Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007869.1 Hibiscus syriacus cultivar Beakdansim tig00110243_pilon, 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: 590314
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:269572 original size:35 final size:35
Alignment explanation
Indices: 269506--269574 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
269496 GTCTTAGGTC
**
269506 TATAAGGAATTACCAGCTCGATCGGTCTGAACCTA
1 TATAAGGAATTACCAGCTCGATAAGTCTGAACCTA
* *
269541 TATAAGGAATTACCAGTTTGACTAAGT-TGAACCT
1 TATAAGGAATTACCAGCTCGA-TAAGTCTGAACCT
269575 GAAGAGACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 26 0.90
36 3 0.10
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (35 bp):
TATAAGGAATTACCAGCTCGATAAGTCTGAACCTA
Found at i:271668 original size:38 final size:38
Alignment explanation
Indices: 271589--271758 Score: 193
Period size: 38 Copynumber: 4.5 Consensus size: 38
271579 TACAATATCA
* * *
271589 TATTTTAATTGAATATAACTTCGT-AATAATATATTCA
1 TATTTTAATTGAATATAAATTCATAAATAATATATTCG
* *
271626 TATTTTAATTGAATATAAGTTCATAAATAATCTAATT-G
1 TATTTTAATTGAATATAAATTCATAAATAATAT-ATTCG
** * *
271664 TA-TTTAATCAAATATAAATTTATAAATAATATATTCC
1 TATTTTAATTGAATATAAATTCATAAATAATATATTCG
* * *
271701 TATTTCAATTGAATATAAATTCGTAAATAATATATTTG
1 TATTTTAATTGAATATAAATTCATAAATAATATATTCG
*
271739 AATTTTAATTGAATATAAAT
1 TATTTTAATTGAATATAAAT
271759 CTTTAAATAA
Statistics
Matches: 110, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
36 3 0.03
37 49 0.45
38 55 0.50
39 3 0.03
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (38 bp):
TATTTTAATTGAATATAAATTCATAAATAATATATTCG
Found at i:271698 original size:75 final size:76
Alignment explanation
Indices: 271613--271770 Score: 212
Period size: 75 Copynumber: 2.1 Consensus size: 76
271603 ATAACTTCGT
* * * *
271613 AATAATATATTCATATTTTAATTGAATATAAGTTCATAAATAATCTAATTGTA-TTTAATCAAAT
1 AATAATATATTCATATTTCAATTGAATATAAATTCATAAATAATATAATTGAATTTTAATCAAAT
271677 ATAAAT-TTATA
66 ATAAATCTT-TA
* * * **
271688 AATAATATATTCCTATTTCAATTGAATATAAATTCGTAAATAATATATTTGAATTTTAATTGAAT
1 AATAATATATTCATATTTCAATTGAATATAAATTCATAAATAATATAATTGAATTTTAATCAAAT
271753 ATAAATCTTTA
66 ATAAATCTTTA
271764 AATAATA
1 AATAATA
271771 GAACAATATC
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
75 46 0.64
76 24 0.33
77 2 0.03
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (76 bp):
AATAATATATTCATATTTCAATTGAATATAAATTCATAAATAATATAATTGAATTTTAATCAAAT
ATAAATCTTTA
Found at i:290239 original size:21 final size:21
Alignment explanation
Indices: 290215--290267 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
290205 TCATTATAAA
290215 TAGATAGT-AAGGGTAAAGGGT
1 TAGATA-TCAAGGGTAAAGGGT
290236 TAGATATCAAGGGTAAAGGGT
1 TAGATATCAAGGGTAAAGGGT
*
290257 TAGTTATCAAG
1 TAGATATCAAG
290268 TTTTCCTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.38, C:0.04, G:0.32, T:0.26
Consensus pattern (21 bp):
TAGATATCAAGGGTAAAGGGT
Found at i:291707 original size:17 final size:19
Alignment explanation
Indices: 291678--291713 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
291668 TAAAAATAAA
291678 ATTTAATAAATCT-TCAAT
1 ATTTAATAAATCTATCAAT
291696 ATTTAA-AAATCTATCAAT
1 ATTTAATAAATCTATCAAT
291714 TTGATCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTTAATAAATCTATCAAT
Found at i:295824 original size:16 final size:18
Alignment explanation
Indices: 295791--295824 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
295781 AGCTTATGAC
295791 AGGTGATCAATAAATGTG
1 AGGTGATCAATAAATGTG
295809 AGGT-ATCAAT-AATGTG
1 AGGTGATCAATAAATGTG
295825 TTTTGAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 6 0.38
18 4 0.25
ACGTcount: A:0.38, C:0.06, G:0.26, T:0.29
Consensus pattern (18 bp):
AGGTGATCAATAAATGTG
Found at i:297541 original size:16 final size:16
Alignment explanation
Indices: 297522--297554 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
297512 TTTTTCCCTT
*
297522 TTTCTCTTTGCATCAG
1 TTTCTATTTGCATCAG
297538 TTTCTATTTGCATCAG
1 TTTCTATTTGCATCAG
297554 T
1 T
297555 GGACAATGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.21, G:0.12, T:0.52
Consensus pattern (16 bp):
TTTCTATTTGCATCAG
Found at i:301095 original size:60 final size:60
Alignment explanation
Indices: 301018--301145 Score: 170
Period size: 60 Copynumber: 2.1 Consensus size: 60
301008 ATAGTGTAGT
* *
301018 AATT-AACACATACTTACA-TCGGTGTAAGTATGTACATCTCTCAATATCTTGATACCTAA
1 AATTAAACACATACTTACACT-GGTGTAAGTATGTACATATATCAATATCTTGATACCTAA
** * *
301077 AATTAAACACATGTTTACACTGGTGTGAGTATGTACATATATCAATATCTTGGTACCTAA
1 AATTAAACACATACTTACACTGGTGTAAGTATGTACATATATCAATATCTTGATACCTAA
*
301137 AAATAAACA
1 AATTAAACA
301146 ATAATTATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
59 4 0.07
60 55 0.92
61 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (60 bp):
AATTAAACACATACTTACACTGGTGTAAGTATGTACATATATCAATATCTTGATACCTAA
Found at i:302420 original size:15 final size:16
Alignment explanation
Indices: 302387--302420 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
302377 TTTACTTTTC
*
302387 TTTTCAAGTTTTTACT
1 TTTTCAAGGTTTTACT
302403 TTTTCAAGGTTTTA-T
1 TTTTCAAGGTTTTACT
302418 TTT
1 TTT
302421 ACTTTCTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.18, C:0.09, G:0.09, T:0.65
Consensus pattern (16 bp):
TTTTCAAGGTTTTACT
Found at i:302505 original size:54 final size:54
Alignment explanation
Indices: 302442--302548 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
302432 AAATTTTAAG
302442 TATGATTTCTATCATACTTAGCTAAGTTTTTCATAGCCAAAGG-TTGAAGCGATA
1 TATGATTTCTATCATACTTAGCTAAGTTTTTCATAGCCAAAGGCTT-AAGCGATA
302496 TATGATTTCTATCATACTTAGCTAAGTTTTTCATAGCCAAAGGCTTAAGCGAT
1 TATGATTTCTATCATACTTAGCTAAGTTTTTCATAGCCAAAGGCTTAAGCGAT
302549 GACTCAATTC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
54 50 0.96
55 2 0.04
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (54 bp):
TATGATTTCTATCATACTTAGCTAAGTTTTTCATAGCCAAAGGCTTAAGCGATA
Found at i:303908 original size:77 final size:78
Alignment explanation
Indices: 303773--303926 Score: 283
Period size: 77 Copynumber: 2.0 Consensus size: 78
303763 AAAGTAAAAG
*
303773 CCAAGTTGATTCATCTTTGACTATGAAATATTTTAATGGAAGATAATACAATGGCATTTGGTAAT
1 CCAAGTTGATTCATCTTTGACTATGAAATATTTTAATGGAAGATAATACAATGACATTTGGTAAT
303838 TTTCAAGTTTCAA
66 TTTCAAGTTTCAA
*
303851 CCAAGTTGATTCATCTTTGACTATGGAAT-TTTTAATGGAAGATAATACAATGACATTTGGTAAT
1 CCAAGTTGATTCATCTTTGACTATGAAATATTTTAATGGAAGATAATACAATGACATTTGGTAAT
303915 TTTCAAGTTTCA
66 TTTCAAGTTTCA
303927 TTAATGACAA
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
77 46 0.62
78 28 0.38
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.39
Consensus pattern (78 bp):
CCAAGTTGATTCATCTTTGACTATGAAATATTTTAATGGAAGATAATACAATGACATTTGGTAAT
TTTCAAGTTTCAA
Found at i:306526 original size:3 final size:3
Alignment explanation
Indices: 306518--306598 Score: 103
Period size: 3 Copynumber: 27.3 Consensus size: 3
306508 TATGTAACAT
* * * *
306518 TAA TAA TAA TAA TAA TAA TGTA TTA TAA T-A TAA TAG TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
306563 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
306599 TTTAATATAA
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
2 4 0.06
3 63 0.91
4 2 0.03
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:306825 original size:54 final size:54
Alignment explanation
Indices: 306766--307577 Score: 1137
Period size: 54 Copynumber: 15.2 Consensus size: 54
306756 CCTCTTCTTT
* * * * *
306766 GAACAAATCTTCTACCTACAGGTTTGCTCCCTCTTGTTTCAAGGAGT-AGAACTC
1 GAAC-AATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTC
*
306820 GAACAATCTTCTGCCTACGGGTT--CTCCCTCTTGCTTCAGGGAG-CAGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTC
*
306871 GAATAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGT-AGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTC
* *
306924 GAACAATCTTCTGCCTACGGGTTTGCTCCCTCTTGTTTCAGGGAGT-AGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTC
* *
306977 GAACAATCTTCTGCCTACGGGTTTGCTCCCTCTTGTTTCAGGGAGTAAGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTC
*
307031 GAACAATCTTCTGTCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGT-AGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTC
* * * * * *
307084 GAACAATCTTTTGTCTATGGGTTCACT-TCTACTTGCTTTAGGGAGTAAGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCT-CTTGCTTCAGGGAGTAAGAACTC
* *
307138 GAACAATC-T-T-CCTACGGGTTCACTCCCTCTTAC-TCAGGGAGTAAGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTC
* * * * *
307188 GAACAATCTTCTTCCTACGGGTTCGTTCCCTCTTGTTTCAGAGAATAAGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTC
*
307242 GAACAATCTTCTACCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTC
* * *
307296 CAACAATCTTCTACCTACGGGTTCACTCCCTCTTGCTTCAGGGAGTAAGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTC
* * * *
307350 GAACAATTTTCTTCCTACGGGTTCGCTCTCTCTTGCTTCAGAGAGTAAGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTC
* * *
307404 GAACAATCTTCTGCCTATGGGTTCGTTCCCTCTTACTTCAGGGAGTAAGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTC
* *
307458 GAACAATCTTCTGCCTATGGGTTCGCTCCCTCTTGATTCA-GGAGGTAAGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGA-GTAAGAACTC
* * *
307512 AAACAATCTTCTGCCTACGGGTTCGCTCCCTGTTGCTTTAGGGAGTAAGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTC
307566 GAACAATCTTCT
1 GAACAATCTTCT
307578 TCTTCAATAC
Statistics
Matches: 688, Mismatches: 56, Indels: 28
0.89 0.07 0.04
Matches are distributed among these distances:
50 24 0.03
51 64 0.09
52 6 0.01
53 208 0.30
54 383 0.56
55 3 0.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (54 bp):
GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAAGAACTC
Found at i:316599 original size:23 final size:25
Alignment explanation
Indices: 316571--316617 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
316561 GAAGTTGCTT
*
316571 CTCTACT-TTTTTAAT-TCGATCTG
1 CTCTACTCTTTTGAATATCGATCTG
316594 CTCTACTCTTTTGAATATCGATCT
1 CTCTACTCTTTTGAATATCGATCT
316618 CCAATCCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 7 0.33
25 7 0.33
ACGTcount: A:0.19, C:0.23, G:0.09, T:0.49
Consensus pattern (25 bp):
CTCTACTCTTTTGAATATCGATCTG
Found at i:321458 original size:3 final size:3
Alignment explanation
Indices: 321450--321526 Score: 63
Period size: 3 Copynumber: 26.7 Consensus size: 3
321440 TATGTAACAT
* * * *
321450 TAA TAA TAA TAA TAA TTTA TTA TAA T-A TAA TAG TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
321495 T-G TAA TAA TAA TAA T-A TAA TAT TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
321527 TTTATAACCC
Statistics
Matches: 59, Mismatches: 10, Indels: 10
0.75 0.13 0.13
Matches are distributed among these distances:
2 7 0.12
3 50 0.85
4 2 0.03
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:321513 original size:11 final size:11
Alignment explanation
Indices: 321450--321526 Score: 61
Period size: 11 Copynumber: 6.9 Consensus size: 11
321440 TATGTAACAT
321450 TAATAATAATAA
1 TAAT-ATAATAA
* *
321462 TAAT-TTATTA
1 TAATATAATAA
*
321472 TAATATAATAG
1 TAATATAATAA
321483 T--TATAATAA
1 TAATATAATAA
321492 TAATGTAATAATAA
1 TAA--T-ATAATAA
*
321506 TAATATAATAT
1 TAATATAATAA
321517 TAATATAATA
1 TAATATAATA
321527 TTTATAACCC
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
9 8 0.15
10 8 0.15
11 20 0.38
12 5 0.10
13 1 0.02
14 10 0.19
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (11 bp):
TAATATAATAA
Found at i:321514 original size:14 final size:14
Alignment explanation
Indices: 321452--321521 Score: 70
Period size: 14 Copynumber: 4.9 Consensus size: 14
321442 TGTAACATTA
321452 ATAATAATAATAATTT
1 ATAATAATAATAA--T
*
321468 ATTATAAT-ATAAT
1 ATAATAATAATAAT
*
321481 AGTTATAATAATAAT
1 A-TAATAATAATAAT
*
321496 GTAATAATAATAAT
1 ATAATAATAATAAT
*
321510 ATAATATTAATA
1 ATAATAATAATA
321522 TAATATTTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
13 2 0.04
14 29 0.62
15 9 0.19
16 7 0.15
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:326999 original size:22 final size:20
Alignment explanation
Indices: 326964--327003 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
326954 CAAGTTCCTA
326964 AACTTTACTTTCTTGTAAAC
1 AACTTTACTTTCTTGTAAAC
326984 AACTTATACTCTTCTTGTAA
1 AACTT-TACT-TTCTTGTAA
327004 TATCCCCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 4 0.22
22 9 0.50
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (20 bp):
AACTTTACTTTCTTGTAAAC
Found at i:329407 original size:26 final size:26
Alignment explanation
Indices: 329371--329423 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
329361 AATGGTTTTA
329371 TTAGAAATATCAAATTGAATCTTGGG
1 TTAGAAATATCAAATTGAATCTTGGG
329397 TTAGAAATATCAAATTGAATCTTGGG
1 TTAGAAATATCAAATTGAATCTTGGG
329423 T
1 T
329424 ATTTTGTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.36
Consensus pattern (26 bp):
TTAGAAATATCAAATTGAATCTTGGG
Found at i:335510 original size:14 final size:14
Alignment explanation
Indices: 335491--335523 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
335481 TTATGGAAGC
335491 CTTCTTACTCTCTT
1 CTTCTTACTCTCTT
335505 CTTCTTACTCTCTT
1 CTTCTTACTCTCTT
335519 CTTCT
1 CTTCT
335524 CCTTCCCGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.06, C:0.36, G:0.00, T:0.58
Consensus pattern (14 bp):
CTTCTTACTCTCTT
Found at i:337383 original size:20 final size:20
Alignment explanation
Indices: 337358--337401 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
337348 ATGTACATGC
337358 ATTTGATAATTTACATATGT
1 ATTTGATAATTTACATATGT
337378 ATTTGATAATTTACATATGT
1 ATTTGATAATTTACATATGT
337398 ATTT
1 ATTT
337402 ATATGTCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.05, G:0.09, T:0.52
Consensus pattern (20 bp):
ATTTGATAATTTACATATGT
Found at i:338250 original size:22 final size:21
Alignment explanation
Indices: 338223--338281 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 21
338213 CTTTTTATAG
338223 TATAAATATAGATTATAGTTTT
1 TATAAATATA-ATTATAGTTTT
* *
338245 TGTAAATAATATAATATAGTTTT
1 TATAAAT-ATA-ATTATAGTTTT
338268 TATAAATATAATTA
1 TATAAATATAATTA
338282 GTATATAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 3 0.10
22 9 0.29
23 19 0.61
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.47
Consensus pattern (21 bp):
TATAAATATAATTATAGTTTT
Found at i:338266 original size:23 final size:23
Alignment explanation
Indices: 338190--338275 Score: 82
Period size: 23 Copynumber: 3.5 Consensus size: 23
338180 TGTTATGTAA
* * *
338190 TTTTTGTAAATAATATTAGTATAC
1 TTTTTATAAATAATA-TAATATAG
*
338214 TTTTTATAGTATAAATATAGATTATAG
1 TTTTTATA-AAT-AATATA-A-TATAG
*
338241 TTTTTGTAAATAATATAATATAG
1 TTTTTATAAATAATATAATATAG
338264 TTTTTATAAATA
1 TTTTTATAAATA
338276 TAATTAGTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
23 16 0.31
24 8 0.16
25 10 0.20
26 6 0.12
27 11 0.22
ACGTcount: A:0.41, C:0.01, G:0.08, T:0.50
Consensus pattern (23 bp):
TTTTTATAAATAATATAATATAG
Found at i:338278 original size:25 final size:24
Alignment explanation
Indices: 338190--338279 Score: 76
Period size: 25 Copynumber: 3.6 Consensus size: 24
338180 TGTTATGTAA
* * *
338190 TTTTTGTAA-ATAATATTAGTATAC
1 TTTTTATAATATAATA-TAATATAG
*
338214 TTTTTATAGTATAAATATAGATTATAG
1 TTTTTATAATAT-AATATA-A-TATAG
*
338241 TTTTTGTAA-ATAATATAATATAG
1 TTTTTATAATATAATATAATATAG
338264 TTTTTATAAATATAAT
1 TTTTTAT-AATATAAT
338280 TAGTATATAA
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
23 11 0.21
24 10 0.19
25 15 0.28
26 6 0.11
27 11 0.21
ACGTcount: A:0.41, C:0.01, G:0.08, T:0.50
Consensus pattern (24 bp):
TTTTTATAATATAATATAATATAG
Found at i:339837 original size:22 final size:22
Alignment explanation
Indices: 339809--339853 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
339799 TGCATTCATG
*
339809 TATTTTA-CATTTTATTTACATT
1 TATTTTATCATATT-TTTACATT
339831 TATTTTATCATATTTTTACATT
1 TATTTTATCATATTTTTACATT
339853 T
1 T
339854 TTATTCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (22 bp):
TATTTTATCATATTTTTACATT
Found at i:339861 original size:20 final size:22
Alignment explanation
Indices: 339823--339864 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
339813 TTACATTTTA
*
339823 TTTACATTTATTTTATCATATT
1 TTTACATTTATTATATCATATT
339845 TTTACATTT-TTAT-TCATATT
1 TTTACATTTATTATATCATATT
339865 AACTCATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 3 0.16
22 9 0.47
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTACATTTATTATATCATATT
Found at i:353039 original size:6 final size:6
Alignment explanation
Indices: 351703--353038 Score: 1703
Period size: 6 Copynumber: 229.0 Consensus size: 6
351693 GAAAGTATTG
351703 TTATAT TTATTTAT TTAATAT TTATAT TTATAT TTATAT TTATAT TTATAT
1 TTATAT TTA--TAT TT-ATAT TTATAT TTATAT TTATAT TTATAT TTATAT
351754 TTATA- TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTAT-T
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
351800 TTATA- TTATA- TT-TAT TT-TAT TTATAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
*
351844 TTATAT TTATAT TTATAT TTAT-T TTATAT TTATAT TTATAT TTATCT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
351891 TTATTTAT TTATAT TTATAT TTA-AT TTATAT TTATAT TTATAT TTATAT
1 TTA--TAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
351940 TTATAT TTATAT TT-TAT TTATA- TTATAT TTATA- TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
*
351985 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TT-TAT ATATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
*
352032 TTATA- TTATAT TTATAT TTATA- -TATAT TTAGAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
*
352077 TTATAT TTATAT TT-TAT TTA-AT TTATAT TTATAT TATTTAT ATTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT T-TATAT -TTATAT
352125 TTATAT TTATAT TTATAT TTATA- TTATA- TTATA- TT-TAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
352169 TTATAT TTATA- TTATAT TTATATTT TTATAT TTATAT TT-TA- TTATAT
1 TTATAT TTATAT TTATAT TTATA--T TTATAT TTATAT TTATAT TTATAT
*
352216 TTATATT TTATAT TTATAT TTAT-T TATATTT ATTATAT TTATA- TTAT-T
1 TTATA-T TTATAT TTATAT TTATAT T-TATAT -TTATAT TTATAT TTATAT
352264 TTATAT TTATA- TTATAT TT-TAT TT-TAT TTATA- TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
352308 TTATA- TTATA- TTATAT TTATAT TTATAT TTATA- TTATA- TT-TAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
*
352351 TTATAT TTATAT TTA-ATT TTATAT ATATAT TATATTAT TTATA- -TATAT
1 TTATAT TTATAT TTATA-T TTATAT TTATAT T-TA-TAT TTATAT TTATAT
* *
352399 TTATAT TTATAT TTATAT TTATTAT ATTATCT TTATAT TTATAT TTCTAT
1 TTATAT TTATAT TTATAT TTA-TAT -TTATAT TTATAT TTATAT TTATAT
352449 TTATAT TTATAT TTAT-T TTATA- -TATAT TTATAT TTATA- TTATTAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTA-TAT
352494 TTATA- TTATAT TTATAT TTATA- TTATA- TT-TAT TTATA- TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
352537 TTATAT TTATAT TTATATT TTATAT TTATA- TTATAT TTAT-T TTATAT
1 TTATAT TTATAT TTATA-T TTATAT TTATAT TTATAT TTATAT TTATAT
352584 TTATAT TTATAT TTATAT TTATAT TTATA- TTATAT TTATA- -TATA-
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
352628 TTATAT TTA-AT TTATA- TTATA- TT-TAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
*
352672 TTATAT TTAT-T TTATAT TATTTAT ATTATAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT T-TATAT -TTATAT TTATAT TTATAT TTATAT
352721 TTATAT TTATAT ATT-TAT TTATA- TTATA- TT-TAT TTATAT TTATAT
1 TTATAT TTATAT -TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
352766 TTATATT TTATTAT TTATA- TTATA- TT-TAT TTATAT TTATAT TTATAT
1 TTATA-T TTA-TAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
352813 TTATAT TTATAT TTATA- TTATAT TTATAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
352860 TTATAT TTATATT TTATAT TTATAT TTATA- TTATAT TTATAT TTATAT
1 TTATAT TTATA-T TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
* *
352908 TTATAT ATTATTAT ATATAT TTATAT TTATAT TTATA- TTATAT TTATTT
1 TTATAT -TTA-TAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
* * * * * * *
352957 TTATGT GTACATAT ATTATAAT ATATAT ATATAT ATATAT ATATAT ATATAT
1 TTATAT -T-TATAT -TTAT-AT TTATAT TTATAT TTATAT TTATAT TTATAT
* * * * *
353009 ATATAT ATATAT ATATAT ATATAT ATATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT
353039 AGTTACGAAA
Statistics
Matches: 1217, Mismatches: 26, Indels: 174
0.86 0.02 0.12
Matches are distributed among these distances:
4 32 0.03
5 241 0.20
6 828 0.68
7 78 0.06
8 37 0.03
9 1 0.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
TTATAT
Found at i:355346 original size:33 final size:33
Alignment explanation
Indices: 355252--355387 Score: 118
Period size: 33 Copynumber: 4.2 Consensus size: 33
355242 TTCGTCCCAA
* *
355252 TATTTTATCAAAATGAAAAATTGTGACAAAT-T
1 TATTTAATCAAAATAAAAAATTGTGACAAATAT
* * *
355284 TATTTAATCAAAATAAAAATTTATAACAAATAT
1 TATTTAATCAAAATAAAAAATTGTGACAAATAT
** *
355317 TAATTT-ATCATTATAAAAAATTGTGACAAATAA
1 T-ATTTAATCAAAATAAAAAATTGTGACAAATAT
* * * *
355350 TATTCT-TTCACAATAACAAATTGTAACAAA-AT
1 TATT-TAATCAAAATAAAAAATTGTGACAAATAT
355382 TATTTA
1 TATTTA
355388 GTCACAGTAA
Statistics
Matches: 83, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
31 1 0.01
32 34 0.41
33 44 0.53
34 4 0.05
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (33 bp):
TATTTAATCAAAATAAAAAATTGTGACAAATAT
Found at i:357922 original size:18 final size:18
Alignment explanation
Indices: 357899--357955 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
357889 CAAACCTATG
*
357899 TTTGTAAAAATGTTTATC
1 TTTGTAAGAATGTTTATC
* *
357917 TTTGTATGAATG---ATG
1 TTTGTAAGAATGTTTATC
357932 TTTGTAAGAATGTTTATC
1 TTTGTAAGAATGTTTATC
357950 TTTGTA
1 TTTGTA
357956 TGAGTGTCGC
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 13 0.42
18 18 0.58
ACGTcount: A:0.28, C:0.04, G:0.18, T:0.51
Consensus pattern (18 bp):
TTTGTAAGAATGTTTATC
Found at i:357938 original size:33 final size:33
Alignment explanation
Indices: 357896--357958 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
357886 TGTCAAACCT
357896 ATGTTTGTAAAAATGTTTATCTTTGTATGAATG
1 ATGTTTGTAAAAATGTTTATCTTTGTATGAATG
*
357929 ATGTTTGTAAGAATGTTTATCTTTGTATGA
1 ATGTTTGTAAAAATGTTTATCTTTGTATGA
357959 GTGTCGCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.03, G:0.19, T:0.49
Consensus pattern (33 bp):
ATGTTTGTAAAAATGTTTATCTTTGTATGAATG
Found at i:358084 original size:17 final size:17
Alignment explanation
Indices: 358062--358095 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
358052 ATGTTTATAA
*
358062 GAAATTAAGACTCTAAT
1 GAAATTAAGAATCTAAT
358079 GAAATTAAGAATCTAAT
1 GAAATTAAGAATCTAAT
358096 ATTTCATAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (17 bp):
GAAATTAAGAATCTAAT
Found at i:359703 original size:23 final size:23
Alignment explanation
Indices: 359677--359778 Score: 107
Period size: 23 Copynumber: 4.4 Consensus size: 23
359667 TGAACATATA
*
359677 TAAACGAACATGTT-AGCGAACGC
1 TAAATGAACATGTTCA-CGAACGC
* *
359700 TAAATGAACATATTCATGAACGC
1 TAAATGAACATGTTCACGAACGC
*
359723 TAAATGAACATGTTCACGAACATC
1 TAAATGAACATGTTCACGAAC-GC
** * *
359747 TAAACAAACATGTTCGCGAACGT
1 TAAATGAACATGTTCACGAACGC
359770 TAAATGAAC
1 TAAATGAAC
359779 TAACAAGAAT
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
23 44 0.69
24 20 0.31
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.23
Consensus pattern (23 bp):
TAAATGAACATGTTCACGAACGC
Found at i:362526 original size:20 final size:21
Alignment explanation
Indices: 362490--362530 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
362480 TTGCTTTAGG
*
362490 GGTATCGATACCCCTGCTACA
1 GGTACCGATACCCCTGCTACA
362511 GGTACCGATA-CCCTGCTACA
1 GGTACCGATACCCCTGCTACA
362531 ATGCTACTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.24, C:0.34, G:0.20, T:0.22
Consensus pattern (21 bp):
GGTACCGATACCCCTGCTACA
Found at i:363301 original size:22 final size:22
Alignment explanation
Indices: 363276--363355 Score: 142
Period size: 22 Copynumber: 3.6 Consensus size: 22
363266 ATGTGAAATT
* *
363276 TGTCCCGAAGGACCTATGTATT
1 TGTCCCGAAGGACCTCTGTATA
363298 TGTCCCGAAGGACCTCTGTATA
1 TGTCCCGAAGGACCTCTGTATA
363320 TGTCCCGAAGGACCTCTGTATA
1 TGTCCCGAAGGACCTCTGTATA
363342 TGTCCCGAAGGACC
1 TGTCCCGAAGGACC
363356 ACGTAGACCC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 56 1.00
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.26
Consensus pattern (22 bp):
TGTCCCGAAGGACCTCTGTATA
Found at i:366260 original size:106 final size:105
Alignment explanation
Indices: 366075--366285 Score: 413
Period size: 106 Copynumber: 2.0 Consensus size: 105
366065 CTTGCAGCAC
366075 CCATATGAACATCACTTGGTTCAGTCATGAACCTTGAAAGAAAACTTACTGCAAACACTAAATCC
1 CCATATGAACATCACTTGGTTCAGTCATGAACCTTGAAAGAAAACTTACTGCAAACACTAAATCC
366140 GGTCTGGTTGCTGTGAGGTAAAGTAGACTTCCAACTAAGCT
66 GGTCTGGTTGCTGTGAGGTAAAGTAGA-TTCCAACTAAGCT
366181 CCATATGAACATCACTTGGTTCAGTCATGAACCTTGAAAGAAAACTTACTGCAAACACTAAATCC
1 CCATATGAACATCACTTGGTTCAGTCATGAACCTTGAAAGAAAACTTACTGCAAACACTAAATCC
366246 GGTCTGGTTGCTGTGAGGTAAAGTAGATTCCAACTAAGCT
66 GGTCTGGTTGCTGTGAGGTAAAGTAGATTCCAACTAAGCT
366286 TCTGTATTCC
Statistics
Matches: 105, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
105 13 0.12
106 92 0.88
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (105 bp):
CCATATGAACATCACTTGGTTCAGTCATGAACCTTGAAAGAAAACTTACTGCAAACACTAAATCC
GGTCTGGTTGCTGTGAGGTAAAGTAGATTCCAACTAAGCT
Found at i:369276 original size:19 final size:18
Alignment explanation
Indices: 369254--369309 Score: 78
Period size: 18 Copynumber: 3.1 Consensus size: 18
369244 GTCTGTTTTC
369254 TACAGTCTGTTTTCTACAA
1 TACAGTCTGTTTTCTAC-A
*
369273 TACAGTCTGTTTTCTTTC-
1 TACAGTCTGTTTTC-TACA
369291 TACAGTCTGTTTTCTACA
1 TACAGTCTGTTTTCTACA
369309 T
1 T
369310 GGTATTAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
17 2 0.06
18 15 0.45
19 14 0.42
20 2 0.06
ACGTcount: A:0.20, C:0.21, G:0.11, T:0.48
Consensus pattern (18 bp):
TACAGTCTGTTTTCTACA
Found at i:369308 original size:14 final size:14
Alignment explanation
Indices: 369244--369271 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
369234 TAACAGACTT
369244 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
369258 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
369272 ATACAGTCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.50
Consensus pattern (14 bp):
GTCTGTTTTCTACA
Found at i:373370 original size:19 final size:19
Alignment explanation
Indices: 373348--373384 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
373338 GTCTGTTTTC
*
373348 TACAGTTTGTTTTCTACAA
1 TACAGTCTGTTTTCTACAA
373367 TACAGTCTGTTTTCTACA
1 TACAGTCTGTTTTCTACA
373385 TTTTCTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.19, G:0.11, T:0.46
Consensus pattern (19 bp):
TACAGTCTGTTTTCTACAA
Found at i:376448 original size:32 final size:32
Alignment explanation
Indices: 376398--376610 Score: 208
Period size: 32 Copynumber: 6.7 Consensus size: 32
376388 AAAAGTGAAA
376398 ATAATAATAAAATATATTTTTAAAAGTTTTAG
1 ATAATAATAAAATATATTTTTAAAAGTTTTAG
* * *
376430 ATGAA-AACAGAATATATTTTTTAAAA-TTAAAATA-
1 AT-AATAATAAAATATA-TTTTTAAAAGTT---TTAG
*
376464 ATAATAATAAAATATATTTTTAAAAGTTTTAT
1 ATAATAATAAAATATATTTTTAAAAGTTTTAG
* *
376496 ATGAA-AATAAAATATATTTTTTAAAA--TTAAA
1 AT-AATAATAAAATATA-TTTTTAAAAGTTTTAG
376527 ATAATAATAAAATATATTTTTAAAAGTTTTAG
1 ATAATAATAAAATATATTTTTAAAAGTTTTAG
* * * * *
376559 ATAAGAATAAAATGTATTTAT-AAA-TTTAAA
1 ATAATAATAAAATATATTTTTAAAAGTTTTAG
376589 ATAATAATAAAATATATTTTTA
1 ATAATAATAAAATATATTTTTA
376611 GTTAAGTTAA
Statistics
Matches: 149, Mismatches: 18, Indels: 29
0.76 0.09 0.15
Matches are distributed among these distances:
30 33 0.22
31 21 0.14
32 47 0.32
33 33 0.22
34 13 0.09
35 2 0.01
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (32 bp):
ATAATAATAAAATATATTTTTAAAAGTTTTAG
Found at i:376568 original size:63 final size:63
Alignment explanation
Indices: 376395--376610 Score: 328
Period size: 66 Copynumber: 3.4 Consensus size: 63
376385 TTCAAAAGTG
* *
376395 AAAATAATAATAAAATATATTTTTAAAAGTTTTAGATGAAAACAGAATATATTTTTTAAAATT
1 AAAATAATAATAAAATATATTTTTAAAAGTTTTAGATGAAAATAAAATATATTTTTTAAAATT
*
376458 AAAATAATAATAATAAAATATATTTTTAAAAGTTTTATATGAAAATAAAATATATTTTTTAAAAT
1 --AA-AATAATAATAAAATATATTTTTAAAAGTTTTAGATGAAAATAAAATATATTTTTTAAAAT
376523 T
63 T
* * *
376524 AAAATAATAATAAAATATATTTTTAAAAGTTTTAGAT-AAGAATAAAATGTA-TTTATAAATTT
1 AAAATAATAATAAAATATATTTTTAAAAGTTTTAGATGAA-AATAAAATATATTTTTTAAAATT
376586 AAAATAATAATAAAATATATTTTTA
1 AAAATAATAATAAAATATATTTTTA
376611 GTTAAGTTAA
Statistics
Matches: 142, Mismatches: 7, Indels: 7
0.91 0.04 0.04
Matches are distributed among these distances:
62 36 0.25
63 44 0.31
64 2 0.01
65 2 0.01
66 58 0.41
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (63 bp):
AAAATAATAATAAAATATATTTTTAAAAGTTTTAGATGAAAATAAAATATATTTTTTAAAATT
Found at i:376656 original size:30 final size:30
Alignment explanation
Indices: 376522--376658 Score: 102
Period size: 30 Copynumber: 4.6 Consensus size: 30
376512 TTTTTTAAAA
* * *
376522 TTAAAATAATAATAAAATATATTTTTAA-AAG
1 TTAAGATAAGAATAAAATATA--TTTAATATG
* * *
376553 TTTTAGATAAGAATAAAATGTATTTATAAAT-
1 -TTAAGATAAGAATAAAATATATTTA-ATATG
* * *
376584 TTAAAATAATAATAAAATATATTT-TTA-G
1 TTAAGATAAGAATAAAATATATTTAATATG
* *
376612 TTAAGTTAAGAATAAAACATATTTAATATG
1 TTAAGATAAGAATAAAATATATTTAATATG
*
376642 TTAAGATAAAAATAAAA
1 TTAAGATAAGAATAAAA
376659 AAAAATTTGA
Statistics
Matches: 82, Mismatches: 18, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
28 21 0.26
29 2 0.02
30 40 0.49
31 1 0.01
32 18 0.22
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.38
Consensus pattern (30 bp):
TTAAGATAAGAATAAAATATATTTAATATG
Found at i:376656 original size:58 final size:60
Alignment explanation
Indices: 376395--376658 Score: 205
Period size: 66 Copynumber: 4.2 Consensus size: 60
376385 TTCAAAAGTG
* * * * *
376395 AAAATAATAATAAAATATATTTTTAAAAGTTTTAGATGAA-AACAGAATATATTTTTTAAAATTA
1 AAAATAATAATAAAATATATTTTT--AAGTTTAAGAT-AAGAATAAAACATA-TTTAT-AAATT-
*
376459 A
60 T
* * * * *
376460 AATAATAATAATAAAATATATTTTTAAAAGTTTTATATGAA-AATAAAATATATTTTTTAAAATT
1 AA-AATAATAATAAAATATATTTTT--AAGTTTAAGAT-AAGAATAAAACATA-TTTATAAATTT
* **
376524 AAAATAATAATAAAATATATTTTTAAAAGTTTTAGATAAGAATAAAATGTATTTATAAATTT
1 AAAATAATAATAAAATATATTTTT--AAGTTTAAGATAAGAATAAAACATATTTATAAATTT
* *
376586 AAAATAATAATAAAATATATTTTT-AG-TTAAGTTAAGAATAAAACATATTTA-ATATGTT
1 AAAATAATAATAAAATATATTTTTAAGTTTAAGATAAGAATAAAACATATTTATAAAT-TT
* *
376644 AAGATAAAAATAAAA
1 AAAATAATAATAAAA
376659 AAAAATTTGA
Statistics
Matches: 180, Mismatches: 16, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
57 3 0.02
58 36 0.20
59 2 0.01
62 35 0.19
63 44 0.24
64 2 0.01
65 6 0.03
66 52 0.29
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.39
Consensus pattern (60 bp):
AAAATAATAATAAAATATATTTTTAAGTTTAAGATAAGAATAAAACATATTTATAAATTT
Found at i:378395 original size:21 final size:21
Alignment explanation
Indices: 378354--378393 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
378344 CTTGAAAATG
378354 TAATGTTATGAATATATTTTA
1 TAATGTTATGAATATATTTTA
*
378375 TAATTTTA-GAATATATTTT
1 TAATGTTATGAATATATTTT
378394 TAGAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (21 bp):
TAATGTTATGAATATATTTTA
Found at i:378405 original size:15 final size:13
Alignment explanation
Indices: 378373--378403 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
378363 GAATATATTT
*
378373 TATAATTTTAGAA
1 TATATTTTTAGAA
378386 TATATTTTTAGAA
1 TATATTTTTAGAA
378399 TATAT
1 TATAT
378404 ATATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (13 bp):
TATATTTTTAGAA
Found at i:384286 original size:3 final size:3
Alignment explanation
Indices: 384278--384341 Score: 65
Period size: 3 Copynumber: 20.3 Consensus size: 3
384268 TTTTAATTGT
* * * *
384278 TTA TTA TTA TTA TTA TTA TTTA TTG TTA TTA CTA TTAA TTG TTA GTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT-A TTA TTA TTA
384325 TTAA TTA TTA TTA TTA T
1 TT-A TTA TTA TTA TTA T
384342 CATCATAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
3 41 0.82
4 9 0.18
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:384306 original size:13 final size:13
Alignment explanation
Indices: 384273--384339 Score: 55
Period size: 13 Copynumber: 4.9 Consensus size: 13
384263 TCGAATTTTA
384273 ATTGTTTATTA-TT
1 ATTG-TTATTATTT
*
384286 ATTATTATTATTT
1 ATTGTTATTATTT
384299 ATTGTTATTACTATT
1 ATTGTTATTA-T-TT
* *
384314 AATTGTTAGTATTA
1 -ATTGTTATTATTT
*
384328 ATTATTATTATT
1 ATTGTTATTATT
384340 ATCATCATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
12 6 0.14
13 24 0.55
14 2 0.05
15 3 0.07
16 9 0.20
ACGTcount: A:0.30, C:0.01, G:0.06, T:0.63
Consensus pattern (13 bp):
ATTGTTATTATTT
Found at i:384306 original size:16 final size:16
Alignment explanation
Indices: 384281--384341 Score: 68
Period size: 16 Copynumber: 3.8 Consensus size: 16
384271 TAATTGTTTA
384281 TTATTATTATTATTAT
1 TTATTATTATTATTAT
* *
384297 TTATTGTTATTACTAT
1 TTATTATTATTATTAT
* * * *
384313 TAATTGTTAGTATTAA
1 TTATTATTATTATTAT
384329 TTATTATTATTAT
1 TTATTATTATTAT
384342 CATCATAAAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (16 bp):
TTATTATTATTATTAT
Found at i:385959 original size:24 final size:24
Alignment explanation
Indices: 385932--385977 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
385922 ATGCGTATAC
*
385932 ATATATTTTTTTACA-TATATTTCA
1 ATATATATTTTTA-ATTATATTTCA
385956 ATATATATTTTTAATTATATTT
1 ATATATATTTTTAATTATATTT
385978 TGTATTCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (24 bp):
ATATATATTTTTAATTATATTTCA
Found at i:386175 original size:9 final size:9
Alignment explanation
Indices: 386162--386232 Score: 72
Period size: 9 Copynumber: 7.3 Consensus size: 9
386152 TAGTAATATT
386162 TTTA-TTTA
1 TTTATTTTA
386170 TTTTATTTTA
1 -TTTATTTTA
386180 TTTATTTTA
1 TTTATTTTA
386189 TTTATTTTA
1 TTTATTTTA
386198 TTATACTTTTA
1 TT-TA-TTTTA
*
386209 TGTTATTTTG
1 T-TTATTTTA
386219 TCTTATTTTTA
1 T-TTA-TTTTA
386230 TTT
1 TTT
386233 TGTTATATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
9 24 0.44
10 16 0.30
11 13 0.24
12 1 0.02
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.75
Consensus pattern (9 bp):
TTTATTTTA
Found at i:386176 original size:5 final size:5
Alignment explanation
Indices: 386161--386233 Score: 71
Period size: 5 Copynumber: 14.8 Consensus size: 5
386151 ATAGTAATAT
*
386161 TTTTA -TTTA TTTTA TTTTA -TTTA TTTTA -TTTA TTTTA TTATA CTTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA
* * *
386209 TGTTA TTTTG TCTTA TTTTTA TTTT
1 TTTTA TTTTA TTTTA -TTTTA TTTT
386234 GTTATATTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
4 12 0.22
5 35 0.64
6 8 0.15
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:386180 original size:14 final size:14
Alignment explanation
Indices: 386161--386217 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
386151 ATAGTAATAT
386161 TTTTATTTATTTTA
1 TTTTATTTATTTTA
386175 TTTTATTTATTTTA
1 TTTTATTTATTTTA
*
386189 -TTTATTTTATTATA
1 TTTTA-TTTATTTTA
386203 CTTTTATGTTATTTT
1 -TTTTAT-TTATTTT
386218 GTCTTATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
13 4 0.11
14 22 0.59
15 1 0.03
16 10 0.27
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (14 bp):
TTTTATTTATTTTA
Found at i:386243 original size:14 final size:14
Alignment explanation
Indices: 386164--386243 Score: 54
Period size: 14 Copynumber: 5.4 Consensus size: 14
386154 GTAATATTTT
*
386164 TATTTATTTTATTT
1 TATTTATTTTATTA
386178 TATTTATTTTATT-
1 TATTTATTTTATTA
* *
386191 TATTTTATTATACTTT
1 TA-TTTATTTTA-TTA
*
386207 TATGTTATTTTGTCTTA
1 TAT-TTA-TTT-TATTA
* *
386224 TTTTTATTTTGTTA
1 TATTTATTTTATTA
386238 TATTTA
1 TATTTA
386244 AATCTAATTA
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
13 2 0.04
14 30 0.57
15 6 0.11
16 8 0.15
17 6 0.11
18 1 0.02
ACGTcount: A:0.21, C:0.03, G:0.04, T:0.72
Consensus pattern (14 bp):
TATTTATTTTATTA
Found at i:391097 original size:727 final size:729
Alignment explanation
Indices: 389903--391232 Score: 2475
Period size: 727 Copynumber: 1.8 Consensus size: 729
389893 TTGCATATTT
*
389903 ACATTGTACATTACATTTACTTAAGTGTTTTCACATGCATCATTCATAAAAACATGAAATCAATT
1 ACATTGTACATTACATTTACTTAAGTGTTTTCACATGCATCATTCATAAAAAAATGAAATCAATT
389968 CATGGAGGATTAGATGAAGTGGTCCTAATCACGTGACACCAAATTAAGAATAGAAGCAAGATTCA
66 CATGGAGGATTAGATGAAGTGGTCCTAATCACGTGACACCAAATTAAGAATAGAAGCAAGATTCA
390033 AAAAATTAAAAGAAGAAGTTGAAATCAGTACGCTGGGAGCATATTCAGCAGATCGTAGGGCTGAA
131 AAAAATTAAAAGAAGAAGTTGAAATCAGTACGCTGGGAGCATATTCAGCAGATCGTAGGGCTGAA
*
390098 CCTTATAGGATGATCTGATAAAAAAGTTAATTTGATCCAATTCCAATGACCTATGAGGAACTACT
196 CCTTATAGGATGATCTGAGAAAAAAGTTAATTTGATCCAATTCCAATGACCTATGAGGAACTACT
*
390163 TCCAACGTTGGTTGAGAATAATCTTGTGACTCTAGTTTAGTCCAAGCCCAAAGAGTCCCCATATC
261 TCCAACGTTGGTTGAGAATAATCTTGTGACTCTAGTTCAGTCCAAGCCCAAAGAGTCCCCATATC
390228 TTGAGGGTTGCATTGTTGATGCCATATGCAACTATCACATAGGAAGTTTAGGGCATTCCAATGAG
326 TTGAGGGTTGCATTGTTGATGCCATATGCAACTATCACATAGGAAGTTTAGGGCATTCCAATGAG
* *
390293 AATTATGGGGCATTGAAGCGAAAGGTCTAGAATCTGATTGATTCAGGGGCATGGACGTTTGATGA
391 AATTATGGGGCATTGAAACGAAAGGTCTAGAATCTGATTGATTAAGGGGCATGGACGTTTGATGA
* *
390358 ATGATGGGGAATTCTGATGTTAATCAAGAAGAGATTTTTGCATATACCGTGAAGTTTTCTTGCAC
456 ATGATAGGGAATTCTGATGCTAATCAAGAAGAGATTTTTGCATATACCGTGAAGTTTTCTTGCAC
*
390423 TTGCATTAAGAGCATTGTTTTGTTTGATCTCGTTTTTGTTCTATCTTTAATATTTGCTTAAAA-T
521 TTGCATTAAGAGCATTGTTTTGTTTGATCTCGTTTTTATTCTATCTTTAATATTTGCTTAAAATT
390487 TTTTAAATCTTTTGATAATTGAACTTATTCCACCTTCTAAGGTTGTGAACAATTGAACAAGTTTT
586 TTTTAAATCTTTTGATAATTGAACTTATTCCACCTTCTAAGGTTGTGAACAATTGAACAAGTTTT
390552 AATCTTATAGTTCTTTGAATATCGAATGAATTACAGATTCTTTTAGTTCTTAAAAAATTATAGAT
651 AATCTTATAGTTCTTTGAATATCGAATGAATTACAGATTCTTTTAGTTCTTAAAAAATTATAGAT
390617 TTTTGACATATGGC
716 TTTTGACATATGGC
* * *
390631 ACATTTTACATTACATTTACTTAAGTGTTTTCATATGCATCATTCATAAAAAAATGAAATTAATT
1 ACATTGTACATTACATTTACTTAAGTGTTTTCACATGCATCATTCATAAAAAAATGAAATCAATT
* **
390696 CATGGAGGATTAGATGAAGTGGTCCTAATCACGTGACACCACATTAAGAATAGAAGCAAGATTTG
66 CATGGAGGATTAGATGAAGTGGTCCTAATCACGTGACACCAAATTAAGAATAGAAGCAAGATTCA
*
390761 AACAATTAAAAGAAGAAGTTGAAATCAGTACGCT-GGAGCATATTCAGCAGATCGTAGGGCTGAA
131 AAAAATTAAAAGAAGAAGTTGAAATCAGTACGCTGGGAGCATATTCAGCAGATCGTAGGGCTGAA
* *
390825 CCTTATAGGATGATCTGAGAAAATAGTTAATTTGATCCAATTCCAATGACCTATGCGGAACTACT
196 CCTTATAGGATGATCTGAGAAAAAAGTTAATTTGATCCAATTCCAATGACCTATGAGGAACTACT
*
390890 TCCATCGTTGGTTGAGAATAATCTTGTGACTCTAGTTCAGTCCAAGCCCAAAGAGTCCCCATATC
261 TCCAACGTTGGTTGAGAATAATCTTGTGACTCTAGTTCAGTCCAAGCCCAAAGAGTCCCCATATC
390955 TTGAGGGTTGCATTGTTGATGCCATATGCAACTATCACATAGGAAGTTTAGGGCATTCCAATGAG
326 TTGAGGGTTGCATTGTTGATGCCATATGCAACTATCACATAGGAAGTTTAGGGCATTCCAATGAG
391020 AATTATGGGGCATTGAAACGAAAGGTCTAGAATCTGATTGATTAAGGGGCATGGACGTTTGATGA
391 AATTATGGGGCATTGAAACGAAAGGTCTAGAATCTGATTGATTAAGGGGCATGGACGTTTGATGA
391085 ATGATAGGGAATTCTGATGCTAATCAAGAAGAGATTTTTGCATATACCGTGAAGTTTTCTTGCAC
456 ATGATAGGGAATTCTGATGCTAATCAAGAAGAGATTTTTGCATATACCGTGAAGTTTTCTTGCAC
*
391150 TTGCATTAAGATCATTGTTTTGTTTGATCTCGTTTTTATTCTATCTTTAATATTTGCTTAAAATT
521 TTGCATTAAGAGCATTGTTTTGTTTGATCTCGTTTTTATTCTATCTTTAATATTTGCTTAAAATT
391215 TTTTAAATCTTTTGATAA
586 TTTTAAATCTTTTGATAA
391233 CAATTGAATG
Statistics
Matches: 582, Mismatches: 19, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
727 407 0.70
728 175 0.30
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (729 bp):
ACATTGTACATTACATTTACTTAAGTGTTTTCACATGCATCATTCATAAAAAAATGAAATCAATT
CATGGAGGATTAGATGAAGTGGTCCTAATCACGTGACACCAAATTAAGAATAGAAGCAAGATTCA
AAAAATTAAAAGAAGAAGTTGAAATCAGTACGCTGGGAGCATATTCAGCAGATCGTAGGGCTGAA
CCTTATAGGATGATCTGAGAAAAAAGTTAATTTGATCCAATTCCAATGACCTATGAGGAACTACT
TCCAACGTTGGTTGAGAATAATCTTGTGACTCTAGTTCAGTCCAAGCCCAAAGAGTCCCCATATC
TTGAGGGTTGCATTGTTGATGCCATATGCAACTATCACATAGGAAGTTTAGGGCATTCCAATGAG
AATTATGGGGCATTGAAACGAAAGGTCTAGAATCTGATTGATTAAGGGGCATGGACGTTTGATGA
ATGATAGGGAATTCTGATGCTAATCAAGAAGAGATTTTTGCATATACCGTGAAGTTTTCTTGCAC
TTGCATTAAGAGCATTGTTTTGTTTGATCTCGTTTTTATTCTATCTTTAATATTTGCTTAAAATT
TTTTAAATCTTTTGATAATTGAACTTATTCCACCTTCTAAGGTTGTGAACAATTGAACAAGTTTT
AATCTTATAGTTCTTTGAATATCGAATGAATTACAGATTCTTTTAGTTCTTAAAAAATTATAGAT
TTTTGACATATGGC
Found at i:392030 original size:5 final size:5
Alignment explanation
Indices: 392020--392067 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
392010 ACATAAAGAA
* *
392020 AAAAG AAAAG AAAAG AAAAG AAAAA ATAAAG AAAA- AGAAG AAAGAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG A-AAAG AAAAG AAAAG AAA-AG AA
392068 CATATTAAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
4 3 0.08
5 25 0.69
6 8 0.22
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:392039 original size:22 final size:20
Alignment explanation
Indices: 392014--392062 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
392004 GCGAGAACAT
392014 AAAGAAAAAAGAAAAGAAAAGA
1 AAAGAAAAAA-AAAAGAAAA-A
*
392036 AAAGAAAAAATAAAGAAAAA
1 AAAGAAAAAAAAAAGAAAAA
*
392056 GAAGAAA
1 AAAGAAA
392063 GAGAACATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.28
21 8 0.32
22 10 0.40
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (20 bp):
AAAGAAAAAAAAAAGAAAAA
Found at i:392056 original size:17 final size:17
Alignment explanation
Indices: 392012--392058 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
392002 AGGCGAGAAC
*
392012 ATAAAGAAAAAAGAAAAG
1 ATAAAG-AAAAAGAAAAA
392030 A-AAAG-AAAAGAAAAA
1 ATAAAGAAAAAGAAAAA
392045 ATAAAGAAAAAGAA
1 ATAAAGAAAAAGAA
392059 GAAAGAGAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 10 0.38
16 4 0.15
17 11 0.42
18 1 0.04
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (17 bp):
ATAAAGAAAAAGAAAAA
Found at i:395248 original size:3 final size:3
Alignment explanation
Indices: 395240--395309 Score: 86
Period size: 3 Copynumber: 22.3 Consensus size: 3
395230 TTTTAATTGT
* * *
395240 TTA TTA TTA TTA TTA TTTA TTG TTA TTA TTA TTAA TTG TTA GTA TTGA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT-A TTA TTA TTA TT-A
395288 TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
395310 CATAAATAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
3 49 0.84
4 9 0.16
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:395260 original size:16 final size:16
Alignment explanation
Indices: 395239--395309 Score: 83
Period size: 16 Copynumber: 4.5 Consensus size: 16
395229 GTTTTAATTG
395239 TTTATTATTATTATTA
1 TTTATTATTATTATTA
*
395255 TTTATTGTTATTATTA
1 TTTATTATTATTATTA
* * *
395271 TTAATTGTTAGTATTGA
1 TTTATTATTATTATT-A
395288 -TTATTATTATTATTA
1 TTTATTATTATTATTA
395303 -TTATTAT
1 TTTATTAT
395310 CATAAATAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
15 8 0.17
16 39 0.81
17 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.65
Consensus pattern (16 bp):
TTTATTATTATTATTA
Found at i:395633 original size:29 final size:30
Alignment explanation
Indices: 395600--395661 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
395590 AAATTTTATC
* *
395600 TAGTGACTAAAATAT-AAGTTTTAAAAGTT
1 TAGTGACTAAAATATAAACTTTGAAAAGTT
* *
395629 TAGTGGCTAAAGTATAAACTTTGAAAAGTT
1 TAGTGACTAAAATATAAACTTTGAAAAGTT
395659 TAG
1 TAG
395662 GAACCAAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 13 0.46
30 15 0.54
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (30 bp):
TAGTGACTAAAATATAAACTTTGAAAAGTT
Found at i:403174 original size:29 final size:30
Alignment explanation
Indices: 403141--403202 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
403131 AAATTTTGTC
**
403141 TAGTGACTAAAATATAAGTTTTG-AAAGTT
1 TAGTGACTAAAATATAAACTTTGAAAAGTT
* *
403170 TAGTGGCTAAAGTATAAACTTTGAAAAGTT
1 TAGTGACTAAAATATAAACTTTGAAAAGTT
403200 TAG
1 TAG
403203 GAACCGAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.35
Consensus pattern (30 bp):
TAGTGACTAAAATATAAACTTTGAAAAGTT
Found at i:404393 original size:20 final size:21
Alignment explanation
Indices: 404370--404462 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
404360 ATTTCCCAAT
*
404370 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
404390 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
404411 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
404431 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
404452 TCGCAATGCGA
1 TCGCAATGCGA
404463 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:404415 original size:41 final size:41
Alignment explanation
Indices: 404370--404462 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
404360 ATTTCCCAAT
404370 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
404411 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
404452 TCGCAATGCGA
1 TCGCAATGCGA
404463 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:404475 original size:41 final size:41
Alignment explanation
Indices: 404389--404523 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
404379 GAATAAGTAA
* *
404389 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
404430 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
404471 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
404512 TTCGCAACGCGA
1 ATCGCAACGCGA
404524 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:404476 original size:20 final size:20
Alignment explanation
Indices: 404451--404565 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
404441 AATTGGGAAA
*
404451 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
404471 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
404492 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
404512 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
404532 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
404552 TTCGCAACGCGATA
1 ATCGCAACGCGATA
404566 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:404524 original size:41 final size:41
Alignment explanation
Indices: 404448--404585 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
404438 GCGAATTGGG
* * *
404448 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
404489 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-AC
** *
404531 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
404570 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
404586 TTTCAAAGCG
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.39
41 44 0.56
42 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:404781 original size:22 final size:22
Alignment explanation
Indices: 404753--404796 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
404743 CACTCTCTCA
*
404753 CCCATCTCTGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
404775 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
404797 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:405084 original size:20 final size:20
Alignment explanation
Indices: 405059--405137 Score: 104
Period size: 20 Copynumber: 4.0 Consensus size: 20
405049 GCGATTCTCT
**
405059 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
405079 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
405099 TGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
405119 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
405138 AGAAACTATT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.16, C:0.18, G:0.23, T:0.43
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:406406 original size:19 final size:20
Alignment explanation
Indices: 406352--406397 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
406342 TAGTTTACTT
* *
406352 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
406372 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
406392 TCGCAA
1 TCGCAA
406398 TTCGAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:406426 original size:14 final size:14
Alignment explanation
Indices: 406407--406464 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
406397 ATTCGAAATG
406407 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
406421 AAAATCGCAATGCGAAAT
1 AAAATCGCAA--CG--AC
406439 AAAATCGCAACGAC
1 AAAATCGCAACGAC
406453 AAAATCGCAACG
1 AAAATCGCAACG
406465 CGAAATGTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:406448 original size:32 final size:33
Alignment explanation
Indices: 406391--406481 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
406381 GGAAATGGCT
*
406391 ATCGCAATTCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
406424 ATCGCAATGCGAAAT-AAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
406456 ATCGCAACGCGAAATGTAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
406482 TGCGATTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 31 0.57
33 23 0.43
ACGTcount: A:0.47, C:0.22, G:0.16, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:406517 original size:14 final size:14
Alignment explanation
Indices: 406498--406555 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
406488 TTGTGTTTCG
406498 CGTTGCGATTTTTT
1 CGTTGCGATTTTTT
*
406512 CGTTGCAATTTCATTT
1 CGTTGCGATTT--TTT
*
406528 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTTT
406544 CGTTGCGATTTT
1 CGTTGCGATTTT
406556 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 22 0.59
16 5 0.14
18 10 0.27
ACGTcount: A:0.10, C:0.17, G:0.22, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTTT
Found at i:406534 original size:32 final size:33
Alignment explanation
Indices: 406493--406571 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 33
406483 GCGATTTGTG
*
406493 TTTCGCGTTGCGATTTTTTCGTTGC-AATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGAATTTCA
*
406525 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGAATTTCA
*
406558 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
406572 AGCCATTTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 24 0.56
33 19 0.44
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGAATTTCA
Found at i:406570 original size:19 final size:19
Alignment explanation
Indices: 406544--406610 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
406534 GCGATTTTGT
**
406544 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
406563 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
406583 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
406602 CGTTGCGAT
1 CGTTGCGAT
406611 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:406590 original size:20 final size:19
Alignment explanation
Indices: 406556--406610 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
406546 TTGCGATTTT
*
406556 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
406575 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
406595 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
406611 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:410246 original size:5 final size:5
Alignment explanation
Indices: 410236--410279 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
410226 ATAATAATTT
* *
410236 TTTTA TTTTA TTTTA -TTTA TTTTA TTATA CTTTTA TGTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTT
410280 TTATGTTCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
4 4 0.12
5 25 0.76
6 4 0.12
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:410256 original size:9 final size:9
Alignment explanation
Indices: 410232--410279 Score: 53
Period size: 9 Copynumber: 5.0 Consensus size: 9
410222 AATGATAATA
410232 ATTT-TTTT
1 ATTTATTTT
410240 ATTTTATTTT
1 A-TTTATTTT
410250 ATTTATTTT
1 ATTTATTTT
410259 ATTATACTTTT
1 ATT-TA-TTTT
410270 ATGTTATTTT
1 AT-TTATTTT
410280 TTATGTTCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
8 1 0.03
9 14 0.40
10 11 0.31
11 8 0.23
12 1 0.03
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (9 bp):
ATTTATTTT
Found at i:410256 original size:14 final size:13
Alignment explanation
Indices: 410232--410281 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 13
410222 AATGATAATA
410232 ATTTTTTTATTTT
1 ATTTTTTTATTTT
410245 ATTTTATTTATTTT
1 ATTTT-TTTATTTT
*
410259 ATTATACTTTTATGTT
1 ATT-T--TTTTATTTT
410275 ATTTTTT
1 ATTTTTT
410282 ATGTTCTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
13 8 0.25
14 11 0.34
15 2 0.06
16 10 0.31
17 1 0.03
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (13 bp):
ATTTTTTTATTTT
Found at i:410718 original size:13 final size:13
Alignment explanation
Indices: 410700--410726 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
410690 AGTTTTTATC
410700 TTTAAAATGATTT
1 TTTAAAATGATTT
410713 TTTAAAATGATTT
1 TTTAAAATGATTT
410726 T
1 T
410727 AAAAGACGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (13 bp):
TTTAAAATGATTT
Found at i:412634 original size:16 final size:16
Alignment explanation
Indices: 412615--412654 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 16
412605 TTAAAAAGAG
412615 AAAAAAATGAAAAATT
1 AAAAAAATGAAAAATT
412631 AAAAAAATGAAAAATT
1 AAAAAAATGAAAAATT
412647 ACAAAAAA
1 A-AAAAAA
412655 AGGAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (16 bp):
AAAAAAATGAAAAATT
Found at i:417675 original size:38 final size:37
Alignment explanation
Indices: 417620--417749 Score: 154
Period size: 38 Copynumber: 3.5 Consensus size: 37
417610 GAAGCAAAAA
*
417620 ATTTATCTCGCTTGAGATAGTTTCACTAGAAACAGAAG
1 ATTTATCTCACTTGAGATAGTTTCACTA-AAACAGAAG
* * ** * *
417658 ATTTATCTCACTCGAGATTGTTTTTCTTAAA-ATAAG
1 ATTTATCTCACTTGAGATAGTTTCACTAAAACAGAAG
* *
417694 ATTCATCTTACTTGAGATAGTTTCACTCAAAACAGAAG
1 ATTTATCTCACTTGAGATAGTTTCACT-AAAACAGAAG
417732 ATTTATCTCACTTGAGAT
1 ATTTATCTCACTTGAGAT
417750 TATTTTTCTT
Statistics
Matches: 73, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
36 25 0.34
37 6 0.08
38 42 0.58
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (37 bp):
ATTTATCTCACTTGAGATAGTTTCACTAAAACAGAAG
Found at i:417711 original size:36 final size:35
Alignment explanation
Indices: 417615--417788 Score: 120
Period size: 38 Copynumber: 4.8 Consensus size: 35
417605 CGCTCGAAGC
* * ** *
417615 AAAAA-ATTTATCTCGCTTGAGATAGTTTCACTAGA
1 AAAAAGATTCATCTCACTTGAGATAGTTTTTCT-TA
* * *
417650 AACAGAAGATTTATCTCACTCGAGATTGTTTTTCTTA
1 AA-A-AAGATTCATCTCACTTGAGATAGTTTTTCTTA
* ** *
417687 AAATAAGATTCATCTTACTTGAGATAGTTTCACTCAA
1 AAA-AAGATTCATCTCACTTGAGATAGTTTTTCT-TA
*
417724 AACAGAAGATTTATCTCACTTGAGATTA-TTTTTCTTA
1 AA-A-AAGATTCATCTCACTTGAGA-TAGTTTTTCTTA
* *
417761 AAAAA-AATCATCTCGCTTGAGATAGTTT
1 AAAAAGATTCATCTCACTTGAGATAGTTT
417789 CACTCACTTG
Statistics
Matches: 109, Mismatches: 23, Indels: 15
0.74 0.16 0.10
Matches are distributed among these distances:
33 2 0.02
34 17 0.16
35 4 0.04
36 27 0.25
37 11 0.10
38 46 0.42
39 2 0.02
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (35 bp):
AAAAAGATTCATCTCACTTGAGATAGTTTTTCTTA
Found at i:417719 original size:74 final size:72
Alignment explanation
Indices: 417615--417794 Score: 254
Period size: 74 Copynumber: 2.5 Consensus size: 72
417605 CGCTCGAAGC
* * * *
417615 AAAAAATTTATCTCGCTTGAGATAGTTTCACT-AGAAACAGAAGATTTATCTCACTCGAGATTGT
1 AAAAAAATCATCTCACTTGAGATAGTTTCACTCA-AAACAGAAGATTTATCTCACTCGAGATTAT
417679 TTTTCTTA
65 TTTTCTTA
* * *
417687 AAATAAGATTCATCTTACTTGAGATAGTTTCACTCAAAACAGAAGATTTATCTCACTTGAGATTA
1 AAA-AA-AATCATCTCACTTGAGATAGTTTCACTCAAAACAGAAGATTTATCTCACTCGAGATTA
417752 TTTTTCTTA
64 TTTTTCTTA
*
417761 AAAAAAATCATCTCGCTTGAGATAGTTTCACTCA
1 AAAAAAATCATCTCACTTGAGATAGTTTCACTCA
417795 CTTGAGATTG
Statistics
Matches: 97, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
72 29 0.30
73 4 0.04
74 63 0.65
75 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (72 bp):
AAAAAAATCATCTCACTTGAGATAGTTTCACTCAAAACAGAAGATTTATCTCACTCGAGATTATT
TTTCTTA
Found at i:417796 original size:53 final size:55
Alignment explanation
Indices: 417738--417848 Score: 181
Period size: 53 Copynumber: 2.1 Consensus size: 55
417728 GAAGATTTAT
417738 CTCACTTGAGATTATTTTTCTTAAAA-AAA-ATCATCTCGCTTGAGATAGTTTCA
1 CTCACTTGAGATTATTTTTCTTAAAATAAATATCATCTCGCTTGAGATAGTTTCA
* * *
417791 CTCACTTGAGATTGTTTTTCTTAAAATAAATTTTATCTCGCTTGAGATAGTTTCA
1 CTCACTTGAGATTATTTTTCTTAAAATAAATATCATCTCGCTTGAGATAGTTTCA
417846 CTC
1 CTC
417849 GAAACATAAG
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
53 25 0.47
54 3 0.06
55 25 0.47
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (55 bp):
CTCACTTGAGATTATTTTTCTTAAAATAAATATCATCTCGCTTGAGATAGTTTCA
Found at i:417819 original size:127 final size:129
Alignment explanation
Indices: 417664--417922 Score: 416
Period size: 127 Copynumber: 2.0 Consensus size: 129
417654 GAAGATTTAT
*
417664 CTCACTCGAGATTGTTTTTCTTAAAATAAGA-TTCATCTTACTTGAGATAGTTTCACTCAAAACA
1 CTCACTCGAGATTGTTTTTCTTAAAATAA-ATTTCATCTCACTTGAGATAGTTTCACTCAAAACA
417728 GAAGATTTATCTCACTTGAGATTATTTTTCTTAAAA-AA-AATCATCTCGCTTGAGATAGTTTCA
65 GAAGATTTATCTCACTTGAGATTATTTTTCTTAAAACAAGAATCATCTCGCTTGAGATAGTTTCA
* * * * *
417791 CTCACTTGAGATTGTTTTTCTTAAAATAAATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAT
1 CTCACTCGAGATTGTTTTTCTTAAAATAAATTTCATCTCACTTGAGATAGTTTCACTCAAAACAG
* *
417856 AAGATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTCA
66 AAGATTTATCTCACTTGAGATTATTTTTCTTAAAACAAGAATCATCTCGCTTGAGATAGTTTCA
417920 CTC
1 CTC
417923 TAAACATAAA
Statistics
Matches: 121, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
126 1 0.01
127 91 0.75
128 2 0.02
129 27 0.22
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (129 bp):
CTCACTCGAGATTGTTTTTCTTAAAATAAATTTCATCTCACTTGAGATAGTTTCACTCAAAACAG
AAGATTTATCTCACTTGAGATTATTTTTCTTAAAACAAGAATCATCTCGCTTGAGATAGTTTCA
Found at i:417867 original size:38 final size:37
Alignment explanation
Indices: 417822--418288 Score: 310
Period size: 38 Copynumber: 12.6 Consensus size: 37
417812 TAAAATAAAT
*
417822 TTTATCTCGCTTGAGATAGTTTCACTCGAAACATAAGA
1 TTTATCTCACTTGAGATAGTTTCACTCGAAACA-AAGA
* ** **
417860 TTTATCTCACTTGAGATTGTTTTTCTTAAAAC-AAGA
1 TTTATCTCACTTGAGATAGTTTCACTCGAAACAAAGA
* * *
417896 TTCATCTCGCTTGAGATAGTTTCACTCTAAACATAA-A
1 TTTATCTCACTTGAGATAGTTTCACTCGAAACA-AAGA
* ** **
417933 TTTTATCCCACTTGAGAT--TTTTTCTTAAAAC-AAGA
1 -TTTATCTCACTTGAGATAGTTTCACTCGAAACAAAGA
* *
417968 TTCATCTCGCTTGAGATAGTTTCACTCGAAACAGAA-A
1 TTTATCTCACTTGAGATAGTTTCACTCGAAACA-AAGA
** **
418005 TTTAATCTCACTTGAGATTA-TTTTTCTTAAAACAAA-A
1 TTT-ATCTCACTTGAGA-TAGTTTCACTCGAAACAAAGA
* * * * *
418042 TTTGTCTCGCTTGAGATATTTTTTACTCGAAACAAGAAA
1 TTTATCTCACTTGAGATA-GTTTCACTCGAAACAA-AGA
* ** * ** **
418081 TTTCATTTCACTCAAGATTGTTTTTCTTAAAAC-AAGA
1 TTT-ATCTCACTTGAGATAGTTTCACTCGAAACAAAGA
* * * *
418118 TTCATCTCGCTTGAGATAGTTTCGCTCGAAGCAAA-A
1 TTTATCTCACTTGAGATAGTTTCACTCGAAACAAAGA
* *
418154 CTTTATCTCCCATGAGATAGTTTCACTCGAAACAAAAGA
1 -TTTATCTCACTTGAGATAGTTTCACTCGAAAC-AAAGA
* * * * *
418193 TTTATCTCACTTGAGATTGTTT--TTCTAAAAATAAGT
1 TTTATCTCACTTGAGATAGTTTCACTCGAAACA-AAGA
* *
418229 TTTATCTCGCTTGAGATATTTTCACTCGAAACAAAAGA
1 TTTATCTCACTTGAGATAGTTTCACTCGAAAC-AAAGA
*
418267 TTTATCTCACTTGAGATTGTTT
1 TTTATCTCACTTGAGATAGTTT
418289 TTCTTAAAAT
Statistics
Matches: 324, Mismatches: 82, Indels: 46
0.72 0.18 0.10
Matches are distributed among these distances:
34 16 0.05
35 4 0.01
36 105 0.32
37 55 0.17
38 117 0.36
39 18 0.06
40 9 0.03
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (37 bp):
TTTATCTCACTTGAGATAGTTTCACTCGAAACAAAGA
Found at i:417903 original size:36 final size:36
Alignment explanation
Indices: 417791--418297 Score: 306
Period size: 36 Copynumber: 13.7 Consensus size: 36
417781 GATAGTTTCA
*
417791 CTCACTTGAGATTGTTTTTCTTAAAATAA-ATTTTAT
1 CTCACTTGAGATTGTTTTTCTTAAAACAAGA-TTTAT
* * ** * *
417827 CTCGCTTGAGATAGTTTCACTCGAAACATAAGATTTAT
1 CTCACTTGAGATTGTTTTTCT-TAAA-ACAAGATTTAT
*
417865 CTCACTTGAGATTGTTTTTCTTAAAACAAGATTCAT
1 CTCACTTGAGATTGTTTTTCTTAAAACAAGATTTAT
* * ** *
417901 CTCGCTTGAGATAGTTTCACTCT-AAACATAAATTTTAT
1 CTCACTTGAGATTGTTTTTCT-TAAAACA-AGA-TTTAT
* *
417939 CCCACTTGAGA-T-TTTTTCTTAAAACAAGATTCAT
1 CTCACTTGAGATTGTTTTTCTTAAAACAAGATTTAT
* * ** ** *
417973 CTCGCTTGAGATAGTTTCACTCGAAACAGAAATTTAAT
1 CTCACTTGAGATTGTTTTTCTTAAAACA-AGATTT-AT
* * *
418011 CTCACTTGAGATTATTTTTCTTAAAACAAAATTTGT
1 CTCACTTGAGATTGTTTTTCTTAAAACAAGATTTAT
* **
418047 CTCGCTTGAGATAT-TTTTTACTCGAAACAAGAAATTTCAT
1 CTCACTTGAGAT-TGTTTTT-CTTAAAACAAG--ATTT-AT
* ** *
418087 TTCACTCAAGATTGTTTTTCTTAAAACAAGATTCAT
1 CTCACTTGAGATTGTTTTTCTTAAAACAAGATTTAT
* * ** ** * *
418123 CTCGCTTGAGATAGTTTCGCTCGAAGCAAAACTTTAT
1 CTCACTTGAGATTGTTTTTCTTAAAACAAGA-TTTAT
* * * ** * *
418160 CTCCCATGAGATAGTTTCACTCGAAACAAAAGATTTAT
1 CTCACTTGAGATTGTTTTTCT-TAAA-ACAAGATTTAT
* * *
418198 CTCACTTGAGATTGTTTTTCTAAAAATAAGTTTTAT
1 CTCACTTGAGATTGTTTTTCTTAAAACAAGATTTAT
* ** * *
418234 CTCGCTTGAGATAT-TTTCACTCGAAACAAAAGATTTAT
1 CTCACTTGAGAT-TGTTTTTCT-TAAA-ACAAGATTTAT
418272 CTCACTTGAGATTGTTTTTCTTAAAA
1 CTCACTTGAGATTGTTTTTCTTAAAA
418298 TAATCTACAC
Statistics
Matches: 355, Mismatches: 92, Indels: 48
0.72 0.19 0.10
Matches are distributed among these distances:
34 13 0.04
35 3 0.01
36 133 0.37
37 64 0.18
38 110 0.31
39 18 0.05
40 14 0.04
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (36 bp):
CTCACTTGAGATTGTTTTTCTTAAAACAAGATTTAT
Found at i:417912 original size:74 final size:74
Alignment explanation
Indices: 417791--418147 Score: 488
Period size: 74 Copynumber: 4.8 Consensus size: 74
417781 GATAGTTTCA
* *
417791 CTCACTTGAGATTGTTTTTCTTAAAATAA-ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACA
1 CTCACTTGAGATTGTTTTTCTTAAAACAAGA-TTCATCTCGCTTGAGATAGTTTCACTCGAAACA
417855 TAAGATTT-AT
65 TAA-ATTTAAT
*
417865 CTCACTTGAGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCTAAACAT
1 CTCACTTGAGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCGAAACAT
*
417930 AAATTTTAT
66 AAATTTAAT
* *
417939 CCCACTTGAGA-T-TTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCGAAACAG
1 CTCACTTGAGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCGAAACAT
418002 AAATTTAAT
66 AAATTTAAT
* * ** * *
418011 CTCACTTGAGATTATTTTTCTTAAAACAAAATTTGTCTCGCTTGAGATATTTTTTACTCGAAACA
1 CTCACTTGAGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTGAGATA-GTTTCACTCGAAAC-
* *
418076 AGAAATTTCAT
64 ATAAATTTAAT
* ** *
418087 TTCACTCAAGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTCGCTCGAA
1 CTCACTTGAGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCGAA
418148 GCAAAACTTT
Statistics
Matches: 253, Mismatches: 24, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
72 67 0.26
73 6 0.02
74 106 0.42
75 22 0.09
76 52 0.21
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.39
Consensus pattern (74 bp):
CTCACTTGAGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCGAAACAT
AAATTTAAT
Found at i:417975 original size:201 final size:197
Alignment explanation
Indices: 417621--418297 Score: 650
Period size: 201 Copynumber: 3.3 Consensus size: 197
417611 AAGCAAAAAA
*
417621 TTTATCTCGCTTGAGATAGTTTCACTAGAAACAGAAGATTTATCTCACTCGAGATTGTTTTTCTT
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAACA-AAGATTTATCTCACTCGAGATTGTTTTTCTT
* ** *
417686 AAAATAAGATTCATCTTACTTGAGATAGTTTCACTCAAAACAGAAGATTTATCTCACTTGAGATT
65 AAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCAAAACA-AA-ATTTATCCCACTTGAGA-T
*
417751 ATTTTTCTTAAAAAAAATCATCTCGCTTGAGATAGTTTCACTCACTTGAGATTGTTTTTCTTAAA
127 ATTTTTCTTAAAACAAATCATCTCGCTTGAGATAGTTTCACTCACTTGAGATTGTTTTTCTTAAA
417816 ATAAAT
192 ATAAAT
*
417822 TTTATCTCGCTTGAGATAGTTTCACTCGAAACATAAGATTTATCTCACTTGAGATTGTTTTTCTT
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAACA-AAGATTTATCTCACTCGAGATTGTTTTTCTT
*
417887 AAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCTAAACATAAATTTTATCCCACTTGAGAT-
65 AAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCAAAACA-AAA-TTTATCCCACTTGAGATA
417951 TTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCGAAACAGAAATTTAATCTCAC
128 TTTTTCTTAAAACAA-A-TCATCTCGCTTGAGATAG-TT---T-----C---------A-CTCAC
* * *
418016 TTGAGATTATTTTTCTTAAAACAAAA
172 TTGAGATTGTTTTTCTTAAAATAAAT
* * * * * *
418042 TTTGTCTCGCTTGAGATATTTTTTACTCGAAACAAGAAATTTCATTTCACTCAAGATTGTTTTTC
1 TTTATCTCGCTTGAGATA-GTTTCACTCGAAACAA-AGATTT-ATCTCACTCGAGATTGTTTTTC
* * * *
418107 TTAAAACAAGATTCATCTCGCTTGAGATAGTTTCGCTCGAAGCAAAACTTTATCTCC-CATGAGA
63 TTAAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCAAAACAAAA-TTTATC-CCACTTGAGA
** ** * *
418171 TAGTTTCACTCGAAACAAA--A----GATT----TA---T--CTCACTTGAGATTGTTTTTCTAA
126 TA-TTTTTCTTAAAACAAATCATCTCGCTTGAGATAGTTTCACTCACTTGAGATTGTTTTTCTTA
*
418221 AAATAAGT
190 AAATAAAT
* *
418229 TTTATCTCGCTTGAGATATTTTCACTCGAAACAAAAGATTTATCTCACTTGAGATTGTTTTTCTT
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAAC-AAAGATTTATCTCACTCGAGATTGTTTTTCTT
418294 AAAA
65 AAAA
418298 TAATCTACAC
Statistics
Matches: 406, Mismatches: 41, Indels: 74
0.78 0.08 0.14
Matches are distributed among these distances:
185 25 0.06
186 18 0.04
187 45 0.11
199 14 0.03
200 3 0.01
201 135 0.33
202 2 0.00
204 1 0.00
205 1 0.00
210 1 0.00
211 2 0.00
215 3 0.01
219 2 0.00
220 46 0.11
221 34 0.08
222 63 0.16
223 11 0.03
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (197 bp):
TTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAGATTTATCTCACTCGAGATTGTTTTTCTTA
AAACAAGATTCATCTCGCTTGAGATAGTTTCACTCAAAACAAAATTTATCCCACTTGAGATATTT
TTCTTAAAACAAATCATCTCGCTTGAGATAGTTTCACTCACTTGAGATTGTTTTTCTTAAAATAA
AT
Found at i:418252 original size:74 final size:74
Alignment explanation
Indices: 418155--418300 Score: 256
Period size: 74 Copynumber: 2.0 Consensus size: 74
418145 GAAGCAAAAC
418155 TTTATCTCCCATGAGATAGTTTCACTCGAAACAAAAGATTTATCTCACTTGAGATTGTTTTTCTA
1 TTTATCTCCCATGAGATAGTTTCACTCGAAACAAAAGATTTATCTCACTTGAGATTGTTTTTCTA
418220 AAAATAAGT
66 AAAATAAGT
* * * *
418229 TTTATCTCGCTTGAGATATTTTCACTCGAAACAAAAGATTTATCTCACTTGAGATTGTTTTTCTT
1 TTTATCTCCCATGAGATAGTTTCACTCGAAACAAAAGATTTATCTCACTTGAGATTGTTTTTCTA
418294 AAAATAA
66 AAAATAA
418301 TCTACACCTC
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 68 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.40
Consensus pattern (74 bp):
TTTATCTCCCATGAGATAGTTTCACTCGAAACAAAAGATTTATCTCACTTGAGATTGTTTTTCTA
AAAATAAGT
Found at i:418316 original size:74 final size:74
Alignment explanation
Indices: 418166--418317 Score: 234
Period size: 74 Copynumber: 2.1 Consensus size: 74
418156 TTATCTCCCA
*
418166 TGAGATAGTTTCACTCGAAACAAAAGATTTATCTCACTTGAGATTGTTTTTCTAAAAATAAGTTT
1 TGAGATAGTTTCACTCGAAACAAAAGATTTATCTCACTTGAGATTGTTTTTCTAAAAATAAGTTA
* * *
418231 TATCTCGCT
66 CACCTCACT
* *
418240 TGAGATATTTTCACTCGAAACAAAAGATTTATCTCACTTGAGATTGTTTTTCTTAAAATAA-TCT
1 TGAGATAGTTTCACTCGAAACAAAAGATTTATCTCACTTGAGATTGTTTTTCTAAAAATAAGT-T
418304 ACACCTCACT
65 ACACCTCACT
418314 TGAG
1 TGAG
418318 GGATTAACAT
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
73 1 0.01
74 70 0.99
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.38
Consensus pattern (74 bp):
TGAGATAGTTTCACTCGAAACAAAAGATTTATCTCACTTGAGATTGTTTTTCTAAAAATAAGTTA
CACCTCACT
Found at i:418438 original size:59 final size:59
Alignment explanation
Indices: 418307--418439 Score: 158
Period size: 59 Copynumber: 2.3 Consensus size: 59
418297 ATAATCTACA
* * * *
418307 CCTCACTTGAGGGATTAACATTTCATTTGCTCAGTTCATGACATTTCGAATCAGCGATG
1 CCTCACTTAAGGGATTAACATTACATTTGCTCAGTTCATGACATTTCAAATCAGCGAAG
* * * * * *
418366 CCTCACTCAAGGGATTAACATTACCTTTTCTCGGTTCATGACATTTCAAATCCGTGAAG
1 CCTCACTTAAGGGATTAACATTACATTTGCTCAGTTCATGACATTTCAAATCAGCGAAG
* *
418425 CCTTACTTTAGGGAT
1 CCTCACTTAAGGGAT
418440 CAATATTTCC
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (59 bp):
CCTCACTTAAGGGATTAACATTACATTTGCTCAGTTCATGACATTTCAAATCAGCGAAG
Found at i:418628 original size:90 final size:90
Alignment explanation
Indices: 418434--418796 Score: 387
Period size: 90 Copynumber: 4.0 Consensus size: 90
418424 GCCTTACTTT
* *
418434 AGGGATCAATATTTCC-GATAGAGAATTCATGAGAAGAACTTATTCAACCTTAG-CTCGATTCAC
1 AGGGACCAACATTTCCAG-TAGAGAATTCATGAGAAGAACTTATTCAACCTT-GTCTCGATTCAC
*
418497 GGCATTTCGAATCAGCAACGCCTCACTCA
64 GG-ATTTCGAATCAGCAACGCCTCACT-G
418526 AGGGACCAACATTTCCAGTAGAGAATTCATGA-AAGAACTTATTCAACCTTGTCTCGATTCACGG
1 AGGGACCAACATTTCCAGTAGAGAATTCATGAGAAGAACTTATTCAACCTTGTCTCGATTCACGG
* * *
418590 TTTTTGAATCAGCGACGCCTCACATG
66 ATTTCGAATCAGCAACGCCTCAC-TG
* * * *
418616 AGGGACCAACATTTCCAGTAGAGAATTAATGAGAAGAACTTATT--TCCTTTTCTTGATTCACGA
1 AGGGACCAACATTTCCAGTAGAGAATTCATGAGAAGAACTTATTCAACCTTGTCTCGATTCACG-
* * * *
418679 CATTTCAAATCAGCGACACCTCACTTG
65 GATTTCGAATCAGCAACGCCTCAC-TG
* * * * * * *
418706 AGGCACCAACATTTCCAATAGAGAATTCATAATGAAGAACTTGTTCAGCCTTTTCCCGATTCAC-
1 AGGGACCAACATTTCCAGTAGAGAATTCATGA-GAAGAACTTATTCAACCTTGTCTCGATTCACG
* *
418770 GATATTATGAATCAGCAACGTCTCACT
65 GAT-TT-CGAATCAGCAACGCCTCACT
418797 CGATGGATTA
Statistics
Matches: 231, Mismatches: 30, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
89 15 0.06
90 101 0.44
91 55 0.24
92 31 0.13
93 29 0.13
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (90 bp):
AGGGACCAACATTTCCAGTAGAGAATTCATGAGAAGAACTTATTCAACCTTGTCTCGATTCACGG
ATTTCGAATCAGCAACGCCTCACTG
Found at i:422347 original size:21 final size:21
Alignment explanation
Indices: 422321--422361 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
422311 TTAAATAGAA
*
422321 TATAGAAATATCCAACTTTTC
1 TATAGAAATATACAACTTTTC
* *
422342 TATAGAGATATAGAACTTTT
1 TATAGAAATATACAACTTTT
422362 ATCCATAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
TATAGAAATATACAACTTTTC
Found at i:428639 original size:57 final size:58
Alignment explanation
Indices: 428527--428802 Score: 364
Period size: 57 Copynumber: 4.8 Consensus size: 58
428517 TGGCACTATA
* *
428527 TGTGCTAAAATGATAATG-AATCATACTGAATGTATGAATTTCCATATGGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATG-ATTTCCATATGGAGCACTGAG
*
428585 TGTGCTAAAATGATAAGAAAATCATACTGAGTGTA-GATTTCCATATGGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGATTTCCATATGGAGCACTGAG
*
428642 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGTATTTCCATATGGAGCACTGAC
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATG-ATTTCCATATGGAGCACTGAG
* * * * * *
428701 TATGCTAAAATGATAAGGAAATCATATTGAATATTTGGATTTCCATATAGG-GCA-TTA-
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTAT-GATTTCCATAT-GGAGCACTGAG
* *
428758 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCA
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTAT-GATTTCCA
428803 GAAAAATCGC
Statistics
Matches: 195, Mismatches: 18, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
57 93 0.48
58 20 0.10
59 79 0.41
60 3 0.02
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.31
Consensus pattern (58 bp):
TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGATTTCCATATGGAGCACTGAG
Found at i:428713 original size:59 final size:59
Alignment explanation
Indices: 428527--428872 Score: 375
Period size: 59 Copynumber: 5.9 Consensus size: 59
428517 TGGCACTATA
* * *
428527 TGTGCTAAAATGATAATG-AATCATACTGAATGTATGAATTTCCATATGGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAG
*
428585 TGTGCTAAAATGATAAGAAAATCATACTGAGTGTA--GATTTCCATATGGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAG
* *
428642 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGTATTTCCATATGGAGCACTGAC
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAG
* * * * * *
428701 TATGCTAAAATGATAAGGAAATCATATTGAATATTTGGATTTCCATATAGG-GCA-TTA-
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATAT-GGAGCACTGAG
* * * *** * * *
428758 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGAAAAATCGCTAAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAG
* * * * *
428817 GGTGCTACAAGGATAAGGAAATCATACT-AATAGTATGGATTTTCATATAGG-GCACT
1 TGTGCTAAAATGATAAGGAAATCATACTGAGT-GTATGGATTTCCATAT-GGAGCACT
428873 TTGTTGAAAA
Statistics
Matches: 238, Mismatches: 41, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
57 95 0.40
58 22 0.09
59 119 0.50
60 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (59 bp):
TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAG
Found at i:428823 original size:116 final size:117
Alignment explanation
Indices: 428518--428873 Score: 409
Period size: 116 Copynumber: 3.1 Consensus size: 117
428508 ATTACCAAAT
* *
428518 GGCACTATATGTGCTAAAATGATAA-TGAATCATACTGAATGTATGAATTTCCATATGGAGCACT
1 GGCACT-TATGTGCTAAAATGATAAGGGAATCATACTGAGTGTATGAATTTCCATATGGAGCACT
* * *
428582 GAGTGTGCTAAAATGATAAGAAAATCATACTGAGTGTA--GATTTCCATAT-G
65 GAGTGTGCTAAAATGATAAGGAAATCATACTGAATATATGGATTTCCATATAG
* * *
428632 GAGCACTGAGTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGTATTTCCATATGGAGCAC
1 G-GCACTTA-TGTGCTAAAATGATAAGGGAATCATACTGAGTGTATGAATTTCCATATGGAGCAC
* * * *
428697 TGACTATGCTAAAATGATAAGGAAATCATATTGAATATTTGGATTTCCATATAG
64 TGAGTGTGCTAAAATGATAAGGAAATCATACTGAATATATGGATTTCCATATAG
* * * *** * * *
428751 GGCA-TTATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGAAAAATCGCTA
1 GGCACTTATGTGCTAAAATGATAAGGGAATCATACTGAGTGTATGAATTTCCATATGGAGCACTG
* * * *
428815 AGGGTGCTACAAGGATAAGGAAATCATACT-AATAGTATGGATTTTCATATAG
66 AGTGTGCTAAAATGATAAGGAAATCATACTGAATA-TATGGATTTCCATATAG
428867 GGCACTT
1 GGCACTT
428874 TGTTGAAAAC
Statistics
Matches: 203, Mismatches: 31, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
114 2 0.01
115 25 0.12
116 156 0.77
117 4 0.02
118 14 0.07
119 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (117 bp):
GGCACTTATGTGCTAAAATGATAAGGGAATCATACTGAGTGTATGAATTTCCATATGGAGCACTG
AGTGTGCTAAAATGATAAGGAAATCATACTGAATATATGGATTTCCATATAG
Found at i:434933 original size:20 final size:21
Alignment explanation
Indices: 434908--434967 Score: 86
Period size: 20 Copynumber: 2.8 Consensus size: 21
434898 TTTGGTGCAG
*
434908 AGGGAATCGATTCCCCCTTT-
1 AGGGAACCGATTCCCCCTTTA
434928 AGGGAACCGATTCCCCCTTTAA
1 AGGGAACCGATTCCCCCTTT-A
434950 AGGGGAACCGATTCCCCC
1 A-GGGAACCGATTCCCCC
434968 CACAGGGGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 19 0.53
22 1 0.03
23 16 0.44
ACGTcount: A:0.23, C:0.33, G:0.22, T:0.22
Consensus pattern (21 bp):
AGGGAACCGATTCCCCCTTTA
Found at i:434976 original size:21 final size:21
Alignment explanation
Indices: 434929--434989 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
434919 TCCCCCTTTA
*
434929 GGGAACCGATTCCCCCTTTAAAG
1 GGGAACCGATTCCCCC--CAAAG
*
434952 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCAAAG
* *
434973 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
434990 TGGGGTTGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 18 0.53
23 16 0.47
ACGTcount: A:0.25, C:0.38, G:0.23, T:0.15
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCAAAG
Found at i:438479 original size:60 final size:60
Alignment explanation
Indices: 438380--438515 Score: 218
Period size: 60 Copynumber: 2.3 Consensus size: 60
438370 TAACTCAACA
*
438380 CACTTCATGTGCTAAAAATGGTAAAGGGATCATACTAATGGTATGGATTCTCAAATAGGG
1 CACTTCATGTGCTAAAAATGGTAAAGGAATCATACTAATGGTATGGATTCTCAAATAGGG
* * *
438440 CACTTCATGTGCTAAAAATGGTAAAGGAATCGTATTAATGGTATGGATTCTCGAATAGGG
1 CACTTCATGTGCTAAAAATGGTAAAGGAATCATACTAATGGTATGGATTCTCAAATAGGG
* *
438500 CACTTCGTGTACTAAA
1 CACTTCATGTGCTAAA
438516 CTGAGAAGGA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 70 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (60 bp):
CACTTCATGTGCTAAAAATGGTAAAGGAATCATACTAATGGTATGGATTCTCAAATAGGG
Found at i:438717 original size:44 final size:44
Alignment explanation
Indices: 438669--439083 Score: 400
Period size: 44 Copynumber: 9.0 Consensus size: 44
438659 TCAGTGATGC
* * *
438669 AAATTATAATAAGTATATTGGTAAAATAAGCTTACGAACTTCTG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
438713 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
438757 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* * * * * ** *
438801 AAATTATAGTAAGTAATGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACG
1 AAATTATAGTAAGT-AT---A-T-TGGTAA-AATA-AGCT--TACGAGCTTATG
** * *
438855 AGCTTAT-GAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAA--GT-------ATATTGGTAAAATAAGCTTACGAGCTTATG
438907 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* * * * *
438951 GAATAATGGTAAGTATATTGATAAAATAAGCTTACGATCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* * * *
438995 GAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAGG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* * *
439039 GATTTAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATT-ATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
439084 GATTAAATGG
Statistics
Matches: 312, Mismatches: 39, Indels: 39
0.80 0.10 0.10
Matches are distributed among these distances:
44 212 0.68
45 40 0.13
48 1 0.00
49 1 0.00
50 5 0.02
51 4 0.01
52 15 0.05
53 6 0.02
54 15 0.05
55 4 0.01
56 5 0.02
57 1 0.00
58 1 0.00
61 2 0.01
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.34
Consensus pattern (44 bp):
AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
Found at i:438821 original size:18 final size:18
Alignment explanation
Indices: 438798--438833 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
438788 TTACGAGCTT
438798 ATGAAATTATAGTAAGTA
1 ATGAAATTATAGTAAGTA
438816 ATGAAATTATAGTAAGTA
1 ATGAAATTATAGTAAGTA
438834 TATTGGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (18 bp):
ATGAAATTATAGTAAGTA
Found at i:438851 original size:62 final size:62
Alignment explanation
Indices: 438754--438877 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
438744 TTACGAGCTT
438754 ATGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATTATAGTAAGTA
1 ATGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATTATAGTAAGTA
438816 ATGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATTATAGTAAGTA
1 ATGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATTATAGTAAGTA
438878 TATTGGTAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.34
Consensus pattern (62 bp):
ATGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATTATAGTAAGTA
Found at i:438896 original size:106 final size:106
Alignment explanation
Indices: 438711--438921 Score: 422
Period size: 106 Copynumber: 2.0 Consensus size: 106
438701 TACGAACTTC
438711 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATTATAGTAAGTATATT
1 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATTATAGTAAGTATATT
438776 GGTAAAATAAGCTTACGAGCTTATGAAATTATAGTAAGTAA
66 GGTAAAATAAGCTTACGAGCTTATGAAATTATAGTAAGTAA
438817 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATTATAGTAAGTATATT
1 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATTATAGTAAGTATATT
438882 GGTAAAATAAGCTTACGAGCTTATGAAATTATAGTAAGTA
66 GGTAAAATAAGCTTACGAGCTTATGAAATTATAGTAAGTA
438922 TATTGGTAAA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 105 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.34
Consensus pattern (106 bp):
TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATTATAGTAAGTATATT
GGTAAAATAAGCTTACGAGCTTATGAAATTATAGTAAGTAA
Found at i:438940 original size:150 final size:150
Alignment explanation
Indices: 438669--438965 Score: 540
Period size: 150 Copynumber: 2.0 Consensus size: 150
438659 TCAGTGATGC
*
438669 AAATTATAATAAGTATATTGGTAAAATAAGCTTACGAACTTCTGAAATTATAGTAAGTATATTGG
1 AAATTATAATAAGTATATTGGTAAAATAAGCTTACGAACTTATGAAATTATAGTAAGTATATTGG
438734 TAAAATAAGCTTACGAGCTTATGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
66 TAAAATAAGCTTACGAGCTTATGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
*
438799 TGAAATTATAGTAAGTAATG
131 TGAAATAATAGTAAGTAATG
* *
438819 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATTATAGTAAGTATATTGG
1 AAATTATAATAAGTATATTGGTAAAATAAGCTTACGAACTTATGAAATTATAGTAAGTATATTGG
438884 TAAAATAAGCTTACGAGCTTATGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
66 TAAAATAAGCTTACGAGCTTATGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
* *
438949 TGGAATAATGGTAAGTA
131 TGAAATAATAGTAAGTA
438966 TATTGATAAA
Statistics
Matches: 141, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
150 141 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.34
Consensus pattern (150 bp):
AAATTATAATAAGTATATTGGTAAAATAAGCTTACGAACTTATGAAATTATAGTAAGTATATTGG
TAAAATAAGCTTACGAGCTTATGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
TGAAATAATAGTAAGTAATG
Found at i:439000 original size:21 final size:21
Alignment explanation
Indices: 438931--439000 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
438921 ATATTGGTAA
*
438931 AATAAGCTTACGAGCTTATGG
1 AATAAGCTTACGATCTTATGG
* * * **
438952 AATAATG-GTAAGTATATTGATAA
1 AATAA-GCTTACG-ATCTT-ATGG
438975 AATAAGCTTACGATCTTATGG
1 AATAAGCTTACGATCTTATGG
438996 AATAA
1 AATAA
439001 TGGTAAGTAT
Statistics
Matches: 34, Mismatches: 11, Indels: 8
0.64 0.21 0.15
Matches are distributed among these distances:
21 15 0.44
22 9 0.26
23 10 0.29
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (21 bp):
AATAAGCTTACGATCTTATGG
Found at i:440585 original size:22 final size:22
Alignment explanation
Indices: 440558--440600 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
440548 TGGTTGACCG
440558 TTGACCGGTCAGACCGTTGACT
1 TTGACCGGTCAGACCGTTGACT
*
440580 TTGACCGGTCTGACCGTTGAC
1 TTGACCGGTCAGACCGTTGAC
440601 CGTTAACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (22 bp):
TTGACCGGTCAGACCGTTGACT
Found at i:442223 original size:31 final size:31
Alignment explanation
Indices: 442187--442290 Score: 86
Period size: 31 Copynumber: 3.2 Consensus size: 31
442177 AGACTCAGAC
*
442187 AGGTTCAGTCGCTGCTGGTAATTTCTTGTAT
1 AGGTTCAGTCGCTGCTGGTAATTCCTTGTAT
* * * *
442218 AGGTTCAACATCG-AG-TGGTAATTCCTATCTCT
1 AGGTTC-A-GTCGCTGCTGGTAATTCCT-TGTAT
*
442250 GGCAGGTTCAGTTGCTGCTGGTAATTCCTTGTAT
1 ---AGGTTCAGTCGCTGCTGGTAATTCCTTGTAT
442284 AGGTTCA
1 AGGTTCA
442291 ACACCGACTG
Statistics
Matches: 55, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
31 23 0.42
32 5 0.09
33 5 0.09
34 5 0.09
35 17 0.31
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (31 bp):
AGGTTCAGTCGCTGCTGGTAATTCCTTGTAT
Found at i:447154 original size:17 final size:17
Alignment explanation
Indices: 447132--447165 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
447122 TTATTTTACC
447132 TTTTTTTACTTAACTTA
1 TTTTTTTACTTAACTTA
*
447149 TTTTTTTATTTAACTTA
1 TTTTTTTACTTAACTTA
447166 AACTTAAGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTTTACTTAACTTA
Found at i:447426 original size:59 final size:59
Alignment explanation
Indices: 447334--447451 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
447324 ACCTGATAAT
*
447334 TTCATGTGTAGGCGGGGATCCGGTATTTTCTGAAACCTTGTGTAAGGAAATACAAAAGA
1 TTCATGTGTAGGAGGGGATCCGGTATTTTCTGAAACCTTGTGTAAGGAAATACAAAAGA
447393 TTCATGTGTAGGAGGGGATCCGGTATTTTCTGAAACCTTGTGTAAGGAAATACAAAAGA
1 TTCATGTGTAGGAGGGGATCCGGTATTTTCTGAAACCTTGTGTAAGGAAATACAAAAGA
447452 ATTTCTTTCA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (59 bp):
TTCATGTGTAGGAGGGGATCCGGTATTTTCTGAAACCTTGTGTAAGGAAATACAAAAGA
Found at i:448794 original size:16 final size:16
Alignment explanation
Indices: 448775--448807 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
448765 AGCAAGCTGC
448775 TATGACATGAGAGCAT
1 TATGACATGAGAGCAT
448791 TATGACATGAGAGCAT
1 TATGACATGAGAGCAT
448807 T
1 T
448808 GATACTTCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.27
Consensus pattern (16 bp):
TATGACATGAGAGCAT
Found at i:449634 original size:152 final size:152
Alignment explanation
Indices: 449358--449658 Score: 593
Period size: 152 Copynumber: 2.0 Consensus size: 152
449348 GAATTTTTGG
449358 ATCGAATCAACGGATTAATGGACTAGATCAATATGATCAAATTTTTTACACCCCTACCACACATA
1 ATCGAATCAACGGATTAATGGACTAGATCAATATGATCAAATTTTTTACACCCCTACCACACATA
449423 CTTTTTCTTTTGGATAAAATTAATATAATTTTTCTTCAGTTTTAACTTTTTTTTCTTCTATTTTG
66 CTTTTTCTTTTGGATAAAATTAATATAATTTTTCTTCAGTTTTAACTTTTTTTTCTTCTATTTTG
449488 GCCCAACCTTTGAAAGCATTCC
131 GCCCAACCTTTGAAAGCATTCC
*
449510 ATCGAATCAACGGATTAATGGACTAGATCAATATGATCAAATTTTTTACACCCCTACCACACATG
1 ATCGAATCAACGGATTAATGGACTAGATCAATATGATCAAATTTTTTACACCCCTACCACACATA
449575 CTTTTTCTTTTGGATAAAATTAATATAATTTTTCTTCAGTTTTAACTTTTTTTTCTTCTATTTTG
66 CTTTTTCTTTTGGATAAAATTAATATAATTTTTCTTCAGTTTTAACTTTTTTTTCTTCTATTTTG
449640 GCCCAACCTTTGAAAGCAT
131 GCCCAACCTTTGAAAGCAT
449659 ACCCTACGTA
Statistics
Matches: 148, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
152 148 1.00
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.42
Consensus pattern (152 bp):
ATCGAATCAACGGATTAATGGACTAGATCAATATGATCAAATTTTTTACACCCCTACCACACATA
CTTTTTCTTTTGGATAAAATTAATATAATTTTTCTTCAGTTTTAACTTTTTTTTCTTCTATTTTG
GCCCAACCTTTGAAAGCATTCC
Found at i:451539 original size:33 final size:33
Alignment explanation
Indices: 451492--451595 Score: 174
Period size: 33 Copynumber: 3.2 Consensus size: 33
451482 ACAAAGTTTA
* *
451492 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
*
451524 CGATAAATTCAAATACTTAAAAACCTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
451557 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
451590 CGATAA
1 CGATAA
451596 TTGAAACAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 4 0.06
33 63 0.94
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.30
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTCCAAGTT
Found at i:451615 original size:21 final size:21
Alignment explanation
Indices: 451590--451631 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
451580 CTTCCAAGTT
451590 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
451611 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
451632 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:465868 original size:32 final size:32
Alignment explanation
Indices: 465824--465886 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
465814 TTTAAATAGG
465824 TTTTTAGTATTTTA-ATTAAGTTTTAGGATATTA
1 TTTTTAGTATTTTATATT-AGTTTTAGG-TATTA
*
465857 TTTTTA-TATTTTATATTTGTTTTAGGTATT
1 TTTTTAGTATTTTATATTAGTTTTAGGTATT
465887 TTAGTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 4 0.14
32 15 0.54
33 9 0.32
ACGTcount: A:0.25, C:0.00, G:0.11, T:0.63
Consensus pattern (32 bp):
TTTTTAGTATTTTATATTAGTTTTAGGTATTA
Found at i:465950 original size:63 final size:62
Alignment explanation
Indices: 465867--465986 Score: 188
Period size: 63 Copynumber: 1.9 Consensus size: 62
465857 TTTTTATATT
*
465867 TTATATTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGT-ATTTAATTAGGATTTAGAATA
1 TTATATTTGTTTTAGGTATTTTAGTTTAAATA-GTTTAAGTGATTTAATTAGGATTTAGAATA
* *
465929 TTATATTATTTTTTAGGTATTTTAGTTTAAATAGTTTAAGTGTTTTAATTAGGATTTA
1 TTATATT-TGTTTTAGGTATTTTAGTTTAAATAGTTTAAGTGATTTAATTAGGATTTA
465987 AGATGTTTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
62 14 0.26
63 39 0.74
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (62 bp):
TTATATTTGTTTTAGGTATTTTAGTTTAAATAGTTTAAGTGATTTAATTAGGATTTAGAATA
Found at i:466692 original size:16 final size:18
Alignment explanation
Indices: 466650--466695 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
466640 AAATCCCCTT
466650 TTATATTTATTACTATTAA
1 TTATA-TTATTACTATTAA
*
466669 TATTTATTATTA-TATT-A
1 T-TATATTATTACTATTAA
466686 TTATATTATT
1 TTATATTATT
466696 TTTCTTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
16 8 0.33
17 2 0.08
18 4 0.17
19 7 0.29
20 3 0.12
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TTATATTATTACTATTAA
Found at i:466729 original size:19 final size:19
Alignment explanation
Indices: 466668--466730 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
466658 ATTACTATTA
*
466668 ATATTTATTATTATATT-AT
1 ATATTTATT-TTATTTTCAT
*
466687 -TATATTATTTTTCTTTTC-T
1 ATAT-TTA-TTTTATTTTCAT
*
466706 TTATTTATTTTATTTTCAT
1 ATATTTATTTTATTTTCAT
466725 ATATTT
1 ATATTT
466731 TTTCAACTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
18 12 0.34
19 18 0.51
20 5 0.14
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (19 bp):
ATATTTATTTTATTTTCAT
Found at i:469384 original size:62 final size:61
Alignment explanation
Indices: 469308--469487 Score: 225
Period size: 62 Copynumber: 2.9 Consensus size: 61
469298 AATATAAAAT
* * * *
469308 ATGGATAATATCATAAAATATTATAATACTGGATAAAAATAAATATAAAATATTAATACTCA
1 ATGGACAATCTCATAAAATATTA-AATACTGGATAAAAATGAATATAAAATATTAAGACTCA
* * * *
469370 ATGGACAATCTCATAATATATTAAATTCCGAAATAAAAATGAATATAAAATATTAAGACTCA
1 ATGGACAATCTCATAAAATATTAAATACTG-GATAAAAATGAATATAAAATATTAAGACTCA
* * *
469432 TTGGACAATCTCATAAAATATTAAAATCCTAGATTAAAAATGAATATAAAATATTA
1 ATGGACAATCTCATAAAATATT-AAATACTGGA-TAAAAATGAATATAAAATATTA
469488 TTGATGTAAA
Statistics
Matches: 101, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
61 5 0.05
62 69 0.68
63 27 0.27
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.31
Consensus pattern (61 bp):
ATGGACAATCTCATAAAATATTAAATACTGGATAAAAATGAATATAAAATATTAAGACTCA
Found at i:474000 original size:25 final size:25
Alignment explanation
Indices: 473966--474023 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
473956 TTTTTTCTTT
*
473966 GTATTTTAGTTTAAATATGTTTTTA
1 GTATTTTAGTTTAAATAGGTTTTTA
473991 GTATTTTAGTTTAAATAGGTTTTTA
1 GTATTTTAGTTTAAATAGGTTTTTA
474016 GTATTTTA
1 GTATTTTA
474024 ATTAAGTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (25 bp):
GTATTTTAGTTTAAATAGGTTTTTA
Found at i:474065 original size:32 final size:32
Alignment explanation
Indices: 474010--474072 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
474000 TTTAAATAGG
474010 TTTTTAGTATTTTAATTAAGTTTTAGGATATTA
1 TTTTTAGTATTTTAATTAAGTTTTAGG-TATTA
*
474043 TTTTTA-TATTTTATATT-TGTTTTAGGTATT
1 TTTTTAGTATTTTA-ATTAAGTTTTAGGTATT
474073 TTAGTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 4 0.14
32 15 0.54
33 9 0.32
ACGTcount: A:0.25, C:0.00, G:0.11, T:0.63
Consensus pattern (32 bp):
TTTTTAGTATTTTAATTAAGTTTTAGGTATTA
Done.