Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000190.1 Hibiscus syriacus cultivar Beakdansim tig00000340_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: 14308945
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 48 of 62
Found at i:11135608 original size:19 final size:19
Alignment explanation
Indices: 11135584--11135635 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
11135574 GAATGCAGTT
11135584 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
*
11135603 AGTGCATCGATACATAAGG
1 AGTGCATCGATGCATAAGG
11135622 AGTGCATCGATGCA
1 AGTGCATCGATGCA
11135636 CCCCCTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:11135676 original size:83 final size:83
Alignment explanation
Indices: 11135539--11135696 Score: 189
Period size: 83 Copynumber: 1.9 Consensus size: 83
11135529 ATGCACAGGA
* *
11135539 AGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAGTTAGTGCATCGATGCATAAGG-
1 AGTGCATCGATGCACCCATTAAAAATGAAAACATCAAATGCAGTTAGTGCATCGATGCAT-AGGT
11135603 AGTGCATCGATACATAAGG
65 AGTGCATCGATACATAAGG
* * * * *
11135622 AGTGCATCGATGCACCCCCTT-AAAATGAAAACATCAAAGGTG-A-TTTGTGTATCGATGTATGG
1 AGTGCATCGATGCA-CCCATTAAAAATGAAAACATCAAA--TGCAGTTAGTGCATCGATGCATAG
11135684 GTAGTGCATCGAT
63 GTAGTGCATCGAT
11135697 GCACATGTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
82 2 0.03
83 54 0.84
84 6 0.09
85 2 0.03
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.25
Consensus pattern (83 bp):
AGTGCATCGATGCACCCATTAAAAATGAAAACATCAAATGCAGTTAGTGCATCGATGCATAGGTA
GTGCATCGATACATAAGG
Found at i:11135733 original size:20 final size:22
Alignment explanation
Indices: 11135688--11135750 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 22
11135678 GTATGGGTAG
11135688 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
11135712 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
11135732 TGCATCGATGCACT-TTAAG
1 TGCATCGATGCACTGTTAAG
11135751 GGGAAATTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
20 19 0.51
21 2 0.05
22 1 0.03
23 2 0.05
24 13 0.35
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:11137320 original size:23 final size:23
Alignment explanation
Indices: 11137294--11137353 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
11137284 ATGGAACTTC
11137294 GGTGCATTTCTACGTGGCACTAT
1 GGTGCATTTCTACGTGGCACTAT
* *
11137317 GGTGCAATTCTACGTGGCACTTT
1 GGTGCATTTCTACGTGGCACTAT
*
11137340 GGTGCATTTATACG
1 GGTGCATTTCTACG
11137354 AGCTGTGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (23 bp):
GGTGCATTTCTACGTGGCACTAT
Found at i:11137719 original size:2 final size:2
Alignment explanation
Indices: 11137706--11137747 Score: 75
Period size: 2 Copynumber: 20.5 Consensus size: 2
11137696 AATATGTAAG
11137706 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11137748 TTATGTTTGG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11139464 original size:22 final size:22
Alignment explanation
Indices: 11139423--11139464 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
11139413 ATGTTCATAA
*
11139423 ACAAACATAAGGAAAAATAAAC
1 ACAAACATAAGAAAAAATAAAC
11139445 ACAAACATAA-AAAAATATAA
1 ACAAACATAAGAAAAA-ATAA
11139465 GCAAATTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.71, C:0.12, G:0.05, T:0.12
Consensus pattern (22 bp):
ACAAACATAAGAAAAAATAAAC
Found at i:11139469 original size:20 final size:21
Alignment explanation
Indices: 11139419--11139469 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
11139409 ATTCATGTTC
11139419 ATAAACAAACATAAGGAAAAAT
1 ATAAACAAACATAA-GAAAAAT
11139441 A-AACACAAACATAA-AAAAAT
1 ATAA-ACAAACATAAGAAAAAT
*
11139461 ATAAGCAAA
1 ATAAACAAA
11139470 TTGATGAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 11 0.42
21 4 0.15
22 11 0.42
ACGTcount: A:0.71, C:0.12, G:0.06, T:0.12
Consensus pattern (21 bp):
ATAAACAAACATAAGAAAAAT
Found at i:11139889 original size:23 final size:23
Alignment explanation
Indices: 11139859--11139929 Score: 124
Period size: 23 Copynumber: 3.1 Consensus size: 23
11139849 CTCCTACCAA
*
11139859 CATTATTATTCGTCCAAGCCGTG
1 CATTATTATTCGTCCAAGCTGTG
11139882 CATTATTATTCGTCCAAGCTGTG
1 CATTATTATTCGTCCAAGCTGTG
*
11139905 CTTTATTATTCGTCCAAGCTGTG
1 CATTATTATTCGTCCAAGCTGTG
11139928 CA
1 CA
11139930 AACGCTAGCT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (23 bp):
CATTATTATTCGTCCAAGCTGTG
Found at i:11144783 original size:29 final size:29
Alignment explanation
Indices: 11144751--11144828 Score: 120
Period size: 29 Copynumber: 2.7 Consensus size: 29
11144741 TGGTAAGAAA
*
11144751 TTCTTACACGTGTAATATGTGATGTGCAG
1 TTCTTACACGTGTAAGATGTGATGTGCAG
* * *
11144780 TTCTTAGACGTGGAAGATGTGCTGTGCAG
1 TTCTTACACGTGTAAGATGTGATGTGCAG
11144809 TTCTTACACGTGTAAGATGT
1 TTCTTACACGTGTAAGATGT
11144829 TAGGGTTATA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (29 bp):
TTCTTACACGTGTAAGATGTGATGTGCAG
Found at i:11144997 original size:9 final size:9
Alignment explanation
Indices: 11144983--11145017 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
11144973 ACTGCTATTC
11144983 TCTATTTCT
1 TCTATTTCT
*
11144992 TCTATTGCT
1 TCTATTTCT
11145001 TCTATTTCT
1 TCTATTTCT
11145010 TCCTATTT
1 T-CTATTT
11145018 TATGTACAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 17 0.74
10 6 0.26
ACGTcount: A:0.11, C:0.23, G:0.03, T:0.63
Consensus pattern (9 bp):
TCTATTTCT
Found at i:11152362 original size:15 final size:15
Alignment explanation
Indices: 11152342--11152371 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
11152332 TTCAAAAGAG
11152342 TTGTAAAGGAGTTTT
1 TTGTAAAGGAGTTTT
11152357 TTGTAAAGGAGTTTT
1 TTGTAAAGGAGTTTT
11152372 GGTTCTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.47
Consensus pattern (15 bp):
TTGTAAAGGAGTTTT
Found at i:11156702 original size:24 final size:24
Alignment explanation
Indices: 11156675--11156760 Score: 64
Period size: 24 Copynumber: 3.3 Consensus size: 24
11156665 CAAGGAAAAT
11156675 CGATACTACTATTATAAGTAGTAG
1 CGATACTACTATTATAAGTAGTAG
* ** * *
11156699 CGATACTTGGACGATTATCGGTACTAAAAAT
1 CGATAC-T--ACTATTATAAGTAGT----AG
11156730 CGATACTACTATTATAAGTAGTAG
1 CGATACTACTATTATAAGTAGTAG
11156754 CGATACT
1 CGATACT
11156761 TGGACGATTA
Statistics
Matches: 45, Mismatches: 10, Indels: 14
0.65 0.14 0.20
Matches are distributed among these distances:
24 14 0.31
25 1 0.02
27 11 0.24
28 11 0.24
30 1 0.02
31 7 0.16
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.31
Consensus pattern (24 bp):
CGATACTACTATTATAAGTAGTAG
Found at i:11156754 original size:55 final size:55
Alignment explanation
Indices: 11156670--11156784 Score: 230
Period size: 55 Copynumber: 2.1 Consensus size: 55
11156660 TGGGTCAAGG
11156670 AAAATCGATACTACTATTATAAGTAGTAGCGATACTTGGACGATTATCGGTACTA
1 AAAATCGATACTACTATTATAAGTAGTAGCGATACTTGGACGATTATCGGTACTA
11156725 AAAATCGATACTACTATTATAAGTAGTAGCGATACTTGGACGATTATCGGTACTA
1 AAAATCGATACTACTATTATAAGTAGTAGCGATACTTGGACGATTATCGGTACTA
11156780 AAAAT
1 AAAAT
11156785 GTATAATGGA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 60 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.30
Consensus pattern (55 bp):
AAAATCGATACTACTATTATAAGTAGTAGCGATACTTGGACGATTATCGGTACTA
Found at i:11159623 original size:55 final size:55
Alignment explanation
Indices: 11159539--11159649 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
11159529 ATATGCTTTT
11159539 ATATTAGATTCGAGGGAGGCTTGCTACAAGCCAACCTCAGAGTTTTCGATCAAAA
1 ATATTAGATTCGAGGGAGGCTTGCTACAAGCCAACCTCAGAGTTTTCGATCAAAA
11159594 ATATTAGATTCGAGGGAGGCTTGCTACAAGCCAACCTCAGAGTTTTCGATCAAAA
1 ATATTAGATTCGAGGGAGGCTTGCTACAAGCCAACCTCAGAGTTTTCGATCAAAA
11159649 A
1 A
11159650 CCATTTTATT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (55 bp):
ATATTAGATTCGAGGGAGGCTTGCTACAAGCCAACCTCAGAGTTTTCGATCAAAA
Found at i:11159960 original size:23 final size:22
Alignment explanation
Indices: 11159908--11159974 Score: 89
Period size: 23 Copynumber: 3.0 Consensus size: 22
11159898 GTTGAGGGTT
* *
11159908 CTATGTGGTCATTCGGGACAAA
1 CTATGTGGTCCTTCGAGACAAA
* *
11159930 CTATGTGGTCCTTCGAAACAATC
1 CTATGTGGTCCTTCGAGACAA-A
11159953 CTATGTGGTCCTTCGAGACAAA
1 CTATGTGGTCCTTCGAGACAAA
11159975 TATATGGCAC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 18 0.47
23 20 0.53
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.28
Consensus pattern (22 bp):
CTATGTGGTCCTTCGAGACAAA
Found at i:11161367 original size:41 final size:41
Alignment explanation
Indices: 11161318--11161453 Score: 125
Period size: 41 Copynumber: 3.3 Consensus size: 41
11161308 TCTACTGAGT
11161318 AGTATCGATACCGATTCAAGTGGTATCGATACCAAGAGGGG
1 AGTATCGATACCGATTCAAGTGGTATCGATACCAAGAGGGG
* * * ** * * * *
11161359 AGTATCGATA-CTA-TGAGGATAATATCGATA-GAATCTACTGAGT
1 AGTATCGATACCGATTCAAG-TGGTATCGATACCAA--GA--GGGG
11161402 AGTATCGATACCGATTCAAGTGGTATCGATACCAAGAGGGG
1 AGTATCGATACCGATTCAAGTGGTATCGATACCAAGAGGGG
11161443 AGTATCGATAC
1 AGTATCGATAC
11161454 TATGAGGATA
Statistics
Matches: 69, Mismatches: 18, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
39 5 0.07
40 11 0.16
41 24 0.35
43 13 0.19
44 11 0.16
45 5 0.07
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (41 bp):
AGTATCGATACCGATTCAAGTGGTATCGATACCAAGAGGGG
Found at i:11161396 original size:84 final size:84
Alignment explanation
Indices: 11161277--11161472 Score: 342
Period size: 84 Copynumber: 2.3 Consensus size: 84
11161267 GATAGAACAA
* *
11161277 TATCGATACTAT-AGGCTTAAAATC-AGTAGAATCTACTGAGTAGTATCGATACCGATTCAAGTG
1 TATCGATACTATGAGG-ATAATATCGA-TAGAATCTACTGAGTAGTATCGATACCGATTCAAGTG
11161340 GTATCGATACCAAGAGGGGAG
64 GTATCGATACCAAGAGGGGAG
11161361 TATCGATACTATGAGGATAATATCGATAGAATCTACTGAGTAGTATCGATACCGATTCAAGTGGT
1 TATCGATACTATGAGGATAATATCGATAGAATCTACTGAGTAGTATCGATACCGATTCAAGTGGT
11161426 ATCGATACCAAGAGGGGAG
66 ATCGATACCAAGAGGGGAG
11161445 TATCGATACTATGAGGATAATATCGATA
1 TATCGATACTATGAGGATAATATCGATA
11161473 CCATTGATCA
Statistics
Matches: 108, Mismatches: 2, Indels: 4
0.95 0.02 0.04
Matches are distributed among these distances:
84 104 0.96
85 4 0.04
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.27
Consensus pattern (84 bp):
TATCGATACTATGAGGATAATATCGATAGAATCTACTGAGTAGTATCGATACCGATTCAAGTGGT
ATCGATACCAAGAGGGGAG
Found at i:11161840 original size:15 final size:15
Alignment explanation
Indices: 11161820--11161851 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
11161810 GTGCATTTAA
11161820 TTGTGTAACTATATG
1 TTGTGTAACTATATG
11161835 TTGTGTAACTATATG
1 TTGTGTAACTATATG
11161850 TT
1 TT
11161852 ATACTAGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (15 bp):
TTGTGTAACTATATG
Found at i:11161970 original size:54 final size:54
Alignment explanation
Indices: 11161907--11162505 Score: 860
Period size: 54 Copynumber: 11.1 Consensus size: 54
11161897 ACCAAATTGA
11161907 CACTAAGTGTGCAAATCACAGAATTCATCATATGTTGATGAATAACCGTTTCGG
1 CACTAAGTGTGCAAATCACAGAATTCATCATATGTTGATGAATAACCGTTTCGG
11161961 CACTAAGTGTGCAAATCACAGAATTCATCATATGTTGATGAATAACCGTTTCGG
1 CACTAAGTGTGCAAATCACAGAATTCATCATATGTTGATGAATAACCGTTTCGG
* *
11162015 CACTAAGTGTGCAAATCACAGAATTCATCATATGTTGATGAATAATCGTTTCGA
1 CACTAAGTGTGCAAATCACAGAATTCATCATATGTTGATGAATAACCGTTTCGG
* *
11162069 CACTAAGTGTGCAAATCACAGAATTCATAATATGTTGATGAATAACTGTTTCGG
1 CACTAAGTGTGCAAATCACAGAATTCATCATATGTTGATGAATAACCGTTTCGG
* * *
11162123 CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGA
1 CACTAAGTGTGCAAATCACAGAATTCATCATATGTTGATGAATAACCGTTTCGG
* * *
11162177 AACTAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAATAACTGTTTCGG
1 CACTAAGTGTGCAAATCACAGAATTCATCATATGTTGATGAATAACCGTTTCGG
* ** **
11162231 CACTAAGTGTGTAAATCATGGAATTCATCATATGTTGATGAATAACTATTTCGG
1 CACTAAGTGTGCAAATCACAGAATTCATCATATGTTGATGAATAACCGTTTCGG
* * * * *
11162285 CATTAAGTGTGTAATTCACGGAATTCATCATATGTTGATGAATAACTGTTTCGG
1 CACTAAGTGTGCAAATCACAGAATTCATCATATGTTGATGAATAACCGTTTCGG
* * *
11162339 CACTAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAATAACCATTTCGA
1 CACTAAGTGTGCAAATCACAGAATTCATCATATGTTGATGAATAACCGTTTCGG
* *
11162393 CAATAAGTGTGCAAAGT-AC-GAAATTCATCATATGTTGATGAATAACCGTTTCAG
1 CACTAAGTGTGCAAA-TCACAG-AATTCATCATATGTTGATGAATAACCGTTTCGG
* ** * * * * * *
11162447 CACGATTTGTGTAAACCACAGAATTCATAATATGTTTATGAATAACCGTATAGG
1 CACTAAGTGTGCAAATCACAGAATTCATCATATGTTGATGAATAACCGTTTCGG
11162501 CACTA
1 CACTA
11162506 CGGATGCATT
Statistics
Matches: 496, Mismatches: 45, Indels: 8
0.90 0.08 0.01
Matches are distributed among these distances:
53 1 0.00
54 493 0.99
55 2 0.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (54 bp):
CACTAAGTGTGCAAATCACAGAATTCATCATATGTTGATGAATAACCGTTTCGG
Found at i:11165982 original size:23 final size:23
Alignment explanation
Indices: 11165949--11166010 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
11165939 GACATTTTAT
*
11165949 ATGGCACTTCGGTGCAATTCTAC
1 ATGGCACTTCGGTGCAATCCTAC
*
11165972 GCT-GCACTTCGGTGCAATCCTAC
1 -ATGGCACTTCGGTGCAATCCTAC
11165995 ATGGCACTTCGGTGCA
1 ATGGCACTTCGGTGCA
11166011 TTTATACGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.03
23 32 0.94
24 1 0.03
ACGTcount: A:0.19, C:0.29, G:0.24, T:0.27
Consensus pattern (23 bp):
ATGGCACTTCGGTGCAATCCTAC
Found at i:11166277 original size:2 final size:2
Alignment explanation
Indices: 11166270--11166335 Score: 118
Period size: 2 Copynumber: 34.0 Consensus size: 2
11166260 TATGAAATGG
11166270 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
11166311 AT A- 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
11166336 GTATTTATGT
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 60 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11170977 original size:23 final size:23
Alignment explanation
Indices: 11170887--11170969 Score: 130
Period size: 23 Copynumber: 3.6 Consensus size: 23
11170877 CATTTTATAT
*
11170887 GGCACTTCGGTGCAATTCTACAC
1 GGCACTTCGGTGCAATTCTACGC
11170910 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* * *
11170933 GGCACTTCGGTACAATCCTACGT
1 GGCACTTCGGTGCAATTCTACGC
11170956 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
11170970 TTTATACGAG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.19, C:0.30, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:11173155 original size:41 final size:41
Alignment explanation
Indices: 11173091--11173170 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 41
11173081 TAGAAGTAAG
* * ** *
11173091 AAAAGTCTGTCAGGTGATGTGAAAGATTGTTTGATTCTGTA
1 AAAAGTATGTCAAGTGAAATGAAAGATTGTTTGAATCTGTA
*
11173132 AAAAGTATGTCAAGTGAAATGAAAGGTTGTTTGAATCTG
1 AAAAGTATGTCAAGTGAAATGAAAGATTGTTTGAATCTG
11173171 CAAAGTGTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (41 bp):
AAAAGTATGTCAAGTGAAATGAAAGATTGTTTGAATCTGTA
Found at i:11175871 original size:23 final size:23
Alignment explanation
Indices: 11175841--11175900 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
11175831 CATTTTATAT
*
11175841 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATCCTACGC
* *
11175864 GGCACTTCGGTGTAATCCTACGT
1 GGCACTTCGGTGCAATCCTACGC
*
11175887 GGCACTTTGGTGCA
1 GGCACTTCGGTGCA
11175901 TTGTACGAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTGCAATCCTACGC
Found at i:11176156 original size:47 final size:49
Alignment explanation
Indices: 11176089--11176185 Score: 180
Period size: 48 Copynumber: 2.0 Consensus size: 49
11176079 AAAGTTGTGA
11176089 ACGTAAATGATGATATGTGTGCATAT-GGTAATTGTTTCATAAAAGAAT
1 ACGTAAATGATGATATGTGTGCATATGGGTAATTGTTTCATAAAAGAAT
11176137 ACGT-AATGATGATATGTGTGCATATGGGTAATTGTTTCATAAAAGAAT
1 ACGTAAATGATGATATGTGTGCATATGGGTAATTGTTTCATAAAAGAAT
11176185 A
1 A
11176186 TATGAGTTGG
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
47 21 0.44
48 27 0.56
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (49 bp):
ACGTAAATGATGATATGTGTGCATATGGGTAATTGTTTCATAAAAGAAT
Found at i:11176318 original size:2 final size:2
Alignment explanation
Indices: 11176311--11176343 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
11176301 AGTATGAAAT
*
11176311 TA TA TA TA TA TC TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11176344 GTTATGCTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11177534 original size:17 final size:17
Alignment explanation
Indices: 11177512--11177545 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
11177502 TGCAAGGGTG
11177512 GCTAGGGTATGTAGAAA
1 GCTAGGGTATGTAGAAA
11177529 GCTAGGGTATGTAGAAA
1 GCTAGGGTATGTAGAAA
11177546 ATGTCCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.35, T:0.24
Consensus pattern (17 bp):
GCTAGGGTATGTAGAAA
Found at i:11180793 original size:64 final size:64
Alignment explanation
Indices: 11180679--11180798 Score: 154
Period size: 64 Copynumber: 1.9 Consensus size: 64
11180669 ATGTACTATC
* * **
11180679 TATGCATCGGTGCATAAATCCTATTCGGTGTTTGTATTTTAGGCAGGTGCATCGATGCACTCCT
1 TATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTTAGAAAGGTGCATCGATGCACTCCT
* *
11180743 TATGCATCGATGCACTAATTGC-ATTCGATGTTTGTATTTTA-AAAGAGTGCATCGAT
1 TATGCATCGATGCA-TAAATCCTATTCGATGTTTGTATTTTAGAAAG-GTGCATCGAT
11180799 ACACCTTGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
63 2 0.04
64 41 0.85
65 5 0.10
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (64 bp):
TATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTTAGAAAGGTGCATCGATGCACTCCT
Found at i:11183467 original size:20 final size:20
Alignment explanation
Indices: 11183438--11183486 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
11183428 AAAATTACAT
*
11183438 AAAAATGGAGCTTAATTCTG
1 AAAAACGGAGCTTAATTCTG
11183458 AAAAACGGAGCTTAATTCTG
1 AAAAACGGAGCTTAATTCTG
11183478 AAAAACGGA
1 AAAAACGGA
11183487 TCGAATCGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.22
Consensus pattern (20 bp):
AAAAACGGAGCTTAATTCTG
Found at i:11185764 original size:24 final size:24
Alignment explanation
Indices: 11185737--11185841 Score: 86
Period size: 24 Copynumber: 4.4 Consensus size: 24
11185727 AAACGGAGAT
*
11185737 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
11185761 ATCAGATATCAGAACAGAATCCACG
1 ATCAGAAATCAAAACAGAATTCA-G
* * * *
11185786 TTAAG-AATCATAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* ** *
11185809 ATTAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
11185833 ATCAGAAAT
1 ATCAGAAAT
11185842 TAGATAAAAT
Statistics
Matches: 59, Mismatches: 20, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
23 4 0.07
24 51 0.86
25 4 0.07
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.23
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:11187088 original size:18 final size:18
Alignment explanation
Indices: 11187065--11187099 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11187055 TTCCATCTAG
*
11187065 TCTTATTATTTAATTTAA
1 TCTTATCATTTAATTTAA
*
11187083 TCTTATCATTTACTTTA
1 TCTTATCATTTAATTTA
11187100 GTTCTTTCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (18 bp):
TCTTATCATTTAATTTAA
Found at i:11190577 original size:106 final size:108
Alignment explanation
Indices: 11190392--11190606 Score: 416
Period size: 106 Copynumber: 2.0 Consensus size: 108
11190382 GCCAATAATC
11190392 ATTCTTGAGTGGAAGTGAGAGCGAGTTACAATAGATTTTGTTTCGGGGCTACCTTTGTCACCAGG
1 ATTCTTGAGTGGAAGTGAGAGCGAGTTACAATAGATTTTGTTTCGGGGCTACCTTTGTCACCAGG
11190457 TAAGAATGACTCGATATAGGTAATAGTAGCCA-ATT-ACCAAG
66 TAAGAATGACTCGATATAGGTAATAGTAGCCAGATTAACCAAG
11190498 ATTCTTGAGTGGAAGTGAGAGCGAGTTACAATAGATTTTGTTTCGGGGCTACCTTTGTCACCAGG
1 ATTCTTGAGTGGAAGTGAGAGCGAGTTACAATAGATTTTGTTTCGGGGCTACCTTTGTCACCAGG
11190563 TAAGAATGACTCGATATAGGTAATAGTAGCCAGATTAACCAAG
66 TAAGAATGACTCGATATAGGTAATAGTAGCCAGATTAACCAAG
11190606 A
1 A
11190607 CTGCTCATTT
Statistics
Matches: 107, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
106 97 0.91
107 3 0.03
108 7 0.07
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.29
Consensus pattern (108 bp):
ATTCTTGAGTGGAAGTGAGAGCGAGTTACAATAGATTTTGTTTCGGGGCTACCTTTGTCACCAGG
TAAGAATGACTCGATATAGGTAATAGTAGCCAGATTAACCAAG
Found at i:11192445 original size:20 final size:20
Alignment explanation
Indices: 11192416--11192460 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
11192406 CAATTCAAGT
11192416 GGTATCGATACCAAGAGGGA
1 GGTATCGATACCAAGAGGGA
* * * *
11192436 GGTATGGATACTATGAGGGT
1 GGTATCGATACCAAGAGGGA
11192456 GGTAT
1 GGTAT
11192461 TAATACCATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.09, G:0.38, T:0.24
Consensus pattern (20 bp):
GGTATCGATACCAAGAGGGA
Found at i:11192833 original size:15 final size:15
Alignment explanation
Indices: 11192813--11192844 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
11192803 CTGCATTTAA
11192813 TTGTGTAACTATATG
1 TTGTGTAACTATATG
11192828 TTGTGTAACTATATG
1 TTGTGTAACTATATG
11192843 TT
1 TT
11192845 ATACTAGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (15 bp):
TTGTGTAACTATATG
Found at i:11192980 original size:54 final size:54
Alignment explanation
Indices: 11192898--11193065 Score: 266
Period size: 54 Copynumber: 3.1 Consensus size: 54
11192888 TTACCAAATA
* *
11192898 GGCACTAAGTGTGTAAATCAC-AGAATTCATCAAATGTTGATGAATAACCATTTC
1 GGCACTAAGTGTGCAAATCACGA-AATTCATCATATGTTGATGAATAACCATTTC
11192952 GGCACTAAGTGTGCAAATCACGAAATTCATCATATGTTGATGAATAACCATTTC
1 GGCACTAAGTGTGCAAATCACGAAATTCATCATATGTTGATGAATAACCATTTC
* * * *
11193006 GGCATTAAGCGTGCAAATCACGAAATTCATCATATGTTGAAGAATAATCATTTC
1 GGCACTAAGTGTGCAAATCACGAAATTCATCATATGTTGATGAATAACCATTTC
11193060 GGCACT
1 GGCACT
11193066 GTAGACACAC
Statistics
Matches: 106, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
54 105 0.99
55 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (54 bp):
GGCACTAAGTGTGCAAATCACGAAATTCATCATATGTTGATGAATAACCATTTC
Found at i:11193115 original size:2 final size:2
Alignment explanation
Indices: 11193108--11193139 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
11193098 ATACGTGTAT
11193108 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11193140 GTAGTATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:11197998 original size:8 final size:8
Alignment explanation
Indices: 11197985--11198021 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
11197975 GAACATTTCA
11197985 TGCATTCT
1 TGCATTCT
11197993 TGCATTCT
1 TGCATTCT
*
11198001 TGCATTTT
1 TGCATTCT
*
11198009 TGCATTTT
1 TGCATTCT
11198017 TGCAT
1 TGCAT
11198022 CTTCATCTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.14, C:0.19, G:0.14, T:0.54
Consensus pattern (8 bp):
TGCATTCT
Found at i:11199157 original size:13 final size:14
Alignment explanation
Indices: 11199139--11199223 Score: 54
Period size: 14 Copynumber: 6.2 Consensus size: 14
11199129 CAATCATAAC
11199139 AAAAAGAG-AA-AA
1 AAAAAGAGAAACAA
11199151 AAAAA-AGAAA-AA
1 AAAAAGAGAAACAA
** *
11199163 GCAAAGAGAAAAGAA
1 AAAAAGAG-AAACAA
11199178 AAAAAGAGAAACAA
1 AAAAAGAGAAACAA
* *
11199192 AAAAACA-AAAGAA
1 AAAAAGAGAAACAA
*
11199205 CAAAAAGAAAGAACAA
1 -AAAAAGAGA-AACAA
11199221 AAA
1 AAA
11199224 TCGAAAGAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
11 2 0.04
12 12 0.21
13 7 0.12
14 20 0.35
15 12 0.21
16 4 0.07
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAGAGAAACAA
Found at i:11199179 original size:26 final size:23
Alignment explanation
Indices: 11199141--11199192 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 23
11199131 ATCATAACAA
11199141 AAAGAGAAAAAAAAAAGAAAAAGC
1 AAAGAGAAAAAAAAAAGAAAAA-C
*
11199165 AAAGAGAAAAGAAAAAAAGAGAAAC
1 AAAGAG-AAA-AAAAAAAGAAAAAC
11199190 AAA
1 AAA
11199193 AAAACAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 6 0.24
25 7 0.28
26 12 0.48
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.00
Consensus pattern (23 bp):
AAAGAGAAAAAAAAAAGAAAAAC
Found at i:11199222 original size:26 final size:25
Alignment explanation
Indices: 11199149--11199222 Score: 76
Period size: 27 Copynumber: 2.8 Consensus size: 25
11199139 AAAAAGAGAA
*
11199149 AAAAAAAAGAAAAAGCAAAGAGAAAAG
1 AAAAAAAAGAAAAA-CAAA-ACAAAAG
*
11199176 AAAAAAAGAGAAACAAAAAAACAAAAG
1 AAAAAAA-AGAAA-AACAAAACAAAAG
*
11199203 AACAAAAAGAAAGAACAAAA
1 AAAAAAAAGAAA-AACAAAA
11199223 ATCGAAAGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
26 11 0.28
27 19 0.47
28 8 0.20
29 2 0.05
ACGTcount: A:0.80, C:0.07, G:0.14, T:0.00
Consensus pattern (25 bp):
AAAAAAAAGAAAAACAAAACAAAAG
Found at i:11199232 original size:28 final size:27
Alignment explanation
Indices: 11199150--11199223 Score: 80
Period size: 26 Copynumber: 2.7 Consensus size: 27
11199140 AAAAGAGAAA
* *
11199150 AAAAAAAGAAAAAGC--AAAGAGAAAAG
1 AAAAAAAGAAAAA-CAAAAAAACAAAAG
*
11199176 AAAAAAAGAGAAACAAAAAAACAAAAG
1 AAAAAAAGAAAAACAAAAAAACAAAAG
11199203 AACAAAAAGAAAGAACAAAAA
1 AA-AAAAAGAAA-AACAAAAA
11199224 TCGAAAGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 1 0.03
26 12 0.30
27 11 0.28
28 8 0.20
29 8 0.20
ACGTcount: A:0.80, C:0.07, G:0.14, T:0.00
Consensus pattern (27 bp):
AAAAAAAGAAAAACAAAAAAACAAAAG
Found at i:11199235 original size:41 final size:40
Alignment explanation
Indices: 11199136--11199223 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 40
11199126 ATTCAATCAT
* * *
11199136 AACAAAAAGAGAAAAAAAAAAGAAAAAGCAAAGAGAAAAG
1 AACAAAAAGAGAAAAAAAAAACAAAAAACAAAAAGAAAAG
11199176 AA-AAAAAGAGAAACAAAAAAACAAAAGAACAAAAAG-AAAG
1 AACAAAAAGAGAAA-AAAAAAACAAAA-AACAAAAAGAAAAG
11199216 AACAAAAA
1 AACAAAAA
11199224 TCGAAAGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
39 11 0.26
40 19 0.45
41 12 0.29
ACGTcount: A:0.80, C:0.07, G:0.14, T:0.00
Consensus pattern (40 bp):
AACAAAAAGAGAAAAAAAAAACAAAAAACAAAAAGAAAAG
Found at i:11200533 original size:42 final size:42
Alignment explanation
Indices: 11200474--11200561 Score: 160
Period size: 42 Copynumber: 2.1 Consensus size: 42
11200464 AAAGCTGTCT
11200474 CAACGGTTTCAACTTCACGGCGAAGGGAATTGTGTCCA-CCCG
1 CAACGGTTTCAACTTCACGGCGAA-GGAATTGTGTCCACCCCG
11200516 CAACGGTTTCAACTTCACGGCGAAGGAATTGTGTCCACCCCG
1 CAACGGTTTCAACTTCACGGCGAAGGAATTGTGTCCACCCCG
11200558 CAAC
1 CAAC
11200562 ATACAATACT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
41 13 0.29
42 32 0.71
ACGTcount: A:0.25, C:0.31, G:0.24, T:0.20
Consensus pattern (42 bp):
CAACGGTTTCAACTTCACGGCGAAGGAATTGTGTCCACCCCG
Found at i:11201710 original size:529 final size:530
Alignment explanation
Indices: 11200672--11201734 Score: 1668
Period size: 529 Copynumber: 2.0 Consensus size: 530
11200662 ATATCGTGCC
* *
11200672 ACTCGAGACAACATAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
*
11200737 AATTTCAGAGCAAATTTCAACTTCACAGCGAAGGATATTGTACTCCAGACAACGCAAGTTCAACT
66 AATTTCAGAGCAAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* *
11200802 TCACGACGAAGGGACCGCTGGTTGTCATTAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
*
11200867 ACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTG
196 ACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACAAAGGGACCGCTGGTTG
* * *
11200932 TCAATAAATAATTTCCCAATTTTAGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCCAG
261 TCAATAAACAACTTCCCAATTTTAGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCAAG
* * * * *
11200997 ACAACGCAAGTTCAAGTTCACGACGAAGGGACCACTGGTTGTCAATAAACAATTTCCCAATTTCA
326 ACAACACAAGTTCAACTTCACAACGAAGGGACCACTGGTTGTCAACAAACAACTTCCCAATTTCA
* * *
11201062 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
391 GAGCCAATTTCAACTTCACAGCGAAGGACATTGGACTCCAGACAACACAAGCTCAACTTCACGAC
* * * * *
11201127 GAAGGGACCACTGGTTGTCAATAAACAGTTTCCCAATTTCAGAGTCAATTTCAACTTCACAGCGA
456 GAAGGGACCACTGGCTGTCAACAAACAATTTCCCAATTCCAGAATCAATTTCAACTTCACAGCGA
11201192 AGGATATTGG
521 AGGATATTGG
* * * *
11201202 ACTCCAGACAACGCAAGTTCAACTTCACGACGAA-GGATC-ACTGGTTGTCAATAAATAATTTCC
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCC
* *
11201265 CAATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
65 CAATTTCAGAGCAAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
11201330 TTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTT
130 TTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTT
* *
11201395 CACAGCGAAGGATATTGGACTCCAGATAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTT
195 CACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACAAAGGGACCGCTGGTT
* *
11201460 GTCAATAAACAACTTCCCAATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAA
260 GTCAATAAACAACTTCCCAATTTTAGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCAA
*
11201525 GATAACACAAGTTCAACTTCACAACGAAGGGA-CAGCTGGTTGTCAACAAACAACTTCCCAATTT
325 GACAACACAAGTTCAACTTCACAACGAAGGGACCA-CTGGTTGTCAACAAACAACTTCCCAATTT
* * *
11201589 CAGAGCCAATTTCAACTTCACAGCGAAGGGCATTGGACTCGAGACAGCACAAGCTCAACTTCAC-
389 CAGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACTCCAGACAACACAAGCTCAACTTCACG
** * * *
11201653 AGCGAAGGGACGGCTGGCTGTCAACAAATAATTTCCCAGTTCCA-AATCCAGTTTCAACTTCACA
454 A-CGAAGGGACCACTGGCTGTCAACAAACAATTTCCCAATTCCAGAAT-CAATTTCAACTTCACA
* *
11201717 GTGGAGGATATTGG
517 GCGAAGGATATTGG
11201731 ACTC
1 ACTC
11201735 GGAGCAAGAC
Statistics
Matches: 486, Mismatches: 43, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
528 5 0.01
529 450 0.93
530 31 0.06
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (530 bp):
ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCAAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
TCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
ACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACAAAGGGACCGCTGGTTG
TCAATAAACAACTTCCCAATTTTAGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCAAG
ACAACACAAGTTCAACTTCACAACGAAGGGACCACTGGTTGTCAACAAACAACTTCCCAATTTCA
GAGCCAATTTCAACTTCACAGCGAAGGACATTGGACTCCAGACAACACAAGCTCAACTTCACGAC
GAAGGGACCACTGGCTGTCAACAAACAATTTCCCAATTCCAGAATCAATTTCAACTTCACAGCGA
AGGATATTGG
Found at i:11201735 original size:106 final size:106
Alignment explanation
Indices: 11200672--11201734 Score: 1628
Period size: 106 Copynumber: 10.0 Consensus size: 106
11200662 ATATCGTGCC
* ** * *
11200672 ACTCGAGACAACATAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAATAAACAATTTCC
* *
11200736 CAATTTCAGAGCAAATTTCAACTTCACAGCGAAGGATATTGT
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
11200778 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCATTAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
11200843 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
11200884 ACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAATAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* * *
11200949 AATTTTAGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
11200990 ACTCCAGACAACGCAAGTTCAAGTTCACGACGAAGGGACCACTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
11201055 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
11201096 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAATAAACAGTTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
11201161 AATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
11201202 ACTCCAGACAACGCAAGTTCAACTTCACGACGAA-GGATCACTGGTTGTCAATAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
11201266 AATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
11201307 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
11201372 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
11201413 ACTCCAGATAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
11201478 AATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
11201519 ACTCAAGATAACACAAGTTCAACTTCACAACGAAGGGACAGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
**
11201584 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGGCATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * * *
11201625 ACTCGAGACAGCACAAGCTCAACTTCAC-AGCGAAGGGACGGCTGGCTGTCAACAAATAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGA-CGAAGGGACCGCTGGTTGTCAATAAACAATTTCC
* * * * * * *
11201689 CAGTTCCAAATCCAGTTTCAACTTCACAGTGGAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
11201731 ACTC
1 ACTC
11201735 GGAGCAAGAC
Statistics
Matches: 893, Mismatches: 61, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
105 101 0.11
106 790 0.88
107 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:11204011 original size:2 final size:2
Alignment explanation
Indices: 11204004--11204028 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11203994 TTAAATTTGT
11204004 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 T
11204029 TGTTTTTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11204578 original size:54 final size:54
Alignment explanation
Indices: 11204486--11204798 Score: 290
Period size: 54 Copynumber: 5.8 Consensus size: 54
11204476 TTGCGACAGG
* * * *
11204486 CACTAAGTGTACAGTTCACGGAATTCATCATATGTTGATGAATAACCGTTTTGA
1 CACTAAGTGTGCAATTAACGAAATTCATCATATGTTGATGAATAACCGTTTTGA
* * * * * *
11204540 CAATAAGTGTGCAATTAATGAAATTTATCATATATTGATGAATAACCATTTTGG
1 CACTAAGTGTGCAATTAACGAAATTCATCATATGTTGATGAATAACCGTTTTGA
* * * * *
11204594 CACTAAGTGTGCAATTCACGGAATTCATCATATGTTCATGAATAACCATTTCGA
1 CACTAAGTGTGCAATTAACGAAATTCATCATATGTTGATGAATAACCGTTTTGA
* * * * *
11204648 CACTAAGTGTGTAAATCAAAG-AATTCATCATATGTTGATGAATAATCGTTTTGG
1 CACTAAGTGTG-CAATTAACGAAATTCATCATATGTTGATGAATAACCGTTTTGA
* * * * * *
11204702 CAGTAAGTGTGCAAAGT-ACGAAATTCATCGTATGTTGATGAATAATCGTTTCGG
1 CACTAAGTGTGC-AATTAACGAAATTCATCATATGTTGATGAATAACCGTTTTGA
*** * * *
11204756 CACTATA-TGTGCAAACCACGGAATTCATAATATGTTTATGAAT
1 CACTA-AGTGTGCAATTAACGAAATTCATCATATGTTGATGAAT
11204799 GAACGTATGG
Statistics
Matches: 212, Mismatches: 42, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
53 4 0.02
54 202 0.95
55 6 0.03
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.34
Consensus pattern (54 bp):
CACTAAGTGTGCAATTAACGAAATTCATCATATGTTGATGAATAACCGTTTTGA
Found at i:11204678 original size:108 final size:108
Alignment explanation
Indices: 11204484--11204760 Score: 351
Period size: 108 Copynumber: 2.6 Consensus size: 108
11204474 GGTTGCGACA
* * * *
11204484 GGCACTAAGTGTACAGTTCACGGAATTCATCATATGTTGATGAATAACCGTTTTGACAATAAGTG
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGACACTAAGTG
* * * *
11204549 TGCAATTAATGAAATTTATCATATATTGATGAATAACCATTTT
66 TGAAATCAAAGAAATTCATCATATATTGATGAATAACCATTTT
* *
11204592 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTCATGAATAACCATTTCGACACTAAGTG
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGACACTAAGTG
* * *
11204657 TGTAAATCAAAG-AATTCATCATATGTTGATGAATAATCGTTTT
66 TG-AAATCAAAGAAATTCATCATATATTGATGAATAACCATTTT
* * * * * *
11204700 GGCAGTAAGTGTGCAAAGT-ACGAAATTCATCGTATGTTGATGAATAATCGTTTCGGCACTA
1 GGCACTAAGTGTGC-AATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGACACTA
11204761 TATGTGCAAA
Statistics
Matches: 146, Mismatches: 21, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
108 137 0.94
109 9 0.06
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33
Consensus pattern (108 bp):
GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGACACTAAGTG
TGAAATCAAAGAAATTCATCATATATTGATGAATAACCATTTT
Found at i:11204760 original size:162 final size:162
Alignment explanation
Indices: 11204506--11204798 Score: 419
Period size: 162 Copynumber: 1.8 Consensus size: 162
11204496 ACAGTTCACG
* * *
11204506 GAATTCATCATATGTTGATGAATAACCGTTTTGACAATAAGTGTGCAATTAATGAAATTTATCAT
1 GAATTCATCATATGTTGATGAATAACCGTTTTGACAATAAGTGTGCAAGTAACGAAATTCATCAT
* ** *
11204571 ATATTGATGAATAACCATTTTGGCACTA-AGTGTGCAATTCACGGAATTCATCATATGTTCATGA
66 ATATTGATGAATAACCATTTCGGCACTATA-TGTGCAAACCACGGAATTCATAATATGTTCATGA
11204635 ATAACCATTTCGACACTAAGTGTGTAAATCAAA
130 ATAACCATTTCGACACTAAGTGTGTAAATCAAA
* * * *
11204668 GAATTCATCATATGTTGATGAATAATCGTTTTGGCAGTAAGTGTGCAAAGT-ACGAAATTCATCG
1 GAATTCATCATATGTTGATGAATAACCGTTTTGACAATAAGTGTGC-AAGTAACGAAATTCATCA
* * * *
11204732 TATGTTGATGAATAATCGTTTCGGCACTATATGTGCAAACCACGGAATTCATAATATGTTTATGA
65 TATATTGATGAATAACCATTTCGGCACTATATGTGCAAACCACGGAATTCATAATATGTTCATGA
11204797 AT
130 AT
11204799 GAACGTATGG
Statistics
Matches: 114, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
162 110 0.96
163 4 0.04
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (162 bp):
GAATTCATCATATGTTGATGAATAACCGTTTTGACAATAAGTGTGCAAGTAACGAAATTCATCAT
ATATTGATGAATAACCATTTCGGCACTATATGTGCAAACCACGGAATTCATAATATGTTCATGAA
TAACCATTTCGACACTAAGTGTGTAAATCAAA
Found at i:11204780 original size:108 final size:108
Alignment explanation
Indices: 11204484--11204798 Score: 350
Period size: 108 Copynumber: 2.9 Consensus size: 108
11204474 GGTTGCGACA
* * * *
11204484 GGCACTAAGTGTAC-AGTTCACGGAATTCATCATATGTTGATGAATAACCGTTTTGACAATAAGT
1 GGCACTAAGTGTGCAAG-TCACGAAATTCATCATATGTTGATGAATAACCGTTTCGACACTAAGT
* * * *
11204548 GTGC-AATTAATGAAATTTATCATATATTGATGAATAACCATTTT
65 GTGCAAATCAA-GGAATTCATCATATGTTGATGAATAACCATTTT
* * * *
11204592 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTCATGAATAACCATTTCGACACTAAGTG
1 GGCACTAAGTGTGCAAGTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGACACTAAGTG
* * * *
11204657 TGTAAATCAAAGAATTCATCATATGTTGATGAATAATCGTTTT
66 TGCAAATCAAGGAATTCATCATATGTTGATGAATAACCATTTT
* * * *
11204700 GGCAGTAAGTGTGCAAAGT-ACGAAATTCATCGTATGTTGATGAATAATCGTTTCGGCACTATA-
1 GGCACTAAGTGTGC-AAGTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGACACTA-AG
* * * *
11204763 TGTGCAAACCACGGAATTCATAATATGTTTATGAAT
64 TGTGCAAATCAAGGAATTCATCATATGTTGATGAAT
11204799 GAACGTATGG
Statistics
Matches: 175, Mismatches: 28, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
108 165 0.94
109 10 0.06
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33
Consensus pattern (108 bp):
GGCACTAAGTGTGCAAGTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGACACTAAGTG
TGCAAATCAAGGAATTCATCATATGTTGATGAATAACCATTTT
Found at i:11211437 original size:21 final size:21
Alignment explanation
Indices: 11211392--11211455 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
11211382 AAAAATTATG
11211392 TGGTCCTTCGGGATA-AAACTATA
1 TGGTCCTTC-GGA-ACAAA-TATA
*
11211415 TGGTCCTTCGGCACAAATATA
1 TGGTCCTTCGGAACAAATATA
11211436 TGG-CACTTCGGAACAAATAT
1 TGGTC-CTTCGGAACAAATAT
11211456 GTGGCACTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
20 1 0.03
21 22 0.59
22 5 0.14
23 9 0.24
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.28
Consensus pattern (21 bp):
TGGTCCTTCGGAACAAATATA
Found at i:11211460 original size:21 final size:21
Alignment explanation
Indices: 11211411--11211467 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
11211401 GGGATAAAAC
*
11211411 TATATGGTC-CTTCGGCACAAA
1 TATATGG-CACTTCGGAACAAA
11211432 TATATGGCACTTCGGAACAAA
1 TATATGGCACTTCGGAACAAA
*
11211453 TATGTGGCACTTCGG
1 TATATGGCACTTCGG
11211468 TGCAATTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 1 0.03
21 32 0.97
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (21 bp):
TATATGGCACTTCGGAACAAA
Found at i:11214606 original size:23 final size:23
Alignment explanation
Indices: 11214580--11214671 Score: 85
Period size: 23 Copynumber: 4.0 Consensus size: 23
11214570 ACCGAAATGT
* *
11214580 CACATAGAAATGTCTCGAAGGAC
1 CACATAGAAATATCCCGAAGGAC
* * *
11214603 CACATAGTATTATCCCGAAGAAC
1 CACATAGAAATATCCCGAAGGAC
** *
11214626 CGTATAGAAATGTCCCGAAGGAC
1 CACATAGAAATATCCCGAAGGAC
* * *
11214649 CACGTAGAATTATCTCGAAGGAC
1 CACATAGAAATATCCCGAAGGAC
11214672 TGCGTAGAAC
Statistics
Matches: 52, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.20
Consensus pattern (23 bp):
CACATAGAAATATCCCGAAGGAC
Found at i:11215505 original size:22 final size:22
Alignment explanation
Indices: 11215488--11215535 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
11215478 AAAAGTTTTC
11215488 CCGGTATCCAAAGAAAGTAGCA
1 CCGGTATCCAAAGAAAGTAGCA
*
11215510 CCGGTATCCAAAGACAGTAGCA
1 CCGGTATCCAAAGAAAGTAGCA
11215532 CCGG
1 CCGG
11215536 CGATTATCCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.35, C:0.27, G:0.25, T:0.12
Consensus pattern (22 bp):
CCGGTATCCAAAGAAAGTAGCA
Found at i:11218544 original size:21 final size:21
Alignment explanation
Indices: 11218511--11218593 Score: 62
Period size: 23 Copynumber: 3.8 Consensus size: 21
11218501 GTCCTTTGAG
11218511 ATATATGTTTGGT-CTTTTGGAA
1 ATATATG--TGGTCCTTTTGGAA
* *
11218533 CATATATGTGGTCCTATGGGATA
1 -ATATATGTGGTCCTTTTGGA-A
* * *
11218556 ATTCTATGTGGTCCTTTAGGAT
1 A-TATATGTGGTCCTTTTGGAA
11218578 ATATATGTGGT-CTTTT
1 ATATATGTGGTCCTTTT
11218594 AAGACATTCT
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
20 4 0.08
21 13 0.27
22 8 0.16
23 24 0.49
ACGTcount: A:0.22, C:0.10, G:0.23, T:0.46
Consensus pattern (21 bp):
ATATATGTGGTCCTTTTGGAA
Found at i:11218577 original size:23 final size:22
Alignment explanation
Indices: 11218537--11218610 Score: 78
Period size: 21 Copynumber: 3.4 Consensus size: 22
11218527 TTGGAACATA
* *
11218537 TATGTGGTCCTATGGGATAATTC
1 TATGTGGTCCTTTAGGAT-ATTC
*
11218560 TATGTGGTCCTTTAGGATA-TA
1 TATGTGGTCCTTTAGGATATTC
* * *
11218581 TATGTGGTCTTTTAAGACATTC
1 TATGTGGTCCTTTAGGATATTC
11218603 TATGTGGT
1 TATGTGGT
11218611 ATTTCGGTGT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
21 17 0.40
22 10 0.23
23 16 0.37
ACGTcount: A:0.22, C:0.11, G:0.24, T:0.43
Consensus pattern (22 bp):
TATGTGGTCCTTTAGGATATTC
Found at i:11218594 original size:21 final size:21
Alignment explanation
Indices: 11218500--11218594 Score: 68
Period size: 21 Copynumber: 4.4 Consensus size: 21
11218490 GGTTCTATAC
* *
11218500 GGTCCTTT-GAGATATATGTTT
1 GGTCCTTTAG-GATATATATGT
* *
11218521 GGT-CTTTTGGAACATATATGT
1 GGTCCTTTAGG-ATATATATGT
* * *
11218542 GGTCCTATGGGATAATTCTATGT
1 GGTCCTTTAGGAT-A-TATATGT
11218565 GGTCCTTTAGGATATATATGT
1 GGTCCTTTAGGATATATATGT
*
11218586 GGTCTTTTA
1 GGTCCTTTA
11218595 AGACATTCTA
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
20 5 0.09
21 29 0.50
22 7 0.12
23 17 0.29
ACGTcount: A:0.21, C:0.11, G:0.24, T:0.44
Consensus pattern (21 bp):
GGTCCTTTAGGATATATATGT
Found at i:11218635 original size:24 final size:24
Alignment explanation
Indices: 11218599--11218646 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
11218589 CTTTTAAGAC
* * *
11218599 ATTCTATGTGGTATTTCGGTGTAT
1 ATTCTACGCGGTACTTCGGTGTAT
*
11218623 ATTCTACGCGGTACTTCGTTGTAT
1 ATTCTACGCGGTACTTCGGTGTAT
11218647 TTTATACGAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.15, G:0.23, T:0.46
Consensus pattern (24 bp):
ATTCTACGCGGTACTTCGGTGTAT
Found at i:11218654 original size:24 final size:24
Alignment explanation
Indices: 11218608--11218654 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
11218598 CATTCTATGT
* *
11218608 GGTATTTCGGTGTATATTCTACGC
1 GGTACTTCGGTGTATATTATACGC
* *
11218632 GGTACTTCGTTGTATTTTATACG
1 GGTACTTCGGTGTATATTATACG
11218655 AGTTGTGGTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.17, C:0.15, G:0.23, T:0.45
Consensus pattern (24 bp):
GGTACTTCGGTGTATATTATACGC
Found at i:11234669 original size:23 final size:23
Alignment explanation
Indices: 11234643--11234734 Score: 105
Period size: 23 Copynumber: 4.0 Consensus size: 23
11234633 CACCACAGCT
* *
11234643 CGTATAAATGCATCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
*
11234666 CGTAGAATTGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
11234689 CGTAGAATTACACTGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
*
11234712 CGTA-AAATTGCACCGTAGTGCCA
1 CGTAGAAA-TGCACCGAAGTGCCA
11234735 TATAAGATTG
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
22 2 0.03
23 57 0.97
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.21
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:11235489 original size:62 final size:65
Alignment explanation
Indices: 11235376--11235535 Score: 172
Period size: 62 Copynumber: 2.5 Consensus size: 65
11235366 ATCCCTTGAC
*
11235376 GGGTGCATCGATGCACTA-TCTATGCATCGATACA-TAAATCCTATTCAATGTTTGTA-TTT-AA
1 GGGTGCATCGATGCACTACT-TGTGCATCGATACACTAAATCCTATTCAATGTTTGTATTTTAAA
11235437 G
65 G
* * * *
11235438 GGGTGCATCGATGCACTACTTGTGCATCGATACACT-GATGGC-ATTCGATGTTTTTATTTTAAA
1 GGGTGCATCGATGCACTACTTGTGCATCGATACACTAAAT-CCTATTCAATGTTTGTATTTTAAA
11235501 G
65 G
* * **
11235502 GAGTGCATCGATGCACTTCAAGT-CATCGATACAC
1 GGGTGCATCGATGCACTACTTGTGCATCGATACAC
11235536 CTTGAACAAT
Statistics
Matches: 84, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
62 45 0.54
63 17 0.20
64 22 0.26
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (65 bp):
GGGTGCATCGATGCACTACTTGTGCATCGATACACTAAATCCTATTCAATGTTTGTATTTTAAAG
Found at i:11237326 original size:20 final size:20
Alignment explanation
Indices: 11237287--11237332 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
11237277 TTGATGATGT
*
11237287 TGATGAGTTATTATGAAATA
1 TGATGAGTTATGATGAAATA
11237307 TGATGAGTTATGGATG-AATA
1 TGATGAGTTAT-GATGAAATA
11237327 -GATGAG
1 TGATGAG
11237333 GTTTTGGGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 6 0.25
20 15 0.62
21 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.28, T:0.35
Consensus pattern (20 bp):
TGATGAGTTATGATGAAATA
Found at i:11237529 original size:23 final size:23
Alignment explanation
Indices: 11237499--11237546 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
11237489 TTGGATGAAA
*
11237499 AATATCGATACCATCGAGCGAAC
1 AATATCGATACCATCGAGCAAAC
11237522 AATATCGATACCATCGAGCAAAC
1 AATATCGATACCATCGAGCAAAC
11237545 AA
1 AA
11237547 GGATAAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.44, C:0.25, G:0.15, T:0.17
Consensus pattern (23 bp):
AATATCGATACCATCGAGCAAAC
Found at i:11238520 original size:24 final size:24
Alignment explanation
Indices: 11238493--11238570 Score: 110
Period size: 24 Copynumber: 3.4 Consensus size: 24
11238483 TGGATAGTGA
11238493 ATCGATGCACATGTTAAGGAATGT
1 ATCGATGCACATGTTAAGGAATGT
*
11238517 ATCGATGCACATGTTAAGGAATGC
1 ATCGATGCACATGTTAAGGAATGT
11238541 ATCGATGCAC-TG-T-A-GAATGT
1 ATCGATGCACATGTTAAGGAATGT
*
11238561 ACCGATGCAC
1 ATCGATGCAC
11238571 TTTAAAGGGA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
20 14 0.27
21 1 0.02
22 1 0.02
23 2 0.04
24 33 0.65
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (24 bp):
ATCGATGCACATGTTAAGGAATGT
Found at i:11239527 original size:2 final size:2
Alignment explanation
Indices: 11239514--11239555 Score: 75
Period size: 2 Copynumber: 20.5 Consensus size: 2
11239504 GAATACAATG
11239514 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11239556 GTGATATGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11239599 original size:30 final size:30
Alignment explanation
Indices: 11239515--11239588 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 30
11239505 AATACAATGT
*
11239515 ATATGATATATATAT-ATAT-ATATATATAT-
1 ATATGATATATATGTGATATGA-AT-TATATG
11239544 ATAT-ATATATATGTGATATGAATTATATG
1 ATATGATATATATGTGATATGAATTATATG
*
11239573 ATATGATATATGTGTG
1 ATATGATATATATGTG
11239589 TTAGTGATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
28 14 0.36
29 14 0.36
30 11 0.28
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (30 bp):
ATATGATATATATGTGATATGAATTATATG
Found at i:11239607 original size:30 final size:31
Alignment explanation
Indices: 11239511--11239612 Score: 92
Period size: 30 Copynumber: 3.5 Consensus size: 31
11239501 ATTGAATACA
*
11239511 ATGTATATGATATATATAT-ATAT--ATATAT
1 ATGTATATGATATATATGTGATATGAAT-TAT
*
11239540 ATATATAT-ATATATATGTGATATGAATTAT
1 ATGTATATGATATATATGTGATATGAATTAT
* *
11239570 ATG-ATATGATATATGTGTGTTAGTG-ATTAT
1 ATGTATATGATATATATGTGATA-TGAATTAT
*
11239600 -TGTATATGTTATA
1 ATGTATATGATATA
11239613 AGATATATGA
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
28 9 0.15
29 17 0.28
30 31 0.51
31 4 0.07
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (31 bp):
ATGTATATGATATATATGTGATATGAATTAT
Found at i:11240581 original size:2 final size:2
Alignment explanation
Indices: 11240576--11240608 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
11240566 ATGTTGTATG
11240576 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11240609 ACATAAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11240915 original size:23 final size:21
Alignment explanation
Indices: 11240816--11240921 Score: 70
Period size: 21 Copynumber: 5.0 Consensus size: 21
11240806 GCGGTAATTT
* *
11240816 GGGACATATATGTGATCCTTC
1 GGGATATATATGTGGTCCTTC
* * * *
11240837 GGGATATATGTTTGGTTCTTT
1 GGGATATATATGTGGTCCTTC
* **
11240858 GGAATATATATGTGGTCCGAC
1 GGGATATATATGTGGTCCTTC
*
11240879 GCGGCA-ATTGTATGTGGTCCTTC
1 G-GG-ATA-TATATGTGGTCCTTC
* *
11240902 GGGACATATATATGGTCCTT
1 GGGATATATATGTGGTCCTT
11240922 TAGGACATTC
Statistics
Matches: 62, Mismatches: 19, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
21 43 0.69
22 5 0.08
23 14 0.23
ACGTcount: A:0.21, C:0.15, G:0.27, T:0.37
Consensus pattern (21 bp):
GGGATATATATGTGGTCCTTC
Found at i:11240983 original size:24 final size:24
Alignment explanation
Indices: 11240935--11240983 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
11240925 GACATTCTAT
*
11240935 GTGGCACTTCGGTGCATATTCTAC
1 GTGGCACTTCGGTGCATATTATAC
* *
11240959 GTGGCACTTCGGTGTATTTTATAC
1 GTGGCACTTCGGTGCATATTATAC
11240983 G
1 G
11240984 AGTTGTGGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (24 bp):
GTGGCACTTCGGTGCATATTATAC
Found at i:11243567 original size:15 final size:15
Alignment explanation
Indices: 11243529--11243567 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
11243519 CGCCTATTGC
11243529 AATTGCACCTTACCG
1 AATTGCACCTTACCG
*
11243544 AA-TGACACCTTACTG
1 AATTG-CACCTTACCG
11243559 AATTGCACC
1 AATTGCACC
11243568 AAAAGAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 2 0.10
15 17 0.81
16 2 0.10
ACGTcount: A:0.31, C:0.31, G:0.13, T:0.26
Consensus pattern (15 bp):
AATTGCACCTTACCG
Found at i:11245070 original size:21 final size:22
Alignment explanation
Indices: 11245030--11245075 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
11245020 AGATTGCTGC
*
11245030 CAGGGAACTGATTCCCCTGCTA
1 CAGGGAACTGATTACCCTGCTA
11245052 CAGGGAACTGA-TACCCTGCTA
1 CAGGGAACTGATTACCCTGCTA
11245073 CAG
1 CAG
11245076 TACTGCTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.26, C:0.30, G:0.24, T:0.20
Consensus pattern (22 bp):
CAGGGAACTGATTACCCTGCTA
Found at i:11245884 original size:31 final size:31
Alignment explanation
Indices: 11245846--11245908 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 31
11245836 CGACCTATGT
*
11245846 AACTGTCCATATGTTCTGA-AGAACATAGGTA
1 AACTGTCCATATGTT-TCATAGAACATAGGTA
11245877 AACTGTCCATATGTTTCATAGAACATAGGTA
1 AACTGTCCATATGTTTCATAGAACATAGGTA
11245908 A
1 A
11245909 CCCTCGACTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 2 0.07
31 28 0.93
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (31 bp):
AACTGTCCATATGTTTCATAGAACATAGGTA
Found at i:11248669 original size:21 final size:21
Alignment explanation
Indices: 11248613--11248713 Score: 62
Period size: 21 Copynumber: 4.8 Consensus size: 21
11248603 TTATGAGGAG
* *
11248613 GAACATATATGTGATCCTTCG
1 GAACATATATGTGGTCCTTCA
* * * * *
11248634 GGATATATGTTTGGTCTTTCA
1 GAACATATATGTGGTCCTTCA
*
11248655 GAACATATATGTGGTCCTAT-G
1 GAACATATATGTGGTCCT-TCA
* *
11248676 GGACAATTCTATGTGGTCCTTC-
1 GAAC-A-TATATGTGGTCCTTCA
*
11248698 GGACATATATGTGGTC
1 GAACATATATGTGGTC
11248714 TTTTAAGACA
Statistics
Matches: 60, Mismatches: 16, Indels: 9
0.71 0.19 0.11
Matches are distributed among these distances:
20 10 0.17
21 31 0.52
22 7 0.12
23 12 0.20
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.37
Consensus pattern (21 bp):
GAACATATATGTGGTCCTTCA
Found at i:11255321 original size:21 final size:22
Alignment explanation
Indices: 11255304--11255367 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
11255294 TTTGTCCTTT
*
11255304 GGAACATATATGTGGTCCTATGA
1 GGAACATATATGTGGTCCT-TCA
* *
11255327 GGCAA-TTCTATGTGGTCCTTCA
1 GG-AACATATATGTGGTCCTTCA
11255349 GG-ACATATATGTGGTCCTT
1 GGAACATATATGTGGTCCTT
11255368 TAAGACATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
20 1 0.03
21 13 0.38
22 4 0.12
23 14 0.41
24 2 0.06
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.34
Consensus pattern (22 bp):
GGAACATATATGTGGTCCTTCA
Found at i:11255374 original size:21 final size:22
Alignment explanation
Indices: 11255310--11255384 Score: 71
Period size: 21 Copynumber: 3.4 Consensus size: 22
11255300 CTTTGGAACA
* * *
11255310 TATATGTGGTCCTATGAGGCAAT
1 TATATGTGGTCCTTTAAGAC-AT
* * *
11255333 TCTATGTGGTCCTTCAGGACA-
1 TATATGTGGTCCTTTAAGACAT
11255354 TATATGTGGTCCTTTAAGACAT
1 TATATGTGGTCCTTTAAGACAT
*
11255376 TTTATGTGG
1 TATATGTGG
11255385 CACTTTGGTG
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
21 18 0.44
22 9 0.22
23 14 0.34
ACGTcount: A:0.23, C:0.15, G:0.24, T:0.39
Consensus pattern (22 bp):
TATATGTGGTCCTTTAAGACAT
Found at i:11262398 original size:21 final size:21
Alignment explanation
Indices: 11262362--11262411 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
11262352 CTACGCAGTC
11262362 CTTTGGG-ACATATATGTGAT
1 CTTTGGGAACATATATGTGAT
*
11262382 CTTTGGGAACTTATATGTGAT
1 CTTTGGGAACATATATGTGAT
11262403 CATTTGGGA
1 C-TTTGGGA
11262412 TTTATGTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 7 0.26
21 13 0.48
22 7 0.26
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.40
Consensus pattern (21 bp):
CTTTGGGAACATATATGTGAT
Found at i:11262497 original size:21 final size:21
Alignment explanation
Indices: 11262459--11262499 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
11262449 GAGATAATTC
*
11262459 TATGTGGTCCTTCGGGACATA
1 TATGTGGTCCTTCAGGACATA
*
11262480 TATGTGGTCCTTTAGGACAT
1 TATGTGGTCCTTCAGGACAT
11262500 TTTATGCAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.37
Consensus pattern (21 bp):
TATGTGGTCCTTCAGGACATA
Found at i:11264390 original size:61 final size:61
Alignment explanation
Indices: 11263775--11264382 Score: 775
Period size: 61 Copynumber: 9.9 Consensus size: 61
11263765 CTCTAAAATG
* * *
11263775 AAAGTTAAATGTCTAACGATGCATTTTTTGCAGAAAGGTGCCACTAATGCAAGTTAGATGA
1 AAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGA
* * * *
11263836 AAAGTTAAATGCCTAACGGTGCATTTTTGGGAAAAAAAATGTGCCACTAATGTAAGTTAGATGA
1 AAAGTTAAATGCCTAACGGTGCATTTTT-GG--CAGAAAGGTGCCACTAATGCAAGTTAGATGA
* * * *
11263900 AAAGTTAAATGCCTAAAGGTGTATTTTTGGTAGAAAGGTTCCACTAATGCAAGTTAGATGA
1 AAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGA
* ** * *
11263961 AAATTTAAATGCCTAACAATGCATTTTTGGTAGAAATGTGCCACTAATGCAAGTTAGATGA
1 AAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGA
* * * *
11264022 AAAGTTAAATGCCTAACGGTGCATTTTTTGCAGCAAGGTGCTACTAATGCAAGTTAGATGG
1 AAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGA
* * * * *
11264083 AAAGTTAAATGCCTAACGGTGTATTCTTGTCAGAAAGATGCTACTAATGCAAGTTAGATGA
1 AAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGA
* * * * *
11264144 AAAGTTAAATGCCTAACAGTGCATTTTTGGCAGCAATGTGCTACTAATGCAAGTTATATGA
1 AAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGA
* * *** *
11264205 AAAGCTAAATTCCTAACGGTGCATTTTTTATAGAAAGGTGCCATTAATGCAAGTTAGATGA
1 AAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGA
* * * *
11264266 AAAGTTAAATGCCTAACGGTGCATTTTTGGCAGTAAGGTTCTACTAATGCAAGATAGATGA
1 AAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGA
** * * * *
11264327 AAAGTTAAATGCCCCACGATGCATTTTTGGCAAAAAGGTGTCACTAATACAAGTTA
1 AAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTA
11264383 AAAGAAAAAC
Statistics
Matches: 468, Mismatches: 76, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
61 412 0.88
62 1 0.00
63 2 0.00
64 53 0.11
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (61 bp):
AAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGA
Found at i:11269700 original size:3 final size:3
Alignment explanation
Indices: 11269692--11269729 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
11269682 AGCTTATTTC
*
11269692 CTT CTT CTT CTT -TT CCTT CTT CTT CTT CTC CTT CTT CT
1 CTT CTT CTT CTT CTT -CTT CTT CTT CTT CTT CTT CTT CT
11269730 CCCCGTAAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.87
4 2 0.06
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:11269708 original size:15 final size:15
Alignment explanation
Indices: 11269688--11269729 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
11269678 TAGAAGCTTA
11269688 TTTCCTTCTTCTTCT
1 TTTCCTTCTTCTTCT
11269703 TTTCCTTCTTCTTCT
1 TTTCCTTCTTCTTCT
*
11269718 TCTCCTTCTTCT
1 TTTCCTTCTTCT
11269730 CCCCGTAAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTCCTTCTTCTTCT
Found at i:11270600 original size:23 final size:23
Alignment explanation
Indices: 11270533--11270592 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
11270523 ATTATTATAT
*
11270533 GGCACTACGGTGCAATTCTACGC
1 GGCACTCCGGTGCAATTCTACGC
*
11270556 GGCACTCCGGTGCAATTCTACGT
1 GGCACTCCGGTGCAATTCTACGC
* *
11270579 GGTACTTCGGTGCA
1 GGCACTCCGGTGCA
11270593 CTTATACGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.25
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTCTACGC
Found at i:11273665 original size:17 final size:17
Alignment explanation
Indices: 11273643--11273677 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
11273633 CTATATAAAT
11273643 ATGATGAAGGCAAAGAG
1 ATGATGAAGGCAAAGAG
11273660 ATGATGAAGGCAAAGAG
1 ATGATGAAGGCAAAGAG
11273677 A
1 A
11273678 AGAGTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.06, G:0.34, T:0.11
Consensus pattern (17 bp):
ATGATGAAGGCAAAGAG
Found at i:11275178 original size:20 final size:19
Alignment explanation
Indices: 11275149--11275223 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 19
11275139 AATGTATTTT
*
11275149 GTGCACCGATGCACAAGTAA
1 GTGCATCGATGCAC-AGTAA
*
11275169 GTGCATCGATGCACCGTTAA
1 GTGCATCGATGCACAG-TAA
* *
11275189 GGATGCATCGATACACTGTATA
1 -G-TGCATCGATGCACAGTA-A
11275211 GTGCATCGATGCA
1 GTGCATCGATGCA
11275224 TACCTTCATT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
19 1 0.02
20 27 0.59
21 4 0.09
22 14 0.30
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (19 bp):
GTGCATCGATGCACAGTAA
Found at i:11276096 original size:23 final size:23
Alignment explanation
Indices: 11276066--11276125 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
11276056 ATGGCACTAT
*
11276066 GGTGCAATTCTACGCGGTACTCC
1 GGTGCAATTCTACGCGGCACTCC
* *
11276089 GGTGCAATTCTACGTGGCACTTC
1 GGTGCAATTCTACGCGGCACTCC
* *
11276112 GGTCCAATTATACG
1 GGTGCAATTCTACG
11276126 AGCTGTGGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.28
Consensus pattern (23 bp):
GGTGCAATTCTACGCGGCACTCC
Found at i:11296202 original size:18 final size:19
Alignment explanation
Indices: 11296166--11296203 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
11296156 TATTTATGGG
11296166 GTATCGATACCTAAAGGGTA
1 GTATCGATACC-AAAGGGTA
11296186 GTATCGATACC-AAGGGTA
1 GTATCGATACCAAAGGGTA
11296204 CCGATACCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (19 bp):
GTATCGATACCAAAGGGTA
Found at i:11299070 original size:25 final size:26
Alignment explanation
Indices: 11299012--11299072 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
11299002 TCGTATAAAT
* * *
11299012 TGCACCGAAGTGCCGCGTAGAGTTTT
1 TGCACCGAAGTGCCACGTAGAATTTG
11299038 TGCACCGAAGTGCCACGTAGAAATTTG
1 TGCACCGAAGTGCCACGTAG-AATTTG
11299065 T-C-CCGAAG
1 TGCACCGAAG
11299073 GATGGCGTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.19
26 20 0.65
27 5 0.16
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.23
Consensus pattern (26 bp):
TGCACCGAAGTGCCACGTAGAATTTG
Found at i:11299791 original size:21 final size:21
Alignment explanation
Indices: 11299767--11299809 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
11299757 TCATATTCGT
*
11299767 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
11299788 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
11299809 T
1 T
11299810 AGCCCGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:11305220 original size:20 final size:20
Alignment explanation
Indices: 11305195--11305240 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
11305185 TGGGAAGTAT
*
11305195 CGATACCCTATAGGGGGTAC
1 CGATACCCTATAGAGGGTAC
11305215 CGATACCCTATAGAGGGTAC
1 CGATACCCTATAGAGGGTAC
*
11305235 GGATAC
1 CGATAC
11305241 TACTCCAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.20
Consensus pattern (20 bp):
CGATACCCTATAGAGGGTAC
Found at i:11305851 original size:22 final size:22
Alignment explanation
Indices: 11305823--11305864 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
11305813 TCGAGGGTTA
*
11305823 CATAGGTTCTTCAGGACATATG
1 CATAGGTCCTTCAGGACATATG
*
11305845 CATAGGTCCTTCGGGACATA
1 CATAGGTCCTTCAGGACATA
11305865 AATTTCACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (22 bp):
CATAGGTCCTTCAGGACATATG
Found at i:11309090 original size:545 final size:545
Alignment explanation
Indices: 11308050--11309137 Score: 2095
Period size: 545 Copynumber: 2.0 Consensus size: 545
11308040 TGAAGAGTCA
*
11308050 ATGATATCGAAATCGTCAATTGGGTTTCGAAATCGTTTACTAACAATAATTTAAAGATGAACTTT
1 ATGACATCGAAATCGTCAATTGGGTTTCGAAATCGTTTACTAACAATAATTTAAAGATGAACTTT
11308115 AAAGGGTTTTATAACCTTTAGTTTAGTTTCAAAACTGACCTAATATCAGTTCGATCGATTAATCG
66 AAAGGGTTTTATAACCTTTAGTTTAGTTTCAAAACTGACCTAATATCAGTTCGATCGATTAATCG
11308180 AAAAAACCGTTCTTTTAGAAAATTGATTTAAAAGGCATTTGGATAAATTCTAATTTTAAACACAA
131 AAAAAACCGTTCTTTTAGAAAATTGATTTAAAAGGCATTTGGATAAATTCTAATTTTAAACACAA
11308245 GTGTGTTAATGTTAACTCGATTGGTTAATCGAAATATACAAAGAGAAGGGTGAAATGACTCTTTA
196 GTGTGTTAATGTTAACTCGATTGGTTAATCGAAATATACAAAGAGAAGGGTGAAATGACTCTTTA
11308310 AAAATTGGTGGAAGTAATTGAAACATAGAGATAAAGTTTGCACAATAATTTAGAGTGATTCGACG
261 AAAATTGGTGGAAGTAATTGAAACATAGAGATAAAGTTTGCACAATAATTTAGAGTGATTCGACG
11308375 TTTAAATTAAGTCTACATCCATTAATTTAGCTATACACTAAGGATTTTTTTAAATATACTAGATT
326 TTTAAATTAAGTCTACATCCATTAATTTAGCTATACACTAAGGATTTTTTTAAATATACTAGATT
*
11308440 TGCTTATCTTTAAAGATAAAGTGTAATCTTACAAACTCCCATAAAGAGTAACTAAACTAGAGGAA
391 TGCTTATCTTTAAAGATAAAGTGTAATCTTACAAACTCCCATAAAGAGTAACTAAACTAAAGGAA
11308505 ATTTGACTAGGCAAATGTGTTTACACGACAGTGAAATTCTATAAAACTCTTTGATGTTGCTATAT
456 ATTTGACTAGGCAAATGTGTTTACACGACAGTGAAATTCTATAAAACTCTTTGATGTTGCTATAT
11308570 TTTTTTCAAGAATGGTTTTTTAAAG
521 TTTTTTCAAGAATGGTTTTTTAAAG
*
11308595 ATGACATCGAGATCGTCAATTGGGTTTCGAAATCGTTTACTAACAATAATTTAAAGATGAACTTT
1 ATGACATCGAAATCGTCAATTGGGTTTCGAAATCGTTTACTAACAATAATTTAAAGATGAACTTT
* *
11308660 AAAGTGTTTTATAACCTTTAGTTTAGTTTCAAAACTGACCTAATATCAGTTTGATCGATTAATCG
66 AAAGGGTTTTATAACCTTTAGTTTAGTTTCAAAACTGACCTAATATCAGTTCGATCGATTAATCG
*
11308725 AAAAAACCGTTCTTTTAGAAAATTGATTTAAAAGGCATTTGGATAAATTCTAATTTTAAATACAA
131 AAAAAACCGTTCTTTTAGAAAATTGATTTAAAAGGCATTTGGATAAATTCTAATTTTAAACACAA
* *
11308790 GTGTGTTAATGTTAACTCGATTGGTTAATCGAAATATACAAAGAGGAGGGTGAATTGACTCTTTA
196 GTGTGTTAATGTTAACTCGATTGGTTAATCGAAATATACAAAGAGAAGGGTGAAATGACTCTTTA
11308855 AAAATTGGTGGAAGTAATTGAAACATAGAGATAAAGTTTGCACAATAATTTAGAGTGATTCGACG
261 AAAATTGGTGGAAGTAATTGAAACATAGAGATAAAGTTTGCACAATAATTTAGAGTGATTCGACG
*
11308920 TTTAAATTAAGTCTACATCCATTAATTTAGCTATACACTAAGGATTTTTTTAAATCTACTAGATT
326 TTTAAATTAAGTCTACATCCATTAATTTAGCTATACACTAAGGATTTTTTTAAATATACTAGATT
11308985 TGCTTATCTTTAAAGATAAAGTGTAATCTTACAAACTCCCATAAAGAGTAACTAAACTAAAGGAA
391 TGCTTATCTTTAAAGATAAAGTGTAATCTTACAAACTCCCATAAAGAGTAACTAAACTAAAGGAA
11309050 ATTTGACTAGGCAAATGTGTTTACACGACAGTGAAATTCTATAAAACTCTTTGATGTTGCTATAT
456 ATTTGACTAGGCAAATGTGTTTACACGACAGTGAAATTCTATAAAACTCTTTGATGTTGCTATAT
11309115 TTTTTTCAAGAATGGTTTTTTAA
521 TTTTTTCAAGAATGGTTTTTTAA
11309138 TGTTGTTAAG
Statistics
Matches: 534, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
545 534 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (545 bp):
ATGACATCGAAATCGTCAATTGGGTTTCGAAATCGTTTACTAACAATAATTTAAAGATGAACTTT
AAAGGGTTTTATAACCTTTAGTTTAGTTTCAAAACTGACCTAATATCAGTTCGATCGATTAATCG
AAAAAACCGTTCTTTTAGAAAATTGATTTAAAAGGCATTTGGATAAATTCTAATTTTAAACACAA
GTGTGTTAATGTTAACTCGATTGGTTAATCGAAATATACAAAGAGAAGGGTGAAATGACTCTTTA
AAAATTGGTGGAAGTAATTGAAACATAGAGATAAAGTTTGCACAATAATTTAGAGTGATTCGACG
TTTAAATTAAGTCTACATCCATTAATTTAGCTATACACTAAGGATTTTTTTAAATATACTAGATT
TGCTTATCTTTAAAGATAAAGTGTAATCTTACAAACTCCCATAAAGAGTAACTAAACTAAAGGAA
ATTTGACTAGGCAAATGTGTTTACACGACAGTGAAATTCTATAAAACTCTTTGATGTTGCTATAT
TTTTTTCAAGAATGGTTTTTTAAAG
Found at i:11311150 original size:25 final size:25
Alignment explanation
Indices: 11311094--11311143 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
11311084 AATTTTATAT
* *
11311094 TAAAATTTTAGGCAGTGCGAGATTA
1 TAAAATTTTAGGCAGTGCGAAATCA
11311119 TAAAATTTTAGG-AGGTGCGAAATCA
1 TAAAATTTTAGGCA-GTGCGAAATCA
11311144 AATAATTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.30
Consensus pattern (25 bp):
TAAAATTTTAGGCAGTGCGAAATCA
Found at i:11312968 original size:22 final size:23
Alignment explanation
Indices: 11312937--11312980 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
11312927 AAAATACATT
11312937 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
11312960 TATT-ATATTTTTAATATTATA
1 TATTAATATTTCTAATAATATA
11312981 TAAACTAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:11313069 original size:21 final size:21
Alignment explanation
Indices: 11313013--11313073 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
11313003 ATACTATAAG
*
11313013 AAATTATATT-TTATTTTAATA
1 AAATTATATTATT-TATTAATA
* * *
11313034 ATA-TATAATAATTATTAATA
1 AAATTATATTATTTATTAATA
11313054 AAATTATATTATTTATTAAT
1 AAATTATATTATTTATTAAT
11313074 TTCATAGAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AAATTATATTATTTATTAATA
Found at i:11314411 original size:64 final size:64
Alignment explanation
Indices: 11314343--11314464 Score: 154
Period size: 64 Copynumber: 1.9 Consensus size: 64
11314333 ATTGTTCAAG
* * * * **
11314343 GTGTATCGATGCACATGAAGTGTATCAATGCACTCTTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGAGGCACAAGAAGTGCATCAATGCACCCGCTTAAAATAAAAACATCGAATGCCATCA
* * * *
11314407 GTGTATCGAGGCACAAGTAGTGCATCGATGCACCCGCTTAAAATACAAACTTCGAATG
1 GTGTATCGAGGCACAAGAAGTGCATCAATGCACCCGCTTAAAATAAAAACATCGAATG
11314465 AGATTTATGT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
64 48 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.25
Consensus pattern (64 bp):
GTGTATCGAGGCACAAGAAGTGCATCAATGCACCCGCTTAAAATAAAAACATCGAATGCCATCA
Found at i:11314523 original size:24 final size:24
Alignment explanation
Indices: 11314491--11314571 Score: 162
Period size: 24 Copynumber: 3.4 Consensus size: 24
11314481 GCATAAATAG
11314491 TGCATCGATGCACCCGTCAAGGGA
1 TGCATCGATGCACCCGTCAAGGGA
11314515 TGCATCGATGCACCCGTCAAGGGA
1 TGCATCGATGCACCCGTCAAGGGA
11314539 TGCATCGATGCACCCGTCAAGGGA
1 TGCATCGATGCACCCGTCAAGGGA
11314563 TGCATCGAT
1 TGCATCGAT
11314572 ACATGGTGTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.19
Consensus pattern (24 bp):
TGCATCGATGCACCCGTCAAGGGA
Found at i:11315145 original size:18 final size:19
Alignment explanation
Indices: 11315119--11315214 Score: 106
Period size: 18 Copynumber: 5.1 Consensus size: 19
11315109 TCGAGGGATT
11315119 ATCAGTGGTCCTTCGGGAC
1 ATCAGTGGTCCTTCGGGAC
* * *
11315138 AT-AGTGGTTCTTCGGAATA
1 ATCAGTGGTCCTTCGGGA-C
11315157 ATCAGTGGTCCTTCGGGAC
1 ATCAGTGGTCCTTCGGGAC
* * *
11315176 AT-AGTGGTTCTTCGGAATA
1 ATCAGTGGTCCTTCGGGA-C
11315195 ATCAGTGGTCCTTCGGGAC
1 ATCAGTGGTCCTTCGGGAC
11315214 A
1 A
11315215 AATATTCAGT
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
18 26 0.43
19 9 0.15
20 26 0.43
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (19 bp):
ATCAGTGGTCCTTCGGGAC
Found at i:11315170 original size:38 final size:38
Alignment explanation
Indices: 11315119--11315214 Score: 192
Period size: 38 Copynumber: 2.5 Consensus size: 38
11315109 TCGAGGGATT
11315119 ATCAGTGGTCCTTCGGGACATAGTGGTTCTTCGGAATA
1 ATCAGTGGTCCTTCGGGACATAGTGGTTCTTCGGAATA
11315157 ATCAGTGGTCCTTCGGGACATAGTGGTTCTTCGGAATA
1 ATCAGTGGTCCTTCGGGACATAGTGGTTCTTCGGAATA
11315195 ATCAGTGGTCCTTCGGGACA
1 ATCAGTGGTCCTTCGGGACA
11315215 AATATTCAGT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 58 1.00
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (38 bp):
ATCAGTGGTCCTTCGGGACATAGTGGTTCTTCGGAATA
Found at i:11321458 original size:65 final size:63
Alignment explanation
Indices: 11321352--11321520 Score: 169
Period size: 64 Copynumber: 2.6 Consensus size: 63
11321342 ATTGTTCAAG
* * * * *
11321352 GTGTATCGATGCACATGAAGTGTATCGATGCACTTCTTTAAAACAAAAAACATCGAATGACATCC
1 GTGTATCGATGCACAAGTAGTGCATCGATGCAC-CCCTTAAAA-AAAAAACATCGAATGACATCC
* * ** **
11321417 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCGCTTAAAATACAAACATCGAATGGGATTT
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCC-CTTAAAAAAAAAACATCGAATGACATCC
* * *
11321481 ATGTATCGATGCA-TAGATAGTGCATCGATGCACCCATTAA
1 GTGTATCGATGCACAAG-TAGTGCATCGATGCACCCCTTAA
11321521 GGGATGCATC
Statistics
Matches: 88, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
63 6 0.07
64 46 0.52
65 36 0.41
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (63 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCTTAAAAAAAAAACATCGAATGACATCC
Found at i:11322107 original size:18 final size:18
Alignment explanation
Indices: 11322084--11322118 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11322074 AGGGATTATC
*
11322084 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGGACAT
11322102 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGGGACA
11322119 AATATTCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:11328826 original size:26 final size:26
Alignment explanation
Indices: 11328791--11328858 Score: 129
Period size: 26 Copynumber: 2.7 Consensus size: 26
11328781 TAGTTATAAC
11328791 ATTG-AAGTTTTCTCAATTATATTTA
1 ATTGAAAGTTTTCTCAATTATATTTA
11328816 ATTGAAAGTTTTCTCAATTATATTTA
1 ATTGAAAGTTTTCTCAATTATATTTA
11328842 ATTGAAAGTTTTCTCAA
1 ATTGAAAGTTTTCTCAA
11328859 AAGACGTAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
25 4 0.10
26 38 0.90
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.49
Consensus pattern (26 bp):
ATTGAAAGTTTTCTCAATTATATTTA
Found at i:11333649 original size:30 final size:30
Alignment explanation
Indices: 11333613--11333672 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
11333603 CTTGGTTAAA
11333613 AACTAAAGCATATTTTCTCAACTAAATAGT
1 AACTAAAGCATATTTTCTCAACTAAATAGT
11333643 AACTAAAGCATATTTTCTCAACTAAATAGT
1 AACTAAAGCATATTTTCTCAACTAAATAGT
11333673 TTATCTTTTC
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:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
AACTAAAGCATATTTTCTCAACTAAATAGT
Found at i:11355261 original size:53 final size:53
Alignment explanation
Indices: 11355168--11355367 Score: 267
Period size: 53 Copynumber: 3.8 Consensus size: 53
11355158 ATGATGTGTC
* * ** *
11355168 CGCTCCCTCTTG-TTCAGGGATTAAGGAACTTGAACAATCTTCTAAAAACGAGTT
1 CGCTCCCTCTTGCTTCAGGGAGT-A-GAACTCGAACAATCTTCTGCATACGAGTT
* * * *
11355222 CGCTCCCTATTTCTTCAGGAAGTAGAACTCGAACAATCTTCTGCTTACGAGTT
1 CGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCATACGAGTT
* * *
11355275 CGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTCCTGCCTACGGGTT
1 CGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCATACGAGTT
11355328 CGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTT
1 CGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTT
11355368 ATGGTTTGAT
Statistics
Matches: 129, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
53 110 0.85
54 11 0.09
55 8 0.06
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.29
Consensus pattern (53 bp):
CGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCATACGAGTT
Found at i:11355820 original size:42 final size:43
Alignment explanation
Indices: 11355773--11355871 Score: 182
Period size: 42 Copynumber: 2.3 Consensus size: 43
11355763 TATCATCTCA
11355773 CTCGAAAGACTTACAAATGACCCGAAGGA-TTTCATCATCATG
1 CTCGAAAGACTTACAAATGACCCGAAGGATTTTCATCATCATG
11355815 CTCGAAAGACTTACAAATGACCCGAAGGATTTTCATCATCATG
1 CTCGAAAGACTTACAAATGACCCGAAGGATTTTCATCATCATG
*
11355858 CTCAAAAGACTTAC
1 CTCGAAAGACTTAC
11355872 TGATGAATTT
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 29 0.53
43 26 0.47
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.24
Consensus pattern (43 bp):
CTCGAAAGACTTACAAATGACCCGAAGGATTTTCATCATCATG
Found at i:11355866 original size:43 final size:43
Alignment explanation
Indices: 11355736--11355871 Score: 174
Period size: 42 Copynumber: 3.3 Consensus size: 43
11355726 CACTCTTCCG
* * * *
11355736 AAAAGGCTTA-AAATGGCTCGAAGGACTTATCATC-TCA--CTC
1 AAAAGACTTACAAATGACCCGAAGGA-TTTTCATCATCATGCTC
*
11355776 GAAAGACTTACAAATGACCCGAAGGA-TTTCATCATCATGCTC
1 AAAAGACTTACAAATGACCCGAAGGATTTTCATCATCATGCTC
*
11355818 GAAAGACTTACAAATGACCCGAAGGATTTTCATCATCATGCTC
1 AAAAGACTTACAAATGACCCGAAGGATTTTCATCATCATGCTC
11355861 AAAAGACTTAC
1 AAAAGACTTAC
11355872 TGATGAATTT
Statistics
Matches: 85, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
39 6 0.07
40 11 0.13
41 13 0.15
42 29 0.34
43 26 0.31
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (43 bp):
AAAAGACTTACAAATGACCCGAAGGATTTTCATCATCATGCTC
Found at i:11355951 original size:80 final size:80
Alignment explanation
Indices: 11355824--11356036 Score: 345
Period size: 80 Copynumber: 2.6 Consensus size: 80
11355814 GCTCGAAAGA
* * *
11355824 CTTACAAATGACCCGAAGGATTTTCATCATCATGCTCAAAAGACTTACTGATGAATTTGCTTCAC
1 CTTACAAATTACCCGAAGGA-TTTAATCATCATGCTCGAAAGACTTACTGATGAATTTGCTTCAC
*
11355889 TACTCTTCGGTGAAGG
65 TACTCTTCGGCGAAGG
*
11355905 CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGATTTGCTTCACT
1 CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGAATTTGCTTCACT
*
11355970 ACTCTTTGGCGAAGG
66 ACTCTTCGGCGAAGG
* *
11355985 CTTACAAATTACCCGAAGAACTTAATCATCATGCTCGAAAGACTTACTGATG
1 CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
11356037 GCCCGAAGGA
Statistics
Matches: 124, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
80 105 0.85
81 19 0.15
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (80 bp):
CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGAATTTGCTTCACT
ACTCTTCGGCGAAGG
Found at i:11356029 original size:22 final size:22
Alignment explanation
Indices: 11356004--11356072 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
11355994 TACCCGAAGA
11356004 ACTTAATCATCATGCTCGAAAG
1 ACTTAATCATCATGCTCGAAAG
* * *
11356026 ACTT-A-C-TGATGGCCCGAAGG
1 ACTTAATCATCAT-GCTCGAAAG
* *
11356046 ACTTCATCATCATGCTTGAAAG
1 ACTTAATCATCATGCTCGAAAG
11356068 ACTTA
1 ACTTA
11356073 CTGATGACAC
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
19 3 0.09
20 12 0.34
21 2 0.06
22 15 0.43
23 3 0.09
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (22 bp):
ACTTAATCATCATGCTCGAAAG
Found at i:11356044 original size:42 final size:42
Alignment explanation
Indices: 11355996--11356078 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
11355986 TTACAAATTA
11355996 CCCGAAGAACTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGAACTTAATCATCATGCTCGAAAGACTTACTGATGG
* * *
11356038 CCCGAAGGACTTCATCATCATGCTTGAAAGACTTACTGATG
1 CCCGAAGAACTTAATCATCATGCTCGAAAGACTTACTGATG
11356079 ACACTTACTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (42 bp):
CCCGAAGAACTTAATCATCATGCTCGAAAGACTTACTGATGG
Found at i:11356349 original size:41 final size:41
Alignment explanation
Indices: 11356294--11356400 Score: 133
Period size: 42 Copynumber: 2.6 Consensus size: 41
11356284 CCCGAAGGTT
* * * *
11356294 TTACGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGC
1 TTACAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGAC
* * *
11356335 TTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGAC
1 TTACAGATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGAC
*
11356377 TTACTGATGGCCCGAAGGACTTAT
1 TTACAGATGGCCCGAAGGACTTAT
11356401 AAATTGTGAA
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 20 0.37
42 34 0.63
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.25
Consensus pattern (41 bp):
TTACAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGAC
Found at i:11356374 original size:214 final size:214
Alignment explanation
Indices: 11356116--11356517 Score: 687
Period size: 214 Copynumber: 1.9 Consensus size: 214
11356106 CTCTTCCGTG
* *
11356116 AAGGCTTACAAATTACCCTAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
1 AAGGCTTACAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
* *
11356181 ACTTAAAAATTGTGAAATTTTGAAAATCGCATTATTTGTTTTCAAAAATTTCATCTTCTCAAAAC
66 ACTTAAAAATTGTGAAATTTTGAAAATCGCATTATTCGTTTTCAAAAATTCCATCTTCTCAAAAC
* *
11356246 ATCGTTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTTTTACGGATGGCCCGAAG
131 ATCATTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTCTTACGGATGGCCCGAAG
11356311 GACTTATCATCTTGCTCTA
196 GACTTATCATCTTGCTCTA
*
11356330 AAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
1 AAGGCTTACAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
* * *
11356395 ACTTATAAATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAAC
66 ACTTAAAAATTGTGAAATTTTGAAAATCGCATTATTCGTTTTCAAAAATTCCATCTTCTCAAAAC
* * *
11356460 ATTATTTTTTATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTCTTATGGATGG
131 ATCATTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTCTTACGGATGG
11356518 TTTGCTTCAC
Statistics
Matches: 175, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
214 175 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (214 bp):
AAGGCTTACAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
ACTTAAAAATTGTGAAATTTTGAAAATCGCATTATTCGTTTTCAAAAATTCCATCTTCTCAAAAC
ATCATTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTCTTACGGATGGCCCGAAG
GACTTATCATCTTGCTCTA
Found at i:11373243 original size:105 final size:104
Alignment explanation
Indices: 11373079--11373299 Score: 262
Period size: 105 Copynumber: 2.1 Consensus size: 104
11373069 TATTGTCCAT
* * *
11373079 AAGGACCACATATAAATTCCTTAAGAACCATATACATATACCAAGGATCAAGTAAGTGTCTCAAA
1 AAGGACCACATAAAAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCTCAAA
*
11373144 AAACCTCATACATGCTCCAAATAATACATATACGTCCCA
66 AAACCTCATACATGCTCCAAAGAATACATATACGTCCCA
* * * * *
11373183 AAGGACCACGTAGAAAATTCCTTAAGAATCATATACATATGCTAAGGACCAAATACGTGTCTCAA
1 AAGGACCACATA-AAAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCTCAA
** * * * * * * *
11373248 AGGACCTCATAGATGTTCCATAGGATACCTATATGTCCCG
65 AAAACCTCATACATGCTCCAAAGAATACATATACGTCCCA
*
11373288 AAGGACCGCATA
1 AAGGACCACATA
11373300 GACCCTCGAC
Statistics
Matches: 96, Mismatches: 20, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
104 11 0.11
105 85 0.89
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (104 bp):
AAGGACCACATAAAAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCTCAAA
AAACCTCATACATGCTCCAAAGAATACATATACGTCCCA
Found at i:11374795 original size:22 final size:22
Alignment explanation
Indices: 11374770--11374850 Score: 119
Period size: 22 Copynumber: 3.7 Consensus size: 22
11374760 TCGGTTGAGG
11374770 GGGTATCGATTCCCCTTTGAAT
1 GGGTATCGATTCCCCTTTGAAT
*
11374792 GGGTATCGATTCCCCCTTGAAT
1 GGGTATCGATTCCCCTTTGAAT
* *
11374814 GGGTACCGATT-CCCATTGAAT
1 GGGTATCGATTCCCCTTTGAAT
*
11374835 GGGTAACGATTCCCCT
1 GGGTATCGATTCCCCT
11374851 AGCCCAGAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
21 19 0.36
22 34 0.64
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (22 bp):
GGGTATCGATTCCCCTTTGAAT
Found at i:11378358 original size:105 final size:104
Alignment explanation
Indices: 11378151--11378366 Score: 261
Period size: 105 Copynumber: 2.1 Consensus size: 104
11378141 GATTGTCCAT
* * * * *
11378151 AAGGATCACATATAAATTCCTTAAGAACCATATACATATACCAATGATCAAGTAAGTGTCTCAAA
1 AAGGACCACATAAAAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCTCAAA
11378216 AAACCTCATACATGCTCCAAAGAATACATATACGTCCCG
66 AAACCTCATACATGCTCCAAAGAATACATATACGTCCCG
* * * *
11378255 AAGGACCACATAGAAAATTCCTTAAGAATCATATACATATGCTAAGGACCAAATACGTGTCTCAA
1 AAGGACCACATA-AAAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCTCAA
** * * * * * *
11378320 AGGACCTCATATATGTTCCATAGGATACCTATATGTCCCG
65 AAAACCTCATACATGCTCCAAAGAATACATATACGTCCCG
*
11378360 AAAGACC
1 AAGGACC
11378367 GCGTAGACCC
Statistics
Matches: 93, Mismatches: 18, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
104 11 0.12
105 82 0.88
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.24
Consensus pattern (104 bp):
AAGGACCACATAAAAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCTCAAA
AAACCTCATACATGCTCCAAAGAATACATATACGTCCCG
Found at i:11378735 original size:22 final size:23
Alignment explanation
Indices: 11378702--11378744 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
11378692 TCACACATGC
*
11378702 TCATAGTTTCTG-GTTATATCAT
1 TCATAGTTTCTGACTTATATCAT
11378724 TCATA-TTCTCTGACTTATATC
1 TCATAGTT-TCTGACTTATATC
11378745 TTATGATCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 2 0.11
22 9 0.50
23 7 0.39
ACGTcount: A:0.23, C:0.19, G:0.09, T:0.49
Consensus pattern (23 bp):
TCATAGTTTCTGACTTATATCAT
Found at i:11379861 original size:22 final size:22
Alignment explanation
Indices: 11379836--11379899 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
11379826 TCTAGTTCGG
11379836 TTGAATGGGTACCGATTCCCCC
1 TTGAATGGGTACCGATTCCCCC
* * *
11379858 TTGAATGGGTACCTAAT-CCCT
1 TTGAATGGGTACCGATTCCCCC
*
11379879 TTGAATGGGTATCGATTCCCC
1 TTGAATGGGTACCGATTCCCC
11379900 TAGCCCAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 17 0.49
22 18 0.51
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (22 bp):
TTGAATGGGTACCGATTCCCCC
Found at i:11383808 original size:57 final size:57
Alignment explanation
Indices: 11383736--11383940 Score: 286
Period size: 57 Copynumber: 3.6 Consensus size: 57
11383726 TATAGTTGGA
*
11383736 GGAAGAATACTTGCAGGTTCCTCGGCTTTGTTCTGAGAGCCTTATTGTTCGTGAAGG
1 GGAAGAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTATTGTTCGTGAAGG
* *
11383793 GGAAGAATACTTGCAGGTTCCTCGACTTTGTGCTGAGAGCCTTATTGTTCGTGACGG
1 GGAAGAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTATTGTTCGTGAAGG
* ** *
11383850 GGAAGAATACTTGTAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACAGTTCGTGACA-T
1 GGAAGAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTATTGTTCGTGA-AGG
** * * *
11383907 GGTTGATTACTTGTAGGTTCCTTGGCTTTGTGCT
1 GGAAGAATACTTGCAGGTTCCTCGGCTTTGTGCT
11383941 CAGGGTCTTA
Statistics
Matches: 134, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
57 134 1.00
ACGTcount: A:0.18, C:0.18, G:0.29, T:0.35
Consensus pattern (57 bp):
GGAAGAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTATTGTTCGTGAAGG
Found at i:11383968 original size:57 final size:57
Alignment explanation
Indices: 11383736--11383965 Score: 282
Period size: 57 Copynumber: 4.0 Consensus size: 57
11383726 TATAGTTGGA
* * * *
11383736 GGAAGAATACTTGCAGGTTCCTCGGCTTTGTTCTGAGAGCCTTATTGTTCGTGAAGG
1 GGAAGAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTATTCGTGACGG
* * *
11383793 GGAAGAATACTTGCAGGTTCCTCGACTTTGTGCTGAGAGCCTTATTGTTCGTGACGG
1 GGAAGAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTATTCGTGACGG
* **
11383850 GGAAGAATACTTGTAGGTTCCTCGGCTTTGTGCTGAGAGCCTTAC-AGTTCGTGACAT
1 GGAAGAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTA-TTCGTGACGG
** * * * * * *
11383907 GGTTGATTACTTGTAGGTTCCTTGGCTTTGTGCTCAGGGTCTTACTATTCGTGACGG
1 GGAAGAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTATTCGTGACGG
11383964 GG
1 GG
11383966 TTGTATGATT
Statistics
Matches: 153, Mismatches: 18, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
57 152 0.99
58 1 0.01
ACGTcount: A:0.18, C:0.18, G:0.30, T:0.34
Consensus pattern (57 bp):
GGAAGAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTATTCGTGACGG
Found at i:11385970 original size:12 final size:12
Alignment explanation
Indices: 11385953--11385992 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
11385943 CCAACCCGAC
*
11385953 CCGACCAGTTGA
1 CCGACCCGTTGA
*
11385965 CCGACCCGTTAA
1 CCGACCCGTTGA
11385977 CCCGACCCGTTGA
1 -CCGACCCGTTGA
11385990 CCG
1 CCG
11385993 TTGATCTGCG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.20, C:0.42, G:0.23, T:0.15
Consensus pattern (12 bp):
CCGACCCGTTGA
Found at i:11386010 original size:17 final size:17
Alignment explanation
Indices: 11385988--11386025 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
11385978 CCGACCCGTT
*
11385988 GACCGTTGATCTGCGTC
1 GACCGTTGATCGGCGTC
*
11386005 GACCGTTGATCGGCGTT
1 GACCGTTGATCGGCGTC
11386022 GACC
1 GACC
11386026 ACATTTGACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.13, C:0.29, G:0.32, T:0.26
Consensus pattern (17 bp):
GACCGTTGATCGGCGTC
Found at i:11388674 original size:57 final size:57
Alignment explanation
Indices: 11388582--11388689 Score: 144
Period size: 57 Copynumber: 1.9 Consensus size: 57
11388572 GGAGGAAGAA
* *
11388582 TACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCATGACGGGGTTGAT
1 TACTTGCAGGTTCCTCGGCTTTATGCTCAGAGCCTTACTGTTCATGACGGGGTTGAT
* * * * **
11388639 TACTTGTAGGTTCTTTGGCTTTATGCTCAGGGCCTTACTGTTTGTGACGGG
1 TACTTGCAGGTTCCTCGGCTTTATGCTCAGAGCCTTACTGTTCATGACGGG
11388690 TTGTATGATT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
57 43 1.00
ACGTcount: A:0.13, C:0.19, G:0.30, T:0.38
Consensus pattern (57 bp):
TACTTGCAGGTTCCTCGGCTTTATGCTCAGAGCCTTACTGTTCATGACGGGGTTGAT
Done.