Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3131
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: 48688
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:1563 original size:40 final size:40
Alignment explanation
Indices: 1479--1662 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
1469 TTGAATGCTG
* * * *
1479 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
1518 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
1559 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
1599 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
1639 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
1663 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:1616 original size:80 final size:81
Alignment explanation
Indices: 1479--1659 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
1469 TTGAATGCTG
* * *
1479 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
1543 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
1559 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
1620 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
1639 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
1660 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:1683 original size:39 final size:38
Alignment explanation
Indices: 1560--1709 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
1550 GTTATTAATT
* ** * *
1560 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
1600 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
1639 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
1679 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
1710 GAGCTAATCC
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
39 30 0.32
40 63 0.68
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Found at i:9404 original size:40 final size:40
Alignment explanation
Indices: 9320--9503 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
9310 TTGAATGCTG
* * * *
9320 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
9359 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
9400 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
9440 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
9480 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
9504 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:9457 original size:80 final size:81
Alignment explanation
Indices: 9320--9500 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
9310 TTGAATGCTG
* * *
9320 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
9384 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
9400 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
9461 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
9480 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
9501 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:9524 original size:39 final size:38
Alignment explanation
Indices: 9401--9550 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
9391 GTTATTAATT
* ** * *
9401 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
9441 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
9480 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
9520 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
9551 GAGCTAAATC
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
39 30 0.32
40 63 0.68
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Found at i:19646 original size:53 final size:54
Alignment explanation
Indices: 19575--19880 Score: 363
Period size: 53 Copynumber: 5.6 Consensus size: 54
19565 AAATTACCAT
* *
19575 TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAACTCACCAA
1 TGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAACTCATCAA
* * * *
19628 TGTCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCGTTATAGTAACTCATCAA
1 TGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTATAG-AACTCATCAA
* * *
19683 TGCCATGTCTTGACATGGTCTTACATGGTATCATTGCCTTAT-GAACTCACCAA
1 TGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAACTCATCAA
* *
19736 TGCCATGCCTTGGCACGGTCTTACATAGG-A-CCTTTGCCTTATAGTAACTCATCAA
1 TGCCATGCCTTGACATGGTCTTACAT-GGTATCC-TTGCCTTATAG-AACTCATCAA
** *
19791 TGCCATGTTCC-AAACATGGTCTTACATGGTATCCTTGCCTTATAGAACTTATCAA
1 TGCCATG--CCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAACTCATCAA
* *
19846 TGCCATGCCTTGGCATGGTCTTACATGATATCCTT
1 TGCCATGCCTTGACATGGTCTTACATGGTATCCTT
19881 ATATTACCAA
Statistics
Matches: 213, Mismatches: 27, Indels: 25
0.80 0.10 0.09
Matches are distributed among these distances:
52 3 0.01
53 78 0.37
54 26 0.12
55 77 0.36
56 25 0.12
57 4 0.02
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (54 bp):
TGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAACTCATCAA
Found at i:19703 original size:108 final size:108
Alignment explanation
Indices: 19575--19872 Score: 488
Period size: 108 Copynumber: 2.7 Consensus size: 108
19565 AAATTACCAT
*
19575 TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGTCATGCCTTG
1 TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTG
*
19640 GCATGGTCTTACATGGGACCTTTGCGTTATAGTAACTCATCAA
66 GCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
*
19683 TGCCATGTCTTGACATGGTCTTACATGGTATCATTGCCTTATGAACTCACCAATGCCATGCCTTG
1 TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTG
* *
19748 GCACGGTCTTACATAGGACCTTTGCCTTATAGTAACTCATCAA
66 GCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
*** * *
19791 TGCCATGTTCCAAACATGGTCTTACATGGTATCCTTGCCTTATAGAACTTATCAATGCCATGCCT
1 TGCCATG-TCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAACTCACCAATGCCATGCCT
19856 TGGCATGGTCTTACATG
64 TGGCATGGTCTTACATG
19873 ATATCCTTAT
Statistics
Matches: 175, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
108 110 0.63
109 31 0.18
110 34 0.19
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (108 bp):
TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTG
GCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
Found at i:24715 original size:40 final size:39
Alignment explanation
Indices: 24622--24723 Score: 127
Period size: 39 Copynumber: 2.6 Consensus size: 39
24612 ACAATTCGGA
*
24622 TATATATGGCACTTAGTGTATGATTCAAGAAAGCTTCGC
1 TATATATGGCACTTAGTGTGTGATTCAAGAAAGCTTCGC
** *
24661 TATAGT-TGGCACTTAGTGTGTGATT-TGGAATGGCTTCGAC
1 TATA-TATGGCACTTAGTGTGTGATTCAAGAA-AGCTTCG-C
24701 TATATATGGCACTTAGTGTGTGA
1 TATATATGGCACTTAGTGTGTGA
24724 GGCTGTGATA
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
38 3 0.05
39 29 0.53
40 23 0.42
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.36
Consensus pattern (39 bp):
TATATATGGCACTTAGTGTGTGATTCAAGAAAGCTTCGC
Found at i:24805 original size:42 final size:42
Alignment explanation
Indices: 24693--24809 Score: 132
Period size: 41 Copynumber: 2.8 Consensus size: 42
24683 ATTTGGAATG
* * * ** *
24693 GCTTCGACTATATAT-GGCACTTAGTGTGTGAGGCTGTGATA
1 GCTTCGGCTATGTATAGGCACTTAGTGTGCGAGATTATGATA
* *
24734 GCTTTGGCTATGTA-AGGCACTTAGCGTGCGAGATTAT-ATTA
1 GCTTCGGCTATGTATAGGCACTTAGTGTGCGAGATTATGA-TA
24775 GCTTCGGCTATGTATAGGCACTTAGTGTGCGAGAT
1 GCTTCGGCTATGTATAGGCACTTAGTGTGCGAGAT
24810 ATTGAGTATT
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
40 1 0.02
41 43 0.68
42 19 0.30
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.33
Consensus pattern (42 bp):
GCTTCGGCTATGTATAGGCACTTAGTGTGCGAGATTATGATA
Found at i:25380 original size:13 final size:13
Alignment explanation
Indices: 25362--25387 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25352 TGGTTTAACC
25362 ATATGAATTATGT
1 ATATGAATTATGT
25375 ATATGAATTATGT
1 ATATGAATTATGT
25388 CTAATAAAAC
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:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
ATATGAATTATGT
Found at i:32645 original size:43 final size:42
Alignment explanation
Indices: 32542--32659 Score: 139
Period size: 43 Copynumber: 2.8 Consensus size: 42
32532 TGTGTTATCG
* *
32542 TGTAAGACCACGTCTGGGACGTTGGCATCGTACTTGATTTCA
1 TGTAAGACCACGTATGGGACGTTGGCATCGTACTTGATTACA
** * *
32584 TGTAAGACCTTGTATGGGACAG-TGGTATCGGTATTTGATTACA
1 TGTAAGACCACGTATGGGAC-GTTGGCATC-GTACTTGATTACA
* *
32627 TGTAAGACCACGTTTGGGACGTTGGCATTGTAC
1 TGTAAGACCACGTATGGGACGTTGGCATCGTAC
32660 GAGCTTTTCA
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
42 27 0.44
43 34 0.56
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (42 bp):
TGTAAGACCACGTATGGGACGTTGGCATCGTACTTGATTACA
Found at i:36259 original size:28 final size:27
Alignment explanation
Indices: 36196--36347 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
36186 ATATTAAGTC
* * *
36196 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
36223 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
36251 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
36278 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
36306 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
36333 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
36348 GCACAATTTA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:36280 original size:55 final size:55
Alignment explanation
Indices: 36196--36347 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
36186 ATATTAAGTC
* * *
36196 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
36251 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
36306 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
36348 GCACAATTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:44336 original size:27 final size:27
Alignment explanation
Indices: 44319--44468 Score: 135
Period size: 27 Copynumber: 5.6 Consensus size: 27
44309 ATATTAAGTC
44319 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* *
44346 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* *
44374 CGCACACTTAGTGCTACAT-ATGCAACT
1 CGCACACTCAGTGCTATATAAT-CAACT
* * * *
44401 CGCACCCTTA-TGC-ACATAGTCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* * * *
44427 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTCAGTGCTATATAATCAACT
*
44454 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
44469 GCACAATTTA
Statistics
Matches: 111, Mismatches: 6, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
25 5 0.05
26 17 0.15
27 57 0.51
28 32 0.29
ACGTcount: A:0.31, C:0.30, G:0.13, T:0.26
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:44436 original size:53 final size:55
Alignment explanation
Indices: 44319--44468 Score: 209
Period size: 53 Copynumber: 2.8 Consensus size: 55
44309 ATATTAAGTC
* *
44319 CGCACACTCAGTGCTATATAAT-CAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACAT-ATGCAACTCGCACACTTAGTGCTACATAATCAAACT
* *
44374 CGCACACTTAGTGCTACATATGCAACTCGCACCCTTA-TGC-ACATAGTCAAACT
1 CGCACACTTAGTGCTACATATGCAACTCGCACACTTAGTGCTACATAATCAAACT
*
44427 CGCACACTTAGTGCTACATA-GTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATATG-CAACTCGCACACTTAGTGCT
44469 GCACAATTTA
Statistics
Matches: 85, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
52 1 0.01
53 45 0.53
54 8 0.09
55 31 0.36
ACGTcount: A:0.31, C:0.30, G:0.13, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATATGCAACTCGCACACTTAGTGCTACATAATCAAACT
Done.