Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1794
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 27282
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Found at i:2737 original size:47 final size:46
Alignment explanation
Indices: 2681--2998 Score: 300
Period size: 47 Copynumber: 6.8 Consensus size: 46
2671 TACTAGATCT
* * * *
2681 TAACACCAATATAGTCAAATAATGGTATAAAGAGTTTGACCAGCTGC
1 TAACGCCAATACAGTCAAATAATGGTA-AAAGAGTTTGACCAGGTCC
* * *
2728 TAACGCCAATACAGCCAAATAATGGTGAAAAGAAGTTTGACTAAGTCC
1 TAACGCCAATACAGTCAAATAATGGT-AAAAG-AGTTTGACCAGGTCC
* *
2776 TAACACCAATACAGTCAAATAATAGTAAAAAGAGTTTGACCAGGTCC
1 TAACGCCAATACAGTCAAATAATGGT-AAAAGAGTTTGACCAGGTCC
* * *
2823 TAACGTCAATACAGTCAAACAATGGTATAAAGAGTTTGACGAGGTCC
1 TAACGCCAATACAGTCAAATAATGGTA-AAAGAGTTTGACCAGGTCC
* * * * *
2870 TAATGCCAATATAGCCAAACAATGGTGAAAAGAAGTTTGACTAGGTCC
1 TAACGCCAATACAGTCAAATAATGGT-AAAAG-AGTTTGACCAGGTCC
* * * * ** *
2918 TAA-TCCATTACACTTAAAGGA-GG-AAAACGAGTTTGACTAGGTCC
1 TAACGCCAATACAGTCAAATAATGGTAAAA-GAGTTTGACCAGGTCC
* *
2962 TAATGCCAATACAGTCAAATGATGGTGAAAAGAGTTT
1 TAACGCCAATACAGTCAAATAATGGT-AAAAGAGTTT
2999 AACTATATGC
Statistics
Matches: 225, Mismatches: 36, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
44 22 0.10
45 14 0.06
46 5 0.02
47 122 0.54
48 62 0.28
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (46 bp):
TAACGCCAATACAGTCAAATAATGGTAAAAGAGTTTGACCAGGTCC
Found at i:2833 original size:95 final size:94
Alignment explanation
Indices: 2681--2920 Score: 302
Period size: 95 Copynumber: 2.5 Consensus size: 94
2671 TACTAGATCT
* * *
2681 TAACACCAATATAGTCAAATAATGGTATAAAGAGTTTGACCAGCTGCTAACGCCAATACAGCCAA
1 TAACACCAATATAGTCAAATAATGGTAAAAAGAGTTTGACCAGGTCCTAACGCCAATACAGCCAA
* *
2746 ATAATGGTGA-AAAGAAGTTTGACTAAGTCC
66 ACAATGGT-ATAAAG-AGTTTGACGAAGTCC
* * * *
2776 TAACACCAATACAGTCAAATAATAGTAAAAAGAGTTTGACCAGGTCCTAACGTCAATACAGTCAA
1 TAACACCAATATAGTCAAATAATGGTAAAAAGAGTTTGACCAGGTCCTAACGCCAATACAGCCAA
*
2841 ACAATGGTATAAAGAGTTTGACGAGGTCC
66 ACAATGGTATAAAGAGTTTGACGAAGTCC
** * * * *
2870 TAATGCCAATATAGCCAAACAATGGTGAAAAGAAGTTTGACTAGGTCCTAA
1 TAACACCAATATAGTCAAATAATGGTAAAAAG-AGTTTGACCAGGTCCTAA
2921 TCCATTACAC
Statistics
Matches: 125, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
94 39 0.31
95 86 0.69
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.23
Consensus pattern (94 bp):
TAACACCAATATAGTCAAATAATGGTAAAAAGAGTTTGACCAGGTCCTAACGCCAATACAGCCAA
ACAATGGTATAAAGAGTTTGACGAAGTCC
Found at i:2900 original size:142 final size:139
Alignment explanation
Indices: 2681--2998 Score: 395
Period size: 142 Copynumber: 2.3 Consensus size: 139
2671 TACTAGATCT
* * *
2681 TAACACCAATATAGTCAAATAATGGTATAAAGAGTTTGACCAGCTGCTAACGCCAATACAGCCAA
1 TAACGCCAATACAGTCAAATAATGGTATAAAGAGTTTGACCAGCTCCTAACGCCAATACAGCCAA
* * * *
2746 ATAATGGTGAAAAGAAGTTTGACTAAGTCCTAACACCAATACAGTCAAATAATAGTAAAAAGAGT
66 ACAATGGTGAAAAGAAGTTTGACTAAGTCCTAA-ACCAATACACT-AAA-AAGAGGAAAAAGAGT
2811 TTGACCAGGTCC
128 TTGACCAGGTCC
* * * * * *
2823 TAACGTCAATACAGTCAAACAATGGTATAAAGAGTTTGACGAGGTCCTAATGCCAATATAGCCAA
1 TAACGCCAATACAGTCAAATAATGGTATAAAGAGTTTGACCAGCTCCTAACGCCAATACAGCCAA
* * * * * *
2888 ACAATGGTGAAAAGAAGTTTGACTAGGTCCTAATCCATTACACTTAAAGGAGGAAAACGAGTTTG
66 ACAATGGTGAAAAGAAGTTTGACTAAGTCCTAAACCAATACACTAAAAAGAGGAAAAAGAGTTTG
*
2953 ACTAGGTCC
131 ACCAGGTCC
* *
2962 TAATGCCAATACAGTCAAATGATGGTGA-AAAGAGTTT
1 TAACGCCAATACAGTCAAATAATGGT-ATAAAGAGTTT
2999 AACTATATGC
Statistics
Matches: 151, Mismatches: 24, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
139 53 0.35
140 3 0.02
141 8 0.05
142 87 0.58
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (139 bp):
TAACGCCAATACAGTCAAATAATGGTATAAAGAGTTTGACCAGCTCCTAACGCCAATACAGCCAA
ACAATGGTGAAAAGAAGTTTGACTAAGTCCTAAACCAATACACTAAAAAGAGGAAAAAGAGTTTG
ACCAGGTCC
Found at i:3112 original size:30 final size:30
Alignment explanation
Indices: 3076--3133 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
3066 TTTGATCAAG
* *
3076 TATAGTCTAA-TGATGAAAGACTTAACTAGA
1 TATAGTC-AAGTGAGGAAAGACCTAACTAGA
3106 TATAGTCAAGTGAGGAAAGACCTAACTA
1 TATAGTCAAGTGAGGAAAGACCTAACTA
3134 AATACAACCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.26
Consensus pattern (30 bp):
TATAGTCAAGTGAGGAAAGACCTAACTAGA
Found at i:6465 original size:20 final size:20
Alignment explanation
Indices: 6440--6514 Score: 80
Period size: 20 Copynumber: 3.6 Consensus size: 20
6430 ATTTGCCTGC
*
6440 ATGTATTGATACAATTATAA
1 ATGTATCGATACAATTATAA
6460 ATGTATCGATACAATT-TGAA
1 ATGTATCGATACAATTAT-AA
* *
6480 GCATGTATCGATACATTTATTA
1 --ATGTATCGATACAATTATAA
*
6502 ATGTATCGGTACA
1 ATGTATCGATACA
6515 TGTCCTTGGC
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
19 1 0.02
20 29 0.62
22 16 0.34
23 1 0.02
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACAATTATAA
Found at i:6565 original size:19 final size:18
Alignment explanation
Indices: 6539--6626 Score: 78
Period size: 19 Copynumber: 4.9 Consensus size: 18
6529 TGCAAGGTGA
6539 TTTGTATCGATACAAAAC
1 TTTGTATCGATACAAAAC
6557 TTATGTATCGATAC---A-
1 TT-TGTATCGATACAAAAC
6572 -TTGTATCGATACAAAAC
1 TTTGTATCGATACAAAAC
**
6589 TTCTGTATCGATACATTTAC
1 TT-TGTATCGATACA-AAAC
6609 TGTTTGTATCGATACAAA
1 --TTTGTATCGATACAAA
6627 TTGTAGAAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
13 11 0.20
14 1 0.02
16 2 0.04
18 3 0.05
19 23 0.41
20 2 0.04
21 12 0.21
22 2 0.04
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACAAAAC
Found at i:6578 original size:13 final size:13
Alignment explanation
Indices: 6560--6584 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6550 ACAAAACTTA
6560 TGTATCGATACAT
1 TGTATCGATACAT
6573 TGTATCGATACA
1 TGTATCGATACA
6585 AAACTTCTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:6581 original size:32 final size:32
Alignment explanation
Indices: 6540--6605 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
6530 GCAAGGTGAT
6540 TTGTATCGATACAAAACTTATGTATCGATACA
1 TTGTATCGATACAAAACTTATGTATCGATACA
*
6572 TTGTATCGATACAAAACTTCTGTATCGATACA
1 TTGTATCGATACAAAACTTATGTATCGATACA
6604 TT
1 TT
6606 TACTGTTTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (32 bp):
TTGTATCGATACAAAACTTATGTATCGATACA
Found at i:9059 original size:32 final size:32
Alignment explanation
Indices: 9004--9064 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
8994 TAGCCAAACT
* *
9004 TGTATCGATACACCAAGTATGTATCGATATAA
1 TGTATCGATACACAAAATATGTATCGATATAA
9036 TGTATCGATACACAAAA-ATTGTATCGATA
1 TGTATCGATACACAAAATA-TGTATCGATA
9065 CATTGGCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 1 0.04
32 25 0.96
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (32 bp):
TGTATCGATACACAAAATATGTATCGATATAA
Found at i:10724 original size:20 final size:20
Alignment explanation
Indices: 10679--10732 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
10669 CACATATTTG
*
10679 TGTGTATCGATACTATGCAA
1 TGTGTATCGATACTATGAAA
* *
10699 TCTGTATCGATAC-ATTTAAA
1 TGTGTATCGATACTA-TGAAA
10719 TGTGTATCGATACT
1 TGTGTATCGATACT
10733 TTTCAGGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTGTATCGATACTATGAAA
Found at i:10797 original size:21 final size:21
Alignment explanation
Indices: 10771--10811 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
10761 GTCAACCTTG
10771 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
10792 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
10812 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:13328 original size:18 final size:18
Alignment explanation
Indices: 13305--13340 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
13295 GTCAACCATC
13305 AATGATGATGAAGATGGT
1 AATGATGATGAAGATGGT
*
13323 AATGATGATGATGATGGT
1 AATGATGATGAAGATGGT
13341 GACTCGGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.31
Consensus pattern (18 bp):
AATGATGATGAAGATGGT
Found at i:18482 original size:79 final size:79
Alignment explanation
Indices: 18399--18548 Score: 196
Period size: 79 Copynumber: 1.9 Consensus size: 79
18389 ATAAAATCGG
* * * *
18399 GGTTGAAGTATTCCCTCGAAAATAACAGGG-TTGGAATGTCCCCGATTGTGAAAAATT-GATGCT
1 GGTTGAAGTATCCCCGCGAAAATAAC-GGGATTGGAATATCCCCGATTATGAAAAATTAG-TGCT
18462 TTAGAAATAAGGCCGA
64 TTAGAAATAAGGCCGA
* * * *
18478 GGTTGGAGTATCCCCGCGAAAATAACGGGATTGGAGTATCCCCGATTATGAAAACTTAGTGTTTT
1 GGTTGAAGTATCCCCGCGAAAATAACGGGATTGGAATATCCCCGATTATGAAAAATTAGTGCTTT
18543 AGAAAT
66 AGAAAT
18549 TAAATAGGGT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
78 3 0.05
79 57 0.93
80 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.27
Consensus pattern (79 bp):
GGTTGAAGTATCCCCGCGAAAATAACGGGATTGGAATATCCCCGATTATGAAAAATTAGTGCTTT
AGAAATAAGGCCGA
Found at i:18575 original size:129 final size:130
Alignment explanation
Indices: 18425--18828 Score: 532
Period size: 129 Copynumber: 3.1 Consensus size: 130
18415 CGAAAATAAC
* * * ** ** * *
18425 AGGGTTGGAATGTCCCCGATTGTGAAAAATTGATGCTTTAGAAATAAGGCCGAGGTTGGAGTATC
1 AGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATC
* * *
18490 CCCGCGAAAATAACGGGATTGGAGTATCCCCGATTATGAAAA-CTTAGTGTTTTAGAAATTAAAT
66 CCCTCGAAAATAACGGGATTGGAGTATCCCCGATTATGAAAAGATTAGTGTTTTAGAAATAAAAT
18554 AGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATC
1 AGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATC
* * *
18619 CCCTCGGAAATAACGGGATTGGAGTATCCCC-ATTTGTGAAAAGATTGGTGTTTTAGAAATAAAA
66 CCCTCGAAAATAACGGGATTGGAGTATCCCCGA-TTATGAAAAGATTAGTGTTTTAGAAATAAAA
18683 T
130 T
*
18684 TGAGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTAT
1 AG-GGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTAT
* * * *
18749 -CCCTTGAAAATAAGGGGATTGGAGTATCCCCGATTATGGAAA-ATT-GATG-CTTAGGAAATAA
65 CCCCTCGAAAATAACGGGATTGGAGTATCCCCGATTATGAAAAGATTAG-TGTTTTA-GAAATAA
18810 AACT
128 AA-T
*
18814 GGGGTTGGAGTATCC
1 AGGGTTGGAGTATCC
18829 TTGAGATGAA
Statistics
Matches: 245, Mismatches: 23, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
128 5 0.02
129 120 0.49
130 57 0.23
131 63 0.26
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (130 bp):
AGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATC
CCCTCGAAAATAACGGGATTGGAGTATCCCCGATTATGAAAAGATTAGTGTTTTAGAAATAAAAT
Found at i:18593 original size:50 final size:50
Alignment explanation
Indices: 18508--18621 Score: 133
Period size: 50 Copynumber: 2.3 Consensus size: 50
18498 AATAACGGGA
* * * *
18508 TTGGAGTATCCCCGATTATGAAAACTTAGTGTTTTAGAAATTAAA-TAGGG
1 TTGGAGTATCCCCGATTATGAAAACTCAATATTTTAGAAA-TAAACCAGGG
* *
18558 TTGGAGTATCCCCGATTGTGAGAAA-TCAATATTTTAGAAATAAAGCCGGGG
1 TTGGAGTATCCCCGATTATGA-AAACTCAATATTTTAGAAATAAA-CCAGGG
18609 TTGGAGTATCCCC
1 TTGGAGTATCCCC
18622 TCGGAAATAA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
49 4 0.07
50 32 0.58
51 19 0.35
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.31
Consensus pattern (50 bp):
TTGGAGTATCCCCGATTATGAAAACTCAATATTTTAGAAATAAACCAGGG
Found at i:24391 original size:18 final size:16
Alignment explanation
Indices: 24360--24393 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
24350 ATCTTGACAA
24360 CTTTTGTTCATGCATT
1 CTTTTGTTCATGCATT
24376 CTTTGTGTTCCATGCATT
1 CTTT-TGTT-CATGCATT
24394 TTCCATGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 4 0.25
18 8 0.50
ACGTcount: A:0.12, C:0.21, G:0.15, T:0.53
Consensus pattern (16 bp):
CTTTTGTTCATGCATT
Found at i:25335 original size:13 final size:13
Alignment explanation
Indices: 25297--25337 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
25287 CCGTTGGGCT
25297 CAATGTATCGATA
1 CAATGTATCGATA
* *
25310 CAGTGTGTCGATA
1 CAATGTATCGATA
*
25323 CAATGTATTGATA
1 CAATGTATCGATA
25336 CA
1 CA
25338 TGAACAATGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.32
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:25517 original size:33 final size:32
Alignment explanation
Indices: 25459--25521 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
25449 CCAATTCATG
25459 ATGTATCGATACCAAGAACATGTATCGATATA
1 ATGTATCGATACCAAGAACATGTATCGATATA
* * *
25491 ATGTGTCGATACTAAGCAATATGTATCGATA
1 ATGTATCGATACCAAG-AACATGTATCGATA
25522 CATCTCGGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.30
Consensus pattern (32 bp):
ATGTATCGATACCAAGAACATGTATCGATATA
Found at i:25666 original size:21 final size:21
Alignment explanation
Indices: 25626--25666 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
25616 CTTTTAGATT
25626 ATTTTTACTTGAAAACATATG
1 ATTTTTACTTGAAAACATATG
*
25647 ATTTATTAGTTGAAAA-ATAT
1 ATTT-TTACTTGAAAACATAT
25667 TTATCGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (21 bp):
ATTTTTACTTGAAAACATATG
Found at i:26730 original size:20 final size:21
Alignment explanation
Indices: 26688--26732 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
26678 TGTAGAAAAT
26688 AGCAAGACAAACATTCATAAA
1 AGCAAGACAAACATTCATAAA
*
26709 AGCAA-ACATAAC-TTCATGAA
1 AGCAAGACA-AACATTCATAAA
26729 AGCA
1 AGCA
26733 TGAATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.53, C:0.20, G:0.11, T:0.16
Consensus pattern (21 bp):
AGCAAGACAAACATTCATAAA
Done.