Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 93 of 132
Found at i:28622266 original size:14 final size:14
Alignment explanation
Indices: 28622247--28622281 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
28622237 TGTTTCACTG
*
28622247 AAAATGGTTTCCGA
1 AAAATGATTTCCGA
*
28622261 AAAATGATTTCTGA
1 AAAATGATTTCCGA
28622275 AAAATGA
1 AAAATGA
28622282 CTTACTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.29
Consensus pattern (14 bp):
AAAATGATTTCCGA
Found at i:28622798 original size:20 final size:20
Alignment explanation
Indices: 28622756--28622796 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
28622746 ATTTATTATT
* *
28622756 AATATTTTTTAATTATAATA
1 AATATTTATTAATTAAAATA
28622776 AATATTTATT-ATTAAAATA
1 AATATTTATTAATTAAAATA
28622795 AA
1 AA
28622797 ATTAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATATTTATTAATTAAAATA
Found at i:28632994 original size:14 final size:15
Alignment explanation
Indices: 28632975--28633012 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
28632965 TATTTTGACT
28632975 AAAAATGATTTTC-A
1 AAAAATGATTTTCTA
*
28632989 AAAAAT-AATTTCTA
1 AAAAATGATTTTCTA
28633003 AAAAATGATT
1 AAAAATGATT
28633013 ATTTTTTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
13 5 0.25
14 13 0.65
15 2 0.10
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (15 bp):
AAAAATGATTTTCTA
Found at i:28633237 original size:21 final size:20
Alignment explanation
Indices: 28633190--28633237 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
28633180 TATCTATTAA
*
28633190 ATTTATATTTTACATTATTT
1 ATTTATATATTACATTATTT
28633210 -TTATATATATTACAATTATTT
1 ATT-TATATATTAC-ATTATTT
28633231 ATTTATA
1 ATTTATA
28633238 AATAAATACA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 2 0.08
20 9 0.38
21 11 0.46
22 2 0.08
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTATATATTACATTATTT
Found at i:28641135 original size:19 final size:20
Alignment explanation
Indices: 28641091--28641135 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
28641081 AGTTGACTGC
* *
28641091 CCCGACCCATTGACTCGTTGA
1 CCCGTCCCATTGACTC-TTAA
28641112 CCCGTCCCATTGACT-TTAA
1 CCCGTCCCATTGACTCTTAA
28641131 CCCGT
1 CCCGT
28641136 TACCCCATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.36
21 14 0.64
ACGTcount: A:0.18, C:0.40, G:0.16, T:0.27
Consensus pattern (20 bp):
CCCGTCCCATTGACTCTTAA
Found at i:28641170 original size:13 final size:13
Alignment explanation
Indices: 28641149--28641179 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
28641139 CCCATTAACC
28641149 TTGACAGTTGACT
1 TTGACAGTTGACT
*
28641162 TTGATAGTTGACT
1 TTGACAGTTGACT
28641175 TTGAC
1 TTGAC
28641180 TTTAACCGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.42
Consensus pattern (13 bp):
TTGACAGTTGACT
Found at i:28643173 original size:28 final size:28
Alignment explanation
Indices: 28643141--28643329 Score: 174
Period size: 28 Copynumber: 6.8 Consensus size: 28
28643131 GAAAATGTTA
28643141 GAAAAT-GAATGCCTTTGTGGCAATCTAT
1 GAAAATGGAA-GCCTTTGTGGCAATCTAT
* *
28643169 GAAAATGGAAGCCTTTATAGCAATCTAT
1 GAAAATGGAAGCCTTTGTGGCAATCTAT
*
28643197 G-AAATGGAAGCCCTTT-TGGTAATCTAT
1 GAAAATGGAAG-CCTTTGTGGCAATCTAT
* * *
28643224 GAAAATAGAAGTCTTTATGGCAATCTAT
1 GAAAATGGAAGCCTTTGTGGCAATCTAT
* * *
28643252 GATAAAT-GAAGCCTTTGTGACAGTATAT
1 GA-AAATGGAAGCCTTTGTGGCAATCTAT
* *
28643280 GATAAA-GGAAGCCTTTGTGGCGATTTAT
1 GA-AAATGGAAGCCTTTGTGGCAATCTAT
* **
28643308 GGAAA-GGAAGTATTTGTGGCAA
1 GAAAATGGAAGCCTTTGTGGCAA
28643330 ATGATGAAAG
Statistics
Matches: 135, Mismatches: 20, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
27 40 0.30
28 88 0.65
29 7 0.05
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (28 bp):
GAAAATGGAAGCCTTTGTGGCAATCTAT
Found at i:28643267 original size:55 final size:54
Alignment explanation
Indices: 28643143--28643270 Score: 168
Period size: 55 Copynumber: 2.3 Consensus size: 54
28643133 AAATGTTAGA
*
28643143 AAATGAATGCCTTTGTGGCAATCTATGAAAATGGAAGCCTTTATAGCAATCTATG
1 AAATGAA-GCCTTTGTGGCAATCTATGAAAATAGAAGCCTTTATAGCAATCTATG
* * *
28643198 AAATGGAAGCCCTTT-TGGTAATCTATGAAAATAGAAGTCTTTATGGCAATCTATG
1 AAAT-GAAG-CCTTTGTGGCAATCTATGAAAATAGAAGCCTTTATAGCAATCTATG
28643253 ATAAATGAAGCCTTTGTG
1 --AAATGAAGCCTTTGTG
28643271 ACAGTATATG
Statistics
Matches: 64, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
55 46 0.72
56 14 0.22
57 4 0.06
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.32
Consensus pattern (54 bp):
AAATGAAGCCTTTGTGGCAATCTATGAAAATAGAAGCCTTTATAGCAATCTATG
Found at i:28643318 original size:83 final size:83
Alignment explanation
Indices: 28643153--28643329 Score: 191
Period size: 83 Copynumber: 2.1 Consensus size: 83
28643143 AAATGAATGC
* * *
28643153 CTTTGTGGCAATCTATGAAAATGGAAGCCTTTATAGCAATCTATGAAATGGAAGCCCTTTTGGTA
1 CTTTGTGGCAATCTATGAAAATGGAAGCCTTTATAGCAATATATGAAAAGGAAGCCCTTTTGGCA
28643218 ATCTATGAAAATAGAAGT
66 ATCTATGAAAATAGAAGT
* * *
28643236 CTTTATGGCAATCTATGATAAAT-GAAGCCTTTGT-GACAGTATATGATAAAGGAAG-CCTTTGT
1 CTTTGTGGCAATCTATGA-AAATGGAAGCCTTTATAG-CAATATATGA-AAAGGAAGCCCTTT-T
* * * *
28643298 GGCGATTTATGGAAA-GGAAGT
62 GGCAATCTATGAAAATAGAAGT
*
28643319 ATTTGTGGCAA
1 CTTTGTGGCAA
28643330 ATGATGAAAG
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
82 1 0.01
83 54 0.69
84 23 0.29
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (83 bp):
CTTTGTGGCAATCTATGAAAATGGAAGCCTTTATAGCAATATATGAAAAGGAAGCCCTTTTGGCA
ATCTATGAAAATAGAAGT
Found at i:28650183 original size:20 final size:21
Alignment explanation
Indices: 28650158--28650196 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
28650148 GCAAGGAAAA
28650158 GGAAAGGAGAAA-GGGGGAAG
1 GGAAAGGAGAAATGGGGGAAG
*
28650178 GGAAAGGGGAAATGGGGGA
1 GGAAAGGAGAAATGGGGGA
28650197 GAGGCTTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.56, T:0.03
Consensus pattern (21 bp):
GGAAAGGAGAAATGGGGGAAG
Found at i:28652716 original size:17 final size:16
Alignment explanation
Indices: 28652675--28652737 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 16
28652665 ACAACCCAAA
28652675 TAAAATAATAAATAAC
1 TAAAATAATAAATAAC
* *
28652691 TAAGTATAATAAATACC
1 TAA-AATAATAAATAAC
* *
28652708 TGAAAATAAAATAATAAGT
1 T-AAAATAATA-AATAA-C
28652727 TAAAATAATAA
1 TAAAATAATAA
28652738 GTCAATAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
16 3 0.08
17 18 0.50
18 14 0.39
19 1 0.03
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (16 bp):
TAAAATAATAAATAAC
Found at i:28652732 original size:13 final size:13
Alignment explanation
Indices: 28652714--28652739 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28652704 TACCTGAAAA
28652714 TAAAATAATAAGT
1 TAAAATAATAAGT
28652727 TAAAATAATAAGT
1 TAAAATAATAAGT
28652740 CAATAATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (13 bp):
TAAAATAATAAGT
Found at i:28653744 original size:20 final size:20
Alignment explanation
Indices: 28653719--28653756 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
28653709 GGTTTCTCGA
28653719 AAAAAGTCAACGGTCAACCC
1 AAAAAGTCAACGGTCAACCC
28653739 AAAAAGTCAACGGTCAAC
1 AAAAAGTCAACGGTCAAC
28653757 AGTCAACAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.26, G:0.16, T:0.11
Consensus pattern (20 bp):
AAAAAGTCAACGGTCAACCC
Found at i:28653754 original size:7 final size:7
Alignment explanation
Indices: 28653743--28653783 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
28653733 CAACCCAAAA
28653743 AGTCAAC
1 AGTCAAC
*
28653750 GGTCAAC
1 AGTCAAC
28653757 AGTCAAC
1 AGTCAAC
*
28653764 AGTCAAT
1 AGTCAAC
*
28653771 AGTTAAC
1 AGTCAAC
28653778 AGTCAA
1 AGTCAA
28653784 TGGGTTGGGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (7 bp):
AGTCAAC
Found at i:28659789 original size:18 final size:18
Alignment explanation
Indices: 28659768--28659802 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28659758 TAAATACCCA
28659768 AAAATAAAATAATAAGTT
1 AAAATAAAATAATAAGTT
*
28659786 AAAATGAAATAATAAGT
1 AAAATAAAATAATAAGT
28659803 CTATAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
AAAATAAAATAATAAGTT
Found at i:28660710 original size:20 final size:20
Alignment explanation
Indices: 28660685--28660722 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
28660675 GGTTTCTCGG
28660685 AAAAAGTCAATGGTCAACTC
1 AAAAAGTCAATGGTCAACTC
28660705 AAAAAGTCAATGGTCAAC
1 AAAAAGTCAATGGTCAAC
28660723 GGTCAACGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAAGTCAATGGTCAACTC
Found at i:28663278 original size:9 final size:10
Alignment explanation
Indices: 28663259--28663287 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
28663249 ATTACGTGTT
28663259 TGAATAGAAA
1 TGAATAGAAA
28663269 TGAA-AGAAA
1 TGAATAGAAA
28663278 TGAATAGAAA
1 TGAATAGAAA
28663288 AAGAGAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.17
Consensus pattern (10 bp):
TGAATAGAAA
Found at i:28668421 original size:18 final size:18
Alignment explanation
Indices: 28668393--28668479 Score: 120
Period size: 18 Copynumber: 4.8 Consensus size: 18
28668383 AATGCTCTTT
*
28668393 ACGAGCTAGTATGCTCAA
1 ACGAGCCAGTATGCTCAA
*
28668411 AAGAGCCAGTATGCTCAA
1 ACGAGCCAGTATGCTCAA
* *
28668429 ATGAGCAAGTATGCTCAA
1 ACGAGCCAGTATGCTCAA
* *
28668447 ACGAACCAGTATGCTTAA
1 ACGAGCCAGTATGCTCAA
28668465 ACGAGCCAGTATGCT
1 ACGAGCCAGTATGCT
28668480 ATTCCTTCTG
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 60 1.00
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.21
Consensus pattern (18 bp):
ACGAGCCAGTATGCTCAA
Found at i:28670623 original size:10 final size:9
Alignment explanation
Indices: 28670600--28670640 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
28670590 TATACACATA
28670600 TTTTTTCTT
1 TTTTTTCTT
* *
28670609 CTTTTCCTTT
1 TTTTTTC-TT
28670619 TTTTTTCTT
1 TTTTTTCTT
28670628 TTTTTTCTT
1 TTTTTTCTT
28670637 TTTT
1 TTTT
28670641 CTATGTGACT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 20 0.74
10 7 0.26
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:28670624 original size:19 final size:19
Alignment explanation
Indices: 28670600--28670640 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
28670590 TATACACATA
28670600 TTTTTTCTTCTTTTCCTTT
1 TTTTTTCTTCTTTTCCTTT
* *
28670619 TTTTTTCTTTTTTTTCTTT
1 TTTTTTCTTCTTTTCCTTT
28670638 TTT
1 TTT
28670641 CTATGTGACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (19 bp):
TTTTTTCTTCTTTTCCTTT
Found at i:28670638 original size:16 final size:18
Alignment explanation
Indices: 28670600--28670642 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
28670590 TATACACATA
*
28670600 TTTTTTCTTCTTTTCCTTT
1 TTTTTTCTTCTTTT-CTTC
28670619 TTTTTTCTT-TTTT-TTC
1 TTTTTTCTTCTTTTCTTC
28670635 TTTTTTCT
1 TTTTTTCT
28670643 ATGTGACTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 10 0.43
18 4 0.17
19 9 0.39
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTTCTTCTTTTCTTC
Found at i:28671256 original size:17 final size:17
Alignment explanation
Indices: 28671200--28671256 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
28671190 AATATATATG
* *
28671200 GAAATGCAATGACAAAT
1 GAAATGCAGTGACAAAA
28671217 GCAAATGCAGTGACAATAA
1 G-AAATGCAGTGACAA-AA
*
28671236 -AAATGCAGGGACAAAA
1 GAAATGCAGTGACAAAA
28671252 GAAAT
1 GAAAT
28671257 TTGATGACAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 2 0.06
17 18 0.53
18 13 0.38
19 1 0.03
ACGTcount: A:0.53, C:0.12, G:0.21, T:0.14
Consensus pattern (17 bp):
GAAATGCAGTGACAAAA
Found at i:28676231 original size:15 final size:15
Alignment explanation
Indices: 28676213--28676242 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28676203 GATGAAATTA
28676213 ATGAGGATCACTTTC
1 ATGAGGATCACTTTC
28676228 ATGAGGATCACTTTC
1 ATGAGGATCACTTTC
28676243 CACTACCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (15 bp):
ATGAGGATCACTTTC
Found at i:28678690 original size:14 final size:14
Alignment explanation
Indices: 28678666--28678704 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
28678656 GCATTTTTGC
28678666 ATTTCCTTTTATCT
1 ATTTCCTTTTATCT
*
28678680 -TTTCACTTTTATTT
1 ATTTC-CTTTTATCT
28678694 ATTTCCTTTTA
1 ATTTCCTTTTA
28678705 AATTCTATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 4 0.18
14 14 0.64
15 4 0.18
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTTCCTTTTATCT
Found at i:28681675 original size:9 final size:10
Alignment explanation
Indices: 28681652--28681702 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
28681642 TCACCTATAA
*
28681652 AAAAAGTAAG
1 AAAAAGAAAG
28681662 AAAAAGAAAG
1 AAAAAGAAAG
28681672 -AAAAGAAAAG
1 AAAAAG-AAAG
*
28681682 AGAAAAGAATG
1 A-AAAAGAAAG
28681693 AAAAAAGAAA
1 -AAAAAGAAA
28681703 TAATTTGCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
9 5 0.15
10 13 0.38
11 10 0.29
12 6 0.18
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:28694477 original size:18 final size:18
Alignment explanation
Indices: 28694456--28694490 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28694446 AAAATGTTAC
*
28694456 TATTTTTAAATTTTTTAA
1 TATTTTTAAATCTTTTAA
*
28694474 TATTTTTCAATCTTTTA
1 TATTTTTAAATCTTTTA
28694491 CAATTTCTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTTTAAATCTTTTAA
Found at i:28694564 original size:19 final size:19
Alignment explanation
Indices: 28694528--28694566 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
28694518 TCAACTCCAA
* * *
28694528 ATAATTTTTATAATTTTTT
1 ATAATTTTCAAAAGTTTTT
28694547 ATAATTTTCAAAAGTTTTT
1 ATAATTTTCAAAAGTTTTT
28694566 A
1 A
28694567 AAAGTTCTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (19 bp):
ATAATTTTCAAAAGTTTTT
Found at i:28694676 original size:16 final size:16
Alignment explanation
Indices: 28694653--28694708 Score: 103
Period size: 16 Copynumber: 3.5 Consensus size: 16
28694643 CGTTTGGTTC
28694653 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
28694669 GGTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
28694685 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
28694701 GCTGTAAT
1 GCTGTAAT
28694709 CAGTAATTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.36, C:0.05, G:0.32, T:0.27
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:28694743 original size:46 final size:44
Alignment explanation
Indices: 28694690--28694783 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
28694680 ATAGAGCTGT
* *
28694690 AATGGAATAGAGCTGTAATCAGTAATTCAAT-TGTTTGGTTGATTGG
1 AATGGAATAGAGCTGTAAT-AAT-ATTC-ATGTGTTTGGTTGAATGG
*
28694736 AATGGAATAGAGCTGTAATAATATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATAATATTCATGTGTTTGGTTGAATGG
28694780 AATG
1 AATG
28694784 ATGCTGTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 22 0.50
45 2 0.05
46 19 0.43
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAGCTGTAATAATATTCATGTGTTTGGTTGAATGG
Found at i:28694947 original size:58 final size:56
Alignment explanation
Indices: 28694878--28695023 Score: 179
Period size: 58 Copynumber: 2.5 Consensus size: 56
28694868 AATTTTAATG
*
28694878 ATTATTATTAAATATAATTTAATAAAAATAT-TAATTTATTTAATTATATTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATATGTAATTTA-ATAA-TAT-TTTTAACATA
* *
28694936 ATTATTATTAAATACAATTTAATAAAATAATATGTAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAATTTAAT-AAA-AATATGTAATTTAATAATATTTTTAACATA
*
28694994 ATTATTATTAAAATATGAA-TTAGTAAAAAT
1 ATTATTATT-AAATAT-AATTTAATAAAAAT
28695024 TATAATATAT
Statistics
Matches: 78, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
57 3 0.04
58 43 0.55
59 15 0.19
60 10 0.13
61 7 0.09
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (56 bp):
ATTATTATTAAATATAATTTAATAAAAATATGTAATTTAATAATATTTTTAACATA
Found at i:28700255 original size:18 final size:18
Alignment explanation
Indices: 28700232--28700266 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
28700222 AGAAGAAAGG
28700232 GGGTAAATTAAAATTTTA
1 GGGTAAATTAAAATTTTA
28700250 GGGTAAATTAAAATTTT
1 GGGTAAATTAAAATTTT
28700267 GGCCAACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (18 bp):
GGGTAAATTAAAATTTTA
Found at i:28706729 original size:75 final size:72
Alignment explanation
Indices: 28706542--28706754 Score: 318
Period size: 72 Copynumber: 2.9 Consensus size: 72
28706532 ATACTCCATC
* * **
28706542 AACTCCTCCTTCAGCTTATCCCAAGCTTGTTTAGGAGTCTCACAAGGGTGAGCTACTGCTGCCTT
1 AACTCCTCCTTCAGCTTATCCCAAGCTTGTTTGGGAGTCTCACAAGGGTGAGTTGTTGCTGCCTT
28706607 ACCTTAG
66 ACCTTAG
* *
28706614 AACTCCTCCTTCAGCTTATCCCAAGCTTGTTTGGGAGTCTCACAGGGGTGAGTTGTTTCTGCCTT
1 AACTCCTCCTTCAGCTTATCCCAAGCTTGTTTGGGAGTCTCACAAGGGTGAGTTGTTGCTGCCTT
*
28706679 ACCTTGG
66 ACCTTAG
* *
28706686 AACTCCTTCTCCTTCAGCTTATCCCAAACTTGTTTGGGAGTCTCACAAAGGTGAGTTGTTGCTGC
1 AACT-C--CTCCTTCAGCTTATCCCAAGCTTGTTTGGGAGTCTCACAAGGGTGAGTTGTTGCTGC
28706751 CTTA
63 CTTA
28706755 ACAAACAGCC
Statistics
Matches: 127, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
72 69 0.54
73 1 0.01
75 57 0.45
ACGTcount: A:0.19, C:0.27, G:0.21, T:0.33
Consensus pattern (72 bp):
AACTCCTCCTTCAGCTTATCCCAAGCTTGTTTGGGAGTCTCACAAGGGTGAGTTGTTGCTGCCTT
ACCTTAG
Found at i:28707851 original size:75 final size:74
Alignment explanation
Indices: 28707651--28707864 Score: 302
Period size: 75 Copynumber: 2.9 Consensus size: 74
28707641 ACTCCATCAA
* * * * ** *
28707651 CTCCTCCTTCAGCTTATCCCAAACTTATTTGGGAGTCTCACAGGAGTGAGCTACTGCTGCCATAC
1 CTCCTCCTTCAGCTTATCCCAAGCTTGTTTGGGAGTCTCAAAGG-GTGAGTTGTTGCTGCCTTAC
*
28707716 CTTGGAACTC
65 CTTGAAACTC
* *
28707726 TTCCTCCTTCAACTTATCCCAAGCTTGTTTGGGAGTCTCACAAGGGTGAGTTGTTGCTGCCTTAC
1 CTCCTCCTTCAGCTTATCCCAAGCTTGTTTGGGAGTCTCA-AAGGGTGAGTTGTTGCTGCCTTAC
28707791 CTTGAAACTC
65 CTTGAAACTC
*
28707801 CTCCTCCTTCAGCTTATGCCAAGCTTGTTTGGGAGTCTCATAAGGGTGAGTTGTTGCTGCCTTA
1 CTCCTCCTTCAGCTTATCCCAAGCTTGTTTGGGAGTCTCA-AAGGGTGAGTTGTTGCTGCCTTA
28707865 ACAAGCAACC
Statistics
Matches: 124, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
75 121 0.98
76 3 0.02
ACGTcount: A:0.19, C:0.27, G:0.21, T:0.33
Consensus pattern (74 bp):
CTCCTCCTTCAGCTTATCCCAAGCTTGTTTGGGAGTCTCAAAGGGTGAGTTGTTGCTGCCTTACC
TTGAAACTC
Found at i:28713405 original size:18 final size:18
Alignment explanation
Indices: 28713382--28713424 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
28713372 GTTCAAAGTG
28713382 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
28713400 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
28713418 TAATTAA
1 TAATTAA
28713425 AAATTATTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:28720999 original size:23 final size:23
Alignment explanation
Indices: 28720924--28721033 Score: 118
Period size: 23 Copynumber: 4.8 Consensus size: 23
28720914 AAGTGCTGGG
*
28720924 GAAACAGTAAGCACACACAGTGC
1 GAAACAGTAGGCACACACAGTGC
* * * *
28720947 -AATCAGTAGGCGCACATAGCGC
1 GAAACAGTAGGCACACACAGTGC
28720969 -AAATCAGTAGGCACACGA-AGTGC
1 GAAA-CAGTAGGCACAC-ACAGTGC
*
28720992 GAAACAGTAGGCACACAAAGTGC
1 GAAACAGTAGGCACACACAGTGC
*
28721015 GAAACAGTAAGCACACACA
1 GAAACAGTAGGCACACACA
28721034 ATGCTGAACG
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
22 20 0.27
23 49 0.67
24 4 0.05
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.10
Consensus pattern (23 bp):
GAAACAGTAGGCACACACAGTGC
Found at i:28721023 original size:46 final size:45
Alignment explanation
Indices: 28720924--28721033 Score: 134
Period size: 46 Copynumber: 2.4 Consensus size: 45
28720914 AAGTGCTGGG
* * *
28720924 GAAACAGTAAGCACACACAGTGCAATCAGTAGGCGCACATAGCGC
1 GAAACAGTAAGCACACACAGTGCAAACAGTAGGCACACAAAGCGC
* *
28720969 -AAATCAGTAGGCACACGA-AGTGCGAAACAGTAGGCACACAAAGTGC
1 GAAA-CAGTAAGCACAC-ACAGTGC-AAACAGTAGGCACACAAAGCGC
28721015 GAAACAGTAAGCACACACA
1 GAAACAGTAAGCACACACA
28721034 ATGCTGAACG
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
44 3 0.06
45 17 0.31
46 31 0.57
47 3 0.06
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.10
Consensus pattern (45 bp):
GAAACAGTAAGCACACACAGTGCAAACAGTAGGCACACAAAGCGC
Found at i:28724920 original size:2 final size:2
Alignment explanation
Indices: 28724913--28724955 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
28724903 AGGATCATAA
28724913 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28724955 A
1 A
28724956 AAGAATTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28736513 original size:29 final size:29
Alignment explanation
Indices: 28736451--28736514 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
28736441 AATTTTAATT
* *
28736451 TTTTTTATATATTTTTTAAAAAAAATTAAG
1 TTTTTTATACATTTTTTAAAAAAAA-TAAA
28736481 TTTTTTAT-CATTTTTTAAAAATATAA-AAA
1 TTTTTTATACATTTTTTAAAAA-A-AATAAA
28736510 TTTTT
1 TTTTT
28736515 GTTATGAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
29 19 0.63
30 9 0.30
31 2 0.07
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (29 bp):
TTTTTTATACATTTTTTAAAAAAAATAAA
Found at i:28739234 original size:40 final size:40
Alignment explanation
Indices: 28739104--28739334 Score: 199
Period size: 40 Copynumber: 5.9 Consensus size: 40
28739094 ATCTACATAT
* * *
28739104 TCGGGCTTTGTGCCTAGTAGGCTTCGTGTCGGTGTA--T-
1 TCGGGCTTAGTGCCTAGTAGGCTTAGTGCCGGTGTATTTA
* * *
28739141 TCGGGCTTTGTGCCTACTAGGATTCA-TGCCGGTGTA-TT-
1 TCGGGCTTAGTGCCTAGTAGGCTT-AGTGCCGGTGTATTTA
*
28739179 T-GGGCTTCGTGCCTAGTAGGCTTAGTGCCGGTGTATTTA
1 TCGGGCTTAGTGCCTAGTAGGCTTAGTGCCGGTGTATTTA
** *
28739218 TTAGGCTTAGTGCCTAGTAGGCTTCA-TGCTGGTGTATTTA
1 TCGGGCTTAGTGCCTAGTAGGCTT-AGTGCCGGTGTATTTA
* * * * *
28739258 TCGGGCTTAATGCCTAGCAGGCTTCGTACCGATGTATTTA
1 TCGGGCTTAGTGCCTAGTAGGCTTAGTGCCGGTGTATTTA
** * * * *
28739298 TAAGGCTTAGTGCATAGCAGGCTTCGTGCTGGTGTAT
1 TCGGGCTTAGTGCCTAGTAGGCTTAGTGCCGGTGTAT
28739335 ACTATCAGGC
Statistics
Matches: 161, Mismatches: 25, Indels: 13
0.81 0.13 0.07
Matches are distributed among these distances:
36 1 0.01
37 60 0.37
38 4 0.02
39 1 0.01
40 94 0.58
41 1 0.01
ACGTcount: A:0.15, C:0.19, G:0.30, T:0.36
Consensus pattern (40 bp):
TCGGGCTTAGTGCCTAGTAGGCTTAGTGCCGGTGTATTTA
Found at i:28739298 original size:80 final size:78
Alignment explanation
Indices: 28739144--28739334 Score: 231
Period size: 80 Copynumber: 2.4 Consensus size: 78
28739134 GGTGTATTCG
* * * * ** * *
28739144 GGCTTTGTGCCTACTAGGATTCATGCCGGTGTA-TTTGGGCTTCGTGCCTAGTAGGCTTAGTGCC
1 GGCTTAGTGCCTAGTAGGCTTCATGCTGGTGTATTTTGGGCTTAATGCCTAGCAGGCTTAGTACC
* *
28739208 GGTGTATTTATTA
66 GATGTATTTATAA
*
28739221 GGCTTAGTGCCTAGTAGGCTTCATGCTGGTGTATTTATCGGGCTTAATGCCTAGCAGGCTTCGTA
1 GGCTTAGTGCCTAGTAGGCTTCATGCTGGTGTATTT-T-GGGCTTAATGCCTAGCAGGCTTAGTA
28739286 CCGATGTATTTATAA
64 CCGATGTATTTATAA
* * *
28739301 GGCTTAGTGCATAGCAGGCTTCGTGCTGGTGTAT
1 GGCTTAGTGCCTAGTAGGCTTCATGCTGGTGTAT
28739335 ACTATCAGGC
Statistics
Matches: 97, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
77 29 0.30
78 2 0.02
79 1 0.01
80 65 0.67
ACGTcount: A:0.17, C:0.18, G:0.29, T:0.36
Consensus pattern (78 bp):
GGCTTAGTGCCTAGTAGGCTTCATGCTGGTGTATTTTGGGCTTAATGCCTAGCAGGCTTAGTACC
GATGTATTTATAA
Found at i:28753856 original size:23 final size:23
Alignment explanation
Indices: 28753801--28753856 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
28753791 TCAGTTAAAT
* *
28753801 TCAACGGTTAGGGTCGTGTTCAG
1 TCAACGGGTCGGGTCGTGTTCAG
* *
28753824 TCAATGGGTCGGGTCAG-GTTCGG
1 TCAACGGGTCGGGTC-GTGTTCAG
28753847 TCAACGGGTC
1 TCAACGGGTC
28753857 AAATCGAGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.16, C:0.20, G:0.38, T:0.27
Consensus pattern (23 bp):
TCAACGGGTCGGGTCGTGTTCAG
Found at i:28754855 original size:17 final size:17
Alignment explanation
Indices: 28754833--28754865 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28754823 TCTACCGAAT
*
28754833 AATTTGATTTAATATTA
1 AATTTGATCTAATATTA
28754850 AATTTGATCTAATATT
1 AATTTGATCTAATATT
28754866 TATCCTGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (17 bp):
AATTTGATCTAATATTA
Found at i:28759866 original size:13 final size:14
Alignment explanation
Indices: 28759837--28759866 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28759827 TTCAGTACAT
28759837 TGACATTTAACTTC
1 TGACATTTAACTTC
28759851 TGACATTTAA-TTC
1 TGACATTTAACTTC
28759864 TGA
1 TGA
28759867 TTACACTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (14 bp):
TGACATTTAACTTC
Found at i:28767103 original size:667 final size:670
Alignment explanation
Indices: 28765822--28767163 Score: 2465
Period size: 667 Copynumber: 2.0 Consensus size: 670
28765812 ATGTCAACAC
28765822 ATTTCTTTACTTACTTTCAGTTATTTTAATTTTACTTGTGTTGTTTCAAATTCTTTTGCAGAAAC
1 ATTTCTTTACTTACTTTCAGTTATTTTAATTTTACTTGTGTTGTTTCAAATTCTTTTGCAGAAAC
* *
28765887 AAAAAAACATCTTTTTGTCGAAGCGTCGAAGCATCAAAGCATGGATTGTCGGCGCATTCTGTGAT
66 AAAAAAACAACTTTTTGT---A--GTCGAAGCATCAAAGCATGAATTGTCGGCGCATTCTGTGAT
*
28765952 GAGTCAGCATTACTTTTTCAGCAAGAATCGCGCCAATTGATTTCTCTTCTCTCCTAACCGAACGA
126 GAGTCAGCATTACTTTTTCAGCAAGAATCACGCCAATTGATTTCTCTTCTCTCCTAACCGAACGA
* *
28766017 TCAAGTGAAATAGTATAATCTACAGCCTGGCAATTAATGACTGCAGACGCAACGTTTCCCCGTAA
191 TCAAGCGAAATAGTACAATCTACAGCCTGGCAATTAATGACTGCAGACGCAACGTTTCCCCGTAA
28766082 TTCTTTTAATCATCACGCCTAGGTTATAAAACCTCTGTCCTGCAGTTTTCTTTTCTCCTCACATC
256 TTCTTTTAATCATCACGCCTAGGTTATAAAACCTCTGTCCTGCAGTTTTCTTTTCTCCTCACATC
*
28766147 TTTCATTGTTGCTACAACTCGTTTTCTTCATCGCTTCTGTATTTTCTTTTTCATTCAATAGAGCA
321 TTCCATTGTTGCTACAACTCGTTTTCTTCATCGCTTCTGTATTTTCTTTTTCATTCAATAGAGCA
*
28766212 ATCATTTTCTGTAACCTTTTCTAACTTCCTTCTTCATTTACAATGGCTAAAACCCATGCCTCGAA
386 ATCATTTTCTGTAACCTCTTCTAACTTCCTTCTTCATTTACAATGGCTAAAACCCATGCCTCGAA
28766277 AAACCTTTCAAAAACTCCTTTCAAGAACACCCCGACAACTTTTACTTGGGCTCCGACCACAACGC
451 AAACCTTTCAAAAACTCCTTTCAAGAACACCCCGACAACTTTTACTTGGGCTCCGACCACAACGC
*
28766342 CACCTCCTTCTACAGACCCAGTTTTATTCTTGACAACTGCGGCCAAAGGCTGCTACCAAAATATC
516 CACCTCCTTCTACAGACCCAGTTTTATTCTTGACAACTGCGGCCAAAGGCTGCTACCAAAATACC
* *
28766407 ATGTTGAAGAGAAACCTCCACCCTGAACAAGGTCTGCAGCTTTCTCCACACCAGACTTTGGGGAA
581 ATGTTAAAGAGAAACCTCCACCCTGAACAAGGTCTGCAGCTTTCTCCACACCAAACTTTGGGGAA
28766472 GCATGTTGTTTGCACTATCAACCAT
646 GCATGTTGTTTGCACTATCAACCAT
28766497 ATTTCTTTACTTACTTTCAGTTATTTTAATTTTACTTGTGTTGTTTCAAATTCTTTTGCAGAAAC
1 ATTTCTTTACTTACTTTCAGTTATTTTAATTTTACTTGTGTTGTTTCAAATTCTTTTGCAGAAAC
28766562 AAAAAAACAAC-TTTT-T-GTCGAAGCATCAAAGCATGAATTGTCGGCGCATTCTGTGATGAGTC
66 AAAAAAACAACTTTTTGTAGTCGAAGCATCAAAGCATGAATTGTCGGCGCATTCTGTGATGAGTC
28766624 AGCATTACTTTTTCAGCAAGAATCACGCCAATTGATTTCTCTTCTCTCCTAACCGAACGATCAAG
131 AGCATTACTTTTTCAGCAAGAATCACGCCAATTGATTTCTCTTCTCTCCTAACCGAACGATCAAG
* *
28766689 CGAAATAGTACAATCTACAGCCTGGCAATTAATGACTGCAGACGCAATGTTTTCCCGTAATTCTT
196 CGAAATAGTACAATCTACAGCCTGGCAATTAATGACTGCAGACGCAACGTTTCCCCGTAATTCTT
* *
28766754 TTAATCATCACGTCTAGGTTATAAAACCTCTGTCCTGCAGTTTTCTTTTCTCCTCACATCTTCCC
261 TTAATCATCACGCCTAGGTTATAAAACCTCTGTCCTGCAGTTTTCTTTTCTCCTCACATCTTCCA
*
28766819 TTGTTGCTACAACTCGTTTTCTTCATCGCTTTTGTATTTTCTTTTTCATTCAATAGAGCAATCAT
326 TTGTTGCTACAACTCGTTTTCTTCATCGCTTCTGTATTTTCTTTTTCATTCAATAGAGCAATCAT
* *
28766884 TTTCTGTAACCTCTTCTAACTTCCTTCTTCATTTACAATGGCTAAAACTCGTGCCTCGAAAAACC
391 TTTCTGTAACCTCTTCTAACTTCCTTCTTCATTTACAATGGCTAAAACCCATGCCTCGAAAAACC
28766949 TTTCAAAAACTCCTTTCAAGAACACCCCGACAACTTTTACTTGGGCTCCGACCACAACGCCACCT
456 TTTCAAAAACTCCTTTCAAGAACACCCCGACAACTTTTACTTGGGCTCCGACCACAACGCCACCT
28767014 CCTTCTACAGACCCAGTTTTATTCTTGACAACTGCGGCCAAAGGCTGCTACCAAAATACCATGTT
521 CCTTCTACAGACCCAGTTTTATTCTTGACAACTGCGGCCAAAGGCTGCTACCAAAATACCATGTT
28767079 AAAGAGAAACCTCCACCCTGAACAAGGTCTGCAGCTTTCTCCACACCAAACTTTGGGGAAGCATG
586 AAAGAGAAACCTCCACCCTGAACAAGGTCTGCAGCTTTCTCCACACCAAACTTTGGGGAAGCATG
28767144 TTGTTTGCACTATCAACCAT
651 TTGTTTGCACTATCAACCAT
28767164 CTTGGTTGGG
Statistics
Matches: 650, Mismatches: 17, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
667 570 0.88
673 1 0.00
674 4 0.01
675 75 0.12
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.34
Consensus pattern (670 bp):
ATTTCTTTACTTACTTTCAGTTATTTTAATTTTACTTGTGTTGTTTCAAATTCTTTTGCAGAAAC
AAAAAAACAACTTTTTGTAGTCGAAGCATCAAAGCATGAATTGTCGGCGCATTCTGTGATGAGTC
AGCATTACTTTTTCAGCAAGAATCACGCCAATTGATTTCTCTTCTCTCCTAACCGAACGATCAAG
CGAAATAGTACAATCTACAGCCTGGCAATTAATGACTGCAGACGCAACGTTTCCCCGTAATTCTT
TTAATCATCACGCCTAGGTTATAAAACCTCTGTCCTGCAGTTTTCTTTTCTCCTCACATCTTCCA
TTGTTGCTACAACTCGTTTTCTTCATCGCTTCTGTATTTTCTTTTTCATTCAATAGAGCAATCAT
TTTCTGTAACCTCTTCTAACTTCCTTCTTCATTTACAATGGCTAAAACCCATGCCTCGAAAAACC
TTTCAAAAACTCCTTTCAAGAACACCCCGACAACTTTTACTTGGGCTCCGACCACAACGCCACCT
CCTTCTACAGACCCAGTTTTATTCTTGACAACTGCGGCCAAAGGCTGCTACCAAAATACCATGTT
AAAGAGAAACCTCCACCCTGAACAAGGTCTGCAGCTTTCTCCACACCAAACTTTGGGGAAGCATG
TTGTTTGCACTATCAACCAT
Found at i:28771053 original size:13 final size:14
Alignment explanation
Indices: 28771024--28771053 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28771014 TTCAGTACAT
28771024 TGACATTTAACTTC
1 TGACATTTAACTTC
28771038 TGACATTTAA-TTC
1 TGACATTTAACTTC
28771051 TGA
1 TGA
28771054 TTGCATTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (14 bp):
TGACATTTAACTTC
Found at i:28772655 original size:27 final size:28
Alignment explanation
Indices: 28772595--28772655 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
28772585 ATGAAGTTCG
*
28772595 CTAGGACAAGTAAACAAGAGGTAGTCCA
1 CTAGGACAACTAAACAAGAGGTAGTCCA
* *
28772623 CCAGGAC-ACTAAACATGAGGTAGTCCA
1 CTAGGACAACTAAACAAGAGGTAGTCCA
*
28772650 TTAGGA
1 CTAGGA
28772656 ATATGGATAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 22 0.79
28 6 0.21
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.16
Consensus pattern (28 bp):
CTAGGACAACTAAACAAGAGGTAGTCCA
Found at i:28773252 original size:76 final size:76
Alignment explanation
Indices: 28773126--28773278 Score: 306
Period size: 76 Copynumber: 2.0 Consensus size: 76
28773116 AACTACTAGG
28773126 AAGGGCATATGCATGGTAACCAAACAATAAATAGTGACGAGAGATGACACACTAGTGGTGGCCTG
1 AAGGGCATATGCATGGTAACCAAACAATAAATAGTGACGAGAGATGACACACTAGTGGTGGCCTG
28773191 TGTTCAGACGA
66 TGTTCAGACGA
28773202 AAGGGCATATGCATGGTAACCAAACAATAAATAGTGACGAGAGATGACACACTAGTGGTGGCCTG
1 AAGGGCATATGCATGGTAACCAAACAATAAATAGTGACGAGAGATGACACACTAGTGGTGGCCTG
28773267 TGTTCAGACGA
66 TGTTCAGACGA
28773278 A
1 A
28773279 CAAAAGATGT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.20
Consensus pattern (76 bp):
AAGGGCATATGCATGGTAACCAAACAATAAATAGTGACGAGAGATGACACACTAGTGGTGGCCTG
TGTTCAGACGA
Found at i:28779710 original size:28 final size:28
Alignment explanation
Indices: 28779662--28779715 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
28779652 TTTTTATTTT
*
28779662 AAAATATTACATTAATAAATTTAACAAA
1 AAAATACTACATTAATAAATTTAACAAA
*
28779690 AAAATACTACTATTAA-CAATTTAACA
1 AAAATACTAC-ATTAATAAATTTAACA
28779716 TGAATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (28 bp):
AAAATACTACATTAATAAATTTAACAAA
Found at i:28788157 original size:9 final size:9
Alignment explanation
Indices: 28788138--28788178 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
28788128 AAGCCTGAAC
28788138 ATTATTAAAT
1 ATTA-TAAAT
28788148 ATTATAAAT
1 ATTATAAAT
28788157 ATTAT-AA-
1 ATTATAAAT
*
28788164 ATTATAAAG
1 ATTATAAAT
28788173 ATTATA
1 ATTATA
28788179 GAAAAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 5 0.17
8 4 0.14
9 16 0.55
10 4 0.14
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (9 bp):
ATTATAAAT
Found at i:28788159 original size:16 final size:16
Alignment explanation
Indices: 28788148--28788178 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28788138 ATTATTAAAT
28788148 ATTATAAATATTATAA
1 ATTATAAATATTATAA
*
28788164 ATTATAAAGATTATA
1 ATTATAAATATTATA
28788179 GAAAAATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
ATTATAAATATTATAA
Found at i:28788280 original size:43 final size:42
Alignment explanation
Indices: 28788200--28788281 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 42
28788190 TCGGTTGTTT
* * *
28788200 AAAAATTATAAACAAATTAGAAGAGATATATAAATATTAGAG
1 AAAAATTATAAAAAAATTAGAAGAAATATAAAAATATTAGAG
28788242 AAAAATTATAAAAAAAGTTATG-AGAAATATAAAAATATTA
1 AAAAATTATAAAAAAA-TTA-GAAGAAATATAAAAATATTA
28788282 ATATATTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
42 15 0.43
43 19 0.54
44 1 0.03
ACGTcount: A:0.62, C:0.01, G:0.10, T:0.27
Consensus pattern (42 bp):
AAAAATTATAAAAAAATTAGAAGAAATATAAAAATATTAGAG
Found at i:28788291 original size:19 final size:19
Alignment explanation
Indices: 28788269--28788332 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
28788259 TTATGAGAAA
28788269 TATAAAAATATTAATATAT
1 TATAAAAATATTAATATAT
* *
28788288 TATAAATA-ATT-ATAATAC
1 TATAAAAATATTAAT-ATAT
*
28788306 TATAAAAACT-TTAAAATAT
1 TATAAAAA-TATTAATATAT
*
28788325 TACAAAAA
1 TATAAAAA
28788333 CTATGAAAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
17 2 0.06
18 13 0.37
19 19 0.54
20 1 0.03
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
TATAAAAATATTAATATAT
Found at i:28788371 original size:10 final size:9
Alignment explanation
Indices: 28788347--28788379 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
28788337 GAAAAGTTAT
28788347 ATAAAAATC
1 ATAAAAATC
28788356 ATAAAAATC
1 ATAAAAATC
28788365 ATAAAAA--
1 ATAAAAATC
28788372 ATAAAAAT
1 ATAAAAAT
28788380 GATTAAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.30
9 16 0.70
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (9 bp):
ATAAAAATC
Found at i:28788790 original size:9 final size:9
Alignment explanation
Indices: 28788696--28788810 Score: 72
Period size: 9 Copynumber: 12.4 Consensus size: 9
28788686 TATTTATTTA
28788696 TTTATAATT
1 TTTATAATT
*
28788705 TTTTTAATT
1 TTTATAATT
*
28788714 TTTGAGTAATG
1 TTT-A-TAATT
* *
28788725 TTAATAATA
1 TTTATAATT
* *
28788734 TATATATTT
1 TTTATAATT
28788743 TTCTATAATT
1 TT-TATAATT
* *
28788753 TTTAAAATA
1 TTTATAATT
28788762 TTTAT-ATT
1 TTTATAATT
* *
28788770 TTAATAAGT
1 TTTATAATT
28788779 TTTATAATTT
1 TTTATAA-TT
*
28788789 TTTAATAAAT
1 TTT-ATAATT
28788799 TTTAT-ATT
1 TTTATAATT
28788807 TTTA
1 TTTA
28788811 ATAAATTCTT
Statistics
Matches: 79, Mismatches: 21, Indels: 13
0.70 0.19 0.12
Matches are distributed among these distances:
8 12 0.15
9 40 0.51
10 17 0.22
11 10 0.13
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (9 bp):
TTTATAATT
Found at i:28788808 original size:18 final size:18
Alignment explanation
Indices: 28788757--28788817 Score: 79
Period size: 18 Copynumber: 3.3 Consensus size: 18
28788747 ATAATTTTTA
28788757 AAATATTTATA-TTTTAAT
1 AAAT-TTTATATTTTTAAT
*
28788775 AAGTTTTATAATTTTTTAAT
1 AAATTTTAT-A-TTTTTAAT
28788795 AAATTTTATATTTTTAAT
1 AAATTTTATATTTTTAAT
28788813 AAATT
1 AAATT
28788818 CTTAGAATCC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
17 5 0.13
18 17 0.45
19 1 0.03
20 15 0.39
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
AAATTTTATATTTTTAAT
Found at i:28792633 original size:2 final size:2
Alignment explanation
Indices: 28792626--28792672 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
28792616 TCAAACAAAG
28792626 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28792668 AT AT A
1 AT AT A
28792673 ATCCTTTTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28804138 original size:22 final size:21
Alignment explanation
Indices: 28804100--28804141 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
28804090 TTGAATATGA
*
28804100 TTTTATTTTAATAATTTTTAT
1 TTTTATTTCAATAATTTTTAT
28804121 TTTTATTTCATATAATTTTTA
1 TTTTATTTCA-ATAATTTTTA
28804142 ATAATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTATTTCAATAATTTTTAT
Found at i:28819373 original size:13 final size:13
Alignment explanation
Indices: 28819355--28819388 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
28819345 ATTAATTATT
28819355 TTTTTAAAAAATA
1 TTTTTAAAAAATA
28819368 TTTTTAAAAAATA
1 TTTTTAAAAAATA
28819381 -TTTTAAAA
1 TTTTTAAAA
28819389 TTATTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TTTTTAAAAAATA
Found at i:28819397 original size:13 final size:12
Alignment explanation
Indices: 28819354--28819400 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
28819344 AATTAATTAT
28819354 TTTTTTAAAAAA
1 TTTTTTAAAAAA
28819366 TATTTTTAAAAAA
1 T-TTTTTAAAAAA
* *
28819379 TATTTTAAAATTA
1 TTTTTTAAAA-AA
28819392 TTTTTTAAA
1 TTTTTTAAA
28819401 TATAAAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.30
13 21 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTTTTTAAAAAA
Found at i:28820374 original size:21 final size:22
Alignment explanation
Indices: 28820349--28820393 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
28820339 AAAATTATTT
*
28820349 AATAATTTT-ATTATTTTAAAA
1 AATAATTTTAATTAATTTAAAA
28820370 AATAATTTTAAATTAATTTAAAA
1 AATAATTTT-AATTAATTTAAAA
28820393 A
1 A
28820394 TATTTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
23 12 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AATAATTTTAATTAATTTAAAA
Found at i:28820403 original size:11 final size:11
Alignment explanation
Indices: 28820367--28820407 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
28820357 TATTATTTTA
28820367 AAAAATAATTT
1 AAAAATAATTT
* *
28820378 TAAATTAATTT
1 AAAAATAATTT
28820389 AAAAAT-ATTT
1 AAAAATAATTT
28820399 AAAAA-AATT
1 AAAAATAATT
28820408 ATATTTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
10 12 0.48
11 13 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AAAAATAATTT
Found at i:28823697 original size:59 final size:62
Alignment explanation
Indices: 28823632--28823748 Score: 159
Period size: 62 Copynumber: 1.9 Consensus size: 62
28823622 ATCACTTTAA
* * * * *
28823632 TATTAAATTAATATAATATTTATC-A-AG-ATAAATATTAGATTAAATTTAATGTTAAATCT
1 TATTAAAATAATAAAATATTTATCTATAGAATAAACATTAAATTAAATTTAATATTAAATCT
*
28823691 TATTAAAATAATAAAATGTTTATCTATAGAATAAACATTAAATTAAATTTAATATTAA
1 TATTAAAATAATAAAATATTTATCTATAGAATAAACATTAAATTAAATTTAATATTAA
28823749 GATACTCAGT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
59 21 0.43
60 1 0.02
61 2 0.04
62 25 0.51
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.42
Consensus pattern (62 bp):
TATTAAAATAATAAAATATTTATCTATAGAATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:28825586 original size:24 final size:24
Alignment explanation
Indices: 28825553--28825599 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
28825543 GTCAAGAGTA
*
28825553 AAAATTGTCAGTGCAAATGTAATAC
1 AAAATTGTCAGAGCAAAT-TAATAC
28825578 AAAA-TGTCAGAGCAAATTAATA
1 AAAATTGTCAGAGCAAATTAATA
28825600 AAAGATGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.26
Consensus pattern (24 bp):
AAAATTGTCAGAGCAAATTAATAC
Found at i:28828186 original size:12 final size:13
Alignment explanation
Indices: 28828169--28828203 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
28828159 CAGGGCTACA
28828169 TCTTCTTCTT-TT
1 TCTTCTTCTTCTT
28828181 TCTTCTT-TTCTT
1 TCTTCTTCTTCTT
28828193 TCTTCTTCTTC
1 TCTTCTTCTTC
28828204 CGCCTTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.10
12 16 0.76
13 3 0.14
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (13 bp):
TCTTCTTCTTCTT
Found at i:28841793 original size:17 final size:17
Alignment explanation
Indices: 28841754--28841802 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
28841744 ATATTTATGG
**
28841754 AAATGCAATGACAATGT
1 AAATGCAATGACAATAA
* *
28841771 AGATGCAGTGACAATAA
1 AAATGCAATGACAATAA
*
28841788 AAATGCAAAGACAAT
1 AAATGCAATGACAAT
28841803 TATACTACAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.51, C:0.12, G:0.18, T:0.18
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:28856349 original size:41 final size:42
Alignment explanation
Indices: 28856303--28856403 Score: 105
Period size: 41 Copynumber: 2.4 Consensus size: 42
28856293 ATATGAATGA
* * *
28856303 AAGACTCGCGACTCGAAACGAGCATGAGGATAT-ATTAAAGG
1 AAGACTCACGACTCGAAACGAGAATGAGAATATGATTAAAGG
* * ** *
28856344 AAGACTCATGTCTCGGGATGAGAATGAGAATATGATTAAAGG
1 AAGACTCACGACTCGAAACGAGAATGAGAATATGATTAAAGG
* *
28856386 AAGACTCATGACTTGAAA
1 AAGACTCACGACTCGAAA
28856404 TGAGCCTAAG
Statistics
Matches: 47, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
41 25 0.53
42 22 0.47
ACGTcount: A:0.40, C:0.14, G:0.26, T:0.21
Consensus pattern (42 bp):
AAGACTCACGACTCGAAACGAGAATGAGAATATGATTAAAGG
Found at i:28856407 original size:42 final size:41
Alignment explanation
Indices: 28856303--28856407 Score: 120
Period size: 42 Copynumber: 2.5 Consensus size: 41
28856293 ATATGAATGA
** * * *
28856303 AAGACTCGCGACTCGAAACGAGCATGAGGATATATTAAAGG
1 AAGACTCATGACTCGAAATGAGAATGAGAATATATTAAAGG
* **
28856344 AAGACTCATGTCTCGGGATGAGAATGAGAATATGATTAAAGG
1 AAGACTCATGACTCGAAATGAGAATGAGAATAT-ATTAAAGG
*
28856386 AAGACTCATGACTTGAAATGAG
1 AAGACTCATGACTCGAAATGAG
28856408 CCTAAGATTA
Statistics
Matches: 51, Mismatches: 12, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
41 25 0.49
42 26 0.51
ACGTcount: A:0.39, C:0.13, G:0.27, T:0.21
Consensus pattern (41 bp):
AAGACTCATGACTCGAAATGAGAATGAGAATATATTAAAGG
Found at i:28856425 original size:42 final size:41
Alignment explanation
Indices: 28856337--28856475 Score: 113
Period size: 42 Copynumber: 3.3 Consensus size: 41
28856327 TGAGGATATA
* ** ** * *
28856337 TTAAAGGAAGACTCATGTCTCGGGATGAGAATGAGAATATGA
1 TTAAAGGAAGACTCATGACTCGAAATGAGCCTAAG-ATATGT
*
28856379 TTAAAGGAAGACTCATGACTTGAAATGAGCCTAAGATTATGT
1 TTAAAGGAAGACTCATGACTCGAAATGAGCCTAAGA-TATGT
* *
28856421 TTAAAAAGGAAGACTTATGACTCGATA-GA-CCATAAGAT-TGT
1 TT--AAAGGAAGACTCATGACTCGAAATGAGCC-TAAGATATGT
28856462 ATTAAAGGAAGACT
1 -TTAAAGGAAGACT
28856476 TGTGAATCCG
Statistics
Matches: 81, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
40 11 0.14
41 4 0.05
42 39 0.48
43 7 0.09
44 20 0.25
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26
Consensus pattern (41 bp):
TTAAAGGAAGACTCATGACTCGAAATGAGCCTAAGATATGT
Found at i:28862101 original size:2 final size:2
Alignment explanation
Indices: 28862094--28862124 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28862084 TAAATTTCAA
28862094 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28862125 AAGTACAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28863789 original size:15 final size:17
Alignment explanation
Indices: 28863758--28863789 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28863748 ACCGAATAGC
28863758 TCAATTTGTTATAAAAT
1 TCAATTTGTTATAAAAT
28863775 TCAATTT-TT-TAAAAT
1 TCAATTTGTTATAAAAT
28863790 AAAATTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (17 bp):
TCAATTTGTTATAAAAT
Found at i:28863801 original size:19 final size:19
Alignment explanation
Indices: 28863768--28863806 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
28863758 TCAATTTGTT
28863768 ATAAAATTCAATTTTTTAAA
1 ATAAAATTCAA-TTTTTAAA
28863788 ATAAAATT-AATTTTTAAA
1 ATAAAATTCAATTTTTAAA
28863806 A
1 A
28863807 AGGAAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
19 2 0.11
20 8 0.42
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAAAATTCAATTTTTAAA
Found at i:28863807 original size:19 final size:20
Alignment explanation
Indices: 28863768--28863807 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
28863758 TCAATTTGTT
*
28863768 ATAAAATTCAATTTTTTAAA
1 ATAAAATTCAATTTTTAAAA
28863788 ATAAAATT-AATTTTTAAAA
1 ATAAAATTCAATTTTTAAAA
28863807 A
1 A
28863808 GGAAAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAAAATTCAATTTTTAAAA
Found at i:28863813 original size:20 final size:20
Alignment explanation
Indices: 28863770--28863813 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
28863760 AATTTGTTAT
* *
28863770 AAAATTCAATTTTTTAAAAT
1 AAAATTCAATTTTTAAAAAG
28863790 AAAATT-AATTTTTAAAAAGG
1 AAAATTCAATTTTTAAAAA-G
28863810 AAAA
1 AAAA
28863814 AGAAAGTGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAATTCAATTTTTAAAAAG
Found at i:28872616 original size:17 final size:17
Alignment explanation
Indices: 28872590--28872623 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28872580 AACACTTAAA
*
28872590 GCGATTCCTTCAACTAT
1 GCGATACCTTCAACTAT
28872607 GCGATACCTTCAACTAT
1 GCGATACCTTCAACTAT
28872624 AACTGATGAT
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:0.26, C:0.29, G:0.12, T:0.32
Consensus pattern (17 bp):
GCGATACCTTCAACTAT
Found at i:28878834 original size:6 final size:6
Alignment explanation
Indices: 28878825--28878858 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
28878815 TTCTCTTTCT
*
28878825 CCTTCC CCTTCC TCTTCC CCTTCC CCTTCC CCTT
1 CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCTT
28878859 TCCTCTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (6 bp):
CCTTCC
Found at i:28878843 original size:12 final size:12
Alignment explanation
Indices: 28878826--28878866 Score: 64
Period size: 12 Copynumber: 3.3 Consensus size: 12
28878816 TCTCTTTCTC
28878826 CTTCCCCTTCCT
1 CTTCCCCTTCCT
*
28878838 CTTCCCCTTCCC
1 CTTCCCCTTCCT
28878850 CTTCCCCTTTCCT
1 CTTCCCC-TTCCT
28878863 CTTC
1 CTTC
28878867 ATTGCGTCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 18 0.69
13 8 0.31
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (12 bp):
CTTCCCCTTCCT
Found at i:28881768 original size:14 final size:14
Alignment explanation
Indices: 28881749--28881784 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
28881739 GAAAAGTAAG
28881749 TCATTTTCCAGAAA
1 TCATTTTCCAGAAA
*
28881763 TCATTTTCCGGAAA
1 TCATTTTCCAGAAA
*
28881777 CCATTTTC
1 TCATTTTC
28881785 AGTCAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.39
Consensus pattern (14 bp):
TCATTTTCCAGAAA
Found at i:28882401 original size:18 final size:19
Alignment explanation
Indices: 28882373--28882409 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
28882363 GTTAAAAGAA
*
28882373 AAATAATTTTTTTGTTTTT
1 AAATAATTTTTTAGTTTTT
28882392 AAAT-ATTTTTTAGTTTTT
1 AAATAATTTTTTAGTTTTT
28882410 TTTAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (19 bp):
AAATAATTTTTTAGTTTTT
Found at i:28882401 original size:19 final size:20
Alignment explanation
Indices: 28882373--28882416 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
28882363 GTTAAAAGAA
28882373 AAATAATTTTT-TTGTTTTT
1 AAATAATTTTTATTGTTTTT
* *
28882392 AAATATTTTTTAGTTTTTTTT
1 AAATAATTTTTA-TTGTTTTT
28882413 AAAT
1 AAAT
28882417 TTTCAAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
21 11 0.52
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (20 bp):
AAATAATTTTTATTGTTTTT
Found at i:28899943 original size:36 final size:36
Alignment explanation
Indices: 28899891--28899983 Score: 107
Period size: 36 Copynumber: 2.6 Consensus size: 36
28899881 AGGACACAAT
* * *
28899891 AAAACATATAATTAAATAAAAAGAAAAAAAATGTAA
1 AAAACATATAAATAAATAAAAACAAAAAAAATATAA
** * *
28899927 ATGACATAAAAATAAATAACAAACAAATAAAATATAA
1 AAAACATATAAATAAATAA-AAACAAAAAAAATATAA
28899964 AAAACA-ATAAATAAATAAAA
1 AAAACATATAAATAAATAAAA
28899984 CTAAATAAAG
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
35 2 0.04
36 26 0.57
37 18 0.39
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.18
Consensus pattern (36 bp):
AAAACATATAAATAAATAAAAACAAAAAAAATATAA
Found at i:28899956 original size:21 final size:21
Alignment explanation
Indices: 28899932--28899978 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
28899922 TGTAAATGAC
*
28899932 ATAAAA-ATAAATAACAAACAA
1 ATAAAATATAAAAAAC-AACAA
*
28899953 ATAAAATATAAAAAACAATAA
1 ATAAAATATAAAAAACAACAA
28899974 ATAAA
1 ATAAA
28899979 TAAAACTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (21 bp):
ATAAAATATAAAAAACAACAA
Found at i:28899975 original size:16 final size:18
Alignment explanation
Indices: 28899942--28899992 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
28899932 ATAAAAATAA
*
28899942 ATAACAAACAAATAAAAT
1 ATAAAAAACAAATAAAAT
28899960 ATAAAAAAC-AAT-AAAT
1 ATAAAAAACAAATAAAAT
28899976 A-AATAAAACTAAATAAA
1 ATAA-AAAAC-AAATAAA
28899993 GTCAAGAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 2 0.07
16 10 0.36
17 3 0.11
18 11 0.39
19 2 0.07
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.18
Consensus pattern (18 bp):
ATAAAAAACAAATAAAAT
Found at i:28901966 original size:102 final size:101
Alignment explanation
Indices: 28901807--28902414 Score: 663
Period size: 102 Copynumber: 6.0 Consensus size: 101
28901797 AGGAAGATAG
* * *
28901807 GATTTGG-GTTTGTAACTTCACTCCATTCCATTACAACTTCAGAGAGATTGAGATCTGCTACGGT
1 GATTTGGTG-TTGTAACTTCACTCCATTCCACTGCAACTTCAGGGAGATTGAGATCTGCTACGGT
*
28901871 TAGTTTTAATCTACCCCTCTGCAACTTTAAGGGTATAA
65 TAGTTTTAATCTGCCCCTCTGCAACTTT-AGGGTATAA
* * ** * * *
28901909 GATTTGATATTGTCTCTTCACTTCATTCCACTGTAACTTTAGGGAGATTGAGATCTGCTACGGTT
1 GATTTGGTGTTGTAACTTCACTCCATTCCACTGCAACTTCAGGGAGATTGAGATCTGCTACGGTT
*
28901974 AGTTTTAATAC-GCCCCTCTACAACTTTAGGGATATAA
66 AGTTTTAAT-CTGCCCCTCTGCAACTTTAGGG-TATAA
* ** * * * *
28902011 GATTTGGTGTTATAACTTCACTCTGTTCCATTGTAACTTCAGGGAGATTAAGATCTGCTACGATT
1 GATTTGGTGTTGTAACTTCACTCCATTCCACTGCAACTTCAGGGAGATTGAGATCTGCTACGGTT
* * *
28902076 AGTTTTAATTTTCCCCTCT--AATCATTTAGAGGTATAG
66 AGTTTTAATCTGCCCCTCTGCAA-C-TTTAG-GGTATAA
* * * * *
28902113 GATTTGGTGTTGTAACTTCATTCCATTCTATTGTAACTTCAGGGAGATTGACATCTGCTACGGTT
1 GATTTGGTGTTGTAACTTCACTCCATTCCACTGCAACTTCAGGGAGATTGAGATCTGCTACGGTT
* *
28902178 AGTTTTAATCTGCCCCTCTGTAACTTTAGGGGTATAG
66 AGTTTTAATCTGCCCCTCTGCAACTTTA-GGGTATAA
* * * * * **
28902215 GATTTGATATTGTAACTTCACTCCATTCCACTGCATCTTTAGGGAGATTAAGATCTATTACGGTT
1 GATTTGGTGTTGTAACTTCACTCCATTCCACTGCAACTTCAGGGAGATTGAGATCTGCTACGGTT
** * *
28902280 AGTTTTAATCCACTCCTCTACAACTTTAGAGGTATAA
66 AGTTTTAATCTGCCCCTCTGCAACTTTAG-GGTATAA
** *
28902317 GATTTGGTGTTGTAACTTCACTCCATTCTGCTGCAACTTCAGGGAGATTGAGATCTGTTAC--TT
1 GATTTGGTGTTGTAACTTCACTCCATTCCACTGCAACTTCAGGGAGATTGAGATCTGCTACGGTT
* * *
28902380 -GTTTTACTCTGCCCTTCTGTAACTTTAAGGGTATA
66 AGTTTTAATCTGCCCCTCTGCAACTTT-AGGGTATA
28902415 GGAGTTGTTG
Statistics
Matches: 424, Mismatches: 70, Indels: 27
0.81 0.13 0.05
Matches are distributed among these distances:
99 25 0.06
100 6 0.01
101 6 0.01
102 380 0.90
103 5 0.01
104 2 0.00
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (101 bp):
GATTTGGTGTTGTAACTTCACTCCATTCCACTGCAACTTCAGGGAGATTGAGATCTGCTACGGTT
AGTTTTAATCTGCCCCTCTGCAACTTTAGGGTATAA
Found at i:28902357 original size:306 final size:306
Alignment explanation
Indices: 28901803--28902373 Score: 849
Period size: 306 Copynumber: 1.9 Consensus size: 306
28901793 CTTCAGGAAG
*
28901803 ATAGGATTTGGGTTTGTAACTTCACTCCATTCCATTACAACTTCAGAGAGATTGAGATCTGCTAC
1 ATAGGATTTGGGTTTGTAACTTCACTCCATTCCATTACAACTTCAGAGAGATTGACATCTGCTAC
** *
28901868 GGTTAGTTTTAATCTACCCCTCTGCAACTTTAAGGGTATAAGATTTGATATTGTCTCTTCACTTC
66 GGTTAGTTTTAATCTACCCCTCTGCAACTTTAAGGGTATAAGATTTGATATTGTAACTTCACTCC
* * * *
28901933 ATTCCACTGTAACTTTAGGGAGATTGAGATCTGCTACGGTTAGTTTTAATACGCCCCTCTACAAC
131 ATTCCACTGCAACTTTAGGGAGATTAAGATCTACTACGGTTAGTTTTAATACACCCCTCTACAAC
** * *
28901998 TTTAGGGATATAAGATTTGGTGTTATAACTTCACTCTGTTCCATTGTAACTTCAGGGAGATTAAG
196 TTTAGGGATATAAGATTTGGTGTTATAACTTCACTCCATTCCACTGCAACTTCAGGGAGATTAAG
28902063 ATCTGCTACGATTAGTTTTAATTTTCCCCTCTAATCATTTAGAGGT
261 ATCTGCTACGATTAGTTTTAATTTTCCCCTCTAATCATTTAGAGGT
* * ** *
28902109 ATAGGATTT-GGTGTTGTAACTTCATTCCATTCTATTGTAACTTCAGGGAGATTGACATCTGCTA
1 ATAGGATTTGGGT-TTGTAACTTCACTCCATTCCATTACAACTTCAGAGAGATTGACATCTGCTA
* * * *
28902173 CGGTTAGTTTTAATCTGCCCCTCTGTAACTTTAGGGGTATAGGATTTGATATTGTAACTTCACTC
65 CGGTTAGTTTTAATCTACCCCTCTGCAACTTTAAGGGTATAAGATTTGATATTGTAACTTCACTC
* * * *
28902238 CATTCCACTGCATCTTTAGGGAGATTAAGATCTATTACGGTTAGTTTTAATCCACTCCTCTACAA
130 CATTCCACTGCAACTTTAGGGAGATTAAGATCTACTACGGTTAGTTTTAATACACCCCTCTACAA
* ** *
28902303 CTTTAGAGG-TATAAGATTTGGTGTTGTAACTTCACTCCATTCTGCTGCAACTTCAGGGAGATTG
195 CTTTAG-GGATATAAGATTTGGTGTTATAACTTCACTCCATTCCACTGCAACTTCAGGGAGATTA
28902367 AGATCTG
259 AGATCTG
28902374 TTACTTGTTT
Statistics
Matches: 234, Mismatches: 29, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
305 3 0.01
306 229 0.98
307 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (306 bp):
ATAGGATTTGGGTTTGTAACTTCACTCCATTCCATTACAACTTCAGAGAGATTGACATCTGCTAC
GGTTAGTTTTAATCTACCCCTCTGCAACTTTAAGGGTATAAGATTTGATATTGTAACTTCACTCC
ATTCCACTGCAACTTTAGGGAGATTAAGATCTACTACGGTTAGTTTTAATACACCCCTCTACAAC
TTTAGGGATATAAGATTTGGTGTTATAACTTCACTCCATTCCACTGCAACTTCAGGGAGATTAAG
ATCTGCTACGATTAGTTTTAATTTTCCCCTCTAATCATTTAGAGGT
Found at i:28903416 original size:102 final size:101
Alignment explanation
Indices: 28903252--28903859 Score: 650
Period size: 102 Copynumber: 6.0 Consensus size: 101
28903242 AAGAAGATAG
* * * *
28903252 GATTTGG-GTTTGTAACTTCAGTTCATTCCACTGCAACTTTAAGGAGATTGAGATCCGTTACGGT
1 GATTTGGTG-TTGTAACTTCACTCCATTCCACTGCAACTTT-AGGAGATTGAGATCTGCTACGGT
* * * * *
28903316 TATTTTTAATCTGCCTCTCTACAACTTTATGGGTATAC
64 TAGTTTTAATCCGCCCCTCTGCAACTTTAGGGGTATAC
* ** ** *
28903354 GATTTGATGTTGTGGCTTCACTCCATTCCACTATAACTTTAGGAAGATTGAGATCTACTACGGTT
1 GATTTGGTGTTGTAACTTCACTCCATTCCACTGCAACTTTAGG-AGATTGAGATCTGCTACGGTT
* * *
28903419 AGTTTTAATACGCCCCTCTGCAAGTTTAGGGGTATAA
65 AGTTTTAATCCGCCCCTCTGCAACTTTAGGGGTATAC
* * * *
28903456 AATTTGGTGTTATAACTTCACTTCATTCCACTGCAACTTTAGGGAGATTGAGATCTGCTACGATT
1 GATTTGGTGTTGTAACTTCACTCCATTCCACTGCAACTTTA-GGAGATTGAGATCTGCTACGGTT
* * * * *
28903521 AGTTTTAATCTGCCCCTTTGTAACTTTATGGGTATAG
65 AGTTTTAATCCGCCCCTCTGCAACTTTAGGGGTATAC
* * * * * *
28903558 GATTTGGTATTGTAACTTCACTCCATTCGACTACAACTTCAAGGAGATTGAGATTTGTTACGGTT
1 GATTTGGTGTTGTAACTTCACTCCATTCCACTGCAACTT-TAGGAGATTGAGATCTGCTACGGTT
* * *
28903623 AATTTTAATCCGCCCCTCTACAACTTTAGGGGTATAG
65 AGTTTTAATCCGCCCCTCTGCAACTTTAGGGGTATAC
* * *
28903660 GATTTGGTTTTGTAACTTCACTCCATTCCACTGCAACTTTAAGAAGATTGAGATTTGCTACGGTT
1 GATTTGGTGTTGTAACTTCACTCCATTCCACTGCAACTTT-AGGAGATTGAGATCTGCTACGGTT
*
28903725 AGTTTTAATCCGCCCCGCTGCAACTTTAGGGGTAT-C
65 AGTTTTAATCCGCCCCTCTGCAACTTTAGGGGTATAC
* * * * * * *
28903761 GAATTTGGTTTTGTAACTTCACTTCATTCCACTGTAGCTTCATGGTGATTGAGATCTGTTA---T
1 G-ATTTGGTGTTGTAACTTCACTCCATTCCACTGCAACTTTA-GGAGATTGAGATCTGCTACGGT
* * * *
28903823 TTGTTTTACTCTGCCCCTCTGTAACTTTAGGGGTATA
64 TAGTTTTAATCCGCCCCTCTGCAACTTTAGGGGTATA
28903860 AGAGTTGTTA
Statistics
Matches: 424, Mismatches: 74, Indels: 18
0.82 0.14 0.03
Matches are distributed among these distances:
99 32 0.08
101 5 0.01
102 383 0.90
103 4 0.01
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (101 bp):
GATTTGGTGTTGTAACTTCACTCCATTCCACTGCAACTTTAGGAGATTGAGATCTGCTACGGTTA
GTTTTAATCCGCCCCTCTGCAACTTTAGGGGTATAC
Found at i:28903622 original size:204 final size:203
Alignment explanation
Indices: 28903264--28903860 Score: 725
Period size: 204 Copynumber: 2.9 Consensus size: 203
28903254 TTTGGGTTTG
* * * *
28903264 TAACTTCAGTTCATTCCACTGCAACTTTAAGGAGATTGAGATCCGTTACGGTTATTTTTAATCTG
1 TAACTTCACTTCATTCCACTGCAACTTTAAGGAGATTGAGATCTGCTACGGTTAGTTTTAATCTG
* * * * * **
28903329 CCTCTCTACAACTTTATGGGTATACGATTTGATGTTGTGGCTTCACTCCATTCCACTATAACTT-
66 CCCCTCTGCAACTTTATGGGTATAGGATTTGGTATTGTAACTTCACTCCATTCCACTATAACTTC
* ** *
28903393 TAGGAAGATTGAGATCTACTACGGTTAGTTTTAATACGCCCCTCTGCAAGTTTAGGGGTATAAAA
131 AAGG-AGATTGAGATCTGTTACGGTTAGTTTTAAT-CGCCCCTCTGCAACTTTAGGGGTATAAAA
28903458 TTTGGTGTTA
194 TTTGGTGTTA
* *
28903468 TAACTTCACTTCATTCCACTGCAACTTTAGGGAGATTGAGATCTGCTACGATTAGTTTTAATCTG
1 TAACTTCACTTCATTCCACTGCAACTTTAAGGAGATTGAGATCTGCTACGGTTAGTTTTAATCTG
* * * *
28903533 CCCCTTTGTAACTTTATGGGTATAGGATTTGGTATTGTAACTTCACTCCATTCGACTACAACTTC
66 CCCCTCTGCAACTTTATGGGTATAGGATTTGGTATTGTAACTTCACTCCATTCCACTATAACTTC
* * * **
28903598 AAGGAGATTGAGATTTGTTACGGTTAATTTTAATCCGCCCCTCTACAACTTTAGGGGTATAGGAT
131 AAGGAGATTGAGATCTGTTACGGTTAGTTTTAAT-CGCCCCTCTGCAACTTTAGGGGTATAAAAT
* *
28903663 TTGGTTTTG
195 TTGGTGTTA
* * * *
28903672 TAACTTCACTCCATTCCACTGCAACTTTAAGAAGATTGAGATTTGCTACGGTTAGTTTTAATCCG
1 TAACTTCACTTCATTCCACTGCAACTTTAAGGAGATTGAGATCTGCTACGGTTAGTTTTAATCTG
* * * * * * * *
28903737 CCCCGCTGCAACTTTAGGGGTATCGAATTTGGTTTTGTAACTTCACTTCATTCCACTGTAGCTTC
66 CCCCTCTGCAACTTTATGGGTATAGGATTTGGTATTGTAACTTCACTCCATTCCACTATAACTTC
* * * * *
28903802 ATGGTGATTGAGATCTGTTA---TTTGTTTTACTCTGCCCCTCTGTAACTTTAGGGGTATAA
131 AAGGAGATTGAGATCTGTTACGGTTAGTTTTAATC-GCCCCTCTGCAACTTTAGGGGTATAA
28903861 GAGTTGTTAT
Statistics
Matches: 335, Mismatches: 56, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
200 1 0.00
201 31 0.09
204 300 0.90
205 3 0.01
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (203 bp):
TAACTTCACTTCATTCCACTGCAACTTTAAGGAGATTGAGATCTGCTACGGTTAGTTTTAATCTG
CCCCTCTGCAACTTTATGGGTATAGGATTTGGTATTGTAACTTCACTCCATTCCACTATAACTTC
AAGGAGATTGAGATCTGTTACGGTTAGTTTTAATCGCCCCTCTGCAACTTTAGGGGTATAAAATT
TGGTGTTA
Found at i:28903813 original size:306 final size:303
Alignment explanation
Indices: 28903248--28903859 Score: 839
Period size: 306 Copynumber: 2.0 Consensus size: 303
28903238 CTTCAAGAAG
* * * *
28903248 ATAGGATTTGGGTTTGTAACTTCAGTTCATTCCACTGCAACTTTAAGGAGATTGAGATCCGTTAC
1 ATAGGATTTGGGTTTGTAACTTCACTCCATTCCACTACAACTTCAAGGAGATTGAGATCCGTTAC
* * * * **
28903313 GGTTATTTTTAATCTGCCTCTCTACAACTTTATGGGTATACGATTTGATGTTGTGGCTTCACTCC
66 GGTTAATTTTAATCCGCCCCTCTACAACTTTAGGGGTATACGATTTGATGTTGTAACTTCACTCC
* * * *
28903378 ATTCCACTATAACTTTAGGAAGATTGAGATCTACTACGGTTAGTTTTAATACGCCCCTCTGCAAG
131 ATTCCACTACAACTTTAAGAAGATTGAGATCTACTACGGTTAGTTTTAATACGCCCCGCTGCAAC
*
28903443 TTTAGGGGTATAAAATTTGGTGTTATAACTTCACTTCATTCCACTGCAACTTTAGGGAGATTGAG
196 TTTAGGGGTATAAAATTTGGTGTTATAACTTCACTTCATTCCACTGCAACTTCAGGGAGATTGAG
* *
28903508 ATCTGCTACGATTAGTTTTAATCTGCCCCTTTGTAACTTTATGGGT
261 ATCTG-T--GATTAGTTTTAATCTGCCCCTCTGTAACTTTAGGGGT
* **
28903554 ATAGGATTT-GGTATTGTAACTTCACTCCATTCGACTACAACTTCAAGGAGATTGAGATTTGTTA
1 ATAGGATTTGGGT-TTGTAACTTCACTCCATTCCACTACAACTTCAAGGAGATTGAGATCCGTTA
* * *
28903618 CGGTTAATTTTAATCCGCCCCTCTACAACTTTAGGGGTATAGGATTTGGTTTTGTAACTTCACTC
65 CGGTTAATTTTAATCCGCCCCTCTACAACTTTAGGGGTATACGATTTGATGTTGTAACTTCACTC
* * * *
28903683 CATTCCACTGCAACTTTAAGAAGATTGAGATTTGCTACGGTTAGTTTTAATCCGCCCCGCTGCAA
130 CATTCCACTACAACTTTAAGAAGATTGAGATCTACTACGGTTAGTTTTAATACGCCCCGCTGCAA
** * * * * * *
28903748 CTTTAGGGGTATCGAATTTGGTTTTGTAACTTCACTTCATTCCACTGTAGCTTCATGGTGATTGA
195 CTTTAGGGGTATAAAATTTGGTGTTATAACTTCACTTCATTCCACTGCAACTTCAGGGAGATTGA
* * *
28903813 GATCTGTTATTTGTTTTACTCTGCCCCTCTGTAACTTTAGGGGT
260 GATCTGTGATTAGTTTTAATCTGCCCCTCTGTAACTTTAGGGGT
28903857 ATA
1 ATA
28903860 AGAGTTGTTA
Statistics
Matches: 267, Mismatches: 38, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
303 35 0.13
305 4 0.01
306 228 0.85
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (303 bp):
ATAGGATTTGGGTTTGTAACTTCACTCCATTCCACTACAACTTCAAGGAGATTGAGATCCGTTAC
GGTTAATTTTAATCCGCCCCTCTACAACTTTAGGGGTATACGATTTGATGTTGTAACTTCACTCC
ATTCCACTACAACTTTAAGAAGATTGAGATCTACTACGGTTAGTTTTAATACGCCCCGCTGCAAC
TTTAGGGGTATAAAATTTGGTGTTATAACTTCACTTCATTCCACTGCAACTTCAGGGAGATTGAG
ATCTGTGATTAGTTTTAATCTGCCCCTCTGTAACTTTAGGGGT
Found at i:28904435 original size:20 final size:20
Alignment explanation
Indices: 28904410--28904459 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
28904400 TTTAAAAATA
*
28904410 TCAAACATTAGTCAAAGATG
1 TCAAACATTAGTAAAAGATG
* *
28904430 TCAAACAATGGTAAAAGATG
1 TCAAACATTAGTAAAAGATG
*
28904450 ACAAACATTA
1 TCAAACATTA
28904460 AACAATGGTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.22
Consensus pattern (20 bp):
TCAAACATTAGTAAAAGATG
Found at i:28904521 original size:20 final size:20
Alignment explanation
Indices: 28904465--28904525 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
28904455 CATTAAACAA
* *
28904465 TGGTAAAAAATTGGAAATAT
1 TGGTAAAAAATAGCAAATAT
* * *
28904485 TGATAAAAAATGGCAAATGT
1 TGGTAAAAAATAGCAAATAT
*
28904505 TGGTAAAAAATAACAAATAT
1 TGGTAAAAAATAGCAAATAT
28904525 T
1 T
28904526 AATCAAGAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.52, C:0.03, G:0.16, T:0.28
Consensus pattern (20 bp):
TGGTAAAAAATAGCAAATAT
Found at i:28907712 original size:28 final size:29
Alignment explanation
Indices: 28907680--28907740 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
28907670 AAAACGAAAC
28907680 TTTTGGATACCCG-GGGGCAAAATAGTAA
1 TTTTGGATACCCGAGGGGCAAAATAGTAA
* * *
28907708 TTTTGGATGCGCGAGGGGCAAAATGGTAA
1 TTTTGGATACCCGAGGGGCAAAATAGTAA
28907737 TTTT
1 TTTT
28907741 TGATTAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 11 0.38
29 18 0.62
ACGTcount: A:0.28, C:0.11, G:0.31, T:0.30
Consensus pattern (29 bp):
TTTTGGATACCCGAGGGGCAAAATAGTAA
Found at i:28907827 original size:58 final size:59
Alignment explanation
Indices: 28907727--28908034 Score: 311
Period size: 58 Copynumber: 5.3 Consensus size: 59
28907717 CGCGAGGGGC
* ** * * *
28907727 AAAATGGTAATTTTTGATTAAATAGAGGTTTAAAATGGAATTTTAGAAAGTTCGAGGGT
1 AAAATGGTAATTTTTGATGAAACCGAGGTTAAAAATGGAATTTTGGAAAGTTCAAGGGT
* * * * * *
28907786 AAAACGATAATTTTTGATGACACCG-GGTTTAAAATGGAATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGATGAAACCGAGGTTAAAAATGGAATTTTGGAAAGTTCAAGGGT
* * *
28907844 AATATGGTAATTTTTGGTGAAACCGAGGTTAAAAAT-GAAGTTTTGGAAAGTTC-GGGGT
1 AAAATGGTAATTTTTGATGAAACCGAGGTTAAAAATGGAA-TTTTGGAAAGTTCAAGGGT
* * * * * *
28907902 AAAATGATAATTTTTGACGAAA-CTAGGGTTGAAAATGGAGTTTT-GAAAGTTTAAGGGT
1 AAAATGGTAATTTTTGATGAAACCGA-GGTTAAAAATGGAATTTTGGAAAGTTCAAGGGT
* * * * * * *
28907960 TAAATGGTAATTTTCGGTGAAATCGAGGTTAAAAATGGAGTTTTGGAAAGTTTAAGAGT
1 AAAATGGTAATTTTTGATGAAACCGAGGTTAAAAATGGAATTTTGGAAAGTTCAAGGGT
28908019 AAAATGGTAATTTTTG
1 AAAATGGTAATTTTTG
28908035 GACCATCCAA
Statistics
Matches: 206, Mismatches: 36, Indels: 14
0.80 0.14 0.05
Matches are distributed among these distances:
57 9 0.04
58 126 0.61
59 71 0.34
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGATGAAACCGAGGTTAAAAATGGAATTTTGGAAAGTTCAAGGGT
Found at i:28907842 original size:117 final size:117
Alignment explanation
Indices: 28907721--28908034 Score: 391
Period size: 117 Copynumber: 2.7 Consensus size: 117
28907711 TGGATGCGCG
* * * * * *
28907721 AGGGGCAAAATGGTAATTTTTGATTAAATAGAGGTTTAAAATGGAATTTTAGAAAGTTCGAGGGT
1 AGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
* * * * *
28907786 AAAACGATAATTTTTGATGACAC-CGGGTTTAAAATGGAATTTTGGAAAGTTT
66 AAAATGATAATTTTTGACGAAACTAGGGTTGAAAATGGAATTTT-GAAAGTTT
* *
28907838 AGGGGTAATATGGTAATTTTTGGTGAAACCGAGGTTAAAAAT-GAAGTTTTGGAAAGTTCG-GGG
1 AGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAA-TTTTGGAAAGTTCGAGGG
*
28907901 TAAAATGATAATTTTTGACGAAACTAGGGTTGAAAATGGAGTTTTGAAAGTTT
65 TAAAATGATAATTTTTGACGAAACTAGGGTTGAAAATGGAATTTTGAAAGTTT
* * * * ** *
28907954 AAGGGTTAAATGGTAATTTTCGGTGAAATCGAGGTTAAAAATGGAGTTTTGGAAAGTTTAAGAGT
1 AGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
*
28908019 AAAATGGTAATTTTTG
66 AAAATGATAATTTTTG
28908035 GACCATCCAA
Statistics
Matches: 169, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
116 84 0.50
117 85 0.50
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (117 bp):
AGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
AAAATGATAATTTTTGACGAAACTAGGGTTGAAAATGGAATTTTGAAAGTTT
Found at i:28908284 original size:162 final size:162
Alignment explanation
Indices: 28908106--28908433 Score: 408
Period size: 162 Copynumber: 2.0 Consensus size: 162
28908096 AGCATCCAGA
** * ** *
28908106 AGTCAAAAGACTAATTTGTAAATCTTGAAAA-ATTCTTGGACCAATTTTGTAATTAAATAAAAGT
1 AGTCAAAAGACTAATTTAAAAATC-TCAAAAGATTCCAGGACCAATTTTGTAATTAAACAAAAGT
* * *** * *
28908170 TGATTTAAGGATTAAATTTAAACAAATTAAAAATGGCAAGGACTAGATATATAAATAAGCC-AAA
65 TAATTTAAGGATTAAATTAAAACAAATTAAAAACAACAAGGACTAAATACA-AAATAAGCCGAAA
*
28908234 AAGTGACACGTGGCAGCCTCTGGTGCAGTCAAAC
129 AAATGACACGTGGCAGCCTCTGGTGCAGTCAAAC
* ** *
28908268 AGTCAAAGGACTAATTTAAAAATCTCAAAAGATTCCAGGGTCAATTTTGTAATTAAGCAAAAGTT
1 AGTCAAAAGACTAATTTAAAAATCTCAAAAGATTCCAGGACCAATTTTGTAATTAAACAAAAGTT
* * *
28908333 AATTTGAGGATTAAATTAAAACAAATTAAACACAACAAGGACTAAATGCAAAATAAGCCGAAAAA
66 AATTTAAGGATTAAATTAAAACAAATTAAAAACAACAAGGACTAAATACAAAATAAGCCGAAAAA
* * *
28908398 ATGACACTTGGCAGCTTCTGGTGCAGTCACAC
131 ATGACACGTGGCAGCCTCTGGTGCAGTCAAAC
28908430 AGTC
1 AGTC
28908434 GGGGGATTAA
Statistics
Matches: 140, Mismatches: 24, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
161 14 0.10
162 126 0.90
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (162 bp):
AGTCAAAAGACTAATTTAAAAATCTCAAAAGATTCCAGGACCAATTTTGTAATTAAACAAAAGTT
AATTTAAGGATTAAATTAAAACAAATTAAAAACAACAAGGACTAAATACAAAATAAGCCGAAAAA
ATGACACGTGGCAGCCTCTGGTGCAGTCAAAC
Found at i:28909390 original size:22 final size:23
Alignment explanation
Indices: 28909359--28909405 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
28909349 GACAGCTTCA
*
28909359 GTTATGAATGCATGTATA-CCTG
1 GTTATGAATGCATGAATAGCCTG
* *
28909381 GTTATTAATGCTTGAATAGCCTG
1 GTTATGAATGCATGAATAGCCTG
28909404 GT
1 GT
28909406 ATTGACTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (23 bp):
GTTATGAATGCATGAATAGCCTG
Found at i:28909992 original size:6 final size:6
Alignment explanation
Indices: 28909993--28910081 Score: 69
Period size: 6 Copynumber: 14.8 Consensus size: 6
28909983 TTAAAGTTAA
* *
28909993 TTAAAT TTAAAT TTAAA- ATAAAT TTAAAT CAGTAAAT TTAAAT TTAAGA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAA-AT
* * *
28910042 -TAAAT TTAAAA ATAAAT TTAAAA TT-AAT TTAAACT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA-T TTAAA
28910082 AAATCAAAAG
Statistics
Matches: 65, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
4 1 0.02
5 11 0.17
6 41 0.63
7 7 0.11
8 5 0.08
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (6 bp):
TTAAAT
Found at i:28910014 original size:17 final size:17
Alignment explanation
Indices: 28909994--28910051 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 17
28909984 TAAAGTTAAT
28909994 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
28910011 TAAATTTAAA--T-CAG
1 TAAATTTAAATTTAAAA
*
28910025 TAAATTTAAATTTAAGA
1 TAAATTTAAATTTAAAA
28910042 TAAATTTAAA
1 TAAATTTAAA
28910052 AATAAATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
14 11 0.33
15 1 0.03
16 1 0.03
17 20 0.61
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:28910032 original size:31 final size:29
Alignment explanation
Indices: 28909994--28910083 Score: 108
Period size: 31 Copynumber: 3.0 Consensus size: 29
28909984 TAAAGTTAAT
*
28909994 TAAATTTAAATTTAAAATAAATTTAAATCAG
1 TAAATTTAAATTTAAAATAAATTTAAA--AA
*
28910025 TAAATTTAAATTTAAGATAAATTTAAAAA
1 TAAATTTAAATTTAAAATAAATTTAAAAA
* **
28910054 TAAATTTAAAATTAATTTAAACTTTAAAAA
1 TAAATTTAAATTTAAAATAAA-TTTAAAAA
28910084 ATCAAAAGCC
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
29 19 0.36
30 8 0.15
31 26 0.49
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (29 bp):
TAAATTTAAATTTAAAATAAATTTAAAAA
Found at i:28910057 original size:23 final size:23
Alignment explanation
Indices: 28910031--28910074 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
28910021 TCAGTAAATT
*
28910031 TAAATTTAAGATAAATTTAAAAA
1 TAAATTTAAAATAAATTTAAAAA
*
28910054 TAAATTTAAAATTAATTTAAA
1 TAAATTTAAAATAAATTTAAA
28910075 CTTTAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
TAAATTTAAAATAAATTTAAAAA
Found at i:28910058 original size:12 final size:11
Alignment explanation
Indices: 28910000--28910074 Score: 66
Period size: 11 Copynumber: 6.9 Consensus size: 11
28909990 TAATTAAATT
28910000 TAAATTTAAAA
1 TAAATTTAAAA
28910011 TAAATTT-AAA
1 TAAATTTAAAA
* * *
28910021 T-CA-GTAAATT
1 TAAATTTAAA-A
*
28910031 TAAATTTAAGA
1 TAAATTTAAAA
28910042 TAAATTTAAAAA
1 TAAATTT-AAAA
28910054 TAAATTTAAAA
1 TAAATTTAAAA
*
28910065 TTAATTTAAA
1 TAAATTTAAA
28910075 CTTTAAAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
8 1 0.02
9 3 0.06
10 5 0.10
11 28 0.56
12 13 0.26
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:28922091 original size:17 final size:18
Alignment explanation
Indices: 28922071--28922107 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
28922061 CTTAAGTTAA
28922071 AATA-ATATGAAA-TTTAT
1 AATATATAT-AAATTTTAT
28922088 AATATATATAAATTTTAT
1 AATATATATAAATTTTAT
28922106 AA
1 AA
28922108 GAAAAAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
AATATATATAAATTTTAT
Found at i:28923436 original size:30 final size:31
Alignment explanation
Indices: 28923383--28923442 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
28923373 TATAGGTTTA
*
28923383 AAAAATGATCTTGGATAAAAAAATATGACCT
1 AAAAATGATCTTGGATAAAAAAATAAGACCT
*
28923414 AAAAATGAGT-TTGGA-CAAAAAATAAGACC
1 AAAAATGA-TCTTGGATAAAAAAATAAGACC
28923443 AACTTTCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 12 0.46
31 13 0.50
32 1 0.04
ACGTcount: A:0.53, C:0.10, G:0.15, T:0.22
Consensus pattern (31 bp):
AAAAATGATCTTGGATAAAAAAATAAGACCT
Found at i:28924171 original size:17 final size:18
Alignment explanation
Indices: 28924141--28924174 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28924131 TAAAAATACC
*
28924141 AAAAGCCAACAAACAAAA
1 AAAAACCAACAAACAAAA
28924159 AAAAACCAA-AAACAAA
1 AAAAACCAACAAACAAA
28924175 GTCTAAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.76, C:0.21, G:0.03, T:0.00
Consensus pattern (18 bp):
AAAAACCAACAAACAAAA
Found at i:28925743 original size:17 final size:17
Alignment explanation
Indices: 28925696--28925743 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
28925686 ACGGACTGAA
28925696 CACATGGTCGTGTGAGC
1 CACATGGTCGTGTGAGC
* *
28925713 CACACGGTTGTGTGAGC
1 CACATGGTCGTGTGAGC
*
28925730 CACATGGTCATGTG
1 CACATGGTCGTGTG
28925744 CCAGACCTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.19, C:0.23, G:0.33, T:0.25
Consensus pattern (17 bp):
CACATGGTCGTGTGAGC
Found at i:28927150 original size:6 final size:6
Alignment explanation
Indices: 28927139--28927164 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
28927129 ATGACAAATA
28927139 AGGGAG AGGGAG AGGGAG AGGGAG AG
1 AGGGAG AGGGAG AGGGAG AGGGAG AG
28927165 AGTGTGAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
AGGGAG
Found at i:28930629 original size:28 final size:29
Alignment explanation
Indices: 28930538--28930673 Score: 79
Period size: 28 Copynumber: 4.7 Consensus size: 29
28930528 TGGATACCCG
*
28930538 GGGGCAAAATGGTAGATTTT-GGTGAA-ATC
1 GGGGTAAAATGGTA-ATTTTAGG-GAAGATC
* * *
28930567 GGAGTTAAAAATGG-AA-TTTAGGGAAGTTT
1 GG-GGT-AAAATGGTAATTTTAGGGAAGATC
*
28930596 GAGGGTAAAATGGTAATTTTAGTGAA-ATC
1 G-GGGTAAAATGGTAATTTTAGGGAAGATC
* * *
28930625 GGGGTTTAAAATGG-GA-TTTAGGGAAGTTTG
1 GGGG--TAAAATGGTAATTTTAGGGAAG-ATC
28930655 GGGGTAAAATGGTAATTTT
1 GGGGTAAAATGGTAATTTT
28930674 TGAAAGTTTT
Statistics
Matches: 81, Mismatches: 13, Indels: 25
0.68 0.11 0.21
Matches are distributed among these distances:
28 32 0.40
29 15 0.19
30 27 0.33
31 7 0.09
ACGTcount: A:0.33, C:0.02, G:0.33, T:0.32
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTAGGGAAGATC
Found at i:28930635 original size:30 final size:30
Alignment explanation
Indices: 28930543--28930638 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
28930533 ACCCGGGGGC
* * *
28930543 AAAATGGTAGATTTTGGTGAAATCGGAGTTA
1 AAAATGGTA-ATTTTAGTGAAATCGGGGTTT
* * *
28930574 AAAATGG-AA-TTTAGGGAAGTTTGAGGG--T
1 AAAATGGTAATTTTAGTGAA-ATCG-GGGTTT
28930602 AAAATGGTAATTTTAGTGAAATCGGGGTTT
1 AAAATGGTAATTTTAGTGAAATCGGGGTTT
28930632 AAAATGG
1 AAAATGG
28930639 GATTTAGGGA
Statistics
Matches: 50, Mismatches: 9, Indels: 13
0.69 0.12 0.18
Matches are distributed among these distances:
28 17 0.34
29 7 0.14
30 19 0.38
31 7 0.14
ACGTcount: A:0.36, C:0.02, G:0.30, T:0.31
Consensus pattern (30 bp):
AAAATGGTAATTTTAGTGAAATCGGGGTTT
Found at i:28930636 original size:58 final size:58
Alignment explanation
Indices: 28930543--28930673 Score: 208
Period size: 58 Copynumber: 2.2 Consensus size: 58
28930533 ACCCGGGGGC
*
28930543 AAAATGGTAGATTTTGGTGAAATCGGAGTTAAAAATGGAATTTAGGGAAGTTTGAGGGT
1 AAAATGGTA-ATTTTAGTGAAATCGGAGTTAAAAATGGAATTTAGGGAAGTTTGAGGGT
* * * *
28930602 AAAATGGTAATTTTAGTGAAATCGGGGTTTAAAATGGGATTTAGGGAAGTTTGGGGGT
1 AAAATGGTAATTTTAGTGAAATCGGAGTTAAAAATGGAATTTAGGGAAGTTTGAGGGT
28930660 AAAATGGTAATTTT
1 AAAATGGTAATTTT
28930674 TGAAAGTTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
58 58 0.87
59 9 0.13
ACGTcount: A:0.34, C:0.02, G:0.31, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTTAGTGAAATCGGAGTTAAAAATGGAATTTAGGGAAGTTTGAGGGT
Found at i:28930680 original size:29 final size:29
Alignment explanation
Indices: 28930590--28930703 Score: 92
Period size: 29 Copynumber: 3.9 Consensus size: 29
28930580 GAATTTAGGG
*
28930590 AAGTTTGAGGGTAAAATGGTAATTTTAGTGA
1 AAGTTTGGGGGTAAAATGGTAATTTT--TGA
* * * ** *
28930621 AA--TCGGGGTTTAAAATGG-GATTTAGGG
1 AAGTTTGGGG-GTAAAATGGTAATTTTTGA
28930648 AAGTTTGGGGGTAAAATGGTAATTTTTGA
1 AAGTTTGGGGGTAAAATGGTAATTTTTGA
*
28930677 AAGTTTTGGGGTAAAAAT-GTAATTTTT
1 AAGTTTGGGGGT-AAAATGGTAATTTTT
28930704 TGGAAATTTT
Statistics
Matches: 64, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
27 3 0.05
28 8 0.12
29 38 0.59
30 13 0.20
31 2 0.03
ACGTcount: A:0.32, C:0.01, G:0.30, T:0.37
Consensus pattern (29 bp):
AAGTTTGGGGGTAAAATGGTAATTTTTGA
Found at i:28930685 original size:30 final size:30
Alignment explanation
Indices: 28930648--28930886 Score: 254
Period size: 30 Copynumber: 8.0 Consensus size: 30
28930638 GGATTTAGGG
* *
28930648 AAGTTTGGGGGT-AAAATGGTAATTTTTG-A
1 AAGTTTTGGGGTCAAAAT-GTAATTTTGGAA
*
28930677 AAGTTTTGGGGTAAAAATGTAATTTTTTGG-A
1 AAGTTTTGGGGTCAAAATGTAA--TTTTGGAA
* * *
28930708 AA-TTTTAGGGTCAAAATATGATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
* *
28930737 AAGTGTTAGGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
* * *
28930767 AAATTTTAGGGTCAAAATGTAATTTCT-AAA
1 AAGTTTTGGGGTCAAAATGTAATTT-TGGAA
* *
28930797 AAGTTTTGGGGTCAAAATATAATTTTGAAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
*
28930827 AAGTTTTGGGGTCAAAATATAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
* *
28930857 AAGTTTTGGGGTCAACATTTAATTTCTGGA
1 AAGTTTTGGGGTCAAAATGTAATTT-TGGA
28930887 CAATTTAGGG
Statistics
Matches: 184, Mismatches: 18, Indels: 14
0.85 0.08 0.06
Matches are distributed among these distances:
28 6 0.03
29 19 0.10
30 146 0.79
31 13 0.07
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.38
Consensus pattern (30 bp):
AAGTTTTGGGGTCAAAATGTAATTTTGGAA
Found at i:28930882 original size:90 final size:89
Alignment explanation
Indices: 28930648--28930883 Score: 287
Period size: 90 Copynumber: 2.6 Consensus size: 89
28930638 GGATTTAGGG
* * * * **
28930648 AAGTTTGGGGGT-AAAATGGTAATTTTTG-AAAGTTTTGGGGTAAAAATGTAATTTTTTGGAAAT
1 AAGTTTTGGGGTCAAAAT-GTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAA-TTTCTAAAAAT
* *
28930711 TTTAGGGTCAAAATATGATTTTGGAA
64 TTTAGGGTCAAAATATAATTTTGAAA
* * * *
28930737 AAGTGTTAGGGTCAAAATGTAATTTTGGAAAAATTTTAGGGTCAAAATGTAATTTCTAAAAAGTT
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTCTAAAAA-TT
*
28930802 TTGGGGTCAAAATATAATTTTGAAA
65 TTAGGGTCAAAATATAATTTTGAAA
* * *
28930827 AAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTTGGGGTCAACATTTAATTTCT
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTCT
28930884 GGACAATTTA
Statistics
Matches: 124, Mismatches: 20, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
89 25 0.20
90 99 0.80
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (89 bp):
AAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTCTAAAAATTT
TAGGGTCAAAATATAATTTTGAAA
Found at i:28931146 original size:163 final size:162
Alignment explanation
Indices: 28930954--28931302 Score: 436
Period size: 163 Copynumber: 2.1 Consensus size: 162
28930944 GGCATCCAGA
* * * * *
28930954 AGTCAAAGGATTAGTTTGAAAATCTTGAAAAATTTTTGGACCAATTTTGTAATTAAATAAAAGTT
1 AGTCAAAGGACTAATTTGAAAACCTTGAAAAATTATTGGACCAATTTTATAATTAAATAAAAGTT
* * * * *
28931019 AATTTAAGGACTAAATTAAAATAAA-CAAAGAAGAGTCAGGGACTATATGCATAAATAAGC-CAG
66 AATTTAAGGACTAAATTAAAACAAATCAAA-AA-AGTCAGGGACTAAATGCAGAAATAAGCAAAA
*
28931082 AAAGTGACACGTGGCAGCC-CTTGGTGCAGTCAAAC
129 AAAGT-ACACGTGGCAGCCTC-TGGTCCAGTCAAAC
*
28931117 AGTCAAAGGACTAATTT-ATAAACCTTGAAAAATTATTGGGCCAATTTTATAATTAAATAAAAGT
1 AGTCAAAGGACTAATTTGA-AAACCTTGAAAAATTATTGGACCAATTTTATAATTAAATAAAAGT
* * * * * *
28931181 TGATTTAGGGATTAAATTAAAACAAATTAAAAATGTCAGGGACTAAATGTAGAAATAAGCAAAAA
65 TAATTTAAGGACTAAATTAAAACAAATCAAAAAAGTCAGGGACTAAATGCAGAAATAAGC-AAAA
28931246 AAAGTACACGTGGCAGCCTCTGGTCCAGTCAAAC
129 AAAGTACACGTGGCAGCCTCTGGTCCAGTCAAAC
* *
28931280 AGTCAAAGGATTAAATTGAAAAC
1 AGTCAAAGGACTAATTTGAAAAC
28931303 TAATTAAAAT
Statistics
Matches: 160, Mismatches: 20, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
162 24 0.15
163 125 0.78
164 11 0.07
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (162 bp):
AGTCAAAGGACTAATTTGAAAACCTTGAAAAATTATTGGACCAATTTTATAATTAAATAAAAGTT
AATTTAAGGACTAAATTAAAACAAATCAAAAAAGTCAGGGACTAAATGCAGAAATAAGCAAAAAA
AGTACACGTGGCAGCCTCTGGTCCAGTCAAAC
Found at i:28932709 original size:20 final size:20
Alignment explanation
Indices: 28932671--28932709 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
28932661 CAGGGCATGG
*
28932671 TGGAGCTTGGTGGTGGCAGA
1 TGGAGCTTGGTGGTAGCAGA
28932691 TGGAGC-TGGTGGTCAGCAG
1 TGGAGCTTGGTGGT-AGCAG
28932710 CAGCATAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.15, C:0.13, G:0.49, T:0.23
Consensus pattern (20 bp):
TGGAGCTTGGTGGTAGCAGA
Found at i:28935274 original size:28 final size:30
Alignment explanation
Indices: 28935233--28935492 Score: 119
Period size: 29 Copynumber: 8.8 Consensus size: 30
28935223 ATATTTTGAC
28935233 CCCTCAAACTTTT-CAAAATTACATATTCA
1 CCCTCAAACTTTTCCAAAATTACATATTCA
* *
28935262 CCCT-AAATTTTTCCAAAATTACATTTTCA
1 CCCTCAAACTTTTCCAAAATTACATATTCA
*** * * *
28935291 CCCCTCAAACTTTTTTGAAATCACATTTTGA
1 -CCCTCAAACTTTTCCAAAATTACATATTCA
* * * *
28935322 CCC-CTAAC--TTCCAAAAATCACATTTTGA
1 CCCTCAAACTTTTCC-AAAATTACATATTCA
* * *
28935350 TCCTAAAACTTTCCCAAAA-T-CATATTTACA
1 CCCTCAAACTTTTCCAAAATTACATA-TT-CA
* * * *
28935380 CCCT-AAACTTTTCAAAAATCACATTTTGA
1 CCCTCAAACTTTTCCAAAATTACATATTCA
* * * *
28935409 CCCCCAAAC-TTTCCTAAAATCACATTTTGA
1 CCCTCAAACTTTTCC-AAAATTACATATTCA
* * * * *
28935439 GCC-CAAACTTTTCCAAAATCATATTTTGA
1 CCCTCAAACTTTTCCAAAATTACATATTCA
* *
28935468 TCCC-AAAACTTTCCCAAAATTACAT
1 -CCCTCAAACTTTTCCAAAATTACAT
28935493 TTTTTTCCTA
Statistics
Matches: 182, Mismatches: 34, Indels: 29
0.74 0.14 0.12
Matches are distributed among these distances:
27 2 0.01
28 26 0.14
29 67 0.37
30 62 0.34
31 25 0.14
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.34
Consensus pattern (30 bp):
CCCTCAAACTTTTCCAAAATTACATATTCA
Found at i:28935359 original size:29 final size:30
Alignment explanation
Indices: 28935203--28935495 Score: 203
Period size: 30 Copynumber: 9.9 Consensus size: 30
28935193 CCCAAGAGAT
* *
28935203 CCCTAAAA-TTTCTAAAAATCATATTTTGA
1 CCCTAAAACTTTCCAAAAATCACATTTTGA
* * * * *
28935232 CCCCTCAAACTTTTC-AAAATTACATATTCA
1 -CCCTAAAACTTTCCAAAAATCACATTTTGA
** * *
28935262 CCCTAAATTTTTCC-AAAATTACATTTTCA
1 CCCTAAAACTTTCCAAAAATCACATTTTGA
* ****
28935291 CCCCTCAAACTTTTTTGAAATCACATTTTGA
1 -CCCTAAAACTTTCCAAAAATCACATTTTGA
28935322 CCCCT--AAC-TTCCAAAAATCACATTTTGA
1 -CCCTAAAACTTTCCAAAAATCACATTTTGA
* * * **
28935350 TCCTAAAACTTTCCCAAAATCATATTTACA
1 CCCTAAAACTTTCCAAAAATCACATTTTGA
*
28935380 CCCT-AAACTTTTCAAAAATCACATTTTGA
1 CCCTAAAACTTTCCAAAAATCACATTTTGA
** *
28935409 CCCCCAAACTTTCCTAAAATCACATTTTGA
1 CCCTAAAACTTTCCAAAAATCACATTTTGA
*
28935439 GCCC--AAACTTTTCC-AAAATCATATTTTGA
1 -CCCTAAAAC-TTTCCAAAAATCACATTTTGA
* *
28935468 TCCC-AAAACTTTCCCAAAATTACATTTT
1 -CCCTAAAACTTTCCAAAAATCACATTTT
28935496 TTTCCTAAAT
Statistics
Matches: 210, Mismatches: 42, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
27 3 0.01
28 16 0.08
29 79 0.38
30 89 0.42
31 23 0.11
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.35
Consensus pattern (30 bp):
CCCTAAAACTTTCCAAAAATCACATTTTGA
Found at i:28935493 original size:59 final size:59
Alignment explanation
Indices: 28935217--28935495 Score: 262
Period size: 59 Copynumber: 4.7 Consensus size: 59
28935207 AAAATTTCTA
* * * * *
28935217 AAAATCATATTTTGACCCCTCAAACTTT-TCAAAATTACATATTCACCCTAAATTTTTCC
1 AAAATCACATTTTGACCCC-CAAACTTTCCCAAAATCACATTTTCACCCTAAACTTTTCC
* * **** *
28935276 AAAATTACATTTTCACCCCTCAAACTTTTTTGAAATCACATTTTGACCCCT-AAC--TTCC
1 AAAATCACATTTTGACCCC-CAAACTTTCCCAAAATCACATTTTCA-CCCTAAACTTTTCC
* ** * * *
28935334 AAAAATCACATTTTGATCCTAAAACTTTCCCAAAATCATATTTACACCCTAAACTTTTCA
1 -AAAATCACATTTTGACCCCCAAACTTTCCCAAAATCACATTTTCACCCTAAACTTTTCC
* *
28935394 AAAATCACATTTTGACCCCCAAACTTTCCTAAAATCACATTTTGAGCCC-AAACTTTTCC
1 AAAATCACATTTTGACCCCCAAACTTTCCCAAAATCACATTTTCA-CCCTAAACTTTTCC
* * * *
28935453 AAAATCATATTTTGATCCCAAAACTTTCCCAAAATTACATTTT
1 AAAATCACATTTTGACCCCCAAACTTTCCCAAAATCACATTTT
28935496 TTTCCTAAAT
Statistics
Matches: 178, Mismatches: 35, Indels: 14
0.78 0.15 0.06
Matches are distributed among these distances:
57 4 0.02
58 25 0.14
59 125 0.70
60 20 0.11
61 4 0.02
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.35
Consensus pattern (59 bp):
AAAATCACATTTTGACCCCCAAACTTTCCCAAAATCACATTTTCACCCTAAACTTTTCC
Found at i:28935514 original size:118 final size:118
Alignment explanation
Indices: 28935216--28935495 Score: 334
Period size: 118 Copynumber: 2.4 Consensus size: 118
28935206 TAAAATTTCT
* * * * *
28935216 AAAAATCATATTTTGACCCCTCAAACTTT-TCAAAATTACATATTCACCCTAAATTTTTCC-AAA
1 AAAAATCATATTTTGATCCC-AAAACTTTCCCAAAATTACATTTTCACCCTAAA-CTTTCCAAAA
* ** * *
28935279 ATTACATTTTCACCCCTCAAACTTTTTTGAAATCACATTTTGACCCCTAACTTCC
64 ATCACATTTTCACCCCTCAAACTTTCCTAAAATCACATTTTGACCCCAAACTTCC
* * * * * *
28935334 AAAAATCACATTTTGATCCTAAAACTTTCCCAAAATCATATTTACACCCTAAACTTTTCAAAAAT
1 AAAAATCATATTTTGATCCCAAAACTTTCCCAAAATTACATTTTCACCCTAAACTTTCCAAAAAT
* *
28935399 CACATTTTGACCCC-CAAACTTTCCTAAAATCACATTTTGAGCCCAAACTTTTCC
66 CACATTTTCACCCCTCAAACTTTCCTAAAATCACATTTTGACCCCAAAC--TTCC
28935453 -AAAATCATATTTTGATCCCAAAACTTTCCCAAAATTACATTTT
1 AAAAATCATATTTTGATCCCAAAACTTTCCCAAAATTACATTTT
28935496 TTTCCTAAAT
Statistics
Matches: 135, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
117 40 0.30
118 91 0.67
119 4 0.03
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (118 bp):
AAAAATCATATTTTGATCCCAAAACTTTCCCAAAATTACATTTTCACCCTAAACTTTCCAAAAAT
CACATTTTCACCCCTCAAACTTTCCTAAAATCACATTTTGACCCCAAACTTCC
Found at i:28935532 original size:118 final size:115
Alignment explanation
Indices: 28935216--28935532 Score: 316
Period size: 118 Copynumber: 2.7 Consensus size: 115
28935206 TAAAATTTCT
* * * * *
28935216 AAAAATCATATTTTGACCCCTCAAACTTT-TCAAAATTACATATTCACCCTAAATTTTTCCAAAA
1 AAAAATCATATTTTGATCCC-AAAACTTTCCCAAAATTACATTTTCACCCTAAA-CTTTCCAAAA
** * *
28935280 TTACATTTTCACCCCTCAAACTTTTTTGAAATCACATTTTGACCCCTAACTTCC
64 TT-CATTTTCACCCC-CAAACTTTCCTAAAATCACATTTTGACCCCAAACTTCC
* * * * * *
28935334 AAAAATCACATTTTGATCCTAAAACTTTCCCAAAATCATATTTACACCCTAAACTTTTCAAAAAT
1 AAAAATCATATTTTGATCCCAAAACTTTCCCAAAATTACATTTTCACCCTAAAC-TTTCCAAAAT
* * *
28935399 CACATTTTGACCCCCAAACTTTCCTAAAATCACATTTTGAGCCCAAACTTTTCC
65 -TCATTTTCACCCCCAAACTTTCCTAAAATCACATTTTGACCCCAAAC--TTCC
***
28935453 -AAAATCATATTTTGATCCCAAAACTTTCCCAAAATTACATTTTTTTCCTAAA-TTCTCCAAAAC
1 AAAAATCATATTTTGATCCCAAAACTTTCCCAAAATTACATTTTCACCCTAAACTT-TCCAAAA-
*
28935516 TTCATTTTTCAACCCCA
64 TTCA-TTTTCACCCCCA
28935533 TTTTTTTATT
Statistics
Matches: 161, Mismatches: 30, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
116 2 0.01
117 44 0.27
118 111 0.69
119 4 0.02
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (115 bp):
AAAAATCATATTTTGATCCCAAAACTTTCCCAAAATTACATTTTCACCCTAAACTTTCCAAAATT
CATTTTCACCCCCAAACTTTCCTAAAATCACATTTTGACCCCAAACTTCC
Found at i:28944500 original size:29 final size:30
Alignment explanation
Indices: 28944466--28944565 Score: 120
Period size: 30 Copynumber: 3.4 Consensus size: 30
28944456 GGTAATATCA
*
28944466 TAATTTTGGAGAAGTTTA-GGGTCAAAATG
1 TAATTTTAGAGAAGTTTAGGGGTCAAAATG
*
28944495 -AGATTTTAGAGAAATTTAGGGGTCAAAATG
1 TA-ATTTTAGAGAAGTTTAGGGGTCAAAATG
*
28944525 TAATTTTAGAAAAGTTT-GGGG--AGAAATG
1 TAATTTTAGAGAAGTTTAGGGGTCA-AAATG
28944553 TAATTTTAGAGAA
1 TAATTTTAGAGAA
28944566 AAACAAGGGC
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
27 1 0.02
28 18 0.29
29 18 0.29
30 24 0.39
31 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.26, T:0.33
Consensus pattern (30 bp):
TAATTTTAGAGAAGTTTAGGGGTCAAAATG
Found at i:28944520 original size:30 final size:30
Alignment explanation
Indices: 28944466--28944566 Score: 115
Period size: 29 Copynumber: 3.5 Consensus size: 30
28944456 GGTAATATCA
* *
28944466 TAATTTTGGAGAAGTTTA-GGGTCAAAATG
1 TAATTTTAGAGAAATTTAGGGGTCAAAATG
28944495 -AGATTTTAGAGAAATTTAGGGGTCAAAATG
1 TA-ATTTTAGAGAAATTTAGGGGTCAAAATG
28944525 TAATTTTAGA-AAAGTTT-GGGG--AGAAATG
1 TAATTTTAGAGAAA-TTTAGGGGTCA-AAATG
28944553 TAATTTTAGAGAAA
1 TAATTTTAGAGAAA
28944567 AACAAGGGCT
Statistics
Matches: 64, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
27 1 0.02
28 16 0.25
29 24 0.38
30 22 0.34
31 1 0.02
ACGTcount: A:0.40, C:0.02, G:0.26, T:0.33
Consensus pattern (30 bp):
TAATTTTAGAGAAATTTAGGGGTCAAAATG
Found at i:28945637 original size:15 final size:15
Alignment explanation
Indices: 28945617--28945647 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28945607 TTTTATTTAA
28945617 AATTATATATTTATT
1 AATTATATATTTATT
*
28945632 AATTATGTATTTATT
1 AATTATATATTTATT
28945647 A
1 A
28945648 CACTTTGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
AATTATATATTTATT
Done.