Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, whole genome shotgun sequence
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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 23 of 195
Found at i:5289738 original size:125 final size:125
Alignment explanation
Indices: 5289446--5289745 Score: 291
Period size: 125 Copynumber: 2.4 Consensus size: 125
5289436 ATGTTATTGT
* * * * ** * * * *
5289446 AAATTTAATATATAATTTAATAGAAATATTATAATAAATTTTAAATAAAATATCATATGTTAAAT
1 AAATTTAATATGTAACTTAATA-AAACATTATAATAAATTTCAAAT-AGGTAACTTTTG-AAAAT
* *
5289511 TTTATGAATTAATGACAAGAGTATTTCAATAATTTAATATGTAATTAATTTTACATTATATTA
63 TTTATGAAGTAATGACAAGAGTATTTCAATAATTTAATATATAATTAATTTTACATTATATTA
* * ** * *
5289574 AAATTTCATATGTAATTTAATAAGGCCTTATAGTAAATTTCAAATAGGTAACTTTTGAAAATTTT
1 AAATTTAATATGTAACTTAATAAAACATTATAATAAATTTCAAATAGGTAACTTTTGAAAATTTT
* * * *
5289639 ATTAAGTAATGACAATGA-TATTTTAGA-AATTTAATATATAATTAATTTTATATTATGTTA
66 ATGAAGTAATGACAA-GAGTATTTCA-ATAATTTAATATATAATTAATTTTACATTATATTA
* * *
5289699 AAATTTAATACT-TAACTTGATAAAAACATTATAATAATTTTAAAATA
1 AAATTTAATA-TGTAACTTAAT-AAAACATTATAATAAATTTCAAATA
5289746 AAATACCACA
Statistics
Matches: 139, Mismatches: 29, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
125 72 0.52
126 30 0.22
127 17 0.12
128 20 0.14
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (125 bp):
AAATTTAATATGTAACTTAATAAAACATTATAATAAATTTCAAATAGGTAACTTTTGAAAATTTT
ATGAAGTAATGACAAGAGTATTTCAATAATTTAATATATAATTAATTTTACATTATATTA
Found at i:5290289 original size:2 final size:2
Alignment explanation
Indices: 5290282--5290310 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5290272 GAATCTTTAC
5290282 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5290311 GAGAAAGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5298521 original size:31 final size:31
Alignment explanation
Indices: 5298486--5298599 Score: 140
Period size: 31 Copynumber: 3.6 Consensus size: 31
5298476 ATCCATGTAT
* * *
5298486 TTATATAAAATTTAAAATTTAATATTTTTAC
1 TTATATAAAATTTAAAATTTAATCTCTATAC
* *
5298517 TTATATAAAATTTAAAATTTACTCTCTGTA-
1 TTATATAAAATTTAAAATTTAATCTCTATAC
* *
5298547 GTATCATAATATTTAAAATTTAATCTCTATAC
1 TTAT-ATAAAATTTAAAATTTAATCTCTATAC
5298579 TTATATAAAATTTTAAAATTT
1 TTATATAAAA-TTTAAAATTT
5298600 TGTTCCTATA
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
30 3 0.04
31 54 0.77
32 13 0.19
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (31 bp):
TTATATAAAATTTAAAATTTAATCTCTATAC
Found at i:5299488 original size:16 final size:14
Alignment explanation
Indices: 5299453--5299490 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
5299443 AATTTTGTTA
5299453 TATTAAT-TTAAAT
1 TATTAATATTAAAT
5299466 TATTAATATTATAAT
1 TATTAATATTA-AAT
5299481 TGATTAATAT
1 T-ATTAATAT
5299491 ATATGATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.32
14 3 0.14
15 4 0.18
16 8 0.36
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
TATTAATATTAAAT
Found at i:5299514 original size:20 final size:19
Alignment explanation
Indices: 5299464--5299518 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
5299454 ATTAATTTAA
*
5299464 ATTATTAATATTATAATTG
1 ATTATTAATATGATAATTG
*
5299483 ATTAATATATATGATAATAAT-
1 ATTATTA-ATATGATAAT--TG
5299504 ATTATTAATATGATA
1 ATTATTAATATGATA
5299519 TTATTAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 6 0.20
20 17 0.57
21 6 0.20
22 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (19 bp):
ATTATTAATATGATAATTG
Found at i:5299537 original size:17 final size:17
Alignment explanation
Indices: 5299516--5299567 Score: 50
Period size: 20 Copynumber: 2.9 Consensus size: 17
5299506 TATTAATATG
*
5299516 ATATTATTAAAAATTAA
1 ATATTATTAAAAATAAA
*
5299533 TTATTTATAATAAAAATAAA
1 ATA-TTAT--TAAAAATAAA
*
5299553 ATATTTTTAAAAATA
1 ATATTATTAAAAATA
5299568 TCTTTTATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
17 10 0.36
18 4 0.14
19 3 0.11
20 11 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATTATTAAAAATAAA
Found at i:5299891 original size:14 final size:14
Alignment explanation
Indices: 5299842--5299902 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
5299832 TAAAATTTTC
*
5299842 AAATTAAAATAATATA
1 AAATT-AAATTATA-A
*
5299858 AAATTAAATTTATAT
1 AAATTAAA-TTATAA
* *
5299873 GAATTATATTATAA
1 AAATTAAATTATAA
*
5299887 AAATTAAATTTTAA
1 AAATTAAATTATAA
5299901 AA
1 AA
5299903 TTTCGTAAAG
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
14 18 0.50
15 9 0.25
16 9 0.25
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (14 bp):
AAATTAAATTATAA
Found at i:5312403 original size:13 final size:13
Alignment explanation
Indices: 5312387--5312411 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5312377 ATTTTTTAAA
5312387 AGTTTTTTTTTTT
1 AGTTTTTTTTTTT
5312400 AGTTTTTTTTTT
1 AGTTTTTTTTTT
5312412 ATTTTATTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (13 bp):
AGTTTTTTTTTTT
Found at i:5314847 original size:22 final size:23
Alignment explanation
Indices: 5314802--5314849 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
5314792 AGATTATAAC
5314802 TTTGTAAGTATTATTATTATTTT
1 TTTGTAAGTATTATTATTATTTT
*
5314825 TTTGTAA-TATT-TTATTTTATTT
1 TTTGTAAGTATTATTATTAT-TTT
5314847 TTT
1 TTT
5314850 ATTTAGTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 6 0.26
22 10 0.43
23 7 0.30
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (23 bp):
TTTGTAAGTATTATTATTATTTT
Found at i:5314848 original size:24 final size:23
Alignment explanation
Indices: 5314812--5314866 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
5314802 TTTGTAAGTA
5314812 TTATTATTATTTTT-TTGTAATATT
1 TTATT-TTATTTTTATT-TAATATT
*
5314836 TTATTTTATTTTTTATTTAGTATT
1 TTATTTTA-TTTTTATTTAATATT
*
5314860 ATATTTT
1 TTATTTT
5314867 TGTGAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 3 0.11
24 22 0.81
25 2 0.07
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.73
Consensus pattern (23 bp):
TTATTTTATTTTTATTTAATATT
Found at i:5316668 original size:26 final size:25
Alignment explanation
Indices: 5316610--5316676 Score: 79
Period size: 26 Copynumber: 2.8 Consensus size: 25
5316600 CGACCCGATA
* *
5316610 TATATATATATAATTTT-T-TTAAT
1 TATATATATTTAATTTTATAATAAT
5316633 TAT-T-TATTTAATTTTATAATAATT
1 TATATATATTTAATTTTATAATAA-T
5316657 TATATATATTTAATTTTATA
1 TATATATATTTAATTTTATA
5316677 TTTATATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
21 10 0.27
22 2 0.05
23 6 0.16
24 4 0.11
25 1 0.03
26 14 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TATATATATTTAATTTTATAATAAT
Found at i:5316676 original size:12 final size:13
Alignment explanation
Indices: 5316627--5316685 Score: 54
Period size: 12 Copynumber: 4.6 Consensus size: 13
5316617 ATATAATTTT
5316627 TTTAATTATT-TA
1 TTTAATTATTATA
5316639 TTTAATT-TTATA
1 TTTAATTATTATA
*
5316651 -ATAATTTATATATA
1 TTTAA-TTAT-TATA
5316665 TTTAATT-TTATA
1 TTTAATTATTATA
5316677 TTTATATTA
1 TTTA-ATTA
5316686 AAAATAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
11 5 0.13
12 19 0.50
13 5 0.13
14 6 0.16
15 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTAATTATTATA
Found at i:5318679 original size:12 final size:13
Alignment explanation
Indices: 5318630--5318688 Score: 52
Period size: 12 Copynumber: 4.6 Consensus size: 13
5318620 ATATAATTTT
5318630 TTTAATTATT-TA
1 TTTAATTATTATA
5318642 TTTAATT-TTATA
1 TTTAATTATTATA
* * *
5318654 ATGATTTATATATA
1 TTTAATTAT-TATA
5318668 TTTAATT-TTATA
1 TTTAATTATTATA
5318680 TTTATATTA
1 TTTA-ATTA
5318689 AAAATAATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
11 2 0.06
12 21 0.58
13 5 0.14
14 8 0.22
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (13 bp):
TTTAATTATTATA
Found at i:5320570 original size:72 final size:73
Alignment explanation
Indices: 5320443--5320603 Score: 166
Period size: 73 Copynumber: 2.2 Consensus size: 73
5320433 TTTAGAAGTA
* * * **
5320443 TCATTTTTTCAACAAATTTATGTTTTTATCTTAAAAATATCATATTTATTAAAATTTGAA-AACT
1 TCATGTTTTCAACAAATTTATGTTTCTATATTAAAAATATCATATTTATTAAAATTTGAACAAAA
5320507 ACATTTTT
66 ACATTTTT
* * * ** * *
5320515 TCATGTTTTCAACAAATATTGTGTTTCTATATTAGAAATGTTGTCTTTATT-AAATTTTAACAAA
1 TCATGTTTTCAACAAAT-TTATGTTTCTATATTAAAAATATCATATTTATTAAAATTTGAACAAA
*
5320579 AATATTTTT
65 AACATTTTT
5320588 TCATG-TTTCTAACAAA
1 TCATGTTTTC-AACAAA
5320604 GACTGTATTT
Statistics
Matches: 73, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
72 28 0.38
73 45 0.62
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (73 bp):
TCATGTTTTCAACAAATTTATGTTTCTATATTAAAAATATCATATTTATTAAAATTTGAACAAAA
ACATTTTT
Found at i:5323490 original size:18 final size:18
Alignment explanation
Indices: 5323453--5323491 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5323443 TGCTCTTGGA
* * *
5323453 AGCCATAGCTTTTCTGGC
1 AGCCATACCTTTCCTAGC
5323471 AGCCATACCTTTCCTAGC
1 AGCCATACCTTTCCTAGC
5323489 AGC
1 AGC
5323492 TCTTGCGTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.33, G:0.18, T:0.28
Consensus pattern (18 bp):
AGCCATACCTTTCCTAGC
Found at i:5325689 original size:5 final size:5
Alignment explanation
Indices: 5325681--5325718 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
5325671 TTTTAAATGT
* *
5325681 TTTTA TTTTA TTTTA TTATA TTTTA TTAT- TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
5325719 TTAAAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
4 3 0.11
5 25 0.89
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:5325866 original size:27 final size:27
Alignment explanation
Indices: 5325784--5325881 Score: 74
Period size: 27 Copynumber: 3.6 Consensus size: 27
5325774 CATATATGAT
* *
5325784 AATTTAAAATAATGATTAT-AAATAATA
1 AATTTAAAATAAT-TTTATAAAAAAATA
* * **
5325811 TATTTGAAATAATTTTA-ATAAAATTTA
1 AATTTAAAATAATTTTATA-AAAAAATA
*
5325838 AATTTAAAATTATTTTATAAAAAAATA
1 AATTTAAAATAATTTTATAAAAAAATA
**
5325865 AACCTAAAATTAATTTT
1 AATTTAAAA-TAATTTT
5325882 TTATTAATTA
Statistics
Matches: 53, Mismatches: 14, Indels: 7
0.72 0.19 0.09
Matches are distributed among these distances:
26 3 0.06
27 43 0.81
28 7 0.13
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (27 bp):
AATTTAAAATAATTTTATAAAAAAATA
Found at i:5326253 original size:19 final size:20
Alignment explanation
Indices: 5326231--5326268 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5326221 ATTTAAAACG
*
5326231 TAATAAATTAAT-TAAATAA
1 TAATAAAATAATATAAATAA
5326250 TAATAAAATAATATAAATA
1 TAATAAAATAATATAAATA
5326269 TTTTCATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TAATAAAATAATATAAATAA
Found at i:5334524 original size:21 final size:19
Alignment explanation
Indices: 5334498--5334542 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
5334488 GTTTATTACA
5334498 TTTTTAAATACATTT-TTTAT
1 TTTTTAAA-ACATTTATTT-T
*
5334518 TTTTTTAAACATTTATTTT
1 TTTTTAAAACATTTATTTT
5334537 TTTTTA
1 TTTTTA
5334543 TTCTCAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTAAAACATTTATTTT
Found at i:5334529 original size:19 final size:18
Alignment explanation
Indices: 5334507--5334542 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5334497 ATTTTTAAAT
*
5334507 ACATTTTTTATTTTTTTAA
1 ACATTTATT-TTTTTTTAA
5334526 ACATTTATTTTTTTTTA
1 ACATTTATTTTTTTTTA
5334543 TTCTCAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (18 bp):
ACATTTATTTTTTTTTAA
Found at i:5335369 original size:11 final size:11
Alignment explanation
Indices: 5335353--5335383 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
5335343 TGTTAATCTA
5335353 TTTTAAAATTT
1 TTTTAAAATTT
*
5335364 TTTTAAAACTT
1 TTTTAAAATTT
5335375 TTTTAAAAT
1 TTTTAAAAT
5335384 GAATTTTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATTT
Found at i:5349191 original size:23 final size:23
Alignment explanation
Indices: 5349165--5349208 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5349155 TTTTAAAAGT
*
5349165 AATTTTTAAATAAAATTTTTTGA
1 AATTTTGAAATAAAATTTTTTGA
* *
5349188 AATTTTGAAATCAATTTTTTT
1 AATTTTGAAATAAAATTTTTT
5349209 TCTCCGCCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (23 bp):
AATTTTGAAATAAAATTTTTTGA
Found at i:5350131 original size:17 final size:17
Alignment explanation
Indices: 5350109--5350146 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
5350099 AAAACGTATT
5350109 AAATAATAC-CTTTAAAA
1 AAATAATACAC-TTAAAA
*
5350126 AAATAATGCACTTAAAA
1 AAATAATACACTTAAAA
5350143 AAAT
1 AAAT
5350147 TAAGGCGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.61, C:0.11, G:0.03, T:0.26
Consensus pattern (17 bp):
AAATAATACACTTAAAA
Found at i:5350201 original size:22 final size:18
Alignment explanation
Indices: 5350153--5350189 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5350143 AAATTAAGGC
5350153 GTTTTTAAATAATCACCT
1 GTTTTTAAATAATCACCT
5350171 GTTTTTAAATAATCACCT
1 GTTTTTAAATAATCACCT
5350189 G
1 G
5350190 ATACATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.43
Consensus pattern (18 bp):
GTTTTTAAATAATCACCT
Found at i:5350689 original size:22 final size:22
Alignment explanation
Indices: 5350653--5350697 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
5350643 AAAAACTAAT
5350653 AAAAAATTACTATAA-TATATCA
1 AAAAAATTACTATAACTAT-TCA
5350675 AAAAAATTA-TGATAACTATTCA
1 AAAAAATTACT-ATAACTATTCA
5350697 A
1 A
5350698 GAATTAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 1 0.05
22 17 0.81
23 3 0.14
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (22 bp):
AAAAAATTACTATAACTATTCA
Found at i:5350812 original size:17 final size:17
Alignment explanation
Indices: 5350777--5350810 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5350767 AAACTTGAGT
5350777 ATCATATTTTTTTATAA
1 ATCATATTTTTTTATAA
5350794 ATCATATTTTTTT-TAA
1 ATCATATTTTTTTATAA
5350810 A
1 A
5350811 ATTTAAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (17 bp):
ATCATATTTTTTTATAA
Found at i:5350950 original size:17 final size:17
Alignment explanation
Indices: 5350926--5350963 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
5350916 TTTTCATATA
*
5350926 AAATAAAAA-AGTAATT
1 AAATAAAAATAATAATT
*
5350942 AAATAAAAATAATATTT
1 AAATAAAAATAATAATT
5350959 AAATA
1 AAATA
5350964 TTCAATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
AAATAAAAATAATAATT
Found at i:5356271 original size:3 final size:3
Alignment explanation
Indices: 5356265--5356331 Score: 127
Period size: 3 Copynumber: 22.7 Consensus size: 3
5356255 ATCCAACTCA
5356265 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5356313 AAT AAT AA- AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
5356332 ACGATTTAGT
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 61 0.97
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5357719 original size:21 final size:21
Alignment explanation
Indices: 5357693--5357740 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
5357683 TGTTATGAAT
5357693 TATTTATAAG-TTGTAACAAAA
1 TATTTATAAGATTGTAA-AAAA
*
5357714 TATTTAATAAGATTTTAAAAAA
1 TATTT-ATAAGATTGTAAAAAA
5357736 T-TTTA
1 TATTTA
5357741 ACGTGATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 8 0.33
22 10 0.42
23 5 0.21
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (21 bp):
TATTTATAAGATTGTAAAAAA
Found at i:5357735 original size:22 final size:22
Alignment explanation
Indices: 5357693--5357741 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
5357683 TGTTATGAAT
5357693 TATTT-ATAAGTTGTAACAAAA
1 TATTTAATAAGTTGTAACAAAA
*
5357714 TATTTAATAAGATTTTAA-AAAA
1 TATTTAATAAG-TTGTAACAAAA
5357736 T-TTTAA
1 TATTTAA
5357742 CGTGATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 10 0.40
22 10 0.40
23 5 0.20
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (22 bp):
TATTTAATAAGTTGTAACAAAA
Found at i:5357799 original size:15 final size:15
Alignment explanation
Indices: 5357779--5357811 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5357769 ATTTAATTAA
*
5357779 TATTTAATTTTAATT
1 TATTTAATTTTAAAT
5357794 TATTTAATTTTAAAT
1 TATTTAATTTTAAAT
5357809 TAT
1 TAT
5357812 AAATAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTTAATTTTAAAT
Found at i:5357883 original size:27 final size:31
Alignment explanation
Indices: 5357828--5357932 Score: 90
Period size: 27 Copynumber: 3.7 Consensus size: 31
5357818 TTAATTTATA
5357828 TAAATATTATATTAATTAATATATCTT-AATT
1 TAAATATTATATTAA-TAATATATCTTAAATT
*
5357859 TAAATATTATATTAA-AA-A-ATTTTAAATT
1 TAAATATTATATTAATAATATATCTTAAATT
5357887 TAAATA-TATATT--TAATAT-T-TTACAATT
1 TAAATATTATATTAATAATATATCTTA-AATT
5357914 T-AATGATTAT-TT-ATAATAT
1 TAAAT-ATTATATTAATAATAT
5357933 TAATGCAAAT
Statistics
Matches: 65, Mismatches: 1, Indels: 19
0.76 0.01 0.22
Matches are distributed among these distances:
26 8 0.12
27 20 0.31
28 20 0.31
29 2 0.03
31 15 0.23
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (31 bp):
TAAATATTATATTAATAATATATCTTAAATT
Found at i:5358253 original size:31 final size:31
Alignment explanation
Indices: 5358197--5358255 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
5358187 AAGTTTAAGT
* *
5358197 TTTAATTTGATTTGATATTTGTTTTTAAAAA
1 TTTAATTTGATTTAATATTTATTTTTAAAAA
5358228 TTTAATTTGATTTAAT-TTTAATTTTTAA
1 TTTAATTTGATTTAATATTT-ATTTTTAA
5358256 TTTCGAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (31 bp):
TTTAATTTGATTTAATATTTATTTTTAAAAA
Found at i:5359214 original size:21 final size:23
Alignment explanation
Indices: 5359169--5359219 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
5359159 CTTAATATTC
* *
5359169 AAATTGTGAAGGTGTTTATGAGA
1 AAATTTTGAAGGTGTTTACGAGA
5359192 AAATTTTG-AGGTGTTT-CGAGA
1 AAATTTTGAAGGTGTTTACGAGA
5359213 AAATTTT
1 AAATTTT
5359220 TTCTTCAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 11 0.42
22 8 0.31
23 7 0.27
ACGTcount: A:0.33, C:0.02, G:0.25, T:0.39
Consensus pattern (23 bp):
AAATTTTGAAGGTGTTTACGAGA
Found at i:5361243 original size:2 final size:2
Alignment explanation
Indices: 5361238--5361275 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5361228 TATATATATA
5361238 TG TG TG TG TG TG 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 TG TG TG TG TG TG
5361276 AAAATAGATT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:5362819 original size:82 final size:82
Alignment explanation
Indices: 5362682--5362846 Score: 312
Period size: 82 Copynumber: 2.0 Consensus size: 82
5362672 AATGCAAAAC
5362682 TACGAAGCTTTACAGCTTAGAAAATAAATGTCCTTGTAACAAGTACATATGTTTCTCATTTGTTG
1 TACGAAGCTTTACAGCTTAGAAAATAAATGTCCTTGTAACAAGTACATATGTTTCTCATTTGTTG
5362747 CCCGTTTTTCATATATA
66 CCCGTTTTTCATATATA
*
5362764 TACGAAGCTTTGCAGCTTAGAAAATAAATGTCCTTGTAACAAGTACATATGTTTCTCATTTGTTG
1 TACGAAGCTTTACAGCTTAGAAAATAAATGTCCTTGTAACAAGTACATATGTTTCTCATTTGTTG
*
5362829 CCTGTTTTTCATATATA
66 CCCGTTTTTCATATATA
5362846 T
1 T
5362847 GTGTGTGTGT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (82 bp):
TACGAAGCTTTACAGCTTAGAAAATAAATGTCCTTGTAACAAGTACATATGTTTCTCATTTGTTG
CCCGTTTTTCATATATA
Found at i:5371699 original size:17 final size:17
Alignment explanation
Indices: 5371673--5371712 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
5371663 GCAATGAAAA
*
5371673 CATTCTGCTCACTGTTT
1 CATTCCGCTCACTGTTT
5371690 CATTCCGCTCACTGTTT
1 CATTCCGCTCACTGTTT
5371707 CATTCC
1 CATTCC
5371713 ATTATCACCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.12, C:0.35, G:0.10, T:0.42
Consensus pattern (17 bp):
CATTCCGCTCACTGTTT
Found at i:5404827 original size:13 final size:14
Alignment explanation
Indices: 5404797--5404829 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5404787 TATTAAAATT
*
5404797 TATTTATTATTAAA
1 TATTTATTAGTAAA
5404811 TATTTATTAGT-AA
1 TATTTATTAGTAAA
5404824 TATTTA
1 TATTTA
5404830 AAAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (14 bp):
TATTTATTAGTAAA
Found at i:5404856 original size:14 final size:15
Alignment explanation
Indices: 5404815--5404882 Score: 50
Period size: 16 Copynumber: 4.5 Consensus size: 15
5404805 ATTAAATATT
*
5404815 TATTAGTAATATTTAA
1 TATTAATAATATTT-A
* * *
5404831 AAATAATTATATTT-
1 TATTAATAATATTTA
5404845 TATTAATAATATTTAA
1 TATTAATAATATTT-A
*
5404861 TATTAAAAATA-TTA
1 TATTAATAATATTTA
*
5404875 TGTTAATA
1 TATTAATA
5404883 TAAAAAATTT
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
14 18 0.45
15 2 0.05
16 20 0.50
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (15 bp):
TATTAATAATATTTA
Found at i:5404866 original size:16 final size:16
Alignment explanation
Indices: 5404815--5404873 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
5404805 ATTAAATATT
*
5404815 TATTAGTAATATTTAA
1 TATTAATAATATTTAA
* * *
5404831 AAATAATTATATTT--
1 TATTAATAATATTTAA
5404845 TATTAATAATATTTAA
1 TATTAATAATATTTAA
*
5404861 TATTAAAAATATT
1 TATTAATAATATT
5404874 ATGTTAATAT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
14 11 0.33
16 22 0.67
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
TATTAATAATATTTAA
Found at i:5404873 original size:30 final size:30
Alignment explanation
Indices: 5404808--5404882 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
5404798 ATTTATTATT
*
5404808 AAATA-TTTATTAGTAATATTTAAAAATAA
1 AAATATTTTATTAATAATATTTAAAAATAA
** * *
5404837 TTATATTTTATTAATAATATTTAATATTAA
1 AAATATTTTATTAATAATATTTAAAAATAA
* *
5404867 AAATATTATGTTAATA
1 AAATATTTTATTAATA
5404883 TAAAAAATTT
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
29 3 0.08
30 33 0.92
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (30 bp):
AAATATTTTATTAATAATATTTAAAAATAA
Found at i:5404952 original size:15 final size:16
Alignment explanation
Indices: 5404936--5404969 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
5404926 ATTAATAGAT
5404936 TATAATATTATTTATTAA
1 TATAATATTATTTA-T-A
5404954 TATAATATTATTTATA
1 TATAATATTATTTATA
5404970 AGTAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 1 0.06
18 14 0.88
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATAATATTATTTATA
Found at i:5416649 original size:41 final size:42
Alignment explanation
Indices: 5416604--5416690 Score: 140
Period size: 41 Copynumber: 2.1 Consensus size: 42
5416594 GCTATTAATT
* * *
5416604 TTTTTTATCTAAGTATGATTTGGCTACTTAAGGAATCTAT-A
1 TTTTTTATCTAAGTATGACTTGGCTACCTAAAGAATCTATCA
5416645 TTTTTTATCTAAGTATGACTTGGCTACCTAAAGAATCTATCA
1 TTTTTTATCTAAGTATGACTTGGCTACCTAAAGAATCTATCA
5416687 TTTT
1 TTTT
5416691 AAAGAGCTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 37 0.88
42 5 0.12
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.46
Consensus pattern (42 bp):
TTTTTTATCTAAGTATGACTTGGCTACCTAAAGAATCTATCA
Found at i:5418387 original size:12 final size:11
Alignment explanation
Indices: 5418371--5418429 Score: 64
Period size: 11 Copynumber: 5.1 Consensus size: 11
5418361 CATCGAAAAC
5418371 TAAAAAATTTT
1 TAAAAAATTTT
5418382 TAAAAAATTTT
1 TAAAAAATTTT
* *
5418393 TCAGAAATTTT
1 TAAAAAATTTT
5418404 CTAAAAAATTTT
1 -TAAAAAATTTT
*
5418416 CAGAAAAATCTTT
1 TA-AAAAAT-TTT
5418429 T
1 T
5418430 TTTTAACCCA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
11 21 0.54
12 15 0.38
13 3 0.08
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (11 bp):
TAAAAAATTTT
Found at i:5418400 original size:22 final size:22
Alignment explanation
Indices: 5418375--5418421 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 22
5418365 GAAAACTAAA
5418375 AAATTTT-TAAAAAATTTTTCAG
1 AAATTTTCTAAAAAA-TTTTCAG
5418397 AAATTTTCTAAAAAATTTTCAG
1 AAATTTTCTAAAAAATTTTCAG
5418419 AAA
1 AAA
5418422 AATCTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40
Consensus pattern (22 bp):
AAATTTTCTAAAAAATTTTCAG
Found at i:5418839 original size:4 final size:4
Alignment explanation
Indices: 5418815--5418852 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
5418805 ATAAACCAGA
* *
5418815 AAAT AATT AAAT AATT AAAT AAAT -AAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
5418853 ATATAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (4 bp):
AAAT
Found at i:5418854 original size:20 final size:20
Alignment explanation
Indices: 5418815--5418855 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
5418805 ATAAACCAGA
*
5418815 AAATAATTAAATAATTAAAT
1 AAATAATTAAATAATAAAAT
5418835 AAATAA-TAAATAAATAAAAT
1 AAATAATTAAAT-AATAAAAT
5418855 A
1 A
5418856 TAAAATAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATAATTAAATAATAAAAT
Found at i:5419542 original size:56 final size:55
Alignment explanation
Indices: 5419471--5419646 Score: 146
Period size: 56 Copynumber: 3.2 Consensus size: 55
5419461 TGAATTTTTC
* *
5419471 TTTTAAATTATTATGTTGTTTATTTTTTTATTAGTTTACATTAATTTGTTAAATTA
1 TTTTAATTTAATATGTT-TTTATTTTTTTATTAGTTTACATTAATTTGTTAAATTA
** * * * *
5419527 TTTTAATTTAATATGTACCTTATTTTTTTA-TATGTTTGCATTAA-TCGATCATATTA
1 TTTTAATTTAATATGT-TTTTATTTTTTTATTA-GTTTACATTAATTTG-TTAAATTA
* * * * * * *
5419583 TTTTAATTCAATA---TTTTATTTTTTTATTTGTTTATATTGATCTATTAGATTA
1 TTTTAATTTAATATGTTTTTATTTTTTTATTAGTTTACATTAATTTGTTAAATTA
5419635 TTTTAATTTAAT
1 TTTTAATTTAAT
5419647 TTGATGACTT
Statistics
Matches: 94, Mismatches: 21, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
52 36 0.38
53 1 0.01
55 4 0.04
56 53 0.56
ACGTcount: A:0.28, C:0.05, G:0.06, T:0.61
Consensus pattern (55 bp):
TTTTAATTTAATATGTTTTTATTTTTTTATTAGTTTACATTAATTTGTTAAATTA
Found at i:5419635 original size:52 final size:53
Alignment explanation
Indices: 5419487--5419642 Score: 170
Period size: 56 Copynumber: 2.9 Consensus size: 53
5419477 ATTATTATGT
* * * *
5419487 TGTTTATTTTTTTATTAGTTTACATTAATTTGTTAAATTATTTTAATTTAATA
1 TGTTTATTTTTTTATTTGTTTACATTAATCTATTAAATTATTTTAATTCAATA
* * * * *
5419540 TGTACCTTATTTTTTTATATGTTTGCATTAATCGATCATATTATTTTAATTCAATA
1 TGT---TTATTTTTTTATTTGTTTACATTAATCTATTAAATTATTTTAATTCAATA
* * *
5419596 T-TTTATTTTTTTATTTGTTTATATTGATCTATTAGATTATTTTAATT
1 TGTTTATTTTTTTATTTGTTTACATTAATCTATTAAATTATTTTAATT
5419643 TAATTTGATG
Statistics
Matches: 84, Mismatches: 16, Indels: 7
0.79 0.15 0.07
Matches are distributed among these distances:
52 38 0.45
53 3 0.04
55 1 0.01
56 42 0.50
ACGTcount: A:0.28, C:0.05, G:0.06, T:0.61
Consensus pattern (53 bp):
TGTTTATTTTTTTATTTGTTTACATTAATCTATTAAATTATTTTAATTCAATA
Found at i:5421682 original size:7 final size:7
Alignment explanation
Indices: 5421667--5421706 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
5421657 TTTGTCATTG
*
5421667 TCTAAGC
1 TCTAGGC
5421674 TCTAGGC
1 TCTAGGC
5421681 TCTAGGC
1 TCTAGGC
5421688 TCTAGGC
1 TCTAGGC
5421695 TCTAGGC
1 TCTAGGC
5421702 TCTAG
1 TCTAG
5421707 CCATTGCCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.17, C:0.28, G:0.25, T:0.30
Consensus pattern (7 bp):
TCTAGGC
Found at i:5434568 original size:23 final size:25
Alignment explanation
Indices: 5434542--5434587 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
5434532 TTAAACTTAT
5434542 TTATGGT-TTTTT-TAAATTTTAAA
1 TTATGGTATTTTTGTAAATTTTAAA
* *
5434565 TTATGTTATTTTTGTATATTTTA
1 TTATGGTATTTTTGTAAATTTTA
5434588 TTCATATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 5 0.26
25 8 0.42
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (25 bp):
TTATGGTATTTTTGTAAATTTTAAA
Found at i:5437158 original size:72 final size:73
Alignment explanation
Indices: 5437071--5437459 Score: 317
Period size: 70 Copynumber: 5.5 Consensus size: 73
5437061 ATTAATTTAT
* * *
5437071 TTTTAAGATCTACTATATTTTTTATGCTT-AAAATGCGATCTTTGTTAAAATTTTA-AATTTTCA
1 TTTTAACATCCACTATATTTTTTAT-CTTAAAAATGCGATCTTTGTTAAAATTTTATAATTTTCG
5437134 AAAATAAAA
65 AAAATAAAA
* ** * *
5437143 TTTTAACATCCAC--TATTTTTTATTTTAAAAATATGATTTTTGTTAAAATTTTATGATTTT-GA
1 TTTTAACATCCACTATATTTTTTATCTTAAAAATGCGATCTTTGTTAAAATTTTATAATTTTCGA
*
5437205 AAATAAAG
66 AAATAAAA
* ** * *
5437213 TTTTAACGT-CTTTATATTTCTTATCTTAAAAGCATG-G-TCTTTGTTAAAATTTCATAA-TTTC
1 TTTTAACATCCACTATATTTTTTATCTTAAAA--ATGCGATCTTTGTTAAAATTTTATAATTTTC
*
5437274 AAAAATAAAA
64 GAAAATAAAA
* * * * * *
5437284 TTTTCACATCTACTATATTTTTTATTTTAAAAACATG-AAT-TTTGTTAAAATTTCAAAATTTT-
1 TTTTAACATCCACTATATTTTTTATCTT-AAAA-ATGCGATCTTTGTTAAAATTTTATAATTTTC
5437346 GAAAATAAAA
64 GAAAATAAAA
* ** * ** *
5437356 TTTTAATATCCACTGCATTTTTTATTTTAAAAAAT---ATCTTTACTAAAATTTTAGAA-TTTCG
1 TTTTAACATCCACTATATTTTTTATCTT-AAAAATGCGATCTTTGTTAAAATTTTATAATTTTCG
5437417 AAAATAAAA
65 AAAATAAAA
* * * *
5437426 TTTTAATAT-CACCATGTTTTTTATCTTGAAAATG
1 TTTTAACATCCACTATATTTTTTATCTTAAAAATG
5437460 AAGTACTTAT
Statistics
Matches: 258, Mismatches: 45, Indels: 31
0.77 0.13 0.09
Matches are distributed among these distances:
68 5 0.02
69 21 0.08
70 85 0.33
71 54 0.21
72 83 0.32
73 10 0.04
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (73 bp):
TTTTAACATCCACTATATTTTTTATCTTAAAAATGCGATCTTTGTTAAAATTTTATAATTTTCGA
AAATAAAA
Found at i:5437360 original size:143 final size:141
Alignment explanation
Indices: 5437084--5437361 Score: 391
Period size: 143 Copynumber: 2.0 Consensus size: 141
5437074 TAAGATCTAC
* *
5437084 TATATTTTTTATGCTTAAAATGCGATCTTTGTTAAAATTTTAAATTTTCAAAAATAAAATTTTAA
1 TATATTTCTTATGCTTAAAATGCGATCTTTGTTAAAATTTCAAATTTTCAAAAATAAAATTTTAA
* * * ** *
5437149 CATCCACTATTTTTTATTTTAAAAATATGATTTTTGTTAAAATTTTATGATTTTGAAAATAAAGT
66 CATCCACTATTTTTTATTTTAAAAACATGAATTTTGTTAAAATTTCAAAATTTTGAAAATAAAAT
5437214 TTTAACGTCTT
131 TTTAACGTCTT
*
5437225 TATATTTCTTAT-CTTAAAA-GCATGGTCTTTGTTAAAATTTCATAA-TTTCAAAAATAAAATTT
1 TATATTTCTTATGCTTAAAATGC--GATCTTTGTTAAAATTTCA-AATTTTCAAAAATAAAATTT
* *
5437287 TCACATCTACTATATTTTTTATTTTAAAAACATGAATTTTGTTAAAATTTCAAAATTTTGAAAAT
63 TAACATCCAC--TATTTTTTATTTTAAAAACATGAATTTTGTTAAAATTTCAAAATTTTGAAAAT
5437352 AAAATTTTAA
126 AAAATTTTAA
5437362 TATCCACTGC
Statistics
Matches: 121, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
139 2 0.02
140 7 0.06
141 53 0.44
142 2 0.02
143 57 0.47
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (141 bp):
TATATTTCTTATGCTTAAAATGCGATCTTTGTTAAAATTTCAAATTTTCAAAAATAAAATTTTAA
CATCCACTATTTTTTATTTTAAAAACATGAATTTTGTTAAAATTTCAAAATTTTGAAAATAAAAT
TTTAACGTCTT
Found at i:5437432 original size:70 final size:72
Alignment explanation
Indices: 5437071--5437449 Score: 348
Period size: 72 Copynumber: 5.3 Consensus size: 72
5437061 ATTAATTTAT
* * * *
5437071 TTTTAAGATCTACTATATTTTTTATGCTTAAAATGC--GATCTTTGTTAAAATTTTA-AATTTTC
1 TTTTAACATCCACTATATTTTTTAT-TTTAAAA-ACATGATCTTTGTTAAAATTTTAGAA-TTTC
*
5437133 AAAAATAAAA
63 GAAAATAAAA
* * *
5437143 TTTTAACATCCAC--TATTTTTTATTTTAAAAATATGATTTTTGTTAAAATTTTATG-ATTTTGA
1 TTTTAACATCCACTATATTTTTTATTTTAAAAACATGATCTTTGTTAAAATTTTA-GAATTTCGA
*
5437205 AAATAAAG
65 AAATAAAA
* ** * * * * * * *
5437213 TTTTAACGT-CTTTATATTTCTTATCTTAAAAGCATGGTCTTTGTTAAAATTTCATAATTTCAAA
1 TTTTAACATCCACTATATTTTTTATTTTAAAAACATGATCTTTGTTAAAATTTTAGAATTTCGAA
5437277 AATAAAA
66 AATAAAA
* * * * *
5437284 TTTTCACATCTACTATATTTTTTATTTTAAAAACATGAAT-TTTGTTAAAATTTCAAAATTTTGA
1 TTTTAACATCCACTATATTTTTTATTTTAAAAACATG-ATCTTTGTTAAAATTTTAGAATTTCGA
5437348 AAATAAAA
65 AAATAAAA
* ** **
5437356 TTTTAATATCCACTGCATTTTTTATTTTAAAAA-AT-ATCTTTACTAAAATTTTAGAATTTCGAA
1 TTTTAACATCCACTATATTTTTTATTTTAAAAACATGATCTTTGTTAAAATTTTAGAATTTCGAA
5437419 AATAAAA
66 AATAAAA
* * *
5437426 TTTTAATAT-CACCATGTTTTTTAT
1 TTTTAACATCCACTATATTTTTTAT
5437450 CTTGAAAATG
Statistics
Matches: 248, Mismatches: 49, Indels: 23
0.77 0.15 0.07
Matches are distributed among these distances:
69 20 0.08
70 83 0.33
71 55 0.22
72 89 0.36
73 1 0.00
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (72 bp):
TTTTAACATCCACTATATTTTTTATTTTAAAAACATGATCTTTGTTAAAATTTTAGAATTTCGAA
AATAAAA
Found at i:5437684 original size:14 final size:15
Alignment explanation
Indices: 5437667--5437701 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
5437657 TTTCTAAACC
5437667 AAAATTAAAAAA-AT
1 AAAATTAAAAAAGAT
5437681 AAAATTAAAAAAGAT
1 AAAATTAAAAAAGAT
5437696 AAAATT
1 AAAATT
5437702 TCAATCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (15 bp):
AAAATTAAAAAAGAT
Found at i:5445430 original size:29 final size:29
Alignment explanation
Indices: 5445398--5445491 Score: 84
Period size: 30 Copynumber: 3.2 Consensus size: 29
5445388 AATTTTAATG
5445398 TAAAAATAAATAATATGTAAAAATTTATT
1 TAAAAATAAATAATATGTAAAAATTTATT
* * *
5445427 TAAAATATTATTAA-AT-TAATAAAATTTAATA
1 TAAAA-ATAAATAATATGT-A-AAAATTT-ATT
* * *
5445458 TAAAGATAAATAATAAGTAAAATTTTATT
1 TAAAAATAAATAATATGTAAAAATTTATT
5445487 TAAAA
1 TAAAA
5445492 TATTATTTAT
Statistics
Matches: 49, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
28 1 0.02
29 14 0.29
30 25 0.51
31 8 0.16
32 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (29 bp):
TAAAAATAAATAATATGTAAAAATTTATT
Found at i:5445453 original size:30 final size:29
Alignment explanation
Indices: 5445408--5445503 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 29
5445398 TAAAAATAAA
*
5445408 TAATATGTAAAAATTTATTTAAAATATTAT
1 TAATAAGT-AAAATTTATTTAAAATATTAT
* *
5445438 TAAATTAA-TAAAATTTAATATAAAGATA--AA
1 T-AA-TAAGTAAAATTT-ATTTAAA-ATATTAT
5445468 TAATAAGTAAAATTTTATTTAAAATATTAT
1 TAATAAGTAAAA-TTTATTTAAAATATTAT
*
5445498 TTATAA
1 TAATAA
5445504 TTTATATTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
28 6 0.12
29 13 0.25
30 19 0.37
31 9 0.17
32 5 0.10
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (29 bp):
TAATAAGTAAAATTTATTTAAAATATTAT
Found at i:5445455 original size:60 final size:60
Alignment explanation
Indices: 5445377--5445498 Score: 192
Period size: 60 Copynumber: 2.0 Consensus size: 60
5445367 AATAAAAGTT
* *
5445377 TTAAATTAAAAAATTTTAATGTAAAAATAAATAATATGTAAAAATTTATTTAAAATATTA
1 TTAAATTAAAAAATTTTAATATAAAAATAAATAATAAGTAAAAATTTATTTAAAATATTA
* *
5445437 TTAAATTAATAAAA-TTTAATATAAAGATAAATAATAAGTAAAATTTTATTTAAAATATTA
1 TTAAATTAA-AAAATTTTAATATAAAAATAAATAATAAGTAAAAATTTATTTAAAATATTA
5445497 TT
1 TT
5445499 TATAATTTAT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
60 53 0.93
61 4 0.07
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (60 bp):
TTAAATTAAAAAATTTTAATATAAAAATAAATAATAAGTAAAAATTTATTTAAAATATTA
Found at i:5445490 original size:12 final size:12
Alignment explanation
Indices: 5445475--5445514 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
5445465 AAATAATAAG
5445475 TAAAATTTTATT
1 TAAAATTTTATT
*
5445487 TAAAATATTATT
1 TAAAATTTTATT
*
5445499 TATAATTTATATT
1 TAAAATTT-TATT
5445512 TAA
1 TAA
5445515 TTGTTATGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
12 17 0.74
13 6 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TAAAATTTTATT
Found at i:5446186 original size:21 final size:22
Alignment explanation
Indices: 5446162--5446227 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 22
5446152 TAATATATTG
5446162 TATAAATTTATAT-TAATTTAA
1 TATAAATTTATATCTAATTTAA
* * *
5446183 TATAAATTTAAATCTTATATAA
1 TATAAATTTATATCTAATTTAA
*
5446205 T-T-AATTTAATATGTAATTTAA
1 TATAAATTT-ATATCTAATTTAA
5446226 TA
1 TA
5446228 GATTTTATTA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
20 5 0.14
21 23 0.66
22 7 0.20
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
TATAAATTTATATCTAATTTAA
Found at i:5446240 original size:36 final size:32
Alignment explanation
Indices: 5446169--5446255 Score: 83
Period size: 31 Copynumber: 2.7 Consensus size: 32
5446159 TTGTATAAAT
5446169 TTAT-ATTAATTTAATATAAATTTAAATCTTA
1 TTATAATTAATTTAATATAAATTTAAATCTTA
* *
5446200 -TATAATTAATTTAATATGTAATTTAATAGATTTTA
1 TTATAATTAATTTAATAT-AAATTT-A-A-ATCTTA
5446235 TTATAA-TAATTTTAATA-AAAT
1 TTATAATTAA-TTTAATATAAAT
5446256 GTAACATATC
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
30 3 0.07
31 13 0.28
32 5 0.11
33 1 0.02
34 4 0.09
35 8 0.17
36 12 0.26
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (32 bp):
TTATAATTAATTTAATATAAATTTAAATCTTA
Found at i:5448520 original size:18 final size:18
Alignment explanation
Indices: 5448489--5448534 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
5448479 TCTTATTAAC
*
5448489 TAAATTAATAACTTAAAAA
1 TAAA-TAATTACTTAAAAA
5448508 TAAATAATTACTTAAAAA
1 TAAATAATTACTTAAAAA
*
5448526 TAAAAAATT
1 TAAATAATT
5448535 TGTGATTTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAATAATTACTTAAAAA
Found at i:5448720 original size:3 final size:3
Alignment explanation
Indices: 5448712--5448751 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
5448702 TTTTCTTTCA
5448712 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5448752 ATACTACTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5449864 original size:21 final size:20
Alignment explanation
Indices: 5449829--5449869 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
5449819 TATATTTTAT
5449829 TTTTAAAAATATCAATATATA
1 TTTTAAAAATATCAA-ATATA
5449850 TTTTATAAAAT-TCAAATATA
1 TTTTA-AAAATATCAAATATA
5449870 AAAATATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTTAAAAATATCAAATATA
Found at i:5456276 original size:3 final size:3
Alignment explanation
Indices: 5456268--5456337 Score: 88
Period size: 3 Copynumber: 22.7 Consensus size: 3
5456258 TAATGAGTAA
*
5456268 AAT AAT AATT AAA AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AA-T AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
5456315 AAT AAT AAC AAT AA- AAT CAAT AA
1 AAT AAT AAT AAT AAT AAT -AAT AA
5456338 AAAATCAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
2 2 0.03
3 48 0.81
4 9 0.15
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:5456280 original size:12 final size:11
Alignment explanation
Indices: 5456253--5456342 Score: 83
Period size: 12 Copynumber: 7.5 Consensus size: 11
5456243 TTGTTCAATT
*
5456253 TAAAATAATGAG
1 TAAAATAAT-AA
5456265 TAAAATAATAA
1 TAAAATAATAA
5456276 TTAAAAATAAATAA
1 -T-AAAAT-AATAA
5456290 TAATAATAATAA
1 TAA-AATAATAA
5456302 TAATAATAATAA
1 TAA-AATAATAA
*
5456314 TAATAATAACAA
1 TAA-AATAATAA
5456326 TAAAATCAATAA
1 TAAAAT-AATAA
5456338 -AAAAT
1 TAAAAT
5456343 CAAAATAGAA
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
11 9 0.13
12 47 0.67
13 9 0.13
14 5 0.07
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:5457522 original size:226 final size:227
Alignment explanation
Indices: 5457124--5457565 Score: 726
Period size: 226 Copynumber: 2.0 Consensus size: 227
5457114 TTTTTCATTT
* * * *
5457124 GTTTGTTGTTTTCTTTTTTTATTGATTATCAATTAATTTTTTATTAAGGTAATAAACTAGAAATA
1 GTTTGTTGTTTTCTTTTTTGATTAATTATCAATTAATTTTTTATTAAGATAATAAACTAAAAATA
*
5457189 GGATAAAAAAAAAGTCAAACGGACCTATGTTAGGCTTAAAGCCCAAAATCAATTCAATGCCCAAT
66 GGATAAAAAAAAAGTCAAACGGACCTATGTTAGGCTGAAAGCCCAAAATCAATTCAATGCCCAAT
* *
5457254 TATTCAAAGCCAATGGGCCCTTCGAAAGCCCAATGGTTTTGACAAAATTGAAATGGAGAATTTCA
131 TATTCAAAGCCAATGGGCCCTTCGAAAGCCCAACGATTTTGACAAAATTGAAATGGAGAATTTCA
*
5457319 ATGCATG-TTCTAGACGAAATGGGGTGTTTACA
196 ATGCATGCCT-TAGACGAAATGGGGTGTTTACA
5457351 GTTTGTTGTTTTCTTTTTTGATTAATTATCAATTAATTTTTTATTAAGATAATAAACTAAAAATA
1 GTTTGTTGTTTTCTTTTTTGATTAATTATCAATTAATTTTTTATTAAGATAATAAACTAAAAATA
* *
5457416 GGAT-TAAAAAAAGTCAAACGGACCTATGTTGGGCTGAAAGCCCAAAATCAATTCAATGCCCAAT
66 GGATAAAAAAAAAGTCAAACGGACCTATGTTAGGCTGAAAGCCCAAAATCAATTCAATGCCCAAT
* * * * *
5457480 TATTCAAAGCTAATGGGCCTTTCGAAAGCGCAACGATTTTGACAAAATTGAAATTGAGAATTTGA
131 TATTCAAAGCCAATGGGCCCTTCGAAAGCCCAACGATTTTGACAAAATTGAAATGGAGAATTTCA
5457545 ATGCATGCCTTAGACGAAATG
196 ATGCATGCCTTAGACGAAATG
5457566 AGATATCTAT
Statistics
Matches: 199, Mismatches: 15, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
226 133 0.67
227 66 0.33
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (227 bp):
GTTTGTTGTTTTCTTTTTTGATTAATTATCAATTAATTTTTTATTAAGATAATAAACTAAAAATA
GGATAAAAAAAAAGTCAAACGGACCTATGTTAGGCTGAAAGCCCAAAATCAATTCAATGCCCAAT
TATTCAAAGCCAATGGGCCCTTCGAAAGCCCAACGATTTTGACAAAATTGAAATGGAGAATTTCA
ATGCATGCCTTAGACGAAATGGGGTGTTTACA
Found at i:5458068 original size:65 final size:64
Alignment explanation
Indices: 5457959--5458101 Score: 155
Period size: 64 Copynumber: 2.2 Consensus size: 64
5457949 TAGTCAGAAT
* * * *
5457959 AAAAAATAAATGACCAAATATTGAATCATAAATAAAAAATTAAATGATCTGGACCAAGCCAAGGC
1 AAAAAATAAGTGACCAAATATTGAATCACAAATAAAAAATTAAATGACCT-AACCAAGCCAAGGC
* * * ***
5458024 AAAAAATAAGTTACCAAA-ATTGAGTCACAAGTTAGAAAAA-TAAATGACCTAATTTAGCCAAGG
1 AAAAAATAAGTGACCAAATATTGAATCACAA-ATA-AAAAATTAAATGACCTAACCAAGCCAAGG
5458087 C
64 C
5458088 AAAAAATAAGTGAC
1 AAAAAATAAGTGAC
5458102 TGGGACTAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
64 33 0.51
65 27 0.42
66 5 0.08
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.20
Consensus pattern (64 bp):
AAAAAATAAGTGACCAAATATTGAATCACAAATAAAAAATTAAATGACCTAACCAAGCCAAGGC
Found at i:5458299 original size:60 final size:60
Alignment explanation
Indices: 5458235--5458376 Score: 171
Period size: 59 Copynumber: 2.4 Consensus size: 60
5458225 AGTGACAGGG
* * * * *
5458235 ATTGAACCGTAGGTAAAAAAATGATTTGAATTGAATCGAGA-TAAAAGATGAGTAACTTAA
1 ATTGAACTGTAGGTAAAAAAATAATTTGAACTGAATCAAGATTAAAA-ATGAGTAACTGAA
* * * * *
5458295 ATTGAATTGTAGTTAAAAAAA-AATTTGGACTGAATCAAGATTGAAAATGAGTGACTGAA
1 ATTGAACTGTAGGTAAAAAAATAATTTGAACTGAATCAAGATTAAAAATGAGTAACTGAA
5458354 ATTGAACTGTAGGTAAAAAAATA
1 ATTGAACTGTAGGTAAAAAAATA
5458377 CAATGTTCTA
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
59 45 0.66
60 23 0.34
ACGTcount: A:0.47, C:0.06, G:0.20, T:0.27
Consensus pattern (60 bp):
ATTGAACTGTAGGTAAAAAAATAATTTGAACTGAATCAAGATTAAAAATGAGTAACTGAA
Found at i:5461041 original size:29 final size:29
Alignment explanation
Indices: 5460985--5461041 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
5460975 TAGGTGTTGG
* *
5460985 ATATGAAGCATAATTTCTGAACTATTACA
1 ATATGAAGCATAATTTCTAAACCATTACA
* *
5461014 ATATGAAGCATAATTTTTAAACCGTTAC
1 ATATGAAGCATAATTTCTAAACCATTAC
5461042 CTTTCAAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (29 bp):
ATATGAAGCATAATTTCTAAACCATTACA
Found at i:5465873 original size:18 final size:18
Alignment explanation
Indices: 5465834--5465881 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
5465824 TAATGAGTCA
*
5465834 AATAATAATAATA-ATAAT
1 AATAA-AATAAAACATAAT
5465852 AATAAAATGAAAACATAA-
1 AATAAAAT-AAAACATAAT
5465870 AATAAAATAAAA
1 AATAAAATAAAA
5465882 AAAGTAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 7 0.26
18 16 0.59
19 4 0.15
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (18 bp):
AATAAAATAAAACATAAT
Found at i:5465882 original size:18 final size:19
Alignment explanation
Indices: 5465847--5465882 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5465837 AATAATAATA
*
5465847 ATAATAATAAAATGAAAAC
1 ATAATAATAAAATAAAAAC
5465866 ATAA-AATAAAATAAAAA
1 ATAATAATAAAATAAAAA
5465883 AAGTAAATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (19 bp):
ATAATAATAAAATAAAAAC
Found at i:5465883 original size:12 final size:13
Alignment explanation
Indices: 5465833--5465889 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
5465823 ATAATGAGTC
5465833 AAATAATAATAATA
1 AAATAATAA-AATA
5465847 ATAATAATAAAATGA
1 A-AATAATAAAAT-A
*
5465862 AAA-CATAAAATA
1 AAATAATAAAATA
*
5465874 AAATAAAAAAAGTA
1 AAATAATAAAA-TA
5465888 AA
1 AA
5465890 TACTTGTGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
12 4 0.11
13 12 0.33
14 10 0.28
15 10 0.28
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.21
Consensus pattern (13 bp):
AAATAATAAAATA
Found at i:5467572 original size:11 final size:10
Alignment explanation
Indices: 5467554--5467578 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5467544 ATAATCTAAC
5467554 AGAAAAAAAA
1 AGAAAAAAAA
5467564 AGAAAAAAAA
1 AGAAAAAAAA
5467574 AGAAA
1 AGAAA
5467579 GAGACTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:5472675 original size:14 final size:15
Alignment explanation
Indices: 5472643--5472672 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5472633 AATTTGTTTA
*
5472643 TATTCATTTAAATTT
1 TATTAATTTAAATTT
5472658 TATTAATTTAAATTT
1 TATTAATTTAAATTT
5472673 ATTTGATTAT
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:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTAATTTAAATTT
Found at i:5473173 original size:23 final size:21
Alignment explanation
Indices: 5473143--5473223 Score: 84
Period size: 23 Copynumber: 4.0 Consensus size: 21
5473133 ATTAGACACA
5473143 AAATAATTTATTTATTATTTAT
1 AAATAATTTATTTA-TATTTAT
5473165 AAATAAATTTA--TATATTTAT
1 AAAT-AATTTATTTATATTTAT
5473185 --AT-ATTTATTTAATATTTAT
1 AAATAATTTATTT-ATATTTAT
5473204 AAATAAATTTATTTA-ATTTA
1 AAAT-AATTTATTTATATTTA
5473224 ATCAAATTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 17
0.75 0.00 0.25
Matches are distributed among these distances:
16 5 0.10
18 3 0.06
19 8 0.16
20 7 0.14
21 9 0.18
22 5 0.10
23 14 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AAATAATTTATTTATATTTAT
Found at i:5473230 original size:23 final size:24
Alignment explanation
Indices: 5473187--5473235 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
5473177 ATATTTATAT
*
5473187 ATTTATTTAATATTTATAAA-TAA
1 ATTTATTTAATATTAATAAATTAA
5473210 ATTTATTTAAT-TTAATCAAATTAA
1 ATTTATTTAATATTAAT-AAATTAA
5473234 AT
1 AT
5473236 AAAAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 14 0.61
24 5 0.22
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTTATTTAATATTAATAAATTAA
Found at i:5474281 original size:7 final size:7
Alignment explanation
Indices: 5474269--5474293 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5474259 AAAGAGATTA
5474269 TAAATAT
1 TAAATAT
5474276 TAAATAT
1 TAAATAT
5474283 TAAATAT
1 TAAATAT
5474290 TAAA
1 TAAA
5474294 ATTTATTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
TAAATAT
Found at i:5478944 original size:65 final size:64
Alignment explanation
Indices: 5478837--5478966 Score: 215
Period size: 65 Copynumber: 2.0 Consensus size: 64
5478827 CTCAAGAAAG
* *
5478837 TGGAACCAGACCTAAACCTATTCTGCTTCCACCTATTTTCTTCTCTTCACCATTGAACGACACC
1 TGGAACCAGACCTAAACCTATTCTGCTTCCACCTATTGTCTTCTCTCCACCATTGAACGACACC
* *
5478901 TGGAACCAGACGTAAATCCTATTCTGCTTCCACCTATTGTCTTCTCTCCACCTTTGAACGACACC
1 TGGAACCAGACCTAAA-CCTATTCTGCTTCCACCTATTGTCTTCTCTCCACCATTGAACGACACC
5478966 T
1 T
5478967 ATTATTTTGT
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
64 15 0.25
65 46 0.75
ACGTcount: A:0.24, C:0.34, G:0.11, T:0.32
Consensus pattern (64 bp):
TGGAACCAGACCTAAACCTATTCTGCTTCCACCTATTGTCTTCTCTCCACCATTGAACGACACC
Found at i:5483121 original size:26 final size:23
Alignment explanation
Indices: 5483092--5483142 Score: 59
Period size: 22 Copynumber: 2.1 Consensus size: 23
5483082 AACAATAATG
5483092 ATTTTAATAATAATAATAAAAAATCA
1 ATTTTAAT--TAA-AATAAAAAATCA
*
5483118 A-TTTAATTAAAATTAAAAATCA
1 ATTTTAATTAAAATAAAAAATCA
5483140 ATT
1 ATT
5483143 AATTATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
22 12 0.52
23 4 0.17
25 6 0.26
26 1 0.04
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (23 bp):
ATTTTAATTAAAATAAAAAATCA
Found at i:5483122 original size:25 final size:22
Alignment explanation
Indices: 5483106--5483147 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5483096 TAATAATAAT
5483106 AATAAAAAATCAATTTAATTAA
1 AATAAAAAATCAATTTAATTAA
*
5483128 AATTAAAAATCAA-TTAATTA
1 AATAAAAAATCAATTTAATTA
5483148 TTAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (22 bp):
AATAAAAAATCAATTTAATTAA
Found at i:5483156 original size:21 final size:20
Alignment explanation
Indices: 5483109--5483157 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
5483099 TAATAATAAT
5483109 AAAAAATCAATTTAATTAAA
1 AAAAAATCAATTTAATTAAA
*
5483129 ATTAAAAATCAA-TTAATTATTA
1 A--AAAAATCAATTTAATTA-AA
5483151 AAAAAAT
1 AAAAAAT
5483158 AAAAAACAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 7 0.28
21 7 0.28
22 11 0.44
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAATCAATTTAATTAAA
Found at i:5484185 original size:18 final size:18
Alignment explanation
Indices: 5484135--5484185 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
5484125 GAATTTTCTA
* * *
5484135 ATTTTTTTATATATCATT
1 ATTTTTTTATATTTAAGT
5484153 ATTTTTGTTAT-TTTAAGT
1 ATTTTT-TTATATTTAAGT
5484171 ATTTTTTTATATTTA
1 ATTTTTTTATATTTA
5484186 TGCACGATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 4 0.14
18 20 0.71
19 4 0.14
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (18 bp):
ATTTTTTTATATTTAAGT
Found at i:5484582 original size:17 final size:16
Alignment explanation
Indices: 5484540--5484584 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
5484530 CTTAAAAACG
* *
5484540 ACCCATAAAATCCAAA
1 ACCCCTAAAATTCAAA
*
5484556 ACCTCTAAAATTCAAA
1 ACCCCTAAAATTCAAA
5484572 ACCCCCTAAAATT
1 A-CCCCTAAAATT
5484585 TGAAATCTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (16 bp):
ACCCCTAAAATTCAAA
Found at i:5484642 original size:14 final size:14
Alignment explanation
Indices: 5484602--5484643 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
5484592 TAAAACCTTT
*
5484602 AAACTCTTAAATCC
1 AAACCCTTAAATCC
*
5484616 AAACCACTAAAATCC
1 AAACC-CTTAAATCC
5484631 AAACCCTTAAATC
1 AAACCCTTAAATC
5484644 AAAATCTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (14 bp):
AAACCCTTAAATCC
Found at i:5497314 original size:109 final size:109
Alignment explanation
Indices: 5497160--5498459 Score: 1338
Period size: 109 Copynumber: 11.9 Consensus size: 109
5497150 TATAGTCACT
* * *
5497160 TTTTATTTCTTTGACTTACGGTTCAGT-CTCAGTTATCTTTAATCTTTGACTCATGGTTTAATTT
1 TTTTATTTCTTTGACTTACGGTTCAGTCCT-GGTTATCTTTAATCTTTGACTCGTGGTTTAATCT
* * * * * *
5497224 CGATCATTCTCATAGCTTCTCGACTTATGGTTTAATCCTAGTTGT
65 CGATCATTCTTATAGCTTTTCGACTTACGATTTAATCCTAGTCGC
* * * * * *
5497269 TTTTATTTCTTTGACTTACGGTTTAGTCCTGATCATCGTTAATCTTTGACTCATGGTTTAATCCC
1 TTTTATTTCTTTGACTTACGGTTCAGTCCTGGTTATCTTTAATCTTTGACTCGTGGTTTAATCTC
* * ** * **
5497334 AATCATTTTTATAATTTTTCAACTTACGATTTAATCCTAGTCATT
66 GATCATTCTTATAGCTTTTCGACTTACGATTTAATCCTAGTC-GC
* * ** * *
5497379 TTTTATTTTTTTGACTTACGGTTCAGTCTTGGTCGTCGTTAATCTTTGACTCGTAGTTTAATCTC
1 TTTTATTTCTTTGACTTACGGTTCAGTCCTGGTTATCTTTAATCTTTGACTCGTGGTTTAATCTC
* * *
5497444 GATCATTCTTATAACTTCTCGACTTACGATTTAATCCTAGTCGT
66 GATCATTCTTATAGCTTTTCGACTTACGATTTAATCCTAGTCGC
* * *
5497488 TTTTATTTCTTTAACTTACGATTCAGT-CTCGGTTATCTTTAATCTTTGACTCGTGATTTAATCT
1 TTTTATTTCTTTGACTTACGGTTCAGTCCT-GGTTATCTTTAATCTTTGACTCGTGGTTTAATCT
* *
5497552 CGATCATTCTTATAGCTTTTTCGACTTACGGTTTAATCCTAGTCAC
65 CGATCATTCTTATAGC-TTTTCGACTTACGATTTAATCCTAGTCGC
* * * *
5497598 TTTTATTTCTTTGAC-TGCGGTT-TGAT-CTCAGTTATCTTTAATCTTTGACTCATGGTTTAATC
1 TTTTATTTCTTTGACTTACGGTTCAG-TCCT-GGTTATCTTTAATCTTTGACTCGTGGTTTAATC
* * *
5497660 TCGATCATTCTCATAGCTTTTCGACTTACGGTTTAATCCTAATCGC
64 TCGATCATTCTTATAGCTTTTCGACTTACGATTTAATCCTAGTCGC
* * ** *
5497706 TTTTATTTTTTTGACTTACGGCTCAGTCCTGGTCGTCATTAATCTTTGACTCGTGGTTTAATC-C
1 TTTTATTTCTTTGACTTACGGTTCAGTCCTGGTTATCTTTAATCTTTGACTCGTGGTTTAATCTC
* * *
5497770 TGATCATTCTTATAGCTTTTCGACTTACGGTTTAATCCTAGCCAC
66 -GATCATTCTTATAGCTTTTCGACTTACGATTTAATCCTAGTCGC
** * *
5497815 TTTTATTTCTTTGACTTGTGATTCAGT-CTCAGTTATCTTTAATCTTTGACTCGTGGTTTAATCT
1 TTTTATTTCTTTGACTTACGGTTCAGTCCT-GGTTATCTTTAATCTTTGACTCGTGGTTTAATCT
* * * *
5497879 CGGTCATTCTTATAGTTTTTCGACTTACGATTTAATCTTAGTCAC
65 CGATCATTCTTATAGCTTTTCGACTTACGATTTAATCCTAGTCGC
* * * * *
5497924 TTTTATTTATTTGACTTATGGTTCAGTCCCGGTCAT-TGTTAATATTTGACTCGTGGTTTAATCT
1 TTTTATTTCTTTGACTTACGGTTCAGTCCTGGTTATCT-TTAATCTTTGACTCGTGGTTTAATCT
* *
5497988 CAATTATTCTTATAG-TTTATCGACTTACGATTTAATCCTAGTCGC
65 CGATCATTCTTATAGCTTT-TCGACTTACGATTTAATCCTAGTCGC
* ** * * *
5498033 TTTTATTTCTTTAACTTGTGATTCAGTCGC-AGTTATCTTTAATCTTTGACTCATGGTTTAATCT
1 TTTTATTTCTTTGACTTACGGTTCAGTC-CTGGTTATCTTTAATCTTTGACTCGTGGTTTAATCT
* * * *
5498097 CGACCATTCTTATAGCTTCTCGACTTACGATTTAATCTTAATCGC
65 CGATCATTCTTATAGCTTTTCGACTTACGATTTAATCCTAGTCGC
* * * ** * * *
5498142 TTTTATTTTTTTGACTTACGGTTCAATCCCGGTCGT-TATTAATATTTAACTCGTGATTTAATCT
1 TTTTATTTCTTTGACTTACGGTTCAGTCCTGGTTATCT-TTAATCTTTGACTCGTGGTTTAATCT
* * *
5498206 CAATCATTCTTATAG-TTTATCGACTTATGATTTAATCCTAATCGC
65 CGATCATTCTTATAGCTTT-TCGACTTACGATTTAATCCTAGTCGC
* ** * * * *
5498251 TTTTATTTCTTTAACTTGTGATTTAGT-CTCGGTTATATTTAATCTTTGACTCATGGTTTAATCT
1 TTTTATTTCTTTGACTTACGGTTCAGTCCT-GGTTATCTTTAATCTTTGACTCGTGGTTTAATCT
* * * * *
5498315 CGGTCATTCTTATACCTTCTCAACTTAC-AGTTTAATCCTAGTCAC
65 CGATCATTCTTATAGCTTTTCGACTTACGA-TTTAATCCTAGTCGC
* * * * * * *
5498360 TTTTATTTCTCTGACTTGCGATTCAGT-CTCAGTTATCTTTAATCTTTGACTTGTGATCTAAT-T
1 TTTTATTTCTTTGACTTACGGTTCAGTCCT-GGTTATCTTTAATCTTTGACTCGTGGTTTAATCT
* * * *
5498423 CTGATCATTTTTATAG-TTTTTGAATTACGGTTTAATC
65 C-GATCATTCTTATAGCTTTTCGACTTACGATTTAATC
5498460 TCAGTCTCTT
Statistics
Matches: 998, Mismatches: 167, Indels: 53
0.82 0.14 0.04
Matches are distributed among these distances:
108 73 0.07
109 777 0.78
110 148 0.15
ACGTcount: A:0.21, C:0.19, G:0.13, T:0.47
Consensus pattern (109 bp):
TTTTATTTCTTTGACTTACGGTTCAGTCCTGGTTATCTTTAATCTTTGACTCGTGGTTTAATCTC
GATCATTCTTATAGCTTTTCGACTTACGATTTAATCCTAGTCGC
Found at i:5497398 original size:37 final size:38
Alignment explanation
Indices: 5497325--5497398 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 38
5497315 TGACTCATGG
5497325 TTTAATCCCAATCATTTTTATAATTTTTCAACTTACGA
1 TTTAATCCCAATCATTTTTATAATTTTTCAACTTACGA
* * * **
5497363 TTTAATCCTAGTCATTTTT-TATTTTTTTGACTTACG
1 TTTAATCCCAATCATTTTTATAATTTTTCAACTTACG
5497399 GTTCAGTCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
37 14 0.45
38 17 0.55
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (38 bp):
TTTAATCCCAATCATTTTTATAATTTTTCAACTTACGA
Found at i:5497712 original size:218 final size:217
Alignment explanation
Indices: 5497152--5498459 Score: 1534
Period size: 218 Copynumber: 6.0 Consensus size: 217
5497142 AGCTCATTTA
*
5497152 TAGTCACTTTTTATTTCTTTGACTTACGGTTCAGTCTCAGTTATCTTTAATCTTTGACTCATGGT
1 TAGTCAC-TTTTATTTCTTTGACTTGCGGTTCAGTCTCAGTTATCTTTAATCTTTGACTCATGGT
* * * * * *
5497217 TTAATTTCGATCATTCTCATAGCTTCTCGACTTATGGTTTAATCCTAGTTGTTTTTATTTCTTTG
65 TTAATCTCGATCATTCTTATAGCTTCTCGACTTACGATTTAATCCTAGTCGCTTTTATTTCTTTG
* * * * * * *
5497282 ACTTACGGTTTAGTCCTGATCATCGTTAATCTTTGACTCATGGTTTAATCCCAATCATTTTTATA
130 ACTTACGGTTCAGTCC-GGTCATCTTTAATCTTTGACTCGTGATTTAATCTCAATCATTCTTATA
* *
5497347 ATTTTTCAACTTACGATTTAATCC
194 GTTTTTCGACTTACGATTTAATCC
* * * ** ** * * *
5497371 TAGTCATTTTTTATTTTTTTGACTTACGGTTCAGTCTTGGTCGTCGTTAATCTTTGACTCGTAGT
1 TAGTCA-CTTTTATTTCTTTGACTTGCGGTTCAGTCTCAGTTATCTTTAATCTTTGACTCATGGT
* * *
5497436 TTAATCTCGATCATTCTTATAACTTCTCGACTTACGATTTAATCCTAGTCGTTTTTATTTCTTTA
65 TTAATCTCGATCATTCTTATAGCTTCTCGACTTACGATTTAATCCTAGTCGCTTTTATTTCTTTG
* * *
5497501 ACTTACGATTCAGTCTCGGTTATCTTTAATCTTTGACTCGTGATTTAATCTCGATCATTCTTATA
130 ACTTACGGTTCAGTC-CGGTCATCTTTAATCTTTGACTCGTGATTTAATCTCAATCATTCTTATA
*
5497566 GCTTTTTCGACTTACGGTTTAATCC
194 G-TTTTTCGACTTACGATTTAATCC
*
5497591 TAGTCACTTTTATTTCTTTGAC-TGCGGTT-TGATCTCAGTTATCTTTAATCTTTGACTCATGGT
1 TAGTCACTTTTATTTCTTTGACTTGCGGTTCAG-TCTCAGTTATCTTTAATCTTTGACTCATGGT
* * * * *
5497654 TTAATCTCGATCATTCTCATAGCTTTTCGACTTACGGTTTAATCCTAATCGCTTTTATTTTTTTG
65 TTAATCTCGATCATTCTTATAGCTTCTCGACTTACGATTTAATCCTAGTCGCTTTTATTTCTTTG
* * * * *
5497719 ACTTACGGCTCAGTCCTGGTCGTCATTAATCTTTGACTCGTGGTTTAATC-CTGATCATTCTTAT
130 ACTTACGGTTCAGTCC-GGTCATCTTTAATCTTTGACTCGTGATTTAATCTC-AATCATTCTTAT
* *
5497783 AGCTTTTCGACTTACGGTTTAATCC
193 AGTTTTTCGACTTACGATTTAATCC
* * * *
5497808 TAGCCACTTTTATTTCTTTGACTTGTGATTCAGTCTCAGTTATCTTTAATCTTTGACTCGTGGTT
1 TAGTCACTTTTATTTCTTTGACTTGCGGTTCAGTCTCAGTTATCTTTAATCTTTGACTCATGGTT
* * * * * *
5497873 TAATCTCGGTCATTCTTATAGTTTTTCGACTTACGATTTAATCTTAGTCACTTTTATTTATTTGA
66 TAATCTCGATCATTCTTATAGCTTCTCGACTTACGATTTAATCCTAGTCGCTTTTATTTCTTTGA
* * * *
5497938 CTTATGGTTCAGTCCCGGTCAT-TGTTAATATTTGACTCGTGGTTTAATCTCAATTATTCTTATA
131 CTTACGGTTCAGT-CCGGTCATCT-TTAATCTTTGACTCGTGATTTAATCTCAATCATTCTTATA
*
5498002 GTTTATCGACTTACGATTTAATCC
194 GTTTTTCGACTTACGATTTAATCC
* * * * *
5498026 TAGTCGCTTTTATTTCTTTAACTTGTGATTCAGTCGCAGTTATCTTTAATCTTTGACTCATGGTT
1 TAGTCACTTTTATTTCTTTGACTTGCGGTTCAGTCTCAGTTATCTTTAATCTTTGACTCATGGTT
* * * *
5498091 TAATCTCGACCATTCTTATAGCTTCTCGACTTACGATTTAATCTTAATCGCTTTTATTTTTTTGA
66 TAATCTCGATCATTCTTATAGCTTCTCGACTTACGATTTAATCCTAGTCGCTTTTATTTCTTTGA
* * * *
5498156 CTTACGGTTCAATCCCGGTCGT-TATTAATATTTAACTCGTGATTTAATCTCAATCATTCTTATA
131 CTTACGGTTCAGT-CCGGTCATCT-TTAATCTTTGACTCGTGATTTAATCTCAATCATTCTTATA
* *
5498220 GTTTATCGACTTATGATTTAATCC
194 GTTTTTCGACTTACGATTTAATCC
* * * * * * * *
5498244 TAATCGCTTTTATTTCTTTAACTTGTGATTTAGTCTCGGTTATATTTAATCTTTGACTCATGGTT
1 TAGTCACTTTTATTTCTTTGACTTGCGGTTCAGTCTCAGTTATCTTTAATCTTTGACTCATGGTT
* * * * *
5498309 TAATCTCGGTCATTCTTATACCTTCTCAACTTAC-AGTTTAATCCTAGTCACTTTTATTTCTCTG
66 TAATCTCGATCATTCTTATAGCTTCTCGACTTACGA-TTTAATCCTAGTCGCTTTTATTTCTTTG
* * * * * * * *
5498373 ACTTGCGATTCAGTCTCAGTTATCTTTAATCTTTGACTTGTGATCTAAT-TCTGATCATTTTTAT
130 ACTTACGGTTCAGTC-CGGTCATCTTTAATCTTTGACTCGTGATTTAATCTC-AATCATTCTTAT
* *
5498437 AGTTTTT-GAATTACGGTTTAATC
193 AGTTTTTCGACTTACGATTTAATC
5498460 TCAGTCTCTT
Statistics
Matches: 946, Mismatches: 128, Indels: 32
0.86 0.12 0.03
Matches are distributed among these distances:
217 63 0.07
218 670 0.71
219 185 0.20
220 28 0.03
ACGTcount: A:0.21, C:0.19, G:0.13, T:0.47
Consensus pattern (217 bp):
TAGTCACTTTTATTTCTTTGACTTGCGGTTCAGTCTCAGTTATCTTTAATCTTTGACTCATGGTT
TAATCTCGATCATTCTTATAGCTTCTCGACTTACGATTTAATCCTAGTCGCTTTTATTTCTTTGA
CTTACGGTTCAGTCCGGTCATCTTTAATCTTTGACTCGTGATTTAATCTCAATCATTCTTATAGT
TTTTCGACTTACGATTTAATCC
Found at i:5498821 original size:45 final size:45
Alignment explanation
Indices: 5498757--5498843 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
5498747 AAATCGCAGT
5498757 TTAATATCAATTGTTGTTATTTTTTGACTCATGATTTAATCCCGA
1 TTAATATCAATTGTTGTTATTTTTTGACTCATGATTTAATCCCGA
* * *
5498802 TTAATCTCGATTGTTGTTATTTTTTGACTCATGGTTTAATCC
1 TTAATATCAATTGTTGTTATTTTTTGACTCATGATTTAATCC
5498844 TGGTCTCTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.23, C:0.14, G:0.13, T:0.51
Consensus pattern (45 bp):
TTAATATCAATTGTTGTTATTTTTTGACTCATGATTTAATCCCGA
Found at i:5500824 original size:17 final size:16
Alignment explanation
Indices: 5500785--5500824 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
5500775 AAAAATGACC
*
5500785 CTAAAATCCAAAATCT
1 CTAAAATCCAAAACCT
5500801 CTAAAATCCAAAACCT
1 CTAAAATCCAAAACCT
5500817 CATAAAAT
1 C-TAAAAT
5500825 TCGAAATCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.23
Consensus pattern (16 bp):
CTAAAATCCAAAACCT
Found at i:5500865 original size:14 final size:14
Alignment explanation
Indices: 5500843--5500884 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
5500833 CCAAACCTTT
*
5500843 AAACTCTTAAATCC
1 AAACCCTTAAATCC
5500857 AAACCCTTAAAATCC
1 AAACCCTT-AAATCC
*
5500872 AAACCGTTAAATC
1 AAACCCTTAAATC
5500885 AAAATCTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.45, C:0.29, G:0.02, T:0.24
Consensus pattern (14 bp):
AAACCCTTAAATCC
Found at i:5500890 original size:20 final size:20
Alignment explanation
Indices: 5500865--5500903 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
5500855 CCAAACCCTT
5500865 AAAATC-CAAACCGTTAAATC
1 AAAATCTCAAACC-TTAAATC
5500885 AAAATCTCAAACCTTAAAT
1 AAAATCTCAAACCTTAAAT
5500904 TTTAATATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.51, C:0.23, G:0.03, T:0.23
Consensus pattern (20 bp):
AAAATCTCAAACCTTAAATC
Found at i:5500933 original size:58 final size:58
Alignment explanation
Indices: 5500788--5500975 Score: 147
Period size: 58 Copynumber: 3.2 Consensus size: 58
5500778 AATGACCCTA
** *
5500788 AAATCCAAAATCTCTAAAATCCAAAACCTCATAAAATTCGAAATCCCAAACCTTTAAACTCTT
1 AAATCCAAACCCT-TAAAATCC-AAA-CTC-TAAAA-TCAAAATCCCAAACCTTTAAACTCTT
* * *
5500851 AAATCCAAACCCTTAAAATCCAAAC-CGTTAAATCAAAATCTCAAACC-TTAAA-TTTT
1 AAATCCAAACCCTTAAAATCCAAACTC-TAAAATCAAAATCCCAAACCTTTAAACTCTT
*
5500907 AATATCGAAACCC-TAAAATCTTCAAACTCTAAAATCAAAA-CCCTAAA-CTTTACATAC-CTT
1 AA-ATCCAAACCCTTAAAATC--CAAACTCTAAAATCAAAATCCC-AAACCTTTA-A-ACTCTT
*
5500967 AAAACCAAA
1 AAATCCAAA
5500976 TTCTAAAACC
Statistics
Matches: 103, Mismatches: 13, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
56 12 0.12
57 17 0.17
58 34 0.33
59 12 0.12
60 6 0.06
61 3 0.03
62 8 0.08
63 11 0.11
ACGTcount: A:0.47, C:0.26, G:0.02, T:0.25
Consensus pattern (58 bp):
AAATCCAAACCCTTAAAATCCAAACTCTAAAATCAAAATCCCAAACCTTTAAACTCTT
Found at i:5503674 original size:141 final size:141
Alignment explanation
Indices: 5503420--5503703 Score: 568
Period size: 141 Copynumber: 2.0 Consensus size: 141
5503410 ATGCAGGCCT
5503420 CGAAAGGCATACCTCATGCGGTCATTCTTAGCCCTTTCTGCCTTCTGTGCAGCCAAACTCTCATC
1 CGAAAGGCATACCTCATGCGGTCATTCTTAGCCCTTTCTGCCTTCTGTGCAGCCAAACTCTCATC
5503485 TCTTTCTGCTATCTTCTTCTTCTTCCATTCTATAAATAACTCGGGAGTCATAGGAGTTGAAGTTT
66 TCTTTCTGCTATCTTCTTCTTCTTCCATTCTATAAATAACTCGGGAGTCATAGGAGTTGAAGTTT
5503550 TTAATTTGGCA
131 TTAATTTGGCA
5503561 CGAAAGGCATACCTCATGCGGTCATTCTTAGCCCTTTCTGCCTTCTGTGCAGCCAAACTCTCATC
1 CGAAAGGCATACCTCATGCGGTCATTCTTAGCCCTTTCTGCCTTCTGTGCAGCCAAACTCTCATC
5503626 TCTTTCTGCTATCTTCTTCTTCTTCCATTCTATAAATAACTCGGGAGTCATAGGAGTTGAAGTTT
66 TCTTTCTGCTATCTTCTTCTTCTTCCATTCTATAAATAACTCGGGAGTCATAGGAGTTGAAGTTT
5503691 TTAATTTGGCA
131 TTAATTTGGCA
5503702 CG
1 CG
5503704 CACCAGCCAA
Statistics
Matches: 143, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
141 143 1.00
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.37
Consensus pattern (141 bp):
CGAAAGGCATACCTCATGCGGTCATTCTTAGCCCTTTCTGCCTTCTGTGCAGCCAAACTCTCATC
TCTTTCTGCTATCTTCTTCTTCTTCCATTCTATAAATAACTCGGGAGTCATAGGAGTTGAAGTTT
TTAATTTGGCA
Found at i:5514141 original size:12 final size:13
Alignment explanation
Indices: 5514117--5514158 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
5514107 AAAAAATATT
5514117 AAATAATAATTAA
1 AAATAATAATTAA
5514130 AAATAA-AATTAA
1 AAATAATAATTAA
*
5514142 TAATTAATAAATTAA
1 -AAATAAT-AATTAA
5514157 AA
1 AA
5514159 TATTTTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 6 0.24
13 11 0.44
14 2 0.08
15 6 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATAATAATTAA
Found at i:5514142 original size:19 final size:21
Alignment explanation
Indices: 5514120--5514159 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
5514110 AAATATTAAA
5514120 TAATAATTAA-AAA-TAAAAT
1 TAATAATTAATAAATTAAAAT
5514139 TAATAATTAATAAATTAAAAT
1 TAATAATTAATAAATTAAAAT
5514160 ATTTTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.53
20 3 0.16
21 6 0.32
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TAATAATTAATAAATTAAAAT
Found at i:5514224 original size:14 final size:15
Alignment explanation
Indices: 5514197--5514238 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
5514187 AATTTTAAAA
5514197 AATAAAATATATTTTT
1 AATAAAA-ATATTTTT
*
5514213 AA-ATAAATATTTTT
1 AATAAAAATATTTTT
5514227 AATAAAAATATT
1 AATAAAAATATT
5514239 AATAAAATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 10 0.43
15 11 0.48
16 2 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAAAAATATTTTT
Found at i:5514300 original size:13 final size:13
Alignment explanation
Indices: 5514284--5514308 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5514274 TTAAATTATA
5514284 AATAATTTTTTTG
1 AATAATTTTTTTG
5514297 AATAATTTTTTT
1 AATAATTTTTTT
5514309 TACATATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
AATAATTTTTTTG
Found at i:5518363 original size:7 final size:6
Alignment explanation
Indices: 5518333--5518359 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5518323 TTCATTCATA
5518333 AAATTT AAATTT AAATTT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAA
5518360 ATTTTATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (6 bp):
AAATTT
Found at i:5518368 original size:12 final size:13
Alignment explanation
Indices: 5518331--5518372 Score: 61
Period size: 12 Copynumber: 3.4 Consensus size: 13
5518321 TTTTCATTCA
5518331 TAAAATTTAAATT
1 TAAAATTTAAATT
5518344 T-AAATTTAAATT
1 TAAAATTTAAATT
*
5518356 TAAAATTT-TATT
1 TAAAATTTAAATT
5518368 TAAAA
1 TAAAA
5518373 AATATTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 20 0.74
13 7 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAAAATTTAAATT
Found at i:5521967 original size:2 final size:2
Alignment explanation
Indices: 5521960--5521988 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5521950 TTGAGTTGTT
5521960 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5521989 TATTAAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5522095 original size:31 final size:32
Alignment explanation
Indices: 5522049--5522114 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
5522039 AGGATTATAT
* *
5522049 TTTGACACTTTTTTAATATTGTAAAATGATCA
1 TTTGACACTTTTTTAATATTATAAAATGACCA
*
5522081 TTTGACA-TTTTTTAATATTATATAATGACCA
1 TTTGACACTTTTTTAATATTATAAAATGACCA
5522112 TTT
1 TTT
5522115 TACCTGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 24 0.77
32 7 0.23
ACGTcount: A:0.33, C:0.09, G:0.08, T:0.50
Consensus pattern (32 bp):
TTTGACACTTTTTTAATATTATAAAATGACCA
Found at i:5523980 original size:26 final size:23
Alignment explanation
Indices: 5523949--5524017 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 23
5523939 AATATTTCTC
5523949 AATATTTTAATTTTTTAAAAATA
1 AATATTTTAATTTTTTAAAAATA
*
5523972 ATATTTATTTT-ATTATTTAAAACATA
1 A-A--TATTTTAATTTTTTAAAA-ATA
5523998 AA-ATTTTAATTTTTTAAAAA
1 AATATTTTAATTTTTTAAAAA
5524018 ATAGTTTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
22 6 0.15
23 11 0.28
24 1 0.03
25 11 0.28
26 10 0.26
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTTAATTTTTTAAAAATA
Found at i:5523993 original size:25 final size:27
Alignment explanation
Indices: 5523951--5524003 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
5523941 TATTTCTCAA
* *
5523951 TATTTTAATTTTTTAAAA-ATAATATT
1 TATTTTAATTATTTAAAACATAAAATT
5523977 TATTTT-ATTATTTAAAACATAAAATT
1 TATTTTAATTATTTAAAACATAAAATT
5524003 T
1 T
5524004 TAATTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (27 bp):
TATTTTAATTATTTAAAACATAAAATT
Found at i:5530581 original size:18 final size:18
Alignment explanation
Indices: 5530560--5530604 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
5530550 TAGCTGGGAA
5530560 AAGTGGAAGTGGTGA-TGC
1 AAGTGGAAGTGG-GAGTGC
* *
5530578 AAGTGGGAGTGGGAGTGG
1 AAGTGGAAGTGGGAGTGC
5530596 AAGTGGAAG
1 AAGTGGAAG
5530605 CAAGGCAGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.29, C:0.02, G:0.51, T:0.18
Consensus pattern (18 bp):
AAGTGGAAGTGGGAGTGC
Found at i:5534707 original size:2 final size:2
Alignment explanation
Indices: 5534691--5534726 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
5534681 ACCATTTCAA
5534691 AT AT A- AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5534727 GATGTTTGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5535883 original size:15 final size:17
Alignment explanation
Indices: 5535863--5535894 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
5535853 TATACCAAAT
5535863 TTAAAA-AAA-TTAATA
1 TTAAAATAAACTTAATA
5535878 TTAAAATAAACTTAATA
1 TTAAAATAAACTTAATA
5535895 AAACAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
TTAAAATAAACTTAATA
Found at i:5536552 original size:3 final size:3
Alignment explanation
Indices: 5536544--5536572 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5536534 TAAGCTCTAT
5536544 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5536573 TGTGTTTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5538597 original size:2 final size:2
Alignment explanation
Indices: 5538590--5538622 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5538580 TTAACAATAC
5538590 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5538623 TTGTATTCCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5541143 original size:17 final size:16
Alignment explanation
Indices: 5541121--5541154 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5541111 ATTTGATAAC
5541121 TTTTAATATAATTTTGA
1 TTTTAATA-AATTTTGA
*
5541138 TTTTAATAACTTTTGA
1 TTTTAATAAATTTTGA
5541154 T
1 T
5541155 AAATTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.59
Consensus pattern (16 bp):
TTTTAATAAATTTTGA
Found at i:5541156 original size:10 final size:10
Alignment explanation
Indices: 5541137--5541244 Score: 67
Period size: 10 Copynumber: 10.5 Consensus size: 10
5541127 TATAATTTTG
*
5541137 ATTTTAATAA
1 ATTTTGATAA
*
5541147 CTTTTGATAA
1 ATTTTGATAA
*
5541157 ATTTTAATAA
1 ATTTTGATAA
*
5541167 CTTTTGATATA
1 ATTTTGATA-A
*
5541178 ATTTTGGT-A
1 ATTTTGATAA
5541187 ATTTATGATATA
1 ATTT-TGATA-A
5541199 ATTTTGATAA
1 ATTTTGATAA
***
5541209 CCATTGATAAA
1 ATTTTGAT-AA
*
5541220 ATTTTGTTAA
1 ATTTTGATAA
*
5541230 TTTTTG-TAAA
1 ATTTTGAT-AA
5541240 ATTTT
1 ATTTT
5541245 AGTAATTTTT
Statistics
Matches: 74, Mismatches: 18, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
9 6 0.08
10 45 0.61
11 18 0.24
12 5 0.07
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.52
Consensus pattern (10 bp):
ATTTTGATAA
Found at i:5541182 original size:21 final size:21
Alignment explanation
Indices: 5541137--5541266 Score: 104
Period size: 21 Copynumber: 6.2 Consensus size: 21
5541127 TATAATTTTG
5541137 ATTTTAATAACTTTTGATA-A
1 ATTTTAATAACTTTTGATATA
5541157 ATTTTAATAACTTTTGATATA
1 ATTTTAATAACTTTTGATATA
**
5541178 ATTTTGGTAA-TTTATGATATA
1 ATTTTAATAACTTT-TGATATA
* ** *
5541199 ATTTTGATAACCATTGATAAA
1 ATTTTAATAACTTTTGATATA
** * *
5541220 ATTTTGTTAATTTTTG-TAAA
1 ATTTTAATAACTTTTGATATA
* * *
5541240 ATTTTAGTAATTTTTTGATGTA
1 ATTTTAATAA-CTTTTGATATA
5541262 ATTTT
1 ATTTT
5541267 GGTAATCTTT
Statistics
Matches: 91, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
20 34 0.37
21 49 0.54
22 8 0.09
ACGTcount: A:0.35, C:0.03, G:0.09, T:0.53
Consensus pattern (21 bp):
ATTTTAATAACTTTTGATATA
Found at i:5541202 original size:12 final size:11
Alignment explanation
Indices: 5541112--5541207 Score: 60
Period size: 11 Copynumber: 8.6 Consensus size: 11
5541102 ATAAGTAAAA
*
5541112 TTTGATA-ACT
1 TTTGATATAAT
*
5541122 TTTAATATAAT
1 TTTGATATAAT
5541133 TTTGATTTTAATAACT
1 TTTGA---T-ATAA-T
5541149 TTTGATA-AAT
1 TTTGATATAAT
5541159 TTT-A-ATAACT
1 TTTGATATAA-T
5541169 TTTGATATAAT
1 TTTGATATAAT
*
5541180 TTTG--GTAAT
1 TTTGATATAAT
5541189 TTATGATATAAT
1 TT-TGATATAAT
5541201 TTTGATA
1 TTTGATA
5541208 ACCATTGATA
Statistics
Matches: 68, Mismatches: 5, Indels: 25
0.69 0.05 0.26
Matches are distributed among these distances:
8 1 0.01
9 9 0.13
10 16 0.24
11 19 0.28
12 11 0.16
13 1 0.01
14 1 0.01
15 4 0.06
16 6 0.09
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.53
Consensus pattern (11 bp):
TTTGATATAAT
Found at i:5541209 original size:42 final size:40
Alignment explanation
Indices: 5541151--5541272 Score: 120
Period size: 42 Copynumber: 2.9 Consensus size: 40
5541141 TAATAACTTT
5541151 TGATAAATTTTAATAACTTTTGATATAATTTTGGTAATTTA
1 TGATAAATTTT-ATAACTTTTGATATAATTTTGGTAATTTA
** * * *
5541192 TGATATAATTTTGATAACCATTGATAAAATTTTGTTAATTTT
1 TGATA-AATTTT-ATAACTTTTGATATAATTTTGGTAATTTA
* *
5541234 TG-TAAAATTTTAGTAATTTTTTGATGTAATTTTGGTAAT
1 TGAT-AAATTTTA-TAA-CTTTTGATATAATTTTGGTAAT
5541273 CTTTTAATAA
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
40 1 0.02
41 15 0.23
42 49 0.75
ACGTcount: A:0.34, C:0.02, G:0.11, T:0.52
Consensus pattern (40 bp):
TGATAAATTTTATAACTTTTGATATAATTTTGGTAATTTA
Found at i:5541432 original size:13 final size:13
Alignment explanation
Indices: 5541414--5541438 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5541404 TTCAAATTTA
5541414 TAATTTTTTTTCC
1 TAATTTTTTTTCC
5541427 TAATTTTTTTTC
1 TAATTTTTTTTC
5541439 TTGAATAGGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (13 bp):
TAATTTTTTTTCC
Found at i:5541590 original size:22 final size:22
Alignment explanation
Indices: 5541549--5541704 Score: 89
Period size: 22 Copynumber: 7.1 Consensus size: 22
5541539 TAAAAAAATT
* * * *
5541549 TTATCAATAATTGACAATTAAG
1 TTATCATTAATTTACTATTAAA
* **
5541571 TTATCATTAATTTATTATTATG
1 TTATCATTAATTTACTATTAAA
* * *
5541593 TTATCAGTAATTTATTACTAAA
1 TTATCATTAATTTACTATTAAA
* * * * *
5541615 TCATCAATGAA-ATATTACTAAA
1 TTATC-ATTAATTTACTATTAAA
* *
5541637 TTATTAATAATTTACTATTAAA
1 TTATCATTAATTTACTATTAAA
* * * *
5541659 TTAACATTTATTTACTATCAAG
1 TTATCATTAATTTACTATTAAA
* *
5541681 TTATGATCAATTTACTATTAAA
1 TTATCATTAATTTACTATTAAA
5541703 TT
1 TT
5541705 GTTAATGATT
Statistics
Matches: 100, Mismatches: 32, Indels: 4
0.74 0.24 0.03
Matches are distributed among these distances:
21 3 0.03
22 94 0.94
23 3 0.03
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (22 bp):
TTATCATTAATTTACTATTAAA
Found at i:5541895 original size:22 final size:22
Alignment explanation
Indices: 5541813--5541895 Score: 69
Period size: 22 Copynumber: 3.8 Consensus size: 22
5541803 ATTTGCTTAT
* * * *
5541813 AATTATCATTTATTTATAACTA
1 AATTATCAATGATTTACATCTA
* *
5541835 AAGTATTAATGATTTACTAT-TA
1 AATTATCAATGATTTAC-ATCTA
* * *
5541857 AGTTATTAATAATTTACATCTA
1 AATTATCAATGATTTACATCTA
5541879 AATTATCAATGATTTAC
1 AATTATCAATGATTTAC
5541896 TATTATGTTA
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
21 2 0.04
22 44 0.94
23 1 0.02
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (22 bp):
AATTATCAATGATTTACATCTA
Found at i:5541906 original size:22 final size:22
Alignment explanation
Indices: 5541842--5541906 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
5541832 CTAAAGTATT
*
5541842 AATGATTTACTATTAAGTTATT
1 AATGATTTACTATTAAGTTATC
* *
5541864 AATAATTTAC-ATCTAAATTATC
1 AATGATTTACTAT-TAAGTTATC
*
5541886 AATGATTTACTATTATGTTAT
1 AATGATTTACTATTAAGTTAT
5541907 TATGCATTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 2 0.06
22 31 0.89
23 2 0.06
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (22 bp):
AATGATTTACTATTAAGTTATC
Found at i:5541928 original size:44 final size:44
Alignment explanation
Indices: 5541824--5541930 Score: 126
Period size: 44 Copynumber: 2.4 Consensus size: 44
5541814 ATTATCATTT
* *
5541824 ATTTATAACTAAAGTATTAATGATTTACTATTAAGTTATTAATA
1 ATTTATAACTAAATTATCAATGATTTACTATTAAGTTATTAATA
* * * *
5541868 ATTTACATCTAAATTATCAATGATTTACTATTATGTTATT-ATGC
1 ATTTATAACTAAATTATCAATGATTTACTATTAAGTTATTAAT-A
* *
5541912 ATTTATTACTATATTATCA
1 ATTTATAACTAAATTATCA
5541931 TTAATTTATT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
43 2 0.04
44 50 0.96
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (44 bp):
ATTTATAACTAAATTATCAATGATTTACTATTAAGTTATTAATA
Found at i:5542003 original size:22 final size:21
Alignment explanation
Indices: 5541951--5542007 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
5541941 ACTTAATTTT
* *
5541951 TTATTATTTATTACAAAATCA
1 TTATAATTTATTACAAAATAA
* *
5541972 TCACAGATTTATTACAAAAGTAA
1 TTATA-ATTTATTACAAAA-TAA
5541995 TTATAATTTATTA
1 TTATAATTTATTA
5542008 TCAAGTTATT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 2 0.07
22 21 0.75
23 5 0.18
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.44
Consensus pattern (21 bp):
TTATAATTTATTACAAAATAA
Done.