Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3708
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: 64088
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:11626 original size:44 final size:44
Alignment explanation
Indices: 11563--11890 Score: 182
Period size: 44 Copynumber: 7.6 Consensus size: 44
11553 ATTATACAGG
*
11563 TCTTATCTCCCTAAGATTACAGTGGA-CAGACCAAAAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAAAA-TTCAGA
* * * *
11607 TCTTATCTCCCTGAGATTACAGCGGAGCGGATCAAAGA-T-AGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAAAATTCAG--A
* * * * ** *
11651 TCCTATCTCCTTGAGATTACAATGGAGCGGA--TTAAA---GGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAAAATTCAGA
* * * * * *
11690 TCTTATCTCTCTGA-AGTTACAGTAGAGAAGATC--ACA-TCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGACCAAAAATTCAGA
*
11731 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAA-AA-TTCAGA
* *** *****
11777 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAAAATTCAGA
* * * *
11821 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGA--CACTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAAAATTCA-GA
*
11864 TCCTATCTCCCTGA-AGTTACAGTGGAG
1 TCTTATCTCCCTGAGA-TTACAGTGGAG
11891 TGGATTAAAA
Statistics
Matches: 219, Mismatches: 49, Indels: 33
0.73 0.16 0.11
Matches are distributed among these distances:
38 1 0.00
39 25 0.11
41 28 0.13
42 7 0.03
43 26 0.12
44 89 0.41
45 8 0.04
46 35 0.16
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAAAATTCAGA
Found at i:11910 original size:87 final size:88
Alignment explanation
Indices: 11731--11930 Score: 217
Period size: 87 Copynumber: 2.3 Consensus size: 88
11721 TCACATCAGG
* * *
11731 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTA
1 TCTTATCTCCCTGAGATTACAGCGGAACAGACCAAAGAA--TCAGATCCTATCTCCCTGAAGTTA
* **
11796 CAGTGGAGCAGATTGAAGCCAGAGA
64 CAGTGGAGCAGATTAAAGAAAGAGA
* * *
11821 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAG-A-CACTATCCTATCTCCCTGAAGTTAC
1 TCTTATCTCCCTGAGATTACAGCGGAACAGACCAAAGAATCA-GATCCTATCTCCCTGAAGTTAC
** *
11884 AGTGGAGTGGATTAAAATAAAG-GA
65 AGTGGAGCAGATT-AAAGAAAGAGA
* *
11908 TCTTATCTCTCTGAGGTTACAGC
1 TCTTATCTCCCTGAGATTACAGC
11931 AGAGTAGGTC
Statistics
Matches: 94, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
86 2 0.02
87 53 0.56
88 4 0.04
89 1 0.01
90 34 0.36
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (88 bp):
TCTTATCTCCCTGAGATTACAGCGGAACAGACCAAAGAATCAGATCCTATCTCCCTGAAGTTACA
GTGGAGCAGATTAAAGAAAGAGA
Found at i:12049 original size:218 final size:214
Alignment explanation
Indices: 11611--12052 Score: 475
Period size: 218 Copynumber: 2.0 Consensus size: 214
11601 TTCAGATCTT
* * * *
11611 ATCTCCCTGAGATTACAGCGGAGCGGATCAAAGATAGTAATCCTATCTCCTTGAGATTACAATGG
1 ATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGATTACAATGG
*
11676 AGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCTTATCTCC
66 AGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAGGTCTTATCTCC
*** * *
11741 CTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCA
131 CTGAGATTACAGTGGAACAGACCAAAGAACAACAGATCTTATCCCCCTGAAGTTACAGTGGAGCA
* **
11806 GATTGAAGCCAGAGATCTT
196 GATTGAAGACAGAGATCCG
*
11825 ATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACT-ATCCTATCTCCCTGA-AGTTACAGTG
1 ATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGA-TTACAATG
* * * * *
11888 GAGTGGATTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGGTCGCATCAGGTCTT
65 GAGCGGA-T----TAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAGGTCTT
* * * *** **
11953 ATTTCCCTGAAGA-TGCAGTGGAATAGATTGAA-AACAAC-GAATCTTATCCCCCTGAAGTTGTA
125 ATCTCCCTG-AGATTACAGTGGAACAGACCAAAGAACAACAG-ATCTTATCCCCCTGAAGTTACA
* *
12015 GTGGGGGCA-AGTTGAAGATATGAG-TCCG
188 GT-GGAGCAGA-TTGAAGACA-GAGATCCG
12043 ATCTCCCTGA
1 ATCTCCCTGA
12053 AGTTGCAGTG
Statistics
Matches: 188, Mismatches: 29, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
212 1 0.01
213 27 0.14
214 36 0.19
216 1 0.01
217 24 0.13
218 93 0.49
219 6 0.03
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (214 bp):
ATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGATTACAATGG
AGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAGGTCTTATCTCC
CTGAGATTACAGTGGAACAGACCAAAGAACAACAGATCTTATCCCCCTGAAGTTACAGTGGAGCA
GATTGAAGACAGAGATCCG
Found at i:13426 original size:3 final size:3
Alignment explanation
Indices: 13418--13458 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
13408 TTTGTTAACT
13418 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
13459 TTCCTTTTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:22772 original size:20 final size:22
Alignment explanation
Indices: 22734--22798 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
22724 TTATTTTCCA
22734 TTAATCAAAATATTATTTTTTG
1 TTAATCAAAATATTATTTTTTG
*
22756 TTAATCAATATATT-TTTTTT-
1 TTAATCAAAATATTATTTTTTG
**
22776 AAAATCATAAATAATTATTTTTT
1 TTAATCA-AAAT-ATTATTTTTT
22799 AATGTTATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 5 0.14
21 9 0.25
22 16 0.44
23 6 0.17
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (22 bp):
TTAATCAAAATATTATTTTTTG
Found at i:29834 original size:42 final size:43
Alignment explanation
Indices: 29733--29853 Score: 147
Period size: 42 Copynumber: 2.8 Consensus size: 43
29723 AGCTCGAATA
** * *
29733 ATGCCAACATCCCAGAC-GTGGTCTTACATGTAATCAAATAATG
1 ATGCCAATGTCCCAGACAG-GGTCTTACACGTAATCAAATAACG
* *
29776 ATGCCACTGTCCCAGACAGGGTCTTACACGTAATCATAT-ACG
1 ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAAATAACG
* *
29818 ATGCCAATGTCCCAGACATGGTCTTACACGAAATCA
1 ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCA
29854 CATATTGGAA
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
42 35 0.51
43 32 0.47
44 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAAATAACG
Found at i:32861 original size:24 final size:24
Alignment explanation
Indices: 32833--32884 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
32823 TTAGTAAGTC
* *
32833 AAATAGACTATGCTAATAAATGCT
1 AAATAGACTATACTAATAAATACT
* *
32857 AAATATATTATACTAATAAATACT
1 AAATAGACTATACTAATAAATACT
32881 AAAT
1 AAAT
32885 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.33
Consensus pattern (24 bp):
AAATAGACTATACTAATAAATACT
Found at i:33616 original size:35 final size:35
Alignment explanation
Indices: 33570--33641 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
33560 TTGATAAACC
33570 TTCATTTTTATACATTATTCTTGATCAATATAAGA
1 TTCATTTTTATACATTATTCTTGATCAATATAAGA
*
33605 TTCATTTTTATACATTATTCTTGATCTATATAAGA
1 TTCATTTTTATACATTATTCTTGATCAATATAAGA
33640 TT
1 TT
33642 GTGAGTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.51
Consensus pattern (35 bp):
TTCATTTTTATACATTATTCTTGATCAATATAAGA
Found at i:33978 original size:22 final size:23
Alignment explanation
Indices: 33947--33990 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
33937 GTCATCAATT
*
33947 AATTAATTTTAAAAATTAAAAAA
1 AATTAATTTTAAAAAATAAAAAA
33970 AATT-ATTTTAAAAAATAAAAA
1 AATTAATTTTAAAAAATAAAAA
33991 CTATTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
AATTAATTTTAAAAAATAAAAAA
Found at i:34579 original size:26 final size:26
Alignment explanation
Indices: 34550--34601 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
34540 ATACTTTTAA
* * * *
34550 AATTTTTTTATTTTTTTTTTTAAAAT
1 AATTTTTTAATGTTTATTTTAAAAAT
34576 AATTTTTTAATGTTTATTTTAAAAAT
1 AATTTTTTAATGTTTATTTTAAAAAT
34602 GGGCCGGGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
AATTTTTTAATGTTTATTTTAAAAAT
Found at i:34595 original size:25 final size:23
Alignment explanation
Indices: 34544--34599 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 23
34534 TTTAAAATAC
* * *
34544 TTTTAAAATTTTTTTATTTTTTT
1 TTTTAAAATTTTTTTAATGTTTA
34567 TTTTAAAATAATTTTTTAATGTTTA
1 TTTTAAAAT--TTTTTTAATGTTTA
34592 TTTTAAAA
1 TTTTAAAA
34600 ATGGGCCGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 9 0.32
25 19 0.68
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (23 bp):
TTTTAAAATTTTTTTAATGTTTA
Found at i:35853 original size:17 final size:17
Alignment explanation
Indices: 35831--35863 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35821 TTCCAGATTT
*
35831 TGATACCTATATCTTTC
1 TGATACCCATATCTTTC
35848 TGATACCCATATCTTT
1 TGATACCCATATCTTT
35864 GACTTTCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:39362 original size:17 final size:17
Alignment explanation
Indices: 39340--39372 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
39330 TCCCAGATTT
*
39340 TGATACCCATATCTTTC
1 TGATACCAATATCTTTC
39357 TGATACCAATATCTTT
1 TGATACCAATATCTTT
39373 GACTTTCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.24, G:0.06, T:0.42
Consensus pattern (17 bp):
TGATACCAATATCTTTC
Found at i:44124 original size:113 final size:113
Alignment explanation
Indices: 43921--44148 Score: 447
Period size: 113 Copynumber: 2.0 Consensus size: 113
43911 CTTCAATCAT
43921 GGCACAACATACTGATAGTAATCATATATTGTATTAAGAACTGTAATATATGCTACCTGGACTCT
1 GGCACAACATACTGATAGTAATCATATATTGTATTAAGAACTGTAATATATGCTACCTGGACTCT
*
43986 TGTTTTACCGTAAATTACATGTTTCGGCATATATTTGGAATAGGTATG
66 TGTTTTACCGTAAATTACATCTTTCGGCATATATTTGGAATAGGTATG
44034 GGCACAACATACTGATAGTAATCATATATTGTATTAAGAACTGTAATATATGCTACCTGGACTCT
1 GGCACAACATACTGATAGTAATCATATATTGTATTAAGAACTGTAATATATGCTACCTGGACTCT
44099 TGTTTTACCGTAAATTACATCTTTCGGCATATATTTGGAATAGGTATG
66 TGTTTTACCGTAAATTACATCTTTCGGCATATATTTGGAATAGGTATG
44147 GG
1 GG
44149 GATATAGTCT
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
113 114 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (113 bp):
GGCACAACATACTGATAGTAATCATATATTGTATTAAGAACTGTAATATATGCTACCTGGACTCT
TGTTTTACCGTAAATTACATCTTTCGGCATATATTTGGAATAGGTATG
Found at i:44764 original size:21 final size:21
Alignment explanation
Indices: 44738--44784 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
44728 TTCTAATTTT
*
44738 ACCGCTACAGTATCCAATCTC
1 ACCGCTACAGTAACCAATCTC
*
44759 ACCGCTACAGTAACTAATCTC
1 ACCGCTACAGTAACCAATCTC
44780 ACCGC
1 ACCGC
44785 CACCGCTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.38, G:0.11, T:0.21
Consensus pattern (21 bp):
ACCGCTACAGTAACCAATCTC
Found at i:45665 original size:23 final size:22
Alignment explanation
Indices: 45635--45679 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
45625 TATAATTTTA
45635 ATAAATTATATGATAAAA-TAAAT
1 ATAAATTATA-GA-AAAATTAAAT
45658 ATAAATTATAGAAAAATTAAAT
1 ATAAATTATAGAAAAATTAAAT
45680 CTCTATTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.19
22 7 0.33
23 10 0.48
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (22 bp):
ATAAATTATAGAAAAATTAAAT
Found at i:46632 original size:12 final size:12
Alignment explanation
Indices: 46612--46654 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
46602 GTTAGACTGG
*
46612 AATAGAAATAGA
1 AATAAAAATAGA
46624 AATAAAAATAGA
1 AATAAAAATAGA
*
46636 AATAAAAAATAAA
1 AAT-AAAAATAGA
46649 AATAAA
1 AATAAA
46655 TGGGTTTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 17 0.61
13 11 0.39
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (12 bp):
AATAAAAATAGA
Found at i:46635 original size:18 final size:19
Alignment explanation
Indices: 46612--46652 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
46602 GTTAGACTGG
*
46612 AATAGAAAT-AGAAATAAA
1 AATAGAAATAAAAAATAAA
46630 AATAGAAATAAAAAATAAA
1 AATAGAAATAAAAAATAAA
46649 AATA
1 AATA
46653 AATGGGTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (19 bp):
AATAGAAATAAAAAATAAA
Found at i:46649 original size:6 final size:6
Alignment explanation
Indices: 46612--46654 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
46602 GTTAGACTGG
* * *
46612 AATAGA AATAGA AATAAA AATAGA AATAAAA AATAAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AAT-AAA AATAAA AATAAA
46655 TGGGTTTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
6 28 0.85
7 5 0.15
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:62752 original size:54 final size:55
Alignment explanation
Indices: 62668--62786 Score: 177
Period size: 54 Copynumber: 2.2 Consensus size: 55
62658 ATTTTCCTTG
* *
62668 TTGAAACAAAAACTAGTGGATTTTTTGCACAAATAAATGGAAAACTTGCTCTCAAA
1 TTGAAA-AAAAACAAGTGGAATTTTTGCACAAATAAATGGAAAACTTGCTCTCAAA
* * *
62724 TTGAAAAAAAA-AAGTGGAATTTTTGCACAAATAATTGTAAAACTTGCTCTCAAG
1 TTGAAAAAAAACAAGTGGAATTTTTGCACAAATAAATGGAAAACTTGCTCTCAAA
62778 TTGAAAAAA
1 TTGAAAAAA
62787 GGTGGATTCT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 47 0.81
55 5 0.09
56 6 0.10
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (55 bp):
TTGAAAAAAAACAAGTGGAATTTTTGCACAAATAAATGGAAAACTTGCTCTCAAA
Found at i:62823 original size:51 final size:50
Alignment explanation
Indices: 62682--62827 Score: 159
Period size: 54 Copynumber: 2.8 Consensus size: 50
62672 AACAAAAACT
62682 AGTGGATTTTTTGCACAAATAAATGGAAAACTTGCTCTCAAATTGAAAAAAAAA
1 AGTGGA-TTTTTGCACAAATAAAT-GAAAACTTGCTCTCAAATTG--AAAAAAA
* *
62736 AGTGGAATTTTTGCACAAATAATTGTAAAACTTGCTCTCAAGTTG-AAAAAA
1 AGTGG-ATTTTTGCACAAATAAATG-AAAACTTGCTCTCAAATTGAAAAAAA
* * * *
62787 GGTGGATTCTTTGCTCAAATAAATGAATATCATGCTCTCAA
1 AGTGGATT-TTTGCACAAATAAATGAA-AACTTGCTCTCAA
62828 CTTATTTTTA
Statistics
Matches: 81, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
50 5 0.06
51 35 0.43
53 1 0.01
54 39 0.48
55 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (50 bp):
AGTGGATTTTTGCACAAATAAATGAAAACTTGCTCTCAAATTGAAAAAAA
Done.