Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 269 of 316
Found at i:89102926 original size:48 final size:48
Alignment explanation
Indices: 89102869--89103121 Score: 424
Period size: 48 Copynumber: 5.4 Consensus size: 48
89102859 TACATATTTC
*
89102869 ACATATCTCATATATATTTCACATTAGCCATTCGGATTTACCACATAT
1 ACATATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATAT
*
89102917 ACTTATCTCATA-A-ATTTCACATTAGCCATTCGGCTTTACCACATAT
1 ACATATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATAT
*
89102963 ACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATAT
1 ACATATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATAT
* *
89103011 ACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATAT
1 ACATATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATAT
*
89103059 ACATA-CTCATATATATTTCACATTAGCCATTCGGCTTTACTACA-AT
1 ACATATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATAT
89103105 ACATATCTCATATATAT
1 ACATATCTCATATATAT
89103122 ATCTTGTACA
Statistics
Matches: 195, Mismatches: 7, Indels: 7
0.93 0.03 0.03
Matches are distributed among these distances:
46 50 0.26
47 49 0.25
48 96 0.49
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.36
Consensus pattern (48 bp):
ACATATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATAT
Found at i:89102974 original size:94 final size:96
Alignment explanation
Indices: 89102869--89103121 Score: 424
Period size: 94 Copynumber: 2.7 Consensus size: 96
89102859 TACATATTTC
* *
89102869 ACATATCTCATATATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCATA-A-AT
1 ACATATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
*
89102932 TTCACATTAGCCATTCGGCTTTACCACATAT
66 TTCACACTAGCCATTCGGCTTTACCACATAT
*
89102963 ACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 ACATATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
89103028 TTCACACTAGCCATTCGGCTTTACCACATAT
66 TTCACACTAGCCATTCGGCTTTACCACATAT
* *
89103059 ACATA-CTCATATATATTTCACATTAGCCATTCGGCTTTACTACA-ATACATATCTCATATATAT
1 ACATATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
89103122 ATCTTGTACA
Statistics
Matches: 150, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
94 75 0.50
95 38 0.25
96 37 0.25
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.36
Consensus pattern (96 bp):
ACATATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
TTCACACTAGCCATTCGGCTTTACCACATAT
Found at i:89123912 original size:40 final size:40
Alignment explanation
Indices: 89123829--89124091 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
89123819 TTGAATGCTG
* * * * * *
89123829 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
89123869 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
89123909 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
89123949 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
89123989 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
89124029 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
89124068 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
89124092 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:89124111 original size:79 final size:80
Alignment explanation
Indices: 89123868--89124126 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
89123858 AAGTGAATAT
* * * * * *
89123868 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
89123932 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
89123948 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
89124013 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
89124028 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
89124092 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
89124107 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
89124127 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:89125540 original size:46 final size:46
Alignment explanation
Indices: 89125473--89125766 Score: 378
Period size: 46 Copynumber: 6.4 Consensus size: 46
89125463 GGGGTGTTAC
* * * *
89125473 AGATACCATGGCAACCTGATATG-AAATGTGTAAGATCATGGTTGAA
1 AGATACCATGGCAACATGACA-GAAAATGAGTAAGACCATGGTTGAA
* * * * *
89125519 AGATACCATGGCAACCTGATATG-AAAGGAATAAGGCCATGGTTGAA
1 AGATACCATGGCAACATGACA-GAAAATGAGTAAGACCATGGTTGAA
89125565 AGATACCATGGCAACATGACAGAAAATGAGTAAGACCATGGTTGAA
1 AGATACCATGGCAACATGACAGAAAATGAGTAAGACCATGGTTGAA
* * *
89125611 AGATACCATGGCAGCGTGACATG-AAATGAATAAGACCATGGTTGAA
1 AGATACCATGGCAACATGACA-GAAAATGAGTAAGACCATGGTTGAA
* *
89125657 AGATACCATGGCAACATGACAGCATATGAGTAAGACCATGGTTGAA
1 AGATACCATGGCAACATGACAGAAAATGAGTAAGACCATGGTTGAA
*
89125703 AGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAA
1 AGATACCATGGCAACATGACAGAAAATGAGTAAGACCATGGTTGAA
* * *
89125749 AGACACTATGGCATCATG
1 AGATACCATGGCAACATG
89125767 TCAAAGATAA
Statistics
Matches: 222, Mismatches: 23, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
45 2 0.01
46 219 0.99
47 1 0.00
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (46 bp):
AGATACCATGGCAACATGACAGAAAATGAGTAAGACCATGGTTGAA
Found at i:89125721 original size:138 final size:138
Alignment explanation
Indices: 89125473--89125761 Score: 427
Period size: 138 Copynumber: 2.1 Consensus size: 138
89125463 GGGGTGTTAC
* ** * *
89125473 AGATACCATGGCAACCTGATATGAAATGTGTAAGATCATGGTTGAAAGATACCATGGCAACCTGA
1 AGATACCATGGCAACCTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGA
* *
89125538 TATGAAAGGAATAAGGCCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCA
66 CATGAAAGGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCA
*
89125603 TGGTTGAA
131 TAGTTGAA
* *
89125611 AGATACCATGGCAGCGTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGA
1 AGATACCATGGCAACCTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGA
* * *
89125676 CA-GCATATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACC
66 CATG-AAAGGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACC
89125740 ATAGTTGAA
130 ATAGTTGAA
* *
89125749 AGACACTATGGCA
1 AGATACCATGGCA
89125762 TCATGTCAAA
Statistics
Matches: 135, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
137 1 0.01
138 134 0.99
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (138 bp):
AGATACCATGGCAACCTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGA
CATGAAAGGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCA
TAGTTGAA
Found at i:89126913 original size:4 final size:4
Alignment explanation
Indices: 89126899--89126930 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
89126889 TTATTATTTG
89126899 TGTT T-TT TGTT TGTT TGTT TGTT TGTT TGTT T
1 TGTT TGTT TGTT TGTT TGTT TGTT TGTT TGTT T
89126931 TATTTGGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (4 bp):
TGTT
Found at i:89127883 original size:3 final size:3
Alignment explanation
Indices: 89127875--89128131 Score: 186
Period size: 3 Copynumber: 84.7 Consensus size: 3
89127865 TAATTTTAAC
* * * *
89127875 ATT ATT ATT ATCT -TT ATT TTT ATT ACT ATT ATT ATT ACT ACT ATT
1 ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
89127920 GTT ATT TTT ATT ACT ATT ATT ATT ATT ATT ATT ATT -TT CATT ACT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT
* * * * *
89127965 ATT A-C ATT ATT -TCT TTT TTT ATTT ATTT ATTT ACCT ATT ACTT TTT
1 ATT ATT ATT ATT AT-T ATT ATT A-TT A-TT A-TT A-TT ATT A-TT ATT
** * * * * * *
89128011 A-T ATT CACGC ATT -TT ATT -TT TTT ATC ATG ACT CTC ATT ATT ATT
1 ATT ATT -A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
89128055 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
89128103 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
89128132 ATCCTTTTAT
Statistics
Matches: 204, Mismatches: 36, Indels: 28
0.76 0.13 0.10
Matches are distributed among these distances:
2 11 0.05
3 172 0.84
4 21 0.10
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:89128158 original size:18 final size:18
Alignment explanation
Indices: 89128135--89128169 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
89128125 TTATTATATC
*
89128135 CTTTTATATCATTCCAAA
1 CTTTTATATCATGCCAAA
89128153 CTTTTATATCATGCCAA
1 CTTTTATATCATGCCAA
89128170 CAATTTTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.23, G:0.03, T:0.43
Consensus pattern (18 bp):
CTTTTATATCATGCCAAA
Found at i:89130899 original size:43 final size:44
Alignment explanation
Indices: 89130851--89131006 Score: 165
Period size: 43 Copynumber: 3.6 Consensus size: 44
89130841 TACCGAGATG
* *
89130851 TGATTACATGTAAGACCATGTCTGGGGCATTGGCATTGTAT-TA
1 TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATATA
** *
89130894 TGATTATGTGTAAGACCATGTCTGGGACATTGGCACCGT-TATA
1 TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATATA
*** * * * *
89130937 TGATTTTGTATAAGACCCTGTCTAGGACAGTGGCATCG-ATATA
1 TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATATA
* *
89130980 TGATAACATGTAAGACCATATCTGGGA
1 TGATTACATGTAAGACCATGTCTGGGA
89131007 TATGGCGTTG
Statistics
Matches: 92, Mismatches: 19, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
42 1 0.01
43 91 0.99
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.32
Consensus pattern (44 bp):
TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATATA
Found at i:89137961 original size:24 final size:24
Alignment explanation
Indices: 89137896--89137976 Score: 74
Period size: 23 Copynumber: 3.4 Consensus size: 24
89137886 TTCCCATTAA
** *
89137896 ATGGCTCTTATTGAGCTTCCTGAT
1 ATGGCTCTTCCTGAACTTCCTGAT
*
89137920 A-GGCTCTTCCTGAGCTTCCTGAT
1 ATGGCTCTTCCTGAACTTCCTGAT
* ** *
89137943 ATGGTTCTTTGTGAACTTCCCGATT
1 ATGGCTCTTCCTGAACTTCCTGA-T
89137968 ATGGCTCTT
1 ATGGCTCTT
89137977 ATGAGCTTCC
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
23 21 0.45
24 17 0.36
25 9 0.19
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.41
Consensus pattern (24 bp):
ATGGCTCTTCCTGAACTTCCTGAT
Found at i:89137985 original size:24 final size:24
Alignment explanation
Indices: 89137882--89137992 Score: 88
Period size: 24 Copynumber: 4.6 Consensus size: 24
89137872 TGGCTATCGG
89137882 GAGCTTCCC-ATTAAATGGCTCTTATT
1 GAGCTTCCCGATT--ATGGCTCTTA-T
* *
89137908 GAGCTTCCTGA-TA-GGCTCTTCCT
1 GAGCTTCCCGATTATGGCTCTT-AT
* * *
89137931 GAGCTTCCTGA-TATGGTTCTTTGT
1 GAGCTTCCCGATTATGGCTC-TTAT
*
89137955 GAACTTCCCGATTATGGCTCTTAT
1 GAGCTTCCCGATTATGGCTCTTAT
89137979 GAGCTTCCCG-TTAT
1 GAGCTTCCCGATTAT
89137993 ATAGCCCGAA
Statistics
Matches: 71, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
23 25 0.35
24 27 0.38
25 9 0.13
26 9 0.13
27 1 0.01
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (24 bp):
GAGCTTCCCGATTATGGCTCTTAT
Found at i:89147646 original size:19 final size:19
Alignment explanation
Indices: 89147618--89147708 Score: 125
Period size: 19 Copynumber: 4.9 Consensus size: 19
89147608 AATCATATCT
*
89147618 TCTAAGATTGTATATCATA
1 TCTAAGATTGCATATCATA
*
89147637 TCTAATATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
*
89147655 TCTAATATTG--TATCATA
1 TCTAAGATTGCATATCATA
*
89147672 TCTAAGATTGCATATCACA
1 TCTAAGATTGCATATCATA
89147691 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
89147709 TGAAGATTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
17 15 0.23
18 16 0.25
19 33 0.52
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:89147676 original size:35 final size:36
Alignment explanation
Indices: 89147618--89147700 Score: 114
Period size: 35 Copynumber: 2.3 Consensus size: 36
89147608 AATCATATCT
* *
89147618 TCTAAGATTGTATATCATATCTAATATTGCA-ATCATA
1 TCTAAGATTG--TATCATATCTAAGATTGCATATCACA
*
89147655 TCTAATATTGTATCATATCTAAGATTGCATATCACA
1 TCTAAGATTGTATCATATCTAAGATTGCATATCACA
89147691 TCTAAGATTG
1 TCTAAGATTG
89147701 CATATCATTG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
35 18 0.44
36 14 0.34
37 9 0.22
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (36 bp):
TCTAAGATTGTATCATATCTAAGATTGCATATCACA
Found at i:89148557 original size:207 final size:207
Alignment explanation
Indices: 89148100--89148686 Score: 951
Period size: 207 Copynumber: 2.8 Consensus size: 207
89148090 AAATCTGCTT
* * * *
89148100 CTTCAATTTGTTCCCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
* * *
89148165 GCGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
* * * * * * *
89148230 AGATC-TGCTTTAGTCTAATCATCTGAAGGTTAGATCTGCTATATGTCTGTCCTCCGTCGAATAT
131 GGATCTTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTGCCCTCCATCGAATAT
89148294 GGAGACGCCAAA
196 GGAGACGCCAAA
* * *
89148306 CTTCGATTTGTTCTTTGAAAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAATGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
**
89148371 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAAAATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
**
89148436 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCCATCGAATAT
131 GGATCTTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTGCCCTCCATCGAATAT
89148501 GGAGACGCCAAA
196 GGAGACGCCAAA
* *
89148513 GTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCCTCAACGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
*
89148578 GTGAAAACCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
89148643 GGATCTTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATG
131 GGATCTTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATG
89148687 CTTTAACCTG
Statistics
Matches: 349, Mismatches: 31, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
206 122 0.35
207 227 0.65
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (207 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
GGATCTTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTGCCCTCCATCGAATAT
GGAGACGCCAAA
Found at i:89148948 original size:84 final size:84
Alignment explanation
Indices: 89148807--89148965 Score: 239
Period size: 84 Copynumber: 1.9 Consensus size: 84
89148797 AGTCGTCGTT
* * * *
89148807 GATCTGTTCCACTACTACTTAGGGAGATAAGATCTGTAATTTTAGCCCATTACCCTACTGCTTAG
1 GATCTGCTCCACTACTACTTAGGGAGATAAGATCTGCAAATTTAACCCATTACCCTACTGCTTAG
89148872 AGGG-TTAAGGTAAGTCTTC
66 -GGGATTAAGGTAAGTCTTC
* **
89148891 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAAATTTAACCTGTTACCCTACTGCTTAG
1 GATCTGCTCCACTACTACTTAGGGAGATAAGATCTGCAAATTTAACCCATTACCCTACTGCTTAG
89148956 GGGATTAAGG
66 GGGATTAAGG
89148966 CGCTGAATTT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
83 3 0.04
84 64 0.96
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.31
Consensus pattern (84 bp):
GATCTGCTCCACTACTACTTAGGGAGATAAGATCTGCAAATTTAACCCATTACCCTACTGCTTAG
GGGATTAAGGTAAGTCTTC
Found at i:89149917 original size:1 final size:1
Alignment explanation
Indices: 89149907--89149987 Score: 63
Period size: 1 Copynumber: 81.0 Consensus size: 1
89149897 GGCCTCTCCA
* * * * * * * * * *
89149907 TTTTTCTTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTTCTCTTTTTC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
89149972 TTTTCTTTTTTTTTTT
1 TTTTTTTTTTTTTTTT
89149988 GAAATAGAAG
Statistics
Matches: 58, Mismatches: 22, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:89149924 original size:7 final size:7
Alignment explanation
Indices: 89149907--89149987 Score: 114
Period size: 7 Copynumber: 11.6 Consensus size: 7
89149897 GGCCTCTCCA
89149907 TTTTTCTT
1 TTTTTC-T
89149915 TTTTTCT
1 TTTTTCT
89149922 TTTTTCT
1 TTTTTCT
89149929 TTTTTCT
1 TTTTTCT
89149936 TTTTTCT
1 TTTTTCT
89149943 TTTTTCT
1 TTTTTCT
89149950 TTTTTCTT
1 TTTTTC-T
89149958 TTTTTCT
1 TTTTTCT
89149965 CTTTTTC-
1 -TTTTTCT
89149972 -TTTTCT
1 TTTTTCT
89149978 TTTTT-T
1 TTTTTCT
89149984 TTTT
1 TTTT
89149988 GAAATAGAAG
Statistics
Matches: 69, Mismatches: 0, Indels: 10
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.07
6 5 0.07
7 40 0.58
8 19 0.28
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTCT
Found at i:89155817 original size:17 final size:18
Alignment explanation
Indices: 89155764--89155871 Score: 157
Period size: 17 Copynumber: 6.0 Consensus size: 18
89155754 AATCATATCT
*
89155764 TCTAAGATTGTATATCATA
1 TCTAAGATTG-CTATCATA
*
89155783 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
89155801 TCTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
*
89155818 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
89155836 TCTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
89155853 TCTAAGATTGCATATCATA
1 TCTAAGATTGC-TATCATA
89155872 GAAGATTATA
Statistics
Matches: 81, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
17 32 0.40
18 32 0.40
19 17 0.21
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (18 bp):
TCTAAGATTGCTATCATA
Found at i:89155822 original size:35 final size:35
Alignment explanation
Indices: 89155764--89155871 Score: 189
Period size: 35 Copynumber: 3.0 Consensus size: 35
89155754 AATCATATCT
89155764 TCTAAGATTGTATATCATATCTAAGATTGCAATCATA
1 TCTAAGATTG--TATCATATCTAAGATTGCAATCATA
89155801 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
89155836 TCTAAGATTGTATCATATCTAAGATTGCATATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCA-ATCATA
89155872 GAAGATTATA
Statistics
Matches: 70, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
35 54 0.77
36 6 0.09
37 10 0.14
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (35 bp):
TCTAAGATTGTATCATATCTAAGATTGCAATCATA
Found at i:89156837 original size:17 final size:18
Alignment explanation
Indices: 89156815--89156852 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
89156805 ACTATATAAG
89156815 ATATTA-ATTATTACAAA
1 ATATTATATTATTACAAA
* *
89156832 ATATTATTTTATTATAAA
1 ATATTATATTATTACAAA
89156850 ATA
1 ATA
89156853 AATTTTAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATTATATTATTACAAA
Found at i:89156859 original size:17 final size:18
Alignment explanation
Indices: 89156822--89156859 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
89156812 AAGATATTAA
*
89156822 TTATTACAAAATATTATT
1 TTATTACAAAATATAATT
*
89156840 TTATTATAAAATA-AATT
1 TTATTACAAAATATAATT
89156857 TTA
1 TTA
89156860 GTTCTCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TTATTACAAAATATAATT
Found at i:89161113 original size:41 final size:41
Alignment explanation
Indices: 89161046--89161296 Score: 265
Period size: 41 Copynumber: 6.1 Consensus size: 41
89161036 ATACAAATTA
* * * *
89161046 CCTGACACAATACACCGCCACAAAGCCTGCTAAGCTCAAGG
1 CCTGATACAATACACTGACACAAAGCCTGCTAGGCTCAAGG
* * * *
89161087 CCTGATACAATACACTGACACGAAGCCTACGAGGCTTACA-G
1 CCTGATACAATACACTGACACAAAGCCTGCTAGGCTCA-AGG
* * ** * *
89161128 CCTAATACAATACAC-CAGCATGAAGCTTGCTAGGCTCAAAG
1 CCTGATACAATACACTGA-CACAAAGCCTGCTAGGCTCAAGG
89161169 CCTGATACAATACACT-AGCACAAAGCCTGCTAGGCTCAAGG
1 CCTGATACAATACACTGA-CACAAAGCCTGCTAGGCTCAAGG
* *
89161210 CCTGATACAATACACTGGCACAAAGCCTGCTAGGCTCAAGT
1 CCTGATACAATACACTGACACAAAGCCTGCTAGGCTCAAGG
* * * * *
89161251 CCTGATACAATACTCCGGCACGAAGCCTGTTAGGCTCAAGG
1 CCTGATACAATACACTGACACAAAGCCTGCTAGGCTCAAGG
89161292 CCTGA
1 CCTGA
89161297 CAGAATATCT
Statistics
Matches: 178, Mismatches: 27, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
40 2 0.01
41 175 0.98
42 1 0.01
ACGTcount: A:0.33, C:0.30, G:0.20, T:0.18
Consensus pattern (41 bp):
CCTGATACAATACACTGACACAAAGCCTGCTAGGCTCAAGG
Found at i:89161276 original size:123 final size:123
Alignment explanation
Indices: 89161046--89161303 Score: 340
Period size: 123 Copynumber: 2.1 Consensus size: 123
89161036 ATACAAATTA
* *
89161046 CCTGACACAATACACCGCCACAAAGCCTGCTAAGCTCAAGGCCTGATACAATACACTGACACGAA
1 CCTGACACAATACACAGCCACAAAGCCTGCTAAGCTCAAGGCCTGATACAATACACTGACACAAA
* * *
89161111 GCCTACGAGGCTTACAGCCTAATACAATACACCAGCATGAAGCTTGCTAGGCTCAAAG
66 GCCTACGAGGCTCACAGCCTAATACAATACACCAGCACGAAGCCTGCTAGGCTCAAAG
* * *
89161169 CCTGATACAATACACTAG-CACAAAGCCTGCTAGGCTCAAGGCCTGATACAATACACTGGCACAA
1 CCTGACACAATACAC-AGCCACAAAGCCTGCTAAGCTCAAGGCCTGATACAATACACTGACACAA
* * * * * * *
89161233 AGCCTGCTAGGCTCA-AGTCCTGATACAATACTCCGGCACGAAGCCTGTTAGGCTCAAGG
65 AGCCTACGAGGCTCACAG-CCTAATACAATACACCAGCACGAAGCCTGCTAGGCTCAAAG
*
89161292 CCTGACAGAATA
1 CCTGACACAATA
89161304 TCTCATGTTT
Statistics
Matches: 116, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
122 2 0.02
123 113 0.97
124 1 0.01
ACGTcount: A:0.33, C:0.30, G:0.19, T:0.17
Consensus pattern (123 bp):
CCTGACACAATACACAGCCACAAAGCCTGCTAAGCTCAAGGCCTGATACAATACACTGACACAAA
GCCTACGAGGCTCACAGCCTAATACAATACACCAGCACGAAGCCTGCTAGGCTCAAAG
Found at i:89161295 original size:82 final size:81
Alignment explanation
Indices: 89161046--89161296 Score: 297
Period size: 82 Copynumber: 3.1 Consensus size: 81
89161036 ATACAAATTA
* * * *
89161046 CCTGACACAATACACCGCCACAAAGCCTGCTAAGCTCAAGGCCTGATACAATACACTGACACGAA
1 CCTGATACAATACACCGGCACAAAGCCTGCTAGGCTCAA-GCCTGATACAATACACTGGCACGAA
* * *
89161111 GCCTACGAGGCTTACA-G
65 GCCTGCTAGGCTCA-AGG
* * ** * * *
89161128 CCTAATACAATACACCAGCATGAAGCTTGCTAGGCTCAAAGCCTGATACAATACACTAGCACAAA
1 CCTGATACAATACACCGGCACAAAGCCTGCTAGGCTC-AAGCCTGATACAATACACTGGCACGAA
89161193 GCCTGCTAGGCTCAAGG
65 GCCTGCTAGGCTCAAGG
* * *
89161210 CCTGATACAATACACTGGCACAAAGCCTGCTAGGCTCAAGTCCTGATACAATACTCCGGCACGAA
1 CCTGATACAATACACCGGCACAAAGCCTGCTAGGCTCAAG-CCTGATACAATACACTGGCACGAA
*
89161275 GCCTGTTAGGCTCAAGG
65 GCCTGCTAGGCTCAAGG
89161292 CCTGA
1 CCTGA
89161297 CAGAATATCT
Statistics
Matches: 141, Mismatches: 25, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
81 4 0.03
82 135 0.96
83 2 0.01
ACGTcount: A:0.33, C:0.30, G:0.20, T:0.18
Consensus pattern (81 bp):
CCTGATACAATACACCGGCACAAAGCCTGCTAGGCTCAAGCCTGATACAATACACTGGCACGAAG
CCTGCTAGGCTCAAGG
Found at i:89169537 original size:20 final size:19
Alignment explanation
Indices: 89169508--89169546 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
89169498 ATTTTTTAAA
*
89169508 ATTTTAAAAATTCAAAAAAT
1 ATTTTAAAAAAT-AAAAAAT
*
89169528 ATTTTTAAAAATAAAAAAT
1 ATTTTAAAAAATAAAAAAT
89169547 CATTAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTTTAAAAAATAAAAAAT
Found at i:89172431 original size:24 final size:23
Alignment explanation
Indices: 89172404--89172706 Score: 113
Period size: 24 Copynumber: 12.5 Consensus size: 23
89172394 TCCCGTAAAC
*
89172404 CCACCTGTTCCAATCTATAAACCT
1 CCACCAGTTCCAATCTA-AAACCT
*
89172428 CCACCAGTTCCAGTCTATAAACCT
1 CCACCAGTTCCAATCTA-AAACCT
* * *
89172452 CCTCCAGTTCCAGT-AAAACCACTTCCT
1 CCACCAGTTCCAATCTAAA--A---CCT
* *
89172479 CCACCTGTTCCGATCTACAAACCT
1 CCACCAGTTCCAATCTA-AAACCT
** * * * *
89172503 CCACCAGTTGAAAAACCACATCCT
1 CCACCAGTT-CCAATCTAAAACCT
*
89172527 CCACCTGTTCCAATCTACAAACCT
1 CCACCAGTTCCAATCTA-AAACCT
** * * * *
89172551 CCACCAGTTGAAAAACCACATCCT
1 CCACCAGTT-CCAATCTAAAACCT
*
89172575 CCACCTGTTCCAATCTACAAACCT
1 CCACCAGTTCCAATCTA-AAACCT
** * * * *
89172599 CCACCAGTTGAAAAACCACATCCT
1 CCACCAGTT-CCAATCTAAAACCT
* * *
89172623 CCACCTGTTCCAGTTTATAAACCT
1 CCACCAGTTCCAATCTA-AAACCT
** * * * *
89172647 CCACCAGTTGAAAAACCACATCCT
1 CCACCAGTT-CCAATCTAAAACCT
* *
89172671 CCACCTGTTCCAGTCTATAAACCT
1 CCACCAGTTCCAATCTA-AAACCT
89172695 CCACCAGTTCCA
1 CCACCAGTTCCA
89172707 GTATATAAGA
Statistics
Matches: 192, Mismatches: 72, Indels: 30
0.65 0.24 0.10
Matches are distributed among these distances:
22 2 0.01
23 14 0.07
24 146 0.76
25 13 0.07
27 14 0.07
28 1 0.01
29 2 0.01
ACGTcount: A:0.30, C:0.39, G:0.07, T:0.23
Consensus pattern (23 bp):
CCACCAGTTCCAATCTAAAACCT
Found at i:89172527 original size:48 final size:48
Alignment explanation
Indices: 89172425--89172703 Score: 425
Period size: 48 Copynumber: 5.8 Consensus size: 48
89172415 AATCTATAAA
* * * * *
89172425 CCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTAAAACCACTT
1 CCTCCACCTGTTCCAGTCTACAAACCTCCACCAGTT---GAAAAACCACAT
89172476 CCTCCACCTGTTCC-GATCTACAAACCTCCACCAGTTGAAAAACCACAT
1 CCTCCACCTGTTCCAG-TCTACAAACCTCCACCAGTTGAAAAACCACAT
*
89172524 CCTCCACCTGTTCCAATCTACAAACCTCCACCAGTTGAAAAACCACAT
1 CCTCCACCTGTTCCAGTCTACAAACCTCCACCAGTTGAAAAACCACAT
*
89172572 CCTCCACCTGTTCCAATCTACAAACCTCCACCAGTTGAAAAACCACAT
1 CCTCCACCTGTTCCAGTCTACAAACCTCCACCAGTTGAAAAACCACAT
* *
89172620 CCTCCACCTGTTCCAGTTTATAAACCTCCACCAGTTGAAAAACCACAT
1 CCTCCACCTGTTCCAGTCTACAAACCTCCACCAGTTGAAAAACCACAT
*
89172668 CCTCCACCTGTTCCAGTCTATAAACCTCCACCAGTT
1 CCTCCACCTGTTCCAGTCTACAAACCTCCACCAGTT
89172704 CCAGTATATA
Statistics
Matches: 216, Mismatches: 10, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
48 184 0.85
50 1 0.00
51 31 0.14
ACGTcount: A:0.30, C:0.39, G:0.08, T:0.23
Consensus pattern (48 bp):
CCTCCACCTGTTCCAGTCTACAAACCTCCACCAGTTGAAAAACCACAT
Found at i:89172734 original size:33 final size:33
Alignment explanation
Indices: 89172692--89172870 Score: 160
Period size: 33 Copynumber: 5.7 Consensus size: 33
89172682 AGTCTATAAA
* **
89172692 CCTCCACCAGTTCCAGTATATAAGAAACCATGT
1 CCTCCTCCAGTTCCAGTATATAAGAAACCACAT
* *
89172725 CCTCCACCAGTTCCAGTCTAT-----A--A-AT
1 CCTCCTCCAGTTCCAGTATATAAGAAACCACAT
* * *
89172750 -CTCCTCCGGTTCCAGTATACAAGAAACCGCAT
1 CCTCCTCCAGTTCCAGTATATAAGAAACCACAT
*
89172782 CCTCCTCCAGTTCCAGTCTATAAGAAACCACAT
1 CCTCCTCCAGTTCCAGTATATAAGAAACCACAT
* * **
89172815 CCACCTCCAGTTCCAGTATACAAGAAACCATGT
1 CCTCCTCCAGTTCCAGTATATAAGAAACCACAT
* *
89172848 CCTCCCCCAGTTCCAGTCTATAA
1 CCTCCTCCAGTTCCAGTATATAA
89172871 ATCTCCTCCA
Statistics
Matches: 117, Mismatches: 20, Indels: 18
0.75 0.13 0.12
Matches are distributed among these distances:
24 16 0.14
25 1 0.01
26 1 0.01
28 1 0.01
29 1 0.01
32 2 0.02
33 95 0.81
ACGTcount: A:0.30, C:0.35, G:0.11, T:0.24
Consensus pattern (33 bp):
CCTCCTCCAGTTCCAGTATATAAGAAACCACAT
Found at i:89172747 original size:57 final size:57
Alignment explanation
Indices: 89172667--89173006 Score: 259
Period size: 57 Copynumber: 6.0 Consensus size: 57
89172657 AAAAACCACA
* *
89172667 TCCTCCACCTGTTCCAGTCTATAAACCTCCACCAGTTCCAGTATATAAGAAACCATG
1 TCCTCCACCAGTTCCAGTCTATAAACCTCCACCAGTTCCAGTATACAAGAAACCATG
* * * ***
89172724 TCCTCCACCAGTTCCAGTCTATAAATCTCCTCCGGTTCCAGTATACAAGAAACCGCA
1 TCCTCCACCAGTTCCAGTCTATAAACCTCCACCAGTTCCAGTATACAAGAAACCATG
*
89172781 TCCTCCTCCAGTTCCAGTCTATAAGAAACCACATCCACCTCCAGTTCCAGTATACAAGAAACCAT
1 TCCTCCACCAGTTCCAGTCTAT---AAA-C-C-TCCA---CCAGTTCCAGTATACAAGAAACCAT
89172846 G
57 G
* * * **
89172847 TCCTCCCCCAGTTCCAGTCTATAAATCTCCTCCAGTTCC-G-------G-AACCACA
1 TCCTCCACCAGTTCCAGTCTATAAACCTCCACCAGTTCCAGTATACAAGAAACCATG
* * * * * *
89172895 TCCTCCGCCAGTTCCAGTCCATAAGCCTCCTCCAGTTCCGGTATACAAGAAACGA-G
1 TCCTCCACCAGTTCCAGTCTATAAACCTCCACCAGTTCCAGTATACAAGAAACCATG
* * * * * * * * *
89172951 TCCCTCCTCCGGTTCCAATCTACAAGCCCCCTCCAGTTCCTGTATACAACAAACCA
1 T-CCTCCACCAGTTCCAGTCTATAAACCTCCACCAGTTCCAGTATACAAGAAACCA
89173007 CTACCTCCCC
Statistics
Matches: 229, Mismatches: 35, Indels: 38
0.76 0.12 0.13
Matches are distributed among these distances:
48 40 0.17
49 2 0.01
56 3 0.01
57 127 0.55
60 6 0.03
61 1 0.00
62 1 0.00
63 6 0.03
66 43 0.19
ACGTcount: A:0.27, C:0.37, G:0.12, T:0.24
Consensus pattern (57 bp):
TCCTCCACCAGTTCCAGTCTATAAACCTCCACCAGTTCCAGTATACAAGAAACCATG
Found at i:89172900 original size:24 final size:24
Alignment explanation
Indices: 89172873--89172935 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
89172863 GTCTATAAAT
* *
89172873 CTCCTCCAGTTCCGGAACCA-CATC
1 CTCCTCCAGTTCCGG-ACCATAAGC
* * *
89172897 CTCCGCCAGTTCCAGTCCATAAGC
1 CTCCTCCAGTTCCGGACCATAAGC
89172921 CTCCTCCAGTTCCGG
1 CTCCTCCAGTTCCGG
89172936 TATACAAGAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
23 3 0.10
24 28 0.90
ACGTcount: A:0.17, C:0.44, G:0.16, T:0.22
Consensus pattern (24 bp):
CTCCTCCAGTTCCGGACCATAAGC
Found at i:89173014 original size:57 final size:57
Alignment explanation
Indices: 89172917--89173024 Score: 146
Period size: 57 Copynumber: 1.9 Consensus size: 57
89172907 TCCAGTCCAT
* * * * *
89172917 AAGCCTCCTCCAGTTCCGGTATACAAGAAACGAGTCCCTCCTCC-GGTTCCAATCTAC
1 AAGCCCCCTCCAGTTCCGGTATACAACAAACCACTACCTCC-CCGGGTTCCAATCTAC
*
89172974 AAGCCCCCTCCAGTTCCTGTATACAACAAACCACTACCTCCCCGGGTTCCA
1 AAGCCCCCTCCAGTTCCGGTATACAACAAACCACTACCTCCCCGGGTTCCA
89173025 GTGTATACGA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
56 2 0.05
57 42 0.95
ACGTcount: A:0.25, C:0.40, G:0.14, T:0.21
Consensus pattern (57 bp):
AAGCCCCCTCCAGTTCCGGTATACAACAAACCACTACCTCCCCGGGTTCCAATCTAC
Found at i:89173026 original size:228 final size:228
Alignment explanation
Indices: 89172619--89173057 Score: 515
Period size: 228 Copynumber: 1.9 Consensus size: 228
89172609 AAAAACCACA
* * * *
89172619 TCCTCCACCTGTTCCAGTTTATAAACCTCCACCAGTTGAAAAACCACATCCTCCACCTGTTCCAG
1 TCCTCCACCAGTTCCAGTCTATAAACCTCCACCAGTTCAAAAACCACATCCTCCACCAGTTCCAG
* * * *
89172684 TCTATAAACCTCCACCAGTTCCAGTATATAAGAAACCATGTCCTCCACCAGTTCCAGTCTATAAA
66 TCCATAAACCTCCACCAGTTCCAGTATACAAGAAACCATGTCCTCCACCAGTTCCAATCTACAAA
* * * * *
89172749 TCTCCTCCGGTTCCAGTATACAAGAAACCGCATCCTCCTCCAGTTCCAGTCTATAAGAAACCACA
131 CCCCCTCCAGTTCCAGTATACAACAAACCACATCCTCCTCCAGTTCCAGTCTATAAGAAACCACA
*
89172814 TCCACCTCCAGTTCCAGTATACAAGAAACCATG
196 TCCACCACCAGTTCCAGTATACAAGAAACCATG
* * * *** *
89172847 TCCTCCCCCAGTTCCAGTCTATAAATCTCCTCCAGTTCCGGAACCACATCCTCCGCCAGTTCCAG
1 TCCTCCACCAGTTCCAGTCTATAAACCTCCACCAGTTCAAAAACCACATCCTCCACCAGTTCCAG
* * * * * *
89172912 TCCATAAGCCTCCTCCAGTTCCGGTATACAAGAAACGA-GTCCCTCCTCCGGTTCCAATCTACAA
66 TCCATAAACCTCCACCAGTTCCAGTATACAAGAAACCATGT-CCTCCACCAGTTCCAATCTACAA
* * * * * *
89172976 GCCCCCTCCAGTTCCTGTATACAACAAACCAC-TACCTCC-CCGGGTTCCAGTGTATACGAAGCC
130 ACCCCCTCCAGTTCCAGTATACAACAAACCACAT-CCTCCTCC-AGTTCCAGTCTATAAGAAACC
* *
89173039 ACTTCCACCACCTGTTCCA
193 ACATCCACCACCAGTTCCA
89173058 ACCTACAATC
Statistics
Matches: 173, Mismatches: 35, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
227 5 0.03
228 168 0.97
ACGTcount: A:0.27, C:0.37, G:0.12, T:0.24
Consensus pattern (228 bp):
TCCTCCACCAGTTCCAGTCTATAAACCTCCACCAGTTCAAAAACCACATCCTCCACCAGTTCCAG
TCCATAAACCTCCACCAGTTCCAGTATACAAGAAACCATGTCCTCCACCAGTTCCAATCTACAAA
CCCCCTCCAGTTCCAGTATACAACAAACCACATCCTCCTCCAGTTCCAGTCTATAAGAAACCACA
TCCACCACCAGTTCCAGTATACAAGAAACCATG
Found at i:89173124 original size:18 final size:18
Alignment explanation
Indices: 89173101--89173136 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
89173091 TACAAGCCAC
89173101 TCCCTCCACTTCCC-AAGA
1 TCCCTCCA-TTCCCTAAGA
89173119 TCCCTCCATTCCCTAAGA
1 TCCCTCCATTCCCTAAGA
89173137 AGCCATGCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.22, C:0.47, G:0.06, T:0.25
Consensus pattern (18 bp):
TCCCTCCATTCCCTAAGA
Found at i:89173208 original size:60 final size:60
Alignment explanation
Indices: 89173144--89173266 Score: 212
Period size: 60 Copynumber: 2.0 Consensus size: 60
89173134 AGAAGCCATG
89173144 CCCTCCCCTTCCTAAGCTACCTCCTCTTCCC-AAGATTCCTCCCAAGTATTTCCACCACCA
1 CCCTCCCCTTCCTAAGCTACCTCCTC-TCCCTAAGATTCCTCCCAAGTATTTCCACCACCA
* *
89173204 CCCTCCTCTTCCTAAGCTGCCTCCTCTCCCTAAGATTCCTCCCAAGTATTTCCACCACCA
1 CCCTCCCCTTCCTAAGCTACCTCCTCTCCCTAAGATTCCTCCCAAGTATTTCCACCACCA
89173264 CCC
1 CCC
89173267 CAAGTTCGGA
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
59 4 0.07
60 56 0.93
ACGTcount: A:0.19, C:0.49, G:0.06, T:0.27
Consensus pattern (60 bp):
CCCTCCCCTTCCTAAGCTACCTCCTCTCCCTAAGATTCCTCCCAAGTATTTCCACCACCA
Found at i:89173244 original size:18 final size:18
Alignment explanation
Indices: 89173205--89173245 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
89173195 CCACCACCAC
* *
89173205 CCTCCTCTTCCTAAGCTG
1 CCTCCTCTCCCTAAGATG
*
89173223 CCTCCTCTCCCTAAGATT
1 CCTCCTCTCCCTAAGATG
89173241 CCTCC
1 CCTCC
89173246 CAAGTATTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.49, G:0.07, T:0.32
Consensus pattern (18 bp):
CCTCCTCTCCCTAAGATG
Found at i:89173286 original size:60 final size:60
Alignment explanation
Indices: 89173163--89173288 Score: 157
Period size: 60 Copynumber: 2.1 Consensus size: 60
89173153 TCCTAAGCTA
** * **
89173163 CCTCCTCTTCCCAAGATTCCTCCCAAGTATTTCCACCACCACCCTCCTCTTCCTAAGCTG
1 CCTCCTCTTCCCAAGATTCCTCCCAAGTATTTCCACCACCACCCTCAACTTCCGAAAATG
* *
89173223 CCTCCTC-TCCCTAAGATTCCTCCCAAGTATTTCCACCACCACCC-CAAGTTCGGAAAATGG
1 CCTCCTCTTCCC-AAGATTCCTCCCAAGTATTTCCACCACCACCCTCAACTTCCGAAAAT-G
89173283 CCTCCT
1 CCTCCT
89173289 TTGCCACCCT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
59 11 0.19
60 46 0.81
ACGTcount: A:0.21, C:0.44, G:0.09, T:0.26
Consensus pattern (60 bp):
CCTCCTCTTCCCAAGATTCCTCCCAAGTATTTCCACCACCACCCTCAACTTCCGAAAATG
Found at i:89174478 original size:36 final size:38
Alignment explanation
Indices: 89174438--89174517 Score: 119
Period size: 40 Copynumber: 2.1 Consensus size: 38
89174428 ATTTTTTTTA
*
89174438 TTTTAAGCTATTTAA-TTTT-TTTTATGTTCTTTTAAC
1 TTTTAAGCAATTTAATTTTTCTTTTATGTTCTTTTAAC
89174474 TTTTAAGCAATTTAATTTTTTTCTTTTATGTTCTTTTAAC
1 TTTTAAGCAATTTAA--TTTTTCTTTTATGTTCTTTTAAC
89174514 TTTT
1 TTTT
89174518 TTTTTCTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
36 14 0.36
39 4 0.10
40 21 0.54
ACGTcount: A:0.21, C:0.09, G:0.05, T:0.65
Consensus pattern (38 bp):
TTTTAAGCAATTTAATTTTTCTTTTATGTTCTTTTAAC
Found at i:89180296 original size:6 final size:6
Alignment explanation
Indices: 89180285--89180331 Score: 76
Period size: 6 Copynumber: 7.7 Consensus size: 6
89180275 TAACATGCAA
*
89180285 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAATAT ATAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA-AT AAAAAT AAAA
89180332 TTGTATTGCC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 33 0.87
7 5 0.13
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAAAT
Found at i:89198384 original size:22 final size:23
Alignment explanation
Indices: 89198350--89198394 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
89198340 ATATGACAAA
*
89198350 AAATATATAAATATTA-AAGATT
1 AAATATATAAATAATAGAAGATT
* *
89198372 AAATTTATTAATAATAGAAGATT
1 AAATATATAAATAATAGAAGATT
89198395 GTAATTAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38
Consensus pattern (23 bp):
AAATATATAAATAATAGAAGATT
Found at i:89202552 original size:26 final size:26
Alignment explanation
Indices: 89202531--89202583 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
89202521 ATTTTTAGTC
89202531 TAAGATTTTTTTAAATTCTTTTACCA
1 TAAGATTTTTTTAAATTCTTTTACCA
89202557 TAAGATTTTTTTAAATTCTTTTACCA
1 TAAGATTTTTTTAAATTCTTTTACCA
89202583 T
1 T
89202584 TATTGTTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.04, T:0.55
Consensus pattern (26 bp):
TAAGATTTTTTTAAATTCTTTTACCA
Found at i:89204214 original size:16 final size:18
Alignment explanation
Indices: 89204189--89204224 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
89204179 CTTAAGTTTA
89204189 TTTATCAAAT-AAATAAT
1 TTTATCAAATAAAATAAT
89204206 TTTAT-AAATAAAATAAT
1 TTTATCAAATAAAATAAT
89204223 TT
1 TT
89204225 CCTTAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTATCAAATAAAATAAT
Found at i:89206815 original size:15 final size:16
Alignment explanation
Indices: 89206790--89206823 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
89206780 AAGATGAAGC
89206790 GTTTGATAAATTTAAA
1 GTTTGATAAATTTAAA
*
89206806 GTTT-ATAAATTTGAA
1 GTTTGATAAATTTAAA
89206821 GTT
1 GTT
89206824 GAACTTCAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (16 bp):
GTTTGATAAATTTAAA
Found at i:89208611 original size:22 final size:22
Alignment explanation
Indices: 89208583--89208627 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
89208573 AATAGAGTAC
89208583 TTAGTTACTTAAAGAAAACTAT
1 TTAGTTACTTAAAGAAAACTAT
89208605 TTAGTTACTTAAAGAAAACTAT
1 TTAGTTACTTAAAGAAAACTAT
89208627 T
1 T
89208628 AACTATGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (22 bp):
TTAGTTACTTAAAGAAAACTAT
Found at i:89209834 original size:20 final size:20
Alignment explanation
Indices: 89209800--89209841 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
89209790 AACTATTTAA
** *
89209800 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
89209820 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
89209840 AT
1 AT
89209842 GTATTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:89211906 original size:21 final size:21
Alignment explanation
Indices: 89211882--89211925 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
89211872 TCTCTAATCT
* *
89211882 AATTT-ATTTATTTCCTTTTAG
1 AATTTGATTT-TTTACTTTGAG
89211903 AATTTGATTTTTTACTTTGAG
1 AATTTGATTTTTTACTTTGAG
89211924 AA
1 AA
89211926 GTTAAGTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.27, C:0.07, G:0.09, T:0.57
Consensus pattern (21 bp):
AATTTGATTTTTTACTTTGAG
Found at i:89213617 original size:68 final size:69
Alignment explanation
Indices: 89213497--89213782 Score: 272
Period size: 68 Copynumber: 4.1 Consensus size: 69
89213487 CCTTCTATGT
* * * * *
89213497 CCAACACAGTTAGCAAGAACGAAGCTCCCAACTGTCATATTAAGGCTCGCAGGTGAAGAGCCGCA
1 CCAACAAAGTTAGCGAGAGCAAAGCTCCCAACTGTCATATTTAGGCTCGCAGGTGAAGAGCCGCA
89213562 GCCC
66 GCCC
* * * *
89213566 CCAA-AAAGTTAGCGAGAGTAAAGCTCCCAACTGTTATATTTAGGCTTGCAGGTGAAGAGCCGTA
1 CCAACAAAGTTAGCGAGAGCAAAGCTCCCAACTGTCATATTTAGGCTCGCAGGTGAAGAGCCGCA
* *
89213630 GTCT
66 GCCC
* *
89213634 CCAACATAGTTAGCGAGAGCAAAGCTCCTAACTGTCATA-TTAGGCTCGCAGGTGAAGAGTCGCA
1 CCAACAAAGTTAGCGAGAGCAAAGCTCCCAACTGTCATATTTAGGCTCGCAGGTGAAGAG-C-C-
*
89213698 GCCTCAGCCT
63 G---CAGCCC
* ** * * * * *
89213708 CCAACACAA-TTAGCGAGAACAAAGCTCCCAGTTGTCATATTAAAGCTTGTAGGTGAAGAGCTGC
1 CCAACA-AAGTTAGCGAGAGCAAAGCTCCCAACTGTCATATTTAGGCTCGCAGGTGAAGAGCCGC
* *
89213772 AGTCT
65 AGCCC
89213777 CCAACA
1 CCAACA
89213783 CAATTAACAA
Statistics
Matches: 179, Mismatches: 29, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
68 76 0.42
69 46 0.26
70 1 0.01
71 1 0.01
72 1 0.01
74 37 0.21
75 17 0.09
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.20
Consensus pattern (69 bp):
CCAACAAAGTTAGCGAGAGCAAAGCTCCCAACTGTCATATTTAGGCTCGCAGGTGAAGAGCCGCA
GCCC
Found at i:89213756 original size:143 final size:137
Alignment explanation
Indices: 89213496--89213784 Score: 348
Period size: 143 Copynumber: 2.1 Consensus size: 137
89213486 ACCTTCTATG
*
89213496 TCCAACACAGTTAGCAAGAACGAAGCTCCCAACTGTCATATTAAGGCTCGCAGGTGAAGAGCCGC
1 TCCAACACAGTTAGCAAGAACAAAGCTCCCAACTGTCATATTAAGGCTCGCAGGTGAAGAGCCGC
** * * *
89213561 AGCCCCCAAAAAGTTAGCGAGAGTAAAGCTCCCAACTGTTATATTTAGGCTTGCAGGTGAAGAGC
66 AGCCCCCAAAAAGTTAGCGAGAACAAAGCTCCCAACTGTCATATTAAAGCTTGCAGGTGAAGAGC
*
89213626 CGTAGTC
131 CGCAGTC
* * * *
89213633 TCCAACATAGTTAGCGAGAGCAAAGCTCCTAACTGTCATATT-AGGCTCGCAGGTGAAGAGTCGC
1 TCCAACACAGTTAGCAAGAACAAAGCTCCCAACTGTCATATTAAGGCTCGCAGGTGAAGAG-C-C
* ** *
89213697 AGCCTCAGCCTCCAACACAA-TTAGCGAGAACAAAGCTCCCAGTTGTCATATTAAAGCTTGTAGG
64 -G---CAGCCCCCAA-A-AAGTTAGCGAGAACAAAGCTCCCAACTGTCATATTAAAGCTTGCAGG
*
89213761 TGAAGAGCTGCAGTC
123 TGAAGAGCCGCAGTC
89213776 TCCAACACA
1 TCCAACACA
89213785 ATTAACAACT
Statistics
Matches: 127, Mismatches: 17, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
136 18 0.14
137 38 0.30
138 1 0.01
139 1 0.01
142 9 0.07
143 58 0.46
144 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.20
Consensus pattern (137 bp):
TCCAACACAGTTAGCAAGAACAAAGCTCCCAACTGTCATATTAAGGCTCGCAGGTGAAGAGCCGC
AGCCCCCAAAAAGTTAGCGAGAACAAAGCTCCCAACTGTCATATTAAAGCTTGCAGGTGAAGAGC
CGCAGTC
Found at i:89213801 original size:143 final size:137
Alignment explanation
Indices: 89213518--89213851 Score: 314
Period size: 143 Copynumber: 2.4 Consensus size: 137
89213508 AGCAAGAACG
89213518 AAGCTCCCAACTGTCATATTAAGGCTCGCAGGTGAAGAGCCGCAGCCCCCAAAAAGTTAGCGAGA
1 AAGCTCCCAACTGTCATATTAAGGCTCGCAGGTGAAGAGCCGCAGCCCCCAAAAAGTTAGCGAGA
** * * * * * * *
89213583 GTAAAGCTCCCAACTGTTATATTTAGGCTTGCAGGTGAAGAGCCGTAGTCTCCAACATAGTTAGC
66 ACAAAGCTCCCAACTGTCATATTAAAGCTTGCAGGTGAAGAGCCGCAGTCTCCAACACAATTAAC
* * *
89213648 GAGAGCA
131 AACAGAA
* *
89213655 AAGCTCCTAACTGTCATATT-AGGCTCGCAGGTGAAGAGTCGCAGCCTCAGCCTCCAACACAA-T
1 AAGCTCCCAACTGTCATATTAAGGCTCGCAGGTGAAGAG-C-C-G---CAGCCCCCAA-A-AAGT
** * *
89213718 TAGCGAGAACAAAGCTCCCAGTTGTCATATTAAAGCTTGTAGGTGAAGAGCTGCAGTCTCCAACA
58 TAGCGAGAACAAAGCTCCCAACTGTCATATTAAAGCTTGCAGGTGAAGAGCCGCAGTCTCCAACA
**
89213783 CAATTAACAACTTAA
123 CAATTAACAACAGAA
* * * * * * * *
89213798 AAGCTCCCAGCTGTTATA-TAGGGGCTCGCAAGTGAAAAACTGCAGCCCCTAAAA
1 AAGCTCCCAACTGTCATATTA-AGGCTCGCAGGTGAAGAGCCGCAGCCCCCAAAA
89213852 TAACTCACGG
Statistics
Matches: 157, Mismatches: 30, Indels: 21
0.75 0.14 0.10
Matches are distributed among these distances:
136 19 0.12
137 21 0.13
138 9 0.06
139 1 0.01
141 1 0.01
142 10 0.06
143 80 0.51
144 16 0.10
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (137 bp):
AAGCTCCCAACTGTCATATTAAGGCTCGCAGGTGAAGAGCCGCAGCCCCCAAAAAGTTAGCGAGA
ACAAAGCTCCCAACTGTCATATTAAAGCTTGCAGGTGAAGAGCCGCAGTCTCCAACACAATTAAC
AACAGAA
Found at i:89215666 original size:18 final size:18
Alignment explanation
Indices: 89215643--89215678 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
89215633 AATAAAATGC
89215643 GTATAATAAA-ATTAAAAT
1 GTATAA-AAATATTAAAAT
89215661 GTATAAAAATATTAAAAT
1 GTATAAAAATATTAAAAT
89215679 AAAATTTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (18 bp):
GTATAAAAATATTAAAAT
Found at i:89216500 original size:26 final size:25
Alignment explanation
Indices: 89216464--89216527 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
89216454 TTTGTTAGAA
*
89216464 TTTTT-TTA-AAAATTCACTTAAAT
1 TTTTTATTATAAAAGTCACTTAAAT
* *
89216487 TTTTTGTTATAAAAGTGACTTAAAT
1 TTTTTATTATAAAAGTCACTTAAAT
*
89216512 TTTTTATTATCAAAGT
1 TTTTTATTATAAAAGT
89216528 GATCAATAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 5 0.14
24 3 0.09
25 27 0.77
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (25 bp):
TTTTTATTATAAAAGTCACTTAAAT
Found at i:89216507 original size:25 final size:25
Alignment explanation
Indices: 89216479--89216529 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
89216469 TTAAAAATTC
*
89216479 ACTTAAATTTTTTGTTATAAAAGTG
1 ACTTAAATTTTTTATTATAAAAGTG
*
89216504 ACTTAAATTTTTTATTATCAAAGTG
1 ACTTAAATTTTTTATTATAAAAGTG
89216529 A
1 A
89216530 TCAATAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (25 bp):
ACTTAAATTTTTTATTATAAAAGTG
Found at i:89219205 original size:16 final size:17
Alignment explanation
Indices: 89219184--89219218 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
89219174 AATTAATTTA
89219184 AATTAATTAA-TTTCTC
1 AATTAATTAATTTTCTC
89219200 AATTAATTAATTTTCTC
1 AATTAATTAATTTTCTC
89219217 AA
1 AA
89219219 CCTAATTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTAATTAATTTTCTC
Found at i:89222559 original size:23 final size:23
Alignment explanation
Indices: 89222533--89222609 Score: 120
Period size: 23 Copynumber: 3.3 Consensus size: 23
89222523 GGTCCATTTA
89222533 CACATTAATATTTAAGCATAAAT
1 CACATTAATATTTAAGCATAAAT
89222556 CACATTAATATTTAAGCATAAAT
1 CACATTAATATTTAAGCATAAAT
*
89222579 CACATTAA-ATTTTAAACATAAAT
1 CACATTAATA-TTTAAGCATAAAT
*
89222602 CATATTAA
1 CACATTAA
89222610 GTTCTAACAC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
22 1 0.02
23 50 0.98
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (23 bp):
CACATTAATATTTAAGCATAAAT
Found at i:89236120 original size:20 final size:21
Alignment explanation
Indices: 89236090--89236132 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
89236080 AGATGGTTTC
*
89236090 TTTTATCTTTTATTTACTTAA
1 TTTTATCTTTTATTTACTAAA
89236111 TTTT-TCTTTTATTTACTAAA
1 TTTTATCTTTTATTTACTAAA
89236131 TT
1 TT
89236133 ATTGCTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTTATTTACTAAA
Found at i:89236141 original size:20 final size:20
Alignment explanation
Indices: 89236096--89236140 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
89236086 TTTCTTTTAT
* *
89236096 CTTTTATTTACTTAATTTTT
1 CTTTTATTTACTAAATTTTG
89236116 CTTTTATTTACTAAATTATTG
1 CTTTTATTTACTAAATT-TTG
89236137 CTTT
1 CTTT
89236141 AACCTTACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.22, C:0.11, G:0.02, T:0.64
Consensus pattern (20 bp):
CTTTTATTTACTAAATTTTG
Found at i:89237739 original size:12 final size:13
Alignment explanation
Indices: 89237722--89237759 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
89237712 ATCCTGGAAT
89237722 ATTAA-GACAAGA
1 ATTAAGGACAAGA
*
89237734 ATTAAGGACACATA
1 ATTAAGGACA-AGA
89237748 ATTAAGGACAAG
1 ATTAAGGACAAG
89237760 TCAAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 5 0.23
13 5 0.23
14 12 0.55
ACGTcount: A:0.53, C:0.11, G:0.18, T:0.18
Consensus pattern (13 bp):
ATTAAGGACAAGA
Found at i:89238916 original size:20 final size:21
Alignment explanation
Indices: 89238886--89238928 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
89238876 AGATGGTTTC
*
89238886 TTTTATCTTTTATTTACTTAA
1 TTTTATCTTTTATTTACTAAA
89238907 TTTT-TCTTTTATTTACTAAA
1 TTTTATCTTTTATTTACTAAA
89238927 TT
1 TT
89238929 ATTGCTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTTATTTACTAAA
Found at i:89238937 original size:20 final size:20
Alignment explanation
Indices: 89238892--89238936 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
89238882 TTTCTTTTAT
* *
89238892 CTTTTATTTACTTAATTTTT
1 CTTTTATTTACTAAATTTTG
89238912 CTTTTATTTACTAAATTATTG
1 CTTTTATTTACTAAATT-TTG
89238933 CTTT
1 CTTT
89238937 AACCTTACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.22, C:0.11, G:0.02, T:0.64
Consensus pattern (20 bp):
CTTTTATTTACTAAATTTTG
Found at i:89240535 original size:12 final size:13
Alignment explanation
Indices: 89240518--89240555 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
89240508 ATCCTGGAAT
89240518 ATTAA-GACAAGA
1 ATTAAGGACAAGA
*
89240530 ATTAAGGACACATA
1 ATTAAGGACA-AGA
89240544 ATTAAGGACAAG
1 ATTAAGGACAAG
89240556 TCAAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 5 0.23
13 5 0.23
14 12 0.55
ACGTcount: A:0.53, C:0.11, G:0.18, T:0.18
Consensus pattern (13 bp):
ATTAAGGACAAGA
Found at i:89241738 original size:19 final size:20
Alignment explanation
Indices: 89241701--89241738 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
89241691 CTTTCTTTTA
89241701 TCTTTTATTTACTTAAATTT
1 TCTTTTATTTACTTAAATTT
89241721 TCTTTTATTTAC-TAAATT
1 TCTTTTATTTACTTAAATT
89241739 ACTGCTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (20 bp):
TCTTTTATTTACTTAAATTT
Found at i:89244280 original size:3 final size:3
Alignment explanation
Indices: 89244272--89244317 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
89244262 GTATGTATTG
* * *
89244272 TAT TAT TAT TAT TGT TAT TAT CAT TAT TAT TAT TAT CAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
89244318 TAGAACAAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:89244292 original size:15 final size:15
Alignment explanation
Indices: 89244267--89244314 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
89244257 TATATGTATG
*
89244267 TATTG-TATTATTAT
1 TATTGTTATTATCAT
89244281 TATTGTTATTATCAT
1 TATTGTTATTATCAT
*
89244296 TATTATTATTATCAT
1 TATTGTTATTATCAT
89244311 TATT
1 TATT
89244315 ATTTAGAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 5 0.16
15 26 0.84
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.62
Consensus pattern (15 bp):
TATTGTTATTATCAT
Found at i:89244315 original size:15 final size:15
Alignment explanation
Indices: 89244272--89244317 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
89244262 GTATGTATTG
* *
89244272 TATTATTATTATTGT
1 TATTATCATTATTAT
89244287 TATTATCATTATTAT
1 TATTATCATTATTAT
89244302 TATTATCATTATTAT
1 TATTATCATTATTAT
89244317 T
1 T
89244318 TAGAACAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.63
Consensus pattern (15 bp):
TATTATCATTATTAT
Found at i:89250749 original size:45 final size:45
Alignment explanation
Indices: 89250685--89250775 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
89250675 ACAAAACATG
89250685 TGTCACATACATCATGAACTCAGACCACAACT-AGATGAGCTCAGA
1 TGTCACATACATCATGAACTCAGACCACAACTCA-ATGAGCTCAGA
* * *
89250730 TGTCACATATATCATGAACTCAGACCATAACTCAATGAGTTCAGA
1 TGTCACATACATCATGAACTCAGACCACAACTCAATGAGCTCAGA
89250775 T
1 T
89250776 CACATTGTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
45 41 0.98
46 1 0.02
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.24
Consensus pattern (45 bp):
TGTCACATACATCATGAACTCAGACCACAACTCAATGAGCTCAGA
Found at i:89250751 original size:24 final size:24
Alignment explanation
Indices: 89250685--89250753 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 24
89250675 ACAAAACATG
*
89250685 TGTCACATACATCATGAACTCAGA
1 TGTCACATATATCATGAACTCAGA
* * *
89250709 --CCACA-ACTA-GATGAGCTCAGA
1 TGTCACATA-TATCATGAACTCAGA
89250730 TGTCACATATATCATGAACTCAGA
1 TGTCACATATATCATGAACTCAGA
89250754 CCATAACTCA
Statistics
Matches: 33, Mismatches: 7, Indels: 10
0.66 0.14 0.20
Matches are distributed among these distances:
21 11 0.33
22 5 0.15
23 6 0.18
24 11 0.33
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.23
Consensus pattern (24 bp):
TGTCACATATATCATGAACTCAGA
Found at i:89275212 original size:24 final size:24
Alignment explanation
Indices: 89275180--89275230 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
89275170 CGTGTTTAAG
*
89275180 TTCATCTATTAATATAAGTTGTCT
1 TTCATCTATTAATATAAGTCGTCT
89275204 TTCATCTATTAATATAAGTCGTCT
1 TTCATCTATTAATATAAGTCGTCT
89275228 TTC
1 TTC
89275231 TATGTTACGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.49
Consensus pattern (24 bp):
TTCATCTATTAATATAAGTCGTCT
Found at i:89280075 original size:13 final size:13
Alignment explanation
Indices: 89280057--89280084 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
89280047 GTGGCTGCAT
89280057 TAGTGCTTGTAAC
1 TAGTGCTTGTAAC
89280070 TAGTGCTTGTAAC
1 TAGTGCTTGTAAC
89280083 TA
1 TA
89280085 CGGTCATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.39
Consensus pattern (13 bp):
TAGTGCTTGTAAC
Found at i:89285266 original size:17 final size:17
Alignment explanation
Indices: 89285244--89285280 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
89285234 CAAAAAAATG
89285244 TGAAAGTATTGAATTCA
1 TGAAAGTATTGAATTCA
89285261 TGAAAGTATTGAATTCA
1 TGAAAGTATTGAATTCA
89285278 TGA
1 TGA
89285281 CTATGTATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.35
Consensus pattern (17 bp):
TGAAAGTATTGAATTCA
Found at i:89289447 original size:16 final size:16
Alignment explanation
Indices: 89289426--89289457 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
89289416 AGAATGGTTT
89289426 GGTTTGATAAATTCTA
1 GGTTTGATAAATTCTA
89289442 GGTTTGATAAATTCTA
1 GGTTTGATAAATTCTA
89289458 CTTTCATACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (16 bp):
GGTTTGATAAATTCTA
Found at i:89293870 original size:13 final size:13
Alignment explanation
Indices: 89293852--89293880 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
89293842 ACCAGTGAGC
89293852 TGGTACTTAACAA
1 TGGTACTTAACAA
89293865 TGGTACTTAACAA
1 TGGTACTTAACAA
89293878 TGG
1 TGG
89293881 CGTTGGTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (13 bp):
TGGTACTTAACAA
Found at i:89296340 original size:41 final size:40
Alignment explanation
Indices: 89296198--89296349 Score: 191
Period size: 40 Copynumber: 3.8 Consensus size: 40
89296188 ATAACCACTC
* * * *
89296198 GCAC-AATGCCTTCGGGTCTTAACCCGGATATGGTCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCGCTA
*
89296237 GCATAAATGCCTTCGGGACTTAGCCCGGATATAGTCGCTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCGCTA
* * *
89296277 GCACAAATGCCCTC-GGATCTTAGTCCGGATGTAGTCGCTTA
1 GCACAAATGCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TA
*
89296318 GCACAAAAGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGACTTAGCCCGGATAT
89296350 CATTCGAGTA
Statistics
Matches: 96, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
39 6 0.06
40 61 0.64
41 26 0.27
42 3 0.03
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCGCTA
Found at i:89297580 original size:38 final size:38
Alignment explanation
Indices: 89297538--89297613 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
89297528 CAAGAACTCC
*
89297538 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAAAATTTTCGGCCAAAAGAAATGAA
89297576 TTCCTCCTTCCTTAAAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAAAATTTTCGGCCAAAAGAAATGAA
89297614 AAAGGATGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.32
Consensus pattern (38 bp):
TTCCTCCTTCCTTAAAATTTTCGGCCAAAAGAAATGAA
Found at i:89298740 original size:17 final size:17
Alignment explanation
Indices: 89298718--89298751 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
89298708 CACAAGGATT
89298718 CTTAGGACAAACCTTCC
1 CTTAGGACAAACCTTCC
89298735 CTTAGGACAAACCTTCC
1 CTTAGGACAAACCTTCC
89298752 TTCTTAGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.35, G:0.12, T:0.24
Consensus pattern (17 bp):
CTTAGGACAAACCTTCC
Found at i:89303276 original size:26 final size:26
Alignment explanation
Indices: 89303215--89303277 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
89303205 GTATCTGACC
* *
89303215 ACTCAATCAAAAGACCATTTCCCGAA
1 ACTCAATCACAAGACCATCTCCCGAA
*
89303241 ACTCAATCACAAGACCATCTCCCGGA
1 ACTCAATCACAAGACCATCTCCCGAA
89303267 ACTCAATCACA
1 ACTCAATCACA
89303278 TGTATTGCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.40, C:0.35, G:0.08, T:0.17
Consensus pattern (26 bp):
ACTCAATCACAAGACCATCTCCCGAA
Found at i:89303330 original size:43 final size:43
Alignment explanation
Indices: 89303282--89303367 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
89303272 ATCACATGTA
*
89303282 TTGCATCCATTATGAACTCAGACCACTCAACAAGCTCGGATGC
1 TTGCATCCATAATGAACTCAGACCACTCAACAAGCTCGGATGC
* * *
89303325 TTGCATCCATAATGAACTCGGACCACTTAACGAGCTCGGATGC
1 TTGCATCCATAATGAACTCAGACCACTCAACAAGCTCGGATGC
89303368 CACATATATC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (43 bp):
TTGCATCCATAATGAACTCAGACCACTCAACAAGCTCGGATGC
Found at i:89303655 original size:14 final size:16
Alignment explanation
Indices: 89303624--89303661 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
89303614 TTTACATAAT
*
89303624 ATATATCACCTATTTC
1 ATATATCACCTATGTC
89303640 ATATATCA-CT-TGTC
1 ATATATCACCTATGTC
89303654 ATATATCA
1 ATATATCA
89303662 TCATTTCCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.52
15 2 0.10
16 8 0.38
ACGTcount: A:0.34, C:0.21, G:0.03, T:0.42
Consensus pattern (16 bp):
ATATATCACCTATGTC
Found at i:89306466 original size:40 final size:40
Alignment explanation
Indices: 89306411--89306517 Score: 133
Period size: 40 Copynumber: 2.6 Consensus size: 40
89306401 ACGACAATTT
* *
89306411 GGCTAAGTGTGGCACTTAGTGTGCGATTCAAGATAGCTTC
1 GGCTAAGTATGGCACTTAGTGTGCGATTCAAGATAACTTC
**
89306451 GGCTAAGTATGGCACTTAGTGTGCGATTTGAGATAACTTC
1 GGCTAAGTATGGCACTTAGTGTGCGATTCAAGATAACTTC
* * **
89306491 GTCTATGTATTAACACTTAGTGTGCGA
1 GGCTAAGTA-TGGCACTTAGTGTGCGA
89306518 GAATTTGAGT
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
40 43 0.74
41 15 0.26
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (40 bp):
GGCTAAGTATGGCACTTAGTGTGCGATTCAAGATAACTTC
Found at i:89328815 original size:85 final size:86
Alignment explanation
Indices: 89328716--89328886 Score: 272
Period size: 86 Copynumber: 2.0 Consensus size: 86
89328706 GTTTTTTTCA
* *
89328716 AAAAAATGCAGCTGCTAGACCTAGG-TTTCTTTTCGTTTTCTTGGTTAATGTTGGTAACACTCTC
1 AAAAAATGCAGCTGCTAGACCTAGGTTTTCTTTTCATTTTCGTGGTTAATGTTGGTAACACTCTC
*
89328780 TCACCTTAGGGTTTTTGTGAT
66 TCACCTTAGGGTTTTTATGAT
** * *
89328801 AAAAAATGTGGCTGCTAGACCTAGGTTTTTTTTTTATTTTCGTGGTTAATGTTGGTAACACTCTC
1 AAAAAATGCAGCTGCTAGACCTAGGTTTTCTTTTCATTTTCGTGGTTAATGTTGGTAACACTCTC
89328866 TCACCTTAGGGTTTTTATGAT
66 TCACCTTAGGGTTTTTATGAT
89328887 TCCCTTTTAT
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
85 23 0.29
86 55 0.71
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.43
Consensus pattern (86 bp):
AAAAAATGCAGCTGCTAGACCTAGGTTTTCTTTTCATTTTCGTGGTTAATGTTGGTAACACTCTC
TCACCTTAGGGTTTTTATGAT
Found at i:89338627 original size:21 final size:21
Alignment explanation
Indices: 89338587--89338627 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
89338577 ATCTGCTCAA
* * *
89338587 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGAAGTAC
89338608 ACTCCACCTGCTGTGAAGTA
1 ACTCCACCTGCTGTGAAGTA
89338628 TTGCTCGTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGAAGTAC
Found at i:89342666 original size:25 final size:25
Alignment explanation
Indices: 89342638--89342688 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
89342628 ATTACTCAGG
*
89342638 TATACCAGTAATAATCTATTAACTT
1 TATACCAGTAATAATCCATTAACTT
89342663 TATACCAGTAATAATCCATTAACTT
1 TATACCAGTAATAATCCATTAACTT
89342688 T
1 T
89342689 GTTCAGAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.39, C:0.18, G:0.04, T:0.39
Consensus pattern (25 bp):
TATACCAGTAATAATCCATTAACTT
Found at i:89344133 original size:43 final size:43
Alignment explanation
Indices: 89344005--89344136 Score: 169
Period size: 43 Copynumber: 3.1 Consensus size: 43
89343995 TATAAAAAAC
* * *
89344005 GCCGTTAAAGAA-CATGACCTTTAGCGGCGCTTTTCTTACAAAC
1 GCCGTTAAA-AATCATGACTTTTAGCGTCGCTTTTCTTACAAAT
** *
89344048 GTTGCTAAAAATCATGACTTTTAGCGTCGCTCTTT-TTACAAAT
1 GCCGTTAAAAATCATGACTTTTAGCGTCGCT-TTTCTTACAAAT
*
89344091 GCCGTTAAAAATCATGATTTTTAGCGTCGCTTTTCTTACAAAT
1 GCCGTTAAAAATCATGACTTTTAGCGTCGCTTTTCTTACAAAT
89344134 GCC
1 GCC
89344137 ACTAAAGAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
42 5 0.07
43 68 0.89
44 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (43 bp):
GCCGTTAAAAATCATGACTTTTAGCGTCGCTTTTCTTACAAAT
Found at i:89344156 original size:43 final size:43
Alignment explanation
Indices: 89344017--89344156 Score: 167
Period size: 43 Copynumber: 3.3 Consensus size: 43
89344007 CGTTAAAGAA
* * * **
89344017 CATGACCTTTAGCGGCGCTTTTCTTACAAACGTTGCTAAAAAT
1 CATGACTTTTAGCGTCGCTTTTCTTACAAATGCCGCTAAAAAT
*
89344060 CATGACTTTTAGCGTCGCTCTTT-TTACAAATGCCGTTAAAAAT
1 CATGACTTTTAGCGTCGCT-TTTCTTACAAATGCCGCTAAAAAT
* *
89344103 CATGATTTTTAGCGTCGCTTTTCTTACAAATGCCACTAAAGAAT
1 CATGACTTTTAGCGTCGCTTTTCTTACAAATGCCGCTAAA-AAT
*
89344147 -AAGACTTTTA
1 CATGACTTTTA
89344157 AAAAATATTT
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
42 3 0.04
43 74 0.89
44 6 0.07
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (43 bp):
CATGACTTTTAGCGTCGCTTTTCTTACAAATGCCGCTAAAAAT
Found at i:89347700 original size:21 final size:21
Alignment explanation
Indices: 89347668--89347708 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
89347658 AGGCTCGAGG
89347668 GGCCTGTTTTAGGCC-ATACAA
1 GGCCTGTTTTA-GCCTATACAA
89347689 GGCCT-TTCTTAGCCTATACA
1 GGCCTGTT-TTAGCCTATACA
89347709 CCAAATGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (21 bp):
GGCCTGTTTTAGCCTATACAA
Found at i:89351375 original size:6 final size:6
Alignment explanation
Indices: 89351364--89351392 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
89351354 TGAGAAATTT
89351364 CTTTCC CTTTCC CTTTCC CTTTCC CTTTC
1 CTTTCC CTTTCC CTTTCC CTTTCC CTTTC
89351393 AGAAGCAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (6 bp):
CTTTCC
Found at i:89354345 original size:46 final size:46
Alignment explanation
Indices: 89353894--89354344 Score: 636
Period size: 46 Copynumber: 9.8 Consensus size: 46
89353884 TGATGTTATA
* * *** *
89353894 GTATCTTTCAACTATGGTTTTACTTGTTTTC-TATCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTAC-ACATTTCATATCACGTTGCCATG
* ** * *
89353940 GTATCTTTTAACCATGGTCTTATTCATTTTC-TCCTCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACA-TTTCAT-ATCACGTTGCCATG
**
89353987 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATG
* * *
89354033 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATG
** *
89354079 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGTCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATG
89354125 GTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATG
89354171 GTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATG
* * *
89354217 GTATCTTTCAACCATGATCTTACACATTTCATGTCACATTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATG
* *
89354263 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGTCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATG
*
89354309 GTATCTTTCAACCATGGTCTTACACATTCCATATCA
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCA
89354345 GAGAGCACAC
Statistics
Matches: 372, Mismatches: 30, Indels: 6
0.91 0.07 0.01
Matches are distributed among these distances:
45 1 0.00
46 333 0.90
47 38 0.10
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATG
Found at i:89359329 original size:46 final size:46
Alignment explanation
Indices: 89359253--89359658 Score: 573
Period size: 46 Copynumber: 8.8 Consensus size: 46
89359243 TGATGTCATA
* * ** * *
89359253 GTATCTTTCAACTATGGTTTTACTTGTTTTC-TGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTAC-TCATTTCATATCAGGTTGCCATG
* * *
89359299 GTATCTTTTAACCATGGTCTTATTCATTTTC-TCCTCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCA-TTTCAT-ATCAGGTTGCCATG
* *
89359346 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
*
89359392 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
* * *
89359438 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGTCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
* *
89359484 GTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
*
89359530 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
* *
89359576 GTATCTTTCAACCATAGTCTTACACATTTCATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
* *
89359622 GTATCTTTCAACCATGGTCTTACACATTCCATATCAG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAG
89359659 AGAGCACACT
Statistics
Matches: 332, Mismatches: 25, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
45 1 0.00
46 293 0.88
47 38 0.11
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
Found at i:89363050 original size:14 final size:14
Alignment explanation
Indices: 89363031--89363057 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
89363021 TATGGACTAA
89363031 AATATTAAATATTG
1 AATATTAAATATTG
89363045 AATATTAAATATT
1 AATATTAAATATT
89363058 TAAGTTTTTT
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:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (14 bp):
AATATTAAATATTG
Found at i:89363084 original size:15 final size:14
Alignment explanation
Indices: 89363064--89363103 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
89363054 TATTTAAGTT
89363064 TTTTATTTTTTAATA
1 TTTTATTTTTTAA-A
89363079 TTTTA-TTTTTAAA
1 TTTTATTTTTTAAA
89363092 TTTTAATTTTTT
1 TTTT-ATTTTTT
89363104 TTGAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 5 0.22
14 8 0.35
15 10 0.43
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTATTTTTTAAA
Found at i:89363087 original size:13 final size:14
Alignment explanation
Indices: 89363064--89363102 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
89363054 TATTTAAGTT
*
89363064 TTTTATTTTTTAATA
1 TTTTAATTTTTAA-A
89363079 TTTT-ATTTTTAAA
1 TTTTAATTTTTAAA
89363092 TTTTAATTTTT
1 TTTTAATTTTT
89363103 TTTGAAGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 5 0.23
14 13 0.59
15 4 0.18
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTAATTTTTAAA
Found at i:89363120 original size:21 final size:20
Alignment explanation
Indices: 89363070--89363124 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
89363060 AGTTTTTTAT
*
89363070 TTTTTAATATTTTATTTTTAAA
1 TTTTTAA-ATTTT-TTTTGAAA
89363092 -TTTT-AATTTTTTTTGAAGA
1 TTTTTAAATTTTTTTTGAA-A
89363111 TTTTTAAATTTTTT
1 TTTTTAAATTTTTT
89363125 AAATTAACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 6 0.21
20 5 0.17
21 12 0.41
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (20 bp):
TTTTTAAATTTTTTTTGAAA
Found at i:89363955 original size:15 final size:15
Alignment explanation
Indices: 89363910--89363957 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
89363900 CTTAAACCCC
* *
89363910 AACCCTTAAACCATA
1 AACCCATAATCCATA
89363925 AA-CCATAATCTC-TA
1 AACCCATAATC-CATA
89363939 AACCCATAATCCATA
1 AACCCATAATCCATA
89363954 AACC
1 AACC
89363958 TTAAAATAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (15 bp):
AACCCATAATCCATA
Found at i:89363962 original size:22 final size:20
Alignment explanation
Indices: 89363913--89363962 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
89363903 AAACCCCAAC
89363913 CCTTAAACCATAAACCATAA
1 CCTTAAACCATAAACCATAA
* *
89363933 TCTCTAAACCCATAATCCATAAA
1 CCT-TAAA-CCATAAACCAT-AA
89363956 CCTTAAA
1 CCTTAAA
89363963 ATAGTAACTC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 2 0.08
21 4 0.17
22 14 0.58
23 4 0.17
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (20 bp):
CCTTAAACCATAAACCATAA
Found at i:89364011 original size:14 final size:14
Alignment explanation
Indices: 89363910--89364011 Score: 55
Period size: 14 Copynumber: 7.1 Consensus size: 14
89363900 CTTAAACCCC
*
89363910 AACCCTTAAACCATA
1 AACCC-TAAACTATA
* * *
89363925 AACCATAATCTCTA
1 AACCCTAAACTATA
* *
89363939 AACCCATAATCCATA
1 AACCC-TAAACTATA
* *
89363954 AACCTTAAAATAGT-
1 AACCCTAAACTA-TA
* *
89363968 AACTCCTACACTTTA
1 AAC-CCTAAACTATA
89363983 AACCCTAAA-TCATA
1 AACCCTAAACT-ATA
89363997 AACCCTAAACTATA
1 AACCCTAAACTATA
89364011 A
1 A
89364012 TGATAATTAA
Statistics
Matches: 64, Mismatches: 17, Indels: 13
0.68 0.18 0.14
Matches are distributed among these distances:
13 1 0.02
14 38 0.59
15 25 0.39
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.25
Consensus pattern (14 bp):
AACCCTAAACTATA
Found at i:89364135 original size:7 final size:7
Alignment explanation
Indices: 89364113--89364212 Score: 62
Period size: 7 Copynumber: 14.0 Consensus size: 7
89364103 AACTAATCAT
89364113 TAAACTCC
1 TAAAC-CC
*
89364121 TAATCCC
1 TAAACCC
89364128 TAAACCC
1 TAAACCC
*
89364135 TAAACCA
1 TAAACCC
*
89364142 TAAATCC
1 TAAACCC
* *
89364149 TAAAACA
1 TAAACCC
89364156 TAAACCC
1 TAAACCC
89364163 TAAA-CC
1 TAAACCC
*
89364169 AAGAACCCC
1 TA-AA-CCC
89364178 T-AACCC
1 TAAACCC
*
89364184 TTAACCC
1 TAAACCC
89364191 -ATAACACC
1 TA-AAC-CC
*
89364199 TAAACCT
1 TAAACCC
89364206 TAAACCC
1 TAAACCC
89364213 CAACCATTAA
Statistics
Matches: 71, Mismatches: 14, Indels: 15
0.71 0.14 0.15
Matches are distributed among these distances:
6 7 0.10
7 52 0.73
8 9 0.13
9 3 0.04
ACGTcount: A:0.44, C:0.37, G:0.01, T:0.18
Consensus pattern (7 bp):
TAAACCC
Found at i:89364176 original size:14 final size:14
Alignment explanation
Indices: 89364113--89364169 Score: 69
Period size: 14 Copynumber: 4.0 Consensus size: 14
89364103 AACTAATCAT
* *
89364113 TAAACTCCTAATCCC
1 TAAAC-CCTAAACCA
89364128 TAAACCCTAAACCA
1 TAAACCCTAAACCA
* *
89364142 TAAATCCTAAAACA
1 TAAACCCTAAACCA
89364156 TAAACCCTAAACCA
1 TAAACCCTAAACCA
89364170 AGAACCCCTA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
14 31 0.86
15 5 0.14
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.19
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:89364253 original size:15 final size:15
Alignment explanation
Indices: 89364231--89364265 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
89364221 AAACCACCCT
*
89364231 TAAA-CCATAATCCC
1 TAAACCCATAATCCA
89364245 TAAACCCATAATCCA
1 TAAACCCATAATCCA
89364260 TAAACC
1 TAAACC
89364266 TTAAAATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.20
Consensus pattern (15 bp):
TAAACCCATAATCCA
Found at i:89364358 original size:315 final size:307
Alignment explanation
Indices: 89363695--89364408 Score: 881
Period size: 310 Copynumber: 2.3 Consensus size: 307
89363685 TTACATAATT
* * * * *
89363695 TAAACTATAATCATAATT--TT-AATATATTAAAATTAGTATTATCTCTTTTACAATTATATAAT
1 TAAACTATAATGATAATTAATTCAATATTTTAAAATTAATACTATCTCTTTTACAATTATATAAG
* * * * * *
89363757 AAATTATTTAAT-ATATAAATTACAAAACATTAATTAATCTAAGCCTTAAACCCCTAACCCCTAC
66 AAAATATTT-ATCATATAAATTAAAAAACACTAATTAAACTAAGCATTAAACCCCTAACCCCTAA
* *
89363821 CCCCTAAACCTTAAATCATAAACATAACCTATAAACCTTAAAAACCTAACACTTAACCCCTAACC
130 ACCCTAAACCATAAATCATAAACATAACCTATAAACC-TAAAAACC--ACACTTAACCCCTAACC
* ** * *
89363886 CCTAACCCGTAAGTCTTAAACCCCAACCCTTAAACCATAAACCATAATCTCTAAACCCATAATCC
192 CATAACCCGTAAACCTTAAACCCCAACCATTAAACCATAAACCATAATCCCTAAACCCATAATCC
* * *
89363951 ATAAACCTTAAAATAGTAACTCCTACACTTTAAACCCTAAATCATAAACCC
257 ATAAACCTTAAAATAGTAACTCATAAACATTAAACCCTAAATCATAAACCC
* *
89364002 TAAACTATAATGATAATTAATTCAATATTTTAAAATTAATACTATCTCTTTTATAATTGTATAAG
1 TAAACTATAATGATAATTAATTCAATATTTTAAAATTAATACTATCTCTTTTACAATTATATAAG
* * *
89364067 AAAATATTTATCATATAAATTAAAAAACACTAATTAAACTAATCATTAAACTCCTAATCCCTAAA
66 AAAATATTTATCATATAAATTAAAAAACACTAATTAAACTAAGCATTAAACCCCTAACCCCTAAA
* * * *
89364132 CCCTAAACCATAAATCCTAAAACATAAACC-CTAAACC-AAGAACC-C-C-TAACCCTTAACCCA
131 CCCTAAACCATAAATCAT-AAACAT-AACCTATAAACCTAAAAACCACACTTAACCCCTAACCCA
89364192 TAACACC-TAAACCTTAAACCCCAACCATTAAACCACCCTTAAACCATAATCCCTAAACCCATAA
194 TAAC-CCGTAAACCTTAAACCCCAACCATTAAACCA----TAAACCATAATCCCTAAACCCATAA
* *
89364256 TCCATAAACCTTAAAATAGTAACTCATAAACATTAAACCCTTCACTATATACCGTAAATCC
254 TCCATAAACCTTAAAATAGTAACTCATAAACATTAAACCC-T-A--A-AT--CATAAACCC
* *
89364317 TAAACTATAATGATAATTAATTCAACATTTTAAAATTAATACTATCTCTTTTACAATTATATGAG
1 TAAACTATAATGATAATTAATTCAATATTTTAAAATTAATACTATCTCTTTTACAATTATATAAG
*
89364382 AAAATATTTAACATATAAATTAAAAAA
66 AAAATATTTATCATATAAATTAAAAAA
89364409 TAATTAGTCA
Statistics
Matches: 352, Mismatches: 37, Indels: 28
0.84 0.09 0.07
Matches are distributed among these distances:
304 41 0.12
305 3 0.01
306 1 0.00
307 17 0.05
308 61 0.17
309 11 0.03
310 105 0.30
311 12 0.03
312 5 0.01
313 2 0.01
315 94 0.27
ACGTcount: A:0.45, C:0.23, G:0.02, T:0.30
Consensus pattern (307 bp):
TAAACTATAATGATAATTAATTCAATATTTTAAAATTAATACTATCTCTTTTACAATTATATAAG
AAAATATTTATCATATAAATTAAAAAACACTAATTAAACTAAGCATTAAACCCCTAACCCCTAAA
CCCTAAACCATAAATCATAAACATAACCTATAAACCTAAAAACCACACTTAACCCCTAACCCATA
ACCCGTAAACCTTAAACCCCAACCATTAAACCATAAACCATAATCCCTAAACCCATAATCCATAA
ACCTTAAAATAGTAACTCATAAACATTAAACCCTAAATCATAAACCC
Found at i:89365009 original size:20 final size:20
Alignment explanation
Indices: 89364984--89365022 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
89364974 TGATATTAAT
*
89364984 TTTTAGTTATTAATTTTTTG
1 TTTTAGGTATTAATTTTTTG
89365004 TTTTAGGTATTAATTTTTT
1 TTTTAGGTATTAATTTTTT
89365023 TCTTTTGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (20 bp):
TTTTAGGTATTAATTTTTTG
Found at i:89365021 original size:21 final size:20
Alignment explanation
Indices: 89364984--89365028 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
89364974 TGATATTAAT
* *
89364984 TTTTAGTTATTAATTTTTTG
1 TTTTAGGTATTAATTTTTTC
89365004 TTTTAGGTATTAATTTTTTTC
1 TTTTAGGTATTAA-TTTTTTC
89365025 TTTT
1 TTTT
89365029 GTGAATTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.18, C:0.02, G:0.09, T:0.71
Consensus pattern (20 bp):
TTTTAGGTATTAATTTTTTC
Found at i:89367363 original size:17 final size:17
Alignment explanation
Indices: 89367343--89367377 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
89367333 TATTACATAA
89367343 ATAATACAATCACAAAT
1 ATAATACAATCACAAAT
* *
89367360 ATAATATAATTACAAAT
1 ATAATACAATCACAAAT
89367377 A
1 A
89367378 CAAATTCGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAATACAATCACAAAT
Found at i:89367374 original size:23 final size:21
Alignment explanation
Indices: 89367339--89367382 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
89367329 TTATTATTAC
89367339 ATAAATAATAC-AATCACAAAT
1 ATAAATAATACAAAT-ACAAAT
89367360 ATAATATAATTACAAATACAAAT
1 ATAA-ATAA-TACAAATACAAAT
89367383 TCGAACCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.20
22 4 0.20
23 9 0.45
24 3 0.15
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.27
Consensus pattern (21 bp):
ATAAATAATACAAATACAAAT
Found at i:89369816 original size:18 final size:18
Alignment explanation
Indices: 89369793--89369828 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
89369783 CCAATTAAAT
89369793 CTTCATGTGTAGTTTTTC
1 CTTCATGTGTAGTTTTTC
89369811 CTTCATGTGTAGTTTTTC
1 CTTCATGTGTAGTTTTTC
89369829 TTACTCCGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.17, G:0.17, T:0.56
Consensus pattern (18 bp):
CTTCATGTGTAGTTTTTC
Found at i:89370023 original size:14 final size:14
Alignment explanation
Indices: 89370004--89370036 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
89369994 TGTTTCACTA
89370004 AAAATGACTTCTGG
1 AAAATGACTTCTGG
*
89370018 AAAATGATTTCTGG
1 AAAATGACTTCTGG
89370032 AAAAT
1 AAAAT
89370037 AATTTACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.30
Consensus pattern (14 bp):
AAAATGACTTCTGG
Found at i:89370041 original size:14 final size:14
Alignment explanation
Indices: 89370012--89370041 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
89370002 TAAAAATGAC
*
89370012 TTCTGGAAAATGAT
1 TTCTGGAAAATAAT
89370026 TTCTGGAAAATAAT
1 TTCTGGAAAATAAT
89370040 TT
1 TT
89370042 ACTTTTCTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.40
Consensus pattern (14 bp):
TTCTGGAAAATAAT
Found at i:89370620 original size:16 final size:16
Alignment explanation
Indices: 89370589--89370625 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
89370579 ATGTGAATAA
89370589 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
89370605 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
89370621 TATTA
1 TATTA
89370626 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:89370677 original size:22 final size:22
Alignment explanation
Indices: 89370637--89370692 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
89370627 AATAAAATTG
*
89370637 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
89370657 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
* * *
89370679 TATTAATAATTTAT
1 AAATAATAAATTAT
89370693 TATATGACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.30
21 2 0.07
22 19 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:89370759 original size:26 final size:25
Alignment explanation
Indices: 89370716--89370776 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
89370706 ATAAATAATT
*
89370716 AAATATATATGTTTAATAATATTGAA
1 AAATATAAATGTTTAAT-ATATTGAA
* *
89370742 AAATATAAAT-TTTAAATATTTTTAA
1 AAATATAAATGTTT-AATATATTGAA
*
89370767 AAATAAAAAT
1 AAATATAAAT
89370777 AAAATTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 18 0.60
26 12 0.40
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (25 bp):
AAATATAAATGTTTAATATATTGAA
Found at i:89375196 original size:15 final size:15
Alignment explanation
Indices: 89375176--89375206 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
89375166 AATAACTAAA
89375176 AAAAAATAGATAGAT
1 AAAAAATAGATAGAT
89375191 AAAAAATAGATAGAT
1 AAAAAATAGATAGAT
89375206 A
1 A
89375207 GATGAGAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.19
Consensus pattern (15 bp):
AAAAAATAGATAGAT
Found at i:89375219 original size:19 final size:19
Alignment explanation
Indices: 89375172--89375209 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
89375162 AGTGAATAAC
*
89375172 TAAAAAA-AAATAGATAGA
1 TAAAAAATAGATAGATAGA
89375190 TAAAAAATAGATAGATAGA
1 TAAAAAATAGATAGATAGA
89375209 T
1 T
89375210 GAGAGATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.66, C:0.00, G:0.13, T:0.21
Consensus pattern (19 bp):
TAAAAAATAGATAGATAGA
Found at i:89380927 original size:187 final size:187
Alignment explanation
Indices: 89380612--89380985 Score: 703
Period size: 187 Copynumber: 2.0 Consensus size: 187
89380602 ATTGCCCTGG
89380612 GCGGATAGCAGGAATCAAACCCGCGTCTTCTCCTTGGCAAAGAGAAATTTTACCATTCGACTATA
1 GCGGATAGCAGGAATCAAACCCGCGTCTTCTCCTTGGCAAAGAGAAATTTTACCATTCGACTATA
*
89380677 TCCACATTTTCGTTCTTGATTCTTGATACGAAAGAATGTTTGGTCAGAGCTAGGACAGATACTTT
66 TCCACATTTTCGTTCTTGATTCTTGATACGAAAGAATATTTGGTCAGAGCTAGGACAGATACTTT
*
89380742 CTTCAGTTCAGGGCAATTTTATCAAATTCCACTACTAAACCAATTAACAATCGAAAT
131 CTTCAGTTCAAGGCAATTTTATCAAATTCCACTACTAAACCAATTAACAATCGAAAT
*
89380799 GCGGATAGGAGGAATCAAACCCGCGTCTTCTCCTTGGCAAAGAGAAATTTTACCATTCGACTATA
1 GCGGATAGCAGGAATCAAACCCGCGTCTTCTCCTTGGCAAAGAGAAATTTTACCATTCGACTATA
*
89380864 TCCGCATTTTCGTTCTTGATTCTTGATACGAAAGAATATTTGGTCAGAGCTAGGACAGATACTTT
66 TCCACATTTTCGTTCTTGATTCTTGATACGAAAGAATATTTGGTCAGAGCTAGGACAGATACTTT
*
89380929 CTTCAGTTCAAGGCAATTTTATCAAATTCCACTACTAAACCAATTAACAATTGAAAT
131 CTTCAGTTCAAGGCAATTTTATCAAATTCCACTACTAAACCAATTAACAATCGAAAT
89380986 TATATAACAA
Statistics
Matches: 182, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
187 182 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Consensus pattern (187 bp):
GCGGATAGCAGGAATCAAACCCGCGTCTTCTCCTTGGCAAAGAGAAATTTTACCATTCGACTATA
TCCACATTTTCGTTCTTGATTCTTGATACGAAAGAATATTTGGTCAGAGCTAGGACAGATACTTT
CTTCAGTTCAAGGCAATTTTATCAAATTCCACTACTAAACCAATTAACAATCGAAAT
Found at i:89381200 original size:26 final size:30
Alignment explanation
Indices: 89381125--89381249 Score: 97
Period size: 32 Copynumber: 4.2 Consensus size: 30
89381115 TCTATATTTC
*
89381125 TATATTATTTA-TTTTATTATTCTATCTATTAT
1 TATATTATCTATTTTTA-TA-T-TATCTATTAT
89381157 TATATTATCTATTTTTATATTATCTA-T-T
1 TATATTATCTATTTTTATATTATCTATTAT
89381185 TATA-TA-CTATTTTTATA-TAT-TATTAT
1 TATATTATCTATTTTTATATTATCTATTAT
*
89381211 TATATATAT-TATTATTTCTATTTAGT-TATTATT
1 TATAT-TATCTATT-TTTATA-TTA-TCTATTA-T
89381244 TATATT
1 TATATT
89381250 TAGTATATTT
Statistics
Matches: 80, Mismatches: 2, Indels: 22
0.77 0.02 0.21
Matches are distributed among these distances:
24 2 0.03
25 4 0.05
26 16 0.20
27 2 0.03
28 11 0.14
29 6 0.08
30 6 0.08
31 3 0.04
32 19 0.24
33 11 0.14
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (30 bp):
TATATTATCTATTTTTATATTATCTATTAT
Found at i:89381203 original size:28 final size:27
Alignment explanation
Indices: 89381151--89381247 Score: 94
Period size: 28 Copynumber: 3.5 Consensus size: 27
89381141 TTATTCTATC
89381151 TATTATTATAT-TATCTA-TTTTTATAT
1 TATTATTATATATA-CTATTTTTTATAT
89381177 TATCTATT-TATATACTATTTTTATATAT
1 TAT-TATTATATATACTATTTTT-TATAT
*
89381205 TATTATTATATATATTATTATTTCTAT-T
1 TATTATTATATATACTATT-TTT-TATAT
*
89381233 TAGTTATTATTTATA
1 TA-TTATTATATATA
89381248 TTTAGTATAT
Statistics
Matches: 61, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
26 9 0.15
27 14 0.23
28 21 0.34
29 17 0.28
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (27 bp):
TATTATTATATATACTATTTTTTATAT
Found at i:89381259 original size:32 final size:30
Alignment explanation
Indices: 89381202--89381282 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 30
89381192 TATTTTTATA
*
89381202 TATTATTATTATATATATTATTATTT-CTATT
1 TATTATTATT-TATAT-TTATTATTTACAATT
*
89381233 TAGTTATTATTTATATTTAGTATATTTAGAATT
1 TA-TTATTATTTATATTTA-T-TATTTACAATT
89381266 TATTATTATTTA-ATTTA
1 TATTATTATTTATATTTA
89381283 AGTTAAATAG
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
30 3 0.07
31 13 0.30
32 23 0.52
33 5 0.11
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (30 bp):
TATTATTATTTATATTTATTATTTACAATT
Found at i:89381259 original size:63 final size:62
Alignment explanation
Indices: 89381117--89381274 Score: 137
Period size: 66 Copynumber: 2.5 Consensus size: 62
89381107 TTTATAAATC
* * *
89381117 TATATTT-CTATATTATTTATTTTATTATTCTATCTATTATTATATTATCTATTTTTATATTA
1 TATATTTAATATATT-TTTATTTTATTATTATATATATTATTATATTATCTATTTTTATATTA
*
89381179 TCTATTTATATACTATTTTTATATATTATTATTATATATATTA-T-TATT-TCTATTTAGTTATT
1 TATATTTA-ATA-TATTTTTAT-T-TTATTATTATATATATTATTATATTATCTATTT--TTA-T
89381241 ATT-
59 ATTA
* ** *
89381244 TATATTTAGTATATTTAGAATTTATTATTAT
1 TATATTTAATATATTTTTATTTTATTATTAT
89381275 TTAATTTAAG
Statistics
Matches: 79, Mismatches: 9, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
61 10 0.13
62 7 0.09
63 13 0.16
64 13 0.16
65 16 0.20
66 20 0.25
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (62 bp):
TATATTTAATATATTTTTATTTTATTATTATATATATTATTATATTATCTATTTTTATATTA
Found at i:89381277 original size:17 final size:16
Alignment explanation
Indices: 89381117--89381282 Score: 105
Period size: 15 Copynumber: 10.5 Consensus size: 16
89381107 TTTATAAATC
*
89381117 TATATTTCTATATTATT
1 TATATTTAT-TATTATT
* *
89381134 TAT-TTTATTATTCTA
1 TATATTTATTATTATT
*
89381149 TCTA-TTATTA-TATT
1 TATATTTATTATTATT
*
89381163 ATCTATTT-TTA-TATT
1 -TATATTTATTATTATT
* *
89381178 ATCTATTTATATACTATT
1 -TATATTTAT-TATTATT
* *
89381196 TTTATATATTATTA-T
1 TATATTTATTATTATT
*
89381211 TATATATATTATTATT
1 TATATTTATTATTATT
*
89381227 TCTATTTAGTTATTATT
1 TATATTTA-TTATTATT
*
89381244 TATATTTAGTA-TATT
1 TATATTTATTATTATT
*
89381259 TAGAATTTATTATTATT
1 TA-TATTTATTATTATT
89381276 TA-ATTTA
1 TATATTTA
89381283 AGTTAAATAG
Statistics
Matches: 123, Mismatches: 16, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
14 2 0.02
15 57 0.46
16 27 0.22
17 33 0.27
18 4 0.03
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (16 bp):
TATATTTATTATTATT
Found at i:89381294 original size:31 final size:32
Alignment explanation
Indices: 89381236--89381343 Score: 114
Period size: 31 Copynumber: 3.4 Consensus size: 32
89381226 TTCTATTTAG
* **
89381236 TTATTATTTATATTT-AGTATATTTAGAATTTA
1 TTATTATTTA-ATTTAAGTATAATTAGAATAAA
*
89381268 TTATTATTTAATTTAAGT-TAAATAGAA-AAA
1 TTATTATTTAATTTAAGTATAATTAGAATAAA
* *
89381298 TTAATAATTTAATTTAAGTATAATTAAAATAAA
1 TT-ATTATTTAATTTAAGTATAATTAGAATAAA
89381331 TTATTAATTTAAT
1 TTATT-ATTTAAT
89381344 AATTTAGAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
30 3 0.05
31 26 0.41
32 22 0.35
33 12 0.19
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (32 bp):
TTATTATTTAATTTAAGTATAATTAGAATAAA
Found at i:89388599 original size:27 final size:27
Alignment explanation
Indices: 89388569--89388662 Score: 98
Period size: 27 Copynumber: 3.5 Consensus size: 27
89388559 GACATAAAAA
* *
89388569 GAAAGCCTTTGTGGCAAAGTATTAAAT
1 GAAAACCTTTGTGGCAAAGCATTAAAT
* ** * * *
89388596 GAAAATCTTTGTGGTGAACCATGAAAA
1 GAAAACCTTTGTGGCAAAGCATTAAAT
*
89388623 GAAAGCCTTTGTGGCAAAGCATTAAAT
1 GAAAACCTTTGTGGCAAAGCATTAAAT
*
89388650 GAAAATCTTTGTG
1 GAAAACCTTTGTG
89388663 AAAAATCTTG
Statistics
Matches: 50, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (27 bp):
GAAAACCTTTGTGGCAAAGCATTAAAT
Found at i:89388690 original size:54 final size:54
Alignment explanation
Indices: 89388565--89388667 Score: 170
Period size: 54 Copynumber: 1.9 Consensus size: 54
89388555 TGGCGACATA
* ***
89388565 AAAAGAAAGCCTTTGTGGCAAAGTATTAAATGAAAATCTTTGTGGTGAACCATG
1 AAAAGAAAGCCTTTGTGGCAAAGCATTAAATGAAAATCTTTGTGAAAAACCATG
89388619 AAAAGAAAGCCTTTGTGGCAAAGCATTAAATGAAAATCTTTGTGAAAAA
1 AAAAGAAAGCCTTTGTGGCAAAGCATTAAATGAAAATCTTTGTGAAAAA
89388668 TCTTGGAAGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (54 bp):
AAAAGAAAGCCTTTGTGGCAAAGCATTAAATGAAAATCTTTGTGAAAAACCATG
Found at i:89388821 original size:27 final size:27
Alignment explanation
Indices: 89388783--89388850 Score: 102
Period size: 27 Copynumber: 2.5 Consensus size: 27
89388773 GAGAACTCTA
*
89388783 ACTCATGGTGAACTTTAAACGAATGGT
1 ACTCATGGTGAACTTTAAAAGAATGGT
*
89388810 ACTCATGGTGAACTTTAAAAGAATTGT
1 ACTCATGGTGAACTTTAAAAGAATGGT
89388837 A-TACATGGTGAACT
1 ACT-CATGGTGAACT
89388851 ACGAAGGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 1 0.03
27 37 0.97
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (27 bp):
ACTCATGGTGAACTTTAAAAGAATGGT
Done.