Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_028040
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: 105001
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Found at i:1626 original size:15 final size:15
Alignment explanation
Indices: 1606--1639 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1596 GCTCAATTAT
1606 TTAATTGGCCGG-CAA
1 TTAATT-GCCGGCCAA
1621 TTAATTGCCGGCCAA
1 TTAATTGCCGGCCAA
1636 TTAA
1 TTAA
1640 ATAATTGAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (15 bp):
TTAATTGCCGGCCAA
Left flanking sequence: Indices 1106 -- 1605
TTTTCGGACAGTATTGCTGAAACTGCCACCATGAAAAGTGGATTCCCCTTATTTTCAAACTGCTA
AGTAATCTACGTCACCGTCAACTTTAATTCATGAGATATGCGTCTCTTTTATTAATTCTCTAAAT
TATGCCAACCTATCTTATAAAACCCAGTCCGGCAGTATAATACTAGCTCGCTCACATATATCCCC
ACATTCATTCGTCAAATCAGGCAATCTCTATTGAATAAGAGATAAAATATTGGTCTGAACTATTA
TAATAAATTGAATAAAAAGCTTCCGAGTACGCAAATAGTAGGAATACGTCAGCAGCATTGGCAAT
CTAAAGTTAGGCCGGCAAAAGGTACAAGAATAGCATGTCGCCACTAGCTGCTGTGTTACGGCATC
GGCCACCTACAATAGATAGGGCCTGCGGCCCTATCGGCCTCATTATATAGCAAGCGCTGCCGCGA
TCTTGCGAGCCTGCGGCCTCGTACGGTCTTTCTGCGCTCAATTAT
Right flanking sequence: Indices 1640 -- 2139
ATAATTGAGCGCAGCTATATAATAGGGCGCAGCCTAATTATATAGCACATTGATAGTATTAACAA
GACTATTGAATCTATTCGTACGCCAATAATAATACGCAAGTCTATTAAATACAGCCAAAGATGGA
GGAATGTTTGCCATCTTTATTAGGAGCTAAAGTGCGATTAATTACAAAATTGATTACATTAAATT
GCTAATTAGTTTTGGCGGGGCTCTGCCCCCCCCCAATGGACTAAGTCCTTAGAGGGCAGAGCGGG
TAAGTGCTTAAGTGGCACTATCTGCTAAGACGTCTAAATGCTTTCTTTGATAACCGGAAGTTCTG
AAAAAGTGTGAAATGCCGGAGGACTTTTGACCATCCATTCAAGTGTCGTTGAATTCTGTTCAACA
GCCCAAGGACTTGGAGCACACTTGTTTTCACTGGTTAGAGTAAAAAAAACCACTACAAAGAAACA
AAAAATTCCTATTACAGAAACATATGAGCCGAAACTACTAAAGGC
Found at i:24987 original size:17 final size:17
Alignment explanation
Indices: 24965--24998 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
24955 TTCGCCCTTC
24965 TAATTTTACTACATTTA
1 TAATTTTACTACATTTA
24982 TAATTTTACTACATTTA
1 TAATTTTACTACATTTA
24999 AGGGTACTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATTTTACTACATTTA
Left flanking sequence: Indices 24465 -- 24964
AGTGACAAAAAAAAACAGGAAAAAGCAAAAACCACTTAAGTAAAATAATTTGTTGTATTTTTTTC
TTTGTTCTTCATAGCAACTAGGAATCAAAAAACACCAAATTTGATAACTTAAAAAAGGAAATAAA
AAGTAGAAGCAGGATATTAAAGAAATAGTAACATACGTGCTTAAGGCCTCTGTTAATTGTGTACA
AATAAAACCTGAATAAGAAAGAATAAGAAAGGGTTTCGCTGACGAAAAAAACAAATCTTCTGAAA
ACCAATAACACGTAAACCATGTTAAACTGAAGCAAATAAATATCCAAAAAAAACGAATTTTAACT
TCTTTCAAAATAGTTTTAAATAAAAAATTCATGATATTTCATTGTGTGTTAAACCTAATAAGAAC
GAAAAAACTGTTGGGTTAGCTTTTACTGCGCCTGGCCACGTGTGCAATCAACCGTAAGGCCCTAC
CAATATTTTATTTTCAGTTTATTAGTAGTTAAAGATTCGCCCTTC
Right flanking sequence: Indices 24999 -- 25498
AGGGTACTCATTCATCATAATGCAATTACTATATACTAAAACCGTATTACAGCTGAGCATTTATA
TGTAATTGAGTAAAAGGCATGGCATAGAGCACCTATAGCCACGCGAATCTATGGCGAAATCATAT
TTTTTTTGCTTCATGTATAACATTTATTTCTGGCGTTATTTCTATGCTGCGCGCCCTTTATTTAT
TCGTTATATGAAGACAGCTTTTTTACTTGTAGTTAACGAATGAATGAAGGTTAGTATTGTACCGC
ATTCTTAGCTCAGTCGGATAGAGCGACAACCTTCTAAGTTGAAGGTCACAGGTTCAAATCCTGTA
GGATGCTTAAAAAAAGTGCATAATGAATTAATCAATAATATATACCAACGGTACATGCATCTATC
GATTAGTTTAAACTCGTTAAAGGTTACATACCATACATACATACACGCGCGGATTGACCAATTTA
GAAATAATTTTTTATTTATTTTGGGGGAGAGTGGCCGAGTGGTTA
Found at i:30085 original size:21 final size:21
Alignment explanation
Indices: 30059--30098 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
30049 ACTGTTTGTT
30059 ATTAAG-CAAGATAAAAAAAAA
1 ATTAAGACAA-ATAAAAAAAAA
*
30080 ATTAAGACTAATAAAAAAA
1 ATTAAGACAAATAAAAAAA
30099 CTAGATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.70, C:0.05, G:0.07, T:0.17
Consensus pattern (21 bp):
ATTAAGACAAATAAAAAAAAA
Left flanking sequence: Indices 29559 -- 30058
GATTCTGCTTTATCATCTCATGCTAAATGAAATATATACTGAAATGTATATATATATATATTTCA
TTACATATTTCATTTAGCAAGCGCCAGCGGACTTGCAGAGAATTATTGAGCAGGCCGATAAACTA
GCCGACAGCCGACGAATATCTCCATTGCTGCTTCTATGGCATACTTTCTTTGCTATCGGGTAAGC
CCTGAGCCTCTTGAGCAGTAGTGCCTTTGTTGTAATCACAAGTGATCTAACGGCCGCCCCTAAGA
AAGCCCCAGAAATTCTATGGAAAATAGAAAAAATAGAAGTAAGCTGTGGCTTATAAATGGTAAGA
TGAGGTGATAACGGTCGATTAATTTTCATGTTTTTAGTTGACTTTGATTTTGACTCAAGGTGACA
GGATTTGAACCTATGACCCTCTGTACCCAAAACAGATGCGCTACCAGACTGCGCTACACCTTGTC
TGATATTCCTTAATAAATATTTGATAAATGCTTAGACTGTTTGTT
Right flanking sequence: Indices 30099 -- 30598
CTAGATTTTTAACGCCACTGAAAAAAGCACTACCATCTCGTTCAGTTTCTTTTTTGCTTGAAAAT
ATTTTTTTGGTGGACGTTTATTATTGTTTCAGCTTTTTAATGCTCGCTCGAGGCCATAAGGGCAA
GTCGGTCATTGTCCGCCTTATTTATAAAGCTTTATAATGCAATTACATGTAATTGCATTATAAAG
CCAAGTATTCAAATAATATATGATTAATCTTTCAGTTATGTTATTAATTAAGTAATTCCATGAGG
AAGAGCCATGAATAATCATAGATAAATAAAAGGGCCCGGATCGAAAAGTATTCCATAAAATATAG
CATACTTACAATATGCAATCACTACGTAAATCCATAATGCGAAAGAAGCATAGCAGTTTATTGGA
TCAAAGGTTCTACATAGGGAATGCATTTTGGTCTATGGGTATCTTGTTATGATGATGATTTAGTT
AGTGATACGCAGAAGTTTTTTATTGGAAGTTTGGTAGGTTCAAAA
Found at i:40994 original size:81 final size:81
Alignment explanation
Indices: 40859--41008 Score: 257
Period size: 81 Copynumber: 1.9 Consensus size: 81
40849 AAAATACTCG
*
40859 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTGAGACTGCCGTGTTTACCATTTTCAC
1 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
40924 CAAGCGAGTATGCTCA
66 CAAGCGAGTATGCTCA
* *
40940 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA
1 CTATCGGA-TTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCA
41004 CCAAG
65 CCAAG
41009 TGAGCTCAGG
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
81 63 0.97
82 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (81 bp):
CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
CAAGCGAGTATGCTCA
Left flanking sequence: Indices 40359 -- 40858
TATGGACAACTTCAATCTACTTTAGTCAATCATATGGATATAAAAAAAGCGGCTAATTTAGAAAT
AACATCAGTATTTCAACAACTTTTTGAGCTCATTTTTTACCCATATAATTCTTTATCTTCTTGTT
TGAACAAGCCAATTTATGCTTCACCCACTATACAAAAAAAGACGCAAGGAGGATTACTTAATCAC
CAGAGCATAACCACTTAGTAATTTGAATCCCCACTTTGCCAATTAAGGCCGCAGGCTTTATTGAC
AGAACTGGGGCGCGTAGTTTGTAGCGAAGGTTTTTTTTCTTCTATTTTGAGAAACCCCCCAAAAA
GATTTTTTGCTGCGAAAAGCAGGGCTTTCAAAGATTGTAATGATTTAAACTACTGGAGAATTTGT
TTTTTTGGCGAATAACGGGATTCGAACCCGTGTTTTCAAATTCACAATCTGACACTTTCACCTAT
TAAGTTATACTCGCCCTTTTTTCAATTTAGACATTAAAATACTCG
Right flanking sequence: Indices 41009 -- 41508
TGAGCTCAGGGAAGCGAAACGCAGAGTGGAAACACAATCTTTTTGTTTCGTTTTATTTTCGCCAT
TTTATTTTATAGACATCCCCGGCTTATTCCGGCTCAGCTGGACCCGCGGCATTTTTTCAAATATT
TGAAAAAGATATAGTCCTTTTTTGTCTTAAGGTGTGTAGAGACTCCTTTTTTATTGATTTATACT
AGTCTATCTTAGACCCGAGATAGTGCCGAAAAAATGATTAAATTGAATCTAACAACGGTTGCCTT
GGCAATGGCAATTACTCTTATACGATACGCAGAATACTCCAAAACCTCTATTTATTCTATTTAGA
ACTAAAATAAGATAATGTTTTTTATAAAAAAACTATAAAGTGCAAAGGTTAAAATTTGGAGCTTT
GTTTTACGTAGTTTTGCCATCTATATAATATAATATAGTAAGAAATAATAAGTTGGCGAGGAAGT
AAAAAAAAATATATATATATATATTTTTTATTCGGTGGTCCTGCA
Found at i:44010 original size:14 final size:14
Alignment explanation
Indices: 43993--44027 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
43983 ATCAGCTTTT
43993 TTTAGATTATATAG
1 TTTAGATTATATAG
44007 TTTAGATTATATAG
1 TTTAGATTATATAG
*
44021 TCTAGAT
1 TTTAGAT
44028 ACGCGGGTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.49
Consensus pattern (14 bp):
TTTAGATTATATAG
Left flanking sequence: Indices 43493 -- 43992
CTATTTTTCAAACAGTAGACTTTTCGACTATTTTTGCTTGTGCCAGCGCCTTTTCCGAACCCCAT
CATTATTTTATTTTTTGCAATATGAAATTTCATGCTATAACTGTTATTTGTATTTTACTTTTCAT
TGGCGCTGTTGGAAAATCTGCACAAATAGGATTGCATACTCGGTTACCTGATGCAATGGAGGGTT
TTCGAATATTTGAGGGCTCTCATGTGCCAGTAGGTACATTATAACAATCTCACTGTATGCTGGGA
TCGTCGATCAAATGAGAGTCCCGATCAGAAAAATATCTCATTTTGACCAATCAGCAGGAAACCTA
TAAGGGAAAGCCAAGCCCACCCAACAAAGTAAAGGTTGAAGGAGCTCTATAGGATCCTCAGAGAC
TGTACGTGAGACCTCTTGTTAGAAATGAAATTTATCCTTGAAAAGAAAAGCTGGCCAGATTTAAC
TAAGATACGAAGCATTCTTTTGTCGTGAAGATTTAATCAGCTTTT
Right flanking sequence: Indices 44028 -- 44527
ACGCGGGTCTTCTGGAATAGAAGGATCCATCTAGGGTTTGGGCATGTAGAAAACCTTGTATTGAA
TCAAATATGCCTCGTTATTTTGGTTAGAAGGTGGAAACGTAAAAAAATATATATATTTTTTTTTT
CAGCGCGGCCTAATGTTACATTCCAACTTTCGGGTTGAGCCCAGCCTTATTGTCATCCTTACCAA
AAAGCTCAAATATTTTCTGTTGCTTCGCAAAATATATATATATTTGCGAGAAGCCTTGGGATGGG
GCTGAGACGTTTTTTCATATATAAAAGAAAAAAAACATCTTAGTTGTTAAGGACGCGGCATTCGT
AAGATTCTTTCTTGGGGGAGTCTCTATTTCATAAGTGGAAGATACAGTCCTTACTCTGGCTAGGC
TTATCAGCTTATTACCTGATGCTCTAAAATATTATTTATTTGCCTTCTGGAAGCGTAAGAGGTTT
TTAAAGAGTAGCCCACTCCAGTATCTGCTTTGATTCATGCAGCTA
Found at i:101536 original size:29 final size:29
Alignment explanation
Indices: 101494--101552 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
101484 AAAGCGAAAG
101494 CGCGGTGAGAAATTACTGTAATATGCCCA
1 CGCGGTGAGAAATTACTGTAATATGCCCA
*
101523 CGCGGTGATAAATTACTGTAATATGCCCA
1 CGCGGTGAGAAATTACTGTAATATGCCCA
101552 C
1 C
101553 TTGGAGACTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (29 bp):
CGCGGTGAGAAATTACTGTAATATGCCCA
Left flanking sequence: Indices 100994 -- 101493
AAAAAAATAGATTTTTTTGGCCGGAACTTAGTATTCTAACTCTTGTCGGATGCAGGTGTAATCCC
TGTCGCGCGGTAATGCCCCGCAGACTCTCGATTATTATATGGGAGTGGCAACCCCGGAATTCATA
GCAGAATGGTCGCAGGAAGAAAACCGAGAGGAACACTTTGGTTAACGAGTTAAAGCTTTGGTGCC
CGATCACCTTCGGTATGCTGAACCCTTACTGAGGGCTAGACCACAAGTCAATGAGGAAGAGTATG
ATTAGCTTGATTTCTAATTATAGGCATTCTGGGAATACGGGAAAAGAGGCCAGGAAAGTAGTTGC
TTCCACTACGTTCTACGCGCGTGTTCCACCTCCCGCAGTATTGCTCGTCTCTTAGGTTTTCGCAA
CAATCCGACTCGGGAACGGGGTAACTACCTTGAACTCCAAACAACTGATCGTAGGGTAGGCTAGC
CAGGCCACATGTTCATTGGTAGCAGGATTCTCCAAAAAGCGAAAG
Right flanking sequence: Indices 101553 -- 102052
TTGGAGACTCATAACTTCAAAAAAAACTGGGTGTTCCGGGTAAAAAATATATATATATTTTTTTT
TAAGTGATATTTTTCAATAAAAAATATATTTTTTTCTTCTTGGTTCACCTAGTTTCTAAGACACA
CGCTTGGTTCGCCACCCGAATCCAGTTGTGAAAAAAAAAACGTAAAACAAAATATATATATTTTT
TTTGTAACGTGATACAATGTACTTAGTTAGATATAAGACTGTCAAAGCTTCTGAGTCAACACGAG
CTTAGGCTCTTGAAGACGAAGGGAAGCCTAGAAGATACAAACATTATGAGAAGAGCCGTATGAGG
CCGTAGGCTCACGTACGGTTCGGAAGCCGAGCTGCGTCAGCAATAGAGTGGCTTAGGTTAACATT
GGAGCAGGAGCAGCTACCATTGCTTTAGCGGGAGCTGCTGTAGGTATTGGAAACGTATTTAGTGT
GCGCCTCGCTAAAGCGCGTTTGGAGCAGTAAAGGTTAATAGATTA
Done.