Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold43
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: 303621
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Found at i:74912 original size:20 final size:20
Alignment explanation
Indices: 74887--74925 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
74877 GTAAGTTTGC
*
74887 TCTTGCTCACGGGGGTTCGT
1 TCTTGCTCACGAGGGTTCGT
*
74907 TCTTGCTCATGAGGGTTCG
1 TCTTGCTCACGAGGGTTCG
74926 CTTTATTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.23, G:0.33, T:0.36
Consensus pattern (20 bp):
TCTTGCTCACGAGGGTTCGT
Left flanking sequence: Indices 74387 -- 74886
GTCACTAAAATGGTCAAGCTCATCGAGCTCATCAAGATCATCAACCTCAAAAGGTTCGTGCTCCT
GCTCACTTTCCGACAACTCAGGCGACGACTCTTTCTTCTCCACGAGTTTAGCACGTTTGCTAACT
TTGTTAGACACCAGCGACGACTTTCTTTTATTGGTAGTTTTCACTCCCATTGCGTAGTTTCCAAA
ATTTGTGAACTTAAATGTAATGATTTATCTCATCGCGGCGCGATGCGCGCATGTTCTAATACACC
ATGAATCCTTTCCCAACCAAAATGGCAAACCAATGTAAATGAGCAATCGCTAGACATTATCAATC
ATAAACCGGAGATCCATAGGGCACATCCCAAGCCTATGCTCTTTCCATCCGCCTTGAATGCAAAT
TCAGAGTAGAACAACCTTTAGACGTGCGAAGTAGGGATTCCTCGTAGAGGGTCAGGAAGGGAAAT
TGAAGATTTATACATCCTTCAACGCCGTTAGCCTTGTAAGTTTGC
Right flanking sequence: Indices 74926 -- 75425
CTTTATTTGATCGCAACCATTACGTAAGCTCACTTTCGACGCATAACTGATATTAATCAACTTTG
GAACGCAATCGACCACGGATGTTGAAACTTGGCCCCAATCCCTTAGCTGCTCGTCATTTTGTCGC
CACCACTCGCCATTTCATCGCTCCAATGCGAATGCTACTGAGCAAAACTCCGAAGGGGAACGTTA
AAGAGTTGACTGATCTTAGTGGCTTCAAAGACTTCATCAAAGCGGAGAAGCTTTCAGTGATAGAT
TTTTATGCCACCTGGTGCGGTCCTTGCAAAGCCATTGAGCCTGTATTTGCTATGTTGTCTGAACG
GATCCCTGAAGTCCAATTCGGTAGGGTTGACGTGGACCAAGCTGCGGAAGTTGCTCAGGAGTATC
AGATTACTGCTATGCCCACTTGCCTCTTCTTCAAAGGGAGCGAGAGAATAGACCAATTAGTGGGT
GCAAACCCTCCTCAGTTGGTAAAGTTGATTAGCCAGCACGGCGAA
Found at i:155765 original size:18 final size:18
Alignment explanation
Indices: 155742--155782 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
155732 AATCCGTCAG
155742 CTAAATAACTCGTATCCT
1 CTAAATAACTCGTATCCT
* *
155760 CTAAATGATTCGTATCCT
1 CTAAATAACTCGTATCCT
155778 CTAAA
1 CTAAA
155783 CAATGACTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.34
Consensus pattern (18 bp):
CTAAATAACTCGTATCCT
Left flanking sequence: Indices 155242 -- 155741
GATAAATAAGGCATACTTTTCTATATGATCGTCCAATGTCTATATATTTCTATACCCTTGTGACG
TTTCTTTTAGTAAAAGGCGGGGTACAAGCGAGTACTACACACGTAATATCGCTAACAATGAAATG
CAAGCGTGCTGTCATATTATATTCCAACAGTTTTAGTCAAATCACAGGTTATGCTGACTGGTGAA
GGAGTGAAGAACAGGGGAGGTGTTTATCAGGAAGATAGTTTTATTGTTTTAGCGGCCGCGGTTCC
CACGAGGAATTACCCCCTCATTGTTTTAGACAAAAGCACGGATTTTAACGTCTACAAGCACTCTC
TCAGTCACTGGACGCCTACGAAGAGTTGAAAGCATAAAAAGATAAAGGCACCCCATATGTTAGGT
TCATTAAATCGTAAAATAAGCTTATGGCCTTTAGACAACTAAGTTTGTTAACGTAGGCAACTTGG
ATTGATTCAGTAACACGTAAACGAGAGTGTTCCCAAATCCGTCAG
Right flanking sequence: Indices 155783 -- 156282
CAATGACTTCGACCTAATAATGTCCACCAGAACGCTCCCCGTCTTCGAATCTCTGGGATTCTCCT
GAAGGTACTAGTGGCAAAACGCCGTTTGCCACGCGTACCTTATTACCACTTCCGGTTTGCCCTCG
GCCGTCAACCCCGTTTCCCGAACATTCCCTCCAGGTCTCATCTAGCGTGGCTCATAGCCGGTCCA
GCTGGTCTCGCGTCCTGCCGGGCCTAGCATCCCTGTAGTGCTGATCGGGGATTTCATACAACATA
TCATCACTACAAAATGTGTAAACTAGGTCTGTAGAAACTGGAACAGTGAGCCGCCAAAATCACCA
GACACAGGGAAGGATTGGTGGTATTTGATCGGGAACTAGTTTGTGAGAGTTACTCAAGAATCTAA
TTGTCTTCATGAAGTTATCAGGTTATGAAGTCAGAGAATTACCGATGAAAATTACAACTGAGAAC
ACCGAGATTAAATACTACGCTGGGCGTCAAAAACGCTCGTTTCTA
Found at i:175059 original size:15 final size:15
Alignment explanation
Indices: 175039--175073 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
175029 CCTTGGTGGA
175039 CCTGGTCCCTACGGC
1 CCTGGTCCCTACGGC
175054 CCTGGTCCCTACGGC
1 CCTGGTCCCTACGGC
175069 CCTGG
1 CCTGG
175074 CCCCGCTGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.06, C:0.46, G:0.29, T:0.20
Consensus pattern (15 bp):
CCTGGTCCCTACGGC
Left flanking sequence: Indices 174539 -- 175038
GTAGTCGAGGTATGAATCCCCGTCGTCACGAGTAATTAACTCGAGTGCGATTCCAGACGTTTTCT
TAAAAGTCTATTTGATGCATTACACATTATTTTTATGCTAAAAGAACCCAAACAATTAAACTCAT
ATGGATTTGTTATTCACCGAAAAGCATATAAAGGCATGATTTTCCTTCCTTCAACTCCAACCCAC
TTCGTTCATTCGCTATGCAGATTACTAAGCTTGCTATCACTACTCTTGCCATCGTCACTGGTGTC
ACTGCTGCTCCTGTCGCAAACCCTGAGGCTGCTCCTCAGGCCGAGGCTGCGCCGCTTTTGGGAAT
CGCTTCAGGCTTGGTTAATACCGTTGGTAGCACTGTTGGCGGGATCCTCCACGGTGACATTCTTG
GTGCCGCTGGTAACTTGGTTCATGGTGTTCTCAACTCTGCTGTGGGTGGCCTCGCCTCGGACATT
GCCAACCCCCTTAACATTGCACCTCCTTTCAATGTCCTTGGTGGA
Right flanking sequence: Indices 175074 -- 175573
CCCCGCTGGCCCCGCTGCCCCTGGTCCTTATTAAATAGTTCGTCGATGAATAGCAAATCTTGATG
CACTTTACAATCTCATTTTCGCTCACTTAGTATTATTCAAGAGGGAGGAACCCAATCACCAACTA
TGCATCCGGTCGGCTGCAATGTCAGAAAGTCCAACTCTCTCTCATTATCGGATTCCAGCCCAGAG
AAGTCTAAATCAAACAGTGGACCACTTGAGGCCGGATAATGTTCACGTTTAAGACTGGTGTGTAG
AAACAGCTTAATAGGCATTTCGCGAACTTGGGCGACACGTGCAAATCTCTCACGTTCCGCAGAGA
TATTCGTTACCATATCACGCCATGTTTTAATTGTATCGATGGGAAAATGGTCTGCAGTTTCCAAA
ACTTTTTTATACAACAACCCTAGACGTCTCCAGAAGTACATGATACATCGAATTAAGTAGGCAGC
AGTGAATTTGAAACGAGGCAATAGAACTTCCTTCCACTCGTTCTC
Found at i:200140 original size:45 final size:45
Alignment explanation
Indices: 200073--200162 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
200063 CAGTATGGTC
200073 GTTTTTTTTTCACTTTTCCTGAAAATTAACTAAATACTTAGAAAA
1 GTTTTTTTTTCACTTTTCCTGAAAATTAACTAAATACTTAGAAAA
*
200118 GTTTTTTTTTCACTTTTGCTGAAAATTAACTAAATACTTAGAAAA
1 GTTTTTTTTTCACTTTTCCTGAAAATTAACTAAATACTTAGAAAA
200163 TTAACGGCAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (45 bp):
GTTTTTTTTTCACTTTTCCTGAAAATTAACTAAATACTTAGAAAA
Left flanking sequence: Indices 199573 -- 200072
GATTTTCGAGGAGAAGGCTGTCGAAAATGCCAAGTTGACTGAAAAGTCGGTCACTGAGGAGATCA
AGCAATTGCAGGCCACCTTAAAGGACATCGAATCGGCTAGACCCTTCGACCAGTTGACTGTGGAC
GACGTTGCCGCCGCTTCCGACTTGGATGCTAAGGTCACTTACATGGTTAAGAATGGTAAATGGGA
GGTGCCCGGTTACAAGGAGAAGTTCGGTGACTTGACTGTTATGTAAGACAAGTATAGCATTTTAT
AAACGATAAAGTATTGGAAAACAACCGTTCAAGCTTGATGACACTGGTGAGGATCTTAAGTGTGT
GTGTTCATATCACGTATAGCATTTGCAAAAATAATACGCCTCTACGCTTAAACCCAATCACAGTA
CTGATTTCTAAATAATAATAAAAAAGAAAGGTCGTACTCGGATTCGAACCGAGGTTAATTGGATC
AGAACCAATGGTGATAACCACTACACTATACAACCCAGTATGGTC
Right flanking sequence: Indices 200163 -- 200662
TTAACGGCATGCGTCTTTTTTCACTTTTCCTGAAAATTAACTAAATACTTAGGTTATAAACGGCA
AGCGTCTTATATGGGGAACCGTTGATCGGAGAAAAACCCATTGCATCTGTCATAACATGTATGTC
ATGGTAATTGGTTGGCTTATGTCAATCTTTGTTGTATGAAGCCAGGTTCGTATTTCTGAATATCA
ACGGTTCGATTCCCCGCTACCCTTCTGTCAACCCTACGAGCAACACGTCGTCATATGACTCCTAC
TCTTTTCGTTACCTATGGCGAGCCTTCTCCCACCAATCGCTCTGGTCTGGCTGATGTTTTTCTCG
TGTTTTACAGTCTGATCTTACGTTTCTAAGTAAATAGTTAGCATATTATATGGAAAAAATACAAA
TCAACATGTTAACTCGGCTTTCACAAACAAGTTCCTTGTTATTACCACCAACCCCTTCCTGCGTC
AGGTTAATTTTAGCGTCACACTGCTCCAGTTTCCATGGGCCCAGT
Found at i:200225 original size:56 final size:56
Alignment explanation
Indices: 200122--200235 Score: 174
Period size: 56 Copynumber: 2.0 Consensus size: 56
200112 AGAAAAGTTT
* * *
200122 TTTTTTCACTTTTGCTGAAAATTAACTAAATACTTAGAAAATTAACGGCATGCGTC
1 TTTTTTCACTTTTCCTGAAAATTAACTAAATACTTAGAAAATAAACGGCAAGCGTC
***
200178 TTTTTTCACTTTTCCTGAAAATTAACTAAATACTTAGGTTATAAACGGCAAGCGTC
1 TTTTTTCACTTTTCCTGAAAATTAACTAAATACTTAGAAAATAAACGGCAAGCGTC
200234 TT
1 TT
200236 ATATGGGGAA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (56 bp):
TTTTTTCACTTTTCCTGAAAATTAACTAAATACTTAGAAAATAAACGGCAAGCGTC
Left flanking sequence: Indices 199622 -- 200121
GTCACTGAGGAGATCAAGCAATTGCAGGCCACCTTAAAGGACATCGAATCGGCTAGACCCTTCGA
CCAGTTGACTGTGGACGACGTTGCCGCCGCTTCCGACTTGGATGCTAAGGTCACTTACATGGTTA
AGAATGGTAAATGGGAGGTGCCCGGTTACAAGGAGAAGTTCGGTGACTTGACTGTTATGTAAGAC
AAGTATAGCATTTTATAAACGATAAAGTATTGGAAAACAACCGTTCAAGCTTGATGACACTGGTG
AGGATCTTAAGTGTGTGTGTTCATATCACGTATAGCATTTGCAAAAATAATACGCCTCTACGCTT
AAACCCAATCACAGTACTGATTTCTAAATAATAATAAAAAAGAAAGGTCGTACTCGGATTCGAAC
CGAGGTTAATTGGATCAGAACCAATGGTGATAACCACTACACTATACAACCCAGTATGGTCGTTT
TTTTTTCACTTTTCCTGAAAATTAACTAAATACTTAGAAAAGTTT
Right flanking sequence: Indices 200236 -- 200735
ATATGGGGAACCGTTGATCGGAGAAAAACCCATTGCATCTGTCATAACATGTATGTCATGGTAAT
TGGTTGGCTTATGTCAATCTTTGTTGTATGAAGCCAGGTTCGTATTTCTGAATATCAACGGTTCG
ATTCCCCGCTACCCTTCTGTCAACCCTACGAGCAACACGTCGTCATATGACTCCTACTCTTTTCG
TTACCTATGGCGAGCCTTCTCCCACCAATCGCTCTGGTCTGGCTGATGTTTTTCTCGTGTTTTAC
AGTCTGATCTTACGTTTCTAAGTAAATAGTTAGCATATTATATGGAAAAAATACAAATCAACATG
TTAACTCGGCTTTCACAAACAAGTTCCTTGTTATTACCACCAACCCCTTCCTGCGTCAGGTTAAT
TTTAGCGTCACACTGCTCCAGTTTCCATGGGCCCAGTTTAGACATTATTAATACAACGAGTTTTT
TCTTCAATTTTTTCTGGAGATTTACTCCCTGCTACCCTGCTGGCT
Found at i:214481 original size:27 final size:25
Alignment explanation
Indices: 214453--214502 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
214443 TTTTATTTTT
*
214453 TTTTTTCACTTTTCCTGAAAATTAA
1 TTTTTTCACTCTTCCTGAAAATTAA
214478 TTTTTTCACTCTTCCTGAAAATTAA
1 TTTTTTCACTCTTCCTGAAAATTAA
214503 CTAAATACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.18, G:0.04, T:0.50
Consensus pattern (25 bp):
TTTTTTCACTCTTCCTGAAAATTAA
Left flanking sequence: Indices 213953 -- 214452
AATGTGTGTTGTATTATTAATGTCTAAACTGGGTCCGTAGAAACTGGAACAGTAAGACGCTAAAA
TCAACCTGACGCAGGGAGGGGTTGTGGTAATAAACTGGGAACTTGTTTGTGAAAGCCGAGGAAAT
CAAGAATCCAATGTCTTCTTGATATTACTAGGCTCTGAAGTTAGAGAATTACCGATGATGGAATA
GCATGAAATCCGATTGTTGTTGCAGGTGAGAACACTGAGTTTAAATACTACGCCGGGCGTCGGAA
ACGCCCGGGTCTACAACACATGGGAGGGTGCCGCACCGCAGCCCAATCCAGCACGTGAGTCTTAT
TGTCGGAGCCGTACGGGAACGTGGTCGTCTCAAACTCTAATCTCAAGTCCTGAACCGGAGCGGAA
TCGGCGTCGCTCGCGCGTGTCCTCAGTGCGCCTAACCTACTAGTACGGATCTAGAGTCGTAATAC
AACATTGTGTTTTTTTATGTTTTTTTAACGTGTTTTTTTATTTTT
Right flanking sequence: Indices 214503 -- 215002
CTAAATACTTAAAAGTGTTGTTTAAATCTCCTGGTTTAGGGGATTCGGGTCAAGTTGACTTAACG
CAGGGGAAGTTCCCTAACGCAGGTCGCGGAGGGGTTGTGTTTGTGTAGTTTCGAGTTTTGAATTT
AATTGGTCCCACTTGCAAGACCTGTAATTCCCAAGACTCTTGTTTTACTCTGGCCCGTCTGTGCT
TATTTATGCTGGGAGGGAAGCCCTTGGAGCTTCCTCATCTCCAACGCATTACTCTACATGCTACT
ACAGGAGGGGGGCTCTTCGAGCTTCCCTGTGCACGTCTGCACTCCTCGTAGCCAGACCGGACGCT
ATGCCACCTGGAGTTCCTCTCCTGGGACTCTACTTGAGTCACTAACCTGAGTTCCTCGAAGGAAC
TTATTCTAATACAAATTGCGGTTTGTTTCTAATATTCTGTGTTCACAAATGACTATTTTTGGAAC
TGTTGTATTATTACGACTAAATCAGGTCCTTAGTACCAGTAATAT
Found at i:253542 original size:6 final size:6
Alignment explanation
Indices: 253534--253591 Score: 71
Period size: 6 Copynumber: 9.7 Consensus size: 6
253524 ACGGGGCCGT
* * * * *
253534 GGTCGT GGTCGT GGTCGT GGTCGC GGCCGT GGTCGC GGTCGC GGTCGC
1 GGTCGC GGTCGC GGTCGC GGTCGC GGTCGC GGTCGC GGTCGC GGTCGC
253582 GGTCGC GGTC
1 GGTCGC GGTC
253592 ACTTTGGGGC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.00, C:0.28, G:0.50, T:0.22
Consensus pattern (6 bp):
GGTCGC
Left flanking sequence: Indices 253034 -- 253533
CGAGTTGAAGGAGGGACGTTGGCGAAAGACCGCTTGCTGACCTTCCCACGAACGCCAGCACGTAG
TATACTTGACAACGTCATTATCATCACTTGGGGTTATCTGAGCATGCCGCATACGTTTGGAGGGG
TAGGGCGGTATCGAGCTCTATATTAACTCCTAGTAACTTGGTTGTTCAGGAGCTATCTTATTCCC
TTCGCTCGCAATATCGTGATTACATATAATCCGCTCCTCTATCGAAGTATTTACTTGATCAATTC
GAATACGCGCAACGTGCATCAGCTCAGTGAGGTTGCACGATCACCATATCCGTCCGTCGATTTGC
TAAAATGTCCCAAAGGATCTCTCAAGTCCCATACGTTGACGGAGAGAAGATACTGGTGCCAGCTT
TGGGGCATGTCACAACCTCCGAAACCACCCTGAGCGATTTTTCAACTTCAACACACAGAACAGAT
CTCTCTGAGCTTCAACTCGGAGGTTTTGATGAATCACGGGGCCGT
Right flanking sequence: Indices 253592 -- 254091
ACTTTGGGGCCGGGAGTACCTGGCACAGGGGGAACTACCTAGTTCGCGAGCCTTCTGCTTATCCT
TTTTTGATCAATGGAGCACCACGTTATGAAACATTAACCAACGATGGGCTCTCAATACATGCATT
GAAGTCGAAGGATTTTCTTTCACATTTGAGGGGACGCACACGAAAAGGCCTTGTTCCTCCTTATG
AGGCTTGGCACTACTCTGTGAATGTCAATAACGTGTTGACGCTAGACCGATCGGGAGGAAGCAAG
TACCAGCCCGATACAGTTGCAAACCTTTCCAAGATTGATTTGAGTTTGGGATGGGAGGAGTACCA
GCCCATTGCCAAAGCTGATCGTCCAGATGGTGGCACAAAACTCGAATCAATGATACTCCATGAGA
AAAGGATGAATAGGCGTGCAGAATTCGATATGGTGTGTCTGCGCCACACTATGGTACTGCTTTTG
TACACCACGTTTGATCCATATCGATCCCCAGTGCTGATTGCCGTC
Found at i:253548 original size:12 final size:12
Alignment explanation
Indices: 253534--253591 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 12
253524 ACGGGGCCGT
*
253534 GGTCGTGGTCGT
1 GGTCGTGGTCGC
253546 GGTCGTGGTCGC
1 GGTCGTGGTCGC
*
253558 GGCCGTGGTCGC
1 GGTCGTGGTCGC
*
253570 GGTCGCGGTCGC
1 GGTCGTGGTCGC
*
253582 GGTCGCGGTC
1 GGTCGTGGTC
253592 ACTTTGGGGC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 42 1.00
ACGTcount: A:0.00, C:0.28, G:0.50, T:0.22
Consensus pattern (12 bp):
GGTCGTGGTCGC
Left flanking sequence: Indices 253034 -- 253533
CGAGTTGAAGGAGGGACGTTGGCGAAAGACCGCTTGCTGACCTTCCCACGAACGCCAGCACGTAG
TATACTTGACAACGTCATTATCATCACTTGGGGTTATCTGAGCATGCCGCATACGTTTGGAGGGG
TAGGGCGGTATCGAGCTCTATATTAACTCCTAGTAACTTGGTTGTTCAGGAGCTATCTTATTCCC
TTCGCTCGCAATATCGTGATTACATATAATCCGCTCCTCTATCGAAGTATTTACTTGATCAATTC
GAATACGCGCAACGTGCATCAGCTCAGTGAGGTTGCACGATCACCATATCCGTCCGTCGATTTGC
TAAAATGTCCCAAAGGATCTCTCAAGTCCCATACGTTGACGGAGAGAAGATACTGGTGCCAGCTT
TGGGGCATGTCACAACCTCCGAAACCACCCTGAGCGATTTTTCAACTTCAACACACAGAACAGAT
CTCTCTGAGCTTCAACTCGGAGGTTTTGATGAATCACGGGGCCGT
Right flanking sequence: Indices 253592 -- 254091
ACTTTGGGGCCGGGAGTACCTGGCACAGGGGGAACTACCTAGTTCGCGAGCCTTCTGCTTATCCT
TTTTTGATCAATGGAGCACCACGTTATGAAACATTAACCAACGATGGGCTCTCAATACATGCATT
GAAGTCGAAGGATTTTCTTTCACATTTGAGGGGACGCACACGAAAAGGCCTTGTTCCTCCTTATG
AGGCTTGGCACTACTCTGTGAATGTCAATAACGTGTTGACGCTAGACCGATCGGGAGGAAGCAAG
TACCAGCCCGATACAGTTGCAAACCTTTCCAAGATTGATTTGAGTTTGGGATGGGAGGAGTACCA
GCCCATTGCCAAAGCTGATCGTCCAGATGGTGGCACAAAACTCGAATCAATGATACTCCATGAGA
AAAGGATGAATAGGCGTGCAGAATTCGATATGGTGTGTCTGCGCCACACTATGGTACTGCTTTTG
TACACCACGTTTGATCCATATCGATCCCCAGTGCTGATTGCCGTC
Found at i:253554 original size:18 final size:18
Alignment explanation
Indices: 253534--253591 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
253524 ACGGGGCCGT
* *
253534 GGTCGTGGTCGTGGTCGT
1 GGTCGCGGTCGTGGTCGC
*
253552 GGTCGCGGCCGTGGTCGC
1 GGTCGCGGTCGTGGTCGC
*
253570 GGTCGCGGTCGCGGTCGC
1 GGTCGCGGTCGTGGTCGC
253588 GGTC
1 GGTC
253592 ACTTTGGGGC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.00, C:0.28, G:0.50, T:0.22
Consensus pattern (18 bp):
GGTCGCGGTCGTGGTCGC
Left flanking sequence: Indices 253034 -- 253533
CGAGTTGAAGGAGGGACGTTGGCGAAAGACCGCTTGCTGACCTTCCCACGAACGCCAGCACGTAG
TATACTTGACAACGTCATTATCATCACTTGGGGTTATCTGAGCATGCCGCATACGTTTGGAGGGG
TAGGGCGGTATCGAGCTCTATATTAACTCCTAGTAACTTGGTTGTTCAGGAGCTATCTTATTCCC
TTCGCTCGCAATATCGTGATTACATATAATCCGCTCCTCTATCGAAGTATTTACTTGATCAATTC
GAATACGCGCAACGTGCATCAGCTCAGTGAGGTTGCACGATCACCATATCCGTCCGTCGATTTGC
TAAAATGTCCCAAAGGATCTCTCAAGTCCCATACGTTGACGGAGAGAAGATACTGGTGCCAGCTT
TGGGGCATGTCACAACCTCCGAAACCACCCTGAGCGATTTTTCAACTTCAACACACAGAACAGAT
CTCTCTGAGCTTCAACTCGGAGGTTTTGATGAATCACGGGGCCGT
Right flanking sequence: Indices 253592 -- 254091
ACTTTGGGGCCGGGAGTACCTGGCACAGGGGGAACTACCTAGTTCGCGAGCCTTCTGCTTATCCT
TTTTTGATCAATGGAGCACCACGTTATGAAACATTAACCAACGATGGGCTCTCAATACATGCATT
GAAGTCGAAGGATTTTCTTTCACATTTGAGGGGACGCACACGAAAAGGCCTTGTTCCTCCTTATG
AGGCTTGGCACTACTCTGTGAATGTCAATAACGTGTTGACGCTAGACCGATCGGGAGGAAGCAAG
TACCAGCCCGATACAGTTGCAAACCTTTCCAAGATTGATTTGAGTTTGGGATGGGAGGAGTACCA
GCCCATTGCCAAAGCTGATCGTCCAGATGGTGGCACAAAACTCGAATCAATGATACTCCATGAGA
AAAGGATGAATAGGCGTGCAGAATTCGATATGGTGTGTCTGCGCCACACTATGGTACTGCTTTTG
TACACCACGTTTGATCCATATCGATCCCCAGTGCTGATTGCCGTC
Found at i:261547 original size:27 final size:27
Alignment explanation
Indices: 261517--261574 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
261507 CGGTGCACCC
* *
261517 GCGGGTTGGCCGTAAGCTGGAGCCGCT
1 GCGGGTTGGCCATAAGCTGGAGCCGCA
*
261544 GCGGGTTGGCCATAAGCTGGAGTCGCA
1 GCGGGTTGGCCATAAGCTGGAGCCGCA
261571 GCGG
1 GCGG
261575 CAGCAGGTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.14, C:0.24, G:0.45, T:0.17
Consensus pattern (27 bp):
GCGGGTTGGCCATAAGCTGGAGCCGCA
Left flanking sequence: Indices 261017 -- 261516
TAGAAATGTTTCATTGCGTCAATGTGTGTGATTTTTCCAACCGATAGTGATTGGGCAGGCTGGAT
CTCTTATAGTCTGGGCAGGAACAAGTTCGTTGCGTGAATCTCGAAATCTCCACATACTTTGTCAG
AGCTAATGTGAGCAGGTGCATCCGAAACCCCAGATAATGAAAGAGACTTTGCCATACTTTTAGAT
GTGGAGTTTAACGTTGCGTGAATCGATAATATACTCGTGGATTCATGGTTGCTTACTTTAGTATT
TAGTTCAACTGGACATAGTTGCCAGGAAAGACGCCCTGTTGCCCGTTGTAGGTACCGGTCCACCA
CCCATTGGCGTCGGCAGTCTTCTCCACAATGGTGATGACAGCGCCCGCGGGGAAAGTCAAATCAC
CGGCCGCCTGGGCGGTGTAGTCGTACAAGGCCGTGCACGTTTGCGCTGCGGGAGACGCCGCGACA
GGTGCAGGAGAAGCGGGAGCAGGCAGCCCGTAAGCCGGTGCACCC
Right flanking sequence: Indices 261575 -- 262074
CAGCAGGTTGGGCGTAAGCCGGGGCTGCTGCGGGCTGGCCGTATGCGGGAGTGGCGCTCGGAGCG
CCATAGCCTGCCTTTTTGTCGTCACCATAGGCTCCACCCATAGCACCAGGGGTGTACTGTGGCAA
ACCACCAGTGGTAGCAGTCCCTGCCGATCCAGCAGTTGGGGTAGGCAGCAACAGTGCGGTAGTCA
GCGCACCGGACATGAGCTGTTGGCGTCGACGTACCTGGTCAAGCTTCGATTTGGCATGACCCACT
TTGAAGTTAGTGATCCCCAACGCGTCCGCGCGTTCCTCGGCATCGCCCTTTTTGTGGGTGTATGC
CTCAACAATGTCGGTTGTCAAGTCAAAGTACGGAATCTTGAGCTCCTCCATCCGGTTGTAAAGAG
TATAGAAGATGTTGAGTTGCATGTAGTAGAACAGGACAAACAACGGCTTGATGAACTCCAGCTGC
AATTGGAACAAAGTTGGGAGCTCCTGCTTCATTAACTCGTTGTAG
Found at i:287759 original size:137 final size:137
Alignment explanation
Indices: 287513--287774 Score: 434
Period size: 137 Copynumber: 1.9 Consensus size: 137
287503 ATACTTCTTT
*
287513 TTTCCTGAAAATTAACTAAATACTTAGAAAATTAACGGCATGCGTCTTGTATGGGGAACCGTTGA
1 TTTCCTGAAAATTAACTAAATACTTAGAAAATTAACGGCATGCGTCTTATATGGGGAACCGTTGA
* *
287578 TCGGAGAAAAACCCATTGCATCTGTCATGACATCTAGGTCATGGTAATTGTTTGGCTTATTGCTT
66 TCGGAGAAAAACCCATTGCATCTGTCATGACATCGAGGTCATGGTAATTGGTTGGCTTATTGCTT
287643 TTTTCAC
131 TTTTCAC
* * * **
287650 TTTCCTGAAAATTAACTAAATATTTAGTAAATTATCGGCATGCGTCTTATATGGGGAATTGTTGA
1 TTTCCTGAAAATTAACTAAATACTTAGAAAATTAACGGCATGCGTCTTATATGGGGAACCGTTGA
* *
287715 TTGGAGAGAAACCCATTGCATCTGTCATGACATCGAGGTCATGGTAATTGGTTGGCTTAT
66 TCGGAGAAAAACCCATTGCATCTGTCATGACATCGAGGTCATGGTAATTGGTTGGCTTAT
287775 GTCAGCTTCA
Statistics
Matches: 115, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
137 115 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.35
Consensus pattern (137 bp):
TTTCCTGAAAATTAACTAAATACTTAGAAAATTAACGGCATGCGTCTTATATGGGGAACCGTTGA
TCGGAGAAAAACCCATTGCATCTGTCATGACATCGAGGTCATGGTAATTGGTTGGCTTATTGCTT
TTTTCAC
Left flanking sequence: Indices 287013 -- 287512
CAGCTAACATTAGATCTTTTATGAGCTCGCAACCAATACCGCCGGCTCCAACCATAAGCACTTTT
GTGTGCCGAAGTCGATTTACGGTGTCATTGCCAAGCACTCTTTGAAGGTAACTGTCGCGGGCCAT
GTCGTGAGATTTTTCGCGCCGCGTTCAAAACTGAAGGTTGCGCGAAGTAGAACCAACTCAGGTCC
TATACGCGTCCAATATAGACATCAAGCAAAGTGCATTGGGATTGACAGGAATAGTCCCTGAACAG
CCCGCATGGTCTGTGATGGGCCAGAAAATAAACACATGCACTAATGTTAAATCTATTTCGGCTTT
AGATGGACCCTTACACGTATATAAACAAACAAAGCAAAAAAACTTCAAAAATGGACGAGTTGGGA
ATCGAACCCAAGACCTTTCGCATGCTAAGCGAACGCTCTACCAACTGAGCTACACGCCCATATTT
TATTTGCTTTTTCACTTTTCCTGAAAATTAACTGAATACTTCTTT
Right flanking sequence: Indices 287775 -- 288274
GTCAGCTTCATGGCAGTGTTTAGCAAAAAAGATCCATATAATTTGCTAACTACGTATTTAGATAC
GTCAGATCTGACTGTAAAACACGAGAAAAACATCAGCCAGACCAGAGCGGTTGGTGGGAGAAGGC
CCGCCATAGGTACCGAAAAGGTAGGAGGCATATGACGACGAGCTGCTCGTGGGGTTGACAAAAGA
ATATTTAGTTAATTTTCAGGAAAAGTGAAAAAAAATGAAGACTAGATGTTATGACAGATGCAATG
GGTTTTTCTCCAATCAACGGTTTTCCCATATAAGACGCATGCCGTTAATTTTCTAAGTATTTAGT
TAATTTTCAGGAAAAGTGAAAAAAAGAAGTGAGGAAAAAAAGAGTTCTGAATTCGGTCCCTTGGC
CCAGTTGGTTAAGGCGTGGTGCTAATAACGCCAAGATCAGCGGTTCGATCCCGCTAGGGACCAAT
TTCCTTTTTAAATCTTTTATTCTGGAAGATTTTTTTGGTTACCTA
Found at i:299298 original size:18 final size:18
Alignment explanation
Indices: 299277--299313 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
299267 CTGCCGCCCC
*
299277 TGCCGCTGCCGCTGGTGG
1 TGCCGCCGCCGCTGGTGG
*
299295 TGCCGCCGCTGCTGGTGG
1 TGCCGCCGCCGCTGGTGG
299313 T
1 T
299314 AACAACAACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.32, G:0.43, T:0.24
Consensus pattern (18 bp):
TGCCGCCGCCGCTGGTGG
Left flanking sequence: Indices 298777 -- 299276
ATCGTTGAGGGCATCGCCAAGCGTCAACTTGAGGACCACGTTAAGCGCATGGAGGACCTTGTTGA
GCGCTTGAACAACGACGCCACTTTGACTTCTCGTGACTTCGCCGACGTTCTCGGTAGCATTGTCT
CTGCTATCTGGAACTCTGGTATTATCCAGAATGTCTACAACTGGGTTGTTGACTGGATCAAGAAC
AACCCGGAGCAATTCCAGAACCTCCTCAACCAGGCTCTCTCCTTCATTGGCTCTTTGGCCGGTCA
GTTGTGGCTGTGGTTGCAGTCTTCTGGTCTCCTCGAAAAGGCTTTCAAGTGGCTTGGTGACAACA
TTGGCAACATTCTCGAGGGTTTGATTAAGTTCATTGGCTCTTTGTTCGGTGGCTCTTCCTCTGGT
GACTCTACCCCCAAGGAGCAGCCCAAGGCCTCCGCCGCTCCCGCCGCTGCCACCCCTGCCGCTGC
CGGTGCTACCGTCACCAAGGCCCCCTCTGCCCCTGCTGCCGCCCC
Right flanking sequence: Indices 299314 -- 299813
AACAACAACGATGTCTTGGCCTCTTTGCAGGCTGAGTACGGTAAGCGTGCTGTTCAGACCACCAT
GGCGCAGAAGAGAATGTTGTACTAGGTTTTGGGCTGGTTCTAATACCCTTTTGTTTTTAGTTTGA
TTTTGGGATGTTGGTTGTCGATACACTAATGGTGTAATCCGATCAACTGTAGATATAGTTAGTTT
TGAATAAAGCGTTAATTTAGAATTTGACAAATTGAGAAATGGCAAAGTGGCGATTTTGAATTGTA
ATCATATCGGATCGGATCTGAAGGTACATCTCGATTTAGGTTAACCTTCGAATTTCCGCTATTCA
TTACAAACTGTAATCATTTATTACCCATACCGTCGATACATTGTTCAAGCGTCTGGCATAAACAC
TAATGAGACACCCTCATCACCAGCGGTTATAAGCTTCCCGTCGTCCATGACGGCAAAGTCAAGCA
CTGGCATGTTGTGGCCAACACCACAAAAGGCTTCGTTCCCCGTCC
Found at i:303553 original size:26 final size:26
Alignment explanation
Indices: 303524--303621 Score: 196
Period size: 26 Copynumber: 3.8 Consensus size: 26
303514 TGTCGTAGTG
303524 TCTTTTCTCAGCATTTGCGGTTAGAA
1 TCTTTTCTCAGCATTTGCGGTTAGAA
303550 TCTTTTCTCAGCATTTGCGGTTAGAA
1 TCTTTTCTCAGCATTTGCGGTTAGAA
303576 TCTTTTCTCAGCATTTGCGGTTAGAA
1 TCTTTTCTCAGCATTTGCGGTTAGAA
303602 TCTTTTCTCAGCATTTGCGG
1 TCTTTTCTCAGCATTTGCGG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 72 1.00
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.43
Consensus pattern (26 bp):
TCTTTTCTCAGCATTTGCGGTTAGAA
Left flanking sequence: Indices 303024 -- 303523
GGACTTGTTCGGCGACGGCGGTCAATTCGTTTCGCAGTGCATAGTCCGCAAGCATCTCAGGTACC
ATCTTAGCGAGACGATCCGTGGAGTACGTATCGTTCGCATCGTATTGGGTCCCCTGATACTTGAT
GGAGAATTGGAAACCACGGCCAACGAGCGACGATTGCTTCAACCGCGGGAAGGTCTCCACCTAAA
GCGAACTTCTTGAATAACGTCGTCTCATCTTCTACGACTTGGAAGTATCCTTCGGGTACCGTCTT
CTTGAGCCGGAGCTGACTGATGTGGAACCACCGGTACTTGCCTTGGTAGCCCGGTACTTCCACGT
AGTAGTTGACGGGTGAGACCTTCTGTACGATTGTGAATGGTCACACGAACTTCAACCGCAACTTA
GGCAGGAGCTCGATATTGTGAGGGTCGGCCAACGTCGGCAACAGGCTGACGTCAACGTAGACTTC
ATCGTCCACGTTGAATTCGACCTTGCGTCGTCGTTTGTCGTAGTG
Right flanking sequence: None
Done.