Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1407
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: 35082
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Found at i:5351 original size:40 final size:40
Alignment explanation
Indices: 5252--5414 Score: 188
Period size: 40 Copynumber: 4.1 Consensus size: 40
5242 TGGATGATAA
* * * * **
5252 CCGGGCTAAGTCCCGAAGGCATCTGCGCTAGTGACTAGTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
5292 CCGGGC-AAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
*
5331 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACCCT-AA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA--CTAAAT
* * * *
5371 CCGGGCTATGTCCCGAAGGCATTTGAGCGAGTTGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
5411 CCGG
1 CCGG
5415 TTAAATTCCG
Statistics
Matches: 106, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.02
39 34 0.32
40 66 0.62
41 2 0.02
42 2 0.02
ACGTcount: A:0.22, C:0.26, G:0.29, T:0.23
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
Found at i:8203 original size:42 final size:41
Alignment explanation
Indices: 8140--8294 Score: 168
Period size: 42 Copynumber: 3.7 Consensus size: 41
8130 CTAAGATTAT
*
8140 GTGTAAGACCATATCTGGGATATGGCATTGATATGAGACTTC
1 GTGTAAGACCATATCTGGGATATGGCATCGATATGAGA-TTC
* *
8182 GTGTAAGACCATATCTTGGATATGGCATCGATGTGAGATTTC
1 GTGTAAGACCATATCTGGGATATGGCATCGATATGAGA-TTC
* * * * *
8224 ATGTAAGACCATGGT-TGGGCTATTGACATCGATATAAGATTC
1 GTGTAAGACCAT-ATCTGGGATA-TGGCATCGATATGAGATTC
* *
8266 GATGTAAAACCATATCTGAGATATGGCAT
1 G-TGTAAGACCATATCTGGGATATGGCAT
8295 TGGTATGGTA
Statistics
Matches: 92, Mismatches: 17, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
42 63 0.68
43 29 0.32
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (41 bp):
GTGTAAGACCATATCTGGGATATGGCATCGATATGAGATTC
Found at i:11617 original size:40 final size:40
Alignment explanation
Indices: 11562--11783 Score: 313
Period size: 40 Copynumber: 5.6 Consensus size: 40
11552 TATTCGAATG
* * *
11562 ATATCTGGGTTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
*
11602 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
*
11642 ATATCCAGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
* * *
11682 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
* * *
11722 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGATT
*
11762 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
11784 TACTTGGGTT
Statistics
Matches: 165, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
39 14 0.08
40 149 0.90
41 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
Found at i:15316 original size:27 final size:27
Alignment explanation
Indices: 15286--15463 Score: 162
Period size: 27 Copynumber: 6.5 Consensus size: 27
15276 AAATTGTACA
15286 GCACTAAGTGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGATTTGACTATGTT
** * *
15313 GCACTAAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCGATTTGACTATGTT
* * **
15340 GCACTAAGTGTGCGAAATTGACCATGCG
1 GCACTAAGTGTGCG-ATTTGACTATGTT
* * *
15368 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGA-TTTGACTATGTT
* * *
15396 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGATTTGACTATGTT
*
15423 GCACTAAGTGTGCGAGTTGA-T-TGTAT
1 GCACTAAGTGTGCGATTTGACTATGT-T
*
15449 AGCACTGAGTGTGCG
1 -GCACTAAGTGTGCG
15464 GGCTCAATAT
Statistics
Matches: 123, Mismatches: 24, Indels: 8
0.79 0.15 0.05
Matches are distributed among these distances:
25 2 0.02
26 1 0.01
27 77 0.63
28 43 0.35
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (27 bp):
GCACTAAGTGTGCGATTTGACTATGTT
Found at i:15400 original size:83 final size:82
Alignment explanation
Indices: 15286--15437 Score: 216
Period size: 83 Copynumber: 1.8 Consensus size: 82
15276 AAATTGTACA
* * * *
15286 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGATCTAACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
15350 TGCGAAATTGACCATGCG
65 TGCGAAATTGACCATGCG
** *
15368 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGA-TCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
15433 TGCGA
65 TGCGA
15438 GTTGATTGTA
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
82 16 0.26
83 45 0.74
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (82 bp):
GCACTAAGTGTGCGATCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAAATTGACCATGCG
Found at i:15426 original size:55 final size:52
Alignment explanation
Indices: 15285--15439 Score: 184
Period size: 55 Copynumber: 2.9 Consensus size: 52
15275 TAAATTGTAC
* *
15285 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG
1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCG-AGTGAATATG
* * * *
15338 ATGCACTAAGTGTGCGAAATTGACCATGCGGCACTAAGTGTGCGAGTCTAACTATG
1 A-GCACTAAGTGTGCG-ATTTGACTATGTGGCACTAAGTGTGCGAGT-GAA-TATG
* *
15394 TAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTGTGCGAGT
1 -AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGT
15440 TGATTGTATA
Statistics
Matches: 86, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
53 1 0.01
54 16 0.19
55 50 0.58
56 18 0.21
57 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (52 bp):
AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTGAATATG
Found at i:23278 original size:27 final size:27
Alignment explanation
Indices: 23247--23420 Score: 176
Period size: 27 Copynumber: 6.6 Consensus size: 27
23237 TAAATTGTAC
*
23247 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
23274 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
23300 ATGCACTAAGTGTGC-AAATGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
23327 GGCACTAAGTGTGCG-AGTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
23353 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
23380 AGCACTAAGTGTGCGAGTTGA-TATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
23406 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
23421 GGCTCAATAT
Statistics
Matches: 123, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
26 61 0.50
27 62 0.50
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:23385 original size:53 final size:52
Alignment explanation
Indices: 23247--23420 Score: 190
Period size: 53 Copynumber: 3.3 Consensus size: 52
23237 TAAATTGTAC
* *
23247 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCG-AGTG-ATATGT
** * **
23300 ATGCACTAAGTGTGC-AAATGACCATGCGGCACTAAGTGTGCGAGTGACTATGT
1 A-GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTGA-TATGT
* * *
23353 AGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGAGTTGATATAT
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAG-TGATATGT
*
23406 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
23421 GGCTCAATAT
Statistics
Matches: 101, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
51 1 0.01
52 20 0.20
53 64 0.63
54 16 0.16
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (52 bp):
AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTGATATGT
Found at i:23416 original size:26 final size:26
Alignment explanation
Indices: 23247--23420 Score: 131
Period size: 26 Copynumber: 6.6 Consensus size: 26
23237 TAAATTGTAC
* *
23247 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGA-TATAT
* **
23274 TGCACTAAGTGTGCGAAATGA-ATAT
1 AGCACTAAGTGTGCGAGTTGATATAT
** * **
23299 GATGCACTAAGTGTGC-AAATGACCATGC
1 -A-GCACTAAGTGTGCGAGTTGA-TATAT
* *
23327 GGCACTAAGTGTGCGAG-TGACTATGT
1 AGCACTAAGTGTGCGAGTTGA-TATAT
*
23353 AGCACTAAGTGTGCGATTTGAT-TACGT
1 AGCACTAAGTGTGCGAGTTGATATA--T
23380 AGCACTAAGTGTGCGAGTTGATATAT
1 AGCACTAAGTGTGCGAGTTGATATAT
*
23406 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
23421 GGCTCAATAT
Statistics
Matches: 122, Mismatches: 16, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
25 4 0.03
26 57 0.47
27 57 0.47
28 4 0.03
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (26 bp):
AGCACTAAGTGTGCGAGTTGATATAT
Found at i:23420 original size:79 final size:80
Alignment explanation
Indices: 23244--23393 Score: 205
Period size: 79 Copynumber: 1.9 Consensus size: 80
23234 GATTAAATTG
* * *
23244 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATGTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
23309 GTGTGCAAATGACCA
66 GTGTGCAAATGACCA
* * ** *
23324 TGCGGCACTAAGTGTGCGA-GTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACTA
1 TACAGCACTAAGTGTGCGATGTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTA
23387 AGTGTGC
65 AGTGTGC
23394 GAGTTGATAT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
78 1 0.02
79 43 0.70
80 17 0.28
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.28
Consensus pattern (80 bp):
TACAGCACTAAGTGTGCGATGTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCAAATGACCA
Done.