Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 56 of 171
Found at i:22387700 original size:21 final size:23
Alignment explanation
Indices: 22387674--22387728 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
22387664 GACTTGATTT
*
22387674 GTATCGGTAGT-TGAAT-TGTAA
1 GTATCGGTAGTATGAATGTGGAA
*
22387695 GTATCGGTAGTACTGTATGTGGAA
1 GTATCGGTAGTA-TGAATGTGGAA
22387719 GTATCGGTAG
1 GTATCGGTAG
22387729 ATTGTGTGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 11 0.38
23 4 0.14
24 14 0.48
ACGTcount: A:0.25, C:0.07, G:0.33, T:0.35
Consensus pattern (23 bp):
GTATCGGTAGTATGAATGTGGAA
Found at i:22400037 original size:17 final size:17
Alignment explanation
Indices: 22400017--22400059 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
22400007 TTTGTTATTT
22400017 ATATTAATTTTTTACA-A
1 ATATT-ATTTTTTACATA
22400034 ATA-TATTTTTTACATA
1 ATATTATTTTTTACATA
22400050 AT-TTATTTTT
1 ATATTATTTTT
22400060 CACCCACATC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 10 0.42
16 11 0.46
17 3 0.12
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATTATTTTTTACATA
Found at i:22400043 original size:15 final size:16
Alignment explanation
Indices: 22400023--22400059 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
22400013 ATTTATATTA
22400023 ATTTTTTACA-AATAT
1 ATTTTTTACATAATAT
*
22400038 ATTTTTTACATAATTT
1 ATTTTTTACATAATAT
22400054 ATTTTT
1 ATTTTT
22400060 CACCCACATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTTTACATAATAT
Found at i:22402954 original size:3 final size:3
Alignment explanation
Indices: 22402946--22402990 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
22402936 AGTTCATTTG
22402946 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
22402991 TTGATGTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:22413301 original size:1 final size:1
Alignment explanation
Indices: 22413295--22413319 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
22413285 GACCCGCCCC
22413295 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
22413320 TTTCAGAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:22414367 original size:6 final size:6
Alignment explanation
Indices: 22414356--22414386 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
22414346 CTTTGATATT
22414356 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG T
1 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG T
22414387 ATGTCAGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (6 bp):
TTTGGG
Found at i:22415354 original size:8 final size:8
Alignment explanation
Indices: 22415341--22415411 Score: 54
Period size: 8 Copynumber: 8.5 Consensus size: 8
22415331 TAGATTATAT
22415341 AAAATTTA
1 AAAATTTA
22415349 AAAATTATA
1 AAAATT-TA
22415358 TAAAATTTA
1 -AAAATTTA
*
22415367 AAATTTTTA
1 AAA-ATTTA
*
22415376 AAAAATTA
1 AAAATTTA
*
22415384 TAAAATATA
1 -AAAATTTA
*
22415393 TAAATTT-
1 AAAATTTA
*
22415400 AAATTTTA
1 AAAATTTA
22415408 AAAA
1 AAAA
22415412 ATGAAAATAT
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
7 5 0.10
8 20 0.42
9 17 0.35
10 6 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
AAAATTTA
Found at i:22415355 original size:18 final size:18
Alignment explanation
Indices: 22415334--22415402 Score: 81
Period size: 18 Copynumber: 3.9 Consensus size: 18
22415324 AAACCGATAG
22415334 ATTATATAAAATTTAAAA
1 ATTATATAAAATTTAAAA
22415352 ATTATATAAAATTTAAAA
1 ATTATATAAAATTTAAAA
* * *
22415370 TTTTTA-AAAAATTATAAA
1 ATTATATAAAATTTA-AAA
22415388 A-TATAT-AAATTTAAA
1 ATTATATAAAATTTAAA
22415403 TTTTAAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
16 2 0.05
17 16 0.37
18 25 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTATATAAAATTTAAAA
Found at i:22415385 original size:26 final size:28
Alignment explanation
Indices: 22415336--22415399 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
22415326 ACCGATAGAT
* *
22415336 TATATAAA-ATTTAAAAATTATATAAAA
1 TATATAAATTTTTAAAAAATATATAAAA
*
22415363 TTTA-AAATTTTTAAAAAAT-TATAAAA
1 TATATAAATTTTTAAAAAATATATAAAA
22415389 TATATAAATTT
1 TATATAAATTT
22415400 AAATTTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
26 13 0.42
27 18 0.58
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
TATATAAATTTTTAAAAAATATATAAAA
Found at i:22415388 original size:9 final size:9
Alignment explanation
Indices: 22415334--22415388 Score: 51
Period size: 10 Copynumber: 6.0 Consensus size: 9
22415324 AAACCGATAG
22415334 ATTATATAAA
1 ATTATA-AAA
22415344 ATT-TAAAA
1 ATTATAAAA
22415352 ATTATATAAA
1 ATTATA-AAA
22415362 ATT-TAAAA
1 ATTATAAAA
* *
22415370 TTTTTAAAAA
1 ATTAT-AAAA
22415380 ATTATAAAA
1 ATTATAAAA
22415389 TATATAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
8 11 0.29
9 11 0.29
10 16 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
ATTATAAAA
Found at i:22415426 original size:33 final size:34
Alignment explanation
Indices: 22415348--22415429 Score: 107
Period size: 32 Copynumber: 2.4 Consensus size: 34
22415338 TATAAAATTT
*
22415348 AAAAATTATATAAAATTTAAAATTTTTAAAAAATT
1 AAAAATTATAT-AAATTTAAAATTTTTAAAAAATG
22415383 ATAAAA-TATATAAATTT-AAA-TTTTAAAAAATG
1 A-AAAATTATATAAATTTAAAATTTTTAAAAAATG
22415415 AAAATATTATATAAA
1 AAAA-ATTATATAAA
22415430 AATTGAAATT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
31 3 0.07
32 13 0.30
33 11 0.26
34 6 0.14
35 6 0.14
36 4 0.09
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (34 bp):
AAAAATTATATAAATTTAAAATTTTTAAAAAATG
Found at i:22415427 original size:35 final size:33
Alignment explanation
Indices: 22415348--22415440 Score: 109
Period size: 35 Copynumber: 2.7 Consensus size: 33
22415338 TATAAAATTT
*
22415348 AAAAATTATATAAAATTTAAAATTTTTAAAAAATT
1 AAAAATTATATAAAATTT-AAA-TTTTAAAAAATG
22415383 ATAAAA-TATAT-AAATTTAAATTTTAAAAAATG
1 A-AAAATTATATAAAATTTAAATTTTAAAAAATG
*
22415415 AAAATATTATATAAAAATTGAAATTT
1 AAAA-ATTATAT-AAAATTTAAATTT
22415441 GTTATAAATT
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
31 3 0.06
32 13 0.25
33 8 0.16
34 6 0.12
35 17 0.33
36 4 0.08
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (33 bp):
AAAAATTATATAAAATTTAAATTTTAAAAAATG
Found at i:22415503 original size:27 final size:26
Alignment explanation
Indices: 22415465--22415519 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 26
22415455 TTTCTTTTTC
*
22415465 AAAAATTCAAA-TTCTAAAAATTCAA
1 AAAAATTCAAATTTCTAAAAATCCAA
*
22415490 AAAAATATCTAAATTTCTAAATATCCAA
1 AAAAAT-TC-AAATTTCTAAAAATCCAA
22415518 AA
1 AA
22415520 TAGACAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.24
26 2 0.08
27 3 0.12
28 14 0.56
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (26 bp):
AAAAATTCAAATTTCTAAAAATCCAA
Found at i:22415584 original size:26 final size:25
Alignment explanation
Indices: 22415550--22415603 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
22415540 ATATATAAAG
* *
22415550 TTTTAAATTTTTAGATATTTAGATTT
1 TTTTAAATTTTTAGA-ATGTAGAGTT
*
22415576 TTTTTAATTTTTAGAATGTAGAGTT
1 TTTTAAATTTTTAGAATGTAGAGTT
22415601 TTT
1 TTT
22415604 GAAAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (25 bp):
TTTTAAATTTTTAGAATGTAGAGTT
Found at i:22415686 original size:23 final size:22
Alignment explanation
Indices: 22415643--22415687 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
22415633 TTTCTATATA
22415643 ATATTTTGATATTTTTAAATTT
1 ATATTTTGATATTTTTAAATTT
22415665 ATATTTT-ATATATTTTAGAATTT
1 ATATTTTGATAT-TTTTA-AATTT
22415688 TTAAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.19
22 12 0.57
23 5 0.24
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (22 bp):
ATATTTTGATATTTTTAAATTT
Found at i:22415730 original size:7 final size:7
Alignment explanation
Indices: 22415718--22415780 Score: 58
Period size: 7 Copynumber: 8.6 Consensus size: 7
22415708 TACATAATAA
22415718 TTTAATT
1 TTTAATT
22415725 TTTAATT
1 TTTAATT
22415732 TTTAA-T
1 TTTAATT
*
22415738 TATATATT
1 TTTA-ATT
22415746 TTATAATT
1 TT-TAATT
22415754 TTT-ATT
1 TTTAATT
22415760 TTTAAACTT
1 TTT-AA-TT
22415769 TTTAAATT
1 TTT-AATT
22415777 TTTA
1 TTTA
22415781 TGATTTTTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
6 10 0.21
7 15 0.31
8 13 0.27
9 10 0.21
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (7 bp):
TTTAATT
Found at i:22415752 original size:37 final size:36
Alignment explanation
Indices: 22415653--22415773 Score: 99
Period size: 37 Copynumber: 3.2 Consensus size: 36
22415643 ATATTTTGAT
22415653 ATTTTTAAATTTATATTTTAT-ATATTTTAGAATTTTTAA
1 ATTTTT-AATTTATATTTTATAATA-TTT--AATTTTTAA
*
22415692 ATTTTT-TTTTCA-ATTTTACATAATAATTTAATTTTT-A
1 ATTTTTAATTT-ATATTTT--ATAAT-ATTTAATTTTTAA
*
22415729 ATTTTTAATTATATATTTTATAAT-TTTTATTTTTAA
1 ATTTTTAATT-TATATTTTATAATATTTAATTTTTAA
22415765 ACTTTTTAA
1 A-TTTTTAA
22415774 ATTTTTATGA
Statistics
Matches: 69, Mismatches: 3, Indels: 22
0.73 0.03 0.23
Matches are distributed among these distances:
35 9 0.13
36 2 0.03
37 27 0.39
38 11 0.16
39 14 0.20
40 5 0.07
41 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (36 bp):
ATTTTTAATTTATATTTTATAATATTTAATTTTTAA
Found at i:22417277 original size:20 final size:20
Alignment explanation
Indices: 22417241--22417279 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
22417231 TTTTATTTTA
*
22417241 TTATTGTATATGTTTTTATT
1 TTATTGTATATGATTTTATT
22417261 TTATTGTATTAT-ATTTTAT
1 TTATTGTA-TATGATTTTAT
22417280 AAAAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (20 bp):
TTATTGTATATGATTTTATT
Found at i:22433551 original size:23 final size:23
Alignment explanation
Indices: 22433525--22433570 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
22433515 AAAGAAAGAT
*
22433525 ATACTATC-TAATGAAGACACCAA
1 ATACAATCATAATGAAGA-ACCAA
*
22433548 ATACAATCATAATTAAGAACCAA
1 ATACAATCATAATGAAGAACCAA
22433571 TAATTTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.52, C:0.20, G:0.07, T:0.22
Consensus pattern (23 bp):
ATACAATCATAATGAAGAACCAA
Found at i:22437597 original size:11 final size:12
Alignment explanation
Indices: 22437573--22437605 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
22437563 TAAAAATTCA
22437573 AAAATAACAATTT
1 AAAATAA-AATTT
22437586 AAAA-AAAATTT
1 AAAATAAAATTT
22437597 AAAATAAAA
1 AAAATAAAA
22437606 AATTAATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.47
12 6 0.32
13 4 0.21
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAATAAAATTT
Found at i:22437611 original size:24 final size:25
Alignment explanation
Indices: 22437564--22437611 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
22437554 TTTTATTCTT
* *
22437564 AAAAATTCAAAAATAACAATTTAAA
1 AAAAATTCAAAAATAAAAAATTAAA
*
22437589 AAAAATT-TAAAATAAAAAATTAA
1 AAAAATTCAAAAATAAAAAATTAA
22437612 TGATTCATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (25 bp):
AAAAATTCAAAAATAAAAAATTAAA
Found at i:22446611 original size:20 final size:21
Alignment explanation
Indices: 22446583--22446621 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
22446573 GTGCATGGGT
*
22446583 GCAATTTC-AGCTTTACAACA
1 GCAAGTTCAAGCTTTACAACA
*
22446603 GCAAGTTCAATCTTTACAA
1 GCAAGTTCAAGCTTTACAA
22446622 GCTGAACTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (21 bp):
GCAAGTTCAAGCTTTACAACA
Found at i:22448449 original size:18 final size:18
Alignment explanation
Indices: 22448426--22448468 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
22448416 GAATTTTGTC
22448426 AATAAATTAATATTTATT
1 AATAAATTAATATTTATT
22448444 AATAAATTAATATTTATT
1 AATAAATTAATATTTATT
22448462 AATAAAT
1 AATAAAT
22448469 GATTGGGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATAAATTAATATTTATT
Found at i:22450715 original size:18 final size:18
Alignment explanation
Indices: 22450692--22450772 Score: 58
Period size: 18 Copynumber: 4.5 Consensus size: 18
22450682 TTTCTTGAAG
22450692 AATTGATAAATTTTATGA
1 AATTGATAAATTTTATGA
* *
22450710 AATTGATGAATTTATAGGA
1 AATTGATAAATTT-TATGA
* * * ** *
22450729 ACTT-TTATATAATAAG-
1 AATTGATAAATTTTATGA
22450745 AATTGATAAATTTTATGA
1 AATTGATAAATTTTATGA
22450763 AATTGCATAA
1 AATTG-ATAA
22450773 TAGGTTACTT
Statistics
Matches: 44, Mismatches: 15, Indels: 7
0.67 0.23 0.11
Matches are distributed among these distances:
16 3 0.07
17 10 0.23
18 20 0.45
19 11 0.25
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.41
Consensus pattern (18 bp):
AATTGATAAATTTTATGA
Found at i:22452338 original size:15 final size:16
Alignment explanation
Indices: 22452320--22452356 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
22452310 GAAAAATAAA
22452320 AAAATAAAAAAAA-CC
1 AAAATAAAAAAAATCC
*
22452335 AAAA-AAAAAAAATCT
1 AAAATAAAAAAAATCC
22452350 AAAATAA
1 AAAATAA
22452357 TAATTTCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 8 0.42
15 9 0.47
16 2 0.11
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.11
Consensus pattern (16 bp):
AAAATAAAAAAAATCC
Found at i:22457374 original size:14 final size:13
Alignment explanation
Indices: 22457350--22457401 Score: 79
Period size: 14 Copynumber: 3.9 Consensus size: 13
22457340 ATTTGGACAT
22457350 AGACCATAGACCTA
1 AGACC-TAGACCTA
22457364 AGACCTAAGACCTA
1 AGACCT-AGACCTA
22457378 AGACCTAGACCT-
1 AGACCTAGACCTA
22457390 AGACCTAGACCT
1 AGACCTAGACCT
22457402 CATGAACGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.32
13 7 0.19
14 18 0.49
ACGTcount: A:0.38, C:0.31, G:0.15, T:0.15
Consensus pattern (13 bp):
AGACCTAGACCTA
Found at i:22457389 original size:6 final size:6
Alignment explanation
Indices: 22457349--22457401 Score: 70
Period size: 7 Copynumber: 8.2 Consensus size: 6
22457339 CATTTGGACA
22457349 TAGACC ATAGACC TAAGACC TAAGACC TAAGACC TAGACC TAGACC TAGACC
1 TAGACC -TAGACC T-AGACC T-AGACC T-AGACC TAGACC TAGACC TAGACC
22457401 T
1 T
22457402 CATGAACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
6 19 0.42
7 26 0.58
ACGTcount: A:0.38, C:0.30, G:0.15, T:0.17
Consensus pattern (6 bp):
TAGACC
Found at i:22457862 original size:6 final size:6
Alignment explanation
Indices: 22457829--22457861 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
22457819 TGAATGAGTA
*
22457829 GCCGGT GCCGGT GCCGGT GCCGGT GCCAGT GCC
1 GCCGGT GCCGGT GCCGGT GCCGGT GCCGGT GCC
22457862 ACCGCTTGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.03, C:0.36, G:0.45, T:0.15
Consensus pattern (6 bp):
GCCGGT
Found at i:22463605 original size:15 final size:14
Alignment explanation
Indices: 22463578--22463611 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
22463568 TAAGAAGCAT
22463578 AAAAATTATAAAAAA
1 AAAAATTA-AAAAAA
*
22463593 AAATATTAAAAAAA
1 AAAAATTAAAAAAA
22463607 AAAAA
1 AAAAA
22463612 CTACACACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (14 bp):
AAAAATTAAAAAAA
Found at i:22464418 original size:17 final size:17
Alignment explanation
Indices: 22464385--22464419 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
22464375 TTTAATTATT
*
22464385 TATATTTTTTGAAAATA
1 TATATTTTTAGAAAATA
*
22464402 TATATTTTTAGACAATA
1 TATATTTTTAGAAAATA
22464419 T
1 T
22464420 TGTTGACCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (17 bp):
TATATTTTTAGAAAATA
Found at i:22469698 original size:21 final size:21
Alignment explanation
Indices: 22469670--22469720 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
22469660 ATAATAACAT
*
22469670 AATCCAAATATAAATTTTAGA
1 AATCCAAATATAAAATTTAGA
* *
22469691 AATTCAAATATAAAATTTATA
1 AATCCAAATATAAAATTTAGA
22469712 AATCCAAAT
1 AATCCAAAT
22469721 TACATAATCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (21 bp):
AATCCAAATATAAAATTTAGA
Found at i:22479152 original size:28 final size:27
Alignment explanation
Indices: 22479106--22479242 Score: 95
Period size: 28 Copynumber: 4.9 Consensus size: 27
22479096 TGCATTTTAG
*
22479106 ATAACTATATTCAAAATTCATAAATTC
1 ATAACTATAATCAAAATTCATAAATTC
22479133 ATAACTATAGATCAAAATTCATAAA-TC
1 ATAACTATA-ATCAAAATTCATAAATTC
* * * *
22479160 -GAA-T-TCA-CAAAACTACACTCTAGATTC
1 ATAACTATAATCAAAA-TTCA---TAAATTC
*
22479187 TAGATAACTATATTCAAAATTCATAAATTC
1 ---ATAACTATAATCAAAATTCATAAATTC
*
22479217 ATAACTATAGATCAAAACTCATAAAT
1 ATAACTATA-ATCAAAATTCATAAAT
22479243 CGAATTCACA
Statistics
Matches: 84, Mismatches: 12, Indels: 27
0.68 0.10 0.22
Matches are distributed among these distances:
22 5 0.06
23 4 0.05
24 1 0.01
25 1 0.01
26 5 0.06
27 22 0.26
28 28 0.33
30 6 0.07
31 2 0.02
32 1 0.01
33 4 0.05
34 5 0.06
ACGTcount: A:0.48, C:0.17, G:0.04, T:0.31
Consensus pattern (27 bp):
ATAACTATAATCAAAATTCATAAATTC
Found at i:22479165 original size:41 final size:41
Alignment explanation
Indices: 22479120--22479250 Score: 126
Period size: 41 Copynumber: 3.1 Consensus size: 41
22479110 CTATATTCAA
*
22479120 AATTCATAAATTCATAACTATAGATCAAAATTCATAAATCG
1 AATTCATAAATTCATAACTATAGATCAAAACTCATAAATCG
* * * * *
22479161 AATTCACAAA-AC-TACACTCTAGATTCTAGATAACT-AT-ATTCAA
1 AATTCATAAATTCATA-ACTATAGA-TC-A-A-AACTCATAAATC-G
22479204 AATTCATAAATTCATAACTATAGATCAAAACTCATAAATCG
1 AATTCATAAATTCATAACTATAGATCAAAACTCATAAATCG
22479245 AATTCA
1 AATTCA
22479251 CAAACTACAC
Statistics
Matches: 69, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
39 2 0.03
40 12 0.17
41 20 0.29
42 8 0.12
43 14 0.20
44 11 0.16
45 2 0.03
ACGTcount: A:0.47, C:0.18, G:0.05, T:0.31
Consensus pattern (41 bp):
AATTCATAAATTCATAACTATAGATCAAAACTCATAAATCG
Found at i:22479200 original size:84 final size:83
Alignment explanation
Indices: 22479103--22479286 Score: 350
Period size: 84 Copynumber: 2.2 Consensus size: 83
22479093 AAATGCATTT
*
22479103 TAGATAACTATATTCAAAATTCATAAATTCATAACTATAGATCAAAATTCATAAATCGAATTCAC
1 TAGATAACTATATTCAAAATTCATAAATTCATAACTATAGATCAAAACTCATAAATCGAATTCAC
22479168 AAAACTACACTCTAGATTC
66 -AAACTACACTCTAGATTC
22479187 TAGATAACTATATTCAAAATTCATAAATTCATAACTATAGATCAAAACTCATAAATCGAATTCAC
1 TAGATAACTATATTCAAAATTCATAAATTCATAACTATAGATCAAAACTCATAAATCGAATTCAC
22479252 AAACTACACTCTAGATTC
66 AAACTACACTCTAGATTC
22479270 TAGATAACTATATTCAA
1 TAGATAACTATATTCAA
22479287 TCAATCAATG
Statistics
Matches: 99, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
83 35 0.35
84 64 0.65
ACGTcount: A:0.46, C:0.18, G:0.05, T:0.31
Consensus pattern (83 bp):
TAGATAACTATATTCAAAATTCATAAATTCATAACTATAGATCAAAACTCATAAATCGAATTCAC
AAACTACACTCTAGATTC
Found at i:22480395 original size:17 final size:17
Alignment explanation
Indices: 22480370--22480411 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
22480360 TAATCAAATT
22480370 ACTCAAGATCACCATTA
1 ACTCAAGATCACCATTA
*
22480387 ACTCCAGATCACCATTA
1 ACTCAAGATCACCATTA
*
22480404 ATTCAAGA
1 ACTCAAGA
22480412 AGTGAATCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.40, C:0.29, G:0.07, T:0.24
Consensus pattern (17 bp):
ACTCAAGATCACCATTA
Found at i:22481035 original size:26 final size:26
Alignment explanation
Indices: 22480989--22481039 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
22480979 AGTACCAAAC
*
22480989 TAAAAAAAAGTAAGTATCAAATTAAG
1 TAAAAAAAAGTAAATATCAAATTAAG
*
22481015 TAAAAAAAATTAAAT-TCCAAATTAA
1 TAAAAAAAAGTAAATAT-CAAATTAA
22481040 AAAAAGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.25
Consensus pattern (26 bp):
TAAAAAAAAGTAAATATCAAATTAAG
Found at i:22487741 original size:7 final size:7
Alignment explanation
Indices: 22487729--22487756 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
22487719 CCCTAATCTC
22487729 TCCTTAA
1 TCCTTAA
22487736 TCCTTAA
1 TCCTTAA
22487743 TCCTTAA
1 TCCTTAA
22487750 TCCTTAA
1 TCCTTAA
22487757 ATAGAAGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (7 bp):
TCCTTAA
Found at i:22489705 original size:17 final size:17
Alignment explanation
Indices: 22489685--22489761 Score: 93
Period size: 17 Copynumber: 4.6 Consensus size: 17
22489675 AATGGATTCA
*
22489685 ATTTTAAATTTTAATTT
1 ATTTTAAATTTGAATTT
*
22489702 A-TTTAAGTTTGAATTT
1 ATTTTAAATTTGAATTT
* *
22489718 ACTTTAAATTTGAACTT
1 ATTTTAAATTTGAATTT
* *
22489735 ATTTTGAATTTAAATTT
1 ATTTTAAATTTGAATTT
22489752 ATTTTAAATT
1 ATTTTAAATT
22489762 AAATTTAAAC
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
16 14 0.28
17 36 0.72
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (17 bp):
ATTTTAAATTTGAATTT
Found at i:22489757 original size:11 final size:11
Alignment explanation
Indices: 22489687--22489776 Score: 60
Period size: 11 Copynumber: 8.0 Consensus size: 11
22489677 TGGATTCAAT
22489687 TTTAAATTTTAA
1 TTTAAA-TTTAA
22489699 TTT--ATTTAA
1 TTTAAATTTAA
* *
22489708 GTTTGAATTTAC
1 -TTTAAATTTAA
22489720 TTTAAATTTGAA
1 TTTAAATTT-AA
* *
22489732 CTT-ATTTTGAA
1 TTTAAATTT-AA
*
22489743 TTTAAATTTAT
1 TTTAAATTTAA
*
22489754 TTTAAATTAAA
1 TTTAAATTTAA
22489765 TTTAAACTTTAA
1 TTTAAA-TTTAA
22489777 AAAGTCCAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
9 5 0.08
10 4 0.07
11 33 0.54
12 19 0.31
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.54
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:22489777 original size:7 final size:6
Alignment explanation
Indices: 22489687--22489777 Score: 50
Period size: 6 Copynumber: 16.0 Consensus size: 6
22489677 TGGATTCAAT
* * * * *
22489687 TTTAAA TTTTAA TTT--A TTTAAG TTTGAA TTT-AC TTTAAA TTTGAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
22489732 CTT-AT TTTGAA TTTAAA TTT-AT TTTAAA -TTAAA TTTAAA CTTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA
22489778 AAGTCCAAAT
Statistics
Matches: 64, Mismatches: 14, Indels: 13
0.70 0.15 0.14
Matches are distributed among these distances:
4 4 0.06
5 16 0.25
6 38 0.59
7 6 0.09
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:22491602 original size:29 final size:29
Alignment explanation
Indices: 22491547--22491995 Score: 229
Period size: 29 Copynumber: 15.4 Consensus size: 29
22491537 AAGGTCCCTG
* * *
22491547 AACTGTCCAAAAATCACGTTTTGAACCCCA
1 AACTTTCCAAAAATTACATTTT-AACCCCA
* * *
22491577 AACTTTTCAAAAACTACATTTTAACCCTTA
1 AACTTTCCAAAAATTACATTTTAACCC-CA
* * *
22491607 AACTTT-CTAAAATTACAATTTAACCCTTA
1 AACTTTCCAAAAATTACATTTTAACCC-CA
* ****
22491636 AACTTTCCAAAAATTACATTTTTGACATTG
1 AACTTTCCAAAAATTACA-TTTTAACCCCA
* *
22491666 AACTTTCCAAAAATCACATTTTGACCCCA
1 AACTTTCCAAAAATTACATTTTAACCCCA
* * *
22491695 TATTTTCCAAATATTACATTTTAACCCCTA
1 AACTTTCCAAAAATTACATTTTAACCCC-A
* *
22491725 AACTTTCCAAAAATTACA-TTTGACCCTA
1 AACTTTCCAAAAATTACATTTTAACCCCA
* * *
22491753 AAC-TTCTCAAAAA-T-CATATTTGACCTCG
1 AACTTTC-CAAAAATTACAT-TTTAACCCCA
** * *
22491781 AACTTTCCAAAAATTACATTTTTTCTCTCG
1 AACTTTCCAAAAATTACATTTTAAC-CCCA
* * *
22491811 AAC-TTCCAAAAATCACATTTTTATCCCTA
1 AACTTTCCAAAAATTACA-TTTTAACCCCA
* * * * *
22491840 CAC-ATCCAAAAATCACATTTTTACCCTCG
1 AACTTTCCAAAAATTACATTTTAACCC-CA
**
22491869 AAC-TTCTCAAAAATTACATTTTTGCCCCCA
1 AACTTTC-CAAAAATTACA-TTTTAACCCCA
* *
22491899 AAC-TTCCAAAAATCACCATTTT-ACTCCCG
1 AACTTTCCAAAAATTA-CATTTTAAC-CCCA
* * * *
22491928 AGCATT-CAAAAATTACCATTTTAACCTCG
1 AACTTTCCAAAAATTA-CATTTTAACCCCA
* * ** *
22491957 AATTTTCCAAAAGTTTGATTTTAATCCC-
1 AACTTTCCAAAAATTACATTTTAACCCCA
*
22491985 AATTTTCCAAA
1 AACTTTCCAAA
22491996 TACTTCAATT
Statistics
Matches: 333, Mismatches: 66, Indels: 42
0.76 0.15 0.10
Matches are distributed among these distances:
26 2 0.01
27 4 0.01
28 45 0.14
29 156 0.47
30 114 0.34
31 12 0.04
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (29 bp):
AACTTTCCAAAAATTACATTTTAACCCCA
Found at i:22491888 original size:88 final size:86
Alignment explanation
Indices: 22491673--22491968 Score: 253
Period size: 88 Copynumber: 3.4 Consensus size: 86
22491663 TTGAACTTTC
* * * ** *
22491673 CAAAAATCACATTTTGACC-CCATATTTTCCAAATATTACATTTTAACCCCTAAACTTTCCAAAA
1 CAAAAATCACA-TTTGACCTCGA-ACTTTCCAAAAATTACATTTTTGCCCCCAAAC-TTCCAAAA
* *
22491737 ATTACA-TTTGACCCTAAACTTCT
63 ATCACATTTTGACCCTAAACATCT
* * * * *
22491760 CAAAAATCATATTTGACCTCGAACTTTCCAAAAATTACATTTTTTCTCTCGAACTTCCAAAAATC
1 CAAAAATCACATTTGACCTCGAACTTTCCAAAAATTACATTTTTGCCCCCAAACTTCCAAAAATC
* *
22491825 ACATTTTTATCCCTACACATC-
66 ACATTTTGA-CCCTAAACATCT
*
22491846 CAAAAATCACATTTTTACCCTCGAAC-TTCTCAAAAATTACATTTTTGCCCCCAAACTTCCAAAA
1 CAAAAATCACA-TTTGA-CCTCGAACTTTC-CAAAAATTACATTTTTGCCCCCAAACTTCCAAAA
** *
22491910 ATCACCATTTT-ACTCCCGAGCAT-T
63 ATCA-CATTTTGAC-CCTAAACATCT
* * *
22491934 CAAAAATTACCATTTTAACCTCGAATTTTCCAAAA
1 CAAAAATCA-CA-TTTGACCTCGAACTTTCCAAAA
22491969 GTTTGATTTT
Statistics
Matches: 171, Mismatches: 27, Indels: 21
0.78 0.12 0.10
Matches are distributed among these distances:
85 13 0.08
86 45 0.26
87 29 0.17
88 68 0.40
89 16 0.09
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.33
Consensus pattern (86 bp):
CAAAAATCACATTTGACCTCGAACTTTCCAAAAATTACATTTTTGCCCCCAAACTTCCAAAAATC
ACATTTTGACCCTAAACATCT
Found at i:22491909 original size:59 final size:59
Alignment explanation
Indices: 22491542--22491920 Score: 258
Period size: 59 Copynumber: 6.4 Consensus size: 59
22491532 CCCAAAAGGT
* * * * * *
22491542 CCCTGAACTGTCCAAAAATCACGTTTTGAACCC-CAAACTTTTCAAAAACTACATTTTAAC
1 CCCTAAACT-TCCAAAAATCACATTTT-TACCCTCAAACTTCTCAAAAATTACATTTTTAC
* * * * * * *
22491602 CCTTAAACTTTCTAAAATTACAATTTAACCCTTAAACTT-TCCAAAAATTACATTTTTGA-
1 CCCTAAACTTCCAAAAATCACATTTTTACCCTCAAACTTCT-CAAAAATTACATTTTT-AC
** * * * * * *
22491661 CATTGAACTTTCCAAAAATCACATTTTGACCC-CATA-TTTTCCAAATATTACATTTTAAC
1 CCCTAAAC-TTCCAAAAATCACATTTTTACCCTCAAACTTCT-CAAAAATTACATTTTTAC
* * *
22491720 CCCTAAACTTTCCAAAAATTACA-TTTGACCCT-AAACTTCTCAAAAA-T-CATATTTGAC
1 CCCTAAAC-TTCCAAAAATCACATTTTTACCCTCAAACTTCTCAAAAATTACAT-TTTTAC
* * * * * * * *
22491777 CTC-GAACTTTCCAAAAATTACATTTTTTCTCTCGAACTTC-CAAAAATCACATTTTTAT
1 CCCTAAAC-TTCCAAAAATCACATTTTTACCCTCAAACTTCTCAAAAATTACATTTTTAC
* * * *
22491835 CCCTACACATCCAAAAATCACATTTTTACCCTCGAACTTCTCAAAAATTACATTTTTGC
1 CCCTAAACTTCCAAAAATCACATTTTTACCCTCAAACTTCTCAAAAATTACATTTTTAC
*
22491894 CCCCAAACTTCCAAAAATCACCATTTT
1 CCCTAAACTTCCAAAAATCA-CATTTT
22491921 ACTCCCGAGC
Statistics
Matches: 252, Mismatches: 51, Indels: 32
0.75 0.15 0.10
Matches are distributed among these distances:
56 21 0.08
57 20 0.08
58 64 0.25
59 115 0.46
60 32 0.13
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.34
Consensus pattern (59 bp):
CCCTAAACTTCCAAAAATCACATTTTTACCCTCAAACTTCTCAAAAATTACATTTTTAC
Found at i:22492006 original size:29 final size:29
Alignment explanation
Indices: 22491945--22492016 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
22491935 AAAAATTACC
* * * **
22491945 ATTTTAACCTCGAATTTTCCAAAAGTTTG
1 ATTTTAATCTCCAATTTTCCAAAACTTCA
22491974 ATTTTAATC-CCAATTTTCCAAATACTTCA
1 ATTTTAATCTCCAATTTTCCAAA-ACTTCA
22492003 ATTTTAATCTCCAA
1 ATTTTAATCTCCAA
22492017 ATTCCTCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 12 0.33
29 20 0.56
30 4 0.11
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.42
Consensus pattern (29 bp):
ATTTTAATCTCCAATTTTCCAAAACTTCA
Found at i:22493596 original size:475 final size:474
Alignment explanation
Indices: 22492706--22493659 Score: 1863
Period size: 475 Copynumber: 2.0 Consensus size: 474
22492696 GAATATCCTC
*
22492706 TTTAAAGTCTTCCAAAATGTCCTTCAATTTCGAAAGTCCGAAAACGTAGTGCCCTAACGTGTTGG
1 TTTAAAGTCTTCCAAAATGTCCTTCAATTTCGAAAGTCCGAAAACATAGTGCCCTAACGTGTTGG
22492771 ACACGACTTCCAATTCTCTTAGAAATTCAAAGCACACGGACGATTTTCCTCAAATAAGATTTTTT
66 ACACGACTTCCAATTCTCTTAGAAATTCAAAGCACACGGACGATTTTCCTCAAATAAGATTTTTT
22492836 GAAAATCATGCAAAGTTTTCTAAAGACAAATATCGTATTTTAAGATTTACTCGAGTTTTCAAATT
131 GAAAATCATGCAAAGTTTTCTAAAGACAAATATCGTATTTTAAGATTTACTCGAGTTTTCAAATT
22492901 TTTAACAAATCAAGACCCGAAAATAGTCAATGTGGTACCAATTTTGGGCGTATGAGGGTGTTAAT
196 TTTAACAAATCAAGACCCGAAAATAGTCAATGTGGTACCAATTTTGGGCGTATGAGGGTGTTAAT
22492966 CCTTCCTCATACGTAACCGACTCCCGAACCTCTTTTTTGGATTTCGAAGACCAAAATATTTTTCA
261 CCTTCCTCATACGTAACCGACTCCCGAACCTCTTTTTTGGATTTCGAAGACCAAAATATTTTTCA
*
22493031 AAACAGATTTTAAACGTTTTGTGGTGATCCAATCACACCATATAAAATGATTGGTGGCCACTTCC
326 AAACAGATTTTAAACGTTTTGTGGTGATCCAATCACACCATATAAAATGATTGGTGGCCACTCCC
*
22493096 ATTTTTTTCGATCATTTAAAATACCTTTTTTTTATTTTTAAATATTGTTTGAGACTTGTTTGTTT
391 ATTTTTTTCGATCATTTAAAATACC-TTTTTTTATTTTTAAATATTGTTTGAGACTTGTTTATTT
22493161 TTCTAAAAGTATTTTTTATT
455 TTCTAAAAGTATTTTTTATT
*
22493181 TTTAAAGTCTTCCAAAATGTCCTTCAATTTCGAAAGTCCGAGAACATAGTGCCCTAACGTGTTGG
1 TTTAAAGTCTTCCAAAATGTCCTTCAATTTCGAAAGTCCGAAAACATAGTGCCCTAACGTGTTGG
22493246 ACACGACTTCCAATTCTCTTAGAAATTCAAAGCACACGGACGATTTTCCTCAAATAAGATTTTTT
66 ACACGACTTCCAATTCTCTTAGAAATTCAAAGCACACGGACGATTTTCCTCAAATAAGATTTTTT
22493311 GAAAATCATGCAAAGTTTTCTAAAGACAAATATCGTATTTTAAGATTTACTCGAGTTTTCAAATT
131 GAAAATCATGCAAAGTTTTCTAAAGACAAATATCGTATTTTAAGATTTACTCGAGTTTTCAAATT
22493376 TTTAACAAATCAAGACCCGAAAATAGTCAATGTGGTACCAATTTTGGGCGTATGAGGGTGTTAAT
196 TTTAACAAATCAAGACCCGAAAATAGTCAATGTGGTACCAATTTTGGGCGTATGAGGGTGTTAAT
22493441 CCTTCCTCATACGTAACCGACTCCCGAACCTCTTTTTTGGATTTCGAAGACCAAAATATTTTTCA
261 CCTTCCTCATACGTAACCGACTCCCGAACCTCTTTTTTGGATTTCGAAGACCAAAATATTTTTCA
22493506 AAACAGATTTTAAACGTTTTGTGGTGATCCAATCACACCATATAAAATGATTGGTGGCCACTCCC
326 AAACAGATTTTAAACGTTTTGTGGTGATCCAATCACACCATATAAAATGATTGGTGGCCACTCCC
22493571 ATTTTTTTCGATCATTTAAAATACCTTTTTTTATTTTTAAATATTGTTTGAGACTTGTTTATTTT
391 ATTTTTTTCGATCATTTAAAATACCTTTTTTTATTTTTAAATATTGTTTGAGACTTGTTTATTTT
22493636 TCTAAAAGTATTTTTTATT
456 TCTAAAAGTATTTTTTATT
22493655 TTTAA
1 TTTAA
22493660 TTTTATAGAT
Statistics
Matches: 475, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
474 63 0.13
475 412 0.87
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (474 bp):
TTTAAAGTCTTCCAAAATGTCCTTCAATTTCGAAAGTCCGAAAACATAGTGCCCTAACGTGTTGG
ACACGACTTCCAATTCTCTTAGAAATTCAAAGCACACGGACGATTTTCCTCAAATAAGATTTTTT
GAAAATCATGCAAAGTTTTCTAAAGACAAATATCGTATTTTAAGATTTACTCGAGTTTTCAAATT
TTTAACAAATCAAGACCCGAAAATAGTCAATGTGGTACCAATTTTGGGCGTATGAGGGTGTTAAT
CCTTCCTCATACGTAACCGACTCCCGAACCTCTTTTTTGGATTTCGAAGACCAAAATATTTTTCA
AAACAGATTTTAAACGTTTTGTGGTGATCCAATCACACCATATAAAATGATTGGTGGCCACTCCC
ATTTTTTTCGATCATTTAAAATACCTTTTTTTATTTTTAAATATTGTTTGAGACTTGTTTATTTT
TCTAAAAGTATTTTTTATT
Found at i:22495585 original size:16 final size:18
Alignment explanation
Indices: 22495553--22495585 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
22495543 GATATTCGTG
22495553 TTATATTTATGAATTTTA
1 TTATATTTATGAATTTTA
22495571 TTATA-TTAT-AATTTT
1 TTATATTTATGAATTTT
22495586 TTAATTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTATATTTATGAATTTTA
Found at i:22497519 original size:192 final size:194
Alignment explanation
Indices: 22497183--22497536 Score: 434
Period size: 192 Copynumber: 1.8 Consensus size: 194
22497173 ATTTAGGTCC
* * * *
22497183 CTTTATAATTTATAAATTTTTAAATTAGTAATGGTAAAATTATACTTTGACCTCCAAAATGATCA
1 CTTTATAATTTATAAAATTTTAAATTAATAATAGTAAAATTACACTTTGACCTCCAAAATGATCA
* * * * * * ** * *
22497248 AAAATTGATTTAATCTTTTAAAAATTATTAAGATGTAGCCTATTAAAATGGAGAAATTGCATTTT
66 AAAATTGATTCAATCTATTAAAAATAATAAAAATATAAACTATTAAAATGAAAAAATTGCATTTT
* * * *
22497313 TATTATCTTAAAAATATACAATTTAATTTCGACCCCCAAAAAATGGAAAAAATTTTTTTAAATTT
131 TACTACCGTAAAAATAAACAA-TTAATTTCGACCCCCAAAAAATGGAAAAAATTTTTTTAAATTT
*
22497378 CTTTATAATTTATAAAATTTTAAATTAATAATAGTAAAATTGCACTTT-ATCC-CC-AAATGAT-
1 CTTTATAATTTATAAAATTTTAAATTAATAATAGTAAAATTACACTTTGA-CCTCCAAAATGATC
22497439 AAAAATTTGATTCAATC-ATTAAAAATAATAAAAATATAAACTATTAAAAT-AATAAAATT-CTA
65 AAAAA-TTGATTCAATCTATTAAAAATAATAAAAATATAAACTATTAAAATGAA-AAAATTGC-A
*
22497501 TTTTTACTACCGTAAAAATAAATAATTAATTTCGAC
127 TTTTTACTACCGTAAAAATAAACAATTAATTTCGAC
22497537 ACACTAAAAA
Statistics
Matches: 135, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
191 13 0.10
192 57 0.42
193 17 0.13
194 3 0.02
195 45 0.33
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (194 bp):
CTTTATAATTTATAAAATTTTAAATTAATAATAGTAAAATTACACTTTGACCTCCAAAATGATCA
AAAATTGATTCAATCTATTAAAAATAATAAAAATATAAACTATTAAAATGAAAAAATTGCATTTT
TACTACCGTAAAAATAAACAATTAATTTCGACCCCCAAAAAATGGAAAAAATTTTTTTAAATTT
Found at i:22499266 original size:30 final size:33
Alignment explanation
Indices: 22499230--22499302 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 33
22499220 TATTTTTAAA
22499230 TTTTAAAAAATTAAATTA-AATTTT-T-ATTAT
1 TTTTAAAAAATTAAATTACAATTTTATCATTAT
*
22499260 TTTTAAAAAGTTAAATTACAATTTTATCATTAT
1 TTTTAAAAAATTAAATTACAATTTTATCATTAT
22499293 TAATTTAAAA
1 T--TTTAAAA
22499303 TTTTATAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
30 17 0.46
31 6 0.16
32 1 0.03
33 6 0.16
35 7 0.19
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (33 bp):
TTTTAAAAAATTAAATTACAATTTTATCATTAT
Found at i:22500724 original size:13 final size:13
Alignment explanation
Indices: 22500706--22500758 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
22500696 AGTTTAGTAT
*
22500706 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
22500719 TGCTTTTAAAAAG
1 TGCTTTTGAAAAG
*
22500732 TGCGTTTGAAAAG
1 TGCTTTTGAAAAG
**
22500745 TAATTTTGAAAAG
1 TGCTTTTGAAAAG
22500758 T
1 T
22500759 TTGGTTTAAG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:22503131 original size:3 final size:3
Alignment explanation
Indices: 22503123--22503161 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
22503113 AAGAGGACAT
* *
22503123 TGA TGA TGA TGA CGA TGA CGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
22503162 ATACGATGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.33, C:0.05, G:0.33, T:0.28
Consensus pattern (3 bp):
TGA
Found at i:22511214 original size:15 final size:15
Alignment explanation
Indices: 22511194--22511233 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
22511184 TAATTTTTAA
22511194 AAATTATAAACAT-AT
1 AAATTATAAA-ATAAT
22511209 AAATTATTAAAATAAT
1 AAATTA-TAAAATAAT
22511225 AAATTATAA
1 AAATTATAA
22511234 TTTTTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (15 bp):
AAATTATAAAATAAT
Found at i:22511240 original size:25 final size:24
Alignment explanation
Indices: 22511212--22511260 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
22511202 AACATATAAA
*
22511212 TTATTAAAATAATAAATTATAATTT
1 TTATTAAAATAA-AAATTACAATTT
**
22511237 TTATTATCATAAAAATTACAATTT
1 TTATTAAAATAAAAATTACAATTT
22511261 AATTTTAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
TTATTAAAATAAAAATTACAATTT
Found at i:22512034 original size:15 final size:15
Alignment explanation
Indices: 22511996--22512046 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
22511986 ACAAAATAAT
* *
22511996 AATATAAGTGATTAA
1 AATATAAATAATTAA
* * *
22512011 AACAT-AATATTTCA
1 AATATAAATAATTAA
22512025 AATATAAATAATTAA
1 AATATAAATAATTAA
22512040 AATATAA
1 AATATAA
22512047 TTTAAAACAA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 9 0.33
15 18 0.67
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (15 bp):
AATATAAATAATTAA
Found at i:22512236 original size:3 final size:3
Alignment explanation
Indices: 22512230--22512263 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
22512220 TATACAGTAT
22512230 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
22512264 AATACAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:22517555 original size:13 final size:14
Alignment explanation
Indices: 22517537--22517566 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
22517527 CTAAACCATT
22517537 ATTTTGTTTCTT-A
1 ATTTTGTTTCTTCA
22517550 ATTTTGTTTCTTCA
1 ATTTTGTTTCTTCA
22517564 ATT
1 ATT
22517567 ATGGTCATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.67
Consensus pattern (14 bp):
ATTTTGTTTCTTCA
Found at i:22521403 original size:19 final size:19
Alignment explanation
Indices: 22521379--22521416 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
22521369 TTTAGGGATT
22521379 TTTTTTTTTGCATTTTTAA
1 TTTTTTTTTGCATTTTTAA
*
22521398 TTTTTTTTTGTATTTTTAA
1 TTTTTTTTTGCATTTTTAA
22521417 GGAATTTTAT
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:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (19 bp):
TTTTTTTTTGCATTTTTAA
Found at i:22523515 original size:3 final size:3
Alignment explanation
Indices: 22523507--22523560 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
22523497 ATTACTAACA
22523507 TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
22523554 TAT TAT T
1 TAT TAT T
22523561 GCTTCTTTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:22523517 original size:17 final size:17
Alignment explanation
Indices: 22523495--22523534 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
22523485 AATATTAAAT
22523495 TTATTACTAACATATTA
1 TTATTACTAACATATTA
* **
22523512 TTATTATTATTATATTA
1 TTATTACTAACATATTA
22523529 TTATTA
1 TTATTA
22523535 TTATTATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (17 bp):
TTATTACTAACATATTA
Found at i:22531004 original size:14 final size:15
Alignment explanation
Indices: 22530978--22531007 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
22530968 TATAATATAT
22530978 TGATAAGATGAACAG
1 TGATAAGATGAACAG
22530993 TGATAA-ATGAACAG
1 TGATAAGATGAACAG
22531007 T
1 T
22531008 AAAACATCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.47, C:0.07, G:0.23, T:0.23
Consensus pattern (15 bp):
TGATAAGATGAACAG
Found at i:22537989 original size:31 final size:31
Alignment explanation
Indices: 22537951--22538042 Score: 184
Period size: 31 Copynumber: 3.0 Consensus size: 31
22537941 TCAGGTAATT
22537951 TCTGAATTTGCAAAAAGTTTTAAATTGCTTG
1 TCTGAATTTGCAAAAAGTTTTAAATTGCTTG
22537982 TCTGAATTTGCAAAAAGTTTTAAATTGCTTG
1 TCTGAATTTGCAAAAAGTTTTAAATTGCTTG
22538013 TCTGAATTTGCAAAAAGTTTTAAATTGCTT
1 TCTGAATTTGCAAAAAGTTTTAAATTGCTT
22538043 ACATGTTTCC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (31 bp):
TCTGAATTTGCAAAAAGTTTTAAATTGCTTG
Found at i:22540341 original size:40 final size:40
Alignment explanation
Indices: 22540286--22540366 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
22540276 GAAATGTATG
22540286 AGGACTCTTATTTTATTTTCTTTTGATTGTTCAAACTTCA
1 AGGACTCTTATTTTATTTTCTTTTGATTGTTCAAACTTCA
22540326 AGGACTCTTATTTTATTTTCTTTTGATTGTTCAAACTTCA
1 AGGACTCTTATTTTATTTTCTTTTGATTGTTCAAACTTCA
22540366 A
1 A
22540367 AAGAGTGTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.52
Consensus pattern (40 bp):
AGGACTCTTATTTTATTTTCTTTTGATTGTTCAAACTTCA
Found at i:22566300 original size:32 final size:31
Alignment explanation
Indices: 22566193--22566318 Score: 121
Period size: 31 Copynumber: 4.0 Consensus size: 31
22566183 AAATTGAATA
*
22566193 TTGGATCCCTTAAAAGTTAGAAAAAAAAATTT
1 TTGGA-CCCTTAAAAGCTAGAAAAAAAAATTT
* * * * * * *
22566225 TAGGCCCCTTAAAAGTTGGTAAAACAATTTT
1 TTGGACCCTTAAAAGCTAGAAAAAAAAATTT
22566256 TTGGACCCTTAAAAGCT-GAAAAAAATAATTT
1 TTGGACCCTTAAAAGCTAGAAAAAAA-AATTT
*
22566287 TTGGACCCTTTAAAAACT-GAAAAATAAAATTT
1 TTGGACCC-TTAAAAGCTAGAAAAA-AAAATTT
22566319 GGATCCCTTT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
30 6 0.08
31 48 0.62
32 22 0.28
33 2 0.03
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.31
Consensus pattern (31 bp):
TTGGACCCTTAAAAGCTAGAAAAAAAAATTT
Found at i:22566327 original size:31 final size:31
Alignment explanation
Indices: 22566254--22566328 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 31
22566244 TAAAACAATT
*
22566254 TTTTGGACCC-TTAAAAGCTGAAAAAAATAA
1 TTTTGGACCCTTTAAAAACTGAAAAAAATAA
22566284 TTTTTGGACCCTTTAAAAACTGAAAAATAA-AA
1 -TTTTGGACCCTTTAAAAACTGAAAAA-AATAA
22566316 -TTTGGATCCCTTT
1 TTTTGGA-CCCTTT
22566329 CAACCTTGGG
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
30 6 0.15
31 16 0.40
32 16 0.40
33 2 0.05
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (31 bp):
TTTTGGACCCTTTAAAAACTGAAAAAAATAA
Found at i:22566327 original size:62 final size:63
Alignment explanation
Indices: 22566193--22566327 Score: 143
Period size: 62 Copynumber: 2.2 Consensus size: 63
22566183 AAATTGAATA
* ** * **
22566193 TTGGATCCCTTAAAAGTTAGAAAAAAAAATTTTAGGCCCCTTAAAAGTTGGTAAAACAATTTT
1 TTGGATCCCTTAAAAGCTAGAAAAAAAAATTTTAGGCCCCTTAAAAACTGGAAAAACAATAAT
* * *
22566256 TTGGA-CCCTTAAAAGCT-GAAAAAAATAATTTTTGGACCCTTTAAAAACT-GAAAAATAA-AAT
1 TTGGATCCCTTAAAAGCTAGAAAAAAA-AATTTTAGG-CCCCTTAAAAACTGGAAAAACAATAAT
22566317 TTGGATCCCTT
1 TTGGATCCCTT
22566328 TCAACCTTGG
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
61 14 0.23
62 31 0.52
63 15 0.25
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.31
Consensus pattern (63 bp):
TTGGATCCCTTAAAAGCTAGAAAAAAAAATTTTAGGCCCCTTAAAAACTGGAAAAACAATAAT
Found at i:22570440 original size:4 final size:4
Alignment explanation
Indices: 22570431--22570458 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
22570421 CCAACCACCC
22570431 CAAA CAAA CAAA CAAA CAAA CAAA CAAA
1 CAAA CAAA CAAA CAAA CAAA CAAA CAAA
22570459 AAGTTCATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.25, G:0.00, T:0.00
Consensus pattern (4 bp):
CAAA
Found at i:22571205 original size:35 final size:35
Alignment explanation
Indices: 22571147--22571248 Score: 197
Period size: 35 Copynumber: 2.9 Consensus size: 35
22571137 AAATTTATTT
22571147 CTTCTATTTTTA-TTTTAAGAATTTAGTTCTTTTA
1 CTTCTATTTTTATTTTTAAGAATTTAGTTCTTTTA
22571181 CTTCTATTTTTATTTTTAAGAATTTAGTTCTTTTA
1 CTTCTATTTTTATTTTTAAGAATTTAGTTCTTTTA
22571216 CTTCTATTTTTATTTTTAAGAATTTAGTTCTTT
1 CTTCTATTTTTATTTTTAAGAATTTAGTTCTTT
22571249 ATTTTTTAAA
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
34 12 0.18
35 55 0.82
ACGTcount: A:0.23, C:0.09, G:0.06, T:0.63
Consensus pattern (35 bp):
CTTCTATTTTTATTTTTAAGAATTTAGTTCTTTTA
Found at i:22576153 original size:3 final size:3
Alignment explanation
Indices: 22576147--22576173 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
22576137 AAAAAAACTA
22576147 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
22576174 TGTTTTCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:22579849 original size:30 final size:30
Alignment explanation
Indices: 22579815--22579872 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
22579805 ATCATAGTCT
*
22579815 TTTTAATCAAAATCTCATTTAATTCAAACA
1 TTTTAATCAAAATCTAATTTAATTCAAACA
22579845 TTTTAATCAAAATCTAATTTAATTCAAA
1 TTTTAATCAAAATCTAATTTAATTCAAA
22579873 TATAAATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (30 bp):
TTTTAATCAAAATCTAATTTAATTCAAACA
Found at i:22579871 original size:17 final size:16
Alignment explanation
Indices: 22579816--22579872 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
22579806 TCATAGTCTT
*
22579816 TTTAATCAAAATCTCA
1 TTTAATCAAAATCTAA
*
22579832 TTTAATTC-AAA-C-AT
1 TTTAA-TCAAAATCTAA
22579846 TTTAATCAAAATCTAA
1 TTTAATCAAAATCTAA
22579862 TTTAATTCAAA
1 TTTAA-TCAAA
22579873 TATAAATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
13 2 0.06
14 8 0.24
15 2 0.06
16 14 0.42
17 7 0.21
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (16 bp):
TTTAATCAAAATCTAA
Found at i:22582430 original size:13 final size:13
Alignment explanation
Indices: 22582405--22582438 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
22582395 TAATTTATTG
22582405 AAATTATATTATAA
1 AAATTA-ATTATAA
22582419 AAATTAATTATAA
1 AAATTAATTATAA
*
22582432 ATATTAA
1 AAATTAA
22582439 AATATCAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATTAATTATAA
Found at i:22600483 original size:23 final size:22
Alignment explanation
Indices: 22600457--22600517 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
22600447 ATTAACATTA
*
22600457 TTCGTGAACATGTTCGTTTAATG
1 TTCGTGAACATGTTCGATTAA-G
22600480 TTCGTGAACATGTTCGATTAAG
1 TTCGTGAACATGTTCGATTAAG
**
22600502 TTAAATGAACATGTTC
1 TT-CGTGAACATGTTC
22600518 ATGAATGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 3 0.09
23 31 0.91
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (22 bp):
TTCGTGAACATGTTCGATTAAG
Found at i:22600492 original size:12 final size:12
Alignment explanation
Indices: 22600457--22600495 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
22600447 ATTAACATTA
22600457 TTCGTGAACATG
1 TTCGTGAACATG
**
22600469 TTCGTTTA-ATG
1 TTCGTGAACATG
22600480 TTCGTGAACATG
1 TTCGTGAACATG
22600492 TTCG
1 TTCG
22600496 ATTAAGTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41
Consensus pattern (12 bp):
TTCGTGAACATG
Found at i:22600527 original size:23 final size:23
Alignment explanation
Indices: 22600484--22600529 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
22600474 TTAATGTTCG
*
22600484 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAGTTAAA
22600507 TGAACATGTTC-ATGAATGTTAAA
1 TGAACATGTTCGATGAA-GTTAAA
22600530 CAACGAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (23 bp):
TGAACATGTTCGATGAAGTTAAA
Found at i:22601243 original size:9 final size:9
Alignment explanation
Indices: 22601231--22601282 Score: 63
Period size: 9 Copynumber: 5.8 Consensus size: 9
22601221 ATTTTTTTTC
22601231 ATAAAAAAT
1 ATAAAAAAT
22601240 ATAAAAAAT
1 ATAAAAAAT
*
22601249 -TCATAAAAT
1 AT-AAAAAAT
22601258 -TATAAAAAT
1 ATA-AAAAAT
22601267 ATAAAAAAT
1 ATAAAAAAT
22601276 ATAAAAA
1 ATAAAAA
22601283 CGGTTAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
8 2 0.05
9 34 0.89
10 2 0.05
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (9 bp):
ATAAAAAAT
Found at i:22601261 original size:19 final size:20
Alignment explanation
Indices: 22601228--22601282 Score: 73
Period size: 18 Copynumber: 3.0 Consensus size: 20
22601218 TTTATTTTTT
22601228 TTCATAAAAAATATAAAAAA
1 TTCATAAAAAATATAAAAAA
*
22601248 TTCAT-AAAATTAT-AAAAA
1 TTCATAAAAAATATAAAAAA
22601266 -T-ATAAAAAATATAAAAA
1 TTCATAAAAAATATAAAAA
22601283 CGGTTAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
16 2 0.06
17 8 0.26
18 9 0.29
19 7 0.23
20 5 0.16
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (20 bp):
TTCATAAAAAATATAAAAAA
Found at i:22601342 original size:9 final size:9
Alignment explanation
Indices: 22601328--22601397 Score: 58
Period size: 10 Copynumber: 7.9 Consensus size: 9
22601318 TTATATAATC
22601328 TTATAAAAA
1 TTATAAAAA
*
22601337 TTATAAACA
1 TTATAAAAA
*
22601346 TGAT--AAA
1 TTATAAAAA
22601353 TTAT-AAAA
1 TTATAAAAA
*
22601361 TTCTAATAAA
1 TTATAA-AAA
22601371 TTATAAAAAA
1 TTAT-AAAAA
22601381 TTAATAAAAA
1 TT-ATAAAAA
22601391 -TATAAAA
1 TTATAAAA
22601398 TTTTGATAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
7 5 0.10
8 12 0.24
9 13 0.26
10 16 0.32
11 4 0.08
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (9 bp):
TTATAAAAA
Found at i:22601397 original size:18 final size:18
Alignment explanation
Indices: 22601234--22601397 Score: 52
Period size: 19 Copynumber: 8.7 Consensus size: 18
22601224 TTTTTTCATA
*
22601234 AAAAATATAAAAAATTCAT
1 AAAAATAT-AAAAATTAAT
*
22601253 AAAATTATAAAAA-T-AT
1 AAAAATATAAAAATTAAT
22601269 AAAAAATATAAAAACGGTTAAAT
1 -AAAAATATAAAAA---TT-AAT
* *
22601292 ATTAAAATATGAAAATTTAT
1 A--AAAATATAAAAATTAAT
* * *
22601312 ATAAACT-TATATAATCTTAT
1 A-AAAATATA-AAAAT-TAAT
* *
22601332 AAAAATTATAAACA-TGAT
1 AAAAA-TATAAAAATTAAT
* *
22601350 -AAATTATAAAATTCTAAT
1 AAAAATATAAAAAT-TAAT
*
22601368 -AAATTATAAAAAATTAAT
1 AAAAATAT-AAAAATTAAT
22601386 AAAAATATAAAA
1 AAAAATATAAAA
22601398 TTTTGATAAA
Statistics
Matches: 111, Mismatches: 17, Indels: 35
0.68 0.10 0.21
Matches are distributed among these distances:
16 8 0.07
17 16 0.14
18 27 0.24
19 30 0.27
20 11 0.10
21 5 0.05
22 1 0.01
23 2 0.02
24 11 0.10
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (18 bp):
AAAAATATAAAAATTAAT
Found at i:22601408 original size:18 final size:18
Alignment explanation
Indices: 22601348--22601409 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
22601338 TATAAACATG
* *
22601348 ATAAATTATAAAATTCTA
1 ATAAAATATAAAATTTTA
* **
22601366 ATAAATTATAAAAAATTA
1 ATAAAATATAAAATTTTA
*
22601384 ATAAAAATATAAAATTTTG
1 AT-AAAATATAAAATTTTA
22601403 ATAAAAT
1 ATAAAAT
22601410 GTATTTAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
18 22 0.61
19 14 0.39
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (18 bp):
ATAAAATATAAAATTTTA
Found at i:22601728 original size:17 final size:17
Alignment explanation
Indices: 22601708--22601757 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
22601698 TTATTAAACT
22601708 TATAAAAATATATAAAA
1 TATAAAAATATATAAAA
22601725 TATAAAAATATA-ATAAA
1 TATAAAAATATATA-AAA
*
22601742 TTTAAAAA-AT-TAAAA
1 TATAAAAATATATAAAA
22601757 T
1 T
22601758 TTTAAATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 4 0.13
16 4 0.13
17 22 0.73
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TATAAAAATATATAAAA
Found at i:22601742 original size:9 final size:8
Alignment explanation
Indices: 22601708--22601749 Score: 57
Period size: 8 Copynumber: 5.0 Consensus size: 8
22601698 TTATTAAACT
22601708 TATAAAAA
1 TATAAAAA
22601716 TATATAAAA
1 TATA-AAAA
22601725 TATAAAAA
1 TATAAAAA
22601733 TATAATAAA
1 TATAA-AAA
*
22601742 TTTAAAAA
1 TATAAAAA
22601750 ATTAAAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 16 0.52
9 15 0.48
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
TATAAAAA
Found at i:22601761 original size:16 final size:18
Alignment explanation
Indices: 22601711--22601763 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 18
22601701 TTAAACTTAT
*
22601711 AAAAATAT-ATAAA-ATA
1 AAAAATATAATAAATTTA
22601727 TAAAAATATAATAAATTTA
1 -AAAAATATAATAAATTTA
*
22601746 AAAAAT-TAA-AATTTTA
1 AAAAATATAATAAATTTA
22601762 AA
1 AA
22601764 TTTTTAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 8 0.25
17 11 0.34
18 11 0.34
19 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAAATATAATAAATTTA
Found at i:22602404 original size:15 final size:15
Alignment explanation
Indices: 22602375--22602408 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
22602365 ACATCAGTAA
22602375 AAAATTAATTATTTT
1 AAAATTAATTATTTT
22602390 AAAATATAATT-TTTT
1 AAAAT-TAATTATTTT
22602405 AAAA
1 AAAA
22602409 ATATTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AAAATTAATTATTTT
Found at i:22602409 original size:16 final size:17
Alignment explanation
Indices: 22602374--22602412 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
22602364 CACATCAGTA
22602374 AAAAAT-TAATTATTTT
1 AAAAATATAATTATTTT
22602390 -AAAATATAATT-TTTT
1 AAAAATATAATTATTTT
22602405 AAAAATAT
1 AAAAATAT
22602413 TTAAAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AAAAATATAATTATTTT
Found at i:22602417 original size:10 final size:10
Alignment explanation
Indices: 22602397--22602435 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
22602387 TTTAAAATAT
*
22602397 AATTTTTTAA
1 AATTATTTAA
*
22602407 AAATATTTAA
1 AATTATTTAA
22602417 AATTAATTTAA
1 AATT-ATTTAA
22602428 AATTATTT
1 AATTATTT
22602436 TTAAATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 15 0.60
11 10 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
AATTATTTAA
Found at i:22604538 original size:16 final size:17
Alignment explanation
Indices: 22604514--22604562 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 17
22604504 AAATTTATCA
*
22604514 TTATTAATT-TAAAATT
1 TTATAAATTATAAAATT
22604530 TTATAAATTATAAAA-T
1 TTATAAATTATAAAATT
* *
22604546 ATCTAAATTA-AAAATT
1 TTATAAATTATAAAATT
22604562 T
1 T
22604563 ATCATTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 4 0.15
16 18 0.67
17 5 0.19
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
TTATAAATTATAAAATT
Found at i:22605197 original size:30 final size:26
Alignment explanation
Indices: 22605138--22605199 Score: 70
Period size: 30 Copynumber: 2.2 Consensus size: 26
22605128 TTCGTTAAGA
*
22605138 ATTTAAAATTTTGTTTATGTTCATTT
1 ATTTAAAATTTTGTTTATATTCATTT
*
22605164 ATTTAAAATTATGTGTGTTCATATTCGTTT
1 ATTTAAAATT-T-TGT-TT-ATATTCATTT
22605194 ATTTAA
1 ATTTAA
22605200 TGTTCATGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 10 0.33
27 1 0.03
28 3 0.10
29 2 0.07
30 14 0.47
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.56
Consensus pattern (26 bp):
ATTTAAAATTTTGTTTATATTCATTT
Found at i:22605258 original size:24 final size:24
Alignment explanation
Indices: 22605206--22605259 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
22605196 TTAATGTTCA
*
22605206 TGAACATGTTCACAAACATGTAAT
1 TGAATATGTTCACAAACATGTAAT
*
22605230 TGAATATGTTCACGAACATGTAAT
1 TGAATATGTTCACAAACATGTAAT
22605254 TGAATA
1 TGAATA
22605260 ATAAACGAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (24 bp):
TGAATATGTTCACAAACATGTAAT
Found at i:22608591 original size:6 final size:6
Alignment explanation
Indices: 22608564--22608631 Score: 77
Period size: 6 Copynumber: 11.5 Consensus size: 6
22608554 TTAAATTTGT
* **
22608564 TTTAAA GTTTAAA TTT-AT TTTAAA TTTAAA TTTATT TTTAAA TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
22608612 TTT-AA TTTAAG TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTT
22608632 GCTTTCAAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
5 9 0.18
6 36 0.71
7 6 0.12
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:22608620 original size:11 final size:11
Alignment explanation
Indices: 22608571--22608627 Score: 60
Period size: 11 Copynumber: 5.0 Consensus size: 11
22608561 TGTTTTAAAG
*
22608571 TTTAAATTTAT
1 TTTAAATTTAA
22608582 TTTAAATTTAAA
1 TTTAAATTT-AA
**
22608594 TTTATTTTTAAA
1 TTTAAATTT-AA
22608606 TTTAAATTTAA
1 TTTAAATTTAA
*
22608617 TTTAAGTTTAA
1 TTTAAATTTAA
22608628 ATTTGCTTTC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
11 21 0.54
12 18 0.46
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:22608660 original size:17 final size:16
Alignment explanation
Indices: 22608536--22608664 Score: 116
Period size: 17 Copynumber: 7.4 Consensus size: 16
22608526 CCAAACCCAT
22608536 TTTAAATTTATCTTAAGA
1 TTTAAATTTAT-TTAA-A
*
22608554 -TTAAATTTGTTTTAAA
1 TTTAAATTT-ATTTAAA
22608570 GTTTAAATTTATTTTAAA
1 -TTTAAATTTA-TTTAAA
22608588 TTTAAATTTATTTTTAAA
1 TTTAAATTTA--TTTAAA
*
22608606 TTTAAATTTAATTTAAG
1 TTTAAATTT-ATTTAAA
*
22608623 TTTAAATTTGCTTTCAAA
1 TTTAAATTT-ATTT-AAA
*
22608641 TTTAAAATTATTATAAA
1 TTTAAATTTATT-TAAA
22608658 TTTAAAT
1 TTTAAAT
22608665 GTCCAATTAC
Statistics
Matches: 94, Mismatches: 9, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
16 1 0.01
17 50 0.53
18 42 0.45
19 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:22608662 original size:35 final size:33
Alignment explanation
Indices: 22608536--22608664 Score: 143
Period size: 35 Copynumber: 3.7 Consensus size: 33
22608526 CCAAACCCAT
22608536 TTTAAATTTATCTTAAGA-TTAAATTTGTTTTAAA
1 TTTAAATTTAT-TTAA-ATTTAAATTTGTTTTAAA
*
22608570 GTTTAAATTTATTTTAAATTTAAATTTATTTTTAAA
1 -TTTAAATTTA-TTTAAATTTAAATTT-GTTTTAAA
* *
22608606 TTTAAATTTAATTTAAGTTTAAATTTGCTTTCAAA
1 TTTAAATTT-ATTTAAATTTAAATTTG-TTTTAAA
*
22608641 TTTAAAATTATTATAAATTTAAAT
1 TTTAAATTTATT-TAAATTTAAAT
22608665 GTCCAATTAC
Statistics
Matches: 82, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
34 4 0.05
35 69 0.84
36 9 0.11
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (33 bp):
TTTAAATTTATTTAAATTTAAATTTGTTTTAAA
Found at i:22609386 original size:24 final size:23
Alignment explanation
Indices: 22609353--22609411 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 23
22609343 TTAAATAAGT
22609353 TTAATATAATATTTAATAATATTCA
1 TTAAT-TAATATTTAATAATATT-A
*
22609378 TTAATTAATAATTTAATGATATTA
1 TTAATTAAT-ATTTAATAATATTA
22609402 TTAATTAATA
1 TTAATTAATA
22609412 ATAAATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 1 0.03
24 14 0.44
25 17 0.53
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
TTAATTAATATTTAATAATATTA
Found at i:22609412 original size:24 final size:25
Alignment explanation
Indices: 22609353--22609413 Score: 90
Period size: 24 Copynumber: 2.5 Consensus size: 25
22609343 TTAAATAAGT
22609353 TTAATATAAT-ATTTAATAATATTCA
1 TTAAT-TAATAATTTAATAATATTCA
*
22609378 TTAATTAATAATTTAATGATATT-A
1 TTAATTAATAATTTAATAATATTCA
22609402 TTAATTAATAAT
1 TTAATTAATAAT
22609414 AAATAAAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 17 0.50
25 17 0.50
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (25 bp):
TTAATTAATAATTTAATAATATTCA
Found at i:22610381 original size:13 final size:12
Alignment explanation
Indices: 22610363--22610406 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
22610353 ATATGAAATA
22610363 AAAGAATAAAAAG
1 AAAGAA-AAAAAG
22610376 AAAGAAACAAAAG
1 AAAGAAA-AAAAG
* *
22610389 AAATAAAAGAAG
1 AAAGAAAAAAAG
22610401 AAAGAA
1 AAAGAA
22610407 CAGAGAGCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (12 bp):
AAAGAAAAAAAG
Found at i:22610387 original size:22 final size:25
Alignment explanation
Indices: 22610357--22610406 Score: 70
Period size: 22 Copynumber: 2.1 Consensus size: 25
22610347 ATATATATAT
*
22610357 GAAATAAAAG-AAT-AAA-AAGAAA
1 GAAACAAAAGAAATAAAAGAAGAAA
22610379 GAAACAAAAGAAATAAAAGAAGAAA
1 GAAACAAAAGAAATAAAAGAAGAAA
22610404 GAA
1 GAA
22610407 CAGAGAGCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 9 0.38
23 3 0.12
24 3 0.12
25 9 0.38
ACGTcount: A:0.76, C:0.02, G:0.16, T:0.06
Consensus pattern (25 bp):
GAAACAAAAGAAATAAAAGAAGAAA
Found at i:22611247 original size:41 final size:40
Alignment explanation
Indices: 22611199--22611299 Score: 100
Period size: 38 Copynumber: 2.6 Consensus size: 40
22611189 TCGACCTCGA
** *
22611199 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
* ** *
22611239 ATTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
*
22611277 GCCGATGAGACACTGGGTGTCAC
1 GTCGATGAGACACTGGGTGTCAC
22611300 TTTATTGCTT
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
37 10 0.22
38 17 0.37
39 4 0.09
40 4 0.09
41 11 0.24
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (40 bp):
GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
Found at i:22616538 original size:24 final size:24
Alignment explanation
Indices: 22616488--22616532 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
22616478 ATATATATAT
*
22616488 GAAATAAAAGAATAAAGAAAGAAA
1 GAAACAAAAGAATAAAGAAAGAAA
22616512 GAAACAAAAGAA-AAA-AAAGAA
1 GAAACAAAAGAATAAAGAAAGAA
22616533 GAAGAACAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (24 bp):
GAAACAAAAGAATAAAGAAAGAAA
Found at i:22617371 original size:29 final size:29
Alignment explanation
Indices: 22617318--22617449 Score: 85
Period size: 29 Copynumber: 4.5 Consensus size: 29
22617308 CAAATAGTCC
**
22617318 AAAAATTA-CATTTTGACCCTGAAACTTCT
1 AAAAATTACCATTTT-ACCCCCAAACTTCT
22617347 AAAAATTACCATTTTACCCCCAAACTT-T
1 AAAAATTACCATTTTACCCCCAAACTTCT
* * * * * *
22617375 CCAAAATT-CCACTTTCAACCCC-GATTTCACC
1 -AAAAATTACCA-TTTTACCCCCAAACTT--CT
*
22617406 AAAAATTACCATTTTACCCCCAAACTTTT
1 AAAAATTACCATTTTACCCCCAAACTTCT
*
22617435 TAAAATT-CCACTTTT
1 AAAAATTACCA-TTTT
22617450 TAAAAGTTTT
Statistics
Matches: 78, Mismatches: 16, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
28 10 0.13
29 42 0.54
30 20 0.26
31 6 0.08
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCCCAAACTTCT
Found at i:22617464 original size:10 final size:10
Alignment explanation
Indices: 22617444--22617481 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
22617434 TTAAAATTCC
22617444 ACTTTTTAAA
1 ACTTTTTAAA
* *
22617454 AGTTTTAAAA
1 ACTTTTTAAA
22617464 ACTTTTTAAA
1 ACTTTTTAAA
22617474 ACTTTTTA
1 ACTTTTTA
22617482 CAGTTTGTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.50
Consensus pattern (10 bp):
ACTTTTTAAA
Found at i:22618566 original size:29 final size:29
Alignment explanation
Indices: 22618519--22618641 Score: 87
Period size: 29 Copynumber: 4.2 Consensus size: 29
22618509 AAACAGTCCA
22618519 AAAAATTA-CATTTTGACCCCGAAACTTCT
1 AAAAATTACCATTTT-ACCCCGAAACTTCT
*
22618548 AAAAATTACCATTTTACCCCCAAACTT-T
1 AAAAATTACCATTTTACCCCGAAACTTCT
* * * *
22618576 CCAAAATT-CCACTTTCAACCCCG--ATTTCACC
1 -AAAAATTACCA-TTT-TACCCCGAAACTT--CT
*
22618607 AAAAATTACCATTTTACCCC-AAACTTTT
1 AAAAATTACCATTTTACCCCGAAACTTCT
*
22618635 TAAAATT
1 AAAAATT
22618642 CCACTTTCAA
Statistics
Matches: 72, Mismatches: 12, Indels: 21
0.69 0.11 0.20
Matches are distributed among these distances:
28 13 0.18
29 33 0.46
30 23 0.32
31 3 0.04
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.32
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCCGAAACTTCT
Found at i:22618612 original size:30 final size:30
Alignment explanation
Indices: 22618578--22618729 Score: 86
Period size: 30 Copynumber: 5.1 Consensus size: 30
22618568 CAAACTTTCC
22618578 AAAATTCCACTTTCAACCCCGATTTCACCA
1 AAAATTCCACTTTCAACCCCGATTTCACCA
* * **
22618608 AAAATTACCA-TTT-TACCCCAAACTTT---TT
1 AAAATT-CCACTTTCAACCCC-GA-TTTCACCA
*
22618636 AAAATTCCACTTTCAAACCTCGATTTCACCA
1 AAAATTCCACTTTC-AACCCCGATTTCACCA
* ** *
22618667 AAAATTACCATTTTACCCCCCCGAACTTC-CC-
1 AAAATT-CCACTTT-CAACCCCG-ATTTCACCA
* *
22618698 AAAATTCCATTTTTAA-CCCGATTTCACCA
1 AAAATTCCACTTTCAACCCCGATTTCACCA
22618727 AAA
1 AAA
22618730 TTACCATTTT
Statistics
Matches: 90, Mismatches: 18, Indels: 29
0.66 0.13 0.21
Matches are distributed among these distances:
27 7 0.08
28 18 0.20
29 9 0.10
30 21 0.23
31 18 0.20
32 12 0.13
33 5 0.06
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.30
Consensus pattern (30 bp):
AAAATTCCACTTTCAACCCCGATTTCACCA
Found at i:22618614 original size:59 final size:59
Alignment explanation
Indices: 22618548--22618744 Score: 283
Period size: 59 Copynumber: 3.3 Consensus size: 59
22618538 CGAAACTTCT
22618548 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCACTTTCAACCCCGATTTCACC
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCACTTTCAACCCCGATTTCACC
** *
22618607 AAAAATTACCATTTTA-CCCCAAACTTTTTAAAATTCCACTTTCAAACCTCGATTTCACC
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCACTTTC-AACCCCGATTTCACC
* * * *
22618666 AAAAATTACCATTTTACCCCCCCGAACTTCCCAAAATTCCATTTTTAA-CCCGATTTCACC
1 AAAAATTACCATTTTA--CCCCCAAACTTTCCAAAATTCCACTTTCAACCCCGATTTCACC
22618726 -AAAATTACCATTTTACCCC
1 AAAAATTACCATTTTACCCC
22618745 GGGTATCCAA
Statistics
Matches: 124, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
57 4 0.03
58 25 0.20
59 61 0.49
60 11 0.09
61 2 0.02
62 21 0.17
ACGTcount: A:0.34, C:0.33, G:0.02, T:0.31
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCACTTTCAACCCCGATTTCACC
Found at i:22618777 original size:59 final size:60
Alignment explanation
Indices: 22618548--22618782 Score: 184
Period size: 59 Copynumber: 4.0 Consensus size: 60
22618538 CGAAACTTCT
* * * * *
22618548 AAAAATTACCATTTTA--CCCCCAAACTTTCCAAAATTCCACTTTCAACCCCGATTTCACC
1 AAAAATTACCATTTTACCCCCCCGAAC-TCCCAAAATCCCATTTTTAACCCCGATTTCACC
* *** * ** *
22618607 AAAAATTACCATTTTA---CCCCAAACTTTTTAAAATTCCACTTTCAAACCTCGATTTCACC
1 AAAAATTACCATTTTACCCCCCCGAAC-TCCCAAAATCCCA-TTTTTAACCCCGATTTCACC
*
22618666 AAAAATTACCATTTTACCCCCCCGAACTTCCCAAAATTCCATTTTTAA-CCCGATTTCACC
1 AAAAATTACCATTTTACCCCCCCGAAC-TCCCAAAATCCCATTTTTAACCCCGATTTCACC
** *
22618726 -AAAATTACCATTTTA-CCCCGGGTA-T-CCAAAAGTCCCATTTTTTTAACCCCGATTTCA
1 AAAAATTACCATTTTACCCCCCCGAACTCCCAAAA-TCCCA--TTTTTAACCCCGATTTCA
22618783 TCGTTTCTTC
Statistics
Matches: 151, Mismatches: 17, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
55 6 0.04
56 5 0.03
58 33 0.22
59 73 0.48
60 11 0.07
61 5 0.03
62 18 0.12
ACGTcount: A:0.33, C:0.32, G:0.04, T:0.31
Consensus pattern (60 bp):
AAAAATTACCATTTTACCCCCCCGAACTCCCAAAATCCCATTTTTAACCCCGATTTCACC
Found at i:22622996 original size:12 final size:12
Alignment explanation
Indices: 22622979--22623003 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22622969 AAGACCAGCT
22622979 AGAGAGAGTACA
1 AGAGAGAGTACA
22622991 AGAGAGAGTACA
1 AGAGAGAGTACA
22623003 A
1 A
22623004 AGGGATATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.32, T:0.08
Consensus pattern (12 bp):
AGAGAGAGTACA
Found at i:22630858 original size:38 final size:38
Alignment explanation
Indices: 22630814--22631013 Score: 141
Period size: 38 Copynumber: 5.3 Consensus size: 38
22630804 ATAACAAGTC
*
22630814 TGAAATTGAAGTAAGAGCAAGATCGTTTCCCATCCTCT
1 TGAAATTGAAGTAAGAGCAAGATCGTTTCCTATCCTCT
* * * *
22630852 TAAAATTGAAGTAGAGTTGGATA-ACACGTCTT--TAT-CTC-
1 TGAAATTGAAGTA-AG-AGCA-AGA-TCGT-TTCCTATCCTCT
*
22630890 TGAAATTGAAGTAAGAGCAAGATCTTTTCCTATCCTCT
1 TGAAATTGAAGTAAGAGCAAGATCGTTTCCTATCCTCT
* * *
22630928 TGAAATTGAAGTAGAGTTGGATA-ACACGTCTT--TAT-CTC-
1 TGAAATTGAAGTA-AG-AGCA-AGA-TCGT-TTCCTATCCTCT
* *
22630966 TGAAATTGTAGTAAGAGCAAGATCATTTCCTATCCTCT
1 TGAAATTGAAGTAAGAGCAAGATCGTTTCCTATCCTCT
22631004 TGAAATTGAA
1 TGAAATTGAA
22631014 ATAGAGCTGG
Statistics
Matches: 122, Mismatches: 20, Indels: 40
0.67 0.11 0.22
Matches are distributed among these distances:
34 4 0.03
35 6 0.05
36 12 0.10
37 10 0.08
38 58 0.48
39 10 0.08
40 11 0.09
41 7 0.06
42 4 0.03
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (38 bp):
TGAAATTGAAGTAAGAGCAAGATCGTTTCCTATCCTCT
Found at i:22630938 original size:76 final size:76
Alignment explanation
Indices: 22630812--22631375 Score: 411
Period size: 76 Copynumber: 7.3 Consensus size: 76
22630802 GGATAACAAG
* * *
22630812 TCTGAAATTGAAGTAAGAGCAAGATCGTTTCCCATCCTCTTAAAATTGAAGTAGAGTTGGATAAC
1 TCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAAC
22630877 ACGTCTTTATC
66 ACGTCTTTATC
*
22630888 TCTGAAATTGAAGTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAAC
1 TCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAAC
22630953 ACGTCTTTATC
66 ACGTCTTTATC
* * * *
22630964 TCTGAAATTGTAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAATAGAGCTGGATATC
1 TCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAAC
*
22631029 AAGTCTTTATCTC
66 ACGTCTTTA--TC
** *** * * **** * *
22631042 TCTGAAATT-AAGTAAGAGCAAGAAGGAGCACCAGCATCATTTCCTATCCTCTTGAAATTGAAGT
1 TCTGAAATTGAAGTAAGAGCAAG-ATCATTTCC--TATC--CT-CT-TGAAATTGAAGTAG-AGT
** * * * *** *
22631106 AAAGCTGGATATCAAGTCTT-TA
58 -TGGAT-AACA-CGTCT-TTATC
** *
22631128 TCTCTGAAATTGAAGTAAGAGCAAGATCATTTTCCTATCTTCTTGAAATTGAAGTAGAGTTGGAT
1 TCT-GAAA-TTGAAGTAAGAGCAAGATCA-TTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGAT
*
22631193 AACACATCTTTATC
63 AACACGTCTTTATC
* * * *
22631207 TC------TG-AGCAAGATC---AT--TTTCCTATCTTTTTGAAATTGAAAGTAGAGTTGGATAA
1 TCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTG-AAGTAGAGTTGGATAA
*
22631260 CACATCTTTATC
65 CACGTCTTTATC
*
22631272 TCTGAAATTGAAGTAAGAGCAAGATCATTGTCCTATCTTCTTGAAATTGAAGT-GAAGTTGGATA
1 TCTGAAATTGAAGTAAGAGCAAGATCATT-TCCTATCCTCTTGAAATTGAAGTAG-AGTTGGATA
* * *
22631336 GCAAGTTTTTATCTC
64 ACACGTCTTTA--TC
* *
22631351 TCTGAAACTGAAGTAAGAGCTAGAT
1 TCTGAAATTGAAGTAAGAGCAAGAT
22631376 AAAGCATCAA
Statistics
Matches: 384, Mismatches: 68, Indels: 69
0.74 0.13 0.13
Matches are distributed among these distances:
64 20 0.05
65 30 0.08
67 2 0.01
70 7 0.02
71 4 0.01
72 7 0.02
75 2 0.01
76 142 0.37
77 34 0.09
78 35 0.09
79 31 0.08
80 5 0.01
81 2 0.01
82 4 0.01
83 10 0.03
84 11 0.03
85 4 0.01
86 6 0.02
87 6 0.02
88 5 0.01
89 17 0.04
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (76 bp):
TCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAAC
ACGTCTTTATC
Found at i:22631459 original size:92 final size:93
Alignment explanation
Indices: 22631295--22631472 Score: 243
Period size: 92 Copynumber: 1.9 Consensus size: 93
22631285 TAAGAGCAAG
* * *
22631295 ATCATTGTCCTATCTTCTTGAAATTGAAGTGAAGTTGGATAGCAAGTTTTTATCTCTCTGAAACT
1 ATCATTGTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAACT
*
22631360 GAAGTAAGAGCTAGATAAAGCATCAAAC
66 GAAGTAAGAGCAAGATAAAGCATCAAAC
* * **
22631388 ATCATT-TCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCGAA-TCTTTATCTCTCTGAAGT
1 ATCATTGTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAGC-AAGTCTTTATCTCTCTGAAAC
* *
22631451 TGCAGTAAGAGCAAGATGAAGC
65 TGAAGTAAGAGCAAGATAAAGC
22631473 TTCGACACCA
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
92 66 0.89
93 8 0.11
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Consensus pattern (93 bp):
ATCATTGTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAACT
GAAGTAAGAGCAAGATAAAGCATCAAAC
Found at i:22631952 original size:17 final size:17
Alignment explanation
Indices: 22631929--22632039 Score: 161
Period size: 17 Copynumber: 6.4 Consensus size: 17
22631919 CCAAACCCAT
*
22631929 TTTAAATTTATCTTAAGA
1 TTTAAATTTATTTTAA-A
*
22631947 -TTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
22631963 GTTTAAATTTATTTTAAA
1 -TTTAAATTTATTTTAAA
22631981 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
22631998 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
*
22632016 TTTAAATTTATTATAAA
1 TTTAAATTTATTTTAAA
22632033 TTTAAAT
1 TTTAAAT
22632040 GTCCAATTAC
Statistics
Matches: 86, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
16 1 0.01
17 53 0.62
18 32 0.37
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:22631968 original size:35 final size:34
Alignment explanation
Indices: 22631929--22632039 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 34
22631919 CCAAACCCAT
* *
22631929 TTTAAATTTATCTTAAGA-TTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAA-ATTTAAATTTATTTTAAA
22631963 GTTTAAATTTATTTTAAATTTAAATTTATTTTAAA
1 -TTTAAATTTATTTTAAATTTAAATTTATTTTAAA
*
22631998 TTTAAATTTATTTTTAAATTTAAATTTATTATAAA
1 TTTAAATTTA-TTTTAAATTTAAATTTATTTTAAA
22632033 TTTAAAT
1 TTTAAAT
22632040 GTCCAATTAC
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
34 11 0.15
35 60 0.85
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.56
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTATTTTAAA
Found at i:22631984 original size:6 final size:6
Alignment explanation
Indices: 22631957--22632039 Score: 84
Period size: 6 Copynumber: 14.2 Consensus size: 6
22631947 TTAAATTTGT
* *
22631957 TTTAAA GTTTAAA TTT-AT TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
**
22632004 TTTATT TTTAAA TTTAAA TTT--A TTATAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA T
22632040 GTCCAATTAC
Statistics
Matches: 63, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
4 3 0.05
5 9 0.14
6 42 0.67
7 9 0.14
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:22631984 original size:11 final size:11
Alignment explanation
Indices: 22631957--22632037 Score: 58
Period size: 11 Copynumber: 7.0 Consensus size: 11
22631947 TTAAATTTGT
22631957 TTTAAAGTTTAAA
1 TTTAAA-TTT-AA
*
22631970 TTT-ATTTTAAA
1 TTTAAATTT-AA
*
22631981 TTTAAATTTAT
1 TTTAAATTTAA
22631992 TTTAAATTTAAA
1 TTTAAATTT-AA
**
22632004 TTTATTTTTAAA
1 TTTAAATTT-AA
22632016 TTTAAATTT-A
1 TTTAAATTTAA
22632026 TTATAAATTTAA
1 TT-TAAATTTAA
22632038 ATGTCCAATT
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
10 3 0.05
11 26 0.46
12 24 0.43
13 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:22631991 original size:52 final size:52
Alignment explanation
Indices: 22631929--22632039 Score: 163
Period size: 52 Copynumber: 2.1 Consensus size: 52
22631919 CCAAACCCAT
*
22631929 TTTAAATTTATCTTAAGA-TTAAATTT-GTTTTAAAGTTTAAATTTATTTTAAA
1 TTTAAATTTATCTTAA-ATTTAAATTTAGTTTTAAA-TTTAAATTTATTATAAA
* *
22631981 TTTAAATTTATTTTAAATTTAAATTTATTTTTAAATTTAAATTTATTATAAA
1 TTTAAATTTATCTTAAATTTAAATTTAGTTTTAAATTTAAATTTATTATAAA
22632033 TTTAAAT
1 TTTAAAT
22632040 GTCCAATTAC
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
51 1 0.02
52 46 0.85
53 7 0.13
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.56
Consensus pattern (52 bp):
TTTAAATTTATCTTAAATTTAAATTTAGTTTTAAATTTAAATTTATTATAAA
Found at i:22632095 original size:29 final size:29
Alignment explanation
Indices: 22632053--22632109 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
22632043 CAATTACAAG
22632053 TCAAGGTATGATATAAGTAAGCATGAAAT
1 TCAAGGTATGATATAAGTAAGCATGAAAT
*
22632082 TCAATGTATGATATAAGTAAGCATGAAA
1 TCAAGGTATGATATAAGTAAGCATGAAA
22632110 GAAAAACATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.28
Consensus pattern (29 bp):
TCAAGGTATGATATAAGTAAGCATGAAAT
Found at i:22633717 original size:16 final size:16
Alignment explanation
Indices: 22633693--22633723 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22633683 AAATTTATCA
*
22633693 TTATTAATTTAAAATT
1 TTATAAATTTAAAATT
22633709 TTATAAATTTAAAAT
1 TTATAAATTTAAAAT
22633724 ATCTAAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATAAATTTAAAATT
Found at i:22633742 original size:16 final size:16
Alignment explanation
Indices: 22633698--22633742 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
22633688 TATCATTATT
* *
22633698 AATTTAAAATTTTATA
1 AATTTAAAATTATCTA
22633714 AATTTAAAA-TATCTA
1 AATTTAAAATTATCTA
*
22633729 AATTAAAAATTATC
1 AATTTAAAATTATC
22633743 ATTTTAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTTAAAATTATCTA
Found at i:22634348 original size:30 final size:26
Alignment explanation
Indices: 22634289--22634350 Score: 70
Period size: 30 Copynumber: 2.2 Consensus size: 26
22634279 TTCGTTAAGA
*
22634289 ATTTAAAATTTTGTTTATGTTCATTT
1 ATTTAAAATTTTGTTTATATTCATTT
*
22634315 ATTTAAAATTATGTGTGTTCATATTCGTTT
1 ATTTAAAATT-T-TGT-TT-ATATTCATTT
22634345 ATTTAA
1 ATTTAA
22634351 TGTTCATGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 10 0.33
27 1 0.03
28 3 0.10
29 2 0.07
30 14 0.47
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.56
Consensus pattern (26 bp):
ATTTAAAATTTTGTTTATATTCATTT
Found at i:22634400 original size:24 final size:23
Alignment explanation
Indices: 22634350--22634421 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 23
22634340 CGTTTATTTA
* * *
22634350 ATGTTCATGAACATTAAATGAAC
1 ATGTTCACGAACATTAATTGAAT
*
22634373 ATGTTCACAAACATGTAATTGAAT
1 ATGTTCACGAACAT-TAATTGAAT
22634397 ATGTTCACGAACATATAATTGAAT
1 ATGTTCACGAACAT-TAATTGAAT
22634421 A
1 A
22634422 ATAAACGAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 12 0.29
24 30 0.71
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (23 bp):
ATGTTCACGAACATTAATTGAAT
Found at i:22639726 original size:175 final size:173
Alignment explanation
Indices: 22639354--22639763 Score: 568
Period size: 175 Copynumber: 2.4 Consensus size: 173
22639344 AGAAATCGGT
* * * * * *
22639354 TTGAATATGCATTAAGTTCAAAGATTGGTGATTATTTCAACACGAATTTTATAATCAATCGATGC
1 TTGAATACGCATT-AGTTCAAAGATCGGTGATTGTTTCAACACTAGTTTCATAATCAATCGATGC
** * * * *
22639419 TTTCTCCTCAATAAAGTATATTGTTTTGTCTTCACTTTTACACATATTTGAATAGATGTTTAATG
65 TTTCTCCTCAATAAAACATATCGTTCTGTCTTCACCTTTACACATATTTGAATAGATGTTTAATA
* * ***
22639484 CATCTAGATCGATTGAACAAATCAATAATGATGTGAAATTGGTA
130 CATCTAGACCGATTGAACAAATCAATAATGATATGAAATCAATA
* *
22639528 TTGAATACGTATTAGTTCAAAGATCGGTGATTGTTTCAACACTAGTTTCATGATCAATCGATGCT
1 TTGAATACGCATTAGTTCAAAGATCGGTGATTGTTTCAACACTAGTTTCATAATCAATCGATGCT
* *
22639593 TTCTCCTCAATAAAACATGTCGTTCTGTCTTCACCTTTGCACATATACTTGAATAGATGTTTAAT
66 TTCTCCTCAATAAAACATATCGTTCTGTCTTCACCTTTACACATAT--TTGAATAGATGTTTAAT
* *
22639658 ACATTTAGACCGATTGAACAAATCAATATTGATATGAAATCAATA
129 ACATCTAGACCGATTGAACAAATCAATAATGATATGAAATCAATA
* *
22639703 TTGAATACACATTAGTTCAAAGATCGATGATTGTTTCAACACTAGTTTCATAATCAATCGA
1 TTGAATACGCATTAGTTCAAAGATCGGTGATTGTTTCAACACTAGTTTCATAATCAATCGA
22639764 AATATACCGT
Statistics
Matches: 207, Mismatches: 27, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
173 85 0.41
174 11 0.05
175 111 0.54
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (173 bp):
TTGAATACGCATTAGTTCAAAGATCGGTGATTGTTTCAACACTAGTTTCATAATCAATCGATGCT
TTCTCCTCAATAAAACATATCGTTCTGTCTTCACCTTTACACATATTTGAATAGATGTTTAATAC
ATCTAGACCGATTGAACAAATCAATAATGATATGAAATCAATA
Found at i:22642217 original size:30 final size:30
Alignment explanation
Indices: 22642116--22642277 Score: 204
Period size: 30 Copynumber: 5.4 Consensus size: 30
22642106 CTTGGGGATA
*
22642116 AAAATGTAATTTTGG-AAAGTTTTAGGGTC
1 AAAATATAATTTTGGAAAAGTTTTAGGGTC
** ***
22642145 AAAATGCAATTTACAAAAAGTTTTAGGGTC
1 AAAATATAATTTTGGAAAAGTTTTAGGGTC
22642175 AAAATATAATTTTGGAAAAGTTTTAGGGTC
1 AAAATATAATTTTGGAAAAGTTTTAGGGTC
*
22642205 AAAATATAATTTTGGAAAAG-TTTAGGGGTT
1 AAAATATAATTTTGGAAAAGTTTTA-GGGTC
* *
22642235 AAAATATAATTTTGTAAAAG-TTTGGGGATC
1 AAAATATAATTTTGGAAAAGTTTTAGGG-TC
22642265 AAAATATAATTTT
1 AAAATATAATTTT
22642278 TGGATAGTTT
Statistics
Matches: 117, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
29 18 0.15
30 99 0.85
ACGTcount: A:0.41, C:0.04, G:0.19, T:0.36
Consensus pattern (30 bp):
AAAATATAATTTTGGAAAAGTTTTAGGGTC
Found at i:22643454 original size:21 final size:21
Alignment explanation
Indices: 22643407--22643456 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 21
22643397 TTGATGCTTT
22643407 TATTT-AAAATTAATTAATAC
1 TATTTAAAAATTAATTAATAC
22643427 TATTTAAAACATTAATTAATAC
1 TATTTAAAA-ATTAATTAATAC
22643449 -ATTTAAAA
1 TATTTAAAA
22643457 TATTCAATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.18
21 11 0.39
22 12 0.43
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (21 bp):
TATTTAAAAATTAATTAATAC
Done.