Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
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: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 17 of 345
Found at i:5239439 original size:92 final size:92
Alignment explanation
Indices: 5239274--5239585 Score: 432
Period size: 92 Copynumber: 3.4 Consensus size: 92
5239264 CGGTGAATCC
* * * * *
5239274 ACAAGTCTTATTTCCCTAAAGTTGCAGTGGAACAGCTTGAAGCTAGAAATTATAGATCTTATCTC
1 ACAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTACAGATCTTATCTC
*
5239339 TCTGAAGTTGCAGTAGAGCAGATAAAA
66 TCTAAAGTTGCAGTAGAGCAGATAAAA
* * *
5239366 ACAAATCTTATTTCCCTGAAGTTGTAGTGGAACAAATTGAAGCTATAAATTACATATCTTATCTC
1 ACAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTACAGATCTTATCTC
5239431 TCTAAAGTTGCAGTAGAGCAGATAAAA
66 TCTAAAGTTGCAGTAGAGCAGATAAAA
* **
5239458 ACAAATCTTATTTCCCTGAAGTTGCAGTGGGATGGATTGAAG-T-TACAA-TATCAGATCTTATC
1 ACAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATA-AATTA-CAGATCTTATC
* *
5239520 TCTCTAAAGTTGCAGTAGAGCAAATCAAA
64 TCTCTAAAGTTGCAGTAGAGCAGATAAAA
* * *
5239549 ACAAATCTTATTTCTCTGAAGTTGCAGTAGAGCAGAT
1 ACAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGAT
5239586 CAAAACAAAT
Statistics
Matches: 195, Mismatches: 23, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
90 4 0.02
91 71 0.36
92 120 0.62
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (92 bp):
ACAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTACAGATCTTATCTC
TCTAAAGTTGCAGTAGAGCAGATAAAA
Found at i:5239935 original size:12 final size:12
Alignment explanation
Indices: 5239920--5239945 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5239910 AATTAACACC
5239920 CCACTAAACCAA
1 CCACTAAACCAA
5239932 CCACTAAACCAA
1 CCACTAAACCAA
5239944 CC
1 CC
5239946 GTTAACTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.46, G:0.00, T:0.08
Consensus pattern (12 bp):
CCACTAAACCAA
Found at i:5240455 original size:15 final size:18
Alignment explanation
Indices: 5240422--5240459 Score: 55
Period size: 15 Copynumber: 2.3 Consensus size: 18
5240412 TTATTATTAT
5240422 TATTATTACTACTACTAC
1 TATTATTACTACTACTAC
5240440 TATTATT-CTA-TA-TAC
1 TATTATTACTACTACTAC
5240455 TATTA
1 TATTA
5240460 CTGTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.40
16 2 0.10
17 3 0.15
18 7 0.35
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTATTACTACTACTAC
Found at i:5240686 original size:15 final size:16
Alignment explanation
Indices: 5240626--5240686 Score: 72
Period size: 15 Copynumber: 3.8 Consensus size: 16
5240616 TGTTTCATTG
5240626 TTATTTTCTATTTTATTA
1 TTATTTTCTA--TTATTA
*
5240644 TTATTTTCTATTACTA
1 TTATTTTCTATTATTA
*
5240660 TT-GTTTCTATTATTA
1 TTATTTTCTATTATTA
5240675 TTATTTTC-ATTA
1 TTATTTTCTATTA
5240687 CTTCCGTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
15 17 0.45
16 11 0.29
18 10 0.26
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (16 bp):
TTATTTTCTATTATTA
Found at i:5240701 original size:30 final size:31
Alignment explanation
Indices: 5240634--5240717 Score: 104
Period size: 30 Copynumber: 2.8 Consensus size: 31
5240624 TGTTATTTTC
*
5240634 TATT-TTATTATTATTTTCTATTACTATTGT
1 TATTATTATTATTATTTTCTATTACTATCGT
5240664 T-TCTATTATTATTATTTTC-ATTACT-TCCGT
1 TAT-TATTATTATTATTTTCTATTACTAT-CGT
*
5240694 TATTATTATCATTATTTTCTATTA
1 TATTATTATTATTATTTTCTATTA
5240718 TCATTAATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
29 2 0.04
30 26 0.55
31 19 0.40
ACGTcount: A:0.24, C:0.11, G:0.02, T:0.63
Consensus pattern (31 bp):
TATTATTATTATTATTTTCTATTACTATCGT
Found at i:5240817 original size:25 final size:23
Alignment explanation
Indices: 5240780--5240832 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 23
5240770 TTATATTTAC
5240780 TTTTTTAAATATTATTACCATTA
1 TTTTTTAAATATTATTACCATTA
*
5240803 TTTTTTAAAACTATTATTACTATTA
1 TTTTTT-AAA-TATTATTACCATTA
5240828 TTTTT
1 TTTTT
5240833 ATTATCCATC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 6 0.22
24 3 0.11
25 18 0.67
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTTTTAAATATTATTACCATTA
Found at i:5240974 original size:15 final size:16
Alignment explanation
Indices: 5240944--5240978 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
5240934 TTATTCCATT
*
5240944 TTTTATCTCTATATTA
1 TTTTATCTCAATATTA
5240960 TTTTATCT-AATATTA
1 TTTTATCTCAATATTA
5240975 TTTT
1 TTTT
5240979 TGTCGGGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTATCTCAATATTA
Found at i:5240979 original size:16 final size:17
Alignment explanation
Indices: 5240943--5240979 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
5240933 GTTATTCCAT
*
5240943 TTTTTATCTCTATATTA
1 TTTTTATCTCAATATTA
5240960 -TTTTATCT-AATATTA
1 TTTTTATCTCAATATTA
5240975 TTTTT
1 TTTTT
5240980 GTCGGGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTATCTCAATATTA
Found at i:5241178 original size:125 final size:127
Alignment explanation
Indices: 5240996--5241257 Score: 323
Period size: 125 Copynumber: 2.1 Consensus size: 127
5240986 ATTTTTCAAG
* * * *
5240996 TAAAGGCAATATTCAGTACTTGGAAATTCAAGAAATCGTGTCCTAACGTACTGGGTTTCGGTTTT
1 TAAAGGCAATATTCAGTACTTAGAAATTCAAGAAATCGTGCCCTAACGTACTGGGTTTCGATTAT
* *
5241061 TCATTTGATCTAAGTA-ACTAATTATCC-TTTT-AAATTAAAATACATGAGTTTTAAATAAAA
66 TCATTTGATCTAAATATACGAA-TATCCTTTTTAAAATTAAAATACATGAGTTTTAAATAAAA
* * * * * * * *
5241121 TAAAGGCAATATTCCGTATTTAGAAATTCGAGTAGTTGTGCCCTAATGTACTGGGTTTTGATTAT
1 TAAAGGCAATATTCAGTACTTAGAAATTCAAGAAATCGTGCCCTAACGTACTGGGTTTCGATTAT
* * * *
5241186 TCGTTTGATCTAAATATCCGAATATCCTTTTTAAAATTTAAATACATGAGTTTTAAATGAAA
66 TCATTTGATCTAAATATACGAATATCCTTTTTAAAATTAAAATACATGAGTTTTAAATAAAA
5241248 TAGAAGGCAA
1 TA-AAGGCAA
5241258 GCTCATACTC
Statistics
Matches: 115, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
125 72 0.63
126 7 0.06
127 29 0.25
128 7 0.06
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (127 bp):
TAAAGGCAATATTCAGTACTTAGAAATTCAAGAAATCGTGCCCTAACGTACTGGGTTTCGATTAT
TCATTTGATCTAAATATACGAATATCCTTTTTAAAATTAAAATACATGAGTTTTAAATAAAA
Found at i:5244609 original size:20 final size:21
Alignment explanation
Indices: 5244580--5244619 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
5244570 TCGATGCTAC
5244580 ATGAAATGTAAAA-AATAAAT
1 ATGAAATGTAAAACAATAAAT
*
5244600 ATGAACTGTAAAACAATAAA
1 ATGAAATGTAAAACAATAAA
5244620 GTAATGTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.23
Consensus pattern (21 bp):
ATGAAATGTAAAACAATAAAT
Found at i:5244761 original size:3 final size:3
Alignment explanation
Indices: 5244753--5244777 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5244743 ATTTAACTCT
5244753 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
5244778 AATAAGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5246046 original size:60 final size:60
Alignment explanation
Indices: 5245919--5246057 Score: 165
Period size: 60 Copynumber: 2.3 Consensus size: 60
5245909 TTTAGTGTTA
* * *
5245919 ACTGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAGTAATAGAGTAT
1 ACTGGGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAGTAAGAGAGTAT
* * *
5245980 ACTGGGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATTACAAGT-CGAGA-TAT
1 ACTGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCC-ATTAC-AGTAAGAGAGTAT
* *
5246040 ATTGGGCCTTGCCCATAT
1 ACTGGGCCTAGCCCATAT
5246058 TGACACAGTT
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
60 50 0.74
61 15 0.22
62 3 0.04
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (60 bp):
ACTGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAGTAAGAGAGTAT
Found at i:5246075 original size:20 final size:19
Alignment explanation
Indices: 5246050--5246105 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
5246040 ATTGGGCCTT
*
5246050 GCCCATATTGACACAGTTGG
1 GCCCATATTAACACAGTT-G
* *
5246070 GCCCATTTTAATACAGTTG
1 GCCCATATTAACACAGTTG
* *
5246089 GCCCATAATAAAACAGT
1 GCCCATATTAACACAGT
5246106 CTCATATGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (19 bp):
GCCCATATTAACACAGTTG
Found at i:5249699 original size:23 final size:25
Alignment explanation
Indices: 5249654--5249700 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
5249644 TAAAAAAAAA
5249654 AAACGTTTTATTTATATGCTATTTC
1 AAACGTTTTATTTATATGCTATTTC
* *
5249679 AAAC-TTTT-TTTTTATGTTATTT
1 AAACGTTTTATTTATATGCTATTT
5249701 ATTTTACATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 4 0.20
25 4 0.20
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.60
Consensus pattern (25 bp):
AAACGTTTTATTTATATGCTATTTC
Found at i:5249823 original size:14 final size:14
Alignment explanation
Indices: 5249806--5249836 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5249796 ATTTTATATG
*
5249806 TATTATTTATTTTA
1 TATTATTTATATTA
5249820 TATTATTTATATTA
1 TATTATTTATATTA
5249834 TAT
1 TAT
5249837 ATATATGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTATTTATATTA
Found at i:5249829 original size:18 final size:19
Alignment explanation
Indices: 5249795--5249834 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
5249785 TATCTTAATC
5249795 TATTTTATATGTATTAT-T
1 TATTTTATATGTATTATAT
5249813 TATTTTATAT-TATTTATAT
1 TATTTTATATGTA-TTATAT
5249832 TAT
1 TAT
5249835 ATATATATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 2 0.10
18 14 0.70
19 4 0.20
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (19 bp):
TATTTTATATGTATTATAT
Found at i:5250199 original size:27 final size:25
Alignment explanation
Indices: 5250150--5250223 Score: 85
Period size: 27 Copynumber: 2.8 Consensus size: 25
5250140 TGTATTATAG
* * * *
5250150 ATTTTAAAATGCTTTATACATTATTT
1 ATTTTAAATTGTTTTAT-TATTATTC
5250176 ATTTTAAACTTGTTTTATGTATTATTC
1 ATTTTAAA-TTGTTTTAT-TATTATTC
5250203 ATTTTAAATTGTTTTATTATT
1 ATTTTAAATTGTTTTATTATT
5250224 TACTTTAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
25 4 0.10
26 17 0.40
27 21 0.50
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (25 bp):
ATTTTAAATTGTTTTATTATTATTC
Found at i:5250238 original size:21 final size:22
Alignment explanation
Indices: 5250195--5250245 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
5250185 TTGTTTTATG
*
5250195 TATTATTCATTTTAAATTGTTT
1 TATTATTCACTTTAAATTGTTT
* *
5250217 TATTATTTACTTT-AATTTTTT
1 TATTATTCACTTTAAATTGTTT
5250238 TATATATT
1 TAT-TATT
5250246 ATCAATTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTATTCACTTTAAATTGTTT
Found at i:5250271 original size:26 final size:26
Alignment explanation
Indices: 5250230--5250279 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
5250220 TATTTACTTT
*
5250230 AATTTTTTTATATATTATCAATTTCA
1 AATTTTTATATATATTATCAATTTCA
* *
5250256 AATTTTTATATGTATTATCTATTT
1 AATTTTTATATATATTATCAATTT
5250280 TTTATATATC
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:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (26 bp):
AATTTTTATATATATTATCAATTTCA
Found at i:5254355 original size:38 final size:38
Alignment explanation
Indices: 5254312--5254387 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
5254302 TATAGTTATA
5254312 GAGTCAGATTTAAATTTGAATGGAATATTTTGCGAGAT
1 GAGTCAGATTTAAATTTGAATGGAATATTTTGCGAGAT
5254350 GAGTCAGATTTAAATTTGAATGGAATATTTTGCGAGAT
1 GAGTCAGATTTAAATTTGAATGGAATATTTTGCGAGAT
5254388 ATATTAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (38 bp):
GAGTCAGATTTAAATTTGAATGGAATATTTTGCGAGAT
Found at i:5255426 original size:10 final size:10
Alignment explanation
Indices: 5255399--5255437 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
5255389 TTAAATTCTA
5255399 AAAGATAAAT
1 AAAGATAAAT
5255409 ACAA-ATAAAT
1 A-AAGATAAAT
*
5255419 AAAGATAATT
1 AAAGATAAAT
5255429 AAAGATAAA
1 AAAGATAAA
5255438 AGCTAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.21
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:5255473 original size:13 final size:12
Alignment explanation
Indices: 5255455--5255487 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
5255445 ATTAAATCTA
5255455 AATAATAATCCTT
1 AATAATAATCC-T
5255468 AATAATAATCCT
1 AATAATAATCCT
5255480 AAT-ATAAT
1 AATAATAAT
5255488 TGGAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.25
12 4 0.20
13 11 0.55
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (12 bp):
AATAATAATCCT
Found at i:5257420 original size:5 final size:5
Alignment explanation
Indices: 5257410--5257497 Score: 69
Period size: 5 Copynumber: 17.6 Consensus size: 5
5257400 ATTAATATCC
* * *
5257410 AAATA AAATA AAGTA ATAA-A TAATA AAATA AAATA AAGT- AAA-A AAATA
1 AAATA AAATA AAATA A-AATA AAATA AAATA AAATA AAATA AAATA AAATA
5257458 AAATAA AAATAA AAATA AGAA-A GAAA-A AAATA AAATA AAA
1 AAAT-A AAAT-A AAATA A-AATA -AAATA AAATA AAATA AAA
5257498 ATAGGGTTGG
Statistics
Matches: 69, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
4 10 0.14
5 44 0.64
6 15 0.22
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (5 bp):
AAATA
Found at i:5257431 original size:25 final size:25
Alignment explanation
Indices: 5257410--5257496 Score: 106
Period size: 25 Copynumber: 3.5 Consensus size: 25
5257400 ATTAATATCC
5257410 AAATAAAATAAAGTAATAAATAATA
1 AAATAAAATAAAGTAATAAATAATA
5257435 AAATAAAATAAAGTAA-AAA-AATA
1 AAATAAAATAAAGTAATAAATAATA
* * * *
5257458 AAATAAAAATAAAAATAAGAAAGAAAA
1 AAAT-AAAAT-AAAGTAATAAATAATA
5257485 AAATAAAATAAA
1 AAATAAAATAAA
5257497 AATAGGGTTG
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
23 8 0.14
24 8 0.14
25 25 0.45
26 8 0.14
27 7 0.12
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (25 bp):
AAATAAAATAAAGTAATAAATAATA
Found at i:5257436 original size:20 final size:18
Alignment explanation
Indices: 5257411--5257496 Score: 68
Period size: 19 Copynumber: 4.6 Consensus size: 18
5257401 TTAATATCCA
5257411 AATAAAATAAAGTAATAAAT
1 AATAAAATAAAG-AA-AAAT
*
5257431 AATAAAATAAA-ATAAAGT
1 AATAAAATAAAGA-AAAAT
* *
5257449 AAAAAAATAAAATAAAAAT
1 AATAAAAT-AAAGAAAAAT
* *
5257468 AAAAATAAGAAAGAAAAA-
1 AATAA-AATAAAGAAAAAT
5257486 AATAAAATAAA
1 AATAAAATAAA
5257497 AATAGGGTTG
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
17 5 0.09
18 15 0.27
19 21 0.38
20 14 0.25
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (18 bp):
AATAAAATAAAGAAAAAT
Found at i:5257490 original size:32 final size:34
Alignment explanation
Indices: 5257424--5257500 Score: 113
Period size: 32 Copynumber: 2.3 Consensus size: 34
5257414 AAAATAAAGT
*
5257424 AATAAATAATAAAATAAAATAAAGTAAAAAAATAA
1 AATAAA-AATAAAATAAAAGAAAGTAAAAAAATAA
*
5257459 AATAAAAATAAAA-ATAAGAAAG-AAAAAAATAA
1 AATAAAAATAAAATAAAAGAAAGTAAAAAAATAA
5257491 AATAAAAATA
1 AATAAAAATA
5257501 GGGTTGGCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
32 20 0.50
33 7 0.17
34 7 0.17
35 6 0.15
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (34 bp):
AATAAAAATAAAATAAAAGAAAGTAAAAAAATAA
Found at i:5262680 original size:10 final size:10
Alignment explanation
Indices: 5262653--5262691 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
5262643 ATAAATTCTA
5262653 AAAGATAAAT
1 AAAGATAAAT
5262663 ACAA-ATAAAT
1 A-AAGATAAAT
*
5262673 AAAGATAATT
1 AAAGATAAAT
5262683 AAAGATAAA
1 AAAGATAAA
5262692 AGCTAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.21
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:5266210 original size:17 final size:17
Alignment explanation
Indices: 5266190--5266223 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5266180 AAATAGATTT
5266190 TTAATTAAAAAATTTAA
1 TTAATTAAAAAATTTAA
*
5266207 TTAATTAAAAATTTTAA
1 TTAATTAAAAAATTTAA
5266224 ACCTAAACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAATTAAAAAATTTAA
Found at i:5269573 original size:19 final size:18
Alignment explanation
Indices: 5269533--5269569 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5269523 AAAAGGGGAC
5269533 ATAAAACAATTTAAAATA
1 ATAAAACAATTTAAAATA
* *
5269551 ATAAAACATTTTTAAATA
1 ATAAAACAATTTAAAATA
5269569 A
1 A
5269570 ATAATACACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAAAACAATTTAAAATA
Found at i:5270956 original size:27 final size:27
Alignment explanation
Indices: 5270926--5271094 Score: 239
Period size: 27 Copynumber: 6.3 Consensus size: 27
5270916 TTAGTTTACC
*
5270926 AAATTACCAAAATACCATTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
* * ** *
5270953 AAATTACTAAAATACCTTTTATTTATA
1 AAATTACCAAAATACCCTTGGTTTGTA
*
5270980 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
5271007 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
* * *
5271034 AAATTATCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
*
5271061 AAATTACCAAAATACCCTTGATTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
5271088 AAATTAC
1 AAATTAC
5271095 TGAAATACTC
Statistics
Matches: 123, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 123 1.00
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.34
Consensus pattern (27 bp):
AAATTACCAAAATACCCTTGGTTTGTA
Found at i:5271119 original size:27 final size:27
Alignment explanation
Indices: 5271089--5271202 Score: 174
Period size: 27 Copynumber: 4.2 Consensus size: 27
5271079 TGATTTGTAA
*
5271089 AATTACTGAAATACTCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
5271116 AATTACTAAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
5271143 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
5271170 AATTACTAAAATACCCCTGTAGGGTGG
1 AATTACTGAAATACCCCTGTAGGGTAG
5271197 AATTAC
1 AATTAC
5271203 CGAGATATCT
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 78 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.26
Consensus pattern (27 bp):
AATTACTGAAATACCCCTGTAGGGTAG
Found at i:5271120 original size:54 final size:54
Alignment explanation
Indices: 5270926--5271185 Score: 229
Period size: 54 Copynumber: 4.8 Consensus size: 54
5270916 TTAGTTTACC
** * ** * * *
5270926 AAATTACCAAAATACCATTGGTTTGTAAAATTACTAAAATACCTTTTATTTATA
1 AAATTACCAAAATACCCCTAGTGGGTAAAATTACTAAAATACCCTTGATTTGTA
* ** * *
5270980 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCCTAGTGGGTAAAATTACTAAAATACCCTTGATTTGTA
* ** *
5271034 AAATTATCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGATTTGTA
1 AAATTACCAAAATACCCCTAGTGGGTAAAATTACTAAAATACCCTTGATTTGTA
** * * * **
5271088 AAATTACTGAAATACTCCT-GTAGGGTAGAATTACTAAAATACCCCT-ATAGGGTA
1 AAATTACCAAAATACCCCTAGT-GGGTAAAATTACTAAAATACCCTTGAT-TTGTA
* * *
5271142 GAATTACCGAAATACCCCT-GTAGGGTAGAATTACTAAAATACCC
1 AAATTACCAAAATACCCCTAGT-GGGTAAAATTACTAAAATACCC
5271186 CTGTAGGGTG
Statistics
Matches: 180, Mismatches: 24, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
53 4 0.02
54 176 0.98
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (54 bp):
AAATTACCAAAATACCCCTAGTGGGTAAAATTACTAAAATACCCTTGATTTGTA
Found at i:5271120 original size:81 final size:79
Alignment explanation
Indices: 5270978--5271202 Score: 224
Period size: 81 Copynumber: 2.8 Consensus size: 79
5270968 CTTTTATTTA
* *
5270978 TAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCT-T-GGTTTGTAAAATTA-
1 TAAAATTACCAAAATACCCCT-GTTTGTAAAATTACTAAAATACCCTGTAGG---GTAGAATTAC
**
5271040 TCAAAATACCCCTAGT-TTG
62 T-AAAATACCCCTA-TAGGG
* *
5271059 TAAAATTACCAAAATACCCTTGATTTGTAAAATTACTGAAATACTCCTGTAGGGTAGAATTACTA
1 TAAAATTACCAAAATACCCCTG-TTTGTAAAATTACTAAAATAC-CCTGTAGGGTAGAATTACTA
5271124 AAATACCCCTATAGGG
64 AAATACCCCTATAGGG
* * ** * *
5271140 TAGAATTACCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTGTAGGGTGGAATTAC
1 TAAAATTACCAAAATACCCCTGT-TTGTAAAATTACTAAAATA-CCCTGTAGGGTAGAATTAC
5271203 CGAGATATCT
Statistics
Matches: 122, Mismatches: 14, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
80 3 0.02
81 111 0.91
82 5 0.04
83 1 0.01
84 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (79 bp):
TAAAATTACCAAAATACCCCTGTTTGTAAAATTACTAAAATACCCTGTAGGGTAGAATTACTAAA
ATACCCCTATAGGG
Found at i:5271186 original size:54 final size:54
Alignment explanation
Indices: 5271089--5271205 Score: 198
Period size: 54 Copynumber: 2.2 Consensus size: 54
5271079 TGATTTGTAA
* *
5271089 AATTACTGAAATACTCCTGTAGGGTAGAATTACTAAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTATAGGGTAG
* *
5271143 AATTACCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTATAGGGTAG
5271197 AATTACCGA
1 AATTACCGA
5271206 GATATCTTGT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.26
Consensus pattern (54 bp):
AATTACCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTATAGGGTAG
Found at i:5271708 original size:22 final size:22
Alignment explanation
Indices: 5271656--5271720 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
5271646 TTAAAGCCTT
* * *
5271656 CTGATTATGACTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
5271678 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
*
5271700 CTGATTATGGCTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
5271721 ACGTATTTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.34
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:5271936 original size:54 final size:53
Alignment explanation
Indices: 5271878--5271980 Score: 134
Period size: 54 Copynumber: 1.9 Consensus size: 53
5271868 TATTCTGTTA
* * * *
5271878 AGTGGCTTTGCCACATTATCTGTTTCTGGTGGCTATGCCACAAATATCTGTTCT
1 AGTGGCTCTGCCACAATATCTGTATCTGGTGACTATGCCAC-AATATCTGTTCT
* * *
5271932 AGTGGCTCTGCCACAATATCTGTATGTGGTGACTCTGTCACAATATCTG
1 AGTGGCTCTGCCACAATATCTGTATCTGGTGACTATGCCACAATATCTG
5271981 ATAACTGAGC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
53 8 0.19
54 34 0.81
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.36
Consensus pattern (53 bp):
AGTGGCTCTGCCACAATATCTGTATCTGGTGACTATGCCACAATATCTGTTCT
Found at i:5271967 original size:27 final size:26
Alignment explanation
Indices: 5271879--5271980 Score: 114
Period size: 27 Copynumber: 3.8 Consensus size: 26
5271869 ATTCTGTTAA
* *
5271879 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTCTGCCACAATATCTG-TTCTG
* *
5271906 GTGGCTATGCCACAAATATCTGTTCTA
1 GTGGCTCTGCCAC-AATATCTGTTCTG
*
5271933 GTGGCTCTGCCACAATATCTGTATGTG
1 GTGGCTCTGCCACAATATCTGT-TCTG
* *
5271960 GTGACTCTGTCACAATATCTG
1 GTGGCTCTGCCACAATATCTG
5271981 ATAACTGAGC
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
26 9 0.14
27 49 0.75
28 7 0.11
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.36
Consensus pattern (26 bp):
GTGGCTCTGCCACAATATCTGTTCTG
Found at i:5272154 original size:6 final size:6
Alignment explanation
Indices: 5272116--5272235 Score: 77
Period size: 6 Copynumber: 19.3 Consensus size: 6
5272106 ATGCATTCAC
* * *
5272116 ATTCTG ATTTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTTTG ATTCT-
1 ATTCTG A-TTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * *
5272165 ATTTCCTG ATACTG ATTCTG ATTCTG ATTCTG -TCACCTA ATTCTA ATTCTG
1 A-TT-CTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG
5272216 ATTCTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG A-TTCTG AT
5272236 AATGTTTCTT
Statistics
Matches: 90, Mismatches: 12, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
5 5 0.06
6 68 0.76
7 14 0.16
8 3 0.03
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:5272162 original size:31 final size:31
Alignment explanation
Indices: 5272116--5272251 Score: 141
Period size: 31 Copynumber: 4.4 Consensus size: 31
5272106 ATGCATTCAC
*
5272116 ATTCTGATTTTTGATTCTGTTACCTGATACTG
1 ATTCTGA-TTCTGATTCTGTTACCTGATACTG
* * *
5272148 ATTCTGATTTTGATTCTATTTCCTGATACTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTG
* * * *
5272179 ATTCTGATTCTGATTCTGTCACCTAATTCTA
1 ATTCTGATTCTGATTCTGTTACCTGATACTG
*
5272210 ATTCTGATTCTGATTCTAGTT--CTGATAATG
1 ATTCTGATTCTGATTCT-GTTACCTGATACTG
* *
5272240 TTTCTTATTCTG
1 ATTCTGATTCTG
5272252 TAATGGGTTA
Statistics
Matches: 87, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
30 15 0.17
31 63 0.72
32 9 0.10
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTTACCTGATACTG
Found at i:5274216 original size:27 final size:27
Alignment explanation
Indices: 5274186--5274391 Score: 279
Period size: 27 Copynumber: 7.6 Consensus size: 27
5274176 TTAGTTTACC
*
5274186 AAATTACCAAAATACCATTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
* ** *
5274213 AAATTACTAAAATACCCTTTATTTATA
1 AAATTACCAAAATACCCTTGGTTTGTA
*
5274240 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
5274267 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
* *
5274294 AAATTATCAAAATA-CCTCTAGTTTGTA
1 AAATTACCAAAATACCCT-TGGTTTGTA
* *
5274321 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
*
5274348 AAATTACCAAAATACCCTTGATTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
**
5274375 AAATTACTGAAATACCC
1 AAATTACCAAAATACCC
5274392 CTGTAGGGTA
Statistics
Matches: 157, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
26 3 0.02
27 152 0.97
28 2 0.01
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (27 bp):
AAATTACCAAAATACCCTTGGTTTGTA
Found at i:5274392 original size:54 final size:53
Alignment explanation
Indices: 5274186--5274447 Score: 285
Period size: 54 Copynumber: 4.8 Consensus size: 53
5274176 TTAGTTTACC
* * *
5274186 AAATTACCAAAATACCATTGGTTTGTAAAATTACTAAAATACCCTTTA-TTTATA
1 AAATTACCAAAATACCCTT-GTTTGTAAAATTACTAAAATACCC-CTAGTTTGTA
* * * *
5274240 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATA-CCCTTGTTTGTAAAATTACTAAAATACCCCTAGTTTGTA
* * *
5274294 AAATTATCAAAATACCTCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACC-CTTGTTTGTAAAATTACTAAAATACCCCTAGTTTGTA
* **
5274348 AAATTACCAAAATACCCTTGATTTGTAAAATTACTGAAATACCCCT-GTAGGGTA
1 AAATTACCAAAATACCCTTG-TTTGTAAAATTACTAAAATACCCCTAGT-TTGTA
* * * **
5274402 GAATTACTAAAATACCCCTGTAGGGTAAAATTACTAAAATACCCCT
1 AAATTACCAAAATACCCTTGT-TTGTAAAATTACTAAAATACCCCT
5274448 GTAGGGTAGA
Statistics
Matches: 181, Mismatches: 21, Indels: 12
0.85 0.10 0.06
Matches are distributed among these distances:
53 10 0.06
54 168 0.93
55 3 0.02
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.32
Consensus pattern (53 bp):
AAATTACCAAAATACCCTTGTTTGTAAAATTACTAAAATACCCCTAGTTTGTA
Found at i:5274406 original size:27 final size:27
Alignment explanation
Indices: 5274210--5274488 Score: 178
Period size: 27 Copynumber: 10.4 Consensus size: 27
5274200 CCATTGGTTT
* **
5274210 GTAAAATTACTAAAATA-CCCTTTATTT
1 GTAAAATTACTAAAATACCCCTGTA-GG
* * **
5274237 ATAAAATTACCAAAATACCCCTGGT-TT
1 GTAAAATTACTAAAATACCCCT-GTAGG
* * **
5274264 GTAAAATTACCAAAATACCCTTGGT-TT
1 GTAAAATTACTAAAATACCCCT-GTAGG
* **
5274291 GTAAAATTA-TCAAAATACCTCTAGT-TT
1 GTAAAATTACT-AAAATACCCCT-GTAGG
* **
5274318 GTAAAATTACCAAAATACCCCTAGT-TT
1 GTAAAATTACTAAAATACCCCT-GTAGG
* * **
5274345 GTAAAATTACCAAAATACCCTTG-ATTT
1 GTAAAATTACTAAAATACCCCTGTA-GG
*
5274372 GTAAAATTACTGAAATACCCCTGTAGG
1 GTAAAATTACTAAAATACCCCTGTAGG
*
5274399 GTAGAATTACTAAAATACCCCTGTAGG
1 GTAAAATTACTAAAATACCCCTGTAGG
5274426 GTAAAATTACTAAAATACCCCTGTAGG
1 GTAAAATTACTAAAATACCCCTGTAGG
* ** * * *
5274453 GTAGAATTACCGAGATA-CCTTGTGGG
1 GTAAAATTACTAAAATACCCCTGTAGG
5274479 GTAAAATTAC
1 GTAAAATTAC
5274489 CAGTTTGCCC
Statistics
Matches: 218, Mismatches: 27, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
26 17 0.08
27 195 0.89
28 5 0.02
29 1 0.00
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.31
Consensus pattern (27 bp):
GTAAAATTACTAAAATACCCCTGTAGG
Found at i:5274407 original size:81 final size:80
Alignment explanation
Indices: 5274186--5274445 Score: 328
Period size: 81 Copynumber: 3.2 Consensus size: 80
5274176 TTAGTTTACC
* * *
5274186 AAATTACCAAAATACCATTGGTTTGTAAAATTACTAAAATA-CCCTTTATTTATAAAATTACCAA
1 AAATTACCAAAATACCCTTGGTTTGTAAAATTACTAAAATACCCCTGTA-TTGTAAAATTACCAA
5274250 AATACCCCTGGTTTGTA
65 AATACCCCT-GTTTGTA
*
5274267 AAATTACCAAAATACCCTTGGTTTGTAAAATTA-TCAAAATACCTCTAGT-TTGTAAAATTACCA
1 AAATTACCAAAATACCCTTGGTTTGTAAAATTACT-AAAATACCCCT-GTATTGTAAAATTACCA
5274330 AAATACCCCTAGTTTGTA
64 AAATACCCCT-GTTTGTA
* * ** * *
5274348 AAATTACCAAAATACCCTTGATTTGTAAAATTACTGAAATACCCCTGTAGGGTAGAATTACTAAA
1 AAATTACCAAAATACCCTTGGTTTGTAAAATTACTAAAATACCCCTGTATTGTAAAATTACCAAA
**
5274413 ATACCCCTGTAGGGTA
66 ATACCCCTGT-TTGTA
*
5274429 AAATTACTAAAATACCC
1 AAATTACCAAAATACCC
5274446 CTGTAGGGTA
Statistics
Matches: 158, Mismatches: 15, Indels: 12
0.85 0.08 0.06
Matches are distributed among these distances:
80 5 0.03
81 148 0.94
82 4 0.03
83 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (80 bp):
AAATTACCAAAATACCCTTGGTTTGTAAAATTACTAAAATACCCCTGTATTGTAAAATTACCAAA
ATACCCCTGTTTGTA
Found at i:5274448 original size:54 final size:54
Alignment explanation
Indices: 5274187--5274488 Score: 197
Period size: 54 Copynumber: 5.6 Consensus size: 54
5274177 TAGTTTACCA
* ** * *** *
5274187 AATTACCAAAATACCATTGGT-TTGTAAAATTACTAAAATA-CCCTTTATTTATAA
1 AATTACCAAAATACCCTT-GTAGGGTAAAATTACTAAAATACCCCTGTA-GGGTAG
* ** * * ** *
5274241 AATTACCAAAATACCCCTGGT-TTGTAAAATTACCAAAATACCCTTGGT-TTGTAA
1 AATTACCAAAATA-CCCTTGTAGGGTAAAATTACTAAAATACCCCT-GTAGGGTAG
* * ** * ** *
5274295 AATTATCAAAATACCTCTAGT-TTGTAAAATTACCAAAATACCCCTAGT-TTGTAA
1 AATTACCAAAATACC-CTTGTAGGGTAAAATTACTAAAATACCCCT-GTAGGGTAG
** *
5274349 AATTACCAAAATACCCTTG-ATTTGTAAAATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCAAAATACCCTTGTA-GGGTAAAATTACTAAAATACCCCTGTAGGGTAG
* *
5274403 AATTACTAAAATACCCCTGTAGGGTAAAATTACTAAAATACCCCTGTAGGGTAG
1 AATTACCAAAATACCCTTGTAGGGTAAAATTACTAAAATACCCCTGTAGGGTAG
* * *
5274457 AATTACCGAGATA-CCTTGTGGGGTAAAATTAC
1 AATTACCAAAATACCCTTGTAGGGTAAAATTAC
5274489 CAGTTTGCCC
Statistics
Matches: 213, Mismatches: 27, Indels: 17
0.83 0.11 0.07
Matches are distributed among these distances:
53 24 0.11
54 181 0.85
55 7 0.03
56 1 0.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (54 bp):
AATTACCAAAATACCCTTGTAGGGTAAAATTACTAAAATACCCCTGTAGGGTAG
Found at i:5274461 original size:81 final size:80
Alignment explanation
Indices: 5274238--5274490 Score: 224
Period size: 81 Copynumber: 3.1 Consensus size: 80
5274228 CCTTTATTTA
* ** * * ** * *
5274238 TAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTGTAAAATTATCA
1 TAAAATTACCAAAATACCCCTAGTGGGTAAAATTACCAAAATACCCCTGATGGGTAAAATTACCG
**
5274303 AAATACCTCTAGT-TTG
66 AAATACC-CT-GTAGGG
** * ** *
5274319 TAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGATTTGTAAAATTACTG
1 TAAAATTACCAAAATACCCCTAGTGGGTAAAATTACCAAAATACCCCTGATGGGTAAAATTACCG
5274384 AAATACCCCTGTAGGG
66 AAATA-CCCTGTAGGG
* * * *
5274400 TAGAATTACTAAAATACCCCT-GTAGGGTAAAATTACTAAAATACCCCTG-TAGGGTAGAATTAC
1 TAAAATTACCAAAATACCCCTAGT-GGGTAAAATTACCAAAATACCCCTGAT-GGGTAAAATTAC
* * *
5274463 CGAGATACCTTGTGGGG
64 CGAAATACCCTGTAGGG
5274480 TAAAATTACCA
1 TAAAATTACCA
5274491 GTTTGCCCCT
Statistics
Matches: 146, Mismatches: 22, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
80 22 0.15
81 122 0.84
82 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (80 bp):
TAAAATTACCAAAATACCCCTAGTGGGTAAAATTACCAAAATACCCCTGATGGGTAAAATTACCG
AAATACCCTGTAGGG
Found at i:5274487 original size:26 final size:27
Alignment explanation
Indices: 5274238--5274490 Score: 203
Period size: 27 Copynumber: 9.4 Consensus size: 27
5274228 CCTTTATTTA
**
5274238 TAAAATTACCAAAATACCCCTGGT-TTG
1 TAAAATTACCAAAATACCCCT-GTAGGG
* **
5274265 TAAAATTACCAAAATACCCTTGGT-TTG
1 TAAAATTACCAAAATACCCCT-GTAGGG
* * **
5274292 TAAAATTATCAAAATACCTCTAGT-TTG
1 TAAAATTACCAAAATACCCCT-GTAGGG
**
5274319 TAAAATTACCAAAATACCCCTAGT-TTG
1 TAAAATTACCAAAATACCCCT-GTAGGG
* **
5274346 TAAAATTACCAAAATACCCTTG-ATTTG
1 TAAAATTACCAAAATACCCCTGTA-GGG
**
5274373 TAAAATTACTGAAATACCCCTGTAGGG
1 TAAAATTACCAAAATACCCCTGTAGGG
* *
5274400 TAGAATTACTAAAATACCCCTGTAGGG
1 TAAAATTACCAAAATACCCCTGTAGGG
*
5274427 TAAAATTACTAAAATACCCCTGTAGGG
1 TAAAATTACCAAAATACCCCTGTAGGG
* * * * *
5274454 TAGAATTACCGAGATA-CCTTGTGGGG
1 TAAAATTACCAAAATACCCCTGTAGGG
5274480 TAAAATTACCA
1 TAAAATTACCA
5274491 GTTTGCCCCT
Statistics
Matches: 199, Mismatches: 24, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
26 18 0.09
27 180 0.90
28 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (27 bp):
TAAAATTACCAAAATACCCCTGTAGGG
Found at i:5274949 original size:22 final size:22
Alignment explanation
Indices: 5274919--5274980 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
5274909 AAGCCTTCTG
* *
5274919 ATTATGGCTTTGTGTCAACCTA
1 ATTATGGCTCTGTGCCAACCTA
5274941 CA-TATGGCTCTGTGCCAACCTA
1 -ATTATGGCTCTGTGCCAACCTA
* *
5274963 ATTATGGCTGTATGCCAA
1 ATTATGGCTCTGTGCCAA
5274981 ACGTATTTGC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 1 0.03
22 32 0.94
23 1 0.03
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (22 bp):
ATTATGGCTCTGTGCCAACCTA
Found at i:5275169 original size:27 final size:27
Alignment explanation
Indices: 5275139--5275240 Score: 107
Period size: 27 Copynumber: 3.8 Consensus size: 27
5275129 ATTCTGTTAA
* *
5275139 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTATGCCACAATATCTGTTTCTG
*
5275166 GTGGCTATGCCACAAATATCT-ATTCTG
1 GTGGCTATGCCAC-AATATCTGTTTCTG
* * *
5275193 GTGGCTCTGCCACAATATCTGTATGTG
1 GTGGCTATGCCACAATATCTGTTTCTG
* * *
5275220 GTGACTCTGTCACAATATCTG
1 GTGGCTATGCCACAATATCTG
5275241 ATAACTGAGT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
26 7 0.11
27 51 0.80
28 6 0.09
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.36
Consensus pattern (27 bp):
GTGGCTATGCCACAATATCTGTTTCTG
Found at i:5275416 original size:25 final size:25
Alignment explanation
Indices: 5275412--5275475 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 25
5275402 ATACTGATTT
*
5275412 TGATTTTGATTCTGTTACCTGATAC
1 TGATTCTGATTCTGTTACCTGATAC
* * *
5275437 TGATTCTGATTCTGTCACCTAATTC
1 TGATTCTGATTCTGTTACCTGATAC
*
5275462 TAATTCTGATTCTG
1 TGATTCTGATTCTG
5275476 ATTCTGATTC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47
Consensus pattern (25 bp):
TGATTCTGATTCTGTTACCTGATAC
Found at i:5275421 original size:31 final size:31
Alignment explanation
Indices: 5275376--5275447 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
5275366 ATGCATTCAC
5275376 ATTCTGATTTTTGATTCTGTTACCTGATACTG
1 ATTCTGA-TTTTGATTCTGTTACCTGATACTG
*
5275408 ATTTTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
5275439 ATTCTGATT
1 ATTCTGATT
5275448 CTGTCACCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 32 0.84
32 6 0.16
ACGTcount: A:0.19, C:0.14, G:0.15, T:0.51
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTTACCTGATACTG
Found at i:5275447 original size:6 final size:6
Alignment explanation
Indices: 5275376--5275495 Score: 68
Period size: 6 Copynumber: 19.3 Consensus size: 6
5275366 ATGCATTCAC
* * * *
5275376 ATTCTG ATTTTTG ATTCTG -TTACCTG ATACTG ATTTTG ATTTTG ATTCTG
1 ATTCTG A-TTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * *
5275426 -TTACCTG ATACTG ATTCTG ATTCTG -TCACCTA ATTCTA ATTCTG ATTCTG
1 ATT--CTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG
5275476 ATTCTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG A-TTCTG AT
5275496 AATGTTTCTT
Statistics
Matches: 90, Mismatches: 12, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
5 6 0.07
6 67 0.74
7 14 0.16
8 3 0.03
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:5276601 original size:15 final size:15
Alignment explanation
Indices: 5276581--5276609 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5276571 TAAAATATTT
5276581 ATTTCCTTTGAAAAC
1 ATTTCCTTTGAAAAC
5276596 ATTTCCTTTGAAAA
1 ATTTCCTTTGAAAA
5276610 TAAGTAACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.41
Consensus pattern (15 bp):
ATTTCCTTTGAAAAC
Found at i:5277042 original size:28 final size:27
Alignment explanation
Indices: 5276941--5277042 Score: 80
Period size: 28 Copynumber: 3.5 Consensus size: 27
5276931 TCAGTGTTAA
* *
5276941 CTGGGCCTTAGCCCATATCAATATTAAT
1 CTGGGCC-TAGCCCATATCAGTATCAAT
*
5276969 CTGGGCCATAGCCCCT-TACAGTATCAGAGTAT
1 CTGGGCC-TAGCCCATAT-CAGTATC--A--AT
*
5277001 ATTGGGCCTAGCCCATATCAGTATCAAT
1 -CTGGGCCTAGCCCATATCAGTATCAAT
5277029 CTGGGCCGTAGCCC
1 CTGGGCC-TAGCCC
5277043 TATTACAAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
27 7 0.12
28 27 0.46
30 2 0.03
32 16 0.27
33 7 0.12
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (27 bp):
CTGGGCCTAGCCCATATCAGTATCAAT
Found at i:5277067 original size:60 final size:59
Alignment explanation
Indices: 5276940--5277069 Score: 156
Period size: 60 Copynumber: 2.2 Consensus size: 59
5276930 ATCAGTGTTA
* *
5276940 ACTGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAGTATCAGAGTAT
1 ACTGGGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAG-ATCAGAGTAT
* * *
5277001 ATTGGGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATTACA-AGTC-GAGATAT
1 ACTGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCC-ATTACAGA-TCAGAG-TAT
5277061 ACTGGGCCT
1 ACTGGGCCT
5277070 TTTCCCATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
59 4 0.07
60 44 0.73
61 12 0.20
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (59 bp):
ACTGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAGATCAGAGTAT
Found at i:5284605 original size:14 final size:14
Alignment explanation
Indices: 5284565--5284614 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
5284555 CACTAGCTTG
5284565 AGCCAATAAAGTAT
1 AGCCAATAAAGTAT
* *
5284579 AGCGAGT---GTAT
1 AGCCAATAAAGTAT
5284590 AGCCAATAAAGTAT
1 AGCCAATAAAGTAT
5284604 AGCCAATAAAG
1 AGCCAATAAAG
5284615 AGCCTCAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
11 9 0.31
14 20 0.69
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.20
Consensus pattern (14 bp):
AGCCAATAAAGTAT
Found at i:5284618 original size:25 final size:25
Alignment explanation
Indices: 5284564--5284618 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
5284554 ACACTAGCTT
* * **
5284564 GAGCCAATAAAGTATAGCGAGTGTA
1 GAGCCAATAAAGTATAGCCAATAAA
*
5284589 TAGCCAATAAAGTATAGCCAATAAA
1 GAGCCAATAAAGTATAGCCAATAAA
5284614 GAGCC
1 GAGCC
5284619 TCAGATTTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.18
Consensus pattern (25 bp):
GAGCCAATAAAGTATAGCCAATAAA
Found at i:5286291 original size:28 final size:28
Alignment explanation
Indices: 5286256--5286326 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
5286246 TGTAAAAATT
* *
5286256 GCACTAAGTGTGCGAG-TCTGATTAT-TGA
1 GCACTAAGTGTGCGAGCT-TAAGTATCT-A
*
5286284 GCACTAAGTGTGCAAGCTTAAGTATCTA
1 GCACTAAGTGTGCGAGCTTAAGTATCTA
5286312 GCACTAAGTGTGCGA
1 GCACTAAGTGTGCGA
5286327 ATCCGATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 35 0.95
29 2 0.05
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGCTTAAGTATCTA
Found at i:5294391 original size:20 final size:20
Alignment explanation
Indices: 5294366--5294403 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5294356 TTTAATACTA
* *
5294366 AACACCGATATCAAATTGGG
1 AACACCAATACCAAATTGGG
5294386 AACACCAATACCAAATTG
1 AACACCAATACCAAATTG
5294404 AAACTACTTA
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:0.45, C:0.24, G:0.13, T:0.18
Consensus pattern (20 bp):
AACACCAATACCAAATTGGG
Found at i:5295160 original size:61 final size:61
Alignment explanation
Indices: 5295065--5295184 Score: 240
Period size: 61 Copynumber: 2.0 Consensus size: 61
5295055 CGAACAAATA
5295065 AACTTGTGAGAAGAAAATTATTCCCCTTTTTCAGTTTTCTTTATGTAAGTGAAGCTTAATG
1 AACTTGTGAGAAGAAAATTATTCCCCTTTTTCAGTTTTCTTTATGTAAGTGAAGCTTAATG
5295126 AACTTGTGAGAAGAAAATTATTCCCCTTTTTCAGTTTTCTTTATGTAAGTGAAGCTTAA
1 AACTTGTGAGAAGAAAATTATTCCCCTTTTTCAGTTTTCTTTATGTAAGTGAAGCTTAA
5295185 AGTCGGTGTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (61 bp):
AACTTGTGAGAAGAAAATTATTCCCCTTTTTCAGTTTTCTTTATGTAAGTGAAGCTTAATG
Found at i:5299221 original size:21 final size:20
Alignment explanation
Indices: 5299166--5299217 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
5299156 AAATTTTCAT
* *
5299166 GAGAAAAAAGTTGAAAATTAA
1 GAGAAAAAA-CTGAAAATCAA
*
5299187 GAGGAAAAAACTGAAAATCAG
1 GA-GAAAAAACTGAAAATCAA
5299208 GAGAAAAAAC
1 GAGAAAAAAC
5299218 CTGATTTGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 8 0.30
21 12 0.44
22 7 0.26
ACGTcount: A:0.62, C:0.06, G:0.21, T:0.12
Consensus pattern (20 bp):
GAGAAAAAACTGAAAATCAA
Found at i:5299645 original size:3 final size:3
Alignment explanation
Indices: 5299637--5299666 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5299627 TGGATCTTTA
5299637 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5299667 TTGTTCTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5300556 original size:33 final size:33
Alignment explanation
Indices: 5300514--5300581 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
5300504 TTTTCAAAAG
5300514 AAAGGAAAATTGACTATTAAAGAGTACTTGGCT
1 AAAGGAAAATTGACTATTAAAGAGTACTTGGCT
5300547 AAAGGAAAATTGACTATTAAAGAGTACTTGGCT
1 AAAGGAAAATTGACTATTAAAGAGTACTTGGCT
5300580 AA
1 AA
5300582 GATCAAAGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (33 bp):
AAAGGAAAATTGACTATTAAAGAGTACTTGGCT
Found at i:5321401 original size:25 final size:25
Alignment explanation
Indices: 5321354--5321401 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
5321344 TTATAACATG
* * *
5321354 AAAATGACCATTTTGCCCCTAGGTA
1 AAAATAACCATTATACCCCTAGGTA
*
5321379 AAAATAACCATTATACCCTTAGG
1 AAAATAACCATTATACCCCTAGG
5321402 GTTTATATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (25 bp):
AAAATAACCATTATACCCCTAGGTA
Found at i:5321468 original size:20 final size:20
Alignment explanation
Indices: 5321445--5321488 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
5321435 TAAACATGGT
5321445 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
5321465 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
5321485 ATGT
1 ATGT
5321489 TCATAAATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:5321562 original size:25 final size:25
Alignment explanation
Indices: 5321534--5321708 Score: 284
Period size: 25 Copynumber: 7.1 Consensus size: 25
5321524 GAGGAAGTGC
*
5321534 AAAAGGGCTTATGCTCCAGTTATTA
1 AAAAGGGCTTATGCCCCAGTTATTA
5321559 AAAAGGGCTTATGCCCCAGTTATT-
1 AAAAGGGCTTATGCCCCAGTTATTA
5321583 AAAAGGGCTTATGCCCCAGTTATT-
1 AAAAGGGCTTATGCCCCAGTTATTA
5321607 AAAAGGGCTTATGCCCCAGTTATTA
1 AAAAGGGCTTATGCCCCAGTTATTA
* *
5321632 AAAAGGGCTTATGCTCCAGTTA-TC
1 AAAAGGGCTTATGCCCCAGTTATTA
*
5321656 AAAAGGACTTATGCCCCAGTTATTA
1 AAAAGGGCTTATGCCCCAGTTATTA
*
5321681 AAAAGGGCTTTTGCCCCAGTTATTA
1 AAAAGGGCTTATGCCCCAGTTATTA
5321706 AAA
1 AAA
5321709 GAGGCTAGGC
Statistics
Matches: 140, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
24 69 0.49
25 71 0.51
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (25 bp):
AAAAGGGCTTATGCCCCAGTTATTA
Found at i:5321709 original size:49 final size:49
Alignment explanation
Indices: 5321534--5321728 Score: 295
Period size: 49 Copynumber: 4.0 Consensus size: 49
5321524 GAGGAAGTGC
*
5321534 AAAAGGGCTTATGCTCCAGTTATTAAAAAGGGCTTATGCCCCAGTTATT-
1 AAAAGGGCTTATGCCCCAGTTATT-AAAAGGGCTTATGCCCCAGTTATTA
5321583 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATTA
1 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATTA
* * *
5321632 AAAAGGGCTTATGCTCCAGTTATCAAAAGGACTTATGCCCCAGTTATTA
1 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATTA
* *
5321681 AAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATTAAAAG-GGCTTATGCC-CCAGTTAT
5321729 ATGATAAAGC
Statistics
Matches: 134, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
48 24 0.18
49 100 0.75
50 10 0.07
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (49 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATTA
Found at i:5321714 original size:25 final size:24
Alignment explanation
Indices: 5321534--5321728 Score: 284
Period size: 24 Copynumber: 8.0 Consensus size: 24
5321524 GAGGAAGTGC
*
5321534 AAAAGGGCTTATGCTCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
5321558 AAAAAGGGCTTATGCCCCAGTTATT
1 -AAAAGGGCTTATGCCCCAGTTATT
5321583 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
5321607 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
5321631 AAAAAGGGCTTATGCTCCAGTTATC
1 -AAAAGGGCTTATGCCCCAGTTATT
*
5321656 AAAAGGACTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
5321680 AAAAAGGGCTTTTGCCCCAGTTATT
1 -AAAAGGGCTTATGCCCCAGTTATT
*
5321705 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
5321729 ATGATAAAGC
Statistics
Matches: 156, Mismatches: 10, Indels: 8
0.90 0.06 0.05
Matches are distributed among these distances:
24 78 0.50
25 78 0.50
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:5324067 original size:17 final size:17
Alignment explanation
Indices: 5324045--5324078 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5324035 GATATGATAC
5324045 TAAAAT-TATTAAAAAAT
1 TAAAATATA-TAAAAAAT
5324062 TAAAATATATAAAAAAT
1 TAAAATATATAAAAAAT
5324079 AGGGAAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAATATATAAAAAAT
Found at i:5324366 original size:22 final size:21
Alignment explanation
Indices: 5324331--5324457 Score: 69
Period size: 19 Copynumber: 6.5 Consensus size: 21
5324321 AAAAGGTATC
* *
5324331 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
5324352 TACAAAATCATATCTTCTGAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
5324375 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
5324394 TGC-AATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
5324412 T--ATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
5324429 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
5324448 TACATATCAT
1 TACAAATCAT
5324458 TGAAGATTAT
Statistics
Matches: 92, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
17 15 0.16
18 15 0.16
19 35 0.38
21 3 0.03
22 15 0.16
23 9 0.10
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:5324395 original size:19 final size:19
Alignment explanation
Indices: 5324371--5324457 Score: 144
Period size: 19 Copynumber: 4.7 Consensus size: 19
5324361 ATATCTTCTG
5324371 AGATTGCATATCATATCTA
1 AGATTGCATATCATATCTA
5324390 AGATTGCA-ATCATATCTA
1 AGATTGCATATCATATCTA
5324408 AGATT--ATATCATATCTA
1 AGATTGCATATCATATCTA
5324425 AGATTGCATATCATATCTA
1 AGATTGCATATCATATCTA
*
5324444 AGATTACATATCAT
1 AGATTGCATATCAT
5324458 TGAAGATTAT
Statistics
Matches: 64, Mismatches: 1, Indels: 6
0.90 0.01 0.08
Matches are distributed among these distances:
16 1 0.02
17 15 0.23
18 15 0.23
19 33 0.52
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (19 bp):
AGATTGCATATCATATCTA
Found at i:5324465 original size:36 final size:36
Alignment explanation
Indices: 5324371--5324457 Score: 140
Period size: 35 Copynumber: 2.4 Consensus size: 36
5324361 ATATCTTCTG
5324371 AGATTGCATATCATATCTAAGATTGCAATCATATCTA
1 AGATT-CATATCATATCTAAGATTGCAATCATATCTA
5324408 AGATT-ATATCATATCTAAGATTGCATATCATATCTA
1 AGATTCATATCATATCTAAGATTGCA-ATCATATCTA
5324444 AGATTACATATCAT
1 AGATT-CATATCAT
5324458 TGAAGATTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
35 20 0.43
36 15 0.32
37 5 0.11
38 7 0.15
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (36 bp):
AGATTCATATCATATCTAAGATTGCAATCATATCTA
Found at i:5328568 original size:23 final size:21
Alignment explanation
Indices: 5328542--5328585 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
5328532 GGTATTTGAG
5328542 TATGAATGCATAAATGTATGTGT
1 TATGAATG-ATAAATG-ATGTGT
* *
5328565 TATGTATGTTAAATGATGTGT
1 TATGAATGATAAATGATGTGT
5328586 ATTGATCGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 6 0.32
23 7 0.37
ACGTcount: A:0.32, C:0.02, G:0.23, T:0.43
Consensus pattern (21 bp):
TATGAATGATAAATGATGTGT
Found at i:5335481 original size:93 final size:93
Alignment explanation
Indices: 5335365--5335537 Score: 292
Period size: 93 Copynumber: 1.9 Consensus size: 93
5335355 ATGTTTGTGC
* * * *
5335365 AAACGAATTGCAGAATTTATATAATTTATAGGGTTCAAATACAAATTAATTATTATTGTAGTTTG
1 AAACGAATTGCAAAATTTATATAATTTATAGGGTTAAAATACAAATTAATTATTATTGCAGTTCG
5335430 TAGAATTACTTGTAAATAAAATGCGTGT
66 TAGAATTACTTGTAAATAAAATGCGTGT
*
5335458 AAACGAATTGCAAAATTTATATAATTTATAGGGTTAAAATACAAATTAATTATTATTGCGGTTCG
1 AAACGAATTGCAAAATTTATATAATTTATAGGGTTAAAATACAAATTAATTATTATTGCAGTTCG
*
5335523 TAGAATTGCTTGTAA
66 TAGAATTACTTGTAA
5335538 TTCATAAAAG
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (93 bp):
AAACGAATTGCAAAATTTATATAATTTATAGGGTTAAAATACAAATTAATTATTATTGCAGTTCG
TAGAATTACTTGTAAATAAAATGCGTGT
Found at i:5335975 original size:25 final size:26
Alignment explanation
Indices: 5335947--5335995 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
5335937 CTGAGTTGTC
5335947 CAAAATCACATATATGG-TATGAACA
1 CAAAATCACATATATGGTTATGAACA
*
5335972 CAAAATCACATATTTGGTTATGAA
1 CAAAATCACATATATGGTTATGAA
5335996 TATGTCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (26 bp):
CAAAATCACATATATGGTTATGAACA
Found at i:5336827 original size:18 final size:19
Alignment explanation
Indices: 5336804--5336839 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5336794 AATCGTGTCG
*
5336804 TTCATTTTCAAAA-CAATA
1 TTCATTTTAAAAATCAATA
5336822 TTCATTTTAAAAATCAAT
1 TTCATTTTAAAAATCAAT
5336840 GTTGAATTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (19 bp):
TTCATTTTAAAAATCAATA
Found at i:5344297 original size:5 final size:5
Alignment explanation
Indices: 5344289--5344355 Score: 59
Period size: 5 Copynumber: 13.2 Consensus size: 5
5344279 ATAATTTATA
* *
5344289 AATAT AATAT AATAT AA-AT CATATAGT AATA- AAAAT ACATAT AATAA
1 AATAT AATAT AATAT AATAT -A-ATA-T AATAT AATAT A-ATAT AATAT
5344336 AATAT -ATAT AATAT AATAT A
1 AATAT AATAT AATAT AATAT A
5344356 TGAGGAAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
4 9 0.18
5 31 0.61
6 8 0.16
7 2 0.04
8 1 0.02
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.34
Consensus pattern (5 bp):
AATAT
Found at i:5344324 original size:17 final size:18
Alignment explanation
Indices: 5344298--5344331 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5344288 AAATATAATA
*
5344298 TAATATAAAT-CATATAG
1 TAATAAAAATACATATAG
5344315 TAATAAAAATACATATA
1 TAATAAAAATACATATA
5344332 ATAAAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (18 bp):
TAATAAAAATACATATAG
Found at i:5344354 original size:14 final size:14
Alignment explanation
Indices: 5344274--5344356 Score: 66
Period size: 14 Copynumber: 6.0 Consensus size: 14
5344264 ATGGTAAAAC
* *
5344274 ATAAAATAATTTAT
1 ATAATATAATATAT
5344288 A-AATATAATATA-
1 ATAATATAATATAT
5344300 AT-ATA-AATCATAT
1 ATAATATAAT-ATAT
* *
5344313 AGTAATAAAAATACAT
1 A-TAAT-ATAATATAT
*
5344329 ATAATAAAATATAT
1 ATAATATAATATAT
5344343 ATAATATAATATAT
1 ATAATATAATATAT
5344357 GAGGAAAAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 14
0.75 0.07 0.18
Matches are distributed among these distances:
11 3 0.05
12 7 0.12
13 10 0.18
14 23 0.40
15 6 0.11
16 5 0.09
17 3 0.05
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.36
Consensus pattern (14 bp):
ATAATATAATATAT
Found at i:5344461 original size:62 final size:61
Alignment explanation
Indices: 5344395--5344600 Score: 151
Period size: 60 Copynumber: 3.3 Consensus size: 61
5344385 TTCATACAAG
** *
5344395 AATATAGTAAAATAATTAATAAATATATAAAAATACATAATATATGCTAAACTTATAAATAA-AA
1 AATATAGTAAAATAATTAATAAATATATAAAAATA-AT-ATATA--CTAAAAATATATATAATAA
* * * *
5344459 TATATAATAATATAATTTATAACATATA-AAAAATAATATATACTAAAAATATATATAATAA
1 AATATAGTAAAATAATTAATAA-ATATATAAAAATAATATATACTAAAAATATATATAATAA
* *
5344520 AATAT-G-AATAATATATATAATAAATATATGATAA-AA-AT-T--TAAAAATATAATAATAGAT
1 AATATAGTAA-AATA-AT-TAATAAATATATAAAAATAATATATACTAAAAATAT-AT-ATA-AT
5344578 AA
60 AA
* *
5344580 AACATAGTAAAATAAATAATA
1 AATATAGTAAAATAATTAATA
5344601 TATACAGTGA
Statistics
Matches: 116, Mismatches: 15, Indels: 27
0.73 0.09 0.17
Matches are distributed among these distances:
57 9 0.08
58 2 0.02
59 11 0.09
60 27 0.23
61 20 0.17
62 15 0.13
63 2 0.02
64 25 0.22
65 5 0.04
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (61 bp):
AATATAGTAAAATAATTAATAAATATATAAAAATAATATATACTAAAAATATATATAATAA
Found at i:5344466 original size:31 final size:30
Alignment explanation
Indices: 5344424--5344535 Score: 77
Period size: 31 Copynumber: 3.5 Consensus size: 30
5344414 TAAATATATA
* *
5344424 AAAATACATAATATATGCTAAACTTATAAAT
1 AAAATATATAATATAT-CTAAAATTATAAAT
* *
5344455 AAAATATATAATA-ATAT-AATTTATAACAT
1 AAAATATATAATATATCTAAAATTATAA-AT
*
5344484 ATAAA-AAATAATATATACTAAAAATATATATAAT
1 A-AAATATATAATATAT-CT-AAAAT-TATA-AAT
5344518 AAAATATGAATAATATAT
1 AAAATAT--ATAATATAT
5344536 ATAATAAATA
Statistics
Matches: 63, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
28 8 0.13
29 11 0.17
30 7 0.11
31 13 0.21
33 6 0.10
34 8 0.13
35 1 0.02
36 9 0.14
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (30 bp):
AAAATATATAATATATCTAAAATTATAAAT
Found at i:5344491 original size:64 final size:63
Alignment explanation
Indices: 5344396--5344548 Score: 147
Period size: 63 Copynumber: 2.4 Consensus size: 63
5344386 TCATACAAGA
* * * *
5344396 ATATAGTAAAATAATTAATAAATATATAAAAATACATAATATATGCT-AAACT-TATA-AATAAA
1 ATATAATAATATAATTAATAAACATATAAAAATA-AT-ATATA--CTAAAAATATATATAATAAA
5344458 AT
62 AT
*
5344460 ATATAATAATATAATTTAT-AACATATAAAAAATAATATATACTAAAAATATATATAATAAAAT
1 ATATAATAATATAATTAATAAACATAT-AAAAATAATATATACTAAAAATATATATAATAAAAT
* *
5344523 AT-GAATAATAT-ATATAATAAATATAT
1 ATATAATAATATAAT-TAATAAACATAT
5344549 GATAAAAATT
Statistics
Matches: 75, Mismatches: 8, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
60 2 0.03
61 6 0.08
62 20 0.27
63 24 0.32
64 23 0.31
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (63 bp):
ATATAATAATATAATTAATAAACATATAAAAATAATATATACTAAAAATATATATAATAAAAT
Found at i:5344494 original size:14 final size:14
Alignment explanation
Indices: 5344477--5344523 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
5344467 AATATAATTT
*
5344477 ATAACATATAAAAA
1 ATAATATATAAAAA
5344491 ATAATATATACTAAAA
1 ATAATATATA--AAAA
5344507 AT-ATATATAATAAA
1 ATAATATATAA-AAA
5344521 ATA
1 ATA
5344524 TGAATAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
13 1 0.04
14 14 0.50
15 7 0.25
16 6 0.21
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAATATATAAAAA
Found at i:5344512 original size:15 final size:16
Alignment explanation
Indices: 5344487--5344557 Score: 58
Period size: 16 Copynumber: 4.4 Consensus size: 16
5344477 ATAACATATA
*
5344487 AAAAATAATATATACT
1 AAAAATAATATATAAT
5344503 AAAAAT-ATATATAAT
1 AAAAATAATATATAAT
5344518 AAAATATGAATA-AT-AT
1 AAAA-AT-AATATATAAT
* *
5344534 ATATAATAAATATATGAT
1 A-AAAAT-AATATATAAT
5344552 AAAAAT
1 AAAAAT
5344558 TTAAAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
15 12 0.27
16 17 0.38
17 10 0.22
18 6 0.13
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.32
Consensus pattern (16 bp):
AAAAATAATATATAAT
Found at i:5344516 original size:36 final size:35
Alignment explanation
Indices: 5344451--5344554 Score: 97
Period size: 36 Copynumber: 2.8 Consensus size: 35
5344441 CTAAACTTAT
* *
5344451 AAATAAAATATATAATAATATAATTTATAACATATAAA
1 AAATAATATATATAATAA-AT-ATATATAA-ATATAAA
5344489 AAATAATATATACTAA-AAATATATAT-AATA-AAA
1 AAATAATATATA-TAATAAATATATATAAATATAAA
5344522 TATGAATAATATATATAATAAATATATGATAAA
1 -A--AATAATATATATAATAAATATAT-ATAAA
5344555 AATTTAAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
33 3 0.05
34 4 0.07
35 4 0.07
36 24 0.42
37 4 0.07
38 15 0.26
39 3 0.05
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (35 bp):
AAATAATATATATAATAAATATATATAAATATAAA
Found at i:5344529 original size:11 final size:11
Alignment explanation
Indices: 5344490--5344574 Score: 66
Period size: 11 Copynumber: 7.4 Consensus size: 11
5344480 ACATATAAAA
5344490 AATAATATATACT
1 AATAA-ATATA-T
*
5344503 AAAAATATATAT
1 AATAA-ATATAT
5344515 AATAAA-ATAT
1 AATAAATATAT
5344525 GAATAATATATAT
1 -AATAA-ATATAT
5344538 AATAAATATAT
1 AATAAATATAT
* * *
5344549 GATAAAAATTT
1 AATAAATATAT
5344560 AA-AAATATAAT
1 AATAAATAT-AT
5344571 AATA
1 AATA
5344575 GATAAAACAT
Statistics
Matches: 59, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
10 9 0.15
11 24 0.41
12 12 0.20
13 14 0.24
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.34
Consensus pattern (11 bp):
AATAAATATAT
Found at i:5344532 original size:14 final size:14
Alignment explanation
Indices: 5344482--5344524 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
5344472 AATTTATAAC
5344482 ATATAA-AAAATAAT
1 ATATAATAAAAT-AT
*
5344496 ATATACTAAAAATAT
1 ATATAAT-AAAATAT
5344511 ATATAATAAAATAT
1 ATATAATAAAATAT
5344525 GAATAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 12 0.48
15 8 0.32
16 5 0.20
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
ATATAATAAAATAT
Found at i:5344536 original size:23 final size:24
Alignment explanation
Indices: 5344506--5344550 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
5344496 ATATACTAAA
5344506 AATATATATAATAAA-ATATGAAT
1 AATATATATAATAAATATATGAAT
5344529 AATATATATAATAAATATATGA
1 AATATATATAATAAATATATGA
5344551 TAAAAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (24 bp):
AATATATATAATAAATATATGAAT
Found at i:5344567 original size:34 final size:36
Alignment explanation
Indices: 5344458--5344574 Score: 93
Period size: 39 Copynumber: 3.3 Consensus size: 36
5344448 TATAAATAAA
* * *
5344458 ATATATAAT-AATATA-ATTTATAACATATAAAAAAT
1 ATATATAATAAATATATA-TAATAAAATATGAAAAAT
* *
5344493 AATATATACTAAAAATATATATAATAAAATATGAATAAT
1 -ATATATA--ATAAATATATATAATAAAATATGAAAAAT
*
5344532 ATATATAATAAATATATGAT-A-AAAAT-TTAAAAAT
1 ATATATAATAAATATAT-ATAATAAAATATGAAAAAT
5344566 ATA-ATAATA
1 ATATATAATA
5344575 GATAAAACAT
Statistics
Matches: 68, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
33 6 0.09
34 9 0.13
35 5 0.07
36 17 0.25
37 2 0.03
38 8 0.12
39 20 0.29
40 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (36 bp):
ATATATAATAAATATATATAATAAAATATGAAAAAT
Found at i:5344598 original size:19 final size:18
Alignment explanation
Indices: 5344484--5344598 Score: 57
Period size: 19 Copynumber: 6.2 Consensus size: 18
5344474 TTTATAACAT
5344484 ATAAAAA-ATAAT-ATATA
1 ATAAAAATATAATAATA-A
*
5344501 CTAAAAATAT-AT-AT-A
1 ATAAAAATATAATAATAA
5344516 AT-AAAATATGAATAATATA
1 ATAAAAATAT-AATAATA-A
5344535 TATAATAAATATATGATAA-AA
1 -ATAA-AAATATA--ATAATAA
*
5344556 ATTTAAAAATATAATAATAG
1 A--TAAAAATATAATAATAA
5344576 ATAAAACATAGTAA-AATAA
1 ATAAAA-ATA-TAATAATAA
5344595 ATAA
1 ATAA
5344599 TATATACAGT
Statistics
Matches: 78, Mismatches: 4, Indels: 30
0.70 0.04 0.27
Matches are distributed among these distances:
14 7 0.09
15 2 0.03
16 2 0.03
17 12 0.15
18 7 0.09
19 16 0.21
20 8 0.10
21 10 0.13
22 10 0.13
23 4 0.05
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.30
Consensus pattern (18 bp):
ATAAAAATATAATAATAA
Found at i:5345831 original size:16 final size:17
Alignment explanation
Indices: 5345796--5345844 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
5345786 TTCCAGATTC
*
5345796 TGTTTAGGCATTGGGCCT
1 TGTTTAGG-ATTGGGTCT
5345814 TGTTTAGG-TTGGGTCT
1 TGTTTAGGATTGGGTCT
* *
5345830 TGTTTGGGTTTGGGT
1 TGTTTAGGATTGGGT
5345845 GTAATAGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 14 0.50
17 6 0.21
18 8 0.29
ACGTcount: A:0.06, C:0.08, G:0.39, T:0.47
Consensus pattern (17 bp):
TGTTTAGGATTGGGTCT
Found at i:5345905 original size:48 final size:48
Alignment explanation
Indices: 5345851--5345946 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
5345841 GGGTGTAATA
*
5345851 GGTTAATAGATTTTGGGCCAAAGGTTTAGGGTAATTGGGTTGTAACCG
1 GGTTAATAGATTTTGGGCCAAAGGTTTAGGCTAATTGGGTTGTAACCG
*
5345899 GGTTAATAGATTTTGGGCTAAAGGTTTAGGCTAATTGGGTTGTAACCG
1 GGTTAATAGATTTTGGGCCAAAGGTTTAGGCTAATTGGGTTGTAACCG
5345947 AGTGCTAAGT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.25, C:0.08, G:0.32, T:0.34
Consensus pattern (48 bp):
GGTTAATAGATTTTGGGCCAAAGGTTTAGGCTAATTGGGTTGTAACCG
Found at i:5346446 original size:93 final size:88
Alignment explanation
Indices: 5346321--5346498 Score: 232
Period size: 93 Copynumber: 2.0 Consensus size: 88
5346311 TTTTTTCTTC
* * * * *
5346321 TTTTTTTTTGCACTGAGTTAGGTATTTGAACTTTCAAATTGCATTAAAAAAG-CCCTCAAACCTT
1 TTTTTTTTTGCACTCAATTAGGTACTTAAACTTTCAAAATGCA-TAAAAAAGACCCTCAAA-CTT
5346385 AAAAAAAAAAGCAATTAAGCCCCTACCT
64 --AAAAAAAA-CAATTAAGCCCCTACCT
* *
5346413 TTTTTTTGTTGCACTCAATTGGGTACTTAAACTTTCAAAATGCATCAAAAAGACCCTCAAACTTA
1 TTTTTTT-TTGCACTCAATTAGGTACTTAAACTTTCAAAATGCATAAAAAAGACCCTCAAACTTA
5346478 AAAAAAACAATTAAGCCCCTA
65 AAAAAAACAATTAAGCCCCTA
5346499 ATTTTATTAA
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
89 14 0.18
90 8 0.10
92 17 0.22
93 38 0.49
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.31
Consensus pattern (88 bp):
TTTTTTTTTGCACTCAATTAGGTACTTAAACTTTCAAAATGCATAAAAAAGACCCTCAAACTTAA
AAAAAACAATTAAGCCCCTACCT
Found at i:5352565 original size:26 final size:26
Alignment explanation
Indices: 5352515--5352567 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
5352505 AGCTGAGTTG
*
5352515 TCCAAAATCACATATATGGTAATGAA
1 TCCAAAATCACATATATGATAATGAA
* *
5352541 TCCAAAATCACATATTTGATTATGAA
1 TCCAAAATCACATATATGATAATGAA
5352567 T
1 T
5352568 ATGTCCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.32
Consensus pattern (26 bp):
TCCAAAATCACATATATGATAATGAA
Found at i:5352577 original size:30 final size:28
Alignment explanation
Indices: 5352513--5352577 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 28
5352503 TTAGCTGAGT
*
5352513 TGTCCAAAATCACATATATGGTAATGAA
1 TGTCCAAAATCACATATATGATAATGAA
* *
5352541 --TCCAAAATCACATATTTGATTATGAATA
1 TGTCCAAAATCACATATATGATAATG-A-A
5352569 TGTCCAAAA
1 TGTCCAAAA
5352578 AAAAAACACA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 21 0.70
27 1 0.03
28 1 0.03
30 7 0.23
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (28 bp):
TGTCCAAAATCACATATATGATAATGAA
Found at i:5354889 original size:12 final size:12
Alignment explanation
Indices: 5354857--5354903 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
5354847 TAAAAAAATG
5354857 TTTTATTTAATA
1 TTTTATTTAATA
**
5354869 TTTCCTTTAATA
1 TTTTATTTAATA
*
5354881 TTTTATTT-ATT
1 TTTTATTTAATA
5354892 TATTTATTTAAT
1 T-TTTATTTAAT
5354904 TTCATTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 3 0.11
12 23 0.82
13 2 0.07
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTATTTAATA
Found at i:5354901 original size:24 final size:24
Alignment explanation
Indices: 5354857--5354903 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5354847 TAAAAAAATG
*
5354857 TTTTATTTAATATTTCCTTTAATA
1 TTTTATTTAATATTTCATTTAATA
*
5354881 TTTTATTTATTTATTT-ATTTAAT
1 TTTTATTTA-ATATTTCATTTAAT
5354904 TTCATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTTATTTAATATTTCATTTAATA
Found at i:5355019 original size:22 final size:22
Alignment explanation
Indices: 5354975--5355020 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5354965 TTGGCTTGTT
* *
5354975 TTATTTTTATTTTTTGCCCTTA
1 TTATTGTTATTTTTTGCCATTA
5354997 TTATTGTTATTTTATT-CCATTA
1 TTATTGTTATTTT-TTGCCATTA
5355019 TT
1 TT
5355021 TATTTGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.17, C:0.11, G:0.04, T:0.67
Consensus pattern (22 bp):
TTATTGTTATTTTTTGCCATTA
Found at i:5355144 original size:3 final size:3
Alignment explanation
Indices: 5355059--5355116 Score: 80
Period size: 3 Copynumber: 19.0 Consensus size: 3
5355049 CAAAATTTAG
* *
5355059 ATT ATT CATT ATT CTT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT
1 ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
5355105 ATT ATT GTT ATT
1 ATT ATT ATT ATT
5355117 TATATTATCG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5358048 original size:14 final size:14
Alignment explanation
Indices: 5358029--5358055 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5358019 TATTAAAATA
5358029 AAAATTAAGAACAC
1 AAAATTAAGAACAC
5358043 AAAATTAAGAACA
1 AAAATTAAGAACA
5358056 AATCAAGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.11, G:0.07, T:0.15
Consensus pattern (14 bp):
AAAATTAAGAACAC
Found at i:5378863 original size:19 final size:19
Alignment explanation
Indices: 5378839--5378885 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
5378829 CGAAGCCCTT
5378839 TTTGCATT-CATCCCATGCA
1 TTTGCATTACATCCCAT-CA
*
5378858 TTTGCATTACATCGCATCA
1 TTTGCATTACATCCCATCA
*
5378877 TATGCATTA
1 TTTGCATTA
5378886 AATTTCACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.38
Consensus pattern (19 bp):
TTTGCATTACATCCCATCA
Found at i:5382772 original size:23 final size:23
Alignment explanation
Indices: 5382725--5382772 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
5382715 CTAATGATAA
* *
5382725 AAGTAAATAAATAAGAATATGTG
1 AAGTAAATAAATAAGAAGATATG
*
5382748 AAGTAAATAAATAAGAGGATATG
1 AAGTAAATAAATAAGAAGATATG
5382771 AA
1 AA
5382773 ACCTATCTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.23
Consensus pattern (23 bp):
AAGTAAATAAATAAGAAGATATG
Found at i:5384897 original size:44 final size:44
Alignment explanation
Indices: 5384834--5385226 Score: 295
Period size: 44 Copynumber: 8.6 Consensus size: 44
5384824 TTATGGCAAG
*
5384834 TCTTATCT-CCTAAAGTTGCAGTGGAGCAGATTGAAGCCACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACAAA
* * * ** *
5384877 TCTTATCTCCCTAAAATTGCAGTGGAGCAGGTTGAAGTTACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACAAA
* * * **
5384921 TCTTATATCCCTGAAGTTGCAGTGAAGCAGACTGAAGATAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCA-CAAA
* * * ** * *
5384966 TCTTATTTCCTTGAAGTTGTAGTGGAATAGATTAAAGCTACAAATTATA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGC--CACA--A-A
* **
5385015 GTTCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGATAGCAAA
1 --TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCA-CAAA
* ** * *
5385062 TCTTATTTCCCTGAAGTTGCAGTGGAATAGATTAAAGCTACAAATTACGAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGC--C-----ACAAA
* *
5385113 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACAAA
* * * * ** *
5385157 -CATTATCTCCCTGAAGTTGCAGTAGAGTAGGTTTAAGTTACGAA
1 TC-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACAAA
5385201 TCTTATCTCCCTGAAGTTGCAGTGGA
1 TCTTATCTCCCTGAAGTTGCAGTGGA
5385227 TCAAGTCAAA
Statistics
Matches: 279, Mismatches: 52, Indels: 37
0.76 0.14 0.10
Matches are distributed among these distances:
43 9 0.03
44 126 0.45
45 65 0.23
46 1 0.00
47 2 0.01
48 2 0.01
49 3 0.01
50 1 0.00
51 69 0.25
52 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACAAA
Found at i:5385039 original size:96 final size:96
Alignment explanation
Indices: 5384921--5385285 Score: 356
Period size: 96 Copynumber: 3.9 Consensus size: 96
5384911 AAGTTACAAG
* * *
5384921 TCTTATATCCCTGAAGTTGCAGTGAAGCAGACTGAAGATAGCAAATCTTATTTCCTTGAAGTTGT
1 TCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGC
*
5384986 AGTGGAATAGATTAAAGCTACAAATTATAG-T
66 AGTGGAATAGATTAAAGCTACAAATTA-AGAA
* * *
5385017 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATTTCCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGC
*
5385082 AGTGGAATAGATTAAAGCTACAAATTACGAA
66 AGTGGAATAGATTAAAGCTACAAATTAAGAA
* * * * ** *
5385113 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCA-CAAA-CATTATCTCCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTGAAGATAGCAAATC-TTATTTCCCTGAAGTTG
* * * * *
5385176 CAGTAGAGTAGGTT-----T--AAGTTACGAA
65 CAGTGGAATAGATTAAAGCTACAAATTAAGAA
* * * ** * * *
5385201 TCTTATCTCCCTGAAGTTGCAGTGGATCAAGTCAAAAGTTA-CAAATCTCATTTCCCTGAAGTAG
1 TCTTATCTCCCTGAAGTTGCAGTGAAGC-AGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTG
* *
5385265 TAGTGGAACAGATTAAAGCTA
65 CAGTGGAATAGATTAAAGCTA
5385286 TAAGTCACAA
Statistics
Matches: 226, Mismatches: 33, Indels: 21
0.81 0.12 0.08
Matches are distributed among these distances:
88 35 0.15
89 34 0.15
90 2 0.01
94 2 0.01
95 32 0.14
96 121 0.54
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (96 bp):
TCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGC
AGTGGAATAGATTAAAGCTACAAATTAAGAA
Found at i:5385042 original size:51 final size:49
Alignment explanation
Indices: 5384966--5385226 Score: 201
Period size: 51 Copynumber: 5.5 Consensus size: 49
5384956 AGATAGCAAA
* * *
5384966 TCTTATTTCCTTGAAGTTGTAGTGGAATAGATTAAAGCTACAAATTATAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAATAGATTAAAGCTACAAATTA-AG
* ** * *
5385016 TTCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGATAGC--A--AA-
1 -TCTTATCTCCCTGAAGTTGCAGTGGAATAGATTAAAGCTA-CAAATTAAG
* *
5385062 TCTTATTTCCCTGAAGTTGCAGTGGAATAGATTAAAGCTACAAATTACGAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAATAGATTAAAGCTACAAATTA--AG
* * *
5385113 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCACAAA--CA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAATAGATTAAAGCTACAAATTAAG
* * * * * *
5385159 --TTATCTCCCTGAAGTTGCAGTAGAGTAGGTTTAAGTTAC----GAA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAATAGATTAAAGCTACAAATTAAG
5385201 TCTTATCTCCCTGAAGTTGCAGTGGA
1 TCTTATCTCCCTGAAGTTGCAGTGGA
5385227 TCAAGTCAAA
Statistics
Matches: 174, Mismatches: 25, Indels: 29
0.76 0.11 0.13
Matches are distributed among these distances:
42 1 0.01
44 58 0.33
45 34 0.20
46 1 0.01
47 2 0.01
48 2 0.01
50 2 0.01
51 73 0.42
52 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Consensus pattern (49 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAATAGATTAAAGCTACAAATTAAG
Found at i:5387004 original size:4 final size:4
Alignment explanation
Indices: 5386995--5387021 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5386985 CCTTTAATAT
5386995 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
5387022 TCATTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:5387141 original size:22 final size:22
Alignment explanation
Indices: 5387097--5387142 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5387087 TGTTTTATTT
* *
5387097 TTATTTTTATTTTTTGCCCTTA
1 TTATTGTTATTTTTTGCCATTA
5387119 TTATTGTTATTTTATT-CCATTA
1 TTATTGTTATTTT-TTGCCATTA
5387141 TT
1 TT
5387143 TATTTGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.17, C:0.11, G:0.04, T:0.67
Consensus pattern (22 bp):
TTATTGTTATTTTTTGCCATTA
Found at i:5388432 original size:3 final size:3
Alignment explanation
Indices: 5388424--5388463 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
5388414 GTTGAGCAGT
5388424 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
5388464 ATGGACATAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:5389373 original size:21 final size:21
Alignment explanation
Indices: 5389340--5389381 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5389330 CAACGTGGAA
5389340 AGTTAACTAGCCA-TATCAGCT
1 AGTTAACTAGCCACT-TCAGCT
* *
5389361 AGTTAATTGGCCACTTCAGCT
1 AGTTAACTAGCCACTTCAGCT
5389382 GTTCCGTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (21 bp):
AGTTAACTAGCCACTTCAGCT
Found at i:5391345 original size:28 final size:29
Alignment explanation
Indices: 5391288--5391345 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
5391278 AATACATAAA
* *
5391288 ATATATATAAAATATATAAAAGAATTAGT
1 ATATATATAAAATATATAAAAAAATGAGT
5391317 ATATATA-AAAATATA-AAATAAAATGAGT
1 ATATATATAAAATATATAAA-AAAATGAGT
5391345 A
1 A
5391346 ATTGTTAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 3 0.12
28 16 0.62
29 7 0.27
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (29 bp):
ATATATATAAAATATATAAAAAAATGAGT
Found at i:5391715 original size:24 final size:24
Alignment explanation
Indices: 5391686--5391735 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
5391676 TGATAGATAA
5391686 TATATAAAAAAATATATAATAAATGT
1 TATAT-AAAAAA-ATATAATAAATGT
* *
5391712 TATATAATAAAATATAATATATGT
1 TATATAAAAAAATATAATAAATGT
5391736 AGGAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 12 0.55
25 5 0.23
26 5 0.23
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (24 bp):
TATATAAAAAAATATAATAAATGT
Found at i:5391821 original size:21 final size:23
Alignment explanation
Indices: 5391785--5391836 Score: 74
Period size: 21 Copynumber: 2.3 Consensus size: 23
5391775 TGGTATTTTT
5391785 AATAATAATAAAT-AAATTATAAA
1 AATAATAATAAATAAAATT-TAAA
5391808 AATAA-AAT-AATAAAATTTAAA
1 AATAATAATAAATAAAATTTAAA
5391829 AATAATAA
1 AATAATAA
5391837 AGAAAGGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 12 0.44
22 10 0.37
23 5 0.19
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (23 bp):
AATAATAATAAATAAAATTTAAA
Found at i:5393829 original size:197 final size:201
Alignment explanation
Indices: 5393491--5394172 Score: 971
Period size: 197 Copynumber: 3.4 Consensus size: 201
5393481 TTCTTTGACA
* * *
5393491 ATACAGAGATGACACATCATCTTAGATTTGCTTCATCGTAAGCACGTGAAAGCCAAATCAGCTAT
1 ATACAGAGATGACAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAACTAT
*
5393556 GCCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTAGATCTTGCTTCAGTCTAAT
66 GTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTAGATCTTGCTTCAGTCTAAT
* * * *
5393621 CGTTTGAAGGTCAGATCTGCTATGTATCTACTCTCTATTGAAGCGGAGATGCCAGACTTCGATTT
131 CGTCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATTGAAGTGGAGATGCCAGACTTCGATTT
5393686 GT-T-C
196 GTCTGC
*
5393690 -T-CAGAGATGACAAATCATCTTATATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAACTAT
1 ATACAGAGATGACAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAACTAT
*
5393753 GTCTTCGATTTGTTCCTTGTAAGCATAAGGATGCCAAATCATCTTAGATCTTGCTTCAGTCTAAT
66 GTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTAGATCTTGCTTCAGTCTAAT
* *
5393818 CGTCTGAAGGTCAGATTTGCTGTGTATCTGCTCTCCATTGAAGTGGAGATGCCAGACTTCGATTT
131 CGTCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATTGAAGTGGAGATGCCAGACTTCGATTT
5393883 GTTCTCTGAC
196 G---TCTG-C
*
5393893 AATACAGAGATGACAAATCATCTTAGATTTGCTTTATCGT-AACACGTGAAAGCCAAATCAACTA
1 -ATACAGAGATGACAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAACTA
* * *
5393957 TGTCTTTGATTTGTTCCTTATAAGCACAAGGATGCCAAATCATCTTGGATCTTGCTTCAGTCTAA
65 TGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTAGATCTTGCTTCAGTCTAA
* * * * ** *
5394022 TCATCTGAAGGTGAGATCTGCCATGTGTCTGC-CTTCCATCAAAGTGGAAATGCCAGACTTCGAC
130 TCGTCTGAAGGTCAGATCTGCTATGTATCTGCTC-TCCATTGAAGTGGAGATGCCAGACTTCGA-
*
5394086 TTGTTCTCTGGC
193 -T-TTGTCT-GC
* * *
5394098 AATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCTAAATCAGCTA
1 -ATACAGAGATGACAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAACTA
*
5394163 TATCTTCGAT
65 TGTCTTCGAT
5394173 CTATTCCCTG
Statistics
Matches: 434, Mismatches: 34, Indels: 23
0.88 0.07 0.05
Matches are distributed among these distances:
197 181 0.42
198 1 0.00
200 1 0.00
201 1 0.00
203 1 0.00
204 1 0.00
205 180 0.41
206 65 0.15
207 1 0.00
208 2 0.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (201 bp):
ATACAGAGATGACAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAACTAT
GTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTAGATCTTGCTTCAGTCTAAT
CGTCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATTGAAGTGGAGATGCCAGACTTCGATTT
GTCTGC
Found at i:5394017 original size:205 final size:206
Alignment explanation
Indices: 5393471--5394172 Score: 1039
Period size: 205 Copynumber: 3.5 Consensus size: 206
5393461 AAATCTGCTT
* * * *
5393471 CTTCGATTCGTTCTTTGACAATACAGAGATGACACATCATCTTAGATTTGCTTCATCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
* *
5393536 GTGAAAGCCAAATCAGCTATGCCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTT
66 GTGAAAGCCAAATCAACTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTT
* * * *
5393601 AGATCTTGCTTCAGTCTAATCGTTTGAAGGTCAGATCTGCTATGTATCTACTCTCTATTGAAGCG
131 AGATCTTGCTTCAGTCTAATCGTCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATTGAAGTG
5393666 GAGATGCCAGA
196 GAGATGCCAGA
*
5393677 CTTCGATTTG---T-T--C--T-CAGAGATGACAAATCATCTTATATTTGCTTCATCGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
*
5393733 GTGAAAGCCAAATCAACTATGTCTTCGATTTGTTCCTTGTAAGCATAAGGATGCCAAATCATCTT
66 GTGAAAGCCAAATCAACTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTT
* *
5393798 AGATCTTGCTTCAGTCTAATCGTCTGAAGGTCAGATTTGCTGTGTATCTGCTCTCCATTGAAGTG
131 AGATCTTGCTTCAGTCTAATCGTCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATTGAAGTG
5393863 GAGATGCCAGA
196 GAGATGCCAGA
*
5393874 CTTCGATTTGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTTATCGT-AACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
* *
5393938 GTGAAAGCCAAATCAACTATGTCTTTGATTTGTTCCTTATAAGCACAAGGATGCCAAATCATCTT
66 GTGAAAGCCAAATCAACTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTT
* * * * * **
5394003 GGATCTTGCTTCAGTCTAATCATCTGAAGGTGAGATCTGCCATGTGTCTGC-CTTCCATCAAAGT
131 AGATCTTGCTTCAGTCTAATCGTCTGAAGGTCAGATCTGCTATGTATCTGCTC-TCCATTGAAGT
*
5394067 GGAAATGCCAGA
195 GGAGATGCCAGA
* * *
5394079 CTTCGACTTGTTCTCTGGCAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
* * *
5394144 GTGAAAGCTAAATCAGCTATATCTTCGAT
66 GTGAAAGCCAAATCAACTATGTCTTCGAT
5394173 CTATTCCCTG
Statistics
Matches: 449, Mismatches: 36, Indels: 22
0.89 0.07 0.04
Matches are distributed among these distances:
197 181 0.40
198 1 0.00
200 2 0.00
201 1 0.00
202 1 0.00
203 2 0.00
204 1 0.00
205 187 0.42
206 73 0.16
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (206 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
GTGAAAGCCAAATCAACTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTT
AGATCTTGCTTCAGTCTAATCGTCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATTGAAGTG
GAGATGCCAGA
Found at i:5399477 original size:37 final size:37
Alignment explanation
Indices: 5399418--5399526 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
5399408 AGCTCAGACG
* *
5399418 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
5399455 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
5399492 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
5399527 ATATATTTCC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:5399727 original size:48 final size:48
Alignment explanation
Indices: 5399673--5399811 Score: 197
Period size: 48 Copynumber: 2.8 Consensus size: 48
5399663 GCACCTCGCC
5399673 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
* *
5399721 TACATATTTCACACTAGCCATTCGGCTTTACCACATATGCATGTCTCA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
* *
5399769 TACATATTTCATCACATTGGCCATTCGGCCTTATCACACATAT
1 TACATATTTCA-CAC--TAGCCATTCGGCTTTA-C-CACATAT
5399812 GCATGCTCAC
Statistics
Matches: 82, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
48 57 0.70
49 3 0.04
51 14 0.17
52 1 0.01
53 7 0.09
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.34
Consensus pattern (48 bp):
TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:5399835 original size:47 final size:47
Alignment explanation
Indices: 5399737--5399926 Score: 213
Period size: 47 Copynumber: 4.0 Consensus size: 47
5399727 TTTCACACTA
*
5399737 GCCATTCGGCTTTA-C-CACATATGCATGTCTCATACATATTTCATCACATTG
1 GCCATTCGGCCTTATCACACATATGCATG-CTC--AC--A-TTCATCACATTG
5399788 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTG
* * * *
5399835 GTCATTCGGCCTTATCACATACATGCATGTTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTG
* * *** *
5399882 GCCATTCGGCCTTATCTCATATATGCACATTCATATTCATCACAT
1 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACAT
5399927 AAAATCCTAA
Statistics
Matches: 126, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
47 94 0.75
48 1 0.01
50 2 0.02
51 13 0.10
52 4 0.03
53 12 0.10
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.34
Consensus pattern (47 bp):
GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTG
Found at i:5403902 original size:40 final size:40
Alignment explanation
Indices: 5403870--5404211 Score: 585
Period size: 40 Copynumber: 8.6 Consensus size: 40
5403860 CCAGCATGAT
* * * * *
5403870 TGCTCTTTGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * *
5403910 TGATTTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
5403950 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
5403990 TGCTCTTTGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
5404030 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
5404070 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
5404110 TGCTCTTCGGGACTTAACCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
5404150 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
5404190 TGCTCTTTGGGACTTAGCCCGG
1 TGCTCTTCGGGACTTAGCCCGG
5404212 GTAGCCACAT
Statistics
Matches: 286, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 286 1.00
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:5405432 original size:37 final size:37
Alignment explanation
Indices: 5405373--5405481 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
5405363 AGCTCAGACG
* *
5405373 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
5405410 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
5405447 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
5405482 ATATATTTCC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:5405687 original size:48 final size:48
Alignment explanation
Indices: 5405629--5405733 Score: 174
Period size: 48 Copynumber: 2.2 Consensus size: 48
5405619 CACCTCGCCT
5405629 ATATATTCACACGAGCCATTCGGCTTTACCACATATACATATCTCATAC
1 ATAT-TTCACACGAGCCATTCGGCTTTACCACATATACATATCTCATAC
* * *
5405678 ATATTTCACACTAGCCATTCGGCTTTACCACATATGCATGTCTCATAC
1 ATATTTCACACGAGCCATTCGGCTTTACCACATATACATATCTCATAC
5405726 ATATTTCA
1 ATATTTCA
5405734 TCACATTGGC
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
48 49 0.92
49 4 0.08
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (48 bp):
ATATTTCACACGAGCCATTCGGCTTTACCACATATACATATCTCATAC
Found at i:5405789 original size:47 final size:47
Alignment explanation
Indices: 5405691--5405880 Score: 231
Period size: 47 Copynumber: 4.0 Consensus size: 47
5405681 TTTCACACTA
*
5405691 GCCATTCGGCTTTA-C-CACATATGCATGTCTCATACATATTTCATCACATTG
1 GCCATTCGGCCTTATCACACATATGCATG-CTC--AC--A-TTCATCACATTG
5405742 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTG
* * *
5405789 GCCATTCGGCCTTATCACATACATGCATGTTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTG
* * ***
5405836 GCCATTCGGCCTTATCTCATATATGCACATTCACATTCATCACAT
1 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACAT
5405881 AAAATCCTAA
Statistics
Matches: 129, Mismatches: 8, Indels: 8
0.89 0.06 0.06
Matches are distributed among these distances:
47 97 0.75
48 1 0.01
50 2 0.02
51 13 0.10
52 4 0.03
53 12 0.09
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.33
Consensus pattern (47 bp):
GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTG
Done.