Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 126 of 193
Found at i:39778503 original size:42 final size:43
Alignment explanation
Indices: 39778457--39778596 Score: 169
Period size: 42 Copynumber: 3.3 Consensus size: 43
39778447 TGGACTTGTT
* * ** * * *
39778457 GGGCTGTAACCTGGTGAACTAGGACTGTAAG-TAGGTGATGTG
1 GGGCTGTAACCAGGCGAGGTAGGACTGTAAGCCAGGAGATGTA
39778499 GGGCTGTAACCAGGCGAGGTAGGACTGT-AGCCAGGAGATGTA
1 GGGCTGTAACCAGGCGAGGTAGGACTGTAAGCCAGGAGATGTA
*
39778541 GGGCTGTAACCAGGCGAGGTAGGACTGT-AGCCAGGAGATGAA
1 GGGCTGTAACCAGGCGAGGTAGGACTGTAAGCCAGGAGATGTA
* *
39778583 GGACTGTAGCCAGG
1 GGGCTGTAACCAGG
39778597 AGATGATGGG
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
41 2 0.02
42 85 0.98
ACGTcount: A:0.26, C:0.16, G:0.40, T:0.19
Consensus pattern (43 bp):
GGGCTGTAACCAGGCGAGGTAGGACTGTAAGCCAGGAGATGTA
Found at i:39778526 original size:21 final size:21
Alignment explanation
Indices: 39778502--39778599 Score: 124
Period size: 21 Copynumber: 4.7 Consensus size: 21
39778492 TGATGTGGGG
* *
39778502 CTGTAACCAGGCGAGGTAGGA
1 CTGTAGCCAGGAGAGGTAGGA
* *
39778523 CTGTAGCCAGGAGATGTAGGG
1 CTGTAGCCAGGAGAGGTAGGA
* *
39778544 CTGTAACCAGGCGAGGTAGGA
1 CTGTAGCCAGGAGAGGTAGGA
* *
39778565 CTGTAGCCAGGAGATGAAGGA
1 CTGTAGCCAGGAGAGGTAGGA
39778586 CTGTAGCCAGGAGA
1 CTGTAGCCAGGAGA
39778600 TGATGGGCTG
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 65 1.00
ACGTcount: A:0.29, C:0.17, G:0.39, T:0.15
Consensus pattern (21 bp):
CTGTAGCCAGGAGAGGTAGGA
Found at i:39778600 original size:21 final size:21
Alignment explanation
Indices: 39778519--39778623 Score: 120
Period size: 21 Copynumber: 5.0 Consensus size: 21
39778509 CAGGCGAGGT
*
39778519 AGGACTGTAGCCAGGAGATGT
1 AGGACTGTAGCCAGGAGATGA
* * * * *
39778540 AGGGCTGTAACCAGGCGAGGT
1 AGGACTGTAGCCAGGAGATGA
39778561 AGGACTGTAGCCAGGAGATGA
1 AGGACTGTAGCCAGGAGATGA
39778582 AGGACTGTAGCCAGGAGATGA
1 AGGACTGTAGCCAGGAGATGA
* * * *
39778603 TGGGCTGTAACCAGGGGATGA
1 AGGACTGTAGCCAGGAGATGA
39778624 CGTGGGAGAG
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 71 1.00
ACGTcount: A:0.29, C:0.15, G:0.40, T:0.16
Consensus pattern (21 bp):
AGGACTGTAGCCAGGAGATGA
Found at i:39778611 original size:42 final size:42
Alignment explanation
Indices: 39778502--39778623 Score: 138
Period size: 42 Copynumber: 2.9 Consensus size: 42
39778492 TGATGTGGGG
* * * *
39778502 CTGTAACCAGGCGAGGTAGGACTGTAGCCAGGAGATGTAGGG
1 CTGTAACCAGGAGAGATAGGACTGTAGCCAGGAGATGAAGGA
* *
39778544 CTGTAACCAGGCGAGGTAGGACTGTAGCCAGGAGATGAAGGA
1 CTGTAACCAGGAGAGATAGGACTGTAGCCAGGAGATGAAGGA
* * * *
39778586 CTGTAGCCAGGAGATGAT-GGGCTGTAACCAGGGGATGA
1 CTGTAACCAGGAGA-GATAGGACTGTAGCCAGGAGATGA
39778624 CGTGGGAGAG
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 69 0.97
43 2 0.03
ACGTcount: A:0.28, C:0.16, G:0.39, T:0.16
Consensus pattern (42 bp):
CTGTAACCAGGAGAGATAGGACTGTAGCCAGGAGATGAAGGA
Found at i:39786276 original size:41 final size:41
Alignment explanation
Indices: 39786214--39786315 Score: 152
Period size: 41 Copynumber: 2.5 Consensus size: 41
39786204 CTCTGACTGT
39786214 GCCGCTAATGCTCTGACCTTTAGCGGCGCTTTCTCATAAAC
1 GCCGCTAATGCTCTGACCTTTAGCGGCGCTTTCTCATAAAC
* * *
39786255 GCCGTTAATGTTCTGACCTTTAGTGGCGCTTTCTCATAAAC
1 GCCGCTAATGCTCTGACCTTTAGCGGCGCTTTCTCATAAAC
* *
39786296 GCCGCTATTGCT-TTACCTTT
1 GCCGCTAATGCTCTGACCTTT
39786316 TGCGATGCGA
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 7 0.13
41 47 0.87
ACGTcount: A:0.18, C:0.28, G:0.19, T:0.35
Consensus pattern (41 bp):
GCCGCTAATGCTCTGACCTTTAGCGGCGCTTTCTCATAAAC
Found at i:39786591 original size:156 final size:156
Alignment explanation
Indices: 39786307--39786623 Score: 625
Period size: 156 Copynumber: 2.0 Consensus size: 156
39786297 CCGCTATTGC
39786307 TTTACCTTTTGCGATGCGATTGGGCTGATGTTAATACTGCTTAGGGAATTAAAAAAGATCAATTT
1 TTTACCTTTTGCGATGCGATTGGGCTGATGTTAATACTGCTTAGGGAATTAAAAAAGATCAATTT
39786372 GGTTTTACAATGGTGAACTTCTTTCGATTAATTCACACTGGGCAACAATTTATGGAGCCGTATGT
66 GGTTTTACAATGGTGAACTTCTTTCGATTAATTCACACTGGGCAACAATTTATGGAGCCGTATGT
39786437 ATTTTCTTCTCAAGTCAAATAAGTTT
131 ATTTTCTTCTCAAGTCAAATAAGTTT
*
39786463 TTTACCTTTTGCGATGTGATTGGGCTGATGTTAATACTGCTTAGGGAATTAAAAAAGATCAATTT
1 TTTACCTTTTGCGATGCGATTGGGCTGATGTTAATACTGCTTAGGGAATTAAAAAAGATCAATTT
39786528 GGTTTTACAATGGTGAACTTCTTTCGATTAATTCACACTGGGCAACAATTTATGGAGCCGTATGT
66 GGTTTTACAATGGTGAACTTCTTTCGATTAATTCACACTGGGCAACAATTTATGGAGCCGTATGT
39786593 ATTTTCTTCTCAAGTCAAATAAGTTT
131 ATTTTCTTCTCAAGTCAAATAAGTTT
39786619 TTTAC
1 TTTAC
39786624 TCGAGAGATC
Statistics
Matches: 160, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
156 160 1.00
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (156 bp):
TTTACCTTTTGCGATGCGATTGGGCTGATGTTAATACTGCTTAGGGAATTAAAAAAGATCAATTT
GGTTTTACAATGGTGAACTTCTTTCGATTAATTCACACTGGGCAACAATTTATGGAGCCGTATGT
ATTTTCTTCTCAAGTCAAATAAGTTT
Found at i:39791681 original size:7 final size:7
Alignment explanation
Indices: 39791669--39791758 Score: 72
Period size: 7 Copynumber: 12.9 Consensus size: 7
39791659 CAAAGTCAAA
39791669 GTCAACG
1 GTCAACG
39791676 GTCAACG
1 GTCAACG
* *
39791683 ATCAACT
1 GTCAACG
*
39791690 GTCAATG
1 GTCAACG
*
39791697 GTCAATG
1 GTCAACG
*
39791704 GTTAACG
1 GTCAACG
39791711 GTCAACG
1 GTCAACG
**
39791718 GTCAATA
1 GTCAACG
*
39791725 GTTAACG
1 GTCAACG
*
39791732 GTCAACT
1 GTCAACG
* *
39791739 ATCAATG
1 GTCAACG
*
39791746 ATCAACG
1 GTCAACG
39791753 GTCAAC
1 GTCAAC
39791759 ACTCGGTCAA
Statistics
Matches: 63, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
7 63 1.00
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.23
Consensus pattern (7 bp):
GTCAACG
Found at i:39793482 original size:33 final size:31
Alignment explanation
Indices: 39793416--39793486 Score: 74
Period size: 33 Copynumber: 2.3 Consensus size: 31
39793406 AGTAAATAAT
*
39793416 AATTATTTATAAAATTTAATTAGAATATATA
1 AATTATTTATAAAATTTAAATAGAATATATA
* *
39793447 AATTATGTTTTAAATATTTAAATATAATCAT-TA
1 AATTAT-TTATAAA-ATTTAAATAGAAT-ATATA
39793480 AA-TATTT
1 AATTATTT
39793487 GTAATTAGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
31 8 0.24
32 9 0.26
33 15 0.44
34 2 0.06
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (31 bp):
AATTATTTATAAAATTTAAATAGAATATATA
Found at i:39794471 original size:33 final size:34
Alignment explanation
Indices: 39794372--39794472 Score: 141
Period size: 34 Copynumber: 3.0 Consensus size: 34
39794362 ACAACTCATT
* *
39794372 TTGTAAGTTTTCAAGCTCAAGAAATCAATATGTA
1 TTGTAAGTTTTCAAACTCAAGAAATTAATATGTA
*
39794406 TTGTAAGTTTTCAAACTCAAGAAATTATTATGTA
1 TTGTAAGTTTTCAAACTCAAGAAATTAATATGTA
* * *
39794440 TTTTAAGTTTTCAAACTGAAG-AATTAGTATGTA
1 TTGTAAGTTTTCAAACTCAAGAAATTAATATGTA
39794473 AAAATGACAC
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
33 11 0.18
34 50 0.82
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.40
Consensus pattern (34 bp):
TTGTAAGTTTTCAAACTCAAGAAATTAATATGTA
Found at i:39795635 original size:17 final size:18
Alignment explanation
Indices: 39795608--39795644 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
39795598 TAAAGCTAAA
39795608 GACATGAGAAACTGCATG
1 GACATGAGAAACTGCATG
39795626 GACA-GAGAAACTGCATG
1 GACATGAGAAACTGCATG
39795643 GA
1 GA
39795645 AATTACATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.41, C:0.16, G:0.30, T:0.14
Consensus pattern (18 bp):
GACATGAGAAACTGCATG
Found at i:39797517 original size:43 final size:43
Alignment explanation
Indices: 39797454--39797596 Score: 207
Period size: 43 Copynumber: 3.3 Consensus size: 43
39797444 TTTTAGCGGG
*
39797454 TCTTTAGCGGCATTTATGGGAGAAGCGCCGCTAAAGACCATGT
1 TCTTTAGCGGCGTTTATGGGAGAAGCGCCGCTAAAGACCATGT
* * * *
39797497 TCTTTAGCGGCGTTTGTGGGAGAAGCGCCACTAAAGACAATAT
1 TCTTTAGCGGCGTTTATGGGAGAAGCGCCGCTAAAGACCATGT
* *
39797540 TCTTTAGCGGCGTTTATGGGA-AAGCGCCGCTAAAAATCATGT
1 TCTTTAGCGGCGTTTATGGGAGAAGCGCCGCTAAAGACCATGT
*
39797582 TCTATAGCGGCGTTT
1 TCTTTAGCGGCGTTT
39797597 TTCCTCATAA
Statistics
Matches: 88, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 30 0.34
43 58 0.66
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (43 bp):
TCTTTAGCGGCGTTTATGGGAGAAGCGCCGCTAAAGACCATGT
Found at i:39798184 original size:10 final size:10
Alignment explanation
Indices: 39798171--39798222 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
39798161 AATAAAATAT
39798171 TTTAATATAA
1 TTTAATATAA
39798181 TTTAATATAAAA
1 TTTAATAT--AA
* * * *
39798193 CTAAAAATAT
1 TTTAATATAA
39798203 TTTAATATAA
1 TTTAATATAA
39798213 TTTAATATAA
1 TTTAATATAA
39798223 AAATAATTAT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
10 25 0.78
12 7 0.22
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (10 bp):
TTTAATATAA
Found at i:39798235 original size:32 final size:31
Alignment explanation
Indices: 39798159--39798228 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 31
39798149 AATATAATTT
39798159 AAAATAAAATATTTTAATATAATTTAATATA
1 AAAATAAAATATTTTAATATAATTTAATATA
*
39798190 AAACTAAAAATATTTTAATATAATTTAATATA
1 AAAAT-AAAATATTTTAATATAATTTAATATA
39798222 AAAATAA
1 AAAATAA
39798229 TTATATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 6 0.17
32 30 0.83
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (31 bp):
AAAATAAAATATTTTAATATAATTTAATATA
Found at i:39799766 original size:53 final size:53
Alignment explanation
Indices: 39799686--39799793 Score: 180
Period size: 53 Copynumber: 2.0 Consensus size: 53
39799676 CGTAAATGCA
* * *
39799686 AAAGGTTCGATGACTTTGTGTCATCGTGAGTTATATGAATCCTATTACGAATT
1 AAAGGTCCGATAACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGAATT
*
39799739 AAAGGTCCGATAACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATT
1 AAAGGTCCGATAACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGAATT
39799792 AA
1 AA
39799794 TGAGTTATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (53 bp):
AAAGGTCCGATAACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGAATT
Found at i:39799808 original size:29 final size:29
Alignment explanation
Indices: 39799765--39799822 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
39799755 TGTGTCATCG
* *
39799765 TGAGTTATATGAATCCTATTACGGATTAA
1 TGAGTTATATAAATCCTATTACAGATTAA
39799794 TGAGTTATATAAATCCTATTACAGATTAA
1 TGAGTTATATAAATCCTATTACAGATTAA
39799823 AGGTTCGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (29 bp):
TGAGTTATATAAATCCTATTACAGATTAA
Found at i:39799849 original size:82 final size:82
Alignment explanation
Indices: 39799712--39799875 Score: 267
Period size: 82 Copynumber: 2.0 Consensus size: 82
39799702 TGTGTCATCG
* *
39799712 TGAGTTATATGAATCCTATTACGAATTAAAGGTCCGATAACTCTGTGTCATCGTGAGTTATATGA
1 TGAGTTATATAAATCCTATTACGAATTAAAGGTCCGATAACTATGTGTCATCGTGAGTTATATGA
39799777 ATCCTATTACGGATTAA
66 ATCCTATTACGGATTAA
* *
39799794 TGAGTTATATAAATCCTATTAC-AGATTAAAGGTTCGATGACTATGTGTCATCGTGAGTTATATG
1 TGAGTTATATAAATCCTATTACGA-ATTAAAGGTCCGATAACTATGTGTCATCGTGAGTTATATG
*
39799858 AATCTTATTACGGATTAA
65 AATCCTATTACGGATTAA
39799876 AGGTCCGATG
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
81 1 0.01
82 75 0.99
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (82 bp):
TGAGTTATATAAATCCTATTACGAATTAAAGGTCCGATAACTATGTGTCATCGTGAGTTATATGA
ATCCTATTACGGATTAA
Found at i:39799874 original size:53 final size:53
Alignment explanation
Indices: 39799794--39799960 Score: 262
Period size: 53 Copynumber: 3.2 Consensus size: 53
39799784 TACGGATTAA
* * * *
39799794 TGAGTTATATAAATCCTATTACAGATTAAAGGTTCGATGACTATGTGTCATCG
1 TGAGTTATATGAATCTTATTACGGATTAAAGGTCCGATGACTATGTGTCATCG
* *
39799847 TGAGTTATATGAATCTTATTACGGATTAAAGGTCCGATGACTCTGTGTCATCA
1 TGAGTTATATGAATCTTATTACGGATTAAAGGTCCGATGACTATGTGTCATCG
* *
39799900 TGAGTTATATGAATCTTATTACGGATTAAAGGTCCGATGACTTTATGTCATCG
1 TGAGTTATATGAATCTTATTACGGATTAAAGGTCCGATGACTATGTGTCATCG
39799953 TGAGTTAT
1 TGAGTTAT
39799961 CAATCATGAA
Statistics
Matches: 105, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 105 1.00
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.37
Consensus pattern (53 bp):
TGAGTTATATGAATCTTATTACGGATTAAAGGTCCGATGACTATGTGTCATCG
Found at i:39799928 original size:135 final size:135
Alignment explanation
Indices: 39799686--39799928 Score: 432
Period size: 135 Copynumber: 1.8 Consensus size: 135
39799676 CGTAAATGCA
*
39799686 AAAGGTTCGATGACTTTGTGTCATCGTGAGTTATATGAATCCTATTACGAATTAAAGGTCCGATA
1 AAAGGTTCGATGACTATGTGTCATCGTGAGTTATATGAATCCTATTACGAATTAAAGGTCCGATA
*
39799751 ACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATTAATGAGTTATATAAATCCTATTAC
66 ACTCTGTGTCATCATGAGTTATATGAATCCTATTACGGATTAATGAGTTATATAAATCCTATTAC
39799816 AGATT
131 AGATT
* * *
39799821 AAAGGTTCGATGACTATGTGTCATCGTGAGTTATATGAATCTTATTACGGATTAAAGGTCCGATG
1 AAAGGTTCGATGACTATGTGTCATCGTGAGTTATATGAATCCTATTACGAATTAAAGGTCCGATA
*
39799886 ACTCTGTGTCATCATGAGTTATATGAATCTTATTACGGATTAA
66 ACTCTGTGTCATCATGAGTTATATGAATCCTATTACGGATTAA
39799929 AGGTCCGATG
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
135 102 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (135 bp):
AAAGGTTCGATGACTATGTGTCATCGTGAGTTATATGAATCCTATTACGAATTAAAGGTCCGATA
ACTCTGTGTCATCATGAGTTATATGAATCCTATTACGGATTAATGAGTTATATAAATCCTATTAC
AGATT
Found at i:39804459 original size:20 final size:21
Alignment explanation
Indices: 39804420--39804459 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
39804410 TTGAAACAAT
*
39804420 TTTTAAATCAAGTTAAAATGA
1 TTTTAAATCAAGTCAAAATGA
*
39804441 TTTTAAA-CATGTCAAAATG
1 TTTTAAATCAAGTCAAAATG
39804460 CTTGCACTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTTAAATCAAGTCAAAATGA
Found at i:39807485 original size:29 final size:29
Alignment explanation
Indices: 39807410--39807494 Score: 100
Period size: 28 Copynumber: 2.9 Consensus size: 29
39807400 TTTTGAAATC
* *
39807410 TAAATAGTTCAAGGACTAAATTACAAAAAAAG
1 TAAAT-GTACAAGGACTAAATT-C-CAAAAAG
* *
39807442 CAAAAGTACAA-GACTAAATTCCAAAAAG
1 TAAATGTACAAGGACTAAATTCCAAAAAG
39807470 TAAATGTACAAGGACTAAATTCCAA
1 TAAATGTACAAGGACTAAATTCCAA
39807495 GTTTGTGAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
28 15 0.33
29 14 0.30
30 9 0.20
31 5 0.11
32 3 0.07
ACGTcount: A:0.54, C:0.14, G:0.12, T:0.20
Consensus pattern (29 bp):
TAAATGTACAAGGACTAAATTCCAAAAAG
Found at i:39825072 original size:28 final size:29
Alignment explanation
Indices: 39825039--39825099 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
39825029 TAATTTATAA
*
39825039 ATTTTAA-A-ATTAATATTGATAAATTTTC
1 ATTTTAACATATTAA-AATGATAAATTTTC
* *
39825067 ATTTTAACATTTTAAAATGATAAATTTTG
1 ATTTTAACATATTAAAATGATAAATTTTC
39825096 ATTT
1 ATTT
39825100 AATCTTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.25
29 17 0.61
30 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (29 bp):
ATTTTAACATATTAAAATGATAAATTTTC
Found at i:39825119 original size:29 final size:29
Alignment explanation
Indices: 39825055--39825111 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
39825045 AAATTAATAT
39825055 TGATAAATTTTCATTTTAACATTTTAAAA
1 TGATAAATTTTCATTTTAACATTTTAAAA
*
39825084 TGATAAATTTTGA-TTTAATC-TTTTAAAA
1 TGATAAATTTTCATTTTAA-CATTTTAAAA
39825112 ATTATAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.49
Consensus pattern (29 bp):
TGATAAATTTTCATTTTAACATTTTAAAA
Found at i:39828774 original size:4 final size:4
Alignment explanation
Indices: 39828765--39828792 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
39828755 TACTTAGACC
39828765 CTAT CTAT CTAT CTAT CTAT CTAT CTAT
1 CTAT CTAT CTAT CTAT CTAT CTAT CTAT
39828793 AAAAGCAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
CTAT
Found at i:39835870 original size:14 final size:13
Alignment explanation
Indices: 39835830--39835886 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 13
39835820 AATTATAGAA
*
39835830 ATAAAATTTAAAGT
1 ATAAAA-TTAAAAT
39835844 ATACCAAATTAAAAT
1 ATA--AAATTAAAAT
*
39835859 ATAAAGATTAAATT
1 ATAAA-ATTAAAAT
*
39835873 ATAAATTTAAAAT
1 ATAAAATTAAAAT
39835886 A
1 A
39835887 GTATAGGGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
13 9 0.25
14 15 0.42
15 9 0.25
16 3 0.08
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (13 bp):
ATAAAATTAAAAT
Found at i:39838883 original size:3 final size:3
Alignment explanation
Indices: 39838871--39838948 Score: 51
Period size: 3 Copynumber: 27.7 Consensus size: 3
39838861 TTGTCATTTG
* * *
39838871 TTA TTA -TA TTA TTA TTA TT- TTG TTA TTA TTA TT- TGA ATA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
39838915 TAA TTT TTA TT- TTA TTA TTAA TT- TTG TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TT
39838949 TTAAATGTAT
Statistics
Matches: 58, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
2 11 0.19
3 44 0.76
4 3 0.05
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:39838944 original size:12 final size:11
Alignment explanation
Indices: 39838871--39838951 Score: 67
Period size: 11 Copynumber: 7.3 Consensus size: 11
39838861 TTGTCATTTG
39838871 TTATTA-TATT
1 TTATTATTATT
39838881 ATTATTATT-TT
1 -TTATTATTATT
39838892 GTTATTATTATT
1 -TTATTATTATT
* * *
39838904 TGAATATTATA
1 TTATTATTATT
* *
39838915 TAATTTTTATT
1 TTATTATTATT
39838926 TTATTATTAATT
1 TTATTATT-ATT
*
39838938 TTGTTATTATT
1 TTATTATTATT
39838949 TTA
1 TTA
39838952 AATGTATTTT
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
11 42 0.76
12 13 0.24
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (11 bp):
TTATTATTATT
Found at i:39844164 original size:17 final size:17
Alignment explanation
Indices: 39844142--39844180 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
39844132 AGGTGGAGAA
* * *
39844142 CTTGTTCTTTGAGAGTT
1 CTTGTTCGTAGAGAATT
39844159 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
39844176 CTTGT
1 CTTGT
39844181 CAAGGTGGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.15, C:0.13, G:0.23, T:0.49
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:39846628 original size:15 final size:16
Alignment explanation
Indices: 39846601--39846642 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 16
39846591 ATATATAAAG
39846601 AATATTATTTAAAATT
1 AATATTATTTAAAATT
39846617 AATATT-TTTAAAATT
1 AATATTATTTAAAATT
39846632 --TATTA-TTAAAA
1 AATATTATTTAAAA
39846643 GAAAATTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 10 0.40
15 9 0.36
16 6 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATATTATTTAAAATT
Found at i:39847698 original size:21 final size:23
Alignment explanation
Indices: 39847673--39847718 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
39847663 CATGTTACAC
39847673 TTTTTA-G-CAAAGATATTCATT
1 TTTTTATGTCAAAGATATTCATT
* *
39847694 TTTTTATGTCAAAGTTATTCGTT
1 TTTTTATGTCAAAGATATTCATT
39847717 TT
1 TT
39847719 ACACTTTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 1 0.05
23 14 0.67
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.54
Consensus pattern (23 bp):
TTTTTATGTCAAAGATATTCATT
Found at i:39855606 original size:11 final size:11
Alignment explanation
Indices: 39855590--39855630 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
39855580 AATTTTTCAG
39855590 TTTTTATGAAT-
1 TTTTTAT-AATA
39855601 TTTTTATAATA
1 TTTTTATAATA
*
39855612 TTTTTTTAATA
1 TTTTTATAATA
39855623 TTTTTATA
1 TTTTTATA
39855631 TTTTTAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 3 0.11
11 24 0.89
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (11 bp):
TTTTTATAATA
Found at i:39856191 original size:24 final size:25
Alignment explanation
Indices: 39856164--39856210 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
39856154 TAATTTTTAT
39856164 TTAACAGAATTAACC-AAATTAAAA
1 TTAACAGAATTAACCAAAATTAAAA
* *
39856188 TTAACCGAATTATCCAAAATTAA
1 TTAACAGAATTAACCAAAATTAA
39856211 CTGAATTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.53, C:0.15, G:0.04, T:0.28
Consensus pattern (25 bp):
TTAACAGAATTAACCAAAATTAAAA
Found at i:39865276 original size:19 final size:20
Alignment explanation
Indices: 39865245--39865283 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
39865235 GAATAAATAA
39865245 ATATTAGAGACAACTCAAAT
1 ATATTAGAGACAACTCAAAT
39865265 ATATTA-AGACAACTCAAAT
1 ATATTAGAGACAACTCAAAT
39865284 TTTAACTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.26
Consensus pattern (20 bp):
ATATTAGAGACAACTCAAAT
Found at i:39867975 original size:22 final size:21
Alignment explanation
Indices: 39867944--39867984 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
39867934 TTTCCAAAAT
*
39867944 TCAAAATATTTTAATTAAATTC
1 TCAAAATATTGTAA-TAAATTC
*
39867966 TCAAAGTATTGTAATAAAT
1 TCAAAATATTGTAATAAAT
39867985 ATAAATTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (21 bp):
TCAAAATATTGTAATAAATTC
Found at i:39877817 original size:17 final size:17
Alignment explanation
Indices: 39877795--39877846 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
39877785 TAAAACCGTA
39877795 TATAAAAAATATATATG
1 TATAAAAAATATATATG
* *
39877812 TATAAAATATACA-ATG
1 TATAAAAAATATATATG
*
39877828 TA-AAAAAGATATGTATG
1 TATAAAAA-ATATATATG
39877845 TA
1 TA
39877847 AAAGTACCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 4 0.14
16 8 0.29
17 16 0.57
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.33
Consensus pattern (17 bp):
TATAAAAAATATATATG
Found at i:39888888 original size:27 final size:26
Alignment explanation
Indices: 39888869--39888926 Score: 89
Period size: 27 Copynumber: 2.2 Consensus size: 26
39888859 TTGTACTTCT
*
39888869 AACATAAGTATTCCTACTTGTTAATAA
1 AACATAACTATTCCTACTTG-TAATAA
39888896 AACATAACTATTCCTACTTGTTAATAA
1 AACATAACTATTCCTACTTG-TAATAA
39888923 AACA
1 AACA
39888927 CTGTTGGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.34
Consensus pattern (26 bp):
AACATAACTATTCCTACTTGTAATAA
Found at i:39889239 original size:29 final size:30
Alignment explanation
Indices: 39889197--39889255 Score: 111
Period size: 29 Copynumber: 2.0 Consensus size: 30
39889187 AGAAAACGTA
39889197 GTTCCAATGAATTTATAT-GTGACTAAATC
1 GTTCCAATGAATTTATATAGTGACTAAATC
39889226 GTTCCAATGAATTTATATAGTGACTAAATC
1 GTTCCAATGAATTTATATAGTGACTAAATC
39889256 ATTTTGTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
Consensus pattern (30 bp):
GTTCCAATGAATTTATATAGTGACTAAATC
Found at i:39890746 original size:32 final size:32
Alignment explanation
Indices: 39890710--39890793 Score: 150
Period size: 32 Copynumber: 2.6 Consensus size: 32
39890700 TTTTAATACA
*
39890710 GTTTTTCTCGCGACTTGTTGCGATGAAATATG
1 GTTTTTCTCGCGACTTGTTGCGACGAAATATG
39890742 GTTTTTCTCGCGACTTGTTGCGACGAAATATG
1 GTTTTTCTCGCGACTTGTTGCGACGAAATATG
*
39890774 GTTTTTCTCGTGACTTGTTG
1 GTTTTTCTCGCGACTTGTTG
39890794 GGAAATGAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.15, C:0.17, G:0.25, T:0.43
Consensus pattern (32 bp):
GTTTTTCTCGCGACTTGTTGCGACGAAATATG
Found at i:39901880 original size:26 final size:27
Alignment explanation
Indices: 39901824--39901883 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
39901814 TAAAATTTAT
** *
39901824 TAATTTTTTTAAAAATATATAAAGTGC
1 TAATTTTTTTAAAAATATATAAAAAGA
*
39901851 TAATTTTTTTAAAAA-ATTTAAAAAGA
1 TAATTTTTTTAAAAATATATAAAAAGA
39901877 TAATTTT
1 TAATTTT
39901884 AAGGACTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 14 0.48
27 15 0.52
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (27 bp):
TAATTTTTTTAAAAATATATAAAAAGA
Found at i:39918083 original size:2 final size:2
Alignment explanation
Indices: 39918076--39918101 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39918066 ACAAATACAA
39918076 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
39918102 GTAGGTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39920809 original size:154 final size:155
Alignment explanation
Indices: 39920576--39920893 Score: 532
Period size: 154 Copynumber: 2.1 Consensus size: 155
39920566 TGTATATATA
* *
39920576 TATTAACACATTTTCGAGATTAGTCGATGCCCTGACTCGATAACTTCAAGTCTCACCTGCAGGTT
1 TATTAACAAATTTTCGAGATTAGTCAATGCCCTGACTCGATAACTTCAAGTCTCACCTGCAGGTT
*
39920641 AAACATTCAAAATAAATATGGCAAATACCAACTACTCATAGCACTTCATTGAAGTTACTCAAGCC
66 AAACATTCAAAATAAATATGGCAAATACCAACTACTCATAGCACTTCATTGAAGTTAATCAAGCC
* *
39920706 ATGTAT-A-TATATATGGATAAACT
131 ATATATAAGTATATATGCATAAACT
* * *
39920729 TATTAACAAATTTTCGAGATTAGTCAATGCCCTGACTTGATAAACTTCGAGTCTCTCCTGCAGGT
1 TATTAACAAATTTTCGAGATTAGTCAATGCCCTGACTCGAT-AACTTCAAGTCTCACCTGCAGGT
39920794 TAAACATTCAAAATAAATATGGCAAATACCAACTACTCATAGCACTTCATTGAAGTTAATCAAGC
65 TAAACATTCAAAATAAATATGGCAAATACCAACTACTCATAGCACTTCATTGAAGTTAATCAAGC
39920859 CATATATAATGTATATATGCATAAACT
130 CATATATAA-GTATATATGCATAAACT
39920886 TATTAACA
1 TATTAACA
39920894 CATATGCCCT
Statistics
Matches: 153, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
153 38 0.25
154 91 0.59
155 1 0.01
157 23 0.15
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (155 bp):
TATTAACAAATTTTCGAGATTAGTCAATGCCCTGACTCGATAACTTCAAGTCTCACCTGCAGGTT
AAACATTCAAAATAAATATGGCAAATACCAACTACTCATAGCACTTCATTGAAGTTAATCAAGCC
ATATATAAGTATATATGCATAAACT
Found at i:39920949 original size:127 final size:125
Alignment explanation
Indices: 39920786--39921017 Score: 394
Period size: 127 Copynumber: 1.8 Consensus size: 125
39920776 CGAGTCTCTC
39920786 CTGCAGGTTAAACATTCAAAATAAATATGGCAAATACCAACTACTCATAGCACTTCATTGAAGTT
1 CTGCAGGTTAAACATTCAAAATAAATATGGCAAATACCAACTACTCATAGCACTTCATTGAAGTT
*
39920851 AATCAAGCCATATATAATGTATATATGCATAAACTTATTAACACATATGCCCTGACTCGAAGT
66 AATCAAG-C-TATAT-ATATATATATGCATAAACTTATTAACACATATGCCCTGACTCGAAGT
*
39920914 CTGCAGGTTAAGCATTC-AAATAAATATGGCAAATACCAACTACTCATAGCACTTCATTGAAGTT
1 CTGCAGGTTAAACATTCAAAATAAATATGGCAAATACCAACTACTCATAGCACTTCATTGAAGTT
* *
39920978 AATCAAGCTATATATATATATGTGCATAAACTTGTTAACA
66 AATCAAGCTATATATATATATATGCATAAACTTATTAACA
39921018 TATTTTCGAG
Statistics
Matches: 100, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
124 24 0.24
125 5 0.05
126 1 0.01
127 54 0.54
128 16 0.16
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.30
Consensus pattern (125 bp):
CTGCAGGTTAAACATTCAAAATAAATATGGCAAATACCAACTACTCATAGCACTTCATTGAAGTT
AATCAAGCTATATATATATATATGCATAAACTTATTAACACATATGCCCTGACTCGAAGT
Found at i:39925364 original size:14 final size:15
Alignment explanation
Indices: 39925345--39925376 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
39925335 ACAATCAAAT
39925345 ATAATTTT-TTATAA
1 ATAATTTTATTATAA
39925359 ATAATTTTATTATAA
1 ATAATTTTATTATAA
39925374 ATA
1 ATA
39925377 TTGATCATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATAATTTTATTATAA
Found at i:39925628 original size:29 final size:29
Alignment explanation
Indices: 39925573--39925683 Score: 96
Period size: 31 Copynumber: 3.7 Consensus size: 29
39925563 ATCTCAAAAT
* * *
39925573 TATACATGAACTTTGATTTAATATGCAATTG
1 TATACATGAACTTTAATTT--GATGCAATTA
39925604 TATACATGAACTTTAATTTGATGCAATTA
1 TATACATGAACTTTAATTTGATGCAATTA
* * * * *
39925633 TACACGTGAAATTCTAATTGTGATTCAAATA
1 TATACATGAACTT-TAATT-TGATGCAATTA
*
39925664 TATACTTGAAACTTTAATTT
1 TATACATG-AACTTTAATTT
39925684 TGATTTAACA
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
29 18 0.27
30 6 0.09
31 38 0.58
32 4 0.06
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (29 bp):
TATACATGAACTTTAATTTGATGCAATTA
Found at i:39926236 original size:20 final size:20
Alignment explanation
Indices: 39926213--39926250 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39926203 TATTAGTCCT
39926213 TATTTTAAAAAATTAAATTC
1 TATTTTAAAAAATTAAATTC
**
39926233 TATTTTTTAAAATTAAAT
1 TATTTTAAAAAATTAAAT
39926251 ATTAATTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
TATTTTAAAAAATTAAATTC
Found at i:39929111 original size:17 final size:17
Alignment explanation
Indices: 39929082--39929123 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
39929072 TTTAATCATT
*
39929082 TAAAATT-TATAAA-AA
1 TAAAATTATTTAAATAA
39929097 TATAAATTATTTAAATAA
1 TA-AAATTATTTAAATAA
39929115 TAAAATTAT
1 TAAAATTAT
39929124 ATTTTTACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 2 0.09
16 5 0.22
17 12 0.52
18 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAAATTATTTAAATAA
Found at i:39929867 original size:2 final size:2
Alignment explanation
Indices: 39929860--39929889 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39929850 ATTGAAGTTC
39929860 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39929890 TAAATTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39929934 original size:19 final size:20
Alignment explanation
Indices: 39929897--39929941 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
39929887 TATTAAATTT
39929897 TAATTTACTGTATATTATAA
1 TAATTTACTGTATATTATAA
39929917 TAATTTA-T-TATAATTATAA
1 TAATTTACTGTAT-ATTATAA
*
39929936 TTATTT
1 TAATTT
39929942 GAATGTATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 3 0.13
19 13 0.57
20 7 0.30
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TAATTTACTGTATATTATAA
Found at i:39936246 original size:14 final size:16
Alignment explanation
Indices: 39936215--39936247 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
39936205 AAACTTGAAT
39936215 AATTAAGAATATTTAA
1 AATTAAGAATATTTAA
39936231 AATTAA-AATA-TTAA
1 AATTAAGAATATTTAA
39936245 AAT
1 AAT
39936248 GACTCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 4 0.24
16 6 0.35
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
AATTAAGAATATTTAA
Found at i:39937281 original size:3 final size:3
Alignment explanation
Indices: 39937273--39937314 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
39937263 GAGTAAATTT
39937273 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
39937315 TCTCTATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:39940711 original size:4 final size:4
Alignment explanation
Indices: 39940702--39940740 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
39940692 TTAAAACTTC
39940702 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
39940741 CAGGTCCTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:39941038 original size:104 final size:103
Alignment explanation
Indices: 39940737--39941253 Score: 515
Period size: 103 Copynumber: 4.9 Consensus size: 103
39940727 TGTATGTATG
*
39940737 TATGCAGGTCCTGCAAGATTTTCCCATGGTTTTAGCTTCAGATTTTTTGCCCCTAGCTCATACAA
1 TATGCAGGTCCTGCAAGATTTTCCCATGGTTTTAGCTTCAAATTTTTTGCCCCTAGCTCATACAA
* *
39940802 TTAAAGCTTAAGACTTGATGTATGTATGTAGGTCTTGCA
66 TCAAAGCTTAA-ACTTCATGTATGTATGTAGGTCTTGCA
* * *
39940841 TATGCAGGTCCTGCAAGA-TTTCCCATGGTTTTAGCTTCAAAATTTTGGCCCCTAGATCATACAA
1 TATGCAGGTCCTGCAAGATTTTCCCATGGTTTTAGCTTCAAATTTTTTGCCCCTAGCTCATACAA
* *
39940905 TTAAAGCTTAAGACTTGATGTATGTATGTAGGTCTTGCA
66 TCAAAGCTTAA-ACTTCATGTATGTATGTAGGTCTTGCA
* * *
39940944 TATGCAGGCCCTGCAAGAATTTCCCCTGGTTTTAGCTTCAAATTTTTTGCCCCTAGCTCATACAA
1 TATGCAGGTCCTGCAAGATTTTCCCATGGTTTTAGCTTCAAATTTTTTGCCCCTAGCTCATACAA
* * *
39941009 TCAAAGCTTATAACTTCATGTATGCATGTATGT-ATGCA
66 TCAAAGCTTA-AACTTCATGTATGTATGTAGGTCTTGCA
* ** * * * * * * * *
39941047 GGTCTTGCATATGCAGGTTC-TGCAAGATTTTCCCATGCTTTTAGCTTCAGATTTTTGGCCCCTA
1 --T-ATGCAGGT-C--CTGCAAG--A-TTTTC-CCATGGTTTTAGCTTCAAATTTTTTGCCCCTA
* * * *
39941111 GCTCATAAAATCAAAGCTTAAAACTTCATGTATGTATGCATGT-ATG--
56 GCTCATACAATCAAAGCTT-AAACTTCATGTATGTATGTAGGTCTTGCA
* * ** * *
39941157 TATGCAGGTCCTGCAATATTTTCCCATGGTTTTAGCTTCACATTTAATGCCTCTGGCTCATACAA
1 TATGCAGGTCCTGCAAGATTTTCCCATGGTTTTAGCTTCAAATTTTTTGCCCCTAGCTCATACAA
*
39941222 CCAAAGCTTAAAACTTCATATGTATGTATGTA
66 TCAAAGCTT-AAACTTC--ATGTATGTATGTA
39941254 CCTGCAAGAA
Statistics
Matches: 349, Mismatches: 48, Indels: 33
0.81 0.11 0.08
Matches are distributed among these distances:
101 50 0.14
102 3 0.01
103 115 0.33
104 89 0.26
105 2 0.01
106 5 0.01
107 6 0.02
108 2 0.01
109 2 0.01
110 1 0.00
111 4 0.01
112 69 0.20
113 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (103 bp):
TATGCAGGTCCTGCAAGATTTTCCCATGGTTTTAGCTTCAAATTTTTTGCCCCTAGCTCATACAA
TCAAAGCTTAAACTTCATGTATGTATGTAGGTCTTGCA
Found at i:39941123 original size:112 final size:113
Alignment explanation
Indices: 39940922--39941171 Score: 367
Period size: 112 Copynumber: 2.2 Consensus size: 113
39940912 TTAAGACTTG
* * *
39940922 ATGTATGTATGTAGGTCTTGCATATGCAGGCCCTGCAAGAATTTCCCCTGGTTTTAGCTTCAAAT
1 ATGTATGTATGCAGGTCTTGCATATGCAGGCCCTGCAAGAATTTCCCATGCTTTTAGCTTCAAAT
* * *
39940987 TTTTTGCCCCTAGCTCATACAATCAAAGCTTATAACTTC-ATGTATGC
66 TTTTGGCCCCTAGCTCATAAAATCAAAGCTTAAAACTTCTATGTATGC
** * *
39941034 ATGTATGTATGCAGGTCTTGCATATGCAGGTTCTGCAAGATTTTCCCATGCTTTTAGCTTCAGAT
1 ATGTATGTATGCAGGTCTTGCATATGCAGGCCCTGCAAGAATTTCCCATGCTTTTAGCTTCAAAT
39941099 TTTTGGCCCCTAGCTCATAAAATCAAAGCTTAAAACTTCATGTATGTATGC
66 TTTTGGCCCCTAGCTCATAAAATCAAAGCTTAAAACTTC---TATGTATGC
*
39941150 ATGTATGTATGCAGGTCCTGCA
1 ATGTATGTATGCAGGTCTTGCA
39941172 ATATTTTCCC
Statistics
Matches: 123, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
112 94 0.76
116 29 0.24
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (113 bp):
ATGTATGTATGCAGGTCTTGCATATGCAGGCCCTGCAAGAATTTCCCATGCTTTTAGCTTCAAAT
TTTTGGCCCCTAGCTCATAAAATCAAAGCTTAAAACTTCTATGTATGC
Found at i:39941154 original size:12 final size:12
Alignment explanation
Indices: 39941137--39941162 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39941127 CTTAAAACTT
39941137 CATGTATGTATG
1 CATGTATGTATG
39941149 CATGTATGTATG
1 CATGTATGTATG
39941161 CA
1 CA
39941163 GGTCCTGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (12 bp):
CATGTATGTATG
Found at i:39943001 original size:34 final size:33
Alignment explanation
Indices: 39942959--39943028 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 33
39942949 AAGGGTTCAA
* *
39942959 TTTTTTTTTAATTTTTAAGGAGTTCAATTTTTTT
1 TTTTTTTTTAATTTTTAAGG-GCTCAAATTTTTT
*
39942993 TTTTTTTTTAGTTTTTAAGGGCTCAAATTTTTT
1 TTTTTTTTTAATTTTTAAGGGCTCAAATTTTTT
39943026 TTT
1 TTT
39943029 ACCAACTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 14 0.42
34 19 0.58
ACGTcount: A:0.19, C:0.04, G:0.10, T:0.67
Consensus pattern (33 bp):
TTTTTTTTTAATTTTTAAGGGCTCAAATTTTTT
Found at i:39944053 original size:15 final size:15
Alignment explanation
Indices: 39944023--39944064 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
39944013 TTTGTGGTTC
* *
39944023 AATAATAATAATAAT
1 AATAATTATTATAAT
*
39944038 AATTATTATTATAAT
1 AATAATTATTATAAT
39944053 AATAATTATTAT
1 AATAATTATTAT
39944065 TAATTTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAATTATTATAAT
Found at i:39944053 original size:18 final size:18
Alignment explanation
Indices: 39944030--39944066 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
39944020 TTCAATAATA
39944030 ATAATAATAATTATTATT
1 ATAATAATAATTATTATT
39944048 ATAATAATAATTATTATT
1 ATAATAATAATTATTATT
39944066 A
1 A
39944067 ATTTTTAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATAATAATAATTATTATT
Found at i:39945104 original size:59 final size:59
Alignment explanation
Indices: 39945023--39945161 Score: 145
Period size: 59 Copynumber: 2.4 Consensus size: 59
39945013 CACGGCCTGT
** * * * *
39945023 CACACGCTTGTGTGTCCCCTGTACCTTAATTCACAAAACAA-TATGCACACACGGTTTGG
1 CACACGCCCGTGTGTCTCCTGTACCTTAATTCACAAAA-AAGTATGCACACACGATCTAG
* * * * *
39945082 CACACGCCCGTGTGTCTTCTGTAGCTTATTTTACAAAAAAGTATGTACACACGATCTAG
1 CACACGCCCGTGTGTCTCCTGTACCTTAATTCACAAAAAAGTATGCACACACGATCTAG
* *
39945141 CACACACCCATGTGTCTCCTG
1 CACACGCCCGTGTGTCTCCTG
39945162 AAGCTTATTT
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
58 2 0.03
59 63 0.97
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.28
Consensus pattern (59 bp):
CACACGCCCGTGTGTCTCCTGTACCTTAATTCACAAAAAAGTATGCACACACGATCTAG
Found at i:39945167 original size:59 final size:59
Alignment explanation
Indices: 39945055--39945171 Score: 146
Period size: 59 Copynumber: 2.0 Consensus size: 59
39945045 ACCTTAATTC
* * * * * * *
39945055 ACAAAACAATATGCACACACGGTTTGGCACACGCCCGTGTGTCTTCTGTAGCTTATTTT
1 ACAAAACAATATGCACACACGATCTAGCACACACCCATGTGTCTCCTGAAGCTTATTTT
*
39945114 ACAAAA-AAGTATGTACACACGATCTAGCACACACCCATGTGTCTCCTGAAGCTTATTT
1 ACAAAACAA-TATGCACACACGATCTAGCACACACCCATGTGTCTCCTGAAGCTTATTT
39945172 ATATGGCACA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
58 2 0.04
59 47 0.96
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (59 bp):
ACAAAACAATATGCACACACGATCTAGCACACACCCATGTGTCTCCTGAAGCTTATTTT
Found at i:39949606 original size:18 final size:18
Alignment explanation
Indices: 39949574--39949625 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
39949564 CTGAGACGAG
39949574 AATAAATTT--TTAATTA
1 AATAAATTTAATTAATTA
39949590 AATAAATTTAATTAATTA
1 AATAAATTTAATTAATTA
*
39949608 AA-AATTTTGAATTAATTA
1 AATAAATTT-AATTAATTA
39949626 CATGAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 9 0.28
17 5 0.16
18 18 0.56
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
AATAAATTTAATTAATTA
Found at i:39951980 original size:168 final size:168
Alignment explanation
Indices: 39951702--39952016 Score: 470
Period size: 168 Copynumber: 1.9 Consensus size: 168
39951692 GTCCCATAGC
* *
39951702 ATGTGCTTGTCATATTATAGGTTCGCGAGGTAAAGGGCTTGAAAAGTCTTGATCTCACAACTTCT
1 ATGTGCTTGTCATATTATAGGTTCACGAGGTAAAGGGCTTGAAAAGTCTTGACCTCACAACTTCT
* * * * * *
39951767 TTAGCAACTTCTACCTCGCAAGCCTATAGCATGGATTAGTGACATCTAAAGGTAGAGGAATTAAG
66 TTAGCAACTTCTAACTCGCAAGCCTATAACATAGATTAGTGACATCTAAAAGCAGAGAAATTAAG
39951832 CTATGTCAAATTAAAGTCACAGAGTGTAGTCCTACAAT
131 CTATGTCAAATTAAAGTCACAGAGTGTAGTCCTACAAT
* * * *
39951870 ATGTGCTTGTCATATTATAGGTTCATGAGGTAAAGGGCTTGCAAAGTTTTGGCCTCACAACTTCT
1 ATGTGCTTGTCATATTATAGGTTCACGAGGTAAAGGGCTTGAAAAGTCTTGACCTCACAACTTCT
* * *
39951935 TTA-CTAGCTTGTAACTCGCAAGCCTATAACATAGATTAGTGACATCTAAAAGCGGAGAAATTAA
66 TTAGC-AACTTCTAACTCGCAAGCCTATAACATAGATTAGTGACATCTAAAAGCAGAGAAATTAA
*
39951999 GTTATGTCAAATTAAAGT
130 GCTATGTCAAATTAAAGT
39952017 GTAAAGATTA
Statistics
Matches: 130, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
167 1 0.01
168 129 0.99
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (168 bp):
ATGTGCTTGTCATATTATAGGTTCACGAGGTAAAGGGCTTGAAAAGTCTTGACCTCACAACTTCT
TTAGCAACTTCTAACTCGCAAGCCTATAACATAGATTAGTGACATCTAAAAGCAGAGAAATTAAG
CTATGTCAAATTAAAGTCACAGAGTGTAGTCCTACAAT
Found at i:39954634 original size:21 final size:22
Alignment explanation
Indices: 39954591--39954653 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
39954581 AGAGAAGGCC
*
39954591 AAGAAGGA-AAGGAAGAAAGAA
1 AAGAAGGAGAAGAAAGAAAGAA
39954612 AAGAAGGAGAAGAAAG--AGAA
1 AAGAAGGAGAAGAAAGAAAGAA
39954632 AA-AACGGGAGAAGAAAGAAAGA
1 AAGAA--GGAGAAGAAAGAAAGA
39954654 GATAAGTCTC
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
19 2 0.06
20 6 0.17
21 19 0.53
22 6 0.17
23 3 0.08
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (22 bp):
AAGAAGGAGAAGAAAGAAAGAA
Found at i:39959150 original size:100 final size:101
Alignment explanation
Indices: 39958998--39959190 Score: 289
Period size: 100 Copynumber: 1.9 Consensus size: 101
39958988 CCTTCAAGAC
* * * *
39958998 CCCCCTATCCGGTAGCTACATTGGAGCTTAACTAAACCCGAAGTTTAGCCGAATTAGACCCTTAA
1 CCCCCTATCCGGTAACTACATTGGAACTTAACTAAACCCGAAGTTCAGCCGAATTAGACCCTAAA
* *
39959063 GAAAGCAAGCTCTACTAGCGGTATTTTCAATCGACT
66 GAAAGCAAGCTCTACTACCAGTATTTTCAATCGACT
* * *
39959099 CCCCCTATCTGGTAACTACATT-GAACTTGACTAAACCCGGAGTTCAGCCGAATTAGACCCTAAA
1 CCCCCTATCCGGTAACTACATTGGAACTTAACTAAACCCGAAGTTCAGCCGAATTAGACCCTAAA
*
39959163 GAAAGCAAGCTCTCCTACCAGTATTTTC
66 GAAAGCAAGCTCTACTACCAGTATTTTC
39959191 TCCGCTAAAA
Statistics
Matches: 82, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
100 62 0.76
101 20 0.24
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (101 bp):
CCCCCTATCCGGTAACTACATTGGAACTTAACTAAACCCGAAGTTCAGCCGAATTAGACCCTAAA
GAAAGCAAGCTCTACTACCAGTATTTTCAATCGACT
Found at i:39967373 original size:84 final size:84
Alignment explanation
Indices: 39967232--39967387 Score: 294
Period size: 84 Copynumber: 1.9 Consensus size: 84
39967222 TGATAACAAA
*
39967232 CTTCCATTTCAATTATTTATATAATCATCTTCCAGTTTACATGACTTGACCATATAACATTTCCT
1 CTTCCATTTCAATTATTTATATAAACATCTTCCAGTTTACATGACTTGACCATATAACATTTCCT
39967297 GTATATACATATATATAAG
66 GTATATACATATATATAAG
*
39967316 CTTCCATTTCAATTATTTATATAAACATCTTCCGGTTTACATGACTTGACCATATAACATTTCCT
1 CTTCCATTTCAATTATTTATATAAACATCTTCCAGTTTACATGACTTGACCATATAACATTTCCT
39967381 GTATATA
66 GTATATA
39967388 TACATATAAA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 70 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (84 bp):
CTTCCATTTCAATTATTTATATAAACATCTTCCAGTTTACATGACTTGACCATATAACATTTCCT
GTATATACATATATATAAG
Found at i:39973557 original size:20 final size:19
Alignment explanation
Indices: 39973520--39973568 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
39973510 TATATCAAAT
*
39973520 AAACTTAAAAACATTAAAAC
1 AAACTTAAAAACAAT-AAAC
39973540 AAACATTAAAAA-AATAAAC
1 AAAC-TTAAAAACAATAAAC
*
39973559 AAATTTAAAA
1 AAACTTAAAA
39973569 TACATTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 6 0.23
19 7 0.27
20 6 0.23
21 7 0.27
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.20
Consensus pattern (19 bp):
AAACTTAAAAACAATAAAC
Found at i:39973740 original size:44 final size:41
Alignment explanation
Indices: 39973685--39973773 Score: 108
Period size: 44 Copynumber: 2.1 Consensus size: 41
39973675 AACAATAGTA
* *
39973685 AAAACGCATAAAAATAACA-TCCAAACAACCAAAATAACAATC
1 AAAACGCATAAAAATAACAGT-AAAACAACAAAAATAACAA-C
*
39973727 AAAACAGCAATAAAAATAACAGTAAAACAACAAAAATAGCAAC
1 AAAAC-GC-ATAAAAATAACAGTAAAACAACAAAAATAACAAC
39973770 AAAA
1 AAAA
39973774 ATAACAGCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
42 5 0.12
43 7 0.17
44 28 0.68
45 1 0.02
ACGTcount: A:0.66, C:0.19, G:0.04, T:0.10
Consensus pattern (41 bp):
AAAACGCATAAAAATAACAGTAAAACAACAAAAATAACAAC
Found at i:39973820 original size:16 final size:16
Alignment explanation
Indices: 39973796--39973859 Score: 65
Period size: 16 Copynumber: 3.7 Consensus size: 16
39973786 AAAATAGTAA
*
39973796 AAAACCAAAAAGCAACC
1 AAAA-CAAAAAACAACC
*
39973813 AAAACAAAAAAAAACC
1 AAAACAAAAAACAACC
39973829 AAAACAGTAAAAACAACACC
1 AAAACA--AAAAAC-A-ACC
39973849 AAAACAAAAAA
1 AAAACAAAAAA
39973860 ACAGCAATCA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
16 16 0.40
17 4 0.10
18 10 0.25
19 1 0.03
20 9 0.22
ACGTcount: A:0.73, C:0.22, G:0.03, T:0.02
Consensus pattern (16 bp):
AAAACAAAAAACAACC
Found at i:39973841 original size:20 final size:21
Alignment explanation
Indices: 39973818--39973896 Score: 67
Period size: 20 Copynumber: 3.9 Consensus size: 21
39973808 CAACCAAAAC
39973818 AAAAAA-AAACCAAAACAGTA
1 AAAAAAGAAACCAAAACAGTA
* *
39973838 AAAACA-ACACCAAAACA--A
1 AAAAAAGAAACCAAAACAGTA
* *
39973856 AAAAACAGCAATCAAAACAGTA
1 AAAAA-AGAAACCAAAACAGTA
*
39973878 AAAAAATAACACCAAAACA
1 AAAAAAGAA-ACCAAAACA
39973897 ACAATATAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
18 5 0.11
19 1 0.02
20 23 0.51
21 2 0.04
22 14 0.31
ACGTcount: A:0.71, C:0.20, G:0.04, T:0.05
Consensus pattern (21 bp):
AAAAAAGAAACCAAAACAGTA
Found at i:39973850 original size:36 final size:39
Alignment explanation
Indices: 39973810--39973897 Score: 110
Period size: 42 Copynumber: 2.3 Consensus size: 39
39973800 CCAAAAAGCA
39973810 ACCAAAACAAAAAA-A-AACCAAAACAGT-AAAAACAAC
1 ACCAAAACAAAAAACACAACCAAAACAGTAAAAAACAAC
* *
39973846 ACCAAAACAAAAAAACAGCAATCAAAACAGTAAAAAAATAAC
1 ACCAAAAC-AAAAAACA-CAACCAAAACAGT-AAAAAACAAC
39973888 ACCAAAACAA
1 ACCAAAACAA
39973898 CAATATAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
36 8 0.18
37 6 0.14
38 1 0.02
40 11 0.25
41 2 0.05
42 16 0.36
ACGTcount: A:0.70, C:0.22, G:0.03, T:0.05
Consensus pattern (39 bp):
ACCAAAACAAAAAACACAACCAAAACAGTAAAAAACAAC
Found at i:39973862 original size:16 final size:16
Alignment explanation
Indices: 39973796--39973862 Score: 62
Period size: 17 Copynumber: 3.9 Consensus size: 16
39973786 AAAATAGTAA
* *
39973796 AAAACCAAAAAGCAACC
1 AAAACAAAAAAAC-ACC
*
39973813 AAAACAAAAAAAAACC
1 AAAACAAAAAAACACC
39973829 AAAACAGTAAAAACAACACC
1 AAAAC---AAAAA-AACACC
39973849 AAAACAAAAAAACA
1 AAAACAAAAAAACA
39973863 GCAATCAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
16 12 0.29
17 15 0.36
19 5 0.12
20 10 0.24
ACGTcount: A:0.73, C:0.22, G:0.03, T:0.01
Consensus pattern (16 bp):
AAAACAAAAAAACACC
Found at i:39978115 original size:51 final size:51
Alignment explanation
Indices: 39978044--39978280 Score: 332
Period size: 51 Copynumber: 4.6 Consensus size: 51
39978034 TTTCATTTAA
* * *
39978044 TACTCACGATGACA-TATAGTCATCGGACCTTTAATTCGTAATGAATTCATT
1 TACTCACGATGACACT-TAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
*
39978095 TACTCACGATGACACTTAGTCATCGAACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* * * *
39978146 TACTCACGATGACACTTAGTTATTGGACTTTTAATCCTTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* * * * *
39978197 CACTCACAATAACACTTAGTCACCGGACCTTTAATCCATAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
39978248 TACTCACGATGACACTTAGTCATCGGACTCTTT
1 TACTCACGATGACACTTAGTCATCGGAC-CTTT
39978281 CATTTATAGC
Statistics
Matches: 163, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
51 158 0.97
52 5 0.03
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
Found at i:39984584 original size:21 final size:21
Alignment explanation
Indices: 39984558--39984610 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
39984548 TGCAGATTTT
*
39984558 TACCGATACATTTACTA-ATTC
1 TACCGATACAATTA-TAGATTC
*
39984579 TACCGATACAATTATAGTTTC
1 TACCGATACAATTATAGATTC
39984600 TACCGATACAA
1 TACCGATACAA
39984611 GTCATGCAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.34
Consensus pattern (21 bp):
TACCGATACAATTATAGATTC
Found at i:39985454 original size:51 final size:51
Alignment explanation
Indices: 39985375--39985483 Score: 175
Period size: 51 Copynumber: 2.1 Consensus size: 51
39985365 TCGTATAGAA
* * *
39985375 ATTCATATACTCACGATGACATTGAGTCATTGGACCTTTAATTCGTAATGG
1 ATTCATTTACTCACGATGACATTGAGTCATTGGACCTTTAATCCGTAAAGG
39985426 ATTCATTTACTCACGATGACACTT-AGTCATTGGACCTTTAATCCGTAAAGG
1 ATTCATTTACTCACGATGACA-TTGAGTCATTGGACCTTTAATCCGTAAAGG
39985477 ATTCATT
1 ATTCATT
39985484 CCGTAAAGGA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
51 52 0.96
52 2 0.04
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (51 bp):
ATTCATTTACTCACGATGACATTGAGTCATTGGACCTTTAATCCGTAAAGG
Found at i:39985488 original size:16 final size:16
Alignment explanation
Indices: 39985467--39985499 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
39985457 GGACCTTTAA
39985467 TCCGTAAAGGATTCAT
1 TCCGTAAAGGATTCAT
39985483 TCCGTAAAGGATTCAT
1 TCCGTAAAGGATTCAT
39985499 T
1 T
39985500 TACTCACGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (16 bp):
TCCGTAAAGGATTCAT
Found at i:39985528 original size:67 final size:67
Alignment explanation
Indices: 39985418--39985550 Score: 230
Period size: 67 Copynumber: 2.0 Consensus size: 67
39985408 ACCTTTAATT
* * *
39985418 CGTAATGGATTCATTTACTCACGATGACACTTAGTCATTGGACCTTTAATCCGTAAAGGATTCAT
1 CGTAAAGGATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCAT
39985483 TC
66 TC
*
39985485 CGTAAAGGATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCTATAAAGGATTCAT
1 CGTAAAGGATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCAT
39985550 T
66 T
39985551 TACTCATGAT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (67 bp):
CGTAAAGGATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCAT
TC
Found at i:39985563 original size:51 final size:51
Alignment explanation
Indices: 39985487--39985634 Score: 242
Period size: 51 Copynumber: 2.9 Consensus size: 51
39985477 ATTCATTCCG
*
39985487 TAAAGGATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCTA
1 TAAAGGATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCGA
* *
39985538 TAAAGGATTCATTTACTCATGATGACACTTAGTCATCGGACCTTTAATCGG
1 TAAAGGATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCGA
* *
39985589 TAAAGGATTCATTTACTCACGATGACATTTAGTCATCAGACTCTTT
1 TAAAGGATTCATTTACTCACGATGACACTTAGTCATCGGAC-CTTT
39985635 TGTTTATAGC
Statistics
Matches: 90, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
51 86 0.96
52 4 0.04
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (51 bp):
TAAAGGATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCGA
Found at i:39985583 original size:118 final size:118
Alignment explanation
Indices: 39985375--39985601 Score: 359
Period size: 118 Copynumber: 1.9 Consensus size: 118
39985365 TCGTATAGAA
* * *
39985375 ATTCATATACTCACGATGACATTGAGTCATTGGACCTTTAATTCGTAATGGATTCATTTACTCAC
1 ATTCATATACTCACGATGACATTGAGTCATCGGACCTTTAATTCATAAAGGATTCATTTACTCAC
*
39985440 GATGACACTTAGTCATTGGACCTTTAATCCGTAAAGGATTCATTCCGTAAAGG
66 GATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTCCGTAAAGG
*
39985493 ATTCATTTACTCACGATGACACTT-AGTCATCGGACCTTTAA-TCTATAAAGGATTCATTTACTC
1 ATTCATATACTCACGATGACA-TTGAGTCATCGGACCTTTAATTC-ATAAAGGATTCATTTACTC
* *
39985556 ATGATGACACTTAGTCATCGGACCTTTAATCGGTAAAGGATTCATT
64 ACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
39985602 TACTCACGAT
Statistics
Matches: 100, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
117 2 0.02
118 96 0.96
119 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (118 bp):
ATTCATATACTCACGATGACATTGAGTCATCGGACCTTTAATTCATAAAGGATTCATTTACTCAC
GATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTCCGTAAAGG
Found at i:39989474 original size:23 final size:22
Alignment explanation
Indices: 39989444--39989640 Score: 143
Period size: 23 Copynumber: 8.5 Consensus size: 22
39989434 ACACTAGCGC
39989444 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGT-T-GT
39989467 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTGT-TGT
* *
39989492 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGT-TGT
* *
39989515 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGT-TGT
* *
39989538 GCTCTCTGATTAGTACT-TTGT
1 GCTCTCTGTTTAGCACTGTTGT
39989559 GTACTCTCTGTTTAGCACTGTGTGT
1 G--CTCTCTGTTTAGCACTGT-TGT
*
39989584 GCTCTCTGTTGCCCAGCACT-TATGT
1 GCTCTCTGTT---TAGCACTGT-TGT
*
39989609 GCTCTCTG-TTAGTACT-TTGGT
1 GCTCTCTGTTTAGCACTGTT-GT
*
39989630 ACTCTCTGTTT
1 GCTCTCTGTTT
39989641 GTTCCGCATA
Statistics
Matches: 151, Mismatches: 11, Indels: 25
0.81 0.06 0.13
Matches are distributed among these distances:
20 1 0.01
21 19 0.13
22 3 0.02
23 83 0.55
24 3 0.02
25 33 0.22
26 9 0.06
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (22 bp):
GCTCTCTGTTTAGCACTGTTGT
Found at i:39989481 original size:25 final size:24
Alignment explanation
Indices: 39989444--39989592 Score: 148
Period size: 23 Copynumber: 6.4 Consensus size: 24
39989434 ACACTAGCGC
39989444 GCTCTCTGT-TTAGCAC-GTCTCGT
1 GCTCTCTGTATTAGCACTGTCT-GT
*
39989467 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-TATTAGCACTGTCTGT
* *
39989492 GCTCTCTG-ATTAGCACTTTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
* *
39989515 GCTCTCTG-ATTAGCACTTTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
* * *
39989538 GCTCTCTG-ATTAGTACTTTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
* *
39989561 ACTCTCTGT-TTAGCACTGTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
39989584 GCTCTCTGT
1 GCTCTCTGT
39989593 TGCCCAGCAC
Statistics
Matches: 115, Mismatches: 7, Indels: 8
0.88 0.05 0.06
Matches are distributed among these distances:
23 94 0.82
24 1 0.01
25 17 0.15
26 3 0.03
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (24 bp):
GCTCTCTGTATTAGCACTGTCTGT
Found at i:39989544 original size:46 final size:46
Alignment explanation
Indices: 39989465--39989591 Score: 200
Period size: 46 Copynumber: 2.7 Consensus size: 46
39989455 AGCACGTCTC
39989465 GTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTG--ATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT
* *
39989513 GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT
* *
39989559 GTACTCTCTGTTTAGCACTGTGTGTGCTCTCTG
1 GTGCTCTCTGATTAGCACTGTGTGTGCTCTCTG
39989592 TTGCCCAGCA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
46 64 0.86
48 10 0.14
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.44
Consensus pattern (46 bp):
GTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT
Found at i:39989583 original size:69 final size:68
Alignment explanation
Indices: 39989444--39989640 Score: 220
Period size: 69 Copynumber: 2.8 Consensus size: 68
39989434 ACACTAGCGC
* * * * * * *
39989444 GCTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACT
1 GCTCTCTGTTCAGCACTTAT-GTGCTCTCTG--ATTAGTACTTTGTGTACTCTCTGTTTAGCACT
*
39989509 TTGTGT
63 GTGTGT
*
39989515 GCTCTCTGATT-AGCACTTTGTGTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTG
1 GCTCTCTG-TTCAGCAC-TTATGTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTG
39989579 TGTGT
64 TGTGT
39989584 GCTCTCTGTTGCCCAGCACTTATGTGCTCTCTG-TTAGTACTTTG-GTACTCTCTGTTT
1 GCTCTCTGTT---CAGCACTTATGTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTT
39989641 GTTCCGCATA
Statistics
Matches: 112, Mismatches: 8, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
68 2 0.02
69 54 0.48
70 11 0.10
71 36 0.32
72 9 0.08
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (68 bp):
GCTCTCTGTTCAGCACTTATGTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTG
TGT
Found at i:39991457 original size:21 final size:21
Alignment explanation
Indices: 39991431--39991484 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
39991421 TAAAACTTAT
*
39991431 TGTATCGGTAGAAGGGTAGGG
1 TGTATCGGTAGAAGGGTAGGA
*
39991452 TGTATCGGTAAAAGGGTAGGA
1 TGTATCGGTAGAAGGGTAGGA
39991473 TGTATCGGTAGA
1 TGTATCGGTAGA
39991485 GCCTAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.06, G:0.41, T:0.26
Consensus pattern (21 bp):
TGTATCGGTAGAAGGGTAGGA
Found at i:39996277 original size:29 final size:29
Alignment explanation
Indices: 39996217--39996280 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
39996207 TAGTTACTTG
* **
39996217 ATTAAATTAATTTCTTTATTATTAAATGA
1 ATTAAATTAATTTCTTCATTATTAAAAAA
*
39996246 ATTAATTTAATTT-TTGCATTATTAAAAAA
1 ATTAAATTAATTTCTT-CATTATTAAAAAA
39996275 ATTAAA
1 ATTAAA
39996281 ATCAAATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (29 bp):
ATTAAATTAATTTCTTCATTATTAAAAAA
Found at i:39997704 original size:17 final size:16
Alignment explanation
Indices: 39997654--39997707 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 16
39997644 TTTAAATAGA
*
39997654 TTAATTAATTTTTAATT
1 TTAATT-ATTTTTATTT
39997671 TTAATTATTCTTCTATTT
1 TTAATTATT-TT-TATTT
*
39997689 TTATGTTATTTTTATTT
1 TTA-ATTATTTTTATTT
39997706 TT
1 TT
39997708 TTCAATGATA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 3 0.09
17 15 0.47
18 9 0.28
19 5 0.16
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (16 bp):
TTAATTATTTTTATTT
Found at i:40008863 original size:2 final size:2
Alignment explanation
Indices: 40008858--40008891 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
40008848 TTTTTATCAA
40008858 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40008892 TTTAAAATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40013925 original size:23 final size:24
Alignment explanation
Indices: 40013896--40013961 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 24
40013886 TTTAATAATA
*
40013896 AATTTAATTTTAAATTTTAAATT-
1 AATTTAAATTTAAATTTTAAATTG
* * **
40013919 ATTTTAAGTTTAAA-TTTATTTTG
1 AATTTAAATTTAAATTTTAAATTG
40013942 AATTTAAATTTAAATTTTAA
1 AATTTAAATTTAAATTTTAA
40013962 TCAAAAATCC
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
22 6 0.18
23 24 0.71
24 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (24 bp):
AATTTAAATTTAAATTTTAAATTG
Found at i:40013936 original size:6 final size:6
Alignment explanation
Indices: 40013894--40013958 Score: 55
Period size: 6 Copynumber: 11.2 Consensus size: 6
40013884 CCTTTAATAA
* * * *
40013894 TAAATT TAATTT TAAATTT TAAA-T T-ATTT TAAGTT TAAATT T-ATTT
1 TAAATT TAAATT TAAA-TT TAAATT TAAATT TAAATT TAAATT TAAATT
*
40013940 TGAATT TAAATT TAAATT T
1 TAAATT TAAATT TAAATT T
40013959 TAATCAAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
4 1 0.02
5 8 0.17
6 32 0.68
7 6 0.13
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (6 bp):
TAAATT
Found at i:40013952 original size:17 final size:17
Alignment explanation
Indices: 40013894--40013953 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
40013884 CCTTTAATAA
*
40013894 TAAATTTAATTTTAAATTT
1 TAAATTT-ATTTT-AAGTT
40013913 TAAA-TTATTTTAAGTT
1 TAAATTTATTTTAAGTT
40013929 TAAATTTATTTTGAA-TT
1 TAAATTTATTTT-AAGTT
40013946 TAAATTTA
1 TAAATTTA
40013954 AATTTTAATC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
16 8 0.21
17 22 0.58
18 4 0.11
19 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TAAATTTATTTTAAGTT
Found at i:40014635 original size:20 final size:21
Alignment explanation
Indices: 40014593--40014647 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
40014583 CATTTTGTAT
* *
40014593 ATATATATATATATATGTATTA
1 ATATATTTAT-TATATATATTA
40014615 ATATATTTATTATATAT-TTA
1 ATATATTTATTATATATATTA
*
40014635 ATACATTTATTAT
1 ATATATTTATTAT
40014648 TTCTTATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 15 0.50
21 6 0.20
22 9 0.30
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
ATATATTTATTATATATATTA
Found at i:40015961 original size:57 final size:58
Alignment explanation
Indices: 40015871--40016046 Score: 266
Period size: 57 Copynumber: 3.1 Consensus size: 58
40015861 AAACTATTTT
40015871 AAAATTACATTTTTGACCTCAAACTTCTCAAAAATTACATTTTACCCCTAAACTTCCA
1 AAAATTACATTTTTGACCTCAAACTTCTCAAAAATTACATTTTACCCCTAAACTTCCA
* * * * *
40015929 AAAATCACA-TTTTAACCTCAAATTTCTAAAAAATTACATTTTACCCCTAAACTTCTA
1 AAAATTACATTTTTGACCTCAAACTTCTCAAAAATTACATTTTACCCCTAAACTTCCA
* *
40015986 AAAATTACATTTTTGACCTCAAACTTC-CAAAAATTATCATTTTACCCCAAAACATCCA
1 AAAATTACATTTTTGACCTCAAACTTCTCAAAAATTA-CATTTTACCCCTAAACTTCCA
40016044 AAA
1 AAA
40016047 TGAGTATTTT
Statistics
Matches: 104, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
57 60 0.58
58 44 0.42
ACGTcount: A:0.41, C:0.24, G:0.01, T:0.33
Consensus pattern (58 bp):
AAAATTACATTTTTGACCTCAAACTTCTCAAAAATTACATTTTACCCCTAAACTTCCA
Found at i:40016150 original size:87 final size:84
Alignment explanation
Indices: 40015871--40016171 Score: 265
Period size: 87 Copynumber: 3.5 Consensus size: 84
40015861 AAACTATTTT
* *
40015871 AAAATTACATTTTTGACCTC-AAACTTCTCAAAAATTACA-TTTT-ACCCCTAAACTTCCAAAAA
1 AAAATTACATTTTT-ACCCCGAAA--TCT-AAAAATTACATTTTTGACCTC-AAACTTCCAAAAA
* * * **
40015933 TCA-CATTTTAACCTCAAATTTC-TAA
61 TTACCATTTT-ACCCCAAA--ACATCC
*
40015958 AAAATTACA-TTTTACCCCTAAACTTCTAAAAATTACATTTTTGACCTCAAACTTCCAAAAATTA
1 AAAATTACATTTTTACCCCGAAA--TCTAAAAATTACATTTTTGACCTCAAACTTCCAAAAATTA
*
40016022 TCATTTTACCCCAAAACATCC
64 CCATTTTACCCCAAAACATCC
* * * *
40016043 AAAATGA-GTATTTTACCCCCGAATATCTAAAAATTACATTTTTTACCTCATACTTTCCAAAAAT
1 AAAATTACAT-TTTTA-CCCCGAA-ATCTAAAAATTACATTTTTGACCTCAAAC-TTCCAAAAAT
*
40016107 TACCATTTTACCCCGAAACATCC
62 TACCATTTTACCCCAAAACATCC
*
40016130 AAAATTACATTTTTGACCCCGAACATCAAAAAATTACCATTT
1 AAAATTACATTTTT-ACCCCGAA-ATCTAAAAATTA-CATTT
40016172 CAAAAATTAT
Statistics
Matches: 183, Mismatches: 18, Indels: 25
0.81 0.08 0.11
Matches are distributed among these distances:
84 1 0.01
85 21 0.11
86 69 0.38
87 84 0.46
88 8 0.04
ACGTcount: A:0.40, C:0.25, G:0.03, T:0.33
Consensus pattern (84 bp):
AAAATTACATTTTTACCCCGAAATCTAAAAATTACATTTTTGACCTCAAACTTCCAAAAATTACC
ATTTTACCCCAAAACATCC
Found at i:40016162 original size:29 final size:28
Alignment explanation
Indices: 40015871--40016171 Score: 222
Period size: 29 Copynumber: 10.4 Consensus size: 28
40015861 AAACTATTTT
*
40015871 AAAATTACATTTTTGACCTCAAACTTCTCA
1 AAAATTACATTTTT-ACCCCAAACTTC-CA
40015901 AAAATTACA-TTTTACCCCTAAACTTCCA
1 AAAATTACATTTTTACCCC-AAACTTCCA
* * * * *
40015929 AAAATCACATTTTAACCTCAAATTTCTAA
1 AAAATTACATTTTTACCCCAAACTTC-CA
*
40015958 AAAATTACA-TTTTACCCCTAAACTTCTA
1 AAAATTACATTTTTACCCC-AAACTTCCA
*
40015986 AAAATTACATTTTTGACCTCAAACTTCCA
1 AAAATTACATTTTT-ACCCCAAACTTCCA
*
40016015 AAAATTATCA-TTTTACCCCAAAACATCC-
1 AAAATTA-CATTTTTACCCC-AAACTTCCA
* * * *
40016043 AAAATGA-GTATTTTACCCCCGAA-TATCTA
1 AAAATTACAT-TTTTA-CCCCAAACT-TCCA
* *
40016072 AAAATTACATTTTTTACCTCATACTTTCCA
1 AAAATTACA-TTTTTACCCCAAAC-TTCCA
*
40016102 AAAATTACCA-TTTTACCCCGAAACATCC-
1 AAAATTA-CATTTTTACCCC-AAACTTCCA
* * *
40016130 AAAATTACATTTTTGACCCCGAACATCAA
1 AAAATTACATTTTT-ACCCCAAACTTCCA
40016159 AAAATTACCATTT
1 AAAATTA-CATTT
40016172 CAAAAATTAT
Statistics
Matches: 217, Mismatches: 31, Indels: 46
0.74 0.11 0.16
Matches are distributed among these distances:
27 2 0.01
28 73 0.34
29 100 0.46
30 38 0.18
31 4 0.02
ACGTcount: A:0.40, C:0.25, G:0.03, T:0.33
Consensus pattern (28 bp):
AAAATTACATTTTTACCCCAAACTTCCA
Found at i:40016237 original size:29 final size:29
Alignment explanation
Indices: 40016205--40016364 Score: 162
Period size: 29 Copynumber: 5.6 Consensus size: 29
40016195 AACTTTTCAC
*
40016205 AAATTACCATTTTACCCTCGAACATCTAA
1 AAATTACCATTTTACCCTCGAACATCCAA
*
40016234 AAATTACCATTTTACCCCCGAACATCCAA
1 AAATTACCATTTTACCCTCGAACATCCAA
****
40016263 AAATTACCATTTTACCCTCGTGTGTCCAA
1 AAATTACCATTTTACCCTCGAACATCCAA
*** * ***
40016292 AAATTATTGTTTTTCCCT-GAGTGTCC-A
1 AAATTACCATTTTACCCTCGAACATCCAA
* *
40016319 AAATTACTATTTTACCCTCAAACATCCAA
1 AAATTACCATTTTACCCTCGAACATCCAA
*
40016348 AAATTACCATATTACCC
1 AAATTACCATTTTACCC
40016365 CCCAGGCATC
Statistics
Matches: 108, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
27 16 0.15
28 11 0.10
29 81 0.75
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.33
Consensus pattern (29 bp):
AAATTACCATTTTACCCTCGAACATCCAA
Found at i:40016251 original size:102 final size:103
Alignment explanation
Indices: 40016071--40016274 Score: 281
Period size: 102 Copynumber: 2.0 Consensus size: 103
40016061 CCGAATATCT
* * * *
40016071 AAAAATTACATTTTTTACCTCATACTTTCCAAAAATTACCATTTTACCCCGAAACATCCAAAATT
1 AAAAATTACATTTTTGACCCCAAACTTTCCAAAAATTACCATTTTACCCCGAAACATCAAAAATT
40016136 ACATTTTTGA-CCCCGAACATCAAAAAATTACCATTTC
66 ACATTTTTGACCCCCGAACATCAAAAAATTACCATTTC
* * *
40016173 AAAAATTATATTTTTGACCCCAAACTTTTCACAAATTACCATTTTACCCTCG-AACATCTAAAAA
1 AAAAATTACATTTTTGACCCCAAACTTTCCAAAAATTACCATTTTACCC-CGAAACATC-AAAAA
*
40016237 TTACCA-TTTT-ACCCCCGAACATCCAAAAATTACCATTT
64 TTA-CATTTTTGACCCCCGAACATCAAAAAATTACCATTT
40016275 TACCCTCGTG
Statistics
Matches: 90, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
102 50 0.56
103 38 0.42
104 2 0.02
ACGTcount: A:0.39, C:0.26, G:0.03, T:0.32
Consensus pattern (103 bp):
AAAAATTACATTTTTGACCCCAAACTTTCCAAAAATTACCATTTTACCCCGAAACATCAAAAATT
ACATTTTTGACCCCCGAACATCAAAAAATTACCATTTC
Found at i:40016390 original size:85 final size:85
Alignment explanation
Indices: 40016233--40016390 Score: 194
Period size: 85 Copynumber: 1.9 Consensus size: 85
40016223 CGAACATCTA
* * * **
40016233 AAAATTACCATTTTACCCCCGAACATCCAAAAATTACCATTTTACCCTCGTGTGTCCAAAAATTA
1 AAAATTACCATTTTACCCCCAAACATCCAAAAATTACCATATTACCCCCGTGCATCCAAAAATTA
**
40016298 TTGTTTTTCCCTGAGTGTCC
66 TCATTTTTCCCTGAGTGTCC
* * *
40016318 AAAATTACTATTTTACCCTCAAACATCCAAAAATTACCATATTACCCCCCAG-GCATCTAAAAAT
1 AAAATTACCATTTTACCCCCAAACATCCAAAAATTACCATATTA-CCCCC-GTGCATCCAAAAAT
40016382 TA-CATTTTT
64 TATCATTTTT
40016391 GACTCCGTTC
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
85 45 0.74
86 15 0.25
87 1 0.02
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.33
Consensus pattern (85 bp):
AAAATTACCATTTTACCCCCAAACATCCAAAAATTACCATATTACCCCCGTGCATCCAAAAATTA
TCATTTTTCCCTGAGTGTCC
Found at i:40022746 original size:66 final size:66
Alignment explanation
Indices: 40022624--40022753 Score: 156
Period size: 66 Copynumber: 2.0 Consensus size: 66
40022614 AGGAGGAGAA
* * *
40022624 GGATCTGAGTAACCGTTATGCCCGCTAACGTAATATTCAAAAGACGGTGCCGTTGGCGCAAAAGA
1 GGATCTGAGTAACCGTTATGCCCGCTAACGGAATATTCAAAAGACGGAGCCATTGGCGCAAAAGA
40022689 C
66 C
** * * *
40022690 GGATCTGAGTAACCGTTATG-GTGACTAACGGAATATTGAGAAGA-GTGAGCCATTGGCGCGAAA
1 GGATCTGAGTAACCGTTATGCCCG-CTAACGGAATATTCAAAAGACG-GAGCCATTGGCGCAAAA
40022753 G
64 G
40022754 GAGGAGGATC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
65 2 0.04
66 52 0.96
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.22
Consensus pattern (66 bp):
GGATCTGAGTAACCGTTATGCCCGCTAACGGAATATTCAAAAGACGGAGCCATTGGCGCAAAAGA
C
Found at i:40027759 original size:77 final size:77
Alignment explanation
Indices: 40027672--40027825 Score: 229
Period size: 77 Copynumber: 2.0 Consensus size: 77
40027662 GAACGTGCTC
* *
40027672 ATATAAGGGCTT-CTCAAATATCGTATATCAGGTTTCAAATCATATTTTTGCTACTTTCTTTTCT
1 ATATAAGGGCTTCCT-AAATATCGTATATCAAGTTTCAAATCATATTTTTACTACTTTCTTTTCT
40027736 TTTCAAGCAATAT
65 TTTCAAGCAATAT
* * * * *
40027749 ATATAAGGGCTTCCTAAATGTTGTATATCAAGTTTCAAATTATGTTTTTATTACTTTCTTTTCTT
1 ATATAAGGGCTTCCTAAATATCGTATATCAAGTTTCAAATCATATTTTTACTACTTTCTTTTCTT
40027814 TTCAAGCAATAT
66 TTCAAGCAATAT
40027826 CTGATTCAAC
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
77 67 0.97
78 2 0.03
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (77 bp):
ATATAAGGGCTTCCTAAATATCGTATATCAAGTTTCAAATCATATTTTTACTACTTTCTTTTCTT
TTCAAGCAATAT
Found at i:40028331 original size:2 final size:2
Alignment explanation
Indices: 40028324--40028355 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
40028314 CAATCTTCAA
40028324 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
40028356 GTTCACCAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:40032517 original size:32 final size:31
Alignment explanation
Indices: 40032452--40032518 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 31
40032442 GCCACTAAAT
*
40032452 TATTCAAAAATTTTTATTTAAATCATTGAGC
1 TATTCAAAAATTTTTATTTAAATAATTGAGC
* * * *
40032483 TATTCGAAAGTTTTTATTTTAAGTAATTGGGC
1 TATTCAAAAATTTTTA-TTTAAATAATTGAGC
40032515 TATT
1 TATT
40032519 TTTTTGAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 14 0.47
32 16 0.53
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.48
Consensus pattern (31 bp):
TATTCAAAAATTTTTATTTAAATAATTGAGC
Found at i:40054849 original size:2 final size:2
Alignment explanation
Indices: 40054844--40054879 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
40054834 ATTTTCAATA
40054844 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40054880 TATTAAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40054907 original size:10 final size:11
Alignment explanation
Indices: 40054841--40054911 Score: 63
Period size: 12 Copynumber: 6.2 Consensus size: 11
40054831 AAAATTTTCA
40054841 ATAATATATAT
1 ATAATATATAT
40054852 ATATATATATAT
1 ATA-ATATATAT
40054864 ATATATATATAT
1 ATA-ATATATAT
* *
40054876 ATATTATTAAAT
1 ATAATA-TATAT
*
40054888 ATTAAAATA-AT
1 A-TAATATATAT
*
40054899 ATAATATAAAT
1 ATAATATATAT
40054910 AT
1 AT
40054912 TTTTAAAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
10 6 0.12
11 12 0.24
12 30 0.59
13 3 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
ATAATATATAT
Found at i:40057473 original size:17 final size:17
Alignment explanation
Indices: 40057425--40057472 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
40057415 GAGATTATTT
* *
40057425 TATTTAATTCATTTGATA
1 TATTTAAAT-ATTTTATA
40057443 TATTTAAATATTTTATA
1 TATTTAAATATTTTATA
40057460 TA-TTAAATATTTT
1 TATTTAAATATTTT
40057473 TTAAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.39
17 9 0.32
18 8 0.29
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (17 bp):
TATTTAAATATTTTATA
Found at i:40057492 original size:12 final size:13
Alignment explanation
Indices: 40057464--40057491 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
40057454 TTTATATATT
40057464 AAATATTTTTTAA
1 AAATATTTTTTAA
40057477 AAATATTTTTTAA
1 AAATATTTTTTAA
40057490 AA
1 AA
40057492 TGAAAAATTA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AAATATTTTTTAA
Found at i:40059452 original size:6 final size:6
Alignment explanation
Indices: 40059441--40059465 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40059431 TTTCAGCCGG
40059441 CTGAGC CTGAGC CTGAGC CTGAGC C
1 CTGAGC CTGAGC CTGAGC CTGAGC C
40059466 GCAGCACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.36, G:0.32, T:0.16
Consensus pattern (6 bp):
CTGAGC
Found at i:40059903 original size:6 final size:6
Alignment explanation
Indices: 40059892--40059938 Score: 69
Period size: 6 Copynumber: 7.8 Consensus size: 6
40059882 GGCCATTAAA
*
40059892 TATGTT TATGTT TATGTT TATGTT TATGTT CT-TATT TATGTT TATGT
1 TATGTT TATGTT TATGTT TATGTT TATGTT -TATGTT TATGTT TATGT
40059939 ATGCAAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
5 1 0.03
6 35 0.95
7 1 0.03
ACGTcount: A:0.17, C:0.02, G:0.15, T:0.66
Consensus pattern (6 bp):
TATGTT
Found at i:40060067 original size:26 final size:26
Alignment explanation
Indices: 40060011--40060087 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
40060001 AGCTAAACCT
*
40060011 AATTAAATAAATTCAAACATAAAAAT
1 AATTAAATAAATTCAAACATAAAAAG
* ** *
40060037 TATTAAATAAATTCAAATTTAAATAG
1 AATTAAATAAATTCAAACATAAAAAG
* *
40060063 AATTAATTCCAAATTCAATCATAAA
1 AATTAAAT--AAATTCAAACATAAA
40060088 CTTAATTAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
26 27 0.69
28 12 0.31
ACGTcount: A:0.57, C:0.09, G:0.01, T:0.32
Consensus pattern (26 bp):
AATTAAATAAATTCAAACATAAAAAG
Found at i:40063020 original size:27 final size:27
Alignment explanation
Indices: 40062982--40063045 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
40062972 GCATTAACAA
40062982 AGGCACCACTAGTGCCGCCTACCCAGT
1 AGGCACCACTAGTGCCGCCTACCCAGT
*
40063009 AGGCACCACTAGTGCCGCCTACCTAGT
1 AGGCACCACTAGTGCCGCCTACCCAGT
40063036 AGGCACCACT
1 AGGCACCACT
40063046 TGTCAAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.23, C:0.39, G:0.22, T:0.16
Consensus pattern (27 bp):
AGGCACCACTAGTGCCGCCTACCCAGT
Found at i:40063248 original size:57 final size:59
Alignment explanation
Indices: 40063126--40063258 Score: 143
Period size: 58 Copynumber: 2.3 Consensus size: 59
40063116 TTTATATTTA
* *
40063126 AATTTTTCTTATATTATTATTGTAAAAATCTGGAGATTATTATTATTTTGATAAATAAAT
1 AATTTTT-TTATATTATTATTGTAAAAATATGGAGATTATTATTATTTTAATAAATAAAT
* * ** *
40063186 -ATTTTTTTATATTATTTATT-TAAAAATATTGAG-TTATTCTTA-TTTAATATTTAATT
1 AATTTTTTTATATTA-TTATTGTAAAAATATGGAGATTATTATTATTTTAATAAATAAAT
40063242 AATTTTTTTA-ATT-TTAT
1 AATTTTTTTATATTATTAT
40063259 AATATTTTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
54 4 0.06
56 13 0.20
57 17 0.27
58 19 0.30
59 11 0.17
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.57
Consensus pattern (59 bp):
AATTTTTTTATATTATTATTGTAAAAATATGGAGATTATTATTATTTTAATAAATAAAT
Found at i:40063250 original size:58 final size:57
Alignment explanation
Indices: 40063108--40063230 Score: 146
Period size: 58 Copynumber: 2.2 Consensus size: 57
40063098 TATAAAAGTG
** * *
40063108 TATTATT-TTTT-ATATTTAAATTTTTCTTATATTATTATTGTAAAAATCTGGAGAT
1 TATTATTATTTTGATAAATAAATTTTTTTTATATTATTATTGTAAAAATATGGAGAT
*
40063163 TATTATTATTTTGATAAATAAATATTTTTTTATATTATTTATT-TAAAAATATTGAG-T
1 TATTATTATTTTGATAAATAAAT-TTTTTTTATATTA-TTATTGTAAAAATATGGAGAT
*
40063220 TATTCTTATTT
1 TATTATTATTT
40063231 AATATTTAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
55 7 0.12
56 4 0.07
57 19 0.33
58 23 0.40
59 5 0.09
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (57 bp):
TATTATTATTTTGATAAATAAATTTTTTTTATATTATTATTGTAAAAATATGGAGAT
Found at i:40063441 original size:27 final size:27
Alignment explanation
Indices: 40063411--40063472 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
40063401 CTTGATAGAA
40063411 AGGCACCATTGGTGCCGCCTGACAGGT
1 AGGCACCATTGGTGCCGCCTGACAGGT
*
40063438 AGGCACCATTGGTGCCGCCTGTCAGGT
1 AGGCACCATTGGTGCCGCCTGACAGGT
40063465 AGGCACCA
1 AGGCACCA
40063473 CCCATTTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.19, C:0.31, G:0.32, T:0.18
Consensus pattern (27 bp):
AGGCACCATTGGTGCCGCCTGACAGGT
Found at i:40068701 original size:18 final size:18
Alignment explanation
Indices: 40068675--40068713 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
40068665 AAATACTTCA
40068675 AAAAAATATA-ATTTTAAT
1 AAAAAATATATA-TTTAAT
*
40068693 AAAAGATATATATTTAAT
1 AAAAAATATATATTTAAT
40068711 AAA
1 AAA
40068714 TATTAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
AAAAAATATATATTTAAT
Found at i:40070428 original size:5 final size:6
Alignment explanation
Indices: 40070412--40070437 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
40070402 GACCAAAGTG
40070412 TAAAAA TAAAAA TAAAAA TAAAAA TA
1 TAAAAA TAAAAA TAAAAA TAAAAA TA
40070438 GCTCTCAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:40073988 original size:15 final size:14
Alignment explanation
Indices: 40073964--40073994 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
40073954 TCGGTTAAAA
40073964 TATCTTAATCGAAT
1 TATCTTAATCGAAT
40073978 TATCATTAATCGAAT
1 TATC-TTAATCGAAT
40073993 TA
1 TA
40073995 CTCAAAATGT
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:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (14 bp):
TATCTTAATCGAAT
Found at i:40075305 original size:33 final size:32
Alignment explanation
Indices: 40075243--40075314 Score: 85
Period size: 34 Copynumber: 2.2 Consensus size: 32
40075233 AAAACTTGTA
40075243 AAAAAAATTACCAAAATTATTTATTAATAACATT
1 AAAAAAATTACCAAAATTATTTATTAAT-A-ATT
**
40075277 AAAAAAATTATTAAAA-TA-TTATTAAATAATT
1 AAAAAAATTACCAAAATTATTTATT-AATAATT
40075308 AAAAAAA
1 AAAAAAA
40075315 ATCATAAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 10 0.29
32 6 0.17
33 5 0.14
34 14 0.40
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (32 bp):
AAAAAAATTACCAAAATTATTTATTAATAATT
Found at i:40076584 original size:23 final size:22
Alignment explanation
Indices: 40076558--40076610 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
40076548 TTTTATGAGG
40076558 ATTAAAATGTAATTTTATTATAT
1 ATTAAAATGTAATTTT-TTATAT
** * *
40076581 ATTAATTTATAATTTTTTATTT
1 ATTAAAATGTAATTTTTTATAT
40076603 A-TAAAATG
1 ATTAAAATG
40076611 ATTGAATTAA
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
21 4 0.17
22 6 0.26
23 13 0.57
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (22 bp):
ATTAAAATGTAATTTTTTATAT
Found at i:40079528 original size:27 final size:27
Alignment explanation
Indices: 40079498--40079593 Score: 90
Period size: 27 Copynumber: 3.6 Consensus size: 27
40079488 TTTTCGTTTA
*
40079498 ATTTAGAGTTAAATTGATTTTAAATTT
1 ATTTAAAGTTAAATTGATTTTAAATTT
* *
40079525 ATTTAAATTTAAATTTATTTTAAATTT
1 ATTTAAAGTTAAATTGATTTTAAATTT
*
40079552 AAATTTAAA-TTTAATT-A-TTTAAATTT
1 --ATTTAAAGTTAAATTGATTTTAAATTT
* *
40079578 AATTTGAATTTAAATT
1 -ATTTAAAGTTAAATT
40079594 TAAATAAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
25 7 0.12
26 15 0.25
27 25 0.42
28 6 0.10
29 7 0.12
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (27 bp):
ATTTAAAGTTAAATTGATTTTAAATTT
Found at i:40079534 original size:6 final size:6
Alignment explanation
Indices: 40079516--40079630 Score: 116
Period size: 6 Copynumber: 19.5 Consensus size: 6
40079506 TTAAATTGAT
*
40079516 TTTAAA TTT--A TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
40079561 TTTAATTA TTTAAA TTT-AA TTTGAA TTTAAA TTTAAA -TAAAA TTAAAA
1 TTTAA--A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
40079609 TATTAAA TTTAACA -TTAAA TTT
1 T-TTAAA TTTAA-A TTTAAA TTT
40079631 TCAATGTCCA
Statistics
Matches: 94, Mismatches: 5, Indels: 20
0.79 0.04 0.17
Matches are distributed among these distances:
4 4 0.04
5 14 0.15
6 64 0.68
7 6 0.06
8 6 0.06
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:40079540 original size:23 final size:21
Alignment explanation
Indices: 40079520--40079598 Score: 90
Period size: 23 Copynumber: 3.6 Consensus size: 21
40079510 ATTGATTTTA
40079520 AATTTATTTAAATTTAAATTT
1 AATTTATTTAAATTTAAATTT
*
40079541 ATTTTAAATTTAAATTTAAATTT
1 AATTT--ATTTAAATTTAAATTT
40079564 AA-TTATTTAAATTT-AATTT
1 AATTTATTTAAATTTAAATTT
40079583 GAATTTAAATTTAAAT
1 -AATTT--ATTTAAAT
40079599 AAAATTAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.10
20 12 0.24
21 6 0.12
22 2 0.04
23 25 0.50
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (21 bp):
AATTTATTTAAATTTAAATTT
Found at i:40079590 original size:11 final size:11
Alignment explanation
Indices: 40079506--40079630 Score: 80
Period size: 11 Copynumber: 11.2 Consensus size: 11
40079496 TAATTTAGAG
* *
40079506 TTAAATTGATT
1 TTAAATTTAAT
40079517 TTAAATTT-AT
1 TTAAATTTAAT
40079527 TTAAATTTAAAT
1 TTAAATTT-AAT
*
40079539 TT-ATTTTAAAT
1 TTAAATTT-AAT
40079550 TTAAATTTAAAT
1 TTAAATTT-AAT
40079562 TT-AA-TT-AT
1 TTAAATTTAAT
40079570 TTAAATTTAAT
1 TTAAATTTAAT
*
40079581 TTGAATTTAAAT
1 TTAAATTT-AAT
**
40079593 TTAAATAAAAT
1 TTAAATTTAAT
*
40079604 TAAAATATTAAAT
1 TTAAAT-TT-AAT
*
40079617 TTAACATTAAAT
1 TTAA-ATTTAAT
40079629 TT
1 TT
40079631 TCAATGTCCA
Statistics
Matches: 91, Mismatches: 13, Indels: 19
0.74 0.11 0.15
Matches are distributed among these distances:
8 4 0.04
9 2 0.02
10 13 0.14
11 36 0.40
12 27 0.30
13 7 0.08
14 2 0.02
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:40079596 original size:17 final size:17
Alignment explanation
Indices: 40079516--40079630 Score: 117
Period size: 17 Copynumber: 6.5 Consensus size: 17
40079506 TTAAATTGAT
40079516 TTTAAATTT-ATTTAAA
1 TTTAAATTTAATTTAAA
*
40079532 TTTAAATTTATTTTAAA
1 TTTAAATTTAATTTAAA
40079549 TTTAAATTTAAATTTAATTA
1 TTTAAATTT-AATTTAA--A
*
40079569 TTTAAATTTAATTTGAA
1 TTTAAATTTAATTTAAA
* *
40079586 TTTAAATTTAAATAAAA
1 TTTAAATTTAATTTAAA
*
40079603 TTAAAATATTAAATTTAACA
1 TTTAAAT-TT-AATTTAA-A
40079623 -TTAAATTT
1 TTTAAATTT
40079631 TCAATGTCCA
Statistics
Matches: 82, Mismatches: 10, Indels: 12
0.79 0.10 0.12
Matches are distributed among these distances:
16 9 0.11
17 36 0.44
18 10 0.12
19 16 0.20
20 11 0.13
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (17 bp):
TTTAAATTTAATTTAAA
Found at i:40079605 original size:37 final size:37
Alignment explanation
Indices: 40079531--40079605 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
40079521 ATTTATTTAA
* **
40079531 ATTTAAATTTATTTTAAATTTAAATTTAAATTTAATT
1 ATTTAAATTTAATTTAAATTTAAATTTAAATAAAATT
*
40079568 ATTTAAATTTAATTTGAATTTAAATTTAAATAAAATT
1 ATTTAAATTTAATTTAAATTTAAATTTAAATAAAATT
40079605 A
1 A
40079606 AAATATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (37 bp):
ATTTAAATTTAATTTAAATTTAAATTTAAATAAAATT
Done.