Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold12
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: 101594
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4963 original size:11 final size:11
Alignment explanation
Indices: 4947--4971 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4937 TGGTTTAGTG
4947 TTTTTTGAATT
1 TTTTTTGAATT
4958 TTTTTTGAATT
1 TTTTTTGAATT
4969 TTT
1 TTT
4972 CGTTTTTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTTTTGAATT
Left flanking sequence: Indices 4447 -- 4946
TCCAGATTTTGTTAATGTGATTTTTGTTGAATGGAGATCCTTTCACAAGAATGCATGGCTGTCTG
ACTAACACACACTGAGTTTCCATTATTTACCACAAACCCCTCCTGCGTCATGTTGTTTTCAAGGC
TCTACCCTTCCGGGTTATTGATTAAGTCGTAATAAATGACAAAATTTTTTTCCATAAGATTTGCT
AACTACGTACATAGATACGTAAGATCTTACTGTAAAACACAAGGAAAACATCAGCCAAACCAGAG
CGGTTGGAGGGAGAAGGCCGCCATAGGTAATGAAAGAGTATGAGGCATATAACGACGAGTTGCTA
GTGGGGTTGACCAAAGGGTAGCAGGAAATGGAACCCTGGTCTCTCACTCGTCGGGAGCATGTTAG
CCATTGACACTACCACCGAAATGGGCTCCCCCTCGGCAGTCGTCTCGTCCCCTTAGTTAATTATT
TTGGATTTTTTGTTTGTAGTGAAAGTCGGATTGTTTGGTTTAGTG
Right flanking sequence: Indices 4972 -- 5471
CGTTTTTTGGTCTCGAGACATCGATCATGCCATGCCCCTGCCCGTCTTGATGTATTCCAATTTGC
TCTTAATCCACTCCTAATAATACAACCAAAAGTTTGGACCTTCTTGAAGATATTGTAGGAAACCA
AGTCGGAACGAGTGCGTACTGTTGCCAGTCGCACGCTCCAGTCCTCGGGCGCCTAACCACTAGAT
GAGGATCGGAGTCATTATACAACAATATTGAGCTTGATAAGAAATGAAACAAAAAAAAATAAGTA
TTTAGTTAATTTTCACGAAAAGTGAAAAAAAAAAAAAAGTTGAAAAATTCTGCATTTGTCGTTGT
TGTGGAAGCAAGGTTGTTTCTCCAATCACGCGTGACGCAGTATGAGTTCGAATCGCACTAATGAT
GATTAACAATGGATAAGTGAACAATCTCTGATGTCAAACGACAATTTGATTAAGAAACCGCATGC
CTTCCTACTGATGAGCGATCAACGTTGATGCTCTACGTCTTTCAA
Found at i:38292 original size:15 final size:15
Alignment explanation
Indices: 38238--38297 Score: 54
Period size: 15 Copynumber: 4.0 Consensus size: 15
38228 CTTGACCACT
*
38238 GAGCAGCCCGCCCCC
1 GAGCAGCCCGCTCCC
38253 GAGCAGCCCGCTCCCTC
1 GAGCAGCCCGCT-CC-C
38270 G-GC--CCCTGCTCCC
1 GAGCAGCCC-GCTCCC
*
38283 GAGCAGCCTGCTCCC
1 GAGCAGCCCGCTCCC
38298 TCTTCTGCGG
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
13 2 0.05
14 7 0.19
15 20 0.54
16 6 0.16
17 2 0.05
ACGTcount: A:0.10, C:0.55, G:0.25, T:0.10
Consensus pattern (15 bp):
GAGCAGCCCGCTCCC
Left flanking sequence: Indices 37738 -- 38237
ACTACCTAACGCCACAACTTAAAGCATATAAATATCATTAGCTCTGTCTCTATAATTTTCATCAC
TGTCTATCGCTTAAAATGAAGTTTTCTACCACTGCCGCTGCCCTCGCTATCGCCACCCCCGCTTT
GGCTCAGTACTCCAACGGCACTGTCACTGATATCCACACCACTGTTGTCACCATCACTTCTTGTG
AGGACAACAAGTGTAACGAGACCCCCGTGACCACTGGTTACCAGGTTGTCACTGAGGAGCACACC
GTGTACACCACCTACTGCCCCTTGACTGATGAGAAGCCCGAGGAGCCTACCCAGGCCCCCGCTCC
CTCTGACGCTCCCGGCACTGAGACCGTGGTGAACCCCATTGACACCACCGTTGTCACTGTCACCT
CGTGCCACCCTGACAAGCCTTGTGAGACTCAGGAGGTCACCACTGGTGTCATCACCTCTTACGAC
GTCGAGAACAAGACTGTGTACACCACTTACTGCCCCTTGACCACT
Right flanking sequence: Indices 38298 -- 38797
TCTTCTGCGGCCCCTGCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCTGCCCCCGAGCAGCC
CGCTCCCTCTTCTGCGGCCCCTGCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCTGCCCCCG
AGCAGCCNCCGCCCCTGCCCCCGAGCAGCCCGCCCCTACTGAGGCTCCCGCCCCCACCACCCAGG
AGGAGGTCCCCTCCCCCACCCTCGCTGGCGAGTCCAAGGTTCCTACCATTGAGACCGCCAACGGT
GCCGCTCGTGCCATGCCCTTCGCTTTGGCCGGTGTTGTCGCTTTCAACCTCTTGTAAGTTGGGTG
ATTTCGTTATTTTCTAAATATTTCGGACTTTTAATACATTAATTTTGGGCTATACAATACCGGTT
TTACAACCACCGTGCTTGTTTCCACTTGACTATTAATCAACAACGAATTTTCCCGCTCGGTTCCG
AAGACGAAACATCTGAGTAACTTCAAGAACAGGGGCAATATAAGT
Found at i:38320 original size:36 final size:36
Alignment explanation
Indices: 38247--38434 Score: 316
Period size: 36 Copynumber: 5.4 Consensus size: 36
38237 TGAGCAGCCC
38247 GCCCCCGAGCAGCCCGCT--C-C--CT-CGGCCCCT
1 GCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
* *
38277 GCTCCCGAGCAGCCTGCTCCCTCTTCTGCGGCCCCT
1 GCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
38313 GCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
1 GCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
38349 GCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
1 GCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
38385 GCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
1 GCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
38421 GCCCCCGAGCAGCC
1 GCCCCCGAGCAGCC
38435 NCCGCCCCTG
Statistics
Matches: 148, Mismatches: 4, Indels: 6
0.94 0.03 0.04
Matches are distributed among these distances:
30 16 0.11
32 1 0.01
33 1 0.01
35 2 0.01
36 128 0.86
ACGTcount: A:0.06, C:0.55, G:0.23, T:0.15
Consensus pattern (36 bp):
GCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCT
Left flanking sequence: Indices 37747 -- 38246
CGCCACAACTTAAAGCATATAAATATCATTAGCTCTGTCTCTATAATTTTCATCACTGTCTATCG
CTTAAAATGAAGTTTTCTACCACTGCCGCTGCCCTCGCTATCGCCACCCCCGCTTTGGCTCAGTA
CTCCAACGGCACTGTCACTGATATCCACACCACTGTTGTCACCATCACTTCTTGTGAGGACAACA
AGTGTAACGAGACCCCCGTGACCACTGGTTACCAGGTTGTCACTGAGGAGCACACCGTGTACACC
ACCTACTGCCCCTTGACTGATGAGAAGCCCGAGGAGCCTACCCAGGCCCCCGCTCCCTCTGACGC
TCCCGGCACTGAGACCGTGGTGAACCCCATTGACACCACCGTTGTCACTGTCACCTCGTGCCACC
CTGACAAGCCTTGTGAGACTCAGGAGGTCACCACTGGTGTCATCACCTCTTACGACGTCGAGAAC
AAGACTGTGTACACCACTTACTGCCCCTTGACCACTGAGCAGCCC
Right flanking sequence: Indices 38435 -- 38934
NCCGCCCCTGCCCCCGAGCAGCCCGCCCCTACTGAGGCTCCCGCCCCCACCACCCAGGAGGAGGT
CCCCTCCCCCACCCTCGCTGGCGAGTCCAAGGTTCCTACCATTGAGACCGCCAACGGTGCCGCTC
GTGCCATGCCCTTCGCTTTGGCCGGTGTTGTCGCTTTCAACCTCTTGTAAGTTGGGTGATTTCGT
TATTTTCTAAATATTTCGGACTTTTAATACATTAATTTTGGGCTATACAATACCGGTTTTACAAC
CACCGTGCTTGTTTCCACTTGACTATTAATCAACAACGAATTTTCCCGCTCGGTTCCGAAGACGA
AACATCTGAGTAACTTCAAGAACAGGGGCAATATAAGTAACGGTGGTGAAAGTATTGTAGTCTTA
AAGTACCCAATTCCATTTTTTACCTAAAGATGCACTTGCTATTTACTCCTTGTATGTCATTCATC
GGTTTTCGTGGTTTCGCCGCTTGAGATTTAAATCATGCTCCAACA
Found at i:38441 original size:23 final size:21
Alignment explanation
Indices: 38415--38464 Score: 82
Period size: 23 Copynumber: 2.3 Consensus size: 21
38405 CTCTTCTGCG
38415 GCCCCTGCCCCCGAGCAGCCNCC
1 GCCCCTGCCCCCGAGCAG-C-CC
38438 GCCCCTGCCCCCGAGCAGCCC
1 GCCCCTGCCCCCGAGCAGCCC
38459 GCCCCT
1 GCCCCT
38465 ACTGAGGCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 8 0.30
22 1 0.04
23 18 0.67
ACGTcount: A:0.08, C:0.62, G:0.22, T:0.06
Consensus pattern (21 bp):
GCCCCTGCCCCCGAGCAGCCC
Left flanking sequence: Indices 37915 -- 38414
TCACCATCACTTCTTGTGAGGACAACAAGTGTAACGAGACCCCCGTGACCACTGGTTACCAGGTT
GTCACTGAGGAGCACACCGTGTACACCACCTACTGCCCCTTGACTGATGAGAAGCCCGAGGAGCC
TACCCAGGCCCCCGCTCCCTCTGACGCTCCCGGCACTGAGACCGTGGTGAACCCCATTGACACCA
CCGTTGTCACTGTCACCTCGTGCCACCCTGACAAGCCTTGTGAGACTCAGGAGGTCACCACTGGT
GTCATCACCTCTTACGACGTCGAGAACAAGACTGTGTACACCACTTACTGCCCCTTGACCACTGA
GCAGCCCGCCCCCGAGCAGCCCGCTCCCTCGGCCCCTGCTCCCGAGCAGCCTGCTCCCTCTTCTG
CGGCCCCTGCCCCCGAGCAGCCCGCTCCCTCTTCTGCGGCCCCTGCCCCCGAGCAGCCCGCTCCC
TCTTCTGCGGCCCCTGCCCCCGAGCAGCCCGCTCCCTCTTCTGCG
Right flanking sequence: Indices 38465 -- 38964
ACTGAGGCTCCCGCCCCCACCACCCAGGAGGAGGTCCCCTCCCCCACCCTCGCTGGCGAGTCCAA
GGTTCCTACCATTGAGACCGCCAACGGTGCCGCTCGTGCCATGCCCTTCGCTTTGGCCGGTGTTG
TCGCTTTCAACCTCTTGTAAGTTGGGTGATTTCGTTATTTTCTAAATATTTCGGACTTTTAATAC
ATTAATTTTGGGCTATACAATACCGGTTTTACAACCACCGTGCTTGTTTCCACTTGACTATTAAT
CAACAACGAATTTTCCCGCTCGGTTCCGAAGACGAAACATCTGAGTAACTTCAAGAACAGGGGCA
ATATAAGTAACGGTGGTGAAAGTATTGTAGTCTTAAAGTACCCAATTCCATTTTTTACCTAAAGA
TGCACTTGCTATTTACTCCTTGTATGTCATTCATCGGTTTTCGTGGTTTCGCCGCTTGAGATTTA
AATCATGCTCCAACAGCGTTAACACGCTGGGCAAATGCTTACTAT
Found at i:40078 original size:15 final size:15
Alignment explanation
Indices: 40060--40097 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
40050 TTTACGCCGT
*
40060 CGTTCTCGTGGTGGA
1 CGTTCTCGTGGTAGA
*
40075 CGTTCTCATGGTAGA
1 CGTTCTCGTGGTAGA
40090 CGTTCTCG
1 CGTTCTCG
40098 CCATAGGCGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.11, C:0.24, G:0.32, T:0.34
Consensus pattern (15 bp):
CGTTCTCGTGGTAGA
Left flanking sequence: Indices 39560 -- 40059
AAAGAGATGGAGTTTGTACGGCTCAACAAAAAATGGCCGCGACACCACGGGCACCCGGGCTTGAA
TCTGGCTGAGAATGTAGTATTCCCACTTCAGAGCCGGTTTCTCTATTTTCAACGCACCATAGGTG
CCATCCAAACACAGCTCAATCAAATAGACCACCCCGTAGCCCCCACGGCCCAACTCGCTTTTGAT
CAGGTACAAGGAGTCACCGCAAAAGTCGATAAGCAGCGCCAGCAGCGCCGGGGTGGGCTTTCCGA
GAAGAAACAAATTGACAAAGTTGCGGCTCCGGTTGATCGTTTTCGAGGAATGGTCGTAGAAACCC
TCGCAGGTCAGTGGACGCATGCTGAGCAACTGCTGGCTGCGCAGGGACAAGTCGGAGACATCGAC
GATGGCCACCTCTGCCAACGGCACCTCTGGATTCATGACAAACAGCAGAGAGTGTTCGGTGACAG
GCGTGACCTCAGACGTCAAGTTCGGGTTGTCGTCATTTACGCCGT
Right flanking sequence: Indices 40098 -- 40597
CCATAGGCGTAATCGCCGTAGGCGCTGTCGTTGTCGTGGTCGTTTTCGTGCGGTAGCCGCGGCAG
GGCTTGCTGGCCCGTGAGGGGGAGCTCAGTGACGTAGTCGGTGAAGTTGGTGAGGGTCGGTTGGT
AGGCTCCAGCAATGGCCAAGTCCTCCTCCTCAGAGTCGTGCAAATCGACCCCGACGTCGTACATT
CCCAACAATTCCTTCTTCGTGTCCTTGCCAAAGAACGTCGTGGTAGGCGACCCCGGCACACGCCC
TACCGACGGAGGCCGCAACGCCAATGGGTGGCTGTCGTCGCCGGAGAAGTTGTCGGGTATCGTGG
CCTGAGAAAGCTGCACAGGTTCGGGGTCTACGGGTGTTTCCTCGAGTGGTTTTCGTATGGTGGAA
GCGGCCTCTCTCGAGCTCAGAGGCTGGAGCCCGGCCTTTGGGTGCGCGTGGGTGGAAACGGTGGC
CAACAACAACTCCAACGAGCAAAGCTCTGTCGCGAAGCTCTTTTG
Found at i:41817 original size:14 final size:14
Alignment explanation
Indices: 41798--41844 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
41788 ACCGGGGATA
41798 TACCGCTAGTTATG
1 TACCGCTAGTTATG
41812 TACCGCTAGTTATG
1 TACCGCTAGTTATG
* * *
41826 TAGCGGTCGTTATG
1 TACCGCTAGTTATG
41840 TACCG
1 TACCG
41845 GTCGTTACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (14 bp):
TACCGCTAGTTATG
Left flanking sequence: Indices 41298 -- 41797
CACTCCAACCACAACCGGACATAGCGGATGTCGTTGGCGTAGCTCTTGTCCTCCATAAAGTGCCG
GGTGGCCGTCTCCAAAACCTCGACAAGCTCGGGGTGTTTCAGGTTGTAGGCAAAAGTGGAGCGGA
GGGACGCGACGTAGTCGACAAACACCAGGAGCGGATCGTCCATCTCGTCGAGCCCCGCTAGTTGC
GCCTCGAAGTGGTCGCGGTCCCTGCGGGTGTCCTCGTCTAGATTCAGCCTCAGGCCCAAACGAAG
CAGTGCCGCTAGCTTTTTTAGCAGCCGCCCGCCTGCGACGGGCTGGATGTTCTCTTTGTGGTCCT
GGAATAGGGAGATATCGCTCATCCGACCCGATTGCGCACCGAGATCCGTGGTGTTTATCTTTGGT
GCGGACGCGCGCACACTACTGACGCGCTACGCGGTGGAAAAACGAGGTGGCCATCACGAGGTTAT
GCTATTCGAAGATACTGATATTCGATGATACTAATACCGGGGATA
Right flanking sequence: Indices 41845 -- 42344
GTCGTTACAACTTGGGTGTGAGGCTCAACGATCTCAAGTGCTTGACGGCCTCCATGCCCAGCCCG
TACGAGAGCTCGTAGCCCATGCCACCCGCACCGTAGTTGTTGATGACATGGTTACGACGCCCGGG
GTGGTCCTGACAACGCTCGAGCAGAGTGTTCAAACCCCCTTCGCGAGCTGGTCTGAACCCGACGT
TGATGTTGACCACGTCAAACTCGCCGTTCCGCATCAACTCGGGGAACAACTTCGCGCCCCGGCGC
TTCAACGAGGCAGTGTCTTCGTCGCGCACCCCTCCGTAGGTGTCACGCACCTGCTTGGTGCCACC
CAAAATCATCCCTCCGTCAAGTGGACGCGGAATGCAAAATGTCCACATGCCATCTGCCAGCTGGT
GGGTCACGGTGGCGTCCGCGTACTTGTTGCCCGGGGGTGGGCGAATCAAGAGGGTCTGACCTCTG
ATGGGGTAGGACATCGGGTCATAGCCTCCGTCGTACTGCAAACCT
Found at i:41846 original size:14 final size:14
Alignment explanation
Indices: 41806--41851 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
41796 TATACCGCTA
* *
41806 GTTATGTACCGCTA
1 GTTATGTACCGGTC
*
41820 GTTATGTAGCGGTC
1 GTTATGTACCGGTC
41834 GTTATGTACCGGTC
1 GTTATGTACCGGTC
41848 GTTA
1 GTTA
41852 CAACTTGGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.37
Consensus pattern (14 bp):
GTTATGTACCGGTC
Left flanking sequence: Indices 41306 -- 41805
CCACAACCGGACATAGCGGATGTCGTTGGCGTAGCTCTTGTCCTCCATAAAGTGCCGGGTGGCCG
TCTCCAAAACCTCGACAAGCTCGGGGTGTTTCAGGTTGTAGGCAAAAGTGGAGCGGAGGGACGCG
ACGTAGTCGACAAACACCAGGAGCGGATCGTCCATCTCGTCGAGCCCCGCTAGTTGCGCCTCGAA
GTGGTCGCGGTCCCTGCGGGTGTCCTCGTCTAGATTCAGCCTCAGGCCCAAACGAAGCAGTGCCG
CTAGCTTTTTTAGCAGCCGCCCGCCTGCGACGGGCTGGATGTTCTCTTTGTGGTCCTGGAATAGG
GAGATATCGCTCATCCGACCCGATTGCGCACCGAGATCCGTGGTGTTTATCTTTGGTGCGGACGC
GCGCACACTACTGACGCGCTACGCGGTGGAAAAACGAGGTGGCCATCACGAGGTTATGCTATTCG
AAGATACTGATATTCGATGATACTAATACCGGGGATATACCGCTA
Right flanking sequence: Indices 41852 -- 42351
CAACTTGGGTGTGAGGCTCAACGATCTCAAGTGCTTGACGGCCTCCATGCCCAGCCCGTACGAGA
GCTCGTAGCCCATGCCACCCGCACCGTAGTTGTTGATGACATGGTTACGACGCCCGGGGTGGTCC
TGACAACGCTCGAGCAGAGTGTTCAAACCCCCTTCGCGAGCTGGTCTGAACCCGACGTTGATGTT
GACCACGTCAAACTCGCCGTTCCGCATCAACTCGGGGAACAACTTCGCGCCCCGGCGCTTCAACG
AGGCAGTGTCTTCGTCGCGCACCCCTCCGTAGGTGTCACGCACCTGCTTGGTGCCACCCAAAATC
ATCCCTCCGTCAAGTGGACGCGGAATGCAAAATGTCCACATGCCATCTGCCAGCTGGTGGGTCAC
GGTGGCGTCCGCGTACTTGTTGCCCGGGGGTGGGCGAATCAAGAGGGTCTGACCTCTGATGGGGT
AGGACATCGGGTCATAGCCTCCGTCGTACTGCAAACCTTGACCCA
Done.