Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold888
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: 55022
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:641 original size:15 final size:13
Alignment explanation
Indices: 621--654 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
611 AAGAATTCAG
*
621 AAAAAAAATTCAA
1 AAAAAAAAATCAA
634 ATAAAAAAAATCAA
1 A-AAAAAAAATCAA
648 AAAAAAA
1 AAAAAAA
655 GGAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAAAAATCAA
Found at i:6707 original size:33 final size:34
Alignment explanation
Indices: 6647--6712 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 34
6637 CATTCTTGTA
6647 AAGAGAAAACAAAGAAAGAAAAGAAAAA-AAAGC
1 AAGAGAAAACAAAGAAAGAAAAGAAAAAGAAAGC
*
6680 AAGAGAGAAA-AAAGAAATG-AAATAAAAAGAAAG
1 AAGAGA-AAACAAAGAAA-GAAAAGAAAAAGAAAG
6713 AGAGGCAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
33 21 0.72
34 8 0.28
ACGTcount: A:0.74, C:0.03, G:0.20, T:0.03
Consensus pattern (34 bp):
AAGAGAAAACAAAGAAAGAAAAGAAAAAGAAAGC
Found at i:8943 original size:30 final size:30
Alignment explanation
Indices: 8909--9004 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
8899 AGCTCACTCC
8909 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
8939 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
*
8969 CAGCTCAACTTTAGCTCACGAGCTAAA-CT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
8998 TAGCTCA
1 TAGCTCA
9005 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
29 9 0.18
30 42 0.82
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:10762 original size:11 final size:13
Alignment explanation
Indices: 10747--10778 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
10737 TCAAAAAAAT
10747 CAAAAAAAAG-GA
1 CAAAAAAAAGTGA
10759 -AAAAAAAAGTGA
1 CAAAAAAAAGTGA
10771 CAAAAAAA
1 CAAAAAAA
10779 TCGAGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.50
12 2 0.11
13 7 0.39
ACGTcount: A:0.78, C:0.06, G:0.12, T:0.03
Consensus pattern (13 bp):
CAAAAAAAAGTGA
Found at i:11730 original size:37 final size:37
Alignment explanation
Indices: 11679--11749 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
11669 CATTCTTGTA
11679 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
11716 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
11750 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:11749 original size:6 final size:6
Alignment explanation
Indices: 11689--11738 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
11679 AAGAGAAAAC
*
11689 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
11738 A
1 A
11739 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:13988 original size:30 final size:30
Alignment explanation
Indices: 13954--14050 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
13944 AGCTCACTCC
13954 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
13984 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
14014 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
14044 TAGCTCA
1 TAGCTCA
14051 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:19799 original size:108 final size:108
Alignment explanation
Indices: 19610--19822 Score: 426
Period size: 108 Copynumber: 2.0 Consensus size: 108
19600 ATCGAAATTA
19610 TAATAGTTCAATGGGAATTATTCTTGAAATATGGAAAAGTGAAATGAAATGAAAATTTATATTAT
1 TAATAGTTCAATGGGAATTATTCTTGAAATATGGAAAAGTGAAATGAAATGAAAATTTATATTAT
19675 GATAAGCTCATCCATGTATGTTTGGCATTCGTATGATGTTGTG
66 GATAAGCTCATCCATGTATGTTTGGCATTCGTATGATGTTGTG
19718 TAATAGTTCAATGGGAATTATTCTTGAAATATGGAAAAGTGAAATGAAATGAAAATTTATATTAT
1 TAATAGTTCAATGGGAATTATTCTTGAAATATGGAAAAGTGAAATGAAATGAAAATTTATATTAT
19783 GATAAGCTCATCCATGTATGTTTGGCATTCGTATGATGTT
66 GATAAGCTCATCCATGTATGTTTGGCATTCGTATGATGTT
19823 ATGTGCCTAA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 105 1.00
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.37
Consensus pattern (108 bp):
TAATAGTTCAATGGGAATTATTCTTGAAATATGGAAAAGTGAAATGAAATGAAAATTTATATTAT
GATAAGCTCATCCATGTATGTTTGGCATTCGTATGATGTTGTG
Found at i:19985 original size:28 final size:28
Alignment explanation
Indices: 19945--20002 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
19935 CATAAATATG
19945 TATGTTAATTTGCTTGAAGTGAATCATA
1 TATGTTAATTTGCTTGAAGTGAATCATA
19973 TATGTTAATTTGCTTGAAGTGAATCATA
1 TATGTTAATTTGCTTGAAGTGAATCATA
20001 TA
1 TA
20003 ACTGAAATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (28 bp):
TATGTTAATTTGCTTGAAGTGAATCATA
Found at i:25995 original size:30 final size:31
Alignment explanation
Indices: 25961--26057 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
25951 AGCTCACTCC
*
25961 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
25991 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
26021 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
26051 TAGCTCA
1 TAGCTCA
26058 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:34684 original size:28 final size:28
Alignment explanation
Indices: 34644--34700 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
34634 ACCATGTCGA
*
34644 TGCCACATTAGTTTAACTAACGAAATTT
1 TGCCACATCAGTTTAACTAACGAAATTT
34672 TGCCACATCAGTTTAACTAACGAAATTT
1 TGCCACATCAGTTTAACTAACGAAATTT
34700 T
1 T
34701 CTTATTTCGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (28 bp):
TGCCACATCAGTTTAACTAACGAAATTT
Found at i:40409 original size:30 final size:30
Alignment explanation
Indices: 40375--40471 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
40365 TAAACTAAAA
40375 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
40405 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
40435 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
40465 TGAGCTA
1 TGAGCTA
40472 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:42653 original size:30 final size:30
Alignment explanation
Indices: 42582--42664 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
42572 CTTTTGTTTC
* *
42582 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
42613 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
42642 ATTTTCTTTTTCTTTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
42665 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.12, C:0.22, G:0.01, T:0.65
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:42682 original size:12 final size:12
Alignment explanation
Indices: 42667--42696 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
42657 TTCTTTTTGC
42667 TTTTCAAAGGCT
1 TTTTCAAAGGCT
42679 TTTT-AAAGGCT
1 TTTTCAAAGGCT
42690 TTTTCAA
1 TTTTCAA
42697 GTTCTCTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:42754 original size:5 final size:5
Alignment explanation
Indices: 42744--42802 Score: 50
Period size: 5 Copynumber: 11.2 Consensus size: 5
42734 CTCTTGCCTC
*
42744 TCTTT TCTTT T-TATT TCATTT TCCTTT TCTTT T-TCT TCTTT TGCTTTT
1 TCTTT TCTTT TCT-TT TC-TTT T-CTTT TCTTT TCTTT TCTTT T-C-TTT
42792 TCTTT TCTTT T
1 TCTTT TCTTT T
42803 TCCTTTATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
4 4 0.09
5 26 0.58
6 9 0.20
7 6 0.13
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.76
Consensus pattern (5 bp):
TCTTT
Found at i:42777 original size:12 final size:12
Alignment explanation
Indices: 42745--42808 Score: 62
Period size: 12 Copynumber: 5.3 Consensus size: 12
42735 TCTTGCCTCT
42745 CTTTTCTTTTT-
1 CTTTTCTTTTTC
* *
42756 -ATTTCATTTTC
1 CTTTTCTTTTTC
42767 CTTTTCTTTTTC
1 CTTTTCTTTTTC
42779 TTCTTTTGCTTTTT-
1 --CTTTT-CTTTTTC
42793 CTTTTCTTTTTC
1 CTTTTCTTTTTC
42805 CTTT
1 CTTT
42809 ATTTTCTCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
10 8 0.19
11 6 0.14
12 18 0.42
14 5 0.12
15 6 0.14
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (12 bp):
CTTTTCTTTTTC
Found at i:42792 original size:21 final size:22
Alignment explanation
Indices: 42745--42797 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
42735 TCTTGCCTCT
*
42745 CTTTTCTTTTTATTTCATTTTC
1 CTTTTCTTTTTACTTCATTTTC
42767 CTTTTCTTTTT-CTTC-TTTTGC
1 CTTTTCTTTTTACTTCATTTT-C
*
42788 TTTTTCTTTT
1 CTTTTCTTTT
42798 CTTTTTCCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 4 0.14
21 13 0.46
22 11 0.39
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.75
Consensus pattern (22 bp):
CTTTTCTTTTTACTTCATTTTC
Found at i:43728 original size:11 final size:11
Alignment explanation
Indices: 43712--43750 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
43702 TAAAACACCC
43712 TTTTTTCAGTT
1 TTTTTTCAGTT
43723 TTTTTTC-GATT
1 TTTTTTCAG-TT
*
43734 TTTTTTCAATT
1 TTTTTTCAGTT
43745 TTTTTT
1 TTTTTT
43751 AACTTGTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 1 0.04
11 24 0.96
ACGTcount: A:0.10, C:0.08, G:0.05, T:0.77
Consensus pattern (11 bp):
TTTTTTCAGTT
Found at i:45442 original size:30 final size:30
Alignment explanation
Indices: 45408--45504 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
45398 TAAACTAAAA
45408 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * *
45438 TGAGCTGAGGC-TAAACTCCTAAGCTAAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
45468 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
45498 TGAGCTA
1 TGAGCTA
45505 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
29 2 0.04
30 43 0.83
31 7 0.13
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:46199 original size:13 final size:13
Alignment explanation
Indices: 46181--46206 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46171 TCACATAGAA
46181 AATTTTTCCATTC
1 AATTTTTCCATTC
46194 AATTTTTCCATTC
1 AATTTTTCCATTC
46207 TATTGAGGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTTTTCCATTC
Found at i:51666 original size:28 final size:27
Alignment explanation
Indices: 51633--51699 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 27
51623 TCTTTGTTTC
*
51633 ATTTCTTTCATCT-TCTTTTCACTCTCAA
1 ATTTCTTTCATCTCT-TTTTCAATCTC-A
*
51661 ATTTCTTTTCGTCTCTTTTTCAATCTCA
1 ATTTC-TTTCATCTCTTTTTCAATCTCA
*
51689 TTTTCTTTCAT
1 ATTTCTTTCAT
51700 TTATTTTGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
27 5 0.15
28 10 0.30
29 17 0.52
30 1 0.03
ACGTcount: A:0.15, C:0.25, G:0.01, T:0.58
Consensus pattern (27 bp):
ATTTCTTTCATCTCTTTTTCAATCTCA
Done.