Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1425
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: 28028
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:3334 original size:12 final size:12
Alignment explanation
Indices: 3317--3341 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3307 CGAAATGATC
3317 TATATATATAAA
1 TATATATATAAA
3329 TATATATATAAA
1 TATATATATAAA
3341 T
1 T
3342 CTGAACACGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TATATATATAAA
Found at i:4145 original size:17 final size:18
Alignment explanation
Indices: 4109--4147 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
4099 TGGTAATTAG
4109 ACAAGTCAAGCAACATGA
1 ACAAGTCAAGCAACATGA
*
4127 ACAAGTCCAGCAA-ATGA
1 ACAAGTCAAGCAACATGA
4144 ACAA
1 ACAA
4148 TTCAGTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.51, C:0.23, G:0.15, T:0.10
Consensus pattern (18 bp):
ACAAGTCAAGCAACATGA
Found at i:5983 original size:21 final size:21
Alignment explanation
Indices: 5957--5999 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5947 GTTTATGCCG
5957 ACACAAATCAGCCAGTAGAGA
1 ACACAAATCAGCCAGTAGAGA
5978 ACACAAATCAGCCAGTAGAGA
1 ACACAAATCAGCCAGTAGAGA
5999 A
1 A
6000 AAACTGATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.23, G:0.19, T:0.09
Consensus pattern (21 bp):
ACACAAATCAGCCAGTAGAGA
Found at i:6517 original size:22 final size:22
Alignment explanation
Indices: 6485--6546 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
6475 TCATGTCTAA
*
6485 AATATTTATATATTT-TTCTTAT
1 AATATTT-TATATTTATTTTTAT
*
6507 AAT-TTTTATATTTATTTTTTT
1 AATATTTTATATTTATTTTTAT
6528 AATATTTTATATTTATTTT
1 AATATTTTATATTTATTTT
6547 ATTTATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.19
21 11 0.31
22 18 0.50
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (22 bp):
AATATTTTATATTTATTTTTAT
Found at i:6527 original size:15 final size:16
Alignment explanation
Indices: 6509--6554 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
6499 TTTCTTATAA
6509 TTTTTATATTTAT-TT
1 TTTTTATATTTATATT
*
6524 TTTTAATATTTTATATT
1 TTTTTATA-TTTATATT
*
6541 TATTT-TATTTATAT
1 TTTTTATATTTATAT
6555 ATGATTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 14 0.54
16 7 0.27
17 5 0.19
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTATATTTATATT
Found at i:6554 original size:22 final size:22
Alignment explanation
Indices: 6486--6554 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
6476 CATGTCTAAA
*
6486 ATATTTATATATTT-TTCTTA-TA
1 ATATTT-TATATTTATT-TTATTT
6508 AT-TTTTATATTTATTTT-TTT
1 ATATTTTATATTTATTTTATTT
6528 AATATTTTATATTTATTTTATTT
1 -ATATTTTATATTTATTTTATTT
6551 ATAT
1 ATAT
6555 ATGATTAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
20 10 0.24
21 7 0.17
22 21 0.51
23 3 0.07
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (22 bp):
ATATTTTATATTTATTTTATTT
Found at i:7651 original size:13 final size:14
Alignment explanation
Indices: 7633--7661 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
7623 CAATAAATTG
7633 CTAAAAA-CACTTT
1 CTAAAAAGCACTTT
7646 CTAAAAAGCACTTT
1 CTAAAAAGCACTTT
7660 CT
1 CT
7662 GTCTCAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.41, C:0.24, G:0.03, T:0.31
Consensus pattern (14 bp):
CTAAAAAGCACTTT
Found at i:14378 original size:14 final size:15
Alignment explanation
Indices: 14359--14387 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
14349 TAAAATTTAT
14359 TTTTGAA-TTAAAAA
1 TTTTGAATTTAAAAA
14373 TTTTGAATTTAAAAA
1 TTTTGAATTTAAAAA
14388 ATTTATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (15 bp):
TTTTGAATTTAAAAA
Found at i:15358 original size:16 final size:16
Alignment explanation
Indices: 15337--15369 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
15327 GATTGATTAA
15337 TTGTTTCTTTTTTCTT
1 TTGTTTCTTTTTTCTT
*
15353 TTGTTTTTTTTTTCTT
1 TTGTTTCTTTTTTCTT
15369 T
1 T
15370 GGCCGTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (16 bp):
TTGTTTCTTTTTTCTT
Found at i:18030 original size:24 final size:24
Alignment explanation
Indices: 17998--18049 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
17988 TTATAATATT
17998 CAAAATAAAAAA-ATTTTAAAATTA
1 CAAAATAAAAAATA-TTTAAAATTA
*
18022 CAAAATAAAATATATTTAAAATTA
1 CAAAATAAAAAATATTTAAAATTA
18046 -AAAA
1 CAAAA
18050 CAAATATTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 4 0.15
24 21 0.81
25 1 0.04
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (24 bp):
CAAAATAAAAAATATTTAAAATTA
Found at i:18483 original size:23 final size:24
Alignment explanation
Indices: 18457--18516 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
18447 ATTTTTTGAA
* *
18457 AAATATATAATTAAATA-ATATTT
1 AAATATATAAATAAATATAAATTT
*
18480 AAATATTTAAATAAATATTAAATTT
1 AAATATATAAATAAATA-TAAATTT
*
18505 AAATATTTAAAT
1 AAATATATAAAT
18517 TTATTATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 15 0.47
25 17 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAATATATAAATAAATATAAATTT
Found at i:18526 original size:13 final size:14
Alignment explanation
Indices: 18476--18519 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
18466 ATTAAATAAT
18476 ATTTAAATATTTAA
1 ATTTAAATATTTAA
18490 A--TAAATA-TTAA
1 ATTTAAATATTTAA
18501 ATTTAAATATTTAA
1 ATTTAAATATTTAA
18515 ATTTA
1 ATTTA
18520 TTATTTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 5 0.19
12 6 0.22
13 6 0.22
14 10 0.37
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTTAAATATTTAA
Found at i:21345 original size:13 final size:13
Alignment explanation
Indices: 21327--21368 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
21317 TTTTTTAAAA
21327 AAATTATATATTT
1 AAATTATATATTT
21340 AAATTAT-TATATT
1 AAATTATATAT-TT
*
21353 AAATT-TATATTC
1 AAATTATATATTT
21365 AAAT
1 AAAT
21369 ATACGTTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 9 0.35
13 17 0.65
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (13 bp):
AAATTATATATTT
Found at i:23587 original size:21 final size:21
Alignment explanation
Indices: 23562--23604 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
23552 ATAAATAAGC
23562 ATAAGAGAGTATTTATAAAGA
1 ATAAGAGAGTATTTATAAAGA
23583 ATAAGAGAGTATTTATAAAGA
1 ATAAGAGAGTATTTATAAAGA
23604 A
1 A
23605 AATCTGACGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (21 bp):
ATAAGAGAGTATTTATAAAGA
Found at i:23751 original size:17 final size:17
Alignment explanation
Indices: 23729--23763 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
23719 ATATCAGAAG
23729 AAAAGCTCTAAAATCAA
1 AAAAGCTCTAAAATCAA
23746 AAAAGCTCTAAAATCAA
1 AAAAGCTCTAAAATCAA
23763 A
1 A
23764 CTCTATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.60, C:0.17, G:0.06, T:0.17
Consensus pattern (17 bp):
AAAAGCTCTAAAATCAA
Found at i:24331 original size:23 final size:22
Alignment explanation
Indices: 24305--24356 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
24295 ATTTTTACTT
24305 TTAATAA-AATAATATTTGATTTA
1 TTAATAATAATAA-ATTT-ATTTA
*
24328 TTAATAATTTATAAATTTATTTA
1 TTAATAA-TAATAAATTTATTTA
24351 TTAATA
1 TTAATA
24357 GTTTATAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 18 0.69
24 4 0.15
25 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TTAATAATAATAAATTTATTTA
Found at i:24361 original size:23 final size:23
Alignment explanation
Indices: 24313--24379 Score: 80
Period size: 23 Copynumber: 2.7 Consensus size: 23
24303 TTTTAATAAA
24313 ATAATATTTGATTTATTAATAATTT
1 ATAA-ATTT-ATTTATTAATAATTT
*
24338 ATAAATTTATTTATTAATAGTTT
1 ATAAATTTATTTATTAATAATTT
24361 ATAAACTTATATTTTATTA
1 ATAAA-TT-TA-TTTATTA
24380 CTATTTCAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
23 19 0.50
24 6 0.16
25 6 0.16
26 7 0.18
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.55
Consensus pattern (23 bp):
ATAAATTTATTTATTAATAATTT
Done.