Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1202
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: 34764
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Found at i:1276 original size:43 final size:43
Alignment explanation
Indices: 1229--1328 Score: 155
Period size: 43 Copynumber: 2.3 Consensus size: 43
1219 GAGTAAATGA
* *
1229 CACTAAGTGTGCGATACAATTATAGCTTCGGCTAATTATTTGG
1 CACTAAGTGTGCGATACAATTATAGCTTCGACTAATTAATTGG
* **
1272 CACTAAGTTTGCGATATGATTATAGCTTCGACTAATTAATTGG
1 CACTAAGTGTGCGATACAATTATAGCTTCGACTAATTAATTGG
1315 CACTAAGTGTGCGA
1 CACTAAGTGTGCGA
1329 GTTCGTTGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (43 bp):
CACTAAGTGTGCGATACAATTATAGCTTCGACTAATTAATTGG
Found at i:9247 original size:48 final size:48
Alignment explanation
Indices: 9167--9430 Score: 336
Period size: 48 Copynumber: 5.8 Consensus size: 48
9157 GGAATGGAAA
*
9167 AACGTGGTGCTAAGTGGATATACCACGATTACACATATTGATACATGT
1 AACGTGGTGCTAAGTGGATATACCACGGTTACACATATTGATACATGT
* * * *
9215 AACGTGGTGCTAAGTGGATATGCCATGGTTACATATATTGATTCAT-T
1 AACGTGGTGCTAAGTGGATATACCACGGTTACACATATTGATACATGT
*
9262 AACGTGGTGCTAAGTGGATATACCACGG---------TT-ATACGTGT
1 AACGTGGTGCTAAGTGGATATACCACGGTTACACATATTGATACATGT
* * *
9300 AACGTGGTGCTAAGTGGATATACCATGATTACACATATTGATACATGC
1 AACGTGGTGCTAAGTGGATATACCACGGTTACACATATTGATACATGT
* *
9348 AACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT-T
1 AACGTGGTGCTAAGTGGATATACCACGGTTACACATATTGATACATGT
*
9395 AACGTGGTGCTAAGTGGATATACCACGGTTAAACAT
1 AACGTGGTGCTAAGTGGATATACCACGGTTACACAT
9431 GTAACGTGGT
Statistics
Matches: 185, Mismatches: 20, Indels: 23
0.81 0.09 0.10
Matches are distributed among these distances:
37 4 0.02
38 29 0.16
47 63 0.34
48 89 0.48
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.31
Consensus pattern (48 bp):
AACGTGGTGCTAAGTGGATATACCACGGTTACACATATTGATACATGT
Found at i:9312 original size:38 final size:38
Alignment explanation
Indices: 9261--9470 Score: 186
Period size: 38 Copynumber: 5.0 Consensus size: 38
9251 ATTGATTCAT
*
9261 TAACGTGGTGCTAAGTGGATATACCACGGTTATACGTG
1 TAACGTGGTGCTAAGTGGATATACCACGGTTATACATG
**
9299 TAACGTGGTGCTAAGTGGATATACCATGATTACACATATTGATACATG
1 TAACGTGGTGCTAAGTGGATATA-C-------CAC-GGTT-ATACATG
* *
9347 CAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTG
1 TAACGTGGTGCTAAGTGGATATACCACGGTT--ATACA-TG
*
9388 ATTCATTAACGTGGTGCTAAGTGGATATACCACGGTTAAACATG
1 ------TAACGTGGTGCTAAGTGGATATACCACGGTTATACATG
*
9432 TAACGTGGTGCTAAGTGGATATGCCACGGTTATACATG
1 TAACGTGGTGCTAAGTGGATATACCACGGTTATACATG
9470 T
1 T
9471 TAATTTGAAA
Statistics
Matches: 141, Mismatches: 13, Indels: 36
0.74 0.07 0.19
Matches are distributed among these distances:
38 60 0.43
39 3 0.02
40 7 0.05
41 2 0.01
44 2 0.01
45 3 0.02
46 3 0.02
47 33 0.23
48 28 0.20
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (38 bp):
TAACGTGGTGCTAAGTGGATATACCACGGTTATACATG
Found at i:9405 original size:133 final size:133
Alignment explanation
Indices: 9167--9468 Score: 523
Period size: 133 Copynumber: 2.3 Consensus size: 133
9157 GGAATGGAAA
*
9167 AACGTGGTGCTAAGTGGATATACCACGATTACACATATTGATACATGTAACGTGGTGCTAAGTGG
1 AACGTGGTGCTAAGTGGATATACCACGATTACACATATTGATACATGCAACGTGGTGCTAAGTGG
* * * *
9232 ATATGCCATGGTTACATATATTGATTCATTAACGTGGTGCTAAGTGGATATACCACGGTTATACG
66 ATATACCACGGTTACATATATTGATTCATTAACGTGGTGCTAAGTGGATATACCACGGTTAAACA
9297 TGT
131 TGT
*
9300 AACGTGGTGCTAAGTGGATATACCATGATTACACATATTGATACATGCAACGTGGTGCTAAGTGG
1 AACGTGGTGCTAAGTGGATATACCACGATTACACATATTGATACATGCAACGTGGTGCTAAGTGG
9365 ATATACCACGGTTACATATATTGATTCATTAACGTGGTGCTAAGTGGATATACCACGGTTAAACA
66 ATATACCACGGTTACATATATTGATTCATTAACGTGGTGCTAAGTGGATATACCACGGTTAAACA
9430 TGT
131 TGT
* * *
9433 AACGTGGTGCTAAGTGGATATGCCACGGTTATACAT
1 AACGTGGTGCTAAGTGGATATACCACGATTACACAT
9469 GTTAATTTGA
Statistics
Matches: 159, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
133 159 1.00
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (133 bp):
AACGTGGTGCTAAGTGGATATACCACGATTACACATATTGATACATGCAACGTGGTGCTAAGTGG
ATATACCACGGTTACATATATTGATTCATTAACGTGGTGCTAAGTGGATATACCACGGTTAAACA
TGT
Found at i:15095 original size:1 final size:1
Alignment explanation
Indices: 15089--15121 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
15079 ATTACAACCA
15089 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
15122 ACATCTCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:17271 original size:40 final size:40
Alignment explanation
Indices: 17194--17325 Score: 153
Period size: 40 Copynumber: 3.3 Consensus size: 40
17184 ACCCAAGTAT
*
17194 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAACAACTAGCACAAATGC
*
17233 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAA-CAACTAGCACAAATGC
* * * * *
17273 CTTCGGGACATAGCCCGGATATAGCAACTCGCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTAGCACAAATGC
*
17313 CTTCGGATCTTAG
1 CTTCGGGTCTTAG
17326 TTTGGTTATC
Statistics
Matches: 78, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
38 1 0.01
39 12 0.15
40 64 0.82
41 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAACAACTAGCACAAATGC
Found at i:25404 original size:40 final size:40
Alignment explanation
Indices: 25346--25508 Score: 213
Period size: 40 Copynumber: 4.1 Consensus size: 40
25336 TCTTTGGGAT
*
25346 TTAG-CCGGATATAACAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGTC
*
25385 TTAGCCCAGATATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGTC
* * * *
25425 TTAGCCCGGATATAATC-ACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATAT-AGCAACTCGCACAAATGCCTTCGGGTC
* * * *
25465 ATAGCCTGGATATAGCAACTCGCACGAATGCCTTCGGATC
1 TTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGTC
25505 TTAG
1 TTAG
25509 TTTGGTTATC
Statistics
Matches: 105, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
39 6 0.06
40 97 0.92
41 2 0.02
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
TTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGTC
Found at i:31921 original size:27 final size:26
Alignment explanation
Indices: 31873--31929 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
31863 GCGAGGCTGC
*
31873 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
31900 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
31926 CAGA
1 CAGA
31930 AATATATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Done.