Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 97 of 125
Found at i:29170418 original size:54 final size:54
Alignment explanation
Indices: 29170328--29170433 Score: 158
Period size: 54 Copynumber: 2.0 Consensus size: 54
29170318 GCAGTTCAAA
* * *
29170328 ACTTCTAGATAGATCCTTCTCACAAAGTTCCTTTTTAGGAGTATCAATTGAAAC
1 ACTTCTAGATAAATCCTTCTCACAAAGTTCCGTTTTAGGAGAATCAATTGAAAC
* * *
29170382 ACTTGTAGATAAATCCTTCTCACAGATTTCCGTTTTAGGAGAATCAATTGAA
1 ACTTCTAGATAAATCCTTCTCACAAAGTTCCGTTTTAGGAGAATCAATTGAA
29170434 TCAGGTACAC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (54 bp):
ACTTCTAGATAAATCCTTCTCACAAAGTTCCGTTTTAGGAGAATCAATTGAAAC
Found at i:29178123 original size:30 final size:29
Alignment explanation
Indices: 29178068--29178128 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
29178058 TTTTTAAAAA
* **
29178068 TTTTAAAAGATTAAATTATTTTTTTATTAT
1 TTTTAAAAGATTAAAGTATAATTTTA-TAT
*
29178098 TTTTAAGAGATTAAAGTATAATTTTATAT
1 TTTTAAAAGATTAAAGTATAATTTTATAT
29178127 TT
1 TT
29178129 ACTAATTTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 5 0.19
30 22 0.81
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (29 bp):
TTTTAAAAGATTAAAGTATAATTTTATAT
Found at i:29179791 original size:17 final size:15
Alignment explanation
Indices: 29179762--29179804 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
29179752 CGGCAGCTTC
29179762 TCAATATAATTAAAATT
1 TCAA-ATAATT-AAATT
29179779 TCAAATAACTTAAATT
1 TCAAATAA-TTAAATT
*
29179795 TAAAATAATT
1 TCAAATAATT
29179805 CAAACCCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 2 0.08
16 16 0.67
17 6 0.25
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (15 bp):
TCAAATAATTAAATT
Found at i:29181376 original size:185 final size:185
Alignment explanation
Indices: 29181064--29181434 Score: 724
Period size: 185 Copynumber: 2.0 Consensus size: 185
29181054 TTTATACCTC
29181064 AATCAAAAACTGTAATCGCAAATAATCAACATGACTATTGAGTATTGAGATGTTCGTTGCACTCC
1 AATCAAAAACTGTAATCGCAAATAATCAACATGACTATTGAGTATTGAGATGTTCGTTGCACTCC
29181129 AAAATAGATACTTAAATAATCACGGGTAGAAACTTTTCACCGAAACCAAACCACTCCAAAATAAG
66 AAAATAGATACTTAAATAATCACGGGTAGAAACTTTTCACCGAAACCAAACCACTCCAAAATAAG
29181194 AAAATCCTCTTATGCACCATTACACCGACTAACCATACATTGGTGCAATATTAAA
131 AAAATCCTCTTATGCACCATTACACCGACTAACCATACATTGGTGCAATATTAAA
29181249 AATCAAAAACTGTAATCGCAAATAATCAACATGACTATTGAGTATTGAGATGTTCGTTGCACTCC
1 AATCAAAAACTGTAATCGCAAATAATCAACATGACTATTGAGTATTGAGATGTTCGTTGCACTCC
*
29181314 ACAATAGATACTTAAATAATCACGGGTAGAAACTTTTCACCGAAACCAAACCACTCCAAAATAAG
66 AAAATAGATACTTAAATAATCACGGGTAGAAACTTTTCACCGAAACCAAACCACTCCAAAATAAG
*
29181379 AAAATCCTCTTATGCATCATTACACCGACTAACCATACATTGGTGCAATATTAAA
131 AAAATCCTCTTATGCACCATTACACCGACTAACCATACATTGGTGCAATATTAAA
29181434 A
1 A
29181435 CAAAATCCGC
Statistics
Matches: 184, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 184 1.00
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.26
Consensus pattern (185 bp):
AATCAAAAACTGTAATCGCAAATAATCAACATGACTATTGAGTATTGAGATGTTCGTTGCACTCC
AAAATAGATACTTAAATAATCACGGGTAGAAACTTTTCACCGAAACCAAACCACTCCAAAATAAG
AAAATCCTCTTATGCACCATTACACCGACTAACCATACATTGGTGCAATATTAAA
Found at i:29185277 original size:2 final size:2
Alignment explanation
Indices: 29185270--29185296 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29185260 GTTCTAAATT
29185270 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
29185297 GCATATGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29187228 original size:24 final size:24
Alignment explanation
Indices: 29187190--29187245 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
29187180 ATTTGAGAAA
*
29187190 TAATT-TTTCAGTTAAA-TTCTGTT
1 TAATTGTTTCAATTAAACTT-TGTT
29187213 TAATTGTTTCAATTAAACTTTGTT
1 TAATTGTTTCAATTAAACTTTGTT
*
29187237 TATTTGTTT
1 TAATTGTTT
29187246 GAGTCAAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 5 0.17
24 22 0.76
25 2 0.07
ACGTcount: A:0.25, C:0.07, G:0.09, T:0.59
Consensus pattern (24 bp):
TAATTGTTTCAATTAAACTTTGTT
Found at i:29187254 original size:24 final size:24
Alignment explanation
Indices: 29187209--29187255 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
29187199 AGTTAAATTC
*
29187209 TGTTTAATTGTTTCAATTAAACTT
1 TGTTTAATTGTTTCAATCAAACTT
* * *
29187233 TGTTTATTTGTTTGAGTCAAACT
1 TGTTTAATTGTTTCAATCAAACT
29187256 CTTATTAGTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.09, G:0.13, T:0.53
Consensus pattern (24 bp):
TGTTTAATTGTTTCAATCAAACTT
Found at i:29189215 original size:24 final size:24
Alignment explanation
Indices: 29189187--29189237 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
29189177 AGAAATAATC
* *
29189187 TTTCATTTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTATTTAATTG
*
29189211 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTATTTAATTG
29189235 TTT
1 TTT
29189238 GAGTCAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.12, G:0.06, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTAATTG
Found at i:29189246 original size:24 final size:24
Alignment explanation
Indices: 29189195--29189249 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
29189185 TCTTTCATTT
* *
29189195 AAACTCTGTTTAATTGTTTCAATT
1 AAACTCTATTTAATTGTTTCAATC
* * *
29189219 AAACTCTATTTATTTGTTTGAGTC
1 AAACTCTATTTAATTGTTTCAATC
29189243 AAACTCT
1 AAACTCT
29189250 TATTAGTCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.47
Consensus pattern (24 bp):
AAACTCTATTTAATTGTTTCAATC
Found at i:29190263 original size:14 final size:14
Alignment explanation
Indices: 29190244--29190285 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
29190234 TGCGTATGTG
29190244 TGTGAAATCATAAA
1 TGTGAAATCATAAA
*
29190258 TGTGAAACCATAAA
1 TGTGAAATCATAAA
* *
29190272 TTTAAAAT-ATAAA
1 TGTGAAATCATAAA
29190285 T
1 T
29190286 ATGTTTAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 6 0.25
14 18 0.75
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (14 bp):
TGTGAAATCATAAA
Found at i:29191215 original size:29 final size:30
Alignment explanation
Indices: 29191182--29191247 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
29191172 CTTTTGTTTT
* *
29191182 TTATTTTAAA-ATTTAATTATTTAAATAAA
1 TTATTTTAAATATTTAATGATTCAAATAAA
* *
29191211 TTATTTTAAATATTTGATGATTCAAATATA
1 TTATTTTAAATATTTAATGATTCAAATAAA
29191241 TT-TTTTA
1 TTATTTTA
29191248 CATAATAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (30 bp):
TTATTTTAAATATTTAATGATTCAAATAAA
Found at i:29191489 original size:16 final size:16
Alignment explanation
Indices: 29191453--29191494 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
29191443 CAAATGGATA
*
29191453 ATTTATTTAATTAATT
1 ATTTATTTAATTAAAT
*
29191469 TTTTATTTAATTAAAT
1 ATTTATTTAATTAAAT
*
29191485 ATTTAGTTAA
1 ATTTATTTAA
29191495 ATTTTAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
ATTTATTTAATTAAAT
Found at i:29193453 original size:21 final size:22
Alignment explanation
Indices: 29193407--29193467 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
29193397 TGATCTAAGG
* *
29193407 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAGAACT
29193428 AAAAATAAAAGAAAATAGAACT
1 AAAAATAAAAGAAAATAGAACT
*
29193450 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
29193468 GGAAGTCGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.31
22 23 0.66
23 1 0.03
ACGTcount: A:0.72, C:0.03, G:0.11, T:0.13
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAACT
Found at i:29193458 original size:15 final size:16
Alignment explanation
Indices: 29193433--29193462 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
29193423 GAATTAAAAA
29193433 TAAAAGAAAATAGAAC
1 TAAAAGAAAATAGAAC
29193449 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
29193463 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.03, G:0.13, T:0.13
Consensus pattern (16 bp):
TAAAAGAAAATAGAAC
Found at i:29194292 original size:19 final size:19
Alignment explanation
Indices: 29194268--29194310 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
29194258 AAACATAAAT
29194268 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
29194287 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
29194306 TAAAT
1 TAAAT
29194311 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:29195746 original size:29 final size:29
Alignment explanation
Indices: 29195713--29195768 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
29195703 TCACACCTTG
* *
29195713 TGTGATATTATTCTGTTTTGTGTTATCTT
1 TGTGATATTAATCTGTATTGTGTTATCTT
*
29195742 TGTGATTTTAATCTGTATTGTGTTATC
1 TGTGATATTAATCTGTATTGTGTTATC
29195769 GCATGTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.16, C:0.07, G:0.18, T:0.59
Consensus pattern (29 bp):
TGTGATATTAATCTGTATTGTGTTATCTT
Found at i:29198498 original size:71 final size:71
Alignment explanation
Indices: 29198382--29198527 Score: 247
Period size: 71 Copynumber: 2.1 Consensus size: 71
29198372 TTCCTATTTT
* *
29198382 TGTACTTTTGTGTTAACCATTTTATTAGAGATTAAACCGTGTTGTAAGTAAAGTTGTTTGGGGTG
1 TGTACTTTTATGTTAACCATTTTATTAGAGATTAAACCGTGTTGTAAGTAAAATTGTTTGGGGTG
29198447 AATGAC
66 AATGAC
* * *
29198453 TGTACTTTTATGTTAATCATTTTATTAGAGATTGAATCGTGTTGTAAGTAAAATTGTTTGGGGTG
1 TGTACTTTTATGTTAACCATTTTATTAGAGATTAAACCGTGTTGTAAGTAAAATTGTTTGGGGTG
29198518 AATGAC
66 AATGAC
29198524 TGTA
1 TGTA
29198528 ATAATTAGAT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.27, C:0.07, G:0.23, T:0.42
Consensus pattern (71 bp):
TGTACTTTTATGTTAACCATTTTATTAGAGATTAAACCGTGTTGTAAGTAAAATTGTTTGGGGTG
AATGAC
Found at i:29199472 original size:11 final size:11
Alignment explanation
Indices: 29199449--29199478 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
29199439 GTCATTTCAC
29199449 TATTATATTTAT
1 TATTAT-TTTAT
29199461 TATTATTTTAT
1 TATTATTTTAT
29199472 TATTATT
1 TATTATT
29199479 GTTTGGATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:29203063 original size:19 final size:19
Alignment explanation
Indices: 29203015--29203051 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
29203005 ATATTTGAGT
* *
29203015 AGAATACTTTGAAGTTTAG
1 AGAATAATTTAAAGTTTAG
29203034 AGAATAATTTAAAGTTTA
1 AGAATAATTTAAAGTTTA
29203052 AGCAATAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (19 bp):
AGAATAATTTAAAGTTTAG
Found at i:29211953 original size:35 final size:34
Alignment explanation
Indices: 29211907--29211978 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 34
29211897 GCAAGATTTG
29211907 GAAAAGGAATAAAATATACTTTCCTAAAAAAAAAA
1 GAAAAGGAATAAAATATACTTTCC-AAAAAAAAAA
* *
29211942 GAAAAGGAATAAAATATACTTTTCAAAAGAAAAA
1 GAAAAGGAATAAAATATACTTTCCAAAAAAAAAA
29211976 GAA
1 GAA
29211979 TAAACTCTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 12 0.34
35 23 0.66
ACGTcount: A:0.62, C:0.07, G:0.11, T:0.19
Consensus pattern (34 bp):
GAAAAGGAATAAAATATACTTTCCAAAAAAAAAA
Found at i:29211992 original size:28 final size:28
Alignment explanation
Indices: 29211938--29211992 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
29211928 TCCTAAAAAA
* *
29211938 AAAAGAAAAGGAATAAAATATACTTTTC
1 AAAAGAAAAAGAATAAAATATAATTTTC
* *
29211966 AAAAGAAAAAGAATAAACTCTAATTTT
1 AAAAGAAAAAGAATAAAATATAATTTT
29211993 TCAGTTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.58, C:0.07, G:0.09, T:0.25
Consensus pattern (28 bp):
AAAAGAAAAAGAATAAAATATAATTTTC
Found at i:29218531 original size:29 final size:27
Alignment explanation
Indices: 29218455--29218539 Score: 73
Period size: 30 Copynumber: 2.9 Consensus size: 27
29218445 GAGTAATTTA
* *
29218455 ATCTTTTTCTTTTATATTATTTTAACTTT
1 ATCTTTTTCTTTTCT-TTATTTT-TCTTT
29218484 -TCTTTTTCTTTCTTTCTTTATTTTTCTTT
1 ATCTTTTTC--T-TTTCTTTATTTTTCTTT
*
29218513 ATCTTTTTCTTATTCCTTTGTTTTTCT
1 ATCTTTTTCTT-TT-CTTTATTTTTCT
29218540 CCCTTTTCCA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
27 1 0.02
28 11 0.23
29 15 0.32
30 16 0.34
31 4 0.09
ACGTcount: A:0.11, C:0.15, G:0.01, T:0.73
Consensus pattern (27 bp):
ATCTTTTTCTTTTCTTTATTTTTCTTT
Found at i:29219742 original size:24 final size:25
Alignment explanation
Indices: 29219701--29219760 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
29219691 AAAAAAGAAG
* *
29219701 AAGAAGAAAAGTTCAAATAACATAA
1 AAGAAAAAAAATTCAAATAACATAA
* *
29219726 AAGAAAAAAAATT-AAATTACTTAA
1 AAGAAAAAAAATTCAAATAACATAA
29219750 AATGAAAAAAA
1 AA-GAAAAAAA
29219761 TATATGAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 11 0.37
25 19 0.63
ACGTcount: A:0.68, C:0.05, G:0.08, T:0.18
Consensus pattern (25 bp):
AAGAAAAAAAATTCAAATAACATAA
Found at i:29221107 original size:26 final size:23
Alignment explanation
Indices: 29221078--29221156 Score: 58
Period size: 23 Copynumber: 3.4 Consensus size: 23
29221068 AAGATGATTG
29221078 TATATGAAAATTTAATAAATAA-ACAA
1 TATAT-AAAA-TTAA-AAATAATA-AA
*
29221104 TATATTAAATTAAAAATAATAAA
1 TATATAAAATTAAAAATAATAAA
* * *
29221127 TATATATATTTTAAAA-AA-AAA
1 TATATAAAATTAAAAATAATAAA
29221148 T-TATAAAAT
1 TATATAAAAT
29221157 AATATGGCAT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
20 6 0.13
21 4 0.09
22 2 0.04
23 20 0.44
24 5 0.11
25 3 0.07
26 5 0.11
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (23 bp):
TATATAAAATTAAAAATAATAAA
Found at i:29221858 original size:2 final size:2
Alignment explanation
Indices: 29221851--29221878 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29221841 TGTTGTGCAC
29221851 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
29221879 GATGTTAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29221974 original size:18 final size:16
Alignment explanation
Indices: 29221942--29221978 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
29221932 AATTAATATT
29221942 TTTATTTTTATTTATG
1 TTTATTTTTATTTATG
29221958 TTTATTTTATGATTTATG
1 TTTATTTT-T-ATTTATG
29221976 TTT
1 TTT
29221979 GGGGTTCGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
17 1 0.05
18 10 0.53
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.73
Consensus pattern (16 bp):
TTTATTTTTATTTATG
Found at i:29234521 original size:20 final size:20
Alignment explanation
Indices: 29234495--29234534 Score: 66
Period size: 18 Copynumber: 2.1 Consensus size: 20
29234485 CAATGTTAAT
29234495 ATTTTTTTT-GTT-AATTTG
1 ATTTTTTTTAGTTAAATTTG
29234513 ATTTTTTTTAGTTAAATTTG
1 ATTTTTTTTAGTTAAATTTG
29234533 AT
1 AT
29234535 CTTCAACCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 9 0.45
19 3 0.15
20 8 0.40
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.68
Consensus pattern (20 bp):
ATTTTTTTTAGTTAAATTTG
Found at i:29234563 original size:32 final size:32
Alignment explanation
Indices: 29234527--29234587 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
29234517 TTTTTAGTTA
* * *
29234527 AATTTGATCTTCAACCTTTTAATAAAAAGTCG
1 AATTTGATCATCAACCTTTAAAAAAAAAGTCG
*
29234559 AATTTGATCATCAATCTTTAAAAAAAAAG
1 AATTTGATCATCAACCTTTAAAAAAAAAG
29234588 AAGTTTAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.34
Consensus pattern (32 bp):
AATTTGATCATCAACCTTTAAAAAAAAAGTCG
Found at i:29237337 original size:31 final size:30
Alignment explanation
Indices: 29237263--29237343 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 30
29237253 GAATTTAGTC
* * *
29237263 AAATCAAAATTTCATGTATAAGTTTTCACA
1 AAATCAAAAGTTCATGTATAAATTTACACA
* *
29237293 AAAT-AAAAGTTCATATATAAATTTACATA
1 AAATCAAAAGTTCATGTATAAATTTACACA
29237322 TTAAATCAAAA-TTCATGTATAA
1 --AAATCAAAAGTTCATGTATAA
29237344 TTTTGATATT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
29 20 0.48
30 4 0.10
31 14 0.33
32 4 0.10
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (30 bp):
AAATCAAAAGTTCATGTATAAATTTACACA
Found at i:29237781 original size:38 final size:40
Alignment explanation
Indices: 29237703--29237781 Score: 108
Period size: 38 Copynumber: 2.0 Consensus size: 40
29237693 TATGTAATTT
29237703 TATAATTACAATTTGTACTACAAAATATAAGAAATTACAA
1 TATAATTACAATTTGTACTACAAAATATAAGAAATTACAA
* * * *
29237743 TATAATTACACTTTGT-CT-GAAATTTTAAGAAATTACAA
1 TATAATTACAATTTGTACTACAAAATATAAGAAATTACAA
29237781 T
1 T
29237782 TTTTTTATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 18 0.51
39 2 0.06
40 15 0.43
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (40 bp):
TATAATTACAATTTGTACTACAAAATATAAGAAATTACAA
Found at i:29238278 original size:31 final size:32
Alignment explanation
Indices: 29238246--29238312 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 32
29238236 TAATTTGTAT
29238246 TTTTATAATTTTT-AAAA-ATAAAAATAAATA
1 TTTTATAATTTTTGAAAAGATAAAAATAAATA
* *
29238276 TTTTATTATTTTTGAAAAGATAAAAATATA-A
1 TTTTATAATTTTTGAAAAGATAAAAATAAATA
29238307 TTTTAT
1 TTTTAT
29238313 TATTACTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 12 0.36
31 11 0.33
32 10 0.30
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (32 bp):
TTTTATAATTTTTGAAAAGATAAAAATAAATA
Found at i:29238313 original size:31 final size:30
Alignment explanation
Indices: 29238246--29238316 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 30
29238236 TAATTTGTAT
*
29238246 TTTTATAATTTTTAAAAATAAAAATAAATA
1 TTTTATTATTTTTAAAAATAAAAATAAATA
*
29238276 TTTTATTATTTTTGAAAAGATAAAAATATA-A
1 TTTTATTATTTTT-AAAA-ATAAAAATAAATA
29238307 TTTTATTATT
1 TTTTATTATT
29238317 ACTAATTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 12 0.32
31 15 0.41
32 10 0.27
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (30 bp):
TTTTATTATTTTTAAAAATAAAAATAAATA
Found at i:29239147 original size:6 final size:6
Alignment explanation
Indices: 29239136--29239168 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
29239126 GAATGGATTT
29239136 ACCATC ACCATC ACCATC ACCATC ACCATC ACC
1 ACCATC ACCATC ACCATC ACCATC ACCATC ACC
29239169 GACAGCTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.00, T:0.15
Consensus pattern (6 bp):
ACCATC
Found at i:29242180 original size:1 final size:1
Alignment explanation
Indices: 29242174--29242200 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
29242164 AGGTGAAGTT
29242174 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGG
29242201 TGTTGAGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:29247566 original size:41 final size:40
Alignment explanation
Indices: 29247359--29247656 Score: 348
Period size: 40 Copynumber: 7.4 Consensus size: 40
29247349 CGTTTAGACA
* * **
29247359 GAAAACGCCACAAAAGGTAGGGCAATAGCGGCGCTT-TTC
1 GAAAGCGCCGCAAAAGGTAGGGCAATAGCGGCGCTTATGG
* * *
29247398 CATAAGCGCCGCAAAAGGCAGGGCAATAACGGCGCTTATGG
1 GA-AAGCGCCGCAAAAGGTAGGGCAATAGCGGCGCTTATGG
29247439 GAAAGCGCCGCAAAAGGTAGGGCAATAGCGGCGCTTATGG
1 GAAAGCGCCGCAAAAGGTAGGGCAATAGCGGCGCTTATGG
* ** *
29247479 GAAAGTGCCGCAAAAGGTAGGGCAACCGTGGCGCTTATGG
1 GAAAGCGCCGCAAAAGGTAGGGCAATAGCGGCGCTTATGG
* * * *
29247519 GAAAGCGCCGCTAAAGGTCAGAGAAATAGCGACGCTTATGG
1 GAAAGCGCCGCAAAAGGT-AGGGCAATAGCGGCGCTTATGG
* **
29247560 GTAAGCGCCGCAAAAGGTAGGGCAATAATGGCGCTTATGG
1 GAAAGCGCCGCAAAAGGTAGGGCAATAGCGGCGCTTATGG
* *
29247600 GGAAGCGCCGCTAAAGGTCAGGGCAATAGCGGCGCTTAT-G
1 GAAAGCGCCGCAAAAGGT-AGGGCAATAGCGGCGCTTATGG
* *
29247640 AAGAAGCGCCGCTAAAG
1 GA-AAGCGCCGCAAAAG
29247657 CTCAATAATA
Statistics
Matches: 219, Mismatches: 35, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
39 1 0.00
40 152 0.69
41 66 0.30
ACGTcount: A:0.31, C:0.21, G:0.34, T:0.14
Consensus pattern (40 bp):
GAAAGCGCCGCAAAAGGTAGGGCAATAGCGGCGCTTATGG
Found at i:29247583 original size:81 final size:81
Alignment explanation
Indices: 29247371--29247656 Score: 380
Period size: 81 Copynumber: 3.6 Consensus size: 81
29247361 AAACGCCACA
* *** * *
29247371 AAAGGT-AGGGCAATAGCGGCGCTTTTCCATAAGCGCCGCAAAAGGCAGGGCAATAACGGCGCTT
1 AAAGGTCAGGGCAATAGCGGCGCTTATGGGTAAGCGCCGCAAAAGGTAGGGCAATAATGGCGCTT
*
29247435 ATGGGAAAGCGCCGCA
66 ATGGGAAAGCGCCGCT
* * ***
29247451 AAAGGT-AGGGCAATAGCGGCGCTTATGGGAAAGTGCCGCAAAAGGTAGGGCAACCGTGGCGCTT
1 AAAGGTCAGGGCAATAGCGGCGCTTATGGGTAAGCGCCGCAAAAGGTAGGGCAATAATGGCGCTT
29247515 ATGGGAAAGCGCCGCT
66 ATGGGAAAGCGCCGCT
* * *
29247531 AAAGGTCAGAGAAATAGCGACGCTTATGGGTAAGCGCCGCAAAAGGTAGGGCAATAATGGCGCTT
1 AAAGGTCAGGGCAATAGCGGCGCTTATGGGTAAGCGCCGCAAAAGGTAGGGCAATAATGGCGCTT
*
29247596 ATGGGGAAGCGCCGCT
66 ATGGGAAAGCGCCGCT
* *
29247612 AAAGGTCAGGGCAATAGCGGCGCTTATGAAG-AAGCGCCGCTAAAG
1 AAAGGTCAGGGCAATAGCGGCGCTTATG-GGTAAGCGCCGCAAAAG
29247657 CTCAATAATA
Statistics
Matches: 178, Mismatches: 26, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
80 74 0.42
81 103 0.58
82 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.35, T:0.15
Consensus pattern (81 bp):
AAAGGTCAGGGCAATAGCGGCGCTTATGGGTAAGCGCCGCAAAAGGTAGGGCAATAATGGCGCTT
ATGGGAAAGCGCCGCT
Found at i:29248515 original size:20 final size:21
Alignment explanation
Indices: 29248466--29248515 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
29248456 ATTTCCTAAC
* * *
29248466 CCTTGGTTCTCTTTAGTTTCT
1 CCTTTGTTCTCTTCAGATTCT
29248487 CCTTT-TTCTCTTCAGATT-T
1 CCTTTGTTCTCTTCAGATTCT
29248506 CCTTTGTTCT
1 CCTTTGTTCT
29248516 ATTACCCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 6 0.24
20 15 0.60
21 4 0.16
ACGTcount: A:0.06, C:0.26, G:0.10, T:0.58
Consensus pattern (21 bp):
CCTTTGTTCTCTTCAGATTCT
Found at i:29251688 original size:43 final size:43
Alignment explanation
Indices: 29251599--29251771 Score: 226
Period size: 42 Copynumber: 4.1 Consensus size: 43
29251589 TGTTAATGGT
* * * *
29251599 GTTTGTG-GAAAAGTGTCGTTAAAGAACATG-TCTTTAGCGGC
1 GTTTGTGAGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGC
* *
29251640 GTTTGTGAGAAAAGCGCCGCTAAAGACCATGATCTATAGCGGC
1 GTTTGTGAGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGC
* * *
29251683 ATTTGTCA-AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGC
1 GTTTGTGAGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGC
* *
29251725 GTTTGTGAGATAAGCGCCACTAAAGACCATGTTCTTTAGCGGC
1 GTTTGTGAGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGC
29251768 GTTT
1 GTTT
29251772 CTCCTCATAA
Statistics
Matches: 114, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
41 7 0.06
42 56 0.49
43 51 0.45
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (43 bp):
GTTTGTGAGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGC
Found at i:29255282 original size:14 final size:14
Alignment explanation
Indices: 29255263--29255295 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
29255253 GTCAATGATG
29255263 ATTACTTAATTCTC
1 ATTACTTAATTCTC
29255277 ATTACTTAATTCTC
1 ATTACTTAATTCTC
29255291 ATTAC
1 ATTAC
29255296 CTACTTAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTACTTAATTCTC
Found at i:29258901 original size:37 final size:39
Alignment explanation
Indices: 29258823--29258905 Score: 125
Period size: 37 Copynumber: 2.2 Consensus size: 39
29258813 AATTTTTACT
*
29258823 AATTCATATTTTAATAATAATTATATTAAAAATATTATTA
1 AATT-ATATTTTAATAATAATTATATTAAAAATATAATTA
*
29258863 AATTATA-TTTAATAATAATTATGTT-AAAATATAATTA
1 AATTATATTTTAATAATAATTATATTAAAAATATAATTA
29258900 AATTAT
1 AATTAT
29258906 TTAATATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
37 17 0.41
38 17 0.41
39 3 0.07
40 4 0.10
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (39 bp):
AATTATATTTTAATAATAATTATATTAAAAATATAATTA
Found at i:29258936 original size:26 final size:26
Alignment explanation
Indices: 29258857--29258948 Score: 69
Period size: 26 Copynumber: 3.3 Consensus size: 26
29258847 ATTAAAAATA
29258857 TTATTAAATTATATTTAATAATAATTAT
1 TTATTAAATTATATTTAATAAT-ATT-T
* * *
29258885 GTTAAAATATAATTA-AATTATTTAATATTT
1 -TT--ATTA-AATTATATTTA-ATAATATTT
* *
29258915 TTATTAAATTATATTTAATAATAATC
1 TTATTAAATTATATTTAATAATATTT
29258941 TTATTAAA
1 TTATTAAA
29258949 ATTTAATAAC
Statistics
Matches: 50, Mismatches: 8, Indels: 13
0.70 0.11 0.18
Matches are distributed among these distances:
26 19 0.38
27 7 0.14
29 4 0.08
30 1 0.02
31 10 0.20
32 9 0.18
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (26 bp):
TTATTAAATTATATTTAATAATATTT
Found at i:29261070 original size:15 final size:16
Alignment explanation
Indices: 29261046--29261075 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
29261036 CCTTCTTTTT
29261046 CATAGCCATATTTTGG
1 CATAGCCATATTTTGG
29261062 CATAG-CATATTTTG
1 CATAGCCATATTTTG
29261076 AAATAGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (16 bp):
CATAGCCATATTTTGG
Found at i:29262605 original size:21 final size:21
Alignment explanation
Indices: 29262581--29262620 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
29262571 AATTAATAAT
29262581 ATTTATATTTGA-TTATTTTTA
1 ATTTATATTT-ATTTATTTTTA
*
29262602 ATTTATGTTTATTTATTTT
1 ATTTATATTTATTTATTTT
29262621 ATTTGTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (21 bp):
ATTTATATTTATTTATTTTTA
Found at i:29264341 original size:13 final size:13
Alignment explanation
Indices: 29264325--29264359 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
29264315 TTTTGTCATT
29264325 TTTAATTTTTTTA
1 TTTAATTTTTTTA
* *
29264338 TTTACTTTTTTTT
1 TTTAATTTTTTTA
29264351 TTTAATTTT
1 TTTAATTTT
29264360 AAAATTTCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTAATTTTTTTA
Found at i:29272545 original size:20 final size:21
Alignment explanation
Indices: 29272504--29272547 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
29272494 TTTAAAGATA
*
29272504 TTTTAATTCTGCTTTTTCTTT
1 TTTTAATTCTGCTATTTCTTT
29272525 TTTTAATTAC-GCTATTT-TTT
1 TTTTAATT-CTGCTATTTCTTT
29272545 TTT
1 TTT
29272548 ATTTTTCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 14 0.67
22 1 0.05
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTTAATTCTGCTATTTCTTT
Found at i:29273283 original size:150 final size:150
Alignment explanation
Indices: 29273006--29273300 Score: 493
Period size: 150 Copynumber: 2.0 Consensus size: 150
29272996 ATAATGAATC
* * *
29273006 TTCATGATGTTAAGGATTAAATTGTAAACTTTGAAAAATTTATAATTGAATCAAAAGAAATGATA
1 TTCAGGATGTTAAGGATTAAATTGTAAACTTTGAAAAAATTATAATTGAAACAAAAGAAATGATA
* * *
29273071 TGCATAAAAATATGTTATGTGAAATAAGATATTATAATGAATTATTTGATTAAAGTGTTTATATG
66 TGCATAAAAATATGTCATGTGAAATAAGATATTATAATGAATTATTTGATTAAAGGGCTTATATG
29273136 ATGAAAAATAAATTAAATAT
131 ATGAAAAATAAATTAAATAT
*
29273156 TTCAGGATGTTGAGGATTAAATTGTAAACTTTGAAAAAAATT-TAATTGAAACAAAAGAAATGAT
1 TTCAGGATGTTAAGGATTAAATTGTAAACTTTG-AAAAAATTATAATTGAAACAAAAGAAATGAT
*
29273220 ATGCATAAAAATTTGTCATGTGAAATAAGATATTATAATGAATTATTTGATTAAAGGGCTTATAT
65 ATGCATAAAAATATGTCATGTGAAATAAGATATTATAATGAATTATTTGATTAAAGGGCTTATAT
*
29273285 GGTGAAAAATAAATTA
130 GATGAAAAATAAATTA
29273301 TATGGCTATA
Statistics
Matches: 135, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
150 128 0.95
151 7 0.05
ACGTcount: A:0.46, C:0.03, G:0.15, T:0.36
Consensus pattern (150 bp):
TTCAGGATGTTAAGGATTAAATTGTAAACTTTGAAAAAATTATAATTGAAACAAAAGAAATGATA
TGCATAAAAATATGTCATGTGAAATAAGATATTATAATGAATTATTTGATTAAAGGGCTTATATG
ATGAAAAATAAATTAAATAT
Found at i:29278815 original size:30 final size:30
Alignment explanation
Indices: 29278779--29278846 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
29278769 ATGTTAATGG
*
29278779 GTGACTGATTTGTCACTTTTC-AATATGTT-A
1 GTGACTGATTTATCACTTTTCGAA-A-GTTGA
*
29278809 GTGACTGATTTATCATTTTTCGAAAGTTGA
1 GTGACTGATTTATCACTTTTCGAAAGTTGA
29278839 GTGACTGA
1 GTGACTGA
29278847 ATTGAAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 3 0.09
30 29 0.85
31 2 0.06
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.43
Consensus pattern (30 bp):
GTGACTGATTTATCACTTTTCGAAAGTTGA
Found at i:29279290 original size:23 final size:23
Alignment explanation
Indices: 29279228--29279284 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
29279218 CTAGTTTTTA
29279228 TCTGTCTTTGTGACACGTTTTTCC
1 TCTG-CTTTGTGACACGTTTTTCC
* * *
29279252 CCTACCTTGTGACACGTTTTTCC
1 TCTGCTTTGTGACACGTTTTTCC
29279275 TCTGCTTTGT
1 TCTGCTTTGT
29279285 AGCACGCTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 25 0.93
24 2 0.07
ACGTcount: A:0.09, C:0.28, G:0.16, T:0.47
Consensus pattern (23 bp):
TCTGCTTTGTGACACGTTTTTCC
Found at i:29280958 original size:2 final size:2
Alignment explanation
Indices: 29280951--29280984 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
29280941 TCACAACCAA
29280951 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29280985 GTAGTGTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29287903 original size:15 final size:15
Alignment explanation
Indices: 29287883--29287912 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29287873 ATTCAATCAA
*
29287883 ATATAAAATTAAAAT
1 ATATAAAAATAAAAT
29287898 ATATAAAAATAAAAT
1 ATATAAAAATAAAAT
29287913 TTTAATTGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
ATATAAAAATAAAAT
Found at i:29287981 original size:2 final size:2
Alignment explanation
Indices: 29287974--29288027 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
29287964 AAATCTTAAC
29287974 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29288016 AT AT AT AT AT AT
1 AT AT AT AT AT AT
29288028 TAAATAAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29291422 original size:24 final size:24
Alignment explanation
Indices: 29291390--29291440 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
29291380 GTAAACTTGT
29291390 TAACCATTCTGGGCTCATAAGAGC
1 TAACCATTCTGGGCTCATAAGAGC
**
29291414 TAACCATTCTGGGCTCATGTGAGC
1 TAACCATTCTGGGCTCATAAGAGC
29291438 TAA
1 TAA
29291441 TATTGTCTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (24 bp):
TAACCATTCTGGGCTCATAAGAGC
Found at i:29292163 original size:21 final size:21
Alignment explanation
Indices: 29292139--29292193 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
29292129 GGAGTTTTTA
*
29292139 GTATCGGTAGAAGAGTCACTT
1 GTATCGGTAGAAGAGTCACAT
* **
29292160 GTATCGGAAGAACTGTCACAT
1 GTATCGGTAGAAGAGTCACAT
29292181 GTATCGGTAGAAG
1 GTATCGGTAGAAG
29292194 TCTACACTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.25
Consensus pattern (21 bp):
GTATCGGTAGAAGAGTCACAT
Found at i:29293280 original size:33 final size:33
Alignment explanation
Indices: 29293238--29293306 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
29293228 CTATGTTCAA
*
29293238 ATAGATAAGGAAATGAAAGTTGATACATTGGGT
1 ATAGATAAGGAAATGAAAGTTGAGACATTGGGT
*
29293271 ATAGATAAGGAAATGAAAGTTGAGGCATTGGGT
1 ATAGATAAGGAAATGAAAGTTGAGACATTGGGT
29293304 ATA
1 ATA
29293307 CGACTTCTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.42, C:0.03, G:0.29, T:0.26
Consensus pattern (33 bp):
ATAGATAAGGAAATGAAAGTTGAGACATTGGGT
Found at i:29302598 original size:21 final size:20
Alignment explanation
Indices: 29302553--29302597 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
29302543 TGGAAAATAA
29302553 TTTTTGAAAAATGAATTATT
1 TTTTTGAAAAATGAATTATT
*
29302573 TTTTTGAAAGAATTAA-TATT
1 TTTTTGAAA-AATGAATTATT
29302593 TTTTT
1 TTTTT
29302598 TTGTATTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (20 bp):
TTTTTGAAAAATGAATTATT
Found at i:29305544 original size:14 final size:14
Alignment explanation
Indices: 29305523--29305583 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
29305513 AAAATAATTC
29305523 AATTTT-AAATTTA
1 AATTTTAAAATTTA
* *
29305536 AATTTTTAATTTTA
1 AATTTTAAAATTTA
*** *
29305550 AAAAATAAAAATTA
1 AATTTTAAAATTTA
29305564 AATTTTAAAAATTTA
1 AATTTT-AAAATTTA
29305579 AATTT
1 AATTT
29305584 AAATTTGTGA
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
13 6 0.17
14 17 0.49
15 12 0.34
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATTTTAAAATTTA
Found at i:29305558 original size:21 final size:22
Alignment explanation
Indices: 29305529--29305589 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 22
29305519 ATTCAATTTT
* *
29305529 AAATTTAAATTTTTAATTTTAA
1 AAATATAAATTTTAAATTTTAA
**
29305551 AAA-ATAAAAATTAAATTTTAA
1 AAATATAAATTTTAAATTTTAA
*
29305572 AAATTTAAA-TTTAAATTT
1 AAATATAAATTTTAAATTT
29305590 GTGAATACTA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 25 0.78
22 7 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AAATATAAATTTTAAATTTTAA
Found at i:29325333 original size:27 final size:27
Alignment explanation
Indices: 29325271--29325336 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 27
29325261 ATAACTCTTT
* *
29325271 TAATTATCAAAATAAAATAATAAATATG
1 TAATTAT-ATAATAAAATAATAAATATA
* *
29325299 TAATTATATAATAAAATATTATATATA
1 TAATTATATAATAAAATAATAAATATA
29325326 TATATATATAT
1 TA-AT-TATAT
29325337 CATTTTGTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 18 0.56
28 9 0.28
29 5 0.16
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (27 bp):
TAATTATATAATAAAATAATAAATATA
Found at i:29325466 original size:102 final size:102
Alignment explanation
Indices: 29325246--29325457 Score: 275
Period size: 102 Copynumber: 2.1 Consensus size: 102
29325236 AAAGTTTTTG
* * *
29325246 AAATCTTTTTAATTAATAACTCTTTTAATTATCAAAATAAAATAATAAATATGTAATTATATAAT
1 AAATATTTTTAATTAATAACTCCTTTAATTATAAAAATAAAATAATAAATATGTAATTATATAAT
* *
29325311 AAAATATTATATATATATATATATATCATTTTGTTAA
66 AAAATATTATATATATATATATATATCATTATATTAA
* * * *
29325348 AAATATTTTTAATTAATAACTCCTTTATTTATAAAAATAGATTACTAAATATGTAATTATATAAT
1 AAATATTTTTAATTAATAACTCCTTTAATTATAAAAATAAAATAATAAATATGTAATTATATAAT
* * * *
29325413 -GAA-ATTATATATTTTTTATATTTATCATTATATTAA
66 AAAATATTATATA-TATATATATATATCATTATATTAA
*
29325449 ATATATTTT
1 AAATATTTT
29325458 ATTTTTAATC
Statistics
Matches: 95, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
100 8 0.08
101 29 0.31
102 58 0.61
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (102 bp):
AAATATTTTTAATTAATAACTCCTTTAATTATAAAAATAAAATAATAAATATGTAATTATATAAT
AAAATATTATATATATATATATATATCATTATATTAA
Found at i:29325586 original size:3 final size:3
Alignment explanation
Indices: 29325578--29325611 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
29325568 AAATCAAAAT
29325578 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
29325612 AATATAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:29337731 original size:18 final size:18
Alignment explanation
Indices: 29337708--29337746 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
29337698 ACTATTATTA
29337708 TTATTATAATATTTAATT
1 TTATTATAATATTTAATT
* *
29337726 TTATTATAATTTTTATTT
1 TTATTATAATATTTAATT
29337744 TTA
1 TTA
29337747 CATTAACCGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATTATAATATTTAATT
Found at i:29339512 original size:6 final size:6
Alignment explanation
Indices: 29339480--29339511 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
29339470 TAATGTTCAA
*
29339480 ATTTAT ATTTAT ATTTAT ATTTAT ATATAT AT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT AT
29339512 AAGAATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
ATTTAT
Found at i:29342522 original size:90 final size:90
Alignment explanation
Indices: 29342368--29342604 Score: 384
Period size: 90 Copynumber: 2.6 Consensus size: 90
29342358 GATCTCTACT
* * * * * * *
29342368 TCTTTCTCATCCTGTACGCCGTTGCTTGATTTTGCTTCGAGTGAATGCTCATCAATTACCCCAGC
1 TCTTTCTCATCCTCTACACCGTTGTTTGGTTCTGCTTCAAGTAAATGCTCATCAATTACCCCAGC
29342433 TGGCAACTCTTTGAACAAGTCGATC
66 TGGCAACTCTTTGAACAAGTCGATC
* * *
29342458 TCTTTCTCATCCTCTACACCATTGTTTGGTTCTGCTTCAAGTAAATGCTCATTAATTACTCCAGC
1 TCTTTCTCATCCTCTACACCGTTGTTTGGTTCTGCTTCAAGTAAATGCTCATCAATTACCCCAGC
29342523 TGGCAACTCTTTGAACAAGTCGATC
66 TGGCAACTCTTTGAACAAGTCGATC
29342548 TCTTTCTCATCCTCTACACCGTTGTTTGGTTCTGCTTCAAGTAAATGCTCATCAATT
1 TCTTTCTCATCCTCTACACCGTTGTTTGGTTCTGCTTCAAGTAAATGCTCATCAATT
29342605 TTGGAAATGG
Statistics
Matches: 135, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 135 1.00
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (90 bp):
TCTTTCTCATCCTCTACACCGTTGTTTGGTTCTGCTTCAAGTAAATGCTCATCAATTACCCCAGC
TGGCAACTCTTTGAACAAGTCGATC
Found at i:29346748 original size:3 final size:3
Alignment explanation
Indices: 29346742--29346767 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
29346732 CTAAAGTATC
29346742 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
29346768 TTGCTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:29347482 original size:39 final size:39
Alignment explanation
Indices: 29347428--29347508 Score: 110
Period size: 39 Copynumber: 2.1 Consensus size: 39
29347418 ACGAGCAGCA
*
29347428 TGGTGGTGGCCGTGGTGGAAGCTTTGGA-TATGGTGATGG
1 TGGTGGTGGCCGTGGTGGAAGCTCTGGATTA-GGTGATGG
** *
29347467 TGGTGGTGGTGGTGGTGGAAGCTCTGGATTAGGTGGTGG
1 TGGTGGTGGCCGTGGTGGAAGCTCTGGATTAGGTGATGG
29347506 TGG
1 TGG
29347509 AGACAATTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 35 0.95
40 2 0.05
ACGTcount: A:0.11, C:0.06, G:0.52, T:0.31
Consensus pattern (39 bp):
TGGTGGTGGCCGTGGTGGAAGCTCTGGATTAGGTGATGG
Found at i:29349631 original size:19 final size:21
Alignment explanation
Indices: 29349604--29349642 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
29349594 CTATTTATTT
29349604 TTATGTTTG-ATA-AATATAA
1 TTATGTTTGTATATAATATAA
*
29349623 TTATTTTTGTATATAATATA
1 TTATGTTTGTATATAATATA
29349643 TAAACATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (21 bp):
TTATGTTTGTATATAATATAA
Found at i:29350030 original size:36 final size:36
Alignment explanation
Indices: 29349990--29350059 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
29349980 AAATTATTAA
* *
29349990 TATTTTTAAATAAATCCTTATAAATTTTTTTAAAAT
1 TATTTTCAAATAAATCCTTATAAAGTTTTTTAAAAT
*
29350026 TATTTTCAAATAAATCCTTATAACGTTTTTTAAA
1 TATTTTCAAATAAATCCTTATAAAGTTTTTTAAA
29350060 TGTTAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.50
Consensus pattern (36 bp):
TATTTTCAAATAAATCCTTATAAAGTTTTTTAAAAT
Found at i:29351986 original size:83 final size:83
Alignment explanation
Indices: 29351847--29352012 Score: 305
Period size: 83 Copynumber: 2.0 Consensus size: 83
29351837 TATGAAAATA
*
29351847 TAATCAAGATTGTTTTGTATTCTGTTGTACTTTATGATAAAAAGTACTTTATTTAAAATATCTGA
1 TAATCAAGATTGTTTTGTATTCTGTTGTACTTTATGATAAAAAGCACTTTATTTAAAATATCTGA
29351912 GATGAATCTTCCAAGTAT
66 GATGAATCTTCCAAGTAT
* *
29351930 TAATCAAGATTGTTTTGTATTCTGTTGTACTTTATGATAAGAAGCACTTTATTTAAAATGTCTGA
1 TAATCAAGATTGTTTTGTATTCTGTTGTACTTTATGATAAAAAGCACTTTATTTAAAATATCTGA
29351995 GATGAATCTTCCAAGTAT
66 GATGAATCTTCCAAGTAT
29352013 CATGTTGGAT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 80 1.00
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (83 bp):
TAATCAAGATTGTTTTGTATTCTGTTGTACTTTATGATAAAAAGCACTTTATTTAAAATATCTGA
GATGAATCTTCCAAGTAT
Found at i:29354642 original size:41 final size:41
Alignment explanation
Indices: 29354585--29354677 Score: 150
Period size: 41 Copynumber: 2.3 Consensus size: 41
29354575 TTTTATTTTA
*
29354585 ACAAGAATTCTAGTCACTAAATTCTAACAATCTCCACCTCC
1 ACAAGAATTCTAGTCACCAAATTCTAACAATCTCCACCTCC
* **
29354626 ACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACCTTG
1 ACAAGAATTCTAGTCACCAAATTCTAACAATCTCCACCTCC
29354667 ACAAGAATTCT
1 ACAAGAATTCT
29354678 CTACGAACAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.37, C:0.30, G:0.06, T:0.27
Consensus pattern (41 bp):
ACAAGAATTCTAGTCACCAAATTCTAACAATCTCCACCTCC
Found at i:29354689 original size:17 final size:17
Alignment explanation
Indices: 29354667--29354705 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
29354657 CTCCACCTTG
* *
29354667 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
29354684 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
29354701 ACAAG
1 ACAAG
29354706 TTCTCCACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:29357915 original size:18 final size:18
Alignment explanation
Indices: 29357892--29357940 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 18
29357882 TATGATGATA
29357892 TATATGTGATGAACAATG
1 TATATGTGATGAACAATG
29357910 TATATGTGAAATATGAACAATG
1 TATATGTG----ATGAACAATG
29357932 TATATGTGA
1 TATATGTGA
29357941 AATATTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
18 9 0.33
22 18 0.67
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.35
Consensus pattern (18 bp):
TATATGTGATGAACAATG
Found at i:29357925 original size:22 final size:22
Alignment explanation
Indices: 29357900--29357945 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
29357890 TATATATGTG
29357900 ATGAACAATGTATATGTGAAAT
1 ATGAACAATGTATATGTGAAAT
29357922 ATGAACAATGTATATGTGAAAT
1 ATGAACAATGTATATGTGAAAT
29357944 AT
1 AT
29357946 TATATGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (22 bp):
ATGAACAATGTATATGTGAAAT
Found at i:29358102 original size:6 final size:6
Alignment explanation
Indices: 29358091--29358128 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
29358081 ATTTGTGATC
*
29358091 GAAAGT GAAAGT GAAAGT GAAAGT GAAATT GAAAGT GA
1 GAAAGT GAAAGT GAAAGT GAAAGT GAAAGT GAAAGT GA
29358129 TATGAATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.32, T:0.18
Consensus pattern (6 bp):
GAAAGT
Found at i:29362001 original size:24 final size:24
Alignment explanation
Indices: 29361971--29362022 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
29361961 AATAGAAAGC
29361971 TTCCTAGCCTCCCAATTCTGCAAT
1 TTCCTAGCCTCCCAATTCTGCAAT
* *
29361995 TTCCTAGCCTCCCAATTTTGTAAT
1 TTCCTAGCCTCCCAATTCTGCAAT
29362019 TTCC
1 TTCC
29362023 GTCTAACCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.19, C:0.35, G:0.08, T:0.38
Consensus pattern (24 bp):
TTCCTAGCCTCCCAATTCTGCAAT
Found at i:29365552 original size:18 final size:18
Alignment explanation
Indices: 29365529--29365586 Score: 98
Period size: 18 Copynumber: 3.2 Consensus size: 18
29365519 TTTTAAAAAA
*
29365529 AATTAAAATATTTTTGAC
1 AATTAAAATATATTTGAC
*
29365547 AATTAAAATATACTTGAC
1 AATTAAAATATATTTGAC
29365565 AATTAAAATATATTTGAC
1 AATTAAAATATATTTGAC
29365583 AATT
1 AATT
29365587 TTAAAATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (18 bp):
AATTAAAATATATTTGAC
Found at i:29372591 original size:23 final size:24
Alignment explanation
Indices: 29372565--29372610 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
29372555 TTTTACACTA
*
29372565 AAATTA-TTTATGCAAGATAGCAC
1 AAATTATTTTATGCAAAATAGCAC
*
29372588 AAATTATTTTATGTAAAATAGCA
1 AAATTATTTTATGCAAAATAGCA
29372611 TTGAAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.35
Consensus pattern (24 bp):
AAATTATTTTATGCAAAATAGCAC
Found at i:29385032 original size:7 final size:7
Alignment explanation
Indices: 29385022--29385049 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
29385012 TATATTACAC
29385022 AATTGAA
1 AATTGAA
29385029 AATTGAA
1 AATTGAA
29385036 AATTGAA
1 AATTGAA
29385043 AATTGAA
1 AATTGAA
29385050 TCAAGCTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (7 bp):
AATTGAA
Found at i:29386177 original size:30 final size:28
Alignment explanation
Indices: 29386115--29386183 Score: 95
Period size: 29 Copynumber: 2.5 Consensus size: 28
29386105 AATTTGTATC
*
29386115 TTTTATATTTTTAAAAAATTAAATTAAA
1 TTTTATATTTTTAAAAAATTAAAATAAA
*
29386143 TTTTATCATTTTTAAAAAATTAAAATATA
1 TTTTAT-ATTTTTAAAAAATTAAAATAAA
*
29386172 GTTT-TATTTTTA
1 TTTTATATTTTTA
29386184 TTAATAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 7 0.19
28 7 0.19
29 23 0.62
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (28 bp):
TTTTATATTTTTAAAAAATTAAAATAAA
Found at i:29391862 original size:19 final size:19
Alignment explanation
Indices: 29391815--29391862 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
29391805 AAAAAATTAT
* **
29391815 TTAAAATTAGTAAACCTTA
1 TTAAAATTAGAAAACAATA
*
29391834 TAAGAAATTAGAAAACAATA
1 TTA-AAATTAGAAAACAATA
29391854 TTAAAATTA
1 TTAAAATTA
29391863 TTTAAAATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.31
Consensus pattern (19 bp):
TTAAAATTAGAAAACAATA
Found at i:29396918 original size:6 final size:6
Alignment explanation
Indices: 29396907--29396933 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
29396897 GTTTCTCATG
29396907 ATCCGA ATCCGA ATCCGA ATCCGA ATC
1 ATCCGA ATCCGA ATCCGA ATCCGA ATC
29396934 TGAAGATGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.33, G:0.15, T:0.19
Consensus pattern (6 bp):
ATCCGA
Found at i:29402383 original size:13 final size:14
Alignment explanation
Indices: 29402365--29402393 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
29402355 ATATTTTAAA
29402365 TTATTTTT-TATTT
1 TTATTTTTATATTT
29402378 TTATTTTTATATTT
1 TTATTTTTATATTT
29402392 TT
1 TT
29402394 TAAAATTTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
TTATTTTTATATTT
Found at i:29406270 original size:22 final size:23
Alignment explanation
Indices: 29406244--29406298 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 23
29406234 ATAATTTCAA
*
29406244 ATTTAAATTTATA-CTAATTATT
1 ATTTTAATTTATATCTAATTATT
*
29406266 -TTTTATTTTATATCTAATTATT
1 ATTTTAATTTATATCTAATTATT
*
29406288 ATTTTGATTTA
1 ATTTTAATTTA
29406299 GTAGTAAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 10 0.37
22 9 0.33
23 8 0.30
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (23 bp):
ATTTTAATTTATATCTAATTATT
Found at i:29408614 original size:7 final size:7
Alignment explanation
Indices: 29408602--29408632 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
29408592 TTATAGTGTT
29408602 TGGTGAA
1 TGGTGAA
29408609 TGGTGAA
1 TGGTGAA
29408616 TGGTGAA
1 TGGTGAA
*
29408623 TGGAGAA
1 TGGTGAA
29408630 TGG
1 TGG
29408633 AGGTTTCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.45, T:0.26
Consensus pattern (7 bp):
TGGTGAA
Found at i:29409235 original size:31 final size:29
Alignment explanation
Indices: 29409197--29409266 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 29
29409187 ATCTCAAAAC
29409197 TATACATGAACTATAG-TTTAATGTGCAATTG
1 TATACATGAACT-TAGATTT--TGTGCAATTG
* *
29409228 TATACATGAACTTTGATTTTGTGCAATTT
1 TATACATGAACTTAGATTTTGTGCAATTG
29409257 TATACATGAA
1 TATACATGAA
29409267 ATTTTGATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
29 19 0.53
30 2 0.06
31 15 0.42
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.41
Consensus pattern (29 bp):
TATACATGAACTTAGATTTTGTGCAATTG
Found at i:29409260 original size:29 final size:30
Alignment explanation
Indices: 29409218--29409276 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
29409208 TATAGTTTAA
29409218 TGTGCAATTGTATACATG-AACTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
* *
29409247 TGTGCAATTTTATACATGAAATTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
29409277 GATCCAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.29, C:0.08, G:0.15, T:0.47
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAACTTTGATTT
Found at i:29409285 original size:30 final size:29
Alignment explanation
Indices: 29409222--29409285 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
29409212 GTTTAATGTG
*
29409222 CAATTGTATACATGAACTTTGATTTTGTG
1 CAATTGTATACATGAACTTTGATTTTGTC
* *
29409251 CAATTTTATACATGAAATTTTGA-TTTGATC
1 CAATTGTATACATG-AACTTTGATTTTG-TC
29409281 CAATT
1 CAATT
29409286 CTTGTAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 17 0.57
30 13 0.43
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.45
Consensus pattern (29 bp):
CAATTGTATACATGAACTTTGATTTTGTC
Found at i:29409494 original size:29 final size:31
Alignment explanation
Indices: 29409423--29409507 Score: 104
Period size: 29 Copynumber: 2.8 Consensus size: 31
29409413 AAATCAAAAG
* * *
29409423 TAAAGTTTCAAGTATA-CATTTCAACCACAAT
1 TAAAGTTTCATGTATATAATTGC-ACCACAAT
*
29409454 TAGAGTTTCATGTATATAATTGCACCA-AAT
1 TAAAGTTTCATGTATATAATTGCACCACAAT
29409484 TAAAG-TTCATGTATATAATTGCAC
1 TAAAGTTTCATGTATATAATTGCAC
29409508 ATTAAATCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
29 19 0.40
30 7 0.15
31 18 0.38
32 4 0.08
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (31 bp):
TAAAGTTTCATGTATATAATTGCACCACAAT
Found at i:29417698 original size:24 final size:26
Alignment explanation
Indices: 29417662--29417709 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
29417652 AGAGAAATGT
29417662 AAATGTGATATATGA-A-ATTATGAG
1 AAATGTGATATATGAGAGATTATGAG
29417686 AAATGATGA-ATATGAGAGATTATG
1 AAATG-TGATATATGAGAGATTATG
29417710 TCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGTGATATATGAGAGATTATGAG
Found at i:29417817 original size:22 final size:22
Alignment explanation
Indices: 29417791--29417894 Score: 120
Period size: 22 Copynumber: 4.6 Consensus size: 22
29417781 TCAACACTTC
*
29417791 GTGTGCTTCTGTTCAGCATTGT
1 GTGTGCTTCTGTTCAGCACTGT
* *
29417813 GTGTGCTTATGTTTAGCACTGT
1 GTGTGCTTCTGTTCAGCACTGT
29417835 GTGTGCTTCTGTTCAGCACTGT
1 GTGTGCTTCTGTTCAGCACTGT
*
29417857 GTGTGCCTACTGTTTCCCAGCACT-T
1 GTGTG-CTTCTG-TT--CAGCACTGT
*
29417882 ATGTGCTTCTGTT
1 GTGTGCTTCTGTT
29417895 TCTCCAGCAC
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
22 44 0.63
23 7 0.10
24 7 0.10
25 5 0.07
26 7 0.10
ACGTcount: A:0.11, C:0.21, G:0.25, T:0.43
Consensus pattern (22 bp):
GTGTGCTTCTGTTCAGCACTGT
Found at i:29417839 original size:44 final size:45
Alignment explanation
Indices: 29417785--29417894 Score: 143
Period size: 44 Copynumber: 2.4 Consensus size: 45
29417775 TACTGATCAA
* *
29417785 CACTTCGTGTGCTTCTGTTCAGCATTGTGTGTGCTTA-TGTTT-AG
1 CACTT-GTGTGCTTCTGTTCAGCACTGTGTGTGCCTACTGTTTCAG
29417829 CACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCCTACTGTTTCCCAG
1 CACT-TGTGTGCTTCTGTTCAGCACTGTGTGTGCCTACTGTTT--CAG
*
29417877 CACTTATGTGCTTCTGTT
1 CACTTGTGTGCTTCTGTT
29417895 TCTCCAGCAC
Statistics
Matches: 58, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
44 33 0.57
45 6 0.10
47 13 0.22
48 6 0.10
ACGTcount: A:0.11, C:0.23, G:0.24, T:0.43
Consensus pattern (45 bp):
CACTTGTGTGCTTCTGTTCAGCACTGTGTGTGCCTACTGTTTCAG
Found at i:29417901 original size:25 final size:24
Alignment explanation
Indices: 29417827--29417944 Score: 134
Period size: 25 Copynumber: 4.8 Consensus size: 24
29417817 GCTTATGTTT
*
29417827 AGCACTGTGTGTGCTTCTG-TT--C
1 AGCACT-TATGTGCTTCTGTTTCCC
* *
29417849 AGCACTGTGTGTGCCTACTGTTTCCC
1 AGCACT-TATGTG-CTTCTGTTTCCC
29417875 AGCACTTATGTGCTTCTGTTTCTCC
1 AGCACTTATGTGCTTCTGTTTC-CC
29417900 AGCACTTATGTGCTTCTGTTTCCCC
1 AGCACTTATGTGCTTCTGTTT-CCC
*
29417925 AGCACTTATGCGCTTCTGTT
1 AGCACTTATGTGCTTCTGTT
29417945 AAGTACTTCG
Statistics
Matches: 86, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.15
23 5 0.06
24 11 0.13
25 49 0.57
26 8 0.09
ACGTcount: A:0.12, C:0.28, G:0.20, T:0.40
Consensus pattern (24 bp):
AGCACTTATGTGCTTCTGTTTCCC
Found at i:29425736 original size:155 final size:155
Alignment explanation
Indices: 29425553--29425866 Score: 601
Period size: 155 Copynumber: 2.0 Consensus size: 155
29425543 TAATTTATAA
29425553 AAAAAAAATCCCGAACTACCCTGGTTGCCATTGGATCTTCGTGATCAAAATAGAGAGAAAAAAAT
1 AAAAAAAATCCCGAACTACCCTGGTTGCCATTGGATCTTCGTGATCAAAATAGAGAGAAAAAAAT
*
29425618 ACGTCTATGTTTCAGTCAAATATTCAAAGTTCGAACGTAAACAAAGAAGGAAGGAAAGATGAACA
66 ACGTCGATGTTTCAGTCAAATATTCAAAGTTCGAACGTAAACAAAGAAGGAAGGAAAGATGAACA
29425683 TTACAACCCCAGTTTCAAAGCATTC
131 TTACAACCCCAGTTTCAAAGCATTC
29425708 AAAAAAAATCCCGAACTACCCTGGTTGCCATTGGATCTTCGTGATCAAAATAGAGAGAAAAAAAT
1 AAAAAAAATCCCGAACTACCCTGGTTGCCATTGGATCTTCGTGATCAAAATAGAGAGAAAAAAAT
29425773 ACGTCGATGTTTCAGTCAAATATTCAAAGTTCGAACGTAAACAAAGAAGGAAGGAAAGATGAACA
66 ACGTCGATGTTTCAGTCAAATATTCAAAGTTCGAACGTAAACAAAGAAGGAAGGAAAGATGAACA
**
29425838 TTACAATTCCAGTTTCAAAGCATTC
131 TTACAACCCCAGTTTCAAAGCATTC
29425863 AAAA
1 AAAA
29425867 CTCCTCCTTA
Statistics
Matches: 156, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
155 156 1.00
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.23
Consensus pattern (155 bp):
AAAAAAAATCCCGAACTACCCTGGTTGCCATTGGATCTTCGTGATCAAAATAGAGAGAAAAAAAT
ACGTCGATGTTTCAGTCAAATATTCAAAGTTCGAACGTAAACAAAGAAGGAAGGAAAGATGAACA
TTACAACCCCAGTTTCAAAGCATTC
Found at i:29430714 original size:14 final size:15
Alignment explanation
Indices: 29430682--29430727 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
29430672 AAAAACTATA
*
29430682 AAAATTAAAATTAAT
1 AAAATTAAAATAAAT
29430697 -AAATTAAAA-AAAT
1 AAAATTAAAATAAAT
*
29430710 AAAATTAGAATACAAT
1 AAAATTAAAATA-AAT
29430726 AA
1 AA
29430728 TTAATTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 3 0.12
14 17 0.65
15 1 0.04
16 5 0.19
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (15 bp):
AAAATTAAAATAAAT
Found at i:29433531 original size:9 final size:9
Alignment explanation
Indices: 29433510--29433556 Score: 51
Period size: 10 Copynumber: 5.1 Consensus size: 9
29433500 TCTAGATATT
29433510 ATTTTTAATA
1 ATTTTTAA-A
29433520 ATTTTTAAA
1 ATTTTTAAA
**
29433529 A-TTTTAGG
1 ATTTTTAAA
29433537 ATTTTTAAA
1 ATTTTTAAA
29433546 ATTTTCTAAA
1 ATTTT-TAAA
29433556 A
1 A
29433557 CGTTAATATG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
8 6 0.19
9 12 0.39
10 13 0.42
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:29436005 original size:19 final size:18
Alignment explanation
Indices: 29435964--29436014 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
29435954 AAAATAAAAT
29435964 CACAAAAATGTGGACAAC
1 CACAAAAATGTGGACAAC
*
29435982 CACAAAATTGTGGGA-AACC
1 CACAAAAATGT-GGACAA-C
*
29436001 CACAAAAATATGGA
1 CACAAAAATGTGGA
29436015 TTGAAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.49, C:0.20, G:0.18, T:0.14
Consensus pattern (18 bp):
CACAAAAATGTGGACAAC
Found at i:29437137 original size:17 final size:17
Alignment explanation
Indices: 29437107--29437139 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29437097 GTGTAATATT
29437107 ATTATAAATGTGTTTGA
1 ATTATAAATGTGTTTGA
29437124 ATTATGAAAT-TGTTTG
1 ATTAT-AAATGTGTTTG
29437140 TCCATAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.48
Consensus pattern (17 bp):
ATTATAAATGTGTTTGA
Found at i:29437395 original size:22 final size:22
Alignment explanation
Indices: 29437370--29437444 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
29437360 CACTTCTATG
29437370 CTCTCTGTTCAACACTTCGGTA
1 CTCTCTGTTCAACACTTCGGTA
* ** *
29437392 CTCTTTGTTCAGTACTTCAGTA
1 CTCTCTGTTCAACACTTCGGTA
** * *
29437414 CTCTCTAATCAACACTTCGATG
1 CTCTCTGTTCAACACTTCGGTA
29437436 CTCTCTGTT
1 CTCTCTGTT
29437445 TAGTAATTCT
Statistics
Matches: 39, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.19, C:0.29, G:0.12, T:0.40
Consensus pattern (22 bp):
CTCTCTGTTCAACACTTCGGTA
Found at i:29437426 original size:44 final size:44
Alignment explanation
Indices: 29437363--29437463 Score: 114
Period size: 44 Copynumber: 2.3 Consensus size: 44
29437353 AGCTTGTCAC
* ** * * *
29437363 TTCTATGCTCTCTGTTCAACACTTCGGTACTCTTTGTTCAGTAC
1 TTCTATACTCTCTAATCAACACTTCGATACTCTCTGTTCAGTAA
* *
29437407 TTC-AGTACTCTCTAATCAACACTTCGATGCTCTCTGTTTAGTAA
1 TTCTA-TACTCTCTAATCAACACTTCGATACTCTCTGTTCAGTAA
29437451 TTCTATACTCTCT
1 TTCTATACTCTCT
29437464 GTTTAGCACT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
43 1 0.02
44 45 0.96
45 1 0.02
ACGTcount: A:0.20, C:0.27, G:0.11, T:0.43
Consensus pattern (44 bp):
TTCTATACTCTCTAATCAACACTTCGATACTCTCTGTTCAGTAA
Found at i:29438871 original size:21 final size:21
Alignment explanation
Indices: 29438823--29438872 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
29438813 TTAAAGCATT
*
29438823 GATATTCTGGATCAGGATACC
1 GATATTTTGGATCAGGATACC
*
29438844 GATATTTTGGATCAGGGTACC
1 GATATTTTGGATCAGGATACC
29438865 GATATTTT
1 GATATTTT
29438873 ACAAGGTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (21 bp):
GATATTTTGGATCAGGATACC
Found at i:29439680 original size:21 final size:21
Alignment explanation
Indices: 29439634--29439680 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
29439624 TTTCAACAAT
*
29439634 ATTTATTATTAAAAAAAGTTA
1 ATTTACTATTAAAAAAAGTTA
* *
29439655 GTTTACTATTAATAATAAG-TA
1 ATTTACTATTAA-AAAAAGTTA
29439676 ATTTA
1 ATTTA
29439681 ATATATATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (21 bp):
ATTTACTATTAAAAAAAGTTA
Found at i:29440154 original size:24 final size:26
Alignment explanation
Indices: 29440116--29440164 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
29440106 AACAATTTCT
29440116 TAAAATAAGATTATTT-TTA-TTAAA
1 TAAAATAAGATTATTTATTACTTAAA
29440140 TAAAATAATGA-TATTTATTACTTAA
1 TAAAATAA-GATTATTTATTACTTAA
29440165 TTTTTAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 13 0.59
25 5 0.23
26 4 0.18
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (26 bp):
TAAAATAAGATTATTTATTACTTAAA
Found at i:29443155 original size:15 final size:15
Alignment explanation
Indices: 29443132--29443171 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
29443122 CACATGCCTC
*
29443132 TCTTATTCTTCATCT
1 TCTTCTTCTTCATCT
29443147 TCTTCTTCTTCATCT
1 TCTTCTTCTTCATCT
*
29443162 TCATCTTCTT
1 TCTTCTTCTT
29443172 TCCTTTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.10, C:0.30, G:0.00, T:0.60
Consensus pattern (15 bp):
TCTTCTTCTTCATCT
Found at i:29443309 original size:113 final size:115
Alignment explanation
Indices: 29443174--29443406 Score: 391
Period size: 113 Copynumber: 2.0 Consensus size: 115
29443164 ATCTTCTTTC
*
29443174 CTTTTGATTCCAATATCTTTAGTTACAAATCTGTCTCAAAGCTTGAATCTTTAAAAC-CTATTAA
1 CTTTTGATTCCAATATCTTTAGTTACAAATCTGTCCCAAAGCTTGAATCTTTAAAACTC-ATTAA
*
29443238 CC-AA-AAGATTCAATATCTTTGGTTCTAATATCTTCTTCCCGTTAAGTTT
65 CCAAAGAAGATTCAATATCTTTGGTTCCAATATCTTCTTCCCGTTAAGTTT
29443287 CTTTTGATTCCAATATCTTTAGTTACAAATCTGTCCCAAAGCTTGAATCTTTAAAACTCATTAAC
1 CTTTTGATTCCAATATCTTTAGTTACAAATCTGTCCCAAAGCTTGAATCTTTAAAACTCATTAAC
* *
29443352 CAAAAGAAGATTTAATATTTTTGGTTCCAATATCTTCTTCCCGTTAAGTTT
66 C-AAAGAAGATTCAATATCTTTGGTTCCAATATCTTCTTCCCGTTAAGTTT
29443403 CTTT
1 CTTT
29443407 GGGTTAATGG
Statistics
Matches: 112, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
113 63 0.56
114 1 0.01
115 2 0.02
116 46 0.41
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (115 bp):
CTTTTGATTCCAATATCTTTAGTTACAAATCTGTCCCAAAGCTTGAATCTTTAAAACTCATTAAC
CAAAGAAGATTCAATATCTTTGGTTCCAATATCTTCTTCCCGTTAAGTTT
Found at i:29446545 original size:14 final size:14
Alignment explanation
Indices: 29446526--29446573 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
29446516 TCATAGTCAT
29446526 TATTATAATTATAA
1 TATTATAATTATAA
29446540 TATTAT-ATTAATAA
1 TATTATAATT-ATAA
29446554 -A-TA-AATTATAA
1 TATTATAATTATAA
29446565 TGATTATAA
1 T-ATTATAA
29446574 ACCCTAGCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 11
0.72 0.00 0.28
Matches are distributed among these distances:
11 4 0.14
12 5 0.18
13 5 0.18
14 12 0.43
15 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (14 bp):
TATTATAATTATAA
Found at i:29448012 original size:12 final size:13
Alignment explanation
Indices: 29447970--29448015 Score: 62
Period size: 12 Copynumber: 3.8 Consensus size: 13
29447960 GGTGGCACCA
*
29447970 GCTGCGGCTGCT-
1 GCTGTGGCTGCTG
29447982 GCTGT-GCTGCTG
1 GCTGTGGCTGCTG
29447994 GCTGTGGCT-CTG
1 GCTGTGGCTGCTG
29448006 GCTGTGGCTG
1 GCTGTGGCTG
29448016 TTTCTCTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
11 6 0.20
12 21 0.70
13 3 0.10
ACGTcount: A:0.00, C:0.26, G:0.43, T:0.30
Consensus pattern (13 bp):
GCTGTGGCTGCTG
Found at i:29448050 original size:18 final size:17
Alignment explanation
Indices: 29448023--29448146 Score: 130
Period size: 18 Copynumber: 7.2 Consensus size: 17
29448013 CTGTTTCTCT
29448023 TCTTCTTTCTTCGGCTCC
1 TCTTCTTTCTT-GGCTCC
* *
29448041 TCTTCCTTCTTGGGTTCC
1 TCTTCTTTCTT-GGCTCC
29448059 TCTTCTTTCTTGGCT--
1 TCTTCTTTCTTGGCTCC
29448074 TCTTCTTTCTTTGGCTCC
1 TCTTCTTTC-TTGGCTCC
* *
29448092 TCTTCCTTCTTGGGT--
1 TCTTCTTTCTTGGCTCC
29448107 TCTTCTTTCTTCGGCTCC
1 TCTTCTTTCTT-GGCTCC
*
29448125 TCCTCTTTCTTGGGCTCC
1 TCTTCTTTCTT-GGCTCC
29448143 TCTT
1 TCTT
29448147 TCTTGGGTTC
Statistics
Matches: 88, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
15 19 0.22
16 9 0.10
17 8 0.09
18 52 0.59
ACGTcount: A:0.00, C:0.34, G:0.14, T:0.52
Consensus pattern (17 bp):
TCTTCTTTCTTGGCTCC
Found at i:29448084 original size:33 final size:34
Alignment explanation
Indices: 29448023--29448153 Score: 142
Period size: 33 Copynumber: 3.9 Consensus size: 34
29448013 CTGTTTCTCT
* *
29448023 TCTTCTTTCTTCGGCTCCTCTTCCTTCTTGGGTTCC
1 TCTTCTTTCTTCGGCT--TCTTCTTTCTTGGGCTCC
*
29448059 TCTTCTTTCTT-GGCTTCTTCTTTCTTTGGCTCC
1 TCTTCTTTCTTCGGCTTCTTCTTTCTTGGGCTCC
* * *
29448092 TCTTCCTTCTT-GGGTTCTTCTTTCTTCGGCTCC
1 TCTTCTTTCTTCGGCTTCTTCTTTCTTGGGCTCC
* * *
29448125 TCCTCTTTCTTGGGC-TCCTCTTTCTTGGG
1 TCTTCTTTCTTCGGCTTCTTCTTTCTTGGG
29448154 TTCTTCCTTT
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
33 66 0.80
34 2 0.02
35 4 0.05
36 11 0.13
ACGTcount: A:0.00, C:0.33, G:0.15, T:0.52
Consensus pattern (34 bp):
TCTTCTTTCTTCGGCTTCTTCTTTCTTGGGCTCC
Found at i:29448090 original size:51 final size:49
Alignment explanation
Indices: 29448021--29448170 Score: 184
Period size: 51 Copynumber: 3.0 Consensus size: 49
29448011 GGCTGTTTCT
29448021 CTTCTTCTTTCTTCGGCTCCTCTTCCTTCTTGGGTTCCTCTTCTTTCTT-GG
1 CTTCTTCTTTCTTCGGCTCCTCTTCCTTCTTGGG-T--TCTTCTTTCTTCGG
*
29448072 CTTCTTCTTTCTTTGGCTCCTCTTCCTTCTTGGGTTCTTCTTTCTTCGG
1 CTTCTTCTTTCTTCGGCTCCTCTTCCTTCTTGGGTTCTTCTTTCTTCGG
* *
29448121 CTCCTCCTCTTTCTTGGGCTCCTC-T--TTCTTGGGTTCTTCCTTT-TTCGG
1 CT--TCTTCTTTCTTCGGCTCCTCTTCCTTCTTGGGTTCTT-CTTTCTTCGG
29448169 CT
1 CT
29448171 CCTCCTTCTT
Statistics
Matches: 92, Mismatches: 3, Indels: 11
0.87 0.03 0.10
Matches are distributed among these distances:
48 31 0.34
49 8 0.09
50 2 0.02
51 51 0.55
ACGTcount: A:0.00, C:0.33, G:0.15, T:0.53
Consensus pattern (49 bp):
CTTCTTCTTTCTTCGGCTCCTCTTCCTTCTTGGGTTCTTCTTTCTTCGG
Found at i:29448161 original size:18 final size:18
Alignment explanation
Indices: 29448026--29448166 Score: 93
Period size: 18 Copynumber: 8.3 Consensus size: 18
29448016 TTTCTCTTCT
* * *
29448026 TCTTTCTTCGGCTCCTCT
1 TCTTTCTTGGGTTCCTCC
* *
29448044 TCCTTCTTGGGTTCCTCT
1 TCTTTCTTGGGTTCCTCC
*
29448062 TCTTTCTTGGCTT-CT--
1 TCTTTCTTGGGTTCCTCC
* * *
29448077 TCTTTCTTTGGCTCCTCT
1 TCTTTCTTGGGTTCCTCC
*
29448095 TCCTTCTTGGGTT-CT--
1 TCTTTCTTGGGTTCCTCC
* *
29448110 TCTTTCTTCGGCTCCTCC
1 TCTTTCTTGGGTTCCTCC
29448128 TCTTTCTTGGG---CTCC
1 TCTTTCTTGGGTTCCTCC
*
29448143 TCTTTCTTGGGTTCTTCC
1 TCTTTCTTGGGTTCCTCC
*
29448161 TTTTTC
1 TCTTTC
29448167 GGCTCCTCCT
Statistics
Matches: 97, Mismatches: 17, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
15 35 0.36
16 4 0.04
17 4 0.04
18 54 0.56
ACGTcount: A:0.00, C:0.33, G:0.14, T:0.53
Consensus pattern (18 bp):
TCTTTCTTGGGTTCCTCC
Found at i:29451726 original size:3 final size:3
Alignment explanation
Indices: 29451718--29451759 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
29451708 AGGAATGTTA
29451718 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29451760 TAAGGATTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:29452213 original size:2 final size:2
Alignment explanation
Indices: 29452206--29452233 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29452196 GATTATGAAC
29452206 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
29452234 TTTGGTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29453433 original size:22 final size:22
Alignment explanation
Indices: 29453408--29453467 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
29453398 TTTTGACAGA
*
29453408 AAATATAAATAA-TAATATTTTT
1 AAATAAAAATAATTAA-ATTTTT
*
29453430 AAATAAAAATAATTAACTTTTT
1 AAATAAAAATAATTAAATTTTT
*
29453452 AAATACAAA-AATTAAA
1 AAATAAAAATAATTAAA
29453468 ATTTAAAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 6 0.18
22 24 0.73
23 3 0.09
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (22 bp):
AAATAAAAATAATTAAATTTTT
Found at i:29460505 original size:1 final size:1
Alignment explanation
Indices: 29460499--29460527 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
29460489 TGTTCGATTT
29460499 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
29460528 GAGGAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:29477510 original size:21 final size:20
Alignment explanation
Indices: 29477485--29477532 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
29477475 ATTGTTCTCT
29477485 TTCAACAAAAGTTACAAAAAA
1 TTCAA-AAAAGTTACAAAAAA
* * *
29477506 TTCAAAATAGTTTCCAAAAA
1 TTCAAAAAAGTTACAAAAAA
*
29477526 TTTAAAA
1 TTCAAAA
29477533 TATTTTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.56, C:0.12, G:0.04, T:0.27
Consensus pattern (20 bp):
TTCAAAAAAGTTACAAAAAA
Found at i:29481395 original size:12 final size:12
Alignment explanation
Indices: 29481378--29481406 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
29481368 GAATATATTC
29481378 TGATTTTTAATT
1 TGATTTTTAATT
29481390 TGATTTTTAATT
1 TGATTTTTAATT
29481402 TGATT
1 TGATT
29481407 ATAGTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.66
Consensus pattern (12 bp):
TGATTTTTAATT
Found at i:29490815 original size:26 final size:23
Alignment explanation
Indices: 29490769--29490816 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
29490759 TTAAATATTT
*
29490769 ATATTATTTTTACATTTTAAATA
1 ATATTATTTTTAAATTTTAAATA
29490792 ATATTATTTTTGAAATGTTATAAAT
1 ATATTATTTTT-AAAT-TT-TAAAT
29490817 TTGTACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 3 0.14
25 2 0.10
26 5 0.24
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (23 bp):
ATATTATTTTTAAATTTTAAATA
Found at i:29491400 original size:17 final size:17
Alignment explanation
Indices: 29491369--29491403 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
29491359 TATTTTAATC
**
29491369 TTTTAAATTTTTAAAAA
1 TTTTAAATTAATAAAAA
29491386 TTTTAAATTAATAAAAA
1 TTTTAAATTAATAAAAA
29491403 T
1 T
29491404 AAAATTACAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTAAATTAATAAAAA
Found at i:29493979 original size:31 final size:31
Alignment explanation
Indices: 29493944--29494023 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 31
29493934 AGATCCCAAA
*
29493944 AAGTTTAAGTATCAACTTAAAAAAAAATATC
1 AAGTTTAAGTATCAAATTAAAAAAAAATATC
* * ** *
29493975 AAGTTTAGGTACCAAATTAGGAAAAATTATC
1 AAGTTTAAGTATCAAATTAAAAAAAAATATC
*
29494006 AAGTTTGAGTATCAAATT
1 AAGTTTAAGTATCAAATT
29494024 GGACAAAAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.31
Consensus pattern (31 bp):
AAGTTTAAGTATCAAATTAAAAAAAAATATC
Found at i:29496181 original size:9 final size:9
Alignment explanation
Indices: 29496167--29496235 Score: 61
Period size: 9 Copynumber: 7.2 Consensus size: 9
29496157 GCAAATGATT
29496167 TTAAAATTA
1 TTAAAATTA
29496176 TTAAAATTA
1 TTAAAATTA
29496185 TTAAAATTAA
1 TTAAAATT-A
29496195 TTTAAAATTAA
1 -TTAAAATT-A
29496206 TTTTTAAAA-TA
1 ---TTAAAATTA
*
29496217 -TAAAATTG
1 TTAAAATTA
29496225 TTAAAATTA
1 TTAAAATTA
29496234 TT
1 TT
29496236 TTAAAATATA
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
7 5 0.10
8 1 0.02
9 26 0.50
10 1 0.02
11 11 0.21
12 1 0.02
13 7 0.13
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (9 bp):
TTAAAATTA
Found at i:29496201 original size:11 final size:10
Alignment explanation
Indices: 29496166--29496242 Score: 58
Period size: 9 Copynumber: 7.8 Consensus size: 10
29496156 AGCAAATGAT
29496166 TTTAAAATTA
1 TTTAAAATTA
29496176 -TTAAAATTA
1 TTTAAAATTA
29496185 -TTAAAATTAA
1 TTTAAAATT-A
29496195 TTTAAAATTAA
1 TTTAAAATT-A
29496206 TTTTTAAAA-TA
1 --TTTAAAATTA
29496217 --TAAAATT-
1 TTTAAAATTA
*
29496224 GTTAAAATTA
1 TTTAAAATTA
29496234 TTTTAAAAT
1 -TTTAAAAT
29496243 ATAGTCATCA
Statistics
Matches: 57, Mismatches: 1, Indels: 17
0.76 0.01 0.23
Matches are distributed among these distances:
7 5 0.09
8 1 0.02
9 24 0.42
10 1 0.02
11 18 0.32
12 1 0.02
13 7 0.12
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (10 bp):
TTTAAAATTA
Done.