Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 143 of 190
Found at i:42138790 original size:25 final size:26
Alignment explanation
Indices: 42138740--42138791 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
42138730 AGTTGTAAAG
42138740 AGAAAATTTTCTAAAGAAATTATTTT
1 AGAAAATTTTCTAAAGAAATTATTTT
* * *
42138766 AGAAAA-TTTCTAGAGATATTTTTTT
1 AGAAAATTTTCTAAAGAAATTATTTT
42138791 A
1 A
42138792 TTTATAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (26 bp):
AGAAAATTTTCTAAAGAAATTATTTT
Found at i:42145807 original size:7 final size:7
Alignment explanation
Indices: 42145787--42145850 Score: 60
Period size: 7 Copynumber: 9.0 Consensus size: 7
42145777 GTTCAAATTC
*
42145787 AAAAAAC
1 AAAAAAG
42145794 AAAAAAG
1 AAAAAAG
42145801 AAAAAAGAG
1 -AAAAA-AG
42145810 AAAAAAG
1 AAAAAAG
42145817 AAAAAA-
1 AAAAAAG
*
42145823 AGAAGAAG
1 A-AAAAAG
42145831 AAAAAAG
1 AAAAAAG
*
42145838 AAAAGA-
1 AAAAAAG
42145844 AAAAAAG
1 AAAAAAG
42145851 GCAGGAGAGG
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
6 6 0.13
7 28 0.60
8 11 0.23
9 2 0.04
ACGTcount: A:0.83, C:0.02, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:42145820 original size:21 final size:22
Alignment explanation
Indices: 42145796--42145848 Score: 83
Period size: 21 Copynumber: 2.5 Consensus size: 22
42145786 CAAAAAACAA
42145796 AAAAGAAAAAAG-AGAAAAAAG
1 AAAAGAAAAAAGAAGAAAAAAG
*
42145817 AAAA-AAAGAAGAAGAAAAAAG
1 AAAAGAAAAAAGAAGAAAAAAG
42145838 AAAAGAAAAAA
1 AAAAGAAAAAA
42145849 AGGCAGGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 6 0.21
21 17 0.61
22 5 0.18
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (22 bp):
AAAAGAAAAAAGAAGAAAAAAG
Found at i:42147345 original size:132 final size:132
Alignment explanation
Indices: 42147079--42148018 Score: 1367
Period size: 132 Copynumber: 7.2 Consensus size: 132
42147069 ACAAACCGGG
* * *
42147079 GAAGACAATAATTCTATCTCCCTGGGTAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCC
1 GAAGCCAATAATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCC
* * * * *
42147144 CT----A--AGTGGAGAAGATTGAAGATGGCAGATTTTACTTCCCTGTGATTACAGTGGAGTATA
66 CTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACA
42147203 TT
131 TT
** * *
42147205 GAAGCCAATAATTCTATCTCATTGGTTGGCAGTGGAATAGATTGAAGACTACAGATCTTATCTCC
1 GAAGCCAATAATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCC
* * * * *
42147270 CTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGGTTTTACCTCTCTGTGATTACAGTGGAGTATA
66 CTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACA
42147335 TT
131 TT
*
42147337 GAAGCCAATAATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAGATTTTATCTCC
1 GAAGCCAATAATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCC
*
42147402 CTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAATGGAGTACA
66 CTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACA
42147467 TT
131 TT
*
42147469 GAAGCCAATAATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAGATTTTATCTCC
1 GAAGCCAATAATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCC
* *
42147534 CTAAGCAATAATGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACA
66 CTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACA
42147599 TT
131 TT
* * *
42147601 GAAGCCAATAATTCTATCTCCCT-G-TGCAGCAGTGGAATAGATTGAAGATTACATATTTTATCT
1 GAAGCCAATAATTCTATCTCCCTGGTTG--GCAGTGGAATAGATTGAAGATTTCAGATCTTATCT
*
42147664 CCCTAAGCAGTAGTGGAGTAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTA
64 CCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTA
*
42147729 TATT
129 CATT
*** * *
42147733 GAAGCCAATAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATATTATCTCC
1 GAAGCCAATAATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCC
* * * *
42147798 CTAAGCAGTAGTGGAACAGATCGAAGATGGTAGATTTTATCTCCCTGTGGTTATAGTGGAGTACA
66 CTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACA
42147863 TT
131 TT
* * * * *
42147865 GAAACCAGTAATTCTATTTCTCTGGTTGGCAGTAGAATAGATTGAAGATTTCAGATCTTATCTCC
1 GAAGCCAATAATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCC
* * ** *
42147930 TTAAGCAGTAGTGGAGTAGATCGAAGATGGC-GAATTTTACCTCCCTGTGACTATAGTGGAGTAC
66 CTAAGCAGTAGTGGAGCAGATCGAAGATGGCAG-ATTTTACCTCCCTGTGGTTACAGTGGAGTAC
42147994 ATT
130 ATT
*
42147997 GAAGCCAGTAATTCTATCTCCC
1 GAAGCCAATAATTCTATCTCCC
42148019 CGACATTGCG
Statistics
Matches: 740, Mismatches: 63, Indels: 16
0.90 0.08 0.02
Matches are distributed among these distances:
126 60 0.08
130 3 0.00
131 2 0.00
132 674 0.91
133 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (132 bp):
GAAGCCAATAATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCC
CTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACA
TT
Found at i:42149476 original size:3 final size:3
Alignment explanation
Indices: 42149468--42149534 Score: 116
Period size: 3 Copynumber: 22.3 Consensus size: 3
42149458 AAGTTAGTAC
* *
42149468 TAT TAT TAT TAT TAT TGT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
42149516 TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
42149535 GTTGTTGTTG
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:42149539 original size:3 final size:3
Alignment explanation
Indices: 42149533--42149600 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
42149523 ATTATTATTA
42149533 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
42149581 TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TT
42149601 ATTATCATCA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:42150006 original size:2 final size:2
Alignment explanation
Indices: 42149999--42150051 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
42149989 ATGCTTACTC
42149999 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42150041 AT AT AT -T AT AT
1 AT AT AT AT AT AT
42150052 TTAATAATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:42150392 original size:15 final size:15
Alignment explanation
Indices: 42150374--42150404 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
42150364 TTATTACTCC
*
42150374 TTTTTGTTCATATTA
1 TTTTTGTTCACATTA
42150389 TTTTTGTTCACATTA
1 TTTTTGTTCACATTA
42150404 T
1 T
42150405 CATATTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.10, G:0.06, T:0.65
Consensus pattern (15 bp):
TTTTTGTTCACATTA
Found at i:42150641 original size:109 final size:109
Alignment explanation
Indices: 42150450--42150770 Score: 522
Period size: 109 Copynumber: 3.0 Consensus size: 109
42150440 ACTTCAAAAA
* * *
42150450 AAAAAATTCAAAGTAAGGCAATATTTTGTGTTTAGAAATTCGAGAAAACGTGCCCTAATGTGCTG
1 AAAAATTTCAAAGTAAGGCAATGTTTTGTGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTG
*
42150515 GGTTTCAATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTT
66 GGTTTCGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTT
* * *
42150559 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGTTG
1 AAAAATTTCAAAGTAAGGCAATGTTTTGTGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTG
42150624 GGTTTCGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTT
66 GGTTTCGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTT
*
42150668 AAAAATTTCAAAGTAAGGCAATGTTTTGTGTTTGGAAATTCGAG-GAACGTGCCCTAATGTGCTG
1 AAAAATTTCAAAGTAAGGCAATGTTTTGTGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTG
* * *
42150732 AGTTTCGA--TTTCTCGTTTAACCAAATAGCCAAATATCCT
66 GGTTTCGATTTTTCTCGTTCAACCAAATAGCTAAATATCCT
42150771 CTTGAATTTT
Statistics
Matches: 198, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
106 29 0.15
108 25 0.13
109 144 0.73
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (109 bp):
AAAAATTTCAAAGTAAGGCAATGTTTTGTGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTG
GGTTTCGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTT
Found at i:42152124 original size:9 final size:9
Alignment explanation
Indices: 42152112--42152156 Score: 58
Period size: 8 Copynumber: 5.1 Consensus size: 9
42152102 TGTAAGTAAT
42152112 TTATTTAAA
1 TTATTTAAA
42152121 TTA-TTAAA
1 TTATTTAAA
*
42152129 ATATATTAAA
1 TTAT-TTAAA
42152139 TTATTTAAA
1 TTATTTAAA
42152148 -TATTTAAA
1 TTATTTAAA
42152156 T
1 T
42152157 ATTGCAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
8 15 0.48
9 8 0.26
10 8 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
TTATTTAAA
Found at i:42152139 original size:18 final size:17
Alignment explanation
Indices: 42152113--42152156 Score: 70
Period size: 18 Copynumber: 2.5 Consensus size: 17
42152103 GTAAGTAATT
42152113 TATTTAAATTATTAAAA
1 TATTTAAATTATTAAAA
*
42152130 TATATTAAATTATTTAAA
1 TAT-TTAAATTATTAAAA
42152148 TATTTAAAT
1 TATTTAAAT
42152157 ATTGCAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTTAAATTATTAAAA
Found at i:42152151 original size:8 final size:8
Alignment explanation
Indices: 42152113--42152159 Score: 58
Period size: 9 Copynumber: 5.5 Consensus size: 8
42152103 GTAAGTAATT
42152113 TATTTAAA
1 TATTTAAA
*
42152121 TTATTAAAA
1 -TATTTAAA
42152130 TATATTAAA
1 TAT-TTAAA
42152139 TTATTTAAA
1 -TATTTAAA
42152148 TATTTAAA
1 TATTTAAA
42152156 TATT
1 TATT
42152160 GCAATAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
8 15 0.44
9 16 0.47
10 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (8 bp):
TATTTAAA
Found at i:42158619 original size:21 final size:21
Alignment explanation
Indices: 42158595--42158657 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
42158585 AATATTTTTT
42158595 AATATTAAAAAGATATTATAA
1 AATATTAAAAAGATATTATAA
* *
42158616 AATATT-AAAATA-ATTACTAG
1 AATATTAAAAAGATATTA-TAA
42158636 AA-ATTATAAAAG-TATTATAA
1 AATATTA-AAAAGATATTATAA
42158656 AA
1 AA
42158658 ATTTTAGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
19 7 0.21
20 13 0.38
21 14 0.41
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (21 bp):
AATATTAAAAAGATATTATAA
Found at i:42158670 original size:30 final size:29
Alignment explanation
Indices: 42158609--42158681 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 29
42158599 TTAAAAAGAT
42158609 ATTATAAAATATTAAAATAATTACTAGAA
1 ATTATAAAATATTAAAATAATTACTAGAA
*
42158638 ATTATAAAAGTATTATAAA-AATT-TTAGAAA
1 ATTATAAAA-TATTA-AAATAATTACTAG-AA
*
42158668 ATTATAAAAAATTA
1 ATTATAAAATATTA
42158682 GAAACTTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 16 0.41
30 20 0.51
31 3 0.08
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (29 bp):
ATTATAAAATATTAAAATAATTACTAGAA
Found at i:42158673 original size:19 final size:19
Alignment explanation
Indices: 42158649--42158697 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
42158639 TTATAAAAGT
42158649 ATTATAAAAATTTTAGAAA
1 ATTATAAAAATTTTAGAAA
*
42158668 ATTATAAAAA-ATTAGAAA
1 ATTATAAAAATTTTAGAAA
*
42158686 CTTATAAAAATT
1 ATTATAAAAATT
42158698 ATTTTTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 16 0.62
19 10 0.38
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (19 bp):
ATTATAAAAATTTTAGAAA
Found at i:42159855 original size:20 final size:20
Alignment explanation
Indices: 42159825--42159862 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42159815 AAGTGTGAAG
42159825 TATTATTGGATTGAATTGAGT
1 TATTATTGGATT-AATTGAGT
42159846 TATT-TTGGATTAATTGA
1 TATTATTGGATTAATTGA
42159863 TTGTGCATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (20 bp):
TATTATTGGATTAATTGAGT
Found at i:42160776 original size:24 final size:24
Alignment explanation
Indices: 42160739--42160790 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
42160729 TGGAGGTAGG
42160739 ATCTATGACCGCATCTATATCTGA
1 ATCTATGACCGCATCTATATCTGA
* * * *
42160763 ATCTATGTCTGCATTTGTATCTGA
1 ATCTATGACCGCATCTATATCTGA
42160787 ATCT
1 ATCT
42160791 GAATATGCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.40
Consensus pattern (24 bp):
ATCTATGACCGCATCTATATCTGA
Found at i:42160799 original size:24 final size:24
Alignment explanation
Indices: 42160772--42160817 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
42160762 AATCTATGTC
* *
42160772 TGCATTTGTATCTGAATCTGAATA
1 TGCATCTGTATCTGAACCTGAATA
*
42160796 TGCATCTGTATTTGAACCTGAA
1 TGCATCTGTATCTGAACCTGAA
42160818 AAATACATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.39
Consensus pattern (24 bp):
TGCATCTGTATCTGAACCTGAATA
Found at i:42171505 original size:2 final size:2
Alignment explanation
Indices: 42171498--42171527 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
42171488 GCAAAGAAGC
42171498 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42171528 GCATACAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42174921 original size:32 final size:32
Alignment explanation
Indices: 42174868--42174946 Score: 113
Period size: 32 Copynumber: 2.4 Consensus size: 32
42174858 CCACTTGCCC
* *
42174868 GTGTAGGCCCACACACTCTACTTGGCCTAGCCT
1 GTGT-GGCCCACACGCCCTACTTGGCCTAGCCT
*
42174901 GTGTGGCCCACACGCCCTACTTGGCTTAGCCT
1 GTGTGGCCCACACGCCCTACTTGGCCTAGCCT
*
42174933 GTGTGGCCTACACG
1 GTGTGGCCCACACG
42174947 GCCACACCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 38 0.90
33 4 0.10
ACGTcount: A:0.15, C:0.35, G:0.25, T:0.24
Consensus pattern (32 bp):
GTGTGGCCCACACGCCCTACTTGGCCTAGCCT
Found at i:42186801 original size:20 final size:20
Alignment explanation
Indices: 42186751--42186790 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
42186741 CACATTGGTG
* *
42186751 AATTATGTAGCGGCTGAAAC
1 AATTTTGTAGCGGCCGAAAC
42186771 AATTTTGTAGCGGCCGAAAC
1 AATTTTGTAGCGGCCGAAAC
42186791 GTTTTGTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (20 bp):
AATTTTGTAGCGGCCGAAAC
Found at i:42191269 original size:18 final size:17
Alignment explanation
Indices: 42191246--42191287 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
42191236 AGTAGTATAG
42191246 GTTCGC-TAGATACCAATA
1 GTTCGCATA-ATACCAA-A
*
42191264 GTTCGCATAATACCTAA
1 GTTCGCATAATACCAAA
42191281 GTTCGCA
1 GTTCGCA
42191288 ACAGGCAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 8 0.36
18 12 0.55
19 2 0.09
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (17 bp):
GTTCGCATAATACCAAA
Found at i:42192522 original size:18 final size:19
Alignment explanation
Indices: 42192501--42192537 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
42192491 TTTTAAAATA
42192501 TATAAA-AT-TTGAAATTTT
1 TATAAATATATTG-AATTTT
42192519 TATAAATATATTGAATTTT
1 TATAAATATATTGAATTTT
42192538 AAAAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
19 8 0.47
20 3 0.18
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
TATAAATATATTGAATTTT
Found at i:42192538 original size:18 final size:19
Alignment explanation
Indices: 42192516--42192554 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
42192506 AATTTGAAAT
*
42192516 TTTTATAAA-TATATTGAA
1 TTTTAAAAATTATATTGAA
*
42192534 TTTTAAAAATTATTTTGAA
1 TTTTAAAAATTATATTGAA
42192553 TT
1 TT
42192555 ATTTTTGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TTTTAAAAATTATATTGAA
Found at i:42194988 original size:4 final size:4
Alignment explanation
Indices: 42194981--42195007 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
42194971 AAATAAATAA
42194981 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
42195008 AATAAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:42199002 original size:12 final size:12
Alignment explanation
Indices: 42198969--42199003 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
42198959 TGCTCATCCA
42198969 CCGCATCCAGCG
1 CCGCATCCAGCG
* *
42198981 CCACAACCAGCG
1 CCGCATCCAGCG
42198993 CCGCATCCAGC
1 CCGCATCCAGC
42199004 TGCACAGGTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.23, C:0.51, G:0.20, T:0.06
Consensus pattern (12 bp):
CCGCATCCAGCG
Found at i:42199627 original size:13 final size:14
Alignment explanation
Indices: 42199609--42199637 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
42199599 CTAACCCCTC
42199609 AAAA-TTTTTATTT
1 AAAATTTTTTATTT
42199622 AAAATTTTTTATTT
1 AAAATTTTTTATTT
42199636 AA
1 AA
42199638 GTCATCTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
AAAATTTTTTATTT
Found at i:42201651 original size:18 final size:17
Alignment explanation
Indices: 42201625--42201666 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
42201615 TCATATTCCT
*
42201625 TTTTA-TATAGTTTTATA
1 TTTTATTATAATTTT-TA
42201642 TTTTATTATAATTTTTA
1 TTTTATTATAATTTTTA
42201659 TTATTATT
1 TT-TTATT
42201667 GTCATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTTATTATAATTTTTA
Found at i:42213196 original size:44 final size:44
Alignment explanation
Indices: 42213128--42213563 Score: 480
Period size: 44 Copynumber: 9.9 Consensus size: 44
42213118 TTATCGTGGA
* * * **
42213128 AAATTTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAAGCCAC
1 AAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTTAC
* *
42213172 ATATCTTATCTCCCTGAAGTTGCAGTGGAG-ATGATTGAAGTTAC
1 AAATCTTATCTCCCTAAAGTTGCAGTGGAGCA-GATTGAAGTTAC
* * * * **
42213216 AAATTTTATCTCCTTGAAGTTGTAGTGGAGCAGATTGAAAATAGC
1 AAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTTA-C
* * *
42213261 AAATCTTATCTCTCTAAAGTTACAGTGGAACAGATTGAAGTTAC
1 AAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTTAC
* * * * *
42213305 AAATCTTATCTTCCTAAAGTTGAAATGGAGAAAATTGAAGTTAC
1 AAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTTAC
* * *
42213349 AAATCTTATCTCCTTGAAGTTGCAGTGGAGTAGATTGAAGTTAC
1 AAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTTAC
42213393 AAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTTAC
1 AAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTTAC
* * * ***
42213437 AAATCTCATCTCCTTAAAGTTGCAGTGGAGTAGATTGAAGACGC
1 AAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTTAC
* * * *
42213481 AAATCTTATCTCCCTAAAGTTGCAGTGGAGTAGGTTAAAGCTAC
1 AAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTTAC
* * * * *
42213525 AAATC-TAGCCTCTCTAAAGTTGTAATGGAGTAGATTGAA
1 AAATCTTA-TCTCCCTAAAGTTGCAGTGGAGCAGATTGAA
42213564 CAACAAATTC
Statistics
Matches: 329, Mismatches: 59, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
43 3 0.01
44 290 0.88
45 36 0.11
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (44 bp):
AAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTTAC
Found at i:42215165 original size:17 final size:16
Alignment explanation
Indices: 42215138--42215169 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
42215128 TTACAAACTG
42215138 TTTTATTTATTTATTA
1 TTTTATTTATTTATTA
42215154 TTTTATTTTATTTATT
1 TTTTA-TTTATTTATT
42215170 TAACTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTATTTATTTATTA
Found at i:42215287 original size:3 final size:3
Alignment explanation
Indices: 42215232--42215272 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
42215222 TTATATTTTG
* * *
42215232 TTA TCA TTA TTA TTA TTG TTA TTA TTA TCA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
42215273 TTTTCCTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:42215768 original size:12 final size:12
Alignment explanation
Indices: 42215751--42215831 Score: 51
Period size: 12 Copynumber: 6.4 Consensus size: 12
42215741 AAATTAAAGT
42215751 TAATATATATTA
1 TAATATATATTA
*
42215763 TAATATATTTTA
1 TAATATATATTA
*
42215775 CTTAAGTAT-TAAGTA
1 --TAA-TATAT-ATTA
42215790 T-ATATATA-TA
1 TAATATATATTA
*
42215800 TATATATTTATATA
1 TA-ATATATAT-TA
42215814 TATATATATATTA
1 TA-ATATATATTA
42215827 TAATA
1 TAATA
42215832 ATAAATGAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
10 3 0.05
11 4 0.07
12 22 0.40
13 5 0.09
14 16 0.29
15 5 0.09
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (12 bp):
TAATATATATTA
Found at i:42215795 original size:2 final size:2
Alignment explanation
Indices: 42215788--42215828 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
42215778 AAGTATTAAG
*
42215788 TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42215829 ATAATAAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:42215906 original size:22 final size:22
Alignment explanation
Indices: 42215866--42215920 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
42215856 AAAAAATAAG
* *
42215866 AAGAGAGAAA-GGAAGGAAAGGA
1 AAGAGAAAAACGGAAAGAAA-GA
42215888 AA-AGAAAAACGGAAAGAAAGA
1 AAGAGAAAAACGGAAAGAAAGA
42215909 AATGAGAAAAAC
1 AA-GAGAAAAAC
42215921 AAGGCTAGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 10 0.36
22 10 0.36
23 8 0.29
ACGTcount: A:0.65, C:0.04, G:0.29, T:0.02
Consensus pattern (22 bp):
AAGAGAAAAACGGAAAGAAAGA
Found at i:42217002 original size:2 final size:2
Alignment explanation
Indices: 42216950--42216991 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
42216940 GATTGCATTG
42216950 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42216992 TATGAATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42222934 original size:4 final size:4
Alignment explanation
Indices: 42222927--42222968 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
42222917 TATTAAATTA
* * *
42222927 ATAT ATAT ATAT ATAT ATAT ATAT ATGT ATGT ATAT GTAT AT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT AT
42222969 GTATTCTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:42222942 original size:10 final size:10
Alignment explanation
Indices: 42222927--42222968 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
42222917 TATTAAATTA
42222927 ATATATATAT
1 ATATATATAT
42222937 ATATATATAT
1 ATATATATAT
*
42222947 ATATATGTAT
1 ATATATATAT
* *
42222957 GTATATGTAT
1 ATATATATAT
42222967 AT
1 AT
42222969 GTATTCTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (10 bp):
ATATATATAT
Found at i:42222972 original size:6 final size:6
Alignment explanation
Indices: 42222927--42222968 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
42222917 TATTAAATTA
* * *
42222927 ATATAT ATATAT ATATAT ATATAT ATGTAT GTATAT GTATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
42222969 GTATTCTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (6 bp):
ATATAT
Found at i:42225016 original size:2 final size:2
Alignment explanation
Indices: 42225009--42225047 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
42224999 TGGTTGGGTG
42225009 AT AT AT AT AT 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 AT AT AT AT AT A
42225048 CACATAAGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42226495 original size:21 final size:20
Alignment explanation
Indices: 42226468--42226521 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
42226458 GAAAGCCAAT
*
42226468 GAAAAGAGAAAGGAAGGAAA
1 GAAAAGAGAAAGGAAAGAAA
*
42226488 GAAAAAGAAAAAGGGAAAGAAA
1 G-AAAAGAGAAA-GGAAAGAAA
*
42226510 GAAAGGAGAAAG
1 GAAAAGAGAAAG
42226522 ACAAGACTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 2 0.07
21 17 0.61
22 9 0.32
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (20 bp):
GAAAAGAGAAAGGAAAGAAA
Found at i:42226509 original size:22 final size:21
Alignment explanation
Indices: 42226469--42226513 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
42226459 AAAGCCAATG
* *
42226469 AAAAGAGAAAGGAAGGAAAGA
1 AAAAGAAAAAGGAAAGAAAGA
42226490 AAAAGAAAAAGGGAAAGAAAGA
1 AAAAGAAAAA-GGAAAGAAAGA
42226512 AA
1 AA
42226514 GGAGAAAGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (21 bp):
AAAAGAAAAAGGAAAGAAAGA
Found at i:42229435 original size:24 final size:24
Alignment explanation
Indices: 42229403--42229450 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
42229393 CACCAGAATG
42229403 GCCCAATAGCAATTGGGGTTTATT
1 GCCCAATAGCAATTGGGGTTTATT
42229427 GCCCAATAGCAATTGGGGTTTATT
1 GCCCAATAGCAATTGGGGTTTATT
42229451 AAACAGTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (24 bp):
GCCCAATAGCAATTGGGGTTTATT
Found at i:42230309 original size:18 final size:20
Alignment explanation
Indices: 42230254--42230312 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 20
42230244 ACCTTTACAC
42230254 CACATTGTGGATAAACCACT
1 CACATTGTGGATAAACCACT
* *
42230274 CATCATTGTGTATGAACCACT
1 CA-CATTGTGGATAAACCACT
42230295 C-C-TTGTGGATAAACCACT
1 CACATTGTGGATAAACCACT
42230313 AGTAAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 14 0.41
19 1 0.03
20 2 0.06
21 17 0.50
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (20 bp):
CACATTGTGGATAAACCACT
Found at i:42234598 original size:24 final size:24
Alignment explanation
Indices: 42234571--42234644 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
42234561 ATGGAAAATT
42234571 GTGAAAAGTAGGTATGGTGTTTCA
1 GTGAAAAGTAGGTATGGTGTTTCA
* * *
42234595 GTGAAGAA--AGCCATATTGAG-TT--
1 GTGAA-AAGTAG--GTATGGTGTTTCA
42234617 GTGAAAAGTAGGTATGGTGTTTCA
1 GTGAAAAGTAGGTATGGTGTTTCA
42234641 GTGA
1 GTGA
42234645 TGAAAACCAT
Statistics
Matches: 36, Mismatches: 6, Indels: 16
0.62 0.10 0.28
Matches are distributed among these distances:
21 7 0.19
22 7 0.19
23 4 0.11
24 11 0.31
25 7 0.19
ACGTcount: A:0.31, C:0.05, G:0.32, T:0.31
Consensus pattern (24 bp):
GTGAAAAGTAGGTATGGTGTTTCA
Found at i:42234621 original size:46 final size:46
Alignment explanation
Indices: 42234569--42234754 Score: 309
Period size: 46 Copynumber: 4.0 Consensus size: 46
42234559 CCATGGAAAA
* *
42234569 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAGCCATATTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
*
42234615 TTGTGAAAAGTAGGTATGGTGTTTCAGTGATGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
*
42234661 TTGTGAAAAGTAGGTATGGTGTTTCAGTGATGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
* * *
42234707 TTGTGAAAAGTAGGTATGGTATTTCAATGAAGGAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
42234753 TT
1 TT
42234755 ATAGCATTGT
Statistics
Matches: 133, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 133 1.00
ACGTcount: A:0.33, C:0.08, G:0.28, T:0.31
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
Found at i:42239594 original size:21 final size:18
Alignment explanation
Indices: 42239551--42239599 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 18
42239541 TTTTAAATTC
*
42239551 TAAAAATGAATAAAATAT
1 TAAAAATAAATAAAATAT
42239569 TAAAAATAATATAAAATCATT
1 TAAAAATAA-ATAAAAT-A-T
42239590 TAAAAATAAA
1 TAAAAATAAA
42239600 AATAGAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 8 0.30
19 7 0.26
20 2 0.07
21 10 0.37
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
TAAAAATAAATAAAATAT
Found at i:42240049 original size:48 final size:48
Alignment explanation
Indices: 42239997--42240102 Score: 140
Period size: 48 Copynumber: 2.2 Consensus size: 48
42239987 GGAGGCGTTT
** * * * * *
42239997 GTGGGTTCACAATAGGTTGTGATGGTGGTGGTAGAATCGATGGTGTTG
1 GTGGGTTCACAATAGGAAGCGATAGAGGTGGTAGAACCGATGGTGTTA
*
42240045 GTGGGTTCACAATTGGAAGCGATAGAGGTGGTAGAACCGATGGTGTTA
1 GTGGGTTCACAATAGGAAGCGATAGAGGTGGTAGAACCGATGGTGTTA
42240093 GTGGGTTCAC
1 GTGGGTTCAC
42240103 TATTGCTGGA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.22, C:0.09, G:0.40, T:0.29
Consensus pattern (48 bp):
GTGGGTTCACAATAGGAAGCGATAGAGGTGGTAGAACCGATGGTGTTA
Found at i:42247350 original size:6 final size:6
Alignment explanation
Indices: 42247341--42247379 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
42247331 GCCTCCGCCT
42247341 CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CAT
1 CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CAT
42247380 ACTCTTCTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.49, G:0.00, T:0.18
Consensus pattern (6 bp):
CATCAC
Found at i:42250028 original size:127 final size:126
Alignment explanation
Indices: 42249751--42250193 Score: 629
Period size: 126 Copynumber: 3.5 Consensus size: 126
42249741 GATAAAATCA
* * * * * *
42249751 AAGCAGGATGATTTATCAGAAGGATTTTTGAAGTCGCGCCCACGTGAACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* *
42249816 AGGTCCTAAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTTT-AAAAAACGCTTC
66 AGGTCCTAAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAACGCTTC
* * *
42249876 AAGCAAGATGCTTTATGAGAAGAATTTGTGAAATCACGCCCTCGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * * *
42249941 TGGTCCTGGAAGAAATAATTTTGAGTTGACGTTTTTAAGCAAATAGTTTAAAAAAACGCTTC
66 AGGTCCT-AAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAACGCTTC
* *
42250003 AAGCAGGATGCTTTATAAGAAGAATTTGTGAAGTCGCGCCCACGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * *
42250068 AGGTCCTAAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAACAACGCTGC
66 AGGTCCTAAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAACGCTTC
* * * *
42250129 AAGCAGCATGCTATT-TGAGAAGAATTTGTGAAATTGTGCCCTCGTGGACGCGCTTTTGCTACAG
1 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAG
42250193 T
65 T
42250194 TGGGGGGGGC
Statistics
Matches: 280, Mismatches: 35, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
125 62 0.22
126 138 0.49
127 80 0.29
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (126 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTAAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAACGCTTC
Found at i:42259966 original size:21 final size:21
Alignment explanation
Indices: 42259941--42259982 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
42259931 CTTTTGCGTA
*
42259941 AAATATGAATTGGATTGAATT
1 AAATATGAATTGGATTAAATT
*
42259962 AAATATGAATTGTATTAAATT
1 AAATATGAATTGGATTAAATT
42259983 GAGTTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.40
Consensus pattern (21 bp):
AAATATGAATTGGATTAAATT
Found at i:42265785 original size:25 final size:25
Alignment explanation
Indices: 42265699--42265792 Score: 93
Period size: 25 Copynumber: 3.8 Consensus size: 25
42265689 AGCAATAAAC
*
42265699 GGGAAGCTCCT-TCGAGCTGAATAAT
1 GGGAAGCTCATAT-GAGCTGAATAAT
* * *
42265724 GGGAAGCTCATGTGAGCTAAATAACA
1 GGGAAGCTCATATGAGCTGAATAA-T
* *
42265750 GGG-AGCTCATATGAGCTGAGTATT
1 GGGAAGCTCATATGAGCTGAATAAT
*
42265774 GGGAAGCTCATAAGAGCTG
1 GGGAAGCTCATATGAGCTG
42265793 TGGTGTGTCC
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
24 3 0.05
25 50 0.88
26 4 0.07
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.22
Consensus pattern (25 bp):
GGGAAGCTCATATGAGCTGAATAAT
Found at i:42267173 original size:32 final size:32
Alignment explanation
Indices: 42267132--42267196 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
42267122 ACCATTGTTG
42267132 ACCCACTAAGGGAATGACATGTGTACAGGGGT
1 ACCCACTAAGGGAATGACATGTGTACAGGGGT
42267164 ACCCACTAAGGGAATGACATGTGTACAGGGGT
1 ACCCACTAAGGGAATGACATGTGTACAGGGGT
42267196 A
1 A
42267197 GGGAAAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.32, C:0.18, G:0.31, T:0.18
Consensus pattern (32 bp):
ACCCACTAAGGGAATGACATGTGTACAGGGGT
Found at i:42268828 original size:19 final size:22
Alignment explanation
Indices: 42268804--42268850 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
42268794 AAAAATATCT
42268804 TTATT-AAAT-TAAT-TAAAAA
1 TTATTAAAATATAATATAAAAA
42268823 TTATTAAAATATAATATAAAAA
1 TTATTAAAATATAATATAAAAA
42268845 TCTATT
1 T-TATT
42268851 TTCATTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.21
20 4 0.17
21 4 0.17
22 7 0.29
23 4 0.17
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TTATTAAAATATAATATAAAAA
Found at i:42280517 original size:20 final size:21
Alignment explanation
Indices: 42280492--42280530 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
42280482 TCCCCATGTG
42280492 GCCCACAC-AGCTTGACCCAA
1 GCCCACACAAGCTTGACCCAA
*
42280512 GCCCACCCAAGCTTGACCC
1 GCCCACACAAGCTTGACCC
42280531 TCGGAGTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.26, C:0.49, G:0.15, T:0.10
Consensus pattern (21 bp):
GCCCACACAAGCTTGACCCAA
Found at i:42283506 original size:42 final size:42
Alignment explanation
Indices: 42283431--42283785 Score: 493
Period size: 42 Copynumber: 8.3 Consensus size: 42
42283421 ACGTCGCTAA
* * *
42283431 CTTTTGCGGCGCTTACAGAAAAAAACGCCGCTAAAGATAATGTT
1 CTTTAGCGGCGCTT--AGGAAAAAACGCCGCTAAAGATCATGTT
*
42283475 CTTTAGCGGCGCTTAAGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
42283517 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGG-AAAAAACGCCGCTAAAGATCATGTT
42283560 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
42283602 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGG-AAAAAACGCCGCTAAAGATCATGTT
*
42283645 CTTTAGCGGCGCTTAGGAAAAAACGCCACTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
* * * *
42283687 CTTTAGCGGCGCTTTGGAAGAAAACTCCTCTAAA-AGTAATGTT
1 CTTTAGCGGCGCTTAGGAA-AAAACGCCGCTAAAGA-TCATGTT
* **
42283730 CTATAGCGGCGCTT-GTTCAAAAACGCCGCTAAA-AGT-AGTGTT
1 CTTTAGCGGCGCTTAG-GAAAAAACGCCGCTAAAGA-TCA-TGTT
42283772 CTTTAGCGGCGCTT
1 CTTTAGCGGCGCTT
42283786 GTTTCACAAA
Statistics
Matches: 289, Mismatches: 16, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
41 1 0.00
42 159 0.55
43 116 0.40
44 13 0.04
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
Found at i:42283550 original size:85 final size:85
Alignment explanation
Indices: 42283431--42283785 Score: 520
Period size: 85 Copynumber: 4.2 Consensus size: 85
42283421 ACGTCGCTAA
* * *
42283431 CTTTTGCGGCGCTTACAGAAAAAAACGCCGCTAAAGATAATGTTCTTTAGCGGCGCTTAAGAAAA
1 CTTTAGCGGCGCTTA-GGAAAAAAACGCCGCTAAAGATAATGTTCTTTAGCGGCGCTTAGGAAAA
42283496 AACGCCGCTAAAGATCATGTT
65 AACGCCGCTAAAGATCATGTT
*
42283517 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAA
1 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAGATAATGTTCTTTAGCGGCGCTTAGGAAAAA
42283582 ACGCCGCTAAAGATCATGTT
66 ACGCCGCTAAAGATCATGTT
*
42283602 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAA
1 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAGATAATGTTCTTTAGCGGCGCTTAGGAAAAA
*
42283667 ACGCCACTAAAGATCATGTT
66 ACGCCGCTAAAGATCATGTT
* * * * * **
42283687 CTTTAGCGGCGCTTTGGAAGAAAACTCCTCTAAA-AGTAATGTTCTATAGCGGCGCTT-GTTCAA
1 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAGA-TAATGTTCTTTAGCGGCGCTTAG-GAAA
42283750 AAACGCCGCTAAA-AGT-AGTGTT
64 AAACGCCGCTAAAGA-TCA-TGTT
42283772 CTTTAGCGGCGCTT
1 CTTTAGCGGCGCTT
42283786 GTTTCACAAA
Statistics
Matches: 251, Mismatches: 14, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
84 4 0.02
85 233 0.93
86 14 0.06
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (85 bp):
CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAGATAATGTTCTTTAGCGGCGCTTAGGAAAAA
ACGCCGCTAAAGATCATGTT
Found at i:42284263 original size:21 final size:21
Alignment explanation
Indices: 42284219--42284263 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
42284209 GCTTCTATCG
* * *
42284219 CTGCTTCTCTCGCTGCGGGAT
1 CTGCTTCCCTCGCTGCCGCAT
*
42284240 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCCCTCGCTGCCGCAT
42284261 CTG
1 CTG
42284264 ATTTAAGTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.02, C:0.42, G:0.24, T:0.31
Consensus pattern (21 bp):
CTGCTTCCCTCGCTGCCGCAT
Found at i:42289851 original size:25 final size:23
Alignment explanation
Indices: 42289823--42289956 Score: 83
Period size: 25 Copynumber: 5.4 Consensus size: 23
42289813 CATGTAAGTA
*
42289823 ATGTAAGCTATGTAAGTAATGTATT
1 ATGTAAGTTATGT-A-TAATGTATT
* *
42289848 ATGTAAGTTGTGTACTACAT-CATT
1 ATGTAAGTTATGTA-TA-ATGTATT
* *
42289872 ATGTGAGTTGTGTATAATGTAAGTT
1 ATGTAAGTTATGTATAATGT-A-TT
* *
42289897 AAG-AAGGTTATGTATAATGTAAGTA
1 ATGTAA-GTTATGTATAATGT-A-TT
*
42289922 ATGTAAGCTATGTAAGTAATGTATT
1 ATGTAAGTTATGT-A-TAATGTATT
42289947 ATGTAAGTTA
1 ATGTAAGTTA
42289957 AGAAGGTTAT
Statistics
Matches: 87, Mismatches: 14, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
22 2 0.02
23 2 0.02
24 21 0.24
25 52 0.60
26 4 0.05
27 6 0.07
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATGTAAGTTATGTATAATGTATT
Found at i:42289853 original size:34 final size:34
Alignment explanation
Indices: 42289814--42289954 Score: 114
Period size: 34 Copynumber: 4.2 Consensus size: 34
42289804 TGTATGCCCC
42289814 ATGTAAGTAATGTAAGCTATGTAAGTAATGTATT
1 ATGTAAGTAATGTAAGCTATGTAAGTAATGTATT
** ** * *
42289848 ATGTAAGTTGTGT-A-CTACATCA-TTATGTGAGTT
1 ATGTAAGTAATGTAAGCTATGTAAGTAATGT-A-TT
* * * * *
42289881 GTGT-A-TAATGTAAGTTAAG-AAGGTTATGTATA
1 ATGTAAGTAATGTAAGCTATGTAA-GTAATGTATT
42289913 ATGTAAGTAATGTAAGCTATGTAAGTAATGTATT
1 ATGTAAGTAATGTAAGCTATGTAAGTAATGTATT
42289947 ATGTAAGT
1 ATGTAAGT
42289955 TAAGAAGGTT
Statistics
Matches: 79, Mismatches: 19, Indels: 18
0.68 0.16 0.16
Matches are distributed among these distances:
31 9 0.11
32 13 0.16
33 10 0.13
34 45 0.57
35 2 0.03
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.39
Consensus pattern (34 bp):
ATGTAAGTAATGTAAGCTATGTAAGTAATGTATT
Found at i:42289861 original size:16 final size:16
Alignment explanation
Indices: 42289814--42289855 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 16
42289804 TGTATGCCCC
*
42289814 ATGTAAGTAATGTAAGCT
1 ATGTAAGTAATGT-A-TT
42289832 ATGTAAGTAATGTATT
1 ATGTAAGTAATGTATT
42289848 ATGTAAGT
1 ATGTAAGT
42289856 TGTGTACTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.39
17 1 0.04
18 13 0.57
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.38
Consensus pattern (16 bp):
ATGTAAGTAATGTATT
Found at i:42289923 original size:9 final size:9
Alignment explanation
Indices: 42289888--42290304 Score: 305
Period size: 9 Copynumber: 47.2 Consensus size: 9
42289878 GTTGTGTATA
42289888 ATGTAAGTT
1 ATGTAAGTT
*
42289897 AAG-AAGGTT
1 ATGTAA-GTT
*
42289906 ATGT-A-TA
1 ATGTAAGTT
*
42289913 ATGTAAGTA
1 ATGTAAGTT
*
42289922 ATGTAAGCT
1 ATGTAAGTT
*
42289931 ATGTAAGTA
1 ATGTAAGTT
42289940 ATGT-A-TT
1 ATGTAAGTT
42289947 ATGTAAGTT
1 ATGTAAGTT
*
42289956 AAG-AAGGTT
1 ATGTAA-GTT
*
42289965 ATGT-A-TA
1 ATGTAAGTT
42289972 ATGTAAGTT
1 ATGTAAGTT
*
42289981 AAT-TAATTT
1 -ATGTAAGTT
42289990 ATGTAAGTT
1 ATGTAAGTT
42289999 ATGTAAGTT
1 ATGTAAGTT
* *
42290008 ATTTAATTTAT
1 ATGTAA-GT-T
42290019 ATGTAAGTT
1 ATGTAAGTT
*
42290028 ATGTAATTT
1 ATGTAAGTT
42290037 ATGTAAGTT
1 ATGTAAGTT
42290046 ATGTAAGTT
1 ATGTAAGTT
42290055 ATGTAAGTT
1 ATGTAAGTT
* *
42290064 ATTTAATTT
1 ATGTAAGTT
*
42290073 ACT-TAATTT
1 A-TGTAAGTT
*
42290082 ACT-TAATTT
1 A-TGTAAGTT
42290091 ATGTAAGTT
1 ATGTAAGTT
42290100 ATGTAAGTT
1 ATGTAAGTT
* *
42290109 ATTTAATTT
1 ATGTAAGTT
42290118 ATGTAAGTT
1 ATGTAAGTT
*
42290127 ATGTAACTT
1 ATGTAAGTT
*
42290136 ATGTAACTT
1 ATGTAAGTT
* *
42290145 ATTTAATTT
1 ATGTAAGTT
42290154 ACT-TAA--T
1 A-TGTAAGTT
*
42290161 -T-TAATTT
1 ATGTAAGTT
*
42290168 ACT-TAATTT
1 A-TGTAAGTT
42290177 ATGTAAGTT
1 ATGTAAGTT
42290186 ATGTAAGTT
1 ATGTAAGTT
* **
42290195 ACGCCAGTT
1 ATGTAAGTT
* *
42290204 ATTTAATTT
1 ATGTAAGTT
*
42290213 TTGTAAGTT
1 ATGTAAGTT
42290222 ATGTAAGTT
1 ATGTAAGTT
*
42290231 ACT-TAATTT
1 A-TGTAAGTT
42290240 ATGTAAGTT
1 ATGTAAGTT
42290249 ATGTAAGTT
1 ATGTAAGTT
42290258 ATGTAAGTT
1 ATGTAAGTT
* *
42290267 ATTTAATTT
1 ATGTAAGTT
*
42290276 TTGTAAGTT
1 ATGTAAGTT
42290285 ATGTAA-TT
1 ATGTAAGTT
42290293 AATGTAAGTT
1 -ATGTAAGTT
42290303 AT
1 AT
42290305 TTAATTTGTG
Statistics
Matches: 331, Mismatches: 51, Indels: 52
0.76 0.12 0.12
Matches are distributed among these distances:
5 4 0.01
7 17 0.05
8 15 0.05
9 280 0.85
10 9 0.03
11 6 0.02
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.48
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:42289945 original size:59 final size:59
Alignment explanation
Indices: 42289882--42290003 Score: 192
Period size: 59 Copynumber: 2.1 Consensus size: 59
42289872 ATGTGAGTTG
42289882 TGTATAATGTAAGTTAAGAAGGTTATGTATAATGTAAG-TAATGTAAGCTATGTAAGTAA
1 TGTATAATGTAAGTTAAGAAGGTTATGTATAATGTAAGTTAAT-TAAGCTATGTAAGTAA
* ** *
42289941 TGTATTATGTAAGTTAAGAAGGTTATGTATAATGTAAGTTAATTAATTTATGTAAGTTA
1 TGTATAATGTAAGTTAAGAAGGTTATGTATAATGTAAGTTAATTAAGCTATGTAAGTAA
42290000 TGTA
1 TGTA
42290004 AGTTATTTAA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
59 54 0.93
60 4 0.07
ACGTcount: A:0.39, C:0.01, G:0.20, T:0.40
Consensus pattern (59 bp):
TGTATAATGTAAGTTAAGAAGGTTATGTATAATGTAAGTTAATTAAGCTATGTAAGTAA
Found at i:42289968 original size:25 final size:25
Alignment explanation
Indices: 42289922--42290065 Score: 81
Period size: 25 Copynumber: 5.8 Consensus size: 25
42289912 AATGTAAGTA
* *
42289922 ATGTAAGCT-ATGTAAGTAATGTATT
1 ATGTAAGTTAATG-AAGTTATGTATT
*
42289947 ATGTAAGTTAA-GAAGGTTATGTATA
1 ATGTAAGTTAATGAA-GTTATGTATT
* *
42289972 ATGTAAGTTAATTAATTTATGTAAGTT
1 ATGTAAGTTAATGAAGTTATGT-A-TT
* *
42289999 ATGTAAGTTATTTAA--T-T-TA-T
1 ATGTAAGTTAATGAAGTTATGTATT
*
42290019 ATGTAAGTT-ATGTAATTTATGTAAGTT
1 ATGTAAGTTAATG-AAGTTATGT-A-TT
42290046 ATGTAAGTT-ATGTAAGTTAT
1 ATGTAAGTTAATG-AAGTTAT
42290066 TTAATTTACT
Statistics
Matches: 96, Mismatches: 10, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
19 1 0.01
20 12 0.12
22 2 0.02
23 2 0.02
24 4 0.04
25 36 0.38
26 4 0.04
27 35 0.36
ACGTcount: A:0.36, C:0.01, G:0.18, T:0.45
Consensus pattern (25 bp):
ATGTAAGTTAATGAAGTTATGTATT
Found at i:42290164 original size:14 final size:14
Alignment explanation
Indices: 42290141--42290177 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
42290131 AACTTATGTA
42290141 ACTT-ATTTAATTT
1 ACTTAATTTAATTT
42290154 ACTTAATTTAATTT
1 ACTTAATTTAATTT
42290168 ACTTAATTTA
1 ACTTAATTTA
42290178 TGTAAGTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (14 bp):
ACTTAATTTAATTT
Found at i:42290525 original size:23 final size:24
Alignment explanation
Indices: 42290485--42290545 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 24
42290475 ATATGAATTT
*
42290485 TAAA-AAATTAATAAAATTTAAGG
1 TAAATAAATTAATAAAATTCAAGG
*
42290508 TAAATAAATT-ATATAATTCAAGG
1 TAAATAAATTAATAAAATTCAAGG
42290531 TAAATAAAATTAATA
1 TAAAT-AAATTAATA
42290546 TCGGAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 20 0.61
24 10 0.30
25 3 0.09
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.33
Consensus pattern (24 bp):
TAAATAAATTAATAAAATTCAAGG
Found at i:42290564 original size:34 final size:34
Alignment explanation
Indices: 42290521--42290821 Score: 291
Period size: 34 Copynumber: 9.1 Consensus size: 34
42290511 ATAAATTATA
42290521 TAATTCAAGGTAAATAAAATTAATATCGGAATAT
1 TAATTCAAGGTAAATAAAATTAATATCGGAATAT
***
42290555 TAATTCAAGGTAAATAAAATTAATAAAATTATATAAATTAT
1 TAATTCAAGGTAAATAAAA-T--T--AA-TATCGGAA-TAT
* *
42290596 ATAAATTTAAGGTAAATAAAATTAATATCAGAATAT
1 -T-AATTCAAGGTAAATAAAATTAATATCGGAATAT
42290632 TAATTCAAGGTAAATAAAATT-ATAT---AA-A-
1 TAATTCAAGGTAAATAAAATTAATATCGGAATAT
42290660 T--TT-AAGGTAAATAAAATTAATATCGGAATAT
1 TAATTCAAGGTAAATAAAATTAATATCGGAATAT
42290691 TAATTCAAGGTAAATAAAATT-ATAT---AA-A-
1 TAATTCAAGGTAAATAAAATTAATATCGGAATAT
42290719 T--TT-AAGGTAAATAAAATTAATATCGGAATAT
1 TAATTCAAGGTAAATAAAATTAATATCGGAATAT
42290750 TAATTCAAGGTAAATAAAATTAATAT--GACTTATAT
1 TAATTCAAGGTAAATAAAATTAATATCGGA---ATAT
* *
42290785 AAATTTAAGGTAAATAAAATTAATATCGGAATAT
1 TAATTCAAGGTAAATAAAATTAATATCGGAATAT
42290819 TAA
1 TAA
42290822 ACAAAAATCA
Statistics
Matches: 224, Mismatches: 11, Indels: 64
0.75 0.04 0.21
Matches are distributed among these distances:
25 30 0.13
26 12 0.05
28 2 0.01
29 6 0.03
30 6 0.03
31 2 0.01
32 2 0.01
33 12 0.05
34 79 0.35
35 30 0.13
36 3 0.01
37 8 0.04
38 2 0.01
39 2 0.01
40 6 0.03
41 3 0.01
42 2 0.01
43 17 0.08
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.34
Consensus pattern (34 bp):
TAATTCAAGGTAAATAAAATTAATATCGGAATAT
Found at i:42290618 original size:77 final size:77
Alignment explanation
Indices: 42290511--42290659 Score: 264
Period size: 77 Copynumber: 1.9 Consensus size: 77
42290501 TTTAAGGTAA
*
42290511 ATAAATTATATAATTCAAGGTAAATAAAATTAATATCGGAATATTAATTCAAGGTAAATAAAATT
1 ATAAATTATATAATTCAAGGTAAATAAAATTAATATCAGAATATTAATTCAAGGTAAATAAAATT
42290576 A-ATAAAATTAT
66 ATATAAAATTAT
*
42290587 ATAAATTATATAAATTTAAGGTAAATAAAATTAATATCAGAATATTAATTCAAGGTAAATAAAAT
1 ATAAATTATAT-AATTCAAGGTAAATAAAATTAATATCAGAATATTAATTCAAGGTAAATAAAAT
42290652 TATATAAA
65 TATATAAA
42290660 TTTAAGGTAA
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
76 11 0.16
77 53 0.77
78 5 0.07
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.34
Consensus pattern (77 bp):
ATAAATTATATAATTCAAGGTAAATAAAATTAATATCAGAATATTAATTCAAGGTAAATAAAATT
ATATAAAATTAT
Found at i:42290653 original size:59 final size:59
Alignment explanation
Indices: 42290589--42290821 Score: 367
Period size: 59 Copynumber: 3.8 Consensus size: 59
42290579 AAAATTATAT
*
42290589 AAATTATATAAATTTAAGGTAAATAAAATTAATATCAGAATATTAATTCAAGGTAAATA
1 AAATTATATAAATTTAAGGTAAATAAAATTAATATCGGAATATTAATTCAAGGTAAATA
42290648 AAATTATATAAATTTAAGGTAAATAAAATTAATATCGGAATATTAATTCAAGGTAAATA
1 AAATTATATAAATTTAAGGTAAATAAAATTAATATCGGAATATTAATTCAAGGTAAATA
42290707 AAATTATATAAATTTAAGGTAAATAAAATTAATATCGGAATATTAATTCAAGGTAAATAAAATTA
1 AAATTATATAAATTTAAGGTAAATAAAATTAATATCGGAATATTAATTCAAGG----T-AAA-TA
42290772 ATATGACTTATATAAATTTAAGGTAAATAAAATTAATATCGGAATATTAA
1 A-A--A-TTATATAAATTTAAGGTAAATAAAATTAATATCGGAATATTAA
42290822 ACAAAAATCA
Statistics
Matches: 163, Mismatches: 1, Indels: 10
0.94 0.01 0.06
Matches are distributed among these distances:
59 111 0.68
63 1 0.01
64 3 0.02
65 3 0.02
66 1 0.01
68 1 0.01
69 43 0.26
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.34
Consensus pattern (59 bp):
AAATTATATAAATTTAAGGTAAATAAAATTAATATCGGAATATTAATTCAAGGTAAATA
Found at i:42290656 original size:25 final size:25
Alignment explanation
Indices: 42290628--42290678 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
42290618 TAATATCAGA
*
42290628 ATATTAATTCAAGGTAAATAAAATT
1 ATATAAATTCAAGGTAAATAAAATT
*
42290653 ATATAAATTTAAGGTAAATAAAATT
1 ATATAAATTCAAGGTAAATAAAATT
42290678 A
1 A
42290679 ATATCGGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (25 bp):
ATATAAATTCAAGGTAAATAAAATT
Found at i:42290715 original size:25 final size:25
Alignment explanation
Indices: 42290687--42290737 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
42290677 TAATATCGGA
*
42290687 ATATTAATTCAAGGTAAATAAAATT
1 ATATAAATTCAAGGTAAATAAAATT
*
42290712 ATATAAATTTAAGGTAAATAAAATT
1 ATATAAATTCAAGGTAAATAAAATT
42290737 A
1 A
42290738 ATATCGGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (25 bp):
ATATAAATTCAAGGTAAATAAAATT
Found at i:42292421 original size:34 final size:34
Alignment explanation
Indices: 42292376--42292453 Score: 147
Period size: 34 Copynumber: 2.3 Consensus size: 34
42292366 TTCTTCCAGC
*
42292376 ATGCAATATCTAAATGCAAAATCATTTTTTACGG
1 ATGCAAAATCTAAATGCAAAATCATTTTTTACGG
42292410 ATGCAAAATCTAAATGCAAAATCATTTTTTACGG
1 ATGCAAAATCTAAATGCAAAATCATTTTTTACGG
42292444 ATGCAAAATC
1 ATGCAAAATC
42292454 ATTTTTTACG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (34 bp):
ATGCAAAATCTAAATGCAAAATCATTTTTTACGG
Found at i:42292449 original size:21 final size:21
Alignment explanation
Indices: 42292423--42292466 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
42292413 CAAAATCTAA
42292423 ATGCAAAATCATTTTTTACGG
1 ATGCAAAATCATTTTTTACGG
42292444 ATGCAAAATCATTTTTTACGG
1 ATGCAAAATCATTTTTTACGG
42292465 AT
1 AT
42292467 ACATAGCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (21 bp):
ATGCAAAATCATTTTTTACGG
Found at i:42293653 original size:261 final size:261
Alignment explanation
Indices: 42293193--42293976 Score: 1319
Period size: 261 Copynumber: 3.0 Consensus size: 261
42293183 TAAAAACGCA
* * *
42293193 ACTAATAACACA-GACAAAACGGCATCGTCATAAGATAACA-T---CATTTTTGCGGCGCTTCAG
1 ACTAATAACA-AGGACAAAACGGCACCGTTATAAGATAACATTAAACATTTTTGCGGCGCTTTAG
* *
42293253 CTAAAGCGCCACTAATAAAAATAGGAAATGGCGCCGTTTCCTCAGCTCGTAATAAATATTTGTGG
65 CTAAAGCGCCACTAATAAAAATAGGAAACGACGCCGTTTCCTCAGCTCGTAATAAATATTTGTGG
* *
42293318 CGTTTTTAAAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTCGTTACGGTTAAAGGA
130 CGTTTTTAAAATGCGCCACTAAAAGAAAACAACAAAACGACACCGTCTTCGTTACAGTTAAAGGA
* * *
42293383 AATTTGTGGCGTTTCTTCATAAAACGCCGGTAATATATCACCTTTTGCGGCGATTTTCAAATGCG
195 AATTTGTGGCGTTTCTTCGTAAAACGCTGGTAATATATCACCTTTTGCGGCGTTTTTCAAATGCG
42293448 CC
260 CC
42293450 ACTAATAACAAGGACAAAACGGCACCGTTATAAGATAACATTAAACATTTTTGCGGCGCTTTAGC
1 ACTAATAACAAGGACAAAACGGCACCGTTATAAGATAACATTAAACATTTTTGCGGCGCTTTAGC
42293515 TAAAGCGCCACTAATAAAAATAGGAAACGACGCCGTTTCCTCAGCTCGTAATAAATATTTGTGGC
66 TAAAGCGCCACTAATAAAAATAGGAAACGACGCCGTTTCCTCAGCTCGTAATAAATATTTGTGGC
* *
42293580 GTTTTTATAATGCACCACTAAAAGAAAACAACAAAACGACACCGTCTTCGTTACAGTTAAAGGAA
131 GTTTTTAAAATGCGCCACTAAAAGAAAACAACAAAACGACACCGTCTTCGTTACAGTTAAAGGAA
* *
42293645 ATTTGTGGCGTTTCTTCGTAAAACGCTGGTAATATATCACCTTTAGCAGCGTTTTTCAAATGCGC
196 ATTTGTGGCGTTTCTTCGTAAAACGCTGGTAATATATCACCTTTTGCGGCGTTTTTCAAATGCGC
*
42293710 A
261 C
* *
42293711 ACTAATAACACGGACAAAACGGCACCGTTATAAGATAACATTAAACATTTTCGCGGCGCTTTAGC
1 ACTAATAACAAGGACAAAACGGCACCGTTATAAGATAACATTAAACATTTTTGCGGCGCTTTAGC
*
42293776 TAAAGCGCCACTAATAAAAATAGGAAACGACGCCGTTTCCTCAGCTCGTAATAAATATTTCTGGC
66 TAAAGCGCCACTAATAAAAATAGGAAACGACGCCGTTTCCTCAGCTCGTAATAAATATTTGTGGC
*
42293841 GTTTTTAAAATGCGCCACTAAAAGAAAACAACAAAACGACACCGTCTTTGTTACAGTTAAAGGAA
131 GTTTTTAAAATGCGCCACTAAAAGAAAACAACAAAACGACACCGTCTTCGTTACAGTTAAAGGAA
*
42293906 ATTTATGGCGTTTCTTCGTAAAACGCTGGTAATATATCA-CTTTTAGCGGCGTTTTTCAAATGCG
196 ATTTGTGGCGTTTCTTCGTAAAACGCTGGTAATATATCACCTTTT-GCGGCGTTTTTCAAATGCG
*
42293970 TC
260 CC
42293972 ACTAA
1 ACTAA
42293977 AAGAAAACAA
Statistics
Matches: 495, Mismatches: 26, Indels: 8
0.94 0.05 0.02
Matches are distributed among these distances:
256 1 0.00
257 36 0.07
258 1 0.00
260 4 0.01
261 453 0.92
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (261 bp):
ACTAATAACAAGGACAAAACGGCACCGTTATAAGATAACATTAAACATTTTTGCGGCGCTTTAGC
TAAAGCGCCACTAATAAAAATAGGAAACGACGCCGTTTCCTCAGCTCGTAATAAATATTTGTGGC
GTTTTTAAAATGCGCCACTAAAAGAAAACAACAAAACGACACCGTCTTCGTTACAGTTAAAGGAA
ATTTGTGGCGTTTCTTCGTAAAACGCTGGTAATATATCACCTTTTGCGGCGTTTTTCAAATGCGC
C
Found at i:42294044 original size:115 final size:115
Alignment explanation
Indices: 42293838--42294076 Score: 388
Period size: 115 Copynumber: 2.1 Consensus size: 115
42293828 AAATATTTCT
42293838 GGCGTTTTTAAAATGCGCCACTAAAAGAAAACAACAAAACGACACCGTCTTTGTTACAGTTAAAG
1 GGCGTTTTTAAAATGCGCCACTAAAAGAAAACAACAAAACGACACCGTCTTTGTTACAGTTAAAG
* ** * *
42293903 GAAATTTATGGCGTTTCTTCGTAAAACGCTGGTAATATATCACTTTTAGC
66 GAAATTTACGGCGTTTCTTCACAAAACGCCGGTAATATATCACCTTTAGC
* * * *
42293953 GGCGTTTTTCAAATGCGTCACTAAAAGAAAACAACGAAACGGCACCGTCTTTGTTACAGTTAAAG
1 GGCGTTTTTAAAATGCGCCACTAAAAGAAAACAACAAAACGACACCGTCTTTGTTACAGTTAAAG
*
42294018 GAAATTTGCGGCGTTTCTTCACAAAACGCCGGTAATATATCACCTTTAGC
66 GAAATTTACGGCGTTTCTTCACAAAACGCCGGTAATATATCACCTTTAGC
42294068 GGCGTTTTT
1 GGCGTTTTT
42294077 TCTGAAGCGC
Statistics
Matches: 114, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
115 114 1.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (115 bp):
GGCGTTTTTAAAATGCGCCACTAAAAGAAAACAACAAAACGACACCGTCTTTGTTACAGTTAAAG
GAAATTTACGGCGTTTCTTCACAAAACGCCGGTAATATATCACCTTTAGC
Found at i:42295401 original size:75 final size:77
Alignment explanation
Indices: 42295258--42295402 Score: 195
Period size: 75 Copynumber: 1.9 Consensus size: 77
42295248 GCCACTAAAG
* * * *
42295258 TAAGCATTAGCGGCGCTTTACTAGAAAACGCTGCTAACGCCACTGAAAGTTAAGAAAACGGTGCC
1 TAAGCAATAGCGGCGCTTCACTAGAAAACGCCGCTAACGCCACTGAAAGATAAGAAAACGGTGCC
42295323 GTTGGGCACCCC
66 GTTGGGCACCCC
* * ** *
42295335 TAAGCAATAGCGGCGCTTCACTA-AAAACGCCGCTAAGGCCTC-GAAAGATCTGAAAACGGTGTC
1 TAAGCAATAGCGGCGCTTCACTAGAAAACGCCGCTAACGCCACTGAAAGATAAGAAAACGGTGCC
42295398 GTTGG
66 GTTGG
42295403 ACATATGTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
75 22 0.37
76 16 0.27
77 21 0.36
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (77 bp):
TAAGCAATAGCGGCGCTTCACTAGAAAACGCCGCTAACGCCACTGAAAGATAAGAAAACGGTGCC
GTTGGGCACCCC
Found at i:42295591 original size:72 final size:71
Alignment explanation
Indices: 42295501--42295698 Score: 213
Period size: 72 Copynumber: 2.8 Consensus size: 71
42295491 AAAGCTGAGA
* * *
42295501 AAACGACACCGTTTGGCTTAGGTTTTTTAGCGGCGCTTCCCCAAAAACACCGCTAAAT-CCCAAA
1 AAACGGCACCGTTTGGCTTAGG-TTTTTAGCGGCGCTTACCCAAAAACGCCGCTAAATCCCCAAA
42295565 AACTACGG
65 AAC-ACGG
* * ** *
42295573 AAACGGCACCGTTTGGCTTAGGATTATTAGTGGCGCTTGA-TTAAAAACGTCGCTAAATCCCCAA
1 AAACGGCACCGTTTGGCTTAGG-TTTTTAGCGGCGCTT-ACCCAAAAACGCCGCTAAATCCCCAA
42295637 AAACACGG
64 AAACACGG
*** * * *
42295645 AAACGGTGTCGTTGGGCTTTGGTTTTT-GCGGCGCTTACCGAAAAACGCCGCTAA
1 AAACGGCACCGTTTGGCTTAGGTTTTTAGCGGCGCTTACCCAAAAACGCCGCTAA
42295699 TTCTTATTTT
Statistics
Matches: 104, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
69 1 0.01
70 21 0.20
71 4 0.04
72 69 0.66
73 9 0.09
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.24
Consensus pattern (71 bp):
AAACGGCACCGTTTGGCTTAGGTTTTTAGCGGCGCTTACCCAAAAACGCCGCTAAATCCCCAAAA
ACACGG
Found at i:42297737 original size:17 final size:18
Alignment explanation
Indices: 42297697--42297737 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
42297687 TTTTTTTTAT
*
42297697 AAAT-ATATTTATTATGT
1 AAATGATATTTATTATGG
*
42297714 AATTGATATTT-TTATGG
1 AAATGATATTTATTATGG
42297731 AAATGAT
1 AAATGAT
42297738 GAATGGTCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (18 bp):
AAATGATATTTATTATGG
Found at i:42298285 original size:32 final size:33
Alignment explanation
Indices: 42298241--42298303 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
42298231 AAAAATTATA
*
42298241 TTTAATACAATAAAATATTTATTAT-TTTATTT
1 TTTAATACAATAAAACATTTATTATATTTATTT
*
42298273 TTTAATATAATAAAACATTTATTATATTTAT
1 TTTAATACAATAAAACATTTATTATATTTAT
42298304 GGTAGTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 23 0.82
33 5 0.18
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (33 bp):
TTTAATACAATAAAACATTTATTATATTTATTT
Found at i:42307208 original size:17 final size:17
Alignment explanation
Indices: 42307188--42307222 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
42307178 AAGTTTAGAG
42307188 AAAATAAACAA-AAATAA
1 AAAATAAA-AATAAATAA
42307205 AAAATAAAAATAAATAA
1 AAAATAAAAATAAATAA
42307222 A
1 A
42307223 GGGTAAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (17 bp):
AAAATAAAAATAAATAA
Found at i:42313586 original size:20 final size:21
Alignment explanation
Indices: 42313565--42313614 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 21
42313555 TTTTGGAAAT
42313565 TTTAATTTTAT-TTTTTAT-A
1 TTTAATTTTATATTTTTATGA
42313584 TTT-ATATTTATATTTTTATGA
1 TTTAAT-TTTATATTTTTATGA
42313605 GTTTAATTTT
1 -TTTAATTTT
42313615 TAAAATTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 2 0.08
19 8 0.31
20 7 0.27
21 1 0.04
22 6 0.23
23 2 0.08
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTAATTTTATATTTTTATGA
Found at i:42314659 original size:2 final size:2
Alignment explanation
Indices: 42314652--42314678 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42314642 TTAGGTTCAA
42314652 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 A
42314679 AAACATCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42314771 original size:17 final size:18
Alignment explanation
Indices: 42314744--42314822 Score: 72
Period size: 17 Copynumber: 4.3 Consensus size: 18
42314734 ATTTTTCTCA
*
42314744 TAAAAATTATAGAATTAT
1 TAAAAATTATAAAATTAT
*
42314762 TAAAAA-TATAAAATTAA
1 TAAAAATTATAAAATTAT
* *
42314779 TATGAACTTATAAAAATTAT
1 TA-AAAATTAT-AAAATTAT
*
42314799 TAAAAAATTATAAAAAT-T
1 T-AAAAATTATAAAATTAT
42314817 TAAAAA
1 TAAAAA
42314823 GATAATAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
17 16 0.33
18 10 0.20
19 8 0.16
20 14 0.29
21 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (18 bp):
TAAAAATTATAAAATTAT
Found at i:42314796 original size:20 final size:20
Alignment explanation
Indices: 42314745--42314816 Score: 62
Period size: 20 Copynumber: 3.8 Consensus size: 20
42314735 TTTTTCTCAT
* *
42314745 AAAAATTAT-AGAATT-ATT
1 AAAAATTATAAAAATTAATA
42314763 AAAAA-TAT-AAAATTAATA
1 AAAAATTATAAAAATTAATA
** * *
42314781 TGAACTTATAAAAATTATTA
1 AAAAATTATAAAAATTAATA
42314801 AAAAATTATAAAAATT
1 AAAAATTATAAAAATT
42314817 TAAAAAGATA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
17 8 0.19
18 9 0.21
19 3 0.07
20 22 0.52
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (20 bp):
AAAAATTATAAAAATTAATA
Found at i:42314894 original size:19 final size:19
Alignment explanation
Indices: 42314851--42314913 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
42314841 TATACATTTA
* *
42314851 ATAAAATATTTTTAAAATAT
1 ATAAAAT-TTTATAAAAAAT
*
42314871 TTAAAATTTTATAAAAAAT
1 ATAAAATTTTATAAAAAAT
** *
42314890 ATAAAAACTTATAAATAAT
1 ATAAAATTTTATAAAAAAT
42314909 ATAAA
1 ATAAA
42314914 TTTCAAAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 30 0.83
20 6 0.17
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAAAATTTTATAAAAAAT
Found at i:42314902 original size:10 final size:9
Alignment explanation
Indices: 42314743--42314913 Score: 81
Period size: 9 Copynumber: 18.6 Consensus size: 9
42314733 TATTTTTCTC
42314743 ATAAAAATT
1 ATAAAAATT
*
42314752 AT-AGAATT
1 ATAAAAATT
42314760 ATTAAAAA-T
1 A-TAAAAATT
42314769 AT-AAAATT
1 ATAAAAATT
* *
42314777 AATATGAACTT
1 -ATA-AAAATT
42314788 ATAAAAATT
1 ATAAAAATT
42314797 ATTAAAAAATT
1 A-T-AAAAATT
42314808 ATAAAAATT
1 ATAAAAATT
*
42314817 -TAAAAA-G
1 ATAAAAATT
42314824 ATAATAAATT
1 ATAA-AAATT
42314834 ATAAAAA-T
1 ATAAAAATT
* *
42314842 AT-ACATTT
1 ATAAAAATT
42314850 AATAAAATATTT
1 -ATAAAA-A-TT
*
42314862 TTAAAATATT
1 ATAAAA-ATT
*
42314872 -TAAAATTTT
1 ATAAAA-ATT
*
42314881 ATAAAAAAT
1 ATAAAAATT
42314890 ATAAAAACTT
1 ATAAAAA-TT
42314900 ATAAATAA-T
1 ATAAA-AATT
42314909 ATAAA
1 ATAAA
42314914 TTTCAAAAAT
Statistics
Matches: 126, Mismatches: 17, Indels: 38
0.70 0.09 0.21
Matches are distributed among these distances:
7 6 0.05
8 21 0.17
9 49 0.39
10 27 0.21
11 21 0.17
12 2 0.02
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (9 bp):
ATAAAAATT
Found at i:42316419 original size:18 final size:20
Alignment explanation
Indices: 42316396--42316439 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
42316386 TAAGTGCTAA
*
42316396 ATTAAAA-AAAT-ATTAATT
1 ATTAAAACAAATGATTAAAT
*
42316414 ATTAAAACAATTGATTAAAT
1 ATTAAAACAAATGATTAAAT
42316434 ATTAAA
1 ATTAAA
42316440 GTTTAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 3 0.14
20 12 0.55
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
ATTAAAACAAATGATTAAAT
Found at i:42320248 original size:21 final size:21
Alignment explanation
Indices: 42320224--42320438 Score: 204
Period size: 21 Copynumber: 10.3 Consensus size: 21
42320214 ATGCTTTACT
*
42320224 TTCTGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTATGAGC
* *
42320245 TTCTGTTTAACTCTTATGAG-
1 TTCTGTTCAGCTCTTATGAGC
* *
42320265 TTTTCGTTTAGCTCTT-TCGAGC
1 TTCT-GTTCAGCTCTTAT-GAGC
* * * *
42320287 TTCTATTCAACTCATATGAGT
1 TTCTGTTCAGCTCTTATGAGC
42320308 TTCTGTTCAGCTCTTATGAGC
1 TTCTGTTCAGCTCTTATGAGC
* * * *
42320329 TTCTGTTCAACCCTTATGGGT
1 TTCTGTTCAGCTCTTATGAGC
*
42320350 TTCTGTTTAGCTCTTATGAGC
1 TTCTGTTCAGCTCTTATGAGC
* * * *
42320371 TTTTGTTTAGCTCTCATAAGC
1 TTCTGTTCAGCTCTTATGAGC
*
42320392 TTCTGTTCAGCTCTTATGAGT
1 TTCTGTTCAGCTCTTATGAGC
*
42320413 TTCTGTTCAGCT-TT-CGAGC
1 TTCTGTTCAGCTCTTATGAGC
42320432 TTCTGTT
1 TTCTGTT
42320439 AATGATGTAC
Statistics
Matches: 156, Mismatches: 34, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
19 10 0.06
20 6 0.04
21 136 0.87
22 4 0.03
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTATGAGC
Found at i:42320279 original size:42 final size:42
Alignment explanation
Indices: 42320223--42320421 Score: 231
Period size: 42 Copynumber: 4.7 Consensus size: 42
42320213 CATGCTTTAC
* *
42320223 TTTCTGTTCAGCTCTTACGAGCTTCTGTTTAACTCTTATGAG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACTCTTATGAG
* * *
42320265 TTT-TCGTTTAGCTCTT-TCGAGCTTCTATTCAACTCATATGAG
1 TTTCT-GTTCAGCTCTTAT-GAGCTTCTGTTCAACTCTTATGAG
* *
42320307 TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGGG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACTCTTATGAG
* * * * * *
42320349 TTTCTGTTTAGCTCTTATGAGCTTTTGTTTAGCTCTCATAAG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACTCTTATGAG
* *
42320391 CTTCTGTTCAGCTCTTATGAGTTTCTGTTCA
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTCA
42320422 GCTTTCGAGC
Statistics
Matches: 130, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.01
42 127 0.98
43 2 0.02
ACGTcount: A:0.16, C:0.21, G:0.17, T:0.46
Consensus pattern (42 bp):
TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACTCTTATGAG
Found at i:42322823 original size:21 final size:21
Alignment explanation
Indices: 42322798--42322840 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
42322788 CAAATTTGAC
* *
42322798 TCAATTTAATACAATTTATAT
1 TCAATTCAATACAATTCATAT
*
42322819 TCAATTCAATCCAATTCATAT
1 TCAATTCAATACAATTCATAT
42322840 T
1 T
42322841 TTAGGCAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (21 bp):
TCAATTCAATACAATTCATAT
Found at i:42326356 original size:2 final size:2
Alignment explanation
Indices: 42326349--42326382 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
42326339 ATTGGTCTAG
42326349 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42326383 TCATTATGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42329224 original size:30 final size:27
Alignment explanation
Indices: 42329152--42329224 Score: 74
Period size: 32 Copynumber: 2.5 Consensus size: 27
42329142 ATGTCATTAA
* *
42329152 AATATAATTAAATAAAAAATTTGTATT
1 AATATAAATAAATAAAAAATTTATATT
42329179 AATATTAATATTAAATAAAAACAATTTATATT
1 AATA-TAA-A-TAAAT-AAAA-AATTTATATT
42329211 AATATCAAATAAAT
1 AATAT-AAATAAAT
42329225 TTTTTTTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
27 4 0.11
28 3 0.08
30 10 0.26
31 6 0.16
32 15 0.39
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (27 bp):
AATATAAATAAATAAAAAATTTATATT
Found at i:42332203 original size:19 final size:20
Alignment explanation
Indices: 42332168--42332217 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
42332158 TTGTAAATCA
42332168 TAAT-CATGAAATAATTACT
1 TAATACATGAAATAATTACT
*
42332187 TAATACATGAAA-CATTACT
1 TAATACATGAAATAATTACT
42332206 T-ATAACATGAAA
1 TAAT-ACATGAAA
42332218 ATTTTTCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 2 0.07
19 19 0.68
20 7 0.25
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.32
Consensus pattern (20 bp):
TAATACATGAAATAATTACT
Found at i:42345999 original size:22 final size:23
Alignment explanation
Indices: 42345958--42346011 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 23
42345948 TTAGAAAACT
42345958 ATAAAAA-TTAAAATTAAAATAA
1 ATAAAAATTTAAAATTAAAATAA
42345980 ATAAAAATTTCAAAA-T-AAATAA
1 ATAAAAATTT-AAAATTAAAATAA
42346002 AGTGAAAAAT
1 A-T-AAAAAT
42346012 GAGGGAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 14 0.50
23 4 0.14
24 10 0.36
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.26
Consensus pattern (23 bp):
ATAAAAATTTAAAATTAAAATAA
Found at i:42346989 original size:2 final size:2
Alignment explanation
Indices: 42346982--42347024 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
42346972 GATATTTTAC
42346982 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42347024 T
1 T
42347025 GGAATTGGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42357276 original size:10 final size:10
Alignment explanation
Indices: 42357261--42357291 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
42357251 TTAAAACTTG
42357261 ACTATTTGAA
1 ACTATTTGAA
42357271 ACTATTTG-A
1 ACTATTTGAA
42357280 ACTATTTGAA
1 ACTATTTGAA
42357290 AC
1 AC
42357292 ACCCCATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.39
Consensus pattern (10 bp):
ACTATTTGAA
Found at i:42364061 original size:25 final size:23
Alignment explanation
Indices: 42364026--42364072 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
42364016 CAAAATCAAA
*
42364026 TGTTAATCTTTATTACTCAAATG
1 TGTTAATCTTTATTACCCAAATG
*
42364049 TGTTCAATCCTTTCTTACCCAAAT
1 TGTT-AAT-CTTTATTACCCAAAT
42364073 AAACTTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 3 0.15
25 13 0.65
ACGTcount: A:0.28, C:0.21, G:0.06, T:0.45
Consensus pattern (23 bp):
TGTTAATCTTTATTACCCAAATG
Found at i:42367832 original size:21 final size:21
Alignment explanation
Indices: 42367806--42367851 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
42367796 AACCAACAAC
42367806 AAAATAACAACAAAACAGTAA
1 AAAATAACAACAAAACAGTAA
* *
42367827 AAAATAACAAGAAAATAGTAA
1 AAAATAACAACAAAACAGTAA
42367848 AAAA
1 AAAA
42367852 AGGTTTTTTT
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:0.74, C:0.09, G:0.07, T:0.11
Consensus pattern (21 bp):
AAAATAACAACAAAACAGTAA
Found at i:42369206 original size:19 final size:20
Alignment explanation
Indices: 42369143--42369214 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
42369133 GAAATTACAA
42369143 AAAAATTCAAAATAATTT-T
1 AAAAATTCAAAATAATTTAT
* *
42369162 CAAATATTCAAAATAATTTTT
1 -AAAAATTCAAAATAATTTAT
*
42369183 TAAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTTAT
*
42369202 AAAAATTCTAAAT
1 AAAAATTCAAAAT
42369215 TTTTACATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
19 16 0.36
20 28 0.62
21 1 0.02
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTAT
Found at i:42381829 original size:16 final size:15
Alignment explanation
Indices: 42381801--42381857 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 15
42381791 TTTTTAAATA
42381801 AATAAATTTTATTTT
1 AATAAATTTTATTTT
42381816 AATAAATTTATATTTT
1 AATAAATTT-TATTTT
*
42381832 AAATTAAAATTTATTCTT
1 -AA-TAAATTTTATT-TT
*
42381850 AATTAATT
1 AATAAATT
42381858 AAAAAATCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
15 9 0.26
16 10 0.29
17 8 0.23
18 8 0.23
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
AATAAATTTTATTTT
Found at i:42381853 original size:17 final size:16
Alignment explanation
Indices: 42381803--42381855 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
42381793 TTTAAATAAA
*
42381803 TAAATTTTATTTTAA-
1 TAAAATTTATTTTAAT
*
42381818 TAAATTTATATTTTAAAT
1 TAAAATT-TATTTT-AAT
42381836 TAAAATTTATTCTTAAT
1 TAAAATTTATT-TTAAT
42381853 TAA
1 TAA
42381856 TTAAAAAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 7 0.21
16 6 0.18
17 12 0.36
18 8 0.24
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
TAAAATTTATTTTAAT
Found at i:42383612 original size:16 final size:16
Alignment explanation
Indices: 42383563--42383605 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
42383553 GAGTGGCAAA
*
42383563 CTAGTGGGGTGGCGAG
1 CTAGCGGGGTGGCGAG
42383579 CTAGCGGGGTGGCGAG
1 CTAGCGGGGTGGCGAG
42383595 CTAGCGGGGTG
1 CTAGCGGGGTG
42383606 TCAAGCTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.12, C:0.16, G:0.56, T:0.16
Consensus pattern (16 bp):
CTAGCGGGGTGGCGAG
Found at i:42385185 original size:106 final size:106
Alignment explanation
Indices: 42384907--42385187 Score: 375
Period size: 106 Copynumber: 2.7 Consensus size: 106
42384897 ACGCGGGTAA
* * * * * * * * *
42384907 CTCCACCACACTAGATAGCTCAATAGAGTGATAACTACACCACACTCAA-ACACCGTAATGTAAA
1 CTCCACCACACCAAATGGCTCAAAAGAGAGTTAACTACACCACAC-CAAGGCACCGTAGTGCAAA
*
42384971 GCCCGTAGGCACAAATATCCTATCATGTAATATATTCCATCC
65 GCTCGTAGGCACAAATATCCTATCATGTAATATATTCCATCC
* * * *
42385013 CTCCACTACACCAAATGGCTCAAAAAAGAGTTAACTACACCACATCAAGGCATCGTAGTGCAAAG
1 CTCCACCACACCAAATGGCTCAAAAGAGAGTTAACTACACCACACCAAGGCACCGTAGTGCAAAG
* * *
42385078 CTCGTATGCATAAATATCCTATCATGTAATATATTTCATCC
66 CTCGTAGGCACAAATATCCTATCATGTAATATATTCCATCC
* *
42385119 CTCCACCACACCAAATGGCTCAAAAGAGCGTTAACTACACCACACCAAGGCACCATAGTGCAAAG
1 CTCCACCACACCAAATGGCTCAAAAGAGAGTTAACTACACCACACCAAGGCACCGTAGTGCAAAG
42385184 CTCG
66 CTCG
42385188 GTATTCCACA
Statistics
Matches: 151, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
105 3 0.02
106 148 0.98
ACGTcount: A:0.37, C:0.29, G:0.13, T:0.21
Consensus pattern (106 bp):
CTCCACCACACCAAATGGCTCAAAAGAGAGTTAACTACACCACACCAAGGCACCGTAGTGCAAAG
CTCGTAGGCACAAATATCCTATCATGTAATATATTCCATCC
Found at i:42389678 original size:9 final size:9
Alignment explanation
Indices: 42389661--42389697 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
42389651 TGAGTTTTCA
42389661 AATTCGAAT
1 AATTCGAAT
*
42389670 AACTCGAAT
1 AATTCGAAT
42389679 AATTCGAAT
1 AATTCGAAT
42389688 AATTCGAAT
1 AATTCGAAT
42389697 A
1 A
42389698 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:42390054 original size:13 final size:13
Alignment explanation
Indices: 42390036--42390060 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42390026 CCTCCAAAAT
42390036 TTTACTTTCCCTA
1 TTTACTTTCCCTA
42390049 TTTACTTTCCCT
1 TTTACTTTCCCT
42390061 CAAACTTTTA
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:0.12, C:0.32, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTACTTTCCCTA
Found at i:42398913 original size:15 final size:15
Alignment explanation
Indices: 42398893--42399000 Score: 69
Period size: 15 Copynumber: 7.2 Consensus size: 15
42398883 TTTATGGAAA
42398893 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
42398908 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
42398922 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
42398938 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
42398952 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
42398968 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
*
42398982 AGTCAGAGATATGGGT
1 A-TCAAAGATATGGGT
42398998 ATC
1 ATC
42399001 GAGATATTGG
Statistics
Matches: 66, Mismatches: 21, Indels: 12
0.67 0.21 0.12
Matches are distributed among these distances:
14 12 0.18
15 42 0.64
16 12 0.18
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:42398930 original size:30 final size:30
Alignment explanation
Indices: 42398887--42399010 Score: 194
Period size: 30 Copynumber: 4.1 Consensus size: 30
42398877 TCCATATTTA
* *
42398887 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
42398917 TAGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
42398947 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
* *
42398977 TGGAAAGTCAGAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
42399008 TGG
1 TGG
42399011 CATAATAAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
30 79 0.91
31 8 0.09
ACGTcount: A:0.43, C:0.06, G:0.25, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:42400791 original size:17 final size:17
Alignment explanation
Indices: 42400769--42400808 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
42400759 CCAATATTGA
42400769 AGAATCCACTTTATGTC
1 AGAATCCACTTTATGTC
*
42400786 AGAATCCACTTTATGTT
1 AGAATCCACTTTATGTC
42400803 AGAATC
1 AGAATC
42400809 AATATTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (17 bp):
AGAATCCACTTTATGTC
Found at i:42402465 original size:23 final size:23
Alignment explanation
Indices: 42402439--42402560 Score: 183
Period size: 23 Copynumber: 5.3 Consensus size: 23
42402429 ATAAGTGCCA
42402439 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
42402462 CACTGATACGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
42402485 CACTG-TAATATAGCCGAAGCTAC
1 CACTGAT-ATGTAGCCGAAGCTAC
*
42402508 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
42402531 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
42402554 CACTGAT
1 CACTGAT
42402561 CAATAACACT
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
22 1 0.01
23 85 0.98
24 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:42402812 original size:18 final size:17
Alignment explanation
Indices: 42402786--42402824 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
42402776 ATTTTCCTTC
42402786 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
42402803 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
42402821 CACA
1 CACA
42402825 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:42408041 original size:15 final size:15
Alignment explanation
Indices: 42408016--42408050 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
42408006 GACTCTATTT
*
42408016 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
42408030 TAATTAATATTAAGA
1 TAATTAATATTAAGA
42408045 TAATTA
1 TAATTA
42408051 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:42410465 original size:18 final size:18
Alignment explanation
Indices: 42410432--42410484 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
42410422 ATTCACCTAA
*
42410432 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAAGT
** *
42410451 ATTCAACCCAACCCAATT
1 ACCCAACCCAACCCAAGT
42410469 ACCCAACCCAACCCAA
1 ACCCAACCCAACCCAA
42410485 TCATAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.42, C:0.45, G:0.02, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAAGT
Found at i:42410958 original size:26 final size:25
Alignment explanation
Indices: 42410924--42410976 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
42410914 AATCATAAGT
* *
42410924 TCACAAAGAACTTTTAATCAGGAAGC
1 TCACAAAGAACCTTCAATCAGG-AGC
* *
42410950 TCACGAAGAGCCTTCAATCAGGAGC
1 TCACAAAGAACCTTCAATCAGGAGC
42410975 TC
1 TC
42410977 CGGATAGCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.21
Consensus pattern (25 bp):
TCACAAAGAACCTTCAATCAGGAGC
Found at i:42413688 original size:22 final size:22
Alignment explanation
Indices: 42413647--42413688 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
42413637 TTCATCTCGT
*
42413647 TAAGCTTTAGTGACACAACACC
1 TAAGCTTTAGTGACAAAACACC
* *
42413669 TAAGCTTTGGTGTCAAAACA
1 TAAGCTTTAGTGACAAAACA
42413689 TCCTCGGTAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (22 bp):
TAAGCTTTAGTGACAAAACACC
Found at i:42414987 original size:12 final size:12
Alignment explanation
Indices: 42414972--42415010 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
42414962 AAAAATGGTA
*
42414972 ATTAAAAACTTG
1 ATTAAAGACTTG
*
42414984 ATTAATGACTTG
1 ATTAAAGACTTG
*
42414996 ATTCAAGACTTG
1 ATTAAAGACTTG
42415008 ATT
1 ATT
42415011 CATGAATGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (12 bp):
ATTAAAGACTTG
Found at i:42415011 original size:12 final size:13
Alignment explanation
Indices: 42414979--42415012 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
42414969 GTAATTAAAA
42414979 ACTTGATT-AATG
1 ACTTGATTCAATG
42414991 ACTTGATTCAA-G
1 ACTTGATTCAATG
42415003 ACTTGATTCA
1 ACTTGATTCA
42415013 TGAATGAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 19 0.90
13 2 0.10
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
ACTTGATTCAATG
Found at i:42416399 original size:7 final size:7
Alignment explanation
Indices: 42416383--42416420 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
42416373 TCCCTACAAA
42416383 AATAAA-
1 AATAAAT
42416389 AATAAAT
1 AATAAAT
42416396 AATAAAT
1 AATAAAT
42416403 AATAAA-
1 AATAAAT
42416409 AATAAAT
1 AATAAAT
42416416 AATAA
1 AATAA
42416421 GAAAAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 12 0.40
7 18 0.60
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AATAAAT
Found at i:42416401 original size:13 final size:13
Alignment explanation
Indices: 42416380--42416431 Score: 70
Period size: 13 Copynumber: 3.9 Consensus size: 13
42416370 GTCTCCCTAC
42416380 AAAAATAAA-AAT
1 AAAAATAAATAAT
42416392 AAATAATAAATAAT
1 AAA-AATAAATAAT
42416406 AAAAATAAATAAT
1 AAAAATAAATAAT
*
42416419 AAGAAAAAAATAA
1 AA-AAATAAATAA
42416432 AATTAAAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
12 3 0.08
13 18 0.50
14 15 0.42
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (13 bp):
AAAAATAAATAAT
Found at i:42416408 original size:20 final size:19
Alignment explanation
Indices: 42416383--42416432 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
42416373 TCCCTACAAA
*
42416383 AATAAAAATAAATAATAAAT
1 AATAAAAATAAATAAT-AAG
42416403 AATAAAAATAAATAATAAG
1 AATAAAAATAAATAATAAG
42416422 AA-AAAAATAAA
1 AATAAAAATAAA
42416433 ATTAAAATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 9 0.31
19 4 0.14
20 16 0.55
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (19 bp):
AATAAAAATAAATAATAAG
Found at i:42416439 original size:13 final size:13
Alignment explanation
Indices: 42416380--42416439 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
42416370 GTCTCCCTAC
42416380 AAAAAT-AAAAAT
1 AAAAATAAAAAAT
*
42416392 AAATAATAAATAAT
1 AAA-AATAAAAAAT
*
42416406 AAAAATAAATAAT
1 AAAAATAAAAAAT
*
42416419 -AAGA-AAAAAAT
1 AAAAATAAAAAAT
*
42416430 AAAATTAAAA
1 AAAAATAAAA
42416440 TGTGTATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 6 0.15
12 8 0.21
13 17 0.44
14 8 0.21
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:42420830 original size:18 final size:18
Alignment explanation
Indices: 42420799--42420836 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
42420789 AAAAAATCAC
*
42420799 ATTTTTTATATTTAATAT
1 ATTTTTTATATTTAAAAT
42420817 ATTTTTTA-ATTTTAAAAT
1 ATTTTTTATA-TTTAAAAT
42420835 AT
1 AT
42420837 ATTGTGACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTTTATATTTAAAAT
Done.