Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000741.1 Hibiscus syriacus cultivar Beakdansim tig00001431_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: 89466
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1717 original size:36 final size:36
Alignment explanation
Indices: 1651--1722 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
1641 AATATCTACC
1651 AAACTTTACCAAACTTTGAAAAAACATTTTTCAAAG
1 AAACTTTACCAAACTTTGAAAAAACATTTTTCAAAG
1687 AAACATTTACCAAACTTTG-AAAAACATTTTTCAAAG
1 AAAC-TTTACCAAACTTTGAAAAAACATTTTTCAAAG
1723 TTGGTTGCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 21 0.60
37 14 0.40
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.31
Consensus pattern (36 bp):
AAACTTTACCAAACTTTGAAAAAACATTTTTCAAAG
Found at i:3497 original size:20 final size:20
Alignment explanation
Indices: 3464--3501 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3454 TATGCTCGGA
3464 GGGAACCGATTTCCCCCCAG
1 GGGAACCGATTTCCCCCCAG
3484 GGGATACCGA-TTCCCCCC
1 GGGA-ACCGATTTCCCCCC
3502 TTGTATAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.18, C:0.42, G:0.24, T:0.16
Consensus pattern (20 bp):
GGGAACCGATTTCCCCCCAG
Found at i:9280 original size:20 final size:20
Alignment explanation
Indices: 9251--9288 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
9241 AGTATACTCG
9251 GAGGGAACCGATTCCCCCCA
1 GAGGGAACCGATTCCCCCCA
*
9271 GAGGGTACCGATTCCCCC
1 GAGGGAACCGATTCCCCC
9289 TTGTATAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.39, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCCA
Found at i:24660 original size:531 final size:531
Alignment explanation
Indices: 23657--24720 Score: 2128
Period size: 531 Copynumber: 2.0 Consensus size: 531
23647 GTTAGAGGTC
23657 AAGGTAGTTTAAAAAAGAATAAGAATCAAAATGATTATTTTATAAAATATTAGTAGTGATTTTTT
1 AAGGTAGTTTAAAAAAGAATAAGAATCAAAATGATTATTTTATAAAATATTAGTAGTGATTTTTT
23722 ACATTATGCCGTTTGTTTATTACGTTAAAATAAAGTCTAGGTCCCTCTAAGTTTTGAAATTTTTT
66 ACATTATGCCGTTTGTTTATTACGTTAAAATAAAGTCTAGGTCCCTCTAAGTTTTGAAATTTTTT
23787 AATTTAACACCATGATCTTAAACTCTTGGAAGTACACGTAGGAGGACTAGTTTATAAAAGTTTGA
131 AATTTAACACCATGATCTTAAACTCTTGGAAGTACACGTAGGAGGACTAGTTTATAAAAGTTTGA
23852 AGAGTACAGCTATTTGGATTCGTCGGAAGTCTTAACATGTGCACGTTATGGTTTTGCTAGGGTTT
196 AGAGTACAGCTATTTGGATTCGTCGGAAGTCTTAACATGTGCACGTTATGGTTTTGCTAGGGTTT
23917 TTGCATGACTGTTCCCAAGCAGTCGGCATAGGTTGTGGTCGGCACCATTGTGATCTCCTCAGTTA
261 TTGCATGACTGTTCCCAAGCAGTCGGCATAGGTTGTGGTCGGCACCATTGTGATCTCCTCAGTTA
23982 GAGGGGCCGGATTCCCCGATAGCAGTGGAGGACCGGTCAGAGATTAAGAAAGGTCGTCTTTATCA
326 GAGGGGCCGGATTCCCCGATAGCAGTGGAGGACCGGTCAGAGATTAAGAAAGGTCGTCTTTATCA
24047 ATTGATCATGAATTGTGTCTCGTCAGCTTCAACGCAAGTTTTGTGGAATGGGGTAACATCTTCGG
391 ATTGATCATGAATTGTGTCTCGTCAGCTTCAACGCAAGTTTTGTGGAATGGGGTAACATCTTCGG
24112 ACTTTAAACCCTCACGAGGGATTCGATAAGGGCTGTCATGAGCTAGAATGCTCCTTTGGTTGTTA
456 ACTTTAAACCCTCACGAGGGATTCGATAAGGGCTGTCATGAGCTAGAATGCTCCTTTGGTTGTTA
24177 TACAAAGGCCG
521 TACAAAGGCCG
24188 AAGGTAGTTTAAAAAAGAATAAGAATCAAAATGATTATTTTATAAAATATTAGTAGTGATTTTTT
1 AAGGTAGTTTAAAAAAGAATAAGAATCAAAATGATTATTTTATAAAATATTAGTAGTGATTTTTT
24253 ACATTATGCCGTTTGTTTATTACGTTAAAATAAAGTCTAGGTCCCTCTAAGTTTTGAAATTTTTT
66 ACATTATGCCGTTTGTTTATTACGTTAAAATAAAGTCTAGGTCCCTCTAAGTTTTGAAATTTTTT
24318 AATTTAACACCATGATCTTAAACTCTTGGAAGTACACGTAGGAGGACTAGTTTATAAAAGTTTGA
131 AATTTAACACCATGATCTTAAACTCTTGGAAGTACACGTAGGAGGACTAGTTTATAAAAGTTTGA
24383 AGAGTACAGCTATTTGGATTCGTCGGAAGTCTTAACATGTGCACGTTATGGTTTTGCTAGGGTTT
196 AGAGTACAGCTATTTGGATTCGTCGGAAGTCTTAACATGTGCACGTTATGGTTTTGCTAGGGTTT
24448 TTGCATGACTGTTCCCAAGCAGTCGGCATAGGTTGTGGTCGGCACCATTGTGATCTCCTCAGTTA
261 TTGCATGACTGTTCCCAAGCAGTCGGCATAGGTTGTGGTCGGCACCATTGTGATCTCCTCAGTTA
24513 GAGGGGCCGGATTCCCCGATAGCAGTGGAGGACCGGTCAGAGATTAAGAAAGGTCGTCTTTATCA
326 GAGGGGCCGGATTCCCCGATAGCAGTGGAGGACCGGTCAGAGATTAAGAAAGGTCGTCTTTATCA
24578 ATTGATCATGAATTGTGTCTCGTCAGCTTCAACGCAAGTTTTGTGGAATGGGGTAACATCTTCGG
391 ATTGATCATGAATTGTGTCTCGTCAGCTTCAACGCAAGTTTTGTGGAATGGGGTAACATCTTCGG
24643 ACTTTAAACCCTCACGAGGGATTCGATAAGGGCTGTCATGAGCTAGAATGCTCCTTTGGTTGTTA
456 ACTTTAAACCCTCACGAGGGATTCGATAAGGGCTGTCATGAGCTAGAATGCTCCTTTGGTTGTTA
24708 TACAAAGGCCG
521 TACAAAGGCCG
24719 AA
1 AA
24721 TCATGACTAA
Statistics
Matches: 533, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
531 533 1.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (531 bp):
AAGGTAGTTTAAAAAAGAATAAGAATCAAAATGATTATTTTATAAAATATTAGTAGTGATTTTTT
ACATTATGCCGTTTGTTTATTACGTTAAAATAAAGTCTAGGTCCCTCTAAGTTTTGAAATTTTTT
AATTTAACACCATGATCTTAAACTCTTGGAAGTACACGTAGGAGGACTAGTTTATAAAAGTTTGA
AGAGTACAGCTATTTGGATTCGTCGGAAGTCTTAACATGTGCACGTTATGGTTTTGCTAGGGTTT
TTGCATGACTGTTCCCAAGCAGTCGGCATAGGTTGTGGTCGGCACCATTGTGATCTCCTCAGTTA
GAGGGGCCGGATTCCCCGATAGCAGTGGAGGACCGGTCAGAGATTAAGAAAGGTCGTCTTTATCA
ATTGATCATGAATTGTGTCTCGTCAGCTTCAACGCAAGTTTTGTGGAATGGGGTAACATCTTCGG
ACTTTAAACCCTCACGAGGGATTCGATAAGGGCTGTCATGAGCTAGAATGCTCCTTTGGTTGTTA
TACAAAGGCCG
Found at i:26723 original size:21 final size:21
Alignment explanation
Indices: 26697--26747 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
26687 GCACAAGGAG
26697 TATCGGTACTGCTATGAACAA
1 TATCGGTACTGCTATGAACAA
*
26718 TATCGGTACTGCTATGAACAG
1 TATCGGTACTGCTATGAACAA
26739 TATCGGTAC
1 TATCGGTAC
26748 AACTTTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (21 bp):
TATCGGTACTGCTATGAACAA
Found at i:28254 original size:33 final size:33
Alignment explanation
Indices: 28209--28276 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
28199 CAAAAACATA
*
28209 ATATATGATCACTTTCATTTTTATTTAATTAAG
1 ATATATGATCACTTTCATTTTTATTTAACTAAG
* *
28242 ATATATGGTCACTTTCATTTTTATTTGACTAAG
1 ATATATGATCACTTTCATTTTTATTTAACTAAG
28275 AT
1 AT
28277 GTTGTCACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.50
Consensus pattern (33 bp):
ATATATGATCACTTTCATTTTTATTTAACTAAG
Found at i:28516 original size:15 final size:16
Alignment explanation
Indices: 28498--28536 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
28488 AGTCATATTT
*
28498 TTAATATATTTT-ATG
1 TTAAAATATTTTGATG
28513 TTAAAATATTTTGATG
1 TTAAAATATTTTGATG
28529 TTAAAATA
1 TTAAAATA
28537 AGAATAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (16 bp):
TTAAAATATTTTGATG
Found at i:29672 original size:20 final size:20
Alignment explanation
Indices: 29636--29673 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29626 ATCCTATTCC
**
29636 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
29656 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
29674 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:29868 original size:31 final size:31
Alignment explanation
Indices: 29832--29891 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 31
29822 CACATATTAT
29832 TGACGTGATA-TTTATACATATATTCAATTCC
1 TGACGTGATACTTT-TACATATATTCAATTCC
29863 TGACGTGATACTTTTACATATATTCAATT
1 TGACGTGATACTTTTACATATATTCAATT
29892 ATTGACCCGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 25 0.89
32 3 0.11
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (31 bp):
TGACGTGATACTTTTACATATATTCAATTCC
Found at i:31560 original size:19 final size:19
Alignment explanation
Indices: 31536--31573 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
31526 AATGTTAGCG
* *
31536 AAAATAATGTTTTTAATAA
1 AAAATAATATTTTAAATAA
31555 AAAATAATATTTTAAATAA
1 AAAATAATATTTTAAATAA
31574 CATTTTACGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
AAAATAATATTTTAAATAA
Found at i:34890 original size:13 final size:13
Alignment explanation
Indices: 34869--34911 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
34859 ATCAAGTGTC
*
34869 AATGACTAAGAAA
1 AATGTCTAAGAAA
34882 AATGTCTAAGAAA
1 AATGTCTAAGAAA
* *
34895 AATTATGTAAGAAA
1 AA-TGTCTAAGAAA
34909 AAT
1 AAT
34912 TTTGAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.58, C:0.05, G:0.14, T:0.23
Consensus pattern (13 bp):
AATGTCTAAGAAA
Found at i:34905 original size:14 final size:14
Alignment explanation
Indices: 34874--34912 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
34864 GTGTCAATGA
*
34874 CTAAGAAAAA-TGT
1 CTAAGAAAAATTAT
34887 CTAAGAAAAATTAT
1 CTAAGAAAAATTAT
*
34901 GTAAGAAAAATT
1 CTAAGAAAAATT
34913 TTGAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.56, C:0.05, G:0.13, T:0.26
Consensus pattern (14 bp):
CTAAGAAAAATTAT
Found at i:44861 original size:14 final size:14
Alignment explanation
Indices: 44842--44868 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44832 CCCACTCTAG
44842 AAATCATTTACTAA
1 AAATCATTTACTAA
44856 AAATCATTTACTA
1 AAATCATTTACTA
44869 TATTAGTCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATCATTTACTAA
Found at i:46254 original size:33 final size:33
Alignment explanation
Indices: 46217--46289 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
46207 TTCCTGATTA
46217 AATAGAAAAATGAAATTTGTTTCAAAGGAGAAC
1 AATAGAAAAATGAAATTTGTTTCAAAGGAGAAC
*
46250 AATAGAAAAATGAAATTTGTTTCAAAGGAGAAT
1 AATAGAAAAATGAAATTTGTTTCAAAGGAGAAC
46283 AATAGAA
1 AATAGAA
46290 GATAGGAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.53, C:0.04, G:0.18, T:0.25
Consensus pattern (33 bp):
AATAGAAAAATGAAATTTGTTTCAAAGGAGAAC
Found at i:47586 original size:21 final size:20
Alignment explanation
Indices: 47562--47690 Score: 66
Period size: 20 Copynumber: 6.3 Consensus size: 20
47552 TCCCAGAATT
47562 GCAACGCGATTATGAAGAATC
1 GCAACGCGATTATGAA-AATC
*
47583 GCAATGCGA-TA-GTACAAATTC
1 GCAACGCGATTATG-A-AAA-TC
** * * *
47604 GCATTGCGATTTTCCAGAATC
1 GCAACGCGATTAT-GAAAATC
* *
47625 GTAACGCGAATATGAAAATC
1 GCAACGCGATTATGAAAATC
**
47645 GCAACGCGAACAT-ATAAATC
1 GCAACGCGATTATGA-AAATC
* **
47665 GCAACGCGATTCTGACTATC
1 GCAACGCGATTATGAAAATC
47685 GCAACG
1 GCAACG
47691 AGTATCCGTA
Statistics
Matches: 81, Mismatches: 19, Indels: 17
0.69 0.16 0.15
Matches are distributed among these distances:
19 2 0.02
20 45 0.56
21 30 0.37
22 3 0.04
23 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
GCAACGCGATTATGAAAATC
Found at i:47650 original size:20 final size:20
Alignment explanation
Indices: 47621--47875 Score: 135
Period size: 20 Copynumber: 12.6 Consensus size: 20
47611 GATTTTCCAG
* *
47621 AATCGTAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
47641 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* *
47661 AATCGCAACGCG-ATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* * * *
47681 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
* *
47702 AATCGCAACGCGTAT-CCATA
1 AATCGCAACGCGAATACGA-A
47722 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * * * *
47743 AATCGCAATGTGTATCCGTA
1 AATCGCAACGCGAATACGAA
* *
47763 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * *
47783 AATCGCAATGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GAA
* *
47803 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * * *
47823 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
47843 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
47864 AATCGCAACGCG
1 AATCGCAACGCG
47876 TATCAGTAAA
Statistics
Matches: 181, Mismatches: 39, Indels: 29
0.73 0.16 0.12
Matches are distributed among these distances:
19 4 0.02
20 129 0.71
21 47 0.26
22 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:47798 original size:40 final size:41
Alignment explanation
Indices: 47682--47892 Score: 318
Period size: 41 Copynumber: 5.2 Consensus size: 41
47672 GATTCTGACT
* * * *
47682 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCATAA
1 ATCGCAACGAGAATACGTAAAATCGCAATGCGTATCCGTAA
* *
47723 ATCGCAACGACAATACGTAAAATCGCAATGTGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAATGCGTATCCGTAA
*
47764 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAATGCGTATCCGTAA
47804 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAATGCGTATCCGTAA
* * *
47844 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCAGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAATGCGTATCCGTAA
47885 ATCGCAAC
1 ATCGCAAC
47893 TCGATTTTTA
Statistics
Matches: 156, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 76 0.49
41 80 0.51
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAATGCGTATCCGTAA
Found at i:47888 original size:20 final size:20
Alignment explanation
Indices: 47682--47892 Score: 148
Period size: 20 Copynumber: 10.4 Consensus size: 20
47672 GATTCTGACT
* *
47682 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCAGT-AA
47703 ATCGCAACGCGTATCCA-TAA
1 ATCGCAACGCGTAT-CAGTAA
*
47723 ATCGCAACGAC-AAT-ACGTAAA
1 ATCGCAACG-CGTATCA-GT-AA
* * *
47744 ATCGCAATGTGTATCCGTAA
1 ATCGCAACGCGTATCAGTAA
* *
47764 ATCGCAACGAGAAT-ACGTAA
1 ATCGCAACGCGTATCA-GTAA
* *
47784 ATCGCAATGCGTATCTGTAA
1 ATCGCAACGCGTATCAGTAA
* *
47804 ATCGCAACGAGAAT-ACGTAA
1 ATCGCAACGCGTATCA-GTAA
* *
47824 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCAGTAA
*
47844 ATCGCAACGAC-AAT-ACGTAAA
1 ATCGCAACG-CGTATCA-GT-AA
47865 ATCGCAACGCGTATCAGTAA
1 ATCGCAACGCGTATCAGTAA
47885 ATCGCAAC
1 ATCGCAAC
47893 TCGATTTTTA
Statistics
Matches: 147, Mismatches: 27, Indels: 33
0.71 0.13 0.16
Matches are distributed among these distances:
18 1 0.01
20 99 0.67
21 45 0.31
22 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGTATCAGTAA
Found at i:48514 original size:21 final size:21
Alignment explanation
Indices: 48453--48531 Score: 85
Period size: 20 Copynumber: 3.9 Consensus size: 21
48443 TTCTAAACTT
48453 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
48473 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
48493 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
*
48514 AAAATCGTAACGAGAGAA
1 AAAATCGCAACGAGAGAA
48532 TCGCAATGCG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
20 30 0.59
21 21 0.41
ACGTcount: A:0.52, C:0.16, G:0.19, T:0.13
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:48554 original size:19 final size:19
Alignment explanation
Indices: 48530--48580 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
48520 GTAACGAGAG
**
48530 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAACCAA
*
48549 AATCGCAACGCGAAACCAA
1 AATCGCAATGCGAAACCAA
*
48568 AATCGCATTGCGA
1 AATCGCAATGCGA
48581 TTTTCATTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.43, C:0.24, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAACCAA
Found at i:48592 original size:19 final size:19
Alignment explanation
Indices: 48570--48701 Score: 112
Period size: 19 Copynumber: 7.1 Consensus size: 19
48560 GAAACCAAAA
*
48570 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
48589 TCGCGTTGCGATTCTC--T
1 TCGCGTTGCGATTTTCATT
* *
48606 T---GTTGCGATTATAATT
1 TCGCGTTGCGATTTTCATT
*
48622 TCACGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
48641 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* **
48660 TCCGCATTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
48680 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
48700 TC
1 TC
48702 AACCAAAAGA
Statistics
Matches: 92, Mismatches: 14, Indels: 14
0.77 0.12 0.12
Matches are distributed among these distances:
14 10 0.11
16 2 0.02
17 2 0.02
19 46 0.50
20 31 0.34
21 1 0.01
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:48671 original size:20 final size:19
Alignment explanation
Indices: 48636--48679 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
48626 GTTGCGATTT
*
48636 TCATTTCGCGTTGCGATAG
1 TCATTTCGCATTGCGATAG
48655 TCATTTCCGCATTGCGATAG
1 TCATTT-CGCATTGCGATAG
48675 TCATT
1 TCATT
48680 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:50555 original size:94 final size:94
Alignment explanation
Indices: 50394--50773 Score: 665
Period size: 94 Copynumber: 4.1 Consensus size: 94
50384 TAGATTGCTT
* * *
50394 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTAAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
50459 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
50488 AGTAAATTTATTCGGTTGTTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
50553 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
50582 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
50647 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
50676 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
50741 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
50769 AGTAA
1 AGTAA
50774 TGCAATCCAT
Statistics
Matches: 277, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
93 26 0.09
94 251 0.91
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:50899 original size:31 final size:32
Alignment explanation
Indices: 50861--50934 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 32
50851 AAAAATGACT
* * *
50861 ATCGCAACGCGAAAT-GAATCGCAACT-AGATA
1 ATCGCAACGAGAAATAAAATCGCAA-TGAGAGA
50892 ATCGCAACGAGAAATAAAAATCGCAATGAGAGA
1 ATCGCAACGAGAAAT-AAAATCGCAATGAGAGA
50925 ATCGCAACGA
1 ATCGCAACGA
50935 CAAAATCGCA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 14 0.38
32 1 0.03
33 22 0.59
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.14
Consensus pattern (32 bp):
ATCGCAACGAGAAATAAAATCGCAATGAGAGA
Found at i:50929 original size:14 final size:14
Alignment explanation
Indices: 50908--50947 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
50898 ACGAGAAATA
* *
50908 AAAATCGCAATGAG
1 AAAATCGCAACGAC
*
50922 AGAATCGCAACGAC
1 AAAATCGCAACGAC
50936 AAAATCGCAACG
1 AAAATCGCAACG
50948 CGAAACCAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:50981 original size:19 final size:19
Alignment explanation
Indices: 50935--50972 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
50925 ATCGCAACGA
50935 CAAAATCGCAACGCGAAAC
1 CAAAATCGCAACGCGAAAC
50954 CAAAATCGCAACGCGAAAC
1 CAAAATCGCAACGCGAAAC
50973 TATAATCGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.32, G:0.16, T:0.05
Consensus pattern (19 bp):
CAAAATCGCAACGCGAAAC
Found at i:51068 original size:20 final size:20
Alignment explanation
Indices: 51016--51082 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
51006 GATTCTCTCG
**
51016 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
51036 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
51056 TTGCGATAGTCATTTTCACG
1 TTGCGATAGTCATTTTCGCA
51076 TTGCGAT
1 TTGCGAT
51083 TTTAAGTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:53046 original size:14 final size:14
Alignment explanation
Indices: 53027--53062 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
53017 ATTGTTTAAT
53027 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
53041 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
53055 TGATTTGT
1 TGATTTGT
53063 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:53252 original size:34 final size:33
Alignment explanation
Indices: 53175--53259 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 33
53165 TCGCAACGTA
**
53175 GAAATGACTATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
*
53208 GAAATGAAAATCGCAACGAGTGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
*
53241 GAAAATGAAAATCACAACG
1 G-AAATGAAAATCGCAACG
53260 CGAAATCTCG
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 31 0.66
34 16 0.34
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:53293 original size:20 final size:19
Alignment explanation
Indices: 53268--53361 Score: 107
Period size: 20 Copynumber: 4.7 Consensus size: 19
53258 CGCGAAATCT
53268 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
53288 CGTTGCGATAGTCAATTTCT
1 CGTTGCGATAGTC-ATTTCG
*
53308 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
* * *
53328 TGTTGCAATAGTCATATTTG
1 CGTTGCGATAGTCAT-TTCG
53348 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
53362 AATGAATGTC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 56 0.90
21 4 0.06
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:53333 original size:40 final size:41
Alignment explanation
Indices: 53265--53361 Score: 135
Period size: 40 Copynumber: 2.4 Consensus size: 41
53255 CAACGCGAAA
*
53265 TCTCGTTGCGATAGTCATTTCCGCGTTGCGATAGTCA-ATT
1 TCTCGTTGCGATAGTCATTTCCGCGTTGCAATAGTCATATT
* * *
53305 TCTCATTGCGATAGTCATTTTCGTGTTGCAATAGTCATATT
1 TCTCGTTGCGATAGTCATTTCCGCGTTGCAATAGTCATATT
*
53346 T-GCGTTGCGATAGTCA
1 TCTCGTTGCGATAGTCA
53362 AATGAATGTC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
40 46 0.92
41 4 0.08
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.39
Consensus pattern (41 bp):
TCTCGTTGCGATAGTCATTTCCGCGTTGCAATAGTCATATT
Found at i:55583 original size:3 final size:3
Alignment explanation
Indices: 55575--55603 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
55565 CTTTGGGGAT
55575 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
55604 TCAGTGTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:56733 original size:20 final size:20
Alignment explanation
Indices: 56695--56802 Score: 137
Period size: 20 Copynumber: 5.4 Consensus size: 20
56685 ATCAGAATCT
*
56695 CGTTGCGATTTATAG-ATTCA
1 CGTTGCGATTTA-CGTATTCA
* *
56715 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATTCA
* * *
56735 CGTTGCGATTTATGTAATCG
1 CGTTGCGATTTACGTATTCA
56755 CGTTGCGATTTACGTATTCA
1 CGTTGCGATTTACGTATTCA
*
56775 CGTTGCGATTTACGTAATCA
1 CGTTGCGATTTACGTATTCA
56795 CGTTGCGA
1 CGTTGCGA
56803 ATTAGGAAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
19 1 0.01
20 76 0.99
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTACGTATTCA
Found at i:56760 original size:60 final size:60
Alignment explanation
Indices: 56690--56802 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
56680 CGATAATCAG
* * *
56690 AATCTCGTTGCGATTTATAG-ATTCACATTGCGATTTACGTATTCGCGTTGCGATTTATGT
1 AATCGCGTTGCGATTTA-AGTATTCACATTGCGATTTACGTAATCACGTTGCGATTTATGT
* *
56750 AATCGCGTTGCGATTTACGTATTCACGTTGCGATTTACGTAATCACGTTGCGA
1 AATCGCGTTGCGATTTAAGTATTCACATTGCGATTTACGTAATCACGTTGCGA
56803 ATTAGGAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 1 0.02
60 46 0.98
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (60 bp):
AATCGCGTTGCGATTTAAGTATTCACATTGCGATTTACGTAATCACGTTGCGATTTATGT
Found at i:56897 original size:20 final size:20
Alignment explanation
Indices: 56874--57046 Score: 186
Period size: 20 Copynumber: 8.6 Consensus size: 20
56864 TACTGGAGAT
*
56874 CGCGTTGCAATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
56894 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
56914 TGTCATTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
56935 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
56955 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
56975 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
**
56995 CTAGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
57015 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
57036 CTCGTTGCGAT
1 CGCGTTGCGAT
57047 AGTCAGAATC
Statistics
Matches: 125, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
20 90 0.72
21 35 0.28
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:56963 original size:40 final size:41
Alignment explanation
Indices: 56876--57046 Score: 256
Period size: 40 Copynumber: 4.2 Consensus size: 41
56866 CTGGAGATCG
* *
56876 CGTTGCAATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
56917 CATTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
56957 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
56997 AGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
57038 CGTTGCGAT
1 CGTTGCGAT
57047 AGTCAGAATC
Statistics
Matches: 117, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
40 74 0.63
41 43 0.37
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:57030 original size:81 final size:80
Alignment explanation
Indices: 56876--57069 Score: 259
Period size: 81 Copynumber: 2.4 Consensus size: 80
56866 CTGGAGATCG
* * *
56876 CGTTGCAATTTACGGATACGCGTTGCGATTTTACGTATTGTCATTGCGATTTACGGATACGCATT
1 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCTCATTGCGATTTACGGATACGCATT
* *
56941 GCGATTTACGTATTCT
65 GCGATTTACGGATACT
*
56957 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT-AGTTGCGATTTACGGATACGCGTT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCA-TTGCGATTTACGGATACGCATT
57021 GCGATTTTACGGATACT
65 GCGA-TTTACGGATACT
*
57038 CGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTA
1 CGTTGCGAT-TTACAGATA-CGCGTTGCGATTTA
57070 TATGTTCGCG
Statistics
Matches: 102, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
79 1 0.01
80 37 0.36
81 63 0.62
82 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (80 bp):
CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCATTGCGATTTACGGATACGCATTG
CGATTTACGGATACT
Found at i:57078 original size:20 final size:20
Alignment explanation
Indices: 57055--57107 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
57045 ATAGTCAGAA
*
57055 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
57075 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
*
57095 TCGCGTTACGATT
1 TCGCGTTGCGATT
57108 CTGGAAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:57099 original size:40 final size:40
Alignment explanation
Indices: 56876--57107 Score: 216
Period size: 40 Copynumber: 5.8 Consensus size: 40
56866 CTGGAGATCG
* * * *
56876 CGTTGCAATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACATATTCT
* * * *
56917 CATTGCGATTTACGGATACGCATTGCGATTTACGTATTCT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTACATATTCT
*
56957 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTACATATTCT
* * ** *
56997 AGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACATATTCT
* * * *
57038 CGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTATATGTTCG
1 CGTTGCGAT-TTACAGATA-CGCGTTGCGATTTACATATTCT
* * * *
57078 CGTTGCGATTTTCATATTCGCGTTACGATT
1 CGTTGCGATTTACAGATACGCGTTGCGATT
57108 CTGGAAAATC
Statistics
Matches: 162, Mismatches: 24, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
39 1 0.01
40 104 0.64
41 56 0.35
42 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.38
Consensus pattern (40 bp):
CGTTGCGATTTACAGATACGCGTTGCGATTTACATATTCT
Found at i:57100 original size:81 final size:81
Alignment explanation
Indices: 56876--57107 Score: 213
Period size: 81 Copynumber: 2.9 Consensus size: 81
56866 CTGGAGATCG
* * * * * *
56876 CGTTGCAATTTACGGATACGCGTTGCGATTTTACGTATT-GTCA-TTGCGATTTACGGATACGCA
1 CGTTGCGATGTACAGATACGCGTTGCGA-TTTACATATTCG--AGTTGCGATTTACAGATACGCG
* *
56939 TTGCGA-TTTACGTATTCT
63 TTGCGATTTTACGGATACT
* * * *
56957 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTAGTTGCGATTTACGGATACGCGTTG
1 CGTTGCGATGTACAGATACGCGTTGCGATTTACATATTCGAGTTGCGATTTACAGATACGCGTTG
57022 CGATTTTACGGATACT
66 CGATTTTACGGATACT
* * * * * *
57038 CGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTATATGTTCGCGTTGCGATTTTCATATTCGCGT
1 CGTTGCGAT-GTACAGATA-CGCGTTGCGATTTACATATTCGAGTTGCGATTTACAGATACGCGT
*
57101 TACGATT
64 TGCGATT
57108 CTGGAAAATC
Statistics
Matches: 129, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
79 1 0.01
80 36 0.28
81 91 0.71
82 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.38
Consensus pattern (81 bp):
CGTTGCGATGTACAGATACGCGTTGCGATTTACATATTCGAGTTGCGATTTACAGATACGCGTTG
CGATTTTACGGATACT
Found at i:57209 original size:20 final size:19
Alignment explanation
Indices: 57157--57210 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
57147 ATTCTTCATA
57157 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* ** *
57176 AACTGATTTACGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
57197 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
57211 TTTATTTCAT
Statistics
Matches: 25, Mismatches: 8, Indels: 3
0.69 0.22 0.08
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:58227 original size:20 final size:20
Alignment explanation
Indices: 58199--58237 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
58189 GAATAGTTTC
58199 TGAAAATGAAAATCGCAACA
1 TGAAAATGAAAATCGCAACA
*
58219 TGAATATGAAAATCGCAAC
1 TGAAAATGAAAATCGCAAC
58238 GCGAATTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.18
Consensus pattern (20 bp):
TGAAAATGAAAATCGCAACA
Found at i:58243 original size:20 final size:20
Alignment explanation
Indices: 58204--58243 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
58194 GTTTCTGAAA
*
58204 ATGAAAATCGCAACATGAAT
1 ATGAAAATCGCAACACGAAT
*
58224 ATGAAAATCGCAACGCGAAT
1 ATGAAAATCGCAACACGAAT
58244 TCGACTATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.17
Consensus pattern (20 bp):
ATGAAAATCGCAACACGAAT
Found at i:58778 original size:20 final size:20
Alignment explanation
Indices: 58752--58808 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
58742 GATTATGTAT
58752 TATCGCGTTGCGAAAGTCAGA
1 TATCGCGTTGCGAAAGTCA-A
58773 -ATCGCGTTGCGAAAGTCAA
1 TATCGCGTTGCGAAAGTCAA
58792 TATCGCGTTGCGAAAGT
1 TATCGCGTTGCGAAAGT
58809 AAGTATATCG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
19 1 0.03
20 34 0.97
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAA
Found at i:58858 original size:20 final size:20
Alignment explanation
Indices: 58752--58866 Score: 86
Period size: 20 Copynumber: 5.7 Consensus size: 20
58742 GATTATGTAT
*
58752 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
58772 AATCGCGTTGCGAAAGTCAA
1 TATCGCGTTGCGATAGTCAG
* *
58792 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGATAGTCAG
** * ** * *
58812 TATATCGTTGCAATTTTTTAT
1 TATCGCGTTGCGA-TAGTCAG
*
58833 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
58853 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
58867 TTTCCCAATT
Statistics
Matches: 73, Mismatches: 21, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
20 62 0.85
21 11 0.15
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:58869 original size:41 final size:41
Alignment explanation
Indices: 58732--58867 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
58722 CGCTTTGAAA
* *
58732 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTATTTATTATCGCGTTGCGAAAGTCAGT
* * * * * *
58773 ATCGCGTTGCGA-AAGTCAATATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTATTTATTATCGCGTTGCGAAAGTCAGT
** * * * * *
58813 ATATCGTTGCAATTTTTTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTATTTATTATCGCGTTGCGAAAGTCAGT
58854 ATCGCATTGCGATT
1 ATCGCATTGCGATT
58868 TTCCCAATTC
Statistics
Matches: 71, Mismatches: 23, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
40 30 0.42
41 41 0.58
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (41 bp):
ATCGCATTGCGATTATTTATTATCGCGTTGCGAAAGTCAGT
Found at i:58884 original size:21 final size:21
Alignment explanation
Indices: 58855--58947 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 21
58845 ATAGTCAGTA
58855 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
58876 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
58896 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * * **
58917 TCGCGTTGC-AATTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
58937 TCGCATTGCGA
1 TCGCATTGCGA
58948 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:58885 original size:41 final size:41
Alignment explanation
Indices: 58855--58947 Score: 141
Period size: 41 Copynumber: 2.3 Consensus size: 41
58845 ATAGTCAGTA
* *
58855 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
* * *
58896 TCGCATTGCGATTTTCCCAATTCGCGTTGCAATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
58937 TCGCATTGCGA
1 TCGCATTGCGA
58948 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:59617 original size:18 final size:18
Alignment explanation
Indices: 59596--59640 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
59586 TCCACTTCGG
*
59596 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
59614 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
59632 GAGCCATCA
1 GAGCCATCA
59641 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:60170 original size:20 final size:20
Alignment explanation
Indices: 60120--60185 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
60110 TAGTTTACTT
*
60120 TCGCAACACGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
60140 TCGCAACGCGAAAATGGCTA
1 TCGCAACGCGAAAATGACTA
* *
60160 TCGCAATGCG-AAATGA-AA
1 TCGCAACGCGAAAATGACTA
60178 TCGCAACG
1 TCGCAACG
60186 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
18 8 0.20
19 5 0.12
20 27 0.68
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:60283 original size:19 final size:19
Alignment explanation
Indices: 60259--60304 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
60249 TTGCGATTTT
*
60259 CATTTCGCATTGTGATAGC
1 CATTTCGCATTGCGATAGC
* *
60278 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCATTGCGATAGC
60298 CATTTCG
1 CATTTCG
60305 TGTTGCGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:60311 original size:19 final size:19
Alignment explanation
Indices: 60247--60313 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
60237 GCGATTTTGT
**
60247 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* * *
60266 CATTGTGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
60286 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
60305 TGTTGCGAT
1 CGTTGCGAT
60314 TTTAAGTTTC
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
19 22 0.58
20 16 0.42
ACGTcount: A:0.15, C:0.21, G:0.24, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:62149 original size:14 final size:14
Alignment explanation
Indices: 62130--62165 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
62120 ATTGTTTAAT
62130 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
62144 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
62158 TGATTTGT
1 TGATTTGT
62166 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:62308 original size:20 final size:20
Alignment explanation
Indices: 62283--62340 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
62273 TCACATTGCG
*
62283 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
62303 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
62323 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
62341 TCAAATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:62694 original size:21 final size:21
Alignment explanation
Indices: 62670--62718 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
62660 TAATACAGAA
62670 TCGCAATGCGAGTTTCAAAGT
1 TCGCAATGCGAGTTTCAAAGT
62691 TCGCAATGCGAGTTTCAAAGT
1 TCGCAATGCGAGTTTCAAAGT
62712 TCGCAAT
1 TCGCAAT
62719 AGGTTTTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (21 bp):
TCGCAATGCGAGTTTCAAAGT
Found at i:65971 original size:33 final size:33
Alignment explanation
Indices: 65929--66053 Score: 191
Period size: 33 Copynumber: 3.8 Consensus size: 33
65919 CGGAATTACT
65929 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
65962 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
65994 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
66028 ATCGCAATGCGAAATG-AAATCGCAAC
1 ATCGCAATGCGAAATGAAAATCGCAAC
66054 ACGAATTTAA
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
32 11 0.13
33 71 0.86
34 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:66021 original size:66 final size:65
Alignment explanation
Indices: 65930--66053 Score: 230
Period size: 66 Copynumber: 1.9 Consensus size: 65
65920 GGAATTACTA
65930 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG-AAATCGCAACGCTAAT
65995 T
65 T
*
65996 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAATCGCAAC
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAATCGCAAC
66054 ACGAATTTAA
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
65 10 0.18
66 47 0.82
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (65 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAATCGCAACGCTAATT
Found at i:66253 original size:14 final size:14
Alignment explanation
Indices: 66234--66270 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
66224 CATCAATTAA
66234 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
66248 ACAAATCACCTTTT
1 ACAAATCAACTTTT
66262 ACAAATCAA
1 ACAAATCAA
66271 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:69734 original size:21 final size:20
Alignment explanation
Indices: 69688--69749 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
69678 TCTTTTGGTT
69688 GAAATGAAAATCGC-AACGA
1 GAAATGAAAATCGCAAACGA
* *
69707 GATAATGAGAATCGCAAACGCG
1 GA-AATGAAAATCGCAAACG-A
**
69729 GAAATGACTATCGC-AACGA
1 GAAATGAAAATCGCAAACGA
69748 GA
1 GA
69750 GAATCGCAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 4 0.11
20 15 0.43
21 14 0.40
22 2 0.06
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (20 bp):
GAAATGAAAATCGCAAACGA
Found at i:69771 original size:33 final size:33
Alignment explanation
Indices: 69713--69812 Score: 137
Period size: 33 Copynumber: 3.0 Consensus size: 33
69703 ACGAGATAAT
*
69713 GAGAATCGCAAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGC-AACGC-GAAATGACTATCGCAACCA
*
69748 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
69781 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
69813 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
33 45 0.76
34 5 0.08
35 9 0.15
ACGTcount: A:0.40, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:69806 original size:19 final size:19
Alignment explanation
Indices: 69688--69911 Score: 209
Period size: 19 Copynumber: 12.1 Consensus size: 19
69678 TCTTTTGGTT
*
69688 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
69707 GATAATGAGAATCGCAAACGC
1 GA-AATGAAAATCGC-AACGC
**
69728 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
69746 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
69762 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
69780 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
69795 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
69815 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
69834 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
69854 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
69873 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
69892 G-AATAAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
69910 GA
1 GA
69912 TTTTGTTTCG
Statistics
Matches: 171, Mismatches: 18, Indels: 32
0.77 0.08 0.14
Matches are distributed among these distances:
14 19 0.11
15 3 0.02
16 2 0.01
17 1 0.01
18 20 0.12
19 61 0.36
20 49 0.29
21 14 0.08
22 2 0.01
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:69827 original size:39 final size:39
Alignment explanation
Indices: 69784--69911 Score: 233
Period size: 39 Copynumber: 3.3 Consensus size: 39
69774 GCGACCAGAC
69784 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
69823 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
69862 AATCGCAACGCGAAATGAAAATCGCAA-CGCG-AATAAA
1 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
*
69899 AATCGCAATGCGA
1 AATCGCAACGCGA
69912 TTTTGTTTCG
Statistics
Matches: 88, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
37 18 0.20
38 4 0.05
39 66 0.75
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.11
Consensus pattern (39 bp):
AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
Found at i:69940 original size:20 final size:19
Alignment explanation
Indices: 69912--69971 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
69902 CGCAATGCGA
*
69912 TTTTGTTTCGCGTTGCGCTT
1 TTTTATTTCGCGTTGCG-TT
*
69932 TTTTATTTCGCGTTGCG-A
1 TTTTATTTCGCGTTGCGTT
*
69950 TATTATTTCGCGTTGCGATT
1 TTTTATTTCGCGTTGCG-TT
69970 TT
1 TT
69972 CATTCGAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
18 16 0.48
20 17 0.52
ACGTcount: A:0.08, C:0.17, G:0.22, T:0.53
Consensus pattern (19 bp):
TTTTATTTCGCGTTGCGTT
Found at i:69977 original size:18 final size:18
Alignment explanation
Indices: 69907--69971 Score: 85
Period size: 18 Copynumber: 3.5 Consensus size: 18
69897 AAAATCGCAA
*
69907 TGCGATTTTGTTTCGCGT
1 TGCGATTTTATTTCGCGT
*
69925 TGCGCTTTTTTATTTCGCGT
1 TGCG--ATTTTATTTCGCGT
*
69945 TGCGATATTATTTCGCGT
1 TGCGATTTTATTTCGCGT
69963 TGCGATTTT
1 TGCGATTTT
69972 CATTCGAAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 24 0.60
20 16 0.40
ACGTcount: A:0.09, C:0.17, G:0.23, T:0.51
Consensus pattern (18 bp):
TGCGATTTTATTTCGCGT
Found at i:70531 original size:20 final size:20
Alignment explanation
Indices: 70483--70535 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
70473 GCGCTATGTA
*
70483 AATCGCGTTACGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
70503 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
70523 TATCTCGTTGCGA
1 AATCGCGTTGCGA
70536 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:70569 original size:20 final size:20
Alignment explanation
Indices: 70544--70597 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
70534 GATTTTGTAT
*
70544 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAC
*
70564 TATCGCATTGCGATAGTCAC
1 TATCGCATTGCGATAGTAAC
70584 TATCGCATTGCGAT
1 TATCGCATTGCGAT
70598 TTTCCCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAC
Found at i:70708 original size:21 final size:21
Alignment explanation
Indices: 70668--70708 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
70658 ATTGTATACC
**
70668 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
70689 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
70709 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:71238 original size:30 final size:30
Alignment explanation
Indices: 71182--71238 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
71172 AAATTTTCGT
* *
71182 TCTTGAAATTTTATAAATTTAAATTCATCC
1 TCTTGAAATTTTAAAAATTCAAATTCATCC
71212 TCTT-AAATTTTAAAAAGTTCAAATTCA
1 TCTTGAAATTTTAAAAA-TTCAAATTCA
71239 CCCCTAACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.40, C:0.12, G:0.04, T:0.44
Consensus pattern (30 bp):
TCTTGAAATTTTAAAAATTCAAATTCATCC
Found at i:74362 original size:18 final size:18
Alignment explanation
Indices: 74330--74366 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
74320 TTTTAACAGA
74330 AAAATATTAAAATAAAAT
1 AAAATATTAAAATAAAAT
74348 AAAA-ATTAAACATAAAAT
1 AAAATATTAAA-ATAAAAT
74366 A
1 A
74367 TGACTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAATATTAAAATAAAAT
Found at i:75162 original size:30 final size:33
Alignment explanation
Indices: 75121--75199 Score: 92
Period size: 35 Copynumber: 2.4 Consensus size: 33
75111 GAAAATCGAA
* *
75121 TTAAACAGGGACGG-A-G-AAAAATCGTTTATG
1 TTAAACGGGGACGGCACGAAAAAACCGTTTATG
75151 TTAAACGGGGACGGTCACGGAAAAAACCGTTTATG
1 TTAAACGGGGACGG-CAC-GAAAAAACCGTTTATG
*
75186 CTAAACGGGGACGG
1 TTAAACGGGGACGG
75200 GGACGGGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 13 0.32
32 1 0.02
34 1 0.02
35 26 0.63
ACGTcount: A:0.35, C:0.15, G:0.30, T:0.19
Consensus pattern (33 bp):
TTAAACGGGGACGGCACGAAAAAACCGTTTATG
Found at i:75182 original size:35 final size:36
Alignment explanation
Indices: 75131--75199 Score: 113
Period size: 35 Copynumber: 1.9 Consensus size: 36
75121 TTAAACAGGG
* *
75131 ACGGAGAAAAATCGTTTATGTTAAACGGGGACGGTC
1 ACGGAGAAAAACCGTTTATGCTAAACGGGGACGGTC
75167 ACGGA-AAAAACCGTTTATGCTAAACGGGGACGG
1 ACGGAGAAAAACCGTTTATGCTAAACGGGGACGG
75200 GGACGGGGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 26 0.84
36 5 0.16
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.19
Consensus pattern (36 bp):
ACGGAGAAAAACCGTTTATGCTAAACGGGGACGGTC
Found at i:75305 original size:19 final size:19
Alignment explanation
Indices: 75281--75338 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
75271 TATATATATA
75281 ATATTAATAAATTTAATTT
1 ATATTAATAAATTTAATTT
* * *
75300 ATATTAAAAAATAT-ATATA
1 ATATTAATAAATTTAAT-TT
* *
75319 ATATTTATATATTTAATTT
1 ATATTAATAAATTTAATTT
75338 A
1 A
75339 AATATATATA
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
18 2 0.07
19 25 0.86
20 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATTAATAAATTTAATTT
Found at i:75624 original size:19 final size:19
Alignment explanation
Indices: 75600--75639 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
75590 CTCCGGTTTA
75600 ACTAAATCTCAACTGTCCC
1 ACTAAATCTCAACTGTCCC
75619 ACTAAATCTCAACTGTCCC
1 ACTAAATCTCAACTGTCCC
75638 AC
1 AC
75640 GTTACCCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.38, G:0.05, T:0.25
Consensus pattern (19 bp):
ACTAAATCTCAACTGTCCC
Found at i:77578 original size:179 final size:172
Alignment explanation
Indices: 77280--77634 Score: 647
Period size: 179 Copynumber: 2.0 Consensus size: 172
77270 ATATTAAATT
77280 TTGAACGAGATATTAAAATGAAACAAAAACTAATTTTTAATAGCATGGTCTAAATAAAATAAAAA
1 TTGAACGAGATATTAAAATGAAACAAAAACTAATTTTTAATAGCATGGTCTAAATAAAATAAAAA
77345 TTAAACTTTAAATATGTTTTGAAAAAATTGAAAGTTTATATACTAAAATGGATAAAAATTTATAA
66 TTAAACTTTAAATATGTTTTGAAAAAATTGAAAGTTTATATACTAAAATGGAT-AAAATTTATAA
77410 TTTACGTACTACACACGTATTTACTAAAAAAACTCTAATTTTTCAAA
130 TTTACG---TACACACGTATTTACTAAAAAAACTCTAA-TTTTCAAA
77457 TTGAACGAGATATTAAAATGAAACAAAAACTAATTTTTTAATAGCATGGTCTAAAATAAAATAAA
1 TTGAACGAGATATTAAAATGAAACAAAAACTAA-TTTTTAATAGCATGGTCT-AAATAAAATAAA
77522 AATTAAACTTTAAATATGTTTTGAAAAAATTGAAAGTTTATATACTAAAATGGATAAAATTTATA
64 AATTAAACTTTAAATATGTTTTGAAAAAATTGAAAGTTTATATACTAAAATGGATAAAATTTATA
77587 ATTTACGTACACACGTATTTACTAAAAAAACTCTAATTTTCAAA
129 ATTTACGTACACACGTATTTACTAAAAAAACTCTAATTTTCAAA
77631 TTGA
1 TTGA
77635 CAGTCATCAC
Statistics
Matches: 176, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
174 12 0.07
175 29 0.16
177 33 0.19
178 35 0.20
179 67 0.38
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (172 bp):
TTGAACGAGATATTAAAATGAAACAAAAACTAATTTTTAATAGCATGGTCTAAATAAAATAAAAA
TTAAACTTTAAATATGTTTTGAAAAAATTGAAAGTTTATATACTAAAATGGATAAAATTTATAAT
TTACGTACACACGTATTTACTAAAAAAACTCTAATTTTCAAA
Found at i:82530 original size:21 final size:24
Alignment explanation
Indices: 82476--82525 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
82466 ATGTATCCAT
*
82476 TATCAGAAATCATGTTTTACTTTAAA
1 TATCAG-AGTCATGTTTTAC-TTAAA
82502 TATCAGAGTCATGTTTTA-TTAAA
1 TATCAGAGTCATGTTTTACTTAAA
82525 T
1 T
82526 CAGAGATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 6 0.26
25 11 0.48
26 6 0.26
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (24 bp):
TATCAGAGTCATGTTTTACTTAAA
Found at i:83267 original size:20 final size:19
Alignment explanation
Indices: 83242--83302 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 19
83232 AACATAATGT
83242 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTAC-GATTCCCC
83262 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTA-CGATT-CCCC
83283 CCA-GGGGTATCGATTCCCC
1 CCAGGGGGTA-CGATTCCCC
83302 C
1 C
83303 TGTCTAACAT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
19 5 0.13
20 25 0.66
21 8 0.21
ACGTcount: A:0.16, C:0.39, G:0.28, T:0.16
Consensus pattern (19 bp):
CCAGGGGGTACGATTCCCC
Found at i:86053 original size:22 final size:21
Alignment explanation
Indices: 86019--86077 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
86009 ATATTGTCTA
*
86019 GGGGTACATATTCCCCCCCTAG
1 GGGGTACAGATTCCCCCCC-AG
*
86041 GGGGAACAGATT-CCCCCCAG
1 GGGGTACAGATTCCCCCCCAG
*
86061 GGGGTACCGATTCCCCC
1 GGGGTACAGATTCCCCC
86078 TGTCTAACGG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 12 0.38
21 10 0.31
22 10 0.31
ACGTcount: A:0.19, C:0.37, G:0.27, T:0.17
Consensus pattern (21 bp):
GGGGTACAGATTCCCCCCCAG
Found at i:87967 original size:19 final size:20
Alignment explanation
Indices: 87928--87967 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
87918 GATCAGAACA
87928 ATTCAAGTTGACTCTGATTG
1 ATTCAAGTTGACTCTGATTG
87948 ATTCAAGTTGACTC-GATTG
1 ATTCAAGTTGACTCTGATTG
87967 A
1 A
87968 CTCAGTCGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.38
Consensus pattern (20 bp):
ATTCAAGTTGACTCTGATTG
Done.