Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2591
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: 34276
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1327 original size:80 final size:80
Alignment explanation
Indices: 1189--1438 Score: 294
Period size: 80 Copynumber: 3.1 Consensus size: 80
1179 CTAACGAGGT
* * * *
1189 TAAGTCCCGAAGACATTTGTGCTAGTGATTAATTCCGGGCTAAGTCCCGAAGGTATTTGTGTGAG
1 TAAGTCCCGAAGGCATTTGTGCGAGTGATTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
*
1254 TTACTA-ATTCTGGGC
66 TTACTATA-TCCGGGC
*
1269 TAAGTCCCGAAGGCATTTGTGCGAGTTATTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
1 TAAGTCCCGAAGGCATTTGTGCGAGTGATTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
1334 TTACTATATCCGGGC
66 TTACTATATCCGGGC
* * ** * *
1349 TAAGTCCCGAAGGCATTTGTGCTAGCGA-CCATATCCGGGCTAAGACCC-AACGGC-CTTGTGCG
1 TAAGTCCCGAAGGCATTTGTGCGAGTGATTAAT-TCCGGGCTAAGTCCCGAA-GGCATTTGTGCG
***
1411 AGTGGTTATAT-CGGGC
64 AGTTACTATATCCGGGC
*
1427 TAAATCCCGAAG
1 TAAGTCCCGAAG
1439 ATAATTGGGT
Statistics
Matches: 150, Mismatches: 17, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
78 16 0.11
79 19 0.13
80 114 0.76
81 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.28
Consensus pattern (80 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTGATTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
TTACTATATCCGGGC
Found at i:1392 original size:40 final size:40
Alignment explanation
Indices: 1189--1373 Score: 266
Period size: 40 Copynumber: 4.6 Consensus size: 40
1179 CTAACGAGGT
* * *
1189 TAAGTCCCGAAGACATTTGTGCTAGTGATTAATTCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCTAGTTACTAATTCCGGGC
* *
1229 TAAGTCCCGAAGGTATTTGTG-TGAGTTACTAATTCTGGGC
1 TAAGTCCCGAAGGCATTTGTGCT-AGTTACTAATTCCGGGC
* *
1269 TAAGTCCCGAAGGCATTTGTGCGAGTTATTAATTCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCTAGTTACTAATTCCGGGC
*
1309 TAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCTAGTTACTAAT-TCCGGGC
1349 TAAGTCCCGAAGGCATTTGTGCTAG
1 TAAGTCCCGAAGGCATTTGTGCTAG
1374 CGACCATATC
Statistics
Matches: 131, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
39 3 0.02
40 128 0.98
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.30
Consensus pattern (40 bp):
TAAGTCCCGAAGGCATTTGTGCTAGTTACTAATTCCGGGC
Found at i:9476 original size:40 final size:40
Alignment explanation
Indices: 9418--9599 Score: 285
Period size: 40 Copynumber: 4.5 Consensus size: 40
9408 CTAACGAGGT
* * * *
9418 TAAGTCCCGAAGACATTTGTGCTAGTGATTAATTCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
* *
9458 TAAGTCCCGAAGGTATTTGTGCGAGTTACTAATTCTGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
9498 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
9538 TAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCCGGGC
*
9578 TAAGTCCCGAAGGAATTTGTGC
1 TAAGTCCCGAAGGCATTTGTGC
9600 TAGCGACCAT
Statistics
Matches: 132, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
39 2 0.02
40 130 0.98
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (40 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
Found at i:9556 original size:80 final size:80
Alignment explanation
Indices: 9418--9667 Score: 294
Period size: 80 Copynumber: 3.1 Consensus size: 80
9408 CTAACGAGGT
* * * *
9418 TAAGTCCCGAAGACATTTGTGCTAGTGATTAATTCCGGGCTAAGTCCCGAAGGTATTTGTGCGAG
1 TAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
*
9483 TTACTA-ATTCTGGGC
66 TTACTATA-TCCGGGC
*
9498 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
1 TAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
9563 TTACTATATCCGGGC
66 TTACTATATCCGGGC
* * * * * *
9578 TAAGTCCCGAAGGAATTTGTGCTAGCGAC-CATATCCGGGCTAAGACCC-AACGGC-CTTGTGCG
1 TAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-TCCGGGCTAAGTCCCGAA-GGCATTTGTGCG
***
9640 AGTGGTTATAT-CGGGC
64 AGTTACTATATCCGGGC
*
9656 TAAATCCCGAAG
1 TAAGTCCCGAAG
9668 ATAATTGGGT
Statistics
Matches: 150, Mismatches: 17, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
78 16 0.11
79 19 0.13
80 114 0.76
81 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (80 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
TTACTATATCCGGGC
Found at i:15055 original size:17 final size:18
Alignment explanation
Indices: 15029--15062 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
15019 AATCTGTGTA
*
15029 GGGCCTACAAG-CCCATT
1 GGGCCCACAAGACCCATT
15046 GGGCCCACAAGACCCAT
1 GGGCCCACAAGACCCAT
15063 CTAGGCCCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.26, C:0.38, G:0.24, T:0.12
Consensus pattern (18 bp):
GGGCCCACAAGACCCATT
Found at i:20280 original size:41 final size:42
Alignment explanation
Indices: 20118--20268 Score: 207
Period size: 42 Copynumber: 3.6 Consensus size: 42
20108 TAATAGTGAT
*
20118 ATATCAGGCTTATTGCCTAACAGGCTTTGATGCCGGTGTATG
1 ATATCAGGCTTATTGCCTAGCAGGCTTTGATGCCGGTGTATG
* * *
20160 ATATTAGGCTTATTGCCTAGCAGGATTTGATGCTGGTGTATG
1 ATATCAGGCTTATTGCCTAGCAGGCTTTGATGCCGGTGTATG
* *
20202 ATATCAGGTTTATTGCCTAGTAGGCTTT-ATGCCGGTGTATTG
1 ATATCAGGCTTATTGCCTAGCAGGCTTTGATGCCGGTGTA-TG
* *
20244 A-ATCAGGTTTATTACCTAGCAGGCT
1 ATATCAGGCTTATTGCCTAGCAGGCT
20269 CTATGTCGGT
Statistics
Matches: 97, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
41 32 0.33
42 65 0.67
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.36
Consensus pattern (42 bp):
ATATCAGGCTTATTGCCTAGCAGGCTTTGATGCCGGTGTATG
Found at i:20297 original size:83 final size:85
Alignment explanation
Indices: 20118--20303 Score: 208
Period size: 83 Copynumber: 2.2 Consensus size: 85
20108 TAATAGTGAT
* *
20118 ATATCAGGC-TTATTGCCTAACAGGCTTTGATGCCGGTGTATGATATTAGGCTTATTGCCTAGCA
1 ATATCAGGCTTTATTGCCTAACAGGCTTTGATGCCGGTGTATGATATCAGGCTTATTACCTAGCA
*
20182 GGATTTGATGCTGGTGTATG
66 GGATCTGATGCTGGTGTATG
** *
20202 ATATCAGG-TTTATTGCCTAGTAGGCTTT-ATGCCGGTGTATTGA-ATCAGGTTTATTACCTAGC
1 ATATCAGGCTTTATTGCCTAACAGGCTTTGATGCCGGTGTA-TGATATCAGGCTTATTACCTAGC
* * *
20264 AGGCTCT-ATG-TCGGTGTTTT
65 AGGATCTGATGCT-GGTGTATG
20284 ATA-CAAGGCTTTA-TGCCTAA
1 ATATC-AGGCTTTATTGCCTAA
20304 TGAATTTTAT
Statistics
Matches: 87, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
81 2 0.02
82 21 0.24
83 36 0.41
84 28 0.32
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (85 bp):
ATATCAGGCTTTATTGCCTAACAGGCTTTGATGCCGGTGTATGATATCAGGCTTATTACCTAGCA
GGATCTGATGCTGGTGTATG
Found at i:22883 original size:33 final size:34
Alignment explanation
Indices: 22840--22927 Score: 106
Period size: 34 Copynumber: 2.6 Consensus size: 34
22830 ACTGTACTGA
* *
22840 TACTGGAATGGGCTTAGGCCC-CACTGATACTAT
1 TACTGAAATGGGCTAAGGCCCACACTGATACTAT
* * *
22873 TACTGAAATGGGCTCAGGCCCAGACTGTTACTAT
1 TACTGAAATGGGCTAAGGCCCACACTGATACTAT
* *
22907 TATTGAAATGAGCTAAGGCCC
1 TACTGAAATGGGCTAAGGCCC
22928 TAACTGAGAC
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 19 0.40
34 28 0.60
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (34 bp):
TACTGAAATGGGCTAAGGCCCACACTGATACTAT
Found at i:29696 original size:40 final size:39
Alignment explanation
Indices: 29646--29870 Score: 272
Period size: 40 Copynumber: 5.7 Consensus size: 39
29636 ACCACTAGCT
*
29646 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
**
29686 CAAATGCCTTCGGGACTTAGCCCGGTATAACAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
* * *
29725 CAAATGCCTTCGGGACTTAGCCCGGACATAATAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* *
29765 CAAACGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* * ** * *
29805 CAAATGCCTTCGGGACTTAGTCCGGAATTAGGCACTAGCT
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAACTCGCA
29845 CAAATG-CTCTCGGGACTTAGCCCGGT
1 CAAATGCCT-TCGGGACTTAGCCCGGT
29871 TATCATCCGA
Statistics
Matches: 163, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
39 39 0.24
40 124 0.76
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
Found at i:29746 original size:79 final size:79
Alignment explanation
Indices: 29623--29869 Score: 293
Period size: 79 Copynumber: 3.1 Consensus size: 79
29613 CTTTCGGAGT
* * * * *
29623 TTAG-CCGGATATAACCACTAGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCAC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGACTTAGCCCGG-AATAGTAACTAGCAC
29687 AAATGCCTTCGGGAC
65 AAATGCCTTCGGGAC
* * *
29702 TTAGCCCGG-TATAACAACTCGCACAAATGCCTTCGGGACTTAGCCCGGACATAATAGCTCGCAC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA-ATAGTAACTAGCAC
*
29766 AAACGCCTTCGGGAC
65 AAATGCCTTCGGGAC
** * * ** *
29781 TTAGCCCGGATATAGTAGCTCGCACAAATGCCTTCGGGACTTAGTCCGGAATTAGGCACTAGCTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAA-TAGTAACTAGCAC
29846 AAATG-CTCTCGGGAC
65 AAATGCCT-TCGGGAC
29861 TTAGCCCGG
1 TTAGCCCGG
29870 TTATCATCCG
Statistics
Matches: 144, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
79 77 0.53
80 67 0.47
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (79 bp):
TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATAGTAACTAGCACA
AATGCCTTCGGGAC
Done.