Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 115 of 120
Found at i:33477892 original size:128 final size:128
Alignment explanation
Indices: 33477664--33477903 Score: 453
Period size: 128 Copynumber: 1.9 Consensus size: 128
33477654 GAGAATTGGG
* *
33477664 TTTTTTTTTTCTCAGCAACCAAACGAGCTAAGAAATCTGAAAGGAAAGTGAAAAAGATATAACCT
1 TTTTTTTTTTCTCAGCAACCAAACAAGCTAAGAAATCTGAAAAGAAAGTGAAAAAGATATAACCT
*
33477729 TGAATTGGAACTAGTGTTTGGCTTTTGAGTCAAAGCAGTCAAATGAATTGGTTCTTCTTTTTT
66 TGAATTGAAACTAGTGTTTGGCTTTTGAGTCAAAGCAGTCAAATGAATTGGTTCTTCTTTTTT
33477792 TTTTTTTTTTCTCAGCAACCAAACAAGCTAAGAAATCTGAAAAGAAAGTGAAAAAGATATAACCT
1 TTTTTTTTTTCTCAGCAACCAAACAAGCTAAGAAATCTGAAAAGAAAGTGAAAAAGATATAACCT
33477857 TGAATTGAAACTAGTGTTTGGCTTTTGAGTCAAAGCAGTCAAATGAA
66 TGAATTGAAACTAGTGTTTGGCTTTTGAGTCAAAGCAGTCAAATGAA
33477904 ATTACTCAAA
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
128 109 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (128 bp):
TTTTTTTTTTCTCAGCAACCAAACAAGCTAAGAAATCTGAAAAGAAAGTGAAAAAGATATAACCT
TGAATTGAAACTAGTGTTTGGCTTTTGAGTCAAAGCAGTCAAATGAATTGGTTCTTCTTTTTT
Found at i:33480239 original size:174 final size:175
Alignment explanation
Indices: 33479940--33480287 Score: 461
Period size: 174 Copynumber: 2.0 Consensus size: 175
33479930 GTTCCTAAGT
* * *
33479940 TGTTTTTTACAATTTTGATCCTATTTCATGTTCAATGAAAACGACCAAAAGTTTGTTTTAATGTG
1 TGTTTTTTACAATTTCGATCCTATTTCATGTTCAATGAAAACGACCAAAAG-TTGTTTGAAGGTG
*
33480005 GTTTTTGAGTTATAAGCAATCATCAAAGCTTTTTGGCTCAAGCTGTGTAACTTGTGGTTGTTTTA
65 GTTTTTGAGTTATAAGCAATCATCAAAGCTTTTTGGCTCAAGCTGTGTAACTTCTGGTTGTTTTA
* *
33480070 TAATATTATGTTGATTGCTAGTTGAGGTCTTTTGGTGGCAATAGTA
130 TAATATTATGTTGATTGCTAGTTGAGATCTTTTGGTGCCAATAGTA
* * *
33480116 TGTTTTTTAGC-ATTTCGATCCTATTTTCATGTTGAATGAAAACGACCAGAAG-TG-TTGGAGGT
1 TGTTTTTTA-CAATTTCGATCCTA-TTTCATGTTCAATGAAAACGACCAAAAGTTGTTTGAAGGT
* ** * * *
33480178 -GTTTTTCGAGTTATATGCCCTTATCAAATCTTTTTGGCTCAAGCTGTGTAATTTCTGGTTGTTT
64 GGTTTTT-GAGTTATAAGCAATCATCAAAGCTTTTTGGCTCAAGCTGTGTAACTTCTGGTTGTTT
* * * *
33480242 TGTAATATTATGTTGGTTGTTTGTTGAGATCTTTTGGTGCCAATAG
128 TATAATATTATGTTGATTGCTAGTTGAGATCTTTTGGTGCCAATAG
33480288 CCTGGTAGCA
Statistics
Matches: 150, Mismatches: 19, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
173 6 0.04
174 95 0.63
175 2 0.01
176 20 0.13
177 27 0.18
ACGTcount: A:0.23, C:0.11, G:0.21, T:0.44
Consensus pattern (175 bp):
TGTTTTTTACAATTTCGATCCTATTTCATGTTCAATGAAAACGACCAAAAGTTGTTTGAAGGTGG
TTTTTGAGTTATAAGCAATCATCAAAGCTTTTTGGCTCAAGCTGTGTAACTTCTGGTTGTTTTAT
AATATTATGTTGATTGCTAGTTGAGATCTTTTGGTGCCAATAGTA
Found at i:33484699 original size:32 final size:32
Alignment explanation
Indices: 33484644--33484742 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
33484634 TAACTATTGG
*
33484644 TAATTAAAATCAATGCT-TAATTAAGCCTTGATT
1 TAATT-AAATCAATGCTAT-ATTAAGGCTTGATT
* *
33484677 TAATTAAATCAAAGCTATATTAAGGTTTGATT
1 TAATTAAATCAATGCTATATTAAGGCTTGATT
* *
33484709 TAATTAAATCAATGCCATATGAAGGCTTGATT
1 TAATTAAATCAATGCTATATTAAGGCTTGATT
33484741 TA
1 TA
33484743 GGCCGGTCTT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
32 52 0.90
33 6 0.10
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.38
Consensus pattern (32 bp):
TAATTAAATCAATGCTATATTAAGGCTTGATT
Found at i:33492861 original size:36 final size:36
Alignment explanation
Indices: 33492812--33492890 Score: 131
Period size: 36 Copynumber: 2.2 Consensus size: 36
33492802 AAACCTTTTT
* *
33492812 ATCAATTCAAACTCGAATTCAAGCAAAAATAATCGA
1 ATCAAGTCAAACTCAAATTCAAGCAAAAATAATCGA
*
33492848 ATCAAGTCGAACTCAAATTCAAGCAAAAATAATCGA
1 ATCAAGTCAAACTCAAATTCAAGCAAAAATAATCGA
33492884 ATCAAGT
1 ATCAAGT
33492891 TTGACTTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.49, C:0.19, G:0.10, T:0.22
Consensus pattern (36 bp):
ATCAAGTCAAACTCAAATTCAAGCAAAAATAATCGA
Found at i:33499259 original size:4 final size:4
Alignment explanation
Indices: 33499250--33499285 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
33499240 AAATCTGCCA
*
33499250 TATG TATG TATG TATG TATG TATG TATG TATA TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG
33499286 CAAAGCTCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:33502596 original size:19 final size:18
Alignment explanation
Indices: 33502566--33502605 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
33502556 TTGTTTTTTT
*
33502566 TTTATATATATTATGTAA
1 TTTATATATATTATATAA
33502584 TTTATAGTATATTATATAA
1 TTTATA-TATATTATATAA
33502603 TTT
1 TTT
33502606 TAAATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
TTTATATATATTATATAA
Found at i:33502613 original size:19 final size:19
Alignment explanation
Indices: 33502565--33502614 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
33502555 TTTGTTTTTT
* *
33502565 TTTTATATATATTATGTAA
1 TTTTAAATATATTATATAA
*
33502584 -TTTATAGTATATTATATAA
1 TTTTA-AATATATTATATAA
33502603 TTTTAAATATAT
1 TTTTAAATATAT
33502615 AATAATATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 4 0.16
19 17 0.68
20 4 0.16
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (19 bp):
TTTTAAATATATTATATAA
Found at i:33502705 original size:21 final size:21
Alignment explanation
Indices: 33502680--33502724 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
33502670 AAAATCATCT
*
33502680 AAAATATTAAATATTAAATTA
1 AAAATAATAAATATTAAATTA
* * *
33502701 AAAATAATATATATTTACTTA
1 AAAATAATAAATATTAAATTA
33502722 AAA
1 AAA
33502725 CGAGCTTAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAATAATAAATATTAAATTA
Found at i:33511174 original size:29 final size:30
Alignment explanation
Indices: 33511140--33511198 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
33511130 TCGCGTGTAT
*
33511140 AATTGCAC-CAAATTAAAATTCATGTATAC
1 AATTGCACACAAATCAAAATTCATGTATAC
*
33511169 AATTGCACATTAAATCAAAATTCATGTATA
1 AATTGCACA-CAAATCAAAATTCATGTATA
33511199 ATTTTGAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
31 18 0.69
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.32
Consensus pattern (30 bp):
AATTGCACACAAATCAAAATTCATGTATAC
Found at i:33511201 original size:29 final size:27
Alignment explanation
Indices: 33511135--33511201 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 27
33511125 GAGTTTCGCG
*
33511135 TGTATAATTGCACCAAATTAAAATTCA
1 TGTATAATTGCACCAAATCAAAATTCA
*
33511162 TGTATACAATTGCACATTAAATCAAAATTCA
1 TGTAT--AATTGCAC--CAAATCAAAATTCA
33511193 TGTATAATT
1 TGTATAATT
33511202 TTGAGATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 5 0.15
29 12 0.35
31 17 0.50
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.36
Consensus pattern (27 bp):
TGTATAATTGCACCAAATCAAAATTCA
Found at i:33513603 original size:29 final size:27
Alignment explanation
Indices: 33513571--33513637 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 27
33513561 TAAATCTCAA
* *
33513571 AATTATACATGAATTTTGATTTAATGTGC
1 AATTATACATGAATTTTAATTT--GGTGC
33513600 AATTGTATACATGAATTTTAATTTGGTGC
1 AA-T-TATACATGAATTTTAATTTGGTGC
33513629 AATTATACA
1 AATTATACA
33513638 CGCGAAACTC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 6 0.18
28 1 0.03
29 8 0.24
30 1 0.03
31 18 0.53
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.43
Consensus pattern (27 bp):
AATTATACATGAATTTTAATTTGGTGC
Found at i:33514872 original size:2 final size:2
Alignment explanation
Indices: 33514865--33514911 Score: 71
Period size: 2 Copynumber: 24.0 Consensus size: 2
33514855 ATCTACTATG
33514865 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
33514907 A- AT AT
1 AT AT AT
33514912 GAATTTGATT
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.05
2 38 0.90
3 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:33522954 original size:21 final size:22
Alignment explanation
Indices: 33522911--33522957 Score: 71
Period size: 20 Copynumber: 2.2 Consensus size: 22
33522901 AAAGTTGTAA
33522911 AAAATAATTTTATATTAAATTT
1 AAAATAATTTTATATTAAATTT
33522933 AAAAT-ATTTT-TATTAAATTT
1 AAAATAATTTTATATTAAATTT
*
33522953 TAAAT
1 AAAAT
33522958 TGGGAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 14 0.58
21 5 0.21
22 5 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AAAATAATTTTATATTAAATTT
Found at i:33525122 original size:4 final size:4
Alignment explanation
Indices: 33525115--33525142 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
33525105 TTTTTTTCCC
33525115 CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT
33525143 AAGTCTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:33526353 original size:3 final size:3
Alignment explanation
Indices: 33526340--33526376 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
33526330 TATAATTTGG
*
33526340 TCT TTT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
33526377 TTTACAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:33530704 original size:16 final size:16
Alignment explanation
Indices: 33530685--33530722 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
33530675 TTTTATATGT
33530685 TATAAATTCTATAAT-A
1 TATAAATTCTA-AATAA
*
33530701 TATAAATTTTAAATAA
1 TATAAATTCTAAATAA
33530717 TATAAA
1 TATAAA
33530723 ACATTACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TATAAATTCTAAATAA
Found at i:33530711 original size:32 final size:32
Alignment explanation
Indices: 33530649--33530711 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
33530639 GATTATAGTA
* *
33530649 ATGTTATATATTACTATAGATTTAATTTTTAT
1 ATGTTATAAATTACTATAGATTTAAATTTTAT
33530681 ATGTTATAAATT-CTATA-ATATATAAATTTTA
1 ATGTTATAAATTACTATAGAT-T-TAAATTTTA
33530712 AATAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 2 0.07
31 6 0.22
32 19 0.70
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (32 bp):
ATGTTATAAATTACTATAGATTTAAATTTTAT
Found at i:33533074 original size:2 final size:2
Alignment explanation
Indices: 33533067--33533096 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
33533057 AAAGAAACGA
33533067 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
33533097 TCATATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33533359 original size:29 final size:30
Alignment explanation
Indices: 33533311--33533390 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
33533301 GAATCAAATC
*
33533311 AAATCAAAATCTCATGTATAAAATTACACA-
1 AAATCAAAAT-TCATATATAAAATTACACAT
* *
33533341 AAATCAAAATTCATATATAACATTATACATT
1 AAATCAAAATTCATATATAAAATTACACA-T
* *
33533372 GAATCAAATTTCATATATA
1 AAATCAAAATTCATATATA
33533391 GTTTTAATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 16 0.37
30 10 0.23
31 17 0.40
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.33
Consensus pattern (30 bp):
AAATCAAAATTCATATATAAAATTACACAT
Found at i:33534466 original size:32 final size:31
Alignment explanation
Indices: 33534430--33534501 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 31
33534420 AAATTAAAGT
* *
33534430 ATGATAAAATTGTAT-TTTGTCTCCTTTCAAAA
1 ATGATAAAATT-TATGTTTAT-TCCCTTCAAAA
33534462 ATGATAAAA-TTATGTTTATTCCCTTCAAAA
1 ATGATAAAATTTATGTTTATTCCCTTCAAAA
*
33534492 ATGATGAAAT
1 ATGATAAAAT
33534502 GATAAATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
30 21 0.60
31 5 0.14
32 9 0.26
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (31 bp):
ATGATAAAATTTATGTTTATTCCCTTCAAAA
Found at i:33545670 original size:22 final size:22
Alignment explanation
Indices: 33545616--33545658 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
33545606 TTTATTGTTC
33545616 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
33545638 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
33545659 TAGCCATGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:33547695 original size:138 final size:138
Alignment explanation
Indices: 33547442--33547726 Score: 561
Period size: 138 Copynumber: 2.1 Consensus size: 138
33547432 ATTCAATCAA
*
33547442 TTTAATTGATTCAACTAGACTAACAATAATTAAATAATTAAAAAAATCATATTTATAAAAAATAT
1 TTTATTTGATTCAACTAGACTAACAATAATTAAATAATTAAAAAAATCATATTTATAAAAAATAT
33547507 TAAATCGCTTCAACCTATTCAACTAGTTAGTTTTCAGTTTTTGCCGATTTCAAGATTCAATCTGT
66 TAAATCGCTTCAACCTATTCAACTAGTTAGTTTTCAGTTTTTGCCGATTTCAAGATTCAATCTGT
33547572 CCAACCCT
131 CCAACCCT
33547580 TTTATTTGATTCAACTAGACTAACAATAATTAAATAATTAAAAAAATCATATTTATAAAAAATAT
1 TTTATTTGATTCAACTAGACTAACAATAATTAAATAATTAAAAAAATCATATTTATAAAAAATAT
33547645 TAAATCGCTTCAACCTATTCAACTAGTTAGTTTTCAGTTTTTGCCGATTTCAAGATTCAATCTGT
66 TAAATCGCTTCAACCTATTCAACTAGTTAGTTTTCAGTTTTTGCCGATTTCAAGATTCAATCTGT
33547710 CCAACCCT
131 CCAACCCT
33547718 TTTATTTGA
1 TTTATTTGA
33547727 ACTAATGTGC
Statistics
Matches: 146, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 146 1.00
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.38
Consensus pattern (138 bp):
TTTATTTGATTCAACTAGACTAACAATAATTAAATAATTAAAAAAATCATATTTATAAAAAATAT
TAAATCGCTTCAACCTATTCAACTAGTTAGTTTTCAGTTTTTGCCGATTTCAAGATTCAATCTGT
CCAACCCT
Found at i:33560487 original size:13 final size:13
Alignment explanation
Indices: 33560469--33560516 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
33560459 TTGAAGGTGA
33560469 TTTTCTTTTTTTC
1 TTTTCTTTTTTTC
* *
33560482 TTTTCTTTGTTTA
1 TTTTCTTTTTTTC
33560495 TTTT-TGTTTTTTC
1 TTTTCT-TTTTTTC
33560508 TTCTTCTTT
1 TT-TTCTTT
33560517 GCAAAACAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
12 1 0.04
13 22 0.79
14 4 0.14
15 1 0.04
ACGTcount: A:0.02, C:0.12, G:0.04, T:0.81
Consensus pattern (13 bp):
TTTTCTTTTTTTC
Found at i:33564937 original size:26 final size:24
Alignment explanation
Indices: 33564884--33564938 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
33564874 CAATTTTTGG
*
33564884 TTATTTTAATTTCTTGTATATTAT
1 TTATTTTAATTTCTTGTACATTAT
33564908 TTATTTTAAATTT-TTGTACATATACT
1 TTATTTT-AATTTCTTGTACAT-TA-T
33564934 TTATT
1 TTATT
33564939 GATTTACAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 14 0.52
25 7 0.26
26 6 0.22
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (24 bp):
TTATTTTAATTTCTTGTACATTAT
Found at i:33571705 original size:51 final size:52
Alignment explanation
Indices: 33571629--33572064 Score: 335
Period size: 51 Copynumber: 8.6 Consensus size: 52
33571619 CCGGTTCACA
* * *
33571629 TAGTAGCATGCACATAGTACTACACAGGTGACCATCA-CTATCCGATACACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCATCAGCTATCCGATACACG
** * * *
33571680 TAGTAGCCTGGACATAGTACTACACACGT-A--ATCGAAGCTATCCGGTACGCA
1 TAGTAGCCTTCACATAGTACTACACACGTGACCATC--AGCTATCCGATACACG
* * * *
33571731 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCA--T-TCTGATACACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACC-ATCAGCTATCCGATACACG
* * * * * * *
33571781 TAGTAGCCTACACATAGTACTACACACGTGATCA--AGTTTTACGGTTCACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCATCAGCTATCCGATACACG
* * * * * *
33571831 AAGTAGCCTTCACATAGTACTACACACGTGATCA-AAGCTTTTC-AGTACACA
1 TAGTAGCCTTCACATAGTACTACACACGTGACCATCAGCTATCCGA-TACACG
* * * **
33571882 TAGTAGCCTTCACTTAGTACTACACATGTGACCATTATTTAT-CGATACACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCATCAGCTATCCGATACACG
* * * * * *
33571933 TAGTAGCCTTCACACAGCACTACACAAGTGACCA-AAGCT-TCTCGGTACACA
1 TAGTAGCCTTCACATAGTACTACACACGTGACCATCAGCTATC-CGATACACG
* * * * **
33571984 TTGTAGCCTTCACTTAGTACTACACATGTGACCATTATTTAT-CGATACACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCATCAGCTATCCGATACACG
*
33572035 TAGTAGCCTTCACACAGTACTACACACGTG
1 TAGTAGCCTTCACATAGTACTACACACGTG
33572065 TTCATCGATA
Statistics
Matches: 307, Mismatches: 60, Indels: 36
0.76 0.15 0.09
Matches are distributed among these distances:
47 1 0.00
48 3 0.01
49 3 0.01
50 79 0.26
51 209 0.68
52 7 0.02
53 2 0.01
55 3 0.01
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.26
Consensus pattern (52 bp):
TAGTAGCCTTCACATAGTACTACACACGTGACCATCAGCTATCCGATACACG
Found at i:33571904 original size:151 final size:153
Alignment explanation
Indices: 33571674--33572060 Score: 408
Period size: 151 Copynumber: 2.5 Consensus size: 153
33571664 CACTATCCGA
* ** * * * *
33571674 TACACGTAGTAGCCTGGACATAGTACTACACACGTAATCGAAGCTATCCGGTACGCATAGTAGCC
1 TACACGAAGTAGCCTTCACATAGTACTACACACGTGATCAAAGCTATCCAGTACACATAGTAGCC
* * *
33571739 TGCACATAGTACTACACATGCGACCTATCA-TTCT-GATACACGTAGTAGCCTACACATAGTACT
66 TGCACATAGTACTACACATGCGACC-ATCATTTATCGATACACGTAGTAGCCTACACACAGCACT
* * *
33571802 ACACACGTGATC-AAG-TTTTACGG
130 ACACAAGTGACCAAAGCTTCT-CGG
* * *
33571825 TTCACGAAGTAGCCTTCACATAGTACTACACACGTGATCAAAGCTTTTCAGTACACATAGTAGCC
1 TACACGAAGTAGCCTTCACATAGTACTACACACGTGATCAAAGCTATCCAGTACACATAGTAGCC
* * * * *
33571890 TTCACTTAGTACTACACATGTGACCATTATTTATCGATACACGTAGTAGCCTTCACACAGCACTA
66 TGCACATAGTACTACACATGCGACCATCATTTATCGATACACGTAGTAGCCTACACACAGCACTA
33571955 CACAAGTGACCAAAGCTTCTCGG
131 CACAAGTGACCAAAGCTTCTCGG
* * * * * ** * *
33571978 TACAC-ATTGTAGCCTTCACTTAGTACTACACATGTGACCATTATTTATCGA-TACACGTAGTAG
1 TACACGA-AGTAGCCTTCACATAGTACTACACACGTGATCA-AAGCTATCCAGTACACATAGTAG
* *
33572041 CCTTCACACAGTACTACACA
64 CCTGCACATAGTACTACACA
33572061 CGTGTTCATC
Statistics
Matches: 195, Mismatches: 35, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
150 3 0.02
151 80 0.41
152 37 0.19
153 68 0.35
154 7 0.04
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (153 bp):
TACACGAAGTAGCCTTCACATAGTACTACACACGTGATCAAAGCTATCCAGTACACATAGTAGCC
TGCACATAGTACTACACATGCGACCATCATTTATCGATACACGTAGTAGCCTACACACAGCACTA
CACAAGTGACCAAAGCTTCTCGG
Found at i:33571969 original size:102 final size:102
Alignment explanation
Indices: 33571731--33572060 Score: 407
Period size: 102 Copynumber: 3.3 Consensus size: 102
33571721 CCGGTACGCA
* * * * * * * * *
33571731 TAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCTGA-TACACGTAGTAGCCTACAC
1 TAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGC-TTCTCAGTACACATAGTAGCCTTCAC
* * * * * *
33571794 ATAGTACTACACACGTGATCAAGT-TTTA-CGGTTCACG
65 TTAGTACTACACATGTGA-CCATTATTTATCGATACACG
* * * * *
33571831 AAGTAGCCTTCACATAGTACTACACACGTGATCAAAGCTTTTCAGTACACATAGTAGCCTTCACT
1 TAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGCTTCTCAGTACACATAGTAGCCTTCACT
33571896 TAGTACTACACATGTGACCATTATTTATCGATACACG
66 TAGTACTACACATGTGACCATTATTTATCGATACACG
* * *
33571933 TAGTAGCCTTCACACAGCACTACACAAGTGACCAAAGCTTCTCGGTACACATTGTAGCCTTCACT
1 TAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGCTTCTCAGTACACATAGTAGCCTTCACT
33571998 TAGTACTACACATGTGACCATTATTTATCGATACACG
66 TAGTACTACACATGTGACCATTATTTATCGATACACG
33572035 TAGTAGCCTTCACACAGTACTACACA
1 TAGTAGCCTTCACACAGTACTACACA
33572061 CGTGTTCATC
Statistics
Matches: 200, Mismatches: 26, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
100 35 0.17
101 39 0.19
102 126 0.63
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (102 bp):
TAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGCTTCTCAGTACACATAGTAGCCTTCACT
TAGTACTACACATGTGACCATTATTTATCGATACACG
Found at i:33579899 original size:33 final size:33
Alignment explanation
Indices: 33579821--33579909 Score: 124
Period size: 33 Copynumber: 2.7 Consensus size: 33
33579811 CACTTATTAG
*
33579821 TTTCCATAATAGTCCTCATCAAATATACATCAA
1 TTTCCATAATAGTCCTCATCAAATACACATCAA
* * *
33579854 TTACGATTATAGTCCTCATCAAATACACATCAA
1 TTTCCATAATAGTCCTCATCAAATACACATCAA
* *
33579887 TTTCCATAATAGTCTTTATCAAA
1 TTTCCATAATAGTCCTCATCAAA
33579910 GTAGCCTAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.35
Consensus pattern (33 bp):
TTTCCATAATAGTCCTCATCAAATACACATCAA
Found at i:33581380 original size:107 final size:107
Alignment explanation
Indices: 33581194--33581410 Score: 382
Period size: 107 Copynumber: 2.0 Consensus size: 107
33581184 GCTCATCTTT
*
33581194 AGTCTCCGTACTTTATCCACTTTAAACTTTCAGTCCTCATGAAACAGTAATTATTAATTTCAAGA
1 AGTCTCCCTACTTTATCCACTTTAAACTTTCAGTCCTCATGAAACAGTAATTATTAATTTCAAGA
33581259 TCTTATGTGGCGAACATAATACTACATATATTATGTCATGTC
66 TCTTATGTGGCGAACATAATACTACATATATTATGTCATGTC
* * *
33581301 AGTCTCCCTACTTTATGCACTTTAAATTTTC-GATCCTCATGAAACAGTTATTATTAATTTCAAG
1 AGTCTCCCTACTTTATCCACTTTAAACTTTCAG-TCCTCATGAAACAGTAATTATTAATTTCAAG
33581365 ATCTTATGTGGCGAACATAATACTACATATATTATGTCATGTC
65 ATCTTATGTGGCGAACATAATACTACATATATTATGTCATGTC
33581408 AGT
1 AGT
33581411 TTACTATTTC
Statistics
Matches: 105, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
106 1 0.01
107 104 0.99
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (107 bp):
AGTCTCCCTACTTTATCCACTTTAAACTTTCAGTCCTCATGAAACAGTAATTATTAATTTCAAGA
TCTTATGTGGCGAACATAATACTACATATATTATGTCATGTC
Found at i:33582257 original size:33 final size:33
Alignment explanation
Indices: 33582220--33582284 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
33582210 TTTAGGCTAC
* *
33582220 TTTGATAAAGACTATTATGGAAATTGATGTGTA
1 TTTGATAAAGACTATAATCGAAATTGATGTGTA
* * *
33582253 TTTGATGAGGACTATAATCGTAATTGATGTGT
1 TTTGATAAAGACTATAATCGAAATTGATGTGT
33582285 CTCCAGCCCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.32, C:0.05, G:0.23, T:0.40
Consensus pattern (33 bp):
TTTGATAAAGACTATAATCGAAATTGATGTGTA
Found at i:33582438 original size:16 final size:16
Alignment explanation
Indices: 33582417--33582452 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
33582407 TGTGGACAAT
33582417 TTTTTTTAATTTTT-AA
1 TTTTTTT-ATTTTTCAA
33582433 TTTTTTTATTTTTCAA
1 TTTTTTTATTTTTCAA
33582449 TTTT
1 TTTT
33582453 CTTTTCCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTTTATTTTTCAA
Found at i:33588530 original size:33 final size:33
Alignment explanation
Indices: 33588484--33588572 Score: 124
Period size: 33 Copynumber: 2.7 Consensus size: 33
33588474 TTTAGGCTAC
* * *
33588484 TTTGATAAAGACTATTATGGAAATTGATGTGTA
1 TTTGATGAGGACTATTATGGAAATTGATGTATA
* * *
33588517 TTTGATGAGGACTATAATCGTAATTGATGTATA
1 TTTGATGAGGACTATTATGGAAATTGATGTATA
33588550 TTTGATGAGGACTATTATGGAAA
1 TTTGATGAGGACTATTATGGAAA
33588573 CTAATAAGTG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.38
Consensus pattern (33 bp):
TTTGATGAGGACTATTATGGAAATTGATGTATA
Found at i:33600340 original size:31 final size:31
Alignment explanation
Indices: 33600302--33600426 Score: 119
Period size: 31 Copynumber: 4.1 Consensus size: 31
33600292 CTTTGCCAAG
* *
33600302 TGTGTATTTTCAGAATAGGAAAACACCGAAA
1 TGTGTATTTTCAGAACAGGACAACACCGAAA
** ** *
33600333 TGTGTATTTAGAGAA-A-GACAACATTGAAG
1 TGTGTATTTTCAGAACAGGACAACACCGAAA
*
33600362 TGGTGTATTTTCAGAACAGGACAATACCGAAA
1 T-GTGTATTTTCAGAACAGGACAACACCGAAA
** * *
33600394 TGCATATTTTCAAAACAAGACAACACCGAAA
1 TGTGTATTTTCAGAACAGGACAACACCGAAA
33600425 TG
1 TG
33600427 CGTAGGACAA
Statistics
Matches: 74, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
29 10 0.14
30 13 0.18
31 41 0.55
32 10 0.14
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (31 bp):
TGTGTATTTTCAGAACAGGACAACACCGAAA
Found at i:33600480 original size:82 final size:81
Alignment explanation
Indices: 33600349--33600498 Score: 194
Period size: 82 Copynumber: 1.8 Consensus size: 81
33600339 TTTAGAGAAA
** * *
33600349 GACAACATTGAAGTGGTGTATTTTCAGAACAGGACAATACCGAAATGCATATTTTCAAAACAAGA
1 GACAACACCGAAGTGGTGTATTTTCAGAACAAGACAACACCGAAATGCATA--TTCAAAACAAGA
33600414 CAACACCGAAATGCGTAG
64 CAACACCGAAATGCGTAG
* * * * *
33600432 GACAACACCGAAGT-GTGTATTTTCATAACAAGACAGCACTGAAGTGCATATTCAGAACAAGACA
1 GACAACACCGAAGTGGTGTATTTTCAGAACAAGACAACACCGAAATGCATATTCAAAACAAGACA
33600496 ACA
66 ACA
33600499 TCAAAGTGTG
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
80 16 0.28
82 30 0.52
83 12 0.21
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (81 bp):
GACAACACCGAAGTGGTGTATTTTCAGAACAAGACAACACCGAAATGCATATTCAAAACAAGACA
ACACCGAAATGCGTAG
Found at i:33600490 original size:29 final size:29
Alignment explanation
Indices: 33600453--33600563 Score: 91
Period size: 29 Copynumber: 3.8 Consensus size: 29
33600443 AGTGTGTATT
* *
33600453 TTCATAACAAGACAGCACTGAAGTGCATA
1 TTCAGAACAAGACAACACTGAAGTGCATA
* * *
33600482 TTCAGAACAAGACAACA-TCAAAGTGTGTATT
1 TTCAGAACAAGACAACACT-GAA--GTGCATA
* *
33600513 TTTAGAACAGGACAACAC-GAAAGTGCATA
1 TTCAGAACAAGACAACACTG-AAGTGCATA
* *
33600542 TTCAGAACAAGGCAACGCTGAA
1 TTCAGAACAAGACAACACTGAA
33600564 ATACGTATTT
Statistics
Matches: 62, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
28 1 0.02
29 38 0.61
30 1 0.02
31 22 0.35
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (29 bp):
TTCAGAACAAGACAACACTGAAGTGCATA
Found at i:33600537 original size:60 final size:60
Alignment explanation
Indices: 33600432--33600557 Score: 173
Period size: 60 Copynumber: 2.1 Consensus size: 60
33600422 AAATGCGTAG
* * *
33600432 GACAACACCGAAGTGTGTATTTTCATAACAAGACAGCACTGAAGTGCATATTCAGAACAA
1 GACAACACCAAAGTGTGTATTTTCAGAACAAGACAACACTGAAGTGCATATTCAGAACAA
* * *
33600492 GACAACATCAAAGTGTGTATTTTTAGAACAGGACAACAC-GAAAGTGCATATTCAGAACAA
1 GACAACACCAAAGTGTGTATTTTCAGAACAAGACAACACTG-AAGTGCATATTCAGAACAA
*
33600552 GGCAAC
1 GACAAC
33600558 GCTGAAATAC
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 1 0.02
60 57 0.98
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (60 bp):
GACAACACCAAAGTGTGTATTTTCAGAACAAGACAACACTGAAGTGCATATTCAGAACAA
Found at i:33600572 original size:60 final size:60
Alignment explanation
Indices: 33600448--33600586 Score: 165
Period size: 60 Copynumber: 2.3 Consensus size: 60
33600438 ACCGAAGTGT
* * * **
33600448 GTATTTTCATAACAAGACAGCACTG-AAGTGCATATTCAGAACAAGACAACATCAAAGTGT
1 GTATTTTCAGAACAGGACAACAC-GAAAGTGCATATTCAGAACAAGACAACATCAAAGTAC
* * * *
33600508 GTATTTTTAGAACAGGACAACACGAAAGTGCATATTCAGAACAAGGCAACGCTGAAA-TAC
1 GTATTTTCAGAACAGGACAACACGAAAGTGCATATTCAGAACAAGACAAC-ATCAAAGTAC
33600568 GTATTTTCAGAACAGGACA
1 GTATTTTCAGAACAGGACA
33600587 GATTAAAGTG
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
59 1 0.01
60 62 0.93
61 4 0.06
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (60 bp):
GTATTTTCAGAACAGGACAACACGAAAGTGCATATTCAGAACAAGACAACATCAAAGTAC
Found at i:33600658 original size:85 final size:91
Alignment explanation
Indices: 33600482--33600689 Score: 207
Period size: 85 Copynumber: 2.4 Consensus size: 91
33600472 GAAGTGCATA
*
33600482 TTCAGAACAAGACAACATCAAAGTGTGTATTTTTAGAACAGGACAACACGAAAGTGCATATTCAG
1 TTCAGAACAAGACAACATCAAAGTGTGTATTTTTAAAACAGGACAACACGAAAGTGCATATTCAG
* * *
33600547 AACAAGGCAACGCTGAAATACGTATT
66 AACAAGACAACACCGAAATACGTATT
* * * *
33600573 TTCAGAACAGGAC-AGATTAAAGTGTGTATTTTTAAAACA-G-C-AC-CG-AAGTGCGTATTCAG
1 TTCAGAACAAGACAACATCAAAGTGTGTATTTTTAAAACAGGACAACACGAAAGTGCATATTCAG
* * *
33600632 AAC-AGTACAACACCGAAGTGCTTATT
66 AACAAG-ACAACACCGAAATACGTATT
* * * *
33600658 TTTAGAATAAGGCAACA-CTAAAGAGTGTATTT
1 TTCAGAACAAGACAACATC-AAAGTGTGTATTT
33600690 AGAACAAGAC
Statistics
Matches: 96, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
84 2 0.02
85 39 0.41
86 16 0.17
87 2 0.02
88 1 0.01
89 1 0.01
90 23 0.24
91 12 0.12
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.25
Consensus pattern (91 bp):
TTCAGAACAAGACAACATCAAAGTGTGTATTTTTAAAACAGGACAACACGAAAGTGCATATTCAG
AACAAGACAACACCGAAATACGTATT
Found at i:33602476 original size:14 final size:14
Alignment explanation
Indices: 33602457--33602488 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
33602447 TCCAATCACC
33602457 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
33602471 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
33602485 GGGC
1 GGGC
33602489 TAAATGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:33607599 original size:14 final size:14
Alignment explanation
Indices: 33607580--33607611 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
33607570 TCCAATCACC
33607580 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
33607594 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
33607608 GGGC
1 GGGC
33607612 TAAATGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:33610108 original size:132 final size:134
Alignment explanation
Indices: 33609843--33610108 Score: 356
Period size: 134 Copynumber: 2.0 Consensus size: 134
33609833 GTAAATATGA
* * * * * *
33609843 GTTTGAACTTTTAAAACGATATTTTTGAGAGAGGTATACATAAATCCTGAATATAGATAGTAAAA
1 GTTTGAACTTTTAAAACGATATTCTTGAGAGAGATACAAATAAATCCTGAACATAGACAGTAAAA
* *
33609908 CAGATATGAAATAAATAAAAAAATGTGAAGTTTGAGAAATGATGCCGAGAACTTGTCTATATATA
66 CAGATATGAAATAAATAAAAAAATGTGAAGTTTGAGAAATGATGACGAGAACTTGCCTATATATA
33609973 AGTG
131 AGTG
* * * * * *
33609977 GTTTGAATTTTTAAAACGGTATTCTTGAGAGAGATACAAATAATTCTTGAACATATACGGTAAAA
1 GTTTGAACTTTTAAAACGATATTCTTGAGAGAGATACAAATAAATCCTGAACATAGACAGTAAAA
** * *
33610042 TGGATATGAAAT-AA-AAAAAAATGTGAAGTTTGAGAAATGATGATGAGAACTTGCCTCTATATA
66 CAGATATGAAATAAATAAAAAAATGTGAAGTTTGAGAAATGATGACGAGAACTTGCCTATATATA
33610105 AGTG
131 AGTG
33610109 CAATCGGGTT
Statistics
Matches: 114, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
132 49 0.43
133 2 0.02
134 63 0.55
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.31
Consensus pattern (134 bp):
GTTTGAACTTTTAAAACGATATTCTTGAGAGAGATACAAATAAATCCTGAACATAGACAGTAAAA
CAGATATGAAATAAATAAAAAAATGTGAAGTTTGAGAAATGATGACGAGAACTTGCCTATATATA
AGTG
Found at i:33611549 original size:19 final size:19
Alignment explanation
Indices: 33611522--33611575 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
33611512 TAATGAGTTC
*
33611522 AAAACTATAAAAAAAAATT
1 AAAAATATAAAAAAAAATT
* *
33611541 AAAAATATAAATAAATATT
1 AAAAATATAAAAAAAAATT
* *
33611560 AATAATTTTAAAAAAA
1 AA-AAATATAAAAAAA
33611576 TCTTAAAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 18 0.64
20 10 0.36
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAAATATAAAAAAAAATT
Found at i:33611872 original size:19 final size:17
Alignment explanation
Indices: 33611850--33611967 Score: 66
Period size: 19 Copynumber: 6.5 Consensus size: 17
33611840 TAGAGGTGCA
33611850 TTTTTATTAATTTTATAA-
1 TTTTTA-TAATTTTA-AAT
33611868 TTTTTATGAATTATT-AAT
1 TTTTTAT-AATT-TTAAAT
*
33611886 ATTTTTAT-ATTTTAATT
1 -TTTTTATAATTTTAAAT
33611903 TAATTTTATAATTTTTAAAAT
1 T--TTTTATAA-TTTT-AAAT
*
33611924 TTTTAAATAATTATTAATAT
1 TTTT-TATAATT-TTAA-AT
33611944 TTTTTATAATTTCT--AT
1 TTTTTATAATTT-TAAAT
33611960 TTTTTATA
1 TTTTTATA
33611968 GTCTCGAATT
Statistics
Matches: 82, Mismatches: 4, Indels: 30
0.71 0.03 0.26
Matches are distributed among these distances:
16 13 0.16
17 8 0.10
18 17 0.21
19 24 0.29
20 16 0.20
21 4 0.05
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.64
Consensus pattern (17 bp):
TTTTTATAATTTTAAAT
Found at i:33611879 original size:10 final size:9
Alignment explanation
Indices: 33611849--33611967 Score: 70
Period size: 9 Copynumber: 13.0 Consensus size: 9
33611839 CTAGAGGTGC
33611849 ATTTTTATTA
1 ATTTTTA-TA
33611859 A-TTTTATA
1 ATTTTTATA
33611867 ATTTTTATGA
1 ATTTTTAT-A
*
33611877 ATTATTA-A
1 ATTTTTATA
33611885 TATTTTTAT-
1 -ATTTTTATA
*
33611894 ATTTTAATTTA
1 ATTTT--TATA
33611905 A-TTTTATA
1 ATTTTTATA
*
33611913 ATTTTTAAA
1 ATTTTTATA
33611922 ATTTTTAAATA
1 ATTTTT--ATA
*
33611933 ATTATTAATA
1 ATT-TTTATA
*
33611943 TTTTTTATA
1 ATTTTTATA
*
33611952 ATTTCTAT-
1 ATTTTTATA
33611960 -TTTTTATA
1 ATTTTTATA
33611968 GTCTCGAATT
Statistics
Matches: 85, Mismatches: 12, Indels: 26
0.69 0.10 0.21
Matches are distributed among these distances:
7 6 0.07
8 13 0.15
9 40 0.47
10 18 0.21
11 6 0.07
12 2 0.02
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (9 bp):
ATTTTTATA
Found at i:33611933 original size:20 final size:20
Alignment explanation
Indices: 33611910--33611947 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
33611900 ATTTAATTTT
*
33611910 ATAATTTTTAAAATTTTTAA
1 ATAATTATTAAAATTTTTAA
*
33611930 ATAATTATTAATATTTTT
1 ATAATTATTAAAATTTTT
33611948 TATAATTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATAATTATTAAAATTTTTAA
Found at i:33613881 original size:21 final size:21
Alignment explanation
Indices: 33613834--33613885 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
33613824 CACAGTATCA
*
33613834 AAATTTTTAAACAATATATTT
1 AAATTTTTAAACAATATAATT
*
33613855 ATAATTTTTAAAGAAT-TAAATT
1 A-AATTTTTAAACAATAT-AATT
33613877 AAATTTTTA
1 AAATTTTTA
33613886 TTATTTTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
AAATTTTTAAACAATATAATT
Found at i:33615719 original size:33 final size:33
Alignment explanation
Indices: 33615682--33615746 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
33615672 CGAGCTAAAG
* * *
33615682 ACACATCAATTACGATTATAGTCCTCATCAAAT
1 ACACATCAAGTACAATAATAGTCCTCATCAAAT
* *
33615715 ACACATCAAGTACAATAATAGTCTTTATCAAA
1 ACACATCAAGTACAATAATAGTCCTCATCAAA
33615747 GTAGCCTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.43, C:0.22, G:0.06, T:0.29
Consensus pattern (33 bp):
ACACATCAAGTACAATAATAGTCCTCATCAAAT
Found at i:33620941 original size:6 final size:6
Alignment explanation
Indices: 33620930--33621014 Score: 98
Period size: 6 Copynumber: 14.2 Consensus size: 6
33620920 AACTAATAAG
* * * *
33620930 TTATTA TTATTA TTATTA TCAATA TTATTA TGATTA TTATTA ATATTA
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA
* * * *
33620978 TTAATA TTAATA TTAATA TTAATA TTATTA TTATTA T
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA T
33621015 CTATGTCTTG
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 69 1.00
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (6 bp):
TTATTA
Found at i:33620957 original size:21 final size:21
Alignment explanation
Indices: 33620931--33621013 Score: 121
Period size: 21 Copynumber: 4.0 Consensus size: 21
33620921 ACTAATAAGT
*
33620931 TATTATTATTATTATTATCAA
1 TATTATTATTATTATTATTAA
*
33620952 TATTATTATGATTATTATTAA
1 TATTATTATTATTATTATTAA
* *
33620973 TATTATTAATATTAATATTAA
1 TATTATTATTATTATTATTAA
*
33620994 TATTAATATTATTATTATTA
1 TATTATTATTATTATTATTA
33621014 TCTATGTCTT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (21 bp):
TATTATTATTATTATTATTAA
Found at i:33631625 original size:24 final size:24
Alignment explanation
Indices: 33631598--33631649 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
33631588 AAATTTAGGG
*
33631598 TTTAGAAATTAGAAATAAAG-GCAA
1 TTTAGAAATTAAAAATAAAGAG-AA
**
33631622 TTTAGGTATTAAAAATAAAGAGAA
1 TTTAGAAATTAAAAATAAAGAGAA
33631646 TTTA
1 TTTA
33631650 AATAATTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.15, T:0.31
Consensus pattern (24 bp):
TTTAGAAATTAAAAATAAAGAGAA
Found at i:33634648 original size:39 final size:39
Alignment explanation
Indices: 33634594--33634704 Score: 186
Period size: 39 Copynumber: 2.8 Consensus size: 39
33634584 TATAAGATTT
*
33634594 TGAAACTAATAGTTACTGTTTGATGAGGATTGAAATTAA
1 TGAAATTAATAGTTACTGTTTGATGAGGATTGAAATTAA
*
33634633 TGAAATTAATAGTTACTGTTTGATAAGGATTGAAATTAA
1 TGAAATTAATAGTTACTGTTTGATGAGGATTGAAATTAA
* *
33634672 TGAAATTATTAGTTACTGTTGGATGAGGATTGA
1 TGAAATTAATAGTTACTGTTTGATGAGGATTGA
33634705 GAGTTTAAAG
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 67 1.00
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.38
Consensus pattern (39 bp):
TGAAATTAATAGTTACTGTTTGATGAGGATTGAAATTAA
Found at i:33639601 original size:33 final size:33
Alignment explanation
Indices: 33639559--33639624 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
33639549 CACAGAGAGT
* *
33639559 TACACATCAATTACGATTATAGTCCTCATCAAA
1 TACACATCAATTACAATAATAGTCCTCATCAAA
* *
33639592 TACACATCAATTACAATAATAGTCTTTATCAAA
1 TACACATCAATTACAATAATAGTCCTCATCAAA
33639625 GTAGCCTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.32
Consensus pattern (33 bp):
TACACATCAATTACAATAATAGTCCTCATCAAA
Found at i:33642330 original size:33 final size:33
Alignment explanation
Indices: 33642293--33642357 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
33642283 TTTAGGCTAC
* *
33642293 TTTGATAAAGACTATT-ATTGTACTTGATGTGTA
1 TTTGATAAAGACT-TTAATCGTAATTGATGTGTA
* *
33642326 TTTGATGAGGACTTTAATCGTAATTGATGTGT
1 TTTGATAAAGACTTTAATCGTAATTGATGTGT
33642358 CTCCAACCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 2 0.07
33 25 0.93
ACGTcount: A:0.28, C:0.06, G:0.22, T:0.45
Consensus pattern (33 bp):
TTTGATAAAGACTTTAATCGTAATTGATGTGTA
Found at i:33645390 original size:33 final size:33
Alignment explanation
Indices: 33645335--33645400 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
33645325 CACAGAGAGT
* *
33645335 TACACATCAATTACGATTATAGTCCTCATCAAA
1 TACACATCAATTACCATAATAGTCCTCATCAAA
* * *
33645368 TACACATCAATTTCCATAATAGTCTTTATCAAA
1 TACACATCAATTACCATAATAGTCCTCATCAAA
33645401 GTAGCCTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.33
Consensus pattern (33 bp):
TACACATCAATTACCATAATAGTCCTCATCAAA
Found at i:33646954 original size:2 final size:2
Alignment explanation
Indices: 33646949--33646978 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
33646939 GTTTTTTATC
33646949 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
33646979 GTCTCACGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33647542 original size:2 final size:2
Alignment explanation
Indices: 33647535--33647560 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
33647525 GAGCTTCATA
33647535 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
33647561 GAATTTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33648397 original size:16 final size:16
Alignment explanation
Indices: 33648373--33648405 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
33648363 GCCCGAATAT
33648373 AATAAATATTTTTAAA
1 AATAAATATTTTTAAA
*
33648389 AATATATATTTTTAAA
1 AATAAATATTTTTAAA
33648405 A
1 A
33648406 TACTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATAAATATTTTTAAA
Found at i:33650926 original size:31 final size:31
Alignment explanation
Indices: 33650888--33651012 Score: 119
Period size: 31 Copynumber: 4.1 Consensus size: 31
33650878 CTTTGCCAAG
*
33650888 TGTGTATTTTCAGAACAGGAAAACACCGAAA
1 TGTGTATTTTCAGAACAGGACAACACCGAAA
** ** *
33650919 TGTGTATTTAGAGAA-A-GACAACATTGAAG
1 TGTGTATTTTCAGAACAGGACAACACCGAAA
*
33650948 TGGTGTATTTTCAGAACAGGACAATACCGAAA
1 T-GTGTATTTTCAGAACAGGACAACACCGAAA
** * * *
33650980 TGCATATTTTCAAAACAAGACAATACCGAAA
1 TGTGTATTTTCAGAACAGGACAACACCGAAA
33651011 TG
1 TG
33651013 CGTAGGACAA
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
29 10 0.13
30 13 0.17
31 42 0.56
32 10 0.13
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (31 bp):
TGTGTATTTTCAGAACAGGACAACACCGAAA
Found at i:33651076 original size:29 final size:29
Alignment explanation
Indices: 33651039--33651143 Score: 104
Period size: 29 Copynumber: 3.6 Consensus size: 29
33651029 AGTGTGTATT
* * *
33651039 TTCATAACAAGACAGCACTGAAGTGCATA
1 TTCAGAACAAGACAACACTAAAGTGCATA
* *
33651068 TTCAGAACAAGACAACA-TCAAAGTGTGTATT
1 TTCAGAACAAGACAACACT-AAA--GTGCATA
* *
33651099 TTCAGAACAGGACAACACCAAAGTGCATA
1 TTCAGAACAAGACAACACTAAAGTGCATA
*
33651128 TTCAGAACAAGGCAAC
1 TTCAGAACAAGACAAC
33651144 GCTGAAATGC
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
28 1 0.02
29 36 0.59
31 24 0.39
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (29 bp):
TTCAGAACAAGACAACACTAAAGTGCATA
Found at i:33651123 original size:60 final size:60
Alignment explanation
Indices: 33651018--33651143 Score: 180
Period size: 60 Copynumber: 2.1 Consensus size: 60
33651008 AAATGCGTAG
* * * **
33651018 GACAACACCGAAGTGTGTATTTTCATAACAAGACAGCACTGAAGTGCATATTCAGAACAA
1 GACAACACCAAAGTGTGTATTTTCAGAACAAGACAACACCAAAGTGCATATTCAGAACAA
* *
33651078 GACAACATCAAAGTGTGTATTTTCAGAACAGGACAACACCAAAGTGCATATTCAGAACAA
1 GACAACACCAAAGTGTGTATTTTCAGAACAAGACAACACCAAAGTGCATATTCAGAACAA
*
33651138 GGCAAC
1 GACAAC
33651144 GCTGAAATGC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (60 bp):
GACAACACCAAAGTGTGTATTTTCAGAACAAGACAACACCAAAGTGCATATTCAGAACAA
Found at i:33651240 original size:29 final size:29
Alignment explanation
Indices: 33651016--33651241 Score: 86
Period size: 29 Copynumber: 7.6 Consensus size: 29
33651006 CGAAATGCGT
* * *
33651016 AGGACAACACCGAAGTGTGTATTTTCATAAC
1 AGGACAACACTGAAGTGCGTA--TTCAGAAC
* * *
33651047 AAGACAGCACTGAAGTGCATATTCAGAAC
1 AGGACAACACTGAAGTGCGTATTCAGAAC
* * *
33651076 AAGACAACA-TCAAAGTGTGTATTTTCAGAAC
1 AGGACAACACT-GAAGTGCGTA--TTCAGAAC
** *
33651107 AGGACAACACCAAAGTGCATATTCAGAAC
1 AGGACAACACTGAAGTGCGTATTCAGAAC
* *
33651136 AAGG-CAACGCTGAAATGCGCGCGTATTTTCAGAAC
1 -AGGACAACACTG-AA---GTGCGTA--TTCAGAAC
* * * * ***
33651171 AGGAC-AGATTAAAGTGTGTATTTTTAA-
1 AGGACAACACTGAAGTGCGTATTCAGAAC
* * *
33651198 A--ATAGCACCGAAGTGCGTATTCAGAAC
1 AGGACAACACTGAAGTGCGTATTCAGAAC
33651225 AGGACAACACTGAAGTG
1 AGGACAACACTGAAGTG
33651242 TTTATTTTTA
Statistics
Matches: 138, Mismatches: 41, Indels: 34
0.65 0.19 0.16
Matches are distributed among these distances:
25 1 0.01
26 13 0.09
27 2 0.01
28 5 0.04
29 46 0.33
30 10 0.07
31 40 0.29
33 7 0.05
34 5 0.04
35 9 0.07
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (29 bp):
AGGACAACACTGAAGTGCGTATTCAGAAC
Found at i:33651292 original size:29 final size:29
Alignment explanation
Indices: 33651214--33651293 Score: 79
Period size: 31 Copynumber: 2.7 Consensus size: 29
33651204 ACCGAAGTGC
* * * *
33651214 GTATTCAGAACAGGACAACACTGAAGTGT
1 GTATTTAGAACAAGACAACACTAAAGAGT
* * *
33651243 TTATTTTTAGAATAAGGCAACACTAAAGAGT
1 GTA--TTTAGAACAAGACAACACTAAAGAGT
33651274 GTATTTAGAACAAGACAACA
1 GTATTTAGAACAAGACAACA
33651294 TCAAAGTGCA
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
29 17 0.44
31 22 0.56
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (29 bp):
GTATTTAGAACAAGACAACACTAAAGAGT
Found at i:33653184 original size:23 final size:23
Alignment explanation
Indices: 33653158--33653203 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
33653148 TCGCTCTCGT
33653158 TGTCAGTCATTGTCTCTTAACCC
1 TGTCAGTCATTGTCTCTTAACCC
33653181 TGTCAGTCATTGTCTCTTAACCC
1 TGTCAGTCATTGTCTCTTAACCC
33653204 ATGCTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.30, G:0.13, T:0.39
Consensus pattern (23 bp):
TGTCAGTCATTGTCTCTTAACCC
Found at i:33655668 original size:131 final size:136
Alignment explanation
Indices: 33655409--33655670 Score: 336
Period size: 136 Copynumber: 1.9 Consensus size: 136
33655399 TAAATATGGA
* * * * * *
33655409 TTTGAATTTTTAAAACGATATTTTTGATAGAGGTACCCATATAAATCTCGAATATAGACAGTAAA
1 TTTGAATTTTTAAAACGATATTCTTAAGAGAGATA-CCAAATAAATCTCGAACATAGACAGTAAA
** * *
33655474 ACGGATATGAAATAAATAAATAAATAAGTGAAGTTTGAGAAATGATGCCGAGAACTTGTCTATAT
65 ACGGATATGAAAT-AATAAATAAATAAGTGAAGTAAGAGAAATGATGACGAGAACTTGCCTATAT
33655539 ATAAGTGG
129 ATAAGTGG
* * *
33655547 TTTGAATTTTTAAAACGATATTCTTAAGAGAGATA-CAAATAATTTTTGAACATAGACAGTAAAA
1 TTTGAATTTTTAAAACGATATTCTTAAGAGAGATACCAAATAAATCTCGAACATAGACAGTAAAA
* *
33655611 CGGATATGAAAT-A-AAA-AAA-AGGTGAAGTAAGAGAAATGATGATGAGAACTTGCCTATATA
66 CGGATATGAAATAATAAATAAATAAGTGAAGTAAGAGAAATGATGACGAGAACTTGCCTATATA
33655671 AGTGCAATCG
Statistics
Matches: 109, Mismatches: 15, Indels: 7
0.83 0.11 0.05
Matches are distributed among these distances:
131 35 0.32
132 3 0.03
133 3 0.03
134 1 0.01
136 36 0.33
138 31 0.28
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.30
Consensus pattern (136 bp):
TTTGAATTTTTAAAACGATATTCTTAAGAGAGATACCAAATAAATCTCGAACATAGACAGTAAAA
CGGATATGAAATAATAAATAAATAAGTGAAGTAAGAGAAATGATGACGAGAACTTGCCTATATAT
AAGTGG
Found at i:33657195 original size:20 final size:20
Alignment explanation
Indices: 33657167--33657213 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
33657157 CAAAACTATG
33657167 AAAAAATATTAATAATTATA
1 AAAAAATATTAATAATTATA
* *
33657187 AACAAATATTAATAATTTTA
1 AAAAAATATTAATAATTATA
33657207 AAAAAAT
1 AAAAAAT
33657214 TCTAAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAAAATATTAATAATTATA
Found at i:33657249 original size:25 final size:28
Alignment explanation
Indices: 33657194--33657247 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
33657184 ATAAACAAAT
* *
33657194 ATTAATAATTTTAAAAAAATTCTAAAAA
1 ATTAATAATTATAAAAAAAGTCTAAAAA
33657222 ATTAA-AATTATAAAAAAAGT-TAAAAA
1 ATTAATAATTATAAAAAAAGTCTAAAAA
33657248 TTTTTTACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 6 0.25
27 13 0.54
28 5 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (28 bp):
ATTAATAATTATAAAAAAAGTCTAAAAA
Found at i:33659697 original size:21 final size:20
Alignment explanation
Indices: 33659626--33659711 Score: 68
Period size: 21 Copynumber: 4.2 Consensus size: 20
33659616 ATTTTATACT
*
33659626 TTTTATGAATTATTAATATTAA
1 TTTTAT-AATTTTTAATA-TAA
* * *
33659648 TATTTTTATTTTTTAATTTAA
1 T-TTTATAATTTTTAATATAA
33659669 TTTTATAATTTTTAA-ATAA
1 TTTTATAATTTTTAATATAA
*
33659688 TTATTAATAATTTTT-TTATAA
1 TT-TT-ATAATTTTTAATATAA
33659709 TTT
1 TTT
33659712 CTTTTTTATA
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
19 5 0.10
20 15 0.29
21 19 0.37
22 9 0.17
23 4 0.08
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (20 bp):
TTTTATAATTTTTAATATAA
Found at i:33662838 original size:2 final size:2
Alignment explanation
Indices: 33662831--33662869 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
33662821 GAATTTACAA
33662831 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
33662870 ACAATGCCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:33663070 original size:30 final size:30
Alignment explanation
Indices: 33663014--33663089 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
33663004 ATTTCTTATG
*
33663014 CCAATATCTCGATACTCATATATTTGACTT-T
1 CCAATAT-TTGATAC-CATATATTTGACTTGT
*
33663045 CCAATATTTGATACCAATATCTTTGACTTGT
1 CCAATATTTGATACC-ATATATTTGACTTGT
*
33663076 -CATTATTTGATACC
1 CCAATATTTGATACC
33663090 CATTGTAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
29 1 0.03
30 31 0.77
31 8 0.20
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (30 bp):
CCAATATTTGATACCATATATTTGACTTGT
Found at i:33663560 original size:7 final size:7
Alignment explanation
Indices: 33663545--33663575 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
33663535 TCTTTTGTAA
*
33663545 TTTTCTT
1 TTTTATT
33663552 TTTTATT
1 TTTTATT
33663559 TTTTATT
1 TTTTATT
33663566 TTTTATT
1 TTTTATT
33663573 TTT
1 TTT
33663576 GGCGATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTATT
Found at i:33663561 original size:13 final size:13
Alignment explanation
Indices: 33663533--33663575 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
33663523 AAAAAGGGAC
* *
33663533 TTTCTTTTGTAAT
1 TTTCTTTTTTATT
33663546 TTTCTTTTTTATTT
1 TTTCTTTTTTA-TT
*
33663560 TTTATTTTTTATT
1 TTTCTTTTTTATT
33663573 TTT
1 TTT
33663576 GGCGATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.12, C:0.05, G:0.02, T:0.81
Consensus pattern (13 bp):
TTTCTTTTTTATT
Found at i:33670164 original size:2 final size:2
Alignment explanation
Indices: 33670157--33670192 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
33670147 GAATTTACAA
33670157 AG AG AG AG AG A- AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
33670193 ACAATGCCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:33670431 original size:30 final size:30
Alignment explanation
Indices: 33670347--33670431 Score: 143
Period size: 30 Copynumber: 2.8 Consensus size: 30
33670337 CCAATATCTC
* *
33670347 GATACCCATATCTTTAACTTTCCAGTATTT
1 GATACCCATATCTTTGACTTTCCATTATTT
33670377 GATACCCATATCTTTGACTTTCCATTATTT
1 GATACCCATATCTTTGACTTTCCATTATTT
*
33670407 GATACTCATATCTTTGACTTTCCAT
1 GATACCCATATCTTTGACTTTCCAT
33670432 AAATATGGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.25, C:0.24, G:0.07, T:0.45
Consensus pattern (30 bp):
GATACCCATATCTTTGACTTTCCATTATTT
Found at i:33673343 original size:11 final size:10
Alignment explanation
Indices: 33673327--33673351 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
33673317 GCACCTAAAA
33673327 TTTTTTTTTC
1 TTTTTTTTTC
33673337 TTTTTTTTTC
1 TTTTTTTTTC
33673347 TTTTT
1 TTTTT
33673352 CGTATATCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:33674780 original size:3 final size:3
Alignment explanation
Indices: 33674772--33674838 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
33674762 AAATGAGCGG
33674772 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
33674820 TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
33674839 CTCAATTCAC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:33677043 original size:43 final size:43
Alignment explanation
Indices: 33676996--33677216 Score: 311
Period size: 43 Copynumber: 5.1 Consensus size: 43
33676986 AAAGGGTACT
* *
33676996 TTTAGCGGCGTTTGTGATAAAAGCGCCACTAGAGGTCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
* * *
33677039 TTTAGCAGCATTTGTGATAAAAGCGCTGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
* * *
33677082 TTTAACGGCTTTTGTGATAAAAGCGCCGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
*
33677125 TTTAGCGGCGTTTGTGGGT-AAAGCGCCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGT-GATAAAAGCGCCGCTAAAGGTCATGTTC
*
33677168 TTTAGCGGCGTTTGTGGAT-AAAGCACCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGT-GATAAAAGCGCCGCTAAAGGTCATGTTC
*
33677211 TATAGC
1 TTTAGC
33677217 AGTGTTTTTT
Statistics
Matches: 160, Mismatches: 17, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
43 158 0.99
44 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
Found at i:33681428 original size:17 final size:17
Alignment explanation
Indices: 33681406--33681451 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
33681396 CTAAGTTTAG
33681406 AAATAATTGTAAATACT
1 AAATAATTGTAAATACT
* * *
33681423 AAATAATTG-GATTATT
1 AAATAATTGTAAATACT
33681439 AAATAATTGTAAA
1 AAATAATTGTAAA
33681452 ATTTTAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.37
Consensus pattern (17 bp):
AAATAATTGTAAATACT
Found at i:33681574 original size:16 final size:16
Alignment explanation
Indices: 33681555--33681585 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33681545 TAGAAAAAAT
33681555 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
33681571 TTTCAAATTTATATG
1 TTTCAAATATATATG
33681586 CTCTAACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:33683184 original size:22 final size:22
Alignment explanation
Indices: 33683157--33683217 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
33683147 TAACGAATTA
33683157 ATTATAAATTATTTTATTTGAT
1 ATTATAAATTATTTTATTTGAT
* *
33683179 TTTATATA-TATGTTTATTT-AT
1 ATTATAAATTAT-TTTATTTGAT
*
33683200 ATT-T-AATTATTTTGTTTG
1 ATTATAAATTATTTTATTTG
33683218 CTAACGTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
19 7 0.23
20 4 0.13
21 7 0.23
22 13 0.42
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (22 bp):
ATTATAAATTATTTTATTTGAT
Found at i:33684170 original size:21 final size:24
Alignment explanation
Indices: 33684141--33684187 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 24
33684131 TATATTGTTG
33684141 ATTACTTAAATT-TAAATT-TATT
1 ATTACTTAAATTATAAATTATATT
33684163 ATTA-TTAAATTAATAAATTATATT
1 ATTACTTAAATT-ATAAATTATATT
33684187 A
1 A
33684188 ATAATTTAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 7 0.32
22 4 0.18
23 6 0.27
24 5 0.23
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTACTTAAATTATAAATTATATT
Found at i:33692911 original size:14 final size:15
Alignment explanation
Indices: 33692888--33692924 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
33692878 TTATCAACAA
*
33692888 TATTTT-AATATTAT
1 TATTTTAAATAATAT
33692902 T-TTTTAAATAATAT
1 TATTTTAAATAATAT
33692916 TATTTTAAA
1 TATTTTAAA
33692925 ACAAAAAGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 4 0.20
14 9 0.45
15 7 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTTTAAATAATAT
Found at i:33693898 original size:2 final size:2
Alignment explanation
Indices: 33693891--33693915 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33693881 GACAAAAGAT
33693891 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 T
33693916 TATTAAATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33707663 original size:17 final size:16
Alignment explanation
Indices: 33707641--33707673 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
33707631 TAATTAAATT
33707641 ATTATAAATTTATAAAA
1 ATTATAAA-TTATAAAA
33707658 ATTATAAATTATAAAA
1 ATTATAAATTATAAAA
33707674 TCCGATTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTATAAATTATAAAA
Found at i:33710245 original size:2 final size:2
Alignment explanation
Indices: 33710238--33710284 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
33710228 TTAAATGTTG
33710238 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
33710280 TA TA T
1 TA TA T
33710285 GATCTAGATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33713169 original size:42 final size:43
Alignment explanation
Indices: 33713009--33713185 Score: 214
Period size: 43 Copynumber: 4.1 Consensus size: 43
33712999 GAAAAAAGTA
* * * *
33713009 CCGCTATAGAACATGACATTTAGCGGCGC-TTTACCCTCAAACG
1 CCGCTAAAGAACATGACCTTTAGCGGCGCTTTTA-TCACAAACG
** * ** *
33713052 CCGCTAAAGGTCATGATCTTTAGCGTTGCTTTTATCACAAACT
1 CCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACG
*
33713095 CCGCTAAAGAACATGACCTTTAGCGGCACTTTTATCACAAACG
1 CCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACG
*
33713138 CCGCTAAAG-ACATGACCTTTAGCGACGCTTTTATCACAAACG
1 CCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACG
*
33713180 CTGCTA
1 CCGCTA
33713186 TAAGTACCGT
Statistics
Matches: 113, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
42 36 0.32
43 73 0.65
44 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.27
Consensus pattern (43 bp):
CCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACG
Found at i:33716680 original size:31 final size:31
Alignment explanation
Indices: 33716642--33716710 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
33716632 TAAAAAAAAA
** *
33716642 TAGTGACTTAAATAAAAACTTTTGAATAGTT
1 TAGTGACTTAAATAAAAACTTTCAAATAATT
*
33716673 TAGTGACTTAAATGAAAACTTTCAAATAATT
1 TAGTGACTTAAATAAAAACTTTCAAATAATT
33716704 TAGTGAC
1 TAGTGAC
33716711 CAAATTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (31 bp):
TAGTGACTTAAATAAAAACTTTCAAATAATT
Found at i:33728349 original size:21 final size:21
Alignment explanation
Indices: 33728325--33728374 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
33728315 TTCTGCTCTG
33728325 CTCTGCTTCCCTCGCTGCAAC
1 CTCTGCTTCCCTCGCTGCAAC
**
33728346 CTCTGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAAC
33728367 CTCTGCTT
1 CTCTGCTT
33728375 TAAGTTGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.04, C:0.48, G:0.16, T:0.32
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAAC
Found at i:33729995 original size:46 final size:45
Alignment explanation
Indices: 33729942--33730080 Score: 188
Period size: 46 Copynumber: 3.0 Consensus size: 45
33729932 ACGTTGTTAT
*
33729942 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTAC-GAAATACCATACCTACTTTTCAC
* * **
33729988 AACTCAGTACGGTTTTCTTTATTGAAATACCATACCTACTTTTTGC
1 AACTCAGTATGGTTTTCTTTA-CGAAATACCATACCTACTTTTCAC
* *
33730034 AACTCAGTATGGTTTTCTTTATCGAAATATCGTACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTA-CGAAATACCATACCTACTTTTCAC
33730080 A
1 A
33730081 CTTTGCCATG
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
46 81 1.00
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (45 bp):
AACTCAGTATGGTTTTCTTTACGAAATACCATACCTACTTTTCAC
Found at i:33740635 original size:28 final size:27
Alignment explanation
Indices: 33740596--33740649 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
33740586 GAAGAAGAAA
*
33740596 TTTAAAATATTTTTAAAT-TAAAAATAC
1 TTTAAAACA-TTTTAAATATAAAAATAC
*
33740623 TTTATAAACATTTTAAATATGAAAATA
1 TTTA-AAACATTTTAAATATAAAAATA
33740650 AACTATGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (27 bp):
TTTAAAACATTTTAAATATAAAAATAC
Found at i:33741025 original size:21 final size:23
Alignment explanation
Indices: 33740986--33741030 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
33740976 AATAAAATAT
* *
33740986 AAGTATAAATAATATAATT-AAG
1 AAGTATAAATAACAAAATTCAAG
33741008 AAGT-TAAATAACAAAATTCAAG
1 AAGTATAAATAACAAAATTCAAG
33741030 A
1 A
33741031 GGGAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.27
Consensus pattern (23 bp):
AAGTATAAATAACAAAATTCAAG
Found at i:33741426 original size:22 final size:23
Alignment explanation
Indices: 33741392--33741435 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
33741382 TTAACAATTT
* *
33741392 TTTAAGTTAAATT-TTTTTAAAC
1 TTTAACTTAAATTAATTTTAAAC
*
33741414 TTTAACTTCAATTAATTTTAAA
1 TTTAACTTAAATTAATTTTAAA
33741436 TATTTTAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (23 bp):
TTTAACTTAAATTAATTTTAAAC
Found at i:33745945 original size:39 final size:39
Alignment explanation
Indices: 33745896--33745974 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
33745886 TGATTCTTTG
33745896 TTGTTATCTTTTCCCTTCCCTCCCAGTATTCATCCTGTT
1 TTGTTATCTTTTCCCTTCCCTCCCAGTATTCATCCTGTT
33745935 TTGTTATCTTTTCCCTTCCCTCCCAGTATTCATCCTGTT
1 TTGTTATCTTTTCCCTTCCCTCCCAGTATTCATCCTGTT
33745974 T
1 T
33745975 ATCTTTTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.10, C:0.33, G:0.08, T:0.49
Consensus pattern (39 bp):
TTGTTATCTTTTCCCTTCCCTCCCAGTATTCATCCTGTT
Found at i:33746816 original size:83 final size:83
Alignment explanation
Indices: 33746677--33746843 Score: 325
Period size: 83 Copynumber: 2.0 Consensus size: 83
33746667 AATGTCATTC
*
33746677 TCCTGCCCCTTCTCTTTCGTTTGTTTTTCTTTTCTGATAGTGCAATCCTCATTGCAACCATAAAT
1 TCCTGCCCCTTCTCTTTCGTTTGTTTTTCTTTTCTGATAGTGCAATCCTCATTGCAACCATAAAC
33746742 GATGATTTAGAGAACATG
66 GATGATTTAGAGAACATG
33746760 TCCTGCCCCTTCTCTTTCGTTTGTTTTTCTTTTCTGATAGTGCAATCCTCATTGCAACCATAAAC
1 TCCTGCCCCTTCTCTTTCGTTTGTTTTTCTTTTCTGATAGTGCAATCCTCATTGCAACCATAAAC
33746825 GATGATTTAGAGAACATG
66 GATGATTTAGAGAACATG
33746843 T
1 T
33746844 TTCCCTTTTC
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (83 bp):
TCCTGCCCCTTCTCTTTCGTTTGTTTTTCTTTTCTGATAGTGCAATCCTCATTGCAACCATAAAC
GATGATTTAGAGAACATG
Found at i:33752626 original size:43 final size:44
Alignment explanation
Indices: 33752552--33752657 Score: 101
Period size: 43 Copynumber: 2.5 Consensus size: 44
33752542 TCGAAAGTGT
* * *
33752552 ATGGCACTAAGTGTGCGAATTCAAGATAGCTTTAGTTGAAT-AA
1 ATGGCACTAAGTGTGCGAACTCAAGAGAGCTTCAGTTGAATGAA
* * * * **
33752595 ATGGCACTAAGTGTGCGGCACT-GAGAGAGCTTCGGTTTAATGTG
1 ATGGCACTAAGTGTGC-GAACTCAAGAGAGCTTCAGTTGAATGAA
33752639 ATGGCACTAAGTGTG-GAAC
1 ATGGCACTAAGTGTGCGAAC
33752658 ATCGTTATAG
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
42 3 0.06
43 30 0.59
44 18 0.35
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.27
Consensus pattern (44 bp):
ATGGCACTAAGTGTGCGAACTCAAGAGAGCTTCAGTTGAATGAA
Found at i:33752883 original size:19 final size:19
Alignment explanation
Indices: 33752838--33752884 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
33752828 AGGTTTGATG
33752838 GAATAT-ATATATATAAAT
1 GAATATGATATATATAAAT
*
33752856 GAGTAATGAT-TATATGAAAT
1 GAAT-ATGATATATAT-AAAT
33752876 GAATATGAT
1 GAATATGAT
33752885 GATCCTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 3 0.12
19 12 0.50
20 9 0.38
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36
Consensus pattern (19 bp):
GAATATGATATATATAAAT
Found at i:33755299 original size:40 final size:40
Alignment explanation
Indices: 33755255--33755386 Score: 142
Period size: 40 Copynumber: 3.3 Consensus size: 40
33755245 CTATGTTTAT
* * *
33755255 CACTTAGTGAGAGAATTGAGATAACTTCAGCTATTTATGG
1 CACTTAGTGTGAGAATTGAGATAGCTTCGGCTATTTATGG
* *
33755295 CACTTAGTGTGCG-ATTGGGAATAGCTTCGGCTATATT-TGG
1 CACTTAGTGTGAGAATTGAG-ATAGCTTCGGCTAT-TTATGG
* * * *
33755335 CACTTAGTGTGTGAGACTGAGATAGCTTCGGCTATGTAAGG
1 CACTTAGTGTGAGA-ATTGAGATAGCTTCGGCTATTTATGG
33755376 CACTTAGTGTG
1 CACTTAGTGTG
33755387 CGAGATTATA
Statistics
Matches: 77, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
39 5 0.06
40 39 0.51
41 29 0.38
42 4 0.05
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (40 bp):
CACTTAGTGTGAGAATTGAGATAGCTTCGGCTATTTATGG
Found at i:33755369 original size:41 final size:40
Alignment explanation
Indices: 33755271--33755391 Score: 120
Period size: 41 Copynumber: 3.0 Consensus size: 40
33755261 GTGAGAGAAT
* * * *
33755271 TGAGATAACTTCAGCTATTTATGGCACTTA--GTGTGCGAT
1 TGAGATAGCTTCGGCTATTT-TGGCACTTAGTGTGTGAGAC
*
33755310 TGGGAATAGCTTCGGCTATATTTGGCACTTAGTGTGTGAGAC
1 TGAG-ATAGCTTCGGCTAT-TTTGGCACTTAGTGTGTGAGAC
** *
33755352 TGAGATAGCTTCGGCTATGTAAGGCACTTAGTGTGCGAGA
1 TGAGATAGCTTCGGCTAT-TTTGGCACTTAGTGTGTGAGA
33755392 TTATAATGGT
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
39 3 0.04
40 21 0.31
41 34 0.50
42 10 0.15
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.32
Consensus pattern (40 bp):
TGAGATAGCTTCGGCTATTTTGGCACTTAGTGTGTGAGAC
Found at i:33759673 original size:11 final size:11
Alignment explanation
Indices: 33759621--33759679 Score: 50
Period size: 11 Copynumber: 5.2 Consensus size: 11
33759611 TATAAATAGA
*
33759621 AATACAATAAT
1 AATATAATAAT
33759632 AATTATAATAAT
1 AA-TATAATAAT
*
33759644 AATACAA-AATT
1 AATATAATAA-T
33759655 AATATAAT-AT
1 AATATAATAAT
33759665 AATAGTAATGAAT
1 AATA-TAAT-AAT
33759678 AA
1 AA
33759680 GTAAATATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
10 7 0.18
11 18 0.46
12 10 0.26
13 4 0.10
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (11 bp):
AATATAATAAT
Found at i:33766730 original size:51 final size:51
Alignment explanation
Indices: 33766620--33766848 Score: 171
Period size: 51 Copynumber: 4.5 Consensus size: 51
33766610 TATCGATGAA
** * * * * *
33766620 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAG-TAATG-G
1 CACGTGTGTAGTACTAAGTGAAGGCTACTATGTGTACCAAGAAGCT-TTGAG
* *
33766670 TCACATGTGTAGTACTAAGTGAAGGCTATTATGTGTACCAAGAAGCTTTGAG
1 -CACGTGTGTAGTACTAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
* ** * * * * * **
33766722 CATGTGTGTAGTACTGTGTGAATGCTACCACGTGT-CTC-GGTAAACTACG-G
1 CACGTGTGTAGTACTAAGTGAAGGCTACTATGTGTAC-CAAG-AAGCTTTGAG
* *
33766772 TTACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
1 -CACGTGTGTAGTACTAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
* *
33766824 CACGAGTGTAGTACTGAGTGAAGGC
1 CACGTGTGTAGTACTAAGTGAAGGC
33766849 GTGAGCCGTA
Statistics
Matches: 133, Mismatches: 37, Indels: 16
0.72 0.20 0.09
Matches are distributed among these distances:
50 3 0.02
51 125 0.94
52 5 0.04
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (51 bp):
CACGTGTGTAGTACTAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
Found at i:33766755 original size:102 final size:102
Alignment explanation
Indices: 33766620--33766848 Score: 343
Period size: 102 Copynumber: 2.2 Consensus size: 102
33766610 TATCGATGAA
* * *
33766620 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGAT-AAGTAATGGTCACATGTGTAGTA
1 CACGTGTGTAGTACTGTGTGAAGGCTACCACGTGTATCGATAAACT-ACGGTCACATGTGTAGTA
*
33766684 CTAAGTGAAGGCTATTATGTGTACCAAGAAGCTTTGAG
65 CTAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
* * * * *
33766722 CATGTGTGTAGTACTGTGTGAATGCTACCACGTGTCTCGGTAAACTACGGTTACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACCACGTGTATCGATAAACTACGGTCACATGTGTAGTAC
33766787 TAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
66 TAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
* *
33766824 CACGAGTGTAGTACTGAGTGAAGGC
1 CACGTGTGTAGTACTGTGTGAAGGC
33766849 GTGAGCCGTA
Statistics
Matches: 113, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
102 110 0.97
103 3 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (102 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACCACGTGTATCGATAAACTACGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
Found at i:33774851 original size:18 final size:18
Alignment explanation
Indices: 33774794--33774840 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
33774784 AGAACTATTT
33774794 ATGGTCAAAATAGAAATG
1 ATGGTCAAAATAGAAATG
33774812 ATGGTCAAAATAGAAATG
1 ATGGTCAAAATAGAAATG
33774830 ATGGTCAAAAT
1 ATGGTCAAAAT
33774841 TGGAATAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.49, C:0.06, G:0.21, T:0.23
Consensus pattern (18 bp):
ATGGTCAAAATAGAAATG
Found at i:33774898 original size:45 final size:45
Alignment explanation
Indices: 33774815--33774906 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
33774805 AGAAATGATG
* *
33774815 GTCAAAATAGAAATGATGGTCAAAATTGGAATAATGGCATGCAAA
1 GTCAAAATAGAAATGATAGTCAAAATTGGAATAATGGCATACAAA
* ** **
33774860 GTCAAAATAGAAATGGTAGTCAAAATTGGGGTGCTGGCATACAAA
1 GTCAAAATAGAAATGATAGTCAAAATTGGAATAATGGCATACAAA
33774905 GT
1 GT
33774907 GAGAAATTGG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.42, C:0.10, G:0.25, T:0.23
Consensus pattern (45 bp):
GTCAAAATAGAAATGATAGTCAAAATTGGAATAATGGCATACAAA
Found at i:33775723 original size:18 final size:18
Alignment explanation
Indices: 33775688--33775723 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
33775678 CCTACTGTTG
*
33775688 ACGGGAGATAATGGTGAC
1 ACGGGAGATAATGCTGAC
*
33775706 ACGGGAGATATTGCTGAC
1 ACGGGAGATAATGCTGAC
33775724 GGGCCGTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.14, G:0.36, T:0.19
Consensus pattern (18 bp):
ACGGGAGATAATGCTGAC
Found at i:33786772 original size:29 final size:29
Alignment explanation
Indices: 33786730--33786787 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
33786720 TTATAACTTT
33786730 TTTTTATTTACCAAAATATTAT-AAAAAAA
1 TTTTTATTTACCAAAATA-TATCAAAAAAA
33786759 TTTTTATTTACCAAAATATATCAAAAAAA
1 TTTTTATTTACCAAAATATATCAAAAAAA
33786788 CAAAAAACAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 3 0.11
29 25 0.89
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.40
Consensus pattern (29 bp):
TTTTTATTTACCAAAATATATCAAAAAAA
Found at i:33787512 original size:37 final size:37
Alignment explanation
Indices: 33787471--33787568 Score: 178
Period size: 37 Copynumber: 2.6 Consensus size: 37
33787461 AAATTTTATA
*
33787471 TTTTAAATGAAAATAGAGTTATTAAATGAGAATAGTT
1 TTTTAAATTAAAATAGAGTTATTAAATGAGAATAGTT
33787508 TTTTAAATTAAAATAGAGTTATTAAATGAGAATAGTT
1 TTTTAAATTAAAATAGAGTTATTAAATGAGAATAGTT
*
33787545 TATTAAATTAAAATAGAGTTATTA
1 TTTTAAATTAAAATAGAGTTATTA
33787569 CTTAATTAGA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (37 bp):
TTTTAAATTAAAATAGAGTTATTAAATGAGAATAGTT
Found at i:33787515 original size:18 final size:19
Alignment explanation
Indices: 33787473--33787568 Score: 115
Period size: 19 Copynumber: 5.2 Consensus size: 19
33787463 ATTTTATATT
33787473 TTAAATGAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* * *
33787492 TTAAATGAGAATAG-TTTT
1 TTAAATGAAAATAGAGTTA
*
33787510 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
33787529 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
33787547 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
33787566 TTA
1 TTA
33787569 CTTAATTAGA
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
18 29 0.47
19 33 0.53
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.39
Consensus pattern (19 bp):
TTAAATGAAAATAGAGTTA
Found at i:33788276 original size:28 final size:29
Alignment explanation
Indices: 33788241--33788307 Score: 109
Period size: 29 Copynumber: 2.3 Consensus size: 29
33788231 TTTTTTGGGT
**
33788241 ATATTTTGGTAAA-TAAAAAAATTTTATA
1 ATATTTTGGTAAATTAAAAAAAAGTTATA
33788269 ATATTTTGGTAAATTAAAAAAAAGTTATA
1 ATATTTTGGTAAATTAAAAAAAAGTTATA
33788298 ATATTTTGGT
1 ATATTTTGGT
33788308 TATTTTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
28 13 0.36
29 23 0.64
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.43
Consensus pattern (29 bp):
ATATTTTGGTAAATTAAAAAAAAGTTATA
Found at i:33788357 original size:2 final size:2
Alignment explanation
Indices: 33788352--33788376 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33788342 CCCGTACATG
33788352 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
33788377 CTTTTTTTTA
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:33792218 original size:21 final size:19
Alignment explanation
Indices: 33792192--33792230 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
33792182 TTTCTTTCAA
33792192 TTCCTTATATACTATTATTCC
1 TTCCTTATAT--TATTATTCC
*
33792213 TTCCTTCTATTATTATTC
1 TTCCTTATATTATTATTC
33792231 TTCAGCTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
21 9 0.53
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (19 bp):
TTCCTTATATTATTATTCC
Found at i:33795032 original size:15 final size:16
Alignment explanation
Indices: 33795014--33795051 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
33795004 TTATTCAATC
*
33795014 TTATTTTATAT-TTTT
1 TTATTTTATATCATTT
33795029 TTATTTT-TATCATTT
1 TTATTTTATATCATTT
33795044 TTATTTTA
1 TTATTTTA
33795052 GTCAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTATATCATTT
Found at i:33797883 original size:17 final size:17
Alignment explanation
Indices: 33797850--33797887 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
33797840 TAACCTACCT
33797850 AATATATCACATCTATA
1 AATATATCACATCTATA
*
33797867 AATA-ATCATATCATATA
1 AATATATCACATC-TATA
33797884 AATA
1 AATA
33797888 CATAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (17 bp):
AATATATCACATCTATA
Found at i:33806617 original size:88 final size:87
Alignment explanation
Indices: 33806388--33806763 Score: 259
Period size: 90 Copynumber: 4.3 Consensus size: 87
33806378 AAAATGTCAA
* * * * *
33806388 CATCGTAGATAAAACAAACCAAAACAATCCA-ACTAT-TGATAATAAACCAAACATGAAAGATGT
1 CATCATAGAAAAAACAAACCAAAACAA-CCAGAATATGT-ATAATAAAACAAACATGAAAGATGC
* *
33806451 CGAT-AAAAGAAA-TTTACTCA-A-
64 CGATAAAAAAAAACATTA-TCACAT
** * * *** * * * **
33806472 CATCATAGCTAAAACAAACTAAAACCATTTGAACATGAACAATAAAACTGACATGAAAGATGCCG
1 CATCATAGAAAAAACAAACCAAAACAACCAGAATATGTATAATAAAACAAACATGAAAGATGCCG
33806537 ATAAAAGAAAAACATTATCA-AT
66 ATAAAA-AAAAACATTATCACAT
* * * *
33806559 GGCATCCTA-AAAAAACAAACCAAAGCAACTC-GAATATAG-ATAATAAAACAAATATGAAAAAT
1 --CATCATAGAAAAAACAAACCAAAACAAC-CAGAATAT-GTATAATAAAACAAACATGAAAGAT
* *
33806621 GCCGATGAGAAAAAACTATTATCAGCAT
62 GCCGATAAAAAAAAAC-ATTATCA-CAT
* * *
33806649 CATCATATGGAAAAACAAACCAAAACAACCAGAATATGTGTAGTAAAACAAACATGAAAGATGCC
1 CATCATA-GAAAAAACAAACCAAAACAACCAGAATATGTATAATAAAACAAACATGAAAGATGCC
* * *
33806714 GACAAAACAAAAACACTATCTGCAT
65 GATAAAA-AAAAACATTATC-ACAT
**
33806739 CATCATAGGTAAAACAAACTCAAAA
1 CATCATAGAAAAAACAAAC-CAAAA
33806764 AAGAAAAAAA
Statistics
Matches: 226, Mismatches: 46, Indels: 34
0.74 0.15 0.11
Matches are distributed among these distances:
84 50 0.22
85 3 0.01
86 8 0.04
87 9 0.04
88 58 0.26
89 20 0.09
90 72 0.32
91 6 0.03
ACGTcount: A:0.53, C:0.18, G:0.11, T:0.18
Consensus pattern (87 bp):
CATCATAGAAAAAACAAACCAAAACAACCAGAATATGTATAATAAAACAAACATGAAAGATGCCG
ATAAAAAAAAACATTATCACAT
Found at i:33820584 original size:24 final size:24
Alignment explanation
Indices: 33820552--33820600 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
33820542 CATACAATAA
33820552 AAGTGTTGCGACTCAAAAGAGTAG
1 AAGTGTTGCGACTCAAAAGAGTAG
33820576 AAGTGTTGCGACTCAAAAGAGTAG
1 AAGTGTTGCGACTCAAAAGAGTAG
33820600 A
1 A
33820601 GGAATACATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.12, G:0.29, T:0.20
Consensus pattern (24 bp):
AAGTGTTGCGACTCAAAAGAGTAG
Found at i:33820717 original size:21 final size:23
Alignment explanation
Indices: 33820675--33820721 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
33820665 TTTATAGTAG
* *
33820675 TAAACTTATATATATTTATTTAT
1 TAAAATTATATATATATATTTAT
33820698 TAAAATTATATATA-AT-TTTAT
1 TAAAATTATATATATATATTTAT
33820719 TAA
1 TAA
33820722 CAACTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
22 1 0.05
23 13 0.59
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TAAAATTATATATATATATTTAT
Found at i:33821260 original size:21 final size:21
Alignment explanation
Indices: 33821236--33821298 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
33821226 ATGGGACAGT
33821236 TGACATGGCTAGTTAACTAGC
1 TGACATGGCTAGTTAACTAGC
* * *
33821257 TGACGTGGCTAATTAACTACC
1 TGACATGGCTAGTTAACTAGC
* * * *
33821278 TGATATGACCAGCTAACTAGC
1 TGACATGGCTAGTTAACTAGC
33821299 CATGATGGAA
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (21 bp):
TGACATGGCTAGTTAACTAGC
Found at i:33823381 original size:7 final size:7
Alignment explanation
Indices: 33823369--33823399 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
33823359 ATTCTAACCT
33823369 TTTAGGG
1 TTTAGGG
33823376 TTTAGGG
1 TTTAGGG
33823383 TTTAGGG
1 TTTAGGG
33823390 TTTAGGG
1 TTTAGGG
33823397 TTT
1 TTT
33823400 CTCGATTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.00, G:0.39, T:0.48
Consensus pattern (7 bp):
TTTAGGG
Found at i:33824211 original size:13 final size:14
Alignment explanation
Indices: 33824176--33824221 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
33824166 ACATGTTAGT
33824176 AAAAT-AATTAATA
1 AAAATAAATTAATA
*
33824189 AAAATGAATTAA-A
1 AAAATAAATTAATA
* *
33824202 ATAATAAATTAAGA
1 AAAATAAATTAATA
33824216 AAAATA
1 AAAATA
33824222 TTTTTAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 16 0.57
14 12 0.43
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (14 bp):
AAAATAAATTAATA
Found at i:33825240 original size:21 final size:21
Alignment explanation
Indices: 33825192--33825240 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
33825182 TAATCAGTAT
*
33825192 ACGACACA-TAGGTGCCTGAA
1 ACGACACACGAGGTGCCTGAA
*
33825212 ACGACACACGAGGTGCCTGAT
1 ACGACACACGAGGTGCCTGAA
*
33825233 ACGGCACA
1 ACGACACA
33825241 TAAAGTGCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.33, C:0.29, G:0.27, T:0.12
Consensus pattern (21 bp):
ACGACACACGAGGTGCCTGAA
Found at i:33825248 original size:21 final size:21
Alignment explanation
Indices: 33825224--33825281 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 21
33825214 GACACACGAG
33825224 GTGCCTGATACGGCACATAAA
1 GTGCCTGATACGGCACATAAA
* *
33825245 GTGCCTGAGATAAGACACATAAA
1 GTGCCT--GATACGGCACATAAA
33825268 GTGCCTGAT-CGGCA
1 GTGCCTGATACGGCA
33825282 AAGCCGATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 3 0.10
21 9 0.29
23 19 0.61
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (21 bp):
GTGCCTGATACGGCACATAAA
Found at i:33826325 original size:3 final size:3
Alignment explanation
Indices: 33826317--33826360 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
33826307 TATTTCTAGT
* *
33826317 TAA TAA TAA TAA TAA TAA TATA TTA TAA TAA TCA T-A TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TA
33826361 TTTTATTCAC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
2 2 0.06
3 32 0.89
4 2 0.06
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Done.