Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold517
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: 22233
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:8703 original size:4 final size:4
Alignment explanation
Indices: 8694--8756 Score: 108
Period size: 4 Copynumber: 15.8 Consensus size: 4
8684 TTGCGTGCAC
* *
8694 CATA CATA CATA CATA CATG CATA CATA CATA CTTA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
8742 CATA CATA CATA CAT
1 CATA CATA CATA CAT
8757 GTAAAGAACT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.46, C:0.25, G:0.02, T:0.27
Consensus pattern (4 bp):
CATA
Found at i:10931 original size:19 final size:19
Alignment explanation
Indices: 10907--10945 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
10897 ACTTTATAAT
10907 ATAATTTTAA-AATAAAATA
1 ATAA-TTTAAGAATAAAATA
10926 ATAATTTAAGTAATAAAATA
1 ATAATTTAAG-AATAAAATA
10946 TATTTATCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 4 0.22
20 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (19 bp):
ATAATTTAAGAATAAAATA
Found at i:13415 original size:16 final size:15
Alignment explanation
Indices: 13394--13424 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
13384 GATGTGAATA
13394 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
13410 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
13425 GTCAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:13618 original size:25 final size:23
Alignment explanation
Indices: 13590--13652 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 23
13580 CGTGATAATA
13590 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATA--TACATAATATAGTG
13615 TTAAAAATATACATAATATA--G
1 TTAAAAATATACATAATATAGTG
*
13636 TTAAGATATATACATAA
1 TTAA-AAATATACATAA
13653 GATAACATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
21 5 0.14
22 11 0.31
23 11 0.31
25 9 0.25
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.35
Consensus pattern (23 bp):
TTAAAAATATACATAATATAGTG
Found at i:13705 original size:33 final size:33
Alignment explanation
Indices: 13641--13714 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 33
13631 TATAGTTAAG
*
13641 ATATATACATAAGATAACATGTAAAAAATATAT
1 ATATATAAATAAGATAACATGTAAAAAATATAT
* * *
13674 ATATATAAATAATATAATAT-T-AAAGATATAT
1 ATATATAAATAAGATAACATGTAAAAAATATAT
*
13705 ACATA-AAATA
1 ATATATAAATA
13715 GTATAATATA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 5 0.14
31 13 0.36
32 1 0.03
33 17 0.47
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.32
Consensus pattern (33 bp):
ATATATAAATAAGATAACATGTAAAAAATATAT
Found at i:13727 original size:25 final size:26
Alignment explanation
Indices: 13670--13728 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
13660 TGTAAAAAAT
*
13670 ATATATATATAAATAATATAATATTA
1 ATATATATATAAATAAAATAATATTA
* * *
13696 A-AGATATATACATAAAATAGTA-TA
1 ATATATATATAAATAAAATAATATTA
13720 ATATATATA
1 ATATATATA
13729 CGTAATCTAG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
24 3 0.11
25 23 0.85
26 1 0.04
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (26 bp):
ATATATATATAAATAAAATAATATTA
Found at i:13801 original size:23 final size:25
Alignment explanation
Indices: 13758--13803 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
13748 TATACCTAAT
13758 ATATTAAAAGAATATATATAATATA
1 ATATTAAAAGAATATATATAATATA
*
13783 ATATTAAGA-AATATA-ATAATA
1 ATATTAAAAGAATATATATAATA
13804 ACAAAAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATTAAAAGAATATATATAATATA
Found at i:14357 original size:30 final size:30
Alignment explanation
Indices: 14279--14423 Score: 170
Period size: 30 Copynumber: 4.8 Consensus size: 30
14269 TAGGTACAAG
* *
14279 TGGTGGTGGAGCAA-GTGTGGTTAGTGGAGT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
* ** * *
14309 AGGTAATGGAGCAA-GTGTGGCTAGTGGATT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
14339 TGGTGGT-GAAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAA-AAGGTGTGGCTAGTGGAGT
*
14369 TGGTGGTGGAAAAGGTATGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
14399 TGGTGGTGGAAAAGGTGTGGCTAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGT
14424 TGAGAAAAGT
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
29 4 0.04
30 93 0.93
31 3 0.03
ACGTcount: A:0.21, C:0.04, G:0.47, T:0.28
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
Found at i:15284 original size:129 final size:121
Alignment explanation
Indices: 15134--15385 Score: 299
Period size: 122 Copynumber: 2.0 Consensus size: 121
15124 ATGTGAACCC
* * * * *
15134 AAGGCTCAACTCACATCTCGCAATATGAGTTGATTTTTTTTTAACAACAGAAATTGAAATTACCT
1 AAGGCTCAACTCACATCTCGCAATATGAG-TCA-----ATTTAA-AACAGAAACTAAAAATACCT
* *
15199 CAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTTGAAAAACAAAAATTAA
59 CAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTG-AAAA-AAAAATTAA
* * * *
15263 AAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTG
1 AAGGCTCAACTCACATCTCGCAATATGAGTCAATTTAAAACAGAAACTAAAAATACCTCAGCGTG
* *
15328 CCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAAAAAATTAA
66 CCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGAAAAAAAAATTAA
15384 AA
1 AA
15386 ATACCTCAAC
Statistics
Matches: 109, Mismatches: 13, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
121 11 0.10
122 59 0.54
123 10 0.09
128 2 0.02
129 27 0.25
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (121 bp):
AAGGCTCAACTCACATCTCGCAATATGAGTCAATTTAAAACAGAAACTAAAAATACCTCAGCGTG
CCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGAAAAAAAAATTAA
Found at i:15412 original size:71 final size:71
Alignment explanation
Indices: 15264--15439 Score: 207
Period size: 71 Copynumber: 2.5 Consensus size: 71
15254 AAAAATTAAA
* * * * * **
15264 AGGCTTAACTCACCTCTCGCAATATGAG-TCA-ATTTAAAACATAAACTAAAAATACCTCGGCGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACAAAAACTAAAAATACCTCAACGT
15327 GCCCCG
66 GCCCCG
*
15333 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAA-AAAAATTAAAAATACCTCAACG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT-AAAACAAAAACTAAAAATACCTCAACG
* **
15397 TGTCTTG
65 TGCCCCG
15404 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTTT
15440 CCTTGGAAAG
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
69 26 0.28
70 3 0.03
71 59 0.64
72 4 0.04
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.29
Consensus pattern (71 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACAAAAACTAAAAATACCTCAACGT
GCCCCG
Done.