Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009001.1 Hibiscus syriacus cultivar Beakdansim tig00112383_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: 4740655
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 24
Found at i:2628348 original size:16 final size:16
Alignment explanation
Indices: 2628323--2628381 Score: 68
Period size: 16 Copynumber: 3.8 Consensus size: 16
2628313 TAATAATAAT
2628323 TATAAT-TATTATTAA
1 TATAATATATTATTAA
*
2628338 TATAATATATTATTAT
1 TATAATATATTATTAA
* *
2628354 TATTATTTATTATT-A
1 TATAATATATTATTAA
2628369 TATATATATATTA
1 TATA-ATATATTA
2628382 CAAATTACAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
15 9 0.25
16 27 0.75
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATAATATATTATTAA
Found at i:2633373 original size:25 final size:24
Alignment explanation
Indices: 2633323--2633390 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 24
2633313 ACAAAAAAAG
2633323 AAATAAATAAATGAAAAAT-AACAAT
1 AAAT-AATAAAT-AAAAATAAACAAT
*
2633348 AAATGAATAAATAAAAATAAATAAT
1 AAAT-AATAAATAAAAATAAACAAT
*
2633373 -AATAAT-AATAATAATAAA
1 AAATAATAAATAAAAATAAA
2633391 ACTATATAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
22 11 0.28
23 3 0.08
24 9 0.23
25 16 0.41
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (24 bp):
AAATAATAAATAAAAATAAACAAT
Found at i:2633388 original size:28 final size:31
Alignment explanation
Indices: 2633324--2633405 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 31
2633314 CAAAAAAAGA
*
2633324 AATAAAT--AAATGAAA-AATAACAATAAATG
1 AATAAATAAAAAT-AAATAATAATAATAAATG
2633353 AATAAATAAAAATAAATAATAATAAT-AAT-
1 AATAAATAAAAATAAATAATAATAATAAATG
* *
2633382 AAT-AATAAAACTATATAAT-ATAAT
1 AATAAATAAAAATAAATAATAATAAT
2633406 TTTTTTTTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
27 5 0.11
28 14 0.30
29 10 0.21
30 6 0.13
31 12 0.26
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (31 bp):
AATAAATAAAAATAAATAATAATAATAAATG
Found at i:2633491 original size:32 final size:31
Alignment explanation
Indices: 2633441--2633528 Score: 124
Period size: 32 Copynumber: 2.8 Consensus size: 31
2633431 ACTATATATT
*
2633441 ATATATAAATTTTCAAAAATGTTTTTTAAAAA
1 ATATAT-AATTTTTAAAAATGTTTTTTAAAAA
*
2633473 ACTATATAATTTTTAAAAATGTTCTTTAAAAA
1 A-TATATAATTTTTAAAAATGTTTTTTAAAAA
2633505 ATCATATAATTTTT-AAAATGTTTT
1 AT-ATATAATTTTTAAAAATGTTTT
2633529 AAATATTATA
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
31 10 0.20
32 36 0.71
33 5 0.10
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (31 bp):
ATATATAATTTTTAAAAATGTTTTTTAAAAA
Found at i:2633629 original size:36 final size:36
Alignment explanation
Indices: 2633519--2633735 Score: 204
Period size: 38 Copynumber: 5.8 Consensus size: 36
2633509 TATAATTTTT
* * *
2633519 AAAATGTTTTAAATATTATATATTATATATAAGTTTTTA
1 AAAATGTTTTAAAAACTATATA-T-TATAT-AGTTTTAA
*
2633558 AAAATGTTTTCAAAAATTATATATTATATAAGTTTTAA
1 AAAATGTTTT-AAAAACTATATATTATAT-AGTTTTAA
**
2633596 AAAATGTTTTCAAAAACTATATATTATAT-GTTTTCT
1 AAAATGTTTT-AAAAACTATATATTATATAGTTTTAA
*
2633632 AAAATGTTTTAAAAACTATATACTATATAGTTTTCAA
1 AAAATGTTTTAAAAACTATATATTATATAGTTTT-AA
* * ** **
2633669 AAATATTTTTTAAAAAATATATATTATATACATTTCC
1 AAA-ATGTTTTAAAAACTATATATTATATAGTTTTAA
*
2633706 AAAATGTTTTTAAATA-TATATATATATATA
1 AAAATG-TTTTAAAAACTATATAT-TATATA
2633736 TATATATATA
Statistics
Matches: 155, Mismatches: 17, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
35 17 0.11
36 29 0.19
37 20 0.13
38 67 0.43
39 11 0.07
40 11 0.07
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (36 bp):
AAAATGTTTTAAAAACTATATATTATATAGTTTTAA
Found at i:2633726 original size:2 final size:2
Alignment explanation
Indices: 2633719--2633767 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
2633709 ATGTTTTTAA
2633719 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2633760 AT AC AT AT
1 AT AT AT AT
2633768 TTTCAACAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2634520 original size:84 final size:80
Alignment explanation
Indices: 2634410--2635045 Score: 512
Period size: 84 Copynumber: 7.7 Consensus size: 80
2634400 GCCTCTGAGT
* ** * *
2634410 TGAGTGTAATCGAACTCGAAGGTCTTTGGTAATAGATAACCCTTCAAGCCTTGAGTTATGATGTA
1 TGAGTGTAATCGAACTCGAAGGTCTTTGGT--CAGATAACCCTTCTCGACTTAAGTTATGAT-TA
*
2634475 GATGATGTGTCCTCGAAGC
63 AATGATGTG-CCTCGAAGC
* * *
2634494 TGAGTGTAATCTAACTCG-AGGATCTTTGG-CAGATAGCCCTTCTCGACTTAAGCTATGATTCAA
1 TGAGTGTAATCGAACTCGAAGG-TCTTTGGTCAGATAACCCTTCTCGACTTAAGTTATGATT-AA
* *
2634557 ATGATGTGCCTTGGAGC
64 ATGATGTGCCTCGAAGC
* * * * *
2634574 TGAGCGTAGTCGAACTCGAAGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTAC
1 TGAGTGTAATCGAACTCGAAGGTCTTT-G--GTCAGATAACCCTTCTCGACTTAAGTTATGAT-T
2634639 AAATGATGTGCCCTCGAAGC
62 AAATGATGTG-CCTCGAAGC
* * * * * * *
2634659 TGAGTGTAATCGAACTTGAGGGTCTTTGG-CAGATAGCCTTTCTCGACTTAAGCTATGCTGCAAA
1 TGAGTGTAATCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTCGACTTAAGTTATGAT-TAAA
* * *
2634723 TGATATGCCTTGGAGC
65 TGATGTGCCTCGAAGC
** * * * * *
2634739 TGAGCATAGTCGAACTCAAAGATCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTAC
1 TGAGTGTAATCGAACTCGAAGGTCTTTGG-T--CAGATAACCCTTCTCGACTTAAGTTATGAT-T
2634804 AAATGATGTGCCCTCGAAGC
62 AAATGATGTG-CCTCGAAGC
* * * * * *
2634824 TGAGCGTAGTCTAACTCGAGGGTCTTTGG-CAGATAGCCCTTCTCGACTTAAGCTATG-TTGCAA
1 TGAGTGTAATCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTCGACTTAAGTTATGATT--AA
* * * *
2634887 ATGATGCGCATTGGAGC
64 ATGATGTGCCTCGAAGC
** * * *
2634904 TGAGCATAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGG
1 TGAGTGTAATCGAACTCGAAGGTCTTTGG-T--CAGATAACCCTTCTCGACTTAAGTTATGAT-T
*
2634969 AAATAATGTGCCCTCGAAGC
62 AAATGATGTG-CCTCGAAGC
* * * * *
2634989 TGAGCGTAGTCGAACTCG-AGAGTCTTTGG-CAGATAGCCCTTCTCGATTTAAGCTATG
1 TGAGTGTAATCGAACTCGAAG-GTCTTTGGTCAGATAACCCTTCTCGACTTAAGTTATG
2635046 CTGCAAATTT
Statistics
Matches: 456, Mismatches: 72, Indels: 51
0.79 0.12 0.09
Matches are distributed among these distances:
80 90 0.20
81 133 0.29
82 1 0.00
83 4 0.01
84 135 0.30
85 93 0.20
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (80 bp):
TGAGTGTAATCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTCGACTTAAGTTATGATTAAAT
GATGTGCCTCGAAGC
Found at i:2634634 original size:165 final size:165
Alignment explanation
Indices: 2634410--2635137 Score: 974
Period size: 165 Copynumber: 4.4 Consensus size: 165
2634400 GCCTCTGAGT
* * *** ** * * * **
2634410 TGAGTGTAATCGAACTCGAAGGTCTTTGG-TAATAGATAACCCTTCAAGCCTTGAGTTATGATGT
1 TGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTAC
* * * *
2634474 AGATGATGTGTCCTCGAAGCTGAGTGTAATCTAACTCGAGGATCTTTGGCAGATAGCCCTTCTCG
66 AAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCGAGGATCTTTGGCAGATAGCCCTTCTCG
* *
2634539 ACTTAAGCTATGATTCAAATGATGTGCCTTGGAGC
131 ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGC
*
2634574 TGAGCGTAGTCGAACTCGAAGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTAC
1 TGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTAC
* * * *
2634639 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCTTTCTCG
66 AAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCGAGGATCTTTGGCAGATAGCCCTTCTCG
*
2634704 ACTTAAGCTATGCTGCAAATGATATGCCTTGGAGC
131 ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGC
* * *
2634739 TGAGCATAGTCGAACTCAAAGATCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTAC
1 TGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTAC
* * *
2634804 AAATGATGTGCCCTCGAAGCTGAGCGTAGTCTAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCG
66 AAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCGAGGATCTTTGGCAGATAGCCCTTCTCG
* * *
2634869 ACTTAAGCTATGTTGCAAATGATGCGCATTGGAGC
131 ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGC
* **
2634904 TGAGCATAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGG
1 TGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTAC
* *
2634969 AAATAATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGA-GAGTCTTTGGCAGATAGCCCTTCTC
66 AAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCGAGGA-TCTTTGGCAGATAGCCCTTCTC
* ** * *
2635033 GATTTAAGCTATGCTGCAAATTTTGTGCCTTTGAAC
130 GACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGC
* * * * * * * *
2635069 TCAGCGTAGTCGAACTCGAAGATCTTTTGTTGGCAGACAACCCTTCTAGCCTTGAGTTATGCTGC
1 TGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTAC
2635134 AAAT
66 AAAT
2635138 AGTTTCTTTT
Statistics
Matches: 503, Mismatches: 59, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
164 27 0.05
165 476 0.95
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (165 bp):
TGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTAC
AAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCGAGGATCTTTGGCAGATAGCCCTTCTCG
ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGC
Found at i:2635046 original size:81 final size:81
Alignment explanation
Indices: 2634476--2635095 Score: 646
Period size: 81 Copynumber: 7.6 Consensus size: 81
2634466 TATGATGTAG
* * * *
2634476 ATGATGTGTCCTCGAAGCTGAGTGTAATCTAACTCGAG-GATCTTTGGCAGATAGCCCTTCTCGA
1 ATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGAG-TCTTTGGCAGATAGCCCTTCTCGA
* *
2634540 CTTAAGCTATGATTCAA
65 CTTAAGCTATGCTGCAA
* * *
2634557 ATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGA-AGGTCTTTAGTTGGCAGATAACCCTTC
1 ATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGA-GTC--T--TTGGCAGATAGCCCTTC
* *
2634620 TCGACTTAAGTTATGCTACAA
61 TCGACTTAAGCTATGCTGCAA
* * * * *
2634641 ATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCTTTCTCGAC
1 ATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGAGTCTTTGGCAGATAGCCCTTCTCGAC
2634706 TTAAGCTATGCTGCAA
66 TTAAGCTATGCTGCAA
* * * * * *
2634722 ATGATATG-CCTTGGAGCTGAGCATAGTCGAACTC-AAAGATCTTTGGTTGGCAGATAACCCTTC
1 ATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGAG-TC--T--TTGGCAGATAGCCCTTC
* *
2634785 TCGACTTAAGTTATGCTACAA
61 TCGACTTAAGCTATGCTGCAA
* *
2634806 ATGATGTGCCCTCGAAGCTGAGCGTAGTCTAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGAC
1 ATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGAGTCTTTGGCAGATAGCCCTTCTCGAC
*
2634871 TTAAGCTATGTTGCAA
66 TTAAGCTATGCTGCAA
* * * * * *
2634887 ATGATGCG-CATTGGAGCTGAGCATAGTCGAACTCGA-AGGTCTTTGGTTGGCAGATAACCCTTC
1 ATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGA-GTC--T--TTGGCAGATAGCCCTTC
* *
2634950 TCGACTTAAGTTATGCTGGAA
61 TCGACTTAAGCTATGCTGCAA
* *
2634971 ATAATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGAGTCTTTGGCAGATAGCCCTTCTCGAT
1 ATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGAGTCTTTGGCAGATAGCCCTTCTCGAC
2635036 TTAAGCTATGCTGCAA
66 TTAAGCTATGCTGCAA
** * * *
2635052 ATTTTGTGCCTTTGAA-CTCAGCGTAGTCGAACTCGA-AGATCTTT
1 ATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGAG-TCTTT
2635096 TGTTGGCAGA
Statistics
Matches: 447, Mismatches: 69, Indels: 47
0.79 0.12 0.08
Matches are distributed among these distances:
79 4 0.01
80 97 0.22
81 137 0.31
82 3 0.01
83 3 0.01
84 123 0.28
85 77 0.17
86 3 0.01
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (81 bp):
ATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGAGTCTTTGGCAGATAGCCCTTCTCGAC
TTAAGCTATGCTGCAA
Found at i:2635574 original size:83 final size:87
Alignment explanation
Indices: 2635482--2635708 Score: 293
Period size: 95 Copynumber: 2.6 Consensus size: 87
2635472 GGCTAGCTGA
2635482 ATCCATAAAGCCGGGGCGTTTAACCAATTACTCTAGAGGGACAACTCAA-TA-TGTA-AG-CACC
1 ATCCATAAAGCCGGGGCGTTTAACCAATTACTCTAGAGGGACAACTCAATTATTGTATAGACACC
* *
2635543 TTTATCAGGTTAGCTGAATCTT
66 TTTATCAGGCTAGCTGAATATT
2635565 ATCCATAAAGCCGGGGCGTTTAACCAATTAC-CTTAGAGGGACAACTCAAGCTTTATTGTATAGT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTACTC-TAGAGGGACAACTCAA---TTATTGTATAG-
*
2635629 ATAATTACCTTTATCAGGCTAGCTGAATATT
61 ---A-CACCTTTATCAGGCTAGCTGAATATT
* *
2635660 ATCCATAAAGCCAGGGCGTTTAACCAATTTCTCTAGAGGGACAACTCAA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTACTCTAGAGGGACAACTCAA
2635709 GCTTTATTGT
Statistics
Matches: 125, Mismatches: 5, Indels: 16
0.86 0.03 0.11
Matches are distributed among these distances:
82 1 0.01
83 47 0.38
87 2 0.02
88 4 0.03
89 2 0.02
95 68 0.54
96 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (87 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTACTCTAGAGGGACAACTCAATTATTGTATAGACACC
TTTATCAGGCTAGCTGAATATT
Found at i:2635703 original size:95 final size:96
Alignment explanation
Indices: 2635540--2635729 Score: 321
Period size: 95 Copynumber: 2.0 Consensus size: 96
2635530 ATATGTAAGC
* * *
2635540 ACCTTTATCAGGTTAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTACCTTAGAGGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATTACCTTAGAGGG
2635605 ACAACTCAAGCTTTATTGTATA-GTATAATT
66 ACAACTCAAGCTTTATTGTATATGTATAATT
*
2635635 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATT-TCTCTAGAGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATTACCT-TAGAGG
2635699 GACAACTCAAGCTTTATTGTATATGTATAAT
65 GACAACTCAAGCTTTATTGTATATGTATAAT
2635730 ATTATAATCT
Statistics
Matches: 89, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
94 2 0.02
95 80 0.90
96 7 0.08
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (96 bp):
ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATTACCTTAGAGGG
ACAACTCAAGCTTTATTGTATATGTATAATT
Found at i:2638691 original size:20 final size:21
Alignment explanation
Indices: 2638647--2638685 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2638637 AAGTAAATAT
2638647 AAAATAAATAAATAAATGAGA
1 AAAATAAATAAATAAATGAGA
*
2638668 AAAATAATTAAA-AAATGA
1 AAAATAAATAAATAAATGA
2638686 ACAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.21
Consensus pattern (21 bp):
AAAATAAATAAATAAATGAGA
Found at i:2638691 original size:21 final size:21
Alignment explanation
Indices: 2638647--2638692 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2638637 AAGTAAATAT
*
2638647 AAAATAAATAAATAAATGAGA
1 AAAATAAATAAATAAATGACA
*
2638668 AAAATAATTAAA-AAATGAACA
1 AAAATAAATAAATAAATG-ACA
2638689 AAAA
1 AAAA
2638693 AAAAGTTAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.17
Consensus pattern (21 bp):
AAAATAAATAAATAAATGACA
Found at i:2640087 original size:38 final size:38
Alignment explanation
Indices: 2640038--2640187 Score: 171
Period size: 38 Copynumber: 3.9 Consensus size: 38
2640028 TTAAAAAATC
2640038 ATATAATTTTTAAAATGTTTT-AAAAATTATATATTAT
1 ATATAATTTTTAAAATGTTTTCAAAAATTATATATTAT
2640075 ATATAAGTTTTTAAAAATGTTTTCAAAAATTATATATTAT
1 ATATAA-TTTTT-AAAATGTTTTCAAAAATTATATATTAT
* * * *
2640115 ATA-AGTTTTAAAAAATATTTTCAAAAACTATATATTAT
1 ATATAATTTT-TAAAATGTTTTCAAAAATTATATATTAT
* ** *
2640153 ATA-CATTTCCAAAATGTTTTTAAAAATATATATAT
1 ATATAATTTTTAAAATGTTTTCAAAAAT-TATATAT
2640188 ATTATACGTA
Statistics
Matches: 97, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
37 20 0.21
38 47 0.48
39 11 0.11
40 19 0.20
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (38 bp):
ATATAATTTTTAAAATGTTTTCAAAAATTATATATTAT
Found at i:2640108 original size:40 final size:40
Alignment explanation
Indices: 2640038--2640155 Score: 174
Period size: 38 Copynumber: 3.1 Consensus size: 40
2640028 TTAAAAAATC
2640038 ATATAA-TTTTT-AAAATGTTTT-AAAAATTATATATTAT
1 ATATAAGTTTTTAAAAATGTTTTCAAAAATTATATATTAT
2640075 ATATAAGTTTTTAAAAATGTTTTCAAAAATTATATA-T-T
1 ATATAAGTTTTTAAAAATGTTTTCAAAAATTATATATTAT
* * *
2640113 ATATAAGTTTTAAAAAATATTTTCAAAAACTATATATTAT
1 ATATAAGTTTTTAAAAATGTTTTCAAAAATTATATATTAT
2640153 ATA
1 ATA
2640156 CATTTCCAAA
Statistics
Matches: 73, Mismatches: 3, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
37 6 0.08
38 39 0.53
39 12 0.16
40 16 0.22
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (40 bp):
ATATAAGTTTTTAAAAATGTTTTCAAAAATTATATATTAT
Found at i:2640206 original size:40 final size:40
Alignment explanation
Indices: 2640043--2640207 Score: 166
Period size: 38 Copynumber: 4.2 Consensus size: 40
2640033 AAATCATATA
*
2640043 ATTTTTAAAATGTTTT-AAAAATTATATATTATATATAAGT
1 ATTTTAAAAATGTTTTCAAAAATTATATA-TATATATAAGT
2640083 -TTTTAAAAATGTTTTCAAAAATTATATAT-TATATAAGT
1 ATTTTAAAAATGTTTTCAAAAATTATATATATATATAAGT
* * * *
2640121 -TTTAAAAAATATTTTCAAAAACTATATAT-TATAT-A-C
1 ATTTTAAAAATGTTTTCAAAAATTATATATATATATAAGT
** * *
2640157 ATTTCCAAAATGTTTTTAAAAA-TATATATATATTATACGT
1 ATTTTAAAAATGTTTTCAAAAATTATATATATA-TATAAGT
2640197 ATTTTCAAAAA
1 ATTTT-AAAAA
2640208 CCGTTTGCAA
Statistics
Matches: 105, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
36 7 0.07
37 20 0.19
38 43 0.41
39 15 0.14
40 16 0.15
41 4 0.04
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (40 bp):
ATTTTAAAAATGTTTTCAAAAATTATATATATATATAAGT
Found at i:2641070 original size:29 final size:29
Alignment explanation
Indices: 2641027--2641109 Score: 148
Period size: 29 Copynumber: 2.8 Consensus size: 29
2641017 CTCACCTAAC
2641027 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
*
2641057 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
2641086 TAAATGATGTAAGCAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
2641110 ATTTAGTTTG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 47 0.92
30 4 0.08
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:2645606 original size:22 final size:22
Alignment explanation
Indices: 2645574--2645625 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
2645564 AAAAAATATT
*
2645574 ACAAGATCACTTTCACTCAAAA
1 ACAAGAACACTTTCACTCAAAA
2645596 ACAAGAACACTTTCACTCAAAA
1 ACAAGAACACTTTCACTCAAAA
2645618 ACAAGAAC
1 ACAAGAAC
2645626 TACAACTCAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.50, C:0.27, G:0.06, T:0.17
Consensus pattern (22 bp):
ACAAGAACACTTTCACTCAAAA
Found at i:2645846 original size:29 final size:29
Alignment explanation
Indices: 2645803--2645885 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
2645793 CTCACCTAAC
*
2645803 TAAATTGATGTAAGCAATGGCATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
*
2645833 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
2645862 TAAATGATGTAAGCAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
2645886 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:2647618 original size:20 final size:20
Alignment explanation
Indices: 2647569--2647618 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
2647559 GAACTTCTTC
*
2647569 AAATCGCAACGCGAATCTAT
1 AAATCACAACGCGAATCTAT
* * *
2647589 AAATCGCAACGCGAATTTGT
1 AAATCACAACGCGAATCTAT
*
2647609 AATTCACAAC
1 AAATCACAAC
2647619 ACAGAAGTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.24, G:0.14, T:0.22
Consensus pattern (20 bp):
AAATCACAACGCGAATCTAT
Found at i:2647654 original size:20 final size:20
Alignment explanation
Indices: 2647609--2647657 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
2647599 GCGAATTTGT
*
2647609 AATTCACAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
*
2647629 AATTCGCAACACATAAGTCA
1 AATTCGCAACACAGAAGTCA
2647649 AATTCGCAA
1 AATTCGCAA
2647658 AGCGCGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.47, C:0.24, G:0.10, T:0.18
Consensus pattern (20 bp):
AATTCGCAACACAGAAGTCA
Found at i:2649419 original size:26 final size:27
Alignment explanation
Indices: 2649383--2649506 Score: 96
Period size: 29 Copynumber: 4.6 Consensus size: 27
2649373 AAAAGGGTGT
*
2649383 TATTTTTGTAATTTTTTTAAAA-ATGC
1 TATTTTTGTAATTTTTTGAAAAGATGC
*
2649409 TATTTTCGTAA-TTTTTGAAAA-ATGAC
1 TATTTTTGTAATTTTTTGAAAAGATG-C
* *
2649435 -ATTTTAGTAAATATTTTGAAAATGATGC
1 TATTTTTGT-AATTTTTTGAAAA-GATGC
* * *
2649463 TATATTGGTAATTAATTTT-AAAATGGTGC
1 TATTTTTGTAATT--TTTTGAAAA-GATGC
2649492 TATTTTTGTAATTTT
1 TATTTTTGTAATTTT
2649507 GTAAATAAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
25 19 0.24
26 13 0.16
27 11 0.14
28 4 0.05
29 29 0.36
30 4 0.05
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51
Consensus pattern (27 bp):
TATTTTTGTAATTTTTTGAAAAGATGC
Found at i:2650261 original size:24 final size:24
Alignment explanation
Indices: 2650234--2650322 Score: 97
Period size: 24 Copynumber: 3.7 Consensus size: 24
2650224 TAGTTATCTG
* *
2650234 ATATGATATTTGACCTGAATTTTT
1 ATATGATACTTGACATGAATTTTT
* * *
2650258 ATATGATACTTGACATGGATTCTG
1 ATATGATACTTGACATGAATTTTT
* * * *
2650282 ATTTGTTACCTGACTTGAATTTTT
1 ATATGATACTTGACATGAATTTTT
2650306 ATATGATACTTGACATG
1 ATATGATACTTGACATG
2650323 GATTATGATC
Statistics
Matches: 49, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.45
Consensus pattern (24 bp):
ATATGATACTTGACATGAATTTTT
Found at i:2650301 original size:48 final size:48
Alignment explanation
Indices: 2650244--2650347 Score: 181
Period size: 48 Copynumber: 2.2 Consensus size: 48
2650234 ATATGATATT
* *
2650244 TGACCTGAATTTTTATATGATACTTGACATGGATTCTGATTTGTTACC
1 TGACCTGAATTTTTATATGATACTTGACATGGATTATGATCTGTTACC
*
2650292 TGACTTGAATTTTTATATGATACTTGACATGGATTATGATCTGTTACC
1 TGACCTGAATTTTTATATGATACTTGACATGGATTATGATCTGTTACC
2650340 TGACCTGA
1 TGACCTGA
2650348 TTTATGTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.42
Consensus pattern (48 bp):
TGACCTGAATTTTTATATGATACTTGACATGGATTATGATCTGTTACC
Found at i:2650343 original size:24 final size:24
Alignment explanation
Indices: 2650258--2650343 Score: 73
Period size: 24 Copynumber: 3.6 Consensus size: 24
2650248 CTGAATTTTT
* * *
2650258 ATATGATACTTGACATGGATTCTG
1 ATATGTTACCTGACATGGATTATG
* * * * *
2650282 ATTTGTTACCTGACTTGAATTTTT
1 ATATGTTACCTGACATGGATTATG
* *
2650306 ATATGATACTTGACATGGATTATG
1 ATATGTTACCTGACATGGATTATG
*
2650330 ATCTGTTACCTGAC
1 ATATGTTACCTGAC
2650344 CTGATTTATG
Statistics
Matches: 45, Mismatches: 17, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (24 bp):
ATATGTTACCTGACATGGATTATG
Found at i:2650816 original size:17 final size:19
Alignment explanation
Indices: 2650791--2650829 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2650781 ATATCTGTAT
2650791 TATTAATATTT-TGTTCTA
1 TATTAATATTTATGTTCTA
2650809 TATT-ATATTTAATGTTCTA
1 TATTAATATTT-ATGTTCTA
2650828 TA
1 TA
2650830 AGTTGTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTAATATTTATGTTCTA
Found at i:2656747 original size:29 final size:30
Alignment explanation
Indices: 2656709--2656766 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
2656699 TTTAGTAAAT
*
2656709 ATTTTGAAAATGGTGCTATATTGGTAATTA
1 ATTTTGAAAATGGTGCTATATTCGTAATTA
*
2656739 ATTTT-AAAATGGTGCTATTTTCGTAATT
1 ATTTTGAAAATGGTGCTATATTCGTAATT
2656767 TTGTAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.47
Consensus pattern (30 bp):
ATTTTGAAAATGGTGCTATATTCGTAATTA
Found at i:2657507 original size:24 final size:24
Alignment explanation
Indices: 2657480--2657565 Score: 100
Period size: 24 Copynumber: 3.6 Consensus size: 24
2657470 TAGTTATATG
*
2657480 ATATGATATTTGACCTGAATTTTT
1 ATATGATACTTGACCTGAATTTTT
* * * *
2657504 ATATGATACTTGACATGGATTCTG
1 ATATGATACTTGACCTGAATTTTT
* * *
2657528 ATCTGTTACCTGACCTGAATTTTT
1 ATATGATACTTGACCTGAATTTTT
2657552 ATATGATACTTGAC
1 ATATGATACTTGAC
2657566 ATGGATTCTG
Statistics
Matches: 47, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (24 bp):
ATATGATACTTGACCTGAATTTTT
Found at i:2657558 original size:48 final size:48
Alignment explanation
Indices: 2657490--2657593 Score: 190
Period size: 48 Copynumber: 2.2 Consensus size: 48
2657480 ATATGATATT
2657490 TGACCTGAATTTTTATATGATACTTGACATGGATTCTGATCTGTTACC
1 TGACCTGAATTTTTATATGATACTTGACATGGATTCTGATCTGTTACC
* *
2657538 TGACCTGAATTTTTATATGATACTTGACATGGATTCTGATTTGTTATC
1 TGACCTGAATTTTTATATGATACTTGACATGGATTCTGATCTGTTACC
2657586 TGACCTGA
1 TGACCTGA
2657594 TTTATGTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.42
Consensus pattern (48 bp):
TGACCTGAATTTTTATATGATACTTGACATGGATTCTGATCTGTTACC
Found at i:2658102 original size:17 final size:19
Alignment explanation
Indices: 2658077--2658115 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2658067 ATATATGTAT
2658077 TATTAATATTT-TGTTCTA
1 TATTAATATTTATGTTCTA
2658095 TATT-ATATTTAATGTTCTA
1 TATTAATATTT-ATGTTCTA
2658114 TA
1 TA
2658116 AGTTGTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTAATATTTATGTTCTA
Found at i:2660462 original size:14 final size:14
Alignment explanation
Indices: 2660441--2660479 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
2660431 TTGCTTGTTT
2660441 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
2660455 AGTTGATTTGTAAA
1 AATTGATTTGTAAA
2660469 AATTGATTTGT
1 AATTGATTTGT
2660480 TTAATTGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:2660516 original size:78 final size:78
Alignment explanation
Indices: 2660427--2660621 Score: 309
Period size: 78 Copynumber: 2.5 Consensus size: 78
2660417 GGGGTACGCT
2660427 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTAAAAATTGATTTGTTTAATTGATAAG
1 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTAAAAATTGATTTGTTTAATTGATAAG
2660492 GAAATAAGAATTA
66 GAAATAAGAATTA
* * **
2660505 TTTTTTGCTTGTTTAGTTGATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGTG
1 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTAAAAATTGATTTGTTTAATTGATAAG
* ***
2660570 TAAATAATTCTTA
66 GAAATAAGAATTA
*
2660583 TTTTTTGTTTGTTTAATTGATTTGTAAAAGTTGATTTGT
1 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGT
2660622 TGTTTTAAAT
Statistics
Matches: 107, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
78 107 1.00
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (78 bp):
TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTAAAAATTGATTTGTTTAATTGATAAG
GAAATAAGAATTA
Found at i:2660538 original size:14 final size:14
Alignment explanation
Indices: 2660519--2660557 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
2660509 TTGCTTGTTT
2660519 AGTTGATTTGTAAA
1 AGTTGATTTGTAAA
2660533 AGTTGATTTGTAAA
1 AGTTGATTTGTAAA
2660547 AGTTGATTTGT
1 AGTTGATTTGT
2660558 TTAATTGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
AGTTGATTTGTAAA
Found at i:2660786 original size:20 final size:20
Alignment explanation
Indices: 2660763--2660848 Score: 118
Period size: 20 Copynumber: 4.3 Consensus size: 20
2660753 CGCGTTGCGA
*
2660763 TTTCGCGTTTCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
2660783 TTTCACGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
***
2660803 TTTCATATTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
2660823 TTTCGCGTTGCAAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
2660843 TTTCGC
1 TTTCGC
2660849 AACAATCGCA
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.43
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:2663407 original size:24 final size:24
Alignment explanation
Indices: 2663380--2663433 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
2663370 TTGAAACATC
*
2663380 ATCAAAATCCAATTATTGACCAAG
1 ATCAAAATCCAAGTATTGACCAAG
* **
2663404 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCAAGTATTGACCAAG
2663428 ATCAAA
1 ATCAAA
2663434 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCAAGTATTGACCAAG
Found at i:2663447 original size:24 final size:24
Alignment explanation
Indices: 2663396--2663447 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
2663386 ATCCAATTAT
** *
2663396 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
2663420 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
2663444 TGAC
1 TGAC
2663448 TAGTACTCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:2664212 original size:14 final size:15
Alignment explanation
Indices: 2664176--2664213 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2664166 GAAATCATTG
2664176 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
2664191 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
2664206 AAAAATTA
1 AAAAATTA
2664214 GAGATTGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:2664394 original size:20 final size:20
Alignment explanation
Indices: 2664369--2664478 Score: 84
Period size: 20 Copynumber: 5.5 Consensus size: 20
2664359 AACTAAAACC
2664369 TGTTGCGAAATTAAAATTCG
1 TGTTGCGAAATTAAAATTCG
2664389 TGTTGCG-AATTCGAAAATT-G
1 TGTTGCGAAATT--AAAATTCG
* **
2664409 AGTTGCGAAAACAAAATTCG
1 TGTTGCGAAATTAAAATTCG
*
2664429 CGTTGCG-AATTCAGAAA-TCG
1 TGTTGCGAAATT-A-AAATTCG
* * *
2664449 AGTTGCGAATTTGAAATTCAG
1 TGTTGCGAAATTAAAATTC-G
2664470 TGTTGCGAA
1 TGTTGCGAA
2664479 TTTGAAAAAT
Statistics
Matches: 71, Mismatches: 10, Indels: 17
0.72 0.10 0.17
Matches are distributed among these distances:
19 15 0.21
20 33 0.46
21 23 0.32
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.30
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCG
Found at i:2664415 original size:40 final size:40
Alignment explanation
Indices: 2664370--2664486 Score: 146
Period size: 40 Copynumber: 2.9 Consensus size: 40
2664360 ACTAAAACCT
*
2664370 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATTGA
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
** *
2664410 GTTGCGAAAACAAAATTCGCGTTGCGAATTC-AGAAATCGA
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGA-AAATCGA
* * *
2664450 GTTGCGAATTTGAAATTCAGTGTTGCGAATTTGAAAA
1 GTTGCGAAATTAAAATTC-GTGTTGCGAATTCGAAAA
2664487 ATCGCAATGC
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
39 1 0.02
40 48 0.75
41 14 0.22
42 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (40 bp):
GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
Found at i:2664682 original size:41 final size:41
Alignment explanation
Indices: 2664637--2664821 Score: 255
Period size: 41 Copynumber: 4.5 Consensus size: 41
2664627 AAAAACTCTT
2664637 TAGCGGCGTTTGTATAAAAACGCCACTAAA-TCACGAGTCTA
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGT-ACGAGTCTA
*** * *
2664678 TAGCGATATTTGAATAAAAACGTCACTAAAGTACGAGTCTA
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTA
* * * *
2664719 TAGCAGTGTTTGTATAAAAACGCCACTAAAGTACGAGTATT
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTA
*
2664760 TAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTA
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTA
*
2664801 TAGCTGCGTTTGTATAAAAAC
1 TAGCGGCGTTTGTATAAAAAC
2664822 TACGAGTTTA
Statistics
Matches: 124, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
41 123 0.99
42 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (41 bp):
TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTA
Found at i:2664826 original size:31 final size:31
Alignment explanation
Indices: 2664791--2664851 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
2664781 GCCACTAAAG
*
2664791 TACGAGTCTATAGCTGCGTTTGTATAAAAAC
1 TACGAGTCTATAGCGGCGTTTGTATAAAAAC
*
2664822 TACGAGTTTATAGCGGCGTTTGTATAAAAA
1 TACGAGTCTATAGCGGCGTTTGTATAAAAA
2664852 TGCCACTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (31 bp):
TACGAGTCTATAGCGGCGTTTGTATAAAAAC
Found at i:2671760 original size:23 final size:23
Alignment explanation
Indices: 2671734--2671781 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
2671724 ATCAAGTACA
* *
2671734 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAACGCTTAT
2671757 ATAATATAATAGGTAACGCTTAT
1 ATAATATAATAGGTAACGCTTAT
2671780 AT
1 AT
2671782 TGACATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTAACGCTTAT
Found at i:2672702 original size:182 final size:181
Alignment explanation
Indices: 2672377--2673016 Score: 969
Period size: 182 Copynumber: 3.5 Consensus size: 181
2672367 CATTTTTTTA
* * *
2672377 TTACCGATTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACTTGTTATATTGTTATAGATCG
1 TTACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATAGATCG
* * * *
2672442 GTACATTTTTTATAAAGTATCGACACTTTATCGGTGCTATAACTTATTCTCTTTTAAATTCCAAA
66 ATACA-TTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTATTCTCTTTTAAATTCTAAA
* **
2672507 AGTGTCGATACTTATAATAAAGTATCAACACTTTCAACATATCTAGTAGTTCT
130 AGTGTCGATACTTATAATAAAGTATCGACACTTTCAACATATC-AGTAGCGCT
**
2672560 TTACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTAGGGATCG
1 TTACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATAGATCG
* * * *
2672625 ATACATTTTTATAAAGTATGGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTTTAAAA
66 ATACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTATTCTCTTTTAAATTCTAAAA
* *
2672690 GTGTCAATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCT
131 GTGTCGATACTTATAATAAAGTATCGACACTTTCAACATAT-CAGTAGCGCT
* * * *
2672742 TTACCGGTTTTGTCATTTCGAGACCAGTTTTGTCATATTTTTACCTATTATATTATTATGGATCG
1 TTACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATAGATCG
*
2672807 ATACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTATTCTCTTTTAAATTCTAAAA
66 ATACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTATTCTCTTTTAAATTCTAAAA
*
2672872 GTGTCGATACTTATAATAAAGTATCGACACTATCAACATATCAGGTAGCGCT
131 GTGTCGATACTTATAATAAAGTATCGACACTTTCAACATATCA-GTAGCGCT
* **
2672924 TTACCTGCTTTT-TCATTTATAGACCGGTTTTGTCAT-TTGTTTACCTGTTATATTGTTATAGAT
1 TTACC-GGTTTTGTCATTTCGAGACCGGTTTTGTCATATT-TTTACCTGTTATATTGTTATAGAT
2672987 CGATACATTTTTATAAAGTATCGACACTTT
64 CGATACATTTTTATAAAGTATCGACACTTT
2673017 CAATATATCT
Statistics
Matches: 416, Mismatches: 37, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
181 3 0.01
182 343 0.82
183 70 0.17
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (181 bp):
TTACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATAGATCG
ATACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTATTCTCTTTTAAATTCTAAAA
GTGTCGATACTTATAATAAAGTATCGACACTTTCAACATATCAGTAGCGCT
Found at i:2673084 original size:112 final size:112
Alignment explanation
Indices: 2672887--2673348 Score: 703
Period size: 112 Copynumber: 4.1 Consensus size: 112
2672877 GATACTTATA
* * *
2672887 ATAAAGTATCGACACTATCAACATATCAGGTAGCGCTTTACCTGCTTTT-TCATTTATAGACCGG
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTG-TTTTGTCATTTATAGACCGG
* * * *
2672951 TTTTGTCATTTGTTTACCTGTTATATTGTTATAGATCGATACATTTTT
65 TTTTGTCATTTTTTTACCTGTTATATTATTATGGATCAATACATTTTT
* *
2672999 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
2673064 TTTGTTATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTATTATGGATCAATACATTTTT
* *
2673111 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTATTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
2673176 TTTGTCATTTTTTTACCTGTTATATTATTATGGATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTATTATGGATCAATACATTTTT
* * *
2673223 ATAAAGTATTGACACTTTCAATATATCCGGTAGCTCTTTACCTGTTTTGTCATTTATAGGCCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* ** *
2673288 TTTGTTA-TTTTTTACCAATTATATTATTATGGATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTATTATGGATCAATACATTTTT
2673334 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
2673349 AAACCGACAA
Statistics
Matches: 325, Mismatches: 24, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
111 55 0.17
112 270 0.83
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.45
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTATTATGGATCAATACATTTTT
Found at i:2693582 original size:58 final size:59
Alignment explanation
Indices: 2693397--2693613 Score: 219
Period size: 59 Copynumber: 3.7 Consensus size: 59
2693387 GTGCTTTATC
*** * * * * * *
2693397 TGGAAATCCATACACTCAGTATGATTCCCTTACCATTTTAGAACATAAAATGCCATATC-
1 TGGAAATCCATATTTTCAATATGATTTCCTTATCATTTTAGCACATAATATGCCCTA-CA
* * *
2693456 TGGAAATCCATATTTTCAATATGATTCCCTTACCATTTTAGCACATAATATGCCCTATA
1 TGGAAATCCATATTTTCAATATGATTTCCTTATCATTTTAGCACATAATATGCCCTACA
* * * *
2693515 TGGAAATCCATATTTTCAATATGATTTCCTTATC-GTTTAGCACACTCA-GTGCTCTACA
1 TGGAAATCCATATTTTCAATATGATTTCCTTATCATTTTAGCACA-TAATATGCCCTACA
* *
2693573 TGGAAATCCATA--CTCAGTATGATTTCCTTATCATTTTAGCA
1 TGGAAATCCATATTTTCAATATGATTTCCTTATCATTTTAGCA
2693614 TACAAAGTGC
Statistics
Matches: 137, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
56 18 0.13
57 7 0.05
58 28 0.20
59 84 0.61
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (59 bp):
TGGAAATCCATATTTTCAATATGATTTCCTTATCATTTTAGCACATAATATGCCCTACA
Found at i:2700548 original size:59 final size:60
Alignment explanation
Indices: 2700417--2700725 Score: 219
Period size: 59 Copynumber: 5.2 Consensus size: 60
2700407 TATGGTTTTG
* * * * *
2700417 TTACCATTTTAGCACC-TGATA-TGCCCTATGTGAAAATCCATAC-CATTAGTATGATTTCC
1 TTACCATTTTAGCACCAT-ATAGTGCTCTATATGGAAATCCATACAC-TCAATATGATTTCC
* * * * * *
2700476 TTATC-TTTATAGCACCCT-TAGTGCTTTATCTGGAAATCCATACACTCAGTATGATTCCC
1 TTACCATTT-TAGCACCATATAGTGCTCTATATGGAAATCCATACACTCAATATGATTTCC
* * *** * *
2700535 TTACCATTTTAGCA-CATAAAATG-TCATATATGGAAATCCATATTTTCAATATGACTCCC
1 TTACCATTTTAGCACCATATAGTGCTC-TATATGGAAATCCATACACTCAATATGATTTCC
* * ***
2700594 TTACCATTTTAGCA-CATAATA-TGCCCTATTTGGAAATCCATATTTTCAATATGATTTCC
1 TTACCATTTTAGCACCAT-ATAGTGCTCTATATGGAAATCCATACACTCAATATGATTTCC
* * * *
2700653 TTA-TAATTTAGCA-CACT-CAGTGCTCTATATGGAAATCCATACACTCAATATGGTTTCC
1 TTACCATTTTAGCACCA-TATAGTGCTCTATATGGAAATCCATACACTCAATATGATTTCC
* *
2700711 TTATCAATTTAGCAC
1 TTACCATTTTAGCAC
2700726 ACAAAGTGCC
Statistics
Matches: 204, Mismatches: 33, Indels: 25
0.78 0.13 0.10
Matches are distributed among these distances:
57 1 0.00
58 53 0.26
59 142 0.70
60 8 0.04
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.37
Consensus pattern (60 bp):
TTACCATTTTAGCACCATATAGTGCTCTATATGGAAATCCATACACTCAATATGATTTCC
Found at i:2703122 original size:20 final size:19
Alignment explanation
Indices: 2703070--2703122 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
2703060 GAGTTCTCCG
* *
2703070 AAATGTTCTAGAAAATTCT
1 AAATTTTCTAGAAAACTCT
* *
2703089 ACATTTCTCCAGAAAACTCT
1 AAATTT-TCTAGAAAACTCT
2703109 AGAATTTTCTAGAA
1 A-AATTTTCTAGAA
2703123 TCTCTCCAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
19 4 0.15
20 18 0.69
21 4 0.15
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (19 bp):
AAATTTTCTAGAAAACTCT
Found at i:2703726 original size:5 final size:5
Alignment explanation
Indices: 2703716--2703925 Score: 351
Period size: 5 Copynumber: 42.6 Consensus size: 5
2703706 ATACCAACTA
2703716 ATTAT ATTAT A-T-T ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
2703764 ATTAT ATTAT ATATAT ATTAT ATTAT A-TAT ATTAT ATTAT ATTATAT
1 ATTAT ATTAT AT-TAT ATTAT ATTAT ATTAT ATTAT ATTAT A-T-TAT
2703811 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A-T-T ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
2703859 ATTAT A-TAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
2703908 ATTAT ATTAT ATTAT ATT
1 ATTAT ATTAT ATTAT ATT
2703926 TCTAACACAC
Statistics
Matches: 196, Mismatches: 0, Indels: 18
0.92 0.00 0.08
Matches are distributed among these distances:
3 4 0.02
4 12 0.06
5 169 0.86
6 7 0.04
7 4 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:2714901 original size:15 final size:14
Alignment explanation
Indices: 2714883--2714918 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
2714873 TAATTTGAGT
2714883 AATTTAAATTTATAC
1 AATTTAAATTT-TAC
2714898 AATTTAAATTTTAC
1 AATTTAAATTTTAC
2714912 ACATTTA
1 A-ATTTA
2714919 TTTTAATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
AATTTAAATTTTAC
Found at i:2716077 original size:16 final size:16
Alignment explanation
Indices: 2716053--2716090 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
2716043 CCGGTCGTCA
*
2716053 ATGGCACCTTTCTCAC
1 ATGGTACCTTTCTCAC
2716069 ATGGTACCTTTCTCAC
1 ATGGTACCTTTCTCAC
2716085 ATGGTA
1 ATGGTA
2716091 TCATTCGCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (16 bp):
ATGGTACCTTTCTCAC
Found at i:2718057 original size:16 final size:16
Alignment explanation
Indices: 2718033--2718065 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2718023 CCGGTCGTCA
2718033 ATGGCACCTTTCTCAC
1 ATGGCACCTTTCTCAC
*
2718049 ATGGTACCTTTCTCAC
1 ATGGCACCTTTCTCAC
2718065 A
1 A
2718066 CTTTGTTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.33, G:0.12, T:0.33
Consensus pattern (16 bp):
ATGGCACCTTTCTCAC
Found at i:2719213 original size:2 final size:2
Alignment explanation
Indices: 2719206--2719246 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2719196 ATGTCGAGCA
2719206 AT AT AT AT 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 AT AT AT AT A
2719247 ATCGAGTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2730577 original size:20 final size:20
Alignment explanation
Indices: 2730552--2730595 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
2730542 AATCAATAGT
2730552 CTTCTTATCTTTTTGGATTG
1 CTTCTTATCTTTTTGGATTG
2730572 CTTCTTATCTTTTTGGATTG
1 CTTCTTATCTTTTTGGATTG
2730592 CTTC
1 CTTC
2730596 ATCTGATGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.09, C:0.18, G:0.14, T:0.59
Consensus pattern (20 bp):
CTTCTTATCTTTTTGGATTG
Found at i:2734466 original size:165 final size:167
Alignment explanation
Indices: 2734188--2734515 Score: 500
Period size: 166 Copynumber: 2.0 Consensus size: 167
2734178 TGCCTTCTAG
* *
2734188 TGTTATCAGGAGAATGGATCAACTTTGTGAATTTTTTTTGGAAAGGTGGTGATGTTCTTACTAAT
1 TGTTATCAAGAGAATAGATCAACTTTGTGAATTTTTTTTGGAAAGGTGGTGATGTTCTTACTAAT
* * * * * *
2734253 TAGGCGAAGGTTAAATGGGAGTGTATTTGTTGCTCCCAAATTTGA-GGGGTCTAGGGATGAAGAA
66 GAAGCCAAGGTTAAATGGGAGTGTATCTGTTGCTCCAAAATCTGAGGGGGTCTAGGGATGAAGAA
*
2734317 TCTGAAAAGCTGGAACAAAACTTGTGTGCTCTTCTGC
131 TCTGAAAAGATGGAACAAAACTTGTGTGCTCTTCTGC
* *
2734354 TGTTATCAAGAGAATAGATCAACTTTGTGTA-TTTTTTTGGAAAGGTGGTGATGTGT-TTGCTAA
1 TGTTATCAAGAGAATAGATCAACTTTGTGAATTTTTTTTGGAAAGGTGGTGATGT-TCTTACTAA
* * *
2734417 TGAAGCCAAGGTTAAGTGGGAGTGTATCTGTTGCTCCAAAATCTGAGGGGGTCTGGGGGTGAAGA
65 TGAAGCCAAGGTTAAATGGGAGTGTATCTGTTGCTCCAAAATCTGAGGGGGTCTAGGGATGAAGA
2734482 ATCTGAAAAGATGGAACAAAACTTGTGTGCTCTT
130 ATCTGAAAAGATGGAACAAAACTTGTGTGCTCTT
2734516 GTTGATGAAG
Statistics
Matches: 146, Mismatches: 14, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
165 68 0.47
166 78 0.53
ACGTcount: A:0.27, C:0.11, G:0.29, T:0.33
Consensus pattern (167 bp):
TGTTATCAAGAGAATAGATCAACTTTGTGAATTTTTTTTGGAAAGGTGGTGATGTTCTTACTAAT
GAAGCCAAGGTTAAATGGGAGTGTATCTGTTGCTCCAAAATCTGAGGGGGTCTAGGGATGAAGAA
TCTGAAAAGATGGAACAAAACTTGTGTGCTCTTCTGC
Found at i:2741390 original size:45 final size:45
Alignment explanation
Indices: 2741326--2741424 Score: 189
Period size: 45 Copynumber: 2.2 Consensus size: 45
2741316 AGTTGACCAC
2741326 TACTATTCAAAAGAAGGGGTTGACAAAGTTGCTGGGATTAGATTA
1 TACTATTCAAAAGAAGGGGTTGACAAAGTTGCTGGGATTAGATTA
*
2741371 TACTATTCAAAAGAAGGGGTTGACAAAGTTGTTGGGATTAGATTA
1 TACTATTCAAAAGAAGGGGTTGACAAAGTTGCTGGGATTAGATTA
2741416 TACTATTCA
1 TACTATTCA
2741425 GTATAGAAAG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.31
Consensus pattern (45 bp):
TACTATTCAAAAGAAGGGGTTGACAAAGTTGCTGGGATTAGATTA
Found at i:2743419 original size:18 final size:19
Alignment explanation
Indices: 2743398--2743433 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2743388 ATTCTCTCAA
2743398 CTTTCTTCTCTC-GAATCT
1 CTTTCTTCTCTCTGAATCT
*
2743416 CTTTCTTTTCTCTGAATC
1 CTTTCTTCTCTCTGAATC
2743434 CATAACACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.11, C:0.31, G:0.06, T:0.53
Consensus pattern (19 bp):
CTTTCTTCTCTCTGAATCT
Found at i:2744313 original size:34 final size:35
Alignment explanation
Indices: 2744274--2744344 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 35
2744264 TTATATATAA
* *
2744274 AAAAAGAATAGATGGCTGCATACACATATAA-TTT
1 AAAAAGAAAAGATGACTGCATACACATATAAGTTT
* *
2744308 AAAAAGAAAAGATGACTGGATATACATATAAGTTT
1 AAAAAGAAAAGATGACTGCATACACATATAAGTTT
2744343 AA
1 AA
2744345 CTATGGAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 27 0.84
35 5 0.16
ACGTcount: A:0.51, C:0.08, G:0.15, T:0.25
Consensus pattern (35 bp):
AAAAAGAAAAGATGACTGCATACACATATAAGTTT
Found at i:2744964 original size:41 final size:41
Alignment explanation
Indices: 2744916--2744993 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
2744906 AACAACGTAC
* *
2744916 GAGTCTTTAGCGGTGTTTATATAAAGACGCCACTAAAATAT
1 GAGTCTTTAGCGGCGTTTATATAAAAACGCCACTAAAATAT
* *
2744957 GAGTCTTTAGCTGCGTTTATATAAAAACGCTACTAAA
1 GAGTCTTTAGCGGCGTTTATATAAAAACGCCACTAAA
2744994 GTACGAGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (41 bp):
GAGTCTTTAGCGGCGTTTATATAAAAACGCCACTAAAATAT
Found at i:2747154 original size:20 final size:20
Alignment explanation
Indices: 2747129--2747200 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 20
2747119 TTGTTACTCT
2747129 AATATTGACAATTCTAATAC
1 AATATTGACAATTCTAATAC
2747149 AATATTGAAACCAATAT-TGAA-ATC
1 AATATTG--A-CAAT-TCT-AATA-C
2747173 AATATTGACAATTCTAATAC
1 AATATTGACAATTCTAATAC
*
2747193 AAGATTGA
1 AATATTGA
2747201 TTTCATTGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 16
0.72 0.02 0.27
Matches are distributed among these distances:
20 18 0.42
21 6 0.14
22 2 0.05
23 6 0.14
24 11 0.26
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.32
Consensus pattern (20 bp):
AATATTGACAATTCTAATAC
Found at i:2747165 original size:12 final size:12
Alignment explanation
Indices: 2747148--2747180 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
2747138 AATTCTAATA
2747148 CAATATTGAAAC
1 CAATATTGAAAC
*
2747160 CAATATTGAAAT
1 CAATATTGAAAC
2747172 CAATATTGA
1 CAATATTGA
2747181 CAATTCTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.30
Consensus pattern (12 bp):
CAATATTGAAAC
Found at i:2748516 original size:31 final size:31
Alignment explanation
Indices: 2748454--2748529 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
2748444 TAAATCGTAA
* * **
2748454 TGACCACATCTTAATTAAATAAAAATTAAAG
1 TGACCATATATTAATTAAATAAAAACGAAAG
* * *
2748485 TGATCATATTTTAATTAAATAAAGACGAAAG
1 TGACCATATATTAATTAAATAAAAACGAAAG
2748516 TGACCATATATTAA
1 TGACCATATATTAA
2748530 GTTTTTAGAA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.32
Consensus pattern (31 bp):
TGACCATATATTAATTAAATAAAAACGAAAG
Found at i:2758445 original size:24 final size:25
Alignment explanation
Indices: 2758395--2758464 Score: 62
Period size: 24 Copynumber: 2.9 Consensus size: 25
2758385 AAATAAATAT
2758395 AATAGATAT-ATATAACAT-AT-ATGA
1 AATA-ATATAATATAA-ATAATAATGA
2758419 AATAATATAATATAAATAATAAT-A
1 AATAATATAATATAAATAATAATGA
*
2758443 AATACTATAA-AT-AATATATAAT
1 AATAATATAATATAAATA-ATAAT
2758465 ACATATATTA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 4 0.10
23 13 0.32
24 22 0.54
25 2 0.05
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (25 bp):
AATAATATAATATAAATAATAATGA
Found at i:2758453 original size:19 final size:20
Alignment explanation
Indices: 2758378--2758465 Score: 78
Period size: 19 Copynumber: 4.3 Consensus size: 20
2758368 TGGACCTAAA
2758378 AATAA-ATAA-ATAAAT-AT
1 AATAATATAATATAAATAAT
2758395 AATAGATAT-ATATAACATATAT
1 AATA-ATATAATATAA-ATA-AT
2758417 GAAATAATATAATATAAATAAT
1 --AATAATATAATATAAATAAT
*
2758439 AATAA-ATACTATAAATAAT
1 AATAATATAATATAAATAAT
2758458 ATATAATA
1 A-ATAATA
2758466 CATATATTAT
Statistics
Matches: 59, Mismatches: 1, Indels: 18
0.76 0.01 0.23
Matches are distributed among these distances:
17 4 0.07
18 2 0.03
19 20 0.34
20 11 0.19
21 1 0.02
22 4 0.07
23 7 0.12
24 10 0.17
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
AATAATATAATATAAATAAT
Found at i:2758460 original size:9 final size:9
Alignment explanation
Indices: 2758377--2758471 Score: 70
Period size: 9 Copynumber: 10.1 Consensus size: 9
2758367 TTGGACCTAA
2758377 AAATAA-AT
1 AAATAATAT
2758385 AAATAA-AT
1 AAATAATAT
2758393 ATAATAGATAT
1 A-AATA-ATAT
* *
2758404 ATATAACAT
1 AAATAATAT
*
2758413 ATATGAA-AT
1 AAAT-AATAT
2758422 AATATAATAT
1 AA-ATAATAT
2758432 AAATAATAAT
1 AAATAAT-AT
*
2758442 AAATACTAT
1 AAATAATAT
2758451 AAATAATAT
1 AAATAATAT
2758460 ATAATACATAT
1 A-AATA-ATAT
2758471 A
1 A
2758472 TTATATATTT
Statistics
Matches: 73, Mismatches: 5, Indels: 15
0.78 0.05 0.16
Matches are distributed among these distances:
8 9 0.12
9 32 0.44
10 24 0.33
11 8 0.11
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (9 bp):
AAATAATAT
Found at i:2758628 original size:17 final size:17
Alignment explanation
Indices: 2758586--2758638 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
2758576 AGCCATATAT
*
2758586 ATTATATGTTTTCAAAA
1 ATTATATATTTTCAAAA
*
2758603 CTATATATATTTTCAAAA
1 AT-TATATATTTTCAAAA
2758621 ATTATATATTTTCAAAA
1 ATTATATATTTTCAAAA
2758638 A
1 A
2758639 CCATATATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
17 17 0.53
18 15 0.47
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (17 bp):
ATTATATATTTTCAAAA
Found at i:2758628 original size:44 final size:41
Alignment explanation
Indices: 2758501--2758629 Score: 120
Period size: 42 Copynumber: 3.1 Consensus size: 41
2758491 ACTATATAAC
* * *
2758501 ATATATTAT-AT-TTTCAAAAACTATGTTTTCAAAAAATAT
1 ATATATTATAATGTTTTAAAAAATATATTTTCAAAAAATAT
* ***
2758540 ATATATTATACATGTTTTAAAAAATCTATTTTCAAAAGCCAT
1 ATATATTATA-ATGTTTTAAAAAATATATTTTCAAAAAATAT
*
2758582 ATATATTAT-ATGTTTTCAAAACTATATATATTTTCAAAAATTAT
1 ATATATTATAATGTTTT-AAAA--A-ATATATTTTCAAAAAATAT
2758626 ATAT
1 ATAT
2758630 TTTCAAAAAC
Statistics
Matches: 72, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
39 9 0.12
40 7 0.10
41 6 0.08
42 30 0.42
43 1 0.01
44 19 0.26
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (41 bp):
ATATATTATAATGTTTTAAAAAATATATTTTCAAAAAATAT
Found at i:2758645 original size:19 final size:18
Alignment explanation
Indices: 2758588--2758646 Score: 68
Period size: 17 Copynumber: 3.3 Consensus size: 18
2758578 CCATATATAT
*
2758588 TATATGTTTTC-AAAACTA
1 TATATATTTTCAAAAAC-A
*
2758606 TATATATTTTCAAAAA-T
1 TATATATTTTCAAAAACA
2758623 TATATATTTTCAAAAACCA
1 TATATATTTTCAAAAA-CA
2758642 TATAT
1 TATAT
2758647 TATATACATC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
17 16 0.46
18 10 0.29
19 9 0.26
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (18 bp):
TATATATTTTCAAAAACA
Found at i:2766002 original size:24 final size:24
Alignment explanation
Indices: 2765974--2766023 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
2765964 TATGGGGCTT
2765974 CAGAGGTTCCACTAGATATGGTGA
1 CAGAGGTTCCACTAGATATGGTGA
*
2765998 CAGAGGTTCCACTGGATATGGTGA
1 CAGAGGTTCCACTAGATATGGTGA
2766022 CA
1 CA
2766024 CCATATGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (24 bp):
CAGAGGTTCCACTAGATATGGTGA
Found at i:2769890 original size:38 final size:39
Alignment explanation
Indices: 2769848--2769926 Score: 97
Period size: 39 Copynumber: 2.1 Consensus size: 39
2769838 ACTTAAAGTT
* *
2769848 AAATTTTGAA-TATCTATACTAAAATGAAACAAAAACTA
1 AAATTTTGAACGATCGATACTAAAATGAAACAAAAACTA
* * * *
2769886 AAATTTTTAACGATGGGTACTAAAATGAAACAAAAATTA
1 AAATTTTGAACGATCGATACTAAAATGAAACAAAAACTA
2769925 AA
1 AA
2769927 CTTTAGGCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
38 9 0.26
39 25 0.74
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.28
Consensus pattern (39 bp):
AAATTTTGAACGATCGATACTAAAATGAAACAAAAACTA
Found at i:2775705 original size:18 final size:18
Alignment explanation
Indices: 2775682--2775716 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2775672 TTCCATCCGG
*
2775682 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
2775700 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
2775717 GTCCTTTCGA
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:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:2777040 original size:13 final size:13
Alignment explanation
Indices: 2777020--2777064 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
2777010 AACGGTCAAT
2777020 GGGTCAACGGGTC
1 GGGTCAACGGGTC
* *
2777033 GAGTCAACAGGTC
1 GGGTCAACGGGTC
*
2777046 GGGTAAACGGGTC
1 GGGTCAACGGGTC
2777059 GGGTCA
1 GGGTCA
2777065 GGTAAACGGG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.42, T:0.16
Consensus pattern (13 bp):
GGGTCAACGGGTC
Found at i:2777063 original size:18 final size:18
Alignment explanation
Indices: 2777042--2777085 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
2777032 CGAGTCAACA
2777042 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
*
2777060 GGTCAGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
2777078 GGTCGGGT
1 GGTCGGGT
2777086 TGTGACCGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.16, G:0.50, T:0.18
Consensus pattern (18 bp):
GGTCGGGTAAACGGGTCG
Found at i:2780875 original size:18 final size:18
Alignment explanation
Indices: 2780852--2780886 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2780842 TTCCATCCGG
*
2780852 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
2780870 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
2780887 GTCCTTTCGA
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:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:2782214 original size:13 final size:13
Alignment explanation
Indices: 2782177--2782227 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
2782167 GTCAACGACG
2782177 GTCAACGGGTCGA
1 GTCAACGGGTCGA
* *
2782190 GTCAGCGAGTCGA
1 GTCAACGGGTCGA
*
2782203 GTCAACGGGTCGG
1 GTCAACGGGTCGA
*
2782216 GTAAACGGGTCG
1 GTCAACGGGTCG
2782228 GGTCGGGTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.22, C:0.22, G:0.41, T:0.16
Consensus pattern (13 bp):
GTCAACGGGTCGA
Found at i:2782231 original size:18 final size:18
Alignment explanation
Indices: 2782208--2782253 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
2782198 GTCGAGTCAA
2782208 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
2782226 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
*
2782244 CGAGTCGGGT
1 CGGGTCGGGT
2782254 TGTGACCAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.15, C:0.17, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:2782245 original size:13 final size:13
Alignment explanation
Indices: 2782206--2782230 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2782196 GAGTCGAGTC
2782206 AACGGGTCGGGTA
1 AACGGGTCGGGTA
2782219 AACGGGTCGGGT
1 AACGGGTCGGGT
2782231 CGGGTAAACG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.48, T:0.16
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:2783379 original size:103 final size:103
Alignment explanation
Indices: 2783200--2783404 Score: 392
Period size: 103 Copynumber: 2.0 Consensus size: 103
2783190 ATTTATTTAA
2783200 ATGTTCGATCATCGAAAAAGCGAACCAAAGAGACCACAAGTCTAATGCAAAGATTCACAGAAGCA
1 ATGTTCGATCATCGAAAAAGCGAACCAAAGAGACCACAAGTCTAATGCAAAGATTCACAGAAGCA
2783265 AAGCTAGAAATTCATCCGAAGGTGATCACACCACTGAT
66 AAGCTAGAAATTCATCCGAAGGTGATCACACCACTGAT
* *
2783303 ATGTTCGATCATCGAAAAAGCGAACCAAAGAGACCACAAGTCTAATGCAAAGATTCAGAGCAGCA
1 ATGTTCGATCATCGAAAAAGCGAACCAAAGAGACCACAAGTCTAATGCAAAGATTCACAGAAGCA
2783368 AAGCTAGAAATTCATCCGAAGGTGATCACACCACTGA
66 AAGCTAGAAATTCATCCGAAGGTGATCACACCACTGA
2783405 GGTCGTTCGA
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 100 1.00
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.17
Consensus pattern (103 bp):
ATGTTCGATCATCGAAAAAGCGAACCAAAGAGACCACAAGTCTAATGCAAAGATTCACAGAAGCA
AAGCTAGAAATTCATCCGAAGGTGATCACACCACTGAT
Found at i:2785475 original size:7 final size:7
Alignment explanation
Indices: 2785465--2785506 Score: 84
Period size: 7 Copynumber: 6.0 Consensus size: 7
2785455 ATTTTTAATT
2785465 TTTTTCC
1 TTTTTCC
2785472 TTTTTCC
1 TTTTTCC
2785479 TTTTTCC
1 TTTTTCC
2785486 TTTTTCC
1 TTTTTCC
2785493 TTTTTCC
1 TTTTTCC
2785500 TTTTTCC
1 TTTTTCC
2785507 CTTCACATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTTCC
Found at i:2788561 original size:2 final size:2
Alignment explanation
Indices: 2788554--2788822 Score: 190
Period size: 2 Copynumber: 141.5 Consensus size: 2
2788544 AGAAGAGGGA
*
2788554 AG AG AG AG AG AG ATG -G A- AG AG AG AG AG AG AG GG A- AG AG AG
1 AG AG AG AG AG AG A-G AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * *
2788594 AG AG AG AG GG A- AG AG AG AG AG AG AG GG AG AG AG AG AG GG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * * * *
2788635 GG A- AG AG AG GG AG AG AG GG A- AG AG AG TG AG AG AG GG A- AA
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * *
2788674 AG AG AG AG AG AG GG A- AA AG AG AG AG AG AG GG A- AA AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * * *
2788714 AG AG AG GG A- AA AG AG AG AG AT AG GG A- AA AG AG AG AG AG -G
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * * *
2788753 GG AA AG AG AG AG AG AG GG A- AG AG AG AG AG AG AG GG A- AG AA
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* *
2788793 AG AG AG AG AG GG A- AA AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2788823 AAAATGAAGA
Statistics
Matches: 206, Mismatches: 45, Indels: 32
0.73 0.16 0.11
Matches are distributed among these distances:
1 15 0.07
2 190 0.92
3 1 0.00
ACGTcount: A:0.49, C:0.00, G:0.50, T:0.01
Consensus pattern (2 bp):
AG
Found at i:2788573 original size:17 final size:17
Alignment explanation
Indices: 2788547--2788819 Score: 417
Period size: 17 Copynumber: 16.2 Consensus size: 17
2788537 AAGGGGAAGA
2788547 AGAGGGAAGAGAGAGAG
1 AGAGGGAAGAGAGAGAG
*
2788564 AGATGGAAGAGAGAGAG
1 AGAGGGAAGAGAGAGAG
2788581 AGAGGGAAGAGAGAGAG
1 AGAGGGAAGAGAGAGAG
2788598 AGAGGGAAGAGAGAGAG
1 AGAGGGAAGAGAGAGAG
2788615 AGAGGG-AGAGAGAGAG
1 AGAGGGAAGAGAGAGAG
* *
2788631 GGAGGGAAGAGAGGGAG
1 AGAGGGAAGAGAGAGAG
*
2788648 AGAGGGAAGAGAGTGAG
1 AGAGGGAAGAGAGAGAG
*
2788665 AGAGGGAAAAGAGAGAG
1 AGAGGGAAGAGAGAGAG
*
2788682 AGAGGGAAAAGAGAGAG
1 AGAGGGAAGAGAGAGAG
*
2788699 AGAGGGAAAAGAGAGAG
1 AGAGGGAAGAGAGAGAG
*
2788716 AGAGGGAAAAGAGAGAG
1 AGAGGGAAGAGAGAGAG
* *
2788733 ATAGGGAAAAGAGAGAG
1 AGAGGGAAGAGAGAGAG
2788750 AG-GGGAA-AGAGAGAG
1 AGAGGGAAGAGAGAGAG
2788765 AGAGGGAAGAGAGAGAG
1 AGAGGGAAGAGAGAGAG
*
2788782 AGAGGGAAGAAAGAGAG
1 AGAGGGAAGAGAGAGAG
*
2788799 AGAGGGAAAAGAGAGAG
1 AGAGGGAAGAGAGAGAG
2788816 AGAG
1 AGAG
2788820 AGAAAAATGA
Statistics
Matches: 240, Mismatches: 13, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
15 10 0.04
16 25 0.10
17 205 0.85
ACGTcount: A:0.48, C:0.00, G:0.51, T:0.01
Consensus pattern (17 bp):
AGAGGGAAGAGAGAGAG
Found at i:2795823 original size:19 final size:19
Alignment explanation
Indices: 2795782--2795829 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
2795772 TATATTTGTT
*
2795782 TTAGGTATTA-TAATTTAA
1 TTAGGTTTTAGTAATTTAA
* *
2795800 ATAGGTTTTAGTATTTTAA
1 TTAGGTTTTAGTAATTTAA
*
2795819 TTAGGATTTAG
1 TTAGGTTTTAG
2795830 AATATTATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (19 bp):
TTAGGTTTTAGTAATTTAA
Found at i:2797392 original size:20 final size:21
Alignment explanation
Indices: 2797369--2797415 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2797359 TTGCATTCGT
2797369 ATTTTTT-TCATTACATTTGC
1 ATTTTTTATCATTACATTTGC
** *
2797389 ATTTTTTATGTTTGCATTTGC
1 ATTTTTTATCATTACATTTGC
2797410 ATTTTT
1 ATTTTT
2797416 ATATTTTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.17, C:0.11, G:0.09, T:0.64
Consensus pattern (21 bp):
ATTTTTTATCATTACATTTGC
Found at i:2797406 original size:21 final size:20
Alignment explanation
Indices: 2797382--2797434 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
2797372 TTTTTCATTA
2797382 CATTTGCATTTTT-TATGTTT
1 CATTTGCATTTTTATAT-TTT
2797402 GCATTTGCATTTTTATATTTT
1 -CATTTGCATTTTTATATTTT
*
2797423 CATTTACATTTT
1 CATTTGCATTTT
2797435 CATTTTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 11 0.37
21 16 0.53
22 3 0.10
ACGTcount: A:0.19, C:0.11, G:0.08, T:0.62
Consensus pattern (20 bp):
CATTTGCATTTTTATATTTT
Found at i:2797416 original size:20 final size:20
Alignment explanation
Indices: 2797382--2797434 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
2797372 TTTTTCATTA
*
2797382 CATTTGCATTTTTTATGTTTG
1 CATTTGCA-TTTTTATATTTG
*
2797403 CATTTGCATTTTTATATTTT
1 CATTTGCATTTTTATATTTG
*
2797423 CATTTACATTTT
1 CATTTGCATTTT
2797435 CATTTTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 21 0.72
21 8 0.28
ACGTcount: A:0.19, C:0.11, G:0.08, T:0.62
Consensus pattern (20 bp):
CATTTGCATTTTTATATTTG
Found at i:2797456 original size:47 final size:47
Alignment explanation
Indices: 2797350--2797459 Score: 127
Period size: 47 Copynumber: 2.3 Consensus size: 47
2797340 CCTTTGTTGC
*
2797350 ATTTGCATTTTGCATTCGTATTTTTTTCATTACATTTGCATTTTTTAT
1 ATTTGCATTTTGCATTCGTATTATTTTCATTACATTTGCA-TTTTTAT
* ** *
2797398 GTTTGCA-TTTGCATTTTTA-TATTTTCATTTACATTTTCA-TTTTAT
1 ATTTGCATTTTGCATTCGTATTATTTTCA-TTACATTTGCATTTTTAT
2797443 ATTTGCATCTTTGCATT
1 ATTTGCAT-TTTGCATT
2797460 GCACAGTTTG
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
45 12 0.23
46 7 0.13
47 28 0.53
48 6 0.11
ACGTcount: A:0.19, C:0.13, G:0.08, T:0.60
Consensus pattern (47 bp):
ATTTGCATTTTGCATTCGTATTATTTTCATTACATTTGCATTTTTAT
Found at i:2799687 original size:72 final size:72
Alignment explanation
Indices: 2799570--2799703 Score: 225
Period size: 72 Copynumber: 1.9 Consensus size: 72
2799560 TACAATAAAG
2799570 CTTGAGTTATCCCCCTAAAGAAATTGATTAATAGCCCCGACTTTATGGATAATATTCAGCTAGTC
1 CTTGAGTTATCCCCCTAAAGAAATTGATTAATAGCCCCGACTTTATGGATAATATTCAGCTAGTC
2799635 TGTTATA
66 TGTTATA
* * *
2799642 CTTGAGTTATCCCCCTAAAGGAATT-AGTTAATCGCCCCGGCTTTATGGATAATATTCAGCTA
1 CTTGAGTTATCCCCCTAAAGAAATTGA-TTAATAGCCCCGACTTTATGGATAATATTCAGCTA
2799704 ACCTATTATA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 1 0.02
72 57 0.98
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (72 bp):
CTTGAGTTATCCCCCTAAAGAAATTGATTAATAGCCCCGACTTTATGGATAATATTCAGCTAGTC
TGTTATA
Found at i:2801933 original size:75 final size:75
Alignment explanation
Indices: 2801807--2801979 Score: 260
Period size: 75 Copynumber: 2.3 Consensus size: 75
2801797 ATCAACAAGA
* *
2801807 AGAAAATGTTGGGGCATGCTAAAAGCCCATTTCAATCAGAATTAGGAATGTTTATATATTTTGAA
1 AGAAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATTAGGAATGTTGATATATTTTGAA
**
2801872 -TGTTTGTATC
66 CT-TTCATATC
* *
2801882 A-ACAAATGTTGGGGCGTGCTGAAAGCCCATTTCAATCAGAATTAGGAATGTTGATGTATTTTGA
1 AGA-AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATTAGGAATGTTGATATATTTTGA
2801946 ACTTTCATATC
65 ACTTTCATATC
2801957 AGAAAATGTTGGGGCATGCTGAA
1 AGAAAATGTTGGGGCATGCTGAA
2801980 GTCCCACATC
Statistics
Matches: 88, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
74 1 0.01
75 85 0.97
76 2 0.02
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (75 bp):
AGAAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATTAGGAATGTTGATATATTTTGAA
CTTTCATATC
Found at i:2802935 original size:54 final size:54
Alignment explanation
Indices: 2802853--2802963 Score: 168
Period size: 54 Copynumber: 2.1 Consensus size: 54
2802843 TTTACTGGCA
* * * *
2802853 AACATCTGTGCAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTATTACG
1 AACATATGTACAGAAGACACAGGAAATGATGAATGTGTTGCCAAATGTATTACG
* *
2802907 AACATATGTACAGAAGACACAGGAAATGATGAATGTGTTGCCAAATGTTTTATG
1 AACATATGTACAGAAGACACAGGAAATGATGAATGTGTTGCCAAATGTATTACG
2802961 AAC
1 AAC
2802964 CAGTTATTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.26
Consensus pattern (54 bp):
AACATATGTACAGAAGACACAGGAAATGATGAATGTGTTGCCAAATGTATTACG
Found at i:2803571 original size:22 final size:23
Alignment explanation
Indices: 2803543--2803600 Score: 84
Period size: 22 Copynumber: 2.6 Consensus size: 23
2803533 TACATCTACA
2803543 TTCTTCAAAGATGATAGATTCT-
1 TTCTTCAAAGATGATAGATTCTC
*
2803565 TTCTTCAAAGATAATAGATTCTC
1 TTCTTCAAAGATGATAGATTCTC
*
2803588 TT-TTCAAATATGA
1 TTCTTCAAAGATGA
2803601 AAGCTTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
22 30 0.94
23 2 0.06
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (23 bp):
TTCTTCAAAGATGATAGATTCTC
Found at i:2804606 original size:22 final size:22
Alignment explanation
Indices: 2804581--2804643 Score: 78
Period size: 20 Copynumber: 3.0 Consensus size: 22
2804571 GGGTCATCTG
2804581 TAAGACCTACAGTGCATGATGA
1 TAAGACCTACAGTGCATGATGA
* *
2804603 TAAGACCT-CAGGGCCATCA--A
1 TAAGACCTACAGTG-CATGATGA
2804623 TAAGACCTACAGTGCATGATG
1 TAAGACCTACAGTGCATGATG
2804644 TGTTCAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
20 13 0.39
21 8 0.24
22 12 0.36
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (22 bp):
TAAGACCTACAGTGCATGATGA
Found at i:2804834 original size:116 final size:117
Alignment explanation
Indices: 2804267--2804864 Score: 930
Period size: 117 Copynumber: 5.1 Consensus size: 117
2804257 CTATTTCCCA
* * *
2804267 CATCCATAAGACCTACAGTGCATGATGTGTTC-AAAAAGCCTTCGGGAGCTTTTTTATATTTAAA
1 CATCCATAAGACCTACAGTGCAGGATGTGTTCAAAAAAGCCTTCAGGAGCTTTTTGATATTTAAA
* * * * * *
2804331 GCCTCCGGGTCATCTGTAAGACCTATAGTGTAAGATGGTAAGACCTCAGGGA
66 ACCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGC
*
2804383 CATCCATAAGACCTACAGTGCAGGATGTGCTCAAAAAAGCCTTCAGGAGCTTTTTGATATTTAAA
1 CATCCATAAGACCTACAGTGCAGGATGTGTTCAAAAAAGCCTTCAGGAGCTTTTTGATATTTAAA
* * *
2804448 ACCTTCGGGTCATATGTAAGACCTACAATACAAGATGATAAGACCTCAGGGC
66 ACCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGC
* *
2804500 CATCTATAAGACCTACAGTGCAGGATGTGTTCAAAAAAGCCTTCGGGAGCTTTTTGATATTTAAA
1 CATCCATAAGACCTACAGTGCAGGATGTGTTCAAAAAAGCCTTCAGGAGCTTTTTGATATTTAAA
*
2804565 ACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGATAAGACCTCAGGGC
66 ACCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGC
* * * *
2804617 CATCAATAAGACCTACAGTGCATGATGTGTTCAAAAAAAACATTCAGGAGCTTTTTGATATTTAA
1 CATCCATAAGACCTACAGTGCAGGATGTGTTC-AAAAAAGCCTTCAGGAGCTTTTTGATATTTAA
* *
2804682 AGCCTTCGGGTCATCTGTAAGACCTACAGTGTAAGATGATAAGACCTCAGGGC
65 AACCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGC
*
2804735 CATCCATAAGACCTACAGTGCAGGATGTTTTC-AAAAAGCCTTCAGGAGCTTTTTGATATTTAAA
1 CATCCATAAGACCTACAGTGCAGGATGTGTTCAAAAAAGCCTTCAGGAGCTTTTTGATATTTAAA
* * *
2804799 ACCTCCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAATACCTCAGGGT
66 ACCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGC
*
2804851 CATTCATAAGACCT
1 CATCCATAAGACCT
2804865 CTTGGCAGAA
Statistics
Matches: 441, Mismatches: 39, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
116 120 0.27
117 213 0.48
118 108 0.24
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (117 bp):
CATCCATAAGACCTACAGTGCAGGATGTGTTCAAAAAAGCCTTCAGGAGCTTTTTGATATTTAAA
ACCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGC
Found at i:2805092 original size:3 final size:3
Alignment explanation
Indices: 2805011--2805083 Score: 116
Period size: 3 Copynumber: 25.3 Consensus size: 3
2805001 CATTTTACTT
*
2805011 TTA TTA TTA TTA ATA -TA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2805057 TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2805084 AAATTATTAC
Statistics
Matches: 66, Mismatches: 1, Indels: 6
0.90 0.01 0.08
Matches are distributed among these distances:
2 6 0.09
3 60 0.91
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2806672 original size:100 final size:99
Alignment explanation
Indices: 2806554--2806746 Score: 350
Period size: 100 Copynumber: 1.9 Consensus size: 99
2806544 AAAAGGTCGA
2806554 TGGCGACTCCAAAACATTTTAATAAAAATCATTTATTTCATTCACATTACTTTTCCACCAAGGAA
1 TGGCGACTCCAAAACATTTTAATAAAAATCATTTATTTCATTCACATTACTTTTCCACCAAGGAA
*
2806619 ATTTTGTACCCGGGCAAAAACCGGTTACGGCAGTT
66 ATTTCGTA-CCGGGCAAAAACCGGTTACGGCAGTT
* *
2806654 TGGCGACTCCGAAACATTTTAATAAAAATCATTTATTTCATTCACATTACTTTTCCGCCAAGGAA
1 TGGCGACTCCAAAACATTTTAATAAAAATCATTTATTTCATTCACATTACTTTTCCACCAAGGAA
2806719 ATTTCGTACCGGGCAAAAACCGGTTACG
66 ATTTCGTACCGGGCAAAAACCGGTTACG
2806747 ACACCTACCA
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
99 20 0.22
100 70 0.78
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.31
Consensus pattern (99 bp):
TGGCGACTCCAAAACATTTTAATAAAAATCATTTATTTCATTCACATTACTTTTCCACCAAGGAA
ATTTCGTACCGGGCAAAAACCGGTTACGGCAGTT
Found at i:2815506 original size:20 final size:20
Alignment explanation
Indices: 2815478--2815521 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2815468 TAAATACATT
2815478 CAATCAACACAGGCAGATTA
1 CAATCAACACAGGCAGATTA
* *
2815498 CAATTAACACAGGCAGATTG
1 CAATCAACACAGGCAGATTA
2815518 CAAT
1 CAAT
2815522 ATTCAAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.23, G:0.16, T:0.18
Consensus pattern (20 bp):
CAATCAACACAGGCAGATTA
Found at i:2817211 original size:18 final size:18
Alignment explanation
Indices: 2817178--2817262 Score: 80
Period size: 18 Copynumber: 4.7 Consensus size: 18
2817168 CGGTCAGAAA
* *
2817178 AGTTTCATCAATCCTAAC
1 AGTTTCACCAACCCTAAC
*
2817196 AGTTTGACCAACCCTAAC
1 AGTTTCACCAACCCTAAC
* *
2817214 AGTTTCAGCAACCCTAAT
1 AGTTTCACCAACCCTAAC
** *
2817232 AGTTTCAGGAACCCTTAC
1 AGTTTCACCAACCCTAAC
* *
2817250 ATTTTCATCAACC
1 AGTTTCACCAACC
2817263 GTAATAGATT
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 55 1.00
ACGTcount: A:0.32, C:0.29, G:0.09, T:0.29
Consensus pattern (18 bp):
AGTTTCACCAACCCTAAC
Found at i:2817245 original size:36 final size:36
Alignment explanation
Indices: 2817178--2817269 Score: 103
Period size: 36 Copynumber: 2.6 Consensus size: 36
2817168 CGGTCAGAAA
* * *
2817178 AGTTTCATCAATCCTAACAGTTTGACCAACCCTAAC
1 AGTTTCATCAACCCTAATAGTTTCACCAACCCTAAC
* ** *
2817214 AGTTTCAGCAACCCTAATAGTTTCAGGAACCCTTAC
1 AGTTTCATCAACCCTAATAGTTTCACCAACCCTAAC
* *
2817250 ATTTTCATCAACCGTAATAG
1 AGTTTCATCAACCCTAATAG
2817270 ATTCGGCCAC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.29
Consensus pattern (36 bp):
AGTTTCATCAACCCTAATAGTTTCACCAACCCTAAC
Found at i:2817282 original size:36 final size:36
Alignment explanation
Indices: 2817205--2817302 Score: 110
Period size: 36 Copynumber: 2.7 Consensus size: 36
2817195 CAGTTTGACC
* * * *
2817205 AACCCTAACAGTTTCAGCAACCCTAATAGTTTCAGG
1 AACCCTTACATTTTCATCAACCCTAATAGATTCAGG
*
2817241 AACCCTTACATTTTCATCAACCGTAATAGATTC-GG
1 AACCCTTACATTTTCATCAACCCTAATAGATTCAGG
*
2817276 CCACCCTTACATTTTCATGC-ACCCTAA
1 -AACCCTTACATTTTCAT-CAACCCTAA
2817303 CAATTTTAGC
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
35 2 0.04
36 50 0.94
37 1 0.02
ACGTcount: A:0.31, C:0.31, G:0.10, T:0.29
Consensus pattern (36 bp):
AACCCTTACATTTTCATCAACCCTAATAGATTCAGG
Found at i:2817383 original size:60 final size:60
Alignment explanation
Indices: 2817306--2817428 Score: 169
Period size: 60 Copynumber: 2.0 Consensus size: 60
2817296 ACCCTAACAA
* * *
2817306 TTTTAGCCAAGTTAATTTCAATATCCAC-TATTGGTTCAGTTTCAATTGGG-CCAAGTTCAG
1 TTTTAGCCAAATCAATTTCAATATCAACAT-TTGGTTCAGTTTCAA-TGGGACCAAGTTCAG
* *
2817366 TTTTAGCCAAATCAATTTCAATATCAACATTTGGTTTAGTTTCAATGGGATCAAGTTCAG
1 TTTTAGCCAAATCAATTTCAATATCAACATTTGGTTCAGTTTCAATGGGACCAAGTTCAG
2817426 TTT
1 TTT
2817429 CAATAAGAGC
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
59 4 0.07
60 51 0.91
61 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.40
Consensus pattern (60 bp):
TTTTAGCCAAATCAATTTCAATATCAACATTTGGTTCAGTTTCAATGGGACCAAGTTCAG
Found at i:2818123 original size:21 final size:21
Alignment explanation
Indices: 2818099--2818151 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
2818089 AATGAAACAA
*
2818099 AACAGTTGCAAAATTGACCAC
1 AACAGTTGCAAAAATGACCAC
2818120 AACAGTTGCAAAAATGACCAC
1 AACAGTTGCAAAAATGACCAC
2818141 AACAGTTGCAA
1 AACAGTTGCAA
2818152 TAACAACAAT
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:0.45, C:0.23, G:0.15, T:0.17
Consensus pattern (21 bp):
AACAGTTGCAAAAATGACCAC
Found at i:2818816 original size:21 final size:21
Alignment explanation
Indices: 2818787--2818839 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2818777 ATTCTGACTA
2818787 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* * **
2818808 TCGCTTTGCGGTTTTCTTAAT
1 TCGCATTGCGATTTTCCAAAT
*
2818829 TCGCAATGCGA
1 TCGCATTGCGA
2818840 ATACATAAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:2818854 original size:20 final size:20
Alignment explanation
Indices: 2818829--2818962 Score: 214
Period size: 20 Copynumber: 6.7 Consensus size: 20
2818819 TTTTCTTAAT
* *
2818829 TCGCAATGCGAATACATAAA
1 TCGCAACGCGAATACGTAAA
** *
2818849 TCGCAACGCGAATTTGGAAAA
1 TCGCAACGCGAA-TACGTAAA
2818870 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
2818890 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
2818910 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
2818930 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
2818950 TCGCAACGCGAAT
1 TCGCAACGCGAAT
2818963 CTAACTATCA
Statistics
Matches: 105, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
20 89 0.85
21 16 0.15
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:2819186 original size:22 final size:21
Alignment explanation
Indices: 2819160--2819225 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 21
2819150 GGCAACATCC
*
2819160 GTCCCTATCTCTGACGAAATCA
1 GTCCC-ATCTCCGACGAAATCA
*
2819182 GTCCCCATCTCCGACGATATCA
1 GT-CCCATCTCCGACGAAATCA
*
2819204 GTCTCCATCTCCGGCGAAATCA
1 GTC-CCATCTCCGACGAAATCA
2819226 TTCACGGTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 34 0.89
23 3 0.08
ACGTcount: A:0.24, C:0.36, G:0.15, T:0.24
Consensus pattern (21 bp):
GTCCCATCTCCGACGAAATCA
Found at i:2819642 original size:20 final size:20
Alignment explanation
Indices: 2819554--2819644 Score: 94
Period size: 20 Copynumber: 4.6 Consensus size: 20
2819544 GCGATTCTGT
2819554 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
* ** **
2819573 CGTTGCAATAGTCAAATTCG
1 CGTTGCGATTTTCATTTTCG
**
2819593 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
2819613 TGTTGCGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
2819633 AGTTGCGATTTT
1 CGTTGCGATTTT
2819645 AAGTTTCAGA
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
19 11 0.18
20 49 0.82
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:2819651 original size:20 final size:20
Alignment explanation
Indices: 2819608--2819651 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2819598 CGATAGTCAT
* * *
2819608 TTTCGTGTTGCGATTTTCAT
1 TTTCGAGTTGCGATTTTAAG
2819628 TTTCGAGTTGCGATTTTAAG
1 TTTCGAGTTGCGATTTTAAG
2819648 TTTC
1 TTTC
2819652 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGAGTTGCGATTTTAAG
Found at i:2821533 original size:20 final size:20
Alignment explanation
Indices: 2821508--2821684 Score: 157
Period size: 20 Copynumber: 9.5 Consensus size: 20
2821498 AGAATAGTTT
2821508 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
2821528 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
2821548 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
2821564 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
2821581 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
2821597 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
2821615 ACTATCGCAATGCGAAAATA
1 ACTATCGCAATGCGAAAATG
**
2821635 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
**
2821655 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
2821675 ACTATCGCAA
1 ACTATCGCAA
2821685 CGAGAGAATC
Statistics
Matches: 135, Mismatches: 8, Indels: 28
0.79 0.05 0.16
Matches are distributed among these distances:
14 14 0.10
16 10 0.07
17 8 0.06
18 5 0.04
19 7 0.05
20 91 0.67
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:2821588 original size:33 final size:33
Alignment explanation
Indices: 2821531--2821611 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
2821521 GAAAATGACT
** * * *
2821531 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAACGCG-AAATGAAAATCGCAACAACAAA
*
2821565 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACAACAAA
2821598 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
2821612 ATGACTATCG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 30 0.75
34 10 0.25
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACAACAAA
Found at i:2821797 original size:20 final size:20
Alignment explanation
Indices: 2821731--2821782 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
2821721 GATTCTCTCG
2821731 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
2821751 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
2821771 TTGCGATAGTCA
1 TTGCGATAGTCA
2821783 TTTTCGCGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:2822371 original size:21 final size:21
Alignment explanation
Indices: 2822280--2822384 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
2822270 GACTCACCTG
*
2822280 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
2822302 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
2822322 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
2822343 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
2822364 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
2822385 CCAACATTCT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:2822377 original size:42 final size:42
Alignment explanation
Indices: 2822277--2822387 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
2822267 CCCGACTCAC
* * * *
2822277 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
2822319 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
2822361 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
2822388 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.93
43 2 0.04
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:2823965 original size:33 final size:34
Alignment explanation
Indices: 2823908--2824003 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 34
2823898 AAAACAGACT
* ** *
2823908 ATCGCAACGCGAAAATGACTATCGCAATGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
*
2823942 ATCGCAATGCG-AAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
2823975 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCGAAAATGAAAATCGCAACG
2824004 CGAAACTAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 29 0.52
34 27 0.48
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
Found at i:2823999 original size:20 final size:19
Alignment explanation
Indices: 2823941--2824008 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
2823931 GCAATGAGAG
2823941 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2823960 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
2823974 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
2823994 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
2824009 CTAATTTCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.20
16 5 0.12
17 2 0.05
18 3 0.08
19 11 0.28
20 11 0.28
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2824076 original size:33 final size:33
Alignment explanation
Indices: 2824018--2824102 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 33
2824008 ACTAATTTCG
* *
2824018 CGTTGCGATTTTCATTTTCGTATTGCTATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
2824052 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
**
2824085 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
2824103 CGCGTTGTGA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 32 0.70
34 14 0.30
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:2824114 original size:20 final size:20
Alignment explanation
Indices: 2824085--2824173 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
2824075 GCGATTCTCT
2824085 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
2824105 CGTTGTGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
2824125 CGTTGTGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
2824145 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
2824165 CGTTGCGAT
1 CGTTGCGAT
2824174 TTCTACGTTG
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
20 60 0.97
21 2 0.03
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:2827339 original size:22 final size:22
Alignment explanation
Indices: 2827310--2827383 Score: 141
Period size: 22 Copynumber: 3.4 Consensus size: 22
2827300 TTCCGGATGG
2827310 GGAA-GGATGTCGTTGGATATA
1 GGAACGGATGTCGTTGGATATA
2827331 GGAACGGATGTCGTTGGATATA
1 GGAACGGATGTCGTTGGATATA
2827353 GGAACGGATGTCGTTGGATATA
1 GGAACGGATGTCGTTGGATATA
2827375 GGAACGGAT
1 GGAACGGAT
2827384 ATCGCCGGAG
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 4 0.08
22 48 0.92
ACGTcount: A:0.28, C:0.08, G:0.38, T:0.26
Consensus pattern (22 bp):
GGAACGGATGTCGTTGGATATA
Found at i:2827588 original size:20 final size:20
Alignment explanation
Indices: 2827544--2827591 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2827534 GAAATTCAGT
*
2827544 ATTGCGATAATCAGAATCTC
1 ATTGCGATAATCAGAATCGC
* *
2827564 ATTGCGATAGTCAGATTCGC
1 ATTGCGATAATCAGAATCGC
*
2827584 GTTGCGAT
1 ATTGCGAT
2827592 TTACGTATTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (20 bp):
ATTGCGATAATCAGAATCGC
Found at i:2827673 original size:21 final size:21
Alignment explanation
Indices: 2827643--2827686 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2827633 TTTGCATTGT
2827643 GAATTAGGAAAATCGCAACGC
1 GAATTAGGAAAATCGCAACGC
* *
2827664 GAATTTGGAAAATCGCAATGC
1 GAATTAGGAAAATCGCAACGC
2827685 GA
1 GA
2827687 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.18
Consensus pattern (21 bp):
GAATTAGGAAAATCGCAACGC
Found at i:2832163 original size:2 final size:2
Alignment explanation
Indices: 2832156--2832220 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
2832146 AACATCACAA
2832156 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2832198 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
2832221 CGAGGATATA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2832712 original size:2 final size:2
Alignment explanation
Indices: 2832639--2832694 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
2832629 ATCATAGCCC
*
2832639 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2832681 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
2832695 AAAGGTTTGA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2834030 original size:140 final size:138
Alignment explanation
Indices: 2833863--2834191 Score: 459
Period size: 141 Copynumber: 2.4 Consensus size: 138
2833853 TCTAAAACAA
2833863 AAAATAGAGGCTCTAATATTAACCCTAATTGATTTT-ACCAATTATTGAATTGAATAATCGATGA
1 AAAATAGAGGCTCTAATA-TAA-CCTAATTGATTTTAACCAATTATTGAATTGAATAATCGATGA
*
2833927 AAACCCTA-GGACATTTTAATAAGAGAGACAAAT-AGAATTATTCCCTAAGTTTAAAGACTTAAG
64 AAACCCTATGG-CATTTTAATAAGAGAGACAAATCA-AATTATTCCCTAAATTTAAAGAC-TAAG
*
2833990 TGTGATTCTACCT
126 TGTAATTCTACCT
* * *
2834003 AAAATTGAGGCTCTAATTAATAACCTAATGGATTTTAACCAATTATTGAATCGAATAATCGATGA
1 AAAATAGAGGCTCTAA-T-ATAACCTAATTGATTTTAACCAATTATTGAATTGAATAATCGATGA
** *
2834068 AAACCCTATGGCATTTTAATGCGAGAGCCAAATCAAATTATTCCCTAAATTTAAAGACTAAGTGT
64 AAACCCTATGGCATTTTAATAAGAGAGACAAATCAAATTATTCCCTAAATTTAAAGACTAAGTGT
2834133 AATTCTACCT
129 AATTCTACCT
* * * *
2834143 GAAATGGAGGCTCTGAT-TAACCTAATTGATTTTAACCAATTACTGAATT
1 AAAATAGAGGCTCTAATATAACCTAATTGATTTTAACCAATTATTGAATT
2834192 AATCCCTAAA
Statistics
Matches: 170, Mismatches: 14, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
137 29 0.17
139 1 0.01
140 56 0.33
141 80 0.47
142 4 0.02
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (138 bp):
AAAATAGAGGCTCTAATATAACCTAATTGATTTTAACCAATTATTGAATTGAATAATCGATGAAA
ACCCTATGGCATTTTAATAAGAGAGACAAATCAAATTATTCCCTAAATTTAAAGACTAAGTGTAA
TTCTACCT
Found at i:2836502 original size:31 final size:31
Alignment explanation
Indices: 2836467--2836544 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
2836457 TTTAACGTCC
* *
2836467 AAGTGATCAAAACTTAATAAAACGATAACGT
1 AAGTGACCAAAACTTAATAAAACAATAACGT
2836498 AAGTGACCAAAACTTAATAAAACAATAACGT
1 AAGTGACCAAAACTTAATAAAACAATAACGT
*
2836529 AATTGACCAAAACTTA
1 AAGTGACCAAAACTTA
2836545 TGTTTTTTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.53, C:0.15, G:0.10, T:0.22
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAACAATAACGT
Done.