Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold791
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: 39194
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.37
Found at i:273 original size:30 final size:30
Alignment explanation
Indices: 236--318 Score: 107
Period size: 30 Copynumber: 2.8 Consensus size: 30
226 TTTAAGAATA
236 AATTAAAAATTAAGAGTTTATTTGTA-TAA-
1 AATTAAAAATTAAGAGTTTATTTG-AGTAAC
* *
265 ACATTAAAAGTTAAGAGTTTATTTGAGTATC
1 A-ATTAAAAATTAAGAGTTTATTTGAGTAAC
*
296 AATTAAAGATTAAGAGTTTATTT
1 AATTAAAAATTAAGAGTTTATTT
319 AAAATAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
29 2 0.04
30 44 0.94
31 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.13, T:0.41
Consensus pattern (30 bp):
AATTAAAAATTAAGAGTTTATTTGAGTAAC
Found at i:4599 original size:17 final size:17
Alignment explanation
Indices: 4572--4611 Score: 66
Period size: 15 Copynumber: 2.5 Consensus size: 17
4562 TTTTTACAAA
4572 ATTAAATATAT-TT-AT
1 ATTAAATATATATTCAT
4587 ATTAAATATATATTCAT
1 ATTAAATATATATTCAT
4604 ATTAAATA
1 ATTAAATA
4612 CTTACTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 11 0.48
16 2 0.09
17 10 0.43
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTAAATATATATTCAT
Found at i:14391 original size:34 final size:34
Alignment explanation
Indices: 14345--14562 Score: 273
Period size: 34 Copynumber: 6.5 Consensus size: 34
14335 GTAAAAACCA
*
14345 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
14379 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
14413 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
14447 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
14480 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* ** *
14514 CCATTTAATCAACAATGGTAAACTATTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
14547 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
14563 TCTCCCACTT
Statistics
Matches: 161, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 45 0.28
34 114 0.71
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:14459 original size:68 final size:67
Alignment explanation
Indices: 14343--14562 Score: 314
Period size: 67 Copynumber: 3.3 Consensus size: 67
14333 TGGTAAAAAC
* * *
14343 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
14408 AT
66 AT
* * *
14410 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
14475 AAT
65 AAT
* * * * * **
14478 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTATTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
14543 AT
66 AT
14545 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
14563 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 74 0.55
68 61 0.45
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:19019 original size:34 final size:34
Alignment explanation
Indices: 18973--19188 Score: 278
Period size: 34 Copynumber: 6.4 Consensus size: 34
18963 GTAAAAACCA
*
18973 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
19007 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
19041 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
19075 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
19108 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
19142 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
19175 CCATTTAATCAACA
1 CCATTTAATCAACA
19189 CTTTTGACGT
Statistics
Matches: 160, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 43 0.27
34 115 0.72
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:19087 original size:68 final size:67
Alignment explanation
Indices: 18971--19188 Score: 319
Period size: 67 Copynumber: 3.2 Consensus size: 67
18961 TGGTAAAAAC
* * *
18971 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
19036 AT
66 AT
* * *
19038 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
19103 AAT
65 AAT
* * * * * *
19106 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
19171 AT
66 AT
19173 CACCATTTAATCAACA
1 CACCATTTAATCAACA
19189 CTTTTGACGT
Statistics
Matches: 134, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 73 0.54
68 61 0.46
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:19792 original size:2 final size:2
Alignment explanation
Indices: 19785--19825 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
19775 AAATGTTCAC
19785 AT 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 AT A
19826 CACACCAGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21337 original size:80 final size:83
Alignment explanation
Indices: 21207--21368 Score: 240
Period size: 80 Copynumber: 2.0 Consensus size: 83
21197 TTGCGTTTAT
* *
21207 TTTTTTTATTTTTACCTTTTTTTTTAATTTTAATATTCTTATTTATAATATCTTTATCTATATTA
1 TTTTTTTATTTTTACC--TTTTTTTAATTTTAATATTCCTATTTATAATATCTTTATCTATACTA
*
21272 AAATTGGTACACTTATTGCA
64 AAATTGGTACACCTATTGCA
*
21292 TTTTTTTATTTTTA-C-TTTTTT-ATTTTAATATTCCTATTTATAATATCTTTATTTATACTAAA
1 TTTTTTTATTTTTACCTTTTTTTAATTTTAATATTCCTATTTATAATATCTTTATCTATACTAAA
*
21354 ATTGTTACACCTATT
66 ATTGGTACACCTATT
21369 ACATGGGTGG
Statistics
Matches: 72, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
80 51 0.71
81 6 0.08
84 1 0.01
85 14 0.19
ACGTcount: A:0.27, C:0.10, G:0.02, T:0.60
Consensus pattern (83 bp):
TTTTTTTATTTTTACCTTTTTTTAATTTTAATATTCCTATTTATAATATCTTTATCTATACTAAA
ATTGGTACACCTATTGCA
Found at i:22116 original size:13 final size:12
Alignment explanation
Indices: 22078--22126 Score: 57
Period size: 13 Copynumber: 4.0 Consensus size: 12
22068 ATGATTTTTT
22078 AAATAATTATTA
1 AAATAATTATTA
22090 AAAT-ATTAATTTA
1 AAATAATT-A-TTA
22103 AAATAAATTATTA
1 AAAT-AATTATTA
22116 AAAT-ATTATTA
1 AAATAATTATTA
22127 TTTTGACATG
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
11 10 0.30
12 5 0.15
13 14 0.42
14 1 0.03
15 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
AAATAATTATTA
Found at i:22517 original size:25 final size:26
Alignment explanation
Indices: 22469--22518 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
22459 TAATTATTTT
* *
22469 AAAATATTTAATTTAATTTTTAATTG
1 AAAATATTTAATTTAAGTTGTAATTG
*
22495 AAAAT-TTTAATTTAGGTTGTAATT
1 AAAATATTTAATTTAAGTTGTAATT
22519 ATATATATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (26 bp):
AAAATATTTAATTTAAGTTGTAATTG
Found at i:22831 original size:14 final size:14
Alignment explanation
Indices: 22788--22832 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
22778 TTTAGATGAC
22788 TAAATTAAA-ATTT
1 TAAATTAAATATTT
**
22801 TAAATTAAATAAAT
1 TAAATTAAATATTT
22815 TAAATTAAATATTT
1 TAAATTAAATATTT
22829 TAAA
1 TAAA
22833 ATAATTATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
13 9 0.33
14 18 0.67
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TAAATTAAATATTT
Found at i:22944 original size:21 final size:19
Alignment explanation
Indices: 22920--22966 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
22910 AATATTATTA
*
22920 TATTTATAATAATATTTCTTT
1 TATTTATAAT-ATAATT-TTT
*
22941 TATTAATAATATAATTTTT
1 TATTTATAATATAATTTTT
22960 TATTTAT
1 TATTTAT
22967 TTTAAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 9 0.39
20 5 0.22
21 9 0.39
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTATAATATAATTTTT
Found at i:23030 original size:14 final size:16
Alignment explanation
Indices: 23011--23042 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
23001 ATTATTAAAA
23011 AATAATAA-AATT-AT
1 AATAATAACAATTGAT
23025 AATAATAACAATTGAT
1 AATAATAACAATTGAT
23041 AA
1 AA
23043 CTAGACGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (16 bp):
AATAATAACAATTGAT
Found at i:23104 original size:32 final size:32
Alignment explanation
Indices: 23062--23122 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
23052 TCCACGTCAT
* *
23062 AATCGGTAAAGTATTTAGCAATTTTATGTAAA
1 AATCGGTAAAGTATCTAGCAATTTCATGTAAA
* *
23094 AATCGTTAAAGTATCTAGCTATTTCATGT
1 AATCGGTAAAGTATCTAGCAATTTCATGT
23123 TGGAATCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (32 bp):
AATCGGTAAAGTATCTAGCAATTTCATGTAAA
Found at i:26033 original size:10 final size:10
Alignment explanation
Indices: 25999--26034 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
25989 TATACCTCTA
25999 TTATATATAT
1 TTATATATAT
*
26009 TTACATATAT
1 TTATATATAT
*
26019 ATATATATAT
1 TTATATATAT
26029 TTATAT
1 TTATAT
26035 GAAAATATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (10 bp):
TTATATATAT
Found at i:31517 original size:18 final size:18
Alignment explanation
Indices: 31482--31537 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
31472 TATTTATGCC
*
31482 ATGTTAATATTAGT-TTTT
1 ATGTTAATATT-TTATTTT
31500 ATGTTAATATTTTATTTT
1 ATGTTAATATTTTATTTT
* *
31518 ATATT-ATGTTTTAATTTT
1 ATGTTAATATTTT-ATTTT
31536 AT
1 AT
31538 TATATCATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 7 0.21
18 26 0.79
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (18 bp):
ATGTTAATATTTTATTTT
Found at i:31878 original size:22 final size:20
Alignment explanation
Indices: 31852--31893 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
31842 GAATGCAATG
*
31852 GTAATTGAAAATTTATCAAAAT
1 GTAATT-AAAATGTAT-AAAAT
31874 GTAATTAAAATGTATAAAAT
1 GTAATTAAAATGTATAAAAT
31894 AAATTAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 8 0.42
22 6 0.32
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (20 bp):
GTAATTAAAATGTATAAAAT
Found at i:32480 original size:16 final size:18
Alignment explanation
Indices: 32449--32484 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
32439 TATTTATGTC
32449 ATATTAATATTTTTTATT
1 ATATTAATATTTTTTATT
32467 ATATT-ATA-TTTTTATT
1 ATATTAATATTTTTTATT
32483 AT
1 AT
32485 TTTTATGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 3 0.17
18 5 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATATTAATATTTTTTATT
Found at i:33419 original size:32 final size:30
Alignment explanation
Indices: 33382--33440 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 30
33372 AATTATAAAA
*
33382 AATATAAATATTAATAAAAATAATATTTTAAT
1 AATATAAATAATAAT-AAAATAA-ATTTTAAT
*
33414 AATATAATTAATAATAAAATAAATTTT
1 AATATAAATAATAATAAAATAAATTTT
33441 TAAAAAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 5 0.20
31 7 0.28
32 13 0.52
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
AATATAAATAATAATAAAATAAATTTTAAT
Found at i:33420 original size:16 final size:17
Alignment explanation
Indices: 33345--33435 Score: 61
Period size: 16 Copynumber: 5.7 Consensus size: 17
33335 TAAAGTTTAA
* *
33345 TAATAAAAATAATATTT
1 TAATAAATATAATATAT
*
33362 TATTTAAAT-TAAT-TA-
1 TA-ATAAATATAATATAT
*
33377 TAAAAAATATAA-ATAT
1 TAATAAATATAATATAT
* *
33393 TAATAAAAATAATATTT
1 TAATAAATATAATATAT
*
33410 TAAT-AATATAAT-TAA
1 TAATAAATATAATATAT
33425 TAATAAA-ATAA
1 TAATAAATATAA
33436 ATTTTTAAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
14 4 0.07
15 16 0.28
16 20 0.35
17 13 0.23
18 4 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAATAAATATAATATAT
Found at i:33448 original size:16 final size:15
Alignment explanation
Indices: 33371--33448 Score: 50
Period size: 16 Copynumber: 5.0 Consensus size: 15
33361 TTATTTAAAT
33371 TAATTA-TAAAAAATA
1 TAATTATTAAAAAA-A
*
33386 TAAATATTAATAAAAA
1 TAATTATTAA-AAAAA
* * *
33402 TAATATTTTAATAATA
1 TAAT-TATTAAAAAAA
* *
33418 TAATTAATAATAAAA
1 TAATTATTAAAAAAA
*
33433 TAAATTTTTAAAAAAA
1 T-AATTATTAAAAAAA
33449 CATAAGCATT
Statistics
Matches: 48, Mismatches: 11, Indels: 7
0.73 0.17 0.11
Matches are distributed among these distances:
15 14 0.29
16 25 0.52
17 9 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAATTATTAAAAAAA
Found at i:36205 original size:2 final size:2
Alignment explanation
Indices: 36198--36227 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
36188 CATTTGACTT
36198 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36228 ATTGCCAAGT
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):
TA
Found at i:37041 original size:5 final size:5
Alignment explanation
Indices: 37031--37083 Score: 54
Period size: 5 Copynumber: 10.6 Consensus size: 5
37021 GAGATATTCA
* * * *
37031 TAAAT TAAAT TAAAT TAAA- TAAAA AAAAT TAAAT TGAAT TGAAAT TAAGT
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT T-AAAT TAAAT
37081 TAA
1 TAA
37084 GTTGATGAGC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
4 4 0.10
5 32 0.80
6 4 0.10
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (5 bp):
TAAAT
Done.