Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2271
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: 3023
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.33
Found at i:187 original size:1 final size:1
Alignment explanation
Indices: 183--226 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
173 GTTTTTTTTT
* * **
183 AAAAAAAAAAAAATAAAATAAAAAAAAAAAATTAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
227 TTCCAAATGT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (1 bp):
A
Found at i:205 original size:14 final size:13
Alignment explanation
Indices: 183--227 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
173 GTTTTTTTTT
183 AAAAAA-AAAAAA
1 AAAAAATAAAAAA
*
195 ATAAAATAAAAAA
1 AAAAAATAAAAAA
*
208 AAAAAATTAAAAA
1 AAAAAATAAAAAA
221 AAAAAAT
1 AAAAAAT
228 TCCAAATGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 5 0.17
13 24 0.83
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (13 bp):
AAAAAATAAAAAA
Found at i:206 original size:19 final size:19
Alignment explanation
Indices: 182--226 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
172 TGTTTTTTTT
182 TAAAAAAAAAAAAATAAAA
1 TAAAAAAAAAAAAATAAAA
*
201 TAAAAAAAAAAAATTAAAA
1 TAAAAAAAAAAAAATAAAA
220 -AAAAAAA
1 TAAAAAAA
227 TTCCAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (19 bp):
TAAAAAAAAAAAAATAAAA
Found at i:207 original size:18 final size:18
Alignment explanation
Indices: 183--226 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
173 GTTTTTTTTT
183 AAAAAAAAAAAAA-TAAA
1 AAAAAAAAAAAAATTAAA
200 ATAAAAAAAAAAAATTAAA
1 A-AAAAAAAAAAAATTAAA
219 AAAAAAAA
1 AAAAAAAA
227 TTCCAAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.04
18 19 0.76
19 5 0.20
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (18 bp):
AAAAAAAAAAAAATTAAA
Found at i:278 original size:20 final size:20
Alignment explanation
Indices: 226--307 Score: 112
Period size: 21 Copynumber: 4.0 Consensus size: 20
216 AAAAAAAAAA
226 ATTC-CAAATGTATCGATAC
1 ATTCACAAATGTATCGATAC
***
245 ATTTGTAGAATGTATCGATAC
1 ATTCACA-AATGTATCGATAC
266 ATTCACAAATGTATCGATAC
1 ATTCACAAATGTATCGATAC
286 ATTCTACAAATGTATCGATAC
1 ATTC-ACAAATGTATCGATAC
307 A
1 A
308 GGGTCCCAAC
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
19 3 0.05
20 18 0.33
21 34 0.62
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (20 bp):
ATTCACAAATGTATCGATAC
Found at i:287 original size:41 final size:40
Alignment explanation
Indices: 226--307 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 40
216 AAAAAAAAAA
* *
226 ATTCCAAATGTATCGATACATTTGTA-GAATGTATCGATAC
1 ATTCCAAATGTATCGATACA-TTCTACAAATGTATCGATAC
266 ATTCACAAATGTATCGATACATTCTACAAATGTATCGATAC
1 ATTC-CAAATGTATCGATACATTCTACAAATGTATCGATAC
307 A
1 A
308 GGGTCCCAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 8 0.21
41 30 0.79
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (40 bp):
ATTCCAAATGTATCGATACATTCTACAAATGTATCGATAC
Found at i:367 original size:19 final size:19
Alignment explanation
Indices: 343--410 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
333 AATTCAACAA
343 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
362 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
*
377 --TGTATCAATACATAAGT
1 TTTGTATCGATACATAAGT
*
394 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
411 TTGGCTACTG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
13 10 0.24
15 2 0.05
17 2 0.05
19 27 0.66
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:388 original size:32 final size:32
Alignment explanation
Indices: 345--407 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
335 TTCAACAATT
* *
345 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCAATACATAAGTATTGTATCGATACAA
377 TGTATCAATACATAAGTATTGTATCGATACA
1 TGTATCAATACATAAGTATTGTATCGATACA
408 TAATTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (32 bp):
TGTATCAATACATAAGTATTGTATCGATACAA
Found at i:442 original size:85 final size:85
Alignment explanation
Indices: 345--560 Score: 371
Period size: 85 Copynumber: 2.5 Consensus size: 85
335 TTCAACAATT
345 TGTATCGATACATAAGTTTTGTATCGATACAATGTATCAATACATAAGTATTGTATCGATACATA
1 TGTATCGATACATAAGTTTTGTATCGATACAATGTATCAATACATAAGTATTGTATCGATACATA
410 ATTGGCTACTGCCAAGGAAA
66 ATTGGCTACTGCCAAGGAAA
430 TGTATCGATACATAAGTTTTGTATCGATACAATGTATCAATACATAAGTATTGTATCGATACATA
1 TGTATCGATACATAAGTTTTGTATCGATACAATGTATCAATACATAAGTATTGTATCGATACATA
495 ATTGGCTACTGCCAAGGAAA
66 ATTGGCTACTGCCAAGGAAA
** * *
515 TGTATCGATACAT-TTTTCTGTGTATCGATACATTGTATCGATACAT
1 TGTATCGATACATAAGTT-T-TGTATCGATACAATGTATCAATACAT
561 GGATCTTTGT
Statistics
Matches: 125, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
84 2 0.02
85 99 0.79
86 24 0.19
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (85 bp):
TGTATCGATACATAAGTTTTGTATCGATACAATGTATCAATACATAAGTATTGTATCGATACATA
ATTGGCTACTGCCAAGGAAA
Found at i:454 original size:19 final size:18
Alignment explanation
Indices: 430--495 Score: 70
Period size: 19 Copynumber: 3.8 Consensus size: 18
420 GCCAAGGAAA
430 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
449 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
*
462 TGTATCAATACATAAGTAT
1 TGTATCGATACATAAGT-T
481 TGTATCGATACATAA
1 TGTATCGATACATAA
496 TTGGCTACTG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
13 10 0.26
15 2 0.05
17 2 0.05
19 25 0.64
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:473 original size:32 final size:32
Alignment explanation
Indices: 428--492 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
418 CTGCCAAGGA
* *
428 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCAATACATAAGTATTGTATCGATAC
460 AATGTATCAATACATAAGTATTGTATCGATAC
1 AATGTATCAATACATAAGTATTGTATCGATAC
492 A
1 A
493 TAATTGGCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (32 bp):
AATGTATCAATACATAAGTATTGTATCGATAC
Found at i:553 original size:13 final size:13
Alignment explanation
Indices: 535--560 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
525 CATTTTTCTG
535 TGTATCGATACAT
1 TGTATCGATACAT
548 TGTATCGATACAT
1 TGTATCGATACAT
561 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:557 original size:33 final size:33
Alignment explanation
Indices: 515--581 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
505 GCCAAGGAAA
***
515 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
548 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
581 T
1 T
582 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Done.