Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 2 of 126
Found at i:467645 original size:16 final size:17
Alignment explanation
Indices: 467624--467656 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
467614 AAATTTTGTT
*
467624 AATATTT-TTTATTAAA
1 AATATTTATTTAATAAA
467640 AATATTTATTTAATAAA
1 AATATTTATTTAATAAA
467657 TACATCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AATATTTATTTAATAAA
Found at i:467743 original size:5 final size:6
Alignment explanation
Indices: 467715--467748 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
467705 ATAATAAATT
*
467715 TTTTTA TATATTA TTTTTA TTTTTA TTTTTA TTT
1 TTTTTA T-TTTTA TTTTTA TTTTTA TTTTTA TTT
467749 ACATATTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:471834 original size:2 final size:2
Alignment explanation
Indices: 471829--471854 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
471819 GGGGGGGGGG
471829 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
471855 AGGACCTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:472683 original size:20 final size:19
Alignment explanation
Indices: 472658--472702 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
472648 CTAAATAAAA
472658 TTATATAT-TTTTATTAATTT
1 TTATATATATTTTA--AATTT
472678 TTATATATAATTTTAAATTT
1 TTATATAT-ATTTTAAATTT
472698 TTATA
1 TTATA
472703 AAATAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 18 0.78
22 5 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATATATATTTTAAATTT
Found at i:472691 original size:22 final size:20
Alignment explanation
Indices: 472659--472702 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
472649 TAAATAAAAT
*
472659 TATATATTTTTATTAATTTTTA
1 TATATAATTTTA--AATTTTTA
472681 TATATAATTTTAAATTTTTA
1 TATATAATTTTAAATTTTTA
472701 TA
1 TA
472703 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
22 11 0.52
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TATATAATTTTAAATTTTTA
Found at i:476870 original size:148 final size:148
Alignment explanation
Indices: 476601--476880 Score: 434
Period size: 148 Copynumber: 1.9 Consensus size: 148
476591 CTAAGACAAG
* * *
476601 CTCCCACATAAGCCAACTAAAACTACACTATGAAGCATGCACAATTCGCTAAAGAGTGTCACTCT
1 CTCCCACATAAGCCAACTAAAACTACACTATGAAGCACGCACAATTCGATAAAGAATGTCACTCT
* *
476666 TGAAAACAATAACGCATGAACCAAACGAAAGCTATTCCTAACAATCATAAAGCATATCCAATGCA
66 TGAAAACAATAACGCATGAACCAAACGAAAGCTATTCCTAACAATCATAAAACATATCAAATGCA
476731 CTCAGCTGCTTACATTTC
131 CTCAGCTGCTTACATTTC
** * *
476749 CTCCCACATAAGCCAACTAAAACTACACTATGAAGCACGTGCAATTCGATAATGAATGTCGCTCT
1 CTCCCACATAAGCCAACTAAAACTACACTATGAAGCACGCACAATTCGATAAAGAATGTCACTCT
* * * **
476814 TGAAAACAATAATGCGTGAACTAAACGAAAGCTATTCCTAACAATTGTAAAACATATCAAATGCA
66 TGAAAACAATAACGCATGAACCAAACGAAAGCTATTCCTAACAATCATAAAACATATCAAATGCA
476879 CT
131 CT
476881 TAGCCACTCA
Statistics
Matches: 118, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
148 118 1.00
ACGTcount: A:0.40, C:0.25, G:0.12, T:0.23
Consensus pattern (148 bp):
CTCCCACATAAGCCAACTAAAACTACACTATGAAGCACGCACAATTCGATAAAGAATGTCACTCT
TGAAAACAATAACGCATGAACCAAACGAAAGCTATTCCTAACAATCATAAAACATATCAAATGCA
CTCAGCTGCTTACATTTC
Found at i:480876 original size:22 final size:21
Alignment explanation
Indices: 480836--480876 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
480826 ATAAAATACA
* *
480836 TATATTTGATTTTGTTAAACC
1 TATATATGATTTTGCTAAACC
480857 TATATATGATTTTTGCTAAA
1 TATATATGA-TTTTGCTAAA
480877 ATTTTAAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (21 bp):
TATATATGATTTTGCTAAACC
Found at i:483553 original size:114 final size:114
Alignment explanation
Indices: 483318--483594 Score: 279
Period size: 114 Copynumber: 2.4 Consensus size: 114
483308 GATTTTGCAT
* * * * ** ** *
483318 ATCCTGAGGCAGTGCTCACCAATCCAGCATGCTGGACCTCAGTAGCCTTATTCCGAGCCAACCCT
1 ATCCTGAGGAAGAGCTCACCACTCCAGCACGCTGGACCTCAGTAGCCACACCCCAAGCCAACCCT
** * ** *
483383 GGAGCCTTTTGGGCAGCCGAGATGACTTCAGATGAGACTGGCTTGATGA
66 GGAGCCACTTGGCCAGCCGAGATGACTTCAGATGAGACTGGCTCAAGGA
* * *
483432 ATCCTGAGGAAGTATC-CACCACTCCAGCACGCTGGACCTCAGTAGCCACACCCCAAGCCATCCT
1 ATCCTGAGGAAG-AGCTCACCACTCCAGCACGCTGGACCTCAGTAGCCACACCCCAAGCCAACCC
* * *
483496 TGGAGCCACTTGGCCAGTCGAGATGGCTTCGGATGAGACCT-GCTCAAGGA
65 TGGAGCCACTTGGCCAGCCGAGATGACTTCAGATGAGA-CTGGCTCAAGGA
* * * * * *
483546 GTTCTGAGGCAGCGCTCACCACTCCAGCACGCTGGAGCTCAGAAGCCAC
1 ATCCTGAGGAAGAGCTCACCACTCCAGCACGCTGGACCTCAGTAGCCAC
483595 CCCTGCAGCC
Statistics
Matches: 132, Mismatches: 28, Indels: 6
0.80 0.17 0.04
Matches are distributed among these distances:
113 1 0.01
114 128 0.97
115 3 0.02
ACGTcount: A:0.23, C:0.32, G:0.26, T:0.19
Consensus pattern (114 bp):
ATCCTGAGGAAGAGCTCACCACTCCAGCACGCTGGACCTCAGTAGCCACACCCCAAGCCAACCCT
GGAGCCACTTGGCCAGCCGAGATGACTTCAGATGAGACTGGCTCAAGGA
Found at i:484115 original size:329 final size:328
Alignment explanation
Indices: 483591--484790 Score: 1411
Period size: 329 Copynumber: 3.7 Consensus size: 328
483581 AGCTCAGAAG
* * * *
483591 CCACCCCTGCAGCCTTTTGGGCAGCTGAGATGGCTTCGGATGAGACCTGGTTGATGACTACG-GG
1 CCACTCCTGCAGCCATTTGGGCAGCCGAGATGGCTTCGGATGAGACCTGGTTGATGACT-GGAGG
* * * * * *
483655 GACAAGATGATCAATCTTGGTCACAGATTCACCAGCCTGCAATAGAAACAAAGAATAATTCTTGA
65 GACAAGACGATCAATCTTAGTCACAGATTCACCAACCTGGAATAAAAACAAAGAAGAATTCTTGA
* * * *
483720 ATCCCCTTTCATTTGCTAGACATAACCAATCATAGGATACTCTCTGTCAATCAAACATTTGAGCT
130 ATCTCCTTTCATTTGCTTGACATCACCAATCTTAGGATACTCTCTGTCAATCAAACATTTGAGCT
* * * * * * *
483785 AAAAAATTCAGTAATTTCTGTCAACCTCCGAAGCCTTTTGGACAGCTAACA-GAGCTTCAGGTGA
195 AAAAAATTCTGTAATTTCTGTTAACCTCTGGAGCCTTTTGGGCAGCCAAGATG-GCTTCAGGTGA
* * * *
483849 GACCTGCTCGATGAATCCCGAGGCAGCGCTCATCACTCCAGCACGCTGGACCTCAATAGCCACAC
259 GACCTGTTCGATGAATCCTGAGGCAGTGCTCATCACTCCAGCACGCTGGACCTCAGTAGCCACAC
483914 CTCCAT
324 C-CCAT
* * * * * *
483920 CCACTCCTGGAGCCTTTTGGTCAGCCGAGATGGCTTCAGATGAAACCTGGTTGATGACTGGAGAG
1 CCACTCCTGCAGCCATTTGGGCAGCCGAGATGGCTTCGGATGAGACCTGGTTGATGACTGGAGGG
* *
483985 ACAAGATGATCAATCTTAGTCACAGATTCACCAACCTGAAATAAAAACAAAGAAGAATTCTTGAA
66 ACAAGACGATCAATCTTAGTCACAGATTCACCAACCTGGAATAAAAACAAAGAAGAATTCTTGAA
*
484050 TCTCCTTTCATTTGCTTGACATCACCAATCTCAGGATACTCTCTGTCAATCAAACATTTGAGCTA
131 TCTCCTTTCATTTGCTTGACATCACCAATCTTAGGATACTCTCTGTCAATCAAACATTTGAGCTA
** * *
484115 AAATGTTCTGTAATTTCTGTTAACATATGGAGCCTTTTGGGCAGCCAAGATGGCTTC-GGATGAG
196 AAAAATTCTGTAATTTCTGTTAACCTCTGGAGCCTTTTGGGCAGCCAAGATGGCTTCAGG-TGAG
* * * *
484179 ACCTGTTTC-AAGAATCCTGAGGCATTGCTCACCGCTCCAGCACGCTGGACCTCAGTAGCCACAC
260 ACCTG-TTCGATGAATCCTGAGGCAGTGCTCATCACTCCAGCACGCTGGACCTCAGTAGCCACAC
484243 CCC-T
324 CCCAT
* * * * * * * *
484247 GGCCACTCCTACGGCCATTTGCGTAGCCAAGATGGCTTTGGATG-GGCCCGGCTTGATGACTGGA
1 --CCACTCCTGCAGCCATTTGGGCAGCCGAGATGGCTTCGGATGAGACCTGG-TTGATGACTGGA
* * * *
484311 GGGACAAGACGATCAATCTTAGTAACAGATTCACCAACCTGGAAT-AAAACAAATAAGAATCCAT
63 GGGACAAGACGATCAATCTTAGTCACAGATTCACCAACCTGGAATAAAAACAAAGAAGAATTCTT
* ** * * * * * *
484375 GAATTTCCTTTCATTTGCCGGACATTATCAAGCTTAGG--A-TCACTGTCAATCAAAAATTTGGG
128 GAATCTCCTTTCATTTGCTTGACATCACCAATCTTAGGATACTCTCTGTCAATCAAACATTTGAG
** * * * * * *
484437 CTAAAAGGTTTTGTAATTTATGTTAACCTCTGGAGTCTCTTGGGCAGCCGAGATGGCTTCAGATG
193 CTAAAAAATTCTGTAATTTCTGTTAACCTCTGGAGCCTTTTGGGCAGCCAAGATGGCTTCAGGTG
* * *
484502 AGACCTGTTTGATGAATCCTGACGCAGTGGTC-TCCACTCCAGCACGCTGGACCTCAGTAGCCAC
258 AGACCTGTTCGATGAATCCTGAGGCAGTGCTCAT-CACTCCAGCACGCTGGACCTCAGTAGCCAC
*
484566 ACCCCCAA
322 A-CCCCAT
* * *
484574 CCACTCCTGCAGTCATTTGGGCAGCTGAGATGGCTTCGGATGAGACCTGCTTGATGACTGGAGGG
1 CCACTCCTGCAGCCATTTGGGCAGCCGAGATGGCTTCGGATGAGACCTGGTTGATGACTGGAGGG
* ** * *
484639 ACAGGACCCTCAATTTTAGTCACAGATTCACCAACCTGGAATAAAACCAAAGAAGAATTCTTGAA
66 ACAAGACGATCAATCTTAGTCACAGATTCACCAACCTGGAATAAAAACAAAGAAGAATTCTTGAA
** * *
484704 TCTCCTTTCATTTGCTAT-ACATCGTCAATCTTAGGGTAC-CTTCTGTCAATCAAACATTTGAAC
131 TCTCCTTTCATTTGCT-TGACATCACCAATCTTAGGATACTC-TCTGTCAATCAAACATTTGAGC
484767 T-AAAAATTCTGTAATTTCTGTTAA
194 TAAAAAATTCTGTAATTTCTGTTAA
484791 AACCTTAGTT
Statistics
Matches: 734, Mismatches: 118, Indels: 39
0.82 0.13 0.04
Matches are distributed among these distances:
324 2 0.00
325 214 0.29
326 56 0.08
327 1 0.00
328 77 0.10
329 381 0.52
330 3 0.00
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.26
Consensus pattern (328 bp):
CCACTCCTGCAGCCATTTGGGCAGCCGAGATGGCTTCGGATGAGACCTGGTTGATGACTGGAGGG
ACAAGACGATCAATCTTAGTCACAGATTCACCAACCTGGAATAAAAACAAAGAAGAATTCTTGAA
TCTCCTTTCATTTGCTTGACATCACCAATCTTAGGATACTCTCTGTCAATCAAACATTTGAGCTA
AAAAATTCTGTAATTTCTGTTAACCTCTGGAGCCTTTTGGGCAGCCAAGATGGCTTCAGGTGAGA
CCTGTTCGATGAATCCTGAGGCAGTGCTCATCACTCCAGCACGCTGGACCTCAGTAGCCACACCC
CAT
Found at i:486825 original size:5 final size:5
Alignment explanation
Indices: 486815--486851 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
486805 AAATTAATAA
* *
486815 AATTT AATTT AATTT AATTA AATTT AATTC AATTT AA
1 AATTT AATTT AATTT AATTT AATTT AATTT AATTT AA
486852 ATTTTTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (5 bp):
AATTT
Found at i:486828 original size:10 final size:10
Alignment explanation
Indices: 486803--486851 Score: 62
Period size: 10 Copynumber: 4.9 Consensus size: 10
486793 AAAATAATAA
*
486803 TAAAATTAAT
1 TAAATTTAAT
*
486813 AAAATTTAAT
1 TAAATTTAAT
*
486823 TTAATTTAAT
1 TAAATTTAAT
486833 TAAATTTAAT
1 TAAATTTAAT
*
486843 TCAATTTAA
1 TAAATTTAA
486852 ATTTTTTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (10 bp):
TAAATTTAAT
Found at i:486831 original size:20 final size:20
Alignment explanation
Indices: 486808--486851 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
486798 AATAATAAAA
*
486808 TTAATAAAATTTAATTTAAT
1 TTAATAAAATTTAATTCAAT
*
486828 TTAATTAAATTTAATTCAAT
1 TTAATAAAATTTAATTCAAT
486848 TTAA
1 TTAA
486852 ATTTTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAATAAAATTTAATTCAAT
Found at i:487194 original size:114 final size:114
Alignment explanation
Indices: 486988--487200 Score: 293
Period size: 114 Copynumber: 1.9 Consensus size: 114
486978 AAAAAAAAAA
*** * *
486988 CTCACCACTCCAGCTTGCTGAACCTCAGTAGCCACATTTCCGGCCACTCCCGCAGCCTTTTGGGT
1 CTCACCACTCCAGCTTGCTGAACCTCAGTAGCCACACCCCCAGCCACTCCCGCAGCCTTTTGGGC
*
487053 AGCCGAGATGGCTTCCGATGAGGCCTGCTCGATGAATCCTGAGGCAGTG
66 AGCCGAGATGGCTTCCGATGAGACCTGCTCGATGAATCCTGAGGCAGTG
* * * *
487102 CTCATCACTCCAGCATT-CTGGACCTCAGTAGCCACACCCCCAGCCACTCCTGGAGCCTTTTGGG
1 CTCACCACTCCAGC-TTGCTGAACCTCAGTAGCCACACCCCCAGCCACTCCCGCAGCCTTTTGGG
* * *
487166 CAGCCGAGATGGCTTCGGATGATACCTGCTTGATG
65 CAGCCGAGATGGCTTCCGATGAGACCTGCTCGATG
487201 GCTGGAGGGA
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
114 83 0.98
115 2 0.02
ACGTcount: A:0.19, C:0.34, G:0.24, T:0.23
Consensus pattern (114 bp):
CTCACCACTCCAGCTTGCTGAACCTCAGTAGCCACACCCCCAGCCACTCCCGCAGCCTTTTGGGC
AGCCGAGATGGCTTCCGATGAGACCTGCTCGATGAATCCTGAGGCAGTG
Found at i:489013 original size:12 final size:13
Alignment explanation
Indices: 488994--489030 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
488984 TTGGTATATA
488994 TATATTTAATTAT
1 TATATTTAATTAT
489007 T-TATTTAATT-T
1 TATATTTAATTAT
489018 TATATTTATATTA
1 TATATTTA-ATTA
489031 AAAATAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.10
12 15 0.71
13 4 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TATATTTAATTAT
Found at i:489040 original size:18 final size:18
Alignment explanation
Indices: 489019--489069 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 18
489009 ATTTAATTTT
489019 ATATTTATATTAAAAATA
1 ATATTTATATTAAAAATA
489037 ATATTTTATATTTAAAAAATA
1 ATA-TTTATA-TT-AAAAATA
489058 ATATTT-TATTAA
1 ATATTTATATTAA
489070 TTTTGAATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.07
18 5 0.17
19 8 0.27
20 5 0.17
21 10 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATTTATATTAAAAATA
Found at i:489046 original size:19 final size:21
Alignment explanation
Indices: 489022--489066 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
489012 TAATTTTATA
489022 TTTATA-TT-AAAAATAATAT
1 TTTATATTTAAAAAATAATAT
489041 TTTATATTTAAAAAATAATAT
1 TTTATATTTAAAAAATAATAT
489062 TTTAT
1 TTTAT
489067 TAATTTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.25
20 2 0.08
21 16 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTATATTTAAAAAATAATAT
Found at i:490931 original size:329 final size:326
Alignment explanation
Indices: 490069--492104 Score: 1680
Period size: 329 Copynumber: 6.4 Consensus size: 326
490059 TTCCCTAACG
* * * *
490069 TGCTAGACATCATCAGTCTTAGAATACTCTCTGTCAATCAAAT-ATTGGAGCT-AAAAGGTCTGA
1 TGCTAGACATCATCAATCTTAGGATACTCTCTGTCAATCAAATAATT-GAGCTAAAAAGTTCTGT
** * * * * * * * *
490132 AAAATCTGTTAACCCCTGAAGCCTTTTGGGCAGTCGAAATGGCTTCGGATGAGAGCTGCCCGATT
65 AATTTCTGCTAACCCCTGGAGCCTTTTGGGCAGCCGAGATAGCTTCGGATGAGACCTGCTCGATG
* * * * *
490197 AACCCTGTGGCAGTGCTCACCACTCCAGCATG-CTGGAC-C-----TCAG-----TAGCCACTCC
130 AATCCTGAGGCAGTGCTCA-CACGCCAGCA-GACTGGACTCAGAAGCCAGACCCCCAGCCACTCC
* ** * * * * * * *
490250 TGCAGCCTTGTCAGCAGCCGAGATGGTTTCAGAAGAGACCTGTTTGATGATTGAAGGGACAAGAC
193 TGCAGCCTTTTGGGCAGCCGAGATGGCTTCGGATGAAACCTG-CTGATGACTGGAGGGACAAGAC
* * * *
490315 CATCAAGCTTAGTCAGAGATTCACCAACCTGCAATAAAAACAAAGATGAATTCTTGAATCTCCTT
257 TATCAATCTTAGTCACAGATTCACCAACCTGCAATAAAAACAAAGAAGAATTCTTGAATCTCCTT
490380 TCATT
322 TCATT
** * * * *
490385 TGCTAGACATCATCAAT-TTCAGTTTA--CACTGTCAATCAAATATTTGGGCTGAAAAGTTCTGT
1 TGCTAGACATCATCAATCTT-AGGATACTCTCTGTCAATCAAATAATTGAGCTAAAAAGTTCTGT
* * * * * * *
490447 AATTTATGCTAACCCCTGAATCCGTTTGGGCTGCCGAGATGGCTTCGGATGAGACCTGCTGGATG
65 AATTTCTGCTAACCCCTGGAGCCTTTTGGGCAGCCGAGATAGCTTCGGATGAGACCTGCTCGATG
* * * * * * *
490512 AATCCTGAGGCATTGCTTAGGACTCCAGCAGAATGGACCTCAGTAGCCACACCCCC-GACCACTC
130 AATCCTGAGGCAGTGCTCA-CACGCCAGCAGACTGGA-CTCAGAAGCCAGACCCCCAG-CCACTC
* * * * * *
490576 CTGCAGCCTTGTCGACAGCCGAGATGGCATCGGATGAAACCTGCTTGATGATTGAAGGGACAAGA
192 CTGCAGCCTTTTGGGCAGCCGAGATGGCTTCGGATGAAACCTGC-TGATGACTGGAGGGACAAGA
* * *
490641 CTATCAAGCTTAGTCACAGATTCACCAACCTGCAATAAAAACGAAGAAGAGTTCTTGAATCTCCT
256 CTATCAATCTTAGTCACAGATTCACCAACCTGCAATAAAAACAAAGAAGAATTCTTGAATCTCC-
490706 TTTC-TT
320 TTTCATT
* * * * * *
490712 TGCTAGACATCATCAATCATAGGGTACCCTTTGTCAATCAAACAATTGAGCTAAAAAGTTCAGTA
1 TGCTAGACATCATCAATCTTAGGATACTCTCTGTCAATCAAATAATTGAGCTAAAAAGTTCTGTA
* * * ** * * *
490777 AATTCGGCTAACCCCTGGAGCCTTTTGAGCAGTTGAGATGGCTTCGGATGAGACCTGCCCAATGA
66 ATTTCTGCTAACCCCTGGAGCCTTTTGGGCAGCCGAGATAGCTTCGGATGAGACCTGCTCGATGA
490842 ATCCTGAGGCAGTGCTCACAACGCCAGCAGACTGGAACTCAGAAGCCAGACCCCCAGCCACTCCT
131 ATCCTGAGGCAGTGCTCAC-ACGCCAGCAGACTGG-ACTCAGAAGCCAGACCCCCAGCCACTCCT
* * * *
490907 GCAGCCTTTTGGGCAGCTGAGATGGCTTCGGATGAAACCTGACTGATGGCTGGAGGGACGAGACG
194 GCAGCCTTTTGGGCAGCCGAGATGGCTTCGGATGAAACCTG-CTGATGACTGGAGGGACAAGACT
* * *
490972 ATTAATCTTAGTCGCAGATTCACCAACCTGCAATAAAAACAAAGAAGAAATCTTGAATCTCCTTT
258 ATCAATCTTAGTCACAGATTCACCAACCTGCAATAAAAACAAAGAAGAATTCTTGAATCTCCTTT
491037 CATT
323 CATT
* * * ** * * * *
491041 GGCCAGGCATCATCGGTCTTATGATACTCTCTGTCAATCAAATTATTAAGTTAAAAAGTTCTGTA
1 TGCTAGACATCATCAATCTTAGGATACTCTCTGTCAATCAAATAATTGAGCTAAAAAGTTCTGTA
* *** ** * ** * *
491106 ATTTCTGTTCGGCTGTGGAGCCTTTTGGGAAGTAGAGATAGCTTAGAATGAGACCTGCTCGATGA
66 ATTTCTGCTAACCCCTGGAGCCTTTTGGGCAGCCGAGATAGCTTCGGATGAGACCTGCTCGATGA
* * ** **
491171 ATCCTGAGGCAGCGCTCAC-CGCTC--CAG-CT---C-CGGCAAGCTGGACCTCAGTAGCCAGC-
131 ATCCTGAGGCAGTGCTCACACGC-CAGCAGACTGGACTCAG-AAGCCAGACC-C-CCAGCCA-CT
* * * *
491227 CCTGCAGCCTTTTGTGCAGCTGAGATGGCTTTGGATGAGACCTGGCTGATGACTGGAGGGACAAG
191 CCTGCAGCCTTTTGGGCAGCCGAGATGGCTTCGGATGAAACCT-GCTGATGACTGGAGGGACAAG
* *
491292 A-TGATCAATTTTAGTCACAGATTCACCAACCTGCAGTAAAAACAAAGAA-AATTTCTTGAATCT
255 ACT-ATCAATCTTAGTCACAGATTCACCAACCTGCAATAAAAACAAAGAAGAA-TTCTTGAATCT
491355 CCTTTCATT
318 CCTTTCATT
* * * *
491364 TGGTAGACATCATCAATCTTAGGACACTCTCTGTCAATCATATATTTGAGCTAAAAAGTTCTGTA
1 TGCTAGACATCATCAATCTTAGGATACTCTCTGTCAATCAAATAATTGAGCTAAAAAGTTCTGTA
* * * * *
491429 ATTTCTGTTAAGCTCTGGAG-CTTTTGGGGCAGCCGAGATAGCTTCAGATGAGACCTGCTCGATT
66 ATTTCTGCTAACCCCTGGAGCCTTTT-GGGCAGCCGAGATAGCTTCGGATGAGACCTGCTCGATG
* * *
491493 AATTCTGAGGCAGTGCTCAC-CGCTCCAGCA-AGCTGGACT------TCAG-----TAGCCACTC
130 AATCCTGAGGCAGTGCTCACACG--CCAGCAGA-CTGGACTCAGAAGCCAGACCCCCAGCCACTC
* * ** * * *
491545 CAGCAGCCTTTTGGGCAGCCAAGATGGCCCCAGATGAGAA-CTGGCCGATGACCGGAGGGACAAG
192 CTGCAGCCTTTTGGGCAGCCGAGATGGCTTCGGATGA-AACCT-GCTGATGACTGGAGGGACAAG
* * *
491609 A-TGATTAATCTTAGTCACAGATTCACCAACCTGTAATAAAACCAAAG--G-ATTCTTGAATCTC
255 ACT-ATCAATCTTAGTCACAGATTCACCAACCTGCAATAAAAACAAAGAAGAATTCTTGAATCTC
*
491670 CTTTCAAT
319 CTTTCATT
*
491678 TGCTAGACATCATCAATCTTAGGATACTCTCTGTCAATCAAATAATTGACCTAAAAAGTTCTGTA
1 TGCTAGACATCATCAATCTTAGGATACTCTCTGTCAATCAAATAATTGAGCTAAAAAGTTCTGTA
* * * * * *
491743 ATTTCTGTTAA-GCC----GCCTTTTGGGCAGCCAAGATAACTTGGGATGAGACCTTCTCGATGA
66 ATTTCTGCTAACCCCTGGAGCCTTTTGGGCAGCCGAGATAGCTTCGGATGAGACCTGCTCGATGA
* * *
491803 ATCCTGAGGCAGTGCTTACTGCTCCAGCA-A---G-CT-----G---G------A--C-C-CCTG
131 ATCCTGAGGCAGTGCTCAC-ACGCCAGCAGACTGGACTCAGAAGCCAGACCCCCAGCCACTCCTG
* * * * * **
491845 CAGCCTTTTGGGCAGTCGAGATAGCTTCGGATGATACTTGCTTGATGACTGGAGGGACAAGCCGG
195 CAGCCTTTTGGGCAGCCGAGATGGCTTCGGATGAAACCTGC-TGATGACTGGAGGGACAAGACTA
** * *
491910 TCAATCTTTTTCACAGATTCAACAACCTGCAATAAAAACAAAGAAGAATTCTTGAATCCCCTTTC
259 TCAATCTTAGTCACAGATTCACCAACCTGCAATAAAAACAAAGAAGAATTCTTGAATCTCCTTTC
491975 ATT
324 ATT
* * * * * * * * * *
491978 TGCTAGACATCATCAATCTGAGGTTATTCTCTCTCAGTCAAACATTTGAGCTAAAATGTTTTGCA
1 TGCTAGACATCATCAATCTTAGGATACTCTCTGTCAATCAAATAATTGAGCTAAAAAGTTCTGTA
* * *
492043 ATTTCTGCTAACCCCTGAAGCCTTTTGGGCAG-C----TGGCTTCAGATGAGACCTGCTCGATGA
66 ATTTCTGCTAACCCCTGGAGCCTTTTGGGCAGCCGAGATAGCTTCGGATGAGACCTGCTCGATGA
492103 AT
131 AT
492105 TCTGTTATTA
Statistics
Matches: 1417, Mismatches: 239, Indels: 144
0.79 0.13 0.08
Matches are distributed among these distances:
296 3 0.00
297 86 0.06
298 1 0.00
299 2 0.00
300 107 0.08
301 3 0.00
302 1 0.00
304 3 0.00
305 14 0.01
309 58 0.04
310 5 0.00
311 1 0.00
313 1 0.00
314 109 0.08
315 94 0.07
316 22 0.02
317 101 0.07
318 1 0.00
320 2 0.00
321 9 0.01
322 10 0.01
323 245 0.17
324 4 0.00
325 3 0.00
326 6 0.00
327 149 0.11
328 10 0.01
329 363 0.26
330 4 0.00
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (326 bp):
TGCTAGACATCATCAATCTTAGGATACTCTCTGTCAATCAAATAATTGAGCTAAAAAGTTCTGTA
ATTTCTGCTAACCCCTGGAGCCTTTTGGGCAGCCGAGATAGCTTCGGATGAGACCTGCTCGATGA
ATCCTGAGGCAGTGCTCACACGCCAGCAGACTGGACTCAGAAGCCAGACCCCCAGCCACTCCTGC
AGCCTTTTGGGCAGCCGAGATGGCTTCGGATGAAACCTGCTGATGACTGGAGGGACAAGACTATC
AATCTTAGTCACAGATTCACCAACCTGCAATAAAAACAAAGAAGAATTCTTGAATCTCCTTTCAT
T
Found at i:491377 original size:652 final size:612
Alignment explanation
Indices: 490575--492075 Score: 1568
Period size: 652 Copynumber: 2.4 Consensus size: 612
490565 CCCGACCACT
* * * *
490575 CCTGCAGCC--TTGTCGACAGCCGAGATGGCATCGGATGAAACCTGCTTGATGATTGAAGGGACA
1 CCTGCAGCCTTTTGT-G-CAGCTGAGATGGCTTCGGATGAAACCTGCTTGATGACTGGAGGGACA
** * *
490638 AGACT-ATCAAGCTTAGTCACAGATTCACCAACCTGCAATAAAAACGAAGAAGAGTTCTTGAATC
64 AGA-TGATCAATTTTAGTCACAGATTCACCAACCTGCAATAAAAACAAAGAA-AATTCTTGAATC
* * * *
490702 TCCTTTTC-TTTGCTAGACATCATCAATCATAGGGTACCCTTTGTCAATCAAACAATTGAGCTAA
127 TCC-TTTCATTTGCTAGACATCATCAATC-TAGGATACTCTCTGTCAATCAAACATTTGAGCTAA
* * * * ** * *
490766 AAAGTTCAGTAAATTCGGCTAACCCCTGGAGCCTTTTGAGCAGTTGAGATGGCTTCGGATGAGAC
190 AAAGTTCTGTAATTTCTGCTAACCCCTGGAGCCTTTTGGGCAGCCGAGATAGCTTCAGATGAGAC
490831 CTGCCCAATGAATCCTGAGGCAGTGCTCACAACGCCAGC-AGACTGGAACTCAGAAGCCAGACCC
255 CTGCCCAATGAATCCTGAGGCAGTGCTCACAACGCCAGCAAG-CTGG-ACT------CCAG----
* ** ** * * * *
490895 CCAGCCACTCCTGCAGCCTTTTGGGCAGCTGAGATGGCTTCGGATGA-AACCTGACTGATGGCTG
308 -CAGCCACTCCAGCAGCCTTTTGGGCAGCCAAGATGGCCCCAGATGAGAA-CTGACCGATGACCG
* *
490959 GAGGGACGAGACGATTAATCTTAGTCGCAGATTCACCAACCTGCAATAAAAACAAAGAAGAAATC
371 GAGGGACAAGACGATTAATCTTAGTCACAGATTCACCAACCTGCAATAAAAACAAAG--G-AATC
* ** * *
491024 TTGAATCTCCTTTC-ATTGGCCAGGCATCATCGGTCTTATGATACTCTCTGTCAATCAAATTATT
433 TTGAATCTCCTTTCAATT-GCCAGACATCATCAATCTTAGGATACTCTCTGTCAATCAAATAATT
** ** * *
491088 AAGTTAAAAAGTTCTGTAATTTCTGTTCGGCTGTGGAGCCTTTTGGGAAG-TAGAGATAGCTTAG
497 AACCTAAAAAGTTCTGTAATTTCTGTTAAGC-----AGCCTTTTGGGAAGCCA-AGATAACTTAG
*
491152 AATGAGACCTGCTCGATGAATCCTGAGGCAGCGCTCACCGCTCCAGCTCCGGCAAGCTGGACCTC
556 AATGAGACCTGCTCGATGAATCCTGAGGCAGCGCTCA---CT---GCTCCAGCAAGCT-G-----
491217 AGTAGCCAGC
609 -G-A--C--C
* *
491227 CCTGCAGCCTTTTGTGCAGCTGAGATGGCTTTGGATGAGACCTGGC-TGATGACTGGAGGGACAA
1 CCTGCAGCCTTTTGTGCAGCTGAGATGGCTTCGGATGAAACCT-GCTTGATGACTGGAGGGACAA
*
491291 GATGATCAATTTTAGTCACAGATTCACCAACCTGCAGTAAAAACAAAGAAAATTTCTTGAATCTC
65 GATGATCAATTTTAGTCACAGATTCACCAACCTGCAATAAAAACAAAGAAAA-TTCTTGAATCTC
* * * *
491356 CTTTCATTTGGTAGACATCATCAATCTTAGGACACTCTCTGTCAATCATATATTTGAGCTAAAAA
129 CTTTCATTTGCTAGACATCATCAATC-TAGGATACTCTCTGTCAATCAAACATTTGAGCTAAAAA
* * *
491421 GTTCTGTAATTTCTGTTAAGCTCTGGAG-CTTTTGGGGCAGCCGAGATAGCTTCAGATGAGACCT
193 GTTCTGTAATTTCTGCTAACCCCTGGAGCCTTTT-GGGCAGCCGAGATAGCTTCAGATGAGACCT
* * * * ** * * *
491485 GCTCGATTAATTCTGAGGCAGTGCTCACCGCTCCAGCAAGCTGGACTTCAGTAGCCACTCCAGCA
257 GCCCAATGAATCCTGAGGCAGTGCTCACAACGCCAGCAAGCTGGACTCCAGCAGCCACTCCAGCA
* *
491550 GCCTTTTGGGCAGCCAAGATGGCCCCAGATGAGAACTGGCCGATGACCGGAGGGACAAGATGATT
322 GCCTTTTGGGCAGCCAAGATGGCCCCAGATGAGAACTGACCGATGACCGGAGGGACAAGACGATT
* * *
491615 AATCTTAGTCACAGATTCACCAACCTGTAATAAAACCAAAGGATTCTTGAATCTCCTTTCAATTG
387 AATCTTAGTCACAGATTCACCAACCTGCAATAAAAACAAAGGAATCTTGAATCTCCTTTCAATTG
* *
491680 CTAGACATCATCAATCTTAGGATACTCTCTGTCAATCAAATAATTGACCTAAAAAGTTCTGTAAT
452 CCAGACATCATCAATCTTAGGATACTCTCTGTCAATCAAATAATTAACCTAAAAAGTTCTGTAAT
* * * * *
491745 TTCTGTTAAGCCGCCTTTTGGGCAGCCAAGATAACTTGGGATGAGACCTTCTCGATGAATCCTGA
517 TTCTGTTAAGCAGCCTTTTGGGAAGCCAAGATAACTTAGAATGAGACCTGCTCGATGAATCCTGA
* *
491810 GGCAGTGCTTACTGCTCCAGCAAGCTGGACC
582 GGCAGCGCTCACTGCTCCAGCAAGCTGGACC
* * * *
491841 CCTGCAGCCTTTTGGGCAG-TCGAGATAGCTTCGGATGATACTTGCTTGATGACTGGAGGGACAA
1 CCTGCAGCCTTTTGTGCAGCT-GAGATGGCTTCGGATGAAACCTGCTTGATGACTGGAGGGACAA
** * * * *
491905 GCCGGTCAATCTTT-TTCACAGATTCAACAACCTGCAATAAAAACAAAGAAGAATTCTTGAATCC
65 GATGATCAAT-TTTAGTCACAGATTCACCAACCTGCAATAAAAACAAAGAA-AATTCTTGAATCT
* * * *
491969 CCTTTCATTTGCTAGACATCATCAATCTGAGGTTATTCTCTCTCAGTCAAACATTTGAGCTAAAA
128 CCTTTCATTTGCTAGACATCATCAATCT-AGGATACTCTCTGTCAATCAAACATTTGAGCTAAAA
* * * *
492034 TGTTTTGCAATTTCTGCTAACCCCTGAAGCCTTTTGGGCAGC
192 AGTTCTGTAATTTCTGCTAACCCCTGGAGCCTTTTGGGCAGC
492076 TGGCTTCAGA
Statistics
Matches: 728, Mismatches: 104, Indels: 72
0.81 0.12 0.08
Matches are distributed among these distances:
613 4 0.01
614 189 0.26
615 10 0.01
616 1 0.00
618 1 0.00
619 1 0.00
625 1 0.00
626 12 0.02
629 2 0.00
632 54 0.07
633 1 0.00
637 83 0.11
638 4 0.01
640 101 0.14
641 2 0.00
645 3 0.00
651 14 0.02
652 236 0.32
653 5 0.01
654 4 0.01
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (612 bp):
CCTGCAGCCTTTTGTGCAGCTGAGATGGCTTCGGATGAAACCTGCTTGATGACTGGAGGGACAAG
ATGATCAATTTTAGTCACAGATTCACCAACCTGCAATAAAAACAAAGAAAATTCTTGAATCTCCT
TTCATTTGCTAGACATCATCAATCTAGGATACTCTCTGTCAATCAAACATTTGAGCTAAAAAGTT
CTGTAATTTCTGCTAACCCCTGGAGCCTTTTGGGCAGCCGAGATAGCTTCAGATGAGACCTGCCC
AATGAATCCTGAGGCAGTGCTCACAACGCCAGCAAGCTGGACTCCAGCAGCCACTCCAGCAGCCT
TTTGGGCAGCCAAGATGGCCCCAGATGAGAACTGACCGATGACCGGAGGGACAAGACGATTAATC
TTAGTCACAGATTCACCAACCTGCAATAAAAACAAAGGAATCTTGAATCTCCTTTCAATTGCCAG
ACATCATCAATCTTAGGATACTCTCTGTCAATCAAATAATTAACCTAAAAAGTTCTGTAATTTCT
GTTAAGCAGCCTTTTGGGAAGCCAAGATAACTTAGAATGAGACCTGCTCGATGAATCCTGAGGCA
GCGCTCACTGCTCCAGCAAGCTGGACC
Found at i:492090 original size:300 final size:300
Alignment explanation
Indices: 490904--492104 Score: 1145
Period size: 323 Copynumber: 3.9 Consensus size: 300
490894 CCCAGCCACT
* * *
490904 CCTGCAGCCTTTTGGGCAGCTGAGATGGCTTCGGATGAAACCTGACTGATGGCTGGAGGGACGAG
1 CCTGCAGCCTTTTGGGCAGC-GAGATGGCTTCGGATGAAA-CTGGCTGATGACTGGAGGGACAAG
* * * * *
490969 ACGATTAATCTTAGTCGCAGATTCACCAACCTGCAATAAAAACAAAGAAGAAATCTTGAATCTCC
64 ATGATCAATCTTTGTCACAGATTCACCAACCTGCAATAAAAACAAAGAAGAATTCTTGAATCTCC
* * * ** * * *
491034 TTTCATTGGCCAGGCATCATCGGTCTTATGATACTCTCTGTCAATCAAAT-TATTAAGTTAAAAA
129 TTTCATTTGCTAGACATCATCAATCTTAGGATACTCTCTGTCAATCAAATAT-TTGAGCTAAAAA
** ** * **
491098 GTTCTGTAATTTCTGTTCGGCTGTGGAGCCTTTTGGGAAGTAGAGATAGCTT-AGAATGAGACCT
193 GTTCTGTAATTTCTGTT-AACCCT-GAGCCTTTT-GG--GCAGCCATAGCTTCAG-ATGAGACCT
*
491162 GCTCGATGAATCCTGAGGCAGCGCTCACCGCTCCAGCTCCGGCAAGCTGGACCTCAGTAGCCAGC
252 GCTCGATGAATCCTGAGGCAGTGCTCACCGCTCCA------GCAAGCTGG-----A-T---CA-C
* * *
491227 CCTGCAGCCTTTTGTGCAGCTGAGATGGCTTTGGATGAGACCTGGCTGATGACTGGAGGGACAAG
1 CCTGCAGCCTTTTGGGCAGC-GAGATGGCTTCGGATGA-AACTGGCTGATGACTGGAGGGACAAG
*
491292 ATGATCAAT-TTTAGTCACAGATTCACCAACCTGCAGTAAAAACAAAGAA-AATTTCTTGAATCT
64 ATGATCAATCTTT-GTCACAGATTCACCAACCTGCAATAAAAACAAAGAAGAA-TTCTTGAATCT
* * *
491355 CCTTTCATTTGGTAGACATCATCAATCTTAGGACACTCTCTGTCAATCATATATTTGAGCTAAAA
127 CCTTTCATTTGCTAGACATCATCAATCTTAGGATACTCTCTGTCAATCAAATATTTGAGCTAAAA
*
491420 AGTTCTGTAATTTCTGTTAAGCTCTGGAG-CTTTTGGGGCAGCCGAGATAGCTTCAGATGAGACC
192 AGTTCTGTAATTTCTGTTAA-CCCT-GAGCCTTTT-GGGCAGCC---ATAGCTTCAGATGAGACC
* *
491484 TGCTCGATTAATTCTGAGGCAGTGCTCACCGCTCCAGCAAGCTGGACTTCAGTAGC
251 TGCTCGATGAATCCTGAGGCAGTGCTCACCGCTCCAGCAAGCTGGA--TC---A-C
* ** * * *
491540 CACTCCAGCAGCCTTTTGGGCAGCCAAGATGGCCCCAGATGAGAACTGGCCGATGACCGGAGGGA
1 C-CT---GCAGCCTTTTGGGCAG-CGAGATGGCTTCGGATGA-AACTGGCTGATGACTGGAGGGA
* * * *
491605 CAAGATGATTAATCTTAGTCACAGATTCACCAACCTGTAATAAAACCAAAG--G-ATTCTTGAAT
60 CAAGATGATCAATCTTTGTCACAGATTCACCAACCTGCAATAAAAACAAAGAAGAATTCTTGAAT
* * *
491667 CTCCTTTCAATTGCTAGACATCATCAATCTTAGGATACTCTCTGTCAATCAAATAATTGACCTAA
125 CTCCTTTCATTTGCTAGACATCATCAATCTTAGGATACTCTCTGTCAATCAAATATTTGAGCTAA
* * **
491732 AAAGTTCTGTAATTTCTGTTAAGCC---GCCTTTTGGGCAGCCAAGATAACTTGGGATGAGACCT
190 AAAGTTCTGTAATTTCTGTTAACCCTGAGCCTTTTGGGCAGCC---ATAGCTTCAGATGAGACCT
* * *
491794 TCTCGATGAATCCTGAGGCAGTGCTTACTGCTCCAGCAAGCTGGA-C-C
252 GCTCGATGAATCCTGAGGCAGTGCTCACCGCTCCAGCAAGCTGGATCAC
* * *
491841 CCTGCAGCCTTTTGGGCAGTCGAGATAGCTTCGGATGATACTTGCTTGATGACTGGAGGGACAAG
1 CCTGCAGCCTTTTGGGCAG-CGAGATGGCTTCGGATGAAACTGGC-TGATGACTGGAGGGACAAG
** * * * *
491906 CCGGTCAATCTTTTTCACAGATTCAACAACCTGCAATAAAAACAAAGAAGAATTCTTGAATCCCC
64 ATGATCAATCTTTGTCACAGATTCACCAACCTGCAATAAAAACAAAGAAGAATTCTTGAATCTCC
* * * * * * *
491971 TTTCATTTGCTAGACATCATCAATCTGAGGTTATTCTCTCTCAGTCAAACATTTGAGCTAAAATG
129 TTTCATTTGCTAGACATCATCAATCTTAGGATACTCTCTGTCAATCAAATATTTGAGCTAAAAAG
* * * *
492036 TTTTGCAATTTCTGCTAACCCCTGAAGCCTTTTGGGCAG-C-TGGCTTCAGATGAGACCTGCTCG
194 TTCTGTAATTTCTGTTAA-CCCTG-AGCCTTTTGGGCAGCCATAGCTTCAGATGAGACCTGCTCG
492099 ATGAAT
257 ATGAAT
492105 TCTGTTATTA
Statistics
Matches: 745, Mismatches: 103, Indels: 83
0.80 0.11 0.09
Matches are distributed among these distances:
296 5 0.01
297 84 0.11
299 1 0.00
300 109 0.15
301 4 0.01
304 1 0.00
305 13 0.02
306 1 0.00
309 67 0.09
310 6 0.01
312 1 0.00
313 6 0.01
314 92 0.12
315 1 0.00
317 99 0.13
318 3 0.00
320 3 0.00
322 12 0.02
323 233 0.31
324 4 0.01
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (300 bp):
CCTGCAGCCTTTTGGGCAGCGAGATGGCTTCGGATGAAACTGGCTGATGACTGGAGGGACAAGAT
GATCAATCTTTGTCACAGATTCACCAACCTGCAATAAAAACAAAGAAGAATTCTTGAATCTCCTT
TCATTTGCTAGACATCATCAATCTTAGGATACTCTCTGTCAATCAAATATTTGAGCTAAAAAGTT
CTGTAATTTCTGTTAACCCTGAGCCTTTTGGGCAGCCATAGCTTCAGATGAGACCTGCTCGATGA
ATCCTGAGGCAGTGCTCACCGCTCCAGCAAGCTGGATCAC
Found at i:494990 original size:2 final size:2
Alignment explanation
Indices: 494983--495010 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
494973 AAGAAAGGAG
494983 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
495011 TTCCTTTGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:495166 original size:19 final size:21
Alignment explanation
Indices: 495144--495184 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
495134 CTTTTTTTCT
*
495144 TCAATTTTCT-CCA-TTGAGA
1 TCAATGTTCTACCATTTGAGA
495163 TCAATGTTCTACCATTTGAGA
1 TCAATGTTCTACCATTTGAGA
495184 T
1 T
495185 TTTAAGCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 3 0.16
21 7 0.37
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (21 bp):
TCAATGTTCTACCATTTGAGA
Found at i:496268 original size:329 final size:327
Alignment explanation
Indices: 495585--496487 Score: 1184
Period size: 329 Copynumber: 2.7 Consensus size: 327
495575 AACTCACCAT
* * * * * * * * *
495585 TCCAGCATGTTGGACCTCAGTAGCCACAGCCCCAACCACGCCTGCAGCCTTTTCGACAGCCGAGA
1 TCCAGCACGCTGGACCTCAGTAGCCACACCCCCAGCCACTCCTGCAGCCTTTTGGGCAGCAGAAA
* * * * * * *
495650 TCGCTTCGGATGAGACCTGCCTGATGATTGGAGGGACAAAACTATCAAGCTTAGCCACAGATTCA
66 TGGCTTCGGATGAGACCTGCTTGATGAATGGAGGGACAAGACCATCAATCTTAG-TACAGATTCA
** * *
495715 CCAACCTGCAAAAAAAACAAAGAAGTATTCTTGAATATCCTTTCATTTGCTAGACATCA-TCAAT
130 CCAACCTGCATTAAAAACAAAGAAGAATTCTTGAATCTCCTTTCATTTGCTAGACAT-ATTCAAT
* * *
495779 TTCAAG-TAACACTCTGTCAATCAAACATTTGAGCTAAAAAG-TCTGTAATTTCTGCTAACCCCT
194 TT-AGGAT-ACACTCTGTCAGTCAAACATTTGAGCTAAAAAGTTCTGTAATTTCTGCTAACCCCA
*
495842 GGAGCCTTTTGGGCAGCCGAGATGGCTTCAGATGAGACCTGCTTGATGAATCCTGAGGCAGTGCT
257 GGAGCCTTTTGGGCAGCCGAGATGGCTTCAGATGAGACCTGCTTGATGAATCCTGAGGCAGAGCT
* *
495907 CACCAC
322 CACAAA
* * * * * * *
495913 CCCAGCAGGCTGGACCGCAGTAGCCACACCCCCGGCCACTCCTGCAGCATTTTGGGTAGCTGAAA
1 TCCAGCACGCTGGACCTCAGTAGCCACACCCCCAGCCACTCCTGCAGCCTTTTGGGCAGCAGAAA
* * * * *
495978 TGGCTTCAGATGAGACTTGCTTGATGAATGGAGGAACAAGACCATCAATCATACGTACTGATTCA
66 TGGCTTCGGATGAGACCTGCTTGATGAATGGAGGGACAAGACCATCAATCTTA-GTACAGATTCA
* * * * *
496043 CCAACCTGCATTAAAAACAAAGAAGAATTTTTTAATCTCCTTTCACTTGCTAGACATTTTCAGTT
130 CCAACCTGCATTAAAAACAAAGAAGAATTCTTGAATCTCCTTTCATTTGCTAGACATATTCAATT
** *
496108 GTAGGATACTTTCTGTCAGTCAAACATTTGAGCTAAAAGGTTCTGTAATTTCTGCTAACCCCAGG
195 -TAGGATACACTCTGTCAGTCAAACATTTGAGCTAAAAAGTTCTGTAATTTCTGCTAACCCCAGG
* * *
496173 AGCCTTTTGGGCAGCGGAGATGGCTTCGGATGAGACCTGCTTGATGAATCCTGAGGCGGAGCTCA
259 AGCCTTTTGGGCAGCCGAGATGGCTTCAGATGAGACCTGCTTGATGAATCCTGAGGCAGAGCTCA
496238 CAAA
324 CAAA
*
496242 TCCAGCACGCTGGACCTCAGTAGCCACACTCCCAGCCACTCCTGCAGCCTTTTGGGCAGCAGAAA
1 TCCAGCACGCTGGACCTCAGTAGCCACACCCCCAGCCACTCCTGCAGCCTTTTGGGCAGCAGAAA
* *
496307 TGGCTTCGGATGAGACCTGCTTGATGACTGGAGGGACAAGACGATCAATCTTAGTCACAGATTCA
66 TGGCTTCGGATGAGACCTGCTTGATGAATGGAGGGACAAGACCATCAATCTTAGT-ACAGATTCA
* *
496372 CCAACCTGCATTAAAAACAAAGAACAATTCTTGAATCTCTTTTCATTTGCTAGACATAATT-AAT
130 CCAACCTGCATTAAAAACAAAGAAGAATTCTTGAATCTCCTTTCATTTGCTAGACAT-ATTCAAT
* * *
496436 CTTAGGATAAACTATGTCAGTCAAACATTTGAGCTAAAAAGTTTTGTAATTT
194 -TTAGGATACACTCTGTCAGTCAAACATTTGAGCTAAAAAGTTCTGTAATTT
496488 ACCACAGTTT
Statistics
Matches: 492, Mismatches: 75, Indels: 15
0.85 0.13 0.03
Matches are distributed among these distances:
328 190 0.39
329 299 0.61
330 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (327 bp):
TCCAGCACGCTGGACCTCAGTAGCCACACCCCCAGCCACTCCTGCAGCCTTTTGGGCAGCAGAAA
TGGCTTCGGATGAGACCTGCTTGATGAATGGAGGGACAAGACCATCAATCTTAGTACAGATTCAC
CAACCTGCATTAAAAACAAAGAAGAATTCTTGAATCTCCTTTCATTTGCTAGACATATTCAATTT
AGGATACACTCTGTCAGTCAAACATTTGAGCTAAAAAGTTCTGTAATTTCTGCTAACCCCAGGAG
CCTTTTGGGCAGCCGAGATGGCTTCAGATGAGACCTGCTTGATGAATCCTGAGGCAGAGCTCACA
AA
Found at i:497858 original size:24 final size:28
Alignment explanation
Indices: 497813--497868 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 28
497803 CGATTTAGTT
*
497813 TATTAGTTTTAAATTTAAAA-TTT-ATA
1 TATTAGTTTTAAATATAAAATTTTAATA
497839 TATT-GTTTT-AATATAAAATTTTAATA
1 TATTAGTTTTAAATATAAAATTTTAATA
497865 TATT
1 TATT
497869 TAAATAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 8 0.30
25 8 0.30
26 11 0.41
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (28 bp):
TATTAGTTTTAAATATAAAATTTTAATA
Found at i:497891 original size:22 final size:22
Alignment explanation
Indices: 497845--497892 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
497835 TATATATTGT
*
497845 TTTAATATAAAATTTTAATATA
1 TTTAATATAAAATTTTAATAAA
497867 TTTAA-AT-AAATTTTGATATAAA
1 TTTAATATAAAATTTT-A-ATAAA
497889 TTTA
1 TTTA
497893 TTATTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 7 0.30
21 3 0.13
22 13 0.57
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTAATATAAAATTTTAATAAA
Found at i:497928 original size:55 final size:56
Alignment explanation
Indices: 497850--497963 Score: 133
Period size: 55 Copynumber: 2.1 Consensus size: 56
497840 ATTGTTTTAA
* * * ****
497850 TATAAAATTTTAATATATTTAAATAAATTTTGATATA-AATTT-ATTATTTTATTTT
1 TATAAAAATTTAAAATATATAAATAAATAAAAATATACAATTTGATT-TTTTATTTT
*
497905 TATAAAAATTTAAAATATATAAATTAATAAAAATATACAATTTGATTTTTTATTTT
1 TATAAAAATTTAAAATATATAAATAAATAAAAATATACAATTTGATTTTTTATTTT
497961 TAT
1 TAT
497964 TTTTTATCCG
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
55 29 0.59
56 17 0.35
57 3 0.06
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.52
Consensus pattern (56 bp):
TATAAAAATTTAAAATATATAAATAAATAAAAATATACAATTTGATTTTTTATTTT
Found at i:499159 original size:27 final size:26
Alignment explanation
Indices: 499095--499160 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 26
499085 GTATATAATT
* * *
499095 AAAATGTTAAATTACTTAATATTTAT
1 AAAATTTTAAATTACTTAAAATTTAA
*
499121 AAAATTAATAAATTA-TTAAAAATATTAA
1 AAAATT-TTAAATTACTT-AAAAT-TTAA
499149 AAAATTTTAAAT
1 AAAATTTTAAAT
499161 CAAATAATGG
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
26 7 0.22
27 16 0.50
28 9 0.28
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (26 bp):
AAAATTTTAAATTACTTAAAATTTAA
Found at i:500054 original size:25 final size:26
Alignment explanation
Indices: 500022--500098 Score: 75
Period size: 25 Copynumber: 2.9 Consensus size: 26
500012 TATATTTATA
500022 TTTATATAAATTATAATATAAA-ATT
1 TTTATATAAATTATAATATAAATATT
* * *
500047 TTTATATAAAATATAGTTTAAATATT
1 TTTATATAAATTATAATATAAATATT
* * *
500073 TTATATTTAAATAATAAAATATAATA
1 TT-TATATAAATTATAATATA-AATA
500099 AAAAAATCAA
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
25 19 0.47
26 5 0.12
27 12 0.30
28 4 0.10
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (26 bp):
TTTATATAAATTATAATATAAATATT
Found at i:502741 original size:19 final size:19
Alignment explanation
Indices: 502694--502741 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
502684 TAAAAATAAT
* *
502694 ATTTTATAAATATTATATTA
1 ATTTTA-AATTATTAAATTA
* *
502714 AATTAAAATTATTAAATTA
1 ATTTTAAATTATTAAATTA
502733 ATTTTAAAT
1 ATTTTAAAT
502742 CAAATCGAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTTAAATTATTAAATTA
Found at i:503211 original size:9 final size:9
Alignment explanation
Indices: 503197--503221 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
503187 CAATTCAAGC
503197 AAAAAAACA
1 AAAAAAACA
503206 AAAAAAACA
1 AAAAAAACA
503215 AAAAAAA
1 AAAAAAA
503222 AGAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:511680 original size:21 final size:21
Alignment explanation
Indices: 511656--511697 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
511646 TAAATTTGAG
511656 ATTTAAATTTTAATATATAAA
1 ATTTAAATTTTAATATATAAA
** *
511677 ATTTATTTTTTAATTTATAAA
1 ATTTAAATTTTAATATATAAA
511698 TTATGATTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTAAATTTTAATATATAAA
Found at i:511701 original size:19 final size:20
Alignment explanation
Indices: 511663--511716 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
511653 GAGATTTAAA
* *
511663 TTTTAATATATAAAATTTATT
1 TTTTAATTTAT-AAATTTATG
511684 TTTTAATTTATAAA-TTATG
1 TTTTAATTTATAAATTTATG
* *
511703 ATTTCATTTATAAA
1 TTTTAATTTATAAA
511717 AAAAAAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 16 0.55
20 3 0.10
21 10 0.34
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTAATTTATAAATTTATG
Found at i:512584 original size:22 final size:24
Alignment explanation
Indices: 512547--512592 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
512537 TATTAAACTT
512547 AATTTATATAATAAAAAATAAAAA
1 AATTTATATAATAAAAAATAAAAA
*
512571 AATTT-TA-AATAAAATATAAAAA
1 AATTTATATAATAAAAAATAAAAA
512593 TCAAAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 2 0.10
24 5 0.24
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (24 bp):
AATTTATATAATAAAAAATAAAAA
Found at i:516764 original size:11 final size:11
Alignment explanation
Indices: 516748--516774 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
516738 TTTAAAATTT
516748 TAATTTTTTAA
1 TAATTTTTTAA
516759 TAATTTTTTAA
1 TAATTTTTTAA
516770 TAATT
1 TAATT
516775 AGTTATATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TAATTTTTTAA
Found at i:518313 original size:14 final size:13
Alignment explanation
Indices: 518294--518342 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 13
518284 ACGTATTTTC
518294 TTAATTTATTTTAA
1 TTAATTTA-TTTAA
518308 TTAATTTAATTTAA
1 TTAATTT-ATTTAA
518322 TTAAATTTATTTAA
1 TT-AATTTATTTAA
*
518336 CTAATTT
1 TTAATTT
518343 TCTAATATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
13 5 0.16
14 21 0.66
15 6 0.19
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (13 bp):
TTAATTTATTTAA
Found at i:518316 original size:5 final size:5
Alignment explanation
Indices: 518294--518335 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
518284 ACGTATTTTC
* *
518294 TTAAT TTATT TTAA- TTAAT TTAAT TTAAT TAAAT TT-AT TTAA
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAA
518336 CTAATTTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
4 8 0.26
5 23 0.74
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTAAT
Found at i:524814 original size:20 final size:20
Alignment explanation
Indices: 524777--524840 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 20
524767 TATATAAATA
***
524777 TAAAATAATAATTTTATAAT
1 TAAAATAATAAAAATATAAT
524797 TAAAATAATAAAAATAT-AT
1 TAAAATAATAAAAATATAAT
*
524816 TAAAAT-TTAAAAAT-TCAAT
1 TAAAATAATAAAAATAT-AAT
524835 TAAAAT
1 TAAAAT
524841 TCGTAAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
17 1 0.03
18 7 0.18
19 16 0.42
20 14 0.37
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAAATAATAAAAATATAAT
Found at i:524873 original size:21 final size:20
Alignment explanation
Indices: 524814--524876 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 20
524804 ATAAAAATAT
524814 ATTAAAATTTAAAA-ATTCA
1 ATTAAAATTTAAAATATTCA
*
524833 ATTAAAATTCGTAAATTATTCTA
1 ATTAAAATT--TAAAATATTC-A
524856 A-TAAAATATTAAAATATTCA
1 ATTAAAAT-TTAAAATATTCA
524876 A
1 A
524877 ACTCAACTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
19 9 0.24
20 2 0.05
21 13 0.35
22 10 0.27
23 3 0.08
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (20 bp):
ATTAAAATTTAAAATATTCA
Found at i:530221 original size:69 final size:70
Alignment explanation
Indices: 530109--530247 Score: 262
Period size: 69 Copynumber: 2.0 Consensus size: 70
530099 AATGGTAAAG
530109 TCACACAACCAAAACTGTGAAAAAAACAGCTTACTTACATTCATTTGTACATCTATAACAGGCTC
1 TCACACAACCAAAACTGTGAAAAAAACAGCTTACTTACATTCATTTGTACATCTATAACAGGCTC
530174 CAAAA
66 CAAAA
*
530179 TCACATAACCAAAACTGTG-AAAAAACAGCTTACTTACATTCATTTGTACATCTATAACAGGCTC
1 TCACACAACCAAAACTGTGAAAAAAACAGCTTACTTACATTCATTTGTACATCTATAACAGGCTC
530243 CAAAA
66 CAAAA
530248 CAGAGCTAGA
Statistics
Matches: 68, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
69 50 0.74
70 18 0.26
ACGTcount: A:0.42, C:0.24, G:0.09, T:0.25
Consensus pattern (70 bp):
TCACACAACCAAAACTGTGAAAAAAACAGCTTACTTACATTCATTTGTACATCTATAACAGGCTC
CAAAA
Found at i:533465 original size:15 final size:15
Alignment explanation
Indices: 533445--533474 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
533435 CATTCTTTAC
533445 ATCAAATTATTAAAG
1 ATCAAATTATTAAAG
533460 ATCAAATTATTAAAG
1 ATCAAATTATTAAAG
533475 CTGCCATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (15 bp):
ATCAAATTATTAAAG
Found at i:547704 original size:20 final size:20
Alignment explanation
Indices: 547679--547716 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
547669 TGATATATAA
547679 AATATTAAAATTTATATATT
1 AATATTAAAATTTATATATT
* *
547699 AATATTATATTTTATATA
1 AATATTAAAATTTATATA
547717 AAAATTATGT
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:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATATTAAAATTTATATATT
Found at i:548600 original size:12 final size:12
Alignment explanation
Indices: 548585--548618 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
548575 CTATTTAAAA
548585 ATATTAAAAATT
1 ATATTAAAAATT
548597 ATATT-AAAATT
1 ATATTAAAAATT
548608 ATATATAAAAA
1 ATAT-TAAAAA
548619 CAAAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 10 0.50
12 6 0.30
13 4 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATATTAAAAATT
Found at i:550288 original size:3 final size:3
Alignment explanation
Indices: 550276--550325 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
550266 CTTACTGCTA
550276 ATT A-T 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
550323 ATT
1 ATT
550326 TTGAAATATT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:552221 original size:28 final size:26
Alignment explanation
Indices: 552167--552225 Score: 86
Period size: 25 Copynumber: 2.3 Consensus size: 26
552157 AATTTTTTAT
552167 TAATTTTTTTTCAATCGTAATTATAA
1 TAATTTTTTTTCAATCGTAATTATAA
*
552193 TAATTTTTTTT-AAT-GATAATTATAG
1 TAATTTTTTTTCAATCG-TAATTATAA
552218 TAATTTTT
1 TAATTTTT
552226 ATTACTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
24 1 0.03
25 19 0.61
26 11 0.35
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (26 bp):
TAATTTTTTTTCAATCGTAATTATAA
Found at i:554915 original size:11 final size:11
Alignment explanation
Indices: 554869--554916 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
554859 GATAATTATT
554869 ATTTATTCTTAA
1 ATTT-TTCTTAA
554881 ATTTTT-TTAA
1 ATTTTTCTTAA
* *
554891 TTTTTTCTTCA
1 ATTTTTCTTAA
*
554902 ATTTTTCTAAA
1 ATTTTTCTTAA
554913 ATTT
1 ATTT
554917 AATCATGTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
10 9 0.30
11 17 0.57
12 4 0.13
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTTTCTTAA
Found at i:554980 original size:20 final size:20
Alignment explanation
Indices: 554938--554980 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
554928 AATACTTTAA
*
554938 AAATAAATAAAAAATAAAGT
1 AAATAAATAAAAAATAAAAT
554958 AAATAAATTAAAAAA-AAAAT
1 AAATAAA-TAAAAAATAAAAT
554978 AAA
1 AAA
554981 ACATGAATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (20 bp):
AAATAAATAAAAAATAAAAT
Found at i:555253 original size:21 final size:21
Alignment explanation
Indices: 555206--555253 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
555196 TCCTCGAATT
*
555206 TTTCTTTTTTCCTCTCTCTCC
1 TTTCTTTTTTCCTCACTCTCC
555227 TCTTCTTTTTTCTCTCACTCT-C
1 T-TTCTTTTTTC-CTCACTCTCC
555249 TTTCT
1 TTTCT
555254 AGAAGCCATG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 5 0.21
22 12 0.50
23 7 0.29
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTCTTTTTTCCTCACTCTCC
Found at i:555639 original size:18 final size:20
Alignment explanation
Indices: 555601--555654 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 20
555591 TTCAAATTTT
*
555601 CTTTAAATTTTAACTTCAAA
1 CTTTAAATTCTAACTTCAAA
555621 CTTTAAA-TCTAAC-TCAAA
1 CTTTAAATTCTAACTTCAAA
555639 CTTTACAATTC-AACTT
1 CTTTA-AATTCTAACTT
555655 AAATTTTACA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
18 10 0.33
19 10 0.33
20 10 0.33
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (20 bp):
CTTTAAATTCTAACTTCAAA
Found at i:555653 original size:19 final size:19
Alignment explanation
Indices: 555616--555675 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
555606 AATTTTAACT
555616 TCAAACTTTA-AA-TCTAAC
1 TCAAACTTTACAATTC-AAC
555634 TCAAACTTTACAATTCAAC
1 TCAAACTTTACAATTCAAC
* * *
555653 TTAAATTTTACAATCCAA-
1 TCAAACTTTACAATTCAAC
555671 TCAAA
1 TCAAA
555676 TAATTTCACA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 14 0.39
19 20 0.56
20 2 0.06
ACGTcount: A:0.45, C:0.22, G:0.00, T:0.33
Consensus pattern (19 bp):
TCAAACTTTACAATTCAAC
Found at i:556090 original size:43 final size:42
Alignment explanation
Indices: 556035--556170 Score: 155
Period size: 43 Copynumber: 3.2 Consensus size: 42
556025 TGACTTTAAA
* * *
556035 AAATAAAACTTCTCTAAACAAAGCTCAATGATTTTAAAAAAAT
1 AAATAAAACTTCTCTAAACAAAGCTTAATGACTTT-GAAAAAT
* *
556078 AAATAAAACTTCTCTAAATAGAAGCTTAATAACTTTGAAAAAT
1 AAATAAAACTTCTCTAAACA-AAGCTTAATGACTTTGAAAAAT
** * * *
556121 AAATAAGGCTTATTTAAGCAAAGGCTTAATGACTTTGAAAAAT
1 AAATAAAACTTCTCTAAACAAA-GCTTAATGACTTTGAAAAAT
556164 AAATAAA
1 AAATAAA
556171 GCTCATTTAA
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
42 2 0.03
43 64 0.82
44 12 0.15
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (42 bp):
AAATAAAACTTCTCTAAACAAAGCTTAATGACTTTGAAAAAT
Found at i:556179 original size:43 final size:43
Alignment explanation
Indices: 556101--556213 Score: 154
Period size: 43 Copynumber: 2.6 Consensus size: 43
556091 CTAAATAGAA
* *
556101 GCTTAATAACTTTGAAAAATAAATAAGGCTTATTTAAGCAAAG
1 GCTTAATAACTTTGAAAAATAAATAAAGCTCATTTAAGCAAAG
* * *
556144 GCTTAATGACTTTGAAAAATAAATAAAGCTCATTTAAGTAGAG
1 GCTTAATAACTTTGAAAAATAAATAAAGCTCATTTAAGCAAAG
* *
556187 GCTCAATAACTTTTAAAAAATAAATAA
1 GCTTAATAAC-TTTGAAAAATAAATAA
556214 GGCCCATCGA
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
43 46 0.75
44 15 0.25
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.30
Consensus pattern (43 bp):
GCTTAATAACTTTGAAAAATAAATAAAGCTCATTTAAGCAAAG
Found at i:556195 original size:86 final size:84
Alignment explanation
Indices: 555968--556216 Score: 236
Period size: 86 Copynumber: 2.9 Consensus size: 84
555958 AGCCCCTCTT
* ** ** *
555968 AACAAGGCTCAAAAACTTTGAAAAAGTAAATAAAAGCTCTTCTAAGTAGAGATTCAATGACTTTA
1 AACAAAGCTCAATGACTTTGAAAAA-TAAAT-AAAGCTCTT-TAAGTAGAGGCTCAATAACTTTA
*
556033 AAAAAT-AA-AA--CTTCTCTA
63 AAAAATAAATAAGGCTTATCTA
* * * * * * * *
556051 AACAAAGCTCAATGATTTTAAAAAAATAAATAAAACTTCTCTAAATAGAAGCTTAATAACTTTGA
1 AACAAAGCTCAATGACTTT-GAAAAATAAATAAAGC-TCTTTAAGTAGAGGCTCAATAACTTTAA
*
556116 AAAATAAATAAGGCTTATTTA
64 AAAATAAATAAGGCTTATCTA
* *
556137 AGCAAAGGCTTAATGACTTTGAAAAATAAATAAAGCTCATTTAAGTAGAGGCTCAATAACTTTTA
1 AACAAA-GCTCAATGACTTTGAAAAATAAATAAAGCTC-TTTAAGTAGAGGCTCAATAAC-TTTA
556202 AAAAATAAATAAGGC
63 AAAAATAAATAAGGC
556217 CCATCGACAA
Statistics
Matches: 131, Mismatches: 26, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
82 26 0.20
83 25 0.19
84 7 0.05
85 2 0.02
86 42 0.32
87 29 0.22
ACGTcount: A:0.49, C:0.12, G:0.11, T:0.28
Consensus pattern (84 bp):
AACAAAGCTCAATGACTTTGAAAAATAAATAAAGCTCTTTAAGTAGAGGCTCAATAACTTTAAAA
AATAAATAAGGCTTATCTA
Found at i:556711 original size:23 final size:23
Alignment explanation
Indices: 556644--556711 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
556634 ATCTAAATTC
*
556644 AAAGGTTCTCATTCAAAAAATTT
1 AAAGGTTCTCATTCAAAAATTTT
** * *
556667 AGGGGTTCACA-TCCAAAATTTT
1 AAAGGTTCTCATTCAAAAATTTT
*
556689 AAAGCTTCTCATTCAAAAATTTT
1 AAAGGTTCTCATTCAAAAATTTT
556712 TGGTGATTCA
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
22 16 0.47
23 18 0.53
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.35
Consensus pattern (23 bp):
AAAGGTTCTCATTCAAAAATTTT
Found at i:557966 original size:16 final size:16
Alignment explanation
Indices: 557945--557975 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
557935 TTTTCTCTTA
557945 TTTTATATTTTTTTTT
1 TTTTATATTTTTTTTT
557961 TTTTATATTTTTTTT
1 TTTTATATTTTTTTT
557976 CATCCATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTATATTTTTTTTT
Found at i:562654 original size:17 final size:18
Alignment explanation
Indices: 562621--562654 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
562611 GTATAAAAAA
*
562621 TCAAATTCTTTTTTTTCC
1 TCAAATTCTTTTCTTTCC
562639 TCAAATT-TTTTCTTTC
1 TCAAATTCTTTTCTTTC
562655 TACTTTCTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.62
Consensus pattern (18 bp):
TCAAATTCTTTTCTTTCC
Found at i:563125 original size:19 final size:19
Alignment explanation
Indices: 563102--563149 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
563092 ATTTTTAATT
563102 CAACTCAAACTTTACAATC
1 CAACTCAAACTTTACAATC
* *
563121 TAACTCAAAATTTTACAATC
1 CAACTC-AAACTTTACAATC
563141 CAA-TCAAAC
1 CAACTCAAAC
563150 AGTTTCACAC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 3 0.12
19 7 0.29
20 14 0.58
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (19 bp):
CAACTCAAACTTTACAATC
Found at i:578078 original size:19 final size:19
Alignment explanation
Indices: 578054--578104 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
578044 TATATATGAA
578054 TAAAATAATAATTTTTAAT
1 TAAAATAATAATTTTTAAT
578073 TAAAATTTAA-AA-TTTTAAT
1 TAAAA--TAATAATTTTTAAT
*
578092 TAAATTAATAATT
1 TAAAATAATAATT
578105 ACTTGATTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
17 3 0.11
18 2 0.07
19 17 0.63
20 2 0.07
21 3 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TAAAATAATAATTTTTAAT
Found at i:580209 original size:30 final size:31
Alignment explanation
Indices: 580170--580232 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
580160 GGCATTCAAA
* *
580170 AAATCCTTAACTTTT-AATTTGTATCTAAAT
1 AAATCCTTAAATTTTGAATTTCTATCTAAAT
* *
580200 AAATTCTTAAATTTTGAATTTCTATTTAAAT
1 AAATCCTTAAATTTTGAATTTCTATCTAAAT
580231 AA
1 AA
580233 GCCCTTAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 13 0.46
31 15 0.54
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.48
Consensus pattern (31 bp):
AAATCCTTAAATTTTGAATTTCTATCTAAAT
Found at i:580240 original size:31 final size:30
Alignment explanation
Indices: 580174--580240 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 30
580164 TTCAAAAAAT
* * *
580174 CCTTAACTTTTAATTTGTATCTAAATAAAT
1 CCTTAAATTTTAATTTCTATCTAAATAAAC
* * *
580204 TCTTAAATTTTGAATTTCTATTTAAATAAGC
1 CCTTAAATTTT-AATTTCTATCTAAATAAAC
580235 CCTTAA
1 CCTTAA
580241 CATAAATAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
30 9 0.31
31 20 0.69
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.46
Consensus pattern (30 bp):
CCTTAAATTTTAATTTCTATCTAAATAAAC
Found at i:580608 original size:101 final size:101
Alignment explanation
Indices: 580378--580691 Score: 364
Period size: 101 Copynumber: 3.1 Consensus size: 101
580368 TATTTTAGCC
* *
580378 AAGAAAATTAAAACAAAAATTTGGTAACACAGTTCAGTTTCCATGCAAGAATGGAAAGTAATCCT
1 AAGAAAATTAAAACAAAAATTTGGTAACACAGTTCAGTTTCCATGCAAGAATGGAAAGTAGTTCT
* *
580443 AGAATGACAAGATCAGCTAGCAAACTGCAGTCTCAG
66 AGGATGACAAGATCAGCTAGCAAACTGCAGTATCAG
* * ***** *
580479 ATGAAAATTAAAAAAAAAAAAAATTAACACAGTTCAGTTTCCATGCAAGAATGGAAAGTAGTTCA
1 AAGAAAATTAAAACAAAAATTTGGTAACACAGTTCAGTTTCCATGCAAGAATGGAAAGTAGTTCT
**
580544 AGGATGGTAAGATCAGCTAGCAAACTGCAGTATCAG
66 AGGATGACAAGATCAGCTAGCAAACTGCAGTATCAG
* ** * * *
580580 AAGAAAATTAAAACAAAAATTTGGTAACATATATAGTTCAGCATCCATCCAAGAGTGAAAAGTAG
1 AAGAAAATTAAAACAAAAATTTGGTAAC----ACAGTTCAGTTTCCATGCAAGAATGGAAAGTAG
* * *
580645 TTCTAGGATGACAAG---AGCTAGAAAATTACAGTATCAG
62 TTCTAGGATGACAAGATCAGCTAGCAAACTGCAGTATCAG
580682 AAGAAAATTA
1 AAGAAAATTA
580692 GACCCCTTTC
Statistics
Matches: 176, Mismatches: 33, Indels: 7
0.81 0.15 0.03
Matches are distributed among these distances:
101 108 0.61
102 29 0.16
105 39 0.22
ACGTcount: A:0.46, C:0.14, G:0.18, T:0.22
Consensus pattern (101 bp):
AAGAAAATTAAAACAAAAATTTGGTAACACAGTTCAGTTTCCATGCAAGAATGGAAAGTAGTTCT
AGGATGACAAGATCAGCTAGCAAACTGCAGTATCAG
Found at i:581291 original size:21 final size:20
Alignment explanation
Indices: 581262--581307 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
581252 GATTAATGAT
*
581262 ATTATTTAATTTAATCATATA
1 ATTAATTAATTTAATCAT-TA
* *
581283 ATTAATTAATTTTATGATTA
1 ATTAATTAATTTAATCATTA
581303 ATTAA
1 ATTAA
581308 ATATGTCACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
ATTAATTAATTTAATCATTA
Found at i:582297 original size:13 final size:13
Alignment explanation
Indices: 582279--582303 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
582269 AATAACTTAA
582279 AATACGATACAAT
1 AATACGATACAAT
582292 AATACGATACAA
1 AATACGATACAA
582304 ATATAATACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.16, G:0.08, T:0.20
Consensus pattern (13 bp):
AATACGATACAAT
Found at i:585059 original size:2 final size:2
Alignment explanation
Indices: 585046--585075 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
585036 CTTTTCTTTC
*
585046 AT AT AA 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
585076 GTTTGTTGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:585515 original size:66 final size:68
Alignment explanation
Indices: 585387--585519 Score: 234
Period size: 66 Copynumber: 2.0 Consensus size: 68
585377 TGCTATTATG
*
585387 TATGATTGACAAGAGTTTCAATTGGTCTGAATATATGGGTCATATTTTTGTTTCAATTATGACAT
1 TATGATTGACAAGAGTTTCAATTGATCTGAATATATGGGTCATATTTTTGTTTCAATTATGACAT
585452 ATA
66 ATA
*
585455 TATGATTGACAAGAGTTTCAATTGATCTG-AT-TATGGGTCATCTTTTTGTTTCAATTATGACAT
1 TATGATTGACAAGAGTTTCAATTGATCTGAATATATGGGTCATATTTTTGTTTCAATTATGACAT
585518 AT
66 AT
585520 GTAAGTTATT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
66 33 0.52
67 2 0.03
68 28 0.44
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (68 bp):
TATGATTGACAAGAGTTTCAATTGATCTGAATATATGGGTCATATTTTTGTTTCAATTATGACAT
ATA
Found at i:589042 original size:22 final size:22
Alignment explanation
Indices: 589016--589057 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
589006 CTTATATTTA
* *
589016 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAAAATTAAG
589038 TATTTGTATCCCTAAAATTA
1 TATTTGTATCCCTAAAATTA
589058 GGATAGACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:595196 original size:6 final size:6
Alignment explanation
Indices: 595185--595209 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
595175 CAATGCCCCA
595185 GTCAAT GTCAAT GTCAAT GTCAAT G
1 GTCAAT GTCAAT GTCAAT GTCAAT G
595210 CAGCAACATG
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (6 bp):
GTCAAT
Found at i:599934 original size:18 final size:19
Alignment explanation
Indices: 599911--599951 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
599901 TCCAAAATTA
*
599911 ATAAAATATTATTTTT-AT
1 ATAAAATAATATTTTTAAT
599929 ATAAAATAATATTTTTAAT
1 ATAAAATAATATTTTTAAT
599948 ATAA
1 ATAA
599952 TTATAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATAAAATAATATTTTTAAT
Found at i:604924 original size:21 final size:21
Alignment explanation
Indices: 604898--604943 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
604888 GTATACCTAT
**
604898 GCAGGATGCATTGCGTCTCTG
1 GCAGGATGCATCACGTCTCTG
604919 GCAGGATGCATCACGTCTCTG
1 GCAGGATGCATCACGTCTCTG
604940 GCAG
1 GCAG
604944 TATTGCATGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.17, C:0.26, G:0.33, T:0.24
Consensus pattern (21 bp):
GCAGGATGCATCACGTCTCTG
Found at i:609933 original size:17 final size:17
Alignment explanation
Indices: 609911--609946 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
609901 CTAGTTAATG
609911 TAATTGAATTTTGATTT
1 TAATTGAATTTTGATTT
**
609928 TAATTGGGTTTTGATTT
1 TAATTGAATTTTGATTT
609945 TA
1 TA
609947 TCTTGGCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.17, T:0.58
Consensus pattern (17 bp):
TAATTGAATTTTGATTT
Found at i:612127 original size:371 final size:371
Alignment explanation
Indices: 611444--614272 Score: 4492
Period size: 371 Copynumber: 7.7 Consensus size: 371
611434 CACAAGGGCA
611444 AATGTCACGGACCTAAGGGGGAGTCCTGAATCCCACATCGAACATAATAGG-AGAGTC-CTTGGG
1 AATGTCACGGACCTAAGGGGGAGTCCTGAATCCCACATCGAACATAATAGGAAG-GTCAC-TGGG
*
611507 GTATAAAAGGGTTCACACCATCTCCGTCTTGTGAGGCGCCTTTTGTAGGACAAAACCGTGAGGCC
64 GTATAAAAGGGTTCACACCATCTCCGCCTTGTGAGGCGCCTTTTGTAGGACAAAACCGTGAGGCC
* *
611572 AGGGGGGCCAGAGCGGACAATACCTCACAAGGATGTGAACTGTGGCAGG-AAGGCTGATCTGGGA
129 AGGGGGGCCAGAGCGGACAATACCTCACAAGGGTGTGAACCGTGGC-GGTAAGGCTGATCTGGGA
* * *
611636 CGCCGGAAGGGTGAATGCCCGGGTCCCGGAGCCGCGCGGGTTCGAAGCTTGAGCCTCGACCCGTG
193 CGCCGGAAGGGTGAATGCCCGGGTCCCGGAGCCGCGCGGGTTCGGAGCTTAAGTCTCGACCCGTG
611701 ACAAGTGGTATCAGAGCCAACCCTAAACCGTTCGATCCACGCCGAGCACCTCGAGGGAGGTAGGC
258 ACAAGTGGTATCAGAGCCAACCCTAAACCGTTCGATCCACGCCGAGCACCTCGAGGGAGGTAGGC
*
611766 AGGGTGGCCGGCCTCCGTGACGAGGGCGTCACGAGGTTGGGTGCGGGAG
323 AGGGTGGCCAGCCTCCGTGACGAGGGCGTCACGAGGTTGGGTGCGGGAG
* * * *
611815 AATGTCACGGACCTAAGGGAGAGTCCTAAATCCCACATCGAACATAATAGGAAGATCGCTGGGGT
1 AATGTCACGGACCTAAGGGGGAGTCCTGAATCCCACATCGAACATAATAGGAAGGTCACTGGGGT
* * *
611880 ATAAAAGGGTTCACACCATCTCCGCCTTATGAGGCGTCTTTTGTAGGACAAAACAGTGAGGCCAG
66 ATAAAAGGGTTCACACCATCTCCGCCTTGTGAGGCGCCTTTTGTAGGACAAAACCGTGAGGCCAG
* *
611945 GGGGGCCAGAGCGGACAATACCTCACAAGGGTGTGAACCGTGGCGGTTAGGCTGAT-TCAGGACG
131 GGGGGCCAGAGCGGACAATACCTCACAAGGGTGTGAACCGTGGCGGTAAGGCTGATCT-GGGACG
* * * *
612009 CCGGAAAGGTGAATGCCCAGGTCCCGGAGCCGCGCGGGTTCAGAGCTTAAGTCTCGACCCGTAAC
195 CCGGAAGGGTGAATGCCCGGGTCCCGGAGCCGCGCGGGTTCGGAGCTTAAGTCTCGACCCGTGAC
* ** *
612074 AAATGGTATCAGAGCCCGCCCTAAACCGTTCGATCCACGCCAAGCACCTCGAGGGAGGTAGGCAG
260 AAGTGGTATCAGAGCCAACCCTAAACCGTTCGATCCACGCCGAGCACCTCGAGGGAGGTAGGCAG
612139 GGTGGCCAGCCTCCGTGACGAGGGCGTCACGAGGTTGGGTGCGGGAG
325 GGTGGCCAGCCTCCGTGACGAGGGCGTCACGAGGTTGGGTGCGGGAG
* *
612186 AATGTCACGGACCTAAGGGGGAGTCCTGAATCCCACATCGAACATAATAGGAGGGTCCCTGGGGT
1 AATGTCACGGACCTAAGGGGGAGTCCTGAATCCCACATCGAACATAATAGGAAGGTCACTGGGGT
612251 ATAAAAGGGTTCACACCATCTCCGCCTTGTGAGGCGCCTTTTGTAGGACAAAACCGTGAGGCCAG
66 ATAAAAGGGTTCACACCATCTCCGCCTTGTGAGGCGCCTTTTGTAGGACAAAACCGTGAGGCCAG
* * *
612316 GGGAGCCAGAGCAGACAATACCTCACAAGGGTGTGAACCGTGGCGGTCAGGCTGAT-TCGGGACG
131 GGGGGCCAGAGCGGACAATACCTCACAAGGGTGTGAACCGTGGCGGTAAGGCTGATCT-GGGACG
* * *
612380 CCGGAAGGGTAAATGCCCGGGTCCGGGAGCCGCGCGGGTTCGGAGCTTGAGTCTCGACCCGTGAC
195 CCGGAAGGGTGAATGCCCGGGTCCCGGAGCCGCGCGGGTTCGGAGCTTAAGTCTCGACCCGTGAC
* * * *
612445 AAGTGGTATCAAAGCCAACCCTAAACCGTTCGATCCATGCCGAGCACCTCGAGGGAGGCATGCAG
260 AAGTGGTATCAGAGCCAACCCTAAACCGTTCGATCCACGCCGAGCACCTCGAGGGAGGTAGGCAG
*
612510 GGTGGTCAGCCTCCGTGACGAGGGCGTCACGAGGTTGGGTGCGGGAG
325 GGTGGCCAGCCTCCGTGACGAGGGCGTCACGAGGTTGGGTGCGGGAG
* *
612557 AATATCACGGACCTAAGGGCGAGTCCTGAATCCCACATCGAACATAATAGGAAGGTCACTGGGGT
1 AATGTCACGGACCTAAGGGGGAGTCCTGAATCCCACATCGAACATAATAGGAAGGTCACTGGGGT
* * *
612622 ATATAAGGGTTCACACCATCTCCGCTTTGTGAGGCACCTTTTGTAGGACAAAACCGTGAGGCCAG
66 ATAAAAGGGTTCACACCATCTCCGCCTTGTGAGGCGCCTTTTGTAGGACAAAACCGTGAGGCCAG
* *
612687 GGAGGCCAGAGCGGACAATACCTCACAAGGGTGTGAACCGTGGCGGTTAGGCTGAT-TCGGGACG
131 GGGGGCCAGAGCGGACAATACCTCACAAGGGTGTGAACCGTGGCGGTAAGGCTGATCT-GGGACG
* * *
612751 CCAGAAAGGTGAATGCCCGGGTCCCGGAGCCGAGCGGGTTCGGAGCTTAAGTCTCGACCCGTGAC
195 CCGGAAGGGTGAATGCCCGGGTCCCGGAGCCGCGCGGGTTCGGAGCTTAAGTCTCGACCCGTGAC
* * * * * *
612816 AAGTAGAATCAGAGCCAGCCCTAAACCATTCGATCCACGCTGAGCGCCTCGAGGGAGGTAGGCAG
260 AAGTGGTATCAGAGCCAACCCTAAACCGTTCGATCCACGCCGAGCACCTCGAGGGAGGTAGGCAG
*
612881 GGTGGCCGGCCTCCGTGACGAGGGCGTCACGAGGTTGGGTGCGGGAG
325 GGTGGCCAGCCTCCGTGACGAGGGCGTCACGAGGTTGGGTGCGGGAG
* *
612928 AATGTCACGGACCTAAGGGGGAGTCCTGAATCCCACATCGAACATAATAGGAGGGTCCCTGGGGT
1 AATGTCACGGACCTAAGGGGGAGTCCTGAATCCCACATCGAACATAATAGGAAGGTCACTGGGGT
612993 ATAAAAGGGTTCACACCATCTCCGCCTTGTGAGGCGCCTTTTGTAGGACAAAACCGTGAGGCCAG
66 ATAAAAGGGTTCACACCATCTCCGCCTTGTGAGGCGCCTTTTGTAGGACAAAACCGTGAGGCCAG
*
613058 GGGGGCCAGAGCGGACAATACCTCACAAGGGTGTGAACTGTGGCAGG-AAGGCTGATCTGGGACG
131 GGGGGCCAGAGCGGACAATACCTCACAAGGGTGTGAACCGTGGC-GGTAAGGCTGATCTGGGACG
* * * *
613122 CCAGAAGGGTGAATGCCCGGGTCCCGGAGCCGCGCGGGTTCGGAGCTTGAGTCTTGATCCGTGAC
195 CCGGAAGGGTGAATGCCCGGGTCCCGGAGCCGCGCGGGTTCGGAGCTTAAGTCTCGACCCGTGAC
613187 AAGTGGTATCAGAGCCAACCCTAAACCGTTCGATCCACGCCGAGCACCTC-----------G-A-
260 AAGTGGTATCAGAGCCAACCCTAAACCGTTCGATCCACGCCGAGCACCTCGAGGGAGGTAGGCAG
613239 -G-GG--AGCCTCCGTGACGAGGGCGTCACGAGGTTGGGTGCGGGAG
325 GGTGGCCAGCCTCCGTGACGAGGGCGTCACGAGGTTGGGTGCGGGAG
*
613282 AATGTCACGGACCTAAGGGGGAGTCCTAAATCCCACATCGAACATAATAGGAAGGTCACTGGGGT
1 AATGTCACGGACCTAAGGGGGAGTCCTGAATCCCACATCGAACATAATAGGAAGGTCACTGGGGT
*
613347 ATAAAAGGGTTCACACCATCTCCGCCTTGTGAGGCGCCTTTTGTAGGACAAAACTGTGAGGCCAG
66 ATAAAAGGGTTCACACCATCTCCGCCTTGTGAGGCGCCTTTTGTAGGACAAAACCGTGAGGCCAG
* * * *
613412 GAGGGCCAGAGCGGACAATACCTCACAAGGGTGTGAACCGTGACGATCAGGCTGATCTGGGACGC
131 GGGGGCCAGAGCGGACAATACCTCACAAGGGTGTGAACCGTGGCGGTAAGGCTGATCTGGGACGC
613477 CGGAAGGGTGAATGCCCGGGTCCCGGAGCCGCGCGGGTTCGGAGCTTAAGTCTCGACCCGTGACA
196 CGGAAGGGTGAATGCCCGGGTCCCGGAGCCGCGCGGGTTCGGAGCTTAAGTCTCGACCCGTGACA
* * *
613542 AGTGGTATCAGAGCCAGCCCTAAACCGTTCGATCCACGCCAAGCACCTCGAGGGAGATAGGCAGG
261 AGTGGTATCAGAGCCAACCCTAAACCGTTCGATCCACGCCGAGCACCTCGAGGGAGGTAGGCAGG
*
613607 GTGGCCAGCCTCCGTGACGAGGGCGTCACGAGGTTGGGTGCAGGAG
326 GTGGCCAGCCTCCGTGACGAGGGCGTCACGAGGTTGGGTGCGGGAG
* * *
613653 AATGTCACGGACCTAAGGGGGAGTCCTGAATCCCACATCAAACATAATAGGAGGGTCCCTGGGGT
1 AATGTCACGGACCTAAGGGGGAGTCCTGAATCCCACATCGAACATAATAGGAAGGTCACTGGGGT
* *
613718 ATAAAAGGGTTCACACCATCTCTGCCTTGTGAGGCGCCTTTTGTAGGATAAAACCGTGAGGCCAG
66 ATAAAAGGGTTCACACCATCTCCGCCTTGTGAGGCGCCTTTTGTAGGACAAAACCGTGAGGCCAG
* * *
613783 GAGGGCCAGAGCGGACAATACCTCACAAGGGTGTGAACCATGACAGG-AAGGCTGATCTGGGACG
131 GGGGGCCAGAGCGGACAATACCTCACAAGGGTGTGAACCGTGGC-GGTAAGGCTGATCTGGGACG
* *
613847 CCGGAAGGGTGAATGCCCAGGTCCCGGAGCCGCGCGGGTTCGGAGCTTGAGTCTCGACCCGTGAC
195 CCGGAAGGGTGAATGCCCGGGTCCCGGAGCCGCGCGGGTTCGGAGCTTAAGTCTCGACCCGTGAC
613912 AAGTGGTATCAGAGCCAACCCTAAACCGTTCGATCCACGCCGAGCACCTCGAGGGAGGTAGGCAG
260 AAGTGGTATCAGAGCCAACCCTAAACCGTTCGATCCACGCCGAGCACCTCGAGGGAGGTAGGCAG
* *
613977 GGTGGCCGGCCTCCGTGACGAAGGG-GTCATGAGGTTGGGTGCGGGAG
325 GGTGGCCAGCCTCCGTGACG-AGGGCGTCACGAGGTTGGGTGCGGGAG
*
614024 AATGTCACGGACCTAAGGGGGAGTCCTAAATCCCACATCGAACATAATAGGAAGGTCACTGGGGT
1 AATGTCACGGACCTAAGGGGGAGTCCTGAATCCCACATCGAACATAATAGGAAGGTCACTGGGGT
* *
614089 ATAAAAGGGTTCACACCATCTCCGCCTTATGAGGCGCCTTTTGTAGGACAAAATCGT---G--A-
66 ATAAAAGGGTTCACACCATCTCCGCCTTGTGAGGCGCCTTTTGTAGGACAAAACCGTGAGGCCAG
* *
614148 ---GGCCAG-G-GGACAATACCTCACAAGGGTGTGAACCGTGGCGGTTAGGCTGAT-TCGGGACA
131 GGGGGCCAGAGCGGACAATACCTCACAAGGGTGTGAACCGTGGCGGTAAGGCTGATCT-GGGACG
* *
614207 CCGGAAAGGTGAATGCCCGGGTCCCGGAGCCGCGCGGGTTCGGAGCTTAAATCTCGACCCGTGAC
195 CCGGAAGGGTGAATGCCCGGGTCCCGGAGCCGCGCGGGTTCGGAGCTTAAGTCTCGACCCGTGAC
614272 A
260 A
614273 CAAGCACCAA
Statistics
Matches: 2278, Mismatches: 152, Indels: 67
0.91 0.06 0.03
Matches are distributed among these distances:
353 1 0.00
354 331 0.15
356 2 0.00
357 1 0.00
359 4 0.00
360 106 0.05
361 1 0.00
362 6 0.00
365 1 0.00
366 2 0.00
368 2 0.00
369 2 0.00
370 3 0.00
371 1805 0.79
372 11 0.00
ACGTcount: A:0.24, C:0.25, G:0.33, T:0.17
Consensus pattern (371 bp):
AATGTCACGGACCTAAGGGGGAGTCCTGAATCCCACATCGAACATAATAGGAAGGTCACTGGGGT
ATAAAAGGGTTCACACCATCTCCGCCTTGTGAGGCGCCTTTTGTAGGACAAAACCGTGAGGCCAG
GGGGGCCAGAGCGGACAATACCTCACAAGGGTGTGAACCGTGGCGGTAAGGCTGATCTGGGACGC
CGGAAGGGTGAATGCCCGGGTCCCGGAGCCGCGCGGGTTCGGAGCTTAAGTCTCGACCCGTGACA
AGTGGTATCAGAGCCAACCCTAAACCGTTCGATCCACGCCGAGCACCTCGAGGGAGGTAGGCAGG
GTGGCCAGCCTCCGTGACGAGGGCGTCACGAGGTTGGGTGCGGGAG
Found at i:614518 original size:24 final size:26
Alignment explanation
Indices: 614472--614519 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
614462 AGATTTGATA
*
614472 GTGTGGAAAAATTAAGAAATAAAATT
1 GTGTGGAAAAACTAAGAAATAAAATT
*
614498 GTGT-GAAAAACTAA-AAGTAAAA
1 GTGTGGAAAAACTAAGAAATAAAA
614520 CTGAATGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 9 0.45
26 4 0.20
ACGTcount: A:0.56, C:0.02, G:0.19, T:0.23
Consensus pattern (26 bp):
GTGTGGAAAAACTAAGAAATAAAATT
Found at i:614691 original size:22 final size:22
Alignment explanation
Indices: 614665--614708 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
614655 ATTTTTTGTC
614665 CTTAATTCTATG-GATACAAATA
1 CTTAATTCTA-GAGATACAAATA
614687 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
614709 TAAATACACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:617051 original size:86 final size:85
Alignment explanation
Indices: 616902--617079 Score: 329
Period size: 86 Copynumber: 2.1 Consensus size: 85
616892 TGAGTTGATG
*
616902 AATACCCCACAAAGATACACTTAATTGCTCTTGATCCAACTTTTCCCTATTATGACTATGAACAT
1 AATATCCCACAAAGATACACTTAATTGCTCTTGATCCAACTTTTCCCTATTATGACTATGAACAT
616967 GAACAAATGATGTACAACCA
66 GAACAAATGATGTACAACCA
616987 AATATCCCACAAAGATACACTTAATTGCTCTTGGATCCAACTTTTCCCTATTATGACTATGAACA
1 AATATCCCACAAAGATACACTTAATTGCTCTT-GATCCAACTTTTCCCTATTATGACTATGAACA
*
617052 TGAACAAATGATGTACAATCA
65 TGAACAAATGATGTACAACCA
617073 AATATCC
1 AATATCC
617080 TAGGTGTGAG
Statistics
Matches: 90, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
85 31 0.34
86 59 0.66
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.29
Consensus pattern (85 bp):
AATATCCCACAAAGATACACTTAATTGCTCTTGATCCAACTTTTCCCTATTATGACTATGAACAT
GAACAAATGATGTACAACCA
Found at i:617168 original size:68 final size:68
Alignment explanation
Indices: 617059--617195 Score: 247
Period size: 68 Copynumber: 2.0 Consensus size: 68
617049 ACATGAACAA
* *
617059 ATGATGTACAATCAAATATCCTAGGTGTGAGGTTGTTTGTGGTATTAAAGTTGTGATAGAATTGT
1 ATGATGTACAACCAAATATCCTAGGTGTGAGGTTGTTTGTGGTATTAAAGTTGGGATAGAATTGT
617124 GAC
66 GAC
*
617127 ATGATGTACAACCAAATATCCTAGGTGTGAGGTTGTTTGTGGTATTAAGGTTGGGATAGAATTGT
1 ATGATGTACAACCAAATATCCTAGGTGTGAGGTTGTTTGTGGTATTAAAGTTGGGATAGAATTGT
617192 GAC
66 GAC
617195 A
1 A
617196 GTAATTTCAT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.29, C:0.08, G:0.28, T:0.35
Consensus pattern (68 bp):
ATGATGTACAACCAAATATCCTAGGTGTGAGGTTGTTTGTGGTATTAAAGTTGGGATAGAATTGT
GAC
Found at i:618609 original size:25 final size:25
Alignment explanation
Indices: 618571--618630 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
618561 AATGGCTATA
* *
618571 AAGGCCTTAGCAGGGTTCGACAATG
1 AAGGCCTAAACAGGGTTCGACAATG
*
618596 AAGGTCTAAACAGGGTTCGACAATG
1 AAGGCCTAAACAGGGTTCGACAATG
618621 AAGGCCTAAA
1 AAGGCCTAAA
618631 ATAGAAATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.18
Consensus pattern (25 bp):
AAGGCCTAAACAGGGTTCGACAATG
Found at i:618722 original size:24 final size:24
Alignment explanation
Indices: 618695--618744 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
618685 TCTGATACCA
618695 TGTG-GAAAAACTAATAAATAAAAC
1 TGTGTGAAAAACTAA-AAATAAAAC
*
618719 TGTGTGAAAAACTAAAAGTAAAAC
1 TGTGTGAAAAACTAAAAATAAAAC
618743 TG
1 TG
618745 AATGTATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.54, C:0.08, G:0.16, T:0.22
Consensus pattern (24 bp):
TGTGTGAAAAACTAAAAATAAAAC
Found at i:618913 original size:22 final size:22
Alignment explanation
Indices: 618888--618931 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
618878 ATTTTTTGTC
**
618888 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAAATACAAATA
618910 CTTAATTCTAGAAATACAAATA
1 CTTAATTCTAGAAATACAAATA
618932 TAAATACACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAAATACAAATA
Found at i:622381 original size:11 final size:11
Alignment explanation
Indices: 622365--622398 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
622355 TCAGTATTTA
622365 AATATTATATT
1 AATATTATATT
622376 AATATTATATT
1 AATATTATATT
622387 AATA--ATATT
1 AATATTATATT
622396 AAT
1 AAT
622399 TATTTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 8 0.35
11 15 0.65
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AATATTATATT
Found at i:622568 original size:8 final size:8
Alignment explanation
Indices: 622555--622580 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
622545 TTTGATTGAA
622555 TTTTTTAT
1 TTTTTTAT
622563 TTTTTTAT
1 TTTTTTAT
622571 TTTTTTAT
1 TTTTTTAT
622579 TT
1 TT
622581 CATAATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTAT
Found at i:622615 original size:20 final size:21
Alignment explanation
Indices: 622592--622638 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
622582 ATAATTTGAA
622592 AATAAATTTAAAGTGAATTT-
1 AATAAATTTAAAGTGAATTTC
* * *
622612 AAT-ATTTTATATTGAATTTC
1 AATAAATTTAAAGTGAATTTC
622632 AATAAAT
1 AATAAAT
622639 ACGAATAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
19 13 0.62
20 6 0.29
21 2 0.10
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (21 bp):
AATAAATTTAAAGTGAATTTC
Found at i:624161 original size:30 final size:30
Alignment explanation
Indices: 624095--624191 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
624085 ATTTGATGAT
* **
624095 TTATATATTTATATTATATAAAATATTAAAA
1 TTATATATTTATATTATGTTTAATA-TAAAA
*
624126 TTTATATATTTATATTATGTTTTATATAAAA
1 -TTATATATTTATATTATGTTTAATATAAAA
*
624157 TTATAT-GTTATAATTTATG-TTAATATAAAA
1 TTATATATTTAT-A-TTATGTTTAATATAAAA
624187 TTATA
1 TTATA
624192 AAATATAATT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
29 4 0.07
30 22 0.39
31 10 0.18
32 21 0.37
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (30 bp):
TTATATATTTATATTATGTTTAATATAAAA
Found at i:624199 original size:30 final size:31
Alignment explanation
Indices: 624140--624202 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
624130 TATATTTATA
* ***
624140 TTATGTTTTATATAAAATTATATGTTATAAT
1 TTATGTTTAATATAAAATTATAAAATATAAT
624171 TTATG-TTAATATAAAATTATAAAATATAAT
1 TTATGTTTAATATAAAATTATAAAATATAAT
624201 TT
1 TT
624203 TTTATTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 23 0.82
31 5 0.18
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (31 bp):
TTATGTTTAATATAAAATTATAAAATATAAT
Found at i:625109 original size:19 final size:20
Alignment explanation
Indices: 625085--625124 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
625075 TATCATTTTT
625085 TTATTAAATTTATA-TAAAA
1 TTATTAAATTTATATTAAAA
* *
625104 TTATTATATTTTTATTAAAA
1 TTATTAAATTTATATTAAAA
625124 T
1 T
625125 CTTGTTGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATTAAATTTATATTAAAA
Found at i:636851 original size:411 final size:394
Alignment explanation
Indices: 636085--636878 Score: 914
Period size: 394 Copynumber: 2.0 Consensus size: 394
636075 TAATAAAAAC
* *
636085 AACAAAAACTCAATTTCATCCAAAATGACAACATGCAAAAGGAAAATCATACAAAAAAACACATC
1 AACAAAAACTCAATTTCATCCAAAATAACAACATGCAAAAAGAAAATCATACAAAAAAACACATC
* * * *
636150 CAAAACATCATGCAAAACCTCCAACCACAAAAATCCAAAACCCATTCAACAATAAAACTCTATTA
66 CAAAACAACATACAAAACCTCCAACCACAAAAACCCAAAACCCATTCAACAATAAAACTCCATTA
* *
636215 AAAAAATTATAATGTATAAAACGAAAATAATGACAATAAAAATCTAAAAGAAAAAGAAACCCACA
131 AAAAAATTATAATGTATAAAACGAAAATAATGACAATAAAAACCCAAAAGAAAAAGAAACCCACA
* * *
636280 CTCAATGACAAAATAAAAGAGAAAAAAATCATACTTAAAAACATCTAAAAAAACCAAAAACCAAA
196 CTCAATGACAAAACAAAAGAGAAAAAAATCATACCTAAAAACAGCTAAAAAAACCAAAAACCAAA
* ** * * *
636345 GAAAAAAGAAAATAAAAACTCACAGGAAAAAGAAGGATATCTTACACGATAGAAGAAGTCTACTA
261 GAAAAAAGAAAATAAAAACTCAAAAAAAAAAAAAGGATACCTTACACGACAGAAGAAGTCTACTA
*
636410 CAAACACAAAAATACACAACTAAAAGAAGTTTCGAAAATAAACAACACAAACACCTGTCAAGAAC
326 CAAACACAAAAATACACAACAAAAAGAAGTTTCGAAAATAAACAACACAAACACCTGTCAAGAAC
636475 AGAA
391 AGAA
* * ** * * * *
636479 AACAAAAATTCATTTTCATTGAAGATAACAACATGCAAAAATAAAATCTTGCAAAAAAACACATC
1 AACAAAAACTCAATTTCATCCAAAATAACAACATGCAAAAAGAAAATCATACAAAAAAACACATC
** * * * * *
636544 CACGATAACATAC-AAACTTCCAATCAC-AAAACCCAAAAACCCATTGAACAATGAAACTCCATT
66 CAAAACAACATACAAAACCTCCAACCACAAAAACCC-AAAACCCATTCAACAATAAAACTCCATT
* *
636607 AAAAAAAATTTATAATGTATAGAACGAAAATAGTGA-ACA-AAAAACCCAAAAG-AAAAGCAAAA
130 -AAAAAAA-TTATAATGTATAAAACGAAAATAATGACA-ATAAAAACCCAAAAGAAAAAG--AAA
* * * * * *
636669 CTCACATTCAATGGCAGAACAAAAGAAGAAAAAATTCATACCTAAAAATAGCTTAAAAAAAAAAG
190 CCCACACTCAATGACAAAACAAAAG-AGAAAAAAATCATACCTAAAAACAGC-T-----AAAAA-
* ** *
636734 AACCAAAAACCAAATAAACTAGAAAGTAAAAACTCATAAAAAAAAAAAAAAAGGAAAGGTACCTT
247 AACCAAAAACCAAAGAAAAAAGAAAATAAAAACTC----AAAAAAAAAAAAAGG--A--TACCTT
* * * *
636799 ACACGCCAGAAGAAGTCTGCTACAAACACAAAGATAGACAACAAAAAGAAGTTTCGAAAATAAAC
304 ACACGACAGAAGAAGTCTACTACAAACACAAAAATACACAACAAAAAGAAGTTTCGAAAATAAAC
636864 AACACAAACACCTGT
369 AACACAAACACCTGT
636879 AAAATCCAAA
Statistics
Matches: 329, Mismatches: 49, Indels: 27
0.81 0.12 0.07
Matches are distributed among these distances:
392 6 0.02
393 42 0.13
394 82 0.25
395 49 0.15
396 22 0.07
397 1 0.00
402 5 0.02
403 31 0.09
407 11 0.03
409 1 0.00
411 79 0.24
ACGTcount: A:0.57, C:0.19, G:0.09, T:0.15
Consensus pattern (394 bp):
AACAAAAACTCAATTTCATCCAAAATAACAACATGCAAAAAGAAAATCATACAAAAAAACACATC
CAAAACAACATACAAAACCTCCAACCACAAAAACCCAAAACCCATTCAACAATAAAACTCCATTA
AAAAAATTATAATGTATAAAACGAAAATAATGACAATAAAAACCCAAAAGAAAAAGAAACCCACA
CTCAATGACAAAACAAAAGAGAAAAAAATCATACCTAAAAACAGCTAAAAAAACCAAAAACCAAA
GAAAAAAGAAAATAAAAACTCAAAAAAAAAAAAAGGATACCTTACACGACAGAAGAAGTCTACTA
CAAACACAAAAATACACAACAAAAAGAAGTTTCGAAAATAAACAACACAAACACCTGTCAAGAAC
AGAA
Found at i:637111 original size:21 final size:22
Alignment explanation
Indices: 637069--637110 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
637059 TTATGCCCCA
*
637069 ATTAAAGATAATTTTTATTTTT
1 ATTAAAGATAATTTATATTTTT
637091 ATTAAA-ATAA-TTATATTTTT
1 ATTAAAGATAATTTATATTTTT
637111 TTTTGCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 4 0.21
22 6 0.32
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
ATTAAAGATAATTTATATTTTT
Found at i:638460 original size:20 final size:21
Alignment explanation
Indices: 638437--638476 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
638427 ACATTGATAT
638437 AAAG-TTTTACTAAATGATTG
1 AAAGATTTTACTAAATGATTG
* *
638457 AAAGATTTTATTAATTGATT
1 AAAGATTTTACTAAATGATT
638477 TCAAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (21 bp):
AAAGATTTTACTAAATGATTG
Found at i:638475 original size:21 final size:19
Alignment explanation
Indices: 638429--638476 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
638419 AGAGATATAC
638429 ATTGATATAAAGTTTTACTA
1 ATTGAT-TAAAGTTTTACTA
* *
638449 AATGATTGAAAGATTTTATTA
1 ATTGATT-AAAG-TTTTACTA
638470 ATTGATT
1 ATTGATT
638477 TCAAAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 9 0.39
21 13 0.57
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (19 bp):
ATTGATTAAAGTTTTACTA
Found at i:640776 original size:30 final size:30
Alignment explanation
Indices: 640736--640797 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
640726 ATGGCCAAGG
*
640736 TAACCAGAGATCTCTTGATTGAGTTTACTA
1 TAACCAGAGATCTCTTGACTGAGTTTACTA
*
640766 TAACCTGAGATCTCTTGACTGAGTTTACTA
1 TAACCAGAGATCTCTTGACTGAGTTTACTA
640796 TA
1 TA
640798 TATGTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (30 bp):
TAACCAGAGATCTCTTGACTGAGTTTACTA
Found at i:641995 original size:2 final size:2
Alignment explanation
Indices: 641988--642015 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
641978 CTTACAGGTT
641988 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
642016 ATGCATACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:646022 original size:81 final size:81
Alignment explanation
Indices: 645882--646042 Score: 232
Period size: 81 Copynumber: 2.0 Consensus size: 81
645872 CCAAGCTACG
* * * * * *
645882 TAGATCATTTTCGCCTTCTCGATTGGCAAACAGATTGGTGTCCCCATTGAAGAGCAGAAAAAGTT
1 TAGATCATTTTCGCCCTCCCAATTGGCAAACAGATTGGTCTCCCCATTGAAGAGAAGAAAAAGCT
**
645947 TGCAAAGTAGTGATGC
66 TGCAAAAAAGTGATGC
* *
645963 TAGATCATTTTCGCCCTCCCAATTTGCAAACAGATTGGTCTCTCCATTGAAGAGAAGAAAAAGCT
1 TAGATCATTTTCGCCCTCCCAATTGGCAAACAGATTGGTCTCCCCATTGAAGAGAAGAAAAAGCT
646028 TGCAAAAAAGTGATG
66 TGCAAAAAAGTGATG
646043 GATCGATGAG
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 70 1.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27
Consensus pattern (81 bp):
TAGATCATTTTCGCCCTCCCAATTGGCAAACAGATTGGTCTCCCCATTGAAGAGAAGAAAAAGCT
TGCAAAAAAGTGATGC
Found at i:652003 original size:17 final size:17
Alignment explanation
Indices: 651977--652010 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
651967 ATTAAATTGA
651977 AATATATATATATTTTT
1 AATATATATATATTTTT
*
651994 AATATTTATATATTTTT
1 AATATATATATATTTTT
652011 TAAAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
AATATATATATATTTTT
Found at i:652005 original size:19 final size:18
Alignment explanation
Indices: 651976--652023 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
651966 AATTAAATTG
*
651976 AAATATATATATATTTTTA
1 AAATTTATATAT-TTTTTA
*
651995 ATATTTATATATTTTTTA
1 AAATTTATATATTTTTTA
*
652013 AAATTTTTATA
1 AAATTTATATA
652024 AAATAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
AAATTTATATATTTTTTA
Found at i:661714 original size:23 final size:23
Alignment explanation
Indices: 661688--661733 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
661678 TCATGAGCAC
661688 ATGCTGATCTATAATAACACAAT
1 ATGCTGATCTATAATAACACAAT
* *
661711 ATGCTGATCTATAGTAGCACAAT
1 ATGCTGATCTATAATAACACAAT
661734 TATAAAGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.30
Consensus pattern (23 bp):
ATGCTGATCTATAATAACACAAT
Found at i:670012 original size:21 final size:21
Alignment explanation
Indices: 669967--670017 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
669957 AACATAATTG
*
669967 AATTTTTA-TGTTTTAATATA
1 AATTTTTATTATTTTAATATA
*
669987 TATTTTTATTATTTTAAT-TA
1 AATTTTTATTATTTTAATATA
*
670007 AA-ATTTATTAT
1 AATTTTTATTAT
670018 ATATATATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 8 0.31
20 10 0.38
21 8 0.31
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
AATTTTTATTATTTTAATATA
Found at i:677923 original size:6 final size:6
Alignment explanation
Indices: 677912--677940 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
677902 CAAATGTAGT
677912 GAAAAG GAAAAG GAAAAG GAAAAG GAAAA
1 GAAAAG GAAAAG GAAAAG GAAAAG GAAAA
677941 AAGTTTCAAA
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:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (6 bp):
GAAAAG
Found at i:684990 original size:3 final size:3
Alignment explanation
Indices: 684982--685023 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
684972 ACATTAGGGT
*
684982 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTA TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
685024 GATTGAGATC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:689048 original size:12 final size:12
Alignment explanation
Indices: 689031--689084 Score: 69
Period size: 12 Copynumber: 4.8 Consensus size: 12
689021 CTCCTCCTTA
689031 TCATCATCAAAC
1 TCATCATCAAAC
* *
689043 TCATCACCAAAT
1 TCATCATCAAAC
689055 TCATCATCAAAC
1 TCATCATCAAAC
689067 TCATCAT--AA-
1 TCATCATCAAAC
689076 TCATCATCA
1 TCATCATCA
689085 TCTTCATCTA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 7 0.19
10 2 0.06
12 27 0.75
ACGTcount: A:0.41, C:0.31, G:0.00, T:0.28
Consensus pattern (12 bp):
TCATCATCAAAC
Found at i:689085 original size:12 final size:11
Alignment explanation
Indices: 689030--689101 Score: 62
Period size: 12 Copynumber: 6.5 Consensus size: 11
689020 CCTCCTCCTT
689030 ATCATCATCAA
1 ATCATCATCAA
*
689041 ACTCATCACCAA
1 A-TCATCATCAA
689053 ATTCATCATCAA
1 A-TCATCATCAA
689065 A-C-TCATCATA
1 ATCATCATCA-A
689075 ATCATCATC--
1 ATCATCATCAA
*
689084 ATCTTCATCTAA
1 ATCATCATC-AA
689096 ATCATC
1 ATCATC
689102 CTCAGGCAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
9 14 0.29
10 3 0.06
11 2 0.04
12 30 0.61
ACGTcount: A:0.39, C:0.31, G:0.00, T:0.31
Consensus pattern (11 bp):
ATCATCATCAA
Found at i:689086 original size:24 final size:23
Alignment explanation
Indices: 689030--689084 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 23
689020 CCTCCTCCTT
689030 ATCATCATCAAACTCATCACCAA
1 ATCATCATCAAACTCATCACCAA
*
689053 ATTCATCATCAAACTCATCA--TA
1 A-TCATCATCAAACTCATCACCAA
689075 ATCATCATCA
1 ATCATCATCA
689085 TCTTCATCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 9 0.30
22 2 0.07
23 1 0.03
24 18 0.60
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.27
Consensus pattern (23 bp):
ATCATCATCAAACTCATCACCAA
Found at i:690672 original size:124 final size:124
Alignment explanation
Indices: 690513--690754 Score: 412
Period size: 124 Copynumber: 2.0 Consensus size: 124
690503 TTTACTAAAT
* * *
690513 TATATTATTTTATTTTCGTTAATCGAATAAAATTTATAAATTTAAAAAATTAATAGACCAAATTT
1 TATATAATTTTATTTTCGTTAATCAAATAAAATTTATAAATTTAAAAAATTAACAGACCAAATTT
* *
690578 AATTCAATTAATTCGATTAATTTTTTCGGTTAATCGAATAATAAATATATTTATTAATA
66 AATTCAATTAATTCGATTAATTTTTTCGGTAAATCAAATAATAAATATATTTATTAATA
* * *
690637 TATATAATTTTATTTTCGTTAATCAAATAAAATTTATTAATTTTAAAAATTAACAGATCAAATTT
1 TATATAATTTTATTTTCGTTAATCAAATAAAATTTATAAATTTAAAAAATTAACAGACCAAATTT
690702 AATTCAATTAATTCGATTAATTTTTTCGGTAAATCAAATAATAAATATATTTA
66 AATTCAATTAATTCGATTAATTTTTTCGGTAAATCAAATAATAAATATATTTA
690755 AATTAAATTA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
124 110 1.00
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (124 bp):
TATATAATTTTATTTTCGTTAATCAAATAAAATTTATAAATTTAAAAAATTAACAGACCAAATTT
AATTCAATTAATTCGATTAATTTTTTCGGTAAATCAAATAATAAATATATTTATTAATA
Found at i:690768 original size:16 final size:16
Alignment explanation
Indices: 690743--690775 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
690733 AATCAAATAA
690743 TAAATATA-TTTAAAT
1 TAAATATATTTTAAAT
690758 TAAATTATATTTTAAAT
1 TAAA-TATATTTTAAAT
690775 T
1 T
690776 CTTAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 4 0.25
17 8 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAAATATATTTTAAAT
Found at i:699878 original size:2 final size:2
Alignment explanation
Indices: 699871--699899 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
699861 CTCACGTCCA
699871 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
699900 AAGATTTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:723351 original size:18 final size:19
Alignment explanation
Indices: 723319--723356 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
723309 TATATAGTAT
*
723319 TTTAATATAATTTTAAATA
1 TTTAATATAAATTTAAATA
723338 TTTAA-ATAAATTTAAATA
1 TTTAATATAAATTTAAATA
723356 T
1 T
723357 AAAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTAATATAAATTTAAATA
Found at i:729635 original size:24 final size:22
Alignment explanation
Indices: 729598--729657 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 22
729588 AATTAGATCT
* *
729598 AATAATTTAAAATATGATATAAT
1 AATAATAT-AAATATGATATAAA
729621 AATACGATATAAATATGATATAAA
1 AATA--ATATAAATATGATATAAA
729645 AATAATATAAATA
1 AATAATATAAATA
729658 AATATTATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 9 0.27
23 4 0.12
24 17 0.52
25 3 0.09
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (22 bp):
AATAATATAAATATGATATAAA
Found at i:729640 original size:11 final size:11
Alignment explanation
Indices: 729607--729657 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
729597 TAATAATTTA
729607 AAATATGATAT
1 AAATATGATAT
*
729618 AATAATACGATAT
1 -A-AATATGATAT
729631 AAATATGATAT
1 AAATATGATAT
* *
729642 AAAAATAATAT
1 AAATATGATAT
729653 AAATA
1 AAATA
729658 AATATTATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
11 22 0.67
12 2 0.06
13 9 0.27
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (11 bp):
AAATATGATAT
Found at i:729647 original size:13 final size:13
Alignment explanation
Indices: 729606--729648 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
729596 CTAATAATTT
729606 AAAATATGATATA
1 AAAATATGATATA
* *
729619 ATAATACGATAT-
1 AAAATATGATATA
729631 -AAATATGATATA
1 AAAATATGATATA
729643 AAAATA
1 AAAATA
729649 ATATAAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 9 0.38
13 15 0.62
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.30
Consensus pattern (13 bp):
AAAATATGATATA
Found at i:729707 original size:27 final size:28
Alignment explanation
Indices: 729643--729707 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
729633 ATATGATATA
729643 AAAATAATATA-AATAAATATTATAATTT
1 AAAATAATA-ACAATAAATATTATAATTT
* *
729671 AAAATTATAACAATAATTA-TATAATTT
1 AAAATAATAACAATAAATATTATAATTT
729698 AATAA-AATAA
1 AA-AATAATAA
729708 AAATTTATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 15 0.47
28 17 0.53
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (28 bp):
AAAATAATAACAATAAATATTATAATTT
Found at i:730481 original size:25 final size:25
Alignment explanation
Indices: 730411--730481 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 25
730401 TTAATATAAC
*
730411 TATTAAAA-TATTAAAAAGTATTTAT
1 TATTAAAATTATT-AAAATTATTTAT
*
730436 TATTAAAATATATTGAAATTATTTAT
1 TATTAAAAT-TATTAAAATTATTTAT
*
730462 TATTAAAATTATTAATATTA
1 TATTAAAATTATTAAAATTA
730482 AAAATAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.43
26 19 0.47
27 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (25 bp):
TATTAAAATTATTAAAATTATTTAT
Found at i:730485 original size:16 final size:16
Alignment explanation
Indices: 730451--730533 Score: 55
Period size: 16 Copynumber: 5.0 Consensus size: 16
730441 AAATATATTG
*
730451 AAATTATTTATTATT-A
1 AAATTA-TTAATATTAA
730467 AAATTATTAATATTAA
1 AAATTATTAATATTAA
* *
730483 AAATAATTATATTTTAA
1 AAATTATTA-ATATTAA
*
730500 TAATAATATTTAATAATTAA
1 -AA-ATTA-TTAAT-ATTAA
730520 AAA-TATTAA-ATTAA
1 AAATTATTAATATTAA
730534 TATAAAAATA
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
14 5 0.09
15 7 0.13
16 19 0.35
17 8 0.15
18 3 0.05
19 6 0.11
20 7 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATTATTAATATTAA
Found at i:730503 original size:14 final size:13
Alignment explanation
Indices: 730484--730518 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
730474 TAATATTAAA
730484 AATAATTATATTTT
1 AATAATTATA-TTT
*
730498 AATAATAATATTT
1 AATAATTATATTT
730511 AATAATTA
1 AATAATTA
730519 AAAATATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
AATAATTATATTT
Found at i:730535 original size:21 final size:20
Alignment explanation
Indices: 730513--730549 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
730503 TAATATTTAA
730513 TAAT-TAAAAATA-TTAAAT
1 TAATATAAAAATACTTAAAT
730531 TAATATAAAAATACTTAAA
1 TAATATAAAAATACTTAAA
730550 ATAAAACTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 8 0.47
20 5 0.29
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (20 bp):
TAATATAAAAATACTTAAAT
Found at i:730548 original size:20 final size:18
Alignment explanation
Indices: 730504--730549 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 18
730494 TTTTAATAAT
*
730504 AATATTTAA-TAATTAAA
1 AATATTAAATTAATTAAA
730521 AATATTAAATTAATATAAA
1 AATATTAAATTAAT-TAAA
730540 AATACTTAAA
1 AATA-TTAAA
730550 ATAAAACTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 8 0.32
18 4 0.16
19 8 0.32
20 5 0.20
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
AATATTAAATTAATTAAA
Found at i:730603 original size:23 final size:22
Alignment explanation
Indices: 730571--730708 Score: 92
Period size: 23 Copynumber: 6.1 Consensus size: 22
730561 TATTATTCTT
730571 TATATTATTTATTAATATATTA
1 TATATTATTTATTAATATATTA
730593 TAGTATTATTTATTAATAATATT-
1 TA-TATTATTTATTAAT-ATATTA
*
730616 TA-ATTAATTA-TAAT-TATTA
1 TATATTATTTATTAATATATTA
730635 TATATT-TATTATATAATATTATT-
1 TATATTAT-TTAT-TAATA-TATTA
* * *
730658 TAT-TAATATATCTAATATTATTTCT
1 TATATTATTTAT-TAATA-TA-TT-A
*
730683 TAATATTATTTTTTAATATATTA
1 T-ATATTATTTATTAATATATTA
730706 TAT
1 TAT
730709 TGATTATATA
Statistics
Matches: 92, Mismatches: 9, Indels: 30
0.70 0.07 0.23
Matches are distributed among these distances:
18 4 0.04
19 2 0.02
20 10 0.11
21 7 0.08
22 20 0.22
23 23 0.25
24 11 0.12
25 3 0.03
26 7 0.08
27 5 0.05
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (22 bp):
TATATTATTTATTAATATATTA
Found at i:730623 original size:14 final size:13
Alignment explanation
Indices: 730576--730709 Score: 79
Period size: 13 Copynumber: 10.6 Consensus size: 13
730566 TTCTTTATAT
730576 TATTTATTAAT-A
1 TATTTATTAATAA
* *
730588 TA-TTA-TAGTAT
1 TATTTATTAATAA
730599 TATTTATTAATAA
1 TATTTATTAATAA
*
730612 TATTTAATTAATTA
1 TATTT-ATTAATAA
*
730626 TAATTATT-AT-A
1 TATTTATTAATAA
730637 TATTTATTATATAA
1 TATTTATTA-ATAA
*
730651 TA-TTATTTATTAA
1 TATTTA-TTAATAA
*
730664 TA--TATCTAATAT
1 TATTTAT-TAATAA
* *
730676 TATTTCTTAATAT
1 TATTTATTAATAA
*
730689 TATTTTTTAAT-A
1 TATTTATTAATAA
730701 TATTATATT
1 TATT-TATT
730710 GATTATATAT
Statistics
Matches: 96, Mismatches: 14, Indels: 23
0.72 0.11 0.17
Matches are distributed among these distances:
10 3 0.03
11 14 0.15
12 19 0.20
13 41 0.43
14 19 0.20
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (13 bp):
TATTTATTAATAA
Found at i:730638 original size:11 final size:11
Alignment explanation
Indices: 730574--730656 Score: 52
Period size: 11 Copynumber: 7.7 Consensus size: 11
730564 TATTCTTTAT
730574 ATTATT-TATTA
1 ATTATTATA-TA
730585 ATATATTATAGT-
1 AT-TATTATA-TA
730597 ATTATT-TATTA
1 ATTATTATA-TA
* *
730608 A-TAATATTTA
1 ATTATTATATA
*
730618 ATTAAT-TATA
1 ATTATTATATA
730628 ATTATTATATA
1 ATTATTATATA
*
730639 TTTATTATATA
1 ATTATTATATA
730650 A-TATTAT
1 ATTATTAT
730657 TTATTAATAT
Statistics
Matches: 58, Mismatches: 8, Indels: 13
0.73 0.10 0.16
Matches are distributed among these distances:
10 23 0.40
11 26 0.45
12 6 0.10
13 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (11 bp):
ATTATTATATA
Found at i:730644 original size:80 final size:82
Alignment explanation
Indices: 730560--730748 Score: 223
Period size: 78 Copynumber: 2.3 Consensus size: 82
730550 ATAAAACTAC
*
730560 TTATTATTCTTTATATTATTTATTAATATAT-TATAGTATTATTTATTAATAATATTTAATTAAT
1 TTATTATTCTTAATATTATTTATTAATATATCTA-A-TATTATTTATTAATAATATTT-ATTAAT
730624 -TA-TA-ATT-ATTATATAT
63 ATATTATATTGATTATATAT
* * * *
730640 TTATTA-T-ATAATATTATTTATTAATATATCTAATATTATTTCTTAATATTATTTTTTAATATA
1 TTATTATTCTTAATATTATTTATTAATATATCTAATATTATTTATTAATAATATTTATTAATATA
730703 TTATATTGATTATATAT
66 TTATATTGATTATATAT
*
730720 TT-TTATTCATATAATATTATTTATAAATA
1 TTATTATTC-T-TAATATTATTTATTAATA
730749 AAATTATGCA
Statistics
Matches: 93, Mismatches: 7, Indels: 15
0.81 0.06 0.13
Matches are distributed among these distances:
76 5 0.05
77 21 0.23
78 23 0.25
79 9 0.10
80 18 0.19
83 17 0.18
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (82 bp):
TTATTATTCTTAATATTATTTATTAATATATCTAATATTATTTATTAATAATATTTATTAATATA
TTATATTGATTATATAT
Found at i:730675 original size:22 final size:20
Alignment explanation
Indices: 730572--730743 Score: 96
Period size: 22 Copynumber: 8.6 Consensus size: 20
730562 ATTATTCTTT
730572 ATATTATTTATTAATATATTA
1 ATATTATTTATTAAT-TATTA
*
730593 TAGTATTATTTATTAATAATATTT
1 -A-TATTATTTATTAAT--TATTA
*
730617 A-ATTAATTA-TAATTATT-
1 ATATTATTTATTAATTATTA
730634 ATA-TATTTATT-A-TA-TA
1 ATATTATTTATTAATTATTA
730650 ATATTATTTATTAATATATCTA
1 ATATTATTTATTAAT-TAT-TA
*
730672 ATATTATTTCTTAA-TATTA
1 ATATTATTTATTAATTATTA
* * *
730691 TTTTTTAATATATTATATTGATTA
1 -ATATT-ATTTATTA-ATT-ATTA
*
730715 TATATT-TTTATTCA-TA-TA
1 -ATATTATTTATTAATTATTA
730733 ATATTATTTAT
1 ATATTATTTAT
730744 AAATAAAATT
Statistics
Matches: 121, Mismatches: 12, Indels: 38
0.71 0.07 0.22
Matches are distributed among these distances:
15 1 0.01
16 5 0.04
17 20 0.17
18 14 0.12
19 3 0.02
20 13 0.11
21 14 0.12
22 22 0.18
23 16 0.13
24 13 0.11
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (20 bp):
ATATTATTTATTAATTATTA
Found at i:730731 original size:28 final size:25
Alignment explanation
Indices: 730688--730744 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
730678 TTTCTTAATA
*
730688 TTAT-TTTTTAATATATTATATTGAT
1 TTATATTTTTAATATATAATATT-AT
*
730713 TATATATTTTTATTCATATAATATTAT
1 T-TATATTTTTAAT-ATATAATATTAT
730740 TTATA
1 TTATA
730745 AATAAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 1 0.04
26 7 0.26
27 10 0.37
28 9 0.33
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (25 bp):
TTATATTTTTAATATATAATATTAT
Found at i:730739 original size:14 final size:13
Alignment explanation
Indices: 730572--730745 Score: 69
Period size: 13 Copynumber: 14.1 Consensus size: 13
730562 ATTATTCTTT
730572 ATATTATT-TATTA
1 ATATTATTATA-TA
730585 ATA-TATTATAGTA
1 ATATTATTATA-TA
*
730598 TTATTTATTA-ATA
1 ATA-TTATTATATA
*
730611 ATATTTAATTA-ATT
1 ATA-TT-ATTATATA
730625 ATAATTATTATAT-
1 AT-ATTATTATATA
730638 AT-TTATTATATA
1 ATATTATTATATA
730650 ATATTATT-TAT-
1 ATATTATTATATA
* *
730661 -TAATA-TATCTA
1 ATATTATTATATA
*
730672 ATATTATT-TCTTA
1 ATATTATTAT-ATA
* *
730685 ATATTATTTTTTA
1 ATATTATTATATA
730698 ATA-TATTATAT-
1 ATATTATTATATA
730709 -TGATTA-TATAT-
1 AT-ATTATTATATA
*
730720 -TTTTATTCATATA
1 ATATTATT-ATATA
730733 ATATTATT-TATA
1 ATATTATTATATA
730745 A
1 A
730746 ATAAAATTAT
Statistics
Matches: 129, Mismatches: 12, Indels: 41
0.71 0.07 0.23
Matches are distributed among these distances:
9 1 0.01
10 10 0.08
11 17 0.13
12 31 0.24
13 44 0.34
14 20 0.16
15 6 0.05
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (13 bp):
ATATTATTATATA
Found at i:732145 original size:52 final size:52
Alignment explanation
Indices: 732009--732145 Score: 186
Period size: 52 Copynumber: 2.6 Consensus size: 52
731999 AAAAATTTTT
* * * *
732009 TAAGACAAATGAGATTCTTAATAGGTAAGTTTAACTTGCAAGAGAAGAATTC
1 TAAGAGAAATGAAATTCTTAATAGGTAAGTTTGACTTACAAGAGAAGAATTC
* * *
732061 TAAGAGAAAAT-ATATTCTTAATAGATAAGTTTGACTTATAAGAGAAGAATTC
1 TAAGAG-AAATGAAATTCTTAATAGGTAAGTTTGACTTACAAGAGAAGAATTC
*
732113 TAAGAGAAATGAAATTTTTAATAGGTAAGTTTG
1 TAAGAGAAATGAAATTCTTAATAGGTAAGTTTG
732146 TATGATTATA
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
51 4 0.05
52 66 0.89
53 4 0.05
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (52 bp):
TAAGAGAAATGAAATTCTTAATAGGTAAGTTTGACTTACAAGAGAAGAATTC
Found at i:735721 original size:15 final size:16
Alignment explanation
Indices: 735695--735726 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
735685 TATAATTTGA
735695 TTTAATTTTTTTAATT
1 TTTAATTTTTTTAATT
735711 TTTAA-TTTTTTAATT
1 TTTAATTTTTTTAATT
735726 T
1 T
735727 AAAATTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTAATTTTTTTAATT
Done.