Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, 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: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 62 of 109
Found at i:12385107 original size:31 final size:30
Alignment explanation
Indices: 12385069--12385164 Score: 104
Period size: 31 Copynumber: 3.1 Consensus size: 30
12385059 ATATATTATC
12385069 AATAAATTAAATAATAATATTTTATTAATAA
1 AATAAATTAAATAATAATATTTTATTAAT-A
* * *
12385100 AATAAATTATATAATATTATTTTATTAATT
1 AATAAATTAAATAATAATATTTTATTAATA
* *
12385130 ATTAAATTTAAAAAATATATATTTATATTAA-A
1 AATAAA-TTAAATAATA-ATATTT-TATTAATA
12385162 AAT
1 AAT
12385165 TAATATTTAT
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
30 5 0.09
31 35 0.66
32 7 0.13
33 6 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
AATAAATTAAATAATAATATTTTATTAATA
Found at i:12385119 original size:26 final size:26
Alignment explanation
Indices: 12385050--12385120 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
12385040 TTTTTAGTAT
* *
12385050 ATAAATTTTAT-ATATTATCAATAAA
1 ATAAATTATATAATATTATTAATAAA
*
12385075 TTAAA-TA-ATAATATTTTATTAATAAA
1 ATAAATTATATAATA--TTATTAATAAA
12385101 ATAAATTATATAATATTATT
1 ATAAATTATATAATATTATT
12385121 TTATTAATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
23 2 0.05
24 4 0.11
25 4 0.11
26 19 0.51
27 2 0.05
28 6 0.16
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (26 bp):
ATAAATTATATAATATTATTAATAAA
Found at i:12385170 original size:21 final size:21
Alignment explanation
Indices: 12385137--12385198 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
12385127 ATTATTAAAT
12385137 TTAAAAAAT-ATATATTTATA
1 TTAAAAAATAATATATTTATA
* *
12385157 TTAAAAATTAATAT-TTATTTA
1 TTAAAAAATAATATATT-TATA
12385178 TTAATAAAATAATATCATTTA
1 TTAA-AAAATAATAT-ATTTA
12385199 ATTTATTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
20 10 0.30
21 11 0.33
22 9 0.27
23 1 0.03
24 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAAAAAATAATATATTTATA
Found at i:12385186 original size:23 final size:23
Alignment explanation
Indices: 12385142--12385210 Score: 68
Period size: 23 Copynumber: 2.9 Consensus size: 23
12385132 TAAATTTAAA
* *
12385142 AAATATATATTTA-TATTAAAAAT
1 AAATATTTATTTATTAAT-AAAAT
*
12385165 TAATATTTATTTATTAATAAAAT
1 AAATATTTATTTATTAATAAAAT
12385188 AATATCATTTAATTTATTAATAA
1 AA-AT-ATTT-ATTTATTAATAA
12385211 TTTATAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
23 17 0.45
24 5 0.13
25 4 0.11
26 12 0.32
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (23 bp):
AAATATTTATTTATTAATAAAAT
Found at i:12386059 original size:25 final size:25
Alignment explanation
Indices: 12386030--12386095 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 25
12386020 TTAATATATC
12386030 TATTAAA-ATATTAAAAATTATTTAT
1 TATTAAAGATATT-AAAATTATTTAT
*
12386055 TATTAAAGTATATTGAAATTATTTAT
1 TATTAAAG-ATATTAAAATTATTTAT
* *
12386081 TTTTAAAGCTATTAA
1 TATTAAAGATATTAA
12386096 TATTCAAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
25 12 0.34
26 18 0.51
27 5 0.14
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (25 bp):
TATTAAAGATATTAAAATTATTTAT
Found at i:12386151 original size:19 final size:18
Alignment explanation
Indices: 12386116--12386160 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
12386106 TAGTTATATT
12386116 TTAATAATAATATTTAATA
1 TTAA-AATAATATTTAATA
*
12386135 TTAAAATATTATATTAATA
1 TTAAAATAATAT-TTAATA
*
12386154 TAAAAAT
1 TTAAAAT
12386161 TACTTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAAATAATATTTAATA
Found at i:12386157 original size:18 final size:18
Alignment explanation
Indices: 12386129--12386184 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
12386119 ATAATAATAT
12386129 TTAATATTAAAATATTATA
1 TTAATA-TAAAATATTATA
*
12386148 TTAATATAAAA-ATTA-C
1 TTAATATAAAATATTATA
*
12386164 TTAAAATAAAACTATT-TA
1 TTAATATAAAA-TATTATA
12386182 TTA
1 TTA
12386185 TTCTTTATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 10 0.32
17 4 0.13
18 11 0.35
19 6 0.19
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAATATAAAATATTATA
Found at i:12387020 original size:13 final size:12
Alignment explanation
Indices: 12386997--12387021 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12386987 AAAATATAAA
12386997 AATCATTTTTTT
1 AATCATTTTTTT
12387009 AATCATTTTTTT
1 AATCATTTTTTT
12387021 A
1 A
12387022 CGAAACAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (12 bp):
AATCATTTTTTT
Found at i:12391346 original size:25 final size:24
Alignment explanation
Indices: 12391300--12391346 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
12391290 TATTTATTTG
*
12391300 ATATTTAAATTTTTGGTGTATTCA
1 ATATTTAAATTTTTGGTATATTCA
* *
12391324 ATATTATAAGTTTTTGTTATATT
1 ATATT-TAAATTTTTGGTATATT
12391347 TGTGTTAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 5 0.26
25 14 0.74
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (24 bp):
ATATTTAAATTTTTGGTATATTCA
Found at i:12393982 original size:2 final size:2
Alignment explanation
Indices: 12393975--12394004 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12393965 TCCAATGTTG
12393975 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
12394005 TTTAAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12399113 original size:1 final size:1
Alignment explanation
Indices: 12399107--12399151 Score: 54
Period size: 1 Copynumber: 45.0 Consensus size: 1
12399097 TAGAATTTAG
* * * *
12399107 AAAAAAAAAAAAAAAAAAACAAAAACAAAAACAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
12399152 CAAATTTTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:12399152 original size:7 final size:7
Alignment explanation
Indices: 12399107--12399155 Score: 68
Period size: 7 Copynumber: 7.4 Consensus size: 7
12399097 TAGAATTTAG
12399107 AAAAAA-
1 AAAAAAC
*
12399113 AAAAAAA
1 AAAAAAC
12399120 AAAAAAC
1 AAAAAAC
12399127 -AAAAAC
1 AAAAAAC
12399133 -AAAAAC
1 AAAAAAC
12399139 AAAAAAC
1 AAAAAAC
12399146 AAAAAAC
1 AAAAAAC
12399153 AAA
1 AAA
12399156 TTTTAAACTA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
6 18 0.45
7 22 0.55
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:12400179 original size:21 final size:21
Alignment explanation
Indices: 12400155--12400195 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
12400145 TTCCTTATTA
12400155 TTGTTTCTTTCTGGGTTTCAG
1 TTGTTTCTTTCTGGGTTTCAG
12400176 TTGTTTCTTTCTGGGTTTCA
1 TTGTTTCTTTCTGGGTTTCA
12400196 TGTTAAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.05, C:0.15, G:0.22, T:0.59
Consensus pattern (21 bp):
TTGTTTCTTTCTGGGTTTCAG
Found at i:12407632 original size:35 final size:35
Alignment explanation
Indices: 12407586--12407652 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
12407576 AAATGATGAG
12407586 ATTGAAACTTATTCACGTGTT-CAATCAATTCTACC
1 ATTGAAACTTATTCACGT-TTCCAATCAATTCTACC
* * *
12407621 ATTGAATCTTATTTATGTTTCCAATCAATTCT
1 ATTGAAACTTATTCACGTTTCCAATCAATTCT
12407653 CTGTTTTCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 2 0.07
35 26 0.93
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.43
Consensus pattern (35 bp):
ATTGAAACTTATTCACGTTTCCAATCAATTCTACC
Found at i:12414091 original size:7 final size:7
Alignment explanation
Indices: 12414079--12414112 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
12414069 CACGATACAT
12414079 AATTTTA
1 AATTTTA
12414086 AATTTTA
1 AATTTTA
*
12414093 AAATTTA
1 AATTTTA
12414100 AATTTTA
1 AATTTTA
*
12414107 TATTTT
1 AATTTT
12414113 TTAAATACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
AATTTTA
Found at i:12418323 original size:2 final size:2
Alignment explanation
Indices: 12418316--12418341 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12418306 TTTGGACATA
12418316 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
12418342 TTTGGAGGAA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12429548 original size:7 final size:8
Alignment explanation
Indices: 12429533--12429559 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
12429523 CCCAACCCCG
12429533 AAATAAAA
1 AAATAAAA
12429541 AAATAAAA
1 AAATAAAA
12429549 AAATAAAA
1 AAATAAAA
12429557 AAA
1 AAA
12429560 AGGGTGAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAATAAAA
Found at i:12433260 original size:32 final size:31
Alignment explanation
Indices: 12433224--12433300 Score: 100
Period size: 32 Copynumber: 2.5 Consensus size: 31
12433214 TAATTAAATA
* *
12433224 TGATTTCATTTGGTATAATATTAATGCACATT
1 TGATTTCATTTGATAAAATATTAATGCACA-T
* *
12433256 TGATTTTATTCGATAAAATATTAATGCACAT
1 TGATTTCATTTGATAAAATATTAATGCACAT
*
12433287 GGATTTCATTTGAT
1 TGATTTCATTTGAT
12433301 TTCATTTATA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 12 0.32
32 26 0.68
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.45
Consensus pattern (31 bp):
TGATTTCATTTGATAAAATATTAATGCACAT
Found at i:12434254 original size:17 final size:17
Alignment explanation
Indices: 12434225--12434257 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12434215 TAAAAGTTAT
12434225 TTTAATATTATTTAATA
1 TTTAATATTATTTAATA
12434242 TTTAA-ATTAATTTAAT
1 TTTAATATT-ATTTAAT
12434258 GATATATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAATATTATTTAATA
Found at i:12440730 original size:30 final size:31
Alignment explanation
Indices: 12440708--12440782 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
12440698 ATTTGCATAT
12440708 AAATAAATAC-TT-AATTTTTAATTTATATTC
1 AAATAAAT-CTTTAAATTTTTAATTTATATTC
12440738 AAATAAATCTTTAAATTTTTAATTTATACTT-
1 AAATAAATCTTTAAATTTTTAATTTATA-TTC
*
12440769 AAATAAATCCTTAA
1 AAATAAATCTTTAA
12440783 CTTAAATTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 1 0.02
30 10 0.24
31 28 0.68
32 2 0.05
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (31 bp):
AAATAAATCTTTAAATTTTTAATTTATATTC
Found at i:12440791 original size:36 final size:33
Alignment explanation
Indices: 12440708--12440799 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 33
12440698 ATTTGCATAT
12440708 AAATAAA--TACTT-AATTTTTAATTTATATTC
1 AAATAAATCTACTTAAATTTTTAATTTATATTC
12440738 AAATAAATCT--TTAAATTTTTAATTTATACTT-
1 AAATAAATCTACTTAAATTTTTAATTTATA-TTC
*
12440769 AAATAAATCCTTAACTTAAATTTTTTATTTA
1 AAATAAAT-C-T-ACTTAAATTTTTAATTTA
12440800 AAATAAGAGT
Statistics
Matches: 52, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
30 9 0.17
31 23 0.44
32 4 0.08
33 1 0.02
36 15 0.29
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (33 bp):
AAATAAATCTACTTAAATTTTTAATTTATATTC
Found at i:12442365 original size:12 final size:12
Alignment explanation
Indices: 12442348--12442388 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
12442338 TTTAAAATTT
12442348 ATATAAAGAATG
1 ATATAAAGAATG
12442360 ATATAAAGAA-G
1 ATATAAAGAATG
*
12442371 ACATTAAA-AATG
1 ATA-TAAAGAATG
12442383 ATATAA
1 ATATAA
12442389 TTTAAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 8 0.32
12 17 0.68
ACGTcount: A:0.61, C:0.02, G:0.12, T:0.24
Consensus pattern (12 bp):
ATATAAAGAATG
Found at i:12449948 original size:20 final size:19
Alignment explanation
Indices: 12449900--12449949 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
12449890 TATACGTTAA
*
12449900 AAAATAA-TAATTTTTTTT
1 AAAATAATTATTTTTTTTT
*
12449918 ATAAAT-TTTATTTTTATTTT
1 A-AAATAATTATTTTT-TTTT
12449938 AAAATAATTATT
1 AAAATAATTATT
12449950 AAAAAATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
18 1 0.04
19 14 0.56
20 10 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
AAAATAATTATTTTTTTTT
Found at i:12467419 original size:12 final size:13
Alignment explanation
Indices: 12467360--12467422 Score: 55
Period size: 12 Copynumber: 5.2 Consensus size: 13
12467350 ATTTTTATTA
*
12467360 AATTAAAAT-ATT
1 AATTAATATAATT
* *
12467372 AAATAATA-ATTT
1 AATTAATATAATT
12467384 AATTAATATAATT
1 AATTAATATAATT
12467397 --TTATATATAATT
1 AATTA-ATATAATT
12467409 AATTAAT-TAATT
1 AATTAATATAATT
12467421 AA
1 AA
12467423 AAATACTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
11 3 0.07
12 30 0.73
13 5 0.12
14 3 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTAATATAATT
Found at i:12468739 original size:20 final size:17
Alignment explanation
Indices: 12468714--12468755 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 17
12468704 TTAAATCGAA
12468714 TTATATATTTTTATTAATTT
1 TTATATA-TTTTA--AATTT
12468734 TTATATATTTTAAATTT
1 TTATATATTTTAAATTT
12468751 TTATA
1 TTATA
12468756 AAATAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.45
19 5 0.23
20 7 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATATATTTTAAATTT
Found at i:12468799 original size:20 final size:20
Alignment explanation
Indices: 12468774--12468813 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12468764 ATAATTATTC
* * *
12468774 TATATTTAAATTTATTTTAA
1 TATATTAAAAATTATATTAA
12468794 TATATTAAAAATTATATTAA
1 TATATTAAAAATTATATTAA
12468814 GATTACATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATATTAAAAATTATATTAA
Found at i:12469645 original size:12 final size:12
Alignment explanation
Indices: 12469627--12469659 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12469617 TGAATGAGTG
12469627 ATAAAATTAA-A
1 ATAAAATTAATA
12469638 ATTAAAATTAATA
1 A-TAAAATTAATA
12469651 ATAAAATTA
1 ATAAAATTA
12469660 TTATATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 1 0.05
12 17 0.85
13 2 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
ATAAAATTAATA
Found at i:12472389 original size:11 final size:10
Alignment explanation
Indices: 12472364--12472396 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
12472354 ATATTTATAA
12472364 TATTTAAATT
1 TATTTAAATT
12472374 TATTTAAATAT
1 TATTTAAAT-T
12472385 TATTTAAATT
1 TATTTAAATT
12472395 TA
1 TA
12472397 ATATTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TATTTAAATT
Found at i:12487147 original size:2 final size:2
Alignment explanation
Indices: 12487135--12487166 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
12487125 TCTTCTTCTT
*
12487135 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12487167 AAGCTAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:12489731 original size:11 final size:11
Alignment explanation
Indices: 12489715--12489739 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12489705 CAGATGTTGA
12489715 GATAAAAGAAG
1 GATAAAAGAAG
12489726 GATAAAAGAAG
1 GATAAAAGAAG
12489737 GAT
1 GAT
12489740 TTTTCTCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.28, T:0.12
Consensus pattern (11 bp):
GATAAAAGAAG
Found at i:12504113 original size:24 final size:25
Alignment explanation
Indices: 12504068--12504123 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
12504058 TATTAAATGT
*
12504068 TATTAAAATATTATGATAAAATTGAA
1 TATTAAAATATTA-GATAAAATAGAA
12504094 TATTAATAATATTA-AT-AAATAGAA
1 TATTAA-AATATTAGATAAAATAGAA
12504118 -ATTAAA
1 TATTAAA
12504124 TGGATATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 1 0.04
23 5 0.18
24 7 0.25
25 2 0.07
26 6 0.21
27 7 0.25
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (25 bp):
TATTAAAATATTAGATAAAATAGAA
Found at i:12505766 original size:493 final size:490
Alignment explanation
Indices: 12504697--12506170 Score: 2366
Period size: 493 Copynumber: 3.0 Consensus size: 490
12504687 TAAAATTTTA
*
12504697 TCTTAATTGATAAAAAAACAATGTTAAGTTTTTTATTCAAATAAAAATTTAATTAAATGCAAATA
1 TCTTAATTGATAAAAAAACAATGTTAAGTTTTTTATTCAAATAAAAATTTAATTAAATGTAAATA
12504762 AATATTAAAGGAATTGATTGATTATAATAAAAAATAAAAACTTGA-TTTTTTTTTCCAATTATAG
66 AATATTAAAGGAATTGATTGATTATAATAAAAAATAAAAACTTGATTTTTTTTTTCCAATTATAG
*
12504826 TTCAACAACTTACATTGTAATGTATAAACTTGCTTTTTTTTATCAACAAGTTGTTGGTTCAATTG
131 TTCAACAACTTACATTGTAATGTATAAACTTACTTTTTTTTATCAACAAGTTGTTGGTTCAATTG
12504891 ATTAAGATTCGTCTTTATCGACGAAAAAGTCTTGAGTTTGAGTCTTACCGATAATCATTTATTGG
196 ATTAAGATTCGTCTTTATCGACG-AAAAGTCTTGAGTTTGAGTCTTACCGATAATCATTTATTGG
* *
12504956 AGTTATCTTGAATACACGACTTGCAGTTATCTATCTTAGATTATCAAGTATGACACATATTATCA
260 AGTTATCTTGAATACATGACCTGCAGTTATCTATCTTAGATTATCAAGTATGACACATATTATCA
* ** *
12505021 TAACTTGAGAGACTGAACAATCTATTTATTTTTAAATTTCTTTAAAAGAAAAAAACTTGTTTTTC
325 TAACTTGAAAGACTGAACAATCTATTTATTTTCGAATTTC-TTAAAA-AAAAAAACTTGCTTTTC
12505086 TTTATAGGACACTTTCAAAGCTAATATTCAAAATTGTCGTTTAATGAAGTCAATGGCATAAAGTT
388 TTTATAGGACACTTTCAAAGCTAATATTCAAAATTGTCGTTTAATGAAGTCAATGGCATAAAGTT
*
12505151 TAATAAACTTGTCTTATTGATATAGACATGATTTTCCT
453 TAATAAGCTTGTCTTATTGATATAGACATGATTTTCCT
* *
12505189 TCTTAATTGATAAAAAAAACAATGTTAATTTTTTTATTCAAATAAAAAATTAATTAAATGTAAAT
1 TCTTAATTGAT-AAAAAAACAATGTTAAGTTTTTTATTCAAATAAAAATTTAATTAAATGTAAAT
12505254 AAATATTAAAGGAATTGATTGATTATAATAAAAAATAAAAACTTGATTTTTTTTTTCCAATTATA
65 AAATATTAAAGGAATTGATTGATTATAATAAAAAATAAAAACTTGATTTTTTTTTTCCAATTATA
* *
12505319 GTTCAACAACTTAAATTGTAATGTATAAACTTACTTTTTTTTATCAACAAGTTGTTGATTCAATT
130 GTTCAACAACTTACATTGTAATGTATAAACTTACTTTTTTTTATCAACAAGTTGTTGGTTCAATT
* * * * *
12505384 GATTAAGATTCGTCTTTATCAACGAAAAGTCTTGAGTTTGAGTCTTACTGATGATCACTTATCGG
195 GATTAAGATTCGTCTTTATCGACGAAAAGTCTTGAGTTTGAGTCTTACCGATAATCATTTATTGG
* *
12505449 AGTTATCTTAAATACATGACCTGCAGTTATCTATCTTAGATTATCAAGTATGACATATATTATCA
260 AGTTATCTTGAATACATGACCTGCAGTTATCTATCTTAGATTATCAAGTATGACACATATTATCA
*
12505514 TAACTTGAAAGACTGAACAATCTATTTATTTTCGAATTTCTTAAAATAAAAAA-TTGCTTTTCTT
325 TAACTTGAAAGACTGAACAATCTATTTATTTTCGAATTTCTTAAAAAAAAAAACTTGCTTTTCTT
*
12505578 TGTAGGACACTTTCAAAGCTAATATTCAAAATTGTCGTTTAATGAAGTCAATGGCATAAAGTTTA
390 TATAGGACACTTTCAAAGCTAATATTCAAAATTGTCGTTTAATGAAGTCAATGGCATAAAGTTTA
12505643 ATAAGCTTGTCTTATTGATATAGACATGATTTTCCT
455 ATAAGCTTGTCTTATTGATATAGACATGATTTTCCT
* *
12505679 TCTTAATTGATAAAAAAACAATGTTAAGTTTTTTATTAAAATAAAATTTTAATTAAATGTAAATA
1 TCTTAATTGATAAAAAAACAATGTTAAGTTTTTTATTCAAATAAAAATTTAATTAAATGTAAATA
* * *
12505744 AATATTAAAGAAATTTATTGATTATAATAAAAAATAAAAACTT--TATTTTTTTTCCAATTATAG
66 AATATTAAAGGAATTGATTGATTATAATAAAAAATAAAAACTTGATTTTTTTTTTCCAATTATAG
* * * *
12505807 GTCAACAACTTACATTGTAATGTATAAACTTACTTTTCTTTATTAATAAGTTGTTGGTTCAATTG
131 TTCAACAACTTACATTGTAATGTATAAACTTACTTTTTTTTATCAACAAGTTGTTGGTTCAATTG
** * * * * * *
12505872 ATTAAGATTTATTTTTATTGACGAAAAGGTCTTGAGTTTAAGTTTTACCGATTATTATTTATTGG
196 ATTAAGATTCGTCTTTATCGACGAAAA-GTCTTGAGTTTGAGTCTTACCGATAATCATTTATTGG
* * * * * * * * * * *
12505937 ACTCATATTGAATATATAACCTACAGTTATCTGTCTTAAATTATTAAATATGATACATATTATCA
260 AGTTATCTTGAATACATGACCTGCAGTTATCTATCTTAGATTATCAAGTATGACACATATTATCA
* * *
12506002 TAA-TTGAAAGACTAAATAATCTATTTATTTTCGAATTT-TAAAAAAAAAAAAACTTGCTTTTCT
325 TAACTTGAAAGACTGAACAATCTATTTATTTTCGAATTTCT-TAAAAAAAAAAACTTGCTTTTCT
*
12506065 TTATAGGACATTTTCAAAGCTAATATTCAAAATTGTCGTTTAATGAAGTCAATGGCATAAAGTTT
389 TTATAGGACACTTTCAAAGCTAATATTCAAAATTGTCGTTTAATGAAGTCAATGGCATAAAGTTT
12506130 AATAAGCTTGTCTTATTGATATAGACATGATTTTCCT
454 AATAAGCTTGTCTTATTGATATAGACATGATTTTCCT
12506167 TCTT
1 TCTT
12506171 GTACTTTTCT
Statistics
Matches: 911, Mismatches: 66, Indels: 14
0.92 0.07 0.01
Matches are distributed among these distances:
486 1 0.00
487 143 0.16
488 199 0.22
489 91 0.10
490 120 0.13
491 6 0.01
492 17 0.02
493 231 0.25
494 103 0.11
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (490 bp):
TCTTAATTGATAAAAAAACAATGTTAAGTTTTTTATTCAAATAAAAATTTAATTAAATGTAAATA
AATATTAAAGGAATTGATTGATTATAATAAAAAATAAAAACTTGATTTTTTTTTTCCAATTATAG
TTCAACAACTTACATTGTAATGTATAAACTTACTTTTTTTTATCAACAAGTTGTTGGTTCAATTG
ATTAAGATTCGTCTTTATCGACGAAAAGTCTTGAGTTTGAGTCTTACCGATAATCATTTATTGGA
GTTATCTTGAATACATGACCTGCAGTTATCTATCTTAGATTATCAAGTATGACACATATTATCAT
AACTTGAAAGACTGAACAATCTATTTATTTTCGAATTTCTTAAAAAAAAAAACTTGCTTTTCTTT
ATAGGACACTTTCAAAGCTAATATTCAAAATTGTCGTTTAATGAAGTCAATGGCATAAAGTTTAA
TAAGCTTGTCTTATTGATATAGACATGATTTTCCT
Found at i:12506245 original size:488 final size:477
Alignment explanation
Indices: 12504759--12506170 Score: 2011
Period size: 488 Copynumber: 2.9 Consensus size: 477
12504749 TTAAATGCAA
* *
12504759 ATAAATATTAAAGGAATTGATTGATTATAATAAAAAATAAAAACTTGATTTTTTTTTCCAATTAT
1 ATAAATATTAAAGAAATTGATTGATTATAATAAAAAATAAAAACTTTA-TTTTTTTTCCAATTAT
*
12504824 AGTTCAACAACTTACATTGTAATGTATAAACTTGCTTTTTTTTATCAACAAGTTGTTGGTTCAAT
65 AGTTCAACAACTTACATTGTAATGTATAAACTTACTTTTTTTTATCAACAAGTTGTTGGTTCAAT
12504889 TGATTAAGATTCGTCTTTATCGACGAAAAAGTCTTGAGTTTGAGTCTTACCGATAATCATTTATT
130 TGATTAAGATTCGTCTTTATCGACG-AAAAGTCTTGAGTTTGAGTCTTACCGATAATCATTTATT
* *
12504954 GGAGTTATCTTGAATACACGACTTGCAGTTATCTATCTTAGATTATCAAGTATGACACATATTAT
194 GGAGTTATCTTGAATACATGACCTGCAGTTATCTATCTTAGATTATCAAGTATGACACATATTAT
* ** * *
12505019 CATAACTTGAGAGACTGAACAATCTATTTATTTTTAAATTTCTTTAAAAGAAAAAAACTTGTTTT
259 CATAACTTGAAAGACTGAACAATCTATTTATTTTCGAA--T-TTTAAAAAAAAAAAACTTGCTTT
12505084 TCTTTATAGGACACTTTCAAAGCTAATATTCAAAATTGTCGTTTAATGAAGTCAATGGCATAAAG
321 TCTTTATAGGACACTTTCAAAGCTAATATTCAAAATTGTCGTTTAATGAAGTCAATGGCATAAAG
*
12505149 TTTAATAAACTTGTCTTATTGATATAGACATGATTTTCCTTCTTAATTGATAAAAAAAACAATGT
386 TTTAATAAGCTTGTCTTATTGATATAGACATGATTTTCCTTCTTAATTGAT-AAAAAAAC-A--T
**
12505214 TAATT-TTTTTATTCAAATAAAAAATTAATTAAATGTAA
447 T-ATTGTTTTTATT--AA-AAAAAATT--TT-AAT-TTT
* *
12505252 ATAAATATTAAAGGAATTGATTGATTATAATAAAAAATAAAAACTTGATTTTTTTTTTCCAATTA
1 ATAAATATTAAAGAAATTGATTGATTATAATAAAAAATAAAAACTT--TATTTTTTTTCCAATTA
* *
12505317 TAGTTCAACAACTTAAATTGTAATGTATAAACTTACTTTTTTTTATCAACAAGTTGTTGATTCAA
64 TAGTTCAACAACTTACATTGTAATGTATAAACTTACTTTTTTTTATCAACAAGTTGTTGGTTCAA
* * * * *
12505382 TTGATTAAGATTCGTCTTTATCAACGAAAAGTCTTGAGTTTGAGTCTTACTGATGATCACTTATC
129 TTGATTAAGATTCGTCTTTATCGACGAAAAGTCTTGAGTTTGAGTCTTACCGATAATCATTTATT
* *
12505447 GGAGTTATCTTAAATACATGACCTGCAGTTATCTATCTTAGATTATCAAGTATGACATATATTAT
194 GGAGTTATCTTGAATACATGACCTGCAGTTATCTATCTTAGATTATCAAGTATGACACATATTAT
* *
12505512 CATAACTTGAAAGACTGAACAATCTATTTATTTTCGAATTTCTTAAAATAAAAAA-TTGCTTTTC
259 CATAACTTGAAAGACTGAACAATCTATTTATTTTCGAATTT-TAAAAAAAAAAAACTTGCTTTTC
*
12505576 TTTGTAGGACACTTTCAAAGCTAATATTCAAAATTGTCGTTTAATGAAGTCAATGGCATAAAGTT
323 TTTATAGGACACTTTCAAAGCTAATATTCAAAATTGTCGTTTAATGAAGTCAATGGCATAAAGTT
* *
12505641 TAATAAGCTTGTCTTATTGATATAGACATGATTTTCCTTCTTAATTGATAAAAAAACAATGTTAA
388 TAATAAGCTTGTCTTATTGATATAGACATGATTTTCCTTCTTAATTGATAAAAAAACATTATT--
12505706 GTTTTTTATTAAAATAAAATTTTAATTAAATGT
451 G-TTTTTATTAAAA-AAAATTTTAATT---T-T
*
12505739 AAATAAATATTAAAGAAATTTATTGATTATAATAAAAAATAAAAACTTTATTTTTTTTCCAATTA
1 --ATAAATATTAAAGAAATTGATTGATTATAATAAAAAATAAAAACTTTATTTTTTTTCCAATTA
* * * *
12505804 TAGGTCAACAACTTACATTGTAATGTATAAACTTACTTTTCTTTATTAATAAGTTGTTGGTTCAA
64 TAGTTCAACAACTTACATTGTAATGTATAAACTTACTTTTTTTTATCAACAAGTTGTTGGTTCAA
** * * * * * *
12505869 TTGATTAAGATTTATTTTTATTGACGAAAAGGTCTTGAGTTTAAGTTTTACCGATTATTATTTAT
129 TTGATTAAGATTCGTCTTTATCGACGAAAA-GTCTTGAGTTTGAGTCTTACCGATAATCATTTAT
* * * * * * * * * * *
12505934 TGGACTCATATTGAATATATAACCTACAGTTATCTGTCTTAAATTATTAAATATGATACATATTA
193 TGGAGTTATCTTGAATACATGACCTGCAGTTATCTATCTTAGATTATCAAGTATGACACATATTA
* *
12505999 TCATAA-TTGAAAGACTAAATAATCTATTTATTTTCGAATTTTAAAAAAAAAAAAACTTGCTTTT
258 TCATAACTTGAAAGACTGAACAATCTATTTATTTTCGAATTTT-AAAAAAAAAAAACTTGCTTTT
*
12506063 CTTTATAGGACATTTTCAAAGCTAATATTCAAAATTGTCGTTTAATGAAGTCAATGGCATAAAGT
322 CTTTATAGGACACTTTCAAAGCTAATATTCAAAATTGTCGTTTAATGAAGTCAATGGCATAAAGT
12506128 TTAATAAGCTTGTCTTATTGATATAGACATGATTTTCCTTCTT
387 TTAATAAGCTTGTCTTATTGATATAGACATGATTTTCCTTCTT
12506171 GTACTTTTCT
Statistics
Matches: 835, Mismatches: 67, Indels: 39
0.89 0.07 0.04
Matches are distributed among these distances:
483 1 0.00
484 3 0.00
485 4 0.00
486 4 0.00
487 151 0.18
488 200 0.24
489 60 0.07
490 122 0.15
491 11 0.01
493 177 0.21
494 102 0.12
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (477 bp):
ATAAATATTAAAGAAATTGATTGATTATAATAAAAAATAAAAACTTTATTTTTTTTCCAATTATA
GTTCAACAACTTACATTGTAATGTATAAACTTACTTTTTTTTATCAACAAGTTGTTGGTTCAATT
GATTAAGATTCGTCTTTATCGACGAAAAGTCTTGAGTTTGAGTCTTACCGATAATCATTTATTGG
AGTTATCTTGAATACATGACCTGCAGTTATCTATCTTAGATTATCAAGTATGACACATATTATCA
TAACTTGAAAGACTGAACAATCTATTTATTTTCGAATTTTAAAAAAAAAAAACTTGCTTTTCTTT
ATAGGACACTTTCAAAGCTAATATTCAAAATTGTCGTTTAATGAAGTCAATGGCATAAAGTTTAA
TAAGCTTGTCTTATTGATATAGACATGATTTTCCTTCTTAATTGATAAAAAAACATTATTGTTTT
TATTAAAAAAAATTTTAATTTT
Found at i:12516644 original size:30 final size:30
Alignment explanation
Indices: 12516610--12516666 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
12516600 GATGTTTATG
12516610 GATTCAATTGAATAAAAATAAATATTTAAA
1 GATTCAATTGAATAAAAATAAATATTTAAA
* * *
12516640 GATTCCATTGGATGAAAATAAATATTT
1 GATTCAATTGAATAAAAATAAATATTT
12516667 GAAGGCTCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.49, C:0.05, G:0.11, T:0.35
Consensus pattern (30 bp):
GATTCAATTGAATAAAAATAAATATTTAAA
Found at i:12529749 original size:164 final size:164
Alignment explanation
Indices: 12529478--12529808 Score: 536
Period size: 164 Copynumber: 2.0 Consensus size: 164
12529468 TGTCGAGAAT
* * *
12529478 GAAGCAAAAGCTCATAGATACTCAAAATCAGTTTCCAAAACTACAAACAAAAATGAAAATTTCAA
1 GAAGCAAAAGCTCACAAATACCCAAAATCAGTTTCCAAAACTACAAACAAAAATGAAAATTTCAA
12529543 AGTGAAATTCAACTTACCCAGTAAAAAAATCACGAAATTTGACTGAGACAGAAAGCTTACCCAAA
66 AGTGAAATTCAACTTACCCAGTAAAAAAATCACGAAATTTGACTGAGACAGAAAGCTTACCCAAA
* *
12529608 TATGCAGAAGCTTACCCAGACAGAGATGCTGGAA
131 TATGCAAAAACTTACCCAGACAGAGATGCTGGAA
* *
12529642 GAAGCAAAAGCTCACAAATACCCAAAATTAGTTTCCAAAACTACAAACAAAAATGAAAATTTCGA
1 GAAGCAAAAGCTCACAAATACCCAAAATCAGTTTCCAAAACTACAAACAAAAATGAAAATTTCAA
* * * * *
12529707 AGTGGAATTCAACTTACCTAGTAAAGAAATCACGAAATTTGACTGAGACGGAAAGCTTACCCAGA
66 AGTGAAATTCAACTTACCCAGTAAAAAAATCACGAAATTTGACTGAGACAGAAAGCTTACCCAAA
* *
12529772 TATGCAAAAACTTACCTAGACGGAGATGCTGGAA
131 TATGCAAAAACTTACCCAGACAGAGATGCTGGAA
12529806 GAA
1 GAA
12529809 CTATAAACTC
Statistics
Matches: 153, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
164 153 1.00
ACGTcount: A:0.46, C:0.19, G:0.16, T:0.20
Consensus pattern (164 bp):
GAAGCAAAAGCTCACAAATACCCAAAATCAGTTTCCAAAACTACAAACAAAAATGAAAATTTCAA
AGTGAAATTCAACTTACCCAGTAAAAAAATCACGAAATTTGACTGAGACAGAAAGCTTACCCAAA
TATGCAAAAACTTACCCAGACAGAGATGCTGGAA
Found at i:12531696 original size:18 final size:19
Alignment explanation
Indices: 12531660--12531697 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
12531650 ATTATTAAAA
*
12531660 ATTTTGTATTTAATATATG
1 ATTTTGTATTAAATATATG
*
12531679 ATTTT-TATTAAATTTATG
1 ATTTTGTATTAAATATATG
12531697 A
1 A
12531698 GAAAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (19 bp):
ATTTTGTATTAAATATATG
Found at i:12532555 original size:12 final size:12
Alignment explanation
Indices: 12532540--12532618 Score: 52
Period size: 12 Copynumber: 7.2 Consensus size: 12
12532530 AAATAACTTT
12532540 TTAAATATTATA
1 TTAAATATTATA
12532552 TT--A-ATTA-A
1 TTAAATATTATA
12532560 -TAAAT-TTATA
1 TTAAATATTATA
12532570 TTTTAAATATTATA
1 --TTAAATATTATA
12532584 TTAAA-A--AT-
1 TTAAATATTATA
*
12532592 TTAAATATTATG
1 TTAAATATTATA
*
12532604 TTAAATATTTTA
1 TTAAATATTATA
12532616 TTA
1 TTA
12532619 TAATTTAAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 24
0.67 0.03 0.30
Matches are distributed among these distances:
7 1 0.02
8 6 0.11
9 11 0.21
10 2 0.04
11 3 0.06
12 20 0.38
13 5 0.09
14 5 0.09
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (12 bp):
TTAAATATTATA
Found at i:12532594 original size:20 final size:20
Alignment explanation
Indices: 12532571--12532613 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
12532561 AAATTTATAT
12532571 TTTAAATATTATATTAAAAA
1 TTTAAATATTATATTAAAAA
* *
12532591 TTTAAATATTATGTTAAATA
1 TTTAAATATTATATTAAAAA
12532611 TTT
1 TTT
12532614 TATTATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TTTAAATATTATATTAAAAA
Found at i:12532608 original size:32 final size:33
Alignment explanation
Indices: 12532540--12532630 Score: 109
Period size: 32 Copynumber: 2.8 Consensus size: 33
12532530 AAATAACTTT
* *
12532540 TTAAATATTATATTAATTAA--TAAATTTATATT
1 TTAAATATTATATTAA-TAATTTAAATATATATG
*
12532572 TTAAATATTATATTAAAAATTTAAATAT-TATG
1 TTAAATATTATATTAATAATTTAAATATATATG
*
12532604 TTAAATATTTTATT-ATAATTTAAATAT
1 TTAAATATTATATTAATAATTTAAATAT
12532631 CATTCATGAT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
31 14 0.27
32 32 0.62
33 6 0.12
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (33 bp):
TTAAATATTATATTAATAATTTAAATATATATG
Found at i:12541765 original size:25 final size:27
Alignment explanation
Indices: 12541737--12541791 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
12541727 ACACTTATTT
*
12541737 TATATTATAGTTTTT-TTTATAAAAATA
1 TATATAATA-TTTTTATTTATAAAAATA
*
12541764 TATATAATATTTTTATTTATAAATATA
1 TATATAATATTTTTATTTATAAAAATA
12541791 T
1 T
12541792 GCATGTGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
TATATAATATTTTTATTTATAAAAATA
Found at i:12544253 original size:26 final size:25
Alignment explanation
Indices: 12544213--12544264 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
12544203 GGGGAACATG
12544213 ATGGAAAAATGTTTTTTAAAAGAAA
1 ATGGAAAAATGTTTTTTAAAAGAAA
*
12544238 ATGGAAAAATGTTTTTTATAAGAAA
1 ATGGAAAAATGTTTTTTAAAAGAAA
12544263 AT
1 AT
12544265 ATCACATCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (25 bp):
ATGGAAAAATGTTTTTTAAAAGAAA
Found at i:12547524 original size:13 final size:13
Alignment explanation
Indices: 12547506--12547531 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12547496 GCAGTCGTCC
12547506 AATAAAATCAGAA
1 AATAAAATCAGAA
12547519 AATAAAATCAGAA
1 AATAAAATCAGAA
12547532 GAAATAGATT
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:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (13 bp):
AATAAAATCAGAA
Found at i:12549067 original size:2 final size:2
Alignment explanation
Indices: 12549055--12549088 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
12549045 TTGTGATTTC
*
12549055 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12549089 ACTTTTACCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:12549532 original size:26 final size:26
Alignment explanation
Indices: 12549496--12549547 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
12549486 TTTTTTCCTT
*
12549496 AGTAAAGATATTATTAGAGGTAGCAA
1 AGTAAAGATATAATTAGAGGTAGCAA
12549522 AGTAAAGATATAATTAGAGGTAGCAA
1 AGTAAAGATATAATTAGAGGTAGCAA
12549548 GTTTTTTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.48, C:0.04, G:0.23, T:0.25
Consensus pattern (26 bp):
AGTAAAGATATAATTAGAGGTAGCAA
Found at i:12556598 original size:21 final size:20
Alignment explanation
Indices: 12556574--12556614 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
12556564 AACTATTTGA
12556574 ATTAAAAAATAAAATTAATAT
1 ATTAAAAAA-AAAATTAATAT
* *
12556595 ATTAAAATAAAAATTTATAT
1 ATTAAAAAAAAAATTAATAT
12556615 TATATATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
ATTAAAAAAAAAATTAATAT
Found at i:12556615 original size:18 final size:18
Alignment explanation
Indices: 12556579--12556616 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
12556569 TTTGAATTAA
12556579 AAAATAAAATTAATATATT
1 AAAATAAAATT-ATATATT
12556598 AAAATAAAAATT-TATATT
1 AAAAT-AAAATTATATATT
12556616 A
1 A
12556617 TATATAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 5 0.28
20 6 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATAAAATTATATATT
Found at i:12557523 original size:29 final size:30
Alignment explanation
Indices: 12557491--12557586 Score: 78
Period size: 29 Copynumber: 3.3 Consensus size: 30
12557481 TTAAAAAAGT
*
12557491 TTTTAAATTATTTTATT-TATTTAAATAAA
1 TTTTATATTATTTTATTATATTTAAATAAA
* * *
12557520 TTTT-TA-TATTTTTATTGTGTTTAAATATA
1 TTTTATATTA-TTTTATTATATTTAAATAAA
*
12557549 TTCTTATATT-TTGTT-TTATATTCAAATAAA
1 TT-TTATATTATT-TTATTATATTTAAATAAA
12557579 TTTT-TATT
1 TTTTATATT
12557587 TCAAATGAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
27 2 0.04
28 12 0.22
29 18 0.33
30 17 0.31
31 4 0.07
32 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.62
Consensus pattern (30 bp):
TTTTATATTATTTTATTATATTTAAATAAA
Found at i:12557589 original size:17 final size:19
Alignment explanation
Indices: 12557562--12557597 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
12557552 TTATATTTTG
12557562 TTTTATATTCAAAT-AAAT
1 TTTTATATTCAAATGAAAT
12557580 TTTTAT-TTCAAATGAAAT
1 TTTTATATTCAAATGAAAT
12557598 AATGATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.50
Consensus pattern (19 bp):
TTTTATATTCAAATGAAAT
Found at i:12559867 original size:18 final size:17
Alignment explanation
Indices: 12559834--12559866 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12559824 ACTTTTTGTT
12559834 AAAAAAATAAATAAAAG
1 AAAAAAATAAATAAAAG
12559851 AAAAGAAAT-AATAAAA
1 AAAA-AAATAAATAAAA
12559867 AAATTTTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (17 bp):
AAAAAAATAAATAAAAG
Found at i:12563821 original size:21 final size:20
Alignment explanation
Indices: 12563791--12563830 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12563781 TTAAATTTTT
*
12563791 AGAAAAAATAAATAAGAAAAG
1 AGAAAAAAT-AATAAAAAAAG
*
12563812 AGAAATAATAATAAAAAAA
1 AGAAAAAATAATAAAAAAA
12563831 TAGCTTTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (20 bp):
AGAAAAAATAATAAAAAAAG
Found at i:12565805 original size:20 final size:20
Alignment explanation
Indices: 12565780--12565819 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
12565770 TGCTTATGAT
12565780 AATACACAACAGAAAGTCAC
1 AATACACAACAGAAAGTCAC
12565800 AATACACAACAGAAAGTCAC
1 AATACACAACAGAAAGTCAC
12565820 TATTGTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.25, G:0.10, T:0.10
Consensus pattern (20 bp):
AATACACAACAGAAAGTCAC
Found at i:12570237 original size:23 final size:23
Alignment explanation
Indices: 12570211--12570259 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
12570201 TGAGAACTTC
* * *
12570211 ATTTATTTGGTTTTAGAGAGAGA
1 ATTTATCTAGTTTTAGAAAGAGA
12570234 ATTTATCTAGTTTTAGAAAGAGA
1 ATTTATCTAGTTTTAGAAAGAGA
12570257 ATT
1 ATT
12570260 AATTGATGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.20, T:0.43
Consensus pattern (23 bp):
ATTTATCTAGTTTTAGAAAGAGA
Found at i:12571260 original size:18 final size:18
Alignment explanation
Indices: 12571230--12571274 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
12571220 TAAAATCTTC
12571230 TATATTTTT-TAATTTTG
1 TATATTTTTATAATTTTG
* *
12571247 TATTTTTTTATAATTTTT
1 TATATTTTTATAATTTTG
12571265 TATATTTTTA
1 TATATTTTTA
12571275 ATATTCAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (18 bp):
TATATTTTTATAATTTTG
Found at i:12571263 original size:10 final size:9
Alignment explanation
Indices: 12571230--12571279 Score: 59
Period size: 8 Copynumber: 5.7 Consensus size: 9
12571220 TAAAATCTTC
12571230 TATATTTTT
1 TATATTTTT
*
12571239 TA-ATTTTG
1 TATATTTTT
12571247 TAT-TTTTT
1 TATATTTTT
12571255 TATAATTTTT
1 TAT-ATTTTT
12571265 TATATTTTT
1 TATATTTTT
*
12571274 AATATT
1 TATATT
12571280 CAAATGAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
8 14 0.40
9 13 0.37
10 8 0.23
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (9 bp):
TATATTTTT
Found at i:12571473 original size:19 final size:21
Alignment explanation
Indices: 12571445--12571488 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
12571435 AGCAAGATAA
12571445 AAAATGTATAAA-T-TTTTTT
1 AAAATGTATAAACTCTTTTTT
*
12571464 AAAATTTATAAACTCTTTTTT
1 AAAATGTATAAACTCTTTTTT
12571485 AAAA
1 AAAA
12571489 CATAAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.50
20 1 0.05
21 10 0.45
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (21 bp):
AAAATGTATAAACTCTTTTTT
Found at i:12571510 original size:28 final size:28
Alignment explanation
Indices: 12571463--12571516 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
12571453 TAAATTTTTT
* *
12571463 TAAAATTTATAAACTCTTTTTTAAAACA
1 TAAAATTTATAAAATCTTTTCTAAAACA
12571491 TAAAATATTATAAAAT-TTTTCTAAAA
1 TAAAAT-TTATAAAATCTTTTCTAAAA
12571517 AAACATAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (28 bp):
TAAAATTTATAAAATCTTTTCTAAAACA
Found at i:12571517 original size:29 final size:28
Alignment explanation
Indices: 12571463--12571517 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
12571453 TAAATTTTTT
* *
12571463 TAAAATTTATAAACTCTTTTTTAAAACA
1 TAAAATTTATAAAATCTTTTTAAAAACA
12571491 TAAAATATTATAAAAT-TTTTCTAAAAA
1 TAAAAT-TTATAAAATCTTTT-TAAAAA
12571518 AACATAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (28 bp):
TAAAATTTATAAAATCTTTTTAAAAACA
Found at i:12576499 original size:13 final size:13
Alignment explanation
Indices: 12576469--12576500 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
12576459 TAGGAATAGT
12576469 TTCTCTGTTACCC
1 TTCTCTGTTACCC
12576482 -T-TCTGTTACCC
1 TTCTCTGTTACCC
12576493 TTCTCTGT
1 TTCTCTGT
12576501 ATTTTGTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
11 10 0.59
12 2 0.12
13 5 0.29
ACGTcount: A:0.06, C:0.34, G:0.09, T:0.50
Consensus pattern (13 bp):
TTCTCTGTTACCC
Found at i:12586587 original size:26 final size:26
Alignment explanation
Indices: 12586538--12586610 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
12586528 TATTAATATA
12586538 ATTATT-AAA-ATATTAAAAATTATTT
1 ATTATTCAAATATATT-AAAATTATTT
* *
12586563 ATTGTTGAAATATATTAAAATTATTT
1 ATTATTCAAATATATTAAAATTATTT
*
12586589 ATTATTCAAAT-TATTAATATTA
1 ATTATTCAAATATATTAAAATTA
12586611 AAATATTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
25 15 0.36
26 22 0.52
27 5 0.12
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (26 bp):
ATTATTCAAATATATTAAAATTATTT
Found at i:12586591 original size:13 final size:14
Alignment explanation
Indices: 12586573--12586624 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 14
12586563 ATTGTTGAAA
12586573 TATATTAAAATTATT
1 TATATTAAAATTA-T
*
12586588 TATTATTCAAATTAT
1 TA-TATTAAAATTAT
12586603 TAATATTAAAA-TAT
1 T-ATATTAAAATTAT
12586617 TATATTAA
1 TATATTAA
12586625 TATAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 7 0.21
14 4 0.12
15 11 0.33
16 11 0.33
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATTAAAATTAT
Found at i:12586680 original size:28 final size:28
Alignment explanation
Indices: 12586642--12586724 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 28
12586632 ATACTTTAAA
12586642 TAAAACTATTTATTTTTATATTAATATT-T
1 TAAAA-TATTTA-TTTTATATTAATATTCT
*** *
12586671 TAAAATATTTAAAATAGTATTACTATTCT
1 TAAAATATTTATTTTA-TATTAATATTCT
12586700 TAAAATA-TTATTTT-TATTAATATTC
1 TAAAATATTTATTTTATATTAATATTC
12586725 AAATAGTAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
26 10 0.23
27 2 0.05
28 19 0.43
29 13 0.30
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.53
Consensus pattern (28 bp):
TAAAATATTTATTTTATATTAATATTCT
Found at i:12586763 original size:17 final size:16
Alignment explanation
Indices: 12586732--12586774 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
12586722 TTCAAATAGT
12586732 AATATTTAT-TATTAA
1 AATATTTATATATTAA
*
12586747 GATATTTATACTATTAA
1 AATATTTATA-TATTAA
*
12586764 AATAGTTATAT
1 AATATTTATAT
12586775 TTTATATTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 8 0.35
16 1 0.04
17 14 0.61
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (16 bp):
AATATTTATATATTAA
Found at i:12588258 original size:33 final size:34
Alignment explanation
Indices: 12588208--12588286 Score: 106
Period size: 34 Copynumber: 2.3 Consensus size: 34
12588198 TAATTATAGG
* *
12588208 AAATGAATTTTTGAAAAATTTTAAGAT-TTCTCAA
1 AAATAAATTTTTAAAAAATTTTAAGATGTT-TCAA
* *
12588242 AAATAAATTTTTAAAAAATTTTAGGATGTTTTAA
1 AAATAAATTTTTAAAAAATTTTAAGATGTTTCAA
12588276 AAATAAATTTT
1 AAATAAATTTT
12588287 CGAGAAGTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 38 0.95
35 2 0.05
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.43
Consensus pattern (34 bp):
AAATAAATTTTTAAAAAATTTTAAGATGTTTCAA
Found at i:12588357 original size:35 final size:34
Alignment explanation
Indices: 12588307--12588386 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
12588297 TAGGGTTTTG
* * *
12588307 AATTATTGAAAAATTTTAAGACTTCTTGA-AAATT
1 AATTTTTGAAAAAATTTAA-AATTCTTGATAAATT
* *
12588341 AATTTTTGAAAAAATTTAAAATTTTTTATAAATT
1 AATTTTTGAAAAAATTTAAAATTCTTGATAAATT
12588375 AATTTTTGAAAA
1 AATTTTTGAAAA
12588387 GCTCAAATAC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 6 0.15
34 34 0.85
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (34 bp):
AATTTTTGAAAAAATTTAAAATTCTTGATAAATT
Found at i:12588359 original size:17 final size:16
Alignment explanation
Indices: 12588335--12588386 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 16
12588325 AGACTTCTTG
12588335 AAAATTAATTTTTGAA
1 AAAATTAATTTTTGAA
*
12588351 AAAATTTAAAATTTTT-TA
1 AAAA-TT--AATTTTTGAA
*
12588369 TAAATTAATTTTTGAA
1 AAAATTAATTTTTGAA
12588385 AA
1 AA
12588387 GCTCAAATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
15 7 0.25
16 6 0.21
17 4 0.14
18 4 0.14
19 7 0.25
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (16 bp):
AAAATTAATTTTTGAA
Found at i:12589531 original size:20 final size:19
Alignment explanation
Indices: 12589506--12589544 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
12589496 TCGTTTGGAG
12589506 ATGTTTTCT-TTTTGTGTTTT
1 ATGTTTT-TGTTTT-TGTTTT
12589526 ATGTTTTTGTTTTTGTTTT
1 ATGTTTTTGTTTTTGTTTT
12589545 TTTAGAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.05, C:0.03, G:0.15, T:0.77
Consensus pattern (19 bp):
ATGTTTTTGTTTTTGTTTT
Found at i:12590848 original size:16 final size:16
Alignment explanation
Indices: 12590816--12590861 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
12590806 AATATATATA
*
12590816 TAATTTTATTCGA-TT
1 TAATTTTTTTCGATTT
12590831 TAATTTTTTTCGATTT
1 TAATTTTTTTCGATTT
*
12590847 TAAATTTTTT-GATTT
1 TAATTTTTTTCGATTT
12590862 GAACCTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.24, C:0.04, G:0.07, T:0.65
Consensus pattern (16 bp):
TAATTTTTTTCGATTT
Found at i:12591013 original size:2 final size:2
Alignment explanation
Indices: 12591001--12591053 Score: 56
Period size: 2 Copynumber: 27.5 Consensus size: 2
12590991 CATCTCCACT
* * *
12591001 TA TA TA AA TA TA TA TA TG TA TA T- TA -A TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
12591041 TA TA TA AA TA TA T
1 TA TA TA TA TA TA T
12591054 CATGGTCAAC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:12593668 original size:22 final size:22
Alignment explanation
Indices: 12593642--12593691 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
12593632 ATAATAAAAC
12593642 TTATCACCAATTGATAATTAAG
1 TTATCACCAATTGATAATTAAG
* * * *
12593664 TTATCACTAATTTATTATTATG
1 TTATCACCAATTGATAATTAAG
12593686 TTATCA
1 TTATCA
12593692 GTGATTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (22 bp):
TTATCACCAATTGATAATTAAG
Found at i:12593698 original size:22 final size:22
Alignment explanation
Indices: 12593658--12593733 Score: 98
Period size: 22 Copynumber: 3.5 Consensus size: 22
12593648 CCAATTGATA
*
12593658 ATTAAGTTATCACTAATTTATT
1 ATTAAGTTATCAATAATTTATT
* * *
12593680 ATTATGTTATCAGTGATTTATT
1 ATTAAGTTATCAATAATTTATT
* *
12593702 ATTAAATTATCAATAATTTAAT
1 ATTAAGTTATCAATAATTTATT
12593724 ATTAAGTTAT
1 ATTAAGTTAT
12593734 GAATGATTAC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (22 bp):
ATTAAGTTATCAATAATTTATT
Found at i:12593741 original size:44 final size:44
Alignment explanation
Indices: 12593658--12593741 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 44
12593648 CCAATTGATA
* * * * *
12593658 ATTAAGTTATCACTAATTTATTATTATGTTATCAGTGATTTATT
1 ATTAAATTATCAATAATTTAATATTAAGTTATCAATGATTTATT
*
12593702 ATTAAATTATCAATAATTTAATATTAAGTTATGAATGATT
1 ATTAAATTATCAATAATTTAATATTAAGTTATCAATGATT
12593742 ACTAAGTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (44 bp):
ATTAAATTATCAATAATTTAATATTAAGTTATCAATGATTTATT
Found at i:12593825 original size:30 final size:30
Alignment explanation
Indices: 12593772--12593831 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
12593762 TTATAAATTA
* *
12593772 TAACTAATTTTCTATGAAGTTATCAATGAT
1 TAACTAATTTACTATGAAATTATCAATGAT
*
12593802 TAACTAATTTACTACT-AAATTATCATTGAT
1 TAACTAATTTACTA-TGAAATTATCAATGAT
12593832 ATGTAACTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (30 bp):
TAACTAATTTACTATGAAATTATCAATGAT
Found at i:12593909 original size:42 final size:44
Alignment explanation
Indices: 12593808--12593923 Score: 116
Period size: 42 Copynumber: 2.7 Consensus size: 44
12593798 TGATTAACTA
* * *
12593808 ATTTACTACTAAATTATCATTGATATGTA--ACTAAATTATAAGTG
1 ATTTACTACTATATTATTATTGAT-T-TACTACTAAATTACAAGTG
** *
12593852 ATTTGTTAGTATATTATTATTGATTTACTACTAAATT-CAA-TG
1 ATTTACTACTATATTATTATTGATTTACTACTAAATTACAAGTG
12593894 ATTTACTACTATATTATTA-TGCATTTACTA
1 ATTTACTACTATATTATTATTG-ATTTACTA
12593924 ATTACCATTG
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
41 2 0.03
42 28 0.47
43 3 0.05
44 27 0.45
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (44 bp):
ATTTACTACTATATTATTATTGATTTACTACTAAATTACAAGTG
Found at i:12594535 original size:22 final size:22
Alignment explanation
Indices: 12594450--12594535 Score: 73
Period size: 22 Copynumber: 3.9 Consensus size: 22
12594440 AATCAGCTAT
* *
12594450 TAAGTTATCAATTATTTACTAC
1 TAAGTTATCAATGAATTACTAC
* *
12594472 TAAATTATTAATTGAATTACTAC
1 TAAGTTATCAA-TGAATTACTAC
** * *
12594495 TAAGTTATTTATGATTTACTAT
1 TAAGTTATCAATGAATTACTAC
* *
12594517 TAATTTATCAATAAATTAC
1 TAAGTTATCAATGAATTAC
12594536 AATATATGAG
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
22 32 0.64
23 18 0.36
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.47
Consensus pattern (22 bp):
TAAGTTATCAATGAATTACTAC
Found at i:12594792 original size:22 final size:21
Alignment explanation
Indices: 12594774--12594938 Score: 120
Period size: 22 Copynumber: 7.5 Consensus size: 21
12594764 ATCTTATCAC
*
12594774 TAATTTACTACTAAATTATGA
1 TAATTTACTACTAAATTATAA
12594795 TCAATTTA-TCACTAAATTATATA
1 T-AATTTACT-ACTAAATTATA-A
* * *
12594818 TGATTTACTTCTAAGTTATAAA
1 TAATTTACTACTAAATTAT-AA
* * *
12594840 TGATTTACTAATAAATTATTGA
1 TAATTTACTACTAAATTA-TAA
* *
12594862 TAATTTACTATTAAGTTATAAA
1 TAATTTACTACTAAATTAT-AA
* *
12594884 TAATTTATTA-TAAAGTTATTAC
1 TAATTTACTACTAAA-TTA-TAA
12594906 TAATTTACTA-TAAAATTATTAA
1 TAATTTACTACT-AAATTA-TAA
12594928 TAATTTACTAC
1 TAATTTACTAC
12594939 GAGTTATTAA
Statistics
Matches: 116, Mismatches: 17, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
21 6 0.05
22 101 0.87
23 9 0.08
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.45
Consensus pattern (21 bp):
TAATTTACTACTAAATTATAA
Found at i:12594846 original size:44 final size:45
Alignment explanation
Indices: 12594774--12594934 Score: 140
Period size: 44 Copynumber: 3.6 Consensus size: 45
12594764 ATCTTATCAC
* * * *
12594774 TAATTTACTACTAAATTAT-GATCAATTTATC-ACTAAATTATAT-A
1 TAATTTACTATTAAGTTATAAAT-AATTTATCTAATAAATTAT-TGA
* *
12594818 TGATTTACT-TCTAAGTTATAAATGATTTA-CTAATAAATTATTGA
1 TAATTTACTAT-TAAGTTATAAATAATTTATCTAATAAATTATTGA
12594862 TAATTTACTATTAAGTTATAAATAATTTAT-T-ATAAAGTTATT-A
1 TAATTTACTATTAAGTTATAAATAATTTATCTAATAAA-TTATTGA
* * *
12594905 CTAATTTACTATAAAATTATTAATAATTTA
1 -TAATTTACTATTAAGTTATAAATAATTTA
12594935 CTACGAGTTA
Statistics
Matches: 98, Mismatches: 11, Indels: 16
0.78 0.09 0.13
Matches are distributed among these distances:
43 8 0.08
44 87 0.89
45 3 0.03
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (45 bp):
TAATTTACTATTAAGTTATAAATAATTTATCTAATAAATTATTGA
Found at i:12594890 original size:66 final size:66
Alignment explanation
Indices: 12594774--12594938 Score: 176
Period size: 66 Copynumber: 2.5 Consensus size: 66
12594764 ATCTTATCAC
* * * *
12594774 TAATTTACTACTAAATTA-TGATCAATTTA-TCACTAAATTATATATGATTTACTTCT-AAGTTA
1 TAATTTACTAATAAATTATTGAT-AATTTACT-ACTAAATTATAAATAATTTA-TTATAAAGTTA
12594836 TAAA
63 TAAA
* * * *
12594840 TGATTTACTAATAAATTATTGATAATTTACTATTAAGTTATAAATAATTTATTATAAAGTTATTA
1 TAATTTACTAATAAATTATTGATAATTTACTACTAAATTATAAATAATTTATTATAAAGTTATAA
*
12594905 C
66 A
*
12594906 TAATTTACT-ATAAAATTATTAATAATTTACTAC
1 TAATTTACTAAT-AAATTATTGATAATTTACTAC
12594939 GAGTTATTAA
Statistics
Matches: 83, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
65 5 0.06
66 73 0.88
67 5 0.06
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.45
Consensus pattern (66 bp):
TAATTTACTAATAAATTATTGATAATTTACTACTAAATTATAAATAATTTATTATAAAGTTATAA
A
Found at i:12595041 original size:22 final size:22
Alignment explanation
Indices: 12594959--12595591 Score: 179
Period size: 22 Copynumber: 29.0 Consensus size: 22
12594949 TAATTAACTA
* * * *
12594959 ATTTACAACTAAATTATCATTA
1 ATTTACTATTAAATTATCAATG
* *
12594981 ATTTA-TAATTAAATTATCACTA
1 ATTTACT-ATTAAATTATCAATG
** *
12595003 ATTTAC-AGCCAAGTTATCAATG
1 ATTTACTA-TTAAATTATCAATG
* * * *
12595025 ATTTACTATGACATTATTAGTG
1 ATTTACTATTAAATTATCAATG
* *
12595047 ATTT-CTTTTAAATTATCAATA
1 ATTTACTATTAAATTATCAATG
12595068 ATTTACTATTAAATTATCAATG
1 ATTTACTATTAAATTATCAATG
**
12595090 ATTTACTATATATTGTTATC--T-
1 ATTTACTAT-TA-AATTATCAATG
* *** * *
12595111 ATTTGCTATTATGGTATCATTA
1 ATTTACTATTAAATTATCAATG
* * * *
12595133 ATTTACTATTGAGTT-TTAGTG
1 ATTTACTATTAAATTATCAATG
* * *
12595154 ATTAACTAATAAATTATCATTG
1 ATTTACTATTAAATTATCAATG
* ** * **
12595176 ATTTATTGCTAAGTTATTTATG
1 ATTTACTATTAAATTATCAATG
* * *
12595198 ATTTACTACTAAGTTTAT-AATTT
1 ATTTACTATTAA-ATTATCAA-TG
* * *
12595221 AATTACTATTAAACTAAAACAA--
1 ATTTACTATTAAA-T-TATCAATG
* * ** *
12595243 ATTTACTGTTAAGTTATCTGTA
1 ATTTACTATTAAATTATCAATG
* * * *
12595265 ATTTACTACTAAAATT-TTATTA
1 ATTTACTA-TTAAATTATCAATG
12595287 ATTTACTATTAAATTATCAATG
1 ATTTACTATTAAATTATCAATG
* * * *
12595309 ATTAACTATTAAGTTATCATTT
1 ATTTACTATTAAATTATCAATG
** * * *
12595331 ATTTTTTATTAAGTTAT-TATT
1 ATTTACTATTAAATTATCAATG
* * *** *
12595352 AATTACTACTATGCTAT-TATG
1 ATTTACTATTAAATTATCAATG
**
12595373 CATTTA-TAGTTATGTTAT-AATTG
1 -ATTTACTA-TTAAATTATCAA-TG
* *
12595396 ATTTACTATTAAGTTAT-TATG
1 ATTTACTATTAAATTATCAATG
* *
12595417 CATTTACTATTAAATTATTATTG
1 -ATTTACTATTAAATTATCAATG
* * *
12595440 ATTTACTACTAAGTTATCAATT
1 ATTTACTATTAAATTATCAATG
* * * * *
12595462 ATTAATTATTAAATTATTATTA
1 ATTTACTATTAAATTATCAATG
* * * *
12595484 ATATACTATTAAGTTATCACTA
1 ATTTACTATTAAATTATCAATG
*
12595506 ATTTACTATATTAAATTATCATTG
1 ATTTAC--TATTAAATTATCAATG
* *
12595530 ATTAACTATTAATTTATCAATG
1 ATTTACTATTAAATTATCAATG
* *
12595552 A-TTACTATTAAGTTAT-ATTG
1 ATTTACTATTAAATTATCAATG
* *
12595572 ATTTACT-TTTAATTTTCAAT
1 ATTTACTATTAAATTATCAAT
12595592 TATTAATTAC
Statistics
Matches: 450, Mismatches: 131, Indels: 61
0.70 0.20 0.10
Matches are distributed among these distances:
19 6 0.01
20 14 0.03
21 86 0.19
22 288 0.64
23 30 0.07
24 24 0.05
25 2 0.00
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (22 bp):
ATTTACTATTAAATTATCAATG
Found at i:12595524 original size:153 final size:152
Alignment explanation
Indices: 12595243--12595655 Score: 378
Period size: 153 Copynumber: 2.7 Consensus size: 152
12595233 ACTAAAACAA
* * * * *
12595243 ATTTACTGTTAAGTTATCTGTAATTTACTACTAAAATT-TTATTAATTTACTATTAAATTATCAA
1 ATTTACTATTAAGTTATATG--ATTTACTA-TTAAATTATTATT-ATTTACTACTAAGTTATCAA
* * * * * * * **
12595307 TGATTAACTATTAAGTTATCATTTATTTTTTATTAAGTTATTATTAATTACTACTATGCTATTAT
62 TTATTAACTATTAAATTATTATTAATTTATTATTAAGTTATCACTAATTACTACTATGAAATTAT
12595372 GCA-T-TT-A-TAGTT-ATGTTAT-AATTG
127 -CATTATTAACTA-TTAAT-TTATCAA-TG
12595396 ATTTACTATTAAGTTATTATGCATTTACTATTAAATTATTATTGATTTACTACTAAGTTATCAAT
1 ATTTACTATTAAGTTA-TATG-ATTTACTATTAAATTATTATT-ATTTACTACTAAGTTATCAAT
* * * *
12595461 TATTAATTATTAAATTATTATTAATATACTATTAAGTTATCACTAATTTACTA-TATTAAATTAT
63 TATTAACTATTAAATTATTATTAATTTATTATTAAGTTATCACTAA-TTACTACTATGAAATTAT
12595525 CATTGATTAACTATTAATTTATCAATG
127 CATT-ATTAACTATTAATTTATCAATG
* * * * *
12595552 A-TTACTATTAAGTTATATTGATTTACTTTTAATTTTCAATTATTAATTACTACTAAGTTCTAAA
1 ATTTACTATTAAGTTATA-TGATTTACTATTAA-ATT--ATTATTATTTACTACTAAGTTATCAA
* *
12595616 TTATTTACTATT-AATTATTATTAGTTTATTATTAAGTTAT
62 TTATTAACTATTAAATTATTATTAATTTATTATTAAGTTAT
12595656 TTATGATTTA
Statistics
Matches: 216, Mismatches: 30, Indels: 26
0.79 0.11 0.10
Matches are distributed among these distances:
152 8 0.04
153 92 0.43
154 22 0.10
155 45 0.21
156 37 0.17
157 12 0.06
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.51
Consensus pattern (152 bp):
ATTTACTATTAAGTTATATGATTTACTATTAAATTATTATTATTTACTACTAAGTTATCAATTAT
TAACTATTAAATTATTATTAATTTATTATTAAGTTATCACTAATTACTACTATGAAATTATCATT
ATTAACTATTAATTTATCAATG
Found at i:12596044 original size:22 final size:23
Alignment explanation
Indices: 12595973--12596062 Score: 82
Period size: 22 Copynumber: 4.1 Consensus size: 23
12595963 TCTTATTTGT
* *
12595973 TATTAAATTATTA-TTAATTTAC
1 TATTAAGTTATCACTTAATTTAC
*
12595995 TACTAAGTTATCA-TTAATTTAC
1 TATTAAGTTATCACTTAATTTAC
*
12596017 TATTAAGTTATCACTT-ATTT-T
1 TATTAAGTTATCACTTAATTTAC
* *
12596038 TATTTAATTTATC-CTTAATTAAC
1 TA-TTAAGTTATCACTTAATTTAC
12596061 TA
1 TA
12596063 CTATCTTGTT
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
21 5 0.09
22 47 0.84
23 4 0.07
ACGTcount: A:0.36, C:0.10, G:0.02, T:0.52
Consensus pattern (23 bp):
TATTAAGTTATCACTTAATTTAC
Found at i:12596158 original size:22 final size:22
Alignment explanation
Indices: 12596098--12596158 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
12596088 TCTATAAATG
*
12596098 ATTTATTATTAAATTATTTGTT
1 ATTTATTATTATATTATTTGTT
** *
12596120 ATTTACGACTATATTATTATG-T
1 ATTTATTATTATATTATT-TGTT
*
12596142 ATTTATTATTATGTTAT
1 ATTTATTATTATATTAT
12596159 CACTAGCATA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
22 28 0.93
23 2 0.07
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.59
Consensus pattern (22 bp):
ATTTATTATTATATTATTTGTT
Found at i:12596247 original size:22 final size:22
Alignment explanation
Indices: 12596177--12596320 Score: 78
Period size: 22 Copynumber: 6.6 Consensus size: 22
12596167 TATAACTATT
*
12596177 TTATCAATT-ATTTACTACTAAA-
1 TTATC-ATTAATTTAATA-TAAAG
* * * *
12596199 TTATTATTTATTTACTATTAAG
1 TTATCATTAATTTAATATAAAG
* * *
12596221 CTATCCTTAATTTAATATACAG
1 TTATCATTAATTTAATATAAAG
*
12596243 TTATCATTGATTTAATATAAAG
1 TTATCATTAATTTAATATAAAG
* * ** * *
12596265 TTATTATTGATTTTGTCTTAA-
1 TTATCATTAATTTAATATAAAG
* * *
12596286 TTATCACTAATTTACTATAAAT
1 TTATCATTAATTTAATATAAAG
*
12596308 TTATCAATAATTT
1 TTATCATTAATTT
12596321 GCTACTATAT
Statistics
Matches: 93, Mismatches: 26, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
21 20 0.22
22 73 0.78
ACGTcount: A:0.36, C:0.10, G:0.04, T:0.50
Consensus pattern (22 bp):
TTATCATTAATTTAATATAAAG
Found at i:12599467 original size:17 final size:17
Alignment explanation
Indices: 12599445--12599478 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
12599435 TTATATTAGA
12599445 AATATTATTAAA-ATATT
1 AATATT-TTAAATATATT
12599462 AATATTTTAAATATATT
1 AATATTTTAAATATATT
12599479 TTAAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AATATTTTAAATATATT
Found at i:12603903 original size:24 final size:24
Alignment explanation
Indices: 12603871--12603917 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
12603861 CTAGTATGAG
12603871 AATCACTTCACTTATCCTTTCTAC
1 AATCACTTCACTTATCCTTTCTAC
*
12603895 AATCACTTCACTTATCTTTTCTA
1 AATCACTTCACTTATCCTTTCTA
12603918 TCTGAGAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.45
Consensus pattern (24 bp):
AATCACTTCACTTATCCTTTCTAC
Found at i:12606213 original size:158 final size:151
Alignment explanation
Indices: 12605936--12606244 Score: 492
Period size: 158 Copynumber: 2.0 Consensus size: 151
12605926 ATCTATCGTG
*
12605936 TCAAAAACATGTCATGAAAATTATTGTATTATACTACATGTCCACATATAAAACATGAATTTTTT
1 TCAAAAACATGTCATGAAAATTATTGTATTATAATACATGTCCACATATAAAACATGAATTTTTT
*
12606001 TTTTGTCAAAATTTTATATTATGATATTTTCATATATTTTTTATATTATTTACCTATCATAATAT
66 TTTTGTCAAAATTTTAAATTATGATATTTTCATATATTTTTTATATTATTTACCTATCATAATAT
12606066 TATATTATGTTTAAAATTATC
131 TATATTATGTTTAAAATTATC
* * *
12606087 TCAAAAACATGTCATTAAAATTATTGTATTATAATACGTGTGCACATATAAAACATGAAAATTTT
1 TCAAAAACATGTCATGAAAATTATTGTATTATAATACATGTCCACATATAAAACATG--AA----
*
12606152 TTTTTATTTTTGTCAAAATTTTAAATTATGATATTTTCATATATTTTTTATATTATTTACCTGTC
60 TTTTT-TTTTTGTCAAAATTTTAAATTATGATATTTTCATATATTTTTTATATTATTTACCTATC
*
12606217 ATAATATTATATTGTGTTTAAAATTATC
124 ATAATATTATATTATGTTTAAAATTATC
12606245 ATAGAAGAAG
Statistics
Matches: 144, Mismatches: 7, Indels: 7
0.91 0.04 0.04
Matches are distributed among these distances:
151 53 0.37
153 2 0.01
157 5 0.03
158 84 0.58
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.48
Consensus pattern (151 bp):
TCAAAAACATGTCATGAAAATTATTGTATTATAATACATGTCCACATATAAAACATGAATTTTTT
TTTTGTCAAAATTTTAAATTATGATATTTTCATATATTTTTTATATTATTTACCTATCATAATAT
TATATTATGTTTAAAATTATC
Found at i:12607885 original size:10 final size:10
Alignment explanation
Indices: 12607866--12607908 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
12607856 ATATTTTCTA
12607866 TTAAAATTTT
1 TTAAAATTTT
12607876 TT-AAA-TTT
1 TTAAAATTTT
*
12607884 TTACAATTTT
1 TTAAAATTTT
12607894 TTGAAAATTTT
1 TT-AAAATTTT
12607905 TTAA
1 TTAA
12607909 TTAATTATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
8 5 0.18
9 5 0.18
10 9 0.32
11 9 0.32
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (10 bp):
TTAAAATTTT
Found at i:12613270 original size:23 final size:22
Alignment explanation
Indices: 12613228--12613291 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
12613218 AAATATAATC
* *
12613228 ATTGA-TAAATAAGTAC-TTTA
1 ATTGATTAAAGAAATACATTTA
12613248 ATTG-TTCAAATGAAATACATTTA
1 ATTGATT-AAA-GAAATACATTTA
*
12613271 TTTGATTAAAGAAATACATTT
1 ATTGATTAAAGAAATACATTT
12613292 CATTCAATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
20 5 0.14
21 3 0.08
22 16 0.44
23 10 0.28
24 2 0.06
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (22 bp):
ATTGATTAAAGAAATACATTTA
Found at i:12615192 original size:57 final size:56
Alignment explanation
Indices: 12615125--12615240 Score: 180
Period size: 57 Copynumber: 2.1 Consensus size: 56
12615115 GCCTACTTAA
* *
12615125 TCATCATTAGAAGTAATAAATTAGAATGTAAAATAAAACA-AATAATTTAGTGTAAAG
1 TCATCATTAGAAGAAATAAATTAGAATGTAAAATAAAA-AGAATAATTTAGTCT-AAG
*
12615182 TCATCTTTAGAAGAAATAAATTAGAATGTAAAATAAAAAGAATAATTTAGTCTAAG
1 TCATCATTAGAAGAAATAAATTAGAATGTAAAATAAAAAGAATAATTTAGTCTAAG
12615238 TCA
1 TCA
12615241 AAACAATATT
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
56 7 0.13
57 48 0.87
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.30
Consensus pattern (56 bp):
TCATCATTAGAAGAAATAAATTAGAATGTAAAATAAAAAGAATAATTTAGTCTAAG
Found at i:12619100 original size:20 final size:20
Alignment explanation
Indices: 12619075--12619114 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
12619065 TGTGATTGTT
12619075 TTGAATGTAGGTATACTTAA
1 TTGAATGTAGGTATACTTAA
12619095 TTGAATGTAGGTATACTTAA
1 TTGAATGTAGGTATACTTAA
12619115 AGGTTCACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.40
Consensus pattern (20 bp):
TTGAATGTAGGTATACTTAA
Found at i:12624051 original size:30 final size:30
Alignment explanation
Indices: 12623987--12624051 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
12623977 CAGCAGCCAC
* * ** * *
12623987 ACCACCCATAATGATCACAGCAGTAGCCAC
1 ACCACCCATAATGACCAAAGCAACAACCAA
12624017 ACCACCCATAATGACCAAAGCAACAACCAA
1 ACCACCCATAATGACCAAAGCAACAACCAA
12624047 ACCAC
1 ACCAC
12624052 TTAGAATGAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.43, C:0.38, G:0.09, T:0.09
Consensus pattern (30 bp):
ACCACCCATAATGACCAAAGCAACAACCAA
Found at i:12624116 original size:33 final size:30
Alignment explanation
Indices: 12624065--12624150 Score: 86
Period size: 30 Copynumber: 2.8 Consensus size: 30
12624055 GAATGACCAT
*
12624065 AGCAGTAG-CAAGCCACCTACAATGACTAGCA
1 AGCAGCAGCCAAGCCACCTACAATGA-TAG-A
* * *
12624096 CAGCAGCAGCCAAGCTACCTATAATGATTGA
1 -AGCAGCAGCCAAGCCACCTACAATGATAGA
12624127 AGCCA-CAGCCAAGCCACCTACAAT
1 AG-CAGCAGCCAAGCCACCTACAAT
12624151 AACCACAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
30 19 0.41
31 3 0.07
32 9 0.20
33 15 0.33
ACGTcount: A:0.37, C:0.31, G:0.17, T:0.14
Consensus pattern (30 bp):
AGCAGCAGCCAAGCCACCTACAATGATAGA
Found at i:12624167 original size:30 final size:30
Alignment explanation
Indices: 12624133--12624227 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 30
12624123 TTGAAGCCAC
* *
12624133 AGCCAAGCCACCTACAATAACCACAA-TTGT
1 AGCCAAGCCACCTATAATAACCA-AAGTAGT
* *
12624163 AGCCAAGTCACCTATAATGACCAAAGTAGT
1 AGCCAAGCCACCTATAATAACCAAAGTAGT
* * *
12624193 AGCCAAGCCACCCATAATAACCAGAGCAGT
1 AGCCAAGCCACCTATAATAACCAAAGTAGT
12624223 AGCCA
1 AGCCA
12624228 CACCACTTAC
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 2 0.04
30 53 0.96
ACGTcount: A:0.40, C:0.31, G:0.15, T:0.15
Consensus pattern (30 bp):
AGCCAAGCCACCTATAATAACCAAAGTAGT
Found at i:12628061 original size:42 final size:39
Alignment explanation
Indices: 12628005--12628106 Score: 105
Period size: 42 Copynumber: 2.5 Consensus size: 39
12627995 TATGTAAATA
* *
12628005 TTAATAAAATTATTATTTAATACTTTAATTTAAAATATTAAT
1 TTAATAAAAATATTATTTAATA-TATAA-TTAAAATA-TAAT
* *
12628047 TTAATAAAAATATTATATTTATATATAATTGAAATATAAT
1 TTAATAAAAATATTAT-TTAATATATAATTAAAATATAAT
*
12628087 TTATATTAAAAATAATATTT
1 TTA-A-TAAAAATATTATTT
12628107 TATGAATATA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
40 7 0.13
41 10 0.19
42 30 0.58
43 5 0.10
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (39 bp):
TTAATAAAAATATTATTTAATATATAATTAAAATATAAT
Found at i:12628109 original size:41 final size:42
Alignment explanation
Indices: 12628037--12628118 Score: 107
Period size: 41 Copynumber: 2.0 Consensus size: 42
12628027 CTTTAATTTA
*
12628037 AAATATTAATTTAATAAAAATATTATATTTAT-ATATAATTG
1 AAATATTAATTTAATAAAAATAATATATTTATAATATAATTG
12628078 AAATA-TAATTTATATTAAAAATAATAT-TTTATGAATATAAT
1 AAATATTAATTTA-A-TAAAAATAATATATTTAT-AATATAAT
12628119 ACTAAATTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
40 7 0.19
41 11 0.31
42 11 0.31
43 7 0.19
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (42 bp):
AAATATTAATTTAATAAAAATAATATATTTATAATATAATTG
Found at i:12630676 original size:199 final size:199
Alignment explanation
Indices: 12630336--12630739 Score: 808
Period size: 199 Copynumber: 2.0 Consensus size: 199
12630326 ATTCATCTAC
12630336 TTCCATCACAAATGAACCAAAATTATCTCTTCAAAATGCCAATCAAACCAATTTGAAACTAAACT
1 TTCCATCACAAATGAACCAAAATTATCTCTTCAAAATGCCAATCAAACCAATTTGAAACTAAACT
12630401 CATTACAATCAGCCCTAAAATATTGTCCATTATTCTTGGAAAAGGAAACATAAAATATATTCCAA
66 CATTACAATCAGCCCTAAAATATTGTCCATTATTCTTGGAAAAGGAAACATAAAATATATTCCAA
12630466 AAAATCAAATCAGGACTCAATTAAAAATTAAGCAAAAGTTACGGAGTTTGACATAAATAAAGCAA
131 AAAATCAAATCAGGACTCAATTAAAAATTAAGCAAAAGTTACGGAGTTTGACATAAATAAAGCAA
12630531 ACCT
196 ACCT
12630535 TTCCATCACAAATGAACCAAAATTATCTCTTCAAAATGCCAATCAAACCAATTTGAAACTAAACT
1 TTCCATCACAAATGAACCAAAATTATCTCTTCAAAATGCCAATCAAACCAATTTGAAACTAAACT
12630600 CATTACAATCAGCCCTAAAATATTGTCCATTATTCTTGGAAAAGGAAACATAAAATATATTCCAA
66 CATTACAATCAGCCCTAAAATATTGTCCATTATTCTTGGAAAAGGAAACATAAAATATATTCCAA
12630665 AAAATCAAATCAGGACTCAATTAAAAATTAAGCAAAAGTTACGGAGTTTGACATAAATAAAGCAA
131 AAAATCAAATCAGGACTCAATTAAAAATTAAGCAAAAGTTACGGAGTTTGACATAAATAAAGCAA
12630730 ACCT
196 ACCT
12630734 TTCCAT
1 TTCCAT
12630740 ACCTGTTCAT
Statistics
Matches: 205, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
199 205 1.00
ACGTcount: A:0.46, C:0.19, G:0.09, T:0.26
Consensus pattern (199 bp):
TTCCATCACAAATGAACCAAAATTATCTCTTCAAAATGCCAATCAAACCAATTTGAAACTAAACT
CATTACAATCAGCCCTAAAATATTGTCCATTATTCTTGGAAAAGGAAACATAAAATATATTCCAA
AAAATCAAATCAGGACTCAATTAAAAATTAAGCAAAAGTTACGGAGTTTGACATAAATAAAGCAA
ACCT
Found at i:12639564 original size:26 final size:26
Alignment explanation
Indices: 12639517--12639566 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
12639507 TTTAGATAAA
**
12639517 ATTTATAAAATATTTTCTTAAAAATT
1 ATTTATAAAATATTTTAATAAAAATT
12639543 ATTTAATAAAA-ATTTTAATAAAAA
1 ATTT-ATAAAATATTTTAATAAAAA
12639567 ATATAAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
ATTTATAAAATATTTTAATAAAAATT
Found at i:12640109 original size:22 final size:21
Alignment explanation
Indices: 12640083--12640130 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
12640073 TTTTTGTTAA
*
12640083 AATATTAAATTATATATTTTTT
1 AATATT-AATTATATAATTTTT
*
12640105 AATATT-TTTATATAATTTTT
1 AATATTAATTATATAATTTTT
12640125 -ATATTA
1 AATATTA
12640131 TATATTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 5 0.22
20 12 0.52
22 6 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
AATATTAATTATATAATTTTT
Found at i:12640117 original size:20 final size:19
Alignment explanation
Indices: 12640092--12640129 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
12640082 AAATATTAAA
*
12640092 TTATATATTTTTTAATATTT
1 TTATATAATTTTT-ATATTT
12640112 TTATATAATTTTTATATT
1 TTATATAATTTTTATATT
12640130 ATATATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATATAATTTTTATATTT
Found at i:12640122 original size:11 final size:11
Alignment explanation
Indices: 12640092--12640128 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
12640082 AAATATTAAA
*
12640092 TTATATATTTT
1 TTATATAATTT
12640103 TTA-AT-ATTT
1 TTATATAATTT
12640112 TTATATAATTT
1 TTATATAATTT
12640123 TTATAT
1 TTATAT
12640129 TATATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
9 6 0.26
10 4 0.17
11 13 0.57
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATATAATTT
Found at i:12641544 original size:23 final size:20
Alignment explanation
Indices: 12641502--12641550 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 20
12641492 TCAAATAGAG
12641502 TATTTTAATAAATATAAAATT
1 TATTTTAATAAATATAAAA-T
*
12641523 TATTTTAATTAATTTATAAAAT
1 TATTTTAA-TAA-ATATAAAAT
12641545 TATTTT
1 TATTTT
12641551 TAAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 8 0.32
22 10 0.40
23 7 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTTTAATAAATATAAAAT
Found at i:12641550 original size:22 final size:21
Alignment explanation
Indices: 12641502--12641559 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 21
12641492 TCAAATAGAG
12641502 TATTTTAATAAATATAAAATT
1 TATTTTAATAAATATAAAATT
*
12641523 TATTTTAATTAATTTATAAAA-T
1 TATTTTAA-TAA-ATATAAAATT
*
12641545 TATTTTTAAAAAATA
1 TA-TTTTAATAAATA
12641560 ATATTCAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 10 0.32
22 8 0.26
23 13 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATTTTAATAAATATAAAATT
Found at i:12642841 original size:20 final size:19
Alignment explanation
Indices: 12642816--12642884 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 19
12642806 CTTGTTAGTG
*
12642816 TTAAAAATTTTTAAAGAATT
1 TTAAAAA-TTTTAAAAAATT
12642836 TTAAAAATTTTAAAAAATTT
1 TTAAAAATTTTAAAAAA-TT
* * * *
12642856 TTAAAACAATCTACAATATT
1 TTAAAA-ATTTTAAAAAATT
12642876 TTAAAAATT
1 TTAAAAATT
12642885 CAAAATATTG
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
19 11 0.27
20 23 0.56
21 7 0.17
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.42
Consensus pattern (19 bp):
TTAAAAATTTTAAAAAATT
Found at i:12642846 original size:9 final size:9
Alignment explanation
Indices: 12642816--12642964 Score: 67
Period size: 9 Copynumber: 16.4 Consensus size: 9
12642806 CTTGTTAGTG
12642816 TTAAAAATTT
1 TTAAAAA-TT
12642826 TTAAAGAATT
1 TTAAA-AATT
12642836 TTAAAAATT
1 TTAAAAATT
12642845 TTAAAAAATTT
1 TT-AAAAA-TT
*
12642856 TTAAAACAAT
1 TTAAAA-ATT
* *
12642866 CTACAATATT
1 TTA-AAAATT
12642876 TTAAAAA--
1 TTAAAAATT
*
12642883 TTCAAAATAT
1 TTAAAAAT-T
* *
12642893 TGAAATATT
1 TTAAAAATT
*
12642902 TTTAAAATT
1 TTAAAAATT
*
12642911 ATAAAAA--
1 TTAAAAATT
*
12642918 TTAAAATTT
1 TTAAAAATT
* *
12642927 TTGAGAA-T
1 TTAAAAATT
*
12642935 TTAAAATTT
1 TTAAAAATT
12642944 TTAAAAA-T
1 TTAAAAATT
* *
12642952 GTATAAATT
1 TTAAAAATT
12642961 TTAA
1 TTAA
12642965 TAAAAATCTA
Statistics
Matches: 99, Mismatches: 28, Indels: 25
0.65 0.18 0.16
Matches are distributed among these distances:
7 11 0.11
8 11 0.11
9 35 0.35
10 33 0.33
11 9 0.09
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (9 bp):
TTAAAAATT
Found at i:12642924 original size:26 final size:26
Alignment explanation
Indices: 12642870--12642928 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
12642860 AACAATCTAC
* *
12642870 AATATTTTAAAAATTCAAAATATTGA
1 AATATTTTAAAAATTCAAAAAATTAA
*
12642896 AATATTTTTAAAATT-ATAAAAATTAA
1 AATATTTTAAAAATTCA-AAAAATTAA
12642922 AAT-TTTT
1 AATATTTT
12642929 GAGAATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 5 0.17
26 24 0.83
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (26 bp):
AATATTTTAAAAATTCAAAAAATTAA
Found at i:12642959 original size:18 final size:16
Alignment explanation
Indices: 12642903--12642977 Score: 62
Period size: 17 Copynumber: 4.4 Consensus size: 16
12642893 TGAAATATTT
*
12642903 TTAAAA-TTATAAAAA
1 TTAAAATTTTTAAAAA
* *
12642918 TTAAAATTTTTGAGAAT
1 TTAAAATTTTT-AAAAA
12642935 TTAAAATTTTTAAAAA
1 TTAAAATTTTTAAAAA
12642951 TGTATAAATTTTAATAAAAA
1 T-TA-AAATTTT--TAAAAA
12642971 TCTAAAA
1 T-TAAAA
12642978 AATTAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
15 6 0.12
16 7 0.15
17 16 0.33
18 7 0.15
19 3 0.06
20 9 0.19
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (16 bp):
TTAAAATTTTTAAAAA
Found at i:12642987 original size:18 final size:18
Alignment explanation
Indices: 12642961--12643004 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
12642951 TGTATAAATT
12642961 TTAATAAAAATCTAAAAAA
1 TTAA-AAAAATCTAAAAAA
* *
12642980 TTAAAAAAATTTGAAAAA
1 TTAAAAAAATCTAAAAAA
12642998 TTAAAAA
1 TTAAAAA
12643005 TATGGAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (18 bp):
TTAAAAAAATCTAAAAAA
Found at i:12643139 original size:19 final size:20
Alignment explanation
Indices: 12643102--12643145 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
12643092 TTTTTTAAAA
*
12643102 TTAAAAAATCTACAATTTTT
1 TTAAAAAAGCTACAATTTTT
*
12643122 TTAAAAAAGCTA-ATTTTTT
1 TTAAAAAAGCTACAATTTTT
12643141 TTAAA
1 TTAAA
12643146 TTCTAAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (20 bp):
TTAAAAAAGCTACAATTTTT
Found at i:12643226 original size:18 final size:19
Alignment explanation
Indices: 12643203--12643246 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
12643193 GAAACATTCT
12643203 TTAAAAAATATT-AAAAAA
1 TTAAAAAATATTGAAAAAA
*
12643221 TTAAAAAATTTTGAAAAAA
1 TTAAAAAATATTGAAAAAA
*
12643240 ATAAAAA
1 TTAAAAA
12643247 TTAAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
TTAAAAAATATTGAAAAAA
Found at i:12643245 original size:27 final size:29
Alignment explanation
Indices: 12643205--12643259 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
12643195 AACATTCTTT
12643205 AAAAAATATTAAAAAATT-AAAAAATTTTG
1 AAAAAATATT-AAAAATTAAAAAAATTTTG
12643234 AAAAAA-A-TAAAAATTAAAAAAATTTT
1 AAAAAATATTAAAAATTAAAAAAATTTT
12643260 CTAATTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 7 0.28
27 11 0.44
28 1 0.04
29 6 0.24
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (29 bp):
AAAAAATATTAAAAATTAAAAAAATTTTG
Found at i:12643293 original size:19 final size:20
Alignment explanation
Indices: 12643266--12643308 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
12643256 TTTTCTAATT
12643266 AAAA-ATTTTTGAAAAATAC
1 AAAATATTTTTGAAAAATAC
* * *
12643285 AAAATTTTTTTGAATAATTC
1 AAAATATTTTTGAAAAATAC
12643305 AAAA
1 AAAA
12643309 ATTATATAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (20 bp):
AAAATATTTTTGAAAAATAC
Found at i:12643311 original size:21 final size:20
Alignment explanation
Indices: 12643271--12643308 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12643261 TAATTAAAAA
12643271 TTTTTGAAAAATACAAAATT
1 TTTTTGAAAAATACAAAATT
* *
12643291 TTTTTGAATAATTCAAAA
1 TTTTTGAAAAATACAAAA
12643309 ATTATATAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (20 bp):
TTTTTGAAAAATACAAAATT
Found at i:12643512 original size:22 final size:21
Alignment explanation
Indices: 12643486--12643534 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
12643476 ATTTTGCAAG
*
12643486 ATTTTTGGATTTTTTAATTAAA
1 ATTTTTAGATTTTTT-ATTAAA
* *
12643508 ATTTTCAGATTTTTTTTTAAA
1 ATTTTTAGATTTTTTATTAAA
12643529 ATTTTT
1 ATTTTT
12643535 TAAGTTTGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (21 bp):
ATTTTTAGATTTTTTATTAAA
Found at i:12643610 original size:11 final size:11
Alignment explanation
Indices: 12643594--12643625 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
12643584 TATAATTTTA
12643594 AAAAATATTTC
1 AAAAATATTTC
12643605 AAAAATA-TTC
1 AAAAATATTTC
12643615 AAAAAT-TTTC
1 AAAAATATTTC
12643625 A
1 A
12643626 GAATTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 13 0.65
11 7 0.35
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.34
Consensus pattern (11 bp):
AAAAATATTTC
Found at i:12643664 original size:20 final size:20
Alignment explanation
Indices: 12643616--12643665 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
12643606 AAAATATTCA
* *
12643616 AAAATTTTCAGAATTTTTTTG
1 AAAATTTT-TGAATTTTTTAG
**
12643637 AACGTTTTTGAATTTTTTAG
1 AAAATTTTTGAATTTTTTAG
12643657 AAAATTTTT
1 AAAATTTTT
12643666 TTAATATTGA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.32, C:0.04, G:0.10, T:0.54
Consensus pattern (20 bp):
AAAATTTTTGAATTTTTTAG
Found at i:12643739 original size:18 final size:18
Alignment explanation
Indices: 12643718--12643753 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12643708 TTTTTTACAT
*
12643718 ATATTAATATTTTATTAG
1 ATATTAATATTATATTAG
*
12643736 ATATTTATATTATATTAG
1 ATATTAATATTATATTAG
12643754 TGGAGAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
ATATTAATATTATATTAG
Found at i:12644276 original size:12 final size:13
Alignment explanation
Indices: 12644253--12644281 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
12644243 TAATTTATCT
12644253 ATTTTGATTTTTG
1 ATTTTGATTTTTG
12644266 ATTTT-ATTTTTG
1 ATTTTGATTTTTG
12644278 ATTT
1 ATTT
12644282 AATTATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.72
Consensus pattern (13 bp):
ATTTTGATTTTTG
Found at i:12645553 original size:2 final size:2
Alignment explanation
Indices: 12645548--12645573 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12645538 GTTATATCTA
12645548 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
12645574 CACACCCCAT
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:12645756 original size:16 final size:16
Alignment explanation
Indices: 12645723--12645755 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
12645713 GTGAAACAAT
12645723 AATTTAAAAAAAATAA
1 AATTTAAAAAAAATAA
*
12645739 AATTT-AATAAAATAA
1 AATTTAAAAAAAATAA
12645754 AA
1 AA
12645756 AACACATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AATTTAAAAAAAATAA
Found at i:12649277 original size:2 final size:2
Alignment explanation
Indices: 12649270--12649299 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12649260 TGTAAACAAA
12649270 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
12649300 GAGATACCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12651392 original size:68 final size:68
Alignment explanation
Indices: 12651311--12651444 Score: 232
Period size: 68 Copynumber: 2.0 Consensus size: 68
12651301 ATTAAAAAGC
*
12651311 ATTGCCTTTAAAATTTGCTAAAAAGAGCCTAAACACCAACAATTTTTACTAAAAATTCAAAGTAT
1 ATTGCCATTAAAATTTGCTAAAAAGAGCCTAAACACCAACAATTTTTACTAAAAATTCAAAGTAT
12651376 AGT
66 AGT
* * *
12651379 ATTGCCATTAAAATTTGCTAAAAAGAGCCTAAATACCAACAATTTTTTCTAAAAATTCAAATTAT
1 ATTGCCATTAAAATTTGCTAAAAAGAGCCTAAACACCAACAATTTTTACTAAAAATTCAAAGTAT
12651444 A
66 A
12651445 AAAGTCATGT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 62 1.00
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.32
Consensus pattern (68 bp):
ATTGCCATTAAAATTTGCTAAAAAGAGCCTAAACACCAACAATTTTTACTAAAAATTCAAAGTAT
AGT
Done.