Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1443
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: 43802
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.30
Found at i:2215 original size:80 final size:79
Alignment explanation
Indices: 1988--2208 Score: 238
Period size: 78 Copynumber: 2.8 Consensus size: 79
1978 CGAATGATGT
* * * * *
1988 CCGGCTAAGTCCCG-AGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATTT
1 CCGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCATTT
* *
2050 GTGCAAGTTACTAATT
64 GTGCGAGTTACTAATA
* * * * *
2066 CCGGCTATG-CCCGAAGGCATTGGTGTGAGTTACTA-AATCTGGGTTAAGTCCCGAAGGCATTTG
1 CCGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTAAGTCCCGAAGGCATTTG
2129 TGCGAGTTACT-ATAA
65 TGCGAGTTACTAAT-A
*
2144 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTTG
1 CC-GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
2209 AACGAGTAGC
Statistics
Matches: 117, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
77 8 0.07
78 50 0.43
79 11 0.09
80 46 0.39
81 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (79 bp):
CCGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGT
GCGAGTTACTAATA
Found at i:2222 original size:40 final size:40
Alignment explanation
Indices: 1990--2208 Score: 236
Period size: 40 Copynumber: 5.5 Consensus size: 40
1980 AATGATGTCC
* * * *
1990 GGCTAAGTCCCG-AGGC-TTTGTGCTAAGTGACCATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCG
* * *
2029 GACTAAGAT-CCGAAGGCATTTGTGCAAGTTACTA-ATTCC-
1 GGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-ACCG
* * * *
2068 GGCTATG-CCCGAAGGCATTGGTGTGAGTTACTA-AATCTG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCG
*
2107 GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCG
2147 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCG
*
2187 GGCTATGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
2209 AACGAGTAGC
Statistics
Matches: 154, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
38 24 0.16
39 20 0.13
40 101 0.66
41 9 0.06
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCG
Found at i:12775 original size:22 final size:22
Alignment explanation
Indices: 12748--12790 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12738 ACAGAAGAAG
* *
12748 AAAAGAATAACAAATGGAGAGA
1 AAAAGAAAAACAAAAGGAGAGA
*
12770 AAAAGAAAAATAAAAGGAGAG
1 AAAAGAAAAACAAAAGGAGAG
12791 GAAGAGTGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.67, C:0.02, G:0.23, T:0.07
Consensus pattern (22 bp):
AAAAGAAAAACAAAAGGAGAGA
Found at i:19295 original size:28 final size:27
Alignment explanation
Indices: 19240--19351 Score: 122
Period size: 27 Copynumber: 4.1 Consensus size: 27
19230 AGCATGGCTG
* * *
19240 CCAGAACAGATAA-AGTGACAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
*
19266 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAATTGTGGCAGAGCCA
19294 CCAGAACAGA-AATATGTGGCAGAGCCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
* *
19321 CCA-AATTAGATAATTGTGGCATAGCCA
1 CCAGAA-CAGATAATTGTGGCAGAGCCA
19348 CCAG
1 CCAG
19352 GACGCTTCGT
Statistics
Matches: 74, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
26 10 0.14
27 46 0.62
28 18 0.24
ACGTcount: A:0.39, C:0.22, G:0.23, T:0.15
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:19332 original size:54 final size:54
Alignment explanation
Indices: 19240--19351 Score: 138
Period size: 54 Copynumber: 2.1 Consensus size: 54
19230 AGCATGGCTG
* *
19240 CCAGAACAGATAAAGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATAAAGTGACAGAGCCACCAAATACAGATAATCGTGGCAGAGCCA
* * * *
19294 CCAGAACAGA-AATATGTGGCAGAGCCACCAAAT-TAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-A-GTGACAGAGCCACCAAATACAGATAATCGTGGCAGAGCCA
19348 CCAG
1 CCAG
19352 GACGCTTCGT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
53 2 0.04
54 33 0.66
55 15 0.30
ACGTcount: A:0.39, C:0.22, G:0.23, T:0.15
Consensus pattern (54 bp):
CCAGAACAGATAAAGTGACAGAGCCACCAAATACAGATAATCGTGGCAGAGCCA
Found at i:20623 original size:22 final size:22
Alignment explanation
Indices: 20571--20624 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
20561 GGGGAACAGA
* *
20571 AGAAGAAAAGAATAACAAATGG
1 AGAAGAAAAGAAAAACAAAAGG
* *
20593 AGAAAAAAAGAAAAATAAAAGG
1 AGAAGAAAAGAAAAACAAAAGG
*
20615 AGAGGAAAAG
1 AGAAGAAAAG
20625 TGATCAGAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.69, C:0.02, G:0.24, T:0.06
Consensus pattern (22 bp):
AGAAGAAAAGAAAAACAAAAGG
Found at i:29297 original size:23 final size:23
Alignment explanation
Indices: 29271--29318 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
29261 TGACACTACC
29271 TATTTTACAAGATATGAAAAACA
1 TATTTTACAAGATATGAAAAACA
29294 TATTTTACAAGATATGAAAAACA
1 TATTTTACAAGATATGAAAAACA
29317 TA
1 TA
29319 CATTGGTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.31
Consensus pattern (23 bp):
TATTTTACAAGATATGAAAAACA
Found at i:32188 original size:40 final size:40
Alignment explanation
Indices: 31936--32181 Score: 406
Period size: 40 Copynumber: 6.2 Consensus size: 40
31926 AACCGAAGTA
* *
31936 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* *
31975 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAGATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
32015 CCTTCGGGACTTAGCCTGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
32055 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
32095 CCTTCGGGACTTAGCCCGGATATAGTAACTAGAACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
32135 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
32175 CCTTCGG
1 CCTTCGG
32182 ATCTTAGTCC
Statistics
Matches: 193, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
39 13 0.07
40 180 0.93
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:33573 original size:13 final size:13
Alignment explanation
Indices: 33555--33580 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33545 ATTTTTATTT
33555 TTAACATAAAATA
1 TTAACATAAAATA
33568 TTAACATAAAATA
1 TTAACATAAAATA
33581 ATTAGAATAT
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:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAACATAAAATA
Found at i:39563 original size:40 final size:40
Alignment explanation
Indices: 39391--39556 Score: 237
Period size: 40 Copynumber: 4.2 Consensus size: 40
39381 AACCGAAGTA
* * *
39391 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATA
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* * *
39430 CCTTCGGGACTTAGCCCGGATATAGTAACTAACACAGATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
39470 CCTTCGGGACTTAGCCTGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
39510 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
39550 CTTTCGG
1 CCTTCGG
39557 ATCTTAGTCC
Statistics
Matches: 113, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
39 13 0.12
40 100 0.88
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:41597 original size:78 final size:79
Alignment explanation
Indices: 41456--41633 Score: 211
Period size: 78 Copynumber: 2.3 Consensus size: 79
41446 TACTCGTTCA
* *
41456 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAG-CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
41521 TTAGTAAC-TCGCACC
65 ATAGTAACTTAGCA-C
**
41536 AATGCCTTCGGG-CTTAGCCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGA
* *
41598 TATGGTCACTTAGCAC
64 TATAGTAACTTAGCAC
*
41614 AAAGCCTTCGGGACTTAGCC
1 AATGCCTTCGGGACTTAGCC
41634 CGGACATCAT
Statistics
Matches: 85, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
77 4 0.05
78 54 0.64
79 15 0.18
80 12 0.14
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (79 bp):
AATGCCTTCGGGACTTAGCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATA
TAGTAACTTAGCAC
Found at i:41637 original size:40 final size:40
Alignment explanation
Indices: 41435--41637 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
41425 CGGAATTTAA
** *
41435 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
41475 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
41515 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAG-
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
41553 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
41593 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
41633 CCGGA
1 CCGGA
41638 CATCATTCGA
Statistics
Matches: 140, Mismatches: 15, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
37 2 0.01
38 27 0.19
39 10 0.07
40 89 0.64
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:42897 original size:82 final size:81
Alignment explanation
Indices: 42788--42959 Score: 301
Period size: 84 Copynumber: 2.1 Consensus size: 81
42778 ATATTTATTG
*
42788 CCATGCTCTTTATTTATTAATCCTTACATAATGCACT-CCAACATGTTTATGACATGTTTTTAGC
1 CCATGCTCTTTATTTATTAATCCTTACATAATGCACTACCAACATGTTTATGACATGTCTTTAGC
42852 CATAACATCTTGTCCA
66 CATAACATCTTGTCCA
42868 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCAACATGTTTATGACATGTCTTT
1 -CCATGCTCTTTA-TTTATTAATCCTTACATAATGCACTA-CCAACATGTTTATGACATGTCTTT
42933 AGCCATAACATCTTGTCCA
63 AGCCATAACATCTTGTCCA
42952 CCATGCTC
1 CCATGCTC
42960 ATGGCCGGCC
Statistics
Matches: 87, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
81 12 0.14
82 25 0.29
83 8 0.09
84 42 0.48
ACGTcount: A:0.27, C:0.26, G:0.09, T:0.38
Consensus pattern (81 bp):
CCATGCTCTTTATTTATTAATCCTTACATAATGCACTACCAACATGTTTATGACATGTCTTTAGC
CATAACATCTTGTCCA
Done.