Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2875
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: 68807
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:5578 original size:30 final size:28
Alignment explanation
Indices: 5519--5646 Score: 163
Period size: 29 Copynumber: 4.5 Consensus size: 28
5509 TAAATTGTAC
5519 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
5547 AGCACTAAAGTGTGCGCACGTTTGA-TATAT
1 AGCACT-AAGTGTGCG-A-GTTTGATTATAT
* * *
5577 AGCACTAAGTGTGCAAGTTTTATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
5605 GAGCACTAAGTGTGCGAG-TT-ATTATAT
1 -AGCACTAAGTGTGCGAGTTTGATTATAT
*
5632 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
5647 GACTTAATAT
Statistics
Matches: 89, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
26 14 0.16
27 11 0.12
28 13 0.15
29 33 0.37
30 12 0.13
31 6 0.07
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:13685 original size:28 final size:28
Alignment explanation
Indices: 13617--13854 Score: 381
Period size: 28 Copynumber: 8.5 Consensus size: 28
13607 CATGAGATTG
* * *
13617 GCACTAAGTGTGC-AGGTTTAAATTGTACA
1 GCACTAAGTGTGCGA-GTTT-GATTATATA
13646 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
13674 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
13702 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
13730 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
13758 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
* *
13786 GCACTAAGTGTGCAAGTTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATATA
13814 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
13841 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
13855 GACTTAATAT
Statistics
Matches: 198, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
27 23 0.12
28 157 0.79
29 17 0.09
30 1 0.01
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.34
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:17541 original size:20 final size:20
Alignment explanation
Indices: 17516--17564 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
17506 ATGGAGCTTA
*
17516 TATAATATATTAAA-TCTATC
1 TATAATATACTAAACT-TATC
*
17536 TCTAATATACTAAACTTATC
1 TATAATATACTAAACTTATC
17556 TATAATATA
1 TATAATATA
17565 ATGGGCTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (20 bp):
TATAATATACTAAACTTATC
Found at i:18852 original size:25 final size:27
Alignment explanation
Indices: 18814--18898 Score: 81
Period size: 25 Copynumber: 3.3 Consensus size: 27
18804 TTATAATTAT
* *
18814 TTTATTTTTATAAT-TTTCATATGTA-A
1 TTTATTTTTTTAATATAT-ATATGTATA
18840 -TTATTTTTTTAATATATATATGTATA
1 TTTATTTTTTTAATATATATATGTATA
* * *
18866 TTTATTTTTTT-ATGTACATATTTATA
1 TTTATTTTTTTAATATATATATGTATA
18892 TTT-TTTT
1 TTTATTTT
18899 AACTAATATT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
25 23 0.45
26 18 0.35
27 10 0.20
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (27 bp):
TTTATTTTTTTAATATATATATGTATA
Found at i:18873 original size:26 final size:25
Alignment explanation
Indices: 18801--18898 Score: 73
Period size: 26 Copynumber: 4.0 Consensus size: 25
18791 TTTAATAATG
18801 TAATTATA-AT-TAT-TTTATTTTT
1 TAATTATATATGTATATTTATTTTT
*
18823 ATAATTTTCATATGTA-A-TTATTTTTT
1 -TAATTAT-ATATGTATATTTA-TTTTT
18849 TAATATATATATGTATATTTATTTTT
1 TAAT-TATATATGTATATTTATTTTT
* * *
18875 TTATGTACATATTTATATTT-TTTT
1 TAAT-TATATATGTATATTTATTTT
18899 AACTAATATT
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
23 6 0.10
24 1 0.02
25 20 0.33
26 31 0.51
27 3 0.05
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (25 bp):
TAATTATATATGTATATTTATTTTT
Found at i:18907 original size:21 final size:22
Alignment explanation
Indices: 18868--18909 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
18858 TATGTATATT
**
18868 TATTTTTTTATGTACATATTTA
1 TATTTTTTTAACTACATATTTA
18890 TATTTTTTTAACTA-ATATTT
1 TATTTTTTTAACTACATATTT
18910 TTCTCATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (22 bp):
TATTTTTTTAACTACATATTTA
Found at i:19429 original size:27 final size:26
Alignment explanation
Indices: 19383--19433 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
19373 ATGTCGTTGG
*
19383 TTATTTTTTTATCTACATTAATTTCGT
1 TTATTTATTTATCTACATT-ATTTCGT
* *
19410 TTATTTATTTATTTATATTATTTC
1 TTATTTATTTATCTACATTATTTC
19434 TATGTCATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 5 0.24
27 16 0.76
ACGTcount: A:0.24, C:0.08, G:0.02, T:0.67
Consensus pattern (26 bp):
TTATTTATTTATCTACATTATTTCGT
Found at i:25554 original size:36 final size:36
Alignment explanation
Indices: 25505--25580 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
25495 GCAGAGCAGA
* *
25505 TTAAAGCTAAGGGCAGCGAATCTTATCTCCCTAGCG
1 TTAAAGCTAAGGGCAGCCAATCTTATATCCCTAGCG
* *
25541 TTAAAGCTGAGGGCAGCCAATCTTATATCCCTGGCG
1 TTAAAGCTAAGGGCAGCCAATCTTATATCCCTAGCG
25577 TTAA
1 TTAA
25581 GACTTGGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (36 bp):
TTAAAGCTAAGGGCAGCCAATCTTATATCCCTAGCG
Found at i:25825 original size:169 final size:169
Alignment explanation
Indices: 25541--25916 Score: 590
Period size: 169 Copynumber: 2.2 Consensus size: 169
25531 CTCCCTAGCG
* * * *
25541 TTAAAGCTGAGGGCAGCCAATCTTATATCCCTGGCGTTAAGACTTGGAATAGCTAAGGTGGAGCG
1 TTAAAGCTGAGGGCAGCGAATCTTATCTCCCTGGCGTTAAGACTTAGAATAGCTAAGGTGGAGCA
* *
25606 GATTAAAGCTGTGGGCAGTGAATCCTATCTCTTTGGCATTATAGTGGAACAGATTAAAGCTAAAC
66 GATTAAAGCGGTGGGCAGTGAATCCTATCTCTTTGGCATTATAATGGAACAGATTAAAGCTAAAC
*
25671 ATAGCGAATCTTGTTTCCCTAGCGTTGCAGCAGAGCAGA
131 ATAGCGAATCTTGTTTCCCTAGCGTTGCAACAGAGCAGA
** * *
25710 TTAAAGCTGAGGGCAGCGAATCTTATCTTTCTGGCTTTAAGACTTAGAATAGCTGAGGTGGAGCA
1 TTAAAGCTGAGGGCAGCGAATCTTATCTCCCTGGCGTTAAGACTTAGAATAGCTAAGGTGGAGCA
* *
25775 GATTACAGCGGTGGGCAGTGAATCCTATCTCTTTGGCATTATAATGGAACAGATTAAAGCTAAAG
66 GATTAAAGCGGTGGGCAGTGAATCCTATCTCTTTGGCATTATAATGGAACAGATTAAAGCTAAAC
* *
25840 GTAGCGAATCTTGTTTCTCTAGCGTTGCAACAGAGCAGA
131 ATAGCGAATCTTGTTTCCCTAGCGTTGCAACAGAGCAGA
* * *
25879 TTAAAGCTGAGGGCAACGAGTCTTATCTCACTGGCGTT
1 TTAAAGCTGAGGGCAGCGAATCTTATCTCCCTGGCGTT
25917 GAGCGGATTA
Statistics
Matches: 187, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
169 187 1.00
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (169 bp):
TTAAAGCTGAGGGCAGCGAATCTTATCTCCCTGGCGTTAAGACTTAGAATAGCTAAGGTGGAGCA
GATTAAAGCGGTGGGCAGTGAATCCTATCTCTTTGGCATTATAATGGAACAGATTAAAGCTAAAC
ATAGCGAATCTTGTTTCCCTAGCGTTGCAACAGAGCAGA
Found at i:26116 original size:44 final size:44
Alignment explanation
Indices: 26045--26158 Score: 158
Period size: 44 Copynumber: 2.6 Consensus size: 44
26035 AGGAAGCAAG
* * *
26045 CCTTATCTCCCTGAACAGTAGTAGAGTAGGTTGAATATTGA-AGA
1 CCTTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATT-ACAGA
*
26089 CCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGA
1 CCTTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATTACAGA
* *
26133 TCTTATCTCCCTAAGCAGTAGTGGAG
1 CCTTATCTCCCTGAGCAGTAGTGGAG
26159 CAAATTGAAG
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 1 0.02
44 61 0.98
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (44 bp):
CCTTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATTACAGA
Found at i:26310 original size:57 final size:56
Alignment explanation
Indices: 26217--26380 Score: 197
Period size: 57 Copynumber: 2.9 Consensus size: 56
26207 ATTGAACCCA
* *
26217 CTAGTCCTATCTCCCTT-GACAGTAGTGGAATAGATTGAAAATTACAGATCAAAGACC
1 CTAGTCCTATCT-CCTTGGACAGCAGTGGAATGGATTGAAAATTACAGATCAAAGA-C
* * * * *
26274 CTAGTCCTATCTCCTTGGACAACAGAGGAGTGGATTGAAAATTACAAATCGAAGAC
1 CTAGTCCTATCTCCTTGGACAGCAGTGGAATGGATTGAAAATTACAGATCAAAGAC
* *
26330 CTCAGTCCTATTTCCCTGGACAGCAGTGGAATAGG-TTGAAAATTACAGATC
1 CT-AGTCCTATCTCCTTGGACAGCAGTGGAAT-GGATTGAAAATTACAGATC
26381 TTATCTCCCT
Statistics
Matches: 91, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
56 7 0.08
57 82 0.90
58 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (56 bp):
CTAGTCCTATCTCCTTGGACAGCAGTGGAATGGATTGAAAATTACAGATCAAAGAC
Found at i:26910 original size:24 final size:24
Alignment explanation
Indices: 26874--26945 Score: 117
Period size: 24 Copynumber: 3.0 Consensus size: 24
26864 TCCAAGCCCC
*
26874 ATGTCCCTAACTTTGCAGTGGAGT
1 ATGTCCCTGACTTTGCAGTGGAGT
*
26898 ATGTCCCTGACTTTGCAGTGGGGT
1 ATGTCCCTGACTTTGCAGTGGAGT
*
26922 ATGTCCTTGACTTTGCAGTGGAGT
1 ATGTCCCTGACTTTGCAGTGGAGT
26946 GGATTGGAGC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.17, C:0.19, G:0.29, T:0.35
Consensus pattern (24 bp):
ATGTCCCTGACTTTGCAGTGGAGT
Found at i:28357 original size:20 final size:21
Alignment explanation
Indices: 28320--28359 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28310 TATGTATATT
**
28320 TATTTTTTATGTACATATTTA
1 TATTTTTTAACTACATATTTA
28341 TATTTTTTAACTA-ATATTT
1 TATTTTTTAACTACATATTT
28360 TTCTCATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (21 bp):
TATTTTTTAACTACATATTTA
Found at i:28537 original size:139 final size:138
Alignment explanation
Indices: 28295--28555 Score: 318
Period size: 139 Copynumber: 1.9 Consensus size: 138
28285 TGTAATTATT
* * ** * *
28295 TTTTTAATCTATATATATGTATATTTATTTTTTATGTACATATTTATATTTTTTAACTAATATTT
1 TTTTTAATCTATATATATATATATTTATTGTACATGTACATATTTATATTTTTTAAATAATATTC
* *
28360 TTCTCATATTTATATATATACACATATTTATTTATTTTTATTAATTTT-GATAATGTAGATATTA
66 TTCTCATATTTATATATATACACATATCTATTTATTTTTATTAATTTTCGAAAATGTAGATATTA
28424 TTTAATTA
131 TTTAATTA
*
28432 TTTTTAATCTATATATATATAT-TTTATATGTACATGTATACATATTTATTTTTTTTAAATGAAT
1 TTTTTAATCTATATATATATATATTTAT-TGTACATG--TACATATTTATATTTTTTAAAT-AAT
* *
28496 ATTCCTT-T-ATATTTATATATATACGTATATATCTA-TT-TTTTTATTTATTTTCGAAAATGT
62 ATT-CTTCTCATATTTATATATATAC--ACATATCTATTTATTTTTATTAATTTTCGAAAATGT
28556 TTAACTACCT
Statistics
Matches: 105, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
136 5 0.05
137 26 0.25
139 49 0.47
140 16 0.15
141 9 0.09
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (138 bp):
TTTTTAATCTATATATATATATATTTATTGTACATGTACATATTTATATTTTTTAAATAATATTC
TTCTCATATTTATATATATACACATATCTATTTATTTTTATTAATTTTCGAAAATGTAGATATTA
TTTAATTA
Found at i:29881 original size:24 final size:24
Alignment explanation
Indices: 29854--29903 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
29844 TCTAGAATAG
*
29854 TTAGAATTTATTAGTATAATATAT
1 TTAGAATTTATTAGCATAATATAT
* *
29878 TTAGCATTTATTAGCATAATTTAT
1 TTAGAATTTATTAGCATAATATAT
29902 TT
1 TT
29904 GACCTATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.52
Consensus pattern (24 bp):
TTAGAATTTATTAGCATAATATAT
Found at i:36277 original size:20 final size:21
Alignment explanation
Indices: 36232--36278 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
36222 ATATATTCCG
*
36232 ACACATATCAATCACATATAA
1 ACACATATCAATCACATACAA
* *
36253 GCACATAT-AATTACATACAA
1 ACACATATCAATCACATACAA
36273 ACACAT
1 ACACAT
36279 TTAGTCATAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.51, C:0.23, G:0.02, T:0.23
Consensus pattern (21 bp):
ACACATATCAATCACATACAA
Found at i:44198 original size:12 final size:12
Alignment explanation
Indices: 44181--44205 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44171 AAACGGAAAA
44181 ATAAAAATAAAT
1 ATAAAAATAAAT
44193 ATAAAAATAAAT
1 ATAAAAATAAAT
44205 A
1 A
44206 GTGAGGGAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAAAAATAAAT
Found at i:60657 original size:77 final size:70
Alignment explanation
Indices: 60566--60753 Score: 200
Period size: 71 Copynumber: 2.6 Consensus size: 70
60556 GTATATAAAA
* * *
60566 GGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCA-CCATATCT
1 GGGGTTGCTATGTGCTGATTCCCCG----A-GGG-GGTGCTAAGTGCGAT-ATCCATCCATATAT
60629 TTGAAATGTGAAAG
59 TTGAAA--TGAAAG
* ***
60643 GGGGTTGCTATGTGCTGATTCCCCGAGGGGTTGCTAAGTGCGATATCCATTGGTATATTTGAAAT
1 GGGGTTGCTATGTGCTGATTCCCCGAGGGGGTGCTAAGTGCGATATCCATCCATATATTTGAAAT
60708 GAAAG
66 GAAAG
*
60713 GGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAAGTG
1 GGGGTTGCTATGTGCTGATT-CCCCGAGGGGGTGCTAAGTG
60754 ATGATTCCCC
Statistics
Matches: 101, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
70 26 0.26
71 36 0.36
72 14 0.14
73 1 0.01
77 24 0.24
ACGTcount: A:0.19, C:0.16, G:0.33, T:0.32
Consensus pattern (70 bp):
GGGGTTGCTATGTGCTGATTCCCCGAGGGGGTGCTAAGTGCGATATCCATCCATATATTTGAAAT
GAAAG
Done.