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 157 of 190
Found at i:45724351 original size:6 final size:6
Alignment explanation
Indices: 45724340--45724369 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
45724330 TTTAAGTTTT
45724340 ATTATA ATTATA ATTATA ATTATA ATTATA
1 ATTATA ATTATA ATTATA ATTATA ATTATA
45724370 GATTTTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTATA
Found at i:45732268 original size:5 final size:5
Alignment explanation
Indices: 45732258--45732282 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
45732248 AAATTGGTTT
45732258 CAATC CAATC CAATC CAATC CAATC
1 CAATC CAATC CAATC CAATC CAATC
45732283 AGAGTAAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (5 bp):
CAATC
Found at i:45734139 original size:28 final size:28
Alignment explanation
Indices: 45734053--45734139 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 28
45734043 CTTCATTTAT
* *
45734053 AAAAAATGTTTAGGTACCAAATTAGGGAA
1 AAAAAATGTTTAGATACCAAATT-GAGAA
* *
45734082 AAAAGA-GTTTAGATACC-ACTTGTA-ACA
1 AAAAAATGTTTAGATACCAAATTG-AGA-A
*
45734109 AAAAAATGTTTAGATACCAAAATGAGAA
1 AAAAAATGTTTAGATACCAAATTGAGAA
45734137 AAA
1 AAA
45734140 TGACATAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
26 2 0.04
27 9 0.20
28 26 0.57
29 9 0.20
ACGTcount: A:0.52, C:0.09, G:0.16, T:0.23
Consensus pattern (28 bp):
AAAAAATGTTTAGATACCAAATTGAGAA
Found at i:45735925 original size:41 final size:41
Alignment explanation
Indices: 45735868--45736149 Score: 288
Period size: 41 Copynumber: 6.9 Consensus size: 41
45735858 CTTACCTTTC
*
45735868 GGGTCTTTAGCGGCGTTTTCAAAAAAGCGCCGCTAATGCTG
1 GGGTCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTG
* * *
45735909 GGGTCTTTAGCTGCGTTTTTAAAAAGGCGCCACTAATGCT-
1 GGGTCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTG
* * *
45735949 GGGTGCTTTAACGGCGTTTTTGAAAAGGCGCCGCTAATGCTTG
1 GGGT-CTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGC-TG
* * **
45735992 GTGT-TTTAGCGGCGTTTTTGAGAAAA-CGCCATTAATGCTTG
1 GGGTCTTTAGCGGCGTTTTT-AAAAAAGCGCCGCTAATGC-TG
* * * *
45736033 GTGT-TTTAGCGGCGTTTTTGAGAAAGTGCCGCTAATGCTAG
1 GGGTCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCT-G
* * **
45736074 GGG-CTTTAGCGGTGTTTTTGAAAAAGTACCGCTAATGCTCG
1 GGGTCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCT-G
*
45736115 GTGT-TTTAGCGGCGTTTTTAAAAAAGCGCCGCTAA
1 GGGTCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAA
45736150 AAACAATTTA
Statistics
Matches: 202, Mismatches: 31, Indels: 16
0.81 0.12 0.06
Matches are distributed among these distances:
40 8 0.04
41 187 0.93
42 4 0.02
43 3 0.01
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.32
Consensus pattern (41 bp):
GGGTCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTG
Found at i:45736009 original size:82 final size:82
Alignment explanation
Indices: 45735868--45736149 Score: 329
Period size: 82 Copynumber: 3.5 Consensus size: 82
45735858 CTTACCTTTC
* *
45735868 GGGT-CTTTAGCGGCGTTTTCAAAAAAGCGCCGCTAATGC-TGGGGTCTTTAGCTGCGTTTTT-A
1 GGGTGCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTTGGGGT-TTTAGCGGCGTTTTTGA
45735930 AAAAGGCGCCACTAATGCT
65 AAAA-GCGCCACTAATGCT
* * * *
45735949 GGGTGCTTTAACGGCGTTTTTGAAAAGGCGCCGCTAATGCTTGGTGTTTTAGCGGCGTTTTTGAG
1 GGGTGCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTTGGGGTTTTAGCGGCGTTTTTGA-
*
45736014 AAAA-CGCCATTAATGCT
65 AAAAGCGCCACTAATGCT
* * * * * * * *
45736031 TGGTGTTTTAGCGGCGTTTTTGAGAAAGTGCCGCTAATGCTAGGGGCTTTAGCGGTGTTTTTGAA
1 GGGTGCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTTGGGGTTTTAGCGGCGTTTTTGAA
** *
45736096 AAAGTACCGCTAATGCT
66 AAAGCGCCACTAATGCT
* *
45736113 CGGTGTTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAA
1 GGGTGCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAA
45736150 AAACAATTTA
Statistics
Matches: 171, Mismatches: 25, Indels: 9
0.83 0.12 0.04
Matches are distributed among these distances:
81 8 0.05
82 153 0.89
83 6 0.04
84 4 0.02
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.32
Consensus pattern (82 bp):
GGGTGCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTTGGGGTTTTAGCGGCGTTTTTGAA
AAAGCGCCACTAATGCT
Found at i:45736092 original size:123 final size:124
Alignment explanation
Indices: 45735873--45736149 Score: 341
Period size: 123 Copynumber: 2.3 Consensus size: 124
45735863 CTTTCGGGTC
* *
45735873 TTTAGCGGCG-TTTTCAAAAAAGCGCCGCTAATGCTGGGGTCTTTAGCTGCGTTTTTAAAAAGGC
1 TTTAGCGGCGTTTTTCAAAAAAGCGCCACTAATGCTGGGGTCTTTAGCGGCGTTTTTAAAAAGGC
* * *
45735937 GCCACTAATGCTGGGTGCTTTAACGGCGTTTTTGAAAAGGCGCCGCTAATGCTTGGTGT
66 GCCACTAATGCTGGGTGCTTTAACGGCGTTTTTGAAAAAGCACCGCTAATGCTCGGTGT
* * * * *
45735996 TTTAGCGGCGTTTTTGAGAAAA-CGCCATTAATGCTTGGTGT-TTTAGCGGCGTTTTTGAGAAA-
1 TTTAGCGGCGTTTTTCAAAAAAGCGCCACTAATGC-TGGGGTCTTTAGCGGCGTTTTT-AAAAAG
* * * * *
45736058 GTGCCGCTAATGCTAGGG-GCTTTAGCGGTGTTTTTGAAAAAGTACCGCTAATGCTCGGTGT
64 GCGCCACTAATGCT-GGGTGCTTTAACGGCGTTTTTGAAAAAGCACCGCTAATGCTCGGTGT
*
45736119 TTTAGCGGCGTTTTT-AAAAAAGCGCCGCTAA
1 TTTAGCGGCGTTTTTCAAAAAAGCGCCACTAA
45736150 AAACAATTTA
Statistics
Matches: 131, Mismatches: 18, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
122 5 0.04
123 105 0.80
124 21 0.16
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (124 bp):
TTTAGCGGCGTTTTTCAAAAAAGCGCCACTAATGCTGGGGTCTTTAGCGGCGTTTTTAAAAAGGC
GCCACTAATGCTGGGTGCTTTAACGGCGTTTTTGAAAAAGCACCGCTAATGCTCGGTGT
Found at i:45736543 original size:21 final size:20
Alignment explanation
Indices: 45736509--45736571 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
45736499 GTATGGATTA
*
45736509 GGGATTATGGTTTAAGGGTT
1 GGGATTAAGGTTTAAGGGTT
*
45736529 GGGATTTAAGGTTTAGGGGTT
1 GGGA-TTAAGGTTTAAGGGTT
*
45736550 AGAGG-TTAAGGGTTTAGGGGTT
1 -G-GGATTAA-GGTTTAAGGGTT
45736572 AGACGTTAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
20 4 0.11
21 18 0.49
22 13 0.35
23 2 0.05
ACGTcount: A:0.21, C:0.00, G:0.43, T:0.37
Consensus pattern (20 bp):
GGGATTAAGGTTTAAGGGTT
Found at i:45736566 original size:22 final size:21
Alignment explanation
Indices: 45736534--45736593 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
45736524 GGGTTGGGAT
*
45736534 TTAAGGTTTAGGGGTTAGAGG
1 TTAAGGTTTAGGGGTTAGACG
45736555 TTAAGGGTTTAGGGGTTAGACG
1 TTAA-GGTTTAGGGGTTAGACG
*
45736577 TTAGACG-TTAGGGGTTA
1 TTA-AGGTTTAGGGGTTA
45736594 AGATACTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.40
22 20 0.57
23 1 0.03
ACGTcount: A:0.23, C:0.03, G:0.40, T:0.33
Consensus pattern (21 bp):
TTAAGGTTTAGGGGTTAGACG
Found at i:45736593 original size:14 final size:14
Alignment explanation
Indices: 45736541--45736593 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
45736531 GATTTAAGGT
45736541 TTAGGGGTTAGAGG
1 TTAGGGGTTAGAGG
* *
45736555 TTAAGGGTTTAGGGG
1 TT-AGGGGTTAGAGG
** *
45736570 TTAGACGTTAGACG
1 TTAGGGGTTAGAGG
45736584 TTAGGGGTTA
1 TTAGGGGTTA
45736594 AGATACTATT
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.23, C:0.04, G:0.42, T:0.32
Consensus pattern (14 bp):
TTAGGGGTTAGAGG
Found at i:45736628 original size:15 final size:14
Alignment explanation
Indices: 45736603--45736735 Score: 99
Period size: 15 Copynumber: 9.4 Consensus size: 14
45736593 AAGATACTAT
*
45736603 TTTAAGGTTTAGGG
1 TTTAGGGTTTAGGG
*
45736617 ATTATGGGTTTAGGG
1 TTTA-GGGTTTAGGG
* * *
45736632 TTTATGATTTATGG
1 TTTAGGGTTTAGGG
* *
45736646 TTTATGGTTTACGGC
1 TTTAGGGTTTA-GGG
*
45736661 TTAAGGG-TT-GGG
1 TTTAGGGTTTAGGG
*
45736673 TTTAAGGTTTAGGG
1 TTTAGGGTTTAGGG
*
45736687 GTTAGGGGTTTAGGG
1 TTTA-GGGTTTAGGG
* *
45736702 TTCAAGGTTTAGGG
1 TTTAGGGTTTAGGG
*
45736716 GTTAGGAGTTTAGGG
1 TTTAGG-GTTTAGGG
45736731 TTTAG
1 TTTAG
45736736 ATTAATTAGT
Statistics
Matches: 90, Mismatches: 23, Indels: 11
0.73 0.19 0.09
Matches are distributed among these distances:
12 7 0.08
13 2 0.02
14 40 0.44
15 41 0.46
ACGTcount: A:0.19, C:0.02, G:0.38, T:0.41
Consensus pattern (14 bp):
TTTAGGGTTTAGGG
Found at i:45736632 original size:7 final size:7
Alignment explanation
Indices: 45736603--45736735 Score: 99
Period size: 7 Copynumber: 18.7 Consensus size: 7
45736593 AAGATACTAT
*
45736603 TTTAAGG
1 TTTAGGG
45736610 TTTAGGG
1 TTTAGGG
*
45736617 ATTATGGG
1 TTTA-GGG
45736625 TTTAGGG
1 TTTAGGG
* *
45736632 TTTATGA
1 TTTAGGG
*
45736639 TTTATGG
1 TTTAGGG
*
45736646 TTTATGG
1 TTTAGGG
*
45736653 TTTACGGC
1 TTTA-GGG
*
45736661 TTAAGGG
1 TTTAGGG
45736668 -TT-GGG
1 TTTAGGG
*
45736673 TTTAAGG
1 TTTAGGG
45736680 TTTAGGG
1 TTTAGGG
*
45736687 GTTAGGGG
1 TTTA-GGG
45736695 TTTAGGG
1 TTTAGGG
* *
45736702 TTCAAGG
1 TTTAGGG
45736709 TTTAGGG
1 TTTAGGG
*
45736716 GTTAGGAG
1 TTTAGG-G
45736724 TTTAGGG
1 TTTAGGG
45736731 TTTAG
1 TTTAG
45736736 ATTAATTAGT
Statistics
Matches: 99, Mismatches: 21, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
5 3 0.03
6 3 0.03
7 71 0.72
8 22 0.22
ACGTcount: A:0.19, C:0.02, G:0.38, T:0.41
Consensus pattern (7 bp):
TTTAGGG
Found at i:45738504 original size:125 final size:123
Alignment explanation
Indices: 45738282--45738561 Score: 490
Period size: 125 Copynumber: 2.3 Consensus size: 123
45738272 TTATTTCGAG
45738282 TTGACGTTTCTG-GTCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGT
*
45738346 GAAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAACAAATTTTTT
65 GAAATCGTGCCCTCGTAGACGCGATTTCGCTACAGTTGGTCATGTAAGAAA-AAA-TTTTT
45738407 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* *
45738472 AAATCGTGCCCTCGTAGATGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTT
66 AAATCGTGCCCTCGTAGACGCGATTTCGCTACAGTTGGTCATGTAAGAAAAAATTTTT
*
45738530 TTGACGTTTCTGAGTAAATAGTATAAAATCGC
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGC
45738562 GCCCTCGTGG
Statistics
Matches: 150, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
123 36 0.24
124 2 0.01
125 111 0.74
126 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (123 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGTGCCCTCGTAGACGCGATTTCGCTACAGTTGGTCATGTAAGAAAAAATTTTT
Found at i:45741889 original size:29 final size:29
Alignment explanation
Indices: 45741752--45742564 Score: 815
Period size: 36 Copynumber: 25.8 Consensus size: 29
45741742 TTTTGTTAAT
*
45741752 GGTTAGGGTTTTTAATTAAATTAAGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
45741781 GGTTTAGGGTTTTTAATTAAATTAGGTT--
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
45741809 -GTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
45741837 GGTTAGGGTTTACAGTTTTTAATTAAATTAGGTTAA
1 GGTTA-GG------GTTTTTAATTAAATTAGGTTAG
45741873 GGTTAGGGTTTTTAATTAAATTAGGATAGGATTAG
1 GGTTAGGGTTTTTAATTAAA-T----TAGG-TTAG
* *
45741908 GGTTTAAGGTTTTTAATTAAATTAGATTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
45741938 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
45741967 GGTTAGGGTTTTTAATTAAATTAGATTAGGGTTAG
1 GGTTAGGGTTTTTAATT--A--A-ATTA-GGTTAG
45742002 GGTTTAGGGTTTTTAATTAAATTAGATTAGGGTTAG
1 GG-TTAGGGTTTTTAATT--A--A-ATTA-GGTTAG
45742038 GGTTTAGGGTTTTTAATTAAATTAGGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
45742068 GGTTAGGGTTTATGGTTTTTAATTAAATTAGGTTAG
1 GGTTA--G-----GGTTTTTAATTAAATTAGGTTAG
45742104 GGTTAGGGTTTTTAATTAAATTAGGTTAGGG
1 GGTTAGGGTTTTTAATTAAATTAGGTTA--G
45742135 TTAGAGTTTAGGGTTTTTAATTAAATTAGGTTTAG
1 ---G-G-TTAGGGTTTTTAATTAAATTAGG-TTAG
* **
45742170 GGTTAGAGTTTAGGGTTTAAATTAGGTTAGGGTTAG
1 GGTTAG-GGTT----TTT-AATTAAATTA-GGTTAG
* *
45742206 GGTTTAGAGTTTTTAATTAAATTAAGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
*
45742236 GGTTAGGG-TTTTAATTAAATTAAGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
45742264 GGTTTAGGGTTTTTAATTAAATTAGGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
*
45742294 AGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAG
1 -GGTTAGGGTTTTTAATT-AA--A--TTA-GGTTAG
*
45742330 GGTTTAGGGTTTTTAATTAAATTAAGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
45742360 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* *
45742389 GGTTTATGATTTTTAATTAAATTAGGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
*
45742419 GGTTAGGATTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
45742448 GGTTAGGATTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
45742477 GGTTTAGGGTTTTTAATTAAATTAGGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
45742507 GGTTAGGGTTTAAGGTTTTTAATTAAATTAGGTTAG
1 GGTTA--G-----GGTTTTTAATTAAATTAGGTTAG
*
45742543 GGTTAGGGTTTTAAATTAAATT
1 GGTTAGGGTTTTTAATTAAATT
45742565 GGGATTTTTA
Statistics
Matches: 691, Mismatches: 26, Indels: 134
0.81 0.03 0.16
Matches are distributed among these distances:
26 25 0.04
27 1 0.00
28 22 0.03
29 200 0.29
30 148 0.21
31 29 0.04
32 5 0.01
33 3 0.00
34 12 0.02
35 27 0.04
36 210 0.30
37 9 0.01
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:45741910 original size:65 final size:63
Alignment explanation
Indices: 45741752--45742564 Score: 734
Period size: 65 Copynumber: 12.9 Consensus size: 63
45741742 TTTTGTTAAT
45741752 GGTTAGGGTTTTTAATTAAATT--A-A-GTTAGGGTTTAGGGTTTTTAATTAAATTAGGTT--
1 GGTTAGGGTTTTTAATTAAATTAGATAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAG
* ** *
45741809 -GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTACAGTTTTTAATTAAATTAGGTTAA
1 GGTTAGGGTTTTTAATTAAATTA-GATA-GGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAG
* *
45741873 GGTTAGGGTTTTTAATTAAATTAGGATAGGATTAGGGTTTAAGGTTTTTAATTAAATTAGATTAG
1 GGTTAGGGTTTTTAATTAAATTA-GATAGG-TTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAG
45741938 GGTTAGGGTTTTTAATTAAA-T---TAGGTTAGGG-TTAGGGTTTTTAATTAAATTAGATTAGGG
1 GGTTAGGGTTTTTAATTAAATTAGATAGGTTAGGGTTTAGGGTTTTTAATT--A--A-ATTA-GG
45741998 TTAG
60 TTAG
45742002 GGTTTAGGGTTTTTAATTAAATTAGATTAGGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTA
1 GG-TTAGGGTTTTTAATTAAATTAGA-TA-GGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTA
45742067 G
63 G
* * *
45742068 GGTTAGGGTTTATGGT-TTTTAATTAAATTAGGTTAGGG-TTAGGGTTTTTAATTAAATTAGGTT
1 GGTTAGGGTTT-T--TAATTAAATTAGA-TAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTT
45742131 AGGG
62 A--G
* * * **
45742135 TTAGAGTTTAGGGTTTTTAATTAAATTAGGTTTAGGGTTAGAGTTTAGGG-TTTAAATTAGGTTA
1 ---G-G-TTAGGGTTTTTAATTAAATTA-G-ATA-GGTTAGGGTTTAGGGTTTTTAATTAAATTA
45742199 GGGTTAG
58 -GGTTAG
* *
45742206 GGTTTAGAGTTTTTAATTAAATT--A-A-GTTAGGG-TTAGGG-TTTTAATTAAATTAAGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGATAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAG
*
45742264 GGTTTAGGGTTTTTAATTAAA-T---TAGGTTAGAGTTTAGGGTTTTTAATTAAATTAGGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGATAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAG
* * *
45742324 GGTTAGGGTTTAGGGTT--TTTAATTAAATTAAGTTAGGG-TTAGGGTTTTTAATTAAATTAGGT
1 GGTTAGGGTTT----TTAATTAAATTAGA-TAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGT
45742386 TAG
61 TAG
* * *
45742389 GGTTTATGATTTTTAATTAAA-T---TAGGTTAGGG-TTAGGATTTTTAATTAAATTAGGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGATAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAG
*
45742448 GGTTAGGATTTTTAATTAAA-T---TAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGATAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAG
* * *
45742507 GGTTAGGG--TTTAAGGTTTTTAATTAAATTAGGTTAGGG-TTAGGGTTTTAAATTAAATT
1 GGTTAGGGTTTTTAA----TTAAATTAGA-TAGGTTAGGGTTTAGGGTTTTTAATTAAATT
45742565 GGGATTTTTA
Statistics
Matches: 646, Mismatches: 44, Indels: 124
0.79 0.05 0.15
Matches are distributed among these distances:
56 21 0.03
57 7 0.01
58 73 0.11
59 108 0.17
60 33 0.05
61 8 0.01
62 37 0.06
63 7 0.01
64 14 0.02
65 177 0.27
66 43 0.07
67 37 0.06
68 3 0.00
69 1 0.00
70 11 0.02
71 13 0.02
72 42 0.07
73 11 0.02
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (63 bp):
GGTTAGGGTTTTTAATTAAATTAGATAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:45741960 original size:24 final size:24
Alignment explanation
Indices: 45741927--45741999 Score: 76
Period size: 29 Copynumber: 2.9 Consensus size: 24
45741917 TTTTTAATTA
*
45741927 AATTAGATTAGGGTTAGGGTTTTT
1 AATTAAATTAGGGTTAGGGTTTTT
45741951 AATTAAATTAGGTTAGGGTTAGGGTTTTT
1 AATT-AA--A--TTAGGGTTAGGGTTTTT
*
45741980 AATTAAATTA-GATTAGGGTT
1 AATTAAATTAGGGTTAGGGTT
45742000 AGGGTTTAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
23 9 0.21
24 7 0.17
25 1 0.02
26 1 0.02
27 1 0.02
28 2 0.05
29 21 0.50
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (24 bp):
AATTAAATTAGGGTTAGGGTTTTT
Found at i:45741999 original size:23 final size:26
Alignment explanation
Indices: 45741915--45741990 Score: 89
Period size: 29 Copynumber: 2.7 Consensus size: 26
45741905 TAGGGTTTAA
*
45741915 GGTTTTTAATTAAATTAGATTAGGGTTAG
1 GGTTTTTAATTAAATTAG-GTA--GTTAG
45741944 GGTTTTTAATTAAATTAGGTTAGGGTTAG
1 GGTTTTTAATTAAATTAGG-TA--GTTAG
45741973 GGTTTTTAATTAAATTAG
1 GGTTTTTAATTAAATTAG
45741991 ATTAGGGTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.46
Consensus pattern (26 bp):
GGTTTTTAATTAAATTAGGTAGTTAG
Found at i:45744927 original size:28 final size:29
Alignment explanation
Indices: 45744886--45744948 Score: 101
Period size: 28 Copynumber: 2.2 Consensus size: 29
45744876 GCCATTGATG
*
45744886 AAAATATAAAAAAATTTAAAATTA-TTTT
1 AAAAAATAAAAAAATTTAAAATTATTTTT
*
45744914 AAAAAATATAAAAATTTAAAATTATTTTT
1 AAAAAATAAAAAAATTTAAAATTATTTTT
45744943 AAAAAA
1 AAAAAA
45744949 AATGAAATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 22 0.69
29 10 0.31
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
AAAAAATAAAAAAATTTAAAATTATTTTT
Found at i:45745010 original size:22 final size:21
Alignment explanation
Indices: 45744985--45745035 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 21
45744975 TAATATGGAT
45744985 TTGAGAGATTTTTAGAAGGAAA
1 TTGAGAGA-TTTTAGAAGGAAA
*
45745007 TTGAGAGGATTTTGGAAGGAAA
1 TTGAGA-GATTTTAGAAGGAAA
45745029 TTGAGAG
1 TTGAGAG
45745036 TTTGAGAGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 1 0.04
22 24 0.89
23 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.29
Consensus pattern (21 bp):
TTGAGAGATTTTAGAAGGAAA
Found at i:45745042 original size:30 final size:30
Alignment explanation
Indices: 45745007--45745064 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
45744997 TAGAAGGAAA
45745007 TTGAGAGGATTTTGGAAGGAAATTGAGAGT
1 TTGAGAGGATTTTGGAAGGAAATTGAGAGT
45745037 TTGAGAGGATTTTGGAAGGAAATTGAGA
1 TTGAGAGGATTTTGGAAGGAAATTGAGA
45745065 TAGGATTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.34, C:0.00, G:0.36, T:0.29
Consensus pattern (30 bp):
TTGAGAGGATTTTGGAAGGAAATTGAGAGT
Found at i:45745730 original size:27 final size:27
Alignment explanation
Indices: 45745692--45745757 Score: 132
Period size: 27 Copynumber: 2.4 Consensus size: 27
45745682 ACCACATTTG
45745692 CTAAGTTTGCTATATTAGGATGTAGTA
1 CTAAGTTTGCTATATTAGGATGTAGTA
45745719 CTAAGTTTGCTATATTAGGATGTAGTA
1 CTAAGTTTGCTATATTAGGATGTAGTA
45745746 CTAAGTTTGCTA
1 CTAAGTTTGCTA
45745758 AGTTTTCTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (27 bp):
CTAAGTTTGCTATATTAGGATGTAGTA
Found at i:45747239 original size:13 final size:13
Alignment explanation
Indices: 45747221--45747245 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45747211 TACATTTTTA
45747221 ATCCTTATATATC
1 ATCCTTATATATC
45747234 ATCCTTATATAT
1 ATCCTTATATAT
45747246 ATATTTTGTA
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:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (13 bp):
ATCCTTATATATC
Found at i:45757244 original size:5 final size:5
Alignment explanation
Indices: 45757227--45757262 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
45757217 ATTTAAGTAA
45757227 ATATT ATTATT ATATT ATATT ATATT ATATT ATATT
1 ATATT A-TATT ATATT ATATT ATATT ATATT ATATT
45757263 GTTATAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
ATATT
Found at i:45757252 original size:15 final size:16
Alignment explanation
Indices: 45757227--45757267 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
45757217 ATTTAAGTAA
45757227 ATATTATTATTATATT
1 ATATTATTATTATATT
45757243 ATATTA-TATTATATT
1 ATATTATTATTATATT
*
45757258 ATATTGTTAT
1 ATATTATTAT
45757268 AATAATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
ATATTATTATTATATT
Found at i:45757348 original size:11 final size:11
Alignment explanation
Indices: 45757293--45757381 Score: 60
Period size: 13 Copynumber: 7.6 Consensus size: 11
45757283 AAATAAATGA
45757293 AAGAAAAAGA-
1 AAGAAAAAGAG
45757303 ATAG-AAAA-AG
1 A-AGAAAAAGAG
45757313 AAGAACAAAGTAG
1 AAGAA-AAAG-AG
*
45757326 AACGAAACAGAG
1 AA-GAAAAAGAG
45757338 AAGAAAAAGAGAG
1 AAG-AAAA-AGAG
45757351 AAAGAAAAAGAG
1 -AAGAAAAAGAG
45757363 AAGGAAAAAGCAG
1 AA-GAAAAAG-AG
45757376 AA-AAAA
1 AAGAAAA
45757382 TTAGGGTTTT
Statistics
Matches: 65, Mismatches: 2, Indels: 23
0.72 0.02 0.26
Matches are distributed among these distances:
9 3 0.05
10 7 0.11
11 12 0.18
12 18 0.28
13 19 0.29
14 6 0.09
ACGTcount: A:0.70, C:0.04, G:0.24, T:0.02
Consensus pattern (11 bp):
AAGAAAAAGAG
Found at i:45757357 original size:14 final size:13
Alignment explanation
Indices: 45757334--45757372 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
45757324 AGAACGAAAC
45757334 AGAGAAGAAAAAG
1 AGAGAAGAAAAAG
45757347 AGAGAAAGAAAAAG
1 AGAG-AAGAAAAAG
*
45757361 AGA-AGGAAAAAG
1 AGAGAAGAAAAAG
45757373 CAGAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 8 0.33
13 4 0.17
14 12 0.50
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
AGAGAAGAAAAAG
Found at i:45757377 original size:25 final size:24
Alignment explanation
Indices: 45757307--45757378 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 24
45757297 AAAAGAATAG
* *
45757307 AAAA-AGAAGAACAAAGTAGAACGA
1 AAAAGAGAAGAA-AAAGCAGAAAGA
* *
45757331 AACAGAGAAGAAAAAGAGAGAAAGA
1 AAAAGAGAAGAAAAAG-CAGAAAGA
45757356 AAAAGAGAAGGAAAAAGCAGAAA
1 AAAAGAGAA-GAAAAAGCAGAAA
45757379 AAATTAGGGT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
24 7 0.17
25 26 0.65
26 7 0.17
ACGTcount: A:0.68, C:0.06, G:0.25, T:0.01
Consensus pattern (24 bp):
AAAAGAGAAGAAAAAGCAGAAAGA
Found at i:45759437 original size:52 final size:52
Alignment explanation
Indices: 45759359--45759460 Score: 195
Period size: 52 Copynumber: 2.0 Consensus size: 52
45759349 GGGCTCATAA
45759359 AAGGGACAATATGATTAAATTATGATGTGTATGCTAGATGATTATATAATAT
1 AAGGGACAATATGATTAAATTATGATGTGTATGCTAGATGATTATATAATAT
*
45759411 AAGGGACAATATGATTAAATTATGATGTGTATGCTAGATGCTTATATAAT
1 AAGGGACAATATGATTAAATTATGATGTGTATGCTAGATGATTATATAAT
45759461 GTTCATATTT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (52 bp):
AAGGGACAATATGATTAAATTATGATGTGTATGCTAGATGATTATATAATAT
Found at i:45761853 original size:12 final size:12
Alignment explanation
Indices: 45761836--45761863 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
45761826 TTTATTAATA
45761836 TTTTGATTTGAT
1 TTTTGATTTGAT
45761848 TTTTGATTTGAT
1 TTTTGATTTGAT
45761860 TTTT
1 TTTT
45761864 TTATTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (12 bp):
TTTTGATTTGAT
Found at i:45761871 original size:8 final size:8
Alignment explanation
Indices: 45761858--45761885 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
45761848 TTTTGATTTG
45761858 ATTTTTTT
1 ATTTTTTT
45761866 ATTTTTTT
1 ATTTTTTT
45761874 ATTTTTTT
1 ATTTTTTT
45761882 ATTT
1 ATTT
45761886 GACATAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (8 bp):
ATTTTTTT
Found at i:45770905 original size:25 final size:27
Alignment explanation
Indices: 45770868--45770928 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 27
45770858 ATCATTACTC
*
45770868 TTTATTTACATAA-AAAAATA-ATATA
1 TTTAATTACATAATAAAAATATATATA
* * *
45770893 TTTAATTATATAATGAAATTATATATA
1 TTTAATTACATAATAAAAATATATATA
45770920 TTTATATTA
1 TTTA-ATTA
45770929 AATATATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 11 0.38
26 5 0.17
27 9 0.31
28 4 0.14
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
TTTAATTACATAATAAAAATATATATA
Found at i:45770928 original size:15 final size:15
Alignment explanation
Indices: 45770888--45770941 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
45770878 TAAAAAAATA
45770888 ATATATTTA-ATTAT
1 ATATATTTATATTAT
* *
45770902 ATA-A-TGAAATTAT
1 ATATATTTATATTAT
*
45770915 ATATATTTATATTAA
1 ATATATTTATATTAT
45770930 ATATATTT-TATT
1 ATATATTTATATT
45770942 TTTTAAAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 2 0.06
13 9 0.27
14 8 0.24
15 14 0.42
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATATTTATATTAT
Found at i:45771511 original size:25 final size:25
Alignment explanation
Indices: 45771435--45771503 Score: 115
Period size: 24 Copynumber: 2.8 Consensus size: 25
45771425 AGCTTTTTAT
45771435 TTTTATATTAAATTAT-TTAAAATA
1 TTTTATATTAAATTATATTAAAATA
*
45771459 TTTTAT-TTTAATTATATTAAAATA
1 TTTTATATTAAATTATATTAAAATA
45771483 TTTTATATTAAATTATATTAA
1 TTTTATATTAAATTATATTAA
45771504 GAGATTTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
23 8 0.20
24 20 0.49
25 13 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TTTTATATTAAATTATATTAAAATA
Found at i:45784084 original size:19 final size:18
Alignment explanation
Indices: 45784053--45784088 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
45784043 GTTTATCAAC
*
45784053 TTTTTTAAGTTTTTTATG
1 TTTTTTAAATTTTTTATG
45784071 TTTTTTATAATTTTTTAT
1 TTTTTTA-AATTTTTTAT
45784089 CATAGATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (18 bp):
TTTTTTAAATTTTTTATG
Found at i:45787040 original size:3 final size:3
Alignment explanation
Indices: 45787032--45787060 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
45787022 AATACTTCAA
45787032 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
45787061 CAACATAGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:45793141 original size:15 final size:15
Alignment explanation
Indices: 45793117--45793146 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
45793107 AACACAAAAC
*
45793117 CTTTTTCTTTTTTTA
1 CTTTTACTTTTTTTA
45793132 CTTTTACTTTTTTTA
1 CTTTTACTTTTTTTA
45793147 TATTTTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (15 bp):
CTTTTACTTTTTTTA
Found at i:45797660 original size:73 final size:72
Alignment explanation
Indices: 45797542--45797745 Score: 282
Period size: 73 Copynumber: 2.8 Consensus size: 72
45797532 TTAGTAAATA
* * * * *
45797542 GATGGCTTGAGATCCAACATGTGTTGTGGATTCTTTGGAGCTTGTGTGAGCGGCATCAAATCATT
1 GATGGCTTGAGATCCAACACGTGTTGCGGATTCTTTGAAGCTTGTGTGAACAGCATCAAATCATT
*
45797607 CTTTATT
66 CTTTATC
*
45797614 GATGGCTTGAGATCCAAACACGTGTTGCGGATTCTTTGAAGCTTGTGTGAACAGCATCGAATCAT
1 GATGGCTTGAGATCC-AACACGTGTTGCGGATTCTTTGAAGCTTGTGTGAACAGCATCAAATCAT
45797679 TCTTTATC
65 TCTTTATC
* * ** * *
45797687 GATGGCTTAAGATCCAGCACGTGTTGCGGATTCTCGGAAGCTTGTTTGAATAGCATCAA
1 GATGGCTTGAGATCCAACACGTGTTGCGGATTCTTTGAAGCTTGTGTGAACAGCATCAA
45797746 TAAAGCTTAC
Statistics
Matches: 117, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
72 53 0.45
73 64 0.55
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (72 bp):
GATGGCTTGAGATCCAACACGTGTTGCGGATTCTTTGAAGCTTGTGTGAACAGCATCAAATCATT
CTTTATC
Found at i:45799009 original size:36 final size:36
Alignment explanation
Indices: 45798969--45799040 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
45798959 ATTTTTTTTA
* *
45798969 TTTGTTAAGATTTTTCTAAACATTGAAGCTAATAAT
1 TTTGTTAAGATTTTTATAAACATCGAAGCTAATAAT
45799005 TTTGTTAAGATTTTTATAAACATCGAAGCTAATAAT
1 TTTGTTAAGATTTTTATAAACATCGAAGCTAATAAT
45799041 GTTATCGGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (36 bp):
TTTGTTAAGATTTTTATAAACATCGAAGCTAATAAT
Found at i:45813272 original size:40 final size:40
Alignment explanation
Indices: 45813228--45813316 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 40
45813218 ACTATGTTTA
* *
45813228 GCACTTAGTATGAAATTTGAGATAACTTCGGCTATTTATG
1 GCACTTAGTATGAAATTTGAAATAACTTCGGCTATATATG
* ** * *
45813268 GCACTTAGTGTGCGATTTGAAATAGCTTCGGCTCTATATG
1 GCACTTAGTATGAAATTTGAAATAACTTCGGCTATATATG
45813308 GCACTTAGT
1 GCACTTAGT
45813317 GTACGAGAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (40 bp):
GCACTTAGTATGAAATTTGAAATAACTTCGGCTATATATG
Found at i:45813317 original size:40 final size:41
Alignment explanation
Indices: 45813244--45813401 Score: 167
Period size: 41 Copynumber: 3.9 Consensus size: 41
45813234 AGTATGAAAT
* * * *
45813244 TTGAGATAACTTCGGCTATTTATGGCACTTAGTGTGCGA-T
1 TTGAAATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGA
* *
45813284 TTGAAATAGCTTCGGCTCTATATGGCACTTAGTGTACGAGA
1 TTGAAATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGA
* * * * *
45813325 ATGAGATAGTTTCGGCTATGTAAGGCACTTAGTGTGCGAGA
1 TTGAAATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGA
* *
45813366 TT-ATAATAGCTTTGGCTATATGATGGCAATTAGTGT
1 TTGA-AATAGCTTCGGCTATAT-ATGGCACTTAGTGT
45813402 ACGAAACATT
Statistics
Matches: 95, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
40 35 0.37
41 48 0.51
42 12 0.13
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (41 bp):
TTGAAATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGA
Found at i:45813342 original size:81 final size:83
Alignment explanation
Indices: 45813245--45813405 Score: 220
Period size: 81 Copynumber: 2.0 Consensus size: 83
45813235 GTATGAAATT
* * * *
45813245 TGAGATAACTTCGGCTATTTATGGCACTTAGTGTGCGA-TTTGA-AATAGCTTCGGCTCTAT-AT
1 TGAGATAACTTCGGCTATGTAAGGCACTTAGTGTGCGAGATT-ATAATAGCTTCGGCTATATGAT
*
45813307 GGCACTTAGTGTACGAGAA
65 GGCAATTAGTGTACGAGAA
** *
45813326 TGAGATAGTTTCGGCTATGTAAGGCACTTAGTGTGCGAGATTATAATAGCTTTGGCTATATGATG
1 TGAGATAACTTCGGCTATGTAAGGCACTTAGTGTGCGAGATTATAATAGCTTCGGCTATATGATG
45813391 GCAATTAGTGTACGA
66 GCAATTAGTGTACGA
45813406 AACATTGAGT
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
81 35 0.51
82 17 0.25
83 17 0.25
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.34
Consensus pattern (83 bp):
TGAGATAACTTCGGCTATGTAAGGCACTTAGTGTGCGAGATTATAATAGCTTCGGCTATATGATG
GCAATTAGTGTACGAGAA
Found at i:45814579 original size:39 final size:39
Alignment explanation
Indices: 45814531--45814658 Score: 220
Period size: 39 Copynumber: 3.3 Consensus size: 39
45814521 GTAACGGTAG
* *
45814531 CAGTAACAGTATTCAACACACAAAGTGCCGAGTCGGTAA
1 CAGTAACAGTATTCGACACACAAAGTGCCGAGTCAGTAA
*
45814570 CAGTAACAGTATTCGACACACAAAGTGCCTAGTCAGTAA
1 CAGTAACAGTATTCGACACACAAAGTGCCGAGTCAGTAA
*
45814609 CAGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAA
1 CAGTAACAGTATTCGACACACAAAGTGCCGAGTCAGTAA
45814648 CAGTAACAGTA
1 CAGTAACAGTA
45814659 GTTGGCACAT
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 84 1.00
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (39 bp):
CAGTAACAGTATTCGACACACAAAGTGCCGAGTCAGTAA
Found at i:45814653 original size:78 final size:77
Alignment explanation
Indices: 45814531--45814685 Score: 231
Period size: 78 Copynumber: 2.0 Consensus size: 77
45814521 GTAACGGTAG
* *
45814531 CAGTAACAGTATTCAACACACAAAGTGCCGAGTCGGTAACAGTAACAGTA-TTCGACACACAAAG
1 CAGTAACAGTATTCAACACACAAAGTGCCGAATCAGTAACAGTAACAGTAGTT-GACACA-AAAG
*
45814595 TGCCTAGTCAGTAA
64 TGCCTAATCAGTAA
* * *
45814609 CAGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAACAGTAACAGTAGTTGGCACATAAGTG
1 CAGTAACAGTATTCAACACACAAAGTGCCGAATCAGTAACAGTAACAGTAGTTGACACAAAAGTG
45814674 CCTAATCAGTAA
66 CCTAATCAGTAA
45814686 GCCGGCAAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
77 16 0.23
78 52 0.74
79 2 0.03
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (77 bp):
CAGTAACAGTATTCAACACACAAAGTGCCGAATCAGTAACAGTAACAGTAGTTGACACAAAAGTG
CCTAATCAGTAA
Found at i:45817546 original size:23 final size:22
Alignment explanation
Indices: 45817520--45817589 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 22
45817510 TGTGGTTGTT
*
45817520 TTTTTATGTTATAATGCTGTCCA
1 TTTTGATG-TATAATGCTGTCCA
*
45817543 TTTTGA-GCATATTAATGTTGTCCA
1 TTTTGATG--TA-TAATGCTGTCCA
*
45817567 ATTTGATGTATAAATGCTGTCCA
1 TTTTGATGTAT-AATGCTGTCCA
45817590 AAACAAGATA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
22 2 0.05
23 19 0.50
24 16 0.42
25 1 0.03
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.46
Consensus pattern (22 bp):
TTTTGATGTATAATGCTGTCCA
Found at i:45817558 original size:24 final size:23
Alignment explanation
Indices: 45817531--45817590 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
45817521 TTTTATGTTA
*
45817531 TAATGCTGTCCATTTTGA-GCATAT
1 TAATGCTGTCCAATTTGATG--TAT
*
45817555 TAATGTTGTCCAATTTGATGTAT
1 TAATGCTGTCCAATTTGATGTAT
*
45817578 AAATGCTGTCCAA
1 TAATGCTGTCCAA
45817591 AACAAGATAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 14 0.45
24 16 0.52
25 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (23 bp):
TAATGCTGTCCAATTTGATGTAT
Found at i:45818137 original size:18 final size:18
Alignment explanation
Indices: 45818114--45818148 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
45818104 TATTCATATC
*
45818114 TATTGTTGAAAATAAGAT
1 TATTGTTAAAAATAAGAT
45818132 TATTGTTAAAAATAAGA
1 TATTGTTAAAAATAAGA
45818149 AATTGAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (18 bp):
TATTGTTAAAAATAAGAT
Found at i:45818153 original size:17 final size:18
Alignment explanation
Indices: 45818115--45818153 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
45818105 ATTCATATCT
* *
45818115 ATTGTTGAAAATAAGATT
1 ATTGTTAAAAATAAGATA
45818133 ATTGTTAAAAATAAGA-A
1 ATTGTTAAAAATAAGATA
45818150 ATTG
1 ATTG
45818154 AATTGAATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36
Consensus pattern (18 bp):
ATTGTTAAAAATAAGATA
Found at i:45821117 original size:94 final size:94
Alignment explanation
Indices: 45820952--45821123 Score: 220
Period size: 94 Copynumber: 1.8 Consensus size: 94
45820942 AATGTTTAAA
* * * * * * **
45820952 TGTAAGACCATAGTTGGGCTATGGCGTTTTAATGAAAAGACCATAACTGGGTTATGGCACATTGA
1 TGTAAGACCATAGCTAGGCTATAGCATTCTAATGAAAAGACCATAACTGAGTTATGGCACATCAA
45821017 ACGTAAGACCATGACAGTATAAATACATG
66 ACGTAAGACCATGACAGTATAAATACATG
* * *
45821046 TGTAAGACCATAGCTAGGCTATAGCATTCTGATGATAAGACCATAACTGAGTTATGTCAC-TACA
1 TGTAAGACCATAGCTAGGCTATAGCATTCTAATGAAAAGACCATAACTGAGTTATGGCACAT-CA
*
45821110 AATGTAAGACCATG
65 AACGTAAGACCATG
45821124 GCAATGTATG
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
93 1 0.02
94 64 0.98
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (94 bp):
TGTAAGACCATAGCTAGGCTATAGCATTCTAATGAAAAGACCATAACTGAGTTATGGCACATCAA
ACGTAAGACCATGACAGTATAAATACATG
Found at i:45822922 original size:19 final size:19
Alignment explanation
Indices: 45822898--45822938 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
45822888 ACATACCTTT
45822898 AATAACATATTCACTACTA
1 AATAACATATTCACTACTA
45822917 AATAACATATTCACTACTA
1 AATAACATATTCACTACTA
45822936 AAT
1 AAT
45822939 TCAACATACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.32
Consensus pattern (19 bp):
AATAACATATTCACTACTA
Found at i:45826194 original size:16 final size:16
Alignment explanation
Indices: 45826173--45826220 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 16
45826163 AAAATAATGT
45826173 AAAATAATAAAATTAA
1 AAAATAATAAAATTAA
** *
45826189 AAAATAATATATTTTTTA
1 AAAATAATA-A-AATTAA
45826207 AAAATAATAAAATT
1 AAAATAATAAAATT
45826221 CGAGAGAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
16 11 0.44
17 2 0.08
18 12 0.48
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATAATAAAATTAA
Found at i:45826987 original size:21 final size:21
Alignment explanation
Indices: 45826963--45827006 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
45826953 GATTCATTCT
45826963 AAATATACCAAATA-TATTAAA
1 AAATATACCAAATATTA-TAAA
* *
45826984 AAATCTATCAAATATTATAAA
1 AAATATACCAAATATTATAAA
45827005 AA
1 AA
45827007 TGAAACATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (21 bp):
AAATATACCAAATATTATAAA
Found at i:45834933 original size:91 final size:91
Alignment explanation
Indices: 45834829--45835015 Score: 356
Period size: 91 Copynumber: 2.1 Consensus size: 91
45834819 TCCCATTGGA
*
45834829 GCCATTTCTTCTTAAATTGCTTTGTTTCATATTTCAGCTTTTCTTTATTCGTGCTGCTGTATTTG
1 GCCATTTCTTCTTAAATTGCTTTGTTTCATATTTCAGCTTTTCTTTATTCGTGCTGCTGTATTTC
45834894 TCTTGCCATGCTACATCATGGCCTGG
66 TCTTGCCATGCTACATCATGGCCTGG
*
45834920 GCCATTTCTTCTTAAATTGCTTTGTTTCATGTTTCAGCTTTTCTTTATTCGTGCTGCTGTATTTC
1 GCCATTTCTTCTTAAATTGCTTTGTTTCATATTTCAGCTTTTCTTTATTCGTGCTGCTGTATTTC
45834985 TCTTGCCATGCTACATCATGGCCTGG
66 TCTTGCCATGCTACATCATGGCCTGG
45835011 GCCAT
1 GCCAT
45835016 CAGTATATTA
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 94 1.00
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.47
Consensus pattern (91 bp):
GCCATTTCTTCTTAAATTGCTTTGTTTCATATTTCAGCTTTTCTTTATTCGTGCTGCTGTATTTC
TCTTGCCATGCTACATCATGGCCTGG
Found at i:45841607 original size:24 final size:24
Alignment explanation
Indices: 45841541--45841612 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 24
45841531 GAGTTATTAA
* * *
45841541 CGAGAAGCTCGTGAGAGTCATATAT
1 CGAGATGCTCATGAGAGACA-ATAT
* *
45841566 CGAG-TAGCTCAAGTGAGACAATAT
1 CGAGAT-GCTCATGAGAGACAATAT
*
45841590 CGAGATGCTCATGAGAGATAATA
1 CGAGATGCTCATGAGAGACAATA
45841613 ATGGGACACT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
24 22 0.59
25 15 0.41
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.22
Consensus pattern (24 bp):
CGAGATGCTCATGAGAGACAATAT
Found at i:45844280 original size:41 final size:43
Alignment explanation
Indices: 45844167--45844286 Score: 131
Period size: 45 Copynumber: 2.8 Consensus size: 43
45844157 AGGATTTTCG
* * *
45844167 ATATGTGTTCTCGTGTAAGACCAC-GTCTGGGACGATGGCATCGAT
1 ATATGTGAT-TCGTGTAAGACC-CTGTCTAGGAC-ATGACATCGAT
*
45844212 ATATGTGATTACGTGTAAGACCATGTCTAGGACATTGACATCG-T
1 ATATGTGATT-CGTGTAAGACCCTGTCTAGGACA-TGACATCGAT
45844256 AT-T-TGATTCGTGTAAGACCCTGTCTAGGACA
1 ATATGTGATTCGTGTAAGACCCTGTCTAGGACA
45844287 ATGGCATCAA
Statistics
Matches: 67, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
41 22 0.33
42 5 0.07
43 1 0.01
44 5 0.07
45 34 0.51
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (43 bp):
ATATGTGATTCGTGTAAGACCCTGTCTAGGACATGACATCGAT
Found at i:45854877 original size:21 final size:20
Alignment explanation
Indices: 45854841--45854886 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
45854831 ACCAATAAAA
45854841 TAAA-TGAGCTGAAATGTAGC
1 TAAATTGAGCTGAAATG-AGC
45854861 TAAATTGAGCTCG-AATGAGC
1 TAAATTGAGCT-GAAATGAGC
45854881 TGAAAT
1 T-AAAT
45854887 AAGCTCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
20 8 0.35
21 14 0.61
22 1 0.04
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (20 bp):
TAAATTGAGCTGAAATGAGC
Found at i:45854881 original size:31 final size:30
Alignment explanation
Indices: 45854843--45854901 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
45854833 CAATAAAATA
*
45854843 AATGAGCTGAAATGTAGCTAAATTGAGCTCG
1 AATGAGCTGAAAT-AAGCTAAATTGAGCTCG
*
45854874 AATGAGCTGAAATAAGCTCAATTGAGCT
1 AATGAGCTGAAATAAGCTAAATTGAGCT
45854902 GGTCGGAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (30 bp):
AATGAGCTGAAATAAGCTAAATTGAGCTCG
Found at i:45861945 original size:14 final size:14
Alignment explanation
Indices: 45861926--45861977 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
45861916 CAAAAATAAC
*
45861926 AAAAATAACAAAAT
1 AAAAATAAAAAAAT
45861940 AAAAATAAAAAAAT
1 AAAAATAAAAAAAT
* * *
45861954 AAAATTTATAAAAT
1 AAAAATAAAAAAAT
45861968 AAAAATAAAA
1 AAAAATAAAA
45861978 TTATAAACAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAAATAAAAAAAT
Found at i:45861956 original size:8 final size:8
Alignment explanation
Indices: 45861917--45861957 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
45861907 ACATGTATAC
45861917 AAAAATAA
1 AAAAATAA
45861925 CAAAAATAA
1 -AAAAATAA
*
45861934 CAAAAT--
1 AAAAATAA
45861940 AAAAATAA
1 AAAAATAA
45861948 AAAAATAA
1 AAAAATAA
45861956 AA
1 AA
45861958 TTTATAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
6 5 0.18
8 15 0.54
9 8 0.29
ACGTcount: A:0.83, C:0.05, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:45861973 original size:20 final size:20
Alignment explanation
Indices: 45861948--45861989 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
45861938 ATAAAAATAA
45861948 AAAAATAAAATTTATAAA-AT
1 AAAAATAAAA-TTATAAACAT
45861968 AAAAATAAAATTATAAACAT
1 AAAAATAAAATTATAAACAT
45861988 AA
1 AA
45861990 TAGACTAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAATAAAATTATAAACAT
Found at i:45862283 original size:3 final size:3
Alignment explanation
Indices: 45862275--45862334 Score: 52
Period size: 3 Copynumber: 19.7 Consensus size: 3
45862265 TGCGGTAAGT
* *
45862275 ATA ATA ATA AAA ATA TATA AT- ATA ATA ATA ATA A-A CTA ATA ATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
45862319 ATTCA GTA ATA ATA AT
1 A-T-A ATA ATA ATA AT
45862335 GTAATATATA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
2 3 0.07
3 37 0.80
4 5 0.11
5 1 0.02
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:45862308 original size:14 final size:14
Alignment explanation
Indices: 45862275--45862320 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
45862265 TGCGGTAAGT
45862275 ATAATAATA-AA-A
1 ATAATAATATAATA
45862287 ATATATAATATAATA
1 ATA-ATAATATAATA
45862302 ATAATAA-ACTAATA
1 ATAATAATA-TAATA
45862316 ATAAT
1 ATAAT
45862321 TCAGTAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 3 0.10
13 7 0.23
14 16 0.53
15 4 0.13
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAATAATATAATA
Found at i:45862319 original size:11 final size:10
Alignment explanation
Indices: 45862277--45862319 Score: 52
Period size: 11 Copynumber: 4.1 Consensus size: 10
45862267 CGGTAAGTAT
45862277 AATAATAA-A
1 AATAATAATA
45862286 AATATATAATA
1 AATA-ATAATA
45862297 TAATAATAATA
1 -AATAATAATA
45862308 AACTAATAATA
1 AA-TAATAATA
45862319 A
1 A
45862320 TTCAGTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.13
10 6 0.20
11 16 0.53
12 4 0.13
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (10 bp):
AATAATAATA
Found at i:45863810 original size:17 final size:16
Alignment explanation
Indices: 45863784--45863822 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
45863774 TTTTGATTGA
*
45863784 TTATTTTTTGAATGTT
1 TTATTTTTTGAATATT
45863800 TTATATTTTTGAATATT
1 TTAT-TTTTTGAATATT
45863817 TTATTT
1 TTATTT
45863823 ATAAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (16 bp):
TTATTTTTTGAATATT
Found at i:45864591 original size:43 final size:43
Alignment explanation
Indices: 45864503--45864596 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 43
45864493 ACCCTTGAAA
* * * * *
45864503 TTAAAACTGAGAAAAAAGGCCCAATAGAGCGGCAGTATTGCTGT
1 TTAAAACTAAGAAAAAAAGCCCAATA-AGCCGAAGTATTGATGT
*
45864547 TTAAAACTAAGAAAAAGAAGCCCAAT-AGCCGAAGTGTTGATGT
1 TTAAAACTAAGAAAAA-AAGCCCAATAAGCCGAAGTATTGATGT
45864590 TTAAAAC
1 TTAAAAC
45864597 CCATTTTAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
43 20 0.47
44 15 0.35
45 8 0.19
ACGTcount: A:0.43, C:0.15, G:0.21, T:0.21
Consensus pattern (43 bp):
TTAAAACTAAGAAAAAAAGCCCAATAAGCCGAAGTATTGATGT
Found at i:45874991 original size:13 final size:13
Alignment explanation
Indices: 45874973--45875001 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
45874963 ATAAAATTGG
45874973 AAAGATGATAAAT
1 AAAGATGATAAAT
45874986 AAAGATGATAAAT
1 AAAGATGATAAAT
45874999 AAA
1 AAA
45875002 AAATAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.14, T:0.21
Consensus pattern (13 bp):
AAAGATGATAAAT
Found at i:45876037 original size:26 final size:26
Alignment explanation
Indices: 45876008--45876189 Score: 97
Period size: 24 Copynumber: 7.4 Consensus size: 26
45875998 CTTATGAGTG
45876008 TCCCGTTATATGGCTCTTCGTGAGCT
1 TCCCGTTATATGGCTCTTCGTGAGCT
* *
45876034 TCCCGATTA-AAGGCTCTTTGTGAGCT
1 TCCCG-TTATATGGCTCTTCGTGAGCT
* *
45876060 TCTCG--ATATGGCTCGTT--TGAACT
1 TCCCGTTATATGGCTC-TTCGTGAGCT
* * * **
45876083 TCCCGATATATGGGT-ATCCAGAGCT
1 TCCCGTTATATGGCTCTTCGTGAGCT
*
45876108 TCCAGTTA-ATGGCTCTTCG-GAG-T
1 TCCCGTTATATGGCTCTTCGTGAGCT
*
45876131 TACCCGTTAT-T-G-TCTTGCATGAGCT
1 T-CCCGTTATATGGCTCTT-CGTGAGCT
* *
45876156 TCCTGATTATA--GCTCTT-ATGAGCT
1 TCCCG-TTATATGGCTCTTCGTGAGCT
45876180 TCCCGTTATA
1 TCCCGTTATA
45876190 CAGCCCGAAT
Statistics
Matches: 121, Mismatches: 19, Indels: 35
0.69 0.11 0.20
Matches are distributed among these distances:
22 4 0.03
23 20 0.17
24 38 0.31
25 28 0.23
26 28 0.23
27 3 0.02
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (26 bp):
TCCCGTTATATGGCTCTTCGTGAGCT
Found at i:45880485 original size:11 final size:11
Alignment explanation
Indices: 45880469--45880513 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
45880459 TTATATACTA
45880469 AATAAAATAAT
1 AATAAAATAAT
45880480 AATAAAAT-AT
1 AATAAAATAAT
* *
45880490 CACTAAAATATT
1 -AATAAAATAAT
45880502 AATAAAATAAT
1 AATAAAATAAT
45880513 A
1 A
45880514 TTTATTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 2 0.07
11 25 0.89
12 1 0.04
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:45886448 original size:22 final size:22
Alignment explanation
Indices: 45886386--45886451 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
45886376 ATTGTTCAAA
* **
45886386 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
45886408 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
45886430 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
45886452 TATGTTTAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:45898634 original size:48 final size:48
Alignment explanation
Indices: 45898567--45898727 Score: 216
Period size: 48 Copynumber: 3.4 Consensus size: 48
45898557 AGGTGAAAGA
* * ** *
45898567 AATAGTGCCT-GACTACCCGTTTGGGTTAAACCTACATGAACAATAAAT
1 AATAGTGCCTAG-TTACCCGTTAGGGTTAAACCTACACAAATAATAAAT
45898615 AATAGTGCCTAGTTACCCGTTAGGGTTAAACCTACACAAATAATAAAT
1 AATAGTGCCTAGTTACCCGTTAGGGTTAAACCTACACAAATAATAAAT
* * *
45898663 AATAGTGCCTGGTTACCCGTTAGGGTTAAACTTACACAAATAATGAAT
1 AATAGTGCCTAGTTACCCGTTAGGGTTAAACCTACACAAATAATAAAT
**
45898711 AATAGTGTTTAGTTACC
1 AATAGTGCCTAGTTACC
45898728 TATTATGTAA
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
48 100 0.99
49 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (48 bp):
AATAGTGCCTAGTTACCCGTTAGGGTTAAACCTACACAAATAATAAAT
Found at i:45899945 original size:41 final size:40
Alignment explanation
Indices: 45899889--45899987 Score: 126
Period size: 41 Copynumber: 2.4 Consensus size: 40
45899879 TATAAAATTC
** *
45899889 GAGATAGCTTCGGCTATTTATGGCACTTAGTGTGCGAGACT
1 GAGATAGCTTCGGCTATGCAAGGCACTTAGTGTGCGAGA-T
*
45899930 GAGATAGCTTCGGCTATGCAAGGCACTTGGTGTGCGAGAT
1 GAGATAGCTTCGGCTATGCAAGGCACTTAGTGTGCGAGAT
* *
45899970 TATAATAGCTTCGGCTAT
1 GA-GATAGCTTCGGCTAT
45899988 ACGATGACAA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
40 2 0.04
41 49 0.96
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.30
Consensus pattern (40 bp):
GAGATAGCTTCGGCTATGCAAGGCACTTAGTGTGCGAGAT
Found at i:45901981 original size:56 final size:50
Alignment explanation
Indices: 45901715--45902009 Score: 277
Period size: 50 Copynumber: 5.8 Consensus size: 50
45901705 TAATAACATA
* * ** * * *
45901715 CCAAAGCCATGTCCCAGACATGGTCTTACATGGAATGTTTCATGT-ACTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTG
* * * ** * *
45901764 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTG
* * * *** * * *
45901814 CCCATGCCATGTCCCAGACATGGCCTTATGGGGGATCTCTCATCCCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTG
*
45901864 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCAGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTG
*
45901914 CCAACGCCATGTCCAAGACATGGTCTTACATGGGACCTCTCATAATCTCAAGAATG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC-AG--TG
* * *
45901970 CCAATGTCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
45902010 TTACCCAAAT
Statistics
Matches: 202, Mismatches: 37, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
49 37 0.18
50 121 0.60
53 4 0.02
54 2 0.01
56 38 0.19
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.26
Consensus pattern (50 bp):
CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTG
Found at i:45904835 original size:24 final size:24
Alignment explanation
Indices: 45904800--45904887 Score: 101
Period size: 24 Copynumber: 3.8 Consensus size: 24
45904790 TTATATGTTA
* *
45904800 TAATGATGTCCATTTTGAGCATAT
1 TAATGCTGTCCAATTTGAGCATAT
* *
45904824 TGATGCTATCCAATTTGATG--TA-
1 TAATGCTGTCCAATTTGA-GCATAT
*
45904846 TAATGCTGTCCATTTTGAGCATAT
1 TAATGCTGTCCAATTTGAGCATAT
45904870 TAATGCTGTCCAATTTGA
1 TAATGCTGTCCAATTTGA
45904888 TGTATAAATG
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
21 1 0.02
22 15 0.29
23 4 0.08
24 31 0.60
25 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (24 bp):
TAATGCTGTCCAATTTGAGCATAT
Found at i:45904856 original size:46 final size:46
Alignment explanation
Indices: 45904798--45904904 Score: 169
Period size: 46 Copynumber: 2.3 Consensus size: 46
45904788 TTTTATATGT
*
45904798 TATAATGATGTCCATTTTGAGCATATTGATGCTATCCAATTTGATG
1 TATAATGATGTCCATTTTGAGCATATTAATGCTATCCAATTTGATG
* *
45904844 TATAATGCTGTCCATTTTGAGCATATTAATGCTGTCCAATTTGATG
1 TATAATGATGTCCATTTTGAGCATATTAATGCTATCCAATTTGATG
*
45904890 TATAAATGTTGTCCA
1 TAT-AATGATGTCCA
45904905 AAACAAGGTA
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
46 46 0.82
47 10 0.18
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (46 bp):
TATAATGATGTCCATTTTGAGCATATTAATGCTATCCAATTTGATG
Found at i:45904902 original size:23 final size:22
Alignment explanation
Indices: 45904826--45904905 Score: 90
Period size: 24 Copynumber: 3.5 Consensus size: 22
45904816 GAGCATATTG
*
45904826 ATGCTATCCAATTTGATGTATA
1 ATGCTGTCCAATTTGATGTATA
*
45904848 ATGCTGTCCATTTTGA-GCATATTA
1 ATGCTGTCCAATTTGATG--TA-TA
45904872 ATGCTGTCCAATTTGATGTATAA
1 ATGCTGTCCAATTTGATGTAT-A
*
45904895 ATGTTGTCCAA
1 ATGCTGTCCAA
45904906 AACAAGGTAG
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
21 1 0.02
22 15 0.31
23 15 0.31
24 17 0.35
25 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (22 bp):
ATGCTGTCCAATTTGATGTATA
Found at i:45908422 original size:22 final size:22
Alignment explanation
Indices: 45908397--45908439 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
45908387 GCACTATTGA
*
45908397 ATAGAGAGCACTAAAGTGCTAT
1 ATAGAGAGCACGAAAGTGCTAT
*
45908419 ATAGAGAGCACGAATGTGCTA
1 ATAGAGAGCACGAAAGTGCTA
45908440 AACGGAGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.14, G:0.26, T:0.21
Consensus pattern (22 bp):
ATAGAGAGCACGAAAGTGCTAT
Found at i:45910501 original size:2 final size:2
Alignment explanation
Indices: 45910494--45910546 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
45910484 GGGGAACTAG
45910494 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
45910536 AT AT AT AT AT A
1 AT AT AT AT AT A
45910547 GTAGTAGTAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:45925550 original size:2 final size:2
Alignment explanation
Indices: 45925543--45925588 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
45925533 TTTTCACACG
*
45925543 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
45925585 CT CT
1 CT CT
45925589 TTTCAGAGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:45931993 original size:3 final size:3
Alignment explanation
Indices: 45931985--45932024 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
45931975 GTGCGATTTT
45931985 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
45932025 AGAATTAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:45932973 original size:19 final size:19
Alignment explanation
Indices: 45932935--45932977 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
45932925 CTGTTTTTGT
*
45932935 TGAAGTTTTAGATTTTTGA
1 TGAAGTTTTAGATTTCTGA
* *
45932954 TGAAGTTTTTGCTTTCTGA
1 TGAAGTTTTAGATTTCTGA
45932973 TGAAG
1 TGAAG
45932978 AAAAGAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (19 bp):
TGAAGTTTTAGATTTCTGA
Found at i:45939607 original size:23 final size:23
Alignment explanation
Indices: 45939581--45939626 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
45939571 GTAATTATAA
45939581 ATACATGTGTAATAAATATATGT
1 ATACATGTGTAATAAATATATGT
* *
45939604 ATACATTTGTAATTAATATATGT
1 ATACATGTGTAATAAATATATGT
45939627 CCATACTTAT
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:0.41, C:0.04, G:0.11, T:0.43
Consensus pattern (23 bp):
ATACATGTGTAATAAATATATGT
Found at i:45940765 original size:20 final size:20
Alignment explanation
Indices: 45940740--45940778 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
45940730 TTCAATTAAG
*
45940740 TCTTTCATT-AAGTGTTTTTT
1 TCTTTC-TTCAAGTATTTTTT
45940760 TCTTTCTTCAAGTATTTTT
1 TCTTTCTTCAAGTATTTTT
45940779 CATCTAGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.15, C:0.13, G:0.08, T:0.64
Consensus pattern (20 bp):
TCTTTCTTCAAGTATTTTTT
Found at i:45940827 original size:14 final size:14
Alignment explanation
Indices: 45940767--45940831 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
45940757 TTTTCTTTCT
* *
45940767 TCAAGTATTTTTCA
1 TCAAGTTTTTTTTA
* *
45940781 TCTAG-TTCTTTTA
1 TCAAGTTTTTTTTA
*
45940794 TCAAGTTTTTAATTA
1 TCAAGTTTTT-TTTA
*
45940809 CCAAGTTTTTTTTA
1 TCAAGTTTTTTTTA
45940823 TCAAGTTTT
1 TCAAGTTTT
45940832 GCAACAAGTT
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
13 9 0.23
14 18 0.46
15 12 0.31
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.55
Consensus pattern (14 bp):
TCAAGTTTTTTTTA
Found at i:45940863 original size:24 final size:25
Alignment explanation
Indices: 45940774--45940890 Score: 94
Period size: 25 Copynumber: 4.6 Consensus size: 25
45940764 TCTTCAAGTA
* *
45940774 TTTTTCATCTAGTTCTTTTATCAAG
1 TTTTTCATCAAGTTCTTTTATAAAG
* * *
45940799 TTTTTAATTACCAAGTTTTTTTTATCAAG
1 TTTTTCA-T--CAAG-TTCTTTTATAAAG
* *
45940828 TTTTGCAACAAGTTCTTTT-TAAAG
1 TTTTTCATCAAGTTCTTTTATAAAG
*
45940852 TTTTTCATCAAG-TCTTTTCATAAAA
1 TTTTTCATCAAGTTCTTTT-ATAAAG
*
45940877 TTTTCCATCAAGTT
1 TTTTTCATCAAGTT
45940891 TTTAATCATT
Statistics
Matches: 73, Mismatches: 12, Indels: 13
0.74 0.12 0.13
Matches are distributed among these distances:
23 6 0.08
24 14 0.19
25 27 0.37
26 6 0.08
28 3 0.04
29 17 0.23
ACGTcount: A:0.26, C:0.15, G:0.08, T:0.51
Consensus pattern (25 bp):
TTTTTCATCAAGTTCTTTTATAAAG
Found at i:45940864 original size:12 final size:12
Alignment explanation
Indices: 45940774--45940898 Score: 63
Period size: 12 Copynumber: 9.8 Consensus size: 12
45940764 TCTTCAAGTA
*
45940774 TTTTTCATCTAG
1 TTTTTCATCAAG
*
45940786 TTCTTTTATCAAG
1 TT-TTTCATCAAG
*
45940799 TTTTTAATTACCAAG
1 TTTTTCA-T--CAAG
*
45940814 TTTTTTTTATCAAG
1 --TTTTTCATCAAG
* *
45940828 TTTTGCAACAAG
1 TTTTTCATCAAG
* *
45940840 TTCTTT-TTAAAG
1 TT-TTTCATCAAG
45940852 TTTTTCATCAAG
1 TTTTTCATCAAG
* *
45940864 TCTTTTCATAAAA
1 T-TTTTCATCAAG
*
45940877 TTTTCCATCAAG
1 TTTTTCATCAAG
*
45940889 TTTTTAATCA
1 TTTTTCATCA
45940899 TTTCGTTTTT
Statistics
Matches: 84, Mismatches: 20, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
11 3 0.04
12 43 0.51
13 23 0.27
14 4 0.05
15 4 0.05
16 1 0.01
17 6 0.07
ACGTcount: A:0.27, C:0.14, G:0.07, T:0.51
Consensus pattern (12 bp):
TTTTTCATCAAG
Found at i:45942211 original size:27 final size:26
Alignment explanation
Indices: 45942181--45942244 Score: 78
Period size: 25 Copynumber: 2.5 Consensus size: 26
45942171 TTAAGGAACT
*
45942181 TTAGCGCGCTCTCTGATTATTAGCACG
1 TTAG-GCGCTCTCTGATTACTAGCACG
*
45942208 TTA-GTGCTCTCTGATTACTAGCACG
1 TTAGGCGCTCTCTGATTACTAGCACG
*
45942233 TTA-GTGCTCTCT
1 TTAGGCGCTCTCT
45942245 ATTTAGCACA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 32 0.91
27 3 0.09
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.38
Consensus pattern (26 bp):
TTAGGCGCTCTCTGATTACTAGCACG
Found at i:45942216 original size:25 final size:25
Alignment explanation
Indices: 45942188--45942297 Score: 112
Period size: 25 Copynumber: 4.6 Consensus size: 25
45942178 ACTTTAGCGC
45942188 GCTCTCTGATTATTAGCACGTTAGT
1 GCTCTCTGATTATTAGCACGTTAGT
*
45942213 GCTCTCTGATTACTAGCACGTTAGT
1 GCTCTCTGATTATTAGCACGTTAGT
*
45942238 GCTCTCT-A-T-TTAGCACATCT-GT
1 GCTCTCTGATTATTAGCACGT-TAGT
45942260 GCTCTCTG--TA-TAGCAC-TTCAGT
1 GCTCTCTGATTATTAGCACGTT-AGT
45942282 GCTCTCTG-TTCATTAG
1 GCTCTCTGATT-ATTAG
45942298 TGCATAACAA
Statistics
Matches: 74, Mismatches: 3, Indels: 16
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.01
21 1 0.01
22 33 0.45
23 3 0.04
24 2 0.03
25 34 0.46
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTTAGT
Found at i:45942289 original size:22 final size:22
Alignment explanation
Indices: 45942201--45942290 Score: 94
Period size: 22 Copynumber: 4.0 Consensus size: 22
45942191 CTCTGATTAT
45942201 TAGCACGTTAGTGCTCTCTGATTA
1 TAGCACGTTAGTGCTCTCTG--TA
* *
45942225 CTAGCACGTTAGTGCTCTCTATT
1 -TAGCACGTTAGTGCTCTCTGTA
*
45942248 TAGCACATCT-GTGCTCTCTGTA
1 TAGCACGT-TAGTGCTCTCTGTA
45942270 TAGCAC-TTCAGTGCTCTCTGT
1 TAGCACGTT-AGTGCTCTCTGT
45942291 TCATTAGTGC
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 34 0.60
23 2 0.04
25 19 0.33
ACGTcount: A:0.18, C:0.26, G:0.19, T:0.38
Consensus pattern (22 bp):
TAGCACGTTAGTGCTCTCTGTA
Found at i:45944502 original size:21 final size:21
Alignment explanation
Indices: 45944476--45944531 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
45944466 AATAGCGGTG
*
45944476 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
45944497 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
45944518 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
45944532 AACAATGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:45960100 original size:8 final size:8
Alignment explanation
Indices: 45960087--45960138 Score: 56
Period size: 8 Copynumber: 6.8 Consensus size: 8
45960077 AAGAATGGGC
45960087 CTTTTTCT
1 CTTTTTCT
45960095 CTTTTT-T
1 CTTTTTCT
45960102 CTTTTT-T
1 CTTTTTCT
*
45960109 -TTTCTCT
1 CTTTTTCT
*
45960116 TTTTTTCTT
1 CTTTTTC-T
45960125 CTTTTTCT
1 CTTTTTCT
45960133 CTTTTT
1 CTTTTT
45960139 TTTCTTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
6 4 0.11
7 9 0.24
8 18 0.47
9 7 0.18
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (8 bp):
CTTTTTCT
Found at i:45960102 original size:9 final size:9
Alignment explanation
Indices: 45960088--45960148 Score: 70
Period size: 9 Copynumber: 6.6 Consensus size: 9
45960078 AGAATGGGCC
45960088 TTTTTCTCT
1 TTTTTCTCT
*
45960097 TTTTTCTTTT
1 TTTTTC-TCT
45960107 TTTTTCTCT
1 TTTTTCTCT
45960116 TTTTT-TCTT
1 TTTTTCTC-T
45960125 CTTTTTCTCT
1 -TTTTTCTCT
*
45960135 TTTTTTTCT
1 TTTTTCTCT
45960144 TTTTT
1 TTTTT
45960149 TTTGCTGGGC
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
8 2 0.04
9 27 0.60
10 14 0.31
11 2 0.04
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTCTCT
Found at i:45960112 original size:19 final size:19
Alignment explanation
Indices: 45960088--45960151 Score: 92
Period size: 20 Copynumber: 3.3 Consensus size: 19
45960078 AGAATGGGCC
45960088 TTTTTCTCTTTTTTCTTTT
1 TTTTTCTCTTTTTTCTTTT
45960107 TTTTTCTCTTTTTTTCTTCTT
1 TTTTTCTC-TTTTTTCTT-TT
* *
45960128 TTTCTCTTTTTTTTCTTTT
1 TTTTTCTCTTTTTTCTTTT
45960147 TTTTT
1 TTTTT
45960152 GCTGGGCTGG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
19 14 0.35
20 18 0.45
21 8 0.20
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTCTCTTTTTTCTTTT
Found at i:45960149 original size:9 final size:9
Alignment explanation
Indices: 45960088--45960150 Score: 81
Period size: 10 Copynumber: 6.6 Consensus size: 9
45960078 AGAATGGGCC
*
45960088 TTTTTCTCT
1 TTTTTCTTT
45960097 TTTTTCTTTT
1 TTTTTC-TTT
45960107 TTTTTCTCTT
1 TTTTTCT-TT
45960117 TTTTTCTTCT
1 TTTTTCTT-T
45960127 TTTTCTCTTT
1 TTTT-TCTTT
45960137 TTTTTCTTT
1 TTTTTCTTT
45960146 TTTTT
1 TTTTT
45960151 TGCTGGGCTG
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
9 18 0.37
10 27 0.55
11 4 0.08
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:45960362 original size:12 final size:12
Alignment explanation
Indices: 45960336--45960385 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
45960326 TGGTCTGCTG
45960336 CTTTT-TTTTT-
1 CTTTTCTTTTTC
*
45960346 C-TTTCCTTTTC
1 CTTTTCTTTTTC
45960357 CTTTTCTTTTTC
1 CTTTTCTTTTTC
* *
45960369 TTTTTCTTTTTT
1 CTTTTCTTTTTC
45960381 CTTTT
1 CTTTT
45960386 TTTCTTCTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 3 0.09
10 5 0.16
11 1 0.03
12 23 0.72
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
CTTTTCTTTTTC
Found at i:45960372 original size:11 final size:11
Alignment explanation
Indices: 45960336--45960398 Score: 60
Period size: 11 Copynumber: 5.8 Consensus size: 11
45960326 TGGTCTGCTG
45960336 CTTTT-TTTTT
1 CTTTTCTTTTT
* *
45960346 CTTTCCTTTTC
1 CTTTTCTTTTT
45960357 CTTTTCTTTTT
1 CTTTTCTTTTT
45960368 CTTTTTCTTTTT
1 C-TTTTCTTTTT
*
45960380 -TCTT-TTTTT
1 CTTTTCTTTTT
45960389 CTTCTTCTTT
1 CTT-TTCTTT
45960399 GGGCCAAACC
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.19
11 16 0.38
12 13 0.31
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
CTTTTCTTTTT
Found at i:45960374 original size:24 final size:23
Alignment explanation
Indices: 45960336--45960394 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
45960326 TGGTCTGCTG
45960336 CTTTTTTTTTC--TTTCCTTTTC
1 CTTTTTTTTTCTTTTTCCTTTTC
* *
45960357 CTTTTCTTTTTCTTTTTCTTTTTT
1 CTTTT-TTTTTCTTTTTCCTTTTC
45960381 CTTTTTTTCTTCTT
1 CTTTTTTT-TTCTT
45960395 CTTTGGGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 5 0.16
22 6 0.19
23 3 0.09
24 18 0.56
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (23 bp):
CTTTTTTTTTCTTTTTCCTTTTC
Found at i:45960397 original size:6 final size:6
Alignment explanation
Indices: 45960347--45960386 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
45960337 TTTTTTTTTC
* *
45960347 TTTCCT TTTCCT TTTCTT TTTCTT TTTCTTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTC-TT TTTCTT TTT
45960387 TTCTTCTTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 26 0.81
7 6 0.19
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTCTT
Found at i:45961015 original size:30 final size:30
Alignment explanation
Indices: 45960944--45961049 Score: 153
Period size: 30 Copynumber: 3.6 Consensus size: 30
45960934 GGAAAAATAT
*
45960944 GGGTCTAAAATG-CATTTATGAAAAGTTTA
1 GGGTCTAAAATGTAATTTATGAAAAGTTTA
*
45960973 GGG-CTCAAATGTAATTTATGAAAAGTTTA
1 GGGTCTAAAATGTAATTTATGAAAAGTTTA
*
45961002 GGGTCTAAAATGTAATTTATAAAAAGTTTA
1 GGGTCTAAAATGTAATTTATGAAAAGTTTA
* *
45961032 GGGGCTAAAATATAATTT
1 GGGTCTAAAATGTAATTT
45961050 CTTTAAAAAG
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
28 7 0.10
29 22 0.32
30 40 0.58
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.35
Consensus pattern (30 bp):
GGGTCTAAAATGTAATTTATGAAAAGTTTA
Found at i:45966203 original size:107 final size:107
Alignment explanation
Indices: 45966017--45966232 Score: 387
Period size: 107 Copynumber: 2.0 Consensus size: 107
45966007 CTATTCAAAA
45966017 AAGATTTTCTAAATAAGGCAATATTTCGCGTTTGGAAATTCGAGAAAACATGCCCTAACGTGCTG
1 AAGATTTTCTAAATAAGGCAATATTTCGCGTTTGGAAATTCGAGAAAACATGCCCTAACGTGCTG
*
45966082 GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
66 GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTCTT
* * *
45966124 AAGATTTTCTAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTG
1 AAGATTTTCTAAATAAGGCAATATTTCGCGTTTGGAAATTCGAGAAAACATGCCCTAACGTGCTG
*
45966189 GGTTTCGATTTCTCGTTCGACTAAATAGCCAAATATCCTCTT
66 GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTCTT
45966231 AA
1 AA
45966233 AACTTCAAAG
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
107 104 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (107 bp):
AAGATTTTCTAAATAAGGCAATATTTCGCGTTTGGAAATTCGAGAAAACATGCCCTAACGTGCTG
GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTCTT
Found at i:45974139 original size:17 final size:16
Alignment explanation
Indices: 45974117--45974156 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
45974107 AAAAGAATTA
*
45974117 TATTTTTTTCATCTTTC
1 TATTTTTTT-ACCTTTC
45974134 TATTTTTTTACCTTTC
1 TATTTTTTTACCTTTC
*
45974150 AATTTTT
1 TATTTTT
45974157 ATATTTCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTTTTTTACCTTTC
Found at i:45974171 original size:16 final size:16
Alignment explanation
Indices: 45974120--45974171 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 16
45974110 AGAATTATAT
*
45974120 TTTTTTCATCTTTCTAT
1 TTTTTT-ATCTTTCTAA
*
45974137 TTTTTTACCTTTC-AA
1 TTTTTTATCTTTCTAA
*
45974152 -TTTTTATATTTCTAA
1 TTTTTTATCTTTCTAA
45974167 TTTTT
1 TTTTT
45974172 ATGAATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
14 10 0.34
15 3 0.10
16 10 0.34
17 6 0.21
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTTTATCTTTCTAA
Found at i:45982959 original size:46 final size:46
Alignment explanation
Indices: 45982892--45983095 Score: 333
Period size: 46 Copynumber: 4.5 Consensus size: 46
45982882 TGATCAGTGA
* *
45982892 CAAGTGACAAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGAT
1 CAAGTGAAAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGAT
45982938 CAAGTGAAAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGAT
1 CAAGTGAAAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGAT
45982984 CAAGTGAAAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGAT
1 CAAGTGAAAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGAT
* *
45983030 CAAGTGACAAAGTGATAAGTGATAGCC-TAGCTACACTTATCTGAT
1 CAAGTGAAAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGAT
* *
45983075 C-AG-GGACAAGTGATAAGTGGT
1 CAAGTGAAAAAGTGATAAGTGGT
45983096 TATACGTAAG
Statistics
Matches: 150, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
43 14 0.09
44 2 0.01
45 19 0.13
46 115 0.77
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.26
Consensus pattern (46 bp):
CAAGTGAAAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGAT
Found at i:45986236 original size:11 final size:11
Alignment explanation
Indices: 45986208--45986247 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
45986198 ACCTAAATTC
45986208 TATATTTTATT
1 TATATTTTATT
45986219 T-TATTTTATT
1 TATATTTTATT
45986229 TATATTTTATAT
1 TATATTTTAT-T
45986241 TA-ATTTT
1 TATATTTT
45986248 TATGATCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.37
11 14 0.52
12 3 0.11
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TATATTTTATT
Found at i:45988234 original size:13 final size:13
Alignment explanation
Indices: 45988216--45988255 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
45988206 GGTTTGATAA
*
45988216 TGCTTTGGAAAAG
1 TGCTTTTGAAAAG
45988229 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
45988242 TGTTTTTGAAAAG
1 TGCTTTTGAAAAG
45988255 T
1 T
45988256 TTGGTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.30, C:0.05, G:0.25, T:0.40
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:45989734 original size:23 final size:24
Alignment explanation
Indices: 45989687--45989730 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
45989677 TGTTCATCTA
45989687 TTTTTTACTTATTATGTATTGTGT
1 TTTTTTACTTATTATGTATTGTGT
*
45989711 TTTTTTTC-TATTAT-TATTGT
1 TTTTTTACTTATTATGTATTGT
45989731 TGTTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 6 0.32
24 7 0.37
ACGTcount: A:0.16, C:0.05, G:0.09, T:0.70
Consensus pattern (24 bp):
TTTTTTACTTATTATGTATTGTGT
Found at i:46002454 original size:31 final size:31
Alignment explanation
Indices: 46002419--46002479 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
46002409 TAACAACCAG
*
46002419 TGACTTCAATAAAACCTATCGAATAGTTCAA
1 TGACTTAAATAAAACCTATCGAATAGTTCAA
* * * *
46002450 TGACTTAAATGAAAGCTTTTGAATAGTTCA
1 TGACTTAAATAAAACCTATCGAATAGTTCA
46002480 GTGATATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (31 bp):
TGACTTAAATAAAACCTATCGAATAGTTCAA
Found at i:46002937 original size:22 final size:23
Alignment explanation
Indices: 46002912--46002954 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
46002902 AATTGAATTT
46002912 TTAAATCT-GAAAAATAAAAGGA
1 TTAAATCTCGAAAAATAAAAGGA
*
46002934 TTAAATTTCGAAAAATAAAAG
1 TTAAATCTCGAAAAATAAAAG
46002955 TAAGAGGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.58, C:0.05, G:0.12, T:0.26
Consensus pattern (23 bp):
TTAAATCTCGAAAAATAAAAGGA
Found at i:46008579 original size:31 final size:31
Alignment explanation
Indices: 46008543--46008621 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
46008533 GGACCCCAAA
* *
46008543 AAGTTTAAGTACCAACTTA-AGAAGAAGTGTC
1 AAGTTTAAGTACCAAATTAGA-AAAAAGTGTC
* *
46008574 AAGTTTAGGTATCAAATTAGAAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAGAAAAAAGTGTC
*
46008605 AAGTTCAAGTACCAAAT
1 AAGTTTAAGTACCAAAT
46008622 GTTATATTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 39 0.98
32 1 0.03
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.27
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAGAAAAAAGTGTC
Found at i:46021734 original size:25 final size:25
Alignment explanation
Indices: 46021680--46021763 Score: 91
Period size: 25 Copynumber: 3.4 Consensus size: 25
46021670 CAGCTCTTAT
* *
46021680 GAGCTTACCGATACTCAACTC-ACATA
1 GAGCTTACCGTTACTCAGCTCGA-A-A
* *
46021706 -AGCTTACCGTTACTCAGCTCGGAG
1 GAGCTTACCGTTACTCAGCTCGAAA
*
46021730 GAGCTTACCGTTATTCAGCTCGAAA
1 GAGCTTACCGTTACTCAGCTCGAAA
46021755 GAGCTTACC
1 GAGCTTACC
46021764 ATTTACAGCT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (25 bp):
GAGCTTACCGTTACTCAGCTCGAAA
Found at i:46026129 original size:18 final size:18
Alignment explanation
Indices: 46026103--46026137 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
46026093 TCATCCATGT
*
46026103 TTTGAATGTTAATGTTGC
1 TTTGAATGTTAAGGTTGC
*
46026121 TTTGTATGTTAAGGTTG
1 TTTGAATGTTAAGGTTG
46026138 ATTTTGCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.03, G:0.26, T:0.51
Consensus pattern (18 bp):
TTTGAATGTTAAGGTTGC
Found at i:46027568 original size:13 final size:13
Alignment explanation
Indices: 46027550--46027576 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
46027540 TGGAATTGGT
46027550 ACGTGCTAATATC
1 ACGTGCTAATATC
46027563 ACGTGCTAATATC
1 ACGTGCTAATATC
46027576 A
1 A
46027577 ATATGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (13 bp):
ACGTGCTAATATC
Found at i:46035073 original size:20 final size:20
Alignment explanation
Indices: 46035034--46035078 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
46035024 TATTAAATTG
*
46035034 TTTTATTTATAAGACCATTA
1 TTTTATTTATAAAACCATTA
**
46035054 TTTTATTTATAAAATTATTA
1 TTTTATTTATAAAACCATTA
46035074 TTTTA
1 TTTTA
46035079 ATAAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTTATTTATAAAACCATTA
Found at i:46041317 original size:15 final size:15
Alignment explanation
Indices: 46041294--46041324 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
46041284 TATTTTAATT
46041294 GAACAAGTTCTTAAG
1 GAACAAGTTCTTAAG
*
46041309 GAACGAGTTCTTAAG
1 GAACAAGTTCTTAAG
46041324 G
1 G
46041325 GAAGAAGTTA
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:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (15 bp):
GAACAAGTTCTTAAG
Found at i:46041333 original size:16 final size:16
Alignment explanation
Indices: 46041294--46041333 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
46041284 TATTTTAATT
46041294 GAAC-AAGTTCTTAAG
1 GAACGAAGTTCTTAAG
46041309 GAACG-AGTTCTTAAGG
1 GAACGAAGTTCTTAA-G
46041325 GAA-GAAGTT
1 GAACGAAGTT
46041334 ATCAATCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.38, C:0.10, G:0.28, T:0.25
Consensus pattern (16 bp):
GAACGAAGTTCTTAAG
Found at i:46044452 original size:3 final size:3
Alignment explanation
Indices: 46044444--46044468 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
46044434 CTTTCATTCC
46044444 ACT ACT ACT ACT ACT ACT ACT ACT A
1 ACT ACT ACT ACT ACT ACT ACT ACT A
46044469 ACAGTTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ACT
Found at i:46055888 original size:18 final size:17
Alignment explanation
Indices: 46055865--46055908 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
46055855 TGCTTTGAAG
*
46055865 TTTTTAATTGTTATAATA
1 TTTTTAATTATT-TAATA
46055883 TTTTTAATTATTTAATA
1 TTTTTAATTATTTAATA
46055900 TATTTTAAT
1 T-TTTTAAT
46055909 AGATTCAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTTTAATTATTTAATA
Found at i:46056405 original size:22 final size:22
Alignment explanation
Indices: 46056343--46056409 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
46056333 ATTGTTCAAA
* **
46056343 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
46056365 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
46056387 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
46056409 C
1 C
46056410 CCAACTTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:46067042 original size:24 final size:24
Alignment explanation
Indices: 46067001--46067047 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
46066991 ATAGAAGATT
**
46067001 TAGTATTTATGAGTATAATATATC
1 TAGTATTTATGAACATAATATATC
*
46067025 TAGTATTTATTAACATAATATAT
1 TAGTATTTATGAACATAATATAT
46067048 TTGACTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (24 bp):
TAGTATTTATGAACATAATATATC
Found at i:46069923 original size:16 final size:15
Alignment explanation
Indices: 46069910--46069942 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
46069900 TCGTTTTTTG
46069910 TTTATTTTCATTTTAT
1 TTTATTTT-ATTTTAT
46069926 TTTATTTTA-TTTAT
1 TTTATTTTATTTTAT
46069940 TTT
1 TTT
46069943 TTGTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 1 0.06
16 8 0.47
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTATTTTATTTTAT
Found at i:46069940 original size:4 final size:5
Alignment explanation
Indices: 46069910--46069942 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
46069900 TCGTTTTTTG
46069910 TTTAT TTTCAT TTTAT TTTAT TTTA- TTTAT TTT
1 TTTAT TTT-AT TTTAT TTTAT TTTAT TTTAT TTT
46069943 TTGTTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 17 0.65
6 5 0.19
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:46069943 original size:10 final size:10
Alignment explanation
Indices: 46069910--46069942 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
46069900 TCGTTTTTTG
46069910 TTTATTTTCAT
1 TTTATTTT-AT
46069921 TTTATTTTAT
1 TTTATTTTAT
46069931 TTTA-TTTAT
1 TTTATTTTAT
46069940 TTT
1 TTT
46069943 TTGTTTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 8 0.36
10 6 0.27
11 8 0.36
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTATTTTAT
Found at i:46070509 original size:3 final size:3
Alignment explanation
Indices: 46070503--46070577 Score: 71
Period size: 3 Copynumber: 24.0 Consensus size: 3
46070493 ATTTTTTTAC
* * *
46070503 ATT ATT ATT A-T ATT TTT ATT ATT ACTT GTTT ATT ATT CTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT -ATT ATT ATT ATT ATT ATT
*
46070549 ATTT ATT ATT ATT AAT ATT ATTT ATT ATT
1 A-TT ATT ATT ATT ATT ATT A-TT ATT ATT
46070578 TTCATGTACT
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
2 2 0.03
3 47 0.80
4 10 0.17
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (3 bp):
ATT
Done.