Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 87 of 226
Found at i:30816697 original size:54 final size:54
Alignment explanation
Indices: 30816598--30816707 Score: 141
Period size: 54 Copynumber: 2.0 Consensus size: 54
30816588 TCATCTCTTA
**
30816598 GGGGTATAACAGTCATTTTACCCTATGGGGGTATTTTGATCATTTTACCATATG
1 GGGGTATAACAGTCATTTTACCCTATGGGGGTATTCAGATCATTTTACCATATG
** * * *
30816652 GGGGTATTTCAGTCATTTTATCCTATGGGGGTAATTCAG-TTATTTTACCCTATG
1 GGGGTATAACAGTCATTTTACCCTATGGGGGT-ATTCAGATCATTTTACCATATG
30816706 GG
1 GG
30816708 TATTTATGTC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
54 44 0.92
55 4 0.08
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.40
Consensus pattern (54 bp):
GGGGTATAACAGTCATTTTACCCTATGGGGGTATTCAGATCATTTTACCATATG
Found at i:30829605 original size:23 final size:22
Alignment explanation
Indices: 30829575--30829617 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
30829565 CTTAGTTAAC
30829575 ATTTATGT-TACTATTAATGTAAA
1 ATTTATGTATA-TATT-ATGTAAA
30829598 ATTTATGTATATATTATGTA
1 ATTTATGTATATATTATGTA
30829618 TTTTGAGCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 12 0.63
24 2 0.11
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.51
Consensus pattern (22 bp):
ATTTATGTATATATTATGTAAA
Found at i:30831205 original size:25 final size:26
Alignment explanation
Indices: 30831167--30831215 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
30831157 GAATTAGTAG
30831167 AAAACAAATAATATTTATTTAATAGA
1 AAAACAAATAATATTTATTTAATAGA
*
30831193 AAAACTAAT-ATATTTATTTAATA
1 AAAACAAATAATATTTATTTAATA
30831216 AAATTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (26 bp):
AAAACAAATAATATTTATTTAATAGA
Found at i:30840983 original size:2 final size:2
Alignment explanation
Indices: 30840976--30841007 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
30840966 TGTAAAAGTC
30840976 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30841008 TATGTATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30850997 original size:18 final size:19
Alignment explanation
Indices: 30850974--30851022 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
30850964 GCAAATATAT
*
30850974 AATAAAAAG-AAATCAACA
1 AATAAAAAGTAAATAAACA
30850992 AAT-AAAAGTAAATAAACA
1 AATAAAAAGTAAATAAACA
*
30851010 AATAAAAATTAAA
1 AATAAAAAGTAAA
30851023 GCACTTAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 5 0.19
18 14 0.52
19 8 0.30
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.16
Consensus pattern (19 bp):
AATAAAAAGTAAATAAACA
Found at i:30853194 original size:46 final size:46
Alignment explanation
Indices: 30853138--30853570 Score: 616
Period size: 46 Copynumber: 9.4 Consensus size: 46
30853128 CTGCTTAGGG
* * * *
30853138 AGACAGGATCTGCAATCTTCGATCTACTTCATTGCCAAATACAGGA
1 AGACAAGATCTGCTATCTTCGATCTACTCCACTGCCAAATACAGGA
*
30853184 AGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATACAGGA
1 AGACAAGATCTGCTATCTTCGATCTACTCCACTGCCAAATACAGGA
* * *
30853230 TGACAAGATCTTCTATCTTCGATCTACTCCACTGCCCAAATATAGGA
1 AGACAAGATCTGCTATCTTCGATCTACTCCACTG-CCAAATACAGGA
*
30853277 AGACAAGATCTTCTATCTTCGATCTACTCCACTGCCAAATACAGGA
1 AGACAAGATCTGCTATCTTCGATCTACTCCACTGCCAAATACAGGA
* *
30853323 AGACAAGATCTTCTATCTTCGATCTACTTCACTGCCAAATACAGGA
1 AGACAAGATCTGCTATCTTCGATCTACTCCACTGCCAAATACAGGA
* *
30853369 AGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAAATACAGGA
1 AGACAAGATCTGCTATCTTCGATCTACTCCACTGCCAAATACAGGA
* * * **
30853415 AGACAAGATCTACTATCTTTGATCTCCTCTGCTGCCAAATACAGGA
1 AGACAAGATCTGCTATCTTCGATCTACTCCACTGCCAAATACAGGA
* * * *
30853461 AGAAAAGATCTGCTATCTACGATCTACTCCGCTACCAAATACAGGA
1 AGACAAGATCTGCTATCTTCGATCTACTCCACTGCCAAATACAGGA
* * *
30853507 AGACAAGATCTGCTTTCTTTGATCTACTCCGCTGCCAAATACAGGA
1 AGACAAGATCTGCTATCTTCGATCTACTCCACTGCCAAATACAGGA
*
30853553 AGACTAGATCTGCT-TCTT
1 AGACAAGATCTGCTATCTT
30853571 TTAGTCCATT
Statistics
Matches: 354, Mismatches: 32, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
45 4 0.01
46 306 0.86
47 44 0.12
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (46 bp):
AGACAAGATCTGCTATCTTCGATCTACTCCACTGCCAAATACAGGA
Found at i:30854645 original size:108 final size:106
Alignment explanation
Indices: 30854459--30854774 Score: 416
Period size: 97 Copynumber: 3.0 Consensus size: 106
30854449 AAATGCTTGA
* * * * *
30854459 AAAAGATTATCAAAATGGACAAGATGAAATTTTATTGAGAATAAGGCTCAAAATGAATAAATTAA
1 AAAAGATTATCACAATGGACAAGATGAAATTTTATTGAAAACAAAGCTCGAAATGAATAAATTAA
* *
30854524 TCAAAATAACAAATTTTGCTAAGATATGAACTGAATAAGATG
66 TCAAGATAGCAAATTTTGCTAAGATATGAA-TGAATAAGATG
*
30854566 AAAAGGGTTATCACAATGGACAAGATGAAATTTTATTGAAAACAAAGCTCGAAATGAATAAATTA
1 AAAA-GATTATCACAATGGACAAGATGAAATTTTATTGAAAACAAAGCTCGAAATGAATAAATTA
30854631 ATCAAGATAGCAAATTTTGCTAAG--AT-AA-G-AT--GA--
65 ATCAAGATAGCAAATTTTGCTAAGATATGAATGAATAAGATG
* * * *
30854664 AAAAGATTATCACAATGGATAAGATGAAATTTTATTGAAAGCACAGCTTGAAATGAATAAATTAA
1 AAAAGATTATCACAATGGACAAGATGAAATTTTATTGAAAACAAAGCTCGAAATGAATAAATTAA
* *
30854729 TTAAGATAGCAAATTTTGCTAAGATACGAAATGAATAAGATG
66 TCAAGATAGCAAATTTTGCTAAGATATG-AATGAATAAGATG
30854771 AAAA
1 AAAA
30854775 CAGGTGCCCC
Statistics
Matches: 183, Mismatches: 15, Indels: 22
0.83 0.07 0.10
Matches are distributed among these distances:
97 78 0.43
98 4 0.02
99 1 0.01
100 2 0.01
101 2 0.01
102 3 0.02
103 3 0.02
105 4 0.02
106 2 0.01
107 8 0.04
108 76 0.42
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.27
Consensus pattern (106 bp):
AAAAGATTATCACAATGGACAAGATGAAATTTTATTGAAAACAAAGCTCGAAATGAATAAATTAA
TCAAGATAGCAAATTTTGCTAAGATATGAATGAATAAGATG
Found at i:30855056 original size:5 final size:5
Alignment explanation
Indices: 30855040--30855120 Score: 57
Period size: 5 Copynumber: 16.8 Consensus size: 5
30855030 CCTCTCCTTT
* * *
30855040 TTTTC ATTTTC TTTTC TTTT- TCTTC TTTTC TTTT- TTATTT TTTTC ATTT-
1 TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC TTTTC
*
30855089 TTTTC -ATT- TTTTC TTTTC -TTTC TTTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC TTTT
30855121 TCTTCTCCTT
Statistics
Matches: 60, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
4 16 0.27
5 33 0.55
6 11 0.18
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:30855060 original size:6 final size:6
Alignment explanation
Indices: 30855039--30855124 Score: 51
Period size: 6 Copynumber: 14.3 Consensus size: 6
30855029 GCCTCTCCTT
*
30855039 TTTTTC ATTTTC -TTTTC TTTTTC TTCTTTTC TTTTT- TATTTT- TTTCATT-
1 TTTTTC TTTTTC TTTTTC TTTTTC -T-TTTTC TTTTTC T-TTTTC TTT--TTC
30855088 TTTTTC ATTTTT- TCTTTTC --TTTC TTTTTC TTTTTC TT
1 TTTTTC -TTTTTC T-TTTTC TTTTTC TTTTTC TTTTTC TT
30855125 CTCCTTTTTT
Statistics
Matches: 67, Mismatches: 1, Indels: 24
0.73 0.01 0.26
Matches are distributed among these distances:
4 4 0.06
5 11 0.16
6 35 0.52
7 12 0.18
8 5 0.07
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:30855083 original size:15 final size:14
Alignment explanation
Indices: 30855046--30855121 Score: 71
Period size: 15 Copynumber: 5.1 Consensus size: 14
30855036 CTTTTTTTCA
*
30855046 TTTTCTTTTCTTTT
1 TTTTTTTTTCTTTT
* *
30855060 TCTTCTTTTCTTTT
1 TTTTTTTTTCTTTT
30855074 TTATTTTTTTCATTTT
1 TT-TTTTTTTC-TTTT
30855090 TTTCATTTTTTCTTTT
1 TTT--TTTTTTCTTTT
*
30855106 CTTTCTTTTTCTTTT
1 -TTTTTTTTTCTTTT
30855121 T
1 T
30855122 CTTCTCCTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
14 15 0.28
15 18 0.34
16 10 0.19
17 10 0.19
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTTTTTCTTTT
Found at i:30855092 original size:32 final size:31
Alignment explanation
Indices: 30855056--30855132 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 31
30855046 TTTTCTTTTC
*
30855056 TTTTTCTTCTTTTCTTTT-TTATTTTTTTCATT
1 TTTTTCTTCTTTTCTTTTCTT-TCTTTTTC-TT
30855088 TTTTTCATT-TTTTCTTTTCTTTCTTTTTCTT
1 TTTTTC-TTCTTTTCTTTTCTTTCTTTTTCTT
*
30855119 TTTCTTCTCCTTTT
1 TTT-TTCTTCTTTT
30855133 TTTGAAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
31 6 0.15
32 29 0.74
33 4 0.10
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (31 bp):
TTTTTCTTCTTTTCTTTTCTTTCTTTTTCTT
Found at i:30855126 original size:15 final size:15
Alignment explanation
Indices: 30855051--30855126 Score: 70
Period size: 16 Copynumber: 5.0 Consensus size: 15
30855041 TTTCATTTTC
30855051 TTTTCTTTTTCTTC-
1 TTTTCTTTTTCTTCT
*
30855065 TTTTCTTTTT-TATTT
1 TTTTCTTTTTCT-TCT
30855080 TTTTCATTTTT-TTCAT
1 TTTTC-TTTTTCTTC-T
30855096 TTTT-TCTTTTCTTTCT
1 TTTTCT-TTTTC-TTCT
30855112 TTTTCTTTTTCTTCT
1 TTTTCTTTTTCTTCT
30855127 CCTTTTTTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
13 1 0.02
14 12 0.23
15 14 0.27
16 21 0.40
17 4 0.08
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTCTTTTTCTTCT
Found at i:30855195 original size:33 final size:33
Alignment explanation
Indices: 30855153--30855215 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
30855143 CTTTGATTGA
30855153 ATTCGAACTCGTAGGATCAGGTAAATCCTTGTT
1 ATTCGAACTCGTAGGATCAGGTAAATCCTTGTT
*
30855186 ATTCGAACTCGTAGGATCATGTAAATCCTT
1 ATTCGAACTCGTAGGATCAGGTAAATCCTT
30855216 ACTATCCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (33 bp):
ATTCGAACTCGTAGGATCAGGTAAATCCTTGTT
Found at i:30859565 original size:18 final size:19
Alignment explanation
Indices: 30859542--30859590 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
30859532 GCAAATATAT
*
30859542 AATAAAAAG-AAATCAACA
1 AATAAAAAGTAAATAAACA
30859560 AAT-AAAAGTAAATAAACA
1 AATAAAAAGTAAATAAACA
*
30859578 AATAAAAATTAAA
1 AATAAAAAGTAAA
30859591 GCACTTAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 5 0.19
18 14 0.52
19 8 0.30
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.16
Consensus pattern (19 bp):
AATAAAAAGTAAATAAACA
Found at i:30862344 original size:23 final size:22
Alignment explanation
Indices: 30862314--30862356 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
30862304 CTTAGTTAAC
30862314 ATTTATGT-TACTATTAATGTAAA
1 ATTTATGTATA-TATT-ATGTAAA
30862337 ATTTATGTATATATTATGTA
1 ATTTATGTATATATTATGTA
30862357 TTTTGAGCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 12 0.63
24 2 0.11
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.51
Consensus pattern (22 bp):
ATTTATGTATATATTATGTAAA
Found at i:30869142 original size:23 final size:22
Alignment explanation
Indices: 30869112--30869154 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
30869102 CTTAGTTAAC
30869112 ATTTATGT-TACTATTAATGTAAA
1 ATTTATGTATA-TATT-ATGTAAA
30869135 ATTTATGTATATATTATGTA
1 ATTTATGTATATATTATGTA
30869155 TTTTGAGCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 12 0.63
24 2 0.11
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.51
Consensus pattern (22 bp):
ATTTATGTATATATTATGTAAA
Found at i:30870741 original size:25 final size:26
Alignment explanation
Indices: 30870703--30870751 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
30870693 GAATTAGTAG
30870703 AAAACAAATAATATTTATTTAATAGA
1 AAAACAAATAATATTTATTTAATAGA
*
30870729 AAAACTAAT-ATATTTATTTAATA
1 AAAACAAATAATATTTATTTAATA
30870752 AAATTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (26 bp):
AAAACAAATAATATTTATTTAATAGA
Found at i:30885805 original size:23 final size:22
Alignment explanation
Indices: 30885775--30885817 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
30885765 CTTAGTTAAC
30885775 ATTTATGT-TACTATTAATGTAAA
1 ATTTATGTATA-TATT-ATGTAAA
30885798 ATTTATGTATATATTATGTA
1 ATTTATGTATATATTATGTA
30885818 TTTTGACCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 12 0.63
24 2 0.11
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.51
Consensus pattern (22 bp):
ATTTATGTATATATTATGTAAA
Found at i:30897932 original size:29 final size:29
Alignment explanation
Indices: 30897890--30897956 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
30897880 CTTCAAGCAA
* *
30897890 TAGGTAAAAGAGTATATGCAGACTGCATT
1 TAGGTAAAAGAGTATATGCAAACTCCATT
*
30897919 TAGGTAAAAGAGTATCTGCAAACTCCATT
1 TAGGTAAAAGAGTATATGCAAACTCCATT
30897948 TAGGTAAAA
1 TAGGTAAAA
30897957 CACTCGACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (29 bp):
TAGGTAAAAGAGTATATGCAAACTCCATT
Found at i:30898372 original size:9 final size:9
Alignment explanation
Indices: 30898355--30898444 Score: 83
Period size: 9 Copynumber: 10.0 Consensus size: 9
30898345 CACCCCACCC
*
30898355 ATCGATTAA
1 ATCGGTTAA
30898364 ATCGGTTAA
1 ATCGGTTAA
*
30898373 GTCGGTTAA
1 ATCGGTTAA
*
30898382 GTCGGTTAA
1 ATCGGTTAA
* *
30898391 TTTGGTTAA
1 ATCGGTTAA
*
30898400 ATTGGTTAA
1 ATCGGTTAA
*
30898409 ATTGAG-TAA
1 ATCG-GTTAA
*
30898418 ATCAGTTAA
1 ATCGGTTAA
*
30898427 ATAGGTTAA
1 ATCGGTTAA
30898436 ATCGGTTAA
1 ATCGGTTAA
30898445 TTATTAACCA
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
8 1 0.01
9 67 0.97
10 1 0.01
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.37
Consensus pattern (9 bp):
ATCGGTTAA
Found at i:30899005 original size:75 final size:75
Alignment explanation
Indices: 30898882--30899034 Score: 306
Period size: 75 Copynumber: 2.0 Consensus size: 75
30898872 GAGAGATTTT
30898882 AGGAGAAAATCAAGGAGTTTGAGAGTGAGGGGGAAGTGTGTCGTTTGGGGGTAATTCAACTTGGA
1 AGGAGAAAATCAAGGAGTTTGAGAGTGAGGGGGAAGTGTGTCGTTTGGGGGTAATTCAACTTGGA
30898947 AAAATGGTCA
66 AAAATGGTCA
30898957 AGGAGAAAATCAAGGAGTTTGAGAGTGAGGGGGAAGTGTGTCGTTTGGGGGTAATTCAACTTGGA
1 AGGAGAAAATCAAGGAGTTTGAGAGTGAGGGGGAAGTGTGTCGTTTGGGGGTAATTCAACTTGGA
30899022 AAAATGGTCA
66 AAAATGGTCA
30899032 AGG
1 AGG
30899035 GAAGGGTTTT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 78 1.00
ACGTcount: A:0.32, C:0.07, G:0.38, T:0.24
Consensus pattern (75 bp):
AGGAGAAAATCAAGGAGTTTGAGAGTGAGGGGGAAGTGTGTCGTTTGGGGGTAATTCAACTTGGA
AAAATGGTCA
Found at i:30900095 original size:27 final size:27
Alignment explanation
Indices: 30900051--30900433 Score: 355
Period size: 27 Copynumber: 14.2 Consensus size: 27
30900041 CTTGGGCCAA
* *
30900051 AAAATTACCGAAATACCCTCGAAGGGT
1 AAAATTATCGAAATACCCTCAAAGGGT
* * * * *
30900078 AAAATTACCAAAAAACCCTTAAAGAGT
1 AAAATTATCGAAATACCCTCAAAGGGT
* *
30900105 AAAATTATCGAAATACCCCCGAAGGGT
1 AAAATTATCGAAATACCCTCAAAGGGT
* * *
30900132 TAAATTATCAAAATACCCTAAAAGGGT
1 AAAATTATCGAAATACCCTCAAAGGGT
* *
30900159 AAAATTATTGAAATA-CCTTAAAGGGT
1 AAAATTATCGAAATACCCTCAAAGGGT
* *
30900185 AAAATTACCAAAAT-CCCTCCCAAAGGGT
1 AAAATTATCGAAATACCCT--CAAAGGGT
* **
30900213 AAAATTATCGAAATACCTTTGAAGGGT
1 AAAATTATCGAAATACCCTCAAAGGGT
* *
30900240 AAAATTACCGAAATACCTTCGAAA-GGT
1 AAAATTATCGAAATACCCTC-AAAGGGT
* * *
30900267 AAAAATATTGAAATACCCTCGAAGGGT
1 AAAATTATCGAAATACCCTCAAAGGGT
* * *
30900294 AAAATTATCGAAATACCCTCGAGGGGA
1 AAAATTATCGAAATACCCTCAAAGGGT
*
30900321 AAAATTATC-AATATCCCCTCAAAGGGT
1 AAAATTATCGAA-ATACCCTCAAAGGGT
* *
30900348 AAAACTATCGAAATACCCTCTAAGGGT
1 AAAATTATCGAAATACCCTCAAAGGGT
* *
30900375 GAAATTA-CTAAAATACCCTCAAAGGGT
1 AAAATTATC-GAAATACCCTCAAAGGGT
* * *
30900402 AAAATGACCGAAATACCGCT-ATAGGGT
1 AAAATTATCGAAATACC-CTCAAAGGGT
30900429 AAAAT
1 AAAAT
30900434 GACTGTTATG
Statistics
Matches: 288, Mismatches: 57, Indels: 22
0.78 0.16 0.06
Matches are distributed among these distances:
26 29 0.10
27 230 0.80
28 26 0.09
29 3 0.01
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.22
Consensus pattern (27 bp):
AAAATTATCGAAATACCCTCAAAGGGT
Found at i:30900623 original size:27 final size:25
Alignment explanation
Indices: 30900586--30900650 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 25
30900576 AGGGGAAGTG
*
30900586 TACTATACTGGTGGCTATGCCACATA
1 TACTATACTGGCGGCTATGCCACA-A
**
30900612 TACTGATACTGGCGGCTATGCTGCAA
1 TACT-ATACTGGCGGCTATGCCACAA
30900638 TACTAATACTGGC
1 TACT-ATACTGGC
30900651 AGTTATGCTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 17 0.50
27 17 0.50
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (25 bp):
TACTATACTGGCGGCTATGCCACAA
Found at i:30900640 original size:26 final size:26
Alignment explanation
Indices: 30900611--30900688 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 26
30900601 TATGCCACAT
*
30900611 ATACTGATACTGGCGGCTATGCTGCA
1 ATACTGATACTGGCAGCTATGCTGCA
* * **
30900637 ATACTAATACTGGCAGTTATGCTGTG
1 ATACTGATACTGGCAGCTATGCTGCA
* * *
30900663 ATACTGTTACTGACAGCTCTGCTGCA
1 ATACTGATACTGGCAGCTATGCTGCA
30900689 TTATTATTAC
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (26 bp):
ATACTGATACTGGCAGCTATGCTGCA
Found at i:30900712 original size:52 final size:52
Alignment explanation
Indices: 30900611--30900717 Score: 117
Period size: 52 Copynumber: 2.1 Consensus size: 52
30900601 TATGCCACAT
* * *
30900611 ATACTGATACTGGCGGCTATGCTGCAATACTAATACTGGCAGTTATGCTGTG
1 ATACTGATACTGACAGCTATGCTGCAATACTAATACTGGCAGTTATGCTGCG
* * * * * *
30900663 ATACTGTTACTGACAGCTCTGCTGCATTATTATTACTGGTAGCTT-TGCTGCG
1 ATACTGATACTGACAGCTATGCTGCAATACTAATACTGGCAG-TTATGCTGCG
30900715 ATA
1 ATA
30900718 TTGGTGTGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
52 43 0.96
53 2 0.04
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (52 bp):
ATACTGATACTGACAGCTATGCTGCAATACTAATACTGGCAGTTATGCTGCG
Found at i:30900895 original size:30 final size:29
Alignment explanation
Indices: 30900826--30900936 Score: 109
Period size: 30 Copynumber: 3.8 Consensus size: 29
30900816 TTTGTACTGA
* *
30900826 TTACTGTTTTGGGCTAAGGCCCACA-CTG
1 TTACTGTATTGGGCTAAGGCCCACACCTC
*
30900854 TTACTGAATTGGGCTAAGGCCCACACTCTC
1 TTACTGTATTGGGCTAAGGCCCACAC-CTC
* *
30900884 TTACTGTATTGGGCTATGACCCACACACTGC
1 TTACTGTATTGGGCTAAGGCCCACAC-CT-C
** *
30900915 -TACTGTATAAGGCTCAGGCCCA
1 TTACTGTATTGGGCTAAGGCCCA
30900937 GACTGATTCT
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
28 23 0.34
30 44 0.65
31 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.28
Consensus pattern (29 bp):
TTACTGTATTGGGCTAAGGCCCACACCTC
Found at i:30907238 original size:27 final size:27
Alignment explanation
Indices: 30907207--30907565 Score: 357
Period size: 27 Copynumber: 13.1 Consensus size: 27
30907197 TGGCCGAATA
* *
30907207 CTCGAAGGGTAAAATTATCGAAGTACA
1 CTCGAAGGGTAAAATTATCGAAATACC
* *
30907234 TTCGAAGGGTAAAATTA-CTAAAATACC
1 CTCGAAGGGTAAAATTATC-GAAATACC
* *
30907261 CTCAAAGGATAAAATTATCGAAATACC
1 CTCGAAGGGTAAAATTATCGAAATACC
* *
30907288 CTAGAAGGGTAAAATTATCGATATACC
1 CTCGAAGGGTAAAATTATCGAAATACC
* *
30907315 CTCGAAGGGTAAAATTATCGATATATC
1 CTCGAAGGGTAAAATTATCGAAATACC
* * * *
30907342 CTCAAAGGGTAAAATGACCAAAATACC
1 CTCGAAGGGTAAAATTATCGAAATACC
*
30907369 CTCGAAGGGTAAAATAATCGAAATACC
1 CTCGAAGGGTAAAATTATCGAAATACC
* * *
30907396 C-CTATAGGGTAAAATGATTGAAATACC
1 CTCGA-AGGGTAAAATTATCGAAATACC
*
30907423 CTCGAAGGGTAAAA-TAACTGAAATACC
1 CTCGAAGGGTAAAATTATC-GAAATACC
*
30907450 CTCGAAGGGTAAGGGTAAAATTATCGATATACC
1 CTC-----G-AAGGGTAAAATTATCGAAATACC
* *
30907483 CTTGAAGGGTAAAATTATAGAAATACC
1 CTCGAAGGGTAAAATTATCGAAATACC
* *
30907510 CCCAAAGGGTAAAATTA-CTGAAATACC
1 CTCGAAGGGTAAAATTATC-GAAATACC
* * *
30907537 TTCGAAGGGTAAAATGATCGAAACACC
1 CTCGAAGGGTAAAATTATCGAAATACC
30907564 CT
1 CT
30907566 TATAAGGTAA
Statistics
Matches: 272, Mismatches: 46, Indels: 28
0.79 0.13 0.08
Matches are distributed among these distances:
26 4 0.01
27 240 0.88
28 5 0.02
32 1 0.00
33 19 0.07
34 3 0.01
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (27 bp):
CTCGAAGGGTAAAATTATCGAAATACC
Found at i:30907469 original size:33 final size:33
Alignment explanation
Indices: 30907427--30907494 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
30907417 AATACCCTCG
30907427 AAGGGTAAAATAA-CTGAAATACCCTCGAAGGGT
1 AAGGGTAAAATAATC-GAAATACCCTCGAAGGGT
* * *
30907460 AAGGGTAAAATTATCGATATACCCTTGAAGGGT
1 AAGGGTAAAATAATCGAAATACCCTCGAAGGGT
30907493 AA
1 AA
30907495 AATTATAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.22
Consensus pattern (33 bp):
AAGGGTAAAATAATCGAAATACCCTCGAAGGGT
Found at i:30907591 original size:27 final size:27
Alignment explanation
Indices: 30907561--30907613 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
30907551 TGATCGAAAC
* *
30907561 ACCCTTATAAGGTAAAATGACTGTTAG
1 ACCCTTAGAAGATAAAATGACTGTTAG
* *
30907588 ACCCTTAGGAGATGAAATGACTGTTA
1 ACCCTTAGAAGATAAAATGACTGTTA
30907614 TGGCCTTATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (27 bp):
ACCCTTAGAAGATAAAATGACTGTTAG
Found at i:30907881 original size:26 final size:26
Alignment explanation
Indices: 30907780--30907881 Score: 93
Period size: 26 Copynumber: 3.9 Consensus size: 26
30907770 CATATACTAA
*
30907780 TACTGGC-GTCTATGCTGCGATACTGA-
1 TACTGGCAG-CTATGCTGCGATA-TTAT
* * *
30907806 TACTGGCAGCTATACTGTGATACTAT
1 TACTGGCAGCTATGCTGCGATATTAT
* *
30907832 TACTGGCAACTCTGCTGC-ATTATTAT
1 TACTGGCAGCTATGCTGCGA-TATTAT
*
30907858 TACTGGCAGCTTTGCTGCGATATT
1 TACTGGCAGCTATGCTGCGATATT
30907882 GATGTGTTAG
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
25 2 0.03
26 57 0.93
27 2 0.03
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (26 bp):
TACTGGCAGCTATGCTGCGATATTAT
Found at i:30908082 original size:30 final size:30
Alignment explanation
Indices: 30907988--30908084 Score: 135
Period size: 30 Copynumber: 3.3 Consensus size: 30
30907978 TTTGTATTGA
*
30907988 TTACTGTTTTGGGCTAAGG-CC-CACACTG
1 TTACTGTATTGGGCTAAGGCCCACACACTG
* *
30908016 TTACTGAATTGGGCTAAGGCCCACACTCTG
1 TTACTGTATTGGGCTAAGGCCCACACACTG
*
30908046 TTACTGTATTGGGCTATGGCCCACACACTG
1 TTACTGTATTGGGCTAAGGCCCACACACTG
*
30908076 CTACTGTAT
1 TTACTGTAT
30908085 AAGGCTCAAG
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
28 17 0.28
29 2 0.03
30 41 0.68
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.31
Consensus pattern (30 bp):
TTACTGTATTGGGCTAAGGCCCACACACTG
Found at i:30910607 original size:23 final size:24
Alignment explanation
Indices: 30910571--30910616 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 24
30910561 TTGAGATTTG
30910571 TATATTTTGATTGAC-ATCTTTTGAC
1 TATATTTT-ATTGACTAT-TTTTGAC
30910596 TATATTTT-TTGACTATTTTTG
1 TATATTTTATTGACTATTTTTG
30910617 TCCAACTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 10 0.50
24 2 0.10
25 8 0.40
ACGTcount: A:0.22, C:0.09, G:0.11, T:0.59
Consensus pattern (24 bp):
TATATTTTATTGACTATTTTTGAC
Found at i:30916613 original size:10 final size:10
Alignment explanation
Indices: 30916598--30916640 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
30916588 TAACATGTTG
30916598 AATTTTAATT
1 AATTTTAATT
*
30916608 AATTTTATATCA
1 AATTTTA-AT-T
30916620 AATTTTAATT
1 AATTTTAATT
*
30916630 AATTTTTATT
1 AATTTTAATT
30916640 A
1 A
30916641 TATTCGACAG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 17 0.61
11 4 0.14
12 7 0.25
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (10 bp):
AATTTTAATT
Found at i:30925114 original size:183 final size:183
Alignment explanation
Indices: 30924806--30925170 Score: 685
Period size: 183 Copynumber: 2.0 Consensus size: 183
30924796 GTAAAAAGTG
30924806 AAAAAGTTGAGTTCTACATGTTAGAAGTGTCCAATCGTTATGAAATTTTAAATTGGAGGTCTTTA
1 AAAAAGTTGAGTTCTACATGTTAGAAGTGTCCAATCGTTATGAAATTTTAAATTGGAGGTCTTTA
*
30924871 TATGGTAATTATACCATTGGTTAAGTTATGGACAAAAATGGACATGAGATAAGTGAAATAGGAAA
66 TATGGTAATTAGACCATTGGTTAAGTTATGGACAAAAATGGACATGAGATAAGTGAAATAGGAAA
*
30924936 TTTTTAAGTTAGGGGCATTTTGGTAATTCGGTAATTAAAATGAATTAAAAGGA
131 TTTTAAAGTTAGGGGCATTTTGGTAATTCGGTAATTAAAATGAATTAAAAGGA
30924989 AAAAAGTTGAGTTCTACATGTTAGAAGTGTCCAATCGTTATGAAATTTTAAATTGGAGGTCTTTA
1 AAAAAGTTGAGTTCTACATGTTAGAAGTGTCCAATCGTTATGAAATTTTAAATTGGAGGTCTTTA
* *
30925054 TATGGTAATTAGACCATTGGTTAAGTTATTGACAAAAGTGGACATGAGATAAGTGAAATAGGAAA
66 TATGGTAATTAGACCATTGGTTAAGTTATGGACAAAAATGGACATGAGATAAGTGAAATAGGAAA
*
30925119 TTTTAAATTTAGGGGCATTTTGGTAATTCGGTAATTAAAATGAATTAAAAGG
131 TTTTAAAGTTAGGGGCATTTTGGTAATTCGGTAATTAAAATGAATTAAAAGG
30925171 GATAAAGATG
Statistics
Matches: 177, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
183 177 1.00
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.34
Consensus pattern (183 bp):
AAAAAGTTGAGTTCTACATGTTAGAAGTGTCCAATCGTTATGAAATTTTAAATTGGAGGTCTTTA
TATGGTAATTAGACCATTGGTTAAGTTATGGACAAAAATGGACATGAGATAAGTGAAATAGGAAA
TTTTAAAGTTAGGGGCATTTTGGTAATTCGGTAATTAAAATGAATTAAAAGGA
Found at i:30926118 original size:50 final size:49
Alignment explanation
Indices: 30926064--30926257 Score: 201
Period size: 50 Copynumber: 3.9 Consensus size: 49
30926054 CATTGAGATT
* *
30926064 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGAC
* * * * *
30926114 ATGAGAGGCCCCCTGTAAGACCATGTTTGGGACATGGCATGGGCACTGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAC-GAC
** * * *
30926164 ATGAGAACTCCCATGTAAGACCATATCTGAGATATGGCATTGGCA-GTAC
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACG-AC
* * ** *
30926213 AAGAAACTTCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
30926258 TGTTATTATC
Statistics
Matches: 118, Mismatches: 24, Indels: 5
0.80 0.16 0.03
Matches are distributed among these distances:
48 1 0.01
49 39 0.33
50 78 0.66
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (49 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACGAC
Found at i:30928656 original size:25 final size:29
Alignment explanation
Indices: 30928600--30928662 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
30928590 TGACATTCAC
30928600 TCTCTCAAATATTTCACATACAAAAAATA
1 TCTCTCAAATATTTCACATACAAAAAATA
30928629 TCTCTCAAATATTTCA-A-A-AAAAAA-A
1 TCTCTCAAATATTTCACATACAAAAAATA
30928654 TCTCTCAAA
1 TCTCTCAAA
30928663 AAAAATTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
25 10 0.29
26 6 0.18
27 1 0.03
28 1 0.03
29 16 0.47
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (29 bp):
TCTCTCAAATATTTCACATACAAAAAATA
Found at i:30934843 original size:68 final size:65
Alignment explanation
Indices: 30934698--30934888 Score: 164
Period size: 68 Copynumber: 2.9 Consensus size: 65
30934688 ACTTAATCAT
* *
30934698 TTTAATATTAAATTAATATAATATTTATCT-T--GATAAATATTAGATTAAATTTAATATTAAAT
1 TTTAATATTAAATTAA-AT--T-TTTATCTATAAGATAAATATTAAATTAAATTTAATATTAAAA
**
30934760 CTTA
62 CCAA
*
30934764 -TTAA-AAT-AATTAAATTTTTATCTATAAGATAAATATTAAATTAAATTTAATATTGAGATAAC
1 TTTAATATTAAATTAAATTTTTATCTATAAGATAAATATTAAATTAAATTTAATATT-A-A-AAC
30934826 CAA
63 CAA
*** *
30934829 TTTAATATTAAATT-AA-TAAAATACTATTAAGATAAGTATTAAATTAAATTTAATATTAAA
1 TTTAATATTAAATTAAATTTTTAT-CTA-TAAGATAAATATTAAATTAAATTTAATATTAAA
30934889 CTATCAAATT
Statistics
Matches: 104, Mismatches: 10, Indels: 23
0.76 0.07 0.17
Matches are distributed among these distances:
59 7 0.07
60 2 0.02
62 28 0.27
63 7 0.07
64 3 0.03
65 8 0.08
66 8 0.08
67 8 0.08
68 33 0.32
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (65 bp):
TTTAATATTAAATTAAATTTTTATCTATAAGATAAATATTAAATTAAATTTAATATTAAAACCAA
Found at i:30940451 original size:67 final size:72
Alignment explanation
Indices: 30940378--30940518 Score: 211
Period size: 74 Copynumber: 2.0 Consensus size: 72
30940368 CTAACCTAAA
30940378 ACCTCACATACAC-AAGCA-T-AA-AA-TAAATTTACTTGACAATTTTTAACAATTCAAAAAGTT
1 ACCTCACATACACTAAGCACTAAACAAGTAAATTTACTTGACAATTTTTAACAATTCAAAAAGTT
30940438 AAAATTT
66 AAAATTT
* *
30940445 ACCTCACATACACTTAATCACTAAACCAAGTCAATTTACTTGACAATTTTTAACAATTCAAAAAG
1 ACCTCACATACAC-TAAGCACTAAA-CAAGTAAATTTACTTGACAATTTTTAACAATTCAAAAAG
30940510 TTAAAATTT
64 TTAAAATTT
30940519 TAGGGCGTTA
Statistics
Matches: 65, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
67 13 0.20
69 4 0.06
70 1 0.02
71 2 0.03
73 2 0.03
74 43 0.66
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.32
Consensus pattern (72 bp):
ACCTCACATACACTAAGCACTAAACAAGTAAATTTACTTGACAATTTTTAACAATTCAAAAAGTT
AAAATTT
Found at i:30940518 original size:37 final size:37
Alignment explanation
Indices: 30940402--30940518 Score: 107
Period size: 37 Copynumber: 3.2 Consensus size: 37
30940392 AGCATAAAAT
30940402 AAATTTACTTGACAATTTTTAACAATTCAAAAAGTTA
1 AAATTTACTTGACAATTTTTAACAATTCAAAAAGTTA
* * *** *
30940439 AAATTTACCTCACATACACTTAATC-ACT-AAACCAAG-T-
1 AAATTTACTTGACA-ATTTTTAA-CAATTCAAA--AAGTTA
*
30940476 CAATTTACTTGACAATTTTTAACAATTCAAAAAGTTA
1 AAATTTACTTGACAATTTTTAACAATTCAAAAAGTTA
30940513 AAATTT
1 AAATTT
30940519 TAGGGCGTTA
Statistics
Matches: 58, Mismatches: 14, Indels: 16
0.66 0.16 0.18
Matches are distributed among these distances:
35 4 0.07
36 8 0.14
37 34 0.59
38 8 0.14
39 4 0.07
ACGTcount: A:0.44, C:0.16, G:0.04, T:0.35
Consensus pattern (37 bp):
AAATTTACTTGACAATTTTTAACAATTCAAAAAGTTA
Found at i:30940738 original size:13 final size:12
Alignment explanation
Indices: 30940700--30940739 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 12
30940690 TATTCTATAT
*
30940700 AAATAAAAT-AA
1 AAATATAATAAA
30940711 AAATATAATAAA
1 AAATATAATAAA
30940723 AAATATTAATAAA
1 AAATA-TAATAAA
30940736 AAAT
1 AAAT
30940740 TTATCACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 8 0.31
12 7 0.27
13 11 0.42
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (12 bp):
AAATATAATAAA
Found at i:30950771 original size:14 final size:14
Alignment explanation
Indices: 30950741--30950806 Score: 59
Period size: 14 Copynumber: 4.8 Consensus size: 14
30950731 CACACATGTA
*
30950741 GTTCACACCT-AGAG
1 GTTCACACATAAG-G
30950755 GTTCACACATAAGG
1 GTTCACACATAAGG
*
30950769 GTTCACTCAAGTAA-G
1 GTTCACAC-A-TAAGG
30950784 G-TCACACAT-AGG
1 GTTCACACATAAGG
30950796 GTTCACACATA
1 GTTCACACATA
30950807 TAGATTTTGC
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
11 1 0.02
12 3 0.07
13 9 0.21
14 22 0.51
15 5 0.12
16 3 0.07
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (14 bp):
GTTCACACATAAGG
Found at i:30950771 original size:41 final size:41
Alignment explanation
Indices: 30950726--30950806 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
30950716 TACATAAGTG
* * *
30950726 GGGTTCACACATGT-AGTTCACACCTAGAGGTTCACACATAA
1 GGGTTCACACAAGTAAGGTCACACATAG-GGTTCACACATAA
*
30950767 GGGTTCACTCAAGTAAGGTCACACATAGGGTTCACACATA
1 GGGTTCACACAAGTAAGGTCACACATAGGGTTCACACATA
30950807 TAGATTTTGC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 24 0.69
42 11 0.31
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.23
Consensus pattern (41 bp):
GGGTTCACACAAGTAAGGTCACACATAGGGTTCACACATAA
Found at i:30952457 original size:23 final size:23
Alignment explanation
Indices: 30952431--30952513 Score: 96
Period size: 23 Copynumber: 3.6 Consensus size: 23
30952421 TTTACATGAT
30952431 ATTTCCTATAGGGTTCGCATAAC
1 ATTTCCTATAGGGTTCGCATAAC
*
30952454 ATTTACTAT-GGGATTCGCATAAC
1 ATTTCCTATAGGG-TTCGCATAAC
* * * * *
30952477 AGTTCCTATACGGTTCACATGAT
1 ATTTCCTATAGGGTTCGCATAAC
30952500 ATTTCCTATAGGGT
1 ATTTCCTATAGGGT
30952514 AAACATATAC
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
22 3 0.06
23 44 0.90
24 2 0.04
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (23 bp):
ATTTCCTATAGGGTTCGCATAAC
Found at i:30952811 original size:23 final size:23
Alignment explanation
Indices: 30952775--30952869 Score: 102
Period size: 23 Copynumber: 4.1 Consensus size: 23
30952765 GGTTTATACA
*
30952775 ATAATAGTTCCTATAGGGTTCAC
1 ATAATAATTCCTATAGGGTTCAC
* * *
30952798 ATAACAATTACTATAGGGTTTAC
1 ATAATAATTCCTATAGGGTTCAC
**
30952821 ATAATAGA-TCCTATAGGGTTGGC
1 ATAATA-ATTCCTATAGGGTTCAC
* *
30952844 ATAATATTTCCTATAGGGTTCGC
1 ATAATAATTCCTATAGGGTTCAC
30952867 ATA
1 ATA
30952870 TACTCATTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
23 59 0.98
24 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (23 bp):
ATAATAATTCCTATAGGGTTCAC
Found at i:30952833 original size:46 final size:48
Alignment explanation
Indices: 30952761--30952863 Score: 129
Period size: 46 Copynumber: 2.2 Consensus size: 48
30952751 AACTAAGTCA
* *
30952761 TATAGGTTTATACAATAATAGTTCCTATAGGGTTCACATAACAATTAC
1 TATAGGGTTATACAATAATAGATCCTATAGGGTTCACATAACAATTAC
** * * *
30952809 TATAGGGTT-TAC-ATAATAGATCCTATAGGGTTGGCATAATATTTCC
1 TATAGGGTTATACAATAATAGATCCTATAGGGTTCACATAACAATTAC
30952855 TATAGGGTT
1 TATAGGGTT
30952864 CGCATATACT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
46 37 0.77
47 3 0.06
48 8 0.17
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (48 bp):
TATAGGGTTATACAATAATAGATCCTATAGGGTTCACATAACAATTAC
Found at i:30954445 original size:32 final size:32
Alignment explanation
Indices: 30954403--30954468 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
30954393 TTAATTTCAC
*
30954403 AAATCGAACCAAAACACGTTATTATATCAAGT
1 AAATCAAACCAAAACACGTTATTATATCAAGT
30954435 AAATCAAACCAAAACACGTTATTATATCAAGT
1 AAATCAAACCAAAACACGTTATTATATCAAGT
30954467 AA
1 AA
30954469 GTTTCGTTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.50, C:0.18, G:0.08, T:0.24
Consensus pattern (32 bp):
AAATCAAACCAAAACACGTTATTATATCAAGT
Found at i:30955279 original size:17 final size:17
Alignment explanation
Indices: 30955238--30955272 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
30955228 GTAAGTTTTT
30955238 TTTCTTTCGTTTTATTC
1 TTTCTTTCGTTTTATTC
30955255 TTTCTTTCGTTTTATTC
1 TTTCTTTCGTTTTATTC
30955272 T
1 T
30955273 GTTTTTCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.06, C:0.17, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTCTTTCGTTTTATTC
Found at i:30970061 original size:21 final size:22
Alignment explanation
Indices: 30970035--30970090 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
30970025 AGTTTCCCCC
30970035 GTTTGCAGTGGCTATACAATT-
1 GTTTGCAGTGGCTATACAATTA
*
30970056 GTTTGCAGTGGCTATATAATTA
1 GTTTGCAGTGGCTATACAATTA
* *
30970078 ATTTGCAGCGGCT
1 GTTTGCAGTGGCT
30970091 CCATCTGCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
21 20 0.65
22 11 0.35
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.38
Consensus pattern (22 bp):
GTTTGCAGTGGCTATACAATTA
Found at i:30973946 original size:16 final size:16
Alignment explanation
Indices: 30973925--30973993 Score: 65
Period size: 16 Copynumber: 4.4 Consensus size: 16
30973915 TAAGTTAATA
30973925 TAAGAATATTAATTAT
1 TAAGAATATTAATTAT
*
30973941 TAAGAATATT-ATGAT
1 TAAGAATATTAATTAT
**
30973956 TTGGTTAA-ATTAA-TA-
1 TAAG--AATATTAATTAT
30973971 TAAGAATATTAATTAT
1 TAAGAATATTAATTAT
30973987 TAAGAAT
1 TAAGAAT
30973994 TTTATTAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
13 2 0.05
14 5 0.12
15 10 0.24
16 21 0.51
17 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (16 bp):
TAAGAATATTAATTAT
Found at i:30974332 original size:122 final size:121
Alignment explanation
Indices: 30973946--30974529 Score: 1010
Period size: 121 Copynumber: 4.8 Consensus size: 121
30973936 ATTATTAAGA
*
30973946 ATATTATGATTTG-GTTAAATTAATAT-AAGAATATTAATTATTAAGAATTTTATTAAATTATAT
1 ATATTATGATTTGAG-TAAATTAATATAAAGAATATTAATTATTAAGAATTTTTTTAAATTATAT
* * * *
30974009 TGTTCAATTAAAATATATTTAATCATATATTATGTTAATTTATATTTTACAGTATCAT
65 AGTTTAATTAAAATTTATTTAATAATA-ATTATGTTAATTTATATTTTACAGTATCAT
* *
30974067 ATATTATGATTTCAGTAAATTAATATAAAGAATATTAATTATTAAGAATTTTTTTAAAATATATA
1 ATATTATGATTTGAGTAAATTAATATAAAGAATATTAATTATTAAGAATTTTTTTAAATTATATA
30974132 GTTTAATTAAAATTTATTTAATAATAATTATGTTAATTTATATTTTACAGTATCAT
66 GTTTAATTAAAATTTATTTAATAATAATTATGTTAATTTATATTTTACAGTATCAT
*
30974188 ATATTATGATGTGAGTAAATTAATATAAAGAATATTAATTATTAAGAATTTTTTTAAATTATATA
1 ATATTATGATTTGAGTAAATTAATATAAAGAATATTAATTATTAAGAATTTTTTTAAATTATATA
30974253 GTTTAATTAAAATTTATTTAATAATAAATTATGTTAATTTATATTTTACAGTATCAT
66 GTTTAATTAAAATTTATTTAATAAT-AATTATGTTAATTTATATTTTACAGTATCAT
*
30974310 ATATTATGATTTGAGTAAATTAATATAAAGAATATTAATTATTAAGAATTTTATTAAATTATATA
1 ATATTATGATTTGAGTAAATTAATATAAAGAATATTAATTATTAAGAATTTTTTTAAATTATATA
30974375 GTTTAATTAAAATTTATTTAATAATAATTATGTTAATTTATATTTTACAGTATCAT
66 GTTTAATTAAAATTTATTTAATAATAATTATGTTAATTTATATTTTACAGTATCAT
* *
30974431 ATATTATGATTTCAGTAAATTAATATAAAGAATATTAATTATTAAGAATTTTTTTTAATTATATA
1 ATATTATGATTTGAGTAAATTAATATAAAGAATATTAATTATTAAGAATTTTTTTAAATTATATA
* *
30974496 TTTTAATTAAAATATATTTAATAATAATTATGTT
66 GTTTAATTAAAATTTATTTAATAATAATTATGTT
30974530 TAAATATGAT
Statistics
Matches: 443, Mismatches: 17, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
121 265 0.60
122 178 0.40
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.48
Consensus pattern (121 bp):
ATATTATGATTTGAGTAAATTAATATAAAGAATATTAATTATTAAGAATTTTTTTAAATTATATA
GTTTAATTAAAATTTATTTAATAATAATTATGTTAATTTATATTTTACAGTATCAT
Found at i:30974400 original size:243 final size:243
Alignment explanation
Indices: 30973946--30974529 Score: 1021
Period size: 243 Copynumber: 2.4 Consensus size: 243
30973936 ATTATTAAGA
*
30973946 ATATTATGATTTG-GTTAAATTAATAT-AAGAATATTAATTATTAAGAATTTTATTAAATTATAT
1 ATATTATGATTTGAG-TAAATTAATATAAAGAATATTAATTATTAAGAATTTTTTTAAATTATAT
* * * *
30974009 TGTTCAATTAAAATATATTTAATCATATATTATGTTAATTTATATTTTACAGTATCATATATTAT
65 AGTTTAATTAAAATATATTTAATAATAAATTATGTTAATTTATATTTTACAGTATCATATATTAT
*
30974074 GATTTCAGTAAATTAATATAAAGAATATTAATTATTAAGAATTTTTTTAAAATATATAGTTTAAT
130 GATTTCAGTAAATTAATATAAAGAATATTAATTATTAAGAATTTTATTAAAATATATAGTTTAAT
30974139 TAAAATTTATTTAATAATAATTATGTTAATTTATATTTTACAGTATCAT
195 TAAAATTTATTTAATAATAATTATGTTAATTTATATTTTACAGTATCAT
*
30974188 ATATTATGATGTGAGTAAATTAATATAAAGAATATTAATTATTAAGAATTTTTTTAAATTATATA
1 ATATTATGATTTGAGTAAATTAATATAAAGAATATTAATTATTAAGAATTTTTTTAAATTATATA
*
30974253 GTTTAATTAAAATTTATTTAATAATAAATTATGTTAATTTATATTTTACAGTATCATATATTATG
66 GTTTAATTAAAATATATTTAATAATAAATTATGTTAATTTATATTTTACAGTATCATATATTATG
* *
30974318 ATTTGAGTAAATTAATATAAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATT
131 ATTTCAGTAAATTAATATAAAGAATATTAATTATTAAGAATTTTATTAAAATATATAGTTTAATT
30974383 AAAATTTATTTAATAATAATTATGTTAATTTATATTTTACAGTATCAT
196 AAAATTTATTTAATAATAATTATGTTAATTTATATTTTACAGTATCAT
* *
30974431 ATATTATGATTTCAGTAAATTAATATAAAGAATATTAATTATTAAGAATTTTTTTTAATTATATA
1 ATATTATGATTTGAGTAAATTAATATAAAGAATATTAATTATTAAGAATTTTTTTAAATTATATA
*
30974496 TTTTAATTAAAATATATTTAATAAT-AATTATGTT
66 GTTTAATTAAAATATATTTAATAATAAATTATGTT
30974530 TAAATATGAT
Statistics
Matches: 325, Mismatches: 15, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
242 32 0.10
243 293 0.90
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.48
Consensus pattern (243 bp):
ATATTATGATTTGAGTAAATTAATATAAAGAATATTAATTATTAAGAATTTTTTTAAATTATATA
GTTTAATTAAAATATATTTAATAATAAATTATGTTAATTTATATTTTACAGTATCATATATTATG
ATTTCAGTAAATTAATATAAAGAATATTAATTATTAAGAATTTTATTAAAATATATAGTTTAATT
AAAATTTATTTAATAATAATTATGTTAATTTATATTTTACAGTATCAT
Found at i:30974742 original size:44 final size:45
Alignment explanation
Indices: 30974677--30974767 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
30974667 ACCTCTATTC
* * *
30974677 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
30974721 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
30974766 CA
1 CA
30974768 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:30974782 original size:17 final size:16
Alignment explanation
Indices: 30974748--30974811 Score: 119
Period size: 16 Copynumber: 3.9 Consensus size: 16
30974738 GATTAGCTAT
30974748 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
30974764 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
30974781 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
30974797 TACACCTCTAATCCA
1 TACACCTCTAATCCA
30974812 TAAATTTAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 31 0.66
17 16 0.34
ACGTcount: A:0.36, C:0.39, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:30974790 original size:33 final size:33
Alignment explanation
Indices: 30974748--30974810 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
30974738 GATTAGCTAT
30974748 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCCAA
30974781 TACACCTCTAATCCAATACACCTCTAATCC
1 TACACCTCTAATCCAATACACCTCTAATCC
30974811 ATAAATTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.35, C:0.40, G:0.00, T:0.25
Consensus pattern (33 bp):
TACACCTCTAATCCAATACACCTCTAATCCCAA
Found at i:30975588 original size:44 final size:45
Alignment explanation
Indices: 30975451--30975674 Score: 126
Period size: 44 Copynumber: 5.1 Consensus size: 45
30975441 GATGGCAAAT
*
30975451 CTTATCTTTCCAAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
1 CTTATCTTTCCTAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
* * * * * * *** **
30975496 CTTATC-TCCCTGAGCAGCAGT-GG-AGTA-AGTTGAAGACGGAAAAT
1 CTTATCTTTCCTAAG-A-TAGTGGGAAGCAGA-TTTAAGCCACCAAGC
30975540 CTTATCTTTCC-AAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
1 CTTATCTTTCCTAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
* * * * * * ** **
30975584 CTTATC--TCCGTGAGCAGCAGT-GG-AGTAGGTTGAAGACGGCAAAT
1 CTTATCTTTCC-TAAG-A-TAGTGGGAAGCAGATTTAAGCCACCAAGC
30975628 CTTATCTTT-CTAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
1 CTTATCTTTCCTAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
30975672 CTT
1 CTT
30975675 GCCCCCTTAA
Statistics
Matches: 121, Mismatches: 43, Indels: 31
0.62 0.22 0.16
Matches are distributed among these distances:
42 9 0.07
43 7 0.06
44 81 0.67
45 17 0.14
46 7 0.06
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.25
Consensus pattern (45 bp):
CTTATCTTTCCTAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
Found at i:30975598 original size:88 final size:88
Alignment explanation
Indices: 30975395--30975707 Score: 502
Period size: 88 Copynumber: 3.5 Consensus size: 88
30975385 CAGATCGGTG
* *
30975395 AAGCCACCAAGCCTTATGTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATGGCAAATCTTATCTTT
1 AAGCCACCAAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGACGGCAAATCTTATCTTT
30975460 CCAAAGATAGTGGGAAGCAGATTT
66 CC-AAGATAGTGGGAAGCAGATTT
* *
30975484 AAGCCACCAAGCCTTATCTCCCTGAGCAGCAGTGGAGTAAGTTGAAGACGGAAAATCTTATCTTT
1 AAGCCACCAAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGACGGCAAATCTTATCTTT
30975549 CCAAGATAGTGGGAAGCAGATTT
66 CCAAGATAGTGGGAAGCAGATTT
*
30975572 AAGCCACCAAGCCTTATCTCCGTGAGCAGCAGTGGAGTAGGTTGAAGACGGCAAATCTTATCTTT
1 AAGCCACCAAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGACGGCAAATCTTATCTTT
*
30975637 CTAAGATAGTGGGAAGCAGATTT
66 CCAAGATAGTGGGAAGCAGATTT
* * * * *
30975660 AAGCCACCAAGCCTT-GCCCCCTTAAGCAGCAGCGAAGTAGGTTGAAGA
1 AAGCCACCAAGCCTTATCTCCC-TGAGCAGCAGTGGAGTAGGTTGAAGA
30975708 TTACAAATCC
Statistics
Matches: 209, Mismatches: 14, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
87 3 0.01
88 143 0.68
89 63 0.30
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (88 bp):
AAGCCACCAAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGACGGCAAATCTTATCTTT
CCAAGATAGTGGGAAGCAGATTT
Found at i:30980560 original size:29 final size:29
Alignment explanation
Indices: 30980524--30980592 Score: 111
Period size: 29 Copynumber: 2.3 Consensus size: 29
30980514 AAATTGTTGT
30980524 GAAAATAAATCACGATGATAATATGTGTA
1 GAAAATAAATCACGATGATAATATGTGTA
*
30980553 GAAAATAAATCACGATGATATTATGTGTA
1 GAAAATAAATCACGATGATAATATGTGTA
*
30980582 GTAATATAAAT
1 G-AAAATAAAT
30980593 GCACCAAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
29 29 0.78
30 8 0.22
ACGTcount: A:0.48, C:0.06, G:0.16, T:0.30
Consensus pattern (29 bp):
GAAAATAAATCACGATGATAATATGTGTA
Found at i:30980813 original size:18 final size:19
Alignment explanation
Indices: 30980790--30980825 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
30980780 GGTTTGTAAT
30980790 CACATAAAAG-AATATGAA
1 CACATAAAAGTAATATGAA
*
30980808 CACATAAATGTAATATGA
1 CACATAAAAGTAATATGA
30980826 TAAAAATGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (19 bp):
CACATAAAAGTAATATGAA
Found at i:30982444 original size:44 final size:42
Alignment explanation
Indices: 30982331--30982486 Score: 120
Period size: 44 Copynumber: 3.6 Consensus size: 42
30982321 TTTTAGTCTA
* * * *
30982331 CTCCACTGCAACGTCAGGGAGATAATATTTGTTATA-TTCAGCCTG
1 CTCCACTGCAACTTCAGGGAGATAAGA-CT-TTA-ACTTCA-ACTG
* * *
30982376 CTCCACTGCGACTTTAGGGTGATAAGACTTATAACTTCAACTTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTT-TAACTTCAAC-TG
* * * *
30982420 CTCCACTGCAACTTCAGGGAGATAAG-GTTT-GCTATGATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTTAACT-TCAACTG
*
30982461 CTCTACTGCAACTTCAGGGAGATAAG
1 CTCCACTGCAACTTCAGGGAGATAAG
30982487 GTTTGCTATG
Statistics
Matches: 92, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
41 29 0.32
42 4 0.04
43 5 0.05
44 32 0.35
45 22 0.24
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (42 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTTAACTTCAACTG
Found at i:30982472 original size:41 final size:40
Alignment explanation
Indices: 30982417--30982527 Score: 159
Period size: 41 Copynumber: 2.7 Consensus size: 40
30982407 TAACTTCAAC
*
30982417 TTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGCTATGA
1 TTGCTCTACTGCAACTTCAGGGAGATAAGGTTTGCTATGA
30982457 TCTGCTCTACTGCAACTTCAGGGAGATAAGGTTTGCTATGA
1 T-TGCTCTACTGCAACTTCAGGGAGATAAGGTTTGCTATGA
* * * *
30982498 TTCACTTTACTGCAACTTTAGAGAGATAAG
1 TT-GCTCTACTGCAACTTCAGGGAGATAAG
30982528 ATATCTAATT
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
40 2 0.03
41 62 0.97
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.32
Consensus pattern (40 bp):
TTGCTCTACTGCAACTTCAGGGAGATAAGGTTTGCTATGA
Found at i:30982837 original size:44 final size:43
Alignment explanation
Indices: 30982681--30982841 Score: 119
Period size: 44 Copynumber: 3.7 Consensus size: 43
30982671 TAAGATTTGT
* **
30982681 TCTACTCCACTGCAACTTCAGAGAGATAAGGTTTATAACTTTAA
1 TCTACTCCACTGCAACTTCAGAGAGATAAGATCCATAAC-TTAA
* * * * *
30982725 TCTGA-TCTACTGCAACTTCAGATAGATAAGAGTTGC-TATCTCTGA
1 TCT-ACTCCACTGCAACTTCAGAGAGATAAGA--TCCATAACT-TAA
* * ** * *
30982770 TTTACACCACTAAAACTTTAGGGAGATAAGATCCATAACTTAAA
1 TCTACTCCACTGCAACTTCAGAGAGATAAGATCCATAACTT-AA
*
30982814 TCTACTCCACTGCAACTTCAGGGAGATA
1 TCTACTCCACTGCAACTTCAGAGAGATA
30982842 GGATTTGTAA
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
43 3 0.03
44 56 0.64
45 27 0.31
46 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (43 bp):
TCTACTCCACTGCAACTTCAGAGAGATAAGATCCATAACTTAA
Found at i:30982988 original size:45 final size:45
Alignment explanation
Indices: 30982892--30983122 Score: 279
Period size: 45 Copynumber: 5.2 Consensus size: 45
30982882 TTAGGGAAAC
* * * * * *
30982892 AAGATTTGCTATCTTTAGTCTGCTCTATTG-TACTTTAGGGAGAT
1 AAGACTTGCTATCTTTAGTCTGCTCCACTGCAACTTCAAGGAGAT
* *
30982936 AAGACTTGCTATCTTTAGTCCGCTCCACTGCAACTTCAGGGAGAT
1 AAGACTTGCTATCTTTAGTCTGCTCCACTGCAACTTCAAGGAGAT
* * *
30982981 TAGACTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAAGGAGAC
1 AAGACTTGCTATCTTTAGTCTGCTCCACTGCAACTTCAAGGAGAT
* * *
30983026 AAGACTTGGTATCTTCAGTCTGATCCACTGCAACTTCAAGGAGAT
1 AAGACTTGCTATCTTTAGTCTGCTCCACTGCAACTTCAAGGAGAT
** *
30983071 AA-ACTTG-TGGCTTTAATCTGCTCCACTGCAACTTCAAGGAGAT
1 AAGACTTGCTATCTTTAGTCTGCTCCACTGCAACTTCAAGGAGAT
*
30983114 AAGATTTGC
1 AAGACTTGC
30983123 AGCCTATCTT
Statistics
Matches: 163, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
43 33 0.20
44 35 0.21
45 95 0.58
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (45 bp):
AAGACTTGCTATCTTTAGTCTGCTCCACTGCAACTTCAAGGAGAT
Found at i:30982990 original size:89 final size:90
Alignment explanation
Indices: 30982870--30983158 Score: 271
Period size: 90 Copynumber: 3.2 Consensus size: 90
30982860 TTTAATATGT
* * * * * * * * * * *
30982870 TCCATTGCAACTTTAGGGAAACAAGATTTGCTATCTTTAGTCTGCTCTATTG-TACTTTAGGGAG
1 TCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAAGGAG
* * *
30982934 ATAAGACTTGCTATCTTTAGTCCGC
66 ACAAGACTTGCTATCTTCAGTCCGA
*
30982959 TCCACTGCAACTTCAGGGAGATTAGACTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAAGGAG
1 TCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAAGGAG
* *
30983024 ACAAGACTTGGTATCTTCAGTCTGA
66 ACAAGACTTGCTATCTTCAGTCCGA
* ** * *
30983049 TCCACTGCAACTTCAAGGAGATAA-ACTTG-TGGCTTTAATCTGCTCCACTGCAACTTCAAGGAG
1 TCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAAGGAG
* * *
30983112 ATAAGATTTGCAGCCTATCTTCAATCC-A
66 ACAAGACTT---G-CTATCTTCAGTCCGA
*
30983140 TCTTACTGCAACTTCAGGG
1 TC-CACTGCAACTTCAGGG
30983159 GCATGGGTAA
Statistics
Matches: 164, Mismatches: 30, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
88 37 0.23
89 48 0.29
90 51 0.31
91 4 0.02
92 24 0.15
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (90 bp):
TCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAAGGAG
ACAAGACTTGCTATCTTCAGTCCGA
Found at i:30983046 original size:134 final size:133
Alignment explanation
Indices: 30982870--30983122 Score: 301
Period size: 134 Copynumber: 1.9 Consensus size: 133
30982860 TTTAATATGT
* * * * * * * * * * *
30982870 TCCATTGCAACTTTAGGGAAACAAGATTTGCTATCTTTAGTCTGCTCTATTG-TACTTTAGGGAG
1 TCCACTGCAACTTCAAGGAAACAAGACTTGCTATCTTCAGTCTGATCCACTGCAACTTCAAGGAG
* * * *
30982934 ATAAGACTTGCTATCTTTAGTCCGCTCCACTGCAACTTCAGGGAGATTAGACTTGCTATCTTCAG
66 ATAA-ACTTG-TAGCTTTAATCCGCTCCACTGCAACTTCAAGGAGATAAGACTTGCTATCTTCAG
30982999 TCTGC
129 TCTGC
* *
30983004 TCCACTGCAACTTCAAGGAGACAAGACTTGGTATCTTCAGTCTGATCCACTGCAACTTCAAGGAG
1 TCCACTGCAACTTCAAGGAAACAAGACTTGCTATCTTCAGTCTGATCCACTGCAACTTCAAGGAG
* * *
30983069 ATAAACTTGTGGCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGC
66 ATAAACTTGTAGCTTTAATCCGCTCCACTGCAACTTCAAGGAGATAAGACTTGC
30983123 AGCCTATCTT
Statistics
Matches: 98, Mismatches: 20, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
133 38 0.39
134 47 0.48
135 13 0.13
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (133 bp):
TCCACTGCAACTTCAAGGAAACAAGACTTGCTATCTTCAGTCTGATCCACTGCAACTTCAAGGAG
ATAAACTTGTAGCTTTAATCCGCTCCACTGCAACTTCAAGGAGATAAGACTTGCTATCTTCAGTC
TGC
Found at i:30983060 original size:90 final size:89
Alignment explanation
Indices: 30982870--30983158 Score: 278
Period size: 89 Copynumber: 3.2 Consensus size: 89
30982860 TTTAATATGT
* * * * * * * * * *
30982870 TCCATTGCAACTTTAGGGAAACAAGATTTGCTATCTTTAGTCTGCTCTATTG-TACTTTAGGGAG
1 TCCACTGCAACTTCAGGGAGA-TAGACTTGCTATCTTTAGTCTGCTCCACTGCAACTTCAAGGAG
* *
30982934 ATAAGACTTGCTATCTTTAGTCCGC
65 ATAAGACTTGCTATCTTCAGTCCGA
*
30982959 TCCACTGCAACTTCAGGGAGATTAGACTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAAGGAG
1 TCCACTGCAACTTCAGGGAGA-TAGACTTGCTATCTTTAGTCTGCTCCACTGCAACTTCAAGGAG
* * *
30983024 ACAAGACTTGGTATCTTCAGTCTGA
65 ATAAGACTTGCTATCTTCAGTCCGA
* * ** *
30983049 TCCACTGCAACTTCAAGGAGATAAACTTG-TGGCTTTAATCTGCTCCACTGCAACTTCAAGGAGA
1 TCCACTGCAACTTCAGGGAGATAGACTTGCTATCTTTAGTCTGCTCCACTGCAACTTCAAGGAGA
* *
30983113 TAAGATTTGCAGCCTATCTTCAATCC-A
66 TAAGACTT---G-CTATCTTCAGTCCGA
*
30983140 TCTTACTGCAACTTCAGGG
1 TC-CACTGCAACTTCAGGG
30983159 GCATGGGTAA
Statistics
Matches: 164, Mismatches: 30, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
88 37 0.23
89 50 0.30
90 49 0.30
91 4 0.02
92 24 0.15
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (89 bp):
TCCACTGCAACTTCAGGGAGATAGACTTGCTATCTTTAGTCTGCTCCACTGCAACTTCAAGGAGA
TAAGACTTGCTATCTTCAGTCCGA
Found at i:30991487 original size:18 final size:18
Alignment explanation
Indices: 30991466--30991500 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30991456 GATGCAATTC
30991466 CAGAGACAGATACAAATA
1 CAGAGACAGATACAAATA
**
30991484 CAGATTCAGATACAAAT
1 CAGAGACAGATACAAAT
30991501 GCGGACACAA
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:0.51, C:0.17, G:0.14, T:0.17
Consensus pattern (18 bp):
CAGAGACAGATACAAATA
Found at i:30993143 original size:15 final size:14
Alignment explanation
Indices: 30993119--30993150 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
30993109 CCACTCTTGG
30993119 TTTCACTAACCCAA
1 TTTCACTAACCCAA
30993133 TTTCTACTAACCCAA
1 TTTC-ACTAACCCAA
30993148 TTT
1 TTT
30993151 TTGAGGTCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (14 bp):
TTTCACTAACCCAA
Found at i:30997207 original size:25 final size:25
Alignment explanation
Indices: 30997191--30997247 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
30997181 ATAGGTAGTA
30997191 TATACTGGGACTACTATAGATAGAC
1 TATACTGGGACTACTATAGATAGAC
* *
30997216 TGTACTGGGACTATTATAGATAGAC
1 TATACTGGGACTACTATAGATAGAC
30997241 TATACTG
1 TATACTG
30997248 AAAACACTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (25 bp):
TATACTGGGACTACTATAGATAGAC
Found at i:31003559 original size:12 final size:13
Alignment explanation
Indices: 31003533--31003566 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
31003523 ACTGATTGAT
31003533 ATTTTATGTCATG
1 ATTTTATGTCATG
31003546 ATTTTATG-CATG
1 ATTTTATGTCATG
31003558 ATTTTATGT
1 ATTTTATGT
31003567 TTTAGCATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.24, C:0.06, G:0.15, T:0.56
Consensus pattern (13 bp):
ATTTTATGTCATG
Found at i:31005300 original size:29 final size:29
Alignment explanation
Indices: 31005238--31005312 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
31005228 GTCATATGAC
* *
31005238 TGGCCGTGTGAGCCACACAAACGTGTGGT
1 TGGCTGTGTCAGCCACACAAACGTGTGGT
* *
31005267 TGGCTGTGTCAGCCACACAGATGTGTGGT
1 TGGCTGTGTCAGCCACACAAACGTGTGGT
* *
31005296 TGGCTATGTTAGCCACA
1 TGGCTGTGTCAGCCACA
31005313 TGGGCGTGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.20, C:0.23, G:0.32, T:0.25
Consensus pattern (29 bp):
TGGCTGTGTCAGCCACACAAACGTGTGGT
Found at i:31005321 original size:29 final size:29
Alignment explanation
Indices: 31005248--31005327 Score: 97
Period size: 29 Copynumber: 2.8 Consensus size: 29
31005238 TGGCCGTGTG
* *
31005248 AGCCACACAAACGTGTGGTTGGCTGTGTC
1 AGCCACACAGACGTGTGGTTGGCTATGTC
* *
31005277 AGCCACACAGATGTGTGGTTGGCTATGTT
1 AGCCACACAGACGTGTGGTTGGCTATGTC
** *
31005306 AGCCACATGGGCGTGTGGTTGG
1 AGCCACACAGACGTGTGGTTGG
31005328 ACATGTAGGC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.19, C:0.20, G:0.35, T:0.26
Consensus pattern (29 bp):
AGCCACACAGACGTGTGGTTGGCTATGTC
Found at i:31010191 original size:23 final size:25
Alignment explanation
Indices: 31010158--31010215 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
31010148 ATAATTTTTT
31010158 AATATTATTTA-ATAA-G-TTTTAAA
1 AATATTATTTATA-AATGTTTTTAAA
*
31010181 AATATTTTTTATAAATGTTTTTAAA
1 AATATTATTTATAAATGTTTTTAAA
*
31010206 AATAATATTT
1 AATATTATTT
31010216 TTTCAATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 12 0.41
24 2 0.07
25 15 0.52
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (25 bp):
AATATTATTTATAAATGTTTTTAAA
Found at i:31011203 original size:60 final size:60
Alignment explanation
Indices: 31011129--31011241 Score: 208
Period size: 60 Copynumber: 1.9 Consensus size: 60
31011119 ATACTAAATT
*
31011129 AAACACAACAATTTATAACATAATCTTAAATTACTAATAAATTAATTTTAAAACAATAAC
1 AAACACAACAATTTATAACATAATCTTAAATTACTAACAAATTAATTTTAAAACAATAAC
*
31011189 AAACACAACCATTTATAACATAATCTTAAATTACTAACAAATTAATTTTAAAA
1 AAACACAACAATTTATAACATAATCTTAAATTACTAACAAATTAATTTTAAAA
31011242 TAATTATAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (60 bp):
AAACACAACAATTTATAACATAATCTTAAATTACTAACAAATTAATTTTAAAACAATAAC
Found at i:31013459 original size:24 final size:24
Alignment explanation
Indices: 31013406--31013460 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
31013396 CTAAAGGCCC
*
31013406 ACACCTCCAAATGTACATCTGGTT
1 ACACCTCCAAATGTACATCTAGTT
** *
31013430 GTACCTCCAAATGTACATTTAGTT
1 ACACCTCCAAATGTACATCTAGTT
31013454 ACACCTC
1 ACACCTC
31013461 TGGCTGTACG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.29, G:0.11, T:0.31
Consensus pattern (24 bp):
ACACCTCCAAATGTACATCTAGTT
Found at i:31017701 original size:18 final size:18
Alignment explanation
Indices: 31017678--31017737 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
31017668 CTGCCCCTTC
31017678 TTCCTCACCTACATCTTT
1 TTCCTCACCTACATCTTT
*
31017696 TTCCTCGA-CTAC-CCTTT
1 TTCCTC-ACCTACATCTTT
*
31017713 CTTCCTCACCTACATCTTC
1 -TTCCTCACCTACATCTTT
31017732 TTCCTC
1 TTCCTC
31017738 TGTCGTATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
17 5 0.14
18 26 0.74
19 4 0.11
ACGTcount: A:0.13, C:0.43, G:0.02, T:0.42
Consensus pattern (18 bp):
TTCCTCACCTACATCTTT
Found at i:31020448 original size:22 final size:21
Alignment explanation
Indices: 31020418--31020477 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
31020408 ATAAAAAATA
*
31020418 TCTTCAATGAGCTCAAGATAAG
1 TCTTAAATG-GCTCAAGATAAG
* *
31020440 TCTTAAAT-GTTCAAGATATG
1 TCTTAAATGGCTCAAGATAAG
*
31020460 TCTTAAAT-GTTCAAGATA
1 TCTTAAATGGCTCAAGATA
31020478 TGCTTCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
20 28 0.80
22 7 0.20
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (21 bp):
TCTTAAATGGCTCAAGATAAG
Found at i:31020478 original size:20 final size:20
Alignment explanation
Indices: 31020430--31020479 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
31020420 TTCAATGAGC
*
31020430 TCAAGATAAGTCTTAAATGT
1 TCAAGATATGTCTTAAATGT
31020450 TCAAGATATGTCTTAAATGT
1 TCAAGATATGTCTTAAATGT
31020470 TCAAGATATG
1 TCAAGATATG
31020480 CTTCAAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (20 bp):
TCAAGATATGTCTTAAATGT
Found at i:31026816 original size:21 final size:22
Alignment explanation
Indices: 31026783--31026823 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
31026773 ATGAATACGG
* *
31026783 GGTATTAGTGTTAC-ATTTAAT
1 GGTATCAGAGTTACGATTTAAT
31026804 GGTATCAGAGTTACGATTTA
1 GGTATCAGAGTTACGATTTA
31026824 GTCAGTTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.41
Consensus pattern (22 bp):
GGTATCAGAGTTACGATTTAAT
Found at i:31033893 original size:25 final size:22
Alignment explanation
Indices: 31033840--31033883 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
31033830 CATATTAGAG
*
31033840 TGTAGTTTAACCACCAATGGTT
1 TGTAGATTAACCACCAATGGTT
*
31033862 TGTAGATTAACTACCAATGGTT
1 TGTAGATTAACCACCAATGGTT
31033884 GTGGATAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (22 bp):
TGTAGATTAACCACCAATGGTT
Found at i:31035086 original size:18 final size:18
Alignment explanation
Indices: 31035063--31035109 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
31035053 TTCTTGTCGA
31035063 AAAATAATTAATTTTTAC
1 AAAATAATTAATTTTTAC
31035081 AAAATAATTAATTTTTAC
1 AAAATAATTAATTTTTAC
31035099 AAAATAATTAA
1 AAAATAATTAA
31035110 AGTGCACTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATAATTAATTTTTAC
Found at i:31041496 original size:19 final size:19
Alignment explanation
Indices: 31041472--31041512 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
31041462 TTTATTTTTA
* *
31041472 AATTAGAATCGAAAAGTTT
1 AATTAGAATAGAAAAGTAT
31041491 AATTAGAATAGAAAAGTAT
1 AATTAGAATAGAAAAGTAT
31041510 AAT
1 AAT
31041513 AAAAGTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.02, G:0.15, T:0.29
Consensus pattern (19 bp):
AATTAGAATAGAAAAGTAT
Found at i:31042455 original size:27 final size:27
Alignment explanation
Indices: 31042412--31042529 Score: 123
Period size: 27 Copynumber: 4.4 Consensus size: 27
31042402 ATCTGGACCA
*
31042412 AAATACCCCCATAGGGTAAAATGACTG
1 AAATACCCCTATAGGGTAAAATGACTG
* * *
31042439 TAATGCCCCTGTAGGGTAAAATGACTG
1 AAATACCCCTATAGGGTAAAATGACTG
* * * *
31042466 AAATACCCCCATAGGGAAAAATAACCG
1 AAATACCCCTATAGGGTAAAATGACTG
31042493 AAATA-CCCTCATAGGGTAAAATGA-TCG
1 AAATACCCCT-ATAGGGTAAAATGACT-G
*
31042520 TAATACCCCT
1 AAATACCCCT
31042530 GTGTGGGTTG
Statistics
Matches: 72, Mismatches: 16, Indels: 5
0.77 0.17 0.05
Matches are distributed among these distances:
26 3 0.04
27 65 0.90
28 4 0.06
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (27 bp):
AAATACCCCTATAGGGTAAAATGACTG
Found at i:31042528 original size:54 final size:54
Alignment explanation
Indices: 31042412--31042516 Score: 140
Period size: 54 Copynumber: 1.9 Consensus size: 54
31042402 ATCTGGACCA
* * * * * *
31042412 AAATACCCCCATAGGGTAAAATGACTGTAATGCCCCTGTAGGGTAAAATGACTG
1 AAATACCCCCATAGGGAAAAATAACCGAAATACCCCTATAGGGTAAAATGACTG
31042466 AAATACCCCCATAGGGAAAAATAACCGAAATA-CCCTCATAGGGTAAAATGA
1 AAATACCCCCATAGGGAAAAATAACCGAAATACCCCT-ATAGGGTAAAATGA
31042517 TCGTAATACC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
53 4 0.09
54 40 0.91
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (54 bp):
AAATACCCCCATAGGGAAAAATAACCGAAATACCCCTATAGGGTAAAATGACTG
Found at i:31042557 original size:21 final size:21
Alignment explanation
Indices: 31042533--31042576 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
31042523 TACCCCTGTG
*
31042533 TGGGTTGTTCGTGATATAAAT
1 TGGGATGTTCGTGATATAAAT
31042554 TGGGATGTTCGTGATATAAAT
1 TGGGATGTTCGTGATATAAAT
31042575 TG
1 TG
31042577 AATTGTGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.25, C:0.05, G:0.30, T:0.41
Consensus pattern (21 bp):
TGGGATGTTCGTGATATAAAT
Found at i:31045035 original size:25 final size:26
Alignment explanation
Indices: 31044985--31045036 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
31044975 TTTAAAACAC
*
31044985 AAAAATAAATACCAAAATGGGTTTAT
1 AAAAATAAATACCAAAATGGGATTAT
31045011 AAAAATAAATACCAAAAT-GGATTAT
1 AAAAATAAATACCAAAATGGGATTAT
31045036 A
1 A
31045037 TGCTTGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.58, C:0.08, G:0.10, T:0.25
Consensus pattern (26 bp):
AAAAATAAATACCAAAATGGGATTAT
Found at i:31045361 original size:51 final size:50
Alignment explanation
Indices: 31045300--31045397 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 50
31045290 GCACAAAAAA
*
31045300 ATACTAGTGCCACCCATCTCTCCCCCTCCACGCTTAAAAAATATATTTTTT
1 ATACTAGTGCCACCCATCTCTCCCCCTCCACCCTTAAAAAAT-TATTTTTT
* * * * * *
31045351 ATACTGGTGCCGCCCATTTCTCCCTCTCTACCCTTAAAATATTATTT
1 ATACTAGTGCCACCCATCTCTCCCCCTCCACCCTTAAAAAATTATTT
31045398 ATATTTTGTA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
50 5 0.12
51 35 0.88
ACGTcount: A:0.24, C:0.33, G:0.07, T:0.36
Consensus pattern (50 bp):
ATACTAGTGCCACCCATCTCTCCCCCTCCACCCTTAAAAAATTATTTTTT
Found at i:31051446 original size:18 final size:20
Alignment explanation
Indices: 31051407--31051446 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
31051397 AAAAATATTG
*
31051407 TATTTAATTTTTTTTCAATA
1 TATTTAATTTATTTTCAATA
31051427 TATTTAA-TTATTTT-AATA
1 TATTTAATTTATTTTCAATA
31051445 TA
1 TA
31051447 AGCTTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 6 0.32
20 7 0.37
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTAATTTATTTTCAATA
Found at i:31055515 original size:25 final size:25
Alignment explanation
Indices: 31055410--31055508 Score: 162
Period size: 25 Copynumber: 4.0 Consensus size: 25
31055400 CTCCAAGTTG
*
31055410 AATAACGGAAAGCTCATGCGAGCTA
1 AATAACGGGAAGCTCATGCGAGCTA
31055435 AATAACGGGAAGCTCATGCGAGCTA
1 AATAACGGGAAGCTCATGCGAGCTA
* *
31055460 AATAATGGGAAGCTCATGCGAGTTA
1 AATAACGGGAAGCTCATGCGAGCTA
*
31055485 AATAACAGGAAGCTCATGCGAGCT
1 AATAACGGGAAGCTCATGCGAGCT
31055509 TTATAACTGG
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 68 1.00
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.18
Consensus pattern (25 bp):
AATAACGGGAAGCTCATGCGAGCTA
Found at i:31055520 original size:25 final size:25
Alignment explanation
Indices: 31055410--31055521 Score: 147
Period size: 25 Copynumber: 4.5 Consensus size: 25
31055400 CTCCAAGTTG
31055410 AATAAC-GGAAAGCTCATGCGAGCTA
1 AATAACTGG-AAGCTCATGCGAGCTA
*
31055435 AATAACGGGAAGCTCATGCGAGCTA
1 AATAACTGGAAGCTCATGCGAGCTA
*
31055460 AATAA-TGGGAAGCTCATGCGAGTTA
1 AATAACT-GGAAGCTCATGCGAGCTA
* *
31055485 AATAACAGGAAGCTCATGCGAGCTT
1 AATAACTGGAAGCTCATGCGAGCTA
*
31055510 TATAACTGGAAG
1 AATAACTGGAAG
31055522 ATATGCAAGC
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
25 75 0.97
26 2 0.03
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.20
Consensus pattern (25 bp):
AATAACTGGAAGCTCATGCGAGCTA
Found at i:31055532 original size:24 final size:25
Alignment explanation
Indices: 31055486--31055532 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
31055476 TGCGAGTTAA
* *
31055486 ATAACAGGAAGCTCATGCGAGCTTT
1 ATAACAGGAAGATCATGCAAGCTTT
*
31055511 ATAACTGGAAGAT-ATGCAAGCT
1 ATAACAGGAAGATCATGCAAGCT
31055533 GTGGTGTGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.23
Consensus pattern (25 bp):
ATAACAGGAAGATCATGCAAGCTTT
Found at i:31056041 original size:8 final size:8
Alignment explanation
Indices: 31056028--31056053 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
31056018 GCCCACATAA
31056028 TTCACAAT
1 TTCACAAT
31056036 TTCACAAT
1 TTCACAAT
31056044 TTCACAAT
1 TTCACAAT
31056052 TT
1 TT
31056054 TACCATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (8 bp):
TTCACAAT
Found at i:31056723 original size:17 final size:15
Alignment explanation
Indices: 31056685--31056721 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
31056675 ATTGTTCTTT
31056685 TATTTTTCATTTATA
1 TATTTTTCATTTATA
31056700 TATTTTTCATTTATA
1 TATTTTTCATTTATA
31056715 TATTTTT
1 TATTTTT
31056722 TTATTTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTTTTCATTTATA
Found at i:31061933 original size:38 final size:36
Alignment explanation
Indices: 31061890--31062005 Score: 95
Period size: 28 Copynumber: 3.3 Consensus size: 36
31061880 CTTTCTAGCC
*
31061890 TCTGCCGATTTGCTCCCTCCGTTTCTTTTCTTTTATTT
1 TCTGCCGATTTGCTCCCT--GTTTCTTTTCTTTTCTTT
*
31061928 TCTGCC------CT--CTGTTTATTTTCTTTTCTTT
1 TCTGCCGATTTGCTCCCTGTTTCTTTTCTTTTCTTT
* *
31061956 TCTACCGATTTGCTCCCTTTGTTTCTTCTCATTTTCTTT
1 TCTGCCGATTTGCTCCC--TGTTTCTTTTC-TTTTCTTT
31061995 TCTGCCGATTT
1 TCTGCCGATTT
31062006 CCGAGTTAGT
Statistics
Matches: 61, Mismatches: 6, Indels: 21
0.69 0.07 0.24
Matches are distributed among these distances:
28 21 0.34
30 2 0.03
32 2 0.03
34 2 0.03
36 1 0.02
38 15 0.25
39 18 0.30
ACGTcount: A:0.06, C:0.28, G:0.09, T:0.57
Consensus pattern (36 bp):
TCTGCCGATTTGCTCCCTGTTTCTTTTCTTTTCTTT
Found at i:31064208 original size:8 final size:8
Alignment explanation
Indices: 31064195--31064221 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
31064185 AAAAGTTATA
31064195 TGCAAAGT
1 TGCAAAGT
31064203 TGCAAAGT
1 TGCAAAGT
31064211 TGCAAAGT
1 TGCAAAGT
31064219 TGC
1 TGC
31064222 GGTTTCTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (8 bp):
TGCAAAGT
Found at i:31064906 original size:16 final size:16
Alignment explanation
Indices: 31064885--31064926 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
31064875 TTATTAAATT
*
31064885 ATATATTTTAATTATA
1 ATATATTTTAATAATA
31064901 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
31064916 AT-TATGTTTAA
1 ATATAT-TTTAA
31064927 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:31064911 original size:15 final size:15
Alignment explanation
Indices: 31064876--31064917 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
31064866 TTAAGAATTT
*
31064876 TATTAAATTAT-ATA
1 TATTTAATTATAATA
31064890 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
31064904 TATTTAATAATAAT
1 TATTTAATTATAAT
31064918 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:31065063 original size:157 final size:162
Alignment explanation
Indices: 31064860--31065185 Score: 554
Period size: 166 Copynumber: 2.0 Consensus size: 162
31064850 ATAAGAATAT
31064860 TAATTATTAAGAATTTTATTAAATTATATA-T-TT-TAAT-TA-TAATATATTTAATAATAATTA
1 TAATTATTAAGAATTTTATTAAATTATATATTATTATAATATATTAATATATTTAATAATAATTA
*
31064920 TGTTTAAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAAT
66 TGTTTAAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAAT
*
31064985 AACAATAATAATTTACCAAAACAAATTTCTGC
131 AACAATAATAATTTACCAAAACAAATTTATGC
31065017 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATATATTTAATAATA
1 TAATTATTAAGAATTTTATTAAATTATATA--TT-ATTATAATATA-TTAATATATTTAATAATA
31065082 ATTATGTTTAAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAA
62 ATTATGTTTAAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAA
*
31065147 CAATAACAATAATCATTTACCAAAACAAATTTATGC
127 CAATAACAATAATAATTTACCAAAACAAATTTATGC
31065183 TAA
1 TAA
31065186 GGGTATTCTA
Statistics
Matches: 157, Mismatches: 3, Indels: 9
0.93 0.02 0.05
Matches are distributed among these distances:
157 30 0.19
160 1 0.01
162 2 0.01
163 4 0.03
164 2 0.01
166 118 0.75
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (162 bp):
TAATTATTAAGAATTTTATTAAATTATATATTATTATAATATATTAATATATTTAATAATAATTA
TGTTTAAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAAT
AACAATAATAATTTACCAAAACAAATTTATGC
Found at i:31065074 original size:25 final size:26
Alignment explanation
Indices: 31065042--31065096 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
31065032 TTATTAAATT
*
31065042 ATATATTTTAATTATAA-TATATTTA
1 ATATATTTTAATAATAATTATATTTA
*
31065067 ATATA-TTTAATAATAATTATGTTTA
1 ATATATTTTAATAATAATTATATTTA
31065092 A-ATAT
1 ATATAT
31065097 GATTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATATTTTAATAATAATTATATTTA
Found at i:31065318 original size:45 final size:43
Alignment explanation
Indices: 31065218--31065327 Score: 120
Period size: 45 Copynumber: 2.6 Consensus size: 43
31065208 TTTTCCATTA
31065218 TGCTATTACACCTCTATTC----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCATTACATTCAACCAAACACAAGAT
* * ***
31065257 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATT-CATTACATTCAACCAAACACAAGA-T
31065302 TGCTATTACACCTCTATTTCATTACA
1 TGCTATTACACCTCTA-TTCATTACA
31065328 CCTCTAATCC
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 22 0.39
46 2 0.04
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (43 bp):
TGCTATTACACCTCTATTCATTACATTCAACCAAACACAAGAT
Found at i:31065665 original size:14 final size:15
Alignment explanation
Indices: 31065633--31065666 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
31065623 AAAGAAAGGG
31065633 AGACAAGGCAGCGGC
1 AGACAAGGCAGCGGC
*
31065648 AGACAAGG-AGCTGC
1 AGACAAGGCAGCGGC
31065662 AGACA
1 AGACA
31065667 CATCAGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.38, C:0.24, G:0.35, T:0.03
Consensus pattern (15 bp):
AGACAAGGCAGCGGC
Found at i:31066202 original size:15 final size:16
Alignment explanation
Indices: 31066171--31066204 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
31066161 TGTCATATGA
31066171 ATTTTTTAAAATATTT
1 ATTTTTTAAAATATTT
*
31066187 ATTTTTTAATAT-TTT
1 ATTTTTTAAAATATTT
31066202 ATT
1 ATT
31066205 ATATTTGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTTTTAAAATATTT
Found at i:31068810 original size:34 final size:35
Alignment explanation
Indices: 31068729--31068849 Score: 122
Period size: 34 Copynumber: 3.5 Consensus size: 35
31068719 AGAACGTTAG
* *
31068729 AAAA-AGAAGTTTTTGAGAAACCAAAGAAGAGCATTT
1 AAAAGAGAAGCTTTTGAAAAACC--AGAAGAGCATTT
* * *
31068765 GAAAGAAAAGCTTTTGAAAAACCAG-AGAGCGTTT
1 AAAAGAGAAGCTTTTGAAAAACCAGAAGAGCATTT
* *
31068799 AAAAGAGAAGCTTTTGAGAAA-CTGAAGAGCATTT
1 AAAAGAGAAGCTTTTGAAAAACCAGAAGAGCATTT
* *
31068833 GAAAGACAAGCTTTTGA
1 AAAAGAGAAGCTTTTGA
31068850 GAGAAGTAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
33 2 0.03
34 49 0.69
35 2 0.03
36 3 0.04
37 15 0.21
ACGTcount: A:0.45, C:0.10, G:0.22, T:0.22
Consensus pattern (35 bp):
AAAAGAGAAGCTTTTGAAAAACCAGAAGAGCATTT
Found at i:31068849 original size:68 final size:69
Alignment explanation
Indices: 31068696--31068849 Score: 190
Period size: 71 Copynumber: 2.2 Consensus size: 69
31068686 TTAAATCATA
* *
31068696 GAAAGAAA-CTTTTGAAAAATCAAAGAACGTTAGAAAAAGAAGTTTTTGAGAAACCAAAGAAGAG
1 GAAAGAAAGCTTTTGAAAAACCAAAGAACGTTAGAAAAAGAAGCTTTTGAGAAACC-AAGAAGAG
31068760 CATTT
65 CATTT
* * * *
31068765 GAAAGAAAAGCTTTTGAAAAACCAGAGAGCGTTTA-AAAGAGAAGCTTTTGAGAAA-C-TGAAGA
1 GAAAG-AAAGCTTTTGAAAAACCAAAGAACG-TTAGAAAAAGAAGCTTTTGAGAAACCAAGAAGA
31068827 GCATTT
64 GCATTT
31068833 GAAAGACAAGCTTTTGA
1 GAAAGA-AAGCTTTTGA
31068850 GAGAAGTAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
67 1 0.01
68 26 0.35
69 5 0.07
70 4 0.05
71 36 0.48
72 3 0.04
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.22
Consensus pattern (69 bp):
GAAAGAAAGCTTTTGAAAAACCAAAGAACGTTAGAAAAAGAAGCTTTTGAGAAACCAAGAAGAGC
ATTT
Found at i:31068850 original size:34 final size:33
Alignment explanation
Indices: 31068754--31068851 Score: 124
Period size: 34 Copynumber: 2.9 Consensus size: 33
31068744 AGAAACCAAA
*
31068754 GAAGAGCATTTGAAAGAAAAGCTTTTGAAAAAC
1 GAAGAGCATTTGAAAGAAAAGCTTTTGAGAAAC
* * * *
31068787 CAGAGAGCGTTTAAAAGAGAAGCTTTTGAGAAAC
1 GA-AGAGCATTTGAAAGAAAAGCTTTTGAGAAAC
*
31068821 TGAAGAGCATTTGAAAGACAAGCTTTTGAGA
1 -GAAGAGCATTTGAAAGAAAAGCTTTTGAGA
31068852 GAAGTAAAAC
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
33 1 0.02
34 52 0.96
35 1 0.02
ACGTcount: A:0.43, C:0.10, G:0.24, T:0.22
Consensus pattern (33 bp):
GAAGAGCATTTGAAAGAAAAGCTTTTGAGAAAC
Found at i:31070803 original size:2 final size:2
Alignment explanation
Indices: 31070796--31070830 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
31070786 TTCTTCAAAT
31070796 TA TA TA 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 TA TA TA T
31070831 TGTAGATGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31071548 original size:30 final size:29
Alignment explanation
Indices: 31071491--31071559 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
31071481 CCTTTTTACT
* *
31071491 TTTTCCCCAAAACTTTTACTTCTTCCCAC
1 TTTTCCCCAAAACTTTTACTCCCTCCCAC
*
31071520 TTTTCTCCAAAACTTTTACTCCCCTCCCATC
1 TTTTCCCCAAAACTTTTACT-CCCTCCCA-C
*
31071551 TTATCCCCA
1 TTTTCCCCA
31071560 TCTACCCCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 19 0.58
30 6 0.18
31 8 0.24
ACGTcount: A:0.20, C:0.41, G:0.00, T:0.39
Consensus pattern (29 bp):
TTTTCCCCAAAACTTTTACTCCCTCCCAC
Found at i:31071817 original size:45 final size:40
Alignment explanation
Indices: 31071712--31071804 Score: 186
Period size: 40 Copynumber: 2.3 Consensus size: 40
31071702 CTCATTTTCC
31071712 CCCCAAAACTTTTACTCCCCTCCCATCCTAGCCCCATCTA
1 CCCCAAAACTTTTACTCCCCTCCCATCCTAGCCCCATCTA
31071752 CCCCAAAACTTTTACTCCCCTCCCATCCTAGCCCCATCTA
1 CCCCAAAACTTTTACTCCCCTCCCATCCTAGCCCCATCTA
31071792 CCCCAAAACTTTT
1 CCCCAAAACTTTT
31071805 TTATTTCTCC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.24, C:0.48, G:0.02, T:0.26
Consensus pattern (40 bp):
CCCCAAAACTTTTACTCCCCTCCCATCCTAGCCCCATCTA
Found at i:31073176 original size:14 final size:14
Alignment explanation
Indices: 31073157--31073196 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
31073147 TTGATTGCCA
31073157 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
31073171 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
31073185 GGAAAATGTTTT
1 GTAAAATGTTTT
31073197 ACTTTTCTGT
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:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:31073205 original size:20 final size:20
Alignment explanation
Indices: 31073180--31073219 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
31073170 CGTAAAATGA
*
31073180 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
31073200 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
31073220 GGAAAATATT
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:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:31073209 original size:34 final size:35
Alignment explanation
Indices: 31073165--31073231 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
31073155 CAGTAAAATG
*
31073165 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
31073199 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
31073232 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:31073235 original size:14 final size:15
Alignment explanation
Indices: 31073159--31073235 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
31073149 GATTGCCAGT
* *
31073159 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
31073173 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
31073187 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
31073207 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
31073222 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
31073236 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:31073918 original size:16 final size:17
Alignment explanation
Indices: 31073879--31073918 Score: 71
Period size: 17 Copynumber: 2.3 Consensus size: 17
31073869 ATCAATGAGA
31073879 CTTTCTTGAACACTTTTT
1 CTTT-TTGAACACTTTTT
31073897 CTTTTTGAACACTTTTT
1 CTTTTTGAACACTTTTT
31073914 CTTTT
1 CTTTT
31073919 ACGTTTGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.15, C:0.20, G:0.05, T:0.60
Consensus pattern (17 bp):
CTTTTTGAACACTTTTT
Found at i:31074623 original size:35 final size:36
Alignment explanation
Indices: 31074577--31074645 Score: 122
Period size: 35 Copynumber: 1.9 Consensus size: 36
31074567 TGTCAATCAT
31074577 TTCAATATCCAACAAGCTTAAAACATAAT-AATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
*
31074612 TTCAATATCCAACAAGGTTAAAACATAATCAATA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATA
31074646 TCTAACAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 28 0.88
36 4 0.12
ACGTcount: A:0.52, C:0.17, G:0.04, T:0.26
Consensus pattern (36 bp):
TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
Found at i:31077122 original size:10 final size:10
Alignment explanation
Indices: 31077107--31077132 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
31077097 TCATTAAGTG
31077107 CTAACAAATA
1 CTAACAAATA
31077117 CTAACAAATA
1 CTAACAAATA
31077127 CTAACA
1 CTAACA
31077133 GATCAGTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.58, C:0.23, G:0.00, T:0.19
Consensus pattern (10 bp):
CTAACAAATA
Found at i:31079601 original size:5 final size:5
Alignment explanation
Indices: 31079596--31079717 Score: 163
Period size: 5 Copynumber: 24.4 Consensus size: 5
31079586 GTTTATTTAA
* * * * * * * * *
31079596 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAT TATAA TATAC
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
31079646 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
31079696 TATAT TATAT TATAT TATAT TA
1 TATAT TATAT TATAT TATAT TA
31079718 AATAAACTAA
Statistics
Matches: 113, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 113 1.00
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (5 bp):
TATAT
Found at i:31079948 original size:22 final size:22
Alignment explanation
Indices: 31079909--31079956 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
31079899 AAATAAAAGA
*
31079909 AAAAGAAACAAAGGAAGA-ACAG
1 AAAAGAAACAAAGAAAGAGAC-G
* *
31079931 AAAAGAAATAGAGAAAGAGACG
1 AAAAGAAACAAAGAAAGAGACG
31079953 AAAA
1 AAAA
31079957 TAGGGGAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.69, C:0.06, G:0.23, T:0.02
Consensus pattern (22 bp):
AAAAGAAACAAAGAAAGAGACG
Found at i:31079986 original size:30 final size:29
Alignment explanation
Indices: 31079933--31079990 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
31079923 AAGAACAGAA
* * *
31079933 AAGAAATAGAGAAAGAGACGAAAATAGGGG
1 AAGAAAAAGAGAAAGAAAAGAAAA-AGGGG
*
31079963 AAGAAAAAGGGAAAGAAAAGAAAAAGGG
1 AAGAAAAAGAGAAAGAAAAGAAAAAGGG
31079991 AAAATTCAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.62, C:0.02, G:0.33, T:0.03
Consensus pattern (29 bp):
AAGAAAAAGAGAAAGAAAAGAAAAAGGGG
Found at i:31084535 original size:51 final size:50
Alignment explanation
Indices: 31084477--31084663 Score: 223
Period size: 51 Copynumber: 3.7 Consensus size: 50
31084467 TCAGTTCACA
* * *
31084477 TAGTAGCCTGCACATATTACTACACATGTGACCATTACCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATCCGGTACACG
* * * * *
31084528 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATCCGGTACACG
* * * * *
31084579 TAGTAGCCTGTACATAGTATTACACATGCGACC-TATCATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATACCA-TCCGGTACACG
31084629 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
31084664 CACTTTCACT
Statistics
Matches: 111, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
49 2 0.02
50 39 0.35
51 68 0.61
52 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATACCATCCGGTACACG
Found at i:31084651 original size:101 final size:101
Alignment explanation
Indices: 31084475--31084659 Score: 291
Period size: 101 Copynumber: 1.8 Consensus size: 101
31084465 GTTCAGTTCA
* *
31084475 CATAGTAGCCTGCACATATTACTACACATGTGACCATTACCATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCATCCGATACACGTAGTAGCCTGCA
31084540 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
65 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
* * * *
31084577 CATAGTAGCCTGTACATAGTATTACACATGCGACC-TATCATTCCGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCA-TCCGATACACGTAGTAGCCTGCA
31084641 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
31084660 CCATCACTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 4 0.05
101 41 0.54
102 31 0.41
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATCCGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCCGGTACG
Found at i:31089359 original size:23 final size:23
Alignment explanation
Indices: 31089326--31089400 Score: 105
Period size: 23 Copynumber: 3.3 Consensus size: 23
31089316 ATAAGTGCCA
* * *
31089326 CACTGATATGTAACCAAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
* *
31089349 CACTGAAATGTAGCTGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
31089372 CACTGAAATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
31089395 CACTGA
1 CACTGA
31089401 TCAATAACAC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (23 bp):
CACTGAAATGTAGCCGAAGCTAC
Done.