Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold265
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: 864291
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
File 4 of 6
Found at i:470549 original size:19 final size:20
Alignment explanation
Indices: 470520--470557 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
470510 ATAAATAAAT
*
470520 TTTATTTATTATTTATAATG
1 TTTATTTATTATATATAATG
470540 TTTA-TTATTATATATAAT
1 TTTATTTATTATATATAAT
470558 ATCTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTATTTATTATATATAATG
Found at i:470824 original size:6 final size:6
Alignment explanation
Indices: 470813--470850 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
470803 TTTTATTAAT
*
470813 TTTATA TTTATA TTTATA TTTATA TTT-TT TTTATA TTT
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTT
470851 CAATCCTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTATA
Found at i:470895 original size:25 final size:23
Alignment explanation
Indices: 470867--470915 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 23
470857 TCAAAATTGA
470867 TTATTGTATTATTTACTTTATTTTT
1 TTATTGTATTATTT-CTTT-TTTTT
*
470892 TTATTTTATTATTTCTTTTTTTT
1 TTATTGTATTATTTCTTTTTTTT
470915 T
1 T
470916 CATTTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.26
24 4 0.17
25 13 0.57
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (23 bp):
TTATTGTATTATTTCTTTTTTTT
Found at i:470926 original size:21 final size:25
Alignment explanation
Indices: 470873--470921 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
470863 TTGATTATTG
*
470873 TATTATTTACTTTATTTTTTTATTT
1 TATTATTTACTTTATTTTTTCATTT
470898 TATTATTT-CTTT-TTTTTTCATTT
1 TATTATTTACTTTATTTTTTCATTT
470921 T
1 T
470922 TATTTGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.48
24 4 0.17
25 8 0.35
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (25 bp):
TATTATTTACTTTATTTTTTCATTT
Found at i:471548 original size:2 final size:2
Alignment explanation
Indices: 471541--471591 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
471531 ATATTGAGTT
471541 TA TA TA TA TA TA 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 TA TA TA TA TA TA
*
471583 TA TA CA TA T
1 TA TA TA TA T
471592 TCATTTTACA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:471725 original size:17 final size:17
Alignment explanation
Indices: 471703--471735 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
471693 ATGAATCAAG
471703 TTATAAATAA-AAATTTT
1 TTATAAA-AAGAAATTTT
471720 TTATAAAAAGAAATTT
1 TTATAAAAAGAAATTT
471736 ATTAAAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
TTATAAAAAGAAATTTT
Found at i:474104 original size:24 final size:23
Alignment explanation
Indices: 474068--474113 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
474058 ATAAAATATA
474068 TATTAAATTTATATATATATTAAT
1 TATTAAATTTATATATAT-TTAAT
*
474092 TATT-AATTATATATTTATTTAA
1 TATTAAATT-TATATATATTTAA
474114 AAAATAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TATTAAATTTATATATATTTAAT
Found at i:474531 original size:14 final size:14
Alignment explanation
Indices: 474514--474583 Score: 50
Period size: 16 Copynumber: 4.6 Consensus size: 14
474504 ATTTTAAATA
474514 TTAAATATATAATT
1 TTAAATATATAATT
* *
474528 TTAATAATAAATATTT
1 TT-A-AATATATAATT
*
474544 TTAAAAATATATATT
1 TTAAATATATA-ATT
474559 TATCAAATTATATAATT
1 T-T-AAA-TATATAATT
*
474576 TTTAATAT
1 TTAAATAT
474584 TTTCATTTGT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
14 11 0.26
15 7 0.16
16 13 0.30
17 7 0.16
18 5 0.12
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAAATATATAATT
Found at i:474538 original size:20 final size:21
Alignment explanation
Indices: 474503--474541 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
474493 CTATTAAAAA
*
474503 AATTTTAAATATTAAATATAT
1 AATTTTAAATAATAAATATAT
474524 AATTTT-AATAATAAATAT
1 AATTTTAAATAATAAATAT
474542 TTTTAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AATTTTAAATAATAAATATAT
Found at i:474545 original size:16 final size:16
Alignment explanation
Indices: 474516--474559 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
474506 TTTAAATATT
* *
474516 AAATATATAATTTTAA
1 AAATAAATATTTTTAA
*
474532 TAATAAATATTTTTAA
1 AAATAAATATTTTTAA
*
474548 AAATATATATTT
1 AAATAAATATTT
474560 ATCAAATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATAAATATTTTTAA
Found at i:474917 original size:16 final size:16
Alignment explanation
Indices: 474885--474916 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
474875 AAAAATAATA
474885 TAATATTTAATAATTT
1 TAATATTTAATAATTT
474901 TAATA-TTAATAATTT
1 TAATATTTAATAATTT
474916 T
1 T
474917 TTTATCGCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAATATTTAATAATTT
Found at i:475957 original size:17 final size:17
Alignment explanation
Indices: 475932--475965 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
475922 AATTTAATGA
475932 AATGATTTATGTTTATT
1 AATGATTTATGTTTATT
* *
475949 AATGCTTTATTTTTATT
1 AATGATTTATGTTTATT
475966 TGTAAAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.09, T:0.62
Consensus pattern (17 bp):
AATGATTTATGTTTATT
Found at i:476544 original size:33 final size:32
Alignment explanation
Indices: 476499--476571 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
476489 ACATAATATA
*
476499 TATATAATATAAATATAC-GAATATATCAAAATT
1 TATATAAAATAAAT-T-CTGAATATATCAAAATT
* * *
476532 TATATAAAATAAATTCTTATTATGTCAAAATT
1 TATATAAAATAAATTCTGAATATATCAAAATT
476564 TATATAAA
1 TATATAAA
476572 TTTATAATAC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 1 0.03
32 21 0.60
33 13 0.37
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (32 bp):
TATATAAAATAAATTCTGAATATATCAAAATT
Found at i:477444 original size:2 final size:2
Alignment explanation
Indices: 477437--477467 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
477427 GATTGCAATA
477437 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 A
477468 ATTGATTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:477770 original size:16 final size:16
Alignment explanation
Indices: 477747--477785 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
477737 TATTTGAGTC
*
477747 AATTTAAATTATTTTG
1 AATTTAAACTATTTTG
*
477763 AGTTTAAACTATTTTG
1 AATTTAAACTATTTTG
477779 AATTTAA
1 AATTTAA
477786 GTTAATCAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (16 bp):
AATTTAAACTATTTTG
Found at i:478135 original size:28 final size:29
Alignment explanation
Indices: 478073--478135 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
478063 AAATTAACCA
*
478073 TTAAATATATATAAAAAAAATAATATTTT
1 TTAAATATATATAAAAAAAATAATATTAT
* *
478102 TATAAATATA-ATAAAAATATTAA-ATTAAT
1 T-TAAATATATATAAAAAAAATAATATT-AT
478131 TTAAA
1 TTAAA
478136 ATTTTACATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
28 7 0.24
29 14 0.48
30 8 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
TTAAATATATATAAAAAAAATAATATTAT
Found at i:478212 original size:18 final size:18
Alignment explanation
Indices: 478186--478223 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
478176 AATAATTAAT
*
478186 TTATTAAAATCTATAAAA
1 TTATAAAAATCTATAAAA
*
478204 TTATAAAAATGTATAAAA
1 TTATAAAAATCTATAAAA
478222 TT
1 TT
478224 TACTAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (18 bp):
TTATAAAAATCTATAAAA
Found at i:479705 original size:34 final size:34
Alignment explanation
Indices: 479667--479769 Score: 197
Period size: 34 Copynumber: 3.0 Consensus size: 34
479657 CCTTTTCATG
479667 CATATGCATCAGTCAGAGCAGAAACTAACATTCT
1 CATATGCATCAGTCAGAGCAGAAACTAACATTCT
479701 CATATGCATCAGTCAGAGCAGAAACTAACATTCT
1 CATATGCATCAGTCAGAGCAGAAACTAACATTCT
*
479735 CTTATGCATCAGTCAGAGCAGAAACTAACATTCT
1 CATATGCATCAGTCAGAGCAGAAACTAACATTCT
479769 C
1 C
479770 TAAGTAAAAT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 68 1.00
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (34 bp):
CATATGCATCAGTCAGAGCAGAAACTAACATTCT
Found at i:485306 original size:2 final size:2
Alignment explanation
Indices: 485299--485329 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
485289 CCTTTTCTTG
485299 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 A
485330 CGTAAACTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:491501 original size:40 final size:40
Alignment explanation
Indices: 491456--491557 Score: 152
Period size: 40 Copynumber: 2.6 Consensus size: 40
491446 TCTCTGATTC
*
491456 AAAATCAGCAAGCAGAAAATAATACACCGGTTTCTTAATA
1 AAAATCAGCAAGTAGAAAATAATACACCGGTTTCTTAATA
* * *
491496 AAAATCAGCAAGTAGATAATAATACGCCGGTTTGTTAATA
1 AAAATCAGCAAGTAGAAAATAATACACCGGTTTCTTAATA
*
491536 AAAATCAGCGAGTAG-AAATAAT
1 AAAATCAGCAAGTAGAAAATAAT
491558 TAAGGAGTAC
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
39 6 0.11
40 50 0.89
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.24
Consensus pattern (40 bp):
AAAATCAGCAAGTAGAAAATAATACACCGGTTTCTTAATA
Found at i:492874 original size:22 final size:21
Alignment explanation
Indices: 492843--492894 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
492833 AAAGGATTTA
492843 ATTTTTATT-ATTTTATTATAT
1 ATTTTTATTAATTTT-TTATAT
492864 ATTTTTAATTAATTTTTTATAT
1 ATTTTT-ATTAATTTTTTATAT
*
492886 -TTCTTATTA
1 ATTTTTATTA
492895 TATTCAAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 4 0.14
21 10 0.36
22 9 0.32
23 5 0.18
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (21 bp):
ATTTTTATTAATTTTTTATAT
Found at i:493162 original size:12 final size:12
Alignment explanation
Indices: 493145--493178 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
493135 GGAAAAAGAT
493145 GAAGAATCAGGA
1 GAAGAATCAGGA
* *
493157 GAAGAACCATGA
1 GAAGAATCAGGA
493169 GAAGAATCAG
1 GAAGAATCAG
493179 AGGAAAGTGG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.29, T:0.09
Consensus pattern (12 bp):
GAAGAATCAGGA
Found at i:496642 original size:17 final size:17
Alignment explanation
Indices: 496620--496674 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
496610 ATCACTTAAG
*
496620 TAAATACATATTTTTAT
1 TAAATACTTATTTTTAT
* * *
496637 TAAATATTTATTATAAT
1 TAAATACTTATTTTTAT
496654 T-AATACTTATTTATTAT
1 TAAATACTTATTT-TTAT
496671 TAAA
1 TAAA
496675 ATTATATATT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
16 9 0.31
17 18 0.62
18 2 0.07
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAATACTTATTTTTAT
Found at i:496688 original size:31 final size:33
Alignment explanation
Indices: 496622--496699 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 33
496612 CACTTAAGTA
*
496622 AATACATATTTTTATTAAATATTTATTATAATT
1 AATACTTATTTTTATTAAATATTTATTATAATT
*
496655 AATACTTATTTATTATTAAA-A-TTA-TATATTT
1 AATACTTATTT-TTATTAAATATTTATTATAATT
*
496686 AATGCTTAATTTTT
1 AATACTT-ATTTTT
496700 TATTTTAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
31 14 0.35
32 7 0.17
33 11 0.28
34 8 0.20
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (33 bp):
AATACTTATTTTTATTAAATATTTATTATAATT
Found at i:499688 original size:26 final size:24
Alignment explanation
Indices: 499656--499704 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
499646 ACAAATTAAA
499656 TATTTTATTTATATTTATATTATTTT
1 TATTTTATTTA-A-TTATATTATTTT
499682 TATTTTATTTAATTATATTATTT
1 TATTTTATTTAATTATATTATTT
499705 AATTATAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 11 0.48
25 1 0.04
26 11 0.48
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (24 bp):
TATTTTATTTAATTATATTATTTT
Found at i:499710 original size:26 final size:28
Alignment explanation
Indices: 499651--499710 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 28
499641 AATTAACAAA
*
499651 TTAAATATTTTATTTATATTTATATTAT
1 TTAATTATTTTATTTATATTTATATTAT
499679 TT--TTATTTTATTTA-A-TTATATTAT
1 TTAATTATTTTATTTATATTTATATTAT
499703 TTAATTAT
1 TTAATTAT
499711 AGTGATATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
24 11 0.38
25 1 0.03
26 15 0.52
28 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (28 bp):
TTAATTATTTTATTTATATTTATATTAT
Found at i:501481 original size:31 final size:31
Alignment explanation
Indices: 501446--501521 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
501436 ATATTATAGT
*
501446 TTTTTATTTTTTAA-ATATATTTTTAATTTAA
1 TTTTTATTTATTAACATATATTTTTAA-TTAA
* *
501477 TTTTTAATTATTAACTATATTTTTTTAATTAA
1 TTTTTATTTATTAAC-ATATATTTTTAATTAA
*
501509 TTTTT-TTTGTTAA
1 TTTTTATTTATTAA
501522 TATTCTTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
31 18 0.47
32 9 0.24
33 11 0.29
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (31 bp):
TTTTTATTTATTAACATATATTTTTAATTAA
Found at i:501481 original size:32 final size:32
Alignment explanation
Indices: 501445--501514 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 32
501435 TATATTATAG
* *
501445 TTTTTTATTTTTTAA-ATATATTTTTAATTTAA
1 TTTTTTAATTATTAACATATATTTTTAA-TTAA
*
501477 -TTTTTAATTATTAACTATATTTTTTTAATTAA
1 TTTTTTAATTATTAAC-ATATATTTTTAATTAA
501509 TTTTTT
1 TTTTTT
501515 TTGTTAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
31 12 0.38
32 4 0.12
33 16 0.50
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (32 bp):
TTTTTTAATTATTAACATATATTTTTAATTAA
Found at i:501740 original size:18 final size:19
Alignment explanation
Indices: 501700--501754 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
501690 TAAGACTCAA
* **
501700 TTTATTTTTTTAAATGGGT
1 TTTATTTTTTTACATAAGT
501719 TTTATTTTTTTACATAAG-
1 TTTATTTTTTTACATAAGT
501737 TTTATTTTTTTAACATAA
1 TTTATTTTTTT-ACATAA
501755 TAATTTTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
18 11 0.34
19 21 0.66
ACGTcount: A:0.27, C:0.04, G:0.07, T:0.62
Consensus pattern (19 bp):
TTTATTTTTTTACATAAGT
Found at i:502562 original size:5 final size:5
Alignment explanation
Indices: 502552--502587 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
502542 TATTGAAATT
*
502552 AAAGA AAAGA AAAGA AAAGA ACAGA AAA-A AAAGA AA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AA
502588 TATTTAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.81, C:0.03, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:503884 original size:26 final size:25
Alignment explanation
Indices: 503855--503923 Score: 67
Period size: 26 Copynumber: 2.9 Consensus size: 25
503845 AAATAATAAT
503855 TAAAATATTATATAATATGTAATATA
1 TAAAATATTATATAATAT-TAATATA
* *
503881 TAAAATATAATGTAA-A-T-ATA-A
1 TAAAATATTATATAATATTAATATA
503902 TATAAAT-TTATATAATATTAAT
1 TA-AAATATTATATAATATTAAT
503924 TATTAATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
21 9 0.26
22 8 0.23
23 2 0.06
24 2 0.06
25 1 0.03
26 13 0.37
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (25 bp):
TAAAATATTATATAATATTAATATA
Found at i:503899 original size:11 final size:11
Alignment explanation
Indices: 503864--503973 Score: 56
Period size: 11 Copynumber: 10.5 Consensus size: 11
503854 TTAAAATATT
*
503864 ATATAATATGTA
1 ATATAATAT-AA
503876 ATAT-ATA-AA
1 ATATAATATAA
*
503885 ATATAATGTAA
1 ATATAATATAA
503896 ATATAATATAA
1 ATATAATATAA
*
503907 AT-TTATAT-A
1 ATATAATATAA
*
503916 ATATTAATTATTA
1 ATA-TAA-TATAA
*
503929 ATAT--TAAAA
1 ATATAATATAA
*
503938 ATATAA-AAAA
1 ATATAATATAA
*
503948 AT-TAATATTA
1 ATATAATATAA
**
503958 ATACGATATAA
1 ATATAATATAA
503969 ATATA
1 ATATA
503974 TATTATCATA
Statistics
Matches: 74, Mismatches: 14, Indels: 21
0.68 0.13 0.19
Matches are distributed among these distances:
9 18 0.24
10 17 0.23
11 27 0.36
12 8 0.11
13 4 0.05
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (11 bp):
ATATAATATAA
Found at i:503930 original size:13 final size:15
Alignment explanation
Indices: 503862--503935 Score: 64
Period size: 16 Copynumber: 4.9 Consensus size: 15
503852 AATTAAAATA
503862 TTATATAATATGTAAT
1 TTATATAATAT-TAAT
* *
503878 ATATAAAATA-TAAT
1 TTATATAATATTAAT
* *
503892 GTAAATATAATATAAAT
1 -T-TATATAATATTAAT
503909 TTATATAATATTAA-
1 TTATATAATATTAAT
503923 TTAT-TAATATTAA
1 TTATATAATATTAA
503936 AAATATAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
13 9 0.19
14 8 0.17
15 11 0.23
16 16 0.34
17 3 0.06
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
TTATATAATATTAAT
Found at i:504032 original size:12 final size:12
Alignment explanation
Indices: 504015--504039 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
504005 TTAATCTTGC
504015 TATTTTTTTTTT
1 TATTTTTTTTTT
504027 TATTTTTTTTTT
1 TATTTTTTTTTT
504039 T
1 T
504040 CTCTTTTTTA
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:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (12 bp):
TATTTTTTTTTT
Found at i:504124 original size:14 final size:14
Alignment explanation
Indices: 504086--504131 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
504076 CTCAAAATAT
**
504086 TAAA-TTAATTTTT
1 TAAATTTAATTTAA
504099 TAAATTTAAATTTAA
1 TAAATTT-AATTTAA
504114 TAAATTTAATTTAA
1 TAAATTTAATTTAA
504128 TAAA
1 TAAA
504132 AAAATATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 4 0.14
14 13 0.45
15 12 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAAATTTAATTTAA
Found at i:504221 original size:15 final size:14
Alignment explanation
Indices: 504182--504231 Score: 68
Period size: 15 Copynumber: 3.6 Consensus size: 14
504172 ATAATTACTT
504182 TTAA-TAAATTTAA
1 TTAATTAAATTTAA
*
504195 AT-ATTAAATTTAA
1 TTAATTAAATTTAA
504208 TTAATTATAATTTAA
1 TTAATTA-AATTTAA
504223 TTAATTAAA
1 TTAATTAAA
504232 ATAATTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 1 0.03
13 11 0.34
14 6 0.19
15 14 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTAATTAAATTTAA
Found at i:504262 original size:18 final size:19
Alignment explanation
Indices: 504214--504265 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
504204 TTAATTAATT
*
504214 ATAATTTAATTAA-TTAAA
1 ATAATTTAAATAATTTAAA
*
504232 ATAATTT-AA-AATTTTAA
1 ATAATTTAAATAATTTAAA
504249 A-AATTTAAATAATTTAA
1 ATAATTTAAATAATTTAA
504266 CTCAACTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 7 0.25
17 8 0.29
18 13 0.46
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAATTTAAATAATTTAAA
Found at i:508009 original size:32 final size:33
Alignment explanation
Indices: 507973--508043 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 33
507963 TATTTTATAT
*
507973 TTATATAAAATTTAATATATTAGTA-ATTCGTA
1 TTATATAAAATTTAAGATATTAGTATATTCGTA
* * * *
508005 TTATATAAATTTTGAGATATTCGTATATTCTTA
1 TTATATAAAATTTAAGATATTAGTATATTCGTA
508038 TTATAT
1 TTATAT
508044 TTTATTTTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
32 21 0.64
33 12 0.36
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (33 bp):
TTATATAAAATTTAAGATATTAGTATATTCGTA
Found at i:509776 original size:3 final size:3
Alignment explanation
Indices: 509768--509808 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
509758 GTTAATTTTA
509768 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
509809 ATAACTAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:510166 original size:52 final size:52
Alignment explanation
Indices: 510104--510205 Score: 161
Period size: 52 Copynumber: 2.0 Consensus size: 52
510094 TTAATAAATA
*
510104 TTTAGTTAGTATTTAAAGGTATTAATTAATCA-AATTTTTTATTAATTAATTT
1 TTTAGCTAGTATTTAAAGGTATTAATTAAT-AGAATTTTTTATTAATTAATTT
* *
510156 TTTAGCTAGTATTTATAGGTATTCATTAATAGAATTTTTTATTAATTAAT
1 TTTAGCTAGTATTTAAAGGTATTAATTAATAGAATTTTTTATTAATTAAT
510206 AAAATAAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 1 0.02
52 45 0.98
ACGTcount: A:0.35, C:0.03, G:0.09, T:0.53
Consensus pattern (52 bp):
TTTAGCTAGTATTTAAAGGTATTAATTAATAGAATTTTTTATTAATTAATTT
Found at i:510827 original size:21 final size:20
Alignment explanation
Indices: 510803--510851 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
510793 TGAGTTTAAA
510803 TTAATTTAAATTTAAAATTTT
1 TTAATTTAAATTTAAAA-TTT
* * *
510824 TTAAATT-ATTTTTAAATTT
1 TTAATTTAAATTTAAAATTT
510843 TTAATTTAA
1 TTAATTTAA
510852 TTAAATTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 9 0.39
20 8 0.35
21 6 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTAATTTAAATTTAAAATTT
Found at i:511076 original size:30 final size:29
Alignment explanation
Indices: 511004--511073 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 29
510994 AATATGATAA
* *
511004 TTTATGTAT-TTAT-ATAATATTTATATAT
1 TTTAT-TATATTATAATTATATTTAAATAT
511032 TTTATTATATTATAATTATATTTAAAGTAT
1 TTTATTATATTATAATTATATTTAAA-TAT
511062 TTTA-TAT-TTATA
1 TTTATTATATTATA
511074 TAAAATTTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
27 3 0.08
28 14 0.38
29 13 0.35
30 7 0.19
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (29 bp):
TTTATTATATTATAATTATATTTAAATAT
Found at i:511145 original size:12 final size:12
Alignment explanation
Indices: 511121--511197 Score: 75
Period size: 12 Copynumber: 6.3 Consensus size: 12
511111 TTTAAGATAT
511121 TTATATATTTATA
1 TTATAT-TTTATA
511134 TTATATTTTATA
1 TTATATTTTATA
511146 TTATATTTTAT-
1 TTATATTTTATA
* *
511157 TTATTTTTTATG
1 TTATATTTTATA
* *
511169 TTATATAATCATA
1 TTATAT-TTTATA
* *
511182 TTATGTTTAATA
1 TTATATTTTATA
511194 TTAT
1 TTAT
511198 CAAATTTAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
11 10 0.19
12 30 0.56
13 14 0.26
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (12 bp):
TTATATTTTATA
Found at i:511149 original size:17 final size:19
Alignment explanation
Indices: 511003--511174 Score: 94
Period size: 18 Copynumber: 9.1 Consensus size: 19
510993 AAATATGATA
* *
511003 ATTTATGTATTTATATAAT
1 ATTTATATATTTATATTAT
511022 ATTTATATATTT-TATTAT
1 ATTTATATATTTATATTAT
511040 A-TTATA-A-TTATATTTAAAGT
1 ATTTATATATTTATA-TT--A-T
* *
511060 ATTT-TATATTTATATAAA
1 ATTTATATATTTATATTAT
*
511078 ATTTGATA-AGTTAATAATTTAT
1 ATTT-ATATA-TTTAT-A-TTAT
* **
511100 ATTATATAAATTT-TAAGAT
1 ATT-TATATATTTATATTAT
511119 ATTTATATATTTATATTAT
1 ATTTATATATTTATATTAT
*
511138 ATTT-TATA-TTATATTTT
1 ATTTATATATTTATATTAT
* *
511155 ATTTAT-TTTTTATGTTAT
1 ATTTATATATTTATATTAT
511173 AT
1 AT
511175 AATCATATTA
Statistics
Matches: 118, Mismatches: 17, Indels: 37
0.69 0.10 0.22
Matches are distributed among these distances:
15 2 0.02
16 3 0.03
17 20 0.17
18 32 0.27
19 27 0.23
20 11 0.09
21 6 0.05
22 15 0.13
23 2 0.02
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
ATTTATATATTTATATTAT
Found at i:511160 original size:23 final size:25
Alignment explanation
Indices: 511121--511174 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
511111 TTTAAGATAT
511121 TTATATATTTATATTATAT-TTTATA
1 TTATAT-TTTATATTATATATTTATA
* *
511146 TTATATTTTAT-TTAT-TTTTTATG
1 TTATATTTTATATTATATATTTATA
511169 TTATAT
1 TTATAT
511175 AATCATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 1 0.04
23 15 0.56
24 5 0.19
25 6 0.22
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (25 bp):
TTATATTTTATATTATATATTTATA
Found at i:511739 original size:18 final size:18
Alignment explanation
Indices: 511716--511753 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
511706 ATGCTGTAAT
511716 ATTATAT-ATATAATAAAA
1 ATTATATAATAT-ATAAAA
511734 ATTATATAATATATAAAA
1 ATTATATAATATATAAAA
511752 AT
1 AT
511754 ATAAAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATTATATAATATATAAAA
Found at i:511745 original size:23 final size:24
Alignment explanation
Indices: 511714--511774 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
511704 TTATGCTGTA
*
511714 ATATTATATATATAATA-AAAATT
1 ATATAATATATATAATATAAAATT
*
511737 ATATAATATATAAAAATATAAAATT
1 ATATAATATAT-ATAATATAAAATT
511762 A-A-AATATACTATA
1 ATATAATATA-TATA
511775 TAATTGTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
23 18 0.56
24 7 0.22
25 7 0.22
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
ATATAATATATATAATATAAAATT
Found at i:511995 original size:16 final size:16
Alignment explanation
Indices: 511969--512018 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
511959 TATTATTTTT
511969 AAAAT-AAAAAATATA
1 AAAATAAAAAAATATA
511984 AAAATAAAAAAATCAT-
1 AAAATAAAAAAAT-ATA
**
512000 ATCATAAAATAAATATA
1 AAAATAAAA-AAATATA
512017 AA
1 AA
512019 GATTAGTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 5 0.18
16 16 0.57
17 7 0.25
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAATAAAAAAATATA
Found at i:512353 original size:2 final size:2
Alignment explanation
Indices: 512346--512374 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
512336 GTTGGCTTCA
512346 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
512375 CGCTGCAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:518585 original size:21 final size:23
Alignment explanation
Indices: 518559--518600 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
518549 ATACAACAAT
518559 TTTATA-AGAAAAAA-TAAAATA
1 TTTATATAGAAAAAATTAAAATA
*
518580 TTTATATTGAAAAAATTAAAA
1 TTTATATAGAAAAAATTAAAA
518601 AAATATTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 7 0.39
23 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (23 bp):
TTTATATAGAAAAAATTAAAATA
Found at i:519139 original size:31 final size:30
Alignment explanation
Indices: 519078--519137 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
519068 TTTCGTAGGC
519078 AAGTCTGGTCTAATTAGTATTTGTTTTTTT
1 AAGTCTGGTCTAATTAGTATTTGTTTTTTT
*
519108 AAGTCTGGTCTAATTTGTATTTGTTTTTTT
1 AAGTCTGGTCTAATTAGTATTTGTTTTTTT
519138 TAGTAAGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.18, C:0.07, G:0.17, T:0.58
Consensus pattern (30 bp):
AAGTCTGGTCTAATTAGTATTTGTTTTTTT
Found at i:519293 original size:23 final size:23
Alignment explanation
Indices: 519253--519296 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
519243 AAATTATAAA
519253 TATTAAAATTTAAATTTTAAATT
1 TATTAAAATTTAAATTTTAAATT
*
519276 TATTAAATATTT-ATTTTTAAA
1 TATTAAA-ATTTAAATTTTAAA
519297 AGTGATTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAAAATTTAAATTTTAAATT
Found at i:522865 original size:3 final size:3
Alignment explanation
Indices: 522857--522885 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
522847 TGAAAACAAA
522857 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
522886 AGAACTGCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:524400 original size:18 final size:18
Alignment explanation
Indices: 524377--524415 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
524367 ATTCCAATTC
*
524377 TTTTTTTTTCTTTTTTCT
1 TTTTTTTTTCTTTTTTAT
524395 TTTTTTTTTCTTTTTTAT
1 TTTTTTTTTCTTTTTTAT
524413 TTT
1 TTT
524416 CCATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.90
Consensus pattern (18 bp):
TTTTTTTTTCTTTTTTAT
Found at i:524401 original size:11 final size:11
Alignment explanation
Indices: 524377--524416 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
524367 ATTCCAATTC
*
524377 TTTTTT-TTTC
1 TTTTTTCTTTT
524387 TTTTTTCTTTT
1 TTTTTTCTTTT
524398 TTTTTTCTTTT
1 TTTTTTCTTTT
524409 TTATTTTC
1 TT-TTTTC
524417 CATTTATTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 6 0.22
11 16 0.59
12 5 0.19
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:524678 original size:31 final size:30
Alignment explanation
Indices: 524631--524704 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
524621 ATCTGTTAAA
*
524631 TTAAATTAATTTTTATATAATTTATA-TTTAT
1 TTAAATTAATTATTATAT--TTTATATTTTAT
*
524662 TTAATTTAATTATTATATTTTATATTTTAT
1 TTAAATTAATTATTATATTTTATATTTTAT
* *
524692 TTATATAAATTAT
1 TTAAATTAATTAT
524705 GCATATTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 6 0.16
30 15 0.41
31 16 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
TTAAATTAATTATTATATTTTATATTTTAT
Found at i:524844 original size:9 final size:9
Alignment explanation
Indices: 524830--524872 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
524820 AATTAAATTA
524830 TTTTTATAT
1 TTTTTATAT
*
524839 TTTTTATAA
1 TTTTTATAT
524848 TTTTTATAT
1 TTTTTATAT
**
524857 AATTTATAT
1 TTTTTATAT
524866 TTGTTTA
1 TT-TTTA
524873 AATTAATTGT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
9 23 0.85
10 4 0.15
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (9 bp):
TTTTTATAT
Found at i:524852 original size:37 final size:38
Alignment explanation
Indices: 524783--524860 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 38
524773 TTAAATATTT
*
524783 ATTAAATTAGTTTTATATATTTTTATAGTTTTTATAAA
1 ATTAAATTAGTTTTATATATTTTTATAATTTTTATAAA
* *
524821 ATTAAATTATTTTTATAT-TTTTTATAATTTTTATATA
1 ATTAAATTAGTTTTATATATTTTTATAATTTTTATAAA
524858 ATT
1 ATT
524861 TATATTTGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
37 20 0.54
38 17 0.46
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (38 bp):
ATTAAATTAGTTTTATATATTTTTATAATTTTTATAAA
Found at i:525339 original size:22 final size:22
Alignment explanation
Indices: 525281--525344 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
525271 TTTATCAAAC
*
525281 AATCATATATATTTAATAATTT
1 AATCATATATATTTAATAAATT
* *
525303 TATCA-A-A-ATTT--TAAAAT
1 AATCATATATATTTAATAAATT
525320 AATCATATATATTTAATAAATT
1 AATCATATATATTTAATAAATT
525342 AAT
1 AAT
525345 ATTTGTTGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 10
0.68 0.11 0.21
Matches are distributed among these distances:
17 8 0.25
18 1 0.03
19 5 0.16
20 5 0.16
21 1 0.03
22 12 0.38
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (22 bp):
AATCATATATATTTAATAAATT
Found at i:525389 original size:25 final size:22
Alignment explanation
Indices: 525361--525405 Score: 63
Period size: 25 Copynumber: 1.9 Consensus size: 22
525351 TGTTTTAAAA
525361 TTATAAAATATTAAGTTTATTTAAT
1 TTATAAAAT-TT-AG-TTATTTAAT
525386 TTATAAAATTTAGTTATTTA
1 TTATAAAATTTAGTTATTTA
525406 TTTGGAGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 2 0.10
25 9 0.45
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (22 bp):
TTATAAAATTTAGTTATTTAAT
Found at i:526584 original size:3 final size:3
Alignment explanation
Indices: 526576--526626 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
526566 TTATTAAGAC
526576 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
526624 AAT
1 AAT
526627 CTAATATAGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:526949 original size:48 final size:45
Alignment explanation
Indices: 526836--526953 Score: 121
Period size: 48 Copynumber: 2.5 Consensus size: 45
526826 TCATTTAATA
*
526836 ATGGGATAATATTTAATGCACTTATGTATAAATATATTAAAATTT
1 ATGGGATAATATTTAATGCACTTATGTATAAATATATTAAAACTT
** * *
526881 AT-TAAAAATTATTTAATAATGCACTTATGTATAAATATATTTAATGCACTT
1 ATGGGATAA-TA-TT--TAATGCACTTATGTATAAATATA-TTAA--AACTT
526932 ATGGGATAATATTTAATGCACT
1 ATGGGATAATATTTAATGCACT
526954 CATTTAATAA
Statistics
Matches: 57, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
44 3 0.05
45 4 0.07
46 2 0.04
48 32 0.56
49 4 0.07
50 2 0.04
51 7 0.12
52 3 0.05
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.42
Consensus pattern (45 bp):
ATGGGATAATATTTAATGCACTTATGTATAAATATATTAAAACTT
Found at i:526970 original size:31 final size:33
Alignment explanation
Indices: 526932--527008 Score: 122
Period size: 31 Copynumber: 2.4 Consensus size: 33
526922 TAATGCACTT
526932 ATGGGATAATATTTAATGCACTCAT-T-TAATA
1 ATGGGATAATATTTAATGCACTCATGTATAATA
*
526963 ATGGGATAATATTTAATGCACTTATGTATAATA
1 ATGGGATAATATTTAATGCACTCATGTATAATA
*
526996 ATGGGATTATATT
1 ATGGGATAATATT
527009 AATTTATTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
31 24 0.57
32 1 0.02
33 17 0.40
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.40
Consensus pattern (33 bp):
ATGGGATAATATTTAATGCACTCATGTATAATA
Found at i:528700 original size:14 final size:15
Alignment explanation
Indices: 528683--528750 Score: 61
Period size: 16 Copynumber: 4.5 Consensus size: 15
528673 TTATTATTTT
*
528683 TAAATATGAT-TATA
1 TAAATATAATATATA
528697 TAAATATAATATATA
1 TAAATATAATATATA
*
528712 TAAAATATAAAATATA
1 T-AAATATAATATATA
*
528728 TGATATATTAA-AT-TA
1 T-AAATA-TAATATATA
528743 TAAATATA
1 TAAATATA
528751 TATTTTAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
13 2 0.04
14 13 0.28
15 8 0.17
16 20 0.43
17 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
TAAATATAATATATA
Found at i:528714 original size:9 final size:9
Alignment explanation
Indices: 528700--528845 Score: 50
Period size: 8 Copynumber: 17.3 Consensus size: 9
528690 GATTATATAA
528700 ATATAATAT
1 ATATAATAT
528709 ATATAA-A-
1 ATATAATAT
*
528716 ATATAAAAT
1 ATATAATAT
*
528725 ATATGATAT
1 ATATAATAT
528734 AT-TAA-AT
1 ATATAATAT
528741 -TATAA-AT
1 ATATAATAT
528748 ATAT-AT-T
1 ATATAATAT
* * *
528755 TTAAAATTT
1 ATATAATAT
528764 ATATAATAT
1 ATATAATAT
*
528773 A-A-ATTAT
1 ATATAATAT
*
528780 A-AAAATAT
1 ATATAATAT
* *
528788 -TAAAATTT
1 ATATAATAT
528796 ATATAA-AT
1 ATATAATAT
*
528804 ATATAAAAT
1 ATATAATAT
*
528813 ATTTTAAATAT
1 A-TAT-AATAT
528824 AATTATAATAT
1 -A-TATAATAT
*
528835 A-ATAAAAT
1 ATATAATAT
528843 ATA
1 ATA
528846 CACAATCGCA
Statistics
Matches: 105, Mismatches: 17, Indels: 30
0.69 0.11 0.20
Matches are distributed among these distances:
6 1 0.01
7 23 0.22
8 34 0.32
9 31 0.30
10 3 0.03
11 9 0.09
12 4 0.04
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.42
Consensus pattern (9 bp):
ATATAATAT
Found at i:528730 original size:39 final size:39
Alignment explanation
Indices: 528686--528845 Score: 112
Period size: 46 Copynumber: 3.9 Consensus size: 39
528676 TTATTTTTAA
528686 ATATGATTATATAAATAT-AATATATATAAAATATAAAAT
1 ATATGA-TATATAAATATAAATATATATAAAATATAAAAT
*
528725 ATATGATATATTAAATTATAAATATATATTTTAAAATTTATATAAT
1 ATATGATATA-TAAA-TATAAATATATA---TAAAA--TATAAAAT
* * *
528771 ATA-AATTATAAAAATATTAAAATTTATATAAATATATAAAAT
1 ATATGA-TATATAAATA-T-AAATATATATAAA-ATATAAAAT
* * * *
528813 ATTTTAAATATAATTAT-AATATA-ATAAAATATA
1 ATATGATATATAAATATAAATATATATAAAATATA
528846 CACAATCGCA
Statistics
Matches: 97, Mismatches: 11, Indels: 28
0.71 0.08 0.21
Matches are distributed among these distances:
37 5 0.05
38 9 0.09
39 15 0.15
40 3 0.03
41 9 0.09
42 16 0.16
43 5 0.05
44 8 0.08
45 5 0.05
46 22 0.23
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (39 bp):
ATATGATATATAAATATAAATATATATAAAATATAAAAT
Found at i:528767 original size:32 final size:31
Alignment explanation
Indices: 528730--528820 Score: 91
Period size: 36 Copynumber: 2.9 Consensus size: 31
528720 AAAATATATG
528730 ATATATTAAATTATAAATATATATTTTAAAATTT
1 ATATATTAAATTATAAA-ATATA--TTAAAATTT
528764 ATATAATATAAATTATAAAA-ATATTAAAA-TT
1 ATAT-AT-TAAATTATAAAATATATTAAAATTT
*
528795 -TATA-TAAATATATAAAATATTTTAAA
1 ATATATTAAAT-TATAAAATATATTAAA
528821 TATAATTATA
Statistics
Matches: 52, Mismatches: 1, Indels: 13
0.79 0.02 0.20
Matches are distributed among these distances:
27 5 0.10
28 7 0.13
29 8 0.15
30 3 0.06
31 2 0.04
32 6 0.12
34 7 0.13
35 3 0.06
36 11 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
ATATATTAAATTATAAAATATATTAAAATTT
Found at i:531448 original size:37 final size:38
Alignment explanation
Indices: 531422--531494 Score: 105
Period size: 37 Copynumber: 1.9 Consensus size: 38
531412 TTTGATAATT
* *
531422 TTAAATATGATAT-AAAAATATTATAAA-ATATAATATA
1 TTAAATA-AATATAAAAAATATAATAAATATATAATATA
531459 TTAAATAAATATAAAAAATATAATAAATATATAATA
1 TTAAATAAATATAAAAAATATAATAAATATATAATA
531495 AGATGTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 4 0.12
37 20 0.62
38 8 0.25
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (38 bp):
TTAAATAAATATAAAAAATATAATAAATATATAATATA
Found at i:531477 original size:9 final size:9
Alignment explanation
Indices: 531431--531489 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
531421 TTTAAATATG
531431 ATAT-AAAA
1 ATATAAAAA
*
531439 ATATTATAAA
1 ATA-TAAAAA
* *
531449 ATATAATAT
1 ATATAAAAA
531458 AT-TAAATAA
1 ATATAAA-AA
531467 ATATAAAAA
1 ATATAAAAA
*
531476 ATATAATAA
1 ATATAAAAA
531485 ATATA
1 ATATA
531490 TAATAAGATG
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
8 6 0.15
9 24 0.60
10 10 0.25
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
ATATAAAAA
Found at i:531493 original size:11 final size:10
Alignment explanation
Indices: 531436--531495 Score: 63
Period size: 10 Copynumber: 6.2 Consensus size: 10
531426 ATATGATATA
*
531436 AAAATATTAT
1 AAAATATAAT
531446 AAAATATAAT
1 AAAATATAAT
* *
531456 ATATTA-AAT
1 AAAATATAAT
531465 -AAATATAA-
1 AAAATATAAT
531473 AAAATATAAT
1 AAAATATAAT
531483 AAATATATAAT
1 AAA-ATATAAT
531494 AA
1 AA
531496 GATGTTTAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
8 3 0.07
9 13 0.32
10 16 0.39
11 9 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAATATAAT
Found at i:533064 original size:13 final size:13
Alignment explanation
Indices: 533037--533074 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
533027 AATGAAAAAT
533037 TATTTTAATAATTA
1 TATTTTAA-AATTA
533051 TATTTTAAAATTA
1 TATTTTAAAATTA
533064 TATTTTTAAAA
1 TA-TTTTAAAA
533075 AGTTTTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTTTAAAATTA
Found at i:534827 original size:22 final size:21
Alignment explanation
Indices: 534802--534843 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
534792 TAAATATTAT
534802 TTAATAAAAATAATTATATAAA
1 TTAATAAAAATAA-TATATAAA
*
534824 TTAATCAAAATAATATATAA
1 TTAATAAAAATAATATATAA
534844 CGACTTGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
TTAATAAAAATAATATATAAA
Found at i:535671 original size:16 final size:16
Alignment explanation
Indices: 535634--535718 Score: 59
Period size: 16 Copynumber: 5.3 Consensus size: 16
535624 TAAATTTGTT
535634 TGATCTAAACTCAAAA
1 TGATCTAAACTCAAAA
* *
535650 TAATCTAAACTCAGAA
1 TGATCTAAACTCAAAA
* *
535666 TGATCTGAA-TACGAAA
1 TGATCTAAACT-CAAAA
* *
535682 TGA-CTCCAACCCAAAA
1 TGATCT-AAACTCAAAA
*
535698 TGA-CTTAAATTCAAAA
1 TGATC-TAAACTCAAAA
535714 TGATC
1 TGATC
535719 AGAACTTGAA
Statistics
Matches: 52, Mismatches: 12, Indels: 9
0.71 0.16 0.12
Matches are distributed among these distances:
15 3 0.06
16 47 0.90
17 2 0.04
ACGTcount: A:0.46, C:0.20, G:0.09, T:0.25
Consensus pattern (16 bp):
TGATCTAAACTCAAAA
Found at i:536053 original size:45 final size:45
Alignment explanation
Indices: 535997--536135 Score: 278
Period size: 45 Copynumber: 3.1 Consensus size: 45
535987 TAAAAATAAA
535997 ATTTTAAATATATTGTATTGATGTGAAAAATTATATCTTTAAAAT
1 ATTTTAAATATATTGTATTGATGTGAAAAATTATATCTTTAAAAT
536042 ATTTTAAATATATTGTATTGATGTGAAAAATTATATCTTTAAAAT
1 ATTTTAAATATATTGTATTGATGTGAAAAATTATATCTTTAAAAT
536087 ATTTTAAATATATTGTATTGATGTGAAAAATTATATCTTTAAAAT
1 ATTTTAAATATATTGTATTGATGTGAAAAATTATATCTTTAAAAT
536132 ATTT
1 ATTT
536136 CAGGGCAAGA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 94 1.00
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (45 bp):
ATTTTAAATATATTGTATTGATGTGAAAAATTATATCTTTAAAAT
Found at i:539285 original size:2 final size:2
Alignment explanation
Indices: 539278--539325 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
539268 TTATTCACTA
* * * *
539278 AT AT AT AT AT AT AT AT AC AT AT AT AC AT AT AC AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
539320 AT AT AT
1 AT AT AT
539326 GTTATGTTGG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:539318 original size:102 final size:102
Alignment explanation
Indices: 539192--539402 Score: 386
Period size: 102 Copynumber: 2.1 Consensus size: 102
539182 ATTTACATAC
*
539192 ACATATATACATATACATCTATATGTATATATGTTATGTTGGGTCACACTCACTGCGTTTTGCTT
1 ACATATATACATATACATATATATGTATATATGTTATGTTGGGTCACACTCACTGCGTTTTGCTT
*
539257 GTTCACAAGTCTTATTCACTAATATATATATATATAT
66 GTTCACAAGTCTTACTCACTAATATATATATATATAT
539294 ACATATATACATATACATATATATGTATATATGTTATGTTGGGTCACACTCACTGCGTTTTGCTT
1 ACATATATACATATACATATATATGTATATATGTTATGTTGGGTCACACTCACTGCGTTTTGCTT
*
539359 GTTTACAAGTCTTACTCACTAATATATATATATATAT
66 GTTCACAAGTCTTACTCACTAATATATATATATATAT
*
539396 ATATATA
1 ACATATA
539403 GGACTGGTGA
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 105 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (102 bp):
ACATATATACATATACATATATATGTATATATGTTATGTTGGGTCACACTCACTGCGTTTTGCTT
GTTCACAAGTCTTACTCACTAATATATATATATATAT
Found at i:540720 original size:13 final size:14
Alignment explanation
Indices: 540701--540731 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
540691 ATTGCCTGAG
*
540701 TTTTTTTTTTTAAA
1 TTTTTTTATTTAAA
540715 TTTTTTTATTTAAA
1 TTTTTTTATTTAAA
540729 TTT
1 TTT
540732 GCATCATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTTTATTTAAA
Found at i:540822 original size:26 final size:26
Alignment explanation
Indices: 540773--540824 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
540763 TTTATTTTTC
** *
540773 ATAATTATATTAAAATTTATATATTT
1 ATAATTATATTAAAATAAAAATATTT
*
540799 ATAATTATATTTAAATAAAAATATTT
1 ATAATTATATTAAAATAAAAATATTT
540825 TTTATTAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
ATAATTATATTAAAATAAAAATATTT
Found at i:542316 original size:16 final size:16
Alignment explanation
Indices: 542298--542331 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
542288 ATTTATTTAT
542298 TTTTTA-AATTTAAT-
1 TTTTTATAATTTAATA
542312 TTTTTATAATTTAATA
1 TTTTTATAATTTAATA
542328 TTTT
1 TTTT
542332 AATTTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 8 0.44
16 4 0.22
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTATAATTTAATA
Found at i:542317 original size:21 final size:23
Alignment explanation
Indices: 542288--542349 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 23
542278 ATATTATATT
542288 ATTTATTTATTTTTTAA-A-TTTA
1 ATTT-TTTATTTTTTAATATTTTA
**
542310 ATTTTTTATAATTTAATATTTTA
1 ATTTTTTATTTTTTAATATTTTA
542333 ATTTTATTATTTTTTAA
1 ATTTT-TTATTTTTTAA
542350 CATATAACCA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.30
22 5 0.15
23 9 0.27
24 9 0.27
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (23 bp):
ATTTTTTATTTTTTAATATTTTA
Found at i:542322 original size:15 final size:14
Alignment explanation
Indices: 542292--542349 Score: 64
Period size: 14 Copynumber: 4.0 Consensus size: 14
542282 TATATTATTT
542292 ATTT-ATTTTTTAA
1 ATTTAATTTTTTAA
542305 ATTTAATTTTTTATA
1 ATTTAATTTTTTA-A
*
542320 ATTTAATATTTTAA
1 ATTTAATTTTTTAA
*
542334 TTTTATTATTTTTTAA
1 ATTTA--ATTTTTTAA
542350 CATATAACCA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
13 4 0.11
14 13 0.34
15 13 0.34
16 8 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTTAATTTTTTAA
Found at i:542439 original size:19 final size:21
Alignment explanation
Indices: 542410--542456 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
542400 TTTTATTTTT
542410 ATATAATAAAAAT-T-AAA-TA
1 ATAT-ATAAAAATATAAAATTA
542429 ATATATAAAAATATAAAATTA
1 ATATATAAAAATATAAAATTA
542450 ATATATA
1 ATATATA
542457 TTATATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.32
19 5 0.20
20 3 0.12
21 9 0.36
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
ATATATAAAAATATAAAATTA
Found at i:542461 original size:26 final size:25
Alignment explanation
Indices: 542414--542477 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 25
542404 ATTTTTATAT
542414 AATAAAAATTAA-ATAATATATAAA
1 AATAAAAATTAATATAATATATAAA
*
542438 AATATAAAATTAATAT-ATATTATATA
1 AATA-AAAATTAATATAATA-TATAAA
*
542464 ATTAAAAAATTAAT
1 AAT-AAAAATTAAT
542478 TAAATTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 4 0.12
25 11 0.32
26 18 0.53
27 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
AATAAAAATTAATATAATATATAAA
Found at i:542767 original size:24 final size:24
Alignment explanation
Indices: 542734--542788 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
542724 TATTTTTATT
542734 TAAAT-TTAATTATAAAA-AATATA
1 TAAATATTAATTA-AAAATAATATA
* *
542757 TAAATATTAATTAAAAATAATTTT
1 TAAATATTAATTAAAAATAATATA
542781 TAAATATT
1 TAAATATT
542789 TTATTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 9 0.32
24 19 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TAAATATTAATTAAAAATAATATA
Found at i:542966 original size:17 final size:18
Alignment explanation
Indices: 542935--542972 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
542925 AACTTTTATT
*
542935 TTTTTAATAAATTATTTA
1 TTTTTAATAAATTATATA
*
542953 TTTTTAA-AATTTATATA
1 TTTTTAATAAATTATATA
542970 TTT
1 TTT
542973 ATATTTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTAATAAATTATATA
Found at i:543360 original size:74 final size:74
Alignment explanation
Indices: 543239--543460 Score: 389
Period size: 74 Copynumber: 3.0 Consensus size: 74
543229 GATTAACGAA
543239 ATAACAGGAAGATGGAGCAACTGTCGACAACTACAGTATTGTAACGAGCTCCAGCATGCATCTCC
1 ATAACAGGAAGATGGAGCAACTGTCGACAACTACAGTATTGTAACGAGCTCCAGCATGCATCTCC
543304 TCTTTGTTC
66 TCTTTGTTC
543313 ATAACAGGAAGATGGAGCAACTGTCGACAACTACAGTATTGTAACGAGCT-C--CATGCATCTCC
1 ATAACAGGAAGATGGAGCAACTGTCGACAACTACAGTATTGTAACGAGCTCCAGCATGCATCTCC
543375 TCTTTGTTC
66 TCTTTGTTC
* *
543384 ATAACAGGAAGATGGAGCAACTGTCGACAA-TACCAATATAGTAACGAGCTCCAGCATGCATCTC
1 ATAACAGGAAGATGGAGCAACTGTCGACAACTA-CAGTATTGTAACGAGCTCCAGCATGCATCTC
543448 CTCTTTGTTC
65 CTCTTTGTTC
543458 ATA
1 ATA
543461 GCAAAAGACT
Statistics
Matches: 142, Mismatches: 2, Indels: 8
0.93 0.01 0.05
Matches are distributed among these distances:
70 2 0.01
71 65 0.46
72 1 0.01
73 1 0.01
74 73 0.51
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (74 bp):
ATAACAGGAAGATGGAGCAACTGTCGACAACTACAGTATTGTAACGAGCTCCAGCATGCATCTCC
TCTTTGTTC
Found at i:544688 original size:21 final size:22
Alignment explanation
Indices: 544658--544698 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
544648 ATATTTTTAT
*
544658 ATTAATATTTATATAATCTATA
1 ATTAATATTTAAATAATCTATA
544680 ATTAA-ATTTAAATAATCTA
1 ATTAATATTTAAATAATCTA
544699 ATTAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (22 bp):
ATTAATATTTAAATAATCTATA
Found at i:544702 original size:19 final size:20
Alignment explanation
Indices: 544658--544704 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
544648 ATATTTTTAT
*
544658 ATTAATATTTATATAATCTATA
1 ATTAA-ATTTAAATAATC-ATA
544680 ATTAAATTTAAATAATC-TA
1 ATTAAATTTAAATAATCATA
544699 ATTAAA
1 ATTAAA
544705 AATTACTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 8 0.33
21 11 0.46
22 5 0.21
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTAAATTTAAATAATCATA
Found at i:545798 original size:96 final size:96
Alignment explanation
Indices: 545736--545924 Score: 288
Period size: 96 Copynumber: 2.0 Consensus size: 96
545726 ATAGATTTGA
*
545736 AATTCTTATTTATGAATGTAATAAATTTTATTGATAATAAAAAAATCAACAAGAAAATTATAATA
1 AATTCTTATTTATGAATGTAATAAATCTTATTGATAATAAAAAAATCAACAAGAAAATTATAATA
* *
545801 TAATTAACAACAATGGGTATATAAATTTTCG
66 TAATTAACAACAATCGGTAGATAAATTTTCG
* ** *
545832 AATTCTTATTTATGAATGTAATAAATCTTATTGATAATAAAAAAATTAATGACAAAATTATAATA
1 AATTCTTATTTATGAATGTAATAAATCTTATTGATAATAAAAAAATCAACAAGAAAATTATAATA
* * *
545897 TAATTACCAACAATGGGTATATAAATTT
66 TAATTAACAACAATCGGTAGATAAATTT
545925 ATTTATTTTT
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
96 87 1.00
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (96 bp):
AATTCTTATTTATGAATGTAATAAATCTTATTGATAATAAAAAAATCAACAAGAAAATTATAATA
TAATTAACAACAATCGGTAGATAAATTTTCG
Found at i:546335 original size:13 final size:15
Alignment explanation
Indices: 546301--546337 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
546291 AATATTTAAA
*
546301 ATATAATATGAATTT
1 ATATAATATGAAATT
546316 ATATAATAT-AAATT
1 ATATAATATGAAATT
546330 AT-TAATAT
1 ATATAATAT
546338 TTTTAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.29
14 6 0.29
15 9 0.43
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (15 bp):
ATATAATATGAAATT
Found at i:548167 original size:2 final size:2
Alignment explanation
Indices: 548160--548188 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
548150 TACCAACATT
548160 TA TA TA TA TA 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 T
548189 TTATTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:548262 original size:3 final size:3
Alignment explanation
Indices: 548254--548280 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
548244 GAGTTGCATA
548254 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
548281 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:549618 original size:25 final size:26
Alignment explanation
Indices: 549610--549662 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
549600 TTTTTGTTTA
549610 TTTTATTTTAAATTAATTTTTAATTT
1 TTTTATTTTAAATTAATTTTTAATTT
* *
549636 TTTTATTTT-GA-TCATTTTTAATTT
1 TTTTATTTTAAATTAATTTTTAATTT
549660 TTT
1 TTT
549663 CGTAATTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 15 0.60
25 1 0.04
26 9 0.36
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (26 bp):
TTTTATTTTAAATTAATTTTTAATTT
Found at i:549878 original size:2 final size:2
Alignment explanation
Indices: 549871--549897 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
549861 TGTATATGTT
549871 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
549898 GAAAACAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:550534 original size:8 final size:7
Alignment explanation
Indices: 550459--550543 Score: 52
Period size: 8 Copynumber: 12.0 Consensus size: 7
550449 AAAATCGAAT
550459 TTAAA-A
1 TTAAATA
550465 TT-AATA
1 TTAAATA
550471 TTAAAT-
1 TTAAATA
*
550477 TAAAATTA
1 TTAAA-TA
550485 TTAAATAA
1 TTAAAT-A
*
550493 TAAAATA
1 TTAAATA
**
550500 TTTTATA
1 TTAAATA
550507 TTTAAAT-
1 -TTAAATA
*
550514 TTAATTA
1 TTAAATA
550521 TTTAAATA
1 -TTAAATA
550529 TATAAATA
1 T-TAAATA
550537 TTAAATA
1 TTAAATA
550544 AAATTAATAT
Statistics
Matches: 60, Mismatches: 10, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
5 2 0.03
6 14 0.23
7 17 0.28
8 27 0.45
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TTAAATA
Found at i:550629 original size:26 final size:26
Alignment explanation
Indices: 550600--550679 Score: 70
Period size: 30 Copynumber: 2.8 Consensus size: 26
550590 AAAAAAGAAA
*
550600 AAAAAAATAAAATATTAAAAATTTAT
1 AAAAAAATAAAATATTAAAAAATTAT
* *
550626 AAAAATATTAAATATTTTAAATAAAATTAT
1 AAAAA-AATAAA-ATATT-AA-AAAATTAT
*
550656 AATAAAAATATAAAAATTAAAAAA
1 AA-AAAAATA-AAATATTAAAAAA
550680 AAAAGTCAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
26 5 0.12
27 5 0.12
28 8 0.19
29 4 0.10
30 15 0.36
31 5 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (26 bp):
AAAAAAATAAAATATTAAAAAATTAT
Found at i:550630 original size:19 final size:18
Alignment explanation
Indices: 550608--550646 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
550598 AAAAAAAAAT
550608 AAAATATTAAAAATTTATA
1 AAAATATTAAAAATTT-TA
*
550627 AAAATATTAAATATTTTA
1 AAAATATTAAAAATTTTA
550645 AA
1 AA
550647 TAAAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATATTAAAAATTTTA
Found at i:550654 original size:19 final size:19
Alignment explanation
Indices: 550608--550659 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
550598 AAAAAAAAAT
* *
550608 AAAATATTAAAAATTTATA
1 AAAAAATTAAATATTTATA
*
550627 AAAATATTAAATATTT-TA
1 AAAAAATTAAATATTTATA
550645 AATAAAATTATAATA
1 AA-AAAATTA-AATA
550660 AAAATATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 4 0.14
19 21 0.72
20 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAAATTAAATATTTATA
Found at i:550676 original size:30 final size:31
Alignment explanation
Indices: 550616--550681 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
550606 ATAAAATATT
*
550616 AAAAATTTATAAAAATATTAAATATTTTAAA
1 AAAAATTTATAAAAATATTAAATATATTAAA
*
550647 TAAAATTATAATAAAAATA-TAAA-A-ATTAAA
1 AAAAATT-T-ATAAAAATATTAAATATATTAAA
550677 AAAAA
1 AAAAA
550682 AAGTCAAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
30 9 0.30
31 7 0.23
32 5 0.17
33 9 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (31 bp):
AAAAATTTATAAAAATATTAAATATATTAAA
Found at i:551887 original size:21 final size:21
Alignment explanation
Indices: 551846--551894 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
551836 TTATTTTTTT
551846 AAATAATTTTAAATATTAATAA
1 AAATAATTTTAAATATTAAT-A
* *
551868 AAATAATTTT-ATTTTTAATA
1 AAATAATTTTAAATATTAATA
551888 AAATAAT
1 AAATAAT
551895 ATCATTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.32
21 7 0.28
22 10 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATAATTTTAAATATTAATA
Found at i:551901 original size:20 final size:21
Alignment explanation
Indices: 551861--551902 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
551851 ATTTTAAATA
* *
551861 TTAATAAAAATAATTTTATTT
1 TTAATAAAAATAATATCATTT
551882 TTAAT-AAAATAATATCATTT
1 TTAATAAAAATAATATCATTT
551902 T
1 T
551903 ATTTATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAATAAAAATAATATCATTT
Found at i:552204 original size:16 final size:16
Alignment explanation
Indices: 552183--552249 Score: 68
Period size: 16 Copynumber: 4.2 Consensus size: 16
552173 TCGATTTAAG
552183 ATTTAAAATTAATTTT
1 ATTTAAAATTAATTTT
552199 ATTTAAAATTTATATATTT
1 ATTTAAAA-TTA-AT-TTT
* *
552218 ATTT--TA-TAATTTA
1 ATTTAAAATTAATTTT
552231 ATTTAAAATTAATTTT
1 ATTTAAAATTAATTTT
552247 ATT
1 ATT
552250 CTAAGTTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
13 6 0.15
14 2 0.05
15 3 0.07
16 17 0.41
17 4 0.10
18 2 0.05
19 7 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTAAAATTAATTTT
Found at i:552223 original size:20 final size:17
Alignment explanation
Indices: 552183--552234 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 17
552173 TCGATTTAAG
552183 ATTTAAAA-TTAATTTT
1 ATTTAAAATTTAATTTT
552199 ATTTAAAATTTATATATTT
1 ATTTAAAATTTA-AT-TTT
*
552218 ATTTTATAATTTAATTT
1 A-TTTAAAATTTAATTT
552235 AAAATTAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
16 8 0.26
17 3 0.10
18 4 0.13
19 6 0.19
20 10 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTAAAATTTAATTTT
Found at i:553547 original size:22 final size:24
Alignment explanation
Indices: 553497--553550 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 24
553487 GATTATATAT
*
553497 ATATTAA--TTAAAAATTATTTAA
1 ATATTAATTTTAAAAAATATTTAA
*
553519 TTATTAATTTTAAAAAAT-TTTAA
1 ATATTAATTTTAAAAAATATTTAA
553542 AT-TTAATTT
1 ATATTAATTT
553551 ATTATTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 13 0.48
23 6 0.22
24 8 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATATTAATTTTAAAAAATATTTAA
Found at i:554008 original size:21 final size:20
Alignment explanation
Indices: 553983--554043 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
553973 TAGTTTATAC
553983 AAATAA-AATAAAGTTATAATA
1 AAATAATAATAAA--TATAATA
*
554004 AAATAATTATTAAATATAATA
1 AAATAA-TAATAAATATAATA
* *
554025 AAATAATTATAATTATAAT
1 AAATAATAATAAATATAAT
554044 TTAATTTGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
20 10 0.29
21 19 0.56
23 5 0.15
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
AAATAATAATAAATATAATA
Found at i:556003 original size:53 final size:53
Alignment explanation
Indices: 555923--556031 Score: 218
Period size: 53 Copynumber: 2.1 Consensus size: 53
555913 AGCTACTTGA
555923 CAATATTTGGTTGATCAGTTAACCTACAATACTTGAATTAAATTCTAAAATAT
1 CAATATTTGGTTGATCAGTTAACCTACAATACTTGAATTAAATTCTAAAATAT
555976 CAATATTTGGTTGATCAGTTAACCTACAATACTTGAATTAAATTCTAAAATAT
1 CAATATTTGGTTGATCAGTTAACCTACAATACTTGAATTAAATTCTAAAATAT
556029 CAA
1 CAA
556032 GAAAAAATCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (53 bp):
CAATATTTGGTTGATCAGTTAACCTACAATACTTGAATTAAATTCTAAAATAT
Found at i:556006 original size:26 final size:26
Alignment explanation
Indices: 555922--556006 Score: 75
Period size: 26 Copynumber: 3.2 Consensus size: 26
555912 AAGCTACTTG
555922 ACAATATTTGGTTGATCAGTTAACCT
1 ACAATATTTGGTTGATCAGTTAACCT
* * * * **
555948 ACAATACTTGAATT-A-AATTCTAAAAT
1 ACAATATTTG-GTTGATCAGT-TAACCT
555974 ATCAATATTTGGTTGATCAGTTAACCT
1 A-CAATATTTGGTTGATCAGTTAACCT
556001 ACAATA
1 ACAATA
556007 CTTGAATTAA
Statistics
Matches: 42, Mismatches: 12, Indels: 10
0.66 0.19 0.16
Matches are distributed among these distances:
25 2 0.05
26 22 0.52
27 16 0.38
28 2 0.05
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (26 bp):
ACAATATTTGGTTGATCAGTTAACCT
Found at i:558148 original size:25 final size:26
Alignment explanation
Indices: 558094--558169 Score: 61
Period size: 25 Copynumber: 3.0 Consensus size: 26
558084 TTTTTTTAAT
* *
558094 TATATAAACTATATTATTTTAATATT
1 TATATAAACTATATAATTTTAATATA
*
558120 TATATATAC-ATATAATTTT-ATATCA
1 TATATAAACTATATAATTTTAATAT-A
*
558145 TATA-AAA-TAAATAAATTTATAATAT
1 TATATAAACTATAT-AATTT-TAATAT
558170 TATGGTTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
24 9 0.22
25 18 0.45
26 9 0.22
27 4 0.10
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (26 bp):
TATATAAACTATATAATTTTAATATA
Found at i:563988 original size:16 final size:16
Alignment explanation
Indices: 563969--564019 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
563959 GCATGAAGTA
563969 AATTTAAAATGATTTG
1 AATTTAAAATGATTTG
* *
563985 AATTTTAAATAATTTG
1 AATTTAAAATGATTTG
* *
564001 AACTTAAAATGATTCG
1 AATTTAAAATGATTTG
564017 AAT
1 AAT
564020 AATTAATTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (16 bp):
AATTTAAAATGATTTG
Found at i:564036 original size:55 final size:55
Alignment explanation
Indices: 563969--564098 Score: 152
Period size: 55 Copynumber: 2.4 Consensus size: 55
563959 GCATGAAGTA
* ** * *** *
563969 AATTTAAAATGATTTGAATTTTAAATAATTTGAACTTAAAATGATTCGAATAATT
1 AATTTGAAATGATTCAAACTTTAAATAATAAAAACTTAAAATGATCCGAATAATT
* *
564024 AATTTGAAATGATTCAAACTTTAAATAATAAAAACTTGAAATGATCCGACTAATT
1 AATTTGAAATGATTCAAACTTTAAATAATAAAAACTTAAAATGATCCGAATAATT
**
564079 AACATGAAATGATTCAAACT
1 AATTTGAAATGATTCAAACT
564099 CAAAAGATGA
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 63 1.00
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.35
Consensus pattern (55 bp):
AATTTGAAATGATTCAAACTTTAAATAATAAAAACTTAAAATGATCCGAATAATT
Found at i:564627 original size:3 final size:3
Alignment explanation
Indices: 564619--564674 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
564609 AATATAGTTG
564619 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
564667 TTA TTA TT
1 TTA TTA TT
564675 GTTGTTTTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:564858 original size:2 final size:2
Alignment explanation
Indices: 564851--564890 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
564841 ATCTAAAATC
564851 AT AT AT AT AT 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 AT AT AT AT AT
564891 GATCCTAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:567077 original size:18 final size:18
Alignment explanation
Indices: 567022--567066 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 18
567012 CATATTGATT
*
567022 TTATTTAAATTTT-AAT-
1 TTATTTTAATTTTAAATA
*
567038 TTA-ATTAATTTTAAATA
1 TTATTTTAATTTTAAATA
567055 TTATTTTAATTT
1 TTATTTTAATTT
567067 AAGTATTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 7 0.30
16 6 0.26
17 3 0.13
18 7 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATTTTAATTTTAAATA
Found at i:567152 original size:14 final size:14
Alignment explanation
Indices: 567133--567163 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
567123 TTGGATCATG
567133 ATTTTATTTTTATT
1 ATTTTATTTTTATT
*
567147 ATTTTATTTTTTTT
1 ATTTTATTTTTATT
567161 ATT
1 ATT
567164 GAAACCCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
ATTTTATTTTTATT
Found at i:567349 original size:69 final size:68
Alignment explanation
Indices: 567236--567367 Score: 228
Period size: 69 Copynumber: 1.9 Consensus size: 68
567226 TTTTTCATTA
* *
567236 TTTTCATTGTTTTAACTTGTTTGTATTCTTCTAATCAATTATTAATGCTCTCTCTCTCTCTCTAT
1 TTTTCATTGTTTTAACTTGTTTATATTCATCTAATCAATTATTAATGCTCTCTCTCTCTCTCTAT
567301 TTG
66 TTG
*
567304 TTTTCATTGTTTTAAGTTGTTTTATATTCATCTAATCAATTATTAATGCTCTCTCTCTCTCTCT
1 TTTTCATTGTTTTAACTTG-TTTATATTCATCTAATCAATTATTAATGCTCTCTCTCTCTCTCT
567368 CTCTTCATAA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
68 18 0.30
69 42 0.70
ACGTcount: A:0.19, C:0.19, G:0.07, T:0.55
Consensus pattern (68 bp):
TTTTCATTGTTTTAACTTGTTTATATTCATCTAATCAATTATTAATGCTCTCTCTCTCTCTCTAT
TTG
Found at i:567752 original size:17 final size:18
Alignment explanation
Indices: 567730--567763 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
567720 TTAAAGATGC
567730 AATTATATT-TTTATTTT
1 AATTATATTATTTATTTT
567747 AATTATATTATTTATTT
1 AATTATATTATTTATTT
567764 ATTTATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
AATTATATTATTTATTTT
Found at i:567764 original size:17 final size:17
Alignment explanation
Indices: 567730--567781 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
567720 TTAAAGATGC
567730 AATTATATT-TTTATTTT
1 AATTATATTATTTA-TTT
567747 AATTATATTATTTATTT
1 AATTATATTATTTATTT
*
567764 -ATT-TATTA-ATATTT
1 AATTATATTATTTATTT
567778 AATT
1 AATT
567782 CGAAATATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.16
15 8 0.25
16 3 0.09
17 12 0.38
18 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
AATTATATTATTTATTT
Found at i:568568 original size:13 final size:13
Alignment explanation
Indices: 568537--568587 Score: 57
Period size: 14 Copynumber: 3.7 Consensus size: 13
568527 ACTTAATAGA
*
568537 AAAAACAAATTATT
1 AAAAATAAATT-TT
568551 AAAAATTAAATTTT
1 AAAAA-TAAATTTT
*
568565 AAAAATATATTTT
1 AAAAATAAATTTT
568578 AAAAAATAAA
1 -AAAAATAAA
568588 AAAATACAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
13 7 0.22
14 20 0.62
15 5 0.16
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAAATAAATTTT
Found at i:568796 original size:18 final size:18
Alignment explanation
Indices: 568773--568828 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 18
568763 TATTTAAAAT
568773 ATTTTATATTTATTATAA
1 ATTTTATATTTATTATAA
*
568791 ATTTTA-ATATATTA-ATA
1 ATTTTATATTTATTATA-A
*
568808 A-TTCATA-TTA-TATAA
1 ATTTTATATTTATTATAA
568823 ATTTTA
1 ATTTTA
568829 AAATTTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
15 4 0.13
16 10 0.33
17 10 0.33
18 6 0.20
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTATATTTATTATAA
Found at i:572378 original size:33 final size:33
Alignment explanation
Indices: 572339--572403 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
572329 CTTTTCTATC
** **
572339 TTTATTTAATTGTATTAGGAATTAATATTATTA
1 TTTATTTAATAATATTAAAAATTAATATTATTA
572372 TTTATTTAATAATATTAAAAATTAATATTATT
1 TTTATTTAATAATATTAAAAATTAATATTATT
572404 TTCAAACTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.54
Consensus pattern (33 bp):
TTTATTTAATAATATTAAAAATTAATATTATTA
Done.