Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008209.1 Hibiscus syriacus cultivar Beakdansim tig00110831_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: 6561538
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 30
Found at i:2811239 original size:3 final size:3
Alignment explanation
Indices: 2811214--2811253 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
2811204 AAAAAAGTAA
2811214 AAT AA- AAT AAGT AAT AA- AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2811254 ATATAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.12
3 27 0.79
4 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:2811342 original size:29 final size:29
Alignment explanation
Indices: 2811310--2811395 Score: 111
Period size: 30 Copynumber: 2.9 Consensus size: 29
2811300 AAACTATATA
*
2811310 TATATAAATTTCCAAAAAT-TTTTAAAAAC
1 TATAT-AATTTTCAAAAATATTTTAAAAAC
* *
2811339 TATATAATTTTCAAAAATGTCTTTAAGAAC
1 TATATAATTTTCAAAAATAT-TTTAAAAAC
*
2811369 CATATAATTTTCAAAAATATTTTAAAA
1 TATATAATTTTCAAAAATATTTTAAAA
2811396 TCATATATTA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
28 12 0.24
29 12 0.24
30 26 0.52
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (29 bp):
TATATAATTTTCAAAAATATTTTAAAAAC
Found at i:2811462 original size:41 final size:36
Alignment explanation
Indices: 2811375--2811560 Score: 162
Period size: 38 Copynumber: 4.9 Consensus size: 36
2811365 GAACCATATA
* *
2811375 ATTTTCAAAAATATTTTAAAATC-ATATATTATA--T
1 ATTTTC-AAAATGTTTTAAAAACTATATATTATATTT
* *
2811409 GTTTTCAAAATGTTTTTTCAAAAATTATATATTCTATATTT
1 ATTTTCAAAATG--TTTT-AAAAACTATATA-T-TATATTT
*
2811450 ATTTTCAAAATGTTTTAAAAACTATATAATATATATAT
1 ATTTTCAAAATGTTTTAAAAACTATAT-AT-TATATTT
* *
2811488 ATTTTCAAAAATGTCTTGAAAACTATATATTATATTT
1 ATTTTC-AAAATGTTTTAAAAACTATATATTATATTT
* * *
2811525 ATTTTCAAAAACGTTTTAAAAAACCATATAATATAT
1 ATTTTC-AAAATGTTTT-AAAAACTATATATTATAT
2811561 AAATGTTTTC
Statistics
Matches: 125, Mismatches: 16, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
33 5 0.04
34 5 0.04
35 4 0.03
36 4 0.03
37 26 0.21
38 41 0.33
39 28 0.22
41 12 0.10
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (36 bp):
ATTTTCAAAATGTTTTAAAAACTATATATTATATTT
Found at i:2811477 original size:75 final size:74
Alignment explanation
Indices: 2811375--2811576 Score: 216
Period size: 77 Copynumber: 2.7 Consensus size: 74
2811365 GAACCATATA
* * * *
2811375 ATTTTCAAAAATATTTTAAAATC--AT-ATAT-TATATGTTTTCAAAATGTTTTTTCAAAAATTA
1 ATTTTCAAAAATGTTTTAAAAACATATAATATATATATGTTTTCAAAATG--TCTT-AAAAACTA
2811436 TATATTCTATATTT
63 TATA-T-TATATTT
* *
2811450 ATTTTC-AAAATGTTTTAAAAACTATATAATATATATATATTTTCAAAAATGTCTTGAAAACTAT
1 ATTTTCAAAAATGTTTTAAAAAC-ATATAATATATATATGTTTTC-AAAATGTCTTAAAAACTAT
2811514 ATATTATATTT
64 ATATTATATTT
* *
2811525 ATTTTCAAAAACGTTTTAAAAAACCATATAATATATAAATGTTTTCAAAATG
1 ATTTTCAAAAATGTTTT-AAAAA-CATATAATATATATATGTTTTCAAAATG
2811577 AAATGTTTTT
Statistics
Matches: 109, Mismatches: 9, Indels: 17
0.81 0.07 0.13
Matches are distributed among these distances:
74 14 0.13
75 19 0.17
76 16 0.15
77 36 0.33
78 8 0.07
79 10 0.09
80 6 0.06
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (74 bp):
ATTTTCAAAAATGTTTTAAAAACATATAATATATATATGTTTTCAAAATGTCTTAAAAACTATAT
ATTATATTT
Found at i:2811485 original size:38 final size:39
Alignment explanation
Indices: 2811398--2811576 Score: 168
Period size: 38 Copynumber: 4.6 Consensus size: 39
2811388 TTTTAAAATC
* * *
2811398 ATATATTATATGTTTTCAAAATGTTTTTTCAAAAATTATATA
1 ATATA-TATATATTTTCAAAATG--TTTTAAAAAACTATATA
* * *
2811440 TTCTATATTTATTTTCAAAATGTTTT-AAAAACTATATA
1 ATATATATATATTTTCAAAATGTTTTAAAAAACTATATA
* *
2811478 ATATATATATATTTTCAAAAATGTCTT-GAAAACTATAT-
1 ATATATATATATTTTC-AAAATGTTTTAAAAAACTATATA
* * *
2811516 AT-TATATTTATTTTCAAAAACGTTTTAAAAAACCATATA
1 ATATATATATATTTTC-AAAATGTTTTAAAAAACTATATA
* *
2811555 ATATATAAATGTTTTCAAAATG
1 ATATATATATATTTTCAAAATG
2811577 AAATGTTTTT
Statistics
Matches: 114, Mismatches: 19, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
37 21 0.18
38 35 0.31
39 30 0.26
40 10 0.09
41 15 0.13
42 3 0.03
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.45
Consensus pattern (39 bp):
ATATATATATATTTTCAAAATGTTTTAAAAAACTATATA
Found at i:2812386 original size:165 final size:165
Alignment explanation
Indices: 2812133--2813143 Score: 1771
Period size: 165 Copynumber: 6.1 Consensus size: 165
2812123 AGTTTTATTG
* * * * * * * * * *
2812133 ACAGATAACCCTTCTTGCATTGAGCTATTCTGTAAGCTTGATTTG-CCTCTAAGTTGAATATAAT
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAA--ATGATGTGCCCTCGAAGCTGAGTGTAAT
** *
2812197 CGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
64 CGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
* *
2812262 GGAACTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTC
129 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
2812299 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
2812364 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
2812429 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
2812464 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
2812529 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
2812594 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
2812629 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
*
2812694 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
2812759 AGCTGAGCGTAGTCGAACTCGAAGGTC--TTGGTC
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
2812792 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
2812857 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
2812922 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
2812957 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
*
2813022 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
* *
2813087 AGCTAAGCGTAGTCGAACTCGAAGGTC--TTGGTG
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
* * *
2813120 GCAGATAGCCCTTCTGGCCTTGAG
1 ACAGATAACCCTTCTAGCCTTGAG
2813144 CTAAGCTACA
Statistics
Matches: 819, Mismatches: 23, Indels: 9
0.96 0.03 0.01
Matches are distributed among these distances:
163 188 0.23
164 6 0.01
165 594 0.73
166 31 0.04
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (165 bp):
ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
Found at i:2812968 original size:328 final size:328
Alignment explanation
Indices: 2812133--2813143 Score: 1790
Period size: 328 Copynumber: 3.1 Consensus size: 328
2812123 AGTTTTATTG
* * * * * * * * * *
2812133 ACAGATAACCCTTCTTGCATTGAGCTATTCTGTAAGCTTGATTTG-CCTCTAAGTTGAATATAAT
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAA--ATGATGTGCCCTCGAAGCTGAGTGTAAT
** *
2812197 CGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
64 CGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
* *
2812262 GGAACTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTAT
129 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTAT
2812327 GCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCT
194 GCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCT
*
2812392 TCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCT
259 TCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-
2812457 TTTGGTC
323 -TTGGTC
2812464 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
2812529 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
2812594 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGC
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGC
2812659 TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTC
196 TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTC
2812724 TCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTG
261 TCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTG
2812789 GTC
326 GTC
2812792 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
2812857 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
2812922 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGC
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGC
2812987 TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTC
196 TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTC
*
2813052 TCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTAAGCGTAGTCGAACTCGAAGGTCTTG
261 TCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTG
*
2813117 GTG
326 GTC
* * *
2813120 GCAGATAGCCCTTCTGGCCTTGAG
1 ACAGATAACCCTTCTAGCCTTGAG
2813144 CTAAGCTACA
Statistics
Matches: 658, Mismatches: 21, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
328 353 0.54
329 6 0.01
330 268 0.41
331 31 0.05
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (328 bp):
ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGC
TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTC
TCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTG
GTC
Found at i:2816541 original size:18 final size:19
Alignment explanation
Indices: 2816500--2816544 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
2816490 AGTTAATGTG
2816500 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
2816519 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
2816537 AATGCAAA
1 AATGCAAA
2816545 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:2818013 original size:69 final size:69
Alignment explanation
Indices: 2817902--2818049 Score: 278
Period size: 69 Copynumber: 2.1 Consensus size: 69
2817892 TGTCCCCAGC
2817902 GGAGTCGCCAAGCTGTCGGAACCGTCTTTCGGTTGGGCCCCAGAATTGGGCTTCGACTTGAAATG
1 GGAGTCGCCAAGCTGTCGGAACCGTCTTTCGGTTGGGCCCCAGAATTGGGCTTCGACTTGAAATG
2817967 AATT
66 AATT
* *
2817971 GGAGTTGCCCAGCTGTCGGAACCGTCTTTCGGTTGGGCCCCAGAATTGGGCTTCGACTTGAAATG
1 GGAGTCGCCAAGCTGTCGGAACCGTCTTTCGGTTGGGCCCCAGAATTGGGCTTCGACTTGAAATG
2818036 AATT
66 AATT
2818040 GGAGTCGCCA
1 GGAGTCGCCA
2818050 CCGACCACTT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 75 1.00
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.26
Consensus pattern (69 bp):
GGAGTCGCCAAGCTGTCGGAACCGTCTTTCGGTTGGGCCCCAGAATTGGGCTTCGACTTGAAATG
AATT
Found at i:2819680 original size:6 final size:5
Alignment explanation
Indices: 2819666--2819731 Score: 51
Period size: 6 Copynumber: 11.8 Consensus size: 5
2819656 TTGGACCTGG
* *
2819666 AAAAA AAAAGT AAAAT AAAAT AAGTAAT AAAAA AAAAT AATAAT AATAAT
1 AAAAT AAAA-T AAAAT AAAAT AA--AAT AAAAT AAAAT AA-AAT AA-AAT
2819716 AATAAT AAATAT AAAA
1 AA-AAT AAA-AT AAAA
2819732 AACTATATAA
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
5 22 0.42
6 26 0.49
7 5 0.09
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:2819707 original size:3 final size:3
Alignment explanation
Indices: 2819679--2819723 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
2819669 AAAAAAGTAA
*
2819679 AAT AA- AAT AAGT AAT AA- AA- AAA AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2819722 AA
1 AA
2819724 ATATAAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
2 6 0.16
3 29 0.76
4 3 0.08
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (3 bp):
AAT
Found at i:2819829 original size:30 final size:30
Alignment explanation
Indices: 2819783--2819871 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 30
2819773 CTATATATTA
*
2819783 TATATAAATTTCCAAAAATATTTTTAAAAAC
1 TATAT-AATTTTCAAAAATATTTTTAAAAAC
* * *
2819814 TATATAATTTTCAAAAATGTCTTTAAGAAC
1 TATATAATTTTCAAAAATATTTTTAAAAAC
*
2819844 CATATAATTTTCAAAAATA-TTTTAAAAA
1 TATATAATTTTCAAAAATATTTTTAAAAA
2819872 TCATATATTA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
29 7 0.14
30 38 0.76
31 5 0.10
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.39
Consensus pattern (30 bp):
TATATAATTTTCAAAAATATTTTTAAAAAC
Found at i:2819949 original size:38 final size:37
Alignment explanation
Indices: 2819845--2820040 Score: 184
Period size: 38 Copynumber: 5.1 Consensus size: 37
2819835 TTTAAGAACC
*
2819845 ATATA-ATTTTCAAAAATATTTTAAAAA-TCATATATT
1 ATATATATTTTCAAAAATGTTTTAAAAACT-ATATATT
* *
2819881 ATATATGTTTTC-AAAATGTTTTTTCAAAAAATTATATATTCT
1 ATATATATTTTCAAAAATG--TTTT--AAAAACTATATA-T-T
*
2819923 ATATTTATTTTC-AAAATGTTTTAAAAACTATATAATAT
1 ATATATATTTTCAAAAATGTTTTAAAAACTATAT-AT-T
* *
2819961 ATATATATTTTCAAAAATGTCTTGAAAACTATATATT
1 ATATATATTTTCAAAAATGTTTTAAAAACTATATATT
* * * *
2819998 ATATTTATTTTCAAAAACGTTTTAAAAACCCATATAAT
1 ATATATATTTTCAAAAATGTTTTAAAAA-CTATATATT
2820036 ATATA
1 ATATA
2820041 AATGTTTTCA
Statistics
Matches: 133, Mismatches: 16, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
36 10 0.08
37 30 0.23
38 40 0.30
39 20 0.15
40 14 0.11
41 2 0.02
42 17 0.13
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (37 bp):
ATATATATTTTCAAAAATGTTTTAAAAACTATATATT
Found at i:2820051 original size:77 final size:77
Alignment explanation
Indices: 2819908--2820053 Score: 215
Period size: 77 Copynumber: 1.9 Consensus size: 77
2819898 GTTTTTTCAA
* * * *
2819908 AAAATTATATATTCTATATTTATTTTCAAAATGTTTTAAAAACTATATAATATATATATATTTTC
1 AAAACTATATATTCTATATTTATTTTCAAAACGTTTTAAAAACCATATAATATATAAATATTTTC
2819973 AAAAATGTCTTG
66 AAAAATGTCTTG
*
2819985 AAAACTATATA-T-TATATTTATTTTCAAAAACGTTTTAAAAACCCATATAATATATAAATGTTT
1 AAAACTATATATTCTATATTTATTTTC-AAAACGTTTTAAAAA-CCATATAATATATAAATATTT
2820048 TCAAAA
64 TCAAAA
2820054 TGAAAATGTT
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
75 13 0.21
76 15 0.24
77 34 0.55
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.43
Consensus pattern (77 bp):
AAAACTATATATTCTATATTTATTTTCAAAACGTTTTAAAAACCATATAATATATAAATATTTTC
AAAAATGTCTTG
Found at i:2820835 original size:29 final size:28
Alignment explanation
Indices: 2820760--2820935 Score: 163
Period size: 29 Copynumber: 6.0 Consensus size: 28
2820750 ATATTAACAT
* * *
2820760 TAAATATATTTTTTATTTTTATTTTAAAT
1 TAAAAATATATTTTATTTTTATTTT-AAC
* * * *
2820789 TATTAAATCTATTTTATTATTGTTTTAATC
1 TA-AAAATATATTTTATTTTTATTTTAA-C
2820819 TAAAAATATATTTTATTTTTATTTTAAC
1 TAAAAATATATTTTATTTTTATTTTAAC
* * * **
2820847 TTAAAATATATTTTAATCTTATCATAAC
1 TAAAAATATATTTTATTTTTATTTTAAC
*
2820875 TTAAAAATATATTTTATTTTTATCTTAAC
1 -TAAAAATATATTTTATTTTTATTTTAAC
*
2820904 TTTTAAAAATATATCTTATTTTTATTTTAAC
1 ---TAAAAATATATTTTATTTTTATTTTAAC
2820935 T
1 T
2820936 TATTACATAT
Statistics
Matches: 120, Mismatches: 22, Indels: 11
0.78 0.14 0.07
Matches are distributed among these distances:
28 25 0.21
29 49 0.41
30 19 0.16
31 27 0.22
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (28 bp):
TAAAAATATATTTTATTTTTATTTTAAC
Found at i:2820885 original size:57 final size:58
Alignment explanation
Indices: 2820754--2820915 Score: 175
Period size: 57 Copynumber: 2.8 Consensus size: 58
2820744 ATTCACATAT
* * * * * * **
2820754 TAACATTAAATATATTTTTTATTTTTATTTTAAATTATTAAATCTATTTTATTATTGTTT
1 TAAC-TTAAAAATATATTTTATTTTTATTTTAACTTA-TAAATATATTTTAATATTATCA
*
2820814 TAA-TCTAAAAATATATTTTATTTTTATTTTAACTTA-AAATATATTTTAATCTTATCA
1 TAACT-TAAAAATATATTTTATTTTTATTTTAACTTATAAATATATTTTAATATTATCA
* * *
2820871 TAACTTAAAAATATATTTTATTTTTATCTTAACTTTTAAAAATAT
1 TAACTTAAAAATATATTTTATTTTTATTTTAACTTATAAATATAT
2820916 ATCTTATTTT
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
57 47 0.54
58 9 0.10
59 28 0.32
60 3 0.03
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.56
Consensus pattern (58 bp):
TAACTTAAAAATATATTTTATTTTTATTTTAACTTATAAATATATTTTAATATTATCA
Found at i:2821042 original size:31 final size:31
Alignment explanation
Indices: 2821001--2821073 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
2820991 AAATTATTAA
*
2821001 ATATAATTTATCCCTTA-TTTTAACATAA-AGT
1 ATATATTTTAT-CCTTATTTTTAACATAATA-T
* *
2821032 ATATATTTTATTCTTATTTTTAACTTAATAT
1 ATATATTTTATCCTTATTTTTAACATAATAT
*
2821063 GTATATTTTAT
1 ATATATTTTAT
2821074 TTCTATTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 4 0.11
31 31 0.86
32 1 0.03
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.55
Consensus pattern (31 bp):
ATATATTTTATCCTTATTTTTAACATAATAT
Found at i:2821050 original size:30 final size:30
Alignment explanation
Indices: 2820753--2821084 Score: 103
Period size: 29 Copynumber: 11.1 Consensus size: 30
2820743 AATTCACATA
* *
2820753 TTAACATTAA-ATATATTTTTTATTTTTATT
1 TTAACA-TAATATATATATTTTATTCTTATT
* * * * *
2820783 TTAA-ATTATTAAATCTATTTTATTATTGTT
1 TTAACA-TAATATATATATTTTATTCTTATT
* *
2820813 TTAATC-TAA-AAATATATTTTATTTTTATT
1 TTAA-CATAATATATATATTTTATTCTTATT
* * *
2820842 TTAACTTAA-A-ATATATTTTAATCTTATC
1 TTAACATAATATATATATTTTATTCTTATT
* * * * *
2820870 ATAACTTAA-AAATATATTTTATTTTTATC
1 TTAACATAATATATATATTTTATTCTTATT
* * * *
2820899 TTAACTTTTAA-AAATATATCTTATTTTTATT
1 TTAAC--ATAATATATATATTTTATTCTTATT
* * * ** * **
2820930 TTAACTTATTACATATATTACATTATTAAC
1 TTAACATAATATATATATTTTATTCTTATT
** * * * * **
2820960 TTAAGTTATTAAATATATTCTAGTC-TACC
1 TTAACATAATATATATATTTTATTCTTATT
* * * *
2820989 TTAA-ATTATTAAATATAATTTATCCCTTATT
1 TTAACA-TAATATATATATTTTAT-TCTTATT
2821020 TTAACATAA-AGTATATATTTTATTCTTATTT
1 TTAACATAATA-TATATATTTTATTCTTA-TT
* *
2821051 TTAACTTAATATGTATATTTTATT-TCTATT
1 TTAACATAATATATATATTTTATTCT-TATT
2821081 TTAA
1 TTAA
2821085 TTTAAAAATA
Statistics
Matches: 239, Mismatches: 47, Indels: 32
0.75 0.15 0.10
Matches are distributed among these distances:
28 25 0.10
29 73 0.31
30 70 0.29
31 69 0.29
32 2 0.01
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.55
Consensus pattern (30 bp):
TTAACATAATATATATATTTTATTCTTATT
Found at i:2821148 original size:29 final size:29
Alignment explanation
Indices: 2821032--2821155 Score: 97
Period size: 31 Copynumber: 4.1 Consensus size: 29
2821022 AACATAAAGT
* * * *
2821032 ATATATTTTATTCTTATTTTTAACTTAATAT
1 ATATATTTTGTTTTTA-TTTTAATTTAA-AA
* * *
2821063 GTATATTTTATTTCTATTTTAATTTAAAA
1 ATATATTTTGTTTTTATTTTAATTTAAAA
* * *
2821092 ATAT-TTATGCTAATTTTGTTTTGATTTAAAA
1 ATATATTTTG-T--TTTTATTTTAATTTAAAA
*
2821123 ATATATTTTGTTTTTATCTTAATTTAAAA
1 ATATATTTTGTTTTTATTTTAATTTAAAA
2821152 ATAT
1 ATAT
2821156 TATAAGAATA
Statistics
Matches: 74, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
28 3 0.04
29 24 0.32
30 10 0.14
31 33 0.45
32 4 0.05
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (29 bp):
ATATATTTTGTTTTTATTTTAATTTAAAA
Found at i:2821235 original size:58 final size:59
Alignment explanation
Indices: 2821172--2821303 Score: 153
Period size: 59 Copynumber: 2.2 Consensus size: 59
2821162 AATATAAATA
* * *
2821172 TTTAAGTTAAGGTAAGAA-AAAAT-TATTTTTTAAGTTAATAAAAAAATTAAA-ATATATT
1 TTTAAGTTAAGATAAGAATAAAATATA-TTTCTAAGTTAAGAAAAAAA-TAAACATATATT
* * *
2821230 TTTAAGTTAAAATAAGAATAAAATATATTTCTAAGTTAAGATAAGAATAAACTATATATT
1 TTTAAGTTAAGATAAGAATAAAATATATTTCTAAGTTAAGAAAAAAATAAAC-ATATATT
2821290 TTTAATGTTAAGAT
1 TTTAA-GTTAAGAT
2821304 GTTAATTTAA
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
58 20 0.32
59 21 0.34
60 14 0.23
61 7 0.11
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (59 bp):
TTTAAGTTAAGATAAGAATAAAATATATTTCTAAGTTAAGAAAAAAATAAACATATATT
Found at i:2821252 original size:29 final size:29
Alignment explanation
Indices: 2821157--2821300 Score: 138
Period size: 29 Copynumber: 5.0 Consensus size: 29
2821147 TAAAAATATT
* *
2821157 ATAAGAATATAA-ATA--TTTAAGTTAAG
1 ATAAGAATAAAATATATTTTTAAGTTAAA
*
2821183 GTAAGAA-AAAAT-TATTTTTTAAGTTAATA
1 ATAAGAATAAAATATA-TTTTTAAGTTAA-A
*
2821212 A-AAAAATTAAAATATATTTTTAAGTTAAA
1 ATAAGAA-TAAAATATATTTTTAAGTTAAA
* *
2821241 ATAAGAATAAAATATATTTCTAAGTTAAG
1 ATAAGAATAAAATATATTTTTAAGTTAAA
2821270 ATAAGAATAAACTATATATTTTTAATGTTAA
1 ATAAGAATAAA--ATATATTTTTAA-GTTAA
2821301 GATGTTAATT
Statistics
Matches: 97, Mismatches: 9, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
25 5 0.05
26 6 0.06
28 14 0.14
29 33 0.34
30 21 0.22
31 13 0.13
32 5 0.05
ACGTcount: A:0.52, C:0.01, G:0.08, T:0.38
Consensus pattern (29 bp):
ATAAGAATAAAATATATTTTTAAGTTAAA
Found at i:2821906 original size:13 final size:15
Alignment explanation
Indices: 2821888--2821917 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2821878 TAAGTGTCAA
2821888 TTTTTT-TTAATATT
1 TTTTTTCTTAATATT
2821902 TTTTTTCTTAATATT
1 TTTTTTCTTAATATT
2821917 T
1 T
2821918 GTTATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTTCTTAATATT
Found at i:2822200 original size:70 final size:71
Alignment explanation
Indices: 2822050--2822201 Score: 164
Period size: 70 Copynumber: 2.2 Consensus size: 71
2822040 ATATTTTATT
* * * * * *
2822050 ACTTTTTATTAGAGATTCAATTTTTTAATATTTGTTATTATGAATATACTCTTAAAATTTATTTT
1 ACTTATTATTAGAGACTCAATTTTTCAATACTTGTTATTATGAAGATACCCTTAAAATTTATTTT
*
2822115 TTTAAT
66 TTTAAC
** * * *
2822121 TTTTATTATTAGGGACT-AATTTTTCAATACTTGTTGTTATG-AGCTACCCTTAAAATTTATTTT
1 ACTTATTATTAGAGACTCAATTTTTCAATACTTGTTATTATGAAGATACCCTTAAAATTTATTTT
2822184 TTTCAAC
66 TTT-AAC
*
2822191 ACTTGTTATTA
1 ACTTATTATTA
2822202 TGAACAATTA
Statistics
Matches: 65, Mismatches: 15, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
69 22 0.34
70 31 0.48
71 12 0.18
ACGTcount: A:0.30, C:0.09, G:0.08, T:0.53
Consensus pattern (71 bp):
ACTTATTATTAGAGACTCAATTTTTCAATACTTGTTATTATGAAGATACCCTTAAAATTTATTTT
TTTAAC
Found at i:2824487 original size:31 final size:31
Alignment explanation
Indices: 2824428--2824497 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
2824418 AAAAGTAATA
*
2824428 TTTTT-GTCACTTACATTATCAGTTTATAAC
1 TTTTTGGTCACTTACATTATCAGTATATAAC
*
2824458 TTTTTGGTCACTTACGTTATC-GATATATAAC
1 TTTTTGGTCACTTACATTATCAG-TATATAAC
**
2824489 AATTTGGTC
1 TTTTTGGTC
2824498 CCTGAGATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 6 0.18
31 28 0.82
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (31 bp):
TTTTTGGTCACTTACATTATCAGTATATAAC
Found at i:2824623 original size:31 final size:31
Alignment explanation
Indices: 2824575--2824656 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 31
2824565 TGACCCACAC
*
2824575 TAGATAAAAT-ACTAATTTAACCCTT-AAATT
1 TAGATAAAATAAC-AATTTAACCCTTAAAATA
* *
2824605 TAAGATAAATTAACAATTTAACTCTTAAAATA
1 T-AGATAAAATAACAATTTAACCCTTAAAATA
*
2824637 TAGATAAAATATCAATTTAA
1 TAGATAAAATAACAATTTAA
2824657 GCTAAGAATC
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
30 1 0.02
31 36 0.82
32 7 0.16
ACGTcount: A:0.51, C:0.10, G:0.04, T:0.35
Consensus pattern (31 bp):
TAGATAAAATAACAATTTAACCCTTAAAATA
Found at i:2826644 original size:41 final size:41
Alignment explanation
Indices: 2826517--2826675 Score: 142
Period size: 41 Copynumber: 3.8 Consensus size: 41
2826507 AGTGGTAAAT
* * *
2826517 TAGTGGCGTTTATACCACAAACGCCGCAATAG-ATTACACATA
1 TAGTGGCGTTTTTA-GACAAACGCCGCAATAGTATTACTCA-A
*** * * *
2826559 TAGTGGCGTTTTTTCCCTCAAATGCCGTAATAGTGA-TAATCAA
1 TAGTGGCG-TTTTT-AGACAAACGCCGCAATAGT-ATTACTCAA
*
2826602 TAGTTGCGTTTTTAGACAAACGCCGCAATAGTATTACTCAA
1 TAGTGGCGTTTTTAGACAAACGCCGCAATAGTATTACTCAA
* *
2826643 TAGTGGCATTTTTAGACAAAACGCCACAATAGT
1 TAGTGGCGTTTTTAGAC-AAACGCCGCAATAGT
2826676 GGTAAATAAG
Statistics
Matches: 94, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
40 1 0.01
41 35 0.37
42 27 0.29
43 26 0.28
44 4 0.04
45 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (41 bp):
TAGTGGCGTTTTTAGACAAACGCCGCAATAGTATTACTCAA
Found at i:2827429 original size:17 final size:17
Alignment explanation
Indices: 2827409--2827452 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
2827399 AAATGTATAT
* *
2827409 AATATATTATTTTTTAA
1 AATATATTATTTCTGAA
*
2827426 AATATATAATTTCTGAA
1 AATATATTATTTCTGAA
2827443 AATATATTAT
1 AATATATTAT
2827453 ATAGTTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
AATATATTATTTCTGAA
Found at i:2830030 original size:24 final size:22
Alignment explanation
Indices: 2830003--2830051 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 22
2829993 TTAACTTTAG
2830003 CAATTAA-GCCAACCTTTTCATCTT
1 CAATTAATG-CAACC-TTT-ATCTT
2830027 CAA-TAATGCAACCTTTATCTT
1 CAATTAATGCAACCTTTATCTT
2830048 CAAT
1 CAAT
2830052 AGAGGTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
21 8 0.35
22 3 0.13
23 8 0.35
24 4 0.17
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.37
Consensus pattern (22 bp):
CAATTAATGCAACCTTTATCTT
Found at i:2833568 original size:21 final size:21
Alignment explanation
Indices: 2833542--2833583 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2833532 AGGTATTGCC
2833542 AAAAGAACCGGATGAGATACT
1 AAAAGAACCGGATGAGATACT
2833563 AAAAGAACCGGATGAGATACT
1 AAAAGAACCGGATGAGATACT
2833584 GGCTTCGAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.14, G:0.24, T:0.14
Consensus pattern (21 bp):
AAAAGAACCGGATGAGATACT
Found at i:2834335 original size:54 final size:54
Alignment explanation
Indices: 2834252--2834369 Score: 166
Period size: 54 Copynumber: 2.2 Consensus size: 54
2834242 CATCATTGCC
* *
2834252 ACCATAAGATGTGATACTCGGTATCGGTTCAAAATCACTAGTGAATGATTTCTT-
1 ACCATAAGAAGTGATACTCGGTATCGGTTCAAAATCACCAGTGAATGATTT-TTG
* * *
2834306 ACCATAAGAAGTGATGCTCGGTATGGGTTCAAAATCACCGGTGAATGATTTTTG
1 ACCATAAGAAGTGATACTCGGTATCGGTTCAAAATCACCAGTGAATGATTTTTG
*
2834360 GCCATAAGAA
1 ACCATAAGAA
2834370 ATGCTCAGTC
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
53 2 0.04
54 55 0.96
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (54 bp):
ACCATAAGAAGTGATACTCGGTATCGGTTCAAAATCACCAGTGAATGATTTTTG
Found at i:2834530 original size:54 final size:54
Alignment explanation
Indices: 2834439--2834545 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 54
2834429 ATCATCGCCT
* * * *
2834439 CCATAAGAAGTGGTGCTTGGTCTCGGTTTGAAATCACTAGTGAATGATTTCTTA
1 CCATAAGAAGTGATGCTCGGTCTCAGTTTCAAATCACTAGTGAATGATTTCTTA
* * *
2834493 CCATAAGATGTGATGCTCGGTCTCAG-TTCAAATTCACTAGTTAATGTTTTCTT
1 CCATAAGAAGTGATGCTCGGTCTCAGTTTCAAA-TCACTAGTGAATGATTTCTT
2834546 CACTCCTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
53 5 0.11
54 40 0.89
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (54 bp):
CCATAAGAAGTGATGCTCGGTCTCAGTTTCAAATCACTAGTGAATGATTTCTTA
Found at i:2834679 original size:135 final size:134
Alignment explanation
Indices: 2834306--2834794 Score: 610
Period size: 135 Copynumber: 3.6 Consensus size: 134
2834296 ATGATTTCTT
* * * ** * *
2834306 ACCATAAGAAGTGATGCTCGGTATGGGTTCAAAATCACCGGTGAATGATTTTTGGCCATAAGAA-
1 ACCATAAGAAGTGGTGCTCGGTCTCGGTTCAAAATCACTAGTGAATGATTTCTGACCATAAGAAG
* * * * *
2834370 --ATGCTCAGTCTCGGTTCAAAATTGCTAGGAAAAGTTTTCTTCACTCCTTTAAGATCAACATCA
66 TGATGCTCGGTCTCGGTTCAAATTTACTA-GTAATGTTTTCTTCACTCCTTTAAGATCAACATCA
2834433 TCGCC
130 TCGCC
* * ** * *
2834438 TCCATAAGAAGTGGTGCTTGGTCTCGGTTTGAAATCACTAGTGAATGATTTCTTACCATAAGATG
1 ACCATAAGAAGTGGTGCTCGGTCTCGGTTCAAAATCACTAGTGAATGATTTCTGACCATAAGAAG
* *
2834503 TGATGCTCGGTCTCAGTTCAAATTCACTAGTTAATGTTTTCTTCACTCCTTTTAAGATCAACATC
66 TGATGCTCGGTCTCGGTTCAAATTTACTAG-TAATGTTTTCTTCACTCC-TTTAAGATCAACATC
*
2834568 ATTGCC
129 ATCGCC
* * *
2834574 ACCATAAGAAGTGGTGCTTGGTCTCGGCTCAAAATCAATAGTGAATGATTT-TGACCATAA-AAC
1 ACCATAAGAAGTGGTGCTCGGTCTCGGTTCAAAATCACTAGTGAATGATTTCTGACCATAAGAA-
*
2834637 GTGATGCTCGGTCTCGGTTCAAATTTACTAGTAATTGATTTCTTCACTCCTTTAAGATCAACATC
65 GTGATGCTCGGTCTCGGTTCAAATTTACTAGTAA-TGTTTTCTTCACTCCTTTAAGATCAACATC
2834702 ATCGCC
129 ATCGCC
* * * * * *
2834708 GCCATAAGATGTGGTACTCGATCTCGGTTTAAAATCACTAGTGAATGATTTCTGGCCATAAGAAG
1 ACCATAAGAAGTGGTGCTCGGTCTCGGTTCAAAATCACTAGTGAATGATTTCTGACCATAAGAAG
*
2834773 TGGTGCTCGGTCTCGGTTCAAA
66 TGATGCTCGGTCTCGGTTCAAA
2834795 ATAGCTCTCC
Statistics
Matches: 306, Mismatches: 42, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
132 51 0.17
134 68 0.22
135 119 0.39
136 68 0.22
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (134 bp):
ACCATAAGAAGTGGTGCTCGGTCTCGGTTCAAAATCACTAGTGAATGATTTCTGACCATAAGAAG
TGATGCTCGGTCTCGGTTCAAATTTACTAGTAATGTTTTCTTCACTCCTTTAAGATCAACATCAT
CGCC
Found at i:2834785 original size:270 final size:268
Alignment explanation
Indices: 2834306--2834794 Score: 685
Period size: 270 Copynumber: 1.8 Consensus size: 268
2834296 ATGATTTCTT
* * * * *
2834306 ACCATAAGAAGTGATGCTCGGTATGGGTTCAAAATCACCGGTGAATGATTTTTGGCCATAAGAAA
1 ACCATAAGAAGTGATGCTCGGTATCGGCTCAAAATCAACAGTGAATGATTTTTGACCATAAGAAA
* *
2834371 TGCTCAGTCTCGGTTCAAAATTGCTAGGAAAAGTTTTCTTCACTCCTTTAAGATCAACATCATCG
66 TGCTCAGTCTCGGTTCAAAATTACTAGGAAAAGATTTCTTCACTCCTTTAAGATCAACATCATCG
* * * * * *
2834436 CCTCCATAAGAAGTGGTGCTTGGTCTCGGTTTGAAATCACTAGTGAATGATTTCTTACCATAAGA
131 CCGCCATAAGAAGTGGTACTCGATCTCGGTTTAAAATCACTAGTGAATGATTTCTGACCATAAGA
*
2834501 TGTGATGCTCGGTCTCAGTTCAAATTCACTAGTTAATGTTTTCTTCACTCCTTTTAAGATCAACA
196 AGTGATGCTCGGTCTCAGTTCAAATTCACTAGTTAATGTTTTCTTCACTCCTTTTAAGATCAACA
2834566 TCATTGCC
261 TCATTGCC
* * * *
2834574 ACCATAAGAAGTGGTGCTTGGTCTCGGCTCAAAATCAATAGTGAATGA-TTTTGACCATAA-AAC
1 ACCATAAGAAGTGATGCTCGGTATCGGCTCAAAATCAACAGTGAATGATTTTTGACCATAAGAA-
* * * **
2834637 GTGATGCTCGGTCTCGGTTCAAATTTACTAGTAATTGATTTCTTCACTCCTTTAAGATCAACATC
65 ---ATGCTCAGTCTCGGTTCAAAATTACTAGGAAAAGATTTCTTCACTCCTTTAAGATCAACATC
* *
2834702 ATCGCCGCCATAAGATGTGGTACTCGATCTCGGTTTAAAATCACTAGTGAATGATTTCTGGCCAT
127 ATCGCCGCCATAAGAAGTGGTACTCGATCTCGGTTTAAAATCACTAGTGAATGATTTCTGACCAT
* *
2834767 AAGAAGTGGTGCTCGGTCTCGGTTCAAA
192 AAGAAGTGATGCTCGGTCTCAGTTCAAA
2834795 ATAGCTCTCC
Statistics
Matches: 190, Mismatches: 27, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
266 2 0.01
267 11 0.06
268 40 0.21
270 137 0.72
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (268 bp):
ACCATAAGAAGTGATGCTCGGTATCGGCTCAAAATCAACAGTGAATGATTTTTGACCATAAGAAA
TGCTCAGTCTCGGTTCAAAATTACTAGGAAAAGATTTCTTCACTCCTTTAAGATCAACATCATCG
CCGCCATAAGAAGTGGTACTCGATCTCGGTTTAAAATCACTAGTGAATGATTTCTGACCATAAGA
AGTGATGCTCGGTCTCAGTTCAAATTCACTAGTTAATGTTTTCTTCACTCCTTTTAAGATCAACA
TCATTGCC
Found at i:2840730 original size:14 final size:14
Alignment explanation
Indices: 2840711--2840770 Score: 59
Period size: 14 Copynumber: 4.2 Consensus size: 14
2840701 CAAATATTCA
*
2840711 AAAAAAGTAAATAT
1 AAAAAATTAAATAT
* *
2840725 AAAAAATAAAAAAT
1 AAAAAATTAAATAT
2840739 -AAAAATTAAATTACT
1 AAAAAATTAAA-TA-T
*
2840754 AAAAAATTGAATAT
1 AAAAAATTAAATAT
2840768 AAA
1 AAA
2840771 TATTAAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 9 0.24
14 16 0.43
15 3 0.08
16 9 0.24
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.23
Consensus pattern (14 bp):
AAAAAATTAAATAT
Found at i:2841541 original size:10 final size:10
Alignment explanation
Indices: 2841526--2841574 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
2841516 ATATCAATTT
*
2841526 AAAATATAAC
1 AAAATATAAA
2841536 AAAATATAAA
1 AAAATATAAA
*
2841546 AAAATAAAAA
1 AAAATATAAA
2841556 TAAAATA-AAA
1 -AAAATATAAA
2841566 AAAATATAA
1 AAAATATAA
2841575 TTATAATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 6 0.17
10 23 0.66
11 6 0.17
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (10 bp):
AAAATATAAA
Found at i:2841557 original size:16 final size:15
Alignment explanation
Indices: 2841536--2841574 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
2841526 AAAATATAAC
2841536 AAAATATAAAAAAATA
1 AAAATATAAAAAAA-A
*
2841552 AAAATA-AAATAAAA
1 AAAATATAAAAAAAA
2841566 AAAATATAA
1 AAAATATAA
2841575 TTATAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 8 0.38
16 6 0.29
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAATATAAAAAAAA
Found at i:2841560 original size:14 final size:14
Alignment explanation
Indices: 2841525--2841571 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
2841515 TATATCAATT
2841525 TAAAATATAACAAAATA
1 TAAAATA-AA-AAAA-A
2841542 TAAAA-AAATAAAAA
1 TAAAATAAA-AAAAA
2841556 TAAAATAAAAAAAA
1 TAAAATAAAAAAAA
2841570 TA
1 TA
2841572 TAATTATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 13 0.46
15 9 0.32
16 1 0.04
17 5 0.18
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (14 bp):
TAAAATAAAAAAAA
Found at i:2841582 original size:20 final size:20
Alignment explanation
Indices: 2841536--2841586 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2841526 AAAATATAAC
2841536 AAAATATAAAAAAATAAAAAT
1 AAAATA-AAAAAAATAAAAAT
* *
2841557 AAAATAAAAAAAATATAATT
1 AAAATAAAAAAAATAAAAAT
*
2841577 ATAATAAAAA
1 AAAATAAAAA
2841587 CATATTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 21 0.78
21 6 0.22
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (20 bp):
AAAATAAAAAAAATAAAAAT
Found at i:2841585 original size:19 final size:19
Alignment explanation
Indices: 2841526--2841591 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
2841516 ATATCAATTT
2841526 AAAATATAACA-AAATATAAA
1 AAAATATAA-ATAAA-ATAAA
*
2841546 AAAATAAAAATAAAATAAAA
1 AAAATATAAATAAAAT-AAA
* *
2841566 AAAATATAATTATAATAAA
1 AAAATATAAATAAAATAAA
*
2841585 AACATAT
1 AAAATAT
2841592 TTTATATAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 12 0.31
20 27 0.69
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAATATAAATAAAATAAA
Found at i:2842443 original size:23 final size:22
Alignment explanation
Indices: 2842412--2842459 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
2842402 AAATATTTGT
2842412 TATGGATTTA-ATAATTTAAATAA
1 TATGGATTTATAT-ATTT-AATAA
*
2842435 TATGTATTTATATATTTAATAA
1 TATGGATTTATATATTTAATAA
2842457 TAT
1 TAT
2842460 AAATAATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 8 0.35
23 13 0.57
24 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (22 bp):
TATGGATTTATATATTTAATAA
Found at i:2850076 original size:17 final size:17
Alignment explanation
Indices: 2850054--2850087 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2850044 TAAAATGTTA
2850054 TGAATAT-ATGTTATATG
1 TGAATATGA-GTTATATG
2850071 TGAATATGAGTTATATG
1 TGAATATGAGTTATATG
2850088 ATTAAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.94
18 1 0.06
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (17 bp):
TGAATATGAGTTATATG
Found at i:2850525 original size:23 final size:24
Alignment explanation
Indices: 2850494--2850546 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
2850484 TTTGAGACAA
*
2850494 ACTTCGGTGCAAACCTATGTGG-C
1 ACTTTGGTGCAAACCTATGTGGTC
2850517 ACTTTGGTGCAAACCTATGTGGTC
1 ACTTTGGTGCAAACCTATGTGGTC
2850541 A-TTTGG
1 ACTTTGG
2850547 GATAATTATG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 26 0.93
24 2 0.07
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (24 bp):
ACTTTGGTGCAAACCTATGTGGTC
Found at i:2856863 original size:16 final size:16
Alignment explanation
Indices: 2856844--2856874 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2856834 ATAAAAATAC
*
2856844 TAAAATATTAATTTAT
1 TAAAAAATTAATTTAT
2856860 TAAAAAATTAATTTA
1 TAAAAAATTAATTTA
2856875 ATTAGTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAAAAATTAATTTAT
Found at i:2857445 original size:81 final size:81
Alignment explanation
Indices: 2857274--2857493 Score: 203
Period size: 81 Copynumber: 2.7 Consensus size: 81
2857264 TTTTTTTCTA
* * * * * * * * * *
2857274 CTTTAAGATTACCATCGTCTCCGTAAGCTGAAACATTTGGTCTCGGTTCGAAATCTTCGGTAAAT
1 CTTTCAGATTAGCATCGACCCCGTAAGCCGAAAGATTTGGCCTCGGCTCGAAATCTTCGGCAAAA
*
2857339 GATGATGATCTCTTTC
66 GATGACGATCTCTTTC
* * *
2857355 GTTTCAGATTAGCATC-ACCACCGTAAGCCGAAAGGTTTGGCCTCGGCTCGAAATCTTTGGCAAA
1 CTTTCAGATTAGCATCGACC-CCGTAAGCCGAAAGATTTGGCCTCGGCTCGAAATCTTCGGCAAA
*
2857419 AGATGACGATTTC-TTC
65 AGATGACGATCTCTTTC
* ** * * *
2857435 ACTTTTAGATTCTCGTCGTCCCCGTAAGCC-AAAGCATTTGGCCTCGGCTCGAGATCTTC
1 -CTTTCAGATTAGCATCGACCCCGTAAGCCGAAAG-ATTTGGCCTCGGCTCGAAATCTTC
2857494 ACAAAATGTG
Statistics
Matches: 111, Mismatches: 24, Indels: 8
0.78 0.17 0.06
Matches are distributed among these distances:
80 8 0.07
81 101 0.91
82 2 0.02
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (81 bp):
CTTTCAGATTAGCATCGACCCCGTAAGCCGAAAGATTTGGCCTCGGCTCGAAATCTTCGGCAAAA
GATGACGATCTCTTTC
Found at i:2858181 original size:31 final size:31
Alignment explanation
Indices: 2858121--2858187 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
2858111 AAAAAGTAAT
*
2858121 ATTTTTGTCACTTACGTTATCAGTTTATAA-
1 ATTTTTGTCACTTACGTTATCAGTATATAAC
2858151 ATTTTTAGTCACTTACGTTATC-GATATATAAC
1 ATTTTT-GTCACTTACGTTATCAG-TATATAAC
2858183 ATTTT
1 ATTTT
2858188 GGTCCTTGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
30 7 0.21
31 21 0.64
32 5 0.15
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.49
Consensus pattern (31 bp):
ATTTTTGTCACTTACGTTATCAGTATATAAC
Found at i:2861162 original size:78 final size:76
Alignment explanation
Indices: 2861014--2861175 Score: 177
Period size: 78 Copynumber: 2.1 Consensus size: 76
2861004 ATAAGAAAAT
* * * * *
2861014 AATATAATATTCTAAATCCTAATTAAAACACTAAAACCTATTTCAACTAAAATACCTAAAACAAA
1 AATATAATATCCTAAAACCTAATTAAAACACTAAAACCAATTTAAACTAAAATACCTAAAAAAAA
2861079 GATAAAACATAA
66 GAT-AAACATAA
* *
2861091 AA-ATAATATCCTAAAACTTAATTAAAAATACTAAAAACCAATTTAAACTAAAATA-C-AAAGAT
1 AATATAATATCCTAAAACCTAATT-AAAACACT-AAAACCAATTTAAACTAAAATACCTAAA-A-
* *
2861153 AAAATATAAAGATAA
62 AAAAGATAAACATAA
2861168 AATATAAT
1 AATATAAT
2861176 GTTTAAATAT
Statistics
Matches: 71, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
76 21 0.30
77 20 0.28
78 30 0.42
ACGTcount: A:0.59, C:0.13, G:0.02, T:0.26
Consensus pattern (76 bp):
AATATAATATCCTAAAACCTAATTAAAACACTAAAACCAATTTAAACTAAAATACCTAAAAAAAA
GATAAACATAA
Found at i:2861172 original size:13 final size:13
Alignment explanation
Indices: 2861139--2861174 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
2861129 CAATTTAAAC
*
2861139 TAAAATACAAAGA
1 TAAAATATAAAGA
2861152 TAAAATATAAAGA
1 TAAAATATAAAGA
2861165 TAAAATATAA
1 TAAAATATAA
2861175 TGTTTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.69, C:0.03, G:0.06, T:0.22
Consensus pattern (13 bp):
TAAAATATAAAGA
Found at i:2862819 original size:14 final size:15
Alignment explanation
Indices: 2862800--2862829 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2862790 TAAGCATCTG
2862800 ATAAAAT-AAAATAA
1 ATAAAATGAAAATAA
2862814 ATAAAATGAAAATAA
1 ATAAAATGAAAATAA
2862829 A
1 A
2862830 ACGAAATGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (15 bp):
ATAAAATGAAAATAA
Found at i:2864823 original size:62 final size:63
Alignment explanation
Indices: 2864712--2864835 Score: 157
Period size: 62 Copynumber: 2.0 Consensus size: 63
2864702 GTCGAGGGTT
*
2864712 TACCTATGTTCTATAGAAAATATGGACATAATTACCTATGTCTTTCGGGACATATAGACAGTA
1 TACCTATGTTCTATAGAAAATATGGACATAATTACCTAGGTCTTTCGGGACATATAGACAGTA
* * *
2864775 TACCTGTGTTCTA-AGAAACATATGGA-A-AATTTACCTAGGT-TCTTCGGGACCTATGGACAGT
1 TACCTATGTTCTATAGAAA-ATATGGACATAA-TTACCTAGGTCT-TTCGGGACATATAGACAGT
2864836 TGCCGAGGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
61 3 0.06
62 32 0.59
63 19 0.35
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (63 bp):
TACCTATGTTCTATAGAAAATATGGACATAATTACCTAGGTCTTTCGGGACATATAGACAGTA
Found at i:2865639 original size:21 final size:22
Alignment explanation
Indices: 2865604--2865646 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
2865594 GCCGAAAGTT
2865604 ACTGTAGCAAGGGTATCAGTAC
1 ACTGTAGCAAGGGTATCAGTAC
*
2865626 ACTGTAGC-AGGGTATCGGTAC
1 ACTGTAGCAAGGGTATCAGTAC
2865647 CATTGTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (22 bp):
ACTGTAGCAAGGGTATCAGTAC
Found at i:2865741 original size:19 final size:19
Alignment explanation
Indices: 2865719--2865762 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
2865709 CATAGAACTG
2865719 TTCATA-CAGTATAGTACTA
1 TTCATACCA-TATAGTACTA
*
2865738 TTCATACCATATATTACTA
1 TTCATACCATATAGTACTA
2865757 TTCATA
1 TTCATA
2865763 AAAATGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 21 0.91
20 2 0.09
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (19 bp):
TTCATACCATATAGTACTA
Found at i:2871514 original size:16 final size:16
Alignment explanation
Indices: 2871495--2871525 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2871485 ATATACTCAT
2871495 TAAATTAATTTTTTAA
1 TAAATTAATTTTTTAA
2871511 TAAATTAATTTTTTA
1 TAAATTAATTTTTTA
2871526 GTATTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TAAATTAATTTTTTAA
Found at i:2873996 original size:2 final size:2
Alignment explanation
Indices: 2873989--2874017 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2873979 ATAATTTTAA
2873989 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 A
2874018 ATCTTGTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2874165 original size:22 final size:22
Alignment explanation
Indices: 2874152--2874195 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2874142 TATATTTTAG
2874152 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
2874174 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
2874196 AATTTTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:2874258 original size:31 final size:31
Alignment explanation
Indices: 2874220--2874278 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
2874210 AGTTGTATGG
*
2874220 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATTTCAGTATTGCAAAACTAAA
2874251 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTGCAAAACT
2874279 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTGCAAAACTAAA
Found at i:2877486 original size:15 final size:15
Alignment explanation
Indices: 2877466--2877563 Score: 97
Period size: 15 Copynumber: 6.5 Consensus size: 15
2877456 ATTTTATTGG
*
2877466 TATGTGAAAATGTTA
1 TATGTGAAAATGTTC
* *
2877481 TATGTGAATATGTTT
1 TATGTGAAAATGTTC
* *
2877496 TATATGAAAAAGTTC
1 TATGTGAAAATGTTC
* *
2877511 TATGTGAAAATATGC
1 TATGTGAAAATGTTC
*
2877526 TAAGTGAAAATGTTC
1 TATGTGAAAATGTTC
* * *
2877541 TACGTGAAAATATCC
1 TATGTGAAAATGTTC
2877556 TATGTGAA
1 TATGTGAA
2877564 TATACTCTAC
Statistics
Matches: 66, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 66 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (15 bp):
TATGTGAAAATGTTC
Found at i:2877573 original size:30 final size:30
Alignment explanation
Indices: 2877509--2877576 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
2877499 ATGAAAAAGT
* * **
2877509 TCTATGTGAAAATATGCTAAGTGAAAATGT
1 TCTACGTGAAAATATCCTAAGTGAAAATAC
* *
2877539 TCTACGTGAAAATATCCTATGTGAATATAC
1 TCTACGTGAAAATATCCTAAGTGAAAATAC
2877569 TCTACGTG
1 TCTACGTG
2877577 GATAAAACAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (30 bp):
TCTACGTGAAAATATCCTAAGTGAAAATAC
Found at i:2884408 original size:15 final size:15
Alignment explanation
Indices: 2884341--2884408 Score: 57
Period size: 15 Copynumber: 4.5 Consensus size: 15
2884331 TTATTGGTAT
* * *
2884341 GTGAAATTGTTATAT
1 GTGAAAATGTTCTAA
* *
2884356 GTGAATATGTTTTATA
1 GTGAAAATGTTCTA-A
*
2884372 -TGAAAAAGTTCTAA
1 GTGAAAATGTTCTAA
*
2884386 GTGAAAATGTTCTAC
1 GTGAAAATGTTCTAA
2884401 GTGAAAAT
1 GTGAAAAT
2884409 ACCCTATGTG
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
14 1 0.02
15 41 0.98
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.38
Consensus pattern (15 bp):
GTGAAAATGTTCTAA
Found at i:2884598 original size:24 final size:24
Alignment explanation
Indices: 2884539--2884611 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
2884529 GATTCGAGGG
*
2884539 TTCTACGTGGTCCTTCGGGACAAT
1 TTCTACGTGGTCCTTCGGGACAAA
* **
2884563 TTTTATATGGTCCTTCGGGACAAA
1 TTCTACGTGGTCCTTCGGGACAAA
* *
2884587 TTCTACGCGGTCATTCGGGACAAA
1 TTCTACGTGGTCCTTCGGGACAAA
2884611 T
1 T
2884612 CTATGTGACA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (24 bp):
TTCTACGTGGTCCTTCGGGACAAA
Found at i:2885231 original size:16 final size:17
Alignment explanation
Indices: 2885200--2885233 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2885190 AATTTTCAAC
*
2885200 AAGTTTTTAAAGAGTCA
1 AAGTTTTGAAAGAGTCA
2885217 AAGTTTTGAAA-AGTCA
1 AAGTTTTGAAAGAGTCA
2885233 A
1 A
2885234 TATGACACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (17 bp):
AAGTTTTGAAAGAGTCA
Found at i:2888547 original size:21 final size:22
Alignment explanation
Indices: 2888523--2888740 Score: 177
Period size: 21 Copynumber: 10.1 Consensus size: 22
2888513 ACTTCGACTA
* *
2888523 TCGCATTGCGA-TAGTCCAAGT
1 TCGCGTTGCGATTATTCCAAGT
2888544 TCGCGTTGCGATTTATTCCAAGT
1 TCGCGTTGCGA-TTATTCCAAGT
* * *
2888567 T--TGTTGCGA-TAGTCGAAGT
1 TCGCGTTGCGATTATTCCAAGT
*
2888586 TCGCGTTGCGATTTATTCCAAAT
1 TCGCGTTGCGA-TTATTCCAAGT
2888609 T--CGTTGCGATTTATTCCAAGT
1 TCGCGTTGCGA-TTATTCCAAGT
* * *
2888630 T--CGTTGCGA-TAGTCGAGGT
1 TCGCGTTGCGATTATTCCAAGT
* * *
2888649 TCGCGTTGCG-GTAGTCGAAGT
1 TCGCGTTGCGATTATTCCAAGT
*
2888670 TCGCGTTGCGATTTATTCCAAAT
1 TCGCGTTGCGA-TTATTCCAAGT
* *
2888693 TCACGTTGCGATTTATTACAAGT
1 TCGCGTTGCGA-TTATTCCAAGT
2888716 TCGCGTTGCGATTTATTCCAAGT
1 TCGCGTTGCGA-TTATTCCAAGT
2888739 TC
1 TC
2888741 ATTGCGATAG
Statistics
Matches: 163, Mismatches: 23, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
19 17 0.10
21 78 0.48
23 68 0.42
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (22 bp):
TCGCGTTGCGATTATTCCAAGT
Found at i:2888575 original size:42 final size:42
Alignment explanation
Indices: 2888528--2888755 Score: 239
Period size: 42 Copynumber: 5.3 Consensus size: 42
2888518 GACTATCGCA
*
2888528 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTTG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
* *
2888570 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
* * * *
2888612 TTGCGATTTATTCCAAGTT--CGTTGCGA--TAGTCGAGGTTCGCG
1 TTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT--CG
* * *
2888654 TTGCGGTAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCACG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT--CG
* * *
2888698 TTGCGATTTATTACAAGTTCGCGTTGCGATTTATTCCAAGTTCA
1 TTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
2888742 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
2888756 AATCGCAACG
Statistics
Matches: 151, Mismatches: 25, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
40 16 0.11
42 74 0.49
44 31 0.21
46 30 0.20
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
Found at i:2888614 original size:63 final size:63
Alignment explanation
Indices: 2888537--2888748 Score: 241
Period size: 63 Copynumber: 3.3 Consensus size: 63
2888527 ATTGCGATAG
*
2888537 TCCAAGTTCGCGTTGCGATTTATTCCAAGTTTGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* * * *
2888602 TCCAAATTCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAGGTTCGCGTTGCG--GTAG
1 TCCAAGTTCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* * *
2888663 TCGAAGTTCGCGTTGCGATTTATTCCAAATTCACGTTGCGATTTATTAC-AAGTTCGCGTTGCGA
1 TCCAAGTT--CGTTGCGATTTATTCCAAGTT--CGTTGCGA--TAGT-CGAAGTTCGCGTTGCGA
2888727 TTTAT
59 TTTAT
*
2888732 TCCAAGTTCATTGCGAT
1 TCCAAGTTCGTTGCGAT
2888749 AGTCCAAAAT
Statistics
Matches: 124, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
61 8 0.06
63 67 0.54
65 15 0.12
67 24 0.19
68 1 0.01
69 9 0.07
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (63 bp):
TCCAAGTTCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
Found at i:2889358 original size:5 final size:5
Alignment explanation
Indices: 2889348--2889426 Score: 122
Period size: 5 Copynumber: 15.6 Consensus size: 5
2889338 GCCGTCCATC
* * *
2889348 TCGGG TCGGG TCGGG TCGGG TCGGG TCGTG TCGTG TCGTG TCGTGG TCGGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCGGG
2889399 TCGGG TCGGG TCGGG TCGGG TCGGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCG
2889427 TGGTAATACG
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
5 67 0.94
6 4 0.06
ACGTcount: A:0.00, C:0.20, G:0.54, T:0.25
Consensus pattern (5 bp):
TCGGG
Found at i:2896429 original size:22 final size:22
Alignment explanation
Indices: 2896401--2896446 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
2896391 TTAACATGCC
2896401 ATATGATCCACGGAAGCCTGCT
1 ATATGATCCACGGAAGCCTGCT
2896423 ATATGATCCACGGAAGCCTGCT
1 ATATGATCCACGGAAGCCTGCT
2896445 AT
1 AT
2896447 GTCAAGATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (22 bp):
ATATGATCCACGGAAGCCTGCT
Found at i:2898062 original size:14 final size:14
Alignment explanation
Indices: 2898020--2898063 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
2898010 TAAGAAGGTG
2898020 CATACACACACATA
1 CATACACACACATA
2898034 C--ACACACACATA
1 CATACACACACATA
2898046 CATACACACACATA
1 CATACACACACATA
2898060 CATA
1 CATA
2898064 ACTTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.43
14 16 0.57
ACGTcount: A:0.50, C:0.36, G:0.00, T:0.14
Consensus pattern (14 bp):
CATACACACACATA
Found at i:2899371 original size:19 final size:19
Alignment explanation
Indices: 2899347--2899395 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
2899337 AGTTAACCTA
2899347 TTTTGTTTCAAATGATCAC
1 TTTTGTTTCAAATGATCAC
2899366 TTTTGTTTCAAATGATCAC
1 TTTTGTTTCAAATGATCAC
*
2899385 TTTTATTTCAA
1 TTTTGTTTCAA
2899396 GAATAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.27, C:0.14, G:0.08, T:0.51
Consensus pattern (19 bp):
TTTTGTTTCAAATGATCAC
Found at i:2900947 original size:74 final size:74
Alignment explanation
Indices: 2900822--2900970 Score: 246
Period size: 74 Copynumber: 2.0 Consensus size: 74
2900812 TATGATAATT
*
2900822 TTAGCTCTAAAACTCTTTTGACGTTGGTTTGATATTGCAATAATCTTTCTTGTTGTTATCCATTT
1 TTAGCTCTAAAACTCTTTTGACGTTGGTTTGATATTGCAATAATCTATCTTGTTGTTATCCATTT
2900887 GAATCTTGG
66 GAATCTTGG
* * *
2900896 TTAGCTCTAAAACTCTTTTGATGTTGGTTTGATATTGCAGTAAAT-TATCTTGTTGTTCTCCATT
1 TTAGCTCTAAAACTCTTTTGACGTTGGTTTGATATTGCAAT-AATCTATCTTGTTGTTATCCATT
2900960 TGAATCTTGG
65 TGAATCTTGG
2900970 T
1 T
2900971 ATCTTTTTTA
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
74 67 0.96
75 3 0.04
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (74 bp):
TTAGCTCTAAAACTCTTTTGACGTTGGTTTGATATTGCAATAATCTATCTTGTTGTTATCCATTT
GAATCTTGG
Found at i:2901671 original size:21 final size:21
Alignment explanation
Indices: 2901645--2901685 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2901635 TTGTTATGAT
* *
2901645 GCTTACATGACAATTTACAAA
1 GCTTACATGAAAATATACAAA
2901666 GCTTACATGAAAATATACAA
1 GCTTACATGAAAATATACAA
2901686 TACTGATGTG
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:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (21 bp):
GCTTACATGAAAATATACAAA
Found at i:2904565 original size:119 final size:120
Alignment explanation
Indices: 2904379--2904817 Score: 528
Period size: 129 Copynumber: 3.5 Consensus size: 120
2904369 TAGTATAATC
*
2904379 TTAAATTCTTAACTAT-AAAA-ATATATTTTATTATTTTTCTTAATTTATCGAATATATATTTTT
1 TTAAATTCTTAACTATAAAAATATATATTTTATTATTTTTCTTAATTTATCGAATATATATATTT
*
2904442 TGGTTTAAAGTAGGCCAAGTTTATTATTTGAGGTAGGAATATATATTTAAAATAT
66 TGGTTTAAAGTAGGCCAAGTTTATTATTTGAGTTAGGAATATATATTTAAAATAT
* *
2904497 TTAAATTCTTAACTATAAAAATATATATTTTATTACTTTT-TAAATTTATCGAATATATATATTT
1 TTAAATTCTTAACTATAAAAATATATATTTTATTATTTTTCTTAATTTATCGAATATATATATTT
* *
2904561 TGGTTTAAAGTAGGCCAAGTTTATTATTTAAGTTAAGAATATATATTTAAAATATTTTAAAATAT
66 TGGTTTAAAGTAGGCCAAGTTTATTATTTGAGTT-AG--GA-ATA--T---ATA-TTTAAAATAT
* *
2904626 TTAAATTCTTAACTATAAAAATATATTTTTTAAATGT-TTTTTCTTAATTTATCAAATATATATA
1 TTAAATTCTTAACTATAAAAATATATATTTT--AT-TATTTTTCTTAATTTATCGAATATATATA
* * *
2904690 TTTTAGTTTAAAGTAGACCAAGTTTATTA-TTGAAGTTAAGAATATATATTTAAAATATATGT
63 TTTTGGTTTAAAGTAGGCCAAGTTTATTATTTG-AGTTAGGAATATATATTT-AAA-ATA--T
*
2904752 TTAAATTCTTAACTATAAAAATATATATAATTTATTATTTTTTTTCTTAATTTATTGAATATATA
1 TTAAATTCTTAACTATAAAAATATATAT--TTTATTA---TTTTTCTTAATTTATCGAATATATA
2904817 T
61 T
2904818 TTTAAAATAT
Statistics
Matches: 276, Mismatches: 18, Indels: 43
0.82 0.05 0.13
Matches are distributed among these distances:
118 16 0.06
119 58 0.21
120 19 0.07
122 4 0.01
123 9 0.03
124 3 0.01
125 2 0.01
126 31 0.11
128 9 0.03
129 65 0.24
131 9 0.03
132 51 0.18
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (120 bp):
TTAAATTCTTAACTATAAAAATATATATTTTATTATTTTTCTTAATTTATCGAATATATATATTT
TGGTTTAAAGTAGGCCAAGTTTATTATTTGAGTTAGGAATATATATTTAAAATAT
Found at i:2904711 original size:132 final size:130
Alignment explanation
Indices: 2904482--2904817 Score: 445
Period size: 132 Copynumber: 2.6 Consensus size: 130
2904472 AGGTAGGAAT
* * *
2904482 ATATATTTAAAATATTTAAATTCTTAACTATAAAAATATATATTTT-ATTACTTTT-TAAATTTA
1 ATAT-TTTAAAATATTTAAATTCTTAACTATAAAAATATATTTTTTAATT-TTTTTCTTAATTTA
* * *
2904545 TCGAATATATATATTTTGGTTTAAAGTAGGCCAAGTTTATTATTTAAGTTAAGAATATATATTTA
64 TCGAATATATATATTTTAGTTTAAAGTAGACCAAGTTTATTATTGAAGTTAAGAATATATATTTA
2904610 AA
129 AA
2904612 ATATTTTAAAATATTTAAATTCTTAACTATAAAAATATATTTTTTAAATGTTTTTTCTTAATTTA
1 ATATTTTAAAATATTTAAATTCTTAACTATAAAAATATATTTTTT-AAT-TTTTTTCTTAATTTA
*
2904677 TCAAATATATATATTTTAGTTTAAAGTAGACCAAGTTTATTATTGAAGTTAAGAATATATATTTA
64 TCGAATATATATATTTTAGTTTAAAGTAGACCAAGTTTATTATTGAAGTTAAGAATATATATTTA
2904742 AA
129 AA
* *
2904744 ATA---T---ATGTTTAAATTCTTAACTATAAAAATATATATAATTTATTATTTTTTTTCTTAAT
1 ATATTTTAAAATATTTAAATTCTTAACTAT-AAAA-ATATAT--TTT-TTAATTTTTTTCTTAAT
*
2904803 TTATTGAATATATAT
61 TTATCGAATATATAT
2904818 TTTAAAATAT
Statistics
Matches: 186, Mismatches: 11, Indels: 19
0.86 0.05 0.09
Matches are distributed among these distances:
126 19 0.10
127 4 0.02
128 6 0.03
129 66 0.35
130 9 0.05
131 8 0.04
132 74 0.40
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (130 bp):
ATATTTTAAAATATTTAAATTCTTAACTATAAAAATATATTTTTTAATTTTTTTCTTAATTTATC
GAATATATATATTTTAGTTTAAAGTAGACCAAGTTTATTATTGAAGTTAAGAATATATATTTAAA
Found at i:2907683 original size:20 final size:20
Alignment explanation
Indices: 2907658--2907714 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
2907648 AGGGTGTCAA
2907658 AGTGTATTCATACACTCTGT
1 AGTGTATTCATACACTCTGT
* *
2907678 AGTGTA-TCGATGCACCCTGT
1 AGTGTATTC-ATACACTCTGT
* *
2907698 AGTGCATCCATACACTC
1 AGTGTATTCATACACTC
2907715 AAACACCGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
19 2 0.07
20 26 0.90
21 1 0.03
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (20 bp):
AGTGTATTCATACACTCTGT
Found at i:2910870 original size:19 final size:19
Alignment explanation
Indices: 2910846--2910883 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2910836 CAACAATTGG
2910846 TAACAATTGATATCTTTTT
1 TAACAATTGATATCTTTTT
*
2910865 TAACAATTGGTATCTTTTT
1 TAACAATTGATATCTTTTT
2910884 CATTAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.53
Consensus pattern (19 bp):
TAACAATTGATATCTTTTT
Found at i:2911137 original size:20 final size:19
Alignment explanation
Indices: 2911114--2911171 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 19
2911104 AAGTGTATTG
2911114 ATGCACCCTGTAGTGCATCC
1 ATGCACCCTGTA-TGCATCC
*
2911134 ATGCA--CTGT-T-CATCG
1 ATGCACCCTGTATGCATCC
2911149 ATGCACCCTGTAATGCATCC
1 ATGCACCCTGT-ATGCATCC
2911169 ATG
1 ATG
2911172 GACTCAAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
15 9 0.29
16 1 0.03
17 4 0.13
18 4 0.13
19 1 0.03
20 12 0.39
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.28
Consensus pattern (19 bp):
ATGCACCCTGTATGCATCC
Found at i:2911370 original size:20 final size:22
Alignment explanation
Indices: 2911332--2911371 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
2911322 TTTTTGTAGA
2911332 AAAACAATCCCCAAACGGCTCC
1 AAAACAATCCCCAAACGGCTCC
2911354 AAAAC-ATCCCC-AACGGCT
1 AAAACAATCCCCAAACGGCT
2911372 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 6 0.33
22 5 0.28
ACGTcount: A:0.40, C:0.40, G:0.10, T:0.10
Consensus pattern (22 bp):
AAAACAATCCCCAAACGGCTCC
Found at i:2911871 original size:20 final size:21
Alignment explanation
Indices: 2911831--2911892 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
2911821 AACATAATGT
2911831 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
**
2911852 CCAGGGGGTATTGATT-CCCC
1 CCAGGGGGTACAGATTCCCCC
* *
2911872 CTAGGGGGAACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
2911893 TTGTCTAACG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 16 0.47
21 18 0.53
ACGTcount: A:0.19, C:0.34, G:0.29, T:0.18
Consensus pattern (21 bp):
CCAGGGGGTACAGATTCCCCC
Found at i:2911893 original size:20 final size:20
Alignment explanation
Indices: 2911833--2911893 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
2911823 CATAATGTCC
*
2911833 AGGGGGTACAGATTCCCCCCC
1 AGGGGGTACAGATT-CCCCCT
**
2911854 AGGGGGTATTGATTCCCCCT
1 AGGGGGTACAGATTCCCCCT
*
2911874 AGGGGGAACAGATTCCCCCT
1 AGGGGGTACAGATTCCCCCT
2911894 TGTCTAACGG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 22 0.65
21 12 0.35
ACGTcount: A:0.20, C:0.31, G:0.30, T:0.20
Consensus pattern (20 bp):
AGGGGGTACAGATTCCCCCT
Found at i:2920772 original size:74 final size:76
Alignment explanation
Indices: 2920590--2920795 Score: 256
Period size: 75 Copynumber: 2.7 Consensus size: 76
2920580 CAAAGCCAAA
* * * **
2920590 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTGAATGG
1 AATTCCAGAATGCTCAGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
2920654 TTTGGCTCCGAG
65 TTTGGCTCCGAG
* *
2920666 ATTTCCAGAATGCTCAGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACATT
1 AATTCCAGAATGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
* *
2920730 TTTGTTCCGAG
66 TTGGCTCCGAG
* * * * *
2920741 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAGAATGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCC
2920796 TGTTCAACGG
Statistics
Matches: 113, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
74 21 0.19
75 60 0.53
76 32 0.28
ACGTcount: A:0.25, C:0.31, G:0.23, T:0.21
Consensus pattern (76 bp):
AATTCCAGAATGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTGGCTCCGAG
Found at i:2929412 original size:75 final size:74
Alignment explanation
Indices: 2929228--2929433 Score: 243
Period size: 74 Copynumber: 2.8 Consensus size: 74
2929218 CAAAGCCAAA
* * * * * **
2929228 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGAAACCGATTCCCCCCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGA-TCCCCCCATAGGAGGAACCGATT-CCCCCTAAACAGT
2929293 TTGGCTCCGAG
64 TTGGCTCCGAG
* * *
2929304 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCTAAACATTTT
1 AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTT
* *
2929369 TGTTCCGAG
66 GGCTCCGAG
* * *
2929378 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGAT-CCCCCCATAGGAGGAACCGATTCCCCCT
2929434 GTTCAACGGT
Statistics
Matches: 112, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
74 62 0.55
75 27 0.24
76 23 0.21
ACGTcount: A:0.25, C:0.31, G:0.23, T:0.21
Consensus pattern (74 bp):
AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTT
GGCTCCGAG
Found at i:2930923 original size:23 final size:22
Alignment explanation
Indices: 2930894--2930998 Score: 131
Period size: 23 Copynumber: 4.7 Consensus size: 22
2930884 TTTGTGCATA
2930894 AGGTATCGATACCCCCTTTGAAT
1 AGGTATCGATACCCCC-TTGAAT
* * *
2930917 AAGTATCGATA-CTCCTGGAAT
1 AGGTATCGATACCCCCTTGAAT
2930938 AGGTATCGATACCTCCCTTGAAT
1 AGGTATCGATACC-CCCTTGAAT
*
2930961 GGGTATCGATACCTCCCTTGAAT
1 AGGTATCGATACC-CCCTTGAAT
*
2930984 GGGTATCGATACCCC
1 AGGTATCGATACCCC
2930999 TGATGGTACC
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
21 15 0.21
22 6 0.08
23 52 0.71
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.29
Consensus pattern (22 bp):
AGGTATCGATACCCCCTTGAAT
Found at i:2930959 original size:44 final size:46
Alignment explanation
Indices: 2930894--2930998 Score: 144
Period size: 44 Copynumber: 2.3 Consensus size: 46
2930884 TTTGTGCATA
2930894 AGGTATCGATACCCCCTTTGAATAAGTATCGATA-CT-CCTGGAAT
1 AGGTATCGATACCCCCTTTGAATAAGTATCGATACCTCCCTGGAAT
** *
2930938 AGGTATCGATACCTCCC-TTGAATGGGTATCGATACCTCCCTTGAAT
1 AGGTATCGATACC-CCCTTTGAATAAGTATCGATACCTCCCTGGAAT
*
2930984 GGGTATCGATACCCC
1 AGGTATCGATACCCC
2930999 TGATGGTACC
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
44 28 0.52
45 7 0.13
46 19 0.35
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.29
Consensus pattern (46 bp):
AGGTATCGATACCCCCTTTGAATAAGTATCGATACCTCCCTGGAAT
Found at i:2933295 original size:13 final size:13
Alignment explanation
Indices: 2933277--2933302 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2933267 AGAGTAAGGG
2933277 GGAGTAATTTTTC
1 GGAGTAATTTTTC
2933290 GGAGTAATTTTTC
1 GGAGTAATTTTTC
2933303 AAAATTGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (13 bp):
GGAGTAATTTTTC
Found at i:2933728 original size:18 final size:20
Alignment explanation
Indices: 2933705--2933748 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
2933695 GTACCAATAC
2933705 CCCCCAT-A-GGTATCGATA
1 CCCCCATAATGGTATCGATA
2933723 CCCCCATGCAATGGTATCGATA
1 CCCCCAT--AATGGTATCGATA
2933745 CCCC
1 CCCC
2933749 TCAGATGGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.32
21 1 0.05
22 14 0.64
ACGTcount: A:0.25, C:0.39, G:0.16, T:0.20
Consensus pattern (20 bp):
CCCCCATAATGGTATCGATA
Found at i:2934489 original size:21 final size:21
Alignment explanation
Indices: 2934463--2934508 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2934453 GGTATAAATT
2934463 CCCCCCAGGGCGAACAGATTC
1 CCCCCCAGGGCGAACAGATTC
* * *
2934484 CCCCCCAGGGGGTACCGATTC
1 CCCCCCAGGGCGAACAGATTC
2934505 CCCC
1 CCCC
2934509 TTGTCTAACG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.17, C:0.48, G:0.24, T:0.11
Consensus pattern (21 bp):
CCCCCCAGGGCGAACAGATTC
Found at i:2934902 original size:34 final size:32
Alignment explanation
Indices: 2934857--2934926 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
2934847 TTTTGTAAAG
* * *
2934857 GGGAAATGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
2934891 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
2934923 GGGA
1 GGGA
2934927 GTTGTAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:2935339 original size:329 final size:328
Alignment explanation
Indices: 2934836--2935496 Score: 1067
Period size: 329 Copynumber: 2.0 Consensus size: 328
2934826 TCTTGTTTAC
* * *
2934836 TTTTCTTATCCTTTTGTAAAGGGGAAATGTTCTAGCTTATCCCGTGTAAAAGCTAGGGAAAGGTT
1 TTTTCTTATCCTTTTGTAAAGGGGAAAGGTTCTAACTTATCCCGTGTAAAAGCTAGGGAAAGATT
*
2934901 CTAGTTTAGCCCGGAAAAACTAGGGAGTTGTAAGGTTATCTCTTTGTCCTCAAAAGAAAGAACAA
66 CTAGTTTAGCCCGGAAAAACTAGGGAGTTGTAAGGTTATCTCTTTGTCCTAAAAAGAAAGAACAA
* *
2934966 ATTAGTGAATTTGTTGGAAAATCCTTGGTGAGGAGTTAAGGTAGTGGACGTAGACTTTGGTTGAG
131 ATTAGTGAATTTGTTGGAAAATCCTTGGTGAGGAGCTAAGGTAGTGGACATAGACTTTGGTTGAG
* *
2935031 AATGTCGAACCACTATAAATCACTGTGCAATTCTCTATCTTTCAATCTCCTTACTCCCTAAACAC
196 AAAGTCGAACCACTATAAATCACTGTGCAATTCTCTATCTCTCAATCTCCTTACTCCCTAAACAC
* * * *
2935096 -AAAATCGTTCCGACCCCTCTTTGCAAACCGTTCCGGTTGTCGATTCGAGCTTCTGAAAATCCCA
261 AAAAACCATTCCGACCCCTCTTTGCAAACCGTTCAGGTTGTCGATTCGAGCTTCCGAAAATCCCA
2935160 ACA
326 ACA
* *
2935163 TTTTCTTATCC-TTTGTAAAGGGGAAAGGTTCTAAC-TATGTCCTTGTAAAAGCTAGGGAAAGAT
1 TTTTCTTATCCTTTTGTAAAGGGGAAAGGTTCTAACTTAT-CCCGTGTAAAAGCTAGGGAAAGAT
** * *
2935226 TCTAGTTTAGCCATTGAAAAACTATGGAGTTGTAAATGTTATCTCTTTGTCCTAAAAAAGAAAGA
65 TCTAGTTTAGCC-CGGAAAAACTAGGGAGTTGT-AAGGTTATCTCTTTGTCCT-AAAAAGAAAGA
*
2935291 ACAAATTAGTGAATTTGTTGGAAAATTCTTGGTGAGGAGCTAAGGTAGTGGACATAGACTTTGGT
127 ACAAATTAGTGAATTTGTTGGAAAATCCTTGGTGAGGAGCTAAGGTAGTGGACATAGACTTTGGT
* *
2935356 TGATAAAGTCGAACCACTATAAATCGCTGTGCAATTCTCTATCTCTCAATCTCCTTACTCCCTAA
192 TGAGAAAGTCGAACCACTATAAATCACTGTGCAATTCTCTATCTCTCAATCTCCTTACTCCCTAA
2935421 ACACAAAAACCATTCCGACCCCTCTTTGCAAACCGTTCAGGTTGTCGATTCGAGCTTCCGAAAAT
257 ACACAAAAACCATTCCGACCCCTCTTTGCAAACCGTTCAGGTTGTCGATTCGAGCTTCCGAAAAT
*
2935486 CCCTACA
322 CCCAACA
2935493 TTTT
1 TTTT
2935497 TTGTTTAAAA
Statistics
Matches: 307, Mismatches: 22, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
325 3 0.01
326 55 0.18
327 28 0.09
328 18 0.06
329 137 0.45
330 66 0.21
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Consensus pattern (328 bp):
TTTTCTTATCCTTTTGTAAAGGGGAAAGGTTCTAACTTATCCCGTGTAAAAGCTAGGGAAAGATT
CTAGTTTAGCCCGGAAAAACTAGGGAGTTGTAAGGTTATCTCTTTGTCCTAAAAAGAAAGAACAA
ATTAGTGAATTTGTTGGAAAATCCTTGGTGAGGAGCTAAGGTAGTGGACATAGACTTTGGTTGAG
AAAGTCGAACCACTATAAATCACTGTGCAATTCTCTATCTCTCAATCTCCTTACTCCCTAAACAC
AAAAACCATTCCGACCCCTCTTTGCAAACCGTTCAGGTTGTCGATTCGAGCTTCCGAAAATCCCA
ACA
Found at i:2938030 original size:32 final size:32
Alignment explanation
Indices: 2937994--2938067 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
2937984 ACCATGTCAT
*
2937994 TTAAAGTGATTATACAGTATGTGCTACATCAC
1 TTAAAGTAATTATACAGTATGTGCTACATCAC
*
2938026 TTAAAGTAATTATACAGTATGTGTTACATCAC
1 TTAAAGTAATTATACAGTATGTGCTACATCAC
*
2938058 TTAAAATAAT
1 TTAAAGTAAT
2938068 GACATTACAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (32 bp):
TTAAAGTAATTATACAGTATGTGCTACATCAC
Found at i:2938422 original size:3 final size:3
Alignment explanation
Indices: 2938414--2938439 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2938404 ACGAGTACAA
2938414 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2938440 ATATAGAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2942209 original size:15 final size:15
Alignment explanation
Indices: 2942191--2942266 Score: 61
Period size: 15 Copynumber: 5.3 Consensus size: 15
2942181 GTGAAATTCT
2942191 AATTATTTAAATAAA
1 AATTATTTAAATAAA
*
2942206 AATTATTTATATAAA
1 AATTATTTAAATAAA
*
2942221 AATTCA-TT-GAT-AA
1 AATT-ATTTAAATAAA
* *
2942234 TA-TATTCAAATAAA
1 AATTATTTAAATAAA
* *
2942248 AAGTATTTATATAAA
1 AATTATTTAAATAAA
2942263 AATT
1 AATT
2942267 CATCGATAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
11 1 0.02
12 2 0.04
13 5 0.11
14 5 0.11
15 33 0.70
16 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (15 bp):
AATTATTTAAATAAA
Found at i:2942246 original size:42 final size:42
Alignment explanation
Indices: 2942190--2942281 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
2942180 AGTGAAATTC
* * *
2942190 TAAT-TATTTAAATAAAAATTATTTATATAAAAATTCATTGA
1 TAATATATTCAAATAAAAAGTATTTATATAAAAATTCATCGA
2942231 TAATATATTCAAATAAAAAGTATTTATATAAAAATTCATCGA
1 TAATATATTCAAATAAAAAGTATTTATATAAAAATTCATCGA
2942273 TAATATATT
1 TAATATATT
2942282 ATTTTATTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 4 0.09
42 43 0.91
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.41
Consensus pattern (42 bp):
TAATATATTCAAATAAAAAGTATTTATATAAAAATTCATCGA
Found at i:2947889 original size:8 final size:8
Alignment explanation
Indices: 2947876--2947920 Score: 65
Period size: 8 Copynumber: 5.6 Consensus size: 8
2947866 ACATGTGATG
2947876 GAAAAAGA
1 GAAAAAGA
2947884 GAAAAAGA
1 GAAAAAGA
2947892 GAAAAAGA
1 GAAAAAGA
2947900 GAAAAAGA
1 GAAAAAGA
*
2947908 -AAAGAAAA
1 GAAA-AAGA
2947916 GAAAA
1 GAAAA
2947921 GCCTAGAAGC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
7 3 0.09
8 28 0.82
9 3 0.09
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (8 bp):
GAAAAAGA
Found at i:2949151 original size:23 final size:23
Alignment explanation
Indices: 2949125--2949179 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
2949115 CATTTGGGAT
2949125 AATTCTATGT-GGTCCTTCAGGAC
1 AATTCTATGTCGGTCCTTC-GGAC
* *
2949148 AATTCT-TCTCGGTTCTTCGGAC
1 AATTCTATGTCGGTCCTTCGGAC
*
2949170 AAATCTATGT
1 AATTCTATGT
2949180 AGTACTTCGG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (23 bp):
AATTCTATGTCGGTCCTTCGGAC
Found at i:2949208 original size:24 final size:24
Alignment explanation
Indices: 2949181--2949226 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2949171 AATCTATGTA
*
2949181 GTACTTCGGTGC-ATATTCTACGTG
1 GTACTTCGATGCAAT-TTCTACGTG
2949205 GTACTTCGATGCAATTTCTACG
1 GTACTTCGATGCAATTTCTACG
2949227 CGACAGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.37
Consensus pattern (24 bp):
GTACTTCGATGCAATTTCTACGTG
Found at i:2955445 original size:23 final size:23
Alignment explanation
Indices: 2955417--2955495 Score: 104
Period size: 23 Copynumber: 3.4 Consensus size: 23
2955407 GAGTCGAGAG
* * *
2955417 TTCTATGTGGTTCTTCGAGATAA
1 TTCTATGTAGTCCTTCGAGACAA
2955440 TTCTATGTAGTCCTTCGAGACAA
1 TTCTATGTAGTCCTTCGAGACAA
* *
2955463 TTCTATGTAATCATTCGAGACAA
1 TTCTATGTAGTCCTTCGAGACAA
*
2955486 ATCTATGTAG
1 TTCTATGTAG
2955496 CACTTTGGTG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (23 bp):
TTCTATGTAGTCCTTCGAGACAA
Found at i:2957720 original size:24 final size:25
Alignment explanation
Indices: 2957671--2957728 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
2957661 ATCACATATC
* *
2957671 AAATTATAAGTTACGATAACATTTT
1 AAATTATAAATAACGATAACATTTT
*
2957696 AAATTATAAATAAC-ATAAATATTTAT
1 AAATTATAAATAACGAT-AACATTT-T
2957722 AAATTAT
1 AAATTAT
2957729 TCGAATAGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 2 0.07
25 18 0.64
26 8 0.29
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (25 bp):
AAATTATAAATAACGATAACATTTT
Found at i:2957892 original size:3 final size:3
Alignment explanation
Indices: 2957884--2957966 Score: 166
Period size: 3 Copynumber: 27.7 Consensus size: 3
2957874 TTGAAACTAT
2957884 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2957932 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2957967 TTTTTATATA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2960276 original size:2 final size:2
Alignment explanation
Indices: 2960269--2960325 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
2960259 CAGATATGAG
2960269 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
2960311 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
2960326 GCTAGAGCTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2960633 original size:9 final size:8
Alignment explanation
Indices: 2960611--2960713 Score: 57
Period size: 9 Copynumber: 11.9 Consensus size: 8
2960601 CGAACCCAAA
*
2960611 AATATTAT
1 AATATAAT
2960619 ATATATAATT
1 A-ATATAA-T
*
2960629 AATATAAAA
1 AATAT-AAT
2960638 AATATAA-
1 AATATAAT
*
2960645 AATATTAT
1 AATATAAT
2960653 ATATATAATT
1 A-ATATAA-T
*
2960663 AATATAAA
1 AATATAAT
2960671 AATATAA-
1 AATATAAT
*
2960678 AATATTAT
1 AATATAAT
2960686 ATATATATAT
1 A-ATATA-AT
2960696 ATATATATAT
1 A-ATATA-AT
2960706 ATATATAA
1 A-ATATAA
2960714 AATCGGGTCG
Statistics
Matches: 79, Mismatches: 7, Indels: 17
0.77 0.07 0.17
Matches are distributed among these distances:
7 12 0.15
8 12 0.15
9 30 0.38
10 25 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
AATATAAT
Found at i:2960649 original size:25 final size:26
Alignment explanation
Indices: 2960621--2960715 Score: 70
Period size: 26 Copynumber: 3.7 Consensus size: 26
2960611 AATATTATAT
2960621 ATATAAT-TAATATAAAAAATAT-AAA
1 ATATAATAT-ATATAAAAAATATAAAA
* **
2960646 ATATTATATATATAATTAATATAAAA
1 ATATAATATATATAAAAAATATAAAA
* * * * *
2960672 ATATAAAATAT-TATATATATATATAT
1 ATATAATATATATA-AAAAATATAAAA
2960698 ATATATATATATATAAAA
1 ATATA-ATATATATAAAA
2960716 TCGGGTCGGG
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
25 19 0.35
26 26 0.48
27 7 0.13
28 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
ATATAATATATATAAAAAATATAAAA
Found at i:2960652 original size:34 final size:33
Alignment explanation
Indices: 2960609--2960716 Score: 162
Period size: 34 Copynumber: 3.2 Consensus size: 33
2960599 CCCGAACCCA
2960609 AAAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATAT-AAAAATAT
2960643 AAAATATTATATATATAATTAATATAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAATAT
* *
2960676 AAAATATTATATATATATATATATATATATATATAT
1 AAAATATTATATATATA-AT-TA-ATATAAAAATAT
2960712 AAAAT
1 AAAAT
2960717 CGGGTCGGGG
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
33 25 0.36
34 27 0.39
35 2 0.03
36 15 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (33 bp):
AAAATATTATATATATAATTAATATAAAAATAT
Found at i:2960655 original size:2 final size:2
Alignment explanation
Indices: 2960646--2960712 Score: 65
Period size: 2 Copynumber: 36.5 Consensus size: 2
2960636 AAAATATAAA
* * *
2960646 AT AT -T AT AT AT AT A- AT -T A- AT AT AA AA AT AT A- AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2960683 -T 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 A
2960713 AAATCGGGTC
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
1 6 0.11
2 50 0.89
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2973357 original size:23 final size:26
Alignment explanation
Indices: 2973331--2973378 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 26
2973321 AATCAACATG
2973331 TAATAG-TAAAGTG-ATG-TTTGTTA
1 TAATAGTTAAAGTGAATGATTTGTTA
*
2973354 TAATAGTTAAATTGAATGATTTGTT
1 TAATAGTTAAAGTGAATGATTTGTT
2973379 TGTAACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 6 0.29
25 3 0.14
26 6 0.29
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (26 bp):
TAATAGTTAAAGTGAATGATTTGTTA
Found at i:2975970 original size:24 final size:24
Alignment explanation
Indices: 2975943--2975989 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
2975933 ATTATAGTGA
* *
2975943 TTTTATAATTTTTTATTAAATTAT
1 TTTTATAATTTATAATTAAATTAT
2975967 TTTTATAATTTATAATTAAATTA
1 TTTTATAATTTATAATTAAATTA
2975990 GTGTTGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTATAATTTATAATTAAATTAT
Found at i:2976509 original size:42 final size:42
Alignment explanation
Indices: 2976396--2976511 Score: 196
Period size: 42 Copynumber: 2.8 Consensus size: 42
2976386 CCCGAAATCT
* * *
2976396 CGTGTTTGTTTCATGTAATTCGTTTTTCGAAAAATATTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCC
*
2976438 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCC
2976480 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
2976512 CGTAATTCAT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.18, C:0.17, G:0.18, T:0.47
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCC
Found at i:2976744 original size:26 final size:24
Alignment explanation
Indices: 2976682--2976744 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
2976672 CATTTTCATC
2976682 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
2976706 AAAATATAT-TTATTAATAT-TTAT
1 AAAATATATATTATTAAAATATT-T
2976729 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
2976745 ATTTTTAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:2976843 original size:30 final size:28
Alignment explanation
Indices: 2976785--2976877 Score: 95
Period size: 28 Copynumber: 3.4 Consensus size: 28
2976775 CTATAATAAT
* *
2976785 ATAAGATATTATATTTTTT-TAT-TTTA
1 ATAATATATAATATTTTTTATATATTTA
2976811 ATAATATATAATAAATTTTTTATATATTTA
1 ATAATATATAAT--ATTTTTTATATATTTA
*
2976841 ATAATGA-ATAATATTATTTATATATTTA
1 ATAAT-ATATAATATTTTTTATATATTTA
*
2976869 A-AACATATA
1 ATAATATATA
2976878 CTAGTAAAGA
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
26 11 0.19
27 5 0.09
28 23 0.40
29 3 0.05
30 14 0.25
31 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (28 bp):
ATAATATATAATATTTTTTATATATTTA
Found at i:2976903 original size:23 final size:23
Alignment explanation
Indices: 2976862--2976923 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
2976852 TATTATTTAT
*
2976862 ATATTTAAAACATATACTAGTAAAG
1 ATATTT-AAA-ATATACTAATAAAG
* *
2976887 ATATTTAAAATATACTAATTAAT
1 ATATTTAAAATATACTAATAAAG
*
2976910 ATTTTTAAAATATA
1 ATATTTAAAATATA
2976924 ATATAACACT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 24 0.73
24 3 0.09
25 6 0.18
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (23 bp):
ATATTTAAAATATACTAATAAAG
Found at i:2977045 original size:18 final size:20
Alignment explanation
Indices: 2977018--2977055 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
2977008 TAATAAAATT
2977018 ATAAAAAAA-TA-TTTAATA
1 ATAAAAAAATTATTTTAATA
*
2977036 ATAAATAAATTATTTTAATA
1 ATAAAAAAATTATTTTAATA
2977056 TTTTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 2 0.12
20 7 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAAAAAAATTATTTTAATA
Found at i:2977262 original size:20 final size:20
Alignment explanation
Indices: 2977204--2977253 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
2977194 TTTCCAGATG
2977204 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
2977224 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
2977244 TTTTCCAGAA
1 TTTTCCAGAA
2977254 TTCAAATTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:2977272 original size:15 final size:15
Alignment explanation
Indices: 2977236--2977291 Score: 87
Period size: 15 Copynumber: 3.8 Consensus size: 15
2977226 TTCCAGAAAT
2977236 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
2977251 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
2977265 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
2977280 GTAATTCATTTT
1 GTAATTCATTTT
2977292 TTGGAAAATC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
14 12 0.33
15 24 0.67
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.45
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:2978963 original size:23 final size:22
Alignment explanation
Indices: 2978908--2978964 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
2978898 CCCTAGAAAA
*
2978908 TAATATTAAAAAAAGATAATTCC
1 TAAT-TTAAAAAAAGATAAATCC
**
2978931 TAAAAATAAAAATAAGATAAATCC
1 T-AATTTAAAAA-AAGATAAATCC
2978955 TAATTTAAAA
1 TAATTTAAAA
2978965 TAAAAAAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.61, C:0.07, G:0.04, T:0.28
Consensus pattern (22 bp):
TAATTTAAAAAAAGATAAATCC
Found at i:2979038 original size:23 final size:23
Alignment explanation
Indices: 2979012--2979056 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2979002 CTGATTGGAT
*
2979012 CTTCTAGAAGCTGCTGACTAGGC
1 CTTCTAGAAGCTACTGACTAGGC
* *
2979035 CTTCTGGAAGCTATTGACTAGG
1 CTTCTAGAAGCTACTGACTAGG
2979057 TGCCACGTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (23 bp):
CTTCTAGAAGCTACTGACTAGGC
Found at i:2985236 original size:40 final size:39
Alignment explanation
Indices: 2985184--2985274 Score: 96
Period size: 40 Copynumber: 2.3 Consensus size: 39
2985174 TTTTTCTCTA
* * * *
2985184 TTTTTCCACTTTTTTCCT-TCCTTTTTGTTTTTTCTTTGT
1 TTTTTCTACTTTTTT-ATGTCCTTTTTGTTATATCTTTGT
*
2985223 TTTTTCTATCTTTTTTATGTCCTTTTTGTTATATCTTTTT
1 TTTTTCTA-CTTTTTTATGTCCTTTTTGTTATATCTTTGT
2985263 TTCTTTCT-CTTT
1 TT-TTTCTACTTT
2985275 GTGTCGTCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
39 12 0.27
40 27 0.61
41 5 0.11
ACGTcount: A:0.05, C:0.18, G:0.04, T:0.73
Consensus pattern (39 bp):
TTTTTCTACTTTTTTATGTCCTTTTTGTTATATCTTTGT
Found at i:2991106 original size:54 final size:54
Alignment explanation
Indices: 2991021--2991402 Score: 487
Period size: 54 Copynumber: 7.1 Consensus size: 54
2991011 TACTACATGA
*
2991021 ACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAATAACCGTACAAGC
1 ACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCGTACAAGC
* * *
2991075 ACCATGTGTGCAATTCATGGAATTCATCATGAGTTTATGAACAACCGTACAAGC
1 ACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCGTACAAGC
* * * * * *
2991129 ACCATGTGTGTAATTCATGGAATTCATCATGTGTTGATGAACAACCGTATAGGC
1 ACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCGTACAAGC
* * * * **
2991183 ACTATGGGTACAATTCACGGAATTCATCTTGTGTTGATGAACAACATTACATA-C
1 ACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCGTACA-AGC
* * * * * * *
2991237 ACTATGTGTGTAATGCACGGAACTCATTATGAGTTGACGAACAATCGTACAATC
1 ACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCGTACAAGC
* * * *
2991291 ACTATGTGTTCAAATCACGGAATTCATCATGAGTTGATGAACAACCGTAGAGGC
1 ACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCGTACAAGC
* *
2991345 ACTATGTGTGCAATTCATGGAATTCATCATGAGTTGATGAACAACCGTACATGC
1 ACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCGTACAAGC
2991399 ACTA
1 ACTA
2991403 AGTATGCATC
Statistics
Matches: 279, Mismatches: 47, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
53 1 0.00
54 278 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (54 bp):
ACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAACAACCGTACAAGC
Found at i:2992501 original size:2 final size:2
Alignment explanation
Indices: 2992494--2992518 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2992484 TTATTTATTT
2992494 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
2992519 TAACATTTTG
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:2992695 original size:4 final size:4
Alignment explanation
Indices: 2992681--2992739 Score: 50
Period size: 4 Copynumber: 14.0 Consensus size: 4
2992671 TTTTATGTCT
*
2992681 TTTA TTTTA TTTA TTTA TTTA TTTA -TT- TTTA TTTTCA TTTC TTTA TTTTA
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTT-A TTTA TTTA -TTTA
2992731 TTTAA TTTA
1 TTT-A TTTA
2992740 CTTGTTATCG
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
3 4 0.09
4 23 0.50
5 18 0.39
6 1 0.02
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:2992725 original size:14 final size:13
Alignment explanation
Indices: 2992671--2992733 Score: 56
Period size: 14 Copynumber: 4.6 Consensus size: 13
2992661 GGACTTTATT
*
2992671 TTTTATGTCTTTTA
1 TTTTATTTC-TTTA
*
2992685 TTTTATTTATTTA
1 TTTTATTTCTTTA
*
2992698 -TTTATTTATTTTTA
1 TTTTA-TT-TCTTTA
2992712 TTTTCATTTCTTTA
1 TTTT-ATTTCTTTA
2992726 TTTTATTT
1 TTTTATTT
2992734 AATTTACTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
12 4 0.10
13 10 0.24
14 21 0.51
15 5 0.12
16 1 0.02
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTTATTTCTTTA
Found at i:2992725 original size:20 final size:19
Alignment explanation
Indices: 2992681--2992733 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
2992671 TTTTATGTCT
*
2992681 TTTATTTTATTTATTTATTTA
1 TTTATTTTA-TT-TTCATTTA
*
2992702 TTTATTTTTATTTTCATTTC
1 TTTA-TTTTATTTTCATTTA
2992722 TTTATTTTATTT
1 TTTATTTTATTT
2992734 AATTTACTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 8 0.28
20 10 0.34
21 6 0.21
22 5 0.17
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTATTTTATTTTCATTTA
Found at i:2992824 original size:16 final size:16
Alignment explanation
Indices: 2992803--2992842 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
2992793 TTATTTTACC
2992803 TTTTCTATTTCATTAG
1 TTTTCTATTTCATTAG
**
2992819 TTTTCTATTTTGTTAG
1 TTTTCTATTTCATTAG
2992835 TTTT-TATT
1 TTTTCTATT
2992843 ACCTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.70
Consensus pattern (16 bp):
TTTTCTATTTCATTAG
Found at i:2996717 original size:32 final size:31
Alignment explanation
Indices: 2996680--2996749 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
2996670 AGGAATAATA
* *
2996680 GGGGCACTTTTGAAGATTCAACATTAAATGTT
1 GGGGCA-TTTTGAAGATTCAACATCAAATATT
** * *
2996712 GGGGCATTTTTTATATTCAACATCGAATATT
1 GGGGCATTTTGAAGATTCAACATCAAATATT
2996743 GGGGCAT
1 GGGGCAT
2996750 CTTCGGGGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 26 0.81
32 6 0.19
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.36
Consensus pattern (31 bp):
GGGGCATTTTGAAGATTCAACATCAAATATT
Done.