Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3389
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: 36995
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:3924 original size:19 final size:20
Alignment explanation
Indices: 3900--3937 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
3890 GGTACCACCA
3900 AAACAT-ATATCAT-ATCTTT
1 AAACATCAT-TCATCATCTTT
3919 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
3938 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:4744 original size:30 final size:30
Alignment explanation
Indices: 4710--4769 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
4700 ATTTAATACG
*
4710 AACTTTAAAAAAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGACCCTA
*** *
4740 AACTTTTGCATAATTACACTTTTGACCCTA
1 AACTTTAAAAAAATTACACTTTTGACCCTA
4770 GGCTCGGGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.37
Consensus pattern (30 bp):
AACTTTAAAAAAATTACACTTTTGACCCTA
Found at i:23206 original size:33 final size:34
Alignment explanation
Indices: 23159--23256 Score: 94
Period size: 33 Copynumber: 2.9 Consensus size: 34
23149 ATTGCATTAC
* * * * *
23159 ACTG-TTACTATATAGGGCTAATGCCTAGATTGT
1 ACTGATTACTGTATAGGGCCAAGGCCCAGACTGT
23192 ACT-ATTACTGTATAGGGCCAAGGCCCAGACTGT
1 ACTGATTACTGTATAGGGCCAAGGCCCAGACTGT
* * *
23225 ATTGATTACTGAATAGGGTTC-AGGCCCAGACT
1 ACTGATTACTGTATAGGG-CCAAGGCCCAGACT
23257 CTTACTGCAT
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
33 29 0.54
34 24 0.44
35 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (34 bp):
ACTGATTACTGTATAGGGCCAAGGCCCAGACTGT
Found at i:28102 original size:39 final size:39
Alignment explanation
Indices: 28028--28204 Score: 241
Period size: 39 Copynumber: 4.5 Consensus size: 39
28018 GCTACTCGTT
*
28028 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGGATT-TAGTAACTCGCA
*
28068 CAAATGCCTTCGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
28107 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
* *
28146 CAAATGCCTTCGGATCTTAGTCCGGA-TTAGTATCTCGCA
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGTAACTCGCA
28185 CAAATGCCTTCGGATCTTAG
1 CAAATGCCTTCGGA-CTTAG
28205 TCATATGGTC
Statistics
Matches: 127, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
39 104 0.82
40 23 0.18
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (39 bp):
CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:28148 original size:78 final size:79
Alignment explanation
Indices: 27995--28197 Score: 247
Period size: 78 Copynumber: 2.6 Consensus size: 79
27985 AAATCACGTA
** *
27995 CCTTCGGAAT-TTAA-CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGCCCGGTTAT
1 CCTTCGG-ATCTTAACCCGGAT-TAG-TAACTCGCACAAATGCCTTCGGGACATAGCCCGGATAT
28057 AGTAACTCGCACAAATG
63 AGTAACTCGCACAAATG
*
28074 CCTTCGGA-CTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGGA-ATTA
1 CCTTCGGATCTTAACCCGGA-TTAGTAACTCGCACAAATGCCTTCGGGACATAGCCCGGATA-TA
*
28136 GTATCTCGCACAAATG
64 GTAACTCGCACAAATG
** *
28152 CCTTCGGATCTTAGTCCGGATTAGTATCTCGCACAAATGCCTTCGG
1 CCTTCGGATCTTAACCCGGATTAGTAACTCGCACAAATGCCTTCGG
28198 ATCTTAGTCA
Statistics
Matches: 110, Mismatches: 8, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
77 1 0.01
78 65 0.59
79 43 0.39
80 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (79 bp):
CCTTCGGATCTTAACCCGGATTAGTAACTCGCACAAATGCCTTCGGGACATAGCCCGGATATAGT
AACTCGCACAAATG
Found at i:31527 original size:39 final size:40
Alignment explanation
Indices: 31450--31596 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
31440 TAGCTCCTCG
* * *
31450 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
31490 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
31529 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
31569 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
31597 ATTAATAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:31607 original size:80 final size:80
Alignment explanation
Indices: 31496--31676 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
31486 CTCATTCAAT
* * *
31496 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
31559 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
31575 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
31639 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
31656 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
31677 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:31636 original size:40 final size:40
Alignment explanation
Indices: 31493--31676 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
31483 TAACTCATTC
* *
31493 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
31533 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
31573 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
31613 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
31654 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
31677 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
Done.