Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167949.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_21, whole genome shotgun sequence
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: 19848060
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Warning! 113000 characters in sequence are not A, C, G, or T
File 20 of 138
Found at i:5512721 original size:16 final size:17
Alignment explanation
Indices: 5512698--5512740 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
5512688 TTATTCAAAA
*
5512698 TCATATATATA-TTATT
1 TCATATATATAGTTAAT
*
5512714 TTATATATA-AGTTAAT
1 TCATATATATAGTTAAT
5512730 TCATATATATA
1 TCATATATATA
5512741 AATTAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (17 bp):
TCATATATATAGTTAAT
Found at i:5520240 original size:17 final size:17
Alignment explanation
Indices: 5520218--5520253 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
5520208 TTGGATATTA
*
5520218 AATAGCAAAATTTGTCT
1 AATAGCAAAATTTATCT
5520235 AATAGCAAAATTTATCT
1 AATAGCAAAATTTATCT
5520252 AA
1 AA
5520254 GTTATTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.33
Consensus pattern (17 bp):
AATAGCAAAATTTATCT
Found at i:5520543 original size:20 final size:21
Alignment explanation
Indices: 5520514--5520563 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
5520504 TTAAGAAAAT
* *
5520514 TAAACA-AAAACTATATATAA
1 TAAACATAAAACCAAATATAA
*
5520534 TAAA-ATAAAACCAAATATAT
1 TAAACATAAAACCAAATATAA
5520554 TAAACATAAA
1 TAAACATAAA
5520564 TAAATGTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 19 0.76
21 5 0.20
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAACATAAAACCAAATATAA
Found at i:5521184 original size:21 final size:23
Alignment explanation
Indices: 5521160--5521202 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
5521150 TTAGCATGTT
*
5521160 TTTA-GCTTT-TATTTTGAAAAG
1 TTTATGCTTTATATTTTAAAAAG
*
5521181 TTTATGTTTTATATTTTAAAAA
1 TTTATGCTTTATATTTTAAAAA
5521203 CTTTTTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 4 0.22
23 10 0.56
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (23 bp):
TTTATGCTTTATATTTTAAAAAG
Found at i:5521914 original size:36 final size:36
Alignment explanation
Indices: 5521856--5521949 Score: 102
Period size: 36 Copynumber: 2.6 Consensus size: 36
5521846 GCACATGTCA
* *
5521856 AAAAATATAATAATAATACCTCTT-TCAGCAATCTA-TT
1 AAAATTATTATAAT-ATACCTCTTATCA-CAAT-TAGTT
* *
5521893 AAAATTATTATAATATCCCTCTTATCATAATTAGTT
1 AAAATTATTATAATATACCTCTTATCACAATTAGTT
*
5521929 AAAATTACTATAATATACCTC
1 AAAATTATTATAATATACCTC
5521950 CCATCATAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
35 2 0.04
36 32 0.65
37 15 0.31
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.38
Consensus pattern (36 bp):
AAAATTATTATAATATACCTCTTATCACAATTAGTT
Found at i:5521956 original size:36 final size:36
Alignment explanation
Indices: 5521891--5521961 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
5521881 CAGCAATCTA
* * **
5521891 TTAAAATTATTATAATATCCCTCTTATCATAATTAG
1 TTAAAATTACTATAATATACCTCCCATCATAATTAG
5521927 TTAAAATTACTATAATATACCTCCCATCATAATTA
1 TTAAAATTACTATAATATACCTCCCATCATAATTA
5521962 TGAAAATATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.41, C:0.17, G:0.01, T:0.41
Consensus pattern (36 bp):
TTAAAATTACTATAATATACCTCCCATCATAATTAG
Found at i:5522538 original size:25 final size:26
Alignment explanation
Indices: 5522483--5522541 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
5522473 CATGATTGAT
* *
5522483 TATAATTATTATAATACCACTCTTAC
1 TATAATTATGAGAATACCACTCTTAC
*
5522509 TATAATTATGAGAATGCC-CTCTTA-
1 TATAATTATGAGAATACCACTCTTAC
5522533 TCATAATTA
1 T-ATAATTA
5522542 AATAAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 1 0.03
25 13 0.45
26 15 0.52
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.41
Consensus pattern (26 bp):
TATAATTATGAGAATACCACTCTTAC
Found at i:5522688 original size:22 final size:25
Alignment explanation
Indices: 5522638--5522690 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
5522628 CTTTGGCCTT
*
5522638 TATTTTATGAAAATTTGACATATAG
1 TATTTTATGAAAATTTGACATATAA
5522663 TATTTTATGAAAA-TT-AC-TATAA
1 TATTTTATGAAAATTTGACATATAA
5522685 TATTTT
1 TATTTT
5522691 TATTAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 10 0.37
23 2 0.07
24 2 0.07
25 13 0.48
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.49
Consensus pattern (25 bp):
TATTTTATGAAAATTTGACATATAA
Found at i:5528152 original size:23 final size:22
Alignment explanation
Indices: 5528122--5528175 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 22
5528112 ATAAAGCGAA
*
5528122 AATGAAAAAAA-AAAGAGAAGAG
1 AATGAAAAAAAGAAA-AGAAAAG
5528144 AATGAAAAAAATGAAAAGAAAAG
1 AATGAAAAAAA-GAAAAGAAAAG
5528167 AATGAAAAA
1 AATGAAAAA
5528176 TGAAAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 11 0.38
23 15 0.52
24 3 0.10
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (22 bp):
AATGAAAAAAAGAAAAGAAAAG
Found at i:5528155 original size:31 final size:29
Alignment explanation
Indices: 5528094--5528208 Score: 94
Period size: 31 Copynumber: 3.8 Consensus size: 29
5528084 AGATAAAAAA
*
5528094 AAAAAAACAAAGAAAAAAAT-AAAGCGAAAATG
1 AAAAAAA-AAAGAGAAAAATGAAA---AAAATG
5528126 AAAAAAAAAAGAGAAGAGAATGAAAAAAATG
1 AAAAAAAAAAGAGAA-A-AATGAAAAAAATG
*
5528157 AAAAGAAAAGAA-TGAAAAATGAAAAAAA--
1 AAAA-AAAA-AAGAGAAAAATGAAAAAAATG
* *
5528185 AATAAAAAAAGAGAAAAAGGAAAA
1 AAAAAAAAAAGAGAAAAATGAAAA
5528209 CTTAAATAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
26 2 0.03
27 15 0.21
28 3 0.04
30 11 0.15
31 18 0.25
32 15 0.21
33 5 0.07
34 3 0.04
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.06
Consensus pattern (29 bp):
AAAAAAAAAAGAGAAAAATGAAAAAAATG
Found at i:5530067 original size:117 final size:117
Alignment explanation
Indices: 5529864--5530095 Score: 290
Period size: 117 Copynumber: 2.0 Consensus size: 117
5529854 ATATTATTGT
** *
5529864 TATTATTTTTATGTTTGAAAATTTCTAAAACATTCTAACACTTTTATAATATTTGAGAAAATTTC
1 TATTATTTTTATACTTGAAAATTTCTAAAACATTCTAACACTTTTAAAATATTT---AAAATTTC
* *
5529929 TTTGTATGAATATTTTCAATAAAATCACCATTTGTGACTTTATTCTTTTTTATAA
63 TTTGTATGAATATTTTCAATAAAATCAACACTTGTGACTTTATTCTTTTTTATAA
* * *
5529984 TATT-TTTTTATACTTGAAAAATTT-TAAAATATTTTTAACACTTTTAAAATATTT-AAATTCTT
1 TATTATTTTTATACTTG-AAAATTTCTAAAACA-TTCTAACACTTTTAAAATATTTAAAATT-TC
* * *
5530046 TTTGTGTGAATATTTTTAATAAAATCAACACTTGTGACTTTATTGTTTTT
63 TTTGTATGAATATTTTCAATAAAATCAACACTTGTGACTTTATTCTTTTT
5530096 ATTATTTAAT
Statistics
Matches: 98, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
116 5 0.05
117 46 0.47
119 16 0.16
120 31 0.32
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (117 bp):
TATTATTTTTATACTTGAAAATTTCTAAAACATTCTAACACTTTTAAAATATTTAAAATTTCTTT
GTATGAATATTTTCAATAAAATCAACACTTGTGACTTTATTCTTTTTTATAA
Found at i:5530294 original size:21 final size:20
Alignment explanation
Indices: 5530261--5530299 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5530251 TAATTAAAAA
5530261 TATTATATATTTTCTATCATT
1 TATTATATATTTT-TATCATT
* *
5530282 TATTTTATTTTTTTATCA
1 TATTATATATTTTTATCA
5530300 AAAGTTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTATATATTTTTATCATT
Found at i:5531638 original size:16 final size:17
Alignment explanation
Indices: 5531619--5531652 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5531609 TTTTGATTGA
*
5531619 TTTTGA-TTTTTTTCTT
1 TTTTGACTTTTTTGCTT
5531635 TTTTGACTTTTTTGCTT
1 TTTTGACTTTTTTGCTT
5531652 T
1 T
5531653 CTTTTTTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.06, C:0.09, G:0.09, T:0.76
Consensus pattern (17 bp):
TTTTGACTTTTTTGCTT
Found at i:5531711 original size:19 final size:17
Alignment explanation
Indices: 5531677--5531714 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 17
5531667 TTCTATATGT
5531677 TTAATAAAAAAATAATA
1 TTAATAAAAAAATAATA
5531694 TTAATAAATAATAATAATA
1 TTAATAAA-AA-AATAATA
5531713 TT
1 TT
5531715 TGAACCCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 2 0.11
19 9 0.47
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TTAATAAAAAAATAATA
Found at i:5532289 original size:57 final size:56
Alignment explanation
Indices: 5532153--5532292 Score: 165
Period size: 57 Copynumber: 2.5 Consensus size: 56
5532143 AACTAACTGT
* * * *
5532153 AAATGATTTTAGATATTACCACCGAAAGAAACTTGGATATCATCATCGAAAAAATAC
1 AAATGAGTTTGGATATTACCACC-AAAGAAACTTGAACATCATCATCGAAAAAATAC
* * * *
5532210 AAATGAGTTCGAATATCACCACCACAAGAAACTTGAACATCATCA-CTAAGAAAATAC
1 AAATGAGTTTGGATATTACCACCA-AAGAAACTTGAACATCATCATCGAA-AAAATAC
*
5532267 AAATGAGTTTGGATATTGCCACCAAA
1 AAATGAGTTTGGATATTACCACCAAA
5532293 CAAAACACGA
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
56 6 0.09
57 63 0.91
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.24
Consensus pattern (56 bp):
AAATGAGTTTGGATATTACCACCAAAGAAACTTGAACATCATCATCGAAAAAATAC
Found at i:5534158 original size:18 final size:19
Alignment explanation
Indices: 5534135--5534184 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
5534125 CCATTATCTC
*
5534135 TTTTATTTTTTCTTTTTT-
1 TTTTATTTTTTATTTTTTG
5534153 TTTTATTTTTTTATTTTTTG
1 TTTTA-TTTTTTATTTTTTG
5534173 TTGTTATTTTTT
1 TT-TTATTTTTT
5534185 TTTGTATCGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 5 0.18
19 12 0.43
20 8 0.29
21 3 0.11
ACGTcount: A:0.08, C:0.02, G:0.04, T:0.86
Consensus pattern (19 bp):
TTTTATTTTTTATTTTTTG
Found at i:5534182 original size:26 final size:25
Alignment explanation
Indices: 5534135--5534187 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
5534125 CCATTATCTC
* *
5534135 TTTTATTTTTTCTTTTTTTTTTATTT
1 TTTTATTTTTTCTTGTTATTTT-TTT
*
5534161 TTTTATTTTTTGTTGTTATTTTTTT
1 TTTTATTTTTTCTTGTTATTTTTTT
5534186 TT
1 TT
5534188 GTATCGTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.08, C:0.02, G:0.04, T:0.87
Consensus pattern (25 bp):
TTTTATTTTTTCTTGTTATTTTTTT
Found at i:5534187 original size:18 final size:17
Alignment explanation
Indices: 5534137--5534187 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
5534127 ATTATCTCTT
*
5534137 TTATTTTTTCTTTTTTTT
1 TTATTTTTT-TTTTTTTG
5534155 TTATTTTTTTATTTTTTG
1 TTATTTTTTT-TTTTTTG
*
5534173 TTGTTATTTTTTTTT
1 TTATT-TTTTTTTTT
5534188 GTATCGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 1 0.03
18 23 0.79
19 5 0.17
ACGTcount: A:0.08, C:0.02, G:0.04, T:0.86
Consensus pattern (17 bp):
TTATTTTTTTTTTTTTG
Found at i:5534189 original size:13 final size:13
Alignment explanation
Indices: 5534137--5534189 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
5534127 ATTATCTCTT
5534137 TTATTTTTTCTTT-
1 TTATTTTTT-TTTG
*
5534150 TT-TTTTTATTTTT
1 TTATTTTT-TTTTG
*
5534163 TTATTTTTTGTTG
1 TTATTTTTTTTTG
5534176 TTATTTTTTTTTG
1 TTATTTTTTTTTG
5534189 T
1 T
5534190 ATCGTTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 8 0.24
13 21 0.62
14 5 0.15
ACGTcount: A:0.08, C:0.02, G:0.06, T:0.85
Consensus pattern (13 bp):
TTATTTTTTTTTG
Found at i:5538745 original size:23 final size:23
Alignment explanation
Indices: 5538719--5538770 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
5538709 TTTAGTTAAC
5538719 TTTTATTTTATT-TAATGGAAAAT
1 TTTTATTTTATTGT-ATGGAAAAT
* * *
5538742 TTTTTTTTTGTTGTATTGAAAAT
1 TTTTATTTTATTGTATGGAAAAT
5538765 TTTTAT
1 TTTTAT
5538771 AAATACTCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (23 bp):
TTTTATTTTATTGTATGGAAAAT
Found at i:5546093 original size:20 final size:20
Alignment explanation
Indices: 5546051--5546094 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5546041 TATTTATATA
* *
5546051 TATTTAATAAATAAATTTTT
1 TATTAAATAAATAAATTTAT
5546071 TATTAAATAATATAAA-TTAT
1 TATTAAATAA-ATAAATTTAT
5546091 TATT
1 TATT
5546095 TAAAATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTAAATAAATAAATTTAT
Found at i:5546097 original size:21 final size:19
Alignment explanation
Indices: 5546051--5546098 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
5546041 TATTTATATA
5546051 TATTT-AATAAATAAATTT
1 TATTTAAATAAATAAATTT
*
5546069 TTTATTAAATAATATAAATTAT
1 TAT-TTAAATAA-ATAAATT-T
5546091 TATTTAAA
1 TATTTAAA
5546099 ATTAATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 2 0.08
19 2 0.08
20 5 0.21
21 12 0.50
22 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TATTTAAATAAATAAATTT
Found at i:5546168 original size:27 final size:28
Alignment explanation
Indices: 5546109--5546172 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
5546099 ATTAATTAAA
* *
5546109 ATTAATATATTTTTATTAAAAAATATAT
1 ATTAATATATATTTATTAAAAAATATAC
5546137 ATTAATATATATTTA-TAAAAAA-AGTAC
1 ATTAATATATATTTATTAAAAAATA-TAC
*
5546164 CTTAATATA
1 ATTAATATA
5546173 CAAGATAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 1 0.03
27 17 0.53
28 14 0.44
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (28 bp):
ATTAATATATATTTATTAAAAAATATAC
Found at i:5546334 original size:17 final size:19
Alignment explanation
Indices: 5546300--5546337 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
5546290 TAAAATATTC
5546300 ATTAGATATAAGTATAAAA
1 ATTAGATATAAGTATAAAA
5546319 ATTA-ATATAA-TATAAAA
1 ATTAGATATAAGTATAAAA
5546336 AT
1 AT
5546338 CTGATGATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 6 0.32
19 4 0.21
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (19 bp):
ATTAGATATAAGTATAAAA
Found at i:5548385 original size:26 final size:26
Alignment explanation
Indices: 5548349--5548404 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
5548339 ACACCTATTT
**
5548349 ATGTCTAGGTCTTATTAGGCTCATTA
1 ATGTCTAGGTCCGATTAGGCTCATTA
* * *
5548375 ATGTCTGGGTCCGATTAGGTTCGTTA
1 ATGTCTAGGTCCGATTAGGCTCATTA
5548401 ATGT
1 ATGT
5548405 TCGGACTCGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.20, C:0.14, G:0.25, T:0.41
Consensus pattern (26 bp):
ATGTCTAGGTCCGATTAGGCTCATTA
Found at i:5560095 original size:41 final size:41
Alignment explanation
Indices: 5559920--5560095 Score: 205
Period size: 40 Copynumber: 4.3 Consensus size: 41
5559910 GAGATAAACA
* * *
5559920 TCCACGTTGATGAAAAATAGTTTTTTTGCTAAAGATGTGCC
1 TCCAGGTTGATGAAAAATAGTTTTTTTACCAAAGATGTGCC
* *
5559961 TCCACGCTGATGAAAAATAG-TTTTTTACCAAAGATGTGCC
1 TCCAGGTTGATGAAAAATAGTTTTTTTACCAAAGATGTGCC
* * * * *
5560001 T-CATGGCTGATGAAAGATGGTTTCTTTACCAAA-ATGCGCC
1 TCCA-GGTTGATGAAAAATAGTTTTTTTACCAAAGATGTGCC
**
5560041 TCCAGGTTGATGAAAAATAGTTTTTTTACCAAAGATGTGTA
1 TCCAGGTTGATGAAAAATAGTTTTTTTACCAAAGATGTGCC
*
5560082 TTCAGGTTGATGAA
1 TCCAGGTTGATGAA
5560096 TGATAATTTT
Statistics
Matches: 115, Mismatches: 16, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
39 2 0.02
40 64 0.56
41 49 0.43
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (41 bp):
TCCAGGTTGATGAAAAATAGTTTTTTTACCAAAGATGTGCC
Found at i:5560116 original size:81 final size:80
Alignment explanation
Indices: 5559925--5560117 Score: 221
Period size: 81 Copynumber: 2.4 Consensus size: 80
5559915 AAACATCCAC
* * *
5559925 GTTGATGAAAAATAGTTTTTTTGCTAAAGATGTGCCTCCACGCTGATGAAAAATAGTTTTTTACC
1 GTTGATGAAAGATAGTTTTTTCGCTAAA-ATGCGCCTCCACGCTGATGAAAAATAGTTTTTTACC
*
5559990 AAAGATGTGCCTCATG
65 AAAGATGTGACTCATG
* * * *
5560006 GCTGATGAAAGATGGTTTCTTTAC-C-AAAATGCGCCTCCAGGTTGATGAAAAATAGTTTTTTTA
1 GTTGATGAAAGATAGTTT-TTT-CGCTAAAATGCGCCTCCACGCTGATGAAAAATAG-TTTTTTA
*
5560069 CCAAAGATGTGTATTCA-G
63 CCAAAGATGTG-ACTCATG
* *
5560087 GTTGATGAATGATAATTTTTTCGCTAAAATG
1 GTTGATGAAAGATAGTTTTTTCGCTAAAATG
5560118 TATAGTGAAG
Statistics
Matches: 93, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
79 1 0.01
80 28 0.30
81 57 0.61
82 7 0.08
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.35
Consensus pattern (80 bp):
GTTGATGAAAGATAGTTTTTTCGCTAAAATGCGCCTCCACGCTGATGAAAAATAGTTTTTTACCA
AAGATGTGACTCATG
Found at i:5560928 original size:62 final size:62
Alignment explanation
Indices: 5560829--5560949 Score: 190
Period size: 62 Copynumber: 2.0 Consensus size: 62
5560819 TCCAGGTCCT
* * *
5560829 ATTAGGCCCATTGATGTCTGGGTTCGATTAGGCTCGTTAACGTTTGGGCCTGATTAGGCATC
1 ATTAGGCCCATTGATGTCAGGCTTCGATTAGGCTCGTTAACGTCTGGGCCTGATTAGGCATC
*
5560891 ATTAGGCCCATTGATGTCCAGGCTT-GATTAGGTTCGTTAACGTCTGGGCCTGATTAGGC
1 ATTAGGCCCATTGATGT-CAGGCTTCGATTAGGCTCGTTAACGTCTGGGCCTGATTAGGC
5560950 CCATTGATGT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
62 49 0.91
63 5 0.09
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.33
Consensus pattern (62 bp):
ATTAGGCCCATTGATGTCAGGCTTCGATTAGGCTCGTTAACGTCTGGGCCTGATTAGGCATC
Found at i:5560953 original size:52 final size:51
Alignment explanation
Indices: 5560891--5561001 Score: 141
Period size: 52 Copynumber: 2.2 Consensus size: 51
5560881 ATTAGGCATC
* * * *
5560891 ATTAGGCCCATTGATGTCCAGGCTTGATTAGGTTCGTTAACGTCTGGGCCTG
1 ATTAGGCCCATTGATGTCCAGGCTCGATTAGG-CCGTTAACGTCTGGGACTA
*** *
5560943 ATTAGGCCCATTGATGTTTGGGCTCGATTAGGCCGTTGACGTCTGGGACTA
1 ATTAGGCCCATTGATGTCCAGGCTCGATTAGGCCGTTAACGTCTGGGACTA
5560994 ATTAGGCC
1 ATTAGGCC
5561002 TATTTGTGTC
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
51 23 0.45
52 28 0.55
ACGTcount: A:0.18, C:0.21, G:0.30, T:0.32
Consensus pattern (51 bp):
ATTAGGCCCATTGATGTCCAGGCTCGATTAGGCCGTTAACGTCTGGGACTA
Found at i:5560997 original size:25 final size:24
Alignment explanation
Indices: 5560915--5561001 Score: 75
Period size: 26 Copynumber: 3.4 Consensus size: 24
5560905 TGTCCAGGCT
* *
5560915 TGATTAGGTTCGTTAACGTCTGGGCC
1 TGATTAGG-CCGTTGACGTCTGGG-C
* * *
5560941 TGATTAGGCCCATTGATGTTTGGGC
1 TGATTAGG-CCGTTGACGTCTGGGC
5560966 TCGATTAGGCCGTTGACGTCTGGGAC
1 T-GATTAGGCCGTTGACGTCTGGG-C
*
5560992 TAATTAGGCC
1 TGATTAGGCC
5561002 TATTTGTGTC
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
25 22 0.45
26 27 0.55
ACGTcount: A:0.17, C:0.20, G:0.31, T:0.32
Consensus pattern (24 bp):
TGATTAGGCCGTTGACGTCTGGGC
Found at i:5561168 original size:52 final size:52
Alignment explanation
Indices: 5561073--5561174 Score: 127
Period size: 52 Copynumber: 2.0 Consensus size: 52
5561063 AAATTATTAT
* * * *
5561073 TATTATTATTACTTTCTTTTTTATTTTTATTTTTTTGTGTTTCTTTTCTTTA
1 TATTATTATTACTTACTATTATATTTCTATTTTTTTGTGTTTCTTTTCTTTA
*
5561125 TATTATTATTA-TTACTATTATATTTCTATTTTCATTT-TTTTTCTTTTCTT
1 TATTATTATTACTTACTATTATATTTCTATTTT--TTTGTGTTTCTTTTCTT
5561175 CTTTGTTCTT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
51 17 0.40
52 23 0.53
53 3 0.07
ACGTcount: A:0.17, C:0.09, G:0.02, T:0.73
Consensus pattern (52 bp):
TATTATTATTACTTACTATTATATTTCTATTTTTTTGTGTTTCTTTTCTTTA
Found at i:5561177 original size:55 final size:55
Alignment explanation
Indices: 5561070--5561178 Score: 141
Period size: 55 Copynumber: 2.0 Consensus size: 55
5561060 TATAAATTAT
* * * * *
5561070 TATTATTATTATTACTTTCTTTTTTATTTTTATTTTTTTGTGTTTCTTTTCTTTA
1 TATTATTATTATTACTTTATTTTCTATTTTCATTTTTTTGTCTTTCTCTTCTTTA
5561125 TATTATTATTATTACTATTATATTTCTATTTTCATTTTTTT-TCTTT-TCTTCTTT
1 TATTATTATTATTACT-TTAT-TTTCTATTTTCATTTTTTTGTCTTTCTCTTCTTT
5561179 GTTCTTTCTT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
55 23 0.49
56 7 0.15
57 17 0.36
ACGTcount: A:0.17, C:0.09, G:0.02, T:0.72
Consensus pattern (55 bp):
TATTATTATTATTACTTTATTTTCTATTTTCATTTTTTTGTCTTTCTCTTCTTTA
Found at i:5561183 original size:15 final size:15
Alignment explanation
Indices: 5561153--5561197 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
5561143 TATATTTCTA
5561153 TTTTCATTT-TTTTTC
1 TTTTC-TTTCTTTTTC
5561168 TTTTC-TTCTTTGTTC
1 TTTTCTTTCTTT-TTC
5561183 -TTTCTTTCTTTTTC
1 TTTTCTTTCTTTTTC
5561197 T
1 T
5561198 GTTCAAATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
13 2 0.08
14 10 0.38
15 14 0.54
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (15 bp):
TTTTCTTTCTTTTTC
Found at i:5564390 original size:2 final size:2
Alignment explanation
Indices: 5564377--5564414 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
5564367 AATTAGAATC
* *
5564377 AT AT AA AT AT AT AT AT GT 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
5564415 TATGAGCTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5585767 original size:24 final size:25
Alignment explanation
Indices: 5585740--5585794 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
5585730 GTTATTCATA
*
5585740 ATTTTATTTAGA-TTA-TAATAAAAT
1 ATTTTATTT-GATTTAGCAATAAAAT
5585764 ATTTATATTTGATTTAGCAATAAAAT
1 ATTT-TATTTGATTTAGCAATAAAAT
5585790 -TTTTA
1 ATTTTA
5585795 CTTAAGCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 8 0.30
25 11 0.41
26 8 0.30
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (25 bp):
ATTTTATTTGATTTAGCAATAAAAT
Found at i:5588643 original size:75 final size:75
Alignment explanation
Indices: 5588490--5588644 Score: 231
Period size: 75 Copynumber: 2.1 Consensus size: 75
5588480 TAGGTGGCCA
*
5588490 ATTGATTGTATGCGTTTTGGGAAGAGTAAATCTAGATCATTGAATTAATAGGTGGGAAAGATTAA
1 ATTGATTATATGCGTTTTGGGAAGAGTAAATCTAGATCATTGAATTAATAGGTGGGAAAGATTAA
*
5588555 ATCCAAACTC
66 ATCCAAACAC
* * * *
5588565 ATTGATTATATGTGTTTTGGGAAGATTAAATCTAGATGATTGAAATTAATAGGTGGGTAAGATTA
1 ATTGATTATATGCGTTTTGGGAAGAGTAAATCTAGATCATTG-AATTAATAGGTGGGAAAGATTA
*
5588630 AATCTAAA-AC
65 AATCCAAACAC
5588640 ATTGA
1 ATTGA
5588645 AATGAGTTAG
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
75 44 0.61
76 28 0.39
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.34
Consensus pattern (75 bp):
ATTGATTATATGCGTTTTGGGAAGAGTAAATCTAGATCATTGAATTAATAGGTGGGAAAGATTAA
ATCCAAACAC
Found at i:5588646 original size:37 final size:35
Alignment explanation
Indices: 5588507--5588681 Score: 129
Period size: 37 Copynumber: 4.7 Consensus size: 35
5588497 GTATGCGTTT
* *
5588507 TGGGAAGAGTAAATCTAGATCATTGAATTAATAGG
1 TGGGAAGATTAAATCTAAATCATTGAATTAATAGG
*
5588542 TGGGAAAGATTAAATCCAAACTCATTG-ATT-ATATGTG
1 TGGG-AAGATTAAATCTAAA-TCATTGAATTAATA-G-G
* *
5588579 TTTTGGGAAGATTAAATCTAGATGATTGAAATTAATAGG
1 ---TGGGAAGATTAAATCTAAATCATTG-AATTAATAGG
* * *
5588618 TGGGTAAGATTAAATCTAAAACATTGAAATGAGTTAGG
1 TGGG-AAGATTAAATCTAAATCATTG-AATTA-ATAGG
* * * *
5588656 TGAGTAGATTTAATCTAGATCATTGA
1 TGGGAAGATTAAATCTAAATCATTGA
5588682 TACGAGTTAG
Statistics
Matches: 112, Mismatches: 16, Indels: 23
0.74 0.11 0.15
Matches are distributed among these distances:
35 7 0.06
36 21 0.19
37 47 0.42
38 12 0.11
39 14 0.12
40 8 0.07
41 3 0.03
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (35 bp):
TGGGAAGATTAAATCTAAATCATTGAATTAATAGG
Found at i:5588689 original size:37 final size:38
Alignment explanation
Indices: 5588614--5588691 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 38
5588604 TTGAAATTAA
* *
5588614 TAGGTGGGTAAGATTAAATCTAAAACATTGAAATGAGT
1 TAGGTGAGTAAGATTAAATCTAAAACATTGAAACGAGT
* * * *
5588652 TAGGTGAGT-AGATTTAATCTAGATCATTGATACGAGT
1 TAGGTGAGTAAGATTAAATCTAAAACATTGAAACGAGT
5588689 TAG
1 TAG
5588692 TTGAAAAAGT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
37 26 0.76
38 8 0.24
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.32
Consensus pattern (38 bp):
TAGGTGAGTAAGATTAAATCTAAAACATTGAAACGAGT
Found at i:5589250 original size:17 final size:17
Alignment explanation
Indices: 5589225--5589258 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5589215 GATAGGTAGA
5589225 CAATCGATTACATGTGT
1 CAATCGATTACATGTGT
*
5589242 CAATTGATTACATGTGT
1 CAATCGATTACATGTGT
5589259 TTTGGCCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (17 bp):
CAATCGATTACATGTGT
Found at i:5589271 original size:71 final size:70
Alignment explanation
Indices: 5589189--5589325 Score: 202
Period size: 71 Copynumber: 1.9 Consensus size: 70
5589179 TGTTTTGTGA
* * * *
5589189 TTGGCCAAATAAAATTGATCTAATGTGATAGGTAGACAATCGATTACATGTGTCAATTGATTACA
1 TTGGCCAAATAAAAATGATCTAACGTGATAGGTAGACAA-CGATTACACGTGTCAATCGATTACA
5589254 TGTGTT
65 TGTGTT
* * *
5589260 TTGGCCAAATAAAAATGATCTAACGTGATAGGTGGCCAACGATTACACGTTTCAATCGATTACAT
1 TTGGCCAAATAAAAATGATCTAACGTGATAGGTAGACAACGATTACACGTGTCAATCGATTACAT
5589325 G
66 G
5589326 GGGAAAATTA
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
70 24 0.41
71 35 0.59
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (70 bp):
TTGGCCAAATAAAAATGATCTAACGTGATAGGTAGACAACGATTACACGTGTCAATCGATTACAT
GTGTT
Found at i:5589387 original size:38 final size:38
Alignment explanation
Indices: 5589327--5589400 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
5589317 GATTACATGG
* * * *
5589327 GGAAAATTAAGTCTAGATCATTG-AGATGAGTTAGGAT
1 GGAAAATTAAATCTAAACCATTGAAAATGAGTTAGGAT
5589364 GGAAACATTAAATCTAAACCATTGAAAATGAGTTAGG
1 GGAAA-ATTAAATCTAAACCATTGAAAATGAGTTAGG
5589401 TGAAAAGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 5 0.16
38 15 0.48
39 11 0.35
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (38 bp):
GGAAAATTAAATCTAAACCATTGAAAATGAGTTAGGAT
Found at i:5589975 original size:15 final size:15
Alignment explanation
Indices: 5589955--5589995 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
5589945 TATAATTATT
*
5589955 TTTTAATATTAATAA
1 TTTTAATATAAATAA
5589970 TTTTAATAATAAATAA
1 TTTTAAT-ATAAATAA
*
5589986 TTTCAATATA
1 TTTTAATATA
5589996 CTTAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTTAATATAAATAA
Found at i:5590025 original size:25 final size:23
Alignment explanation
Indices: 5589971--5590029 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 23
5589961 TATTAATAAT
5589971 TTTAATAATAAATAATTTCAATA
1 TTTAATAATAAATAATTTCAATA
*
5589994 TACTTAATAATAAATAATTTTTAATA
1 T--TTAATAATAAATAA-TTTCAATA
5590020 GTTTAATAAT
1 -TTTAATAAT
5590030 TATATTAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
23 1 0.03
25 22 0.71
26 7 0.23
27 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (23 bp):
TTTAATAATAAATAATTTCAATA
Found at i:5593148 original size:18 final size:19
Alignment explanation
Indices: 5593125--5593160 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
5593115 TATATGACAA
5593125 AAAATTGTGATA-AATATG
1 AAAATTGTGATAGAATATG
5593143 AAAATTGTGATAGAATAT
1 AAAATTGTGATAGAATAT
5593161 TATAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (19 bp):
AAAATTGTGATAGAATATG
Found at i:5593194 original size:13 final size:13
Alignment explanation
Indices: 5593176--5593210 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
5593166 TAAAATTTTC
* *
5593176 AATATTGTAATAG
1 AATATTATAAGAG
5593189 AATATTATAAGAG
1 AATATTATAAGAG
5593202 AATATTATA
1 AATATTATA
5593211 GTGATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.37
Consensus pattern (13 bp):
AATATTATAAGAG
Found at i:5595074 original size:34 final size:34
Alignment explanation
Indices: 5595031--5595096 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
5595021 AAATTAAAAA
* * *
5595031 ACTCCTCTGATCAGAGGTTATGAAACTTTAAATG
1 ACTCATCTGACCAGAGGCTATGAAACTTTAAATG
*
5595065 ACTCATCTGACCAGAGGCTATGATACTTTAAA
1 ACTCATCTGACCAGAGGCTATGAAACTTTAAA
5595097 GAAAACTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (34 bp):
ACTCATCTGACCAGAGGCTATGAAACTTTAAATG
Found at i:5595144 original size:70 final size:70
Alignment explanation
Indices: 5595050--5595273 Score: 238
Period size: 70 Copynumber: 3.2 Consensus size: 70
5595040 ATCAGAGGTT
* * * * * * *
5595050 ATGAAACTTTAAAT-GACTCATCTGACCAGAGGCTATGATACTTTAAAGAAAACTTCTCTGACCA
1 ATGAAACTTTAAATAG-CTCTTCTGACTAAAGGCTATGAAACTTTAAAGAAAGCTTCTTTGACTA
*
5595114 AAGGCA
65 GAGGCA
* * * * * *
5595120 ATAAAACTTTAAATAGCTCTTCTGAGTAAAGTCAATGAAACTTTAGAGAAAGTTTCTTTGACTAG
1 ATGAAACTTTAAATAGCTCTTCTGACTAAAGGCTATGAAACTTTAAAGAAAGCTTCTTTGACTAG
**
5595185 AGGTT
66 AGGCA
* *
5595190 ATGAAACTTTAAATAGCTCCTT-TGACTAAAGGCTATGACAGTTTAAAGAAAGC-TCATTTGACT
1 ATGAAACTTTAAATAGCT-CTTCTGACTAAAGGCTATGAAACTTTAAAGAAAGCTTC-TTTGACT
5595253 AGAGGCA
64 AGAGGCA
5595260 ATGAAACTTTAAAT
1 ATGAAACTTTAAAT
5595274 TTAAAAATTT
Statistics
Matches: 125, Mismatches: 26, Indels: 6
0.80 0.17 0.04
Matches are distributed among these distances:
69 2 0.02
70 119 0.95
71 4 0.03
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (70 bp):
ATGAAACTTTAAATAGCTCTTCTGACTAAAGGCTATGAAACTTTAAAGAAAGCTTCTTTGACTAG
AGGCA
Found at i:5595272 original size:36 final size:35
Alignment explanation
Indices: 5595079--5595272 Score: 144
Period size: 36 Copynumber: 5.5 Consensus size: 35
5595069 ATCTGACCAG
* * * * *
5595079 AGGCTATGATACTTTAAAGAAAACTTCTCTGACCAA
1 AGGCAATGAAACTTTAAAGAAAGC-TCTTTGACTAA
* * *
5595115 AGGCAATAAAACTTT-AA-ATAGCTCTTCTGAGTAA
1 AGGCAATGAAACTTTAAAGAAAGCTCTT-TGACTAA
* * * *
5595149 AGTCAATGAAACTTTAGAGAAAGTTTCTTTGACTAG
1 AGGCAATGAAACTTTAAAGAAAG-CTCTTTGACTAA
** *
5595185 AGGTTATGAAACTTT-AA-ATAGCTCCTTTGACTAA
1 AGGCAATGAAACTTTAAAGAAAGCT-CTTTGACTAA
* * * *
5595219 AGGCTATGACAGTTTAAAGAAAGCTCATTTGACTAG
1 AGGCAATGAAACTTTAAAGAAAGCTC-TTTGACTAA
5595255 AGGCAATGAAACTTTAAA
1 AGGCAATGAAACTTTAAA
5595273 TTTAAAAATT
Statistics
Matches: 120, Mismatches: 30, Indels: 16
0.72 0.18 0.10
Matches are distributed among these distances:
33 4 0.03
34 45 0.38
35 7 0.06
36 60 0.50
37 4 0.03
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (35 bp):
AGGCAATGAAACTTTAAAGAAAGCTCTTTGACTAA
Found at i:5606616 original size:20 final size:18
Alignment explanation
Indices: 5606589--5606634 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 18
5606579 ATAAATTGTA
5606589 AAAAAAATCTTAAA-CAAAT
1 AAAAAAATC--AAATCAAAT
5606608 AACAAAAATCAAATCAAAT
1 AA-AAAAATCAAATCAAAT
5606627 AAAAAAAT
1 AAAAAAAT
5606635 AAAACTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 9 0.36
19 9 0.36
20 7 0.28
ACGTcount: A:0.72, C:0.11, G:0.00, T:0.17
Consensus pattern (18 bp):
AAAAAAATCAAATCAAAT
Found at i:5606645 original size:19 final size:19
Alignment explanation
Indices: 5606604--5606645 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
5606594 AATCTTAAAC
* *
5606604 AAATAACAAAAATCAAATC
1 AAATAACAAAAATAAAATA
5606623 AAATAA-AAAAATAAAACTA
1 AAATAACAAAAATAAAA-TA
5606642 AAAT
1 AAAT
5606646 GGAAAAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.17
Consensus pattern (19 bp):
AAATAACAAAAATAAAATA
Found at i:5608422 original size:25 final size:25
Alignment explanation
Indices: 5608393--5608450 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
5608383 TAAAGATAAC
5608393 TATTAAA-ATATCAAAATATATTTAT
1 TATTAAAGATATCAAAAT-TATTTAT
**
5608418 TATTAAAGTATATTGAAATTATTTAT
1 TATTAAAG-ATATCAAAATTATTTAT
5608444 TATTAAA
1 TATTAAA
5608451 TTATTAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 7 0.24
26 14 0.48
27 8 0.28
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (25 bp):
TATTAAAGATATCAAAATTATTTAT
Found at i:5608512 original size:19 final size:18
Alignment explanation
Indices: 5608463--5608522 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
5608453 ATTAATATGC
* *
5608463 ATAATAATTATATTTTAATA
1 ATAATATTTA-ATATTAA-A
5608483 ATAATATTTAATATTAAA
1 ATAATATTTAATATTAAA
* *
5608501 ATATTATATTAATATAAAA
1 ATAATAT-TTAATATTAAA
5608520 ATA
1 ATA
5608523 CTTCAAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 7 0.20
19 19 0.54
20 9 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAATATTTAATATTAAA
Found at i:5608655 original size:17 final size:15
Alignment explanation
Indices: 5608624--5608665 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
5608614 TTAAAATAGT
5608624 AATATTTATTATTAA
1 AATATTTATTATTAA
5608639 AATATTTATACTATTAA
1 AATATTTAT--TATTAA
*
5608656 AATATATATT
1 AATATTTATT
5608666 TTATATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 10 0.42
17 14 0.58
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
AATATTTATTATTAA
Found at i:5608899 original size:41 final size:41
Alignment explanation
Indices: 5608831--5608910 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
5608821 GAAAAAAATT
5608831 TATTATTATATTATTTAACATTAATTATTAAAATAATAAAA
1 TATTATTATATTATTTAACATTAATTATTAAAATAATAAAA
** *
5608872 TATTATTATA-TATGTTATTATTTATTATTAAAATAATAA
1 TATTATTATATTAT-TTAACATTAATTATTAAAATAATAA
5608911 TCTAATACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
40 3 0.09
41 32 0.91
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (41 bp):
TATTATTATATTATTTAACATTAATTATTAAAATAATAAAA
Found at i:5609045 original size:24 final size:23
Alignment explanation
Indices: 5609014--5609068 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
5609004 GCTAATATTT
5609014 TAATATTTTAATTAAAATTAAATAA
1 TAATATTTTAATTAAAA-T-AATAA
* *
5609039 -AATATTTTTATTAATATAATAA
1 TAATATTTTAATTAAAATAATAA
5609061 TAATATTT
1 TAATATTT
5609069 CAAATCAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 5 0.19
23 8 0.30
24 14 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATATTTTAATTAAAATAATAA
Found at i:5609175 original size:17 final size:17
Alignment explanation
Indices: 5609153--5609234 Score: 55
Period size: 17 Copynumber: 4.9 Consensus size: 17
5609143 TTAATATTAA
5609153 AATATTAAAATATTTTT
1 AATATTAAAATATTTTT
5609170 AATATT--AATA-TTTT
1 AATATTAAAATATTTTT
* * **
5609184 AATTTTAAAGTATAATT
1 AATATTAAAATATTTTT
*
5609201 AA-ATAAAAATATTATTT
1 AATATTAAAATATT-TTT
* *
5609218 ATTTATTACAATATTTT
1 A-ATATTAAAATATTTT
5609235 GGATCTGGTC
Statistics
Matches: 47, Mismatches: 12, Indels: 11
0.67 0.17 0.16
Matches are distributed among these distances:
14 9 0.19
15 4 0.09
16 10 0.21
17 13 0.28
18 2 0.04
19 9 0.19
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (17 bp):
AATATTAAAATATTTTT
Found at i:5609179 original size:23 final size:23
Alignment explanation
Indices: 5609134--5609181 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
5609124 AGTATAACTA
5609134 TAAAAATATTTAATATTAAAATAT
1 TAAAAATATTTAATATT-AAATAT
*
5609158 TAAAATATTTTTAATATT-AATAT
1 TAAAA-ATATTTAATATTAAATAT
5609181 T
1 T
5609182 TTAATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 6 0.27
24 5 0.23
25 11 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TAAAAATATTTAATATTAAATAT
Found at i:5609961 original size:33 final size:34
Alignment explanation
Indices: 5609924--5610021 Score: 112
Period size: 33 Copynumber: 2.9 Consensus size: 34
5609914 AAAAATGATG
* *
5609924 TTACTTTGGTGGCATTTGTAATTGAAAATGCC-C
1 TTACTTTAGAGGCATTTGTAATTGAAAATGCCAC
* * *
5609957 TTACTTTAGAGGTATTTATAACTGAAAATGCCAC
1 TTACTTTAGAGGCATTTGTAATTGAAAATGCCAC
*
5609991 -TACTTTAGAGGCGTTTGT-ATCTGAAAATGCC
1 TTACTTTAGAGGCATTTGTAAT-TGAAAATGCC
5610022 TCTATTTTAG
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
32 1 0.02
33 52 0.96
34 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (34 bp):
TTACTTTAGAGGCATTTGTAATTGAAAATGCCAC
Found at i:5610043 original size:33 final size:33
Alignment explanation
Indices: 5609938--5610031 Score: 102
Period size: 33 Copynumber: 2.8 Consensus size: 33
5609928 TTTGGTGGCA
**
5609938 TTTGTAAT-TGAAAATGCC-CTTACTTTAGAGGTA
1 TTTGT-ATCTGAAAATGCCAC-TACTTTAGAGGCG
* *
5609971 TTTATAACTGAAAATGCCACTACTTTAGAGGCG
1 TTTGTATCTGAAAATGCCACTACTTTAGAGGCG
* *
5610004 TTTGTATCTGAAAATGCCTCTATTTTAG
1 TTTGTATCTGAAAATGCCACTACTTTAG
5610032 CAGTGTTTGT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
32 1 0.02
33 49 0.96
34 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (33 bp):
TTTGTATCTGAAAATGCCACTACTTTAGAGGCG
Found at i:5610136 original size:134 final size:134
Alignment explanation
Indices: 5609991--5610244 Score: 318
Period size: 134 Copynumber: 1.9 Consensus size: 134
5609981 AAAATGCCAC
* * **
5609991 TACTTTAGAGGCGTTTGTATCTGAAAAT-GCC-TCTATTTTAGC-AGTGTTTGTATATTTGAGAC
1 TACTTTAGAGGCATTTGTATCTG-AAATCGCCTTC-ATATTAGCGA-CATTTGTATATTTGAGAC
* *
5610053 GCT-GCTAATTTAGTGACATTTTTATGAGAAAAACGCCATTGCTTTGGTGGCATTTGTAAATGAA
63 G-TAGCTAATTTAGTGACATTCTTATGAGAAAAACGCCATTGCTTTGGTGACATTTGTAAATGAA
5610117 AATACCGT
127 AATACCGT
* *
5610125 TACTTTAGAGGCATTTGTATCTGAAATCGCCTTCATATTAGCGACATTTGTATCTTTGAGATGTA
1 TACTTTAGAGGCATTTGTATCTGAAATCGCCTTCATATTAGCGACATTTGTATATTTGAGACGTA
* *** * *
5610190 GTTAATTTAGTGGTGTTCTTATGAGAAAAACGCCGTTGCTTTGGTGACGTTTGTA
66 GCTAATTTAGTGACATTCTTATGAGAAAAACGCCATTGCTTTGGTGACATTTGTA
5610245 TCAAAAACGT
Statistics
Matches: 102, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
133 5 0.05
134 94 0.92
135 3 0.03
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (134 bp):
TACTTTAGAGGCATTTGTATCTGAAATCGCCTTCATATTAGCGACATTTGTATATTTGAGACGTA
GCTAATTTAGTGACATTCTTATGAGAAAAACGCCATTGCTTTGGTGACATTTGTAAATGAAAATA
CCGT
Found at i:5616457 original size:19 final size:20
Alignment explanation
Indices: 5616420--5616457 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
5616410 CATCTTCTTT
* *
5616420 GATTTCTTACAAGATTTAAG
1 GATTTCTTACAAAAGTTAAG
5616440 GATTT-TTACAAAAGTTAA
1 GATTTCTTACAAAAGTTAA
5616458 CATTTTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (20 bp):
GATTTCTTACAAAAGTTAAG
Found at i:5620297 original size:80 final size:80
Alignment explanation
Indices: 5620164--5620493 Score: 405
Period size: 80 Copynumber: 4.1 Consensus size: 80
5620154 CTTAAATATT
* * * *
5620164 ATGGTTTGCTAAACCTTGTTGTTTGATATTTTTTTGTTGAATGGTATTGTATGATATTGGAGGGC
1 ATGGTTTGCTGAACCTTGTTGTCTGATATTATTTTGCTGAATGGTATTGTATGATATTGGAGGGC
5620229 TGAATCATATG-TCGA
66 TGAATCATATGCT-GA
* ** * *
5620244 ATGGTTTGCTGAACCTTGTTGTATGATATTATATTACCT-AATGGTAATGTATGATATTGGGGGG
1 ATGGTTTGCTGAACCTTGTTGTCTGATATTAT-TTTGCTGAATGGTATTGTATGATATTGGAGGG
*
5620308 CCGAATCATATGCTGA
65 CTGAATCATATGCTGA
* * * *
5620324 ATGGTTTGTTGAACCTTATTGTCTGATATTATTTTGCTGAATGGTTTTGTATGATATTGGAGAGC
1 ATGGTTTGCTGAACCTTGTTGTCTGATATTATTTTGCTGAATGGTATTGTATGATATTGGAGGGC
5620389 TGAATCATATGCTGA
66 TGAATCATATGCTGA
* * * * * *
5620404 ATGGATTGTTGAATCTTGTTGTCTGATATTATTTTGCTAAATGATTTTGTATGATATT-GAGGGG
1 ATGGTTTGCTGAACCTTGTTGTCTGATATTATTTTGCTGAATGGTATTGTATGATATTGGA-GGG
* * *
5620468 CTAAATCGTATTCTGA
65 CTGAATCATATGCTGA
5620484 ATGGTTTGCT
1 ATGGTTTGCT
5620494 AAATAGTGTT
Statistics
Matches: 216, Mismatches: 30, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
79 6 0.03
80 206 0.95
81 4 0.02
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.43
Consensus pattern (80 bp):
ATGGTTTGCTGAACCTTGTTGTCTGATATTATTTTGCTGAATGGTATTGTATGATATTGGAGGGC
TGAATCATATGCTGA
Found at i:5620362 original size:40 final size:39
Alignment explanation
Indices: 5620318--5620446 Score: 104
Period size: 40 Copynumber: 3.2 Consensus size: 39
5620308 CCGAATCATA
5620318 TGCTGAATGGTTTGTTGAACCTTATTGTCTGATATTATTT
1 TGCTGAATGGTTTGTTGAA-CTTATTGTCTGATATTATTT
** * *
5620358 TGCTGAATGGTTTTGTATGATA-TTGGAGAG-CTGA-ATCA-TA
1 TGCTGAATGG-TTTGT-TGA-ACTT--ATTGTCTGATATTATTT
* *
5620398 TGCTGAATGGATTGTTGAATCTTGTTGTCTGATATTATTT
1 TGCTGAATGGTTTGTTGAA-CTTATTGTCTGATATTATTT
*
5620438 TGCTAAATG
1 TGCTGAATG
5620447 ATTTTGTATG
Statistics
Matches: 68, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
37 2 0.03
38 7 0.10
39 9 0.13
40 30 0.44
41 10 0.15
42 7 0.10
43 3 0.04
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.45
Consensus pattern (39 bp):
TGCTGAATGGTTTGTTGAACTTATTGTCTGATATTATTT
Found at i:5620881 original size:33 final size:33
Alignment explanation
Indices: 5620844--5620910 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
5620834 TGGCTACTCA
*
5620844 TATTGGAGCTATCGTCCATCGTAAGATTTCCAT
1 TATTGGAGCTATCGTCCATCATAAGATTTCCAT
5620877 TATTGGAGCTATCGTCCATCATAAGATTTCCAT
1 TATTGGAGCTATCGTCCATCATAAGATTTCCAT
5620910 T
1 T
5620911 TTGTATAGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.37
Consensus pattern (33 bp):
TATTGGAGCTATCGTCCATCATAAGATTTCCAT
Found at i:5630289 original size:22 final size:22
Alignment explanation
Indices: 5630260--5630302 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5630250 AAAAAAATTC
5630260 AAACACAAAAACAA-AATCTAG
1 AAACACAAAAACAATAATCTAG
*
5630281 AAACTACAAAAATAATAATCTA
1 AAAC-ACAAAAACAATAATCTA
5630303 TACAATGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 9 0.47
23 6 0.32
ACGTcount: A:0.65, C:0.16, G:0.02, T:0.16
Consensus pattern (22 bp):
AAACACAAAAACAATAATCTAG
Found at i:5630448 original size:25 final size:25
Alignment explanation
Indices: 5630421--5630467 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
5630411 CACAAAAGGA
5630421 AAAAAT-AAAA-AAAATGAAGAAATC
1 AAAAATGAAAAGAAAA-GAAGAAATC
5630445 AAAAATGAAAAGAAAAGAAGAAA
1 AAAAATGAAAAGAAAAGAAGAAA
5630468 CTCTGCCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.29
25 11 0.52
26 4 0.19
ACGTcount: A:0.77, C:0.02, G:0.13, T:0.09
Consensus pattern (25 bp):
AAAAATGAAAAGAAAAGAAGAAATC
Found at i:5633852 original size:21 final size:21
Alignment explanation
Indices: 5633826--5633898 Score: 85
Period size: 22 Copynumber: 3.4 Consensus size: 21
5633816 AATTTGAATC
*
5633826 TTCTTTTTTCATTTTTTTCAT
1 TTCTTTTTTCTTTTTTTTCAT
* *
5633847 TTCTTTCTTCTTTTTTTTTCCT
1 TTCTTTTTTC-TTTTTTTTCAT
5633869 TT-TTTTTTCTTTTTTTTCAT
1 TTCTTTTTTCTTTTTTTTCAT
*
5633889 CATCTTTTTT
1 -TTCTTTTTT
5633899 TTCTCATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
20 10 0.23
21 16 0.37
22 17 0.40
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.78
Consensus pattern (21 bp):
TTCTTTTTTCTTTTTTTTCAT
Found at i:5633886 original size:9 final size:10
Alignment explanation
Indices: 5633824--5633885 Score: 63
Period size: 10 Copynumber: 6.0 Consensus size: 10
5633814 TCAATTTGAA
*
5633824 TCTTCTTTTT
1 TCTTTTTTTT
*
5633834 TC-ATTTTTT
1 TCTTTTTTTT
*
5633843 TCATTTCTTTCT
1 TC-TTT-TTTTT
5633855 TCTTTTTTTT
1 TCTTTTTTTT
5633865 TCCTTTTTTTT
1 T-CTTTTTTTT
5633876 TCTTTTTTTT
1 TCTTTTTTTT
5633886 CATCATCTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
9 7 0.16
10 16 0.37
11 14 0.33
12 6 0.14
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:5633896 original size:24 final size:23
Alignment explanation
Indices: 5633829--5633913 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 23
5633819 TTGAATCTTC
* *
5633829 TTTTTTCATTTTTTTCAT--TTC
1 TTTTTTCTTTTTTTTCATCATTT
* *
5633850 TTTCTTCTTTTTTTT--TCCTTT
1 TTTTTTCTTTTTTTTCATCATTT
5633871 TTTTTTCTTTTTTTTCATCATCTT
1 TTTTTTCTTTTTTTTCATCAT-TT
**
5633895 TTTTTTCTCATTTTTCATC
1 TTTTTTCTTTTTTTTCATC
5633914 CATTGTTGAT
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.02
21 29 0.56
23 3 0.06
24 19 0.37
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (23 bp):
TTTTTTCTTTTTTTTCATCATTT
Found at i:5633905 original size:14 final size:15
Alignment explanation
Indices: 5633876--5633909 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
5633866 CCTTTTTTTT
5633876 TCTTTTTTTTCATCA
1 TCTTTTTTTTCATCA
5633891 TCTTTTTTTTC-TCA
1 TCTTTTTTTTCATCA
5633905 T-TTTT
1 TCTTTT
5633910 CATCCATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.21
14 4 0.21
15 11 0.58
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.74
Consensus pattern (15 bp):
TCTTTTTTTTCATCA
Found at i:5637823 original size:59 final size:59
Alignment explanation
Indices: 5637724--5638187 Score: 623
Period size: 59 Copynumber: 7.7 Consensus size: 59
5637714 TTTTTTGTAG
*
5637724 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA--TTTTTTGGAAATTTCGATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGAAATTT--ATTTCT-AA
* *** *
5637783 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTGAAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGAAATTTATTTCTAA
* *
5637842 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTGAAATTTTGATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGAAA-TTT-ATTTCTAA
5637903 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATATTTTTTTTGGAAATTTATTTTTCTTTTA
1 GGAAAATTGATACTTTCAACTTTTCCCC-AAAA-ATATTTTTTTTGGAAATTTA--TTTC---TA
5637968 A
59 A
* * *
5637969 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTCGAAATTTATTTCTGA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGAAATTTATTTCTAA
* * *
5638028 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTGAAGTTTATTTCTGA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGAAATTTATTTCTAA
* *
5638087 GGAAAATTGATACTTTCAACTTTTTCCCAAAAATA--TTTTTTGAAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGAAATTTATTTCTAA
*
5638144 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATAT-TTTTTTT
5638188 TTGGAATTTT
Statistics
Matches: 363, Mismatches: 27, Indels: 29
0.87 0.06 0.07
Matches are distributed among these distances:
57 51 0.14
59 171 0.47
60 10 0.03
61 49 0.13
62 11 0.03
63 18 0.05
64 19 0.05
65 4 0.01
66 30 0.08
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.45
Consensus pattern (59 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGAAATTTATTTCTAA
Found at i:5638039 original size:245 final size:242
Alignment explanation
Indices: 5637710--5638193 Score: 726
Period size: 245 Copynumber: 2.0 Consensus size: 242
5637700 GGAAAGAATG
* * *
5637710 ATTTTTTTTTGTAGGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTCG
1 ATTTTTCTTTGTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTCGAAATTTC-
* *
5637775 ATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAA-CCCTTTTTTTGAAAATTTATTTC
65 ATTTTCAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATACCTTTTTTTG-AAATTTATTTC
* *
5637839 TAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTGAAATTTTGATTTTTAAG
129 TAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATA---TTTTTTGAAAATTT-ATTTCTAAG
5637904 GAAAATTGATACTTTCAACTTTTCCCCAAAAATATA-TTTTTTTTGGAAATTT
190 GAAAATTGATACTTTCAACTTTTCCCCAAAAATATATTTTTTTTTGGAAATTT
5637956 ATTTTTCTTT-TAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTCGAAATTT
1 ATTTTTCTTTGTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATA--TTTTTTCGAAATTT
* ** *
5638020 -A-TTTCTGAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTGAAGTTTATTT
64 CATTTTC-AAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATACCTTTTTTTGAAATTTATTT
* *
5638083 CTGAGGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGAAAATTTATTTCTAAGGAA
128 CTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTCTAAGGAA
*
5638148 AATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTTTTGGAA
193 AATTGATACTTTCAACTTTTCCCCAAAAATATATTTTTTTTTGGAA
5638194 TTTTTTATTT
Statistics
Matches: 219, Mismatches: 14, Indels: 14
0.89 0.06 0.06
Matches are distributed among these distances:
241 43 0.20
242 25 0.11
244 4 0.02
245 117 0.53
246 17 0.08
247 13 0.06
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.46
Consensus pattern (242 bp):
ATTTTTCTTTGTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTCGAAATTTCA
TTTTCAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATACCTTTTTTTGAAATTTATTTCTA
AGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTCTAAGGAAAAT
TGATACTTTCAACTTTTCCCCAAAAATATATTTTTTTTTGGAAATTT
Found at i:5638286 original size:16 final size:14
Alignment explanation
Indices: 5638265--5638333 Score: 54
Period size: 16 Copynumber: 4.8 Consensus size: 14
5638255 AACCTAATCT
5638265 AATAAATAAAAATTAA
1 AATAAA-AAAAATT-A
*
5638281 AATAAACAAAGAAATA
1 AATAAA-AAA-AATTA
5638297 AATAAAAAAAATTCA
1 AATAAAAAAAATT-A
*
5638312 AAGAAAAAAAA--A
1 AATAAAAAAAATTA
5638324 AA-AAAAAAAA
1 AATAAAAAAAA
5638334 AACCTGAAGC
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
11 8 0.17
12 3 0.06
14 3 0.06
15 14 0.30
16 16 0.34
17 3 0.06
ACGTcount: A:0.81, C:0.03, G:0.03, T:0.13
Consensus pattern (14 bp):
AATAAAAAAAATTA
Found at i:5638313 original size:23 final size:23
Alignment explanation
Indices: 5638287--5638330 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
5638277 TTAAAATAAA
* *
5638287 CAAAGAAATAAATAAAAAAAATT
1 CAAAGAAAAAAAAAAAAAAAATT
5638310 CAAAGAAAAAAAAAAAAAAAA
1 CAAAGAAAAAAAAAAAAAAAA
5638331 AAAAACCTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.82, C:0.05, G:0.05, T:0.09
Consensus pattern (23 bp):
CAAAGAAAAAAAAAAAAAAAATT
Found at i:5638335 original size:31 final size:31
Alignment explanation
Indices: 5638272--5638335 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 31
5638262 TCTAATAAAT
* * * * *
5638272 AAAAATTAAAATAAACAAAGAAATAAATAAA
1 AAAAATTAAAAGAAAAAAAAAAAAAAAAAAA
*
5638303 AAAAATTCAAAGAAAAAAAAAAAAAAAAAAA
1 AAAAATTAAAAGAAAAAAAAAAAAAAAAAAA
5638334 AA
1 AA
5638336 CCTGAAGCGG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.83, C:0.03, G:0.03, T:0.11
Consensus pattern (31 bp):
AAAAATTAAAAGAAAAAAAAAAAAAAAAAAA
Found at i:5638678 original size:20 final size:20
Alignment explanation
Indices: 5638653--5638690 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5638643 GAACACCGGT
*
5638653 GCCGGATTCTGGAAATTTTC
1 GCCGGAATCTGGAAATTTTC
5638673 GCCGGAATCTGGAAATTT
1 GCCGGAATCTGGAAATTT
5638691 CACCGGAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
GCCGGAATCTGGAAATTTTC
Found at i:5638696 original size:19 final size:20
Alignment explanation
Indices: 5638654--5638698 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
5638644 AACACCGGTG
* *
5638654 CCGGATTCTGGAAATTTTCG
1 CCGGAATCTGGAAATTTTCA
5638674 CCGGAATCTGGAAA-TTTCA
1 CCGGAATCTGGAAATTTTCA
5638693 CCGGAA
1 CCGGAA
5638699 GTTGGCCGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (20 bp):
CCGGAATCTGGAAATTTTCA
Found at i:5638789 original size:31 final size:31
Alignment explanation
Indices: 5638751--5638821 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
5638741 ACTGGGCAGG
* ** *
5638751 TCGCCGGAAACTTCAATGTTGGCCGGAATTT
1 TCGCCGGAAAATTCAAACTTCGCCGGAATTT
5638782 TCGCCGGAAAATTCAAACTTCGCCGGAATTT
1 TCGCCGGAAAATTCAAACTTCGCCGGAATTT
*
5638813 TCGTCGGAA
1 TCGCCGGAA
5638822 TCTGGAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (31 bp):
TCGCCGGAAAATTCAAACTTCGCCGGAATTT
Found at i:5638869 original size:26 final size:24
Alignment explanation
Indices: 5638830--5638883 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
5638820 AATCTGGAAA
*
5638830 TTTCCCAGAAATTTCCAGAAAAAAT
1 TTTCCCAAAAATTTCCA-AAAAAAT
* *
5638855 TTTCGCCAAAAATTTCTAAAAAATT
1 TTTC-CCAAAAATTTCCAAAAAAAT
5638880 TTTC
1 TTTC
5638884 TCACTCCCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.35
Consensus pattern (24 bp):
TTTCCCAAAAATTTCCAAAAAAAT
Found at i:5639364 original size:3 final size:3
Alignment explanation
Indices: 5639356--5639382 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5639346 AAAGATATAC
5639356 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
5639383 GAATACATAA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5639591 original size:20 final size:20
Alignment explanation
Indices: 5639563--5639600 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5639553 TTAAATCTCA
5639563 TCGTAGGATAAAAATTTTTT
1 TCGTAGGATAAAAATTTTTT
*
5639583 TCGTTGGATAAAAATTTT
1 TCGTAGGATAAAAATTTT
5639601 CTTTTCTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (20 bp):
TCGTAGGATAAAAATTTTTT
Found at i:5639705 original size:12 final size:12
Alignment explanation
Indices: 5639685--5639730 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
5639675 ATATCAAAAA
*
5639685 ATTTAATTATAT
1 ATTTTATTATAT
5639697 ATTTTATTATAT
1 ATTTTATTATAT
5639709 AATTTTATTA-AT
1 -ATTTTATTATAT
*
5639721 -TATTATTATA
1 ATTTTATTATA
5639731 AAATAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
10 7 0.23
11 1 0.03
12 13 0.43
13 9 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
ATTTTATTATAT
Found at i:5639713 original size:13 final size:13
Alignment explanation
Indices: 5639684--5639718 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
5639674 AATATCAAAA
*
5639684 AATTTAATTATAT
1 AATTTTATTATAT
5639697 -ATTTTATTATAT
1 AATTTTATTATAT
5639709 AATTTTATTA
1 AATTTTATTA
5639719 ATTATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AATTTTATTATAT
Found at i:5640737 original size:23 final size:23
Alignment explanation
Indices: 5640690--5640738 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
5640680 TTTATAGAGC
*
5640690 TTTTTAGGATTCAAATCCCATAT
1 TTTTTAGGATTCAAATCCCAGAT
*
5640713 TTTTTAGGATTCAAATCCTAGAT
1 TTTTTAGGATTCAAATCCCAGAT
5640736 TTT
1 TTT
5640739 CAAGCCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.47
Consensus pattern (23 bp):
TTTTTAGGATTCAAATCCCAGAT
Found at i:5640916 original size:15 final size:15
Alignment explanation
Indices: 5640894--5640958 Score: 62
Period size: 15 Copynumber: 4.3 Consensus size: 15
5640884 AGAAAAAAGG
5640894 AAAA-AATATATGA-A
1 AAAATAATA-ATGATA
5640908 AAAATAATAATGATA
1 AAAATAATAATGATA
* *
5640923 ATAATAATAATAATA
1 AAAATAATAATGATA
* *
5640938 ATAATAATAATAATA
1 AAAATAATAATGATA
5640953 CAAAAT
1 -AAAAT
5640959 GGTGTTCACA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
14 8 0.18
15 33 0.73
16 4 0.09
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.28
Consensus pattern (15 bp):
AAAATAATAATGATA
Found at i:5640918 original size:3 final size:3
Alignment explanation
Indices: 5640910--5640952 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
5640900 TATATGAAAA
*
5640910 AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5640953 CAAAATGGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5641155 original size:44 final size:45
Alignment explanation
Indices: 5641106--5641345 Score: 152
Period size: 48 Copynumber: 5.1 Consensus size: 45
5641096 TCAATGACAT
** * * *
5641106 TTTTGAAAATTTAAGGAA-GCTCCTCTAAGTAGAGGCTCAATAAC
1 TTTTGAAAATTTAAAAAAGGCTCATCTAAGCAGAGGCTCAACAAC
5641150 TTTTGAAAATTTTAAAAAAGGCTCATCTAAGCAGAGGCTCAACAAC
1 TTTTGAAAA-TTTAAAAAAGGCTCATCTAAGCAGAGGCTCAACAAC
* * *
5641196 -TTT-AAAATTTATCATCCTGGAAAA-ACTCCTCTAAGCAGAGTCTCAACAAC
1 TTTTGAAAATTTA--A------AAAAGGCTCATCTAAGCAGAGGCTCAACAAC
* *
5641246 -TTTAAAAATCTTATCTGAAAAA-GCTCCTCTAAGCAGAGGCTCAACAAC
1 TTTTGAAAAT-TTA----AAAAAGGCTCATCTAAGCAGAGGCTCAACAAC
* *
5641294 -TTTAAAAATCTCATCTAAAAAAGACTCATCTAAGCAGAGGCTCAACAAC
1 TTTTGAAAA--T--T-TAAAAAAGGCTCATCTAAGCAGAGGCTCAACAAC
5641343 TTT
1 TTT
5641346 ACTTTAAAAT
Statistics
Matches: 162, Mismatches: 14, Indels: 34
0.77 0.07 0.16
Matches are distributed among these distances:
43 4 0.02
44 13 0.08
45 11 0.07
46 23 0.14
48 41 0.25
49 24 0.15
50 29 0.18
51 10 0.06
52 5 0.03
54 2 0.01
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (45 bp):
TTTTGAAAATTTAAAAAAGGCTCATCTAAGCAGAGGCTCAACAAC
Found at i:5641346 original size:49 final size:48
Alignment explanation
Indices: 5641122--5641760 Score: 526
Period size: 49 Copynumber: 12.9 Consensus size: 48
5641112 AAATTTAAGG
* * * *
5641122 AAGCTCCTCTAAGTAGAGGCTCAATAACTTTTGAAAAT-T--T-TAAAA
1 AAGCTCATCTAAGTAGAGGCTCAACAAC-TTTAAAAATCTCATCTGAAA
* * *
5641167 AAGGCTCATCTAAGCAGAGGCTCAACAACTTTAAAATTTATCATCCTGGAAA
1 AA-GCTCATCTAAGTAGAGGCTCAACAACTTTAAAA-ATCTCAT-CT-GAAA
* * * *
5641219 AA-CTCCTCTAAGCAGAGTCTCAACAACTTTAAAAATCTTATCTGAAA
1 AAGCTCATCTAAGTAGAGGCTCAACAACTTTAAAAATCTCATCTGAAA
* * *
5641266 AAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAAATCTCATCTAAAA
1 AAGCTCATCTAAGTAGAGGCTCAACAACTTTAAAAATCTCATCTGAAA
*
5641314 AAGACTCATCTAAGCAGAGGCTCAACAACTTTACTTTAAAATTCATCATCCT-AGAA
1 AAG-CTCATCTAAGTAGAGGCTCAACAACTTTA----AAAA-TC-TCAT-CTGA-AA
* * * *
5641370 AAGCTTC-TCTAAGTAGAGGCTCAATAATTTTAAAAATATTATCTGAAA
1 AAGC-TCATCTAAGTAGAGGCTCAACAACTTTAAAAATCTCATCTGAAA
* * * * * *
5641418 AAGGCT-ATTCTAAGCAGATGTTTAACAACTTTAAAATTTTTCATCCT-AAA
1 AA-GCTCA-TCTAAGTAGAGGCTCAACAACTTTAAAA-ATCTCAT-CTGAAA
*
5641468 AAGGCTCCTCTAAGTAGAGGCTCAACAACTTTAAAAATCTCATCT-AGAA
1 AA-GCTCATCTAAGTAGAGGCTCAACAACTTTAAAAATCTCATCTGA-AA
* * * *
5641517 AAGCTCTTTTAAGTAGAGGCTCAACAACTTTAAAAATTTCATATGAAAA
1 AAGCTCATCTAAGTAGAGGCTCAACAACTTTAAAAATCTCATCTG-AAA
* *
5641566 AAGCTCATCTAAGCAGATGCTCAACAACTTTAAAAATCATCATCTTGAAA
1 AAGCTCATCTAAGTAGAGGCTCAACAACTTTAAAAATC-TCATC-TGAAA
* ** * *
5641616 AAGTTTC-TCTAAACAAAGGCTCAACAATTTTAAAAATCCATCATCTTGAAA
1 AAG-CTCATCTAAGTAGAGGCTCAACAACTTTAAAAAT-C-TCATC-TGAAA
* * *
5641667 AAGCTCATCTAAATATAAGCTCAACAACTTTAAAAATCTCATCTTGAAA
1 AAGCTCATCTAAGTAGAGGCTCAACAACTTTAAAAATCTCATC-TGAAA
* * * * * *
5641716 AAGCTCCTCTAAGTAAAAGCTTAACAATTTTAAAAATTTCATCTG
1 AAGCTCATCTAAGTAGAGGCTCAACAACTTTAAAAATCTCATCTG
5641761 TTCTCAAAAT
Statistics
Matches: 498, Mismatches: 62, Indels: 65
0.80 0.10 0.10
Matches are distributed among these distances:
45 8 0.02
46 24 0.05
47 7 0.01
48 97 0.19
49 153 0.31
50 108 0.22
51 53 0.11
52 5 0.01
53 4 0.01
54 2 0.00
55 28 0.06
56 9 0.02
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.29
Consensus pattern (48 bp):
AAGCTCATCTAAGTAGAGGCTCAACAACTTTAAAAATCTCATCTGAAA
Found at i:5641402 original size:104 final size:102
Alignment explanation
Indices: 5641164--5641728 Score: 433
Period size: 99 Copynumber: 5.6 Consensus size: 102
5641154 GAAAATTTTA
* * * * * *
5641164 AAAAAGGCTCATCTAAGCAGAGGCTCAACAACTTTAAAATTTATCATCCTGGAAAAA-CTCCTCT
1 AAAAA-GCTCCTCTAAGTAGAGGCTCAACAACTTTAAAA-ATCTCAT-CT-AAAAAAGCTCATCT
* *
5641228 AAGCAGAGTCTCAACAACTTTA----AAAA-TC-TTAT-CT
62 AAGCAGAGGCTCAACAACTTTACTTTAAAATTCATCATCCT
*
5641262 GAAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAAATCTCATCTAAAAAAGACTCATCTAA
1 -AAAAAGCTCCTCTAAGTAGAGGCTCAACAACTTTAAAAATCTCATCTAAAAAAG-CTCATCTAA
5641327 GCAGAGGCTCAACAACTTTACTTTAAAATTCATCATCCT
64 GCAGAGGCTCAACAACTTTACTTTAAAATTCATCATCCT
* * * * * *
5641366 AGAAAAGCTTCTCTAAGTAGAGGCTCAATAATTTTAAAAATATTATCTGAAAAAGGCT-ATTCTA
1 A-AAAAGCTCCTCTAAGTAGAGGCTCAACAACTTTAAAAATCTCATCT-AAAAAAGCTCA-TCTA
* * * **
5641430 AGCAGATGTTTAAC-A----ACTTTAAAATTTTTCATCCT
63 AGCAGAGGCTCAACAACTTTACTTTAAAATTCATCATCCT
* * *
5641465 AAAAAGGCTCCTCTAAGTAGAGGCTCAACAACTTTAAAAATCTCATCTAGAAAAGCTCTTTTAAG
1 AAAAA-GCTCCTCTAAGTAGAGGCTCAACAACTTTAAAAATCTCATCTAAAAAAGCTCATCTAAG
* **
5641530 TAGAGGCTCAACAACTTTA----AAAATTTCAT-AT-GA
65 CAGAGGCTCAACAACTTTACTTTAAAA-TTCATCATCCT
* * * * *
5641563 AAAAAGCTCATCTAAGCAGATGCTCAACAACTTTAAAAATCATCATCTTGAAAAAGTTTC-TCTA
1 AAAAAGCTCCTCTAAGTAGAGGCTCAACAACTTTAAAAATC-TCATC-TAAAAAAG-CTCATCTA
* * * * *
5641627 AACAAAGGCTCAACAA--TT--TTAAAAATCCATCATCTT
63 AGCAGAGGCTCAACAACTTTACTTTAAAATTCATCATCCT
* * * * * *
5641663 GAAAAAGCTCATCTAAATATAAGCTCAACAACTTTAAAAATCTCATCTTGAAAAAGCTCCTCTAA
1 -AAAAAGCTCCTCTAAGTAGAGGCTCAACAACTTTAAAAATCTCATC-TAAAAAAGCTCATCTAA
5641728 G
64 G
5641729 TAAAAGCTTA
Statistics
Matches: 381, Mismatches: 55, Indels: 59
0.77 0.11 0.12
Matches are distributed among these distances:
95 5 0.01
96 2 0.01
97 67 0.18
98 70 0.18
99 98 0.26
100 24 0.06
101 41 0.11
102 2 0.01
103 7 0.02
104 59 0.15
105 6 0.02
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (102 bp):
AAAAAGCTCCTCTAAGTAGAGGCTCAACAACTTTAAAAATCTCATCTAAAAAAGCTCATCTAAGC
AGAGGCTCAACAACTTTACTTTAAAATTCATCATCCT
Found at i:5641553 original size:147 final size:148
Alignment explanation
Indices: 5641162--5641718 Score: 583
Period size: 147 Copynumber: 3.7 Consensus size: 148
5641152 TTGAAAATTT
* * * * *
5641162 TAAAAAAGGCTCATCTAAGCAGAGGCTCAACAACTTTAAAATTTATCATCCTGGAAAAACTCCTC
1 TAAAAAAGGCTCATCTAAGCAGAGGCTCAACAACTTTAAAAATCATCATCCTAGAAAAGCTCTTC
* * * *
5641227 TAAGCAGAGTCTCAACAACTTTAAAAATCTTATCTGAAAAA-GCTCCTCTAAGCAGAGGCTCAAC
66 TAAGTAGAGGCTCAACAACTTTAAAAATCTTATCTGAAAAAGGCT-ATCTAAGCAGATGCTCAAC
* *
5641291 AACTTTAAAAATCTCAT-C
130 AACTTTAAAATTATCATCC
*
5641309 TAAAAAAGACTCATCTAAGCAGAGGCTCAACAACTTTACTTTAAAATTCATCATCCTAGAAAAGC
1 TAAAAAAGGCTCATCTAAGCAGAGGCTCAACAACTTTA----AAAA-TCATCATCCTAGAAAAGC
* * *
5641374 T-TCTCTAAGTAGAGGCTCAATAATTTTAAAAATATTATCTGAAAAAGGCTATTCTAAGCAGATG
61 TCT-TCTAAGTAGAGGCTCAACAACTTTAAAAATCTTATCTGAAAAAGGCTA-TCTAAGCAGATG
* * *
5641438 TTTAACAACTTTAAAATTTTTCATCC
124 CTCAACAACTTTAAAA-TTATCATCC
* * *
5641464 T-AAAAAGGCTCCTCTAAGTAGAGGCTCAACAACTTTAAAAATC-TCAT-CTAGAAAAGCTCTTT
1 TAAAAAAGGCTCATCTAAGCAGAGGCTCAACAACTTTAAAAATCATCATCCTAGAAAAGCTCTTC
* *
5641526 TAAGTAGAGGCTCAACAACTTTAAAAAT-TTCATATGAAAAAAGCTCATCTAAGCAGATGCTCAA
66 TAAGTAGAGGCTCAACAACTTTAAAAATCTT-ATCTGAAAAAGGCT-ATCTAAGCAGATGCTCAA
* *
5641590 CAACTTTAAAAATCATCATCT
129 CAACTTT-AAAATTATCATCC
* ** * * * * *
5641611 TGAAAAAGTTTC-TCTAAACAAAGGCTCAACAATTTTAAAAATCCATCAT-CTTGAAAAAGCTCA
1 TAAAAAAGGCTCATCTAAGCAGAGGCTCAACAACTTTAAAAAT-CATCATCCTAG-AAAAGCTCT
* * * *
5641674 TCTAAATATAAGCTCAACAACTTTAAAAATCTCATCTTGAAAAAG
64 TCTAAGTAGAGGCTCAACAACTTTAAAAATCTTATC-TGAAAAAG
5641719 CTCCTCTAAG
Statistics
Matches: 345, Mismatches: 45, Indels: 36
0.81 0.11 0.08
Matches are distributed among these distances:
146 2 0.01
147 142 0.41
148 19 0.06
149 9 0.03
150 40 0.12
151 11 0.03
152 54 0.16
153 28 0.08
154 38 0.11
155 2 0.01
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (148 bp):
TAAAAAAGGCTCATCTAAGCAGAGGCTCAACAACTTTAAAAATCATCATCCTAGAAAAGCTCTTC
TAAGTAGAGGCTCAACAACTTTAAAAATCTTATCTGAAAAAGGCTATCTAAGCAGATGCTCAACA
ACTTTAAAATTATCATCC
Found at i:5648685 original size:16 final size:16
Alignment explanation
Indices: 5648655--5648696 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
5648645 CAGATAAAAA
5648655 ATTTTT-TTCTTATATT
1 ATTTTTATT-TTATATT
5648671 -TTTATTATTTTATATT
1 ATTT-TTATTTTATATT
5648687 ATTTTTATTT
1 ATTTTTATTT
5648697 AATTATAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 3 0.13
16 15 0.65
17 5 0.22
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (16 bp):
ATTTTTATTTTATATT
Found at i:5648782 original size:13 final size:12
Alignment explanation
Indices: 5648751--5648784 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
5648741 TTATAAAAAA
5648751 ATTTTATTATAT
1 ATTTTATTATAT
5648763 ATTTTATTATAT
1 ATTTTATTATAT
5648775 ATTTTTATTA
1 A-TTTTATTA
5648785 ATTATTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.62
13 8 0.38
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATTTTATTATAT
Found at i:5648897 original size:23 final size:23
Alignment explanation
Indices: 5648850--5648902 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
5648840 CATAAATATT
*
5648850 AATAATAATAATTAAAATAACAAA
1 AATAATAATAA-TAAAATAAAAAA
5648874 AATAATATATAA-AAAATAAAAAA
1 AATAATA-ATAATAAAATAAAAAA
5648897 AATAAT
1 AATAAT
5648903 TTTTTTACCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 16 0.59
24 7 0.26
25 4 0.15
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.25
Consensus pattern (23 bp):
AATAATAATAATAAAATAAAAAA
Found at i:5649512 original size:18 final size:16
Alignment explanation
Indices: 5649480--5649526 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
5649470 GGTCAAACCC
5649480 TCTTTTTTATTTTGACTT
1 TCTTTTTT-TTTTGA-TT
5649498 TCTTTTTTTTATTGATT
1 TCTTTTTTTT-TTGATT
*
5649515 T-TTTTCTTTTTG
1 TCTTTTTTTTTTG
5649527 TTTGCAGGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 3 0.11
16 7 0.26
17 5 0.19
18 12 0.44
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.77
Consensus pattern (16 bp):
TCTTTTTTTTTTGATT
Found at i:5649892 original size:24 final size:24
Alignment explanation
Indices: 5649860--5649908 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
5649850 ATTAAACTGG
* * *
5649860 AGAAGGAAAGAAGAAGAAGGAAAA
1 AGAAAGAAAGAAAAAGAAAGAAAA
5649884 AGAAAGAAAGAAAAAGAAAGAAAA
1 AGAAAGAAAGAAAAAGAAAGAAAA
5649908 A
1 A
5649909 ATAATAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (24 bp):
AGAAAGAAAGAAAAAGAAAGAAAA
Found at i:5649902 original size:14 final size:14
Alignment explanation
Indices: 5649860--5649906 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
5649850 ATTAAACTGG
*
5649860 AGAAGGAAAGAAG-A
1 AGAAAGAAA-AAGAA
*
5649874 AGAAGGAAAAAGAA
1 AGAAAGAAAAAGAA
5649888 AGAAAGAAAAAGAA
1 AGAAAGAAAAAGAA
5649902 AGAAA
1 AGAAA
5649907 AAATAATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 3 0.10
14 28 0.90
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (14 bp):
AGAAAGAAAAAGAA
Found at i:5649916 original size:3 final size:3
Alignment explanation
Indices: 5649908--5649952 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
5649898 AGAAAGAAAA
5649908 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5649953 CAAAATGTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5650227 original size:26 final size:27
Alignment explanation
Indices: 5650197--5650272 Score: 66
Period size: 26 Copynumber: 2.8 Consensus size: 27
5650187 ATATTAAGAG
5650197 TTAATATTAAATTTTATTACTAT-ACT
1 TTAATATTAAATTTTATTACTATGACT
* * **
5650223 TTAATTTCATTAAATTTTAATAATATGTTT
1 TTAA--T-ATTAAATTTTATTACTATGACT
*
5650253 TTAA-ATAAAATTTTATTACT
1 TTAATATTAAATTTTATTACT
5650273 TACATAGATA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
26 17 0.44
28 1 0.03
29 16 0.41
30 5 0.13
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.54
Consensus pattern (27 bp):
TTAATATTAAATTTTATTACTATGACT
Found at i:5662013 original size:2 final size:2
Alignment explanation
Indices: 5662006--5662038 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5661996 CCACCTTAGG
5662006 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5662039 AGTTTTACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5662429 original size:25 final size:25
Alignment explanation
Indices: 5662392--5662452 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
5662382 AAATATTGCA
*
5662392 AATCTATCAATATAATAAATCTTTC
1 AATCTATCCATATAATAAATCTTTC
* *
5662417 AATCCATCCATATAATAAATCTTTG
1 AATCTATCCATATAATAAATCTTTC
5662442 AATCTATCCAT
1 AATCTATCCAT
5662453 CCTTACATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.41, C:0.20, G:0.02, T:0.38
Consensus pattern (25 bp):
AATCTATCCATATAATAAATCTTTC
Found at i:5662523 original size:7 final size:8
Alignment explanation
Indices: 5662505--5662538 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
5662495 AAACTATTTG
5662505 TTTTTACT
1 TTTTTACT
5662513 TTTTTACT
1 TTTTTACT
*
5662521 TTTTTGCT
1 TTTTTACT
5662529 TTTTTA-T
1 TTTTTACT
5662536 TTT
1 TTT
5662539 ATAATTAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 4 0.17
8 20 0.83
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.79
Consensus pattern (8 bp):
TTTTTACT
Found at i:5662906 original size:13 final size:13
Alignment explanation
Indices: 5662888--5662913 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5662878 TCTATTTAAT
5662888 TATATATATATTA
1 TATATATATATTA
5662901 TATATATATATTA
1 TATATATATATTA
5662914 ATAAAATTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATTA
Found at i:5663022 original size:18 final size:18
Alignment explanation
Indices: 5662995--5663039 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
5662985 ATTATCTTTT
* *
5662995 TTTTTATTTTTTGTT-TA
1 TTTTTCTTTTTTATTATA
5663012 TTTTTCTTTTTTATTATA
1 TTTTTCTTTTTTATTATA
5663030 TTTTTCTTTT
1 TTTTTCTTTT
5663040 ACCTTAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.11, C:0.04, G:0.02, T:0.82
Consensus pattern (18 bp):
TTTTTCTTTTTTATTATA
Found at i:5663039 original size:24 final size:24
Alignment explanation
Indices: 5662986--5663039 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
5662976 ACACCTTTAA
* *
5662986 TTATCTTT-TTTTTTATTTTTTGT
1 TTATTTTTCTTTTTTATTTATTGT
5663009 TTATTTTTCTTTTTTATTATATT-T
1 TTATTTTTCTTTTTTATT-TATTGT
*
5663033 TTCTTTT
1 TTATTTT
5663040 ACCTTAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 7 0.27
24 16 0.62
25 3 0.12
ACGTcount: A:0.11, C:0.06, G:0.02, T:0.81
Consensus pattern (24 bp):
TTATTTTTCTTTTTTATTTATTGT
Found at i:5663813 original size:15 final size:15
Alignment explanation
Indices: 5663776--5663817 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
5663766 ATCATTAAAG
*
5663776 ATTCAAAATCTATTTT
1 ATTCAAAA-ATATTTT
*
5663792 -TTAAAAAATATTTT
1 ATTCAAAAATATTTT
5663806 ATTCAAAAATAT
1 ATTCAAAAATAT
5663818 CTTTTAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTCAAAAATATTTT
Found at i:5666042 original size:53 final size:51
Alignment explanation
Indices: 5665976--5666100 Score: 160
Period size: 51 Copynumber: 2.4 Consensus size: 51
5665966 ATCAAGCACG
5665976 TAGTTTTTTATTGAAAAAAAATTACAAAGACTACGTTTATAAAAATAGAAACA
1 TAGTTTTTTATTGAAAAAAAATTACAAAGA-T-CGTTTATAAAAATAGAAACA
* * * * * * *
5666029 TAGTCTTTGATTGAAAAAAAATTACAGAGATTGTTTATGAAAGTAGAAACT
1 TAGTTTTTTATTGAAAAAAAATTACAAAGATCGTTTATAAAAATAGAAACA
*
5666080 TAGTTTTTTCTTGAAAAAAAA
1 TAGTTTTTTATTGAAAAAAAA
5666101 AATTTATAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
51 34 0.55
52 1 0.02
53 27 0.44
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.34
Consensus pattern (51 bp):
TAGTTTTTTATTGAAAAAAAATTACAAAGATCGTTTATAAAAATAGAAACA
Found at i:5666101 original size:53 final size:53
Alignment explanation
Indices: 5665976--5666328 Score: 185
Period size: 53 Copynumber: 6.6 Consensus size: 53
5665966 ATCAAGCACG
5665976 TAGTTTTTTATTGAAAAAAAATTACAAAGACTACGTTTATAAAAATAGAAACA
1 TAGTTTTTTATTGAAAAAAAATTACAAAGACTACGTTTATAAAAATAGAAACA
* * * * * * *
5666029 TAGTCTTTGATTGAAAAAAAATTACAGAGA-T-TGTTTATGAAAGTAGAAACT
1 TAGTTTTTTATTGAAAAAAAATTACAAAGACTACGTTTATAAAAATAGAAACA
* * * * * * * * **
5666080 TAGTTTTTTCTTGAAAAAAAAAATTTATAAAGACTACATTTTTTAGAGTAGACATG
1 TAGTTTTTTATTG--AAAAAAAA-TTACAAAGACTACGTTTATAAAAATAGAAACA
* * * * * ** * * *
5666136 TAGTTTTTGATTGAAAAAAATTTTACAAACACTATGTTTTTGTAAGTAAAAACG
1 TAGTTTTTTATTGAAAAAAA-ATTACAAAGACTACGTTTATAAAAATAGAAACA
* * * * *** **
5666190 TAGTTTTTTATTG-AAAAAAATATATAAATACTACATTTTTAATTGTAGAAATG
1 TAGTTTTTTATTGAAAAAAAAT-TACAAAGACTACGTTTATAAAAATAGAAACA
* ** * * ** *
5666243 TAATTTTTTATTGAAAAAATTTTACAAA-ACTACATTTTTGAAAGTTA-CAACA
1 TAGTTTTTTATTGAAAAAAAATTACAAAGACTACGTTTAT-AAAAATAGAAACA
**
5666295 TAGTTTTAGATTGAAAAAAAAAATTACAAAGACT
1 TAGTTTTTTATTG--AAAAAAAATTACAAAGACT
5666329 CATTTTTTAT
Statistics
Matches: 228, Mismatches: 60, Indels: 22
0.74 0.19 0.07
Matches are distributed among these distances:
51 26 0.11
52 25 0.11
53 83 0.36
54 67 0.29
55 4 0.02
56 23 0.10
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (53 bp):
TAGTTTTTTATTGAAAAAAAATTACAAAGACTACGTTTATAAAAATAGAAACA
Found at i:5666145 original size:107 final size:107
Alignment explanation
Indices: 5665973--5666314 Score: 309
Period size: 107 Copynumber: 3.2 Consensus size: 107
5665963 AAAATCAAGC
* * * * * ** *
5665973 ACGTAGTTTTTTATTGAAAAAAA-ATTACAAAGACTACGTTTATAAAAATAGAAACATAGTCTTT
1 ACGTAGTTTTTTATTGAAAAAAATA-TATAAAGACTACATTTTTAAGAGTAGAAATGTAGTTTTT
* * *
5666037 GATTGAAAAAAA-ATTACAGAGA-T-TGTTTATGAAAGTAGAA
65 GATTGAAAAAAATATTACAAACACTATGTTTATGAAAGTAAAA
* * * * *
5666077 ACTTAGTTTTTTCTTGAAAAAAAAAATTTATAAAGACTACATTTTTTAGAGTAGACATGTAGTTT
1 ACGTAGTTTTTTATTG---AAAAAAATATATAAAGACTACATTTTTAAGAGTAGAAATGTAGTTT
* * *
5666142 TTGATTGAAAAAAATTTTACAAACACTATGTTTTTGTAAGTAAAA
63 TTGATTGAAAAAAATATTACAAACACTATGTTTATGAAAGTAAAA
* ** * *
5666187 ACGTAGTTTTTTATTGAAAAAAATATATAAATACTACATTTTTAATTGTAGAAATGTAATTTTTT
1 ACGTAGTTTTTTATTGAAAAAAATATATAAAGACTACATTTTTAAGAGTAGAAATGTAGTTTTTG
* ** * * *
5666252 ATTG-AAAAAATTTTACAAA-ACTACATTTTTGAAAGTTACA
66 ATTGAAAAAAATATTACAAACACTATGTTTATGAAAGTAAAA
* **
5666292 ACATAGTTTTAGATTGAAAAAAA
1 ACGTAGTTTTTTATTGAAAAAAA
5666315 AAATTACAAA
Statistics
Matches: 194, Mismatches: 37, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
104 14 0.07
105 36 0.19
106 15 0.08
107 93 0.48
108 7 0.04
109 1 0.01
110 28 0.14
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (107 bp):
ACGTAGTTTTTTATTGAAAAAAATATATAAAGACTACATTTTTAAGAGTAGAAATGTAGTTTTTG
ATTGAAAAAAATATTACAAACACTATGTTTATGAAAGTAAAA
Found at i:5666315 original size:107 final size:108
Alignment explanation
Indices: 5666066--5666373 Score: 306
Period size: 107 Copynumber: 2.9 Consensus size: 108
5666056 AGATTGTTTA
* * *** * **
5666066 TGAAAGTAGAAACTTAGTTTTTTCTTGAAAAAAAAAATTTATAAAGACTACATTTTTTAGAGTAG
1 TGAAAGTAAAAACATAGTTTTAGATTG-AAAAAAAAATATATAAAGACTACATTTTTTATTGTAG
* * **
5666131 ACATGTAGTTTTTGATTGAAAAAAATTTTACAAACACTATGTTTT
65 AAATGTAATTTTTGATTG-AAAAAATTTTACAAACACTACATTTT
* * ** * *
5666176 TGTAAGTAAAAACGTAGTTTTTTATTG--AAAAAAATATATAAATACTACATTTTTAATTGTAGA
1 TGAAAGTAAAAACATAGTTTTAGATTGAAAAAAAAATATATAAAGACTACATTTTTTATTGTAGA
*
5666239 AATGTAATTTTTTATTGAAAAAATTTTACAAA-ACTACATTTT
66 AATGTAATTTTTGATTGAAAAAATTTTACAAACACTACATTTT
* * * * *
5666281 TGAAAGTTACAACATAGTTTTAGATTGAAAAAAAAA-ATTACAAAGACT-CATTTTTTATTGCAA
1 TGAAAGTAAAAACATAGTTTTAGATTGAAAAAAAAATA-TATAAAGACTACATTTTTTATTGTAG
* *
5666344 AAACGTAATGTTTGA-TGAAAAAA-TTTACAA
65 AAATGTAATTTTTGATTGAAAAAATTTTACAA
5666374 TGACTATAGT
Statistics
Matches: 167, Mismatches: 28, Indels: 12
0.81 0.14 0.06
Matches are distributed among these distances:
104 7 0.04
105 37 0.22
106 40 0.24
107 60 0.36
110 23 0.14
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (108 bp):
TGAAAGTAAAAACATAGTTTTAGATTGAAAAAAAAATATATAAAGACTACATTTTTTATTGTAGA
AATGTAATTTTTGATTGAAAAAATTTTACAAACACTACATTTT
Found at i:5668932 original size:23 final size:23
Alignment explanation
Indices: 5668906--5668952 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
5668896 ATTAGCTTAC
* *
5668906 ATATTTATTTAAATATAATATAT
1 ATATTCATTCAAATATAATATAT
*
5668929 ATATTCATTCATATATAATATAT
1 ATATTCATTCAAATATAATATAT
5668952 A
1 A
5668953 CTGGTATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (23 bp):
ATATTCATTCAAATATAATATAT
Found at i:5670070 original size:24 final size:23
Alignment explanation
Indices: 5669962--5670114 Score: 108
Period size: 24 Copynumber: 6.4 Consensus size: 23
5669952 TGTAAATATT
* *
5669962 TTTTTCATTAATAGAAGTCCAAA
1 TTTTTCATTTATACAAGTCCAAA
* * * *
5669985 TTTTATAATTAAGACAAATCCAAAA
1 TTTT-TCATTTATACAAGTCC-AAA
* * **
5670010 TTTTTTATTTAAACGTGTCCAAA
1 TTTTTCATTTATACAAGTCCAAA
*
5670033 TTTTATGATTTATACAAGTCCAAA
1 TTTT-TCATTTATACAAGTCCAAA
* *
5670057 GTTTTTCATATATACAAATCCTAAA
1 -TTTTTCATTTATACAAGTCC-AAA
* * *
5670082 ATTTTCATTTATATAAGTCCAAC
1 TTTTTCATTTATACAAGTCCAAA
5670105 TTTTGTCATT
1 TTTT-TCATT
5670115 CATATGTGGC
Statistics
Matches: 101, Mismatches: 23, Indels: 11
0.75 0.17 0.08
Matches are distributed among these distances:
23 16 0.16
24 71 0.70
25 14 0.14
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (23 bp):
TTTTTCATTTATACAAGTCCAAA
Found at i:5670480 original size:52 final size:53
Alignment explanation
Indices: 5670418--5670520 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 53
5670408 TTTAATTACT
* *
5670418 TTTGTATGTAATCCTTTCTAAATTCATGTGGCAGTGTAAAAAA-AAATCAAAA
1 TTTGTATGTAATCCTTTCTAAATTCATGTAGCAGTGCAAAAAAGAAATCAAAA
*
5670470 TTTGTATGTAATCCTTTCTAAATTCATGTAGTAGTGCAAAAAAGAAATCAA
1 TTTGTATGTAATCCTTTCTAAATTCATGTAGCAGTGCAAAAAAGAAATCAA
5670521 CTTTGTTAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 40 0.85
53 7 0.15
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (53 bp):
TTTGTATGTAATCCTTTCTAAATTCATGTAGCAGTGCAAAAAAGAAATCAAAA
Found at i:5671564 original size:21 final size:21
Alignment explanation
Indices: 5671525--5671575 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
5671515 TGAAAAATGT
5671525 ATAAAAT-AAAATTATAAAAA
1 ATAAAATAAAAATTATAAAAA
*
5671545 GTAAAATAAAAATGTA-AAAAA
1 ATAAAATAAAAAT-TATAAAAA
5671566 ATAAAATAAA
1 ATAAAATAAA
5671576 TCGATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 6 0.22
21 19 0.70
22 2 0.07
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.22
Consensus pattern (21 bp):
ATAAAATAAAAATTATAAAAA
Found at i:5675168 original size:149 final size:148
Alignment explanation
Indices: 5674890--5675179 Score: 381
Period size: 149 Copynumber: 1.9 Consensus size: 148
5674880 TGTGGTCTTT
*
5674890 ATGATCAAAGACTACTTTTTAAAAGAAAAAAATGTGGTCTTTAAATAATATCCACCAGTTTGTAT
1 ATGATCAAAGACTACTTTTTAAAAGAAAAAAA-GTGATCTTTAAATAATATCCACCAGTTTGTAT
* * * * * *
5674955 GTTAGAAATATAATCTTTATAATGTACTCAAAGATTACATTTCTTATGTAAAAAATGTGATCTTT
65 GTAAAAAATATAATCTTTATAATATACTCAAAGACTACAGTTCTTATGTAAAAAATATGATCTTT
*
5675020 GTAGATCAAAGTCTACAAA
130 ATAGATCAAAGTCTACAAA
* * *
5675039 ATGATCAAAGACTACTTTTTGATAGAAAAAACA-TGATCTTTAAATGATAAT-CACCACGTTT-T
1 ATGATCAAAGACTACTTTTTAAAAGAAAAAA-AGTGATCTTTAAATAAT-ATCCACCA-GTTTGT
* *
5675101 ATAGGTAAAAAATATGATCTTTATAATATACTCAAAGACTAC-GTTCTTATGTAAAAAATATGGT
63 AT--GTAAAAAATATAATCTTTATAATATACTCAAAGACTACAGTTCTTATGTAAAAAATATGAT
5675165 CTTTATAGATCAAAG
126 CTTTATAGATCAAAG
5675180 ACTATGTTTA
Statistics
Matches: 123, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
148 21 0.17
149 68 0.55
150 34 0.28
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (148 bp):
ATGATCAAAGACTACTTTTTAAAAGAAAAAAAGTGATCTTTAAATAATATCCACCAGTTTGTATG
TAAAAAATATAATCTTTATAATATACTCAAAGACTACAGTTCTTATGTAAAAAATATGATCTTTA
TAGATCAAAGTCTACAAA
Found at i:5676826 original size:3 final size:3
Alignment explanation
Indices: 5676813--5676865 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
5676803 TTTTCTCTTA
*
5676813 AAT ACT 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
5676861 AAT AA
1 AAT AA
5676866 AATGAAACAG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5677201 original size:22 final size:21
Alignment explanation
Indices: 5677176--5677233 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 21
5677166 ATTCATTTTG
*
5677176 AATAAATAGAAAAA-ATTAAATA
1 AATAAATA-AAAAAGAAT-AATA
*
5677198 AATACATAAAAAAGAATAATA
1 AATAAATAAAAAAGAATAATA
5677219 AATATAATAATAAAA
1 AATA-AATAA-AAAA
5677234 TCACAAGTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 13 0.43
22 13 0.43
23 4 0.13
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.22
Consensus pattern (21 bp):
AATAAATAAAAAAGAATAATA
Found at i:5677330 original size:9 final size:8
Alignment explanation
Indices: 5677313--5677337 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5677303 GAATCTTTTC
5677313 AATAAAAA
1 AATAAAAA
5677321 AATAAAAA
1 AATAAAAA
5677329 AATAAAAA
1 AATAAAAA
5677337 A
1 A
5677338 TATTTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AATAAAAA
Found at i:5683376 original size:17 final size:17
Alignment explanation
Indices: 5683356--5683397 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
5683346 TTTAGGGAAA
5683356 AAAATAAAATTTTGAAG
1 AAAATAAAATTTTGAAG
*
5683373 AAAA-AATAATTTTGAGG
1 AAAATAA-AATTTTGAAG
5683390 AAAATAAA
1 AAAATAAA
5683398 TGGCACAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.09
17 18 0.82
18 2 0.09
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (17 bp):
AAAATAAAATTTTGAAG
Found at i:5684298 original size:42 final size:42
Alignment explanation
Indices: 5684186--5684301 Score: 144
Period size: 42 Copynumber: 2.8 Consensus size: 42
5684176 ATTAAAATTC
** *
5684186 TAAATTTTATTTT-TTCAATAGTGATATCAAAGTGTTAAAGCT
1 TAAATTTTATTTTCTT-GGTAGTGATATCTAAGTGTTAAAGCT
* ** * *
5684228 AAAATTGCATTTTCTTGGTGGTGATATCTGAGTGTTAAAGCT
1 TAAATTTTATTTTCTTGGTAGTGATATCTAAGTGTTAAAGCT
5684270 TAAATTTTATTTTCTTGGTAGTGATATCTAAG
1 TAAATTTTATTTTCTTGGTAGTGATATCTAAG
5684302 ACATTTTTAA
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 58 0.97
43 2 0.03
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (42 bp):
TAAATTTTATTTTCTTGGTAGTGATATCTAAGTGTTAAAGCT
Found at i:5684465 original size:57 final size:58
Alignment explanation
Indices: 5684348--5684530 Score: 165
Period size: 57 Copynumber: 3.2 Consensus size: 58
5684338 TAAAGTTTGA
* * *
5684348 ATTTGCATTTTTTCGATAGGTGATATTCAAGTTTACTTTGGTAGTGATATCCAAAGTC
1 ATTTGCATTTTTTCGATAGGTGATATCCAAGTTTACTTTGATAGTGATATCCAAACTC
* * * * *
5684406 ATTTGCATTTCTTT-GAT-GGTGATATCCGAGTTTTCTTTGATTGTGATATCTACACTC
1 ATTTGCATTT-TTTCGATAGGTGATATCCAAGTTTACTTTGATAGTGATATCCAAACTC
* * * * ** * * * * *
5684463 ATTTGTATTTTCTCAAT-GATGATATTTAAATTTTCTTTTATAGCGATATCTAAACTC
1 ATTTGCATTTTTTCGATAGGTGATATCCAAGTTTACTTTGATAGTGATATCCAAACTC
5684520 ATTTGCATTTT
1 ATTTGCATTTT
5684531 CTTAGTGATG
Statistics
Matches: 102, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
56 2 0.02
57 84 0.82
58 13 0.13
59 3 0.03
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.48
Consensus pattern (58 bp):
ATTTGCATTTTTTCGATAGGTGATATCCAAGTTTACTTTGATAGTGATATCCAAACTC
Done.