Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 183 of 226
Found at i:58485503 original size:38 final size:38
Alignment explanation
Indices: 58485452--58485528 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
58485442 GATAACTCTA
* *
58485452 CAATCCTATATTTTCCTCCTAAAGTCACTCCAACACTC
1 CAATCCCATATTTTCCTCCTAAAATCACTCCAACACTC
*
58485490 CAATCCCATATTTTCCTCCTAAAATCACTCCAACGCTC
1 CAATCCCATATTTTCCTCCTAAAATCACTCCAACACTC
58485528 C
1 C
58485529 CCCACCAAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.29, C:0.39, G:0.03, T:0.30
Consensus pattern (38 bp):
CAATCCCATATTTTCCTCCTAAAATCACTCCAACACTC
Found at i:58488192 original size:11 final size:10
Alignment explanation
Indices: 58488164--58488218 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
58488154 AATTAAAATG
58488164 TTAAAATAAA
1 TTAAAATAAA
*
58488174 TTTAAATAAA
1 TTAAAATAAA
58488184 TTAACAAT--A
1 TTAA-AATAAA
* *
58488193 TTGAAATAAT
1 TTAAAATAAA
*
58488203 TTGAAATAAA
1 TTAAAATAAA
58488213 TTAAAA
1 TTAAAA
58488219 AATGTTAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
8 3 0.08
9 4 0.11
10 26 0.72
11 3 0.08
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (10 bp):
TTAAAATAAA
Found at i:58488201 original size:29 final size:28
Alignment explanation
Indices: 58488154--58488268 Score: 92
Period size: 29 Copynumber: 4.0 Consensus size: 28
58488144 ATAATATATG
*
58488154 AATTAAAATGTTAAAATAAATTT-AAATA
1 AATTAAAATATTAAAAT-AATTTGAAATA
*
58488182 AATTAACAATATTGAAATAATTTGAAATA
1 AATTAA-AATATTAAAATAATTTGAAATA
* *
58488211 AATTAAAAAATGTTAAAAT-ATTTGAAAGA
1 AATT--AAAATATTAAAATAATTTGAAATA
* *
58488240 GA-TAAAATATTTATATAATAATATGAAAT
1 AATTAAAATA-TTA-A-AATAATTTGAAAT
58488269 TAACAATAGA
Statistics
Matches: 70, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
26 5 0.07
27 3 0.04
28 13 0.19
29 31 0.44
30 16 0.23
31 2 0.03
ACGTcount: A:0.57, C:0.01, G:0.07, T:0.35
Consensus pattern (28 bp):
AATTAAAATATTAAAATAATTTGAAATA
Found at i:58488608 original size:19 final size:19
Alignment explanation
Indices: 58488563--58488610 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
58488553 TCAAAATAAT
* *
58488563 AATATATT-ATAATATTGA
1 AATATATTAATAAAATTAA
58488581 AATAGTATTAATAAAATTAA
1 AATA-TATTAATAAAATTAA
58488601 AATATATTAA
1 AATATATTAA
58488611 ACTTAAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 4 0.15
19 10 0.38
20 12 0.46
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
AATATATTAATAAAATTAA
Found at i:58490306 original size:50 final size:50
Alignment explanation
Indices: 58490252--58490934 Score: 394
Period size: 50 Copynumber: 13.7 Consensus size: 50
58490242 TACACCGCCT
* * *
58490252 GGGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCG
1 GGGAAGTAAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCG
** * *
58490302 GGGAAACAAGATTCACCGTTGTGGCTTTAAT-TTGTTT-CCATGC-ATCGCTTG
1 GGGAAGTAAGATTCACCGTTGTGGCTTTAATCTT-TTTAAC-TGCAAT-G-TCG
* * **
58490353 GGG-GGTAAGATTCGCCACTGTGGCTTTAATCTTTTTAACTGCAATGTCG
1 GGGAAGTAAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCG
* * * * ** ** * * *
58490402 GGGAAGCAAGATTCACTGATATGGCTTTAATCTACTCCACGGC-ATCGCCA
1 GGGAAGTAAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAAT-GTCG
* * *
58490452 GGGCAGTAGGATTCACCGTTGTGGCTTTAATCTTTTTATCTGCAATGTCG
1 GGGAAGTAAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCG
* * * ** ** * *
58490502 GGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACCGCCA
1 GGGAAGTAAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCG
** ** *
58490552 GGGAAGTAAGATTTGCCACTCTGGCTTTAATCTTTTTAACTGCAATGTCG
1 GGGAAGTAAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCG
** * ** ** * *
58490602 GGGAAGCGAGATTCACCGATGTGGCTTTAATCTACTCCACTGCACT-TCCA
1 GGGAAGTAAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGT-CG
* * *
58490652 GGGAAGTAGGATTCACCGCTGTGGCTTTAATCTTTTTAACTGCAACGTCG
1 GGGAAGTAAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCG
** * ** ** ** ** *
58490702 GGGAAGCGAGATTCACCGATGTGGCTTTAATCTGCTCCACTATACCG-CTA
1 GGGAAGTAAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTC-G
* * ** * *
58490752 GAGAAGTAGGATTTGCCGTTGTGGCTTTAACCTTTTTAACTGCTATTGTCG
1 GGGAAGTAAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGC-AATGTCG
* ** * * ** * * * *
58490803 GGGAAGTGAGATTTGCCGTTGTGGTTTTAATCTATTCCAC-GTAACCGCCA
1 GGGAAGTAAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAA-TGTCG
* * * * * * * *
58490853 GAGAAGTAAGATTCGCTGCTATAGCTTTAATCTTTTTAACTGTAATG-CC
1 GGGAAGTAAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCG
** * *
58490902 GGGAAGCGAGATTCACCGATGTGGTTTTAATCT
1 GGGAAGTAAGATTCACCGTTGTGGCTTTAATCT
58490935 GCTCCACTGC
Statistics
Matches: 460, Mismatches: 156, Indels: 35
0.71 0.24 0.05
Matches are distributed among these distances:
49 40 0.09
50 368 0.80
51 51 0.11
52 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.32
Consensus pattern (50 bp):
GGGAAGTAAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCG
Found at i:58490313 original size:100 final size:100
Alignment explanation
Indices: 58490196--58490946 Score: 730
Period size: 100 Copynumber: 7.5 Consensus size: 100
58490186 TTTAATAGTG
* * * * * * * * *
58490196 ATGTCGAGGAAGTAAGATTCGCTATTGTAGCTTCAATTTGTTCCACTACACCGCCTGGGAAGTAA
1 ATGTCGGGGAAGCAAGATTCCCGATTGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAA
* * *
58490261 GATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCA
66 GATTCGCCGCTGTGGCTTTAATCTTTTTAACTGCA
* * * ** **
58490296 ATGTCGGGGAAACAAGATTCACCG-TTGTGGCTTTAATTTGTTTCCA-TGCATCGCTTGGGGGGT
1 ATGTCGGGGAAGCAAGATTC-CCGATTGTGGCTTTAATCTG-TTCCACTGCACCGCCAGGGAAGT
*
58490359 AAGATTCGCCACTGTGGCTTTAATCTTTTTAACTGCA
64 AAGATTCGCCGCTGTGGCTTTAATCTTTTTAACTGCA
* * ** * * *
58490396 ATGTCGGGGAAGCAAGATTCACTGA-TATGGCTTTAATCTACTCCACGGCATCGCCAGGGCAGTA
1 ATGTCGGGGAAGCAAGATTC-CCGATTGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTA
* * * *
58490460 GGATTCACCGTTGTGGCTTTAATCTTTTTATCTGCA
65 AGATTCGCCGCTGTGGCTTTAATCTTTTTAACTGCA
58490496 ATGTCGGGGAAGCAAGATTCACCGA-TGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTA
1 ATGTCGGGGAAGCAAGATTC-CCGATTGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTA
* * *
58490560 AGATTTGCCACTCTGGCTTTAATCTTTTTAACTGCA
65 AGATTCGCCGCTGTGGCTTTAATCTTTTTAACTGCA
* ** **
58490596 ATGTCGGGGAAGCGAGATTCACCGA-TGTGGCTTTAATCTACTCCACTGCACTTCCAGGGAAGTA
1 ATGTCGGGGAAGCAAGATTC-CCGATTGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTA
* *
58490660 GGATTCACCGCTGTGGCTTTAATCTTTTTAACTGCA
65 AGATTCGCCGCTGTGGCTTTAATCTTTTTAACTGCA
* * * ** * *
58490696 ACGTCGGGGAAGCGAGATTCACCGA-TGTGGCTTTAATCTGCTCCACTATACCGCTAGAGAAGTA
1 ATGTCGGGGAAGCAAGATTC-CCGATTGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTA
* * * *
58490760 GGATTTGCCGTTGTGGCTTTAACCTTTTTAACTGCTA
65 AGATTCGCCGCTGTGGCTTTAATCTTTTTAACTGC-A
* ** * * * * *
58490797 TTGTCGGGGAAGTGAGATTTGCCG-TTGTGGTTTTAATCTATTCCAC-GTAACCGCCAGAGAAGT
1 ATGTCGGGGAAGCAAGA-TTCCCGATTGTGGCTTTAATCTGTTCCACTG-CACCGCCAGGGAAGT
* * * *
58490860 AAGATTCGCTGCTATAGCTTTAATCTTTTTAACTGTA
64 AAGATTCGCCGCTGTGGCTTTAATCTTTTTAACTGCA
* * * *
58490897 ATG-CCGGGAAGCGAGATTCACCGA-TGTGGTTTTAATCTGCTCCACTGCAC
1 ATGTCGGGGAAGCAAGATTC-CCGATTGTGGCTTTAATCTGTTCCACTGCAC
58490947 TGCCTGAAAG
Statistics
Matches: 547, Mismatches: 93, Indels: 23
0.83 0.14 0.03
Matches are distributed among these distances:
98 2 0.00
99 39 0.07
100 421 0.77
101 83 0.15
102 2 0.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (100 bp):
ATGTCGGGGAAGCAAGATTCCCGATTGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAA
GATTCGCCGCTGTGGCTTTAATCTTTTTAACTGCA
Found at i:58490519 original size:200 final size:200
Alignment explanation
Indices: 58490252--58490946 Score: 811
Period size: 200 Copynumber: 3.5 Consensus size: 200
58490242 TACACCGCCT
* * * * *
58490252 GGGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAACAAGATTCA
1 GGGAAGTAGGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCA
* * * ** ** *
58490317 CCGTTGTGGCTTTAATTTGTTTCCA-TGCATCGCTTGGGGGGTAAGATTCGCCACTGTGGCTTTA
66 CCGATGTGGCTTTAATCTG-TTCCACTGCACCGCCAGGGAAGTAAGATTCGCCACTCTGGCTTTA
*
58490381 ATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACTGATATGGCTTTAATCTACTCCACGGCA
130 ATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATATGGCTTTAATCTACTCCACGGCA
58490446 -TCGCCA
195 CT-GCCA
* *
58490452 GGGCAGTAGGATTCACCGTTGTGGCTTTAATCTTTTTATCTGCAATGTCGGGGAAGCAAGATTCA
1 GGGAAGTAGGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCA
*
58490517 CCGATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTTGCCACTCTGGCTTTAA
66 CCGATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGCCACTCTGGCTTTAA
* * *
58490582 TCTTTTTAACTGCAATGTCGGGGAAGCGAGATTCACCGATGTGGCTTTAATCTACTCCACTGCAC
131 TCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATATGGCTTTAATCTACTCCACGGCAC
*
58490647 TTCCA
196 TGCCA
* * *
58490652 GGGAAGTAGGATTCACCGCTGTGGCTTTAATCTTTTTAACTGCAACGTCGGGGAAGCGAGATTCA
1 GGGAAGTAGGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCA
* ** * * * * ** *
58490717 CCGATGTGGCTTTAATCTGCTCCACTATACCGCTAGAGAAGTAGGATTTGCCGTTGTGGCTTTAA
66 CCGATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGCCACTCTGGCTTTAA
* * ** ** * * * * **
58490782 CCTTTTTAACTGCTATTGTCGGGGAAGTGAGATTTGCCGTTGTGGTTTTAATCTATTCCACGTAA
131 TCTTTTTAACTGC-AATGTCGGGGAAGCAAGATTCACCGATATGGCTTTAATCTACTCCACGGCA
*
58490847 CCGCCA
195 CTGCCA
* * * * * * * * * *
58490853 GAGAAGTAAGATTCGCTGCTATAGCTTTAATCTTTTTAACTGTAATG-CCGGGAAGCGAGATTCA
1 GGGAAGTAGGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCA
* *
58490917 CCGATGTGGTTTTAATCTGCTCCACTGCAC
66 CCGATGTGGCTTTAATCTGTTCCACTGCAC
58490947 TGCCTGAAAG
Statistics
Matches: 432, Mismatches: 60, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
199 5 0.01
200 342 0.79
201 85 0.20
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (200 bp):
GGGAAGTAGGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCA
CCGATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGCCACTCTGGCTTTAA
TCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATATGGCTTTAATCTACTCCACGGCAC
TGCCA
Found at i:58491155 original size:142 final size:142
Alignment explanation
Indices: 58490984--58491351 Score: 592
Period size: 142 Copynumber: 2.6 Consensus size: 142
58490974 TTCGGTCTAT
* * *
58490984 TCCACCGTAATCTTAGGGAAATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGA
1 TCCACTGTAATCTTAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGA
* *
58491049 TAAGATTTCTGGCTTTAATCTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGACCCTTT
66 TAAGATTTCTGGCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGACCCTTT
***
58491114 ATTTTAATCCGT
131 ATTTTAATCAAC
* * *
58491126 TCTACTGTAATCTTAGGGAGATAGGATTACTGGCTTCAATCTGCTCCGCTGTAATTTCAGGGAGA
1 TCCACTGTAATCTTAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGA
*
58491191 TAAGATTTCTGGCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTT
66 TAAGATTTCTGGCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGACCCTTT
58491256 ATTTTAATCAAC
131 ATTTTAATCAAC
* * * *
58491268 TCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGTTTCACTGTAATCTCAGGGAGA
1 TCCACTGTAATCTTAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGA
58491333 TAAGATTTCTGGCTTCAAT
66 TAAGATTTCTGGCTTCAAT
58491352 TTGCTTCCTT
Statistics
Matches: 207, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
142 207 1.00
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (142 bp):
TCCACTGTAATCTTAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGA
TAAGATTTCTGGCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGACCCTTT
ATTTTAATCAAC
Found at i:58497894 original size:19 final size:19
Alignment explanation
Indices: 58497849--58497896 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
58497839 TCAAAATAAT
* *
58497849 AATATATT-ATAATATTGA
1 AATATATTAATAAAATTAA
58497867 AATAGTATTAATAAAATTAA
1 AATA-TATTAATAAAATTAA
58497887 AATATATTAA
1 AATATATTAA
58497897 ACTTAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 4 0.15
19 10 0.38
20 12 0.46
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
AATATATTAATAAAATTAA
Found at i:58504013 original size:24 final size:24
Alignment explanation
Indices: 58503985--58504036 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
58503975 TTTCTAGAAG
* *
58503985 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
*
58504009 ATTTAGCATTTATTAGCATAATTT
1 ATTTAGCATTTATTAGCATAATAT
58504033 ATTT
1 ATTT
58504037 GACCTACTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:58507463 original size:6 final size:7
Alignment explanation
Indices: 58507442--58507466 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
58507432 ATTTATATAA
58507442 TTTATTT
1 TTTATTT
58507449 TTTATTT
1 TTTATTT
58507456 TTTATTT
1 TTTATTT
58507463 TTTA
1 TTTA
58507467 CTACATCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTATTT
Found at i:58507636 original size:3 final size:3
Alignment explanation
Indices: 58507628--58507670 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
58507618 AATTTTTTAC
58507628 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
58507671 CCACACATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:58508142 original size:46 final size:47
Alignment explanation
Indices: 58508089--58508177 Score: 153
Period size: 47 Copynumber: 1.9 Consensus size: 47
58508079 CGTCGCACCA
58508089 TTTTCTTTCACTTT-CTCCCATCCAAACACCCACCACTTCATTATAG
1 TTTTCTTTCACTTTCCTCCCATCCAAACACCCACCACTTCATTATAG
* *
58508135 TTTTCTTTCACTTTCCTCCTATCCAAACACCGACCACTTCATT
1 TTTTCTTTCACTTTCCTCCCATCCAAACACCCACCACTTCATT
58508178 CCTAGCAACA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
46 14 0.35
47 26 0.65
ACGTcount: A:0.22, C:0.37, G:0.02, T:0.38
Consensus pattern (47 bp):
TTTTCTTTCACTTTCCTCCCATCCAAACACCCACCACTTCATTATAG
Found at i:58509223 original size:118 final size:118
Alignment explanation
Indices: 58509015--58509241 Score: 454
Period size: 118 Copynumber: 1.9 Consensus size: 118
58509005 ACCTCATGCA
58509015 AAAATTAGATTAGAGAGCGTTGCAAGGTTTTAGGTTGTATTTTTCGTTTAAAATTGTTTCTGTTA
1 AAAATTAGATTAGAGAGCGTTGCAAGGTTTTAGGTTGTATTTTTCGTTTAAAATTGTTTCTGTTA
58509080 AGTATGGCTCCTATTTTCAGTCAAATTTGAGAAATAATCTTTTAAAATTGTTT
66 AGTATGGCTCCTATTTTCAGTCAAATTTGAGAAATAATCTTTTAAAATTGTTT
58509133 AAAATTAGATTAGAGAGCGTTGCAAGGTTTTAGGTTGTATTTTTCGTTTAAAATTGTTTCTGTTA
1 AAAATTAGATTAGAGAGCGTTGCAAGGTTTTAGGTTGTATTTTTCGTTTAAAATTGTTTCTGTTA
58509198 AGTATGGCTCCTATTTTCAGTCAAATTTGAGAAATAATCTTTTA
66 AGTATGGCTCCTATTTTCAGTCAAATTTGAGAAATAATCTTTTA
58509242 GTTAAACTCT
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 109 1.00
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.44
Consensus pattern (118 bp):
AAAATTAGATTAGAGAGCGTTGCAAGGTTTTAGGTTGTATTTTTCGTTTAAAATTGTTTCTGTTA
AGTATGGCTCCTATTTTCAGTCAAATTTGAGAAATAATCTTTTAAAATTGTTT
Found at i:58517830 original size:119 final size:115
Alignment explanation
Indices: 58517571--58518027 Score: 397
Period size: 119 Copynumber: 3.9 Consensus size: 115
58517561 CACATGTCCA
* * * * *
58517571 TGTACCATGACAAATTCCATTTATTGTCACTTTAAGATGTAAATATTTGAAATTTTTTATTTT--
1 TGTACAATGACAAATTCCATTTATTGTTACTTTAAAATGTAAATATTTG-AATTTATGATTTTGA
* * * * * *
58517634 CA-AAGG-AGCCAATATTTGATCTCTCTGTTAGACCAAGAC-G-TGTGTGTC
65 CATAAGGTA-CCAATGTTTGATCTGTCTCTGAGACAAAGACAGATATGTGTC
** *
58517682 TGTGTAGTATGACTAATTCCATTTATTGTTACTTTAAAATGTAAATATTTGAATTTCATGATTTT
1 --TGTACAATGACAAATTCCATTTATTGTTACTTTAAAATGTAAATATTTGAATTT-ATGA-TTT
* *
58517747 TGACATAAGGTACCAAGGTTTGATCTGTCTCTGAGACAAAGACAGAT-TCGCTTGTG
62 TGACATAAGGTACCAATGTTTGATCTGTCTCTGAGACAAAGACAGATAT-G--TGTC
* * * * *
58517803 TGTTCTATGGCAAATTCCATTTATTGTTGCTTTAAAATGTAAATATTTGAATTTTATCATTTTGA
1 TGTACAATGACAAATTCCATTTATTGTTACTTTAAAATGTAAATATTTGAA-TTTATGATTTTGA
* * * * *
58517868 CATAAAGTACCAATGTTTGGTCCGTGTCTCTTAGACCAAGGACATATATGTGTC
65 CATAAGGTACCAATGTTTGAT-C-TGTCTCTGAGA-CAAAGACAGATATGTGTC
* * * * *
58517922 TGTACAATGACAAATTCCTTTTATTATTACTTCAAAGTGTAAAGATTTGAAATTTATGATTTTGA
1 TGTACAATGACAAATTCCATTTATTGTTACTTTAAAATGTAAATATTTG-AATTTATGATTTTGA
* * * * *
58517987 GATAAGGTAGCATTGTTTGAGATGTGTCTCTGAGACCAAGA
65 CATAAGGTACCAATGTTT--GATCTGTCTCTGAGACAAAGA
58518028 ATTATGTCAT
Statistics
Matches: 279, Mismatches: 46, Indels: 33
0.78 0.13 0.09
Matches are distributed among these distances:
112 5 0.02
113 46 0.16
114 4 0.01
116 2 0.01
117 29 0.10
118 31 0.11
119 131 0.47
120 15 0.05
121 15 0.05
122 1 0.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (115 bp):
TGTACAATGACAAATTCCATTTATTGTTACTTTAAAATGTAAATATTTGAATTTATGATTTTGAC
ATAAGGTACCAATGTTTGATCTGTCTCTGAGACAAAGACAGATATGTGTC
Found at i:58521356 original size:11 final size:11
Alignment explanation
Indices: 58521330--58521364 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
58521320 GTCCGGTTGG
58521330 ATTAAATAAATT
1 ATTAAA-AAATT
*
58521342 ATTAAAAATTT
1 ATTAAAAAATT
58521353 ATTAAAAAATT
1 ATTAAAAAATT
58521364 A
1 A
58521365 AAAATTCAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATTAAAAAATT
Found at i:58525261 original size:15 final size:15
Alignment explanation
Indices: 58525241--58525308 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 15
58525231 ATACTACAAA
58525241 ATATTTATTATTAAT
1 ATATTTATTATTAAT
58525256 ATATTTA-TAGTTGTAAT
1 ATATTTATTA--T-TAAT
*
58525273 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
*
58525290 ATA-TTAATATTAA-
1 ATATTTATTATTAAT
58525303 ATATTT
1 ATATTT
58525309 TAATAAAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
13 3 0.07
14 13 0.30
15 10 0.23
16 1 0.02
17 7 0.16
18 1 0.02
19 7 0.16
20 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:58525311 original size:15 final size:15
Alignment explanation
Indices: 58525272--58525313 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
58525262 ATAGTTGTAA
*
58525272 TAAATA-TTTATTAT
1 TAAATATTTTAATAT
*
58525286 TAAA-ATATTAATAT
1 TAAATATTTTAATAT
58525300 TAAATATTTTAATA
1 TAAATATTTTAATA
58525314 AAATTTGAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 1 0.04
14 14 0.61
15 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAATATTTTAATAT
Found at i:58525357 original size:16 final size:16
Alignment explanation
Indices: 58525326--58525362 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
58525316 ATTTGAAGAA
58525326 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
58525342 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
58525358 TATTA
1 TATTA
58525363 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:58525394 original size:25 final size:28
Alignment explanation
Indices: 58525366--58525420 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 28
58525356 ATTATTAAAA
58525366 TAAAAATAA-AAATTA-AATAATT-TAT
1 TAAAAATAATAAATTATAATAATTATAT
*
58525391 T-AAAATAATAAATTATATTAATTATAT
1 TAAAAATAATAAATTATAATAATTATAT
58525418 TAA
1 TAA
58525421 TAATTTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
24 7 0.28
25 7 0.28
26 6 0.24
27 4 0.16
28 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
TAAAAATAATAAATTATAATAATTATAT
Found at i:58525422 original size:25 final size:25
Alignment explanation
Indices: 58525369--58525433 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
58525359 ATTAAAATAA
*
58525369 AAATAA-AAATTA-AATAATTTATT
1 AAATAATAAATTATATTAATTTATT
58525392 AAAATAATAAATTATATTAATTATATT
1 -AAATAATAAATTATATTAATT-TATT
**
58525419 -AATAATTTATTATAT
1 AAATAATAAATTATAT
58525434 GACTAAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 6 0.17
25 19 0.54
26 6 0.17
27 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
AAATAATAAATTATATTAATTTATT
Found at i:58528293 original size:63 final size:63
Alignment explanation
Indices: 58528134--58528312 Score: 184
Period size: 63 Copynumber: 2.8 Consensus size: 63
58528124 GTTCTAAACC
* * * * * *
58528134 AATTTATTTGACACAAGCACCACAACACACACAATCATT-CCTCGAATCAAAACCTTCAGCTCT
1 AATTTATTTTACACAAGCACCACAACATACACAATCATTCCCT-GCATCAACACATTCAGCGCT
** * *
58528197 AATTTATTTTACACTAA-CACTGCAGCATGCACAATCATTCCCTGCATCAACACATTCAGCAGC-
1 AATTTATTTTACAC-AAGCACCACAACATACACAATCATTCCCTGCATCAACACATTCAGC-GCT
* * **
58528260 AGTTTATTTTACACAAGCACCACAACATACACAATTATTCATTGCATCAACAC
1 AATTTATTTTACACAAGCACCACAACATACACAATCATTCCCTGCATCAACAC
58528313 CTTCTCCAAG
Statistics
Matches: 94, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
62 2 0.02
63 86 0.91
64 6 0.06
ACGTcount: A:0.37, C:0.30, G:0.07, T:0.26
Consensus pattern (63 bp):
AATTTATTTTACACAAGCACCACAACATACACAATCATTCCCTGCATCAACACATTCAGCGCT
Found at i:58533241 original size:27 final size:27
Alignment explanation
Indices: 58533161--58533242 Score: 67
Period size: 27 Copynumber: 3.0 Consensus size: 27
58533151 GCATCAAAGA
* *
58533161 AGTCTAATGGGACTTTAAACACGAGAT
1 AGTCTGATGGGACATTAAACACGAGAT
* * * ** **
58533188 TGTATGACT-AGATGTTAAACATAAGAT
1 AGTCTGA-TGGGACATTAAACACGAGAT
58533215 AGTCTGATGGGACATTAAACACGAGAT
1 AGTCTGATGGGACATTAAACACGAGAT
58533242 A
1 A
58533243 CTTCGACGAG
Statistics
Matches: 38, Mismatches: 15, Indels: 4
0.67 0.26 0.07
Matches are distributed among these distances:
26 1 0.03
27 36 0.95
28 1 0.03
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27
Consensus pattern (27 bp):
AGTCTGATGGGACATTAAACACGAGAT
Found at i:58533259 original size:54 final size:53
Alignment explanation
Indices: 58533157--58533260 Score: 129
Period size: 54 Copynumber: 1.9 Consensus size: 53
58533147 TATGGCATCA
* ** * *
58533157 AAGAAGTCTAATGGGACTTTAAACACGAGATTGTATGACTAGATGTTAAACAT
1 AAGAAGTCTAATGGGACATTAAACACGAGATACTATGACGAGACGTTAAACAT
*
58533210 AAGATAGTCTGATGGGACATTAAACACGAGATACT-TCGACGAGACGTTAAA
1 AAGA-AGTCTAATGGGACATTAAACACGAGATACTAT-GACGAGACGTTAAA
58533261 TTTAGGGTAG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
53 5 0.12
54 38 0.88
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.25
Consensus pattern (53 bp):
AAGAAGTCTAATGGGACATTAAACACGAGATACTATGACGAGACGTTAAACAT
Found at i:58554301 original size:9 final size:9
Alignment explanation
Indices: 58554287--58554312 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
58554277 TTAATTGAGA
58554287 AATTAATTT
1 AATTAATTT
58554296 AATTAATTT
1 AATTAATTT
58554305 AATTAATT
1 AATTAATT
58554313 GAATAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
AATTAATTT
Found at i:58564456 original size:37 final size:37
Alignment explanation
Indices: 58564407--58564481 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
58564397 ATTTCACCAT
*
58564407 TTTTAACCATAAATCATGCTAGCCAGTTTTTACTTAA
1 TTTTAACCATAAATCATGCTAGCCAATTTTTACTTAA
58564444 TTTTAACCATAAATCATGCTAGCCAATTTTTACTTAA
1 TTTTAACCATAAATCATGCTAGCCAATTTTTACTTAA
58564481 T
1 T
58564482 CTTATAACAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (37 bp):
TTTTAACCATAAATCATGCTAGCCAATTTTTACTTAA
Found at i:58572765 original size:78 final size:78
Alignment explanation
Indices: 58572638--58572800 Score: 211
Period size: 78 Copynumber: 2.1 Consensus size: 78
58572628 CAAATTAGTT
* * * * * * *
58572638 CCCCTCTCCTCGAAGTCCTTAAATTTTTTTCCCAGACCCCTTTCTTTTTTTCCCTAATTTC-TTT
1 CCCCTCTCCCCGAAATCCCTAAATTTCTTTCCCAGACCCCTTTC-ATTTTTCCCCAATTCCTTTT
58572702 CCCTAAATCAATTC
65 CCCTAAATCAATTC
* * *
58572716 CCCCTCTCCCCGAAATCCCTAAGTTTCTTTCCGAGACCTCTTTCATTTTTCCCCAATTCCTTTTC
1 CCCCTCTCCCCGAAATCCCTAAATTTCTTTCCCAGACCCCTTTCATTTTTCCCCAATTCCTTTTC
*
58572781 CCTAAATCAGTTC
66 CCTAAATCAATTC
58572794 CCCCTCT
1 CCCCTCT
58572801 GTGAAATCAC
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
77 13 0.18
78 60 0.82
ACGTcount: A:0.17, C:0.38, G:0.05, T:0.40
Consensus pattern (78 bp):
CCCCTCTCCCCGAAATCCCTAAATTTCTTTCCCAGACCCCTTTCATTTTTCCCCAATTCCTTTTC
CCTAAATCAATTC
Found at i:58573472 original size:13 final size:13
Alignment explanation
Indices: 58573455--58573485 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
58573445 ATAGAAGGCA
58573455 AAAATTTTATTAG
1 AAAATTTTATTAG
*
58573468 GAAATTTTATTAG
1 AAAATTTTATTAG
58573481 AAAAT
1 AAAAT
58573486 AATTAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (13 bp):
AAAATTTTATTAG
Found at i:58574616 original size:25 final size:25
Alignment explanation
Indices: 58574588--58574637 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
58574578 GAATATTATA
*
58574588 TTTTTT-TAATTTGGTACTTAAATT
1 TTTTTTCTAATTTGATACTTAAATT
*
58574612 TTTTTTCTAATTTGATATTTAAATT
1 TTTTTTCTAATTTGATACTTAAATT
58574637 T
1 T
58574638 ATCAAACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.64
Consensus pattern (25 bp):
TTTTTTCTAATTTGATACTTAAATT
Found at i:58575324 original size:35 final size:35
Alignment explanation
Indices: 58575278--58575347 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
58575268 AGAATAAAAT
*
58575278 TTAATGATTATCATAACTTACATAAACATTTAAAG
1 TTAATGATTATCATAACTTACACAAACATTTAAAG
58575313 TTAATGATTATCATAACTTACACAAACATTTAAAG
1 TTAATGATTATCATAACTTACACAAACATTTAAAG
58575348 AATATAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.36
Consensus pattern (35 bp):
TTAATGATTATCATAACTTACACAAACATTTAAAG
Found at i:58581659 original size:22 final size:23
Alignment explanation
Indices: 58581608--58581670 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
58581598 AGCTCATTGA
58581608 AGCTTACCGTTTCAGCTCGTATG
1 AGCTTACCGTTTCAGCTCGTATG
* *
58581631 AGGTTACTG-TTCAGCTCGTCA-G
1 AGCTTACCGTTTCAGCTCGT-ATG
* *
58581653 AGCTTACCATTTTAGCTC
1 AGCTTACCGTTTCAGCTC
58581671 AATAGAGCCT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
22 17 0.53
23 15 0.47
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (23 bp):
AGCTTACCGTTTCAGCTCGTATG
Found at i:58581880 original size:20 final size:20
Alignment explanation
Indices: 58581855--58581912 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
58581845 AAGATATGTA
*
58581855 TTTATATGGATGAATTATTG
1 TTTATATGGATGAATTACTG
* * *
58581875 TTTATACGGATGGACTACTG
1 TTTATATGGATGAATTACTG
* *
58581895 GTTATATGAATGAATTAC
1 TTTATATGGATGAATTAC
58581913 AGTTATACGA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (20 bp):
TTTATATGGATGAATTACTG
Found at i:58588989 original size:24 final size:23
Alignment explanation
Indices: 58588961--58589019 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 23
58588951 CAGCTTGTAA
58588961 GAGCTTACTGTTTTCAGCACGT-T
1 GAGCTTACTGTTTT-AGCACGTAT
* *
58588984 GAAGCTTACCGTTTTAGCTCGTAT
1 G-AGCTTACTGTTTTAGCACGTAT
58589008 GAGCTTACTGTT
1 GAGCTTACTGTT
58589020 CAGCTCGTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 17 0.55
24 14 0.45
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (23 bp):
GAGCTTACTGTTTTAGCACGTAT
Found at i:58589259 original size:20 final size:20
Alignment explanation
Indices: 58589234--58589291 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
58589224 AAGATATGTA
*
58589234 TTTATATGGATGAATTATTG
1 TTTATATGGATGAATTACTG
* * *
58589254 TTTATACGGATGGACTACTG
1 TTTATATGGATGAATTACTG
* *
58589274 GTTATATGAATGAATTAC
1 TTTATATGGATGAATTAC
58589292 AGTTATACAA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (20 bp):
TTTATATGGATGAATTACTG
Found at i:58595705 original size:3 final size:3
Alignment explanation
Indices: 58595697--58595730 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
58595687 CACGAAAGGA
58595697 AAT AAT AAT ATAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
58595731 TTTAACACCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:58599595 original size:64 final size:64
Alignment explanation
Indices: 58599486--58599609 Score: 162
Period size: 64 Copynumber: 1.9 Consensus size: 64
58599476 ACAAAGAGCC
* * * * *
58599486 TATATCAGGACGCTCATAAAGAGCTGCGATATGTCCGCAATATATGCAGGATC-AATACCGGTCA
1 TATAACAGGACGCTCACAAAGAGCTACGATATATCCGCAACATATGCAGGA-CAAATACCGGTCA
*
58599550 TATAACAGGACGCTCACAAAGAGCTAC-AGTATATCCGCAACATATGTAGGACAAATACCG
1 TATAACAGGACGCTCACAAAGAGCTACGA-TATATCCGCAACATATGCAGGACAAATACCG
58599610 ATCGAGATGC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
63 2 0.04
64 50 0.96
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (64 bp):
TATAACAGGACGCTCACAAAGAGCTACGATATATCCGCAACATATGCAGGACAAATACCGGTCA
Found at i:58603107 original size:21 final size:22
Alignment explanation
Indices: 58603059--58603109 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
58603049 GGTCAATACG
*
58603059 CCCGTGTGGAATGAGGCACACG
1 CCCGTGTGGAATGAGGCACACA
** *
58603081 GTCGTGTGG-CTGAGGCACACA
1 CCCGTGTGGAATGAGGCACACA
58603102 CCCGTGTG
1 CCCGTGTG
58603110 AGCTAGGGAC
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.18, C:0.27, G:0.37, T:0.18
Consensus pattern (22 bp):
CCCGTGTGGAATGAGGCACACA
Found at i:58603850 original size:16 final size:16
Alignment explanation
Indices: 58603829--58603862 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
58603819 ACAGAGAGAA
**
58603829 AAAAAAGAGGAAAAAG
1 AAAAAAGAAAAAAAAG
58603845 AAAAAAGAAAAAAAAG
1 AAAAAAGAAAAAAAAG
58603861 AA
1 AA
58603863 CGTGCTACTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAAAAG
Found at i:58604810 original size:5 final size:5
Alignment explanation
Indices: 58604800--58604826 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
58604790 TAATATAAGT
58604800 ATTAA ATTAA ATTAA ATTAA ATTAA AT
1 ATTAA ATTAA ATTAA ATTAA ATTAA AT
58604827 ATTAAATCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATTAA
Found at i:58605479 original size:17 final size:18
Alignment explanation
Indices: 58605452--58605492 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
58605442 ACGAAAAACA
58605452 AAAACCAAAACC-AAGCCC
1 AAAA-CAAAACCAAAGCCC
*
58605470 AAAACAAAACCAAAGCCT
1 AAAACAAAACCAAAGCCC
58605488 AAAAC
1 AAAAC
58605493 TTAGTTCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.61, C:0.32, G:0.05, T:0.02
Consensus pattern (18 bp):
AAAACAAAACCAAAGCCC
Found at i:58615963 original size:16 final size:17
Alignment explanation
Indices: 58615929--58615963 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
58615919 TTTTCGTTTA
*
58615929 AAAAATAAAATAATTTT
1 AAAAATAAAATAATATT
58615946 AAAAATAAAAT-ATATT
1 AAAAATAAAATAATATT
58615962 AA
1 AA
58615964 TTATTTAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAAATAAAATAATATT
Found at i:58616206 original size:16 final size:16
Alignment explanation
Indices: 58616163--58616208 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
58616153 ATTTATAAAA
*
58616163 ATAATTTAAAATTTGT
1 ATAATTTAAAATTTAT
*
58616179 AAAATATTAAAATTTAT
1 ATAAT-TTAAAATTTAT
*
58616196 TTAATTTAAAATT
1 ATAATTTAAAATT
58616209 ATAAAAAGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
ATAATTTAAAATTTAT
Found at i:58616250 original size:25 final size:25
Alignment explanation
Indices: 58616222--58616275 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
58616212 AAAAGTAATT
58616222 ATAAACA-ATAACTATTATTTA-ATAA
1 ATAAACATATAA--ATTATTTATATAA
**
58616247 ATAATTATATAAATTATTTATATAA
1 ATAAACATATAAATTATTTATATAA
58616272 ATAA
1 ATAA
58616276 TTATTCTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 8 0.32
25 13 0.52
26 4 0.16
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (25 bp):
ATAAACATATAAATTATTTATATAA
Found at i:58616269 original size:13 final size:13
Alignment explanation
Indices: 58616235--58616273 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
58616225 AACAATAACT
58616235 ATTATTTA-ATAA
1 ATTATTTATATAA
*
58616247 A-TAATTATATAA
1 ATTATTTATATAA
58616259 ATTATTTATATAA
1 ATTATTTATATAA
58616272 AT
1 AT
58616274 AATTATTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 5 0.22
12 6 0.26
13 12 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATTATTTATATAA
Found at i:58616379 original size:18 final size:18
Alignment explanation
Indices: 58616358--58616418 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
58616348 TATCTATTAT
58616358 ATTTAATTTATATAAATA
1 ATTTAATTTATATAAATA
*
58616376 ATTTAAATTT-TATAAATT
1 ATTT-AATTTATATAAATA
* *
58616394 ATTAAATTTATAAAAATTA
1 ATTTAATTTATATAAA-TA
58616413 ATTTAA
1 ATTTAA
58616419 AATGTATTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
17 5 0.14
18 19 0.54
19 11 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTAATTTATATAAATA
Found at i:58619702 original size:22 final size:22
Alignment explanation
Indices: 58619677--58619723 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
58619667 TTTTTTTTTA
*
58619677 CTTTTA-AAATTTTTTATATATT
1 CTTTTAGAAACTTTTTATA-ATT
58619699 C-TTTAGAAACTTTTTATAATT
1 CTTTTAGAAACTTTTTATAATT
58619720 -TTTT
1 CTTTT
58619724 GAGTTATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (22 bp):
CTTTTAGAAACTTTTTATAATT
Found at i:58628096 original size:22 final size:22
Alignment explanation
Indices: 58628071--58628129 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
58628061 GAGAAATAAA
* *
58628071 AATTGAGTGAGAATTAAGAGGG
1 AATTGAGAGAGAATTAAAAGGG
58628093 AATTGAGAGA-AATTTAAAAGGG
1 AATTGAGAGAGAA-TTAAAAGGG
*
58628115 ATTTGAGAGAGAATT
1 AATTGAGAGAGAATT
58628130 GAGAATGTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 2 0.06
22 28 0.88
23 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.31, T:0.25
Consensus pattern (22 bp):
AATTGAGAGAGAATTAAAAGGG
Found at i:58628965 original size:18 final size:18
Alignment explanation
Indices: 58628938--58628972 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
58628928 ACTAAGCCTA
58628938 CCCAAATACAACCCAAAC
1 CCCAAATACAACCCAAAC
*
58628956 CCCAATTACAACCCAAA
1 CCCAAATACAACCCAAA
58628973 TCGAAGCCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.43, G:0.00, T:0.09
Consensus pattern (18 bp):
CCCAAATACAACCCAAAC
Found at i:58629989 original size:20 final size:20
Alignment explanation
Indices: 58629948--58629989 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
58629938 TTTTTAGCAT
* *
58629948 TTTTATTATTTTCTTCATTA
1 TTTTATTATTTTCATCAATA
58629968 TTTTATTATTATT-ATCAATA
1 TTTTATTATT-TTCATCAATA
58629988 TT
1 TT
58629990 ATGGTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTATTATTTTCATCAATA
Found at i:58631439 original size:30 final size:29
Alignment explanation
Indices: 58631405--58631461 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
58631395 AGGTGGAATG
* *
58631405 GGAAGAGAATAAAAGTTTTAGGGGAAAAGT
1 GGAAGAGAATAAAAATTTT-GGGAAAAAGT
* *
58631435 GGAAGGGAGTAAAAATTTTGGGAAAAA
1 GGAAGAGAATAAAAATTTTGGGAAAAA
58631462 ATAAAAGGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 7 0.30
30 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.33, T:0.19
Consensus pattern (29 bp):
GGAAGAGAATAAAAATTTTGGGAAAAAGT
Found at i:58631692 original size:9 final size:9
Alignment explanation
Indices: 58631674--58631710 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
58631664 TATAGTTTGA
58631674 TATTCGAAT
1 TATTCGAAT
*
58631683 TATTCTAAT
1 TATTCGAAT
*
58631692 TATTCGAGT
1 TATTCGAAT
58631701 TATTCGAAT
1 TATTCGAAT
58631710 T
1 T
58631711 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:58635105 original size:23 final size:22
Alignment explanation
Indices: 58635082--58635126 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
58635072 TCTCAACTTA
58635082 GTTTTGTTTATTAAAATATTTTAG
1 GTTTT-TTTATTAAAA-ATTTTAG
*
58635106 GTTTTTTTATTAACAATTTTA
1 GTTTTTTTATTAAAAATTTTA
58635127 TTATTCAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 9 0.45
24 5 0.25
ACGTcount: A:0.29, C:0.02, G:0.09, T:0.60
Consensus pattern (22 bp):
GTTTTTTTATTAAAAATTTTAG
Found at i:58644407 original size:27 final size:26
Alignment explanation
Indices: 58644369--58644455 Score: 120
Period size: 27 Copynumber: 3.2 Consensus size: 26
58644359 GTCAGGAAGT
58644369 AAAAGCCTTTGTGGCGTAATATGAAAG
1 AAAAG-CTTTGTGGCGTAATATGAAAG
* *
58644396 AAAAGTCTTTGTGACGTAATATAAAAG
1 AAAAG-CTTTGTGGCGTAATATGAAAG
*
58644423 AAAAGCTTTTGTGGCATAATATGAAAG
1 AAAAGC-TTTGTGGCGTAATATGAAAG
58644450 AAAAGC
1 AAAAGC
58644456 CTGTGGAGGC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
26 1 0.02
27 52 0.98
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.26
Consensus pattern (26 bp):
AAAAGCTTTGTGGCGTAATATGAAAG
Found at i:58648588 original size:4 final size:4
Alignment explanation
Indices: 58648579--58648635 Score: 105
Period size: 4 Copynumber: 14.2 Consensus size: 4
58648569 TCTGAGCATA
*
58648579 TATG TATG TATG TATG TATG TATG TATG TATA TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
58648627 TATG TATG T
1 TATG TATG T
58648636 TTACTTTGAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:58649754 original size:22 final size:22
Alignment explanation
Indices: 58649726--58649768 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
58649716 GTGGATACTA
58649726 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTC
58649748 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
58649769 GAACAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTC
Found at i:58653797 original size:21 final size:21
Alignment explanation
Indices: 58653768--58653814 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
58653758 AGTCAGCGTC
* * *
58653768 CACGGGCGTGTGAGGTAGTCA
1 CACGAGCGTGTGAAGTAGCCA
58653789 CACGAGCGTGTGAAGTAGCCA
1 CACGAGCGTGTGAAGTAGCCA
58653810 CACGA
1 CACGA
58653815 CCATATTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.26, C:0.23, G:0.36, T:0.15
Consensus pattern (21 bp):
CACGAGCGTGTGAAGTAGCCA
Found at i:58654436 original size:13 final size:13
Alignment explanation
Indices: 58654418--58654442 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58654408 TGGCATAATT
58654418 TAAAATGAAAATA
1 TAAAATGAAAATA
58654431 TAAAATGAAAAT
1 TAAAATGAAAAT
58654443 GAATATTGTA
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:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (13 bp):
TAAAATGAAAATA
Found at i:58654531 original size:18 final size:18
Alignment explanation
Indices: 58654510--58654544 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
58654500 TTCACTCTCT
58654510 TTTTTCGATTTTACTTTA
1 TTTTTCGATTTTACTTTA
*
58654528 TTTTTCGTTTTTACTTT
1 TTTTTCGATTTTACTTT
58654545 TAAAACTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.11, G:0.06, T:0.71
Consensus pattern (18 bp):
TTTTTCGATTTTACTTTA
Found at i:58660265 original size:21 final size:21
Alignment explanation
Indices: 58660224--58660267 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
58660214 CCTATTTTAT
*
58660224 ATTTATTATTTTCTCTTTCTC
1 ATTTATTATTTTCTCTCTCTC
*
58660245 ATTTATTGTTTTCTTGCTCTCTC
1 ATTTATTATTTTC-T-CTCTCTC
58660268 CGACGCCTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.63
22 1 0.05
23 6 0.32
ACGTcount: A:0.11, C:0.20, G:0.05, T:0.64
Consensus pattern (21 bp):
ATTTATTATTTTCTCTCTCTC
Found at i:58662830 original size:100 final size:100
Alignment explanation
Indices: 58662657--58662855 Score: 380
Period size: 100 Copynumber: 2.0 Consensus size: 100
58662647 AATCAACATA
58662657 TGGGTTTCAATAACACACACTTCCACACATTCATCATCTTAGTAGGCATAAAAAAATATTTTGAC
1 TGGGTTTCAATAACACACACTTCCACACATTCATCATCTTAGTAGGCATAAAAAAATATTTTGAC
58662722 ATTTCCTCAAGTTAAAGGTGAATATGCAACTAATG
66 ATTTCCTCAAGTTAAAGGTGAATATGCAACTAATG
*
58662757 TGGGTTTCAATAACACACATTTCCACACATTCATCATCTTAGTAGGCATAAAAAAATATTTTGAC
1 TGGGTTTCAATAACACACACTTCCACACATTCATCATCTTAGTAGGCATAAAAAAATATTTTGAC
*
58662822 ATTTCCTCAAGTTAAAGGTGCATATGCAACTAAT
66 ATTTCCTCAAGTTAAAGGTGAATATGCAACTAAT
58662856 ATGATTTTTA
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 97 1.00
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.32
Consensus pattern (100 bp):
TGGGTTTCAATAACACACACTTCCACACATTCATCATCTTAGTAGGCATAAAAAAATATTTTGAC
ATTTCCTCAAGTTAAAGGTGAATATGCAACTAATG
Found at i:58663888 original size:24 final size:24
Alignment explanation
Indices: 58663821--58663889 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
58663811 ACAAAGATTT
*
58663821 TTATACTAATAAATGCCAAATATA
1 TTATACTAATAAATGCTAAATATA
* *
58663845 TTATGCTAATAAATGTTAAATATA
1 TTATACTAATAAATGCTAAATATA
* *
58663869 TTTTACTAATAAATACTAAAT
1 TTATACTAATAAATGCTAAAT
58663890 TTTCTAGAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (24 bp):
TTATACTAATAAATGCTAAATATA
Found at i:58666168 original size:24 final size:24
Alignment explanation
Indices: 58666148--58666247 Score: 137
Period size: 24 Copynumber: 4.2 Consensus size: 24
58666138 AAGAAATAAA
* * **
58666148 AAATATTTTATAATAATAAATGTT
1 AAATATATTATACTAATAAATACT
* *
58666172 AAATATATTATGCTAATAAGTACT
1 AAATATATTATACTAATAAATACT
58666196 AAATATATTATACTAATAAATACT
1 AAATATATTATACTAATAAATACT
*
58666220 AAATATATTATACTAATAAATTCT
1 AAATATATTATACTAATAAATACT
58666244 AAAT
1 AAAT
58666248 CTTCTAAAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 67 1.00
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:58666211 original size:14 final size:14
Alignment explanation
Indices: 58666192--58666235 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
58666182 TGCTAATAAG
58666192 TACTAAATATATTA
1 TACTAAATATATTA
58666206 TACT-AATA-A--A
1 TACTAAATATATTA
58666216 TACTAAATATATTA
1 TACTAAATATATTA
58666230 TACTAA
1 TACTAA
58666236 TAAATTCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
10 5 0.19
11 4 0.15
12 2 0.08
13 4 0.15
14 11 0.42
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (14 bp):
TACTAAATATATTA
Found at i:58666521 original size:49 final size:49
Alignment explanation
Indices: 58666449--58666591 Score: 182
Period size: 49 Copynumber: 2.9 Consensus size: 49
58666439 GATAAGTCTG
* * *
58666449 CCTACATCCACGGTGC-AGTTATTCTGCAAAATATAGTACAATAAAGCTA
1 CCTACATCCATGGTTCTA-TTATTCTGAAAAATATAGTACAATAAAGCTA
*
58666498 CCTACATCCATGGTTCTATTATTCTGAAAAATATAGTACAATAAAGCTG
1 CCTACATCCATGGTTCTATTATTCTGAAAAATATAGTACAATAAAGCTA
* * * *
58666547 TCTACAACCATGGTGT-TGTTATTTTGAAAAATATAGTACAATAAA
1 CCTACATCCATGGT-TCTATTATTCTGAAAAATATAGTACAATAAA
58666592 ACTTCCTTGA
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
49 82 0.98
50 2 0.02
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.31
Consensus pattern (49 bp):
CCTACATCCATGGTTCTATTATTCTGAAAAATATAGTACAATAAAGCTA
Found at i:58666986 original size:22 final size:21
Alignment explanation
Indices: 58666960--58667013 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
58666950 ATGAAACCAG
58666960 AAAGGAGAAAACAAAAGAAGAA
1 AAAGGAGAAAAC-AAAGAAGAA
* * *
58666982 AAAGGAAGAAATCAAATAAGAG
1 AAAGG-AGAAAACAAAGAAGAA
58667004 AAA-GAGAAAA
1 AAAGGAGAAAA
58667014 TAGACTTGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 5 0.19
21 1 0.04
22 15 0.56
23 6 0.22
ACGTcount: A:0.70, C:0.04, G:0.22, T:0.04
Consensus pattern (21 bp):
AAAGGAGAAAACAAAGAAGAA
Found at i:58667554 original size:15 final size:15
Alignment explanation
Indices: 58667534--58667564 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
58667524 GTTAGAAAAC
58667534 TCCATTTTTTAGGTT
1 TCCATTTTTTAGGTT
58667549 TCCATTTTTTAGGTT
1 TCCATTTTTTAGGTT
58667564 T
1 T
58667565 TAAGGTTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.61
Consensus pattern (15 bp):
TCCATTTTTTAGGTT
Found at i:58673105 original size:42 final size:43
Alignment explanation
Indices: 58672869--58673125 Score: 234
Period size: 43 Copynumber: 6.0 Consensus size: 43
58672859 AAACAGTTTT
* ** * *
58672869 ATAAGTTGTGTAATCAACAAAACTATCCTCATGAGTTTAAGTG
1 ATAAGTTGTGTAATCAACAAAGCTCCCCTCGTGAGCTTAAGTG
* * * *
58672912 ATAAGTTGTGTAATCAGCGAAA-CTCCCTTCGTTAACTTAAGTG
1 ATAAGTTGTGTAATCAAC-AAAGCTCCCCTCGTGAGCTTAAGTG
* * ** * * *
58672955 ATAAGCTGTGTAACCAATGAAGCTTCCCTCATGAGCTTAAATG
1 ATAAGTTGTGTAATCAACAAAGCTCCCCTCGTGAGCTTAAGTG
* * ** *
58672998 ATAAGTTGAGTAATTAGTAAAGCT-CCCTCGTGAACTTAAGTG
1 ATAAGTTGTGTAATCAACAAAGCTCCCCTCGTGAGCTTAAGTG
** **
58673040 ATAAACTGTGTAATCAGTAAAGCTCCCCTCGTGAGCTTAAGTG
1 ATAAGTTGTGTAATCAACAAAGCTCCCCTCGTGAGCTTAAGTG
*
58673083 ATAAGTTGTGT-ATCAACCAAGCTCCCCAT-GTGAGCTTAAGTG
1 ATAAGTTGTGTAATCAACAAAGCTCCCC-TCGTGAGCTTAAGTG
58673125 A
1 A
58673126 CAACCTATGT
Statistics
Matches: 172, Mismatches: 38, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
42 64 0.37
43 105 0.61
44 3 0.02
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (43 bp):
ATAAGTTGTGTAATCAACAAAGCTCCCCTCGTGAGCTTAAGTG
Found at i:58673121 original size:85 final size:85
Alignment explanation
Indices: 58672895--58673125 Score: 270
Period size: 85 Copynumber: 2.7 Consensus size: 85
58672885 ACAAAACTAT
* *
58672895 CCTCATGAGTTTAAGTGATAAGTTGTGTAATCAGCGAAA-CTCCCTTCGTTAACTTAAGTGATAA
1 CCTCATGAGCTTAAGTGATAAGTTGTGTAATCAGC-AAAGCTCCC-TCGTGAACTTAAGTGATAA
* * *
58672959 GCTGTGTAACCAATGAAGCTTC
64 ACTGTGTAACCAATAAAGCTCC
* * * *
58672981 CCTCATGAGCTTAAATGATAAGTTGAGTAATTAGTAAAGCTCCCTCGTGAACTTAAGTGATAAAC
1 CCTCATGAGCTTAAGTGATAAGTTGTGTAATCAGCAAAGCTCCCTCGTGAACTTAAGTGATAAAC
* *
58673046 TGTGTAATCAGTAAAGCTCC
66 TGTGTAACCAATAAAGCTCC
* * * *
58673066 CCTCGTGAGCTTAAGTGATAAGTTGTGT-ATCAACCAAGCTCCC-CATGTGAGCTTAAGTGA
1 CCTCATGAGCTTAAGTGATAAGTTGTGTAATCAGCAAAGCTCCCTC--GTGAACTTAAGTGA
58673126 CAACCTATGT
Statistics
Matches: 123, Mismatches: 19, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
83 1 0.01
84 11 0.09
85 76 0.62
86 35 0.28
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (85 bp):
CCTCATGAGCTTAAGTGATAAGTTGTGTAATCAGCAAAGCTCCCTCGTGAACTTAAGTGATAAAC
TGTGTAACCAATAAAGCTCC
Found at i:58673137 original size:42 final size:42
Alignment explanation
Indices: 58673059--58673163 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 42
58673049 GTAATCAGTA
* ** *
58673059 AAGCTCCCC-TCGTGAGCTTAAGTGATAAGTTGTGTATCAACC
1 AAGCTCCCCAT-GTGAGCTTAAGTGACAACCTATGTATCAACC
* * *
58673101 AAGCTCCCCATGTGAGCTTAAGTGACAACCTATGTATTAGCG
1 AAGCTCCCCATGTGAGCTTAAGTGACAACCTATGTATCAACC
*
58673143 AAGCTCCCCATGCGAGCTTAA
1 AAGCTCCCCATGTGAGCTTAA
58673164 ATGATTGTGC
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
42 53 0.98
43 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (42 bp):
AAGCTCCCCATGTGAGCTTAAGTGACAACCTATGTATCAACC
Found at i:58676493 original size:24 final size:25
Alignment explanation
Indices: 58676455--58676501 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
58676445 TAAAAAATAA
*
58676455 AAATATAGTTCAAAAGATAAAAACC
1 AAATATAGTTCAAAAAATAAAAACC
*
58676480 AAATA-AGTTTAAAAAATAAAAA
1 AAATATAGTTCAAAAAATAAAAA
58676502 TAAACATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.21
Consensus pattern (25 bp):
AAATATAGTTCAAAAAATAAAAACC
Found at i:58676502 original size:6 final size:6
Alignment explanation
Indices: 58676491--58676524 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
58676481 AATAAGTTTA
*
58676491 AAAAAT AAAAAT AAACAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
58676525 CAAATAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:58676510 original size:25 final size:24
Alignment explanation
Indices: 58676447--58676510 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 24
58676437 AACAACCATA
*
58676447 AAAAATAAAAATATAGTTCAAAAGAT
1 AAAAAT-AAAATA-AGTTCAAAAAAT
** *
58676473 AAAAACCAAATAAGTTTAAAAAAT
1 AAAAATAAAATAAGTTCAAAAAAT
58676497 AAAAATAAACATAA
1 AAAAATAAA-ATAA
58676511 AAATAAAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
24 17 0.55
25 9 0.29
26 5 0.16
ACGTcount: A:0.69, C:0.06, G:0.05, T:0.20
Consensus pattern (24 bp):
AAAAATAAAATAAGTTCAAAAAAT
Found at i:58687685 original size:23 final size:23
Alignment explanation
Indices: 58687656--58687820 Score: 134
Period size: 23 Copynumber: 7.2 Consensus size: 23
58687646 GGTAAGTTAC
* *
58687656 CTGTGAAGCCTTTATGGCGCATT
1 CTGTGAAGCCTTTGTGGCGTATT
**
58687679 CTGTGAAGCCTTTGTGATGTATT
1 CTGTGAAGCCTTTGTGGCGTATT
* * * *
58687702 TTGTGGAGCATTTGTGGTGTATT
1 CTGTGAAGCCTTTGTGGCGTATT
* * * *
58687725 CTGTGAAACATTTATGGCATATT
1 CTGTGAAGCCTTTGTGGCGTATT
* * *
58687748 CTGTGGAGACTTTGTGGCATATT
1 CTGTGAAGCCTTTGTGGCGTATT
*
58687771 CTGT-AGAGCCTTTGTGGCCTATT
1 CTGTGA-AGCCTTTGTGGCGTATT
* * **
58687794 CTATGAAGCCTTTATGGTATATT
1 CTGTGAAGCCTTTGTGGCGTATT
58687817 CTGT
1 CTGT
58687821 AACTCCTAAA
Statistics
Matches: 113, Mismatches: 27, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
23 112 0.99
24 1 0.01
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.41
Consensus pattern (23 bp):
CTGTGAAGCCTTTGTGGCGTATT
Found at i:58687785 original size:69 final size:69
Alignment explanation
Indices: 58687656--58687820 Score: 186
Period size: 69 Copynumber: 2.4 Consensus size: 69
58687646 GGTAAGTTAC
** * ** * * **
58687656 CTGTGAAGCCTTTATGGCGCATTCTGTGAAGCCTTTGTGATGTATTTTGTGGAGCATTTGTGGTG
1 CTGTGAAGCCTTTATGGCATATTCTGTGAAGACTTTGTGACATATTCTGTAGAGCATTTGTGGCC
58687721 TATT
66 TATT
* * * * *
58687725 CTGTGAAACATTTATGGCATATTCTGTGGAGACTTTGTGGCATATTCTGTAGAGCCTTTGTGGCC
1 CTGTGAAGCCTTTATGGCATATTCTGTGAAGACTTTGTGACATATTCTGTAGAGCATTTGTGGCC
58687790 TATT
66 TATT
* *
58687794 CTATGAAGCCTTTATGGTATATTCTGT
1 CTGTGAAGCCTTTATGGCATATTCTGT
58687821 AACTCCTAAA
Statistics
Matches: 78, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
69 78 1.00
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.41
Consensus pattern (69 bp):
CTGTGAAGCCTTTATGGCATATTCTGTGAAGACTTTGTGACATATTCTGTAGAGCATTTGTGGCC
TATT
Found at i:58697170 original size:17 final size:17
Alignment explanation
Indices: 58697148--58697200 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
58697138 CTAAAATTTT
58697148 AACATATTAAACAATAA
1 AACATATTAAACAATAA
* *
58697165 AAC--A-TAGACAA-GA
1 AACATATTAAACAATAA
*
58697178 GACATATTAAACAATAA
1 AACATATTAAACAATAA
58697195 AACATA
1 AACATA
58697201 GACAAGAGAT
Statistics
Matches: 26, Mismatches: 6, Indels: 8
0.65 0.15 0.20
Matches are distributed among these distances:
13 3 0.12
14 6 0.23
15 2 0.08
16 6 0.23
17 9 0.35
ACGTcount: A:0.62, C:0.13, G:0.06, T:0.19
Consensus pattern (17 bp):
AACATATTAAACAATAA
Found at i:58697185 original size:30 final size:30
Alignment explanation
Indices: 58697149--58697209 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
58697139 TAAAATTTTA
58697149 ACATATTAAACAATAAAACATAGACAAGAG
1 ACATATTAAACAATAAAACATAGACAAGAG
58697179 ACATATTAAACAATAAAACATAGACAAGAG
1 ACATATTAAACAATAAAACATAGACAAGAG
58697209 A
1 A
58697210 TAGAAATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.61, C:0.13, G:0.10, T:0.16
Consensus pattern (30 bp):
ACATATTAAACAATAAAACATAGACAAGAG
Found at i:58697224 original size:30 final size:30
Alignment explanation
Indices: 58697155--58697226 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
58697145 TTTAACATAT
* *
58697155 TAAACAATAAAACATAGACAAGAGACATAT
1 TAAACAATAAAACATAGACAAGAGACAAAA
*
58697185 TAAACAATAAAACATAGACAAGAGATAGAAA
1 TAAACAATAAAACATAGACAAGAGACA-AAA
*
58697216 TATA-AATAAAA
1 TAAACAATAAAA
58697227 AGTAAGCCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 33 0.89
31 4 0.11
ACGTcount: A:0.64, C:0.10, G:0.10, T:0.17
Consensus pattern (30 bp):
TAAACAATAAAACATAGACAAGAGACAAAA
Found at i:58698860 original size:11 final size:11
Alignment explanation
Indices: 58698822--58698889 Score: 86
Period size: 11 Copynumber: 6.2 Consensus size: 11
58698812 TAAATCCTTT
*
58698822 CTCTC-AATTT
1 CTCTCAAATTC
58698832 CTCTCTAATATT-
1 CTCTC-AA-ATTC
58698844 CTCTCAAATTC
1 CTCTCAAATTC
58698855 CTCTCAAATTC
1 CTCTCAAATTC
*
58698866 CTCTCAAGTTC
1 CTCTCAAATTC
58698877 CTCTCAAATTC
1 CTCTCAAATTC
58698888 CT
1 CT
58698890 ATTTAAAATA
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
10 8 0.15
11 35 0.67
12 6 0.12
13 3 0.06
ACGTcount: A:0.24, C:0.34, G:0.01, T:0.41
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:58700719 original size:18 final size:18
Alignment explanation
Indices: 58700696--58700738 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
58700686 TGCCAGGTGC
* *
58700696 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
58700714 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
58700732 GTTTCCT
1 GTATCCT
58700739 TTTTCTAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:58701004 original size:21 final size:21
Alignment explanation
Indices: 58700979--58701037 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
58700969 CCAACACCGA
58700979 CAACCAG-ATCCCCTACCGGAG
1 CAACCAGAATCCCC-ACCGGAG
* *
58701000 GAACCAGAATCCCCGCCGGAG
1 CAACCAGAATCCCCACCGGAG
* *
58701021 CAACCACAACCCCCACC
1 CAACCAGAATCCCCACC
58701038 AGAAGTTGGA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 25 0.81
22 6 0.19
ACGTcount: A:0.31, C:0.47, G:0.17, T:0.05
Consensus pattern (21 bp):
CAACCAGAATCCCCACCGGAG
Found at i:58701209 original size:32 final size:28
Alignment explanation
Indices: 58701165--58701245 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 28
58701155 TTATCTGATG
* * *
58701165 TAATAAAATAGAAATTCTTCTATATTATT
1 TAATATAATAGAAATTCTTATACATT-TT
58701194 TCATATACTAATAGAAATTTACTTATACATTTT
1 T-A-ATA-TAATAGAAA-TT-CTTATACATTTT
58701227 TAATATAATAGAAATTCTT
1 TAATATAATAGAAATTCTT
58701246 TTAAATAAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
28 3 0.07
29 3 0.07
30 10 0.23
31 6 0.14
32 9 0.20
33 5 0.11
34 8 0.18
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (28 bp):
TAATATAATAGAAATTCTTATACATTTT
Found at i:58704650 original size:126 final size:126
Alignment explanation
Indices: 58704425--58705093 Score: 1140
Period size: 126 Copynumber: 5.3 Consensus size: 126
58704415 CCAAACATGC
* *
58704425 GCTACTGTAGCAAAAGCGCGTTCACGTGGGAGCTTCTTTCAGTACTTCCGCTGACAAAGCATCCT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
*
58704490 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCAGGA
66 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
*
58704551 GCTACTGTAGCAAAAGCGCGTCCACGTGAGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
* *
58704616 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTATTCGAAATTATTTTTTTAGGA
66 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
*
58704677 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTAACAAAGCATCCT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
* * *
58704742 GCTTAAAGCGTTTTTGACACTATTTGCTTAGAAAAGTCTACTCGAAATTATTTTTTCAAGA
66 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
* *
58704803 GCTACTGTAGCAAAAGCGCGTCCATGTGGGACCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
* *
58704868 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTATTCGAAATTATTTTTTTAGGA
66 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
* * * **
58704929 GCTACTGTAGCGAAAGCGCGTCCACATGAGAGCTTCTTTCAAAACTTCTGCTGACAAAGCATCCT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
*
58704994 GCTTAAAGCATTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
66 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
* *
58705055 GCTACTGTAGCAAAAGTGCGTCCACCTGGGAGCTTCTTT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTT
58705094 AAATTAACAA
Statistics
Matches: 508, Mismatches: 35, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 508 1.00
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.32
Consensus pattern (126 bp):
GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCT
GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
Found at i:58705349 original size:96 final size:96
Alignment explanation
Indices: 58705115--58705348 Score: 335
Period size: 95 Copynumber: 2.4 Consensus size: 96
58705105 TAATTTAATT
* *
58705115 AAGTAACCCTAAACCCTAACTTATTTGAGTTTTTACTTAAAAACCCTAAACTCTAAACCCTAACC
1 AAGTAACCCTAAACCCTAATTTATTTGA-TTTTTACTTAAAAACCCTAAACACTAAACCCTAACC
*
58705180 TAATTTTATAAAACATTATAATTAATTTACTC
65 TAATTTTATAAAACATTATAATTAAATTACTC
* * *
58705212 AAGTAACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTTAACACTAAACCCTAATCT
1 AAGTAACCCTAAACCCTAATTTATTTGATTTTTACTTAAAAACCCTAAACACTAAACCCTAACCT
* ** *
58705277 GATTTT-TAAAATTTTTTAATTAAATTACTC
66 AATTTTATAAAACATTATAATTAAATTACTC
* * *
58705307 AAGTAAACCTAAACCCTAATTTAATTGATTTTTTCTTAAAAA
1 AAGTAACCCTAAACCCTAATTTATTTGATTTTTACTTAAAAA
58705349 ATAATAAACA
Statistics
Matches: 124, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
95 59 0.48
96 38 0.31
97 27 0.22
ACGTcount: A:0.39, C:0.20, G:0.03, T:0.38
Consensus pattern (96 bp):
AAGTAACCCTAAACCCTAATTTATTTGATTTTTACTTAAAAACCCTAAACACTAAACCCTAACCT
AATTTTATAAAACATTATAATTAAATTACTC
Found at i:58705370 original size:95 final size:95
Alignment explanation
Indices: 58705115--58705394 Score: 278
Period size: 95 Copynumber: 2.9 Consensus size: 95
58705105 TAATTTAATT
* * * * ** * *
58705115 AAGTAACCCTAAACCCTAACTTATTTGAGTTTTTACTTAAAAACCCTAAACTCTAAACCCTAA-C
1 AAGTAAACCTAAACCCTAATTTAATTGA-TTTTTCCTTAAAAACAATAAACACGAAACCCTAATC
* *
58705179 CTAATTTT-ATAAAACATTATAATTAATTTACTC
65 C-AATTTTGA-AAAA-TTTATAATTAAATTACTC
* * ** * * *
58705212 AAGTAACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTTAACACTAAACCCTAATCT
1 AAGTAAACCTAAACCCTAATTTAATTGATTTTTCCTTAAAAACAATAAACACGAAACCCTAATCC
* * * *
58705277 GATTTTTAAAATTTTTTAATTAAATTACTC
66 AATTTTGAAAAATTTATAATTAAATTACTC
* * *
58705307 AAGTAAACCTAAACCCTAATTTAATTGATTTTTTCTTAAAAAATAATAAACACGAAA-CTTAATC
1 AAGTAAACCTAAACCCTAATTTAATTGATTTTTCCTT-AAAAACAATAAACACGAAACCCTAATC
58705371 CAATTTTGAAAAATTTATAATTAA
65 CAATTTTGAAAAATTTATAATTAA
58705395 TTTAATTGAC
Statistics
Matches: 156, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
95 74 0.47
96 53 0.34
97 29 0.19
ACGTcount: A:0.41, C:0.18, G:0.04, T:0.37
Consensus pattern (95 bp):
AAGTAAACCTAAACCCTAATTTAATTGATTTTTCCTTAAAAACAATAAACACGAAACCCTAATCC
AATTTTGAAAAATTTATAATTAAATTACTC
Found at i:58706770 original size:16 final size:16
Alignment explanation
Indices: 58706749--58706779 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
58706739 GATTACAAAT
*
58706749 TTTTTTGGAATTTCGA
1 TTTTTTGAAATTTCGA
58706765 TTTTTTGAAATTTCG
1 TTTTTTGAAATTTCG
58706780 GTTAACGGCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.06, G:0.16, T:0.58
Consensus pattern (16 bp):
TTTTTTGAAATTTCGA
Found at i:58710316 original size:68 final size:68
Alignment explanation
Indices: 58710236--58710377 Score: 266
Period size: 68 Copynumber: 2.1 Consensus size: 68
58710226 TGACATTGTT
58710236 TATATCTGAAATATTACGATTGAATTGGAGATAAAATGGATTGAAATGTAAACTGTTATACAATT
1 TATATCTGAAATATTACGATTGAATTGGAGATAAAATGGATTGAAATGTAAACTGTTATACAATT
58710301 ACG
66 ACG
* *
58710304 TATATCTGAAATATTACGATTGAATTGGTGATAAAATGGATTGAAATGTAAACTGTTATACGATT
1 TATATCTGAAATATTACGATTGAATTGGAGATAAAATGGATTGAAATGTAAACTGTTATACAATT
58710369 ACG
66 ACG
58710372 TATATC
1 TATATC
58710378 AAGCCTGAAT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 72 1.00
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (68 bp):
TATATCTGAAATATTACGATTGAATTGGAGATAAAATGGATTGAAATGTAAACTGTTATACAATT
ACG
Found at i:58711019 original size:13 final size:13
Alignment explanation
Indices: 58711001--58711044 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
58710991 TAAAGGTGTA
58711001 ATATGAAATGGTT
1 ATATGAAATGGTT
*
58711014 ATATGAGATGGTT
1 ATATGAAATGGTT
*
58711027 AT-TCGAAATGTTT
1 ATAT-GAAATGGTT
58711040 ATATG
1 ATATG
58711045 GATAGATATG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 1 0.04
13 24 0.92
14 1 0.04
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.41
Consensus pattern (13 bp):
ATATGAAATGGTT
Found at i:58715010 original size:40 final size:38
Alignment explanation
Indices: 58714889--58715026 Score: 109
Period size: 40 Copynumber: 3.5 Consensus size: 38
58714879 AACTTTGAGT
* *
58714889 CGATGAGACACT-GGATGTCAATTTATTACTTCAAATTTATT
1 CGATGAGACACTAGG-TGTC-ATTTA-TACTTCGAA-TTATC
* * * ** *
58714930 CGATGAGGCACTAGGTGCCAATT-TACTTCGGTTTAAC
1 CGATGAGACACTAGGTGTCATTTATACTTCGAATTATC
*
58714967 CGATGAGACACTAAGTGTCAGTTTACTACTTCGAATTATC
1 CGATGAGACACTAGGTGTCA-TTTA-TACTTCGAATTATC
* *
58715007 CGATGAGGCACTGGGTGTCA
1 CGATGAGACACTAGGTGTCA
58715027 AACTGGTGTG
Statistics
Matches: 75, Mismatches: 18, Indels: 9
0.74 0.18 0.09
Matches are distributed among these distances:
37 20 0.27
38 8 0.11
40 31 0.41
41 14 0.19
42 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.32
Consensus pattern (38 bp):
CGATGAGACACTAGGTGTCATTTATACTTCGAATTATC
Found at i:58717001 original size:2 final size:2
Alignment explanation
Indices: 58716996--58717035 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
58716986 TCCACAAACT
58716996 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58717036 AATGACCATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58717315 original size:23 final size:23
Alignment explanation
Indices: 58717289--58717334 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
58717279 ATACAATTAC
58717289 ATGCTCAAGTTATAGTAAATGAT
1 ATGCTCAAGTTATAGTAAATGAT
58717312 ATGCTCAAGTTATAGTAAATGAT
1 ATGCTCAAGTTATAGTAAATGAT
58717335 GTTATGCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (23 bp):
ATGCTCAAGTTATAGTAAATGAT
Found at i:58717626 original size:58 final size:58
Alignment explanation
Indices: 58717564--58717679 Score: 205
Period size: 58 Copynumber: 2.0 Consensus size: 58
58717554 TGCAATTTAA
*
58717564 TACATTGTCACTAGTGATCATTCAATTCAAATTCACATCTCATAAAATTGTTTCAAGG
1 TACATTGTCACTAGTGATCATTCAATTCAAATTCACATATCATAAAATTGTTTCAAGG
* *
58717622 TACATTGTCACTAGTGATCATTCAATTTAAATTCGCATATCATAAAATTGTTTCAAGG
1 TACATTGTCACTAGTGATCATTCAATTCAAATTCACATATCATAAAATTGTTTCAAGG
58717680 AATAGCTTAC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.37
Consensus pattern (58 bp):
TACATTGTCACTAGTGATCATTCAATTCAAATTCACATATCATAAAATTGTTTCAAGG
Found at i:58721694 original size:48 final size:48
Alignment explanation
Indices: 58721638--58721734 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
58721628 CGATTGTCCC
58721638 TTCTGTTCACTGATGATTGATCCCAAGTGTTATTTTCATTTTTAAAAA
1 TTCTGTTCACTGATGATTGATCCCAAGTGTTATTTTCATTTTTAAAAA
58721686 TTCTGTTCACTGATGATTGATCCCAAGTGTTATTTTCATTTTTAAAAA
1 TTCTGTTCACTGATGATTGATCCCAAGTGTTATTTTCATTTTTAAAAA
58721734 T
1 T
58721735 CCTCTCGATG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.46
Consensus pattern (48 bp):
TTCTGTTCACTGATGATTGATCCCAAGTGTTATTTTCATTTTTAAAAA
Found at i:58735957 original size:12 final size:12
Alignment explanation
Indices: 58735940--58735964 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58735930 GGTGTTCATT
58735940 CGGTTAACCGAC
1 CGGTTAACCGAC
58735952 CGGTTAACCGAC
1 CGGTTAACCGAC
58735964 C
1 C
58735965 CGAAATAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:58736159 original size:27 final size:27
Alignment explanation
Indices: 58736121--58736223 Score: 161
Period size: 27 Copynumber: 3.8 Consensus size: 27
58736111 TTTGTTTAAA
*
58736121 AATTAACCGAATTACCCGAATTACCCG
1 AATTAACCGAATTAACCGAATTACCCG
*
58736148 AATTACCCGAATTAACCGAATTACCCG
1 AATTAACCGAATTAACCGAATTACCCG
*
58736175 AATTACCCGAATTAACCGAATTACCCG
1 AATTAACCGAATTAACCGAATTACCCG
* *
58736202 AATTAACCAAATTAACCAAATT
1 AATTAACCGAATTAACCGAATT
58736224 GAATCACTAC
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 71 1.00
ACGTcount: A:0.41, C:0.27, G:0.09, T:0.23
Consensus pattern (27 bp):
AATTAACCGAATTAACCGAATTACCCG
Found at i:58736207 original size:18 final size:18
Alignment explanation
Indices: 58736121--58736223 Score: 143
Period size: 18 Copynumber: 5.7 Consensus size: 18
58736111 TTTGTTTAAA
58736121 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
*
58736139 AATTACCCGAATTACCCG
1 AATTAACCGAATTACCCG
58736157 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
* *
58736175 AATTACCCGAATTAACCG
1 AATTAACCGAATTACCCG
* * *
58736193 AATTACCCGAATTAACCA
1 AATTAACCGAATTACCCG
*
58736211 AATTAACCAAATT
1 AATTAACCGAATT
58736224 GAATCACTAC
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 78 1.00
ACGTcount: A:0.41, C:0.27, G:0.09, T:0.23
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:58736223 original size:9 final size:9
Alignment explanation
Indices: 58736121--58736206 Score: 145
Period size: 9 Copynumber: 9.6 Consensus size: 9
58736111 TTTGTTTAAA
*
58736121 AATTAACCG
1 AATTACCCG
58736130 AATTACCCG
1 AATTACCCG
58736139 AATTACCCG
1 AATTACCCG
58736148 AATTACCCG
1 AATTACCCG
*
58736157 AATTAACCG
1 AATTACCCG
58736166 AATTACCCG
1 AATTACCCG
58736175 AATTACCCG
1 AATTACCCG
*
58736184 AATTAACCG
1 AATTACCCG
58736193 AATTACCCG
1 AATTACCCG
58736202 AATTA
1 AATTA
58736207 ACCAAATTAA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 72 1.00
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:58738080 original size:7 final size:7
Alignment explanation
Indices: 58738068--58738094 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
58738058 ATTAAGTAAG
58738068 AAAATTT
1 AAAATTT
58738075 AAAATTT
1 AAAATTT
58738082 AAAATTT
1 AAAATTT
58738089 AAAATT
1 AAAATT
58738095 AAACTATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAAATTT
Found at i:58739905 original size:20 final size:20
Alignment explanation
Indices: 58739880--58739920 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
58739870 ATTCAGAAGA
58739880 ATTTCACACATATATGTTAT
1 ATTTCACACATATATGTTAT
58739900 ATTTCACACATATATGTTAT
1 ATTTCACACATATATGTTAT
58739920 A
1 A
58739921 AACACAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.44
Consensus pattern (20 bp):
ATTTCACACATATATGTTAT
Found at i:58743010 original size:28 final size:28
Alignment explanation
Indices: 58742979--58743037 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
58742969 TAGTACTGTA
58742979 TGGGCCTTAGCCCAATACAGTAACAGTG
1 TGGGCCTTAGCCCAATACAGTAACAGTG
**
58743007 TGGGCCTTAGCGTAATACAGTAACAGTG
1 TGGGCCTTAGCCCAATACAGTAACAGTG
58743035 TGG
1 TGG
58743038 TAATGCAACC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (28 bp):
TGGGCCTTAGCCCAATACAGTAACAGTG
Found at i:58743178 original size:26 final size:26
Alignment explanation
Indices: 58743136--58743185 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
58743126 ACCAATATTG
*
58743136 CAGCAAAGCTGCCAGTAAAAGTATCA
1 CAGCAAAGCTGACAGTAAAAGTATCA
* *
58743162 CAGCAAAGCTGATAGTAACAGTAT
1 CAGCAAAGCTGACAGTAAAAGTAT
58743186 ATGTGGCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (26 bp):
CAGCAAAGCTGACAGTAAAAGTATCA
Found at i:58744299 original size:19 final size:18
Alignment explanation
Indices: 58744275--58744321 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 18
58744265 GTTCTCAGTC
58744275 AAAAGGAAAACA-AAATAAT
1 AAAAGGAAAA-ATAAA-AAT
58744294 AAAAGGTAAAAATAAAAAT
1 AAAAGG-AAAAATAAAAAT
58744313 AGAAAGGAA
1 A-AAAGGAA
58744322 GAGAAGAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.72, C:0.02, G:0.15, T:0.11
Consensus pattern (18 bp):
AAAAGGAAAAATAAAAAT
Found at i:58746106 original size:25 final size:25
Alignment explanation
Indices: 58746077--58746142 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
58746067 ATCGAGTCCA
*
58746077 AGCTCGTATGAGCTTACCGATTTAC
1 AGCTCGTATGAGCATACCGATTTAC
* *
58746102 GGCTCGTGA-GAGCATACCGATTTAT
1 AGCTCGT-ATGAGCATACCGATTTAC
58746127 AGCTCGTATGAGCATA
1 AGCTCGTATGAGCATA
58746143 AACGTACAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
24 1 0.03
25 33 0.94
26 1 0.03
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (25 bp):
AGCTCGTATGAGCATACCGATTTAC
Found at i:58747933 original size:37 final size:35
Alignment explanation
Indices: 58747881--58747951 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 35
58747871 ATTTCAAAAA
*
58747881 TAATATTATTTTAATAGT-TTAGTATTTAATTTAATG
1 TAATATTATCTTAATAGTATT-GTA-TTAATTTAATG
*
58747917 TAATACTTATCTTAATAGTATTTTATTAATTTAAT
1 TAATA-TTATCTTAATAGTATTGTATTAATTTAAT
58747952 ATTAAAGTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 15 0.48
37 14 0.45
38 2 0.06
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.55
Consensus pattern (35 bp):
TAATATTATCTTAATAGTATTGTATTAATTTAATG
Found at i:58748599 original size:21 final size:21
Alignment explanation
Indices: 58748555--58748599 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
58748545 ATTTGAGACA
* *
58748555 TTTATTTTTCTTCTTCTTTTC
1 TTTATTTTTCTTATTCTTTCC
58748576 TTTATTTTTCTTATT-TTGTCC
1 TTTATTTTTCTTATTCTT-TCC
58748597 TTT
1 TTT
58748600 TTGGGCCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.07, C:0.16, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTATTTTTCTTATTCTTTCC
Found at i:58749247 original size:20 final size:20
Alignment explanation
Indices: 58749213--58749250 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
58749203 TTTTTTTAGT
*
58749213 AATTTTAAAGGAAAGTTTAA
1 AATTTTAAAAGAAAGTTTAA
*
58749233 AATTTTAAAATAAAGTTT
1 AATTTTAAAAGAAAGTTT
58749251 TGATTTCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (20 bp):
AATTTTAAAAGAAAGTTTAA
Found at i:58749401 original size:148 final size:147
Alignment explanation
Indices: 58749005--58749427 Score: 541
Period size: 154 Copynumber: 2.8 Consensus size: 147
58748995 AGTTTTGATT
* *
58749005 TTTTTTTAAAGAGAAAGTTTAGATTTT-AACAAAT-AAAA-AT-TTGTTTTTATAGTTATTTTAA
1 TTTTTTTAAAGAGAAAGTTTAGATTTTGAA-AAATAAAAATATATTTTTTTTA-AGTAATTTTAA
* * * * * *
58749066 AGGAAATTTTAAATTTTTAAAACAAATTTTTTTATTTTTTTTCAACTATTTCAAAGTAAAAGCTT
64 AGGAAAGTTTAAAATTTTAAAATAAA-GTTTTGA-TTTTTTTCAACTATTTCAAAATAAAAGCTT
* *
58749131 TAATTTTTAAGAAAAATAGTA
127 GAATCTTTAAGAAAAATAGTA
*
58749152 TTTTTTTCAAAAAAAAGGAGAAAGTTTAGTTTTTGAAAAATAAAAATATATTTTTTTT-AGTAAT
1 TTTTTTT------AAA-GAGAAAGTTTAGATTTTGAAAAATAAAAATATATTTTTTTTAAGTAAT
*
58749216 TTTAAAGGAAAGTTTAAAATTTTAAAATAAAGTTTTGATTTCTTTTCAACTACTTCAAAATAAAA
59 TTTAAAGGAAAGTTTAAAATTTTAAAATAAAGTTTTGATTT-TTTTCAACTATTTCAAAATAAAA
* *
58749281 GCTTGCATCTTTAAGAAAAATAGTG
123 GCTTGAATCTTTAAGAAAAATAGTA
* *
58749306 TTTTTTTAAAGAGAAAATTTAGATTTTGAAAAATAAAAATATATTTTTTTTAAGTCATTTTAAAG
1 TTTTTTTAAAGAGAAAGTTTAGATTTTGAAAAATAAAAATATATTTTTTTTAAGTAATTTTAAAG
* *
58749371 GAAAGTTTAAAATTTTAAAATAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAA
66 GAAAGTTTAAAATTTTAAAATAAAGTTTTGATTTTTTTCAACTATTTCAAAATAAAA
58749428 TTTTGATTTT
Statistics
Matches: 243, Mismatches: 20, Indels: 26
0.84 0.07 0.09
Matches are distributed among these distances:
147 66 0.27
148 49 0.20
153 6 0.02
154 74 0.30
155 39 0.16
156 2 0.01
157 7 0.03
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.44
Consensus pattern (147 bp):
TTTTTTTAAAGAGAAAGTTTAGATTTTGAAAAATAAAAATATATTTTTTTTAAGTAATTTTAAAG
GAAAGTTTAAAATTTTAAAATAAAGTTTTGATTTTTTTCAACTATTTCAAAATAAAAGCTTGAAT
CTTTAAGAAAAATAGTA
Found at i:58749447 original size:147 final size:145
Alignment explanation
Indices: 58749005--58749493 Score: 519
Period size: 147 Copynumber: 3.3 Consensus size: 145
58748995 AGTTTTGATT
* * *
58749005 TTTTTTTAAAGAGAAAGTTTAGATTTT-AACAAAT-AAAA-AT-TTGTTTTTATAGTTATTTTAA
1 TTTTTTTAAAGAGAAAATTTAGATTTTGAA-AAATAAAAATATATTTTTTTTA-AGTAATTTTAA
* * * * *
58749066 AGGAAATTTTAAATTTTTAAAACAAATTTTTTTATTTTTTTTCAACTATTTCAAAGTAAAAGCTT
64 AGGAAAGTTTAAAATTTTAAAATAAA-GTTTTGATTTTTTTT-AACTATTTCAAA-TAAAA-CTT
* *
58749131 TAATTTTTAAGAAAAATAGTA
125 TGATTTTTAAGAAAAATAGTG
* *
58749152 TTTTTTTCAAAAAAAAGGAGAAAGTTTAGTTTTTGAAAAATAAAAATATATTTTTTTT-AGTAAT
1 TTTTTTT------AAA-GAGAAAATTTAGATTTTGAAAAATAAAAATATATTTTTTTTAAGTAAT
* *
58749216 TTTAAAGGAAAGTTTAAAATTTTAAAATAAAGTTTTGATTTCTTTTCAACTACTTCAAAATAAAA
59 TTTAAAGGAAAGTTTAAAATTTTAAAATAAAGTTTTGATTT-TTTTTAACTATTTC-AAATAAAA
*
58749281 GC-TTGCATCTTTAAGAAAAATAGTG
122 -CTTTG-ATTTTTAAGAAAAATAGTG
*
58749306 TTTTTTTAAAGAGAAAATTTAGATTTTGAAAAATAAAAATATATTTTTTTTAAGTCATTTTAAAG
1 TTTTTTTAAAGAGAAAATTTAGATTTTGAAAAATAAAAATATATTTTTTTTAAGTAATTTTAAAG
*
58749371 GAAAGTTTAAAATTTTAAAATAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAATTTTGATT
66 GAAAGTTTAAAATTTTAAAATAAAGTTTTGATTTTTTTTAACTATTTC-AAATAAAACTTTGATT
* *
58749436 TTTAAAAAAAAATTAATG
130 TTT-AAGAAAAA-TAGTG
*
58749454 ATTTTTTCTAAA-A-AAAACTTT-GATTTTGCAAAAAAAAAAA
1 -TTTTTT-TAAAGAGAAAA-TTTAGATTTTG-AAAAATAAAAA
58749494 ATTTCGGCCA
Statistics
Matches: 296, Mismatches: 24, Indels: 42
0.82 0.07 0.12
Matches are distributed among these distances:
146 5 0.02
147 76 0.26
148 64 0.22
149 20 0.07
150 4 0.01
153 5 0.02
154 67 0.23
155 46 0.16
156 2 0.01
157 7 0.02
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (145 bp):
TTTTTTTAAAGAGAAAATTTAGATTTTGAAAAATAAAAATATATTTTTTTTAAGTAATTTTAAAG
GAAAGTTTAAAATTTTAAAATAAAGTTTTGATTTTTTTTAACTATTTCAAATAAAACTTTGATTT
TTAAGAAAAATAGTG
Found at i:58749477 original size:22 final size:22
Alignment explanation
Indices: 58749434--58749480 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
58749424 AAAATTTTGA
58749434 TTTTTAAAAAAAAATTAATGATT
1 TTTTTAAAAAAAAATT-ATGATT
*
58749457 TTTTCTAAAAAAAACTT-TGATT
1 TTTT-TAAAAAAAAATTATGATT
58749479 TT
1 TT
58749481 GCAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 4 0.18
24 11 0.50
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (22 bp):
TTTTTAAAAAAAAATTATGATT
Found at i:58749479 original size:148 final size:146
Alignment explanation
Indices: 58749004--58749493 Score: 507
Period size: 148 Copynumber: 3.3 Consensus size: 146
58748994 AAGTTTTGAT
* * * *
58749004 TTTTTTTTAAAGAGAAAGTTTAGATTTT-AACAAAT-AAAA-AT-TTGTTTTTATAGTTATTTTA
1 TTTTTTCTAAA-AGAAAATTTAGATTTTGAA-AAATAAAAATATATTTTTTTTA-AGTAATTTTA
* * * * *
58749065 AAGGAAATTTTAAATTTTTAAAACAAATTTTTTTATTTTTTTTCAACTATTTCAAAGTAAAAGCT
63 AAGGAAAGTTTAAAATTTTAAAATAAA-GTTTTGATTTTTTTT-AACTATTTCAAA-TAAAA-CT
*
58749130 TTAATTTTTAAGAAAAATAGT-A
124 TTGATTTTTAAGAAAAATAGTGA
* *
58749152 TTTTTTTCAAAAAAAAGGAGAAAGTTTAGTTTTTGAAAAATAAAAATATATTTTTTTT-AGTAAT
1 -TTTTTTC---TAAAA-GA-AAA-TTTAGATTTTGAAAAATAAAAATATATTTTTTTTAAGTAAT
* *
58749216 TTTAAAGGAAAGTTTAAAATTTTAAAATAAAGTTTTGATTTCTTTTCAACTACTTCAAAATAAAA
59 TTTAAAGGAAAGTTTAAAATTTTAAAATAAAGTTTTGATTT-TTTTTAACTATTTC-AAATAAAA
*
58749281 GC-TTGCATCTTTAAGAAAAATAGTG-
122 -CTTTG-ATTTTTAAGAAAAATAGTGA
*
58749306 TTTTTT-TAAAGAGAAAATTTAGATTTTGAAAAATAAAAATATATTTTTTTTAAGTCATTTTAAA
1 TTTTTTCTAAA-AGAAAATTTAGATTTTGAAAAATAAAAATATATTTTTTTTAAGTAATTTTAAA
*
58749370 GGAAAGTTTAAAATTTTAAAATAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAATTTTGAT
65 GGAAAGTTTAAAATTTTAAAATAAAGTTTTGATTTTTTTTAACTATTTC-AAATAAAACTTTGAT
* *
58749435 TTTTAAAAAAAAATTAATGA
129 TTTT-AAGAAAAA-TAGTGA
*
58749455 TTTTTTCTAAAA-AAAACTTT-GATTTTGCAAAAAAAAAAA
1 TTTTTTCTAAAAGAAAA-TTTAGATTTTG-AAAAATAAAAA
58749494 ATTTCGGCCA
Statistics
Matches: 292, Mismatches: 26, Indels: 46
0.80 0.07 0.13
Matches are distributed among these distances:
146 5 0.02
147 63 0.22
148 64 0.22
149 31 0.11
150 5 0.02
151 1 0.00
152 5 0.02
153 10 0.03
154 53 0.18
155 46 0.16
156 2 0.01
157 7 0.02
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (146 bp):
TTTTTTCTAAAAGAAAATTTAGATTTTGAAAAATAAAAATATATTTTTTTTAAGTAATTTTAAAG
GAAAGTTTAAAATTTTAAAATAAAGTTTTGATTTTTTTTAACTATTTCAAATAAAACTTTGATTT
TTAAGAAAAATAGTGA
Found at i:58749480 original size:21 final size:21
Alignment explanation
Indices: 58749415--58749492 Score: 61
Period size: 21 Copynumber: 3.7 Consensus size: 21
58749405 TTTTTAACTA
* * *
58749415 TTTCGAAATAAAATTTTGA-T
1 TTTCTAAAAAAAAATTTGATT
58749435 TTT-TAAAAAAAAATTAATGATTT
1 TTTCTAAAAAAAAATT--TGA-TT
*
58749458 TTTCTAAAAAAAACTTTGATT
1 TTTCTAAAAAAAAATTTGATT
* *
58749479 TTGCAAAAAAAAAA
1 TTTCTAAAAAAAAA
58749493 AATTTCGGCC
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
19 9 0.20
20 3 0.07
21 16 0.35
22 3 0.07
23 4 0.09
24 11 0.24
ACGTcount: A:0.50, C:0.05, G:0.06, T:0.38
Consensus pattern (21 bp):
TTTCTAAAAAAAAATTTGATT
Found at i:58750467 original size:11 final size:11
Alignment explanation
Indices: 58750451--58750476 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
58750441 TGTAAGAGTA
58750451 AAATTAGTTTT
1 AAATTAGTTTT
58750462 AAATTAGTTTT
1 AAATTAGTTTT
58750473 AAAT
1 AAAT
58750477 ATTGTATAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (11 bp):
AAATTAGTTTT
Found at i:58750777 original size:3 final size:3
Alignment explanation
Indices: 58750769--58750806 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
58750759 AATCTTTTAA
58750769 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
58750807 AAGATCGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:58752121 original size:19 final size:18
Alignment explanation
Indices: 58752099--58752142 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
58752089 TTTAATTTCA
58752099 TATTTTTTTCATTTGACTT
1 TATTTTTTTCA-TTGACTT
*
58752118 TATTATTTTTTATTGACTT
1 TATT-TTTTTCATTGACTT
*
58752137 TGTTTT
1 TATTTT
58752143 CTTGTGTCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 14 0.64
20 6 0.27
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.70
Consensus pattern (18 bp):
TATTTTTTTCATTGACTT
Found at i:58752814 original size:30 final size:30
Alignment explanation
Indices: 58752778--58752836 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
58752768 CCAGCGGTGA
58752778 TAGACATTTGGCACTGTTCACGTTTGCCGC
1 TAGACATTTGGCACTGTTCACGTTTGCCGC
58752808 TAGACATTTGGCACTGTTCACGTTTGCCG
1 TAGACATTTGGCACTGTTCACGTTTGCCG
58752837 TATATGAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.34
Consensus pattern (30 bp):
TAGACATTTGGCACTGTTCACGTTTGCCGC
Found at i:58754753 original size:16 final size:16
Alignment explanation
Indices: 58754732--58754764 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
58754722 GTATATTGTG
*
58754732 AAGATTTACCGCTTCA
1 AAGATTTACAGCTTCA
58754748 AAGATTTACAGCTTCA
1 AAGATTTACAGCTTCA
58754764 A
1 A
58754765 GCGCCAGGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.30
Consensus pattern (16 bp):
AAGATTTACAGCTTCA
Found at i:58762147 original size:34 final size:35
Alignment explanation
Indices: 58762082--58762158 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 35
58762072 TCGAAAAAAG
*
58762082 AAAAAAAGAAAAAATAGGGAAAGTGAATAAGAAGA
1 AAAAAAAGAAAAAATAGGGAAAGTGAATAAGAACA
*
58762117 AAAAAAAGAAAGGAAATA-GG-AAG-GAGTAAGAACA
1 AAAAAAAGAAA--AAATAGGGAAAGTGAATAAGAACA
*
58762151 AAGAAAAG
1 AAAAAAAG
58762159 TGATTAAGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
34 16 0.43
35 14 0.38
36 2 0.05
37 5 0.14
ACGTcount: A:0.68, C:0.01, G:0.25, T:0.06
Consensus pattern (35 bp):
AAAAAAAGAAAAAATAGGGAAAGTGAATAAGAACA
Found at i:58763204 original size:42 final size:43
Alignment explanation
Indices: 58763135--58763431 Score: 347
Period size: 42 Copynumber: 7.1 Consensus size: 43
58763125 AAGGAGAACA
* *
58763135 TTCATTGCATTTAG-AGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAAGACCCAGGTGTGGAGGTCCATTTACTT
** *
58763177 TTCATTGCATTTAGAAG-CCCAAATGTGGAGGTTCATTTACTT
1 TTCATTGCATTTAGAAGACCCAGGTGTGGAGGTCCATTTACTT
* *
58763219 TTCATTGCATTTA-AAGACCCAGCTGTGGAGATCCATTTACTT
1 TTCATTGCATTTAGAAGACCCAGGTGTGGAGGTCCATTTACTT
* * * * *
58763261 TTCATTGTATTTAG-AGGCCCAGGTATTGAGGTCCATTCACTT
1 TTCATTGCATTTAGAAGACCCAGGTGTGGAGGTCCATTTACTT
* * * * *
58763303 TTCATTGCATTTAG-AGACCTAAGTATTGAGGTCCATTCACTT
1 TTCATTGCATTTAGAAGACCCAGGTGTGGAGGTCCATTTACTT
* * * *
58763345 TTCATTGCATTTAG-AGACCTAAGTGTAGAGGTCCATTGACTT
1 TTCATTGCATTTAGAAGACCCAGGTGTGGAGGTCCATTTACTT
*
58763387 TTCATTGCATTTAG-AGACCCAGGTGTTGAGGTCCATTTACTT
1 TTCATTGCATTTAGAAGACCCAGGTGTGGAGGTCCATTTACTT
58763429 TTC
1 TTC
58763432 TAGTTTACTT
Statistics
Matches: 226, Mismatches: 26, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
41 3 0.01
42 221 0.98
43 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.38
Consensus pattern (43 bp):
TTCATTGCATTTAGAAGACCCAGGTGTGGAGGTCCATTTACTT
Found at i:58763281 original size:84 final size:84
Alignment explanation
Indices: 58763135--58763431 Score: 387
Period size: 84 Copynumber: 3.5 Consensus size: 84
58763125 AAGGAGAACA
* * * *
58763135 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAAGCCCAAA
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAAG
* * *
58763200 TGTGGAGGTTCATTTACTT
66 TGTAGAGGTCCATTCACTT
* * * * *
58763219 TTCATTGCATTTAAAGACCCAGCTGTGGAGATCCATTTACTTTTCATTGTATTTAGAGGCCCAGG
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAAG
* *
58763284 TATTGAGGTCCATTCACTT
66 TGTAGAGGTCCATTCACTT
* * * * * * *
58763303 TTCATTGCATTTAGAGACCTAAGTATTGAGGTCCATTCACTTTTCATTGCATTTAGAGACCTAAG
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAAG
*
58763368 TGTAGAGGTCCATTGACTT
66 TGTAGAGGTCCATTCACTT
*
58763387 TTCATTGCATTTAGAGACCCAGGTGTTGAGGTCCATTTACTTTTC
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTTTTC
58763432 TAGTTTACTT
Statistics
Matches: 181, Mismatches: 32, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
84 181 1.00
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.38
Consensus pattern (84 bp):
TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAAG
TGTAGAGGTCCATTCACTT
Found at i:58763363 original size:126 final size:126
Alignment explanation
Indices: 58763135--58763431 Score: 409
Period size: 126 Copynumber: 2.4 Consensus size: 126
58763125 AAGGAGAACA
* *
58763135 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAAGCCCAAA
1 TTCATTGCATTTAGAGGCCCAGGTGTTGAGGTCCATTTACTTTTCATTGCATTTAGAAGCCCAAA
* * * * * *
58763200 TGTGGAGGTTCATTTACTTTTCATTGCATTTAAAGACC-CAGCTGTGGAGATCCATTTACTT
66 TATGGAGGTCCATTCACTTTTCATTGCATTTAAAGACCTAAG-TGTAGAGATCCATTGACTT
* * * *
58763261 TTCATTGTATTTAGAGGCCCAGGTATTGAGGTCCATTCACTTTTCATTGCATTTAG-AGACCTAA
1 TTCATTGCATTTAGAGGCCCAGGTGTTGAGGTCCATTTACTTTTCATTGCATTTAGAAG-CCCAA
* * * *
58763325 GTATTGAGGTCCATTCACTTTTCATTGCATTTAGAGACCTAAGTGTAGAGGTCCATTGACTT
65 ATATGGAGGTCCATTCACTTTTCATTGCATTTAAAGACCTAAGTGTAGAGATCCATTGACTT
*
58763387 TTCATTGCATTTAGAGACCCAGGTGTTGAGGTCCATTTACTTTTC
1 TTCATTGCATTTAGAGGCCCAGGTGTTGAGGTCCATTTACTTTTC
58763432 TAGTTTACTT
Statistics
Matches: 149, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
125 2 0.01
126 145 0.97
127 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.38
Consensus pattern (126 bp):
TTCATTGCATTTAGAGGCCCAGGTGTTGAGGTCCATTTACTTTTCATTGCATTTAGAAGCCCAAA
TATGGAGGTCCATTCACTTTTCATTGCATTTAAAGACCTAAGTGTAGAGATCCATTGACTT
Found at i:58763459 original size:16 final size:16
Alignment explanation
Indices: 58763438--58763468 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
58763428 TTTCTAGTTT
58763438 ACTTTTCATTGCATTG
1 ACTTTTCATTGCATTG
58763454 ACTTTTCATTGCATT
1 ACTTTTCATTGCATT
58763469 TAGAGGCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.19, G:0.10, T:0.52
Consensus pattern (16 bp):
ACTTTTCATTGCATTG
Done.