Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397266.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_20.0, 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: 7441454
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 92215 characters in sequence are not A, C, G, or T
File 14 of 18
Found at i:5732550 original size:26 final size:26
Alignment explanation
Indices: 5732514--5732567 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
5732504 GTAATAACTT
*
5732514 TTTTTTTCAACATAACATATAACAAC
1 TTTTTTCCAACATAACATATAACAAC
* * *
5732540 TTTTTTCCAACATGACGTATAGCAAC
1 TTTTTTCCAACATAACATATAACAAC
5732566 TT
1 TT
5732568 GTTGATAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.39
Consensus pattern (26 bp):
TTTTTTCCAACATAACATATAACAAC
Found at i:5745599 original size:21 final size:21
Alignment explanation
Indices: 5745575--5745640 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
5745565 ATTATCAAAA
*
5745575 TTGTTTGAATGATCTTTGAAC
1 TTGTTTGAATGATTTTTGAAC
* * *
5745596 TTGTTTTAATAATTTTTGAAA
1 TTGTTTGAATGATTTTTGAAC
*
5745617 TGGTTTGAATGAGTTTTTGAAC
1 TTGTTTGAATGA-TTTTTGAAC
5745639 TT
1 TT
5745641 AATTTATTAA
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
21 26 0.74
22 9 0.26
ACGTcount: A:0.26, C:0.05, G:0.18, T:0.52
Consensus pattern (21 bp):
TTGTTTGAATGATTTTTGAAC
Found at i:5745675 original size:142 final size:142
Alignment explanation
Indices: 5745419--5745779 Score: 482
Period size: 142 Copynumber: 2.6 Consensus size: 142
5745409 TTAAAATGAT
* * * * *
5745419 AAAAATTATCAAAATTGCTTGAATAATCTTTAAACTTATTTAAATAATTTTTGAAGTGGTTTAAA
1 AAAAATTATCAAAATTGCTTGAATGATCTTTGAACTTGTTTAAATAATTTTTGAAATGGTTTGAA
*
5745484 TGAGTTTTTGAACTTAATTTATTAATGTTAAAAAATTCTATATATTTGCTTTTTAAGT-ACGAAG
66 TGAGTTTTTGAACTTAATTTATTAATGTTAAAAAATTCTATATATTTGCTTTTGAAGTGACGAAG
5745548 TATTTCCATGTG
131 TATTTCCATGTG
* *
5745560 AAAAAATTATCAAAATTGTTTGAATGATCTTTGAACTTGTTTTAATAATTTTTGAAATGGTTTGA
1 -AAAAATTATCAAAATTGCTTGAATGATCTTTGAACTTGTTTAAATAATTTTTGAAATGGTTTGA
* * *
5745625 ATGAGTTTTTGAACTTAATTTATTAATGTT-AAAAACTCTTATATATTTGCTTTTGAAGTGCCTA
65 ATGAGTTTTTGAACTTAATTTATTAATGTTAAAAAATTC-TATATATTTGCTTTTGAAGTGACGA
*
5745689 AGTGTTTCCATGTG
129 AGTATTTCCATGTG
* * * * * **
5745703 AAAAGTT-TCAAAATTGCTTGAATGA-GTTTGATA-TTGTTTAAATGAGTTTTGAACTTATTTGA
1 AAAAATTATCAAAATTGCTTGAATGATCTTTGA-ACTTGTTTAAATAATTTTTGAAATGGTTTGA
5745765 AT-AGTTTTTGAACTT
65 ATGAGTTTTTGAACTT
5745780 GTTTGAATTG
Statistics
Matches: 195, Mismatches: 21, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
139 13 0.07
140 30 0.15
141 25 0.13
142 112 0.57
143 15 0.08
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (142 bp):
AAAAATTATCAAAATTGCTTGAATGATCTTTGAACTTGTTTAAATAATTTTTGAAATGGTTTGAA
TGAGTTTTTGAACTTAATTTATTAATGTTAAAAAATTCTATATATTTGCTTTTGAAGTGACGAAG
TATTTCCATGTG
Found at i:5745773 original size:21 final size:21
Alignment explanation
Indices: 5745736--5745815 Score: 99
Period size: 21 Copynumber: 3.8 Consensus size: 21
5745726 GAGTTTGATA
*
5745736 TTGTTTAAATGAG-TTTTGAAC
1 TTGTTTGAAT-AGTTTTTGAAC
*
5745757 TTATTTGAATAGTTTTTGAAC
1 TTGTTTGAATAGTTTTTGAAC
*
5745778 TTGTTTGAATTGTTTTTGAAC
1 TTGTTTGAATAGTTTTTGAAC
*
5745799 TTGTTTAAATAAGTTTT
1 TTGTTTGAAT-AGTTTT
5745816 AAACCTCCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
20 2 0.04
21 44 0.86
22 5 0.10
ACGTcount: A:0.26, C:0.04, G:0.16, T:0.54
Consensus pattern (21 bp):
TTGTTTGAATAGTTTTTGAAC
Found at i:5745802 original size:12 final size:12
Alignment explanation
Indices: 5745768--5745804 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
5745758 TATTTGAATA
5745768 GTTTTTGAACTT
1 GTTTTTGAACTT
5745780 G--TTTGAA-TT
1 GTTTTTGAACTT
5745789 GTTTTTGAACTT
1 GTTTTTGAACTT
5745801 GTTT
1 GTTT
5745805 AAATAAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 3 0.14
10 6 0.27
11 6 0.27
12 7 0.32
ACGTcount: A:0.16, C:0.05, G:0.19, T:0.59
Consensus pattern (12 bp):
GTTTTTGAACTT
Found at i:5746053 original size:22 final size:20
Alignment explanation
Indices: 5746018--5746061 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
5746008 ATTTATATTT
5746018 AAACTTAAAAATAAAACATA
1 AAACTTAAAAATAAAACATA
*
5746038 AAACTATAAAGAATAAAATATA
1 AAACT-TAAA-AATAAAACATA
5746060 AA
1 AA
5746062 TAATTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 4 0.19
22 12 0.57
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.20
Consensus pattern (20 bp):
AAACTTAAAAATAAAACATA
Found at i:5746069 original size:15 final size:14
Alignment explanation
Indices: 5746023--5746078 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
5746013 TATTTAAACT
5746023 TAAAA-ATAAA-ACA
1 TAAAATATAAATA-A
*
5746036 TAAAACTATAAAGAA
1 TAAAA-TATAAATAA
5746051 TAAAATATAAATAA
1 TAAAATATAAATAA
*
5746065 TTAAATATGAAATA
1 TAAAATAT-AAATA
5746079 CAAGATTTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
13 5 0.14
14 15 0.41
15 16 0.43
16 1 0.03
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (14 bp):
TAAAATATAAATAA
Found at i:5746069 original size:22 final size:20
Alignment explanation
Indices: 5746022--5746069 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 20
5746012 ATATTTAAAC
*
5746022 TTAAAAATAAAACATAAAAC
1 TTAAAAATAAAACATAAAAA
*
5746042 TATAAAGAATAAAATATAAATAA
1 T-TAAA-AATAAAACATAAA-AA
5746065 TTAAA
1 TTAAA
5746070 TATGAAATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.04
21 4 0.17
22 16 0.70
23 2 0.09
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (20 bp):
TTAAAAATAAAACATAAAAA
Found at i:5746321 original size:6 final size:6
Alignment explanation
Indices: 5746273--5746320 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
5746263 TAAAATACAA
* * *
5746273 AAAAAA AAAAAG -AAGAG AAAAAG AAAAAG AAAAAG AAAAAG AGAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
5746320 A
1 A
5746321 GGTGTAGAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
5 4 0.11
6 33 0.89
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:5747802 original size:108 final size:108
Alignment explanation
Indices: 5747610--5747819 Score: 305
Period size: 108 Copynumber: 1.9 Consensus size: 108
5747600 TAAAATGACT
* * *
5747610 AAATATGTTGATTTAGTTACAACTTTCACAATTTTCGAAAACACATTCTTTTGAAATTATTTAAC
1 AAATATGTTGATTTAATTACAACTTTCACAATTTACGAAAACACATTCTTATGAAATTATTTAAC
* *
5747675 TCTTACCCAATTTATCTTTTATTTAAATTTACTCAAATTAGCA
66 TCTCACCCAATTTACCTTTTATTTAAATTTACTCAAATTAGCA
* * * *
5747718 AAATATGTTGATTTAATTGCAACTTTTACAATTTAC-AAATACTCATTCTTATGCAATTATTTAA
1 AAATATGTTGATTTAATTACAACTTTCACAATTTACGAAA-ACACATTCTTATGAAATTATTTAA
* *
5747782 CTCTCATCTAATTTACCTTTTATTTAAATTTACTCAAA
65 CTCTCACCCAATTTACCTTTTATTTAAATTTACTCAAA
5747820 ATTTCTAATA
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
107 3 0.03
108 87 0.97
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.44
Consensus pattern (108 bp):
AAATATGTTGATTTAATTACAACTTTCACAATTTACGAAAACACATTCTTATGAAATTATTTAAC
TCTCACCCAATTTACCTTTTATTTAAATTTACTCAAATTAGCA
Found at i:5749290 original size:14 final size:14
Alignment explanation
Indices: 5749257--5749291 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
5749247 CCACTATCTA
5749257 CTAATAAGTTATAT
1 CTAATAAGTTATAT
5749271 -TAAATAAGTTATAT
1 CT-AATAAGTTATAT
5749285 CTAATAA
1 CTAATAA
5749292 TAATTACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 1 0.05
14 17 0.89
15 1 0.05
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (14 bp):
CTAATAAGTTATAT
Found at i:5750483 original size:28 final size:28
Alignment explanation
Indices: 5750448--5750515 Score: 136
Period size: 28 Copynumber: 2.4 Consensus size: 28
5750438 TATACTTGAT
5750448 CTTTAAAAGGCAATAGATATGCTTGAAC
1 CTTTAAAAGGCAATAGATATGCTTGAAC
5750476 CTTTAAAAGGCAATAGATATGCTTGAAC
1 CTTTAAAAGGCAATAGATATGCTTGAAC
5750504 CTTTAAAAGGCA
1 CTTTAAAAGGCA
5750516 TTGCATTGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.28
Consensus pattern (28 bp):
CTTTAAAAGGCAATAGATATGCTTGAAC
Found at i:5753831 original size:4 final size:4
Alignment explanation
Indices: 5753824--5753848 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5753814 TCAAGAAAGA
5753824 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
5753849 GAAAATGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:5755246 original size:31 final size:31
Alignment explanation
Indices: 5755211--5755288 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
5755201 ACATCATAAA
*
5755211 AATTAAATTGAATAAAAATATA-ACGTACATG
1 AATTAAATTGAACAAAAATATAGA-GTACATG
*
5755242 AATTAAATTGAACAAAATTATAGAGTACATG
1 AATTAAATTGAACAAAAATATAGAGTACATG
*
5755273 GATTAAATTGAACAAA
1 AATTAAATTGAACAAA
5755289 GATCTATTAG
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
31 42 0.98
32 1 0.02
ACGTcount: A:0.54, C:0.06, G:0.12, T:0.28
Consensus pattern (31 bp):
AATTAAATTGAACAAAAATATAGAGTACATG
Found at i:5755500 original size:22 final size:22
Alignment explanation
Indices: 5755469--5755511 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5755459 AAATACTAAT
5755469 AAATAATCTCATTTCATTAAAA
1 AAATAATCTCATTTCATTAAAA
*
5755491 AAATATTCTCATTTCATTAAA
1 AAATAATCTCATTTCATTAAA
5755512 GGAATGAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATAATCTCATTTCATTAAAA
Found at i:5756438 original size:7 final size:7
Alignment explanation
Indices: 5756426--5756450 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5756416 ACAAGGCAAT
5756426 ACAACCA
1 ACAACCA
5756433 ACAACCA
1 ACAACCA
5756440 ACAACCA
1 ACAACCA
5756447 ACAA
1 ACAA
5756451 TACAATCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.40, G:0.00, T:0.00
Consensus pattern (7 bp):
ACAACCA
Found at i:5757615 original size:2 final size:2
Alignment explanation
Indices: 5757608--5757642 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5757598 TGTTGAGTTC
*
5757608 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5757643 GCAAATTACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:5762875 original size:2 final size:2
Alignment explanation
Indices: 5762868--5762895 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5762858 AACAGAATTC
5762868 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
5762896 GGCATTTGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5762945 original size:2 final size:2
Alignment explanation
Indices: 5762938--5762968 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5762928 TCCTTTGATC
5762938 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5762969 GCTAAGGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5767984 original size:43 final size:43
Alignment explanation
Indices: 5767922--5768008 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
5767912 TATTAAAATA
*
5767922 TATTTCTAATACTTGTAATTGCTTGATTAATAACTACCTGATT
1 TATTTCTAATACTTGTAATTGCTTGATCAATAACTACCTGATT
* *
5767965 TATTTCTAATACTTTTAATTGCTTGATCAATAACTATCTGATT
1 TATTTCTAATACTTGTAATTGCTTGATCAATAACTACCTGATT
5768008 T
1 T
5768009 GTGAATCTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.48
Consensus pattern (43 bp):
TATTTCTAATACTTGTAATTGCTTGATCAATAACTACCTGATT
Found at i:5772669 original size:29 final size:29
Alignment explanation
Indices: 5772636--5772695 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
5772626 TTTATCTTTG
5772636 AGATAATGATGAAAACTAAATGATATCAA
1 AGATAATGATGAAAACTAAATGATATCAA
5772665 AGATAATGATGAAAACTAAATGATATCAA
1 AGATAATGATGAAAACTAAATGATATCAA
5772694 AG
1 AG
5772696 CTTGAGAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.55, C:0.07, G:0.15, T:0.23
Consensus pattern (29 bp):
AGATAATGATGAAAACTAAATGATATCAA
Found at i:5779370 original size:20 final size:22
Alignment explanation
Indices: 5779326--5779380 Score: 80
Period size: 20 Copynumber: 2.6 Consensus size: 22
5779316 GAATAACCAA
5779326 CTATCGATAGAT-AGTCTTCAT
1 CTATCGATAGATGAGTCTTCAT
5779347 CTATCGATAGATGAGTC-T-AT
1 CTATCGATAGATGAGTCTTCAT
*
5779367 CTATGGATAGATGA
1 CTATCGATAGATGA
5779381 AAAACATCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 15 0.47
21 13 0.41
22 4 0.12
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.35
Consensus pattern (22 bp):
CTATCGATAGATGAGTCTTCAT
Found at i:5781127 original size:17 final size:17
Alignment explanation
Indices: 5781102--5781173 Score: 53
Period size: 17 Copynumber: 4.4 Consensus size: 17
5781092 ATGATTGATC
5781102 AAAAATATT-ATTTAATT
1 AAAAATATTAATTT-ATT
*
5781119 AAAATTATTAATTTATT
1 AAAAATATTAATTTATT
*
5781136 --AAGTATTAATTTA-T
1 AAAAATATTAATTTATT
* * *
5781150 AGAAATTTTAATATATT
1 AAAAATATTAATTTATT
5781167 AGAAAAT
1 A-AAAAT
5781174 TTTTTTAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
14 1 0.02
15 12 0.27
16 10 0.23
17 13 0.30
18 8 0.18
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (17 bp):
AAAAATATTAATTTATT
Found at i:5793744 original size:2 final size:2
Alignment explanation
Indices: 5793737--5793768 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5793727 AACCAACCAA
5793737 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5793769 CATAGCAGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5795939 original size:100 final size:101
Alignment explanation
Indices: 5795746--5795941 Score: 340
Period size: 101 Copynumber: 2.0 Consensus size: 101
5795736 AACTATTAAC
*
5795746 AAAAATAGAAGACCCAACAACAAAATATCAAAATCTAAAATTTTTTTGTTCTTACAAAAATTAAG
1 AAAAACAGAAGACCCAACAACAAAATATCAAAATCTAAAATTTTTTTGTTCTTACAAAAATTAAG
5795811 AAAAAAAAAATCTAAAATTCAAAACTGCATTTAGAA
66 AAAAAAAAAATCTAAAATTCAAAACTGCATTTAGAA
* * * *
5795847 AAAAACAGAAGACCCAACAACAGAATATCAAAATCTAGAATTTTTTTGTTTTTACAAAGATTAAG
1 AAAAACAGAAGACCCAACAACAAAATATCAAAATCTAAAATTTTTTTGTTCTTACAAAAATTAAG
5795912 -AAAAAAAAATCTAAAATTCAAAACTGCATT
66 AAAAAAAAAATCTAAAATTCAAAACTGCATT
5795942 CAGATACTAT
Statistics
Matches: 90, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
100 30 0.33
101 60 0.67
ACGTcount: A:0.54, C:0.13, G:0.07, T:0.26
Consensus pattern (101 bp):
AAAAACAGAAGACCCAACAACAAAATATCAAAATCTAAAATTTTTTTGTTCTTACAAAAATTAAG
AAAAAAAAAATCTAAAATTCAAAACTGCATTTAGAA
Found at i:5805990 original size:40 final size:40
Alignment explanation
Indices: 5805935--5806010 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
5805925 AAACTTCAAT
* *
5805935 TTTGTGAAGCTTGAGGGTTAGAGATTAGAAGATTGTCGAC
1 TTTGTGAAGCTTGAGGATGAGAGATTAGAAGATTGTCGAC
* *
5805975 TTTGTGAAGTTTGAGGATGAGAGATTAGAGGATTGT
1 TTTGTGAAGCTTGAGGATGAGAGATTAGAAGATTGT
5806011 GTTGATAACG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.28, C:0.04, G:0.34, T:0.34
Consensus pattern (40 bp):
TTTGTGAAGCTTGAGGATGAGAGATTAGAAGATTGTCGAC
Found at i:5807391 original size:32 final size:33
Alignment explanation
Indices: 5807319--5807392 Score: 80
Period size: 32 Copynumber: 2.2 Consensus size: 33
5807309 GACATTGCAA
* * *
5807319 TGACATGTTGCATTGACATGATGATGTGGCAATG
1 TGACATG-TGCATTAACATGATAACGTGGCAATG
*
5807353 TTACATG-GCATTAACATGATAACGTGG-AATG
1 TGACATGTGCATTAACATGATAACGTGGCAATG
5807384 CTGACATGT
1 -TGACATGT
5807393 TGGTGCCACA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
31 4 0.12
32 23 0.70
34 6 0.18
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.31
Consensus pattern (33 bp):
TGACATGTGCATTAACATGATAACGTGGCAATG
Found at i:5821938 original size:265 final size:264
Alignment explanation
Indices: 5821453--5822105 Score: 1054
Period size: 265 Copynumber: 2.5 Consensus size: 264
5821443 TGAGCAGTGA
5821453 GGGGTCATTACTCTCTTCCCCATAAACCGGCTTATAGGGGTGTGCAGCACACCCGCTTATAAGGA
1 GGGGTCATTACTCTC-TCCCCATAAACCGGCTTATAGGGGTGTGCAGCACACCCGCTTATAAGGA
* * *
5821518 GCCCAAGACCTCCCGTTCCTGTCTGATGTAGGATAGAGGTATTTTCCTTGTGACACTTTCACCCA
65 GCCCAAGACCTCCCGTTCTTGTCTGATGTGGGATAGAGGTATTTTCCTTGTGACACTCTCACCCA
* * * *
5821583 CTCGAATCGGCAACGCTCCCGTTGCCGTTGGCCACCCTGCCTACCCCGTTGGGCCCCACTGGACC
130 CCCGAATCGGCAACGCCCCCGTTGCCGTCGGCCACCCTGCCTACCCCATTGGGCCCCACTGGACC
*
5821648 AGCCCCACCGGGCCGGGCACTTGGCGTGAGTCAGAATGATGATCGGTCTGCTCTGATACCACTTT
195 AGCCCCACAGGGCCGGGCACTTGGCGTGAGTCAGAATGATGATCGGTCTGCTCTGATACCACTTT
5821713 ATCAC
260 ATCAC
* *
5821718 GGGGTCATTACTCTCTCCTCCATAAACCGGCTTATAGGGGTGTGTAGCACACTCGCTTATAAGGA
1 GGGGTCATTACTCTCTCC-CCATAAACCGGCTTATAGGGGTGTGCAGCACACCCGCTTATAAGGA
* * * * *
5821783 GCCTAGGACCTCCTGTTCTTGTCTGATGTGGGATAGAGGCACTTTCCTTGTGACACTCTCACCCA
65 GCCCAAGACCTCCCGTTCTTGTCTGATGTGGGATAGAGGTATTTTCCTTGTGACACTCTCACCCA
* * * * *
5821848 CCCGAATCGGTAACGCCCCCGTTGCCGTCGGCCACCCTGCCTACTCCATTGGGCCCCATTGGGCT
130 CCCGAATCGGCAACGCCCCCGTTGCCGTCGGCCACCCTGCCTACCCCATTGGGCCCCACTGGACC
* *
5821913 AGCCCCACAGGGTCGGGCGCTTGGCGTGAGTCAGAATGATGATCGGTCTGCTCTGATACCACTTT
195 AGCCCCACAGGGCCGGGCACTTGGCGTGAGTCAGAATGATGATCGGTCTGCTCTGATACCACTTT
5821978 ATCAC
260 ATCAC
5821983 GGGGTCATTACTCTCTCCCCCATAAACCGGCTTATAGGGGTGTGCAGCACACCCGCTTATAAGGA
1 GGGGTCATTACTCTCT-CCCCATAAACCGGCTTATAGGGGTGTGCAGCACACCCGCTTATAAGGA
* * *
5822048 GCCCAAGACCTCCCGTTCTTATCTGATGTGGGATAGAAGTATTTTTCTTGTGACACTC
65 GCCCAAGACCTCCCGTTCTTGTCTGATGTGGGATAGAGGTATTTTCCTTGTGACACTC
5822106 GTTTAGAATC
Statistics
Matches: 354, Mismatches: 32, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
264 3 0.01
265 349 0.99
266 2 0.01
ACGTcount: A:0.19, C:0.31, G:0.24, T:0.26
Consensus pattern (264 bp):
GGGGTCATTACTCTCTCCCCATAAACCGGCTTATAGGGGTGTGCAGCACACCCGCTTATAAGGAG
CCCAAGACCTCCCGTTCTTGTCTGATGTGGGATAGAGGTATTTTCCTTGTGACACTCTCACCCAC
CCGAATCGGCAACGCCCCCGTTGCCGTCGGCCACCCTGCCTACCCCATTGGGCCCCACTGGACCA
GCCCCACAGGGCCGGGCACTTGGCGTGAGTCAGAATGATGATCGGTCTGCTCTGATACCACTTTA
TCAC
Found at i:5830224 original size:8 final size:8
Alignment explanation
Indices: 5830213--5830255 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
5830203 AGTGAGAGTA
5830213 AGAGAGAC
1 AGAGAGAC
5830221 --AGAGAC
1 AGAGAGAC
5830227 AGAGAGAC
1 AGAGAGAC
*
5830235 AGAGAGAG
1 AGAGAGAC
*
5830243 AGAGAGAA
1 AGAGAGAC
5830251 AGAGA
1 AGAGA
5830256 ATCAACATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 6 0.19
8 25 0.81
ACGTcount: A:0.53, C:0.07, G:0.40, T:0.00
Consensus pattern (8 bp):
AGAGAGAC
Found at i:5830230 original size:14 final size:14
Alignment explanation
Indices: 5830213--5830247 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
5830203 AGTGAGAGTA
5830213 AGAGAGACAGAGAC
1 AGAGAGACAGAGAC
*
5830227 AGAGAGACAGAGAG
1 AGAGAGACAGAGAC
5830241 AGAGAGA
1 AGAGAGA
5830248 GAAAGAGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.51, C:0.09, G:0.40, T:0.00
Consensus pattern (14 bp):
AGAGAGACAGAGAC
Found at i:5830254 original size:14 final size:14
Alignment explanation
Indices: 5830213--5830255 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
5830203 AGTGAGAGTA
*
5830213 AGAGAGACAGAGAC
1 AGAGAGAAAGAGAC
*
5830227 AGAGAGACAGAGAGAG
1 AGAGAGA-A-AGAGAC
5830243 AGAGAGAAAGAGA
1 AGAGAGAAAGAGA
5830256 ATCAACATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 12 0.48
15 1 0.04
16 12 0.48
ACGTcount: A:0.53, C:0.07, G:0.40, T:0.00
Consensus pattern (14 bp):
AGAGAGAAAGAGAC
Found at i:5830256 original size:6 final size:6
Alignment explanation
Indices: 5830213--5830255 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
5830203 AGTGAGAGTA
* * * *
5830213 AGAGAG ACAGAG ACAGAG AGACAG AGAGAG AGAGAG AAAGAG A
1 AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG A
5830256 ATCAACATGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.53, C:0.07, G:0.40, T:0.00
Consensus pattern (6 bp):
AGAGAG
Found at i:5842352 original size:17 final size:17
Alignment explanation
Indices: 5842332--5842383 Score: 65
Period size: 15 Copynumber: 3.2 Consensus size: 17
5842322 CAATCAAAAA
5842332 TATT-ATTTAATCGAGGT
1 TATTAATTT-ATCGAGGT
*
5842349 TATTAATTTATTGA-G-
1 TATTAATTTATCGAGGT
5842364 TATTAATTTATCGAGGT
1 TATTAATTTATCGAGGT
5842381 TAT
1 TAT
5842384 ATTGTAGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 13 0.43
16 2 0.07
17 11 0.37
18 4 0.13
ACGTcount: A:0.31, C:0.04, G:0.15, T:0.50
Consensus pattern (17 bp):
TATTAATTTATCGAGGT
Found at i:5847818 original size:2 final size:2
Alignment explanation
Indices: 5847811--5847837 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5847801 CACAAGAAAC
5847811 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 A
5847838 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5847842 original size:2 final size:2
Alignment explanation
Indices: 5847837--5847861 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5847827 ATATATATAT
5847837 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 A
5847862 TTGTTAATTG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5853406 original size:4 final size:4
Alignment explanation
Indices: 5853397--5853424 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
5853387 TGGTTGTGCA
5853397 AAGG AAGG AAGG AAGG AAGG AAGG AAGG
1 AAGG AAGG AAGG AAGG AAGG AAGG AAGG
5853425 GGCAAATTTT
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (4 bp):
AAGG
Found at i:5865492 original size:27 final size:27
Alignment explanation
Indices: 5865462--5865527 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
5865452 GGTGCTTCCA
* * *
5865462 CACTTGGAATACCTTGGGGTGCTTTTG
1 CACTTGGAACACCTTCGGGCGCTTTTG
* * *
5865489 CACTTAGAACACCTTCTGGCGTTTTTG
1 CACTTGGAACACCTTCGGGCGCTTTTG
5865516 CACTTGGAACAC
1 CACTTGGAACAC
5865528 TTTTGAGCAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.33
Consensus pattern (27 bp):
CACTTGGAACACCTTCGGGCGCTTTTG
Found at i:5865817 original size:27 final size:27
Alignment explanation
Indices: 5865787--5865881 Score: 79
Period size: 27 Copynumber: 3.5 Consensus size: 27
5865777 ATGATTCCCT
*
5865787 ACTTGGAACACCATTAGGCGTTTTC-GC
1 ACTTAGAACACC-TTAGGCGTTTTCAGC
* *
5865814 ACTTAGAACAACCCTAGGCG-TTTCAGT
1 ACTTAGAAC-ACCTTAGGCGTTTTCAGC
* *
5865841 ATTTAGAACACCTTTAGGCGTTTTTA-C
1 ACTTAGAACACC-TTAGGCGTTTTCAGC
* *
5865868 GCTTAAAACACCTT
1 ACTTAGAACACCTT
5865882 GATGTACTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
26 9 0.17
27 38 0.70
28 7 0.13
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (27 bp):
ACTTAGAACACCTTAGGCGTTTTCAGC
Found at i:5866147 original size:36 final size:37
Alignment explanation
Indices: 5866059--5866150 Score: 98
Period size: 36 Copynumber: 2.5 Consensus size: 37
5866049 GATGTGTTCC
**
5866059 AATACAACTCGCAATGCTTCTTCTTTTAAGTGTTCTA
1 AATACAACTCGCAATGCTTCTTCTTAGAAGTGTTCTA
* * * * *
5866096 AATATAACTTGCAATGTTTC-TCTTAGATGTGCTT-TG
1 AATACAACTCGCAATGCTTCTTCTTAGAAGTG-TTCTA
5866132 AATACAACTCGCAATGCTT
1 AATACAACTCGCAATGCTT
5866151 TTTATTTTCA
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
36 25 0.57
37 19 0.43
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (37 bp):
AATACAACTCGCAATGCTTCTTCTTAGAAGTGTTCTA
Found at i:5869161 original size:27 final size:27
Alignment explanation
Indices: 5869131--5869197 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
5869121 GTCCTTTGGC
*
5869131 GCTTTTGCACTTGGAACACTATTGGAT
1 GCTTTTGCACTTGGAACACCATTGGAT
* *
5869158 GCTTCTGCACTTGGAACACCCTTGGAT
1 GCTTTTGCACTTGGAACACCATTGGAT
*
5869185 GCTTTTGCGCTTG
1 GCTTTTGCACTTG
5869198 AAACCAACCT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (27 bp):
GCTTTTGCACTTGGAACACCATTGGAT
Found at i:5869410 original size:27 final size:27
Alignment explanation
Indices: 5869380--5869436 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
5869370 TCTTTGGGAG
* *
5869380 TTTTTGTGATTGGAAC-ACCCTTAGGCA
1 TTTTCGTGATTCGAACGA-CCTTAGGCA
**
5869407 TTTTCGTTCTTCGAACGACCTTAGGCA
1 TTTTCGTGATTCGAACGACCTTAGGCA
5869434 TTT
1 TTT
5869437 CAACGCTTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (27 bp):
TTTTCGTGATTCGAACGACCTTAGGCA
Found at i:5870294 original size:2 final size:2
Alignment explanation
Indices: 5870287--5870331 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
5870277 CGTATACTAC
5870287 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5870328 -T AT A
1 AT AT A
5870332 AAATCCAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5871585 original size:16 final size:16
Alignment explanation
Indices: 5871561--5871591 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5871551 ATTTAAAATC
*
5871561 AAAATATAAAAATTAT
1 AAAAAATAAAAATTAT
5871577 AAAAAATAAAAATTA
1 AAAAAATAAAAATTA
5871592 AATTAAAATT
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAAATAAAAATTAT
Found at i:5883057 original size:13 final size:14
Alignment explanation
Indices: 5883030--5883064 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
5883020 TTAATGCATA
5883030 AAATAAAATTAAAT
1 AAATAAAATTAAAT
5883044 AAATAAAA-TAAAT
1 AAATAAAATTAAAT
*
5883057 AATTAAAA
1 AAATAAAA
5883065 AGTATAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATAAAATTAAAT
Found at i:5893540 original size:23 final size:23
Alignment explanation
Indices: 5893510--5893558 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
5893500 TAGTATTCAT
5893510 GCAGTGACCT-ACCAACCACTCAC
1 GCAGTGA-CTAACCAACCACTCAC
*
5893533 GCAGTGACTAATCAACCACTCAC
1 GCAGTGACTAACCAACCACTCAC
5893556 GCA
1 GCA
5893559 ACAACATACC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.33, C:0.39, G:0.14, T:0.14
Consensus pattern (23 bp):
GCAGTGACTAACCAACCACTCAC
Found at i:5893571 original size:23 final size:22
Alignment explanation
Indices: 5893518--5893571 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
5893508 ATGCAGTGAC
***
5893518 CTACCAACCACTCACGCAGTGA
1 CTACCAACCACTCACGCAACAA
*
5893540 CTAATCAACCACTCACGCAACAA
1 CT-ACCAACCACTCACGCAACAA
5893563 CATACCAAC
1 C-TACCAAC
5893572 TAGTCACTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 2 0.08
23 22 0.88
24 1 0.04
ACGTcount: A:0.39, C:0.41, G:0.07, T:0.13
Consensus pattern (22 bp):
CTACCAACCACTCACGCAACAA
Found at i:5893673 original size:23 final size:23
Alignment explanation
Indices: 5893643--5893703 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
5893633 TAATATTCAC
* *
5893643 GCAATGACTTATCAACTACTCAT
1 GCAATGACATATCAACCACTCAT
*
5893666 GCAATGACCTATCAACCACTCAT
1 GCAATGACATATCAACCACTCAT
5893689 GCAATGACATATCAA
1 GCAATGACATATCAA
5893704 TCAGTCACGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.25
Consensus pattern (23 bp):
GCAATGACATATCAACCACTCAT
Found at i:5893717 original size:23 final size:23
Alignment explanation
Indices: 5893639--5893717 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 23
5893629 TGAATAATAT
* *
5893639 TCACGCAATGACTTATCAACTAC
1 TCACGCAATGACATATCAACCAC
* *
5893662 TCATGCAATGACCTATCAACCAC
1 TCACGCAATGACATATCAACCAC
* * *
5893685 TCATGCAATGACATATCAATCAG
1 TCACGCAATGACATATCAACCAC
*
5893708 TCACGTAATG
1 TCACGCAATG
5893718 TTAAACTCTA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.35, C:0.28, G:0.11, T:0.25
Consensus pattern (23 bp):
TCACGCAATGACATATCAACCAC
Found at i:5893718 original size:133 final size:130
Alignment explanation
Indices: 5893480--5893893 Score: 479
Period size: 133 Copynumber: 3.1 Consensus size: 130
5893470 ACGCACGCAT
* * * * * * *
5893480 TAAGTGACGCCATGTTTGAATAGTATTCATGCAGTGACCTACCAACCACTCACGCAGTGA-CTAA
1 TAAGTGATGCCATGCTTGAATAATATTCACGCAATGACCTATCAACCACTCACGCAATGACCT-A
** *
5893544 TCAACCACTCACGCAACAACATACCAACTAGTCACTCAATGTTAAACCCTAATGCAATCACACAC
65 TCAACCACTCACGCAATGACATATCAAC-AGTCACT-AATGTTAAACCCTAATGCAATCACACAC
5893609 ACAC
128 AC-C
* * *
5893613 TAAGTGATGCCATGCTTGAATAATATTCACGCAATGACTTATCAACTACTCATGCAATGACCTAT
1 TAAGTGATGCCATGCTTGAATAATATTCACGCAATGACCTATCAACCACTCACGCAATGACCTAT
* * * *
5893678 CAACCACTCATGCAATGACATATCAATCAGTCACGTAATGTTAAACTCTAATGCAATCACGCATA
66 CAACCACTCACGCAATGACATATCAA-CAGTCAC-TAATGTTAAACCCTAATGCAATCACACACA
5893743 CCC
129 -CC
* * * * * *
5893746 TAAGTGATGCCATGCCTAAACAATATTTACGCAATGACCCATCAACCACTCACGTAATGACCTAT
1 TAAGTGATGCCATGCTTGAATAATATTCACGCAATGACCTATCAACCACTCACGCAATGACCTAT
* * * * *
5893811 CAACCACTCACGTAATGACCTATCAACCAGTCACACAATGTTAAACCTTAATGCAATCACACACG
66 CAACCACTCACGCAATGACATATCAA-CAGTCAC-TAATGTTAAACCCTAATGCAATCACACACA
5893876 CC
129 CC
5893878 TTAAGTGATGCCATGC
1 -TAAGTGATGCCATGC
5893894 CAAAATCTAG
Statistics
Matches: 239, Mismatches: 37, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
132 2 0.01
133 232 0.97
134 5 0.02
ACGTcount: A:0.36, C:0.29, G:0.12, T:0.24
Consensus pattern (130 bp):
TAAGTGATGCCATGCTTGAATAATATTCACGCAATGACCTATCAACCACTCACGCAATGACCTAT
CAACCACTCACGCAATGACATATCAACAGTCACTAATGTTAAACCCTAATGCAATCACACACACC
Found at i:5893812 original size:23 final size:23
Alignment explanation
Indices: 5893778--5893844 Score: 116
Period size: 23 Copynumber: 2.9 Consensus size: 23
5893768 ATATTTACGC
*
5893778 AATGACCCATCAACCACTCACGT
1 AATGACCTATCAACCACTCACGT
5893801 AATGACCTATCAACCACTCACGT
1 AATGACCTATCAACCACTCACGT
*
5893824 AATGACCTATCAACCAGTCAC
1 AATGACCTATCAACCACTCAC
5893845 ACAATGTTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.36, C:0.36, G:0.09, T:0.19
Consensus pattern (23 bp):
AATGACCTATCAACCACTCACGT
Found at i:5893850 original size:23 final size:23
Alignment explanation
Indices: 5893774--5893850 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
5893764 AACAATATTT
*
5893774 ACGCAATGACCCATCAACCACTC
1 ACGCAATGACCTATCAACCACTC
*
5893797 ACGTAATGACCTATCAACCACTC
1 ACGCAATGACCTATCAACCACTC
* *
5893820 ACGTAATGACCTATCAACCAGTC
1 ACGCAATGACCTATCAACCACTC
*
5893843 ACACAATG
1 ACGCAATG
5893851 TTAAACCTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.36, C:0.35, G:0.10, T:0.18
Consensus pattern (23 bp):
ACGCAATGACCTATCAACCACTC
Found at i:5895501 original size:2 final size:2
Alignment explanation
Indices: 5895496--5895524 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5895486 TGTGTTGGTT
5895496 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5895525 GTAAGTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5904028 original size:291 final size:295
Alignment explanation
Indices: 5903498--5904087 Score: 848
Period size: 291 Copynumber: 2.0 Consensus size: 295
5903488 GTTAGTCAAT
5903498 ATCACATAAATACTTTAGGCACAAATACCTTCATTTATGGAAAACAAAAAAAAAAGATAAAATAC
1 ATCACATAAATACTTTAGGCACAAATACCTTCATTTATGG--AACAAAAAAAAAAGATAAAATAC
* * * * * *
5903563 CTGTACCGCTTAACTTTTAAGTATAATTTCATGCAGATCCATTAATATTAAAAATAGATAGTCTA
64 CTCTACCGCTTAACTTTTAAGTATAATTTCACGCAGATCCATTAATAGTAAAAATAAACAGTCCA
5903628 ACTCAAACAATTTTGTTATGCTAGACAAAGAAATCATATAGTCAATCTTGCCATCAACCTCCATT
129 ACTCAAACAATTTTGTTATGCTAGACAAAGAAATCATATAGTCAATCTTGCCATCAACCTCCATT
* * * *
5903693 TATTTGATGAAATTTATGATAATTTTACCCCTCTTTCCATGTTCTTGCTGAAACTAAGAAGCCCC
194 TATTTGATAAAATTTATGACAATTTTACCCATCTTTCAATGTTCTTGCTGAAACTAAGAAGCCCC
*
5903758 TCATACCAGAAGTTAAAAAACCAAATTTTTTGTTGAA
259 TCAAACCAGAAGTTAAAAAACCAAATTTTTTGTTGAA
*
5903795 ATCACATAAATACTTTAGGCACAAATACCTTCATTTAT-G-A-AAAAAAAAGAG-TAAAATACCT
1 ATCACATAAATACTTTAGGCACAAATACCTTCATTTATGGAACAAAAAAAAAAGATAAAATACCT
* * * *
5903856 CTACC-CTTTAACTTTTAAGTATAATTTCACGTAGGTCCATTATTGGTAAAAATAAACAGTCCAA
66 CTACCGC-TTAACTTTTAAGTATAATTTCACGCAGATCCATTAATAGTAAAAATAAACAGTCCAA
* * * * * * * * * *
5903920 CTCAAACAATTTTTTTCTGCTAGATAAAGAAATTATATCGTCAGTCTTGTCGTTAACCTCCGTTT
130 CTCAAACAATTTTGTTATGCTAGACAAAGAAATCATATAGTCAATCTTGCCATCAACCTCCATTT
* * *
5903985 ATTTGATAAAATTTATGACAATTTTACCCATTTTTCAATGTTCTTGCTGAAACTAAGAAGTCTCT
195 ATTTGATAAAATTTATGACAATTTTACCCATCTTTCAATGTTCTTGCTGAAACTAAGAAGCCCCT
*
5904050 CAAACCAGAAGTTAAAAAACTAAATTTTTTGTTGAA
260 CAAACCAGAAGTTAAAAAACCAAATTTTTTGTTGAA
5904086 AT
1 AT
5904088 GTTATAGATT
Statistics
Matches: 262, Mismatches: 30, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
290 1 0.00
291 211 0.81
292 10 0.04
293 1 0.00
296 1 0.00
297 38 0.15
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.34
Consensus pattern (295 bp):
ATCACATAAATACTTTAGGCACAAATACCTTCATTTATGGAACAAAAAAAAAAGATAAAATACCT
CTACCGCTTAACTTTTAAGTATAATTTCACGCAGATCCATTAATAGTAAAAATAAACAGTCCAAC
TCAAACAATTTTGTTATGCTAGACAAAGAAATCATATAGTCAATCTTGCCATCAACCTCCATTTA
TTTGATAAAATTTATGACAATTTTACCCATCTTTCAATGTTCTTGCTGAAACTAAGAAGCCCCTC
AAACCAGAAGTTAAAAAACCAAATTTTTTGTTGAA
Found at i:5905433 original size:36 final size:36
Alignment explanation
Indices: 5905386--5905459 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
5905376 ACACCATGAC
5905386 CAAGTCTTGAAGCATTAGTAGCAGTAGGTCTTTTTA
1 CAAGTCTTGAAGCATTAGTAGCAGTAGGTCTTTTTA
5905422 CAAGTCTTGAAGCATTAGTAGCAGTAGGTCTTTTTA
1 CAAGTCTTGAAGCATTAGTAGCAGTAGGTCTTTTTA
5905458 CA
1 CA
5905460 CATCAGCGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (36 bp):
CAAGTCTTGAAGCATTAGTAGCAGTAGGTCTTTTTA
Found at i:5914765 original size:21 final size:22
Alignment explanation
Indices: 5914730--5914773 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
5914720 CTCTTAAAGT
5914730 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
5914752 AATTT-AATTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
5914773 A
1 A
5914774 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:5915813 original size:29 final size:30
Alignment explanation
Indices: 5915771--5915838 Score: 104
Period size: 29 Copynumber: 2.3 Consensus size: 30
5915761 CTTAAATATC
* *
5915771 TAAATTAGGGAATTAGGGTTA-GGGTTTTA
1 TAAATTAGGGAATTAGGGTTATGGATTTGA
5915800 TAAATTAGGGAATTAGGGTTATGGATTTGA
1 TAAATTAGGGAATTAGGGTTATGGATTTGA
5915830 -AAATTAGGG
1 TAAATTAGGG
5915839 TTTTCAAGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 30 0.83
30 6 0.17
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.35
Consensus pattern (30 bp):
TAAATTAGGGAATTAGGGTTATGGATTTGA
Found at i:5918983 original size:81 final size:79
Alignment explanation
Indices: 5918844--5919005 Score: 225
Period size: 81 Copynumber: 2.0 Consensus size: 79
5918834 TGGGGCGTTG
* * * **
5918844 CACAAATAGTGGGATAGAATATCATGGATGCCACATCAATAATAAATGGAGTGAGTTTTGAATAT
1 CACAAATAGTGGGATAAAATATCATAGATACCACATCAATAATAAATAAAGTGAGTTTTG-A-AT
*
5918909 ATAAATATGAATCTTT
64 ATAAATATGAATATTT
* * *
5918925 CACAATTAGTGGGGTAAAATATCATAGATACCACATCAATAATAAATAAAGTGGGTTTTGAATAT
1 CACAAATAGTGGGATAAAATATCATAGATACCACATCAATAATAAATAAAGTGAGTTTTGAATAT
5918990 AAATATGAATATTT
66 AAATATGAATATTT
5919004 CA
1 CA
5919006 TTATTTAGTA
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
79 19 0.26
80 1 0.01
81 52 0.72
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.31
Consensus pattern (79 bp):
CACAAATAGTGGGATAAAATATCATAGATACCACATCAATAATAAATAAAGTGAGTTTTGAATAT
AAATATGAATATTT
Found at i:5919867 original size:247 final size:250
Alignment explanation
Indices: 5919513--5920694 Score: 911
Period size: 247 Copynumber: 4.8 Consensus size: 250
5919503 AGAATTGATA
* * * * *
5919513 TAAAAACTTG-TAAATGTAGAATAACTAAATTTAAAATCTTAACGTA-AATATGT--GAGAATTA
1 TAAAAAC-TGATAAA-GAAGAACAACTAAATTTTAAATCTTAAC-TATAACATGTAAGAGAGTTA
* * * *
5919574 ACGTAACAAGTTAATTAAGGAAAATAATCTAATTTTAATGAAAAATAAATA-TTAAATTTATATT
63 ACGTAACAAGTCAATTAAGTAAAAAAATCTAATTTTAATAAAAAATAAATATTTAAATTTATATT
* * * *
5919638 CTCCGACTAAAAATGTTTAACAATATAAAAATTTTAATTTTTAAATAAAAATAATAAGGATAAAA
128 ATCAGACTAAAAGTATTTAACAATATAAAAATTTTAATTTTTAAATAAAAATAATAA-GATAAAA
* ** * *
5919703 CTAATTATAATTCAAAATTGAAATAGATAAGTTTTGACATAAAACTGTATCGATTGACG
192 ATAATTATAATTCAAAATTGAAATAGATAAACTTTGACATAAAACTGTAACAATTGACG
* * * * *
5919762 TAAAAACTGATAAA-AAAAATAATTAAATTTTAAATCTTAA-TATAA-ATGAAAGAGAGTTAATG
1 TAAAAACTGATAAAGAAGAACAACTAAATTTTAAATCTTAACTATAACATGTAAGAGAGTTAACG
* * * * *
5919824 TAACAAGTCAATTAAATAAAAAAATTTAATTTTAGTAAAAAATAAATATTTAAATTTATATTCTT
66 TAACAAGTCAATTAAGTAAAAAAATCTAATTTTAATAAAAAATAAATATTTAAATTTATATTATC
* * * * * *
5919889 AGACTAAAAGTAATTAACGATATATAAATTTTAATTTTTAAGTAAAAAATAATAACA-AAAAAAA
131 AGACTAAAAGTATTTAACAATATAAAAATTTTAATTTTTAAAT-AAAAATAATAAGATAAAAATA
* * *** * * * *
5919953 ATTATAGTTCAAAATTGACATAGAT-TTTTTTGACGTAAAACTATAAAAATTGATG
195 ATTATAATTCAAAATTGAAATAGATAAACTTTGACATAAAACTGTAACAATTGACG
* ** * *
5920008 TAAAAACTTATAAAGGTGGAACAATTAAATTTTAAATCTTAACGTA-AATATGTAA-A-AGTTAA
1 TAAAAACTGATAAA-GAAGAACAACTAAATTTTAAATCTTAAC-TATAACATGTAAGAGAGTTAA
* * * * * * *
5920070 CATAATAAG-CTAATTAAATAATAAAATCTAATTTTAATAAAAAAACAAACATTTATATTTATAT
64 CGTAACAAGTC-AATTAAGTAAAAAAATCTAATTTTAAT-AAAAAATAAATATTTAAATTTATAT
** ** * * ** * *
5920134 TATTGGGGTAAAAGTATGTAATAATATTCAAATTTTCATTTTT-AGTAAAGAATAATAAAGATAA
127 TATCAGACTAAAAGTATTTAACAATATAAAAATTTTAATTTTTAAATAAA-AATAAT-AAGATAA
* ** * * * * * * **
5920198 AAATAATTATAATAT-ACAATTGGCACAAAAAAACCCTTGACGTAAAATTGTAAGGATTGACG
190 AAATAATTATAAT-TCAAAATTGAAATAGATAAA-CTTTGACATAAAACTGTAACAATTGACG
* * * * *
5920260 TAAAAATTTATAAAGGTAGAACAACTAAATTTTAAATCTTAACT-TAGACGTGTTA-A-AGTTAA
1 TAAAAACTGATAAA-GAAGAACAACTAAATTTTAAATCTTAACTATA-ACATGTAAGAGAGTTAA
*
5920322 CCTAACAAGTCAATTAAGTAAAAAAGA-CTAATTTTAATAAAAAATAAATATTTAAATTTATATT
64 CGTAACAAGTCAATTAAGTAAAAAA-ATCTAATTTTAATAAAAAATAAATATTTAAATTTATATT
* * * * *
5920386 TTCAGATTAAAAGTATTTAACGATATATAAATTTTTA-TTTTAAATAAAAATAAT-A-ATAAAAA
128 ATCAGACTAAAAGTATTTAACAATATAAAAATTTTAATTTTTAAATAAAAATAATAAGATAAAAA
* * * * * * *
5920448 TAATTATAA-TCTAAAATTGACATAAATAAACATTAACATGAAATTGTAACAATTGATG
193 TAATTATAATTC-AAAATTGAAATAGATAAACTTTGACATAAAACTGTAACAATTGACG
** ** * **
5920506 TAAAAACATG-TAAAAGTGGAGTAACTAAATTTTAAATCTTAA-TGTAA-ATGTGTGAGAGTTAA
1 TAAAAAC-TGAT-AAAGAAGAACAACTAAATTTTAAATCTTAACTATAACATGTAAGAGAGTTAA
* * * * *
5920568 CTTAATAAGTTAATTAAGTAAAAAAA-CTTAATTTTAAT--GAAA-AAATATTTATATTTATATT
64 CGTAACAAGTCAATTAAGTAAAAAAATC-TAATTTTAATAAAAAATAAATATTTAAATTTATATT
* * * * *
5920629 ATCATACTAAAAATATGTAACAA-A-AATTAAATTTTTA-TTTTAAATAAAAAATAATAAAAATA
128 ATCAGACTAAAAGTATTTAACAATATAA--AAATTTTAATTTTTAAAT-AAAAATAAT-AAGATA
5920691 AAAA
189 AAAA
5920695 ATTATTGTTA
Statistics
Matches: 761, Mismatches: 134, Indels: 78
0.78 0.14 0.08
Matches are distributed among these distances:
241 1 0.00
242 1 0.00
243 52 0.07
244 15 0.02
245 11 0.01
246 130 0.17
247 145 0.19
248 122 0.16
249 82 0.11
250 40 0.05
251 57 0.07
252 103 0.14
253 2 0.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (250 bp):
TAAAAACTGATAAAGAAGAACAACTAAATTTTAAATCTTAACTATAACATGTAAGAGAGTTAACG
TAACAAGTCAATTAAGTAAAAAAATCTAATTTTAATAAAAAATAAATATTTAAATTTATATTATC
AGACTAAAAGTATTTAACAATATAAAAATTTTAATTTTTAAATAAAAATAATAAGATAAAAATAA
TTATAATTCAAAATTGAAATAGATAAACTTTGACATAAAACTGTAACAATTGACG
Found at i:5920626 original size:500 final size:497
Alignment explanation
Indices: 5919500--5920694 Score: 1275
Period size: 498 Copynumber: 2.4 Consensus size: 497
5919490 ACGTAAAGTA
* * * * *
5919500 ATAAGAATTGATATAAAAACTTGTAAATGTAGAATAACTAAATTTAAAATCTTAACGTAAATATG
1 ATAAAAATTGATGTAAAAACTTGTAAAAGTGGAATAACTAAATTTTAAATCTTAACGTAAATATG
* * * * *
5919565 TGAGAATTAACGTAACAAGTTAATTAAGGAAAATAATCTAATTTTAATG-AAAAATAAATA-TTA
66 TGAGAGTTAACATAATAAGTTAATTAAGTAAAAAAATCTAATTTTAATGAAAAAATAAATATTTA
* * * *
5919628 AATTTATATTCTCCGACTAAAAATGTTTAACAATATAAAAATTTTAATTTTTAAATAAAAATAAT
131 TATTTATATTATCCGACTAAAAATATGTAACAATATAAAAATTTTAATTTTTAAATAAAAATAAT
* * * *** *
5919693 AAGGATAAAACTAATTATAATTCAAAATTGAAATAGATAAGTTTTGACATAAAACTGTATCGATT
196 AAAGATAAAAATAATTATAATTCAAAATTGAAATAGAAAACCCTTGACATAAAACTGTAACGATT
* * *
5919758 GACGTAAAAACTGATAAAAAAAATAATTAAATTTTAAATCTTAATATAAATGAAAGAGAGTTAAT
261 GACGTAAAAACTGATAAAAAAAACAACTAAATTTTAAATCTTAATATAAATGAAAGAGAGTTAAC
* * *
5919823 GTAACAAGTCAATTAAATAAAAAAATTTAATTTTAGTAAAAAATAAATATTTAAATTTATATTCT
326 CTAACAAGTCAATTAAATAAAAAAATCTAATTTTAATAAAAAATAAATATTTAAATTTATATTCT
*
5919888 TAGACTAAAAGTAATTAACGATATATAAATTTTAATTTTTAAGTAAAAAATAATAACAAAAAAAA
391 TAGACTAAAAGTAATTAACGATATATAAATTTTAATTTTTAAATAAAAAATAATAACAAAAAAAA
* * **** * *
5919953 ATTATAGTTCAAAATTGACATAGATTTTTTTGACGTAAAACT
456 ATTATAATTCAAAATTGACATAAATAACATTAACATAAAACT
* * * *
5919995 ATAAAAATTGATGTAAAAACTTATAAAGGTGGAACAATTAAATTTTAAATCTTAACGTAAATATG
1 ATAAAAATTGATGTAAAAACTTGTAAAAGTGGAATAACTAAATTTTAAATCTTAACGTAAATATG
* * * * * * * *
5920060 TAAAAGTTAACATAATAAGCTAATTAAATAATAAAATCTAATTTTAATAAAAAAACAAACATTTA
66 TGAGAGTTAACATAATAAGTTAATTAAGTAAAAAAATCTAATTTTAATGAAAAAATAAATATTTA
** ** * * ** * *
5920125 TATTTATATTATTGGGGTAAAAGTATGTAATAATATTCAAATTTTCATTTTT-AGTAAAGAATAA
131 TATTTATATTATCCGACTAAAAATATGTAACAATATAAAAATTTTAATTTTTAAATAAA-AATAA
* * *
5920189 TAAAGATAAAAATAATTATAATAT-ACAATTGGCACAA-A-AAAACCCTTGACGTAAAATTGTAA
195 TAAAGATAAAAATAATTATAAT-TCAAAATT-G-A-AATAGAAAACCCTTGACATAAAACTGTAA
* * * * * * **
5920251 GGATTGACGTAAAAATTTATAAAGGTAGAACAACTAAATTTTAAATCTTAACT-TAGACGTGTTA
256 CGATTGACGTAAAAACTGATAAA--AAAAACAACTAAATTTTAAATCTTAA-TATA-A-ATGAAA
*
5920315 -A-AGTTAACCTAACAAGTCAATTAAGTAAAAAAGA-CTAATTTTAATAAAAAATAAATATTTAA
316 GAGAGTTAACCTAACAAGTCAATTAAATAAAAAA-ATCTAATTTTAATAAAAAATAAATATTTAA
* * *
5920377 ATTTATATT-TTCAGATTAAAAGTATTTAACGATATATAAATTTTTA-TTTTAAAT-AAAAATAA
380 ATTTATATTCTT-AGACTAAAAGTAATTAACGATATATAAATTTTAATTTTTAAATAAAAAATAA
* * * *
5920439 TAA-TAAAAATAATTATAA-TCTAAAATTGACATAAATAAACATTAACATGAAATT
444 TAACAAAAAAAAATTATAATTC-AAAATTGACATAAAT-AACATTAACATAAAACT
* * * * * *
5920493 GTAACAATTGATGTAAAAACATGTAAAAGTGGAGTAACTAAATTTTAAATCTTAATGTAAATGTG
1 ATAAAAATTGATGTAAAAACTTGTAAAAGTGGAATAACTAAATTTTAAATCTTAACGTAAATATG
*
5920558 TGAGAGTTAACTTAATAAGTTAATTAAGTAAAAAAA-CTTAATTTTAATG---AAA-AAATATTT
66 TGAGAGTTAACATAATAAGTTAATTAAGTAAAAAAATC-TAATTTTAATGAAAAAATAAATATTT
** *
5920618 ATATTTATATTATCATACTAAAAATATGTAACAA-A-AATTAAATTTTTA-TTTTAAATAAAAAA
130 ATATTTATATTATCCGACTAAAAATATGTAACAATATAA--AAATTTTAATTTTTAAAT-AAAAA
*
5920680 TAATAAAAATAAAAA
192 TAATAAAGATAAAAA
5920695 ATTATTGTTA
Statistics
Matches: 573, Mismatches: 106, Indels: 43
0.79 0.15 0.06
Matches are distributed among these distances:
493 5 0.01
494 60 0.10
495 101 0.18
496 16 0.03
497 99 0.17
498 154 0.27
499 11 0.02
500 120 0.21
501 4 0.01
502 3 0.01
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (497 bp):
ATAAAAATTGATGTAAAAACTTGTAAAAGTGGAATAACTAAATTTTAAATCTTAACGTAAATATG
TGAGAGTTAACATAATAAGTTAATTAAGTAAAAAAATCTAATTTTAATGAAAAAATAAATATTTA
TATTTATATTATCCGACTAAAAATATGTAACAATATAAAAATTTTAATTTTTAAATAAAAATAAT
AAAGATAAAAATAATTATAATTCAAAATTGAAATAGAAAACCCTTGACATAAAACTGTAACGATT
GACGTAAAAACTGATAAAAAAAACAACTAAATTTTAAATCTTAATATAAATGAAAGAGAGTTAAC
CTAACAAGTCAATTAAATAAAAAAATCTAATTTTAATAAAAAATAAATATTTAAATTTATATTCT
TAGACTAAAAGTAATTAACGATATATAAATTTTAATTTTTAAATAAAAAATAATAACAAAAAAAA
ATTATAATTCAAAATTGACATAAATAACATTAACATAAAACT
Found at i:5920750 original size:20 final size:22
Alignment explanation
Indices: 5920725--5920767 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
5920715 TTTAAAAGGC
*
5920725 TTAACGTTAAAT-T-ATAAAAA
1 TTAACGTAAAATCTAATAAAAA
5920745 TTAACGTAAAATCTAATAAAAA
1 TTAACGTAAAATCTAATAAAAA
5920767 T
1 T
5920768 AAAATAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 1 0.05
22 8 0.40
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.33
Consensus pattern (22 bp):
TTAACGTAAAATCTAATAAAAA
Found at i:5922331 original size:15 final size:15
Alignment explanation
Indices: 5922311--5922340 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5922301 TTGACATTTC
5922311 AATGAAATTCACTAA
1 AATGAAATTCACTAA
5922326 AATGAAATTCACTAA
1 AATGAAATTCACTAA
5922341 CTACTTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.07, T:0.27
Consensus pattern (15 bp):
AATGAAATTCACTAA
Found at i:5936438 original size:2 final size:2
Alignment explanation
Indices: 5936431--5936483 Score: 74
Period size: 2 Copynumber: 27.5 Consensus size: 2
5936421 TTGTCACTCT
* *
5936431 GA GA GA GA GA GA GA AA GA G- GA -A GA TA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5936471 GA GA GA GA GA GA G
1 GA GA GA GA GA GA G
5936484 GGCCACACAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.51, C:0.00, G:0.47, T:0.02
Consensus pattern (2 bp):
GA
Found at i:5937363 original size:19 final size:18
Alignment explanation
Indices: 5937339--5937379 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 18
5937329 TTTGCCTTTG
5937339 TTTTCCTCTTCTTTTTTTC-
1 TTTTCCT-TT-TTTTTTTCA
5937358 TTTTCCTTTTTTTTTTCA
1 TTTTCCTTTTTTTTTTCA
5937376 TTTT
1 TTTT
5937380 GTACTTTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.38
18 6 0.29
19 7 0.33
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTCCTTTTTTTTTTCA
Found at i:5938138 original size:23 final size:23
Alignment explanation
Indices: 5938066--5938139 Score: 58
Period size: 24 Copynumber: 3.0 Consensus size: 23
5938056 AAATAATTGT
*
5938066 TTTTATATAATTTTAATTATAAACTA
1 TTTTA-AT-ATTTTAATGATAAA-TA
* * * *
5938092 TATTTAAAATATCAATGTAAAAATA
1 T-TTTAATATTTTAATG-ATAAATA
5938117 TTTTAATATTTTAATGATAAATA
1 TTTTAATATTTTAATGATAAATA
5938140 ACTGTTAATT
Statistics
Matches: 37, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
23 6 0.16
24 12 0.32
25 9 0.24
26 6 0.16
27 4 0.11
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (23 bp):
TTTTAATATTTTAATGATAAATA
Found at i:5950071 original size:20 final size:19
Alignment explanation
Indices: 5950046--5950090 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
5950036 TAATTAACAT
5950046 TATTATA-TTAATATATAATA
1 TATTATAGTT-ATATATAA-A
*
5950066 TATTATAGTTATCTATAAA
1 TATTATAGTTATATATAAA
5950085 TATTAT
1 TATTAT
5950091 TTTATACATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 7 0.30
20 14 0.61
21 2 0.09
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
TATTATAGTTATATATAAA
Found at i:5950102 original size:20 final size:20
Alignment explanation
Indices: 5950046--5950104 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
5950036 TAATTAACAT
5950046 TATTATA-TTAAT-ATATAATA
1 TATTATAGTT-ATCATATAA-A
5950066 TATTATAGTTATC-TATAAA
1 TATTATAGTTATCATATAAA
*
5950085 TATTAT-TTTATACATATAAA
1 TATTATAGTTAT-CATATAAA
5950105 AAATATTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 4 0.12
19 8 0.24
20 20 0.59
21 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (20 bp):
TATTATAGTTATCATATAAA
Found at i:5960795 original size:7 final size:7
Alignment explanation
Indices: 5960780--5960810 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
5960770 TCTTAGATAA
5960780 GCAAAAT
1 GCAAAAT
*
5960787 GCAATAT
1 GCAAAAT
5960794 GCAAAAT
1 GCAAAAT
5960801 GCAAAAT
1 GCAAAAT
5960808 GCA
1 GCA
5960811 CAACCAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (7 bp):
GCAAAAT
Found at i:5963501 original size:309 final size:307
Alignment explanation
Indices: 5962941--5963544 Score: 716
Period size: 309 Copynumber: 2.0 Consensus size: 307
5962931 ATGTTATTTA
* ** * * *
5962941 TTTATTAATATAAAAACAGGGTGAGTAATCGGTTAAATTGACTAAAATATATTTTTAACCAACTT
1 TTTATTAATATAAAAACAGGGTGAGCAATCAATTAAATTGACTAAAAAATATTATTAACAAACTT
* * ** * * *
5963006 AATTGATTTTCATACATTTTAATTAAATCTATCTACTTTCGTATATTAATTGAATTAACCAATTA
66 AATCGATTTCCATACATTTTAACCAAATCCATCAACTATCGTATATTAATTGAATTAACCAATTA
* **
5963071 ATCAACTAAATTCAATTAATTCGATTTTAACTGATTTAATTGAAATATTTTTTAAGAAATGGACA
131 AACAACTAAATTCAATTAATTCGATTTTAAAAGATTTAATTGAAATATTTTTTAAGAAATGGACA
* *
5963136 TGGATGCACTCAAACCTATTTTCAAGCTTTCTTTATATAAAAAATATAAAAATGTTTCCCATGCG
196 TGAATGCACTCAAACCTATTTTCAAGCTTTCTTTATATAAAAAATATAAAAATGTTTCCCATGCA
5963201 TACATCGAACAGAAAAGATATAAGTAATCTTAAAACCATTTAGTGGAT
261 TACATCGAAC-GAAAAGATATAAGTAATCTTAAAACCATTTAGTGGAT
** *
5963249 TTTATTAATATAAAATTAGGGTGAGCAATCAATTAAATTTA-TCAAAAAATATTATTAACAAACT
1 TTTATTAATATAAAAACAGGGTGAGCAATCAATTAAATTGACT-AAAAAATATTATTAACAAACT
* * * *
5963313 TAATCGATTTCCCTATATATTTTAACCAAA-CCATCAACTATCTTATTTTAATTGAATTAATCAA
65 TAATCGATTT-CC-ATACATTTTAACCAAATCCATCAACTATCGTATATTAATTGAATTAACCAA
* * * * * * * *
5963377 TTAAACGATTGAATTCAATTAATTTG-TTTCTAAAAGATTTAATTGAATTTTTTTTTAAGGAATT
128 TTAAACAACTAAATTCAATTAATTCGATTT-TAAAAGATTTAATTGAAATATTTTTTAAGAAATG
* * * *
5963441 GACTTGAATGCACTCAAA-CTATTCTTCAAGCCATTT-TTT-TTTATAAAATATAACAATGTTTC
192 GACATGAATGCACTCAAACCTATT-TTCAAG-C-TTTCTTTATATAAAAAATATAAAAATGTTTC
* ** * *
5963503 CTATGCATACATCTTACGAAAAGATATAAGTAGTCTTGAAAC
254 CCATGCATACATCGAACGAAAAGATATAAGTAATCTTAAAAC
5963545 TCTAAAGTGA
Statistics
Matches: 247, Mismatches: 42, Indels: 14
0.82 0.14 0.05
Matches are distributed among these distances:
307 1 0.00
308 93 0.38
309 133 0.54
310 17 0.07
311 3 0.01
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.39
Consensus pattern (307 bp):
TTTATTAATATAAAAACAGGGTGAGCAATCAATTAAATTGACTAAAAAATATTATTAACAAACTT
AATCGATTTCCATACATTTTAACCAAATCCATCAACTATCGTATATTAATTGAATTAACCAATTA
AACAACTAAATTCAATTAATTCGATTTTAAAAGATTTAATTGAAATATTTTTTAAGAAATGGACA
TGAATGCACTCAAACCTATTTTCAAGCTTTCTTTATATAAAAAATATAAAAATGTTTCCCATGCA
TACATCGAACGAAAAGATATAAGTAATCTTAAAACCATTTAGTGGAT
Found at i:5963883 original size:33 final size:34
Alignment explanation
Indices: 5963842--5963913 Score: 110
Period size: 33 Copynumber: 2.1 Consensus size: 34
5963832 TTTTAATGTA
*
5963842 ATATATTTTATTTTCATTTCTTATTATAA-TCTT
1 ATATATTTTATTTTCATTTCTTAATATAATTCTT
*
5963875 ATATATTTTATTTTTATTTCTTAATATAATTTCTT
1 ATATATTTTATTTTCATTTCTTAATATAA-TTCTT
5963910 ATAT
1 ATAT
5963914 TATATATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 27 0.77
35 8 0.23
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (34 bp):
ATATATTTTATTTTCATTTCTTAATATAATTCTT
Found at i:5967042 original size:23 final size:24
Alignment explanation
Indices: 5966991--5967042 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
5966981 CCTCCCTATG
*
5966991 CTTTT-CTTCCCCAATTCCGTTTA
1 CTTTTCCTTCCCCAATTCCCTTTA
*
5967014 CGTTTCCTTCCCC-ATTCCCTTTA
1 CTTTTCCTTCCCCAATTCCCTTTA
*
5967037 TTTTTC
1 CTTTTC
5967043 TCTTTTGCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.10, C:0.37, G:0.04, T:0.50
Consensus pattern (24 bp):
CTTTTCCTTCCCCAATTCCCTTTA
Found at i:5968131 original size:42 final size:40
Alignment explanation
Indices: 5968085--5968405 Score: 218
Period size: 42 Copynumber: 7.7 Consensus size: 40
5968075 TTTGCATCAT
* *
5968085 AGTTCAAATAATATAAATTAATTTTATATTTGTTAGTTTACA
1 AGTTCAACTAATATAAA--AATTTTATATTTGTTAATTTACA
*
5968127 AGTTCAACTAATATAAAAATTTTATATATT-TAAATTTACATTA
1 AGTTCAACTAATATAAAAATTTTATAT-TTGTTAATTTAC---A
* * *
5968170 TAGTTCAAGTAATATAAATTAATTTTACATTTGTTTATTTACA
1 -AGTTCAACTAATATAAA--AATTTTATATTTGTTAATTTACA
* * * *
5968213 AGTTCGACTAGTATAAAAATTTTATATAT-TTAAGTTTGCA
1 AGTTCAACTAATATAAAAATTTTATATTTGTTAA-TTTACA
* *
5968253 TTATGGTTCAAGTAATATAAATTAATTTTATATTTGTTAATTTAGA
1 --A--GTTCAACTAATATAAA--AATTTTATATTTGTTAATTTACA
* *
5968299 AGTTCAACTAATATAAAAATTTTATATAT-TTAACTTTGCA
1 AGTTCAACTAATATAAAAATTTTATATTTGTTAA-TTTACA
*** * * * * *
5968339 TCAT-AAGTAATAGAAATCAATTTTACATTTGTTAGTTTATA
1 AGTTCAACTAATATAAA--AATTTTATATTTGTTAATTTACA
* * *
5968380 AATTTAACTAATATAAAAATCTTATA
1 AGTTCAACTAATATAAAAATTTTATA
5968406 AATAATATAA
Statistics
Matches: 217, Mismatches: 41, Indels: 44
0.72 0.14 0.15
Matches are distributed among these distances:
39 17 0.08
40 55 0.25
41 17 0.08
42 59 0.27
43 2 0.01
44 30 0.14
45 2 0.01
46 31 0.14
47 4 0.02
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (40 bp):
AGTTCAACTAATATAAAAATTTTATATTTGTTAATTTACA
Found at i:5968175 original size:86 final size:86
Alignment explanation
Indices: 5968070--5968405 Score: 441
Period size: 86 Copynumber: 4.0 Consensus size: 86
5968060 TGATATGTTA
* * * *
5968070 TTAAGTTTGCATCATAGTTCAAATAATATAAATTAATTTTATATTTGTTAGTTTACAAGTTCAAC
1 TTAAATTTGCATTATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAAC
5968135 TAATATAAAAATTTTATATAT
66 TAATATAAAAATTTTATATAT
* *
5968156 TTAAATTTACATTATAGTTCAAGTAATATAAATTAATTTTACATTTGTTTA-TTTACAAGTTCGA
1 TTAAATTTGCATTATAGTTCAAGTAATATAAATTAATTTTACATTTG-TTAGTTTACAAGTTCAA
*
5968220 CTAGTATAAAAATTTTATATAT
65 CTAATATAAAAATTTTATATAT
* * * * *
5968242 TTAAGTTTGCATTATGGTTCAAGTAATATAAATTAATTTTATATTTGTTAATTTAGAAGTTCAAC
1 TTAAATTTGCATTATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAAC
5968307 TAATATAAAAATTTTATATAT
66 TAATATAAAAATTTTATATAT
* * * * * * *
5968328 TTAACTTTGCA-T-CA--T-AAGTAATAGAAATCAATTTTACATTTGTTAGTTTATAAATTTAAC
1 TTAAATTTGCATTATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAAC
*
5968388 TAATATAAAAATCTTATA
66 TAATATAAAAATTTTATA
5968406 AATAATATAA
Statistics
Matches: 223, Mismatches: 25, Indels: 9
0.87 0.10 0.04
Matches are distributed among these distances:
81 55 0.25
82 1 0.00
85 4 0.02
86 160 0.72
87 3 0.01
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (86 bp):
TTAAATTTGCATTATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAAC
TAATATAAAAATTTTATATAT
Found at i:5969075 original size:25 final size:27
Alignment explanation
Indices: 5969021--5969078 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 27
5969011 TTGAACAAAA
*
5969021 ATCATA-TCTCAAAACTAAAACAGATG
1 ATCATATTCTCAAAACCAAAACAGATG
*
5969047 -TCATATTC-CAAAACCAAAATAGA-G
1 ATCATATTCTCAAAACCAAAACAGATG
5969071 ATCATATT
1 ATCATATT
5969079 TATTTATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 1 0.04
25 25 0.89
26 2 0.07
ACGTcount: A:0.48, C:0.19, G:0.07, T:0.26
Consensus pattern (27 bp):
ATCATATTCTCAAAACCAAAACAGATG
Found at i:5969799 original size:18 final size:18
Alignment explanation
Indices: 5969776--5969837 Score: 115
Period size: 18 Copynumber: 3.4 Consensus size: 18
5969766 TTTCTTCTTC
5969776 TTCTTCTGTAAGGTTAAT
1 TTCTTCTGTAAGGTTAAT
5969794 TTCTTCTGTAAGGTTAAT
1 TTCTTCTGTAAGGTTAAT
*
5969812 TTCTTCTGTAAGGTTAAC
1 TTCTTCTGTAAGGTTAAT
5969830 TTCTTCTG
1 TTCTTCTG
5969838 ACTGTCTTTC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.19, C:0.15, G:0.16, T:0.50
Consensus pattern (18 bp):
TTCTTCTGTAAGGTTAAT
Found at i:5974335 original size:25 final size:25
Alignment explanation
Indices: 5974300--5974360 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
5974290 GCATACATTG
*
5974300 AACAAAAATCATATCCCAAAACCAA
1 AACAAAGATCATATCCCAAAACCAA
* * *
5974325 AATAGAGATCATATTCCAAAACCAA
1 AACAAAGATCATATCCCAAAACCAA
5974350 AACAAAGATCA
1 AACAAAGATCA
5974361 AATTTACTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.57, C:0.23, G:0.05, T:0.15
Consensus pattern (25 bp):
AACAAAGATCATATCCCAAAACCAA
Found at i:5976021 original size:34 final size:30
Alignment explanation
Indices: 5975940--5976014 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 30
5975930 TTTGTTCACG
5975940 TACA-CTTTTTTCTCTTGTACCTATTTACA
1 TACATCTTTTTTCTCTTGTACCTATTTACA
*
5975969 TATATCTTTTTTCTCTTGTACCTATTTACA
1 TACATCTTTTTTCTCTTGTACCTATTTACA
5975999 TACATCTTTTTCTCTC
1 TACATCTTTTT-TCTC
5976015 AACTTGTTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
29 3 0.07
30 35 0.83
31 4 0.10
ACGTcount: A:0.19, C:0.24, G:0.03, T:0.55
Consensus pattern (30 bp):
TACATCTTTTTTCTCTTGTACCTATTTACA
Found at i:5977009 original size:18 final size:18
Alignment explanation
Indices: 5976986--5977020 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5976976 AAATAAATAT
*
5976986 AATTGTTTGAACAAACAA
1 AATTGTTTAAACAAACAA
5977004 AATTGTTTAAACAAACA
1 AATTGTTTAAACAAACA
5977021 TAACTGTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AATTGTTTAAACAAACAA
Found at i:5982964 original size:31 final size:31
Alignment explanation
Indices: 5982929--5982989 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
5982919 AAAATTCTAT
*
5982929 ATTTTTATTTT-AAGTTAAATAAATTTTTATA
1 ATTTTTATTTTGAA-TCAAATAAATTTTTATA
5982960 ATTTTTATTTTGAATCAAATAAATTTTTAT
1 ATTTTTATTTTGAATCAAATAAATTTTTAT
5982990 TATTAATAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 26 0.93
32 2 0.07
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (31 bp):
ATTTTTATTTTGAATCAAATAAATTTTTATA
Found at i:5983356 original size:19 final size:19
Alignment explanation
Indices: 5983332--5983368 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5983322 ATTTAATTAG
*
5983332 TAAAATTTACTAATTTGAT
1 TAAAATTTACTAACTTGAT
*
5983351 TAAAATTTCCTAACTTGA
1 TAAAATTTACTAACTTGA
5983369 AAATAGTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (19 bp):
TAAAATTTACTAACTTGAT
Found at i:5992701 original size:15 final size:15
Alignment explanation
Indices: 5992681--5992719 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
5992671 TAGAAAAATT
5992681 AATAATAAATAAGTA
1 AATAATAAATAAGTA
5992696 AATAATAAATAAGTA
1 AATAATAAATAAGTA
*
5992711 AATACTAAA
1 AATAATAAA
5992720 ACGTGTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.26
Consensus pattern (15 bp):
AATAATAAATAAGTA
Found at i:5992704 original size:7 final size:7
Alignment explanation
Indices: 5992681--5992719 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
5992671 TAGAAAAATT
5992681 AATAATA
1 AATAATA
5992688 AATAAGTA
1 AATAA-TA
5992696 AATAATA
1 AATAATA
5992703 AATAAGTA
1 AATAA-TA
*
5992711 AATACTA
1 AATAATA
5992718 AA
1 AA
5992720 ACGTGTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
7 16 0.55
8 13 0.45
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.26
Consensus pattern (7 bp):
AATAATA
Found at i:5996302 original size:29 final size:30
Alignment explanation
Indices: 5996269--5996341 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 30
5996259 AGCACTTTTT
5996269 CAATTAAAGGCCAAACATTTCAATT-GTCA
1 CAATTAAAGGCCAAACATTTCAATTCGTCA
* *
5996298 CAATT-AAGGACCAAACATTTCAATTCTTTA
1 CAATTAAAGG-CCAAACATTTCAATTCGTCA
5996328 CAATTAAAGGCCAA
1 CAATTAAAGGCCAA
5996342 GTTGATTGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
28 4 0.10
29 20 0.51
30 11 0.28
31 4 0.10
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (30 bp):
CAATTAAAGGCCAAACATTTCAATTCGTCA
Found at i:5996445 original size:27 final size:27
Alignment explanation
Indices: 5996386--5996448 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
5996376 TAAAAAATCT
* * **
5996386 TATTGAAAATGCAGTTATTGCACGTTG
1 TATTGAAAATGCAGTTATTACACATAA
5996413 TATTGAAAATGCAGTTATTACACATAA
1 TATTGAAAATGCAGTTATTACACATAA
*
5996440 TGTTGAAAA
1 TATTGAAAA
5996449 CTGTAGTGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (27 bp):
TATTGAAAATGCAGTTATTACACATAA
Found at i:5996487 original size:27 final size:27
Alignment explanation
Indices: 5996452--5996617 Score: 86
Period size: 27 Copynumber: 6.1 Consensus size: 27
5996442 TTGAAAACTG
*
5996452 TAGTGGTTACACGTCATATTAAAAATT
1 TAGTAGTTACACGTCATATTAAAAATT
* * *
5996479 TAGTAGTTACACGCCTTATTGAAAATT
1 TAGTAGTTACACGTCATATTAAAAATT
* * ** ** *
5996506 TACTTGTTACACACCAGGTTGAAAAATA
1 TAGTAGTTACACGTCATATT-AAAAATT
* * *
5996534 TAGTTA-TTACAC-ACTATGTTGAAAAATA
1 TAG-TAGTTACACGTC-ATATT-AAAAATT
* * *
5996562 CAGTTA-TTACACGTTATGTTAAAAATT
1 TAG-TAGTTACACGTCATATTAAAAATT
* * *
5996589 TAGTTGTTATATGTCATATTAAAAATT
1 TAGTAGTTACACGTCATATTAAAAATT
5996616 TA
1 TA
5996618 ATTGTTATAC
Statistics
Matches: 108, Mismatches: 26, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
26 1 0.01
27 65 0.60
28 41 0.38
29 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (27 bp):
TAGTAGTTACACGTCATATTAAAAATT
Found at i:5996579 original size:28 final size:28
Alignment explanation
Indices: 5996512--5996587 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
5996502 AATTTACTTG
* * *
5996512 TTACACACCAGGTTGAAAAATATAGTTA
1 TTACACACTATGTTGAAAAATACAGTTA
5996540 TTACACACTATGTTGAAAAATACAGTTA
1 TTACACACTATGTTGAAAAATACAGTTA
**
5996568 TTACACGTTATGTT-AAAAAT
1 TTACACACTATGTTGAAAAAT
5996588 TTAGTTGTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 6 0.14
28 37 0.86
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (28 bp):
TTACACACTATGTTGAAAAATACAGTTA
Found at i:5996584 original size:110 final size:110
Alignment explanation
Indices: 5996425--5996655 Score: 266
Period size: 110 Copynumber: 2.1 Consensus size: 110
5996415 TTGAAAATGC
* ** *
5996425 AGTTATTACACATAATGTTGAAAACTGTAGTGGTTACACGTCATATTAAAAATTTAGTAGTTACA
1 AGTTATTACACATAATGTTGAAAAATACAGTGATTACACGTCATATTAAAAATTTAGTAGTTACA
* * * *
5996490 CGCCTTATTGAAAATTTACTTGTTACACACCAGGTTGAAAAATAT
66 CGCCATATTAAAAATTTAATTGTTACACACCAGGCTGAAAAATAT
* * * * *
5996535 AGTTATTACACACT-ATGTTGAAAAATACAGTTATTACACGTTATGTTAAAAATTTAGTTGTTAT
1 AGTTATTACACA-TAATGTTGAAAAATACAGTGATTACACGTCATATTAAAAATTTAGTAGTTAC
* * * * * *
5996599 ATGTCATATTAAAAATTTAATTGTTATACATCATGCTGAACAATAT
65 ACGCCATATTAAAAATTTAATTGTTACACACCAGGCTGAAAAATAT
*
5996645 AGTTGTTACAC
1 AGTTATTACAC
5996656 GTCACGTTAT
Statistics
Matches: 100, Mismatches: 20, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
110 99 0.99
111 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (110 bp):
AGTTATTACACATAATGTTGAAAAATACAGTGATTACACGTCATATTAAAAATTTAGTAGTTACA
CGCCATATTAAAAATTTAATTGTTACACACCAGGCTGAAAAATAT
Found at i:5996632 original size:27 final size:27
Alignment explanation
Indices: 5996580--5996632 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
5996570 ACACGTTATG
* **
5996580 TTAAAAATTTAGTTGTTATATGTCATA
1 TTAAAAATTTAATTGTTATACATCATA
5996607 TTAAAAATTTAATTGTTATACATCAT
1 TTAAAAATTTAATTGTTATACATCAT
5996633 GCTGAACAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.47
Consensus pattern (27 bp):
TTAAAAATTTAATTGTTATACATCATA
Found at i:5997227 original size:10 final size:10
Alignment explanation
Indices: 5997212--5997259 Score: 64
Period size: 10 Copynumber: 5.0 Consensus size: 10
5997202 CTTAATCCCG
5997212 TTTTCTTTTT
1 TTTTCTTTTT
5997222 TTTTC-TTTT
1 TTTTCTTTTT
*
5997231 CTTTCTTTTT
1 TTTTCTTTTT
5997241 TTTTC-TTTT
1 TTTTCTTTTT
*
5997250 CTTTCTTTTT
1 TTTTCTTTTT
5997260 AGAACCTAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 16 0.48
10 17 0.52
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:5997232 original size:15 final size:15
Alignment explanation
Indices: 5997212--5997259 Score: 64
Period size: 15 Copynumber: 3.2 Consensus size: 15
5997202 CTTAATCCCG
5997212 TTTTCTTTT-TTTTT
1 TTTTCTTTTCTTTTT
5997226 CTTTTC-TTTCTTTTT
1 -TTTTCTTTTCTTTTT
5997241 TTTTCTTTTCTTTCTT
1 TTTTCTTTTCTTT-TT
5997257 TTT
1 TTT
5997260 AGAACCTAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 8 0.27
15 17 0.57
16 5 0.17
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTCTTTTCTTTTT
Found at i:5997237 original size:19 final size:19
Alignment explanation
Indices: 5997213--5997259 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
5997203 TTAATCCCGT
5997213 TTTCTTTTTTTTTCTTTTC
1 TTTCTTTTTTTTTCTTTTC
5997232 TTTCTTTTTTTTTCTTTTC
1 TTTCTTTTTTTTTCTTTTC
5997251 TTTCTTTTT
1 TTTCTTTTT
5997260 AGAACCTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (19 bp):
TTTCTTTTTTTTTCTTTTC
Found at i:5998819 original size:26 final size:27
Alignment explanation
Indices: 5998765--5998822 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 27
5998755 TATAATACTA
5998765 AATATTAAACTATAATGTATAAAATATT
1 AATATTAAACTATAA-GTATAAAATATT
5998793 AATAGTTAAA-TATAA-TATAAAGA-ATT
1 AATA-TTAAACTATAAGTATAAA-ATATT
5998819 AATA
1 AATA
5998823 ATTTTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
26 13 0.46
27 1 0.04
28 9 0.32
29 5 0.18
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (27 bp):
AATATTAAACTATAAGTATAAAATATT
Found at i:6008832 original size:352 final size:353
Alignment explanation
Indices: 6008161--6008855 Score: 1275
Period size: 352 Copynumber: 2.0 Consensus size: 353
6008151 AATCAGGTTT
*
6008161 TGACTAATTGACAAGTGTTACACAAAAATTATATATATAAAATTTGAAATCGAGAATGATTATAA
1 TGACTAATTGACAAGCGTTACAC-AAAATTATATATATAAAATTTGAAATCGAGAATGATTATAA
6008226 AATATTGCAAAAAATTTACAAATTAAAGATTCAATTTTCATACTATAGTAATAACATTATTGTAG
65 AATATTGCAAAAAATTTACAAATTAAAGATTCAATTTTCATACTATAGTAATAACATTATTGTAG
*
6008291 ACACTAGTTATTTATTTTCTTTCTTTCTTTATTTATTTTTAGTAATGTAGAGGCCCTTATCTTAT
130 ACACTAGTTATTTATTTTCTTTCTTTCTTTATTTATTTTTAGTAATGTAAAGGCCCTTATCTTAT
6008356 TTTTATTTTTATATTTCATTTTAGATGTTTATTTTATTATCATTTAAATCAAGTCCAAAGATCAG
195 TTTTATTTTTATATTTCATTTTAGATGTTTATTTTATTATCATTTAAATCAAGTCCAAAGATCAG
* * **
6008421 TGGGCTTTGGGCACCCCAAGTATTATATTAACGTCCATATAGGGAGCAGAGGGCTTAAAGTTGTT
260 TGGGCTTTGGGCACCCCAAGCATTATATTAACGTCCATATAGGGAGCAAAGCACTTAAAGTTGTT
6008486 GATCCTAAAGAAATGTGCCAAAGGGGGCA
325 GATCCTAAAGAAATGTGCCAAAGGGGGCA
6008515 TGACTAATTGACAAGCGTTACAC-AAATTATATATATAAAATTTGAAATCGAGAATGATTATAAA
1 TGACTAATTGACAAGCGTTACACAAAATTATATATATAAAATTTGAAATCGAGAATGATTATAAA
*
6008579 ATATTGCAAAGAATTTACAAATTAAAGATTCAATTTTCATACTATAGTAATAACATTATTGTAGA
66 ATATTGCAAAAAATTTACAAATTAAAGATTCAATTTTCATACTATAGTAATAACATTATTGTAGA
6008644 CACTAGTTATTTATTTTCTTTCTTTCTTTATTTATTTTTAGTAATGTAAAGGCCCTTATCTTATT
131 CACTAGTTATTTATTTTCTTTCTTTCTTTATTTATTTTTAGTAATGTAAAGGCCCTTATCTTATT
*
6008709 TTTATTTTTATATTTCATTTTAGATGTTTATTTTATTATTATTTAAATCAAGTCCAAAGATCAGT
196 TTTATTTTTATATTTCATTTTAGATGTTTATTTTATTATCATTTAAATCAAGTCCAAAGATCAGT
** *
6008774 GGGCTTTGGGCACCCCAAGCATTATATTAGTGTCCATATAGGGATCAAAGCACTTAAAGTTGTTG
261 GGGCTTTGGGCACCCCAAGCATTATATTAACGTCCATATAGGGAGCAAAGCACTTAAAGTTGTTG
6008839 ATCCTAAAGAAATGTGC
326 ATCCTAAAGAAATGTGC
6008856 TTGAGAGGGC
Statistics
Matches: 330, Mismatches: 11, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
352 308 0.93
354 22 0.07
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.40
Consensus pattern (353 bp):
TGACTAATTGACAAGCGTTACACAAAATTATATATATAAAATTTGAAATCGAGAATGATTATAAA
ATATTGCAAAAAATTTACAAATTAAAGATTCAATTTTCATACTATAGTAATAACATTATTGTAGA
CACTAGTTATTTATTTTCTTTCTTTCTTTATTTATTTTTAGTAATGTAAAGGCCCTTATCTTATT
TTTATTTTTATATTTCATTTTAGATGTTTATTTTATTATCATTTAAATCAAGTCCAAAGATCAGT
GGGCTTTGGGCACCCCAAGCATTATATTAACGTCCATATAGGGAGCAAAGCACTTAAAGTTGTTG
ATCCTAAAGAAATGTGCCAAAGGGGGCA
Found at i:6009714 original size:74 final size:74
Alignment explanation
Indices: 6009606--6009803 Score: 283
Period size: 74 Copynumber: 2.7 Consensus size: 74
6009596 CAAACAGAGT
** * *
6009606 GCTCTTAGTTGACTAA-CAAACTTCTTAGTCGATTAAGTCTTCTCTGTCTTGTAATTGAATTCTC
1 GCTCTTAGTTGACTAACCATGCTTCTTAGTCGATTAAGTCTTCTCTGTCTTGTAATTAAAGTCTC
6009670 TAGCAGTGA
66 TAGCAGTGA
* *
6009679 GCTGTTAGTTGACTAACCATGCTTCTTAGTTGATTAAGTTCTT-TCTGTCTTGTAATTAAAGTCT
1 GCTCTTAGTTGACTAACCATGCTTCTTAGTCGATTAAG-TCTTCTCTGTCTTGTAATTAAAGTCT
* *
6009743 TTGGCAGTGA
65 CTAGCAGTGA
* *
6009753 GCTCTTAGTTGACTAACCATGCATCTTAGTCGACTAAGTCTTCTCTGTCTT
1 GCTCTTAGTTGACTAACCATGCTTCTTAGTCGATTAAGTCTTCTCTGTCTT
6009804 TGAACCGGTC
Statistics
Matches: 110, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
73 19 0.17
74 87 0.79
75 4 0.04
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (74 bp):
GCTCTTAGTTGACTAACCATGCTTCTTAGTCGATTAAGTCTTCTCTGTCTTGTAATTAAAGTCTC
TAGCAGTGA
Found at i:6011852 original size:2 final size:2
Alignment explanation
Indices: 6011845--6011870 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6011835 AATTTGAAAG
6011845 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
6011871 GTAAATAATA
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:6014196 original size:11 final size:12
Alignment explanation
Indices: 6014172--6014208 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
6014162 ACGGAAATTT
*
6014172 AATTTCCATTGG
1 AATTTCCGTTGG
6014184 AATTT-CGTTGG
1 AATTTCCGTTGG
6014195 AATTTCCGTTGG
1 AATTTCCGTTGG
6014207 AA
1 AA
6014209 CATTTGGTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.41
Consensus pattern (12 bp):
AATTTCCGTTGG
Found at i:6015641 original size:28 final size:28
Alignment explanation
Indices: 6015601--6015659 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
6015591 ATTTATCATG
*
6015601 TTGGTGTTAGGATTAGGCCTGTGGCTAA
1 TTGGTGTTAGGATTAGCCCTGTGGCTAA
6015629 TTGGTGTTAGGATTAGCCCTGTGGCTAA
1 TTGGTGTTAGGATTAGCCCTGTGGCTAA
6015657 TTG
1 TTG
6015660 TAATTGGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.17, C:0.12, G:0.34, T:0.37
Consensus pattern (28 bp):
TTGGTGTTAGGATTAGCCCTGTGGCTAA
Found at i:6016758 original size:35 final size:35
Alignment explanation
Indices: 6016716--6016939 Score: 286
Period size: 35 Copynumber: 6.3 Consensus size: 35
6016706 ATCAAATTAG
6016716 AAGTTATTGGGCCTAATTGATTAAATTATTTAATT
1 AAGTTATTGGGCCTAATTGATTAAATTATTTAATT
* *
6016751 AAGTTATTGGGCCTAATTGATTAAATTTGTTTAATC
1 AAGTTATTGGGCCTAATTGATTAAA-TTATTTAATT
* * *
6016787 AAGTTGTTGGGCTTAATTGATTAAATTGTTTAATT
1 AAGTTATTGGGCCTAATTGATTAAATTATTTAATT
** * ***
6016822 AAGTTATTAAGCCTCATTGATTAAATTAAACAATT
1 AAGTTATTGGGCCTAATTGATTAAATTATTTAATT
* *
6016857 AAGTTATTAGGCCTAATTGATTAAATTGTTTAATT
1 AAGTTATTGGGCCTAATTGATTAAATTATTTAATT
***
6016892 AAGTTATTGGGCCTAATTGATTAAATTAAACAATT
1 AAGTTATTGGGCCTAATTGATTAAATTATTTAATT
6016927 AAGTTAATTGGGC
1 AAGTT-ATTGGGC
6016940 TTCTTAAGAA
Statistics
Matches: 162, Mismatches: 25, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
35 124 0.77
36 38 0.23
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (35 bp):
AAGTTATTGGGCCTAATTGATTAAATTATTTAATT
Found at i:6016891 original size:70 final size:70
Alignment explanation
Indices: 6016716--6016939 Score: 322
Period size: 70 Copynumber: 3.2 Consensus size: 70
6016706 ATCAAATTAG
* **
6016716 AAGTTATTGGGCCTAATTGATTAAATTATTTAATTAAGTTATTGGGCCTAATTGATTAAATTTGT
1 AAGTTATTGGGCCTAATTGATTAAATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAA-TTAA
** *
6016781 TTAATC
65 ACAATT
* * ** *
6016787 AAGTTGTTGGGCTTAATTGATTAAATTGTTTAATTAAGTTATTAAGCCTCATTGATTAAATTAAA
1 AAGTTATTGGGCCTAATTGATTAAATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAATTAAA
6016852 CAATT
66 CAATT
*
6016857 AAGTTATTAGGCCTAATTGATTAAATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAATTAAA
1 AAGTTATTGGGCCTAATTGATTAAATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAATTAAA
6016922 CAATT
66 CAATT
6016927 AAGTTAATTGGGC
1 AAGTT-ATTGGGC
6016940 TTCTTAAGAA
Statistics
Matches: 134, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
70 74 0.55
71 60 0.45
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (70 bp):
AAGTTATTGGGCCTAATTGATTAAATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAATTAAA
CAATT
Found at i:6017666 original size:36 final size:36
Alignment explanation
Indices: 6017619--6017688 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
6017609 GTTGAGAGTT
6017619 TGTACATGATCATTGGGAAGACTTTTACCAGTTGTC
1 TGTACATGATCATTGGGAAGACTTTTACCAGTTGTC
6017655 TGTACATGATCATTGGGAAGACTTTTACCAGTTG
1 TGTACATGATCATTGGGAAGACTTTTACCAGTTG
6017689 ACTCAATAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.36
Consensus pattern (36 bp):
TGTACATGATCATTGGGAAGACTTTTACCAGTTGTC
Found at i:6043867 original size:5 final size:5
Alignment explanation
Indices: 6043857--6043884 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
6043847 AAAAGGGCCG
6043857 AAGAA AAGAA AAGAA AAGAA AAGAA AAG
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAG
6043885 TGGAGATCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:6046933 original size:26 final size:26
Alignment explanation
Indices: 6046897--6046948 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
6046887 TTTAAGGTTA
6046897 GAAACATATCCAGAGCAAACTTGGAT
1 GAAACATATCCAGAGCAAACTTGGAT
6046923 GAAACATATCCAGAGCAAACTTGGAT
1 GAAACATATCCAGAGCAAACTTGGAT
6046949 CTTCTCATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (26 bp):
GAAACATATCCAGAGCAAACTTGGAT
Found at i:6048689 original size:21 final size:22
Alignment explanation
Indices: 6048638--6048690 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
6048628 AAACATGTAA
*
6048638 GATACGATTAGACACAAAACAC
1 GATACGATTACACACAAAACAC
* * * *
6048660 GTTAAGATTACACAC-GAGCAC
1 GATACGATTACACACAAAACAC
6048681 GATACGATTA
1 GATACGATTA
6048691 ATATTCGTGT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (22 bp):
GATACGATTACACACAAAACAC
Found at i:6052482 original size:31 final size:31
Alignment explanation
Indices: 6052446--6052514 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
6052436 TAATTTTTGT
6052446 TTTGTAGCAAGTATCTAGCTTTGTTTTACAA
1 TTTGTAGCAAGTATCTAGCTTTGTTTTACAA
*
6052477 TTTGTAGCAAGTATCTAGTTTTGTTTTACAA
1 TTTGTAGCAAGTATCTAGCTTTGTTTTACAA
*
6052508 TGTGTAG
1 TTTGTAG
6052515 AGCTAGAGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.25, C:0.10, G:0.19, T:0.46
Consensus pattern (31 bp):
TTTGTAGCAAGTATCTAGCTTTGTTTTACAA
Found at i:6053030 original size:17 final size:17
Alignment explanation
Indices: 6053008--6053048 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
6052998 TGAAAGGGAA
6053008 AAGAAGAAAAAGAATTG
1 AAGAAGAAAAAGAATTG
*
6053025 AAGAAGAAAAATAATTG
1 AAGAAGAAAAAGAATTG
6053042 AAGAAGA
1 AAGAAGA
6053049 GAAGAAAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.22, T:0.12
Consensus pattern (17 bp):
AAGAAGAAAAAGAATTG
Found at i:6055350 original size:13 final size:13
Alignment explanation
Indices: 6055329--6055367 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
6055319 AAAAAGAAAA
*
6055329 GAGGAGGGGGGGG
1 GAGGGGGGGGGGG
6055342 GAGGGGGGGGGGG
1 GAGGGGGGGGGGG
6055355 G-GGGGGGGGGGG
1 GAGGGGGGGGGGG
6055367 G
1 G
6055368 GGGTGTGGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 12 0.48
13 13 0.52
ACGTcount: A:0.08, C:0.00, G:0.92, T:0.00
Consensus pattern (13 bp):
GAGGGGGGGGGGG
Found at i:6055379 original size:1 final size:1
Alignment explanation
Indices: 6055334--6055370 Score: 65
Period size: 1 Copynumber: 37.0 Consensus size: 1
6055324 GAAAAGAGGA
*
6055334 GGGGGGGGGAGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
6055371 TGTGGGGGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.03, C:0.00, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:6055794 original size:3 final size:3
Alignment explanation
Indices: 6055786--6055813 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
6055776 TTGGCTTGCT
6055786 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
6055814 ATATATATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:6065167 original size:12 final size:12
Alignment explanation
Indices: 6065150--6065187 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
6065140 CTTGGGTAAG
6065150 ATACGTGAGGAA
1 ATACGTGAGGAA
6065162 ATACGTGAGGAA
1 ATACGTGAGGAA
* *
6065174 ATGCGTGAAGAA
1 ATACGTGAGGAA
6065186 AT
1 AT
6065188 TAAGAATGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.32, T:0.18
Consensus pattern (12 bp):
ATACGTGAGGAA
Found at i:6065947 original size:19 final size:18
Alignment explanation
Indices: 6065910--6065948 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
6065900 TTTTCATGGG
*
6065910 AAATGCTTTTCCAACAAA
1 AAATGCTTTTCAAACAAA
*
6065928 AAATGCTTTTTCAAATAAA
1 AAATGC-TTTTCAAACAAA
6065947 AA
1 AA
6065949 TTCCGTTGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (18 bp):
AAATGCTTTTCAAACAAA
Found at i:6065976 original size:29 final size:29
Alignment explanation
Indices: 6065935--6065991 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
6065925 AAAAAATGCT
*
6065935 TTTTCAAATAAAAATTCCGTTGGAAATTC
1 TTTTCAAACAAAAATTCCGTTGGAAATTC
* *
6065964 TTTTCGAACAAAAATTTCGTTGGAAATT
1 TTTTCAAACAAAAATTCCGTTGGAAATT
6065992 TTCAACGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (29 bp):
TTTTCAAACAAAAATTCCGTTGGAAATTC
Found at i:6066000 original size:29 final size:29
Alignment explanation
Indices: 6065944--6066000 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
6065934 TTTTTCAAAT
**
6065944 AAAAATTCCGTTGGAAATTCTTTTCGAAC
1 AAAAATTCCGTTGGAAATTCTTAACGAAC
*
6065973 AAAAATTTCGTTGGAAATT-TTCAACGAA
1 AAAAATTCCGTTGGAAATTCTT-AACGAA
6066001 ATTATTACGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (29 bp):
AAAAATTCCGTTGGAAATTCTTAACGAAC
Found at i:6074739 original size:14 final size:15
Alignment explanation
Indices: 6074721--6074775 Score: 65
Period size: 17 Copynumber: 3.4 Consensus size: 15
6074711 TTTAAGCTTT
6074721 TTTTTTAAAAAATTA
1 TTTTTTAAAAAATTA
*
6074736 TTTTTTAAAAAATTTTG
1 TTTTTTAAAAAA--TTA
6074753 TTTTTTAAAAAAATTA
1 TTTTTT-AAAAAATTA
6074769 CTTTTTT
1 -TTTTTT
6074776 TAATAGGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
15 12 0.35
16 2 0.06
17 14 0.41
18 6 0.18
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (15 bp):
TTTTTTAAAAAATTA
Found at i:6074739 original size:16 final size:16
Alignment explanation
Indices: 6074720--6074778 Score: 75
Period size: 15 Copynumber: 3.6 Consensus size: 16
6074710 TTTTAAGCTT
6074720 TTTTTTTAAAAAATTA
1 TTTTTTTAAAAAATTA
*
6074736 -TTTTTTAAAAAATTT
1 TTTTTTTAAAAAATTA
6074751 TGTTTTTTAAAAAAATTA
1 T-TTTTTT-AAAAAATTA
6074769 CTTTTTTTAA
1 -TTTTTTTAA
6074779 TAGGTTTTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
15 14 0.38
17 8 0.22
18 14 0.38
19 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (16 bp):
TTTTTTTAAAAAATTA
Found at i:6074777 original size:18 final size:17
Alignment explanation
Indices: 6074719--6074778 Score: 70
Period size: 18 Copynumber: 3.5 Consensus size: 17
6074709 TTTTTAAGCT
*
6074719 TTTTTTTTAAAAAATTA
1 TTTTTTTAAAAAAATTA
*
6074736 -TTTTTT-AAAAAATTT
1 TTTTTTTAAAAAAATTA
6074751 TGTTTTTTAAAAAAATTA
1 T-TTTTTTAAAAAAATTA
6074769 CTTTTTTTAA
1 -TTTTTTTAA
6074779 TAGGTTTTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
15 8 0.22
16 6 0.16
17 6 0.16
18 16 0.43
19 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (17 bp):
TTTTTTTAAAAAAATTA
Found at i:6079227 original size:2 final size:2
Alignment explanation
Indices: 6079220--6079247 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6079210 CTGTATCATC
6079220 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
6079248 TGATGAACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6080788 original size:16 final size:16
Alignment explanation
Indices: 6080767--6080800 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
6080757 CTTCCTTTTT
6080767 CAAGTGGCTACAACGA
1 CAAGTGGCTACAACGA
6080783 CAAGTGGCTACAACGA
1 CAAGTGGCTACAACGA
6080799 CA
1 CA
6080801 TATAGATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.26, G:0.24, T:0.12
Consensus pattern (16 bp):
CAAGTGGCTACAACGA
Found at i:6085241 original size:84 final size:84
Alignment explanation
Indices: 6085087--6085258 Score: 218
Period size: 84 Copynumber: 2.0 Consensus size: 84
6085077 TCCTCAAATC
* * * * * ** *
6085087 AGCTAGAAAGAATTAGGGCTCTTGAGCAAAAGCTACTTGCTAGAGGAAAACATCAAGGAGTTCCA
1 AGCTAGAAAGAATTAGGGCTATTGAGAAAAAGCCACTTGCTAAAGGAAAACAGCAAAAAGATCCA
6085152 AAAGAGCAAAAGGGTCAAA
66 AAAGAGCAAAAGGGTCAAA
* * *
6085171 AGCTAGAAAGAATTGGGGGTATTGAGAAAAAGCCACTTGCTAAAGGAAAGCAGCAAAAAGATCCA
1 AGCTAGAAAGAATTAGGGCTATTGAGAAAAAGCCACTTGCTAAAGGAAAACAGCAAAAAGATCCA
* * *
6085236 CAAGAGCAGAAGGTTCAAA
66 AAAGAGCAAAAGGGTCAAA
6085255 AGCT
1 AGCT
6085259 CAACATTCCA
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
84 74 1.00
ACGTcount: A:0.44, C:0.15, G:0.26, T:0.16
Consensus pattern (84 bp):
AGCTAGAAAGAATTAGGGCTATTGAGAAAAAGCCACTTGCTAAAGGAAAACAGCAAAAAGATCCA
AAAGAGCAAAAGGGTCAAA
Found at i:6087566 original size:2 final size:2
Alignment explanation
Indices: 6087559--6087583 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6087549 GATTATTTAG
6087559 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
6087584 TTGTATGTAT
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:6093322 original size:21 final size:21
Alignment explanation
Indices: 6093292--6093348 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
6093282 GGATATGTTC
*
6093292 ATGCAATTCATGACTAAGACTG
1 ATGC-ATTCATGACAAAGACTG
** *
6093314 ATGCATTCAAAACAAAGATTG
1 ATGCATTCATGACAAAGACTG
*
6093335 ATGCATTTATGACA
1 ATGCATTCATGACA
6093349 GGGATTGATG
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (21 bp):
ATGCATTCATGACAAAGACTG
Found at i:6093610 original size:18 final size:18
Alignment explanation
Indices: 6093591--6093624 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6093581 AAGAAATTGA
6093591 AAAATA-TGTTGAAAAAG
1 AAAATATTGTTGAAAAAG
*
6093608 AAATTATTGTTGAAAAA
1 AAAATATTGTTGAAAAA
6093625 TCTCTTGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.29
Consensus pattern (18 bp):
AAAATATTGTTGAAAAAG
Done.