Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2021
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: 49307
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Found at i:49 original size:24 final size:25
Alignment explanation
Indices: 13--60 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
3 ATTTCTTACC
*
13 CCTTCTCCATCCC-CCGTTTCTTTT
1 CCTTCTCCATCCCTCCCTTTCTTTT
* *
37 CCTTTTCCTTCCCTCCCTTTCTTT
1 CCTTCTCCATCCCTCCCTTTCTTT
61 GCTCTCCCCG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.02, C:0.46, G:0.02, T:0.50
Consensus pattern (25 bp):
CCTTCTCCATCCCTCCCTTTCTTTT
Found at i:409 original size:34 final size:34
Alignment explanation
Indices: 371--589 Score: 255
Period size: 34 Copynumber: 6.5 Consensus size: 34
361 GTAAAAATCA
* *
371 CCATTTAATCAGCAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
405 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* * * *
439 CCATTTAATCAACAATGGTAAGCTACCATATTTT
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
473 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
507 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * * *
541 CCATTTAATCAATAATGGTAAACTGCCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
574 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
590 TCTCCCACTT
Statistics
Matches: 157, Mismatches: 24, Indels: 9
0.83 0.13 0.05
Matches are distributed among these distances:
33 19 0.12
34 133 0.85
35 5 0.03
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:477 original size:68 final size:67
Alignment explanation
Indices: 365--589 Score: 288
Period size: 68 Copynumber: 3.3 Consensus size: 67
355 GGTTTGGTAA
* * * *
365 AAATCACCATTTAATCAGCAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCA
1 AAATCACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTA
430 CC
66 CC
* * * * *
432 AAATCACCCATTTAATCAACAATGGTAAGCTACCATATTTTCCATTTAATCAACAATGGTAAGCT
1 AAATCA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCT
497 ACC
65 ACC
* * * * * *
500 AAATCTCCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAATAATGGTAAACT
1 AAATC-ACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCT
*
565 GCC
65 ACC
568 AAATCACCATTTAATCAACAAT
1 AAATCACCATTTAATCAACAAT
590 TCTCCCACTT
Statistics
Matches: 134, Mismatches: 22, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
67 21 0.16
68 113 0.84
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
AAATCACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTA
CC
Found at i:547 original size:102 final size:101
Alignment explanation
Indices: 365--589 Score: 342
Period size: 102 Copynumber: 2.2 Consensus size: 101
355 GGTTTGGTAA
* * *
365 AAATCACCATTTAATCAGCAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCA
1 AAATCACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCA
*
430 CCAAATCACCCATTTAATCAACAATGGTAAGCTACC
66 CCAAATCACCCATTTAATCAACAATGGTAAACTACC
* ** * *
466 ATATTTTCCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACC
1 A-AATCACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACC
* *
531 ACCAAATCACCCATTTAATCAATAATGGTAAACTGCC
65 ACCAAATCACCCATTTAATCAACAATGGTAAACTACC
568 AAATCACCATTTAATCAACAAT
1 AAATCACCATTTAATCAACAAT
590 TCTCCCACTT
Statistics
Matches: 109, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
101 19 0.17
102 90 0.83
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (101 bp):
AAATCACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCA
CCAAATCACCCATTTAATCAACAATGGTAAACTACC
Found at i:4671 original size:19 final size:19
Alignment explanation
Indices: 4649--4703 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
4639 TACAGTAACC
4649 GTATACTTGAATAGTACTT
1 GTATACTTGAATAGTACTT
*
4668 GTATACGTGAATAGTACTT
1 GTATACTTGAATAGTACTT
*
4687 ATATA-TGTGAATAGTAC
1 GTATACT-TGAATAGTAC
4704 CTAGACAACC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (19 bp):
GTATACTTGAATAGTACTT
Found at i:5057 original size:34 final size:34
Alignment explanation
Indices: 5012--5227 Score: 215
Period size: 34 Copynumber: 6.4 Consensus size: 34
5002 TAAAAACTAC
* *
5012 CATTTAATCAACAATGGCAACCTACCAAATCTCT
1 CATTTAATCAACAATGGTAACCTACCAAATCACT
* * *
5046 CATTTAGTCAACAATAGTAAGCC-ACCAAATCACC
1 CATTTAATCAACAATGGTAA-CCTACCAAATCACT
* * **
5080 CATTTAATCAACAATAGTAAGCTACCAAATTTCT
1 CATTTAATCAACAATGGTAACCTACCAAATCACT
** *
5114 CATTTAATCAACAATGGTAAGTTACCAAATCTCT
1 CATTTAATCAACAATGGTAACCTACCAAATCACT
* * *
5148 CATTTAGTCAACAATGGCAAACC-ATCAAATCAC-
1 CATTTAATCAACAATGG-TAACCTACCAAATCACT
* * *
5181 CTATTAAATCAACAATGATAAACTACCAAATCAC-
1 C-ATTTAATCAACAATGGTAACCTACCAAATCACT
5215 CATTTAATCAACA
1 CATTTAATCAACA
5228 TTTTTAACAT
Statistics
Matches: 151, Mismatches: 26, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
33 16 0.11
34 131 0.87
35 4 0.03
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.26
Consensus pattern (34 bp):
CATTTAATCAACAATGGTAACCTACCAAATCACT
Found at i:5125 original size:68 final size:67
Alignment explanation
Indices: 5011--5227 Score: 240
Period size: 68 Copynumber: 3.2 Consensus size: 67
5001 GTAAAAACTA
* * *
5011 CCATTTAATCAACAATGGCAACCTACCAAATCTCTCATTTAGTCAACAATAGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATCTCTCATTTAATCAACAAT-GTAAGCTACCAAAT
5076 CAC
65 CAC
* * * * *
5079 CCATTTAATCAACAATAGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGTTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATCTCTCATTTAATCAACAAT-GTAAGCTACCAAAT
*
5144 CTC
65 CAC
* * * * * * *
5147 TCATTTAGTCAACAATGGCAAACCATCAAATCAC-CTATTAAATCAACAATGATAAACTACCAAA
1 CCATTTAATCAACAATGGCAAACTACCAAATCTCTC-ATTTAATCAACAATG-TAAGCTACCAAA
5211 TCA-
64 TCAC
5214 CCATTTAATCAACA
1 CCATTTAATCAACA
5228 TTTTTAACAT
Statistics
Matches: 123, Mismatches: 24, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
67 14 0.11
68 109 0.89
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.26
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATCTCTCATTTAATCAACAATGTAAGCTACCAAATC
AC
Found at i:5191 original size:102 final size:101
Alignment explanation
Indices: 5010--5227 Score: 303
Period size: 102 Copynumber: 2.1 Consensus size: 101
5000 GGTAAAAACT
* *
5010 ACCATTTAATCAACAATGGCAACCTACCAAATCTCTCATTTAGTCAACAATAGTAAGCCACCAAA
1 ACCATTTAATCAACAATGGCAACCTACCAAATCTCTCATTTAGTCAACAATAGCAAACCACCAAA
* * *
5075 TCACCCATTTAATCAACAAT-AGTAAGCTACCAAATT
66 TCACCCATTAAATCAACAATGA-TAAACTACCAAATC
* * ** * *
5111 TCTCATTTAATCAACAATGGTAAGTTACCAAATCTCTCATTTAGTCAACAATGGCAAACCATCAA
1 AC-CATTTAATCAACAATGGCAACCTACCAAATCTCTCATTTAGTCAACAATAGCAAACCACCAA
*
5176 ATCACCTATTAAATCAACAATGATAAACTACCAAATC
65 ATCACCCATTAAATCAACAATGATAAACTACCAAATC
5213 ACCATTTAATCAACA
1 ACCATTTAATCAACA
5228 TTTTTAACAT
Statistics
Matches: 102, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
101 14 0.14
102 87 0.85
103 1 0.01
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.26
Consensus pattern (101 bp):
ACCATTTAATCAACAATGGCAACCTACCAAATCTCTCATTTAGTCAACAATAGCAAACCACCAAA
TCACCCATTAAATCAACAATGATAAACTACCAAATC
Found at i:6442 original size:25 final size:24
Alignment explanation
Indices: 6412--6496 Score: 68
Period size: 25 Copynumber: 3.5 Consensus size: 24
6402 ATTTTCGATT
*
6412 ATATTAATGATAACAAATATAATAA
1 ATATTAATAATAA-AAATATAATAA
* * *
6437 ATATTATCACAAT-TAATTATAATAA
1 ATATTA--ATAATAAAAATATAATAA
*
6462 ATATTAATAATAAAAAAATAA-AA
1 ATATTAATAATAAAAATATAATAA
*
6485 ATTTTAA-AATAA
1 ATATTAATAATAA
6497 CTATCATAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 9
0.73 0.14 0.14
Matches are distributed among these distances:
22 5 0.10
23 12 0.25
24 6 0.12
25 22 0.46
27 3 0.06
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (24 bp):
ATATTAATAATAAAAATATAATAA
Found at i:7422 original size:14 final size:15
Alignment explanation
Indices: 7383--7423 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
7373 CTTTTATTTA
7383 TATAAATTTTAATACT
1 TATAAATTTT-ATACT
7399 T-TATAATTTTAT-CT
1 TATA-AATTTTATACT
7413 TATAAATTTTA
1 TATAAATTTTA
7424 ATATATTCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 10 0.43
15 6 0.26
16 7 0.30
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (15 bp):
TATAAATTTTATACT
Found at i:7643 original size:119 final size:118
Alignment explanation
Indices: 7428--7662 Score: 353
Period size: 119 Copynumber: 2.0 Consensus size: 118
7418 ATTTTAATAT
* * * *
7428 ATTCGTATAATTATATCATATTTATATTTATTTTTCATCTAATTTAAGTTTTAATTATTTTGTTC
1 ATTCATATAATCATATCATATTCATATTGATTTTTCATCTAATTTAAGTTTTAATTATTTTGTTC
* *
7493 AACCTAATGTATCGATCTTGTAAACTTACGAAAGTCTAATAATTCAATCTTGC
66 AACCTAATGTATCGATCTTATAAACTTACGAAAGTCCAATAATTCAATCTTGC
* * * *
7546 ATTCATATAATCATATCGTATTCATATTGATTTTTTATTTAATGTTAATTTTTAATTATTTTGTT
1 ATTCATATAATCATATCATATTCATATTGATTTTTCATCTAAT-TTAAGTTTTAATTATTTTGTT
* *
7611 CAACCTAATGTATCGATCTTATAAACTTACGAAGGTCCAATAATTCGATCTT
65 CAACCTAATGTATCGATCTTATAAACTTACGAAAGTCCAATAATTCAATCTT
7663 ACATGATTTA
Statistics
Matches: 104, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
118 36 0.35
119 68 0.65
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (118 bp):
ATTCATATAATCATATCATATTCATATTGATTTTTCATCTAATTTAAGTTTTAATTATTTTGTTC
AACCTAATGTATCGATCTTATAAACTTACGAAAGTCCAATAATTCAATCTTGC
Found at i:12861 original size:21 final size:20
Alignment explanation
Indices: 12835--12876 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
12825 TTAGGATAAA
12835 AAAATTAAAATATAAAATTTT
1 AAAATTAAAATA-AAAATTTT
*
12856 AAAATTAAAATAAAATTTTT
1 AAAATTAAAATAAAAATTTT
12876 A
1 A
12877 CTATCTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATTAAAATAAAAATTTT
Found at i:14534 original size:15 final size:15
Alignment explanation
Indices: 14510--14540 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
14500 CACAAATCAT
*
14510 ATTGTTTACAAAGCA
1 ATTGTGTACAAAGCA
14525 ATTGTGTACAAAGCA
1 ATTGTGTACAAAGCA
14540 A
1 A
14541 ATTTCAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (15 bp):
ATTGTGTACAAAGCA
Found at i:14680 original size:29 final size:29
Alignment explanation
Indices: 14626--14681 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
14616 AAACTTTAAC
* *
14626 AAAATCATCTTTAAAATCATATCAAAACA
1 AAAATCATCTTTAAAATCAAAACAAAACA
*
14655 AAAATCA-CTTTTCAAATCAAAACAAAA
1 AAAATCATC-TTTAAAATCAAAACAAAA
14682 AAATCACATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 1 0.04
29 22 0.96
ACGTcount: A:0.57, C:0.18, G:0.00, T:0.25
Consensus pattern (29 bp):
AAAATCATCTTTAAAATCAAAACAAAACA
Found at i:16394 original size:2 final size:2
Alignment explanation
Indices: 16387--16411 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16377 TATAATTGTA
16387 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 A
16412 ATCGGATGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16705 original size:24 final size:24
Alignment explanation
Indices: 16678--16725 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
16668 AAAAAATATG
16678 ATATAATATAGTTAA-ATATGATTA
1 ATATAATATAGTTAATATAT-ATTA
*
16702 ATATAATATATTTAATATATATTA
1 ATATAATATAGTTAATATATATTA
16726 TTTTTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (24 bp):
ATATAATATAGTTAATATATATTA
Found at i:16721 original size:16 final size:16
Alignment explanation
Indices: 16702--16751 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
16692 AATATGATTA
16702 ATATAATATATTTAAT
1 ATATAATATATTTAAT
* * *
16718 ATATATTATTTTTATT
1 ATATAATATATTTAAT
16734 ATATAATA-ATTT-AT
1 ATATAATATATTTAAT
16748 ATAT
1 ATAT
16752 TATTTATATT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
14 5 0.18
15 3 0.11
16 20 0.71
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATATAATATATTTAAT
Found at i:18518 original size:5 final size:5
Alignment explanation
Indices: 18502--18531 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
18492 TTTGGTGAGC
*
18502 ATATT ATGTT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT
18532 TTTCACCTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:21939 original size:17 final size:18
Alignment explanation
Indices: 21897--21941 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
21887 ACTCGTAAGG
21897 TAATATAT-TTTATTTAT
1 TAATATATATTTATTTAT
*
21914 T--TATTTATTTATTT-T
1 TAATATATATTTATTTAT
21929 TAATATATATTTA
1 TAATATATATTTA
21942 AAAATTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
15 6 0.26
16 7 0.30
17 10 0.43
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TAATATATATTTATTTAT
Found at i:22362 original size:25 final size:24
Alignment explanation
Indices: 22320--22374 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
22310 ATTTATGATA
22320 ATAATAAATATAATAAATATTATT
1 ATAATAAATATAATAAATATTATT
*
22344 ATAATTAATTATAATAAATATTA--
1 ATAA-TAAATATAATAAATATTATT
22367 ATAATAAA
1 ATAATAAA
22375 AAAAATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 3 0.11
23 4 0.14
24 4 0.14
25 17 0.61
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
ATAATAAATATAATAAATATTATT
Found at i:22370 original size:13 final size:12
Alignment explanation
Indices: 22328--22374 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
22318 TAATAATAAA
22328 TATAATAAATAT
1 TATAATAAATAT
* *
22340 TATTATAATTAAT
1 TATAATAAAT-AT
22353 TATAATAAATAT
1 TATAATAAATAT
22365 TAATAATAAA
1 T-ATAATAAA
22375 AAAAATTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TATAATAAATAT
Found at i:23109 original size:29 final size:29
Alignment explanation
Indices: 23071--23129 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
23061 ATAATATATT
23071 TAATATATATCATATTCT-TATTTATATAA
1 TAATATATATCATATT-TATATTTATATAA
* *
23100 TAATTTATATTATATTTATATTTATATAA
1 TAATATATATCATATTTATATTTATATAA
23129 T
1 T
23130 TAAGAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 1 0.04
29 26 0.96
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (29 bp):
TAATATATATCATATTTATATTTATATAA
Found at i:23890 original size:30 final size:32
Alignment explanation
Indices: 23829--23890 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
23819 TATGATTTAA
* *
23829 AAAATAAAAAATTACAATAATTACATCATAAT
1 AAAATAAAAAATTACAATAATAAAATCATAAT
23861 AAAATAAAAAA-TA-AATAAATAAAAT-ATAAT
1 AAAATAAAAAATTACAAT-AATAAAATCATAAT
23891 TACATAAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 8 0.30
31 8 0.30
32 11 0.41
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (32 bp):
AAAATAAAAAATTACAATAATAAAATCATAAT
Found at i:27357 original size:34 final size:34
Alignment explanation
Indices: 27311--27528 Score: 282
Period size: 34 Copynumber: 6.5 Consensus size: 34
27301 GTAAAAACCA
*
27311 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
27345 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
27379 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
27413 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
27446 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
27480 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
27513 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
27529 TCTCCCACTT
Statistics
Matches: 162, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 45 0.28
34 115 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:27425 original size:68 final size:67
Alignment explanation
Indices: 27309--27528 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
27299 TGGTAAAAAC
* * *
27309 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
27374 AT
66 AT
* * *
27376 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
27441 AAT
65 AAT
* * * * * *
27444 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
27509 AT
66 AT
27511 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
27529 TCTCCCACTT
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 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:31621 original size:19 final size:19
Alignment explanation
Indices: 31594--31656 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
31584 TCACGTGTAC
* *
31594 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
31613 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
31632 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
31651 AGTACC
1 AGTACC
31657 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:32008 original size:34 final size:34
Alignment explanation
Indices: 31962--32177 Score: 267
Period size: 34 Copynumber: 6.4 Consensus size: 34
31952 GTAAAAACCA
*
31962 CCATTTAATCAACAATGGCAA-CTTACCAAATCTC
1 CCATTTAATCAACAATGGTAAGC-TACCAAATCTC
* * *
31996 CCATTTAGTCAACAATGGTAAGCCACCAAATCAC
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
*
32030 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
32064 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
* * * * *
32097 CCATTTAGTCAACAATGGTAAACCACTAAATCAC
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
* * * *
32131 TCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
*
32164 CTATTTAATCAACA
1 CCATTTAATCAACA
32178 GAAAGTTGAA
Statistics
Matches: 160, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
33 40 0.25
34 119 0.74
35 1 0.01
ACGTcount: A:0.40, C:0.25, G:0.08, T:0.27
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAAGCTACCAAATCTC
Found at i:32138 original size:67 final size:67
Alignment explanation
Indices: 31960--32177 Score: 285
Period size: 67 Copynumber: 3.2 Consensus size: 67
31950 TGGTAAAAAC
* * *
31960 CACCATTTAATCAACAATGG-CAACTTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCA
1 CACCATTTAATCAACAATGGTAAAC-TACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
32024 AAT
65 AAT
* *
32027 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGTAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
32092 AAT
65 AAT
* * * * * * * *
32095 CTCCATTTAGTCAACAATGGTAAACCACTAAATCACTCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGTAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
32160 AT
66 AT
*
32162 CACTATTTAATCAACA
1 CACCATTTAATCAACA
32178 GAAAGTTGAA
Statistics
Matches: 131, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
67 71 0.54
68 58 0.44
69 2 0.02
ACGTcount: A:0.40, C:0.25, G:0.08, T:0.27
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGTAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:32867 original size:19 final size:19
Alignment explanation
Indices: 32835--32884 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
32825 AAACCTGGGG
* *
32835 AAAGAAAGAAAGAAAAAAA
1 AAAGAGAGAGAGAAAAAAA
* *
32854 AAAGAGAGAGAGAAAAGAG
1 AAAGAGAGAGAGAAAAAAA
32873 AAAGAGAGAGAG
1 AAAGAGAGAGAG
32885 TACAGTCCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
AAAGAGAGAGAGAAAAAAA
Found at i:32869 original size:15 final size:15
Alignment explanation
Indices: 32834--32881 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
32824 AAAACCTGGG
*
32834 GAAAGAAAGAAAGAAA
1 GAAA-AAAGAAAGAGA
* *
32850 AAAAAAAGAGAGAGA
1 GAAAAAAGAAAGAGA
*
32865 GAAAAGAGAAAGAGA
1 GAAAAAAGAAAGAGA
32880 GA
1 GA
32882 GAGTACAGTC
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
15 23 0.88
16 3 0.12
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (15 bp):
GAAAAAAGAAAGAGA
Found at i:37854 original size:6 final size:6
Alignment explanation
Indices: 37843--37867 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
37833 CACTTAACTG
37843 AGTCTT AGTCTT AGTCTT AGTCTT A
1 AGTCTT AGTCTT AGTCTT AGTCTT A
37868 TAATCAACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (6 bp):
AGTCTT
Found at i:48460 original size:13 final size:13
Alignment explanation
Indices: 48442--48466 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48432 GAATTAAAGA
48442 GAGAGAGAGAGAG
1 GAGAGAGAGAGAG
48455 GAGAGAGAGAGA
1 GAGAGAGAGAGA
48467 AACGCTTACA
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (13 bp):
GAGAGAGAGAGAG
Done.