Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3258
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: 22326
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Found at i:1855 original size:68 final size:67
Alignment explanation
Indices: 1774--1906 Score: 257
Period size: 68 Copynumber: 2.0 Consensus size: 67
1764 TGGACAAATA
1774 AACAGCAAGAGGCTTTTGAGAAGTTAAAGAAGGTCCTGACAGAAGTGCCAGTGTTAATTCAGCTA
1 AACAGCAAGAGGCTTTTGAGAAGTTAAAGAAGGTCCTGACAGAAGTGCCAGTGTTAATTCAGCTA
1839 AT
66 AT
1841 AACAGCAAGAAGGCTTTTGAGAAGTTAAAGAAGGTCCTGACAGAAGTGCCAGTGTTAATTCAGCT
1 AACAGCAAG-AGGCTTTTGAGAAGTTAAAGAAGGTCCTGACAGAAGTGCCAGTGTTAATTCAGCT
1906 A
65 A
1907 GAGTCTGGTA
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
67 9 0.14
68 56 0.86
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (67 bp):
AACAGCAAGAGGCTTTTGAGAAGTTAAAGAAGGTCCTGACAGAAGTGCCAGTGTTAATTCAGCTA
AT
Found at i:3424 original size:77 final size:78
Alignment explanation
Indices: 3323--3490 Score: 225
Period size: 77 Copynumber: 2.2 Consensus size: 78
3313 GCTCCTCGTT
* *
3323 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGAC-TAACCCGG
1 CAAATGCCTTCGGGACATAACCCGGATTTA--AACTCACACGAATGCCTTCGGGACTTAACCCGG
3386 ATTTA-AAACTCGCA
64 ATTTAGAAACTCGCA
* * * *
3400 CGAATGCCTTCGGGACTTAACCCGGATTTAATCTCGCACGAATGCCTTCGGGACTTAACCCGGAT
1 CAAATGCCTTCGGGACATAACCCGGATTTAAACTCACACGAATGCCTTCGGGACTTAACCCGGAT
* *
3465 TTAGTATCTCGCA
66 TTAGAAACTCGCA
3478 CAAATGCCTTCGG
1 CAAATGCCTTCGG
3491 ATCTTAGTCC
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
75 7 0.09
76 14 0.18
77 39 0.49
78 19 0.24
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAAACTCACACGAATGCCTTCGGGACTTAACCCGGAT
TTAGAAACTCGCA
Found at i:3485 original size:40 final size:39
Alignment explanation
Indices: 3323--3543 Score: 227
Period size: 38 Copynumber: 5.7 Consensus size: 39
3313 GCTCCTCGTT
* * * *
3323 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTA-TAACTCGCA
*
3363 C-AATGCCTTCGGGAC-TAACCCGGATTTAAAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTATAACTCGCA
* *
3400 CGAATGCCTTCGGGACTTAACCCGGATTTA-ATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTATAACTCGCA
* *
3438 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTA-TAACTCGCA
** * * *
3478 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTA-TAAC-TCGCA
*
3519 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
3544 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 14, Indels: 14
0.85 0.07 0.07
Matches are distributed among these distances:
37 8 0.05
38 62 0.39
39 30 0.19
40 49 0.31
41 11 0.07
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTATAACTCGCA
Found at i:3552 original size:41 final size:41
Alignment explanation
Indices: 3475--3552 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
3465 TTAGTATCTC
* * *
3475 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
3516 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
3553 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:11382 original size:40 final size:40
Alignment explanation
Indices: 11200--11422 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
11190 TCCTCGTTCA
* * * * *
11200 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
11239 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
11279 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
11319 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
11359 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
11399 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
11423 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 115 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:11431 original size:41 final size:41
Alignment explanation
Indices: 11354--11431 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
11344 TTAGTATCTC
* * *
11354 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
11395 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
11432 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:19039 original size:27 final size:27
Alignment explanation
Indices: 19008--19185 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
18998 TAAATTGTAC
19008 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
19035 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
19061 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
19089 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
19117 AGCACTAAGTGTGCGATTTGATTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
19144 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
19171 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
19186 GACTCGATAT
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 108 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:19122 original size:82 final size:81
Alignment explanation
Indices: 19009--19164 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
18999 AAATTGTACA
*
19009 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTA-GCACTAAGTG
19073 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
19090 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTG
*
19155 TGCGAGTTGA
65 TGCGAATTGA
19165 TTATATAGCA
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 15 0.22
82 52 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:19176 original size:82 final size:81
Alignment explanation
Indices: 19005--19185 Score: 238
Period size: 82 Copynumber: 2.2 Consensus size: 81
18995 GATTAAATTG
*
19005 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
19070 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
19086 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGAT-GCACT
* **
19150 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
19168 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
19186 GACTCGATAT
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
81 18 0.21
82 67 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
GTGTGCGAATTGACCA
Done.