Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001838.1 Hibiscus syriacus cultivar Beakdansim tig00003721_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3924084
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 18
Found at i:2571879 original size:41 final size:43
Alignment explanation
Indices: 2571815--2571931 Score: 116
Period size: 42 Copynumber: 2.8 Consensus size: 43
2571805 AAAAACATTC
* * * *
2571815 TGCTCGAGAGTCTTA-TAGATGACCTGAAGGACTT-ATCAACA
1 TGCTCGAAAGACTTACTAGATGACCCGAAGGACTTAAACAACA
* * *
2571856 TGCTCGAAAGACTTACTAG-TGACCCAAAGGATTTAAACATCA
1 TGCTCGAAAGACTTACTAGATGACCCGAAGGACTTAAACAACA
* * *
2571898 TGATCGAAAGACTTACT-GATGGCCGGAAGGACTT
1 TGCTCGAAAGACTTACTAGATGACCCGAAGGACTT
2571932 GTTTCTAAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
41 26 0.43
42 35 0.57
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (43 bp):
TGCTCGAAAGACTTACTAGATGACCCGAAGGACTTAAACAACA
Found at i:2572271 original size:74 final size:74
Alignment explanation
Indices: 2572147--2572370 Score: 308
Period size: 74 Copynumber: 3.0 Consensus size: 74
2572137 CCAAAGGATT
* * * ** * *
2572147 TAATCATCAAGAACTCTTTGAAAATGAAAGTTGGCTTGTTTAAAACTTCATTTGAAAACATCATA
1 TAATCATCAAGAAATCTTTGAAAATCAAACTTGAATTCTTTAAAAATTCATTTGAAAACATCATA
*
2572212 TCAATCGGG
66 TCAGTCGGG
* * *
2572221 TAATCATTAAGAAATCTTTGAAAATCAAACTTGTATTCTTTAAAAATTCATTTGAAAACTTCATA
1 TAATCATCAAGAAATCTTTGAAAATCAAACTTGAATTCTTTAAAAATTCATTTGAAAACATCATA
*
2572286 TCGGTCGGG
66 TCAGTCGGG
*
2572295 TAAT-ATCAAGAAACCTTTGAAAATCAAACTT-AACTTCTTTAAAAATTCATTTGAAAACATCAT
1 TAATCATCAAGAAATCTTTGAAAATCAAACTTGAA-TTCTTTAAAAATTCATTTGAAAACATCAT
2572358 ATCAGTCGGG
65 ATCAGTCGGG
2572368 TAA
1 TAA
2572371 CATACCCTAC
Statistics
Matches: 133, Mismatches: 16, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
72 1 0.01
73 65 0.49
74 67 0.50
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (74 bp):
TAATCATCAAGAAATCTTTGAAAATCAAACTTGAATTCTTTAAAAATTCATTTGAAAACATCATA
TCAGTCGGG
Found at i:2572339 original size:73 final size:74
Alignment explanation
Indices: 2572147--2572370 Score: 301
Period size: 73 Copynumber: 3.0 Consensus size: 74
2572137 CCAAAGGATT
* * ** * *
2572147 TAATCATCAAG-AACTCTTTGAAAATGAAAGTTGGCTTGTTTAAAACTTCATTTGAAAACATCAT
1 TAATCATCAAGAAAC-CTTTGAAAATCAAACTTAACTTCTTTAAAAATTCATTTGAAAACATCAT
*
2572211 ATCAATCGGG
65 ATCAGTCGGG
* * * *
2572221 TAATCATTAAGAAATCTTTGAAAATCAAACTTGTA-TTCTTTAAAAATTCATTTGAAAACTTCAT
1 TAATCATCAAGAAACCTTTGAAAATCAAACTT-AACTTCTTTAAAAATTCATTTGAAAACATCAT
*
2572285 ATCGGTCGGG
65 ATCAGTCGGG
2572295 TAAT-ATCAAGAAACCTTTGAAAATCAAACTTAACTTCTTTAAAAATTCATTTGAAAACATCATA
1 TAATCATCAAGAAACCTTTGAAAATCAAACTTAACTTCTTTAAAAATTCATTTGAAAACATCATA
2572359 TCAGTCGGG
66 TCAGTCGGG
2572368 TAA
1 TAA
2572371 CATACCCTAC
Statistics
Matches: 131, Mismatches: 16, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
72 1 0.01
73 65 0.50
74 63 0.48
75 2 0.02
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (74 bp):
TAATCATCAAGAAACCTTTGAAAATCAAACTTAACTTCTTTAAAAATTCATTTGAAAACATCATA
TCAGTCGGG
Found at i:2574916 original size:21 final size:24
Alignment explanation
Indices: 2574889--2574948 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 24
2574879 AACCAAAAGG
2574889 AGTAGTATCGGTACCA-TA-ACTA
1 AGTAGTATCGGTACCACTACACTA
*
2574911 AG-AGTATCGGTACTACTACACTA
1 AGTAGTATCGGTACCACTACACTA
*
2574934 AGTAGTATCGATACC
1 AGTAGTATCGGTACC
2574949 GTATATGGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 12 0.38
22 4 0.12
23 6 0.19
24 10 0.31
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (24 bp):
AGTAGTATCGGTACCACTACACTA
Found at i:2578558 original size:18 final size:18
Alignment explanation
Indices: 2578535--2578571 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2578525 TGTCGAAATG
2578535 GTCCTTAAGCTCGGGAAA
1 GTCCTTAAGCTCGGGAAA
2578553 GTCCTTAAGCTCGGGAAA
1 GTCCTTAAGCTCGGGAAA
2578571 G
1 G
2578572 CCACTCGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.22
Consensus pattern (18 bp):
GTCCTTAAGCTCGGGAAA
Found at i:2584547 original size:14 final size:14
Alignment explanation
Indices: 2584525--2584589 Score: 76
Period size: 14 Copynumber: 4.6 Consensus size: 14
2584515 TCTAGTCACT
* *
2584525 GAGTTAACTCATCC
1 GAGTCAACTCGTCC
*
2584539 GAGTCAACTCGGTCT
1 GAGTCAACTC-GTCC
* *
2584554 GAGTCAACCCGTCT
1 GAGTCAACTCGTCC
2584568 GAGTCAACTCGTCC
1 GAGTCAACTCGTCC
2584582 GAGTCAAC
1 GAGTCAAC
2584590 CCGTAAACTT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
14 33 0.75
15 11 0.25
ACGTcount: A:0.25, C:0.31, G:0.22, T:0.23
Consensus pattern (14 bp):
GAGTCAACTCGTCC
Found at i:2584556 original size:29 final size:29
Alignment explanation
Indices: 2584523--2584591 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
2584513 GGTCTAGTCA
* *
2584523 CTGAGTTAACTCATCCGAGTCAACTCGGT
1 CTGAGTCAACCCATCCGAGTCAACTCGGT
* *
2584552 CTGAGTCAACCCGTCTGAGTCAACTC-GT
1 CTGAGTCAACCCATCCGAGTCAACTCGGT
*
2584580 CCGAGTCAACCC
1 CTGAGTCAACCC
2584592 GTAAACTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
28 13 0.37
29 22 0.63
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.23
Consensus pattern (29 bp):
CTGAGTCAACCCATCCGAGTCAACTCGGT
Found at i:2584592 original size:28 final size:29
Alignment explanation
Indices: 2584539--2584593 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
2584529 TAACTCATCC
*
2584539 GAGTCAACTCGGTCTGAGTCAACCCGTCT
1 GAGTCAACTCGGTCCGAGTCAACCCGTCT
2584568 GAGTCAACTC-GTCCGAGTCAACCCGT
1 GAGTCAACTCGGTCCGAGTCAACCCGT
2584594 AAACTTTGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 15 0.60
29 10 0.40
ACGTcount: A:0.22, C:0.33, G:0.24, T:0.22
Consensus pattern (29 bp):
GAGTCAACTCGGTCCGAGTCAACCCGTCT
Found at i:2588221 original size:29 final size:28
Alignment explanation
Indices: 2588187--2588269 Score: 112
Period size: 29 Copynumber: 2.9 Consensus size: 28
2588177 GGTCCAGTCA
2588187 CCGAGTCAACTGGGTCTGAGTCAACCAGT
1 CCGAGTCAACT-GGTCTGAGTCAACCAGT
* *
2588216 CCGAGTCAACTCGGTCTGAGTTAACCTGT
1 CCGAGTCAACT-GGTCTGAGTCAACCAGT
* *
2588245 CTGAGTCAACTCGTCTGAGTCAACC
1 CCGAGTCAACTGGTCTGAGTCAACC
2588270 CGTTGACTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 12 0.25
29 36 0.75
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.24
Consensus pattern (28 bp):
CCGAGTCAACTGGTCTGAGTCAACCAGT
Found at i:2588223 original size:14 final size:13
Alignment explanation
Indices: 2588200--2588269 Score: 77
Period size: 14 Copynumber: 5.0 Consensus size: 13
2588190 AGTCAACTGG
2588200 GTCTGAGTCAACC
1 GTCTGAGTCAACC
*
2588213 AGTCCGAGTCAACTC
1 -GTCTGAGTCAAC-C
*
2588228 GGTCTGAGTTAACC
1 -GTCTGAGTCAACC
2588242 TGTCTGAGTCAACTC
1 -GTCTGAGTCAAC-C
2588257 GTCTGAGTCAACC
1 GTCTGAGTCAACC
2588270 CGTTGACTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
13 1 0.02
14 35 0.73
15 12 0.25
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.26
Consensus pattern (13 bp):
GTCTGAGTCAACC
Found at i:2591414 original size:22 final size:25
Alignment explanation
Indices: 2591371--2591423 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
2591361 TGAAAATATG
* *
2591371 TTTTATTTTTTTATACTGAT-AATT-
1 TTTTACTTTTGTATAC-GATAAATTA
2591395 TTTTACTTTTGTATAC-ATAAATTA
1 TTTTACTTTTGTATACGATAAATTA
2591419 TTTTA
1 TTTTA
2591424 TGAGTTTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 2 0.08
23 4 0.16
24 19 0.76
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (25 bp):
TTTTACTTTTGTATACGATAAATTA
Found at i:2597379 original size:21 final size:22
Alignment explanation
Indices: 2597343--2597383 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2597333 TTAAATATTA
*
2597343 TAAAGGTAGTATCGATACTCAT
1 TAAAGGTAGTACCGATACTCAT
2597365 TAAAGG-AGTACCGATACTC
1 TAAAGGTAGTACCGATACTC
2597384 CCTGTCCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (22 bp):
TAAAGGTAGTACCGATACTCAT
Found at i:2612290 original size:2 final size:2
Alignment explanation
Indices: 2612285--2612330 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2612275 ATATTTCACA
2612285 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
2612327 AT AT
1 AT AT
2612331 GTTTAATATC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2613178 original size:45 final size:45
Alignment explanation
Indices: 2613114--2613203 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
2613104 ATAACTAATT
2613114 TAAGAATCACTTATCATTTGTACTTGTAACTTTTCCCCACATCAA
1 TAAGAATCACTTATCATTTGTACTTGTAACTTTTCCCCACATCAA
2613159 TAAGAATCACTTATCATTTGTACTTGTAACTTTTCCCCACATCAA
1 TAAGAATCACTTATCATTTGTACTTGTAACTTTTCCCCACATCAA
2613204 ATTATAAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (45 bp):
TAAGAATCACTTATCATTTGTACTTGTAACTTTTCCCCACATCAA
Found at i:2615967 original size:2 final size:2
Alignment explanation
Indices: 2615960--2616034 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
2615950 ACCCTACAGA
2615960 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2616002 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2616035 ATATATATAT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2616039 original size:2 final size:2
Alignment explanation
Indices: 2616034--2616060 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2616024 TCTCTCTCTC
2616034 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2616061 GCAAAATGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2617683 original size:15 final size:15
Alignment explanation
Indices: 2617663--2617731 Score: 50
Period size: 15 Copynumber: 4.3 Consensus size: 15
2617653 AATGTAAAAT
2617663 ATAAAATAAAAATAC
1 ATAAAATAAAAATAC
2617678 ATAAAATACAAAAAAATCAC
1 ATAAAAT----AAAAAT-AC
*
2617698 AT-AAATTAAAATATC
1 ATAAAATAAAAATA-C
* *
2617713 ATAAAATATAATTAC
1 ATAAAATAAAAATAC
2617728 ATAA
1 ATAA
2617732 GTAATGGTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
14 1 0.02
15 20 0.47
16 8 0.19
19 10 0.23
20 4 0.09
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.25
Consensus pattern (15 bp):
ATAAAATAAAAATAC
Found at i:2621522 original size:10 final size:10
Alignment explanation
Indices: 2621507--2621540 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
2621497 CGAAGACTTC
2621507 CTCTCTTTCT
1 CTCTCTTTCT
*
2621517 CTCTCTTTTT
1 CTCTCTTTCT
*
2621527 CTCTCTGTCT
1 CTCTCTTTCT
2621537 CTCT
1 CTCT
2621541 AATGTTCATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.00, C:0.38, G:0.03, T:0.59
Consensus pattern (10 bp):
CTCTCTTTCT
Found at i:2622216 original size:16 final size:17
Alignment explanation
Indices: 2622179--2622221 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
2622169 AATAAAATTT
2622179 TAAAATAAATATCATCAA
1 TAAAATAAATA-CATCAA
*
2622197 TAAAATAAATA-ATTAA
1 TAAAATAAATACATCAA
2622213 TAAAATAAA
1 TAAAATAAA
2622222 ATTTAAGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 13 0.54
18 11 0.46
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (17 bp):
TAAAATAAATACATCAA
Found at i:2622287 original size:16 final size:17
Alignment explanation
Indices: 2622254--2622292 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
2622244 AATAATTTTC
2622254 AAAATAAATATCATTAAT
1 AAAATAAATA-CATTAAT
2622272 AAAATAAATA-ATTAAT
1 AAAATAAATACATTAAT
*
2622288 CAAAT
1 AAAAT
2622293 TTTAAGATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 10 0.50
18 10 0.50
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAATAAATACATTAAT
Found at i:2623370 original size:8 final size:8
Alignment explanation
Indices: 2623357--2623424 Score: 59
Period size: 8 Copynumber: 8.4 Consensus size: 8
2623347 TTTTATTATA
2623357 TTTAATTT
1 TTTAATTT
2623365 TTTAATTT
1 TTTAATTT
2623373 TTT-ATTT
1 TTTAATTT
*
2623380 ATTTAAGTAT
1 -TTTAA-TTT
*
2623390 TTAAATTT
1 TTTAATTT
*
2623398 TTTAATAT
1 TTTAATTT
2623406 TTT-ATTT
1 TTTAATTT
*
2623413 AATTAATTT
1 -TTTAATTT
2623422 TTT
1 TTT
2623425 TGTAGATATA
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
7 7 0.15
8 29 0.62
9 9 0.19
10 2 0.04
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.69
Consensus pattern (8 bp):
TTTAATTT
Found at i:2623375 original size:25 final size:25
Alignment explanation
Indices: 2623347--2623424 Score: 81
Period size: 24 Copynumber: 3.2 Consensus size: 25
2623337 TTAATATATA
2623347 TTTTATTATATTTAATTTTTTAATT
1 TTTTATTATATTTAATTTTTTAATT
* *
2623372 TTTTATT-TATTTAAGTATTTAAATT
1 TTTTATTATATTTAA-TTTTTTAATT
* *
2623397 TTTTA--ATATTTTATTTAATTAATT
1 TTTTATTATATTTAATTT-TTTAATT
2623421 TTTT
1 TTTT
2623425 TGTAGATATA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
23 2 0.05
24 22 0.50
25 20 0.45
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.69
Consensus pattern (25 bp):
TTTTATTATATTTAATTTTTTAATT
Found at i:2623402 original size:33 final size:32
Alignment explanation
Indices: 2623330--2623418 Score: 103
Period size: 33 Copynumber: 2.8 Consensus size: 32
2623320 TATTCTCTTA
* * *
2623330 TAATTGTTTAATA-TATATTTTATT-A-TATT
1 TAATTTTTTAATATTTTATTTAATTAAGTATT
* *
2623359 TAATTTTTTAATTTTTTATTTATTTAAGTATT
1 TAATTTTTTAATATTTTATTTAATTAAGTATT
2623391 TAAATTTTTTAATATTTTATTTAATTAA
1 T-AATTTTTTAATATTTTATTTAATTAA
2623419 TTTTTTTGTA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
29 11 0.22
30 8 0.16
31 1 0.02
32 5 0.10
33 24 0.49
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (32 bp):
TAATTTTTTAATATTTTATTTAATTAAGTATT
Found at i:2625754 original size:34 final size:33
Alignment explanation
Indices: 2625687--2625774 Score: 99
Period size: 34 Copynumber: 2.6 Consensus size: 33
2625677 TAATACTTAC
*
2625687 TTTATTTCGTT-AATTTGGTTGGATTTATTTTAA
1 TTTATTTTGTTAAATTT-GTTGGATTTATTTTAA
2625720 TTTATTTTGTTAAATTTGTTGGACTTT-TTGTTAA
1 TTTATTTTGTTAAATTTGTTGGA-TTTATT-TTAA
* *
2625754 TGTATTTTGGTTAATTTTGTT
1 TTTATTTT-GTTAAATTTGTT
2625775 TATTACCATT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
33 18 0.38
34 19 0.40
35 11 0.23
ACGTcount: A:0.19, C:0.02, G:0.16, T:0.62
Consensus pattern (33 bp):
TTTATTTTGTTAAATTTGTTGGATTTATTTTAA
Found at i:2629803 original size:3 final size:3
Alignment explanation
Indices: 2629795--2629831 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2629785 CATGTCAACA
2629795 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
2629832 CCATAACAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2640247 original size:25 final size:24
Alignment explanation
Indices: 2640197--2640247 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 24
2640187 AAAGTGTTCG
* * *
2640197 AATATAACAAAAAACCATCAACAA
1 AATACAACAAAAAAACAACAACAA
*
2640221 AATACAACTAAAAAAACAACAAGAA
1 AATACAAC-AAAAAAACAACAACAA
2640246 AA
1 AA
2640248 ATAGAAAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.71, C:0.18, G:0.02, T:0.10
Consensus pattern (24 bp):
AATACAACAAAAAAACAACAACAA
Found at i:2640263 original size:14 final size:16
Alignment explanation
Indices: 2640241--2640279 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
2640231 AAAAAACAAC
2640241 AAGAAAAAT-A-GAAA
1 AAGAAAAATGAGGAAA
2640255 AAGAAAAATGAGGAAA
1 AAGAAAAATGAGGAAA
*
2640271 AAGGAAAAT
1 AAGAAAAAT
2640280 TTTGATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.41
15 1 0.05
16 12 0.55
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.08
Consensus pattern (16 bp):
AAGAAAAATGAGGAAA
Found at i:2643639 original size:22 final size:22
Alignment explanation
Indices: 2643614--2643658 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2643604 AATCAATGTT
*
2643614 AAATAAAATAAAATAAAATAAA
1 AAATAAAATAAAATAAAACAAA
* * *
2643636 AAATATATTAAATTAAAACAAA
1 AAATAAAATAAAATAAAACAAA
2643658 A
1 A
2643659 CAATCATTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (22 bp):
AAATAAAATAAAATAAAACAAA
Found at i:2644721 original size:3 final size:3
Alignment explanation
Indices: 2644708--2644788 Score: 69
Period size: 3 Copynumber: 27.0 Consensus size: 3
2644698 CAAAAACTGA
* *
2644708 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT -AG AAT AAA AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* * *
2644752 AAT ATT AAT -AT AAT ATAT AAT AAA AACT AAA AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AA-T AAT AAT AAT
2644789 TTGTTTTCAA
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
2 5 0.08
3 49 0.79
4 8 0.13
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2644847 original size:39 final size:38
Alignment explanation
Indices: 2644798--2644931 Score: 153
Period size: 39 Copynumber: 3.4 Consensus size: 38
2644788 TTTGTTTTCA
* * *
2644798 AAAATTATATATTATATATG-TTTCCAAAAAATCATTTTT
1 AAAACTATATAATATATATGCTTT-C-AAAAATTATTTTT
* * *
2644837 AAAACTATATATTATATATGCTTTCAAAAATTGTTTTC
1 AAAACTATATAATATATATGCTTTCAAAAATTATTTTT
* *
2644875 GAAACTATATAATATATATGTTTTTCAAAAATTATTTTT
1 AAAACTATATAATATATATG-CTTTCAAAAATTATTTTT
2644914 CAAAACTATATAATATAT
1 -AAAACTATATAATATAT
2644932 TTCAATTTTT
Statistics
Matches: 82, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
38 28 0.34
39 35 0.43
40 19 0.23
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (38 bp):
AAAACTATATAATATATATGCTTTCAAAAATTATTTTT
Found at i:2644990 original size:36 final size:37
Alignment explanation
Indices: 2644949--2645029 Score: 110
Period size: 37 Copynumber: 2.2 Consensus size: 37
2644939 TTTTTTAAAT
*
2644949 TATATATTATACATTTTC-AAAAAAAAATTTCAAAAC
1 TATATATTATACATTTTCAAAAAAAAAAATTCAAAAC
* **
2644985 TATATAATATATGTTTTCAAAAAAAAAAATTCAAAAC
1 TATATATTATACATTTTCAAAAAAAAAAATTCAAAAC
*
2645022 CATATATT
1 TATATATT
2645030 TATGATATGT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
36 15 0.39
37 23 0.61
ACGTcount: A:0.53, C:0.10, G:0.01, T:0.36
Consensus pattern (37 bp):
TATATATTATACATTTTCAAAAAAAAAAATTCAAAAC
Found at i:2646948 original size:21 final size:22
Alignment explanation
Indices: 2646922--2646968 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
2646912 AACACCTAAC
*
2646922 TTTGAATTC-TAAGCAGCCCCA
1 TTTGAATGCTTAAGCAGCCCCA
* *
2646943 TTTGAATGCTTTAGCCGCCCCA
1 TTTGAATGCTTAAGCAGCCCCA
2646965 TTTG
1 TTTG
2646969 TTGTTTTTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (22 bp):
TTTGAATGCTTAAGCAGCCCCA
Found at i:2646987 original size:24 final size:25
Alignment explanation
Indices: 2646955--2647013 Score: 84
Period size: 27 Copynumber: 2.3 Consensus size: 25
2646945 TGAATGCTTT
2646955 AGCCGCCCCATTTG-TTGTTTTTCC
1 AGCCGCCCCATTTGATTGTTTTTCC
*
2646979 AGCCGCCCCATTTGCATTTGTTTTTCT
1 AGCCGCCCCATTTG-A-TTGTTTTTCC
2647006 AGCCGCCC
1 AGCCGCCC
2647014 ATGTTTTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
24 14 0.45
27 17 0.55
ACGTcount: A:0.10, C:0.36, G:0.17, T:0.37
Consensus pattern (25 bp):
AGCCGCCCCATTTGATTGTTTTTCC
Found at i:2650702 original size:22 final size:20
Alignment explanation
Indices: 2650683--2650757 Score: 53
Period size: 23 Copynumber: 3.5 Consensus size: 20
2650673 AGAGGGAATC
2650683 GATACCCCCTTAAAGGGGAACT
1 GATACCCCCTT-AA-GGGAACT
*
2650705 GATTCCCCCTTTGAATGGGAACT
1 GATACCCCC-TT-AA-GGGAACT
* *
2650728 GATTCCCTCCTTTAGGGAA-T
1 GATACCC-CCTTAAGGGAACT
2650748 CGATACCCCC
1 -GATACCCCC
2650758 ATGAGTTCTA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
20 3 0.07
21 11 0.24
22 9 0.20
23 20 0.44
24 2 0.04
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (20 bp):
GATACCCCCTTAAGGGAACT
Found at i:2650746 original size:21 final size:22
Alignment explanation
Indices: 2650687--2650741 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 22
2650677 GGAATCGATA
* *
2650687 CCCCCTTAAAGGGGAACTGATT
1 CCCCCTTTAATGGGAACTGATT
2650709 CCCCCTTTGAATGGGAACTGATT
1 CCCCCTTT-AATGGGAACTGATT
2650732 CCCTCCTTTA
1 CCC-CCTTTA
2650742 GGGAATCGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 7 0.24
23 17 0.59
24 5 0.17
ACGTcount: A:0.22, C:0.31, G:0.18, T:0.29
Consensus pattern (22 bp):
CCCCCTTTAATGGGAACTGATT
Found at i:2657520 original size:30 final size:30
Alignment explanation
Indices: 2657486--2657553 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
2657476 TGGGATGATT
2657486 TTGAAGCTAAATGGATTAGGGTATTTATAG
1 TTGAAGCTAAATGGATTAGGGTATTTATAG
*
2657516 TTGAAGCTAAATGGATTAGGTTATTTATAG
1 TTGAAGCTAAATGGATTAGGGTATTTATAG
2657546 TTGAAGCT
1 TTGAAGCT
2657554 TAAGGACTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.32, C:0.04, G:0.25, T:0.38
Consensus pattern (30 bp):
TTGAAGCTAAATGGATTAGGGTATTTATAG
Found at i:2657782 original size:2 final size:2
Alignment explanation
Indices: 2657775--2657818 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2657765 TTTGTTTTGC
2657775 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
2657817 AT
1 AT
2657819 GTGTGTGTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2657823 original size:2 final size:2
Alignment explanation
Indices: 2657818--2657858 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2657808 TATATATATA
*
2657818 TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2657859 TGCGTTAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.02, C:0.00, G:0.46, T:0.51
Consensus pattern (2 bp):
TG
Found at i:2659659 original size:20 final size:20
Alignment explanation
Indices: 2659634--2659674 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
2659624 GAAAAAATCG
2659634 CATTGCGATAATATTGTTTA
1 CATTGCGATAATATTGTTTA
*
2659654 CATTGCGATAGTATTGTTTA
1 CATTGCGATAATATTGTTTA
2659674 C
1 C
2659675 CTATATCGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (20 bp):
CATTGCGATAATATTGTTTA
Found at i:2659715 original size:20 final size:20
Alignment explanation
Indices: 2659690--2659736 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
2659680 TCGGTAATTA
2659690 GCGTTGCAAATTTGAAAATC
1 GCGTTGCAAATTTGAAAATC
*
2659710 GCGTTGCGAATTTGAAAATC
1 GCGTTGCAAATTTGAAAATC
*
2659730 GCATTGC
1 GCGTTGC
2659737 GATAGTACTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (20 bp):
GCGTTGCAAATTTGAAAATC
Found at i:2659754 original size:20 final size:20
Alignment explanation
Indices: 2659731--2659770 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2659721 TTGAAAATCG
2659731 CATTGCGATAGTACTGTTTA
1 CATTGCGATAGTACTGTTTA
2659751 CATTGCGATAGTACTGTTTA
1 CATTGCGATAGTACTGTTTA
2659771 TCTATATCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (20 bp):
CATTGCGATAGTACTGTTTA
Found at i:2659799 original size:97 final size:100
Alignment explanation
Indices: 2659627--2659917 Score: 378
Period size: 97 Copynumber: 3.0 Consensus size: 100
2659617 CACGGTAGAA
* * *
2659627 AAAATCGCATTGCGATAATATTGTTTACATTGCGATAGTATTGTTTACCTATATCGGTAATTAGC
1 AAAATCGCATTGCGATAGTACTGTTTACATTGCGATAGTACTGTTTACCTATATCGGTAATTAGC
* * *
2659692 GTTGCAAATTTGAAAATCGCGTTGCGA-A-T-TTG
66 GTTGCGAATTTAAAAATCGCATTGCGATAGTATTG
* *
2659724 AAAATCGCATTGCGATAGTACTGTTTACATTGCGATAGTACTGTTTATCTATATCGGTAATTCGC
1 AAAATCGCATTGCGATAGTACTGTTTACATTGCGATAGTACTGTTTACCTATATCGGTAATTAGC
*
2659789 GTTACGAATTTAAAAATCGCATTGCGATAGTATTG
66 GTTGCGAATTTAAAAATCGCATTGCGATAGTATTG
* ** * * * * *
2659824 ---TTTTCATTGCGATAGCACTGTTTACATTGCAATAGTACTATTTACCTATATCGGTCATTAAC
1 AAAATCGCATTGCGATAGTACTGTTTACATTGCGATAGTACTGTTTACCTATATCGGTAATTAGC
*
2659886 GTTGCGAATTTAAAAATCGCATTACGATAGTA
66 GTTGCGAATTTAAAAATCGCATTGCGATAGTA
2659918 CTGTTTACCT
Statistics
Matches: 170, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
97 165 0.97
98 1 0.01
99 1 0.01
100 3 0.02
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (100 bp):
AAAATCGCATTGCGATAGTACTGTTTACATTGCGATAGTACTGTTTACCTATATCGGTAATTAGC
GTTGCGAATTTAAAAATCGCATTGCGATAGTATTG
Found at i:2659833 original size:20 final size:20
Alignment explanation
Indices: 2659808--2659868 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
2659798 TTAAAAATCG
* *
2659808 CATTGCGATAGTATTGTTTT
1 CATTGCGATAGTACTGTTTA
*
2659828 CATTGCGATAGCACTGTTTA
1 CATTGCGATAGTACTGTTTA
* *
2659848 CATTGCAATAGTACTATTTA
1 CATTGCGATAGTACTGTTTA
2659868 C
1 C
2659869 CTATATCGGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.41
Consensus pattern (20 bp):
CATTGCGATAGTACTGTTTA
Found at i:2659981 original size:21 final size:21
Alignment explanation
Indices: 2659949--2660019 Score: 108
Period size: 21 Copynumber: 3.4 Consensus size: 21
2659939 TACCGTTGCA
*
2659949 AATTTG-AAAATCGTGTTTCG
1 AATTTGAAAAATCGCGTTTCG
2659969 AATTTGAAAAATCGCGTTTCG
1 AATTTGAAAAATCGCGTTTCG
*
2659990 AATTTGAAAAATCGCGTTGCG
1 AATTTGAAAAATCGCGTTTCG
*
2660011 ATTTTGAAA
1 AATTTGAAA
2660020 CCTGTGTTGC
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 6 0.13
21 41 0.87
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (21 bp):
AATTTGAAAAATCGCGTTTCG
Found at i:2662343 original size:10 final size:10
Alignment explanation
Indices: 2662328--2662369 Score: 59
Period size: 10 Copynumber: 4.1 Consensus size: 10
2662318 CTCTCTAAGG
2662328 TATATTTTAT
1 TATATTTTAT
2662338 TATATTTTAT
1 TATATTTTAT
2662348 TATATTTTGTAT
1 TATA-TTT-TAT
2662360 T-TATTTTAT
1 TATATTTTAT
2662369 T
1 T
2662370 TAAGTATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 4 0.13
10 17 0.57
11 5 0.17
12 4 0.13
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (10 bp):
TATATTTTAT
Found at i:2662376 original size:17 final size:17
Alignment explanation
Indices: 2662343--2662394 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 17
2662333 TTTATTATAT
* *
2662343 TTTATTATATTT-TGTA
1 TTTATTTTATTTAAGTA
2662359 TTTATTTTATTTAAGTA
1 TTTATTTTATTTAAGTA
*
2662376 TTTAATTTATTTAA-TA
1 TTTATTTTATTTAAGTA
2662392 TTT
1 TTT
2662395 TACTTATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
16 16 0.50
17 16 0.50
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (17 bp):
TTTATTTTATTTAAGTA
Found at i:2662396 original size:17 final size:17
Alignment explanation
Indices: 2662359--2662410 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
2662349 ATATTTTGTA
*
2662359 TTTATTTTATTTAAGTA-
1 TTTAATTTATTTAA-TAT
2662376 TTTAATTTATTTAATAT
1 TTTAATTTATTTAATAT
*
2662393 TTT-ACTTATTTAAT-T
1 TTTAATTTATTTAATAT
2662408 TTT
1 TTT
2662411 TTTACAGATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 4 0.12
16 12 0.38
17 16 0.50
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTAATTTATTTAATAT
Found at i:2662401 original size:16 final size:16
Alignment explanation
Indices: 2662365--2662410 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
2662355 TGTATTTATT
* *
2662365 TTATTTAAGTATTTAAT
1 TTATTTAA-TATTTTAC
2662382 TTATTTAATATTTTAC
1 TTATTTAATATTTTAC
2662398 TTATTTAAT-TTTT
1 TTATTTAATATTTT
2662411 TTTACAGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
17 8 0.30
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATTTAATATTTTAC
Found at i:2664116 original size:27 final size:27
Alignment explanation
Indices: 2664053--2664116 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
2664043 CTTCACAGTA
* *
2664053 GCCACCACCATTCCCTTACCCGATGCC
1 GCCACCGCCATTCCCTTACCCGATACC
*
2664080 GCCACTGCCATTCCCTTACCCGATACC
1 GCCACCGCCATTCCCTTACCCGATACC
*
2664107 GCCGCCGCCA
1 GCCACCGCCA
2664117 CCATCACCTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.17, C:0.52, G:0.14, T:0.17
Consensus pattern (27 bp):
GCCACCGCCATTCCCTTACCCGATACC
Found at i:2664168 original size:33 final size:33
Alignment explanation
Indices: 2664105--2664172 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
2664095 TTACCCGATA
* * *
2664105 CCGCCGCCGCCACCATCACCTGGTTTTATGACC
1 CCGCCACCGCCACCATCACCAGGTTATATGACC
*
2664138 CCGCCACCGCCACCGTCA-CAGAGTTATATGACC
1 CCGCCACCGCCACCATCACCAG-GTTATATGACC
2664171 CC
1 CC
2664173 TCATGGAGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 2 0.07
33 28 0.93
ACGTcount: A:0.19, C:0.46, G:0.18, T:0.18
Consensus pattern (33 bp):
CCGCCACCGCCACCATCACCAGGTTATATGACC
Found at i:2668202 original size:51 final size:50
Alignment explanation
Indices: 2668130--2668242 Score: 113
Period size: 51 Copynumber: 2.2 Consensus size: 50
2668120 TCGCGCCCTA
* * * * *
2668130 GGGGTCGCGCTTTAACCACGTGTATCCAACTCAGCATAAGGCGTG-TCGCAG
1 GGGGT-GCGCCTTAACCACGTGGATCCAAATCAGCATAAAGCGCGCT-GCAG
* * *
2668181 GGGGTGCGCCTTACCCTACGTGGCTCCAAATCAGCGTAAAGCGCGCTGCAG
1 GGGGTGCGCCTTAACC-ACGTGGATCCAAATCAGCATAAAGCGCGCTGCAG
2668232 GGGG-GCGCCTT
1 GGGGTGCGCCTT
2668243 TCTGCAAAGG
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
50 16 0.31
51 35 0.67
52 1 0.02
ACGTcount: A:0.19, C:0.29, G:0.33, T:0.19
Consensus pattern (50 bp):
GGGGTGCGCCTTAACCACGTGGATCCAAATCAGCATAAAGCGCGCTGCAG
Found at i:2668487 original size:24 final size:24
Alignment explanation
Indices: 2668443--2668488 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2668433 ATCTCAAGAT
*
2668443 TTTTATAAAATTATCTTTTTAAAA
1 TTTTATAAAATTATCTCTTTAAAA
*
2668467 TTTTATAAATTTAT-TCCTTTAA
1 TTTTATAAAATTATCT-CTTTAA
2668489 TATGAAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.05
24 18 0.95
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTATAAAATTATCTCTTTAAAA
Found at i:2669612 original size:44 final size:42
Alignment explanation
Indices: 2669556--2669640 Score: 109
Period size: 44 Copynumber: 2.0 Consensus size: 42
2669546 TTTAGAAATA
* *
2669556 GAAACATAATTAAATAATTTATATA-ATTTTATAAAAATTATAT
1 GAAACATAATTAAAAAATATATATATA-TTTAT-AAAATTATAT
*
2669599 GAAATCATTATTAAAAAATATATATATATTTATAAAATTATA
1 GAAA-CATAATTAAAAAATATATATATATTTATAAAATTATA
2669641 AAAATATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 13 0.35
44 23 0.62
45 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (42 bp):
GAAACATAATTAAAAAATATATATATATTTATAAAATTATAT
Found at i:2669634 original size:21 final size:20
Alignment explanation
Indices: 2669575--2669635 Score: 54
Period size: 23 Copynumber: 2.9 Consensus size: 20
2669565 TTAAATAATT
*
2669575 TATATAAT-TTTATAAAAAT
1 TATATAATATTTATAAAAAA
2669594 TATATGAA-ATCATTATTAAAAAA
1 TATAT-AATAT--TTA-TAAAAAA
2669617 TATATATATATTTATAAAA
1 TATATA-ATATTTATAAAA
2669636 TTATAAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
19 5 0.15
20 3 0.09
21 5 0.15
22 7 0.21
23 12 0.35
24 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
TATATAATATTTATAAAAAA
Found at i:2669657 original size:28 final size:27
Alignment explanation
Indices: 2669608--2669664 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
2669598 TGAAATCATT
2669608 ATTAAAAAATATATATATATTTATAAA
1 ATTAAAAAATATATATATATTTATAAA
* *
2669635 ATTATAAAAATAT-TATTTAATTTTTAAA
1 ATTA-AAAAATATATATAT-ATTTATAAA
2669663 AT
1 AT
2669665 CAAATTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATTAAAAAATATATATATATTTATAAA
Found at i:2669694 original size:23 final size:23
Alignment explanation
Indices: 2669643--2669699 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 23
2669633 AAATTATAAA
*
2669643 AATATTATTTAATTTTTAAAATC
1 AATATTAATTAATTTTTAAAATC
* *
2669666 AA-ATTAATTATTTATTTGAAAT-
1 AATATTAATTAATT-TTTAAAATC
*
2669688 AATATTATTTAA
1 AATATTAATTAA
2669700 ATTATCTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
22 11 0.41
23 16 0.59
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
AATATTAATTAATTTTTAAAATC
Found at i:2669726 original size:33 final size:32
Alignment explanation
Indices: 2669666--2669731 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 32
2669656 TTTTAAAATC
2669666 AAATTAATTATTTATTTGAAATAATATTATTT
1 AAATTAATTATTTATTTGAAATAATATTATTT
*
2669698 AAATT-ATCTATTTAGTTTTAAATAATATTATTT
1 AAATTAAT-TATTTA-TTTGAAATAATATTATTT
2669731 A
1 A
2669732 GGATAAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
31 2 0.06
32 11 0.35
33 18 0.58
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (32 bp):
AAATTAATTATTTATTTGAAATAATATTATTT
Found at i:2669862 original size:23 final size:23
Alignment explanation
Indices: 2669812--2669883 Score: 81
Period size: 23 Copynumber: 3.0 Consensus size: 23
2669802 AATCTAAAAA
* * *
2669812 AATATTACTTGAAATAAATAATT
1 AATATTATTTTAAATAAATAAAT
*
2669835 GATATTATTTTAAATAAATAAAT
1 AATATTATTTTAAATAAATAAAT
*
2669858 AATATGATTTTAAAATTAAATAAAT
1 AATATTATTTT-AAA-TAAATAAAT
2669883 A
1 A
2669884 TTTGTTATGT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 28 0.68
24 3 0.07
25 10 0.24
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.40
Consensus pattern (23 bp):
AATATTATTTTAAATAAATAAAT
Found at i:2675458 original size:26 final size:27
Alignment explanation
Indices: 2675409--2675460 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
2675399 TTTATGTTTC
* * *
2675409 TTTTTTAAAATTAATAATATTTTAAAG
1 TTTTTTAAAATTAAAAAAAATTTAAAG
2675436 TTTTTTAAAA-TAAAAAAAATTTAAA
1 TTTTTTAAAATTAAAAAAAATTTAAA
2675461 TTACATGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (27 bp):
TTTTTTAAAATTAAAAAAAATTTAAAG
Found at i:2687416 original size:22 final size:21
Alignment explanation
Indices: 2687392--2687431 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2687382 GAGAAATTAT
2687392 TTTTAAAATAT-AAAAATGATG
1 TTTTAAAAT-TGAAAAATGATG
2687413 TTTTAAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
2687432 AAACAAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATG
Found at i:2691277 original size:23 final size:21
Alignment explanation
Indices: 2691228--2691290 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
2691218 TTTTAGTGCA
*
2691228 GAGGGAATCGATCCCCCCCTT
1 GAGGGAACCGATCCCCCCCTT
*
2691249 GAGGGAACCGATCCCCCCTTT
1 GAGGGAACCGATCCCCCCCTT
*
2691270 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATCCCCCCC
2691291 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
21 20 0.56
22 1 0.03
23 15 0.42
ACGTcount: A:0.21, C:0.38, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCCTT
Found at i:2697507 original size:40 final size:40
Alignment explanation
Indices: 2697452--2697573 Score: 208
Period size: 40 Copynumber: 3.0 Consensus size: 40
2697442 TGTAGGTTTA
*
2697452 TAATACACTTCGGTGTATATGATGGGAACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGAACGACCTTATGTG
* *
2697492 TAATACACTTTGGTGTATATGGTGGGTACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGAACGACCTTATGTG
*
2697532 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGAACGACCTTATGTG
2697572 TA
1 TA
2697574 GCACTACGGT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 77 1.00
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGAACGACCTTATGTG
Found at i:2697773 original size:45 final size:45
Alignment explanation
Indices: 2697678--2698070 Score: 630
Period size: 45 Copynumber: 8.8 Consensus size: 45
2697668 GTAAGCATGC
2697678 AAATAAGCTTACGAGCTTATGGAAT-AATG-TCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGAT-AAGTATATTGGTA
2697722 AAATAAGCTTACGAGCTTATGGAATAAATGATAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGATAAGTATATTGGTA
*
2697767 AAATAAGCTTACGAGCTTATGGAATAAATGATAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGATAAGTATATTGGTA
2697812 AAATAAGCTTACGAGCTTATGGAATAAATGATAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGATAAGTATATTGGTA
*
2697857 AAACAAGCTTACGAGCTTATGGAATAAATGATAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGATAAGTATATTGGTA
* *
2697902 AAACAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGATAAGTATATTGGTA
* * *
2697947 AAATAAGCTTATGAGCTTATGGAGT-AATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGATAAGTATATTGGTA
* * * *
2697991 AAATACGATTATGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGATAAGTATATTGGTA
* * *
2698036 GAATAAGCTTACTAGCTTATAGAATAAATGATAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGATAAG
2698071 AAATTTTATA
Statistics
Matches: 329, Mismatches: 17, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
44 66 0.20
45 262 0.80
46 1 0.00
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGATAAGTATATTGGTA
Found at i:2698443 original size:2 final size:2
Alignment explanation
Indices: 2698436--2698472 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2698426 TTTTGTGAGT
2698436 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2698473 TGTTGAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2702031 original size:15 final size:15
Alignment explanation
Indices: 2701932--2702031 Score: 55
Period size: 15 Copynumber: 6.5 Consensus size: 15
2701922 ACATAAATAC
2701932 ATAT-TTATATTATT
1 ATATATTATATTATT
*
2701946 -TATAAATATATT-TT
1 ATAT-ATTATATTATT
* *
2701960 TTACTATTTTATTATTT
1 ATA-TATTATATTA-TT
2701977 ATATATTTATATTATT
1 ATATA-TTATATTATT
*
2701993 A-ATATGTAAATATATAT
1 ATATAT-TATAT-TAT-T
* *
2702010 CTTTATTATATTATT
1 ATATATTATATTATT
2702025 ATATATT
1 ATATATT
2702032 TTTATATCTG
Statistics
Matches: 64, Mismatches: 11, Indels: 21
0.67 0.11 0.22
Matches are distributed among these distances:
13 3 0.05
14 3 0.05
15 27 0.42
16 12 0.19
17 16 0.25
18 3 0.05
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (15 bp):
ATATATTATATTATT
Found at i:2702037 original size:8 final size:9
Alignment explanation
Indices: 2701933--2702038 Score: 57
Period size: 8 Copynumber: 12.0 Consensus size: 9
2701923 CATAAATACA
2701933 TATTTATAT
1 TATTTATAT
2701942 TATTTATA-
1 TATTTATAT
*
2701950 -A-ATATAT
1 TATTTATAT
*
2701957 T-TTT-TAC
1 TATTTATAT
2701964 TATTT-TAT
1 TATTTATAT
2701972 TATTTATA-
1 TATTTATAT
2701980 TATTTATAT
1 TATTTATAT
*
2701989 TATTAATAT
1 TATTTATAT
*
2701998 GTAAATATATAT
1 -T--ATTTATAT
*
2702010 CTTTATTATAT
1 -TAT-TTATAT
2702021 TATTATATAT
1 TATT-TATAT
2702031 T-TTTATAT
1 TATTTATAT
2702039 CTGTTATGAA
Statistics
Matches: 75, Mismatches: 11, Indels: 23
0.69 0.10 0.21
Matches are distributed among these distances:
6 4 0.05
7 4 0.05
8 24 0.32
9 21 0.28
10 10 0.13
11 5 0.07
12 7 0.09
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (9 bp):
TATTTATAT
Found at i:2706775 original size:665 final size:667
Alignment explanation
Indices: 2705736--2707472 Score: 2459
Period size: 665 Copynumber: 2.6 Consensus size: 667
2705726 GAGGTTACCC
* * * *
2705736 ATTGTAATACCCCAAATTTTAGCTAGTGACAAAAATGTAAATTTTGAAAGTATGGTTGCCAAAAT
1 ATTGTAATACCCCAAATTTTAGCTAGTGACCAAAATGTAAATTTTG-AAGTTTGGTGGCCAAAGT
* * * * *
2705801 ATAAATTTGTAAAAATTCAAAGACTAAAAATG----TTTTAAGAGTTATATATCTTGGCTCGTAA
65 ATAAATTTGTAAAAATTCAAAGACCAAAAATGTAATTTTTAAAAGTTATATATTTTGACCCGTAA
2705862 ATGAATAGTAGTATACTAAGTTATGTTTTAAATGTTATCAGTATGGATTTTATAGTATGTAGATT
130 ATGAATAGTAGTATACTAAGTTATGTTTTAAATGTTATCAGTATGGATTTTATAGTATGTAGATT
* * *
2705927 TTAGACAATTTTAAATGTTATTTGAAACAGTATTGAATGACAACATTACTGCCTAAAATCAAGTT
195 TTAGACAGTTTTAAATGTTATATGAAACAGTATTGAATGACTACATTACTGCCTAAAATC-AGTT
* *
2705992 TGAAATTAATGATAAAATATTTCTTTTCAATTTTTACTCGATTAAATATTTTAGTGATTAAAGTA
259 TGAAATGAATGATAAAATATTTCTTTTCAATTTTTACTAGATTAAATATTTTAGTGATTAAAGTA
*
2706057 AATTTGATGTTTATGAAAGAAACAAAATTTTACGGGTTTTTGAGTAAGAAATGTTATAAAAGGTC
324 AATTTGATGTTT-TGAAAGAAACAAAATTTTACGGGTTTTTGAGTAGGAAATGTTATAAAAGGTC
*
2706122 AGTGTGACATCTTTAACTCCTATTAATTCATAGGAGATTCAAATGGATTTGATATACG-AAGAAA
388 AGTGTGACATCTTTAACTCCTATTAATTCATAGGAGATTCAAATGGATTTGATATACGAAAAAAA
* * *
2706186 AATTAGTAAATTTATTAGCACATAAATTCAAAGGACTAAGAAATAAAATGA-ACCCGTTTGTTAA
453 AATTAGAAAATATATTAGCACATAAAGTCAAAGGACTAAGAAATAAAAT-ATACCCGTTTGTTAA
* * *
2706250 AGTTTTGTTTTTCCTTAGCAAAGTATAGGATTGAGGAAACTACTTGGGAACGAGAAGAAGACATG
517 AGTTTTGTTTTTCCTTAGCAAAGCATAAGATCGAGGAAACTACTTGGGAACGAGAAGAAGACATG
* * * * *
2706315 AAAAAGCAATTTCCTTATCTATTT-CATCAGGTATGTAAATACGTGTGGAAAATTTAAGGACAAA
582 AAAAAGCAATTTCCTCATCTATTTACATCAGGCATGTAAATACGTATGGAAAATTCAAAGACAAA
* *
2706379 TTTTC-TTGAAGGTAAAGAGA
647 TTTTCTTTAAAGGGAAAGAGA
*
2706399 ATTGTAATACCCCAAA-TTTATGCTAGTGACCAAATTGTAAATTTTG-AGTTTGGTGGCCAAAGT
1 ATTGTAATACCCCAAATTTTA-GCTAGTGACCAAAATGTAAATTTTGAAGTTTGGTGGCCAAAGT
* *
2706462 ATAAATTTGTAAAAATTCAAGGACCAAAAATGTAATTTTTAAAATTTATATATTTTTGACCCGTA
65 ATAAATTTGTAAAAATTCAAAGACCAAAAATGTAATTTTTAAAAGTTATATA-TTTTGACCCGTA
* *
2706527 AATGAATAGTAGTCTACTAAGTTATGTTTTAAATGTTATCAGTATGGATTTTATATTATGTAGAT
129 AATGAATAGTAGTATACTAAGTTATGTTTTAAATGTTATCAGTATGGATTTTATAGTATGTAGAT
* *
2706592 TTTAGA-TGTTTTAAATGTTATATGAAATAGTATTGAATGACTACATTACTGCCTAAAATCAGTT
194 TTTAGACAGTTTTAAATGTTATATGAAACAGTATTGAATGACTACATTACTGCCTAAAATCAG-T
* ** * * *
2706656 TTGAAATGAATGGTAAAATATTTCTTTTTTATTTTCACTAGATTAAATAATTTAGTGATTAAATT
258 TTGAAATGAATGATAAAATATTTCTTTTCAATTTTTACTAGATTAAATATTTTAGTGATTAAAGT
* ** * * *
2706721 AAATTTGATATTTCTGAAAGAAATGAAATTTTACGAGTTTTTAAGTAGGAAATGTTATAAAAAGT
323 AAATTTGATGTTT-TGAAAGAAACAAAATTTTACGGGTTTTTGAGTAGGAAATGTTATAAAAGGT
* * *
2706786 CAGTGTGACATCTTTAACTCTTATTCATTCATAGGAGATTCAAATGGATTTGATATGCGAAAAAA
387 CAGTGTGACATCTTTAACTCCTATTAATTCATAGGAGATTCAAATGGATTTGATATACGAAAAAA
* * * **
2706851 AAATTAGAAAATATATTAGTACATAAAGTCAAAGGACTCAGAAATAAGATATACTTGTTTGTTAA
452 AAATTAGAAAATATATTAGCACATAAAGTCAAAGGACTAAGAAATAAAATATACCCGTTTGTTAA
* *
2706916 AGTTTTGTTTTTCCTTAGTAAAGCATAAGATCGAGGAAGCTACTTGGGAACGAGAAGAAGACATG
517 AGTTTTGTTTTTCCTTAGCAAAGCATAAGATCGAGGAAACTACTTGGGAACGAGAAGAAGACATG
*
2706981 AAAAAGCATTTTCCTCATCTATTTACATCAGGCATGTAAATACGTATGGAAAATTCAAAGACAAA
582 AAAAAGCAATTTCCTCATCTATTTACATCAGGCATGTAAATACGTATGGAAAATTCAAAGACAAA
*
2707046 TTTTCTTTAAAGGGGAAGAGA
647 TTTTCTTTAAAGGGAAAGAGA
* *
2707067 ATTGTAATACCCCAAATTTTGGCTAGTGACCAAAATGTAAATATTGAAAGTTTGGTGGCCAAAGT
1 ATTGTAATACCCCAAATTTTAGCTAGTGACCAAAATGTAAATTTTG-AAGTTTGGTGGCCAAAGT
* * * *
2707132 ATAAACTTATAAAAATTTAAAGA-CAAAAATGTAATTTTTAAAAGTTATATATTTTGACCTGTAA
65 ATAAATTTGTAAAAATTCAAAGACCAAAAATGTAATTTTTAAAAGTTATATATTTTGACCCGTAA
* * * * * * * *
2707196 ATGAATAGTAATATACTAATTTATGTTTCAAATGTTTTCAATATAGATTTTATGGTATGCA-ATT
130 ATGAATAGTAGTATACTAAGTTATGTTTTAAATGTTATCAGTATGGATTTTATAGTATGTAGATT
* * * * *
2707260 TTAGACAG-TTTAAACGTTATATGAAACAATATT---T-ACTATATTATTGTCTAAAATCAGGTT
195 TTAGACAGTTTTAAATGTTATATGAAACAGTATTGAATGACTACATTACTGCCTAAAATCA-GTT
* *
2707320 TGAAATGAATGATAAAATATTTCTTTTCGATTTTTACTCA-ATTAAATGTTTTAGTGATTAAAGT
259 TGAAATGAATGATAAAATATTTCTTTTCAATTTTTACT-AGATTAAATATTTTAGTGATTAAAGT
* * * *
2707384 ATATTTGATGTTTTGAAAGAAACAAAATTTTACGGGCTTTTGAGTAGGAAATATTATAAAAGGTT
323 AAATTTGATGTTTTGAAAGAAACAAAATTTTACGGGTTTTTGAGTAGGAAATGTTATAAAAGGTC
* *
2707449 AGTGTGACATCTTAAACTCGTATT
388 AGTGTGACATCTTTAACTCCTATT
2707473 TAAGTACGTA
Statistics
Matches: 951, Mismatches: 106, Indels: 35
0.87 0.10 0.03
Matches are distributed among these distances:
661 44 0.05
662 70 0.07
663 126 0.13
664 5 0.01
665 235 0.25
666 219 0.23
667 71 0.07
668 115 0.12
669 30 0.03
670 36 0.04
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.37
Consensus pattern (667 bp):
ATTGTAATACCCCAAATTTTAGCTAGTGACCAAAATGTAAATTTTGAAGTTTGGTGGCCAAAGTA
TAAATTTGTAAAAATTCAAAGACCAAAAATGTAATTTTTAAAAGTTATATATTTTGACCCGTAAA
TGAATAGTAGTATACTAAGTTATGTTTTAAATGTTATCAGTATGGATTTTATAGTATGTAGATTT
TAGACAGTTTTAAATGTTATATGAAACAGTATTGAATGACTACATTACTGCCTAAAATCAGTTTG
AAATGAATGATAAAATATTTCTTTTCAATTTTTACTAGATTAAATATTTTAGTGATTAAAGTAAA
TTTGATGTTTTGAAAGAAACAAAATTTTACGGGTTTTTGAGTAGGAAATGTTATAAAAGGTCAGT
GTGACATCTTTAACTCCTATTAATTCATAGGAGATTCAAATGGATTTGATATACGAAAAAAAAAT
TAGAAAATATATTAGCACATAAAGTCAAAGGACTAAGAAATAAAATATACCCGTTTGTTAAAGTT
TTGTTTTTCCTTAGCAAAGCATAAGATCGAGGAAACTACTTGGGAACGAGAAGAAGACATGAAAA
AGCAATTTCCTCATCTATTTACATCAGGCATGTAAATACGTATGGAAAATTCAAAGACAAATTTT
CTTTAAAGGGAAAGAGA
Found at i:2708179 original size:52 final size:52
Alignment explanation
Indices: 2708122--2708222 Score: 193
Period size: 52 Copynumber: 1.9 Consensus size: 52
2708112 CTTTATCACG
*
2708122 CCAAGCAGCCATAAATGTTTTTCTTCTTGCTTGACCCCTTCTTCTTTAGACT
1 CCAAGCAGCCATAAATGTTTTTCTTCTTGCTTGACCCATTCTTCTTTAGACT
2708174 CCAAGCAGCCATAAATGTTTTTCTTCTTGCTTGACCCATTCTTCTTTAG
1 CCAAGCAGCCATAAATGTTTTTCTTCTTGCTTGACCCATTCTTCTTTAG
2708223 GAGGGGACAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.20, C:0.28, G:0.12, T:0.41
Consensus pattern (52 bp):
CCAAGCAGCCATAAATGTTTTTCTTCTTGCTTGACCCATTCTTCTTTAGACT
Found at i:2712657 original size:32 final size:31
Alignment explanation
Indices: 2712565--2712695 Score: 93
Period size: 32 Copynumber: 4.2 Consensus size: 31
2712555 TTACGAACAT
* * *
2712565 AAGGTGAC-CCTTGGGTAGGCTCTTAGGTCCT
1 AAGGT-ACTCCTTGGGTAGGCTCTAAGGCCCC
* * * * *
2712596 AAGATGCTTTCTTGGGTAGGCTATTAGGCCCC
1 AAGGTAC-TCCTTGGGTAGGCTCTAAGGCCCC
* *
2712628 AAGGTACTCCATTGGGTAGGTTCTAAGGCCCT
1 AAGGTACTCC-TTGGGTAGGCTCTAAGGCCCC
* * * **
2712660 ATGGGATTCCTTATGTAGGCTCTAAGGCCCC
1 AAGGTACTCCTTGGGTAGGCTCTAAGGCCCC
2712691 AAGGT
1 AAGGT
2712696 GTTCCCTTAA
Statistics
Matches: 75, Mismatches: 22, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
30 1 0.01
31 26 0.35
32 48 0.64
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (31 bp):
AAGGTACTCCTTGGGTAGGCTCTAAGGCCCC
Found at i:2714943 original size:47 final size:48
Alignment explanation
Indices: 2714856--2714952 Score: 169
Period size: 47 Copynumber: 2.0 Consensus size: 48
2714846 TGGGTTCCTT
2714856 AAAAATTATCTTGTAACAAGGGTTGTATCTGAATAGGAATCTCTTGTGTA
1 AAAAATTATCTTGTAACAA--GTTGTATCTGAATAGGAATCTCTTGTGTA
2714906 AAAAATTATCTTGTAACAA-TTGTATCTGAATAGGAATCTCTTGTGTA
1 AAAAATTATCTTGTAACAAGTTGTATCTGAATAGGAATCTCTTGTGTA
2714953 GCGACTTCCA
Statistics
Matches: 47, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
47 28 0.60
50 19 0.40
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (48 bp):
AAAAATTATCTTGTAACAAGTTGTATCTGAATAGGAATCTCTTGTGTA
Found at i:2715372 original size:18 final size:17
Alignment explanation
Indices: 2715349--2715395 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
2715339 TGTTTCTGAG
2715349 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
* *
2715367 GGAATTGGAATATGTTA
1 GGAATTGGAATCTGTAA
2715384 GGAATTGGAATC
1 GGAATTGGAATC
2715396 CAATTCCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.34, C:0.04, G:0.32, T:0.30
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:2716238 original size:259 final size:256
Alignment explanation
Indices: 2715746--2716271 Score: 817
Period size: 259 Copynumber: 2.0 Consensus size: 256
2715736 CTCCATCCGA
*
2715746 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCTGAATATATGAATTAGAAACCCGAC
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGAC
* *
2715811 CCGACCCGAAATAATAATAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAATAT
66 CCGACCCGAAATAATAAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAATAT
*
2715876 ATATATATAGAGGGGTATTACTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTTG
131 ATATATATAGAGGGGTATTACTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTATTT-
** *
2715941 GGTCGGGTTGGGTATTTTTCACCCTAAACCCGACCCGACCCGAGTATCACACTTTAAAAAAACC
195 -GTCGGGTCAGGTATTTTTCACCCTAAACCCGACCCGACCCGAATATCACA-TTTAAAAAAACC
* **
2716005 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGACTATATGAATTAGAAATTCGAC
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGAC
2716070 CCGACCCGAAATAATAAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAA-AT
66 CCGACCCGAAATAATAAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAATAT
* * *
2716134 -TGTATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAGGGTAAAATTATATA-TATTT-
131 ATATATATAGAGGGGTATTACTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTATTTG
*
2716196 TCGGGTCAGGTATTTTTCACCCTAAACCCGAACTCTACCCGACCCGAATATCACATTTAAAAAAT
196 TCGGGTCAGGTATTTTTCACCCTAAACCCG------ACCCGACCCGAATATCACATTTAAAAAAA
2716261 CC
255 CC
2716263 GACCCGACC
1 GACCCGACC
2716272 AAAATAAAGT
Statistics
Matches: 247, Mismatches: 14, Indels: 13
0.90 0.05 0.05
Matches are distributed among these distances:
253 28 0.11
256 4 0.02
257 54 0.22
258 22 0.09
259 139 0.56
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (256 bp):
GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGAC
CCGACCCGAAATAATAAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAATAT
ATATATATAGAGGGGTATTACTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTATTTG
TCGGGTCAGGTATTTTTCACCCTAAACCCGACCCGACCCGAATATCACATTTAAAAAAACC
Found at i:2717615 original size:32 final size:32
Alignment explanation
Indices: 2717548--2717621 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
2717538 TAAGGTGACC
* * * *
2717548 CTTGGGTAGGCTCTTAGGTCCCGAGATGCTTT
1 CTTGGGTAGGCTATTAGGTCCCAAGATACTCT
*
2717580 CTTGGGTAGGCTATTAGG-CCCAAAGGTACTCT
1 CTTGGGTAGGCTATTAGGTCCC-AAGATACTCT
2717612 CTTGGGTAGG
1 CTTGGGTAGG
2717622 TTCTAAGGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
31 3 0.08
32 33 0.92
ACGTcount: A:0.16, C:0.20, G:0.32, T:0.31
Consensus pattern (32 bp):
CTTGGGTAGGCTATTAGGTCCCAAGATACTCT
Found at i:2718597 original size:20 final size:20
Alignment explanation
Indices: 2718572--2718613 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2718562 TACCTTTGAC
* *
2718572 ATCGGTACTTCAAGAATAAT
1 ATCGGTACTACAAGAACAAT
2718592 ATCGGTACTACAAGAACAAT
1 ATCGGTACTACAAGAACAAT
2718612 AT
1 AT
2718614 TGATATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (20 bp):
ATCGGTACTACAAGAACAAT
Found at i:2719864 original size:50 final size:49
Alignment explanation
Indices: 2719787--2719887 Score: 166
Period size: 50 Copynumber: 2.0 Consensus size: 49
2719777 GTGGGTTCCT
* *
2719787 TAAAAATTATCTTGTAACAAGGGTTGTATCTGAATAGGAATCTCTTGTG
1 TAAAAATTATCTTGTAACAAGGCTTGTATCTGAATAGGAATCTCTAGTG
*
2719836 TAAAATATTATCTTGTATCAAGGCTTGTATCTGAATAGGAATCTCTAGTG
1 TAAAA-ATTATCTTGTAACAAGGCTTGTATCTGAATAGGAATCTCTAGTG
2719886 TA
1 TA
2719888 GCGACTTCCA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 5 0.10
50 43 0.90
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.38
Consensus pattern (49 bp):
TAAAAATTATCTTGTAACAAGGCTTGTATCTGAATAGGAATCTCTAGTG
Found at i:2727886 original size:166 final size:165
Alignment explanation
Indices: 2727581--2727914 Score: 643
Period size: 166 Copynumber: 2.0 Consensus size: 165
2727571 AAACCCTAGG
2727581 AGCCCCCACTATATAAAGCTAAGGACACCCACATTAAAGGTAGAATGAGTTTATGAGATAAGAAA
1 AGCCCCCACTATATAAAGCTAAGGACACCCACATTAAAGGTAGAATGAGTTTATGAGATAAGAAA
2727646 GAGAAAAGTGAGAGGCGACCACTCTTCCTTTTCTCTATTCTTTTTGGTGACCTCAATTGTTAGAG
66 GAGAAAAGTGAGAGGCGACCACTCTTCCTTTTCTCTATTCTTTTTGGTGACCTCAATTGTTAGAG
2727711 CTCCAAGGGGATAAAGCTTGATGGCCTTTGAGAGA
131 CTCCAAGGGGATAAAGCTTGATGGCCTTTGAGAGA
2727746 AGCCCCCACTATATAAAGCTAAGGACACCCACATTAAAGGTAGAATGAGTTTTATGAGATAAGAA
1 AGCCCCCACTATATAAAGCTAAGGACACCCACATTAAAGGTAGAATGAG-TTTATGAGATAAGAA
2727811 AGAGAAAAGTGAGAGGCGACCACTCTTCCTTTTCTCTTATTCTTTTTGGTGACCTCAATTGTTAG
65 AGAGAAAAGTGAGAGGCGACCACTCTTCCTTTTCTC-TATTCTTTTTGGTGACCTCAATTGTTAG
2727876 AGCT-CAAGGGGATAAAGCTTGATGGCCTTTGAGAGA
129 AGCTCCAAGGGGATAAAGCTTGATGGCCTTTGAGAGA
2727912 AGC
1 AGC
2727915 AACAACGCTT
Statistics
Matches: 167, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
165 49 0.29
166 86 0.51
167 32 0.19
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (165 bp):
AGCCCCCACTATATAAAGCTAAGGACACCCACATTAAAGGTAGAATGAGTTTATGAGATAAGAAA
GAGAAAAGTGAGAGGCGACCACTCTTCCTTTTCTCTATTCTTTTTGGTGACCTCAATTGTTAGAG
CTCCAAGGGGATAAAGCTTGATGGCCTTTGAGAGA
Found at i:2731388 original size:24 final size:23
Alignment explanation
Indices: 2731356--2731404 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
2731346 TAACAATACA
2731356 AAAATAAATAGAAGATA-A-AAAAT
1 AAAATAAAT-GAA-ATATATAAAAT
2731379 AAAATAAAATGAAATATATAAAAT
1 AAAAT-AAATGAAATATATAAAAT
2731403 AA
1 AA
2731405 TAAATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
22 3 0.13
23 9 0.39
24 11 0.48
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.20
Consensus pattern (23 bp):
AAAATAAATGAAATATATAAAAT
Found at i:2731411 original size:16 final size:16
Alignment explanation
Indices: 2731390--2731421 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2731380 AAATAAAATG
2731390 AAATATATAAAATAAT
1 AAATATATAAAATAAT
*
2731406 AAATATATAATATAAT
1 AAATATATAAAATAAT
2731422 TATAGTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATATATAAAATAAT
Found at i:2731448 original size:28 final size:29
Alignment explanation
Indices: 2731391--2731454 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
2731381 AATAAAATGA
*
2731391 AATATATA-AAATAATAAATATATAATAT
1 AATATATAGTAATAATAAATATATAATAT
2731419 AAT-TATAGTAATAA-AAATAT-TATATAAT
1 AATATATAGTAATAATAAATATATA-AT-AT
2731447 AATATATA
1 AATATATA
2731455 TGAAAGAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 2 0.06
27 12 0.39
28 13 0.42
29 4 0.13
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (29 bp):
AATATATAGTAATAATAAATATATAATAT
Found at i:2744671 original size:29 final size:29
Alignment explanation
Indices: 2744613--2744675 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
2744603 AAAAATGTAG
* *
2744613 TAAAAATGAATAAAATAAAGAAGGTGAAA
1 TAAAAATAAATAAAATAAAGAAGGTAAAA
* *
2744642 TAAAAATAAATACAATAAAGTAGAG-AAAA
1 TAAAAATAAATAAAATAAAGAAG-GTAAAA
2744671 TAAAA
1 TAAAA
2744676 CAGATAAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.68, C:0.02, G:0.13, T:0.17
Consensus pattern (29 bp):
TAAAAATAAATAAAATAAAGAAGGTAAAA
Found at i:2744807 original size:15 final size:15
Alignment explanation
Indices: 2744787--2744818 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2744777 ATACAAAAAT
*
2744787 AAAAATAGAAGATAA
1 AAAAATAAAAGATAA
2744802 AAAAATAAAAGATAA
1 AAAAATAAAAGATAA
2744817 AA
1 AA
2744819 TGAAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.12
Consensus pattern (15 bp):
AAAAATAAAAGATAA
Found at i:2745179 original size:30 final size:30
Alignment explanation
Indices: 2745129--2745198 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
2745119 TGGGTCAACT
* *
2745129 CGTTAACTTTGACCGAGTCAACCCATTGAC
1 CGTTGACTTTAACCGAGTCAACCCATTGAC
* *
2745159 CGTTGACTTTAACCGGGTCAACCCGTTGAC
1 CGTTGACTTTAACCGAGTCAACCCATTGAC
*
2745189 CATTGACTTT
1 CGTTGACTTT
2745199 GACCAAAAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.30
Consensus pattern (30 bp):
CGTTGACTTTAACCGAGTCAACCCATTGAC
Found at i:2745230 original size:17 final size:17
Alignment explanation
Indices: 2745204--2745241 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2745194 ACTTTGACCA
* *
2745204 AAAAGTCAAAAATTTCG
1 AAAAGGCAAAAAGTTCG
2745221 AAAAGGCAAAAAGTTCG
1 AAAAGGCAAAAAGTTCG
2745238 AAAA
1 AAAA
2745242 TTTATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.58, C:0.11, G:0.16, T:0.16
Consensus pattern (17 bp):
AAAAGGCAAAAAGTTCG
Found at i:2751545 original size:27 final size:28
Alignment explanation
Indices: 2751508--2751565 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
2751498 TCGGTCAAAG
2751508 TCAACGAGTTAACCCAG-TGA-GTTGAC
1 TCAACGAGTTAACCCAGCTGAGGTTGAC
* *
2751534 TCAACCGAGTTAACTCAGCTTAGGTTGAC
1 TCAA-CGAGTTAACCCAGCTGAGGTTGAC
2751563 TCA
1 TCA
2751566 GTCGGCTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 4 0.15
27 12 0.44
28 2 0.07
29 9 0.33
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (28 bp):
TCAACGAGTTAACCCAGCTGAGGTTGAC
Found at i:2754920 original size:20 final size:20
Alignment explanation
Indices: 2754894--2754946 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
2754884 TGATTCAATT
2754894 GGTATCGATACCAAAGGG-A
1 GGTATCGATACCAAAGGGAA
**
2754913 GAGTATCGATACTGAAGGGAA
1 G-GTATCGATACCAAAGGGAA
2754934 GGTATCGATACCA
1 GGTATCGATACCA
2754947 TTTAAAAGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.04
20 25 0.89
21 2 0.07
ACGTcount: A:0.36, C:0.15, G:0.30, T:0.19
Consensus pattern (20 bp):
GGTATCGATACCAAAGGGAA
Found at i:2755017 original size:20 final size:20
Alignment explanation
Indices: 2754969--2755021 Score: 79
Period size: 22 Copynumber: 2.5 Consensus size: 20
2754959 ATGAAAAAAT
2754969 GGTATCGATACCATAGTATG
1 GGTATCGATACCATAGTATG
*
2754989 GTAGTATCGATACCATGGTATG
1 G--GTATCGATACCATAGTATG
2755011 GGTATCGATAC
1 GGTATCGATAC
2755022 TGATGAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 11 0.37
22 19 0.63
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (20 bp):
GGTATCGATACCATAGTATG
Found at i:2755566 original size:54 final size:54
Alignment explanation
Indices: 2755344--2755535 Score: 278
Period size: 54 Copynumber: 3.6 Consensus size: 54
2755334 TTACCAAATA
*
2755344 GGCACTAAATGTGCATTTCACGGAATTCATCCTATGTGGATGAATAATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAATCGTTTC
* * * * *
2755398 GGTACTAAGTGTGCATTTCATGGAATTGATCCTATGTGGATGAATAACCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAATCGTTTC
* * *
2755452 GGCACTGAGTGTGCATTTCACAGAATTCATTCTATGTGGATGAATAA-CTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAATC-GTTTC
*
2755506 GGCACTAAGTGTGCATTTCATGGAATTCAT
1 GGCACTAAGTGTGCATTTCACGGAATTCAT
2755536 AATATATTTA
Statistics
Matches: 121, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
53 1 0.01
54 120 0.99
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAATCGTTTC
Found at i:2761757 original size:22 final size:21
Alignment explanation
Indices: 2761716--2761770 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
2761706 TACCATAGCA
* *
2761716 TAGTATCGGTACCATAGTATTG
1 TAGTATCGATACTATAGTA-TG
*
2761738 TAGTATCGATACTATGGTATG
1 TAGTATCGATACTATAGTATG
*
2761759 -GGTATCGATACT
1 TAGTATCGATACT
2761771 GAGGAGCCAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 11 0.38
21 2 0.07
22 16 0.55
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (21 bp):
TAGTATCGATACTATAGTATG
Found at i:2762158 original size:53 final size:53
Alignment explanation
Indices: 2762090--2762218 Score: 170
Period size: 53 Copynumber: 2.4 Consensus size: 53
2762080 GATTACCAAA
* * * * *
2762090 TAGGCATTAAATGTGCATTTCATGGAATTCATCTTATGTGGATG-ATAACCGTT
1 TAGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGAATGAATAACCG-T
*
2762143 TAGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGAATGAATAACTGT
1 TAGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGAATGAATAACCGT
* *
2762196 TCGGCACTAAGTATGCATTTCAC
1 TAGGCACTAAGTGTGCATTTCAC
2762219 ATTTGCTTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
53 61 0.91
54 6 0.09
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (53 bp):
TAGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGAATGAATAACCGT
Found at i:2762668 original size:54 final size:54
Alignment explanation
Indices: 2762338--2762637 Score: 438
Period size: 54 Copynumber: 5.6 Consensus size: 54
2762328 TTACCAAATA
* * * * * *
2762338 GGCATTAAATGTGCATTTCATGGAATTCATCTTATGTGGATGAATAACCGTTTA
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTC
*
2762392 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGAATGAATAACTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTC
* **
2762446 GGCACTAAGTATGCATTTCACATAATTCATCCTATGTGGATGAATAACTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTC
* * *
2762500 GACACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAATTATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTC
* * * *
2762554 GGCACTAAGTGTGCATTTCACAGAATTTATTCTATGTGGATGAATAACAGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTC
*
2762608 GGCACTAAGTGAGCATTTCACGGAATTCAT
1 GGCACTAAGTGTGCATTTCACGGAATTCAT
2762638 AATATGTTTA
Statistics
Matches: 219, Mismatches: 27, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 219 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTC
Found at i:2763356 original size:2 final size:2
Alignment explanation
Indices: 2763351--2763387 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2763341 TTTCTTTCAT
2763351 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2763388 TTTATTTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2764202 original size:13 final size:12
Alignment explanation
Indices: 2764181--2764214 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2764171 TATTGCATGG
2764181 TAATTTTTTTTT
1 TAATTTTTTTTT
*
2764193 CAATTTTTTTTT
1 TAATTTTTTTTT
*
2764205 TACTTTTTTT
1 TAATTTTTTT
2764215 GTAATTACCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (12 bp):
TAATTTTTTTTT
Found at i:2768127 original size:34 final size:34
Alignment explanation
Indices: 2768089--2768211 Score: 120
Period size: 34 Copynumber: 3.4 Consensus size: 34
2768079 TTTATAAATA
2768089 ATATTCTGTAAAATTAAAAGAAACATACTTTAGT
1 ATATTCTGTAAAATTAAAAGAAACATACTTTAGT
* * * * *
2768123 ATATTCTGTAAATTTTAAAAAATCAATGATAAATTTATAAAT
1 ATATTCTGTAAA-ATTAAAAGA--AA-CAT--ACTT-T-AGT
2768165 AATATTCTGTAAAATTAAAAGAAACATACTTTAGT
1 -ATATTCTGTAAAATTAAAAGAAACATACTTTAGT
2768200 ATATTCTGTAAA
1 ATATTCTGTAAA
2768212 TTGGGTTGGG
Statistics
Matches: 70, Mismatches: 10, Indels: 18
0.71 0.10 0.18
Matches are distributed among these distances:
34 24 0.34
35 9 0.13
36 1 0.01
37 5 0.07
38 2 0.03
39 2 0.03
40 5 0.07
41 1 0.01
42 9 0.13
43 12 0.17
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (34 bp):
ATATTCTGTAAAATTAAAAGAAACATACTTTAGT
Found at i:2768177 original size:22 final size:20
Alignment explanation
Indices: 2768123--2768177 Score: 51
Period size: 22 Copynumber: 2.6 Consensus size: 20
2768113 ATACTTTAGT
2768123 ATATTCTGTAAATTTTAAAA
1 ATATTCTGTAAATTTTAAAA
2768143 A-A-TCAATGATAAATTTATAAATA
1 ATATTC--TG-TAAATTT-TAAA-A
2768166 ATATTCTGTAAA
1 ATATTCTGTAAA
2768178 ATTAAAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
18 2 0.07
19 1 0.04
20 3 0.11
21 7 0.25
22 8 0.29
23 4 0.14
24 1 0.04
25 2 0.07
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.40
Consensus pattern (20 bp):
ATATTCTGTAAATTTTAAAA
Found at i:2768187 original size:77 final size:77
Alignment explanation
Indices: 2768060--2768213 Score: 308
Period size: 77 Copynumber: 2.0 Consensus size: 77
2768050 ACCTATACCA
2768060 TTAAAAAATCAATGATAAATTTATAAATAATATTCTGTAAAATTAAAAGAAACATACTTTAGTAT
1 TTAAAAAATCAATGATAAATTTATAAATAATATTCTGTAAAATTAAAAGAAACATACTTTAGTAT
2768125 ATTCTGTAAATT
66 ATTCTGTAAATT
2768137 TTAAAAAATCAATGATAAATTTATAAATAATATTCTGTAAAATTAAAAGAAACATACTTTAGTAT
1 TTAAAAAATCAATGATAAATTTATAAATAATATTCTGTAAAATTAAAAGAAACATACTTTAGTAT
2768202 ATTCTGTAAATT
66 ATTCTGTAAATT
2768214 GGGTTGGGAT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.38
Consensus pattern (77 bp):
TTAAAAAATCAATGATAAATTTATAAATAATATTCTGTAAAATTAAAAGAAACATACTTTAGTAT
ATTCTGTAAATT
Found at i:2768228 original size:22 final size:22
Alignment explanation
Indices: 2768200--2768244 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2768190 ATACTTTAGT
2768200 ATATTCTGTAAATTGGGTTGGG
1 ATATTCTGTAAATTGGGTTGGG
2768222 ATATTCTGTAAATTGGGTTGGG
1 ATATTCTGTAAATTGGGTTGGG
2768244 A
1 A
2768245 GGGTAGACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.04, G:0.31, T:0.40
Consensus pattern (22 bp):
ATATTCTGTAAATTGGGTTGGG
Found at i:2770392 original size:24 final size:25
Alignment explanation
Indices: 2770336--2770394 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 25
2770326 TATATTATGT
2770336 TATTAATTAAATATATATAAAAATAC
1 TATTAATT-AATATATATAAAAATAC
*
2770362 TA-T-ATTAATA-ATAT-AAATTGAC
1 TATTAATTAATATATATAAAAAT-AC
2770384 TATTAATTAAT
1 TATTAATTAAT
2770395 TAATTGTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
21 4 0.14
22 8 0.28
23 5 0.17
24 9 0.31
25 1 0.03
26 2 0.07
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (25 bp):
TATTAATTAATATATATAAAAATAC
Found at i:2772521 original size:35 final size:35
Alignment explanation
Indices: 2772450--2772522 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
2772440 ACACATCATA
**
2772450 TAAGGCCCTAAGCACAAAGCCGAGGAACTGGTAAG
1 TAAGGCCCTAAGCACAAAGCCGAGGAACTGCCAAG
* *
2772485 TAAGGCCCTGAGCACACAGCCGAGGAACCT-CCAAG
1 TAAGGCCCTAAGCACAAAGCCGAGGAA-CTGCCAAG
2772520 TAA
1 TAA
2772523 TCTTCCTCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 31 0.94
36 2 0.06
ACGTcount: A:0.36, C:0.27, G:0.26, T:0.11
Consensus pattern (35 bp):
TAAGGCCCTAAGCACAAAGCCGAGGAACTGCCAAG
Found at i:2772626 original size:24 final size:24
Alignment explanation
Indices: 2772599--2772659 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
2772589 AATAATTTAA
*
2772599 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
2772623 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
2772647 GTCAA-TATCAGAT
1 GTCAAGTATCAGAT
2772660 AAAATATTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
23 8 0.24
24 25 0.76
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:2777594 original size:12 final size:12
Alignment explanation
Indices: 2777577--2777627 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
2777567 TTCAAAGAGG
2777577 TTTTATATTTAA
1 TTTTATATTTAA
2777589 TTTTATA-TTATA
1 TTTTATATTTA-A
*
2777601 TTTGAT-TTTAA
1 TTTTATATTTAA
2777612 TTTTA-ATATTAA
1 TTTTATAT-TTAA
2777624 TTTT
1 TTTT
2777628 TAAATAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
11 9 0.27
12 24 0.73
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:2777731 original size:17 final size:18
Alignment explanation
Indices: 2777669--2777725 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
2777659 ATATTATAGA
2777669 TATT-AAATTTTATATCA-
1 TATTAAAATTTTATAT-AT
2777686 TA-TAAATTATTTTATATAT
1 TATTAAA--ATTTTATATAT
2777705 TATTAAAATTTTATAT-T
1 TATTAAAATTTTATATAT
2777722 TATT
1 TATT
2777726 TTAATTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
16 1 0.03
17 9 0.26
18 10 0.29
19 11 0.31
20 4 0.11
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTAAAATTTTATATAT
Found at i:2777735 original size:20 final size:19
Alignment explanation
Indices: 2777675--2777736 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
2777665 TAGATATTAA
*
2777675 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
2777694 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
2777712 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
2777732 ATTTT
1 ATTTT
2777737 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:2778003 original size:25 final size:24
Alignment explanation
Indices: 2777967--2778014 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
2777957 ATATTTTCTA
*
2777967 AAATTATCATATA-ATTATAAAAAT
1 AAATTATAATATATATT-TAAAAAT
2777991 AAATTATGAATATATATTTAAAAA
1 AAATTAT-AATATATATTTAAAAA
2778015 AATTAAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 11 0.52
26 3 0.14
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
AAATTATAATATATATTTAAAAAT
Found at i:2778243 original size:31 final size:32
Alignment explanation
Indices: 2778191--2778251 Score: 106
Period size: 31 Copynumber: 1.9 Consensus size: 32
2778181 TAGCTGTATG
*
2778191 AATTATTTAAATTTTCAGTATTGTAAAACTAA
1 AATTATTTAAATTCTCAGTATTGTAAAACTAA
2778223 AATTATTTAAA-TCTCAGTATTGTAAAACT
1 AATTATTTAAATTCTCAGTATTGTAAAACT
2778252 CTTTTAAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 17 0.61
32 11 0.39
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.43
Consensus pattern (32 bp):
AATTATTTAAATTCTCAGTATTGTAAAACTAA
Found at i:2778505 original size:2 final size:2
Alignment explanation
Indices: 2778490--2778566 Score: 124
Period size: 2 Copynumber: 40.0 Consensus size: 2
2778480 AAGAATCAAT
*
2778490 TA TA -A TA T- TA TA TA TA TA TA TA GA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2778530 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2778567 GTTAATGATA
Statistics
Matches: 70, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
1 3 0.04
2 67 0.96
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2778663 original size:15 final size:15
Alignment explanation
Indices: 2778629--2778661 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2778619 ATATGACTAA
*
2778629 ATTTATTATTTTCAT
1 ATTTATTATTTTAAT
2778644 ATTTATT-TTTTAAT
1 ATTTATTATTTTAAT
2778658 ATTT
1 ATTT
2778662 TAAAACTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTATTATTTTAAT
Found at i:2779873 original size:22 final size:21
Alignment explanation
Indices: 2779819--2779896 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
2779809 CGGTGTTTGA
2779819 GTACATGGATGCAC-TGCATG
1 GTACATGGATGCACTTGCATG
* *
2779839 GTGCATCGATGCACTAGTGCAT-
1 GTACATGGATGCACT--TGCATG
*
2779861 GTACATGGATGCAC-TGCAGG
1 GTACATGGATGCACTTGCATG
*
2779881 GATGCATGGATGCACT
1 G-TACATGGATGCACT
2779897 GCAGGGGTGC
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
19 4 0.09
20 13 0.28
21 12 0.26
22 12 0.26
23 5 0.11
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.24
Consensus pattern (21 bp):
GTACATGGATGCACTTGCATG
Found at i:2779890 original size:21 final size:21
Alignment explanation
Indices: 2779822--2779909 Score: 92
Period size: 21 Copynumber: 4.2 Consensus size: 21
2779812 TGTTTGAGTA
*
2779822 CATGGATGCACTGCATGG-TG
1 CATGGATGCACTGCAGGGATG
* *
2779842 CATCGATGCACT--AGTGCATG
1 CATGGATGCACTGCAG-GGATG
2779862 TACATGGATGCACTGCAGGGATG
1 --CATGGATGCACTGCAGGGATG
*
2779885 CATGGATGCACTGCAGGGGTG
1 CATGGATGCACTGCAGGGATG
2779906 CATG
1 CATG
2779910 CACTTTGACA
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
18 1 0.02
19 1 0.02
20 13 0.23
21 24 0.43
22 11 0.20
23 4 0.07
24 2 0.04
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (21 bp):
CATGGATGCACTGCAGGGATG
Found at i:2780020 original size:29 final size:31
Alignment explanation
Indices: 2779988--2780047 Score: 90
Period size: 29 Copynumber: 2.0 Consensus size: 31
2779978 AAACTTTGAA
2779988 TAAATTCAATT-AAGT-CTAAAAA-CATTTTG
1 TAAATTCAATTCAAGTGC-AAAAACCATTTTG
2780017 TAAATTCAATTCAAGTGCAAAAACCATTTTG
1 TAAATTCAATTCAAGTGCAAAAACCATTTTG
2780048 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 11 0.39
30 9 0.32
31 8 0.29
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTGCAAAAACCATTTTG
Found at i:2783310 original size:21 final size:20
Alignment explanation
Indices: 2783266--2783339 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
2783256 GCAACCTTCG
* *
2783266 TGCATGGATGCACA-ACAGGA
1 TGCATCGATGCACAGA-ATGA
**
2783286 TGCATCGATGCACAGCCTTGA
1 TGCATCGATGCACAG-AATGA
* *
2783307 TGCATAGATGCAAAGAATGA
1 TGCATCGATGCACAGAATGA
2783327 TGCATCGATGCAC
1 TGCATCGATGCAC
2783340 TAATTGCATT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (20 bp):
TGCATCGATGCACAGAATGA
Found at i:2783393 original size:22 final size:23
Alignment explanation
Indices: 2783359--2783403 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
2783349 TCGGTGTTTG
2783359 AGTGCATGGTGCATCGATGCACT
1 AGTGCATGGTGCATCGATGCACT
*
2783382 AGTGCA-GGTGCATGGATGCACT
1 AGTGCATGGTGCATCGATGCACT
2783404 GCAGGGGTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.24
Consensus pattern (23 bp):
AGTGCATGGTGCATCGATGCACT
Found at i:2783563 original size:31 final size:31
Alignment explanation
Indices: 2783504--2783565 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
2783494 AAACTTTGAA
*
2783504 TAAATTCAATTAAGTATATAAAAACATTTTG
1 TAAATTCAATTAAGTACATAAAAACATTTTG
* *
2783535 TAAATTCAATTCAAGTCCA-AAAACCATTTTG
1 TAAATTCAATT-AAGTACATAAAAACATTTTG
2783566 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTAAGTACATAAAAACATTTTG
Found at i:2784281 original size:16 final size:16
Alignment explanation
Indices: 2784257--2784287 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2784247 CTATTTCTAT
*
2784257 TTCTTCGATTCTCTTC
1 TTCTCCGATTCTCTTC
2784273 TTCTCCGATTCTCTT
1 TTCTCCGATTCTCTT
2784288 GGGTCATAAC
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:0.06, C:0.32, G:0.06, T:0.55
Consensus pattern (16 bp):
TTCTCCGATTCTCTTC
Found at i:2785100 original size:21 final size:21
Alignment explanation
Indices: 2785074--2785115 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2785064 TTTCTACTAT
2785074 ATTGAAGTTGGGTATATGGAG
1 ATTGAAGTTGGGTATATGGAG
2785095 ATTGAAGTTGGGTATATGGAG
1 ATTGAAGTTGGGTATATGGAG
2785116 CAATCTCAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.38, T:0.33
Consensus pattern (21 bp):
ATTGAAGTTGGGTATATGGAG
Found at i:2787466 original size:18 final size:19
Alignment explanation
Indices: 2787443--2787480 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2787433 TGAATTGTTC
2787443 TCTTCT-TCAACCTCTATT
1 TCTTCTCTCAACCTCTATT
* *
2787461 TCTTCTCTTAATCTCTATT
1 TCTTCTCTCAACCTCTATT
2787480 T
1 T
2787481 TTATTTCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.16, C:0.29, G:0.00, T:0.55
Consensus pattern (19 bp):
TCTTCTCTCAACCTCTATT
Found at i:2787509 original size:16 final size:16
Alignment explanation
Indices: 2787485--2787515 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2787475 CTATTTTTAT
*
2787485 TTCTTCGATTCTCTTC
1 TTCTCCGATTCTCTTC
2787501 TTCTCCGATTCTCTT
1 TTCTCCGATTCTCTT
2787516 GGGTCATAAC
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:0.06, C:0.32, G:0.06, T:0.55
Consensus pattern (16 bp):
TTCTCCGATTCTCTTC
Found at i:2789389 original size:3 final size:3
Alignment explanation
Indices: 2789383--2789408 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2789373 GAAGAAGAAA
2789383 AGC AGC AGC AGC AGC AGC AGC AGC AG
1 AGC AGC AGC AGC AGC AGC AGC AGC AG
2789409 ACACGTGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.35, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:2795258 original size:20 final size:20
Alignment explanation
Indices: 2795229--2795268 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2795219 TTTGGGAAAA
* *
2795229 ATCGGTTTTTTTTTAACCGG
1 ATCGGATTTTTTTAAACCGG
2795249 ATCGGATTTTTTTAAACCGG
1 ATCGGATTTTTTTAAACCGG
2795269 TTATTTTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (20 bp):
ATCGGATTTTTTTAAACCGG
Found at i:2796108 original size:78 final size:79
Alignment explanation
Indices: 2796009--2796165 Score: 280
Period size: 78 Copynumber: 2.0 Consensus size: 79
2795999 TTTGAGGCAC
* *
2796009 GGTATCTGGTATAACATTGTGTCGAGAAGGTATTTCGTCCGGCGAAATCAAGTGTCGTTATTTTC
1 GGTATCTGGTATAACATTGTGTCGAGAAAGTATTTCGCCCGGCGAAATCAAGTGTCGTTATTTTC
2796074 TAAATCTCGTCTCG
66 TAAATCTCGTCTCG
*
2796088 GGTATCTGGTAT-ACATTGTGTCGAGAAAGTATTTCGCCCGGCGAAATCAAGTGTCGTTATTTTT
1 GGTATCTGGTATAACATTGTGTCGAGAAAGTATTTCGCCCGGCGAAATCAAGTGTCGTTATTTTC
2796152 TAAATCTCGTCTCG
66 TAAATCTCGTCTCG
2796166 AAAAAGTAAG
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
78 63 0.84
79 12 0.16
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.36
Consensus pattern (79 bp):
GGTATCTGGTATAACATTGTGTCGAGAAAGTATTTCGCCCGGCGAAATCAAGTGTCGTTATTTTC
TAAATCTCGTCTCG
Found at i:2797813 original size:13 final size:13
Alignment explanation
Indices: 2797795--2797820 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2797785 TGATCTTTAC
2797795 TGTAAATGGGCTT
1 TGTAAATGGGCTT
2797808 TGTAAATGGGCTT
1 TGTAAATGGGCTT
2797821 CTGATTTGTT
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:0.23, C:0.08, G:0.31, T:0.38
Consensus pattern (13 bp):
TGTAAATGGGCTT
Done.