Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold80
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: 303919
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Found at i:37 original size:26 final size:26
Alignment explanation
Indices: 1--99 Score: 198
Period size: 26 Copynumber: 3.8 Consensus size: 26
1 AACCGCAAATGCTGAGAAAAGATTCT
1 AACCGCAAATGCTGAGAAAAGATTCT
27 AACCGCAAATGCTGAGAAAAGATTCT
1 AACCGCAAATGCTGAGAAAAGATTCT
53 AACCGCAAATGCTGAGAAAAGATTCT
1 AACCGCAAATGCTGAGAAAAGATTCT
79 AACCGCAAATGCTGAGAAAAG
1 AACCGCAAATGCTGAGAAAAG
100 GTTCCACATC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.43, C:0.19, G:0.20, T:0.17
Consensus pattern (26 bp):
AACCGCAAATGCTGAGAAAAGATTCT
Left flanking sequence: None
Right flanking sequence: Indices 100 -- 599
GTTCCACATCAGTCAGCTCCGGCTCAAGAAGACGGTACCCGAAGGATACTTCCAAGTCGTAGAAG
ATGAGACGACGTTATTCAAGAAGTTCGCTTTAGGTGGAGACCTTCCCGCGGTTGAAGCAATCGTC
GCTCGTTGGCCGTGGTTTCCAATTCTCCATCAAGTATCAGGGGACCCAATACGATGCGAACGATA
CGTACTCCACGGATCGTCTCGCTAAGATGGTACCTGAGATGCTTGCGGACTATGCACTGCGAAAC
GAATTGACCGCCGTCGCCGAACAAGTCCGGAAGCGGGTTTCGAAGTCCCATAGTTGGGAGGCTGT
AAGGGCATAGGTGCCAACCTAGGTCCTGTACGCGTCCAATATGGACGTCGCACGAAGTGCATTGA
GGTTACAGGAATGGAGCCTACGCAGTCCGCAGGGTCTGCGATGGCCCAGTACATAGACGCATGCA
ATAGTGCAATAAAAATTAGTTGTTGTTAAAGATGGCAGACCAAGG
Found at i:4122 original size:18 final size:18
Alignment explanation
Indices: 4099--4135 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4089 CGTTGTTGTT
*
4099 ACCACCAGCAGCGGCGGC
1 ACCACCAGCAGCAGCGGC
*
4117 ACCACCAGCGGCAGCGGC
1 ACCACCAGCAGCAGCGGC
4135 A
1 A
4136 GGGGCGGCAG
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:0.24, C:0.43, G:0.32, T:0.00
Consensus pattern (18 bp):
ACCACCAGCAGCAGCGGC
Left flanking sequence: Indices 3599 -- 4098
GGACGGGGAACGAAGCCTTTTGTGGTGTTGGCCACAACATGCCAGTGCTTGACTTTGCCGTCATG
GACGACGGGAAGCTTATAACCGCTGGTGATGAGGGTGTCTCATTAGTGTTTATGCCAGACGCTTG
AACAATGTATCGACGGTATGGGTAATAAATGATTACAGTTTGTAATGAATAGCGGAAATTCGAAG
GTTAACCTAAATCGAGATGTACCTTCAGATCCGATCCGATATGATTACAATTCAAAATCGCCACT
TTGCCATTTCTCAATTTGTCAAATTCTAAATTAACGCTTTATTCAAAACTAACTATATCTACAGT
TGATCGGATTACACCATTAGTGTATCGACAACCAACATCCCAAAATCAAACTAAAAACAAAAGGG
TATTAGAACCAGCCCAAAACCTAGTACAACATTCTCTTCTGCGCCATGGTGGTCTGAACAGCACG
CTTACCGTACTCAGCCTGCAAAGAGGCCAAGACATCGTTGTTGTT
Right flanking sequence: Indices 4136 -- 4635
GGGGCGGCAGCAGGGGCAGAGGGGGCCTTGGTGACGGTAGCACCGGCAGCGGCAGGGGTGGCAGC
GGCGGGAGCGGCGGAGGCCTTGGGCTGCTCCTTGGGGGTAGAGTCACCAGAGGAAGAGCCACCGA
ACAAAGAGCCAATGAACTTAATCAAACCCTCGAGAATGTTGCCAATGTTGTCACCAAGCCACTTG
AAAGCCTTTTCGAGGAGACCAGAAGACTGCAACCACAGCCACAACTGACCGGCCAAAGAGCCAAT
GAAGGAGAGAGCCTGGTTGAGGAGGTTCTGGAATTGCTCCGGGTTGTTCTTGATCCAGTCAACAA
CCCAGTTGTAGACATTCTGGATAATACCAGAGTTCCAGATAGCAGAGACAATGCTACCGAGAACG
TCGGCGAAGTCACGAGAAGTCAAAGTGGCGTCGTTGTTCAAGCGCTCAACAAGGTCCTCCATGCG
CTTAACGTGGTCCTCAAGTTGACGCTTGGCGATGCCCTCAACGAT
Found at i:41738 original size:27 final size:27
Alignment explanation
Indices: 41699--41756 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
41689 CAACCTGCTG
* *
41699 CCGCTGCGACTCCAGCTTATGGCCAAC
1 CCGCAGCGACTCCAGCTTACGGCCAAC
*
41726 CCGCAGCGGCTCCAGCTTACGGCCAAC
1 CCGCAGCGACTCCAGCTTACGGCCAAC
41753 CCGC
1 CCGC
41757 GGGTGCACCG
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:0.17, C:0.45, G:0.24, T:0.14
Consensus pattern (27 bp):
CCGCAGCGACTCCAGCTTACGGCCAAC
Left flanking sequence: Indices 41199 -- 41698
CTACAACGAGTTAATGAAGCAGGAGCTCCCAACTTTGTTCCAATTGCAGCTGGAGTTCATCAAGC
CGTTGTTTGTCCTGTTCTACTACATGCAACTCAACATCTTCTATACTCTTTACAACCGGATGGAG
GAGCTCAAGATTCCGTACTTTGACTTGACAACCGACATTGTTGAGGCGTACACCCACAAAAAGGG
CGATGCCGAGGAACGCGCGGACGCGTTGGGGATCACTAACTTCAAAGTGGGTCATGCCAAATCGA
AGCTTGACCAGGTACGTCGACGCCAACAGCTCATGTCCGGTGCGCTGACTACCGCACTGTTGCTG
CCTACCCCAACTGCTGGATCGGCAGGGACTGCTACCACTGGTGGTTTGCCACAGTACACCCCTGG
TGCTATGGGTGGAGCCTATGGTGACGACAAAAAGGCAGGCTATGGCGCTCCGAGCGCCACTCCCG
CATACGGCCAGCCCGCAGCAGCCCCGGCTTACGCCCAACCTGCTG
Right flanking sequence: Indices 41757 -- 42256
GGGTGCACCGGCTTACGGGCTGCCTGCTCCCGCTTCTCCTGCACCTGTCGCGGCGTCTCCCGCAA
CGCAAACGTGCACGGCCTTGTACGACTACACCGCCCAGGCGGCCGGTGATTTGACTTTCCCCGCG
GGCGCTGTCATCACCATTGTGGAGAAGACTGCCGACGCCAATGGGTGGTGGACCGGTACCTACAA
CGGGCAACAGGGCGTCTTTCCTGGCAACTATGTCCAGTTGAACTAAATACTAAAGTAAGCAACCA
TGAATCCACGAGTATATTATCGATTCACGCAACGTTAAACTCCACATCTAAAAGTATGGCAAAGT
CTCTTTCATTATCTGGGGTTTCGGATGCACCTGCTCACATTAGCTCTGACAAAGTATGTGGAGAT
TTCGAGATTCACGCAACGAACTTGTTCCTGCCCAGACTATAGGAGATCCAGCCTGCCCAATCACT
ATCGGTTGGAAAAATCACACACATTGACGCAATGAAACATTTCTA
Found at i:41770 original size:27 final size:27
Alignment explanation
Indices: 41710--41774 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
41700 CGCTGCGACT
* *
41710 CCAGCTTATGGCCAACCCGCAGCGGCT
1 CCAGCTTACGGCCAACCCGCAGCGGCA
*
41737 CCAGCTTACGGCCAACCCGC-GGGTGCA
1 CCAGCTTACGGCCAACCCGCAGCG-GCA
*
41764 CCGGCTTACGG
1 CCAGCTTACGG
41775 GCTGCCTGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 2 0.06
27 31 0.94
ACGTcount: A:0.17, C:0.40, G:0.29, T:0.14
Consensus pattern (27 bp):
CCAGCTTACGGCCAACCCGCAGCGGCA
Left flanking sequence: Indices 41210 -- 41709
TAATGAAGCAGGAGCTCCCAACTTTGTTCCAATTGCAGCTGGAGTTCATCAAGCCGTTGTTTGTC
CTGTTCTACTACATGCAACTCAACATCTTCTATACTCTTTACAACCGGATGGAGGAGCTCAAGAT
TCCGTACTTTGACTTGACAACCGACATTGTTGAGGCGTACACCCACAAAAAGGGCGATGCCGAGG
AACGCGCGGACGCGTTGGGGATCACTAACTTCAAAGTGGGTCATGCCAAATCGAAGCTTGACCAG
GTACGTCGACGCCAACAGCTCATGTCCGGTGCGCTGACTACCGCACTGTTGCTGCCTACCCCAAC
TGCTGGATCGGCAGGGACTGCTACCACTGGTGGTTTGCCACAGTACACCCCTGGTGCTATGGGTG
GAGCCTATGGTGACGACAAAAAGGCAGGCTATGGCGCTCCGAGCGCCACTCCCGCATACGGCCAG
CCCGCAGCAGCCCCGGCTTACGCCCAACCTGCTGCCGCTGCGACT
Right flanking sequence: Indices 41775 -- 42274
GCTGCCTGCTCCCGCTTCTCCTGCACCTGTCGCGGCGTCTCCCGCAACGCAAACGTGCACGGCCT
TGTACGACTACACCGCCCAGGCGGCCGGTGATTTGACTTTCCCCGCGGGCGCTGTCATCACCATT
GTGGAGAAGACTGCCGACGCCAATGGGTGGTGGACCGGTACCTACAACGGGCAACAGGGCGTCTT
TCCTGGCAACTATGTCCAGTTGAACTAAATACTAAAGTAAGCAACCATGAATCCACGAGTATATT
ATCGATTCACGCAACGTTAAACTCCACATCTAAAAGTATGGCAAAGTCTCTTTCATTATCTGGGG
TTTCGGATGCACCTGCTCACATTAGCTCTGACAAAGTATGTGGAGATTTCGAGATTCACGCAACG
AACTTGTTCCTGCCCAGACTATAGGAGATCCAGCCTGCCCAATCACTATCGGTTGGAAAAATCAC
ACACATTGACGCAATGAAACATTTCTAGACCGACGTTAAGCGCAT
Found at i:49694 original size:6 final size:6
Alignment explanation
Indices: 49683--49740 Score: 71
Period size: 6 Copynumber: 9.7 Consensus size: 6
49673 GCCCCAAAGT
* * * *
49683 GACCGC GACCGC GACCGC GACCGC GACCAC GGCCGC GACCAC GACCAC
1 GACCGC GACCGC GACCGC GACCGC GACCGC GACCGC GACCGC GACCGC
*
49731 GACCAC GACC
1 GACCGC GACC
49741 ACGGCCCCGT
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:0.22, C:0.50, G:0.28, T:0.00
Consensus pattern (6 bp):
GACCGC
Left flanking sequence: Indices 49183 -- 49682
GACGGCAATCAGCACTGGGGATCGATATGGATCAAACGTGGTGTACAAAAGCAGTACCATAGTGT
GGCGCAGACACACCATATCGAATTCTGCACGCCTATTCATCCTTTTCTCATGGAGTATCATTGAT
TCGAGTTTTGTGCCACCATCTGGACGATCAGCTTTGGCAATGGGCTGGTACTCCTCCCATCCCAA
ACTCAAATCAATCTTGGAAAGGTTTGCAACTGTATCGGGCTGGTACTTGCTTCCTCCCGATCGGT
CTAGCGTCAACACGTTATTGACATTCACAGAGTAGTGCCAAGCCTCATAAGGAGGAACAAGGCCT
TTTCGTGTGCGTCCCCTCAAATGTGAAAGAAAATCCTTCGACTTCAATGCATGTATTGAGAGCCC
ATCGTTGGTTAATGTTTCATAACGTGGTGCTCCATTGATCAAAAAAGGATAAGCAGAAGGCTCGC
GAACTAGGTAGTTCCCCCTGTGCCAGGTACTCCCGGCCCCAAAGT
Right flanking sequence: Indices 49741 -- 50240
ACGGCCCCGTGATTCATCAAAACCTCCGAGTTGAAGCTCAGAGAGATCTGTTCTGTGTGTTGAAG
TTGAAAAATCGCTCAGGGTGGTTTCGGAGGTTGTGACATGCCCCAAAGCTGGCACCAGTATCTTC
TCTCCGTCAACGTATGGGACTTGAGAGATCCTTTGGGACATTTTAGCAAATCGACGGACGGATAT
GGTGATCGTGCAACCTCACTGAGCTGATGCACGTTGCGCGTATTCGAATTGATCAAGTAAATACT
TCGATAGAGGAGCGGATTATATGTAATCACGATATTGCGAGCGAAGGGAATAAGATAGCTCCTGA
ACAACCAAGTTACTAGGAGTTAATATAGAGCTCGATACCGCCCTACCCCTCCAAACGTATGCGGC
ATGCTCAGATAACCCCAAGTGATGATAATGACGTTGTCAAGTATACTACGTGCTGGCGTTCGTGG
GAAGGTCAGCAAGCGGTCTTTCGCCAACGTCCCTCCTTCAACTCG
Found at i:49706 original size:18 final size:18
Alignment explanation
Indices: 49683--49740 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
49673 GCCCCAAAGT
*
49683 GACCGCGACCGCGACCGC
1 GACCGCGACCACGACCGC
*
49701 GACCGCGACCACGGCCGC
1 GACCGCGACCACGACCGC
* *
49719 GACCACGACCACGACCAC
1 GACCGCGACCACGACCGC
49737 GACC
1 GACC
49741 ACGGCCCCGT
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:0.22, C:0.50, G:0.28, T:0.00
Consensus pattern (18 bp):
GACCGCGACCACGACCGC
Left flanking sequence: Indices 49183 -- 49682
GACGGCAATCAGCACTGGGGATCGATATGGATCAAACGTGGTGTACAAAAGCAGTACCATAGTGT
GGCGCAGACACACCATATCGAATTCTGCACGCCTATTCATCCTTTTCTCATGGAGTATCATTGAT
TCGAGTTTTGTGCCACCATCTGGACGATCAGCTTTGGCAATGGGCTGGTACTCCTCCCATCCCAA
ACTCAAATCAATCTTGGAAAGGTTTGCAACTGTATCGGGCTGGTACTTGCTTCCTCCCGATCGGT
CTAGCGTCAACACGTTATTGACATTCACAGAGTAGTGCCAAGCCTCATAAGGAGGAACAAGGCCT
TTTCGTGTGCGTCCCCTCAAATGTGAAAGAAAATCCTTCGACTTCAATGCATGTATTGAGAGCCC
ATCGTTGGTTAATGTTTCATAACGTGGTGCTCCATTGATCAAAAAAGGATAAGCAGAAGGCTCGC
GAACTAGGTAGTTCCCCCTGTGCCAGGTACTCCCGGCCCCAAAGT
Right flanking sequence: Indices 49741 -- 50240
ACGGCCCCGTGATTCATCAAAACCTCCGAGTTGAAGCTCAGAGAGATCTGTTCTGTGTGTTGAAG
TTGAAAAATCGCTCAGGGTGGTTTCGGAGGTTGTGACATGCCCCAAAGCTGGCACCAGTATCTTC
TCTCCGTCAACGTATGGGACTTGAGAGATCCTTTGGGACATTTTAGCAAATCGACGGACGGATAT
GGTGATCGTGCAACCTCACTGAGCTGATGCACGTTGCGCGTATTCGAATTGATCAAGTAAATACT
TCGATAGAGGAGCGGATTATATGTAATCACGATATTGCGAGCGAAGGGAATAAGATAGCTCCTGA
ACAACCAAGTTACTAGGAGTTAATATAGAGCTCGATACCGCCCTACCCCTCCAAACGTATGCGGC
ATGCTCAGATAACCCCAAGTGATGATAATGACGTTGTCAAGTATACTACGTGCTGGCGTTCGTGG
GAAGGTCAGCAAGCGGTCTTTCGCCAACGTCCCTCCTTCAACTCG
Found at i:49743 original size:12 final size:12
Alignment explanation
Indices: 49683--49740 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 12
49673 GCCCCAAAGT
*
49683 GACCGCGACCGC
1 GACCACGACCGC
*
49695 GACCGCGACCGC
1 GACCACGACCGC
*
49707 GACCACGGCCGC
1 GACCACGACCGC
*
49719 GACCACGACCAC
1 GACCACGACCGC
49731 GACCACGACC
1 GACCACGACC
49741 ACGGCCCCGT
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:0.22, C:0.50, G:0.28, T:0.00
Consensus pattern (12 bp):
GACCACGACCGC
Left flanking sequence: Indices 49183 -- 49682
GACGGCAATCAGCACTGGGGATCGATATGGATCAAACGTGGTGTACAAAAGCAGTACCATAGTGT
GGCGCAGACACACCATATCGAATTCTGCACGCCTATTCATCCTTTTCTCATGGAGTATCATTGAT
TCGAGTTTTGTGCCACCATCTGGACGATCAGCTTTGGCAATGGGCTGGTACTCCTCCCATCCCAA
ACTCAAATCAATCTTGGAAAGGTTTGCAACTGTATCGGGCTGGTACTTGCTTCCTCCCGATCGGT
CTAGCGTCAACACGTTATTGACATTCACAGAGTAGTGCCAAGCCTCATAAGGAGGAACAAGGCCT
TTTCGTGTGCGTCCCCTCAAATGTGAAAGAAAATCCTTCGACTTCAATGCATGTATTGAGAGCCC
ATCGTTGGTTAATGTTTCATAACGTGGTGCTCCATTGATCAAAAAAGGATAAGCAGAAGGCTCGC
GAACTAGGTAGTTCCCCCTGTGCCAGGTACTCCCGGCCCCAAAGT
Right flanking sequence: Indices 49741 -- 50240
ACGGCCCCGTGATTCATCAAAACCTCCGAGTTGAAGCTCAGAGAGATCTGTTCTGTGTGTTGAAG
TTGAAAAATCGCTCAGGGTGGTTTCGGAGGTTGTGACATGCCCCAAAGCTGGCACCAGTATCTTC
TCTCCGTCAACGTATGGGACTTGAGAGATCCTTTGGGACATTTTAGCAAATCGACGGACGGATAT
GGTGATCGTGCAACCTCACTGAGCTGATGCACGTTGCGCGTATTCGAATTGATCAAGTAAATACT
TCGATAGAGGAGCGGATTATATGTAATCACGATATTGCGAGCGAAGGGAATAAGATAGCTCCTGA
ACAACCAAGTTACTAGGAGTTAATATAGAGCTCGATACCGCCCTACCCCTCCAAACGTATGCGGC
ATGCTCAGATAACCCCAAGTGATGATAATGACGTTGTCAAGTATACTACGTGCTGGCGTTCGTGG
GAAGGTCAGCAAGCGGTCTTTCGCCAACGTCCCTCCTTCAACTCG
Found at i:88800 original size:25 final size:25
Alignment explanation
Indices: 88766--88815 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
88756 AAGTATTTAG
*
88766 TTAATTTTCAGGAAGAGTGAAAAAA
1 TTAATTTTCAGGAAAAGTGAAAAAA
88791 TTAATTTTCAGGAAAAGTGAAAAAA
1 TTAATTTTCAGGAAAAGTGAAAAAA
88816 AAAAATAAAA
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:0.50, C:0.04, G:0.18, T:0.28
Consensus pattern (25 bp):
TTAATTTTCAGGAAAAGTGAAAAAA
Left flanking sequence: Indices 88266 -- 88765
ATATTACTGGTACTAAGGACCTGATTTAGTCGTAATAATACAACAGTTCCAAAAATAGTCATTTG
TGAACACAGAATATTAGAAACAAACCGCAATTTGTATTAGAATAAGTTCCTTCGAGGAACTCAGG
TTAGTGACTCAAGTAGAGTCCCAGGAGAGGAACTCCAGGTGGCATAGCGTCCGGTCTGGCTACGA
GGAGTGCAGACGTGCACAGGGAAGCTCGAAGAGCCCCCCTCCTGTAGTAGCATGTAGAGTAATGC
GTTGGAGATGAGGAAGCTCCAAGGGCTTCCCTCCCAGCATAAATAAGCACAGACGGGCCAGAGTA
AAACAAGAGTCTTGGGAATTACAGGTCTTGCAAGTGGGACCAATTAAATTCAAAACTCGAAACTA
CACAAACACAACCCCTCCGCGACCTGCGTTAGGGAACTTCCCCTGCGTTAAGTCAACTTGACCCG
AATCCCCTAAACCAGGAGATTTAAACAACACTTTTAAGTATTTAG
Right flanking sequence: Indices 88816 -- 89315
AAAAATAAAAAAACAAGTTAAAAAAACATAAAAAAACACAATGTTGTATTACGACTCTAGATCCG
TACTAGTAGGTTAGGCGCACTGAGGACACGCGCGAGCGACGCCGATTCCGCTCCGGTTCAGGACT
TGAGATTAGAGTTTGAGACGACCACGTTCCCGTACGGCTCCGACAATAAGACTCACGTGCTGGAT
TGGGCTGCGGTGCGGCACCCTCCCATGTGTTGTAGACCCGGGCGTTTCCGACGCCCGGCGTAGTA
TTTAAACTCAGTGTTCTCACCTGCAACAACAATCGGATTTCATGCTATTCCATCATCGGTAATTC
TCTAACTTCAGAGCCTAGTAATATCAAGAAGACATTGGATTCTTGATTTCCTCGGCTTTCACAAA
CAAGTTCCCAGTTTATTACCACAACCCCTCCCTGCGTCAGGTTGATTTTAGCGTCTTACTGTTCC
AGTTTCTACGGACCCAGTTTAGACATTAATAATACAACACACATT
Found at i:148083 original size:21 final size:19
Alignment explanation
Indices: 148065--148105 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
148055 GAAGTCATTG
148065 TTTAGAGGATACGAA-TCA
1 TTTAGAGGATACGAAGTCA
*
148083 TTTAGAGGATACG-AGTTA
1 TTTAGAGGATACGAAGTCA
148101 TTTAG
1 TTTAG
148106 CTGACGGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.34
Consensus pattern (19 bp):
TTTAGAGGATACGAAGTCA
Left flanking sequence: Indices 147565 -- 148064
TAGAAACGAGCGTTTTTGACGCCCAGCGTAGTATTTAATCTCGGTGTTCTCAGTTGTAATTTTCA
TCGGTAATTCTCTGACTTCATAACCTGATAACTTCATGAAGACAATTAGATTCTTGAGTAACTCT
CACAAACTAGTTCCCGATCAAATACCACCAATCCTTCCCTGTGTCTGGTGATTTTGGCGGCACAC
TGTTCCAGTTTCTACAGACCTAGTTTACACATTTTGTAGTGATGATATGTTGTATGAAATCCCCG
ATCAGCACTACAGGGATGCTAGGCCCGGCAGGACGCGAGACCAGCTGGACCGGCTATGAGCCACG
CTAGATGAGACCTGGAGGGAAGGTTCGGGAAACGGGGTTGACGGCCGAGGGCAAACCGGAAGTGG
TAATAAGGTACGCGTGGCAAACGGCGTTTTGCCACTAGTACCTTCAGGAGAATCCCAGAGATTCG
AAGACGGGGAGCGTTCTGGTGGACATTATTAGGTCGAAGTCATTG
Right flanking sequence: Indices 148106 -- 148605
CTGACGGATTTGGGAACACTCTCGTTTACGTGTTACTGAATCAATCCAAGTTGCCTACGTTAACA
AACTTAGTTGTCTAAAGGCCATAAGCTTATTTTACGATTTAATGAACCTAACATATGGGGTGCCT
TTATCTTTTTATGCTTTCAACTCTTCGTAGGCGTCCAGTGACTGAGAGAGTGCTTGTAGACGTTA
AAATCCGTGCTTTTGTCTAAAACAATGAGGGGGTAATTCCTCGTGGGAACCGCGGCCGCTAAAAC
AATAAAACTATCTTCCTGATAAACACCTCCCCTGTTCTTCACTCCTTCACCAGTCAGCATAACCT
GTGATTTGACTAAAACTGTTGGAATATAATATGACAGCACGCTTGCATTTCATTGTTAGCGATAT
TACGTGTGTAGTACTCGCTTGTACCCCGCCTTTTACTAAAAGAAACGTCACAAGGGTATAGAAAT
ATATAGACATTGGACGATCATATAGAAAAGTATGCCTTATTTATC
Found at i:228945 original size:20 final size:20
Alignment explanation
Indices: 228920--228958 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
228910 TCAAATAAAG
*
228920 CGAACCCTCATGAGCAAGAA
1 CGAACCCCCATGAGCAAGAA
*
228940 CGAACCCCCGTGAGCAAGA
1 CGAACCCCCATGAGCAAGA
228959 GCAAACTTAC
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:0.36, C:0.33, G:0.23, T:0.08
Consensus pattern (20 bp):
CGAACCCCCATGAGCAAGAA
Left flanking sequence: Indices 228420 -- 228919
TTCGCCGTGCTGGCTAATCAACTTTACCAACTGAGGAGGGTTTGCACCCACTAATTGGTCTATTC
TCTCGCTTCCTTTGAAGAAGAGGCAAGTGGGCATAGCAGTAATCTGATACTCCTGAGCAACTTCC
GCAGCTTGGTCCACGTCAACCCTACCGAATTGGACTTCAGGGATCCGTTCAGACAACATAGCAAA
TACAGGCTCAATGGCTTTGCAAGGACCGCACCAGGTGGCATAAAAATCTATCACTGAAAGCTTCT
CCGCTTTGATGAAGTCTTTGAAGCCACTAAGATCAGTCAACTCTTTAACGTTCCCCTTCGGAGTT
TTGCTCAGTAGCATTCGCATTGGAGCGATGAAATGGCGAGTGGTGGCGACAAAATGACGAGCAGC
TAAGGGATTGGGGCCAAGTTTCAACATCCGTGGTCGATTGCGTTCCAAAGTTGATTAATATCAGT
TATGCGTCGAAAGTGAGCTTACGTAATGGTTGCGATCAAATAAAG
Right flanking sequence: Indices 228959 -- 229458
GCAAACTTACAAGGCTAACGGCGTTGAAGGATGTATAAATCTTCAATTTCCCTTCCTGACCCTCT
ACGAGGAATCCCTACTTCGCACGTCTAAAGGTTGTTCTACTCTGAATTTGCATTCAAGGCGGATG
GAAAGAGCATAGGCTTGGGATGTGCCCTATGGATCTCCGGTTTATGATTGATAATGTCTAGCGAT
TGCTCATTTACATTGGTTTGCCATTTTGGTTGGGAAAGGATTCATGGTGTATTAGAACATGCGCG
CATCGCGCCGCGATGAGATAAATCATTACATTTAAGTTCACAAATTTTGGAAACTACGCAATGGG
AGTGAAAACTACCAATAAAAGAAAGTCGTCGCTGGTGTCTAACAAAGTTAGCAAACGTGCTAAAC
TCGTGGAGAAGAAAGAGTCGTCGCCTGAGTTGTCGGAAAGTGAGCAGGAGCACGAACCTTTTGAG
GTTGATGATCTTGATGAGCTCGATGAGCTTGACCATTTTAGTGAC
Done.