Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 190 of 206
Found at i:57682771 original size:18 final size:18
Alignment explanation
Indices: 57682748--57682782 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
57682738 CTCAGGTTAG
*
57682748 GATTTTTAGGGTTTTTAA
1 GATTTTTAGGGGTTTTAA
57682766 GATTTTTAGGGGTTTTA
1 GATTTTTAGGGGTTTTA
57682783 GGGAAAAAGT
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:0.20, C:0.00, G:0.26, T:0.54
Consensus pattern (18 bp):
GATTTTTAGGGGTTTTAA
Found at i:57683177 original size:127 final size:125
Alignment explanation
Indices: 57682896--57683588 Score: 948
Period size: 127 Copynumber: 5.5 Consensus size: 125
57682886 GATTAAATCA
* * * * * *
57682896 AAGCAGGATGATTTATCAGAAGGATTTTTGAAGTCGCGCCCACGTGTACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * *
57682961 AGGTCCTGGAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACACTTC
66 AGGTCCTGGAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTTTAAAAAACGCTTC
* * *
57683021 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACTCGCTTTTGCTACAAT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* *
57683086 TGGTCCTGGAAGAAATAATTTCGAGTTGACATTTTTGAGCAAATAGTTTAAAAAACCGCTTC
66 AGGTCCTGGAA-AAATAATTTCGAGTTGACATTTCTGAGCAAATAGTTTAAAAAA-CGCTTC
* * *
57683148 AAGAAGGATGCTTTATGAGAAGAATTTGTGACATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAG-
57683213 TA-GTCCTGGAAGAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTTTAAAAAACCGCTTC
65 TAGGTCCTGGAA-AAATAATTTCGAGTTGACATTTCTGAGCAAATAGTTTAAAAAA-CGCTTC
* * * *
57683275 AAGCAGGATGCTTTATGAGAAGAGTTTGTGAAATTGCACCCACATGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * * * *
57683340 AGGTCTTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAACAATGCTGC
66 AGGTCCTGGAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTTTAAAA-AACGCTTC
* * *
57683401 AAGCAGGATGCTATT-TGAGAAGAATTTGTAAAATCGCGCCCTCATGGACGCGCTTTTGCTACAG
1 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAG
* * * *
57683465 TAGGTCCTGGAAAAATAATTTTGAGATG---TTTCTGAGCAAATAGTAT-AAAATCGCTTC
65 TAGGTCCTGGAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTTTAAAAAACGCTTC
* * *
57683522 TAGCAGGATGCTATATGAGAAGAATTTATGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
57683587 AG
66 AG
57683589 CATATTTGGG
Statistics
Matches: 510, Mismatches: 51, Indels: 18
0.88 0.09 0.03
Matches are distributed among these distances:
120 1 0.00
121 64 0.13
122 3 0.01
123 18 0.04
125 66 0.13
126 165 0.32
127 192 0.38
128 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (125 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTGGAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTTTAAAAAACGCTTC
Found at i:57683380 original size:253 final size:250
Alignment explanation
Indices: 57682900--57683588 Score: 951
Period size: 253 Copynumber: 2.7 Consensus size: 250
57682890 AAATCAAAGC
* * * * * *
57682900 AGGATGATTTATCAGAAGGATTTTTGAAGTCGCGCCCACGTGTACGCGCTTTTGCTACAGTAGGT
1 AGGATGCTTTATGAGAAGAATTTGTGAA-TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGT
*
57682965 CCTGGAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACACTTCAAGCAGGAT
65 CCTGGAAAAATAATTTTGAGTTGAC-TTTCTGAGCAAATAGTTTAAAAAACGCTTCAAGCAGGAT
* * * *
57683030 GCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACTCGCTTTTGCTACAATTGGTCCTGG
129 GCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGG
* * * *
57683095 AAGAAATAATTTCGAGTTGACATTTTTGAGCAAATAGTTTAAAA-AACCGCTTCAAGA
194 AAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAACAA-CGCTGCAAGA
57683152 AGGATGCTTTATGAGAAGAATTTGTGACATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTTA-G
1 AGGATGCTTTATGAGAAGAATTTGTGA-ATCGCGCCCTCGTGGACGCGCTTTTGCTACAG-TAGG
*
57683216 TCCTGGAAGAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTTTAAAAAACCGCTTCAAGCAG
64 TCCTGGAA-AAATAATTTTGAGTTGAC-TTTCTGAGCAAATAGTTTAAAAAA-CGCTTCAAGCAG
* * * *
57683281 GATGCTTTATGAGAAGAGTTTGTGAAATTGCACCCACATGGACGCGCTTTTGCTACAGTAGGT-C
126 GATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCC
* * * *
57683345 TTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAACAATGCTGCAAGC
191 TGGAAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAACAACGCTGCAAGA
* *
57683405 AGGATGCTATT-TGAGAAGAATTTGTAAAATCGCGCCCTCATGGACGCGCTTTTGCTACAGTAGG
1 AGGATGCT-TTATGAGAAGAATTTGT-GAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGG
* * * *
57683469 TCCTGGAAAAATAATTTTGAGATG--TTTCTGAGCAAATAGTAT-AAAATCGCTTCTAGCAGGAT
64 TCCTGGAAAAATAATTTTGAGTTGACTTTCTGAGCAAATAGTTTAAAAAACGCTTCAAGCAGGAT
* *
57683531 GCTATATGAGAAGAATTTATGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAG
129 GCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAG
57683589 CATATTTGGG
Statistics
Matches: 391, Mismatches: 38, Indels: 21
0.87 0.08 0.05
Matches are distributed among these distances:
247 66 0.17
248 4 0.01
249 17 0.04
252 77 0.20
253 156 0.40
254 71 0.18
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.29
Consensus pattern (250 bp):
AGGATGCTTTATGAGAAGAATTTGTGAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTC
CTGGAAAAATAATTTTGAGTTGACTTTCTGAGCAAATAGTTTAAAAAACGCTTCAAGCAGGATGC
TTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAA
AAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAACAACGCTGCAAGA
Found at i:57686599 original size:18 final size:17
Alignment explanation
Indices: 57686566--57686604 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
57686556 TTGTATAAAT
57686566 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
57686584 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
57686601 TGTG
1 TGTG
57686605 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:57686722 original size:8 final size:8
Alignment explanation
Indices: 57686709--57686737 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
57686699 CACTAGAGAC
57686709 CAGTGTTA
1 CAGTGTTA
57686717 CAGTGTTA
1 CAGTGTTA
57686725 CAGTGTTA
1 CAGTGTTA
57686733 CAGTG
1 CAGTG
57686738 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:57689492 original size:22 final size:21
Alignment explanation
Indices: 57689448--57690428 Score: 197
Period size: 21 Copynumber: 45.0 Consensus size: 21
57689438 TCAAATTATA
57689448 TTTAAATTAAGGGTTAGGGTT
1 TTTAAATTAAGGGTTAGGGTT
*
57689469 TTTAAATTAAGTGTTAGGGGTT
1 TTTAAATTAAGGGTTA-GGGTT
* *
57689491 TTT-ATTTAAGGGTTACGG-T
1 TTTAAATTAAGGGTTAGGGTT
*
57689510 TTTAAAGTTAAGGGTTTAGGGTA
1 TTTAAA-TTAAGGG-TTAGGGTT
* *
57689533 TTTAATTTAAGGGTTATGGTT
1 TTTAAATTAAGGGTTAGGGTT
* *
57689554 TTTAAGTTAAGGGTATATGG-T
1 TTTAAATTAAGGGT-TAGGGTT
57689575 TTTAAAGTTAA-GGTTAGGG-T
1 TTTAAA-TTAAGGGTTAGGGTT
* *
57689595 TTTAAAGTTATAGGTTTATGGTT
1 TTTAAA-TTA-AGGGTTAGGGTT
*
57689618 TTTAAGA-TAAGGGTTTAGTGTTTTAGGGT
1 TTTAA-ATTAAGGG-TTA--G-----GGTT
* * * * ** *
57689647 TTTTAATTTAAGGGTTTATAGTT
1 TTTAAATTAAGGGTTAG--GGTT
*
57689670 TTTAAGTTAAGGGTTTAGGG-T
1 TTTAAATTAAGGG-TTAGGGTT
** *
57689691 TTTAAAGTTAAAAGTTA-TGTCT
1 TTTAAA-TTAAGGGTTAGGGT-T
* **
57689713 TTTAATTTAAGGGTTACAGTT
1 TTTAAATTAAGGGTTAGGGTT
*
57689734 TTTAAGTTAAGGGTTTAGGG-T
1 TTTAAATTAAGGG-TTAGGGTT
* *
57689755 TTTAAAGTTAAGGATTAGTGTT
1 TTTAAA-TTAAGGGTTAGGGTT
* **
57689777 TTTAATTTAAGGGTTATAGTT
1 TTTAAATTAAGGGTTAGGGTT
* ** *
57689798 TTTAAGTTAATGATTTAAGG-T
1 TTTAAATTAA-GGGTTAGGGTT
** * *
57689819 TTTAGGGTTTTTAA--TTTAACGGTTT
1 TTTA----AATTAAGGGTT-A-GGGTT
** **
57689844 ACAGTTTTTAAGTTAAGGGTTTAGGG-T
1 ----TTTAAATT--AAGGG-TTAGGGTT
*
57689871 TTTAAAGTTAAGGGTTAGGGCT
1 TTTAAA-TTAAGGGTTAGGGTT
* ***
57689893 TTTAATTTAAGGGTTATAATT
1 TTTAAATTAAGGGTTAGGGTT
* *
57689914 TTTAAGTTAAGGGTTTATGG-T
1 TTTAAATTAAGGG-TTAGGGTT
*
57689935 TTTAAAGTTAAGGGTTAGGGCT
1 TTTAAA-TTAAGGGTTAGGGTT
* * ***
57689957 TTTAATTTAAGGGCTACATTT
1 TTTAAATTAAGGGTTAGGGTT
* *
57689978 TTTAAGTTAAGGGTTTAAGG-T
1 TTTAAATTAAGGG-TTAGGGTT
57689999 TTTAAAGTTAAGGGTTAGGGTT
1 TTTAAA-TTAAGGGTTAGGGTT
*
57690021 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAATTAAGGG-TTAGGGTT
* *
57690043 TTTAAGTTAAAGGCTTAGGG--
1 TTTAAATT-AAGGGTTAGGGTT
*
57690063 -TT---TT-AGGGTTTATGGTT
1 TTTAAATTAAGGG-TTAGGGTT
* * *
57690080 TTTAATTTAAGGGTTCACGATT
1 TTTAAATTAAGGGTT-AGGGTT
* *
57690102 TTTAAGTTAAGGGTTTATGGTT
1 TTTAAATTAAGGG-TTAGGGTT
* * *
57690124 TTTAAGTTAAGTGTTAAGG-T
1 TTTAAATTAAGGGTTAGGGTT
*
57690144 TTTAATTTAA-----A-GGTT
1 TTTAAATTAAGGGTTAGGGTT
* * * * **
57690159 TATGATTTTAGGGTTTTAGAATT
1 TTTAAATTAAGGG--TTAGGGTT
* *
57690182 TTTAATTTAAAGGTTTAGGGTT
1 TTTAAATT-AAGGGTTAGGGTT
**
57690204 TTTATGTTAAGGGTTAGGGTTTTT
1 TTTAAATTAAGGGTTAGGG---TT
* * ** *
57690228 AATTTATGAATTTAAGGTTTTAGGGT
1 --TTTA--AATTAAGGGTTAG-GGTT
* * * **
57690254 TTTAAATTTAAGGGTTTAGGGTT
1 TTTAAATTAAGGGTTAG--GGTT
* *
57690277 TTTAAATTAAGAGTTTAGGG-C
1 TTTAAATTAAG-GGTTAGGGTT
*
57690298 TTTAAGTTAAGGGTTTAGGG-T
1 TTTAAATTAAGGG-TTAGGGTT
*
57690319 TTTAAAGTTTTAAGGTTTAGGGTT
1 TTTAAA---TTAAGGGTTAGGGTT
* *
57690343 TTTAAGTTAAGTGTTAGGGTT
1 TTTAAATTAAGGGTTAGGGTT
*
57690364 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAATTAAGGG-TTAGGGTT
* * * *
57690386 TTCAAGTTAAGGATTTAGTGTT
1 TTTAAATTAAGG-GTTAGGGTT
* * *
57690408 TTTAAGTTTATGGTTAGGGTT
1 TTTAAATTAAGGGTTAGGGTT
57690429 AGGGTTTTTA
Statistics
Matches: 712, Mismatches: 156, Indels: 184
0.68 0.15 0.17
Matches are distributed among these distances:
14 5 0.01
15 14 0.02
16 2 0.00
18 2 0.00
19 6 0.01
20 30 0.04
21 283 0.40
22 241 0.34
23 59 0.08
24 26 0.04
25 6 0.01
26 5 0.01
27 3 0.00
28 11 0.02
29 17 0.02
30 2 0.00
ACGTcount: A:0.27, C:0.01, G:0.26, T:0.46
Consensus pattern (21 bp):
TTTAAATTAAGGGTTAGGGTT
Found at i:57689543 original size:43 final size:43
Alignment explanation
Indices: 57689448--57690428 Score: 587
Period size: 43 Copynumber: 22.5 Consensus size: 43
57689438 TCAAATTATA
* * *
57689448 TTTAAATTAAGGGTTAGGGTTTTTAAATTAAGTG-TTAGGGGTT
1 TTTAATTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTA-GGGTT
* * *
57689491 TTT-ATTTAAGGGTTACGGTTTTAAAGTTAAGGGTTTAGGGTA
1 TTTAATTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
57689533 TTTAATTTAAGGGTTATGGTTTTTAAGTTAAGGGTATATGGTT
1 TTTAATTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * *
57689576 TTAAAGTTAA-GGTTAGGGTTTTAAAGTTATA-GGTTTATGGTT
1 TTTAATTTAAGGGTTAGGGTTTTTAAGTTA-AGGGTTTAGGGTT
* * * **
57689618 TTTAAGATAAGGGTTTAGTGTTTTAGGGTTTTTAATTTAAGGGTTTATAGTT
1 TTT-A-AT-----TTAAG-G-GTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * ** *
57689670 TTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAAAAG-TTA-TGTCT
1 TTTAATTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGT-T
**
57689713 TTTAATTTAAGGGTTACAGTTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAATTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * * * **
57689756 TTAAAGTTAAGGATTAGTGTTTTTAATTTAAGGGTTATAGTTTT
1 TTTAATTTAAGGGTTAGGGTTTTTAAGTTAAGGGTT-TAGGGTT
* * * **
57689800 TAAGTTAATGATTTAAGGTTTTAGGGTTTTTAATTTAACGGTTTACAGTT
1 T---TT-A--ATTTAAGG-GTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
57689850 TTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAAGGG-TTAGGGCT
1 TTTAATTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
*** *
57689893 TTTAATTTAAGGGTTATAATTTTTAAGTTAAGGGTTTATGGTT
1 TTTAATTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * * * ***
57689936 TTAAAGTTAAGGGTTAGGGCTTTTAATTTAAGGG-CTACATTT
1 TTTAATTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
57689978 TTTAAGTTAAGGGTTTAAGGTTTTAAAGTTAAGGG-TTAGGGTT
1 TTTAATTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
57690021 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAAGGCTTAGGG--
1 TTTAATTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * * *
57690063 --T--TTT-AGGGTTTATGGTTTTTAATTTAAGGGTTCACGATT
1 TTTAATTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * *
57690102 TTTAAGTTAAGGGTTTATGGTTTTTAAGTTAAGTG-TTAAGG-T
1 TTTAATTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * * **
57690144 TTTAATTTAAAGGTTTA-TGATTTT-AG----GGTTTTAGAATT
1 TTTAATTT-AAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* *
57690182 TTTAATTTAAAGGTTTAGGGTTTTTATGTTAAGGG-TTAGGGTTTTTAAT
1 TTTAATTT-AAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGG----T--T
* * *
57690231 TTATGAATTTAAGGTTTTAGGGTTTTAAATTTAAGGGTTTAGGGTT
1 TT-T-AATTTAAGG-GTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
57690277 TTTAAATTAAGAGTTTAGGG-CTTTAAGTTAAGGGTTTAGGGTT
1 TTTAATTTAAG-GGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
57690320 TTAAAGTTTTAAGGTTTAGGGTTTTTAAGTTAAGTG-TTAGGGTT
1 TTTAA--TTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * *
57690364 TTTAAGTTAAGGGTTTAGGGTTTTCAAGTTAAGGATTTAGTGTT
1 TTTAATTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
*
57690408 TTTAAGTTT-ATGGTTAGGGTT
1 TTTAA-TTTAAGGGTTAGGGTT
57690429 AGGGTTTTTA
Statistics
Matches: 734, Mismatches: 141, Indels: 126
0.73 0.14 0.13
Matches are distributed among these distances:
36 1 0.00
37 29 0.04
38 20 0.03
39 5 0.01
40 4 0.01
41 6 0.01
42 129 0.18
43 266 0.36
44 133 0.18
45 25 0.03
46 4 0.01
47 4 0.01
48 2 0.00
49 6 0.01
50 18 0.02
51 48 0.07
52 34 0.05
ACGTcount: A:0.27, C:0.01, G:0.26, T:0.46
Consensus pattern (43 bp):
TTTAATTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
Found at i:57689663 original size:52 final size:52
Alignment explanation
Indices: 57689588--57689694 Score: 153
Period size: 52 Copynumber: 2.1 Consensus size: 52
57689578 AAAGTTAAGG
* *
57689588 TTAGGGTTTTAAAGTTATAGGTTTATGGTTTTTAAGATAAGGGTTTAGTGTT
1 TTAGGGTTTTAAAGTTATAGGTTTATAGTTTTTAAGATAAGGGTTTAGGGTT
* * *
57689640 TTAGGGTTTTTAATTTA-AGGGTTTATAGTTTTTAAGTTAAGGGTTTAGGGTT
1 TTAGGGTTTTAAAGTTATA-GGTTTATAGTTTTTAAGATAAGGGTTTAGGGTT
57689692 TTA
1 TTA
57689695 AAGTTAAAAG
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
51 1 0.02
52 48 0.98
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (52 bp):
TTAGGGTTTTAAAGTTATAGGTTTATAGTTTTTAAGATAAGGGTTTAGGGTT
Found at i:57689671 original size:30 final size:30
Alignment explanation
Indices: 57689602--57689671 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
57689592 GGTTTTAAAG
* *
57689602 TTATAGGTTTATGGTTTTTAAGATAAGGGT
1 TTATAGTTTTAGGGTTTTTAAGATAAGGGT
**
57689632 TTAGT-GTTTTAGGGTTTTTAATTTAAGGGT
1 TTA-TAGTTTTAGGGTTTTTAAGATAAGGGT
57689662 TTATAGTTTT
1 TTATAGTTTT
57689672 TAAGTTAAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 1 0.03
30 32 0.94
31 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.24, T:0.53
Consensus pattern (30 bp):
TTATAGTTTTAGGGTTTTTAAGATAAGGGT
Found at i:57689693 original size:116 final size:115
Alignment explanation
Indices: 57689520--57689758 Score: 313
Period size: 116 Copynumber: 2.1 Consensus size: 115
57689510 TTTAAAGTTA
* *
57689520 AGGG-TTTAGGGTATTTAATTTAAGGGTTATGGTTTTTAAGTTAAGGGTATATGGTTTTAAAGTT
1 AGGGTTTTAGGGTATTTAATTTAAGGGTTATAGTTTTTAAGTTAAGGGTATAGGGTTTTAAAGTT
* * **
57689584 -AAGGTTAGGGT-TTTAAAGTTATAGGTTTATGGTTTTTAAGATAAGGGTTT
66 AAAAGTTA-GGTCTTTAAAGTTA-AGGGTTACAGTTTTTAAGATAAGGGTTT
* * *
57689634 AGTGTTTTAGGGTTTTTAATTTAAGGGTTTATAGTTTTTAAGTTAAGGGTTTAGGGTTTTAAAGT
1 AGGGTTTTAGGGTATTTAATTTAAGGG-TTATAGTTTTTAAGTTAAGGGTATAGGGTTTTAAAGT
* * * *
57689699 TAAAAGTTATGTCTTTTAATTTAAGGGTTACAGTTTTTAAGTTAAGGGTTT
65 TAAAAGTTAGGTCTTTAAAGTTAAGGGTTACAGTTTTTAAGATAAGGGTTT
57689750 AGGGTTTTA
1 AGGGTTTTA
57689759 AAGTTAAGGA
Statistics
Matches: 107, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
114 3 0.03
115 21 0.20
116 69 0.64
117 14 0.13
ACGTcount: A:0.27, C:0.01, G:0.26, T:0.46
Consensus pattern (115 bp):
AGGGTTTTAGGGTATTTAATTTAAGGGTTATAGTTTTTAAGTTAAGGGTATAGGGTTTTAAAGTT
AAAAGTTAGGTCTTTAAAGTTAAGGGTTACAGTTTTTAAGATAAGGGTTT
Found at i:57689762 original size:180 final size:179
Alignment explanation
Indices: 57689488--57690002 Score: 671
Period size: 180 Copynumber: 2.9 Consensus size: 179
57689478 AGTGTTAGGG
* * **
57689488 GTTTTT-ATTTAAGGG-TTACGGTTTTAAAGTTAAGGGTTTAGGG-TATTTAATTTAAGGGTTAT
1 GTTTTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAAAAG-TTAGGGCT-TTTAATTTAAGGGTTAT
* * * *
57689550 GGTTTTTAAGTTAAGGGTATATGGTTTTAAAGTTAAGGTTAGGGTTTTAAAGTTATAGGTTTATG
64 AGTTTTTAAGTTAAGGGTTTATGGTTTTAAAGTTAAGGTTAGGGTTTTAAAGTTA-AGGGTTATA
* * *
57689615 GTTTTTAAGATAAGGGTTT-AGTGTTTTAGGGTTTTTAATTTAAGGGTTTATA
128 GTTTTTAAGATAAGGATTTAAG-GTTTTAGGGTTTTTAATTTAACGGTTTACA
* * *
57689667 GTTTTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAAAAGTTATGTCTTTTAATTTAAGGGTTACAG
1 GTTTTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAAAAGTTAGGGCTTTTAATTTAAGGGTTATAG
* * * *
57689732 TTTTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAAGGATTAGTGTTTTTAATTTAAGGGTTATAGT
66 TTTTTAAGTTAAGGGTTTATGGTTTTAAAGTTAAGG-TTAGGGTTTTAAAGTTAAGGGTTATAGT
* *
57689797 TTTTAAGTTAATGATTTAAGGTTTTAGGGTTTTTAATTTAACGGTTTACA
130 TTTTAAGATAAGGATTTAAGGTTTTAGGGTTTTTAATTTAACGGTTTACA
** *
57689847 GTTTTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAAGGGTTAGGGCTTTTAATTTAAGGGTTATAA
1 GTTTTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAAAAGTTAGGGCTTTTAATTTAAGGGTTATAG
* * * *
57689912 TTTTTAAGTTAAGGGTTTATGGTTTTAAAGTTAAGGGTTAGGGCTTTT-AATTTAAGGGCTACAT
66 TTTTTAAGTTAAGGGTTTATGGTTTTAAAGTTAA-GGTTAGGG-TTTTAAAGTTAAGGGTTATAG
* *
57689976 TTTTTAAGTTAAGGGTTTAAGGTTTTA
129 TTTTTAAGATAAGGATTTAAGGTTTTA
57690003 AAGTTAAGGG
Statistics
Matches: 296, Mismatches: 33, Indels: 13
0.87 0.10 0.04
Matches are distributed among these distances:
179 6 0.02
180 249 0.84
181 41 0.14
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.46
Consensus pattern (179 bp):
GTTTTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAAAAGTTAGGGCTTTTAATTTAAGGGTTATAG
TTTTTAAGTTAAGGGTTTATGGTTTTAAAGTTAAGGTTAGGGTTTTAAAGTTAAGGGTTATAGTT
TTTAAGATAAGGATTTAAGGTTTTAGGGTTTTTAATTTAACGGTTTACA
Found at i:57689846 original size:116 final size:115
Alignment explanation
Indices: 57689712--57689938 Score: 373
Period size: 116 Copynumber: 2.0 Consensus size: 115
57689702 AAGTTATGTC
* *
57689712 TTTTAATTTAAGGGTTACAGTTTTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAAGGATTAGTGTT
1 TTTTAATTTAAGGGTTACAGTTTTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAAGGATTAGGGCT
* *
57689777 TTTAATTTAAGGGTTATAGTTTTTAAGTTAATGATTTAAGGTTTTAGGGT
66 TTTAATTTAAGGGTTATAATTTTTAAGTTAAGGATTTAAGGTTTTAGGGT
* *
57689827 TTTTAATTTAACGGTTTACAGTTTTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAAGGGTTAGGGC
1 TTTTAATTTAA-GGGTTACAGTTTTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAAGGATTAGGGC
* *
57689892 TTTTAATTTAAGGGTTATAATTTTTAAGTTAAGGGTTTATGGTTTTA
65 TTTTAATTTAAGGGTTATAATTTTTAAGTTAAGGATTTAAGGTTTTA
57689939 AAGTTAAGGG
Statistics
Matches: 103, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
115 11 0.11
116 92 0.89
ACGTcount: A:0.27, C:0.02, G:0.23, T:0.48
Consensus pattern (115 bp):
TTTTAATTTAAGGGTTACAGTTTTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAAGGATTAGGGCT
TTTAATTTAAGGGTTATAATTTTTAAGTTAAGGATTTAAGGTTTTAGGGT
Found at i:57689851 original size:30 final size:30
Alignment explanation
Indices: 57689795--57689853 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
57689785 AAGGGTTATA
*
57689795 GTTTTTAAGTTAATGATTTAAGGTTTTAGG
1 GTTTTTAAGTTAACGATTTAAGGTTTTAGG
* * *
57689825 GTTTTTAATTTAACGGTTTACAGTTTTTA
1 GTTTTTAAGTTAACGATTTA-AGGTTTTA
57689854 AGTTAAGGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 17 0.71
31 7 0.29
ACGTcount: A:0.25, C:0.03, G:0.19, T:0.53
Consensus pattern (30 bp):
GTTTTTAAGTTAACGATTTAAGGTTTTAGG
Found at i:57689858 original size:52 final size:51
Alignment explanation
Indices: 57689769--57689874 Score: 149
Period size: 52 Copynumber: 2.1 Consensus size: 51
57689759 AAGTTAAGGA
* * *
57689769 TTAGTGTTTTTAATTTAAGGGTTATAGTTTTTAAGTTAATGATTTAAGGTT
1 TTAGGGTTTTTAATTTAAGGGTTACAGTTTTTAAGTTAAGGATTTAAGGTT
* * *
57689820 TTAGGGTTTTTAATTTAACGGTTTACAGTTTTTAAGTTAAGGGTTTAGGGTT
1 TTAGGGTTTTTAATTTAA-GGGTTACAGTTTTTAAGTTAAGGATTTAAGGTT
57689872 TTA
1 TTA
57689875 AAGTTAAGGG
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
51 17 0.35
52 31 0.65
ACGTcount: A:0.25, C:0.02, G:0.22, T:0.51
Consensus pattern (51 bp):
TTAGGGTTTTTAATTTAAGGGTTACAGTTTTTAAGTTAAGGATTTAAGGTT
Found at i:57690082 original size:59 final size:58
Alignment explanation
Indices: 57690009--57690125 Score: 153
Period size: 59 Copynumber: 2.0 Consensus size: 58
57689999 TTTAAAGTTA
* * *
57690009 AGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAAGGCTTAGGGTTTT
1 AGGGTTAGGGTTTTTAAGTTAAGGGTTCACGATTTTTAAGTTAAAGGCTTAGGGTTTT
* * * * *
57690067 AGGGTTTATGGTTTTTAATTTAAGGGTTCACGATTTTTAAGTTAAGGGTTTATGGTTTT
1 AGGG-TTAGGGTTTTTAAGTTAAGGGTTCACGATTTTTAAGTTAAAGGCTTAGGGTTTT
57690126 TAAGTTAAGT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
58 4 0.08
59 46 0.92
ACGTcount: A:0.22, C:0.03, G:0.29, T:0.46
Consensus pattern (58 bp):
AGGGTTAGGGTTTTTAAGTTAAGGGTTCACGATTTTTAAGTTAAAGGCTTAGGGTTTT
Found at i:57690146 original size:80 final size:77
Alignment explanation
Indices: 57689987--57690387 Score: 257
Period size: 80 Copynumber: 5.0 Consensus size: 77
57689977 TTTTAAGTTA
* * *
57689987 AGGGTTTAAGGTTTTAAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTA
1 AGGGTTTAAGGTTTTTAATTTAAGGGTTA-GATTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTT-
57690052 AAGGCTTAGGGTTTT
64 AAGG-TTAGGGTTTT
* *
57690067 AGGGTTTATGGTTTTTAATTTAAGGGTTCACGATTTTTAAGTTAAGGGTTTATGGTTTTTAAGTT
1 AGGGTTTAAGGTTTTTAATTTAAGGGTT-A-GATTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTT
*
57690132 AAGTGTTAAGGTTTT
64 AAG-GTTAGGGTTTT
* * * * * * *
57690147 A--ATTTAAAGGTTTATGATTTTAGGGTTTTAGAATTTTTAATTTAAAGGTTTAGGGTTTTTATG
1 AGGGTTT-AAGGTTTTTAATTTAAGGG--TTAG-ATTTTTAAGTTAAGGGTTTAGGGTTTTTAAG
57690210 TTAAGGGTTAGGG--TT
62 TTAA-GGTTAGGGTTTT
* * * * * * *
57690225 ----TTTAA--TTTATGAATTTAAGGTTTTAGGGTTTTAAATTTAAGGGTTTAGGGTTTTTAAAT
1 AGGGTTTAAGGTTT-TTAATTTAAGG-GTT-AGATTTTTAAGTTAAGGGTTTAGGGTTTTTAAGT
57690284 TAAGAGTTTAGGGCTTTAAGTT
63 TAAG-G-TTAGGG--TT---TT
* * * * *
57690306 AAGGGTTTAGGGTTTTAAAGTTTTAAGGTTTAGGGTTTTTAAGTTAAGTG-TTAGGGTTTTTAAG
1 -AGGGTTTAAGGTTTTTAA--TTTAAGGGTTA-GATTTTTAAGTTAAGGGTTTAGGGTTTTTAAG
57690370 TTAAGGGTTTAGGGTTTT
62 TTAA-GG-TTAGGGTTTT
57690388 CAAGTTAAGG
Statistics
Matches: 256, Mismatches: 35, Indels: 58
0.73 0.10 0.17
Matches are distributed among these distances:
72 1 0.00
73 36 0.14
74 14 0.05
75 2 0.01
76 3 0.01
78 5 0.02
79 16 0.06
80 76 0.30
81 39 0.15
82 2 0.01
85 2 0.01
86 4 0.02
87 28 0.11
88 21 0.08
89 7 0.03
ACGTcount: A:0.25, C:0.01, G:0.27, T:0.47
Consensus pattern (77 bp):
AGGGTTTAAGGTTTTTAATTTAAGGGTTAGATTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAA
GGTTAGGGTTTT
Found at i:57690223 original size:51 final size:52
Alignment explanation
Indices: 57690165--57690278 Score: 146
Period size: 51 Copynumber: 2.2 Consensus size: 52
57690155 GGTTTATGAT
* *
57690165 TTTAGGGTTTTAGAATTT-TTAATTTAAAGG-TTTAGGGTTTT-TATGTTAAGGG
1 TTTAGGGTTTT-GAATTTATGAATTT-AAGGTTTTAGGGTTTTAAAT-TTAAGGG
*
57690217 -TTAGGGTTTTTAATTTATGAATTTAAGGTTTTAGGGTTTTAAATTTAAGGG
1 TTTAGGGTTTTGAATTTATGAATTTAAGGTTTTAGGGTTTTAAATTTAAGGG
57690268 TTTAGGGTTTT
1 TTTAGGGTTTT
57690279 TAAATTAAGA
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
50 9 0.16
51 34 0.62
52 12 0.22
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (52 bp):
TTTAGGGTTTTGAATTTATGAATTTAAGGTTTTAGGGTTTTAAATTTAAGGG
Found at i:57690234 original size:73 final size:73
Alignment explanation
Indices: 57690099--57690387 Score: 243
Period size: 73 Copynumber: 4.0 Consensus size: 73
57690089 AGGGTTCACG
* * * * * *
57690099 ATTTTTAAGTTAAGGGTTTATGGTTTTTAAGTTAAGTGTTAAGGTTTTAATTTAAAGGTTTATGA
1 ATTTTTAATTTAAAGGTTTAGGGTTTTTAAGTTAAGGGTT-AGG-GTT--TTT-AA-G-TTAAGA
*
57690164 TTTTAGGGTTTTAGA
59 GTTTAGGGTTTTAGA
* * * * *
57690179 ATTTTTAATTTAAAGGTTTAGGGTTTTTATGTTAAGGGTTAGGGTTTTTAATTTATGAATTTAAG
1 ATTTTTAATTTAAAGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGAGTTTAGG
*
57690244 GTTTTAGG
66 GTTTTAGA
* * * * * * *
57690252 GTTTTAAATTTAAGGGTTTAGGGTTTTTAAATTAAGAGTTTAGGG-CTTTAAGTTAAGGGTTTAG
1 ATTTTTAATTTAAAGGTTTAGGGTTTTTAAGTTAAG-GGTTAGGGTTTTTAAGTTAAGAGTTTAG
57690316 GGTTTTA-A
65 GGTTTTAGA
* * *
57690324 A---GT--TTT-AAGGTTTAGGGTTTTTAAGTTAAGTGTTAGGGTTTTTAAGTTAAGGGTTTAGG
1 ATTTTTAATTTAAAGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGAGTTTAGG
57690383 GTTTT
66 GTTTT
57690388 CAAGTTAAGG
Statistics
Matches: 176, Mismatches: 31, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
65 6 0.03
66 46 0.26
67 3 0.02
73 69 0.39
74 7 0.04
75 2 0.01
76 3 0.02
78 2 0.01
79 3 0.02
80 35 0.20
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.48
Consensus pattern (73 bp):
ATTTTTAATTTAAAGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGAGTTTAGG
GTTTTAGA
Found at i:57690353 original size:66 final size:65
Alignment explanation
Indices: 57690239--57690415 Score: 243
Period size: 66 Copynumber: 2.7 Consensus size: 65
57690229 ATTTATGAAT
* *
57690239 TTAAGGTTTTAGGGTTTTAAA-TTTAAGGGTTTAGGGTTTTTAAATTAAGAGTTTAGGG-CTTTA
1 TTAAGGGTTTAGGGTTTTAAAGTTTAA-GGTTTAGGGTTTTTAAGTTAAGAG-TTAGGGTCTTTA
57690302 AG
64 AG
* *
57690304 TTAAGGGTTTAGGGTTTTAAAGTTTTAAGGTTTAGGGTTTTTAAGTTAAGTGTTAGGGTTTTTAA
1 TTAAGGGTTTAGGGTTTTAAAG-TTTAAGGTTTAGGGTTTTTAAGTTAAGAGTTAGGGTCTTTAA
57690369 G
65 G
* *
57690370 TTAAGGGTTTAGGGTTTTCAAG-TTAAGGATTTAGTGTTTTTAAGTT
1 TTAAGGGTTTAGGGTTTTAAAGTTTAAGG-TTTAGGGTTTTTAAGTT
57690416 TATGGTTAGG
Statistics
Matches: 102, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
64 6 0.06
65 42 0.41
66 49 0.48
67 5 0.05
ACGTcount: A:0.25, C:0.01, G:0.27, T:0.46
Consensus pattern (65 bp):
TTAAGGGTTTAGGGTTTTAAAGTTTAAGGTTTAGGGTTTTTAAGTTAAGAGTTAGGGTCTTTAAG
Found at i:57691026 original size:18 final size:18
Alignment explanation
Indices: 57691000--57691043 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
57690990 GACTCGAAAA
* *
57691000 AGGAAACATATAAGGGTT
1 AGGAAACATAAAAGGGCT
*
57691018 AGGATACATAAAAGGGCT
1 AGGAAACATAAAAGGGCT
57691036 AGGAAACA
1 AGGAAACA
57691044 CACTTGGCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.48, C:0.09, G:0.27, T:0.16
Consensus pattern (18 bp):
AGGAAACATAAAAGGGCT
Found at i:57692691 original size:15 final size:15
Alignment explanation
Indices: 57692671--57692701 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
57692661 ATAATTATCT
57692671 AAAAATTCATAAATA
1 AAAAATTCATAAATA
*
57692686 AAAAATTCTTAAATA
1 AAAAATTCATAAATA
57692701 A
1 A
57692702 TATTTAAAAA
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:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAAATTCATAAATA
Found at i:57692913 original size:51 final size:50
Alignment explanation
Indices: 57692858--57692957 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 50
57692848 AATTATTTAA
57692858 AAATAAGGATTTAAGAGAAATTT-AAGAGGAACTTGAGAGCAAATTGAGATT
1 AAATAAGGATTTAAGAGAAATTTGAA-AGG-ACTTGAGAGCAAATTGAGATT
* * * *
57692909 AAATATGGATTTGAGAGAAATTTGGAACGGATTTGAGAGCAAATTGAGA
1 AAATAAGGATTTAAGAGAAATTT-GAAAGGACTTGAGAGCAAATTGAGA
57692958 GGAAATTTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
51 39 0.91
52 2 0.05
53 2 0.05
ACGTcount: A:0.44, C:0.04, G:0.26, T:0.26
Consensus pattern (50 bp):
AAATAAGGATTTAAGAGAAATTTGAAAGGACTTGAGAGCAAATTGAGATT
Found at i:57692931 original size:11 final size:11
Alignment explanation
Indices: 57692917--57692993 Score: 56
Period size: 11 Copynumber: 6.9 Consensus size: 11
57692907 TTAAATATGG
57692917 ATTTGAGAGAA
1 ATTTGAGAGAA
*
57692928 ATTTG-GA-ACGG
1 ATTTGAGAGA--A
57692939 ATTTGAGAGCAA
1 ATTTGAGAG-AA
57692951 A-TTGAGAGGAA
1 ATTTGAGA-GAA
57692962 ATTT-AGAGGAA
1 ATTTGAGA-GAA
57692973 A-TTGAGAGGAA
1 ATTTGAGA-GAA
57692984 ATTTGAGAGA
1 ATTTGAGAGA
57692994 GGATTAGTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
9 1 0.02
10 4 0.07
11 37 0.67
12 12 0.22
14 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.31, T:0.25
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:57692974 original size:22 final size:23
Alignment explanation
Indices: 57692939--57692992 Score: 92
Period size: 22 Copynumber: 2.4 Consensus size: 23
57692929 TTTGGAACGG
57692939 ATTTGAGAGCAAATTGAGAGGAA
1 ATTTGAGAGCAAATTGAGAGGAA
*
57692962 ATTT-AGAGGAAATTGAGAGGAA
1 ATTTGAGAGCAAATTGAGAGGAA
57692984 ATTTGAGAG
1 ATTTGAGAG
57692993 AGGATTAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 21 0.72
23 8 0.28
ACGTcount: A:0.43, C:0.02, G:0.31, T:0.24
Consensus pattern (23 bp):
ATTTGAGAGCAAATTGAGAGGAA
Found at i:57697075 original size:26 final size:27
Alignment explanation
Indices: 57697015--57697075 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 27
57697005 TTTTATTTTT
*
57697015 TTAAAAATTGTGTAAATTAAATAAAAA
1 TTAAAATTTGTGTAAATTAAATAAAAA
** *
57697042 TT-TTATTTGTGT-AATTAAATTAAAA
1 TTAAAATTTGTGTAAATTAAATAAAAA
57697067 TTAAAATTT
1 TTAAAATTT
57697076 TTAGTATATA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
25 14 0.52
26 11 0.41
27 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (27 bp):
TTAAAATTTGTGTAAATTAAATAAAAA
Found at i:57701568 original size:27 final size:27
Alignment explanation
Indices: 57701516--57701568 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
57701506 ATAGAGATAA
* **
57701516 TTTTAATTACTTTTAAATTTTGAAATG
1 TTTTAATTAATTTTAAATTTAAAAATG
57701543 TTTTAATTAAATTTTAAA-TTAAAAAT
1 TTTTAATT-AATTTTAAATTTAAAAAT
57701569 TAGGTTCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 14 0.64
28 8 0.36
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (27 bp):
TTTTAATTAATTTTAAATTTAAAAATG
Found at i:57701916 original size:23 final size:23
Alignment explanation
Indices: 57701886--57701930 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
57701876 AGTTCTTTTG
57701886 AATTTTAA-AATATATATATTTAA
1 AATTTTAATAA-ATATATATTTAA
*
57701909 AATTTTAATAAATATATTTTTA
1 AATTTTAATAAATATATATTTA
57701931 TATATGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AATTTTAATAAATATATATTTAA
Found at i:57701948 original size:19 final size:20
Alignment explanation
Indices: 57701924--57701970 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
57701914 TAATAAATAT
57701924 ATTTTTAT-AT-ATGTTTTAA
1 ATTTTTATAATAAT-TTTTAA
57701943 ATTTTT-TAATAATTTTTAA
1 ATTTTTATAATAATTTTTAA
57701962 ATTATTTAT
1 ATT-TTTAT
57701971 CAATGTGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
18 1 0.04
19 17 0.71
20 5 0.21
21 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
ATTTTTATAATAATTTTTAA
Found at i:57705753 original size:6 final size:6
Alignment explanation
Indices: 57705742--57705770 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
57705732 AAGTATGTAT
57705742 TTTGAC TTTGAC TTTGAC TTTGAC TTTGA
1 TTTGAC TTTGAC TTTGAC TTTGAC TTTGA
57705771 TATTTTCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.52
Consensus pattern (6 bp):
TTTGAC
Found at i:57705976 original size:24 final size:25
Alignment explanation
Indices: 57705940--57705986 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
57705930 ATATAATTTA
* *
57705940 ATATATTATAAA-TAAAATATTAGT
1 ATATATTAGAAATTAAAAAATTAGT
*
57705964 ATATTTTAGAAATTAAAAAATTA
1 ATATATTAGAAATTAAAAAATTA
57705987 AAATGTTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (25 bp):
ATATATTAGAAATTAAAAAATTAGT
Found at i:57707057 original size:28 final size:28
Alignment explanation
Indices: 57707022--57707075 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
57707012 TCGACGTGGA
*
57707022 GAACAACATACCTCGGCCTCGGGGAGTC
1 GAACAACATACCTCGGCCTCGAGGAGTC
57707050 GAACAACATACCTCGGCCTCGAGGAG
1 GAACAACATACCTCGGCCTCGAGGAG
57707076 ATTCAATAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.28, C:0.31, G:0.28, T:0.13
Consensus pattern (28 bp):
GAACAACATACCTCGGCCTCGAGGAGTC
Found at i:57709919 original size:38 final size:39
Alignment explanation
Indices: 57709877--57709983 Score: 110
Period size: 38 Copynumber: 2.7 Consensus size: 39
57709867 TCGGATAGTT
* *
57709877 CGAAGCAAAGTTGACACCCAGTGTCTCATCG-GCCTAGC
1 CGAAGTAAAGTTGACACCCAGTGTCTCATCGAACCTAGC
* * * * *
57709915 CGAAGTAAAG-TGATACCCAATATCTCATCGAATCTATC
1 CGAAGTAAAGTTGACACCCAGTGTCTCATCGAACCTAGC
*
57709953 CGAAGTAAAATAGTGACACCCAGTGTCTCAT
1 CGAAGTAAAGT--TGACACCCAGTGTCTCAT
57709984 TGACTCGAGG
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
37 17 0.31
38 22 0.41
41 15 0.28
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (39 bp):
CGAAGTAAAGTTGACACCCAGTGTCTCATCGAACCTAGC
Found at i:57710114 original size:18 final size:19
Alignment explanation
Indices: 57710078--57710131 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 19
57710068 TTTCCAATTC
57710078 TCAA-TTCAAA-TTCACTT
1 TCAATTTCAAATTTCACTT
*
57710095 TC-ATTTCAAATTTTACTT
1 TCAATTTCAAATTTCACTT
*
57710113 TCAATATCAAA-TTCACTT
1 TCAATTTCAAATTTCACTT
57710131 T
1 T
57710132 TTCATTCACT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 1 0.03
17 8 0.26
18 15 0.48
19 7 0.23
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.46
Consensus pattern (19 bp):
TCAATTTCAAATTTCACTT
Found at i:57710699 original size:29 final size:29
Alignment explanation
Indices: 57710651--57710708 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
57710641 TTAATCAATT
57710651 CTAATCAATAATTCTATCAA-ATAAACCC
1 CTAATCAATAATTCTATCAACATAAACCC
* *
57710679 CTAATTCAATCATT-TATTCAACATGAACCC
1 CTAA-TCAATAATTCTA-TCAACATAAACCC
57710709 TACTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 6 0.24
29 12 0.48
30 7 0.28
ACGTcount: A:0.41, C:0.26, G:0.02, T:0.31
Consensus pattern (29 bp):
CTAATCAATAATTCTATCAACATAAACCC
Found at i:57710892 original size:25 final size:25
Alignment explanation
Indices: 57710853--57710904 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
57710843 CCTATTTCTC
* *
57710853 CTTTCTTTCTTTCCCTTTTTCTTTT
1 CTTTCTTTCTTTCCCTGTTTCGTTT
57710878 CTTTCTTT-TTCTCCCTGTTTCGTTT
1 CTTTCTTTCTT-TCCCTGTTTCGTTT
57710903 CT
1 CT
57710905 ATTATGTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.00, C:0.29, G:0.04, T:0.67
Consensus pattern (25 bp):
CTTTCTTTCTTTCCCTGTTTCGTTT
Found at i:57710918 original size:15 final size:16
Alignment explanation
Indices: 57710893--57710922 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
57710883 TTTTTCTCCC
57710893 TGTTTCGTTTCTATTA
1 TGTTTCGTTTCTATTA
57710909 TGTTTC-TTTCTATT
1 TGTTTCGTTTCTATT
57710923 TCTTTTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.10, C:0.13, G:0.10, T:0.67
Consensus pattern (16 bp):
TGTTTCGTTTCTATTA
Found at i:57711403 original size:8 final size:8
Alignment explanation
Indices: 57711390--57711450 Score: 58
Period size: 8 Copynumber: 8.0 Consensus size: 8
57711380 AATTTATTTC
57711390 ATAATATA
1 ATAATATA
57711398 ATAATATA
1 ATAATATA
57711406 ATCAAT-T-
1 AT-AATATA
*
57711413 -TAAT-TT
1 ATAATATA
57711419 ATAATATA
1 ATAATATA
*
57711427 ATAAAATA
1 ATAATATA
*
57711435 ATAAAATA
1 ATAATATA
57711443 ATAATATA
1 ATAATATA
57711451 TTTTATAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
5 4 0.09
6 1 0.02
7 4 0.09
8 34 0.74
9 3 0.07
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (8 bp):
ATAATATA
Found at i:57711422 original size:29 final size:29
Alignment explanation
Indices: 57711380--57711436 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
57711370 GTCTTTTCTT
*
57711380 AATTTATTTCATAATATAATAATATAATC
1 AATTTATTTCATAATATAATAAAATAATC
57711409 AATTTAATTT-ATAATATAATAAAATAAT
1 AATTT-ATTTCATAATATAATAAAATAAT
57711437 AAAATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (29 bp):
AATTTATTTCATAATATAATAAAATAATC
Found at i:57711450 original size:29 final size:29
Alignment explanation
Indices: 57711390--57711450 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
57711380 AATTTATTTC
* ** *
57711390 ATAATATAATAATATAATCAATTTAATTT
1 ATAATATAATAAAATAATCAAAATAATAT
57711419 ATAATATAATAAAATAAT-AAAATAATAAT
1 ATAATATAATAAAATAATCAAAATAAT-AT
57711448 ATA
1 ATA
57711451 TTTTATAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (29 bp):
ATAATATAATAAAATAATCAAAATAATAT
Found at i:57715485 original size:37 final size:37
Alignment explanation
Indices: 57715425--57715499 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
57715415 AATTTTTGCC
*
57715425 TGCTCTTACTGTATTTGTATGATTTAGGAACTCTGAT
1 TGCTCTTACCGTATTTGTATGATTTAGGAACTCTGAT
*
57715462 TGCTGTTACCGTATTTGTATGATTTAGGAACTCTGAT
1 TGCTCTTACCGTATTTGTATGATTTAGGAACTCTGAT
57715499 T
1 T
57715500 TATACTTGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.21, C:0.13, G:0.20, T:0.45
Consensus pattern (37 bp):
TGCTCTTACCGTATTTGTATGATTTAGGAACTCTGAT
Found at i:57723717 original size:23 final size:23
Alignment explanation
Indices: 57723691--57723742 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
57723681 AAAAGCTATC
*
57723691 TACAAAATCAAATC-TCTAATATT
1 TACAAAATCAAATCTTCTAAGA-T
*
57723714 TACAAAGTCAAATCTTCTAAGAT
1 TACAAAATCAAATCTTCTAAGAT
57723737 TACAAA
1 TACAAA
57723743 TCCTATAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.17, G:0.04, T:0.31
Consensus pattern (23 bp):
TACAAAATCAAATCTTCTAAGAT
Found at i:57727838 original size:110 final size:109
Alignment explanation
Indices: 57727596--57728432 Score: 1237
Period size: 110 Copynumber: 7.6 Consensus size: 109
57727586 GTTAAACGAG
* * * * * *
57727596 AAATCGAAACCCAGCACATTAGGGCACG-CTCCTCGAATTTCCAAACGCAAAACATTGTCTTATT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
** * * *
57727660 TTGAAATTTTTGGAAGGATATTTAGCTATTTTGTTGAACGAGAA
66 TTGAAATTTTTAAAAGGATATTAAGCCATTTGGTTGAACGAGAA
* *
57727704 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACACAAAACATTGCCATATT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
* *
57727769 TTGAAATTTTTAAAAAAGATATTAAGCAATTTGGTTGAACGAGAA
66 TTGAAATTTTT-AAAAGGATATTAAGCCATTTGGTTGAACGAGAA
* * *
57727814 AAGTAGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTTCAAACGCAAAACATTGCCTTATT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
* * *
57727879 TTAAAATTTTTTAAAAGGATATTTAGCTATTTGGTTGAACGAGAA
66 TTGAAA-TTTTTAAAAGGATATTAAGCCATTTGGTTGAACGAGAA
* *
57727924 AAATCGACACCGAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCATATT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
*
57727989 TTGAAATTTTTAAAAAGGATATTAAGTCATTTGGTTGAACGAGAA
66 TTGAAATTTTT-AAAAGGATATTAAGCCATTTGGTTGAACGAGAA
*
57728034 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCATATT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
57728099 TTGAAATTTTTTAAAAAGGATATTAAGCCATTTGGTTGAACGAGAA
66 TTGAAA-TTTTT-AAAAGGATATTAAGCCATTTGGTTGAACGAGAA
57728145 AAATCGACA-CCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
*
57728209 TTAAAATTTTTAAAAGGATATTAAGCCATTTGGTTGAACGAGAA
66 TTGAAATTTTTAAAAGGATATTAAGCCATTTGGTTGAACGAGAA
57728253 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAGTTTTCTCGAATTTCCAAACGCAAAACA
1 AAATCGACACCCAGCACCTTAGGGCA-------T---GTTTTCTCGAATTTCCAAACGCAAAACA
* * *
57728318 TTGCCTTATTTTAAAATTTTTAAAAGGATATTAAACCATTTAGTTGAACGAGAA
56 TTGCCTTATTTTGAAATTTTTAAAAGGATATTAAGCCATTTGGTTGAACGAGAA
* * *
57728372 AAATAGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCTAAATATTGCCT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCT
57728433 GGATTAGAAA
Statistics
Matches: 672, Mismatches: 41, Indels: 31
0.90 0.06 0.04
Matches are distributed among these distances:
108 67 0.10
109 100 0.15
110 346 0.51
111 52 0.08
112 1 0.00
116 1 0.00
119 105 0.16
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.31
Consensus pattern (109 bp):
AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
TTGAAATTTTTAAAAGGATATTAAGCCATTTGGTTGAACGAGAA
Found at i:57728382 original size:119 final size:119
Alignment explanation
Indices: 57728171--57728408 Score: 449
Period size: 119 Copynumber: 2.0 Consensus size: 119
57728161 CTTAGGGCAT
*
57728171 GTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCC
1 GTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAACC
* *
57728236 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGA
66 ATTTAGTTGAACGAGAAAAATAGACACCCAGCACCTTAGGGCATGTTTTCTCGA
57728290 GTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAACC
1 GTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAACC
57728355 ATTTAGTTGAACGAGAAAAATAGACACCCAGCACCTTAGGGCATGTTTTCTCGA
66 ATTTAGTTGAACGAGAAAAATAGACACCCAGCACCTTAGGGCATGTTTTCTCGA
57728409 ATTTCCAAAC
Statistics
Matches: 116, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
119 116 1.00
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (119 bp):
GTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAACC
ATTTAGTTGAACGAGAAAAATAGACACCCAGCACCTTAGGGCATGTTTTCTCGA
Found at i:57728684 original size:39 final size:39
Alignment explanation
Indices: 57728641--57728715 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
57728631 AAAATATATG
* *
57728641 AAAATTA-TAAAATATGAAA-AATATGTATATGTATATTTT
1 AAAATTATTAAAATA--AAATAATATATATATATATATTTT
57728680 AAAATTATTAAAATAAAATAATATATATATATATAT
1 AAAATTATTAAAATAAAATAATATATATATATATAT
57728716 ATGAGTATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
38 3 0.09
39 22 0.69
40 7 0.22
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (39 bp):
AAAATTATTAAAATAAAATAATATATATATATATATTTT
Found at i:57728781 original size:16 final size:16
Alignment explanation
Indices: 57728762--57728808 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
57728752 TATATAGATA
57728762 TACATATATAAATATG
1 TACATATATAAATATG
* *
57728778 TACATATAAAAAGTATT
1 TACATATATAAA-TATG
57728795 TA-ATATATTAAATA
1 TACATATA-TAAATA
57728809 AGTTAGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 18 0.69
17 8 0.31
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (16 bp):
TACATATATAAATATG
Found at i:57728871 original size:16 final size:16
Alignment explanation
Indices: 57728852--57728892 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 16
57728842 TATATATATA
57728852 TATATATATAAACAAT
1 TATATATATAAACAAT
57728868 TATATA-AT-AACAAT
1 TATATATATAAACAAT
*
57728882 AATATAT-TAAA
1 TATATATATAAA
57728893 ACACATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
14 12 0.55
15 4 0.18
16 6 0.27
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (16 bp):
TATATATATAAACAAT
Found at i:57728873 original size:2 final size:2
Alignment explanation
Indices: 57728819--57728861 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
57728809 AGTTAGAAAA
* *
57728819 AT AT AT AT AC GT 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
57728861 A
1 A
57728862 AACAATTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:57737907 original size:17 final size:16
Alignment explanation
Indices: 57737880--57737911 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
57737870 TGGAATACTT
57737880 TAATTTTTTTTTAATA
1 TAATTTTTTTTTAATA
57737896 TAATTATTTTTTTAAT
1 TAATT-TTTTTTTAAT
57737912 CTTTTTAAAG
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TAATTTTTTTTTAATA
Found at i:57738276 original size:2 final size:2
Alignment explanation
Indices: 57738269--57738295 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
57738259 TTTCCTCTTT
57738269 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
57738296 TTCTTTCTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57742163 original size:13 final size:13
Alignment explanation
Indices: 57742145--57742169 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57742135 GAGTTCAAAT
57742145 TATATATATAATA
1 TATATATATAATA
57742158 TATATATATAAT
1 TATATATATAAT
57742170 CATTGCATGC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATATATATAATA
Found at i:57743165 original size:19 final size:18
Alignment explanation
Indices: 57743126--57743164 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
57743116 TTTATTTTAA
*
57743126 TTTAATTTTTGGGTTTTT
1 TTTAATTTTTGAGTTTTT
57743144 TTTAATATTTTGA-TTTTT
1 TTTAAT-TTTTGAGTTTTT
57743162 TTT
1 TTT
57743165 TGGATTGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.15, C:0.00, G:0.10, T:0.74
Consensus pattern (18 bp):
TTTAATTTTTGAGTTTTT
Found at i:57743703 original size:26 final size:27
Alignment explanation
Indices: 57743673--57743732 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
57743663 TAAGATTATT
*
57743673 ATATAAAAATT-TTCAATAAATAAAA-A
1 ATATAAAAATTATTAAAT-AATAAAATA
*
57743699 ATATATAAAATTATTAAATATTAAAATA
1 ATATA-AAAATTATTAAATAATAAAATA
57743727 ATATAA
1 ATATAA
57743733 TATAAACATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 5 0.17
27 13 0.45
28 11 0.38
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (27 bp):
ATATAAAAATTATTAAATAATAAAATA
Found at i:57743718 original size:28 final size:28
Alignment explanation
Indices: 57743672--57743731 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
57743662 TTAAGATTAT
*
57743672 TATATAAAAATTTTCAATAAATAAAA-AA
1 TATATAAAAATTTTAAAT-AATAAAATAA
*
57743700 TATAT-AAAATTATTAAATATTAAAATAA
1 TATATAAAAATT-TTAAATAATAAAATAA
57743728 TATA
1 TATA
57743732 ATATAAACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 12 0.43
28 16 0.57
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (28 bp):
TATATAAAAATTTTAAATAATAAAATAA
Found at i:57748070 original size:24 final size:24
Alignment explanation
Indices: 57748033--57748080 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
57748023 GGACACACCA
57748033 TAGCTCGAAAGAGCATCCCGTTAT
1 TAGCTCGAAAGAGCATCCCGTTAT
* * *
57748057 TAGCTCTAATGAGCTTCCCGTTAT
1 TAGCTCGAAAGAGCATCCCGTTAT
57748081 ATGGTTCTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (24 bp):
TAGCTCGAAAGAGCATCCCGTTAT
Found at i:57750168 original size:31 final size:31
Alignment explanation
Indices: 57750133--57750191 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
57750123 TTTAATTTGA
* * *
57750133 TTAATTTTAATCTTTGTACTTTTCGAATTGG
1 TTAATTTTAACCCTTATACTTTTCGAATTGG
*
57750164 TTAATTTTAACCCTTATACTTTTTGAAT
1 TTAATTTTAACCCTTATACTTTTCGAAT
57750192 GTTAAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.54
Consensus pattern (31 bp):
TTAATTTTAACCCTTATACTTTTCGAATTGG
Found at i:57751959 original size:20 final size:20
Alignment explanation
Indices: 57751934--57751974 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
57751924 GGTGAACTTA
57751934 ACTAAGAATAGCAAGAGGAT
1 ACTAAGAATAGCAAGAGGAT
57751954 ACTAAGAATAGCAAGAGGAT
1 ACTAAGAATAGCAAGAGGAT
57751974 A
1 A
57751975 TGTTAGACCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.10, G:0.24, T:0.15
Consensus pattern (20 bp):
ACTAAGAATAGCAAGAGGAT
Found at i:57763734 original size:25 final size:25
Alignment explanation
Indices: 57763700--57763750 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
57763690 AGACTGTTGA
57763700 GGAGTTAATTGAAACGGGGAGTTTT
1 GGAGTTAATTGAAACGGGGAGTTTT
*
57763725 GGAGTTAATTGAAACGGGGCGTTTT
1 GGAGTTAATTGAAACGGGGAGTTTT
57763750 G
1 G
57763751 TGTTTTTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.06, G:0.37, T:0.31
Consensus pattern (25 bp):
GGAGTTAATTGAAACGGGGAGTTTT
Found at i:57768825 original size:19 final size:18
Alignment explanation
Indices: 57768797--57768832 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
57768787 TTTAACCACC
*
57768797 ACTCCAGAAATTTTGTCT
1 ACTCCAGAAAATTTGTCT
57768815 ACTCTCAGAAAATTTGTC
1 ACTC-CAGAAAATTTGTC
57768833 ATGAATGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (18 bp):
ACTCCAGAAAATTTGTCT
Found at i:57774986 original size:43 final size:43
Alignment explanation
Indices: 57774938--57775024 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
57774928 GACAACACGT
*
57774938 GGTTTTTGTGGGCATGGATCTGAGGAGGTGTTGCATGTTTTCA
1 GGTTTTTGTGGGCATGGATCTGAGGAGGTGTTGCATGTTCTCA
*
57774981 GGTTTTTGTGGGCATGGATCTGAGGAGTTGTTGCATGTTCTCA
1 GGTTTTTGTGGGCATGGATCTGAGGAGGTGTTGCATGTTCTCA
57775024 G
1 G
57775025 AGATTGCCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.14, C:0.10, G:0.37, T:0.39
Consensus pattern (43 bp):
GGTTTTTGTGGGCATGGATCTGAGGAGGTGTTGCATGTTCTCA
Found at i:57775011 original size:22 final size:22
Alignment explanation
Indices: 57774943--57775011 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 22
57774933 CACGTGGTTT
57774943 TTGTGGGCATGGATCTGAGGAG
1 TTGTGGGCATGGATCTGAGGAG
* * * * * **
57774965 GTGT-TGCAT-GTTTTCAGGTTT
1 TTGTGGGCATGGATCTGAGG-AG
57774986 TTGTGGGCATGGATCTGAGGAG
1 TTGTGGGCATGGATCTGAGGAG
57775008 TTGT
1 TTGT
57775012 TGCATGTTCT
Statistics
Matches: 30, Mismatches: 14, Indels: 6
0.60 0.28 0.12
Matches are distributed among these distances:
20 6 0.20
21 7 0.23
22 11 0.37
23 6 0.20
ACGTcount: A:0.14, C:0.09, G:0.39, T:0.38
Consensus pattern (22 bp):
TTGTGGGCATGGATCTGAGGAG
Found at i:57778792 original size:24 final size:24
Alignment explanation
Indices: 57778765--57778817 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
57778755 ATAGTAACAT
*
57778765 CCCAACGGTCAAATTTCAAATCCG
1 CCCAACAGTCAAATTTCAAATCCG
*
57778789 CCCAACAGTCAAATTTCAAATCCT
1 CCCAACAGTCAAATTTCAAATCCG
57778813 CCCAA
1 CCCAA
57778818 TGGCTAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.36, C:0.36, G:0.08, T:0.21
Consensus pattern (24 bp):
CCCAACAGTCAAATTTCAAATCCG
Found at i:57782180 original size:23 final size:22
Alignment explanation
Indices: 57782152--57782205 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
57782142 TTGGAATGGA
*
57782152 TATGAAATGCTAATTTGTTTATG
1 TATGAAATGCTAATGT-TTTATG
* *
57782175 TTTG-AATGGTTAATGTTTTATG
1 TATGAAAT-GCTAATGTTTTATG
57782197 TATGAAATG
1 TATGAAATG
57782206 TGGTGTCAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.48
Consensus pattern (22 bp):
TATGAAATGCTAATGTTTTATG
Found at i:57783779 original size:69 final size:69
Alignment explanation
Indices: 57783687--57783849 Score: 191
Period size: 69 Copynumber: 2.4 Consensus size: 69
57783677 AGAGGTTTAC
* * * *
57783687 GGTGTAAGACCATAACTCGGCTATGACGACCAATAAAATCTGCTAGGACAATAAACATGGGGATT
1 GGTGTAAGACCATAGCTCGGCTATGACGACCAATAAAACCTGCTAGGACAATAAACATAGGGATA
*
57783752 GCGA
66 ACGA
* * ** * * * *
57783756 GGTTTAAGACCATAGGTCGGCTATGGTGACCAATAGAGCCTGTTGGGACAATAAACATAGGGATA
1 GGTGTAAGACCATAGCTCGGCTATGACGACCAATAAAACCTGCTAGGACAATAAACATAGGGATA
57783821 ACGA
66 ACGA
* *
57783825 GGTGTAGGACCATAGCTCAGCTATG
1 GGTGTAAGACCATAGCTCGGCTATG
57783850 CCAACCATTG
Statistics
Matches: 77, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
69 77 1.00
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (69 bp):
GGTGTAAGACCATAGCTCGGCTATGACGACCAATAAAACCTGCTAGGACAATAAACATAGGGATA
ACGA
Found at i:57783873 original size:69 final size:69
Alignment explanation
Indices: 57783687--57783882 Score: 167
Period size: 69 Copynumber: 2.8 Consensus size: 69
57783677 AGAGGTTTAC
* * * * * ** ** * *
57783687 GGTGTAAGACCATAACTCGGCTATGACGACCAATAAAATCTGCTAGGACAATAAACATGGGGATT
1 GGTGTAAGACCATAGCTCAGCTATGCCAACCAATAGAGCCTGCCGGGACAATAAACATAGGGATA
*
57783752 GCGA
66 ACGA
* * * *** **
57783756 GGTTTAAGACCATAGGTCGGCTATGGTGACCAATAGAGCCTGTTGGGACAATAAACATAGGGATA
1 GGTGTAAGACCATAGCTCAGCTATGCCAACCAATAGAGCCTGCCGGGACAATAAACATAGGGATA
57783821 ACGA
66 ACGA
* * * * *
57783825 GGTGTAGGACCATAGCTCAGCTATGCCAACCATTGGAGTCTGCCGGGACGATAAACAT
1 GGTGTAAGACCATAGCTCAGCTATGCCAACCAATAGAGCCTGCCGGGACAATAAACAT
57783883 GGGGTATACT
Statistics
Matches: 101, Mismatches: 26, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
69 101 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (69 bp):
GGTGTAAGACCATAGCTCAGCTATGCCAACCAATAGAGCCTGCCGGGACAATAAACATAGGGATA
ACGA
Found at i:57787368 original size:30 final size:30
Alignment explanation
Indices: 57787334--57787396 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
57787324 ACTTATTTTA
57787334 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
*
57787364 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
57787394 TTG
1 TTG
57787397 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:57787550 original size:12 final size:12
Alignment explanation
Indices: 57787520--57787552 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
57787510 TATATATTTT
57787520 AAAATT-ATATA
1 AAAATTAATATA
57787531 AAAA-TAATATA
1 AAAATTAATATA
57787542 AAAATTAATAT
1 AAAATTAATAT
57787553 GGCGGGCCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:57797469 original size:3 final size:3
Alignment explanation
Indices: 57797461--57797493 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
57797451 TCATAAAAGT
57797461 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
57797494 ATATTTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:57802304 original size:17 final size:17
Alignment explanation
Indices: 57802277--57802317 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
57802267 GTAAAAAAAT
*
57802277 ATTTTTATATTTTAATA
1 ATTTATATATTTTAATA
* *
57802294 GTTTATATATTTTTATA
1 ATTTATATATTTTAATA
57802311 ATTTATA
1 ATTTATA
57802318 AAGATTAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
ATTTATATATTTTAATA
Found at i:57802336 original size:29 final size:29
Alignment explanation
Indices: 57802297--57802364 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
57802287 TTTAATAGTT
* *
57802297 TATATATTTTTATAATTTATAAAGATTAAAT
1 TATA-ATTTTTATAATTTA-AAAAATTAAAA
*
57802328 TA-AATTTTTATTATTTAAAAAATTAAAA
1 TATAATTTTTATAATTTAAAAAATTAAAA
57802356 TATAATTTT
1 TATAATTTT
57802365 ATCATTATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 11 0.33
29 19 0.58
30 1 0.03
31 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (29 bp):
TATAATTTTTATAATTTAAAAAATTAAAA
Found at i:57802365 original size:28 final size:29
Alignment explanation
Indices: 57802298--57802366 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
57802288 TTAATAGTTT
* *
57802298 ATATATTTTTATAATTTATAAAGATTAAA
1 ATATAATTTTATAATTTATAAAAATTAAA
* *
57802327 TTA-AATTTTTATTATTTA-AAAAATTAAA
1 ATATAA-TTTTATAATTTATAAAAATTAAA
57802355 ATATAATTTTAT
1 ATATAATTTTAT
57802367 CATTATTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
28 18 0.55
29 15 0.45
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (29 bp):
ATATAATTTTATAATTTATAAAAATTAAA
Found at i:57807410 original size:25 final size:25
Alignment explanation
Indices: 57807373--57807421 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
57807363 CGGCCCTTAC
57807373 AAAAACAAATAAAA-TCAAAAAATT
1 AAAAACAAATAAAAGTCAAAAAATT
* *
57807397 AAAAATAAATTAAAAGTCCAAAAAT
1 AAAAACAAA-TAAAAGTCAAAAAAT
57807422 ACAGGAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 5 0.24
26 8 0.38
ACGTcount: A:0.71, C:0.08, G:0.02, T:0.18
Consensus pattern (25 bp):
AAAAACAAATAAAAGTCAAAAAATT
Found at i:57807772 original size:8 final size:8
Alignment explanation
Indices: 57807759--57807787 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
57807749 AATCGGCATC
57807759 AAAAAAAG
1 AAAAAAAG
57807767 AAAAAAAG
1 AAAAAAAG
57807775 AAAAAAAG
1 AAAAAAAG
57807783 AAAAA
1 AAAAA
57807788 GAAAAATGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:57808572 original size:15 final size:15
Alignment explanation
Indices: 57808552--57808583 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
57808542 TTTAGTGTGT
*
57808552 TTTTTATTTTTATTA
1 TTTTTATTTTTAATA
57808567 TTTTTATTTTTAATA
1 TTTTTATTTTTAATA
57808582 TT
1 TT
57808584 AGATTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTATTTTTAATA
Found at i:57809554 original size:18 final size:19
Alignment explanation
Indices: 57809531--57809568 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
57809521 TATCATGAAA
*
57809531 ATATGTGTGTATGTA-AAT
1 ATATGTATGTATGTACAAT
57809549 ATATGTATGTATGTACAAT
1 ATATGTATGTATGTACAAT
57809568 A
1 A
57809569 CGTATATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.37, C:0.03, G:0.18, T:0.42
Consensus pattern (19 bp):
ATATGTATGTATGTACAAT
Found at i:57809679 original size:34 final size:34
Alignment explanation
Indices: 57809624--57809695 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 34
57809614 TAAAAAAATG
*
57809624 TAAATATATATACTATAAAAATGA-ATGTATATTT
1 TAAATATATATACTATAAAAAT-ATATGTATATTC
57809658 TAAAT-TATAATA-TATAGAAAATATATGTATATTC
1 TAAATATAT-ATACTATA-AAAATATATGTATATTC
57809692 TAAA
1 TAAA
57809696 ATGTACATGT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
33 8 0.24
34 26 0.76
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (34 bp):
TAAATATATATACTATAAAAATATATGTATATTC
Found at i:57809864 original size:3 final size:3
Alignment explanation
Indices: 57809856--57809936 Score: 121
Period size: 3 Copynumber: 27.7 Consensus size: 3
57809846 AATATAAATG
* *
57809856 ATA ATA ATA ATA ACA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
57809904 ATA ATA ATA ATA ATA ATA AT- ATA A-A AAA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
57809937 TAAACAGTAA
Statistics
Matches: 73, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
2 4 0.05
3 69 0.95
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:57816776 original size:37 final size:38
Alignment explanation
Indices: 57816675--57816778 Score: 120
Period size: 37 Copynumber: 2.7 Consensus size: 38
57816665 ACTTCGAGTC
**
57816675 GATGAGACACTGGGTGTCAATTTATTGCTTCGGATTTATTT
1 GATGAGACACTGGGTGTCAATTTA---CTTCGGATTTAACT
* * *
57816716 GATGAGGCACTGGGTGCCGATTTACTTCGG-TTTAACT
1 GATGAGACACTGGGTGTCAATTTACTTCGGATTTAACT
*
57816753 GATGAGACACTAGGTGTCAATTTACT
1 GATGAGACACTGGGTGTCAATTTACT
57816779 ACTTCGAATT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
37 27 0.50
38 6 0.11
41 21 0.39
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (38 bp):
GATGAGACACTGGGTGTCAATTTACTTCGGATTTAACT
Found at i:57818217 original size:13 final size:14
Alignment explanation
Indices: 57818201--57818240 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
57818191 TTTCAGATAT
57818201 AGATA-ACAGAATC
1 AGATATACAGAATC
*
57818214 AGATATGCAGAA-C
1 AGATATACAGAATC
57818227 AGATATACAGAATC
1 AGATATACAGAATC
57818241 TTACCCCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 17 0.74
14 6 0.26
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.17
Consensus pattern (14 bp):
AGATATACAGAATC
Found at i:57819079 original size:24 final size:25
Alignment explanation
Indices: 57819050--57819108 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
57819040 AATATTATTT
57819050 AAATTTATCATGCAT-C-ATAGTTTA
1 AAATTTATCATG-ATACTATAGTTTA
*
57819074 AAATTTATCA-GATACTATAGTTTT
1 AAATTTATCATGATACTATAGTTTA
*
57819098 AAACTTATCAT
1 AAATTTATCAT
57819109 AGATTATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 2 0.07
23 2 0.07
24 26 0.87
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (25 bp):
AAATTTATCATGATACTATAGTTTA
Found at i:57822568 original size:3 final size:3
Alignment explanation
Indices: 57822560--57822584 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
57822550 TGTCTCCATG
57822560 ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC A
57822585 CCGCCACCAT
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):
ATC
Found at i:57825498 original size:16 final size:16
Alignment explanation
Indices: 57825477--57825509 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
57825467 GCAATTTTTG
57825477 TTCCCTCATGAAAAAC
1 TTCCCTCATGAAAAAC
57825493 TTCCCTCATGAAAAAC
1 TTCCCTCATGAAAAAC
57825509 T
1 T
57825510 AACATCGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.30, G:0.06, T:0.27
Consensus pattern (16 bp):
TTCCCTCATGAAAAAC
Found at i:57829370 original size:3 final size:3
Alignment explanation
Indices: 57829362--57829397 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
57829352 CAGACTATAT
57829362 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
57829398 GTTTATGACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:57830165 original size:41 final size:41
Alignment explanation
Indices: 57830120--57830254 Score: 128
Period size: 41 Copynumber: 3.1 Consensus size: 41
57830110 AAAATAAGTG
57830120 AAAACATCTTTACTTATAAATGTTTACAATTGACTTGAAAT
1 AAAACATCTTTACTTATAAATGTTTACAATTGACTTGAAAT
* ** ** *
57830161 AAAACATCTTTACTTATAAAACATCTTTACTCAAAATAAAAAT-AAGT
1 AAAACATCTTTACTTAT--AA-ATGTTTA--C--AATTGACTTGAAAT
57830208 GAAAACATCTTTACTTATAAATGTTTACAATTGACTTGAAATT
1 -AAAACATCTTTACTTATAAATGTTTACAATTGACTTGAAA-T
57830251 AAAA
1 AAAA
57830255 AAAAAAAAAC
Statistics
Matches: 72, Mismatches: 12, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
41 22 0.31
42 6 0.08
43 4 0.06
44 6 0.08
45 6 0.08
46 3 0.04
47 3 0.04
48 22 0.31
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.36
Consensus pattern (41 bp):
AAAACATCTTTACTTATAAATGTTTACAATTGACTTGAAAT
Found at i:57830181 original size:17 final size:17
Alignment explanation
Indices: 57830159--57830191 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
57830149 TTGACTTGAA
57830159 ATAAAACATCTTTACTT
1 ATAAAACATCTTTACTT
57830176 ATAAAACATCTTTACT
1 ATAAAACATCTTTACT
57830192 CAAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAAAACATCTTTACTT
Found at i:57830816 original size:29 final size:30
Alignment explanation
Indices: 57830758--57830833 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 30
57830748 AAACTGAATC
* *
57830758 AAATCAAAATTTTATGTATGAAATCGCACA-
1 AAATC-AAAGTTTATGTATGAAATCACACAT
* *
57830788 AAATCAAAGTTTATGTATGACATTACACATT
1 AAATCAAAGTTTATGTATGAAATCACACA-T
57830819 AAATCAAAGTTTATG
1 AAATCAAAGTTTATG
57830834 AATAGTTTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 20 0.50
30 5 0.12
31 15 0.38
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.33
Consensus pattern (30 bp):
AAATCAAAGTTTATGTATGAAATCACACAT
Found at i:57832544 original size:40 final size:40
Alignment explanation
Indices: 57832489--57832570 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
57832479 AGTGGCTAAT
*
57832489 AGGTGATCGGGATCCTATAACTTAAAATGTTGCTTGACAA
1 AGGTGATCAGGATCCTATAACTTAAAATGTTGCTTGACAA
*
57832529 AGGTGATCAGGATCCTATAGCTTAAAATGTTGCTTGACAA
1 AGGTGATCAGGATCCTATAACTTAAAATGTTGCTTGACAA
57832569 AG
1 AG
57832571 TCATCAATCC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (40 bp):
AGGTGATCAGGATCCTATAACTTAAAATGTTGCTTGACAA
Found at i:57835215 original size:17 final size:15
Alignment explanation
Indices: 57835193--57835227 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
57835183 CCTCCCCATC
57835193 TTTCTTTTTCTTTTTCT
1 TTTCTTTTT-TTTTT-T
57835210 TTTCTTTTTTTTTTT
1 TTTCTTTTTTTTTTT
57835225 TTT
1 TTT
57835228 GTTGGTGCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 5 0.28
17 9 0.50
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTCTTTTTTTTTTT
Found at i:57839032 original size:19 final size:20
Alignment explanation
Indices: 57838991--57839032 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
57838981 AAAATTTTTA
* *
57838991 ATATTAGAATTGATATGTGC
1 ATATTAGAATTGAAATGTAC
*
57839011 ATATTAGTA-TGAAATGTAC
1 ATATTAGAATTGAAATGTAC
57839030 ATA
1 ATA
57839033 GATTGCCAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (20 bp):
ATATTAGAATTGAAATGTAC
Found at i:57844019 original size:28 final size:29
Alignment explanation
Indices: 57843967--57844021 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
57843957 TGTTGCAGGA
*
57843967 GCTGGTGAGTTAAAGAAGAAAAAGAATAG
1 GCTGGTGAGTGAAAGAAGAAAAAGAATAG
* *
57843996 GCTGGTGAG-GAATGAAGAAGAAGAAT
1 GCTGGTGAGTGAAAGAAGAAAAAGAAT
57844022 GAAGGGAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.45, C:0.04, G:0.35, T:0.16
Consensus pattern (29 bp):
GCTGGTGAGTGAAAGAAGAAAAAGAATAG
Found at i:57853509 original size:13 final size:13
Alignment explanation
Indices: 57853491--57853515 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57853481 AGAAACATGG
57853491 TTTAATATTTTAC
1 TTTAATATTTTAC
57853504 TTTAATATTTTA
1 TTTAATATTTTA
57853516 ATATTTTTTA
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:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTAATATTTTAC
Found at i:57856028 original size:2 final size:2
Alignment explanation
Indices: 57856021--57856053 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
57856011 TCGAATTTAA
57856021 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 A
57856054 ATAGTTATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57861513 original size:21 final size:21
Alignment explanation
Indices: 57861487--57861528 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
57861477 TCCATTCAGC
57861487 CTTTATTTATTCTTAATCTGT
1 CTTTATTTATTCTTAATCTGT
57861508 CTTTATTTATTCTTAATCTGT
1 CTTTATTTATTCTTAATCTGT
57861529 GCAGAGGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.14, G:0.05, T:0.62
Consensus pattern (21 bp):
CTTTATTTATTCTTAATCTGT
Found at i:57866924 original size:57 final size:57
Alignment explanation
Indices: 57866836--57866944 Score: 157
Period size: 57 Copynumber: 1.9 Consensus size: 57
57866826 AATTCGGATT
*
57866836 ACCCGTCCGAGCTAAATCCATTTTCCACATATTCTTCGGGAGGGCTATATCAAGATC
1 ACCCGTCCGAGCTAAATCCATTTTCCACATATTCTTCAGGAGGGCTATATCAAGATC
* * * *
57866893 ACCCGTCCGGGCTAGAT-CTTTTTCACACATATTCTTTAGGAGGGCTATATCA
1 ACCCGTCCGAGCTAAATCCATTTTC-CACATATTCTTCAGGAGGGCTATATCA
57866945 GGATAGGATC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
56 6 0.13
57 40 0.87
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (57 bp):
ACCCGTCCGAGCTAAATCCATTTTCCACATATTCTTCAGGAGGGCTATATCAAGATC
Found at i:57876133 original size:2 final size:2
Alignment explanation
Indices: 57876126--57876173 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
57876116 CCTCTTTACC
57876126 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
57876168 AT AT AT
1 AT AT AT
57876174 TAGCTATTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57876436 original size:89 final size:88
Alignment explanation
Indices: 57876341--57876513 Score: 231
Period size: 89 Copynumber: 2.0 Consensus size: 88
57876331 TTTTTTTTTT
* * ** * *
57876341 TTTTTTTTGCACTCAATTGAGCACTTGAACTTTTAAAATACATCAAAAAGGCTCTC-AAACTTCT
1 TTTTTTTTGCACTCAATTGAGCACTTGAACATTCAAAATACATCAAAAAAACCCTCAAAAATT-T
57876405 TCACAAAAAGCAATTAAGCCCCTAC
65 TCA-AAAAAGCAATTAAGCCCCTAC
* * * *
57876430 TTTTTTTTTCACTCAATTGGGTACTTGAACATTCAAAATTCATCAAAAAAACCCTCAAAAATTTT
1 TTTTTTTTGCACTCAATTGAGCACTTGAACATTCAAAATACATCAAAAAAACCCTCAAAAATTTT
57876495 CAAAAAAGCAATTAAGCCC
66 CAAAAAAGCAATTAAGCCC
57876514 ATGTTCTTAT
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
88 17 0.23
89 51 0.70
90 5 0.07
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.32
Consensus pattern (88 bp):
TTTTTTTTGCACTCAATTGAGCACTTGAACATTCAAAATACATCAAAAAAACCCTCAAAAATTTT
CAAAAAAGCAATTAAGCCCCTAC
Found at i:57876549 original size:9 final size:9
Alignment explanation
Indices: 57876537--57876670 Score: 58
Period size: 9 Copynumber: 14.6 Consensus size: 9
57876527 AAATTAGAAA
57876537 AAAAATTAT
1 AAAAATTAT
*
57876546 AAAAATAAT
1 AAAAATTAT
** *
57876555 AAATTTTAG
1 AAAAATTAT
57876564 AAAAATTATT
1 AAAAATTA-T
***
57876574 AATTTTTAAT
1 AAAAATT-AT
57876584 AAAAA-TAT
1 AAAAATTAT
57876592 AAAAATTATT
1 AAAAATTA-T
*
57876602 AAAAATTAG
1 AAAAATTAT
**
57876611 AAATTTTTAT
1 AAA-AATTAT
*
57876621 ATAAAAATAGT
1 A-AAAATTA-T
*
57876632 AAAAA-TAA
1 AAAAATTAT
57876640 AAAAATTA-
1 AAAAATTAT
**
57876648 AAATTTTAT
1 AAAAATTAT
*
57876657 AAAAATAAT
1 AAAAATTAT
57876666 AAAAA
1 AAAAA
57876671 ATTAATGACC
Statistics
Matches: 89, Mismatches: 27, Indels: 18
0.66 0.20 0.13
Matches are distributed among these distances:
8 18 0.20
9 40 0.45
10 26 0.29
11 5 0.06
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (9 bp):
AAAAATTAT
Found at i:57876652 original size:37 final size:39
Alignment explanation
Indices: 57876543--57876674 Score: 134
Period size: 38 Copynumber: 3.5 Consensus size: 39
57876533 GAAAAAAAAT
* * **
57876543 TATAAAAATA-ATAAATTTTAGAAAAATTATTAATTTTTA
1 TATAAAAATATAAAAATTATA-AAAAATTAGAAATTTTTA
*
57876582 -ATAAAAATATAAAAATTATTAAAAATTAGAAATTTTTA
1 TATAAAAATATAAAAATTATAAAAAATTAGAAATTTTTA
57876620 TATAAAAATAGTAAAAA-TA-AAAAAATTA-AAA-TTTTA
1 TATAAAAATA-TAAAAATTATAAAAAATTAGAAATTTTTA
*
57876656 TAAAAATAATA-AAAAATTA
1 TATAAA-AATATAAAAATTA
57876675 ATGACCCCTA
Statistics
Matches: 81, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
35 5 0.06
36 12 0.15
37 7 0.09
38 33 0.41
39 18 0.22
40 6 0.07
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (39 bp):
TATAAAAATATAAAAATTATAAAAAATTAGAAATTTTTA
Found at i:57876814 original size:9 final size:9
Alignment explanation
Indices: 57876800--57876830 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
57876790 GTTAAACGAA
57876800 TCGAGTTAT
1 TCGAGTTAT
*
57876809 TCGAGTTAA
1 TCGAGTTAT
57876818 TCGAGTTAT
1 TCGAGTTAT
57876827 TCGA
1 TCGA
57876831 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:57876902 original size:9 final size:9
Alignment explanation
Indices: 57876883--57876919 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
57876873 TGAGTTTTCG
*
57876883 AATTTGAAT
1 AATTCGAAT
*
57876892 AACTCGAAT
1 AATTCGAAT
57876901 AATTCGAAT
1 AATTCGAAT
57876910 AATTCGAAT
1 AATTCGAAT
57876919 A
1 A
57876920 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:57878159 original size:29 final size:28
Alignment explanation
Indices: 57878110--57878211 Score: 98
Period size: 29 Copynumber: 3.5 Consensus size: 28
57878100 AGAGTCTACC
**
57878110 TTTATAATTTTCTTACGATTTTATAAAAT
1 TTTATAATTTT-TTTTGATTTTATAAAAT
*
57878139 TTTATAATTTTTTTTGTATTTT-TATATAT
1 TTTATAATTTTTTTTG-ATTTTATA-AAAT
57878168 TTTATAATTTTTTTATGATTTTTATAAAAAT
1 TTTATAATTTTTTT-TGA-TTTTAT-AAAAT
* *
57878199 TTTACAGTTTTTT
1 TTTATAATTTTTT
57878212 ATATTTTTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
28 5 0.08
29 34 0.56
30 6 0.10
31 15 0.25
32 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.64
Consensus pattern (28 bp):
TTTATAATTTTTTTTGATTTTATAAAAT
Found at i:57878180 original size:20 final size:20
Alignment explanation
Indices: 57878157--57878231 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
57878147 TTTTTTTGTA
57878157 TTTTTAT-ATATTTTATAATT
1 TTTTTATGAT-TTTTATAATT
**
57878177 TTTTTATGATTTTTATAAAA
1 TTTTTATGATTTTTATAATT
* * *
57878197 ATTTTACAGTTTTTTAT-ATT
1 TTTTTA-TGATTTTTATAATT
*
57878217 TTTTTACGATTTTTA
1 TTTTTATGATTTTTA
57878232 CTTTTTCTAA
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
19 7 0.16
20 26 0.60
21 10 0.23
ACGTcount: A:0.28, C:0.03, G:0.04, T:0.65
Consensus pattern (20 bp):
TTTTTATGATTTTTATAATT
Found at i:57878210 original size:58 final size:58
Alignment explanation
Indices: 57878110--57878219 Score: 143
Period size: 58 Copynumber: 1.9 Consensus size: 58
57878100 AGAGTCTACC
* *
57878110 TTTATAATTTTCTTACGATTTTATAAAATTTTATAATTTTTTTTGTATTTTTATATAT
1 TTTATAATTTTCTTACGATTTTATAAAATTTTATAATGTTTTTTATATTTTTATATAT
* * *
57878168 TTTATAATTTTTTTATGATTTTTATAAAAATTTTA-CA-GTTTTTTATATTTTT
1 TTTATAATTTTCTTACGA-TTTTAT-AAAATTTTATAATGTTTTTTATATTTTT
57878220 TTACGATTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
58 29 0.64
59 7 0.16
60 9 0.20
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.65
Consensus pattern (58 bp):
TTTATAATTTTCTTACGATTTTATAAAATTTTATAATGTTTTTTATATTTTTATATAT
Found at i:57878324 original size:17 final size:17
Alignment explanation
Indices: 57878302--57878453 Score: 62
Period size: 18 Copynumber: 8.7 Consensus size: 17
57878292 TTATTGATTT
57878302 TAATTTTATAATTTTTA
1 TAATTTTATAATTTTTA
**
57878319 TAATTTTTATAAAAGTTTA
1 TAA-TTTTAT-AATTTTTA
* *
57878338 CAATTTTTTATATTTTTA
1 TAATTTTATA-ATTTTTA
** *
57878356 CCATTTT-TAATTTTTC
1 TAATTTTATAATTTTTA
*
57878372 TAATTTT-TAATATTTGA
1 TAATTTTATAAT-TTTTA
* *
57878389 -AATTTTTATTAAAATTTAA
1 TAA-TTTTA-T-AATTTTTA
* *
57878408 TCATATTTATATTTTTTA
1 TAAT-TTTATAATTTTTA
* *
57878426 TTGATTTTA-ATTTTTTA
1 -TAATTTTATAATTTTTA
57878443 TAATTTT-TAAT
1 TAATTTTATAAT
57878454 AAAAGCAGAG
Statistics
Matches: 102, Mismatches: 21, Indels: 25
0.69 0.14 0.17
Matches are distributed among these distances:
16 25 0.25
17 21 0.21
18 31 0.30
19 18 0.18
20 7 0.07
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (17 bp):
TAATTTTATAATTTTTA
Found at i:57878377 original size:16 final size:16
Alignment explanation
Indices: 57878358--57878396 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
57878348 TATTTTTACC
* *
57878358 ATTTTTAATTTTTCTA
1 ATTTTTAATATTTCAA
*
57878374 ATTTTTAATATTTGAA
1 ATTTTTAATATTTCAA
57878390 ATTTTTA
1 ATTTTTA
57878397 TTAAAATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (16 bp):
ATTTTTAATATTTCAA
Found at i:57878383 original size:133 final size:133
Alignment explanation
Indices: 57878166--57878451 Score: 405
Period size: 133 Copynumber: 2.1 Consensus size: 133
57878156 ATTTTTATAT
* * * *
57878166 ATTTTATAATTTTTTTATGATTTTTATAAAAATTTTACAGTTTTTTATATTTTTTTACGATTTTT
1 ATTTTATAA--TTTTTATAATTTTTATAAAAAGTTTACAATTTTTTATA-TTTTTTACCATTTTT
* * *
57878231 ACTTTTTCTAATTTCTAATATTTTAATTTTTTTAATTAAAATTTAATAATATTTATACTTTTTAT
63 AATTTTTCTAATTTCTAATATTTGAA-ATTTTT-ATTAAAATTTAATAATATTTATACTTTTTAT
57878296 TGATTTTA
126 TGATTTTA
57878304 ATTTTATAATTTTTATAATTTTTAT-AAAAGTTTACAATTTTTTATA-TTTTTACCATTTTTAAT
1 ATTTTATAATTTTTATAATTTTTATAAAAAGTTTACAATTTTTTATATTTTTTACCATTTTTAAT
* * *
57878367 TTTTCTAATTTTTAATATTTGAAATTTTTATTAAAATTTAATCATATTTATATTTTTTATTGATT
66 TTTTCTAATTTCTAATATTTGAAATTTTTATTAAAATTTAATAATATTTATACTTTTTATTGATT
57878432 TTA
131 TTA
57878435 ATTTTTTATAATTTTTA
1 A--TTTTATAATTTTTA
57878452 ATAAAAGCAG
Statistics
Matches: 136, Mismatches: 10, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
131 38 0.28
132 5 0.04
133 50 0.37
135 19 0.14
136 15 0.11
138 9 0.07
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (133 bp):
ATTTTATAATTTTTATAATTTTTATAAAAAGTTTACAATTTTTTATATTTTTTACCATTTTTAAT
TTTTCTAATTTCTAATATTTGAAATTTTTATTAAAATTTAATAATATTTATACTTTTTATTGATT
TTA
Found at i:57878451 original size:9 final size:9
Alignment explanation
Indices: 57878305--57878380 Score: 59
Period size: 9 Copynumber: 8.6 Consensus size: 9
57878295 TTGATTTTAA
57878305 TTTTATAAT
1 TTTTATAAT
57878314 TTTTATAAT
1 TTTTATAAT
*
57878323 TTTTATAAAA
1 TTTTAT-AAT
* *
57878333 GTTTACAAT
1 TTTTATAAT
57878342 TTTT-TATAT
1 TTTTATA-AT
**
57878351 TTTTACCA-
1 TTTTATAAT
57878359 TTTT-TAAT
1 TTTTATAAT
*
57878367 TTTTCTAAT
1 TTTTATAAT
57878376 TTTTA
1 TTTTA
57878381 ATATTTGAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
7 1 0.02
8 9 0.18
9 35 0.69
10 6 0.12
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:57885325 original size:20 final size:19
Alignment explanation
Indices: 57885281--57885330 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
57885271 TATGTATTTT
* *
57885281 TTAAATAATATTGATACAT
1 TTAAAAAATATTGATACAA
*
57885300 TTAAAACATATTGATGACAA
1 TTAAAAAATATTGAT-ACAA
57885320 TTAAAAAATAT
1 TTAAAAAATAT
57885331 ATTATTATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (19 bp):
TTAAAAAATATTGATACAA
Found at i:57886442 original size:12 final size:13
Alignment explanation
Indices: 57886425--57886454 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
57886415 CGATTTACAG
57886425 AAAATAGAGAA-A
1 AAAATAGAGAATA
57886437 AAAATAGAGAATA
1 AAAATAGAGAATA
57886450 AAAAT
1 AAAAT
57886455 CAATCCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (13 bp):
AAAATAGAGAATA
Found at i:57886740 original size:44 final size:44
Alignment explanation
Indices: 57886654--57886809 Score: 147
Period size: 44 Copynumber: 3.5 Consensus size: 44
57886644 ATCTACTCTG
* * * *
57886654 CTGTAA-CTTCAGAGAGATAAGA-TACTTTGTTTTAATCCGCTCCA
1 CTGTAATC-TCAGAGAGATAAGATTAC-TAGCTTCAATCTGCTCCA
* *
57886698 CTGTAATCTCAGAGAGATAGGATTACTAGCTTCAATCTGCTCCG
1 CTGTAATCTCAGAGAGATAAGATTACTAGCTTCAATCTGCTCCA
** * * *
57886742 CTGTAATCTCA-AGGAGATAAGATTTTTGGCTTCAGTCTGCCCCA
1 CTGTAATCTCAGA-GAGATAAGATTACTAGCTTCAATCTGCTCCA
* *
57886786 CTGTGACCTCAGAGAGATAAGATT
1 CTGTAATCTCAGAGAGATAAGATT
57886810 GATTTCTTCT
Statistics
Matches: 93, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
43 1 0.01
44 87 0.94
45 5 0.05
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (44 bp):
CTGTAATCTCAGAGAGATAAGATTACTAGCTTCAATCTGCTCCA
Found at i:57904325 original size:91 final size:84
Alignment explanation
Indices: 57904160--57904376 Score: 236
Period size: 91 Copynumber: 2.4 Consensus size: 84
57904150 TTAATGGTGC
* * * * *
57904160 AAAAAGCTCTCAAATGTTTTCAAAAAAAAATAATTAAGCCCTTTTTTTTTGCACTTATTTGGGTA
1 AAAAAGCTCTCAAAT-TTTTC--AAAAAAGTAATTAAGCCCTCTTTTTTTGCACTCAATTGGATA
*
57904225 TTTAAACTTTCAAAATGCATCAA
63 CTTAAACTTTCAAAATGCAT-AA
57904248 AAAAAGCTCTCAAACTTTTTCAAGAAAAGTAATTAAGCCTTGACTCTTTTTTTGCACTCAATTGG
1 AAAAAGCTCTCAAA-TTTTTCAA-AAAAGTAATTAAGCC----CTCTTTTTTTGCACTCAATTGG
57904313 ATACTTAAACTTTCAAAATGCATAA
60 ATACTTAAACTTTCAAAATGCATAA
* * *
57904338 AAAAAACCCTCAAATTTTTTTCCAAAAAAGCAATTAAGC
1 AAAAAGCTCTCAAA--TTTTT-CAAAAAAGTAATTAAGC
57904377 TCATGCTTTT
Statistics
Matches: 111, Mismatches: 10, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
86 2 0.02
87 14 0.13
88 19 0.17
89 1 0.01
90 14 0.13
91 58 0.52
92 3 0.03
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (84 bp):
AAAAAGCTCTCAAATTTTTCAAAAAAGTAATTAAGCCCTCTTTTTTTGCACTCAATTGGATACTT
AAACTTTCAAAATGCATAA
Found at i:57904504 original size:27 final size:27
Alignment explanation
Indices: 57904474--57904526 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
57904464 AAAAATTAGG
*
57904474 AAAAGAATATAAAATTGTAAAAAAATA
1 AAAAAAATATAAAATTGTAAAAAAATA
* * *
57904501 AAAAAAATTTAAAATTTTATAAAAAT
1 AAAAAAATATAAAATTGTAAAAAAAT
57904527 CATAAAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (27 bp):
AAAAAAATATAAAATTGTAAAAAAATA
Found at i:57904505 original size:18 final size:19
Alignment explanation
Indices: 57904464--57904505 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
57904454 TTCAAATATT
*
57904464 AAAAATTAGGAAAAGAATA
1 AAAAATTAGGAAAAAAATA
* *
57904483 TAAAATT-GTAAAAAAATA
1 AAAAATTAGGAAAAAAATA
57904501 AAAAA
1 AAAAA
57904506 AATTTAAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (19 bp):
AAAAATTAGGAAAAAAATA
Found at i:57904684 original size:11 final size:11
Alignment explanation
Indices: 57904668--57904700 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
57904658 AGAAGTATTT
*
57904668 TATAATTTTTC
1 TATAATTTTTA
57904679 TATAATTTTTA
1 TATAATTTTTA
57904690 T-TAATTTTTA
1 TATAATTTTTA
57904700 T
1 T
57904701 TTATTTATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (11 bp):
TATAATTTTTA
Found at i:57904694 original size:10 final size:10
Alignment explanation
Indices: 57904665--57904706 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
57904655 AAAAGAAGTA
57904665 TTTTA-TAAT
1 TTTTATTAAT
*
57904674 TTTTCTATAAT
1 TTTTAT-TAAT
57904685 TTTTATTAAT
1 TTTTATTAAT
*
57904695 TTTTATTTAT
1 TTTTATTAAT
57904705 TT
1 TT
57904707 ATCATTTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 4 0.14
10 15 0.54
11 9 0.32
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTATTAAT
Found at i:57905130 original size:91 final size:89
Alignment explanation
Indices: 57904951--57905145 Score: 230
Period size: 91 Copynumber: 2.2 Consensus size: 89
57904941 TTTTAATAAG
* * *
57904951 AGCAGGGGCTTAATTGCTTTTTTGAAAAATTTTGAGAGTCTTTTTTATGCATTTTGAAAGTTCAA
1 AGCAGGGACTTAATTGCTTTTTTGAAAAAGTTTGAGAGCCTTTTTTATGCATTTTGAAAGTTCAA
** *
57905016 GTACCCAGTTGAGTGAAAAAAAAA
66 GTACCCAACTAAGTGAAAAAAAAA
* *
57905040 AGCAGGGCCTTAATTGCTTTTTTTGAAGAAGTTTGAGTA-CCTTTTTTGATGCATTTTGAAAGTT
1 AGCAGGGACTTAATTGC-TTTTTTGAAAAAGTTTGAG-AGCCTTTTTT-ATGCATTTTGAAAGTT
* *** *
57905104 TAAGTGGTCAACTAAGTGCAAAAAAAA
63 CAAGTACCCAACTAAGTGAAAAAAAAA
*
57905131 AGGAGGGACTTAATT
1 AGCAGGGACTTAATT
57905146 ATTATTATTA
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
89 16 0.18
90 24 0.27
91 49 0.55
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (89 bp):
AGCAGGGACTTAATTGCTTTTTTGAAAAAGTTTGAGAGCCTTTTTTATGCATTTTGAAAGTTCAA
GTACCCAACTAAGTGAAAAAAAAA
Found at i:57909554 original size:30 final size:31
Alignment explanation
Indices: 57909514--57909581 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
57909504 TTACAAAATG
*
57909514 GTCACTGAATTATT-TAAAGTTTTCATTTAA
1 GTCACTGAATTATTCGAAAGTTTTCATTTAA
*
57909544 GTCATTGAATTATTCGAAAGTTTTCATTTAA
1 GTCACTGAATTATTCGAAAGTTTTCATTTAA
*
57909575 GTTACTG
1 GTCACTG
57909582 CGTTGTTAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 13 0.39
31 20 0.61
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (31 bp):
GTCACTGAATTATTCGAAAGTTTTCATTTAA
Found at i:57911523 original size:24 final size:23
Alignment explanation
Indices: 57911496--57911544 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
57911486 CCCTGTTAGA
*
57911496 GTAATTAATGAAGTTGTTTAGTCT
1 GTAACTAATGAAGTTG-TTAGTCT
**
57911520 GTAACTGCTGAAGTTGTTAGTCT
1 GTAACTAATGAAGTTGTTAGTCT
57911543 GT
1 GT
57911545 TAGTAGTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.43
Consensus pattern (23 bp):
GTAACTAATGAAGTTGTTAGTCT
Found at i:57916087 original size:24 final size:23
Alignment explanation
Indices: 57916060--57916108 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
57916050 GAATGTTAGA
*
57916060 GTAATTAATGAAGTTGTTTAGTCT
1 GTAACTAATGAAGTTG-TTAGTCT
**
57916084 GTAACTGCTGAAGTTGTTAGTCT
1 GTAACTAATGAAGTTGTTAGTCT
57916107 GT
1 GT
57916109 TAGTAGTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.43
Consensus pattern (23 bp):
GTAACTAATGAAGTTGTTAGTCT
Found at i:57918581 original size:6 final size:6
Alignment explanation
Indices: 57918570--57918594 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
57918560 CCTTGATTTG
57918570 TGGTGC TGGTGC TGGTGC TGGTGC T
1 TGGTGC TGGTGC TGGTGC TGGTGC T
57918595 ACTACTTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TGGTGC
Found at i:57923695 original size:16 final size:17
Alignment explanation
Indices: 57923664--57923701 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
57923654 TAAATTCTAT
*
57923664 AAAAGAAATCAAATTTTA
1 AAAAGAAA-CAAATTTGA
57923682 AAAAGAAA-AAATTTGA
1 AAAAGAAACAAATTTGA
57923698 AAAA
1 AAAA
57923702 CTTAAAGGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 11 0.58
18 8 0.42
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.21
Consensus pattern (17 bp):
AAAAGAAACAAATTTGA
Done.