Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3481
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: 51441
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5284 original size:13 final size:13
Alignment explanation
Indices: 5266--5290 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5256 AAACAAACCC
5266 AAAAACCCAAATT
1 AAAAACCCAAATT
5279 AAAAACCCAAAT
1 AAAAACCCAAAT
5291 CGAGAGCCCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.24, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAACCCAAATT
Found at i:15609 original size:17 final size:17
Alignment explanation
Indices: 15578--15611 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
15568 CATGGTAAAT
* *
15578 AATAAAAAGTCAACAAA
1 AATAAAAAATAAACAAA
15595 AATAAAAAATAAACAAA
1 AATAAAAAATAAACAAA
15612 CAAGAATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.09, G:0.03, T:0.12
Consensus pattern (17 bp):
AATAAAAAATAAACAAA
Found at i:16101 original size:14 final size:14
Alignment explanation
Indices: 16064--16097 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
16054 GCACATATAT
16064 ATATGAATAATAATA
1 ATAT-AATAATAATA
16079 ATATAATAATAATA
1 ATATAATAATAATA
16093 A-ATAA
1 ATATAA
16098 ATAAATGAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.21
14 11 0.58
15 4 0.21
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (14 bp):
ATATAATAATAATA
Found at i:19038 original size:22 final size:22
Alignment explanation
Indices: 19010--19054 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
19000 ATTCTACTTT
19010 TGTTGAGTAAAATAATAAGAAA
1 TGTTGAGTAAAATAATAAGAAA
19032 TGTTGAGTAAAATAATAAGAAA
1 TGTTGAGTAAAATAATAAGAAA
19054 T
1 T
19055 TCAATATCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (22 bp):
TGTTGAGTAAAATAATAAGAAA
Found at i:19381 original size:33 final size:33
Alignment explanation
Indices: 19339--19405 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
19329 TAAGTGATAC
19339 TAAGCTTGAAATCTTACCTTGCGTGTAGGGGGA
1 TAAGCTTGAAATCTTACCTTGCGTGTAGGGGGA
*
19372 TAAGCTTGAAATCTTACCTTGCTTGTAGGGGGA
1 TAAGCTTGAAATCTTACCTTGCGTGTAGGGGGA
19405 T
1 T
19406 GCAAGTTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (33 bp):
TAAGCTTGAAATCTTACCTTGCGTGTAGGGGGA
Found at i:20071 original size:22 final size:24
Alignment explanation
Indices: 20040--20095 Score: 80
Period size: 22 Copynumber: 2.4 Consensus size: 24
20030 ATATCTAATA
* *
20040 ATTTAAATATAAATTTTTATTT-T
1 ATTTATATATAAATATTTATTTAT
20063 ATTT-TATATAAATATTTATTTAT
1 ATTTATATATAAATATTTATTTAT
20086 ATTTATATAT
1 ATTTATATAT
20096 TTGTTTACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 15 0.52
23 9 0.31
24 5 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
ATTTATATATAAATATTTATTTAT
Found at i:20095 original size:18 final size:18
Alignment explanation
Indices: 20060--20102 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
20050 AAATTTTTAT
20060 TTTATTT-TATATAAATA
1 TTTATTTATATATAAATA
* *
20077 TTTATTTATATTTATATA
1 TTTATTTATATATAAATA
*
20095 TTTGTTTA
1 TTTATTTA
20103 CTAACATGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTATTTATATATAAATA
Found at i:22307 original size:22 final size:23
Alignment explanation
Indices: 22282--22341 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
22272 TGGACTGAAT
22282 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
22304 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
22326 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
22342 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:22309 original size:4 final size:4
Alignment explanation
Indices: 22291--22324 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
22281 TATAAAAATT
22291 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
22325 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:23727 original size:23 final size:22
Alignment explanation
Indices: 23676--23727 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
23666 CCTCGTCTTT
*
23676 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
23698 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
23721 TTCTTTT
1 TTCTTTT
23728 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:26122 original size:22 final size:23
Alignment explanation
Indices: 26097--26156 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
26087 TGGACTGAAT
26097 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
26119 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
26141 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
26157 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:26124 original size:4 final size:4
Alignment explanation
Indices: 26106--26139 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
26096 TATAAAAATT
26106 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
26140 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:29937 original size:13 final size:13
Alignment explanation
Indices: 29919--29961 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
29909 AAAAGAAAAT
29919 TGTTGTGTTTTGC
1 TGTTGTGTTTTGC
29932 TG-T-TGTTTTGC
1 TGTTGTGTTTTGC
* *
29943 CGTTGTGTTTTGT
1 TGTTGTGTTTTGC
29956 TGTTGT
1 TGTTGT
29962 TTTGTTATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 9 0.36
12 2 0.08
13 14 0.56
ACGTcount: A:0.00, C:0.07, G:0.30, T:0.63
Consensus pattern (13 bp):
TGTTGTGTTTTGC
Found at i:29947 original size:24 final size:24
Alignment explanation
Indices: 29920--29965 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
29910 AAAGAAAATT
29920 GTTGTGTTTTGCTGTTGTTTTGCC
1 GTTGTGTTTTGCTGTTGTTTTGCC
*
29944 GTTGTGTTTTGTTGTTGTTTTG
1 GTTGTGTTTTGCTGTTGTTTTG
29966 TTATCATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.00, C:0.07, G:0.30, T:0.63
Consensus pattern (24 bp):
GTTGTGTTTTGCTGTTGTTTTGCC
Found at i:32956 original size:100 final size:100
Alignment explanation
Indices: 32778--32962 Score: 275
Period size: 100 Copynumber: 1.9 Consensus size: 100
32768 TCCTTCTCAG
* *
32778 ACAAATTTTATTAAATTATATCTATTTTAAAACTTAATAAAACAAAAGTAATCAAGAACTAAAAA
1 ACAAATTTTATTAAACTATATCTATTTTAAAACTTAATAAAACAAAAGTAATCAAAAACTAAAAA
32843 AATAAATTAGAAAATATACTTTAATCAAATTTCAA
66 AATAAATTAGAAAATATACTTTAATCAAATTTCAA
* * *
32878 ACAAATTTTGTTAAACTATATCTATTTTAAAACTTAATAAAACAAAAGGT-ATTAAAATACT-AC
1 ACAAATTTTATTAAACTATATCTATTTTAAAACTTAATAAAACAAAA-GTAATCAAAA-ACTAAA
* *
32941 AAATTAAATTGGAAAATATACT
64 AAAATAAATTAGAAAATATACT
32963 CTCTCTTTTT
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
100 71 0.93
101 5 0.07
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (100 bp):
ACAAATTTTATTAAACTATATCTATTTTAAAACTTAATAAAACAAAAGTAATCAAAAACTAAAAA
AATAAATTAGAAAATATACTTTAATCAAATTTCAA
Found at i:40121 original size:27 final size:27
Alignment explanation
Indices: 40083--40165 Score: 94
Period size: 27 Copynumber: 3.1 Consensus size: 27
40073 ATACATACAT
*
40083 GTTGCGCCTATCTGACAGGCGCAACTA
1 GTTGAGCCTATCTGACAGGCGCAACTA
* *
40110 GTTGAGCCTATCTGACAGGCACGACTA
1 GTTGAGCCTATCTGACAGGCGCAACTA
* * * **
40137 GTTGTGCCTTTTTGGTAGGCGCAACTA
1 GTTGAGCCTATCTGACAGGCGCAACTA
40164 GT
1 GT
40166 GGGGCCCACA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.28
Consensus pattern (27 bp):
GTTGAGCCTATCTGACAGGCGCAACTA
Found at i:44455 original size:10 final size:10
Alignment explanation
Indices: 44434--44476 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
44424 AAAATTTATA
44434 TTTTTATATTT
1 TTTTTAT-TTT
44445 TTTTTATTTT
1 TTTTTATTTT
*
44455 TTTGTATTTT
1 TTTTTATTTT
* *
44465 CTTTTATGTT
1 TTTTTATTTT
44475 TT
1 TT
44477 AATATATGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
10 20 0.74
11 7 0.26
ACGTcount: A:0.12, C:0.02, G:0.05, T:0.81
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:44456 original size:19 final size:20
Alignment explanation
Indices: 44428--44481 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
44418 AAGGTAAAAA
44428 TTTATATTTTTATATTTT-T
1 TTTATATTTTTATATTTTCT
* *
44447 TTTATTTTTTTGTATTTTCT
1 TTTATATTTTTATATTTTCT
* *
44467 TTTATGTTTTAATAT
1 TTTATATTTTTATAT
44482 ATGTATAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.19, C:0.02, G:0.04, T:0.76
Consensus pattern (20 bp):
TTTATATTTTTATATTTTCT
Found at i:45819 original size:72 final size:72
Alignment explanation
Indices: 45584--45835 Score: 389
Period size: 73 Copynumber: 3.5 Consensus size: 72
45574 ACATGTGAAC
* * *
45584 TGAGGCTCAACTCACTTT-TCGTAATATGAGTTGATTTTTTGACAACAGAAATTGAAATTACCTC
1 TGAGGCTCAACTCA-TTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTC
* *
45648 AGCGTGTCC
64 AACGTGTCT
* *
45657 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAAATACCTTA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA-CAGAAATTGAAATTACCTCA
45722 ACGTGTCT
65 ACGTGTCT
45730 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAA
*
45795 TGTGTCT
66 CGTGTCT
*
45802 TGAAGCTCAACTCATTTCTCGCAATATGAGTTGA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
45836 TTCTTTCAAA
Statistics
Matches: 166, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
72 69 0.42
73 97 0.58
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (72 bp):
TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAA
CGTGTCT
Found at i:45917 original size:88 final size:87
Alignment explanation
Indices: 45768--46014 Score: 273
Period size: 88 Copynumber: 2.8 Consensus size: 87
45758 AGTTGAATTT
* ** * * **
45768 TGAAAACAGAAATTGAAATTACCTCAATGTGTCTTGAAGCTCAACTCATTTCTCGCAATATGAGT
1 TGAAAACAGAAATTGAAAATACCTCGGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
45833 TGA-TTCTTTCAAAAACATAATAA
66 TGATTTCTTTCAAAAACA-AA-AA
* *
45856 TGAAAACAGAAATGGAAAATACCTCGGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 TGAAAACAGAAATTGAAAATACCTCGGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
* * *
45921 TGATTTTTTTTGAAAAACAGAAA
66 TGA-TTTCTTTCAAAAACAAAAA
* ** *
45944 TCAAAAGGC-TTAATTGAAAATACCTCGGCGTGTGTCCTGAGGCTCAACTTACCTCTCGCAATAT
1 TGAAAA--CAGAAATTGAAAATACCTC-G-GTGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
46008 GAGTTGA
62 GAGTTGA
46015 AATTAAAACA
Statistics
Matches: 135, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
88 66 0.49
89 15 0.11
90 14 0.10
91 40 0.30
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (87 bp):
TGAAAACAGAAATTGAAAATACCTCGGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTCTTTCAAAAACAAAAA
Found at i:46345 original size:76 final size:74
Alignment explanation
Indices: 46236--46573 Score: 403
Period size: 76 Copynumber: 4.5 Consensus size: 74
46226 AGTGTGTAAT
* *
46236 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAACAGAATTTGAAAATACCT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAACAGAAATTGAAAATACCT
*
46301 CAGCATGTGAAC
66 CAGC--GTG-TC
* *
46313 C-GAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTGAAAACAGAAATTGAAAATACC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTAAAAACAGAAATTGAAAATACC
**
46377 TCAATGTGTC
65 TCAGCGTGTC
* ** * * * * *
46387 TTGAGGCTCAACTCATTTCTCGCAATATAAGTTGA--ATTTTGAAAACAAAAATTGAAATTACCT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAACAGAAATTGAAAATACCT
46450 CAGCGTGTC
66 CAGCGTGTC
** * * *
46459 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTAACAACAGAACTTGAAATTAC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTAAAAACAGAAATTGAAAATAC
*
46524 ATCAGCGTGTC
64 CTCAGCGTGTC
*
46535 CTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
46574 GAAAAACAAA
Statistics
Matches: 229, Mismatches: 26, Indels: 15
0.85 0.10 0.06
Matches are distributed among these distances:
72 65 0.28
74 5 0.02
75 34 0.15
76 94 0.41
77 31 0.14
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (74 bp):
CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAACAGAAATTGAAAATACCT
CAGCGTGTC
Found at i:46738 original size:70 final size:70
Alignment explanation
Indices: 46591--46765 Score: 212
Period size: 70 Copynumber: 2.5 Consensus size: 70
46581 AAAAATTAAA
* * * * * **
46591 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCGGCGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAAATACCTCAACGTG
46655 CCCCG
66 CCCCG
*
46660 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAA-AAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT-AAAACAAAAACTAAAAATACCTCAACGT
* **
46724 GTCTTG
65 GCCCCG
46730 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTTT
46766 CCTTGGAAAG
Statistics
Matches: 92, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
69 27 0.29
70 61 0.66
71 4 0.04
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.29
Consensus pattern (70 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAAATACCTCAACGTG
CCCCG
Done.