Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold9
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 331816
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.26
Found at i:206 original size:39 final size:39
Alignment explanation
Indices: 1--195 Score: 336
Period size: 39 Copynumber: 5.0 Consensus size: 39
*
1 AGCGGAGTCAGAAGGACCAGTAGGACCAGTGGGCTCAGA
1 AGCGGAGTCAGAAGGACCAGTAGGACCAGTAGGCTCAGA
*
40 AGCGGAGTCGGAAGGACCAGTAGGACCAGTAGGCTCAGA
1 AGCGGAGTCAGAAGGACCAGTAGGACCAGTAGGCTCAGA
* *
79 AGCGGAGTCAGAAGGACCAGTGGGACCAGTAGGCTCCGA
1 AGCGGAGTCAGAAGGACCAGTAGGACCAGTAGGCTCAGA
118 AGCGGAGTCAGAAGGACCAGTAGGACCAGTAGGCTCAGA
1 AGCGGAGTCAGAAGGACCAGTAGGACCAGTAGGCTCAGA
* *
157 AGCGGAGTCGGAAGGACCAGTGGGACCAGTAGGCTCAGA
1 AGCGGAGTCAGAAGGACCAGTAGGACCAGTAGGCTCAGA
196 GACTGAGTCG
Statistics
Matches: 147, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 147 1.00
ACGTcount: A:0.30, C:0.21, G:0.38, T:0.10
Consensus pattern (39 bp):
AGCGGAGTCAGAAGGACCAGTAGGACCAGTAGGCTCAGA
Left flanking sequence: None
Right flanking sequence: Indices 196 -- 695
GACTGAGTCGGTGGGTTCAGGCGATGAGATATCACCGGTATTTGACGCCGTACCAGGCTTGGAAG
ACTCGGAGCTCTCGCTAGTGGGAGTGGTAATAGTGATGGTGGTAGGGGGAGGGGTCACAGTCACC
GACACCGTAGTGCAAGGGCTAGGAAGACTGGTGGTCACAGTGATAGGGGGAGGGGTTACAGTGAC
AGTGGTCGATGTACAAGGAGGGAGGGGAGTGGTAGTAGGCTTCGGGCGAGTGGTGGTGTCGGGGC
AATCACAATCCCAACAGTATTGAGGGAACTTGTGCTTGCGGATGGCACAGCCCTTAAGGAGGTTG
GAGATAAATCTAAGGTCTCTCTTCTCAGCGGGAGTAAACTCGCCAAAAGTGCCTTCGTCTCTCTT
CTTGTAGTTGGTAACCATCAGATTCAAAAGATCATCAGCCAGGTCGTAGTTGTCGTAGTTGGAGG
CAGCCTCAATGCCGTAAGAAATATCAAGGCCGAACTTGGACTTGA
Found at i:9029 original size:16 final size:16
Alignment explanation
Indices: 9008--9043 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
8998 CTTCGAATTC
9008 ATTGATAAACTGTAGG
1 ATTGATAAACTGTAGG
9024 ATTGATAAACTGTAGG
1 ATTGATAAACTGTAGG
9040 ATTG
1 ATTG
9044 CACCCTGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.33
Consensus pattern (16 bp):
ATTGATAAACTGTAGG
Left flanking sequence: Indices 8508 -- 9007
CAAATCCGCCTGAGGAAACTTCACATTGCAGGTATTGCAGGTGAACTGGGATTTCGTGGGATCGC
CGTGAGTAGGTAACTCCATTGCTTTAGACTTATTTCGAATGGTTGCGAAAAAAGGTGGCGACTAT
ATGCTAGTTGTGCATGAAGGTGGCAATCTTACTAACTGAAAAAAAAAGCCTTATCGAGTGTTCTA
ACTCCTGGGCTTGAGAGCGTTACTTTAGACTAGATTCAGAGGGCTCCGAAGTCTCTATATGGCCG
CGTTGACGCGGCGACGGGGACCCGATAGAAAGCAGTGATCGTTTTCGTTTTGGTCAGCAGCGTTT
TACACGTGATGGGACCATTCCTTTTCCAGGGTTTTCATGGAAACAACGTAGTGCTTGAACAAACA
AATTCACGATTGCACAGGATTTGAATAGCTCATACACGAGTAACCGTTCGAGAACAACCTTGCAA
CTTTTGACAACCCAATGAACAACGCAGTCAGAAGACTTCGAATTC
Right flanking sequence: Indices 9044 -- 9543
CACCCTGTATAGGATATTTTGATGGCCTGAGAGCTACGCGAAAGACTCTTGCACCACCAGAATCG
CGAACTGAAAAACTAAGACTTCATTCACCTCGAGAGCAGGAATTAAACACGAGATGGCAGTGCAC
ATTTTTGGTCACAACATCAGACACAACGCTTTGGTATGGCTTGGATTGAAGAATGCCATTTTTGG
GATTGGTTCCAAGACAGCACAGCGGATCTGCGCAAAGGTGGCCATCTACCCTCAGATGAGAATGA
AGGACTTGACCGAGCCCCAGATCATGGACCTTAACAAAGAGATTTCCGCGTTGACCGTTGATGGC
GCTCTCAAGGCTCAAATCAACGAAAATATCAAGTTTAAGAAGGACATTGGCTCCTACGTGGGTCT
GCGCCACGTGATGGGGTTACCTGTGCGTGGCCAAAAGACCAGAAACAACGCCAAGACAGCCGGAA
AGTTGAACAAGTTGGAGCGTTACAAGGTTTGAACACGTTTCATAC
Found at i:28413 original size:9 final size:9
Alignment explanation
Indices: 28399--28423 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
28389 AGTTTACCTT
28399 GTTGCTGAG
1 GTTGCTGAG
28408 GTTGCTGAG
1 GTTGCTGAG
28417 GTTGCTG
1 GTTGCTG
28424 GTTCTGCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.12, G:0.44, T:0.36
Consensus pattern (9 bp):
GTTGCTGAG
Left flanking sequence: Indices 27899 -- 28398
CTTACATAGTGAATAGTCACTGGGCCGCAATGCAATTAAATATACTAAACCAATTTAGTCCTTGC
TTTTACCGAAAAGCTTTCGTAACTTGCCGAACTTCTTTTTGTCCTTTTGCGGGCTGCCTTGTCCA
TCTCGGGACGATGCCTCCAGGGCGCGAACAAATGGCACCGCCAGCGCTTGTTCTTCATTCCGCAC
TGATGGTAAAATGAAGTTGTTGGTGATGAAGCCACCAGTCTTTTGAGGCTTCTTTTGCTCCTGTT
GGTGGCGGCCAAAACCCATGTGATGACCACGGCCACCAGTAGCAGGGGAGGGTCCCGAAGCCGCA
GCAACTACACCGGGTTCATAGTCTTCATCGTCAGAGTCAGCAAACCGCGACTTGAAGGCACCGGA
ATTACCAGAAAGCGGCACAACCCCGTCGGGAGCGCGCTGTGAACCATTGTTGTAGTACTGTTGCT
GGTTTTGTCCCGACAGCCCATTACGCAAAGTGAGTAGTTTACCTT
Right flanking sequence: Indices 28424 -- 28923
GTTCTGCTGAGGGTTTGCCCGCAATGTCGTGGCACCCTGAGGGACAGCGCTGGCACGATTAGCTT
GGGCACGAGCCTGCACCTGAGCCTGCTGCTGGGGAGTGATTTTGAGGGAACCCGACAGCGAGCGG
TTGTGACCTTTAGGAGGAGGCGGGGCAACCGACCCGTTCTGGGCGGCCTTGAACCCAGCATTGGG
GTCCGATTCATTTTCCTTAGAGAAAGACGACTTACGAGCCAAACCGAATTGCGACACGGGTCGCG
AGCTGGCTTTGGCATACAACTGCGCTGCTTTAACCTTCGAAGGCAGTTGATAGCCGGGCTGAAGA
GTTGGGTGGGGGGCAATAGGCTGAACATAGCCACCAGTCGCAGGGGCTCCATGTGTCAGCTGGCG
AAGCGAGCGCAGCAGCATCTTGGCCCCAGGTTGCTGGCGAGGTTCTGCGTACAGTTGCGGGCGCA
TAGTCCGTTGCTTTTCTTGGGCAGGCGGCTGAGGTGCCCGTAAAC
Found at i:87472 original size:21 final size:21
Alignment explanation
Indices: 87439--87478 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
87429 AAGGAGGCCC
* *
87439 CTGCTCCTACCCCTGCTGCTG
1 CTGCTCCCACCCCCGCTGCTG
*
87460 CTGCTCCCGCCCCCGCTGC
1 CTGCTCCCACCCCCGCTGC
87479 CGGTGGCGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.03, C:0.55, G:0.20, T:0.23
Consensus pattern (21 bp):
CTGCTCCCACCCCCGCTGCTG
Left flanking sequence: Indices 86939 -- 87438
CAAACCTACTCCAACAAATCGAATTGTAAGTTGTGAAAGCCAGACGAAGAATCTCAAGGGTAATG
ATTGCTGTTTTCCTTAAATCATGAAGGACCTGATCAAGACAAAAGTATCCAGTCACCAAGAGTCA
AAATTCTTGATTGTTGGGTCTGGAAAATACGTTAAGTTCTTCTTGATAAGCGACGCAATGATGTT
GATGACCACATGCCGACACAGCATTCAGCTGAGGGCGTTTTCAAAGATTTCCATTCCCAAACGAA
TGGGTTAACTTATTCGGTTGCTTTCGATATCATAATATCTATCACATAATTACTAACTTCACTAG
AAAATGGGTTCCGCTTATCAGATTTTTGGCAAACAAGTTCCTGCTCATGTGGTAAGTTATTTCGA
CTGGTTTGCAGATTTGCATTTACCAAATACTAACAAATTGTAGCTTGCCCTTGCGACTTTAGGGT
CGGTCACTGCCATAGCTGCTTGGCCCAGAGCTAAAAAGGAGGCCC
Right flanking sequence: Indices 87479 -- 87978
CGGTGGCGATGACTTTGACTTGGAAAAGTTCTTGAATGACTTAACCAAGGAGGAATTTAAGTAAT
CATGCATATCCTTATATATTTTTCCATATTTTATGCCATACCAATGCGCCGTAAAATTCATGTCA
AGTCAAGTGACGGCGTTCTAGATTGGATTGAGGTATCGAAACTGCCAGTTTTGGCCCCTTATCCC
CCAATCAAGACAAGGTTCGTGATCAAGTTAGAGGCGCGGAGCAAAGTGCAAGGCCACTTGTCGTC
TAATGAAGTCGTTTACGGGGTGATTTGACCAAATTAACTCTACACATTGCTTTTTGTGGATGTTA
TTCAAATTCGAGCATAGTGACTGGGTCTGCAAACGAGATGCATATCTAAGCTACCACCAGCTTTG
ACAGCATTTTCATGCGATATGAAATATCAACCTATTAACTCGCATGGACATTCCCGACCCGCTAT
CGTTTACTTCTCCCCACCCCGAGTACGGATATTTGAAATCGTTTG
Found at i:190327 original size:12 final size:12
Alignment explanation
Indices: 190310--190336 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
190300 GGCGGCAGGT
190310 AAGAAGAAAGAC
1 AAGAAGAAAGAC
190322 AAGAAGAAAGAC
1 AAGAAGAAAGAC
190334 AAG
1 AAG
190337 CATGGGACTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.26, T:0.00
Consensus pattern (12 bp):
AAGAAGAAAGAC
Left flanking sequence: Indices 189810 -- 190309
ACCCATGGAGCTAAAGAAAGCGTCACTATGGTGCCTGATATTACACGATTTCTACGAAAAGGGGT
ATCCTGGTCCGAAATTCTTGGTTTTGCATGTCTGAGCTTGTCAACCTGAGTTTCAAGAATTGGGT
CGCTCTCATGAGCAAAGTTATACACAACCCAAGCCATGAGGCTTGCAATAAAGCTGAAGCCTCGT
ATGAGGTATGTATAACAATCAATATCTGGTTTCGTTGGTAGCGCTGACAGTTATGGAGAGTTCCC
AAATGTGCGACTGCGAAAGTGAAACGGTTACTGGTTTGCCGTCGTCCACTACTGCTGCCTGAAAT
GGACATAGATCGCCCACGTTACGTGCCGCCGCTCAACTTTGCCCTTGTTGAGGACGGCATCTACC
GCCTGGGTTTTCCCATGCCCATCAATTATCCTTTCCTTCAGCAGCTAGGACTCAAGACGATCATC
TACTTAGGTGACCTCGGTCAACCACCAAAGACGCTGGCGGCAGGT
Right flanking sequence: Indices 190337 -- 190836
CATGGGACTGCTGAAATTATGGCAAACTACGAACTGTGGATTACCAACGAGACCGATGTCAAATT
CCACCGACTCTTATTTGAACTGCCCCAAGAGCCATTCACACTAGTAGAGGCAGAGGCCCAAGCCC
ACGCTCTGTTGACCGAAGCGCTTCAACTCATGTTAGATCGGAGCAACTTTCCCATTCTTATCCAC
TCAAATAAGGGTAAACACCGTATTGGAGTTTTGGTCGGCCTCATGCGCAAAATACTTCAAGGATG
GGGTTTGGCTAGCATCTTCGATGAGTATGAGAAGTTTGCTATGGGCAAGGCGGAATATGATCTTG
AATTTATCGAATTGTGGCAGCCTGAGTTGGAGGTTGATGACGACAACAAACCGGAATTTGTTCGC
GTTTGAAACAGGGCCAGCCTCTGATAAAAACTCAGACCGCCCCAACATCTTATATTAATCTAGAT
ATAAGATACTACGGCACCGCACCACTCGTTGATTTCGTCACAACC
Found at i:211175 original size:15 final size:15
Alignment explanation
Indices: 211155--211184 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
211145 CGTCTTTCAA
*
211155 CTCATCGCGCGCAGC
1 CTCATCGCCCGCAGC
211170 CTCATCGCCCGCAGC
1 CTCATCGCCCGCAGC
211185 ATATTGCGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.50, G:0.23, T:0.13
Consensus pattern (15 bp):
CTCATCGCCCGCAGC
Left flanking sequence: Indices 210655 -- 211154
GATGGCTTTGCCTATGATGACCTGGGAATCTACGTTGCACTCTTCGGGGACGGGAAGGTGGCCCA
TTACAACTGGCGAGGGGAGCACGTTGGTGAGTACACCGTAGGGGGTAAGCGTGTCACATGTGTCG
GTGGCCAAGGTTACGTCACCACTGCCCATGCACTGCTTCAGAACCAGGTGGAGCCTCTGGATCAT
GGGGGTCGTCTCTACCAAATCCCGGTCAAGATTGACCAGCAATTGCACAAGTGGCTGCTTTAAGC
GGCTGTCTCTAAGTAGGATAATACAGCCTGGATAAACTCCTCAACCTCGGTGTTGGCCTCAAACC
CTCCTTTGCGTAAACTGTTGAGCTTGAGCTTGGCCACATCCCATTGGCGATTGGCAACGTCAGTG
ATGGGTCGATTGACAATCTCGAGAAGAGTAACCAAGTGGAACTGGAGCGTAGGCAGCTTAAGCAT
AGCCTGGATCTCAGGCGGGATGCTAAAGCCCGGCTCGTCTTTCAA
Right flanking sequence: Indices 211185 -- 211684
ATATTGCGAAGGCACCAGAGTCCCCGGTTCCAGCATCGGGGTCAGGTTCGGGGCATGGTCACGGG
ACATGTGCTCCTTGTAGCACTTAACTGAGCAATATCTGGCCCCACATTTGCACTTGTACTTTGCT
TCGTCACCACAGTGGCACTGGATCATATTGTGATAGTGAGAGACGATTTTGGAAACGGGCTCCTG
TGCAAGCACTCTACGCGACCCGAAGGCATAATTGTCGGGACAACGCCCGCCCAAAGCGTCCCGCG
CCTCGTACGTTGTCTGTGAACCGGCGTTGCCGACGTTGCGCAATCTACAATGTGTTCCAACCCAA
ATCGTAATTCATTAAAATCTATAATATGCAAATAGTCAGGGCATGGCTAATAGCCATGATGCAAA
TGGGGTGCCACCAGCGCCACGGGCGGGCAGTACCACTGAGGCTTGGCGATGGCGTCGGCGGGAGG
CGTCAAAGGCAAAGCCATCAGTTGAGGACCTTGGGCGGCCACTCC
Found at i:223223 original size:27 final size:27
Alignment explanation
Indices: 223181--223233 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
223171 GCCCAGAGCG
*
223181 CCCAGCACGCTGCCGTGGCGCGAAATC
1 CCCAGCACGCTCCCGTGGCGCGAAATC
223208 CCCAGCACGCTCCCGTGGCGCGAAAT
1 CCCAGCACGCTCCCGTGGCGCGAAAT
223234 GGACTCGTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.19, C:0.42, G:0.28, T:0.11
Consensus pattern (27 bp):
CCCAGCACGCTCCCGTGGCGCGAAATC
Left flanking sequence: Indices 222681 -- 223180
CATCCTCCCCTTCACTGGGCCCGCTGTCCTTCGCGCCATTCTCTTTCACCTGCAAATCTTGCGAC
TCGAGCACCAGTGTGTCATTAGTGGTGGACGTGTCAAGCGGAAGATCGCTGGGGGCAGAGTCGCT
GGGTAAGTCTGAAGAGTCATCGCGGGGACCGTCCCCACCAAGATTAGTGGTTTGGTGAGGCGGCG
CGTGGCCCGTGTAGCTGGGCGGCCCAAGCGGCTGGTCATGGGGCCCGAGCTCGTCATCATCGATG
GGCCGACGCGTGGGTGACACCTCGTCGTCATAGTGCAGCACGTAGCTCGGCGGGTTCATCAATGG
CGGGCGCAAGCCCTGGTTGGGCGAGATCACGGGGGACTCCAACGGCGTGGGCGCCTCTGCCACTG
CTCCGAGCATGTCACCGCCTTGAGTGGTTACTGGAGGCGGTGGCAGCATGGTGGCCCGCAGCGGC
GAGAAACTCAGGCGGGTGGGCGAGCCCACCAGGAAGCCCAGAGCG
Right flanking sequence: Indices 223234 -- 223733
GGACTCGTCGTCCCACACCAGGTTGCTGCGTTCAGTACGGATGGCCTCTTCAAACGACGGCAACT
GGCCGCGGCCCCACGATTCGGGATCGAACGTGTCGTCGTCCACGGCGAGCGGGGCAACCGACACC
CCGTTGAAGTCCGGGTTGCGGAAGGTGACCTCGTCGTACTTGGGCAACTGCATCAGCTCGTCGTG
ACACCGTGCCAGCAACAAAATGAGCGGGGTGTCCACCACCACCTCGTAGTGGTGCATTTTGTAGT
TGTCGCTGGCGTCGGGCTTCAGGATCCGGAAGCAGATCTGCAACCGGTGGTGGATCTGGATGTGG
CGGAAGTTGGAGTCCGGGTAGAGCGCGCGTCCCAACGTGGTGACACCGGGCACCGGCGCCCCTGG
GCCGGCATCGGCCAGGTAGTGCAGCACATTGGGCACCAGCAGCCGTCGCTGTGCCGTGACAAGCG
TTTCCTGGCACCCCATCGCCGGTGGGTCCACTCCTGGCGGCGCGT
Found at i:224969 original size:12 final size:12
Alignment explanation
Indices: 224954--224988 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
224944 CAGCACCGGC
224954 CGCAGAGCCAGA
1 CGCAGAGCCAGA
*
224966 CGCAGAGCCAGG
1 CGCAGAGCCAGA
*
224978 CGCAGCGCCAG
1 CGCAGAGCCAG
224989 CGCCGAGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.26, C:0.37, G:0.37, T:0.00
Consensus pattern (12 bp):
CGCAGAGCCAGA
Left flanking sequence: Indices 224454 -- 224953
CCGAGGCCGCAGTGGCGGTGGCGGCGCAGGCGTCGCCCGCGAGCTCGGGCTCGGGGTCCACGCCG
TTGGCCAACTGGCGGATTTGCGCAAGCTTGTACTCGCGGGTGCGGTTGGCGAGTCCGTGCGGGCC
TAGCGGCTTGGCGCGGGCCAGGTGCGAGTTGTGGAGAGGGATGAAGTAGTCCGCGTCGCCAAAGC
AGTAGCGCCACCGCAAATGCCCGATCTTGAACTTCTCCAGGTACAGCAGCCCGTCCGCACACGGC
CAGAGCGTGGTCACGTCCGACGACAAGTCGACGTTGATCGGTGCCGCGTCTCTCATCAGTTGCTG
CAACTCCACCACCACGGCAAACGTGTGGGGGATCGGGGTTTCCAGATCGATCTTGGTGCAGAGGT
AGTTGGGCAGGTTGAACTTGGTGAAGTGGCGCGGAAGCTGGCTGGCGGCGTCAGACGCCTCGCTG
GTGGGCGGGGTGTCCACGTAGTCGCTGTTGCGACGCAGCACCGGC
Right flanking sequence: Indices 224989 -- 225488
CGCCGAGCTTGCGTCGTCATCGGTGGGGATCGCTTCCTGGGGCATGTTGGTCTGCCCGTCGGCAT
CCTCGTAGGTGAACAGCAGCAGCAGCGCCGGCGCCAAAAACACCACGTCGTTGGTGTTGGCCACG
TGGAAGCGCACGCCGTGGGGGGTGGTGCCACAGGCCACCGGGTCCTGCAACCCGAGCTCCAGAAG
CACGCCGGCCAACTTGCGGTTGACCACCAGGAGGGTCTCGTCCATCACGAGCTGGTGGGTGGACG
GATGCGACGGGTAGAGGATGGGGGAGCGCAGCGGTTCTAACAGCGGCGACTGCGACCCGAGCGAC
AGCGCACGTGCCCGGCCGATCAGCTTGGCCGCCTCCGACACCATGGCGATCGACAGACGCCGCGG
CCGCTGCAGCGGGGTGGGCAGGGTATGGCGGACGGCGGTTGCGCCAGCACCTACGCCAAACGCCC
CCACCGCCGGCACCTCGAGGAAGCCCAGGTCACTCAGCCGTCGCA
Found at i:284986 original size:12 final size:12
Alignment explanation
Indices: 284959--285018 Score: 77
Period size: 12 Copynumber: 5.0 Consensus size: 12
284949 TTATTAATTA
284959 CATACCCATG-GG
1 CATACCC-TGAGG
*
284971 CATCCCCTGAGG
1 CATACCCTGAGG
* *
284983 CATCCCCTGGGG
1 CATACCCTGAGG
284995 CATACCCTGAGG
1 CATACCCTGAGG
285007 CATACCCTGAGG
1 CATACCCTGAGG
285019 ACCACCCAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
11 2 0.05
12 41 0.95
ACGTcount: A:0.20, C:0.37, G:0.27, T:0.17
Consensus pattern (12 bp):
CATACCCTGAGG
Left flanking sequence: Indices 284459 -- 284958
GAGATCAAGCGCACCGAGTTGGCAAGCTTGAAGCGCCGCGAGGACAACGACCGCCGCCATACCCG
GGCCGAGAAGATCCCGGAGAAGGAAAAGCATATTCGCGGCACCGCGATCAAGGACGACGAGTAAC
AGGTTTTAATAGAATGGGACAAGAAATAGAGAAACGTAAGAAGGGCCTAACTGTGGGTTCGTGAG
GTTAGCTGTGTACTTAGCTGTAGTGGTTGGGCGGTGGCAACACGTGCCTGTGCACGTGCTCACGT
CAAGAGGTCCGCGTGTCGCTGGTACATGTCAATAAACGTTCAATGTCGATAAATGTGTCAAATAT
TATCGGTGCGCACACGAAAAGATGTATGATTTGGTTCACGAACGACCTTCAGTATCGAGATGAAC
ACTCTAATTCTATTTACTAGACGACCTGTGTAGTCTCGTTCTAACTGTACGTCCCCTATATAAGC
TTACGGACCTCTCAGCAACCCTACCATGTTACCTATTATTAATTA
Right flanking sequence: Indices 285019 -- 285518
ACCACCCAGGGGGTCCTGCTTCAACGACGAGCGGCCCGCCTTCAACAACTCGTCGCACAACAACA
AGTTCAGCGCAATCCCGGTGGCAGCCAGGATGGCGTTGCGGAGCACGCGGTACAGGTCCCACACC
CCGTCGACGGTGGGGTCCATAGGCTCGCCCACCTTCAAGTCCACACCGACAATGTTAGAATCGTT
CACCTCGTCCTCACACGCGGCCAACACCTCCAAGGTATCGAGCCCGGCGTTGGTCACAAGCGTCT
TGGGCACCACCAACAACGCCTCGGCAAAGGCAGTGAACCCAGCCTTGTTCTTCCCCTTGGCCAAC
TGGGGCAACCGCAAGTGGTGCGAGGCACACATCCAAAAGGCACCAGCACCCGGGATCACCGAGCC
GTCCCGCAACACGTTGGCGACCAGCCGCAACCCGTCGCGCACAGCGTCCTTGACCTGCTGCACCA
CGTGGTTGTTGGACCCGTGGATCAACACCGTGGCCGCCTTGGGGT
Found at i:285025 original size:24 final size:24
Alignment explanation
Indices: 284959--285025 Score: 59
Period size: 24 Copynumber: 2.8 Consensus size: 24
284949 TTATTAATTA
284959 CATACCCATGGG-CATC-CCCTGAGG
1 CATACCC-TGGGACA-CACCCTGAGG
* * *
284983 CATCCCCTGGGGCATACCCTGAGG
1 CATACCCTGGGACACACCCTGAGG
285007 CATACCCTGAGGAC-CACCC
1 CATACCCTG-GGACACACCC
285026 AGGGGGTCCT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
23 4 0.11
24 28 0.80
25 3 0.09
ACGTcount: A:0.21, C:0.40, G:0.24, T:0.15
Consensus pattern (24 bp):
CATACCCTGGGACACACCCTGAGG
Left flanking sequence: Indices 284459 -- 284958
GAGATCAAGCGCACCGAGTTGGCAAGCTTGAAGCGCCGCGAGGACAACGACCGCCGCCATACCCG
GGCCGAGAAGATCCCGGAGAAGGAAAAGCATATTCGCGGCACCGCGATCAAGGACGACGAGTAAC
AGGTTTTAATAGAATGGGACAAGAAATAGAGAAACGTAAGAAGGGCCTAACTGTGGGTTCGTGAG
GTTAGCTGTGTACTTAGCTGTAGTGGTTGGGCGGTGGCAACACGTGCCTGTGCACGTGCTCACGT
CAAGAGGTCCGCGTGTCGCTGGTACATGTCAATAAACGTTCAATGTCGATAAATGTGTCAAATAT
TATCGGTGCGCACACGAAAAGATGTATGATTTGGTTCACGAACGACCTTCAGTATCGAGATGAAC
ACTCTAATTCTATTTACTAGACGACCTGTGTAGTCTCGTTCTAACTGTACGTCCCCTATATAAGC
TTACGGACCTCTCAGCAACCCTACCATGTTACCTATTATTAATTA
Right flanking sequence: Indices 285026 -- 285525
AGGGGGTCCTGCTTCAACGACGAGCGGCCCGCCTTCAACAACTCGTCGCACAACAACAAGTTCAG
CGCAATCCCGGTGGCAGCCAGGATGGCGTTGCGGAGCACGCGGTACAGGTCCCACACCCCGTCGA
CGGTGGGGTCCATAGGCTCGCCCACCTTCAAGTCCACACCGACAATGTTAGAATCGTTCACCTCG
TCCTCACACGCGGCCAACACCTCCAAGGTATCGAGCCCGGCGTTGGTCACAAGCGTCTTGGGCAC
CACCAACAACGCCTCGGCAAAGGCAGTGAACCCAGCCTTGTTCTTCCCCTTGGCCAACTGGGGCA
ACCGCAAGTGGTGCGAGGCACACATCCAAAAGGCACCAGCACCCGGGATCACCGAGCCGTCCCGC
AACACGTTGGCGACCAGCCGCAACCCGTCGCGCACAGCGTCCTTGACCTGCTGCACCACGTGGTT
GTTGGACCCGTGGATCAACACCGTGGCCGCCTTGGGGTCCTTGGG
Found at i:299831 original size:15 final size:15
Alignment explanation
Indices: 299811--299844 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
299801 TCGGCGTCGA
*
299811 CCTCTTCTTCCTCTT
1 CCTCTTCCTCCTCTT
299826 CCTCTTCCTCCTCTT
1 CCTCTTCCTCCTCTT
299841 CCTC
1 CCTC
299845 AGCATCGCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (15 bp):
CCTCTTCCTCCTCTT
Left flanking sequence: Indices 299311 -- 299810
TTGGACACGTTGGTAGACAAGCTGGAGGCCTTGTCGTCGTCGCTGAGAATGTTCTACAAACAGGC
GAAAAAGACCAACTCGTGCTGTGTGCTTATGTAGCGTTTTTGTACATTAATACCTTATGCCATGT
CGTACGGCTTACAAACCTTCTTTCCAATGTCATTTGATTCTATTATACACACCTTACTTCAACTT
GGCCAACTCCTTCTTCTTCTTCTTCTCGAGCTGCGACTTCTTTTTAGAGAGCTCCTTCTGGCGGG
TCTCCTTCTTGTCAAGACCGTACTGCATCTTGTTGTAAAGCTTGCGCTGCTTCTGGGTCATCATG
ATCTTCTTGAGCTCCTTCTCGTCGTCCTCGGGCGCCGCTCTCTTCTTGCCCTTCTTGGGCTTGGC
GTCGTCGAGGTTAGCCTCAGAGTACTTGACACCGGCGGCCTCCATCTCAAGCTCGCGCTGAGCAG
CGAGGTCTTCGTCCTCTTCTTCCTCCTCGGCGTCCTCGGCGTCGA
Right flanking sequence: Indices 299845 -- 300344
AGCATCGCCCTCAGCAACCTCGGCTTCAGGGTTGTAGATACCGCGGTCACCCCAGGGGGACAAAT
GAGGAGGCAAGGTCTCACCGGGAGCGTACTGGTTGACAGGAACCAACTGAGACTTGTTAATGCAA
TCAAACACCCATTGCGGCTGCACGTAGGTGCGACCCGCCACCTTTTGGGGAACCTTGGGACGGTC
GGTGATGTGATGGGTGACGTTACCAAAGTCCAAGCGGGCGTAAGCGGTGGGGTTGCTGGCCTGCA
ACTCGTCAAGAGCAATTTCCAGCACCAACTTACCACCGCAGGCGAGAATGGGGAGTTCCAAGAGG
TCCAAAGAAACCTCACGGCCAACGTAGAAGGTGAACTTGCTGAACAACTCCAGGGTGGGGGACGC
GTATTTGTTGGGCTGCGAGAGCACGTCGCCCTTGGCGGCATCACCCGAGAACTCGTCGAGGTCCG
CTTCCTCAACGTTGTCATCCTCAGCCTCCTCCTCGGCGTCGTCAA
Found at i:321807 original size:48 final size:48
Alignment explanation
Indices: 321752--321952 Score: 249
Period size: 48 Copynumber: 4.2 Consensus size: 48
321742 TGGACAACTT
* * * * * *
321752 CAAAACCCTCAAGCTGCTCCTGTGCAACAAATCAATGACGGCCAGATT
1 CAAAACCCTCAAGCTGCTCCCGTACAACAGATCACTGATGGCCAGATC
* * * *
321800 CAGAACCCTCAAGCTGCGCCCGTACAACAGATTACTGATGGCCAAATC
1 CAAAACCCTCAAGCTGCTCCCGTACAACAGATCACTGATGGCCAGATC
* * * *
321848 CAGAACCCTCAAGCTGCACCCGTACAGCAGATCACTGATGGTCAGATC
1 CAAAACCCTCAAGCTGCTCCCGTACAACAGATCACTGATGGCCAGATC
* * *
321896 CAAAACCCTCAAGCAGCTCCCGTACAACAGATCACCGATGGACAGATC
1 CAAAACCCTCAAGCTGCTCCCGTACAACAGATCACTGATGGCCAGATC
321944 CAAAACCCT
1 CAAAACCCT
321953 GGTTCTGCTC
Statistics
Matches: 132, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 132 1.00
ACGTcount: A:0.33, C:0.34, G:0.17, T:0.16
Consensus pattern (48 bp):
CAAAACCCTCAAGCTGCTCCCGTACAACAGATCACTGATGGCCAGATC
Left flanking sequence: Indices 321252 -- 321751
CTAAGAGAGGATTTCTTGACGATCTCACCGGTGGGGCGTCTGCAGACGTCATTGTCACCACCGAC
CTAGTTTCGAAGATCAGCGACGCAGGGGCCGCGACAGCGATTGCAGATGACAAACCCGCACCCGC
GCCAACCGACACCACCGAGGGTGGTTTGTTTGATGGTATTTTTGGAGGCTCCCCTTCAACGACTA
CGTCTCCTTCAGCCACTTCTACTGGCGGCGGTTTCTTAGATGGAATTTTTGGTGGATCACCATCC
ACAACGCCTTCTGCTACCTCCACTTCCACTAGCGGTGGATTTTTAGATAGTTTGTTTGGTCTTTT
TGGTGATTCATCGAACGATAAGGACACTGCAACCACTGCAACCACTACTGGTGGAGGGTTTTTGG
ACAGTTTATTCGGTGGTGGTTCCTCGGCCGCATCCAAACCTACTGGTGATGCTAACGTGACAGGT
GGTTCCTCTCCTGCTCCGGTGCAACAGATTAACGATGGACAACTT
Right flanking sequence: Indices 321953 -- 322452
GGTTCTGCTCCTGCCCCCGCGCCAGCTCCCGAAAACGTTTCTCCGAAGCCTGATGCTCCCAAGCC
TGACGCAAATGAGGTTCAGCAGATTACCGACGGCCAAATCCAAAACCCTGTATCATCGGGACCTA
AGCCTGACGCTGACAAGCCCGACGCCGGTAAACCCGATGCTGGAACTCCTGAAGCCGGTAAGCCT
GATTCTGGCAATCCGGGTAATGAGGTTCAACAGATCACTGATGGCCAAATTCAAAACCCCGGTCC
TGCTGCCCCTGGCCCTGCTGCCCCTGGCCCCAACGACAAACCCGATGACTCGAAGCCTGAGGACT
CCAAGCCTGAAGACTCGAAGCCTGGTGACAATGTTCAACAGATTACCGATGGTCAAATTCAAAAC
CCTGGCCCCAATAACGGTGGTTCTGATGGAGCCAAACCTGATAACAACGGGGCTGAACAAATCAA
CGATGGGCAGGTTCAGAACCAAAAGGGTAACACAGCGGCCACTGG
Found at i:321963 original size:48 final size:48
Alignment explanation
Indices: 321717--321952 Score: 242
Period size: 48 Copynumber: 4.9 Consensus size: 48
321707 GGTTCCTCTC
* * * *
321717 CTGCTCCGGTGCAACAGATTAAC-GATGGACA-ACTTCAAAACCCTCAAG
1 CTGCTCCCGTACAACAGA-TCACTGATGGACAGA-TCCAAAACCCTCAAG
* * * * * * * *
321765 CTGCTCCTGTGCAACAAATCAATGACGGCCAGATTCAGAACCCTCAAG
1 CTGCTCCCGTACAACAGATCACTGATGGACAGATCCAAAACCCTCAAG
* * * * *
321813 CTGCGCCCGTACAACAGATTACTGATGGCCAAATCCAGAACCCTCAAG
1 CTGCTCCCGTACAACAGATCACTGATGGACAGATCCAAAACCCTCAAG
* * *
321861 CTGCACCCGTACAGCAGATCACTGATGGTCAGATCCAAAACCCTCAAG
1 CTGCTCCCGTACAACAGATCACTGATGGACAGATCCAAAACCCTCAAG
* *
321909 CAGCTCCCGTACAACAGATCACCGATGGACAGATCCAAAACCCT
1 CTGCTCCCGTACAACAGATCACTGATGGACAGATCCAAAACCCT
321953 GGTTCTGCTC
Statistics
Matches: 159, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
47 2 0.01
48 156 0.98
49 1 0.01
ACGTcount: A:0.32, C:0.33, G:0.18, T:0.17
Consensus pattern (48 bp):
CTGCTCCCGTACAACAGATCACTGATGGACAGATCCAAAACCCTCAAG
Left flanking sequence: Indices 321217 -- 321716
TATCCAAATTATCAATGCAGGTGAGCCCGCTCCGTCTAAGAGAGGATTTCTTGACGATCTCACCG
GTGGGGCGTCTGCAGACGTCATTGTCACCACCGACCTAGTTTCGAAGATCAGCGACGCAGGGGCC
GCGACAGCGATTGCAGATGACAAACCCGCACCCGCGCCAACCGACACCACCGAGGGTGGTTTGTT
TGATGGTATTTTTGGAGGCTCCCCTTCAACGACTACGTCTCCTTCAGCCACTTCTACTGGCGGCG
GTTTCTTAGATGGAATTTTTGGTGGATCACCATCCACAACGCCTTCTGCTACCTCCACTTCCACT
AGCGGTGGATTTTTAGATAGTTTGTTTGGTCTTTTTGGTGATTCATCGAACGATAAGGACACTGC
AACCACTGCAACCACTACTGGTGGAGGGTTTTTGGACAGTTTATTCGGTGGTGGTTCCTCGGCCG
CATCCAAACCTACTGGTGATGCTAACGTGACAGGTGGTTCCTCTC
Right flanking sequence: Indices 321953 -- 322452
GGTTCTGCTCCTGCCCCCGCGCCAGCTCCCGAAAACGTTTCTCCGAAGCCTGATGCTCCCAAGCC
TGACGCAAATGAGGTTCAGCAGATTACCGACGGCCAAATCCAAAACCCTGTATCATCGGGACCTA
AGCCTGACGCTGACAAGCCCGACGCCGGTAAACCCGATGCTGGAACTCCTGAAGCCGGTAAGCCT
GATTCTGGCAATCCGGGTAATGAGGTTCAACAGATCACTGATGGCCAAATTCAAAACCCCGGTCC
TGCTGCCCCTGGCCCTGCTGCCCCTGGCCCCAACGACAAACCCGATGACTCGAAGCCTGAGGACT
CCAAGCCTGAAGACTCGAAGCCTGGTGACAATGTTCAACAGATTACCGATGGTCAAATTCAAAAC
CCTGGCCCCAATAACGGTGGTTCTGATGGAGCCAAACCTGATAACAACGGGGCTGAACAAATCAA
CGATGGGCAGGTTCAGAACCAAAAGGGTAACACAGCGGCCACTGG
Found at i:322231 original size:15 final size:15
Alignment explanation
Indices: 322211--322242 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
322201 AAACCCCGGT
322211 CCTGCTGCCCCTGGC
1 CCTGCTGCCCCTGGC
322226 CCTGCTGCCCCTGGC
1 CCTGCTGCCCCTGGC
322241 CC
1 CC
322243 CAACGACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.56, G:0.25, T:0.19
Consensus pattern (15 bp):
CCTGCTGCCCCTGGC
Left flanking sequence: Indices 321711 -- 322210
CCTCTCCTGCTCCGGTGCAACAGATTAACGATGGACAACTTCAAAACCCTCAAGCTGCTCCTGTG
CAACAAATCAATGACGGCCAGATTCAGAACCCTCAAGCTGCGCCCGTACAACAGATTACTGATGG
CCAAATCCAGAACCCTCAAGCTGCACCCGTACAGCAGATCACTGATGGTCAGATCCAAAACCCTC
AAGCAGCTCCCGTACAACAGATCACCGATGGACAGATCCAAAACCCTGGTTCTGCTCCTGCCCCC
GCGCCAGCTCCCGAAAACGTTTCTCCGAAGCCTGATGCTCCCAAGCCTGACGCAAATGAGGTTCA
GCAGATTACCGACGGCCAAATCCAAAACCCTGTATCATCGGGACCTAAGCCTGACGCTGACAAGC
CCGACGCCGGTAAACCCGATGCTGGAACTCCTGAAGCCGGTAAGCCTGATTCTGGCAATCCGGGT
AATGAGGTTCAACAGATCACTGATGGCCAAATTCAAAACCCCGGT
Right flanking sequence: Indices 322243 -- 322742
CAACGACAAACCCGATGACTCGAAGCCTGAGGACTCCAAGCCTGAAGACTCGAAGCCTGGTGACA
ATGTTCAACAGATTACCGATGGTCAAATTCAAAACCCTGGCCCCAATAACGGTGGTTCTGATGGA
GCCAAACCTGATAACAACGGGGCTGAACAAATCAACGATGGGCAGGTTCAGAACCAAAAGGGTAA
CACAGCGGCCACTGGTGGACGTCCTCAAGCTTGCTCGTCTGATACCGCTCTTAAGGCTACCTTGA
AGGATGGTATTTTACGTGACAGCAAGGGGCGCGTTGGTCTGATCGTCTCCAACCGTCAGTTTCAA
TTCGATGGACCTCCCCCTCAAGCTGGTGCCATCTACGCAAACGGTTGGAGTATTACCAAGGATGG
TTATCTTGCTCTTGGAAGCAGCGATGAATTTTTCCAGTGCTTGCTGGGTGATTTCTACAACTTAT
ACGACCAGAACGTTGCCGCGCAATGTCACCCTGTCAAAATTCAAG
Found at i:322283 original size:15 final size:15
Alignment explanation
Indices: 322259--322301 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
322249 CAAACCCGAT
*
322259 GACTCGAAGCCTGAG
1 GACTCGAAGCCTGAA
*
322274 GACTCCAAGCCTGAA
1 GACTCGAAGCCTGAA
322289 GACTCGAAGCCTG
1 GACTCGAAGCCTG
322302 GTGACAATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.28, C:0.30, G:0.28, T:0.14
Consensus pattern (15 bp):
GACTCGAAGCCTGAA
Left flanking sequence: Indices 321759 -- 322258
CTCAAGCTGCTCCTGTGCAACAAATCAATGACGGCCAGATTCAGAACCCTCAAGCTGCGCCCGTA
CAACAGATTACTGATGGCCAAATCCAGAACCCTCAAGCTGCACCCGTACAGCAGATCACTGATGG
TCAGATCCAAAACCCTCAAGCAGCTCCCGTACAACAGATCACCGATGGACAGATCCAAAACCCTG
GTTCTGCTCCTGCCCCCGCGCCAGCTCCCGAAAACGTTTCTCCGAAGCCTGATGCTCCCAAGCCT
GACGCAAATGAGGTTCAGCAGATTACCGACGGCCAAATCCAAAACCCTGTATCATCGGGACCTAA
GCCTGACGCTGACAAGCCCGACGCCGGTAAACCCGATGCTGGAACTCCTGAAGCCGGTAAGCCTG
ATTCTGGCAATCCGGGTAATGAGGTTCAACAGATCACTGATGGCCAAATTCAAAACCCCGGTCCT
GCTGCCCCTGGCCCTGCTGCCCCTGGCCCCAACGACAAACCCGAT
Right flanking sequence: Indices 322302 -- 322801
GTGACAATGTTCAACAGATTACCGATGGTCAAATTCAAAACCCTGGCCCCAATAACGGTGGTTCT
GATGGAGCCAAACCTGATAACAACGGGGCTGAACAAATCAACGATGGGCAGGTTCAGAACCAAAA
GGGTAACACAGCGGCCACTGGTGGACGTCCTCAAGCTTGCTCGTCTGATACCGCTCTTAAGGCTA
CCTTGAAGGATGGTATTTTACGTGACAGCAAGGGGCGCGTTGGTCTGATCGTCTCCAACCGTCAG
TTTCAATTCGATGGACCTCCCCCTCAAGCTGGTGCCATCTACGCAAACGGTTGGAGTATTACCAA
GGATGGTTATCTTGCTCTTGGAAGCAGCGATGAATTTTTCCAGTGCTTGCTGGGTGATTTCTACA
ACTTATACGACCAGAACGTTGCCGCGCAATGTCACCCTGTCAAAATTCAAGTGATTGAATTCGTG
CAGTGTTAAATCACTATAGTATATACCCGTGTGTCGCGTTAATGA
Done.