Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007908.1 Hibiscus syriacus cultivar Beakdansim tig00110302_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: 529382
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:400355 original size:14 final size:14
Alignment explanation
Indices: 400338--400389 Score: 70
Period size: 14 Copynumber: 3.8 Consensus size: 14
400328 TGCGATTTTT
400338 ATTTTTGAGTTGCG
1 ATTTTTGAGTTGCG
400352 ATTTTTGAGTTGCG
1 ATTTTTGAGTTGCG
* *
400366 ATTTTCGTGTTGCG
1 ATTTTTGAGTTGCG
*
400380 A-ATTTGAGTT
1 ATTTTTGAGTT
400390 TCTTGAGGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
13 6 0.18
14 27 0.82
ACGTcount: A:0.15, C:0.08, G:0.27, T:0.50
Consensus pattern (14 bp):
ATTTTTGAGTTGCG
Found at i:404587 original size:21 final size:21
Alignment explanation
Indices: 404563--404774 Score: 232
Period size: 21 Copynumber: 10.1 Consensus size: 21
404553 TGAAACAATC
*
404563 TCACGTAGAGCACCTACCTCA
1 TCACGTAAAGCACCTACCTCA
* * **
404584 TCACATAAAGCATC-ATTGTCA
1 TCACGTAAAGCACCTA-CCTCA
*
404605 TCACGTAAAGCACATACCTCA
1 TCACGTAAAGCACCTACCTCA
**
404626 TCACGTAAAGCACC-ATTTTCA
1 TCACGTAAAGCACCTA-CCTCA
404647 TCACGTAAAGCACCTACCTCA
1 TCACGTAAAGCACCTACCTCA
* **
404668 TCACGTAAAGCATC-ATTGTCA
1 TCACGTAAAGCACCTA-CCTCA
*
404689 TCACGTAAAGCACCGACCTCA
1 TCACGTAAAGCACCTACCTCA
*
404710 TCACGTAAAGCACCGACCTCA
1 TCACGTAAAGCACCTACCTCA
*
404731 TCACGTAAAGCATCTACCTCA
1 TCACGTAAAGCACCTACCTCA
* *
404752 TCACGTAAAGTACCTAACTCA
1 TCACGTAAAGCACCTACCTCA
404773 TC
1 TC
404775 TCGTGGAGGT
Statistics
Matches: 159, Mismatches: 26, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
20 3 0.02
21 153 0.96
22 3 0.02
ACGTcount: A:0.34, C:0.33, G:0.11, T:0.22
Consensus pattern (21 bp):
TCACGTAAAGCACCTACCTCA
Found at i:404609 original size:42 final size:42
Alignment explanation
Indices: 404563--404761 Score: 292
Period size: 42 Copynumber: 4.7 Consensus size: 42
404553 TGAAACAATC
* * *
404563 TCACGTAGAGCACCTACCTCATCACATAAAGCATCATTGTCA
1 TCACGTAAAGCACCTACCTCATCACGTAAAGCACCATTGTCA
* *
404605 TCACGTAAAGCACATACCTCATCACGTAAAGCACCATTTTCA
1 TCACGTAAAGCACCTACCTCATCACGTAAAGCACCATTGTCA
*
404647 TCACGTAAAGCACCTACCTCATCACGTAAAGCATCATTGTCA
1 TCACGTAAAGCACCTACCTCATCACGTAAAGCACCATTGTCA
* **
404689 TCACGTAAAGCACCGACCTCATCACGTAAAGCACCGA-CCTCA
1 TCACGTAAAGCACCTACCTCATCACGTAAAGCACC-ATTGTCA
*
404731 TCACGTAAAGCATCTACCTCATCACGTAAAG
1 TCACGTAAAGCACCTACCTCATCACGTAAAG
404762 TACCTAACTC
Statistics
Matches: 142, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
42 141 0.99
43 1 0.01
ACGTcount: A:0.34, C:0.32, G:0.12, T:0.22
Consensus pattern (42 bp):
TCACGTAAAGCACCTACCTCATCACGTAAAGCACCATTGTCA
Found at i:404975 original size:42 final size:42
Alignment explanation
Indices: 404876--405081 Score: 220
Period size: 42 Copynumber: 5.0 Consensus size: 42
404866 GATGGAATAT
* ** *
404876 GTGATGGATCTCGGTGTCGAGGTATAGAGTCGGCT--A-GAG
1 GTGATGGATCTCGGTGTCGAAGTGGAGAATCGGCTCGATGAG
* * * *
404915 GTGATGGATCTCGGTGTCGAGGTGTATAATCGGTTCGATGAG
1 GTGATGGATCTCGGTGTCGAAGTGGAGAATCGGCTCGATGAG
* *
404957 ATGATGGATCTCGGTGTCGAAGTGGAGAATCGACTCGATGAG
1 GTGATGGATCTCGGTGTCGAAGTGGAGAATCGGCTCGATGAG
* * * * *
404999 GTGATGAATCTCGATATCGAAGTGGAGAGTCGGCTAGATGAG
1 GTGATGGATCTCGGTGTCGAAGTGGAGAATCGGCTCGATGAG
* * * *
405041 GTGATGGATATCGGTGTCAAAGTGGAGAATCGACTCAATGA
1 GTGATGGATCTCGGTGTCGAAGTGGAGAATCGGCTCGATGA
405082 AAAAGTAGGG
Statistics
Matches: 138, Mismatches: 26, Indels: 3
0.83 0.16 0.02
Matches are distributed among these distances:
39 31 0.22
41 1 0.01
42 106 0.77
ACGTcount: A:0.25, C:0.13, G:0.36, T:0.26
Consensus pattern (42 bp):
GTGATGGATCTCGGTGTCGAAGTGGAGAATCGGCTCGATGAG
Found at i:407479 original size:20 final size:20
Alignment explanation
Indices: 407397--407473 Score: 59
Period size: 20 Copynumber: 3.9 Consensus size: 20
407387 ACAAATTCAA
407397 AAAATCGAGTTGCGAAAACG
1 AAAATCGAGTTGCGAAAACG
* * * **
407417 AAATTCGCGTTG-TAAAATT
1 AAAATCGAGTTGCGAAAACG
* *
407436 AAAACTCGTGTTGCGAATTA-G
1 AAAA-TCGAGTTGCGAA-AACG
407457 AAAATCGAGTTGCGAAA
1 AAAATCGAGTTGCGAAA
407474 CAGAAATTTG
Statistics
Matches: 42, Mismatches: 12, Indels: 7
0.69 0.20 0.11
Matches are distributed among these distances:
19 7 0.17
20 28 0.67
21 6 0.14
22 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.25
Consensus pattern (20 bp):
AAAATCGAGTTGCGAAAACG
Found at i:407556 original size:20 final size:19
Alignment explanation
Indices: 407527--407596 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 19
407517 CTACTTCTGT
* *
407527 GTTGTGAATTCCAAATTCGA
1 GTTGCGAATTCAAAATT-GA
* * * *
407547 GTTGCAAATTCGGAAACTGT
1 GTTGCGAATTC-AAAATTGA
407567 GTTGCGAATTCAAAATTGA
1 GTTGCGAATTCAAAATTGA
407586 GTTGCGAATTC
1 GTTGCGAATTC
407597 GTTGGTTATT
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
19 16 0.40
20 20 0.50
21 4 0.10
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (19 bp):
GTTGCGAATTCAAAATTGA
Found at i:418968 original size:38 final size:38
Alignment explanation
Indices: 418889--418975 Score: 104
Period size: 38 Copynumber: 2.3 Consensus size: 38
418879 AAATTAATGC
** *
418889 TTTTGTCTATGACATTTTAAGAGTCTTTCCTTCTACTT
1 TTTTGTCTATGACATTTTAAGAGTCTCCCCTTCTACCT
* *
418927 TTTTGTCTATGCCATTTTAGGAGTCTCCCCCTT-TACCT
1 TTTTGTCTATGACATTTTAAGAGTCT-CCCCTTCTACCT
*
418965 TTTTGTTTATG
1 TTTTGTCTATG
418976 TCATCATGGG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 38 0.90
39 4 0.10
ACGTcount: A:0.15, C:0.21, G:0.13, T:0.52
Consensus pattern (38 bp):
TTTTGTCTATGACATTTTAAGAGTCTCCCCTTCTACCT
Found at i:419059 original size:15 final size:15
Alignment explanation
Indices: 419049--419084 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
419039 GTTATATATT
419049 TTTTTAATATATTAA
1 TTTTTAATATATTAA
* *
419064 TTTTTAATATTTTAG
1 TTTTTAATATATTAA
419079 TTTTTA
1 TTTTTA
419085 GTCAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTTTAATATATTAA
Found at i:419514 original size:22 final size:22
Alignment explanation
Indices: 419471--419515 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
419461 CTGAATTATA
*
419471 AATTTTCTAAATATTAAAATAT
1 AATTTTCTAAATAATAAAATAT
* * *
419493 AATTTTGTAATTAATAAGATAT
1 AATTTTCTAAATAATAAAATAT
419515 A
1 A
419516 TAAATAAGTT
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:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (22 bp):
AATTTTCTAAATAATAAAATAT
Found at i:422760 original size:2 final size:2
Alignment explanation
Indices: 422753--422792 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
422743 TCATAAATGA
422753 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
422793 TGCACTTATG
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:423035 original size:24 final size:23
Alignment explanation
Indices: 423003--423101 Score: 78
Period size: 23 Copynumber: 4.2 Consensus size: 23
422993 ATTTTTTTAG
* *
423003 AAAAAATAAAAATATTCTAAATTT
1 AAAATATAAAAA-ATTCTAAAATT
*
423027 AAAATATAAAAACATTC-AAAA-C
1 AAAATATAAAAA-ATTCTAAAATT
* *
423049 ATAATTATAAAAAATACTAAAATT
1 A-AAATATAAAAAATTCTAAAATT
423073 AAAAT-TAAAAAATTACTAGAAAATT
1 AAAATATAAAAAATT-CT--AAAATT
423098 AAAA
1 AAAA
423102 CTTGAATTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
22 12 0.20
23 22 0.37
24 16 0.27
25 10 0.17
ACGTcount: A:0.66, C:0.06, G:0.01, T:0.27
Consensus pattern (23 bp):
AAAATATAAAAAATTCTAAAATT
Found at i:423083 original size:23 final size:25
Alignment explanation
Indices: 423051--423101 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
423041 TTCAAAACAT
423051 AATTATAAAAAATACT-AAAATTAA
1 AATTATAAAAAATACTAAAAATTAA
*
423075 AATTA-AAAAATTACTAGAAAATTAA
1 AATTATAAAAAATACTA-AAAATTAA
423100 AA
1 AA
423102 CTTGAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 9 0.38
24 5 0.21
25 10 0.42
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (25 bp):
AATTATAAAAAATACTAAAAATTAA
Found at i:423842 original size:6 final size:6
Alignment explanation
Indices: 423817--423855 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
423807 ACTTCTTAAG
*
423817 AAAAAT AAAATAA AATAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAA-AT AA-AAAT AAAAAT AAAAAT AAAAAT A
423856 CTCTTTTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 21 0.72
7 6 0.21
8 2 0.07
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:424975 original size:47 final size:45
Alignment explanation
Indices: 424905--425030 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
424895 TATAAAATCT
*
424905 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
424950 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCTATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * **
424997 CTTGCCA-TTATTCCGTAAGCTCACAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
425031 GCATAGTTAC
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 22 0.31
45 10 0.14
46 2 0.03
47 37 0.52
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:425210 original size:40 final size:40
Alignment explanation
Indices: 425135--425255 Score: 217
Period size: 40 Copynumber: 3.0 Consensus size: 40
425125 ACCGTAGTGC
*
425135 TACACATAAGGTCGTTCCCA-CATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
425174 TACACATAAGGTCGTGCCCACCATATACACTGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
425214 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
425254 TA
1 TA
425256 TAAACCTGCA
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
39 19 0.24
40 59 0.76
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.25
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:427943 original size:19 final size:19
Alignment explanation
Indices: 427906--427943 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
427896 TTCAACTTTG
*
427906 TTAGTAATTTTTTTTATTT
1 TTAGTAATTTTTTTAATTT
427925 TTAGT-ATTTTTTATAATTT
1 TTAGTAATTTTTT-TAATTT
427944 AAAATTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (19 bp):
TTAGTAATTTTTTTAATTT
Found at i:432085 original size:30 final size:29
Alignment explanation
Indices: 432046--432104 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
432036 GAGAATTTAC
* *
432046 ATGAACTACGTGATTTA-ATGTATATGTGA
1 ATGAACTACGAG-TTTATATGAATATGTGA
432075 ATGAAGCTACGAGTTTATATGAATATGTGA
1 ATGAA-CTACGAGTTTATATGAATATGTGA
432105 TATGTTTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.36
Consensus pattern (29 bp):
ATGAACTACGAGTTTATATGAATATGTGA
Found at i:432366 original size:23 final size:23
Alignment explanation
Indices: 432332--432399 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
432322 CATCTTATAT
432332 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
432355 GGCACTTAGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
432378 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
432400 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:435110 original size:15 final size:17
Alignment explanation
Indices: 435076--435114 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
435066 TTTTATTTGA
*
435076 TAAAATAGATATCTAAT
1 TAAAATAGATATCAAAT
435093 TAAAATA-ATAT-AAAT
1 TAAAATAGATATCAAAT
435108 TAAAATA
1 TAAAATA
435115 TTATTACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.48
16 4 0.19
17 7 0.33
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (17 bp):
TAAAATAGATATCAAAT
Found at i:448470 original size:23 final size:23
Alignment explanation
Indices: 448444--448506 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
448434 CACCATAGCT
* *
448444 CGTATAAATACACCGAAGTGCCA-
1 CGTAGAAATGCACCGAAGTG-CAG
* *
448467 CGTAGAATTGCACCAAAGTGCAG
1 CGTAGAAATGCACCGAAGTGCAG
448490 CGTAGAAATGCACCGAA
1 CGTAGAAATGCACCGAA
448507 ATTCCATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 2 0.06
23 31 0.94
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCAG
Found at i:450147 original size:26 final size:25
Alignment explanation
Indices: 450102--450152 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
450092 CAAATTTAAC
* *
450102 CTCAAAATTCACTTACAAACTCTTT
1 CTCAAAATTCACTCAAAAACTCTTT
450127 CTCAACAATTCACTCAAAAACTCTTT
1 CTCAA-AATTCACTCAAAAACTCTTT
450153 ATATTAAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.33
Consensus pattern (25 bp):
CTCAAAATTCACTCAAAAACTCTTT
Found at i:453379 original size:21 final size:21
Alignment explanation
Indices: 453355--453444 Score: 72
Period size: 21 Copynumber: 4.2 Consensus size: 21
453345 TGTTCTGAAT
453355 GACCACATAGATGTCCCAAAG
1 GACCACATAGATGTCCCAAAG
* ** *
453376 GACCACATATATGTTTCGAAG
1 GACCACATAGATGTCCCAAAG
* * *
453397 GACCACGTAGAATTATCCCGAAG
1 GACCACATAG-A-TGTCCCAAAG
* * *
453420 GACCACATATATGTCCTAAAT
1 GACCACATAGATGTCCCAAAG
453441 GACC
1 GACC
453445 GCGTAGAACC
Statistics
Matches: 52, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
21 35 0.67
22 2 0.04
23 15 0.29
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.21
Consensus pattern (21 bp):
GACCACATAGATGTCCCAAAG
Found at i:453450 original size:44 final size:44
Alignment explanation
Indices: 453368--453452 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
453358 CACATAGATG
* *
453368 TCCCAAAGGACCACATATATGTTTCGAAGGACCACGTAGAATTA
1 TCCCAAAGGACCACATATATGTCTCAAAGGACCACGTAGAATTA
* * *
453412 TCCCGAAGGACCACATATATGTC-CTAAATGACCGCGTAGAA
1 TCCCAAAGGACCACATATATGTCTC-AAAGGACCACGTAGAA
453453 CCCCGAACTC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 1 0.03
44 34 0.97
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (44 bp):
TCCCAAAGGACCACATATATGTCTCAAAGGACCACGTAGAATTA
Found at i:454608 original size:26 final size:25
Alignment explanation
Indices: 454563--454613 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
454553 CAAATTTAAC
* *
454563 CTCAAAATTCACTTACAAACTCTTT
1 CTCAAAATTCACTCAAAAACTCTTT
454588 CTCAACAATTCACTCAAAAACTCTTT
1 CTCAA-AATTCACTCAAAAACTCTTT
454614 ATATTAAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.33
Consensus pattern (25 bp):
CTCAAAATTCACTCAAAAACTCTTT
Found at i:456026 original size:25 final size:26
Alignment explanation
Indices: 455998--456048 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
455988 CAAATTTAAC
* *
455998 CTCAA-AATTCACTTACAAACTCTTT
1 CTCAACAATTCACTTAAAAACCCTTT
456023 CTCAACAATTCACTTAAAAACCCTTT
1 CTCAACAATTCACTTAAAAACCCTTT
456049 ATATTAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.33
Consensus pattern (26 bp):
CTCAACAATTCACTTAAAAACCCTTT
Found at i:457212 original size:17 final size:18
Alignment explanation
Indices: 457175--457216 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
457165 AGAAAATGAT
*
457175 ACAACTCAAAAAATCAAA
1 ACAACTCAAAAAATAAAA
*
457193 ACAACT-AAATAATAAAA
1 ACAACTCAAAAAATAAAA
457210 ACAACTC
1 ACAACTC
457217 GAACAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.64, C:0.21, G:0.00, T:0.14
Consensus pattern (18 bp):
ACAACTCAAAAAATAAAA
Found at i:461465 original size:64 final size:64
Alignment explanation
Indices: 461386--461512 Score: 245
Period size: 64 Copynumber: 2.0 Consensus size: 64
461376 ACTGAGTGTC
*
461386 CTATACAAACTTGCCATAATAATGTATAACTTCGTCATTGTAGACCCACGGAGCACTCATTGGT
1 CTATACAAACTTGCCATAATAATGTACAACTTCGTCATTGTAGACCCACGGAGCACTCATTGGT
461450 CTATACAAACTTGCCATAATAATGTACAACTTCGTCATTGTAGACCCACGGAGCACTCATTGG
1 CTATACAAACTTGCCATAATAATGTACAACTTCGTCATTGTAGACCCACGGAGCACTCATTGG
461513 CGTGAGTGAC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.28
Consensus pattern (64 bp):
CTATACAAACTTGCCATAATAATGTACAACTTCGTCATTGTAGACCCACGGAGCACTCATTGGT
Found at i:468441 original size:153 final size:153
Alignment explanation
Indices: 468190--468473 Score: 469
Period size: 153 Copynumber: 1.9 Consensus size: 153
468180 TTAGAAATCC
*
468190 GACCTGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGA
1 GACCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGA
* * * *
468255 TCCAACCCGAATTTTATATATTTTCGGACCGGTCCGGTTTTTTTCACCCTAAACCCGAACTCGAC
66 CCCAACCCGAATTATATATATTTTCGGACCGGTCCAGTTTTTTTCACCCTAAACCCGAACCCGAC
468320 CCGAACAAAATAAAGTTTCATCT
131 CCGAACAAAATAAAGTTTCATCT
* *
468343 GACCCGACCCGACCCGAAATAATTAAAAATTATTTTTATTTAATAAAAATAGTGACTTAATCCGA
1 GACCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGA
* * **
468408 CCCGACCTGAATTATATATATTTTCGGGTCGGTCCAGTTTTTTTCACCCTAAACCCGAACCCGAC
66 CCCAACCCGAATTATATATATTTTCGGACCGGTCCAGTTTTTTTCACCCTAAACCCGAACCCGAC
468473 C
131 C
468474 GACCCGAATA
Statistics
Matches: 120, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
153 120 1.00
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (153 bp):
GACCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGA
CCCAACCCGAATTATATATATTTTCGGACCGGTCCAGTTTTTTTCACCCTAAACCCGAACCCGAC
CCGAACAAAATAAAGTTTCATCT
Found at i:468942 original size:6 final size:6
Alignment explanation
Indices: 468931--469033 Score: 206
Period size: 6 Copynumber: 17.2 Consensus size: 6
468921 TTCTTGGTGT
468931 CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA
1 CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA
468979 CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA
1 CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA
469027 CTCTCA C
1 CTCTCA C
469034 AAATAAAGCA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 97 1.00
ACGTcount: A:0.17, C:0.50, G:0.00, T:0.33
Consensus pattern (6 bp):
CTCTCA
Found at i:469697 original size:20 final size:19
Alignment explanation
Indices: 469674--469720 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
469664 CGATATACCA
469674 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
469694 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
469714 GGTAAAA
1 GGTAAAA
469721 CGTTACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:469797 original size:181 final size:182
Alignment explanation
Indices: 469462--469934 Score: 732
Period size: 181 Copynumber: 2.6 Consensus size: 182
469452 GATCCAAATT
* * * **
469462 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATTGAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * *
469527 AAACCGGTAAAGCGCTACTGGATACATTTAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* *
469592 GTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
131 GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
*
469644 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
469709 AAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
** * *
469773 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTTGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
* * *
469825 AAAAATATATCGATCCACAACGATGTAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
*
469890 AAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
469935 CGTAAGTACG
Statistics
Matches: 267, Mismatches: 24, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
181 168 0.63
182 99 0.37
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
Found at i:469903 original size:17 final size:19
Alignment explanation
Indices: 469864--469906 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
469854 AGGTAAAAAT
469864 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
469884 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
469901 ATGATA
1 ATGATA
469907 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:472186 original size:21 final size:21
Alignment explanation
Indices: 472122--472174 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
472112 AAGACAATCA
*
472122 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
472143 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
472164 AGAGTCGAAGA
1 AGAGTCGAAGA
472175 TACATTTGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.43, C:0.09, G:0.32, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:474035 original size:19 final size:19
Alignment explanation
Indices: 474011--474078 Score: 118
Period size: 19 Copynumber: 3.6 Consensus size: 19
474001 AATGTAGGGT
474011 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
474030 TAATTTTGTATATGATTTA
1 TAATTTTGTATAAGATTTA
*
474049 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
474068 TAATTTTGTAT
1 TAATTTTGTAT
474079 GTGAATATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.32, C:0.01, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:475293 original size:200 final size:200
Alignment explanation
Indices: 474311--475274 Score: 1651
Period size: 200 Copynumber: 4.8 Consensus size: 200
474301 AATTTACAAT
*
474311 ATGGCAAACAGGGTGCAACCATAAAGTGTCTATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
474376 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTAAAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
474441 ATGAGAGAATATGTCTAAATAATGTATTGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
474506 AATGA
196 AATGA
* * *
474511 ATGGCAAACAGGGTACAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
474576 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
474641 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
474706 AATGA
196 AATGA
* *
474711 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * * *
474776 CGAAACACATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATATCGATTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * *
474841 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCTAT
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
474906 AATGA
196 AATGA
* * *
474911 ATGGCAAATAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCTCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
474976 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCAGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
475041 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATAATTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
475106 AATGA
196 AATGA
475111 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
475176 CGAAACCCAAAAGTATAATGTATTAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * * *
475241 ATGGGAGAATTGGTATATAA-CATGTATCGACACT
131 ATGAGAGAATAGGTCTA-AATAATGTATCGACACT
475275 GTTTAATGTT
Statistics
Matches: 723, Mismatches: 40, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
200 721 1.00
201 2 0.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.31
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
AATGA
Found at i:476755 original size:6 final size:6
Alignment explanation
Indices: 476744--476801 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
476734 CAAGCGGTCA
* * * * *
476744 ATGAAG ATGAAG CTGATG ATGAAG ATGACG ATGAAG ATGACG ATGATG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
*
476792 ATGATG ATGA
1 ATGAAG ATGA
476802 TCCAAACAAG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.40, C:0.05, G:0.33, T:0.22
Consensus pattern (6 bp):
ATGAAG
Found at i:476765 original size:3 final size:3
Alignment explanation
Indices: 476757--476802 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
476747 AAGATGAAGC
* * * *
476757 TGA TGA TGA AGA TGA CGA TGA AGA TGA CGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
476803 CCAAACAAGT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.37, C:0.04, G:0.33, T:0.26
Consensus pattern (3 bp):
TGA
Found at i:476765 original size:18 final size:18
Alignment explanation
Indices: 476744--476801 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
476734 CAAGCGGTCA
*
476744 ATGAAGATGAAGCTGATG
1 ATGAAGATGAAGATGATG
* *
476762 ATGAAGATGACGATGAAG
1 ATGAAGATGAAGATGATG
* *
476780 ATGACGATGATGATGATG
1 ATGAAGATGAAGATGATG
476798 ATGA
1 ATGA
476802 TCCAAACAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.40, C:0.05, G:0.33, T:0.22
Consensus pattern (18 bp):
ATGAAGATGAAGATGATG
Found at i:476802 original size:12 final size:12
Alignment explanation
Indices: 476744--476801 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
476734 CAAGCGGTCA
*
476744 ATGAAGATGAAG
1 ATGACGATGAAG
* *
476756 CTGATGATGAAG
1 ATGACGATGAAG
476768 ATGACGATGAAG
1 ATGACGATGAAG
*
476780 ATGACGATGATG
1 ATGACGATGAAG
*
476792 ATGATGATGA
1 ATGACGATGA
476802 TCCAAACAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.40, C:0.05, G:0.33, T:0.22
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:478436 original size:183 final size:183
Alignment explanation
Indices: 478012--479323 Score: 2314
Period size: 183 Copynumber: 7.2 Consensus size: 183
478002 CAAAGTTTTC
* *
478012 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCCATACCTTTT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* * *
478077 CAAAAAGTGTCG--ATTGAAAAAACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAA
66 CAAAAAGTGTCGACATT---TACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAA
* * *
478140 TATAATCGGTATAAATATACCGATTTTATGAGCG-A-A--T-TACAACCTATATAG
128 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
478191 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCATAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
*
478256 CAAAAAGTGTCGACATTTACACATCGGAGCCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
*
478321 AACCGGTATAAATATACCAGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
478374 ACACTTTTTAATATTGTGTCGGTACTTTATATCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
*
478439 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTATAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
*
478504 AACCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
478557 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATAGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* **
478622 CAAAAAGTTTCGACATTTACACATCAAAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
478687 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
478740 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
*
478805 CAAAAAGTGTCGACATTTACACATCGGAACCTAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
478870 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
* *
478923 ATACTTTTTAATATTGTGTTGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* *
478988 CAAAAAGTATCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTATAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
**
479053 AACCGGTATAAATATACCATTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
479106 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
479171 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
479236 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
479289 ACACTTTTTAATTTTGTGTCGGTACTTTATGTCCA
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCA
479324 AAATTATAAT
Statistics
Matches: 1083, Mismatches: 43, Indels: 10
0.95 0.04 0.01
Matches are distributed among these distances:
178 72 0.07
179 75 0.07
180 1 0.00
181 3 0.00
182 1 0.00
183 931 0.86
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (183 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:479418 original size:120 final size:120
Alignment explanation
Indices: 479205--479440 Score: 418
Period size: 120 Copynumber: 2.0 Consensus size: 120
479195 CGGAACCCAG
479205 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
1 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
*
479270 AGGTCTACAACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGTCCAA
66 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAA
* * * *
479325 AATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACTGGTTTTATTAGCGAAT
1 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
*
479390 AGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGT
66 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
479441 ACAGAATGGA
Statistics
Matches: 110, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 110 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (120 bp):
AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAA
Found at i:479569 original size:303 final size:303
Alignment explanation
Indices: 479022--479612 Score: 1056
Period size: 303 Copynumber: 2.0 Consensus size: 303
479012 CGGAACCCAG
*
479022 AATTATAATGTAATAGATAATTTTATAATATAACCGGTATAAATATACCATTTTTATGAGCGAAT
1 AATTATAATGTAATAGATAATTTTATAATATAACCGGTATAAATATACCAGTTTTATGAGCGAAT
*
479087 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAA
66 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTACAGAATGGAAGAA
*
479152 AAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTA
131 AAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAAAATTATAATGTA
* *
479217 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACC
196 ATAGATAATTTTGTAATATAACAGGTATAAATATACCAGTTTTATGAGCGAATAGGTCTACAACC
*
479282 TATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGTCCAA
261 TATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAA
* * * ** *
479325 AATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACTGGTTTTATTAGCGAAT
1 AATTATAATGTAATAGATAATTTTATAATATAACCGGTATAAATATACCAGTTTTATGAGCGAAT
*
479390 AGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTACAGAATGGAAGAA
66 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTACAGAATGGAAGAA
*
479455 AAATGTGTTGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAAAATTATAATGTA
131 AAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAAAATTATAATGTA
479520 ATAGATAATTTTGTAATATAACAGGTATAAATATACCAGTTTTATGAGCGAATAGGTCTACAACC
196 ATAGATAATTTTGTAATATAACAGGTATAAATATACCAGTTTTATGAGCGAATAGGTCTACAACC
479585 TATATCGACACTTTTTAATATTGTGTCG
261 TATATCGACACTTTTTAATATTGTGTCG
479613 CTAATTTTAA
Statistics
Matches: 274, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
303 274 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (303 bp):
AATTATAATGTAATAGATAATTTTATAATATAACCGGTATAAATATACCAGTTTTATGAGCGAAT
AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTACAGAATGGAAGAA
AAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAAAATTATAATGTA
ATAGATAATTTTGTAATATAACAGGTATAAATATACCAGTTTTATGAGCGAATAGGTCTACAACC
TATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAA
Found at i:482905 original size:260 final size:260
Alignment explanation
Indices: 482439--483107 Score: 1230
Period size: 260 Copynumber: 2.6 Consensus size: 260
482429 CCATAAGTAT
* * *
482439 AATGTTCAATGAAACCGATATAATTATACCGGTTTTATGAGAGAATATGTCTAAATCATGTATCG
1 AATGGTCAATGAAACCGGTATAATTATACCGGTTTTATGAGAGAATAGGTCTAAATCATGTATCG
*
482504 ACACTTTTTTAGTTTGTGTCGATATTTTTGTCCAGAATAAAATATTAAAACCAACGAGGTGCAAG
66 ACACTTTTTTAGTTTGTGTCGATATTTTTGTCCAGAATGAAATATTAAAACCAACGAGGTGCAAG
482569 CATAAAGTGTCGATACTTACGGTCTAGAATGAATGCCAAAAAAGGTGTACCCTTAAAAAGTATCG
131 CATAAAGTGTCGATACTTACGGTCTAGAATGAATGCCAAAAAAGGTGTACCCTTAAAAAGTATCG
*
482634 ATACATTTATTAAAAAAATATCGATCCCTAAAACATCGAAACCCATAAGTATAATGTAATAGGTA
196 ATACATTTATTAAAAAAATATCGATCCCTAAAACATCGAAACCCATAAGTATAATGTAACAGGTA
482699 AATGGTCAATGAAACCGGTATAATTATACCGGTTTTATGAGAGAATAGGTCTAAATCATGTATCG
1 AATGGTCAATGAAACCGGTATAATTATACCGGTTTTATGAGAGAATAGGTCTAAATCATGTATCG
*
482764 ACATTTTTTTAGTTTGTGTCGATATTTTTGTCCAGAATGAAATATTAAAACCAACGAGGTGCAAG
66 ACACTTTTTTAGTTTGTGTCGATATTTTTGTCCAGAATGAAATATTAAAACCAACGAGGTGCAAG
*
482829 CATAAAGTGTCGATACTTACGGTCTAGAATGAATGCCAAAAAAGGTGTACCCTTAAAAAGTGTCG
131 CATAAAGTGTCGATACTTACGGTCTAGAATGAATGCCAAAAAAGGTGTACCCTTAAAAAGTATCG
482894 ATACATTTATTAAAAAAATATCGATCCCTAAAACATCGAAACCCATAAGTATAATGTAACAGGTA
196 ATACATTTATTAAAAAAATATCGATCCCTAAAACATCGAAACCCATAAGTATAATGTAACAGGTA
*
482959 AATGGTCAATGAAACCGGTATAATTATACCAGTTTTATGAGAGAATAGGTCTAAATCATGTATCG
1 AATGGTCAATGAAACCGGTATAATTATACCGGTTTTATGAGAGAATAGGTCTAAATCATGTATCG
** *
483024 ACACTTTTTTAGTTTGTGTCGATATTTTTGTCCAGAATGAAATATTAATGCCCAACGACGTGCAA
66 ACACTTTTTTAGTTTGTGTCGATATTTTTGTCCAGAATGAAATATTAA-AACCAACGAGGTGCAA
483089 GCATAAAGTGTCGATACTT
130 GCATAAAGTGTCGATACTT
483108 TTATAAAAAG
Statistics
Matches: 396, Mismatches: 12, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
260 364 0.92
261 32 0.08
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (260 bp):
AATGGTCAATGAAACCGGTATAATTATACCGGTTTTATGAGAGAATAGGTCTAAATCATGTATCG
ACACTTTTTTAGTTTGTGTCGATATTTTTGTCCAGAATGAAATATTAAAACCAACGAGGTGCAAG
CATAAAGTGTCGATACTTACGGTCTAGAATGAATGCCAAAAAAGGTGTACCCTTAAAAAGTATCG
ATACATTTATTAAAAAAATATCGATCCCTAAAACATCGAAACCCATAAGTATAATGTAACAGGTA
Found at i:483813 original size:23 final size:23
Alignment explanation
Indices: 483753--483825 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
483743 ATAGGTAAAA
* *
483753 ATATGATGTAATAGATAGCGTTT
1 ATATAATGTAATAGGTAGCGTTT
483776 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGTTT
* *
483799 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGTTT
483822 ATAT
1 ATAT
483826 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGTTT
Found at i:484273 original size:23 final size:23
Alignment explanation
Indices: 484242--484291 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
484232 ATAGGTAAAA
*
484242 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
484265 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
484288 ATAT
1 ATAT
484292 TGTAAAGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.36
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:484625 original size:466 final size:472
Alignment explanation
Indices: 483338--484694 Score: 2226
Period size: 489 Copynumber: 2.8 Consensus size: 472
483328 TTATATAAGC
* * *
483338 GTAAAATATCTATCCTTTTTATAAAAGTG-TCTATACTTTTTTCACTGTAGAAAATATTAATTTA
1 GTAAAGTATCTATCCTTTTTATAAAAGTGTTC-ATACTTTTTTCACTGTGGAAAACATTAATTTA
*
483402 AGGTTATATTTTGAGTGAGTTTTAAGATATCAATTTAGTAATTATATGTATCTAATGATTTATTT
65 AGGTTATCTTTTGAGTGAGTTTTAAGATATCAATTTAGTAATTATATGTATCTAATGATTTATTT
483467 TTTATGTTACGGTATATATTATCATTAAATTAAAAACAATAAACATATATATTACATATTTATTA
130 TTTATGTTACGGTATATATTATCATTAAATTAAAAACAATAAACATATATATTACATATTTATTA
483532 TTATCTTTGGTTAATATTGTTAAATTTAAATTATAAATATTATTTTATAAAATATCAAAACAATC
195 TTATCTTTGGTTAATATTGTTAAATTTAAATTATAAATATTATTTTATAAAATATCAAAACAATC
483597 AAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTAT
260 AAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTA-
* *
483662 TAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAATATCGATCCTTTTTATAAAAAGTAT
324 TAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTAT
483727 GGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGATAGCGTTTATATAATGTAATAGGT
389 GGACACTTTCAATATAATAGGT---AATA-GA--TAATA-ATA--G------T-ATGTAATAGGT
* *
483792 AGCGTTTATATAATGTAATAGGTAGTGCTTATATT
438 AGCGCTTATATAATGTAATAGGTAGCGCTTATATT
* * *
483827 GTAAAGTATCTATCCTTTTTATAAAAGTGTCCACACTTTTTTCACTGTGTAAAACATTAATTTAA
1 GTAAAGTATCTATCCTTTTTATAAAAGTGTTCATACTTTTTTCACTGTGGAAAACATTAATTTAA
*
483892 TGTTATCTTTTGAGTGAGTTTTAAGATATCAATTTAGTAATTATATGTATCTAATGATTTATTTT
66 GGTTATCTTTTGAGTGAGTTTTAAGATATCAATTTAGTAATTATATGTATCTAATGATTTATTTT
*
483957 TTATATTACGGTATATATTATCATTAAATTAAAAACAATAAACATATATATTACATATTTATTAT
131 TTATGTTACGGTATATATTATCATTAAATTAAAAACAATAAACATATATATTACATATTTATTAT
**
484022 TATCTTTGGTTAATATTGTTAAATTTAAATTCGAAATATTATTTTATAAAATATCAAAACAATCA
196 TATCTTTGGTTAATATTGTTAAATTTAAATTATAAATATTATTTTATAAAATATCAAAACAATCA
*
484087 AATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTT
261 AATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACT-AT
*
484152 AAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTACCGATCATTTTTATAAAAAGTATG
325 AAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATG
484217 GACACTTTCAATATAATAGGT-A-A-A-AAT-AT-G-ATGTAATAGGTAGCGCTTATATAATGTA
390 GACACTTTCAATATAATAGGTAATAGATAATAATAGTATGTAATAGGTAGCGCTTATATAATGTA
484275 ATAGGTAGCGCTTATATT
455 ATAGGTAGCGCTTATATT
* * *
484293 GTAAAGTATCTATCATTTTTATAGAAGTGTTCATACTTATTTCACTGTGGAAAACATTAATTTAA
1 GTAAAGTATCTATCCTTTTTATAAAAGTGTTCATACTTTTTTCACTGTGGAAAACATTAATTTAA
*
484358 GGTTATCTTTTGAGTGAGTTTTAAGATATCAATTTAATAATTATATGTATCTAATGATTTATTTT
66 GGTTATCTTTTGAGTGAGTTTTAAGATATCAATTTAGTAATTATATGTATCTAATGATTTATTTT
*
484423 TTATGTTACGATATATATTATCATTAAATTAAAAACAATAAACATATATATTACATATTTATTAT
131 TTATGTTACGGTATATATTATCATTAAATTAAAAACAATAAACATATATATTACATATTTATTAT
484488 TATCTTTGGTTAATATTGTTAAATTTAAATTATAAATATTATTTTATAAAATATCAAAACAATCA
196 TATCTTTGGTTAATATTGTTAAATTTAAATTATAAATATTATTTTATAAAATATCAAAACAATCA
*
484553 AATAATTTTTTTGTGCAAATAAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTAT
261 AATAA-TTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTAT
* * *
484618 GAAAAAATTAAAACATAAATTACATAACTTTAAAAAAAGTATCGATCTTTTTTATAAAAAAGTAT
325 AAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTAT-AAAAAGTAT
*
484683 AGACACTTTCAA
389 GGACACTTTCAA
484695 CATATTATAA
Statistics
Matches: 828, Mismatches: 36, Indels: 30
0.93 0.04 0.03
Matches are distributed among these distances:
466 349 0.42
467 76 0.09
474 1 0.00
477 2 0.00
479 3 0.00
482 1 0.00
484 1 0.00
485 1 0.00
489 393 0.47
490 1 0.00
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.41
Consensus pattern (472 bp):
GTAAAGTATCTATCCTTTTTATAAAAGTGTTCATACTTTTTTCACTGTGGAAAACATTAATTTAA
GGTTATCTTTTGAGTGAGTTTTAAGATATCAATTTAGTAATTATATGTATCTAATGATTTATTTT
TTATGTTACGGTATATATTATCATTAAATTAAAAACAATAAACATATATATTACATATTTATTAT
TATCTTTGGTTAATATTGTTAAATTTAAATTATAAATATTATTTTATAAAATATCAAAACAATCA
AATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATA
AAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGG
ACACTTTCAATATAATAGGTAATAGATAATAATAGTATGTAATAGGTAGCGCTTATATAATGTAA
TAGGTAGCGCTTATATT
Found at i:485856 original size:60 final size:59
Alignment explanation
Indices: 485689--485857 Score: 180
Period size: 60 Copynumber: 2.8 Consensus size: 59
485679 TCATATACAT
*
485689 ATAGTTTAGGATGAAATTAGAATGTTCAAAATGTTTGAA-GAGCAATTTAGAATGAAGATC
1 ATAGTTTAGGATGAAATTAGAATGTTCAAAA-GTTT-AAGGAACAATTTAGAATGAAGATC
** * ** **
485749 ATAGTCTGGGGATGAAATTAAAATGTTCAAAAGTTCGAGGATTAATTTAGAATGATAG-TC
1 ATAGT-TTAGGATGAAATTAGAATGTTCAAAAGTTTAAGGAACAATTTAGAATGA-AGATC
* * *
485809 ATAGTTTAAGGATGAAATTAGAATATTTAAAAATTTAAGGAACAATTTA
1 ATAGTTT-AGGATGAAATTAGAATGTTCAAAAGTTTAAGGAACAATTTA
485858 AAAAGGTGAC
Statistics
Matches: 88, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
59 2 0.02
60 61 0.69
61 25 0.28
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.33
Consensus pattern (59 bp):
ATAGTTTAGGATGAAATTAGAATGTTCAAAAGTTTAAGGAACAATTTAGAATGAAGATC
Found at i:486654 original size:28 final size:28
Alignment explanation
Indices: 486573--486658 Score: 109
Period size: 28 Copynumber: 3.0 Consensus size: 28
486563 AGTCCTTCGA
*
486573 CTATTAAAAGTTATAAAATAATCATTTAA
1 CTATTAAAAGTTATAAAATAATCATTT-T
* * * *
486602 CTATTCATATGTTATAAACTCATCATTTT
1 CTATT-AAAAGTTATAAAATAATCATTTT
486631 CTATTAAAAGTTATAAAATAATCATTTT
1 CTATTAAAAGTTATAAAATAATCATTTT
486659 AATGACGTCT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
28 19 0.40
29 10 0.21
30 18 0.38
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.43
Consensus pattern (28 bp):
CTATTAAAAGTTATAAAATAATCATTTT
Found at i:507198 original size:24 final size:20
Alignment explanation
Indices: 507145--507202 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
507135 TTTCCCTTGA
*
507145 AGTGCATCGATGAATTCTAC
1 AGTGCATCGATGCATTCTAC
507165 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
507188 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
507203 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:510662 original size:23 final size:24
Alignment explanation
Indices: 510627--510675 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
510617 CCACTAGGGG
*
510627 CTATGAATTTGTCCCAAAGAACCA
1 CTATGAATATGTCCCAAAGAACCA
* *
510651 CTATGAA-ATGTCCCGAAGGACCA
1 CTATGAATATGTCCCAAAGAACCA
510674 CT
1 CT
510676 GTATGTCCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (24 bp):
CTATGAATATGTCCCAAAGAACCA
Found at i:510943 original size:28 final size:26
Alignment explanation
Indices: 510905--510957 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 26
510895 GTTCTTGTAT
510905 ATCATATATA-TCACATATGCACATAG
1 ATCATATATATTCACATA-GCACATAG
510931 ATCATTATCATATTCACATAGCACATA
1 ATCA-TAT-ATATTCACATAGCACATA
510958 CAAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 4 0.17
27 3 0.12
28 10 0.42
29 7 0.29
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATATATATTCACATAGCACATAG
Found at i:511330 original size:20 final size:20
Alignment explanation
Indices: 511305--511342 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
511295 TTCCCCTTGA
511305 AGTGCATCGATGAATTCTAT
1 AGTGCATCGATGAATTCTAT
*
511325 AGTGCATCGATGCATTCT
1 AGTGCATCGATGAATTCT
511343 TTAACATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATGAATTCTAT
Found at i:511463 original size:64 final size:63
Alignment explanation
Indices: 511350--511490 Score: 142
Period size: 64 Copynumber: 2.2 Consensus size: 63
511340 TCTTTAACAT
* * * *
511350 GTGCATCGATTCACTACCCATGCATCGATACACAAATCACCTTCAATGTTTTCAT-TTTAAGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCAATG-TTTCATCTTTAAAGA
* * * ** * *
511413 GATGCATCGATGCACT-CCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTACC-CATGCATCGATACACAAATCACATTCAATGTTTCATCTTTAAAGA
511477 GTGCATCGATGCAC
1 GTGCATCGATGCAC
511491 ATTGAATGTG
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
63 21 0.33
64 43 0.67
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCAATGTTTCATCTTTAAAGA
Found at i:512763 original size:16 final size:17
Alignment explanation
Indices: 512732--512764 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
512722 TAATTCAATC
*
512732 CCTTTCATTTCTTTATT
1 CCTTTCATTCCTTTATT
512749 CCTTT-ATTCCTTTATT
1 CCTTTCATTCCTTTATT
512765 TATTCCTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (17 bp):
CCTTTCATTCCTTTATT
Found at i:514824 original size:23 final size:24
Alignment explanation
Indices: 514789--514837 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
514779 CCACTAGGGG
*
514789 CTATGAATTTGTCCCAAAGAACCA
1 CTATGAATATGTCCCAAAGAACCA
* *
514813 CTATGAA-ATGTCCCGAAGGACCA
1 CTATGAATATGTCCCAAAGAACCA
514836 CT
1 CT
514838 GTATGTCCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (24 bp):
CTATGAATATGTCCCAAAGAACCA
Found at i:515104 original size:28 final size:26
Alignment explanation
Indices: 515066--515118 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 26
515056 GTTCTTGTAT
515066 ATCATATATA-TCACATATGCACATAG
1 ATCATATATATTCACATA-GCACATAG
515092 ATCATTATCATATTCACATAGCACATA
1 ATCA-TAT-ATATTCACATAGCACATA
515119 CAAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 4 0.17
27 3 0.12
28 10 0.42
29 7 0.29
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATATATATTCACATAGCACATAG
Found at i:515491 original size:20 final size:20
Alignment explanation
Indices: 515466--515503 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
515456 TTCCCCTTGA
515466 AGTGCATCGATGAATTCTAT
1 AGTGCATCGATGAATTCTAT
*
515486 AGTGCATCGATGCATTCT
1 AGTGCATCGATGAATTCT
515504 TTAACATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATGAATTCTAT
Found at i:515624 original size:64 final size:63
Alignment explanation
Indices: 515511--515651 Score: 142
Period size: 64 Copynumber: 2.2 Consensus size: 63
515501 TCTTTAACAT
* * * *
515511 GTGCATCGATTCACTACCCATGCATCGATACACAAATCACCTTCAATGTTTTCAT-TTTAAGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCAATG-TTTCATCTTTAAAGA
* * * ** * *
515574 GATGCATCGATGCACT-CCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTACC-CATGCATCGATACACAAATCACATTCAATGTTTCATCTTTAAAGA
515638 GTGCATCGATGCAC
1 GTGCATCGATGCAC
515652 ATTGAATGTG
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
63 21 0.33
64 43 0.67
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCAATGTTTCATCTTTAAAGA
Found at i:516924 original size:16 final size:17
Alignment explanation
Indices: 516893--516925 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
516883 TAATTCAATC
*
516893 CCTTTCATTTCTTTATT
1 CCTTTCATTCCTTTATT
516910 CCTTT-ATTCCTTTATT
1 CCTTTCATTCCTTTATT
516926 TATTCCTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (17 bp):
CCTTTCATTCCTTTATT
Found at i:518629 original size:2 final size:2
Alignment explanation
Indices: 518624--518663 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
518614 ATATATCCAT
518624 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
518664 AAATACACAC
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):
TA
Found at i:519240 original size:23 final size:24
Alignment explanation
Indices: 519205--519253 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
519195 CCACTAGGGG
*
519205 CTATGAATTTGTCCCAAAGAACCA
1 CTATGAATATGTCCCAAAGAACCA
* *
519229 CTATGAA-ATGTCCCGAAGGACCA
1 CTATGAATATGTCCCAAAGAACCA
519252 CT
1 CT
519254 GTATGTCCCG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (24 bp):
CTATGAATATGTCCCAAAGAACCA
Found at i:519936 original size:24 final size:20
Alignment explanation
Indices: 519879--519916 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
519869 TTCCCCTTGA
519879 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
519899 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
519917 TTAACATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:524300 original size:3 final size:3
Alignment explanation
Indices: 524294--524338 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
524284 TATTATAACC
* *
524294 ATT ATT ATT ATT ATT ATT ATT AATT -TT AAT ATT ATT ATG ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT
524339 TTTCATGTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:524326 original size:21 final size:21
Alignment explanation
Indices: 524302--524355 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
524292 CCATTATTAT
524302 TATTATTATTATTAATTTTAA
1 TATTATTATTATTAATTTTAA
* * *
524323 TATTATTATGATTATTTTTCA
1 TATTATTATTATTAATTTTAA
*
524344 TGTTATT-TTATT
1 TATTATTATTATT
524356 TGTTTATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (21 bp):
TATTATTATTATTAATTTTAA
Found at i:524650 original size:20 final size:21
Alignment explanation
Indices: 524625--524666 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
524615 ATATATATCG
*
524625 TTTATTTGTTT-CTTTTATTT
1 TTTATTTGTTTCCTTTGATTT
*
524645 TTTATTTTTTTCCTTTGATTT
1 TTTATTTGTTTCCTTTGATTT
524666 T
1 T
524667 GTTTTCTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.79
Consensus pattern (21 bp):
TTTATTTGTTTCCTTTGATTT
Done.