Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1018
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: 64083
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:17325 original size:41 final size:41
Alignment explanation
Indices: 17280--17399 Score: 177
Period size: 41 Copynumber: 2.9 Consensus size: 41
17270 GGTTTGGACC
* * *
17280 AAAAACGCCGCAAAAGGTCAAGCAGTAGTGTCGTTTATGAG
1 AAAAACGCCGCAAAAGGTCAAGTAGTAGCGGCGTTTATGAG
* *
17321 AAAAATGCCGTAAAAGGTCAAGTAGTAGCGGCGTTTATGAG
1 AAAAACGCCGCAAAAGGTCAAGTAGTAGCGGCGTTTATGAG
* *
17362 AAAAACGCCACAAAAGGTCAAGTAGTAGCGGCATTTAT
1 AAAAACGCCGCAAAAGGTCAAGTAGTAGCGGCGTTTAT
17400 ATATGAGAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 70 1.00
ACGTcount: A:0.38, C:0.16, G:0.26, T:0.20
Consensus pattern (41 bp):
AAAAACGCCGCAAAAGGTCAAGTAGTAGCGGCGTTTATGAG
Found at i:18143 original size:26 final size:27
Alignment explanation
Indices: 18102--18192 Score: 109
Period size: 27 Copynumber: 3.5 Consensus size: 27
18092 AACCCATCTT
18102 TACATCGCCG--GACCCGACCATCTG-
1 TACATCGCCGTCGACCCGACCATCTGC
*
18126 TCACCTCG-CGTCGACCCGACCATCTGC
1 T-ACATCGCCGTCGACCCGACCATCTGC
*
18153 TACATCGCCGTTGACCCGACCATCTGC
1 TACATCGCCGTCGACCCGACCATCTGC
* *
18180 TGCGTCGCCGTCG
1 TACATCGCCGTCG
18193 CACTCCTCTA
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
24 3 0.05
25 5 0.09
26 19 0.34
27 29 0.52
ACGTcount: A:0.15, C:0.43, G:0.22, T:0.20
Consensus pattern (27 bp):
TACATCGCCGTCGACCCGACCATCTGC
Found at i:20201 original size:22 final size:22
Alignment explanation
Indices: 20176--20256 Score: 56
Period size: 22 Copynumber: 3.5 Consensus size: 22
20166 TTCTAAATTT
20176 TTATTTTTATTTATATAAATAA
1 TTATTTTTATTTATATAAATAA
* *** *
20198 TTATTATTCAAAGATATACAATTAG
1 TTATT-TTTATTTATATA-AA-TAA
*
20223 TTATTTTTATTTAT-TTAATAA
1 TTATTTTTATTTATATAAATAA
*
20244 TATATTTCTATTT
1 T-TATTTTTATTT
20257 CATGTAATAT
Statistics
Matches: 43, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
21 3 0.07
22 17 0.40
23 9 0.21
24 7 0.16
25 7 0.16
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (22 bp):
TTATTTTTATTTATATAAATAA
Found at i:20682 original size:9 final size:9
Alignment explanation
Indices: 20657--20745 Score: 68
Period size: 9 Copynumber: 10.6 Consensus size: 9
20647 TTTTTTAATG
20657 CATAACTT-
1 CATAACTTA
20665 -ATAACTTA
1 CATAACTTA
*
20673 CATAATTTA
1 CATAACTTA
20682 CATAACTTA
1 CATAACTTA
* *
20691 AATAA-ATA
1 CATAACTTA
20699 TCAT-A--T-
1 -CATAACTTA
20705 CATAACTTA
1 CATAACTTA
20714 CATAACTTA
1 CATAACTTA
*
20723 CCA-AATTTA
1 -CATAACTTA
20732 CATAACTTA
1 CATAACTTA
20741 CATAA
1 CATAA
20746 ATAAATATCA
Statistics
Matches: 65, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
5 3 0.05
6 1 0.02
7 8 0.12
8 6 0.09
9 45 0.69
10 2 0.03
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (9 bp):
CATAACTTA
Found at i:20688 original size:18 final size:18
Alignment explanation
Indices: 20665--20782 Score: 79
Period size: 18 Copynumber: 6.8 Consensus size: 18
20655 TGCATAACTT
20665 ATAACTTACATAATTTAC
1 ATAACTTACATAATTTAC
* *
20683 ATAACTTAAATAA-ATATC
1 ATAACTTACATAATTTA-C
*
20701 AT-A--T-CATAACTTAC
1 ATAACTTACATAATTTAC
20715 ATAACTTACCA-AATTTAC
1 ATAACTTA-CATAATTTAC
* *
20733 ATAACTTACATAA-ATAA
1 ATAACTTACATAATTTAC
* * *
20750 ATATCATATCGTAATTTAC
1 ATAACTTA-CATAATTTAC
*
20769 ATAACTTACGTAAT
1 ATAACTTACATAAT
20783 ACATAAATAT
Statistics
Matches: 76, Mismatches: 14, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
14 7 0.09
15 4 0.05
17 14 0.18
18 41 0.54
19 10 0.13
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.36
Consensus pattern (18 bp):
ATAACTTACATAATTTAC
Found at i:20730 original size:50 final size:53
Alignment explanation
Indices: 20657--20777 Score: 164
Period size: 54 Copynumber: 2.4 Consensus size: 53
20647 TTTTTTAATG
20657 CATAACTT--ATAACTTA-CATAATTTACATAAC-T-TAAATAAATATCATAT
1 CATAACTTACATAACTTACCATAATTTACATAACTTATAAATAAATATCATAT
20705 CATAACTTACATAACTTACCA-AATTTACATAACTTACATAAATAAATATCATAT
1 CATAACTTACATAACTTACCATAATTTACATAACTT--ATAAATAAATATCATAT
* *
20759 CGTAATTTACATAACTTAC
1 CATAACTTACATAACTTAC
20778 GTAATACATA
Statistics
Matches: 64, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
48 8 0.12
50 20 0.31
51 3 0.05
54 33 0.52
ACGTcount: A:0.46, C:0.17, G:0.01, T:0.36
Consensus pattern (53 bp):
CATAACTTACATAACTTACCATAATTTACATAACTTATAAATAAATATCATAT
Found at i:25141 original size:153 final size:153
Alignment explanation
Indices: 24863--25170 Score: 433
Period size: 153 Copynumber: 2.0 Consensus size: 153
24853 ATTATTTTGG
* * * * * *
24863 TGATTGTATATTATAAATGATGTGATTAAGTTATTAATGTGGAATGATGTGTATATTTCAATTCT
1 TGATTGTATACTATAAATGATGTGATTAAATGATTAACGTGAAATGATGTGTATATTCCAATTCT
* *
24928 CATGACGTGATTTTATGACGAAATTGATTATGCATGATATATATATATGTTTTAATCATGCTACT
66 CATGACGTGATTTTATGACGAAATTAATTACGCATGATATATATATATGTTTTAATCATGCTACT
24993 ATTATATTAATTGACATTTGATT
131 ATTATATTAATTGACATTTGATT
* *
25016 TGATTGTATGCTATAAATGATGTGATTAAATGATTAACGTGAAATTATGTGTAT-TTACCAATTC
1 TGATTGTATACTATAAATGATGTGATTAAATGATTAACGTGAAATGATGTGTATATT-CCAATTC
* * **
25080 TTATTACATGTGATTTTATGGTGAAATTAATTACGCATGATAT-T-TATATGTTTTAATCATGCT
65 TCATGAC--GTGATTTTATGACGAAATTAATTACGCATGATATATATATATGTTTTAATCATGCT
*
25143 ACTGTTATATTAATTGACATTTGATT
128 ACTATTATATTAATTGACATTTGATT
25169 TG
1 TG
25171 CATGTTAAGC
Statistics
Matches: 137, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
152 2 0.01
153 104 0.76
154 1 0.01
155 30 0.22
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.45
Consensus pattern (153 bp):
TGATTGTATACTATAAATGATGTGATTAAATGATTAACGTGAAATGATGTGTATATTCCAATTCT
CATGACGTGATTTTATGACGAAATTAATTACGCATGATATATATATATGTTTTAATCATGCTACT
ATTATATTAATTGACATTTGATT
Found at i:25208 original size:42 final size:42
Alignment explanation
Indices: 25161--25264 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 42
25151 ATTAATTGAC
*
25161 ATTTGATTTGCATGTTAAGCAAGCT-GACTATGATAAACTGAT
1 ATTTGATTTGCATGTTAAGCAAG-TAGACTATGATAAACTGAG
* * * * *
25203 ATTTGATTTGCATGTTAAGCATGTAGACTATGTTGATCTTAG
1 ATTTGATTTGCATGTTAAGCAAGTAGACTATGATAAACTGAG
*
25245 ATTTGATTTGCATATTAAGC
1 ATTTGATTTGCATGTTAAGC
25265 GTGCCTATTG
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 1 0.02
42 53 0.98
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (42 bp):
ATTTGATTTGCATGTTAAGCAAGTAGACTATGATAAACTGAG
Found at i:27799 original size:20 final size:20
Alignment explanation
Indices: 27774--27819 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
27764 AGACTATGAA
27774 CCATTCCATCTACTTACTTT
1 CCATTCCATCTACTTACTTT
*
27794 CCATTCCATTTACTTACTTT
1 CCATTCCATCTACTTACTTT
*
27814 ACATTC
1 CCATTC
27820 ATTTACTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.46
Consensus pattern (20 bp):
CCATTCCATCTACTTACTTT
Found at i:28637 original size:40 final size:40
Alignment explanation
Indices: 28593--28721 Score: 170
Period size: 40 Copynumber: 3.2 Consensus size: 40
28583 GGGAATTGAT
* * *
28593 GTGCATTCAGGGGTACCGAAGTACAAACAAGGGCACATAA
1 GTGCAATCAAGGGTACCGAAGTACAAACAAGGGCACGTAA
* * *
28633 GTGCAATCAAGGGCACCAAATTACAAACAAGGGCACGTAA
1 GTGCAATCAAGGGTACCGAAGTACAAACAAGGGCACGTAA
* *
28673 GTGCAATCAAGGGTATCGAAGTACAAA-TAGCGGCACGTAA
1 GTGCAATCAAGGGTACCGAAGTACAAACAAG-GGCACGTAA
28713 GTGCAATCA
1 GTGCAATCA
28722 TTCAATAATT
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
39 2 0.03
40 75 0.97
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.16
Consensus pattern (40 bp):
GTGCAATCAAGGGTACCGAAGTACAAACAAGGGCACGTAA
Found at i:28643 original size:20 final size:20
Alignment explanation
Indices: 28620--28685 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
28610 GAAGTACAAA
28620 CAAGGGCACATAAGTGCAAT
1 CAAGGGCACATAAGTGCAAT
* * *
28640 CAAGGGCACCA-AATTACAAA
1 CAAGGGCA-CATAAGTGCAAT
*
28660 CAAGGGCACGTAAGTGCAAT
1 CAAGGGCACATAAGTGCAAT
28680 CAAGGG
1 CAAGGG
28686 TATCGAAGTA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 1 0.03
20 34 0.92
21 2 0.05
ACGTcount: A:0.41, C:0.21, G:0.26, T:0.12
Consensus pattern (20 bp):
CAAGGGCACATAAGTGCAAT
Found at i:28694 original size:20 final size:19
Alignment explanation
Indices: 28609--28721 Score: 68
Period size: 20 Copynumber: 5.7 Consensus size: 19
28599 TCAGGGGTAC
* *
28609 CGAAGTACAAACAAGGGCA
1 CGAAGTGCAATCAAGGGCA
*
28628 CATAAGTGCAATCAAGGGCA
1 C-GAAGTGCAATCAAGGGCA
* * * *
28648 CCAAATTACAAACAAGGGCA
1 -CGAAGTGCAATCAAGGGCA
*
28668 CGTAAGTGCAATCAAGGGTA
1 CG-AAGTGCAATCAAGGGCA
*
28688 TCGAAGTACAA--ATAGCGGCA
1 -CGAAGTGCAATCA-AG-GGCA
28708 CGTAAGTGCAATCA
1 CG-AAGTGCAATCA
28722 TTCAATAATT
Statistics
Matches: 70, Mismatches: 15, Indels: 15
0.70 0.15 0.15
Matches are distributed among these distances:
18 1 0.01
19 6 0.09
20 59 0.84
21 3 0.04
22 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.14
Consensus pattern (19 bp):
CGAAGTGCAATCAAGGGCA
Found at i:42201 original size:41 final size:40
Alignment explanation
Indices: 42145--42224 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 40
42135 AAATGATTCA
42145 GGTTCAGGTCAAATCTGAACATTTGCAATCTGTTCCCTTG
1 GGTTCAGGTCAAATCTGAACATTTGCAATCTGTTCCCTTG
*
42185 GGTTCGGGTCCAAATCTGAACATTTGCAATCTGTTCCCTT
1 GGTTCAGGT-CAAATCTGAACATTTGCAATCTGTTCCCTT
42225 ACTCAAACTA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 8 0.21
41 30 0.79
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (40 bp):
GGTTCAGGTCAAATCTGAACATTTGCAATCTGTTCCCTTG
Found at i:43571 original size:28 final size:28
Alignment explanation
Indices: 43505--43576 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
43495 CAAACAGATA
43505 AATA-TTTTT-ATTAAATAAATAAGTTT
1 AATATTTTTTAATTAAATAAATAAGTTT
* *
43531 -ATATTATTATAATTAAATAAATTAGTTT
1 AATATT-TTTTAATTAAATAAATAAGTTT
*
43559 AATATTTTTTAATAAAAT
1 AATATTTTTTAATTAAAT
43577 CTAATTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
25 3 0.08
26 1 0.03
27 3 0.08
28 26 0.68
29 5 0.13
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (28 bp):
AATATTTTTTAATTAAATAAATAAGTTT
Found at i:46745 original size:16 final size:16
Alignment explanation
Indices: 46724--46754 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46714 TATTTTAAAA
*
46724 ATTTAATTATAATTTT
1 ATTTAATTAAAATTTT
46740 ATTTAATTAAAATTT
1 ATTTAATTAAAATTT
46755 CAAACAAACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTAATTAAAATTTT
Found at i:51454 original size:28 final size:29
Alignment explanation
Indices: 51400--51461 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 29
51390 GAGAGCATGA
*
51400 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGAGATTTGGGCCTAATGGGCC
*
51429 ATATGAATGAGA-TTGGGCCTAGTGGGCC
1 ATATGAATGAGATTTGGGCCTAATGGGCC
51457 ATATG
1 ATATG
51462 TATGTATGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 20 0.65
29 11 0.35
ACGTcount: A:0.26, C:0.13, G:0.32, T:0.29
Consensus pattern (29 bp):
ATATGAATGAGATTTGGGCCTAATGGGCC
Found at i:57698 original size:29 final size:29
Alignment explanation
Indices: 57665--57784 Score: 179
Period size: 29 Copynumber: 4.2 Consensus size: 29
57655 GAACACATGA
*
57665 ATATGGATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
57694 ATATGAATGTAATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
57723 ATACGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* * *
57752 ATATGAATGAGA-TTGGGCCTAGTAGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
57780 ATATG
1 ATATG
57785 TTTGTATGTG
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
28 19 0.23
29 64 0.77
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:63719 original size:9 final size:10
Alignment explanation
Indices: 63697--63734 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
63687 TTTCAAAATC
63697 TATCTATCTA
1 TATCTATCTA
63707 TATCTAT-TA
1 TATCTATCTA
*
63716 TATCTATCTC
1 TATCTATCTA
*
63726 TCTCTATCT
1 TATCTATCT
63735 TTATTTCGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.53
Consensus pattern (10 bp):
TATCTATCTA
Found at i:63724 original size:23 final size:22
Alignment explanation
Indices: 63694--63738 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
63684 CACTTTCAAA
63694 ATCTATCTATCTATATCTATTAT
1 ATCTATCTATCTATATCT-TTAT
* *
63717 ATCTATCTCTCTCTATCTTTAT
1 ATCTATCTATCTATATCTTTAT
63739 TTCGGTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.24, C:0.22, G:0.00, T:0.53
Consensus pattern (22 bp):
ATCTATCTATCTATATCTTTAT
Done.