Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008514.1 Hibiscus syriacus cultivar Beakdansim tig00111377_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: 567339
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:10876 original size:14 final size:14
Alignment explanation
Indices: 10857--10889 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
10847 TGGGGAGTAA
*
10857 TCCCTGTAAATAAT
1 TCCCTGCAAATAAT
10871 TCCCTGCAAATAAT
1 TCCCTGCAAATAAT
10885 TCCCT
1 TCCCT
10890 ACATAGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.33
Consensus pattern (14 bp):
TCCCTGCAAATAAT
Found at i:17532 original size:5 final size:5
Alignment explanation
Indices: 17524--17966 Score: 628
Period size: 5 Copynumber: 89.4 Consensus size: 5
17514 GTTATATAAT
17524 ATATA ATATA ATATA ATAT- A-ATA ATATA ATATAA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATAT-A ATATA ATATA ATATA
* * * * * *
17573 A-ACA ATACA ATACA ATACA ATACA ATACA ATAT- ATAATA TATATA ATAT-
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT-ATA -ATATA ATATA
17622 ATATA ATAT- ATAT- ATATA ATATA ATATA ATATA ATATA ATATA ATAT-
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
17669 ATATA ATATA ATATA ATATA ATATA ATATA ATATA A-ATA A-ATA TATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA -ATATA
17718 ATATA ATATA ATAT- ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
17767 ATATAA ATATA ATATA ATAT- ATA-A TATAATA ATATA ATATA ATATA
1 ATAT-A ATATA ATATA ATATA ATATA -AT-ATA ATATA ATATA ATATA
17813 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATAT- ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
17862 ATAT- ATATA ATATA ATATA ATATAA TATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA
17913 ATAAATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 AT--ATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
17965 AT
1 AT
17967 GGATTATTAG
Statistics
Matches: 412, Mismatches: 2, Indels: 48
0.89 0.00 0.10
Matches are distributed among these distances:
3 2 0.00
4 45 0.11
5 332 0.81
6 21 0.05
7 12 0.03
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:19677 original size:21 final size:21
Alignment explanation
Indices: 19651--19748 Score: 87
Period size: 21 Copynumber: 4.7 Consensus size: 21
19641 ATCAGTTTCC
19651 AAAATCGCAACGCGATTATTG
1 AAAATCGCAACGCGATTATTG
* *
19672 AAAATCGCAATGCGA-TAGT-
1 AAAATCGCAACGCGATTATTG
** *
19691 ACAAATTCGCATTGCGATT-TTCC
1 A-AAA-TCGCAACGCGATTATT-G
*
19714 AAAATCGCAACGCGAATA-TG
1 AAAATCGCAACGCGATTATTG
19734 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
19749 ACACATAAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
19 1 0.02
20 21 0.33
21 36 0.57
22 4 0.06
23 1 0.02
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (21 bp):
AAAATCGCAACGCGATTATTG
Found at i:19739 original size:20 final size:20
Alignment explanation
Indices: 19715--19908 Score: 210
Period size: 20 Copynumber: 9.7 Consensus size: 20
19705 CGATTTTCCA
** *
19715 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
19735 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
*
19755 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
19775 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGT
* **
19795 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGAATCCGT
* *
19815 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
19835 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
19855 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
19875 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
19895 AAATCGCAACGCGA
1 AAATCGCAACGCGA
19909 TATTTAAAGC
Statistics
Matches: 149, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 148 0.99
21 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:20328 original size:33 final size:33
Alignment explanation
Indices: 20289--20359 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
20279 TTCACTTAGA
* *
20289 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
20322 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
20355 TTTCA
1 TTTCA
20360 GTTAGTATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:20473 original size:19 final size:19
Alignment explanation
Indices: 20437--20541 Score: 94
Period size: 19 Copynumber: 5.6 Consensus size: 19
20427 TGCAGAAGAG
20437 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAG--AAATGAAAA
***
20458 TCGCAACGAGAAATGACTG
1 TCGCAACGAGAAATGAAAA
*
20477 TCGCAACGAGAGAAATGACAA
1 TCGCAAC--GAGAAATGAAAA
20498 TCGCAACGAG--A-G--AA
1 TCGCAACGAGAAATGAAAA
*
20512 TCGCAACGCGAAATGAAAA
1 TCGCAACGAGAAATGAAAA
20531 TCGCAACGAGA
1 TCGCAACGAGA
20542 GAATCGCAAC
Statistics
Matches: 70, Mismatches: 7, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 28 0.40
21 27 0.39
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (19 bp):
TCGCAACGAGAAATGAAAA
Found at i:20509 original size:21 final size:21
Alignment explanation
Indices: 20437--20511 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
20427 TGCAGAAGAG
* *
20437 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGACAA
**
20458 TCGCAAC--GAGAAATGACTG
1 TCGCAACGAGAGAAATGACAA
20477 TCGCAACGAGAGAAATGACAA
1 TCGCAACGAGAGAAATGACAA
20498 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
20512 TCGCAACGCG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 15 0.33
21 31 0.67
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGACAA
Found at i:20515 original size:14 final size:14
Alignment explanation
Indices: 20496--20552 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
20486 GAGAAATGAC
20496 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
20510 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
20529 AATCGCAACGAGAG
1 AATCGCAACGAGAG
20543 AATCGCAACG
1 AATCGCAACG
20553 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:20533 original size:33 final size:33
Alignment explanation
Indices: 20488--20568 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
20478 CGCAACGAGA
*
20488 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
20521 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
20554 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
20569 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.46, C:0.23, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:20586 original size:19 final size:19
Alignment explanation
Indices: 20564--20661 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
20554 GAAACCAAAA
*
20564 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
20583 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
20597 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
20616 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
20630 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
20649 TCGCGTTGCGATT
1 TCGCGTTGCGATT
20662 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 20 0.33
16 4 0.07
17 5 0.08
19 32 0.52
ACGTcount: A:0.10, C:0.24, G:0.23, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:20605 original size:14 final size:14
Alignment explanation
Indices: 20586--20675 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
20576 TTTCATTTCG
20586 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
20600 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
20619 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
20633 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
20650 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
20666 CGTTGCGATT
1 CGTTGCGATT
20676 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 2 0.03
16 7 0.11
17 7 0.11
18 2 0.03
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.24, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:20615 original size:33 final size:33
Alignment explanation
Indices: 20569--20683 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
20559 CAAAATCGCA
*
20569 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
20602 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
*
20635 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
*
20668 TTGCGATTTTCATTTC
1 TTGCGATTGTCATTTC
20684 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.44
Consensus pattern (33 bp):
TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
Found at i:22540 original size:93 final size:93
Alignment explanation
Indices: 22381--22811 Score: 835
Period size: 93 Copynumber: 4.6 Consensus size: 93
22371 TAGATTGCTT
*
22381 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
22446 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
22474 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
22539 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
22567 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTGTTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
22632 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
22660 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
22725 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
22753 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAA
22812 TGGATAAATT
Statistics
Matches: 333, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 333 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:24858 original size:19 final size:19
Alignment explanation
Indices: 24834--24930 Score: 150
Period size: 19 Copynumber: 5.4 Consensus size: 19
24824 AAAATTGACT
24834 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
24853 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
24872 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
24886 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
24905 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
24924 ATCGCAA
1 ATCGCAA
24931 CGAGATAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 10
0.86 0.02 0.12
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 55 0.77
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:24912 original size:52 final size:52
Alignment explanation
Indices: 24834--25163 Score: 229
Period size: 52 Copynumber: 6.2 Consensus size: 52
24824 AAAATTGACT
24834 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
24886 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *** * ** ** ** ** ** *
24938 ATCGCAATGCGAAATTATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGA-A
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAAT-CGCAACGAGAGA
* * ** *** ** * ** * * **
24990 AT-GTAATGGTTGATTTTGTTGATTTCAAT-CTGCATTATGTTGAA-GGCAA-AATTGACT
1 ATCGCAAT-G-CGA-AATGAAAATCGCAATGC-G-A-AATG-AAAATCGCAACGA--GAGA
25047 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
25099 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
25152 ATCGCAATGCGA
1 ATCGCAATGCGA
25164 TTTTCATTTC
Statistics
Matches: 207, Mismatches: 55, Indels: 31
0.71 0.19 0.11
Matches are distributed among these distances:
51 4 0.02
52 115 0.56
53 52 0.25
54 9 0.04
55 13 0.06
56 7 0.03
57 3 0.01
58 4 0.02
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:25071 original size:19 final size:19
Alignment explanation
Indices: 25047--25144 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
25037 AAAATTGACT
25047 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
25066 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
25085 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
25099 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
25118 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
25138 ATCGCAA
1 ATCGCAA
25145 CGAGAGAATC
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:25176 original size:53 final size:53
Alignment explanation
Indices: 25047--25163 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
25037 AAAATTGACT
25047 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
25099 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
25152 ATCGCAATGCGA
1 ATCGCAATGCGA
25164 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:27495 original size:12 final size:12
Alignment explanation
Indices: 27478--27502 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27468 TCTTCGGGGA
27478 CTTTTTCTTCTT
1 CTTTTTCTTCTT
27490 CTTTTTCTTCTT
1 CTTTTTCTTCTT
27502 C
1 C
27503 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:27711 original size:24 final size:24
Alignment explanation
Indices: 27677--27723 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
27667 CTGAAACATC
27677 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
27701 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
27724 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:28434 original size:20 final size:20
Alignment explanation
Indices: 28406--28655 Score: 243
Period size: 20 Copynumber: 12.5 Consensus size: 20
28396 AAATTTCAGT
* * *
28406 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
28426 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
28446 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
28466 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* * *
28486 GTTACGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
28506 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
28526 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
28546 ATTGCGATTTACCCATAT-GC
1 GTTGCGATTTACGGAT-TCGC
*
28566 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
28586 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
28606 GTTGCGATTTATGTG-TTCGT
1 GTTGCGATTTACG-GATTCGC
* **
28626 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
28646 GTTGCGATTT
1 GTTGCGATTT
28656 TGGAAAATCG
Statistics
Matches: 194, Mismatches: 32, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
20 193 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:28672 original size:21 final size:21
Alignment explanation
Indices: 28642--28724 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
28632 ATTTTCATAT
*
28642 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
28663 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
28684 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
28705 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
28725 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:29410 original size:29 final size:29
Alignment explanation
Indices: 29368--29429 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
29358 ACCATTGAAC
29368 TTTTTTTGTCTCAATCATACCACCAAACT
1 TTTTTTTGTCTCAATCATACCACCAAACT
29397 TTTTTTTGTCTCAATCATACCACCAAACT
1 TTTTTTTGTCTCAATCATACCACCAAACT
29426 TTTT
1 TTTT
29430 AATTGATTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.26, C:0.26, G:0.03, T:0.45
Consensus pattern (29 bp):
TTTTTTTGTCTCAATCATACCACCAAACT
Found at i:29443 original size:30 final size:29
Alignment explanation
Indices: 29365--29450 Score: 122
Period size: 29 Copynumber: 3.0 Consensus size: 29
29355 TTGACCATTG
29365 AACTTTTT-TTGTCTCAATCATACCACCA
1 AACTTTTTATTGTCTCAATCATACCACCA
*
29393 AACTTTTTTTTGTCTCAATCATACCACCA
1 AACTTTTTATTGTCTCAATCATACCACCA
*
29422 AACTTTTTAATTGAT-TCAATCAGACCACC
1 AACTTTTT-ATTG-TCTCAATCATACCACC
29451 GGGCCATTAA
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
28 8 0.15
29 28 0.53
30 16 0.30
31 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.05, T:0.38
Consensus pattern (29 bp):
AACTTTTTATTGTCTCAATCATACCACCA
Found at i:29869 original size:16 final size:17
Alignment explanation
Indices: 29832--29869 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
29822 GTTAAAAAAA
* *
29832 TTAAGCAAATTATTTGT
1 TTAAACAAATTATTTAT
29849 TTAAACAAATTA-TTAT
1 TTAAACAAATTATTTAT
29865 TTAAA
1 TTAAA
29870 TTAATTGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (17 bp):
TTAAACAAATTATTTAT
Found at i:30115 original size:29 final size:29
Alignment explanation
Indices: 30083--30146 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
30073 AAAAAATTGG
30083 TTAATTCGGTTCAGTTAATAATTTTCAAA
1 TTAATTCGGTTCAGTTAATAATTTTCAAA
**
30112 TTAATTCGGTTTGGTTAATAATTTTCAAA
1 TTAATTCGGTTCAGTTAATAATTTTCAAA
*
30141 TAAATT
1 TTAATT
30147 TTGGTTCAAT
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:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (29 bp):
TTAATTCGGTTCAGTTAATAATTTTCAAA
Found at i:30138 original size:137 final size:139
Alignment explanation
Indices: 29979--30398 Score: 582
Period size: 140 Copynumber: 3.0 Consensus size: 139
29969 ACAAAATTTG
* * * *
29979 TTCGGTTCGATTAATAAATTTCAAATAAATTTTGGTTCGATTAACCGAACCGAATTAACTGAATT
1 TTCGGTTTGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAACTGAATTAACTGAATT
* *
30044 TTTGCTTCGATTAATTCAATTAATAA-TT-AAAAAAATTGGTTAATTCGGTTCAGTTAATAATTT
66 TTTGCTTCGATTAATTCGATTAATAATTTAAAAAAAATTGGTTAATTCGGTTCGGTTAATAATTT
30107 TCAAATTAA
131 TCAAATTAA
* *
30116 TTCGGTTTGGTTAATAATTTTCAAATAAATTTTGGTTCAATTAACC-AAGTTGAATTAACCT-AA
1 TTCGGTTTGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAA-CTGAATTAA-CTGAA
* *
30179 TTTTTACTTCGATTAATTTGATTAATAATTTAAAAAAAATTGGTTAATTCGGTTCGGTTAATAAT
64 TTTTTGCTTCGATTAATTCGATTAATAATTTAAAAAAAATTGGTTAATTCGGTTCGGTTAATAA-
* *
30244 TTTTTAAATTAT
128 TTTTCAAATTAA
** *
30256 TTTAGTTTGGTTAATAATTTTCAAATAAATTTTGGTTCGATGAACCGAACTGAATTAACTGAATT
1 TTCGGTTTGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAACTGAATTAACTGAATT
*
30321 TTTGCTTCGATTAATTCGGTTAA-AATTTTCAAAAAAAAATCT-GTTAATTCGGTTCGGTTAATA
66 TTTGCTTCGATTAATTCGATTAATAA-TTT--AAAAAAAAT-TGGTTAATTCGGTTCGGTTAATA
*
30384 ATTTTCAAATAAA
127 ATTTTCAAATTAA
30397 TT
1 TT
30399 TTGGTTCGAT
Statistics
Matches: 249, Mismatches: 23, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
136 2 0.01
137 76 0.31
138 4 0.02
139 35 0.14
140 87 0.35
141 13 0.05
142 31 0.12
143 1 0.00
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.43
Consensus pattern (139 bp):
TTCGGTTTGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAACTGAATTAACTGAATT
TTTGCTTCGATTAATTCGATTAATAATTTAAAAAAAATTGGTTAATTCGGTTCGGTTAATAATTT
TCAAATTAA
Found at i:30149 original size:25 final size:27
Alignment explanation
Indices: 30096--30152 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 27
30086 ATTCGGTTCA
*
30096 GTTAATAATTTTCAAATTAATTCGGTTTG
1 GTTAATAATTTTCAAATTAAAT--GTTTG
30125 GTTAATAATTTTCAAA-TAAAT-TTTG
1 GTTAATAATTTTCAAATTAAATGTTTG
30150 GTT
1 GTT
30153 CAATTAACCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 7 0.26
28 4 0.15
29 16 0.59
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.49
Consensus pattern (27 bp):
GTTAATAATTTTCAAATTAAATGTTTG
Found at i:31180 original size:12 final size:12
Alignment explanation
Indices: 31163--31187 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31153 TTGGATTCAA
31163 TGATTTGCTTTT
1 TGATTTGCTTTT
31175 TGATTTGCTTTT
1 TGATTTGCTTTT
31187 T
1 T
31188 ATATTAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.16, T:0.68
Consensus pattern (12 bp):
TGATTTGCTTTT
Found at i:32769 original size:28 final size:26
Alignment explanation
Indices: 32721--32778 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
32711 AGGGGTGCAC
32721 AAAAAATTCGAATATCCGATTTTGCGA
1 AAAAAATTCGAATATCCGA-TTTGCGA
* *
32748 AAAAAATATCTGAA-ATCGGATTTGGGA
1 AAAAAAT-TC-GAATATCCGATTTGCGA
32775 AAAA
1 AAAA
32779 CTGATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 17 0.63
28 7 0.26
29 3 0.11
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.26
Consensus pattern (26 bp):
AAAAAATTCGAATATCCGATTTGCGA
Found at i:32875 original size:12 final size:12
Alignment explanation
Indices: 32860--32905 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
32850 CGGTTTTTTT
*
32860 ACCGGATAAAAA
1 ACCGGTTAAAAA
32872 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
32887 ACCGGTTAAAAA
1 ACCGGTTAAAAA
32899 ACCGGTT
1 ACCGGTT
32906 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:32887 original size:15 final size:13
Alignment explanation
Indices: 32866--32906 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
32856 TTTTACCGGA
32866 TAAAAAACCGGTT
1 TAAAAAACCGGTT
32879 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
32893 TAAAAAACCGGTT
1 TAAAAAACCGGTT
32906 T
1 T
32907 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:35218 original size:21 final size:21
Alignment explanation
Indices: 35194--35233 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
35184 TTTATTTTAT
35194 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
35215 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
35234 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:35281 original size:33 final size:33
Alignment explanation
Indices: 35228--35326 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
35218 TTTGTTTCAA
35228 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
35260 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
35293 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
35326 T
1 T
35327 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:35355 original size:13 final size:13
Alignment explanation
Indices: 35312--35366 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
35302 TTGGAAGTAT
35312 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
35325 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
35339 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
35352 TTAAGTATTTGAA
1 TTAAGTATTTCAA
35365 TT
1 TT
35367 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:35814 original size:15 final size:15
Alignment explanation
Indices: 35762--35817 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
35752 ATCTGGAATA
*
35762 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
* *
35777 TTATAACTGGTTTTT
1 TTAAAACCGGTTTTT
*
35792 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
35809 TTAAAACCG
1 TTAAAACCG
35818 AAACCGGTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
15 20 0.62
17 12 0.38
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:35934 original size:15 final size:17
Alignment explanation
Indices: 35908--35939 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
35898 TTCTATGGGA
35908 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
35924 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
35940 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:36193 original size:2 final size:2
Alignment explanation
Indices: 36180--36219 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
36170 ACTTTGCATG
* *
36180 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36220 CCCATATGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:36640 original size:3 final size:3
Alignment explanation
Indices: 36632--36662 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
36622 CTTGAGAAAA
36632 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG A
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG A
36663 CTTTTACCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:36745 original size:77 final size:76
Alignment explanation
Indices: 36619--36771 Score: 245
Period size: 77 Copynumber: 2.0 Consensus size: 76
36609 ATGAAAGAAA
*
36619 GTGCTTGAGAAAAAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGACTTTTACCTTCCCCAATCAAC
1 GTGCTTGAGAAAAAGGAGGAAGAGGAGGAGGAGGAGGAGGAGGACTTTTACCTTCCCCAATCAAC
36684 TACTCATATTC
66 TACTCATATTC
**
36695 GTGCTTGAGAAATATA-GAGGAAGAGGAGGAGGAGGAGGAGGAGTCCTTTTACCTTCCCCAATCA
1 GTGCTTGAGAAA-A-AGGAGGAAGAGGAGGAGGAGGAGGAGGAGGACTTTTACCTTCCCCAATCA
*
36759 GCTACTCATATTC
64 ACTACTCATATTC
36772 ATCGGTTTCG
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
76 12 0.17
77 58 0.82
78 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.30, T:0.22
Consensus pattern (76 bp):
GTGCTTGAGAAAAAGGAGGAAGAGGAGGAGGAGGAGGAGGAGGACTTTTACCTTCCCCAATCAAC
TACTCATATTC
Found at i:38442 original size:38 final size:38
Alignment explanation
Indices: 38391--38470 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 38
38381 AATTTAATGT
38391 TAAATTTTGAACGATT-GTACTAAAATGAAACAAAAAC
1 TAAATTTTGAACGATTAGTACTAAAATGAAACAAAAAC
* * *
38428 TAAAGTTTTTAACGATTAGTATTAAAATGAAATAAAAAC
1 TAAA-TTTTGAACGATTAGTACTAAAATGAAACAAAAAC
38467 TAAA
1 TAAA
38471 CTTTAGATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 4 0.11
38 11 0.29
39 23 0.61
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (38 bp):
TAAATTTTGAACGATTAGTACTAAAATGAAACAAAAAC
Found at i:52339 original size:19 final size:19
Alignment explanation
Indices: 52295--52331 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
52285 GATAAGCTGG
* *
52295 GAATTAATGTTAGAGTGTT
1 GAATTGATGTTAGAATGTT
52314 GAATTGATGTTAGAATGT
1 GAATTGATGTTAGAATGT
52332 GAAATTGAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.27, T:0.41
Consensus pattern (19 bp):
GAATTGATGTTAGAATGTT
Found at i:56919 original size:23 final size:23
Alignment explanation
Indices: 56868--56924 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
56858 AAGCTACCAA
56868 AAGG-CAGAGAAAAACGTGCCAC
1 AAGGACAGAGAAAAACGTGCCAC
* * * *
56890 AAAGACAGAGATAAACGTGTCAT
1 AAGGACAGAGAAAAACGTGCCAC
56913 AAGGACAGAGAA
1 AAGGACAGAGAA
56925 CATGTCACAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 3 0.11
23 25 0.89
ACGTcount: A:0.49, C:0.16, G:0.26, T:0.09
Consensus pattern (23 bp):
AAGGACAGAGAAAAACGTGCCAC
Found at i:56939 original size:20 final size:21
Alignment explanation
Indices: 56887--56939 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
56877 AAAAACGTGC
*
56887 CACAAAGACAGAGATAAACGTGT
1 CACAAAGACAGAG--AAACATGT
* *
56910 CATAAGGACAGAG-AACATGT
1 CACAAAGACAGAGAAACATGT
56930 CACAAAGACA
1 CACAAAGACA
56940 TAATTATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 14 0.56
23 11 0.44
ACGTcount: A:0.49, C:0.19, G:0.21, T:0.11
Consensus pattern (21 bp):
CACAAAGACAGAGAAACATGT
Found at i:70216 original size:174 final size:174
Alignment explanation
Indices: 69922--70263 Score: 542
Period size: 174 Copynumber: 2.0 Consensus size: 174
69912 TGGACTGGAC
* *
69922 CATCCTCTGATGGTATGTTTACACTCTTCAAACTTGGTCTATTACCAGACAGCACAGATGATTCC
1 CATCCTCTGATGGTATGTTTACACGCTTCAAACTTAGTCTATTACCAGACAGCACAGATGATTCC
* *
69987 CATCTTCCATTTTCTTCAATGGGTTGCCTCTGCTAAATTAGTCTACTCAGTTGTAAGCTTCATTA
66 CATCTTCCATTTTCTTCAATGGCTTGCCTCTGCTAAATCAGTCTACTCAGTTGTAAGCTTCATTA
* *
70052 TTTTCAAGTTAATTGAGAT-ACCTCAGTGGTAAAAGAGACTGTAT
131 TTTTCAAGTTAATCGAG-TGACCTCAGTGATAAAAGAGACTGTAT
70096 CATCCTCTGATGGTATGTTTACACGCTTCAAACTTAGTCTATTACCAGACAGCACAGATGATTCC
1 CATCCTCTGATGGTATGTTTACACGCTTCAAACTTAGTCTATTACCAGACAGCACAGATGATTCC
* * * * ** *
70161 CATCTTCCATTTTCTTTAATTGCTTGCCTCTGTTAAATCAGTCTATTTGGTTGTAATCTTCATTA
66 CATCTTCCATTTTCTTCAATGGCTTGCCTCTGCTAAATCAGTCTACTCAGTTGTAAGCTTCATTA
*
70226 TTTTCAAGTTAATCGAGTGACTTCAGTGATAAAAGAGA
131 TTTTCAAGTTAATCGAGTGACCTCAGTGATAAAAGAGA
70264 GTGCCGTTCT
Statistics
Matches: 153, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
173 1 0.01
174 152 0.99
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (174 bp):
CATCCTCTGATGGTATGTTTACACGCTTCAAACTTAGTCTATTACCAGACAGCACAGATGATTCC
CATCTTCCATTTTCTTCAATGGCTTGCCTCTGCTAAATCAGTCTACTCAGTTGTAAGCTTCATTA
TTTTCAAGTTAATCGAGTGACCTCAGTGATAAAAGAGACTGTAT
Found at i:72332 original size:25 final size:26
Alignment explanation
Indices: 72284--72332 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
72274 GACAATAAGT
* *
72284 TTTTTAAAAATATATGAAATTTATAA
1 TTTTTAAAAATATATAAAAATTATAA
*
72310 TTTTTAAAATTATA-AAAAATTAT
1 TTTTTAAAAATATATAAAAATTAT
72333 TATTAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 7 0.35
26 13 0.65
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (26 bp):
TTTTTAAAAATATATAAAAATTATAA
Found at i:77165 original size:22 final size:22
Alignment explanation
Indices: 77129--77172 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
77119 CTTCGATGGT
77129 AATAAAATTATTATTATATTTA
1 AATAAAATTATTATTATATTTA
77151 AATAAATATTA-TATTATATTTA
1 AATAAA-ATTATTATTATATTTA
77173 CTTTGGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATAAAATTATTATTATATTTA
Found at i:77901 original size:8 final size:8
Alignment explanation
Indices: 77862--77903 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
77852 TAAAAATAAA
77862 ATTATTAT
1 ATTATTAT
*
77870 AATATTAT
1 ATTATTAT
*
77878 ACTATTAT
1 ATTATTAT
*
77886 -TTAATAT
1 ATTATTAT
77893 ATTATTAT
1 ATTATTAT
77901 ATT
1 ATT
77904 GTTTGATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
7 5 0.18
8 23 0.82
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (8 bp):
ATTATTAT
Found at i:78844 original size:18 final size:19
Alignment explanation
Indices: 78811--78851 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
78801 TATTTTAAAA
* *
78811 TTTAAGAGAAATTAATTTT
1 TTTAAGAGAAAATAATATT
78830 TTTAA-AGAAAATAATATT
1 TTTAAGAGAAAATAATATT
78848 TTTA
1 TTTA
78852 TTTTTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (19 bp):
TTTAAGAGAAAATAATATT
Found at i:79322 original size:281 final size:282
Alignment explanation
Indices: 78820--79390 Score: 1110
Period size: 281 Copynumber: 2.0 Consensus size: 282
78810 ATTTAAGAGA
78820 AATTAATTTTTTTAAAGAAAATAATATTTTTATTTTTTAAAAAGTAAATTTCAAAATCACTTAAT
1 AATTAATTTTTTTAAAGAAAATAATATTTTTATTTTTTAAAAAGTAAATTTCAAAATCACTTAAT
78885 TTTGACATGTGTCATATACGGGAGAAATTAATGTCATTGACGACTCGGACACCTAAATGGGTAAT
66 TTTGACATGTGTCATATACGGGAGAAATTAATGTCATTGACGACTCGGACACCTAAATGGGTAAT
78950 ATTTGTAACGTTAGACACCTGTGTAGGAAATTAATCTAGTTTTATATGTTAAGTAACTTGATATA
131 ATTTGTAACGTTAGACACCTGTGTAGGAAATTAATCTAGTTTTATATGTTAAGTAACTTGATATA
79015 ATTTAAAAAAATCTCGAGTTCGAG-TTTTGTGTATGTAAAAAATCT-CGTTAAAAGATTCCCTCA
196 ATTTAAAAAAATCTCGAGTTCGAGTTTTTGTGTATGTAAAAAATCTCCGTTAAAAGATTCCCTCA
79078 CCAAAATCAGATGTACAATCCG
261 CCAAAATCAGATGTACAATCCG
79100 AATTAATTTTTTTAAAGAAAATAATATTTTTATTTTTTAAAAAGTAAATTTCAAAATCACTTAAT
1 AATTAATTTTTTTAAAGAAAATAATATTTTTATTTTTTAAAAAGTAAATTTCAAAATCACTTAAT
79165 TTTGACATGTGTCATATAACGGGAGAAATTAATGTCATTGACGACTCGGACACCTAAATGGGTAA
66 TTTGACATGTGTCATAT-ACGGGAGAAATTAATGTCATTGACGACTCGGACACCTAAATGGGTAA
79230 TATTTGTAACGTTAGACACCTGTGTAGGAAATTAATCTAGTTTTATATGTTAAGTAACTTGATAT
130 TATTTGTAACGTTAGACACCTGTGTAGGAAATTAATCTAGTTTTATATGTTAAGTAACTTGATAT
*
79295 AATTTAAAAAAATCTCGAGTTCGAGTTTTTGTGTTTGTAAAAAATCTCCGTTAAAAGATTCCCTC
195 AATTTAAAAAAATCTCGAGTTCGAGTTTTTGTGTATGTAAAAAATCTCCGTTAAAAGATTCCCTC
79360 ACCAAAATCAGATGTACAATCCG
260 ACCAAAATCAGATGTACAATCCG
79383 AATTAATT
1 AATTAATT
79391 CGGATTAATC
Statistics
Matches: 287, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
280 82 0.29
281 137 0.48
282 20 0.07
283 48 0.17
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (282 bp):
AATTAATTTTTTTAAAGAAAATAATATTTTTATTTTTTAAAAAGTAAATTTCAAAATCACTTAAT
TTTGACATGTGTCATATACGGGAGAAATTAATGTCATTGACGACTCGGACACCTAAATGGGTAAT
ATTTGTAACGTTAGACACCTGTGTAGGAAATTAATCTAGTTTTATATGTTAAGTAACTTGATATA
ATTTAAAAAAATCTCGAGTTCGAGTTTTTGTGTATGTAAAAAATCTCCGTTAAAAGATTCCCTCA
CCAAAATCAGATGTACAATCCG
Found at i:79542 original size:22 final size:22
Alignment explanation
Indices: 79506--79549 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
79496 CTTCGATGGT
79506 AATAAAATTATTATTATATTTA
1 AATAAAATTATTATTATATTTA
79528 AATAAATATTA-TATTATATTTA
1 AATAAA-ATTATTATTATATTTA
79550 CTTTGGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATAAAATTATTATTATATTTA
Found at i:80461 original size:2 final size:2
Alignment explanation
Indices: 80454--80508 Score: 60
Period size: 2 Copynumber: 28.5 Consensus size: 2
80444 ATCGGGCCGG
* * * *
80454 AT AT AT AT AT AT TT AA AT -T AA AT AT AT AA AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
80494 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
80509 ATAATTATTT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:84611 original size:19 final size:19
Alignment explanation
Indices: 84589--84645 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
84579 ATCGAAACCA
84589 GGTTTTTTCAGTTCGGTTC
1 GGTTTTTTCAGTTCGGTTC
**
84608 GGTTTTTT-A-AACGGTTC
1 GGTTTTTTCAGTTCGGTTC
* *
84625 GGGTTTTTCGGTTCGGTTC
1 GGTTTTTTCAGTTCGGTTC
84644 GG
1 GG
84646 GTTATCGGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
17 13 0.43
18 1 0.03
19 16 0.53
ACGTcount: A:0.07, C:0.14, G:0.32, T:0.47
Consensus pattern (19 bp):
GGTTTTTTCAGTTCGGTTC
Found at i:90000 original size:47 final size:48
Alignment explanation
Indices: 89945--90036 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
89935 GACACTTGTG
**
89945 GAGGGGTTGCTTGGGATA-CCGGGCACCATGGAGGTCCACCCCTGGAT
1 GAGGGGTTGCCCGGGATACCCGGGCACCATGGAGGTCCACCCCTGGAT
* *
89992 GAGGGGTTGCCCGGGATACCCGGGCTCCATGGAGGTCCGCCCCTG
1 GAGGGGTTGCCCGGGATACCCGGGCACCATGGAGGTCCACCCCTG
90037 AATGTAGACC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 16 0.40
48 24 0.60
ACGTcount: A:0.14, C:0.29, G:0.39, T:0.17
Consensus pattern (48 bp):
GAGGGGTTGCCCGGGATACCCGGGCACCATGGAGGTCCACCCCTGGAT
Found at i:90217 original size:21 final size:20
Alignment explanation
Indices: 90180--90218 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
90170 AATTTCGGTA
**
90180 AAATATTATTTTTTTACCGG
1 AAATATTATTTCGTTACCGG
90200 AAATATTAATTTCGTTACC
1 AAATATT-ATTTCGTTACC
90219 TAATTTTCGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (20 bp):
AAATATTATTTCGTTACCGG
Found at i:92289 original size:373 final size:374
Alignment explanation
Indices: 91582--92325 Score: 1456
Period size: 373 Copynumber: 2.0 Consensus size: 374
91572 GATGATCGGA
91582 AAGGGGCGAAAGGAGGCAATCACCCTTAAATTTTTAAATATTTTTTTATATTTTCAATTGATAAT
1 AAGGGGCGAAAGGAGGCAAT-ACCCTTAAATTTTTAAATATTTTTTTATATTTTCAATTGATAAT
91647 CTATTTTCGTCCCTAGAATTTTATTGGCTCACTCCAAAATTTTAGAAGACCGTTTTCTAACATAA
65 CTATTTTCGTCCCTAGAATTTTATTGGCTCACTCCAAAATTTTAGAAGACCGTTTTCTAACATAA
91712 AAATTTTACGTAAATGCCAGCATTCATCGGAGGCTTTATAGTAGAAAGCTTCAACAAAATTGAAC
130 AAATTTTACGTAAATGCCAGCATTCATCGGAGGCTTTATAGTAGAAAGCTTCAACAAAATTGAAC
91777 CCCAACAATAAATGTTTAAAATTTTATCTATCACATTTCTGGTCCCTATTTGAGGTTACCATAGC
195 CCCAACAATAAATGTTTAAAATTTTATCTATCACATTTCTGGTCCCTATTTGAGGTTACCATAGC
91842 TTTCACTATGATTTCAGAGTCTGTAAAGGCATCCTGGATTAGAGTTTTATATGATAAGGTACCGA
260 TTTCACTATGATTTCAGAGTCTGTAAAGGCATCCTGGATTAGAGTTTTATATGATAAGGTACCGA
91907 TATCACAAATCCATGGATTATTCCAAAACACCGCAATCTTTCTATAGCAT
325 TATCACAAATCCATGGATTATTCCAAAACACCGCAATCTTTCTATAGCAT
91957 AAGGGGCGAAAGGAGGCAAT-CCCTT-AATTTTTAAATATTTTTTTATATTTTCAATTGATAATC
1 AAGGGGCGAAAGGAGGCAATACCCTTAAATTTTTAAATATTTTTTTATATTTTCAATTGATAATC
92020 TATTTTCGTCCCTAGAATTTTATTGGCTCACTCCTAAAATTTTAGAAGACCGTTTTCTAACATAA
66 TATTTTCGTCCCTAGAATTTTATTGGCTCACTCC-AAAATTTTAGAAGACCGTTTTCTAACATAA
92085 AAATTTTACGTAAATGCCAGCATTCATCGGAGGCTTTATAGTAGAAAGCTTCAACAAAATTGAAC
130 AAATTTTACGTAAATGCCAGCATTCATCGGAGGCTTTATAGTAGAAAGCTTCAACAAAATTGAAC
92150 CCCAACAATAAATGTTTAAAATTTTATCTATCACATTTCTGGTCCCTATTTGAGGTTACCATAGC
195 CCCAACAATAAATGTTTAAAATTTTATCTATCACATTTCTGGTCCCTATTTGAGGTTACCATAGC
92215 TTTCACTATGATTTCAGAGTCTGTAAAGGCATCCTGGATTAGAGTTTTATATGATAAGGTACCGA
260 TTTCACTATGATTTCAGAGTCTGTAAAGGCATCCTGGATTAGAGTTTTATATGATAAGGTACCGA
92280 TATCACAAATCCATGGATTATTCCAAAACACCGCAATCTTTCTATA
325 TATCACAAATCCATGGATTATTCCAAAACACCGCAATCTTTCTATA
92326 TACATCCATT
Statistics
Matches: 368, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
372 72 0.20
373 276 0.75
375 20 0.05
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (374 bp):
AAGGGGCGAAAGGAGGCAATACCCTTAAATTTTTAAATATTTTTTTATATTTTCAATTGATAATC
TATTTTCGTCCCTAGAATTTTATTGGCTCACTCCAAAATTTTAGAAGACCGTTTTCTAACATAAA
AATTTTACGTAAATGCCAGCATTCATCGGAGGCTTTATAGTAGAAAGCTTCAACAAAATTGAACC
CCAACAATAAATGTTTAAAATTTTATCTATCACATTTCTGGTCCCTATTTGAGGTTACCATAGCT
TTCACTATGATTTCAGAGTCTGTAAAGGCATCCTGGATTAGAGTTTTATATGATAAGGTACCGAT
ATCACAAATCCATGGATTATTCCAAAACACCGCAATCTTTCTATAGCAT
Found at i:96294 original size:304 final size:305
Alignment explanation
Indices: 95741--96343 Score: 1064
Period size: 304 Copynumber: 2.0 Consensus size: 305
95731 CTCAAACATG
*
95741 AATATTAATTATATGAAGACCTTATACTATGTTTTTTTTAAATCAACATATAAATGTTAATATTA
1 AATATTAATTATATGAAGACCTTATACTATGTTTTTTTAAAATCAACATATAAATGTTAATATTA
* *
95806 TTAATAATTTATTTCTTAAAAACATAAAATCTTAATACATTATATTTTTGAGTTGCTCACGAGCT
66 TTAATAATTCATTTCTTAAAAACATAAAATCTTAATACATTATATTTTCGAGTTGCTCACGAGCT
*
95871 TTTTGAGTCGAATATCAAATAACTCGTTTCGGCTAGTTAAGAACTCAAACTCGAGCATTGAACGA
131 TTTTGAGTCGAATATCAAATAACTCGTTTCGGCTAGTTAAGAACTCAAACTCGAACATTGAACGA
* *
95936 GTCTATCTTAAATAGCTCGTGATCTGTCTCGTCTCATTTACATCATTTGCTTTTGTAGATAATTT
196 GTCTATCTTAAATAGCTCGTGATCTGTCTCGTCTCATTTACAGCATTAGCTTTTGTAGATAATTT
96001 TGGCCCAATACTATAGGCGTACTAATTATTTAGCATTTAAATGTT
261 TGGCCCAATACTATAGGCGTACTAATTATTTAGCATTTAAATGTT
*
96046 AATATTAATTATATGAAGACCTTATACTATGTTTTTTTAAAATTAACATATAAATGTTAATATTA
1 AATATTAATTATATGAAGACCTTATACTATGTTTTTTTAAAATCAACATATAAATGTTAATATTA
* *
96111 TTAATAATTCATTTCTTAAAAACA-AAAATTTTAATATATTATATTTTCGAGTTGCTCACGAGCT
66 TTAATAATTCATTTCTTAAAAACATAAAATCTTAATACATTATATTTTCGAGTTGCTCACGAGCT
* * *
96175 TTTTGAGTCGAGTATCAAATAGCTCGTTTCGGCTAGTTAAGAACTCAAGCTCGAACATTGAACGA
131 TTTTGAGTCGAATATCAAATAACTCGTTTCGGCTAGTTAAGAACTCAAACTCGAACATTGAACGA
* * *
96240 GTCTATCTTAAGTAGTTCGTGATCTGTCTCGTCTCATTTACAGCCTTAGCTTTTGTAGATAATTT
196 GTCTATCTTAAATAGCTCGTGATCTGTCTCGTCTCATTTACAGCATTAGCTTTTGTAGATAATTT
96305 TGGCCCAATACTATAGGCGTACTAATTATTTAGCATTTA
261 TGGCCCAATACTATAGGCGTACTAATTATTTAGCATTTA
96344 CCGTAGATCC
Statistics
Matches: 283, Mismatches: 15, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
304 197 0.70
305 86 0.30
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (305 bp):
AATATTAATTATATGAAGACCTTATACTATGTTTTTTTAAAATCAACATATAAATGTTAATATTA
TTAATAATTCATTTCTTAAAAACATAAAATCTTAATACATTATATTTTCGAGTTGCTCACGAGCT
TTTTGAGTCGAATATCAAATAACTCGTTTCGGCTAGTTAAGAACTCAAACTCGAACATTGAACGA
GTCTATCTTAAATAGCTCGTGATCTGTCTCGTCTCATTTACAGCATTAGCTTTTGTAGATAATTT
TGGCCCAATACTATAGGCGTACTAATTATTTAGCATTTAAATGTT
Found at i:99452 original size:12 final size:12
Alignment explanation
Indices: 99435--99460 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
99425 GGGGGCTACG
99435 TCTTGGTATTGC
1 TCTTGGTATTGC
99447 TCTTGGTATTGC
1 TCTTGGTATTGC
99459 TC
1 TC
99461 GGGCTTTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.19, G:0.23, T:0.50
Consensus pattern (12 bp):
TCTTGGTATTGC
Found at i:113869 original size:31 final size:29
Alignment explanation
Indices: 113802--113877 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 29
113792 TAAAAATTTA
* ***
113802 GATACTAAAATAAAATAAAATTTAATGGC
1 GATACTAAAAGAAAATAAAATTTAACAAC
113831 GAGTACTAAAAGAAAATAAAAATTTAACAAC
1 GA-TACTAAAAGAAAAT-AAAATTTAACAAC
113862 GGATACTAAAATGAAA
1 -GATACTAAAA-GAAA
113878 CAAAAAGTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
29 2 0.05
30 13 0.33
31 18 0.46
32 6 0.15
ACGTcount: A:0.58, C:0.08, G:0.12, T:0.22
Consensus pattern (29 bp):
GATACTAAAAGAAAATAAAATTTAACAAC
Found at i:117110 original size:249 final size:246
Alignment explanation
Indices: 116614--117114 Score: 548
Period size: 249 Copynumber: 2.0 Consensus size: 246
116604 TATTTTTAAA
* *
116614 TAGGGTAAATTACGCTTTAGTTTTAAACTATTAGTTTTGATACATTTTAGTACTTGAAGTTTTAA
1 TAGGGTAAATTACGCTTTAGTTTTAAACTATTAGTTTTGATACATTTTAGTACTTAAACTTTTAA
* ** **
116679 AATTTTCAAAATTATATTTAAAGTTTAGTTTTTTGTTTTATTTCAGTATTCTTGTTTGAAATTTA
66 AATTTTCAAAATCATACCTAAAGTTTAGTTTTTTGTTTTATTTCAGTATTCTTGTTCAAAATTTA
* *
116744 ACGTGAATTTTTGAAAAAAATTCAAAAGTTTAGGTATTAAACTGATCAAATTTAATAGTTTAGAT
131 ACGTGAAATTTT--AAAAAATTCAAAAGTTTAGGTATAAAACTGATCAAATTTAATAGTTTAGAT
* ** * *
116809 ACTAAATGTATTATTTTTTTAACAGTGCTAAAATAGAAAAAAAAACTATACAT
194 ACTAAATGCATTAAGTTTTTAACAATACTAAAATAGAAAAAAAAACTATACAT
*
116862 TAGGGTAAATTACTGC-TTAGTATTTAAACTA-TAGGTTTTGATATATTTTAGTACTTAAACTTT
1 TAGGGTAAATTAC-GCTTTAGT-TTTAAACTATTA-GTTTTGATACATTTTAGTACTTAAACTTT
** ** *
116925 TAATTTTTTTTAAATCATACCTAAAGTTTAG-TTTTTGTTTTATTTTAGTA-TCATTGTTCAAAA
63 TAAAATTTTCAAAATCATACCTAAAGTTTAGTTTTTTGTTTTATTTCAGTATTC-TTGTTCAAAA
* *** ** * * *
116988 TTTAACTTGAAATTTT-AATTTTTTTAAAGTTTATGTACTAAAACTGATCAAATTTGATAATTTT
127 TTTAACGTGAAATTTTAAAAAATTCAAAAGTTTAGGTA-TAAAACTGATCAAATTTAAT-AGTTT
* * * *
117052 AG-TACTAAATGCCTTAAGTTTTTAACCGCGAATATTAAAATAG-AACAAAAATTATACAT
190 AGATACTAAATGCATTAAGTTTTTAA---C-AATACTAAAATAGAAAAAAAAACTATACAT
117111 TAGG
1 TAGG
117115 TATGTTTTTT
Statistics
Matches: 210, Mismatches: 33, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
245 15 0.07
246 37 0.18
247 8 0.04
248 60 0.29
249 80 0.38
250 10 0.05
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.45
Consensus pattern (246 bp):
TAGGGTAAATTACGCTTTAGTTTTAAACTATTAGTTTTGATACATTTTAGTACTTAAACTTTTAA
AATTTTCAAAATCATACCTAAAGTTTAGTTTTTTGTTTTATTTCAGTATTCTTGTTCAAAATTTA
ACGTGAAATTTTAAAAAATTCAAAAGTTTAGGTATAAAACTGATCAAATTTAATAGTTTAGATAC
TAAATGCATTAAGTTTTTAACAATACTAAAATAGAAAAAAAAACTATACAT
Found at i:121653 original size:129 final size:129
Alignment explanation
Indices: 121423--121681 Score: 464
Period size: 129 Copynumber: 2.0 Consensus size: 129
121413 TCTACATGCT
* *
121423 TGAATTTTGAGTGAAGAACTGGGTTAGCACACATCGCTACCGTGCTCGTATTGTCACACCACAAC
1 TGAATTTTGAGTGAAGAACCGGGTTAGCACACATCGCTACCGTGCTCGTATTATCACACCACAAC
121488 GTTGCCTTTCCATGAGGAACTACATGTAACTCACTTAACAGCGATTTAAGCCAAACCATTTCAG
66 GTTGCCTTTCCATGAGGAACTACATGTAACTCACTTAACAGCGATTTAAGCCAAACCATTTCAG
* *
121552 TGAATTTTGAGTGAAGAACCGGGTTAGTACACATCGCTACCGTGCTCGTATTATCACACCACAAT
1 TGAATTTTGAGTGAAGAACCGGGTTAGCACACATCGCTACCGTGCTCGTATTATCACACCACAAC
* *
121617 GTTGCCTTTTCATGAGGAACTACATGTAACTCACTTAACAGCGATTTAAGCCAACCCATTTCAG
66 GTTGCCTTTCCATGAGGAACTACATGTAACTCACTTAACAGCGATTTAAGCCAAACCATTTCAG
121681 T
1 T
121682 CGCAGCACAA
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
129 124 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (129 bp):
TGAATTTTGAGTGAAGAACCGGGTTAGCACACATCGCTACCGTGCTCGTATTATCACACCACAAC
GTTGCCTTTCCATGAGGAACTACATGTAACTCACTTAACAGCGATTTAAGCCAAACCATTTCAG
Found at i:123783 original size:15 final size:15
Alignment explanation
Indices: 123755--123799 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
123745 TTGAGACCTT
* *
123755 ACCCGTCCCGCATCC
1 ACCCGCCCCACATCC
*
123770 ACCCGCCTCACATCC
1 ACCCGCCCCACATCC
*
123785 ACTCGCCCCACATCC
1 ACCCGCCCCACATCC
123800 GCCCACCTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.18, C:0.60, G:0.09, T:0.13
Consensus pattern (15 bp):
ACCCGCCCCACATCC
Found at i:125654 original size:19 final size:20
Alignment explanation
Indices: 125610--125656 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
125600 TTTTTTTTAA
125610 TTTTTTAATAATAAAAATAT
1 TTTTTTAATAATAAAAATAT
125630 TATTTTTAAATAA-AAAAAGT-T
1 T-TTTTT-AATAATAAAAA-TAT
125651 TTTTTT
1 TTTTTT
125657 TGAAAACCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 6 0.25
21 12 0.50
22 6 0.25
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TTTTTTAATAATAAAAATAT
Found at i:125657 original size:22 final size:21
Alignment explanation
Indices: 125610--125657 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
125600 TTTTTTTTAA
125610 TTTTTTAATAATAAAAATATT
1 TTTTTTAATAATAAAAATATT
*
125631 ATTTTTAAATAA-AAAAAGT-TT
1 -TTTTTTAATAATAAAAA-TATT
125652 TTTTTT
1 TTTTTT
125658 GAAAACCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 5 0.22
21 7 0.30
22 11 0.48
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TTTTTTAATAATAAAAATATT
Found at i:126776 original size:54 final size:54
Alignment explanation
Indices: 126717--126826 Score: 202
Period size: 54 Copynumber: 2.0 Consensus size: 54
126707 AATATGATCC
*
126717 TTGAACTTCTTTTCTCGCTCAATGGTCTTTCAACTATTTTTTAATAATTTAATT
1 TTGAACTTCTTTTCTCGCTCAATGGTCTTTCAACTATTTTCTAATAATTTAATT
*
126771 TTGAACTTCTTTTCTCGCTCAATGGTCTTTCAATTATTTTCTAATAATTTAATT
1 TTGAACTTCTTTTCTCGCTCAATGGTCTTTCAACTATTTTCTAATAATTTAATT
126825 TT
1 TT
126827 ATAATATTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.24, C:0.16, G:0.07, T:0.53
Consensus pattern (54 bp):
TTGAACTTCTTTTCTCGCTCAATGGTCTTTCAACTATTTTCTAATAATTTAATT
Found at i:127568 original size:28 final size:28
Alignment explanation
Indices: 127546--127610 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 28
127536 ATTTTCAAAA
*
127546 AAACTGAAAATA-AAAACTATTTTCAAAA
1 AAACTGAAAACAGAAAA-TATTTTCAAAA
*
127574 AAA-TAAAAACAGAAAATATTTTCTAAAA
1 AAACTGAAAACAGAAAATATTTTC-AAAA
127602 TCAAACTGA
1 --AAACTGA
127611 GTTTAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
27 13 0.45
28 11 0.38
30 3 0.10
31 2 0.07
ACGTcount: A:0.60, C:0.11, G:0.05, T:0.25
Consensus pattern (28 bp):
AAACTGAAAACAGAAAATATTTTCAAAA
Found at i:127582 original size:27 final size:28
Alignment explanation
Indices: 127536--127601 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
127526 ATGTTTTCTA
* *
127536 ATTTTCAAAAAAACTGAAAATA-AAAACT
1 ATTTTCAAAAAAACTAAAAACAGAAAA-T
127564 ATTTTCAAAAAAA-TAAAAACAGAAAAT
1 ATTTTCAAAAAAACTAAAAACAGAAAAT
*
127591 ATTTTCTAAAA
1 ATTTTCAAAAA
127602 TCAAACTGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 17 0.50
28 17 0.50
ACGTcount: A:0.61, C:0.09, G:0.03, T:0.27
Consensus pattern (28 bp):
ATTTTCAAAAAAACTAAAAACAGAAAAT
Found at i:138840 original size:101 final size:100
Alignment explanation
Indices: 138666--138854 Score: 333
Period size: 101 Copynumber: 1.9 Consensus size: 100
138656 TAATTTATTA
*
138666 AAAGTATGACTATATTGAGAGAATATATAAATAACATGATTAAATATGTGATTGTACCAAAATAT
1 AAAGTATGACTATATTGAGAGAATATATAAATAACATGATCAAATATGTGATTGTACCAAAATAT
* *
138731 CATGTTACTTAATCTGTTCACTACAATTAACCTAT
66 CACGTTACTTAATCTGTTAACTACAATTAACCTAT
138766 AAAGTATGACTATATTGAGAGAATATATAAATAACAATGATCAAATATGTGATTGTACCAAAATA
1 AAAGTATGACTATATTGAGAGAATATATAAATAAC-ATGATCAAATATGTGATTGTACCAAAATA
*
138831 TCACGTTACTTAATTTGTTAACTA
65 TCACGTTACTTAATCTGTTAACTA
138855 TTAACTACAA
Statistics
Matches: 84, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
100 35 0.42
101 49 0.58
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (100 bp):
AAAGTATGACTATATTGAGAGAATATATAAATAACATGATCAAATATGTGATTGTACCAAAATAT
CACGTTACTTAATCTGTTAACTACAATTAACCTAT
Found at i:138946 original size:31 final size:30
Alignment explanation
Indices: 138886--138946 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
138876 TAACTACATC
138886 TTAAATAAATAAAAACAAATGATACCATATA
1 TTAAATAAATAAAAACAAATGATA-CATATA
*
138917 TTAATTAAATAAAAACGAAAGTGAT-CATAT
1 TTAAATAAATAAAAAC-AAA-TGATACATAT
138947 CTTATGTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 20 0.74
32 3 0.11
33 4 0.15
ACGTcount: A:0.57, C:0.08, G:0.07, T:0.28
Consensus pattern (30 bp):
TTAAATAAATAAAAACAAATGATACATATA
Found at i:141976 original size:40 final size:39
Alignment explanation
Indices: 141850--141976 Score: 114
Period size: 40 Copynumber: 3.2 Consensus size: 39
141840 ACACTTTTGT
*
141850 TAAATTACATTAGGTTAATATTTATTATTAAGGTTTATA
1 TAAATTACATTAGGTTAATATTTATTATTAATGTTTATA
* * * * * * *
141889 TTAATTAAGATTA-GATATTTTTTATATGTTAATATATT-TA
1 TAAATT-ACATTAGGTTAATATTTAT-TATTAATGT-TTATA
*
141929 AATAATTACATTAGGTTAATATTTATTATTAATGTTTATA
1 TA-AATTACATTAGGTTAATATTTATTATTAATGTTTATA
141969 CTAAATTA
1 -TAAATTA
141977 AATTTTGAAG
Statistics
Matches: 64, Mismatches: 17, Indels: 13
0.68 0.18 0.14
Matches are distributed among these distances:
39 16 0.25
40 32 0.50
41 16 0.25
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.50
Consensus pattern (39 bp):
TAAATTACATTAGGTTAATATTTATTATTAATGTTTATA
Found at i:143249 original size:12 final size:12
Alignment explanation
Indices: 143232--143272 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
143222 GAATTCATAT
143232 TAAATTATTATA
1 TAAATTATTATA
*
143244 TAAA-T-TTAAA
1 TAAATTATTATA
143254 TTAAATTATTATA
1 -TAAATTATTATA
143267 TAAATT
1 TAAATT
143273 TAAATTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 4 0.17
11 5 0.21
12 11 0.46
13 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
TAAATTATTATA
Found at i:143249 original size:23 final size:23
Alignment explanation
Indices: 143230--143285 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
143220 TTGAATTCAT
143230 ATTAAATTATTATATAAATTTAA
1 ATTAAATTATTATATAAATTTAA
143253 ATTAAATTATTATATAAATTTAA
1 ATTAAATTATTATATAAATTTAA
143276 ATTAAATTAT
1 ATTAAATTAT
143286 CATCTCTAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTAAATTATTATATAAATTTAA
Found at i:144099 original size:17 final size:18
Alignment explanation
Indices: 144064--144103 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
144054 ACACTCTAAC
144064 TTAAA-ATTTTAAACGAT
1 TTAAATATTTTAAACGAT
144081 TTAAATATTTTAAAC-AT
1 TTAAATATTTTAAACGAT
144098 TTAAAT
1 TTAAAT
144104 GACTTCGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (18 bp):
TTAAATATTTTAAACGAT
Found at i:154503 original size:35 final size:35
Alignment explanation
Indices: 154453--154526 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
154443 CTGAAATTGT
* *
154453 AGATAGAGTCAGTGGCATATTCAAAAATATTTTTG
1 AGATAGAGTCAGTGGCAGATTCAAAAATATTTTTA
* * *
154488 AGATAGAGTCGGTGGCGGATTCAGAAATATTTTTA
1 AGATAGAGTCAGTGGCAGATTCAAAAATATTTTTA
154523 AGAT
1 AGAT
154527 GAACACAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.32
Consensus pattern (35 bp):
AGATAGAGTCAGTGGCAGATTCAAAAATATTTTTA
Found at i:155934 original size:35 final size:35
Alignment explanation
Indices: 155869--155935 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
155859 ACCTTAGGTC
* *
155869 TATAAAGAATTACCAGTTTGATCAGTCTGAACTTA
1 TATAAAGAATTACCAATTTGACCAGTCTGAACTTA
*
155904 TATAAGGAATTACCAATTTGACCGAG-CTGAAC
1 TATAAAGAATTACCAATTTGACC-AGTCTGAAC
155936 ATGCAGAGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 26 0.93
36 2 0.07
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (35 bp):
TATAAAGAATTACCAATTTGACCAGTCTGAACTTA
Found at i:156694 original size:19 final size:19
Alignment explanation
Indices: 156670--156708 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
156660 TGACTTTTTG
*
156670 GGTCAAAGTCAACGGGTCA
1 GGTCAAAGTCAACAGGTCA
156689 GGTCAAAGTCAACAGGTCA
1 GGTCAAAGTCAACAGGTCA
156708 G
1 G
156709 ACTGGTTCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.21, G:0.31, T:0.15
Consensus pattern (19 bp):
GGTCAAAGTCAACAGGTCA
Found at i:162112 original size:18 final size:18
Alignment explanation
Indices: 162080--162114 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
162070 TTGTATTTAG
*
162080 AATTTTCTATGTTTTCCC
1 AATTTTCTATCTTTTCCC
*
162098 AATTTTCTTTCTTTTCC
1 AATTTTCTATCTTTTCC
162115 TCCCCTTTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.23, G:0.03, T:0.60
Consensus pattern (18 bp):
AATTTTCTATCTTTTCCC
Found at i:167941 original size:23 final size:23
Alignment explanation
Indices: 167915--167962 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
167905 ATTTTTATAA
167915 TATAGTTCTCAAATTTGGATTAT
1 TATAGTTCTCAAATTTGGATTAT
167938 TATAGTTCTCAAATTTGGATTAT
1 TATAGTTCTCAAATTTGGATTAT
167961 TA
1 TA
167963 AAACAATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.48
Consensus pattern (23 bp):
TATAGTTCTCAAATTTGGATTAT
Found at i:174398 original size:23 final size:23
Alignment explanation
Indices: 174372--174485 Score: 192
Period size: 23 Copynumber: 5.0 Consensus size: 23
174362 CACCACAGCT
* * *
174372 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCG
174395 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGGAGTGCCG
174418 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGGAGTGCCG
174441 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGGAGTGCCG
*
174464 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGGAGTGCC
174486 ATATAATAAT
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 87 1.00
ACGTcount: A:0.24, C:0.26, G:0.31, T:0.19
Consensus pattern (23 bp):
CGTAGAATTGCACCGGAGTGCCG
Found at i:174688 original size:103 final size:103
Alignment explanation
Indices: 174509--174709 Score: 348
Period size: 103 Copynumber: 2.0 Consensus size: 103
174499 CATAAGGACC
* * *
174509 ACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACCAGACTTCA
1 ACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCA
174574 CACATGTTCCAAAGAATACATATACGTCCCGAATGACA
66 CACATGTTCCAAAGAATACATATACGTCCCGAATGACA
* *
174612 ACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTTA
1 ACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCA
*
174677 CACATGTTCCAAAGAATACATATATGTCCCGAA
66 CACATGTTCCAAAGAATACATATACGTCCCGAA
174710 GGACCGCGTA
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 92 1.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.28
Consensus pattern (103 bp):
ACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCA
CACATGTTCCAAAGAATACATATACGTCCCGAATGACA
Found at i:186076 original size:13 final size:13
Alignment explanation
Indices: 186058--186083 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
186048 AATATGACAT
186058 TTAAAAAATTAAA
1 TTAAAAAATTAAA
186071 TTAAAAAATTAAA
1 TTAAAAAATTAAA
186084 CTTCAATGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAAAAAATTAAA
Found at i:194983 original size:16 final size:17
Alignment explanation
Indices: 194958--194995 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
194948 CTTGATAAAA
194958 ACTC-AACTCG-GGTTG
1 ACTCGAACTCGAGGTTG
*
194973 ACTCGAACTCGAGTTTG
1 ACTCGAACTCGAGGTTG
194990 ACTCGA
1 ACTCGA
194996 TACCTTAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 6 0.30
17 10 0.50
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (17 bp):
ACTCGAACTCGAGGTTG
Found at i:198910 original size:37 final size:37
Alignment explanation
Indices: 198831--198913 Score: 100
Period size: 35 Copynumber: 2.3 Consensus size: 37
198821 ATTAAACCTT
* *
198831 TTTTATATTTTTAATTTTGTAGAAAAATTATATAAATA
1 TTTTATA-ATTTAATTTTGTAGAAAAAATATATAAATA
*
198869 --TTATAATTTAATTTTTTA-AAGAAAATATATAAATA
1 TTTTATAATTTAATTTTGTAGAA-AAAATATATAAATA
198904 TTTTATAATT
1 TTTTATAATT
198914 AATATTATAC
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
34 2 0.05
35 24 0.62
36 5 0.13
37 8 0.21
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (37 bp):
TTTTATAATTTAATTTTGTAGAAAAAATATATAAATA
Found at i:199111 original size:20 final size:20
Alignment explanation
Indices: 199055--199102 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
199045 ATCTTATTCT
199055 CTGGTAATCTTTTATTCACA
1 CTGGTAATCTTTTATTCACA
*
199075 CTGGTAATCTTTTATTCTCA
1 CTGGTAATCTTTTATTCACA
199095 CTGGTAAT
1 CTGGTAAT
199103 TTTACATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.46
Consensus pattern (20 bp):
CTGGTAATCTTTTATTCACA
Found at i:204501 original size:154 final size:155
Alignment explanation
Indices: 204219--204528 Score: 577
Period size: 154 Copynumber: 2.0 Consensus size: 155
204209 GGATAAAATG
* *
204219 TAGTGATTGCTTTAGATGCAAAAACAATGAAAATTTTGGATGGATAAAGATGATTTAGGGATGGT
1 TAGTGATTGCTTTAGATGCAAAAACAATGAAAATTTTGGACGGATAAAGATGATTTAGGGATGGC
204284 AATAGGTCGAGTTAAGATCGGGTTTTTGTCAATCTGATTTGATCCGAAAATATGTATCCCCACTT
66 AATAGGTCGAGTTAAGATCGGGTTTTTGTCAATCTGATTTGATCCGAAAATATGTATCCCCACTT
204349 GAATCTAATCTGATCCGAAAATATT
131 GAATCTAATCTGATCCGAAAATATT
*
204374 TAGTGATTGCTTTAGATGCAAAAACAATGAAAATTTTGGACGTATAAAGATGATTTAGGGAT-GC
1 TAGTGATTGCTTTAGATGCAAAAACAATGAAAATTTTGGACGGATAAAGATGATTTAGGGATGGC
*
204438 AATGGGTCGAGTTAAGATCGGGTTTTTGTCAATCTGATTTGATCCGAAAATATGTATCCCCACTT
66 AATAGGTCGAGTTAAGATCGGGTTTTTGTCAATCTGATTTGATCCGAAAATATGTATCCCCACTT
204503 GAATCTAATCTGATCCGAAAATATT
131 GAATCTAATCTGATCCGAAAATATT
204528 T
1 T
204529 TATTCTCCAT
Statistics
Matches: 151, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
154 91 0.60
155 60 0.40
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Consensus pattern (155 bp):
TAGTGATTGCTTTAGATGCAAAAACAATGAAAATTTTGGACGGATAAAGATGATTTAGGGATGGC
AATAGGTCGAGTTAAGATCGGGTTTTTGTCAATCTGATTTGATCCGAAAATATGTATCCCCACTT
GAATCTAATCTGATCCGAAAATATT
Found at i:215632 original size:32 final size:30
Alignment explanation
Indices: 215596--215658 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 30
215586 TAAGGTAAAT
*
215596 TATGTATTCAGTATCT-AAATTATCAATTTTTC
1 TATGT-TTCAATATCTAAAATT-TC-ATTTTTC
*
215628 TATGTTTTAATATCTAAAATTTCATTTTTC
1 TATGTTTCAATATCTAAAATTTCATTTTTC
215658 T
1 T
215659 CAAAATTGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 8 0.29
31 10 0.36
32 10 0.36
ACGTcount: A:0.30, C:0.11, G:0.05, T:0.54
Consensus pattern (30 bp):
TATGTTTCAATATCTAAAATTTCATTTTTC
Found at i:216201 original size:32 final size:32
Alignment explanation
Indices: 216129--216189 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
216119 TGTATGGCTT
216129 TGAAA-AAAACTTGATAGTTTAAGTTCTAAAA
1 TGAAACAAAACTTGATAGTTTAAGTTCTAAAA
*
216160 TGAACCAAAACTT-ATAGTTT-AGTTACTAAA
1 TGAAACAAAACTTGATAGTTTAAGTT-CTAAA
216190 TGTAATACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 4 0.15
31 16 0.59
32 7 0.26
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.33
Consensus pattern (32 bp):
TGAAACAAAACTTGATAGTTTAAGTTCTAAAA
Found at i:228126 original size:16 final size:16
Alignment explanation
Indices: 228098--228138 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
228088 AAAAAAAAGC
228098 TAAGATAAATAAATAAA
1 TAAGAT-AATAAATAAA
*
228115 TAAGATAATAAATTAA
1 TAAGATAATAAATAAA
*
228131 TAAAATAA
1 TAAGATAA
228139 AAACAAACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (16 bp):
TAAGATAATAAATAAA
Found at i:228654 original size:30 final size:29
Alignment explanation
Indices: 228615--228672 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
228605 GACATATATA
228615 AAAAGAATAGAAATAGAATATAAATAAAAG
1 AAAAGAATAGAAATAGAA-ATAAATAAAAG
* * *
228645 AAAATAATAGTAATATAAATAAATAAAA
1 AAAAGAATAGAAATAGAAATAAATAAAA
228673 TATTAAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (29 bp):
AAAAGAATAGAAATAGAAATAAATAAAAG
Found at i:229842 original size:7 final size:7
Alignment explanation
Indices: 229821--229865 Score: 67
Period size: 7 Copynumber: 6.7 Consensus size: 7
229811 AATAATATTG
229821 ATATAAT
1 ATATAAT
229828 ATAT-AT
1 ATATAAT
*
229834 ATGTAAT
1 ATATAAT
229841 ATATAAT
1 ATATAAT
229848 ATATAAT
1 ATATAAT
229855 ATATAA-
1 ATATAAT
229861 ATATA
1 ATATA
229866 TGTTCTTTCG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
6 10 0.29
7 25 0.71
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (7 bp):
ATATAAT
Found at i:230117 original size:20 final size:20
Alignment explanation
Indices: 230094--230135 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
230084 GAATCCTTCG
230094 TCGTGAAGTTGAAATCGAAC
1 TCGTGAAGTTGAAATCGAAC
230114 TCGTGAAGTTGAAATCGAAC
1 TCGTGAAGTTGAAATCGAAC
230134 TC
1 TC
230136 AGAGTTCTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (20 bp):
TCGTGAAGTTGAAATCGAAC
Found at i:230667 original size:105 final size:105
Alignment explanation
Indices: 230386--230904 Score: 845
Period size: 105 Copynumber: 5.0 Consensus size: 105
230376 GTTGTGAAGT
* *
230386 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGC
1 TGAAATTGAGAAA-TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
230451 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
** * ***
230492 TGAAATTGAG-AA-G----TTGACAGTCAGCGGTCCCTTCGTCTTGAAGTTGAACTTGTACTGTC
1 TGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
*
230551 TTGAGTCCAATATCCTTCGTTG-GAAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTG-AAGTTGAAATTGGCTC
*
230591 TGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTC
1 TGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
230656 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
230696 TGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTC
1 TGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
*
230761 TGGTGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
230801 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
*
230866 TGGAGTCCAATATCCTTCGTTGTGAAGTTGGAATTGGCT
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
230905 TTGGGTAAAA
Statistics
Matches: 383, Mismatches: 22, Indels: 17
0.91 0.05 0.04
Matches are distributed among these distances:
98 1 0.00
99 86 0.22
100 2 0.01
101 1 0.00
103 1 0.00
105 282 0.74
106 10 0.03
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (105 bp):
TGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
Found at i:242471 original size:19 final size:20
Alignment explanation
Indices: 242426--242478 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
242416 CCACCGAAAA
* *
242426 TAGAAAAAGGGATACGAATT
1 TAGAAAAAAGGATACAAATT
*
242446 TAAAAAAAAGGATACAAATT
1 TAGAAAAAAGGATACAAATT
242466 T-GAAAAAAGGATA
1 TAGAAAAAAGGATA
242479 AAGGTTTGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.58, C:0.04, G:0.19, T:0.19
Consensus pattern (20 bp):
TAGAAAAAAGGATACAAATT
Found at i:242742 original size:30 final size:29
Alignment explanation
Indices: 242703--242760 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
242693 GACATATATA
242703 AAAAGAATAGAAATAGAATATAAATAAAAG
1 AAAAGAATAGAAATAGAA-ATAAATAAAAG
* * *
242733 AAAATAATAGTAATATAAATAAATAAAA
1 AAAAGAATAGAAATAGAAATAAATAAAA
242761 TATTAAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (29 bp):
AAAAGAATAGAAATAGAAATAAATAAAAG
Found at i:243909 original size:13 final size:13
Alignment explanation
Indices: 243890--243928 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
243880 AATAATATTG
243890 ATATAATATATAT
1 ATATAATATATAT
*
243903 ATGTAATATATAAT
1 ATATAATATAT-AT
243917 ATATAA-ATATAT
1 ATATAATATATAT
243929 GTTCTTTCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 2 0.09
13 14 0.61
14 7 0.30
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (13 bp):
ATATAATATATAT
Found at i:243911 original size:7 final size:7
Alignment explanation
Indices: 243890--243927 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
243880 AATAATATTG
243890 ATATAAT
1 ATATAAT
243897 ATAT-AT
1 ATATAAT
*
243903 ATGTAAT
1 ATATAAT
243910 ATATAAT
1 ATATAAT
243917 ATATAA-
1 ATATAAT
243923 ATATA
1 ATATA
243928 TGTTCTTTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 10 0.36
7 18 0.64
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (7 bp):
ATATAAT
Found at i:243926 original size:24 final size:24
Alignment explanation
Indices: 243882--243930 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
243872 TTTAAAATAA
* *
243882 TAATATTGATATAATATATATATG
1 TAATATTAATATAATAAATATATG
243906 TAATATATAATAT-ATAAATATATG
1 TAATAT-TAATATAATAAATATATG
243930 T
1 T
243931 TCTTTCGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (24 bp):
TAATATTAATATAATAAATATATG
Found at i:244167 original size:2 final size:2
Alignment explanation
Indices: 244160--244209 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
244150 CATGAGATGA
244160 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
244202 AT AT AT AT
1 AT AT AT AT
244210 CAATATCATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:248746 original size:32 final size:32
Alignment explanation
Indices: 248690--248779 Score: 96
Period size: 32 Copynumber: 2.8 Consensus size: 32
248680 TCTTGAACAG
* * *
248690 TACTCATTACTTTCAT--GAGTCTTCAACATAG
1 TACTCATTAC-TTCATCGGTGTCTTCAACACAA
248721 TACTC-TTAACTTCATCGGTGTCTTCAACACAA
1 TACTCATT-ACTTCATCGGTGTCTTCAACACAA
* *
248753 TACTCATTACTTCATTGTTGTCTTCAA
1 TACTCATTACTTCATCGGTGTCTTCAA
248780 AACATTCAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
30 7 0.14
31 7 0.14
32 34 0.68
33 2 0.04
ACGTcount: A:0.27, C:0.24, G:0.09, T:0.40
Consensus pattern (32 bp):
TACTCATTACTTCATCGGTGTCTTCAACACAA
Found at i:250481 original size:29 final size:32
Alignment explanation
Indices: 250448--250507 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
250438 TTAATCTGTT
*
250448 AAAATTT-TT-CTCGACTCG-TGATCGTTAAG
1 AAAATTTGTTGCTCGACTCGTTGATCATTAAG
250477 AAAATTTGTTGCTCGACTCGTTGATCATTAA
1 AAAATTTGTTGCTCGACTCGTTGATCATTAA
250508 ATTCGTTACT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 7 0.26
30 2 0.07
31 9 0.33
32 9 0.33
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (32 bp):
AAAATTTGTTGCTCGACTCGTTGATCATTAAG
Found at i:252927 original size:31 final size:31
Alignment explanation
Indices: 252888--252979 Score: 105
Period size: 31 Copynumber: 2.9 Consensus size: 31
252878 AGTGACAAAT
252888 CTTGATAAGTTTAA-GAACCATTTTATAACAG
1 CTTGATAAGTTTAATG-ACCATTTTATAACAG
* * * *
252919 TTTGATAAGTTAAATGACTATTTTATAATAG
1 CTTGATAAGTTTAATGACCATTTTATAACAG
* *
252950 CTTGATAAATTTTAATGACCATTTTGTAAC
1 CTTGAT-AAGTTTAATGACCATTTTATAAC
252980 TTCCAAAACT
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
31 30 0.61
32 19 0.39
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (31 bp):
CTTGATAAGTTTAATGACCATTTTATAACAG
Found at i:266070 original size:21 final size:21
Alignment explanation
Indices: 266028--266070 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
266018 TTTCTGGGCT
*
266028 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
266049 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
266070 A
1 A
266071 CGTATATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:266440 original size:14 final size:15
Alignment explanation
Indices: 266406--266444 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
266396 TTATGAGACG
266406 TGACATGAATTCATA
1 TGACATGAATTCATA
* *
266421 TAACATGCATT-ATA
1 TGACATGAATTCATA
266435 TGACATGAAT
1 TGACATGAAT
266445 ATGCAGGAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (15 bp):
TGACATGAATTCATA
Found at i:266777 original size:23 final size:23
Alignment explanation
Indices: 266733--266777 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
266723 ATTATTATAT
*
266733 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
266756 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
266778 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:272845 original size:21 final size:21
Alignment explanation
Indices: 272803--272845 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
272793 TTTCTGGGCT
*
272803 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
272824 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
272845 A
1 A
272846 CGTATATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:273236 original size:14 final size:15
Alignment explanation
Indices: 273201--273240 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
273191 ATTATGAGAC
273201 ATGACATGAATTCAT
1 ATGACATGAATTCAT
*
273216 ATAACATGAATT-AT
1 ATGACATGAATTCAT
273230 ATGACATGAAT
1 ATGACATGAAT
273241 ATGCATGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (15 bp):
ATGACATGAATTCAT
Found at i:273564 original size:23 final size:23
Alignment explanation
Indices: 273531--273575 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
273521 ATTATTATAT
273531 GGCACTACGGTGCAATTT-TACGC
1 GGCACTACGGTGC-ATTTATACGC
*
273554 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCATTTATACG
273576 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (23 bp):
GGCACTACGGTGCATTTATACGC
Found at i:282091 original size:158 final size:157
Alignment explanation
Indices: 281837--282239 Score: 506
Period size: 158 Copynumber: 2.5 Consensus size: 157
281827 TTAGTCATTG
* * * * *
281837 ATTTCATTATTTCTTCAATTTC-TCCTTCATTTTAAGTCCATTTTTACCAAATTTGAACCCGCAT
1 ATTTCCTTATTTCTTCAA-TTCGTCATTTATTTTAAGTCTATTTTTACCAAATTTGAA-CCACAT
* * *
281901 GCTCATAAACCATAATAGAATACATGTTTACTTTCAATTCCTCA-TTTTGATAAAT-TTTTTTTA
64 GCTCATAAACCATAATAAAATACATGTGTACTTTCAATTCCT-ATTTTTGATAAATAATTTTTTA
* *
281964 TTTTTCAATTCAGTCATTCGATTTTTCGTA
128 TTTTTCAATTCAGTCATTCAATTTTTCATA
* *
281994 ATTTCCTTATTTCTTCAATTCGTCATTTATTTTAAGTCTGTTTTTTTACCAAATTTGAGCCACAT
1 ATTTCCTTATTTCTTCAATTCGTCATTTATTTTAAGTC--TATTTTTACCAAATTTGAACCACAT
* * *
282059 GCTCCTAAACCATAGTAAAATACATGTGTACTTTCAATTCCTATTTTTGATAACTAATTTTTTAT
64 GCTCATAAACCATAATAAAATACATGTGTACTTTCAATTCCTATTTTTGATAAATAATTTTTTAT
* *
282124 TTTTTAATTTAGTCATTCAATTTTTCATA
129 TTTTCAATTCAGTCATTCAATTTTTCATA
* * * * *
282153 ATCTCCTTATTCCTTCAATTTGTTATTTATTTTTAAGTCTCTTTTTACCAAATTTGAACCACATG
1 ATTTCCTTATTTCTTCAATTCGTCATTTA-TTTTAAGTCTATTTTTACCAAATTTGAACCACATG
* * *
282218 CTCATACACCACAATAGAATAC
65 CTCATAAACCATAATAAAATAC
282240 GTATGTAACT
Statistics
Matches: 212, Mismatches: 28, Indels: 11
0.84 0.11 0.04
Matches are distributed among these distances:
156 3 0.01
157 32 0.15
158 94 0.44
159 74 0.35
160 9 0.04
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (157 bp):
ATTTCCTTATTTCTTCAATTCGTCATTTATTTTAAGTCTATTTTTACCAAATTTGAACCACATGC
TCATAAACCATAATAAAATACATGTGTACTTTCAATTCCTATTTTTGATAAATAATTTTTTATTT
TTCAATTCAGTCATTCAATTTTTCATA
Found at i:290401 original size:35 final size:35
Alignment explanation
Indices: 290350--290435 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 35
290340 AAAACAGTCA
* * * *
290350 TCAATTTCATTATAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
290385 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
290420 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
290436 ATACTTCAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.42, C:0.20, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:290429 original size:21 final size:21
Alignment explanation
Indices: 290404--290446 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
290394 TTCTAAACCC
290404 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
290425 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
290446 T
1 T
290447 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:290601 original size:16 final size:18
Alignment explanation
Indices: 290569--290602 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
290559 TATTAATGTA
290569 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
290587 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
290603 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:291268 original size:130 final size:130
Alignment explanation
Indices: 291065--291312 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
291055 AATTTTCTTC
* * * *
291065 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATATCAGAT
*
291130 CCTGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
291195 TAATTAGGTGGTAACACGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATATCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATATCAGAT
291260 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
291313 TATATAAATA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.35
Consensus pattern (130 bp):
TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATATCAGAT
CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:297022 original size:29 final size:30
Alignment explanation
Indices: 296964--297023 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
296954 CCCTTTTAGC
*
296964 TTATTTTCTTTTTCAGTCCTTGACTGTAGT
1 TTATTTTCTTTTTCAGTCCTTAACTGTAGT
** *
296994 TTATTTTCTTTTTTGGTCTTTAAC-GTAGT
1 TTATTTTCTTTTTCAGTCCTTAACTGTAGT
297023 T
1 T
297024 AAGTATAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.60
Consensus pattern (30 bp):
TTATTTTCTTTTTCAGTCCTTAACTGTAGT
Found at i:297453 original size:20 final size:19
Alignment explanation
Indices: 297424--297464 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
297414 ATGCAAAACG
*
297424 TTACCTAAAATATTATATTT
1 TTACCGAAAATATTAT-TTT
*
297444 TTACCGAAAATGTTATTTT
1 TTACCGAAAATATTATTTT
297463 TT
1 TT
297465 CTAATTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (19 bp):
TTACCGAAAATATTATTTT
Found at i:299122 original size:12 final size:11
Alignment explanation
Indices: 299099--299138 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
299089 ACATTTTTAA
299099 ATTTTTTAATT
1 ATTTTTTAATT
299110 ATTTTTTATATT
1 ATTTTTTA-ATT
*
299122 ATTATTTAATT
1 ATTTTTTAATT
299133 GATTTT
1 -ATTTT
299139 ATTCAACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 11 0.44
12 14 0.56
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (11 bp):
ATTTTTTAATT
Found at i:302578 original size:34 final size:34
Alignment explanation
Indices: 302533--302628 Score: 174
Period size: 34 Copynumber: 2.8 Consensus size: 34
302523 GGTTACCAAC
*
302533 GATGGAGAAGATGAACAACTAGAAGCCGATACAA
1 GATGGAAAAGATGAACAACTAGAAGCCGATACAA
302567 GATGGAAAAGATGAACAACTAGAAGCCGATACAA
1 GATGGAAAAGATGAACAACTAGAAGCCGATACAA
*
302601 GATGGAAAAGATGAACAGCTAGAAGCCG
1 GATGGAAAAGATGAACAACTAGAAGCCG
302629 GTGCCAGGGG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 60 1.00
ACGTcount: A:0.47, C:0.15, G:0.27, T:0.11
Consensus pattern (34 bp):
GATGGAAAAGATGAACAACTAGAAGCCGATACAA
Found at i:302966 original size:32 final size:32
Alignment explanation
Indices: 302925--303017 Score: 177
Period size: 32 Copynumber: 2.9 Consensus size: 32
302915 CAAACTAATG
302925 ACATTCACCATCTAAATGACCAAATTTTATTA
1 ACATTCACCATCTAAATGACCAAATTTTATTA
302957 ACATTCACCATCTAAATGACCAAATTTTATTA
1 ACATTCACCATCTAAATGACCAAATTTTATTA
*
302989 ACATTCACCATCTAAATGACCAAAATTTA
1 ACATTCACCATCTAAATGACCAAATTTTA
303018 ATAAAATGAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 60 1.00
ACGTcount: A:0.42, C:0.23, G:0.03, T:0.32
Consensus pattern (32 bp):
ACATTCACCATCTAAATGACCAAATTTTATTA
Found at i:311868 original size:16 final size:16
Alignment explanation
Indices: 311842--311879 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
311832 TAAATTTTTG
*
311842 ATTTCATCTATCTATTT
1 ATTTCATCTAT-AATTT
311859 ATTT-ATCTATAATTT
1 ATTTCATCTATAATTT
311874 ATTTCA
1 ATTTCA
311880 CTTGAATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 8 0.42
16 7 0.37
17 4 0.21
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTCATCTATAATTT
Found at i:312071 original size:16 final size:16
Alignment explanation
Indices: 312050--312083 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
312040 TTATTGGTAC
312050 TCAAATCTGTTACTCT
1 TCAAATCTGTTACTCT
312066 TCAAATCTGTTACTCT
1 TCAAATCTGTTACTCT
312082 TC
1 TC
312084 TCAATAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.26, G:0.06, T:0.44
Consensus pattern (16 bp):
TCAAATCTGTTACTCT
Found at i:335745 original size:185 final size:184
Alignment explanation
Indices: 335418--335783 Score: 590
Period size: 185 Copynumber: 2.0 Consensus size: 184
335408 TCAAAAATAA
335418 CTAAATATGTATAACTAGAATCAACTAGAAGTGTGTGTTTTAGACCAAAGAAGAATGAACTAGTT
1 CTAAATATGTATAACTAGAATCAACTAGAAGTGTGTGTTTTAGACCAAAGAAGAATGAACTAGTT
* *
335483 CCAATTGTGGGAAGTCCAAAGCGAGACATCAATAAAGCACGTTGATATCGCTCAAAGTACTTCCC
66 CCAATAGTGGGAAGTCCAAAGCGAGACATCAATAAAGCACATTGATATCGCTCAAAGTACTTCCC
*
335548 CTTATAGAAACAAATCAAAACCCGTAACGCTTGAGCATAATGAAGTAGATTGTG
131 CTTATAGAAACAAATCAAAACCCATAACGCTTGAGCATAATGAAGTAGATTGTG
* * * *
335602 CTAAATTTGTATAACTAGAATCAACTAGAAGTGTGTTTTTTCCGACCAAAGTAGAATGAACTAGT
1 CTAAATATGTATAACTAGAATCAACTAGAAGTGTGTGTTTT-AGACCAAAGAAGAATGAACTAGT
* * *
335667 TCCAATAGTGGGAAGTCCAAAGTGAGGA-ATCAATAAAGCACATTGATATCGCTCAACGTACTTT
65 TCCAATAGTGGGAAGTCCAAAGCGA-GACATCAATAAAGCACATTGATATCGCTCAAAGTACTTC
* * *
335731 CCCTTCTGGAAACAAATCAAAATCCATAACGCTTGAGCATAATGAAGTAGATT
129 CCCTTATAGAAACAAATCAAAACCCATAACGCTTGAGCATAATGAAGTAGATT
335784 ATACGTTCAG
Statistics
Matches: 167, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
184 39 0.23
185 126 0.75
186 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.26
Consensus pattern (184 bp):
CTAAATATGTATAACTAGAATCAACTAGAAGTGTGTGTTTTAGACCAAAGAAGAATGAACTAGTT
CCAATAGTGGGAAGTCCAAAGCGAGACATCAATAAAGCACATTGATATCGCTCAAAGTACTTCCC
CTTATAGAAACAAATCAAAACCCATAACGCTTGAGCATAATGAAGTAGATTGTG
Found at i:339648 original size:12 final size:12
Alignment explanation
Indices: 339600--339648 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
339590 TTTAGTAATC
*
339600 CCCGTCCCGATTA
1 CCCGGCCCGA-TA
* *
339613 TCCGGCCCAATA
1 CCCGGCCCGATA
*
339625 CCCGGCCTGATA
1 CCCGGCCCGATA
339637 CCCGGCCCGATA
1 CCCGGCCCGATA
339649 AATATTAAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
12 22 0.76
13 7 0.24
ACGTcount: A:0.18, C:0.45, G:0.20, T:0.16
Consensus pattern (12 bp):
CCCGGCCCGATA
Done.