Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 140 of 193
Found at i:43882249 original size:16 final size:16
Alignment explanation
Indices: 43882226--43882297 Score: 108
Period size: 16 Copynumber: 4.5 Consensus size: 16
43882216 CGTTTGGTTC
*
43882226 GCTGTAATAGAATAGA
1 GCTGTAATGGAATAGA
*
43882242 GGTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* *
43882258 ACTGTAATGGAATATA
1 GCTGTAATGGAATAGA
43882274 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
43882290 GCTGTAAT
1 GCTGTAAT
43882298 CAGTAATTCA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.39, C:0.06, G:0.28, T:0.28
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:43882338 original size:46 final size:44
Alignment explanation
Indices: 43882279--43882372 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
43882269 ATATAGCTGT
* *
43882279 AATGGAATAGAGCTGTAATCAGTAATTCAAT-TGTTTGGTTGATTGG
1 AATGGAATAGAGCTGTAAT-AAT-ATTC-ATGTGTTTGGTTGAATGG
*
43882325 AATGGAATAGAGCTGTAATAATATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATAATATTCATGTGTTTGGTTGAATGG
43882369 AATG
1 AATG
43882373 ATGCTGTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 22 0.50
45 2 0.05
46 19 0.43
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAGCTGTAATAATATTCATGTGTTTGGTTGAATGG
Found at i:43882538 original size:58 final size:55
Alignment explanation
Indices: 43882467--43882612 Score: 168
Period size: 58 Copynumber: 2.5 Consensus size: 55
43882457 AATTTTAATG
*
43882467 ATTATTATTAAATATAATTGAATAAAAATAT-TAATTTATTTAATTATATTTTAATATA
1 ATTATTATTAAATATAATT-AATAAAAATATGTAATTTA-ATAA-TAT-TTTTAATATA
* *
43882525 ATTATTATTAAATAAAATTTAATAAAATAATATGTAATTTAATAATGTTTTTAATATA
1 ATTATTATTAAATATAA-TTAAT-AAA-AATATGTAATTTAATAATATTTTTAATATA
*
43882583 ATTATTATTAAAATATGAATTAGTAAAAAT
1 ATTATTATT-AAATAT-AATTAATAAAAAT
43882613 TATAATATAT
Statistics
Matches: 77, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
57 3 0.04
58 41 0.53
59 16 0.21
60 10 0.13
61 7 0.09
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (55 bp):
ATTATTATTAAATATAATTAATAAAAATATGTAATTTAATAATATTTTTAATATA
Found at i:43884468 original size:11 final size:11
Alignment explanation
Indices: 43884452--43884484 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
43884442 AGTATTGAGG
43884452 GAAAAATAATT
1 GAAAAATAATT
*
43884463 GAAAAATAATG
1 GAAAAATAATT
43884474 GAAAAATAATT
1 GAAAAATAATT
43884485 TTGTTAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (11 bp):
GAAAAATAATT
Found at i:43886574 original size:75 final size:75
Alignment explanation
Indices: 43886451--43886602 Score: 268
Period size: 75 Copynumber: 2.0 Consensus size: 75
43886441 GAAAATGAAG
*
43886451 ACTTACCTGCAGGCATTTGACTTATGGGAAGTGGTAAATGTTGATGTCGAGCCACCACGTTTGAG
1 ACTTACCTGCAGGCATTTGACTTATGGGAAGTGGTAAATGTTGATGTCGAGCCACCACATTTGAG
43886516 AGCTAACCCA
66 AGCTAACCCA
* * *
43886526 ACTTACCTGTAGGCATTTGACTTGTGGGAAGTGGTAAATGTTGATGTCGAGCCACCTCATTTGAG
1 ACTTACCTGCAGGCATTTGACTTATGGGAAGTGGTAAATGTTGATGTCGAGCCACCACATTTGAG
43886591 AGCTAACCCA
66 AGCTAACCCA
43886601 AC
1 AC
43886603 AGTAGCTCAG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (75 bp):
ACTTACCTGCAGGCATTTGACTTATGGGAAGTGGTAAATGTTGATGTCGAGCCACCACATTTGAG
AGCTAACCCA
Found at i:43893600 original size:40 final size:41
Alignment explanation
Indices: 43893555--43893631 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 41
43893545 GAATTTTTTT
43893555 TCGAATTTCGAGTT-AAAT-GAATTGAGTTATTCGAATCAAC
1 TCGAATTTCGAGTTCAAATCGAATTGAGTT-TTCGAATCAAC
* * *
43893595 TCGAATTTCGTGTTCGAATCGAGTTGAGTTTTCGAAT
1 TCGAATTTCGAGTTCAAATCGAATTGAGTTTTCGAAT
43893632 TCGAATAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
40 13 0.41
41 10 0.31
42 9 0.28
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGAATTTCGAGTTCAAATCGAATTGAGTTTTCGAATCAAC
Found at i:43893908 original size:19 final size:20
Alignment explanation
Indices: 43893869--43893911 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
43893859 CCCAAACATC
* *
43893869 CTCAAAACTTTTTATTTTCT
1 CTCAAAACTTTTTACTCTCT
43893889 CTCAAAAC-TTTTACTCTCT
1 CTCAAAACTTTTTACTCTCT
43893908 CTCA
1 CTCA
43893912 CTTTCCCCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.26, C:0.28, G:0.00, T:0.47
Consensus pattern (20 bp):
CTCAAAACTTTTTACTCTCT
Found at i:43895391 original size:15 final size:15
Alignment explanation
Indices: 43895349--43895391 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
43895339 CACTGATTAA
* *
43895349 TTAATATTTCAATAT
1 TTAATATTTTAACAT
*
43895364 TTAAATTTTTTAACAT
1 TT-AATATTTTAACAT
43895380 TTAATATTTTAA
1 TTAATATTTTAA
43895392 ATAAGAAACG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (15 bp):
TTAATATTTTAACAT
Found at i:43902516 original size:58 final size:58
Alignment explanation
Indices: 43902454--43902769 Score: 231
Period size: 59 Copynumber: 5.4 Consensus size: 58
43902444 TGATAAATGA
* * * *
43902454 TGAAATCGGGGTGAAAAATGGGACTTATGGATACCCAGGGGCAAAATGGTAATTTTGG
1 TGAAATCGGGGTTAAAAATGGGAATTATGGATACTCAGGGGTAAAATGGTAATTTTGG
* * * *
43902512 TGAAATCAGGGTTAAAAAT-GGAATTTTAAAGG-T-TTCAGGGGTAAAATGGTAATTTTTAG
1 TGAAATCGGGGTTAAAAATGGGAA--TT-ATGGATACTCAGGGGTAAAATGGTAA-TTTTGG
* * *
43902571 TGAAATCGGGGTTAAAAAT-AGAATTTTAGA-AGCTTC-GTGGGTAAAATGGTAAATTTTGG
1 TGAAATCGGGGTTAAAAATGGGAATTATGGATA-C-TCAG-GGGTAAAATGGT-AATTTTGG
* * ** *
43902630 TGAAATCGGGGTTAAAAAT-GGAATTTTAAAGG-T-TTTGGGGGTAAAATGGTAATTTTCAG
1 TGAAATCGGGGTTAAAAATGGGAA--TT-ATGGATACTCAGGGGTAAAATGGTAATTTT-GG
* * ** *
43902689 TGAAATCGGGGTTAAAAAT-GGAATTTTAGA-AGCTTTGGGGTAAAATGGTAAATTTTAG
1 TGAAATCGGGGTTAAAAATGGGAATTATGGATA-CTCAGGGGTAAAATGGT-AATTTTGG
*
43902747 TGAAATTGGGGTTAAAAATGGGA
1 TGAAATCGGGGTTAAAAATGGGA
43902770 TTTAGGAAAT
Statistics
Matches: 209, Mismatches: 28, Indels: 41
0.75 0.10 0.15
Matches are distributed among these distances:
56 2 0.01
57 7 0.03
58 75 0.36
59 116 0.56
60 6 0.03
61 2 0.01
62 1 0.00
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.31
Consensus pattern (58 bp):
TGAAATCGGGGTTAAAAATGGGAATTATGGATACTCAGGGGTAAAATGGTAATTTTGG
Found at i:43902532 original size:30 final size:29
Alignment explanation
Indices: 43902496--43902717 Score: 114
Period size: 29 Copynumber: 7.5 Consensus size: 29
43902486 ACCCAGGGGC
*
43902496 AAAATGGTAATTTTGGTGAAATCAGGGTTA
1 AAAATGG-AATTTTAGTGAAATCAGGGTTA
** *** *
43902526 AAAATGGAATTTTAAAGGTTTCAGGGGT-
1 AAAATGGAATTTTAGTGAAATCAGGGTTA
*
43902554 AAAATGGTAATTTTTAGTGAAATCGGGGTTA
1 AAAATGG-AA-TTTTAGTGAAATCAGGGTTA
* * *
43902585 AAAATAGAATTTTA--GAAGCTTC-GTGGGT-
1 AAAATGGAATTTTAGTGAA--ATCAG-GGTTA
* *
43902613 AAAATGGTAAATTTTGGTGAAATCGGGGTTA
1 AAAATGG--AATTTTAGTGAAATCAGGGTTA
** *** ** *
43902644 AAAATGGAATTTTAAAGGTTTTGGGGGT-
1 AAAATGGAATTTTAGTGAAATCAGGGTTA
*
43902672 AAAATGGTAATTTTCAGTGAAATCGGGGTTA
1 AAAATGG-AATTTT-AGTGAAATCAGGGTTA
43902703 AAAATGGAATTTTAG
1 AAAATGGAATTTTAG
43902718 AAGCTTTGGG
Statistics
Matches: 141, Mismatches: 36, Indels: 31
0.68 0.17 0.15
Matches are distributed among these distances:
27 3 0.02
28 21 0.15
29 47 0.33
30 46 0.33
31 21 0.15
32 3 0.02
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (29 bp):
AAAATGGAATTTTAGTGAAATCAGGGTTA
Found at i:43902595 original size:59 final size:59
Alignment explanation
Indices: 43902491--43902772 Score: 387
Period size: 59 Copynumber: 4.8 Consensus size: 59
43902481 TGGATACCCA
* * *
43902491 GGGGCAAAATGGT-AATTTTGGTGAAATCAGGGTTAAAAATGGAATTTTA-AAGGTTTC
1 GGGGTAAAATGGTAAATTTTAGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTTC
* * *
43902548 AGGGGTAAAATGGTAATTTTTAGTGAAATCGGGGTTAAAAATAGAATTTTAGAA-GCTTC
1 -GGGGTAAAATGGTAAATTTTAGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTTC
* *
43902607 GTGGGTAAAATGGTAAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTA-AAGGTTTTG
1 G-GGGTAAAATGGTAAATTTTAGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGG-TTTC
*
43902667 GGGGTAAAATGGT-AATTTTCAGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTT-
1 GGGGTAAAATGGTAAATTTT-AGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTTC
* *
43902725 GGGGTAAAATGGTAAATTTTAGTGAAATTGGGGTTAAAAATGGGATTT
1 GGGGTAAAATGGTAAATTTTAGTGAAATCGGGGTTAAAAATGGAATTT
43902773 AGGAAATTTT
Statistics
Matches: 201, Mismatches: 15, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
58 60 0.30
59 133 0.66
60 8 0.04
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (59 bp):
GGGGTAAAATGGTAAATTTTAGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTTC
Found at i:43902645 original size:118 final size:117
Alignment explanation
Indices: 43902491--43902772 Score: 458
Period size: 118 Copynumber: 2.4 Consensus size: 117
43902481 TGGATACCCA
* *
43902491 GGGGCAAAATGGT-AATTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAAAGGTTTCAGGGGTA
1 GGGGTAAAATGGTAAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAGGTTTCAGGGGTA
*
43902555 AAATGGTAATTTTTAGTGAAATCGGGGTTAAAAATAGAATTTTAGAAGCTTC
66 AAATGGTAATTTTCAGTGAAATCGGGGTTAAAAATAGAATTTTAGAAGCTTC
**
43902607 GTGGGTAAAATGGTAAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAGGTTTTGGGGGT
1 G-GGGTAAAATGGTAAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAGGTTTCAGGGGT
* *
43902672 AAAATGGTAATTTTCAGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTT
65 AAAATGGTAATTTTCAGTGAAATCGGGGTTAAAAATAGAATTTTAGAAGCTTC
* * *
43902725 GGGGTAAAATGGTAAATTTTAGTGAAATTGGGGTTAAAAATGGGATTT
1 GGGGTAAAATGGTAAATTTTGGTGAAATCGGGGTTAAAAATGGAATTT
43902773 AGGAAATTTT
Statistics
Matches: 154, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
116 1 0.01
117 55 0.36
118 98 0.64
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (117 bp):
GGGGTAAAATGGTAAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAGGTTTCAGGGGTA
AAATGGTAATTTTCAGTGAAATCGGGGTTAAAAATAGAATTTTAGAAGCTTC
Found at i:43902728 original size:29 final size:27
Alignment explanation
Indices: 43902513--43902772 Score: 97
Period size: 29 Copynumber: 8.9 Consensus size: 27
43902503 TAATTTTGGT
*
43902513 GAAATCAGGGTTAAAAATGGAATTTTA
1 GAAATCGGGGTTAAAAATGGAATTTTA
*
43902540 -AAGGTTTCAGGGG-T-AAAATGGTAATTTTTA
1 GAA---ATC-GGGGTTAAAAATGG-AA-TTTTA
*
43902570 GTGAAATCGGGGTTAAAAATAGAATTTTA
1 --GAAATCGGGGTTAAAAATGGAATTTTA
* *
43902599 GAAGCTTCGTGGG-T-AAAATGGTAAATTTTGGT
1 GAA--ATCG-GGGTTAAAAATGG--AATTTT--A
43902631 GAAATCGGGGTTAAAAATGGAATTTTA
1 GAAATCGGGGTTAAAAATGGAATTTTA
* * *
43902658 -AAGGTTTTGGGGGT-AAAATGGTAATTTTCA
1 GAA---ATCGGGGTTAAAAATGG-AATTTT-A
43902688 GTGAAATCGGGGTTAAAAATGGAATTTTA
1 --GAAATCGGGGTTAAAAATGGAATTTTA
* *
43902717 GAAGCTTTGGGG-T-AAAATGGTAAATTTTA
1 GAA--ATCGGGGTTAAAAATGG--AATTTTA
* *
43902746 GTGAAATTGGGGTTAAAAATGGGATTT
1 --GAAATCGGGGTTAAAAATGGAATTT
43902773 AGGAAATTTT
Statistics
Matches: 177, Mismatches: 19, Indels: 72
0.66 0.07 0.27
Matches are distributed among these distances:
26 4 0.02
27 13 0.07
28 21 0.12
29 62 0.35
30 40 0.23
31 30 0.17
32 3 0.02
33 4 0.02
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (27 bp):
GAAATCGGGGTTAAAAATGGAATTTTA
Found at i:43902841 original size:30 final size:30
Alignment explanation
Indices: 43902780--43903070 Score: 374
Period size: 30 Copynumber: 9.8 Consensus size: 30
43902770 TTTAGGAAAT
*
43902780 TTTTAGGGTCAAAATGTAATTTTTG-AAAG
1 TTTTAGGGTCAAAATGTAATTTTGGAAAAG
43902809 TTTTAGGGTCAAAATGTAATTTTGGAAAAG
1 TTTTAGGGTCAAAATGTAATTTTGGAAAAG
* * *
43902839 TTTAAGGGTCGAAATGTAATTTTGAAAAAG
1 TTTTAGGGTCAAAATGTAATTTTGGAAAAG
* *
43902869 TTTT-GAGGTTAAAATGTAATTTTGGGAAAG
1 TTTTAG-GGTCAAAATGTAATTTTGGAAAAG
*
43902899 TTTTGGGGTCAAAATGTAATTTTGGAAAAG
1 TTTTAGGGTCAAAATGTAATTTTGGAAAAG
* * **
43902929 TTTTGGGGTTAAAATGTAATTTCTGGATTA-
1 TTTTAGGGTCAAAATGTAATTT-TGGAAAAG
* * *
43902959 TTGTGGGGTTAAAATGTAATTTTGG-AAAG
1 TTTTAGGGTCAAAATGTAATTTTGGAAAAG
* *
43902988 TTTTAGGGTCAAAATATAATTTTGGAAGAG
1 TTTTAGGGTCAAAATGTAATTTTGGAAAAG
*
43903018 TTTTGGGGTCAAAATGTAATTTTGGAAAAG
1 TTTTAGGGTCAAAATGTAATTTTGGAAAAG
*
43903048 TTTTAGGGTTAAAATGTAATTTT
1 TTTTAGGGTCAAAATGTAATTTT
43903071 CGAATTGTTT
Statistics
Matches: 229, Mismatches: 27, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
28 1 0.00
29 49 0.21
30 173 0.76
31 6 0.03
ACGTcount: A:0.34, C:0.02, G:0.24, T:0.40
Consensus pattern (30 bp):
TTTTAGGGTCAAAATGTAATTTTGGAAAAG
Found at i:43902897 original size:119 final size:117
Alignment explanation
Indices: 43902769--43903070 Score: 394
Period size: 119 Copynumber: 2.5 Consensus size: 117
43902759 TAAAAATGGG
* * * * *
43902769 ATTTAGGAAATTTTTAGGGTCAAAATGTAATTTTTG-AAAGTTTTAGGGTCAAAATGTAATTTTG
1 ATTTTGGAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTTAAAATGTAATTTTG
* * *
43902833 GAAAAGTT-TAAGGGTCGAAATGTAATTTTGAAAAAGTTTT-GAGGTTAAAATGTA
66 GAAAA-TTGT-AGGGTCAAAATGTAATTTTG-AAAAGTTTTAG-GGTCAAAATATA
*
43902887 ATTTTGGGAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTTAAAATGTAATTTC
1 ATTTT-GGAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTTAAAATGTAATTT-
** * * *
43902952 TGGATTATTGTGGGGTTAAAATGTAATTTTGGAAAGTTTTAGGGTCAAAATATA
64 TGGAAAATTGTAGGGTCAAAATGTAATTTTGAAAAGTTTTAGGGTCAAAATATA
43903006 ATTTTGGAAGAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTTAAAATGTAATTTT
1 ATTTTGGAA-AGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTTAAAATGTAATTTT
43903071 CGAATTGTTT
Statistics
Matches: 163, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
118 9 0.06
119 104 0.64
120 44 0.27
121 6 0.04
ACGTcount: A:0.34, C:0.02, G:0.24, T:0.39
Consensus pattern (117 bp):
ATTTTGGAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTTAAAATGTAATTTTG
GAAAATTGTAGGGTCAAAATGTAATTTTGAAAAGTTTTAGGGTCAAAATATA
Found at i:43904607 original size:15 final size:15
Alignment explanation
Indices: 43904584--43904614 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
43904574 ATGGTGGATG
43904584 GAGCAGGTGGTGGCA
1 GAGCAGGTGGTGGCA
*
43904599 GAGCTGGTGGTGGCA
1 GAGCAGGTGGTGGCA
43904614 G
1 G
43904615 CGGCATAGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.13, G:0.55, T:0.16
Consensus pattern (15 bp):
GAGCAGGTGGTGGCA
Found at i:43904811 original size:29 final size:29
Alignment explanation
Indices: 43904785--43904850 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
43904775 TTTAATTTTT
*
43904785 ATTTAAATTTAAATTCAAAGTAAATTTAA
1 ATTTAAATTTAAATTCAAAATAAATTTAA
*
43904814 ATTTAAATTTAAATTTAAAATAAATTTAA
1 ATTTAAATTTAAATTCAAAATAAATTTAA
43904843 ATTTAAAT
1 ATTTAAAT
43904851 AAAATCAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (29 bp):
ATTTAAATTTAAATTCAAAATAAATTTAA
Found at i:43904814 original size:6 final size:6
Alignment explanation
Indices: 43904785--43904850 Score: 91
Period size: 6 Copynumber: 11.3 Consensus size: 6
43904775 TTTAATTTTT
* *
43904785 ATTTAA ATTTAA ATTCAA A-GTAA ATTTAA ATTTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
43904832 A-ATAA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA AT
43904851 AAAATCAATT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
5 7 0.13
6 45 0.87
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:43904815 original size:23 final size:22
Alignment explanation
Indices: 43904785--43904853 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 22
43904775 TTTAATTTTT
*
43904785 ATTTAAATTTAAATTCAAAGTAA
1 ATTTAAATTTAAATTTAAA-TAA
43904808 ATTTAAATTTAAATTTAAATTTAA
1 ATTTAAATTTAAATTTAAA--TAA
*
43904832 A-ATAAATTTAAATTTAAATAA
1 ATTTAAATTTAAATTTAAATAA
43904853 A
1 A
43904854 ATCAATTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
21 4 0.10
23 34 0.81
24 4 0.10
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (22 bp):
ATTTAAATTTAAATTTAAATAA
Found at i:43905316 original size:69 final size:69
Alignment explanation
Indices: 43905205--43905890 Score: 1155
Period size: 69 Copynumber: 10.0 Consensus size: 69
43905195 ATGATCTCGT
* * * * * *
43905205 TCTTACTTCAATTTCAGAAATAAAG-GTGTGTTATCCAACTCTATTTCGATTTCAAGAGGACGAC
1 TCTTACTTCAATTTCAGAGATGAAGACT-TGTTATCCAACTCTACTTCAATTTCAAGAGGATGAC
43905269 GTTGC
65 GTTGC
* *
43905274 TCTTACTTCAATTTCAGAGATCAAGACTTGTTATCCAACTCTACTTCAATTTTAAGAGGATGACG
1 TCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACG
43905339 TTGC
66 TTGC
* *
43905343 TCTTACTTCAATTTCAGAGATCAAGACTTGTTATCCAACTCTACTTTAATTTCAAGAGGATGACG
1 TCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACG
43905408 TTGC
66 TTGC
43905412 TCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACG
1 TCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACG
43905477 TTGC
66 TTGC
* * *
43905481 TCTTACTTCAATTTCAGAGATCAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGATGACG
1 TCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACG
43905545 TTGC
66 TTGC
*
43905549 TCTTACTTCAATTTCAGAGATGAAGACTTGTTATCC-ACTCTACTTCAATTTCAAGGGGATGACG
1 TCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACG
43905613 TTGC
66 TTGC
*
43905617 TCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACT
1 TCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACG
43905682 TTGC
66 TTGC
43905686 TCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACG
1 TCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACG
43905751 TTGC
66 TTGC
* * * *
43905755 TCTTACTTCAATTTCAGAGATCAAGACCTGATATCCAACTCTACTTTAATTTCAAGAGGATGACG
1 TCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACG
43905820 TTGC
66 TTGC
*
43905824 TCTTACTTCAATTTCAGAGATGAAGACTTGTTATCC-ACTCTACTTCAATTTCAAGGGGATGACG
1 TCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACG
43905888 TTG
66 TTG
43905891 AGACCTGCAG
Statistics
Matches: 587, Mismatches: 28, Indels: 5
0.95 0.05 0.01
Matches are distributed among these distances:
68 162 0.28
69 424 0.72
70 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.35
Consensus pattern (69 bp):
TCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACG
TTGC
Found at i:43905838 original size:31 final size:32
Alignment explanation
Indices: 43905242--43905890 Score: 326
Period size: 31 Copynumber: 19.0 Consensus size: 32
43905232 GTGTTATCCA
* * *
43905242 ACTCTATTTCGATTTCAAGAGGACGACGTTGC
1 ACTCTACTTCAATTTCAAGAGGATGACGTTGC
* ** * *
43905274 TCT-TACTTCAATTTCAGAGATCAAGACTTGTTATCC
1 ACTCTACTTCAATTTCA-AGAGGATGAC--G-T-TGC
*
43905310 AACTCTACTTCAATTTTAAGAGGATGACGTTGC
1 -ACTCTACTTCAATTTCAAGAGGATGACGTTGC
* ** * *
43905343 TCT-TACTTCAATTTCAGAGATCAAGACTTGTTATCC
1 ACTCTACTTCAATTTCA-AGAGGATGAC--G-T-TGC
*
43905379 AACTCTACTTTAATTTCAAGAGGATGACGTTGC
1 -ACTCTACTTCAATTTCAAGAGGATGACGTTGC
* * * *
43905412 TCT-TACTTCAATTTCAGAGATGAAGACTTGTTATCC
1 ACTCTACTTCAATTTCA-AGAGGATGAC--G-T-TGC
43905448 AACTCTACTTCAATTTCAAGAGGATGACGTTGC
1 -ACTCTACTTCAATTTCAAGAGGATGACGTTGC
* ** * *
43905481 TCT-TACTTCAATTTCAGAGATCAAGACGTGTTATCC
1 ACTCTACTTCAATTTCA-AGAGGATGAC--G-T-TGC
*
43905517 ACTCTACTTCAATTTCAAGGGGATGACGTTGC
1 ACTCTACTTCAATTTCAAGAGGATGACGTTGC
* * * *
43905549 TCT-TACTTCAATTTCAGAGATGAAGACTTGTTATCC
1 ACTCTACTTCAATTTCA-AGAGGATGAC--G-T-TGC
*
43905585 ACTCTACTTCAATTTCAAGGGGATGACGTTGC
1 ACTCTACTTCAATTTCAAGAGGATGACGTTGC
* * * *
43905617 TCT-TACTTCAATTTCAGAGATGAAGACTTGTTATCC
1 ACTCTACTTCAATTTCA-AGAGGATGAC--G-T-TGC
*
43905653 AACTCTACTTCAATTTCAAGAGGATGACTTTGC
1 -ACTCTACTTCAATTTCAAGAGGATGACGTTGC
* * * *
43905686 TCT-TACTTCAATTTCAGAGATGAAGACTTGTTATCC
1 ACTCTACTTCAATTTCA-AGAGGATGAC--G-T-TGC
43905722 AACTCTACTTCAATTTCAAGAGGATGACGTTGC
1 -ACTCTACTTCAATTTCAAGAGGATGACGTTGC
* ** * *
43905755 TCT-TACTTCAATTTCAGAGATCAAGACCTGATATCC
1 ACTCTACTTCAATTTCA-AGAGGATGA-C-G-T-TGC
*
43905791 AACTCTACTTTAATTTCAAGAGGATGACGTTGC
1 -ACTCTACTTCAATTTCAAGAGGATGACGTTGC
* * * *
43905824 TCT-TACTTCAATTTCAGAGATGAAGACTTGTTATCC
1 ACTCTACTTCAATTTCA-AGAGGATGAC--G-T-TGC
*
43905860 ACTCTACTTCAATTTCAAGGGGATGACGTTG
1 ACTCTACTTCAATTTCAAGAGGATGACGTTG
43905891 AGACCTGCAG
Statistics
Matches: 462, Mismatches: 95, Indels: 120
0.68 0.14 0.18
Matches are distributed among these distances:
31 112 0.24
32 88 0.19
33 16 0.03
34 17 0.04
35 14 0.03
36 45 0.10
37 95 0.21
38 75 0.16
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (32 bp):
ACTCTACTTCAATTTCAAGAGGATGACGTTGC
Found at i:43905879 original size:343 final size:344
Alignment explanation
Indices: 43905205--43905890 Score: 1187
Period size: 343 Copynumber: 2.0 Consensus size: 344
43905195 ATGATCTCGT
* * *
43905205 TCTTACTTCAATTTCAGAAATAAAGGTGTGTTATCCAACTCTATTTCGATTTCAAGAGGACGACG
1 TCTTACTTCAATTTCAGAAATAAAGCTGTGTTATCCAACTCTACTTCAATTTCAAGAGGACGACG
*
43905270 TTGCTCTTACTTCAATTTCAGAGATCAAGACTTGTTATCCAACTCTACTTCAATTTTAAGAGGAT
66 TTGCTCTTACTTCAATTTCAGAGATCAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
*
43905335 GACGTTGCTCTTACTTCAATTTCAGAGATCAAGACTTGTTATCCAACTCTACTTTAATTTCAAGA
131 GACGTTGCTCTTACTTCAATTTCAGAGATCAAGACTTGTTATCCAACTCTACTTCAATTTCAAGA
* * *
43905400 GGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTC
196 GGATGACGTTGCTCTTACTTCAATTTCAGAGATCAAGACCTGATATCCAACTCTACTTCAATTTC
43905465 AAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATCAAGACGTGTTATCCACTCTACTTCAAT
261 AAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATCAAGACGTGTTATCCACTCTACTTCAAT
43905530 TTCAAGGGGATGACGTTGC
326 TTCAAGGGGATGACGTTGC
* * * *
43905549 TCTTACTTCAATTTCAGAGATGAAGACT-TGTTATCC-ACTCTACTTCAATTTCAAGGGGATGAC
1 TCTTACTTCAATTTCAGAAATAAAG-CTGTGTTATCCAACTCTACTTCAATTTCAAGAGGACGAC
*
43905612 GTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGA
65 GTTGCTCTTACTTCAATTTCAGAGATCAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGA
* *
43905677 TGACTTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAG
130 TGACGTTGCTCTTACTTCAATTTCAGAGATCAAGACTTGTTATCCAACTCTACTTCAATTTCAAG
*
43905742 AGGATGACGTTGCTCTTACTTCAATTTCAGAGATCAAGACCTGATATCCAACTCTACTTTAATTT
195 AGGATGACGTTGCTCTTACTTCAATTTCAGAGATCAAGACCTGATATCCAACTCTACTTCAATTT
* *
43905807 CAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCACTCTACTTCAA
260 CAAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATCAAGACGTGTTATCCACTCTACTTCAA
43905872 TTTCAAGGGGATGACGTTG
325 TTTCAAGGGGATGACGTTG
43905891 AGACCTGCAG
Statistics
Matches: 323, Mismatches: 18, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
343 291 0.90
344 31 0.10
345 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.35
Consensus pattern (344 bp):
TCTTACTTCAATTTCAGAAATAAAGCTGTGTTATCCAACTCTACTTCAATTTCAAGAGGACGACG
TTGCTCTTACTTCAATTTCAGAGATCAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
GACGTTGCTCTTACTTCAATTTCAGAGATCAAGACTTGTTATCCAACTCTACTTCAATTTCAAGA
GGATGACGTTGCTCTTACTTCAATTTCAGAGATCAAGACCTGATATCCAACTCTACTTCAATTTC
AAGAGGATGACGTTGCTCTTACTTCAATTTCAGAGATCAAGACGTGTTATCCACTCTACTTCAAT
TTCAAGGGGATGACGTTGC
Found at i:43921024 original size:31 final size:31
Alignment explanation
Indices: 43920979--43921233 Score: 162
Period size: 31 Copynumber: 7.7 Consensus size: 31
43920969 TAACACATCT
43920979 TCATCT-CT-GAAATTGAAGTAAGAGCAACG
1 TCATCTCCTCGAAATTGAAGTAAGAGCAACG
*
43921008 TCATCTCCTCGAAATTGAAGT-AGAATGGATAAC-
1 TCATCTCCTCGAAATTGAAGTAAG-A--G-CAACG
*
43921041 ACATCTTCATCTCTGAAATTGAAGTAAGAGCAACG
1 TCATC-TC--CTC-GAAATTGAAGTAAGAGCAACG
* *
43921076 TCATCTCCTCGAAATTGAAGTAGAGTGGATAAC-
1 TCATCTCCTCGAAATTGAAGTA-AG-AG-CAACG
* *
43921109 ACATCTTTATCTCTGAAATTGAAGTAAGAGCAACG
1 TCATC--T-CCTC-GAAATTGAAGTAAGAGCAACG
* *
43921144 TCATCTCCTCGAAATTGAAGTAGAGTGGATAAC-
1 TCATCTCCTCGAAATTGAAGTA-AG-AG-CAACG
* *
43921177 ACATCTTTATCTCTGAAATTGAAGTAAGAGCAACG
1 TCATC--T-CCTC-GAAATTGAAGTAAGAGCAACG
* *
43921212 TCATCCCCTTGAAATTGAAGTA
1 TCATCTCCTCGAAATTGAAGTA
43921234 GAGTGGATAA
Statistics
Matches: 176, Mismatches: 22, Indels: 54
0.70 0.09 0.21
Matches are distributed among these distances:
29 6 0.03
30 4 0.02
31 48 0.27
32 12 0.07
33 16 0.09
34 22 0.12
35 17 0.10
36 13 0.07
37 36 0.20
38 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (31 bp):
TCATCTCCTCGAAATTGAAGTAAGAGCAACG
Found at i:43921045 original size:68 final size:68
Alignment explanation
Indices: 43920936--43921382 Score: 718
Period size: 68 Copynumber: 6.6 Consensus size: 68
43920926 TGCAGGTCTT
*
43920936 AACGTCATCTCCTCGAAATTGAAGTAGAGTGGATAACACATCTTCATCTCTGAAATTGAAGTAAG
1 AACGTCATCTCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAAG
43921001 AGC
66 AGC
* *
43921004 AACGTCATCTCCTCGAAATTGAAGTAGAATGGATAACACATCTTCATCTCTGAAATTGAAGTAAG
1 AACGTCATCTCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAAG
43921069 AGC
66 AGC
43921072 AACGTCATCTCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAAG
1 AACGTCATCTCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAAG
43921137 AGC
66 AGC
43921140 AACGTCATCTCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAAG
1 AACGTCATCTCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAAG
43921205 AGC
66 AGC
* * ** *
43921208 AACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTTATCTCTGAAATTGAAGTGAG
1 AACGTCATCTCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAAG
43921273 AGC
66 AGC
* * * * **
43921276 AACGCCATC-CTCTTGAAGTTGAAGTAAAGTGGATAACATGTCTTTATCTCTGAAATTGAAGTAA
1 AACGTCATCTC-CTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAA
43921340 GAGC
65 GAGC
*
43921344 AACGTCATC-CTCTTGAAATTGAAAGTAGAGTGGATAACA
1 AACGTCATCTC-CTCGAAATTG-AAGTAGAGTGGATAACA
43921383 TGACTTTGAA
Statistics
Matches: 362, Mismatches: 15, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
67 1 0.00
68 345 0.95
69 16 0.04
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (68 bp):
AACGTCATCTCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAAG
AGC
Found at i:43921464 original size:62 final size:60
Alignment explanation
Indices: 43921331--43921492 Score: 267
Period size: 62 Copynumber: 2.7 Consensus size: 60
43921321 ATCTCTGAAA
43921331 TTGAAGTAAGAGCAACGTCATCCTCTTGAAATT--G-AAAGTAGAGTGGATAACATGACT
1 TTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAGTAAAGTAGAGTGGATAACATGACT
43921388 TTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGAAGTAGAGTGGATAACATGACT
1 TTGAAGTAAGAGCAACGTCATCCTCTTGAAATTG-AGTA-AAGTAGAGTGGATAACATGACT
*
43921450 TTGAAGTAAAAGCAACGTCATCCTCTTGAAATTGGAGTAAAGT
1 TTGAAGTAAGAGCAACGTCATCCTCTTGAAATT-GAGTAAAGT
43921493 TGGATAGCAA
Statistics
Matches: 98, Mismatches: 1, Indels: 8
0.92 0.01 0.07
Matches are distributed among these distances:
57 33 0.34
60 1 0.01
61 5 0.05
62 58 0.59
63 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.27
Consensus pattern (60 bp):
TTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAGTAAAGTAGAGTGGATAACATGACT
Found at i:43921858 original size:31 final size:29
Alignment explanation
Indices: 43921803--43921873 Score: 97
Period size: 31 Copynumber: 2.4 Consensus size: 29
43921793 AATGTTTGAA
*
43921803 TTAATTTTAAATTCATTTTTAAATTTATC
1 TTAAATTTAAATTCATTTTTAAATTTATC
* *
43921832 TTAAATTTAAATTTACTTATTTAAATTTATT
1 TTAAATTTAAATTCA-TT-TTTAAATTTATC
43921863 TTAAATTTAAA
1 TTAAATTTAAA
43921874 CCTAATTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 13 0.35
30 2 0.05
31 22 0.59
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.56
Consensus pattern (29 bp):
TTAAATTTAAATTCATTTTTAAATTTATC
Found at i:43921870 original size:11 final size:11
Alignment explanation
Indices: 43921801--43921871 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
43921791 TTAATGTTTG
*
43921801 AATTAATTTTA
1 AATTTATTTTA
*
43921812 AATTCATTTTTA
1 AATTTA-TTTTA
*
43921824 AATTTATCTTA
1 AATTTATTTTA
*
43921835 AATTTAAATTT-
1 AATTT-ATTTTA
*
43921846 -ACTTA-TTTA
1 AATTTATTTTA
43921855 AATTTATTTTA
1 AATTTATTTTA
43921866 AATTTA
1 AATTTA
43921872 AACCTAATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
8 3 0.06
9 1 0.02
10 7 0.15
11 24 0.50
12 13 0.27
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.56
Consensus pattern (11 bp):
AATTTATTTTA
Found at i:43921968 original size:16 final size:17
Alignment explanation
Indices: 43921947--43921980 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
43921937 CCAAATTAAA
43921947 GGCCCGATTACAA-AAG
1 GGCCCGATTACAAGAAG
43921963 GGCCCGATTACAAGAAG
1 GGCCCGATTACAAGAAG
43921980 G
1 G
43921981 CCAATTGGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.35, C:0.24, G:0.29, T:0.12
Consensus pattern (17 bp):
GGCCCGATTACAAGAAG
Found at i:43921982 original size:16 final size:15
Alignment explanation
Indices: 43921944--43921982 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
43921934 GGCCCAAATT
43921944 AAAGGCCCGATTACA
1 AAAGGCCCGATTACA
43921959 AAAGGGCCCGATTACA
1 AAA-GGCCCGATTACA
43921975 AGAAGGCC
1 A-AAGGCC
43921983 AATTGGGCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.14
16 17 0.77
17 2 0.09
ACGTcount: A:0.38, C:0.26, G:0.26, T:0.10
Consensus pattern (15 bp):
AAAGGCCCGATTACA
Found at i:43922897 original size:20 final size:18
Alignment explanation
Indices: 43922869--43922912 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 18
43922859 AAAACCAAAC
43922869 AAAAAAATAGA-AAGAAATA
1 AAAAAAATA-ATAAG-AATA
43922888 AAAAATAATAATAAGAATA
1 AAAAA-AATAATAAGAATA
43922907 AAAAAA
1 AAAAAA
43922913 GAAGCTTTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 1 0.04
19 15 0.65
20 7 0.30
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.14
Consensus pattern (18 bp):
AAAAAAATAATAAGAATA
Found at i:43923579 original size:161 final size:162
Alignment explanation
Indices: 43923392--43923736 Score: 421
Period size: 161 Copynumber: 2.1 Consensus size: 162
43923382 AATTTTAATT
* **
43923392 GGTTTATAATTTAGTCCTTTGACTGTTTGACTGTGCCAGAGGCTGCCACGTGTC-ATGTTTTGGA
1 GGTTTATAAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCAAT-TTTTGGA
* * * *
43923456 TTATTTATGAATTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCC-CAAATCAACT-TTA
65 TTATTTATGAATTTAGTCCCTTCTATTTTTAATTTATTTTAATTCAATCCTCAAATCAACTGTTA
*
43923519 TTTTAATTACGAAATTAGCCCAATAA-ATTTTCAA
130 -TTTAATTACAAAATTAGCCCAA-AATATTTTCAA
* * * *
43923553 GGTTTATAAACTAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGTCACGTGTCAATTTTTGGCT
1 GGTTTATAAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCAATTTTTGGAT
* * * * * *
43923618 TATTTCTGCATTTAGTCCCTTCTATTTTTAATTTATTTTTATTCAGTCCTTAAATTAACTGTTAT
66 TATTTATGAATTTAGTCCCTTCTATTTTTAATTTATTTTAATTCAATCCTCAAATCAACTGTTAT
* * *
43923683 TTAATTACAAAATTGGTCCAAAATTTTTTCAA
131 TTAATTACAAAATTAGCCCAAAATATTTTCAA
*
43923715 AGTTT-TCAAATTAGTCCTTTGA
1 GGTTTAT-AAATTAGTCCTTTGA
43923737 AATCTGGATA
Statistics
Matches: 156, Mismatches: 23, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
161 99 0.63
162 54 0.35
163 3 0.02
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (162 bp):
GGTTTATAAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCAATTTTTGGAT
TATTTATGAATTTAGTCCCTTCTATTTTTAATTTATTTTAATTCAATCCTCAAATCAACTGTTAT
TTAATTACAAAATTAGCCCAAAATATTTTCAA
Found at i:43923854 original size:30 final size:30
Alignment explanation
Indices: 43923808--43923892 Score: 116
Period size: 30 Copynumber: 2.8 Consensus size: 30
43923798 CCTTAAATTG
* *
43923808 TCCAGAAATCATATTTTGACCCCAAAACTTT
1 TCCA-AAATTATATTTTGACCCCAAAACGTT
*
43923839 TCTAAAATTATATTTTGACCCCAAAACGTT
1 TCCAAAATTATATTTTGACCCCAAAACGTT
* *
43923869 TCCAAAATTACATTTTAACCCCAA
1 TCCAAAATTATATTTTGACCCCAA
43923893 TTTCATCGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 45 0.94
31 3 0.06
ACGTcount: A:0.38, C:0.25, G:0.05, T:0.33
Consensus pattern (30 bp):
TCCAAAATTATATTTTGACCCCAAAACGTT
Found at i:43923946 original size:59 final size:59
Alignment explanation
Indices: 43923872--43924330 Score: 599
Period size: 59 Copynumber: 7.8 Consensus size: 59
43923862 AAACGTTTCC
* * * *
43923872 AAAATTACA-TTTTAACCCCAATTTCATCGAAAATTACAATTTTACCCCCAAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAATCTTTT
* * * *
43923930 AGAATTCCATTTTTAACCCTGATTTCACCGAAAATTACCATTTTACGCCCGAAA-CTTCT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTAC-CCCCAAATCTTTT
* * *
43923989 AATATTCCATTTTTAACCCTGATTTCACAC-AAAATTACCATTTTACCCCCGAAA-CTTCT
1 AAAATTCCATTTTTAACCCCGATTTCAC-CGAAAATTACCATTTTACCCCC-AAATCTTTT
* *
43924048 -AAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAAGCTTCT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAATCTTTT
* * *
43924106 AAAATTCTATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCTCGAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAATCTTTT
* * * * * *
43924165 AAAATTCTATTTTTAACCCTGATTTCATCAAAAATTACCATTTTACCCCCGAAGCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAATCTTTT
*
43924224 AAAATTCCATTTTTAACCCCGATTTCACCGAAATTTA-CATTTTACCCCCAAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAATCTTTT
* ** *
43924282 AAAATTCCATTTTTAACCCCGATTACGTC-AAAATTACCATTTTGCCCCC
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCC
43924331 GGGTATCCAT
Statistics
Matches: 358, Mismatches: 35, Indels: 16
0.88 0.09 0.04
Matches are distributed among these distances:
57 10 0.03
58 116 0.32
59 225 0.63
60 7 0.02
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (59 bp):
AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAATCTTTT
Found at i:43924060 original size:28 final size:28
Alignment explanation
Indices: 43923961--43924068 Score: 80
Period size: 28 Copynumber: 3.8 Consensus size: 28
43923951 ATTTCACCGA
43923961 AAATTACCATTTT-ACGCCCGAAACTTCT
1 AAATTACCATTTTAAC-CCCGAAACTTCT
* * * *
43923989 AATATT-CCATTTTTAACCCTGATTTCAC-ACA
1 AA-ATTACCA-TTTTAACCCCGA---AACTTCT
*
43924020 AAATTACCATTTTACCCCCGAAACTTCT
1 AAATTACCATTTTAACCCCGAAACTTCT
43924048 AAATT-CCATTTTTAACCCCGA
1 AAATTACCA-TTTTAACCCCGA
43924069 TTTCACCGAA
Statistics
Matches: 61, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
27 5 0.08
28 22 0.36
29 11 0.18
30 15 0.25
31 6 0.10
32 2 0.03
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (28 bp):
AAATTACCATTTTAACCCCGAAACTTCT
Found at i:43924085 original size:117 final size:117
Alignment explanation
Indices: 43923872--43924329 Score: 613
Period size: 117 Copynumber: 3.9 Consensus size: 117
43923862 AAACGTTTCC
* * * * *
43923872 AAAATTACA-TTTTAACCCCAATTTCATCGAAAATTACAATTTTACCCCCAAATCTTTTAGAATT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAATCTTTTAAAATT
*
43923936 CCATTTTTAACCCTGATTTCACCGAAAATTACCATTTTACGCCCGAAACTTCT
66 CCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTAC-CCCGAAACTTCT
* * *
43923989 AATATTCCATTTTTAACCCTGATTTCACAC-AAAATTACCATTTTACCCCCGAAA-CTTCT-AAA
1 AAAATTCCATTTTTAACCCCGATTTCAC-CGAAAATTACCATTTTACCCCC-AAATCTTTTAAAA
*
43924051 TTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAAGCTTCT
64 TTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCGAAA-CTTCT
* * *
43924106 AAAATTCTATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCTCGAATCTTTTAAAATT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAATCTTTTAAAATT
* * * * * *
43924171 CTATTTTTAACCCTGATTTCATCAAAAATTACCATTTTACCCCCGAAGCTTTT
66 CCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTA-CCCCGAAACTTCT
*
43924224 AAAATTCCATTTTTAACCCCGATTTCACCGAAATTTA-CATTTTACCCCCAAATCTTTTAAAATT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAATCTTTTAAAATT
* ** *
43924288 CCATTTTTAACCCCGATTACGTC-AAAATTACCATTTTGCCCC
66 CCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCC
43924330 CGGGTATCCA
Statistics
Matches: 301, Mismatches: 32, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
115 4 0.01
116 23 0.08
117 147 0.49
118 117 0.39
119 10 0.03
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (117 bp):
AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAATCTTTTAAAATT
CCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCGAAACTTCT
Found at i:43924179 original size:176 final size:177
Alignment explanation
Indices: 43923872--43924324 Score: 675
Period size: 176 Copynumber: 2.6 Consensus size: 177
43923862 AAACGTTTCC
* * * * *
43923872 AAAATTACA-TTTTAACCCCAATTTCATCGAAAATTACAATTTTACCCCCAAATCTTTTAGAATT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAATCTTTTAAAATT
* *
43923936 CCATTTTTAACCCTGATTTCACCGAAAATTACCATTTTACGCCCGAAACTTCTAATATTCCATTT
66 CCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACGCCCGAAACTTCTAAAATTCCATTT
43924001 TTAACCCTGATTTCA-CACAAAATTACCATTTTACCCCCGAAACTTCT
131 TTAACCCTGATTTCATCA-AAAATTACCATTTTACCCCCGAAACTTCT
* *
43924048 -AAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAAGCTTCTAAAATT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAATCTTTTAAAATT
* * * *
43924112 CTATTTTTAACCCCGATTTCACCGAAAATTACCATTTTAC-CCTCGAATCTTTTAAAATTCTATT
66 CCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACGCC-CGAAACTTCTAAAATTCCATT
* *
43924176 TTTAACCCTGATTTCATCAAAAATTACCATTTTACCCCCGAAGCTTTT
130 TTTAACCCTGATTTCATCAAAAATTACCATTTTACCCCCGAAACTTCT
*
43924224 AAAATTCCATTTTTAACCCCGATTTCACCGAAATTTA-CATTTTACCCCCAAATCTTTTAAAATT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAATCTTTTAAAATT
* **
43924288 CCATTTTTAACCCCGATTACGTC-AAAATTACCATTTT
66 CCATTTTTAACCCCGATTTCACCGAAAATTACCATTTT
43924325 GCCCCCGGGT
Statistics
Matches: 251, Mismatches: 22, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
175 23 0.09
176 191 0.76
177 37 0.15
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.36
Consensus pattern (177 bp):
AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAATCTTTTAAAATT
CCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACGCCCGAAACTTCTAAAATTCCATTT
TTAACCCTGATTTCATCAAAAATTACCATTTTACCCCCGAAACTTCT
Found at i:43924296 original size:29 final size:28
Alignment explanation
Indices: 43924019--43924294 Score: 97
Period size: 29 Copynumber: 9.5 Consensus size: 28
43924009 GATTTCACAC
43924019 AAAATTACCATTTTACCCCCGAAA-CTTCT
1 AAAATT-CCATTTTACCCCC-AAATCTTCT
* ** ** *
43924048 -AAATTCCATTTTTAACCCCGATTTCACCG
1 AAAATTCCA-TTTT-ACCCCCAAATCTTCT
*
43924077 AAAATTACCATTTTACCCCCAAAGCTTCT
1 AAAATT-CCATTTTACCCCCAAATCTTCT
* * ** ** *
43924106 AAAATTCTATTTTTAACCCCGATTTCACCG
1 AAAATTCCA-TTTT-ACCCCCAAATCTTCT
* * *
43924136 AAAATTACCATTTTACCCTCGAATCTTTT
1 AAAATT-CCATTTTACCCCCAAATCTTCT
* ** ** * *
43924165 AAAATTCTATTTTTAACCCTGATTTCATCA
1 AAAATTCCA-TTTT-ACCCCCAAATCTTCT
* * *
43924195 AAAATTACCATTTTACCCCCGAAGCTTTT
1 AAAATT-CCATTTTACCCCCAAATCTTCT
* ** ** *
43924224 AAAATTCCATTTTTAACCCCGATTTCACCG
1 AAAATTCCA-TTTT-ACCCCCAAATCTTCT
* * *
43924254 AAATTTACATTTTACCCCCAAATCTTTT
1 AAAATTCCATTTTACCCCCAAATCTTCT
43924282 AAAATTCCATTTT
1 AAAATTCCATTTT
43924295 TAACCCCGAT
Statistics
Matches: 165, Mismatches: 69, Indels: 27
0.63 0.26 0.10
Matches are distributed among these distances:
27 3 0.02
28 36 0.22
29 61 0.37
30 58 0.35
31 7 0.04
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.37
Consensus pattern (28 bp):
AAAATTCCATTTTACCCCCAAATCTTCT
Found at i:43924301 original size:29 final size:28
Alignment explanation
Indices: 43923820--43924301 Score: 105
Period size: 30 Copynumber: 16.4 Consensus size: 28
43923810 CAGAAATCAT
* * **
43923820 ATTTTGACCCCAAAACTTTTCTAAAATTAT
1 ATTTTAACCCC-AAA-TCTTCTAAAATTCC
* * * *
43923850 ATTTTGACCCCAAAACGTTTCCAAAATTAC
1 ATTTTAACCCCAAATC--TTCTAAAATTCC
* * * *
43923880 ATTTTAACCCCAATTTCATCGAAAATTACA
1 ATTTTAACCCCAA-ATCTTCTAAAATT-CC
* * *
43923910 ATTTTACCCCCAAATCTTTTAGAATTCC
1 ATTTTAACCCCAAATCTTCTAAAATTCC
* ** ** *
43923938 ATTTTTAACCCTGATTTCACCGAAAATTACC
1 A-TTTTAACCC-CAAATCTTCTAAAATT-CC
*
43923969 ATTTT-ACGCCCGAAA-CTTCTAATATTCC
1 ATTTTAAC-CCC-AAATCTTCTAAAATTCC
** *
43923997 ATTTTTAA-CCCTGAT-TTCACACAAAATTACC
1 A-TTTTAACCCCAAATCTT--C-TAAAATT-CC
*
43924028 ATTTTACCCCCGAAA-CTTCT-AAATTCC
1 ATTTTAACCCC-AAATCTTCTAAAATTCC
** ** *
43924055 ATTTTTAACCCCGATTTCACCGAAAATTACC
1 A-TTTTAACCCC-AAATCTTCTAAAATT-CC
* * *
43924086 ATTTTACCCCCAAAGCTTCTAAAATTCT
1 ATTTTAACCCCAAATCTTCTAAAATTCC
** ** *
43924114 ATTTTTAACCCCGATTTCACCGAAAATTACC
1 A-TTTTAACCCC-AAATCTTCTAAAATT-CC
* * *
43924145 ATTTT-ACCCTCGAATCTTTTAAAATTCT
1 ATTTTAACCC-CAAATCTTCTAAAATTCC
* ** * *
43924173 ATTTTTAACCCTGATTTCATCAAAAATTACC
1 A-TTTTAACCC-CAAATCTTCTAAAATT-CC
* * * *
43924204 ATTTTACCCCCGAAGCTTTTAAAATTCC
1 ATTTTAACCCCAAATCTTCTAAAATTCC
** ** * * *
43924232 ATTTTTAACCCCGATTTCACCGAAATTTAC
1 A-TTTTAACCCC-AAATCTTCTAAAATTCC
* *
43924262 ATTTTACCCCCAAATCTTTTAAAATTCC
1 ATTTTAACCCCAAATCTTCTAAAATTCC
43924290 ATTTTTAACCCC
1 A-TTTTAACCCC
43924302 GATTACGTCA
Statistics
Matches: 309, Mismatches: 110, Indels: 67
0.64 0.23 0.14
Matches are distributed among these distances:
27 6 0.02
28 41 0.13
29 112 0.36
30 130 0.42
31 17 0.06
32 3 0.01
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (28 bp):
ATTTTAACCCCAAATCTTCTAAAATTCC
Found at i:43927056 original size:20 final size:20
Alignment explanation
Indices: 43927018--43927056 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
43927008 CGTATTAAAA
*
43927018 ATTAGAAATGAACTCTTGAT
1 ATTAGAAATGAAATCTTGAT
* *
43927038 ATTAGTAATGAAATGTTGA
1 ATTAGAAATGAAATCTTGA
43927057 AGATGATTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.36
Consensus pattern (20 bp):
ATTAGAAATGAAATCTTGAT
Found at i:43927998 original size:30 final size:30
Alignment explanation
Indices: 43927962--43928055 Score: 188
Period size: 30 Copynumber: 3.1 Consensus size: 30
43927952 ATATAAAACA
43927962 TTTGACCTAAAGGCATGTACAGTTTATACC
1 TTTGACCTAAAGGCATGTACAGTTTATACC
43927992 TTTGACCTAAAGGCATGTACAGTTTATACC
1 TTTGACCTAAAGGCATGTACAGTTTATACC
43928022 TTTGACCTAAAGGCATGTACAGTTTATACC
1 TTTGACCTAAAGGCATGTACAGTTTATACC
43928052 TTTG
1 TTTG
43928056 GCTTACCTCA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (30 bp):
TTTGACCTAAAGGCATGTACAGTTTATACC
Found at i:43933933 original size:30 final size:31
Alignment explanation
Indices: 43933899--43933961 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 31
43933889 AATAAATAGA
43933899 TAATAT-CAAATTTATACATGAAGTTTGATT
1 TAATATGCAAATTTATACATGAAGTTTGATT
* ** * *
43933929 TAATATGTATTTTTATATATGAATTTTGATT
1 TAATATGCAAATTTATACATGAAGTTTGATT
43933960 TA
1 TA
43933962 GTGTAATTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 6 0.22
31 21 0.78
ACGTcount: A:0.37, C:0.03, G:0.10, T:0.51
Consensus pattern (31 bp):
TAATATGCAAATTTATACATGAAGTTTGATT
Found at i:43935510 original size:30 final size:28
Alignment explanation
Indices: 43935414--43935583 Score: 134
Period size: 29 Copynumber: 5.9 Consensus size: 28
43935404 ACCCCTGAAC
* *
43935414 TTTCC-AAAATT-CCATTTAAACCTCGAT
1 TTTCCAAAAATTACCATTT-TACCCCGAT
*
43935441 TTCTCCAAAAATTACCATTTTACCCCTGAA
1 TT-TCCAAAAATTACCATTTTACCCC-GAT
*
43935471 CTTCCAAAAATT-CCATTTTTAACCCCGATT
1 TTTCCAAAAATTACCA-TTTT-ACCCCGA-T
*
43935501 TTTCTAAAAATTACCATTTTACCTCCGGA-
1 TTTCCAAAAATTACCATTTTACC-CC-GAT
* *
43935530 TGTCTAAAAATT-CCATTTTTGACCCCGAAT
1 TTTCCAAAAATTACCA-TTTT-ACCCCG-AT
*
43935560 TTTCCCAAAATTACCATTTTACCC
1 TTTCCAAAAATTACCATTTTACCC
43935584 TTAATTGTCT
Statistics
Matches: 117, Mismatches: 11, Indels: 28
0.75 0.07 0.18
Matches are distributed among these distances:
27 2 0.02
28 10 0.09
29 51 0.44
30 46 0.39
31 8 0.07
ACGTcount: A:0.31, C:0.28, G:0.05, T:0.36
Consensus pattern (28 bp):
TTTCCAAAAATTACCATTTTACCCCGAT
Found at i:43935513 original size:59 final size:59
Alignment explanation
Indices: 43935398--43935583 Score: 227
Period size: 59 Copynumber: 3.2 Consensus size: 59
43935388 TAAAAATCAT
* * *
43935398 ATTTTGACCCCTGAACTTTCC-AAAATTCCA-TTTAAACCTCGATTTCTCCAAAAATTACC
1 ATTTT-ACCCCTGAAC-TTCCAAAAATTCCATTTTTAACCCCGATTTTTCCAAAAATTACC
*
43935457 ATTTTACCCCTGAACTTCCAAAAATTCCATTTTTAACCCCGATTTTTCTAAAAATTACC
1 ATTTTACCCCTGAACTTCCAAAAATTCCATTTTTAACCCCGATTTTTCCAAAAATTACC
* * * * *
43935516 ATTTTACCTCC-GGA-TGTCTAAAAATTCCATTTTTGACCCCGAATTTTCCCAAAATTACC
1 ATTTTACC-CCTGAACT-TCCAAAAATTCCATTTTTAACCCCGATTTTTCCAAAAATTACC
43935575 ATTTTACCC
1 ATTTTACCC
43935584 TTAATTGTCT
Statistics
Matches: 113, Mismatches: 10, Indels: 9
0.86 0.08 0.07
Matches are distributed among these distances:
57 4 0.04
58 21 0.19
59 86 0.76
60 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.05, T:0.36
Consensus pattern (59 bp):
ATTTTACCCCTGAACTTCCAAAAATTCCATTTTTAACCCCGATTTTTCCAAAAATTACC
Found at i:43935593 original size:59 final size:58
Alignment explanation
Indices: 43935419--43935609 Score: 208
Period size: 59 Copynumber: 3.2 Consensus size: 58
43935409 TGAACTTTCC
* * *
43935419 AAAATTCCA-TTTAAACCTCG-ATTTCTCCAAAAATTACCATTTTACCCCTGAACT-TCCA
1 AAAATTCCATTTTTAACCCCGAATTT-TCCAAAAATTACCATTTTA-CCCTGAA-TGTCTA
* * * *
43935477 AAAATTCCATTTTTAACCCCGATTTTTCTAAAAATTACCATTTTACCTCCGGATGTCTA
1 AAAATTCCATTTTTAACCCCGAATTTTCCAAAAATTACCATTTTACC-CTGAATGTCTA
* * *
43935536 AAAATTCCATTTTTGACCCCGAATTTTCCCAAAATTACCATTTTACCCTTAATTGTCTAA
1 AAAATTCCATTTTTAACCCCGAATTTTCCAAAAATTACCATTTTACCCTGAA-TGTCT-A
43935596 AAAATTACCATTTT
1 AAAATT-CCATTTT
43935610 GCCCCTCGGT
Statistics
Matches: 112, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
58 14 0.12
59 81 0.72
60 10 0.09
61 7 0.06
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (58 bp):
AAAATTCCATTTTTAACCCCGAATTTTCCAAAAATTACCATTTTACCCTGAATGTCTA
Found at i:43937728 original size:3 final size:3
Alignment explanation
Indices: 43937682--43937712 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
43937672 TGCTGATCAT
43937682 GAA GAA GAAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA G-AA GAA GAA GAA GAA GAA GAA GAA
43937713 TCAGAGGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:43938461 original size:19 final size:20
Alignment explanation
Indices: 43938439--43938480 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
43938429 AAATAATTTT
43938439 AATAAAATAAAATTAAA-AA
1 AATAAAATAAAATTAAATAA
* * *
43938458 AATATATTATAATTAAATAA
1 AATAAAATAAAATTAAATAA
43938478 AAT
1 AAT
43938481 TAATTTTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AATAAAATAAAATTAAATAA
Found at i:43938475 original size:29 final size:28
Alignment explanation
Indices: 43938429--43938483 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
43938419 AATAGTTTAT
*
43938429 AAATAATTTTAATAAAATAAAATTAAAA
1 AAATAATTATAATAAAATAAAATTAAAA
*
43938457 AAATATATTATAATTAAATAAAATTAA
1 AAATA-ATTATAATAAAATAAAATTAA
43938484 TTTTTGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (28 bp):
AAATAATTATAATAAAATAAAATTAAAA
Found at i:43939364 original size:92 final size:92
Alignment explanation
Indices: 43939241--43940388 Score: 1912
Period size: 92 Copynumber: 12.5 Consensus size: 92
43939231 CAGATCAAAA
*
43939241 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAGGAGCAAGATGAAGCTTCAAACGTCATTTCTT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCATTTCTT
43939306 ATCCTCTTGAAGTTATAGTAAAGTTGG
66 ATCCTCTTGAAGTTATAGTAAAGTTGG
* *
43939333 ATAATGAACCTTTATCTCTCTGAAGTTATAGTAGGAGCAAGATGAAGCTTCAAACGTCATTTCTT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCATTTCTT
*
43939398 ATCCTCTTG--GTTATAGTAAGGTTGG
66 ATCCTCTTGAAGTTATAGTAAAGTTGG
*
43939423 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCATTTCTT
* *
43939488 ATCCTCTTGAAGTTATAGAAAAGTCGG
66 ATCCTCTTGAAGTTATAGTAAAGTTGG
* * * *
43939515 ATAATGAACCTTTATCTTTCTGAAGTTATAGTAAGAGCAAGATGAAGTTTCAAACATCATTTCTT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCATTTCTT
*
43939580 ATCCTCTTGAAGTTATAGTAAAG-GGG
66 ATCCTCTTGAAGTTATAGTAAAGTTGG
* * * *
43939606 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAGGAGCAAGATAAAACTTCAAACATCATTTCTT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCATTTCTT
43939671 ATCCTCTTGAAGTTATAGTAAAGTTGG
66 ATCCTCTTGAAGTTATAGTAAAGTTGG
*
43939698 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAGGAGCAAGATGAAGCTTCAAACGTCATTTCTT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCATTTCTT
43939763 ATCCTCTTGAAGTTATAGTAAAGTTGG
66 ATCCTCTTGAAGTTATAGTAAAGTTGG
* *
43939790 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGATTCAAAACGTCAATTCT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTC-AAACGTCATTTCT
43939855 TATCCTCTTGAAGTTATAGTAAAGTTGG
65 TATCCTCTTGAAGTTATAGTAAAGTTGG
43939883 ATAACGAACCTTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCATTTCT
1 ATAACGAACC-TTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCATTTCT
43939948 TATCCTCTTGAAGTTATAGTAAAGTTGG
65 TATCCTCTTGAAGTTATAGTAAAGTTGG
* * *
43939976 ATAACAAACCTTTATCTCTCTGAAGTTATAGCAAGAGCAAGATGAAGCTTCAAACGTCAATTCTT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCATTTCTT
43940041 ATCCTCTTGAAGTTATAGTAAA-TTGG
66 ATCCTCTTGAAGTTATAGTAAAGTTGG
*
43940067 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCA-ATCTT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCATTTCTT
* *
43940131 ATCCTCTTAAAATTATAGTAAAGTTGG
66 ATCCTCTTGAAGTTATAGTAAAGTTGG
* * *
43940158 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGACGAAGCTTCAAGCGTCAATTCTT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCATTTCTT
*
43940223 ATCCT-TTGAAGTTATAGTAAAGTGGG
66 ATCCTCTTGAAGTTATAGTAAAGTTGG
* * * *
43940249 ACAACGAACCTTTATCTTTCTGAAGTTATAGTAAGAGAAAGATGAAGCTTCAAACGTCAATTCTT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCATTTCTT
43940314 ATCCTCTTGAAGTTATAGTAAAGTTGG
66 ATCCTCTTGAAGTTATAGTAAAGTTGG
* * *
43940341 ATAACGAACCTTTATCTCTCTGAAGTTGTAGTAAGAGTAAGATAAAGC
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGC
43940389 CTCGACATCA
Statistics
Matches: 993, Mismatches: 55, Indels: 16
0.93 0.05 0.02
Matches are distributed among these distances:
90 110 0.11
91 289 0.29
92 455 0.46
93 99 0.10
94 40 0.04
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Consensus pattern (92 bp):
ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCATTTCTT
ATCCTCTTGAAGTTATAGTAAAGTTGG
Found at i:43939555 original size:182 final size:183
Alignment explanation
Indices: 43939241--43940388 Score: 1892
Period size: 182 Copynumber: 6.3 Consensus size: 183
43939231 CAGATCAAAA
* *
43939241 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAGGAGCAAGATGAAGCTTCAAACGTCATTTCTT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTT
* *
43939306 ATCCTCTTGAAGTTATAGTAAAGTTGGATAATGAACCTTTATCTCTCTGAAGTTATAGTAGGAGC
66 ATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGC
*
43939371 AAGATGAAGCTTCAAACGTCATTTCTTATCCTCTTG-GTTATAGTAAGGTTGG
131 AAGATGAAGCTTCAAACGTCATTTCTTATCCTCTTGAGTTATAGTAAAGTTGG
43939423 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTT
* * * *
43939488 ATCCTCTTGAAGTTATAGAAAAGTCGGATAATGAACCTTTATCTTTCTGAAGTTATAGTAAGAGC
66 ATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGC
* * *
43939553 AAGATGAAGTTTCAAACATCATTTCTTATCCTCTTGAAGTTATAGTAAAG-GGG
131 AAGATGAAGCTTCAAACGTCATTTCTTATCCTCTTG-AGTTATAGTAAAGTTGG
* * * * *
43939606 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAGGAGCAAGATAAAACTTCAAACATCATTTCTT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTT
*
43939671 ATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACCTTTATCTCTCTGAAGTTATAGTAGGAGC
66 ATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGC
43939736 AAGATGAAGCTTCAAACGTCATTTCTTATCCTCTTGAAGTTATAGTAAAGTTGG
131 AAGATGAAGCTTCAAACGTCATTTCTTATCCTCTTG-AGTTATAGTAAAGTTGG
*
43939790 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGATTCAAAACGTCAATTCT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTC-AAACGTCAATTCT
43939855 TATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACCTTTTATCTCTCTGAAGTTATAGTAAGA
65 TATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACC-TTTATCTCTCTGAAGTTATAGTAAGA
43939920 GCAAGATGAAGCTTCAAACGTCATTTCTTATCCTCTTGAAGTTATAGTAAAGTTGG
129 GCAAGATGAAGCTTCAAACGTCATTTCTTATCCTCTTG-AGTTATAGTAAAGTTGG
* *
43939976 ATAACAAACCTTTATCTCTCTGAAGTTATAGCAAGAGCAAGATGAAGCTTCAAACGTCAATTCTT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTT
43940041 ATCCTCTTGAAGTTATAGTAAA-TTGGATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGC
66 ATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGC
* * *
43940105 AAGATGAAGCTTCAAACGTCA-ATCTTATCCTCTTAAAATTATAGTAAAGTTGG
131 AAGATGAAGCTTCAAACGTCATTTCTTATCCTCTT-GAGTTATAGTAAAGTTGG
* *
43940158 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGACGAAGCTTCAAGCGTCAATTCTT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTT
* * * *
43940223 ATCCT-TTGAAGTTATAGTAAAGTGGGACAACGAACCTTTATCTTTCTGAAGTTATAGTAAGAGA
66 ATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGC
*
43940287 AAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTGG
131 AAGATGAAGCTTCAAACGTCATTTCTTATCCTCTTG-AGTTATAGTAAAGTTGG
* * *
43940341 ATAACGAACCTTTATCTCTCTGAAGTTGTAGTAAGAGTAAGATAAAGC
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGC
43940389 CTCGACATCA
Statistics
Matches: 906, Mismatches: 51, Indels: 17
0.93 0.05 0.02
Matches are distributed among these distances:
181 16 0.02
182 311 0.34
183 291 0.32
184 74 0.08
185 85 0.09
186 129 0.14
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Consensus pattern (183 bp):
ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTT
ATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGC
AAGATGAAGCTTCAAACGTCATTTCTTATCCTCTTGAGTTATAGTAAAGTTGG
Found at i:43939724 original size:40 final size:40
Alignment explanation
Indices: 43939669--43939823 Score: 125
Period size: 40 Copynumber: 3.6 Consensus size: 40
43939659 ACATCATTTC
43939669 TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACCT
1 TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACCT
* * * **
43939709 TTAT-CTCTCTGAAGTTATAGTAGGAGCAAGATGAAGCTTCAAACGTCATTT
1 TTATCCTCT-TGAAGTTATAGT---A--AAGTTG--G-AT--AACG-AACCT
43939760 CTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACCT
1 -TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACCT
43939801 TTAT-CTCTCTGAAGTTATAGTAA
1 TTATCCTCT-TGAAGTTATAGTAA
43939824 GAGCAAGATG
Statistics
Matches: 90, Mismatches: 10, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
39 8 0.09
40 34 0.38
41 2 0.02
42 4 0.04
43 1 0.01
44 1 0.01
45 6 0.07
47 6 0.07
48 1 0.01
49 1 0.01
50 4 0.04
51 2 0.02
52 16 0.18
53 4 0.04
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Consensus pattern (40 bp):
TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACCT
Found at i:43952055 original size:59 final size:59
Alignment explanation
Indices: 43951816--43952039 Score: 337
Period size: 59 Copynumber: 3.8 Consensus size: 59
43951806 ATGGATACCC
*
43951816 GGGGGCAAAATGGT-AATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAGGTTTT
1 GGGGGTAAAATGGTAAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAGGTTTT
* * * *
43951874 GGGGGTAAAATGGTAATTTTTAGTGAAATCGGGGTT-AAAATAGAATTTTAGAA-GCTTT
1 GGGGGTAAAATGGTAAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTA-AAGGTTTT
** *
43951932 GGGGGTAAAATGGTAAATTTTGGTGAAATCAAGGTTAAAAATGGAATTTTAAAGGTTTC
1 GGGGGTAAAATGGTAAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAGGTTTT
*
43951991 GGGGGTAAAATGGTAAATTTTGGTGAAATCGGGGTTAAAAATGGGATTT
1 GGGGGTAAAATGGTAAATTTTGGTGAAATCGGGGTTAAAAATGGAATTT
43952040 AGGAAATTTT
Statistics
Matches: 147, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
58 64 0.44
59 83 0.56
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (59 bp):
GGGGGTAAAATGGTAAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAGGTTTT
Found at i:43952069 original size:117 final size:116
Alignment explanation
Indices: 43951816--43952030 Score: 367
Period size: 117 Copynumber: 1.8 Consensus size: 116
43951806 ATGGATACCC
* ** *
43951816 GGGGGCAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAGGTTTTGGGGGTA
1 GGGGGTAAAATGGTAATTTTGGTGAAATCAAGGTTAAAAATGGAATTTTAAAGGTTTCGGGGGTA
*
43951881 AAATGGTAATTTTTAGTGAAATCGGGGTTAAAATAGAATTTTAGAAGCTTT
66 AAATGGTAAATTTTAGTGAAATCGGGGTTAAAATAGAATTTTAGAAGCTTT
43951932 GGGGGTAAAATGGTAAATTTTGGTGAAATCAAGGTTAAAAATGGAATTTTAAAGGTTTCGGGGGT
1 GGGGGTAAAATGGT-AATTTTGGTGAAATCAAGGTTAAAAATGGAATTTTAAAGGTTTCGGGGGT
*
43951997 AAAATGGTAAATTTTGGTGAAATCGGGGTTAAAA
65 AAAATGGTAAATTTTAGTGAAATCGGGGTTAAAA
43952031 ATGGGATTTA
Statistics
Matches: 92, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
116 13 0.14
117 79 0.86
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.32
Consensus pattern (116 bp):
GGGGGTAAAATGGTAATTTTGGTGAAATCAAGGTTAAAAATGGAATTTTAAAGGTTTCGGGGGTA
AAATGGTAAATTTTAGTGAAATCGGGGTTAAAATAGAATTTTAGAAGCTTT
Found at i:43952071 original size:59 final size:59
Alignment explanation
Indices: 43951816--43952071 Score: 331
Period size: 59 Copynumber: 4.4 Consensus size: 59
43951806 ATGGATACCC
* *
43951816 GGGGGCAAAATGGT-AATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAGGTTTT
1 GGGGGTAAAATGGTAAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGTTTT
* * * * *
43951874 GGGGGTAAAATGGTAATTTTTAGTGAAATCGGGGTT-AAAATAGAATTTTAGAAGCTTT
1 GGGGGTAAAATGGTAAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGTTTT
** * *
43951932 GGGGGTAAAATGGTAAATTTTGGTGAAATCAAGGTTAAAAATGGAATTTTAAAGGTTTC
1 GGGGGTAAAATGGTAAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGTTTT
* *
43951991 GGGGGTAAAATGGTAAATTTTGGTGAAATCGGGGTTAAAAATGGGA-TTTAGGAAATTTTT
1 GGGGGTAAAATGGTAAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTA--AAAGTTTT
* *
43952051 GGGGTTAAAAT-GTAATTTTTG
1 GGGGGTAAAATGGTAAATTTTG
43952072 AAAGTTTTAG
Statistics
Matches: 170, Mismatches: 24, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
58 67 0.39
59 88 0.52
60 15 0.09
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (59 bp):
GGGGGTAAAATGGTAAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGTTTT
Found at i:43952108 original size:30 final size:30
Alignment explanation
Indices: 43952047--43952367 Score: 405
Period size: 30 Copynumber: 10.7 Consensus size: 30
43952037 TTTAGGAAAT
* *
43952047 TTTTGGGGTTAAAATGTAATTTTTG-AAAG
1 TTTTGGGGTCAAAATGTAATTTTGGAAAAG
*
43952076 TTTTAGGGTCAAAATGTAATTTTGGAAAAG
1 TTTTGGGGTCAAAATGTAATTTTGGAAAAG
** *
43952106 TTTAAGGGTCGAAATGTAATTTTGGAAAAG
1 TTTTGGGGTCAAAATGTAATTTTGGAAAAG
* * *
43952136 TTTTGGGGTCAAAATATAATTTTAGAAAAT
1 TTTTGGGGTCAAAATGTAATTTTGGAAAAG
*
43952166 TTTTAGGGTCAAAATGTAATTTTTGG-AAAG
1 TTTTGGGGTCAAAATGTAA-TTTTGGAAAAG
*
43952196 TTTTAGGGTCAAAATGTAATTTTGGAAAAG
1 TTTTGGGGTCAAAATGTAATTTTGGAAAAG
* * **
43952226 TTTTGGGGTTAAAATGCAATTTCTGG-ATTG
1 TTTTGGGGTCAAAATGTAATTT-TGGAAAAG
*
43952256 TTTTGGGGTCAAACTGTAATTTTGGAAAAG
1 TTTTGGGGTCAAAATGTAATTTTGGAAAAG
* * *
43952286 TTTTAGGGTCAAAATATAATTTTGGAAGAG
1 TTTTGGGGTCAAAATGTAATTTTGGAAAAG
*
43952316 TTTTGGGGTCAAAATGTAATTTTGGAAAAA
1 TTTTGGGGTCAAAATGTAATTTTGGAAAAG
* *
43952346 TTTTGGGGTTAAAATGCAATTT
1 TTTTGGGGTCAAAATGTAATTT
43952368 CCGGATTGTT
Statistics
Matches: 252, Mismatches: 35, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
29 31 0.12
30 213 0.85
31 8 0.03
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.39
Consensus pattern (30 bp):
TTTTGGGGTCAAAATGTAATTTTGGAAAAG
Found at i:43952350 original size:120 final size:119
Alignment explanation
Indices: 43952037--43952382 Score: 471
Period size: 120 Copynumber: 2.9 Consensus size: 119
43952027 AAAAATGGGA
* * * * *
43952037 TTTAGGAAATTTTTGGGGTTAAAATGTAATTTTTGAAAGTTTTAGGGTCAAAATGTAATTTTGGA
1 TTTAGAAAAGTTTTAGGGTCAAAATGTAATTTTGGAAAGTTTTAGGGTCAAAATGTAATTTTGGA
** ** * **
43952102 AAAGTTTAAGGGTCGAAATGTAATTT-TGGAAAAGTTTTGGGGTCAAAATATAAT
66 AAAGTTTTGGGGTTAAAATGCAATTTCTGG-ATTGTTTTGGGGTCAAAATATAAT
*
43952156 TTTAGAAAATTTTTAGGGTCAAAATGTAATTTTTGGAAAGTTTTAGGGTCAAAATGTAATTTTGG
1 TTTAGAAAAGTTTTAGGGTCAAAATGTAA-TTTTGGAAAGTTTTAGGGTCAAAATGTAATTTTGG
* *
43952221 AAAAGTTTTGGGGTTAAAATGCAATTTCTGGATTGTTTTGGGGTCAAACTGTAAT
65 AAAAGTTTTGGGGTTAAAATGCAATTTCTGGATTGTTTTGGGGTCAAAATATAAT
* * *
43952276 TTTGGAAAAGTTTTAGGGTCAAAATATAATTTTGGAAGAGTTTTGGGGTCAAAATGTAATTTTGG
1 TTTAGAAAAGTTTTAGGGTCAAAATGTAATTTTGGAA-AGTTTTAGGGTCAAAATGTAATTTTGG
* *
43952341 AAAAATTTTGGGGTTAAAATGCAATTTCCGGATTG-TTTGGGG
65 AAAAGTTTTGGGGTTAAAATGCAATTTCTGGATTGTTTTGGGG
43952383 ACCTATAAGC
Statistics
Matches: 205, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
119 41 0.20
120 161 0.79
121 3 0.01
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.39
Consensus pattern (119 bp):
TTTAGAAAAGTTTTAGGGTCAAAATGTAATTTTGGAAAGTTTTAGGGTCAAAATGTAATTTTGGA
AAAGTTTTGGGGTTAAAATGCAATTTCTGGATTGTTTTGGGGTCAAAATATAAT
Found at i:43953879 original size:15 final size:15
Alignment explanation
Indices: 43953856--43953886 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
43953846 ATGGTGGATG
43953856 GAGCAGGTGGTGGCA
1 GAGCAGGTGGTGGCA
*
43953871 GAGCTGGTGGTGGCA
1 GAGCAGGTGGTGGCA
43953886 G
1 G
43953887 CGGCATAGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.13, G:0.55, T:0.16
Consensus pattern (15 bp):
GAGCAGGTGGTGGCA
Found at i:43954089 original size:17 final size:17
Alignment explanation
Indices: 43954066--43954151 Score: 113
Period size: 17 Copynumber: 5.1 Consensus size: 17
43954056 TTTAATTTTT
*
43954066 ATTTAAATTTAAATTCAA
1 ATTTAAATTTAAAAT-AA
* *
43954084 A-GTAAATTTAAATTTAA
1 ATTTAAATTTAAA-ATAA
43954101 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
43954118 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
43954135 ATTTAAATTT-AAATAA
1 ATTTAAATTTAAAATAA
43954151 A
1 A
43954152 ATCAATTTAA
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.11
17 43 0.68
18 13 0.21
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:43954092 original size:29 final size:29
Alignment explanation
Indices: 43954066--43954130 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
43954056 TTTAATTTTT
*
43954066 ATTTAAATTTAAATTCAAAGTAAATTTAA
1 ATTTAAATTTAAATTCAAAATAAATTTAA
*
43954095 ATTTAAATTTAAATTTAAAATAAATTTAA
1 ATTTAAATTTAAATTCAAAATAAATTTAA
43954124 ATTTAAA
1 ATTTAAA
43954131 ATAAATTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (29 bp):
ATTTAAATTTAAATTCAAAATAAATTTAA
Found at i:43954095 original size:6 final size:6
Alignment explanation
Indices: 43954066--43954148 Score: 109
Period size: 6 Copynumber: 14.3 Consensus size: 6
43954056 TTTAATTTTT
* *
43954066 ATTTAA ATTTAA ATTCAA A-GTAA ATTTAA ATTTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* *
43954113 A-ATAA ATTTAA ATTTAA A-ATAA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT
43954149 AAAATCAATT
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
5 11 0.17
6 55 0.83
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (6 bp):
ATTTAA
Found at i:43954096 original size:23 final size:23
Alignment explanation
Indices: 43954066--43954161 Score: 117
Period size: 23 Copynumber: 4.3 Consensus size: 23
43954056 TTTAATTTTT
* *
43954066 ATTTAAATTTAAATTCAAAGTAA
1 ATTTAAATTTAAATTTAAAATAA
*
43954089 ATTTAAATTTAAATTTAAATTTAA
1 ATTTAAATTTAAATTTAAA-ATAA
*
43954113 A-ATAAATTTAAATTTAAAATAA
1 ATTTAAATTTAAATTTAAAATAA
*
43954135 ATTTAAATTTAAA--TAAAATCA
1 ATTTAAATTTAAATTTAAAATAA
43954156 ATTTAA
1 ATTTAA
43954162 CTCAAAAGGT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.20
22 4 0.06
23 44 0.68
24 4 0.06
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (23 bp):
ATTTAAATTTAAATTTAAAATAA
Found at i:43959534 original size:28 final size:28
Alignment explanation
Indices: 43959485--43959578 Score: 134
Period size: 28 Copynumber: 3.3 Consensus size: 28
43959475 CGAAACACTG
* *
43959485 AAGTGCTATTACAGAATAGAGAGCATACA
1 AAGTGCTAAT-CAGAATAGAGAGCACACA
*
43959514 AAGTGCTAATCAGAATGGAGAGCACACA
1 AAGTGCTAATCAGAATAGAGAGCACACA
* *
43959542 AAGTGCTAATCAAAATAGAGAGCACATA
1 AAGTGCTAATCAGAATAGAGAGCACACA
43959570 AAGTGCTAA
1 AAGTGCTAA
43959579 ATACACGTAG
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 50 0.85
29 9 0.15
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.18
Consensus pattern (28 bp):
AAGTGCTAATCAGAATAGAGAGCACACA
Found at i:43960026 original size:19 final size:19
Alignment explanation
Indices: 43959990--43960027 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
43959980 GACTACAAAA
*
43959990 TTCATATATTCTTGTATTT
1 TTCATATATGCTTGTATTT
43960009 TTCACTATATGCTT-TATTT
1 TTCA-TATATGCTTGTATTT
43960028 ATCCATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.21, C:0.13, G:0.05, T:0.61
Consensus pattern (19 bp):
TTCATATATGCTTGTATTT
Found at i:43961368 original size:29 final size:29
Alignment explanation
Indices: 43961327--43961690 Score: 170
Period size: 29 Copynumber: 12.5 Consensus size: 29
43961317 ACTCGGGGGC
* *
43961327 AAAATGGTGATTTTGGTGAAATCGGGGTT
1 AAAATGGTAATTTTGGAGAAATCGGGGTT
* *
43961356 AAAAATGG-AATTTT--AAAAGATACGGGGGT
1 -AAAATGGTAATTTTGGAGAA-AT-CGGGGTT
* ** *
43961385 AAAATGGTAATTTTTGGTGAAATCAAGGTA
1 AAAATGGTAA-TTTTGGAGAAATCGGGGTT
** * *
43961415 AAAATGG-AATTTTAAAAGATAT-GGGGGT
1 AAAATGGTAATTTT-GGAGAAATCGGGGTT
*
43961443 AAAATGGTAATTTTTGGTGAAATCGGGGTT
1 AAAATGGTAA-TTTTGGAGAAATCGGGGTT
** * * *
43961473 AAAATGG-AATTTTAAAGGATTCGGGGGT
1 AAAATGGTAATTTTGGAGAAATCGGGGTT
*
43961501 AAAATGGTAATTTTTGGTGAAATCGGGGTT
1 AAAATGGTAA-TTTTGGAGAAATCGGGGTT
*
43961531 AAAAATAG-AATTTT--AGAAGATTCGGGG-T
1 -AAAATGGTAATTTTGGAGAA-A-TCGGGGTT
** *
43961559 AAAATGGTAATTTTTGGA-AGTTTCGAGGTT
1 AAAATGGTAA-TTTTGGAGA-AATCGGGGTT
* *
43961589 AAAAATAG-AATTTT--AAAAGATTCGAGGG-T
1 -AAAATGGTAATTTTGGAGAA-A-TCG-GGGTT
* *
43961618 AAAATGGTAATTTTCGGTGAAATCGAGGTT
1 AAAATGGTAATTTT-GGAGAAATCGGGGTT
*
43961648 AAAAATGG-AATTTT--AGAAGATTCGGGGGT
1 -AAAATGGTAATTTTGGAGAA-A-TCGGGGTT
43961677 AAAATGGTAATTTT
1 AAAATGGTAATTTT
43961691 TGGAAGTTTT
Statistics
Matches: 247, Mismatches: 52, Indels: 71
0.67 0.14 0.19
Matches are distributed among these distances:
27 15 0.06
28 61 0.25
29 76 0.31
30 68 0.28
31 23 0.09
32 4 0.02
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.32
Consensus pattern (29 bp):
AAAATGGTAATTTTGGAGAAATCGGGGTT
Found at i:43961619 original size:117 final size:117
Alignment explanation
Indices: 43961352--43961699 Score: 524
Period size: 117 Copynumber: 3.0 Consensus size: 117
43961342 GTGAAATCGG
* *
43961352 GGTTAAAAATGGAATTTTAAAAGATACGGGGGTAAAATGGTAATTTTTGGTGAAATCAAGG-TAA
1 GGTTAAAAATGGAATTTTAAAAGATTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAA
* * * *
43961416 AAATGGAATTTTAAAAGATATGGGGGTAAAATGGTAATTTTTGGTGAA--ATCGG
66 AAATGGAATTTTAGAAGAT-TCGGGGTAAAATGGTAATTTTT-G-GAAGTTTCGA
* *
43961469 GGTT-AAAATGGAATTTTAAAGGATTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAA
1 GGTTAAAAATGGAATTTTAAAAGATTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAA
*
43961533 AAATAGAATTTTAGAAGATTCGGGGTAAAATGGTAATTTTTGGAAGTTTCGA
66 AAATGGAATTTTAGAAGATTCGGGGTAAAATGGTAATTTTTGGAAGTTTCGA
* * *
43961585 GGTTAAAAATAGAATTTTAAAAGATTCGAGGGTAAAATGGTAATTTTCGGTGAAATCGAGGTTAA
1 GGTTAAAAATGGAATTTTAAAAGATTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAA
43961650 AAATGGAATTTTAGAAGATTCGGGGGTAAAATGGTAATTTTTGGAAGTTT
66 AAATGGAATTTTAGAAGATTC-GGGGTAAAATGGTAATTTTTGGAAGTTT
43961700 TTGGGTTCAG
Statistics
Matches: 211, Mismatches: 15, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
114 3 0.01
115 1 0.00
116 80 0.38
117 99 0.47
118 28 0.13
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.32
Consensus pattern (117 bp):
GGTTAAAAATGGAATTTTAAAAGATTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAA
AAATGGAATTTTAGAAGATTCGGGGTAAAATGGTAATTTTTGGAAGTTTCGA
Found at i:43961647 original size:59 final size:59
Alignment explanation
Indices: 43961319--43961693 Score: 539
Period size: 58 Copynumber: 6.4 Consensus size: 59
43961309 TTGTGGATAC
* * *
43961319 TCGGGGGCAAAATGGTGA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGAT
1 TCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGAT
* *
43961377 ACGGGGGTAAAATGGTAATTTTTGGTGAAATCAAGG-TAAAAATGGAATTTTAAAAGAT
1 TCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGAT
* *
43961435 AT-GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGGAATTTTAAAGGAT
1 -TCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGAT
* * *
43961493 TCGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTAGAAGAT
1 TCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGAT
* *
43961552 TC-GGGGTAAAATGGTAATTTTT-G-GAAGTTTCGAGGTTAAAAATAGAATTTTAAAAGAT
1 TCGGGGGTAAAATGGTAATTTTTGGTGAA--ATCGAGGTTAAAAATGGAATTTTAAAAGAT
* * *
43961610 TCGAGGGTAAAATGGTAATTTTCGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGAT
1 TCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGAT
43961669 TCGGGGGTAAAATGGTAATTTTTGG
1 TCGGGGGTAAAATGGTAATTTTTGG
43961694 AAGTTTTTGG
Statistics
Matches: 285, Mismatches: 22, Indels: 19
0.87 0.07 0.06
Matches are distributed among these distances:
56 3 0.01
57 2 0.01
58 173 0.61
59 103 0.36
60 1 0.00
61 3 0.01
ACGTcount: A:0.36, C:0.04, G:0.29, T:0.32
Consensus pattern (59 bp):
TCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGAT
Found at i:43963481 original size:6 final size:6
Alignment explanation
Indices: 43963460--43963550 Score: 78
Period size: 6 Copynumber: 15.0 Consensus size: 6
43963450 ATTTTTTATG
* * ** * *
43963460 TTAAAT TTAATGT TTTAAT TTTTAT TTAAAT TTAAAT TCAAA- GTAAAT
1 TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
43963508 TTAAAT AATTAAAT TTAAAT TTAAA- ATAAAT TTAAAT TTAAAT
1 TTAAAT --TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
43963551 AAAATTAAAA
Statistics
Matches: 68, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
5 7 0.10
6 51 0.75
7 4 0.06
8 6 0.09
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (6 bp):
TTAAAT
Found at i:43963506 original size:17 final size:16
Alignment explanation
Indices: 43963486--43963559 Score: 89
Period size: 17 Copynumber: 4.6 Consensus size: 16
43963476 AATTTTTATT
*
43963486 TAAATTTAAATTCAAA
1 TAAATTTAAATTTAAA
*
43963502 GTAAATTTAAA--TAAT
1 -TAAATTTAAATTTAAA
43963517 TAAATTTAAATTTAAAA
1 TAAATTTAAATTT-AAA
43963534 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
*
43963550 TAAAATTAAA
1 TAAATTTAAA
43963560 AATCAATTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
14 10 0.20
15 2 0.04
16 13 0.26
17 25 0.50
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:43963520 original size:31 final size:31
Alignment explanation
Indices: 43963485--43963569 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 31
43963475 TAATTTTTAT
*
43963485 TTAAATTTAAATTCAAAGTAAATTTAAATAA
1 TTAAATTTAAATTCAAAATAAATTTAAATAA
*
43963516 TTAAATTTAAATTTAAAATAAATTTAAAT--
1 TTAAATTTAAATTCAAAATAAATTTAAATAA
* * *
43963545 TTAAA-TAAAATTAAAAATCAATTTA
1 TTAAATTTAAATTCAAAATAAATTTA
43963570 TCTCTAAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
28 17 0.35
29 5 0.10
31 27 0.55
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (31 bp):
TTAAATTTAAATTCAAAATAAATTTAAATAA
Found at i:43964204 original size:68 final size:69
Alignment explanation
Indices: 43963915--43964534 Score: 1005
Period size: 69 Copynumber: 9.0 Consensus size: 69
43963905 GGAAATGATC
*
43963915 TTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTCTACTTCGATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
43963980 GACG
66 GACG
* * *
43963984 TTGCTCTTACTTCAATTTCAGAGATCAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
43964049 GACG
66 GACG
* * * *
43964053 TTGCTCTTACTTCAATTTCAGAGATGAAGACCTGTTATCCAACTCTACTTCGATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
43964118 GACG
66 GACG
*
43964122 TTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCC-TCTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
43964186 GACG
66 GACG
* * * *
43964190 TTGCTCTCACTTCAATTTCAGAGATGAAGACCTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
43964255 GACG
66 GACG
*
43964259 TTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCC-TCTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
43964323 GACG
66 GACG
* * * **
43964327 TTGCTCTCACTTCAATTTCAGAGATGAAGACCAGTTATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
43964392 GACG
66 GACG
*
43964396 TTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCC-TCTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
43964460 GACG
66 GACG
* * *
43964464 TGGTTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCC-TCTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
43964528 GACG
66 GACG
43964532 TTG
1 TTG
43964535 AGACCTACAG
Statistics
Matches: 512, Mismatches: 37, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
68 219 0.43
69 293 0.57
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (69 bp):
TTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
GACG
Found at i:43964233 original size:137 final size:137
Alignment explanation
Indices: 43963915--43964534 Score: 1062
Period size: 137 Copynumber: 4.5 Consensus size: 137
43963905 GGAAATGATC
* * * *
43963915 TTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTCTACTTCGATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACCTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
* * * *
43963980 GACGTTGCTCTTACTTCAATTTCAGAGATCAAGACTTGTTATCCAACTCTACTTCAATTTCAAGA
66 GACGTTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCC-TCTCTACTTCAATTTCAAGA
43964045 GGATGACG
130 GGATGACG
*
43964053 TTGCTCTTACTTCAATTTCAGAGATGAAGACCTGTTATCCAACTCTACTTCGATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACCTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
43964118 GACGTTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCTCTCTACTTCAATTTCAAGAG
66 GACGTTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCTCTCTACTTCAATTTCAAGAG
43964183 GATGACG
131 GATGACG
*
43964190 TTGCTCTCACTTCAATTTCAGAGATGAAGACCTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACCTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
43964255 GACGTTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCTCTCTACTTCAATTTCAAGAG
66 GACGTTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCTCTCTACTTCAATTTCAAGAG
43964320 GATGACG
131 GATGACG
* *
43964327 TTGCTCTCACTTCAATTTCAGAGATGAAGACCAGTTATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACCTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
43964392 GACGTTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCTCTCTACTTCAATTTCAAGAG
66 GACGTTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCTCTCTACTTCAATTTCAAGAG
43964457 GATGACG
131 GATGACG
* * * * * *
43964464 TGGTTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCC-TCTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACCTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
43964528 GACGTTG
66 GACGTTG
43964535 AGACCTACAG
Statistics
Matches: 464, Mismatches: 18, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
136 30 0.06
137 331 0.71
138 103 0.22
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (137 bp):
TTGCTCTTACTTCAATTTCAGAGATGAAGACCTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
GACGTTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCTCTCTACTTCAATTTCAAGAG
GATGACG
Found at i:43976470 original size:29 final size:30
Alignment explanation
Indices: 43976429--43976675 Score: 172
Period size: 29 Copynumber: 8.5 Consensus size: 30
43976419 ACCCGGGGGC
* *
43976429 AAAATGGTGATTTT-GGTGAAATCGGGGTTT
1 AAAATGGTAATTTTCGATGAAATCGGGG-TT
** * * *
43976459 AAAATGG-AATTTTAAAAGATA-CGGGGGT
1 AAAATGGTAATTTTCGATGAAATCGGGGTT
* * *
43976487 AAAATGGTAATTTTCGGTGAAATTGGGGTA
1 AAAATGGTAATTTTCGATGAAATCGGGGTT
** * * *
43976517 AAAATGG-AATTTTAAAAGATAT-GGGGGT
1 AAAATGGTAATTTTCGATGAAATCGGGGTT
43976545 AAAATGGTAATTTTCGATGAAATCGGGGTT
1 AAAATGGTAATTTTCGATGAAATCGGGGTT
* * * *
43976575 AAAATGG-AATTTT-AAAGGATTCGAGGG-T
1 AAAATGGTAATTTTCGATGAAATCG-GGGTT
*
43976603 AAAATGGTAATTTTCGGTGAAATCGGGGTT
1 AAAATGGTAATTTTCGATGAAATCGGGGTT
* * * * *
43976633 AAAAAT-GAAATTTTAGAAG-ATTCGGGGGT
1 -AAAATGGTAATTTTCGATGAAATCGGGGTT
43976662 AAAATGGTAATTTT
1 AAAATGGTAATTTT
43976676 TGGAAGTTTT
Statistics
Matches: 164, Mismatches: 42, Indels: 23
0.72 0.18 0.10
Matches are distributed among these distances:
28 38 0.23
29 73 0.45
30 48 0.29
31 5 0.03
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32
Consensus pattern (30 bp):
AAAATGGTAATTTTCGATGAAATCGGGGTT
Found at i:43976484 original size:58 final size:58
Alignment explanation
Indices: 43976422--43976675 Score: 366
Period size: 58 Copynumber: 4.4 Consensus size: 58
43976412 TGTGGATACC
* * *
43976422 CGGGGGCAAAATGGTGATTTT-GGTGAAATCGGGGTTTAAAATGGAATTTTAAAAGATA
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGG-TAAAAATGGAATTTTAAAAGATA
*
43976480 CGGGGGTAAAATGGTAATTTTCGGTGAAATTGGGGTAAAAATGGAATTTTAAAAGATA
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTAAAAATGGAATTTTAAAAGATA
* * * * *
43976538 TGGGGGTAAAATGGTAATTTTCGATGAAATCGGGGTTAAAATGGAATTTTAAAGGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTAAAAATGGAATTTTAAAAGATA
* * * *
43976596 CGAGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGAAATTTTAGAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGG-TAAAAATGGAATTTTAAAAGATA
43976655 CGGGGGTAAAATGGTAATTTT
1 CGGGGGTAAAATGGTAATTTT
43976676 TGGAAGTTTT
Statistics
Matches: 176, Mismatches: 18, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
58 125 0.71
59 51 0.29
ACGTcount: A:0.35, C:0.04, G:0.30, T:0.31
Consensus pattern (58 bp):
CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTAAAAATGGAATTTTAAAAGATA
Found at i:43977051 original size:34 final size:32
Alignment explanation
Indices: 43977013--43977077 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
43977003 TTACATGGCA
* *
43977013 AAATTGCAAATAATTAAAAAATGCAGAAAGGACT
1 AAATTG-AAACAAATAAAAAATGC-GAAAGGACT
*
43977047 AAATTGAAGCAAATAAAAAATGCGAAAGGAC
1 AAATTGAAACAAATAAAAAATGCGAAAGGAC
43977078 CAATTACACA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 8 0.29
33 14 0.50
34 6 0.21
ACGTcount: A:0.57, C:0.09, G:0.17, T:0.17
Consensus pattern (32 bp):
AAATTGAAACAAATAAAAAATGCGAAAGGACT
Found at i:43978469 original size:6 final size:6
Alignment explanation
Indices: 43978448--43978538 Score: 78
Period size: 6 Copynumber: 15.0 Consensus size: 6
43978438 ATTTTTTATG
* * ** * *
43978448 TTAAAT TTAATGT TTTAAT TTTTAT TTAAAT TTAAAT TCAAA- GTAAAT
1 TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
43978496 TTAAAT AATTAAAT TTAAAT TTAAA- ATAAAT TTAAAT TTAAAT
1 TTAAAT --TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
43978539 AAAATTAAAA
Statistics
Matches: 68, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
5 7 0.10
6 51 0.75
7 4 0.06
8 6 0.09
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (6 bp):
TTAAAT
Found at i:43978494 original size:17 final size:16
Alignment explanation
Indices: 43978474--43978547 Score: 89
Period size: 17 Copynumber: 4.6 Consensus size: 16
43978464 AATTTTTATT
*
43978474 TAAATTTAAATTCAAA
1 TAAATTTAAATTTAAA
*
43978490 GTAAATTTAAA--TAAT
1 -TAAATTTAAATTTAAA
43978505 TAAATTTAAATTTAAAA
1 TAAATTTAAATTT-AAA
43978522 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
*
43978538 TAAAATTAAA
1 TAAATTTAAA
43978548 AATCAATTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
14 10 0.20
15 2 0.04
16 13 0.26
17 25 0.50
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:43978508 original size:31 final size:31
Alignment explanation
Indices: 43978473--43978557 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 31
43978463 TAATTTTTAT
*
43978473 TTAAATTTAAATTCAAAGTAAATTTAAATAA
1 TTAAATTTAAATTCAAAATAAATTTAAATAA
*
43978504 TTAAATTTAAATTTAAAATAAATTTAAAT--
1 TTAAATTTAAATTCAAAATAAATTTAAATAA
* * *
43978533 TTAAA-TAAAATTAAAAATCAATTTA
1 TTAAATTTAAATTCAAAATAAATTTA
43978558 TCTCTAAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
28 17 0.35
29 5 0.10
31 27 0.55
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (31 bp):
TTAAATTTAAATTCAAAATAAATTTAAATAA
Found at i:43979776 original size:3 final size:3
Alignment explanation
Indices: 43979768--43979809 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
43979758 TATCTTTGTA
43979768 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
43979810 TATTTTCTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:43980755 original size:21 final size:21
Alignment explanation
Indices: 43980725--43980764 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
43980715 AAAAAAGATA
*
43980725 AATAATAGAAAAAGGTGAGGC
1 AATAAAAGAAAAAGGTGAGGC
*
43980746 AATAAAAGAAACAGGTGAG
1 AATAAAAGAAAAAGGTGAG
43980765 ACAACAAAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.05, G:0.28, T:0.12
Consensus pattern (21 bp):
AATAAAAGAAAAAGGTGAGGC
Found at i:43982031 original size:59 final size:57
Alignment explanation
Indices: 43981934--43982129 Score: 166
Period size: 59 Copynumber: 3.4 Consensus size: 57
43981924 TGGGTTTTTA
* *
43981934 GGGGTAAAATGGT-AATTTTGTG--GAATCG-GGGCTAAAAATGGAATTTGGAAAGTTT
1 GGGGTAAAATGGTAAATTTTG-GCAAAATCGAGGTC-AAAAATGGAATTTGGAAAGTTT
* *
43981989 GGGGAATAAAATGGTAAATTTTGGCAAAATCGAGGTCAAAAATGAAATTTTGGAAAGTTC
1 GGGG--TAAAATGGTAAATTTTGGCAAAATCGAGGTCAAAAATGGAA-TTTGGAAAGTTT
* * * ** * * * *
43982049 GGAGGCAAAACGGTAAGTTTTGGTGAAATCGGGGTTAAAAATGGGATTTAGGGAAGTTT
1 GG-GGTAAAATGGTAAATTTTGGCAAAATCGAGGTCAAAAATGGAATTT-GGAAAGTTT
*
43982108 GAGGGTAAAATGGTAATTTTTG
1 G-GGGTAAAATGGTAAATTTTG
43982130 AAAGTTTTGG
Statistics
Matches: 113, Mismatches: 18, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
55 4 0.04
57 10 0.09
58 10 0.09
59 70 0.62
60 17 0.15
61 2 0.02
ACGTcount: A:0.35, C:0.05, G:0.31, T:0.29
Consensus pattern (57 bp):
GGGGTAAAATGGTAAATTTTGGCAAAATCGAGGTCAAAAATGGAATTTGGAAAGTTT
Found at i:43982057 original size:29 final size:28
Alignment explanation
Indices: 43981959--43982058 Score: 78
Period size: 29 Copynumber: 3.4 Consensus size: 28
43981949 TTTTGTGGAA
*
43981959 TCGGGGCTAAAAATGGAA-TTTGGAAAGT
1 TCGGGGC-AAAAATGAAATTTTGGAAAGT
* * *
43981987 TTGGGGAATAAAATGGTAAATTTTGGCAAA-A
1 TCGGGGCA-AAAAT-G-AAATTTTGG-AAAGT
*
43982018 TCGAGGTCAAAAATGAAATTTTGGAAAGT
1 TCG-GGGCAAAAATGAAATTTTGGAAAGT
43982047 TCGGAGGCAAAA
1 TCGG-GGCAAAA
43982059 CGGTAAGTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
27 1 0.02
28 14 0.25
29 19 0.35
30 3 0.05
31 12 0.22
32 6 0.11
ACGTcount: A:0.40, C:0.07, G:0.28, T:0.25
Consensus pattern (28 bp):
TCGGGGCAAAAATGAAATTTTGGAAAGT
Found at i:43982166 original size:30 final size:29
Alignment explanation
Indices: 43982121--43982456 Score: 321
Period size: 30 Copynumber: 11.2 Consensus size: 29
43982111 GGTAAAATGG
** *
43982121 TAATTTTTGAAAGTTTTGGGGTCAAAGTA
1 TAATTTTAAAAAGTTTTGGGGTCAAAATA
** *
43982150 TAATTTTCAAAAAGTTTTGGGGTTGAAATG
1 TAATTTT-AAAAAGTTTTGGGGTCAAAATA
* *
43982180 TAATTTTGGAAAAGTTTTAGGGTCAAAATA
1 TAATTTT-AAAAAGTTTTGGGGTCAAAATA
* * *
43982210 TAATTTTAGAAAAGTTTAGGGGTAAAAATG
1 TAATTTTA-AAAAGTTTTGGGGTCAAAATA
** * * *
43982240 TAATTTTTGGAAAGTTTCGAGGTTAAAATA
1 TAA-TTTTAAAAAGTTTTGGGGTCAAAATA
* *
43982270 TAATTTTCAAAAAGTTTTGGGGTCGAAATG
1 TAATTTT-AAAAAGTTTTGGGGTCAAAATA
*
43982300 TAATTTTAGAAAAGTTTTAGGGTCAAAATA
1 TAATTTTA-AAAAGTTTTGGGGTCAAAATA
* *
43982330 TAATTTTGGAAAAGTTTTAGGGTCAAAATA
1 TAATTTT-AAAAAGTTTTGGGGTCAAAATA
* ** *
43982360 TAATTTTGGAAAAGTTTAAGGGTCAAAATG
1 TAATTTT-AAAAAGTTTTGGGGTCAAAATA
*
43982390 TAATATTTAGAAAGTTTTGGGGTCAAAATA
1 TAAT-TTTAAAAAGTTTTGGGGTCAAAATA
* * *
43982420 TAATTTTCAGAAAGTTTTGGGGTCGAAATG
1 TAATTTT-AAAAAGTTTTGGGGTCAAAATA
43982450 TAATTTT
1 TAATTTT
43982457 TGGATAATTT
Statistics
Matches: 256, Mismatches: 43, Indels: 15
0.82 0.14 0.05
Matches are distributed among these distances:
29 15 0.06
30 234 0.91
31 7 0.03
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.38
Consensus pattern (29 bp):
TAATTTTAAAAAGTTTTGGGGTCAAAATA
Found at i:43982203 original size:60 final size:59
Alignment explanation
Indices: 43982105--43982456 Score: 381
Period size: 60 Copynumber: 5.9 Consensus size: 59
43982095 TTTAGGGAAG
* * *
43982105 TTTGAGGGT-AAAATGGTAATTTTTG-AAAGTTTTGGGGTCAAAGTATAATTTTCAAAAAGT
1 TTTG-GGGTCAAAAT-GTAATTTTGGAAAAGTTTTAGGGTCAAAATATAATTTT-AAAAAGT
**
43982165 TTTGGGGTTGAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATATAATTTTAGAAAAGT
1 TTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATATAATTTTA-AAAAGT
* * * *
43982225 TTAGGGGTAAAAATGTAATTTTTGG-AAAG-TTTCGAGGTTAAAATATAATTTTCAAAAAGT
1 TTTGGGGTCAAAATGTAA-TTTTGGAAAAGTTTTAG-GGTCAAAATATAATTTT-AAAAAGT
* * *
43982285 TTTGGGGTCGAAATGTAATTTTAGAAAAGTTTTAGGGTCAAAATATAATTTTGGAAAAGT
1 TTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATATAATTTT-AAAAAGT
* * * * *
43982345 TTTAGGGTCAAAATATAATTTTGGAAAAGTTTAAGGGTCAAAATGTAATATTTAGAAAGT
1 TTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATATAAT-TTTAAAAAGT
* * * * *
43982405 TTTGGGGTCAAAATATAATTTT-CAGAAAGTTTTGGGGTCGAAATGTAATTTT
1 TTTGGGGTCAAAATGTAATTTTGGA-AAAGTTTTAGGGTCAAAATATAATTTT
43982457 TGGATAATTT
Statistics
Matches: 252, Mismatches: 30, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
59 27 0.11
60 211 0.84
61 14 0.06
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.38
Consensus pattern (59 bp):
TTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATATAATTTTAAAAAGT
Found at i:43982468 original size:90 final size:90
Alignment explanation
Indices: 43982102--43982470 Score: 415
Period size: 90 Copynumber: 4.1 Consensus size: 90
43982092 GGATTTAGGG
* * * *
43982102 AAGTTTGAGGGT-AAAATGGTAATTTTTG-AAAGTTTTGGGGTCAAAGTATAATTTTCAAAAAGT
1 AAGTTTAAGGGTCAAAAT-GTAATTTTAGAAAAGTTTTGGGGTCAAAATATAATTTTCAGAAAGT
** *
43982165 TTTGGGGTTGAAATGTAATTTTGGAA
65 TTTGGGGTCAAAATATAATTTTGGAA
* * * * * **
43982191 AAGTTTTAGGGTCAAAATATAATTTTAGAAAAGTTTAGGGGTAAAAATGTAATTTTTGGAAAGTT
1 AAGTTTAAGGGTCAAAATGTAATTTTAGAAAAGTTTTGGGGTCAAAATATAATTTTCAGAAAGTT
* * * **
43982256 TCGAGGTTAAAATATAATTTTCAAA
66 TTGGGGTCAAAATATAATTTTGGAA
** * * *
43982281 AAGTTTTGGGGTCGAAATGTAATTTTAGAAAAGTTTTAGGGTCAAAATATAATTTT-GGAAAAGT
1 AAGTTTAAGGGTCAAAATGTAATTTTAGAAAAGTTTTGGGGTCAAAATATAATTTTCAG-AAAGT
*
43982345 TTTAGGGTCAAAATATAATTTTGGAA
65 TTTGGGGTCAAAATATAATTTTGGAA
43982371 AAGTTTAAGGGTCAAAATGTAATATTTAG-AAAGTTTTGGGGTCAAAATATAATTTTCAGAAAGT
1 AAGTTTAAGGGTCAAAATGTAAT-TTTAGAAAAGTTTTGGGGTCAAAATATAATTTTCAGAAAGT
* * *
43982435 TTTGGGGTCGAAATGTAATTTTTGGAT
65 TTTGGGGTCAAAATATAA-TTTTGGAA
43982462 AA-TTTAAGG
1 AAGTTTAAGG
43982471 ACTTACAAAG
Statistics
Matches: 236, Mismatches: 38, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
89 21 0.09
90 200 0.85
91 15 0.06
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.37
Consensus pattern (90 bp):
AAGTTTAAGGGTCAAAATGTAATTTTAGAAAAGTTTTGGGGTCAAAATATAATTTTCAGAAAGTT
TTGGGGTCAAAATATAATTTTGGAA
Found at i:43984434 original size:25 final size:25
Alignment explanation
Indices: 43984396--43984474 Score: 95
Period size: 25 Copynumber: 3.0 Consensus size: 25
43984386 AATTTGTTTT
*
43984396 ATAATTTAAATTTAAGGTAAATTTAA
1 ATAA-TTAAATTTAAGATAAATTTAA
43984422 ATAATTAAATTTAAGATAAATTTAA
1 ATAATTAAATTTAAGATAAATTTAA
* * *
43984447 ATTCAAATAAATTTAAAATCAATTTAA
1 A-T-AATTAAATTTAAGATAAATTTAA
43984474 A
1 A
43984475 CTCTTAATTA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
25 21 0.45
26 5 0.11
27 21 0.45
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.39
Consensus pattern (25 bp):
ATAATTAAATTTAAGATAAATTTAA
Found at i:43984456 original size:16 final size:16
Alignment explanation
Indices: 43984413--43984468 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
43984403 AAATTTAAGG
*
43984413 TAAATTTAAAT-AA-T
1 TAAATTCAAATAAATT
*
43984427 TAAATTTAAGATAAATT
1 TAAATTCAA-ATAAATT
43984444 TAAATTCAAATAAATT
1 TAAATTCAAATAAATT
*
43984460 TAAAATCAA
1 TAAATTCAA
43984469 TTTAAACTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
14 9 0.24
15 2 0.05
16 17 0.46
17 9 0.24
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (16 bp):
TAAATTCAAATAAATT
Found at i:43984974 original size:68 final size:68
Alignment explanation
Indices: 43984864--43985466 Score: 1107
Period size: 68 Copynumber: 8.8 Consensus size: 68
43984854 TTATCCACTC
*
43984864 TACTTCAATTTCAAGAGATAAAGACGTGTTATCCACTCTACTTTAATTTCAAGAGGATGACGTTG
1 TACTTCAATTTC-AGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTG
43984929 CTCT
65 CTCT
43984933 TACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGC
1 TACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGC
43984998 TCT
66 TCT
* * *
43985001 TACTTTAATTTTAGAGATAAAGACGTGTTATCCATTCTACTTCAATTTCAAGAGGATGACGTTGC
1 TACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGC
43985066 TCT
66 TCT
43985069 TACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGC
1 TACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGC
43985134 TCT
66 TCT
*
43985137 TACTTCAATTTCAGAGATAAAGACGTGTTATCCATTCTACTTCAATTTCAAGAGGATGACGTTGC
1 TACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGC
*
43985202 TTT
66 TCT
*
43985205 TACTTCAATTTCAGAGATAAAGACGTGTTATCCATTCTACTTCAATTTCAAGAGGATGACGTTGC
1 TACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGC
43985270 TCT
66 TCT
43985273 TACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGC
1 TACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGC
43985338 TCT
66 TCT
43985341 TACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGC
1 TACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGC
43985406 TCT
66 TCT
* *
43985409 TACTTCAATTTCAGAGATAAAGACGTGATATCCAGCTTTACTTCAATTTCAAGAGGAT
1 TACTTCAATTTCAGAGATAAAGACGTGTTATCCA-CTCTACTTCAATTTCAAGAGGAT
43985467 AGGAAATAAT
Statistics
Matches: 520, Mismatches: 13, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
68 486 0.93
69 34 0.07
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (68 bp):
TACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGC
TCT
Found at i:43997270 original size:59 final size:57
Alignment explanation
Indices: 43997174--43997369 Score: 157
Period size: 59 Copynumber: 3.4 Consensus size: 57
43997164 TGGGTTTTTA
* *
43997174 GGGGTAAAACGGT-AATTTTGTG--AAATCG-GGGCTAAAAATGGAATTTGGAAAGTTT
1 GGGGTAAAATGGTAAATTTTG-GCAAAATCGAGGTC-AAAAATGGAATTTGGAAAGTTT
* *
43997229 GGGGAATAAAATGGTAAATTTTGGCAAAATCGAGGTCAAAAATGAAATTTTGGAAAGTTCA
1 GGGG--TAAAATGGTAAATTTTGGCAAAATCGAGGTCAAAAATGGAA-TTTGGAAAGTT-T
** * * ** * * * *
43997290 AAGGTAAAACGGTAAGTTTTGGTGAAATCGGGGTTAAAAATGGGATTTAGGGAAGTTT
1 GGGGTAAAATGGTAAATTTTGGCAAAATCGAGGTCAAAAATGGAATTT-GGAAAGTTT
*
43997348 AGGGGTAAAATGGTAATTTTTG
1 -GGGGTAAAATGGTAAATTTTG
43997370 AAAGTTTTGG
Statistics
Matches: 111, Mismatches: 20, Indels: 16
0.76 0.14 0.11
Matches are distributed among these distances:
55 4 0.04
57 9 0.08
58 10 0.09
59 72 0.65
60 14 0.13
61 2 0.02
ACGTcount: A:0.37, C:0.05, G:0.30, T:0.29
Consensus pattern (57 bp):
GGGGTAAAATGGTAAATTTTGGCAAAATCGAGGTCAAAAATGGAATTTGGAAAGTTT
Found at i:43997406 original size:30 final size:30
Alignment explanation
Indices: 43997342--43997699 Score: 325
Period size: 30 Copynumber: 12.0 Consensus size: 30
43997332 GGATTTAGGG
* * *
43997342 AAGTTTAGGGGT-AAAATGGTAATTTTTG-A
1 AAGTTTTGGGGTCAAAAT-ATAATTTTGGAA
* **
43997371 AAGTTTTGGGGTCAAAGTATAATTTTCAAA
1 AAGTTTTGGGGTCAAAATATAATTTTGGAA
* *
43997401 AAGTTTTGGGGTCGAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATATAATTTTGGAA
43997431 AAGTTTTGGGGTCAAAATATAATTTTGGAA
1 AAGTTTTGGGGTCAAAATATAATTTTGGAA
* *
43997461 AAGTTTAGGGGTC-AAATGTAATTTTTGG-A
1 AAGTTTTGGGGTCAAAATATAA-TTTTGGAA
* * *
43997490 AAGTTTCGGGGTTAAAATATAATTTT-TAGA
1 AAGTTTTGGGGTCAAAATATAATTTTGGA-A
* ** *
43997520 AAGTTTTGGGCTTGAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATATAATTTTGGAA
* *
43997550 AAGTTTTGGGGTTAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATATAATTTTGGAA
* * *
43997580 AAGTTGTAGGGTTAAAATATAATTTTGGAA
1 AAGTTTTGGGGTCAAAATATAATTTTGGAA
** * * * *
43997610 AAGTTTAAGGGTTAAAATGTAATATT-CAGA
1 AAGTTTTGGGGTCAAAATATAATTTTGGA-A
*
43997640 AAGTTTTGGGGTCAAAATATAATTTT-TAGA
1 AAGTTTTGGGGTCAAAATATAATTTTGGA-A
* * *
43997670 AAGTTTTAGGGTCGAAATGTAATTTCTGGA
1 AAGTTTTGGGGTCAAAATATAATTT-TGGA
43997700 CAATTTAGGG
Statistics
Matches: 276, Mismatches: 43, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
29 42 0.15
30 231 0.84
31 2 0.01
32 1 0.00
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (30 bp):
AAGTTTTGGGGTCAAAATATAATTTTGGAA
Found at i:43998819 original size:16 final size:16
Alignment explanation
Indices: 43998789--43998840 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
43998779 TTTTATTTTA
43998789 TATTATTATTA-TTAT
1 TATTATTATTAGTTAT
43998804 TATTATTATTAGTTAT
1 TATTATTATTAGTTAT
**
43998820 TATTATTAAAAGTTAT
1 TATTATTATTAGTTAT
43998836 TATTA
1 TATTA
43998841 CCATTAATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
15 11 0.32
16 23 0.68
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (16 bp):
TATTATTATTAGTTAT
Found at i:43998840 original size:3 final size:3
Alignment explanation
Indices: 43998781--43998827 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
43998771 GCCTTCTTTT
43998781 TTA TT- TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA GTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
43998825 TTA
1 TTA
43998828 AAAGTTATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:43999673 original size:6 final size:6
Alignment explanation
Indices: 43999657--43999768 Score: 101
Period size: 6 Copynumber: 19.0 Consensus size: 6
43999647 TTAAATTTGT
**
43999657 TTTATAA TTTAAA TTTAAA TTTAAA TTT-AA GGTAAA TTTAAA TTTAAA
1 TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
**
43999705 TTTAAA TTT-AA GGTAAA TTTAAA TAATTAAA TTTAAGA --TAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA TTTAA-A TTTAAA TTTAAA
*
43999753 TTCAAA --TAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
43999769 ATCAATTTAA
Statistics
Matches: 86, Mismatches: 10, Indels: 19
0.75 0.09 0.17
Matches are distributed among these distances:
4 4 0.05
5 9 0.10
6 62 0.72
7 5 0.06
8 6 0.07
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:43999694 original size:29 final size:28
Alignment explanation
Indices: 43999662--43999767 Score: 148
Period size: 29 Copynumber: 3.9 Consensus size: 28
43999652 TTTGTTTTAT
43999662 AATTTAAATTTAAATTTAAATTTAAGGTA
1 AATTTAAATTTAAA-TTAAATTTAAGGTA
43999691 AATTTAAATTTAAATTTAAATTTAAGGTA
1 AATTTAAATTTAAA-TTAAATTTAAGGTA
*
43999720 AATTTAAA--T-AATTAAATTTAAGATA
1 AATTTAAATTTAAATTAAATTTAAGGTA
*
43999745 AATTTAAATTCAAA-TAAATTTAA
1 AATTTAAATTTAAATTAAATTTAA
43999768 AATCAATTTA
Statistics
Matches: 72, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
25 21 0.29
26 2 0.03
27 10 0.14
28 2 0.03
29 37 0.51
ACGTcount: A:0.52, C:0.01, G:0.05, T:0.42
Consensus pattern (28 bp):
AATTTAAATTTAAATTAAATTTAAGGTA
Found at i:43999728 original size:23 final size:23
Alignment explanation
Indices: 43999666--43999709 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
43999656 TTTTATAATT
43999666 TAAATTTAAATTTAAATTTAAGG
1 TAAATTTAAATTTAAATTTAAGG
43999689 TAAATTTAAATTTAAATTTAA
1 TAAATTTAAATTTAAATTTAA
43999710 ATTTAAGGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (23 bp):
TAAATTTAAATTTAAATTTAAGG
Found at i:43999779 original size:17 final size:17
Alignment explanation
Indices: 43999657--43999768 Score: 95
Period size: 17 Copynumber: 6.4 Consensus size: 17
43999647 TTAAATTTGT
43999657 TTTATAATTTAAATTTAAA
1 TTTA-AATTTAAA-TTAAA
**
43999676 TTTAAATTTAAGGTAAA
1 TTTAAATTTAAATTAAA
43999693 TTTAAATTTAAATTTAAA
1 TTTAAATTTAAA-TTAAA
**
43999711 TTT-AAGGTAAATTTAAA
1 TTTAAATTTAAA-TTAAA
43999728 TAATTAAATTTAAGA-TAAA
1 T--TTAAATTTAA-ATTAAA
*
43999747 TTTAAATTCAAA-TAAA
1 TTTAAATTTAAATTAAA
43999763 TTTAAA
1 TTTAAA
43999769 ATCAATTTAA
Statistics
Matches: 79, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
16 11 0.14
17 37 0.47
18 14 0.18
19 11 0.14
20 5 0.06
21 1 0.01
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAATTAAA
Found at i:44003199 original size:133 final size:135
Alignment explanation
Indices: 44003038--44003309 Score: 476
Period size: 133 Copynumber: 2.0 Consensus size: 135
44003028 TTTTTTTTAT
* *
44003038 AATGTCATTTCATTTCTCTATTACTATAATTTAATTTTAATGTCTAAATTCATTTTTAATAAGGC
1 AATGTCATTTCATTTATCTATTACTATAATTTAATTTTAACGTCTAAATTCATTTTTAATAAGGC
44003103 AAAACTTTATT-AAATG-TTTTTTTAAGATAACGTTTGGTGGGAGATGTTTGATATGTCAATCTA
66 AAAACTTTATTAAAATGTTTTTTTTAAGATAACGTTTGGTGGGAGATGTTTGATATGTCAATCTA
44003166 TTGGC
131 TTGGC
*
44003171 AATGTCATTTCATTTATCTATTATTATAATTTAATTTTAACGTCTAAATTCATTTTTAATAAGGC
1 AATGTCATTTCATTTATCTATTACTATAATTTAATTTTAACGTCTAAATTCATTTTTAATAAGGC
* *
44003236 AAAACTTTATTAAAATGTTTTTTTTTAAGATAACGTTTGGTGGGAGATGTTTGATATTTTAATCT
66 AAAACTTTATTAAAATG-TTTTTTTTAAGATAACGTTTGGTGGGAGATGTTTGATATGTCAATCT
44003301 ATTGGC
130 ATTGGC
44003307 AAT
1 AAT
44003310 AGCTCCTTTT
Statistics
Matches: 131, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
133 73 0.56
134 5 0.04
136 53 0.40
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.47
Consensus pattern (135 bp):
AATGTCATTTCATTTATCTATTACTATAATTTAATTTTAACGTCTAAATTCATTTTTAATAAGGC
AAAACTTTATTAAAATGTTTTTTTTAAGATAACGTTTGGTGGGAGATGTTTGATATGTCAATCTA
TTGGC
Found at i:44008598 original size:97 final size:96
Alignment explanation
Indices: 44008361--44008837 Score: 523
Period size: 97 Copynumber: 4.9 Consensus size: 96
44008351 CAATCTTTTT
* * *
44008361 TAAGGTACAAGGTTCGCCGTTGCGGCTTCAAACTTTCCCTCACATCTCCATGGTACAAGATT-TA
1 TAAGGTACAAGGTTCGCCGTTACGGCTTCAACCTTTCCCTCGCATCTCCATGGTACAAGATTCT-
* *
44008425 TCGTTGCGGCTTGAATCTTTCCCATTATC-TTC
65 CCGTTGCGG-TTTAATCTTTCCCATTATCTTTC
* * * *
44008457 TAAGGTACAAGGTTCGTCGTTACGACTTCAACGTTTCCCTCGCATCTTCATGGTACAAGATTCTC
1 TAAGGTACAAGGTTCGCCGTTACGGCTTCAACCTTTCCCTCGCATCTCCATGGTACAAGATTCTC
* *
44008522 TGTTTCGGTTTCAATCTTTCCCATTATCTTTC
66 CGTTGCGGTTT-AATCTTTCCCATTATCTTTC
* * *
44008554 TAAGGTACAAGGTTCACCGTTACGGCTTCGACTTTTCCCTCGCATCTCCATGGTACAAGATTCGT
1 TAAGGTACAAGGTTCGCCGTTACGGCTTCAACCTTTCCCTCGCATCTCCATGGTACAAGATTC-T
* * * **
44008619 -CGTTACGGCTTCAATCCTTCATATTATCTTTC
65 CCGTTGCGG-TTTAATCTTTCCCATTATCTTTC
* * * * *
44008651 TAAGGTACAAGGCTCGCCGTTACGGCTTCGACCTTTCCCTCGCATCTTCGTGGTACAAGATTCAC
1 TAAGGTACAAGGTTCGCCGTTACGGCTTCAACCTTTCCCTCGCATCTCCATGGTACAAGATTCTC
*
44008716 CGTTGCGGCTTTAATCTTTCCTATTAT-TCTTC
66 CGTTGCGG-TTTAATCTTTCCCATTATCT-TTC
* * * ** * *
44008748 TAAAGTATAAGGTTCACTATTGCGGCTTCAACCTTTCCCTC-CATATCTCCATGGTACATGATTC
1 TAAGGTACAAGGTTCGCCGTTACGGCTTCAACCTTTCCCTCGC--ATCTCCATGGTACAAGATTC
* *
44008812 GCCATTGCGGCTTTAATCTTTCCCAT
64 TCCGTTGCGG-TTTAATCTTTCCCAT
44008838 CAAACCTATA
Statistics
Matches: 325, Mismatches: 47, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
95 2 0.01
96 79 0.24
97 201 0.62
98 43 0.13
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.36
Consensus pattern (96 bp):
TAAGGTACAAGGTTCGCCGTTACGGCTTCAACCTTTCCCTCGCATCTCCATGGTACAAGATTCTC
CGTTGCGGTTTAATCTTTCCCATTATCTTTC
Found at i:44008719 original size:48 final size:47
Alignment explanation
Indices: 44008364--44008736 Score: 218
Period size: 48 Copynumber: 7.7 Consensus size: 47
44008354 TCTTTTTTAA
* * * * *
44008364 GGTACAAGGTTCGCCGTTGCGGCTTCAAACTTTCCCTCACATCTCCAT
1 GGTACAAGATTCGCCGTTACGGCTTCAACCTTTCCCTCGCATCTTC-T
*** * * * *
44008412 GGTACAAGATTTATCGTTGCGGCTTGAATCTTTCCCAT--TATCTTCT
1 GGTACAAGATTCGCCGTTACGGCTTCAACCTTTCCC-TCGCATCTTCT
* * * *
44008458 AAGGTACAAGGTTCGTCGTTACGACTTCAACGTTTCCCTCGCATCTTCAT
1 --GGTACAAGATTCGCCGTTACGGCTTCAACCTTTCCCTCGCATCTTC-T
* * * * * *
44008508 GGTACAAGATTCTCTGTTTCGGTTTCAATCTTTCCCAT--TATCTTTCT
1 GGTACAAGATTCGCCGTTACGGCTTCAACCTTTCCC-TCGCATC-TTCT
* * * * *
44008555 AAGGTACAAGGTTCACCGTTACGGCTTCGACTTTTCCCTCGCATCTCCAT
1 --GGTACAAGATTCGCCGTTACGGCTTCAACCTTTCCCTCGCATCTTC-T
* * ***
44008605 GGTACAAGATTCGTCGTTACGGCTTCAATCC-TT-CATATTATCTTTCT
1 GGTACAAGATTCGCCGTTACGGCTTCAA-CCTTTCCCTCGCATC-TTCT
** *
44008652 AAGGTACAAGGCTCGCCGTTACGGCTTCGACCTTTCCCTCGCATCTTCGT
1 --GGTACAAGATTCGCCGTTACGGCTTCAACCTTTCCCTCGCATCTTC-T
* * * *
44008702 GGTACAAGATTCACCGTTGCGGCTTTAATCTTTCC
1 GGTACAAGATTCGCCGTTACGGCTTCAACCTTTCC
44008737 TATTATTCTT
Statistics
Matches: 243, Mismatches: 62, Indels: 40
0.70 0.18 0.12
Matches are distributed among these distances:
46 1 0.00
47 16 0.07
48 147 0.60
49 68 0.28
50 11 0.05
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (47 bp):
GGTACAAGATTCGCCGTTACGGCTTCAACCTTTCCCTCGCATCTTCT
Found at i:44016155 original size:51 final size:51
Alignment explanation
Indices: 44016066--44016166 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
44016056 AAAGGAGAGC
* * * *
44016066 CTGACATGATTCATTCTGATTCTGTATAGCTGATGAGCTTAAATGTTCTGT
1 CTGACATGATTCATTCTGATCCTGAATAGCTGACGAGCTTAAACGTTCTGT
* * * *
44016117 CTGACATGATTTATTTTGATCCTGAATAGTTGGCGAGCTTAAACGTTCTG
1 CTGACATGATTCATTCTGATCCTGAATAGCTGACGAGCTTAAACGTTCTG
44016167 CAATCACGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (51 bp):
CTGACATGATTCATTCTGATCCTGAATAGCTGACGAGCTTAAACGTTCTGT
Found at i:44016317 original size:25 final size:25
Alignment explanation
Indices: 44016285--44016335 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
44016275 GGTTAAATGA
*
44016285 GAATGATTCTGAATTATTGATTTAT
1 GAATGATTCTAAATTATTGATTTAT
44016310 GAATGATTCTAAATTATTGATTTAT
1 GAATGATTCTAAATTATTGATTTAT
44016335 G
1 G
44016336 TTTCTTGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (25 bp):
GAATGATTCTAAATTATTGATTTAT
Found at i:44020702 original size:29 final size:29
Alignment explanation
Indices: 44020669--44020725 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
44020659 AAATGGGACA
44020669 ATCAGATCTAATTCGAGGAGAAGTTAAGT
1 ATCAGATCTAATTCGAGGAGAAGTTAAGT
*
44020698 ATCAGTTCTAATTCGAGGAGAAGTTAAG
1 ATCAGATCTAATTCGAGGAGAAGTTAAG
44020726 GATTTGGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.28
Consensus pattern (29 bp):
ATCAGATCTAATTCGAGGAGAAGTTAAGT
Found at i:44026913 original size:13 final size:14
Alignment explanation
Indices: 44026895--44026926 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
44026885 ATATTTTGAT
44026895 ATAAATAAAA-AAA
1 ATAAATAAAAGAAA
44026908 ATAAATAAAAGAAA
1 ATAAATAAAAGAAA
44026922 ATAAA
1 ATAAA
44026927 AATGAGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (14 bp):
ATAAATAAAAGAAA
Found at i:44028414 original size:15 final size:15
Alignment explanation
Indices: 44028394--44028424 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
44028384 TAAGAGAACA
44028394 TGTCATAATTTATGG
1 TGTCATAATTTATGG
*
44028409 TGTCATAATTTTTGG
1 TGTCATAATTTATGG
44028424 T
1 T
44028425 TGAGTATTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.06, G:0.19, T:0.52
Consensus pattern (15 bp):
TGTCATAATTTATGG
Found at i:44038846 original size:22 final size:22
Alignment explanation
Indices: 44038821--44038865 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
44038811 AAGCACCAAC
* *
44038821 ATTACCGTCGCACATCACCGTT
1 ATTACCGCCACACATCACCGTT
*
44038843 ATTACTGCCACACATCACCGTT
1 ATTACCGCCACACATCACCGTT
44038865 A
1 A
44038866 CTGTTACACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.36, G:0.11, T:0.27
Consensus pattern (22 bp):
ATTACCGCCACACATCACCGTT
Found at i:44040382 original size:24 final size:24
Alignment explanation
Indices: 44040315--44040373 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
44040305 TTAAATTCTG
44040315 TCTGGGCTCGTAAGAGCTAACCAT
1 TCTGGGCTCGTAAGAGCTAACCAT
* *
44040339 TCTGGGCTCATAAGAGCTAATCAT
1 TCTGGGCTCGTAAGAGCTAACCAT
44040363 TCTGGGCTCGT
1 TCTGGGCTCGT
44040374 GTGGGCTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (24 bp):
TCTGGGCTCGTAAGAGCTAACCAT
Found at i:44053520 original size:18 final size:18
Alignment explanation
Indices: 44053486--44053520 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
44053476 TTTTAACTAG
*
44053486 TTTATTTTTTTTATTTTC
1 TTTATTTTGTTTATTTTC
*
44053504 TTTATTTTGTTTCTTTT
1 TTTATTTTGTTTATTTT
44053521 TAGATGTAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.06, G:0.03, T:0.83
Consensus pattern (18 bp):
TTTATTTTGTTTATTTTC
Found at i:44053588 original size:62 final size:62
Alignment explanation
Indices: 44053513--44053698 Score: 354
Period size: 62 Copynumber: 3.0 Consensus size: 62
44053503 CTTTATTTTG
44053513 TTTCTTTTTAGATGTAAGTTTATAGTGAATTACCTGGATTTGAGGCTTTATAGTGAAAAATC
1 TTTCTTTTTAGATGTAAGTTTATAGTGAATTACCTGGATTTGAGGCTTTATAGTGAAAAATC
* *
44053575 TTTTTTTTTAGATGTAAGTTTATAGTGAATTACCTGAATTTGAGGCTTTATAGTGAAAAATC
1 TTTCTTTTTAGATGTAAGTTTATAGTGAATTACCTGGATTTGAGGCTTTATAGTGAAAAATC
44053637 TTTCTTTTTAGATGTAAGTTTATAGTGAATTACCTGGATTTGAGGCTTTATAGTGAAAAATC
1 TTTCTTTTTAGATGTAAGTTTATAGTGAATTACCTGGATTTGAGGCTTTATAGTGAAAAATC
44053699 AATTTATCTT
Statistics
Matches: 120, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 120 1.00
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.44
Consensus pattern (62 bp):
TTTCTTTTTAGATGTAAGTTTATAGTGAATTACCTGGATTTGAGGCTTTATAGTGAAAAATC
Found at i:44053602 original size:34 final size:34
Alignment explanation
Indices: 44053559--44053665 Score: 93
Period size: 34 Copynumber: 3.3 Consensus size: 34
44053549 GATTTGAGGC
*
44053559 TTTATAGTGAAAAATCTTTTTTTTTAGATGTAAG
1 TTTATAGTGAAAAATCTTTCTTTTTAGATGTAAG
** * ***
44053593 TTTATAGTGAATTA-C-CTGAATTT-GA-G---G
1 TTTATAGTGAAAAATCTTTCTTTTTAGATGTAAG
44053620 CTTTATAGTGAAAAATCTTTCTTTTTAGATGTAAG
1 -TTTATAGTGAAAAATCTTTCTTTTTAGATGTAAG
44053655 TTTATAGTGAA
1 TTTATAGTGAA
44053666 TTACCTGGAT
Statistics
Matches: 53, Mismatches: 12, Indels: 16
0.65 0.15 0.20
Matches are distributed among these distances:
27 1 0.02
28 12 0.23
29 1 0.02
30 5 0.09
31 4 0.08
32 5 0.09
33 1 0.02
34 23 0.43
35 1 0.02
ACGTcount: A:0.32, C:0.06, G:0.17, T:0.46
Consensus pattern (34 bp):
TTTATAGTGAAAAATCTTTCTTTTTAGATGTAAG
Found at i:44053912 original size:28 final size:25
Alignment explanation
Indices: 44053881--44053931 Score: 75
Period size: 28 Copynumber: 1.9 Consensus size: 25
44053871 CAATTAGTTT
44053881 TAGTTTTTTCTAAAAAGATGAAAAATTA
1 TAGTTTTTTC-AAAAA-AT-AAAAATTA
44053909 TAGTTTTTTCAAAAAATAAAAAT
1 TAGTTTTTTCAAAAAATAAAAAT
44053932 AATTCTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 6 0.26
26 2 0.09
27 5 0.22
28 10 0.43
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (25 bp):
TAGTTTTTTCAAAAAATAAAAATTA
Found at i:44057275 original size:30 final size:30
Alignment explanation
Indices: 44057222--44057386 Score: 181
Period size: 30 Copynumber: 5.6 Consensus size: 30
44057212 AAAATTCAAA
* *
44057222 TTTGA-CCCTTAACTTTCT-AAAATTGCAT
1 TTTGACCCCTAAACTTTCTAAAAATTTCAT
* * * *
44057250 TTTGGCCCCCAAACTTTTTGAAAATTTCAT
1 TTTGACCCCTAAACTTTCTAAAAATTTCAT
* *
44057280 TTTAACCCTTAAACTTTCTAAAAATTTCAT
1 TTTGACCCCTAAACTTTCTAAAAATTTCAT
*
44057310 TTTGACCCCTAAACTTTCTAAAAATTACAT
1 TTTGACCCCTAAACTTTCTAAAAATTTCAT
* * * *
44057340 TTTGGCCCCCAAACTTTTTAAAAACTTCAT
1 TTTGACCCCTAAACTTTCTAAAAATTTCAT
* *
44057370 TTTGACCTCTTAACTTT
1 TTTGACCCCTAAACTTT
44057387 TTGAAAACTA
Statistics
Matches: 112, Mismatches: 23, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
28 4 0.04
29 10 0.09
30 98 0.88
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.41
Consensus pattern (30 bp):
TTTGACCCCTAAACTTTCTAAAAATTTCAT
Found at i:44057387 original size:30 final size:29
Alignment explanation
Indices: 44057201--44057419 Score: 174
Period size: 30 Copynumber: 7.4 Consensus size: 29
44057191 TTTTAACCTT
* *
44057201 TAAATTTTTTAAAAATTCAAATTTGA-CCC
1 TAAACTTTTTAAAAATTC-ATTTTGACCCC
* * *
44057230 TTAACTTTCT-AAAATTGCATTTTGGCCCC
1 TAAACTTTTTAAAAATT-CATTTTGACCCC
* * * *
44057259 CAAACTTTTTGAAAATTTCATTTTAACCCT
1 TAAACTTTTT-AAAAATTCATTTTGACCCC
*
44057289 TAAACTTTCTAAAAATTTCATTTTGACCCC
1 TAAACTTTTTAAAAA-TTCATTTTGACCCC
* *
44057319 TAAACTTTCTAAAAATTACATTTTGGCCCC
1 TAAACTTTTTAAAAATT-CATTTTGACCCC
* *
44057349 CAAACTTTTTAAAAACTTCATTTTGACCTC
1 TAAACTTTTTAAAAA-TTCATTTTGACCCC
* * * * * *
44057379 TTAACTTTTTGAAAACTACACTTCGA-TCC
1 TAAACTTTTT-AAAAATTCATTTTGACCCC
44057408 TAAACTTTTTAA
1 TAAACTTTTTAA
44057420 CATTTTGATT
Statistics
Matches: 151, Mismatches: 31, Indels: 17
0.76 0.16 0.09
Matches are distributed among these distances:
28 13 0.09
29 34 0.23
30 93 0.62
31 11 0.07
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (29 bp):
TAAACTTTTTAAAAATTCATTTTGACCCC
Found at i:44063909 original size:27 final size:27
Alignment explanation
Indices: 44063877--44063952 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
44063867 TCTCATTCCT
* ***
44063877 ATTTTACCCCCGATAAATTTTTTGTTG
1 ATTTTACCCCCGATAAAATTTTTGACA
*
44063904 ATTTTA-CCCCTAGTAAAATTTTTGACA
1 ATTTTACCCCCGA-TAAAATTTTTGACA
44063931 ATTTTACCCCCTGATAAAATTT
1 ATTTTACCCCC-GATAAAATTT
44063953 CGAGAAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
26 5 0.12
27 22 0.55
28 12 0.30
29 1 0.03
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.43
Consensus pattern (27 bp):
ATTTTACCCCCGATAAAATTTTTGACA
Found at i:44065632 original size:6 final size:6
Alignment explanation
Indices: 44065607--44065651 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
44065597 ACAATTCATA
* * *
44065607 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
44065652 ATTTTGATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (6 bp):
TCACTT
Found at i:44065803 original size:15 final size:15
Alignment explanation
Indices: 44065771--44065810 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
44065761 TCTTTATAAC
44065771 CACATA-ATATTTCA
1 CACATATATATTTCA
* *
44065785 CACATATATTTTTCT
1 CACATATATATTTCA
44065800 CACATATATAT
1 CACATATATAT
44065811 CATTATATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (15 bp):
CACATATATATTTCA
Found at i:44070101 original size:16 final size:16
Alignment explanation
Indices: 44070077--44070121 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
44070067 TCTGACTTGG
44070077 TTTGGGTTTGGTTCAA
1 TTTGGGTTTGGTTCAA
* *
44070093 TTTGAGTTTGGGTCAA
1 TTTGGGTTTGGTTCAA
*
44070109 CTTGGGTTTGGTT
1 TTTGGGTTTGGTT
44070122 TTTTAAAAGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.11, C:0.07, G:0.33, T:0.49
Consensus pattern (16 bp):
TTTGGGTTTGGTTCAA
Found at i:44071437 original size:16 final size:16
Alignment explanation
Indices: 44071414--44071469 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
44071404 CGTTTGGTTC
44071414 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* *
44071430 GGTGTAATAGAATAGA
1 GCTGTAATGGAATAGA
*
44071446 ACTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
44071462 GCTGTAAT
1 GCTGTAAT
44071470 CAGTAATTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.39, C:0.05, G:0.29, T:0.27
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:44071734 original size:15 final size:15
Alignment explanation
Indices: 44071722--44071759 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
44071712 AATTTAATAA
44071722 AATAATATGTAATTT
1 AATAATATGTAATTT
44071737 AATAATATGTAATTT
1 AATAATATGTAATTT
44071752 AATAATAT
1 AATAATAT
44071760 TTTTAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (15 bp):
AATAATATGTAATTT
Found at i:44071764 original size:12 final size:14
Alignment explanation
Indices: 44071722--44071767 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
44071712 AATTTAATAA
44071722 AATAATATGTAATTT
1 AATAATATGT-ATTT
44071737 AATAATATGTAATTT
1 AATAATATGT-ATTT
44071752 AATAATAT-T-TTT
1 AATAATATGTATTT
44071764 AATA
1 AATA
44071768 TAATTATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.23
14 1 0.03
15 23 0.74
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (14 bp):
AATAATATGTATTT
Found at i:44071821 original size:23 final size:23
Alignment explanation
Indices: 44071773--44071832 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 23
44071763 TAATATAATT
*
44071773 ATTATTAAAATATGAATTAGTAAAA
1 ATTA-TAATATAT-AATTAGTAAAA
44071798 ATTATAATATATAATTA-TAGAAA
1 ATTATAATATATAATTAGTA-AAA
44071821 A--ATAATATATAA
1 ATTATAATATATAA
44071833 CCTATTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 11 0.33
22 2 0.06
23 9 0.27
24 7 0.21
25 4 0.12
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (23 bp):
ATTATAATATATAATTAGTAAAA
Found at i:44076619 original size:26 final size:26
Alignment explanation
Indices: 44076580--44076635 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
44076570 CATTAACTAT
44076580 ATCTGGATCGTAGGCCTATCCTTTAC
1 ATCTGGATCGTAGGCCTATCCTTTAC
*
44076606 ATCTGGATCTTAGGCCTATCCTTTAC
1 ATCTGGATCGTAGGCCTATCCTTTAC
44076632 ATCT
1 ATCT
44076636 TCCTCCTGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.38
Consensus pattern (26 bp):
ATCTGGATCGTAGGCCTATCCTTTAC
Found at i:44077489 original size:13 final size:15
Alignment explanation
Indices: 44077450--44077489 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
44077440 AGAAAAAGGC
44077450 CAAAACAGAGAGTAT
1 CAAAACAGAGAGTAT
44077465 CAAAACAGAGAGTAT
1 CAAAACAGAGAGTAT
*
44077480 CAAAATAGAG
1 CAAAACAGAG
44077490 GGAGAGCTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.55, C:0.12, G:0.20, T:0.12
Consensus pattern (15 bp):
CAAAACAGAGAGTAT
Done.