Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3579
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: 48115
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:10423 original size:3 final size:3
Alignment explanation
Indices: 10415--10440 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
10405 AACAAATAGG
10415 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
10441 GGACTAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:12711 original size:18 final size:18
Alignment explanation
Indices: 12684--12718 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
12674 TTTATTTACT
12684 TGTTTGTTGG-TTTTCAA
1 TGTTTGTTGGCTTTTCAA
12701 TGTTCTGTTGGCTTTTCA
1 TGTT-TGTTGGCTTTTCA
12719 TTTTCAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 6 0.38
19 6 0.38
ACGTcount: A:0.09, C:0.11, G:0.23, T:0.57
Consensus pattern (18 bp):
TGTTTGTTGGCTTTTCAA
Found at i:14658 original size:40 final size:40
Alignment explanation
Indices: 14596--14690 Score: 145
Period size: 40 Copynumber: 2.3 Consensus size: 40
14586 CTTTTCTTTC
* *
14596 TTTCTTTCCTTCCTTCCTTCTCTGTTTCGTTTTGCTCTCTG
1 TTTCTTT-CTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTG
*
14637 TTTCTTTCTTTCTCCCTTCTCTGTTTTGTTTTGCTCTCTG
1 TTTCTTTCTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTG
14677 TTTCTTTTCTTTCT
1 TTTC-TTTCTTTCT
14691 TTCTTTGTCA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
40 34 0.68
41 16 0.32
ACGTcount: A:0.00, C:0.28, G:0.08, T:0.63
Consensus pattern (40 bp):
TTTCTTTCTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTG
Found at i:14716 original size:5 final size:5
Alignment explanation
Indices: 14700--14814 Score: 175
Period size: 5 Copynumber: 23.2 Consensus size: 5
14690 TTTCTTTGTC
14700 ATATA TATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA -ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
14751 ATATA ATATA ATATA ATATA ATAT- AT-TA ATAATA ATATA ATAT- AT-TA
1 ATATA ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA ATATA ATATA
14798 ATAATA ATATA ATATA A
1 AT-ATA ATATA ATATA A
14815 AAACATAATT
Statistics
Matches: 103, Mismatches: 0, Indels: 13
0.89 0.00 0.11
Matches are distributed among these distances:
3 2 0.02
4 8 0.08
5 80 0.78
6 13 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:15489 original size:10 final size:10
Alignment explanation
Indices: 15476--15506 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
15466 TTTTTTTTAG
15476 TTTTTAATTT
1 TTTTTAATTT
15486 TTTTTAATTT
1 TTTTTAATTT
15496 TTTTATAATTT
1 TTTT-TAATTT
15507 CCAACTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.70
11 6 0.30
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTAATTT
Found at i:19872 original size:16 final size:16
Alignment explanation
Indices: 19843--19883 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
19833 TCAAATTCAA
*
19843 AACTTAAATTTAGTTC
1 AACTTAAATATAGTTC
*
19859 AACTTCAATATAGTTC
1 AACTTAAATATAGTTC
19875 AACTTAAAT
1 AACTTAAAT
19884 TCAAAACTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.39
Consensus pattern (16 bp):
AACTTAAATATAGTTC
Found at i:32592 original size:44 final size:44
Alignment explanation
Indices: 32441--32599 Score: 152
Period size: 44 Copynumber: 3.7 Consensus size: 44
32431 AGCTTGTACA
* *
32441 ATGCCAACGTCCCAGACGTGGTCTTACATGT-AATC-AAATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAATCTCAA-ATCG
* * *
32484 ATACC-ACTGTCCTAGACAGT-GTCTTACACG-AAA--TCATATACG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAAATCTCAAAT-CG
* * *
32526 ATGCTAATGTCCCAGACATGGTCTTACACGTAAATCTCAAATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAATCTCAAATCG
*
32570 ATGCCAACGTCCCAAACGTGGTCTTACACG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG
32600 AGATCACATA
Statistics
Matches: 91, Mismatches: 15, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
41 3 0.03
42 26 0.29
43 27 0.30
44 30 0.33
45 5 0.05
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (44 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAATCTCAAATCG
Found at i:32597 original size:86 final size:85
Alignment explanation
Indices: 32449--32605 Score: 194
Period size: 86 Copynumber: 1.8 Consensus size: 85
32439 CAATGCCAAC
* * * *
32449 GTCCCAGACGTGGTCTTACATGTAATCAAATATCGATACCACTGTCCTAGACAGTGTCTTACACG
1 GTCCCAGACATGGTCTTACACGTAATCAAATATCGATACCACTGTCCCAAACAGTGTCTTACACG
32514 AAATCATATACGATGCTAAT
66 AAATCATATACGATGCTAAT
* *
32534 GTCCCAGACATGGTCTTACACGTAAATCTCAA-ATCGATGCCAAC-GTCCCAAAC-GTGGTCTTA
1 GTCCCAGACATGGTCTTACACGT-AATC-AAATATCGATACC-ACTGTCCCAAACAGT-GTCTTA
*
32596 CACGAGATCA
62 CACGAAATCA
32606 CATATCAGAA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
85 23 0.38
86 34 0.56
87 4 0.07
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.25
Consensus pattern (85 bp):
GTCCCAGACATGGTCTTACACGTAATCAAATATCGATACCACTGTCCCAAACAGTGTCTTACACG
AAATCATATACGATGCTAAT
Found at i:36890 original size:26 final size:26
Alignment explanation
Indices: 36851--36903 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
36841 TGCAATTAGC
36851 AGATACATGACAAATC-CTGGTAAAAA
1 AGATACATGACAAATCTC-GGTAAAAA
* *
36877 AGATATATGGCAAATCTCGGTAAAAA
1 AGATACATGACAAATCTCGGTAAAAA
36903 A
1 A
36904 CATTGGAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.49, C:0.13, G:0.17, T:0.21
Consensus pattern (26 bp):
AGATACATGACAAATCTCGGTAAAAA
Found at i:37522 original size:29 final size:29
Alignment explanation
Indices: 37480--37536 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
37470 TTATGGAAAA
* * *
37480 GATGGAGAACTTGTTCGTTGAGAGTTCAC
1 GATGAAGAACTTGTTCATTGAGAATTCAC
37509 GATGAAGAACTTGTTCATTGAGAATTCA
1 GATGAAGAACTTGTTCATTGAGAATTCA
37537 TGTCAAGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (29 bp):
GATGAAGAACTTGTTCATTGAGAATTCAC
Found at i:37630 original size:62 final size:62
Alignment explanation
Indices: 37554--37677 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
37544 GTGGAGATTG
37554 TTAGAATTAAGTGAGTTGAATCATTATTTAAATAAAATACAGTGGTAAAATAAAATAAAAGT
1 TTAGAATTAAGTGAGTTGAATCATTATTTAAATAAAATACAGTGGTAAAATAAAATAAAAGT
*
37616 TTAGAATTAAGTGAGTTGAATCCTTATTTAAATAAAATACAGTGGTAAAATAAAATAAAAGT
1 TTAGAATTAAGTGAGTTGAATCATTATTTAAATAAAATACAGTGGTAAAATAAAATAAAAGT
37678 AAAATCCATA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.49, C:0.04, G:0.15, T:0.32
Consensus pattern (62 bp):
TTAGAATTAAGTGAGTTGAATCATTATTTAAATAAAATACAGTGGTAAAATAAAATAAAAGT
Done.