Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009162.1 Hibiscus syriacus cultivar Beakdansim tig00112697_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: 148633
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 1 of 2
Found at i:389 original size:45 final size:45
Alignment explanation
Indices: 288--444 Score: 129
Period size: 45 Copynumber: 3.5 Consensus size: 45
278 CTAGCCAGAC
** * * * * *
288 AAGGTGTCGATATTGTGTGACCCAGACCTAGCCTAAGGTA-TTGG
1 AAGGTGTCGATGCTATGTGACCCTGACCTCGCCTGAGATACTTGG
* * *
332 GAGGTGTTGATGCTATGTAACCCTGACCTCGCCTGAGATACTTGG
1 AAGGTGTCGATGCTATGTGACCCTGACCTCGCCTGAGATACTTGG
* * *
377 AAGGTGTCGATGCGATGTGA-CCTAGACCTCACTTGAGATACTTGG
1 AAGGTGTCGATGCTATGTGACCCT-GACCTCGCCTGAGATACTTGG
* * * * *
422 GAGATGTTGATACTGTGTGACCC
1 AAGGTGTCGATGCTATGTGACCC
445 AGGTCTACCC
Statistics
Matches: 88, Mismatches: 22, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
44 33 0.38
45 53 0.60
46 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (45 bp):
AAGGTGTCGATGCTATGTGACCCTGACCTCGCCTGAGATACTTGG
Found at i:1581 original size:45 final size:45
Alignment explanation
Indices: 1530--1708 Score: 277
Period size: 45 Copynumber: 4.0 Consensus size: 45
1520 CATTTAAAGA
*
1530 ATCCTTTCATGCCTTTAATGCATCGTTATGCATTTCATTTATGGC
1 ATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGC
* *
1575 ATCCTTTCATGCCTTTCATGAACCGTTATGCATTTCATTTATGGC
1 ATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGC
*
1620 ATCCTTTCATGCCTTTCATGCACCGTTATGCATTTCATTTATGGC
1 ATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGC
* * * * *
1665 ATCTTTTCATGCCTTTAATGTATCATTATGCGTTTCATTTATGG
1 ATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGG
1709 ATTCGTTTTA
Statistics
Matches: 124, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 124 1.00
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.45
Consensus pattern (45 bp):
ATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGC
Found at i:1636 original size:26 final size:26
Alignment explanation
Indices: 1602--1676 Score: 74
Period size: 26 Copynumber: 3.2 Consensus size: 26
1592 ATGAACCGTT
1602 ATGCATTTCATTTATGGCATCCTTTC
1 ATGCATTTCATTTATGGCATCCTTTC
* *
1628 ATGCCTTTC----AT-GCA-CCGTT-
1 ATGCATTTCATTTATGGCATCCTTTC
*
1647 ATGCATTTCATTTATGGCATCTTTTC
1 ATGCATTTCATTTATGGCATCCTTTC
1673 ATGC
1 ATGC
1677 CTTTAATGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 14
0.66 0.09 0.25
Matches are distributed among these distances:
19 8 0.22
20 4 0.11
21 3 0.08
22 2 0.05
23 2 0.05
24 3 0.08
25 3 0.08
26 12 0.32
ACGTcount: A:0.19, C:0.24, G:0.13, T:0.44
Consensus pattern (26 bp):
ATGCATTTCATTTATGGCATCCTTTC
Found at i:2288 original size:95 final size:94
Alignment explanation
Indices: 2125--2307 Score: 253
Period size: 95 Copynumber: 1.9 Consensus size: 94
2115 ACTACCATGA
* * *
2125 TATCGATACTTCTATACTATGGTACCGATACCCTCTCTCAGTATCGATACCATTTATACATTCTG
1 TATCGATACTTCTATACTATAGTACCGATACCCCCTCTCAGTATCGATACCATTTATACATTATG
*
2190 TAATGCATGGCATCGATACCTTTCTCTCAG
66 TAATCCATGGCATCGATA-CTTTCTCTCAG
** *
2220 TATCGATACTAT-TATACTATAGTATTGATACCCCCTTTCAGTATCGATACCATTT-TGACATTA
1 TATCGATACT-TCTATACTATAGTACCGATACCCCCTCTCAGTATCGATACCATTTAT-ACATTA
*
2283 TGTAATCCATGGTATCGATACTTTC
64 TGTAATCCATGGCATCGATACTTTC
2308 CCTTTTAGTA
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
94 6 0.08
95 71 0.91
96 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (94 bp):
TATCGATACTTCTATACTATAGTACCGATACCCCCTCTCAGTATCGATACCATTTATACATTATG
TAATCCATGGCATCGATACTTTCTCTCAG
Found at i:4867 original size:18 final size:18
Alignment explanation
Indices: 4844--4878 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4834 CTACCGGTTT
*
4844 ACTGGTTCAACCGGTCGA
1 ACTGGTCCAACCGGTCGA
*
4862 ACTGGTCCGACCGGTCG
1 ACTGGTCCAACCGGTCG
4879 GAAGAACCGG
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:0.17, C:0.31, G:0.31, T:0.20
Consensus pattern (18 bp):
ACTGGTCCAACCGGTCGA
Found at i:5954 original size:2 final size:2
Alignment explanation
Indices: 5947--5972 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5937 TATCACAATA
5947 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
5973 CCAACCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6893 original size:39 final size:39
Alignment explanation
Indices: 6784--6902 Score: 120
Period size: 39 Copynumber: 3.1 Consensus size: 39
6774 TTAAATGTTT
* *
6784 ATTTATAATTT-TCAAATTATTTCAC-TCTAATATTCTAA
1 ATTTATAATTTCTTAAATTATTTCACAT-TAACATTCTAA
** *
6822 ATTCCTAATTTCTTAAATT-TTACTATCA-TAACATTCTAA
1 ATTTATAATTTCTTAAATTATTTC-A-CATTAACATTCTAA
* *
6861 ATTTTTAATTTCTTAAATTATTTCACATTAACATCCTAA
1 ATTTATAATTTCTTAAATTATTTCACATTAACATTCTAA
6900 ATT
1 ATT
6903 ATTTTTTAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
38 14 0.21
39 48 0.73
40 4 0.06
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.49
Consensus pattern (39 bp):
ATTTATAATTTCTTAAATTATTTCACATTAACATTCTAA
Found at i:7063 original size:2 final size:2
Alignment explanation
Indices: 7056--7087 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
7046 AATTTAGAAT
7056 TA TA TA TA TA TA TA TA TA TA TA TA -A TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7088 ATTTAAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:12609 original size:21 final size:21
Alignment explanation
Indices: 12558--12610 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
12548 ATTATGACTA
12558 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
12579 TCGCGTTGCGATTTTTCCAA-T
1 TCGCAATGCGA-TTTTCCAATT
12600 TCGCAATGCGA
1 TCGCAATGCGA
12611 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:12672 original size:21 final size:21
Alignment explanation
Indices: 12600--12664 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
12590 TTTTTCCAAT
** *
12600 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
12620 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
12641 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
12662 TCG
1 TCG
12665 TAACGCGATA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 12 0.29
21 29 0.71
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:12689 original size:20 final size:20
Alignment explanation
Indices: 12661--12770 Score: 96
Period size: 20 Copynumber: 5.5 Consensus size: 20
12651 AATTTGGAAA
*
12661 ATCGTAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
12681 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
12702 ATCGCAACGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * * *
12722 TTCGCAACGTGATACTTAAT
1 ATCGCAACGCGATACTGACT
* *
12742 TTCGCAACGCGATACTGAAT
1 ATCGCAACGCGATACTGACT
*
12762 TTCGCAACG
1 ATCGCAACG
12771 AAATAATATA
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.03
20 58 0.75
21 15 0.19
22 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:12765 original size:40 final size:41
Alignment explanation
Indices: 12658--12795 Score: 143
Period size: 41 Copynumber: 3.4 Consensus size: 41
12648 GCGAATTTGG
* *
12658 AAAATCGTAACGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * * *
12699 AAAATCGCAACGCGATACTTACTTTCGCAACGTGATACT-T
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
** * ** *
12739 AATTTCGCAACGCGATACTGAATTTCGCAACGAAATAATAT
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
12780 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
12796 TTTCAAAGCG
Statistics
Matches: 79, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 32 0.41
41 47 0.59
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:12992 original size:22 final size:22
Alignment explanation
Indices: 12964--13007 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
12954 CACTCTCTCA
12964 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
12986 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
13008 TATCTCCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:13295 original size:20 final size:20
Alignment explanation
Indices: 13270--13318 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
13260 TTTATTCTCT
13270 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* * **
13290 CGTTGCAATTGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
13310 TGTTGCGAT
1 CGTTGCGAT
13319 TTTCATTTTC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:13324 original size:20 final size:20
Alignment explanation
Indices: 13286--13328 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
13276 GATAGTCAAA
13286 TTCGCGTTGCAATTGTCATT
1 TTCGCGTTGCAATTGTCATT
* * *
13306 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCAATTGTCATT
13326 TTC
1 TTC
13329 AGAAACTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.12, C:0.19, G:0.19, T:0.51
Consensus pattern (20 bp):
TTCGCGTTGCAATTGTCATT
Found at i:13519 original size:25 final size:24
Alignment explanation
Indices: 13465--13519 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
13455 TGTTTATTAT
* *
13465 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
13489 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
13515 TGTTT
1 TGTTT
13520 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:14670 original size:18 final size:18
Alignment explanation
Indices: 14649--14696 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
14639 TCCACTTCGG
14649 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
14667 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
14685 GAGCCATCACCT
1 GAGCCATCACCT
14697 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:15265 original size:20 final size:19
Alignment explanation
Indices: 15242--15284 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
15232 CGCAACACGA
15242 AAATGACTATCGCAATGTGG
1 AAATGACTATCGCAATGT-G
*
15262 AAATGGCTATCGCAATGTG
1 AAATGACTATCGCAATGTG
15281 AAAT
1 AAAT
15285 AAAAATCGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (19 bp):
AAATGACTATCGCAATGTG
Found at i:15292 original size:19 final size:19
Alignment explanation
Indices: 15270--15352 Score: 95
Period size: 19 Copynumber: 4.6 Consensus size: 19
15260 GGAAATGGCT
* *
15270 ATCGCAATGTGAAATAAAA
1 ATCGCAATGCGAAATGAAA
*
15289 ATCGCAA--CGACA--A-A
1 ATCGCAATGCGAAATGAAA
15303 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
15322 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
15341 ATCGCAATGCGA
1 ATCGCAATGCGA
15353 TTTGTGTTTC
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
14 8 0.15
15 1 0.02
16 4 0.07
17 3 0.06
18 1 0.02
19 37 0.69
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:15424 original size:20 final size:20
Alignment explanation
Indices: 15390--15444 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
15380 TTGCGATTTT
*
15390 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
15409 CATTTCCGCGTTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
15429 CATTTCCGTGTTGCGA
1 CATTTCCGCGTTGCGA
15445 AAGTAAGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 5 0.15
20 28 0.85
ACGTcount: A:0.16, C:0.27, G:0.24, T:0.33
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:15845 original size:21 final size:20
Alignment explanation
Indices: 15819--15886 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
15809 CTGTCATCTC
15819 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
15840 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
*
15861 TCAAGAGTCCCC-CCACCGT
1 TCAAGAGTCCCCTCCATCGT
15880 TCAAGAG
1 TCAAGAG
15887 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
19 10 0.27
21 26 0.70
22 1 0.03
ACGTcount: A:0.25, C:0.40, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:15898 original size:40 final size:42
Alignment explanation
Indices: 15809--15898 Score: 130
Period size: 40 Copynumber: 2.2 Consensus size: 42
15799 CCTGACTCAC
* * *
15809 CTGTCATCTCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
*
15851 CTATCATCCCTCAAGAGTCCCC-CC-ACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
15891 CTGTCATC
1 CTGTCATC
15899 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 21 0.49
41 2 0.05
42 20 0.47
ACGTcount: A:0.22, C:0.40, G:0.16, T:0.22
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:17341 original size:14 final size:14
Alignment explanation
Indices: 17307--17345 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
17297 TTGATTGTTT
17307 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
17321 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
17335 TGTTGATTTGT
1 AATTGATTTGT
17346 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:17496 original size:20 final size:20
Alignment explanation
Indices: 17473--17524 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
17463 AAACTGACTA
* *
17473 TCGCATTGCGATAGTCATTT
1 TCGCGTTGCGATAGCCATTT
17493 TCGCGTTGCGATAGCCATTT
1 TCGCGTTGCGATAGCCATTT
17513 TCGCGTTGCGAT
1 TCGCGTTGCGAT
17525 TTCTCCGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.15, C:0.23, G:0.25, T:0.37
Consensus pattern (20 bp):
TCGCGTTGCGATAGCCATTT
Found at i:17772 original size:20 final size:20
Alignment explanation
Indices: 17747--17823 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 20
17737 ATTACGATTT
*
17747 TCAGAATCTCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
*
17767 TCAGAATCGCGTTGTGAAAG
1 TCAGAATCGCGTTGCGAAAG
* *
17787 TCAGTATCGTGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
* *
17807 TTAGTATCGCGTTGCGA
1 TCAGAATCGCGTTGCGA
17824 TTTTGTATTA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (20 bp):
TCAGAATCGCGTTGCGAAAG
Found at i:17865 original size:20 final size:20
Alignment explanation
Indices: 17756--17864 Score: 103
Period size: 20 Copynumber: 5.4 Consensus size: 20
17746 TTCAGAATCT
*
17756 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGTATCG
*
17776 CGTTGTGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGTATCG
* *
17796 TGTTGCGAAAGTTAGTATCG
1 CGTTGCGAAAGTCAGTATCG
** * *
17816 CGTTGCGATTTTGT-ATTATCA
1 CGTTGCGA--AAGTCAGTATCG
*
17837 CGTTGCGATAGTCAGTATCG
1 CGTTGCGAAAGTCAGTATCG
*
17857 CATTGCGA
1 CGTTGCGA
17865 TTTTCCAAAT
Statistics
Matches: 72, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
19 3 0.04
20 54 0.75
21 13 0.18
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.32
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGTATCG
Found at i:17940 original size:20 final size:21
Alignment explanation
Indices: 17854--17947 Score: 154
Period size: 21 Copynumber: 4.5 Consensus size: 21
17844 ATAGTCAGTA
17854 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
17875 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
17896 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* **
17917 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCAAAT
17937 TCGCATTGCGA
1 TCGCATTGCGA
17948 ATTGGGAAAA
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
20 17 0.24
21 53 0.76
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:17962 original size:41 final size:42
Alignment explanation
Indices: 17854--17962 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 42
17844 ATAGTCAGTA
* * * *
17854 TCGCATTGCGATTTTCCAAATTCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGAATTGCCAAAATCGCATTGCGATTTTACAAAT
* * * **
17896 TCGCATTGCGATTTTCCAAATTCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGAATTGCCAAAATCGCATTGCGATTTTACAAAT
**
17937 TCGCATTGCGAATTGGGAAAATCGCA
1 TCGCATTGCGAATTGCCAAAATCGCA
17963 ACGCGATACT
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
41 27 0.46
42 32 0.54
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (42 bp):
TCGCATTGCGAATTGCCAAAATCGCATTGCGATTTTACAAAT
Found at i:17983 original size:20 final size:20
Alignment explanation
Indices: 17958--18090 Score: 158
Period size: 20 Copynumber: 6.7 Consensus size: 20
17948 ATTGGGAAAA
*
17958 TCGCAACGCGATACTTACTT
1 TCGCAACGCGATACTGACTT
*
17978 TCGCAACGCGATACTTACTT
1 TCGCAACGCGATACTGACTT
* * *
17998 TCACAACGTGATACTTACTT
1 TCGCAACGCGATACTGACTT
* *
18018 TCGCAACGTGATTCTGACTT
1 TCGCAACGCGATACTGACTT
*
18038 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
* * *
18058 TCGCAACGAGATTCTGACTA
1 TCGCAACGCGATACTGACTT
*
18078 TCGCAACGAGATA
1 TCGCAACGCGATA
18091 ATACAGAATC
Statistics
Matches: 104, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 104 1.00
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.29
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:19077 original size:12 final size:12
Alignment explanation
Indices: 19060--19096 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
19050 ATATAATCCT
19060 GAAGAAGAAAAA
1 GAAGAAGAAAAA
19072 GAAGAAGAAAAA
1 GAAGAAGAAAAA
19084 GAAGAAGAAAAA
1 GAAGAAGAAAAA
19096 G
1 G
19097 TCTCCGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:21444 original size:33 final size:33
Alignment explanation
Indices: 21407--21533 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
21397 CTTAATGTCT
*
21407 ATCGCAATACGAAATGAAAATCACAACGAGAGA
1 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
*
21440 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
* * *
21473 ATCACAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
21506 ATCGCAA-AGCGAAATGAAAATCGCAACG
1 ATCGCAATA-CGAAATGAAAATCGCAACG
21534 CGAATTTAGT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (33 bp):
ATCGCAATACGAAATGAAAATCGCAACGAGAGA
Found at i:21463 original size:19 final size:18
Alignment explanation
Indices: 21439--21537 Score: 70
Period size: 19 Copynumber: 5.7 Consensus size: 18
21429 ACAACGAGAG
21439 AATCGCAATGCGAAATGAA
1 AATCGCAA-GCGAAATGAA
*
21458 AATCGCAA-CG--A-GAG
1 AATCGCAAGCGAAATGAA
*
21472 AATCACAATGCGAAATGAA
1 AATCGCAA-GCGAAATGAA
**
21491 AATCGCAA-CG--A-GGG
1 AATCGCAAGCGAAATGAA
21505 AATCGCAAAGCGAAATGAA
1 AATCGC-AAGCGAAATGAA
21524 AATCGCAACGCGAA
1 AATCGCAA-GCGAA
21538 TTTAGTTTCG
Statistics
Matches: 61, Mismatches: 8, Indels: 22
0.67 0.09 0.24
Matches are distributed among these distances:
14 16 0.26
15 4 0.07
16 4 0.07
17 4 0.07
18 4 0.07
19 29 0.48
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.11
Consensus pattern (18 bp):
AATCGCAAGCGAAATGAA
Found at i:21568 original size:19 final size:18
Alignment explanation
Indices: 21533--21614 Score: 110
Period size: 19 Copynumber: 4.3 Consensus size: 18
21523 AAATCGCAAC
*
21533 GCGAATTTAGTTTCGCGTT
1 GCGATTTTA-TTTCGCGTT
21552 GCGATTTTAGTTTCGCGTT
1 GCGATTTTA-TTTCGCGTT
*
21571 GCGATTTTTATTTAGCGTT
1 GCGA-TTTTATTTCGCGTT
21590 GCGATTTTCATTTCGCGTT
1 GCGATTTT-ATTTCGCGTT
21609 GCGATT
1 GCGATT
21615 CTCTCGTTAC
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
18 4 0.07
19 49 0.84
20 5 0.09
ACGTcount: A:0.13, C:0.16, G:0.24, T:0.46
Consensus pattern (18 bp):
GCGATTTTATTTCGCGTT
Found at i:21604 original size:38 final size:39
Alignment explanation
Indices: 21538--21614 Score: 122
Period size: 38 Copynumber: 2.0 Consensus size: 39
21528 GCAACGCGAA
*
21538 TTTAGTTTCGCGTTGCGATTTTAGTTTCGCGTTGCGATT
1 TTTAGTTTAGCGTTGCGATTTTAGTTTCGCGTTGCGATT
21577 TTTA-TTTAGCGTTGCGATTTTCA-TTTCGCGTTGCGATT
1 TTTAGTTTAGCGTTGCGATTTT-AGTTTCGCGTTGCGATT
21615 CTCTCGTTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
38 31 0.86
39 5 0.14
ACGTcount: A:0.12, C:0.16, G:0.23, T:0.49
Consensus pattern (39 bp):
TTTAGTTTAGCGTTGCGATTTTAGTTTCGCGTTGCGATT
Found at i:21772 original size:14 final size:14
Alignment explanation
Indices: 21753--21789 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
21743 CATCAATTAA
21753 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
21767 ACAAATCACCTTTT
1 ACAAATCAACTTTT
21781 ACAAATCAA
1 ACAAATCAA
21790 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:23206 original size:21 final size:21
Alignment explanation
Indices: 23140--23206 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
23130 GTGAATCATG
*
23140 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
23160 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
23182 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
23203 CTCT
1 CTCT
23207 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:23657 original size:91 final size:90
Alignment explanation
Indices: 23480--23664 Score: 284
Period size: 91 Copynumber: 2.0 Consensus size: 90
23470 ATTTTAAACT
23480 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAAT--A-AGTTTAGC
23545 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
*
23573 TTCAACCAAAAGATAAAACAAAAAGACAAATACTAACTTCACAGTGTTAATA-AAT-AGTTTAGC
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAA-AGAATAAGTTTAGC
*
23636 AGTATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
23664 T
1 T
23665 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
91 36 0.41
93 18 0.21
95 32 0.37
96 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:25378 original size:20 final size:19
Alignment explanation
Indices: 25351--25535 Score: 122
Period size: 14 Copynumber: 10.7 Consensus size: 19
25341 TCTTTTGGTT
25351 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
25370 GATAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGA
**
25390 GTAAATGACTATCGCAACGA
1 G-AAATGAAAATCGCAACGA
*
25410 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
25424 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
25443 G--A-G--AATCGCAATGC
1 GAAATGAAAATCGCAACGA
25457 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
25476 G--A-G--AATCACAACGC
1 GAAATGAAAATCGCAACGA
*
25490 GAAATGAAAATCGCAATGA
1 GAAATGAAAATCGCAACGA
*
25509 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
25523 GAAATGAAAATCG
1 GAAATGAAAATCG
25536 TAATGCGATT
Statistics
Matches: 126, Mismatches: 18, Indels: 44
0.67 0.10 0.23
Matches are distributed among these distances:
14 40 0.32
16 8 0.06
17 8 0.06
19 37 0.29
20 32 0.25
21 1 0.01
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:25437 original size:33 final size:33
Alignment explanation
Indices: 25351--25535 Score: 262
Period size: 33 Copynumber: 5.4 Consensus size: 33
25341 TCTTTTGGTT
25351 GAAATGAAAATCGCAACGAGATAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAG---A-G--AATCGCAACGC
**
25390 GTAAATGACTATCGCAACGAGAGAATCGCAACGC
1 G-AAATGAAAATCGCAACGAGAGAATCGCAACGC
*
25424 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
25457 GAAATGAAAATCGCAACGAGAGAATCACAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
25490 GAAATGAAAATCGCAATGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
25523 GAAATGAAAATCG
1 GAAATGAAAATCG
25536 TAATGCGATT
Statistics
Matches: 136, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
33 104 0.76
34 12 0.09
36 1 0.01
37 1 0.01
39 1 0.01
40 17 0.12
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:26156 original size:20 final size:20
Alignment explanation
Indices: 26131--26242 Score: 109
Period size: 20 Copynumber: 5.5 Consensus size: 20
26121 GCTATGTAAA
26131 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-GTAAGTAT
* *
26151 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
* ***
26171 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATGTAAGT-AT
* *
26192 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
* *
26212 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
26232 TCGCATTGCGA
1 TCGCATTGCGA
26243 ATTATGAAAA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
19 3 0.04
20 63 0.75
21 18 0.21
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATGTAAGTAT
Found at i:26257 original size:41 final size:41
Alignment explanation
Indices: 26123--26380 Score: 163
Period size: 41 Copynumber: 6.3 Consensus size: 41
26113 CGAATGGTGC
* * * *
26123 TATGTAAATCGCATTGCGATAGTAAG-ATTCGCATTGCGATT
1 TATGAAAATCGCATTGCGAT-TTACGTATTCGCATTGCGAAT
* * * * * *
26164 TACG-TATTCGCATTGCGATTTTCCTAATTCGCATTGCGATT
1 TATGAAAATCGCATTGCGATTTACGT-ATTCGCATTGCGAAT
* * *
26205 TACG-TATTCGCATTGCGATTTACGTATTCGCATTGCGAAT
1 TATGAAAATCGCATTGCGATTTACGTATTCGCATTGCGAAT
** * *
26245 TATGAAAATCGCAACGCGA-ATACGTAAATT-GCAATGCGAAT
1 TATGAAAATCGCATTGCGATTTACGT--ATTCGCATTGCGAAT
* * *
26286 TAGGAAAATTGCATTGCGATAGT-CAGTA-TCGCATTGCG-AT
1 TATGAAAATCGCATTGCGAT-TTAC-GTATTCGCATTGCGAAT
* * * *
26326 TTTCCAAATTCGCATTGCGATTTACTTATTCGCATTGCGAAT
1 TAT-GAAAATCGCATTGCGATTTACGTATTCGCATTGCGAAT
**
26368 TGGGAAAATCGCA
1 TATGAAAATCGCA
26381 ACGCGAAATT
Statistics
Matches: 170, Mismatches: 34, Indels: 26
0.74 0.15 0.11
Matches are distributed among these distances:
39 1 0.01
40 42 0.25
41 117 0.69
42 7 0.04
43 3 0.02
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (41 bp):
TATGAAAATCGCATTGCGATTTACGTATTCGCATTGCGAAT
Found at i:26257 original size:61 final size:60
Alignment explanation
Indices: 26123--26380 Score: 184
Period size: 61 Copynumber: 4.2 Consensus size: 60
26113 CGAATGGTGC
* * *
26123 TATGTAAATCGCATTGCGATAGTAAG-ATTCGCATTGCGATTTACGTATTCGCATTGCGAT
1 TATGAAAATCGCATTGCGAT-TTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGAT
* ** *
26183 TTTCCTAATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGAAT
1 TAT-GAAAATCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCG-AT
** * * * * *
26245 TATGAAAATCGCAACGCGA-ATACGTAAATT-GCAATGCGAATTAGGAAAATT-GCATTGCGA-
1 TATGAAAATCGCATTGCGATTTACGT--ATTCGCATTGCGATTTACG--TATTCGCATTGCGAT
* ** * ** *
26305 TAGTCAGTATCGCATTGCGATTTTCCAAATTCGCATTGCGATTTACTTATTCGCATTGCGAAT
1 TA-TGAAAATCGCATTGCGA-TTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCG-AT
**
26368 TGGGAAAATCGCA
1 TATGAAAATCGCA
26381 ACGCGAAATT
Statistics
Matches: 149, Mismatches: 35, Indels: 26
0.71 0.17 0.12
Matches are distributed among these distances:
60 15 0.10
61 94 0.63
62 34 0.23
63 6 0.04
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (60 bp):
TATGAAAATCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGAT
Found at i:26263 original size:21 final size:21
Alignment explanation
Indices: 26239--26294 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
26229 TATTCGCATT
*
26239 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* * *
26260 GCGAA-TACGTAAATTGCAAT
1 GCGAATTACGAAAATCGCAAC
*
26280 GCGAATTAGGAAAAT
1 GCGAATTACGAAAAT
26295 TGCATTGCGA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.21
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:26296 original size:21 final size:21
Alignment explanation
Indices: 26238--26304 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
26228 GTATTCGCAT
* *
26238 TGCGAATTATGAAAATCGCAA
1 TGCGAATTACGAAAATTGCAA
* *
26259 CGCGAA-TACGTAAATTGCAA
1 TGCGAATTACGAAAATTGCAA
* *
26279 TGCGAATTAGGAAAATTGCAT
1 TGCGAATTACGAAAATTGCAA
26300 TGCGA
1 TGCGA
26305 TAGTCAGTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 16 0.43
21 21 0.57
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (21 bp):
TGCGAATTACGAAAATTGCAA
Found at i:26358 original size:20 final size:21
Alignment explanation
Indices: 26314--26365 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
26304 ATAGTCAGTA
*
26314 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
26335 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
26355 TCGCATTGCGA
1 TCGCATTGCGA
26366 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:26407 original size:21 final size:22
Alignment explanation
Indices: 26355--26407 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
26345 ATTTACTTAT
26355 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
26376 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
26397 TCGCATTGCGA
1 TCGCATTGCGA
26408 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:27623 original size:16 final size:17
Alignment explanation
Indices: 27597--27631 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
27587 TCTAAATTCA
*
27597 AATATAAAATTTAATTT
1 AATATAAAATTAAATTT
27614 AATA-AAAATTAAATTT
1 AATATAAAATTAAATTT
27630 AA
1 AA
27632 AATTAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATATAAAATTAAATTT
Found at i:29347 original size:19 final size:19
Alignment explanation
Indices: 29323--29361 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
29313 TCTAATTTAC
29323 TCTTATTATTATTAACCCA
1 TCTTATTATTATTAACCCA
29342 TCTTATTATTATTAACCCA
1 TCTTATTATTATTAACCCA
29361 T
1 T
29362 GCAAGCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.49
Consensus pattern (19 bp):
TCTTATTATTATTAACCCA
Found at i:34982 original size:2 final size:2
Alignment explanation
Indices: 34975--35003 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
34965 GATAAAACAT
34975 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35004 TAAAAACAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35688 original size:16 final size:16
Alignment explanation
Indices: 35664--35694 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35654 ATCACATAAT
*
35664 ATGTGGAAAATGCTTC
1 ATGTAGAAAATGCTTC
35680 ATGTAGAAAATGCTT
1 ATGTAGAAAATGCTT
35695 TTTTTTACCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.32
Consensus pattern (16 bp):
ATGTAGAAAATGCTTC
Found at i:39586 original size:36 final size:37
Alignment explanation
Indices: 39542--39611 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
39532 TCCCATTATC
*
39542 ATTTTTC-AACAAACATCTACCAAAATTTTAAAAATT
1 ATTTTTCAAACAAACATCTACCAAAATTTGAAAAATT
* * *
39578 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAA
1 ATTTTTCAAACAAACATCTACCAAAATTTGAAAA
39612 CCATTTTCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 7 0.24
37 22 0.76
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.34
Consensus pattern (37 bp):
ATTTTTCAAACAAACATCTACCAAAATTTGAAAAATT
Found at i:39618 original size:36 final size:37
Alignment explanation
Indices: 39541--39631 Score: 89
Period size: 36 Copynumber: 2.5 Consensus size: 37
39531 ATCCCATTAT
* * * *
39541 CATTTTTC-AACAAACATCTACCAAAATTTTAAAAAT
1 CATTTTTCAAAAAAACATTTACCAAAACTTTAAAAAC
* * *
39577 TATTTTTCAAAGAAACATTTACC-AAACTTTGAAAAC
1 CATTTTTCAAAAAAACATTTACCAAAACTTTAAAAAC
*
39613 CA-TTTTCAAAAAAATATTT
1 CATTTTTCAAAAAAACATTT
39632 TTGGTAGTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
35 15 0.33
36 18 0.40
37 12 0.27
ACGTcount: A:0.46, C:0.16, G:0.02, T:0.35
Consensus pattern (37 bp):
CATTTTTCAAAAAAACATTTACCAAAACTTTAAAAAC
Found at i:43043 original size:13 final size:13
Alignment explanation
Indices: 43007--43035 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
42997 ATGCTTCACC
43007 CGATTATCTTCGT
1 CGATTATCTTCGT
43020 CGATTATCTTCGT
1 CGATTATCTTCGT
43033 CGA
1 CGA
43036 ATTTCTTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.41
Consensus pattern (13 bp):
CGATTATCTTCGT
Found at i:44096 original size:36 final size:36
Alignment explanation
Indices: 44052--44169 Score: 132
Period size: 35 Copynumber: 3.3 Consensus size: 36
44042 TCCCATTATC
* * * *
44052 ATTTTTCAACAAACATCTATTAAACTTTGAAAAATT
1 ATTTTTCAAAAAATATTTATTAAACTTTGAAAAATA
**
44088 ATTTTTCAAAAAAATATTTACCAAACTTTG-AAAATA
1 ATTTTTC-AAAAAATATTTATTAAACTTTGAAAAATA
* *
44124 ATTTTTAAAAAAATATTTATTAAACTTT-AAAAATC
1 ATTTTTCAAAAAATATTTATTAAACTTTGAAAAATA
*
44159 ATTTTTTAAAA
1 ATTTTTCAAAA
44170 TTAATTTCCA
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
35 34 0.49
36 18 0.26
37 17 0.25
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (36 bp):
ATTTTTCAAAAAATATTTATTAAACTTTGAAAAATA
Found at i:44173 original size:20 final size:20
Alignment explanation
Indices: 44132--44173 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
44122 TAATTTTTAA
*
44132 AAAAATATTTATTAAACTTT
1 AAAAATATTTATTAAACATT
*
44152 AAAAATCATTTTTTAAA-ATT
1 AAAAAT-ATTTATTAAACATT
44172 AA
1 AA
44174 TTTCCAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (20 bp):
AAAAATATTTATTAAACATT
Found at i:44188 original size:34 final size:35
Alignment explanation
Indices: 44073--44188 Score: 128
Period size: 35 Copynumber: 3.3 Consensus size: 35
44063 AACATCTATT
*
44073 AAACTTTGAAAAATTATTTTTCAAAAAAATATTTACC
1 AAACTTT-AAAAA-TATTTTTTAAAAAAATATTTACC
* * **
44110 AAACTTTGAAAATAATTTTTAAAAAAATATTTATT
1 AAACTTTAAAAATATTTTTTAAAAAAATATTTACC
**
44145 AAACTTTAAAAATCATTTTTTAAAATTA-ATTT-CC
1 AAACTTTAAAAAT-ATTTTTTAAAAAAATATTTACC
44179 AAACTTTAAA
1 AAACTTTAAA
44189 CTTAACAATA
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
34 10 0.15
35 35 0.52
36 15 0.22
37 7 0.10
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.41
Consensus pattern (35 bp):
AAACTTTAAAAATATTTTTTAAAAAAATATTTACC
Found at i:45559 original size:19 final size:19
Alignment explanation
Indices: 45535--45571 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
45525 CATGGAATTG
45535 TTGATTCATAATTTTATCA
1 TTGATTCATAATTTTATCA
45554 TTGATTCATAATTTTATC
1 TTGATTCATAATTTTATC
45572 TGGGGCAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.11, G:0.05, T:0.54
Consensus pattern (19 bp):
TTGATTCATAATTTTATCA
Found at i:46826 original size:21 final size:21
Alignment explanation
Indices: 46777--46837 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
46767 GCATCAGTAA
*
46777 TAATATTATATTTATATATTT
1 TAATATTATATTTATATATAT
*
46798 TACA-ATTATCTTT-TAATATAT
1 TA-ATATTATATTTAT-ATATAT
*
46819 TAATATTAATATTAATATA
1 TAATATT-ATATTTATATA
46838 CTCTTTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
20 2 0.06
21 20 0.65
22 8 0.26
23 1 0.03
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (21 bp):
TAATATTATATTTATATATAT
Found at i:47345 original size:21 final size:21
Alignment explanation
Indices: 47321--47391 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
47311 GTAGTTGAAC
47321 TTTATTTTATTTATAATATTA
1 TTTATTTTATTTATAATATTA
* ** *
47342 TTTATTTTGTCAAGAAATATATA
1 TTTATTTTATTTA-TAATAT-TA
47365 TATT-TTTTATTTATAATATTA
1 T-TTATTTTATTTATAATATTA
47386 TTTATT
1 TTTATT
47392 AATTTATTCT
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
20 2 0.05
21 15 0.39
22 10 0.26
23 9 0.24
24 2 0.05
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (21 bp):
TTTATTTTATTTATAATATTA
Found at i:47389 original size:16 final size:17
Alignment explanation
Indices: 47359--47414 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 17
47349 TGTCAAGAAA
*
47359 TATATATATTTTTTATT
1 TATATATATTATTTATT
47376 TATA-ATATTATTTA-T
1 TATATATATTATTTATT
* *
47391 TA-ATTTATTCTTTATAT
1 TATATATATTATTTAT-T
47408 TATATAT
1 TATATAT
47415 TAGATAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
14 1 0.03
15 11 0.35
16 9 0.29
17 7 0.23
18 3 0.10
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TATATATATTATTTATT
Found at i:47396 original size:20 final size:20
Alignment explanation
Indices: 47360--47398 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
47350 GTCAAGAAAT
*
47360 ATATATATTTTTTATTTATA
1 ATATATATTTTTAATTTATA
47380 ATAT-TATTTATTAATTTAT
1 ATATATATTT-TTAATTTAT
47399 TCTTTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
ATATATATTTTTAATTTATA
Found at i:47398 original size:24 final size:24
Alignment explanation
Indices: 47357--47416 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
47347 TTTGTCAAGA
*
47357 AATA-TATATATT-TTTTATT-TAT
1 AATATTATATATTAATTTATTCT-T
*
47379 AATATTATTTATTAATTTATTCTT
1 AATATTATATATTAATTTATTCTT
*
47403 TATATTATATATTA
1 AATATTATATATTA
47417 GATAAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 4 0.13
23 7 0.23
24 19 0.61
25 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
AATATTATATATTAATTTATTCTT
Found at i:47785 original size:15 final size:15
Alignment explanation
Indices: 47765--47952 Score: 182
Period size: 15 Copynumber: 12.0 Consensus size: 15
47755 TAATAAGGTT
47765 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
47780 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
47795 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
47810 ATTTATTATAAAAT-
1 ATTTATTTTAAAATA
*
47824 ATTTTTTTTAAAATA
1 ATTTATTTTAAAATA
* *
47839 AATTATTATAAAATA
1 ATTTATTTTAAAATA
*
47854 AATTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
47869 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
47888 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
47906 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
* *
47920 ATTTATTAGTATAAATTG
1 ATTTATT--T-TAAAATA
47938 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
47953 TGGATTGATT
Statistics
Matches: 145, Mismatches: 16, Indels: 24
0.78 0.09 0.13
Matches are distributed among these distances:
14 24 0.17
15 88 0.61
16 6 0.04
17 3 0.02
18 11 0.08
19 1 0.01
20 2 0.01
21 4 0.03
22 6 0.04
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:47801 original size:30 final size:30
Alignment explanation
Indices: 47765--48006 Score: 202
Period size: 30 Copynumber: 7.5 Consensus size: 30
47755 TAATAAGGTT
47765 ATTTATTTTAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATA
47795 ATTTATTTTAAAATAATTTATTATAAAAT-
1 ATTTATTTTAAAATAATTTATTATAAAATA
* *
47824 ATTTTTTTTAAAATAAATTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATA
* *
47854 AATTATTTTAAAATAAATTATTATAAAATATGGA
1 ATTTATTTTAAAATAATTTATTAT-AAA-AT--A
*
47888 TTGATTTATTTTAAAATAATTTATT-TTAAATA
1 ---ATTTATTTTAAAATAATTTATTATAAAATA
* * *
47920 ATTTATTAGTATAAATTGATTTATTTTAAAATATGGA
1 ATTTATT--T-TAAAATAATTTATTAT-AAA-AT--A
*
47957 TTGATTTATTTT-AAATAATTTATTAGTATAGATTA
1 ---ATTTATTTTAAAATAATTTATTA-TA-A-AATA
47992 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
48007 TGGATTGATT
Statistics
Matches: 175, Mismatches: 14, Indels: 43
0.75 0.06 0.19
Matches are distributed among these distances:
29 34 0.19
30 51 0.29
31 4 0.02
32 24 0.14
33 6 0.03
34 5 0.03
35 5 0.03
36 12 0.07
37 25 0.14
38 2 0.01
40 7 0.04
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.50
Consensus pattern (30 bp):
ATTTATTTTAAAATAATTTATTATAAAATA
Found at i:47838 original size:59 final size:59
Alignment explanation
Indices: 47764--47884 Score: 206
Period size: 59 Copynumber: 2.1 Consensus size: 59
47754 TTAATAAGGT
* * *
47764 TATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAATTTATTATAAAA
1 TATTTATTTTAAAATAAATTATTATAAAATAAATTATTTTAAAATAAATTATTATAAAA
*
47823 TATTTTTTTTAAAATAAATTATTATAAAATAAATTATTTTAAAATAAATTATTATAAAA
1 TATTTATTTTAAAATAAATTATTATAAAATAAATTATTTTAAAATAAATTATTATAAAA
47882 TAT
1 TAT
47885 GGATTGATTT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (59 bp):
TATTTATTTTAAAATAAATTATTATAAAATAAATTATTTTAAAATAAATTATTATAAAA
Found at i:47897 original size:37 final size:37
Alignment explanation
Indices: 47856--48302 Score: 163
Period size: 32 Copynumber: 12.4 Consensus size: 37
47846 ATAAAATAAA
*
47856 TTATTTTAAAATAAATTATTATAAAATATGGATTGAT
1 TTATTTTAAAATAATTTATTATAAAATATGGATTGAT
* *
47893 TTATTTTAAAATAATTTATT-TTAAATA---ATTTA-
1 TTATTTTAAAATAATTTATTATAAAATATGGATTGAT
* * * * *
47925 TTAGTATAAATTGATTTATTTTAAAATATGGATTGAT
1 TTATTTTAAAATAATTTATTATAAAATATGGATTGAT
*
47962 TTATTTT-AAATAATTTATTAGT---ATA--GATTAAT
1 TTATTTTAAAATAATTTATTA-TAAAATATGGATTGAT
* * *
47994 TTATTTTAAAATATGGATTGATTTATTTTAAATA---ATTTA-
1 TTATTTTAAAATA---ATTTA-TTA--TAAAATATGGATTGAT
* * * * * * *
48033 TTAGTATAGATTGATTTATTTTAAAATATAGATTGAT
1 TTATTTTAAAATAATTTATTATAAAATATGGATTGAT
*
48070 TTATTTT-AAATAATTTA-T-T--AGTATGGATTGAT
1 TTATTTTAAAATAATTTATTATAAAATATGGATTGAT
*** *
48102 TTATTTTAAAATATGAATTGATTTATTATTGTAGTTGTATAGATTGAT
1 TTATTTT-AAA-AT--A---ATTTATTA---TA-AAATATGGATTGAT
* *
48150 TTATTTT-AAATCATTTA-T-T--AGTATGGATTGAT
1 TTATTTTAAAATAATTTATTATAAAATATGGATTGAT
*
48182 TTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGAT
1 TTATTTT-AAA-AT--A---ATTTATTATAAAATATGGATTGAT
*
48226 TTATTTT-AAATAATTTA-T-T--AGTATGGATTGAT
1 TTATTTTAAAATAATTTATTATAAAATATGGATTGAT
*
48258 TTATTTT-AAATAATTTATT-T---GTATGGATTGAT
1 TTATTTTAAAATAATTTATTATAAAATATGGATTGAT
48290 TTATTTTAAAATA
1 TTATTTTAAAATA
48303 TAGATTGATT
Statistics
Matches: 319, Mismatches: 42, Indels: 102
0.69 0.09 0.22
Matches are distributed among these distances:
32 113 0.35
33 28 0.09
34 9 0.03
35 9 0.03
36 44 0.14
37 34 0.11
38 1 0.00
39 10 0.03
40 19 0.06
41 7 0.02
42 3 0.01
44 19 0.06
45 3 0.01
46 2 0.01
48 18 0.06
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (37 bp):
TTATTTTAAAATAATTTATTATAAAATATGGATTGAT
Found at i:47945 original size:32 final size:32
Alignment explanation
Indices: 47906--48111 Score: 175
Period size: 32 Copynumber: 7.4 Consensus size: 32
47896 TTTTAAAATA
*
47906 ATTTATTTTAAATAATTTATTAGTATAAATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
47938 ATTTATTTT-AA-AA--TA-T-G----GATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
*
47960 ATTTATTTTAAATAATTTATTAGTATAGATTA
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
47992 ATTTATTTT-AA-AA--TA-T-G----GATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
48014 ATTTATTTTAAATAATTTATTAGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
48046 ATTTA-TTT---TAA---A--A-TATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
*
48068 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
48100 ATTTATTTTAAA
1 ATTTATTTTAAA
48112 ATATGAATTG
Statistics
Matches: 140, Mismatches: 4, Indels: 60
0.69 0.02 0.29
Matches are distributed among these distances:
22 40 0.29
23 8 0.06
24 4 0.03
25 1 0.01
26 9 0.06
27 4 0.03
28 9 0.06
29 1 0.01
30 4 0.03
31 8 0.06
32 52 0.37
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.52
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATAGATTG
Found at i:47956 original size:69 final size:67
Alignment explanation
Indices: 47824--48006 Score: 208
Period size: 69 Copynumber: 2.7 Consensus size: 67
47814 ATTATAAAAT
* *
47824 ATTTTTTTTAAAATAAATTATTATAAAATAAATTATTTTAAAATAAATTATTATAAAATATGGAT
1 ATTTATTTTAAAATAATTTATTATAAAATAAATTATTTTAAAATAAATTATTATAAAATATGGAT
47889 TG
66 TG
* * * * * *
47891 ATTTATTTTAAAATAATTTATT-TTAAATAATTTATTAGTATAAATTGATTTATTTTAAAATATG
1 ATTTATTTTAAAATAATTTATTATAAAATAAATTATT--T-TAAAATAAATTATTATAAAATATG
47955 GATTG
63 GATTG
* *
47960 ATTTATTTT-AAATAATTTATTAGTATAGATTAATTTATTTTAAAATA
1 ATTTATTTTAAAATAATTTATTA-TA-A-AATAAATTATTTTAAAATA
48007 TGGATTGATT
Statistics
Matches: 97, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
66 12 0.12
67 20 0.21
68 13 0.13
69 39 0.40
70 2 0.02
71 1 0.01
72 10 0.10
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.50
Consensus pattern (67 bp):
ATTTATTTTAAAATAATTTATTATAAAATAAATTATTTTAAAATAAATTATTATAAAATATGGAT
TG
Found at i:47965 original size:54 final size:54
Alignment explanation
Indices: 47906--48411 Score: 536
Period size: 54 Copynumber: 9.4 Consensus size: 54
47896 TTTTAAAATA
*
47906 ATTTATTTTAAATAATTTATTAGTATAAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
*
47960 ATTTATTTTAAATAATTTATTAGTATAGATTAATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
*
48014 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
* *
48068 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
* **
48122 ATTTA--TT--AT--TGTAGTT-GTATAGATTGATTTATTTT-AAATCATTTATTAG
1 ATTTATTTTAAATAATTTA-TTAGTATAGATTGATTTATTTTAAAAT-ATGGATT-G
** * ** * * * *
48171 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTTTAAAATATGGATTG
1 -ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
* *
48224 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
* * ** * * * ***
48274 ATTTGTATGGATTGATTTATTTTAAAATATAGATTGATTTATTATTGTAGTTGTATGGATTG
1 ATTTATTTTAAATAATTTA--TT--AGTATAGATTGATTTA-T-TT-TA-AAATATGGATTG
*
48336 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
48390 ATTTATTTTAAATAATTTATTA
1 ATTTATTTTAAATAATTTATTA
48412 TTGTAGTTGT
Statistics
Matches: 374, Mismatches: 53, Indels: 50
0.78 0.11 0.10
Matches are distributed among these distances:
47 4 0.01
48 26 0.07
49 3 0.01
50 21 0.06
51 1 0.00
52 7 0.02
53 16 0.04
54 246 0.66
55 10 0.03
56 4 0.01
57 2 0.01
58 14 0.04
59 2 0.01
60 2 0.01
62 16 0.04
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
Found at i:48062 original size:22 final size:22
Alignment explanation
Indices: 48037--48235 Score: 103
Period size: 22 Copynumber: 8.0 Consensus size: 22
48027 AATTTATTAG
48037 TATAGATTGATTTATTTTAAAA
1 TATAGATTGATTTATTTTAAAA
48059 TATAGATTGATTTATTTTAAATAA
1 TATAGATTGATTTATTTT-AA-AA
*
48083 TTTATTAGTATGGATTGATTTATTTTAAAA
1 --TA-TAG-ATTGA-T---TTATTTTAAAA
***
48113 TAT-GAATTGATTTATTATTGTAGTTG
1 TATAG-ATTGATTTA-T-TT-TA-AAA
48139 TATAGATTGATTTATTTTAAATCA
1 TATAGATTGATTTATTTTAAA--A
*
48163 TTTATTAGTATGGATTGATTTATTTTAAAA
1 --TA-TAG-ATTGA-T---TTATTTTAAAA
*
48193 TATGGATTGATTTATTTTAAAA
1 TATAGATTGATTTATTTTAAAA
*
48215 TATGGATTGATTTATTTTAAA
1 TATAGATTGATTTATTTTAAA
48236 TAATTTATTA
Statistics
Matches: 140, Mismatches: 12, Indels: 50
0.69 0.06 0.25
Matches are distributed among these distances:
22 53 0.38
23 5 0.04
24 6 0.04
25 5 0.04
26 25 0.18
27 10 0.07
28 12 0.09
29 2 0.01
30 3 0.02
31 2 0.01
32 17 0.12
ACGTcount: A:0.35, C:0.01, G:0.13, T:0.52
Consensus pattern (22 bp):
TATAGATTGATTTATTTTAAAA
Found at i:48159 original size:80 final size:76
Alignment explanation
Indices: 48042--48411 Score: 394
Period size: 80 Copynumber: 4.6 Consensus size: 76
48032 ATTAGTATAG
48042 ATTGATTTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT
1 ATTGATTTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT
48107 TTAAAATATGA
66 TTAAAATATGA
*** *
48118 ATTGATTTATTATTGTAGTTGTATAGATTGATTTATTTTAAATCATTTATTAGTATGGATTGATT
1 ATTGATTTA-T-TT-TA-AAATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATT
*
48183 TATTTTAAAATATGG
62 TATTTTAAAATATGA
*
48198 ATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT
1 ATTGATTTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT
48263 TTAAATAATTTATTTGTA
66 TT-AA-AA--TA--TG-A
*
48281 TGGATTGATTTATTTTAAAATATAGATTGATTTA--TT--AT--TGTAGTT-GTATGGATTGATT
1 ---ATTGATTTATTTTAAAATATAGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATT
48339 TATTTTAAATAATTTATTAGTA
62 TATTTT-AA-AA--TA-T-G-A
*
48361 TGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
1 ---ATTGATTTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTA
48412 TTGTAGTTGT
Statistics
Matches: 256, Mismatches: 15, Indels: 36
0.83 0.05 0.12
Matches are distributed among these distances:
76 57 0.22
77 5 0.02
78 6 0.02
79 5 0.02
80 136 0.53
81 2 0.01
82 6 0.02
84 4 0.02
85 2 0.01
86 33 0.13
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (76 bp):
ATTGATTTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT
TTAAAATATGA
Found at i:48168 original size:188 final size:183
Alignment explanation
Indices: 47955--48411 Score: 700
Period size: 188 Copynumber: 2.4 Consensus size: 183
47945 TTAAAATATG
* *
47955 GATTGATTTATTTTAAATAATTTATTAGTATAGATTAATTTATTTTAAAATATGGATTGATTTAT
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
* *
48020 TTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGATTTATTTTAAATAATT
66 TTTAAATAATTTATTAGTATA-AATAATTTA--TT--AATATAGATTGATTTATTTTAAATAATT
48085 TATTAGTATGGATTGATTTATTTTAAAATAT-GAATTGATTTATTATTGTAGTTGTATA
126 TATTAGTATGGATTGATTTATTTTAAAATATAG-ATTGATTTATTATTGTAGTTGTATA
*
48143 GATTGATTTATTTTAAATCATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
* * * * *
48208 TTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATT
66 TTT-AAATA---ATTTA-TTAGTATAAATAATTTATTAATATAGATTGATTTATTTTAAATAATT
* *
48273 TATTTGTATGGATTGATTTATTTTAAAATATAGATTGATTTATTATTGTAGTTGTATG
126 TATTAGTATGGATTGATTTATTTTAAAATATAGATTGATTTATTATTGTAGTTGTATA
48331 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
48396 TTTAAATAATTTATTA
66 TTTAAATAATTTATTA
48412 TTGTAGTTGT
Statistics
Matches: 249, Mismatches: 14, Indels: 17
0.89 0.05 0.06
Matches are distributed among these distances:
183 3 0.01
184 4 0.02
187 5 0.02
188 212 0.85
189 6 0.02
190 2 0.01
192 11 0.04
193 6 0.02
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (183 bp):
GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
TTTAAATAATTTATTAGTATAAATAATTTATTAATATAGATTGATTTATTTTAAATAATTTATTA
GTATGGATTGATTTATTTTAAAATATAGATTGATTTATTATTGTAGTTGTATA
Found at i:48384 original size:22 final size:22
Alignment explanation
Indices: 48359--48401 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
48349 AATTTATTAG
48359 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
48381 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
48402 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:48461 original size:31 final size:31
Alignment explanation
Indices: 48426--48484 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
48416 AGTTGTATGG
*
48426 ATTATTTAAATTTCAGTATTGTAAAACTAAT
1 ATTATTTAAATCTCAGTATTGTAAAACTAAT
48457 ATTATTTAAATCTCAGTATTGTAAAACT
1 ATTATTTAAATCTCAGTATTGTAAAACT
48485 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGTAAAACTAAT
Found at i:50493 original size:27 final size:27
Alignment explanation
Indices: 50463--50516 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
50453 TAGAATCAAA
50463 TTAA-ATCAAATCAAATTTTATTTTTAT
1 TTAATATCAAATC-AATTTTATTTTTAT
* **
50490 TTAATTTGTAATCAATTTTATTTTTAT
1 TTAATATCAAATCAATTTTATTTTTAT
50517 AATATAAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (27 bp):
TTAATATCAAATCAATTTTATTTTTAT
Found at i:56113 original size:30 final size:28
Alignment explanation
Indices: 56063--56215 Score: 94
Period size: 31 Copynumber: 5.1 Consensus size: 28
56053 TCCTTTAATT
56063 TAAGGACTAATGTGGT-AAAAATCTAAAATCC
1 TAAGGACTAA-GT-GTAAAAAATCT-AAAT-C
* * *
56094 TAAGGACCTAAGTGTAAAAAATCTCTAGTT
1 TAAGGA-CTAAGTGTAAAAAATCT-AAATC
*
56124 TAGGGACCTAAGTGTAAAAAAT-TAAATTC
1 TAAGGA-CTAAGTGTAAAAAATCTAAA-TC
* ** *
56153 TAGGGACTAAAGTGTAAAAACCCATAAAGTA
1 TAAGGACT-AAGTGTAAAAAATC-TAAA-TC
*
56184 TAAGCACTAAGGTGTAAAAAATCTAAAGTC
1 TAAGGACTAA-GTGTAAAAAATCTAAA-TC
56214 TA
1 TA
56216 GGGGTTAAGG
Statistics
Matches: 98, Mismatches: 17, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
28 3 0.03
29 19 0.19
30 33 0.34
31 39 0.40
32 4 0.04
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.25
Consensus pattern (28 bp):
TAAGGACTAAGTGTAAAAAATCTAAATC
Found at i:56156 original size:29 final size:31
Alignment explanation
Indices: 56079--56172 Score: 106
Period size: 30 Copynumber: 3.1 Consensus size: 31
56069 CTAATGTGGT
* *
56079 AAAAATCTAAAATCCTAAGGACCTAAGTGTA
1 AAAAATCTAAAATTCTAGGGACCTAAGTGTA
** *
56110 AAAAATCTCTAGTT-TAGGGACCTAAGTGTA
1 AAAAATCTAAAATTCTAGGGACCTAAGTGTA
56140 AAAAAT-T-AAATTCTAGGGA-CTAAAGTGTA
1 AAAAATCTAAAATTCTAGGGACCT-AAGTGTA
56169 AAAA
1 AAAA
56173 CCCATAAAGT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
28 5 0.09
29 18 0.33
30 21 0.39
31 10 0.19
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.26
Consensus pattern (31 bp):
AAAAATCTAAAATTCTAGGGACCTAAGTGTA
Found at i:56253 original size:29 final size:30
Alignment explanation
Indices: 56189--56266 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 30
56179 AAGTATAAGC
* *
56189 ACTAAGGTGTAAAAAATCTAAAGTCTAGGGG
1 ACTAAGGTAT-AAAAATATAAAGTCTAGGGG
* *
56220 -TTAAGGTATAAAACTATAAAGTCT-GGGG
1 ACTAAGGTATAAAAATATAAAGTCTAGGGG
*
56248 ACTAAGATA-AAAAATATAA
1 ACTAAGGTATAAAAATATAA
56267 TAATTCAGGG
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
28 13 0.33
29 19 0.49
30 7 0.18
ACGTcount: A:0.47, C:0.08, G:0.21, T:0.24
Consensus pattern (30 bp):
ACTAAGGTATAAAAATATAAAGTCTAGGGG
Found at i:57266 original size:29 final size:29
Alignment explanation
Indices: 57231--57312 Score: 110
Period size: 29 Copynumber: 2.8 Consensus size: 29
57221 AAACTAAATT
* *
57231 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
57260 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
* *
57289 GATTTCATTGTTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
57313 GTTAGGTGAG
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 42 0.89
30 5 0.11
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:58612 original size:15 final size:15
Alignment explanation
Indices: 58589--58618 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
58579 ACGAGGCTGG
58589 AATTACAACAACAAC
1 AATTACAACAACAAC
*
58604 AATTCCAACAACAAC
1 AATTACAACAACAAC
58619 TATAAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.13
Consensus pattern (15 bp):
AATTACAACAACAAC
Found at i:62022 original size:29 final size:29
Alignment explanation
Indices: 61987--62068 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
61977 AAACTAAATT
* *
61987 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
62016 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
62045 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
62069 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:77759 original size:21 final size:22
Alignment explanation
Indices: 77735--77808 Score: 96
Period size: 23 Copynumber: 3.3 Consensus size: 22
77725 CACCGAAATG
*
77735 CCACATA-TTTATCTCGAAGGA
1 CCACATAGTTTGTCTCGAAGGA
77756 CCACATAGGTTTGTCTCGAAGGA
1 CCACATA-GTTTGTCTCGAAGGA
* *
77779 TCACATAGTTTTGTCCCGAAGGA
1 CCACATAG-TTTGTCTCGAAGGA
77802 CCACATA
1 CCACATA
77809 AAACCCTCGA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
21 7 0.15
22 1 0.02
23 38 0.83
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (22 bp):
CCACATAGTTTGTCTCGAAGGA
Found at i:77775 original size:23 final size:23
Alignment explanation
Indices: 77746--77808 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
77736 CACATATTTA
77746 TCTCGAAGGACCACATAGGTTTG
1 TCTCGAAGGACCACATAGGTTTG
* *
77769 TCTCGAAGGATCACATAGTTTTG
1 TCTCGAAGGACCACATAGGTTTG
*
77792 TCCCGAAGGACCACATA
1 TCTCGAAGGACCACATA
77809 AAACCCTCGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (23 bp):
TCTCGAAGGACCACATAGGTTTG
Found at i:78665 original size:20 final size:20
Alignment explanation
Indices: 78620--78671 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
78610 TCTTTACTTA
*
78620 CAGTATCGATACCTTATCCT
1 CAGTATCGATACCTTATCAT
**
78640 TGGTATCGATACCTTCA-CAT
1 CAGTATCGATACCTT-ATCAT
*
78660 CAGTATTGATAC
1 CAGTATCGATAC
78672 TTCTTCAACC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (20 bp):
CAGTATCGATACCTTATCAT
Found at i:80941 original size:136 final size:136
Alignment explanation
Indices: 80769--81040 Score: 517
Period size: 136 Copynumber: 2.0 Consensus size: 136
80759 AAGTAATTTG
80769 TCTATCCTCAATAACTTAGTCATAGAAAATACAATCATTGATTATATTCTTATCAATCCTTGTAA
1 TCTATCCTCAATAACTTAGTCATAGAAAATACAATCATTGATTATATTCTTATCAATCCTTGTAA
*
80834 TTTCATTCAACTAAATCTCAAGTTTCCTTAATACACATATCATTTTCCTCTTAGCTGAGTTTACA
66 TTTCATTCAACTAAATCTCAAGTTTCCTTAATACACATATCATTTTCCTCTTAGCCGAGTTTACA
80899 TGGCAA
131 TGGCAA
80905 TCTATCCTCAATAACTTAGTCATAGAAAATACAATCATTGATTATATTCTTATCAATCCTTGTAA
1 TCTATCCTCAATAACTTAGTCATAGAAAATACAATCATTGATTATATTCTTATCAATCCTTGTAA
* *
80970 TTTCATTCAACTATATCTCAAGTTTCCTTAATACACATATCCTTTTCCTCTTAGCCGAGTTTACA
66 TTTCATTCAACTAAATCTCAAGTTTCCTTAATACACATATCATTTTCCTCTTAGCCGAGTTTACA
81035 TGGCAA
131 TGGCAA
81041 AGGAATATAA
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
136 133 1.00
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.39
Consensus pattern (136 bp):
TCTATCCTCAATAACTTAGTCATAGAAAATACAATCATTGATTATATTCTTATCAATCCTTGTAA
TTTCATTCAACTAAATCTCAAGTTTCCTTAATACACATATCATTTTCCTCTTAGCCGAGTTTACA
TGGCAA
Found at i:83532 original size:14 final size:14
Alignment explanation
Indices: 83498--83535 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
83488 TAATAAAATC
83498 ATAAAACATTT-AT
1 ATAAAACATTTCAT
*
83511 -TTAAACATTTCAT
1 ATAAAACATTTCAT
83524 ATAAAACATTTC
1 ATAAAACATTTC
83536 TCAAATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 9 0.43
13 2 0.10
14 10 0.48
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
ATAAAACATTTCAT
Found at i:83746 original size:23 final size:23
Alignment explanation
Indices: 83703--83785 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 23
83693 ATAATTTGCA
83703 CCGAAGTG-CCACATA--TTTGTC
1 CCGAAG-GACCACATAGGTTTGTC
*
83724 CCGAAGGACCAGATAGGTTTGTC
1 CCGAAGGACCACATAGGTTTGTC
* * *
83747 CCAAAGGACTACATAGTTTTGTC
1 CCGAAGGACCACATAGGTTTGTC
*
83770 CCGAAAGACCACATAG
1 CCGAAGGACCACATAG
83786 AACCCTCGAC
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
20 1 0.02
21 12 0.24
23 38 0.75
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (23 bp):
CCGAAGGACCACATAGGTTTGTC
Found at i:84668 original size:20 final size:21
Alignment explanation
Indices: 84627--84676 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
84617 CTTCACATTC
84627 GTATCGATACTTCTTCAACCA
1 GTATCGATACTTCTTCAACCA
* *
84648 GTATCGATA-TTGTTCATCCA
1 GTATCGATACTTCTTCAACCA
84668 GT-TC-ATACT
1 GTATCGATACT
84677 ATTTCCTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 3 0.12
19 3 0.12
20 11 0.42
21 9 0.35
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (21 bp):
GTATCGATACTTCTTCAACCA
Found at i:88899 original size:3 final size:3
Alignment explanation
Indices: 88893--88947 Score: 67
Period size: 3 Copynumber: 17.7 Consensus size: 3
88883 AGTTTTAATA
*
88893 ATT ATT ATT ATC A-T ATTT ATT ATT ATT ATT ATT ATTT ATT ATT ACTT
1 ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT A-TT ATT ATT A-TT
88940 ATT ATT AT
1 ATT ATT AT
88948 AAATAAAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
2 1 0.02
3 37 0.80
4 8 0.17
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:88931 original size:10 final size:10
Alignment explanation
Indices: 88893--88947 Score: 71
Period size: 10 Copynumber: 5.8 Consensus size: 10
88883 AGTTTTAATA
88893 ATTATTA-TT
1 ATTATTATTT
*
88902 ATCA-TATTT
1 ATTATTATTT
88911 ATTATTA-TT
1 ATTATTATTT
88920 ATTATTATTT
1 ATTATTATTT
*
88930 ATTATTACTT
1 ATTATTATTT
88940 ATTATTAT
1 ATTATTAT
88948 AAATAAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
8 2 0.05
9 17 0.44
10 20 0.51
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (10 bp):
ATTATTATTT
Found at i:90864 original size:16 final size:15
Alignment explanation
Indices: 90824--90852 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
90814 TTTATCTTTT
90824 AAAATTATTTTTCTA
1 AAAATTATTTTTCTA
90839 AAAATTATTTTTCT
1 AAAATTATTTTTCT
90853 CCAAATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (15 bp):
AAAATTATTTTTCTA
Found at i:101004 original size:6 final size:6
Alignment explanation
Indices: 100993--101100 Score: 52
Period size: 6 Copynumber: 18.3 Consensus size: 6
100983 GAAGAAAAAT
* * *
100993 AAGAAA AAGAAA AAG-AA AA-AAA TAGAAA AATGAAA AGGAAA ATGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AA-GAAA AAGAAA AAGAAA
* * *
101040 ATGAAAA AAGAGAA AA-AATG AA-AAA ATGAAA AA-ATGAA AA-AAA AAG-AA
1 AAG-AAA AAGA-AA AAGAA-A AAGAAA AAGAAA AAGA--AA AAGAAA AAGAAA
101088 AAG-AA AAGAAA AA
1 AAGAAA AAGAAA AA
101101 AAATAAATAA
Statistics
Matches: 82, Mismatches: 9, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
5 24 0.29
6 39 0.48
7 19 0.23
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (6 bp):
AAGAAA
Found at i:101004 original size:15 final size:15
Alignment explanation
Indices: 100984--101114 Score: 79
Period size: 16 Copynumber: 8.3 Consensus size: 15
100974 ACTTCACCTG
*
100984 AAGAAAAATAAGAAA
1 AAGAAAAATAAAAAA
*
100999 AAGAAAAAGAAAAAA
1 AAGAAAAATAAAAAA
101014 ATAGAAAAATGAAAAGGAA
1 A-AGAAAAAT-AAAA--AA
101033 AATG-AAAATGAAAAAA
1 AA-GAAAAAT-AAAAAA
* *
101049 GAGAAAAAATGAAAAA
1 AAG-AAAAATAAAAAA
*
101065 ATGAAAAAATGAAAAAA
1 AAG-AAAAAT-AAAAAA
* *
101082 AA-AGAAAAGAAAAGA
1 AAGA-AAAATAAAAAA
*
101097 AA-AAAAATAAATAA
1 AAGAAAAATAAAAAA
101111 AAGA
1 AAGA
101115 GGGTTCAAGA
Statistics
Matches: 92, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
14 10 0.11
15 25 0.27
16 27 0.29
17 15 0.16
18 11 0.12
19 4 0.04
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.08
Consensus pattern (15 bp):
AAGAAAAATAAAAAA
Found at i:101022 original size:23 final size:23
Alignment explanation
Indices: 100987--101112 Score: 73
Period size: 23 Copynumber: 5.2 Consensus size: 23
100977 TCACCTGAAG
100987 AAAAATA-AGAAAAAGAAAAAGAA
1 AAAAATAGA-AAAAAGAAAAAGAA
* *
101010 AAAAATAGAAAAATGAAAAGGAA
1 AAAAATAGAAAAAAGAAAAAGAA
*
101033 AATGAAA-ATGAAAAAAGAGAAAAAATGA
1 AA--AAATA-GAAAAAAGA-AAAAGA--A
101061 AAAAAT-GAAAAAATGAAAAA-AA
1 AAAAATAGAAAAAA-GAAAAAGAA
* *
101083 AAGAAA-AGAAAAGAAAAAAAATAA
1 AA-AAATAGAAAA-AAGAAAAAGAA
101107 ATAAAA
1 A-AAAA
101113 GAGGGTTCAA
Statistics
Matches: 83, Mismatches: 6, Indels: 27
0.72 0.05 0.23
Matches are distributed among these distances:
22 3 0.04
23 34 0.41
24 11 0.13
25 23 0.28
26 9 0.11
28 3 0.04
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (23 bp):
AAAAATAGAAAAAAGAAAAAGAA
Found at i:101054 original size:34 final size:36
Alignment explanation
Indices: 100995--101063 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 36
100985 AGAAAAATAA
*
100995 GAAAAAGAAAAAGAAAAAAATAG-AAAAATGAAAAG
1 GAAAAAGAAAAAGAAAAAAAGAGAAAAAATGAAAAG
* *
101030 GAAAATGAAAATG-AAAAAAGAGAAAAAATGAAAA
1 GAAAAAGAAAAAGAAAAAAAGAGAAAAAATGAAAA
101064 AATGAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 8 0.27
35 22 0.73
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.07
Consensus pattern (36 bp):
GAAAAAGAAAAAGAAAAAAAGAGAAAAAATGAAAAG
Found at i:101062 original size:8 final size:8
Alignment explanation
Indices: 101037--101081 Score: 72
Period size: 8 Copynumber: 5.5 Consensus size: 8
101027 AAGGAAAATG
101037 AAAATGAA
1 AAAATGAA
*
101045 AAAAGAGAA
1 AAAA-TGAA
101054 AAAATGAA
1 AAAATGAA
101062 AAAATGAA
1 AAAATGAA
101070 AAAATGAA
1 AAAATGAA
101078 AAAA
1 AAAA
101082 AAAGAAAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
8 27 0.79
9 7 0.21
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (8 bp):
AAAATGAA
Found at i:101112 original size:10 final size:9
Alignment explanation
Indices: 101002--101114 Score: 61
Period size: 8 Copynumber: 11.8 Consensus size: 9
100992 TAAGAAAAAG
101002 AAAAAGAAA
1 AAAAAGAAA
101011 AAAATAGAAAA
1 AAAA-AG-AAA
101022 ATGAAAAGGAAA
1 A--AAAA-GAAA
101034 ATGAAAATGAAA
1 A--AAAA-GAAA
*
101046 AAAGAG-AA
1 AAAAAGAAA
*
101054 AAAATG-AA
1 AAAAAGAAA
*
101062 AAAATG-AA
1 AAAAAGAAA
*
101070 AAAATGAAAA
1 AAAAAG-AAA
101080 AAAAAGAAA
1 AAAAAGAAA
101089 AGAAAAGAAA
1 A-AAAAGAAA
*
101099 AAAAATAAA
1 AAAAAGAAA
*
101108 TAAAAGA
1 AAAAAGA
101115 GGGTTCAAGA
Statistics
Matches: 88, Mismatches: 8, Indels: 16
0.79 0.07 0.14
Matches are distributed among these distances:
8 22 0.25
9 21 0.24
10 21 0.24
11 4 0.05
12 16 0.18
13 4 0.05
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:101114 original size:18 final size:19
Alignment explanation
Indices: 100984--101103 Score: 64
Period size: 21 Copynumber: 5.6 Consensus size: 19
100974 ACTTCACCTG
*
100984 AAGAAAAATAAGAAAAAGAAA
1 AAGAAAAAAAAG-AAAAG-AA
101005 AAGAAAAAAATAGAAAAATGAA
1 AAGAAAAAAA-AG-AAAA-GAA
101027 AAGGAAAATGAAAATGAAAA-AA
1 AA-GAAAA--AAAA-GAAAAGAA
*
101049 GAGAAAAAATGAA-AAAATGAAAA
1 AAGAAAAAA--AAGAAAA-G--AA
101072 AATGAAAAAAAAAGAAAAGAA
1 AA-G-AAAAAAAAGAAAAGAA
101093 AAGAAAAAAAA
1 AAGAAAAAAAA
101104 TAAATAAAAG
Statistics
Matches: 81, Mismatches: 3, Indels: 32
0.70 0.03 0.28
Matches are distributed among these distances:
19 14 0.17
20 1 0.01
21 20 0.25
22 14 0.17
23 12 0.15
24 10 0.12
25 10 0.12
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (19 bp):
AAGAAAAAAAAGAAAAGAA
Found at i:102588 original size:134 final size:132
Alignment explanation
Indices: 102348--102789 Score: 507
Period size: 134 Copynumber: 3.3 Consensus size: 132
102338 ACAAATCGAA
* * * * *
102348 CTCGATTCAATCTTCCTTGAGTAACAGTGGAATGAATTAATGAACC-CATAA-ATGATTTTCCCT
1 CTCGATTCAATCTTCCCTGAGGAACAGTGGAAAGAATCAATG-TCCTCA-AATATGATTTTCCCT
* * *
102411 CAAGAAGAAGTCGAACAGATCCATCTCATTCAAGATTTGATATTCCATAAGTAACAGTGGAACAA
64 CAAGAAGAAG-CGAACA-ATCTATCTCTTTCAAGATTTGATATTCCATGAGTAACAGTGGAACAA
* *
102476 GTTTTC
127 GTCTAC
* * * * *
102482 CTCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCGACGTCCTCAGATATGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAGGAACAGTGGAAAGAATCAATGTCCTCAAATATGATTTTCCCTCA
102547 AGAAGAAGCGGAACATATCTATCTCTTTCAAGATTTGATATT-CACTGAGTAACAGTGGAACAAG
66 AGAAGAAGC-GAACA-ATCTATCTCTTTCAAGATTTGATATTCCA-TGAGTAACAGTGGAACAAG
*
102611 TCTGC
128 TCTAC
* * *** * * *
102616 CTCCATTCAATATTCCCTGAGGAACAACAGAAAGAATCAATAT-TTCCAAATATGGTTTTCCCTC
1 CTCGATTCAATCTTCCCTGAGGAACAGTGGAAAGAATCAATGTCCT-CAAATATGATTTTCCCTC
* *
102680 AAGAAGAAGCAGAACAAGTCTATCTCTTTCAATATTTGATATTTCCA-GAGTAATAGTGGAACAA
65 AAGAAGAAGC-GAACAA-TCTATCTCTTTCAAGATTTGATA-TTCCATGAGTAACAGTGGAACAA
102744 GTCTAC
127 GTCTAC
*
102750 CTCGATTCAATCTTCCCTGAGGAAAAGTGGAAAGAATCAA
1 CTCGATTCAATCTTCCCTGAGGAACAGTGGAAAGAATCAA
102790 CAACCCCAGA
Statistics
Matches: 265, Mismatches: 35, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
133 8 0.03
134 253 0.95
135 2 0.01
136 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (132 bp):
CTCGATTCAATCTTCCCTGAGGAACAGTGGAAAGAATCAATGTCCTCAAATATGATTTTCCCTCA
AGAAGAAGCGAACAATCTATCTCTTTCAAGATTTGATATTCCATGAGTAACAGTGGAACAAGTCT
AC
Found at i:106760 original size:39 final size:39
Alignment explanation
Indices: 106706--106786 Score: 126
Period size: 39 Copynumber: 2.1 Consensus size: 39
106696 CTCATGATTT
*
106706 TATCAAAACCATGATAAACAATATCACATATAATAGTCA
1 TATCAAAACCATGATAAACAATATCACACATAATAGTCA
** *
106745 TATCAAAGTCATGATAAACAATATCATACATAATAGTCA
1 TATCAAAACCATGATAAACAATATCACACATAATAGTCA
106784 TAT
1 TAT
106787 TATATTCTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.49, C:0.16, G:0.06, T:0.28
Consensus pattern (39 bp):
TATCAAAACCATGATAAACAATATCACACATAATAGTCA
Found at i:106984 original size:19 final size:19
Alignment explanation
Indices: 106942--106994 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
106932 CTCAAAACAT
106942 ATTTCAGATTCATA-ACTTA
1 ATTTCA-ATTCATAGACTTA
106961 ATTTCATATTCATAGA-TTA
1 ATTTCA-ATTCATAGACTTA
*
106980 TTTTCAAGTTCATAG
1 ATTTCAA-TTCATAG
106995 CCCAATACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 1 0.03
19 28 0.93
20 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (19 bp):
ATTTCAATTCATAGACTTA
Found at i:115039 original size:19 final size:20
Alignment explanation
Indices: 114988--115039 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 20
114978 TATGATGATG
*
114988 AAAACATATATATTTGTATA
1 AAAATATATATATTTGTATA
** *
115008 AATCT-TATTTATTT-TATA
1 AAAATATATATATTTGTATA
115026 AAAATATATATATT
1 AAAATATATATATT
115040 ATGAGGTATA
Statistics
Matches: 24, Mismatches: 7, Indels: 3
0.71 0.21 0.09
Matches are distributed among these distances:
18 7 0.29
19 15 0.62
20 2 0.08
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (20 bp):
AAAATATATATATTTGTATA
Found at i:116941 original size:42 final size:42
Alignment explanation
Indices: 116869--116949 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
116859 TATCAAATGA
*
116869 GTTCTTTTTAATAATTCTGAAAAAAATTAAAATTTTCTATCG
1 GTTCATTTTAATAATTCTGAAAAAAATTAAAATTTTCTATCG
* * **
116911 GTTCATTTTAATATTTCTGGAAAAGTTTAAAATTTTCTA
1 GTTCATTTTAATAATTCTGAAAAAAATTAAAATTTTCTA
116950 ATCCTGTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.47
Consensus pattern (42 bp):
GTTCATTTTAATAATTCTGAAAAAAATTAAAATTTTCTATCG
Found at i:118831 original size:38 final size:37
Alignment explanation
Indices: 118781--118854 Score: 130
Period size: 38 Copynumber: 2.0 Consensus size: 37
118771 TTTCAACTTT
*
118781 TTTCTAACAATTGTTAATGCACATATTGGTAAAAATA
1 TTTCTAACAATTGATAATGCACATATTGGTAAAAATA
118818 TTTCTTAACAATTGATAATGCACATATTGGTAAAAAT
1 TTTC-TAACAATTGATAATGCACATATTGGTAAAAAT
118855 CTATAATATC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 4 0.11
38 31 0.89
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (37 bp):
TTTCTAACAATTGATAATGCACATATTGGTAAAAATA
Found at i:121423 original size:24 final size:24
Alignment explanation
Indices: 121391--121441 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
121381 TTATAATTTT
*
121391 AAAATTATTT-AT-TTTTATTCAAA
1 AAAATTATTTCATATTAT-TTCAAA
121414 AAAATGTATTTCATATTATTTCAAA
1 AAAAT-TATTTCATATTATTTCAAA
121439 AAA
1 AAA
121442 TTTCATTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 5 0.21
24 5 0.21
25 11 0.46
26 3 0.12
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (24 bp):
AAAATTATTTCATATTATTTCAAA
Found at i:124133 original size:28 final size:29
Alignment explanation
Indices: 124073--124134 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
124063 TAATATTTTG
* *
124073 ATAAAATATTTAATGTGCATATATATATT
1 ATAAAATATTTAATATGAATATATATATT
*
124102 -TAAAATATTTAATAT-AATATTTATATT
1 ATAAAATATTTAATATGAATATATATATT
124129 ATAAAA
1 ATAAAA
124135 AAGATTGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 10 0.34
28 19 0.66
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (29 bp):
ATAAAATATTTAATATGAATATATATATT
Found at i:124354 original size:16 final size:18
Alignment explanation
Indices: 124312--124358 Score: 66
Period size: 16 Copynumber: 2.8 Consensus size: 18
124302 CTAAAATATT
124312 AAAATATAT--ATATTAC
1 AAAATATATAGATATTAC
124328 AAAATATATAGATATTAC
1 AAAATATATAGATATTAC
124346 AAAA-A-ATAGATAT
1 AAAATATATAGATAT
124359 ATTCAAACTC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 17 0.59
17 1 0.03
18 11 0.38
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (18 bp):
AAAATATATAGATATTAC
Found at i:124360 original size:18 final size:18
Alignment explanation
Indices: 124312--124365 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
124302 CTAAAATATT
124312 AAAATATATATATTACAA
1 AAAATATATATATTACAA
* *
124330 AATATATAGATATTACAA
1 AAAATATATATATTACAA
*
124348 AAAATAGATATATT-CAA
1 AAAATATATATATTACAA
124365 A
1 A
124366 CTCATATCAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
17 4 0.13
18 27 0.87
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (18 bp):
AAAATATATATATTACAA
Found at i:124781 original size:16 final size:18
Alignment explanation
Indices: 124756--124793 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
124746 CTATAAAGAT
*
124756 AAAATAT-AAATTATTAA
1 AAAATATAAAATAATTAA
124773 AAAAT-TAAAATAATTAA
1 AAAATATAAAATAATTAA
124790 AAAA
1 AAAA
124794 CATATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 1 0.05
17 18 0.95
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATATAAAATAATTAA
Found at i:126021 original size:52 final size:47
Alignment explanation
Indices: 125965--126132 Score: 174
Period size: 54 Copynumber: 3.3 Consensus size: 47
125955 TTTTAAAATA
*
125965 ATTTATTTTAAAATAATTTATTTTAAAATAAATTATTATAAAATATGGATTG
1 ATTTATTTTAAAATAATTTATTTT-AAAT-AA-T-TTAT-AAATATGAATTG
* *
126017 ATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAAATAATTTATTTTAAATAATTTATAAATATGAATTG
* * *
126064 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTT-AAA-AT--A---ATTTATTTTAAATAATTTATAAATATGAATTG
126118 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
126133 TTGATTGATT
Statistics
Matches: 105, Mismatches: 4, Indels: 16
0.84 0.03 0.13
Matches are distributed among these distances:
47 18 0.17
48 7 0.07
49 3 0.03
50 3 0.03
51 5 0.05
52 26 0.25
53 3 0.03
54 40 0.38
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (47 bp):
ATTTATTTTAAAATAATTTATTTTAAATAATTTATAAATATGAATTG
Found at i:126046 original size:14 final size:15
Alignment explanation
Indices: 125949--126052 Score: 111
Period size: 15 Copynumber: 6.5 Consensus size: 15
125939 TAATAAGGTT
125949 ATTTATTTTTAAAATA
1 ATTTA-TTTTAAAATA
125965 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
125980 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
125995 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
126014 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
126032 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
126046 ATTTATT
1 ATTTATT
126053 AGTATGAATT
Statistics
Matches: 77, Mismatches: 4, Indels: 16
0.79 0.04 0.16
Matches are distributed among these distances:
14 12 0.16
15 40 0.52
16 9 0.12
17 2 0.03
18 1 0.01
19 1 0.01
20 2 0.03
21 4 0.05
22 6 0.08
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:126071 original size:22 final size:22
Alignment explanation
Indices: 126055--126097 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
126045 AATTTATTAG
126055 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
126077 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
126098 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:126071 original size:32 final size:31
Alignment explanation
Indices: 126032--126183 Score: 133
Period size: 32 Copynumber: 5.4 Consensus size: 31
126022 TTTTAAAATA
126032 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATG-ATTG
126064 ATTTATTTT-AA-AA--TA-T-G---GATTG
1 ATTTATTTTAAATAATTTATTAGTATGATTG
126086 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTAT-GATTG
126118 ATTTATTTT--A-AA---A-TA-T-TGATTG
1 ATTTATTTTAAATAATTTATTAGTATGATTG
* *
126140 ATTTATTTTAAATAGTTTATTAGTATAGTTTG
1 ATTTATTTTAAATAATTTATTAGTAT-GATTG
126172 ATTTATTTTAAA
1 ATTTATTTTAAA
126184 ATATGAATTG
Statistics
Matches: 98, Mismatches: 2, Indels: 40
0.70 0.01 0.29
Matches are distributed among these distances:
22 27 0.28
23 4 0.04
24 4 0.04
25 3 0.03
26 4 0.04
27 2 0.02
28 4 0.04
29 4 0.04
30 4 0.04
31 3 0.03
32 39 0.40
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.54
Consensus pattern (31 bp):
ATTTATTTTAAATAATTTATTAGTATGATTG
Found at i:126088 original size:69 final size:67
Alignment explanation
Indices: 125949--126106 Score: 221
Period size: 69 Copynumber: 2.3 Consensus size: 67
125939 TAATAAGGTT
125949 ATTTATTTTTAAAATAATTTATTTTAAAATAATTTATTTTAAAATAAATTATTATAAAATATGGA
1 ATTTA-TTTTAAAATAATTTATTTTAAAATAATTTATTTTAAAATAAATTATTATAAAATATGGA
126014 TTG
65 TTG
* * * * *
126017 ATTTATTTTAAAATAATTTATTTT-AAATAATTTATTAGTATGAATTGATTTATTTTAAAATATG
1 ATTTATTTTAAAATAATTTATTTTAAAATAATTTATT--T-TAAAATAAATTATTATAAAATATG
126081 GATTG
63 GATTG
126086 ATTTATTTT-AAATAATTTATT
1 ATTTATTTTAAAATAATTTATT
126107 AGTATGGATT
Statistics
Matches: 82, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
66 12 0.15
67 19 0.23
68 18 0.22
69 33 0.40
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (67 bp):
ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTTTAAAATAAATTATTATAAAATATGGAT
TG
Found at i:126097 original size:54 final size:54
Alignment explanation
Indices: 126032--126200 Score: 277
Period size: 54 Copynumber: 3.1 Consensus size: 54
126022 TTTTAAAATA
126032 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
* *
126086 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATTGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
* * *
126140 ATTTATTTTAAATAGTTTATTAGTAT-AGTTTGATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGA-ATTGATTTATTTTAAAATATGGATTG
126194 ATTTATT
1 ATTTATT
126201 ATTGTAGTTG
Statistics
Matches: 107, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
54 107 1.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.54
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
Found at i:126231 original size:134 final size:134
Alignment explanation
Indices: 125997--126397 Score: 533
Period size: 134 Copynumber: 3.1 Consensus size: 134
125987 TTAAAATAAA
* * *
125997 TTATTATAAAATATGGATTGATTTATTTTAAAATAATTTATT--T-T-AAATAATTTA--TT--A
1 TTATTTTAAAATATGGATTGATTTATTTT-AAATAATTTATTAGTATGAATTGATTTATTTTAAA
* *** * *
126054 GTATGAATTGATTTA-T-TT-TA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGA
65 ATATGAATTGATTTATTATTGTAGTTGTATGAATTGATTTATTTTAAATAATTTATTAGTATGAA
126115 TTGAT
130 TTGAT
* * *
126120 TTATTTTAAAATATTGATTGATTTATTTTAAATAGTTTATTAGTAT-AGTTTGATTTATTTTAAA
1 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGA-ATTGATTTATTTTAAA
126184 ATATGAATTGATTTATTATTGTAGTTGTATGAATTGATTTATTTTAAATAATTTATTAGTATGAA
65 ATATGAATTGATTTATTATTGTAGTTGTATGAATTGATTTATTTTAAATAATTTATTAGTATGAA
*
126249 CTGAT
130 TTGAT
*
126254 TTATTTTAAAATGTGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
1 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
* *
126319 TATGGATTGATTTATTATTGTAGTTGTAT-AGATTGATTTATTTTAAATAATTTATTAGTATGTA
66 TATGAATTGATTTATTATTGTAGTTGTATGA-ATTGATTTATTTTAAATAATTTATTAGTATGAA
126383 TTGAT
130 TTGAT
126388 TTATTTTAAA
1 TTATTTTAAA
126398 TAATTTATTA
Statistics
Matches: 244, Mismatches: 20, Indels: 17
0.87 0.07 0.06
Matches are distributed among these distances:
122 11 0.05
123 27 0.11
124 1 0.00
125 2 0.01
126 6 0.02
128 2 0.01
130 15 0.06
131 1 0.00
132 2 0.01
133 3 0.01
134 173 0.71
135 1 0.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (134 bp):
TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
TATGAATTGATTTATTATTGTAGTTGTATGAATTGATTTATTTTAAATAATTTATTAGTATGAAT
TGAT
Found at i:126254 original size:32 final size:32
Alignment explanation
Indices: 126210--126317 Score: 128
Period size: 32 Copynumber: 3.7 Consensus size: 32
126200 TATTGTAGTT
126210 GTATGAATTGATTTATTTTAAATAATTTATTA
1 GTATGAATTGATTTATTTTAAATAATTTATTA
*
126242 GTATGAACTGATTTATTTT--A-AA---A-T-
1 GTATGAATTGATTTATTTTAAATAATTTATTA
*
126266 G--TGGATTGATTTATTTTAAATAATTTATTA
1 GTATGAATTGATTTATTTTAAATAATTTATTA
126296 GTATGAATTGATTTATTTTAAA
1 GTATGAATTGATTTATTTTAAA
126318 ATATGGATTG
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
22 14 0.23
24 2 0.03
25 3 0.05
26 1 0.02
28 1 0.02
29 3 0.05
30 2 0.03
32 36 0.58
ACGTcount: A:0.36, C:0.01, G:0.12, T:0.51
Consensus pattern (32 bp):
GTATGAATTGATTTATTTTAAATAATTTATTA
Found at i:126284 original size:54 final size:54
Alignment explanation
Indices: 126211--126334 Score: 221
Period size: 54 Copynumber: 2.3 Consensus size: 54
126201 ATTGTAGTTG
*
126211 TATGAATTGATTTATTTTAAATAATTTATTAGTATGAACTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAACTGATTTATTTTAAAA
* *
126265 TGTGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAACTGATTTATTTTAAAA
126319 TATGGATTGATTTATT
1 TATGGATTGATTTATT
126335 ATTGTAGTTG
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 66 1.00
ACGTcount: A:0.35, C:0.01, G:0.12, T:0.52
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGAACTGATTTATTTTAAAA
Found at i:126479 original size:31 final size:31
Alignment explanation
Indices: 126421--126480 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
126411 TAGTTGTATG
*** *
126421 AATTATTTAAATTTTAGTATTATAAAACTAA
1 AATTATTTAAATCACAGTATTACAAAACTAA
*
126452 AATTATTTAAATCACAGTATTGCAAAACT
1 AATTATTTAAATCACAGTATTACAAAACT
126481 CTTTTAAGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCACAGTATTACAAAACTAA
Found at i:130367 original size:3 final size:3
Alignment explanation
Indices: 130359--130420 Score: 72
Period size: 3 Copynumber: 19.3 Consensus size: 3
130349 ATTAATAAAC
130359 ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATAA ATA ATA ATA A-A TATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA -ATA
130406 TATAA ATA ATA ATA A
1 -AT-A ATA ATA ATA A
130421 AAAAGACCCG
Statistics
Matches: 54, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
2 1 0.02
3 40 0.74
4 12 0.22
5 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Done.