Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1245
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: 41028
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Found at i:1410 original size:68 final size:68
Alignment explanation
Indices: 1338--1513 Score: 175
Period size: 68 Copynumber: 2.6 Consensus size: 68
1328 CATCATGTGT
** * * *
1338 ACAAGAGAGCTACGAGATACTATGTAGTAGCTAGGTCACATGTGTGA-T-ACGGGATGTATC-CC
1 ACAAGAGAGCTACGAGATA-TAAAT-GTAGCTAGGTCACATGTGTGATTCAAGGGAAGGA-CACC
1400 ATGTAG
63 ATGTAG
* * *
1406 ACAAGAGAGCTACGGAGAGGATAAATGTAGCTAGGTCGCATGTGTGATTCCAAGTGAAGGACACC
1 ACAAGAGAGCTAC-GAGA-TATAAATGTAGCTAGGTCACATGTGTGATT-CAAGGGAAGGACACC
1471 ATGTAG
63 ATGTAG
*
1477 ACAAGAGAGCTACGAG--ATAAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGAGATATAAATGTAGCTAGGTCACATG
1514 GGTGGTACTA
Statistics
Matches: 92, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
66 13 0.14
67 6 0.07
68 33 0.36
69 8 0.09
70 5 0.05
71 27 0.29
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.22
Consensus pattern (68 bp):
ACAAGAGAGCTACGAGATATAAATGTAGCTAGGTCACATGTGTGATTCAAGGGAAGGACACCATG
TAG
Found at i:16458 original size:66 final size:69
Alignment explanation
Indices: 16330--16460 Score: 160
Period size: 66 Copynumber: 1.9 Consensus size: 69
16320 GGGATGTATC
* * *
16330 CCATGCAGACAAGAGAGCTACGGGAGAGGATAAATGTAGCTAGGTCGCATGTGTGATTCTAAGTG
1 CCATGCAGACAAGAGAGCTAC--G-GAGGATAAATGTAGCTAGGTCACATGGGTGATACTAAGTG
16395 AAAGACA
63 AAAGACA
* * *
16402 CCATGTAGACAAGAGAGCTAC-GA-GATAAAT-TGGCTAGGTCACATGGGTGGTACTAAGTG
1 CCATGCAGACAAGAGAGCTACGGAGGATAAATGTAGCTAGGTCACATGGGTGATACTAAGTG
16461 TTCACCATGT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
66 24 0.45
67 7 0.13
68 2 0.04
72 20 0.38
ACGTcount: A:0.34, C:0.15, G:0.31, T:0.21
Consensus pattern (69 bp):
CCATGCAGACAAGAGAGCTACGGAGGATAAATGTAGCTAGGTCACATGGGTGATACTAAGTGAAA
GACA
Found at i:24503 original size:40 final size:40
Alignment explanation
Indices: 24271--24496 Score: 289
Period size: 40 Copynumber: 5.7 Consensus size: 40
24261 TTGAATGATG
* * * *
24271 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAGGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGA-GTTACTAAA
* * *
24311 TCCGGACTAAGAT-CCAAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
24351 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
24391 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
24431 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
24472 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
24497 AACGAGTAGC
Statistics
Matches: 169, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
39 1 0.01
40 158 0.93
41 10 0.06
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:24503 original size:120 final size:120
Alignment explanation
Indices: 24271--24529 Score: 287
Period size: 120 Copynumber: 2.2 Consensus size: 120
24261 TTGAATGATG
* * *
24271 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAGGTGACCATATCCGGACTAAGATCCAAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGTGACCAAATCCGGACTAAGATCCAAAGGCATTT
**
24336 GTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTA-CTAAA
66 GTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAG-TAGCTAAA
* * ** *
24391 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-GTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCGAGGTGACCAAATCCGGACTAAGAT-CCAAAGGCAT
* * * *
24454 TTGTGCGAGTTACTATAA-CCGGGCTATG-TCCCGAAGGCATTTGAACGAGTAGCTATA
64 TTGTACGAGTTACTA-AATCCGGACTAAGAT-CCGAAGGCATTTGAACGAGTAGCTAAA
* *
24511 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
24530 TACGTGATTT
Statistics
Matches: 118, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
119 18 0.15
120 90 0.76
121 10 0.08
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (120 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGTGACCAAATCCGGACTAAGATCCAAAGGCATTT
GTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTAGCTAAA
Found at i:30959 original size:39 final size:39
Alignment explanation
Indices: 30822--31044 Score: 260
Period size: 40 Copynumber: 5.7 Consensus size: 39
30812 GCTCCTCGTT
* *
30822 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAT-TAGT-ATCTCGCA
* *
30862 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGA-TTAGTATCTCGCA
30902 CAAATGCCTTCGGG-CTTAGCCCGGATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTAGTATCTCGCA
*
30940 CAAATGCCTTC-GGATCTTAGTCCGGATTAGTATCTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTAGTATCTCGCA
* * *
30979 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TAGT-ATC-TCGCA
31020 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
31045 CATCATTCAA
Statistics
Matches: 165, Mismatches: 10, Indels: 16
0.86 0.05 0.08
Matches are distributed among these distances:
37 2 0.01
38 23 0.14
39 61 0.37
40 66 0.40
41 13 0.08
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTAGTATCTCGCA
Found at i:31004 original size:117 final size:119
Alignment explanation
Indices: 30822--31044 Score: 287
Period size: 117 Copynumber: 1.9 Consensus size: 119
30812 GCTCCTCGTT
*
30822 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
30887 ATTTAGTAAC-TCGCACAAATGCCTTCGGG-CTTAGCCCGGATTAGTATCTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGATTAGTATCTCGCA
* * **
30940 CAAATGCCTTC-GGATCTTAGTCCGGAT-TAGT-ATCTCGCACAAATGCCTTC-GGATCTTAGTC
1 CAAATGCCTTCGGGA-CATAGCCCGGATATAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAACC
* *
31001 CGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
63 CGGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
31045 CATCATTCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
116 5 0.05
117 47 0.52
118 39 0.43
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (119 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGGATTAGTATCTCGCA
Found at i:38759 original size:39 final size:40
Alignment explanation
Indices: 38716--38938 Score: 239
Period size: 39 Copynumber: 5.7 Consensus size: 40
38706 GCTCCTCGTT
* *
38716 CAAATGCCTTCGGGACATAGCCCGGTTATAGTA-ATCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTATATCGCA
* *
38755 CAAATGCCTTCGGGACTTAACCCGGATTTAGTA-ACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTATA-TCGCA
*
38795 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTATATCGCA
* *
38834 CAAATGCCTTC-GGATCTTAGTCCGGAT-TAGTATCTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTATATCGCA
* * *
38873 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACT-TAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGT-A-TATCGCA
38914 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
38939 CATCATTCAA
Statistics
Matches: 163, Mismatches: 11, Indels: 19
0.84 0.06 0.10
Matches are distributed among these distances:
38 2 0.01
39 100 0.61
40 48 0.29
41 12 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTATATCGCA
Found at i:38834 original size:79 final size:77
Alignment explanation
Indices: 38716--38938 Score: 263
Period size: 79 Copynumber: 2.8 Consensus size: 77
38706 GCTCCTCGTT
* * * *
38716 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATCGCACAAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
38781 TTTAGTAACTCGCA
65 -TTAGTAACTCGCA
*
38795 CAAATGCCTTCGGGCTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 CAAATGCCTTCGGGCTTAGCCCGGATA-TAGTA-CTCGCACAAATGCCTTCGGGA-CTTAGCCCG
*
38858 GATTAGTATCTCGCA
63 GATTAGTAACTCGCA
* * * *
38873 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGGATATAGT-AC-TCGCACAAATGCCTTCGGGACTTAGCCCG
38937 GA
63 GA
38939 CATCATTCAA
Statistics
Matches: 125, Mismatches: 11, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
77 1 0.01
78 42 0.34
79 69 0.55
80 13 0.10
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (77 bp):
CAAATGCCTTCGGGCTTAGCCCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGAT
TAGTAACTCGCA
Found at i:38898 original size:118 final size:119
Alignment explanation
Indices: 38716--38938 Score: 285
Period size: 118 Copynumber: 1.9 Consensus size: 119
38706 GCTCCTCGTT
*
38716 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATCGCACAAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAATCGCACAAATGCCTTCGGGACTTAACCCGGA
* *
38781 TTTAGTAAC-TCGCACAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
66 TATAGTAACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* * * **
38834 CAAATGCCTTC-GGATCTTAGTCCGGAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGA-CATAGCCCGGATATAGTA-ATCGCACAAATGCCTTCGGGA-CTTAACCC
* *
38896 GGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
63 GGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
38939 CATCATTCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
117 11 0.12
118 60 0.67
119 19 0.21
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (119 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAATCGCACAAATGCCTTCGGGACTTAACCCGGA
TATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Done.