Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1499
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: 23693
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:1438 original size:28 final size:28
Alignment explanation
Indices: 1381--1444 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
1371 AATGTCACTC
* *
1381 TTTGTA-TTTGTCAAATTAGTAGTTTCT
1 TTTGTATTTTGTCAAATTAGTAGGTTAT
*
1408 TTTGTATTTTGTCAAATATGGT-GGTTAT
1 TTTGTATTTTGTCAAAT-TAGTAGGTTAT
*
1436 TTTTTATTT
1 TTTGTATTT
1445 GTAAACAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 6 0.19
28 22 0.71
29 3 0.10
ACGTcount: A:0.20, C:0.05, G:0.16, T:0.59
Consensus pattern (28 bp):
TTTGTATTTTGTCAAATTAGTAGGTTAT
Found at i:5556 original size:27 final size:28
Alignment explanation
Indices: 5491--5568 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 28
5481 AATTCCATCC
5491 TTTGTATTTGTCAAATATGGTGGTTTCT
1 TTTGTATTTGTCAAATATGGTGGTTTCT
5519 TTTGTATTTGTCAAATATGGTGGTTAT-T
1 TTTGTATTTGTCAAATATGGTGGTT-TCT
* * *
5547 TTT-TGTTTGTAAAAAATGGTGG
1 TTTGTATTTGTCAAATATGGTGG
5569 CTTGTTGTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 16 0.35
28 29 0.63
29 1 0.02
ACGTcount: A:0.22, C:0.04, G:0.23, T:0.51
Consensus pattern (28 bp):
TTTGTATTTGTCAAATATGGTGGTTTCT
Found at i:5576 original size:24 final size:24
Alignment explanation
Indices: 5549--5594 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
5539 TGGTTATTTT
5549 TTGTTTGTAAAAAATGGTGGCTTG
1 TTGTTTGTAAAAAATGGTGGCTTG
* *
5573 TTGTTTGTCAAAATTGGTGGCT
1 TTGTTTGTAAAAAATGGTGGCT
5595 AATTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.22, C:0.07, G:0.28, T:0.43
Consensus pattern (24 bp):
TTGTTTGTAAAAAATGGTGGCTTG
Found at i:6318 original size:35 final size:33
Alignment explanation
Indices: 6260--6340 Score: 92
Period size: 35 Copynumber: 2.4 Consensus size: 33
6250 ATGTAAACAT
* **
6260 TAAAAAATATATTAAATATTTATATTTTAAATCA
1 TAAAAAAAATATTAAATATTTATAAATTAAAT-A
6294 TAATAAAAAATATTAAAT-TATTATAAATTAAATA
1 TAA-AAAAAATATTAAATAT-TTATAAATTAAATA
*
6328 TAAAAAATATATT
1 TAAAAAAAATATT
6341 TTTTAAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
33 9 0.22
34 8 0.20
35 24 0.59
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (33 bp):
TAAAAAAAATATTAAATATTTATAAATTAAATA
Found at i:6460 original size:16 final size:15
Alignment explanation
Indices: 6439--6470 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
6429 ATTATAATTA
6439 AATCTAACTTAAACTT
1 AATCTAACTT-AACTT
6455 AATCTAACTTAACTT
1 AATCTAACTTAACTT
6470 A
1 A
6471 TAAACATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (15 bp):
AATCTAACTTAACTT
Found at i:7935 original size:23 final size:23
Alignment explanation
Indices: 7905--7953 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
7895 TGACCATGCA
7905 TTTTTTATTATGTTTCATGCATT
1 TTTTTTATTATGTTTCATGCATT
7928 TTTTTTATTATGTTTCATGCATT
1 TTTTTTATTATGTTTCATGCATT
7951 TTT
1 TTT
7954 AACATGTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.67
Consensus pattern (23 bp):
TTTTTTATTATGTTTCATGCATT
Found at i:7960 original size:20 final size:21
Alignment explanation
Indices: 7899--7953 Score: 92
Period size: 23 Copynumber: 2.5 Consensus size: 21
7889 AGCCTTTGAC
7899 CATGCATTTTTTATTATGTTT
1 CATGCATTTTTTATTATGTTT
7920 CATGCATTTTTTTTATTATGTTT
1 CATGCA--TTTTTTATTATGTTT
7943 CATGCATTTTT
1 CATGCATTTTT
7954 AACATGTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
21 11 0.34
23 21 0.66
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (21 bp):
CATGCATTTTTTATTATGTTT
Found at i:13869 original size:1 final size:1
Alignment explanation
Indices: 13863--13887 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
13853 CCTCTCTTTT
13863 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
13888 TCCTTTGCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:14434 original size:13 final size:12
Alignment explanation
Indices: 14412--14443 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
14402 ACCCAATCCT
14412 AAAAAAAAACAA
1 AAAAAAAAACAA
14424 AAAACAAAAACAA
1 AAAA-AAAAACAA
14437 AAAAAAA
1 AAAAAAA
14444 CCTTTCACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAACAA
Found at i:15527 original size:27 final size:27
Alignment explanation
Indices: 15496--16236 Score: 1081
Period size: 27 Copynumber: 27.0 Consensus size: 27
15486 GTGACATTTT
* *
15496 CTTTTAAAGTCCACAACTCTGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* * *
15524 TTTTTAAGTCCATAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
15551 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
15579 CTTTTTAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
15606 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
15633 CTTTTAAGTCCACAACTTCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
15660 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
15687 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
15715 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
15743 CTTTTAAGTCCACAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
15771 CTTTTAAGTCTACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
15798 CTTTTAAGTCCACAACTCCGTGGCAACC
1 CTTTTAAGTCCACAACTCCGTGGC-ACC
** *
15826 CTTTTAAGTCCACAACTTTGTGGCATGC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
15854 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* **
15881 CTTTTAAGTCCACAACTCTGTGGCATT
1 CTTTTAAGTCCACAACTCCGTGGCACC
15908 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
15935 TTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
15962 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
15989 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* * * *
16017 CTTTTAAGACTACAACTCTGTAGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
16044 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
16071 CTTTTAAGTCCA-TACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
16098 ATTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
16125 CTTTTAAAGTCCACAAACTCCGTGGCACC
1 CTTTT-AAGTCCAC-AACTCCGTGGCACC
*
16154 CTTTTAAGTCCACAACTTCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
16181 CTTTTAAGTCCACAACT-CATGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
16207 CTTTTAAATCACACAACTCTTGTGGCACC
1 CTTTTAAGTC-CACAACTC-CGTGGCACC
16236 C
1 C
16237 ATTCCAAAGC
Statistics
Matches: 648, Mismatches: 53, Indels: 23
0.90 0.07 0.03
Matches are distributed among these distances:
26 27 0.04
27 389 0.60
28 207 0.32
29 25 0.04
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:16252 original size:32 final size:32
Alignment explanation
Indices: 16228--16728 Score: 819
Period size: 32 Copynumber: 15.7 Consensus size: 32
16218 CACAACTCTT
16228 GTGGC-ACCCATTCCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
*
16259 GTGGCAACCTATTCCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
*
16291 GTGGCAACCCATTTCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
16323 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
16355 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
16387 GT-GCAACCCATTCCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
*
16418 GTGGCAACCCATTTCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
* * *
16450 GTGGCAACCTATTTCAAAGCCCACACAAGTCC
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
16482 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
16514 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
*
16546 GTGGCAACCCATTTCAAAGCCCACACAAGTCG
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
* *
16578 GTGGCAACCCATTTCAAAGCCCACACAAGTCC
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
*
16610 GTGGCAACCCATTCCAAAGCCCACATAAGTCG
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
* *
16642 GTGGGCAACTCATTTCAAAGCCCACACAAGTCG
1 GT-GGCAACCCATTCCAAAGCCCACACAAGTCG
* * *
16675 GTGGCGACCCTTTTCAAAG-CCACACAAGTCG
1 GTGGCAACCCATTCCAAAGCCCACACAAGTCG
**
16706 GTGGCAACCCATTTAAAAGCCCA
1 GTGGCAACCCATTCCAAAGCCCA
16729 TGTAAATCAG
Statistics
Matches: 442, Mismatches: 24, Indels: 7
0.93 0.05 0.01
Matches are distributed among these distances:
31 64 0.14
32 349 0.79
33 29 0.07
ACGTcount: A:0.31, C:0.35, G:0.19, T:0.15
Consensus pattern (32 bp):
GTGGCAACCCATTCCAAAGCCCACACAAGTCG
Found at i:17328 original size:20 final size:19
Alignment explanation
Indices: 17281--17337 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
17271 TTTTACCTTG
* * *
17281 ATGTATCGATACTTTTTCA
1 ATGTATCGATACATTATGA
*
17300 ATATATCGATACATGTATGA
1 ATGTATCGATACAT-TATGA
17320 ATGTATCGATACATTATG
1 ATGTATCGATACATTATG
17338 TCTTTTTACC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (19 bp):
ATGTATCGATACATTATGA
Found at i:18257 original size:20 final size:20
Alignment explanation
Indices: 18232--18284 Score: 79
Period size: 23 Copynumber: 2.5 Consensus size: 20
18222 AGCCTTTGAC
18232 CATGCATTTTTATTATGTTT
1 CATGCATTTTTATTATGTTT
18252 CATGCATTTTTTTTATTATGTTT
1 CATGCA---TTTTTATTATGTTT
18275 CATGCATTTT
1 CATGCATTTT
18285 AACATGTCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 10 0.33
23 20 0.67
ACGTcount: A:0.19, C:0.11, G:0.09, T:0.60
Consensus pattern (20 bp):
CATGCATTTTTATTATGTTT
Found at i:18268 original size:23 final size:23
Alignment explanation
Indices: 18238--18284 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
18228 TGACCATGCA
18238 TTTTTATTATGTTTCATGCATTT
1 TTTTTATTATGTTTCATGCATTT
18261 TTTTTATTATGTTTCATGCATTT
1 TTTTTATTATGTTTCATGCATTT
18284 T
1 T
18285 AACATGTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.17, C:0.09, G:0.09, T:0.66
Consensus pattern (23 bp):
TTTTTATTATGTTTCATGCATTT
Done.