Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 186 of 208
Found at i:56881257 original size:247 final size:249
Alignment explanation
Indices: 56880844--56881573 Score: 949
Period size: 247 Copynumber: 2.9 Consensus size: 249
56880834 CTAGTACTAT
* * * *
56880844 TATTATA-ATTTATAATAAAAGATATAATATTACATAACATTATAATGTTTAATCATTGATGCAT
1 TATTATAGA-TTATAATAAAAGATATAGTATTATATGATATTATAATGTTTAATCATTGATGCA-
56880908 ATATATAAACTATTAATATATTATATACTATATGATATGATATAACATTATATAATATAGTAGGA
64 ATATATAAACTATTAATATATTATATACTATATGATATGATATAACATTATATAATATAGTAGGA
* * * * *
56880973 TGGCTACCTTTCATATGTAC-AAAAACTATAAGGACTTAGAGCATATTTCAACCAGTATAATAAT
129 GGGTTAACTTTCAAATGTACGAAAAA-TATAGGGACTTAGAGCATATTTCAACCAGTATAATAAT
*
56881037 AAACAATAATAATTAATATATAATATATAATGTACTACTATTTTATAT-A-ATTATTA
193 AAACAATAATAATTAATA-ATAATATATAATGTACTACTATTATATATAACATTATTA
* * *
56881093 TCTTATAGATTATAATAAAAGATATAGTATTATATGATACTATAATGTTTAATTATTGATGC-AT
1 TATTATAGATTATAATAAAAGATATAGTATTATATGATATTATAATGTTTAATCATTGATGCAAT
* * *
56881157 ATATAAACTATTATTATATTATATTA-TATACGATATGATATAGCATTATATAATATAGTAGGAG
66 ATATAAACTATTAATATATTATA-TACTATATGATATGATATAACATTATATAATATAGTAGGAG
56881221 GGTTAACTTTCAAATGTACGAAAAATATAGGGACTTAGAGCATATTTCAA-C----TAAT-AT--
130 GGTTAACTTTCAAATGTACGAAAAATATAGGGACTTAGAGCATATTTCAACCAGTATAATAATAA
*
56881278 --AATAAT-A--AATAATAATATATAATGTACTACCATTATATATAACTATTATTA
195 ACAATAATAATTAATAATAATATATAATGTACTACTATTATATATAAC-ATTATTA
* * * *
56881329 TATTATTGATTATAATAAAATATATAGTATTATATGATATTATAATGTCTAAACATTGATGCATA
1 TATTATAGATTATAATAAAAGATATAGTATTATATGATATTATAATGTTTAATCATTGATGCA-A
*
56881394 TATGTGTATAAACTATTAAAATATATTATATACTATATGATATGATACAACATTATATAATATAG
65 TA----TATAAACTATT--AATATATTATATACTATATGATATGATATAACATTATATAATATAG
* * *
56881459 TAGGAGGGTTAACTTTCAAATGTACGAAAAGTATAGAGACTTAGAGTATATTTCAACCAGTATAA
124 TAGGAGGGTTAACTTTCAAATGTACGAAAAATATAGGGACTTAGAGCATATTTCAACCAGTATAA
56881524 TAATAAACAATAATATATGTTAATAATTAATATATAATGTACTACTATTA
189 TAATAAACAATAATA-A--TTAATAA-TAATATATAATGTACTACTATTA
56881574 GATTACAGAA
Statistics
Matches: 417, Mismatches: 32, Indels: 52
0.83 0.06 0.10
Matches are distributed among these distances:
233 27 0.06
234 5 0.01
236 63 0.15
237 6 0.01
238 3 0.01
241 2 0.00
242 15 0.04
243 2 0.00
244 92 0.22
245 1 0.00
246 1 0.00
247 99 0.24
248 7 0.02
249 57 0.14
250 3 0.01
254 6 0.01
256 1 0.00
260 5 0.01
261 22 0.05
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.39
Consensus pattern (249 bp):
TATTATAGATTATAATAAAAGATATAGTATTATATGATATTATAATGTTTAATCATTGATGCAAT
ATATAAACTATTAATATATTATATACTATATGATATGATATAACATTATATAATATAGTAGGAGG
GTTAACTTTCAAATGTACGAAAAATATAGGGACTTAGAGCATATTTCAACCAGTATAATAATAAA
CAATAATAATTAATAATAATATATAATGTACTACTATTATATATAACATTATTA
Found at i:56881469 original size:244 final size:233
Alignment explanation
Indices: 56881042--56881541 Score: 696
Period size: 244 Copynumber: 2.1 Consensus size: 233
56881032 ATAATAAACA
* * * *
56881042 ATAATAATTAATATATAATATATAATGTACTACTATTTTATATAATTATTATCTTATAGATTATA
1 ATAATAATAAATA-ATAATATATAATGTACTACCATTATATATAATTATTATATTATAGATTATA
* ** *
56881107 ATAAAAGATATAGTATTATATGATACTATAATGTTTAATTATTGATGCATATATAAACTATTATT
65 ATAAAAGATATAGTATTATATGATACTATAATGTCTAAACATTGATGCATATATAAACTATTAAT
* *
56881172 ATATTATATTATATACGATATGATATAGCATTATATAATATAGTAGGAGGGTTAACTTTCAAATG
130 ATATTATATTATATACGATATGATACAACATTATATAATATAGTAGGAGGGTTAACTTTCAAATG
* *
56881237 TACGAAAAATATAGGGACTTAGAGCATATTTCAACTAAT
195 TACGAAAAATATAGAGACTTAGAGCATATTTCAACCAAT
*
56881276 ATAATAATAAATAATAATATATAATGTACTACCATTATATATAACTATTATTATATTATTGATTA
1 ATAATAATAAATAATAATATATAATGTACTACCATTATATAT-A--ATTATTATATTATAGATTA
* *
56881341 TAATAAAATATATAGTATTATATGATATTATAATGTCTAAACATTGATGCATATATGTGTATAAA
63 TAATAAAAGATATAGTATTATATGATACTATAATGTCTAAACATTGATGC--ATA----TATAAA
*
56881406 CTATTAAAATATATTATA-TACTATATGATATGATACAACATTATATAATATAGTAGGAGGGTTA
122 CTATT--AATATATTATATTA-TATACGATATGATACAACATTATATAATATAGTAGGAGGGTTA
* * *
56881470 ACTTTCAAATGTACGAAAAGTATAGAGACTTAGAGTATATTTCAACCAGT
184 ACTTTCAAATGTACGAAAAATATAGAGACTTAGAGCATATTTCAACCAAT
*
56881520 ATAATAATAAACAATAATATAT
1 ATAATAATAAATAATAATATAT
56881542 GTTAATAATT
Statistics
Matches: 234, Mismatches: 20, Indels: 14
0.87 0.07 0.05
Matches are distributed among these distances:
233 27 0.12
234 13 0.06
236 62 0.26
238 3 0.01
242 11 0.05
243 2 0.01
244 116 0.50
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (233 bp):
ATAATAATAAATAATAATATATAATGTACTACCATTATATATAATTATTATATTATAGATTATAA
TAAAAGATATAGTATTATATGATACTATAATGTCTAAACATTGATGCATATATAAACTATTAATA
TATTATATTATATACGATATGATACAACATTATATAATATAGTAGGAGGGTTAACTTTCAAATGT
ACGAAAAATATAGAGACTTAGAGCATATTTCAACCAAT
Found at i:56882989 original size:23 final size:24
Alignment explanation
Indices: 56882937--56882991 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
56882927 TGGTATCGTA
*
56882937 TTAAAATAAAATGAATTATTATCT
1 TTAAAATTAAATGAATTATTATCT
*
56882961 TCAAAATTAAAT-AATTATTA-CT
1 TTAAAATTAAATGAATTATTATCT
56882983 TATAAAATT
1 T-TAAAATT
56882992 TAAAATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.11
23 14 0.52
24 10 0.37
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (24 bp):
TTAAAATTAAATGAATTATTATCT
Found at i:56884196 original size:34 final size:35
Alignment explanation
Indices: 56884152--56884218 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
56884142 CAGTAAAATG
* *
56884152 TTTTCCGTAAAATGATTT-TTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTATTAGAAAATATTTTAC
*
56884186 TTTTCTGTAAAATGATTTATTAGAAAATATTTT
1 TTTTCCGTAAAATGATTTATTAGAAAATATTTT
56884219 CTGAAAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.49
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTATTAGAAAATATTTTAC
Found at i:56884226 original size:13 final size:13
Alignment explanation
Indices: 56884186--56884238 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 13
56884176 AATGTTTTAC
56884186 TTTTCTGTAAAATGA
1 TTTTCTG-AAAAT-A
56884201 TTTAT-TAGAAAATA
1 TTT-TCT-GAAAATA
56884215 TTTTCTGAAAATA
1 TTTTCTGAAAATA
*
56884228 TTTTCCGAAAA
1 TTTTCTGAAAA
56884239 AGTTGTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
13 18 0.53
14 5 0.15
15 9 0.26
16 2 0.06
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (13 bp):
TTTTCTGAAAATA
Found at i:56885189 original size:17 final size:19
Alignment explanation
Indices: 56885148--56885192 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 19
56885138 TGTTGCTACT
56885148 ATTTTGTTGTTATTATATA
1 ATTTTGTTGTTATTATATA
*
56885167 ACTTTTGTT-TTATTGT-TA
1 A-TTTTGTTGTTATTATATA
56885185 ATTTTGTT
1 ATTTTGTT
56885193 ACTATTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 7 0.29
18 3 0.12
19 7 0.29
20 7 0.29
ACGTcount: A:0.20, C:0.02, G:0.11, T:0.67
Consensus pattern (19 bp):
ATTTTGTTGTTATTATATA
Found at i:56885589 original size:41 final size:39
Alignment explanation
Indices: 56885535--56885685 Score: 135
Period size: 41 Copynumber: 4.1 Consensus size: 39
56885525 TTATTTTTTA
*
56885535 TTTTTTAACTTTAAAATACTTTTAAAATACTTTTTTTAAAT
1 TTTTTTAATTTTAAAATACTTTTAAAAT--TTTTTTTAAAT
* *
56885576 TTTTTTAATTTTAAAATATTTTTAAAATTTTTTTAAAAT
1 TTTTTTAATTTTAAAATACTTTTAAAATTTTTTTTAAAT
**
56885615 ACTTTT--TTTTAAAATAC--------TTTTTTTT-AAT
1 TTTTTTAATTTTAAAATACTTTTAAAATTTTTTTTAAAT
* *
56885643 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAAAT
1 TTTTTTAATTTTAAAATACTTTTAAAAT-TTTTTTTAAAT
56885683 TTT
1 TTT
56885686 AAAATAAAAT
Statistics
Matches: 87, Mismatches: 11, Indels: 25
0.71 0.09 0.20
Matches are distributed among these distances:
28 7 0.08
29 7 0.08
30 10 0.11
37 10 0.11
38 1 0.01
39 20 0.23
40 6 0.07
41 26 0.30
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (39 bp):
TTTTTTAATTTTAAAATACTTTTAAAATTTTTTTTAAAT
Found at i:56885623 original size:15 final size:15
Alignment explanation
Indices: 56885603--56885641 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
56885593 ATTTTTAAAA
56885603 TTTTTTTAAAATACT
1 TTTTTTTAAAATACT
56885618 TTTTTTTAAAATACT
1 TTTTTTTAAAATACT
56885633 TTTTTTTAA
1 TTTTTTTAA
56885642 TTTTTTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTTTTAAAATACT
Found at i:56885629 original size:67 final size:68
Alignment explanation
Indices: 56885554--56885681 Score: 231
Period size: 67 Copynumber: 1.9 Consensus size: 68
56885544 TTTAAAATAC
56885554 TTTTAAAATACTTTTTTTAAATTTTTTTAATTTTAAAATATTTTTAAAAT-TTTTTTAAAATACT
1 TTTTAAAATACTTTTTTTAAATTTTTTTAATTTTAAAATATTTTTAAAATATTTTTTAAAATACT
56885618 TTT
66 TTT
*
56885621 TTTTAAAATACTTTTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAAA
1 TTTTAAAATACTTTTTTTAAATTTTTTTAATTTTAAAATATTTTTAAAATA-TTTTTTAAA
56885682 TTTTAAAATA
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
67 49 0.84
69 9 0.16
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (68 bp):
TTTTAAAATACTTTTTTTAAATTTTTTTAATTTTAAAATATTTTTAAAATATTTTTTAAAATACT
TTT
Found at i:56885635 original size:11 final size:11
Alignment explanation
Indices: 56885544--56885568 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
56885534 ATTTTTTAAC
56885544 TTTAAAATACT
1 TTTAAAATACT
56885555 TTTAAAATACT
1 TTTAAAATACT
56885566 TTT
1 TTT
56885569 TTTAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTAAAATACT
Found at i:56885682 original size:12 final size:11
Alignment explanation
Indices: 56885584--56885621 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
56885574 ATTTTTTTAA
56885584 TTTTAAAATAT
1 TTTTAAAATAT
*
56885595 TTTTAAAATTT
1 TTTTAAAATAT
56885606 TTTTAAAATACT
1 TTTTAAAATA-T
56885618 TTTT
1 TTTT
56885622 TTTAAAATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 19 0.79
12 5 0.21
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:56889794 original size:2 final size:2
Alignment explanation
Indices: 56889777--56889818 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
56889767 TTATATCTAC
* * *
56889777 AT AT AC AT AC AT AT AT AT AT AT AT AT GT 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
56889819 TAAGTTTTCT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:56890310 original size:16 final size:15
Alignment explanation
Indices: 56890274--56890323 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
56890264 CCAACTAGCA
*
56890274 AAACCCGAATAGCCC
1 AAACCCGAACAGCCC
56890289 AAACCCGAACAGCCC
1 AAACCCGAACAGCCC
**
56890304 AATACCC-TTCAGCCC
1 AA-ACCCGAACAGCCC
56890319 AAACC
1 AAACC
56890324 AATGCCCAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 3 0.10
15 24 0.77
16 4 0.13
ACGTcount: A:0.38, C:0.44, G:0.10, T:0.08
Consensus pattern (15 bp):
AAACCCGAACAGCCC
Found at i:56894914 original size:11 final size:11
Alignment explanation
Indices: 56894898--56894922 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
56894888 TGACTATGCC
56894898 ATTACAAGCCT
1 ATTACAAGCCT
56894909 ATTACAAGCCT
1 ATTACAAGCCT
56894920 ATT
1 ATT
56894923 TTGCAGGCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (11 bp):
ATTACAAGCCT
Found at i:56898187 original size:18 final size:17
Alignment explanation
Indices: 56898161--56898196 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
56898151 TTTGGTTATA
56898161 TTTAATTTTCGATATGTT
1 TTTAATTTT-GATATGTT
*
56898179 TTTATTTTTGATATGTT
1 TTTAATTTTGATATGTT
56898196 T
1 T
56898197 CATTTAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.19, C:0.03, G:0.11, T:0.67
Consensus pattern (17 bp):
TTTAATTTTGATATGTT
Found at i:56898739 original size:14 final size:14
Alignment explanation
Indices: 56898705--56898737 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
56898695 TAAAAACACA
56898705 TTCTTTTCTTTTCT
1 TTCTTTTCTTTTCT
56898719 TTCTTTT-TTTT-T
1 TTCTTTTCTTTTCT
56898731 TTCTTTT
1 TTCTTTT
56898738 TTGGGTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
13 4 0.21
14 7 0.37
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TTCTTTTCTTTTCT
Found at i:56900779 original size:11 final size:11
Alignment explanation
Indices: 56900709--56900751 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
56900699 CACTAAATTT
56900709 TTTTAAAAA-A
1 TTTTAAAAATA
*
56900719 -TATAAAAAGTA
1 TTTTAAAAA-TA
56900730 TTTTAAAAATA
1 TTTTAAAAATA
56900741 TTTTAAAAATA
1 TTTTAAAAATA
56900752 AAAATAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
9 7 0.25
11 14 0.50
12 7 0.25
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
TTTTAAAAATA
Found at i:56900784 original size:29 final size:27
Alignment explanation
Indices: 56900734--56900790 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 27
56900724 AAAGTATTTT
56900734 AAAAATATTTTAAAAATAAAAATAATAA
1 AAAAATATTTTAAAAATAAAAAT-ATAA
56900762 AAAAATATTTTAAAAATAAAAAATATAA
1 AAAAATATTTTAAAAAT-AAAAATATAA
56900790 A
1 A
56900791 TTCATTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 22 0.79
29 6 0.21
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (27 bp):
AAAAATATTTTAAAAATAAAAATATAA
Found at i:56902624 original size:58 final size:58
Alignment explanation
Indices: 56902523--56902642 Score: 152
Period size: 58 Copynumber: 2.1 Consensus size: 58
56902513 TTTAATTCAT
* *
56902523 ATAATAATTATATTAAGAATTTTATTAAATTATATACTATTTTATTAAATTATATTTA
1 ATAATAATTATATTAAGAATATGATTAAATTATATACTATTTTATTAAATTATATTTA
* * * * * *
56902581 ATAATAATTATTTTAA-AATATGGTTAAATTATTTATTATTTTTATTATATTATTTTTA
1 ATAATAATTATATTAAGAATATGATTAAATTATATACTA-TTTTATTAAATTATATTTA
56902639 ATAA
1 ATAA
56902643 CAATCTTATT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
57 17 0.32
58 36 0.68
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (58 bp):
ATAATAATTATATTAAGAATATGATTAAATTATATACTATTTTATTAAATTATATTTA
Found at i:56902633 original size:14 final size:13
Alignment explanation
Indices: 56902609--56902638 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
56902599 TATGGTTAAA
56902609 TTATTTATTATTT
1 TTATTTATTATTT
56902622 TTATTATATTATTT
1 TTATT-TATTATTT
56902636 TTA
1 TTA
56902639 ATAACAATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTATTTATTATTT
Found at i:56902655 original size:58 final size:57
Alignment explanation
Indices: 56902523--56902657 Score: 146
Period size: 58 Copynumber: 2.3 Consensus size: 57
56902513 TTTAATTCAT
* * **
56902523 ATAATAATTATATTAAGAATTTTATTAAATTATATACTATTTTATTAAATTATATTTA
1 ATAACAATTATATTAA-AATATGGTTAAATTATATACTATTTTATTAAATTATATTTA
* * * * * *
56902581 ATAATAATTATTTTAAAATATGGTTAAATTATTTATTATTTTTATTATATTATTTTTA
1 ATAACAATTATATTAAAATATGGTTAAATTATATACTA-TTTTATTAAATTATATTTA
56902639 ATAACAATCT-TATTAAAAT
1 ATAACAAT-TATATTAAAAT
56902658 TTAATAACAA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
57 17 0.26
58 47 0.72
59 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (57 bp):
ATAACAATTATATTAAAATATGGTTAAATTATATACTATTTTATTAAATTATATTTA
Found at i:56902671 original size:6 final size:6
Alignment explanation
Indices: 56902660--56902688 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
56902650 ATTAAAATTT
56902660 AATAAC AATAAC AATAAC AATAAC AATAA
1 AATAAC AATAAC AATAAC AATAAC AATAA
56902689 TCATCTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.14, G:0.00, T:0.17
Consensus pattern (6 bp):
AATAAC
Found at i:56902871 original size:16 final size:16
Alignment explanation
Indices: 56902852--56902890 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
56902842 GTTTTATTCC
56902852 ATTACAACTCTATCCA
1 ATTACAACTCTATCCA
* * *
56902868 ATTACAGCTCTATTCT
1 ATTACAACTCTATCCA
56902884 ATTACAA
1 ATTACAA
56902891 TGAACCAAAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACAACTCTATCCA
Found at i:56902946 original size:16 final size:16
Alignment explanation
Indices: 56902907--56902950 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
56902897 AAACGTACCC
56902907 TAACTTCTTTAACAG-
1 TAACTTCTTTAACAGT
56902922 ---CTT-TTTAACAGT
1 TAACTTCTTTAACAGT
56902934 TAACTTCTTTAACAGT
1 TAACTTCTTTAACAGT
56902950 T
1 T
56902951 TAGCTTCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 9
0.73 0.00 0.27
Matches are distributed among these distances:
11 8 0.33
12 3 0.12
15 3 0.12
16 10 0.42
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.45
Consensus pattern (16 bp):
TAACTTCTTTAACAGT
Found at i:56907962 original size:15 final size:14
Alignment explanation
Indices: 56907942--56907980 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
56907932 TATTTACTCT
*
56907942 AAAAATCATTTTTTA
1 AAAAAT-ATTTATTA
56907957 AAAAATATTTATTA
1 AAAAATATTTATTA
56907971 AAAAA-ATTTA
1 AAAAATATTTA
56907981 AAATTTATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 5 0.22
14 12 0.52
15 6 0.26
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAAATATTTATTA
Found at i:56926744 original size:15 final size:15
Alignment explanation
Indices: 56926724--56926759 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
56926714 TTTTTTTATC
*
56926724 ATTATTATTATTGCT
1 ATTATTATTATTCCT
*
56926739 ATTATTGTTATTCCT
1 ATTATTATTATTCCT
56926754 ATTATT
1 ATTATT
56926760 TCATGTTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.61
Consensus pattern (15 bp):
ATTATTATTATTCCT
Found at i:56926860 original size:18 final size:18
Alignment explanation
Indices: 56926818--56926864 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
56926808 AAGTCGTATA
56926818 TTATTATTGTATGTTAATG
1 TTATTATT-TATGTTAATG
*
56926837 TT-TTATTTATGTT-TTAG
1 TTATTATTTATGTTAAT-G
56926854 TTATTATTTAT
1 TTATTATTTAT
56926865 AAATTCATGG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 1 0.04
17 9 0.36
18 13 0.52
19 2 0.08
ACGTcount: A:0.23, C:0.00, G:0.11, T:0.66
Consensus pattern (18 bp):
TTATTATTTATGTTAATG
Found at i:56935140 original size:24 final size:24
Alignment explanation
Indices: 56935111--56935159 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
56935101 ATTTGATATA
56935111 AATCATTCATTCCATTCCACACCT
1 AATCATTCATTCCATTCCACACCT
56935135 AATCATTCATTCCATTCCACACCT
1 AATCATTCATTCCATTCCACACCT
56935159 A
1 A
56935160 CCATGTAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.37, G:0.00, T:0.33
Consensus pattern (24 bp):
AATCATTCATTCCATTCCACACCT
Found at i:56935943 original size:22 final size:21
Alignment explanation
Indices: 56935918--56935970 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
56935908 TAGGCACCAG
*
56935918 AGTGCAGAATAATAGGCATAAA
1 AGTGC-GAATAATAGGAATAAA
* *
56935940 AGTGCGAACCAATAGGAATAGA
1 AGTGCGAA-TAATAGGAATAAA
56935962 AGTGCGAAT
1 AGTGCGAAT
56935971 TAGAATACAC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.45, C:0.11, G:0.26, T:0.17
Consensus pattern (21 bp):
AGTGCGAATAATAGGAATAAA
Found at i:56936423 original size:18 final size:19
Alignment explanation
Indices: 56936388--56936427 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
56936378 TAAATTTTAG
*
56936388 TTTTCACAATTTCCTTAAA
1 TTTTCACAATTTCATTAAA
*
56936407 TTTTCAC-ATTTTATTAAA
1 TTTTCACAATTTCATTAAA
56936425 TTT
1 TTT
56936428 AATCCCTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTTCACAATTTCATTAAA
Found at i:56945437 original size:2 final size:2
Alignment explanation
Indices: 56945403--56945428 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
56945393 AAAAAGTAAA
56945403 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
56945429 GTTTATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56945580 original size:18 final size:17
Alignment explanation
Indices: 56945553--56945595 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
56945543 GTTTAAAAAA
56945553 ATAA-AAATAAAA-AGAT
1 ATAATAAATAAAACA-AT
56945569 ATAAATAAATAAAACAAT
1 AT-AATAAATAAAACAAT
56945587 ATAATAAAT
1 ATAATAAAT
56945596 TAAATGTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.08
17 9 0.38
18 12 0.50
19 1 0.04
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (17 bp):
ATAATAAATAAAACAAT
Found at i:56946690 original size:18 final size:18
Alignment explanation
Indices: 56946664--56946699 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
56946654 CTAGGTACGG
56946664 CGCACCTAGGGTTAGGTT
1 CGCACCTAGGGTTAGGTT
*
56946682 CGCATCTAGGGTTAGGTT
1 CGCACCTAGGGTTAGGTT
56946700 TTTTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.31
Consensus pattern (18 bp):
CGCACCTAGGGTTAGGTT
Found at i:56947223 original size:44 final size:43
Alignment explanation
Indices: 56947173--56947649 Score: 302
Period size: 44 Copynumber: 10.6 Consensus size: 43
56947163 ATCTTGAGTG
* *
56947173 TACTCCACTACAACTTTAGGGAGATAAGACTTGTAACTTTAACC
1 TACTCCACTGCAACTTCAGGGAGATAAGA-TTGTAACTTTAACC
* * * *** *
56947217 TACTCCACTGTAACTTCAGGGAGATAAGGTT-T-GCTACGATC
1 TACTCCACTGCAACTTCAGGGAGATAAGATTGTAACTTTAACC
* **
56947258 TACTCTACTGCAACTTCAAAGAGATAAGATTCGTAA-TTTATAGCTTC
1 TACTCCACTGCAACTTCAGGGAGATAAGATT-GTAACTTTA-A-C--C
* * * ** **
56947305 AATCTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTTTCTTTAGTC
1 TA-C---TCCACTGCAACTTCAGGGAGATAAGATT-G-TAACTTTAACC
* *
56947354 TACTCCACTGCAACTTCAGAGAGATAAGACTTGTAACTTCAACC
1 TACTCCACTGCAACTTCAGGGAGATAAGA-TTGTAACTTTAACC
* * * * * **
56947398 TGCTCCACTGCAACTTCAGGGAGATAAGGTT-T-GCTATGATA
1 TACTCCACTGCAACTTCAGGGAGATAAGATTGTAACTTTAACC
* * *
56947439 TACTCTACTGCAACTTTAGAGAGATAAGATCTGTAA-TTTATAGCTTC
1 TACTCCACTGCAACTTCAGGGAGATAAGAT-TGTAACTTTA-A-C--C
* * * * **
56947486 AATCTGTTCCACTGCAATTTCAGGGAAATAAGATTCGCTATA-TTCAGTC
1 TA-C---TCCACTGCAACTTCAGGGAGATAAGATT-G-TA-ACTTTAACC
* *
56947535 TGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACC
1 TACTCCACTGCAACTTCAGGGAGATAAGA-TTGTAACTTTAACC
*
56947579 TACTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACC
1 TACTCCACTGCAACTTCAGGGAGATAAGA-TTGTAACTTTAACC
56947623 TACTCCACTGCAACTTCAGGGAGATAA
1 TACTCCACTGCAACTTCAGGGAGATAA
56947650 TGTTTTCTAT
Statistics
Matches: 330, Mismatches: 73, Indels: 60
0.71 0.16 0.13
Matches are distributed among these distances:
41 58 0.18
42 3 0.01
43 10 0.03
44 136 0.41
45 49 0.15
46 4 0.01
47 3 0.01
48 4 0.01
49 3 0.01
50 1 0.00
51 48 0.15
52 3 0.01
53 8 0.02
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.30
Consensus pattern (43 bp):
TACTCCACTGCAACTTCAGGGAGATAAGATTGTAACTTTAACC
Found at i:56947380 original size:96 final size:93
Alignment explanation
Indices: 56947256--56947649 Score: 352
Period size: 89 Copynumber: 4.3 Consensus size: 93
56947246 TTTGCTACGA
* * *
56947256 TCTACTCTACTGCAACTTCAAAGAGATAAGATTCGTAATTTATAGCTTCAATCTGTTCCACTACA
1 TCTACTCCACTGCAACTTCAGAGAGATAAGA-TCGTAATTTATAGCTTCAATCTGTTCCACTGCA
*
56947321 ACTTCAGGGAAATAAGATTCGCTTTCTTTAG
65 ACTTCAGGGAAATAAGATTCGC-TT-TTCAG
* * *
56947352 TCTACTCCACTGCAACTTCAGAGAGATAAGA-C-T--TGTA-A-CTTCAACCTGCTCCACTGCAA
1 TCTACTCCACTGCAACTTCAGAGAGATAAGATCGTAATTTATAGCTTCAATCTGTTCCACTGCAA
* * * * *
56947411 CTTCAGGGAGATAAGGTTTGC-TATGA-
66 CTTCAGGGAAATAAGATTCGCTTTTCAG
* * *
56947437 TATACTCTACTGCAACTTTAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGTTCCACTGCA
1 TCTACTCCACTGCAACTTCAGAGAGATAAGATC-GTAATTTATAGCTTCAATCTGTTCCACTGCA
*
56947502 ATTTCAGGGAAATAAGATTCGCTATATTCAG
65 ACTTCAGGGAAATAAGATTCGCT-T-TTCAG
* * * * **
56947533 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-C-T--TGTA-A-CTTCAACCTACTCCACTGCAA
1 TCTACTCCACTGCAACTTCAGAGAGATAAGATCGTAATTTATAGCTTCAATCTGTTCCACTGCAA
* * *
56947592 CTTCAGGGAGATAAGACTT-G-TAACTTCAA
66 CTTCAGGGAAATAAGA-TTCGCT--TTTCAG
* *
56947621 CCTACTCCACTGCAACTTCAGGGAGATAA
1 TCTACTCCACTGCAACTTCAGAGAGATAA
56947650 TGTTTTCTAT
Statistics
Matches: 247, Mismatches: 38, Indels: 34
0.77 0.12 0.11
Matches are distributed among these distances:
85 28 0.11
86 3 0.01
87 1 0.00
88 33 0.13
89 70 0.28
90 7 0.03
91 7 0.03
92 36 0.15
93 2 0.01
94 2 0.01
95 3 0.01
96 55 0.22
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (93 bp):
TCTACTCCACTGCAACTTCAGAGAGATAAGATCGTAATTTATAGCTTCAATCTGTTCCACTGCAA
CTTCAGGGAAATAAGATTCGCTTTTCAG
Found at i:56947389 original size:181 final size:181
Alignment explanation
Indices: 56947151--56947606 Score: 718
Period size: 181 Copynumber: 2.5 Consensus size: 181
56947141 GTTTGATATG
* * * * *
56947151 ATAAGATTCG-TTATCTTGAGTGTACTCCACTACAACTTTAGGGAGATAAGACTTGTAACTTTAA
1 ATAAGATTCGCTT-TCTTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAA
* *
56947215 CCTACTCCACTGTAACTTCAGGGAGATAAGGTTTGCTACGATCTACTCTACTGCAACTTCAAAGA
65 CCTACTCCACTGCAACTTCAGGGAGATAAGGTTTGCTACGATATACTCTACTGCAACTTCAAAGA
56947280 GATAAGAT-TCGTAATTTATAGCTTCAATCTGTTCCACTACAACTTCAGGGAA
130 GATAAGATCT-GTAATTTATAGCTTCAATCTGTTCCACTACAACTTCAGGGAA
* *
56947332 ATAAGATTCGCTTTCTTTAGTCTACTCCACTGCAACTTCAGAGAGATAAGACTTGTAACTTCAAC
1 ATAAGATTCGCTTTCTTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAAC
* * * *
56947397 CTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGCTATGATATACTCTACTGCAACTTTAGAGAG
66 CTACTCCACTGCAACTTCAGGGAGATAAGGTTTGCTACGATATACTCTACTGCAACTTCAAAGAG
* *
56947462 ATAAGATCTGTAATTTATAGCTTCAATCTGTTCCACTGCAATTTCAGGGAA
131 ATAAGATCTGTAATTTATAGCTTCAATCTGTTCCACTACAACTTCAGGGAA
* * *
56947513 ATAAGATTCGCTATATTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAAC
1 ATAAGATTCGCTTTCTTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAAC
56947578 CTACTCCACTGCAACTTCAGGGAGATAAG
66 CTACTCCACTGCAACTTCAGGGAGATAAG
56947607 ACTTGTAACT
Statistics
Matches: 253, Mismatches: 20, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
181 250 0.99
182 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (181 bp):
ATAAGATTCGCTTTCTTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAAC
CTACTCCACTGCAACTTCAGGGAGATAAGGTTTGCTACGATATACTCTACTGCAACTTCAAAGAG
ATAAGATCTGTAATTTATAGCTTCAATCTGTTCCACTACAACTTCAGGGAA
Found at i:56947903 original size:274 final size:274
Alignment explanation
Indices: 56947581--56948147 Score: 956
Period size: 274 Copynumber: 2.1 Consensus size: 274
56947571 CTTCAACCTA
* * * *
56947581 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTACTCCACTGCAACTTCAGGGAG
1 CTCCACTGCAACTTCAAGGAGATAAGACTGGTAACTTCAACATACTCCACTACAACTTCAGGGAG
* *
56947646 ATAATGTTTTCTATGATAGATTTAATCTGACCTACTGCAACCTCAGAGGTATAAGATTTCTAGTT
66 ATAATGTTTGCTATGATAGATTTAATCTGACCTACTGCAAACTCAGAGGTATAAGATTTCTAGTT
* *
56947711 TTAATCCGCTCCATTGCAACTTCAGGGAGATAGGATTACTATGATCTGCTCTATTGCAACTTCAG
131 TTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTACTATGATCTGCCCTATTGCAACTTCAG
56947776 AGAGATAAGATCTGTAATTTGTAGCTTTAATCTATTCCAATGTAACTTTAGGGAAATAAGATTCA
196 AGAGATAAGATCTGTAATTTGTAGCTTTAATCTATTCCAATGTAACTTTAGGGAAATAAGATTCA
*
56947841 CTATCTTCAGTCTG
261 CTAACTTCAGTCTG
* *
56947855 CTCCGCTGCAACTTCAAGGAGATAAGTCTGGTAACTTCAACATACTCCACTACAACTTCAGGGAG
1 CTCCACTGCAACTTCAAGGAGATAAGACTGGTAACTTCAACATACTCCACTACAACTTCAGGGAG
*
56947920 ATAATGTTTGCTATGATAGATTTAATCTGACCTACTGCAAACTCAGAGGTATAGGATTTCTAGTT
66 ATAATGTTTGCTATGATAGATTTAATCTGACCTACTGCAAACTCAGAGGTATAAGATTTCTAGTT
56947985 TTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTACTATGATCTGCCCTATTGCAACTTCAG
131 TTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTACTATGATCTGCCCTATTGCAACTTCAG
* * *
56948050 AGAGATAAGATCTGTAATTTGTAGCTTTAATTTGTTCCAATGTAACTTTAGGGAAATAAGATTCG
196 AGAGATAAGATCTGTAATTTGTAGCTTTAATCTATTCCAATGTAACTTTAGGGAAATAAGATTCA
* **
56948115 CTAACTTCAATCCAA
261 CTAACTTCAGT-CTG
56948130 C-CCACTGCAACTTCAAGG
1 CTCCACTGCAACTTCAAGG
56948148 GTATAGGATT
Statistics
Matches: 273, Mismatches: 19, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
274 271 0.99
275 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (274 bp):
CTCCACTGCAACTTCAAGGAGATAAGACTGGTAACTTCAACATACTCCACTACAACTTCAGGGAG
ATAATGTTTGCTATGATAGATTTAATCTGACCTACTGCAAACTCAGAGGTATAAGATTTCTAGTT
TTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTACTATGATCTGCCCTATTGCAACTTCAG
AGAGATAAGATCTGTAATTTGTAGCTTTAATCTATTCCAATGTAACTTTAGGGAAATAAGATTCA
CTAACTTCAGTCTG
Found at i:56949002 original size:11 final size:11
Alignment explanation
Indices: 56948983--56949039 Score: 53
Period size: 11 Copynumber: 4.9 Consensus size: 11
56948973 TGGCCTCTCT
56948983 TTTTATTTTTC
1 TTTTATTTTTC
*
56948994 TTTTCTTTTTTC
1 TTTT-ATTTTTC
56949006 ATTTT-TTCCTTTC
1 -TTTTATT--TTTC
56949019 TTTTATTTTTC
1 TTTTATTTTTC
*
56949030 TTTTCTTTTT
1 TTTTATTTTT
56949040 TTTATGAAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
11 19 0.49
12 10 0.26
13 10 0.26
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTATTTTTC
Found at i:56949013 original size:20 final size:18
Alignment explanation
Indices: 56948982--56949040 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
56948972 TTGGCCTCTC
56948982 TTTTTATTTTTCTTTTCT
1 TTTTTATTTTTCTTTTCT
*
56949000 TTTTTCATTTTTTCCTTTC-
1 TTTTT-A-TTTTTCTTTTCT
56949019 -TTTTATTTTTCTTTTCT
1 TTTTTATTTTTCTTTTCT
56949036 TTTTT
1 TTTTT
56949041 TTATGAAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
16 10 0.29
17 1 0.03
18 13 0.37
19 1 0.03
20 10 0.29
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTTATTTTTCTTTTCT
Found at i:56949029 original size:16 final size:16
Alignment explanation
Indices: 56948983--56949042 Score: 68
Period size: 16 Copynumber: 3.6 Consensus size: 16
56948973 TGGCCTCTCT
56948983 TTTTATTTTTCTTTTC
1 TTTTATTTTTCTTTTC
*
56948999 TTTTTTCATTTTTTCCTTTC
1 --TTTT-A-TTTTTCTTTTC
56949019 TTTTATTTTTCTTTTC
1 TTTTATTTTTCTTTTC
56949035 TTTT-TTTT
1 TTTTATTTT
56949043 ATGAAACATT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
15 4 0.11
16 14 0.37
17 1 0.03
18 8 0.21
19 1 0.03
20 10 0.26
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTATTTTTCTTTTC
Found at i:56949042 original size:20 final size:20
Alignment explanation
Indices: 56948982--56949044 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
56948972 TTGGCCTCTC
56948982 TTTTTATTTTTCTTTTC-TT
1 TTTTTATTTTTCTTTTCTTT
* *
56949001 TTTTCA--TTT-TTTCCTTT
1 TTTTTATTTTTCTTTTCTTT
*
56949018 CTTTTATTTTTCTTTTCTTT
1 TTTTTATTTTTCTTTTCTTT
56949038 TTTTTAT
1 TTTTTAT
56949045 GAAACATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
16 4 0.12
17 9 0.26
19 8 0.24
20 13 0.38
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTTATTTTTCTTTTCTTT
Found at i:56954199 original size:18 final size:17
Alignment explanation
Indices: 56954172--56954214 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
56954162 AGTTTAAAAA
56954172 ATAA-AAATAAAA-AGAT
1 ATAATAAATAAAACA-AT
56954188 ATAAATAAATAAAACAAT
1 AT-AATAAATAAAACAAT
56954206 ATAATAAAT
1 ATAATAAAT
56954215 TAAATGTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.08
17 9 0.38
18 12 0.50
19 1 0.04
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (17 bp):
ATAATAAATAAAACAAT
Found at i:56954392 original size:71 final size:65
Alignment explanation
Indices: 56954243--56954392 Score: 144
Period size: 71 Copynumber: 2.2 Consensus size: 65
56954233 TTAGGTAAAT
56954243 AAATATAAAAAGAAATATAATAGAAATAATAATGTGAAACTAATTAATTAAATAAAATAGTAAGT
1 AAATATAAAAAGAAATATAATAGAAATAATAATGTGAAACTAATTAATTAAATAAAATAGTAAG-
56954308 A
65 A
* * *
56954309 AATAAATAAAAAAGGAAA-ATAATAATGACAATAATAATGTTAAATTAATTAATTTTAATTATAA
1 AA-ATAT-AAAAA-GAAATATAAT-A-GA-AATAATAATGTGAAACTAATTAA--TTAA--ATAA
56954373 AATAG-AA-A
56 AATAGTAAGA
56954381 AAATGATAAAAA
1 AAAT-ATAAAAA
56954393 AAGACTAAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
66 2 0.03
67 3 0.04
68 10 0.14
69 5 0.07
70 2 0.03
71 27 0.39
72 5 0.07
73 4 0.06
74 2 0.03
75 9 0.13
ACGTcount: A:0.63, C:0.01, G:0.08, T:0.28
Consensus pattern (65 bp):
AAATATAAAAAGAAATATAATAGAAATAATAATGTGAAACTAATTAATTAAATAAAATAGTAAGA
Found at i:56954485 original size:13 final size:13
Alignment explanation
Indices: 56954467--56954491 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56954457 GAAGTTATAT
56954467 GTGTGAAAATTTC
1 GTGTGAAAATTTC
56954480 GTGTGAAAATTT
1 GTGTGAAAATTT
56954492 GATAGTTTGA
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:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:56955226 original size:2 final size:2
Alignment explanation
Indices: 56955221--56955246 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
56955211 CGCAGAATCC
56955221 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
56955247 GATTTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56956184 original size:57 final size:59
Alignment explanation
Indices: 56956096--56956238 Score: 202
Period size: 57 Copynumber: 2.4 Consensus size: 59
56956086 AATTCGGATT
* * *
56956096 ACCCGTCCGGACTAAATCAATTTTCCACATATTCTTCGGGAGGGCTATATCA-AT-ATC
1 ACCCGTCCGGGCTAGATCATTTTTCCACATATTCTTCGGGAGGGCTATATCAGATGATC
56956153 ACCCGTCCGGGCTAGATC-TTTTTCACACATATTCTTCGGGAGGGCTATATCAGGATAGGATC
1 ACCCGTCCGGGCTAGATCATTTTTC-CACATATTCTTCGGGAGGGCTATATCA-GAT--GATC
56956215 ACCCGTCCGGGCTAGATCATTTTT
1 ACCCGTCCGGGCTAGATCATTTTT
56956239 ACTGTCAATT
Statistics
Matches: 76, Mismatches: 3, Indels: 8
0.87 0.03 0.09
Matches are distributed among these distances:
56 5 0.07
57 43 0.57
59 2 0.03
62 21 0.28
63 5 0.07
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (59 bp):
ACCCGTCCGGGCTAGATCATTTTTCCACATATTCTTCGGGAGGGCTATATCAGATGATC
Found at i:56961971 original size:13 final size:13
Alignment explanation
Indices: 56961953--56961977 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56961943 TAAGTTATAT
56961953 GTGTGAAAATTTC
1 GTGTGAAAATTTC
56961966 GTGTGAAAATTT
1 GTGTGAAAATTT
56961978 GATAGTTTGA
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:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:56963408 original size:41 final size:41
Alignment explanation
Indices: 56963351--56963457 Score: 162
Period size: 41 Copynumber: 2.6 Consensus size: 41
56963341 ATAATTGGTT
* *
56963351 TTCAGGCTTAATGTCTAGCAGGCTTGATGCCGGTGAATTAC
1 TTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAATTAC
* *
56963392 TTCAGACTTTATGTCTAGCAAGCTTGATGCCGGTGAATTAT
1 TTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAATTAC
56963433 TTCAGAC-TTATTGTCTAGCAGGCTT
1 TTCAGACTTTA-TGTCTAGCAGGCTT
56963458 CGTGCTGGTG
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 3 0.05
41 57 0.95
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (41 bp):
TTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAATTAC
Found at i:56964963 original size:32 final size:32
Alignment explanation
Indices: 56964922--56964985 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
56964912 TTTGAGTGCC
*
56964922 AATATAAGTAAAAATTTTAAAATAAAAATCAT
1 AATATAAGTAAAAAATTTAAAATAAAAATCAT
56964954 AATATAAGTAAAAAATTTAAAATAAAAATCAT
1 AATATAAGTAAAAAATTTAAAATAAAAATCAT
56964986 TTGTTTCATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (32 bp):
AATATAAGTAAAAAATTTAAAATAAAAATCAT
Found at i:56970335 original size:21 final size:22
Alignment explanation
Indices: 56970300--56970341 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
56970290 ATTCATAAAA
* *
56970300 TTAAGTCAATTCAAACTAATTT
1 TTAAGTCAATACAAACAAATTT
56970322 TTAA-TCAATACAAACAAATT
1 TTAAGTCAATACAAACAAATT
56970342 AATTCAAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (22 bp):
TTAAGTCAATACAAACAAATTT
Found at i:56976310 original size:2 final size:2
Alignment explanation
Indices: 56976303--56976332 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
56976293 GTCTATGTGA
56976303 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
56976333 TCGGAGTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56988795 original size:105 final size:101
Alignment explanation
Indices: 56988615--56988863 Score: 258
Period size: 105 Copynumber: 2.4 Consensus size: 101
56988605 AATTGACGGA
* *
56988615 TAAGACCATGGTTGGACCATGGCAATGTTTAAATGTAAGATCATAACTAGGCAATGGCATTTTAA
1 TAAGACCATGGTTGGACCATGGCAATGTATAAATGTAAGACCATAACTAGGCAATGGCATTTTAA
56988680 TGAAAAGACCATAACTGGGTTATGGCACCTTAAACT
66 TGAAAAGACCATAACTGGGTTATGGCACCTTAAACT
* * * *
56988716 TAAGACCATGGTTGGACCATGGCAGTATAG-ATACATGTGTAAGACCATAGCTGGGCTATGGCAT
1 TAAGACCATGGTTGGACCATGGCA--AT-GTATA-A-ATGTAAGACCATAACTAGGCAATGGCAT
* * * * *
56988780 TTTGATTATAAGACCATAACTGGGTTATGGTA-C-TACAAAT
61 TTTAATGAAAAGACCATAACTGGGTTATGGCACCTTA-AACT
** *
56988820 GTAAGACCATGGCAGGGA-CATGGCAATGCAT--ATGTAAGACCATA
1 -TAAGACCATGG-TTGGACCATGGCAATGTATAAATGTAAGACCATA
56988864 GTTGGACTAT
Statistics
Matches: 125, Mismatches: 14, Indels: 20
0.79 0.09 0.13
Matches are distributed among these distances:
99 12 0.10
101 24 0.19
102 1 0.01
103 10 0.08
104 6 0.05
105 69 0.55
106 3 0.02
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGGCAATGTATAAATGTAAGACCATAACTAGGCAATGGCATTTTAA
TGAAAAGACCATAACTGGGTTATGGCACCTTAAACT
Found at i:57001817 original size:9 final size:9
Alignment explanation
Indices: 57001803--57001836 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
57001793 CTAATCTTAC
57001803 AGGAAAATG
1 AGGAAAATG
57001812 AGGAAAATG
1 AGGAAAATG
57001821 AGGAAAATG
1 AGGAAAATG
57001830 AGGAAAA
1 AGGAAAA
57001837 CAAGTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.32, T:0.09
Consensus pattern (9 bp):
AGGAAAATG
Found at i:57009642 original size:14 final size:14
Alignment explanation
Indices: 57009620--57009651 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
57009610 CATGCAATGC
*
57009620 ACACTTCTTATTTT
1 ACACATCTTATTTT
57009634 ACACATCTTATTTT
1 ACACATCTTATTTT
57009648 ACAC
1 ACAC
57009652 TCGTACACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
ACACATCTTATTTT
Found at i:57015919 original size:2 final size:2
Alignment explanation
Indices: 57015912--57015936 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
57015902 AATTAGGATT
57015912 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
57015937 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:57016575 original size:9 final size:9
Alignment explanation
Indices: 57016561--57016616 Score: 55
Period size: 9 Copynumber: 6.2 Consensus size: 9
57016551 AAATTATAAT
57016561 AAAATATTA
1 AAAATATTA
57016570 AAAATATTA
1 AAAATATTA
*
57016579 AAAAT-GTA
1 AAAATATTA
57016587 AAATATATTTA
1 AAA-ATA-TTA
57016598 AAAAT-TGTA
1 AAAATAT-TA
57016607 AAAA-ATTA
1 AAAATATTA
57016615 AA
1 AA
57016617 TGTTGTTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
8 10 0.25
9 23 0.57
10 2 0.05
11 5 0.12
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (9 bp):
AAAATATTA
Found at i:57016606 original size:20 final size:19
Alignment explanation
Indices: 57016568--57016686 Score: 86
Period size: 20 Copynumber: 6.2 Consensus size: 19
57016558 AATAAAATAT
57016568 TAAAAATA-TTAAAAA-TG
1 TAAAAATATTTAAAAATTG
57016585 TAAAATATATTTAAAAATTG
1 TAAAA-ATATTTAAAAATTG
**
57016605 TAAAAA-A-TTAAATGTTG
1 TAAAAATATTTAAAAATTG
* *
57016622 TTAAAAATATTTCAAAATTC
1 -TAAAAATATTTAAAAATTG
**
57016642 TAAAAA-AGTTGTTAAAAATAA
1 TAAAAATA--T-TTAAAAATTG
*
57016663 TAAAAATTTATTAAAAATTG
1 TAAAAATAT-TTAAAAATTG
57016683 TAAA
1 TAAA
57016687 TAATTAACAA
Statistics
Matches: 79, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
17 13 0.16
18 11 0.14
19 15 0.19
20 27 0.34
21 13 0.16
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (19 bp):
TAAAAATATTTAAAAATTG
Found at i:57016691 original size:21 final size:20
Alignment explanation
Indices: 57016653--57016691 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
57016643 AAAAAAGTTG
*
57016653 TTAAAAATAATAAAAATTTA
1 TTAAAAATTATAAAAATTTA
*
57016673 TTAAAAATTGTAAATAATT
1 TTAAAAATTATAAA-AATT
57016692 AACAAATCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
TTAAAAATTATAAAAATTTA
Found at i:57016706 original size:3 final size:3
Alignment explanation
Indices: 57016698--57016727 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
57016688 AATTAACAAA
*
57016698 TCT TCT TCT TCT TCT CCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
57016728 ATGTTGTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:57016903 original size:19 final size:20
Alignment explanation
Indices: 57016875--57017063 Score: 94
Period size: 21 Copynumber: 9.6 Consensus size: 20
57016865 CCATCAATTC
*
57016875 ACAATTTTTTAATCATTATTT
1 ACAA-TTTTTAATAATTATTT
57016896 ACAATTTTTTAATAATTATTT
1 ACAA-TTTTTAATAATTATTT
* *
57016917 GC-ATTTTTAAT-ATT-TTCC
1 ACAATTTTTAATAATTATT-T
*
57016935 CCAATTTTTAATAATT-TTT
1 ACAATTTTTAATAATTATTT
* *
57016954 ACAAATTTTAGATAAGGT-TTT
1 ACAATTTTTA-ATAA-TTATTT
* *
57016975 ATAATTTTTAATAACTTTTTTT
1 ACAATTTTTAATAA--TTATTT
** *
57016997 ACAA-CATTAA-AATATTTTT
1 ACAATTTTTAATAAT-TATTT
*
57017016 AACAATATTTAATAATTA-TT
1 -ACAATTTTTAATAATTATTT
**
57017036 ACAATAATTAAT--TT-TTT
1 ACAATTTTTAATAATTATTT
57017053 ACAATTTTTAA
1 ACAATTTTTAA
57017064 ATGTTTTTTT
Statistics
Matches: 135, Mismatches: 21, Indels: 28
0.73 0.11 0.15
Matches are distributed among these distances:
17 15 0.11
18 5 0.04
19 41 0.30
20 22 0.16
21 43 0.32
22 9 0.07
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (20 bp):
ACAATTTTTAATAATTATTT
Found at i:57016950 original size:10 final size:10
Alignment explanation
Indices: 57016937--57016994 Score: 50
Period size: 10 Copynumber: 5.7 Consensus size: 10
57016927 TATTTTCCCC
57016937 AATTTTTAAT
1 AATTTTTAAT
57016947 AATTTTTACA-
1 AATTTTTA-AT
57016957 AA-TTTTAGAT
1 AATTTTTA-AT
*
57016967 AAGGTTTT-AT
1 AA-TTTTTAAT
57016977 AATTTTTAAT
1 AATTTTTAAT
57016987 AACTTTTT
1 AA-TTTTT
57016995 TTACAACATT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
9 10 0.25
10 20 0.50
11 6 0.15
12 4 0.10
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.55
Consensus pattern (10 bp):
AATTTTTAAT
Found at i:57017089 original size:18 final size:18
Alignment explanation
Indices: 57016991--57017159 Score: 65
Period size: 19 Copynumber: 8.9 Consensus size: 18
57016981 TTTAATAACT
** *
57016991 TTTTTTACAACATTAAAA
1 TTTTTTACAATTTTTAAA
*
57017009 TATTTTTAACAATATTTAATA
1 T-TTTTT-ACAATTTTTAA-A
* * **
57017030 ATTATTACAATAATT-AA
1 TTTTTTACAATTTTTAAA
57017047 TTTTTTACAATTTTTAAA
1 TTTTTTACAATTTTTAAA
57017065 TGTTTTTTTA-AATTTTTAACA
1 ---TTTTTTACAATTTTTAA-A
* *
57017086 TTTTTTA-ATAATTTAAATA
1 TTTTTTACA-ATTTTTAA-A
* *
57017105 TTTTTTACAATTTATATA
1 TTTTTTACAATTTTTAAA
* * *
57017123 TATATTACGATTTTTAATA
1 TTTTTTACAATTTTTAA-A
*
57017142 TTCTTTTATAAATTTTTA
1 TT-TTTTA-CAATTTTTA
57017160 CAATATTTTG
Statistics
Matches: 113, Mismatches: 25, Indels: 23
0.70 0.16 0.14
Matches are distributed among these distances:
17 12 0.11
18 25 0.22
19 33 0.29
20 27 0.24
21 16 0.14
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.56
Consensus pattern (18 bp):
TTTTTTACAATTTTTAAA
Found at i:57017125 original size:20 final size:19
Alignment explanation
Indices: 57016991--57017149 Score: 78
Period size: 18 Copynumber: 8.4 Consensus size: 19
57016981 TTTAATAACT
* *
57016991 TTTTTTACAACATTAAAATA
1 TTTTTTACAA-TTTATAATA
*
57017011 TTTTTAACAATATT-TAATA
1 TTTTTTACAAT-TTATAATA
* * * *
57017030 ATTATTACAA-TAATTA-A
1 TTTTTTACAATTTATAATA
* *
57017047 TTTTTTACAATTTTTAAATGT
1 TTTTTTACAATTTAT-AAT-A
* *
57017068 TTTTTTA-AATTTTTAACA
1 TTTTTTACAATTTATAATA
*
57017086 TTTTTTAATAATTTA-AATA
1 TTTTTT-ACAATTTATAATA
57017105 TTTTTTACAATTTAT-ATA
1 TTTTTTACAATTTATAATA
* * * *
57017123 TATATTACGATTTTTAATA
1 TTTTTTACAATTTATAATA
57017142 TTCTTTTA
1 TT-TTTTA
57017150 TAAATTTTTA
Statistics
Matches: 103, Mismatches: 25, Indels: 22
0.69 0.17 0.15
Matches are distributed among these distances:
17 10 0.10
18 31 0.30
19 28 0.27
20 27 0.26
21 7 0.07
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.55
Consensus pattern (19 bp):
TTTTTTACAATTTATAATA
Found at i:57018654 original size:17 final size:17
Alignment explanation
Indices: 57018620--57018654 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
57018610 TAAAAAAATT
*
57018620 ATAAAAACTATTTAAAA
1 ATAAAAACTATTAAAAA
*
57018637 ATAAAAATTATTAAAAA
1 ATAAAAACTATTAAAAA
57018654 A
1 A
57018655 GTATAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAAACTATTAAAAA
Found at i:57019517 original size:5 final size:5
Alignment explanation
Indices: 57019507--57019532 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
57019497 ATGCACTTGC
57019507 AGGTG AGGTG AGGTG AGGTG AGGTG A
1 AGGTG AGGTG AGGTG AGGTG AGGTG A
57019533 CCATATAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.58, T:0.19
Consensus pattern (5 bp):
AGGTG
Found at i:57021408 original size:26 final size:26
Alignment explanation
Indices: 57021379--57021431 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
57021369 GACACTTAAT
* *
57021379 ATCTCTTAAAGAGTAGACAAAAAAAC
1 ATCTCATAAAGAATAGACAAAAAAAC
* **
57021405 ATCTGATGGAGAATAGACAAAAAAAC
1 ATCTCATAAAGAATAGACAAAAAAAC
57021431 A
1 A
57021432 CATATGTCAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.55, C:0.13, G:0.15, T:0.17
Consensus pattern (26 bp):
ATCTCATAAAGAATAGACAAAAAAAC
Found at i:57023147 original size:42 final size:42
Alignment explanation
Indices: 57023088--57023173 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
57023078 CCCTGTAGGA
57023088 CTCCCAAAGTTCCATCTGCATAAAACTTCGGAGTATCAAAAC
1 CTCCCAAAGTTCCATCTGCATAAAACTTCGGAGTATCAAAAC
57023130 CTCCCAAAGTTCCATCTGCATAAAACTTCGGAGTATCAAAAC
1 CTCCCAAAGTTCCATCTGCATAAAACTTCGGAGTATCAAAAC
57023172 CT
1 CT
57023174 TTCTTTTTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.24
Consensus pattern (42 bp):
CTCCCAAAGTTCCATCTGCATAAAACTTCGGAGTATCAAAAC
Found at i:57033585 original size:20 final size:19
Alignment explanation
Indices: 57033547--57033585 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
57033537 GGTGAACACC
*
57033547 AGAACACTCGATACAAAGA
1 AGAACACCCGATACAAAGA
*
57033566 AGAACACCCAGATTCAAAGA
1 AGAACACCC-GATACAAAGA
57033586 TGCCCAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.51, C:0.23, G:0.15, T:0.10
Consensus pattern (19 bp):
AGAACACCCGATACAAAGA
Found at i:57041964 original size:14 final size:14
Alignment explanation
Indices: 57041945--57041972 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
57041935 GGCTTGAGAA
57041945 CTTAAATGGAAATT
1 CTTAAATGGAAATT
57041959 CTTAAATGGAAATT
1 CTTAAATGGAAATT
57041973 AACCAAAGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (14 bp):
CTTAAATGGAAATT
Found at i:57045394 original size:23 final size:20
Alignment explanation
Indices: 57045377--57045417 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
57045367 GTAGAAATTA
*
57045377 TTATTCTCAGAAAATAGAAT
1 TTATTCTAAGAAAATAGAAT
57045397 TTATTCTAAGAAAATA-AAT
1 TTATTCTAAGAAAATAGAAT
57045416 TT
1 TT
57045418 CCTCTACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (20 bp):
TTATTCTAAGAAAATAGAAT
Found at i:57045423 original size:19 final size:20
Alignment explanation
Indices: 57045385--57045423 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
57045375 TATTATTCTC
*
57045385 AGAAAATAGAATTTATTCTA
1 AGAAAATAGAATTTACTCTA
*
57045405 AGAAAATA-AATTTCCTCTA
1 AGAAAATAGAATTTACTCTA
57045424 CTTTCTGGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (20 bp):
AGAAAATAGAATTTACTCTA
Found at i:57045682 original size:11 final size:11
Alignment explanation
Indices: 57045668--57045708 Score: 82
Period size: 11 Copynumber: 3.7 Consensus size: 11
57045658 ATTTTAAAAA
57045668 TAAAATTATTT
1 TAAAATTATTT
57045679 TAAAATTATTT
1 TAAAATTATTT
57045690 TAAAATTATTT
1 TAAAATTATTT
57045701 TAAAATTA
1 TAAAATTA
57045709 AAAATAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
TAAAATTATTT
Found at i:57046474 original size:4 final size:4
Alignment explanation
Indices: 57046467--57046505 Score: 51
Period size: 4 Copynumber: 9.2 Consensus size: 4
57046457 CAAAATAAAT
*
57046467 ATTA ATTA ATTA ATTA ATTTA GTTA ATTAA ATTA ATTA A
1 ATTA ATTA ATTA ATTA A-TTA ATTA ATT-A ATTA ATTA A
57046506 ACTAATTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 24 0.77
5 7 0.23
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (4 bp):
ATTA
Found at i:57046501 original size:9 final size:9
Alignment explanation
Indices: 57046470--57046512 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
57046460 AATAAATATT
57046470 AATTAATT-
1 AATTAATTA
*
57046478 AATTAATTT
1 AATTAATTA
*
57046487 AGTTAATTA
1 AATTAATTA
57046496 AATTAATTA
1 AATTAATTA
*
57046505 AACTAATT
1 AATTAATT
57046513 TTCTAATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
8 8 0.27
9 22 0.73
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (9 bp):
AATTAATTA
Found at i:57046505 original size:13 final size:13
Alignment explanation
Indices: 57046470--57046505 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
57046460 AATAAATATT
57046470 AATTAATTAATTA
1 AATTAATTAATTA
* *
57046483 ATTTAGTTAATTA
1 AATTAATTAATTA
57046496 AATTAATTAA
1 AATTAATTAA
57046506 ACTAATTTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
AATTAATTAATTA
Found at i:57046529 original size:16 final size:17
Alignment explanation
Indices: 57046499--57046532 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
57046489 TTAATTAAAT
57046499 TAATTAAACTAATTTTC
1 TAATTAAACTAATTTTC
57046516 TAATTAAA-TAATTTTC
1 TAATTAAACTAATTTTC
57046532 T
1 T
57046533 TAACTCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATTAAACTAATTTTC
Found at i:57049243 original size:31 final size:31
Alignment explanation
Indices: 57049208--57049821 Score: 357
Period size: 31 Copynumber: 19.7 Consensus size: 31
57049198 AATATTGCCG
* *
57049208 AATTAATTCGTATATAATTATACATTGCTGA
1 AATTAATTTGTATATGATTATACATTGCTGA
* * *
57049239 AATTAATTTGTATATGGTTATACATTGGTTA
1 AATTAATTTGTATATGATTATACATTGCTGA
*
57049270 AATTGAA-TTGTATATGGATATATATGGTTGTACATTGCTAA
1 AATT-AATTTGTATAT-G--AT-TA------TACATTGCTGA
* ** *
57049311 AATTTATTTGTATATGAAGATA-AGTTGCCG-
1 AATTAATTTGTATATGATTATACA-TTGCTGA
* * *
57049341 AATTAATTCGTATATGAATATACTTTGCTGA
1 AATTAATTTGTATATGATTATACATTGCTGA
* *
57049372 AATTAATTTGTATATGGTTATACATTGTTGA
1 AATTAATTTGTATATGATTATACATTGCTGA
57049403 AATTGAA-TTGTATATGGA-TATA-AGTTGCTG-
1 AATT-AATTTGTATAT-GATTATACA-TTGCTGA
** * * *
57049433 AATTAATTCATATATGGTTGTACATTGCTAA
1 AATTAATTTGTATATGATTATACATTGCTGA
* * * *
57049464 AATTTATTTGTATTTGGTTATACATT-ATCGA
1 AATTAATTTGTATATGATTATACATTGCT-GA
* ** *
57049495 AATTGATTTGTATATGAAGATA-AGTTGCCG-
1 AATTAATTTGTATATGATTATACA-TTGCTGA
* * * *
57049525 AATTAATTCGTATATGGTTGTACATTGCTAA
1 AATTAATTTGTATATGATTATACATTGCTGA
* * * *
57049556 AATTTATTTGTATCTGGTTATACATT-ATCGA
1 AATTAATTTGTATATGATTATACATTGCT-GA
* ** *
57049587 AATTGATTTGTATATGAAGATA-AGTTGCCG-
1 AATTAATTTGTATATGATTATACA-TTGCTGA
* *
57049617 AATTAATTCGTATATAATTATACATTGCTGA
1 AATTAATTTGTATATGATTATACATTGCTGA
* *
57049648 AATTAATTTGTATATGGTTATACATT-TTGA
1 AATTAATTTGTATATGATTATACATTGCTGA
* *
57049678 AATTAAATTGTATATGGA-TATA-AGTTGCCG-
1 AATTAATTTGTATAT-GATTATACA-TTGCTGA
* *
57049708 AATTAATTCGTATATGATTATACATTGC-CA
1 AATTAATTTGTATATGATTATACATTGCTGA
* ** * **
57049738 AACTTGATTCATATATGGTTATACATT-CCCA
1 AA-TTAATTTGTATATGATTATACATTGCTGA
* * *
57049769 AATTGATTTGTATATGATTATACATTACCGA
1 AATTAATTTGTATATGATTATACATTGCTGA
* * *
57049800 ATTTGATTTGTATATGAATATA
1 AATTAATTTGTATATGATTATA
57049822 TATATTGTTG
Statistics
Matches: 451, Mismatches: 91, Indels: 82
0.72 0.15 0.13
Matches are distributed among these distances:
29 6 0.01
30 158 0.35
31 253 0.56
32 6 0.01
34 1 0.00
35 2 0.00
37 1 0.00
38 1 0.00
40 2 0.00
41 21 0.05
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (31 bp):
AATTAATTTGTATATGATTATACATTGCTGA
Found at i:57049304 original size:41 final size:41
Alignment explanation
Indices: 57049249--57049326 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
57049239 AATTAATTTG
* *
57049249 TATATGGTTATACATTGGTTAAATTGAATTGTATATGGATA
1 TATATGGTTATACATTGCTAAAATTGAATTGTATATGGATA
* * *
57049290 TATATGGTTGTACATTGCTAAAATTTATTTGTATATG
1 TATATGGTTATACATTGCTAAAATTGAATTGTATATG
57049327 AAGATAAGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.32, C:0.04, G:0.18, T:0.46
Consensus pattern (41 bp):
TATATGGTTATACATTGCTAAAATTGAATTGTATATGGATA
Found at i:57049375 original size:61 final size:61
Alignment explanation
Indices: 57049290--57049821 Score: 269
Period size: 61 Copynumber: 8.7 Consensus size: 61
57049280 TATATGGATA
* * * * *
57049290 TATATGGTTGTACATTGCTAAAATTTATTTGTATATGAAGATA-AGTTGCCGAATTAATTCG
1 TATATGGTTATACTTTGCTGAAATTAATTTGTATATGAATATACA-TTGCCGAATTAATTCG
** ** **
57049351 TATATGAATATACTTTGCTGAAATTAATTTGTATATGGTTATACATTGTTGAAATTGAATT-G
1 TATATGGTTATACTTTGCTGAAATTAATTTGTATATGAATATACATTGCCG-AATT-AATTCG
* ** ** ** * ** * *
57049413 TATATGGATATAAGTTGCTG-AATTAATTCATATATGGTTGTACATTGCTAAAATTTATTTG
1 TATATGGTTATACTTTGCTGAAATTAATTTGTATATGAATATACATTGC-CGAATTAATTCG
* * *
57049474 TATTTGGTTATACATTAT-C-GAAATTGATTTGTATATGAAGATA-AGTTGCCGAATTAATTCG
1 TATATGGTTATAC-TT-TGCTGAAATTAATTTGTATATGAATATACA-TTGCCGAATTAATTCG
* * * * * ** ** * *
57049535 TATATGGTTGTACATTGCTAAAATTTATTTGTATCTGGTTATACATTATCGAAATTGATTTG
1 TATATGGTTATACTTTGCTGAAATTAATTTGTATATGAATATACATTGCCG-AATTAATTCG
*** ** * * * *
57049597 TATATGAAGATAAGTTGCCG-AATTAATTCGTATAT-AATTATACATTGCTGAAATTAATTTG
1 TATATGGTTATACTTTGCTGAAATTAATTTGTATATGAA-TATACATTGCCG-AATTAATTCG
* *
57049658 TATATGGTTATACATTT--TGAAATTAAATTGTATATGGATATA-AGTTGCCGAATTAATTCG
1 TATATGGTTATAC-TTTGCTGAAATTAATTTGTATATGAATATACA-TTGCCGAATTAATTCG
* * * * ** ** * * * *
57049718 TATATGATTATACATTGC-CAAACTTGATTCATATATGGTTATACATTCCCAAATTGATTTG
1 TATATGGTTATACTTTGCTGAAA-TTAATTTGTATATGAATATACATTGCCGAATTAATTCG
* * * * * *
57049779 TATATGATTATACATTACCGAATTTGATTTGTATATGAATATA
1 TATATGGTTATACTTTGCTGAAATTAATTTGTATATGAATATA
57049822 TATATTGTTG
Statistics
Matches: 352, Mismatches: 96, Indels: 46
0.71 0.19 0.09
Matches are distributed among these distances:
59 3 0.01
60 31 0.09
61 242 0.69
62 71 0.20
63 5 0.01
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.43
Consensus pattern (61 bp):
TATATGGTTATACTTTGCTGAAATTAATTTGTATATGAATATACATTGCCGAATTAATTCG
Found at i:57049447 original size:92 final size:92
Alignment explanation
Indices: 57049290--57049785 Score: 636
Period size: 92 Copynumber: 5.4 Consensus size: 92
57049280 TATATGGATA
* ** * *
57049290 TATATGGTTGTACATTGCTAAAATTTATTTGTATATGAAGATAAGTTGCCGAATTAATTCGTATA
1 TATATGGTTATACATTATTGAAATTGATTTGTATATGAAGATAAGTTGCCGAATTAATTCGTATA
* * *
57049355 TGAATATACTTTGCTGAAATTAATTTG
66 TGATTATACATTGCTAAAATTAATTTG
* * * * * *
57049382 TATATGGTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCTGAATTAATTCATATA
1 TATATGGTTATACATTATTGAAATTGATTTGTATATGAAGATAAGTTGCCGAATTAATTCGTATA
* * *
57049447 TGGTTGTACATTGCTAAAATTTATTTG
66 TGATTATACATTGCTAAAATTAATTTG
* *
57049474 TATTTGGTTATACATTATCGAAATTGATTTGTATATGAAGATAAGTTGCCGAATTAATTCGTATA
1 TATATGGTTATACATTATTGAAATTGATTTGTATATGAAGATAAGTTGCCGAATTAATTCGTATA
* * *
57049539 TGGTTGTACATTGCTAAAATTTATTTG
66 TGATTATACATTGCTAAAATTAATTTG
* *
57049566 TATCTGGTTATACATTATCGAAATTGATTTGTATATGAAGATAAGTTGCCGAATTAATTCGTATA
1 TATATGGTTATACATTATTGAAATTGATTTGTATATGAAGATAAGTTGCCGAATTAATTCGTATA
* *
57049631 TAATTATACATTGCTGAAATTAATTTG
66 TGATTATACATTGCTAAAATTAATTTG
* * * *
57049658 TATATGGTTATACATT-TTGAAATTAAATTGTATATGGATATAAGTTGCCGAATTAATTCGTATA
1 TATATGGTTATACATTATTGAAATTGATTTGTATATGAAGATAAGTTGCCGAATTAATTCGTATA
* * * **
57049722 TGATTATACATTGCCAAACTTGATTCA
66 TGATTATACATTGCTAAAATTAATTTG
***
57049749 TATATGGTTATACATT-CCCAAATTGATTTGTATATGA
1 TATATGGTTATACATTATTGAAATTGATTTGTATATGA
57049786 TTATACATTA
Statistics
Matches: 356, Mismatches: 48, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
91 94 0.26
92 262 0.74
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (92 bp):
TATATGGTTATACATTATTGAAATTGATTTGTATATGAAGATAAGTTGCCGAATTAATTCGTATA
TGATTATACATTGCTAAAATTAATTTG
Found at i:57052721 original size:25 final size:24
Alignment explanation
Indices: 57052693--57052740 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
57052683 ATCTAGGCAA
57052693 TATAACGGGAAGCTCACAAAGAGCC
1 TATAACGGGAAGCTC-CAAAGAGCC
* *
57052718 TATAATGGGTAGCTCCAAAGAGC
1 TATAACGGGAAGCTCCAAAGAGC
57052741 AATTAACGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.17
Consensus pattern (24 bp):
TATAACGGGAAGCTCCAAAGAGCC
Found at i:57052751 original size:24 final size:25
Alignment explanation
Indices: 57052689--57052778 Score: 96
Period size: 24 Copynumber: 3.7 Consensus size: 25
57052679 GCTTATCTAG
*
57052689 GCAATATAACGGGAAGCTCACAAAGA
1 GCAATATAACGGGTAGCTC-CAAAGA
* *
57052715 GC-CTATAATGGGTAGCTCCAAAGA
1 GCAATATAACGGGTAGCTCCAAAGA
* *
57052739 GCAAT-TAACGGGTAGTTCCGAAGA
1 GCAATATAACGGGTAGCTCCAAAGA
*
57052763 GCAAT-TAAAGGGTAGC
1 GCAATATAACGGGTAGC
57052779 ACCGGGTAGC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
24 38 0.70
25 14 0.26
26 2 0.04
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.18
Consensus pattern (25 bp):
GCAATATAACGGGTAGCTCCAAAGA
Found at i:57052874 original size:26 final size:25
Alignment explanation
Indices: 57052818--57052875 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
57052808 GTGAACACTG
* *
57052818 ACGGGAAGCTCACAAAGAGCCTTTA
1 ACGGGAAACTCACAAAGAGCCTATA
* *
57052843 ATCGGGAAATTCACGAAGAGCCATATA
1 A-CGGGAAACTCACAAAGAGCC-TATA
57052870 ACGGGA
1 ACGGGA
57052876 CGCTCATAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 1 0.04
26 22 0.81
27 4 0.15
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.16
Consensus pattern (25 bp):
ACGGGAAACTCACAAAGAGCCTATA
Found at i:57059147 original size:33 final size:33
Alignment explanation
Indices: 57059110--57059176 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
57059100 CTAAATTGAA
57059110 AATAGTGTAAAATTTGTTAAATTGTGATTAAAT
1 AATAGTGTAAAATTTGTTAAATTGTGATTAAAT
*
57059143 AATAGTGTAAATTTTGTTAAATTGTGATTAAAT
1 AATAGTGTAAAATTTGTTAAATTGTGATTAAAT
57059176 A
1 A
57059177 GCTTAAGTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.43
Consensus pattern (33 bp):
AATAGTGTAAAATTTGTTAAATTGTGATTAAAT
Found at i:57060211 original size:36 final size:36
Alignment explanation
Indices: 57060170--57060278 Score: 209
Period size: 36 Copynumber: 3.0 Consensus size: 36
57060160 GGTAGCTTTA
57060170 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
*
57060206 GCTACACTTATCTGATCAAGTGACAAAGTGATAATT
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
57060242 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
57060278 G
1 G
57060279 GTAGCCTAGC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 71 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
Found at i:57062180 original size:57 final size:57
Alignment explanation
Indices: 57062115--57062242 Score: 150
Period size: 57 Copynumber: 2.2 Consensus size: 57
57062105 AAAAACATAA
** * * * * *
57062115 ATTCATTTCCAGGTCATTTTCATTT-TTCTTTTTCTTTTTCTTTTTGGAGAAAACCAC
1 ATTCATTTCCAAATCA-TTTCATTTCTCCATTTTCATTTTCATTTAGGAGAAAACCAC
* *
57062172 ATTCATTTCCAAATGATTTCATTTCTCCATTTTCATTTTCATTTAGGAGAAAACCAT
1 ATTCATTTCCAAATCATTTCATTTCTCCATTTTCATTTTCATTTAGGAGAAAACCAC
*
57062229 AATCATTTCCAAAT
1 ATTCATTTCCAAAT
57062243 GTTTCTCATA
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
56 8 0.13
57 52 0.87
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.47
Consensus pattern (57 bp):
ATTCATTTCCAAATCATTTCATTTCTCCATTTTCATTTTCATTTAGGAGAAAACCAC
Found at i:57070800 original size:13 final size:13
Alignment explanation
Indices: 57070782--57070823 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
57070772 AGATTTTTCT
57070782 TAAATATTATCAC
1 TAAATATTATCAC
*
57070795 TAAATA--AT-TC
1 TAAATATTATCAC
57070805 TAAATATTATCAC
1 TAAATATTATCAC
57070818 TAAATA
1 TAAATA
57070824 ATTCAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 7 0.29
11 2 0.08
12 2 0.08
13 13 0.54
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAATATTATCAC
Found at i:57070809 original size:23 final size:23
Alignment explanation
Indices: 57070782--57070832 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
57070772 AGATTTTTCT
57070782 TAAATATTATCACTAAATAATTC
1 TAAATATTATCACTAAATAATTC
57070805 TAAATATTATCACTAAATAATTC
1 TAAATATTATCACTAAATAATTC
*
57070828 AAAAT
1 TAAAT
57070833 TTAAAAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (23 bp):
TAAATATTATCACTAAATAATTC
Found at i:57071058 original size:35 final size:35
Alignment explanation
Indices: 57071019--57071085 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
57071009 TTCATTCCTG
57071019 ATAAGAAAAATCCAAATTTAATAGCATTTTATCTT
1 ATAAGAAAAATCCAAATTTAATAGCATTTTATCTT
*
57071054 ATAAGAAAAATCTAAATTTAATAGCATTTTAT
1 ATAAGAAAAATCCAAATTTAATAGCATTTTAT
57071086 TTGATAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.37
Consensus pattern (35 bp):
ATAAGAAAAATCCAAATTTAATAGCATTTTATCTT
Found at i:57074056 original size:50 final size:51
Alignment explanation
Indices: 57073958--57074090 Score: 160
Period size: 50 Copynumber: 2.6 Consensus size: 51
57073948 CCATGACAGC
* * * *
57073958 GGTATATGGCGTAAGACCATAGATGAAAGAGGTTATGCCAGTCTGGTATAA
1 GGTATATGGCATAAAACCATAGACGAAAGAGGTTATGACAGTCTGGTATAA
* * *
57074009 GGTATATGGCATAAAACTATAGACGAACGA-GTTATGACTGTCTGGTATAA
1 GGTATATGGCATAAAACCATAGACGAAAGAGGTTATGACAGTCTGGTATAA
* * * *
57074059 GGTATATGGCGTAAGATCATAGATGAAAGAGG
1 GGTATATGGCATAAAACCATAGACGAAAGAGG
57074091 CTATTTGTAA
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
50 42 0.62
51 26 0.38
ACGTcount: A:0.35, C:0.11, G:0.29, T:0.26
Consensus pattern (51 bp):
GGTATATGGCATAAAACCATAGACGAAAGAGGTTATGACAGTCTGGTATAA
Found at i:57074520 original size:17 final size:17
Alignment explanation
Indices: 57074499--57074535 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
57074489 AAAATGAAAC
*
57074499 AAAAAGAAAAAGAAATA
1 AAAAAGAAAAAGAAAGA
*
57074516 AAAAAGAAGAAGAAAGA
1 AAAAAGAAAAAGAAAGA
57074533 AAA
1 AAA
57074536 TGGAGAAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (17 bp):
AAAAAGAAAAAGAAAGA
Found at i:57080509 original size:23 final size:23
Alignment explanation
Indices: 57080466--57080509 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
57080456 ACACATAAAG
* *
57080466 GAACAAAAAGCATGCAGTGAAAA
1 GAACAAAAAACAAGCAGTGAAAA
57080489 GAACAAAAAACACAGCA-TGAA
1 GAACAAAAAACA-AGCAGTGAA
57080510 GGCCTAGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.59, C:0.16, G:0.18, T:0.07
Consensus pattern (23 bp):
GAACAAAAAACAAGCAGTGAAAA
Found at i:57088345 original size:96 final size:96
Alignment explanation
Indices: 57088181--57088526 Score: 451
Period size: 96 Copynumber: 3.6 Consensus size: 96
57088171 TTGGAGTCTG
* * * * * * **
57088181 GGGCTAACTCTAGTATTTGGTGTCTTTCTTGAATCGGGTACATTCTGTATCTTCTCAATGTTTGA
1 GGGCTAACTCTAGTATTTGATGTCTTTCTTGAGTCAGTTGCATCCCATATCTTCTCAATGTTTGA
* *
57088246 GTTATCACCATTTGGTAGAGTTTGAAACCTT
66 GTTATCACCATTTGGTAGATTTTGGAACCTT
* * * *
57088277 GGGCTAACTCTAGTATTTAACGTCTTTCTTGAGTCAGTTGGATCCCATGTCTTCTCAATGTTTGA
1 GGGCTAACTCTAGTATTTGATGTCTTTCTTGAGTCAGTTGCATCCCATATCTTCTCAATGTTTGA
* *
57088342 GTTATCAACATTTGGTACATTTTGGAACCTT
66 GTTATCACCATTTGGTAGATTTTGGAACCTT
* ** * * *
57088373 GGGCTAACTCTAGTATTTGATGTCTTTATTGAGAGAGTTGCATCCCTTAAT-TTCTCAGTGTTGG
1 GGGCTAACTCTAGTATTTGATGTCTTTCTTGAGTCAGTTGCATCCCAT-ATCTTCTCAATGTTTG
*
57088437 AGTTATCACCATTAGGTAGATTTTGGAACCTT
65 AGTTATCACCATTTGGTAGATTTTGGAACCTT
* *
57088469 GGGCTAACTCTAGTATTTGATGTCTTTCTTGGGTCGGTTGCATCCCATATCTTCTCAA
1 GGGCTAACTCTAGTATTTGATGTCTTTCTTGAGTCAGTTGCATCCCATATCTTCTCAA
57088527 ATTTTGGTAG
Statistics
Matches: 212, Mismatches: 36, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
95 2 0.01
96 209 0.99
97 1 0.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (96 bp):
GGGCTAACTCTAGTATTTGATGTCTTTCTTGAGTCAGTTGCATCCCATATCTTCTCAATGTTTGA
GTTATCACCATTTGGTAGATTTTGGAACCTT
Found at i:57088590 original size:81 final size:80
Alignment explanation
Indices: 57088451--57088606 Score: 251
Period size: 81 Copynumber: 1.9 Consensus size: 80
57088441 ATCACCATTA
57088451 GGTAGATTTTGGAACCTTGGGCTAACTCTAGTATTTGATGTCTTTCTTGGGTCGGTTGCATCCCA
1 GGTAGATTTTGGAACCTTGGGCTAACTCTAGTATTTGATGTCTTTCTTGGG-CGGTTGCATCCCA
57088516 TATCTTCTCAAATTTT
65 TATCTTCTCAAATTTT
*
57088532 GGTAGATTTTGGAACCTTGGGCTAACTCTAGTATTTGATGTCTTTGTTGAGG-GAGTTGCATCCC
1 GGTAGATTTTGGAACCTTGGGCTAACTCTAGTATTTGATGTCTTTCTTG-GGCG-GTTGCATCCC
* *
57088596 TTTTCTTCTCA
64 ATATCTTCTCA
57088607 TTGTTGGAGT
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
80 1 0.01
81 67 0.96
82 2 0.03
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (80 bp):
GGTAGATTTTGGAACCTTGGGCTAACTCTAGTATTTGATGTCTTTCTTGGGCGGTTGCATCCCAT
ATCTTCTCAAATTTT
Found at i:57088648 original size:177 final size:177
Alignment explanation
Indices: 57088352--57088931 Score: 950
Period size: 177 Copynumber: 3.3 Consensus size: 177
57088342 GTTATCAACA
* *
57088352 TTTGGTACATTTTGGAACCTTGGGCTAACTCTAGTATTTGATGTCTTTATTGAGAGAGTTGCATC
1 TTTGGTAGATTTTGGAACCTTGGGCTAACTCTAGTATTTGATGTCTTTGTTGAGAGAGTTGCATC
* * * *
57088417 CCTTAAT-TTCTCAGTGTTGGAGTTATCACCATTAGGTAGATTTTGGAACCTTGGGCTAACTCTA
66 CCTT-TTCTTCTCATTGTTGGAGTTACCACCATTAGGTAGATTTTGAAACCTTGGGCTAACTCTA
*
57088481 GTATTTGATGTCTTTCTTGGGTCGGTTGCATCCCATATCTTCTCAAAT
130 GTATTTGATGTCTTTCTTGAGTCGGTTGCATCCCATATCTTCTCAAAT
*
57088529 TTTGGTAGATTTTGGAACCTTGGGCTAACTCTAGTATTTGATGTCTTTGTTGAGGGAGTTGCATC
1 TTTGGTAGATTTTGGAACCTTGGGCTAACTCTAGTATTTGATGTCTTTGTTGAGAGAGTTGCATC
57088594 CCTTTTCTTCTCATTGTTGGAGTTACCACCATTAGGTAGATTTTGAAACCTTGGGCTAACTCTAG
66 CCTTTTCTTCTCATTGTTGGAGTTACCACCATTAGGTAGATTTTGAAACCTTGGGCTAACTCTAG
*
57088659 TATTTGATGT-TGTTCTTGAGTCGGTTGCACCCCATATCTTCTC-AAT
131 TATTTGATGTCT-TTCTTGAGTCGGTTGCATCCCATATCTTCTCAAAT
*
57088705 ATTTGGTAGATTTTGGAACCTTGGGCTAGCTCTAGTATTTGATGTCTTTGTTGAGAGAGTTGCAT
1 -TTTGGTAGATTTTGGAACCTTGGGCTAACTCTAGTATTTGATGTCTTTGTTGAGAGAGTTGCAT
57088770 CCCTTTTCTTCTCATTGTTGGAGTTACCACCATTAGGTAGATTTTGAAACCTTGGGCTAACTCTA
65 CCCTTTTCTTCTCATTGTTGGAGTTACCACCATTAGGTAGATTTTGAAACCTTGGGCTAACTCTA
* * * ** *
57088835 GTATTTGATTTCTTTCTTGTGTCAGTTGCATCCCGCATCTTCACAAAT
130 GTATTTGATGTCTTTCTTGAGTCGGTTGCATCCCATATCTTCTCAAAT
* *
57088883 TTTGGTAGATTTTGGAACCTCGGGCTAACTCTAGTATTTGATATCTTTG
1 TTTGGTAGATTTTGGAACCTTGGGCTAACTCTAGTATTTGATGTCTTTG
57088932 CCGAGTCAGT
Statistics
Matches: 377, Mismatches: 21, Indels: 10
0.92 0.05 0.02
Matches are distributed among these distances:
176 5 0.01
177 368 0.98
178 4 0.01
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (177 bp):
TTTGGTAGATTTTGGAACCTTGGGCTAACTCTAGTATTTGATGTCTTTGTTGAGAGAGTTGCATC
CCTTTTCTTCTCATTGTTGGAGTTACCACCATTAGGTAGATTTTGAAACCTTGGGCTAACTCTAG
TATTTGATGTCTTTCTTGAGTCGGTTGCATCCCATATCTTCTCAAAT
Found at i:57088767 original size:81 final size:81
Alignment explanation
Indices: 57088628--57088783 Score: 217
Period size: 81 Copynumber: 1.9 Consensus size: 81
57088618 ACCACCATTA
*
57088628 GGTAGATTTTGAAACCTTGGGCTAACTCTAGTATTTGATGTTGTTCTTGAGTCGGTTGCACCCCA
1 GGTAGATTTTGAAACCTTGGGCTAACTCTAGTATTTGATGTTGTTCTTGAGTAGGTTGCACCCCA
57088693 TATCTTCTCAATATTT
66 TATCTTCTCAATATTT
* * * *
57088709 GGTAGATTTTGGAACCTTGGGCTAGCTCTAGTATTTGATGTCT-TTGTTGAG-AGAGTTGCATCC
1 GGTAGATTTTGAAACCTTGGGCTAACTCTAGTATTTGATGT-TGTTCTTGAGTAG-GTTGCACCC
* *
57088772 CTTTTCTTCTCA
64 CATATCTTCTCA
57088784 TTGTTGGAGT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
80 1 0.02
81 64 0.97
82 1 0.02
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (81 bp):
GGTAGATTTTGAAACCTTGGGCTAACTCTAGTATTTGATGTTGTTCTTGAGTAGGTTGCACCCCA
TATCTTCTCAATATTT
Found at i:57088940 original size:81 final size:82
Alignment explanation
Indices: 57088805--57088966 Score: 220
Period size: 81 Copynumber: 2.0 Consensus size: 82
57088795 ACCACCATTA
* * * *
57088805 GGTAGATTTTGAAACCTTGGGCTAACTCTAGTATTTGATTTCTTTCTTGTGTCAGTTGCATCCCG
1 GGTAGATTTTGAAACCTCGGGCTAACTCTAGTATTTGATATCTTTCTCGAGTCAGTTGCATCCCG
*
57088870 CATCTTCACAA-ATTTT
66 CATCATCACAATATTTT
* * *
57088886 GGTAGATTTTGGAACCTCGGGCTAACTCTAGTATTTGATATCTTTGC-CGAGTCAGTTTCATTCC
1 GGTAGATTTTGAAACCTCGGGCTAACTCTAGTATTTGATATCTTT-CTCGAGTCAGTTGCATCCC
*
57088950 GTATCATCACAATATTT
65 GCATCATCACAATATTT
57088967 GAGTTAGGGC
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
81 65 0.93
82 5 0.07
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (82 bp):
GGTAGATTTTGAAACCTCGGGCTAACTCTAGTATTTGATATCTTTCTCGAGTCAGTTGCATCCCG
CATCATCACAATATTTT
Found at i:57089017 original size:69 final size:69
Alignment explanation
Indices: 57088904--57089040 Score: 186
Period size: 69 Copynumber: 2.0 Consensus size: 69
57088894 TTGGAACCTC
**
57088904 GGGCTAACTCTAGTATTTGATATCTTTGCCGAGTCAGTTTCATTCCGTATCATCACAATATTTGA
1 GGGCTAACTCTAGTATTTGATATCTTTGCCGAGTCAGTCGCATTCCGTATCATCACAATATTTGA
57088969 GTTA
66 GTTA
* * * * * *
57088973 GGGCTAGCTCTAGTATTTGATTTCTTT-CCTGAGTCAGTCGCATTCCTTATCTTCTCAATGTTTG
1 GGGCTAACTCTAGTATTTGATATCTTTGCC-GAGTCAGTCGCATTCCGTATCATCACAATATTTG
57089037 AGTT
65 AGTT
57089041 CCCAACATTT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
68 2 0.03
69 57 0.97
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (69 bp):
GGGCTAACTCTAGTATTTGATATCTTTGCCGAGTCAGTCGCATTCCGTATCATCACAATATTTGA
GTTA
Found at i:57089112 original size:96 final size:96
Alignment explanation
Indices: 57088973--57089175 Score: 255
Period size: 96 Copynumber: 2.1 Consensus size: 96
57088963 ATTTGAGTTA
* * * *
57088973 GGGCTAGCTCTAGTATTTGATTTCTTTCCTGAGTCAGTCGCATTCCTTATCTTCTCAATGTTTGA
1 GGGCTAACTCTAGTATTTAATTTCTTTCCTGAGTCAGTCGCATTCCATATCTTCTCAATGTTCGA
*
57089038 GTTCCCAACATTTAGTAGATTTTGAAACCTT
66 GTTACCAACATTTAGTAGATTTTGAAACCTT
* * * * *
57089069 GGGCTACCTCTAGTATTTAATGTT-TTTCTTGATTTAGTTGCATTCCATATCTTCTCAATGTTCG
1 GGGCTAACTCTAGTATTTAAT-TTCTTTCCTGAGTCAGTCGCATTCCATATCTTCTCAATGTTCG
* * * *
57089133 AGTTACTACCGTTTGGTAGATTTTGAAACCTT
65 AGTTACCAACATTTAGTAGATTTTGAAACCTT
*
57089165 GGACTAACTCT
1 GGGCTAACTCT
57089176 TCGCTGTATT
Statistics
Matches: 91, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
96 89 0.98
97 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.42
Consensus pattern (96 bp):
GGGCTAACTCTAGTATTTAATTTCTTTCCTGAGTCAGTCGCATTCCATATCTTCTCAATGTTCGA
GTTACCAACATTTAGTAGATTTTGAAACCTT
Found at i:57093632 original size:56 final size:56
Alignment explanation
Indices: 57093543--57093667 Score: 189
Period size: 56 Copynumber: 2.2 Consensus size: 56
57093533 TATGTAAAAC
* **
57093543 TATGTAAAATTATTAAGCCCAATAACTTCTGTTAATGGTTAGTAA-ATTTATCAAAT
1 TATGTAAAATTATTAAGCCCAAAAAAGTCTGTTAATGGTTAGTAAGA-TTATCAAAT
*
57093599 TATGTAAAATTATTAAGCCCAAAAAAGTGTGTTAATGGTTAGTAAGATTATCAAAT
1 TATGTAAAATTATTAAGCCCAAAAAAGTCTGTTAATGGTTAGTAAGATTATCAAAT
*
57093655 TAGGTAAAATTAT
1 TATGTAAAATTAT
57093668 GTTATGGTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
56 62 0.98
57 1 0.02
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.37
Consensus pattern (56 bp):
TATGTAAAATTATTAAGCCCAAAAAAGTCTGTTAATGGTTAGTAAGATTATCAAAT
Found at i:57096420 original size:11 final size:11
Alignment explanation
Indices: 57096400--57096449 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
57096390 GCCATTGATG
*
57096400 AAAATATAAAA
1 AAAATTTAAAA
57096411 AAAATTTAAAA
1 AAAATTTAAAA
**
57096422 TTAATTT-AAA
1 AAAATTTAAAA
*
57096432 AAAATATAAAA
1 AAAATTTAAAA
57096443 AAAATTT
1 AAAATTT
57096450 GAAATTATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
10 7 0.23
11 24 0.77
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AAAATTTAAAA
Found at i:57096448 original size:21 final size:21
Alignment explanation
Indices: 57096408--57096449 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
57096398 TGAAAATATA
* **
57096408 AAAAAAATTTAAAATTAATTT
1 AAAAAAATATAAAAAAAATTT
57096429 AAAAAAATATAAAAAAAATTT
1 AAAAAAATATAAAAAAAATTT
57096450 GAAATTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAAAAATATAAAAAAAATTT
Found at i:57096460 original size:31 final size:32
Alignment explanation
Indices: 57096400--57096467 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
57096390 GCCATTGATG
57096400 AAAATATAAAAAAAATTTAAAATTAATTTAAA
1 AAAATATAAAAAAAATTTAAAATTAATTTAAA
*
57096432 AAAATATAAAAAAAATTTGAAATT-ATTTAAA
1 AAAATATAAAAAAAATTTAAAATTAATTTAAA
57096463 AAAAT
1 AAAAT
57096468 GAAATTGAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 12 0.34
32 23 0.66
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (32 bp):
AAAATATAAAAAAAATTTAAAATTAATTTAAA
Found at i:57096526 original size:22 final size:21
Alignment explanation
Indices: 57096501--57096551 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 21
57096491 TAATATGGAT
*
57096501 TTGAGAGATTTTTGGAATGAAA
1 TTGAGAGA-TTTTGGAAGGAAA
57096523 TTGAGAGGATTTTGGAAGGAAA
1 TTGAGA-GATTTTGGAAGGAAA
57096545 TTGAGAG
1 TTGAGAG
57096552 TTTAAGAGAA
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:0.35, C:0.00, G:0.33, T:0.31
Consensus pattern (21 bp):
TTGAGAGATTTTGGAAGGAAA
Found at i:57096568 original size:52 final size:52
Alignment explanation
Indices: 57096504--57096602 Score: 180
Period size: 52 Copynumber: 1.9 Consensus size: 52
57096494 TATGGATTTG
* *
57096504 AGAGATTTTTGGAATGAAATTGAGAGGATTTTGGAAGGAAATTGAGAGTTTA
1 AGAGAATTTTGGAAGGAAATTGAGAGGATTTTGGAAGGAAATTGAGAGTTTA
57096556 AGAGAATTTTGGAAGGAAATTGAGAGGATTTTGGAAGGAAATTGAGA
1 AGAGAATTTTGGAAGGAAATTGAGAGGATTTTGGAAGGAAATTGAGA
57096603 TAGGATTTGT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.29
Consensus pattern (52 bp):
AGAGAATTTTGGAAGGAAATTGAGAGGATTTTGGAAGGAAATTGAGAGTTTA
Found at i:57096586 original size:22 final size:22
Alignment explanation
Indices: 57096556--57096602 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
57096546 TGAGAGTTTA
57096556 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
*
57096578 AGAGGATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
57096600 AGA
1 AGA
57096603 TAGGATTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.34, T:0.26
Consensus pattern (22 bp):
AGAGAATTTTGGAAGGAAATTG
Found at i:57096778 original size:40 final size:40
Alignment explanation
Indices: 57096734--57096828 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 40
57096724 TCCACGTCAA
**
57096734 GGACGCGATTTCCTTCCACGT-CAG-CAGGTCGCGCTGACGT
1 GGACGCGATTTCCTGACACGTCCAGACA--TCGCGCTGACGT
* *
57096774 GGACGCGATGTCCTGACACGTACCCTGACATCGCGCTGACGT
1 GGACGCGATTTCCTGACACGT--CCAGACATCGCGCTGACGT
57096816 GGACGCGATTTCC
1 GGACGCGATTTCC
57096829 CGAAAAATGG
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
40 18 0.39
42 24 0.52
43 2 0.04
44 2 0.04
ACGTcount: A:0.17, C:0.33, G:0.29, T:0.21
Consensus pattern (40 bp):
GGACGCGATTTCCTGACACGTCCAGACATCGCGCTGACGT
Found at i:57108990 original size:41 final size:41
Alignment explanation
Indices: 57108890--57108990 Score: 105
Period size: 41 Copynumber: 2.5 Consensus size: 41
57108880 TTAGTGGCAC
** * * *
57108890 TAGCGGCGTTTTTTG-AAAAATGCCGCTATAGATCGAGCTT
1 TAGCGGCACTTTTTGAAAAAACGCCGCTATAGATCGACCAT
* * ** *
57108930 TAGCAGCTCTTTTAAAAAAAACGCCGCTATAGGTCGACCAT
1 TAGCGGCACTTTTTGAAAAAACGCCGCTATAGATCGACCAT
57108971 TAGCGGCACTTTTTGAAAAA
1 TAGCGGCACTTTTTGAAAAA
57108991 TGCCGCAAAA
Statistics
Matches: 47, Mismatches: 13, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
40 10 0.21
41 37 0.79
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (41 bp):
TAGCGGCACTTTTTGAAAAAACGCCGCTATAGATCGACCAT
Found at i:57109001 original size:156 final size:156
Alignment explanation
Indices: 57108797--57109089 Score: 460
Period size: 156 Copynumber: 1.9 Consensus size: 156
57108787 TAGGGGCGTT
**
57108797 CCGCCATAGGTCGACCATTAGCGGTGCTTTTTAAAAAATGCCGCAAAAAAATTAAGCACAACACC
1 CCGCCATAGGTCGACCATTAGCGGCACTTTTTAAAAAATGCCGCAAAAAAATTAAGCACAACACC
* ** * * *
57108862 GTTGTTTTATGTTGAGCTTTAGTGGCACTAGCGGCGTTTTTTGAAAAATGCCGCTATAGATCGAG
66 ATCATTTTATGTTGAGCTTTAGTGGCACTAACGGCGCTTTTTGAAAAACGCCGCTATAGATCGAG
57108927 CTTTAGCAGCTCTTTTAAAAAAAACG
131 CTTTAGCAGCTCTTTTAAAAAAAACG
* * * *
57108953 CCGCTATAGGTCGACCATTAGCGGCACTTTTTGAAAAATGCCGCAAAAAAATTAATCACAACGCC
1 CCGCCATAGGTCGACCATTAGCGGCACTTTTTAAAAAATGCCGCAAAAAAATTAAGCACAACACC
* *
57109018 ATCATTTTATGTTGAGCTTTAGTGGCATTAACGGCGCTTTTTGAAAAACGTCGCTATAGATCGAG
66 ATCATTTTATGTTGAGCTTTAGTGGCACTAACGGCGCTTTTTGAAAAACGCCGCTATAGATCGAG
57109083 CTTTAGC
131 CTTTAGC
57109090 GGTGCTTTAT
Statistics
Matches: 123, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
156 123 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.29
Consensus pattern (156 bp):
CCGCCATAGGTCGACCATTAGCGGCACTTTTTAAAAAATGCCGCAAAAAAATTAAGCACAACACC
ATCATTTTATGTTGAGCTTTAGTGGCACTAACGGCGCTTTTTGAAAAACGCCGCTATAGATCGAG
CTTTAGCAGCTCTTTTAAAAAAAACG
Found at i:57113125 original size:26 final size:25
Alignment explanation
Indices: 57113091--57113249 Score: 72
Period size: 26 Copynumber: 6.5 Consensus size: 25
57113081 TATATTTTTA
57113091 TTAAATTATATTTAATAATAATTATT
1 TTAAATTATATTT-ATAATAATTATT
*
57113117 TTAAATTATATTT-T-AT-AGTATT
1 TTAAATTATATTTATAATAATTATT
* * *
57113139 ATATATTATGATTT-TAGTAAATTCA-T
1 TTAAATTAT-ATTTATAAT-AATT-ATT
* * **
57113165 ATAAGA--ATATTTAATATTAAGAATT
1 TTAA-ATTATATTT-ATAATAATTATT
*
57113190 TT--ATTA-AATTAT-ATATATT-TT
1 TTAAATTATATTTATAATA-ATTATT
*
57113211 TTAAATTATATTTAATAATAATTATG
1 TTAAATTATATTT-ATAATAATTATT
57113237 TTAAATTATATTT
1 TTAAATTATATTT
57113250 TATAGTATTA
Statistics
Matches: 99, Mismatches: 16, Indels: 36
0.66 0.11 0.24
Matches are distributed among these distances:
21 6 0.06
22 16 0.16
23 14 0.14
24 11 0.11
25 11 0.11
26 39 0.39
27 2 0.02
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.53
Consensus pattern (25 bp):
TTAAATTATATTTATAATAATTATT
Found at i:57113203 original size:120 final size:121
Alignment explanation
Indices: 57113072--57113361 Score: 512
Period size: 120 Copynumber: 2.4 Consensus size: 121
57113062 CAAACTTTAG
*
57113072 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTA
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATATTAAATTATATTTTATAGTA
* *
57113137 TTATATATTATGATTTTAGTAAATTCATA-TAAGAATATTTAATATTAAGAATTTT
66 TTATATATTATGATTTTAGTAAATTAATATTAAGAATATCTAATATTAAGAATTTT
*
57113192 ATTAAATTATATATATTTT-TTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGT
1 ATTAAATTATATAT-TTTTATTAAATTATATTTAATAATAATTATATTAAATTATATTTTATAGT
*
57113256 ATTATATATTATGATTTTAGTAATTTAATATTAAGAATATCTAATATTAAGAATTTT
65 ATTATATATTATGATTTTAGTAAATTAATATTAAGAATATCTAATATTAAGAATTTT
57113313 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATATTAA
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATATTAA
57113362 GATATGATTA
Statistics
Matches: 162, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
120 90 0.56
121 72 0.44
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (121 bp):
ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATATTAAATTATATTTTATAGTA
TTATATATTATGATTTTAGTAAATTAATATTAAGAATATCTAATATTAAGAATTTT
Found at i:57113286 original size:22 final size:21
Alignment explanation
Indices: 57113237--57113288 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
57113227 AATAATTATG
*
57113237 TTAA-ATTATATTTTATAGTA
1 TTAATATTATATTTTATAATA
57113257 TTATATATTATGATTTTAGTAAT-
1 TTA-ATATTAT-ATTTTA-TAATA
57113280 TTAATATTA
1 TTAATATTA
57113289 AGAATATCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.11
21 1 0.04
22 11 0.41
23 9 0.33
24 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (21 bp):
TTAATATTATATTTTATAATA
Found at i:57117675 original size:14 final size:13
Alignment explanation
Indices: 57117653--57117694 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
57117643 AAGTGTTTTC
*
57117653 TTTCTTCAAGTGTT
1 TTTCATCAAGT-TT
57117667 TTTCATCAAGTTCT
1 TTTCATCAAGTT-T
57117681 TTT-ATCAAGTTT
1 TTTCATCAAGTTT
57117693 TT
1 TT
57117695 AATTACCAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 3 0.12
13 9 0.35
14 14 0.54
ACGTcount: A:0.19, C:0.14, G:0.10, T:0.57
Consensus pattern (13 bp):
TTTCATCAAGTTT
Found at i:57117746 original size:23 final size:22
Alignment explanation
Indices: 57117719--57117788 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 22
57117709 TTTTATTATT
57117719 AAGTTTTGCATAAAGTTCTTTTA
1 AAGTTTTGCATAAAG-TCTTTTA
* *
57117742 AAGTTTTTCATCAAGTCTTTTCATA
1 AAGTTTTGCATAAAGTC-TTT--TA
* *
57117767 AAGTTTTCCATCAAGT-TTTTA
1 AAGTTTTGCATAAAGTCTTTTA
57117788 A
1 A
57117789 TCATTAAGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
21 3 0.07
22 2 0.05
23 19 0.46
25 17 0.41
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.47
Consensus pattern (22 bp):
AAGTTTTGCATAAAGTCTTTTA
Found at i:57117771 original size:25 final size:26
Alignment explanation
Indices: 57117740--57117803 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 26
57117730 AAAGTTCTTT
57117740 TAAAGTTTTTCATCAAGTCTTT-TCA
1 TAAAGTTTTTCATCAAGTCTTTATCA
* *
57117765 TAAAGTTTTCCATCAAGTTTTTAATCA
1 TAAAGTTTTTCATCAAGTCTTT-ATCA
*
57117792 TTAAGTTTTTCA
1 TAAAGTTTTTCA
57117804 ATTAAGCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 20 0.61
27 13 0.39
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.48
Consensus pattern (26 bp):
TAAAGTTTTTCATCAAGTCTTTATCA
Found at i:57117809 original size:13 final size:12
Alignment explanation
Indices: 57117742--57117791 Score: 64
Period size: 12 Copynumber: 4.1 Consensus size: 12
57117732 AGTTCTTTTA
57117742 AAGTTTTTCATC
1 AAGTTTTTCATC
*
57117754 AAGTCTTTTCATA
1 AAGT-TTTTCATC
*
57117767 AAGTTTTCCATC
1 AAGTTTTTCATC
*
57117779 AAGTTTTTAATC
1 AAGTTTTTCATC
57117791 A
1 A
57117792 TTAAGTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
12 21 0.66
13 11 0.34
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (12 bp):
AAGTTTTTCATC
Found at i:57119396 original size:23 final size:23
Alignment explanation
Indices: 57119365--57119410 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
57119355 CGAGGTGGGC
57119365 TTCGCGCACCCTATAACCATACA
1 TTCGCGCACCCTATAACCATACA
* * *
57119388 TTCGGGCACCCTATTACTATACA
1 TTCGCGCACCCTATAACCATACA
57119411 GCAGTTACGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.28, C:0.35, G:0.11, T:0.26
Consensus pattern (23 bp):
TTCGCGCACCCTATAACCATACA
Found at i:57121689 original size:2 final size:2
Alignment explanation
Indices: 57121682--57121708 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
57121672 ACATGTACAA
57121682 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
57121709 CATAAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57122864 original size:114 final size:114
Alignment explanation
Indices: 57122678--57123156 Score: 696
Period size: 114 Copynumber: 4.2 Consensus size: 114
57122668 GTTTCCCAAA
* * * * *
57122678 AAGCGCCGCTAATGTTTA-GGCTTTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAAACCTAAGCC
1 AAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCC
* *
57122742 CAACGACGCCGTTTTCTGAGCTTTAGGGGATTTAGTGGCGTTTTTAAAT
66 CAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTAAGT
* *
57122791 ATGCGCCGCTAATGCTCAGGGCTTTAGCGGAGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCC
1 AAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCC
*
57122856 CAACGACGCCGTTTTGTGAGCTTTCGGGGATTTAGT-GCGTTTTTAAGT
66 CAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTAAGT
* * * *
57122904 -AGCGCCGCTAATGCTCAAGGCTTTATCGGCGGTTTTGGGAAGGCGCCGC-AAAATACCTAAGCC
1 AAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCC
* * *
57122967 CAAACGACGCCGTTTACTGAGCTTTCGGTGATTTAGTGGCGTTTTTATGT
66 C-AACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTAAGT
* *
57123017 AAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCCCCGCAAAAATACTTAAGCC
1 AAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCC
* * * *
57123082 CAACGACGCCGTTTTTTGACCTTTCGGGGATTTAGTGGCGTTTGTATGT
66 CAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTAAGT
* *
57123131 AAGCGCCGCTAATACTCAGGGATTTA
1 AAGCGCCGCTAATGCTCAGGGCTTTA
57123157 AAATAATTTA
Statistics
Matches: 328, Mismatches: 33, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
111 15 0.05
112 75 0.23
113 37 0.11
114 187 0.57
115 14 0.04
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (114 bp):
AAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCC
CAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTAAGT
Found at i:57123072 original size:226 final size:228
Alignment explanation
Indices: 57122678--57123148 Score: 707
Period size: 226 Copynumber: 2.1 Consensus size: 228
57122668 GTTTCCCAAA
** *
57122678 AAGCGCCGCTAATG-TTTAGGCTTTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAAACCTAAGCC
1 AAGCGCCGCTAATGCTCAAGGCTTTAGCGGCGGTTTTGAGAAAGCGCCACAAAAAAACCTAAGCC
* *
57122742 CAACGACGCCGTTTTCTGAGCTTTAGGGGATTTAGTGGCGTTTTTAAATATGCGCCGCTAATGCT
66 CAACGACGCCGTTTACTGAGCTTTAGGGGATTTAGTGGCGTTTTTAAATAAGCGCCGCTAATGCT
*
57122807 CAGGGCTTTAGCGGAGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCCCAACGACGCCGTTTTG
131 CAGGGCTTTAGCGGAGTTTTTGGGAAAGCCCCGCAAAAATACCTAAGCCCAACGACGCCGTTTTG
* *
57122872 TGAGCTTTCGGGGATTTAGT-GCGTTTTTAAGT
196 TGACCTTTCGGGGATTTAGTGGCGTTTGTAAGT
* * * * *
57122904 -AGCGCCGCTAATGCTCAAGGCTTTATCGGCGGTTTTGGGAAGGCGCCGC-AAAATACCTAAGCC
1 AAGCGCCGCTAATGCTCAAGGCTTTAGCGGCGGTTTTGAGAAAGCGCCACAAAAAAACCTAAGCC
* * **
57122967 CAAACGACGCCGTTTACTGAGCTTTCGGTGATTTAGTGGCGTTTTTATGTAAGCGCCGCTAATGC
66 C-AACGACGCCGTTTACTGAGCTTTAGGGGATTTAGTGGCGTTTTTAAATAAGCGCCGCTAATGC
* *
57123032 TCAGGGCTTTAGCGGCGTTTTTGGGAAAGCCCCGCAAAAATACTTAAGCCCAACGACGCCGTTTT
130 TCAGGGCTTTAGCGGAGTTTTTGGGAAAGCCCCGCAAAAATACCTAAGCCCAACGACGCCGTTTT
* *
57123097 TTGACCTTTCGGGGATTTAGTGGCGTTTGTATGT
195 GTGACCTTTCGGGGATTTAGTGGCGTTTGTAAGT
*
57123131 AAGCGCCGCTAATACTCA
1 AAGCGCCGCTAATGCTCA
57123149 GGGATTTAAA
Statistics
Matches: 219, Mismatches: 22, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
225 27 0.12
226 166 0.76
227 10 0.05
228 16 0.07
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (228 bp):
AAGCGCCGCTAATGCTCAAGGCTTTAGCGGCGGTTTTGAGAAAGCGCCACAAAAAAACCTAAGCC
CAACGACGCCGTTTACTGAGCTTTAGGGGATTTAGTGGCGTTTTTAAATAAGCGCCGCTAATGCT
CAGGGCTTTAGCGGAGTTTTTGGGAAAGCCCCGCAAAAATACCTAAGCCCAACGACGCCGTTTTG
TGACCTTTCGGGGATTTAGTGGCGTTTGTAAGT
Done.