Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold258
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: 5730937
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 25
Found at i:5335095 original size:14 final size:14
Alignment explanation
Indices: 5335071--5335104 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5335061 AATGAAAACA
*
5335071 TTATCAAAAATTTAT
1 TTAT-AAAAATTTAG
5335086 TTATAAAAATTTAG
1 TTATAAAAATTTAG
5335100 TTATA
1 TTATA
5335105 GTTCAAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (14 bp):
TTATAAAAATTTAG
Found at i:5335126 original size:3 final size:3
Alignment explanation
Indices: 5335118--5335167 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
5335108 CAAGTAAAAC
5335118 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
5335166 GA
1 GA
5335168 TATGGTATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5337612 original size:15 final size:14
Alignment explanation
Indices: 5337589--5337622 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
5337579 GTATCAATAT
5337589 TTATATAAATATAAA
1 TTATATAAATAT-AA
*
5337604 TTATTTAAATATAA
1 TTATATAAATATAA
5337618 TTATA
1 TTATA
5337623 ATATAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TTATATAAATATAA
Found at i:5337974 original size:2 final size:2
Alignment explanation
Indices: 5337967--5337995 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5337957 GCAATAGAAT
5337967 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
5337996 TAGCAGATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5340661 original size:2 final size:2
Alignment explanation
Indices: 5340656--5340690 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5340646 GGGGGAATGT
5340656 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5340691 TTACTGAAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5342691 original size:37 final size:37
Alignment explanation
Indices: 5342641--5342719 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
5342631 ATCAGGTTCA
*
5342641 AACATTCTCAATAAAATAAAAAAGAAAATAAGAACTC
1 AACATTCTCAATAAAATAAAAAAGAAAATAAGAACCC
**
5342678 AACATTCTCAATAAAATTTAAAAGAAAATAAGAACCC
1 AACATTCTCAATAAAATAAAAAAGAAAATAAGAACCC
5342715 AACAT
1 AACAT
5342720 GACATTTTCT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.59, C:0.15, G:0.05, T:0.20
Consensus pattern (37 bp):
AACATTCTCAATAAAATAAAAAAGAAAATAAGAACCC
Found at i:5344722 original size:55 final size:55
Alignment explanation
Indices: 5344638--5344747 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
5344628 CCAACATGAA
5344638 TTTGAACTGGCGGATAAACCAGACAAGCATCAAATAAAGAGGAAAGAATTCCACC
1 TTTGAACTGGCGGATAAACCAGACAAGCATCAAATAAAGAGGAAAGAATTCCACC
5344693 TTTGAACTGGCGGATAAACCAGACAAGCATCAAATAAAGAGGAAAGAATTCCACC
1 TTTGAACTGGCGGATAAACCAGACAAGCATCAAATAAAGAGGAAAGAATTCCACC
5344748 AAGTATCCAC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.44, C:0.20, G:0.20, T:0.16
Consensus pattern (55 bp):
TTTGAACTGGCGGATAAACCAGACAAGCATCAAATAAAGAGGAAAGAATTCCACC
Found at i:5345163 original size:2 final size:2
Alignment explanation
Indices: 5345156--5345189 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5345146 TAAAATTAAA
5345156 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
5345190 CCCCATGTCA
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:5347170 original size:6 final size:6
Alignment explanation
Indices: 5347159--5347190 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
5347149 TTGAAAAACT
5347159 CCCTAA CCCTAA CCCTAA CCCTAA CCCTAA CC
1 CCCTAA CCCTAA CCCTAA CCCTAA CCCTAA CC
5347191 ACCGCATTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.53, G:0.00, T:0.16
Consensus pattern (6 bp):
CCCTAA
Found at i:5351625 original size:31 final size:31
Alignment explanation
Indices: 5351590--5351652 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
5351580 TATCTCGAAG
5351590 TATTTAGAAGTTAGTTCTACCCAACTGGATT
1 TATTTAGAAGTTAGTTCTACCCAACTGGATT
5351621 TATTTAGAAGTTAGTTCTACCCAACTGGATT
1 TATTTAGAAGTTAGTTCTACCCAACTGGATT
5351652 T
1 T
5351653 GTGCCTCTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (31 bp):
TATTTAGAAGTTAGTTCTACCCAACTGGATT
Found at i:5351664 original size:22 final size:22
Alignment explanation
Indices: 5351636--5351680 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
5351626 AGAAGTTAGT
5351636 TCTACCCAACTGGATTTGTGCC
1 TCTACCCAACTGGATTTGTGCC
5351658 TCTACCCAACTGGATTTGTGCC
1 TCTACCCAACTGGATTTGTGCC
5351680 T
1 T
5351681 GAAGATCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.31, G:0.18, T:0.33
Consensus pattern (22 bp):
TCTACCCAACTGGATTTGTGCC
Found at i:5352941 original size:15 final size:15
Alignment explanation
Indices: 5352921--5352950 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5352911 TTTTTAACTG
5352921 ATGGTTTCATTTCCA
1 ATGGTTTCATTTCCA
5352936 ATGGTTTCATTTCCA
1 ATGGTTTCATTTCCA
5352951 TCTGTGCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47
Consensus pattern (15 bp):
ATGGTTTCATTTCCA
Found at i:5355969 original size:20 final size:20
Alignment explanation
Indices: 5355928--5355986 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
5355918 ATTAAAATTA
*
5355928 ATTTGAAAATT-TATATTATT
1 ATTTTAAAATTATAT-TTATT
*
5355948 ATTTTAAAATTATATTTTTT
1 ATTTTAAAATTATATTTATT
5355968 ATTAATTAAAATTA-ATTTA
1 ATT--TTAAAATTATATTTA
5355987 ATCTAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 17 0.52
21 7 0.21
22 9 0.27
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTTTAAAATTATATTTATT
Found at i:5358796 original size:15 final size:15
Alignment explanation
Indices: 5358762--5358803 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
5358752 TAATTAATTT
*
5358762 ATATAATTATTTTTAAA
1 ATATAA-TA-TTTCAAA
5358779 ATATAATATTTCAAA
1 ATATAATATTTCAAA
5358794 ATATAATATT
1 ATATAATATT
5358804 CAATTCTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 16 0.67
16 2 0.08
17 6 0.25
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATAATATTTCAAA
Found at i:5361796 original size:19 final size:19
Alignment explanation
Indices: 5361772--5361822 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
5361762 TCCTAATTTT
5361772 TATTTAATTATTAT-CAAAA
1 TATTTAATTATTATGC-AAA
* *
5361791 TATTTAATTTTTATGCACA
1 TATTTAATTATTATGCAAA
5361810 TATTT-ATTATTAT
1 TATTTAATTATTAT
5361823 ATAGATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 7 0.25
19 20 0.71
20 1 0.04
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (19 bp):
TATTTAATTATTATGCAAA
Found at i:5368600 original size:2 final size:2
Alignment explanation
Indices: 5368593--5368617 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5368583 GGTATATTTG
5368593 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
5368618 CCCCCCCCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:5369152 original size:17 final size:17
Alignment explanation
Indices: 5369130--5369165 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
5369120 TTGATACTGC
5369130 TGTATTGGTATACCATA
1 TGTATTGGTATACCATA
5369147 TGTATTGGTATACCATA
1 TGTATTGGTATACCATA
5369164 TG
1 TG
5369166 ATTTTGTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (17 bp):
TGTATTGGTATACCATA
Found at i:5369306 original size:19 final size:17
Alignment explanation
Indices: 5369262--5369305 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
5369252 GTTTGGTAGG
*
5369262 AAGAAAAAAGTGGAGGA
1 AAGAAAAAAGGGGAGGA
*
5369279 AAGTAAAAAGGGTGAGGA
1 AAGAAAAAAGGG-GAGGA
5369297 AAGAAAAAA
1 AAGAAAAAA
5369306 AAAAAAAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.61, C:0.00, G:0.32, T:0.07
Consensus pattern (17 bp):
AAGAAAAAAGGGGAGGA
Found at i:5373343 original size:25 final size:27
Alignment explanation
Indices: 5373312--5373383 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 27
5373302 ATATTATAAT
* *
5373312 TTATTTATTTAAGTTATAAACA-TTAA
1 TTATTTATTTAAATTAAAAACATTTAA
** *
5373338 TT-TTTAAATAAATTAAAAATATTTAA
1 TTATTTATTTAAATTAAAAACATTTAA
5373364 TTATTTATTT-AATATAAAAA
1 TTATTTATTTAAAT-TAAAAA
5373384 TAATTATGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
25 14 0.39
26 11 0.31
27 11 0.31
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (27 bp):
TTATTTATTTAAATTAAAAACATTTAA
Found at i:5373381 original size:27 final size:26
Alignment explanation
Indices: 5373284--5373385 Score: 84
Period size: 27 Copynumber: 3.8 Consensus size: 26
5373274 CGATTTATAC
*
5373284 TTATTTAATTTAATT-AATATATTATAA
1 TTATTT-ATTTAATTAAAAATATT-TAA
* *
5373311 TTTATTTATTTAAGTTATAAACA-TTAA
1 -TTATTTATTTAA-TTAAAAATATTTAA
* *
5373338 TT-TTTAAATAAATTAAAAATATTTAA
1 TTATTT-ATTTAATTAAAAATATTTAA
5373364 TTATTTATTTAATATAAAAATA
1 TTATTTATTTAAT-TAAAAATA
5373386 ATTATGAAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
25 10 0.17
26 17 0.29
27 20 0.34
28 9 0.15
29 3 0.05
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (26 bp):
TTATTTATTTAATTAAAAATATTTAA
Found at i:5373479 original size:25 final size:27
Alignment explanation
Indices: 5373422--5373480 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
5373412 ATATTATAAT
* *
5373422 AAAATAATTATCAAATTTAAAATTTATT
1 AAAATAATTATC-AATATAAAATTTATA
5373450 AAAATAATTATC-ATATAAAA-TTATA
1 AAAATAATTATCAATATAAAATTTATA
5373475 AAAATA
1 AAAATA
5373481 TATAAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 10 0.34
26 7 0.24
28 12 0.41
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.37
Consensus pattern (27 bp):
AAAATAATTATCAATATAAAATTTATA
Found at i:5377607 original size:11 final size:10
Alignment explanation
Indices: 5377575--5377627 Score: 51
Period size: 9 Copynumber: 5.6 Consensus size: 10
5377565 AATATAAAAT
5377575 TAATTTTTTA
1 TAATTTTTTA
5377585 T-ATTTTTT-
1 TAATTTTTTA
5377593 TAATTTTTATA
1 TAATTTTT-TA
*
5377604 TAA-TTTATA
1 TAATTTTTTA
*
5377613 T-ATTTTTTT
1 TAATTTTTTA
5377622 TAATTT
1 TAATTT
5377628 GATTGTTGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
8 2 0.06
9 21 0.60
10 9 0.26
11 3 0.09
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:5381356 original size:16 final size:17
Alignment explanation
Indices: 5381319--5381357 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
5381309 AAATAAAATG
*
5381319 ATAAAATTTAAATTTAT
1 ATAAATTTTAAATTTAT
*
5381336 TTAAATTTTAAATTT-T
1 ATAAATTTTAAATTTAT
5381352 ATAAAT
1 ATAAAT
5381358 AAGTATTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATAAATTTTAAATTTAT
Found at i:5381944 original size:7 final size:7
Alignment explanation
Indices: 5381932--5381964 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
5381922 TAACAGAATT
5381932 TAAAAAA
1 TAAAAAA
5381939 TAAAAAA
1 TAAAAAA
5381946 TAAAAAA
1 TAAAAAA
*
5381953 -ATAAAA
1 TAAAAAA
5381959 TAAAAA
1 TAAAAA
5381965 GCAATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:5382708 original size:8 final size:8
Alignment explanation
Indices: 5382673--5382719 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
5382663 CCACTTCAAA
5382673 GCCCCCTCC
1 GCCCCC-CC
*
5382682 ACCCCCCC
1 GCCCCCCC
*
5382690 TCCCACCCC
1 GCCC-CCCC
5382699 GCCCCCCC
1 GCCCCCCC
5382707 GCCCCCCC
1 GCCCCCCC
5382715 -CCCCC
1 GCCCCC
5382720 GGCCCTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
7 5 0.15
8 17 0.50
9 12 0.35
ACGTcount: A:0.04, C:0.85, G:0.06, T:0.04
Consensus pattern (8 bp):
GCCCCCCC
Found at i:5393589 original size:16 final size:16
Alignment explanation
Indices: 5393560--5393593 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5393550 AATAATTTAT
* *
5393560 ATTATTTTTTATTAAA
1 ATTATATTTAATTAAA
5393576 ATTATATTTAATTAAA
1 ATTATATTTAATTAAA
5393592 AT
1 AT
5393594 GTTATATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTATATTTAATTAAA
Found at i:5393668 original size:6 final size:6
Alignment explanation
Indices: 5393649--5393702 Score: 51
Period size: 6 Copynumber: 9.0 Consensus size: 6
5393639 TAAATTTAAA
*
5393649 TATATT TATGTATT TATATT TATA-T TATA-T TATATT TTTAATT T-TATT
1 TATATT TA--TATT TATATT TATATT TATATT TATATT TAT-ATT TATATT
5393697 TATATT
1 TATATT
5393703 ATAAATGCAT
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
5 14 0.33
6 18 0.43
7 4 0.10
8 6 0.14
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:5394943 original size:25 final size:23
Alignment explanation
Indices: 5394914--5394972 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 23
5394904 GATAAATATA
5394914 TTAAAAGAATAAAAAGTAATTATTT
1 TTAAAAGAATAAAAA--AATTATTT
*
5394939 TTAAAA-AATTAAAAAATTATTT
1 TTAAAAGAATAAAAAAATTATTT
5394961 TT-AAAGAATAAA
1 TTAAAAGAATAAA
5394973 TATGATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 3 0.10
22 15 0.48
24 7 0.23
25 6 0.19
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (23 bp):
TTAAAAGAATAAAAAAATTATTT
Found at i:5395805 original size:6 final size:6
Alignment explanation
Indices: 5395796--5395828 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
5395786 ATTTTTAAAA
5395796 TATATT TATATT TATATT TATATT TAATATT TA
1 TATATT TATATT TATATT TATATT T-ATATT TA
5395829 ACACCTTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
TATATT
Found at i:5396034 original size:26 final size:25
Alignment explanation
Indices: 5396004--5396070 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 25
5395994 AATTTATTTA
5396004 AAGTATTTAAATATATATTTAAATAT
1 AAGTATTTAAATATATATTTAAA-AT
** **
5396030 AAGTATAAAAATAT-TATTTTTAAT
1 AAGTATTTAAATATATATTTAAAAT
* *
5396054 AATTTTTTAAATATATA
1 AAGTATTTAAATATATA
5396071 AAAATTTAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
24 12 0.38
25 8 0.25
26 12 0.38
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (25 bp):
AAGTATTTAAATATATATTTAAAAT
Found at i:5396733 original size:24 final size:26
Alignment explanation
Indices: 5396706--5396755 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
5396696 AATTGAGGGC
5396706 AAATAG-GGTTTTTTTT-TTTTTTTT
1 AAATAGCGGTTTTTTTTCTTTTTTTT
* *
5396730 AAATTGCTGTTTTTTTTCTTTTTTTT
1 AAATAGCGGTTTTTTTTCTTTTTTTT
5396756 TCTTCTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.23
25 9 0.41
26 8 0.36
ACGTcount: A:0.14, C:0.04, G:0.10, T:0.72
Consensus pattern (26 bp):
AAATAGCGGTTTTTTTTCTTTTTTTT
Found at i:5397164 original size:17 final size:17
Alignment explanation
Indices: 5397128--5397178 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
5397118 TTATGTAATA
*
5397128 AAAATTATTA-ATAAATT
1 AAAATTATTATA-AAAAT
5397145 AAAATTATTATAAAAAT
1 AAAATTATTATAAAAAT
*
5397162 AAAA-TATT-TAAATAT
1 AAAATTATTATAAAAAT
5397177 AA
1 AA
5397179 TTATAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 8 0.26
16 4 0.13
17 18 0.58
18 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAATTATTATAAAAAT
Found at i:5398505 original size:17 final size:17
Alignment explanation
Indices: 5398483--5398526 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
5398473 TCTCTTCCTA
*
5398483 TTTTTTTTCTTTTAGTT
1 TTTTTTTTCTTTTAATT
* *
5398500 TTTTTTGTCCTTTAATT
1 TTTTTTTTCTTTTAATT
5398517 TTTTTTTTCT
1 TTTTTTTTCT
5398527 GCATATTCAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.07, C:0.09, G:0.05, T:0.80
Consensus pattern (17 bp):
TTTTTTTTCTTTTAATT
Found at i:5404127 original size:27 final size:27
Alignment explanation
Indices: 5404070--5404127 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
5404060 AACATGCATG
* * *
5404070 TAAAGATATAATTTATTAAAAATTTAT
1 TAAAGATATAATTTATTAAAAAATAAA
* *
5404097 TAAATATATAATTTTTTAAAAAATAAA
1 TAAAGATATAATTTATTAAAAAATAAA
5404124 TAAA
1 TAAA
5404128 ATCCGACATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (27 bp):
TAAAGATATAATTTATTAAAAAATAAA
Found at i:5404353 original size:2 final size:2
Alignment explanation
Indices: 5404346--5404378 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5404336 TTAGGAGTAA
5404346 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5404379 GAGTGAGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5404459 original size:18 final size:20
Alignment explanation
Indices: 5404422--5404465 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
5404412 ATTAAATTAA
*
5404422 TTTTATATATTTTTATTATT
1 TTTTATATATATTTATTATT
5404442 TTTTATATA-ATTTA-TATT
1 TTTTATATATATTTATTATT
5404460 TATTTA
1 T-TTTA
5404466 ATTCGATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 5 0.23
19 8 0.36
20 9 0.41
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTATATATATTTATTATT
Found at i:5404757 original size:2 final size:2
Alignment explanation
Indices: 5404750--5404784 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5404740 TCTATCCTTT
5404750 TA TA TA TA 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 TA TA TA TA T
5404785 GGATACTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5413360 original size:16 final size:17
Alignment explanation
Indices: 5413336--5413373 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
5413326 CAAAATGGTT
5413336 TTTTGCAA-GAA-ATAA
1 TTTTGCAAGGAAGATAA
5413351 TTTTGTCAAGGAAGATAA
1 TTTTG-CAAGGAAGATAA
5413369 TTTTG
1 TTTTG
5413374 AAAGATCGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 5 0.25
16 3 0.15
17 3 0.15
18 9 0.45
ACGTcount: A:0.37, C:0.05, G:0.18, T:0.39
Consensus pattern (17 bp):
TTTTGCAAGGAAGATAA
Found at i:5413370 original size:18 final size:15
Alignment explanation
Indices: 5413336--5413378 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 15
5413326 CAAAATGGTT
5413336 TTTTGCAAGAAATAA
1 TTTTGCAAGAAATAA
5413351 TTTTGTCAAGGAAGATAA
1 TTTTG-CAA-GAA-ATAA
*
5413369 TTTTGAAAGA
1 TTTTGCAAGA
5413379 TCGGGCAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 5 0.21
16 5 0.21
17 5 0.21
18 9 0.38
ACGTcount: A:0.42, C:0.05, G:0.19, T:0.35
Consensus pattern (15 bp):
TTTTGCAAGAAATAA
Found at i:5419815 original size:19 final size:18
Alignment explanation
Indices: 5419791--5419839 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
5419781 GTAATTACAC
5419791 AAATATAAAAAAATAATAT
1 AAATATAAAAAAATAA-AT
*
5419810 AAATATAACAAAATAAAT
1 AAATATAAAAAAATAAAT
*
5419828 AATATTTAAAAA
1 AA-ATATAAAAA
5419840 TTTATATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (18 bp):
AAATATAAAAAAATAAAT
Found at i:5420813 original size:21 final size:20
Alignment explanation
Indices: 5420767--5420833 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 20
5420757 ATAAAAATTT
5420767 ATATAAATATAA--AATAT-
1 ATATAAATATAATTAATATA
*
5420784 -TTTAAATATAATTATAATATA
1 ATATAAATATAA-T-TAATATA
5420805 ATA-AAATAT-ATTAATATA
1 ATATAAATATAATTAATATA
5420823 ATATAAATATA
1 ATATAAATATA
5420834 TAAATTATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
16 10 0.25
18 10 0.25
19 7 0.17
20 6 0.15
21 6 0.15
22 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATATAAATATAATTAATATA
Found at i:5420825 original size:13 final size:14
Alignment explanation
Indices: 5420749--5420845 Score: 53
Period size: 13 Copynumber: 6.9 Consensus size: 14
5420739 AATACAATAC
5420749 ATAA-ATATATAA-
1 ATAATATATATAAT
*
5420761 A-AATTTATATAAAT
1 ATAATATATAT-AAT
* *
5420775 ATAAAATATTTTAAAT
1 ATAATATA-TAT-AAT
5420791 ATAATTATAATATAAT
1 ATAA-TAT-ATATAAT
*
5420807 AAAATATAT-TAAT
1 ATAATATATATAAT
*
5420820 ATAATATAAAT-AT
1 ATAATATATATAAT
5420833 ATAA-ATTATATAA
1 ATAATA-TATATAA
5420846 CGAGAACATG
Statistics
Matches: 65, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
11 2 0.03
12 7 0.11
13 23 0.35
14 5 0.08
15 7 0.11
16 16 0.25
17 4 0.06
18 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAATATATATAAT
Found at i:5420844 original size:9 final size:8
Alignment explanation
Indices: 5420708--5420845 Score: 59
Period size: 8 Copynumber: 15.9 Consensus size: 8
5420698 AATAAAATAT
5420708 TATATAAA
1 TATATAAA
5420716 TATA-AAA
1 TATATAAA
* *
5420723 AAAATAAA
1 TATATAAA
* *
5420731 -ATACATA
1 TATATAAA
5420738 TA-ATACAA
1 TATATA-AA
*
5420746 TACATAAA
1 TATATAAA
5420754 TATATAAAAA
1 TATAT--AAA
5420764 TTTATATAAA
1 --TATATAAA
5420774 TATA-AAA
1 TATATAAA
*
5420781 TATTTTAAA
1 TA-TATAAA
5420790 TATAATTATAA
1 TAT-A-TA-AA
5420801 TATAATAAAA
1 TAT-AT-AAA
5420811 TATATTAATA
1 TATA-TAA-A
5420821 TAATATAAA
1 T-ATATAAA
5420830 TATATAAA
1 TATATAAA
5420838 TTATATAA
1 -TATATAA
5420846 CGAGAACATG
Statistics
Matches: 102, Mismatches: 10, Indels: 35
0.69 0.07 0.24
Matches are distributed among these distances:
7 16 0.16
8 30 0.29
9 20 0.20
10 20 0.20
11 11 0.11
12 5 0.05
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (8 bp):
TATATAAA
Found at i:5422042 original size:18 final size:18
Alignment explanation
Indices: 5422021--5422066 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
5422011 TACAGTTTAA
5422021 TTTAATTTAAATTATTAT
1 TTTAATTTAAATTATTAT
5422039 TTTAATATT-AATTATTAT
1 TTTAAT-TTAAATTATTAT
5422057 TTTAATTTAA
1 TTTAATTTAA
5422067 TTTTAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 2 0.08
18 22 0.85
19 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTAATTTAAATTATTAT
Found at i:5422063 original size:12 final size:11
Alignment explanation
Indices: 5422016--5422072 Score: 53
Period size: 11 Copynumber: 5.0 Consensus size: 11
5422006 TTAAGTACAG
5422016 TTTAA-TTTAA
1 TTTAATTTTAA
*
5422026 TTTAAATTATTAT
1 TTT-AATT-TTAA
*
5422039 TTTAATATTAA
1 TTTAATTTTAA
*
5422050 TTATTATTTTAA
1 TT-TAATTTTAA
5422062 TTTAATTTTAA
1 TTTAATTTTAA
5422073 AATATAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
10 3 0.08
11 15 0.41
12 13 0.35
13 6 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTAATTTTAA
Found at i:5422495 original size:15 final size:16
Alignment explanation
Indices: 5422461--5422504 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
5422451 TTTTTTAAAT
5422461 TTTTAAATACTTTATA
1 TTTTAAATACTTTATA
*
5422477 -TTTATATA-TTTATA
1 TTTTAAATACTTTATA
5422491 TTTTAAATTACTTT
1 TTTTAAA-TACTTT
5422505 TTTATATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
14 6 0.26
15 12 0.52
16 2 0.09
17 3 0.13
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTAAATACTTTATA
Found at i:5423028 original size:2 final size:2
Alignment explanation
Indices: 5423021--5423051 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5423011 TGGGTTGGAA
5423021 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5423052 ATTTTTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5423098 original size:16 final size:16
Alignment explanation
Indices: 5423043--5423101 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 16
5423033 ATATATATAT
*
5423043 ATATATATAATTTTTAA
1 ATATATTTAA-TTTTAA
5423060 A-ATATTTAAATTTTAA
1 ATATATTT-AATTTTAA
*
5423076 ATTTATTTAA-TTTAA
1 ATATATTTAATTTTAA
5423091 ATGATATTTAA
1 AT-ATATTTAA
5423102 ATCATCAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
15 7 0.19
16 21 0.58
17 8 0.22
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
ATATATTTAATTTTAA
Found at i:5423336 original size:17 final size:17
Alignment explanation
Indices: 5423314--5423355 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
5423304 AGTAATATTC
*
5423314 ATTAAATATCAGAATCT
1 ATTAAATATCAAAATCT
*
5423331 ATTAAATATCAAAATTT
1 ATTAAATATCAAAATCT
5423348 ATTCAAAT
1 ATT-AAAT
5423356 TTATTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (17 bp):
ATTAAATATCAAAATCT
Found at i:5424643 original size:2 final size:2
Alignment explanation
Indices: 5424636--5424667 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5424626 AAAAGCAAAT
*
5424636 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5424668 CACACACATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5428298 original size:8 final size:7
Alignment explanation
Indices: 5428269--5428300 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
5428259 TTATCTTCCT
5428269 AATTTTA
1 AATTTTA
5428276 AATTTTA
1 AATTTTA
5428283 AATTTTA
1 AATTTTA
5428290 AATTTTTA
1 AA-TTTTA
5428298 AAT
1 AAT
5428301 ATTTTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTTTA
Found at i:5431882 original size:36 final size:36
Alignment explanation
Indices: 5431817--5431886 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
5431807 TTTTTAACAA
* * *
5431817 TAAAAATATTATATATTGATATATAAAATTTTTACT
1 TAAAAATATTAAATATTGAAAAATAAAATTTTTACT
* *
5431853 TAAAAATATTAAATATTTAAAAATTAAATTTTTA
1 TAAAAATATTAAATATTGAAAAATAAAATTTTTA
5431887 TTTTCATATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (36 bp):
TAAAAATATTAAATATTGAAAAATAAAATTTTTACT
Found at i:5432401 original size:15 final size:14
Alignment explanation
Indices: 5432381--5432463 Score: 78
Period size: 14 Copynumber: 5.9 Consensus size: 14
5432371 ACATATGCAT
5432381 TTTGGCATAAGTATC
1 TTTGGCATAAGTA-C
*
5432396 TTTGGCATAAGTGC
1 TTTGGCATAAGTAC
*
5432410 TTTGACATAAGTAC
1 TTTGGCATAAGTAC
* *
5432424 TTTGACATAGGTA-
1 TTTGGCATAAGTAC
* * **
5432437 TTGGGCACAACCAC
1 TTTGGCATAAGTAC
5432451 TTTGGCATAAGTA
1 TTTGGCATAAGTA
5432464 TTTTTGACAC
Statistics
Matches: 53, Mismatches: 14, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
13 7 0.13
14 34 0.64
15 12 0.23
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.34
Consensus pattern (14 bp):
TTTGGCATAAGTAC
Found at i:5432418 original size:14 final size:14
Alignment explanation
Indices: 5432381--5432516 Score: 69
Period size: 14 Copynumber: 9.6 Consensus size: 14
5432371 ACATATGCAT
*
5432381 TTTGGCATAAGTATC
1 TTTGACATAAGTA-C
* *
5432396 TTTGGCATAAGTGC
1 TTTGACATAAGTAC
5432410 TTTGACATAAGTAC
1 TTTGACATAAGTAC
*
5432424 TTTGACATAGGTA-
1 TTTGACATAAGTAC
* * * **
5432437 TTGGGCACAACCAC
1 TTTGACATAAGTAC
* *
5432451 TTTGGCATAAGTATT
1 TTTGACATAAGTA-C
* *
5432466 TTTGACACAAGTATA
1 TTTGACATAAGTA-C
* *
5432481 TTTGGCATATGTAC
1 TTTGACATAAGTAC
* * *
5432495 CTTGACACAGGTAC
1 TTTGACATAAGTAC
5432509 -TTGACATA
1 TTTGACATA
5432517 GGCACTTTTG
Statistics
Matches: 92, Mismatches: 27, Indels: 6
0.74 0.22 0.05
Matches are distributed among these distances:
13 14 0.15
14 44 0.48
15 34 0.37
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (14 bp):
TTTGACATAAGTAC
Found at i:5432469 original size:15 final size:15
Alignment explanation
Indices: 5432451--5432489 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
5432441 GCACAACCAC
*
5432451 TTTGGCATAAGTATT
1 TTTGGCATAAGTATA
* *
5432466 TTTGACACAAGTATA
1 TTTGGCATAAGTATA
5432481 TTTGGCATA
1 TTTGGCATA
5432490 TGTACCTTGA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (15 bp):
TTTGGCATAAGTATA
Found at i:5435378 original size:15 final size:15
Alignment explanation
Indices: 5435357--5435388 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
5435347 TAAATTAAAA
5435357 ATAAAAAAATATTATT
1 ATAAAAAAA-ATTATT
5435373 ATAAAAAAAATTATT
1 ATAAAAAAAATTATT
5435388 A
1 A
5435389 GTTTTATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAAAAAAAATTATT
Found at i:5435407 original size:14 final size:14
Alignment explanation
Indices: 5435390--5435419 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5435380 AAATTATTAG
5435390 TTTTATCTTATTTT
1 TTTTATCTTATTTT
*
5435404 TTTTTTCTTATTTT
1 TTTTATCTTATTTT
5435418 TT
1 TT
5435420 ATTGATAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTATCTTATTTT
Found at i:5440308 original size:3 final size:3
Alignment explanation
Indices: 5440300--5440329 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5440290 TAAGGAAACA
5440300 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5440330 TACTTAAATA
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:5442099 original size:19 final size:18
Alignment explanation
Indices: 5442075--5442114 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
5442065 AAACATGATA
*
5442075 ATTTATATGTTTATATCAT
1 ATTTATATATTT-TATCAT
*
5442094 ATTTATATATTTTATTAT
1 ATTTATATATTTTATCAT
5442112 ATT
1 ATT
5442115 ATAATTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (18 bp):
ATTTATATATTTTATCAT
Found at i:5442204 original size:18 final size:18
Alignment explanation
Indices: 5442092--5442205 Score: 58
Period size: 18 Copynumber: 5.9 Consensus size: 18
5442082 TGTTTATATC
**
5442092 ATATTTATATATTTTATT
1 ATATTTATATATTTTAAA
5442110 ATA-TTATAATTATATTTAAA
1 ATATTTAT-A-TAT-TTTAAA
5442130 ATATTT-TATATTTATATAA
1 ATATTTATATATTT-TA-AA
5442149 A-ATTTGATATA--TTAATA
1 ATATTT-ATATATTTTAA-A
*
5442166 ATTCAAATTATATTAATTTTAAA
1 A-T--ATTTATA-T-ATTTTAAA
5442189 ATATTTATATATTTTAA
1 ATATTTATATATTTTAA
5442206 TTATATTGAT
Statistics
Matches: 75, Mismatches: 4, Indels: 34
0.66 0.04 0.30
Matches are distributed among these distances:
16 1 0.01
17 10 0.13
18 21 0.28
19 8 0.11
20 21 0.28
21 6 0.08
22 2 0.03
23 2 0.03
24 4 0.05
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (18 bp):
ATATTTATATATTTTAAA
Found at i:5442207 original size:39 final size:40
Alignment explanation
Indices: 5442146--5442227 Score: 98
Period size: 39 Copynumber: 2.1 Consensus size: 40
5442136 TATATTTATA
5442146 TAAAATTTGATATATTAATAATTCAAATT-ATATTA-ATTT
1 TAAAATTTGATATATTAATAATT-AAATTGATATTATATTT
* * *
5442185 TAAAATATTTATATATT-TTAATTATATTGATATTATATTT
1 TAAAAT-TTGATATATTAATAATTAAATTGATATTATATTT
5442225 TAA
1 TAA
5442228 TTATTTTTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
38 4 0.11
39 17 0.46
40 16 0.43
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (40 bp):
TAAAATTTGATATATTAATAATTAAATTGATATTATATTT
Found at i:5442212 original size:11 final size:11
Alignment explanation
Indices: 5442196--5442236 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
5442186 AAAATATTTA
5442196 TATATTTTAAT
1 TATATTTTAAT
*
5442207 TATA-TTGATAT
1 TATATTTTA-AT
5442218 TATATTTTAAT
1 TATATTTTAAT
5442229 TAT-TTTTA
1 TATATTTTA
5442237 CATTCATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 8 0.31
11 15 0.58
12 3 0.12
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
TATATTTTAAT
Found at i:5446293 original size:2 final size:2
Alignment explanation
Indices: 5446286--5446317 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5446276 GCCAAATGAA
5446286 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
5446318 GAGTTATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5450297 original size:4 final size:4
Alignment explanation
Indices: 5450288--5450325 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
5450278 ATATTGGTCA
* *
5450288 CTGG CTGG CTGG CTGG CTGG CCGG CTGG ATGG CTGG CT
1 CTGG CTGG CTGG CTGG CTGG CTGG CTGG CTGG CTGG CT
5450326 TACAAGCTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.03, C:0.26, G:0.47, T:0.24
Consensus pattern (4 bp):
CTGG
Found at i:5452944 original size:2 final size:2
Alignment explanation
Indices: 5452937--5452979 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5452927 GCCCATAATG
5452937 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5452979 T
1 T
5452980 GTCCACACAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5458794 original size:84 final size:84
Alignment explanation
Indices: 5458653--5458820 Score: 327
Period size: 84 Copynumber: 2.0 Consensus size: 84
5458643 TTCCTTGAAG
*
5458653 CATAGATTCAAATGTTTCAAAATGACAGGAGTACAGCAAATCTAGAATATTTTAAATCAACAAAT
1 CATAGATTCAAATGTTTCAAAATGACAGGAGTACAGCAAATCTAGAATATTTTAAATCAACAAAC
5458718 TCCATGCACCTTCAAAAAT
66 TCCATGCACCTTCAAAAAT
5458737 CATAGATTCAAATGTTTCAAAATGACAGGAGTACAGCAAATCTAGAATATTTTAAATCAACAAAC
1 CATAGATTCAAATGTTTCAAAATGACAGGAGTACAGCAAATCTAGAATATTTTAAATCAACAAAC
5458802 TCCATGCACCTTCAAAAAT
66 TCCATGCACCTTCAAAAAT
5458821 TAACTTAACA
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (84 bp):
CATAGATTCAAATGTTTCAAAATGACAGGAGTACAGCAAATCTAGAATATTTTAAATCAACAAAC
TCCATGCACCTTCAAAAAT
Found at i:5467971 original size:23 final size:23
Alignment explanation
Indices: 5467920--5467997 Score: 70
Period size: 23 Copynumber: 3.3 Consensus size: 23
5467910 TATTTAATAT
*
5467920 TTAATATTAAATTTAA-TATTATA
1 TTAATATTAAATATAATTATT-TA
*
5467943 TAAATATTAAATATAATTATTTA
1 TTAATATTAAATATAATTATTTA
*
5467966 TTAATA-AAAATATATATTTCATTTA
1 TTAATATTAAATATA-A-TT-ATTTA
*
5467991 ATAATAT
1 TTAATAT
5467998 AATTTTTAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
22 7 0.16
23 22 0.49
24 6 0.13
25 10 0.22
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (23 bp):
TTAATATTAAATATAATTATTTA
Found at i:5468272 original size:19 final size:19
Alignment explanation
Indices: 5468235--5468272 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5468225 TCATCTATTT
*
5468235 TTTTATATATTTATCATAA
1 TTTTATATAATTATCATAA
5468254 TTTTATATTAATTAT-ATAA
1 TTTTATA-TAATTATCATAA
5468273 ATATAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTATATAATTATCATAA
Found at i:5468571 original size:26 final size:25
Alignment explanation
Indices: 5468526--5468574 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
5468516 ACTTAGATTT
5468526 TTTATTATTTTTAAAAATATTTATG
1 TTTATTATTTTTAAAAATATTTATG
*
5468551 TTTATTAATTTTTAAATATATTTA
1 TTTATT-ATTTTTAAAAATATTTA
5468575 AATATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
TTTATTATTTTTAAAAATATTTATG
Found at i:5468574 original size:10 final size:10
Alignment explanation
Indices: 5468561--5468594 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
5468551 TTTATTAATT
5468561 TTTAAATATA
1 TTTAAATATA
5468571 TTTAAATATA
1 TTTAAATATA
*
5468581 TATAAATATTA
1 TTTAAATA-TA
5468592 TTT
1 TTT
5468595 TTTAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 17 0.81
11 4 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TTTAAATATA
Found at i:5469176 original size:2 final size:2
Alignment explanation
Indices: 5469111--5469158 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
5469101 TTAAACAAAC
5469111 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5469153 TA TA TA
1 TA TA TA
5469159 CAGAAAAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5469251 original size:30 final size:31
Alignment explanation
Indices: 5469215--5469276 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
5469205 ATATAATTTA
* *
5469215 TATTTATTTA-ATTTAATTAT-CATATTTAAT
1 TATTTATTTATA-TAAATTATACATATTAAAT
5469245 TATTTATTTATATAAATTATACATATTAAAT
1 TATTTATTTATATAAATTATACATATTAAAT
5469276 T
1 T
5469277 TTGAAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.56
Consensus pattern (31 bp):
TATTTATTTATATAAATTATACATATTAAAT
Found at i:5476024 original size:165 final size:165
Alignment explanation
Indices: 5475836--5476135 Score: 408
Period size: 165 Copynumber: 1.8 Consensus size: 165
5475826 TTCATATCCA
*
5475836 AATTCAGCACCAGCCAATAACAATCAGCTGTTGAGTGGCTCTCAGGATAGCCT-CAACTTCAACT
1 AATTCAGCACCAGCCAATAACAATCAGCTGTTGACTGGCTCTCAGGAT-GCCTACAACTTCAA-T
* * ** * * * *
5475900 TTG-CAGATCATCCTCCAACTTCATCTGCCATAGCACGTCCAACGCAAATGGT-GATAGGAGGAC
64 CTGAAAGATCATCCAACAACTTCATCTCCCACAGCACATCCAACGC-AAGGGTCGATAGGAGGAC
*
5475963 AATCATCAGAACAAGTCCACCTATCATCTGCAAATTTG
128 AACCATCAGAACAAGTCCACCTATCATCTGCAAATTTG
* * *
5476001 AATTCAGCACTAGCCAATAACAATCAGCTGTTGACTGGCTCTCAGGATGGCTACAATTTCAATCT
1 AATTCAGCACCAGCCAATAACAATCAGCTGTTGACTGGCTCTCAGGATGCCTACAACTTCAATCT
* * *
5476066 GAAAGATCATCCAACAAGTTCATTTCCCACAGCACATCCAATGCAAGGGTCGATAGGAGGACAAC
66 GAAAGATCATCCAACAACTTCATCTCCCACAGCACATCCAACGCAAGGGTCGATAGGAGGACAAC
5476131 CATCA
131 CATCA
5476136 CAGCAAGGCC
Statistics
Matches: 116, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
164 11 0.09
165 105 0.91
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (165 bp):
AATTCAGCACCAGCCAATAACAATCAGCTGTTGACTGGCTCTCAGGATGCCTACAACTTCAATCT
GAAAGATCATCCAACAACTTCATCTCCCACAGCACATCCAACGCAAGGGTCGATAGGAGGACAAC
CATCAGAACAAGTCCACCTATCATCTGCAAATTTG
Found at i:5476173 original size:165 final size:165
Alignment explanation
Indices: 5475836--5476185 Score: 395
Period size: 165 Copynumber: 2.1 Consensus size: 165
5475826 TTCATATCCA
* * *
5475836 AATTCAGCACCAGCCAATAACAATCAGCTGTTGAGTGGCTCTCAGGATAGCCTCAACTTCAACTT
1 AATTCAGCACTAGCCAATAACAATCAGCTGTTGACTGGCTCTCAGGATAGCCTCAACTTCAACTC
* ** * * * * *
5475901 TGCAGATCATCCTCCAACTTCATCTGCCATAGCACGTCCAACGCAAATGGTGATAGGAGGACAAT
66 TGAAGATCATCCAACAACTTCATCTCCCACAGCACATCCAACGCAAAGGGTGATAGGAGGACAAC
* * * * *
5475966 CATCAGAACAAGTCCACCTATCATCTGCAAATTTG
131 CATCACAACAAGGCCACCTAACATCTCCAAATTAG
* *
5476001 AATTCAGCACTAGCCAATAACAATCAGCTGTTGACTGGCTCTCAGGAT-GGCTACAATTTCAA-T
1 AATTCAGCACTAGCCAATAACAATCAGCTGTTGACTGGCTCTCAGGATAGCCT-CAACTTCAACT
* * *
5476064 CTGAAAGATCATCCAACAAGTTCATTTCCCACAGCACATCCAATGC-AAGGGTCGATAGGAGGAC
65 CTG-AAGATCATCCAACAACTTCATCTCCCACAGCACATCCAACGCAAAGGGT-GATAGGAGGAC
* * *
5476128 AACCATCACAGCAAGGCCAACC-AACATTTCCACATCTAG
128 AACCATCACAACAAGGCC-ACCTAACATCTCCAAAT-TAG
*
5476167 -ATTCAGCACTAGTCAATAA
1 AATTCAGCACTAGCCAATAA
5476186 TCAAACAATT
Statistics
Matches: 155, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
164 11 0.07
165 139 0.90
166 5 0.03
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (165 bp):
AATTCAGCACTAGCCAATAACAATCAGCTGTTGACTGGCTCTCAGGATAGCCTCAACTTCAACTC
TGAAGATCATCCAACAACTTCATCTCCCACAGCACATCCAACGCAAAGGGTGATAGGAGGACAAC
CATCACAACAAGGCCACCTAACATCTCCAAATTAG
Found at i:5480515 original size:24 final size:22
Alignment explanation
Indices: 5480474--5480526 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
5480464 AGCGTGGAAC
5480474 CAAGCTTCTATTTAGCTCAAGCT
1 CAAGC-TCTATTTAGCTCAAGCT
*
5480497 CAAGCTCTATCTCTAGCTCAATCT
1 CAAGCTCTAT-T-TAGCTCAAGCT
*
5480521 GAAGCT
1 CAAGCT
5480527 GAAGCTGCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 5 0.19
23 6 0.23
24 15 0.58
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.32
Consensus pattern (22 bp):
CAAGCTCTATTTAGCTCAAGCT
Found at i:5481292 original size:32 final size:34
Alignment explanation
Indices: 5481256--5481320 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
5481246 CTGATTCTGT
*
5481256 TGCTAACACTATTTTTCT-C-TTTCAGTTCCTGC
1 TGCTAACACTATATTTCTCCTTTTCAGTTCCTGC
5481288 TGCTAACACTATATTTCTCCTTTTCAGTTCCTG
1 TGCTAACACTATATTTCTCCTTTTCAGTTCCTG
5481321 TTCCAAGTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 17 0.57
33 1 0.03
34 12 0.40
ACGTcount: A:0.17, C:0.28, G:0.09, T:0.46
Consensus pattern (34 bp):
TGCTAACACTATATTTCTCCTTTTCAGTTCCTGC
Found at i:5487006 original size:2 final size:2
Alignment explanation
Indices: 5486999--5487040 Score: 50
Period size: 2 Copynumber: 20.0 Consensus size: 2
5486989 CTATATTTAC
5486999 TA TA TA TA TA TA TA TA TA TA TA CTA CTA CTA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA -TA -TA TA TA TA TA TA TA
5487041 CAGAGAAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 29 0.76
3 8 0.21
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:5491269 original size:16 final size:16
Alignment explanation
Indices: 5491248--5491283 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
5491238 GAACATTTCA
5491248 TAATTAGTAAATAA-AT
1 TAATTA-TAAATAATAT
5491264 TAATTATAAATAATAT
1 TAATTATAAATAATAT
5491280 TAAT
1 TAAT
5491284 AGCAATCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TAATTATAAATAATAT
Found at i:5495715 original size:14 final size:14
Alignment explanation
Indices: 5495698--5495728 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5495688 TCTTTTTTTC
*
5495698 CAAAAATAAGAAAA
1 CAAAAAAAAGAAAA
5495712 CAAAAAAAAGAAAA
1 CAAAAAAAAGAAAA
5495726 CAA
1 CAA
5495729 GGGACCTTTT
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:0.81, C:0.10, G:0.06, T:0.03
Consensus pattern (14 bp):
CAAAAAAAAGAAAA
Found at i:5504165 original size:19 final size:19
Alignment explanation
Indices: 5504128--5504165 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5504118 TCATCTATTT
*
5504128 TTTTATATATTTATCATAA
1 TTTTATATAATTATCATAA
5504147 TTTTATATTAATTAT-ATAA
1 TTTTATA-TAATTATCATAA
5504166 ATATAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTATATAATTATCATAA
Found at i:5504464 original size:10 final size:10
Alignment explanation
Indices: 5504451--5504484 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
5504441 TTATTAAATT
5504451 TTTAAATATA
1 TTTAAATATA
5504461 TTTAAATATA
1 TTTAAATATA
*
5504471 TATAAATATTA
1 TTTAAATA-TA
5504482 TTT
1 TTT
5504485 TTTAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 17 0.81
11 4 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TTTAAATATA
Found at i:5504520 original size:19 final size:17
Alignment explanation
Indices: 5504503--5504535 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5504493 TATAAATTAA
5504503 AAAAGTAAATATATATT
1 AAAAGTAAATATATATT
*
5504520 AAATGTAAATATATAT
1 AAAAGTAAATATATAT
5504536 ATATATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (17 bp):
AAAAGTAAATATATATT
Found at i:5505079 original size:8 final size:8
Alignment explanation
Indices: 5505066--5505100 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
5505056 AATTAAATTA
5505066 TTTTATAT
1 TTTTATAT
5505074 TTTTATAT
1 TTTTATAT
5505082 TTTTATAT
1 TTTTATAT
*
5505090 AATTTATAT
1 -TTTTATAT
5505099 TT
1 TT
5505101 ATTTAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
TTTTATAT
Found at i:5505097 original size:17 final size:16
Alignment explanation
Indices: 5505066--5505100 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
5505056 AATTAAATTA
*
5505066 TTTTATATTTTTATAT
1 TTTTATATATTTATAT
5505082 TTTTATATAATTTATAT
1 TTTTATAT-ATTTATAT
5505099 TT
1 TT
5505101 ATTTAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTATATATTTATAT
Found at i:5507439 original size:20 final size:19
Alignment explanation
Indices: 5507411--5507450 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
5507401 ATGAGATATG
*
5507411 ATATTTTAAATATTTTTTAA
1 ATATATTAAA-ATTTTTTAA
5507431 ATATATTAAAATTTTTTAA
1 ATATATTAAAATTTTTTAA
5507450 A
1 A
5507451 AAAATTAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATATTAAAATTTTTTAA
Found at i:5507457 original size:19 final size:20
Alignment explanation
Indices: 5507416--5507459 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
5507406 ATATGATATT
* *
5507416 TTAAATATTTTTTAAATATA
1 TTAAATATTTTTTAAAAAAA
5507436 TTAAA-ATTTTTTAAAAAAA
1 TTAAATATTTTTTAAAAAAA
5507455 TTAAA
1 TTAAA
5507460 CATACTTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTAAATATTTTTTAAAAAAA
Found at i:5511880 original size:165 final size:165
Alignment explanation
Indices: 5511692--5511991 Score: 417
Period size: 165 Copynumber: 1.8 Consensus size: 165
5511682 TTCATATCCA
*
5511692 AATTCAGCACCAGCCAATAACAATCAGCTGTTGAGTGGCTCTCAGGATAGCCT-CAACTTCAACT
1 AATTCAGCACCAGCCAATAACAATCAGCTGTTGACTGGCTCTCAGGAT-GCCTACAACTTCAA-T
* * ** * * *
5511756 TTG-CAGATCATCCTCCAACTTCATCTGCCATAGCACGTCCAACGCAAGGGGT-GATAGGAGGAC
64 CTGAAAGATCATCCAACAACTTCATCTCCCACAGCACATCCAACGCAA-GGGTCGATAGGAGGAC
*
5511819 AATCATCAGAACAAGTCCACCTATCATCTGCAAATTTG
128 AACCATCAGAACAAGTCCACCTATCATCTGCAAATTTG
* * *
5511857 AATTCAGCACTAGCCAATAACAATCAGCTGTTGACTGGCTCTCAGGATGGCTACAATTTCAATCT
1 AATTCAGCACCAGCCAATAACAATCAGCTGTTGACTGGCTCTCAGGATGCCTACAACTTCAATCT
* * *
5511922 GAAAGATCATCCAACAAGTTCATTTCCCACAGCACATCCAATGCAAGGGTCGATAGGAGGACAAC
66 GAAAGATCATCCAACAACTTCATCTCCCACAGCACATCCAACGCAAGGGTCGATAGGAGGACAAC
5511987 CATCA
131 CATCA
5511992 CAGCAAGGCC
Statistics
Matches: 117, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
164 10 0.09
165 107 0.91
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (165 bp):
AATTCAGCACCAGCCAATAACAATCAGCTGTTGACTGGCTCTCAGGATGCCTACAACTTCAATCT
GAAAGATCATCCAACAACTTCATCTCCCACAGCACATCCAACGCAAGGGTCGATAGGAGGACAAC
CATCAGAACAAGTCCACCTATCATCTGCAAATTTG
Found at i:5512029 original size:165 final size:165
Alignment explanation
Indices: 5511692--5512041 Score: 404
Period size: 165 Copynumber: 2.1 Consensus size: 165
5511682 TTCATATCCA
* * *
5511692 AATTCAGCACCAGCCAATAACAATCAGCTGTTGAGTGGCTCTCAGGATAGCCTCAACTTCAACTT
1 AATTCAGCACTAGCCAATAACAATCAGCTGTTGACTGGCTCTCAGGATAGCCTCAACTTCAACTC
* ** * * * *
5511757 TGCAGATCATCCTCCAACTTCATCTGCCATAGCACGTCCAACGCAAGGGGTGATAGGAGGACAAT
66 TGAAGATCATCCAACAACTTCATCTCCCACAGCACATCCAACGCAAGGGGTGATAGGAGGACAAC
* * * * *
5511822 CATCAGAACAAGTCCACCTATCATCTGCAAATTTG
131 CATCACAACAAGGCCACCTAACATCTCCAAATTAG
* *
5511857 AATTCAGCACTAGCCAATAACAATCAGCTGTTGACTGGCTCTCAGGAT-GGCTACAATTTCAA-T
1 AATTCAGCACTAGCCAATAACAATCAGCTGTTGACTGGCTCTCAGGATAGCCT-CAACTTCAACT
* * *
5511920 CTGAAAGATCATCCAACAAGTTCATTTCCCACAGCACATCCAATGCAA-GGGTCGATAGGAGGAC
65 CTG-AAGATCATCCAACAACTTCATCTCCCACAGCACATCCAACGCAAGGGGT-GATAGGAGGAC
* * *
5511984 AACCATCACAGCAAGGCCAACC-AACATTTCCACATCTAG
128 AACCATCACAACAAGGCC-ACCTAACATCTCCAAAT-TAG
*
5512023 -ATTCAGCACTAGTCAATAA
1 AATTCAGCACTAGCCAATAA
5512042 TCAAACAATT
Statistics
Matches: 156, Mismatches: 24, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
164 10 0.06
165 141 0.90
166 5 0.03
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.22
Consensus pattern (165 bp):
AATTCAGCACTAGCCAATAACAATCAGCTGTTGACTGGCTCTCAGGATAGCCTCAACTTCAACTC
TGAAGATCATCCAACAACTTCATCTCCCACAGCACATCCAACGCAAGGGGTGATAGGAGGACAAC
CATCACAACAAGGCCACCTAACATCTCCAAATTAG
Found at i:5516366 original size:24 final size:22
Alignment explanation
Indices: 5516325--5516377 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
5516315 AGCGTGGAAC
5516325 CAAGCTTCTATTTAGCTCAAGCT
1 CAAGC-TCTATTTAGCTCAAGCT
*
5516348 CAAGCTCTATCTCTAGCTCAATCT
1 CAAGCTCTAT-T-TAGCTCAAGCT
*
5516372 GAAGCT
1 CAAGCT
5516378 GAAGCTGCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 5 0.19
23 6 0.23
24 15 0.58
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.32
Consensus pattern (22 bp):
CAAGCTCTATTTAGCTCAAGCT
Found at i:5517148 original size:32 final size:34
Alignment explanation
Indices: 5517112--5517176 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
5517102 CTGATTCTGT
*
5517112 TGCTAACACTATTTTTCT-C-TTTCAGTTCCTGC
1 TGCTAACACTATATTTCTCCTTTTCAGTTCCTGC
5517144 TGCTAACACTATATTTCTCCTTTTCAGTTCCTG
1 TGCTAACACTATATTTCTCCTTTTCAGTTCCTG
5517177 TTCCAAGTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 17 0.57
33 1 0.03
34 12 0.40
ACGTcount: A:0.17, C:0.28, G:0.09, T:0.46
Consensus pattern (34 bp):
TGCTAACACTATATTTCTCCTTTTCAGTTCCTGC
Found at i:5522630 original size:35 final size:34
Alignment explanation
Indices: 5522588--5522655 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 34
5522578 TAAAAATTTA
*
5522588 TAAATATAACATTATATAAATATTAAAAT-TATATT
1 TAAATATAAAATTAT-TAAATA-TAAAATATATATT
*
5522623 TAAATATAAAATTATTACATATAAAATATATAT
1 TAAATATAAAATTATTAAATATAAAATATATAT
5522656 AATAATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 6 0.20
34 10 0.33
35 14 0.47
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (34 bp):
TAAATATAAAATTATTAAATATAAAATATATATT
Found at i:5522700 original size:36 final size:36
Alignment explanation
Indices: 5522660--5522730 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
5522650 ATATATAATA
* *
5522660 ATATATAAATATATCAATTATTAAATTTTTTAAAAC
1 ATATATAAATATACCAATTATTAAATTTCTTAAAAC
5522696 ATATATAAATATACCAATTATTAAATTTCTTAAAA
1 ATATATAAATATACCAATTATTAAATTTCTTAAAA
5522731 GCAATAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (36 bp):
ATATATAAATATACCAATTATTAAATTTCTTAAAAC
Found at i:5524495 original size:22 final size:23
Alignment explanation
Indices: 5524463--5524506 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
5524453 TATAAATACC
*
5524463 TTTATATATATTTATGTTATTTT
1 TTTATATATATTTATATTATTTT
5524486 TTTAT-TATATTTATATTATTT
1 TTTATATATATTTATATTATTT
5524507 AATTCGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (23 bp):
TTTATATATATTTATATTATTTT
Found at i:5524502 original size:11 final size:11
Alignment explanation
Indices: 5524463--5524504 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
5524453 TATAAATACC
5524463 TTTATA-TATA
1 TTTATATTATA
* *
5524473 TTTATGTTATT
1 TTTATATTATA
*
5524484 TTTTTATTATA
1 TTTATATTATA
5524495 TTTATATTAT
1 TTTATATTAT
5524505 TTAATTCGTA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
10 5 0.20
11 20 0.80
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (11 bp):
TTTATATTATA
Found at i:5524982 original size:15 final size:16
Alignment explanation
Indices: 5524951--5524981 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5524941 AAGCTTTGTT
5524951 TGATAAAAAATAAAAA
1 TGATAAAAAATAAAAA
*
5524967 TGATAAAAATTAAAA
1 TGATAAAAAATAAAA
5524982 TTTTTATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (16 bp):
TGATAAAAAATAAAAA
Found at i:5525224 original size:28 final size:29
Alignment explanation
Indices: 5525187--5525277 Score: 87
Period size: 30 Copynumber: 3.2 Consensus size: 29
5525177 AATAAGTTAT
*
5525187 AATATAAATATATTTAATTTTTATATTT-
1 AATAAAAATATATTTAATTTTTATATTTA
** * *
5525215 TTTAAAAATAT-TTTTATATTTATATTTA
1 AATAAAAATATATTTAATTTTTATATTTA
* *
5525243 AATAAAAATGATATATAATTATTATATTTA
1 AATAAAAAT-ATATTTAATTTTTATATTTA
*
5525273 GATAA
1 AATAA
5525278 TTTAAGAAAA
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
27 14 0.29
28 15 0.31
29 2 0.04
30 17 0.35
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (29 bp):
AATAAAAATATATTTAATTTTTATATTTA
Found at i:5525607 original size:23 final size:22
Alignment explanation
Indices: 5525577--5525619 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
5525567 ATATATATTT
**
5525577 GTTTTTTAATTTTATTTTATCA
1 GTTTTTTAATAATATTTTATCA
5525599 GTTTATTTAATAATATTTTAT
1 GTTT-TTTAATAATATTTTAT
5525620 TTTGGGATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (22 bp):
GTTTTTTAATAATATTTTATCA
Found at i:5525812 original size:16 final size:16
Alignment explanation
Indices: 5525780--5525817 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5525770 TTTTAAATTT
5525780 AAATTTTATAAATAAA
1 AAATTTTATAAATAAA
*
5525796 AAATTATTATTAA-AAA
1 AAATT-TTATAAATAAA
5525812 AAATTT
1 AAATTT
5525818 ACATTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 13 0.65
17 6 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATTTTATAAATAAA
Found at i:5529539 original size:13 final size:13
Alignment explanation
Indices: 5529521--5529554 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
5529511 GTTTATTTTT
*
5529521 TTTAATATTTATG
1 TTTAATATTTATA
5529534 TTTAATATTTATA
1 TTTAATATTTATA
5529547 TTTAATAT
1 TTTAATAT
5529555 AAATTTAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (13 bp):
TTTAATATTTATA
Found at i:5533042 original size:82 final size:82
Alignment explanation
Indices: 5532898--5533062 Score: 294
Period size: 82 Copynumber: 2.0 Consensus size: 82
5532888 TCATGCATTA
* *
5532898 TCTTCAGCCCAAACATTTGTGCACATCAAAACAATGTTAACAACAATAAATATTGGACGGTGATA
1 TCTTCAGCCCAAACATTTGTGCACATCAAAACAATGGTAACAACAATAAATACTGGACGGTGATA
5532963 GCATTTAAAGCCAACCT
66 GCATTTAAAGCCAACCT
**
5532980 TCTTCAGCCCAAACATTTGTGCACATCAAAACAATGGTAACAACAATAAATACTGGGTGGTGATA
1 TCTTCAGCCCAAACATTTGTGCACATCAAAACAATGGTAACAACAATAAATACTGGACGGTGATA
5533045 GCATTTAAAGCCAACCT
66 GCATTTAAAGCCAACCT
5533062 T
1 T
5533063 GTTGCTATAA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (82 bp):
TCTTCAGCCCAAACATTTGTGCACATCAAAACAATGGTAACAACAATAAATACTGGACGGTGATA
GCATTTAAAGCCAACCT
Found at i:5535262 original size:43 final size:43
Alignment explanation
Indices: 5535204--5535303 Score: 157
Period size: 43 Copynumber: 2.3 Consensus size: 43
5535194 ATAATTTTGT
*
5535204 TTAAAT-ATATTTTAAAATAAAATTAACTTTAAATATTAGGCA
1 TTAAATGATAATTTAAAATAAAATTAACTTTAAATATTAGGCA
* * *
5535246 TTAGATGATAATTTAAAATAAAATTAACTTTACATGTTAGGCA
1 TTAAATGATAATTTAAAATAAAATTAACTTTAAATATTAGGCA
5535289 TTAAATGATAATTTA
1 TTAAATGATAATTTA
5535304 GATCTTTACA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
42 5 0.10
43 47 0.90
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (43 bp):
TTAAATGATAATTTAAAATAAAATTAACTTTAAATATTAGGCA
Found at i:5536183 original size:24 final size:25
Alignment explanation
Indices: 5536146--5536195 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
5536136 AATTTGATAG
*
5536146 AATTATTTTAATTTGAATTAAATTTA
1 AATTATTTTAATTTAAATT-AATTTA
5536172 AATT-TTTT-ATTTAAATTAATTTA
1 AATTATTTTAATTTAAATTAATTTA
5536195 A
1 A
5536196 TTTAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 7 0.30
24 8 0.35
25 4 0.17
26 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
AATTATTTTAATTTAAATTAATTTA
Found at i:5536187 original size:19 final size:19
Alignment explanation
Indices: 5536163--5536245 Score: 61
Period size: 19 Copynumber: 4.5 Consensus size: 19
5536153 TTAATTTGAA
5536163 TTAAATTTAAATTTTTTAT
1 TTAAATTTAAATTTTTTAT
*
5536182 TTAAA-TT-AA--TTTAAT
1 TTAAATTTAAATTTTTTAT
* *
5536197 TTAAA-ATAATATTTTTTAA
1 TTAAATTTAA-ATTTTTTAT
*
5536216 TT-AATATTATATATTTTTAT
1 TTAAAT-TTAAAT-TTTTTAT
5536236 TTAAATTTAA
1 TTAAATTTAA
5536246 TTATAAATAT
Statistics
Matches: 48, Mismatches: 8, Indels: 15
0.68 0.11 0.21
Matches are distributed among these distances:
15 11 0.23
16 1 0.02
17 3 0.06
18 4 0.08
19 13 0.27
20 13 0.27
21 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTAAATTTAAATTTTTTAT
Found at i:5536200 original size:15 final size:15
Alignment explanation
Indices: 5536161--5536206 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
5536151 TTTTAATTTG
*
5536161 AATTAAATTTAAATT
1 AATTTAATTTAAATT
*
5536176 --TTTTATTTAAATT
1 AATTTAATTTAAATT
*
5536189 AATTTAATTTAAAAT
1 AATTTAATTTAAATT
5536204 AAT
1 AAT
5536207 ATTTTTTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 11 0.44
15 14 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AATTTAATTTAAATT
Found at i:5536201 original size:34 final size:35
Alignment explanation
Indices: 5536153--5536224 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 35
5536143 TAGAATTATT
* *
5536153 TTAATTTGAATTAAATTTAA-ATTTTTTATTTAA-A
1 TTAATTTGAATTAAA-ATAATATTTTTTAATTAATA
5536187 TTAATTT-AATTTAAAATAATATTTTTTAATTAATA
1 TTAATTTGAA-TTAAAATAATATTTTTTAATTAATA
5536222 TTA
1 TTA
5536225 TATATTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
33 5 0.15
34 24 0.73
35 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (35 bp):
TTAATTTGAATTAAAATAATATTTTTTAATTAATA
Found at i:5536216 original size:20 final size:21
Alignment explanation
Indices: 5536191--5536240 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
5536181 TTTAAATTAA
5536191 TTTAATTTAAAATAATAT-TT
1 TTTAATTTAAAATAATATATT
* *
5536211 TTTAA-TTAATATTATATATT
1 TTTAATTTAAAATAATATATT
5536231 TTT-ATTTAAA
1 TTTAATTTAAA
5536241 TTTAATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTAATTTAAAATAATATATT
Found at i:5536430 original size:13 final size:13
Alignment explanation
Indices: 5536412--5536440 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5536402 TTATTTTTTA
5536412 AAATATTTATATT
1 AAATATTTATATT
5536425 AAATATTTATATT
1 AAATATTTATATT
5536438 AAA
1 AAA
5536441 AATATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AAATATTTATATT
Found at i:5536445 original size:15 final size:15
Alignment explanation
Indices: 5536411--5536476 Score: 57
Period size: 15 Copynumber: 4.4 Consensus size: 15
5536401 TTTATTTTTT
5536411 AAAATATTTATATT-
1 AAAATATTTATATTA
5536425 -AAATATTTATATTA
1 AAAATATTTATATTA
*
5536439 AAAATATATT-TTTTA
1 AAAATAT-TTATATTA
* *
5536454 AATATATATTCATATAA
1 AA-A-ATATTTATATTA
5536471 AAAATA
1 AAAATA
5536477 AATCCAAATC
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
13 13 0.31
15 15 0.36
16 5 0.12
17 9 0.21
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAATATTTATATTA
Found at i:5536456 original size:13 final size:14
Alignment explanation
Indices: 5536403--5536460 Score: 52
Period size: 15 Copynumber: 4.2 Consensus size: 14
5536393 TTAAAATTTT
5536403 TATTT-TTTAAA-A
1 TATTTATTTAAATA
5536415 TATTTATATTAAATA
1 TATTTAT-TTAAATA
*
5536430 T-TTATATTAAAAATA
1 TATT-TATT-TAAATA
5536445 TATTT-TTTAAATA
1 TATTTATTTAAATA
5536458 TAT
1 TAT
5536461 ATTCATATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
12 5 0.13
13 9 0.24
14 10 0.26
15 12 0.32
16 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TATTTATTTAAATA
Found at i:5536702 original size:2 final size:2
Alignment explanation
Indices: 5536695--5536730 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5536685 TAAAAAGTTT
*
5536695 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5536731 AAGAAAGACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5540412 original size:3 final size:3
Alignment explanation
Indices: 5540398--5540442 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
5540388 AAAATATGAA
*
5540398 ACT ACC ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT
1 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT
5540443 TCTTTGCCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (3 bp):
ACT
Found at i:5541904 original size:15 final size:17
Alignment explanation
Indices: 5541882--5541922 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
5541872 ATTAAAAATA
5541882 AATA-AAATTATAATTT
1 AATATAAATTATAATTT
5541898 -AT-TAAATT-TAATTT
1 AATATAAATTATAATTT
5541912 AATATAAATTA
1 AATATAAATTA
5541923 AATGAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
14 6 0.29
15 9 0.43
16 6 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATATAAATTATAATTT
Found at i:5542248 original size:25 final size:28
Alignment explanation
Indices: 5542210--5542272 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 28
5542200 TTTTATATCA
*
5542210 TAAATATAAGAAAA-ATAA-AAAT-TAT
1 TAAATATATGAAAATATAATAAATGTAT
* *
5542235 TAAATATATTAAAATTATAATATATGTAT
1 TAAATATATGAAAA-TATAATAAATGTAT
5542264 TAAATATAT
1 TAAATATAT
5542273 CTTATTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 12 0.39
27 4 0.13
28 3 0.10
29 12 0.39
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (28 bp):
TAAATATATGAAAATATAATAAATGTAT
Found at i:5542305 original size:22 final size:23
Alignment explanation
Indices: 5542263--5542312 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
5542253 AATATATGTA
5542263 TTAAATATATCTTATTAATTATAT
1 TTAAATATATCTTATTAATTAT-T
*
5542287 TTAAATATAT-TT-TTTATTATT
1 TTAAATATATCTTATTAATTATT
5542308 TTAAA
1 TTAAA
5542313 AATTATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 6 0.24
22 7 0.28
23 2 0.08
24 10 0.40
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
TTAAATATATCTTATTAATTATT
Found at i:5543115 original size:24 final size:25
Alignment explanation
Indices: 5543069--5543208 Score: 85
Period size: 25 Copynumber: 5.5 Consensus size: 25
5543059 TTCGAATTTG
**
5543069 ATATATAAATAAGGATTATAAATATA
1 ATATA-AAATAATTATTATAAATATA
5543095 ATATAAAATAATTATTA-AAATATA
1 ATATAAAATAATTATTATAAATATA
*
5543119 ATA-AAAAT-ATTATT-T-TATATA
1 ATATAAAATAATTATTATAAATATA
* * * *
5543140 CATGTAAAGACAATAATTTTAAACTTGATA
1 -ATATAAA-ATAATTATTATAAA--T-ATA
*
5543170 TATAAATAAATAATTGA-TATAAATATA
1 -ATATA-AAATAATT-ATTATAAATATA
5543197 ATATAAAATAAT
1 ATATAAAATAAT
5543209 AAGAATATAC
Statistics
Matches: 88, Mismatches: 14, Indels: 25
0.69 0.11 0.20
Matches are distributed among these distances:
21 5 0.06
22 8 0.09
23 8 0.09
24 11 0.12
25 22 0.25
26 10 0.11
27 4 0.05
28 1 0.01
29 1 0.01
30 15 0.17
31 3 0.03
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.37
Consensus pattern (25 bp):
ATATAAAATAATTATTATAAATATA
Found at i:5543122 original size:22 final size:25
Alignment explanation
Indices: 5543083--5543132 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 25
5543073 ATAAATAAGG
5543083 ATTATAAATATAATAT-AAAATAATT
1 ATTATAAATATAATATAAAAAT-ATT
5543108 ATTA-AAATAT-A-ATAAAAATATT
1 ATTATAAATATAATATAAAAATATT
5543130 ATT
1 ATT
5543133 TTATATACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 8 0.33
23 6 0.25
24 6 0.25
25 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
ATTATAAATATAATATAAAAATATT
Found at i:5543197 original size:19 final size:20
Alignment explanation
Indices: 5543164--5543202 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
5543154 AATTTTAAAC
5543164 TTGATATATAAATAA-ATAA
1 TTGATATATAAATAATATAA
5543183 TTGATATA-AATATAATATAA
1 TTGATATATAA-ATAATATAA
5543203 AATAATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 12 0.67
20 4 0.22
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
TTGATATATAAATAATATAA
Found at i:5543463 original size:2 final size:2
Alignment explanation
Indices: 5543456--5543485 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5543446 TTTATGTACG
5543456 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5543486 ACTCTTCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5543993 original size:30 final size:31
Alignment explanation
Indices: 5543958--5544021 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
5543948 AAATTTAAAA
*
5543958 ATTAAATTTATCTT-AAGATTTAAA-AATATT
1 ATTAAATTAAT-TTAAAGATTTAAACAATATT
* *
5543988 ATTAAATTAATTTAAATATTTAAACAATTTT
1 ATTAAATTAATTTAAAGATTTAAACAATATT
5544019 ATT
1 ATT
5544022 TAATCATAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 2 0.07
30 19 0.66
31 8 0.28
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (31 bp):
ATTAAATTAATTTAAAGATTTAAACAATATT
Found at i:5545977 original size:42 final size:42
Alignment explanation
Indices: 5545925--5546007 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
5545915 TAATAGTTTT
*
5545925 GATAAATAGCTTTGTTGTAGATTTTAAGAA-ATTAACAATTAA
1 GATAAATAGCTTTGTTGTAGATATTAA-AAGATTAACAATTAA
* * *
5545967 GATAAGTAGCTTTGTTGTTGATATTAAAAGATTGACAATTA
1 GATAAATAGCTTTGTTGTAGATATTAAAAGATTAACAATTA
5546008 CTCCAGGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 2 0.06
42 34 0.94
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.39
Consensus pattern (42 bp):
GATAAATAGCTTTGTTGTAGATATTAAAAGATTAACAATTAA
Done.