Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 34 of 120
Found at i:8764393 original size:123 final size:123
Alignment explanation
Indices: 8764241--8764516 Score: 371
Period size: 123 Copynumber: 2.2 Consensus size: 123
8764231 CAAGTGATGC
* *
8764241 GGTCATCTTCCTTATGAGATATTGAGAAGTAGACCAAATCAATGAAA-CAAGGCTCAAAGTGAGC
1 GGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAA-GCTCAAAGTGAGC
* *
8764305 AAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCAGGTCGAAGCCAAAAAGT
65 AAATCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCCAAAAAGT
* *
8764364 GGTCGTCTTCCTGATGA-AGTACTGAGAAGTAGACCAAATCAATGAAACCAAGCTCAATGTGAGC
1 GGTCATCTTCCTGATGAGA-TACTGAGAAGTAGACCAAATCAATGAAACCAAGCTCAAAGTGAGC
* * * *
8764428 GAATCTTCGAACCACAGCTTTCTGATGAGATACTGAGAAGTAGGTCGAAG-CAATAAAGC
65 AAATCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCCAA-AAAGT
* * *
8764487 GGTTACCTTCCTGATTAGATA-TAGAGAAGT
1 GGTCATCTTCCTGATGAGATACT-GAGAAGT
8764517 GAACCAGATC
Statistics
Matches: 134, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
122 5 0.04
123 125 0.93
124 4 0.03
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (123 bp):
GGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAGCTCAAAGTGAGCA
AATCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCCAAAAAGT
Found at i:8764680 original size:332 final size:324
Alignment explanation
Indices: 8764082--8764682 Score: 835
Period size: 332 Copynumber: 1.8 Consensus size: 324
8764072 TAGGAGCATC
* *
8764082 TGAAACCAAGCTTAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGTAG
1 TGAAACCAAGCTCAAAGTGAGCAAATCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGTAG
* * * * ** **
8764147 GTTAAAGCAATAAAACAGTTCCCTTCCCGATGAGAAGTGAACCATATCTGTCTTTTTGATGAGAA
66 GTCAAAGCAATAAAACAGTTACCTTCCAGATGAGAAGTGAACCAGATCCATCTTCCTGATGAGAA
** * * * * *
8764212 ATGGAGAAGTGGATCAAAACAAGTGATGCGGTCATCTTCCTTATGAGATATTGAGAAGTAGACCA
131 ACAGAGAACTGGATCAAAACAAGTGATGCGATCATCTTCCTGATGACATACTGAGAAGTAGACCA
*
8764277 AATCAATGAAACAAGGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAG
196 AATCAATGAAACAAGGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAG
8764342 AAGCAGGTCGAAGCCAAAAAGTGGTCGTCTTCCTGATGAAGTACTGAGAAGTAGACCAAATCAA
261 AAGCAGGTCGAAGCCAAAAAGTGGTCGTCTTCCTGATGAAGTACTGAGAAGTAGACCAAATCAA
* * *
8764406 TGAAACCAAGCTCAATGTGAGCGAATCTTCGAACCACAGCTTTCTGATGAGATACTGAGAAGTAG
1 TGAAACCAAGCTCAAAGTGAGCAAATCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGTAG
* * *
8764471 GTCGAAGCAATAAAGCGGTTACCTTCCTGATTAGATATAGAGAAGTGAACCAGATCCATCTTCCT
66 GTCAAAGCAATAAAACAGTTACCTTCC-----AG--AT-GAGAAGTGAACCAGATCCATCTTCCT
* *
8764536 GATGAGACACAGAGAACTGGATCAAAACAAGTGATGCGATCATCTTTCTGATGACATACTGAGAA
123 GATGAGAAACAGAGAACTGGATCAAAACAAGTGATGCGATCATCTTCCTGATGACATACTGAGAA
*** *
8764601 GTAGACCAAATCAATGAAACCAA-GCTCAAAGTGAGCAAATCTTCGAACCTTGGCTTCTTGATGA
188 GTAGACCAAATCAATGAAA-CAAGGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGA
*
8764665 GGTACTGAGAAGCAGGTC
252 GATACTGAGAAGCAGGTC
8764683 AAACCAATAA
Statistics
Matches: 237, Mismatches: 31, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
324 82 0.35
329 1 0.00
331 2 0.01
332 149 0.63
333 3 0.01
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.23
Consensus pattern (324 bp):
TGAAACCAAGCTCAAAGTGAGCAAATCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGTAG
GTCAAAGCAATAAAACAGTTACCTTCCAGATGAGAAGTGAACCAGATCCATCTTCCTGATGAGAA
ACAGAGAACTGGATCAAAACAAGTGATGCGATCATCTTCCTGATGACATACTGAGAAGTAGACCA
AATCAATGAAACAAGGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAG
AAGCAGGTCGAAGCCAAAAAGTGGTCGTCTTCCTGATGAAGTACTGAGAAGTAGACCAAATCAA
Found at i:8764734 original size:209 final size:209
Alignment explanation
Indices: 8764364--8765030 Score: 914
Period size: 209 Copynumber: 3.2 Consensus size: 209
8764354 GCCAAAAAGT
*
8764364 GGTCGTCTTCCTGATGA-AGTACTGAGAAGTAGACCAAATCAATGAAACCAAGCTCAATGTGAGC
1 GGTCATCTTCCTGATGAGA-TACTGAGAAGTAGACCAAATCAATGAAACCAAGCTCAATGTGAGC
* * **
8764428 GAATCTTCGAACCACAGCTT-TCTGATGAGATACTGAGAAGTAGGTCGAAGCAATAAAGCGGTTA
65 AAATCTTCGAACCACAGCTTCT-TGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTA
* * * *
8764492 CCTTCCTGATTAGATATAGAGAAGTGAACCAGATCCATCTTCCTGATGAGACACAGAGAACTGGA
129 CCTTCCTGATAAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGA
*
8764557 TCAAAACAAGTGATGC
194 TCAAAACAAGTGAAGC
* * * *
8764573 GATCATCTTTCTGATGACATACTGAGAAGTAGACCAAATCAATGAAACCAAGCTCAAAGTGAGCA
1 GGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAGCTCAATGTGAGCA
*** * * * *
8764638 AATCTTCGAACCTTGGCTTCTTGATGAGGTACTGAGAAGCAGGTCAAACCAATAAAATAGTTACC
66 AATCTTCGAACCACAGCTTCTTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTACC
* * *
8764703 TTCCCGATAAGATACAGAGAAGTGAACCAGATCCGTCTTCTTAATGAGACAC--AGAAGTGGATC
131 TTCCTGATAAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGATC
* *
8764766 AAAACAAATGAGGC
196 AAAACAAGTGAAGC
* * *
8764780 GGTCATCTTCCTGATGAGATACTGAGAAGTAGACTAACTCAATG-AACCAAAGCTTAATGTGAGC
1 GGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACC-AAGCTCAATGTGAGC
* * * *
8764844 TAAA-CTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTCA
65 -AAATCTTCGAACCACAGCTTCTTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTA
* * *
8764908 GCTTCCTAATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGA
129 CCTTCCTGATAAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGA
8764973 TCAAAACAAGTGAAGC
194 TCAAAACAAGTGAAGC
* *
8764989 GGTCATCTTCCTGATGAGGTACAGAGAAGTAGACCAAATCAA
1 GGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAA
8765031 ATGCGATTGA
Statistics
Matches: 399, Mismatches: 53, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
206 4 0.01
207 172 0.43
208 3 0.01
209 218 0.55
210 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (209 bp):
GGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAGCTCAATGTGAGCA
AATCTTCGAACCACAGCTTCTTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTACC
TTCCTGATAAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGATC
AAAACAAGTGAAGC
Found at i:8765562 original size:23 final size:23
Alignment explanation
Indices: 8765542--8765615 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
8765532 GTCGTTAATA
*
8765542 TTAAATTAAAATTTATTTTAAGT
1 TTAAATTAAAATTTAATTTAAGT
*
8765565 TTAAATTTAAATTTAATTT-A-T
1 TTAAATTAAAATTTAATTTAAGT
* * *
8765586 TCTAAATTTAAA-TTAAATTAAAT
1 T-TAAATTAAAATTTAATTTAAGT
8765609 TTAAATT
1 TTAAATT
8765616 TATTCTAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
21 8 0.18
22 18 0.40
23 19 0.42
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (23 bp):
TTAAATTAAAATTTAATTTAAGT
Found at i:8765567 original size:6 final size:6
Alignment explanation
Indices: 8765542--8765638 Score: 84
Period size: 6 Copynumber: 17.2 Consensus size: 6
8765532 GTCGTTAATA
* * *
8765542 TTAAAT TAAAAT TT-ATT TTAAGT TTAAAT TTAAAT TT-AAT TT--AT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
8765586 TCTAAAT TTAAA- TTAAA- TTAAAT TTAAAT TT--AT TCTAAAT TTAATT
1 T-TAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT T-TAAAT TTAAAT
8765632 TTAAAT T
1 TTAAAT T
8765639 GAGTTATTAA
Statistics
Matches: 76, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
4 6 0.08
5 21 0.28
6 43 0.57
7 6 0.08
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (6 bp):
TTAAAT
Found at i:8765582 original size:11 final size:11
Alignment explanation
Indices: 8765536--8765638 Score: 79
Period size: 11 Copynumber: 9.1 Consensus size: 11
8765526 AAGCCAGTCG
8765536 TTAATATTAAAT
1 TTAAT-TTAAAT
* *
8765548 TAAAATTT-ATT
1 T-TAATTTAAAT
8765559 TTAAGTTTAAAT
1 TTAA-TTTAAAT
8765571 TTAAATTT-AAT
1 TT-AATTTAAAT
8765582 TT-ATTCTAAAT
1 TTAATT-TAAAT
*
8765593 TTAAATTAAAT
1 TTAATTTAAAT
*
8765604 TAAATTTAAAT
1 TTAATTTAAAT
8765615 TT-ATTCTAAAT
1 TTAATT-TAAAT
8765626 TTAATTTTAAAT
1 TTAA-TTTAAAT
8765638 T
1 T
8765639 GAGTTATTAA
Statistics
Matches: 73, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
9 3 0.04
10 6 0.08
11 38 0.52
12 19 0.26
13 7 0.10
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (11 bp):
TTAATTTAAAT
Found at i:8765593 original size:16 final size:17
Alignment explanation
Indices: 8765572--8765634 Score: 85
Period size: 16 Copynumber: 3.8 Consensus size: 17
8765562 AGTTTAAATT
8765572 TAAATTT-AATTTATTC
1 TAAATTTAAATTTATTC
* *
8765588 TAAATTTAAATTAAAT-
1 TAAATTTAAATTTATTC
8765604 TAAATTTAAATTTATTC
1 TAAATTTAAATTTATTC
*
8765621 TAAATTTAATTTTA
1 TAAATTTAAATTTA
8765635 AATTGAGTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
16 21 0.52
17 19 0.47
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TAAATTTAAATTTATTC
Found at i:8765604 original size:33 final size:35
Alignment explanation
Indices: 8765565--8765638 Score: 118
Period size: 33 Copynumber: 2.2 Consensus size: 35
8765555 TATTTTAAGT
8765565 TTAAATTTAAATTT-AATTTATTCTAAATTTAA-A
1 TTAAATTTAAATTTAAATTTATTCTAAATTTAATA
*
8765598 TTAAA-TTAAATTTAAATTTATTCTAAATTTAATT
1 TTAAATTTAAATTTAAATTTATTCTAAATTTAATA
8765632 TTAAATT
1 TTAAATT
8765639 GAGTTATTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
32 8 0.22
33 23 0.62
34 5 0.14
35 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (35 bp):
TTAAATTTAAATTTAAATTTATTCTAAATTTAATA
Found at i:8767075 original size:29 final size:29
Alignment explanation
Indices: 8766960--8767273 Score: 238
Period size: 29 Copynumber: 10.8 Consensus size: 29
8766950 CCTTTGAATT
* *
8766960 TTCCAAAAATCA-TATTTTAACCCTCGAAC
1 TTCCAAAAATTACCATTTT-ACCCTCGAAC
* *
8766989 TTCCTGAAAATCA-CATTTT-CCCTCGAAC
1 TTCC-AAAAATTACCATTTTACCCTCGAAC
* *
8767017 TTTCAAAAATTACCATTTTA-ACTCGAAC
1 TTCCAAAAATTACCATTTTACCCTCGAAC
*
8767045 TTCCAAAAATTACCATTTTACCCTCAAAC
1 TTCCAAAAATTACCATTTTACCCTCGAAC
* * *
8767074 TTCCCAAAAATCA-CATTTTGCCCCCGAAC
1 TT-CCAAAAATTACCATTTTACCCTCGAAC
** *
8767103 TTTTAAAAATGACCATTTTACTCC-CGAAC
1 TTCCAAAAATTACCATTTTAC-CCTCGAAC
* *
8767132 TTCTCAAAAATCA-CATTTTTGTCCC-CGAAC
1 TTC-CAAAAATTACCA-TTTT-ACCCTCGAAC
* * *
8767162 TTCCAAAAATTACCATTTTCCCCCCAAAC
1 TTCCAAAAATTACCATTTTACCCTCGAAC
* *
8767191 TTTCC-AAAA-TATCATTTTTGATCCT-GAAC
1 -TTCCAAAAATTACCA-TTTT-ACCCTCGAAC
* *
8767220 TTTCCAAAAATTATCGATTTGA-CCTCGAAC
1 -TTCCAAAAATTA-CCATTTTACCCTCGAAC
8767250 TTCCAAAAATTACCATTTTACCCT
1 TTCCAAAAATTACCATTTTACCCT
8767274 TGGGTATCCT
Statistics
Matches: 231, Mismatches: 34, Indels: 40
0.76 0.11 0.13
Matches are distributed among these distances:
27 6 0.03
28 64 0.28
29 93 0.40
30 61 0.26
31 6 0.03
32 1 0.00
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.33
Consensus pattern (29 bp):
TTCCAAAAATTACCATTTTACCCTCGAAC
Found at i:8767111 original size:58 final size:58
Alignment explanation
Indices: 8767040--8767268 Score: 223
Period size: 59 Copynumber: 3.9 Consensus size: 58
8767030 CATTTTAACT
8767040 CGAACTTCCAAAAATTACCATTTTACCCTCAAACTTCCCAAAAATCACA-TTTTGCCCC
1 CGAACTTCCAAAAATTACCATTTTACCC-CAAACTTCCCAAAAATCACATTTTTGCCCC
** * * * *
8767098 CGAACTTTTAAAAATGACCATTTTACTCCCGAACTTCTCAAAAATCACATTTTTGTCCC
1 CGAACTTCCAAAAATTACCATTTTAC-CCCAAACTTCCCAAAAATCACATTTTTGCCCC
* * **
8767157 CGAACTTCCAAAAATTACCATTTTCCCCCCAAACTTTCC-AAAAT-ATCATTTTTGATCC
1 CGAACTTCCAAAAATTACCATTTT-ACCCCAAACTTCCCAAAAATCA-CATTTTTGCCCC
* * * * * *
8767215 TGAACTTTCCAAAAATTATCGATTTGACCTCGAACTT-CCAAAAATTACCATTTT
1 CGAAC-TTCCAAAAATTA-CCATTTTACCCCAAACTTCCCAAAAATCA-CATTTT
8767269 ACCCTTGGGT
Statistics
Matches: 141, Mismatches: 22, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
57 1 0.01
58 62 0.44
59 65 0.46
60 13 0.09
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (58 bp):
CGAACTTCCAAAAATTACCATTTTACCCCAAACTTCCCAAAAATCACATTTTTGCCCC
Found at i:8767192 original size:88 final size:86
Alignment explanation
Indices: 8766973--8767268 Score: 259
Period size: 88 Copynumber: 3.4 Consensus size: 86
8766963 CAAAAATCAT
* * *
8766973 ATTTTAACCCTCGAACTTCCTGAAAATCACATTTTCCCTCGAACTTTCAAAAATTACCATTTTAA
1 ATTTTGACCC-CGAACTTCC-AAAAATCACATTTTCCCCCGAACTTTCAAAAA-TACCATTTTAA
8767038 CT--CGAACTTC-CAAAAATTACC
63 CTCCCGAACTTCTCAAAAATTACC
* *
8767059 ATTTT-ACCCTCAAACTTCCCAAAAATCACATTTTGCCCCCGAACTTTTAAAAATGACCATTTT-
1 ATTTTGACCC-CGAACTT-CCAAAAATCACATTTT-CCCCCGAACTTTCAAAAAT-ACCATTTTA
*
8767122 ACTCCCGAACTTCTCAAAAATCA-C
62 ACTCCCGAACTTCTCAAAAATTACC
* * * * * *
8767146 ATTTTTGTCCCCGAACTTCCAAAAATTACCATTTTCCCCCCAAACTTTCCAAAATATCATTTTTG
1 A-TTTTGACCCCGAACTTCCAAAAATCA-CATTTT-CCCCCGAACTTTCAAAAATACCA-TTTTA
* *
8767211 A-TCCTGAACTT-TCCAAAAATTATCG
62 ACTCCCGAACTTCT-CAAAAATTA-CC
* *
8767236 A-TTTGACCTCGAACTTCCAAAAATTACCATTTT
1 ATTTTGACCCCGAACTTCCAAAAATCA-CATTTT
8767269 ACCCTTGGGT
Statistics
Matches: 178, Mismatches: 18, Indels: 26
0.80 0.08 0.12
Matches are distributed among these distances:
85 28 0.16
86 31 0.17
87 23 0.13
88 91 0.51
89 4 0.02
90 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.33
Consensus pattern (86 bp):
ATTTTGACCCCGAACTTCCAAAAATCACATTTTCCCCCGAACTTTCAAAAATACCATTTTAACTC
CCGAACTTCTCAAAAATTACC
Found at i:8770505 original size:52 final size:53
Alignment explanation
Indices: 8770427--8770535 Score: 211
Period size: 52 Copynumber: 2.1 Consensus size: 53
8770417 AATTGGTGAT
8770427 TTAACTGGTGCAATCGATATTTAAAAATTATAAGAAGATAGAACTGGAAC-AA
1 TTAACTGGTGCAATCGATATTTAAAAATTATAAGAAGATAGAACTGGAACAAA
8770479 TTAACTGGTGCAATCGATATTTAAAAATTATAAGAAGATAGAACTGGAACAAA
1 TTAACTGGTGCAATCGATATTTAAAAATTATAAGAAGATAGAACTGGAACAAA
8770532 TTAA
1 TTAA
8770536 TTAAACCAGG
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 50 0.89
53 6 0.11
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.28
Consensus pattern (53 bp):
TTAACTGGTGCAATCGATATTTAAAAATTATAAGAAGATAGAACTGGAACAAA
Found at i:8770685 original size:13 final size:14
Alignment explanation
Indices: 8770667--8770695 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
8770657 TTATATTTCT
8770667 TTATTTTTT-ATGA
1 TTATTTTTTAATGA
8770680 TTATTTTTTAATGA
1 TTATTTTTTAATGA
8770694 TT
1 TT
8770696 TTTGAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (14 bp):
TTATTTTTTAATGA
Found at i:8780327 original size:21 final size:21
Alignment explanation
Indices: 8780288--8780337 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
8780278 TTTTTAGTAC
* * *
8780288 CGGTAGAAGCATGATTTGTTT
1 CGGTAGAAGCATCACTTGTAT
* *
8780309 TGGTAGAAGCTTCACTTGTAT
1 CGGTAGAAGCATCACTTGTAT
8780330 CGGTAGAA
1 CGGTAGAA
8780338 CTGTCATATG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (21 bp):
CGGTAGAAGCATCACTTGTAT
Found at i:8786694 original size:24 final size:24
Alignment explanation
Indices: 8786666--8786739 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
8786656 GTATACTGGT
8786666 TAACCATTCTGGGCTCGTAAGAGC
1 TAACCATTCTGGGCTCGTAAGAGC
* **
8786690 TAACCATTCTGGGGTTTTAAGAGC
1 TAACCATTCTGGGCTCGTAAGAGC
* *
8786714 TAACCATTC-GGGCTCGTGAGAAC
1 TAACCATTCTGGGCTCGTAAGAGC
8786737 TAA
1 TAA
8786740 TATTGTTTTG
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 12 0.29
24 30 0.71
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (24 bp):
TAACCATTCTGGGCTCGTAAGAGC
Found at i:8808549 original size:15 final size:16
Alignment explanation
Indices: 8808529--8808558 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
8808519 TTTAATTTTT
8808529 TTATTT-ACTTTTCAG
1 TTATTTCACTTTTCAG
8808544 TTATTTCACTTTTCA
1 TTATTTCACTTTTCA
8808559 TCGTGTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.20, C:0.17, G:0.03, T:0.60
Consensus pattern (16 bp):
TTATTTCACTTTTCAG
Found at i:8808976 original size:11 final size:11
Alignment explanation
Indices: 8808949--8808978 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
8808939 AACTCGTGCA
8808949 TCCAAAAATAC
1 TCCAAAAATAC
8808960 TCCCAAAAATAC
1 T-CCAAAAATAC
8808972 TCCAAAA
1 TCCAAAA
8808979 CCTTCATCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.53, C:0.30, G:0.00, T:0.17
Consensus pattern (11 bp):
TCCAAAAATAC
Found at i:8817095 original size:69 final size:69
Alignment explanation
Indices: 8816817--8817128 Score: 257
Period size: 69 Copynumber: 4.5 Consensus size: 69
8816807 AGCTTGCAGC
* * * * * ** * *
8816817 TCAAAACAGCTAGTGGACCTACGTTCCCAGCTAATATTACAAAGGCTCATTGATTTATGATCGTA
1 TCAAAATAGCTAGCGGACCTACGTTCCCAGCTGATATTATAAAGGCTTACCGGTTTATGATCGCA
8816882 GCCT
66 GCCT
* * ** * * * * * * * *
8816886 CCAAAACAGCTAGTAGACCTATGTTTCTAACTAAAATTATAAAGGCTTGCCGGTTTATGATCACA
1 TCAAAATAGCTAGCGGACCTACGTTCCCAGCTGATATTATAAAGGCTTACCGGTTTATGATCGCA
**
8816951 -ATT
66 GCCT
* * * * * *
8816954 TCCAAAATAACTAGCGGACTTGCCTTCCCAGCTGACATTATAAAGGCTAACCGGTTTATGATCGC
1 T-CAAAATAGCTAGCGGACCTACGTTCCCAGCTGATATTATAAAGGCTTACCGGTTTATGATCGC
*
8817019 AACCT
65 AGCCT
* * * *
8817024 TCAAAATAGCTAGCGGACCTACGTTCTCAGCTGATATTATAAAAGCTTACTGGTTTATGACCGCA
1 TCAAAATAGCTAGCGGACCTACGTTCCCAGCTGATATTATAAAGGCTTACCGGTTTATGATCGCA
*
8817089 GGCT
66 GCCT
* ** *
8817093 TCAAAATAGTTAGAAGACCTACGTTCCCAACTGATA
1 TCAAAATAGCTAGCGGACCTACGTTCCCAGCTGATA
8817129 CTGAAAGGTT
Statistics
Matches: 188, Mismatches: 53, Indels: 4
0.77 0.22 0.02
Matches are distributed among these distances:
68 1 0.01
69 185 0.98
70 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (69 bp):
TCAAAATAGCTAGCGGACCTACGTTCCCAGCTGATATTATAAAGGCTTACCGGTTTATGATCGCA
GCCT
Found at i:8820403 original size:14 final size:14
Alignment explanation
Indices: 8820384--8820419 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
8820374 TTGTTTGACT
*
8820384 GAAAATGGTTTCCG
1 GAAAATGATTTCCG
*
8820398 GAAAATGATTTCTG
1 GAAAATGATTTCCG
8820412 GAAAATGA
1 GAAAATGA
8820420 ATTACTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.28
Consensus pattern (14 bp):
GAAAATGATTTCCG
Found at i:8822412 original size:18 final size:17
Alignment explanation
Indices: 8822364--8822416 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
8822354 AGAAACAAAT
*
8822364 CAAAAGCAGTGAAGAAA
1 CAAAAGCAGTAAAGAAA
* *
8822381 CAAAAG-TG-AAAGAACC
1 CAAAAGCAGTAAAGAA-A
8822397 CAAAAGCAGTAAAGAAA
1 CAAAAGCAGTAAAGAAA
8822414 CAA
1 CAA
8822417 GATAGGAATG
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 5 0.18
16 7 0.25
17 10 0.36
18 6 0.21
ACGTcount: A:0.60, C:0.15, G:0.19, T:0.06
Consensus pattern (17 bp):
CAAAAGCAGTAAAGAAA
Found at i:8823856 original size:6 final size:6
Alignment explanation
Indices: 8823845--8823881 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
8823835 CGCAATGAAT
*
8823845 GGGGAA GGGGAA AGGGAA GGGGAA GGGGAA GGGGAA G
1 GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA G
8823882 AACGTTTAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
GGGGAA
Found at i:8824069 original size:14 final size:14
Alignment explanation
Indices: 8824050--8824076 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
8824040 AGAAAATTTT
8824050 GAAAAGCTTTTACG
1 GAAAAGCTTTTACG
8824064 GAAAAGCTTTTAC
1 GAAAAGCTTTTAC
8824077 AACTAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (14 bp):
GAAAAGCTTTTACG
Found at i:8825575 original size:22 final size:22
Alignment explanation
Indices: 8825550--8825591 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
8825540 ATTTAAAAGT
8825550 TTTCTATA-GTTTCAAAATCACA
1 TTTCTA-ACGTTTCAAAATCACA
8825572 TTTCTAACGTTTCAAAATCA
1 TTTCTAACGTTTCAAAATCA
8825592 TAACTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.40
Consensus pattern (22 bp):
TTTCTAACGTTTCAAAATCACA
Found at i:8826509 original size:19 final size:19
Alignment explanation
Indices: 8826485--8826523 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
8826475 ATGATCGTAT
* *
8826485 CAATGCATATTTTTTAAAA
1 CAATGCACATTTTGTAAAA
8826504 CAATGCACATTTTGTAAAA
1 CAATGCACATTTTGTAAAA
8826523 C
1 C
8826524 GTTCCTACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (19 bp):
CAATGCACATTTTGTAAAA
Found at i:8828369 original size:37 final size:37
Alignment explanation
Indices: 8828319--8828403 Score: 152
Period size: 37 Copynumber: 2.3 Consensus size: 37
8828309 AGGTTAGTTA
8828319 ATTTAAGATCATAACCTAATTTTCTTCGAGTTCGTTG
1 ATTTAAGATCATAACCTAATTTTCTTCGAGTTCGTTG
*
8828356 ATTTAAGATCATAACCTAATTTTCTTTGAGTTCGTTG
1 ATTTAAGATCATAACCTAATTTTCTTCGAGTTCGTTG
*
8828393 ATTTAATATCA
1 ATTTAAGATCA
8828404 CAACTCAGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (37 bp):
ATTTAAGATCATAACCTAATTTTCTTCGAGTTCGTTG
Found at i:8828834 original size:18 final size:18
Alignment explanation
Indices: 8828808--8828848 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
8828798 TATTGGGACT
*
8828808 TCGTTTCTATAAACTGAA
1 TCGTATCTATAAACTGAA
8828826 TCGTATCTATAAACTGAA
1 TCGTATCTATAAACTGAA
8828844 TCGTA
1 TCGTA
8828849 AATATTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (18 bp):
TCGTATCTATAAACTGAA
Found at i:8830436 original size:20 final size:20
Alignment explanation
Indices: 8830412--8830544 Score: 158
Period size: 20 Copynumber: 6.7 Consensus size: 20
8830402 AATGAAGAAG
* * *
8830412 TGCCCCTGTATGCATTTTGG
1 TGCCCCTGTTTGCACTTTGA
8830432 TGCCCCTGTTTGCACTTTGA
1 TGCCCCTGTTTGCACTTTGA
* * *
8830452 TGCCCTTGTATGCACTTTGG
1 TGCCCCTGTTTGCACTTTGA
*
8830472 TGCCCCTGTTTGCACTTCGA
1 TGCCCCTGTTTGCACTTTGA
* *
8830492 TGCCCCTGTATGCACTTCGA
1 TGCCCCTGTTTGCACTTTGA
* *
8830512 TGCCCCTATTTGCACTTCGA
1 TGCCCCTGTTTGCACTTTGA
*
8830532 TGCCCCTATTTGC
1 TGCCCCTGTTTGC
8830545 GTTTTGGTGC
Statistics
Matches: 100, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 100 1.00
ACGTcount: A:0.11, C:0.32, G:0.20, T:0.37
Consensus pattern (20 bp):
TGCCCCTGTTTGCACTTTGA
Found at i:8830456 original size:40 final size:40
Alignment explanation
Indices: 8830412--8830587 Score: 205
Period size: 40 Copynumber: 4.4 Consensus size: 40
8830402 AATGAAGAAG
* *
8830412 TGCCCCTGTATGCATTTTGGTGCCCCTGTTTGCACTTTGA
1 TGCCCCTGTATGCACTTTGGTGCCCCTGTTTGCACTTCGA
*
8830452 TGCCCTTGTATGCACTTTGGTGCCCCTGTTTGCACTTCGA
1 TGCCCCTGTATGCACTTTGGTGCCCCTGTTTGCACTTCGA
* * *
8830492 TGCCCCTGTATGCACTTCGATGCCCCTATTTGCACTTCGA
1 TGCCCCTGTATGCACTTTGGTGCCCCTGTTTGCACTTCGA
* * ** *
8830532 TGCCCCTATTTGCGTTTTGGTG-CCCT-TTAATGCACACTCG-
1 TGCCCCTGTATGCACTTTGGTGCCCCTGTT--TGCAC-TTCGA
8830572 TGCCCCTGTATGCACT
1 TGCCCCTGTATGCACT
8830588 CCGATGCCCC
Statistics
Matches: 115, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
38 2 0.02
39 4 0.03
40 106 0.92
41 3 0.03
ACGTcount: A:0.12, C:0.31, G:0.20, T:0.36
Consensus pattern (40 bp):
TGCCCCTGTATGCACTTTGGTGCCCCTGTTTGCACTTCGA
Found at i:8830556 original size:60 final size:60
Alignment explanation
Indices: 8830412--8830599 Score: 200
Period size: 60 Copynumber: 3.1 Consensus size: 60
8830402 AATGAAGAAG
* * * * * *
8830412 TGCCCCTGTATGCATTTTGGTGCCCCTGTTTGCACTTTGATGCCCTTGTATGCACTTTGG
1 TGCCCCTGTTTGCATTTTGGTGCCCCTGTATGCACTTCGATGCCCCTGTATGCACTTCGA
* * * * *
8830472 TGCCCCTGTTTGCACTTCGATGCCCCTGTATGCACTTCGATGCCCCTATTTGCACTTCGA
1 TGCCCCTGTTTGCATTTTGGTGCCCCTGTATGCACTTCGATGCCCCTGTATGCACTTCGA
* * * * *
8830532 TGCCCCTATTTGCGTTTTGGTG-CCCTTTAATGCACACTCG-TGCCCCTGTATGCACTCCGA
1 TGCCCCTGTTTGCATTTTGGTGCCCCTGT-ATGCAC-TTCGATGCCCCTGTATGCACTTCGA
8830592 TGCCCCTG
1 TGCCCCTG
8830600 ATGGTATAGT
Statistics
Matches: 104, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
59 5 0.05
60 96 0.92
61 3 0.03
ACGTcount: A:0.12, C:0.32, G:0.21, T:0.35
Consensus pattern (60 bp):
TGCCCCTGTTTGCATTTTGGTGCCCCTGTATGCACTTCGATGCCCCTGTATGCACTTCGA
Found at i:8830584 original size:20 final size:20
Alignment explanation
Indices: 8830561--8830599 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
8830551 GTGCCCTTTA
8830561 ATGCACACTCG-TGCCCCTGT
1 ATGCACAC-CGATGCCCCTGT
*
8830581 ATGCACTCCGATGCCCCTG
1 ATGCACACCGATGCCCCTG
8830600 ATGGTATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.15, C:0.41, G:0.21, T:0.23
Consensus pattern (20 bp):
ATGCACACCGATGCCCCTGT
Found at i:8833005 original size:447 final size:447
Alignment explanation
Indices: 8832171--8833066 Score: 1641
Period size: 447 Copynumber: 2.0 Consensus size: 447
8832161 GTCAAGGTGG
8832171 AGATTTGTTGAATTATGACTCCTATTTCAAGTCAAATTTGAGAAATAATCTTTCAGTTAAACTCT
1 AGATTTGTTGAATTATGACTCCTATTTCAAGTCAAATTTGAGAAATAATCTTTCAGTTAAACTCT
8832236 ATTCATTTATTTGAGTCAAACTCTTATTACTCTAGATTATTTTATTATTATTTGACTTAGGAATT
66 ATTCATTTATTTGAGTCAAACTCTTATTACTCTAGATTATTTTATTATTATTTGACTTAGGAATT
8832301 TAGCCTATAAATAAGCTCTTTTACAACCTTAAAAATATACCCATTTAAACATACCCATCATAGTT
131 TAGCCTATAAATAAGCTCTTTTACAACCTTAAAAATATACCCATTTAAACATACCCATCATAGTT
* *
8832366 TAGAACTCCTAATACTTTTGGAAAATTTAGTGTTTACGTTTTGAGGGTTTTTTATTTTTGGATTT
196 TAGAACTCCTAACACTTTTGGAAAATTTAGTGTTTACGTTTTGAGGGTTCTTTATTTTTGGATTT
8832431 TTGGGATTTAGTTTTTATCTCCATCTTTTGTACTCTTCGTTCTTTGCCAATATAGTAAAATTATC
261 TTGGGATTTAGTTTTTATCTCCATCTTTTGTACTCTTCGTTCTTTGCCAATATAGTAAAATTATC
* *
8832496 TTTGCCCGTGGTTTTTTATCCTCTTCGAAGGGGTTTTTCCACGTTAAATTTGTGTGTTCAATTTC
326 TTTGCCCATGATTTTTTATCCTCTTCGAAGGGGTTTTTCCACGTTAAATTTGTGTGTTCAATTTC
8832561 TCAATTTCTTCCGCTATTTTTAACTTGTTCGTTGCTTAATCGGGTCGATCCCCAACA
391 TCAATTTCTTCCGCTATTTTTAACTTGTTCGTTGCTTAATCGGGTCGATCCCCAACA
8832618 AGATTTGTTGAATTATGACTCCTATTTCAAGTCAAATTTGAGAAATAATCTTTCAGTTAAACTCT
1 AGATTTGTTGAATTATGACTCCTATTTCAAGTCAAATTTGAGAAATAATCTTTCAGTTAAACTCT
* * *
8832683 GTTTATTTGTTTGAGTCAAACTCTTATTACTCTAGATTATTTTATTATTATTTGACTTAGGAATT
66 ATTCATTTATTTGAGTCAAACTCTTATTACTCTAGATTATTTTATTATTATTTGACTTAGGAATT
* * * *
8832748 TAGCCTATAAATAGGCTCTTTTACAATCTTAAAAATATACCCATTTAGACATACCTATCATAGTT
131 TAGCCTATAAATAAGCTCTTTTACAACCTTAAAAATATACCCATTTAAACATACCCATCATAGTT
* *
8832813 TAGAACTCCTAACACTTTTGGAGAATTTAGTGTTTACGTTTTGAGGGTTCTTTATTTTTGGGTTT
196 TAGAACTCCTAACACTTTTGGAAAATTTAGTGTTTACGTTTTGAGGGTTCTTTATTTTTGGATTT
*
8832878 TTGAGG-TTTAGTTTTTATCTCCATCTTTTGTACTCTTCGTTCTTTGCCATTATAGTAAAATTAT
261 TTG-GGATTTAGTTTTTATCTCCATCTTTTGTACTCTTCGTTCTTTGCCAATATAGTAAAATTAT
*
8832942 CTTTGCCCATGATTTTTTATCCTCTTCGGAGGGGTTTTTCCACGTTAAATTTGTGTGTTCAATTT
325 CTTTGCCCATGATTTTTTATCCTCTTCGAAGGGGTTTTTCCACGTTAAATTTGTGTGTTCAATTT
8833007 CTCAATTTCTTCCGCTATTTTTAACTTGTTCGTTGCTTAATCGGGTCGATCCCCAACA
390 CTCAATTTCTTCCGCTATTTTTAACTTGTTCGTTGCTTAATCGGGTCGATCCCCAACA
8833065 AG
1 AG
8833067 TGGTATCAGA
Statistics
Matches: 433, Mismatches: 15, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
447 431 1.00
448 2 0.00
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (447 bp):
AGATTTGTTGAATTATGACTCCTATTTCAAGTCAAATTTGAGAAATAATCTTTCAGTTAAACTCT
ATTCATTTATTTGAGTCAAACTCTTATTACTCTAGATTATTTTATTATTATTTGACTTAGGAATT
TAGCCTATAAATAAGCTCTTTTACAACCTTAAAAATATACCCATTTAAACATACCCATCATAGTT
TAGAACTCCTAACACTTTTGGAAAATTTAGTGTTTACGTTTTGAGGGTTCTTTATTTTTGGATTT
TTGGGATTTAGTTTTTATCTCCATCTTTTGTACTCTTCGTTCTTTGCCAATATAGTAAAATTATC
TTTGCCCATGATTTTTTATCCTCTTCGAAGGGGTTTTTCCACGTTAAATTTGTGTGTTCAATTTC
TCAATTTCTTCCGCTATTTTTAACTTGTTCGTTGCTTAATCGGGTCGATCCCCAACA
Found at i:8840197 original size:17 final size:18
Alignment explanation
Indices: 8840171--8840210 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
8840161 AGAGGATTGA
*
8840171 ACTTTAATTT-TTTTAAG
1 ACTTTGATTTCTTTTAAG
8840188 ACTTTGATTTCTTTTAAG
1 ACTTTGATTTCTTTTAAG
8840206 A-TTTG
1 ACTTTG
8840211 TAATCTTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.25, C:0.07, G:0.10, T:0.57
Consensus pattern (18 bp):
ACTTTGATTTCTTTTAAG
Found at i:8842936 original size:22 final size:24
Alignment explanation
Indices: 8842892--8842936 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
8842882 CAACTTTTTG
*
8842892 CTTTTATTTTTGATGTTATTTTAC
1 CTTTTATTTTTGATGCTATTTTAC
8842916 CTTTTA-TTTT-ATGCTATTTTA
1 CTTTTATTTTTGATGCTATTTTA
8842937 AATCAACTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
23 4 0.20
24 6 0.30
ACGTcount: A:0.18, C:0.09, G:0.07, T:0.67
Consensus pattern (24 bp):
CTTTTATTTTTGATGCTATTTTAC
Found at i:8850763 original size:21 final size:21
Alignment explanation
Indices: 8850739--8850789 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
8850729 TATAAAATAA
8850739 TTATAAATAATT-TTGTAAAAC
1 TTATAAATAATTATT-TAAAAC
* *
8850760 TTATTTAA-AATTATTTAAAAG
1 TTA-TAAATAATTATTTAAAAC
8850781 TTATAAATA
1 TTATAAATA
8850790 GTATAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
20 3 0.12
21 16 0.67
22 5 0.21
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (21 bp):
TTATAAATAATTATTTAAAAC
Found at i:8850858 original size:10 final size:10
Alignment explanation
Indices: 8850830--8850939 Score: 60
Period size: 10 Copynumber: 11.8 Consensus size: 10
8850820 ATTCAATATC
8850830 ATTTTTAAT-
1 ATTTTTAATA
*
8850839 -TTTTTTATA
1 ATTTTTAATA
8850848 ATTTTTAATA
1 ATTTTTAATA
**
8850858 AAATTTAA-A
1 ATTTTTAATA
8850867 A-TTTT-A-A
1 ATTTTTAATA
* *
8850874 ATTTTTTACA
1 ATTTTTAATA
* *
8850884 GTTTTTTATA
1 ATTTTTAATA
8850894 ATTTTT-ATAA
1 ATTTTTAAT-A
*
8850904 ATTATTAA-A
1 ATTTTTAATA
8850913 TATTTTT-AT-
1 -ATTTTTAATA
8850922 ATTTTTAATA
1 ATTTTTAATA
8850932 ATTTTTAA
1 ATTTTTAA
8850940 ATAAAATTAT
Statistics
Matches: 80, Mismatches: 10, Indels: 21
0.72 0.09 0.19
Matches are distributed among these distances:
7 3 0.04
8 20 0.25
9 9 0.11
10 47 0.59
11 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:8850895 original size:46 final size:47
Alignment explanation
Indices: 8850831--8850927 Score: 128
Period size: 46 Copynumber: 2.1 Consensus size: 47
8850821 TTCAATATCA
*
8850831 TTTTTAATTTTTTTATAATTTTTAATAAAAT-TTAAA-A-TTTTAAAT
1 TTTTTAAGTTTTTTATAATTTTT-ATAAAATATTAAATATTTTTAAAT
* *
8850876 TTTTTACAGTTTTTTATAATTTTTATAAATTATTAAATATTTTTATAT
1 TTTTTA-AGTTTTTTATAATTTTTATAAAATATTAAATATTTTTAAAT
8850924 TTTT
1 TTTT
8850928 AATAATTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
45 12 0.27
46 21 0.47
47 1 0.02
48 11 0.24
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (47 bp):
TTTTTAAGTTTTTTATAATTTTTATAAAATATTAAATATTTTTAAAT
Found at i:8850912 original size:38 final size:35
Alignment explanation
Indices: 8850832--8850940 Score: 128
Period size: 36 Copynumber: 3.0 Consensus size: 35
8850822 TCAATATCAT
* **
8850832 TTTTAATTTTTTTATAATTTTTAATAAAATTTAAAA
1 TTTTAAATTTTTTAT-ATTTTTAATAATTTTTAAAA
* *
8850868 TTTTAAATTTTTTACAGTTTTTTATAATTTTTATAAA
1 TTTTAAATTTTTTATA-TTTTTAATAATTTTTA-AAA
8850905 TTATTAAATATTTTTATATTTTTAATAATTTTTAAA
1 TT-TTAAAT-TTTTTATATTTTTAATAATTTTTAAA
8850941 TAAAATTATT
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
35 1 0.02
36 26 0.42
37 7 0.11
38 21 0.34
39 7 0.11
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.61
Consensus pattern (35 bp):
TTTTAAATTTTTTATATTTTTAATAATTTTTAAAA
Found at i:8850918 original size:28 final size:28
Alignment explanation
Indices: 8850886--8850942 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
8850876 TTTTTACAGT
8850886 TTTTTATAATTTTT-ATAAATTATTAAATA
1 TTTTTAT-ATTTTTAAT-AATTATTAAATA
*
8850915 TTTTTATATTTTTAATAATTTTTAAATA
1 TTTTTATATTTTTAATAATTATTAAATA
8850943 AAATTATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTTTATATTTTTAATAATTATTAAATA
Found at i:8850935 original size:18 final size:18
Alignment explanation
Indices: 8850830--8850938 Score: 71
Period size: 18 Copynumber: 5.9 Consensus size: 18
8850820 ATTCAATATC
*
8850830 ATTTTTAAT-TTTTTTAT
1 ATTTTTAATAATTTTTAT
** *
8850847 AATTTTTAATAAAATTTAA
1 -ATTTTTAATAATTTTTAT
* * *
8850866 AATTTTAA-ATTTTTTAC
1 ATTTTTAATAATTTTTAT
*
8850883 AGTTTTTTATAATTTTTAT
1 A-TTTTTAATAATTTTTAT
*
8850902 AAATTATTAA-ATATTTTTAT
1 --ATTTTTAATA-ATTTTTAT
8850922 ATTTTTAATAATTTTTA
1 ATTTTTAATAATTTTTA
8850939 AATAAAATTA
Statistics
Matches: 68, Mismatches: 16, Indels: 14
0.69 0.16 0.14
Matches are distributed among these distances:
17 6 0.09
18 35 0.51
19 13 0.19
20 13 0.19
21 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (18 bp):
ATTTTTAATAATTTTTAT
Found at i:8850962 original size:26 final size:27
Alignment explanation
Indices: 8850931--8850986 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
8850921 TATTTTTAAT
*
8850931 AATTTTTA-AATAAAATTATT-TTTTC
1 AATTTTTATAATAAAATTATTAATTTC
*
8850956 AATTTTTATAATAATATTATTAATTTC
1 AATTTTTATAATAAAATTATTAATTTC
8850983 AATT
1 AATT
8850987 AAATTCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 8 0.30
26 11 0.41
27 8 0.30
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (27 bp):
AATTTTTATAATAAAATTATTAATTTC
Found at i:8855264 original size:21 final size:21
Alignment explanation
Indices: 8855240--8855283 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
8855230 AAAGAAAAAA
*
8855240 TAGAGGGTTCGAAAT-TTTTTT
1 TAGAGGGTT-AAAATGTTTTTT
*
8855261 TAGAGTGTTAAAATGTTTTTT
1 TAGAGGGTTAAAATGTTTTTT
8855282 TA
1 TA
8855284 ATTATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.27, C:0.02, G:0.20, T:0.50
Consensus pattern (21 bp):
TAGAGGGTTAAAATGTTTTTT
Found at i:8861351 original size:10 final size:9
Alignment explanation
Indices: 8861320--8861393 Score: 62
Period size: 10 Copynumber: 8.1 Consensus size: 9
8861310 TATTTCACCT
8861320 AAAAGAGAG
1 AAAAGAGAG
*
8861329 AGATAGAGAG
1 A-AAAGAGAG
8861339 AAAGAGAGAG
1 AAA-AGAGAG
*
8861349 AAAAGAAAG
1 AAAAGAGAG
*
8861358 AAAAGAAAAG
1 AAAAG-AGAG
*
8861368 AAAAGAAAG
1 AAAAGAGAG
8861377 AAAA-AGA-
1 AAAAGAGAG
*
8861384 AAAAAAGAG
1 AAAAGAGAG
8861393 A
1 A
8861394 GGTCAAGATG
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
7 4 0.07
8 5 0.09
9 21 0.38
10 26 0.46
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.01
Consensus pattern (9 bp):
AAAAGAGAG
Found at i:8861362 original size:5 final size:5
Alignment explanation
Indices: 8861347--8861386 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
8861337 AGAAAGAGAG
8861347 AGAAA AG-AA AGAAA AGAAA AGAAA AG-AA AGAAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AG-AAA AGAAA A
8861387 AAAGAGAGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 8 0.25
5 20 0.62
6 4 0.12
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:8862588 original size:46 final size:46
Alignment explanation
Indices: 8862535--8862789 Score: 295
Period size: 46 Copynumber: 5.6 Consensus size: 46
8862525 AAAGTTATCT
* * *
8862535 AATCTTTTACCCTTAAGTCCAGAGGGGCAGATTGAAGCCACCATTC
1 AATCTTTTACCCTTAAATCAAGAGGGGCAGATTGAAGCCACCATCC
* * * *
8862581 AATCTTTTACCCTTAAATCAAAAAGGGCAAATTAAAGCCACCATCC
1 AATCTTTTACCCTTAAATCAAGAGGGGCAGATTGAAGCCACCATCC
* * * * *
8862627 AATCTTTTACCC-CAAA-C-AGA-GGGTAGATTGAAGTCACTATCT
1 AATCTTTTACCCTTAAATCAAGAGGGGCAGATTGAAGCCACCATCC
*
8862669 AATCTTTTACCCGTAAATCAAGAGGGGCAGATTGAAGCCACCATCC
1 AATCTTTTACCCTTAAATCAAGAGGGGCAGATTGAAGCCACCATCC
* * *
8862715 AATCTTTTA-CCTCTAAGTCAAGAGGGGCAAATTGAAGCTACCATCC
1 AATCTTTTACCCT-TAAATCAAGAGGGGCAGATTGAAGCCACCATCC
* * *
8862761 AATCTTTTGCCCTTAAATTAAAAGGGGCA
1 AATCTTTTACCCTTAAATCAAGAGGGGCA
8862790 AATTAAAGTC
Statistics
Matches: 175, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
42 28 0.16
43 5 0.03
44 2 0.01
45 8 0.05
46 129 0.74
47 3 0.02
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (46 bp):
AATCTTTTACCCTTAAATCAAGAGGGGCAGATTGAAGCCACCATCC
Found at i:8862678 original size:88 final size:90
Alignment explanation
Indices: 8862554--8862797 Score: 298
Period size: 88 Copynumber: 2.7 Consensus size: 90
8862544 CCCTTAAGTC
*
8862554 CAGAGGGGCAGATTGAAGCCACCAT-TCAATCTTTTACCCTTAAATCAAAAAGGGCAAATTAAAG
1 CAGAGGGGCAGATTGAAG-CACCATCT-AATCTTTTACCCTTAAATCAAAAGGGGCAAATTAAAG
8862618 CCACCATCCAATCTTTTACC-CCAA-A
64 CCACCATCCAATCTTTTACCTCCAAGA
* * * * * *
8862643 CAGA-GGGTAGATTGAAGTCACTATCTAATCTTTTACCCGTAAATCAAGAGGGGCAGATTGAAGC
1 CAGAGGGGCAGATTGAAG-CACCATCTAATCTTTTACCCTTAAATCAAAAGGGGCAAATTAAAGC
* *
8862707 CACCATCCAATCTTTTACCTCTAAGT
65 CACCATCCAATCTTTTACCTCCAAGA
* * * *
8862733 CAAGAGGGGCAAATTGAAGCTACCATCCAATCTTTTGCCCTTAAATTAAAAGGGGCAAATTAAAG
1 C-AGAGGGGCAGATTGAAGC-ACCATCTAATCTTTTACCCTTAAATCAAAAGGGGCAAATTAAAG
8862798 TCACAGAAGC
Statistics
Matches: 129, Mismatches: 20, Indels: 9
0.82 0.13 0.06
Matches are distributed among these distances:
88 69 0.53
89 8 0.06
90 1 0.01
91 4 0.03
92 47 0.36
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (90 bp):
CAGAGGGGCAGATTGAAGCACCATCTAATCTTTTACCCTTAAATCAAAAGGGGCAAATTAAAGCC
ACCATCCAATCTTTTACCTCCAAGA
Found at i:8862725 original size:134 final size:132
Alignment explanation
Indices: 8862490--8862778 Score: 395
Period size: 134 Copynumber: 2.2 Consensus size: 132
8862480 TACATCACCA
* * * *
8862490 CATCCAATCTTTTGCCCCTAAATCAAGGGTAGATTAAAGTTATCTAATCTTTTACCCTTAAGTCC
1 CATCCAATCTTTTACCCCTAAATCAAGGGTAGATTAAAGTTATCTAATCTTTTACCCGTAAATCA
*
8862555 AGAGGGGCAGATTGAAGCCACCATTCAATCTTTTACC-CTTAAATCAAAAAGGGCAAATTAAAGC
66 AGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCTC-TAAATCAAAAAGGGCAAATTAAAGC
8862619 CAC
130 CAC
*
8862622 CATCCAATCTTTTACCCC-AAA-CAGAGGGTAGATTGAAGTCACTATCTAATCTTTTACCCGTAA
1 CATCCAATCTTTTACCCCTAAATCA-AGGGTAGATTAAAGT---TATCTAATCTTTTACCCGTAA
* * * *
8862685 ATCAAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCTCTAAGTCAAGAGGGGCAAATTGA
62 ATCAAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCTCTAAATCAAAAAGGGCAAATTAA
*
8862750 AGCTAC
127 AGCCAC
* *
8862756 CATCCAATCTTTTGCCCTTAAAT
1 CATCCAATCTTTTACCCCTAAAT
8862779 TAAAAGGGGC
Statistics
Matches: 137, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
130 2 0.01
131 17 0.12
132 17 0.12
134 97 0.71
135 4 0.03
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (132 bp):
CATCCAATCTTTTACCCCTAAATCAAGGGTAGATTAAAGTTATCTAATCTTTTACCCGTAAATCA
AGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCTCTAAATCAAAAAGGGCAAATTAAAGCC
AC
Found at i:8864591 original size:26 final size:26
Alignment explanation
Indices: 8864536--8864592 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
8864526 TTCTTTTAAA
* * *
8864536 AATT-TGTAATCCTTTTATTCTATTT
1 AATTATGTAACCCTTTTAATCTATTC
8864561 AATTATGTAACCCTTTTAAT-TATTC
1 AATTATGTAACCCTTTTAATCTATTC
8864586 ATATTAT
1 A-ATTAT
8864593 TTATTTAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 9 0.33
26 18 0.67
ACGTcount: A:0.30, C:0.12, G:0.04, T:0.54
Consensus pattern (26 bp):
AATTATGTAACCCTTTTAATCTATTC
Found at i:8864956 original size:110 final size:109
Alignment explanation
Indices: 8864748--8864946 Score: 265
Period size: 110 Copynumber: 1.8 Consensus size: 109
8864738 GTAATTTTCT
* * * * * *
8864748 TTTATTTTAGGGAACTCGAGAAGTTGTGCCCTAACGTGTTGGGTATTGTTTTTCTTCGAACCTAA
1 TTTATTTTAAGGAACTCGAAAAATTGTGCCCTAACGTGCTGGGTATAGTTTTTCTTCAAACCTAA
*
8864813 GTAATCAAATATCCTATTTAAAATAGATAAATGTTCAATGTTCA
66 GTAATCAAACATCCTATTTAAAATAGATAAATGTTCAATGTTCA
* *
8864857 TTTATTTTAAAGG-ACTCGAAAAATTGTGTCCTAACGTGCTGGGTATGAGTTTTTCTTTAAACCT
1 TTTATTTT-AAGGAACTCGAAAAATTGTGCCCTAACGTGCTGGGTAT-AGTTTTTCTTCAAACCT
** *
8864921 AAGTAATTGAACATCTTATTTAAAAT
64 AAGTAATCAAACATCCTATTTAAAAT
8864947 CAATGAATGT
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
109 37 0.49
110 39 0.51
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (109 bp):
TTTATTTTAAGGAACTCGAAAAATTGTGCCCTAACGTGCTGGGTATAGTTTTTCTTCAAACCTAA
GTAATCAAACATCCTATTTAAAATAGATAAATGTTCAATGTTCA
Found at i:8875090 original size:21 final size:19
Alignment explanation
Indices: 8875062--8875100 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
8875052 TATTTTATCC
8875062 AATTTTTTATGATTCTATAA
1 AATTTTTTATGATT-TATAA
*
8875082 AATTGTTTTATTATTTATA
1 AATT-TTTTATGATTTATA
8875101 TTCTTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (19 bp):
AATTTTTTATGATTTATAA
Found at i:8877477 original size:20 final size:21
Alignment explanation
Indices: 8877448--8877494 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
8877438 ATGTTTATAT
* * *
8877448 TTTTTATCAATTTAATTTTTA
1 TTTTTATCAAGTTAAATTTGA
8877469 TTTTT-TCAAGTTAAATTTGA
1 TTTTTATCAAGTTAAATTTGA
8877489 TTTTTA
1 TTTTTA
8877495 ATTTTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTTTATCAAGTTAAATTTGA
Found at i:8882374 original size:28 final size:28
Alignment explanation
Indices: 8882316--8882766 Score: 182
Period size: 28 Copynumber: 15.9 Consensus size: 28
8882306 TTACCATTCC
* **
8882316 AGAGTTT-ACCACAAAGGTTTTCCTTTC-
1 AGAGTTTCGCCACAAAGGCGTT-CTTTCT
*
8882343 AGAGGTTCGCCACAAAGGCGTTCTTTCT
1 AGAGTTTCGCCACAAAGGCGTTCTTTCT
* * *
8882371 AGAGCTTT-GTCATAGAGGCGTTCCTTTCT
1 AGAG-TTTCGCCACAAAGGCGTT-CTTTCT
* ** * *
8882400 AGAATTTCTTCACGAAA-GTGTTCTTTCC
1 AGAGTTTCGCCAC-AAAGGCGTTCTTTCT
* * * *
8882428 ATAGTTTCACCACAAAGGCATTCTGTTCC
1 AGAGTTTCGCCACAAAGGCGTTCT-TTCT
* * * *
8882457 A-AATTTTGCCCACAAAGGCTTTCTTTCCC
1 AGAGTTTCG-CCACAAAGGCGTTCTTT-CT
* * *
8882486 AAAGCTTT-ACCATAAAGGCGTTCTTT-T
1 AGAG-TTTCGCCACAAAGGCGTTCTTTCT
* ** * ** *
8882513 CAAAGCATCGCCACAGAGGTTTTCTTTTCC
1 -AGAGTTTCGCCACAAAGGCGTTC-TTTCT
* * * *
8882543 AAAGTTTCGCCATAAAGGCGCTCTTTTT
1 AGAGTTTCGCCACAAAGGCGTTCTTTCT
* * * *
8882571 CAGAGTTTCACCACAAAGGTGCTCTTTTT
1 -AGAGTTTCGCCACAAAGGCGTTCTTTCT
* * ** *
8882600 TGAGGTTCCGCCACAAAGGTATTCTTTCCC
1 AGA-GTTTCGCCACAAAGGCGTTCTTT-CT
* ** * * *
8882630 AAAGTTTTACCACGAAGGCATTCTTTCC
1 AGAGTTTCGCCACAAAGGCGTTCTTTCT
* * *
8882658 AGAGCTTCGCCACAAAGGTGTTCTTTTT
1 AGAGTTTCGCCACAAAGGCGTTCTTTCT
* *
8882686 AAAGTTTTGCCACAAAGGCGTTCTTTCT
1 AGAGTTTCGCCACAAAGGCGTTCTTTCT
* *
8882714 AGAGATT-GCCACAAAGGCATTCTTTCT
1 AGAGTTTCGCCACAAAGGCGTTCTTTCT
** *
8882741 AGAGATTT-TTCACAAAAGCGTTCTTT
1 AGAG-TTTCGCCACAAAGGCGTTCTTT
8882767 ATTAGTGCTT
Statistics
Matches: 318, Mismatches: 86, Indels: 39
0.72 0.19 0.09
Matches are distributed among these distances:
27 38 0.12
28 138 0.43
29 135 0.42
30 4 0.01
31 3 0.01
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (28 bp):
AGAGTTTCGCCACAAAGGCGTTCTTTCT
Found at i:8882567 original size:29 final size:29
Alignment explanation
Indices: 8882419--8882711 Score: 175
Period size: 29 Copynumber: 10.2 Consensus size: 29
8882409 TCACGAAAGT
*
8882419 GTTC-TTTCCATAGTTTCACCACAAAGGC
1 GTTCTTTTCCAAAGTTTCACCACAAAGGC
* * *
8882447 ATTCTGTTCCAAATTTTGC-CCACAAAGGC
1 GTTCTTTTCCAAAGTTT-CACCACAAAGGC
* * *
8882476 TTTCTTTCCCAAAGCTTT-ACCATAAAGGC
1 GTTCTTTTCCAAAG-TTTCACCACAAAGGC
** * * *
8882505 GTTCTTTT-CAAAGCATCGCCACAGAGGT
1 GTTCTTTTCCAAAGTTTCACCACAAAGGC
* * *
8882533 TTTCTTTTCCAAAGTTTCGCCATAAAGGC
1 GTTCTTTTCCAAAGTTTCACCACAAAGGC
* * * *
8882562 GCTCTTTTTCAGAGTTTCACCACAAAGGT
1 GTTCTTTTCCAAAGTTTCACCACAAAGGC
* *** * * * *
8882591 GCTCTTTTTTGAGGTTCCGCCACAAAGGT
1 GTTCTTTTCCAAAGTTTCACCACAAAGGC
* * * *
8882620 ATTCTTTCCCAAAGTTTTACCACGAAGGC
1 GTTCTTTTCCAAAGTTTCACCACAAAGGC
* * * * *
8882649 ATTC-TTTCCAGAGCTTCGCCACAAAGGT
1 GTTCTTTTCCAAAGTTTCACCACAAAGGC
* **
8882677 GTTCTTTT-TAAAGTTTTGCCACAAAGGC
1 GTTCTTTTCCAAAGTTTCACCACAAAGGC
8882705 GTTCTTT
1 GTTCTTT
8882712 CTAGAGATTG
Statistics
Matches: 197, Mismatches: 61, Indels: 14
0.72 0.22 0.05
Matches are distributed among these distances:
27 1 0.01
28 64 0.32
29 128 0.65
30 4 0.02
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.34
Consensus pattern (29 bp):
GTTCTTTTCCAAAGTTTCACCACAAAGGC
Found at i:8882648 original size:87 final size:86
Alignment explanation
Indices: 8882521--8882685 Score: 204
Period size: 87 Copynumber: 1.9 Consensus size: 86
8882511 TTCAAAGCAT
* * * * * * * *
8882521 CGCCACAGAGGTTTTCTTTTCCAAAGTTTCGCCATAAAGGCGCTCTTTTTCAGAGTTTCACCACA
1 CGCCACAAAGGTATTCTTTCCCAAAGTTTCACCACAAAGGCACTC-TTTCCAGAGCTTCACCACA
8882586 AAGGTGCTCTTTTTTGAGGTTC
65 AAGGTGCTCTTTTTTGAGGTTC
* * * *
8882608 CGCCACAAAGGTATTCTTTCCCAAAGTTTTACCACGAAGGCATTCTTTCCAGAGCTTCGCCACAA
1 CGCCACAAAGGTATTCTTTCCCAAAGTTTCACCACAAAGGCACTCTTTCCAGAGCTTCACCACAA
*
8882673 AGGTGTTCTTTTT
66 AGGTGCTCTTTTT
8882686 AAAGTTTTGC
Statistics
Matches: 65, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
86 29 0.45
87 36 0.55
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.34
Consensus pattern (86 bp):
CGCCACAAAGGTATTCTTTCCCAAAGTTTCACCACAAAGGCACTCTTTCCAGAGCTTCACCACAA
AGGTGCTCTTTTTTGAGGTTC
Found at i:8882755 original size:55 final size:56
Alignment explanation
Indices: 8882608--8882766 Score: 178
Period size: 55 Copynumber: 2.8 Consensus size: 56
8882598 TTTGAGGTTC
* * * *
8882608 CGCCACAAAGGTATTCTTTCCCAAAGTTTTACCACGAAGGCATTCTTTCCAGAGCTT
1 CGCCACAAAGGTATTCTTT-CTAAAGTTTTACCACAAAGGCGTTCTTTCCAGAGATT
* * * *
8882665 CGCCACAAAGGTGTTCTTTTTAAAGTTTTGCCACAAAGGCGTTCTTTCTAGAGATT
1 CGCCACAAAGGTATTCTTTCTAAAGTTTTACCACAAAGGCGTTCTTTCCAGAGATT
* * * *
8882721 -GCCACAAAGGCATTCTTTCTAGAGATTTT-TCACAAAAGCGTTCTTT
1 CGCCACAAAGGTATTCTTTCTAAAG-TTTTACCACAAAGGCGTTCTTT
8882767 ATTAGTGCTT
Statistics
Matches: 87, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
55 35 0.40
56 34 0.39
57 18 0.21
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.33
Consensus pattern (56 bp):
CGCCACAAAGGTATTCTTTCTAAAGTTTTACCACAAAGGCGTTCTTTCCAGAGATT
Found at i:8882886 original size:27 final size:28
Alignment explanation
Indices: 8882847--8882913 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
8882837 ACACTTAGAG
*
8882847 ATTCTTTCTAGAGA-TTGCCACAAAGGC
1 ATTCTTTCTAGAGATTTGCCACAAAAGC
* *
8882874 GTTCTTTCTAGAGATTTTCCACAAAAGC
1 ATTCTTTCTAGAGATTTGCCACAAAAGC
8882902 ATTCTTTACTAG
1 ATTCTTT-CTAG
8882914 TGTTTTAGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 13 0.38
28 17 0.50
29 4 0.12
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (28 bp):
ATTCTTTCTAGAGATTTGCCACAAAAGC
Found at i:8882962 original size:142 final size:142
Alignment explanation
Indices: 8882706--8882969 Score: 456
Period size: 142 Copynumber: 1.9 Consensus size: 142
8882696 CACAAAGGCG
* * *
8882706 TTCTTTCTAGAGATTGCCACAAAGGCATTCTTTCTAGAGATTTTTCACAAAAGCGTTCTTTATTA
1 TTCTTTCTAGAGATTGCCACAAAGGCATTCTTTCTAGAGATTTTCCACAAAAGCATTCTTTACTA
*
8882771 GTGCTTTAGGTGATAGGGATTTGCCTAGACTCATATTTCGTGAGGTTTTCCCCTCATTGTCCTAG
66 GTGCTTTAGGTGATAGGGATTTGCCTAGACTCACATTTCGTGAGGTTTTCCCCTCATTGTCCTAG
8882836 AACACTTAGAGA
131 AACACTTAGAGA
*
8882848 TTCTTTCTAGAGATTGCCACAAAGGCGTTCTTTCTAGAGATTTTCCACAAAAGCATTCTTTACTA
1 TTCTTTCTAGAGATTGCCACAAAGGCATTCTTTCTAGAGATTTTCCACAAAAGCATTCTTTACTA
* * *
8882913 GTGTTTTAGGTGATAGGGATTTGCTTAGACTCACATTTTGTGAGGTTTTCCCCTCAT
66 GTGCTTTAGGTGATAGGGATTTGCCTAGACTCACATTTCGTGAGGTTTTCCCCTCAT
8882970 CCTCTCAGAA
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
142 114 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (142 bp):
TTCTTTCTAGAGATTGCCACAAAGGCATTCTTTCTAGAGATTTTCCACAAAAGCATTCTTTACTA
GTGCTTTAGGTGATAGGGATTTGCCTAGACTCACATTTCGTGAGGTTTTCCCCTCATTGTCCTAG
AACACTTAGAGA
Found at i:8883310 original size:21 final size:20
Alignment explanation
Indices: 8883261--8883310 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
8883251 TGAGTTAAAC
* * *
8883261 TAAGTATAAATAGGTTTAAT
1 TAAGTTTAAAAAGGGTTAAT
*
8883281 TAAGATTAAAAAGGGTTAAT
1 TAAGTTTAAAAAGGGTTAAT
8883301 TAAAGTTTAA
1 T-AAGTTTAA
8883311 TGATGAAAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (20 bp):
TAAGTTTAAAAAGGGTTAAT
Found at i:8884224 original size:42 final size:42
Alignment explanation
Indices: 8884113--8884310 Score: 206
Period size: 42 Copynumber: 4.7 Consensus size: 42
8884103 TGATGTATAA
* *
8884113 AAAGGAAGACTCATGTCTC-AGGTTGAGCATGAGAATTTG-TAT
1 AAAGGAAGACTCATGTCTCGA-GATGAGCATGAGAATATGAT-T
* * *
8884155 AAATGGAAGACTCGTGACTCG-GAATGAGCATGAAAATATGATT
1 AAA-GGAAGACTCATGTCTCGAG-ATGAGCATGAGAATATGATT
* *
8884198 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGATT
1 AAAGGAAGACTCATGTCTCGAGATGAGCATGAGAATATGATT
* * **
8884240 AAAGGAAGACTCGTGTCTCGGGATGAAAATGAGAATATGATT
1 AAAGGAAGACTCATGTCTCGAGATGAGCATGAGAATATGATT
* * *
8884282 AAAGGAAGACTTATGACTCGATA-GAGCAT
1 AAAGGAAGACTCATGTCTCGAGATGAGCAT
8884311 AAGATTGATT
Statistics
Matches: 130, Mismatches: 21, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.03
42 92 0.71
43 33 0.25
44 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (42 bp):
AAAGGAAGACTCATGTCTCGAGATGAGCATGAGAATATGATT
Found at i:8884280 original size:84 final size:86
Alignment explanation
Indices: 8884113--8884302 Score: 246
Period size: 84 Copynumber: 2.2 Consensus size: 86
8884103 TGATGTATAA
* *
8884113 AAAGGAAGACTCATGTCTC-AGGTTGAGCATGAGAATTTGTATAAATGGAAGACTCGTGACTCGG
1 AAAGGAAGACTCATGTCTCGAGGATGAGAATGAGAATTTGTATAAATGGAAGACTCGTGACTCGG
**
8884177 AATGAGCATGAAAATATGATT
66 AATGAAAATGAAAATATGATT
*
8884198 AAAGGAAGACTCATGTCTCGA-GATGAGAATGAG-ATTATG-ATTAAA-GGAAGACTCGTGTCTC
1 AAAGGAAGACTCATGTCTCGAGGATGAGAATGAGAATT-TGTA-TAAATGGAAGACTCGTGACTC
* *
8884259 GGGATGAAAATGAGAATATGATT
64 GGAATGAAAATGAAAATATGATT
* *
8884282 AAAGGAAGACTTATGACTCGA
1 AAAGGAAGACTCATGTCTCGA
8884303 TAGAGCATAA
Statistics
Matches: 93, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
84 57 0.61
85 35 0.38
86 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (86 bp):
AAAGGAAGACTCATGTCTCGAGGATGAGAATGAGAATTTGTATAAATGGAAGACTCGTGACTCGG
AATGAAAATGAAAATATGATT
Found at i:8893743 original size:42 final size:42
Alignment explanation
Indices: 8893641--8893869 Score: 280
Period size: 42 Copynumber: 5.4 Consensus size: 42
8893631 TGTATAAAAT
* * *
8893641 GGAAGACTCATGTCTCGAGTTGAGCATGAGAATTTG-TATAAA
1 GGAAGACTCATGTCTCGAGATGAGAATGAGAATATGAT-TAAA
* * * * *
8893683 TGAAAGACTCATGACTCGAAATGAGCATGAAAATATGATTAAA
1 -GGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATTAAA
*
8893726 GGAAGACTCATGTCTCGAGATGAGAATGAGATTATGATTAAA
1 GGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATTAAA
* * * *
8893768 AGAAGACTTATGTCTCGAGATGAGAATGATATTATGATTAAA
1 GGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATTAAA
* *
8893810 GGAAGACTCATGTCTTGGGATGAGAATGAGAATATGATTAAA
1 GGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATTAAA
* *
8893852 GGAAGACTTATGACTCGA
1 GGAAGACTCATGTCTCGA
8893870 TAAAGCATAA
Statistics
Matches: 160, Mismatches: 25, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
42 125 0.78
43 34 0.21
44 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (42 bp):
GGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATTAAA
Found at i:8907982 original size:16 final size:15
Alignment explanation
Indices: 8907949--8907986 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
8907939 TATAAAAAAT
8907949 ATATAAAATAATTAA
1 ATATAAAATAATTAA
8907964 ATACTAAAATAA-TATA
1 ATA-TAAAATAATTA-A
8907980 ATATAAA
1 ATATAAA
8907987 TATTTCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
ATATAAAATAATTAA
Found at i:8909504 original size:5 final size:5
Alignment explanation
Indices: 8909494--8909527 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
8909484 TTTAGACTTG
8909494 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAA
8909528 AGTGTTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:8912259 original size:101 final size:101
Alignment explanation
Indices: 8912084--8912282 Score: 326
Period size: 101 Copynumber: 2.0 Consensus size: 101
8912074 ATGATCTCCA
* * *
8912084 CAAATCAAATCTCTTGAAAACATAGAACAACTGAAAATAAATTCTAAAAACCTACAAAAGAAAGA
1 CAAATCAAATCTCTTGAAAAAAGAGAACAACTGAAAATAAATCCTAAAAACCTACAAAAGAAAGA
* * *
8912149 AAACTAAACTAAATTTAAAAGACTTATTCTAGGCTC
66 AAACTAAACTAAATTCAAAAGACTAATTATAGGCTC
* *
8912185 CAAATCAGATCTCTTGAAAAAAGAGAACAACTGAAAATAAATCCTAAAAACCTACGAAAGAAAGA
1 CAAATCAAATCTCTTGAAAAAAGAGAACAACTGAAAATAAATCCTAAAAACCTACAAAAGAAAGA
8912250 AAACTAAACTAAATTCAAAAGACTAATTATAGG
66 AAACTAAACTAAATTCAAAAGACTAATTATAGG
8912283 TTAAGTGAAT
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
101 90 1.00
ACGTcount: A:0.54, C:0.16, G:0.10, T:0.21
Consensus pattern (101 bp):
CAAATCAAATCTCTTGAAAAAAGAGAACAACTGAAAATAAATCCTAAAAACCTACAAAAGAAAGA
AAACTAAACTAAATTCAAAAGACTAATTATAGGCTC
Found at i:8912995 original size:4 final size:4
Alignment explanation
Indices: 8912986--8913011 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
8912976 ACAGAACATA
8912986 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
8913012 GCAAAAAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:8914897 original size:20 final size:21
Alignment explanation
Indices: 8914869--8914909 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
8914859 GTGTTCTATA
8914869 TAGGATGC-ATGTCGCGACAT
1 TAGGATGCAATGTCGCGACAT
* *
8914889 TAGGGTGCAATGTCGTGACAT
1 TAGGATGCAATGTCGCGACAT
8914910 CGAGCCCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (21 bp):
TAGGATGCAATGTCGCGACAT
Found at i:8914958 original size:15 final size:14
Alignment explanation
Indices: 8914934--8914964 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
8914924 AGCTTATTCG
8914934 ATTTTTATTTTTTT
1 ATTTTTATTTTTTT
8914948 ATTTATTATTTTTTT
1 ATTT-TTATTTTTTT
8914963 AT
1 AT
8914965 GGTTCTGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
ATTTTTATTTTTTT
Found at i:8915061 original size:11 final size:11
Alignment explanation
Indices: 8915042--8915071 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
8915032 AAAATAGACG
8915042 AACAAAATAAA
1 AACAAAATAAA
*
8915053 AATAAAATAAA
1 AACAAAATAAA
8915064 AACAAAAT
1 AACAAAAT
8915072 TTAAAGCGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (11 bp):
AACAAAATAAA
Found at i:8918877 original size:11 final size:11
Alignment explanation
Indices: 8918861--8918885 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
8918851 TATTTAATAT
8918861 TTACGAGGTCA
1 TTACGAGGTCA
8918872 TTACGAGGTCA
1 TTACGAGGTCA
8918883 TTA
1 TTA
8918886 GTATTGTATT
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:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (11 bp):
TTACGAGGTCA
Found at i:8919937 original size:28 final size:28
Alignment explanation
Indices: 8919892--8919969 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
8919882 TGAGGAGTAA
* *
8919892 TCTGA-TTCTGGCTCGAAAGAGCGTTAT
1 TCTGATTTTTGGCTCGAAAGAGCATTAT
* *
8919919 TTTGATTTTTGGCTTGAAAGAGCATTAT
1 TCTGATTTTTGGCTCGAAAGAGCATTAT
* * *
8919947 TCTGATTCTGGGCTCGTAAGAGC
1 TCTGATTTTTGGCTCGAAAGAGC
8919970 TAACCATTCT
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
27 4 0.10
28 37 0.90
ACGTcount: A:0.22, C:0.15, G:0.26, T:0.37
Consensus pattern (28 bp):
TCTGATTTTTGGCTCGAAAGAGCATTAT
Found at i:8920041 original size:25 final size:24
Alignment explanation
Indices: 8919952--8920037 Score: 118
Period size: 24 Copynumber: 3.5 Consensus size: 24
8919942 ATTATTCTGA
*
8919952 TTCTGGGCTCGTAAGAGCTAACCA
1 TTCTGGGCTCGTAAGAGCTAACCT
8919976 TTCTGGGCTCGTAAGAGCTAACCT
1 TTCTGGGCTCGTAAGAGCTAACCT
* * **
8920000 ATCTGGGCTCGTATGAGCTAATTTT
1 TTCTGGGCTCGTAAGAGCTAA-CCT
8920025 TTCTGGGCTCGTA
1 TTCTGGGCTCGTA
8920038 TGAGTTAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
24 42 0.76
25 13 0.24
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.33
Consensus pattern (24 bp):
TTCTGGGCTCGTAAGAGCTAACCT
Found at i:8923363 original size:116 final size:116
Alignment explanation
Indices: 8923225--8923572 Score: 529
Period size: 116 Copynumber: 3.0 Consensus size: 116
8923215 GCAGTTTTTA
* * *
8923225 AACCTTGAAAA-GAGTATTCGATTATTTCGGTTTGAAGAAAAATCGCACCTAATAAGTTAAGGCA
1 AACCTTGAAAAGGA-TATCCGATTATTTCGGTTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCA
** *
8923289 CAAATTTTCAAAACCTGAAATAAAGGAATATTGCCTCGATTTTAAATATTTG
65 CAAATTTTCAAAACCCAAAATAAAGGAATATTGCCTCGATTTTAAATACTTG
* * * * * *
8923341 AACCTTGAAAAGGATATCCGATTGTTCCGGCTTCAAGAAAAATCGTGCCTAGTAAGTTAAGGTAC
1 AACCTTGAAAAGGATATCCGATTATTTCGGTTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCAC
8923406 AAATTTTCAAAACCCAAAATAAAGGAATATTGCCTCGATTTTAAATACTTG
66 AAATTTTCAAAACCCAAAATAAAGGAATATTGCCTCGATTTTAAATACTTG
* *
8923457 AACCTTGAAAAGGGTATCCGATTA-TTCTGGTTTGAAGAAAAATCGCGTCTAGTAAGTTAAGGCA
1 AACCTTGAAAAGGATATCCGATTATTTC-GGTTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCA
*
8923521 CAAATTTTTAAAACCCAAAATAAAGGAATATTGCCTCGATTTTAAATACTTG
65 CAAATTTTCAAAACCCAAAATAAAGGAATATTGCCTCGATTTTAAATACTTG
8923573 TATTTTGGAG
Statistics
Matches: 209, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
115 2 0.01
116 205 0.98
117 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (116 bp):
AACCTTGAAAAGGATATCCGATTATTTCGGTTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCAC
AAATTTTCAAAACCCAAAATAAAGGAATATTGCCTCGATTTTAAATACTTG
Found at i:8923854 original size:28 final size:28
Alignment explanation
Indices: 8923823--8923913 Score: 103
Period size: 29 Copynumber: 3.2 Consensus size: 28
8923813 AAAGGGGTCG
* *
8923823 AAAATG-AAGTTTTGGAGAGTTTAGGGTT
1 AAAATGTAA-TTTTGGAAAGTTTAGGGTA
* *
8923851 AAAATGTAATTTTGAAAAATTTAGGGGTA
1 AAAATGTAATTTTGGAAAGTTTA-GGGTA
*
8923880 AAAATGTAATTTTGGGAAAGTTCAGGGTA
1 AAAATGTAATTTT-GGAAAGTTTAGGGTA
8923909 AAAAT
1 AAAAT
8923914 ATGATTCTTG
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
28 17 0.32
29 29 0.55
30 7 0.13
ACGTcount: A:0.41, C:0.01, G:0.25, T:0.33
Consensus pattern (28 bp):
AAAATGTAATTTTGGAAAGTTTAGGGTA
Found at i:8923907 original size:29 final size:28
Alignment explanation
Indices: 8923823--8923979 Score: 102
Period size: 29 Copynumber: 5.5 Consensus size: 28
8923813 AAAGGGGTCG
* * *
8923823 AAAATG-AAGTTTTGGAGAGTTTAGGGTT
1 AAAATGTAA-TTTTGGAAAGTTCAGGGTA
* * *
8923851 AAAATGTAATTTTGAAAAATTTAGGGGTA
1 AAAATGTAATTTTGGAAAGTTCA-GGGTA
8923880 AAAATGTAATTTTGGGAAAGTTCAGGGTA
1 AAAATGTAATTTT-GGAAAGTTCAGGGTA
* * * *
8923909 AAAATATGATTCTTGG-AAGTTCGGGAGCA
1 AAAATGTAATT-TTGGAAAGTTCAGG-GTA
* * * * * *
8923938 AAAATATGATTTTGAAAAAATTCGGGGTT
1 AAAATGTAATTTTG-GAAAGTTCAGGGTA
8923967 AAAATGTAATTTT
1 AAAATGTAATTTT
8923980 TAAAGAAAAT
Statistics
Matches: 105, Mismatches: 17, Indels: 13
0.78 0.13 0.10
Matches are distributed among these distances:
28 28 0.27
29 60 0.57
30 17 0.16
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (28 bp):
AAAATGTAATTTTGGAAAGTTCAGGGTA
Found at i:8925800 original size:86 final size:86
Alignment explanation
Indices: 8925665--8925866 Score: 332
Period size: 86 Copynumber: 2.3 Consensus size: 86
8925655 GATTTGGTGT
* * *
8925665 ACTTCTCTGTATCTCATCAGGAAGACGACCGCATCACTTGTTTTAATCCACTTTTCTGTGTCTCA
1 ACTTCTCTGTATCTCATTAGGAAGACGACCGCATCACTTGTTTTAATCCACTTCTCTGTATCTCA
8925730 TCAAGAAGACGGATTTGATCC
66 TCAAGAAGACGGATTTGATCC
8925751 ACTTCTCTGTATCTCATTAGGAAGACGACCGCATCACTTGTTTTAATCCACTTCTCTGTATCTCA
1 ACTTCTCTGTATCTCATTAGGAAGACGACCGCATCACTTGTTTTAATCCACTTCTCTGTATCTCA
* * *
8925816 TTAGGAAGACGGATTTGGTCC
66 TCAAGAAGACGGATTTGATCC
* *
8925837 AATTCTCTATATCTCATTAGGAAGACGACC
1 ACTTCTCTGTATCTCATTAGGAAGACGACC
8925867 ATTTTATTGC
Statistics
Matches: 108, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
86 108 1.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (86 bp):
ACTTCTCTGTATCTCATTAGGAAGACGACCGCATCACTTGTTTTAATCCACTTCTCTGTATCTCA
TCAAGAAGACGGATTTGATCC
Found at i:8926026 original size:295 final size:295
Alignment explanation
Indices: 8925496--8926041 Score: 862
Period size: 295 Copynumber: 1.9 Consensus size: 295
8925486 CGTTTTATTA
* * * *
8925496 TTTTAATCCACTTCTCTGTATCTAATTAGGAAGACGGATTTGGTCCACTTCTCTGTGTCTTATCA
1 TTTTAATCCACTTCTCTGTATCTAATTAGGAAGACGGATTTGGTCCAATTCTCTATATCTCATCA
* * * *
8925561 GGAAGACGATCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCAATACGAAGCTGGGGTTCGAA
66 GGAAGACGACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCAATACGAAGCTAGGGTTCAAA
** * *
8925626 GTTTTTCTCACATTGAGTTTTGTTTCATTGATTTGGTGTACTTCTCTGTATCTCATCAGGAAGAC
131 GTTTCGCTCACATTGAGCTTTGTTTCATTGATTTGGTATACTTCTCTGTATCTCATCAGGAAGAC
*
8925691 GACCGCATCACTTGTTTTAATCCACTTTTCTGTGTCTCATCAAGAAGACGGATTTGATCCACTTC
196 GACCGCATCACTTGTTTTAATCCACTTTTCTGTATCTCATCAAGAAGACGGATTTGATCCACTTC
8925756 TCTGTATCTCATTAGGAAGACGACCGCATCACTTG
261 TCTGTATCTCATTAGGAAGACGACCGCATCACTTG
* *
8925791 TTTTAATCCACTTCTCTGTATCTCATTAGGAAGACGGATTTGGTCCAATTCTCTATATCTCATTA
1 TTTTAATCCACTTCTCTGTATCTAATTAGGAAGACGGATTTGGTCCAATTCTCTATATCTCATCA
* * *
8925856 GGAAGACGACCATTTTATTGCTTTGACCTGCTTCTCAGTATCTC-ATCAGGAAGCTAGGGTTCAA
66 GGAAGACGACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCAAT-ACGAAGCTAGGGTTCAA
*
8925920 AGTTTCGCTCATATTGAGCTTTGTTTCATTGATTTGGTATACTTCTCTGTATCTCATCAGGAAGA
130 AGTTTCGCTCACATTGAGCTTTGTTTCATTGATTTGGTATACTTCTCTGTATCTCATCAGGAAGA
** *
8925985 CGATTGCATCACTTGTTTTAATCCACTTCTT-TGTATCTCATCAGGAAGACGGATTTG
195 CGACCGCATCACTTGTTTTAATCCACTT-TTCTGTATCTCATCAAGAAGACGGATTTG
8926042 GATTACTTTT
Statistics
Matches: 227, Mismatches: 22, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
294 2 0.01
295 223 0.98
296 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (295 bp):
TTTTAATCCACTTCTCTGTATCTAATTAGGAAGACGGATTTGGTCCAATTCTCTATATCTCATCA
GGAAGACGACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCAATACGAAGCTAGGGTTCAAA
GTTTCGCTCACATTGAGCTTTGTTTCATTGATTTGGTATACTTCTCTGTATCTCATCAGGAAGAC
GACCGCATCACTTGTTTTAATCCACTTTTCTGTATCTCATCAAGAAGACGGATTTGATCCACTTC
TCTGTATCTCATTAGGAAGACGACCGCATCACTTG
Found at i:8926070 original size:295 final size:294
Alignment explanation
Indices: 8925496--8926116 Score: 858
Period size: 295 Copynumber: 2.1 Consensus size: 294
8925486 CGTTTTATTA
* * * * *
8925496 TTTTAATCCACTTCTCTGTATCTAATTAGGAAGACGGATTTGGTCCACTTCTCTGTGTCTTATCA
1 TTTTAATCCACTTCTCTGTATCTCATTAGGAAGACGGATTTGGTCCAATTCTCTATATCTCATCA
* * * *
8925561 GGAAGACGATCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCAATACGAAGCTGGGGTTCGAA
66 GGAAGACGACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCAATACGAAGCTAGGGTTCAAA
** * *
8925626 GTTTTTCTCACATTGAGTTTTGTTTCATTGATTTGGTGTACTTCTCTGTATCTCATCAGGAAGAC
131 GTTTCGCTCACATTGAGCTTTGTTTCATTGATTTGGTATACTTCTCTGTATCTCATCAGGAAGAC
*
8925691 GACCGCATCACTTGTTTTAATCCACTTTTCTGTGTCTCATCAAGAAGACGGATTTGATCCACTTC
196 GACCGCATCACTTGTTTTAATCCACTTTTCTGTATCTCATCAAGAAGACGGATTTGATCCACTTC
* *
8925756 TCTGTATCTCATTAGGAAGACGACCGCATCACTTG
261 TCTGTATCTCATCAGGAAGACGACCACATCA-TTG
*
8925791 TTTTAATCCACTTCTCTGTATCTCATTAGGAAGACGGATTTGGTCCAATTCTCTATATCTCATTA
1 TTTTAATCCACTTCTCTGTATCTCATTAGGAAGACGGATTTGGTCCAATTCTCTATATCTCATCA
* * *
8925856 GGAAGACGACCATTTTATTGCTTTGACCTGCTTCTCAGTATCTC-ATCAGGAAGCTAGGGTTCAA
66 GGAAGACGACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCAAT-ACGAAGCTAGGGTTCAA
*
8925920 AGTTTCGCTCATATTGAGCTTTGTTTCATTGATTTGGTATACTTCTCTGTATCTCATCAGGAAGA
130 AGTTTCGCTCACATTGAGCTTTGTTTCATTGATTTGGTATACTTCTCTGTATCTCATCAGGAAGA
** * *
8925985 CGATTGCATCACTTGTTTTAATCCACTTCTT-TGTATCTCATCAGGAAGACGGATTTGGAT-TAC
195 CGACCGCATCACTTGTTTTAATCCACTT-TTCTGTATCTCATCAAGAAGACGGATTT-GATCCAC
* * * * *
8926048 TTTTCTACGTCT-TC-TCAGGAAGATGACCACGTTATTG
258 TTCTCT--GTATCTCATCAGGAAGACGACCACATCATTG
*
8926085 TTTTGA-CCTACTTCTCTGTATCTCATTAGGAA
1 TTTTAATCC-ACTTCTCTGTATCTCATTAGGAA
8926117 AATAAGGTTT
Statistics
Matches: 289, Mismatches: 31, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
293 2 0.01
294 33 0.11
295 244 0.84
296 7 0.02
297 3 0.01
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (294 bp):
TTTTAATCCACTTCTCTGTATCTCATTAGGAAGACGGATTTGGTCCAATTCTCTATATCTCATCA
GGAAGACGACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCAATACGAAGCTAGGGTTCAAA
GTTTCGCTCACATTGAGCTTTGTTTCATTGATTTGGTATACTTCTCTGTATCTCATCAGGAAGAC
GACCGCATCACTTGTTTTAATCCACTTTTCTGTATCTCATCAAGAAGACGGATTTGATCCACTTC
TCTGTATCTCATCAGGAAGACGACCACATCATTG
Found at i:8928237 original size:3 final size:3
Alignment explanation
Indices: 8928229--8928255 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
8928219 AGTCATCCCT
8928229 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
8928256 AATATCATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:8937759 original size:117 final size:116
Alignment explanation
Indices: 8937471--8937811 Score: 486
Period size: 108 Copynumber: 3.0 Consensus size: 116
8937461 GCAATTTTTA
* *
8937471 AACCTTGAAAAGGGTATCCGATTATTTCGGTTTGAAGAAAAATCGCACCTAGTATGTTAAGGCAC
1 AACCTTGAAAAGGGTATCCGATTATTCCGGTTTGAAGAAAAATCGCGCCTAGTATGTTAAGGCAC
* *
8937536 AAATTTTCAAAACCCGGAATAAATGAATATTTTG-CTCGATTTTAAATACTTG
66 AAATTTTCAAAACCCGAAATAAAAGAATA--TTGCCTCGATTTTAAATACTTG
* ** *
8937588 AACCTTGAAAA--G-----GA-TA-TCCGATTTGAAGAAAAATTACGCCTAGTAAGTTAAGGCAC
1 AACCTTGAAAAGGGTATCCGATTATTCCGGTTTGAAGAAAAATCGCGCCTAGTATGTTAAGGCAC
8937644 AAAATTTTCAAAACCCGAAATAAAAGAATATTGCCTCGATTTTAAATACTTG
66 -AAATTTTCAAAACCCGAAATAAAAGAATATTGCCTCGATTTTAAATACTTG
8937696 AACCTTGAAAAGGGTATCCGATTATTCCGGTTTGAAGAAAAATCGCGCCTAGTATGTTAAGGCAC
1 AACCTTGAAAAGGGTATCCGATTATTCCGGTTTGAAGAAAAATCGCGCCTAGTATGTTAAGGCAC
* * *
8937761 AAATTTTCGAAACCCAAAATAAAGGAATATTGCCTCGATTTTAAATACTTG
66 AAATTTTCAAAACCCGAAATAAAAGAATATTGCCTCGATTTTAAATACTTG
8937812 TATTTTGGAG
Statistics
Matches: 198, Mismatches: 15, Indels: 23
0.84 0.06 0.10
Matches are distributed among these distances:
107 3 0.02
108 63 0.32
109 29 0.15
110 3 0.02
115 3 0.02
116 50 0.25
117 47 0.24
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (116 bp):
AACCTTGAAAAGGGTATCCGATTATTCCGGTTTGAAGAAAAATCGCGCCTAGTATGTTAAGGCAC
AAATTTTCAAAACCCGAAATAAAAGAATATTGCCTCGATTTTAAATACTTG
Found at i:8937962 original size:14 final size:14
Alignment explanation
Indices: 8937933--8937984 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
8937923 CACGAAAAAT
8937933 TATACGAATGAATAAA
1 TATACGAA--AATAAA
8937949 TATACGAAAATAAA
1 TATACGAAAATAAA
*
8937963 TATAAGAAAAATAAA
1 TATACG-AAAATAAA
8937978 -ATACGAA
1 TATACGAA
8937985 TCATGAATCA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
13 2 0.06
14 15 0.45
15 8 0.24
16 8 0.24
ACGTcount: A:0.63, C:0.06, G:0.10, T:0.21
Consensus pattern (14 bp):
TATACGAAAATAAA
Found at i:8938162 original size:29 final size:28
Alignment explanation
Indices: 8938072--8938235 Score: 107
Period size: 29 Copynumber: 5.6 Consensus size: 28
8938062 AGAAAAAAAG
*
8938072 GGGTCAAAAATG-AAGTTTTGGAGAGTTCA
1 GGGT-AAAAATGTAA-TTTTGGAAAGTTCA
* * * * *
8938101 GGGTTAAAATGTAACTTTAGAAAATTTAA
1 GGGTAAAAATGTAA-TTTTGGAAAGTTCA
*
8938130 GGGTAAAAATGTAATTTTGGGAAAGTTCG
1 GGGTAAAAATGTAATTTT-GGAAAGTTCA
* * *
8938159 GGGTAAAAATATGATTATTTG-AAGTTCGA
1 GGGTAAAAATGTAATT-TTGGAAAGTTC-A
* * * *
8938188 GAGCAAAAATGTGATTTTGGAAAAATTCAA
1 GGGTAAAAATGTAATTTTGG-AAAGTTC-A
*
8938218 GGGTCAAAATGTAATTTT
1 GGGTAAAAATGTAATTTT
8938236 TAAAGAAAAT
Statistics
Matches: 102, Mismatches: 27, Indels: 11
0.73 0.19 0.08
Matches are distributed among these distances:
28 18 0.18
29 62 0.61
30 22 0.22
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (28 bp):
GGGTAAAAATGTAATTTTGGAAAGTTCA
Found at i:8951279 original size:24 final size:24
Alignment explanation
Indices: 8951247--8951302 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
8951237 GCAACTTGTT
8951247 TGTTAGCATAGTGCTGCACCCTTC
1 TGTTAGCATAGTGCTGCACCCTTC
8951271 TGTTAGCATAGTGCTGCACCCTTC
1 TGTTAGCATAGTGCTGCACCCTTC
*
8951295 TGTGAGCA
1 TGTTAGCA
8951303 CAATCGTCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.18, C:0.27, G:0.23, T:0.32
Consensus pattern (24 bp):
TGTTAGCATAGTGCTGCACCCTTC
Found at i:8957114 original size:27 final size:27
Alignment explanation
Indices: 8957061--8957349 Score: 247
Period size: 27 Copynumber: 10.5 Consensus size: 27
8957051 TTCATCATAG
*
8957061 AGGCGTTCCTTTAAAAGAGATTGCCACAA
1 AGGC-TTCCTTT-ACAGAGATTGCCACAA
* * **
8957090 AGTCTTCCTTTATAGAGATCACCACAA
1 AGGCTTCCTTTACAGAGATTGCCACAA
* ** ** *
8957117 TGAATTTATTTACAAAGATTGCCACAA
1 AGGCTTCCTTTACAGAGATTGCCACAA
* * * *
8957144 AGGCTTCTTTTAATAAAGATTGGCACAA
1 AGGCTTCCTTT-ACAGAGATTGCCACAA
* *
8957172 AGGCTTCCTTTACAAAGATTGACACAA
1 AGGCTTCCTTTACAGAGATTGCCACAA
* * *
8957199 AGGCTTCCTTTAATAGAGATCGCTACAA
1 AGGCTTCCTTT-ACAGAGATTGCCACAA
* *
8957227 AGACTTCCTTTACAGAGATTGCCACAG
1 AGGCTTCCTTTACAGAGATTGCCACAA
* *
8957254 A-GCTTTCCTTTAAAGAGATTGACACAA
1 AGGC-TTCCTTTACAGAGATTGCCACAA
* *
8957281 AGGCTTCCTTTAACAGAGATTACTACAA
1 AGGCTTCCTTT-ACAGAGATTGCCACAA
* *
8957309 AGGCTTCCTTTAATAAAGATTGCCACAA
1 AGGCTTCCTTT-ACAGAGATTGCCACAA
*
8957337 AGGCTTCTTTTAC
1 AGGCTTCCTTTAC
8957350 TAGTGTTTTA
Statistics
Matches: 208, Mismatches: 47, Indels: 12
0.78 0.18 0.04
Matches are distributed among these distances:
26 1 0.00
27 104 0.50
28 100 0.48
29 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (27 bp):
AGGCTTCCTTTACAGAGATTGCCACAA
Found at i:8957188 original size:55 final size:55
Alignment explanation
Indices: 8957061--8957349 Score: 280
Period size: 55 Copynumber: 5.2 Consensus size: 55
8957051 TTCATCATAG
* * * ***
8957061 AGGCGTTCCTTTAAAAGAGATTGCCACAAAGTCTTCCTTT-ATAGAGATCACCACAA
1 AGGC-TTCCTTTACAA-AGATTGCCACAAAGGCTTCCTTTAATAAAGATTGGCACAA
* ** ** *
8957117 TGAATTTATTTACAAAGATTGCCACAAAGGCTTCTTTTAATAAAGATTGGCACAA
1 AGGCTTCCTTTACAAAGATTGCCACAAAGGCTTCCTTTAATAAAGATTGGCACAA
* * *
8957172 AGGCTTCCTTTACAAAGATTGACACAAAGGCTTCCTTTAATAGAGA-TCGCTACAA
1 AGGCTTCCTTTACAAAGATTGCCACAAAGGCTTCCTTTAATAAAGATTGGC-ACAA
* * * * *
8957227 AGACTTCCTTTACAGAGATTGCCACAGA-GCTTTCCTTTAA-AGAGATTGACACAA
1 AGGCTTCCTTTACAAAGATTGCCACAAAGGC-TTCCTTTAATAAAGATTGGCACAA
* * * *
8957281 AGGCTTCCTTTAACAGAGATTACTACAAAGGCTTCCTTTAATAAAGATTGCCACAA
1 AGGCTTCCTTT-ACAAAGATTGCCACAAAGGCTTCCTTTAATAAAGATTGGCACAA
*
8957337 AGGCTTCTTTTAC
1 AGGCTTCCTTTAC
8957350 TAGTGTTTTA
Statistics
Matches: 192, Mismatches: 34, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
54 45 0.23
55 122 0.64
56 25 0.13
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (55 bp):
AGGCTTCCTTTACAAAGATTGCCACAAAGGCTTCCTTTAATAAAGATTGGCACAA
Found at i:8957246 original size:82 final size:84
Alignment explanation
Indices: 8957140--8957349 Score: 275
Period size: 82 Copynumber: 2.5 Consensus size: 84
8957130 AAAGATTGCC
* * * *
8957140 ACAAAGGCTTCTTTTAATAAAGATTGGCACAAAGGCTTCCTTTACAA-AGATTGACACAAAGGCT
1 ACAAAGACTTCCTTTAACAAAGATTGCCACAAAGGCTTCCTTTACAAGAGATTGACACAAAGGCT
* *
8957204 TCCTTTAATAGAGATCGCT
66 TCCTTTAACAGAGATCACT
* *
8957223 ACAAAGACTTCCTTT-ACAGAGATTGCCACAGA-GCTTTCCTTTA-AAGAGATTGACACAAAGGC
1 ACAAAGACTTCCTTTAACAAAGATTGCCACAAAGGC-TTCCTTTACAAGAGATTGACACAAAGGC
*
8957285 TTCCTTTAACAGAGATTACT
65 TTCCTTTAACAGAGATCACT
* * *
8957305 ACAAAGGCTTCCTTTAATAAAGATTGCCACAAAGGCTTCTTTTAC
1 ACAAAGACTTCCTTTAACAAAGATTGCCACAAAGGCTTCCTTTAC
8957350 TAGTGTTTTA
Statistics
Matches: 108, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
81 4 0.04
82 68 0.63
83 34 0.31
84 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (84 bp):
ACAAAGACTTCCTTTAACAAAGATTGCCACAAAGGCTTCCTTTACAAGAGATTGACACAAAGGCT
TCCTTTAACAGAGATCACT
Found at i:8961748 original size:27 final size:27
Alignment explanation
Indices: 8961718--8961866 Score: 106
Period size: 27 Copynumber: 5.5 Consensus size: 27
8961708 ATCTTTATAC
* * *
8961718 AGGAACCCTTTGTGGCTAACTATGTAA
1 AGGAAGCCTTTGTGGCTATCTAAGTAA
* * **
8961745 AGGAAGTCATTGTGGC-AGTCTCCGTAA
1 AGGAAGCCTTTGTGGCTA-TCTAAGTAA
*
8961772 AGGAAGCCTTTATGGCTATCTAAGTAA
1 AGGAAGCCTTTGTGGCTATCTAAGTAA
* ** * *
8961799 AGGAAGCCTTCGTAACAATCTTTA-TAA
1 AGGAAGCCTTTGTGGCTATC-TAAGTAA
* * *
8961826 TGGAAGCCTTTGTGGCTGT-TCGAGTAA
1 AGGAAGCCTTTGTGGCTATCT-AAGTAA
8961853 AGGAAGCCTTTGTG
1 AGGAAGCCTTTGTG
8961867 AAGGATATGG
Statistics
Matches: 92, Mismatches: 25, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
25 1 0.01
26 2 0.02
27 86 0.93
28 3 0.03
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (27 bp):
AGGAAGCCTTTGTGGCTATCTAAGTAA
Found at i:8964519 original size:28 final size:28
Alignment explanation
Indices: 8964488--8964546 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
8964478 TCCTTTAAAT
* **
8964488 GATCAGACACAA-GAGTTTCTTTTATAGA
1 GATCA-ACACAACGACTTTCTTCAATAGA
*
8964516 GATCACCACAACGACTTTCTTCAATAGA
1 GATCAACACAACGACTTTCTTCAATAGA
8964544 GAT
1 GAT
8964547 TGCCATAAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (28 bp):
GATCAACACAACGACTTTCTTCAATAGA
Found at i:8964593 original size:28 final size:28
Alignment explanation
Indices: 8964513--8964730 Score: 156
Period size: 28 Copynumber: 7.8 Consensus size: 28
8964503 TTTCTTTTAT
* * * *
8964513 AGAGATCACCACAACGACTTTCTTCAAT
1 AGAGATCACCACAAAGACTTCCTTTAAC
** * * *
8964541 AGAGATTGCCATAAGGACTTCCTTTAAT
1 AGAGATCACCACAAAGACTTCCTTTAAC
*
8964569 AGAGATCGCCACAAAGACTTCCTTTAGA-
1 AGAGATCACCACAAAGACTTCCTTTA-AC
* *
8964597 A-ATGATTACCACAAAGGCTTCCTTTAAC
1 AGA-GATCACCACAAAGACTTCCTTTAAC
* * * * *
8964625 AAAAATCTCCACAAAGGCTTTCTTTAAC
1 AGAGATCACCACAAAGACTTCCTTTAAC
* * *
8964653 AAAGATCACCATAAAGGCTTCCTTTAAC
1 AGAGATCACCACAAAGACTTCCTTTAAC
*
8964681 AGAGATCACCACAAATG-TTTCCTTT-AC
1 AGAGATCACCACAAA-GACTTCCTTTAAC
* **
8964708 AAAGATTTCCACAAAGACATTCC
1 AGAGATCACCACAAAGAC-TTCC
8964731 CTTTCAGAGG
Statistics
Matches: 156, Mismatches: 27, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
26 1 0.01
27 16 0.10
28 136 0.87
29 3 0.02
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.27
Consensus pattern (28 bp):
AGAGATCACCACAAAGACTTCCTTTAAC
Found at i:8964618 original size:56 final size:53
Alignment explanation
Indices: 8964513--8964723 Score: 172
Period size: 56 Copynumber: 3.8 Consensus size: 53
8964503 TTTCTTTTAT
* * * * * *
8964513 AGAGATCACCACAACGACTTTCTTCAATAGAGATTGCCA-TAAGGACTTCCTTTAAT
1 AGAGATCACCACAAAG-CTTCCTTTAA-A-AGATTACCACAAAGG-CTTCCTTTAAC
*
8964569 AGAGATCGCCACAAAGACTTCCTTTAGAAATGATTACCACAAAGGCTTCCTTTAAC
1 AGAGATCACCACAAAG-CTTCCTTTA-AAA-GATTACCACAAAGGCTTCCTTTAAC
* * * * * *
8964625 AAAAATCTCCACAAAGGCTTTCTTTAACAAAGATCACCATAAAGGCTTCCTTTAAC
1 AGAGATCACCACAAA-GCTTCCTTT-A-AAAGATTACCACAAAGGCTTCCTTTAAC
* *
8964681 AGAGATCACCACAAATGTTTCCTTTACAAAGATTTCCACAAAG
1 AGAGATCACCACAAA-GCTTCCTTTA-AAAGATTACCACAAAG
8964724 ACATTCCCTT
Statistics
Matches: 127, Mismatches: 23, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
55 16 0.13
56 101 0.80
57 10 0.08
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (53 bp):
AGAGATCACCACAAAGCTTCCTTTAAAAGATTACCACAAAGGCTTCCTTTAAC
Found at i:8964819 original size:28 final size:29
Alignment explanation
Indices: 8964788--8964862 Score: 73
Period size: 28 Copynumber: 2.6 Consensus size: 29
8964778 AAAGGTGTTT
*
8964788 CCTTTCAGAGGTTTGCCAT-AAGGGC-TCA
1 CCTTTAAGAGGTTTGCCATGAA-GGCTTCA
* * * **
8964816 CCTTTTAGAGTTTTTCCATGAAGGCTTTT
1 CCTTTAAGAGGTTTGCCATGAAGGCTTCA
8964845 CCTTTAAGAGGTTTGCCA
1 CCTTTAAGAGGTTTGCCA
8964863 CAGAGGCTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
28 19 0.51
29 18 0.49
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.37
Consensus pattern (29 bp):
CCTTTAAGAGGTTTGCCATGAAGGCTTCA
Found at i:8964902 original size:57 final size:55
Alignment explanation
Indices: 8964778--8964906 Score: 136
Period size: 57 Copynumber: 2.3 Consensus size: 55
8964768 GTTTTTCCAA
* * * *
8964778 AAAGGTGTTTCCTTTCAGAGGTTTGCCATAAGGGCTCACCTTTTAGAGTTTTTCC
1 AAAGGTTTTTCCTTTAAGAGGTTTGCCACAAGGGCTCACCTTTTAGAGTTTGTCC
* * *
8964833 ATGAAGGCTTTTCCTTTAAGAGGTTTGCCAC-AGAGGCTTATCTTTCTAGAGTTTGTCAC
1 A--AAGGTTTTTCCTTTAAGAGGTTTGCCACAAG-GGCTCACCTTT-TAGAGTTTGTC-C
8964892 AAAGGTTTTT-CTTTA
1 AAAGGTTTTTCCTTTA
8964907 CTGGTGTTTC
Statistics
Matches: 61, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
55 1 0.02
56 7 0.11
57 41 0.67
58 10 0.16
59 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.40
Consensus pattern (55 bp):
AAAGGTTTTTCCTTTAAGAGGTTTGCCACAAGGGCTCACCTTTTAGAGTTTGTCC
Found at i:8973311 original size:15 final size:15
Alignment explanation
Indices: 8973291--8973323 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
8973281 CACTCATAAA
*
8973291 GTTCATTATCCAATC
1 GTTCATTAGCCAATC
8973306 GTTCATTAGCCAATC
1 GTTCATTAGCCAATC
8973321 GTT
1 GTT
8973324 AGACCTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.39
Consensus pattern (15 bp):
GTTCATTAGCCAATC
Found at i:8983391 original size:26 final size:25
Alignment explanation
Indices: 8983356--8983563 Score: 98
Period size: 26 Copynumber: 8.2 Consensus size: 25
8983346 TGAATTGTAA
*
8983356 TAAACACATAAATAACTTGACGAGCG
1 TAAACGCATAAATAAC-TGACGAGCG
* *
8983382 TAAACGCATAAATTAGCTGACAAGCG
1 TAAACGCATAAA-TAACTGACGAGCG
* * ** ** *
8983408 TAAAAGTATGCA-AGTTGGCGAGCG
1 TAAACGCATAAATAACTGACGAGCG
*
8983432 TAAACGCATAAATAAGCTGATGAGCG
1 TAAACGCATAAATAA-CTGACGAGCG
** ** * **
8983458 TAAACGTGTGCA-AGCTGGTGAGCG
1 TAAACGCATAAATAACTGACGAGCG
* *
8983482 TAAACGCATAAATAAGCTGATGAGCA
1 TAAACGCATAAATAA-CTGACGAGCG
** ** * *
8983508 TAAACGTGTGCA-AGCTGGCGAGCG
1 TAAACGCATAAATAACTGACGAGCG
* *
8983532 TAAACGCATAACTAAGCTAACGAGCG
1 TAAACGCATAAATAA-CTGACGAGCG
8983558 TAAACG
1 TAAACG
8983564 TGTATAAGAT
Statistics
Matches: 128, Mismatches: 47, Indels: 14
0.68 0.25 0.07
Matches are distributed among these distances:
24 48 0.38
25 5 0.04
26 72 0.56
27 3 0.02
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (25 bp):
TAAACGCATAAATAACTGACGAGCG
Found at i:8983451 original size:50 final size:50
Alignment explanation
Indices: 8983376--8983566 Score: 283
Period size: 50 Copynumber: 3.8 Consensus size: 50
8983366 AATAACTTGA
* * * * *
8983376 CGAGCGTAAACGCATAAATTAGCTGACAAGCGTAAAAGTATGCAAGTTGG
1 CGAGCGTAAACGCATAAATAAGCTGACGAGCGTAAACGTGTGCAAGCTGG
*
8983426 CGAGCGTAAACGCATAAATAAGCTGATGAGCGTAAACGTGTGCAAGCTGG
1 CGAGCGTAAACGCATAAATAAGCTGACGAGCGTAAACGTGTGCAAGCTGG
* * *
8983476 TGAGCGTAAACGCATAAATAAGCTGATGAGCATAAACGTGTGCAAGCTGG
1 CGAGCGTAAACGCATAAATAAGCTGACGAGCGTAAACGTGTGCAAGCTGG
* *
8983526 CGAGCGTAAACGCATAACTAAGCTAACGAGCGTAAACGTGT
1 CGAGCGTAAACGCATAAATAAGCTGACGAGCGTAAACGTGT
8983567 ATAAGATGGC
Statistics
Matches: 128, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 128 1.00
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Consensus pattern (50 bp):
CGAGCGTAAACGCATAAATAAGCTGACGAGCGTAAACGTGTGCAAGCTGG
Found at i:8983479 original size:24 final size:24
Alignment explanation
Indices: 8983445--8983537 Score: 96
Period size: 24 Copynumber: 3.8 Consensus size: 24
8983435 ACGCATAAAT
8983445 AAGCTGATGAGCGTAAACGTGTGC
1 AAGCTGATGAGCGTAAACGTGTGC
* ****
8983469 AAGCTGGTGAGCGTAAACGCATAAAT
1 AAGCTGATGAGCGTAAACG--TGTGC
*
8983495 AAGCTGATGAGCATAAACGTGTGC
1 AAGCTGATGAGCGTAAACGTGTGC
**
8983519 AAGCTGGCGAGCGTAAACG
1 AAGCTGATGAGCGTAAACG
8983538 CATAACTAAG
Statistics
Matches: 53, Mismatches: 14, Indels: 4
0.75 0.20 0.06
Matches are distributed among these distances:
24 35 0.66
26 18 0.34
ACGTcount: A:0.33, C:0.17, G:0.31, T:0.18
Consensus pattern (24 bp):
AAGCTGATGAGCGTAAACGTGTGC
Found at i:8984755 original size:43 final size:43
Alignment explanation
Indices: 8984642--8984774 Score: 167
Period size: 43 Copynumber: 3.1 Consensus size: 43
8984632 CAAATGCCAC
* * **
8984642 TAAAGAACATGGTCTTTAGCAGCACTTTTCCCACAAACGCTAT
1 TAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGT
* * *
8984685 TAAAGAACATGATCTTTAACGACGCTTTTCCCACAAACGCCGT
1 TAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGT
* ** *
8984728 TAAAGAACATGGTCTTTAGCGGTGCTTTTATCACAAACGCCGC
1 TAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGT
8984771 TAAA
1 TAAA
8984775 ATTAACAGAT
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 76 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (43 bp):
TAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGT
Found at i:8988584 original size:41 final size:41
Alignment explanation
Indices: 8988525--8989015 Score: 565
Period size: 41 Copynumber: 11.8 Consensus size: 41
8988515 ATTAAATAAA
** * * *
8988525 TTAGCGGCGCTTTCCCATAAGCGTTGTTATTGTTCTGATCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
* * * *
8988566 TTAGCGGCGCTTTTCCATAAGCGCCCCTATTGTTCTGATCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
*
8988607 TTAGCGGCGCTTTACCATAAGCGCCGCTATTGCTCTGACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
* *
8988648 TTAGCGGCACTTGCCCATAAGCGCCGCTATTGCTCT-ACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
* * *
8988688 TTAGTGGCGCTTTCCCATAAGCGTCGCTATTGCTCTGACTT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
* * * *
8988729 TTAGCGGCGCTTGCCCTTAGGCACCGCTATTGC-CTTGACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTC-TGACCT
* *
8988770 TTAGCGGTGCTTGCCCATAAGCGCCGCTATTGCTCTGACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
* *
8988811 TTAGCAGCGCTTTCCCATAAGCGCCGCTATTGCCGCTATTGCTCTACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATT---GC---T-CT-GACCT
* * *
8988860 TTAGTGGCGCTTTCCCAAAAGCGCCGCTATTGCTCTGACTT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
* * * * *
8988901 TTAGCGACGCTTGCCCTTAGGCACCGCTATTGC-CTTGACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTC-TGACCT
* *
8988942 TTAGCGGTGCTTGCCCATAAGCGCCGCTATTGCTCTGACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
*
8988983 TTAGCAGCGCTTTCCCATAAGCGCCGCTATTGC
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGC
8989016 CGCTATTGCT
Statistics
Matches: 384, Mismatches: 53, Indels: 26
0.83 0.11 0.06
Matches are distributed among these distances:
40 38 0.10
41 302 0.79
42 4 0.01
43 1 0.00
44 2 0.01
46 2 0.01
47 1 0.00
48 2 0.01
49 32 0.08
ACGTcount: A:0.15, C:0.31, G:0.22, T:0.32
Consensus pattern (41 bp):
TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
Found at i:8988871 original size:49 final size:50
Alignment explanation
Indices: 8988792--8988892 Score: 168
Period size: 49 Copynumber: 2.0 Consensus size: 50
8988782 GCCCATAAGC
*
8988792 GCCGCTATTGCTCTGACCTTTAGCAGCGCTTTCCCATAAGCGCCGCTATT
1 GCCGCTATTGCTCTGACCTTTAGCAGCGCTTTCCCAAAAGCGCCGCTATT
**
8988842 GCCGCTATTGCTCT-ACCTTTAGTGGCGCTTTCCCAAAAGCGCCGCTATT
1 GCCGCTATTGCTCTGACCTTTAGCAGCGCTTTCCCAAAAGCGCCGCTATT
8988891 GC
1 GC
8988893 TCTGACTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 34 0.71
50 14 0.29
ACGTcount: A:0.16, C:0.34, G:0.21, T:0.30
Consensus pattern (50 bp):
GCCGCTATTGCTCTGACCTTTAGCAGCGCTTTCCCAAAAGCGCCGCTATT
Found at i:8988913 original size:131 final size:132
Alignment explanation
Indices: 8988712--8988974 Score: 343
Period size: 131 Copynumber: 2.0 Consensus size: 132
8988702 CCATAAGCGT
* ** * *
8988712 CGCTATTGCTCTGACTTTTAGCGGCGCTTGCCCTTAGGCACCGCTATTGCCTTGACCTTTAGCGG
1 CGCTATTGCTCTGACCTTTAGCGGCGCTTGCCCAAAAGCACCGCTATTGCCTTGACCTTTAGCGA
* * *
8988777 TGCTTGCCCATAAGCGCCGCTATTG-CTCTGACCTTTAGCAGCGCTTTCCCATAAGCGCCGCTAT
66 CGCTTGCCCATAAGCACCGCTATTGCCT-TGACCTTTAGCAGCGCTTGCCCATAAGCGCCGCTAT
8988841 TGC
130 TGC
* * * *
8988844 CGCTATTGCTCT-ACCTTTAGTGGCGCTTTCCCAAAAGCGCCGCTATTG-CTCTGACTTTTAGCG
1 CGCTATTGCTCTGACCTTTAGCGGCGCTTGCCCAAAAGCACCGCTATTGCCT-TGACCTTTAGCG
* * * *
8988907 ACGCTTGCCCTTAGGCACCGCTATTGCCTTGACCTTTAGCGGTGCTTGCCCATAAGCGCCGCTAT
65 ACGCTTGCCCATAAGCACCGCTATTGCCTTGACCTTTAGCAGCGCTTGCCCATAAGCGCCGCTAT
8988972 TGC
130 TGC
8988975 TCTGACCTTT
Statistics
Matches: 113, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
130 2 0.02
131 97 0.86
132 14 0.12
ACGTcount: A:0.15, C:0.32, G:0.22, T:0.30
Consensus pattern (132 bp):
CGCTATTGCTCTGACCTTTAGCGGCGCTTGCCCAAAAGCACCGCTATTGCCTTGACCTTTAGCGA
CGCTTGCCCATAAGCACCGCTATTGCCTTGACCTTTAGCAGCGCTTGCCCATAAGCGCCGCTATT
GC
Found at i:8988914 original size:172 final size:172
Alignment explanation
Indices: 8988605--8989040 Score: 719
Period size: 172 Copynumber: 2.6 Consensus size: 172
8988595 TTGTTCTGAT
* ** * * *
8988605 CTTTAGCGGCGCTTTACCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCACTTGCCCATAA--
1 CTTTAGCGGTGCTTGCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCAGCGCTTTCCCATAAGC
* *
8988668 ---GC----GCCGCTATTGCTCTACCTTTAGTGGCGCTTTCCCATAAGCGTCGCTATTGCTCTGA
66 GCCGCTATTGCCGCTATTGCTCTACCTTTAGTGGCGCTTTCCCAAAAGCGCCGCTATTGCTCTGA
*
8988726 CTTTTAGCGGCGCTTGCCCTTAGGCACCGCTATTGCCTTGAC
131 CTTTTAGCGACGCTTGCCCTTAGGCACCGCTATTGCCTTGAC
8988768 CTTTAGCGGTGCTTGCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCAGCGCTTTCCCATAAGC
1 CTTTAGCGGTGCTTGCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCAGCGCTTTCCCATAAGC
8988833 GCCGCTATTGCCGCTATTGCTCTACCTTTAGTGGCGCTTTCCCAAAAGCGCCGCTATTGCTCTGA
66 GCCGCTATTGCCGCTATTGCTCTACCTTTAGTGGCGCTTTCCCAAAAGCGCCGCTATTGCTCTGA
8988898 CTTTTAGCGACGCTTGCCCTTAGGCACCGCTATTGCCTTGAC
131 CTTTTAGCGACGCTTGCCCTTAGGCACCGCTATTGCCTTGAC
8988940 CTTTAGCGGTGCTTGCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCAGCGCTTTCCCATAAGC
1 CTTTAGCGGTGCTTGCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCAGCGCTTTCCCATAAGC
*
8989005 GCCGCTATTGCCGCTATTGCTCTACCTTTTGTGGCG
66 GCCGCTATTGCCGCTATTGCTCTACCTTTAGTGGCG
8989041 TTTTTTTTTC
Statistics
Matches: 254, Mismatches: 10, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
163 57 0.22
168 2 0.01
172 195 0.77
ACGTcount: A:0.15, C:0.32, G:0.22, T:0.31
Consensus pattern (172 bp):
CTTTAGCGGTGCTTGCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCAGCGCTTTCCCATAAGC
GCCGCTATTGCCGCTATTGCTCTACCTTTAGTGGCGCTTTCCCAAAAGCGCCGCTATTGCTCTGA
CTTTTAGCGACGCTTGCCCTTAGGCACCGCTATTGCCTTGAC
Found at i:8989165 original size:28 final size:28
Alignment explanation
Indices: 8989134--8989190 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
8989124 TTCATTGGGT
*
8989134 AAAAGAATGATGTGGATTGAATAGTAAC
1 AAAAAAATGATGTGGATTGAATAGTAAC
8989162 AAAAAAATGATGTGGATTGAATAGTAAC
1 AAAAAAATGATGTGGATTGAATAGTAAC
8989190 A
1 A
8989191 CTCTGTATCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.49, C:0.04, G:0.23, T:0.25
Consensus pattern (28 bp):
AAAAAAATGATGTGGATTGAATAGTAAC
Found at i:8993176 original size:45 final size:47
Alignment explanation
Indices: 8993091--8993186 Score: 169
Period size: 45 Copynumber: 2.1 Consensus size: 47
8993081 ACCTACTACC
8993091 ATAAAATCTATTCCCAAAACTTTTTTTTAGTGAGATACAAAAATAAG
1 ATAAAATCTATTCCCAAAACTTTTTTTTAGTGAGATACAAAAATAAG
*
8993138 ATAAAATCTA-TCCCCAAAC-TTTTTTTAGTGAGATACAAAAATAAG
1 ATAAAATCTATTCCCAAAACTTTTTTTTAGTGAGATACAAAAATAAG
8993183 ATAA
1 ATAA
8993187 CGCTTAAACA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 30 0.62
46 8 0.17
47 10 0.21
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (47 bp):
ATAAAATCTATTCCCAAAACTTTTTTTTAGTGAGATACAAAAATAAG
Found at i:8994608 original size:51 final size:51
Alignment explanation
Indices: 8994553--8994671 Score: 157
Period size: 51 Copynumber: 2.3 Consensus size: 51
8994543 ACCCTCAAAT
* * * *
8994553 TTTACATATTCTATCAATTTTGTCTTGGTTTAACAAATTTAGCCGGTAACA
1 TTTACATATTCTATCAATTTGGTCATGATTTAACAAATTTAACCGGTAACA
* * * *
8994604 TTTACACATTTTATCAATTTGGTCATGATTTAACAAATTTAACCTGTAATA
1 TTTACATATTCTATCAATTTGGTCATGATTTAACAAATTTAACCGGTAACA
*
8994655 TTTGCATATTCTATCAA
1 TTTACATATTCTATCAA
8994672 CATTTACATA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (51 bp):
TTTACATATTCTATCAATTTGGTCATGATTTAACAAATTTAACCGGTAACA
Found at i:8995011 original size:16 final size:16
Alignment explanation
Indices: 8994992--8995024 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
8994982 ATATATAAAA
8994992 AAAT-ATATATTATTAT
1 AAATCATATA-TATTAT
8995008 AAATCATATATATTAT
1 AAATCATATATATTAT
8995024 A
1 A
8995025 TTATAAAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATCATATATATTAT
Found at i:9008650 original size:162 final size:163
Alignment explanation
Indices: 9008197--9008846 Score: 759
Period size: 161 Copynumber: 4.1 Consensus size: 163
9008187 TATGTATAAA
* * *
9008197 AATAATTTTATATGACATTATATGATCATAATTGACATGATAGGCTTCCATTTCTAATAATTTAT
1 AATAATTTTATATGACATTATATGATCATAATTGACATGATAGGATCCCATTCCTAATAA-TTAT
* * * ** * *
9008262 TTGATTGATTACGAAT-GAATTATTTTGATAATTGACAAAAGATAGTTCGTGAAGATTTCATTCA
65 CTGATTGATTACGAATAG-GTTGTTTCAATAATTGACAAAACATGGTTCGTGAAGATTTCATTCA
*
9008326 TCACATTTTAGTGGAAAATGTGTAGGTAAAATTTC
129 TCACATTTGAGTGGAAAATGTGTAGGTAAAATTTC
* * ** *
9008361 AATAA-TTT-TATGTCATTTTATGATCATAATTGTTATGATAGGA-CTCATTCCTAATAATTTAT
1 AATAATTTTATATGACATTATATGATCATAATTGACATGATAGGATCCCATTCCTAATAA-TTAT
* *
9008423 CTGATTGATTACAAATCA-GTTGTTTCAATAATTGACAAAACATGATTCGTGAAGATTTCATTCA
65 CTGATTGATTACGAAT-AGGTTGTTTCAATAATTGACAAAACATGGTTCGTGAAGATTTCATTCA
*
9008487 TCATATTTGAGTGGAAAATGTGTAGGTAAAATTTC
129 TCACATTTGAGTGGAAAATGTGTAGGTAAAATTTC
9008522 AATAATTTTATATGACATTATATGATCATAATTGACATGATAGGATCCCATTCCTAATAA-TATC
1 AATAATTTTATATGACATTATATGATCATAATTGACATGATAGGATCCCATTCCTAATAATTATC
** * * * *
9008586 CAATTGATTAGGAATAGGTTGTTTCAACAATTGACAAAATATGGTTTGTGAAGATTTCATTCATC
66 TGATTGATTACGAATAGGTTGTTTCAATAATTGACAAAACATGGTTCGTGAAGATTTCATTCATC
9008651 ACA-TTGAGTGGAAAATGTGTAGGTAAAATTTC
131 ACATTTGAGTGGAAAATGTGTAGGTAAAATTTC
*
9008683 AAT-A----AT-T----TTATATGA-C---ATT-ACATGATAGGACCCCATTCCTAATAATTTAT
1 AATAATTTTATATGACATTATATGATCATAATTGACATGATAGGATCCCATTCCTAATAA-TTAT
* *
9008733 ATGATTGATTACGAAT-GGTTTGTTTCAATAATTGACAAAATATGGTTCGTG-A-A--TCA-TCA
65 CTGATTGATTACGAATAGG-TTGTTTCAATAATTGACAAAACATGGTTCGTGAAGATTTCATTCA
* *
9008792 T---ATTTGTGTGGAAAATGTGTAGGTAAAATTTT
129 TCACATTTGAGTGGAAAATGTGTAGGTAAAATTTC
9008824 AATAATTTTATATGACATTATAT
1 AATAATTTTATATGACATTATAT
9008847 AATGGACAGA
Statistics
Matches: 424, Mismatches: 42, Indels: 53
0.82 0.08 0.10
Matches are distributed among these distances:
140 1 0.00
141 30 0.07
142 1 0.00
143 4 0.01
144 3 0.01
146 28 0.07
147 7 0.02
148 45 0.11
150 1 0.00
151 14 0.03
155 1 0.00
156 2 0.00
160 1 0.00
161 140 0.33
162 94 0.22
163 34 0.08
164 18 0.04
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (163 bp):
AATAATTTTATATGACATTATATGATCATAATTGACATGATAGGATCCCATTCCTAATAATTATC
TGATTGATTACGAATAGGTTGTTTCAATAATTGACAAAACATGGTTCGTGAAGATTTCATTCATC
ACATTTGAGTGGAAAATGTGTAGGTAAAATTTC
Found at i:9008833 original size:141 final size:145
Alignment explanation
Indices: 9008556--9008843 Score: 401
Period size: 141 Copynumber: 2.0 Consensus size: 145
9008546 ATCATAATTG
* * *
9008556 ACATGATAGGATCCCATTCCTAATAATATCCAATTGATTAGGAATAGGTTGTTTCAACAATTGAC
1 ACATGATAGGACCCCATTCCTAATAATATACAATTGATTACGAATAGGTTGTTTCAACAATTGAC
*
9008621 AAAATATGGTTTGTGAAGATTTCATTCATCACATTGAGTGGAAAATGTGTAGGTAAAATTTCAAT
66 AAAATATGGTTCGTGAAGA-TTCATTCATCACATTGAGTGGAAAATGTGTAGGTAAAATTTCAAT
9008686 AATTTTATATGACATT
130 AATTTTATATGACATT
** *
9008702 ACATGATAGGACCCCATTCCTAATAATTTATATGATTGATTACGAAT-GGTTTGTTTCAATAATT
1 ACATGATAGGACCCCATTCCTAATAA--TATACAATTGATTACGAATAGG-TTGTTTCAACAATT
* * *
9008766 GACAAAATATGGTTCGTG-A-A-TCA-TCAT-A-TTTGTGTGGAAAATGTGTAGGTAAAATTTTA
63 GACAAAATATGGTTCGTGAAGATTCATTCATCACATTGAGTGGAAAATGTGTAGGTAAAATTTCA
9008825 ATAATTTTATATGACATT
128 ATAATTTTATATGACATT
9008843 A
1 A
9008844 TATAATGGAC
Statistics
Matches: 129, Mismatches: 10, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
141 47 0.36
142 1 0.01
143 4 0.03
144 3 0.02
146 26 0.20
147 3 0.02
148 45 0.35
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (145 bp):
ACATGATAGGACCCCATTCCTAATAATATACAATTGATTACGAATAGGTTGTTTCAACAATTGAC
AAAATATGGTTCGTGAAGATTCATTCATCACATTGAGTGGAAAATGTGTAGGTAAAATTTCAATA
ATTTTATATGACATT
Found at i:9014219 original size:2 final size:2
Alignment explanation
Indices: 9014212--9014282 Score: 65
Period size: 2 Copynumber: 36.0 Consensus size: 2
9014202 AAACTTACAA
* * * * *
9014212 AT AT AT AT AG AGT AT A- AT AA AT AA AT AT AA AT AC AT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
9014254 A- AT AT AT AT GT 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
9014283 CGGAAGAAGA
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
1 2 0.04
2 51 0.94
3 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (2 bp):
AT
Found at i:9015250 original size:39 final size:39
Alignment explanation
Indices: 9015207--9016389 Score: 519
Period size: 39 Copynumber: 30.3 Consensus size: 39
9015197 TCATGATCGA
*
9015207 GGTAAGAGATTGGCTGATGGTGATCTACCTCAGGCTCGG
1 GGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGG
* * ** *** * * *
9015246 GGTAAAAGATCGAATGACT-ACAATTTACCCCAAGCTCAG
1 GGTAAGAGATTGGCTGA-TGGTGATCTACCCCAGGCTCGG
** * * **
9015285 GGTAAGAGATTGATTGATGGTGATATACCTCAACCTCGG
1 GGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGG
* * ** ** *
9015324 GGTAAAAGATCGAATGACT-GCAATC-AGCCCTAGGCTCGG
1 GGTAAGAGATTGGCTGA-TGGTGATCTA-CCCCAGGCTCGG
* * *
9015363 GGTAAGAGATTGACTGGTGGTGATTTACCCCAGGCTCGG
1 GGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGG
* * * * *
9015402 GGTAAAAAAAT--C-GAATGGCTGCAATCTGCCCCAGGCTCAG
1 GGTAAGAGATTGGCTG-ATGG-TG--ATCTACCCCAGGCTCGG
* * * **
9015442 GGTAAGAGATTGGTTGATGGTGATCTGCCCCATGCTCAA
1 GGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGG
* * * *
9015481 GGTAAAAGA-T--C-GAATGGCTACAATCTGCCCCAGGCTCGA
1 GGTAAGAGATTGGCTG-ATGG-T--GATCTACCCCAGGCTCGG
* * * * *
9015520 GGTAAGAGATTGGCTGATGGTGATTTGCCTCATGCTCGA
1 GGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGG
* * * * *
9015559 GGTAAGAGATCGGATGATTGTAATTTACCCCAGGCTCGG
1 GGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGG
* *
9015598 GGTAAGAGATTGGCTGATGGTGATCTACCCCATGCTCGA
1 GGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGG
* * * * * * *
9015637 GGTAAGAGATCGGATGATTGTAATATGCCCCAAGCTCGG
1 GGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGG
* * * * *
9015676 GGTAAGAGATTAGCTGACT-GCGATCTGCCCCAAGCTCGA
1 GGTAAGAGATTGGCTGA-TGGTGATCTACCCCAGGCTCGG
* * *
9015715 GGTAAAAGATT-G--GATGGCTGCAATCTACCCTAAGCTCGG
1 GGTAAGAGATTGGCTGATGG-TG--ATCTACCCCAGGCTCGG
* * * * *
9015754 GGTAAGATATTGGCTGATGGTGACCTGCCCCATGCTCGA
1 GGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGG
* * * **
9015793 GGTAAGAGA-T--CGGATGGCTACAATCTGCCTTAGGCTCGG
1 GGTAAGAGATTGGCTGATGG-T--GATCTACCCCAGGCTCGG
* * *
9015832 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCAG
1 GGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGG
* * * * * ** * *
9015871 AGTAAGAGATCGGATGGTTGCAATCTGCCTCAGGCTCGG
1 GGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGG
* * * * * * **
9015910 GGTAAAAGGTTGGCTGATGGTGATTTGCCTCATGCTCAA
1 GGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGG
* ** * ** * ** *
9015949 GGTAAAAGATCAGATGACT-GCAATTTGTCCTAGGCTCGG
1 GGTAAGAGATTGGCTGA-TGGTGATCTACCCCAGGCTCGG
* ** * *
9015988 GGTAAGAGATTGGCTAATTATGATCT-CTCCTAAGCTCGG
1 GGTAAGAGATTGGCTGATGGTGATCTAC-CCCAGGCTCGG
* ** ** * *
9016027 GGTAAAAGATTGAATGACT-GCAATCTGCCCCAAGCTCGG
1 GGTAAGAGATTGGCTGA-TGGTGATCTACCCCAGGCTCGG
* * * * *
9016066 GGTAAGAGATTGACTGATGGTAATCTGCCCCAAGCTTGG
1 GGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGG
* * * ** *
9016105 GGTAAAAAAAT--CAAATGGCTGTAATCTACCCTAGGCTCGG
1 GGTAAGAGATTGGCTGATGG-TG--ATCTACCCCAGGCTCGG
* * *
9016145 GGTAAGAGATTGACTGATGGTGATCTACTCTAGGCTCGG
1 GGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGG
* * * * *
9016184 GGTAAAAAAAT--CGGATGGCTGTAATTTACCCCAGGCTCGG
1 GGTAAGAGATTGGCTGATGG-TG--ATCTACCCCAGGCTCGG
* *
9016224 GGTAATAGATTGGCTGATGGTGATCTACCCTAGGCTCGG
1 GGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGG
* * * *
9016263 GGTAAGAGATTAGCTGATGGTAATCTACCCTAGGCTTGG
1 GGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGG
* * * * * *
9016302 GGTAAAAGATCGGATGACT--TCAATCTACCCGAGGCTCGA
1 GGTAAGAGATTGGCTGA-TGGT-GATCTACCCCAGGCTCGG
* * * *
9016341 GGTAAGAGACTGACTGATGGTGATCTGCCTCAGGCTCGG
1 GGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGG
*
9016380 GGTAAAAGAT
1 GGTAAGAGAT
9016390 CGAATGGCTT
Statistics
Matches: 861, Mismatches: 228, Indels: 110
0.72 0.19 0.09
Matches are distributed among these distances:
35 2 0.00
36 14 0.02
37 18 0.02
38 15 0.02
39 692 0.80
40 77 0.09
41 10 0.01
42 31 0.04
43 2 0.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (39 bp):
GGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTCGG
Found at i:9015306 original size:78 final size:78
Alignment explanation
Indices: 9015177--9016272 Score: 1028
Period size: 78 Copynumber: 14.0 Consensus size: 78
9015167 CTTTATTGCT
* * * * * * * *
9015177 TCGAATGACTGCAATCTGCCTCATGATCGAGGTAAGAGATTGGCTGATGGTGATCTACCTCAGGC
1 TCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
9015242 TCGGGGTAAAAGA
66 TCGGGGTAAAAGA
* * * * * * ** * * * *
9015255 TCGAATGACTACAATTTACCCCAAGCTCAGGGTAAGAGATTGATTGATGGTGATATACCTCAACC
1 TCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
9015320 TCGGGGTAAAAGA
66 TCGGGGTAAAAGA
* * * * * * * *
9015333 TCGAATGACTGCAATCAGCCCTAGGCTCGGGGTAAGAGATTGACTGGTGGTGATTTACCCCAGGC
1 TCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
*
9015398 TCGGGGTAAAAAAA
66 TCGGGGT-AAAAGA
* * *
9015412 TCGAATGGCTGCAATCTGCCCCAGGCTCAGGGTAAGAGATTGGTTGATGGTGATCTGCCCCATGC
1 TCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
**
9015477 TCAAGGTAAAAGA
66 TCGGGGTAAAAGA
* * * * *
9015490 TCGAATGGCTACAATCTGCCCCAGGCTCGAGGTAAGAGATTGGCTGATGGTGATTTGCCTCATGC
1 TCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
* *
9015555 TCGAGGTAAGAGA
66 TCGGGGTAAAAGA
* ** * * * * *
9015568 TCGGATGATTGTAATTTACCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTACCCCATGC
1 TCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
* *
9015633 TCGAGGTAAGAGA
66 TCGGGGTAAAAGA
* ** * * * * *
9015646 TCGGATGATTGTAATATGCCCCAAGCTCGGGGTAAGAGATTAGCTGACT-GCGATCTGCCCCAAG
1 TCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGA-TGGTGATCTGCCCCAAG
*
9015710 CTCGAGGTAAAAGA
65 CTCGGGGTAAAAGA
* * * * * * * *
9015724 TTGGATGGCTGCAATCTACCCTAAGCTCGGGGTAAGATATTGGCTGATGGTGACCTGCCCCATGC
1 TCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
* *
9015789 TCGAGGTAAGAGA
66 TCGGGGTAAAAGA
* * **
9015802 TCGGATGGCTACAATCTGCCTTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
1 TCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
* * *
9015867 TCAGAGTAAGAGA
66 TCGGGGTAAAAGA
* * * * * * * *
9015880 TCGGATGGTTGCAATCTGCCTCAGGCTCGGGGTAAAAGGTTGGCTGATGGTGATTTGCCTCATGC
1 TCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
**
9015945 TCAAGGTAAAAGA
66 TCGGGGTAAAAGA
* * * * * ** *
9015958 TC-AGATGACTGCAATTTGTCCTAGGCTCGGGGTAAGAGATTGGCTAATTATGATCT-CTCCTAA
1 TCGA-ATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGC-CCCAA
9016021 GCTCGGGGTAAAAGA
64 GCTCGGGGTAAAAGA
* * * * *
9016036 TTGAATGACTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGACTGATGGTAATCTGCCCCAAGC
1 TCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
* *
9016101 TTGGGGTAAAAAAA
66 TCGGGGT-AAAAGA
* * * * * * * * *
9016115 TCAAATGGCTGTAATCTACCCTAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTACTCTAGGC
1 TCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
*
9016180 TCGGGGTAAAAAAA
66 TCGGGGT-AAAAGA
* * * * * * * *
9016194 TCGGATGGCTGTAATTTACCCCAGGCTCGGGGTAATAGATTGGCTGATGGTGATCTACCCTAGGC
1 TCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
*
9016259 TCGGGGTAAGAGA
66 TCGGGGTAAAAGA
9016272 T
1 T
9016273 TAGCTGATGG
Statistics
Matches: 855, Mismatches: 155, Indels: 16
0.83 0.15 0.02
Matches are distributed among these distances:
77 2 0.00
78 649 0.76
79 204 0.24
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.24
Consensus pattern (78 bp):
TCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
TCGGGGTAAAAGA
Found at i:9016147 original size:40 final size:40
Alignment explanation
Indices: 9016085--9016228 Score: 132
Period size: 40 Copynumber: 3.6 Consensus size: 40
9016075 TTGACTGATG
* * * *
9016085 GTAATCTGCCCCAAGCTTGGGGTAAAAAAATCAAATGGCT
1 GTAATCTACCCCAGGCTCGGGGTAAAAAAATCAGATGGCT
* * * * *
9016125 GTAATCTACCCTAGGCTCGGGGTAAGAGATTGACTGATGG-T
1 GTAATCTACCCCAGGCTCGGGGTAAAAAAAT--CAGATGGCT
* * *
9016166 G--ATCTACTCTAGGCTCGGGGTAAAAAAATCGGATGGCT
1 GTAATCTACCCCAGGCTCGGGGTAAAAAAATCAGATGGCT
*
9016204 GTAATTTACCCCAGGCTCGGGGTAA
1 GTAATCTACCCCAGGCTCGGGGTAA
9016229 TAGATTGGCT
Statistics
Matches: 82, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
37 6 0.07
38 2 0.02
39 24 0.29
40 43 0.52
41 2 0.02
42 5 0.06
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (40 bp):
GTAATCTACCCCAGGCTCGGGGTAAAAAAATCAGATGGCT
Found at i:9016893 original size:49 final size:49
Alignment explanation
Indices: 9016715--9017297 Score: 360
Period size: 49 Copynumber: 11.8 Consensus size: 49
9016705 TAAGGTGCTA
* * * * *
9016715 GGTTCGTCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCATGGTACTG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTACCG
* *** * * * *
9016764 GGTTTGTTATTGTGGCCTCAACCTTTCTCATCACACATCTTCTAAGGTATCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCAT--CACATCTTC-ATGGTACCG
* * * * * * *
9016816 GATTCGTCGTCGTGGCCTCAA-TTCTTCCCTTCATC-TCTTCATGGAACCG
1 GGTTCGCCGTTGCGGCCTCAACCT-TTCCCATCA-CATCTTCATGGTACCG
* *
9016865 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAAGTACCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCAT-GGTACCG
* * ** * * * * *
9016915 AGCTCATCATTGCGGCGTCAACCTTTCCCTTCATC-TCTTCTTGGTACTG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCA-CATCTTCATGGTACCG
* * * * *
9016964 GGTTCGCCGTTGCGGCCTTAACTTTTTCCATCACATCTTCTAAGGTACCA
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTC-ATGGTACCG
* * * * *
9017014 GATTCACCGTTGCAGCCTCAATCC-TTCCCTTCATC-TCTTTC-TGGTATCG
1 GGTTCGCCGTTGCGGCCTCAA-CCTTTCCCATCA-CATC-TTCATGGTACCG
* * * ** *
9017063 GGTTTGTCGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAAGTATCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATC-TTCATGGTACCG
* * * * * **
9017113 GATTTGCCATCGCGGCCTCAATCC-TTCCCTTCATC-TCTTCATGGTTTCG
1 GGTTCGCCGTTGCGGCCTCAA-CCTTTCCCATCA-CATCTTCATGGTACCG
* ** * **
9017162 GGTTTGATGTTGCGGCCTCAACCTTT-CCATCACATCTTCTTAGGTGTCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCAT-GGTACCG
* * * *
9017211 GGTTTGCCGTTGCGGCCTCAACCTTTCTCATCACATCTTCTTAGG-ACTG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCAT-GGTACCG
*
9017260 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCA-ATCTT
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTT
9017298 TTAAGGTATC
Statistics
Matches: 414, Mismatches: 97, Indels: 47
0.74 0.17 0.08
Matches are distributed among these distances:
47 1 0.00
48 23 0.06
49 217 0.52
50 127 0.31
51 19 0.05
52 27 0.07
ACGTcount: A:0.15, C:0.31, G:0.18, T:0.36
Consensus pattern (49 bp):
GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTACCG
Found at i:9016967 original size:99 final size:98
Alignment explanation
Indices: 9016715--9017314 Score: 499
Period size: 99 Copynumber: 6.1 Consensus size: 98
9016705 TAAGGTGCTA
* * * * *** *
9016715 GGTTCGTCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCATGGTACTGGGTTTGTTATTGTGGC
1 GGTTCATCGTTGCGGCCTCAACCTTTCCCTTCATCTCTTCATGGTACTGGGTTCGCCGTTGCGGC
*
9016780 CTCAACCTTTCTCATCACACATCTTC-TAAGGTATC
66 CTCAACCTTTCCCAT--CACATCTTCTTAA-GTATC
* * * * * *
9016815 GGATTCGTCGTCGTGGCCTCAA-TTCTTCCCTTCATCTCTTCATGGAACCGGGTTCGCCGTTGCG
1 GG-TTCATCGTTGCGGCCTCAACCT-TTCCCTTCATCTCTTCATGGTACTGGGTTCGCCGTTGCG
*
9016879 GCCTCAACCTTTCCCATCACATCTTCTTAAGTACC
64 GCCTCAACCTTTCCCATCACATCTTCTTAAGTATC
* * * *
9016914 GAGCTCATCATTGCGGCGTCAACCTTTCCCTTCATCTCTTCTTGGTACTGGGTTCGCCGTTGCGG
1 G-GTTCATCGTTGCGGCCTCAACCTTTCCCTTCATCTCTTCATGGTACTGGGTTCGCCGTTGCGG
* * * *
9016979 CCTTAACTTTTTCCATCACATCTTC-TAAGGTACC
65 CCTCAACCTTTCCCATCACATCTTCTTAA-GTATC
* * * * *
9017013 AGATTCACCGTTGCAGCCTCAATCC-TTCCCTTCATCTCTTTC-TGGTA-TCGGGTTTGTCGTTG
1 -GGTTCATCGTTGCGGCCTCAA-CCTTTCCCTTCATCTC-TTCATGGTACT-GGGTTCGCCGTTG
9017075 CGGCCTCAACCTTTCCCATCACATCTT-TTAAAGTATC
62 CGGCCTCAACCTTTCCCATCACATCTTCTT-AAGTATC
*** * * * * **
9017112 GGATTTGCCATCGCGGCCTCAATCC-TTCCCTTCATCTCTTCATGGT-TTCGGGTTTGATGTTGC
1 GG-TTCATCGTTGCGGCCTCAA-CCTTTCCCTTCATCTCTTCATGGTACT-GGGTTCGCCGTTGC
* *
9017175 GGCCTCAACCTTT-CCATCACATCTTCTTAGGTGTC
63 GGCCTCAACCTTTCCCATCACATCTTCTTAAGTATC
*** * * *
9017210 GGGTTTGCCGTTGCGGCCTCAACCTTTCTCATCA-CATCTTCTTAGG-ACTGGGTTCGCCGTTGC
1 -GGTTCATCGTTGCGGCCTCAACCTTTCCCTTCATC-TCTTCAT-GGTACTGGGTTCGCCGTTGC
*
9017273 GGCCTCAACCTTTCCCTTCA-ATCTT-TTAAGGTATC
63 GGCCTCAACCTTTCCCATCACATCTTCTTAA-GTATC
9017308 GGATTCA
1 GG-TTCA
9017315 CCGTCGTGAC
Statistics
Matches: 415, Mismatches: 61, Indels: 50
0.79 0.12 0.10
Matches are distributed among these distances:
97 8 0.02
98 90 0.22
99 236 0.57
100 16 0.04
101 65 0.16
ACGTcount: A:0.15, C:0.31, G:0.18, T:0.36
Consensus pattern (98 bp):
GGTTCATCGTTGCGGCCTCAACCTTTCCCTTCATCTCTTCATGGTACTGGGTTCGCCGTTGCGGC
CTCAACCTTTCCCATCACATCTTCTTAAGTATC
Found at i:9017076 original size:198 final size:196
Alignment explanation
Indices: 9016728--9017311 Score: 583
Period size: 198 Copynumber: 3.0 Consensus size: 196
9016718 TCGTCGTTGT
* * * *
9016728 GGCCTCAACCTTTCCCTTCATATCTTCATGGTACTGGGTTTGTTATTGTGGCCTCAACCTTTCTC
1 GGCCTCAACCTTTCCCTTCATCTCTTCATGGTACTGGGTTTGATGTTGCGGCCTCAACCTTTC-C
* * ** ** *
9016793 ATCACACATCTTCTAAGGTATCGGATTCGTCGTCGTGGCCTCAATTCTTCCCTTCATCTCTTCAT
65 AT--CACATCTTCTAAGGTACCAGATTCACCGTCGCAGCCTCAATCCTTCCCTTCATCTCTTCAT
*
9016858 GGAACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTT-AAGTACCGAGCTCAT
128 GGAACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTT-TTAAAGTACCG-GAT-AT
*
9016922 -CATTGC
190 CCATCGC
* * * ** * *
9016928 GGCGTCAACCTTTCCCTTCATCTCTTCTTGGTACTGGGTTCGCCGTTGCGGCCTTAACTTTTTCC
1 GGCCTCAACCTTTCCCTTCATCTCTTCATGGTACTGGGTTTGATGTTGCGGCCTCAAC-CTTTCC
*
9016993 ATCACATCTTCTAAGGTACCAGATTCACCGTTGCAGCCTCAATCCTTCCCTTCATCTCTTTC-TG
65 ATCACATCTTCTAAGGTACCAGATTCACCGTCGCAGCCTCAATCCTTCCCTTCATCTC-TTCATG
* * * * * *
9017057 GTATCGGGTTTGTCGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAAGTATCGGATTTGCCA
129 GAACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAAGTACCGGATAT-CCA
9017122 TCGC
193 TCGC
*
9017126 GGCCTCAATCC-TTCCCTTCATCTCTTCATGGT-TTCGGGTTTGATGTTGCGGCCTCAACCTTTC
1 GGCCTCAA-CCTTTCCCTTCATCTCTTCATGGTACT-GGGTTTGATGTTGCGGCCTCAACCTTTC
* ** * * ** * * * * *
9017189 CATCACATCTTCTTAGGTGTCGGGTTTGCCGTTGCGGCCTCAA-CCTTTCTCATCA-CATCTTCT
64 CATCACATCTTCTAAGGTACCAGATTCACCGTCGCAGCCTCAATCC-TTCCCTTCATC-TCTTCA
* * * *
9017252 TAGG-ACTGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCA-ATCTTTTAAGGTATCGGAT
127 T-GGAACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAAGTACCGGAT
9017312 TCACCGTCGT
Statistics
Matches: 323, Mismatches: 50, Indels: 26
0.81 0.13 0.07
Matches are distributed among these distances:
196 25 0.08
197 86 0.27
198 151 0.47
199 5 0.02
200 52 0.16
201 4 0.01
ACGTcount: A:0.16, C:0.31, G:0.18, T:0.35
Consensus pattern (196 bp):
GGCCTCAACCTTTCCCTTCATCTCTTCATGGTACTGGGTTTGATGTTGCGGCCTCAACCTTTCCA
TCACATCTTCTAAGGTACCAGATTCACCGTCGCAGCCTCAATCCTTCCCTTCATCTCTTCATGGA
ACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAAGTACCGGATATCCATCG
C
Found at i:9017934 original size:104 final size:107
Alignment explanation
Indices: 9017738--9017935 Score: 231
Period size: 105 Copynumber: 1.9 Consensus size: 107
9017728 TGTTGACCAC
* * * * * * *
9017738 TAACCGTTATTTCAAATGCAAAGATGCTTGAATCAAGGTTATAAGGTGGATGAAATTGGATTTGA
1 TAACCGTTATTTCAAATGCAAAAATGCTTGAATCAAGGTCATAAGGTGAATAAAATTGAATCTCA
*** *
9017803 TTGAAGGCAAAGCTTGCATGAATGAAAAGATCATTGGTTCAT
66 TTGAAGGCAAAGCTCAAATGAAAGAAAAGATCATTGGTTCAT
** * * *
9017845 TAACCGTTATTT-TGATGCAAAAATGCTTGAA-CATGGTCGTAAGGTGAATAAAATTGAATCTCT
1 TAACCGTTATTTCAAATGCAAAAATGCTTGAATCAAGGTCATAAGGTGAATAAAATTGAATCTCA
9017908 TTG-AGGCAAAGCTCAAATGAAAGAAAAG
66 TTGAAGGCAAAGCTCAAATGAAAGAAAAG
9017936 GATTAAAAAT
Statistics
Matches: 75, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
104 21 0.28
105 26 0.35
106 16 0.21
107 12 0.16
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.29
Consensus pattern (107 bp):
TAACCGTTATTTCAAATGCAAAAATGCTTGAATCAAGGTCATAAGGTGAATAAAATTGAATCTCA
TTGAAGGCAAAGCTCAAATGAAAGAAAAGATCATTGGTTCAT
Found at i:9030641 original size:14 final size:14
Alignment explanation
Indices: 9030612--9030645 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
9030602 TTCAAGTAGA
9030612 AATATGTTAATTAT
1 AATATGTTAATTAT
9030626 AATAT-TTAATTAAT
1 AATATGTTAATT-AT
9030640 AATATG
1 AATATG
9030646 ATATGATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (14 bp):
AATATGTTAATTAT
Found at i:9034419 original size:26 final size:26
Alignment explanation
Indices: 9034380--9034432 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
9034370 ATAAAGATTT
*
9034380 ATGATTGTTTAGATTGAAGGATATAA
1 ATGATTGTTCAGATTGAAGGATATAA
*
9034406 ATGATTGTTCAGATTGAAGGATTTAA
1 ATGATTGTTCAGATTGAAGGATATAA
9034432 A
1 A
9034433 CAACATAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.38
Consensus pattern (26 bp):
ATGATTGTTCAGATTGAAGGATATAA
Found at i:9036604 original size:25 final size:25
Alignment explanation
Indices: 9036576--9036623 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
9036566 TTATATATTT
9036576 ATAAATATAAAATA-AATAATATTAA
1 ATAAATATAAAATATAA-AATATTAA
* *
9036601 ATAAATTTCAAATATAAAATATT
1 ATAAATATAAAATATAAAATATT
9036624 TATCAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (25 bp):
ATAAATATAAAATATAAAATATTAA
Found at i:9042823 original size:21 final size:20
Alignment explanation
Indices: 9042799--9042840 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
9042789 TCTTTTATTG
9042799 AAAATAATTGAAG-GAAAATAT
1 AAAATAA-TGAAGAG-AAATAT
*
9042820 AAAATTATGAAGAGAAATAT
1 AAAATAATGAAGAGAAATAT
9042840 A
1 A
9042841 CCTTTTGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.62, C:0.00, G:0.14, T:0.24
Consensus pattern (20 bp):
AAAATAATGAAGAGAAATAT
Found at i:9043270 original size:135 final size:135
Alignment explanation
Indices: 9043002--9043401 Score: 491
Period size: 135 Copynumber: 3.0 Consensus size: 135
9042992 TTAAAGTATT
* * * *
9043002 GATAAAAGTATATACACTTAATTTAGGGCACTTTTGAATTGGACA-TACGTTTATATATGGTTAG
1 GATAAAAATATATACACTTAATTTAAGGCCCCTTTGAA-TGGACAGTACGTTTATATATGGTTAG
* * * * *
9043066 TGT-AAAATAGCGGTGGCGGTGAGATTAGATGTTGTAGCGATATTATAGTGTAAGATAAAAAGAA
65 TGTAAAAATAACGGTGACGGTGAGATTAGATGTTGTAGCGATACTATAGCGTGAGATAAAAAGAA
9043130 AGCTAC
130 AGCTAC
* * * *
9043136 GATAAAAATGTATATACTTAATTTAAGGCCCCTTTGAATGGACAGTGCGTTTATTTATGGTTAGT
1 GATAAAAATATATACACTTAATTTAAGGCCCCTTTGAATGGACAGTACGTTTATATATGGTTAGT
* * * *
9043201 GTAAAAACAACGGTGATGGTGAAATTAGATGTTGTAGCGATACTGTAGCGTGAGATAAAAAGAAA
66 GTAAAAATAACGGTGACGGTGAGATTAGATGTTGTAGCGATACTATAGCGTGAGATAAAAAGAAA
9043266 GCTAC
131 GCTAC
* * * * * *
9043271 GGTAAAAATATATACACTTCATTT-AGAGTCCCTTTGAATTGACAGTACGTTTATCTGTGGTTAG
1 GATAAAAATATATACACTTAATTTAAG-GCCCCTTTGAATGGACAGTACGTTTATATATGGTTAG
* * * * * * *
9043335 TGTAAAAATAACAGTGACGGTGAGAGTAGATGTTATAGTGATACTATAACATGAGATAAAAAAAA
65 TGTAAAAATAACGGTGACGGTGAGATTAGATGTTGTAGCGATACTATAGCGTGAGATAAAAAGAA
9043400 AG
130 AG
9043402 TTAAACACCC
Statistics
Matches: 226, Mismatches: 37, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
133 6 0.03
134 54 0.24
135 166 0.73
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.31
Consensus pattern (135 bp):
GATAAAAATATATACACTTAATTTAAGGCCCCTTTGAATGGACAGTACGTTTATATATGGTTAGT
GTAAAAATAACGGTGACGGTGAGATTAGATGTTGTAGCGATACTATAGCGTGAGATAAAAAGAAA
GCTAC
Found at i:9049339 original size:41 final size:41
Alignment explanation
Indices: 9049294--9049383 Score: 103
Period size: 41 Copynumber: 2.2 Consensus size: 41
9049284 AGAATTCTAG
* *
9049294 AAAAATACTTCCACAT-GGAAGCACTTTTCCTTGAA-TGAGAC
1 AAAAACACCTCCACATAGG-AGCACTTTTCCTT-AATTGAGAC
* **
9049335 AAAAACGCCTCCACATAGGAGCGTTTTTCCTTAATTGAGAC
1 AAAAACACCTCCACATAGGAGCACTTTTCCTTAATTGAGAC
9049376 AAAAACAC
1 AAAAACAC
9049384 TGTGAAAACA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
40 2 0.05
41 37 0.90
42 2 0.05
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.24
Consensus pattern (41 bp):
AAAAACACCTCCACATAGGAGCACTTTTCCTTAATTGAGAC
Found at i:9068700 original size:11 final size:11
Alignment explanation
Indices: 9068684--9068713 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
9068674 GCCTCTAATC
9068684 ATTTTTTTATA
1 ATTTTTTTATA
9068695 A-TTTTTTATA
1 ATTTTTTTATA
9068705 ATTTTTTTA
1 ATTTTTTTA
9068714 AAGTCGGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTTTTTTATA
Done.