Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold355
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: 41870
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.31
Found at i:7407 original size:40 final size:40
Alignment explanation
Indices: 7363--7594 Score: 331
Period size: 40 Copynumber: 5.8 Consensus size: 40
7353 GGATATAGCT
* * * * *
7363 ACTCGCTCGAATGCCTTCGGGGCATAGCCCGG-TTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TGGTA
* *
7403 ACTCGCACCAATGCCTTCGGGACTTAGCCCAGATTTGGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTGGTA
*
7443 ACTCGCACAAATGCCTTCAGGACTTAGCCCGGATTTGGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTGGTA
*
7483 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTGGAA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTGGTA
* * *
7523 ACTCACACAAATGCCTTCAGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTGGTA
*
7563 GCTCGCACAAATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
7595 TTATCATCCG
Statistics
Matches: 173, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 171 0.99
41 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTGGTA
Found at i:12266 original size:47 final size:47
Alignment explanation
Indices: 12179--12534 Score: 595
Period size: 47 Copynumber: 7.6 Consensus size: 47
12169 CCCTTCGGGA
* * * * * *
12179 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
12226 CCTGTTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12273 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
12320 CTTCTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12367 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
12414 CTTATCACATATATACACTTTCACATTCATCACATCGGTCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
12461 CTTATCACATATATACACTTCCACATTCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12508 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
12535 ACCAACCCTT
Statistics
Matches: 290, Mismatches: 19, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 290 1.00
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:12796 original size:40 final size:38
Alignment explanation
Indices: 12759--12849 Score: 130
Period size: 38 Copynumber: 2.3 Consensus size: 38
12749 GCTACTCGTT
*
12759 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGG-C-TAGCCCGGAAT-TAGTAACTCGCA
*
12799 CAAATGCCTTCGGGCTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTAGCCCGGAATTAGTAACTCGCA
12837 CAAATGCCTTCGG
1 CAAATGCCTTCGG
12850 ATCTTAGTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
38 32 0.67
39 2 0.04
40 14 0.29
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (38 bp):
CAAATGCCTTCGGGCTAGCCCGGAATTAGTAACTCGCA
Found at i:12829 original size:38 final size:40
Alignment explanation
Indices: 12740--12898 Score: 141
Period size: 40 Copynumber: 4.0 Consensus size: 40
12730 CGAAATTTAA
**
12740 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACATAGC
*
12780 CCGGTTATAGTAACTCGCACAAATGCCTTCGGG-C-TAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACATAGC
* * *
12818 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CATAGC
* * * * *
12858 TCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACATAGC
12898 C
1 C
12899 TAGACATCAT
Statistics
Matches: 98, Mismatches: 13, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
37 3 0.03
38 30 0.31
39 3 0.03
40 50 0.51
41 12 0.12
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACATAGC
Found at i:16458 original size:51 final size:51
Alignment explanation
Indices: 16395--16640 Score: 386
Period size: 51 Copynumber: 4.8 Consensus size: 51
16385 TACACGGTGA
* *
16395 CCTTCACTTAGTACCACCCTTGTAG-CCAAAGCTATTTTATTCACAAAGTGG
1 CCTTCACATAGTACCACACTTGT-GTCCAAAGCTATTTTATTCACAAAGTGG
* * *
16446 CCTTCACATAGTACCCCACTTGTGTCCAAAGCTATTTTATTCAAAAAATGG
1 CCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAAGTGG
* * *
16497 CTTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTAACAAAGTGG
1 CCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAAGTGG
* *
16548 CCTTCACATAGTACCAAACTTGTGTCCAAAGCTATTATATTCACAAAGTGG
1 CCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAAGTGG
16599 CCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTC
1 CCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTC
16641 CTAAGGTTCA
Statistics
Matches: 178, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
50 1 0.01
51 177 0.99
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (51 bp):
CCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAAGTGG
Found at i:16701 original size:28 final size:28
Alignment explanation
Indices: 16666--16734 Score: 120
Period size: 28 Copynumber: 2.5 Consensus size: 28
16656 GAAATTTCTT
16666 ACTTAGCACAATGCCATGGACTTATTTC
1 ACTTAGCACAATGCCATGGACTTATTTC
* *
16694 ACTTAGCACATTGCCATGGTCTTATTTC
1 ACTTAGCACAATGCCATGGACTTATTTC
16722 ACTTAGCACAATG
1 ACTTAGCACAATG
16735 TCATATCCTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (28 bp):
ACTTAGCACAATGCCATGGACTTATTTC
Found at i:19684 original size:35 final size:35
Alignment explanation
Indices: 19643--19715 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
19633 TTTTATATTA
* *
19643 TTTAAATGTTTATATTAGTTATGACAATCATTTAC
1 TTTAAATGTTTATATAAGTTATGACAATCATTAAC
* *
19678 TTTAAATGTTTATGTAAGTTATGATAATCATTAAC
1 TTTAAATGTTTATATAAGTTATGACAATCATTAAC
19713 TTT
1 TTT
19716 TATTCTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (35 bp):
TTTAAATGTTTATATAAGTTATGACAATCATTAAC
Found at i:21539 original size:12 final size:12
Alignment explanation
Indices: 21522--21547 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
21512 CTTTCTGCCT
21522 TAACAAACAAAA
1 TAACAAACAAAA
21534 TAACAAACAAAA
1 TAACAAACAAAA
21546 TA
1 TA
21548 TTTTAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.73, C:0.15, G:0.00, T:0.12
Consensus pattern (12 bp):
TAACAAACAAAA
Found at i:23226 original size:17 final size:19
Alignment explanation
Indices: 23192--23230 Score: 69
Period size: 19 Copynumber: 2.0 Consensus size: 19
23182 TTATTATTTA
23192 CTTGTTTTTCCTTCTTCTT
1 CTTGTTTTTCCTTCTTCTT
23211 CTTGTTTTTCTCTTCTTCTT
1 CTTGTTTTTC-CTTCTTCTT
23231 TTTTTTGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.00, C:0.26, G:0.05, T:0.69
Consensus pattern (19 bp):
CTTGTTTTTCCTTCTTCTT
Found at i:23236 original size:17 final size:17
Alignment explanation
Indices: 23192--23235 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 17
23182 TTATTATTTA
23192 CTTGTTTTTCCTTCTTCTT
1 CTTGTTTTT-C-TCTTCTT
23211 CTTGTTTTTCTCTTCTT
1 CTTGTTTTTCTCTTCTT
23228 CTT-TTTTT
1 CTTGTTTTT
23236 TGTTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.20
17 10 0.40
18 1 0.04
19 9 0.36
ACGTcount: A:0.00, C:0.23, G:0.05, T:0.73
Consensus pattern (17 bp):
CTTGTTTTTCTCTTCTT
Found at i:26017 original size:33 final size:34
Alignment explanation
Indices: 25975--26054 Score: 119
Period size: 33 Copynumber: 2.4 Consensus size: 34
25965 TTGTTTCCTT
* *
25975 TTGGAAATCAAG-AGTTTGTCATTTTATTTACTG
1 TTGGAAATCAAGCAGTTTGTCATTATATCTACTG
*
26008 TTGGAAATC-AGCAGTTTGTCGTTATATCTACTG
1 TTGGAAATCAAGCAGTTTGTCATTATATCTACTG
26041 TTGGAAATCAAGCA
1 TTGGAAATCAAGCA
26055 CATTAACTGC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
32 2 0.05
33 36 0.86
34 4 0.10
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (34 bp):
TTGGAAATCAAGCAGTTTGTCATTATATCTACTG
Found at i:29305 original size:74 final size:76
Alignment explanation
Indices: 29167--29344 Score: 229
Period size: 74 Copynumber: 2.4 Consensus size: 76
29157 ATATATCAGG
* * * ** *
29167 GAGGGGGAACTGATTTTGGGG-AAAAATTCGAGAAAAAAGGAAAGGGATTTTGAAAAAAATTTAG
1 GAGGGGGAATTGA-TTTGGGGAAAAAATTAGAGAAAAAAGAAAAGGGATTAGGAAAAAAACTTAG
*
29231 GGATTTCGTGGA
65 GGATTTCGGGGA
* *
29243 -A-GGGGAATTGATTTGGGGAAAAAATTAGGGAAAAAAGAAAAGGG-TCTAGGAAAGAAACTTAG
1 GAGGGGGAATTGATTTGGGGAAAAAATTAGAGAAAAAAGAAAAGGGAT-TAGGAAAAAAACTTAG
29305 GGATTTCGGGGA
65 GGATTTCGGGGA
29317 GAGGGGGAATTGATTTGGGGAAAAAATT
1 GAGGGGGAATTGATTTGGGGAAAAAATT
29345 TGACGTTCCG
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
73 8 0.09
74 54 0.61
75 2 0.02
76 25 0.28
ACGTcount: A:0.40, C:0.03, G:0.35, T:0.22
Consensus pattern (76 bp):
GAGGGGGAATTGATTTGGGGAAAAAATTAGAGAAAAAAGAAAAGGGATTAGGAAAAAAACTTAGG
GATTTCGGGGA
Found at i:29517 original size:41 final size:41
Alignment explanation
Indices: 29472--29563 Score: 123
Period size: 41 Copynumber: 2.2 Consensus size: 41
29462 GCTATAGTTC
*
29472 TACCTTTTTTCGGCGTTTAT-TCAAAAACACCGCTAATGCCT
1 TACCTTTTGT-GGCGTTTATCTCAAAAACACCGCTAATGCCT
* * * *
29513 TACCTTTTGTGGCTTTTTTCTCATAAACGCCGCTAATGCCT
1 TACCTTTTGTGGCGTTTATCTCAAAAACACCGCTAATGCCT
29554 TACCTTTTGT
1 TACCTTTTGT
29564 AGCATTTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
40 7 0.16
41 38 0.84
ACGTcount: A:0.20, C:0.26, G:0.13, T:0.41
Consensus pattern (41 bp):
TACCTTTTGTGGCGTTTATCTCAAAAACACCGCTAATGCCT
Found at i:30124 original size:24 final size:25
Alignment explanation
Indices: 30072--30124 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
30062 TCAATTATCT
* * *
30072 TAATTAGAGTGGCTAAATTGAAAAA
1 TAATTAGAGTGACCAAAATGAAAAA
30097 TAATTAGAGTGACCAAAAT-AAAAA
1 TAATTAGAGTGACCAAAATGAAAAA
30121 TAAT
1 TAAT
30125 ACTATTTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.53, C:0.06, G:0.15, T:0.26
Consensus pattern (25 bp):
TAATTAGAGTGACCAAAATGAAAAA
Found at i:35501 original size:40 final size:40
Alignment explanation
Indices: 35419--35675 Score: 342
Period size: 40 Copynumber: 6.5 Consensus size: 40
35409 AAGCCAAGTA
* * * *
35419 CCTTCGGGATTTA-ACCGGATATAGCT-ACTTGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
35457 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
35497 CCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACAAATT
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
35537 CCTTCGGGACTTAGCCCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
35577 CCTTCAGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
35617 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
35657 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
35676 TTATCATCCG
Statistics
Matches: 195, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
38 12 0.06
39 17 0.09
40 166 0.85
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Done.