Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3338
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: 47620
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5591 original size:80 final size:80
Alignment explanation
Indices: 5480--5660 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
5470 CTCATTCAAT
* * *
5480 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
5543 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
5559 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
5623 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
5640 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
5661 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:5620 original size:40 final size:40
Alignment explanation
Indices: 5477--5660 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
5467 TAACTCATTC
* *
5477 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
5517 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
5557 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
5597 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
5638 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
5661 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:13355 original size:39 final size:40
Alignment explanation
Indices: 13278--13384 Score: 119
Period size: 40 Copynumber: 2.7 Consensus size: 40
13268 TAGCTCCTCG
* * *
13278 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATATTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATATAAACTCA
* *
13318 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATATAAACTCA
**
13357 CACGAATGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
13385 ATTAGTATCT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 25 0.43
40 33 0.57
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATATAAACTCA
Found at i:13383 original size:79 final size:80
Alignment explanation
Indices: 13284--13504 Score: 193
Period size: 80 Copynumber: 2.8 Consensus size: 80
13274 CTCGTTCAAG
* * * ** * *
13284 TGCCTTCGGGACATAGCCCGG-TTATATTAACTCATTC-AATGCCTTCGGGACTTAACCCGGATT
1 TGCCTTCGGGACATAACCCGGAAT-TAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGA-A
*
13347 TTAA-AACTCGCACGAA
64 TTAATAACTCGCACAAA
* * *
13363 TGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAGGCCTTCGGGACTTAACCCGGAATT
1 TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATT
13428 AATAACTCGCACAAA
66 AATAACTCGCACAAA
* * ** * * *
13443 TACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGA-CATAACCCGGAAT-TAGTAACTCA-CACAAAGGCCTTCGGGACTTAACCCGGA
13505 CAGCATTCAA
Statistics
Matches: 117, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
79 36 0.31
80 75 0.64
81 6 0.05
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (80 bp):
TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATT
AATAACTCGCACAAA
Found at i:13435 original size:80 final size:80
Alignment explanation
Indices: 13324--13504 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
13314 CTCATTCAAT
* * *
13324 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
13387 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
13403 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
13467 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
13484 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
13505 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:13464 original size:40 final size:40
Alignment explanation
Indices: 13321--13504 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
13311 TAACTCATTC
* *
13321 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
13361 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
13401 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
13441 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
13482 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
13505 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:28909 original size:24 final size:24
Alignment explanation
Indices: 28855--28982 Score: 106
Period size: 24 Copynumber: 5.4 Consensus size: 24
28845 AGTCATGGTT
*
28855 GGTAAGCTCCACTTGAGCTGATAAAC
1 GGTAAGCTCTA-TTGAGCTGA-AAAC
* *
28881 AGTAAGCTCTATTAAGCTGAAAAC
1 GGTAAGCTCTATTGAGCTGAAAAC
28905 GGTAAGCTCTATTGAGCTGAACAA-
1 GGTAAGCTCTATTGAGCTGAA-AAC
* *
28929 --TAAGCTCTTTTGAGCTGAATTA-
1 GGTAAGCTCTATTGAGCTGAA-AAC
* *
28951 -GTAAGCTCCAATGAGCTG-AAAC
1 GGTAAGCTCTATTGAGCTGAAAAC
*
28973 AGTAAGCTCT
1 GGTAAGCTCT
28983 TACGAGCTCT
Statistics
Matches: 85, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
21 1 0.01
22 20 0.24
23 22 0.26
24 23 0.27
25 10 0.12
26 9 0.11
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.27
Consensus pattern (24 bp):
GGTAAGCTCTATTGAGCTGAAAAC
Found at i:28945 original size:46 final size:47
Alignment explanation
Indices: 28855--28983 Score: 147
Period size: 46 Copynumber: 2.7 Consensus size: 47
28845 AGTCATGGTT
*
28855 GGTAAGCTCCACTTGAGCTGATAAACAGTAAGCTCTATTAAGCTGAA-AA
1 GGTAAGCTCCA-TTGAGCTG--AAACAGTAAGCTCTTTTAAGCTGAATAA
* * * *
28904 CGGTAAGCTCTATTGAGCTG-AACAATAAGCTCTTTTGAGCTGAATTA
1 -GGTAAGCTCCATTGAGCTGAAACAGTAAGCTCTTTTAAGCTGAATAA
*
28951 -GTAAGCTCCAATGAGCTGAAACAGTAAGCTCTT
1 GGTAAGCTCCATTGAGCTGAAACAGTAAGCTCTT
28984 ACGAGCTCTG
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
45 16 0.23
46 34 0.49
47 1 0.01
49 8 0.12
50 10 0.14
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (47 bp):
GGTAAGCTCCATTGAGCTGAAACAGTAAGCTCTTTTAAGCTGAATAA
Found at i:28989 original size:23 final size:23
Alignment explanation
Indices: 28868--28990 Score: 99
Period size: 23 Copynumber: 5.3 Consensus size: 23
28858 AAGCTCCACT
28868 TGAGCTGATAAACAGTAAGCTC-TA
1 TGAGCTG--AAACAGTAAGCTCTTA
* *
28892 TTAAGCTGAAAACGGTAAGCTC-TA
1 -TGAGCTG-AAACAGTAAGCTCTTA
* *
28916 TTGAGCTG-AACAATAAGCTCTTT
1 -TGAGCTGAAACAGTAAGCTCTTA
** **
28939 TGAGCTGAATTAGTAAGCTCCAA
1 TGAGCTGAAACAGTAAGCTCTTA
28962 TGAGCTGAAACAGTAAGCTCTTA
1 TGAGCTGAAACAGTAAGCTCTTA
*
28985 CGAGCT
1 TGAGCT
28991 CTGGTGAGTC
Statistics
Matches: 78, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
22 17 0.22
23 34 0.44
24 21 0.27
25 6 0.08
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (23 bp):
TGAGCTGAAACAGTAAGCTCTTA
Found at i:35228 original size:19 final size:19
Alignment explanation
Indices: 35204--35242 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
35194 GAATAAATTG
35204 ATAAACATATAAAAATTTC
1 ATAAACATATAAAAATTTC
* *
35223 ATAAACTTATAGAAATTTC
1 ATAAACATATAAAAATTTC
35242 A
1 A
35243 ACATTTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (19 bp):
ATAAACATATAAAAATTTC
Found at i:36603 original size:24 final size:25
Alignment explanation
Indices: 36561--36619 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
36551 TATGCTCCTC
*
36561 TTGAGCTGATAAACAGTAAGCTCTA
1 TTGAGCTGAAAAACAGTAAGCTCTA
* *
36586 TTGAGCT-AAAAACGGTAAGCTTTA
1 TTGAGCTGAAAAACAGTAAGCTCTA
*
36610 CTGAGCTGAA
1 TTGAGCTGAA
36620 TAATAAGAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 20 0.69
25 9 0.31
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (25 bp):
TTGAGCTGAAAAACAGTAAGCTCTA
Found at i:36652 original size:23 final size:23
Alignment explanation
Indices: 36626--36677 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
36616 TGAATAATAA
**
36626 GAGCTGAATTAGTAAGCTCCAAT
1 GAGCTGAAACAGTAAGCTCCAAT
* **
36649 GAGCTAAAACAGTAAGCTCTTAT
1 GAGCTGAAACAGTAAGCTCCAAT
36672 GAGCTG
1 GAGCTG
36678 TGGTGAGTCC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (23 bp):
GAGCTGAAACAGTAAGCTCCAAT
Found at i:39558 original size:30 final size:30
Alignment explanation
Indices: 39524--39584 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
39514 TTCCCGAGCC
39524 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * * *
39554 TAGGGGCAAAATTGTAATTTTTCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
39584 T
1 T
39585 GAGTTAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:44803 original size:63 final size:63
Alignment explanation
Indices: 44705--44906 Score: 194
Period size: 65 Copynumber: 3.1 Consensus size: 63
44695 CATCATGTGT
* * *
44705 ACAAGAGAGCTACAAGACAATGATTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG
1 ACAAGAGAGCTACGAGATAA--ATTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAG
* * * * * * *
44770 ACAAGA-AGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGTGAAGGACACCATGTA
1 ACAAGAGAGCTACGAGATAAAT-TAGCTAGGTCGCATGGGTGGTACTA-TG-TGTACACCATGTA
44834 G
63 G
* * * *
44835 ACAAGAGAGCTACGAGATAAATTGGCTAGGTCACACGGGTGGTACTGA-GTGTTCACCATGT-G
1 ACAAGAGAGCTACGAGATAAATTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG
44897 TACAAGAGAG
1 -ACAAGAGAG
44907 TCGAACTATA
Statistics
Matches: 110, Mismatches: 21, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
62 3 0.03
63 39 0.35
64 12 0.11
65 42 0.38
66 14 0.13
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (63 bp):
ACAAGAGAGCTACGAGATAAATTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAG
Done.