Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2042
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: 21280
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Found at i:87 original size:2 final size:2
Alignment explanation
Indices: 80--115 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
70 CAAATCAAAG
80 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
116 AATAAAAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1331 original size:2 final size:2
Alignment explanation
Indices: 1324--1362 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1314 TTAGTTCTGT
1324 TA TA TA TA TA -A TA TA TA TA T- TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1363 TCGCATCACT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1338 original size:11 final size:10
Alignment explanation
Indices: 1324--1362 Score: 64
Period size: 9 Copynumber: 4.1 Consensus size: 10
1314 TTAGTTCTGT
1324 TATATATATA
1 TATATATATA
1334 -ATATATATA
1 TATATATATA
1343 T-TATATATA
1 TATATATATA
1352 TATATATATA
1 TATATATATA
1362 T
1 T
1363 TCGCATCACT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 18 0.67
10 9 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
TATATATATA
Found at i:1997 original size:28 final size:28
Alignment explanation
Indices: 1944--2012 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 28
1934 TTAAATTATT
**
1944 ATTTAATAATAAAAAATATTTTATTTAA
1 ATTTAATAATAAAAAATATTGAATTTAA
* *
1972 ATTTAATTAT-AAAAATATATGAATTTTA
1 ATTTAATAATAAAAAATAT-TGAATTTAA
* *
2000 ATATAAAAATAAA
1 ATTTAATAATAAA
2013 GTTTAAATTT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
27 8 0.25
28 22 0.69
29 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (28 bp):
ATTTAATAATAAAAAATATTGAATTTAA
Found at i:2797 original size:16 final size:17
Alignment explanation
Indices: 2776--2807 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2766 AGTTAATTAA
2776 TAAATTTAATT-TTATG
1 TAAATTTAATTATTATG
2792 TAAATTTAATTATTAT
1 TAAATTTAATTATTAT
2808 AATGTGTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TAAATTTAATTATTATG
Found at i:4205 original size:13 final size:13
Alignment explanation
Indices: 4189--4228 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
4179 GTGAAAAGTT
4189 GAAAGAAAAAAAA
1 GAAAGAAAAAAAA
4202 GAAAGAAATAAAATA
1 GAAAGAAA-AAAA-A
4217 -AAAGAAAAAAAA
1 GAAAGAAAAAAAA
4229 AGGAGAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.04
13 12 0.48
14 11 0.44
15 1 0.04
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.05
Consensus pattern (13 bp):
GAAAGAAAAAAAA
Found at i:4325 original size:6 final size:6
Alignment explanation
Indices: 4314--4382 Score: 63
Period size: 6 Copynumber: 11.3 Consensus size: 6
4304 TTGATCATTT
* *
4314 TTTATA TTTATA -TTATA TTTATA TTATATA TTTTTA TATTA-A -TTATT
1 TTTATA TTTATA TTTATA TTTATA TT-TATA TTTATA T-TTATA TTTATA
4361 TTTATTA TATTATA TTTATA TT
1 TTTA-TA T-TTATA TTTATA TT
4383 ATACAATTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
4 3 0.06
5 5 0.10
6 28 0.54
7 13 0.25
8 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTATA
Found at i:4331 original size:11 final size:11
Alignment explanation
Indices: 4315--4385 Score: 76
Period size: 11 Copynumber: 6.5 Consensus size: 11
4305 TGATCATTTT
4315 TTATATTTATA
1 TTATATTTATA
4326 TTATATTTATA
1 TTATATTTATA
4337 TTATATATT-T-
1 TTATAT-TTATA
*
4347 TTATATTAATTA
1 TTATATTTA-TA
*
4359 TT-TTTATTATA
1 TTATAT-TTATA
4370 TTATATTTATA
1 TTATATTTATA
4381 TTATA
1 TTATA
4386 CAATTATATC
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
9 1 0.02
10 6 0.12
11 35 0.70
12 8 0.16
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTATATTTATA
Found at i:13636 original size:16 final size:16
Alignment explanation
Indices: 13617--13669 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 16
13607 TTTCGTTTAG
13617 TTTTCTTTCTTTCTTC
1 TTTTCTTTCTTTCTTC
*
13633 TTTTCTTTTCTTTTCTTT
1 TTTTC-TTTC-TTTCTTC
* *
13651 TTTTTTTTTTTTC-TC
1 TTTTCTTTCTTTCTTC
13666 TTTT
1 TTTT
13670 GGTTTATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
15 5 0.16
16 9 0.29
17 7 0.23
18 10 0.32
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTCTTTCTTTCTTC
Found at i:13638 original size:5 final size:5
Alignment explanation
Indices: 13617--13669 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 5
13607 TTTCGTTTAG
13617 TTTTC -TTTC TTTCTTC TTTTC TTTTC TTTTC TTTT- TTTT- TTTT- TTTCTC
1 TTTTC TTTTC -TT-TTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTT-TC
13666 TTTT
1 TTTT
13670 GGTTTATTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
4 15 0.35
5 19 0.44
6 6 0.14
7 3 0.07
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:13649 original size:26 final size:23
Alignment explanation
Indices: 13617--13669 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 23
13607 TTTCGTTTAG
13617 TTTTCTTTCTTTCTTCTTTTCTTT-TC
1 TTTTCTTT-TTT-TT-TTTT-TTTCTC
13643 TTTTCTTTTTTTTTTTTTTTCTC
1 TTTTCTTTTTTTTTTTTTTTCTC
13666 TTTT
1 TTTT
13670 GGTTTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 3 0.12
23 10 0.38
24 2 0.08
25 3 0.12
26 8 0.31
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (23 bp):
TTTTCTTTTTTTTTTTTTTTCTC
Found at i:14420 original size:2 final size:2
Alignment explanation
Indices: 14413--14451 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
14403 TCAGTTTACA
14413 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14452 AAACATGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15078 original size:2 final size:2
Alignment explanation
Indices: 15071--15100 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15061 TTGATGATAC
15071 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15101 GTACACAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16519 original size:32 final size:33
Alignment explanation
Indices: 16483--16567 Score: 109
Period size: 32 Copynumber: 2.6 Consensus size: 33
16473 ATTTAATGAT
* *
16483 AAAATATTTTCCTCAAATTTAATCAAAACTA-C
1 AAAATATTTTACTCAAATTTAATCAAAACTATA
* * * *
16515 AAAATATTTTACTCAAACTCAATCTAAATTATA
1 AAAATATTTTACTCAAATTTAATCAAAACTATA
16548 AAAATATTTTACTCAAATTT
1 AAAATATTTTACTCAAATTT
16568 TACTTAAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
32 26 0.59
33 18 0.41
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (33 bp):
AAAATATTTTACTCAAATTTAATCAAAACTATA
Found at i:17804 original size:23 final size:22
Alignment explanation
Indices: 17778--17829 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 22
17768 TATTTTTCAT
17778 TTTGTTTAAAATATATATATATA
1 TTTGTTT-AAATATATATATATA
*
17801 TTTGTATT--ATATTTATATATA
1 TTTGT-TTAAATATATATATATA
17822 TTT-TTTAA
1 TTTGTTTAA
17830 TAATTAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
19 2 0.08
20 1 0.04
21 15 0.60
23 5 0.20
24 2 0.08
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (22 bp):
TTTGTTTAAATATATATATATA
Found at i:17839 original size:21 final size:23
Alignment explanation
Indices: 17792--17839 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
17782 TTTAAAATAT
* *
17792 ATATATATATTTGTATTATATTT
1 ATATATATATTTGTAATATATTA
*
17815 ATATATAT-TTTTTAATA-ATTA
1 ATATATATATTTGTAATATATTA
17836 ATAT
1 ATAT
17840 TTAAAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 7 0.32
22 7 0.32
23 8 0.36
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
ATATATATATTTGTAATATATTA
Found at i:17871 original size:27 final size:26
Alignment explanation
Indices: 17819--17903 Score: 86
Period size: 27 Copynumber: 3.2 Consensus size: 26
17809 ATATTTATAT
* *
17819 ATATTTTTTAATAATTAATATTTAAAA
1 ATATTTTTT-ATAAATAAGATTTAAAA
*
17846 ATATTTTTTATAAATACGATTATAAAA
1 ATATTTTTTATAAATAAGATT-TAAAA
17873 ATATAATTTTTATAAA-AA-ATTT-AAA
1 ATAT--TTTTTATAAATAAGATTTAAAA
17898 ATATTT
1 ATATTT
17904 ATATCAAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
23 2 0.04
25 7 0.14
26 10 0.20
27 21 0.41
28 1 0.02
29 10 0.20
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (26 bp):
ATATTTTTTATAAATAAGATTTAAAA
Found at i:19504 original size:24 final size:25
Alignment explanation
Indices: 19463--19522 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
19453 GAATATGAAT
* * * *
19463 TTATTTTTTTATATTTTTTTATAAA
1 TTATATTTTTAAAATTTTTTAAAAA
19488 TT-TATTTTTAAAATTTTTTAAAAA
1 TTATATTTTTAAAATTTTTTAAAAA
*
19512 TTATATCTTTA
1 TTATATTTTTA
19523 TATTCAATTC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 20 0.69
25 9 0.31
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (25 bp):
TTATATTTTTAAAATTTTTTAAAAA
Done.