Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold8
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 4373
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Found at i:22 original size:12 final size:12
Alignment explanation
Indices: 5--98 Score: 89
Period size: 12 Copynumber: 7.8 Consensus size: 12
1 TGAG
*
5 GAGCCTACCGTT
1 GAGCCTACTGTT
**
17 GAGCCTACTGAG
1 GAGCCTACTGTT
*
29 GAGCCTACCGTT
1 GAGCCTACTGTT
**
41 GAGCCTACTGAG
1 GAGCCTACTGTT
*
53 GAGCCTACCGTT
1 GAGCCTACTGTT
* **
65 GAGCCCACTGAG
1 GAGCCTACTGTT
77 GAGCCTACTGTT
1 GAGCCTACTGTT
*
89 GAGCCCACTG
1 GAGCCTACTG
99 AAGAGCCCAC
Statistics
Matches: 62, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 62 1.00
ACGTcount: A:0.20, C:0.31, G:0.29, T:0.20
Consensus pattern (12 bp):
GAGCCTACTGTT
Left flanking sequence: Indices 1 -- 4
TGAG
Right flanking sequence: Indices 99 -- 598
AAGAGCCCACTGATATTTGCACTGCTTGCACCGAGTACACAACCACTTGGACCACCACTGATGCT
AACGGCCAACCGACTACCATTACTGGTATTGTTGCTGTGATGACTGGCGAAGACGGGTCTTTGGT
GACAGTTACCTCCGAGATACCTGTTGAGCCCACTGAGGAGCCTACCGTTGAGCCTACTGAGGAGC
CTACCGTTGAGCCTACCGAGGAGCCTACCGTTGAGCCCACTGAGGAGCCTACTGTTGAGCCCACT
GAAGAGCCCACTGATGTTTGCACTGCTTGCACCGAGTACACCACCACCTGGACCATTACTGGCGC
GGACGGTAAGCCTACCACCGTCAGCGGCATCGTTGCCGTCATGACTGGCGAAGACGGGTCTTTGG
TGACGGTTACTTCTGAAATTCCCCCTGTTATCTGCACCGAATGTTCCGAGTACACCACCACATGG
ACTACCACCGGCGAGGATGGCAAGCCCACTACTGGCTCGGGCGTT
Found at i:104 original size:12 final size:12
Alignment explanation
Indices: 65--111 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
55 GCCTACCGTT
*
65 GAGCCCACTGAG
1 GAGCCCACTGAA
* **
77 GAGCCTACTGTT
1 GAGCCCACTGAA
89 GAGCCCACTGAA
1 GAGCCCACTGAA
101 GAGCCCACTGA
1 GAGCCCACTGA
112 TATTTGCACT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.15
Consensus pattern (12 bp):
GAGCCCACTGAA
Left flanking sequence: Indices 1 -- 64
TGAGGAGCCTACCGTTGAGCCTACTGAGGAGCCTACCGTTGAGCCTACTGAGGAGCCTACCGTT
Right flanking sequence: Indices 112 -- 611
TATTTGCACTGCTTGCACCGAGTACACAACCACTTGGACCACCACTGATGCTAACGGCCAACCGA
CTACCATTACTGGTATTGTTGCTGTGATGACTGGCGAAGACGGGTCTTTGGTGACAGTTACCTCC
GAGATACCTGTTGAGCCCACTGAGGAGCCTACCGTTGAGCCTACTGAGGAGCCTACCGTTGAGCC
TACCGAGGAGCCTACCGTTGAGCCCACTGAGGAGCCTACTGTTGAGCCCACTGAAGAGCCCACTG
ATGTTTGCACTGCTTGCACCGAGTACACCACCACCTGGACCATTACTGGCGCGGACGGTAAGCCT
ACCACCGTCAGCGGCATCGTTGCCGTCATGACTGGCGAAGACGGGTCTTTGGTGACGGTTACTTC
TGAAATTCCCCCTGTTATCTGCACCGAATGTTCCGAGTACACCACCACATGGACTACCACCGGCG
AGGATGGCAAGCCCACTACTGGCTCGGGCGTTGTCGACGTGACCA
Found at i:110 original size:24 final size:24
Alignment explanation
Indices: 1--105 Score: 174
Period size: 24 Copynumber: 4.4 Consensus size: 24
*
1 TGAGGAGCCTACCGTTGAGCCTAC
1 TGAGGAGCCTACCGTTGAGCCCAC
*
25 TGAGGAGCCTACCGTTGAGCCTAC
1 TGAGGAGCCTACCGTTGAGCCCAC
49 TGAGGAGCCTACCGTTGAGCCCAC
1 TGAGGAGCCTACCGTTGAGCCCAC
*
73 TGAGGAGCCTACTGTTGAGCCCAC
1 TGAGGAGCCTACCGTTGAGCCCAC
*
97 TGAAGAGCC
1 TGAGGAGCC
106 CACTGATATT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 78 1.00
ACGTcount: A:0.22, C:0.30, G:0.30, T:0.19
Consensus pattern (24 bp):
TGAGGAGCCTACCGTTGAGCCCAC
Left flanking sequence: None
Right flanking sequence: Indices 106 -- 605
CACTGATATTTGCACTGCTTGCACCGAGTACACAACCACTTGGACCACCACTGATGCTAACGGCC
AACCGACTACCATTACTGGTATTGTTGCTGTGATGACTGGCGAAGACGGGTCTTTGGTGACAGTT
ACCTCCGAGATACCTGTTGAGCCCACTGAGGAGCCTACCGTTGAGCCTACTGAGGAGCCTACCGT
TGAGCCTACCGAGGAGCCTACCGTTGAGCCCACTGAGGAGCCTACTGTTGAGCCCACTGAAGAGC
CCACTGATGTTTGCACTGCTTGCACCGAGTACACCACCACCTGGACCATTACTGGCGCGGACGGT
AAGCCTACCACCGTCAGCGGCATCGTTGCCGTCATGACTGGCGAAGACGGGTCTTTGGTGACGGT
TACTTCTGAAATTCCCCCTGTTATCTGCACCGAATGTTCCGAGTACACCACCACATGGACTACCA
CCGGCGAGGATGGCAAGCCCACTACTGGCTCGGGCGTTGTCGACG
Found at i:359 original size:12 final size:12
Alignment explanation
Indices: 253--374 Score: 91
Period size: 12 Copynumber: 10.2 Consensus size: 12
243 AGATACCTGT
*
253 TGAGCCCACTGA
1 TGAGCCTACTGA
* * *
265 GGAGCCTACCGT
1 TGAGCCTACTGA
277 TGAGCCTACTGA
1 TGAGCCTACTGA
* * *
289 GGAGCCTACCGT
1 TGAGCCTACTGA
*
301 TGAGCCTACCGA
1 TGAGCCTACTGA
* * *
313 GGAGCCTACCGT
1 TGAGCCTACTGA
*
325 TGAGCCCACTGA
1 TGAGCCTACTGA
* *
337 GGAGCCTACTGT
1 TGAGCCTACTGA
*
349 TGAGCCCACTGA
1 TGAGCCTACTGA
* *
361 AGAGCCCACTGA
1 TGAGCCTACTGA
373 TG
1 TG
375 TTTGCACTGC
Statistics
Matches: 84, Mismatches: 26, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 84 1.00
ACGTcount: A:0.22, C:0.31, G:0.29, T:0.18
Consensus pattern (12 bp):
TGAGCCTACTGA
Left flanking sequence: Indices 1 -- 252
TGAGGAGCCTACCGTTGAGCCTACTGAGGAGCCTACCGTTGAGCCTACTGAGGAGCCTACCGTTG
AGCCCACTGAGGAGCCTACTGTTGAGCCCACTGAAGAGCCCACTGATATTTGCACTGCTTGCACC
GAGTACACAACCACTTGGACCACCACTGATGCTAACGGCCAACCGACTACCATTACTGGTATTGT
TGCTGTGATGACTGGCGAAGACGGGTCTTTGGTGACAGTTACCTCCGAGATACCTGT
Right flanking sequence: Indices 375 -- 874
TTTGCACTGCTTGCACCGAGTACACCACCACCTGGACCATTACTGGCGCGGACGGTAAGCCTACC
ACCGTCAGCGGCATCGTTGCCGTCATGACTGGCGAAGACGGGTCTTTGGTGACGGTTACTTCTGA
AATTCCCCCTGTTATCTGCACCGAATGTTCCGAGTACACCACCACATGGACTACCACCGGCGAGG
ATGGCAAGCCCACTACTGGCTCGGGCGTTGTCGACGTGACCACCGACTCGAATGGGCTGTTGGTG
ACCTCTACATCTCCTATTATTGAGGAGTGCATTATTTGCACTGAGTACACGACTACTTGGACCAC
GACTTGCACCGAGGGCAAACCGACCACGTGCCTGGGTCTTGTCGAGGTTACTACGGACTCTCTCG
GGCTGGCTGTGACTTGCACTCAATCAACTACCGAGACTATCACCTGCTATGTTTGCGAAACAAAA
GCCACCGAGATTGTGACTGTAGTCGATTCCACGGTGACTATTACC
Found at i:371 original size:24 final size:24
Alignment explanation
Indices: 246--366 Score: 188
Period size: 24 Copynumber: 5.0 Consensus size: 24
236 ACCTCCGAGA
246 TACCTGTTGAGCCCACTGAGGAGCC
1 TACC-GTTGAGCCCACTGAGGAGCC
*
271 TACCGTTGAGCCTACTGAGGAGCC
1 TACCGTTGAGCCCACTGAGGAGCC
* *
295 TACCGTTGAGCCTACCGAGGAGCC
1 TACCGTTGAGCCCACTGAGGAGCC
319 TACCGTTGAGCCCACTGAGGAGCC
1 TACCGTTGAGCCCACTGAGGAGCC
* *
343 TACTGTTGAGCCCACTGAAGAGCC
1 TACCGTTGAGCCCACTGAGGAGCC
367 CACTGATGTT
Statistics
Matches: 90, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
24 86 0.96
25 4 0.04
ACGTcount: A:0.21, C:0.31, G:0.28, T:0.19
Consensus pattern (24 bp):
TACCGTTGAGCCCACTGAGGAGCC
Left flanking sequence: Indices 1 -- 245
TGAGGAGCCTACCGTTGAGCCTACTGAGGAGCCTACCGTTGAGCCTACTGAGGAGCCTACCGTTG
AGCCCACTGAGGAGCCTACTGTTGAGCCCACTGAAGAGCCCACTGATATTTGCACTGCTTGCACC
GAGTACACAACCACTTGGACCACCACTGATGCTAACGGCCAACCGACTACCATTACTGGTATTGT
TGCTGTGATGACTGGCGAAGACGGGTCTTTGGTGACAGTTACCTCCGAGA
Right flanking sequence: Indices 367 -- 866
CACTGATGTTTGCACTGCTTGCACCGAGTACACCACCACCTGGACCATTACTGGCGCGGACGGTA
AGCCTACCACCGTCAGCGGCATCGTTGCCGTCATGACTGGCGAAGACGGGTCTTTGGTGACGGTT
ACTTCTGAAATTCCCCCTGTTATCTGCACCGAATGTTCCGAGTACACCACCACATGGACTACCAC
CGGCGAGGATGGCAAGCCCACTACTGGCTCGGGCGTTGTCGACGTGACCACCGACTCGAATGGGC
TGTTGGTGACCTCTACATCTCCTATTATTGAGGAGTGCATTATTTGCACTGAGTACACGACTACT
TGGACCACGACTTGCACCGAGGGCAAACCGACCACGTGCCTGGGTCTTGTCGAGGTTACTACGGA
CTCTCTCGGGCTGGCTGTGACTTGCACTCAATCAACTACCGAGACTATCACCTGCTATGTTTGCG
AAACAAAAGCCACCGAGATTGTGACTGTAGTCGATTCCACGGTGA
Found at i:470 original size:261 final size:261
Alignment explanation
Indices: 1--498 Score: 784
Period size: 261 Copynumber: 1.9 Consensus size: 261
*
1 TGAGGAGCCTACCGTTGAGCCTACTGAGGAGCCTACCGTTGAGCCTACTGAGGAGCCTACCGTTG
1 TGAGGAGCCTACCGTTGAGCCTACTGAGGAGCCTACCGTTGAGCCTACCGAGGAGCCTACCGTTG
66 AGCCCACTGAGGAGCCTACTGTTGAGCCCACTGAAGAGCCCACTGATATTTGCACTGCTTGCACC
66 AGCCCACTGAGGAGCCTACTGTTGAGCCCACTGAAGAGCCCACTGATATTTGCACTGCTTGCACC
* * * * * * *
131 GAGTACACAACCACTTGGACCACCACTGATGCTAACGGCCAACCGACTACCATTACTGGTATTGT
131 GAGTACACAACCACCTGGACCACCACTGACGCGAACGGCCAACCGACCACCATCACTGGCATCGT
* *
196 TGCTGTGATGACTGGCGAAGACGGGTCTTTGGTGACAGTTACCTCCGAGATACCTGTTGAGCCCA
196 TGCCGTCATGACTGGCGAAGACGGGTCTTTGGTGACAGTTACCTCCGAGATACCTGTTGAGCCCA
261 C
261 C
262 TGAGGAGCCTACCGTTGAGCCTACTGAGGAGCCTACCGTTGAGCCTACCGAGGAGCCTACCGTTG
1 TGAGGAGCCTACCGTTGAGCCTACTGAGGAGCCTACCGTTGAGCCTACCGAGGAGCCTACCGTTG
*
327 AGCCCACTGAGGAGCCTACTGTTGAGCCCACTGAAGAGCCCACTGATGTTTGCACTGCTTGCACC
66 AGCCCACTGAGGAGCCTACTGTTGAGCCCACTGAAGAGCCCACTGATATTTGCACTGCTTGCACC
* ** * * * * *
392 GAGTACACCACCACCTGGACCATTACTGGCGCGGACGG-TAAGCCTACCACCGTCAGC-GGCATC
131 GAGTACACAACCACCTGGACCACCACTGACGCGAACGGCCAA-CCGACCACCATCA-CTGGCATC
*
455 GTTGCCGTCATGACTGGCGAAGACGGGTCTTTGGTGACGGTTAC
194 GTTGCCGTCATGACTGGCGAAGACGGGTCTTTGGTGACAGTTAC
499 TTCTGAAATT
Statistics
Matches: 215, Mismatches: 20, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
260 2 0.01
261 212 0.99
262 1 0.00
ACGTcount: A:0.22, C:0.30, G:0.27, T:0.21
Consensus pattern (261 bp):
TGAGGAGCCTACCGTTGAGCCTACTGAGGAGCCTACCGTTGAGCCTACCGAGGAGCCTACCGTTG
AGCCCACTGAGGAGCCTACTGTTGAGCCCACTGAAGAGCCCACTGATATTTGCACTGCTTGCACC
GAGTACACAACCACCTGGACCACCACTGACGCGAACGGCCAACCGACCACCATCACTGGCATCGT
TGCCGTCATGACTGGCGAAGACGGGTCTTTGGTGACAGTTACCTCCGAGATACCTGTTGAGCCCA
C
Left flanking sequence: None
Right flanking sequence: Indices 499 -- 998
TTCTGAAATTCCCCCTGTTATCTGCACCGAATGTTCCGAGTACACCACCACATGGACTACCACCG
GCGAGGATGGCAAGCCCACTACTGGCTCGGGCGTTGTCGACGTGACCACCGACTCGAATGGGCTG
TTGGTGACCTCTACATCTCCTATTATTGAGGAGTGCATTATTTGCACTGAGTACACGACTACTTG
GACCACGACTTGCACCGAGGGCAAACCGACCACGTGCCTGGGTCTTGTCGAGGTTACTACGGACT
CTCTCGGGCTGGCTGTGACTTGCACTCAATCAACTACCGAGACTATCACCTGCTATGTTTGCGAA
ACAAAAGCCACCGAGATTGTGACTGTAGTCGATTCCACGGTGACTATTACCCAACCTTGTTATAT
TGTGGTGACCACGAACAGCGAGGGGTCCATTTACACAACTACCGAATTTGAAGGCCAAAAGACTG
TGACTGTCTACACTTCCAAGATTTCTCCAGAGGTTGTGTATATGT
Done.