Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold606
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: 20949
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.30
Warning! 2432 characters in sequence are not A, C, G, or T
Found at i:1113 original size:47 final size:47
Alignment explanation
Indices: 1061--1162 Score: 159
Period size: 47 Copynumber: 2.1 Consensus size: 47
1051 ATGCATAGAT
* * *
1061 TTTTTTAAGTTATATTTATAAAAATTAGATAAAATTAAAAATTTTAG
1 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATCAAAAAGTTTAG
*
1108 TTTTTTAAGTAATATTTTTAAAAATTAGATAAAATCAAAAAGTTTAG
1 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATCAAAAAGTTTAG
1155 TGTTTTTA
1 T-TTTTTA
1163 TTTCATTTTC
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 44 0.88
48 6 0.12
ACGTcount: A:0.44, C:0.01, G:0.08, T:0.47
Consensus pattern (47 bp):
TTTTTTAAGTAATATTTATAAAAATTAGATAAAATCAAAAAGTTTAG
Found at i:1195 original size:19 final size:19
Alignment explanation
Indices: 1157--1195 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1147 AAGTTTAGTG
*
1157 TTTTTATTTCATTTTCATT
1 TTTTTATTTAATTTTCATT
1176 TTTTTATTTTAATTTT-ATT
1 TTTTTA-TTTAATTTTCATT
1195 T
1 T
1196 CTTATAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTATTTAATTTTCATT
Found at i:1693 original size:15 final size:15
Alignment explanation
Indices: 1658--1695 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
1648 AACCCTTAAT
1658 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
1672 T-AATCCATAATCCC
1 TAAATCCATAATCCC
1686 TAAATCCATA
1 TAAATCCATA
1696 TATATAGTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 12 0.55
15 8 0.36
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:2002 original size:17 final size:17
Alignment explanation
Indices: 1976--2019 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
1966 CCAACCCTTA
*
1976 ATTAAACCATAATCCCT
1 ATTAATCCATAATCCCT
1993 ATTAATCCATAATCCCT
1 ATTAATCCATAATCCCT
2010 A--AATCCATAA
1 ATTAATCCATAA
2020 ATACTCCCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 9 0.35
17 17 0.65
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (17 bp):
ATTAATCCATAATCCCT
Found at i:2801 original size:114 final size:114
Alignment explanation
Indices: 2379--2795 Score: 680
Period size: 114 Copynumber: 3.7 Consensus size: 114
2369 ATTAAACACT
* * ** *
2379 GCTAAATCCCCGAAAGCGCAAAAAAAAGCGTCGTTTTGGCTTAGGTTTTTTGCGGCGCTTTCTCA
1 GCTAAATCCCCGAAAGCTCACAAAACTGCGTCGTTTTGGATTAGGTTTTTTGCGGCGCTTTCTCA
2444 AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCC
66 AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCC
2493 GCTAAATCCCCGAAAGCTCACAAAACTGCGTCGTTTTGGATTAGGTTTTTTGCGGCGCTTTCTCA
1 GCTAAATCCCCGAAAGCTCACAAAACTGCGTCGTTTTGGATTAGGTTTTTTGCGGCGCTTTCTCA
* *
2558 AAAATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTATTAAAAACGCC
66 AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCC
*
2607 GCTAAATCCCTGAAAGCTCACAAAA---CGTCGTTTTGGATTAGGTTTTTTGCGGCGCTTTCTCA
1 GCTAAATCCCCGAAAGCTCACAAAACTGCGTCGTTTTGGATTAGGTTTTTTGCGGCGCTTTCTCA
* *
2669 AAAACGCCGCTAAAG-CTTAGAGCATTAGCGGCGCTTTCTTAAAAACGCT
66 AAAACGCCGCTAAAGCCCT-GAGCATTAGCGGCGCTTTCTTAAAAACGCC
* * *
2718 ACTAAATCCCCGAAAGCTTACAAAACTGCGTCGTTTTGGATTAGGTTTTTTGTGGCGCTTTCTCA
1 GCTAAATCCCCGAAAGCTCACAAAACTGCGTCGTTTTGGATTAGGTTTTTTGCGGCGCTTTCTCA
2783 AAAACGCCGCTAA
66 AAAACGCCGCTAA
2796 TGCTTATTGT
Statistics
Matches: 283, Mismatches: 16, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
110 2 0.01
111 101 0.36
114 180 0.64
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.28
Consensus pattern (114 bp):
GCTAAATCCCCGAAAGCTCACAAAACTGCGTCGTTTTGGATTAGGTTTTTTGCGGCGCTTTCTCA
AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCC
Found at i:3151 original size:27 final size:29
Alignment explanation
Indices: 3094--3152 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
3084 TTTGTTTTAA
*
3094 ATGTAGTGTATTTTAAAAATAAAAAATAT
1 ATGTAGTATATTTTAAAAATAAAAAATAT
3123 ATGTAGTATATTTTAAAAATAAAAAATAT
1 ATGTAGTATATTTTAAAAATAAAAAATAT
3152 A
1 A
3153 GTTTTTATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.37
Consensus pattern (29 bp):
ATGTAGTATATTTTAAAAATAAAAAATAT
Found at i:3608 original size:13 final size:14
Alignment explanation
Indices: 3590--3633 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
3580 TTTAAAAGTG
3590 TCATAATAATAA-A
1 TCATAATAATAATA
*
3603 TCATAATACTAATA
1 TCATAATAATAATA
3617 TGCATAAATAATAATA
1 T-CAT-AATAATAATA
3633 T
1 T
3634 TGAAAATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 11 0.42
14 2 0.08
15 3 0.12
16 10 0.38
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (14 bp):
TCATAATAATAATA
Found at i:3645 original size:22 final size:22
Alignment explanation
Indices: 3598--3653 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 22
3588 TGTCATAATA
* *
3598 ATAAATCATAATACTAATATGC
1 ATAAATAATAATACTAAAATGC
*
3620 ATAAATAATAATATTGAAAATG-
1 ATAAATAATAATACT-AAAATGC
*
3642 AT-AATAACAATA
1 ATAAATAATAATA
3654 ACAAAAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 9 0.31
22 15 0.52
23 5 0.17
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (22 bp):
ATAAATAATAATACTAAAATGC
Found at i:5194 original size:12 final size:11
Alignment explanation
Indices: 5161--5193 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
5151 AAAATAAAAA
*
5161 AAAAATATTTT
1 AAAAGTATTTT
5172 AAAAGTATTTT
1 AAAAGTATTTT
5183 AAAAGTATTTT
1 AAAAGTATTTT
5194 TTGTCCAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:7754 original size:15 final size:15
Alignment explanation
Indices: 7734--7763 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
7724 CACTTTCAAG
7734 CTCAAATCGATATAA
1 CTCAAATCGATATAA
*
7749 CTCAAATTGATATAA
1 CTCAAATCGATATAA
7764 AAAAAATAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.30
Consensus pattern (15 bp):
CTCAAATCGATATAA
Found at i:10291 original size:18 final size:18
Alignment explanation
Indices: 10255--10301 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
10245 TAAACTCAAT
* **
10255 CCAAACCCAAGTATTCAA
1 CCAAACCCAATTACCCAA
10273 CCAAACCCAATTACCCAA
1 CCAAACCCAATTACCCAA
*
10291 CCCAACCCAAT
1 CCAAACCCAAT
10302 CATAAAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.43, C:0.43, G:0.02, T:0.13
Consensus pattern (18 bp):
CCAAACCCAATTACCCAA
Found at i:10357 original size:19 final size:19
Alignment explanation
Indices: 10329--10371 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
10319 ATTTAATAAA
10329 TAAAAATAAAATCTAAAG-C
1 TAAAAATAAAA-CTAAAGTC
*
10348 TAAAACTAAAACTAAAGTC
1 TAAAAATAAAACTAAAGTC
10367 TAAAA
1 TAAAA
10372 GTCTAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.63, C:0.12, G:0.05, T:0.21
Consensus pattern (19 bp):
TAAAAATAAAACTAAAGTC
Found at i:10357 original size:25 final size:27
Alignment explanation
Indices: 10329--10379 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
10319 ATTTAATAAA
10329 TAAAAATAAAATCT-AAAG-CTAAAAC
1 TAAAAATAAAATCTAAAAGTCTAAAAC
* *
10354 TAAAACTAAAGTCTAAAAGTCTAAAA
1 TAAAAATAAAATCTAAAAGTCTAAAA
10380 ATAATTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 12 0.55
26 4 0.18
27 6 0.27
ACGTcount: A:0.61, C:0.12, G:0.06, T:0.22
Consensus pattern (27 bp):
TAAAAATAAAATCTAAAAGTCTAAAAC
Found at i:10362 original size:12 final size:13
Alignment explanation
Indices: 10329--10371 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
10319 ATTTAATAAA
*
10329 TAAAAATAAAATC
1 TAAAACTAAAATC
*
10342 TAAAGCTAAAA-C
1 TAAAACTAAAATC
*
10354 TAAAACTAAAGTC
1 TAAAACTAAAATC
10367 TAAAA
1 TAAAA
10372 GTCTAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.63, C:0.12, G:0.05, T:0.21
Consensus pattern (13 bp):
TAAAACTAAAATC
Found at i:10417 original size:9 final size:9
Alignment explanation
Indices: 10403--10478 Score: 98
Period size: 9 Copynumber: 8.4 Consensus size: 9
10393 GTAGTGATTC
*
10403 AATTCGGTT
1 AATTCGGGT
10412 AATTCGGGT
1 AATTCGGGT
*
10421 AATTCGGTT
1 AATTCGGGT
10430 AATTCGGGT
1 AATTCGGGT
* *
10439 AATCCGGTT
1 AATTCGGGT
10448 AATTCGGGT
1 AATTCGGGT
*
10457 AATTCGGTT
1 AATTCGGGT
*
10466 AAATCGGGT
1 AATTCGGGT
10475 AATT
1 AATT
10479 TTTAACCAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 56 1.00
ACGTcount: A:0.25, C:0.12, G:0.26, T:0.37
Consensus pattern (9 bp):
AATTCGGGT
Found at i:10426 original size:18 final size:18
Alignment explanation
Indices: 10403--10478 Score: 134
Period size: 18 Copynumber: 4.2 Consensus size: 18
10393 GTAGTGATTC
10403 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
10421 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
10439 AATCCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
10457 AATTCGGTTAAATCGGGT
1 AATTCGGTTAATTCGGGT
10475 AATT
1 AATT
10479 TTTAACCAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 55 1.00
ACGTcount: A:0.25, C:0.12, G:0.26, T:0.37
Consensus pattern (18 bp):
AATTCGGTTAATTCGGGT
Found at i:13257 original size:23 final size:22
Alignment explanation
Indices: 13223--13267 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
13213 AAATAAGATA
**
13223 AAATAAATAATTAGTTAATAAT
1 AAATAAATAATTAAATAATAAT
*
13245 AAATAATTAAATTAAATAATAAT
1 AAATAAAT-AATTAAATAATAAT
13268 GGTATTAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
AAATAAATAATTAAATAATAAT
Found at i:14638 original size:36 final size:34
Alignment explanation
Indices: 14598--14685 Score: 88
Period size: 36 Copynumber: 2.5 Consensus size: 34
14588 AAGCATCTCG
* * *
14598 ATAAATATATAATATATGTGTGGTCTTGTTATATAT
1 ATAAATATATAATATATCTATGGTC--ATTATATAT
* *
14634 ATAAAATAAATACATACATCTATGGTCATTATATAT
1 AT-AAATATATA-ATATATCTATGGTCATTATATAT
14670 AT-AATATATAATATAT
1 ATAAATATATAATATAT
14686 ATGCCTATAT
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
33 5 0.12
34 7 0.16
36 12 0.28
37 8 0.19
38 11 0.26
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (34 bp):
ATAAATATATAATATATCTATGGTCATTATATAT
Found at i:16356 original size:23 final size:23
Alignment explanation
Indices: 16316--16368 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
16306 ATAGAAAAAG
*
16316 ATATA-TATGCAACGATATATATT
1 ATATATTATGAAACGATATATA-T
16339 ATATATTATGAAAC-ATATATAT
1 ATATATTATGAAACGATATATAT
16361 ATATATTA
1 ATATATTA
16369 ACATTGTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 9 0.32
23 12 0.43
24 7 0.25
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (23 bp):
ATATATTATGAAACGATATATAT
Done.