Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: MW717909
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: 146907
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Found at i:19524 original size:15 final size:15
Alignment explanation
Indices: 19504--19533 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19494 TCACTAAATA
19504 GTACTTACTTAACTT
1 GTACTTACTTAACTT
*
19519 GTACTTACTTGACTT
1 GTACTTACTTAACTT
19534 CATTCTACAG
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:0.23, C:0.20, G:0.10, T:0.47
Consensus pattern (15 bp):
GTACTTACTTAACTT
Left flanking sequence: Indices 19004 -- 19503
CGCCTTTGTTTTGGGTACAAAATGTCACGGGGTCCAATCCTGTCATTCCTACCTATTACTTCTCC
TCTGGGCAGTAACGAGGGATCCATTGAGATCGATGAAAATTGAGGACATAAAAAATCTTTCATTT
AATGATACTATATGCATGCAAGATTTAGTGGGGGTACAAAAAGAATCCTTTTCTTTACAGTCGTT
ATCTACTGTGATAAGAAAGCGCTCTTAGTTCAGTTCGGTAGAACGTGGGTCTCCAAAACCCGATG
TCGTAGGTTCAAATCCTACAGAGCGTGATTCCGTTCTTGTTAGGTCTAATTACAATGAAATAACT
TCACTAACTTGAACAGCAACCTGAATTTGACCTCCTGCGGATTAAAGAAAGGAGGAAGTAAAAAC
ATAAAAGAGACCTATTACCAGTGTGATTTCTCTATGAGGTGCAACAAAGGAAGATCTAGGGGAGG
TTGAGTGCTTGCTTTCCTTTTTCCCGGCCTTGCTTTCACTAAATA
Right flanking sequence: Indices 19534 -- 20033
CATTCTACAGCGGCGCAACCCATTGATTGAATTTCCATTCCAACCCACGACATTTATTTTATTTT
CAACCCATGAGTCAAGGAGTCAAGGATTTACAACCACGCCTAGTTCCCTTAGTTCCGAGCCTGCC
GTTAGGAGAACTGATTCCAAGGCGGCGGCCGTTAGCTTTAATAGTTCTGTTCCAAGCAAGCGAGA
TTTCAATAGGCTTAGCCAGGTCCAACTTTGCGGAGAAGCCAAGGGGAAAGGGTGATTCACCAACA
AAACCGGCTTTCTTCACCTGATTCTTCCTCCGATGAAGCAGTCGAGAAGTCAATGGAAAAGGTAC
CATACCCGCGGGGGATATCTCAATCGAAGTCTCCAAATCGAGAAACGTTCGAAATGCCCTTAAAT
CATCGTTTTAAGCCGCGTTCCGCTGATTAGATAGTAAATTCTCCATTGGACGCTTCAAATGACGA
TGACGCCCACTTTTCTTAAGAAATGGATGAATTCTTCTAATTTAA
Found at i:23127 original size:18 final size:18
Alignment explanation
Indices: 23087--23129 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
23077 ACCGCCCTGC
23087 CATAGTCGCGAGTCTGTTT
1 CATAGTCGCGAG-CTGTTT
23106 -ATAGTCGCGA-CTGTTGT
1 CATAGTCGCGAGCTGTT-T
23123 CATAGTC
1 CATAGTC
23130 AACAAGGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 1 0.05
18 16 0.73
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.35
Consensus pattern (18 bp):
CATAGTCGCGAGCTGTTT
Left flanking sequence: Indices 22587 -- 23086
GTAACGAGAAATCCTGTGAAAAACACGATCGCCTGCCAGTGGAAGGCTTTCTGCGTTCAGTCAAT
CTACGCAGAGTGAATCGGTCCCTAAGGAACCCCCGAAAGGGCTGCCGTCCGATGGGTACACGAAA
GTGACGAAGTTGCTTTGACTACAGAACCATGCCTGTCTGTTGGAGCGAATTGGATGATCGGGCCG
AGGGCTGCCCCCTCTTCCCCTCACTCTCCTTTCCCTAATATGAACCTTGAGTCATCAAAGCCTTT
CTGACTCGGCCTGGCCCGGTCGCCCTACGCGACTGGCGCTTCAAAAGGTAGTTTACTTGCTTACT
TGTTATCTAAAGACGAAACTCTCGTCGTAGTTTGTTTGGCGACCTAAGGTAAGGGGCGGACACTT
TTTGTTATCTAATTTCTCATTTCAGTGCTCGCCTTTTTTTTTCTTCAGTAGGGGCCTTTAGTCTT
TTGATTAGAGTAGGGGTCGCGAGAGAGCAGAGCGTACCGCCCTGC
Right flanking sequence: Indices 23130 -- 23629
AACAAGGTGGAAACTTCCAGGAAAAAACTTCGAATTGGGAGGGCGATCCTCCCGGTGAACTGACC
GTACCCCAAACCGACACAGGTGAACAAGTAGAGTATACTAGGGCGCTTGAGAGAACCATGTCGAA
GGAACTCGGCAAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTCCTATCTTTTGATTAGGAA
AGCGGCACATACCAGGGGGTAGCGACTGTTTATTAAAAACACAGGACTCTGCTAAGTGGTAACAC
GATGTATAGAGTCTGACACCTGCCCGGTGCTGGAAGGTCGGAAGGAGAAGTGTTATAAGCTTTGA
ATGGAAGCCCCGGTAAACGGCGGCAGTAACTCTAACTGTCCTAAGGTAGCGAAATTCCTTGTCGC
ATAAGTAGCGACCTGCACGAATGGTGTAACGACTGCCCCGCTGTCTCCGACATGGACCCGGTGAA
ATTGAATTCTCCGTGAAGATGCGGAGTACCAACGGCTAGACGGTA
Found at i:67567 original size:28 final size:26
Alignment explanation
Indices: 67519--67570 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
67509 TTGACCTGAG
*
67519 CTATTCCCTGAGCTATAAAGCAAGTC
1 CTATTCCCCGAGCTATAAAGCAAGTC
*
67545 CTATTGCCCCGAGTCTATGAAGCAAG
1 CTATT-CCCCGAG-CTATAAAGCAAG
67571 GATAGCATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 6 0.27
28 11 0.50
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (26 bp):
CTATTCCCCGAGCTATAAAGCAAGTC
Left flanking sequence: Indices 67019 -- 67518
GAGCAATCTCCCCACCCTCACTCAGTATCACTGAAATACTGAATGGTGCCTAAAAGTAAAAAAGG
GACAAGGAACGAGTAGAAAAACAATTCGAATTGGAAGGAAGGATTCAATCCAGCGTAGAAAACTC
CAGTGCGCGGATGCATAGCGTCGTAGCATTCTTGGAGACGGGTGAGAGTCGGAATGAGCTTAGTC
AAGACTGACTCCTATTCATATTCTTCCTACTTGCTTTCCTATTCCAGATGGCTTTACTTACAGCG
GGTGTGCTGACTTGACCCGAGGAGATCCGATTGCTTGTGCTTATGTACCAGTTCCTATTGCTTGC
TTTACTATTCTGATTCCGATTTCTATTTCTATTGGCAGGCTATTAAGCTGAAAAAGCCTTTCGTT
ATCTTAAATCGACTAGTAACGCGATGTCTTCCCATAAAAAACAACGGCTAGAGCTCAAGCAAATC
TAAAGTTCGAAATTCCCTACTACACCGGGTCTTTATTGACCTGAG
Right flanking sequence: Indices 67571 -- 68070
GATAGCATTACCCAAGGCGATAGTTCCAGTTCTTCTTCCTTTTATTCTATGGTCTATGGTCTTTT
TTTTTTTTTTTAAGCTTCCGGAATAGAATTTAGCTCGCCAGGGCGTGAAGGTGAATCTTTGAGTC
TGACTCACTTTGTAATTACCTTGAGTTTAGCGACCAAGGAAGGGTAGGAGTTTCGATCCTTTGTT
CGGCTTTGGATCGATCATTTCATTTCAGTTGATGCAGACGGACGAGTCAATAAGGAAGAATTAGC
GGATGCGGATGAGCTTATGAAGAAGAGTTCCATTCCAATAGTTGCTCGAAAAAGAGTTCCAATAG
CAGCTCCGGGGGATCAACTAAGTTAGCGATGAATTGCTGAATCTATTAGTGACGAATGGATGAGG
ACCCTTGCAAACAGATCTCGGTGACTACCTTGGCAACTATTTCAGAAAAGAGAACAAGGGCAAAG
GAAAAGAAAAGGACACCCTGAAATTAAATAGAAATAAGAGAATGA
Found at i:69517 original size:13 final size:12
Alignment explanation
Indices: 69499--69523 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
69489 ACCTTTTTAT
69499 AAAAAAATACAG
1 AAAAAAATACAG
69511 AAAAAAATACAG
1 AAAAAAATACAG
69523 A
1 A
69524 GAGTTTATCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAAAAATACAG
Left flanking sequence: Indices 68999 -- 69498
GAGAATCTATCGGACTTGACGAGTTGGCCAATGATCTCATAGAGCTCTATCTATTCCTCTACAAG
ACTGAACTTAATGAGTCTATCTATTCTTCTATAAAGCTCGACCTAGTAGACTTCTCTAGCTTGTG
GCACTAACTAAATGAGAGCACTTGCCGGCCCCTACTTGAGAAGGTGGAGGAGCGCAGCGAGAGTG
CCCCGCGGTTCAGCACCCGAAGCTAGGGAATTACAGCCTTTTGGTTTACAGCTTTTTTCCTTTCT
AACTGGTTCTTGGCATGATCTTTCTTCGTGGAAAGCCCCATAAGAAGTCTAGCTTGGTTAGTAGT
TGAAAGTCCCCTTTAGCTCCCCTTTGGTGCTAGAATATGAAAGAAGGGATTCATTCAATAAAGAT
AGGCCTTCGCTTTCTTCTTTTGTAGTTTAATCATATAAATAAGTTACCTCTTTCTGTTGGAGTGA
CTGAAGCACCATCATCCTCTTTCACCGAGCGTTGAACCTTTTTAT
Right flanking sequence: Indices 69524 -- 70023
GAGTTTATCCATACATAGCACAAACAGATAAGGACGTCCTTATTCAATGTCCAGGGACAAGCCTT
TTATAACTATAACAGATTTCACTAACGAAATAAAAAAAGAAACAGATACATTAAAAAAATAAAAA
ACCTTGTCAGAGTATATACCAATAGGAGACCTCAGGGCGAGGTCTTTTTCTATATTCCGTGGCCA
TCTTGATAACTGGACTGAATGTCTCATCATAGTCGTTTACCCTCTTGCTGCTTGTAGCCAAAGGC
CACCACGCGAACCTTGTAGCGATCAATAGTTCCATCAGACTTTTACTTTACTTTCTCTTGTATAA
CCAAGACCACTTGCAGCCGAAAACTTTCTTATCCGAAGGTAGTTTACTTGCTTATTTGCTAGAAT
AAGGGCTTTTTCCCGGCAATGAGATTAATCACGCAGCTTTTACTATATAAGATACCTAAGCTGGA
GCTTGAAACTAAACCAGAAAGTGGGATAGCCGGATCCGGATACGA
Found at i:81601 original size:19 final size:19
Alignment explanation
Indices: 81577--81614 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
81567 CGGAAAATCA
81577 GATGCTTAATTTCGTATAT
1 GATGCTTAATTTCGTATAT
81596 GATGCTTAATTTCGTATAT
1 GATGCTTAATTTCGTATAT
81615 ATATAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (19 bp):
GATGCTTAATTTCGTATAT
Left flanking sequence: Indices 81077 -- 81576
GATTTCCAAAGCATTTGAGTGTATTTCTATCGTGGTAGCAAAAGAAGAAAAAAAAAAAAAAGAAT
TTCATTATCATATTGGAGTAAGGAATAAGAGTGCTTCAAGGTATACAGCTAAAAAGATCGTACAC
AAAACGTTTCCAGAATTAAAATAAAATCAATGCCTTACGAAGTTTCATAAGGGATGGGGAACAAT
ATGCAGCTACTTGATTACGCAAGACGAAGAACCTTATGTATGGGGATAATATACACAAGAACAAA
TAATGAACGAGGGCGAAGCCAGCCGGAAACACAAAAAGCCCGAAGAAAACAAGAAGGCAGAGGAA
ATCAACATCGACCTCGTATTTGAAAGACTAGCTAGACATGAAGAATGGATAGATGTACTAAACGA
CCCACTCTTAAGGAGACATTGTTGGAAAAAATATAACACCATTCGAAAATTATGGAGGGACATTC
AAATAAATAAAAAACAACCGATATGCGCAAAAAGGCGGAAAATCA
Right flanking sequence: Indices 81615 -- 82114
ATATAATAATGGTCGAAATCACCAATGGCGTGGCGGAAATGAACGAAAAGCGATATGAACGTGCT
ATTTTAAAATCGATTGATAGATAGCCGGATTTGTTCTGATAGATCGAAAGAGTATGAATGGAAAA
GGGGTGCTGCGGATTTTCTAGTTGGCTATGTTGATATAGATCGTTAATAAGTTGCTCTTTACTTA
TTGTATTTTATGCACTAGGCTTAATGGTATTGTCATTGCATTCAGGGCTTAATGAATATCTGAGT
TTGGGACCCCTGCGAATAGGGGGCCAAAACGGTACCTAATTAACATTAACTTCTTTATTCTAGTG
GGAGTGCCCGAAACGGATTCTCCGATCGGCTAATCGGATGTAATTGCGTAAATAAATTAAGTAAT
GGTCTCATCTTGTCCCATTACACTGCATTAGTGAAAGAAGGACCAAGGATGATTCTAACCCTAAA
CTACAGAGGAGCCATTTTACCGGTAGATAATAGTGAAGTGGAATA
Found at i:115003 original size:66 final size:66
Alignment explanation
Indices: 114895--115023 Score: 213
Period size: 66 Copynumber: 2.0 Consensus size: 66
114885 CTTCGTCTTT
* * * *
114895 ATTACCGTCGAGCCCCTCCAACGGCCCGACCACGCCTTTCCCTTTATTACCGTCTATCCCATCAA
1 ATTACCGTCGAGCCCCTCCAACGGCCCGACCACGCCTGTCCCTTTACTACCGCCTACCCCATCAA
114960 A
66 A
*
114961 ATTACCGTCGAGCCCCTCCAACGGCCCGACTACGCCTGTCCCTTTACTACCGCCTACCCCATC
1 ATTACCGTCGAGCCCCTCCAACGGCCCGACCACGCCTGTCCCTTTACTACCGCCTACCCCATC
115024 CAAGGGTACC
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.19, C:0.45, G:0.13, T:0.22
Consensus pattern (66 bp):
ATTACCGTCGAGCCCCTCCAACGGCCCGACCACGCCTGTCCCTTTACTACCGCCTACCCCATCAA
A
Left flanking sequence: Indices 114395 -- 114894
CCATCATATCATCCAAAGAAACTGAAAATACCAAAAAGTTCAAATTCACTGCTAATAACATTAAT
TCAATTGACATTAACATAATAAGAATATTTCGTCTATTAAGGAGGATTCCCCAAATACCTAAAAT
AAAGATGATCATAGAAAATGTGAAATATTTGATAGGATCCATTTCAGGAACGTAGAATGTAAGAG
AAATTCAAATGTTATAACTCCCTCCAGTACGTCAGGAAACACCAGGCTCTTCCAACTTCAAATTA
CCTACGACGCTTCCGATCTTCCCAGTATTGGGGAAGATTTTTATAAAATCGATAGGCATTTTTTC
GAACTTTGAGGTGTTTCGAGAGTTTTTCGGCTTCGGCTAAAAGCTTTTTTTTTTCTGCCTCATAT
TGTTCGAATAAACACTGAATACGGCGTATTAGCTCCTCTTTTGTTTGGGCATCGTCCGGATACTC
ATTGAGGTCCGGAATTTGTGGGTGTGACGGTCCGGCTTCGTCTTT
Right flanking sequence: Indices 115024 -- 115523
CAAGGGTACCCCTTCCATAAGAGAAAGGAGCTCATTTAATAAATGAATGGATGTAGATAGGGTTG
AAAAGAGAACAAAAGCAATCAAAAAATAAAATACGCAGTCCGAAATCGGATTTCCTTTTCGTGCC
ATATGCGCTTAGACTTTACTTTTTCCCCCTTTTTCTTCCCGGTCCAATATTTGTTCTCGAAAGTC
TTCGTTTCCGTGTAAAAGCAAACTCTCCAAATTTATGACCAACCTTTTCTTCAGTGATCTTACAA
CGAACAAAAGTTTTTCCATTGTAAATTCGTACAGAGCAATCAACAAATTCCGGCAAAATAGAAGA
TCTACGTGACCAAATTTTCCTGTTCAAAAGAAGATCTCTCTTCTTCTTCATTCTCAACAGGAATG
CATCAACAAAACTGCCCTTCCATATAGATCGTCGTGGCATGAACTCATTTCTGCGTTTCCCCACC
ACTGCCCGAAATCCAGCTTTGGTGGGCTTCCCTCAAGTTGACACC
Done.