Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold4
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: 5986281
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.33
Warning! 213817 characters in sequence are not A, C, G, or T
File 29 of 31
Found at i:5644173 original size:22 final size:23
Alignment explanation
Indices: 5644148--5644194 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
5644138 ATTTATAAAT
5644148 AAATTTATTT-ATAAATCATTTA
1 AAATTTATTTAATAAATCATTTA
**
5644170 AAATTTATTTAATTCATCATTTA
1 AAATTTATTTAATAAATCATTTA
5644193 AA
1 AA
5644195 CTCGATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (23 bp):
AAATTTATTTAATAAATCATTTA
Found at i:5644748 original size:9 final size:10
Alignment explanation
Indices: 5644725--5644897 Score: 60
Period size: 11 Copynumber: 17.0 Consensus size: 10
5644715 TGTATTTGTG
5644725 TATTTATATAA
1 TATTTATAT-A
5644736 TATTTATAT-
1 TATTTATATA
5644745 TATTT-T-TA
1 TATTTATATA
* * *
5644753 TGTTAAAATTA
1 TATTTATA-TA
5644764 TATTTATATA
1 TATTTATATA
*
5644774 AATTT-TAATA
1 TATTTAT-ATA
* *
5644784 TATTAATAAA
1 TATTTATATA
5644794 TTATATTATATAA
1 -TAT-TTATAT-A
*
5644807 AATTTA-ATA
1 TATTTATATA
*
5644816 TATTAATAATTTA
1 TATT--T-ATATA
*
5644829 TAGTTTATAAA
1 TA-TTTATATA
5644840 T-TTTA-ATA
1 TATTTATATA
5644848 TA-TT-TATA
1 TATTTATATA
5644856 TATTTATAT-
1 TATTTATATA
5644865 TATTTTATATTA
1 TA-TTTATA-TA
* *
5644877 TATTTATTTT
1 TATTTATATA
5644887 TATATTATATA
1 TAT-TTATATA
5644898 ATTATATTTT
Statistics
Matches: 118, Mismatches: 22, Indels: 44
0.64 0.12 0.24
Matches are distributed among these distances:
7 1 0.01
8 14 0.12
9 18 0.15
10 29 0.25
11 39 0.33
12 10 0.08
13 5 0.04
14 2 0.02
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (10 bp):
TATTTATATA
Found at i:5644809 original size:15 final size:16
Alignment explanation
Indices: 5644758--5644810 Score: 56
Period size: 15 Copynumber: 3.3 Consensus size: 16
5644748 TTTTATGTTA
5644758 AAATTATATT-TATAT
1 AAATTATATTATATAT
* *
5644773 AAATTTTAATATATTAAT
1 AAATTATATTATA-T-AT
5644791 AAATTATATTATATA-
1 AAATTATATTATATAT
5644806 AAATT
1 AAATT
5644811 TAATATATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
15 13 0.42
16 3 0.10
17 2 0.06
18 13 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAATTATATTATATAT
Found at i:5644813 original size:32 final size:33
Alignment explanation
Indices: 5644758--5644851 Score: 147
Period size: 32 Copynumber: 2.9 Consensus size: 33
5644748 TTTTATGTTA
*
5644758 AAATTATATTTATATAAATTTTAATATATTAAT
1 AAATTATAGTTATATAAATTTTAATATATTAAT
*
5644791 AAATTATA-TTATATAAAATTTAATATATTAAT
1 AAATTATAGTTATATAAATTTTAATATATTAAT
*
5644823 AATTTATAGTT-TATAAATTTTAATATATT
1 AAATTATAGTTATATAAATTTTAATATATT
5644852 TATATATTTA
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 47 0.82
33 10 0.18
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (33 bp):
AAATTATAGTTATATAAATTTTAATATATTAAT
Found at i:5644828 original size:16 final size:16
Alignment explanation
Indices: 5644777--5644828 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
5644767 TTATATAAAT
5644777 TTTAATATATTAATAA
1 TTTAATATATTAATAA
*
5644793 ATT-ATATTATATAA-AA
1 TTTAATA-TAT-TAATAA
5644809 TTTAATATATTAATAA
1 TTTAATATATTAATAA
5644825 TTTA
1 TTTA
5644829 TAGTTTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
15 6 0.20
16 18 0.60
17 6 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTAATATATTAATAA
Found at i:5644855 original size:18 final size:18
Alignment explanation
Indices: 5644770--5644873 Score: 73
Period size: 18 Copynumber: 6.2 Consensus size: 18
5644760 ATTATATTTA
5644770 TATAAATTTTAATATATT
1 TATAAATTTTAATATATT
* *
5644788 AATAAA--TT-ATAT-TA
1 TATAAATTTTAATATATT
*
5644802 TATAAAATTTAATATATT
1 TATAAATTTTAATATATT
* *
5644820 AAT-AA-TTT-ATA-GTT
1 TATAAATTTTAATATATT
5644834 TATAAATTTTAATATATT
1 TATAAATTTTAATATATT
* *
5644852 TATATATTTATATTAT-TT
1 TATAAATTT-TAATATATT
5644870 TATA
1 TATA
5644874 TTATATTTAT
Statistics
Matches: 67, Mismatches: 10, Indels: 18
0.71 0.11 0.19
Matches are distributed among these distances:
14 10 0.15
15 9 0.13
16 10 0.15
17 9 0.13
18 24 0.36
19 5 0.07
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (18 bp):
TATAAATTTTAATATATT
Found at i:5644868 original size:17 final size:16
Alignment explanation
Indices: 5644848--5644902 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 16
5644838 AATTTTAATA
5644848 TATTTATATATTTATAT
1 TATTT-TATATTTATAT
5644865 TATTTTATA-TTATATT
1 TATTTTATATTTATA-T
5644881 TATTTTTATATTATATAAT
1 TA-TTTTATATT-TAT-AT
5644900 TAT
1 TAT
5644903 ATTTTTTCGA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
15 5 0.15
16 7 0.21
17 12 0.36
18 2 0.06
19 6 0.18
20 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTTATATTTATAT
Found at i:5644869 original size:27 final size:26
Alignment explanation
Indices: 5644818--5644894 Score: 88
Period size: 27 Copynumber: 3.0 Consensus size: 26
5644808 ATTTAATATA
* *
5644818 TTAATA-ATTTATAGTTTATA-AATT
1 TTAATATATTTATATTTTATATTATT
5644842 TTAATATATTTATATATTTATATTATT
1 TTAATATATTTATAT-TTTATATTATT
5644869 TTATATTATATTTAT-TTTTATATTAT
1 TTA-A-TATATTTATATTTTATATTAT
5644895 ATAATTATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
24 6 0.13
25 7 0.15
26 6 0.13
27 16 0.35
28 2 0.04
29 9 0.20
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (26 bp):
TTAATATATTTATATTTTATATTATT
Found at i:5646373 original size:21 final size:20
Alignment explanation
Indices: 5646339--5646382 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 20
5646329 AATATTTCAT
5646339 TATTAAAAATTAAATTAAAATA
1 TATTAAAAATTAAA--AAAATA
5646361 TATTAAAAA-TAAAAAAATA
1 TATTAAAAATTAAAAAAATA
5646380 TAT
1 TAT
5646383 GAATGGGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.41
21 4 0.18
22 9 0.41
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TATTAAAAATTAAAAAAATA
Found at i:5660711 original size:5 final size:5
Alignment explanation
Indices: 5660701--5660735 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
5660691 CTGCAGATCC
5660701 CCTAG CCTAG CCTAG CCTAG CCTAG CCTAG CCTAG
1 CCTAG CCTAG CCTAG CCTAG CCTAG CCTAG CCTAG
5660736 TCTATGAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.20, C:0.40, G:0.20, T:0.20
Consensus pattern (5 bp):
CCTAG
Found at i:5666459 original size:198 final size:198
Alignment explanation
Indices: 5666089--5666491 Score: 655
Period size: 198 Copynumber: 2.0 Consensus size: 198
5666079 ATTTGAGCTT
*
5666089 AACTCTACTCTTCTGTCTCAGCATTAATATTACATTCTACCTGTGTAGATATATTTGTATGGGTT
1 AACTCTACTCCTCTGTCTCAGCATTAATATTACATTCTACCTGTGTAGATATATTTGTATGGGTT
* * * * *
5666154 GATTTTTTTATTATTTTTTTATAGTAATCATTATTATTTACATATTTAAAATTTTAAATACGTGT
66 GATTTTTTTATAATTTTTTTATAATAATCATCATTATTTACATAGTTAAAATTTTAAATACGTAT
* * *
5666219 AAAATTTAATTATAAATTATAAAATTTGGTAACAGAAAAAAAAGGAAACTAAACCTATTTTTGAC
131 AAAATTTAAATATAAATTATAAAATTTAGTAACAGAAAAAAAAGAAAACTAAACCTATTTTTGAC
5666284 ATC
196 ATC
5666287 AACTCTACTCCTCTGTCTCAGCATTAATATTACATTCTACCTGTGTAGATATATTTGTATGGGTT
1 AACTCTACTCCTCTGTCTCAGCATTAATATTACATTCTACCTGTGTAGATATATTTGTATGGGTT
* *
5666352 GATTTTTTTA-AATTTTTTCATATAATAATCATCATTATTTACCTAGTTAAAATTTTAAATATGT
66 GATTTTTTTATAATTTTTT--TATAATAATCATCATTATTTACATAGTTAAAATTTTAAATACGT
*
5666416 ATAAAATTTAAATATAAATTATAAAATTTATTAACAGAAAAAAAAAAGAAAACTAAACCTATTTT
129 ATAAAATTTAAATATAAATTATAAAATTTAGTAACAG--AAAAAAAAGAAAACTAAACCTATTTT
5666481 TGACATC
192 TGACATC
5666488 AACT
1 AACT
5666492 TTCTTCGTCA
Statistics
Matches: 189, Mismatches: 12, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
197 7 0.04
198 74 0.39
199 72 0.38
201 36 0.19
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.42
Consensus pattern (198 bp):
AACTCTACTCCTCTGTCTCAGCATTAATATTACATTCTACCTGTGTAGATATATTTGTATGGGTT
GATTTTTTTATAATTTTTTTATAATAATCATCATTATTTACATAGTTAAAATTTTAAATACGTAT
AAAATTTAAATATAAATTATAAAATTTAGTAACAGAAAAAAAAGAAAACTAAACCTATTTTTGAC
ATC
Found at i:5666611 original size:20 final size:21
Alignment explanation
Indices: 5666574--5666632 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
5666564 CTAATAGTTT
* *
5666574 ATATATT-TATTTATTATTTT
1 ATATATTATAATTATTATTTA
*
5666594 TTATATTATAATTA-TATTTA
1 ATATATTATAATTATTATTTA
*
5666614 ATATATTATATATTTTTAT
1 ATATATTATA-ATTATTAT
5666633 AAATTTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 20 0.65
21 8 0.26
22 3 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATATATTATAATTATTATTTA
Found at i:5666611 original size:27 final size:27
Alignment explanation
Indices: 5666572--5666627 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
5666562 ATCTAATAGT
* * *
5666572 TTATATATTTATTTATTATTTTTTATA
1 TTATATATTTATTTAATATATTATATA
5666599 TTATA-ATTATATTTAATATATTATATA
1 TTATATATT-TATTTAATATATTATATA
5666626 TT
1 TT
5666628 TTTATAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 3 0.12
27 22 0.88
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (27 bp):
TTATATATTTATTTAATATATTATATA
Found at i:5666631 original size:18 final size:17
Alignment explanation
Indices: 5666584--5666666 Score: 52
Period size: 17 Copynumber: 5.0 Consensus size: 17
5666574 ATATATTTAT
5666584 TTAT-TATTTTT-TATA
1 TTATATATTTTTATATA
*
5666599 TTATAATTATATTTAATATA
1 TTAT-A-TAT-TTTTATATA
*
5666619 TTATATATTTTTATAAA
1 TTATATATTTTTATATA
*
5666636 TTTTA-ATTTATTA-ATA
1 TTATATATTT-TTATATA
*
5666652 TT-T-TATTTTAATATA
1 TTATATATTTTTATATA
5666667 AATTTTAACA
Statistics
Matches: 54, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
14 2 0.04
15 12 0.22
16 8 0.15
17 14 0.26
18 6 0.11
19 4 0.07
20 8 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTATATATTTTTATATA
Found at i:5666673 original size:17 final size:16
Alignment explanation
Indices: 5666625--5666674 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
5666615 TATATTATAT
*
5666625 ATTTTTATAAATTTTA
1 ATTTATATAAATTTTA
5666641 ATTTAT-TAATATTTTA
1 ATTTATATAA-ATTTTA
*
5666657 TTTTAATATAAATTTTA
1 ATTT-ATATAAATTTTA
5666674 A
1 A
5666675 CATATTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 3 0.11
16 14 0.50
17 8 0.29
18 3 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTATATAAATTTTA
Found at i:5666700 original size:19 final size:19
Alignment explanation
Indices: 5666676--5666712 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5666666 AAATTTTAAC
*
5666676 ATATTTTTATATTTATATT
1 ATATTTTTATATTGATATT
5666695 ATATTTTTATATTGATAT
1 ATATTTTTATATTGATAT
5666713 CAAGTTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
ATATTTTTATATTGATATT
Found at i:5667056 original size:26 final size:26
Alignment explanation
Indices: 5666995--5667056 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 26
5666985 AAATAGTAAT
*
5666995 AAATTTAATGCCTTTTTTTATTAAATA
1 AAATATAATGCC-TTTTTTATTAAATA
*
5667022 AAATTTAATGCC-TTTTTA-TAAATGA
1 AAATATAATGCCTTTTTTATTAAAT-A
5667047 ACAATATAAT
1 A-AATATAAT
5667057 AAGCATTATC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
24 5 0.16
25 8 0.25
26 7 0.22
27 12 0.38
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (26 bp):
AAATATAATGCCTTTTTTATTAAATA
Found at i:5667396 original size:19 final size:17
Alignment explanation
Indices: 5667371--5667419 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 17
5667361 ACTTGTAAAA
5667371 AATTTTAAATATTTTATT
1 AATTTTAAATATTTT-TT
*
5667389 ACATTTTACATTAATTTTTT
1 A-ATTTTA-AAT-ATTTTTT
5667409 AATTTTAAATA
1 AATTTTAAATA
5667420 AATATAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
17 1 0.04
18 3 0.12
19 12 0.46
20 5 0.19
21 5 0.19
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (17 bp):
AATTTTAAATATTTTTT
Found at i:5669392 original size:26 final size:28
Alignment explanation
Indices: 5669345--5669398 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 28
5669335 TTTCTTCTAA
* *
5669345 TTAAAAAATTAATTTATATAATTATTTT
1 TTAAAAAATTAATATATATAATAATTTT
*
5669373 TTAAAAAA-TAA-ATATTTAATAATTTT
1 TTAAAAAATTAATATATATAATAATTTT
5669399 AAATTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 12 0.52
27 3 0.13
28 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
TTAAAAAATTAATATATATAATAATTTT
Found at i:5675144 original size:21 final size:20
Alignment explanation
Indices: 5675118--5675163 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
5675108 TATTGAAGAT
*
5675118 AAAAAATAGAAAAAAATGAAA
1 AAAAAAGAGAAAAAAA-GAAA
**
5675139 AAAAAAGAGAGGAAAAGAAA
1 AAAAAAGAGAAAAAAAGAAA
5675159 AAAAA
1 AAAAA
5675164 TGAAGGAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.04
Consensus pattern (20 bp):
AAAAAAGAGAAAAAAAGAAA
Found at i:5675170 original size:19 final size:21
Alignment explanation
Indices: 5675130--5675171 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
5675120 AAAATAGAAA
5675130 AAAATGAAAAAAAAAGAGAGG
1 AAAATGAAAAAAAAAGAGAGG
*
5675151 AAAA-GAAAAAAAATGA-AGG
1 AAAATGAAAAAAAAAGAGAGG
5675170 AA
1 AA
5675172 TGGAAAGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 11 0.55
21 4 0.20
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (21 bp):
AAAATGAAAAAAAAAGAGAGG
Found at i:5675316 original size:30 final size:32
Alignment explanation
Indices: 5675259--5675321 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 32
5675249 TAATTATGTT
*
5675259 CAAATTATTATATATTTATATAAATTTTGACA
1 CAAATAATTATATATTTATATAAATTTTGACA
* *
5675291 CAAATAATT-TAT-TTTGTATAGATTTTGACA
1 CAAATAATTATATATTTATATAAATTTTGACA
5675321 C
1 C
5675322 GTTCTTGTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 17 0.61
31 3 0.11
32 8 0.29
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (32 bp):
CAAATAATTATATATTTATATAAATTTTGACA
Found at i:5675675 original size:2 final size:2
Alignment explanation
Indices: 5675668--5675695 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5675658 TTAAATTGTA
5675668 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5675696 GCTAAATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5683080 original size:2 final size:2
Alignment explanation
Indices: 5683073--5683108 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5683063 GAAAGTTGTA
5683073 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5683109 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5689614 original size:58 final size:58
Alignment explanation
Indices: 5689506--5689667 Score: 243
Period size: 58 Copynumber: 2.8 Consensus size: 58
5689496 GCTTGTTCGT
* * * *
5689506 ATTTTTAGCATGTATGCATGGCAACTTTTGTTGCTCGTTTCTATGTTGTTGGAATGTCC
1 ATTTGTAGCATGTATGCGTGGCAAC-TTTGTTGCTCGCTTCTATGCTGTTGGAATGTCC
* *
5689565 ATTTGTGGCATGTATGCGTGGCAACTTTGTTGCTCACTTCTATGCTGTTGGAATGTCC
1 ATTTGTAGCATGTATGCGTGGCAACTTTGTTGCTCGCTTCTATGCTGTTGGAATGTCC
* *
5689623 ATTTGTAGCATATATGCGTGGTAACTTTGTTGCTCGCTTCTATGC
1 ATTTGTAGCATGTATGCGTGGCAACTTTGTTGCTCGCTTCTATGC
5689668 CGGCCATTGA
Statistics
Matches: 93, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
58 71 0.76
59 22 0.24
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (58 bp):
ATTTGTAGCATGTATGCGTGGCAACTTTGTTGCTCGCTTCTATGCTGTTGGAATGTCC
Found at i:5696994 original size:2 final size:2
Alignment explanation
Indices: 5696967--5697013 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
5696957 CATTAAATTT
*
5696967 TA TA -A TA TA TA CTA TA -A TA T- TT TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5697007 TA TA TA T
1 TA TA TA T
5697014 GTAGACACCA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
1 3 0.08
2 35 0.88
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5697236 original size:20 final size:20
Alignment explanation
Indices: 5697211--5697281 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
5697201 TTTTACCTAG
5697211 ATATATCGATATATTTTTCA
1 ATATATCGATATATTTTTCA
* * * *
5697231 ATATATCGATACATGTATGA
1 ATATATCGATATATTTTTCA
* *
5697251 ATGTATCGATATATTCTTCA
1 ATATATCGATATATTTTTCA
*
5697271 ATGTATCGATA
1 ATATATCGATA
5697282 CATTATGTCT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.42
Consensus pattern (20 bp):
ATATATCGATATATTTTTCA
Found at i:5700610 original size:26 final size:27
Alignment explanation
Indices: 5700557--5700610 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
5700547 TCATTTATTT
*
5700557 TTTAATTATATAATATATAAATATAAA
1 TTTAATTATATAATATATAAATAAAAA
* *
5700584 TTTAA-TATATATTATATAATTAAAAA
1 TTTAATTATATAATATATAAATAAAAA
5700610 T
1 T
5700611 AAATTAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
TTTAATTATATAATATATAAATAAAAA
Found at i:5700688 original size:17 final size:17
Alignment explanation
Indices: 5700666--5700716 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 17
5700656 TTTTTAAATA
5700666 AAATTTATATTTTATTT
1 AAATTTATATTTTATTT
5700683 AAA-TT-TATTTT-TTT
1 AAATTTATATTTTATTT
5700697 -AATTTAATATATTTATTT
1 AAATTT-ATAT-TTTATTT
5700715 AA
1 AA
5700717 TTTTTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 2 0.07
14 5 0.18
15 6 0.21
16 5 0.18
17 6 0.21
18 3 0.11
19 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
AAATTTATATTTTATTT
Found at i:5700709 original size:18 final size:19
Alignment explanation
Indices: 5700675--5700719 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
5700665 AAAATTTATA
*
5700675 TTTT-ATTTAAATTTATTT
1 TTTTAATTTAAATATATTT
5700693 TTTTAATTT-AATATATTT
1 TTTTAATTTAAATATATTT
*
5700711 ATTTAATTT
1 TTTTAATTT
5700720 TTTAAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTAATTTAAATATATTT
Found at i:5700727 original size:22 final size:22
Alignment explanation
Indices: 5700652--5700729 Score: 60
Period size: 22 Copynumber: 3.7 Consensus size: 22
5700642 AAAATTTAAC
*
5700652 TAATTTTTTAAATAAAATTTATAT
1 TAATTTTTTAAAT-ATATTTAT-T
* * *
5700676 T--TTATTTAAATTTATTTTTT
1 TAATTTTTTAAATATATTTATT
5700696 TAA---TTT-AATATATTTATT
1 TAATTTTTTAAATATATTTATT
5700714 TAATTTTTTAAATATA
1 TAATTTTTTAAATATA
5700730 AAATAAATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
18 13 0.31
19 3 0.07
20 2 0.05
21 8 0.19
22 15 0.36
24 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TAATTTTTTAAATATATTTATT
Found at i:5701115 original size:24 final size:24
Alignment explanation
Indices: 5701086--5701151 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 24
5701076 GTAATATATG
*
5701086 TAAAAATATATTTA-AAATAATAT
1 TAAAAATATATTTATAAATAACAT
5701109 TATAAAATATTATTTCATAAATAACAT
1 TA-AAAATA-TATTT-ATAAATAACAT
*
5701136 TAAATATATATTTATA
1 TAAAAATATATTTATA
5701152 CATTATATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
23 2 0.05
24 9 0.24
25 10 0.27
26 6 0.16
27 10 0.27
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (24 bp):
TAAAAATATATTTATAAATAACAT
Found at i:5701116 original size:13 final size:12
Alignment explanation
Indices: 5701088--5701179 Score: 64
Period size: 12 Copynumber: 7.3 Consensus size: 12
5701078 AATATATGTA
5701088 AAAAT-ATATTT
1 AAAATAATATTT
5701099 AAAATAATATTAT
1 AAAATAATATT-T
*
5701112 AAAATATTATTT
1 AAAATAATATTT
*
5701124 CATAAATAACA-TT
1 -A-AAATAATATTT
5701137 -AAATATATATTT
1 AAAATA-ATATTT
*
5701149 ATACATTATATATTT
1 A-A-AATA-ATATTT
*
5701164 CAAATAATATTT
1 AAAATAATATTT
5701176 AAAA
1 AAAA
5701180 ATATATGCCA
Statistics
Matches: 64, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
10 5 0.08
11 7 0.11
12 17 0.27
13 17 0.27
14 8 0.12
15 10 0.16
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (12 bp):
AAAATAATATTT
Found at i:5701185 original size:12 final size:12
Alignment explanation
Indices: 5701078--5701185 Score: 53
Period size: 12 Copynumber: 8.6 Consensus size: 12
5701068 ACATATTAGT
*
5701078 AATATATGTAAA
1 AATATATTTAAA
5701090 AATATATTT-AA
1 AATATATTTAAA
5701101 AATA-ATATTATAA
1 AATATAT-TTA-AA
*
5701114 AATATTATTTCATA
1 AATA-TATTT-AAA
*
5701128 AATA-ACATTAAA
1 AATATA-TTTAAA
*
5701140 TATATATTTATACA
1 AATATATTTA-A-A
* *
5701154 TTATATATTT-CA
1 -AATATATTTAAA
5701166 AATAATATTTAAA
1 AAT-ATATTTAAA
5701179 AATATAT
1 AATATAT
5701186 GCCAAAAATA
Statistics
Matches: 74, Mismatches: 9, Indels: 26
0.68 0.08 0.24
Matches are distributed among these distances:
10 2 0.03
11 10 0.14
12 28 0.38
13 14 0.19
14 8 0.11
15 12 0.16
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.43
Consensus pattern (12 bp):
AATATATTTAAA
Found at i:5701886 original size:2 final size:2
Alignment explanation
Indices: 5701879--5701903 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5701869 TATTCATGTC
5701879 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5701904 AAAAATCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5702619 original size:14 final size:14
Alignment explanation
Indices: 5702602--5702631 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5702592 TAATGATAAA
5702602 ATTAAAAATTTTTT
1 ATTAAAAATTTTTT
*
5702616 ATTAAAATTTTTTT
1 ATTAAAAATTTTTT
5702630 AT
1 AT
5702632 AATTAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTAAAAATTTTTT
Found at i:5702794 original size:22 final size:23
Alignment explanation
Indices: 5702746--5702808 Score: 69
Period size: 25 Copynumber: 2.8 Consensus size: 23
5702736 ATTATTTATA
*
5702746 TAAATTTATTATATATTTAATAGT
1 TAAATTTATTATATAATTAATA-T
*
5702770 TAATTTTTATTATATAATT-AT-T
1 TAA-ATTTATTATATAATTAATAT
5702792 TAAATTTATT-TATAATT
1 TAAATTTATTATATAATT
5702809 TTAAATAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 7 0.20
21 6 0.17
22 4 0.11
24 5 0.14
25 13 0.37
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TAAATTTATTATATAATTAATAT
Found at i:5702847 original size:10 final size:11
Alignment explanation
Indices: 5702818--5702846 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
5702808 TTTAAATAAA
5702818 TAAAAAAATTT
1 TAAAAAAATTT
5702829 TAAAAAAATTT
1 TAAAAAAATTT
5702840 TAAAAAA
1 TAAAAAA
5702847 TAAAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
TAAAAAAATTT
Found at i:5706475 original size:24 final size:24
Alignment explanation
Indices: 5706443--5706492 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
5706433 GGTAGGATTT
5706443 CTTGTTCCACCCTAAATGATGTTG
1 CTTGTTCCACCCTAAATGATGTTG
5706467 CTTGTTCCACCCTAAATGATGTTG
1 CTTGTTCCACCCTAAATGATGTTG
5706491 CT
1 CT
5706493 ATCTATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.26, G:0.16, T:0.38
Consensus pattern (24 bp):
CTTGTTCCACCCTAAATGATGTTG
Found at i:5708670 original size:2 final size:2
Alignment explanation
Indices: 5708663--5708697 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5708653 CCGGCCAACT
*
5708663 TC TC TC TC TC TC TC TC TC TG TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5708698 ATATATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.46, G:0.03, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5709303 original size:29 final size:29
Alignment explanation
Indices: 5709269--5709350 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 29
5709259 ATTACTTATT
5709269 TTTATTAA-TAATTATATAACAAAAATTTA
1 TTTATTAATTAATTATATAA-AAAAATTTA
* * *
5709298 TTTATTAATTTATTATGTAATAAAATTTA
1 TTTATTAATTAATTATATAAAAAAATTTA
5709327 TTTATTATATTAA--AT-TAAAAAAAT
1 TTTATTA-ATTAATTATATAAAAAAAT
5709351 AATTCACATT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
27 8 0.17
28 2 0.04
29 23 0.50
30 13 0.28
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (29 bp):
TTTATTAATTAATTATATAAAAAAATTTA
Found at i:5710442 original size:2 final size:2
Alignment explanation
Indices: 5710435--5710459 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5710425 GAAAAACTTG
5710435 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5710460 CTTTTTCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5711238 original size:17 final size:17
Alignment explanation
Indices: 5711197--5711238 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5711187 TTTAAGTAAG
*
5711197 ATTAATTAATATTTTAT
1 ATTAAATAATATTTTAT
*
5711214 -TTATAATAATATTTTTT
1 ATTA-AATAATATTTTAT
5711231 ATTAAATA
1 ATTAAATA
5711239 TGATCGTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 3 0.14
17 15 0.71
18 3 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTAAATAATATTTTAT
Found at i:5713574 original size:2 final size:2
Alignment explanation
Indices: 5713567--5713625 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
5713557 CTCCTTTCAT
5713567 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5713609 TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC T
5713626 TTGTACGCAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5715418 original size:2 final size:2
Alignment explanation
Indices: 5715400--5715448 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
5715390 AACAAAAGAG
* *
5715400 CT CT TT CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5715442 CT CT CT C
1 CT CT CT C
5715449 ATATATTTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:5718632 original size:20 final size:19
Alignment explanation
Indices: 5718579--5718635 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 19
5718569 TAATAAAAAT
5718579 TATATCAAAATTTATATAA
1 TATATCAAAATTTATATAA
5718598 -A-A-C-AAA-TTAT-TAA
1 TATATCAAAATTTATATAA
5718611 TATATCAAAATTTATATAAA
1 TATATCAAAATTTATAT-AA
5718631 TATAT
1 TATAT
5718636 ATTTTAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 13
0.70 0.00 0.30
Matches are distributed among these distances:
13 3 0.10
14 5 0.16
15 4 0.13
16 2 0.06
17 4 0.13
18 5 0.16
19 1 0.03
20 7 0.23
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
TATATCAAAATTTATATAA
Found at i:5719765 original size:2 final size:2
Alignment explanation
Indices: 5719752--5719788 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5719742 TCACGAAAGC
*
5719752 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5719789 ATGATAAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:5719838 original size:68 final size:68
Alignment explanation
Indices: 5719722--5719852 Score: 210
Period size: 68 Copynumber: 1.9 Consensus size: 68
5719712 GAAGCCTGTT
*
5719722 TGATAAGTTTCAAGCAATAATCACGAAAGCATATACATATATATATATATATATATATATATATA
1 TGATAAGTTTCAAGCAATAATCACGAAAGCATATACATATATACATATATATATATATATATATA
5719787 TAA
66 TAA
* * *
5719790 TGATAAGTTTGAAGCAATAATCACGAGAGCATATACA-ATTATACATATATATATATATGTATA
1 TGATAAGTTTCAAGCAATAATCACGAAAGCATATACATA-TATACATATATATATATATATATA
5719853 ATTCTTTTAA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
67 1 0.02
68 57 0.98
ACGTcount: A:0.47, C:0.09, G:0.10, T:0.34
Consensus pattern (68 bp):
TGATAAGTTTCAAGCAATAATCACGAAAGCATATACATATATACATATATATATATATATATATA
TAA
Found at i:5724623 original size:2 final size:2
Alignment explanation
Indices: 5724616--5724649 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5724606 AAGACATTAA
5724616 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5724650 GCAAGCAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5726354 original size:9 final size:9
Alignment explanation
Indices: 5726340--5726364 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5726330 AAATTAAATA
5726340 TTTAATTTT
1 TTTAATTTT
5726349 TTTAATTTT
1 TTTAATTTT
5726358 TTTAATT
1 TTTAATT
5726365 CAAATATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTAATTTT
Found at i:5726686 original size:16 final size:16
Alignment explanation
Indices: 5726633--5726696 Score: 62
Period size: 16 Copynumber: 3.9 Consensus size: 16
5726623 ATAGATAATA
5726633 AAAAATTTAAAT-TTT
1 AAAAATTTAAATATTT
*
5726648 AAATAAATTAAATAAATTT
1 AAA-AATTTAAAT--ATTT
5726667 --AAATTTAAATATTT
1 AAAAATTTAAATATTT
5726681 AAAAATTATAAATATT
1 AAAAATT-TAAATATT
5726697 AAATCTACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
14 4 0.10
15 3 0.08
16 21 0.52
17 9 0.22
19 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAAATTTAAATATTT
Found at i:5730786 original size:25 final size:26
Alignment explanation
Indices: 5730734--5730786 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
5730724 GTACCTCTTC
*
5730734 AGGTTCCTTCTTTTCAACCGAAATTCG
1 AGGTTCCTTCTTTTCAACC-AAACTCG
*
5730761 AGGTTCCTTTTTTTCAACC-AACTCG
1 AGGTTCCTTCTTTTCAACCAAACTCG
5730786 A
1 A
5730787 ATTTTGGTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 6 0.25
27 18 0.75
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (26 bp):
AGGTTCCTTCTTTTCAACCAAACTCG
Found at i:5730961 original size:3 final size:3
Alignment explanation
Indices: 5730953--5730997 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
5730943 TCTTAGGCAA
5730953 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTCC TTC -TC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC TTC TTC
5730998 CTCAATGCCA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:5731783 original size:2 final size:2
Alignment explanation
Indices: 5731778--5731803 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5731768 CATTTAAAGG
5731778 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5731804 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5731808 original size:2 final size:2
Alignment explanation
Indices: 5731803--5731828 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5731793 TATATATATA
5731803 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
5731829 CAAGTATTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:5732044 original size:22 final size:23
Alignment explanation
Indices: 5732004--5732049 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
5731994 AGATAATTAT
*
5732004 TTTAAAAAATAATTTAATTTTTA
1 TTTAAAAAATAATTAAATTTTTA
5732027 TTTAAAAAATAA-TAAATTTTTA
1 TTTAAAAAATAATTAAATTTTTA
5732049 T
1 T
5732050 CATTAAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTTAAAAAATAATTAAATTTTTA
Found at i:5733016 original size:30 final size:29
Alignment explanation
Indices: 5732980--5733072 Score: 82
Period size: 30 Copynumber: 3.1 Consensus size: 29
5732970 AAGTTAAAGC
5732980 TTATTTATATATAAATTAATGATTAAAGAT
1 TTATTTATATATAAATTAAT-ATTAAAGAT
* * *
5733010 TTATTTA-AGTAAAAATTAAAATTCAAGAGT
1 TTATTTATA-TATAAATTAATATTAAAGA-T
* *
5733040 TTATTT-TAATATAAAATAAATATTAAGGAT
1 TTATTTAT-ATAT-AAATTAATATTAAAGAT
5733070 TTA
1 TTA
5733073 CTTGAACGTA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
29 8 0.16
30 29 0.58
31 13 0.26
ACGTcount: A:0.48, C:0.01, G:0.08, T:0.43
Consensus pattern (29 bp):
TTATTTATATATAAATTAATATTAAAGAT
Found at i:5733409 original size:15 final size:14
Alignment explanation
Indices: 5733389--5733418 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
5733379 TAAGAGTTAA
5733389 AATAAAATAATAATT
1 AATAAAATAA-AATT
5733404 AATAAAATAAAATT
1 AATAAAATAAAATT
5733418 A
1 A
5733419 CAAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AATAAAATAAAATT
Found at i:5733470 original size:19 final size:18
Alignment explanation
Indices: 5733448--5733491 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
5733438 AAATTTGAAC
5733448 AATAATAACCCACTAAAAA
1 AATAATAA-CCACTAAAAA
* *
5733467 AATAATTAATCACTTAAAA
1 AATAA-TAACCACTAAAAA
5733486 AATAAT
1 AATAAT
5733492 TGCTTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 1 0.05
19 18 0.82
20 3 0.14
ACGTcount: A:0.61, C:0.14, G:0.00, T:0.25
Consensus pattern (18 bp):
AATAATAACCACTAAAAA
Found at i:5733761 original size:29 final size:30
Alignment explanation
Indices: 5733699--5733761 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
5733689 ATTATTTCAT
* *
5733699 TTAATTTAATCATATTATATAAATATATAA
1 TTAATTTAATCATATTATATAAATAAAAAA
5733729 -TAATTTAA-CATAATTATA-AAATAAAAAA
1 TTAATTTAATCAT-ATTATATAAATAAAAAA
5733757 TTAAT
1 TTAAT
5733762 ACAAAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
28 11 0.38
29 18 0.62
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (30 bp):
TTAATTTAATCATATTATATAAATAAAAAA
Found at i:5733779 original size:16 final size:18
Alignment explanation
Indices: 5733758--5733791 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
5733748 AATAAAAAAT
5733758 TAATACA-AAA-TATTAA
1 TAATACATAAATTATTAA
5733774 TAATACATAAATTATTAA
1 TAATACATAAATTATTAA
5733792 ATCTATCTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 3 0.19
18 6 0.38
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (18 bp):
TAATACATAAATTATTAA
Found at i:5734198 original size:13 final size:13
Alignment explanation
Indices: 5734182--5734228 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
5734172 TTTATATATT
5734182 TATATTATGTTTA
1 TATATTATGTTTA
5734195 TATATTTATGTATTA
1 TATA-TTATGT-TTA
*
5734210 TA-ATTATTTTTA
1 TATATTATGTTTA
*
5734222 AATATTA
1 TATATTA
5734229 AATATTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 4 0.14
13 13 0.45
14 7 0.24
15 5 0.17
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (13 bp):
TATATTATGTTTA
Found at i:5734208 original size:27 final size:27
Alignment explanation
Indices: 5734170--5734227 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
5734160 TGCATACTGT
*
5734170 TATTTATATATT-TATATTATGTTTATA
1 TATTTATATATTATA-ATTATGTTTAAA
* *
5734197 TATTTATGTATTATAATTATTTTTAAA
1 TATTTATATATTATAATTATGTTTAAA
5734224 TATT
1 TATT
5734228 AAATATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 25 0.93
28 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (27 bp):
TATTTATATATTATAATTATGTTTAAA
Found at i:5734216 original size:21 final size:19
Alignment explanation
Indices: 5734173--5734216 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
5734163 ATACTGTTAT
**
5734173 TTATATATTTATATTATGT
1 TTATATATTTATATTATAA
5734192 TTATATATTTATGTATTATAA
1 TTATATATTTA--TATTATAA
5734213 TTAT
1 TTAT
5734217 TTTTAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 11 0.52
21 10 0.48
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
TTATATATTTATATTATAA
Found at i:5734350 original size:22 final size:22
Alignment explanation
Indices: 5734320--5734363 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
5734310 TATTTTTTTA
*
5734320 TTTTGTATTATA-TTATAATTAT
1 TTTTATATTATATTTA-AATTAT
*
5734342 TTTTATATTTTATTTAAATTAT
1 TTTTATATTATATTTAAATTAT
5734364 GAGATAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (22 bp):
TTTTATATTATATTTAAATTAT
Found at i:5738933 original size:25 final size:25
Alignment explanation
Indices: 5738901--5738978 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 25
5738891 TTAATTTAAA
5738901 TTATTTTAATTAATAAAATTTATTT
1 TTATTTTAATTAATAAAATTTATTT
* * *
5738926 TTATTTTAAATTTA-AAAATATATAT
1 TTATTTT-AATTAATAAAATTTATTT
** *
5738951 AAATATTAATATAAT-AAATTTATTT
1 TTATTTTAAT-TAATAAAATTTATTT
5738976 TTA
1 TTA
5738979 ATATTTTAAT
Statistics
Matches: 39, Mismatches: 11, Indels: 6
0.70 0.20 0.11
Matches are distributed among these distances:
24 3 0.08
25 31 0.79
26 5 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TTATTTTAATTAATAAAATTTATTT
Found at i:5742575 original size:2 final size:2
Alignment explanation
Indices: 5742568--5742605 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5742558 CAAGCCACTT
5742568 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
5742606 TCCATCTTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5744326 original size:45 final size:43
Alignment explanation
Indices: 5744280--5744365 Score: 110
Period size: 43 Copynumber: 2.0 Consensus size: 43
5744270 TAATTTTTTT
5744280 ATTTAT-ATTTA-T-TTTTA-ATTAATAAATTTATAT-TATTTATA
1 ATTTATAATTTATTATTTTATATTAAT--ATTTATATAT-TTTATA
5744321 ATTTATAATTTATTATTTTATATTAATATTTATATATTTTATA
1 ATTTATAATTTATTATTTTATATTAATATTTATATATTTTATA
5744364 AT
1 AT
5744366 AAATTTAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
41 6 0.15
42 5 0.12
43 17 0.43
44 6 0.15
45 6 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (43 bp):
ATTTATAATTTATTATTTTATATTAATATTTATATATTTTATA
Found at i:5744336 original size:21 final size:20
Alignment explanation
Indices: 5744284--5744365 Score: 62
Period size: 21 Copynumber: 3.9 Consensus size: 20
5744274 TTTTTTATTT
*
5744284 ATATTTATT-TTTAATTAATAA
1 ATATTTATTATTT-A-TAATTA
*
5744305 AT-TTATATTATTTATAATTT
1 ATATT-TATTATTTATAATTA
5744325 ATAATTTATTATTT-TATATTA
1 AT-ATTTATTATTTATA-ATTA
5744346 ATATTTATATATTTTATAAT
1 ATATTTAT-TA-TTTATAAT
5744366 AAATTTAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
20 16 0.32
21 22 0.44
22 10 0.20
23 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATATTTATTATTTATAATTA
Found at i:5745114 original size:22 final size:21
Alignment explanation
Indices: 5745089--5745140 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
5745079 ATTATTATCA
5745089 TTATAAATATA-ATTTTTATAAT
1 TTATAAATATACA-TTTTAT-AT
*
5745111 TTATTAATATACATTTTATAT
1 TTATAAATATACATTTTATAT
*
5745132 GTATAAATA
1 TTATAAATA
5745141 ATGTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 9 0.35
22 16 0.62
23 1 0.04
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
TTATAAATATACATTTTATAT
Found at i:5745253 original size:2 final size:2
Alignment explanation
Indices: 5745246--5745280 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5745236 TGGTAATAAC
5745246 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5745281 ATTACTTGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5746704 original size:15 final size:15
Alignment explanation
Indices: 5746684--5746713 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5746674 TCGATTTTTT
5746684 TTATTTTCAAAAAAA
1 TTATTTTCAAAAAAA
*
5746699 TTATTTTTAAAAAAA
1 TTATTTTCAAAAAAA
5746714 AAAATGATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
TTATTTTCAAAAAAA
Found at i:5748325 original size:17 final size:18
Alignment explanation
Indices: 5748303--5748344 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
5748293 AATCCAAATT
*
5748303 TAAAATGATTTC-ATTAA
1 TAAAATGATTTCAAATAA
5748320 TAAAAT-A-TTCAAATAA
1 TAAAATGATTTCAAATAA
5748336 TAAAATGAT
1 TAAAATGAT
5748345 CAAATCTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
15 3 0.14
16 11 0.52
17 7 0.33
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (18 bp):
TAAAATGATTTCAAATAA
Found at i:5751061 original size:9 final size:9
Alignment explanation
Indices: 5751044--5751072 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
5751034 TTTTTTTTTT
5751044 GGGGG-GGG
1 GGGGGTGGG
5751052 GGGGGTGGG
1 GGGGGTGGG
5751061 GGGGGTGGG
1 GGGGGTGGG
5751070 GGG
1 GGG
5751073 AATAAAGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.25
9 15 0.75
ACGTcount: A:0.00, C:0.00, G:0.93, T:0.07
Consensus pattern (9 bp):
GGGGGTGGG
Found at i:5762543 original size:12 final size:12
Alignment explanation
Indices: 5762526--5762551 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5762516 TGATATGAGA
5762526 ATAGTTATTTCC
1 ATAGTTATTTCC
5762538 ATAGTTATTTCC
1 ATAGTTATTTCC
5762550 AT
1 AT
5762552 CCTACCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.50
Consensus pattern (12 bp):
ATAGTTATTTCC
Found at i:5764987 original size:33 final size:33
Alignment explanation
Indices: 5764930--5764998 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
5764920 TCAAACAAAG
* *
5764930 TAATGAAAGCTAATGCTCACCATCGGACGGCTA
1 TAATCAAAGCTAATGCTCAACATCGGACGGCTA
*
5764963 TAATCAAAGCTAATTCTCAACATCGGACGGCTA
1 TAATCAAAGCTAATGCTCAACATCGGACGGCTA
5764996 TAA
1 TAA
5764999 AGAACAAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.23
Consensus pattern (33 bp):
TAATCAAAGCTAATGCTCAACATCGGACGGCTA
Found at i:5767308 original size:11 final size:11
Alignment explanation
Indices: 5767294--5767321 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
5767284 ATAAAAAACT
5767294 TATTTTATATA
1 TATTTTATATA
5767305 TATTTTATATA
1 TATTTTATATA
5767316 TATTTT
1 TATTTT
5767322 TTTAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TATTTTATATA
Found at i:5767755 original size:52 final size:51
Alignment explanation
Indices: 5767682--5767783 Score: 161
Period size: 52 Copynumber: 2.0 Consensus size: 51
5767672 ATATATTTCG
5767682 TAATTAAAATTAAATAAAAATATTTT-ATTTATTATTAAATATTAATTTAAA
1 TAATTAAAATTAAATAAAAATATTTTAATTT-TTATTAAATATTAATTTAAA
* *
5767733 TAATTAAAAGTTAAATACAAATATTTTAATTTTTGTTAAATATTAATTTAA
1 TAATTAAAA-TTAAATAAAAATATTTTAATTTTTATTAAATATTAATTTAA
5767784 GTTTGTTTGA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
51 9 0.19
52 34 0.72
53 4 0.09
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (51 bp):
TAATTAAAATTAAATAAAAATATTTTAATTTTTATTAAATATTAATTTAAA
Found at i:5767872 original size:19 final size:19
Alignment explanation
Indices: 5767848--5767885 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5767838 AAGAGATTAC
5767848 ATAAGTTAAAATTCAAATT
1 ATAAGTTAAAATTCAAATT
*
5767867 ATAAGTTAAAATTTAAATT
1 ATAAGTTAAAATTCAAATT
5767886 TTAATTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (19 bp):
ATAAGTTAAAATTCAAATT
Found at i:5768102 original size:2 final size:2
Alignment explanation
Indices: 5768097--5768123 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5768087 TGATAGTGTG
5768097 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5768124 TTGTCTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5768399 original size:26 final size:26
Alignment explanation
Indices: 5768360--5768411 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
5768350 ACAGCCAGAT
5768360 TGTTTGCTAAGAATGGCGTAAAGGTC
1 TGTTTGCTAAGAATGGCGTAAAGGTC
*
5768386 TGTTTGCTAGGAATGGCGTAAAGGTC
1 TGTTTGCTAAGAATGGCGTAAAGGTC
5768412 ACAATTGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.12, G:0.33, T:0.31
Consensus pattern (26 bp):
TGTTTGCTAAGAATGGCGTAAAGGTC
Found at i:5769614 original size:2 final size:2
Alignment explanation
Indices: 5769607--5769634 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5769597 ATCTTATCAC
5769607 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5769635 TTGTACATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5772156 original size:8 final size:8
Alignment explanation
Indices: 5772143--5772175 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
5772133 AATATACATT
5772143 AGCAAAAC
1 AGCAAAAC
5772151 AGCAAAAC
1 AGCAAAAC
5772159 AGCAAAAC
1 AGCAAAAC
5772167 AGCAAAAC
1 AGCAAAAC
5772175 A
1 A
5772176 AAAGAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.64, C:0.24, G:0.12, T:0.00
Consensus pattern (8 bp):
AGCAAAAC
Found at i:5772974 original size:16 final size:16
Alignment explanation
Indices: 5772933--5772974 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
5772923 AATTTTAAAA
5772933 AATTT-AATT-AATTT
1 AATTTAAATTAAATTT
5772947 -ATTTAAATTTAAATTT
1 AATTTAAA-TTAAATTT
5772963 AATTTAAATTAA
1 AATTTAAATTAA
5772975 TAAAAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 4 0.17
14 2 0.08
15 2 0.08
16 9 0.38
17 7 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTTAAATTAAATTT
Found at i:5772995 original size:14 final size:14
Alignment explanation
Indices: 5772962--5773000 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 14
5772952 AATTTAAATT
5772962 TAATTT-AAATTAA
1 TAATTTAAAATTAA
5772975 TAA---AAAATTAA
1 TAATTTAAAATTAA
5772986 TAATTTAAAATTAA
1 TAATTTAAAATTAA
5773000 T
1 T
5773001 CAATCTGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
11 10 0.45
13 3 0.14
14 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAATTTAAAATTAA
Found at i:5773038 original size:16 final size:16
Alignment explanation
Indices: 5773008--5773050 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
5772998 AATCAATCTG
*
5773008 ATTTCAAAATAATTTCA
1 ATTT-AAAATAATTTAA
*
5773025 ATTTAAAATGATTTAA
1 ATTTAAAATAATTTAA
5773041 ATTTAAAATA
1 ATTTAAAATA
5773051 GTCTGAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (16 bp):
ATTTAAAATAATTTAA
Found at i:5773106 original size:22 final size:22
Alignment explanation
Indices: 5773075--5773124 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
5773065 TGACTGAAAT
5773075 AATT-AATTTAAAATAATTCAA
1 AATTAAATTTAAAATAATTCAA
* *
5773096 ATTTAAATTTAAAATATTTCAA
1 AATTAAATTTAAAATAATTCAA
5773118 AATTAAA
1 AATTAAA
5773125 ATGACTTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (22 bp):
AATTAAATTTAAAATAATTCAA
Found at i:5773140 original size:16 final size:15
Alignment explanation
Indices: 5773117--5773170 Score: 65
Period size: 14 Copynumber: 3.6 Consensus size: 15
5773107 AAATATTTCA
*
5773117 AAATTAAAATGACTT
1 AAATTAAAATAACTT
*
5773132 GAATCTAAAATAACTT
1 AAAT-TAAAATAACTT
*
5773148 AAATTAAAA-AATTT
1 AAATTAAAATAACTT
5773162 AAATTAAAA
1 AAATTAAAA
5773171 ATTTTAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
14 13 0.38
15 8 0.24
16 13 0.38
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (15 bp):
AAATTAAAATAACTT
Found at i:5773165 original size:14 final size:14
Alignment explanation
Indices: 5773094--5773179 Score: 64
Period size: 14 Copynumber: 5.7 Consensus size: 14
5773084 AAAATAATTC
5773094 AAATTTAAATTTAAA
1 AAATTTAAA-TTAAA
*
5773109 ATATTTCAAAATTAAA
1 AAATTT--AAATTAAA
* * *
5773125 ATGACTTGAATCTAAA
1 A-AATTTAAAT-TAAA
*
5773141 ATAACTTAAATTAAA
1 A-AATTTAAATTAAA
5773156 AAATTTAAATTAAA
1 AAATTTAAATTAAA
*
5773170 AATTTTAAAT
1 AAATTTAAAT
5773180 ATTAAGATAA
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
14 21 0.36
15 13 0.22
16 19 0.32
17 6 0.10
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (14 bp):
AAATTTAAATTAAA
Found at i:5775609 original size:10 final size:10
Alignment explanation
Indices: 5775594--5775628 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
5775584 TAAAGTGTTT
5775594 ATAAAAATAA
1 ATAAAAATAA
5775604 ATAAAAATAA
1 ATAAAAATAA
5775614 AT-AAAAT-A
1 ATAAAAATAA
5775622 ATAAAAA
1 ATAAAAA
5775629 ATTTTATAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 3 0.12
9 9 0.38
10 12 0.50
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (10 bp):
ATAAAAATAA
Found at i:5775723 original size:30 final size:29
Alignment explanation
Indices: 5775689--5775761 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
5775679 GTTATATTCG
*
5775689 AATAAATTTTTAATTTTTAACTTATATAAA
1 AATAAATTTTTAA-CTTTAACTTATATAAA
* * *
5775719 AATAAATCTCTTAACTTTAATTTATATATA
1 AATAAAT-TTTTAACTTTAACTTATATAAA
*
5775749 AATAAACTTTTAA
1 AATAAATTTTTAA
5775762 AATAAATTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 5 0.14
30 26 0.72
31 5 0.14
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (29 bp):
AATAAATTTTTAACTTTAACTTATATAAA
Found at i:5776294 original size:21 final size:21
Alignment explanation
Indices: 5776251--5776294 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5776241 GATGCAATGG
**
5776251 TTGGATAAAAGAATGTATTTT
1 TTGGATAAAAGAATGTAACTT
5776272 TTGGATGAAAA-AATGTAACTT
1 TTGGAT-AAAAGAATGTAACTT
5776293 TT
1 TT
5776295 AATAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.39, C:0.02, G:0.18, T:0.41
Consensus pattern (21 bp):
TTGGATAAAAGAATGTAACTT
Found at i:5780036 original size:13 final size:14
Alignment explanation
Indices: 5780008--5780041 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
5779998 TTGAACCTCT
5780008 ATGTTAGCCTAATG
1 ATGTTAGCCTAATG
5780022 ATGTTAGCC-AATG
1 ATGTTAGCCTAATG
5780035 ATGTTAG
1 ATGTTAG
5780042 ATCAACAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (14 bp):
ATGTTAGCCTAATG
Found at i:5780112 original size:21 final size:20
Alignment explanation
Indices: 5780088--5780148 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 20
5780078 ATATAAAAGC
5780088 ATATTAATATGTATATGTTAA
1 ATATTAATATGTATAT-TTAA
*
5780109 ATATAAAATTATGT-TATTTAA
1 ATAT-TAA-TATGTATATTTAA
*
5780130 TTCATTAATAATGTATATT
1 AT-ATTAAT-ATGTATATT
5780149 AAGGCTAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
20 1 0.03
21 15 0.47
22 11 0.34
23 5 0.16
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (20 bp):
ATATTAATATGTATATTTAA
Found at i:5782440 original size:2 final size:2
Alignment explanation
Indices: 5782433--5782466 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5782423 AGGTGAATCA
5782433 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5782467 GCACTGCACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5782805 original size:16 final size:16
Alignment explanation
Indices: 5782785--5782815 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
5782775 TTCTAGGTGA
5782785 AAAAAATAA-TATTTT
1 AAAAAATAAGTATTTT
5782800 AAAAAATAAGTATTTT
1 AAAAAATAAGTATTTT
5782816 TTAAATAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
AAAAAATAAGTATTTT
Found at i:5783220 original size:22 final size:22
Alignment explanation
Indices: 5783195--5783236 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
5783185 TAATAAAAAA
5783195 ATATTTTTAT-ATTAATATTTAT
1 ATATTTTTATAATTAA-ATTTAT
5783217 ATATTTTTATAATTAAATTT
1 ATATTTTTATAATTAAATTT
5783237 TAATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
ATATTTTTATAATTAAATTTAT
Found at i:5784132 original size:14 final size:15
Alignment explanation
Indices: 5784090--5784157 Score: 61
Period size: 15 Copynumber: 4.5 Consensus size: 15
5784080 ATATTTAAAA
*
5784090 AATATTA-ATATATT
1 AATATTATATATTTT
* *
5784104 AATATAAAATTATTTT
1 AATATTATA-TATTTT
5784120 AATATTATA-ATTTTT
1 AATATTATATA-TTTT
5784135 AATATT-TATATTTT
1 AATATTATATATTTT
5784149 GAATATTAT
1 -AATATTAT
5784158 TAAACATACA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
14 13 0.30
15 18 0.41
16 13 0.30
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (15 bp):
AATATTATATATTTT
Found at i:5784334 original size:17 final size:17
Alignment explanation
Indices: 5784314--5784372 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 17
5784304 ATTAAAATTG
5784314 TAATAATATTTTTATAA
1 TAATAATATTTTTATAA
* ** *
5784331 TAATTATATTAAT-TGA
1 TAATAATATTTTTATAA
*
5784347 -AATAATATTTTAATAA
1 TAATAATATTTTTATAA
*
5784363 TAATTATATT
1 TAATAATATT
5784373 AATTGAAATA
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
15 8 0.27
16 4 0.13
17 18 0.60
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
TAATAATATTTTTATAA
Found at i:5784350 original size:29 final size:29
Alignment explanation
Indices: 5784318--5784392 Score: 114
Period size: 32 Copynumber: 2.5 Consensus size: 29
5784308 AAATTGTAAT
5784318 AATATTTTTATAATAATTATATTAATTGA
1 AATATTTTTATAATAATTATATTAATTGA
5784347 AATAATATTTTAATAATAATTATATTAATTGA
1 AAT-AT-TTTT-ATAATAATTATATTAATTGA
*
5784379 AATATTTATATAAT
1 AATATTTTTATAAT
5784393 TATGTTTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
29 8 0.19
30 5 0.12
31 6 0.14
32 23 0.55
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (29 bp):
AATATTTTTATAATAATTATATTAATTGA
Found at i:5784351 original size:32 final size:32
Alignment explanation
Indices: 5784309--5784382 Score: 130
Period size: 32 Copynumber: 2.3 Consensus size: 32
5784299 ATTCTATTAA
* *
5784309 AATTGTAATAATATTTTTATAATAATTATATT
1 AATTGAAATAATATTTTAATAATAATTATATT
5784341 AATTGAAATAATATTTTAATAATAATTATATT
1 AATTGAAATAATATTTTAATAATAATTATATT
5784373 AATTGAAATA
1 AATTGAAATA
5784383 TTTATATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (32 bp):
AATTGAAATAATATTTTAATAATAATTATATT
Found at i:5784468 original size:13 final size:14
Alignment explanation
Indices: 5784450--5784490 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
5784440 AATATTTTAG
5784450 CATT-AAATATTAT
1 CATTAAAATATTAT
5784463 CATTAAAATATTA-
1 CATTAAAATATTAT
5784476 CTATTTAAAATATTA
1 C-A-TTAAAATATTA
5784491 ATATTAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.20
14 9 0.36
15 11 0.44
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (14 bp):
CATTAAAATATTAT
Found at i:5784485 original size:15 final size:15
Alignment explanation
Indices: 5784465--5784508 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
5784455 AATATTATCA
*
5784465 TTAAAATATTACTAT
1 TTAAAATATTAATAT
5784480 TTAAAATATTAATA-
1 TTAAAATATTAATAT
5784494 TTAAACATTATTAAT
1 TTAAA-A-TATTAAT
5784509 TTAATGATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 5 0.19
15 14 0.54
16 7 0.27
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAAATATTAATAT
Found at i:5784510 original size:29 final size:28
Alignment explanation
Indices: 5784454--5784512 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 28
5784444 TTTTAGCATT
5784454 AAATATTATCATTAAAATATTACTATTTA
1 AAATATTATCATTAAAATATTAC-ATTTA
5784483 AAATATTAAT-ATTAAACATTATTA-ATTTA
1 AAATATT-ATCATTAAA-A-TATTACATTTA
5784512 A
1 A
5784513 TGATAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
29 19 0.70
30 3 0.11
31 5 0.19
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (28 bp):
AAATATTATCATTAAAATATTACATTTA
Found at i:5786733 original size:94 final size:95
Alignment explanation
Indices: 5786629--5786814 Score: 329
Period size: 94 Copynumber: 2.0 Consensus size: 95
5786619 GTATAAAAGT
5786629 TTATACAATAATATAAGAAAATTTTCATTTAACAACATTCACCTTCTCACTTAAGCTTTTTTTTT
1 TTATACAATAATATAAGAAAATTTTCATTTAACAACATTCACCTTCTCACTTAAGCTTTTTTTTT
**
5786694 -TTAATTTTTTTCTTTGTACCTAAATTTTC
66 AAAAATTTTTTTCTTTGTACCTAAATTTTC
* *
5786723 TTATACAATAATATAAGAAAATTTTCATTTAACAACATTTACCTTCTCATTTAAGCTTTTTTTTT
1 TTATACAATAATATAAGAAAATTTTCATTTAACAACATTCACCTTCTCACTTAAGCTTTTTTTTT
5786788 AAAAATTTTTTTCTTTGTACCTAAATT
66 AAAAATTTTTTTCTTTGTACCTAAATT
5786815 AAACTAAATA
Statistics
Matches: 87, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
94 63 0.72
95 24 0.28
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.49
Consensus pattern (95 bp):
TTATACAATAATATAAGAAAATTTTCATTTAACAACATTCACCTTCTCACTTAAGCTTTTTTTTT
AAAAATTTTTTTCTTTGTACCTAAATTTTC
Found at i:5787798 original size:8 final size:8
Alignment explanation
Indices: 5787785--5787827 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
5787775 TTTTTTTAAT
5787785 ATAAATTA
1 ATAAATTA
*
5787793 ATAAATAA
1 ATAAATTA
5787801 ATAAATTTA
1 ATAAA-TTA
*
5787810 ATTAATTA
1 ATAAATTA
*
5787818 ATTAATTA
1 ATAAATTA
5787826 AT
1 AT
5787828 TTTTTTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
8 25 0.81
9 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
ATAAATTA
Found at i:5787812 original size:21 final size:21
Alignment explanation
Indices: 5787788--5787829 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5787778 TTTTAATATA
5787788 AATTAATAAATAAATAAATTT
1 AATTAATAAATAAATAAATTT
* * *
5787809 AATTAATTAATTAATTAATTT
1 AATTAATAAATAAATAAATTT
5787830 TTTTATTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTAATAAATAAATAAATTT
Found at i:5788592 original size:25 final size:23
Alignment explanation
Indices: 5788564--5788613 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
5788554 TACTTTAAAA
*
5788564 TAAAATAAATTTATATTTAGTTTTT
1 TAAAAT-AATTTA-ATTTAATTTTT
*
5788589 TAAAATATTTTAATTTAATTTTT
1 TAAAATAATTTAATTTAATTTTT
5788612 TA
1 TA
5788614 TTTGTAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 12 0.52
24 5 0.22
25 6 0.26
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TAAAATAATTTAATTTAATTTTT
Found at i:5790340 original size:20 final size:20
Alignment explanation
Indices: 5790317--5790359 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
5790307 ATAATTGATC
5790317 TTTCTTAAAAAAAATCAAAT
1 TTTCTTAAAAAAAATCAAAT
**
5790337 TTTCTTAAAAATGATCAAAT
1 TTTCTTAAAAAAAATCAAAT
5790357 TTT
1 TTT
5790360 AAAAATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (20 bp):
TTTCTTAAAAAAAATCAAAT
Found at i:5791454 original size:17 final size:17
Alignment explanation
Indices: 5791396--5791457 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
5791386 ATTTTTATCA
*
5791396 ATATTAAAAATTTATTTT
1 ATATTAAAAATAT-TTTT
***
5791414 ATTATTTAAAAAATATTAAA
1 A-TA-TT-AAAAATATTTTT
5791434 ATATTAAAAATATTTTT
1 ATATTAAAAATATTTTT
5791451 ATATTAA
1 ATATTAA
5791458 TTTTTAATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 7
0.71 0.15 0.15
Matches are distributed among these distances:
17 16 0.47
18 3 0.09
19 4 0.12
20 4 0.12
21 7 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATTAAAAATATTTTT
Found at i:5792775 original size:35 final size:35
Alignment explanation
Indices: 5792736--5792807 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
5792726 TTAAACACAC
5792736 GTAAGAATGAAACGTATGTGGCGTTAATGATGCAT
1 GTAAGAATGAAACGTATGTGGCGTTAATGATGCAT
*
5792771 GTAAGAATGAAACGTATGTGGTGTTAATGATGCAT
1 GTAAGAATGAAACGTATGTGGCGTTAATGATGCAT
5792806 GT
1 GT
5792808 CGTAACGACA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.33, C:0.07, G:0.29, T:0.31
Consensus pattern (35 bp):
GTAAGAATGAAACGTATGTGGCGTTAATGATGCAT
Found at i:5793862 original size:3 final size:3
Alignment explanation
Indices: 5793856--5793886 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
5793846 ATAATAATAA
5793856 TAT TAT TAT TAT TAT TAT TAT TAT TACT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
5793887 AAATTCACAG
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:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:5794061 original size:11 final size:12
Alignment explanation
Indices: 5794032--5794064 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
5794022 TATGTTTTAC
5794032 AAATATAATATA
1 AAATATAATATA
5794044 AAA-ATAAT-TA
1 AAATATAATATA
5794054 AAATATAATAT
1 AAATATAATAT
5794065 GATATAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 5 0.26
11 10 0.53
12 4 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAATATAATATA
Found at i:5794103 original size:33 final size:31
Alignment explanation
Indices: 5794046--5794137 Score: 105
Period size: 31 Copynumber: 2.9 Consensus size: 31
5794036 ATAATATAAA
* *
5794046 AATA-ATTAAAATATAATATGATATAAATATAT
1 AATATATTAAAAT-TTATATAATATAAAT-TAT
*
5794078 GAATATTTTAAAATTTATATAATATAAATTAT
1 -AATATATTAAAATTTATATAATATAAATTAT
*
5794110 AATGTATTAAAATTTATATAAATATAAA
1 AATATATTAAAATTTATAT-AATATAAA
5794138 ATTAAAATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
31 17 0.33
32 11 0.21
33 17 0.33
34 7 0.13
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (31 bp):
AATATATTAAAATTTATATAATATAAATTAT
Found at i:5794123 original size:31 final size:33
Alignment explanation
Indices: 5794033--5794137 Score: 110
Period size: 33 Copynumber: 3.2 Consensus size: 33
5794023 ATGTTTTACA
** *
5794033 AATAT-AATATAAAAATA-ATTAAAATATAATAT
1 AATATAAATATATGAATATATTAAAAT-TTATAT
* *
5794065 GATATAAATATATGAATATTTTAAAATTTATAT
1 AATATAAATATATGAATATATTAAAATTTATAT
*
5794098 AATATAAAT-TAT-AATGTATTAAAATTTATAT
1 AATATAAATATATGAATATATTAAAATTTATAT
5794129 AAATATAAA
1 -AATATAAA
5794138 ATTAAAATTT
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
31 17 0.27
32 15 0.24
33 23 0.37
34 7 0.11
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (33 bp):
AATATAAATATATGAATATATTAAAATTTATAT
Found at i:5794137 original size:17 final size:17
Alignment explanation
Indices: 5794086--5794140 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
5794076 ATGAATATTT
5794086 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
**
5794102 T-AAA-TTATA-ATGTA
1 TAAAATTTATATAAATA
5794116 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
5794134 TAAAATT
1 TAAAATT
5794141 AAAATTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 9
0.70 0.09 0.21
Matches are distributed among these distances:
14 7 0.23
15 4 0.13
16 4 0.13
17 12 0.40
18 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:5794152 original size:32 final size:31
Alignment explanation
Indices: 5794051--5794152 Score: 98
Period size: 33 Copynumber: 3.2 Consensus size: 31
5794041 ATAAAAATAA
* * * *
5794051 TTAAAATATAATATGATATAAATATATGAATATT
1 TTAAAAT-TTATATAATATAAAT-TA-AAATGTT
* *
5794085 TTAAAATTTATATAATATAAATTATAATGTA
1 TTAAAATTTATATAATATAAATTAAAATGTT
5794116 TTAAAATTTATATAAATATAAAATTAAAAT-TT
1 TTAAAATTTATAT-AATAT-AAATTAAAATGTT
5794148 TTAAA
1 TTAAA
5794153 TATGATTATG
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
31 17 0.29
32 13 0.22
33 22 0.37
34 7 0.12
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (31 bp):
TTAAAATTTATATAATATAAATTAAAATGTT
Found at i:5794409 original size:24 final size:25
Alignment explanation
Indices: 5794355--5794409 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
5794345 AAAAAATTAA
*
5794355 AATATTAAAATTTTTATAATTAAAT
1 AATAATAAAATTTTTATAATTAAAT
**
5794380 TTTAATAAAA-TTTTATTAA-TAAAT
1 AATAATAAAATTTTTA-TAATTAAAT
5794404 AATAAT
1 AATAAT
5794410 TTAAATTAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AATAATAAAATTTTTATAATTAAAT
Found at i:5795335 original size:17 final size:19
Alignment explanation
Indices: 5795313--5795347 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
5795303 AATTACAAAT
5795313 TAATATT-TA-ATTAACAC
1 TAATATTATATATTAACAC
5795330 TAATATTATATATTAACA
1 TAATATTATATATTAACA
5795348 AATTATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (19 bp):
TAATATTATATATTAACAC
Found at i:5796050 original size:20 final size:20
Alignment explanation
Indices: 5796026--5796077 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
5796016 ATTAAATATT
5796026 ATATTTATTTAAAA-TTAAA
1 ATATTTATTTAAAATTTAAA
*
5796045 ATTATTT-TTAAAAAATTTAAA
1 A-TATTTATT-TAAAATTTAAA
5796066 AT-TTTATTTAAA
1 ATATTTATTTAAA
5796078 TCAATAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
19 9 0.33
20 12 0.44
21 6 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTTATTTAAAATTTAAA
Done.