Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004693.1 Hibiscus syriacus cultivar Beakdansim tig00010533_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: 2620943
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 3 of 12
Found at i:492777 original size:2 final size:2
Alignment explanation
Indices: 492770--492856 Score: 174
Period size: 2 Copynumber: 43.5 Consensus size: 2
492760 TAATAAACGT
492770 TA TA TA TA TA TA TA TA TA TA TA TA TA 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
492812 TA TA TA TA TA TA TA TA TA TA TA TA TA 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
492854 TA T
1 TA T
492857 GGGACAACCA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 85 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:496254 original size:22 final size:22
Alignment explanation
Indices: 496229--496293 Score: 103
Period size: 22 Copynumber: 3.0 Consensus size: 22
496219 GAAAGTCAAC
*
496229 GGTCAACGGTCCGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
496251 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
* *
496273 GTTCAACAGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
496294 AGACCGGTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.11, C:0.25, G:0.45, T:0.20
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:496337 original size:19 final size:18
Alignment explanation
Indices: 496296--496377 Score: 65
Period size: 19 Copynumber: 4.3 Consensus size: 18
496286 GTCGGGTCAG
* **
496296 ACCGGTCAAACTGGTTTA
1 ACCGGTCAAACCGGTCGA
*
496314 GACCGGTCAAATCGGTTCGA
1 -ACCGGTCAAACCGG-TCGA
* *
496334 ACCGATTGAAACCGGTCGA
1 ACCG-GTCAAACCGGTCGA
*
496353 ACCGGTCGAACCGGTCAGA
1 ACCGGTCAAACCGGTC-GA
496372 ACCGGT
1 ACCGGT
496378 TGAAAACCGG
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
18 9 0.18
19 32 0.64
20 9 0.18
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.18
Consensus pattern (18 bp):
ACCGGTCAAACCGGTCGA
Found at i:496357 original size:9 final size:9
Alignment explanation
Indices: 496315--496377 Score: 63
Period size: 9 Copynumber: 6.7 Consensus size: 9
496305 ACTGGTTTAG
*
496315 ACCGGTCAA
1 ACCGGTCGA
*
496324 ATCGGTTCGA
1 ACCGG-TCGA
* *
496334 ACCGATTGAA
1 ACCGGTCG-A
496344 ACCGGTCGA
1 ACCGGTCGA
496353 ACCGGTCGA
1 ACCGGTCGA
496362 ACCGGTCAGA
1 ACCGGTC-GA
496372 ACCGGT
1 ACCGGT
496378 TGAAAACCGG
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
9 23 0.52
10 21 0.48
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.16
Consensus pattern (9 bp):
ACCGGTCGA
Found at i:496374 original size:38 final size:39
Alignment explanation
Indices: 496315--496397 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 39
496305 ACTGGTTTAG
* *
496315 ACCGGTCAAATCGGTTCGAACCGATTG-AAACCGGTCGA
1 ACCGGTCAAACCGGTTCGAACCGATTGAAAACCGGTCAA
* * *
496353 ACCGGTCGAACCGG-TCAGAACCGGTTGAAAACCGGTTAA
1 ACCGGTCAAACCGGTTC-GAACCGATTGAAAACCGGTCAA
496392 ACCGGT
1 ACCGGT
496398 TTCCAGCAGC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
37 2 0.05
38 21 0.55
39 15 0.39
ACGTcount: A:0.29, C:0.27, G:0.28, T:0.17
Consensus pattern (39 bp):
ACCGGTCAAACCGGTTCGAACCGATTGAAAACCGGTCAA
Found at i:500961 original size:25 final size:25
Alignment explanation
Indices: 500923--500979 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
500913 TTATATCATA
*
500923 AATATTCATGTTAAGTAACGAAATT
1 AATATTTATGTTAAGTAACGAAATT
* * **
500948 AATATTTATTTTAATTAGTGAAATT
1 AATATTTATGTTAAGTAACGAAATT
500973 AATATTT
1 AATATTT
500980 TTGATTAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.46
Consensus pattern (25 bp):
AATATTTATGTTAAGTAACGAAATT
Found at i:511335 original size:12 final size:12
Alignment explanation
Indices: 511314--511343 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
511304 ATTCACTCAT
*
511314 TTACACCGCAGA
1 TTACATCGCAGA
511326 TTACATCGCAGA
1 TTACATCGCAGA
511338 TTACAT
1 TTACAT
511344 GATTGGTCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (12 bp):
TTACATCGCAGA
Found at i:520853 original size:21 final size:20
Alignment explanation
Indices: 520826--520924 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
520816 AATCAGTTTC
520826 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
520847 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
520868 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
520888 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
520909 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
520925 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 16 0.26
21 45 0.74
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:520915 original size:20 final size:20
Alignment explanation
Indices: 520891--521161 Score: 292
Period size: 20 Copynumber: 13.5 Consensus size: 20
520881 CGATTTTCCA
* ** *
520891 AAATCGCAACGCGAATATGA
1 AAATCGCAACGAGAATCCGT
* *
520911 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGAGAATC-CGT
* *
520931 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* *
520951 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
520971 TAATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
520991 AAATCGCAACGATAATACAT
1 AAATCGCAACGAGAATCCGT
* *
521011 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGAGAATCCGT
*
521032 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
521052 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
521072 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
521092 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
521112 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
521132 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
521152 AAATCACAAC
1 AAATCGCAAC
521162 ACTGAAATTT
Statistics
Matches: 214, Mismatches: 34, Indels: 6
0.84 0.13 0.02
Matches are distributed among these distances:
20 198 0.93
21 16 0.07
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGAGAATCCGT
Found at i:521022 original size:101 final size:101
Alignment explanation
Indices: 520910--521161 Score: 282
Period size: 101 Copynumber: 2.5 Consensus size: 101
520900 CGCGAATATG
* * * *
520910 AAAATCGCAACGCG-AACACATAAATCGCAACGCGT-ATCCGTAAATCGCAACGTGTATCCGTTA
1 AAAATCGCAACGCGTAAC-CATAAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCCGTAA
*
520973 ATCGCAACGCGT-ATCCGTAAATCGCAACGATAATACAT
64 ATCGCAACG-ATAATCCGTAAATCGCAACGATAATACAT
* * *
521011 AAAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAAAT
1 AAAATCGCAACGCGTAACCATAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCCGTAAAT
*
521076 CGCAACGATAATCCGTAAATCGCAACGAGAAT-C-T
66 CGCAACGATAATCCGTAAATCGCAACGATAATACAT
* * * * * *
521110 GTAAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCTGTAAATCACAAC
1 -AAAATCGCAACGCGTAA-CCATAAATCGCAACGATAATCCGTAAATCGCAAC
521162 ACTGAAATTT
Statistics
Matches: 131, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
99 3 0.02
100 45 0.34
101 81 0.62
102 2 0.02
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (101 bp):
AAAATCGCAACGCGTAACCATAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCCGTAAAT
CGCAACGATAATCCGTAAATCGCAACGATAATACAT
Found at i:521883 original size:24 final size:24
Alignment explanation
Indices: 521844--521890 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
521834 AAATTTGGTC
521844 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
521868 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
521891 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:523680 original size:42 final size:42
Alignment explanation
Indices: 523633--523718 Score: 129
Period size: 42 Copynumber: 2.0 Consensus size: 42
523623 AGATTAGGGT
* *
523633 AATGCTTAGGATTTT-CTTTATGTGAAGGCAACTTTCCATACG
1 AATGCTTAGGATTTTGCTTTAGGTAAAGGCAAC-TTCCATACG
*
523675 AATGCTTAGGGTTTTGCTTTAGGTAAAGGCAACTTCCATACG
1 AATGCTTAGGATTTTGCTTTAGGTAAAGGCAACTTCCATACG
523717 AA
1 AA
523719 GCGATGGAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 25 0.62
43 15 0.38
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (42 bp):
AATGCTTAGGATTTTGCTTTAGGTAAAGGCAACTTCCATACG
Found at i:524009 original size:2 final size:2
Alignment explanation
Indices: 524002--524030 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
523992 ATTCCTCTAT
524002 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
524031 GATCCACTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:525282 original size:81 final size:81
Alignment explanation
Indices: 525147--525314 Score: 318
Period size: 81 Copynumber: 2.1 Consensus size: 81
525137 GATATGACAG
* *
525147 TCAGCAATGGTTGACAACATGACGGATGATATGGCAAATTGACTAAATTAGTAACTCAATCATGG
1 TCAGCAATGGTTGACAACATGACGGATGATAGGGCAAATTGACTAAATTAGTAACCCAATCATGG
525212 CAAATGAACTTTCACA
66 CAAATGAACTTTCACA
525228 TCAGCAATGGTTGACAACATGACGGATGATAGGGCAAATTGACTAAATTAGTAACCCAATCATGG
1 TCAGCAATGGTTGACAACATGACGGATGATAGGGCAAATTGACTAAATTAGTAACCCAATCATGG
525293 CAAATGAACTTTCACA
66 CAAATGAACTTTCACA
525309 TCAGCA
1 TCAGCA
525315 CCGTGGACAA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 85 1.00
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.24
Consensus pattern (81 bp):
TCAGCAATGGTTGACAACATGACGGATGATAGGGCAAATTGACTAAATTAGTAACCCAATCATGG
CAAATGAACTTTCACA
Found at i:527529 original size:45 final size:45
Alignment explanation
Indices: 527465--527555 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
527455 GTGAAGAAAG
527465 AGAAAAAAGCAAGATAATTAGAGATTAGTTGAGGTTTGTGGATTA
1 AGAAAAAAGCAAGATAATTAGAGATTAGTTGAGGTTTGTGGATTA
527510 AGAAAAAAGCAAGATAATTAGAGATTAGTTGAGGTTTGTGGATTA
1 AGAAAAAAGCAAGATAATTAGAGATTAGTTGAGGTTTGTGGATTA
527555 A
1 A
527556 TTACAGTGTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.43, C:0.02, G:0.26, T:0.29
Consensus pattern (45 bp):
AGAAAAAAGCAAGATAATTAGAGATTAGTTGAGGTTTGTGGATTA
Found at i:533542 original size:17 final size:17
Alignment explanation
Indices: 533520--533569 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
533510 AGAAATGCTT
533520 TTGCATGCAACTATTTA
1 TTGCATGCAACTATTTA
533537 TTGCATGCAACTATTTA
1 TTGCATGCAACTATTTA
* **
533554 TTACATTTAACTATTT
1 TTGCATGCAACTATTT
533570 TCAAATGGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (17 bp):
TTGCATGCAACTATTTA
Found at i:543000 original size:64 final size:64
Alignment explanation
Indices: 542899--543025 Score: 200
Period size: 64 Copynumber: 2.0 Consensus size: 64
542889 AATCAGGCAT
* * *
542899 TCCTATTTGCAACACTATCAAAGAAACCATTTGCTAGTTTACCATACCTAGACTATCAATATTA
1 TCCTATTTACAACACTACCAAAGAAACAATTTGCTAGTTTACCATACCTAGACTATCAATATTA
* * *
542963 TCCTATTTACAACACTACCAAAGAAACAATTTGCTAGTTTACCATAGCTAGATTATCGATATT
1 TCCTATTTACAACACTACCAAAGAAACAATTTGCTAGTTTACCATACCTAGACTATCAATATT
543026 CTTTAGCATA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.33
Consensus pattern (64 bp):
TCCTATTTACAACACTACCAAAGAAACAATTTGCTAGTTTACCATACCTAGACTATCAATATTA
Found at i:544422 original size:13 final size:13
Alignment explanation
Indices: 544401--544455 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
544391 AAGTTCGATA
*
544401 AATTCAAATACTT
1 AATTGAAATACTT
544414 AATTGAAATACTT
1 AATTGAAATACTT
* *
544427 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
544441 AATTGAAATACTT
1 AATTGAAATACTT
544454 AA
1 AA
544456 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:544537 original size:32 final size:33
Alignment explanation
Indices: 544441--544539 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
544431 AACTCAACAT
* * *
544441 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
544474 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
544507 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
544539 A
1 A
544540 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:544558 original size:21 final size:21
Alignment explanation
Indices: 544534--544573 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
544524 ACTTCAAGTT
544534 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
544555 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
544574 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:546871 original size:12 final size:12
Alignment explanation
Indices: 546854--546900 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
546844 TCCGAATAAA
546854 AACCGGTTTTTT
1 AACCGGTTTTTT
546866 AACCGGTTTTTTT
1 AACCGG-TTTTTT
546879 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
546893 ATCCGGTT
1 AACCGGTT
546901 AAAAAACCGG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 13 0.42
13 6 0.19
14 6 0.19
15 6 0.19
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:546884 original size:15 final size:14
Alignment explanation
Indices: 546853--546892 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
546843 TTCCGAATAA
546853 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
546866 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
546879 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
546893 ATCCGGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:549695 original size:31 final size:28
Alignment explanation
Indices: 549621--549696 Score: 73
Period size: 31 Copynumber: 2.5 Consensus size: 28
549611 TTGGGCTGAT
549621 TAAAATAAGTCATATATTAATAAAATAA
1 TAAAATAAGTCATATATTAATAAAATAA
*
549649 GAATAATGAATGTCATATCA-TACATAAATATTAA
1 TAA-AAT-AA-GTCATAT-ATTA-ATAAA-A-TAA
549683 TAAAATAAGTCATA
1 TAAAATAAGTCATA
549697 ATGATTAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
28 2 0.05
29 3 0.08
30 2 0.05
31 15 0.38
32 8 0.21
33 4 0.10
34 5 0.13
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.32
Consensus pattern (28 bp):
TAAAATAAGTCATATATTAATAAAATAA
Found at i:550106 original size:31 final size:31
Alignment explanation
Indices: 550064--550123 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
550054 TATTATTTTT
* *
550064 AAAAAATTAAGAGTTGTGACTACTTTAATAA
1 AAAAAAATAAGAGTTGCGACTACTTTAATAA
*
550095 AAAAAAATAAGAGTTGCGACTCCTTTAAT
1 AAAAAAATAAGAGTTGCGACTACTTTAAT
550124 TTAAAGATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.30
Consensus pattern (31 bp):
AAAAAAATAAGAGTTGCGACTACTTTAATAA
Found at i:550794 original size:6 final size:7
Alignment explanation
Indices: 550778--550802 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
550768 GTAAAACACT
550778 AAAAAGA
1 AAAAAGA
550785 AAAAAGA
1 AAAAAGA
550792 AAAAAGA
1 AAAAAGA
550799 AAAA
1 AAAA
550803 CCCACAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:559360 original size:71 final size:71
Alignment explanation
Indices: 559240--559442 Score: 284
Period size: 71 Copynumber: 2.9 Consensus size: 71
559230 CCCGACCCAC
* * * *
559240 AAATATGCATCATCCACCCAAACCGAAAAATATATATCATCCACCCGAAAATATCCTACATCAA-
1 AAATATGCATCATCCACTCGAACCGAAAACTATATATCATCCACACGAAAATATCCTACATCAAC
*
559304 TCTTGA
66 TCCTGA
* *
559310 AAATATGCATCATCCACTCGAACTGAAAGACTATATATCGTCCACACGAAAATATCCTACAT-AA
1 AAATATGCATCATCCACTCGAACCGAAA-ACTATATATCATCCACACGAAAATATCCTACATCAA
559374 CTCCTGA
65 CTCCTGA
* * * *
559381 AAATATACACCATCCACTCGAACCGAAAACTATGTATCCTCCACACGAAAATATCCTACATC
1 AAATATGCATCATCCACTCGAACCGAAAACTATATATCATCCACACGAAAATATCCTACATC
559443 CGACCCGACT
Statistics
Matches: 118, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
70 58 0.49
71 60 0.51
ACGTcount: A:0.41, C:0.29, G:0.07, T:0.23
Consensus pattern (71 bp):
AAATATGCATCATCCACTCGAACCGAAAACTATATATCATCCACACGAAAATATCCTACATCAAC
TCCTGA
Found at i:561698 original size:121 final size:121
Alignment explanation
Indices: 561536--561810 Score: 336
Period size: 121 Copynumber: 2.3 Consensus size: 121
561526 TAATGTTAAG
* * ** * *
561536 TTTTGAAAAAATTTAAAAGTTCATGTACTAAAACATACCAAAGTTGATAGTTTAGGTACTAGATG
1 TTTTGAAAAAA-TTAAAAGTTTATGTACTAAAACAGACCAAAACTGATAGTTTAGGTACTAAACG
** * *
561601 AGTTAAGTTTTTAACGACGGGTATTAAAATAAAACAAAAACTAAATATTAAGTATGA
65 AGTTAAGTTTTTAACGACAAGTACTAAAATAAAACAAAAACTAAACATTAAGTATGA
* * * *
561658 TTTT-AAAAAAGTTGAAAGTTTATGTATTAAAACGGGCCAAAACTGATAGTTTAGGTACTAAACG
1 TTTTGAAAAAA-TTAAAAGTTTATGTACTAAAACAGACCAAAACTGATAGTTTAGGTACTAAACG
* * * ** *
561722 AGTTAATTTTTTAACGACAAGTACTAAAATGAAACAAAAACTAAACGTTGGGTATGG
65 AGTTAAGTTTTTAACGACAAGTACTAAAATAAAACAAAAACTAAACATTAAGTATGA
*
561779 TTTTGAAAAAATTAAAAGTTTAGGTACTAAAA
1 TTTTGAAAAAATTAAAAGTTTATGTACTAAAA
561811 TGAATCAAAA
Statistics
Matches: 128, Mismatches: 24, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
121 118 0.92
122 10 0.08
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.31
Consensus pattern (121 bp):
TTTTGAAAAAATTAAAAGTTTATGTACTAAAACAGACCAAAACTGATAGTTTAGGTACTAAACGA
GTTAAGTTTTTAACGACAAGTACTAAAATAAAACAAAAACTAAACATTAAGTATGA
Found at i:563525 original size:18 final size:18
Alignment explanation
Indices: 563502--563536 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
563492 AAGGCGATGA
* *
563502 CAGCATTATATATGGCTG
1 CAGCATCATAAATGGCTG
563520 CAGCATCATAAATGGCT
1 CAGCATCATAAATGGCT
563537 ACGATGGCTG
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:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (18 bp):
CAGCATCATAAATGGCTG
Found at i:565190 original size:111 final size:111
Alignment explanation
Indices: 565048--565261 Score: 401
Period size: 111 Copynumber: 1.9 Consensus size: 111
565038 ATTACAAAAA
* * *
565048 TTAATTCTTAATCTAATAATCATGTATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATAATGCATTAAATAAATAAACTAATTATTACTAATAATTTAAATTA
565113 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGATATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGATATAT
565159 TTAATTCTTAATCTAATAATAATGCATTAAATAAATAAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATAATGCATTAAATAAATAAACTAATTATTACTAATAATTTAAATTA
565224 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGT
565262 AAAGATATAT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 100 1.00
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATAATGCATTAAATAAATAAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGATATAT
Found at i:565374 original size:17 final size:18
Alignment explanation
Indices: 565333--565371 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
565323 ATTATATTAC
565333 TAAAATA-TTAAATAAAG
1 TAAAATACTTAAATAAAG
*
565350 TAAAATACTTAAATAAAT
1 TAAAATACTTAAATAAAG
565368 TAAA
1 TAAA
565372 TACATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (18 bp):
TAAAATACTTAAATAAAG
Found at i:566707 original size:40 final size:42
Alignment explanation
Indices: 566662--566744 Score: 134
Period size: 40 Copynumber: 2.0 Consensus size: 42
566652 TAGCAATAAC
* *
566662 TACAAATTTAACATGTATTTTA-TTTTTAAT-GATAAATTAT
1 TACAAATTTAACATATATTTTATTTTTTAATAAATAAATTAT
566702 TACAAATTTAACATATATTTTATTTTTTAATAAATAAATTAT
1 TACAAATTTAACATATATTTTATTTTTTAATAAATAAATTAT
566744 T
1 T
566745 TATTTGTAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 21 0.54
41 8 0.21
42 10 0.26
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (42 bp):
TACAAATTTAACATATATTTTATTTTTTAATAAATAAATTAT
Found at i:569478 original size:17 final size:18
Alignment explanation
Indices: 569456--569489 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
569446 ATATCTAAAG
*
569456 TTTAGT-TTTTGTTTTAT
1 TTTAGTATTTTCTTTTAT
569473 TTTAGTATTTTCTTTTA
1 TTTAGTATTTTCTTTTA
569490 AAAAAGTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.03, G:0.09, T:0.74
Consensus pattern (18 bp):
TTTAGTATTTTCTTTTAT
Found at i:569602 original size:27 final size:27
Alignment explanation
Indices: 569571--569626 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
569561 AAAACTTATC
*
569571 GATAAATTTTGAACAATGAATTAAAAT
1 GATAAATTTTGAACAATGAACTAAAAT
*
569598 GATAAGTTTTGAACAATGAACTAAAAT
1 GATAAATTTTGAACAATGAACTAAAAT
569625 GA
1 GA
569627 AACAAAAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.30
Consensus pattern (27 bp):
GATAAATTTTGAACAATGAACTAAAAT
Found at i:573458 original size:27 final size:27
Alignment explanation
Indices: 573422--573477 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
573412 ATTATTTGAC
573422 TAAAAAGTATTGTTTAATTTCTTTATT
1 TAAAAAGTATTGTTTAATTTCTTTATT
* *
573449 TAAAAGGTATTGTTTCATTTCTTTATT
1 TAAAAAGTATTGTTTAATTTCTTTATT
573476 TA
1 TA
573478 GAAATGATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.55
Consensus pattern (27 bp):
TAAAAAGTATTGTTTAATTTCTTTATT
Found at i:574704 original size:286 final size:286
Alignment explanation
Indices: 574192--574769 Score: 1156
Period size: 286 Copynumber: 2.0 Consensus size: 286
574182 TTCTCAGAAA
574192 CATTTTTACAAACAGTTTGAAGACATGTAATGCAAAGAGTCTGGATTTCGAAAACTTCCGGACCT
1 CATTTTTACAAACAGTTTGAAGACATGTAATGCAAAGAGTCTGGATTTCGAAAACTTCCGGACCT
574257 TATTGACGAGGTAGTAATCGGCGAACAATACTCCTCGAGACCTTGTTCTTGCAACTCGATAACCC
66 TATTGACGAGGTAGTAATCGGCGAACAATACTCCTCGAGACCTTGTTCTTGCAACTCGATAACCC
574322 GAGTTCAAAACCGAGAACGGCTAGTTAAAAGTTTCACCGACCGGTAAAGTTAGAAAGTGAAACAA
131 GAGTTCAAAACCGAGAACGGCTAGTTAAAAGTTTCACCGACCGGTAAAGTTAGAAAGTGAAACAA
574387 ACTTGAGGGGAAAAAAGTGTGGGGAGATAGCTGCTTCGGTTGCCGCTGGCACCGTAAACTCTTAT
196 ACTTGAGGGGAAAAAAGTGTGGGGAGATAGCTGCTTCGGTTGCCGCTGGCACCGTAAACTCTTAT
574452 CTCCGGCTGAGAATTCATGGTGCACT
261 CTCCGGCTGAGAATTCATGGTGCACT
574478 CATTTTTACAAACAGTTTGAAGACATGTAATGCAAAGAGTCTGGATTTCGAAAACTTCCGGACCT
1 CATTTTTACAAACAGTTTGAAGACATGTAATGCAAAGAGTCTGGATTTCGAAAACTTCCGGACCT
574543 TATTGACGAGGTAGTAATCGGCGAACAATACTCCTCGAGACCTTGTTCTTGCAACTCGATAACCC
66 TATTGACGAGGTAGTAATCGGCGAACAATACTCCTCGAGACCTTGTTCTTGCAACTCGATAACCC
574608 GAGTTCAAAACCGAGAACGGCTAGTTAAAAGTTTCACCGACCGGTAAAGTTAGAAAGTGAAACAA
131 GAGTTCAAAACCGAGAACGGCTAGTTAAAAGTTTCACCGACCGGTAAAGTTAGAAAGTGAAACAA
574673 ACTTGAGGGGAAAAAAGTGTGGGGAGATAGCTGCTTCGGTTGCCGCTGGCACCGTAAACTCTTAT
196 ACTTGAGGGGAAAAAAGTGTGGGGAGATAGCTGCTTCGGTTGCCGCTGGCACCGTAAACTCTTAT
574738 CTCCGGCTGAGAATTCATGGTGCACT
261 CTCCGGCTGAGAATTCATGGTGCACT
574764 CATTTT
1 CATTTT
574770 GCACGAAACT
Statistics
Matches: 292, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
286 292 1.00
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.25
Consensus pattern (286 bp):
CATTTTTACAAACAGTTTGAAGACATGTAATGCAAAGAGTCTGGATTTCGAAAACTTCCGGACCT
TATTGACGAGGTAGTAATCGGCGAACAATACTCCTCGAGACCTTGTTCTTGCAACTCGATAACCC
GAGTTCAAAACCGAGAACGGCTAGTTAAAAGTTTCACCGACCGGTAAAGTTAGAAAGTGAAACAA
ACTTGAGGGGAAAAAAGTGTGGGGAGATAGCTGCTTCGGTTGCCGCTGGCACCGTAAACTCTTAT
CTCCGGCTGAGAATTCATGGTGCACT
Found at i:579407 original size:24 final size:25
Alignment explanation
Indices: 579356--579410 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 25
579346 CAATAGAAAA
579356 AATAACAAAATCGGTAAAACGCTCAAT
1 AATAACAAAATCGGTAAAA--CTCAAT
579383 AATAACAAAATCGGTATAAA-T-AAT
1 AATAACAAAATCGGTA-AAACTCAAT
579407 AATA
1 AATA
579411 TTTTCGATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
24 7 0.26
25 1 0.04
27 16 0.59
28 3 0.11
ACGTcount: A:0.56, C:0.13, G:0.09, T:0.22
Consensus pattern (25 bp):
AATAACAAAATCGGTAAAACTCAAT
Found at i:581811 original size:59 final size:60
Alignment explanation
Indices: 581673--581812 Score: 137
Period size: 60 Copynumber: 2.3 Consensus size: 60
581663 GTGCAAAGGT
581673 AAATTACATAAATGATC-CCTCAATTATAGAAAATTACTTTGTCAAATCCCCAAATAATAA
1 AAATTACA-AAATGATCACCTCAATTATAGAAAATTACTTTGTCAAATCCCCAAATAATAA
* * ** * * *
581733 AAACTTATAAAAT-ATTCACC-CAATTATATG-ATATTA-TTTGTTGAGTCCCTCAACTATTAA
1 AAA-TTACAAAATGA-TCACCTCAATTATA-GAAAATTACTTTGTCAAATCCC-CAAATAATAA
581793 AAATTACAAAATGATCACCT
1 AAATTACAAAATGATCACCT
581813 AACTATTCAT
Statistics
Matches: 65, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
59 24 0.37
60 34 0.52
61 7 0.11
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.33
Consensus pattern (60 bp):
AAATTACAAAATGATCACCTCAATTATAGAAAATTACTTTGTCAAATCCCCAAATAATAA
Found at i:582124 original size:54 final size:53
Alignment explanation
Indices: 582052--582153 Score: 159
Period size: 54 Copynumber: 1.9 Consensus size: 53
582042 AACAAAATAA
* *
582052 TATCTTATAATCAGAAATTATTTTATAACTTTTTGATAACCAAGGACCAAGTAG
1 TATCCTATAATCAAAAATTATTTTATAACTTTTT-ATAACCAAGGACCAAGTAG
* *
582106 TATCCTATAATTAAAAATTATTTTATAACTTTTTATAATCAAGGACCA
1 TATCCTATAATCAAAAATTATTTTATAACTTTTTATAACCAAGGACCA
582154 TTAGTTTACT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 13 0.30
54 31 0.70
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (53 bp):
TATCCTATAATCAAAAATTATTTTATAACTTTTTATAACCAAGGACCAAGTAG
Found at i:586889 original size:18 final size:20
Alignment explanation
Indices: 586857--586895 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
586847 GATATATAAT
586857 AAGAAAATTATAAA-TTCGA
1 AAGAAAATTATAAATTTCGA
*
586876 AAGAAATTTA-AAATTTCGA
1 AAGAAAATTATAAATTTCGA
586895 A
1 A
586896 TTGATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.28
Consensus pattern (20 bp):
AAGAAAATTATAAATTTCGA
Found at i:590703 original size:3 final size:3
Alignment explanation
Indices: 590695--590720 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
590685 ACGGTGTTCT
590695 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
590721 ATAGTAGGTA
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:593198 original size:16 final size:16
Alignment explanation
Indices: 593170--593217 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
593160 ACTATTCACT
*
593170 TGAATAGTGAATTTCG
1 TGAATAGTAAATTTCG
*
593186 TGAATGGTAAATTTCG
1 TGAATAGTAAATTTCG
*
593202 TGAATAGTAAAATTCG
1 TGAATAGTAAATTTCG
593218 GTCGGCGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.35
Consensus pattern (16 bp):
TGAATAGTAAATTTCG
Found at i:598613 original size:2 final size:2
Alignment explanation
Indices: 598597--598671 Score: 134
Period size: 2 Copynumber: 38.0 Consensus size: 2
598587 AAAATTATCT
*
598597 TA TA TA T- TA TG TA TA TA TA TA TA TA 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
598638 TA TA TA TA TA TA TA TA TA 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
598672 CACACACACT
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
1 1 0.01
2 69 0.99
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:607832 original size:54 final size:57
Alignment explanation
Indices: 607774--607914 Score: 141
Period size: 54 Copynumber: 2.5 Consensus size: 57
607764 ATATTATTTC
* *
607774 TATAATTATATA-TATGTATATTA-AA-ACTATTATAAT-TTATTAAAATGA-AAATAT
1 TATAATTATATATTAT-T-TATTACAATAATATTATAATATTATTAAAATAATAAATAT
* * *
607828 TATAAGTATA-ATTATTTATTACAATAATATTATTATATTATTAACATAATAAATAT
1 TATAATTATATATTATTTATTACAATAATATTATAATATTATTAAAATAATAAATAT
*
607884 TACTAATTATATTAATTATTTATTAAAATAA
1 TA-TAATTATA-T-ATTATTTATTACAATAA
607915 GAATATTATT
Statistics
Matches: 71, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
52 5 0.07
53 4 0.06
54 21 0.30
55 10 0.14
56 8 0.11
57 7 0.10
60 16 0.23
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (57 bp):
TATAATTATATATTATTTATTACAATAATATTATAATATTATTAAAATAATAAATAT
Found at i:607868 original size:22 final size:21
Alignment explanation
Indices: 607829--607914 Score: 58
Period size: 22 Copynumber: 4.2 Consensus size: 21
607819 TGAAAATATT
607829 ATAAGTATAATTATTTATT-AC
1 ATAA-TATAATTATTTATTAAC
*
607850 AATAATATTATTATATTATTAAC
1 -ATAATATAATTAT-TTATTAAC
*
607873 ATAATA-AA-TA-TTACT-A-
1 ATAATATAATTATTTATTAAC
* *
607889 ATTATATTAATTATTTATTAAA
1 ATAATA-TAATTATTTATTAAC
607911 ATAA
1 ATAA
607915 GAATATTATT
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
16 5 0.10
17 1 0.02
18 6 0.12
19 2 0.04
20 6 0.12
21 10 0.20
22 18 0.36
23 2 0.04
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (21 bp):
ATAATATAATTATTTATTAAC
Found at i:607877 original size:38 final size:38
Alignment explanation
Indices: 607844--607934 Score: 109
Period size: 38 Copynumber: 2.5 Consensus size: 38
607834 TATAATTATT
*
607844 TATTAC-AATAATATT-ATTATATTATTAACATAATAAA
1 TATTACTAATAATATTAATTAT-TTATTAAAATAATAAA
* *
607881 TATTACTAATTATATTAATTATTTATTAAAATAA-GAA
1 TATTACTAATAATATTAATTATTTATTAAAATAATAAA
*
607918 TATTA-TTATAATATTAA
1 TATTACTAATAATATTAA
607935 AAATTATAGT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
36 10 0.21
37 13 0.28
38 19 0.40
39 5 0.11
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (38 bp):
TATTACTAATAATATTAATTATTTATTAAAATAATAAA
Found at i:607942 original size:15 final size:15
Alignment explanation
Indices: 607922--607951 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
607912 TAAGAATATT
607922 ATTATAATATTAAAA
1 ATTATAATATTAAAA
*
607937 ATTATAGTATTAAAA
1 ATTATAATATTAAAA
607952 TAGAAATGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
ATTATAATATTAAAA
Found at i:608178 original size:22 final size:23
Alignment explanation
Indices: 608130--608191 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 23
608120 TATTAATAAA
*
608130 TAAATTTTAATAATCAATATTTTTAT
1 TAAA-TTTAATAA--AATATTTATAT
608156 TAAATTTAATAAAATA-TTATAT
1 TAAATTTAATAAAATATTTATAT
*
608178 TAATATTAAATAAA
1 TAA-ATTTAATAAA
608192 TCAAATAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 8 0.24
23 13 0.39
25 8 0.24
26 4 0.12
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TAAATTTAATAAAATATTTATAT
Found at i:611341 original size:21 final size:20
Alignment explanation
Indices: 611292--611342 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
611282 CCATCTTTAT
* *
611292 TTTTAACTTTTCATATATAA
1 TTTTAACTATTCATAAATAA
*
611312 TTGTAAACTATTCATAAATAA
1 TT-TTAACTATTCATAAATAA
611333 CTTTTAACTA
1 -TTTTAACTA
611343 AACACAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 2 0.08
21 21 0.84
22 2 0.08
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.47
Consensus pattern (20 bp):
TTTTAACTATTCATAAATAA
Found at i:612361 original size:18 final size:18
Alignment explanation
Indices: 612324--612361 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
612314 AATAGTAAAA
*
612324 TTAAATATTTTATCTTAC
1 TTAAATATTTTATCTAAC
612342 TTAAA-ATTTTATCCTAAC
1 TTAAATATTTTAT-CTAAC
612360 TT
1 TT
612362 TACTTTAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAAATATTTTATCTAAC
Found at i:612462 original size:21 final size:20
Alignment explanation
Indices: 612415--612465 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
612405 TATAGTGGCG
*
612415 GATTTAAAATTTTAATATTA
1 GATTTAAAATTTTAATAATA
*
612435 GAGTTTAAAATTTTTATAATA
1 GA-TTTAAAATTTTAATAATA
*
612456 TTATTTAAAA
1 -GATTTAAAA
612466 AAATGAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 2 0.08
21 23 0.88
22 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (20 bp):
GATTTAAAATTTTAATAATA
Found at i:614267 original size:19 final size:19
Alignment explanation
Indices: 614224--614267 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
614214 TTAGAGGTGG
614224 GTAAAATTCGATTCGACTC
1 GTAAAATTCGATTCGACTC
* *
614243 GAAAAATTCGAATT-GATTC
1 GTAAAATTCG-ATTCGACTC
614262 GTAAAA
1 GTAAAA
614268 GTTTTAAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
GTAAAATTCGATTCGACTC
Found at i:615150 original size:29 final size:29
Alignment explanation
Indices: 615117--615202 Score: 145
Period size: 29 Copynumber: 3.0 Consensus size: 29
615107 ATCCCAACAC
* *
615117 ATAGGTCGTCATGCCCTCCGGACGACCTT
1 ATAGGTCGCCATGCCCTCCGGGCGACCTT
615146 ATAGGTCGCCATGCCCTCCGGGCGACCTT
1 ATAGGTCGCCATGCCCTCCGGGCGACCTT
*
615175 ATAGGTCGCCATGCACTCCGGGCGACCT
1 ATAGGTCGCCATGCCCTCCGGGCGACCT
615203 ACCCTTGCTC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.16, C:0.36, G:0.27, T:0.21
Consensus pattern (29 bp):
ATAGGTCGCCATGCCCTCCGGGCGACCTT
Found at i:615267 original size:33 final size:33
Alignment explanation
Indices: 615222--615329 Score: 108
Period size: 33 Copynumber: 3.3 Consensus size: 33
615212 CGCTCGCTCG
*
615222 CTCGGATGCCCTCACATAGCTCACTCGGTTGCC
1 CTCGGATGCCCTCACATAGCTCACTCGGATGCC
* * * *
615255 CTCGGATTCCCTCGCATAGCTCGCTCGGATGGC
1 CTCGGATGCCCTCACATAGCTCACTCGGATGCC
* ** ** *
615288 CTCGGATGCTCTTGCATAGCTCGGTCGGATGAC
1 CTCGGATGCCCTCACATAGCTCACTCGGATGCC
*
615321 CTCGAATGC
1 CTCGGATGC
615330 TCAGCGTGTT
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.15, C:0.34, G:0.26, T:0.25
Consensus pattern (33 bp):
CTCGGATGCCCTCACATAGCTCACTCGGATGCC
Found at i:615644 original size:25 final size:25
Alignment explanation
Indices: 615610--615668 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
615600 ATGCGGCTTG
615610 GCCGACAACTGTCTGCACCCGCCTC
1 GCCGACAACTGTCTGCACCCGCCTC
615635 GCCGACAACTGTCTGCACCCGCCTC
1 GCCGACAACTGTCTGCACCCGCCTC
*
615660 GCCAACAAC
1 GCCGACAAC
615669 AAAACTAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.20, C:0.47, G:0.19, T:0.14
Consensus pattern (25 bp):
GCCGACAACTGTCTGCACCCGCCTC
Found at i:617371 original size:3 final size:3
Alignment explanation
Indices: 617363--617387 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
617353 GTGCAATGTG
617363 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
617388 AACCCTGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:619809 original size:3 final size:3
Alignment explanation
Indices: 619801--619828 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
619791 GAATAGGGTC
619801 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
619829 AGTTAAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:627660 original size:5 final size:5
Alignment explanation
Indices: 627650--627787 Score: 235
Period size: 5 Copynumber: 27.4 Consensus size: 5
627640 ATTTCAATAA
627650 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
627700 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATAT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATAT-T ATATT
627751 -TA-T ATATT ATATT ATATT ATATTAT ATATT ATATT AT
1 ATATT ATATT ATATT ATATT ATA-T-T ATATT ATATT AT
627788 TAGCTAAAAA
Statistics
Matches: 128, Mismatches: 0, Indels: 10
0.93 0.00 0.07
Matches are distributed among these distances:
3 1 0.01
4 4 0.03
5 112 0.88
6 7 0.05
7 4 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:629214 original size:21 final size:21
Alignment explanation
Indices: 629163--629215 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
629153 ATTATTACTA
629163 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
629184 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
629205 TCGCAATGCGA
1 TCGCAATGCGA
629216 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:629230 original size:20 final size:21
Alignment explanation
Indices: 629205--629256 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
629195 TTTTCCCAAT
*
629205 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
629225 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
629246 TCGCAATGCGA
1 TCGCAATGCGA
629257 TACTTACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:629343 original size:39 final size:40
Alignment explanation
Indices: 629287--629373 Score: 131
Period size: 39 Copynumber: 2.2 Consensus size: 40
629277 TAATACAAAA
*
629287 TCGCAACGCAATACTGACTTTCGCAACGCG-TACTGACTT
1 TCGCAACGCAATACTGACTTTCGCAACGAGATACTGACTT
* * *
629326 TCGCAACGCGATTCTGACTTTCGCAACGAGATTCTGACTT
1 TCGCAACGCAATACTGACTTTCGCAACGAGATACTGACTT
629366 TCGCAACG
1 TCGCAACG
629374 AGATAATACA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 27 0.63
40 16 0.37
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (40 bp):
TCGCAACGCAATACTGACTTTCGCAACGAGATACTGACTT
Found at i:629374 original size:20 final size:20
Alignment explanation
Indices: 629287--629378 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
629277 TAATACAAAA
629287 TCGCAACGCA-ATACTGACTT
1 TCGCAACG-AGATACTGACTT
*
629307 TCGCAACGCG-TACTGACTT
1 TCGCAACGAGATACTGACTT
* *
629326 TCGCAACGCGATTCTGACTT
1 TCGCAACGAGATACTGACTT
*
629346 TCGCAACGAGATTCTGACTT
1 TCGCAACGAGATACTGACTT
629366 TCGCAACGAGATA
1 TCGCAACGAGATA
629379 ATACAGAATC
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
19 19 0.29
20 47 0.71
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (20 bp):
TCGCAACGAGATACTGACTT
Found at i:629957 original size:24 final size:24
Alignment explanation
Indices: 629930--629983 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
629920 GTATTCGAAA
*
629930 TTTGATCTTGGTCAATACCCAGAC
1 TTTGATATTGGTCAATACCCAGAC
* *
629954 TTTGATATTGGTCAATACTCAGAT
1 TTTGATATTGGTCAATACCCAGAC
629978 TTTGAT
1 TTTGAT
629984 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCAGAC
Found at i:632513 original size:20 final size:19
Alignment explanation
Indices: 632485--632539 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
632475 CAATCATCTT
*
632485 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGC-GA
*
632505 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
632524 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
632540 AGGGAATCGT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:632527 original size:19 final size:20
Alignment explanation
Indices: 632446--632539 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
632436 GACAATCATT
*
632446 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* **
632466 TGACGT-TCGCAATCATC-TTAA
1 TGAC-TATCGCAA-C-GCGGAAA
*
632487 TGTCTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
*
632507 TGACTATCGCAATGC-GAAA
1 TGACTATCGCAACGCGGAAA
**
632526 TGAAAATCGCAACG
1 TGACTATCGCAACG
632540 AGGGAATCGT
Statistics
Matches: 57, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
19 16 0.28
20 27 0.47
21 13 0.23
22 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.21
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:632594 original size:19 final size:19
Alignment explanation
Indices: 632572--632646 Score: 63
Period size: 19 Copynumber: 4.2 Consensus size: 19
632562 AAATCATAAC
*
632572 GCGAATTT-AGTTTCGCGTT
1 GCGAATTTCA-TTTCGCATT
*
632591 GCGATTTTCATTTCGCATT
1 GCGAATTTCATTTCGCATT
*
632610 GCG-A-TTC-TCTCG--TT
1 GCGAATTTCATTTCGCATT
*
632624 GCGATTTTCATTTCGCATT
1 GCGAATTTCATTTCGCATT
632643 GCGA
1 GCGA
632647 TAGTCATTTC
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
14 5 0.11
16 7 0.16
17 7 0.16
19 24 0.55
20 1 0.02
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (19 bp):
GCGAATTTCATTTCGCATT
Found at i:632656 original size:19 final size:19
Alignment explanation
Indices: 632582--632647 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
632572 GCGAATTTAG
*
632582 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
632601 TTTCGCATTGCGA--TTC-
1 TTTCGCATTGCGATTTTCA
*
632617 TCTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
632634 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
632648 AGTCATTTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 6 0.15
16 7 0.18
17 7 0.18
19 19 0.49
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:632773 original size:14 final size:14
Alignment explanation
Indices: 632754--632790 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
632744 CATCAATTAA
*
632754 ACAAATTAACTTTT
1 ACAAATCAACTTTT
*
632768 ACAAATCATCTTTT
1 ACAAATCAACTTTT
632782 ACAAATCAA
1 ACAAATCAA
632791 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:634207 original size:21 final size:21
Alignment explanation
Indices: 634141--634207 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
634131 GTGAATCGGG
*
634141 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
634161 CATCTTCAACGATGACAGTGGC
1 C-TCTTGAACGGTGGGAGGGGA
634183 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
634204 CTCT
1 CTCT
634208 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 28 0.88
22 3 0.09
ACGTcount: A:0.21, C:0.19, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:634226 original size:42 final size:42
Alignment explanation
Indices: 634180--634259 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
634170 CGATGACAGT
* * *
634180 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAAG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAAG
* * *
634222 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
634260 CAGGCGAGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAAG
Found at i:636340 original size:20 final size:20
Alignment explanation
Indices: 636315--636353 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
636305 TTTTGGTTGA
636315 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
636335 AATGAAAATCGCAACGAGA
1 AATGAAAATCGCAACGAGA
636354 TAATCGCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.15, G:0.23, T:0.10
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:637579 original size:30 final size:30
Alignment explanation
Indices: 637520--637638 Score: 177
Period size: 30 Copynumber: 4.0 Consensus size: 30
637510 CCCGAAGGAC
* * *
637520 CTATCCAGAGGTCACACAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
637549 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
637579 CTGTCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
637609 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
637639 ACTGTCCATA
Statistics
Matches: 83, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
29 18 0.22
30 65 0.78
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:637695 original size:31 final size:31
Alignment explanation
Indices: 637634--637701 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
637624 AAAGATCCTC
**
637634 GGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAAACTGTCCATATGTTCCAAAGAACATA
* *
637665 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTAAACTGTCCATATGT-TCCAAAGAACATA
637696 GGTAAA
1 GGTAAA
637702 ACCCTCGACT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (31 bp):
GGTAAACTGTCCATATGTTCCAAAGAACATA
Found at i:638450 original size:21 final size:21
Alignment explanation
Indices: 638426--638470 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
638416 CTATGTTCGT
* * *
638426 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
638447 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
638468 TTG
1 TTG
638471 CCCAGAATCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:639348 original size:20 final size:20
Alignment explanation
Indices: 639325--639459 Score: 153
Period size: 20 Copynumber: 6.7 Consensus size: 20
639315 CGATAGTCAG
*
639325 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACCT
*
639345 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACCT
*
639365 AATTCGCATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACCT
* * *
639386 AATCGCGTTGCGATTTTCCT
1 ATTCGCATTGCGATTTACCT
* *
639406 AATTTGCATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACCT
* * *
639427 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACCT
639447 ATTCGCATTGCGA
1 ATTCGCATTGCGA
639460 ATTGGGAAAA
Statistics
Matches: 94, Mismatches: 19, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
20 61 0.65
21 33 0.35
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACCT
Found at i:639377 original size:41 final size:41
Alignment explanation
Indices: 639325--639459 Score: 209
Period size: 41 Copynumber: 3.3 Consensus size: 41
639315 CGATAGTCAG
* * *
639325 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTTCCTA
639366 ATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTTCCTA
1 ATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTTCCTA
* * *
639407 ATTTGCATTGCGATTTACTTAATCGCGTTGCGATTTACGT-
1 ATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTTCCTA
639447 ATTCGCATTGCGA
1 ATTCGCATTGCGA
639460 ATTGGGAAAA
Statistics
Matches: 87, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
40 12 0.14
41 75 0.86
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.41
Consensus pattern (41 bp):
ATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTTCCTA
Found at i:639438 original size:61 final size:61
Alignment explanation
Indices: 639327--639459 Score: 169
Period size: 61 Copynumber: 2.2 Consensus size: 61
639317 ATAGTCAGAT
* * *
639327 TCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACTTAA
1 TCGCATTGCGATTTACCTATTCGCATTGCGATTTACCTAATTCGCATTGCGATTTACGTAA
* * * * * *
639388 TCGCGTTGCGATTTTCCTAATTTGCATTGCGATTTACTTAA-TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACCT-ATTCGCATTGCGATTTACCTAATTCGCATTGCGATTTACGTAA
639449 TCGCATTGCGA
1 TCGCATTGCGA
639460 ATTGGGAAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
61 42 0.69
62 19 0.31
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.41
Consensus pattern (61 bp):
TCGCATTGCGATTTACCTATTCGCATTGCGATTTACCTAATTCGCATTGCGATTTACGTAA
Found at i:639500 original size:21 final size:22
Alignment explanation
Indices: 639449--639501 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
639439 ATTTACGTAT
639449 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
* *
639470 TCACAATGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
639491 TCGCATTGCGA
1 TCGCATTGCGA
639502 TAGTAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:640598 original size:31 final size:31
Alignment explanation
Indices: 640555--640628 Score: 130
Period size: 31 Copynumber: 2.4 Consensus size: 31
640545 ACTTAATACA
*
640555 TTTAATACCTAAGCTATCAGTTTTTGTCCGT
1 TTTAATACCTAAGCTATCAGTTTTGGTCCGT
*
640586 TTTAGTACCTAAGCTATCAGTTTTGGTCCGT
1 TTTAATACCTAAGCTATCAGTTTTGGTCCGT
640617 TTTAATACCTAA
1 TTTAATACCTAA
640629 ACCTCCAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (31 bp):
TTTAATACCTAAGCTATCAGTTTTGGTCCGT
Found at i:642689 original size:17 final size:18
Alignment explanation
Indices: 642669--642702 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
642659 TTTTTTTATA
*
642669 ATTTTT-ATAGTATTTTC
1 ATTTTTAATAATATTTTC
642686 ATTTTTAATAATATTTT
1 ATTTTTAATAATATTTT
642703 GATCTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (18 bp):
ATTTTTAATAATATTTTC
Found at i:643375 original size:21 final size:22
Alignment explanation
Indices: 643338--643385 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
643328 AAGGTTAGAG
*
643338 TTTA-GGTTTAAGATTTA-AGT
1 TTTATGGTTTAAGATTTAGAAT
* *
643358 TTTATGGTTTAGGGTTTAGAAT
1 TTTATGGTTTAAGATTTAGAAT
643380 TTTATG
1 TTTATG
643386 ACTTGGCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 4 0.17
21 11 0.48
22 8 0.35
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.52
Consensus pattern (22 bp):
TTTATGGTTTAAGATTTAGAAT
Found at i:643851 original size:2 final size:2
Alignment explanation
Indices: 643844--643900 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
643834 CATCAGGTAA
643844 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
*
643886 AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT A
643901 GCAATGGTGC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:644803 original size:297 final size:294
Alignment explanation
Indices: 644259--646036 Score: 3029
Period size: 294 Copynumber: 6.0 Consensus size: 294
644249 ATTCGTTAAG
* ** * * *
644259 ATGACGATTATTATTATATTGTTGACATTTCTTGTTTTTTATCGTCGGATTGGATTTAGATATAC
1 ATGACGGTTATTATTATATTGTTGACATTTCTTGTTTTGGATTGTCGGATTGGATTTGGATACAC
* * *
644324 ATTATACGTTTGT-AGATAGTTTTTTTACATCGTTAGAGTCTGATTTATGATTTGTCAGAGGTAT
66 ATTATACGTTTGTCA-ATAGTTTTTTTACATCGTTAGAGTCTGATTTGTGATTTGTCGGAGGTCT
*
644388 TTTAGTAGTTTGATCTTATTTTATGGTTCGTTTACCGATAAAATCAAATTTGTGTGTATCTATAT
130 TTTAGTAGTTTGATCTTATTTTATGGTTCGTTTACCGAT-GAATCAAATTTGTGTGTATCTATAT
* * *
644453 TTGTTCGAGTTTTTTTAGTTATAATTTAATATTTTATTGTATGATATGTGATCTAAAATTGCTAG
194 TTGTTCGAGTTTTTTTAGTTATGATTTAATATTTTCTTGTATGATATGTGATCTTAAATTGCTAG
644518 TTTTGTTTCAATGATTTTAAAAAATTGAAGTTTAATTT
259 --TTGTTTCAATGATTTTAAAAAATTGAAGTTTAATTT
644556 ATGACGGTTATTATTATATTGTTGACATTTCTTGTTTTGGATTGTCGGATTGGATTTGGATACAC
1 ATGACGGTTATTATTATATTGTTGACATTTCTTGTTTTGGATTGTCGGATTGGATTTGGATACAC
* *
644621 ATTATACGTTTGTCAATAGTTTTTTTACATCGCTAGAGTCTGATTTGTGATTTGTCAGAGGTCTT
66 ATTATACGTTTGTCAATAGTTTTTTTACATCGTTAGAGTCTGATTTGTGATTTGTCGGAGGTCTT
644686 TTAGTAGTTTGATCTTATTTTATGGTTCGTTTACCGATAGAATCAAATTTGTGTGTATCTATATT
131 TTAGTAGTTTGATCTTATTTTATGGTTCGTTTACCGAT-GAATCAAATTTGTGTGTATCTATATT
* *
644751 TGTTCGAGTTTTTTTAGTTATGATTTAATATTTTCTTGTATGATACGTGATCTTTAATTGCTAGT
195 TGTTCGAGTTTTTTTAGTTATGATTTAATATTTTCTTGTATGATATGTGATCTTAAATTGCTAG-
*
644816 TTTGTTTCAATGATTTTAAAAAAATTAAAGTTTAATTT
259 -TTGTTTCAATGATTTT-AAAAAATTGAAGTTTAATTT
** * * * *
644854 ATGATAGTTATTATTATATTGTTGACATTTATTATTTTGGATCGTCAGATTGGATTTGGATACAC
1 ATGACGGTTATTATTATATTGTTGACATTTCTTGTTTTGGATTGTCGGATTGGATTTGGATACAC
* *
644919 TTTATACGTTTGTCAATAGTTTTTTTACATCGCTAGAGTCTGATTTGTGATTTGTCGGAGGTCTT
66 ATTATACGTTTGTCAATAGTTTTTTTACATCGTTAGAGTCTGATTTGTGATTTGTCGGAGGTCTT
644984 TTAGTAGTTTGATCTTATTTTATGGTTCGTTTACCGATGAATCAAATTTGTGTGTATCTATATTT
131 TTAGTAGTTTGATCTTATTTTATGGTTCGTTTACCGATGAATCAAATTTGTGTGTATCTATATTT
* *
645049 GTTCGAGTTTTTTTAGTTACGATTTAATATTTTCTTGTATGTTATGTGATCTTAAATTGCTAGTT
196 GTTCGAGTTTTTTTAGTTATGATTTAATATTTTCTTGTATGATATGTGATCTTAAATTGCTAGTT
645114 GTTTCAATGATTTTAAAAAATTGAAGTTTAATTT
261 GTTTCAATGATTTTAAAAAATTGAAGTTTAATTT
* *
645148 ATGACGGTTCTTATTATATTGTTGACATTTCTTGTTTTGGATTGTCGGATTGGATTTGAATACAC
1 ATGACGGTTATTATTATATTGTTGACATTTCTTGTTTTGGATTGTCGGATTGGATTTGGATACAC
* * *
645213 ATTATACGTTTGTCGATAGTTTTTTTACATAGTTAGAGTCTGATTTGTAATTTGTCGGAGGTCTT
66 ATTATACGTTTGTCAATAGTTTTTTTACATCGTTAGAGTCTGATTTGTGATTTGTCGGAGGTCTT
645278 TTAGTAGTTTGATCTTATTTTATGGTTCGTTTACCGATGAATCAAATTTGTGTGTATCTATATTT
131 TTAGTAGTTTGATCTTATTTTATGGTTCGTTTACCGATGAATCAAATTTGTGTGTATCTATATTT
* *
645343 GTTCGAGTTTTTTTAGTTATGATTTAATATTTTATTGTATGATATGTGATCTTATATTGCTAGTT
196 GTTCGAGTTTTTTTAGTTATGATTTAATATTTTCTTGTATGATATGTGATCTTAAATTGCTAGTT
645408 GTTTCAATGATTTTAAAAAATTGAAGTTTAATTT
261 GTTTCAATGATTTTAAAAAATTGAAGTTTAATTT
* *
645442 ATGACGGTTATTATTATATTGTTGACATTTCTTGTTTTGGATTGTCGAATTGGATTTGAATACAC
1 ATGACGGTTATTATTATATTGTTGACATTTCTTGTTTTGGATTGTCGGATTGGATTTGGATACAC
*
645507 ATTATACGTTTGTCAATAGTTTTTTTACATCGTTAGAGTCTGATTTGTGATTTGTCGGATGTCTT
66 ATTATACGTTTGTCAATAGTTTTTTTACATCGTTAGAGTCTGATTTGTGATTTGTCGGAGGTCTT
645572 TTAGTAGTTTGATCTTATTTTATGGTTCGTTTACCGATGAATCAAATTTGTGTGTATCTATATTT
131 TTAGTAGTTTGATCTTATTTTATGGTTCGTTTACCGATGAATCAAATTTGTGTGTATCTATATTT
* *
645637 GTTCGAGTTTTTTTAGTTACGATTTAATATTTTCTTGTATGTTATGTGATCTTAAATTGCTAGTT
196 GTTCGAGTTTTTTTAGTTATGATTTAATATTTTCTTGTATGATATGTGATCTTAAATTGCTAGTT
645702 GTTTCAATGATTTTAAAAAATTGAAGTTTAATTT
261 GTTTCAATGATTTTAAAAAATTGAAGTTTAATTT
645736 ATGACGGTTATTATTATATTGTTGACATTTCTTGTTTTGGATTGTCGGATTGGATTTGGATACAC
1 ATGACGGTTATTATTATATTGTTGACATTTCTTGTTTTGGATTGTCGGATTGGATTTGGATACAC
*
645801 ATTATACGTTTGTCGATAGTTTTTTTACATCGTTAGAGTCTGATTTGTGATTTGTCGGAGGTCTT
66 ATTATACGTTTGTCAATAGTTTTTTTACATCGTTAGAGTCTGATTTGTGATTTGTCGGAGGTCTT
*
645866 TTAGTAGTTTGATCTTATTTTATGGTTCGTTTA-CTATTGAAATCAAATTTGTGTGTATCTATAT
131 TTAGTAGTTTGATCTTATTTTATGGTTCGTTTACCGA-TG-AATCAAATTTGTGTGTATCTATAT
645930 TTGTTCGAGTTTTTTTAGTTATGATTTAATATTTTCTTGTATGATATGTGATCTTAAATTGCTAG
194 TTGTTCGAGTTTTTTTAGTTATGATTTAATATTTTCTTGTATGATATGTGATCTTAAATTGCTAG
* **
645995 TTTTGTTTCAATAATTTTAAAATTTTGAAGTTTAATTT
259 --TTGTTTCAATGATTTTAAAAAATTGAAGTTTAATTT
646033 ATGA
1 ATGA
646037 TTATTATGGT
Statistics
Matches: 1409, Mismatches: 66, Indels: 12
0.95 0.04 0.01
Matches are distributed among these distances:
293 2 0.00
294 741 0.53
295 103 0.07
297 383 0.27
298 180 0.13
ACGTcount: A:0.25, C:0.08, G:0.18, T:0.50
Consensus pattern (294 bp):
ATGACGGTTATTATTATATTGTTGACATTTCTTGTTTTGGATTGTCGGATTGGATTTGGATACAC
ATTATACGTTTGTCAATAGTTTTTTTACATCGTTAGAGTCTGATTTGTGATTTGTCGGAGGTCTT
TTAGTAGTTTGATCTTATTTTATGGTTCGTTTACCGATGAATCAAATTTGTGTGTATCTATATTT
GTTCGAGTTTTTTTAGTTATGATTTAATATTTTCTTGTATGATATGTGATCTTAAATTGCTAGTT
GTTTCAATGATTTTAAAAAATTGAAGTTTAATTT
Found at i:646153 original size:15 final size:16
Alignment explanation
Indices: 646121--646153 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
646111 AAATAAATAA
*
646121 AATAACACAAATATTT
1 AATAAAACAAATATTT
646137 AATAAAACAAA-ATTT
1 AATAAAACAAATATTT
646152 AA
1 AA
646154 ATTTTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (16 bp):
AATAAAACAAATATTT
Found at i:650434 original size:20 final size:20
Alignment explanation
Indices: 650390--650717 Score: 300
Period size: 20 Copynumber: 16.2 Consensus size: 20
650380 AATGACCAAC
*
650390 AAAATCGCAACGCGA--AATA
1 AAAATCGCAACGCGATTAA-G
*
650409 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
650429 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
650449 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
650469 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
650490 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
650511 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
* *
650532 AAGAATCGCAATGCGATTCAG
1 AA-AATCGCAACGCGATTAAG
650553 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
650575 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
650593 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
650615 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
650633 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
*
650655 --AATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
650673 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
*
650693 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
650713 AAAAT
1 AAAAT
650718 GAGTAAATTC
Statistics
Matches: 258, Mismatches: 28, Indels: 45
0.78 0.08 0.14
Matches are distributed among these distances:
18 9 0.03
19 15 0.06
20 185 0.72
21 14 0.05
22 35 0.14
ACGTcount: A:0.42, C:0.23, G:0.20, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:650460 original size:40 final size:40
Alignment explanation
Indices: 650390--650717 Score: 342
Period size: 40 Copynumber: 8.1 Consensus size: 40
650380 AATGACCAAC
* * *
650390 AAAATCGCAACGCGA-AATAAAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATAACAAGAATCGCAACGCGATTAAG
* * * *
650429 AAAATCGCAACGTTGAAAAGAA-AATCGCAACG-G-TCAAAAG
1 AAAATCGCAACG-CGATAACAAGAATCGCAACGCGAT--TAAG
* *
650469 AAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCGATA--ACAAGAATCGCAACGCGATTAAG
* ** * *
650511 AGAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCAG
1 AAAATCGCAACGCGA--TAACAAGAATCGCAACGCGATTAAG
**
650553 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATAACAAGAATCGCAACGCGATTAAG
**
650593 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATAACAAGAATCGCAACGCGATTAAG
** *
650633 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATAACAAGAATCGCAACGCGATTAAG
* *
650673 AAAATCGCAACGCGATTAAGAA-AATCGCAACGCGATTCAG
1 AAAATCGCAACGCGA-TAACAAGAATCGCAACGCGATTAAG
650713 AAAAT
1 AAAAT
650718 GAGTAAATTC
Statistics
Matches: 257, Mismatches: 20, Indels: 23
0.86 0.07 0.08
Matches are distributed among these distances:
38 1 0.00
39 16 0.06
40 166 0.65
41 9 0.04
42 62 0.24
43 1 0.00
44 2 0.01
ACGTcount: A:0.42, C:0.23, G:0.20, T:0.16
Consensus pattern (40 bp):
AAAATCGCAACGCGATAACAAGAATCGCAACGCGATTAAG
Found at i:650824 original size:6 final size:6
Alignment explanation
Indices: 650813--650971 Score: 318
Period size: 6 Copynumber: 26.5 Consensus size: 6
650803 GACACGTATT
650813 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
650861 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
650909 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
650957 ACCACG ACCACG ACC
1 ACCACG ACCACG ACC
650972 CGAGACGAGA
Statistics
Matches: 153, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 153 1.00
ACGTcount: A:0.33, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:651492 original size:6 final size:6
Alignment explanation
Indices: 651472--651616 Score: 267
Period size: 6 Copynumber: 24.5 Consensus size: 6
651462 TCTCGTCTCG
*
651472 GGTCG- GGTCG- GGTCGG GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
651518 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
651566 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
651614 GGT
1 GGT
651617 AATACGTGTC
Statistics
Matches: 138, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
5 10 0.07
6 128 0.93
ACGTcount: A:0.00, C:0.17, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:651828 original size:42 final size:42
Alignment explanation
Indices: 651712--651924 Score: 244
Period size: 42 Copynumber: 5.2 Consensus size: 42
651702 GAATTTACTT
*
651712 ATTTTCTTAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
1 ATTTTCTTAATCGCATTGCGATTCTTGGAATATCGCGTTGCG
* *
651752 ATTTTCTGAATCGCA-TGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCATTGCGATTCTTGGAATATCGCGTTGCG
*
651793 ATTCTCTTAATCGCATTGCGATTCTTGGAATATCGCGTTGCG
1 ATTTTCTTAATCGCATTGCGATTCTTGGAATATCGCGTTGCG
* * ** * *
651835 ATTTTCTT--TTGACCGTTGCGATT-TT--CTTTTCAACGTTGCG
1 ATTTTCTTAATCG--CATTGCGATTCTTGGAATATC-GCGTTGCG
*
651875 ATTTTCTAAATCGCATTGCGATTCTTGGAATATCGCGTTGCG
1 ATTTTCTTAATCGCATTGCGATTCTTGGAATATCGCGTTGCG
651917 ATTTTCTT
1 ATTTTCTT
651925 TTGACCGTTG
Statistics
Matches: 142, Mismatches: 20, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
39 15 0.11
40 39 0.27
41 28 0.20
42 57 0.40
43 3 0.02
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (42 bp):
ATTTTCTTAATCGCATTGCGATTCTTGGAATATCGCGTTGCG
Found at i:651890 original size:82 final size:82
Alignment explanation
Indices: 651786--652000 Score: 364
Period size: 82 Copynumber: 2.7 Consensus size: 82
651776 TGGAAGATCG
* *
651786 CGTTGCGATTCTCTTAATCGCATTGCGATTCTTGGAATATCGCGTTGCGATTTTCTTTTGACCGT
1 CGTTGCGATTTTCTAAATCGCATTGCGATTCTTGGAATATCGCGTTGCGATTTTCTTTTGACCGT
651851 TGCGATTTTCTTTTCAA
66 TGCGATTTTCTTTTCAA
651868 CGTTGCGATTTTCTAAATCGCATTGCGATTCTTGGAATATCGCGTTGCGATTTTCTTTTGACCGT
1 CGTTGCGATTTTCTAAATCGCATTGCGATTCTTGGAATATCGCGTTGCGATTTTCTTTTGACCGT
651933 TGCGATTTTCTTTTCAA
66 TGCGATTTTCTTTTCAA
* * *
651950 CGTTGCGATTTTCTAAATCGCGTTGCGATT-TT--TATTTCGCGTTGCGATTTT
1 CGTTGCGATTTTCTAAATCGCATTGCGATTCTTGGAATATCGCGTTGCGATTTT
652001 GTTGGTCATT
Statistics
Matches: 128, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
79 17 0.13
81 2 0.02
82 109 0.85
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.45
Consensus pattern (82 bp):
CGTTGCGATTTTCTAAATCGCATTGCGATTCTTGGAATATCGCGTTGCGATTTTCTTTTGACCGT
TGCGATTTTCTTTTCAA
Found at i:651956 original size:62 final size:60
Alignment explanation
Indices: 651848--652000 Score: 168
Period size: 62 Copynumber: 2.5 Consensus size: 60
651838 TTCTTTTGAC
* *
651848 CGTTGCGATTTTCTTTTCAACGTTGCGATTTTCTAAATCGCATTGCGATTCTTGGAATATCG
1 CGTTGCGATTTTCTTTTCAACGTTGCGATTTTCTAAATCACATTGCGATT-TTCGAA-ATCG
* * ** * *
651910 CGTTGCGATTTTCTTTTGACCGTTGCGATTTTCT-TTTCAACGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTTTTCAACGTTGCGATTTTCTAAATC-ACATTGCGATTTTCGAAATCG
*
651970 CGTTGCGATTTT-TATTTC-GCGTTGCGATTTT
1 CGTTGCGATTTTCT-TTTCAACGTTGCGATTTT
652001 GTTGGTCATT
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
59 13 0.16
60 19 0.24
61 6 0.08
62 41 0.52
ACGTcount: A:0.16, C:0.19, G:0.20, T:0.46
Consensus pattern (60 bp):
CGTTGCGATTTTCTTTTCAACGTTGCGATTTTCTAAATCACATTGCGATTTTCGAAATCG
Found at i:651973 original size:20 final size:20
Alignment explanation
Indices: 651712--652000 Score: 155
Period size: 20 Copynumber: 14.2 Consensus size: 20
651702 GAATTTACTT
*
651712 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
651732 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
* *
651752 ATTTTCTGAATCGC-ATGCG
1 ATTTTCTAAATCGCGTTGCG
**
651771 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* * *
651793 ATTCTCTTAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
**
651813 ATTCTTGGAATATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* *
651835 ATTTTCT--TTTGACCGTTGCG
1 ATTTTCTAAATCG--CGTTGCG
** *
651855 ATTTTCT-TTTCAACGTTGCG
1 ATTTTCTAAATC-GCGTTGCG
*
651875 ATTTTCTAAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
**
651895 ATTCTTGGAATATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* *
651917 ATTTTCT--TTTGACCGTTGCG
1 ATTTTCTAAATCG--CGTTGCG
** *
651937 ATTTTCT-TTTCAACGTTGCG
1 ATTTTCTAAATC-GCGTTGCG
651957 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
651977 ATTTT-TATTTCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
651996 ATTTT
1 ATTTT
652001 GTTGGTCATT
Statistics
Matches: 208, Mismatches: 42, Indels: 39
0.72 0.15 0.13
Matches are distributed among these distances:
18 4 0.02
19 26 0.12
20 118 0.57
21 27 0.13
22 33 0.16
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (20 bp):
ATTTTCTAAATCGCGTTGCG
Found at i:653164 original size:2 final size:2
Alignment explanation
Indices: 653157--653183 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
653147 AATGAAGGGT
653157 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
653184 CTACTTACAC
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:656097 original size:14 final size:14
Alignment explanation
Indices: 656078--656107 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
656068 TATGGTGAAC
656078 TACGTCTATTTTAG
1 TACGTCTATTTTAG
656092 TACGTCTATTTTAG
1 TACGTCTATTTTAG
656106 TA
1 TA
656108 TCGAAACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.50
Consensus pattern (14 bp):
TACGTCTATTTTAG
Found at i:656355 original size:17 final size:17
Alignment explanation
Indices: 656330--656374 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
656320 ATACTTTCAT
*
656330 TTTATATTTAAATTTTA
1 TTTAAATTTAAATTTTA
** *
656347 TTTAAATTTTTATTTTT
1 TTTAAATTTAAATTTTA
656364 TTTAAATTTAA
1 TTTAAATTTAA
656375 CATTAATTTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTAAATTTAAATTTTA
Found at i:656359 original size:12 final size:12
Alignment explanation
Indices: 656328--656361 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
656318 CAATACTTTC
656328 ATTTTATATTTAA
1 ATTTT-TATTTAA
656341 A-TTTTATTTAA
1 ATTTTTATTTAA
656352 ATTTTTATTT
1 ATTTTTATTT
656362 TTTTTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 8 0.40
12 11 0.55
13 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATTTTTATTTAA
Found at i:660114 original size:22 final size:22
Alignment explanation
Indices: 660075--660119 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
660065 CGACGACACC
660075 CCAACCTCCGCCCTCGCCGCCG
1 CCAACCTCCGCCCTCGCCGCCG
*
660097 CCAA-CTCCGCCCTCCGCCTCCG
1 CCAACCTCCGCCCT-CGCCGCCG
660119 C
1 C
660120 TTCTACAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.09, C:0.64, G:0.16, T:0.11
Consensus pattern (22 bp):
CCAACCTCCGCCCTCGCCGCCG
Found at i:669069 original size:21 final size:20
Alignment explanation
Indices: 669027--669069 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
669017 TAATATTTTT
*
669027 TATATTTAATAATTAAATAA
1 TATATTTAAAAATTAAATAA
669047 TATATTTTAAAAATATAAA-AA
1 TATA-TTTAAAAAT-TAAATAA
669068 TA
1 TA
669070 AAAATTCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TATATTTAAAAATTAAATAA
Found at i:670817 original size:2 final size:2
Alignment explanation
Indices: 670810--670849 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
670800 GGGATTAATA
670810 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
670850 TCAAATAATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:672549 original size:21 final size:21
Alignment explanation
Indices: 672525--672569 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
672515 AAGAAAGCAA
672525 AAAT-AAAATAGTAAATAAA-AT
1 AAATAAAAATA-TAAA-AAATAT
672546 AAATAAAAATATAAAAAATAT
1 AAATAAAAATATAAAAAATAT
672567 AAA
1 AAA
672570 AAATAAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 3 0.14
21 13 0.59
22 6 0.27
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (21 bp):
AAATAAAAATATAAAAAATAT
Found at i:672550 original size:9 final size:9
Alignment explanation
Indices: 672536--672667 Score: 53
Period size: 9 Copynumber: 14.0 Consensus size: 9
672526 AATAAAATAG
672536 TAAATAAAA
1 TAAATAAAA
672545 TAAATAAAAA
1 TAAAT-AAAA
672555 TATAA-AAAA
1 TA-AATAAAA
672564 TATAA-AAAA
1 TA-AATAAAA
*
672573 TAAAGAAAA
1 TAAATAAAA
*
672582 -AGAAGAAAA
1 TA-AATAAAA
672591 -AATATATAAA
1 TAA-ATA-AAA
672601 TAAA-ACAAA
1 TAAATA-AAA
672610 TAAATAAAA
1 TAAATAAAA
*
672619 -CAATAATAA
1 TAAATAA-AA
672628 -AAAGTAAAAA
1 TAAA-T-AAAA
*
672638 TAATATATATA
1 TAA-ATA-AAA
*
672649 TATATAATAA
1 TAAATAA-AA
672659 TAAATAAAA
1 TAAATAAAA
672668 ACATAAAAAA
Statistics
Matches: 100, Mismatches: 8, Indels: 30
0.72 0.06 0.22
Matches are distributed among these distances:
8 9 0.09
9 52 0.52
10 25 0.25
11 13 0.13
12 1 0.01
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.22
Consensus pattern (9 bp):
TAAATAAAA
Found at i:672564 original size:15 final size:17
Alignment explanation
Indices: 672537--672576 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
672527 ATAAAATAGT
672537 AAATA-AAATAAATA-A
1 AAATATAAATAAATATA
672552 AAATATAAA-AAATATA
1 AAATATAAATAAATATA
*
672568 AAAAATAAA
1 AAATATAAA
672577 GAAAAAGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (17 bp):
AAATATAAATAAATATA
Found at i:672612 original size:13 final size:12
Alignment explanation
Indices: 672596--672629 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
672586 GAAAAAATAT
672596 ATAAATAAAACAA
1 ATAAATAAAAC-A
672609 ATAAATAAAACA
1 ATAAATAAAACA
672621 AT-AATAAAA
1 ATAAATAAAA
672630 AGTAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.33
12 3 0.14
13 11 0.52
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (12 bp):
ATAAATAAAACA
Found at i:672637 original size:46 final size:46
Alignment explanation
Indices: 672587--672745 Score: 117
Period size: 46 Copynumber: 3.4 Consensus size: 46
672577 GAAAAAGAAG
672587 AAAAAATATATAAATAAAACAAATAAATAAAACA-ATAATAAAAAGT
1 AAAAAATATATAAATAAAA-AAATAAATAAAACACATAATAAAAAGT
* *
672633 AAAAATAATATATATATATATAATAATAAATAAAA-ACATAA-AAAATAGT
1 -AAAA-AATATATA-A-ATAAAAAAATAAATAAAACACATAATAAAA-AGT
* * * * * * * *
672682 ATATATATATATATATATATAAATTAATAAAACATATAATAAAAAAT
1 A-AAAAATATATAAATAAAAAAATAAATAAAACACATAATAAAAAGT
* * *
672729 AACATATATATATATAA
1 AAAAAATATATAAATAA
672746 TCTAAAAAAA
Statistics
Matches: 92, Mismatches: 12, Indels: 17
0.76 0.10 0.14
Matches are distributed among these distances:
46 29 0.32
47 12 0.13
48 25 0.27
49 21 0.23
50 5 0.05
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (46 bp):
AAAAAATATATAAATAAAAAAATAAATAAAACACATAATAAAAAGT
Found at i:672694 original size:50 final size:50
Alignment explanation
Indices: 672608--672744 Score: 142
Period size: 50 Copynumber: 2.8 Consensus size: 50
672598 AAATAAAACA
* *
672608 AATAAAT-AAAACAATAATAAAA-AGTAAAAATA-ATATATATATATATAA-T
1 AATAAATAAAAAC-ATAA-AAAATAGTATATATATATATATATATATA-AATT
672657 AATAAATAAAAACATAAAAAATAGTATATATATATATATATATATAAATT
1 AATAAATAAAAACATAAAAAATAGTATATATATATATATATATATAAATT
* **
672707 AATAAA-ACATATA-ATAAAAAATAACATATATATATATA
1 AATAAATA-A-AAACATAAAAAATAGTATATATATATATA
672745 ATCTAAAAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
48 4 0.05
49 22 0.29
50 49 0.64
51 2 0.03
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (50 bp):
AATAAATAAAAACATAAAAAATAGTATATATATATATATATATATAAATT
Found at i:672712 original size:38 final size:40
Alignment explanation
Indices: 672633--672762 Score: 122
Period size: 40 Copynumber: 3.1 Consensus size: 40
672623 AATAAAAAGT
672633 AAAAATAATATATATATATATAATAATAAATAAAAACATA
1 AAAAATAATATATATATATATAATAATAAATAAAAACATA
*
672673 AAAAATAGTATATATATATATATATATATAAATTAATAAAACATA
1 AAAAATAATATATATATATATA-ATA-ATAAA-T-A-AAAACATA
* * *
672718 TAATAAAAAATA-ACATATATATATATAATCTAA-AAAAA-ATA
1 -AA-AAATAATATATATATATATA-ATAAT-AAATAAAAACATA
672759 AAAA
1 AAAA
672763 TATATACCAA
Statistics
Matches: 77, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
39 2 0.03
40 23 0.30
41 6 0.08
42 9 0.12
43 2 0.03
44 1 0.01
45 10 0.13
46 18 0.23
47 6 0.08
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (40 bp):
AAAAATAATATATATATATATAATAATAAATAAAAACATA
Found at i:672737 original size:19 final size:21
Alignment explanation
Indices: 672692--672742 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
672682 ATATATATAT
*
672692 ATATATATATAAATTAATAAA
1 ATATATATATAAATAAATAAA
* *
672713 ACATATA-ATAAA-AAATAAC
1 ATATATATATAAATAAATAAA
672732 ATATATATATA
1 ATATATATATA
672743 TAATCTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 11 0.44
20 8 0.32
21 6 0.24
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (21 bp):
ATATATATATAAATAAATAAA
Found at i:673352 original size:37 final size:37
Alignment explanation
Indices: 673311--673418 Score: 162
Period size: 37 Copynumber: 2.9 Consensus size: 37
673301 TTCTGGATCC
*
673311 TATTTTTAGGAGTTTGAATCATAATATAACTCTATCA
1 TATTTTTAGGAGTTTGAATCATAATAAAACTCTATCA
* *
673348 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCC
1 TATTTTTAGGAGTTTGAATCATAATAAAACTCTATCA
* * *
673385 TATTTTTAGGAGTTTGAATCGTACTAAAATTCTA
1 TATTTTTAGGAGTTTGAATCATAATAAAACTCTA
673419 ACGTTTGTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (37 bp):
TATTTTTAGGAGTTTGAATCATAATAAAACTCTATCA
Found at i:674152 original size:14 final size:14
Alignment explanation
Indices: 674133--674160 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
674123 AGCTGGGCAT
674133 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
674147 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
674161 GAGTATCCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.29, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:674200 original size:33 final size:33
Alignment explanation
Indices: 674131--674238 Score: 144
Period size: 33 Copynumber: 3.2 Consensus size: 33
674121 AGAGCTGGGC
* *
674131 ATCCGAGGCCATCCGACCGAGGCCATCCGAGAGT
1 ATCCGAGGCCATCCGACCGA-GCTATGCGAGAGT
674165 ATCCGAGGCCATCCGACCGAGCTATGCGAGAGT
1 ATCCGAGGCCATCCGACCGAGCTATGCGAGAGT
* * * * *
674198 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
1 ATCCGAGGCCATCCGACCGAGCTATGCGAGAGT
674231 ATCCGAGG
1 ATCCGAGG
674239 GAAGCCGAGC
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
33 47 0.70
34 20 0.30
ACGTcount: A:0.25, C:0.30, G:0.33, T:0.12
Consensus pattern (33 bp):
ATCCGAGGCCATCCGACCGAGCTATGCGAGAGT
Found at i:674239 original size:33 final size:33
Alignment explanation
Indices: 674131--674251 Score: 118
Period size: 33 Copynumber: 3.6 Consensus size: 33
674121 AGAGCTGGGC
* * * * * *
674131 ATCCGAGGCCATCCGACCGAGGCCATCCGAGAGT
1 ATCCGAGGGCAACCGAGCGA-GCTATGCGAGAGA
* * * *
674165 ATCCGAGGCCATCCGACCGAGCTATGCGAGAGT
1 ATCCGAGGGCAACCGAGCGAGCTATGCGAGAGA
*
674198 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
1 ATCCGAGGGCAACCGAGCGAGCTATGCGAGAGA
674231 ATCCGAGGG-AAGCCGAGCGAG
1 ATCCGAGGGCAA-CCGAGCGAG
674252 GGTAGGTCAC
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
32 2 0.03
33 57 0.72
34 20 0.25
ACGTcount: A:0.26, C:0.29, G:0.35, T:0.11
Consensus pattern (33 bp):
ATCCGAGGGCAACCGAGCGAGCTATGCGAGAGA
Found at i:674324 original size:36 final size:36
Alignment explanation
Indices: 674277--674346 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
674267 GTGCATGGCG
* *
674277 ACCTACAAGGTCTACCGGAGGGCATGGTGACCTACA
1 ACCTACAAGGTCGACCGGAGGGCATGGCGACCTACA
*
674313 ACCTACAAGGTCGCCCGGAGGGCATGGCGACCTA
1 ACCTACAAGGTCGACCGGAGGGCATGGCGACCTA
674347 TGTGTTGGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.26, C:0.30, G:0.30, T:0.14
Consensus pattern (36 bp):
ACCTACAAGGTCGACCGGAGGGCATGGCGACCTACA
Found at i:678884 original size:30 final size:30
Alignment explanation
Indices: 678850--678909 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
678840 ATTTTTTTTC
678850 CCCTAACATTTGACATAATAAACACTTTGT
1 CCCTAACATTTGACATAATAAACACTTTGT
678880 CCCTAACATTTGACATAATAAACACTTTGT
1 CCCTAACATTTGACATAATAAACACTTTGT
678910 TCCTTATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.33
Consensus pattern (30 bp):
CCCTAACATTTGACATAATAAACACTTTGT
Found at i:680218 original size:15 final size:16
Alignment explanation
Indices: 680198--680230 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
680188 AAAATTTTAT
680198 AAAAT-ATAATATAAA
1 AAAATAATAATATAAA
680213 AAAATACATAATATAAA
1 AAAATA-ATAATATAAA
680230 A
1 A
680231 TTTTAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
17 11 0.69
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAATAATAATATAAA
Found at i:680245 original size:22 final size:21
Alignment explanation
Indices: 680185--680262 Score: 65
Period size: 22 Copynumber: 3.8 Consensus size: 21
680175 CAGATAAATT
*
680185 TATAAAATTTTATAAAATATAA
1 TATAAAATTTTA-AATATATAA
*
680207 TATAAAA----AAATACATAA
1 TATAAAATTTTAAATATATAA
680224 TATAAAATTTTAAATTATATAA
1 TATAAAATTTTAAA-TATATAA
* *
680246 AATTTAAATTTTAAATA
1 TA-TAAAATTTTAAATA
680263 AAAATTACCA
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
17 14 0.31
18 1 0.02
21 3 0.07
22 16 0.36
23 11 0.24
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (21 bp):
TATAAAATTTTAAATATATAA
Found at i:680253 original size:16 final size:17
Alignment explanation
Indices: 680223--680255 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
680213 AAAATACATA
680223 ATATAAAATTTTAAATT
1 ATATAAAATTTTAAATT
680240 ATATAAAA-TTTAAATT
1 ATATAAAATTTTAAATT
680256 TTAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATAAAATTTTAAATT
Found at i:683572 original size:31 final size:31
Alignment explanation
Indices: 683534--683594 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
683524 TAGTTGAGGG
*
683534 ACTAAAATCGAACGGATCGATAACGTTAGGA
1 ACTAAAATCGAACAGATCGATAACGTTAGGA
*
683565 ACTAAAATCGAACAGATCGGTAACGTTAGG
1 ACTAAAATCGAACAGATCGATAACGTTAGG
683595 GACCACGTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (31 bp):
ACTAAAATCGAACAGATCGATAACGTTAGGA
Found at i:695241 original size:19 final size:22
Alignment explanation
Indices: 695205--695262 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 22
695195 TTATAATTAT
695205 ATTATAT-TTCAATTATAAAA-A
1 ATTATATATT-AATTATAAAAGA
695226 ATTAT-TA-TAATTATAAAAGTA
1 ATTATATATTAATTATAAAAG-A
695247 ATTATATATTAATTAT
1 ATTATATATTAATTAT
695263 TTATTTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
19 10 0.31
20 2 0.06
21 11 0.34
22 2 0.06
23 7 0.22
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
ATTATATATTAATTATAAAAGA
Found at i:695270 original size:19 final size:19
Alignment explanation
Indices: 695248--695292 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
695238 ATAAAAGTAA
*
695248 TTATATATTA-ATTATTTAT
1 TTATATATTAGATAATTT-T
695267 TTATATATTAGATAATTTT
1 TTATATATTAGATAATTTT
695286 TTATATA
1 TTATATA
695293 AAAAAGGGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TTATATATTAGATAATTTT
Found at i:701766 original size:25 final size:25
Alignment explanation
Indices: 701736--701786 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
701726 CGAATTTGAC
*
701736 CTTACAAGTTCAGATTCTTGAATCT
1 CTTACAAGCTCAGATTCTTGAATCT
701761 CTTACAAGCTCAGATTCTTGAATCT
1 CTTACAAGCTCAGATTCTTGAATCT
701786 C
1 C
701787 AACCACTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (25 bp):
CTTACAAGCTCAGATTCTTGAATCT
Found at i:701907 original size:19 final size:17
Alignment explanation
Indices: 701843--701966 Score: 79
Period size: 19 Copynumber: 7.3 Consensus size: 17
701833 GCATAACAAA
701843 TGATATTTTTAAGTAAACT
1 TGATATTTTTAA-T-AACT
*
701862 TGACA-TTTTAA-AA--
1 TGATATTTTTAATAACT
701875 TGATATTCTTTTAATTATACT
1 TGATA-T-TTTTAA-TA-ACT
701896 TGATATTTTTAA-AA-T
1 TGATATTTTTAATAACT
701911 T-ATATTTTTAAGTAAACT
1 TGATATTTTTAA-T-AACT
701929 TGATATTTTTAA-AA-T
1 TGATATTTTTAATAACT
701944 T-ATATTTTTAATTGAACT
1 TGATATTTTTAA-T-AACT
701962 TGATA
1 TGATA
701967 AATTCTTAGT
Statistics
Matches: 85, Mismatches: 2, Indels: 36
0.69 0.02 0.29
Matches are distributed among these distances:
13 4 0.05
14 20 0.24
15 6 0.07
16 9 0.11
17 5 0.06
18 11 0.13
19 24 0.28
20 1 0.01
21 5 0.06
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (17 bp):
TGATATTTTTAATAACT
Done.