Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008338.1 Hibiscus syriacus cultivar Beakdansim tig00111059_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: 2210178
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 12
Found at i:1983988 original size:33 final size:33
Alignment explanation
Indices: 1983946--1984069 Score: 158
Period size: 33 Copynumber: 3.5 Consensus size: 33
1983936 CAAAATCGCA
*
1983946 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
1983979 TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
*
1984012 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCACGTT--G-C-G--ATTCTCTCG
1984053 TTGCGATTTTCATTTCA
1 TTGCGATTTTCATTTCA
1984070 ACCAAAAGAC
Statistics
Matches: 80, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
33 44 0.55
34 2 0.03
35 6 0.08
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.03
41 21 0.26
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
Found at i:1984030 original size:21 final size:21
Alignment explanation
Indices: 1984004--1984068 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
1983994 CACGTTGCGA
1984004 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1984025 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1984045 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
1984066 TTC
1 TTC
1984069 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1985925 original size:93 final size:93
Alignment explanation
Indices: 1985766--1986048 Score: 550
Period size: 93 Copynumber: 3.1 Consensus size: 93
1985756 TAGATTGCTT
*
1985766 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1985831 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1985859 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1985924 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1985952 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1986017 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1986044 AGTAA
1 AGTAA
1986049 TGCAATCCAT
Statistics
Matches: 189, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
92 6 0.03
93 183 0.97
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1986136 original size:19 final size:19
Alignment explanation
Indices: 1986096--1986224 Score: 134
Period size: 19 Copynumber: 7.3 Consensus size: 19
1986086 TAGTTTACTT
* *
1986096 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1986116 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1986135 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1986154 TCGCAA--C--AA-CAGAA
1 TCGCAACGCGAAACCAAAA
1986168 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1986187 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAACCAAAA
1986201 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1986220 TCGCA
1 TCGCA
1986225 TTGCGATTTT
Statistics
Matches: 92, Mismatches: 7, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.22
15 3 0.03
16 3 0.03
17 3 0.03
18 3 0.03
19 47 0.51
20 13 0.14
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1986175 original size:33 final size:33
Alignment explanation
Indices: 1986130--1986224 Score: 154
Period size: 33 Copynumber: 2.9 Consensus size: 33
1986120 AACGCGAAAC
**
1986130 CAAAATCGCAACGCGAAATGAAAATCGCAACAA
1 CAAAATCGCAACGCGAAACCAAAATCGCAACAA
* *
1986163 CAGAATCGCAACGCGAAACCAAAATCGCAACGA
1 CAAAATCGCAACGCGAAACCAAAATCGCAACAA
1986196 CAAAATCGCAACGCGAAACCAAAATCGCA
1 CAAAATCGCAACGCGAAACCAAAATCGCA
1986225 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.48, C:0.28, G:0.16, T:0.07
Consensus pattern (33 bp):
CAAAATCGCAACGCGAAACCAAAATCGCAACAA
Found at i:1986201 original size:14 final size:14
Alignment explanation
Indices: 1986150--1986208 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
1986140 ACGCGAAATG
*
1986150 AAAATCGCAACAAC
1 AAAATCGCAACGAC
*
1986164 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
1986183 AAAATCGCAACGAC
1 AAAATCGCAACGAC
1986197 AAAATCGCAACG
1 AAAATCGCAACG
1986209 CGAAACCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 22 0.59
15 1 0.03
16 1 0.03
17 2 0.05
18 1 0.03
19 10 0.27
ACGTcount: A:0.49, C:0.29, G:0.15, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1986222 original size:52 final size:51
Alignment explanation
Indices: 1986096--1986224 Score: 145
Period size: 52 Copynumber: 2.5 Consensus size: 51
1986086 TAGTTTACTT
* * *
1986096 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGCGAAACCAAAATCGCAACGCAAAA
* * *
1986148 T-GAAAATCGC-AACAACAGAATCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCG-CAA-CGCGAA-ACCAAAATCGCAACGCGAAACCAAAATCGCAACG-CAAAA
1986201 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
1986225 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
51 1 0.02
52 48 0.77
53 12 0.19
54 1 0.02
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (51 bp):
TCGCAACGCGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGCAAAA
Found at i:1986242 original size:19 final size:19
Alignment explanation
Indices: 1986220--1986392 Score: 168
Period size: 19 Copynumber: 9.6 Consensus size: 19
1986210 GAAACCAAAA
*
1986220 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1986239 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1986255 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1986272 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1986288 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1986305 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
1986324 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
1986343 TCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATT
*
1986362 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1986382 TCGTGTTGCGA
1 TCGCGTTGCGA
1986393 AAGTAAACTA
Statistics
Matches: 128, Mismatches: 15, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
14 15 0.12
16 11 0.09
17 11 0.09
19 79 0.62
20 12 0.09
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1986261 original size:14 final size:14
Alignment explanation
Indices: 1986242--1986298 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1986232 TTTCATTTCG
1986242 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1986256 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1986273 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1986289 CGTTGCGATT
1 CGTTGCGATT
1986299 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1986350 original size:38 final size:38
Alignment explanation
Indices: 1986220--1986392 Score: 168
Period size: 33 Copynumber: 4.8 Consensus size: 38
1986210 GAAACCAAAA
*
1986220 TCGCATTGCGATTTTCATTTCGCGTTGCGA-T-TC-TT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* *
1986255 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* **
1986288 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
** *
1986324 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* *
1986362 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
1986393 AAGTAAACTA
Statistics
Matches: 116, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
33 56 0.48
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.38
39 11 0.09
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
Found at i:1988334 original size:14 final size:14
Alignment explanation
Indices: 1988315--1988350 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1988305 ATTGTTTAAT
1988315 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1988329 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1988343 TGATTTGT
1 TGATTTGT
1988351 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1988473 original size:19 final size:19
Alignment explanation
Indices: 1988457--1988554 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1988447 AAAAATGACT
1988457 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1988476 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1988495 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1988509 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1988528 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1988548 ATCGCAA
1 ATCGCAA
1988555 CGATTGCGAT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1988535 original size:52 final size:53
Alignment explanation
Indices: 1988457--1988557 Score: 195
Period size: 52 Copynumber: 1.9 Consensus size: 53
1988447 AAAAATGACT
1988457 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1988509 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGA
1988558 TTGCGATTCT
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.60
53 19 0.40
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:1988595 original size:33 final size:33
Alignment explanation
Indices: 1988557--1988703 Score: 138
Period size: 33 Copynumber: 4.3 Consensus size: 33
1988547 AATCGCAACG
1988557 ATTGCGATTCTCTCGTTGCGATTTTCATTTCGC
1 ATTGCGATTCTCTCGTTGCGATTTTCATTTCGC
* * *
1988590 ATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG-
1 ATTGCGA--TTC-TCTCG--TTGCGATT-T-TCATTTCGC
* * *
1988629 ATTTTC-ATT-TCGCATTGCGATTTTCATTTCCGC
1 A-TTGCGATTCTCTCGTTGCGATTTTCATTT-CGC
1988662 ATTGCGATTCTCTCGTTGCGATTTTCATTTCGC
1 ATTGCGATTCTCTCGTTGCGATTTTCATTTCGC
1988695 ATTGCGATT
1 ATTGCGATT
1988704 TTCATTTCCG
Statistics
Matches: 90, Mismatches: 12, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
31 4 0.04
32 6 0.07
33 31 0.34
34 18 0.20
35 5 0.06
36 4 0.04
37 2 0.02
38 8 0.09
39 3 0.03
40 9 0.10
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTGCGATTCTCTCGTTGCGATTTTCATTTCGC
Found at i:1988596 original size:19 final size:19
Alignment explanation
Indices: 1988572--1988756 Score: 220
Period size: 19 Copynumber: 10.4 Consensus size: 19
1988562 GATTCTCTCG
1988572 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1988591 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1988610 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1988624 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1988643 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
*
1988663 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1988677 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1988696 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1988716 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
1988730 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1988749 TTGCGATT
1 TTGCGATT
1988757 CTCTCGTTGC
Statistics
Matches: 143, Mismatches: 6, Indels: 34
0.78 0.03 0.19
Matches are distributed among these distances:
14 23 0.16
16 14 0.10
17 14 0.10
18 4 0.03
19 62 0.43
20 26 0.18
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1988701 original size:86 final size:84
Alignment explanation
Indices: 1988591--1988770 Score: 242
Period size: 86 Copynumber: 2.1 Consensus size: 84
1988581 TCATTTCGCA
1988591 TTGCGATTTTCATTTCGCATTGCGA-TTC-TCT-CG-TTGCGATTTTCATTTCGCATTGCGATTT
1 TTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGATTGCGATTTTCA--T-G--TTGCGATTT
1988652 TCATTTCCGCATTGCGATTCTCTCG
61 TCATTT-CGCATTGCGATTCTCTCG
* *
1988677 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGA-TTTCATCTCCG-ATTGCGATTTTCATGTTGCGATTTTCA
1988742 TTTCGCATTGCGATTCTCTCG
64 TTTCGCATTGCGATTCTCTCG
1988763 TTGCGATT
1 TTGCGATT
1988771 GTAATTTCCG
Statistics
Matches: 86, Mismatches: 2, Indels: 12
0.86 0.02 0.12
Matches are distributed among these distances:
86 51 0.59
87 14 0.16
88 3 0.03
89 3 0.03
90 3 0.03
92 12 0.14
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (84 bp):
TTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGATTGCGATTTTCATGTTGCGATTTTCATT
TCGCATTGCGATTCTCTCG
Found at i:1988754 original size:33 final size:34
Alignment explanation
Indices: 1988572--1988770 Score: 185
Period size: 33 Copynumber: 5.7 Consensus size: 34
1988562 GATTCTCTCG
1988572 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCA--TCG--TTGCGATTTTCATTTCGCA
*
1988610 TTGCGATTCTC-TCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATCGTTGCGATTTTCATTTCGCA
* * * *
1988643 TTGCGATTTTCAT--TTCCGCA-TTGCGATTCTCTCG
1 TTGCGATTTTCATCGTTGCG-ATTTTC-ATT-TCGCA
1988677 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCA--TCG--TTGCGATTTTCATTT-CGCA
*
1988716 TTGCGATTTTCAT-GTTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATCGTTGCGATTTTCATTTCGCA
*
1988749 TTGCGATTCTC-TCGTTGCGATT
1 TTGCGATTTTCATCGTTGCGATT
1988771 GTAATTTCCG
Statistics
Matches: 135, Mismatches: 13, Indels: 31
0.75 0.07 0.17
Matches are distributed among these distances:
32 8 0.06
33 55 0.41
34 30 0.22
35 3 0.02
36 2 0.01
37 1 0.01
38 11 0.08
39 18 0.13
40 7 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (34 bp):
TTGCGATTTTCATCGTTGCGATTTTCATTTCGCA
Found at i:1988785 original size:53 final size:53
Alignment explanation
Indices: 1988557--1988756 Score: 359
Period size: 53 Copynumber: 3.8 Consensus size: 53
1988547 AATCGCAACG
1988557 ATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGC
1 ATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGC
1988609 ATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGC
1 ATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGC
1988662 ATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGC
1 ATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGC
* *
1988715 ATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCATTGCGATT
1 ATTGCGATTCTC-TCGTTGCGATTTTCATTTCGCATTGCGATT
1988757 CTCTCGTTGC
Statistics
Matches: 144, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
52 49 0.34
53 94 0.65
54 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (53 bp):
ATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGC
Found at i:1991282 original size:24 final size:24
Alignment explanation
Indices: 1991248--1991294 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1991238 CTAAAACATC
1991248 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1991272 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1991295 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1992010 original size:20 final size:20
Alignment explanation
Indices: 1991982--1992210 Score: 235
Period size: 20 Copynumber: 11.4 Consensus size: 20
1991972 AAATTTCAGT
* * *
1991982 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1992002 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1992022 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
* **
1992042 GTTGCGATTTACAGATTATC
1 GTTGCGATTTACGGATTCGC
*
1992062 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1992082 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1992102 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
1992122 ATTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
1992142 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1992162 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1992182 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1992202 GTTGCGATT
1 GTTGCGATT
1992211 CTGGAAAATC
Statistics
Matches: 185, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
20 184 0.99
21 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1993241 original size:14 final size:15
Alignment explanation
Indices: 1993224--1993253 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1993214 ATTATTTAAA
1993224 CTTTAAAA-TTAATC
1 CTTTAAAATTTAATC
1993238 CTTTAAAATTTAATC
1 CTTTAAAATTTAATC
1993253 C
1 C
1993254 AGTTACTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (15 bp):
CTTTAAAATTTAATC
Found at i:1998521 original size:14 final size:14
Alignment explanation
Indices: 1998502--1998530 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1998492 TAGCAAGCCT
1998502 TGTAAAACTTCTAA
1 TGTAAAACTTCTAA
1998516 TGTAAAACTTCTAA
1 TGTAAAACTTCTAA
1998530 T
1 T
1998531 AATTCTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (14 bp):
TGTAAAACTTCTAA
Found at i:1999139 original size:20 final size:21
Alignment explanation
Indices: 1999114--1999162 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
1999104 TGAATTCGCC
1999114 AATTTGAAAACT-GAGTTGCG
1 AATTTGAAAACTCGAGTTGCG
* * *
1999134 AATTTGGCAAATTCGTGTTGCG
1 AATTT-GAAAACTCGAGTTGCG
1999156 AATTTGA
1 AATTTGA
1999163 CCAATTTCGC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 5 0.22
21 6 0.26
22 12 0.52
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.35
Consensus pattern (21 bp):
AATTTGAAAACTCGAGTTGCG
Found at i:2003145 original size:20 final size:19
Alignment explanation
Indices: 2003122--2003210 Score: 63
Period size: 19 Copynumber: 4.5 Consensus size: 19
2003112 TACTTCTGTA
2003122 TTGCGAATTTCAAATTCGAG
1 TTGCGAA-TTCAAATTCGAG
* * *
2003142 TTGCGGATTCAGAA-ACTGTG
1 TTGCGAATTCA-AATTC-GAG
** *
2003162 TTGCGAAATTGGATTTCGAG
1 TTGCG-AATTCAAATTCGAG
* *
2003182 TTGCGAATCCGAATTCGAG
1 TTGCGAATTCAAATTCGAG
2003201 TTGCGAATTC
1 TTGCGAATTC
2003211 GTGAGTTATT
Statistics
Matches: 52, Mismatches: 13, Indels: 9
0.70 0.18 0.12
Matches are distributed among these distances:
19 25 0.48
20 23 0.44
21 4 0.08
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (19 bp):
TTGCGAATTCAAATTCGAG
Found at i:2003314 original size:19 final size:21
Alignment explanation
Indices: 2003275--2003317 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
2003265 TTTTCGGTCA
2003275 ATAAACTCTAAATATATTTAT
1 ATAAACTCTAAATATATTTAT
*
2003296 ATAAACT-TACATA-ATTTAT
1 ATAAACTCTAAATATATTTAT
2003315 ATA
1 ATA
2003318 TCCTCAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.43
20 5 0.24
21 7 0.33
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (21 bp):
ATAAACTCTAAATATATTTAT
Found at i:2009371 original size:39 final size:39
Alignment explanation
Indices: 2009327--2009442 Score: 171
Period size: 39 Copynumber: 3.0 Consensus size: 39
2009317 AGCAATTAGC
*
2009327 AGAGTATGTGTAAATTGTAAATTGATTAAGAAAATTTTG
1 AGAGTATGTGCAAATTGTAAATTGATTAAGAAAATTTTG
2009366 AGAGTATGTGCAAATTGTAAATTGATTAAGAAAATTTTG
1 AGAGTATGTGCAAATTGTAAATTGATTAAGAAAATTTTG
* * **
2009405 A-AATACTCTGCAAACGGTAAATTGATTAAGAAAATTTT
1 AGAGTA-TGTGCAAATTGTAAATTGATTAAGAAAATTTT
2009443 TGAATAAATA
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
38 3 0.04
39 68 0.96
ACGTcount: A:0.42, C:0.04, G:0.18, T:0.35
Consensus pattern (39 bp):
AGAGTATGTGCAAATTGTAAATTGATTAAGAAAATTTTG
Found at i:2011060 original size:4 final size:4
Alignment explanation
Indices: 2011051--2011077 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2011041 CATAATTCTC
2011051 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
2011078 ATAATATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:2011214 original size:15 final size:14
Alignment explanation
Indices: 2011196--2011245 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 14
2011186 TGAAAGTAAA
2011196 TAAAAAAATAAATAG
1 TAAAAAAATAAA-AG
2011211 TAAATAAAAATAAAGAG
1 T-AA-AAAAATAAA-AG
*
2011228 AAAAAAAATAAAAG
1 TAAAAAAATAAAAG
2011242 TAAA
1 TAAA
2011246 TAAAGTAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 5 0.17
15 10 0.33
16 4 0.13
17 11 0.37
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (14 bp):
TAAAAAAATAAAAG
Found at i:2011221 original size:17 final size:16
Alignment explanation
Indices: 2011188--2011249 Score: 74
Period size: 15 Copynumber: 3.8 Consensus size: 16
2011178 AAAATTAATG
2011188 AAAGTAAATAAAAAAATA
1 AAAGTAAAT--AAAAATA
2011206 AATAGTAAATAAAAATA
1 AA-AGTAAATAAAAATA
2011223 AAGAG-AAA-AAAAATA
1 AA-AGTAAATAAAAATA
2011238 AAAGTAAATAAA
1 AAAGTAAATAAA
2011250 GTAGAAGAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
14 2 0.05
15 12 0.30
16 6 0.15
17 11 0.28
18 2 0.05
19 7 0.17
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (16 bp):
AAAGTAAATAAAAATA
Found at i:2011252 original size:9 final size:10
Alignment explanation
Indices: 2011188--2011249 Score: 56
Period size: 10 Copynumber: 6.2 Consensus size: 10
2011178 AAAATTAATG
2011188 AAAGTAAATA
1 AAAGTAAATA
2011198 AAA--AAATA
1 AAAGTAAATA
2011206 AATAGTAAATA
1 AA-AGTAAATA
* *
2011217 AAAATAAAGA
1 AAAGTAAATA
**
2011227 GAAAAAAAATA
1 -AAAGTAAATA
2011238 AAAGTAAATA
1 AAAGTAAATA
2011248 AA
1 AA
2011250 GTAGAAGAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
8 7 0.17
9 1 0.02
10 19 0.45
11 15 0.36
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (10 bp):
AAAGTAAATA
Found at i:2014541 original size:17 final size:16
Alignment explanation
Indices: 2014519--2014565 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
2014509 AATTGAGGAG
2014519 GAAAGAAGAAATGAATA
1 GAAAGAAGAAATGAA-A
*
2014536 GAAAGAAGAGATG-AA
1 GAAAGAAGAAATGAAA
2014551 GAAATGAAGAAATGA
1 GAAA-GAAGAAATGA
2014566 GAGGGAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 5 0.19
16 9 0.35
17 12 0.46
ACGTcount: A:0.62, C:0.00, G:0.28, T:0.11
Consensus pattern (16 bp):
GAAAGAAGAAATGAAA
Found at i:2014557 original size:8 final size:8
Alignment explanation
Indices: 2014519--2014565 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
2014509 AATTGAGGAG
2014519 GAAA-GAA
1 GAAATGAA
2014526 GAAATGAATA
1 GAAATG-A-A
2014536 GAAA-GAA
1 GAAATGAA
*
2014543 GAGATGAA
1 GAAATGAA
2014551 GAAATGAA
1 GAAATGAA
2014559 GAAATGA
1 GAAATGA
2014566 GAGGGAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
7 8 0.24
8 19 0.56
9 2 0.06
10 5 0.15
ACGTcount: A:0.62, C:0.00, G:0.28, T:0.11
Consensus pattern (8 bp):
GAAATGAA
Found at i:2015673 original size:12 final size:10
Alignment explanation
Indices: 2015653--2015690 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
2015643 TTGTTTTTTC
2015653 TTTTTTATTA
1 TTTTTTATTA
2015663 TATTTTGTATTA
1 T-TTTT-TATTA
2015675 TTTTTTATT-
1 TTTTTTATTA
2015684 TTTTTTA
1 TTTTTTA
2015691 ATTTACAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 7 0.27
10 5 0.19
11 8 0.31
12 6 0.23
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (10 bp):
TTTTTTATTA
Found at i:2016495 original size:2 final size:2
Alignment explanation
Indices: 2016488--2016515 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2016478 TTAATACGTC
2016488 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
2016516 CAACACATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2016880 original size:25 final size:25
Alignment explanation
Indices: 2016852--2016900 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2016842 TGTATTGAAT
* *
2016852 ATCTTAATA-ATTGTTTATATTTTTA
1 ATCTAAATACATT-TTTAAATTTTTA
2016877 ATCTAAATACATTTTTAAATTTTT
1 ATCTAAATACATTTTTAAATTTTT
2016901 TTTAAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (25 bp):
ATCTAAATACATTTTTAAATTTTTA
Found at i:2022192 original size:25 final size:25
Alignment explanation
Indices: 2022155--2022202 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
2022145 AGTATAAAAA
* *
2022155 TTTTAAATTTATATAATTTATATAT
1 TTTTAAATATATATAATTCATATAT
* *
2022180 TTTTTAATATATATTATTCATAT
1 TTTTAAATATATATAATTCATAT
2022203 TTTATTTTTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTTAAATATATATAATTCATATAT
Found at i:2023089 original size:13 final size:13
Alignment explanation
Indices: 2023071--2023097 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2023061 ATGTGACCGG
2023071 CACATCAGCAGGT
1 CACATCAGCAGGT
2023084 CACATCAGCAGGT
1 CACATCAGCAGGT
2023097 C
1 C
2023098 CCCATCCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.33, G:0.22, T:0.15
Consensus pattern (13 bp):
CACATCAGCAGGT
Found at i:2024342 original size:15 final size:16
Alignment explanation
Indices: 2024311--2024348 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2024301 ATAAAAGTTC
2024311 TTCTTTTTCTTTAATT
1 TTCTTTTTCTTTAATT
* *
2024327 TTGTTTTT-TTTTATT
1 TTCTTTTTCTTTAATT
2024342 TTCTTTT
1 TTCTTTT
2024349 AAAATGCTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.82
Consensus pattern (16 bp):
TTCTTTTTCTTTAATT
Found at i:2025433 original size:41 final size:42
Alignment explanation
Indices: 2025388--2025514 Score: 140
Period size: 41 Copynumber: 3.1 Consensus size: 42
2025378 TATTATAACT
*
2025388 TTTGTATAAAAACATC-ACTAAAGTATGAGTCTTTAGCAGCG
1 TTTGTATAAAAACATCTACTAAAGTATGAGTCTTTAGCGGCG
* * *
2025429 TTTGTAT-AAAA-ATGCTGCTAAAGTACGAGT-TTATAGTGGCG
1 TTTGTATAAAAACAT-CTACTAAAGTATGAGTCTT-TAGCGGCG
* *
2025470 TTT-TATAAAAAC-GCTACTAAAGTATGAATCTTTAGCGGCG
1 TTTGTATAAAAACATCTACTAAAGTATGAGTCTTTAGCGGCG
2025510 TTTGT
1 TTTGT
2025515 GTTGAGTTAA
Statistics
Matches: 70, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
39 2 0.03
40 33 0.47
41 35 0.50
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.35
Consensus pattern (42 bp):
TTTGTATAAAAACATCTACTAAAGTATGAGTCTTTAGCGGCG
Found at i:2026261 original size:18 final size:17
Alignment explanation
Indices: 2026207--2026255 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
2026197 CTGGATCCTT
* *
2026207 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
2026225 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
2026243 AGTGCATTCGATG
1 AGTGCA-TCGATG
2026256 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:2026360 original size:65 final size:64
Alignment explanation
Indices: 2026201--2026386 Score: 216
Period size: 65 Copynumber: 2.9 Consensus size: 64
2026191 TGACCGCTGG
* * *
2026201 ATCCTTAGTGCATCGGTGCACTAAG-AGTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAA
1 ATCCTCAGTGCATCGGTGCA-T-GGTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAA
2026264 T
64 T
* ** * * *
2026265 AGCCAGAGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCAATGTTTTCATAAA
1 ATCCTCAGTGCATCGGTGCATGG-TAGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAA
2026330 -
64 T
*
2026330 ATCCTCAGTGCATCGGTGCATGGTATGTGCATCGATGCATGAAATGCATTCGATGTT
1 ATCCTCAGTGCATCGGTGCATGGTA-GTGCATCGATGCATCAAATGCATTCGATGTT
2026387 CAATTTATTT
Statistics
Matches: 102, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 44 0.43
65 53 0.52
66 3 0.03
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.30
Consensus pattern (64 bp):
ATCCTCAGTGCATCGGTGCATGGTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAT
Found at i:2034953 original size:18 final size:17
Alignment explanation
Indices: 2034899--2034947 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
2034889 TTAGATCCTT
* *
2034899 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
2034917 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
2034935 AGTGCATTCGATG
1 AGTGCA-TCGATG
2034948 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:2035052 original size:65 final size:65
Alignment explanation
Indices: 2034919--2035078 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
2034909 TGCACTAAGA
*
2034919 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAAAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCAAAGTGCATCGATGCATGGCTG
* ** * *
2034983 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTTCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCAAAGTGCATCGATGCATGGCT
*
2035046 AT
65 -G
*
2035048 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
2035079 CAATTTATTT
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 29 0.34
65 53 0.62
66 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCAAAGTGCATCGATGCATGGCTG
Found at i:2037275 original size:16 final size:18
Alignment explanation
Indices: 2037254--2037293 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
2037244 AACGTCTTTT
2037254 AAAAATA-ATTTTAAGA-
1 AAAAATATATTTTAAGAC
*
2037270 AAAAATATTTTTTAAGAC
1 AAAAATATATTTTAAGAC
2037288 AAAAAT
1 AAAAAT
2037294 GGTCTGTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
17 8 0.38
18 6 0.29
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.33
Consensus pattern (18 bp):
AAAAATATATTTTAAGAC
Found at i:2037877 original size:10 final size:10
Alignment explanation
Indices: 2037854--2037919 Score: 51
Period size: 10 Copynumber: 6.2 Consensus size: 10
2037844 GTAAAGAATA
2037854 AAATAAACAAT
1 AAATAAA-AAT
2037865 AAATAAAAAT
1 AAATAAAAAT
*
2037875 AAATATGAAAT
1 AAATA-AAAAT
*
2037886 GAAATGAAATAT
1 -AAAT-AAAAAT
*
2037898 AAATATAAAT
1 AAATAAAAAT
* *
2037908 ATATAATAAT
1 AAATAAAAAT
2037918 AA
1 AA
2037920 TACATCTATA
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
10 20 0.47
11 15 0.35
12 7 0.16
13 1 0.02
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.26
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:2037885 original size:17 final size:16
Alignment explanation
Indices: 2037853--2037908 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
2037843 AGTAAAGAAT
*
2037853 AAAATAAACAATAAATA
1 AAAATAAA-TATAAATA
2037870 AAAATAAATATGAAAT-
1 AAAATAAATAT-AAATA
*
2037886 GAAATGAAATATAAATA
1 AAAAT-AAATATAAATA
*
2037903 TAAATA
1 AAAATA
2037909 TATAATAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 11 0.33
17 22 0.67
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (16 bp):
AAAATAAATATAAATA
Found at i:2037921 original size:19 final size:19
Alignment explanation
Indices: 2037899--2037943 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2037889 ATGAAATATA
2037899 AATATAAATATATAATAAT
1 AATATAAATATATAATAAT
* **
2037918 AATACATCTATATAATAAT
1 AATATAAATATATAATAAT
2037937 ATATATA
1 A-ATATA
2037944 CACAAATAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (19 bp):
AATATAAATATATAATAAT
Found at i:2038319 original size:30 final size:31
Alignment explanation
Indices: 2038280--2038352 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 31
2038270 GAATAATATG
*
2038280 AGGGACTAAAAT-GATAAAAACAGAAGC-TAA
1 AGGGACTAAAATAGA-AAAAACAGAAACTTAA
* *
2038310 AGGGTCTAAAATAGAAAAATCAGAAACTTAA
1 AGGGACTAAAATAGAAAAAACAGAAACTTAA
2038341 A-GGACTATAAAT
1 AGGGACTA-AAAT
2038353 TAATTACAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 26 0.72
31 10 0.28
ACGTcount: A:0.55, C:0.10, G:0.18, T:0.18
Consensus pattern (31 bp):
AGGGACTAAAATAGAAAAAACAGAAACTTAA
Found at i:2038583 original size:75 final size:76
Alignment explanation
Indices: 2038501--2038666 Score: 174
Period size: 75 Copynumber: 2.2 Consensus size: 76
2038491 ATCAAACATT
* * * *
2038501 GACTAAAATAAAATATTTATAAATTTAATGTCCAAATTCGAACA-CCAAGGAAAATAT-ACAAAA
1 GACTAAAATAAAATATTTATAAATGTAATGGCCAAATTCAAACATCAAAGG-AAATATCACAAAA
*
2038564 TATTAAATCAGG
65 TATGAAATCAGG
* ** * * * **
2038576 GACTAAAATGAAGGATTTATAAATGTCATGGCCAACTTCAAACATCAAAGGAAATTTCACAACTT
1 GACTAAAATAAAATATTTATAAATGTAATGGCCAAATTCAAACATCAAAGGAAATATCACAAAAT
*
2038641 ATGAAATCAGT
66 ATGAAATCAGG
*
2038652 GACTAAAATATAATA
1 GACTAAAATAAAATA
2038667 ACAAAATACA
Statistics
Matches: 71, Mismatches: 18, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
75 41 0.58
76 30 0.42
ACGTcount: A:0.49, C:0.13, G:0.11, T:0.27
Consensus pattern (76 bp):
GACTAAAATAAAATATTTATAAATGTAATGGCCAAATTCAAACATCAAAGGAAATATCACAAAAT
ATGAAATCAGG
Found at i:2039971 original size:14 final size:14
Alignment explanation
Indices: 2039952--2039989 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2039942 ACAAAAGTGT
*
2039952 AATAATAATATTAA
1 AATAATAATAATAA
2039966 AATAATAATAATAA
1 AATAATAATAATAA
*
2039980 ATTAA-AATAA
1 AATAATAATAA
2039990 AATTAAATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AATAATAATAATAA
Found at i:2040529 original size:134 final size:134
Alignment explanation
Indices: 2040195--2040738 Score: 743
Period size: 134 Copynumber: 4.1 Consensus size: 134
2040185 GTCCAAGGGT
* * * * *
2040195 GGATGACACGGCTCATAC-TGATGAAGAGTTCTGGTCATCTTTAGGAATGGTGATAACTAGGTTC
1 GGATGACACGACTCATACGCGATGAAGAGTTCTGGCCATCTTTAGGAAAGGTGATAACTCGGTTC
* * * ** * * *
2040259 CTACGTGATGAGGACAACTGGTTATCTAAGGGTGATACGACTCCTACGTGATGAGGAGATCTGGT
66 CTACGTGATGAGGACGACTGGTTATCTAAAGTTGACGCGGCTCCTACGTGATGAGGAGGTATGGT
*
2040324 C-GG
131 CAAG
* * * * * * **
2040327 GGATGACACGATTCCTACGTGATGAGGA-TAGCTGGCCATATTTAGGAGTGGTGATAACTCGGTT
1 GGATGACACGACTCATACGCGATGAAGAGT-TCTGGCCATCTTTAGGAAAGGTGATAACTCGGTT
* ** * **
2040391 CCTACGCGATGATAACGGCTGGTTATCTACGGTTGACGCGGCTCCTACGTGATGAGGAGGTATGG
65 CCTACGTGATGAGGACGACTGGTTATCTAAAGTTGACGCGGCTCCTACGTGATGAGGAGGTATGG
2040456 TCAAG
130 TCAAG
* *
2040461 GGATGACACTACTCATACGCGATGAAGAGTTTTGGCCATCTTTAGGAAAGGTGATAACTCGGTTC
1 GGATGACACGACTCATACGCGATGAAGAGTTCTGGCCATCTTTAGGAAAGGTGATAACTCGGTTC
2040526 CTACGTGATGAGGACGACTGGTTATCTAAAGTTGACGCGGCTCCTACGTGATGAGGAGGTATGGT
66 CTACGTGATGAGGACGACTGGTTATCTAAAGTTGACGCGGCTCCTACGTGATGAGGAGGTATGGT
*
2040591 CAAT
131 CAAG
* *
2040595 GGATGACACTACTCATACGCGATGAAGAGTTTTGGCCATCTTTAGGAAAGGTGATAACTCGGTTC
1 GGATGACACGACTCATACGCGATGAAGAGTTCTGGCCATCTTTAGGAAAGGTGATAACTCGGTTC
*
2040660 CTACGTGATGAGGACGACTGGTTATCTAAAGTTGACGCGGCTCCTACGTGATGAGGAGGTCTGGT
66 CTACGTGATGAGGACGACTGGTTATCTAAAGTTGACGCGGCTCCTACGTGATGAGGAGGTATGGT
*
2040725 CGAG
131 CAAG
2040729 GGATGACACG
1 GGATGACACG
2040739 GTTTCGACGT
Statistics
Matches: 365, Mismatches: 43, Indels: 6
0.88 0.10 0.01
Matches are distributed among these distances:
132 16 0.04
133 92 0.25
134 256 0.70
135 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (134 bp):
GGATGACACGACTCATACGCGATGAAGAGTTCTGGCCATCTTTAGGAAAGGTGATAACTCGGTTC
CTACGTGATGAGGACGACTGGTTATCTAAAGTTGACGCGGCTCCTACGTGATGAGGAGGTATGGT
CAAG
Found at i:2040901 original size:64 final size:64
Alignment explanation
Indices: 2040809--2041000 Score: 224
Period size: 64 Copynumber: 3.0 Consensus size: 64
2040799 AAGATAATTT
* * * *
2040809 GTTTCAAAAGAAATTGTCTCAAAAGAGACAAAACTCGTTTCAAGGGAAGCGACTCAAAGATGAC
1 GTTTCAAAGGAAACTGTCTCAAAAGAGACAAAATTCGTTTCAAGGGAAACGACTCAAAGATGAC
* ** * * * *
2040873 GTTTTAAAGGAAACTGTCTCAAGCGAGACAAAATTTGTTTTTAAGGGAAAC-TCTCAAAGATCGG
1 GTTTCAAAGGAAACTGTCTCAAAAGAGACAAAATTCG-TTTCAAGGGAAACGACTCAAAGAT-GA
*
2040937 T
64 C
* *
2040938 GTTTCATAGGAAACTGTCTCAAATGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATG
1 GTTTCAAAGGAAACTGTCTCAAAAGAGACAAAATTCGTTTCAAGGGAAACGA-CTCAAAGATG
2041001 TTTGTTTTGT
Statistics
Matches: 105, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
64 51 0.49
65 45 0.43
66 9 0.09
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.25
Consensus pattern (64 bp):
GTTTCAAAGGAAACTGTCTCAAAAGAGACAAAATTCGTTTCAAGGGAAACGACTCAAAGATGAC
Found at i:2041058 original size:36 final size:35
Alignment explanation
Indices: 2041005--2041137 Score: 111
Period size: 36 Copynumber: 3.9 Consensus size: 35
2040995 AAGATGTTTG
2041005 TTTTGTTT-CAAATGAAACAGACTCAAAGATAGTAAA
1 TTTTGTTTCCAAA-GAAACAGACTCAAAGATAG-AAA
2041041 TTTTGTTTCCAAAGAAACAGACTC----A-A-AAA
1 TTTTGTTTCCAAAGAAACAGACTCAAAGATAGAAA
* * * * * *
2041070 TTTT-TCTCAAAAGAAACTGTCTCAAGAGAGACAAAA
1 TTTTGTTTCCAAAGAAACAGACTCAA-AGATA-GAAA
*
2041106 TTTTGTTTCCAAAGAAACAGACCCAAAGATAG
1 TTTTGTTTCCAAAGAAACAGACTCAAAGATAG
2041138 GTTACGTTTT
Statistics
Matches: 76, Mismatches: 11, Indels: 21
0.70 0.10 0.19
Matches are distributed among these distances:
28 15 0.20
29 7 0.09
31 1 0.01
32 1 0.01
33 1 0.01
34 1 0.01
36 30 0.39
37 20 0.26
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.27
Consensus pattern (35 bp):
TTTTGTTTCCAAAGAAACAGACTCAAAGATAGAAA
Found at i:2041263 original size:66 final size:66
Alignment explanation
Indices: 2041152--2041309 Score: 257
Period size: 66 Copynumber: 2.4 Consensus size: 66
2041142 CGTTTTAAGT
*
2041152 GAGACAAAATTTG-TTTCAAATGAAACAATCTCAAAGGTTGGTTTTTCATTA-AAAATTGTCTCA
1 GAGACAAAATTTGTTTTCAAA-GAAACAATCTCAAAGGTTGATTTTTCATTAGAAAA-TGTCTCA
2041215 AGA
64 AGA
2041218 GAGACAAAATTTGTTTTCAAAGAAACAATCTCAAAGGTTGATTTTTCATTAGAAAATGTCTCAAG
1 GAGACAAAATTTGTTTTCAAAGAAACAATCTCAAAGGTTGATTTTTCATTAGAAAATGTCTCAAG
2041283 A
66 A
*
2041284 GAGATAAAATTTGTTTTTCAAAGAAA
1 GAGACAAAATTTG-TTTTCAAAGAAA
2041310 TAGACTCGAA
Statistics
Matches: 87, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
66 64 0.74
67 23 0.26
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (66 bp):
GAGACAAAATTTGTTTTCAAAGAAACAATCTCAAAGGTTGATTTTTCATTAGAAAATGTCTCAAG
A
Found at i:2041823 original size:71 final size:70
Alignment explanation
Indices: 2041742--2041932 Score: 190
Period size: 70 Copynumber: 2.7 Consensus size: 70
2041732 AGGAAAAAAA
** * * * * *
2041742 TGTCTCAAGCGAGATGAAGTTTGTTTT-AAGATAAATTGTCTTAGGTGAGACAAAATTTGTTTTT
1 TGTCTCAAGCGAGACAAAGTTTGTTTTCAAGA-AAACTGTCTCAAGCGAGACAAAATGTG-TTTT
2041806 CAAG-AAC
64 -AAGAAAC
* * *
2041813 TGTCTCAAGCGAGACAAATTTTTTTTTCAAGAAAACTGTCTCAAGCGAGACAAAATGTGTTTTGA
1 TGTCTCAAGCGAGACAAAGTTTGTTTTCAAGAAAACTGTCTCAAGCGAGACAAAATGTGTTTTAA
*
2041878 GAAAT
66 GAAAC
* ** *
2041883 TGTCTCAAGCGAGACAAAGTTTATTTTTGAGAAAAC-GTTCTCAAGTGAGA
1 TGTCTCAAGCGAGACAAAGTTTGTTTTCAAGAAAACTG-TCTCAAGCGAGA
2041933 TCAACTTTGT
Statistics
Matches: 101, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
69 3 0.03
70 49 0.49
71 45 0.45
72 4 0.04
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (70 bp):
TGTCTCAAGCGAGACAAAGTTTGTTTTCAAGAAAACTGTCTCAAGCGAGACAAAATGTGTTTTAA
GAAAC
Found at i:2041839 original size:34 final size:35
Alignment explanation
Indices: 2041788--2041910 Score: 142
Period size: 34 Copynumber: 3.5 Consensus size: 35
2041778 TGTCTTAGGT
*
2041788 GAGACAAAATTTGTTTTTCAAG-AACTGTCTCAAGC
1 GAGAC-AAATTTTTTTTTCAAGAAACTGTCTCAAGC
2041823 GAGACAAATTTTTTTTTCAAGAAAACTGTCTCAAGC
1 GAGACAAATTTTTTTTTCAAG-AAACTGTCTCAAGC
* * * * *
2041859 GAGACAAAATGTGTTTT-GAGAAATTGTCTCAAGC
1 GAGACAAATTTTTTTTTCAAGAAACTGTCTCAAGC
*
2041893 GAGACAAAGTTTATTTTT
1 GAGACAAA-TTTTTTTTT
2041911 GAGAAAACGT
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
34 36 0.48
35 12 0.16
36 27 0.36
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (35 bp):
GAGACAAATTTTTTTTTCAAGAAACTGTCTCAAGC
Found at i:2041857 original size:36 final size:35
Alignment explanation
Indices: 2041737--2041932 Score: 148
Period size: 36 Copynumber: 5.5 Consensus size: 35
2041727 CTCAAAGGAA
* ** * *
2041737 AAAAATGTCTCAAGCGAGATGAAGTTTGTTTTAAG
1 AAAACTGTCTCAAGCGAGACAAATTTTTTTTTAAG
* * * * *
2041772 ATAAATTGTCTTAGGTGAGACAAAATTTGTTTTTCAAG
1 A-AAACTGTCTCAAGCGAGAC-AAATTT-TTTTTTAAG
2041810 --AACTGTCTCAAGCGAGACAAATTTTTTTTTCAAG
1 AAAACTGTCTCAAGCGAGACAAATTTTTTTTT-AAG
* * * *
2041844 AAAACTGTCTCAAGCGAGACAAAATGTGTTTTGAG
1 AAAACTGTCTCAAGCGAGACAAATTTTTTTTTAAG
* * *
2041879 -AAATTGTCTCAAGCGAGACAAAGTTTATTTTTGAG
1 AAAACTGTCTCAAGCGAGACAAA-TTTTTTTTTAAG
*
2041914 AAAAC-GTTCTCAAGTGAGA
1 AAAACTG-TCTCAAGCGAGA
2041933 TCAACTTTGT
Statistics
Matches: 127, Mismatches: 25, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
33 5 0.04
34 30 0.24
35 26 0.20
36 55 0.43
37 4 0.03
38 7 0.06
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (35 bp):
AAAACTGTCTCAAGCGAGACAAATTTTTTTTTAAG
Found at i:2045045 original size:19 final size:18
Alignment explanation
Indices: 2045017--2045057 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
2045007 AAAATGCTTA
*
2045017 AAAATGAAATACGTATGC
1 AAAATGAAATACATATGC
*
2045035 AAAATGCAAATGCATATGC
1 AAAATG-AAATACATATGC
2045054 AAAA
1 AAAA
2045058 ATGTTGATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.54, C:0.12, G:0.15, T:0.20
Consensus pattern (18 bp):
AAAATGAAATACATATGC
Found at i:2047528 original size:6 final size:6
Alignment explanation
Indices: 2047488--2047546 Score: 54
Period size: 6 Copynumber: 10.2 Consensus size: 6
2047478 AAAATAAACA
* *
2047488 ATAAAT A-AAA- ATAAAT ATGAAAT -GAAAT -GAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT AT-AAAT ATAAAT ATAAAT ATAAAT ATAAAT
2047533 ATAAAT ATATAAT A
1 ATAAAT ATA-AAT A
2047547 ATAATACATC
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
4 1 0.02
5 15 0.33
6 22 0.48
7 8 0.17
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (6 bp):
ATAAAT
Found at i:2047538 original size:23 final size:23
Alignment explanation
Indices: 2047488--2047539 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
2047478 AAAATAAACA
2047488 ATAAATAAAAATAAATATGAAAT
1 ATAAATAAAAATAAATATGAAAT
* *
2047511 -GAAATGAAATATAAATAT-AAAT
1 ATAAAT-AAAAATAAATATGAAAT
2047533 ATAAATA
1 ATAAATA
2047540 TATAATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (23 bp):
ATAAATAAAAATAAATATGAAAT
Found at i:2047552 original size:19 final size:19
Alignment explanation
Indices: 2047517--2047574 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
2047507 AAATGAAATG
2047517 AAATATA-AAT-ATAAATAT
1 AAATATATAATAAT-AATAT
*
2047535 AAATATATAATAATAATAC
1 AAATATATAATAATAATAT
**
2047554 ATCTATATAATAATATATAT
1 AAATATATAATAATA-ATAT
2047574 A
1 A
2047575 CACAAATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 7 0.21
19 20 0.61
20 6 0.18
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATATATAATAATAATAT
Found at i:2047948 original size:30 final size:31
Alignment explanation
Indices: 2047909--2047981 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 31
2047899 GAATAATATG
*
2047909 AGGGACTAAAAT-GATAAAAACAGAAGC-TAA
1 AGGGACTAAAATAGA-AAAAACAGAAACTTAA
* *
2047939 AGGGTCTAAAATAGAAAAATCAGAAACTTAA
1 AGGGACTAAAATAGAAAAAACAGAAACTTAA
2047970 A-GGACTATAAAT
1 AGGGACTA-AAAT
2047982 TAATTACAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 26 0.72
31 10 0.28
ACGTcount: A:0.55, C:0.10, G:0.18, T:0.18
Consensus pattern (31 bp):
AGGGACTAAAATAGAAAAAACAGAAACTTAA
Found at i:2048212 original size:75 final size:76
Alignment explanation
Indices: 2048130--2048295 Score: 174
Period size: 75 Copynumber: 2.2 Consensus size: 76
2048120 ATCAAACATT
* * * *
2048130 GACTAAAATAAAATATTTATAAATTTAATGTCCAAATTCGAACA-CCAAGGAAAATAT-ACAAAA
1 GACTAAAATAAAATATTTATAAATGTAATGGCCAAATTCAAACATCAAAGG-AAATATCACAAAA
*
2048193 TATTAAATCAGG
65 TATGAAATCAGG
* ** * * * **
2048205 GACTAAAATGAAGGATTTATAAATGTCATGGCCAACTTCAAACATCAAAGGAAATTTCACAACTT
1 GACTAAAATAAAATATTTATAAATGTAATGGCCAAATTCAAACATCAAAGGAAATATCACAAAAT
*
2048270 ATGAAATCAGT
66 ATGAAATCAGG
*
2048281 GACTAAAATATAATA
1 GACTAAAATAAAATA
2048296 ACAAAAAGTA
Statistics
Matches: 71, Mismatches: 18, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
75 41 0.58
76 30 0.42
ACGTcount: A:0.49, C:0.13, G:0.11, T:0.27
Consensus pattern (76 bp):
GACTAAAATAAAATATTTATAAATGTAATGGCCAAATTCAAACATCAAAGGAAATATCACAAAAT
ATGAAATCAGG
Found at i:2049576 original size:3 final size:3
Alignment explanation
Indices: 2049568--2049605 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
2049558 TACAAAAGTG
*
2049568 TAA TAA TAA TAT TAA -AA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2049606 ATTAAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2056706 original size:29 final size:29
Alignment explanation
Indices: 2056646--2056729 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
2056636 ATTCTACAGT
* ***
2056646 GACCAAGGAGGTCGCCATGCACTCCGGGC
1 GACCAAGGAGGTCGCCATGCACGCCCAAC
2056675 GACCAAGGAGGTCGCCATGCACGCCCAAC
1 GACCAAGGAGGTCGCCATGCACGCCCAAC
* *
2056704 GACCTTA-TAGGTCGCCATGCACGCCC
1 GACC-AAGGAGGTCGCCATGCACGCCC
2056730 GGCGTCCTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
29 47 0.98
30 1 0.02
ACGTcount: A:0.23, C:0.37, G:0.29, T:0.12
Consensus pattern (29 bp):
GACCAAGGAGGTCGCCATGCACGCCCAAC
Found at i:2056738 original size:29 final size:29
Alignment explanation
Indices: 2056683--2056764 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
2056673 GCGACCAAGG
** *
2056683 AGGTCGCCATGCACGCCCAACGACCTTAT
1 AGGTCGCCATGCACGCCCGGCGTCCTTAT
2056712 AGGTCGCCATGCACGCCCGGCGTCCTTAT
1 AGGTCGCCATGCACGCCCGGCGTCCTTAT
2056741 AGGTCGCCATGCACGCCCGGCGTC
1 AGGTCGCCATGCACGCCCGGCGTC
2056765 ATTTCGTTCC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.17, C:0.39, G:0.27, T:0.17
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGTCCTTAT
Found at i:2057454 original size:8 final size:8
Alignment explanation
Indices: 2057441--2057466 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2057431 TATATAAAAA
2057441 AATTAGTT
1 AATTAGTT
2057449 AATTAGTT
1 AATTAGTT
2057457 AATTAGTT
1 AATTAGTT
2057465 AA
1 AA
2057467 AGTTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (8 bp):
AATTAGTT
Found at i:2057598 original size:21 final size:21
Alignment explanation
Indices: 2057573--2057612 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2057563 GTTAATTAGT
2057573 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
2057594 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
2057613 CATATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:2057854 original size:22 final size:22
Alignment explanation
Indices: 2057829--2057909 Score: 81
Period size: 22 Copynumber: 3.3 Consensus size: 22
2057819 AATCATTTAT
2057829 TAGTTTAAGTTATATTAAAGAA
1 TAGTTTAAGTTATATTAAAGAA
2057851 TAGTTTATTAGTTAACGTTATATTAAAGAA
1 TAG-----T--TTAA-GTTATATTAAAGAA
*
2057881 TAGTTAAAGTTATATTAAAGAA
1 TAGTTTAAGTTATATTAAAGAA
2057903 TAGTTTA
1 TAGTTTA
2057910 TTAGTTGTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
22 23 0.47
23 3 0.06
25 1 0.02
27 1 0.02
29 4 0.08
30 17 0.35
ACGTcount: A:0.43, C:0.01, G:0.14, T:0.42
Consensus pattern (22 bp):
TAGTTTAAGTTATATTAAAGAA
Found at i:2057857 original size:327 final size:326
Alignment explanation
Indices: 2057256--2057860 Score: 756
Period size: 327 Copynumber: 1.8 Consensus size: 326
2057246 TTGCTTGATG
* *
2057256 GTTATATTATTGTTAGTTTAAGTTATATCATACATAAATATAAAATTATTTAATTAGTTTGTTTG
1 GTTATATTATTGTTAGTTTAAGTTATATCATACAGAAATATAAAATTATTTAATTAGTATGTTTG
* *
2057321 ATGGTTATATATTAAAAATAATAATTAATTAGTGTGTTAGTTAGTCTAATTTTTAATTAGTTTGT
66 ATAGTTACATATTAAAAATAATAATTAATTAGTGTGTTAGTTAGTCTAATTTTTAATTAGTTTGT
*
2057386 AGTTAGTTAAATAGTTACGTAATATTTTGGTTGTTGAATTTATATTATATAAAAAAATTAGTTAA
131 AGTTAGTTAAATAGTTAAGTAATATTTTGGTTGTTGAATTTATATTATATAAAAAAATTAGTTAA
* **
2057451 TTAGTTAATTAGTTAAAGTTATATAAAAGAATAATTATTTAAATTAGTTTATTTTTATAAATTAT
196 TTAGTTAATTAGTTAAAGTTATATAAAAGAATAATCATTT-AATTAGTTTATAGTTAT-AATTAT
*
2057516 TAGTTAATTAGTTTATTATTATAAATTAGGGTAAAACAAAAAAATTAGTTAATTAGTTTGTTAGT
259 AAG-TAATTAGTTTATTATTATAAATTAGGGTAAAACAAAAAAATTAGTTAATTAGTTTGTTAGT
2057581 TTAA
323 TTAA
*
2057585 GTTATATTATTGTTAGTTTAAGTTATATCATATAGAAA-A-AAAATTATTTAATTAGTATGTTTG
1 GTTATATTATTGTTAGTTTAAGTTATATCATACAGAAATATAAAATTATTTAATTAGTATGTTTG
* *
2057648 ATAGTTACATATTAATAAA-AATAATTAGTTAGTTTGTTAGTCGTTAGT-TATATATAAAAAAAT
66 ATAGTTACATATTAA-AAATAATAATTAATTAGTGTGTTA---GTTAGTCTA-AT-T-------T
* *
2057711 ATGTAATTAGTTTGT-GTTAGTTAAATAGTTAAGTTATA-TTTGTTTGTTGAATTTATATTATAT
118 -T-TAATTAGTTTGTAGTTAGTTAAATAGTTAAGTAATATTTTGGTTGTTGAATTTATATTATAT
** **
2057774 AAAAAAATTAGTTAATTAGTTTTTTAGTAGTAAA-TTATA-ATTA-AA-AATCATTT-ATTAGTT
181 AAAAAAATTAGTTAATTAGTTAATTAGT--TAAAGTTATATAAAAGAATAATCATTTAATTAGTT
2057834 TA-AGTTAT-ATTA-AAG-AA-TAGTTTATTA
244 TATAGTTATAATTATAAGTAATTAGTTTATTA
2057861 GTTAACGTTA
Statistics
Matches: 241, Mismatches: 18, Indels: 36
0.82 0.06 0.12
Matches are distributed among these distances:
327 64 0.27
328 6 0.02
329 38 0.16
330 10 0.04
331 5 0.02
333 4 0.02
334 9 0.04
336 7 0.03
337 2 0.01
338 53 0.22
339 27 0.11
340 16 0.07
ACGTcount: A:0.40, C:0.01, G:0.12, T:0.47
Consensus pattern (326 bp):
GTTATATTATTGTTAGTTTAAGTTATATCATACAGAAATATAAAATTATTTAATTAGTATGTTTG
ATAGTTACATATTAAAAATAATAATTAATTAGTGTGTTAGTTAGTCTAATTTTTAATTAGTTTGT
AGTTAGTTAAATAGTTAAGTAATATTTTGGTTGTTGAATTTATATTATATAAAAAAATTAGTTAA
TTAGTTAATTAGTTAAAGTTATATAAAAGAATAATCATTTAATTAGTTTATAGTTATAATTATAA
GTAATTAGTTTATTATTATAAATTAGGGTAAAACAAAAAAATTAGTTAATTAGTTTGTTAGTTTA
A
Found at i:2057858 original size:30 final size:30
Alignment explanation
Indices: 2057790--2057915 Score: 112
Period size: 30 Copynumber: 4.4 Consensus size: 30
2057780 ATTAGTTAAT
* * *
2057790 TAGTTTTTTAGTAGTAAATTATAATTAAA-AA
1 TAGTTTATTAGT-TTAAGTTAT-ATTAAAGAA
2057821 TCA-TTTATTAGTTTAAGTTATATTAAAGAA
1 T-AGTTTATTAGTTTAAGTTATATTAAAGAA
2057851 TAGTTTATTAG-TTAACGTTATATTAAAGAA
1 TAGTTTATTAGTTTAA-GTTATATTAAAGAA
2057881 TAG----TTA----AAGTTATATTAAAGAA
1 TAGTTTATTAGTTTAAGTTATATTAAAGAA
2057903 TAGTTTATTAGTT
1 TAGTTTATTAGTT
2057916 GTTTAAGGAA
Statistics
Matches: 81, Mismatches: 3, Indels: 24
0.75 0.03 0.22
Matches are distributed among these distances:
22 17 0.21
23 2 0.02
26 6 0.07
29 11 0.14
30 35 0.43
31 9 0.11
32 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (30 bp):
TAGTTTATTAGTTTAAGTTATATTAAAGAA
Found at i:2060372 original size:59 final size:59
Alignment explanation
Indices: 2060237--2060372 Score: 138
Period size: 59 Copynumber: 2.3 Consensus size: 59
2060227 AATATTTAGT
* * *
2060237 AATTCGACTATTTTAAATCATTAGTATCAAATAATTAAATATTAATAATAAATCATTATT
1 AATTTGACTATTATAAATCATTAGTATCAAATAATTAAATATT-ATAATAAATCATTATA
* * *
2060297 AA--T-AATAATTAGTAAATCATTAGTATCGAATCATTAAATATT-TAA-AAATCATTAATA
1 AATTTGACT-ATTA-TAAATCATTAGTATCAAATAATTAAATATTATAATAAATCATT-ATA
2060354 AATTTGACTATGTATAAAT
1 AATTTGACTAT-TATAAAT
2060373 TTAAACTCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
56 8 0.13
57 9 0.15
58 3 0.05
59 36 0.58
60 6 0.10
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (59 bp):
AATTTGACTATTATAAATCATTAGTATCAAATAATTAAATATTATAATAAATCATTATA
Found at i:2060456 original size:14 final size:13
Alignment explanation
Indices: 2060437--2060578 Score: 79
Period size: 14 Copynumber: 11.1 Consensus size: 13
2060427 TAGTAATAAT
2060437 TATTAAATCATTA
1 TATTAAATCATTA
2060450 GTATTAAATCATTA
1 -TATTAAATCATTA
*
2060464 TTATAAAATCA-T-
1 -TATTAAATCATTA
* *
2060476 TACTAAATAATTA
1 TATTAAATCATTA
2060489 CTATTAAATCA-T-
1 -TATTAAATCATTA
* *
2060501 TATTATCATTATTA
1 TATTA-AATCATTA
2060515 TAATTAAATCA-T-
1 T-ATTAAATCATTA
2060527 TATT--ATCATTA
1 TATTAAATCATTA
2060538 TTATTAAATC-TT-
1 -TATTAAATCATTA
*
2060550 TATTATAATGATTA
1 TATTA-AATCATTA
*
2060564 TTACTAAATCATTA
1 -TATTAAATCATTA
2060578 T
1 T
2060579 TATAATGATT
Statistics
Matches: 98, Mismatches: 14, Indels: 33
0.68 0.10 0.23
Matches are distributed among these distances:
9 4 0.04
10 1 0.01
11 20 0.20
12 12 0.12
13 9 0.09
14 44 0.45
15 8 0.08
ACGTcount: A:0.43, C:0.08, G:0.01, T:0.47
Consensus pattern (13 bp):
TATTAAATCATTA
Found at i:2060510 original size:9 final size:9
Alignment explanation
Indices: 2060496--2060541 Score: 67
Period size: 9 Copynumber: 5.2 Consensus size: 9
2060486 TTACTATTAA
2060496 ATCATTATT
1 ATCATTATT
2060505 ATCATTATT
1 ATCATTATT
* *
2060514 ATAATTA-A
1 ATCATTATT
2060522 ATCATTATT
1 ATCATTATT
2060531 ATCATTATT
1 ATCATTATT
2060540 AT
1 AT
2060542 TAAATCTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
8 6 0.19
9 26 0.81
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (9 bp):
ATCATTATT
Found at i:2060511 original size:17 final size:17
Alignment explanation
Indices: 2060505--2060537 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2060495 AATCATTATT
2060505 ATCATTATTATAATTAA
1 ATCATTATTATAATTAA
*
2060522 ATCATTATTATCATTA
1 ATCATTATTATAATTA
2060538 TTATTAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (17 bp):
ATCATTATTATAATTAA
Found at i:2060514 original size:26 final size:25
Alignment explanation
Indices: 2060437--2060714 Score: 162
Period size: 26 Copynumber: 11.0 Consensus size: 25
2060427 TAGTAATAAT
* *
2060437 TATTAAATCATTAGTATTAAATCATTA
1 TATTAAATCATTATTA-T-AATTATTA
* * *
2060464 TTATAAAATCATTACTA-AATAATTA
1 -TATTAAATCATTATTATAATTATTA
*
2060489 CTATTAAATCATTATTATCATTATTA
1 -TATTAAATCATTATTATAATTATTA
*
2060515 TAATTAAATCATTATTATCATTA-T-
1 T-ATTAAATCATTATTATAATTATTA
* *
2060539 TATTAAATCTTTATTATAATGATTA
1 TATTAAATCATTATTATAATTATTA
* *
2060564 TTACTAAATCATTATTATAATGATTA
1 -TATTAAATCATTATTATAATTATTA
* * * *
2060590 TTATCAAATCATTACTA-AATCATCAAA
1 -TATTAAATCATTATTATAATTAT--TA
*
2060617 TAATTAAAT-A-T-TTA-AATCA-T-
1 T-ATTAAATCATTATTATAATTATTA
* **
2060637 TATTAAATTATTATTATAATGGTTA
1 TATTAAATCATTATTATAATTATTA
* *
2060662 TTACTAAATCATTATTATAATGATTA
1 -TATTAAATCATTATTATAATTATTA
* * *
2060688 TTATCAAATCATTACTATAATGATTA
1 -TATTAAATCATTATTATAATTATTA
2060714 T
1 T
2060715 TATCAAACCA
Statistics
Matches: 206, Mismatches: 29, Indels: 33
0.77 0.11 0.12
Matches are distributed among these distances:
19 7 0.03
20 2 0.01
21 1 0.00
22 3 0.01
23 21 0.10
24 10 0.05
25 30 0.15
26 111 0.54
27 7 0.03
28 14 0.07
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (25 bp):
TATTAAATCATTATTATAATTATTA
Found at i:2060528 original size:23 final size:23
Alignment explanation
Indices: 2060502--2060552 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
2060492 TTAAATCATT
*
2060502 ATTATCATTATTATAATTAAATC
1 ATTATCATCATTATAATTAAATC
* *
2060525 ATTATTATCATTATTATTAAATC
1 ATTATCATCATTATAATTAAATC
*
2060548 TTTAT
1 ATTAT
2060553 TATAATGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTATCATCATTATAATTAAATC
Found at i:2060553 original size:49 final size:49
Alignment explanation
Indices: 2060422--2060714 Score: 211
Period size: 52 Copynumber: 5.8 Consensus size: 49
2060412 TTATTCTATA
* * * *
2060422 ATTATTAGTAATAATTATTAAATCATTAGTATTAAATCATTATTA-TAAAATC
1 ATTATTA-TAATTATTATTAAATCATTATTA-T-AATGATTATAACT-AAATC
* * * * *
2060474 ATTACTAAATAATTACTATTAAATCATTATTATCATTATTATAATTAAATC
1 ATTA-T-TATAATTATTATTAAATCATTATTATAATGATTATAACTAAATC
* * *
2060525 ATTATTATCATTATTATTAAATCTTTATTATAATGATTATTACTAAATC
1 ATTATTATAATTATTATTAAATCATTATTATAATGATTATAACTAAATC
* * * * *
2060574 ATTATTATAATGATTATTATCAAATCATTACTA-AATCATCAAATAATTAAAT-
1 ATTATTAT-A--ATTATTATTAAATCATTATTATAATGAT--TATAACTAAATC
* * * *
2060626 A-T-TTA-AATCATTATTAAATTATTATTATAATGGTTATTACTAAATC
1 ATTATTATAATTATTATTAAATCATTATTATAATGATTATAACTAAATC
* *
2060672 ATTATTATAATGATTATTATCAAATCATTACTATAATGATTAT
1 ATTATTAT-A--ATTATTATTAAATCATTATTATAATGATTAT
2060715 TATCAAACCA
Statistics
Matches: 188, Mismatches: 37, Indels: 32
0.73 0.14 0.12
Matches are distributed among these distances:
45 8 0.04
46 18 0.10
47 5 0.03
48 4 0.02
49 44 0.23
50 5 0.03
51 23 0.12
52 51 0.27
53 29 0.15
54 1 0.01
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (49 bp):
ATTATTATAATTATTATTAAATCATTATTATAATGATTATAACTAAATC
Found at i:2060664 original size:12 final size:12
Alignment explanation
Indices: 2060635--2060717 Score: 78
Period size: 12 Copynumber: 6.7 Consensus size: 12
2060625 TATTTAAATC
*
2060635 ATTATTA-AATT
1 ATTATTATAATG
2060646 ATTATTATAATG
1 ATTATTATAATG
* *
2060658 GTTATTACTAAATC
1 ATTATTA-T-AATG
2060672 ATTATTATAATG
1 ATTATTATAATG
*
2060684 ATTATTATCAAATC
1 ATTATTAT--AATG
*
2060698 ATTACTATAATG
1 ATTATTATAATG
2060710 ATTATTAT
1 ATTATTAT
2060718 CAAACCATTA
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
11 7 0.12
12 30 0.52
13 2 0.03
14 19 0.33
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (12 bp):
ATTATTATAATG
Found at i:2060680 original size:124 final size:124
Alignment explanation
Indices: 2060422--2060750 Score: 382
Period size: 124 Copynumber: 2.6 Consensus size: 124
2060412 TTATTCTATA
* * * * *
2060422 ATTATTAGTAATAATTA-T-TAAATCATTAGTATTAAATCATTATTATAAAATCATTACTAAATA
1 ATTATTA-TAATGATTATTATAAATCATTACTA-T-AATGATTATTATCAAATCATTACTAAATC
* * * * *
2060485 AT-TACTATTAAATCATTATTATCATTATTATAATTAAATCATTATTATCATTATTATTAAATC
63 ATCAAATATTAAAT-ATTATAATCATTATTATAATT-AATCATTATAATCATTATTACTAAATC
* *
2060548 TTTATTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCAT
1 ATTATTATAATGATTATTA-TAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCAT
* **
2060613 CAAATAATTAAATATT-TAAATCATTATTA-AATT-ATTATTATAATGGTTATTACTAAATC
65 CAAAT-ATTAAATATTAT-AATCATTATTATAATTAATCATTATAATCATTATTACTAAATC
*
2060672 ATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAACCATTACTAAATCAT
1 ATTATTATAATGATTATTAT-AAATCATTACTATAATGATTATTATCAAATCATTACTAAATCAT
2060737 CAAATCATTAAATA
65 CAAAT-ATTAAATA
2060751 GTCACGTACC
Statistics
Matches: 178, Mismatches: 18, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
123 1 0.01
124 94 0.53
125 8 0.04
126 40 0.22
127 16 0.09
128 19 0.11
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (124 bp):
ATTATTATAATGATTATTATAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATC
AAATATTAAATATTATAATCATTATTATAATTAATCATTATAATCATTATTACTAAATC
Found at i:2060715 original size:26 final size:26
Alignment explanation
Indices: 2060635--2060730 Score: 122
Period size: 26 Copynumber: 3.7 Consensus size: 26
2060625 TATTTAAATC
* * * *
2060635 ATTATTAAATTATTATTATAATGGTT
1 ATTATCAAATCATTACTATAATGATT
*
2060661 ATTA-CTAAATCATTATTATAATGATT
1 ATTATC-AAATCATTACTATAATGATT
2060687 ATTATCAAATCATTACTATAATGATT
1 ATTATCAAATCATTACTATAATGATT
*
2060713 ATTATCAAACCATTACTA
1 ATTATCAAATCATTACTA
2060731 AATCATCAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
26 62 0.98
27 1 0.02
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (26 bp):
ATTATCAAATCATTACTATAATGATT
Found at i:2063196 original size:28 final size:29
Alignment explanation
Indices: 2063155--2063217 Score: 101
Period size: 28 Copynumber: 2.2 Consensus size: 29
2063145 TTTTTTTATA
2063155 TAATATAATTTATAACTTAAACCAACAAAC
1 TAATATAA-TTATAACTTAAACCAACAAAC
*
2063185 TAATATAA-TATAACTTAAACTAACAAAC
1 TAATATAATTATAACTTAAACCAACAAAC
2063213 TAATA
1 TAATA
2063218 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 24 0.75
30 8 0.25
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.30
Consensus pattern (29 bp):
TAATATAATTATAACTTAAACCAACAAAC
Found at i:2063224 original size:28 final size:28
Alignment explanation
Indices: 2063159--2063224 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
2063149 TTTATATAAT
2063159 ATAATTTATAACTTAAACCAACAAACTA
1 ATAATTTATAACTTAAACCAACAAACTA
* *
2063187 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-TTATAACTTAAACCAACAAACTA
2063215 ATAATTTATA
1 ATAATTTATA
2063225 CTAACAAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATTTATAACTTAAACCAACAAACTA
Found at i:2063227 original size:21 final size:21
Alignment explanation
Indices: 2063194--2063242 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
2063184 CTAATATAAT
2063194 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
2063215 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
2063236 ATTAACT
1 A-TAACT
2063243 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:2064613 original size:24 final size:21
Alignment explanation
Indices: 2064595--2064649 Score: 89
Period size: 18 Copynumber: 2.8 Consensus size: 21
2064585 GCGTAGAATT
2064595 TGTCCCGAAGGACCACGTAGA
1 TGTCCCGAAGGACCACGTAGA
2064616 TGTCCCGAAGGACCAC-T--A
1 TGTCCCGAAGGACCACGTAGA
2064634 TGTCCCGAAGGACCAC
1 TGTCCCGAAGGACCAC
2064650 ATATAACACA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
18 17 0.50
20 1 0.03
21 16 0.47
ACGTcount: A:0.27, C:0.33, G:0.25, T:0.15
Consensus pattern (21 bp):
TGTCCCGAAGGACCACGTAGA
Found at i:2066229 original size:41 final size:43
Alignment explanation
Indices: 2066177--2066289 Score: 185
Period size: 41 Copynumber: 2.7 Consensus size: 43
2066167 GTTTGTAAAG
2066177 ACAAACGCCGCTATTGACTGTGTATTTAGCG-CATTTTT-TTT
1 ACAAACGCCGCTATTGACTGTGTATTTAGCGACATTTTTCTTT
* *
2066218 ACAAACACCGCTATTGACTGTGTATTTAGCGACGTTTTTCTTT
1 ACAAACGCCGCTATTGACTGTGTATTTAGCGACATTTTTCTTT
*
2066261 ACAAACGCCGCTACTGACTGTGTATTTAG
1 ACAAACGCCGCTATTGACTGTGTATTTAG
2066290 TGGCATTTAT
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
41 30 0.45
42 6 0.09
43 30 0.45
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (43 bp):
ACAAACGCCGCTATTGACTGTGTATTTAGCGACATTTTTCTTT
Found at i:2066310 original size:43 final size:41
Alignment explanation
Indices: 2066177--2066312 Score: 155
Period size: 43 Copynumber: 3.2 Consensus size: 41
2066167 GTTTGTAAAG
* *
2066177 ACAAACGCCGCTATTGACTGTGTATTTAGCGCATTTTTTTT
1 ACAAACGCCGCTATTGACTGTGTATTTAGGGCATTTTATTT
* * * *
2066218 ACAAACACCGCTATTGACTGTGTATTTAGCGACGTTTTTCTTT
1 ACAAACGCCGCTATTGACTGTGTATTTAG-GGC-ATTTTATTT
* *
2066261 ACAAACGCCGCTACTGACTGTGTATTTAGTGGCATTTATAATT
1 ACAAACGCCGCTATTGACTGTGTATTTAG-GGCATTT-TATTT
*
2066304 AAAAACGCC
1 ACAAACGCC
2066313 ACAAATAAGC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
41 28 0.35
42 4 0.05
43 47 0.59
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (41 bp):
ACAAACGCCGCTATTGACTGTGTATTTAGGGCATTTTATTT
Found at i:2069098 original size:10 final size:11
Alignment explanation
Indices: 2069075--2069184 Score: 56
Period size: 10 Copynumber: 10.6 Consensus size: 11
2069065 TTTAATGTTT
*
2069075 ATTTTATAATA
1 ATTTAATAATA
2069086 ATTTAATAA-A
1 ATTTAATAATA
*
2069096 ATTTAATAATC
1 ATTTAATAATA
2069107 A-TTAATAATA
1 ATTTAATAATA
* *
2069117 AATTGAT--TA
1 ATTTAATAATA
*
2069126 ATTTAA-AAAA
1 ATTTAATAATA
* *
2069136 TATTTGATAATT
1 -ATTTAATAATA
* *
2069148 ATTTAA-AGTT
1 ATTTAATAATA
*
2069158 ATTTAATAA-C
1 ATTTAATAATA
2069168 ATTTAAT-ATA
1 ATTTAATAATA
*
2069178 CTTTAAT
1 ATTTAAT
2069185 CGATATGTCA
Statistics
Matches: 75, Mismatches: 16, Indels: 17
0.69 0.15 0.16
Matches are distributed among these distances:
9 7 0.09
10 42 0.56
11 24 0.32
12 2 0.03
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (11 bp):
ATTTAATAATA
Found at i:2069582 original size:41 final size:41
Alignment explanation
Indices: 2069530--2069885 Score: 304
Period size: 41 Copynumber: 8.9 Consensus size: 41
2069520 TTGTAAACAC
**
2069530 AAACGCCACTAAAACACGAGTCTATAGCGGCGTTTGTATAA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
* *** **
2069571 AAACGTCACTAAATCGTGAGTCTATAGCAACGTTTGTA-AA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
*
2069611 AAACACCACT--A--A--A-TCTATAGCGGCGTTTGTA-ACA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATA-A
* * * * *
2069645 AACACGTCACTAAAGTACGAGTCTTTAGCGGAGTTTATATAA
1 AA-ACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
** * *
2069687 AAACATCACTAAATCATGAGTCTATAGCGGCGTTTGTATAA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
* * *
2069728 AAACGCTACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
* * * *
2069769 AAATGCCACTAAATTAC-AGACTTTAGCGACGTTTGTATAA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
* * *
2069809 AAACGCCACTAAATTA-TATTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
* * * * *
2069849 AAACACCGCTATAA-TAGGAGTCTTTAGCGACGTTTGT
1 AAACGCCACTA-AATTACGAGTCTATAGCGGCGTTTGT
2069886 TCTTAAAATG
Statistics
Matches: 258, Mismatches: 44, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
33 17 0.07
34 4 0.02
35 6 0.02
37 1 0.00
38 1 0.00
39 1 0.00
40 77 0.30
41 132 0.51
42 18 0.07
43 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (41 bp):
AAACGCCACTAAATTACGAGTCTATAGCGGCGTTTGTATAA
Found at i:2069638 original size:33 final size:34
Alignment explanation
Indices: 2069591--2069658 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
2069581 AAATCGTGAG
2069591 TCTATAGCAACGTTTGTAAAAAACAC-CACTAAA
1 TCTATAGCAACGTTTGTAAAAAACACGCACTAAA
** *
2069624 TCTATAGCGGCGTTTGTAACAAACACGTCACTAAA
1 TCTATAGCAACGTTTGTAAAAAACACG-CACTAAA
2069659 GTACGAGTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 23 0.77
35 7 0.23
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.25
Consensus pattern (34 bp):
TCTATAGCAACGTTTGTAAAAAACACGCACTAAA
Found at i:2069874 original size:81 final size:80
Alignment explanation
Indices: 2069547--2069885 Score: 320
Period size: 81 Copynumber: 4.2 Consensus size: 80
2069537 ACTAAAACAC
* * * * **
2069547 GAGTCTATAGCGGCGTTTGTATAAAAACGTCACTAAA-T-CGTGAGTCTATAGCAACGTTTGTA-
1 GAGTCTTTAGCGACGTTTGTATAAAAACGCCACTAAAGTAC--GAGTCTTTAGCGGCGTTTGTAT
2069609 AAAAACACCACT--A-A
64 AAAAACACCACTAAATA
* * * * *
2069623 -A-TCTATAGCGGCGTTTGTA-ACAAACACGTCACTAAAGTACGAGTCTTTAGCGGAGTTTATAT
1 GAGTCTTTAGCGACGTTTGTATA-AAA-ACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTAT
*
2069685 AAAAACATCACTAAATCA
64 AAAAACACCACTAAAT-A
* * *
2069703 TGAGTCTATAGCGGCGTTTGTATAAAAACGCTACTAAAGTACGAGTCTTTAGCGGCGTTTGTATA
1 -GAGTCTTTAGCGACGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATA
**
2069768 AAAATGCCACTAAATTA
65 AAAACACCACTAAA-TA
* * * * *
2069785 CAGACTTTAGCGACGTTTGTATAAAAACGCCACTAAATTA-TATTCTTTAGCGGCGTTTGTATAA
1 GAGTCTTTAGCGACGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
*
2069849 AAACACCGCTATAATA
66 AAACACCACTA-AATA
2069865 GGAGTCTTTAGCGACGTTTGT
1 -GAGTCTTTAGCGACGTTTGT
2069886 TCTTAAAATG
Statistics
Matches: 221, Mismatches: 26, Indels: 27
0.81 0.09 0.10
Matches are distributed among these distances:
73 1 0.00
74 21 0.10
75 28 0.13
76 12 0.05
77 1 0.00
78 1 0.00
80 33 0.15
81 54 0.24
82 47 0.21
83 22 0.10
84 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (80 bp):
GAGTCTTTAGCGACGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
AAACACCACTAAATA
Found at i:2070522 original size:29 final size:29
Alignment explanation
Indices: 2070489--2070552 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
2070479 CATGCATCGC
*
2070489 TCCTTGGTCGCCCCGAGTGCATGGCGACA
1 TCCTTGGTCGCCCCGAGTGCATGACGACA
* *
2070518 TCCTTGGTCGCCCGGAGTGCATGACGACC
1 TCCTTGGTCGCCCCGAGTGCATGACGACA
2070547 TCCTTG
1 TCCTTG
2070553 ATCACTGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.12, C:0.34, G:0.30, T:0.23
Consensus pattern (29 bp):
TCCTTGGTCGCCCCGAGTGCATGACGACA
Found at i:2072811 original size:223 final size:226
Alignment explanation
Indices: 2072401--2072988 Score: 1008
Period size: 223 Copynumber: 2.6 Consensus size: 226
2072391 TAAATAATAT
*
2072401 ATATCAAAACAATCAAATAATTTTGTG-GTAAATGAAATTATTAAATTAATATTGTAGGTGGAAA
1 ATATCAAAA-AATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATA-TGTAGGTGGAAA
*
2072465 ACATGAAACACTATTAAAAAAAATTGAAACATAAATTACAT-AACTTAAAAAAAGTATATATCAT
64 ACATGAAACACTATT-AAAAAAATTGAAACATAAATTACATAAATTTAAAAAAAGTATATATCAT
*
2072529 TTTATAAAAGTGTCTATACTTATTTCACTGTGGAAAACATATTTACTATTATCTTTGGTTAATAT
128 TTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTACTATTATCTTTGGTTAATAT
2072594 TGTTAAATTTAAATTCTAAATAATATTTTATAAA
193 TGTTAAATTTAAATTCTAAATAATATTTTATAAA
2072628 ATATCAAAAAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATA-GTAGGTGGAAAAC
1 ATATCAAAAAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATGTAGGTGGAAAAC
*
2072692 ATGAAACACTATTAAAAAATTTGAAACAT-AATTACATAAATTTAAAAAAAGTATATATCATTTT
66 ATGAAACACTATTAAAAAAATTGAAACATAAATTACATAAATTTAAAAAAAGTATATATCATTTT
*
2072756 ATAAAAGTGTCCATACTTA-TTCACTGTGGAAAACATATTTATTATTATCTTTGGTTAATATTGT
131 ATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTACTATTATCTTTGGTTAATATTGT
2072820 TAAATTTAAATTCTAAATAATATTTTATAAA
196 TAAATTTAAATTCTAAATAATATTTTATAAA
*
2072851 ATATCAAATAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAA
1 ATATCAAAAAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATA-TGTAGGTGGAAAA
* *
2072916 CATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTAT-TGATTCTT
65 CATGAAACACTATTAAAAAAATTGAAACATAAATTACATAAATTTAAAAAAAGTATAT-A-TCAT
2072980 TTTATAAAA
128 TTTATAAAA
2072989 AGTATGGACA
Statistics
Matches: 345, Mismatches: 9, Indels: 14
0.94 0.02 0.04
Matches are distributed among these distances:
223 133 0.39
224 58 0.17
225 68 0.20
226 41 0.12
227 45 0.13
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (226 bp):
ATATCAAAAAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATGTAGGTGGAAAAC
ATGAAACACTATTAAAAAAATTGAAACATAAATTACATAAATTTAAAAAAAGTATATATCATTTT
ATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTACTATTATCTTTGGTTAATATTGT
TAAATTTAAATTCTAAATAATATTTTATAAA
Found at i:2073002 original size:22 final size:22
Alignment explanation
Indices: 2072958--2073002 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2072948 ATTACATAAC
* **
2072958 TTTAAAAAAAGTATTGATTCTT
1 TTTAAAAAAAGTATGGACACTT
*
2072980 TTTATAAAAAGTATGGACACTT
1 TTTAAAAAAAGTATGGACACTT
2073002 T
1 T
2073003 CAATATATAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (22 bp):
TTTAAAAAAAGTATGGACACTT
Found at i:2073051 original size:23 final size:23
Alignment explanation
Indices: 2073020--2073083 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
2073010 TAGGTAAAAA
*
2073020 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
2073043 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
2073066 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
2073084 TTGTAAAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:2073524 original size:23 final size:23
Alignment explanation
Indices: 2073493--2073556 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
2073483 ATAGGTAAAA
* *
2073493 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCACTT
* *
2073516 ATATAATGTAATAGGTATCATTT
1 ATATAATGTAATAGGTAGCACTT
2073539 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
2073557 TTGTAAAGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCACTT
Found at i:2074016 original size:22 final size:23
Alignment explanation
Indices: 2073967--2074029 Score: 101
Period size: 22 Copynumber: 2.8 Consensus size: 23
2073957 AATAGGTAAA
*
2073967 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
2073990 ATATAATGTAATAGGTATCG-TT
1 ATATAATGTAATAGGTAGCGCTT
2074012 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
2074030 TTGTAAAGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
22 19 0.51
23 18 0.49
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:2074275 original size:475 final size:480
Alignment explanation
Indices: 2072788--2075382 Score: 4612
Period size: 475 Copynumber: 5.5 Consensus size: 480
2072778 ACTGTGGAAA
*
2072788 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAAT
1 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
*
2072853 ATC-AAATAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
66 ATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
* *
2072917 ATGAAACACTATT-AAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATTGATTCTTT
131 ATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTT
2072981 TTATAAAAAGTATGGACACTTTCAATAT-ATAGGTAAAAAATATGATGTAATAGGTAGCGCTTAT
196 TTATAAAAAGTATGGACACTTTCAATATAATAGGT-AAAAATATGATGTAATAGGTAGCGCTTAT
2073045 ATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTTGTAAAGTATCTATCCTTTTTATAA
260 ATAATGTAATAGGTATCG-TTATATAATGTAATAGGTAGTTGTAAAGTATCTATCCTTTTTATAA
2073110 AAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
324 AAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
2073175 GATATTAATTTAGTAATTATAGGCGTCTAATGATTTA-TTTTTACGTTACG--ATATATATT-TT
389 GATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATATTATT
*
2073236 ATATTAAAAACAATAAACATATATATT
454 AAATTAAAAACAATAAACATATATATT
2073263 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTA-TTTATAAAAT
1 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
2073327 ATCAAAACAATCAAATAA-TTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
66 ATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
2073391 ATGAAACACTATT--AAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTT
131 ATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTT
2073454 TT-TAAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTAT
196 TTAT-AAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTAT
*
2073518 ATAATGTAATAGGTATCATTTATATAATGTAATAGGTAGTTGTAAAGTATCTATCCTTTTTAT-A
260 ATAATGTAATAGGTATC-GTTATATAATGTAATAGGTAGTTGTAAAGTATCTATCCTTTTTATAA
*
2073582 AAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATC-TTTGAGTGAGTTTTAA
324 AAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
*
2073646 GATATTAATTTAGTAATTATAGG-GTCTAATGATTTATTTTTTACATTACGATATATATATTATT
389 GATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATATTATT
2073710 AAATTAAAAA-AATAAACATATATATT
454 AAATTAAAAACAATAAACATATATATT
2073736 ACATATTTATTATTATCTTTGGTT-ATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
1 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
*
2073800 ATCAAAACAATCAAATGATTTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAA
66 ATCAAAACAATCAAAT-AATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAA
*
2073865 CATAAAACACTATT-AAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTT
130 CATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTT
2073929 TTTAT-AAAAGTATGGACACTTTCAATATAATAGGT-AAAATATGATGTAATAGGTAGCGCTTAT
195 TTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTAT
2073992 ATAATGTAATAGGTATCGTTATATAATGTAATAGGTAGTTGTAAAG-ATCTATCCTTTTTATAAA
260 ATAATGTAATAGGTATCGTTATATAATGTAATAGGTAGTTGTAAAGTATCTATCCTTTTTATAAA
2074056 AGTGTCCATAC-TTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAG
325 AGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAG
2074120 ATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATT
390 ATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATA-TATTATT
* *
2074185 ATATTAAAAACAATAAATATATATATT
454 AAATTAAAAACAATAAACATATATATT
2074212 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTA-TTT-TAAAAT
1 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
2074275 ATCAAAACAATCAAAT-ATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
66 ATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
*
2074339 ATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATTGATCCTTT
131 ATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTT
*
2074404 TTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCACTTATA
196 TTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATA
* *
2074469 TAATATAATAGGTATCATTTATATAATGTAATAGGTAGTTGTAAAGTATCTATCCTTTTTATAAA
261 TAATGTAATAGGTATC-GTTATATAATGTAATAGGTAGTTGTAAAGTATCTATCCTTTTTATAAA
*
2074534 AGTGTCTATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAG
325 AGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAG
2074599 ATATTAATTTAGTAATTATAGGCGTCTAATGA-TTATTTTTTACGTTACGATATATATATTATTA
390 ATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATATTATTA
*
2074663 AATTAAAAATAATAAACATATATATT
455 AATTAAAAACAATAAACATATATATT
2074689 --ATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTAT-AAAT
1 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
2074751 ATCAAAACAATCAAATAATTTTTTGTGT-AATGAAA--ATTAAATTAATATTGTAGGTGGAAAAC
66 ATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
2074813 ATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAAGTATCGATCCTT
131 ATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTT-AAAAAAAGTATCGATCCTT
*
2074878 TTTATAAAAAGTATAGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTAT
195 TTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTAT
2074943 ATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTTGTAAAGTATCTATCCTTTTTATAA
260 ATAATGTAATAGGTATCG-TTATATAATGTAATAGGTAGTTGTAAAGTATCTATCCTTTTTATAA
* * *
2075008 AAGTGTCCATACTTTTTTCACTGTGGAAAATATTAATTTAAGGTTATCTTTTAAGTGAGTTTTAA
324 AAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
2075073 GATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATAT-TATTATT
389 GATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATATTATT
*
2075137 AAATTAAAAACAATAAATATATATATT
454 AAATTAAAAACAATAAACATATATATT
2075164 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
1 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
* * *
2075229 ATCAAAACAATCAAATAAATTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGAAAAAC
66 ATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
*
2075294 ATGAAACA-TATTAAAAAAAATTGAAACATAAATTACAT-ACTTTAAAAAAAATTATCGATCCTT
131 ATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTT-AAAAAAAGTATCGATCCTT
2075357 TTTATAAAAAGTATGGACACTTTCAA
195 TTTATAAAAAGTATGGACACTTTCAA
2075383 CATATTATAA
Statistics
Matches: 2042, Mismatches: 41, Indels: 70
0.95 0.02 0.03
Matches are distributed among these distances:
470 13 0.01
471 51 0.02
472 127 0.06
473 378 0.19
474 294 0.14
475 543 0.27
476 190 0.09
477 159 0.08
478 82 0.04
479 141 0.07
480 30 0.01
481 34 0.02
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (480 bp):
ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
ATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
ATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTT
TTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATA
TAATGTAATAGGTATCGTTATATAATGTAATAGGTAGTTGTAAAGTATCTATCCTTTTTATAAAA
GTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGA
TATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATATTATTAA
ATTAAAAACAATAAACATATATATT
Found at i:2074477 original size:23 final size:23
Alignment explanation
Indices: 2074451--2074506 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
2074441 AAATATGATG
2074451 TAATAGGTAGCACTTATATAATA
1 TAATAGGTAGCACTTATATAATA
* * *
2074474 TAATAGGTATCATTTATATAATG
1 TAATAGGTAGCACTTATATAATA
2074497 TAATAGGTAG
1 TAATAGGTAG
2074507 TTGTAAAGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (23 bp):
TAATAGGTAGCACTTATATAATA
Found at i:2074949 original size:23 final size:23
Alignment explanation
Indices: 2074918--2074981 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
2074908 ATAGGTAAAA
*
2074918 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
2074941 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
2074964 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
2074982 TTGTAAAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:2076585 original size:21 final size:21
Alignment explanation
Indices: 2076558--2076757 Score: 135
Period size: 21 Copynumber: 9.6 Consensus size: 21
2076548 GTTTTCAGAT
*
2076558 TCGCAACGCGAACTTCAACTA
1 TCGCAACGCGAACTTCGACTA
* *
2076579 TCACAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
* * * *
2076600 TCGTAA--CGAATTTAGAATAAA
1 TCGCAACGCGAACTTCGACT--A
2076621 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
2076642 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
** *
2076663 TCGCAATACGAA-TAT-G-CAAA
1 TCGCAACGCGAACT-TCGAC-TA
* * * *
2076683 TCGC-A-TCGAATTTGGAATAAA
1 TCGCAACGCGAACTTCGACT--A
*
2076704 TCGCAACGCAAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
*
2076725 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
* *
2076746 TCACAATGCGAA
1 TCGCAACGCGAA
2076758 TATGTAAATC
Statistics
Matches: 139, Mismatches: 27, Indels: 26
0.72 0.14 0.14
Matches are distributed among these distances:
18 5 0.04
19 13 0.09
20 7 0.05
21 96 0.69
22 1 0.01
23 17 0.12
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.21
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:2076704 original size:83 final size:83
Alignment explanation
Indices: 2076558--2076770 Score: 284
Period size: 83 Copynumber: 2.6 Consensus size: 83
2076548 GTTTTCAGAT
* ** * * * *
2076558 TCGCAACGCGAACTTCAACTATCACAACGCGAACT-TGGACTATCGTAACGAATTTAGAATAAAT
1 TCGCAACGCGAACTTCGACTATCACAATACGAA-TATGCA-AATCGCATCGAATTTAGAATAAAT
*
2076622 CGCAACGCGAACTTCGACTA
64 CGCAACGCAAACTTCGACTA
* *
2076642 TCGCAACGCGAACTTCGACTATCGCAATACGAATATGCAAATCGCATCGAATTTGGAATAAATCG
1 TCGCAACGCGAACTTCGACTATCACAATACGAATATGCAAATCGCATCGAATTTAGAATAAATCG
2076707 CAACGCAAACTTCGACTA
66 CAACGCAAACTTCGACTA
* * *
2076725 TCGCAACGCGAACTTGGACTATCACAATGCGAATATGTAAATCGCA
1 TCGCAACGCGAACTTCGACTATCACAATACGAATATGCAAATCGCA
2076771 ATGCGATAGT
Statistics
Matches: 114, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
83 82 0.72
84 32 0.28
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (83 bp):
TCGCAACGCGAACTTCGACTATCACAATACGAATATGCAAATCGCATCGAATTTAGAATAAATCG
CAACGCAAACTTCGACTA
Found at i:2078842 original size:2 final size:2
Alignment explanation
Indices: 2078829--2078860 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2078819 CATTTTCGCC
*
2078829 TA TA TT 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
2078861 GATTTTATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2078940 original size:37 final size:36
Alignment explanation
Indices: 2078876--2079230 Score: 299
Period size: 37 Copynumber: 9.8 Consensus size: 36
2078866 TATAGTTTGC
2078876 AAACAGTTTTTGAAAATATGTATATAATATATAATTTTTAA
1 AAACA-TTTTTG-AAA-AT-TATATAATATATAATTTTT-A
*
2078917 AAACA-TTTTGAAAATGTATATAATATATAGTTTTTA
1 AAACATTTTTGAAAAT-TATATAATATATAATTTTTA
** *
2078953 AAACACCTTTGAAAACTATATAATATATAATTTTTA
1 AAACATTTTTGAAAATTATATAATATATAATTTTTA
* *
2078989 AAACATTTTAGAAAATATATATAATATATAGTTTTTA
1 AAACATTTTTGAAAAT-TATATAATATATAATTTTTA
*
2079026 AAATCA-TTTTGAAAACTTATATAATATATATTTTTTGA
1 AAA-CATTTTTGAAAA-TTATATAATATATAATTTTT-A
*
2079064 AAACATTTTTGAAATTTTATATATAATATATAATTTTTA
1 AAACATTTTTGAAA--AT-TATATAATATATAATTTTTA
* * *
2079103 AAACATTTTT--TAA--A-AT--TATATAGTTTTAA
1 AAACATTTTTGAAAATTATATAATATATAATTTTTA
* *
2079132 AAACATTTTTAAAAATTATAT-A-AT-T--TTTTAA
1 AAACATTTTTGAAAATTATATAATATATAATTTTTA
* *
2079163 AAATATTTTTGAAAATTTATATATAATATATAGTTTTTAAA
1 AAACATTTTTGAAAA--T-TATATAATATATAATTTTT--A
*
2079204 AAACATTTTTGAAAATT-TATATTATAT
1 AAACATTTTTGAAAATTATATAATATAT
2079231 GTTTTTTTAG
Statistics
Matches: 266, Mismatches: 23, Indels: 54
0.78 0.07 0.16
Matches are distributed among these distances:
29 21 0.08
31 23 0.09
32 1 0.00
33 3 0.01
34 9 0.03
35 1 0.00
36 39 0.15
37 90 0.34
38 19 0.07
39 22 0.08
40 18 0.07
41 20 0.08
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (36 bp):
AAACATTTTTGAAAATTATATAATATATAATTTTTA
Found at i:2078984 original size:73 final size:72
Alignment explanation
Indices: 2078896--2079124 Score: 300
Period size: 73 Copynumber: 3.1 Consensus size: 72
2078886 TGAAAATATG
*
2078896 TATATAATATATAATTTTTAAAAACATTTTGAAAATGTATATAATATATAGTTTTTAAAACACCT
1 TATATAATATATAATTTTT-AAAACATTTTGAAAATATATATAATATATAGTTTTTAAAACA-CT
2078961 TTGAAAAC-
64 TTGAAAACT
*
2078969 TATATAATATATAATTTTTAAAACATTTTAGAAAATATATATAATATATAGTTTTTAAAATCATT
1 TATATAATATATAATTTTTAAAACATTTT-GAAAATATATATAATATATAGTTTTTAAAA-CACT
2079034 TTGAAAACT
64 TTGAAAACT
* * *
2079043 TATATAATATATATTTTTTGAAAACATTTTTGAAATTTTATATATAATATATAATTTTTAAAACA
1 TATATAATATATAATTTTT-AAAACA-TTTTGAAA--ATATATATAATATATAGTTTTTAAAACA
* *
2079108 TTTTTTAAAA-T
62 -CTTTGAAAACT
2079119 TATATA
1 TATATA
2079125 GTTTTAAAAA
Statistics
Matches: 142, Mismatches: 6, Indels: 13
0.88 0.04 0.08
Matches are distributed among these distances:
72 10 0.07
73 57 0.40
74 20 0.14
75 10 0.07
76 13 0.09
77 32 0.23
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (72 bp):
TATATAATATATAATTTTTAAAACATTTTGAAAATATATATAATATATAGTTTTTAAAACACTTT
GAAAACT
Found at i:2079085 original size:31 final size:31
Alignment explanation
Indices: 2079050--2079186 Score: 111
Period size: 31 Copynumber: 4.2 Consensus size: 31
2079040 ACTTATATAA
*
2079050 TATATATTTTTTGAAAACATTTTTGAAATTTTATAT
1 TATATATTTTTTAAAAACATTTTTGAAA----A-AT
*
2079086 ATAATATATAATTTTT-AAAACATTTTT-TAAAAT
1 -T-ATATAT--TTTTTAAAAACATTTTTGAAAAAT
*
2079119 TATATA-GTTTTAAAAACATTTTT-AAAAAT
1 TATATATTTTTTAAAAACATTTTTGAAAAAT
* *
2079148 TATATAATTTTTTAAAAATATTTTTGAAAATT
1 TATAT-ATTTTTTAAAAACATTTTTGAAAAAT
2079180 TATATAT
1 TATATAT
2079187 AATATATAGT
Statistics
Matches: 87, Mismatches: 6, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
28 4 0.05
29 21 0.24
30 1 0.01
31 22 0.25
32 11 0.13
33 2 0.02
34 1 0.01
37 1 0.01
38 8 0.09
39 11 0.13
40 5 0.06
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (31 bp):
TATATATTTTTTAAAAACATTTTTGAAAAAT
Found at i:2079122 original size:29 final size:29
Alignment explanation
Indices: 2079090--2079185 Score: 122
Period size: 29 Copynumber: 3.2 Consensus size: 29
2079080 TTATATATAA
2079090 TATATAATTTTTAAAACATTTTTTAAAAT
1 TATATAATTTTTAAAACATTTTTTAAAAT
* * *
2079119 TATATAGTTTTAAAAACATTTTTAAAAAT
1 TATATAATTTTTAAAACATTTTTTAAAAT
2079148 TATATAATTTTTTAAAA-ATATTTTTGAAAATT
1 TATATAA-TTTTTAAAACAT-TTTTT-AAAA-T
2079180 TATATA
1 TATATA
2079186 TAATATATAG
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
29 34 0.60
30 12 0.21
31 4 0.07
32 7 0.12
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (29 bp):
TATATAATTTTTAAAACATTTTTTAAAAT
Found at i:2079254 original size:41 final size:41
Alignment explanation
Indices: 2079148--2079225 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
2079138 TTTTAAAAAT
* *
2079148 TATATAATTTTTTAAAAATATTTTTGAAAATTTATATATAA
1 TATATAGTTTTTAAAAAATATTTTTGAAAATTTATATATAA
*
2079189 TATATAGTTTTTAAAAAACATTTTTGAAAATTTATAT
1 TATATAGTTTTTAAAAAATATTTTTGAAAATTTATAT
2079226 TATATGTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (41 bp):
TATATAGTTTTTAAAAAATATTTTTGAAAATTTATATATAA
Found at i:2079265 original size:15 final size:15
Alignment explanation
Indices: 2079247--2079290 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
2079237 TTAGAAAAAA
2079247 TATTTTTTTTATATT
1 TATTTTTTTTATATT
*
2079262 TATTTATTTATTATTTT
1 TATTT-TTT-TTATATT
*
2079279 TATTTTTATTAT
1 TATTTTTTTTAT
2079291 TACCTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 9 0.36
16 5 0.20
17 11 0.44
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TATTTTTTTTATATT
Found at i:2079276 original size:26 final size:25
Alignment explanation
Indices: 2079247--2079309 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
2079237 TTAGAAAAAA
*
2079247 TATTTTTTTTATATTTATTTA-TTTAT
1 TATTTTTTTTATA-TTA-TTACCTTAT
*
2079273 TATTTTTATTTTTATTATTACCTTAT
1 TATTTTT-TTTATATTATTACCTTAT
2079299 TATTATTTTTT
1 TATT-TTTTTT
2079310 GTTTCAGGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 3 0.09
26 21 0.66
27 8 0.25
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (25 bp):
TATTTTTTTTATATTATTACCTTAT
Found at i:2079291 original size:15 final size:15
Alignment explanation
Indices: 2079247--2079291 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
2079237 TTAGAAAAAA
* *
2079247 TATTTTTTTTATATT
1 TATTTTTATTATTTT
2079262 TATTTATTTATTATTTT
1 TA-TT-TTTATTATTTT
2079279 TATTTTTATTATT
1 TATTTTTATTATT
2079292 ACCTTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 11 0.42
16 4 0.15
17 11 0.42
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (15 bp):
TATTTTTATTATTTT
Found at i:2080528 original size:14 final size:15
Alignment explanation
Indices: 2080497--2080559 Score: 58
Period size: 14 Copynumber: 4.2 Consensus size: 15
2080487 TTATTTAAAT
*
2080497 TTTCTTTTTTTTATTA
1 TTTC-TTTTATTATTA
2080513 TTTCTTTTATTA-TA
1 TTTCTTTTATTATTA
**
2080527 TTTCTTTGCTTATTTA
1 TTTCTTTTATTA-TTA
*
2080543 TTTATTTTATT-TTA
1 TTTCTTTTATTATTA
2080557 TTT
1 TTT
2080560 TATATATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
14 18 0.46
15 7 0.18
16 14 0.36
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTCTTTTATTATTA
Found at i:2080532 original size:30 final size:32
Alignment explanation
Indices: 2080497--2080598 Score: 100
Period size: 33 Copynumber: 3.1 Consensus size: 32
2080487 TTATTTAAAT
2080497 TTTCTTTTT-TTTA-TTATTTCTTTTATTATA
1 TTTCTTTTTATTTATTTATTTCTTTTATTATA
* *
2080527 TTTCTTTGCTTATTTATTTATTTTATTTTATTTTA
1 TTTCTTT--TTATTTATTTA-TTTCTTTTATTATA
* * *
2080562 TATATTTTTATTTATTTATCTTCTATTTGTTATA
1 TTTCTTTTTATTTATTTAT-TTCT-TTTATTATA
2080596 TTT
1 TTT
2080599 TTGCACATTG
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
30 7 0.12
32 3 0.05
33 18 0.32
34 12 0.21
35 17 0.30
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.74
Consensus pattern (32 bp):
TTTCTTTTTATTTATTTATTTCTTTTATTATA
Found at i:2080547 original size:37 final size:34
Alignment explanation
Indices: 2080506--2080589 Score: 80
Period size: 35 Copynumber: 2.4 Consensus size: 34
2080496 TTTTCTTTTT
* * *
2080506 TTTATTATTTCTTTTATTATATTTCTTTGCTTATTTA
1 TTTATT-TTTATTTTATTATATATATTT--TTATTTA
*
2080543 TTTA-TTTTATTTTATTTTATATATTTTTATTTA
1 TTTATTTTTATTTTATTATATATATTTTTATTTA
*
2080576 TTTATCTTCTATTT
1 TTTAT-TTTTATTT
2080590 GTTATATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
33 11 0.28
35 24 0.60
36 1 0.03
37 4 0.10
ACGTcount: A:0.20, C:0.06, G:0.01, T:0.73
Consensus pattern (34 bp):
TTTATTTTTATTTTATTATATATATTTTTATTTA
Found at i:2080599 original size:30 final size:29
Alignment explanation
Indices: 2080539--2080600 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
2080529 TCTTTGCTTA
2080539 TTTATTTATTTTATTTTATTTTATATATT
1 TTTATTTATTTTATTTTATTTTATATATT
2080568 TTTATTTA-TTTATCTTCTATTTGT-TATATT
1 TTTATTTATTTTAT-TT-TATTT-TATATATT
2080598 TTT
1 TTT
2080601 GCACATTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
28 5 0.17
29 10 0.33
30 14 0.47
31 1 0.03
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (29 bp):
TTTATTTATTTTATTTTATTTTATATATT
Found at i:2084196 original size:95 final size:94
Alignment explanation
Indices: 2084024--2084286 Score: 312
Period size: 95 Copynumber: 2.7 Consensus size: 94
2084014 AGATTATAAT
* * * *
2084024 ATTATATATATACAATAAAGCTTGAGTTGTCCCACTAAAGCAATTGGTTAAGCGCCGCGACTTTA
1 ATTATA-ATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCG-CTTTA
* * *
2084089 TGAATAAGATTCAGTTAGCCTGATAAAGGTG
64 TGGATAAGATTCAGCTAGCCTGATAAAGGCG
2084120 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTAT
1 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCC-GCTTTAT
*
2084185 GGATAATATTCAGCTAGCCTGATAAAGGCG
65 GGATAAGATTCAGCTAGCCTGATAAAGGCG
* * * * * * *
2084215 ATTATAATAT-CTATACAATGATATTAAATTGTCCATCTAGAGCAATTGGTTAAACACTCCGGCT
1 ATTATAATATACAATA-AA-G--CTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGC-CCCGCT
2084279 TTATGGAT
61 TTATGGAT
2084287 TCAGGTAGCC
Statistics
Matches: 146, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
94 4 0.03
95 91 0.62
96 8 0.05
98 41 0.28
99 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Consensus pattern (94 bp):
ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGCTTTATG
GATAAGATTCAGCTAGCCTGATAAAGGCG
Found at i:2085551 original size:84 final size:83
Alignment explanation
Indices: 2085373--2086664 Score: 1421
Period size: 84 Copynumber: 15.4 Consensus size: 83
2085363 GAAACTATCA
* *
2085373 GCAGCATAACTCAAGG-TGAGAAGGGTTATCTGTC-AGCAAAGACCTTCGAGTTCGACTACGCTC
1 GCAGCATAACTCAAGGCT-AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTC
* * * *
2085436 AGCTCCAATGTAGATAATTTT
65 AGC-CCAAGGCACATCA-TTT
* * * *
2085457 GCAAG-ATAACTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTTGACTACGCTC
1 GC-AGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTC
*
2085521 AGCCCTAAGGCATATCATTT
65 AGCCC-AAGGCACATCATTT
* * * * ** * *
2085541 GTAGCATAACTCAAGGTTATAAGGGTTATCTGTCAACCAAAGACCTTTAAGTTTGACTATGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
*
2085606 GCTCCAAGACACATCATTT
66 GC-CCAAGGCACATCATTT
* * * * *
2085625 GCAGTATAACTCAAGGCTAGAAGGGTTATCTTCC-ACAAAAATACCTTTGAGTTCGACTACGCTC
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAC-CAAAGACCTTCGAGTTCGACTACGCTC
2085689 AGCTCCAAGGCACATCATTT
65 AGC-CCAAGGCACATCATTT
* * * * *
2085709 ACAGTATAACTCAAGGCTAGAAGGGTTATCTGTCAACCAAAGACTTTCGAGTTTGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
* *
2085774 GCTTCAAGGCTCATCATTT
66 GC-CCAAGGCACATCATTT
* * *
2085793 GCAGCATAGCTCAAGGCTAGAAGGGTTATCTGCC-ACTAAAAGACCTTCGAGTTTGACTACGCTC
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAC-CAAAGACCTTCGAGTTCGACTACGCTC
* *
2085857 AGCTCCAAGGTATATCATTT
65 AGC-CCAAGGCACATCATTT
* *
2085877 GCATCATAACTCAAGGCTAGAAGGGTTATTTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
*
2085942 GCTTCAAGGCACATCATTT
66 GC-CCAAGGCACATCATTT
** * * *
2085961 ATAGTATAACTCAAGGCTAGAAGGGCTATCT-CCCACCAAAAGACCTTCGAGTTCGACTACGCTC
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTACGCTC
**
2086025 AGTTTCAAGGCACATCATTT
65 AG-CCCAAGGCACATCATTT
* * *
2086045 GCAGCATAACTCAAGGCTATAAGGGTTATCTGCAAACCAAAGACCTTCGAGTTTGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
2086110 GCTCCAAGGCACATCATTT
66 GC-CCAAGGCACATCATTT
* *
2086129 GCAGTATAGA-TCAAGGCTAGAAGGGTTATCTGCC-ACCAAAAGACATTCGAGTTCGACTACGCT
1 GCAGCATA-ACTCAAGGCTAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTACGCT
* *
2086192 CAGCTCAAAGGCATATCATTT
64 CAGC-CCAAGGCACATCATTT
* *
2086213 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
* * *
2086278 GCTCAAATGCATATCATTT
66 GC-CCAAGGCACATCATTT
** * * * ** *
2086297 GCAATATAGCTCAAGGCGAGAAGGGCTATCTGCCAATAAAAGACCTTCGAGTTTGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
* * * *
2086362 GCTCAAAGACATATAATTT
66 GC-CCAAGGCACATCATTT
* *
2086381 ACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
*
2086446 GCTCCAAGGCACATTATTT
66 GC-CCAAGGCACATCATTT
* * * ** * * * *
2086465 GTAACATAGCTCAAGGAAAGAAGGGTTATTTGCCAACGAGAGACCTTTGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
* *
2086530 GCTCAAAGGCATATCATTT
66 GC-CCAAGGCACATCATTT
* * * * * * * *
2086549 GCAGTATAACTTAAGTCGAGAAGGGGTATCTGCCAACCAAAGACCTTTGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
* * * *
2086614 TCTCAAAGGCACGTAATTTT
66 GC-CCAAGGCACATCA-TTT
* *
2086634 ACAGCATAACTCAAGGCAAGAAGGGTTATCT
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCT
2086665 ATTAACAAAA
Statistics
Matches: 1034, Mismatches: 155, Indels: 37
0.84 0.13 0.03
Matches are distributed among these distances:
83 15 0.01
84 939 0.91
85 80 0.08
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (83 bp):
GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
GCCCAAGGCACATCATTT
Found at i:2085653 original size:168 final size:168
Alignment explanation
Indices: 2085373--2086664 Score: 1626
Period size: 168 Copynumber: 7.7 Consensus size: 168
2085363 GAAACTATCA
* *
2085373 GCAGCATAACTCAAGG-TGAGAAGGGTTATCTGTC-AGCAAAGACCTTCGAGTTCGACTACGCTC
1 GCAGCATAACTCAAGGCT-AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTC
* * * * * *
2085436 AGCTCCAATGTAGATAATTTTGCAAG-ATAACTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGA
65 AGCTCCAAGGCACATCA-TTTGC-AGTATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGA
* * *
2085500 CCTTCGAGTTTGACTACGCTCAGCCCTAAGGCATATCATTT
128 CCTTCGAGTTCGACTACGCTCAGCTCAAAGGCATATCATTT
* * * * ** * *
2085541 GTAGCATAACTCAAGGTTATAAGGGTTATCTGTCAACCAAAGACCTTTAAGTTTGACTATGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
* * *
2085606 GCTCCAAGACACATCATTTGCAGTATAACTCAAGGCTAGAAGGGTTATCTTCC-ACAAAAATACC
66 GCTCCAAGGCACATCATTTGCAGTATAACTCAAGGCTAGAAGGGTTATCTGCCAAC-AAAAGACC
* * *
2085670 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
130 TTCGAGTTCGACTACGCTCAGCTCAAAGGCATATCATTT
* * * * *
2085709 ACAGTATAACTCAAGGCTAGAAGGGTTATCTGTCAACCAAAGACTTTCGAGTTTGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
* * * *
2085774 GCTTCAAGGCTCATCATTTGCAGCATAGCTCAAGGCTAGAAGGGTTATCTGCC-ACTAAAAGACC
66 GCTCCAAGGCACATCATTTGCAGTATAACTCAAGGCTAGAAGGGTTATCTGCCAAC-AAAAGACC
* * *
2085838 TTCGAGTTTGACTACGCTCAGCTCCAAGGTATATCATTT
130 TTCGAGTTCGACTACGCTCAGCTCAAAGGCATATCATTT
* *
2085877 GCATCATAACTCAAGGCTAGAAGGGTTATTTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
* ** * * *
2085942 GCTTCAAGGCACATCATTTATAGTATAACTCAAGGCTAGAAGGGCTATCTCCCACCAAAAGACCT
66 GCTCCAAGGCACATCATTTGCAGTATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCT
* *
2086007 TCGAGTTCGACTACGCTCAGTTTC-AAGGCACATCATTT
131 TCGAGTTCGACTACGCTCAG-CTCAAAGGCATATCATTT
* * *
2086045 GCAGCATAACTCAAGGCTATAAGGGTTATCTGCAAACCAAAGACCTTCGAGTTTGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
* *
2086110 GCTCCAAGGCACATCATTTGCAGTATAGA-TCAAGGCTAGAAGGGTTATCTGCCACCAAAAGACA
66 GCTCCAAGGCACATCATTTGCAGTATA-ACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACC
2086174 TTCGAGTTCGACTACGCTCAGCTCAAAGGCATATCATTT
130 TTCGAGTTCGACTACGCTCAGCTCAAAGGCATATCATTT
* *
2086213 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
* * * * * * * *
2086278 GCTCAAATGCATATCATTTGCAATATAGCTCAAGGCGAGAAGGGCTATCTGCCAATAAAAGACCT
66 GCTCCAAGGCACATCATTTGCAGTATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCT
* * *
2086343 TCGAGTTTGACTACGCTCAGCTCAAAGACATATAATTT
131 TCGAGTTCGACTACGCTCAGCTCAAAGGCATATCATTT
* *
2086381 ACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
* * ** * ** * * *
2086446 GCTCCAAGGCACATTATTTGTAACATAGCTCAAGGAAAGAAGGGTTATTTGCCAACGAGAGACCT
66 GCTCCAAGGCACATCATTTGCAGTATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCT
*
2086511 TTGAGTTCGACTACGCTCAGCTCAAAGGCATATCATTT
131 TCGAGTTCGACTACGCTCAGCTCAAAGGCATATCATTT
* * * * * * * *
2086549 GCAGTATAACTTAAGTCGAGAAGGGGTATCTGCCAACCAAAGACCTTTGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
* * * * * * *
2086614 TCTCAAAGGCACGTAATTTTACAGCATAACTCAAGGCAAGAAGGGTTATCT
66 GCTCCAAGGCACATCA-TTTGCAGTATAACTCAAGGCTAGAAGGGTTATCT
2086665 ATTAACAAAA
Statistics
Matches: 983, Mismatches: 131, Indels: 19
0.87 0.12 0.02
Matches are distributed among these distances:
167 6 0.01
168 908 0.92
169 69 0.07
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (168 bp):
GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
GCTCCAAGGCACATCATTTGCAGTATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCT
TCGAGTTCGACTACGCTCAGCTCAAAGGCATATCATTT
Found at i:2087225 original size:2 final size:2
Alignment explanation
Indices: 2087218--2087252 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2087208 ACATACATAA
2087218 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 A
2087253 GTTTTCAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2087356 original size:37 final size:36
Alignment explanation
Indices: 2087236--2087552 Score: 268
Period size: 37 Copynumber: 8.7 Consensus size: 36
2087226 ATATATATAT
* ***
2087236 ATATATATATATATATAGTTTTCAAATGGTTTTTGAAA
1 ATATATATA-ATATATAGTTTTTAAA-ACATTTTGAAA
2087274 ATACTTATATAATATATAGTTTTTAAAACATGTTTGAAA
1 ATA--TATATAATATATAGTTTTTAAAACAT-TTTGAAA
* *
2087313 A-CTATATAATATATAGTTTTTTAAACATTTTAGAAA
1 ATATATATAATATATAGTTTTTAAAACATTTT-GAAA
2087349 ATATATATAATATATAGTTTTTAAAATCATTTTGAAA
1 ATATATATAATATATAGTTTTTAAAA-CATTTTGAAA
2087386 ACT-TATATAATATATAGTTTTTGAAAACAGTTTTGAAA
1 A-TATATATAATATATAGTTTTT-AAAACA-TTTTGAAA
* *
2087424 ACTTATATATAATATATAATTTTTAAAACATTTT--TA
1 A--TATATATAATATATAGTTTTTAAAACATTTTGAAA
**
2087460 A-A-A-AT--TATATAGTTTTTAAAAACATTTT-TTA
1 ATATATATAATATATAGTTTTT-AAAACATTTTGAAA
*
2087491 A-A-A-AT--TATATAGTTTTAAAAAAACATTTTTGAAA
1 ATATATATAATATATAGTTTT--TAAAACA-TTTTGAAA
2087525 ATTTATATATAATATATAGTTTTTAAAA
1 A--TATATATAATATATAGTTTTTAAAA
2087553 AAAAATTTAA
Statistics
Matches: 239, Mismatches: 16, Indels: 47
0.79 0.05 0.16
Matches are distributed among these distances:
29 11 0.05
30 10 0.04
31 20 0.08
32 7 0.03
33 5 0.02
34 2 0.01
35 3 0.01
36 32 0.13
37 49 0.21
38 29 0.12
39 36 0.15
40 24 0.10
41 11 0.05
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (36 bp):
ATATATATAATATATAGTTTTTAAAACATTTTGAAA
Done.