Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1239
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: 27323
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:4037 original size:14 final size:15
Alignment explanation
Indices: 4013--4041 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4003 TAATTATAAA
4013 AATATATAAATTATT
1 AATATATAAATTATT
4028 AATATA-AAATTATT
1 AATATATAAATTATT
4042 GTTTTAGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATATATAAATTATT
Found at i:4645 original size:6 final size:6
Alignment explanation
Indices: 4634--4676 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
4624 ATTAAGTTAT
*
4634 AAATAA AAATAA AAATTA AAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA A
4677 TTTTATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AAATAA
Found at i:5127 original size:22 final size:22
Alignment explanation
Indices: 5037--5127 Score: 57
Period size: 25 Copynumber: 4.1 Consensus size: 22
5027 TTTATTTTAT
5037 TATT-TTTTATATTATT-AA-AA
1 TATTATTTT-TATTATTAAATAA
* * *
5057 TGTTATTTTTA-TA-TGAATATT
1 TATTATTTTTATTATTAAATA-A
*
5078 TATATATTTTTATAATTAAATAAAAA
1 TAT-TATTTTTATTATTAAAT---AA
5104 TATTATTTTTATTATTAAATAA
1 TATTATTTTTATTATTAAATAA
5126 TA
1 TA
5128 ATTTAAACTG
Statistics
Matches: 54, Mismatches: 7, Indels: 18
0.68 0.09 0.23
Matches are distributed among these distances:
18 1 0.02
19 4 0.07
20 6 0.11
21 6 0.11
22 12 0.22
23 1 0.02
24 4 0.07
25 16 0.30
26 3 0.06
27 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TATTATTTTTATTATTAAATAA
Found at i:6016 original size:12 final size:12
Alignment explanation
Indices: 5973--6018 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
5963 ATTTTTATCT
5973 AAATTTAAA-TA
1 AAATTTAAATTA
*
5984 AAATTTAATTTCA
1 AAATTTAAATT-A
5997 AAATTTAAATTA
1 AAATTTAAATTA
*
6009 ATATTTAAAT
1 AAATTTAAAT
6019 ATCAATAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
11 8 0.27
12 11 0.37
13 11 0.37
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
AAATTTAAATTA
Found at i:7611 original size:13 final size:13
Alignment explanation
Indices: 7593--7618 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7583 CAAGTTTTTG
7593 TGTATCGATACAT
1 TGTATCGATACAT
7606 TGTATCGATACAT
1 TGTATCGATACAT
7619 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:7643 original size:19 final size:18
Alignment explanation
Indices: 7573--7643 Score: 53
Period size: 19 Copynumber: 4.0 Consensus size: 18
7563 TACAAGCCAA
*
7573 TGTATCGATACAAGTTTTTG
1 TGTATCGATACAA--TTTGG
7593 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
7606 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
7625 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
7644 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:9984 original size:21 final size:21
Alignment explanation
Indices: 9960--10006 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
9950 TTTGATGCTG
9960 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
*
9980 AATTTGAAGTGAAAAACAAGT
1 ATTTTGAAGTGAAAAACAAGT
10001 ATTTTG
1 ATTTTG
10007 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 5 0.22
21 10 0.43
22 8 0.35
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:10145 original size:13 final size:13
Alignment explanation
Indices: 10127--10167 Score: 82
Period size: 13 Copynumber: 3.2 Consensus size: 13
10117 ATAATCACCC
10127 TGTATCGATACAA
1 TGTATCGATACAA
10140 TGTATCGATACAA
1 TGTATCGATACAA
10153 TGTATCGATACAA
1 TGTATCGATACAA
10166 TG
1 TG
10168 AAAAATGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:10176 original size:20 final size:20
Alignment explanation
Indices: 10151--10189 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
10141 GTATCGATAC
10151 AATGTATCGATACAATGAAA
1 AATGTATCGATACAATGAAA
*
10171 AATGTATCGATACATTGAA
1 AATGTATCGATACAATGAA
10190 TTTCCAGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.28
Consensus pattern (20 bp):
AATGTATCGATACAATGAAA
Found at i:12257 original size:15 final size:15
Alignment explanation
Indices: 12237--12266 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12227 TGTTCATCAA
12237 TTTCATTTGGAGCTT
1 TTTCATTTGGAGCTT
*
12252 TTTCATTTTGAGCTT
1 TTTCATTTGGAGCTT
12267 CCCCAATTTG
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:0.13, C:0.13, G:0.17, T:0.57
Consensus pattern (15 bp):
TTTCATTTGGAGCTT
Found at i:16362 original size:13 final size:13
Alignment explanation
Indices: 16344--16368 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16334 CAAGTTTTTG
16344 TGTATCGATACAA
1 TGTATCGATACAA
16357 TGTATCGATACA
1 TGTATCGATACA
16369 TACTTGGTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:16384 original size:32 final size:32
Alignment explanation
Indices: 16321--16388 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
16311 CGTTACAAGC
* *
16321 CAATGTATCGATACAAGTTTTTGTGTATCGATA
1 CAATGTATCGATACAAG-CTTGGTGTATCGATA
16354 CAATGTATCGATACATA-CTTGGTGTATCGATA
1 CAATGTATCGATACA-AGCTTGGTGTATCGATA
16386 CAA
1 CAA
16389 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 16 0.50
33 15 0.47
34 1 0.03
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACAAGCTTGGTGTATCGATA
Found at i:16394 original size:19 final size:18
Alignment explanation
Indices: 16324--16394 Score: 53
Period size: 19 Copynumber: 4.0 Consensus size: 18
16314 TACAAGCCAA
*
16324 TGTATCGATACAAGTTTTTG
1 TGTATCGATACAA--TTTGG
16344 TGTATCGATACAA-----
1 TGTATCGATACAATTTGG
*
16357 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
16376 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
16395 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 12 0.28
14 1 0.02
18 1 0.02
19 16 0.37
20 13 0.30
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:17253 original size:32 final size:32
Alignment explanation
Indices: 17217--17293 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
17207 ATGCATTCAT
* *
17217 ATGCATTTATTCAAAAAAATTCATTCATCTAA
1 ATGCATTTATTCAAAAAAATTCATTCACCCAA
* * *
17249 ATGCATTCATTTAAATAAATTCATTCACCCAA
1 ATGCATTTATTCAAAAAAATTCATTCACCCAA
**
17281 ATATATTTATTCA
1 ATGCATTTATTCA
17294 TCTAAATGTA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.39
Consensus pattern (32 bp):
ATGCATTTATTCAAAAAAATTCATTCACCCAA
Found at i:17300 original size:18 final size:18
Alignment explanation
Indices: 17246--17300 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
17236 TTCATTCATC
* *
17246 TAAATGCATTCATTTAAA
1 TAAATTCATTCATCTAAA
* *
17264 TAAATTCATTCACCCAAA
1 TAAATTCATTCATCTAAA
* *
17282 TATATTTATTCATCTAAA
1 TAAATTCATTCATCTAAA
17300 T
1 T
17301 GTATCTTGTT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.40
Consensus pattern (18 bp):
TAAATTCATTCATCTAAA
Found at i:17728 original size:13 final size:15
Alignment explanation
Indices: 17710--17741 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
17700 GATAGATTGG
17710 TTTACTT-TATAT-A
1 TTTACTTGTATATGA
17723 TTTACTTGTATATGA
1 TTTACTTGTATATGA
17738 TTTA
1 TTTA
17742 AAGTTAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 5 0.29
15 5 0.29
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.59
Consensus pattern (15 bp):
TTTACTTGTATATGA
Found at i:19215 original size:22 final size:22
Alignment explanation
Indices: 19189--19230 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
19179 TAAAAACATT
*
19189 ATCATTGATATTC-TAGCTTTGC
1 ATCATT-AGATTCTTAGCTTTGC
19211 ATCATTAGATTCTTAGCTTT
1 ATCATTAGATTCTTAGCTTT
19231 TCATTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.48
Consensus pattern (22 bp):
ATCATTAGATTCTTAGCTTTGC
Found at i:20853 original size:22 final size:22
Alignment explanation
Indices: 20825--20867 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
20815 ATTCATCACA
*
20825 GTATCGATACATTACTGTTCAT
1 GTATCGATACATCACTGTTCAT
20847 GTATCGATACATCACTGTTCA
1 GTATCGATACATCACTGTTCA
20868 CACTATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (22 bp):
GTATCGATACATCACTGTTCAT
Found at i:21371 original size:34 final size:36
Alignment explanation
Indices: 21308--21374 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
21298 CTAAGTGATT
*
21308 GAGAGGTTTTATCTTAGCTTTTGGAAAAGATAGAGA
1 GAGAGGTTTTATCTTAGCTCTTGGAAAAGATAGAGA
21344 GAGAGGTTTCTATCTTAGC-CTT-G-AAAGATAG
1 GAGAGGTTT-TATCTTAGCTCTTGGAAAAGATAG
21375 TGTTGTAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 8 0.28
35 1 0.03
36 11 0.38
37 9 0.31
ACGTcount: A:0.31, C:0.09, G:0.27, T:0.33
Consensus pattern (36 bp):
GAGAGGTTTTATCTTAGCTCTTGGAAAAGATAGAGA
Found at i:23074 original size:84 final size:84
Alignment explanation
Indices: 22901--23061 Score: 202
Period size: 84 Copynumber: 1.9 Consensus size: 84
22891 ACTCAAAGAA
* * * *
22901 GAAAATAAATCAATAAGTGTAGAGAATGATATTCTTGAAAAGAAATTAAGTGAATTAGAGAAGAA
1 GAAAATAAATCAATAAGTGTAGAAAATGATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAA
*
22966 TATGAAAGAGTTACAAAAT
66 TAAGAAAGAGTTACAAAAT
* * *
22985 GAAAATAAATCAATGAGTTTAGAAAAT-A-ATTCTTTTAAAAAGAAAATAAATGAATTAGAGGAG
1 GAAAATAAATCAATAAGTGTAGAAAATGATATTC--TTAAAAAGAAAATAAATGAATTAGAGAAG
23048 AA-AAGAAATGAGTT
64 AATAAGAAA-GAGTT
23062 GCAAGTGAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
82 4 0.06
83 6 0.09
84 56 0.85
ACGTcount: A:0.53, C:0.03, G:0.18, T:0.25
Consensus pattern (84 bp):
GAAAATAAATCAATAAGTGTAGAAAATGATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAA
TAAGAAAGAGTTACAAAAT
Found at i:27203 original size:52 final size:51
Alignment explanation
Indices: 27118--27241 Score: 212
Period size: 52 Copynumber: 2.4 Consensus size: 51
27108 ATATGAAAAG
* *
27118 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
*
27169 TTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
27221 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
27242 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 21 0.30
52 48 0.70
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:27254 original size:51 final size:51
Alignment explanation
Indices: 27118--27261 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
27108 ATATGAAAAG
*
27118 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
27170 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
27221 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
27262 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
50 2 0.02
51 34 0.40
52 48 0.57
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:27268 original size:13 final size:13
Alignment explanation
Indices: 27250--27274 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27240 CAAAGATCAG
27250 TGTATCGATACAA
1 TGTATCGATACAA
27263 TGTATCGATACA
1 TGTATCGATACA
27275 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Done.