Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011750.1 Kokia drynarioides strain JFW-HI SEQ_126744, 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: 255262
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 5 characters in sequence are not A, C, G, or T
Found at i:4350 original size:35 final size:35
Alignment explanation
Indices: 4311--4391 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 35
4301 TTAGAAATCT
* ** * *
4311 ATTAAACTAGGGTTTTTTTAATAGTATATATGTTA
1 ATTAAACTAGGGTTCTACTAACAGTATAGATGTTA
* *
4346 ATTAAAATAGGGTTCTACTAACAGTATAGATGTTG
1 ATTAAACTAGGGTTCTACTAACAGTATAGATGTTA
*
4381 ACTAAACTAGG
1 ATTAAACTAGG
4392 ATGTTATTAC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.38
Consensus pattern (35 bp):
ATTAAACTAGGGTTCTACTAACAGTATAGATGTTA
Found at i:6258 original size:110 final size:110
Alignment explanation
Indices: 6065--6273 Score: 294
Period size: 110 Copynumber: 1.9 Consensus size: 110
6055 TTGTCCGTTT
* *
6065 TGTATTCAAAGATTAGCATATTCCAACTGCGACTATATGAACGGAGCATCCATGATTTCTTTTGA
1 TGTATTCAAAGATTAGCATATTCCAACTGCGACTATATGAACGGAGCATCCATGATTTCTTCTAA
* * * *
6130 TAGCTTTTATTTGCAAGGGATTGTGGATCCTCAATCAATCCACTG
66 CAGCTTTTATCTACAAGGGATCGTGGATCCTCAATCAATCCACTG
* * * *
6175 TGTATTCATAGATTAGCATATTCCAATTGTGACTATATGAATGGAGCATCCATGATTT-TCTCTA
1 TGTATTCAAAGATTAGCATATTCCAACTGCGACTATATGAACGGAGCATCCATGATTTCT-TCTA
* *
6239 ACAGCTTTTATCTACAAGGGGTCGTGGATTCTCAA
65 ACAGCTTTTATCTACAAGGGATCGTGGATCCTCAA
6274 CTGTCGAAAC
Statistics
Matches: 86, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
109 1 0.01
110 85 0.99
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (110 bp):
TGTATTCAAAGATTAGCATATTCCAACTGCGACTATATGAACGGAGCATCCATGATTTCTTCTAA
CAGCTTTTATCTACAAGGGATCGTGGATCCTCAATCAATCCACTG
Found at i:7567 original size:29 final size:31
Alignment explanation
Indices: 7533--7603 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 31
7523 TAGACATCTG
* *
7533 GGGGGTAAAATGGTA-AATTTTGG-AAGTTT
1 GGGGGTAAAATGATAGAATTTTGGAAAGTTC
*
7562 TGGGGTCAAAA--ATAGAATTTTGGAAAGTTC
1 GGGGGT-AAAATGATAGAATTTTGGAAAGTTC
7592 GGGGGTAAAATG
1 GGGGGTAAAATG
7604 TAATTTATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
28 2 0.06
29 17 0.52
30 14 0.42
ACGTcount: A:0.34, C:0.03, G:0.34, T:0.30
Consensus pattern (31 bp):
GGGGGTAAAATGATAGAATTTTGGAAAGTTC
Found at i:7571 original size:60 final size:60
Alignment explanation
Indices: 7179--7574 Score: 448
Period size: 59 Copynumber: 6.7 Consensus size: 60
7169 AGACGCTCGA
* * * * * * **
7179 GGGTGAAATGGTAATTTTTGGAAGGCTCGCGG-TCAAAAATAGAATTTTTGGACATCCGA-
1 GGGTAAAATGGTAAATTTTGGAAGGTTCG-GGATCAAAAATGGAGTTTTTAGACATCTTAG
* * *
7238 GGGTAAAATGGTAATTTTTGGAAGGTTCGGGATAAAAAAATGGAGTTTTTAGACAT-TTGG
1 GGGTAAAATGGTAAATTTTGGAAGGTTCGGGAT-CAAAAATGGAGTTTTTAGACATCTTAG
* *
7298 GGGTTAAATGGTAATTTTTGGAAGGTTTC-GGATCAAAAATGGAGTTTTTAGACAT-TTAG
1 GGGTAAAATGGTAAATTTTGGAAGG-TTCGGGATCAAAAATGGAGTTTTTAGACATCTTAG
* *
7357 GGGTAAAATGGTAAATTTTGGAAGGTTTC-GGATCAAAAATGGAGTTTTTAGACATC-CAA
1 GGGTAAAATGGTAAATTTTGGAAGG-TTCGGGATCAAAAATGGAGTTTTTAGACATCTTAG
* * *
7416 GGGTAAAATGGTAAATTTTGGAAGGTTCGAGATCAAAAACGAAGTTTTTAGACATC-TAG
1 GGGTAAAATGGTAAATTTTGGAAGGTTCGGGATCAAAAATGGAGTTTTTAGACATCTTAG
* ** * * **
7475 GGGTAAAATGGTAATTTTTGGAAGGTTCGGGATCAAAAGCGAAGATTTTAGACATCTGGG
1 GGGTAAAATGGTAAATTTTGGAAGGTTCGGGATCAAAAATGGAGTTTTTAGACATCTTAG
* * *
7535 GGGTAAAATGGTAAATTTTGGAAGTTTTGGGGTCAAAAAT
1 GGGTAAAATGGTAAATTTTGGAAGGTTCGGGATCAAAAAT
7575 AGAATTTTGG
Statistics
Matches: 297, Mismatches: 33, Indels: 13
0.87 0.10 0.04
Matches are distributed among these distances:
58 5 0.02
59 208 0.70
60 81 0.27
61 3 0.01
ACGTcount: A:0.33, C:0.07, G:0.28, T:0.31
Consensus pattern (60 bp):
GGGTAAAATGGTAAATTTTGGAAGGTTCGGGATCAAAAATGGAGTTTTTAGACATCTTAG
Found at i:8800 original size:3 final size:3
Alignment explanation
Indices: 8792--8830 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
8782 ATACTATTTT
8792 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
8831 ATGCTATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:11180 original size:42 final size:42
Alignment explanation
Indices: 11112--11199 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
11102 ATTTCACAAA
* * *
11112 ATTTTAAAATTTTAACGGGTTAAATTTTAAGGA-CAAATAAT
1 ATTTTAAAATTTTAACGAGTTAAATTTTAAGAATAAAATAAT
* * *
11153 ATTTTAAATATTTTAACTATTTTAATTTTAAGAATAAAATAAT
1 ATTTTAAA-ATTTTAACGAGTTAAATTTTAAGAATAAAATAAT
11196 ATTT
1 ATTT
11200 ATCCTTTCAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 8 0.21
42 20 0.51
43 11 0.28
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.45
Consensus pattern (42 bp):
ATTTTAAAATTTTAACGAGTTAAATTTTAAGAATAAAATAAT
Found at i:11272 original size:137 final size:136
Alignment explanation
Indices: 11041--11374 Score: 358
Period size: 137 Copynumber: 2.5 Consensus size: 136
11031 AGCTTGACAG
** * * *
11041 TTTTAATTTTAATTATAAAAT-AT-TTTATCCTTTCAT-GAAATTTAAAAAATA-AATATTTATT
1 TTTTAATTTTAAGAACAAAATAATATTTATCCTTTCATAAAAATTTAAAAAATATATTATTTATT
** ** * * * *
11102 ATTTC-ACAAAATTTT-AAAATTTTAACGGGTTAAATTTTAAGGACAAATAATATTTTAAATATT
66 -CGTCGGTAAAATTTTCATACTTTTAACGGGTTAAATATTAAAGACAAATAATATTTTAAATATT
11165 TTAACTA
130 TTAACTA
* ** *
11172 TTTTAATTTTAAGAATAAAATAATATTTATCCTTTCATAAATTTTTTTTAAAAA-ATATTATTTA
1 TTTTAATTTTAAGAACAAAATAATATTTATCCTTTCATAAA--AATTTAAAAAATATATTATTTA
* * * *
11236 TTCGTCGGTAAAATTTTCATACTTTTAACTGTTTAAATATTAAAGATAAATAATATTTTGAATAT
64 TTCGTCGGTAAAATTTTCATACTTTTAACGGGTTAAATATTAAAGACAAATAATATTTTAAATAT
* *
11301 TTTGACTG
129 TTTAACTA
* * *
11309 TTTTTATTTTAAGGACAAAATATTATTTATCCTTTCATAAAAATTTAAAAAATATATTATTTATT
1 TTTTAATTTTAAGAACAAAATAATATTTATCCTTTCATAAAAATTTAAAAAATATATTATTTATT
11374 C
66 C
11375 TTTCATAAAA
Statistics
Matches: 166, Mismatches: 28, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
131 19 0.11
132 2 0.01
133 13 0.08
134 1 0.01
135 11 0.07
136 38 0.23
137 82 0.49
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (136 bp):
TTTTAATTTTAAGAACAAAATAATATTTATCCTTTCATAAAAATTTAAAAAATATATTATTTATT
CGTCGGTAAAATTTTCATACTTTTAACGGGTTAAATATTAAAGACAAATAATATTTTAAATATTT
TAACTA
Found at i:11390 original size:33 final size:34
Alignment explanation
Indices: 11328--11392 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
11318 TAAGGACAAA
11328 ATATTATTTATCCTTTCATAAAAATTTAAAAAAT
1 ATATTATTTATCCTTTCATAAAAATTTAAAAAAT
*
11362 ATATTATTTATTCTTTCAT-AAAATTTAAAAA
1 ATATTATTTATCCTTTCATAAAAATTTAAAAA
11393 TTTTAATTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 12 0.40
34 18 0.60
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (34 bp):
ATATTATTTATCCTTTCATAAAAATTTAAAAAAT
Found at i:11592 original size:31 final size:32
Alignment explanation
Indices: 11532--11598 Score: 104
Period size: 29 Copynumber: 2.2 Consensus size: 32
11522 AATTTTAAGA
11532 AAAAAAATATTTTATCCTTTCATAAATTTTTT
1 AAAAAAATATTTTATCCTTTCATAAATTTTTT
*
11564 AAAAAAA-A-TTTATCCTTTCAT-AATATTTT
1 AAAAAAATATTTTATCCTTTCATAAATTTTTT
11593 AAAAAA
1 AAAAAA
11599 TAATATTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 13 0.38
30 13 0.38
31 1 0.03
32 7 0.21
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (32 bp):
AAAAAAATATTTTATCCTTTCATAAATTTTTT
Found at i:12403 original size:24 final size:23
Alignment explanation
Indices: 12369--12415 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
12359 ATAAATATTA
12369 TTTTTTAAAATATTATGAAAGGAT
1 TTTTTTAAAAT-TTATGAAAGGAT
*
12393 TTTTTTTAAATTTATGAAAGGAT
1 TTTTTTAAAATTTATGAAAGGAT
12416 AAATAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (23 bp):
TTTTTTAAAATTTATGAAAGGAT
Found at i:12435 original size:31 final size:32
Alignment explanation
Indices: 12393--12460 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
12383 ATGAAAGGAT
*
12393 TTTTTTTAAA-TTTATGAAAGGATAAATAATA
1 TTTTTTAAAATTTTATGAAAGGATAAATAATA
12424 TTTTTTAAAATTTTTATGAAAGGATAAATAATA
1 TTTTTTAAAA-TTTTATGAAAGGATAAATAATA
12457 TTTT
1 TTTT
12461 ATCCTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 9 0.26
33 25 0.74
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (32 bp):
TTTTTTAAAATTTTATGAAAGGATAAATAATA
Found at i:12805 original size:42 final size:41
Alignment explanation
Indices: 12753--12831 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 41
12743 TAAATAATAT
*
12753 TTTATCCTTAAAA-TTATAACAGTCAAAATATTTAAAATATGA
1 TTTATCCTTAAAATTTA-AACAGTCAAAAT-TTGAAAATATGA
* * *
12795 TTTATTCTTAATATTTAAACAGTTAAAATTTGAAAAT
1 TTTATCCTTAAAATTTAAACAGTCAAAATTTGAAAAT
12832 TTTATGAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 7 0.22
42 22 0.69
43 3 0.09
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.42
Consensus pattern (41 bp):
TTTATCCTTAAAATTTAAACAGTCAAAATTTGAAAATATGA
Found at i:24630 original size:16 final size:16
Alignment explanation
Indices: 24593--24647 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
24583 AAATGACATG
*
24593 AAAATAAA-AAACAAC
1 AAAATAAATAAACAAA
*
24608 AACATAAATAAACAAA
1 AAAATAAATAAACAAA
*
24624 AAAATAAGTAAA-AATA
1 AAAATAAATAAACAA-A
24640 AAAATAAA
1 AAAATAAA
24648 ATGCTAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
15 9 0.27
16 24 0.73
ACGTcount: A:0.78, C:0.07, G:0.02, T:0.13
Consensus pattern (16 bp):
AAAATAAATAAACAAA
Found at i:24668 original size:13 final size:13
Alignment explanation
Indices: 24594--24682 Score: 51
Period size: 13 Copynumber: 6.6 Consensus size: 13
24584 AATGACATGA
*
24594 AAATAAAAAACAAC
1 AAATAAAATA-AAC
24608 AACAT-AAATAAAC
1 AA-ATAAAATAAAC
*
24621 AAA-AAAATAAGTAA
1 AAATAAAATAA--AC
24635 AAATAAAAATAAA-
1 AAAT-AAAATAAAC
**
24648 ATGCTAAAATAAAC
1 A-AATAAAATAAAC
24662 AAATAAATATAAAC
1 AAATAAA-ATAAAC
24676 -AATAAAA
1 AAATAAAA
24683 ATAATTTGGA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
12 8 0.13
13 24 0.40
14 19 0.32
15 2 0.03
16 7 0.12
ACGTcount: A:0.74, C:0.08, G:0.02, T:0.16
Consensus pattern (13 bp):
AAATAAAATAAAC
Found at i:24686 original size:13 final size:14
Alignment explanation
Indices: 24653--24686 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
24643 ATAAAATGCT
24653 AAAATAAACAAATA
1 AAAATAAACAAATA
*
24667 AATATAAAC-AATA
1 AAAATAAACAAATA
24680 AAAATAA
1 AAAATAA
24687 TTTGGATTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (14 bp):
AAAATAAACAAATA
Found at i:24736 original size:15 final size:15
Alignment explanation
Indices: 24702--24743 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
24692 ATTAGTCATG
*
24702 AAAATAAAT-GACAA
1 AAAATAAATAAACAA
24716 ATAAATAAATAAACAA
1 A-AAATAAATAAACAA
*
24732 AAAATTAATAAA
1 AAAATAAATAAA
24744 TTAAATGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 1 0.04
15 18 0.75
16 5 0.21
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (15 bp):
AAAATAAATAAACAA
Found at i:25669 original size:46 final size:44
Alignment explanation
Indices: 25617--26016 Score: 403
Period size: 46 Copynumber: 8.8 Consensus size: 44
25607 GGTGTTGTAA
* * *
25617 CTTCAATCTGTCCCTTTGGATTTTAGGGTAAAATATTGAATGGTTG
1 CTTCAATCTG-CCCTTTGGA-TTTAGGGTAAAAGATTGGATGGTGG
* * *
25663 CTTCAATCTGCCCCTCTAGATTTAGGGGTAAAAGATTGGATGGAGG
1 CTTCAATCTG-CCCTTTGGATTTA-GGGTAAAAGATTGGATGGTGG
*
25709 CTTCAATCTGCCCTTCTGGA-TTATGGGTAAAAGATTTGATGGTGG
1 CTTCAATCTGCCCTT-TGGATTTA-GGGTAAAAGATTGGATGGTGG
* *
25754 CTTCAATCTGCCCCTCTGGATTTAGAGGTAAAATATTGGATGGTGG
1 CTTCAATCTG-CCCTTTGGATTTAG-GGTAAAAGATTGGATGGTGG
* * * *
25800 CTTTAATCTGTCCTTTTGGTTTTAGGGGTAAAATATTGGATGGTGG
1 CTTCAATCTG-CCCTTTGGATTTA-GGGTAAAAGATTGGATGGTGG
* * *
25846 CTTCAATTTGCCTCTTTGGATTTATGGTAAAAGATTGTATGGT-G
1 CTTCAATCTGCC-CTTTGGATTTAGGGTAAAAGATTGGATGGTGG
25890 CTTTCAATCTGCCCTTCTGGA-TTAGAGGTAAAAGATTGGATGGTGG
1 C-TTCAATCTGCCCTT-TGGATTTAG-GGTAAAAGATTGGATGGTGG
* * * * * *
25936 CTTAAATTTTCCCCTTTGGATTAATGGTAAAAAATTGGATGGTGG
1 CTTCAA-TCTGCCCTTTGGATTTAGGGTAAAAGATTGGATGGTGG
* **
25981 CTTCAATTTGCCCCCTGGA-TTAGAGGTAAAAGATTG
1 CTTCAATCTGCCCTTTGGATTTAG-GGTAAAAGATTG
26017 AATTCGGTGA
Statistics
Matches: 297, Mismatches: 43, Indels: 30
0.80 0.12 0.08
Matches are distributed among these distances:
43 2 0.01
44 29 0.10
45 126 0.42
46 139 0.47
47 1 0.00
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.36
Consensus pattern (44 bp):
CTTCAATCTGCCCTTTGGATTTAGGGTAAAAGATTGGATGGTGG
Found at i:25750 original size:45 final size:45
Alignment explanation
Indices: 25617--26016 Score: 388
Period size: 45 Copynumber: 8.8 Consensus size: 45
25607 GGTGTTGTAA
* * * *
25617 CTTCAATCTGTCCCTT-TGGATTTTAGGGTAAAATATTGAATGGTTG
1 CTTCAATCTG-CCCTTCTGGATTAT-GGGTAAAAGATTGGATGGTGG
* * * *
25663 CTTCAATCTGCCCCTCTAGATTTAGGGGTAAAAGATTGGATGGAGG
1 CTTCAATCTGCCCTTCTGGA-TTATGGGTAAAAGATTGGATGGTGG
*
25709 CTTCAATCTGCCCTTCTGGATTATGGGTAAAAGATTTGATGGTGG
1 CTTCAATCTGCCCTTCTGGATTATGGGTAAAAGATTGGATGGTGG
* *
25754 CTTCAATCTGCCCCTCTGGATT-TAGAGGTAAAATATTGGATGGTGG
1 CTTCAATCTGCCCTTCTGGATTAT-G-GGTAAAAGATTGGATGGTGG
* * * * * *
25800 CTTTAATCTGTCCTTTTGGTTTTAGGGGTAAAATATTGGATGGTGG
1 CTTCAATCTGCCCTTCTGG-ATTATGGGTAAAAGATTGGATGGTGG
* *
25846 CTTCAATTTGCCTCTT-TGGATTTAT-GGTAAAAGATTGTATGGT-G
1 CTTCAATCTGCC-CTTCTGGA-TTATGGGTAAAAGATTGGATGGTGG
25890 CTTTCAATCTGCCCTTCTGGATTA-GAGGTAAAAGATTGGATGGTGG
1 C-TTCAATCTGCCCTTCTGGATTATG-GGTAAAAGATTGGATGGTGG
* * * *
25936 CTTAAATTTTCCCCTT-TGGATTAAT-GGTAAAAAATTGGATGGTGG
1 CTTCAA-TCTGCCCTTCTGGATT-ATGGGTAAAAGATTGGATGGTGG
* *
25981 CTTCAATTTGCCC-CCTGGATTA-GAGGTAAAAGATTG
1 CTTCAATCTGCCCTTCTGGATTATG-GGTAAAAGATTG
26017 AATTCGGTGA
Statistics
Matches: 296, Mismatches: 39, Indels: 40
0.79 0.10 0.11
Matches are distributed among these distances:
43 1 0.00
44 32 0.11
45 129 0.44
46 126 0.43
47 8 0.03
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.36
Consensus pattern (45 bp):
CTTCAATCTGCCCTTCTGGATTATGGGTAAAAGATTGGATGGTGG
Found at i:25786 original size:137 final size:137
Alignment explanation
Indices: 25617--26015 Score: 483
Period size: 137 Copynumber: 2.9 Consensus size: 137
25607 GGTGTTGTAA
* * * * * * *
25617 CTTCAATCTGTCCCTTTGGATTTTAG-GGTAAAATATTGAATGGTTGCTTCAATCTGCCCCTCTA
1 CTTCAATCTGCCCCTCTGGA-TTTAGAGGTAAAATATTGGATGGTGGCTTAAATCTGCCCCTTTG
* * *
25681 GATTTAGGGGTAAAAGATTGGATGGAGGCTTCAATCTGCCCTTCTGGATTATGGGTAAAAGATTT
65 GATTTAGGGGTAAAAAATTGGATGGTGGCTTCAATTTGCCCTTCTGGATTATGGGTAAAAGATTT
25746 G-ATGGTGG
130 GTATGGT-G
* * *
25754 CTTCAATCTGCCCCTCTGGATTTAGAGGTAAAATATTGGATGGTGGCTTTAATCTGTCCTTTTGG
1 CTTCAATCTGCCCCTCTGGATTTAGAGGTAAAATATTGGATGGTGGCTTAAATCTGCCCCTTTGG
* *
25819 TTTTAGGGGTAAAATATTGGATGGTGGCTTCAATTTGCCTCTT-TGGATTTAT-GGTAAAAGA-T
66 ATTTAGGGGTAAAAAATTGGATGGTGGCTTCAATTTGCC-CTTCTGGA-TTATGGGTAAAAGATT
25881 TGTATGGTG
129 TGTATGGTG
* * * *
25890 CTTTCAATCTGCCCTTCTGGA-TTAGAGGTAAAAGATTGGATGGTGGCTTAAATTTTCCCCTTTG
1 C-TTCAATCTGCCCCTCTGGATTTAGAGGTAAAATATTGGATGGTGGCTTAAATCTGCCCCTTTG
** *
25954 GA-TTAATGGTAAAAAATTGGATGGTGGCTTCAATTTGCCC-CCTGGATTA-GAGGTAAAAGATT
65 GATTTAGGGGTAAAAAATTGGATGGTGGCTTCAATTTGCCCTTCTGGATTATG-GGTAAAAGATT
26016 GAATTCGGTG
Statistics
Matches: 228, Mismatches: 25, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
133 3 0.01
134 14 0.06
135 35 0.15
136 48 0.21
137 121 0.53
138 7 0.03
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.36
Consensus pattern (137 bp):
CTTCAATCTGCCCCTCTGGATTTAGAGGTAAAATATTGGATGGTGGCTTAAATCTGCCCCTTTGG
ATTTAGGGGTAAAAAATTGGATGGTGGCTTCAATTTGCCCTTCTGGATTATGGGTAAAAGATTTG
TATGGTG
Found at i:26100 original size:55 final size:55
Alignment explanation
Indices: 26034--26145 Score: 197
Period size: 55 Copynumber: 2.0 Consensus size: 55
26024 TGATTTAACT
* *
26034 TCACTCTGTTCCACTACAACTTCAGGGATATTGAGATCCGCTACTATAATTTTAA
1 TCACTCTGTTCCACTACAACTTCAGGGATATTAAGATCCACTACTATAATTTTAA
*
26089 TCACTCTGTTCCACTACAACTTCAGGGATATTAAGATCCATTACTATAATTTTAA
1 TCACTCTGTTCCACTACAACTTCAGGGATATTAAGATCCACTACTATAATTTTAA
26144 TC
1 TC
26146 CACTTCTCTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (55 bp):
TCACTCTGTTCCACTACAACTTCAGGGATATTAAGATCCACTACTATAATTTTAA
Found at i:26897 original size:20 final size:20
Alignment explanation
Indices: 26874--26911 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
26864 CCAAAGATTA
26874 CAAACATCGGTCAAAAATAG
1 CAAACATCGGTCAAAAATAG
**
26894 CAAATGTCGGTCAAAAAT
1 CAAACATCGGTCAAAAAT
26912 GAAAAAAATT
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:0.47, C:0.18, G:0.16, T:0.18
Consensus pattern (20 bp):
CAAACATCGGTCAAAAATAG
Found at i:27787 original size:52 final size:52
Alignment explanation
Indices: 27727--27830 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
27717 CCCTAGTAAA
27727 AGATCTGATAGACGTTCTATAGGTGTAGAGAGAAAATGGTAACTTCTCATGC
1 AGATCTGATAGACGTTCTATAGGTGTAGAGAGAAAATGGTAACTTCTCATGC
27779 AGATCTGATAGACGTTCTATAGGTGTAGAGAGAAAATGGTAACTTCTCATGC
1 AGATCTGATAGACGTTCTATAGGTGTAGAGAGAAAATGGTAACTTCTCATGC
27831 CAATCTTTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (52 bp):
AGATCTGATAGACGTTCTATAGGTGTAGAGAGAAAATGGTAACTTCTCATGC
Found at i:33944 original size:30 final size:28
Alignment explanation
Indices: 33883--33963 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 28
33873 CCTGGGGTTG
* *
33883 AAATG-AATCTTTGGAGAGTTTGGGGTTA
1 AAATGTAAT-TTTGGAAAGTTTGGGGTAA
33911 AAATGTAATTTTGGAAAGCTTTAGGGGTAA
1 AAATGTAATTTTGGAAAG-TTT-GGGGTAA
* *
33941 AAATGTCATTTTAGGAAAATTTG
1 AAATGTAATTTT-GGAAAGTTTG
33964 CTTTGGAAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
28 13 0.29
29 7 0.16
30 20 0.44
31 5 0.11
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.36
Consensus pattern (28 bp):
AAATGTAATTTTGGAAAGTTTGGGGTAA
Found at i:33998 original size:29 final size:29
Alignment explanation
Indices: 33965--34243 Score: 184
Period size: 29 Copynumber: 9.6 Consensus size: 29
33955 GAAAATTTGC
33965 TTTGGAAGTTTGAGGGCAAAAATGGAATT
1 TTTGGAAGTTTGAGGGCAAAAATGGAATT
* * *
33994 TTTGGAAGTTCG-GGAGTAAAAATATG-ATT
1 TTTGGAAGTTTGAGG-GCAAAAAT-GGAATT
* *
34023 TTTGGAAGTTCGAGGGCAAAAATGAAATT
1 TTTGGAAGTTTGAGGGCAAAAATGGAATT
* *
34052 TTTAGAAGTTTGAGGTG--AAAATGTAATTT
1 TTTGGAAGTTTGAGG-GCAAAAATGGAA-TT
** * *
34081 TTTAAAAGTTAG-GGGCAAAAATATG-A-T
1 TTTGGAAGTTTGAGGGCAAAAAT-GGAATT
34108 TTTGGAAGTTT-AGGGGCAAAAATGGAATT
1 TTTGGAAGTTTGA-GGGCAAAAATGGAATT
* *
34137 TTTGAGAAATTT-AGGGGTC-AAAATGTAATT
1 TTTG-GAAGTTTGA-GGG-CAAAAATGGAATT
** *
34167 TTTGAGAAGTTT-AGTGGTTAAAATGTAATT
1 TTTG-GAAGTTTGAG-GGCAAAAATGGAATT
* ** *
34197 TTTGGAAGTTTAAGGGTTAAAATGTAATT
1 TTTGGAAGTTTGAGGGCAAAAATGGAATT
*
34226 TTTAGAAAGTTTGAGGGC
1 TTT-GGAAGTTTGAGGGC
34244 CTTTTGGGCA
Statistics
Matches: 207, Mismatches: 24, Indels: 37
0.77 0.09 0.14
Matches are distributed among these distances:
27 11 0.05
28 23 0.11
29 105 0.51
30 67 0.32
31 1 0.00
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (29 bp):
TTTGGAAGTTTGAGGGCAAAAATGGAATT
Found at i:34083 original size:58 final size:57
Alignment explanation
Indices: 33965--34241 Score: 206
Period size: 58 Copynumber: 4.8 Consensus size: 57
33955 GAAAATTTGC
* * * * * * *
33965 TTTGGAAGTTTGAGGGCAAAAATGGAATTTTTGGAAGTTCGGGAGTAAAAATATGATT
1 TTTGGAAGTTTGAGGGCAAAAATGAAATTTTTAGAAGTTTGAG-GTGAAAATGTAATT
*
34023 TTTGGAAGTTCGAGGGCAAAAATGAAATTTTTAGAAGTTTGAGGTGAAAATGTAATTT
1 TTTGGAAGTTTGAGGGCAAAAATGAAATTTTTAGAAGTTTGAGGTGAAAATGTAA-TT
** * * * * *
34081 TTTAAAAGTTAG-GGGCAAAAAT-ATGA-TTTTGGAAGTTT-AGGGGCAAAAATGGAATT
1 TTTGGAAGTTTGAGGGCAAAAATGA-AATTTTTAGAAGTTTGAGGTG--AAAATGTAATT
* * * *
34137 TTTGAGAAATTT-AGGGGTC-AAAATGTAATTTTTGAGAAGTTTAGTGGTTAAAATGTAATT
1 TTTG-GAAGTTTGA-GGG-CAAAAATGAAATTTTT-AGAAGTTT-GAGGTGAAAATGTAATT
* ** *
34197 TTTGGAAGTTTAAGGGTTAAAATGTAATTTTTAGAAAGTTTGAGG
1 TTTGGAAGTTTGAGGGCAAAAATGAAATTTTTAG-AAGTTTGAGG
34242 GCCTTTTGGG
Statistics
Matches: 174, Mismatches: 29, Indels: 32
0.74 0.12 0.14
Matches are distributed among these distances:
55 4 0.02
56 17 0.10
57 32 0.18
58 63 0.36
59 34 0.20
60 22 0.13
62 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (57 bp):
TTTGGAAGTTTGAGGGCAAAAATGAAATTTTTAGAAGTTTGAGGTGAAAATGTAATT
Found at i:36769 original size:18 final size:18
Alignment explanation
Indices: 36748--36782 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
36738 AGTTACTTGA
36748 GCTCTTTTAAGATCAAGG
1 GCTCTTTTAAGATCAAGG
36766 GCTCTTTTAAGATCAAG
1 GCTCTTTTAAGATCAAG
36783 ATGTTTAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (18 bp):
GCTCTTTTAAGATCAAGG
Found at i:47683 original size:33 final size:33
Alignment explanation
Indices: 47641--47704 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
47631 TGCTTGATGT
*
47641 TGAGCAAGAGGAACAACTAGGGAGTAAGCCTGG
1 TGAGCAAGAGGAACAACTAAGGAGTAAGCCTGG
*
47674 TGAGCAAGAGGAACAATTAAGGAGTAAGCCT
1 TGAGCAAGAGGAACAACTAAGGAGTAAGCCT
47705 AGTAGTCTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.39, C:0.14, G:0.33, T:0.14
Consensus pattern (33 bp):
TGAGCAAGAGGAACAACTAAGGAGTAAGCCTGG
Found at i:66051 original size:23 final size:24
Alignment explanation
Indices: 66025--66069 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
66015 GTCCCACTCC
66025 ATCTCACC-TCCTTATTTCTCCTT
1 ATCTCACCTTCCTTATTTCTCCTT
*
66048 ATCTTACCTTCCTTATTTCTCC
1 ATCTCACCTTCCTTATTTCTCC
66070 ATTTTGAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.13, C:0.38, G:0.00, T:0.49
Consensus pattern (24 bp):
ATCTCACCTTCCTTATTTCTCCTT
Found at i:68494 original size:19 final size:19
Alignment explanation
Indices: 68470--68506 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
68460 CTCAAAATTA
*
68470 CAAGTCTTTAAAATAAATC
1 CAAGTCTTAAAAATAAATC
68489 CAAGTCTTAAAAATAAAT
1 CAAGTCTTAAAAATAAAT
68507 TAAAATTCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (19 bp):
CAAGTCTTAAAAATAAATC
Found at i:71711 original size:21 final size:22
Alignment explanation
Indices: 71682--71724 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
71672 CTTGGAATAA
71682 AGTACTTTC-TTTATATTTTTAT
1 AGTACTTTCATTTA-ATTTTTAT
*
71704 AGTA-TTTCATTTAGTTTTTAT
1 AGTACTTTCATTTAATTTTTAT
71725 CTTTGAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.63
Consensus pattern (22 bp):
AGTACTTTCATTTAATTTTTAT
Found at i:74064 original size:23 final size:20
Alignment explanation
Indices: 74037--74085 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
74027 CCCTAATTTA
74037 AATTTTGTTAGTTCCTTATTATT
1 AATTTTGTTA-TT-CTT-TTATT
* *
74060 TATTTTTTTATTCTTTTATT
1 AATTTTGTTATTCTTTTATT
74080 AATTTT
1 AATTTT
74086 AATCAAGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 10 0.43
21 3 0.13
22 2 0.09
23 8 0.35
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.69
Consensus pattern (20 bp):
AATTTTGTTATTCTTTTATT
Found at i:77118 original size:24 final size:23
Alignment explanation
Indices: 77082--77128 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
77072 AACTATTCAT
77082 TTTATCTTAATTTGC-TCTGACAA
1 TTTATCTTAATTTGCGT-TGACAA
*
77105 TTTATTTTATATTTGCGTTGACAA
1 TTTATCTTA-ATTTGCGTTGACAA
77129 ATTAATTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 12 0.57
25 1 0.05
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.51
Consensus pattern (23 bp):
TTTATCTTAATTTGCGTTGACAA
Found at i:80772 original size:37 final size:38
Alignment explanation
Indices: 80674--80773 Score: 98
Period size: 38 Copynumber: 2.7 Consensus size: 38
80664 ATATTTCTAG
* * *
80674 ATTGCA-CCAGAGATTGTCGCTGAAAAAATATTCTTCAA
1 ATTGCATCCAGA-ACTGTCGCTGCATAAATATTCTTCAA
* * *
80712 ATTGCATCCAGAACTATCACTGCATAAGTATTCTTC-A
1 ATTGCATCCAGAACTGTCGCTGCATAAATATTCTTCAA
*
80749 ATTGCATCTAGGAA-TGTCGCTGCAT
1 ATTGCATCCA-GAACTGTCGCTGCAT
80774 GAACATGTAC
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
37 19 0.37
38 27 0.53
39 5 0.10
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (38 bp):
ATTGCATCCAGAACTGTCGCTGCATAAATATTCTTCAA
Found at i:80797 original size:26 final size:26
Alignment explanation
Indices: 80755--80816 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
80745 TTCAATTGCA
*
80755 TCTAGGAA-TGTCGCTGCATGAACATG
1 TCTA-GAATTGTCACTGCATGAACATG
*
80781 TAC-AGAATTGTCACTGCATGAACGTG
1 T-CTAGAATTGTCACTGCATGAACATG
80807 TCTAGAATTG
1 TCTAGAATTG
80817 CGCCCACAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
25 4 0.13
26 26 0.84
27 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (26 bp):
TCTAGAATTGTCACTGCATGAACATG
Found at i:85326 original size:24 final size:24
Alignment explanation
Indices: 85276--85343 Score: 93
Period size: 24 Copynumber: 2.8 Consensus size: 24
85266 TACAATCTAA
85276 ATCATTCA-TCAAAGATTTGAAGATAC
1 ATCATTCAGTC-AA-ATTT-AAGATAC
85302 ATCATTCAGTCAAATTTAAGATAC
1 ATCATTCAGTCAAATTTAAGATAC
*
85326 ATCATTTAGTCAAATTTA
1 ATCATTCAGTCAAATTTA
85344 TCCAATTCAT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
24 24 0.60
25 4 0.10
26 10 0.25
27 2 0.05
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (24 bp):
ATCATTCAGTCAAATTTAAGATAC
Found at i:90425 original size:18 final size:17
Alignment explanation
Indices: 90402--90450 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
90392 TGGCAATATA
*
90402 TTTCTTTTCTTTTCTTTT
1 TTTCTTTTCTTTT-TTTG
90420 TTTCTTTTCTTCTTTTTG
1 TTTCTTTTCTT-TTTTTG
90438 TTTC-TTTCTTTTT
1 TTTCTTTTCTTTTT
90451 GTGAATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 3 0.10
17 6 0.21
18 18 0.62
19 2 0.07
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (17 bp):
TTTCTTTTCTTTTTTTG
Found at i:90452 original size:14 final size:14
Alignment explanation
Indices: 90402--90449 Score: 66
Period size: 13 Copynumber: 3.6 Consensus size: 14
90392 TGGCAATATA
90402 TTTCTTTTCTTTTC
1 TTTCTTTTCTTTTC
90416 TTT-TTTTCTTTTC
1 TTTCTTTTCTTTTC
90429 -TTCTTTT-TGTTTC
1 TTTCTTTTCT-TTTC
90442 TTTCTTTT
1 TTTCTTTT
90450 TGTGAATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
12 3 0.10
13 18 0.58
14 10 0.32
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (14 bp):
TTTCTTTTCTTTTC
Found at i:91049 original size:17 final size:17
Alignment explanation
Indices: 91011--91070 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
91001 TATAAGAATG
91011 GAAATGCAACT-AC-AAT
1 GAAATGC-ACTAACAAAT
*
91027 GCAAATGTACTAACAAAT
1 G-AAATGCACTAACAAAT
* *
91045 GAAATGCAGTGACAAAT
1 GAAATGCACTAACAAAT
91062 GAAAATGCA
1 G-AAATGCA
91071 ATGAAAACTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 4 0.11
17 21 0.58
18 11 0.31
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.18
Consensus pattern (17 bp):
GAAATGCACTAACAAAT
Found at i:91231 original size:18 final size:21
Alignment explanation
Indices: 91192--91240 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
91182 CTCACCTTTT
91192 TCTTTGCGCTTCTTCTTCTTA
1 TCTTTGCGCTTCTTCTTCTTA
*
91213 TCTTTGCGCTT-TCTCTTATTA
1 TCTTTGCGCTTCT-TCTTCTTA
91234 TCCTTTG
1 T-CTTTG
91241 AATCAACCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 1 0.04
21 19 0.76
22 5 0.20
ACGTcount: A:0.06, C:0.27, G:0.10, T:0.57
Consensus pattern (21 bp):
TCTTTGCGCTTCTTCTTCTTA
Found at i:103378 original size:21 final size:21
Alignment explanation
Indices: 103325--103378 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
103315 TGAAGAGTGT
*
103325 TGTGGCTGCATATGATTCTAA
1 TGTGGCTGCATCTGATTCTAA
* **
103346 TGTGCCTGCATCTGATTCTGG
1 TGTGGCTGCATCTGATTCTAA
*
103367 TGTGGCTACATC
1 TGTGGCTGCATC
103379 AAAGTTTGCT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (21 bp):
TGTGGCTGCATCTGATTCTAA
Found at i:107600 original size:39 final size:39
Alignment explanation
Indices: 107546--107624 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
107536 GGACGGTAGC
107546 AGACCTAGGGTTAATGAAAATAGCCGACCAAGACAATAA
1 AGACCTAGGGTTAATGAAAATAGCCGACCAAGACAATAA
*
107585 AGACCTAGGGTTAATGAAAATAGCCGACCAAGATAATAA
1 AGACCTAGGGTTAATGAAAATAGCCGACCAAGACAATAA
107624 A
1 A
107625 TAGGGTATTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.47, C:0.16, G:0.20, T:0.16
Consensus pattern (39 bp):
AGACCTAGGGTTAATGAAAATAGCCGACCAAGACAATAA
Found at i:110657 original size:119 final size:120
Alignment explanation
Indices: 110435--110668 Score: 296
Period size: 119 Copynumber: 2.0 Consensus size: 120
110425 CCTCCTTTGG
* *
110435 GTACGATCCTCAGAATACTTCCAAGTGTTTCATTGTAAACACACTATATTTACAACCTAACCCGT
1 GTACGATCCTCAGAACACTACCAAGTGTTTCATTGTAAACACACTATATTTACAACCTAACCCGT
* * *
110500 ATACTTACGGAAAGCCGAAATCTACACCGAACAGGAGTAAGTTTGGAGGCAGTTA
66 ATACTTACGGAAAGCCAAAACCTACACCGAACAGGAGTAAGTTCGGAGGCAGTTA
* * *
110555 GTACGATCCTC-GAAACACTACCAAGTGTTTCGTTGT-AACACACTATATTTATAACCTGACCCG
1 GTACGATCCTCAG-AACACTACCAAGTGTTTCATTGTAAACACACTATATTTACAACCTAACCCG
** * * *
110618 TATACTTGTGG-AAGCCAAAAACCTATACTGAAC-GAGAGTACGTTCGGAGGC
65 TATACTTACGGAAAGCC-AAAACCTACACCGAACAG-GAGTAAGTTCGGAGGC
110669 GATCATGTTG
Statistics
Matches: 98, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
118 6 0.06
119 61 0.62
120 31 0.32
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (120 bp):
GTACGATCCTCAGAACACTACCAAGTGTTTCATTGTAAACACACTATATTTACAACCTAACCCGT
ATACTTACGGAAAGCCAAAACCTACACCGAACAGGAGTAAGTTCGGAGGCAGTTA
Found at i:115039 original size:15 final size:16
Alignment explanation
Indices: 115014--115046 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
115004 TTTGCTGTTC
115014 TTTTCTTTCTTCTTTA
1 TTTTCTTTCTTCTTTA
115030 TTTT-TTTCTTCTTTA
1 TTTTCTTTCTTCTTTA
115045 TT
1 TT
115047 CGAACTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTCTTTCTTCTTTA
Found at i:117613 original size:17 final size:17
Alignment explanation
Indices: 117591--117624 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
117581 TAAGAATTTA
*
117591 AAGAAAGTAAATTTAAG
1 AAGAAACTAAATTTAAG
*
117608 AAGAAACTAAGTTTAAG
1 AAGAAACTAAATTTAAG
117625 TAACAACCTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.03, G:0.18, T:0.24
Consensus pattern (17 bp):
AAGAAACTAAATTTAAG
Found at i:119482 original size:19 final size:19
Alignment explanation
Indices: 119458--119502 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
119448 TGTTTCGAAG
*
119458 GTGCTCGGAAACTAATCTA
1 GTGCTCAGAAACTAATCTA
119477 GTGCTCAGAAACTAATCTA
1 GTGCTCAGAAACTAATCTA
119496 GTGCTCA
1 GTGCTCA
119503 ATTGGGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (19 bp):
GTGCTCAGAAACTAATCTA
Found at i:126663 original size:18 final size:19
Alignment explanation
Indices: 126640--126690 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
126630 CGAACCATAG
126640 CAAATTTTGAACTTTAA-A
1 CAAATTTTGAACTTTAATA
126658 CAAATTTTGAAGAC-TTAATA
1 CAAATTTTG-A-ACTTTAATA
126678 -AAATTTTGAACTT
1 CAAATTTTGAACTT
126691 AAGTGAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
17 2 0.07
18 11 0.38
19 13 0.45
20 3 0.10
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (19 bp):
CAAATTTTGAACTTTAATA
Found at i:126692 original size:17 final size:17
Alignment explanation
Indices: 126641--126706 Score: 64
Period size: 17 Copynumber: 3.7 Consensus size: 17
126631 GAACCATAGC
126641 AAATTTTGAACTTTAA-A
1 AAATTTTGAAC-TTAATA
126658 CAAATTTTGAAGACTTAATA
1 -AAATTTTG-A-ACTTAATA
126678 AAATTTTGAACTTAAGT-
1 AAATTTTGAACTTAA-TA
*
126695 GAATTTTGAACT
1 AAATTTTGAACT
126707 ATGTTATTGA
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
17 17 0.40
18 10 0.23
19 13 0.30
20 3 0.07
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (17 bp):
AAATTTTGAACTTAATA
Found at i:129969 original size:107 final size:107
Alignment explanation
Indices: 129818--130248 Score: 299
Period size: 123 Copynumber: 3.7 Consensus size: 107
129808 ATGGAAGAAC
* * * *
129818 ATTATATCCTTTCTAAAAGGATAGTAACTTTCATGTTTTTAATATCCAATTTCCTTTTATTTAAT
1 ATTATATCATTTCCAAAAGGATAGTAACTTCCATATTTTTAATATCCAATTTCCTTTTATTTAAT
* *
129883 ATCTGATATTAAAATAAAAATATATAGAAGGTTTATTAAAAT
66 ATCTCATATTAAAACAAAAATATATAGAAGGTTTATTAAAAT
* * * * *
129925 ATTATATCATTTCCAAGAGGATATTAACTTCCATATTTTTAATATTCAGTTTTCTTTTATTTAAT
1 ATTATATCATTTCCAAAAGGATAGTAACTTCCATATTTTTAATATCCAATTTCCTTTTATTTAAT
*
129990 ATCTCATATTAAAACGAAAATATCCCCTTAGAGAAATATATGGAAGGTTTATTAAAAC
66 ATCTCATATTAAAAC-AAAA-A------T------ATATA--GAAGGTTTATTAAAAT
* * * * * * **
130048 ATTATATTC-TTTCCAAAAAGATATTGACTTTCATGTTCTTAATATTTAATTTCCTTTTATTTAA
1 ATTATA-TCATTTCCAAAAGGATAGTAACTTCCATATTTTTAATATCCAATTTCCTTTTATTTAA
* *
130112 TATCTCATGTTAAAACGAAATTATTTCTTTATAGAAATATATGGAAGGTTTATTAAAAC
65 TATCTCATATTAAAAC-AAA--A-------AT----ATATA--GAAGGTTTATTAAAAT
* * * * *
130171 ATTATATCCTTTCAAAAAGGATATTAACTTCCATGTTTTTAATATTCAA-TTCCTTTTATTTAAT
1 ATTATATCATTTCCAAAAGGATAGTAACTTCCATATTTTTAATATCCAATTTCCTTTTATTTAAT
*
130235 ATCTCAAATTAAAA
66 ATCTCATATTAAAA
130249 TGGAATTGTT
Statistics
Matches: 268, Mismatches: 30, Indels: 37
0.80 0.09 0.11
Matches are distributed among these distances:
107 69 0.26
108 4 0.01
109 1 0.00
115 1 0.00
121 5 0.02
122 29 0.11
123 153 0.57
124 2 0.01
125 2 0.01
131 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (107 bp):
ATTATATCATTTCCAAAAGGATAGTAACTTCCATATTTTTAATATCCAATTTCCTTTTATTTAAT
ATCTCATATTAAAACAAAAATATATAGAAGGTTTATTAAAAT
Found at i:130037 original size:123 final size:121
Alignment explanation
Indices: 129900--130248 Score: 482
Period size: 123 Copynumber: 2.8 Consensus size: 121
129890 ATTAAAATAA
* * * *
129900 AAATATATAGAAGGTTTATTAAAATATTATATCATTTCCAAGAGGATATTAACTTCCATATTTTT
1 AAATATATGGAAGGTTTATTAAAACATTATATC-TTTCCAAAAGGATATTAACTTCCATGTTTTT
*
129965 AATATTCAGTTTTCTTTTATTTAATATCTCATATTAAAACGAAAATATCCCCTTAGAG
65 AATATTCA-TTTCCTTTTATTTAATATCTCATATTAAAACGAAAATATCCCCTTAGAG
* * * *
130023 AAATATATGGAAGGTTTATTAAAACATTATATTCTTTCCAAAAAGATATTGACTTTCATGTTCTT
1 AAATATATGGAAGGTTTATTAAAACATTATA-TCTTTCCAAAAGGATATTAACTTCCATGTTTTT
* * * ** * *
130088 AATATTTAATTTCCTTTTATTTAATATCTCATGTTAAAACGAAATTATTTCTTTATAG
65 AATA-TTCATTTCCTTTTATTTAATATCTCATATTAAAACGAAAATATCCCCTTAGAG
*
130146 AAATATATGGAAGGTTTATTAAAACATTATATCCTTTCAAAAAGGATATTAACTTCCATGTTTTT
1 AAATATATGGAAGGTTTATTAAAACATTATAT-CTTTCCAAAAGGATATTAACTTCCATGTTTTT
* *
130211 AATATTCAATTCCTTTTATTTAATATCTCAAATTAAAA
65 AATATTCATTTCCTTTTATTTAATATCTCATATTAAAA
130249 TGGAATTGTT
Statistics
Matches: 198, Mismatches: 25, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
122 31 0.16
123 162 0.82
124 5 0.03
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (121 bp):
AAATATATGGAAGGTTTATTAAAACATTATATCTTTCCAAAAGGATATTAACTTCCATGTTTTTA
ATATTCATTTCCTTTTATTTAATATCTCATATTAAAACGAAAATATCCCCTTAGAG
Found at i:130223 original size:21 final size:22
Alignment explanation
Indices: 130191--130241 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
130181 TTCAAAAAGG
130191 ATATT-AACTTCCATGTT-TTTA
1 ATATTCAACTTCC-TGTTATTTA
*
130212 ATATTCAA-TTCCTTTTATTTA
1 ATATTCAACTTCCTGTTATTTA
130233 ATATCTCAA
1 ATAT-TCAA
130242 ATTAAAATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 3 0.12
21 17 0.65
22 6 0.23
ACGTcount: A:0.31, C:0.16, G:0.02, T:0.51
Consensus pattern (22 bp):
ATATTCAACTTCCTGTTATTTA
Found at i:130280 original size:14 final size:14
Alignment explanation
Indices: 130261--130289 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
130251 GAATTGTTCC
130261 TTTATAGAAATATA
1 TTTATAGAAATATA
130275 TTTATAGAAATATA
1 TTTATAGAAATATA
130289 T
1 T
130290 GAAAGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (14 bp):
TTTATAGAAATATA
Found at i:133033 original size:23 final size:24
Alignment explanation
Indices: 133002--133048 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
132992 TAAATCAAAA
133002 AAATATCTCT-AGAG-ATTTTCTG
1 AAATATCTCTCAGAGAATTTTCTG
133024 AAATAATCTCTCCAGAGAATTTTCT
1 AAAT-ATCTCT-CAGAGAATTTTCT
133049 CTCTACAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 4 0.19
23 6 0.29
25 4 0.19
26 7 0.33
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (24 bp):
AAATATCTCTCAGAGAATTTTCTG
Found at i:141533 original size:22 final size:22
Alignment explanation
Indices: 141508--141551 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
141498 AACAAAACAA
141508 AATT-AAAAATAAAAGAAAATAG
1 AATTGAAAAA-AAAAGAAAATAG
* *
141530 AATTGAAAGAAATAGAAAATAG
1 AATTGAAAAAAAAAGAAAATAG
141552 GGAAGTCGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.18
Consensus pattern (22 bp):
AATTGAAAAAAAAAGAAAATAG
Found at i:145421 original size:40 final size:41
Alignment explanation
Indices: 145284--145562 Score: 182
Period size: 40 Copynumber: 6.9 Consensus size: 41
145274 TTTGAACAGA
* ** *
145284 AAACGCCGCAAAAAGTAAAGCAATAGTAGCG-TTTA-CCAT
1 AAACGCCGCAAAAGGTAAAGCAATAGCGGCGTTTTATGCAT
** * * *
145323 AAACGCCGCAAAAAATAAAGAGCAATA-AGGC-ATTTATTG-AA
1 AAACGCCGCAAAAGGT-AA-AGCAATAGCGGCGTTTTA-TGCAT
* * *
145364 AAATGTCACAAAAGGTAAAGCAATAGCGGCGTTTTAT-CAT
1 AAACGCCGCAAAAGGTAAAGCAATAGCGGCGTTTTATGCAT
* * * *
145404 AAACGCAGCAAAAGGTAAAGAGCAATAGCAGCG-TTTATGGAA
1 AAACGCCGCAAAAGGT-AA-AGCAATAGCGGCGTTTTATGCAT
* * ** * *
145446 AAAAGCCGCAAAAAGTAAAGTTATAGCGGCATTTTA-CCAT
1 AAACGCCGCAAAAGGTAAAGCAATAGCGGCGTTTTATGCAT
* *
145486 AAACGCCGC-AAATGTAAAGCAATAGCGGCG-TTTATGGAT
1 AAACGCCGCAAAAGGTAAAGCAATAGCGGCGTTTTATGCAT
* *
145525 AAAACGCCGCAAAATGTAAAGAGCATTAGCGGCGTTTT
1 -AAACGCCGCAAAAGGT-AA-AGCAATAGCGGCGTTTT
145563 TCCCAAAAAC
Statistics
Matches: 184, Mismatches: 38, Indels: 31
0.73 0.15 0.12
Matches are distributed among these distances:
38 4 0.02
39 41 0.22
40 54 0.29
41 42 0.23
42 28 0.15
43 12 0.07
44 3 0.02
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.20
Consensus pattern (41 bp):
AAACGCCGCAAAAGGTAAAGCAATAGCGGCGTTTTATGCAT
Found at i:145555 original size:82 final size:83
Alignment explanation
Indices: 145283--145562 Score: 249
Period size: 82 Copynumber: 3.4 Consensus size: 83
145273 ATTTGAACAG
* ** * **
145283 AAAACGCCGCAAAAAGT-AA-AGCAATAGTAGCG-TTTACCATAAACGCCGCAAAAAATAAAGAG
1 AAAAAGCCGCAAAAAGTAAAGAGC-ATAGCGGCGTTTTACCATAAACGCAGCAAAAGGTAAAGAG
* *
145345 CAATA--AGGCATTTATTGA
65 CAATAGCA-GCGTTTATGGA
* * * * *
145363 AAAATGTCACAAAAGGT-AA-AGCAATAGCGGCGTTTTATCATAAACGCAGCAAAAGGTAAAGAG
1 AAAAAGCCGCAAAAAGTAAAGAGC-ATAGCGGCGTTTTACCATAAACGCAGCAAAAGGTAAAGAG
145426 CAATAGCAGCGTTTATGGA
65 CAATAGCAGCGTTTATGGA
** * * *
145445 AAAAAGCCGCAAAAAGTAAAG-TTATAGCGGCATTTTACCATAAACGCCGC-AAATGT-AA-AGC
1 AAAAAGCCGCAAAAAGTAAAGAGCATAGCGGCGTTTTACCATAAACGCAGCAAAAGGTAAAGAGC
*
145506 AATAGCGGCGTTTATGGA
66 AATAGCAGCGTTTATGGA
* *
145524 TAAAACGCCGCAAAATGTAAAGAGCATTAGCGGCGTTTT
1 -AAAAAGCCGCAAAAAGTAAAGAGCA-TAGCGGCGTTTT
145563 TCCCAAAAAC
Statistics
Matches: 164, Mismatches: 28, Indels: 14
0.80 0.14 0.07
Matches are distributed among these distances:
79 20 0.12
80 47 0.29
81 37 0.23
82 57 0.35
83 3 0.02
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.20
Consensus pattern (83 bp):
AAAAAGCCGCAAAAAGTAAAGAGCATAGCGGCGTTTTACCATAAACGCAGCAAAAGGTAAAGAGC
AATAGCAGCGTTTATGGA
Found at i:145903 original size:29 final size:31
Alignment explanation
Indices: 145842--145904 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 31
145832 ATGTTAAATT
* * * *
145842 TGGTACTTGTACTTTTATAAAATGTTCATTG
1 TGGTACATGTACTTTTAGAAAATGTCCAATG
145873 TGGTACATGTAC-TTT-GAAAATGTCCAATG
1 TGGTACATGTACTTTTAGAAAATGTCCAATG
145902 TGG
1 TGG
145905 CACTTGAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 14 0.50
30 3 0.11
31 11 0.39
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41
Consensus pattern (31 bp):
TGGTACATGTACTTTTAGAAAATGTCCAATG
Found at i:145915 original size:29 final size:29
Alignment explanation
Indices: 145860--145916 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
145850 GTACTTTTAT
* * * *
145860 AAAATGTTCATTGTGGTACATGTACTTTG
1 AAAATGTCCAATGTGGCACATGAACTTTG
*
145889 AAAATGTCCAATGTGGCACTTGAACTTT
1 AAAATGTCCAATGTGGCACATGAACTTT
145917 CAATTTGTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (29 bp):
AAAATGTCCAATGTGGCACATGAACTTTG
Found at i:146518 original size:92 final size:93
Alignment explanation
Indices: 146355--146535 Score: 310
Period size: 92 Copynumber: 1.9 Consensus size: 93
146345 CATCAACTTC
* *
146355 AATTATATTCCGAAATCCTCAAAAAAAAATAATTAATAAATAATTACAAACAATCAAATTAAAAT
1 AATTATATTACGAAATCCTC-AAAAAAAATAATTAATAAATAATTACAAACAATCAAACTAAAAT
*
146420 CTTATTTCTTTATGACCTTTCATAACTCT
65 CCTATTTCTTTATGACCTTTCATAACTCT
*
146449 AATTATATTATGAAATCCTC-AAAAAAATAATTAATAAATAATTACAAACAATCAAACTAAAATC
1 AATTATATTACGAAATCCTCAAAAAAAATAATTAATAAATAATTACAAACAATCAAACTAAAATC
146513 CTATTTCTTTATGACCTTTCATA
66 CTATTTCTTTATGACCTTTCATA
146536 CATACCCACC
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
92 65 0.78
94 18 0.22
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35
Consensus pattern (93 bp):
AATTATATTACGAAATCCTCAAAAAAAATAATTAATAAATAATTACAAACAATCAAACTAAAATC
CTATTTCTTTATGACCTTTCATAACTCT
Found at i:147375 original size:42 final size:41
Alignment explanation
Indices: 147249--147376 Score: 132
Period size: 42 Copynumber: 3.1 Consensus size: 41
147239 AATAATCACG
* *
147249 TTTATGGGAAAAACACCACTAAAGGTTAAGCAATAGCGGCA
1 TTTATGGGAAAAACGCCGCTAAAGGTTAAGCAATAGCGGCA
* * * * * ***
147290 GTTATGGG-AAAACGTCGCAAAAGGTAAAGAGAATTAATTGCA
1 TTTATGGGAAAAACGCCGCTAAAGGTTAAG-CAA-TAGCGGCA
147332 TTTATGGGAAAAATCGCCGCTAAAGGTTAAGCAATAGCGGCA
1 TTTATGGGAAAAA-CGCCGCTAAAGGTTAAGCAATAGCGGCA
147374 TTT
1 TTT
147377 TCCCATAAAC
Statistics
Matches: 65, Mismatches: 18, Indels: 7
0.72 0.20 0.08
Matches are distributed among these distances:
40 16 0.25
41 9 0.14
42 20 0.31
43 6 0.09
44 14 0.22
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (41 bp):
TTTATGGGAAAAACGCCGCTAAAGGTTAAGCAATAGCGGCA
Found at i:150402 original size:30 final size:30
Alignment explanation
Indices: 150318--150395 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
150308 GACTAGTCCA
*
150318 TTAATTATTTAATTCAA-AATATTTAATTAT
1 TTAATTATTTAATTCAACAA-AATTAATTAT
* ** *
150348 TTAATTATTAAAAACAACTAAATTAATTAT
1 TTAATTATTTAATTCAACAAAATTAATTAT
150378 TTAATTATTTAATTCAAC
1 TTAATTATTTAATTCAAC
150396 CCAATTATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 38 0.97
31 1 0.03
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.47
Consensus pattern (30 bp):
TTAATTATTTAATTCAACAAAATTAATTAT
Found at i:150681 original size:6 final size:6
Alignment explanation
Indices: 150667--150699 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
150657 TAGGATGATA
*
150667 AAATAT AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
150700 CATATAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:156820 original size:43 final size:42
Alignment explanation
Indices: 156741--156966 Score: 256
Period size: 43 Copynumber: 5.3 Consensus size: 42
156731 TCTATTAATG
*
156741 TTAGCGGCGTTTGTGGGAAAATGTCGCTAAAGAACATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGGTCGCTAAAGAACATGTTCT
* * *
156783 ATAGCGGCGTTTGTGGGGAAAAGGTCGTTAAAAAACATGTTCT
1 TTAGCGGCGTTTGT-GGGAAAAGGTCGCTAAAGAACATGTTCT
* * * *
156826 TTAGTGGCATTTATGGGAAAAGCGTCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAG-GTCGCTAAAGAACATGTTCT
* *
156869 TTAGTGGCGTTTTTGGGAAAAGAGTCGCTATAA-AACATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAG-GTCGCTA-AAGAACATGTTCT
* * * *
156912 TTAGCGGCATTTGTGGGAAAAGGGCCGTTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAA-GGTCGCTAAAGAACATGTTCT
* *
156955 ATAACGGCGTTT
1 TTAGCGGCGTTT
156967 TTCGAAAAGC
Statistics
Matches: 155, Mismatches: 24, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
42 23 0.15
43 129 0.83
44 3 0.02
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (42 bp):
TTAGCGGCGTTTGTGGGAAAAGGTCGCTAAAGAACATGTTCT
Found at i:156968 original size:86 final size:85
Alignment explanation
Indices: 156741--157008 Score: 306
Period size: 86 Copynumber: 3.1 Consensus size: 85
156731 TCTATTAATG
* * * *
156741 TTAGCGGCGTTTGTGGGAAAA-TGTCGCTAAAGAACATGTTCTATAGCGGCGTTTGTGGGGAAAA
1 TTAGCGGCATTTGTGGGAAAAGCGTCGCTAAAGACCATGTTCTATAGCGGCGTTT-TTGGGAAAA
*
156805 GGTCGTTAAAAAACATGTTCT
65 GGTCGCTAAAAAACATGTTCT
* * * *
156826 TTAGTGGCATTTATGGGAAAAGCGTCGCTAAAGACCATGTTCTTTAGTGGCGTTTTTGGGAAAAG
1 TTAGCGGCATTTGTGGGAAAAGCGTCGCTAAAGACCATGTTCTATAGCGGCGTTTTTGGGAAAAG
*
156891 AGTCGCTATAAAACATGTTCT
66 -GTCGCTAAAAAACATGTTCT
* * * * *
156912 TTAGCGGCATTTGTGGGAAAAGGGCCGTTAAAGACCATGTTCTATAACGGCGTTTTT-CGAAAAG
1 TTAGCGGCATTTGTGGGAAAAGCGTCGCTAAAGACCATGTTCTATAGCGGCGTTTTTGGGAAAAG
** * * *
156976 CACCACTAAAGATCATGTTCT
66 -GTCGCTAAAAAACATGTTCT
*
156997 ATAGCGGCATTT
1 TTAGCGGCATTT
157009 TTTCGCACAA
Statistics
Matches: 154, Mismatches: 27, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
85 58 0.38
86 96 0.62
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (85 bp):
TTAGCGGCATTTGTGGGAAAAGCGTCGCTAAAGACCATGTTCTATAGCGGCGTTTTTGGGAAAAG
GTCGCTAAAAAACATGTTCT
Found at i:157011 original size:129 final size:128
Alignment explanation
Indices: 156742--157010 Score: 310
Period size: 128 Copynumber: 2.1 Consensus size: 128
156732 CTATTAATGT
* * *
156742 TAGCGGCGTTTGTGGGAAAATGTCGCTAAAGAACATGTTCTATAGCGGCGTTTGTGGGGAAAAGG
1 TAGCGGCGTTTTTGGGAAAAAGTCGCTAAAGAACATGTTCTATAGCGGCATTTGTGGGGAAAAGG
* * ** * ** * *
156807 TCGTTAAAAAACATGTTCTTTAGTGGCATTTATGGGAAAAGCGTCGCTAAAGACCATGTTCTT
66 CCGTTAAAAAACATGTTCTATAACGGCATTTATGCGAAAAGCACCACTAAAGACCATGTTCTA
* *
156870 TAGTGGCGTTTTTGGGAAAAGAGTCGCTATAA-AACATGTTCTTTAGCGGCATTTGT-GGGAAAA
1 TAGCGGCGTTTTTGGGAAAA-AGTCGCTA-AAGAACATGTTCTATAGCGGCATTTGTGGGGAAAA
* * * * *
156933 GGGCCGTTAAAGACCATGTTCTATAACGGCGTTT-TTCGAAAAGCACCACTAAAGATCATGTTCT
64 -GGCCGTTAAAAAACATGTTCTATAACGGCATTTATGCGAAAAGCACCACTAAAGACCATGTTCT
156997 A
128 A
*
156998 TAGCGGCATTTTT
1 TAGCGGCGTTTTT
157011 TCGCACAAAT
Statistics
Matches: 117, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
128 60 0.51
129 55 0.47
130 2 0.02
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (128 bp):
TAGCGGCGTTTTTGGGAAAAAGTCGCTAAAGAACATGTTCTATAGCGGCATTTGTGGGGAAAAGG
CCGTTAAAAAACATGTTCTATAACGGCATTTATGCGAAAAGCACCACTAAAGACCATGTTCTA
Found at i:158033 original size:23 final size:24
Alignment explanation
Indices: 157973--158024 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
157963 TCTTTTTTTG
157973 CCATTGAAGATGTTTCTTTTTCAT
1 CCATTGAAGATGTTTCTTTTTCAT
157997 CCATTGAAGATGTTTC-TTTTCAT
1 CCATTGAAGATGTTTCTTTTTCAT
158020 CCATT
1 CCATT
158025 ACATATGTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 12 0.43
24 16 0.57
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (24 bp):
CCATTGAAGATGTTTCTTTTTCAT
Found at i:159466 original size:26 final size:25
Alignment explanation
Indices: 159436--159512 Score: 77
Period size: 24 Copynumber: 3.1 Consensus size: 25
159426 TTGTGGCATT
*
159436 TTGTTTACCTTTGTGGCATAATCTA
1 TTGTTTACCTTTGTGGCGTAATCTA
** *
159461 TATGTTGGCCTTTGTGGTGT-ATCCT-
1 T-TGTTTACCTTTGTGGCGTAAT-CTA
*
159486 TTATTTACCTTTGTGGCGTAATCTA
1 TTGTTTACCTTTGTGGCGTAATCTA
159511 TT
1 TT
159513 TGGACCTTGT
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
24 16 0.40
25 8 0.20
26 16 0.40
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.49
Consensus pattern (25 bp):
TTGTTTACCTTTGTGGCGTAATCTA
Found at i:159519 original size:24 final size:25
Alignment explanation
Indices: 159442--159524 Score: 70
Period size: 24 Copynumber: 3.4 Consensus size: 25
159432 CATTTTGTTT
*
159442 ACCTTTGTGGCATAATCTATATGTTGG
1 ACCTTTGTGGCGTAATCT-TAT-TTGG
*
159469 -CCTTTGTGGTGT-ATCCTTTATTT--
1 ACCTTTGTGGCGTAAT-C-TTATTTGG
159492 ACCTTTGTGGCGTAATC-TATTTGG
1 ACCTTTGTGGCGTAATCTTATTTGG
159516 ACC-TTGTGG
1 ACCTTTGTGG
159525 TGTACTCTGC
Statistics
Matches: 47, Mismatches: 3, Indels: 16
0.71 0.05 0.24
Matches are distributed among these distances:
22 5 0.11
23 6 0.13
24 15 0.32
25 6 0.13
26 14 0.30
27 1 0.02
ACGTcount: A:0.16, C:0.17, G:0.23, T:0.45
Consensus pattern (25 bp):
ACCTTTGTGGCGTAATCTTATTTGG
Found at i:159703 original size:15 final size:16
Alignment explanation
Indices: 159676--159705 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
159666 AATCAAAAGA
159676 TTCTTATAAAAGAAGC
1 TTCTTATAAAAGAAGC
159692 TTCTTA-AAAAGAAG
1 TTCTTATAAAAGAAG
159706 TATGTATCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.30
Consensus pattern (16 bp):
TTCTTATAAAAGAAGC
Found at i:164828 original size:33 final size:33
Alignment explanation
Indices: 164791--164853 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
164781 GGCACTAGGG
164791 TTAATGATGGATCATTG-TTGACAAAGCTAACTA
1 TTAATGATGGATCATTGCTT-ACAAAGCTAACTA
*
164824 TTAATGATGGATCATTGCTTACAGAGCTAA
1 TTAATGATGGATCATTGCTTACAAAGCTAA
164854 TTGTTAAGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (33 bp):
TTAATGATGGATCATTGCTTACAAAGCTAACTA
Found at i:199732 original size:19 final size:19
Alignment explanation
Indices: 199708--199744 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
199698 ATGAACAGAT
*
199708 TTAAAACAAGTTTGAAAGC
1 TTAAAACAAGTTGGAAAGC
*
199727 TTAAAAGAAGTTGGAAAG
1 TTAAAACAAGTTGGAAAG
199745 AATAGATGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.05, G:0.22, T:0.24
Consensus pattern (19 bp):
TTAAAACAAGTTGGAAAGC
Found at i:200719 original size:37 final size:37
Alignment explanation
Indices: 200676--200807 Score: 183
Period size: 37 Copynumber: 3.6 Consensus size: 37
200666 CGCAAAGGCT
* *
200676 TGCTAGGCACAAAGCCCGAACACACCAGCACAAAGCC
1 TGCTAGGCACATAGCCCGAATACACCAGCACAAAGCC
* ** * **
200713 TGCTAGGCACATAGCCCAAATACACTGGCACGAATTC
1 TGCTAGGCACATAGCCCGAATACACCAGCACAAAGCC
200750 TGCTAGGCACATAGCCCGAATACACCAGCACAAAGCC
1 TGCTAGGCACATAGCCCGAATACACCAGCACAAAGCC
*
200787 TGCTAGGCACATAGCCTGAAT
1 TGCTAGGCACATAGCCCGAAT
200808 TCTTAGATGT
Statistics
Matches: 80, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 80 1.00
ACGTcount: A:0.34, C:0.33, G:0.20, T:0.14
Consensus pattern (37 bp):
TGCTAGGCACATAGCCCGAATACACCAGCACAAAGCC
Found at i:207450 original size:31 final size:29
Alignment explanation
Indices: 207415--207491 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
207405 TTAACAGGTT
*
207415 AATGACTAAAATGTTACAATGCGATAACATA
1 AATGACTAAAATGTAACAATGC-A-AACATA
* * *
207446 AATGACTAAAACGTAACATTTCAAACATA
1 AATGACTAAAATGTAACAATGCAAACATA
*
207475 AGTGACTAAAATGTAAC
1 AATGACTAAAATGTAAC
207492 TTCAGGCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 21 0.52
30 1 0.03
31 18 0.45
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.25
Consensus pattern (29 bp):
AATGACTAAAATGTAACAATGCAAACATA
Found at i:207664 original size:43 final size:45
Alignment explanation
Indices: 207590--207697 Score: 116
Period size: 43 Copynumber: 2.4 Consensus size: 45
207580 AGCACAAATT
** *
207590 TTAAATTATAACATTTTTAAATGTGTAATAATTATCACAA-TTACTA
1 TTAAATTATAATTTTTTTAAA-GTGTAATAATTACCACAACTT-CTA
207636 TTAAATTATAATTTTTTTAAA-TGT-ATAATTACCACAACTTCTA
1 TTAAATTATAATTTTTTTAAAGTGTAATAATTACCACAACTTCTA
**
207679 TTTTATT-TCAATTTTTTTA
1 TTAAATTAT-AATTTTTTTA
207698 TTTTAAAATG
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
42 1 0.02
43 30 0.55
44 5 0.09
46 19 0.35
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.50
Consensus pattern (45 bp):
TTAAATTATAATTTTTTTAAAGTGTAATAATTACCACAACTTCTA
Found at i:207893 original size:41 final size:41
Alignment explanation
Indices: 207848--207935 Score: 158
Period size: 41 Copynumber: 2.1 Consensus size: 41
207838 GTCTCTTTAA
207848 AAATTAATCTAAACTCGTACTTTTATATATTATAGAATTAT
1 AAATTAATCTAAACTCGTACTTTTATATATTATAGAATTAT
*
207889 AAATTAATCTAAACTCGTATTTTTATATATTATAGAATTAT
1 AAATTAATCTAAACTCGTACTTTTATATATTATAGAATTAT
*
207930 AGATTA
1 AAATTA
207936 TAGAGATTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (41 bp):
AAATTAATCTAAACTCGTACTTTTATATATTATAGAATTAT
Found at i:208278 original size:18 final size:18
Alignment explanation
Indices: 208255--208307 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
208245 TTTTTAGTTG
208255 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
208273 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
208291 TAATTAA--AAAATTATT
1 TAATTAATTAAAATTATT
208307 T
1 T
208308 TCATCCAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 9 0.28
17 7 0.22
18 16 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:208305 original size:16 final size:17
Alignment explanation
Indices: 208264--208307 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
208254 GTAATTAATT
208264 TAAAATT-TTTAATTAA
1 TAAAATTATTTAATTAA
*
208280 TTAAATTTATTTAATTAA
1 -TAAAATTATTTAATTAA
208298 -AAAATTATTT
1 TAAAATTATTT
208308 TCATCCAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 9 0.38
17 6 0.25
18 9 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TAAAATTATTTAATTAA
Found at i:212792 original size:23 final size:23
Alignment explanation
Indices: 212734--213269 Score: 736
Period size: 23 Copynumber: 23.3 Consensus size: 23
212724 TCATGAGTCC
*
212734 ATTTACGCATAAATCACATTAAT
1 ATTTAAGCATAAATCACATTAAT
212757 ATTTAAAGCATAAATCACATTAAT
1 ATTT-AAGCATAAATCACATTAAT
* *
212781 ATTTAAGCATAAATCATATTAAC
1 ATTTAAGCATAAATCACATTAAT
* * *
212804 AGTTAAGTACAAATCACATTAAT
1 ATTTAAGCATAAATCACATTAAT
212827 ATTTAAGCATAAATCACATTAACT
1 ATTTAAGCATAAATCACATTAA-T
* * *
212851 -TTTAAGCATAAGTCATATTAAC
1 ATTTAAGCATAAATCACATTAAT
212873 ATTTAAGCATAAATCACATTAAT
1 ATTTAAGCATAAATCACATTAAT
* * *
212896 ATTTAAGCACAAATTAAATTAAT
1 ATTTAAGCATAAATCACATTAAT
*
212919 ATTTAAGAATAAATCACATTAAT
1 ATTTAAGCATAAATCACATTAAT
* *
212942 ATTTAAGCACAAATCAAATTAAT
1 ATTTAAGCATAAATCACATTAAT
212965 ATTTAAGCATAAATCACATTAAT
1 ATTTAAGCATAAATCACATTAAT
*
212988 ATTTAAGTATAAATCACATTAAT
1 ATTTAAGCATAAATCACATTAAT
* *
213011 ATTTAAGCACAAATGACATTAAT
1 ATTTAAGCATAAATCACATTAAT
*
213034 ATTTAAGAATAAATCACATTAAT
1 ATTTAAGCATAAATCACATTAAT
*
213057 ATTTAAGCATAAATCACATCAAT
1 ATTTAAGCATAAATCACATTAAT
*
213080 ATTTAAGCAAAAATCACATTAAT
1 ATTTAAGCATAAATCACATTAAT
*
213103 ATTTAAGCACAAATCACATTAAT
1 ATTTAAGCATAAATCACATTAAT
*
213126 ATTTAAGCATAAATCACATTACT
1 ATTTAAGCATAAATCACATTAAT
** *
213149 ATTTAATTACAAATCACATTAAT
1 ATTTAAGCATAAATCACATTAAT
*
213172 ATTTCAA-CACAAATCACATTAAT
1 ATTT-AAGCATAAATCACATTAAT
*
213195 ATTTAAACATAAATCACATTAACT
1 ATTTAAGCATAAATCACATTAA-T
* *
213219 -TTTAAGCATAAATCATATTAAC
1 ATTTAAGCATAAATCACATTAAT
*
213241 ATTTAAGTATAAATCACATTAAT
1 ATTTAAGCATAAATCACATTAAT
213264 ATTTAA
1 ATTTAA
213270 CACATTTAAT
Statistics
Matches: 451, Mismatches: 55, Indels: 14
0.87 0.11 0.03
Matches are distributed among these distances:
22 2 0.00
23 423 0.94
24 26 0.06
ACGTcount: A:0.48, C:0.13, G:0.04, T:0.34
Consensus pattern (23 bp):
ATTTAAGCATAAATCACATTAAT
Found at i:215027 original size:59 final size:58
Alignment explanation
Indices: 214771--215423 Score: 335
Period size: 58 Copynumber: 11.1 Consensus size: 58
214761 AAAAAAAAGC
* * * * **
214771 AATTTTTGGA-TGCTCGAGGGTAAAATGGTAATTTTTGGAAGTTTG-GGGCAAAAATGT
1 AATTTTTGGACAGTTCG-GGGTAAAATGGTAATTTTTGAAAGTTCGAGGTTAAAAATGT
* * * * * * * *
214828 AATTTTTAGATA-TTCAGGGTGTAAATTGGTAATTTTCGGATGATC--GGTAGTAAAAAGGT
1 AATTTTTGGACAGTTC-GGG-GTAAAATGGTAATTTTTGAAAGTTCGAGGT--TAAAAATGT
* * * * * *
214887 AATTTTTGGACACTTGGGAGGTCAAAAGGGTAATTTTTGGATGTTCGAGGGT-AAAATGAT
1 AATTTTTGGACAGTTCGG-GGT-AAAATGGTAATTTTTGAAAGTTCGAGGTTAAAAATG-T
* * *
214947 AATTTTTAGACACTTGGGGGTAAAATGGTAATTTTTGAAAAGTTCGAGGTTAAAAATGT
1 AATTTTTGGACAGTTCGGGGTAAAATGGTAATTTTTG-AAAGTTCGAGGTTAAAAATGT
* * *
215006 AATTTTTGGACA-TTCGTGGGTAAAATGGTAATTTTTGGATGTTCG-GTGGT-AAAATGGT
1 AATTTTTGGACAGTTCG-GGGTAAAATGGTAATTTTTGAAAGTTCGAG-GTTAAAAAT-GT
* * * * * *
215064 AATTTTTAGAAAGTTCGGGGTCAAAAT-GTAATTTTTAGACA-CTCGAGGGT-AAAATGGA
1 AATTTTTGGACAGTTCGGGGT-AAAATGGTAATTTTT-GAAAGTTCGAGGTTAAAAAT-GT
** * * * *
215122 AATTTTT-GA-ATGTTTTAGGGTAAAATGGTATTTTTTTGAAATTTTTG-GGTCAAAAATGT
1 AATTTTTGGACA-G-TTCGGGGTAAAATGGTA-ATTTTTGAAA-GTTCGAGGTTAAAAATGT
* * *
215181 AA-TTTTAGACA-TTCGAGGGTAAATTGGTAATTTTTGAAAGTTCGAGGGGGATAAAAATGT
1 AATTTTTGGACAGTTCG-GGGTAAAATGGTAATTTTTGAAAGTTCGA---GGTTAAAAATGT
* * * * * * *
215241 GATTTTTGGA-AGTTTAGGGGTAAAATGATAATTTTTGGAATGTTTGGGGGTCAAAAATGT
1 AATTTTTGGACAG-TTCGGGGTAAAATGGTAATTTTT-GAAAG-TTCGAGGTTAAAAATGT
* * * *
215301 GATTTTTGGA-AGTTTGGGGTCAAAAT-GTAATTTTTGAAAAGTTTGAGGGTT-AAAATAT
1 AATTTTTGGACAGTTCGGGGT-AAAATGGTAATTTTTG-AAAGTTCGA-GGTTAAAAATGT
* * * * **
215359 AATTTTTGGATAGTTTGTGGCAAAAT-GTAATTTTTGGAAAGTTTAAGGGTT-AAAATGT
1 AATTTTTGGACAGTTCGGGGTAAAATGGTAATTTTT-GAAAGTTCGA-GGTTAAAAATGT
*
215417 GATTTTT
1 AATTTTT
215424 AGAGAGTTTA
Statistics
Matches: 475, Mismatches: 77, Indels: 87
0.74 0.12 0.14
Matches are distributed among these distances:
56 4 0.01
57 40 0.08
58 178 0.37
59 124 0.26
60 94 0.20
61 23 0.05
62 9 0.02
63 3 0.01
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38
Consensus pattern (58 bp):
AATTTTTGGACAGTTCGGGGTAAAATGGTAATTTTTGAAAGTTCGAGGTTAAAAATGT
Found at i:215129 original size:87 final size:85
Alignment explanation
Indices: 214771--215365 Score: 423
Period size: 87 Copynumber: 6.7 Consensus size: 85
214761 AAAAAAAAGC
* * *
214771 AATTTTTGGATGCTCGAGGGTAAAATGGTAATTTTTGGAAGTTTGGGG-CAAAAATGTAATTTTT
1 AATTTTTGGATGTTCG-GGGTAAAATGGTAATTTTTGAAAGTTCGGGGTC-AAAATGTAATTTTT
* *
214835 AGATATTC-AGGGTGTAAATTGGT
64 AGACATTCGA-GG-GTAAAATGGT
* * * * * * * *
214858 AATTTTCGGATGATCGGTAGTAAAAAGGTAATTTTTGGACACTTGGGAGGTCAAAAGGGTAATTT
1 AATTTTTGGATGTTCGG-GGTAAAATGGTAATTTTT-GAAAGTTCGG-GGTCAAAA-TGTAATTT
* ** *
214923 TTGGATGTTCGAGGGTAAAATGAT
62 TTAGACATTCGAGGGTAAAATGGT
* ** * * *
214947 AATTTTTAGACACTTGGGGGTAAAATGGTAATTTTTGAAAAGTTCGAGGTTAAAAATGTAATTTT
1 AATTTTTGGA-TGTTCGGGGTAAAATGGTAATTTTTG-AAAGTTCG-GGGTCAAAATGTAATTTT
* *
215012 TGGACATTCGTGGGTAAAATGGT
63 TAGACATTCGAGGGTAAAATGGT
215035 AATTTTTGGATGTTCGGTGGTAAAATGGTAATTTTTAGAAAGTTCGGGGTCAAAATGTAATTTTT
1 AATTTTTGGATGTTCGG-GGTAAAATGGTAATTTTT-GAAAGTTCGGGGTCAAAATGTAATTTTT
* *
215100 AGACACTCGAGGGTAAAATGGA
64 AGACATTCGAGGGTAAAATGGT
* ** * * **
215122 AATTTTTGAATGTTTTAGGGTAAAATGGTATTTTTTTGAAATTTTTGGGTCAAAAATGTAA-TTT
1 AATTTTTGGATG-TTCGGGGTAAAATGGTA-ATTTTTGAAAGTTCGGGGTC-AAAATGTAATTTT
*
215186 TAGACATTCGAGGGTAAATTGGT
63 TAGACATTCGAGGGTAAAATGGT
* * * * *
215209 AATTTTTGAAAGTTCGAGGGGGATAAAAAT-GTGATTTTTGGAAGTTTAGGGGT-AAAATGATAA
1 AATTTTTGGATGTTC---GGGG-T-AAAATGGTAATTTTTGAAAG-TTCGGGGTCAAAATG-TAA
* * *
215272 TTTTTGGA-ATGTTTGGGGGTCAAAAAT-GT
59 TTTTTAGACA--TTCGAGGGT--AAAATGGT
* * * * * *
215301 GATTTTTGGAAGTTTGGGGTCAAAAT-GTAATTTTTGAAAAGTTTGAGGGTTAAAATATAATTTT
1 AATTTTTGGATGTTCGGGGT-AAAATGGTAATTTTTG-AAAGTTCG-GGGTCAAAATGTAATTTT
215365 T
63 T
215366 GGATAGTTTG
Statistics
Matches: 407, Mismatches: 72, Indels: 56
0.76 0.13 0.10
Matches are distributed among these distances:
86 3 0.01
87 137 0.34
88 110 0.27
89 84 0.21
90 42 0.10
91 13 0.03
92 14 0.03
93 4 0.01
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (85 bp):
AATTTTTGGATGTTCGGGGTAAAATGGTAATTTTTGAAAGTTCGGGGTCAAAATGTAATTTTTAG
ACATTCGAGGGTAAAATGGT
Found at i:215316 original size:30 final size:27
Alignment explanation
Indices: 214788--215432 Score: 285
Period size: 29 Copynumber: 22.0 Consensus size: 27
214778 GGATGCTCGA
214788 GGGTAAAATGGTAATTTTTGGAAGTTTG
1 GGGTAAAAT-GTAATTTTTGGAAGTTTG
* * *
214816 GGGCAAAAATGTAATTTTTAGATA-TTCAG
1 GGG-TAAAATGTAATTTTTGGA-AGTT-TG
* * * * *
214845 GGTGTAAATTGGTAATTTTCGGATGATCG
1 GG-GTAAAAT-GTAATTTTTGGAAGTTTG
* * * *
214874 GTAGTAAAAAGGTAATTTTTGGACACTTGG
1 G-GGT-AAAATGTAATTTTTGGA-AGTTTG
* * *
214904 GAGGTCAAAAGGGTAATTTTTGGATGTTCG
1 G-GGT-AAAA-TGTAATTTTTGGAAGTTTG
* * *
214934 AGGGTAAAATGATAATTTTTAGACACTTGG
1 -GGGTAAAATG-TAATTTTTGGA-AGTTTG
* *
214964 GGGTAAAATGGTAATTTTTGAAAAGTTCG
1 GGGTAAAAT-GTAATTTTTG-GAAGTTTG
* *
214993 AGGTTAAAAATGTAATTTTTGGACA-TTCG
1 -GGGT-AAAATGTAATTTTTGGA-AGTTTG
* *
215022 TGGGTAAAATGGTAATTTTTGGATGTTCG
1 -GGGTAAAAT-GTAATTTTTGGAAGTTTG
* *
215051 GTGGTAAAATGGTAATTTTTAGAAAGTTCG
1 G-GGTAAAAT-GTAATTTTT-GGAAGTTTG
* * *
215081 GGGTCAAAATGTAATTTTTAGACA-CTCG
1 GGGT-AAAATGTAATTTTTGGA-AGTTTG
* *
215109 AGGGTAAAATGGAAATTTTT-GAATGTTTTA
1 -GGGTAAAAT-GTAATTTTTGGAA-G-TTTG
* * * *
215139 GGGTAAAATGGTATTTTTTTGAAATTTTT
1 GGGTAAAAT-GTA-ATTTTTGGAAGTTTG
* *
215168 GGGTCAAAAATGTAA-TTTTAGACA-TTCG
1 GGGT--AAAATGTAATTTTTGGA-AGTTTG
* * *
215196 AGGGTAAATTGGTAATTTTTGAAAGTTCGAGG
1 -GGGTAAAAT-GTAATTTTTGGAAGTT---TG
*
215228 GGGATAAAAATGTGATTTTTGGAAGTTTAG
1 GGG-T-AAAATGTAATTTTTGGAAGTTT-G
215258 GGGTAAAATGATAATTTTTGGAATGTTTGG
1 GGGTAAAATG-TAATTTTTGGAA-GTTT-G
*
215288 GGGTCAAAAATGTGATTTTTGGAAGTTTG
1 GGGT--AAAATGTAATTTTTGGAAGTTTG
*
215317 GGGTCAAAATGTAATTTTTGAAAAGTTTG
1 GGGT-AAAATGTAATTTTTG-GAAGTTTG
*
215346 AGGGTTAAAATATAATTTTTGGATAGTTTG
1 -GGG-TAAAATGTAATTTTTGGA-AGTTTG
* *
215376 TGGCAAAATGTAATTTTTGGAAAGTTTAAG
1 GGGTAAAATGTAATTTTTGG-AAGTTT--G
* * *
215406 GGTTAAAATGTGATTTTTAGAGAGTTT
1 GGGTAAAATGTAATTTTTGGA-AGTTT
215433 AGGGACCTTC
Statistics
Matches: 480, Mismatches: 81, Indels: 110
0.72 0.12 0.16
Matches are distributed among these distances:
27 5 0.01
28 86 0.18
29 190 0.40
30 132 0.28
31 41 0.09
32 22 0.05
33 4 0.01
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38
Consensus pattern (27 bp):
GGGTAAAATGTAATTTTTGGAAGTTTG
Found at i:217239 original size:17 final size:17
Alignment explanation
Indices: 217217--217322 Score: 124
Period size: 17 Copynumber: 6.2 Consensus size: 17
217207 GACTTTCATT
*
217217 AATTTAAATTTAGAATA
1 AATTTAAATTTAAAATA
*
217234 ATTTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
* *
217251 AATTTAAACTTAAATTA
1 AATTTAAATTTAAAATA
* *
217268 AATTTAATTTTAAAACA
1 AATTTAAATTTAAAATA
*
217285 AATCTAAATTTAAAATA
1 AATTTAAATTTAAAATA
*
217302 AATTT-AATCTTACAATA
1 AATTTAAAT-TTAAAATA
217319 AATT
1 AATT
217323 AAAAAAAGTG
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
16 3 0.04
17 71 0.96
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.42
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:218044 original size:209 final size:209
Alignment explanation
Indices: 217669--218686 Score: 1303
Period size: 209 Copynumber: 4.9 Consensus size: 209
217659 ATTTCCTAGA
* * * ** * * *
217669 AAGACGGATTTGGTTCACTTCTCTG-AGTCTCGCCAGGAAGATGACCACTTTATTGCTTTGACCT
1 AAGACGAATTTGGTCCACTTCTCAGTA-TCTCATCAGGAAGTTGACCATTTTATTGCTTCGACCT
* * * * ** *
217733 GCTTCTCCA-TATTTCATCAGGAAGCTGGGGTTCAAAGTTTTGCTTACATAAAACTTTGTTTCAT
65 GCTTCT-CAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCAT
* * * **
217797 TGATTTGGTATACTTCTTTGAATCTCATCAGGAAGATGACCTCCTCACTTGTTTCAATCCATTTC
129 TGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCTCCTCACTTGTTTCAATCCGCTTC
*
217862 TCTGTATCTTATCAGG
194 TCTGTATCTCATCAGG
*
217878 AAGACGAATTGGGTCCACTTCTCAGTATCTCATCAGGAAGTTGACCATTTTATTGCTTCGACCTG
1 AAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGTTGACCATTTTATTGCTTCGACCTG
* * * *
217943 CTTCACAATATCTCATCAGGAAGCTAGGGTTCGAAGTTTCACTCACATTGAGCTTTGTTTCATTG
66 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTG
*
218008 AGTTGGTATACTTCTCTGTATCTCATTAGGAAGATGACCGT-CTCACTTGTTTCAATCCGCTTCT
131 AGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACC-TCCTCACTTGTTTCAATCCGCTTCT
* *
218072 CTGTATCTCATAAAG
195 CTGTATCTCATCAGG
218087 AAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGTTGACCATTTTATTGCTTCGACCTG
1 AAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGTTGACCATTTTATTGCTTCGACCTG
* *
218152 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTTGCTCACATTGAGATTTGTTTCATTG
66 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTG
* * *
218217 AGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTTTTT
131 AGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCTCCTCACTTGTTTCAATCCGCTTCTC
218282 TGTATCTCATCAGG
196 TGTATCTCATCAGG
* *
218296 AAGACGAATTTGGTCCATTTCTCAGTATCTCATCAGGAAGTTGACCATTTTATTGCTTCAACCTG
1 AAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGTTGACCATTTTATTGCTTCGACCTG
* *
218361 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTT-GCTCACTTTGAGCTTGGTTTCATT
66 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAG-TTTCGCTCACATTGAGCTTTGTTTCATT
* * ** * * * * * *
218425 GACTTGGTCTACTTCTCAATATCTCATCAGGAAGATGACCGCATCATTTATTTTAATCCGCTTAT
130 GAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCTCCTCACTTGTTTCAATCCGCTTCT
218490 CTGTATCTCATCAGG
195 CTGTATCTCATCAGG
* ** * * * *** *
218505 AAGAC-AGATTTGATTTACTTCTCTGTATCTCATCAGGAAGGTAACTGCTTTATTGCTTCAACCT
1 AAGACGA-ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGTTGACCATTTTATTGCTTCGACCT
* * * * * *
218569 GCTTCTCAGTACCTCATCAGAAAGCTGGAGTTCGAAGTTTCGCTCACATCGATCCTTAGTTTCAT
65 GCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCACATTGA-GCTTTGTTTCAT
* * * * *
218634 CGATTTGGTCTACTTCTCAGTATCTTATCAGGAAGATGA-CTGCCTCA-TTGTTT
129 TGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCT-CCTCACTTGTTT
218687 TGGATAATCG
Statistics
Matches: 720, Mismatches: 80, Indels: 18
0.88 0.10 0.02
Matches are distributed among these distances:
208 6 0.01
209 660 0.92
210 54 0.08
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (209 bp):
AAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGTTGACCATTTTATTGCTTCGACCTG
CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTG
AGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCTCCTCACTTGTTTCAATCCGCTTCTC
TGTATCTCATCAGG
Found at i:218758 original size:39 final size:39
Alignment explanation
Indices: 218712--219154 Score: 248
Period size: 39 Copynumber: 11.4 Consensus size: 39
218702 TACCCCATGA
*
218712 TCGGGGTAAGAAATTGGCTGATGGTGATCTGCCCCAAGC
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
* ** * * * *
218751 TCGGGGTAAAAGATCAGATGACT-GTAATCT-ACCCAGGC
1 TCGGGGTAAGAGATTGGCTGA-TGGTGATCTGCCCCAAGC
** *
218789 TTAGGTTAAGAGATTGGCTGATGGTGATCTGCCCC-AGAC
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAG-C
** * * *
218828 TTAGGGTAAAAGA-T--CAGATGGCTGCAATCTGTCCCAAGC
1 TCGGGGTAAGAGATTGGCTGATGG-TG--ATCTGCCCCAAGC
* * * * *
218867 TCGGGTTAAGAGATTGGCTAATGGTGATCTACCCTAGGC
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
* * ** *
218906 TCGGGGTAAAAGA-T--C-GAATGGCTACAATCTGCCTTAGGC
1 TCGGGGTAAGAGATTGGCTG-ATGG-T--GATCTGCCCCAAGC
* *
218945 TCGGGGTAAGAGATTGGCTGATGGTGATCTACCTCAAGC
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
* * * * * *
218984 TCGGGGGAAGAGATCGGAT-A-GCTACAATCTGCCCCAGGC
1 TCGGGGTAAGAGATTGGCTGATGGT--GATCTGCCCCAAGC
* * *
219023 TCGGGGTAAAAGATTGGCTGATGGTGATTTGCCCCATGC
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
* * * * * *
219062 TTGGGGTAAGAGATCGGAT-A-GCTGCAATCTACCCCAGGC
1 TCGGGGTAAGAGATTGGCTGATGGTG--ATCTGCCCCAAGC
* *
219101 TCGGGGTAAGAGATTGGTTGATGGTGATCTACCCCCAAGC
1 TCGGGGTAAGAGATTGGCTGATGGTGATCT-GCCCCAAGC
*
219141 TTGGGGTAAGAGAT
1 TCGGGGTAAGAGAT
219155 CGAATCTTCA
Statistics
Matches: 302, Mismatches: 74, Indels: 55
0.70 0.17 0.13
Matches are distributed among these distances:
36 11 0.04
37 9 0.03
38 31 0.10
39 205 0.68
40 27 0.09
41 8 0.03
42 10 0.03
43 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (39 bp):
TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
Found at i:218913 original size:78 final size:78
Alignment explanation
Indices: 218698--219155 Score: 499
Period size: 78 Copynumber: 5.9 Consensus size: 78
218688 GGATAATCGT
* * * * *
218698 AATCTACCCCATGATCGGGGTAAGAAATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAG
1 AATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTACCCCAAGCTCGGGGTAAAAG
* *
218763 ATCAGATGACTGT
66 ATCAGATGGCTGC
* ** * * **
218776 AATCT-ACCCAGGCTTAGGTTAAGAGATTGGCTGATGGTGATCTGCCCC-AGACTTAGGGTAAAA
1 AATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTACCCCAAG-CTCGGGGTAAAA
218839 GATCAGATGGCTGC
65 GATCAGATGGCTGC
* * * * * *
218853 AATCTGTCCCAAGCTCGGGTTAAGAGATTGGCTAATGGTGATCTACCCTAGGCTCGGGGTAAAAG
1 AATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTACCCCAAGCTCGGGGTAAAAG
*
218918 ATC-GAATGGCTAC
66 ATCAG-ATGGCTGC
** * * *
218931 AATCTGCCTTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTACCTCAAGCTCGGGGGAAGAG
1 AATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTACCCCAAGCTCGGGGTAAAAG
* * *
218996 ATCGGATAGCTAC
66 ATCAGATGGCTGC
* * * * * *
219009 AATCTGCCCCAGGCTCGGGGTAAAAGATTGGCTGATGGTGATTTGCCCCATGCTTGGGGTAAGAG
1 AATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTACCCCAAGCTCGGGGTAAAAG
* *
219074 ATCGGATAGCTGC
66 ATCAGATGGCTGC
* * * *
219087 AATCTACCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTACCCCCAAGCTTGGGGTAAGA
1 AATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTA-CCCCAAGCTCGGGGTAAAA
219152 GATC
65 GATC
219156 GAATCTTCAG
Statistics
Matches: 324, Mismatches: 50, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
76 2 0.01
77 64 0.20
78 234 0.72
79 24 0.07
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (78 bp):
AATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTACCCCAAGCTCGGGGTAAAAG
ATCAGATGGCTGC
Found at i:219480 original size:50 final size:50
Alignment explanation
Indices: 219421--219561 Score: 167
Period size: 50 Copynumber: 2.8 Consensus size: 50
219411 CCTTCTTATT
* * * **
219421 TTCTAAGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCTCTTCATCTC
1 TTCTAAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTAAAATC
* * *
219471 TTCTAAGGTACCAGGTTCGTCGTTGCTGCCTCAACCTTTCCCTTAAAATC
1 TTCTAAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTAAAATC
* * * *
219521 TTC-ATGGTACCGGGTTCACCATTGCGGCCTCAACATTTCCC
1 TTCTAAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCC
219562 ATCAGATTTC
Statistics
Matches: 76, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
49 31 0.41
50 45 0.59
ACGTcount: A:0.16, C:0.32, G:0.18, T:0.33
Consensus pattern (50 bp):
TTCTAAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTAAAATC
Found at i:219551 original size:49 final size:49
Alignment explanation
Indices: 219427--219669 Score: 166
Period size: 50 Copynumber: 4.9 Consensus size: 49
219417 TATTTTCTAA
* * ** *
219427 GGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCTCTTCATCTCTTCTAA
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTC-AT
* * * *
219477 GGTACCAGGTTCGTCGTTGCTGCCTCAACCTTTCCCTTAAAATCTTCAT
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTCAT
* * * * *
219526 GGTACCGGGTTCACCATTGCGGCCTCAACATTTCCCATCAGAT-TTCAT
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTCAT
* ** ** * * * ** * *
219574 GGTACTGAATTTTCCATTGCGGCCTTAATCTTTCCAATCACATCTTCTT
1 GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTCAT
** * * *
219623 AGGTATTGGATTCGCCGTCGCGACCTCAATCC-TTCCCTTCAAATCTT
1 -GGTACCGGGTTCGCCGTTGCGGCCTCAA-CCTTTCCCTTCAAATCTT
219670 TTATGTTTTT
Statistics
Matches: 149, Mismatches: 41, Indels: 6
0.76 0.21 0.03
Matches are distributed among these distances:
48 38 0.26
49 39 0.26
50 71 0.48
51 1 0.01
ACGTcount: A:0.18, C:0.30, G:0.17, T:0.35
Consensus pattern (49 bp):
GGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTCAT
Found at i:220621 original size:22 final size:21
Alignment explanation
Indices: 220590--220643 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 21
220580 CGACCTCTCC
220590 TTTTCTTTTTCTCCTTTTTCCT-T
1 TTTTC-TTTTCTCC--TTTCCTCT
*
220613 TTTTCTTTTTTCCTTTCCTCT
1 TTTTCTTTTCTCCTTTCCTCT
220634 TTTT-TTTTCT
1 TTTTCTTTTCT
220644 TTCTTTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 11 0.39
21 5 0.18
22 7 0.25
23 5 0.18
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTCTTTTCTCCTTTCCTCT
Found at i:220638 original size:15 final size:15
Alignment explanation
Indices: 220590--220638 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
220580 CGACCTCTCC
* *
220590 TTTTCTTTTTCTCCT
1 TTTTCCTTTTCTCTT
*
220605 TTTTCCTTTTTTCTT
1 TTTTCCTTTTCTCTT
*
220620 TTTTCCTTTCCTCTT
1 TTTTCCTTTTCTCTT
220635 TTTT
1 TTTT
220639 TTTCTTTCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTCCTTTTCTCTT
Found at i:220646 original size:22 final size:20
Alignment explanation
Indices: 220590--220664 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 20
220580 CGACCTCTCC
220590 TTTTCTTTTTCTCCTTTTTCCTT
1 TTTTCTTTTT-TCC--TTTCCTT
220613 TTTTCTTTTTTCCTTTCCTCT
1 TTTTCTTTTTTCCTTTCCT-T
* *
220634 TTTT-TTTTCTTTCTTTTCTT
1 TTTTCTTTT-TTCCTTTCCTT
* *
220654 TCTCCTTTTTT
1 TTTTCTTTTTT
220665 ATTTATTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
20 15 0.33
21 17 0.38
22 3 0.07
23 10 0.22
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTCTTTTTTCCTTTCCTT
Found at i:220654 original size:26 final size:24
Alignment explanation
Indices: 220590--220664 Score: 82
Period size: 25 Copynumber: 3.1 Consensus size: 24
220580 CGACCTCTCC
*
220590 TTTTCTTTTTCTCCTTTTTCC--TT
1 TTTTCTTTTT-TCCTTTCTCCTTTT
*
220613 TTTTCTTTTTTCCTTTCCTCTTTTT
1 TTTTCTTTTTTCCTTT-CTCCTTTT
*
220638 TTTTCTTTCTTTTCTTTCTCCTTTT
1 TTTTCTTT-TTTCCTTTCTCCTTTT
220663 TT
1 TT
220665 ATTTATTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
22 6 0.14
23 12 0.27
25 19 0.43
26 7 0.16
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTTCTTTTTTCCTTTCTCCTTTT
Found at i:220664 original size:14 final size:14
Alignment explanation
Indices: 220585--220664 Score: 62
Period size: 14 Copynumber: 5.8 Consensus size: 14
220575 CACCTCGACC
220585 TCTCCTTTTCTT-TT
1 TCTCCTTTT-TTCTT
*
220599 TCTCCTTTTTCCTT
1 TCTCCTTTTTTCTT
* *
220613 TTTTCTTTTTTCCTT
1 TCTCCTTTTTT-CTT
220628 TC-CTCTTTTTT-TT
1 TCTC-CTTTTTTCTT
220641 TCT--TTCTTTTCTT
1 TCTCCTT-TTTTCTT
220654 TCTCCTTTTTT
1 TCTCCTTTTTT
220665 ATTTATTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
11 2 0.04
12 4 0.08
13 10 0.19
14 23 0.44
15 13 0.25
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (14 bp):
TCTCCTTTTTTCTT
Found at i:226015 original size:28 final size:28
Alignment explanation
Indices: 225697--226061 Score: 155
Period size: 28 Copynumber: 12.8 Consensus size: 28
225687 TTTGGATGCC
225697 CGAGGGTAAAATGGTAATTTTTGAAAGTT
1 CGAGGGTAAAATGGTAA-TTTTGAAAGTT
* * * * * *
225726 CG-TGGAAAAAT-GCAATTTTTAGATGCT
1 CGAGGGTAAAATGGTAATTTTGA-AAGTT
* * *
225753 CGAGGGTAAAATGGTAATTTTGGGATGAT
1 CGAGGGTAAAATGGTAATTTT-GAAAGTT
* * *
225782 CGAGGGTAAAACGGTAATTTTTGGACACTT
1 CGAGGGTAAAATGGTAA-TTTT-GAAAGTT
** * * *
225812 -G-GGGGGAAATGATAATATTTGGACACTT
1 CGAGGGTAAAATGGTAAT-TTT-GAAAGTT
225840 -GAGGGATAAAATGGTAATTTTTGAAAAGTT
1 CGAGGG-TAAAATGGTAA-TTTTG-AAAGTT
225870 C-AGGGTCAAAAAT-GTAATTTT-AACA-TT
1 CGAGGGT--AAAATGGTAATTTTGAA-AGTT
* *
225897 CGAGAGTAAAATGGTAATTTTGAATGTT
1 CGAGGGTAAAATGGTAATTTTGAAAGTT
* * *
225925 TGAGGGCAAAATAGTAATTTTGGAAAGTT
1 CGAGGGTAAAATGGTAATTTT-GAAAGTT
* * *
225954 TG-GGCTAAAAAAT-GTAATTTTAGACA--T
1 CGAGGGT--AAAATGGTAATTTT-GAAAGTT
225981 CTGAGGGTAAAATGGTAATTTTGAAAGTT
1 C-GAGGGTAAAATGGTAATTTTGAAAGTT
* * * *
226010 CAAGGGGACAAAAAT-GTGATTTTTGGAAGTT
1 CGA-GGG--TAAAATGGT-AATTTTGAAAGTT
* *
226041 CTAGGGTAAAACGGTAATTTT
1 CGAGGGTAAAATGGTAATTTT
226062 TGGAATGCTC
Statistics
Matches: 256, Mismatches: 49, Indels: 63
0.70 0.13 0.17
Matches are distributed among these distances:
26 10 0.04
27 31 0.12
28 83 0.32
29 68 0.27
30 40 0.16
31 24 0.09
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.32
Consensus pattern (28 bp):
CGAGGGTAAAATGGTAATTTTGAAAGTT
Found at i:226050 original size:59 final size:58
Alignment explanation
Indices: 225984--226120 Score: 163
Period size: 59 Copynumber: 2.4 Consensus size: 58
225974 TAGACATCTG
* *
225984 AGGGTAAAATGGTAA-TTTT-GAAAGTTCAAGGGGACAAAAATGTGATTTTTGGAAGTTCT
1 AGGGTAAAATGGTAATTTTTGGAAAGCTC-A-GGGACAAAAATGTGATTTTTGCAAGTT-T
* * * *
226043 AGGGTAAAACGGTAATTTTTGGAATGCTCAGGGTCAAGAATGTGATTTTTGCAAGTTT
1 AGGGTAAAATGGTAATTTTTGGAAAGCTCAGGGACAAAAATGTGATTTTTGCAAGTTT
*
226101 AGGGTAAAAT-GTATTTTTTG
1 AGGGTAAAATGGTAATTTTTG
226121 AGAAGTTTGA
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
57 9 0.13
58 10 0.15
59 38 0.56
60 5 0.07
61 6 0.09
ACGTcount: A:0.32, C:0.06, G:0.27, T:0.35
Consensus pattern (58 bp):
AGGGTAAAATGGTAATTTTTGGAAAGCTCAGGGACAAAAATGTGATTTTTGCAAGTTT
Found at i:226061 original size:29 final size:27
Alignment explanation
Indices: 225699--226300 Score: 204
Period size: 29 Copynumber: 20.8 Consensus size: 27
225689 TGGATGCCCG
*
225699 AGGGTAAAATGGTAATTTTTGAAAG-TT
1 AGGGTAAAAT-GTAATTTTTGGAAGTTT
* * * * * **
225726 CGTGGAAAAATGCAATTTTTAGATGCTCG
1 AG-GGTAAAATGTAATTTTTGGAAG-TTT
* * **
225755 AGGGTAAAATGGTAATTTTGGGATGATCG
1 AGGGTAAAAT-GTAATTTTTGGAAG-TTT
* *
225784 AGGGTAAAACGGTAATTTTTGGACA-CTT
1 AGGGTAAAA-TGTAATTTTTGGA-AGTTT
* ** * * *
225812 GGGGGGAAATGATAATATTTGGACACTTG
1 AGGGTAAAATG-TAATTTTTGGA-AGTTT
* *
225841 AGGGATAAAATGGTAATTTTTGAAAAGTTC
1 AGGG-TAAAAT-GTAATTTTTG-GAAGTTT
* *
225871 AGGGTCAAAAATGTAA-TTTT--AACATTCG
1 AGGGT--AAAATGTAATTTTTGGAA-GTT-T
*
225899 AGAGTAAAATGGTAA-TTTT-GAATGTTT
1 AGGGTAAAAT-GTAATTTTTGGAA-GTTT
*
225926 GAGGGCAAAATAGTAA-TTTTGGAAAGTTT
1 -AGGGTAAAAT-GTAATTTTTGG-AAGTTT
* *
225955 -GGGCTAAAAAATGTAA-TTTTAGACA-TCTG
1 AGGG-T--AAAATGTAATTTTTGGA-AGT-TT
* *
225984 AGGGTAAAATGGTAA-TTTTGAAAGTTCA
1 AGGGTAAAAT-GTAATTTTTGGAAGTT-T
* *
226012 AGGGGACAAAAATGTGATTTTTGGAAGTTCT
1 A-GGG--TAAAATGTAATTTTTGGAAGTT-T
* * *
226043 AGGGTAAAACGGTAATTTTTGGAATGCTC
1 AGGGTAAAA-TGTAATTTTTGGAA-GTTT
* *
226072 AGGGTCAAGAATGTGATTTTTGCAAGTTT
1 AGGGT-AA-AATGTAATTTTTGGAAGTTT
*
226101 AGGGTAAAATGTATTTTTTGAGAAGTTT
1 AGGGTAAAATGTAATTTTTG-GAAGTTT
* *
226129 GAGGTTTAAAATGTTATTTTTGGAAGTTT
1 -AGG-GTAAAATGTAATTTTTGGAAGTTT
* *
226158 GGGGTAAAAATGTAATTATTTGGATGTTT
1 AGGGT-AAAATGTAATT-TTTGGAAGTTT
* *
226187 -GAGGTCAAATTTTTAATTTTTGAGAAGTTT
1 AG-GGT-AAA-ATGTAATTTTTG-GAAGTTT
*
226217 AGGGGTCAAAATATAATTTTTGGAAGTTT
1 A-GGGT-AAAATGTAATTTTTGGAAGTTT
*
226246 GAGAGTAAAAATGTAATTTTTGGAAAGTTT
1 -AGGGT-AAAATGTAATTTTTGG-AAGTTT
* *
226276 AAGGGTTAAAAATATGATTTTTGGA
1 -AGGG-T-AAAATGTAATTTTTGGA
226301 GAGGTCAAGG
Statistics
Matches: 439, Mismatches: 86, Indels: 97
0.71 0.14 0.16
Matches are distributed among these distances:
26 7 0.02
27 44 0.10
28 94 0.21
29 143 0.33
30 101 0.23
31 49 0.11
32 1 0.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (27 bp):
AGGGTAAAATGTAATTTTTGGAAGTTT
Found at i:226246 original size:59 final size:57
Alignment explanation
Indices: 226087--226300 Score: 211
Period size: 59 Copynumber: 3.7 Consensus size: 57
226077 CAAGAATGTG
* * * *
226087 ATTTTTGCAAGTTTA-GGGT-AAAATGTATTTTTTGAGAAGTTTGAGGTTTAAAATGTT-
1 ATTTTTGGAAGTTTAGGGGTAAAAATATAATTTTTG-GAAGTTTGAGG--TAAAATTTTA
* * *
226144 ATTTTTGGAAGTTT-GGGGTAAAAATGTAATTATTTGGATGTTTGAGGTCAAATTTTTA
1 ATTTTTGGAAGTTTAGGGGTAAAAATATAATT-TTTGGAAGTTTGAGGT-AAAATTTTA
* * *
226202 ATTTTTGAGAAGTTTAGGGGTCAAAATATAATTTTTGGAAGTTTGAGAGTAAAAATGTA
1 ATTTTTG-GAAGTTTAGGGGTAAAAATATAATTTTTGGAAGTTTGAG-GTAAAATTTTA
* *
226261 ATTTTTGGAAAGTTTAAGGGTTAAAAATATGATTTTTGGA
1 ATTTTTGG-AAGTTT-AGGGGTAAAAATATAATTTTTGGA
226301 GAGGTCAAGG
Statistics
Matches: 133, Mismatches: 14, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
56 1 0.01
57 23 0.17
58 28 0.21
59 43 0.32
60 38 0.29
ACGTcount: A:0.33, C:0.01, G:0.23, T:0.43
Consensus pattern (57 bp):
ATTTTTGGAAGTTTAGGGGTAAAAATATAATTTTTGGAAGTTTGAGGTAAAATTTTA
Found at i:228131 original size:17 final size:17
Alignment explanation
Indices: 228109--228215 Score: 135
Period size: 17 Copynumber: 6.3 Consensus size: 17
228099 GACTTTCATT
*
228109 AATTTAAATTTAGAATA
1 AATTTAAATTTAAAATA
*
228126 ATTTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
* *
228143 AATTTAAACTTAAATTA
1 AATTTAAATTTAAAATA
* *
228160 AATTTAAATTTTAAACA
1 AATTTAAATTTAAAATA
*
228177 AATCTAAATTTAAAATA
1 AATTTAAATTTAAAATA
228194 AATTT-AATCTTAAAATA
1 AATTTAAAT-TTAAAATA
228211 AATTT
1 AATTT
228216 TAAAAAAGTG
Statistics
Matches: 76, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
16 3 0.04
17 73 0.96
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:228174 original size:7 final size:6
Alignment explanation
Indices: 228109--228200 Score: 63
Period size: 6 Copynumber: 16.2 Consensus size: 6
228099 GACTTTCATT
* * *
228109 AATTTA AATTTA GAA--TA ATTTTA AATTTA AA-ATA AATTTA AACTTA
1 AATTTA AATTTA -AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* * *
228155 AA-TTA AATTTA AATTTTA AA--CA AATCTA AATTTA AA-ATA AATTTA
1 AATTTA AATTTA AA-TTTA AATTTA AATTTA AATTTA AATTTA AATTTA
228200 A
1 A
228201 TCTTAAAATA
Statistics
Matches: 67, Mismatches: 10, Indels: 18
0.71 0.11 0.19
Matches are distributed among these distances:
4 4 0.06
5 15 0.22
6 40 0.60
7 8 0.12
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (6 bp):
AATTTA
Found at i:229141 original size:28 final size:28
Alignment explanation
Indices: 229107--229188 Score: 130
Period size: 28 Copynumber: 2.9 Consensus size: 28
229097 GTGTTATTAT
*
229107 AGAACAGAGAACACATAAAGTGCTAATC
1 AGAACAGAGAACACACAAAGTGCTAATC
229135 -GAAACAGAGAACACACAAAGTGCTAATC
1 AG-AACAGAGAACACACAAAGTGCTAATC
*
229163 AGAACAGAGAGCACACAAAGTGCTAA
1 AGAACAGAGAACACACAAAGTGCTAA
229189 ATGCACGTAG
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
27 1 0.02
28 48 0.96
29 1 0.02
ACGTcount: A:0.50, C:0.20, G:0.20, T:0.11
Consensus pattern (28 bp):
AGAACAGAGAACACACAAAGTGCTAATC
Found at i:229653 original size:19 final size:19
Alignment explanation
Indices: 229617--229654 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
229607 GACTACAAAA
229617 TTCATATATGCTTGTATTT
1 TTCATATATGCTTGTATTT
229636 TTCACTATATGCTT-TATTT
1 TTCA-TATATGCTTGTATTT
229655 ATCCATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.21, C:0.13, G:0.08, T:0.58
Consensus pattern (19 bp):
TTCATATATGCTTGTATTT
Found at i:231323 original size:36 final size:36
Alignment explanation
Indices: 231262--231594 Score: 421
Period size: 36 Copynumber: 9.5 Consensus size: 36
231252 CATTAGCACA
* *
231262 ACATATTCACCGTCACATGGCATGAATAACATACCC
1 ACATATTTACTGTCACATGGCATGAATAACATACCC
* * *
231298 ACATATTTATTGTCATATGGTATGAATAACATACCC
1 ACATATTTACTGTCACATGGCATGAATAACATACCC
* * *
231334 ACATATGTATTGTCACATGGCATAAATAACATACCC
1 ACATATTTACTGTCACATGGCATGAATAACATACCC
* *
231370 ACATATTTACTGTCTCATGACATGAATAACAT----
1 ACATATTTACTGTCACATGGCATGAATAACATACCC
* *
231402 ---TATTTACTATCTCATGGCATGAATAACATACCC
1 ACATATTTACTGTCACATGGCATGAATAACATACCC
*
231435 ACACATTTACTGTCACATGGCATGAATAACATACCC
1 ACATATTTACTGTCACATGGCATGAATAACATACCC
**
231471 ACATATTTACTGTCACATCTCATGAATAACATA-CC
1 ACATATTTACTGTCACATGGCATGAATAACATACCC
* *
231506 ACACATTTACTGTCACATGACATGAATAACATACCC
1 ACATATTTACTGTCACATGGCATGAATAACATACCC
* * *
231542 ACATATTTACTGTCTCGTGGCATGAATAACATACTC
1 ACATATTTACTGTCACATGGCATGAATAACATACCC
*
231578 ACACATTTACTGTCACA
1 ACATATTTACTGTCACA
231595 ACAATTATCA
Statistics
Matches: 256, Mismatches: 33, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
29 27 0.11
35 32 0.12
36 197 0.77
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.30
Consensus pattern (36 bp):
ACATATTTACTGTCACATGGCATGAATAACATACCC
Found at i:231405 original size:29 final size:29
Alignment explanation
Indices: 231373--231430 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
231363 CATACCCACA
*
231373 TATTTACTGTCTCATGACATGAATAACAT
1 TATTTACTATCTCATGACATGAATAACAT
*
231402 TATTTACTATCTCATGGCATGAATAACAT
1 TATTTACTATCTCATGACATGAATAACAT
231431 ACCCACACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.38
Consensus pattern (29 bp):
TATTTACTATCTCATGACATGAATAACAT
Found at i:231432 original size:101 final size:102
Alignment explanation
Indices: 231314--231594 Score: 366
Period size: 101 Copynumber: 2.7 Consensus size: 102
231304 TTATTGTCAT
* * * *
231314 ATGGTATGAATAACATACCCACATATGTATTGTCACATGGCATAAATAACATACCCACATATTTA
1 ATGGCATGAATAACATACCCACATATTTACTGTCACATGGCATGAATAACATACCCACATATTTA
* * * *
231379 CTGTCTCATGACATGAATAACAT-TATTTACTATCTC
66 CTGTCACATCACATGAATAACATACATTTACTATCAC
*
231415 ATGGCATGAATAACATACCCACACATTTACTGTCACATGGCATGAATAACATACCCACATATTTA
1 ATGGCATGAATAACATACCCACATATTTACTGTCACATGGCATGAATAACATACCCACATATTTA
* *
231480 CTGTCACATCTCATGAATAACATACCACACATTTACTGTCAC
66 CTGTCACATCACATGAATAACAT-----ACATTTACTATCAC
* * * * *
231522 ATGACATGAATAACATACCCACATATTTACTGTCTCGTGGCATGAATAACATACTCACACATTTA
1 ATGGCATGAATAACATACCCACATATTTACTGTCACATGGCATGAATAACATACCCACATATTTA
231587 CTGTCACA
66 CTGTCACA
231595 ACAATTATCA
Statistics
Matches: 157, Mismatches: 17, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
101 80 0.51
107 77 0.49
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.30
Consensus pattern (102 bp):
ATGGCATGAATAACATACCCACATATTTACTGTCACATGGCATGAATAACATACCCACATATTTA
CTGTCACATCACATGAATAACATACATTTACTATCAC
Found at i:231530 original size:71 final size:71
Alignment explanation
Indices: 231402--231594 Score: 296
Period size: 71 Copynumber: 2.7 Consensus size: 71
231392 TGAATAACAT
* * * *
231402 TATTTACTATCTCATGGCATGAATAACATACCCACACATTTACTGTCACATGGCATGAATAACAT
1 TATTTACTGTCACATCGCATGAATAACATA-CCACACATTTACTGTCACATGACATGAATAACAT
231467 ACCCACA
65 ACCCACA
*
231474 TATTTACTGTCACATCTCATGAATAACATACCACACATTTACTGTCACATGACATGAATAACATA
1 TATTTACTGTCACATCGCATGAATAACATACCACACATTTACTGTCACATGACATGAATAACATA
231539 CCCACA
66 CCCACA
* * *
231545 TATTTACTGTCTCGTGGCATGAATAACATACTCACACATTTACTGTCACA
1 TATTTACTGTCACATCGCATGAATAACATAC-CACACATTTACTGTCACA
231595 ACAATTATCA
Statistics
Matches: 111, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
71 67 0.60
72 44 0.40
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (71 bp):
TATTTACTGTCACATCGCATGAATAACATACCACACATTTACTGTCACATGACATGAATAACATA
CCCACA
Found at i:233495 original size:18 final size:18
Alignment explanation
Indices: 233472--233534 Score: 108
Period size: 18 Copynumber: 3.5 Consensus size: 18
233462 AGAAATAGCA
233472 TACTAGCTCGTTTGAGCG
1 TACTAGCTCGTTTGAGCG
233490 TACTAGCTCGTTTGAGCG
1 TACTAGCTCGTTTGAGCG
*
233508 TACTAGCTCGTTTGAGCA
1 TACTAGCTCGTTTGAGCG
*
233526 TACTGGCTC
1 TACTAGCTC
233535 ATAAGAGCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.17, C:0.24, G:0.25, T:0.33
Consensus pattern (18 bp):
TACTAGCTCGTTTGAGCG
Found at i:233550 original size:19 final size:19
Alignment explanation
Indices: 233521--233569 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
233511 TAGCTCGTTT
233521 GAGCA-TACTGGCTCATAA
1 GAGCATTACTGGCTCATAA
233539 GAGCATTACTGGCTCATAA
1 GAGCATTACTGGCTCATAA
233558 GAGCATTACTGG
1 GAGCATTACTGG
233570 ATCGCAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 5 0.17
19 25 0.83
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (19 bp):
GAGCATTACTGGCTCATAA
Found at i:236094 original size:24 final size:24
Alignment explanation
Indices: 236067--236114 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
236057 TCGTAGGTAA
*
236067 ATTATACTAATAAATGCTAAATAT
1 ATTATACTAATAAATACTAAATAT
*
236091 ATTATATTAATAAATACTAAATAT
1 ATTATACTAATAAATACTAAATAT
236115 TTTAGAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (24 bp):
ATTATACTAATAAATACTAAATAT
Found at i:237298 original size:22 final size:22
Alignment explanation
Indices: 237273--237317 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
237263 CCACAAGCAT
237273 AGCTACCATTCAAAGTACCCCC
1 AGCTACCATTCAAAGTACCCCC
237295 AGCTACCATTCAAAGTACCCCC
1 AGCTACCATTCAAAGTACCCCC
237317 A
1 A
237318 ACTAGATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.40, G:0.09, T:0.18
Consensus pattern (22 bp):
AGCTACCATTCAAAGTACCCCC
Found at i:241956 original size:27 final size:27
Alignment explanation
Indices: 241914--241991 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
241904 ACACGTCATG
241914 AAAA-AATAGCTTTTGTGGCGAACTCT
1 AAAAGAATAGCTTTTGTGGCGAACTCT
* * *
241940 GAGAGAATAACTTTTGTGGCGAACTCT
1 AAAAGAATAGCTTTTGTGGCGAACTCT
* *
241967 AAAAGAGTAGCCTTTGTGGCGAACT
1 AAAAGAATAGCTTTTGTGGCGAACT
241992 TGAAAGAGTA
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 2 0.05
27 41 0.95
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.28
Consensus pattern (27 bp):
AAAAGAATAGCTTTTGTGGCGAACTCT
Found at i:242030 original size:27 final size:27
Alignment explanation
Indices: 241992--242061 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
241982 GTGGCGAACT
* *
241992 TGAAAGAGTAGCCTTTACGACGAAATA
1 TGAAAGAATAGCCTTTACGACAAAATA
* *
242019 TGAAAGAATAGCTTTTATGACAAAATA
1 TGAAAGAATAGCCTTTACGACAAAATA
242046 TGAAAGAATAGCCTTT
1 TGAAAGAATAGCCTTT
242062 GTGGTGAAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27
Consensus pattern (27 bp):
TGAAAGAATAGCCTTTACGACAAAATA
Found at i:242119 original size:27 final size:27
Alignment explanation
Indices: 242047--242153 Score: 76
Period size: 27 Copynumber: 4.0 Consensus size: 27
242037 GACAAAATAT
* * * *
242047 GAAAGAATAGCCTTTGTGGTGAAACGT-
1 GAAAGAATAACCCTTGTGGCG-AACTTA
* * *
242074 GAAAGAATGA-CCTTCGTGGTGAACTTT
1 GAAAGAATAACCCTT-GTGGCGAACTTA
* *
242101 GAGAGACTAACCCTTGTGGCGAACTTA
1 GAAAGAATAACCCTTGTGGCGAACTTA
* *
242128 GAAAGAATAACCTTTGTGACG-ACTTA
1 GAAAGAATAACCCTTGTGGCGAACTTA
242154 TGAAGTAAAT
Statistics
Matches: 64, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
26 12 0.19
27 48 0.75
28 4 0.06
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (27 bp):
GAAAGAATAACCCTTGTGGCGAACTTA
Found at i:245578 original size:21 final size:21
Alignment explanation
Indices: 245552--245601 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
245542 GGAGTTTTTG
**
245552 GTATCGGTAGTTA-CATGACTT
1 GTATCGGTAGAAATCAT-ACTT
245573 GTATCGGTAGAAATCATACTT
1 GTATCGGTAGAAATCATACTT
245594 GTATCGGT
1 GTATCGGT
245602 GAACTAGTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (21 bp):
GTATCGGTAGAAATCATACTT
Found at i:254486 original size:23 final size:23
Alignment explanation
Indices: 254456--254565 Score: 111
Period size: 23 Copynumber: 4.8 Consensus size: 23
254446 GCTGGGGAAA
254456 CAGTAAGCACACACAGTGC-AAT
1 CAGTAAGCACACACAGTGCAAAT
254478 CCAGTAAGCACACACAGTGC-AAT
1 -CAGTAAGCACACACAGTGCAAAT
* * * *
254501 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
*
254524 CAGTAGGCACACGA-AGTGCGAAA-
1 CAGTAAGCACAC-ACAGTGC-AAAT
*
254547 GAGTAAGCACACACAGTGC
1 CAGTAAGCACACACAGTGC
254566 TGAACAGTAA
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
22 16 0.21
23 55 0.73
24 4 0.05
ACGTcount: A:0.38, C:0.26, G:0.24, T:0.12
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGCAAAT
Found at i:254574 original size:23 final size:22
Alignment explanation
Indices: 254428--254577 Score: 101
Period size: 23 Copynumber: 6.5 Consensus size: 22
254418 CGAAGTACTT
254428 AACAGTAAGCACACA-AGTGCTGGGG
1 AACAGTAAGCACACACAGTGC----G
254453 AAACAGTAAGCACACACAGTGC-
1 -AACAGTAAGCACACACAGTGCG
254475 AATCCAGTAAGCACACACAGTGC-
1 AA--CAGTAAGCACACACAGTGCG
* * * * *
254498 AATCAGTAGGCGCACATAGCGCA
1 AA-CAGTAAGCACACACAGTGCG
*
254521 AATCAGTAGGCACACGA-AGTGCG
1 AA-CAGTAAGCACAC-ACAGTGCG
*
254544 AAAGAGTAAGCACACACAGTGCTG
1 -AACAGTAAGCACACACAGTGC-G
254568 AACAGTAAGC
1 AACAGTAAGC
254578 GCGCTAGCGT
Statistics
Matches: 105, Mismatches: 11, Indels: 19
0.78 0.08 0.14
Matches are distributed among these distances:
21 2 0.02
22 16 0.15
23 63 0.60
24 4 0.04
26 15 0.14
27 5 0.05
ACGTcount: A:0.39, C:0.24, G:0.25, T:0.12
Consensus pattern (22 bp):
AACAGTAAGCACACACAGTGCG
Found at i:254678 original size:24 final size:26
Alignment explanation
Indices: 254640--254687 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
254630 TCTACATGGG
254640 TATAATCTCTCATAT-TCATCATTTCT
1 TATAATCTCTCATATATCA-CATTTCT
254666 TATAAT-T-TCATATATCACATTT
1 TATAATCTCTCATATATCACATTT
254688 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (26 bp):
TATAATCTCTCATATATCACATTTCT
Done.