Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024505.1 Corchorus olitorius cultivar O-4 contig24538, 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: 134932
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:4129 original size:19 final size:19
Alignment explanation
Indices: 4102--4161 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
4092 AATTAAAGCA
4102 CAATGACAACTTCATGTGT
1 CAATGACAACTTCATGTGT
* * *
4121 CAATAACAAATTAATAGTG-
1 CAATGACAACTTCAT-GTGT
*
4140 CATATGACAACTTCGTGTGT
1 CA-ATGACAACTTCATGTGT
4160 CA
1 CA
4162 TTTTGAAAGG
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (19 bp):
CAATGACAACTTCATGTGT
Found at i:4215 original size:32 final size:32
Alignment explanation
Indices: 4172--4388 Score: 155
Period size: 30 Copynumber: 6.9 Consensus size: 32
4162 TTTTGAAAGG
*
4172 TAAAATCATGACAACTTATGGTTTCAATTGAA
1 TAAAATCATGACAACTTATGGTGTCAATTGAA
* * * *
4204 TAAAATTATGACATCTTCA-AGTGTCTATTGGAA
1 TAAAATCATGACAACTT-ATGGTGTCAATT-GAA
** *
4237 -ATTTATCATGACAACTTCTGGTGTCAATTGAA
1 TA-AAATCATGACAACTTATGGTGTCAATTGAA
* * *
4269 TAAAATTATGACATCTTCA-AGTGTCAATTG--
1 TAAAATCATGACAACTT-ATGGTGTCAATTGAA
* *
4299 CAAGATCATGACAACTTATGGTGTCAATTG--
1 TAAAATCATGACAACTTATGGTGTCAATTGAA
* * * *
4329 CAAGATCATGACAGCTTCTGGTGTCAATTG--
1 TAAAATCATGACAACTTATGGTGTCAATTGAA
* * *
4359 CAAAATCATGACAGCTTCTGGTGTCAATTG
1 TAAAATCATGACAACTTATGGTGTCAATTG
4389 CAAGACCATG
Statistics
Matches: 152, Mismatches: 26, Indels: 16
0.78 0.13 0.08
Matches are distributed among these distances:
29 1 0.01
30 80 0.53
32 47 0.31
33 24 0.16
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Consensus pattern (32 bp):
TAAAATCATGACAACTTATGGTGTCAATTGAA
Found at i:4248 original size:33 final size:33
Alignment explanation
Indices: 4172--4298 Score: 109
Period size: 32 Copynumber: 3.9 Consensus size: 33
4162 TTTTGAAAGG
* * *
4172 TAAAATCATGACAACTT-ATGGTTTCAATT-GAA
1 TAAAATCATGACATCTTCA-AGTGTCAATTGGAA
* *
4204 TAAAATTATGACATCTTCAAGTGTCTATTGGAA
1 TAAAATCATGACATCTTCAAGTGTCAATTGGAA
** * **
4237 -ATTTATCATGACAACTTCTGGTGTCAATT-GAA
1 TA-AAATCATGACATCTTCAAGTGTCAATTGGAA
*
4269 TAAAATTATGACATCTTCAAGTGTCAATTG
1 TAAAATCATGACATCTTCAAGTGTCAATTG
4299 CAAGATCATG
Statistics
Matches: 72, Mismatches: 18, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
32 47 0.65
33 25 0.35
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (33 bp):
TAAAATCATGACATCTTCAAGTGTCAATTGGAA
Found at i:4252 original size:65 final size:62
Alignment explanation
Indices: 4176--4388 Score: 252
Period size: 65 Copynumber: 3.4 Consensus size: 62
4166 GAAAGGTAAA
* * *
4176 ATCATGACAACTTATGGTTTCAATTGAATAAAATTATGACATCTTCAAGTGTCTATTGGAAATTT
1 ATCATGACAACTTATGGTGTCAATTGAATAAAATTATGACATCTTCAAGTGTCAATT-GAAA--G
* *
4241 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAGTGTCAATTGCAAG
1 ATCATGACAACTTATGGTGTCAATTGAATAAAATTATGACATCTTCAAGTGTCAATTGAAAG
* * * * **
4303 ATCATGACAACTTATGGTGTCAATTG--CAAGATCATGACAGCTTCTGGTGTCAATTGCAAA-
1 ATCATGACAACTTATGGTGTCAATTGAATAAAATTATGACATCTTCAAGTGTCAATTG-AAAG
* *
4363 ATCATGACAGCTTCTGGTGTCAATTG
1 ATCATGACAACTTATGGTGTCAATTG
4389 CAAGACCATG
Statistics
Matches: 132, Mismatches: 15, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
60 48 0.36
61 2 0.02
62 25 0.19
64 3 0.02
65 54 0.41
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (62 bp):
ATCATGACAACTTATGGTGTCAATTGAATAAAATTATGACATCTTCAAGTGTCAATTGAAAG
Found at i:4323 original size:30 final size:30
Alignment explanation
Indices: 4241--4422 Score: 238
Period size: 30 Copynumber: 6.0 Consensus size: 30
4231 TTGGAAATTT
* * *
4241 ATCATGACAACTTCTGGTGTCAATTGAATAAA
1 ATCATGACAGCTTCTGGTGTCAATTG--CAAG
* * **
4273 ATTATGACATCTTCAAGTGTCAATTGCAAG
1 ATCATGACAGCTTCTGGTGTCAATTGCAAG
* *
4303 ATCATGACAACTTATGGTGTCAATTGCAAG
1 ATCATGACAGCTTCTGGTGTCAATTGCAAG
*
4333 ATCATGACAGCTTCTGGTGTCAATTGCAAA
1 ATCATGACAGCTTCTGGTGTCAATTGCAAG
4363 ATCATGACAGCTTCTGGTGTCAATTGCAAG
1 ATCATGACAGCTTCTGGTGTCAATTGCAAG
* *
4393 ACCATGACAGCTTCCGGTGTCAATTGCAAG
1 ATCATGACAGCTTCTGGTGTCAATTGCAAG
4423 GCGTGTCATT
Statistics
Matches: 133, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
30 111 0.83
32 22 0.17
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (30 bp):
ATCATGACAGCTTCTGGTGTCAATTGCAAG
Found at i:4368 original size:60 final size:60
Alignment explanation
Indices: 4241--4946 Score: 772
Period size: 60 Copynumber: 11.4 Consensus size: 60
4231 TTGGAAATTT
* * * * **
4241 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTG--CAAGATCATGACAACTTCTGGTGTCAATTGCAAG
* * *
4303 ATCATGACAACTTATGGTGTCAATTGCAAGATCATGACAGCTTCTGGTGTCAATTGCAAA
1 ATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAAG
* * * *
4363 ATCATGACAGCTTCTGGTGTCAATTGCAAGACCATGACAGCTTCCGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAAG
* * * * * * *
4423 -GCGTGTC-ATTTGCAAGGCCATGACAACTTCTGGTGTCATTTGCAAGACCATGACAACTTCTGG
1 ATCATGACAACTT-C-TGG---TGTCAA----T--TG-C------AAGATCATGACAACTTCTGG
4486 TGTCAATTGCAAG
48 TGTCAATTGCAAG
* *
4499 ATCATGACAAATTCTGGTGTCAATTGCAAGATGCCATGACAACTTCTGGTGTCATTTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAGAT--CATGACAACTTCTGGTGTCAATTGCAAG
* *
4561 ACCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAAATTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAAG
* * *
4621 ATCATGACAACTTCTGGTGTCATTTGCAAGACCATGACAACTTCTGGTGTCATTTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAAG
* * * *
4681 A-C-CGACAACTTCTGGTGTCAATTGAATAAAATTATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTG--CAAGATCATGACAACTTCTGGTGTCAATTGCAAG
* *
4741 ATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCATTTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAAG
* * * * *
4801 ACCATGACAACTTCTGGTGTCATTTGTAAGACCATGACAAATTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAAG
* * * * *
4861 ATCATGACAACTTCTGGTGTCATTTGTAAGACCATGACAACTTCTGGTGTCATTTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAAG
*
4921 ACCATGACAACTTCTGGTGTCAATTG
1 ATCATGACAACTTCTGGTGTCAATTG
4947 TAAGTATAAT
Statistics
Matches: 553, Mismatches: 65, Indels: 54
0.82 0.10 0.08
Matches are distributed among these distances:
58 22 0.04
59 6 0.01
60 362 0.65
61 1 0.00
62 103 0.19
63 5 0.01
66 1 0.00
67 3 0.01
69 3 0.01
70 1 0.00
73 5 0.01
76 33 0.06
77 5 0.01
78 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (60 bp):
ATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAAG
Found at i:4430 original size:16 final size:16
Alignment explanation
Indices: 4409--4440 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4399 ACAGCTTCCG
4409 GTGTCAATTGCAAGGC
1 GTGTCAATTGCAAGGC
*
4425 GTGTCATTTGCAAGGC
1 GTGTCAATTGCAAGGC
4441 CATGACAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (16 bp):
GTGTCAATTGCAAGGC
Found at i:4446 original size:46 final size:46
Alignment explanation
Indices: 4379--4468 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
4369 ACAGCTTCTG
*
4379 GTGTCAATTGCAAGACCATGACAGCTTCCGGTGTCAATTGCAAGGC
1 GTGTCAATTGCAAGACCATGACAACTTCCGGTGTCAATTGCAAGGC
* * * *
4425 GTGTCATTTGCAAGGCCATGACAACTTCTGGTGTCATTTGCAAG
1 GTGTCAATTGCAAGACCATGACAACTTCCGGTGTCAATTGCAAG
4469 ACCATGACAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (46 bp):
GTGTCAATTGCAAGACCATGACAACTTCCGGTGTCAATTGCAAGGC
Found at i:4461 original size:30 final size:30
Alignment explanation
Indices: 4425--4942 Score: 752
Period size: 30 Copynumber: 17.2 Consensus size: 30
4415 ATTGCAAGGC
*
4425 GTGTCATTTGCAAGGCCATGACAACTTCTG
1 GTGTCATTTGCAAGACCATGACAACTTCTG
4455 GTGTCATTTGCAAGACCATGACAACTTCTG
1 GTGTCATTTGCAAGACCATGACAACTTCTG
* * *
4485 GTGTCAATTGCAAGATCATGACAAATTCTG
1 GTGTCATTTGCAAGACCATGACAACTTCTG
*
4515 GTGTCAATTGCAAGATGCCATGACAACTTCTG
1 GTGTCATTTGCAAGA--CCATGACAACTTCTG
4547 GTGTCATTTGCAAGACCATGACAACTTCTG
1 GTGTCATTTGCAAGACCATGACAACTTCTG
* * *
4577 GTGTCAATTGCAAGATCATGACAAATTCTG
1 GTGTCATTTGCAAGACCATGACAACTTCTG
* *
4607 GTGTCAATTGCAAGATCATGACAACTTCTG
1 GTGTCATTTGCAAGACCATGACAACTTCTG
4637 GTGTCATTTGCAAGACCATGACAACTTCTG
1 GTGTCATTTGCAAGACCATGACAACTTCTG
4667 GTGTCATTTGCAAGACC--GACAACTTCTG
1 GTGTCATTTGCAAGACCATGACAACTTCTG
* * * **
4695 GTGTCAATTGAATAAAATTATGACAACTTCTG
1 GTGTCATTTG--CAAGACCATGACAACTTCTG
* *
4727 GTGTCAATTGCAAGATCATGACAACTTCTG
1 GTGTCATTTGCAAGACCATGACAACTTCTG
* *
4757 GTGTCAATTGCAAGATCATGACAACTTCTG
1 GTGTCATTTGCAAGACCATGACAACTTCTG
*
4787 GTGTCATTTGTAAGACCATGACAACTTCTG
1 GTGTCATTTGCAAGACCATGACAACTTCTG
* *
4817 GTGTCATTTGTAAGACCATGACAAATTCTG
1 GTGTCATTTGCAAGACCATGACAACTTCTG
* *
4847 GTGTCAATTGCAAGATCATGACAACTTCTG
1 GTGTCATTTGCAAGACCATGACAACTTCTG
*
4877 GTGTCATTTGTAAGACCATGACAACTTCTG
1 GTGTCATTTGCAAGACCATGACAACTTCTG
*
4907 GTGTCATTTGTAAGACCATGACAACTTCTG
1 GTGTCATTTGCAAGACCATGACAACTTCTG
4937 GTGTCA
1 GTGTCA
4943 ATTGTAAGTA
Statistics
Matches: 450, Mismatches: 32, Indels: 12
0.91 0.06 0.02
Matches are distributed among these distances:
28 20 0.04
30 382 0.85
32 48 0.11
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (30 bp):
GTGTCATTTGCAAGACCATGACAACTTCTG
Found at i:6031 original size:22 final size:25
Alignment explanation
Indices: 5996--6049 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
5986 ATAAATGTTG
* *
5996 TTGATAA-TCTTCT-CTTTTATCTC
1 TTGATAATTCTTCTCCATTTATCAC
6019 -TGATAATTC-TCTCCATTTATCAC
1 TTGATAATTCTTCTCCATTTATCAC
6042 TTGATAAT
1 TTGATAAT
6050 ATCTAGCTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 9 0.35
23 10 0.38
24 7 0.27
ACGTcount: A:0.24, C:0.20, G:0.06, T:0.50
Consensus pattern (25 bp):
TTGATAATTCTTCTCCATTTATCAC
Found at i:15727 original size:52 final size:52
Alignment explanation
Indices: 15666--15769 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
15656 CATGTTATAG
15666 TTATTATTATGTTATAATGTTACAATAATTAGGTGGAGGCCGTTCACTTTTA
1 TTATTATTATGTTATAATGTTACAATAATTAGGTGGAGGCCGTTCACTTTTA
*
15718 TTATTATTATGTTATAATGTTATAATAATTAGGTGGAGGCCGTTCACTTTTA
1 TTATTATTATGTTATAATGTTACAATAATTAGGTGGAGGCCGTTCACTTTTA
15770 AGATGAAATG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.45
Consensus pattern (52 bp):
TTATTATTATGTTATAATGTTACAATAATTAGGTGGAGGCCGTTCACTTTTA
Found at i:18077 original size:15 final size:15
Alignment explanation
Indices: 18047--18094 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
18037 TTCAAAAGTT
18047 TGAAG-ATTTTAGAAA
1 TGAAGCATTTTA-AAA
18062 TGAAGCATTTTAAAA
1 TGAAGCATTTTAAAA
* * *
18077 TGCATCATTTCAAAA
1 TGAAGCATTTTAAAA
18092 TGA
1 TGA
18095 TAGTGATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 22 0.79
16 6 0.21
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (15 bp):
TGAAGCATTTTAAAA
Found at i:18691 original size:34 final size:34
Alignment explanation
Indices: 18653--18724 Score: 126
Period size: 34 Copynumber: 2.1 Consensus size: 34
18643 TGGAGATCTG
* *
18653 GGAGTTAGCCAGGAAGGAATCAACGTTATGCGAA
1 GGAGTTAGCCAAGAAGGAATCAACGTTAAGCGAA
18687 GGAGTTAGCCAAGAAGGAATCAACGTTAAGCGAA
1 GGAGTTAGCCAAGAAGGAATCAACGTTAAGCGAA
18721 GGAG
1 GGAG
18725 CTTGCTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.38, C:0.14, G:0.33, T:0.15
Consensus pattern (34 bp):
GGAGTTAGCCAAGAAGGAATCAACGTTAAGCGAA
Found at i:18850 original size:60 final size:60
Alignment explanation
Indices: 18784--18909 Score: 225
Period size: 60 Copynumber: 2.1 Consensus size: 60
18774 ATAAGCAAGA
*
18784 AGGAAGGAATCAACATTATGCGAAGGAGCTTGCTTCATTATGGAGATCCGGGAGTTAGCT
1 AGGAAGGAATCAACATTATACGAAGGAGCTTGCTTCATTATGGAGATCCGGGAGTTAGCT
* *
18844 AGGAAGGAATCAACGTTATACGAAGGAGCTTGCTTCATTATGGAGATTCGGGAGTTAGCT
1 AGGAAGGAATCAACATTATACGAAGGAGCTTGCTTCATTATGGAGATCCGGGAGTTAGCT
18904 AGGAAG
1 AGGAAG
18910 CTAATATTTG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.25
Consensus pattern (60 bp):
AGGAAGGAATCAACATTATACGAAGGAGCTTGCTTCATTATGGAGATCCGGGAGTTAGCT
Found at i:20932 original size:49 final size:47
Alignment explanation
Indices: 20872--21000 Score: 163
Period size: 49 Copynumber: 2.7 Consensus size: 47
20862 TTACATTTCC
*
20872 TGCATTTTTTCTCAATTTTTACTACAAAATTGAACTTTTA-TTTTTACT
1 TGCACTTTTTCTCAATTTTTA-TACAAAATTGAACTTTTACTTTTTA-T
* *
20920 TGCACATTTTTCTCAATTTTTAAGACAAAATTGATCTTTTACTTTTTAT
1 TGCAC-TTTTTCTCAATTTTT-ATACAAAATTGAACTTTTACTTTTTAT
*
20969 TGCACTTTTTATCAATTTTT-TGACAAAATTGA
1 TGCACTTTTTCTCAATTTTTAT-ACAAAATTGA
21001 TTGGCACGCT
Statistics
Matches: 72, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
47 10 0.14
48 18 0.25
49 37 0.51
50 7 0.10
ACGTcount: A:0.29, C:0.14, G:0.06, T:0.51
Consensus pattern (47 bp):
TGCACTTTTTCTCAATTTTTATACAAAATTGAACTTTTACTTTTTAT
Found at i:21688 original size:19 final size:19
Alignment explanation
Indices: 21664--21722 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
21654 AGTTAGCCAG
21664 GAAGGAATCAACGTTATGC
1 GAAGGAATCAACGTTATGC
* * **
21683 GAAGGAGT-TA-GCCA-G-
1 GAAGGAATCAACGTTATGC
21698 GAAGGAATCAACGTTATGC
1 GAAGGAATCAACGTTATGC
21717 GAAGGA
1 GAAGGA
21723 GCTTTCTTTA
Statistics
Matches: 28, Mismatches: 8, Indels: 8
0.64 0.18 0.18
Matches are distributed among these distances:
15 7 0.25
16 2 0.07
17 4 0.14
18 2 0.07
19 13 0.46
ACGTcount: A:0.37, C:0.14, G:0.32, T:0.17
Consensus pattern (19 bp):
GAAGGAATCAACGTTATGC
Found at i:21690 original size:34 final size:34
Alignment explanation
Indices: 21652--21723 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
21642 TGGAGATCTG
21652 GGAGTTAGCCAGGAAGGAATCAACGTTATGCGAA
1 GGAGTTAGCCAGGAAGGAATCAACGTTATGCGAA
21686 GGAGTTAGCCAGGAAGGAATCAACGTTATGCGAA
1 GGAGTTAGCCAGGAAGGAATCAACGTTATGCGAA
21720 GGAG
1 GGAG
21724 CTTTCTTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.35, C:0.14, G:0.35, T:0.17
Consensus pattern (34 bp):
GGAGTTAGCCAGGAAGGAATCAACGTTATGCGAA
Found at i:21849 original size:60 final size:60
Alignment explanation
Indices: 21783--21908 Score: 225
Period size: 60 Copynumber: 2.1 Consensus size: 60
21773 ATAAACAAGA
*
21783 AGGAAGGAATCAACATTATGCGAAGGAGCTTGCTTCATTATGGAGATCCGGGAGTTAGCT
1 AGGAAGGAATCAACATTATACGAAGGAGCTTGCTTCATTATGGAGATCCGGGAGTTAGCT
* *
21843 AGGAAGGAATCAACGTTATACGAAGGAGCTTGCTTCATTATGGAGATTCGGGAGTTAGCT
1 AGGAAGGAATCAACATTATACGAAGGAGCTTGCTTCATTATGGAGATCCGGGAGTTAGCT
21903 AGGAAG
1 AGGAAG
21909 CTAATATTTG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.25
Consensus pattern (60 bp):
AGGAAGGAATCAACATTATACGAAGGAGCTTGCTTCATTATGGAGATCCGGGAGTTAGCT
Found at i:23171 original size:23 final size:23
Alignment explanation
Indices: 23141--23184 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
23131 TGGAGGAAGA
23141 GGGTTAGTGGTGACTGTTTTGAT
1 GGGTTAGTGGTGACTGTTTTGAT
23164 GGGTTAGTGGTGACTGTTTTG
1 GGGTTAGTGGTGACTGTTTTG
23185 GTGCATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.11, C:0.05, G:0.41, T:0.43
Consensus pattern (23 bp):
GGGTTAGTGGTGACTGTTTTGAT
Found at i:23685 original size:22 final size:22
Alignment explanation
Indices: 23638--23685 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
23628 ATTACACTAT
* *
23638 TTTTGATGATCTCCTTATGAAC
1 TTTTGATGATCTCCTTAGGAAA
23660 TTTTGATGATCTTCC-TAGGAAA
1 TTTTGATGATC-TCCTTAGGAAA
23682 TTTT
1 TTTT
23686 AATAACGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.48
Consensus pattern (22 bp):
TTTTGATGATCTCCTTAGGAAA
Found at i:23930 original size:22 final size:22
Alignment explanation
Indices: 23905--24187 Score: 129
Period size: 22 Copynumber: 13.0 Consensus size: 22
23895 GAATTGTTAG
*
23905 TAATCACACTCTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
*
23927 TAATCACACTATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
* *
23949 TAACCTCACTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
23971 TAAACATTC-CTATAAAATTTTGA
1 TAATCA--CACTATGAAATTTTGA
* * * *
23994 TAAACCTCCCTATAAAATTTTGA
1 T-AATCACACTATGAAATTTTGA
* *
24017 TAATCTC-CTTATGAAATCTTG-
1 TAATCACAC-TATGAAATTTTGA
*
24038 --AT-A-ACTA-CAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * * **
24055 TAACCTCCCTATGATTTTTTGA
1 TAATCACACTATGAAATTTTGA
* ** * * *
24077 TAACCTTATTATCAAATTTTGT
1 TAATCACACTATGAAATTTTGA
* *
24099 TAATCTCCCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
24121 T-CTACATACTATGAAATTTTGA
1 TAAT-CACACTATGAAATTTTGA
* * *
24143 -AAACTAAACTATAAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
* *
24165 TAAGCTTCA-TATGAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
24187 T
1 T
24188 TATCCTGCCT
Statistics
Matches: 198, Mismatches: 47, Indels: 32
0.71 0.17 0.12
Matches are distributed among these distances:
16 7 0.04
17 2 0.01
18 1 0.01
19 3 0.02
21 6 0.03
22 141 0.71
23 34 0.17
24 4 0.02
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:24015 original size:46 final size:44
Alignment explanation
Indices: 23918--24019 Score: 125
Period size: 46 Copynumber: 2.3 Consensus size: 44
23908 TCACACTCTG
* * *
23918 AAATTTTGATAATCACACTATGAAATTGTGATAACCTCACTATG
1 AAATTTTGATAAACACACTATAAAATTGTGATAACCTCACTATA
* *
23962 AAATTTTGATAAACATTC-CTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACA--CACTATAAAATTGTGAT-AACCTCACTATA
24008 AAATTTTGATAA
1 AAATTTTGATAA
24020 TCTCCTTATG
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
44 14 0.28
45 13 0.26
46 23 0.46
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (44 bp):
AAATTTTGATAAACACACTATAAAATTGTGATAACCTCACTATA
Found at i:24138 original size:44 final size:43
Alignment explanation
Indices: 23653--24208 Score: 210
Period size: 44 Copynumber: 12.8 Consensus size: 43
23643 ATGATCTCCT
* * * * *
23653 TATGAACTTTTGATGATCTTCCTAGGAAATTTTAATAACGATAC
1 TATGAAATTTTGATAATCTCCCTATGAAATTTTGATAAC-ATAC
* * * *** **
23697 TATGGAATTTTGAGAACCTTTTTAT-AAATTTTTTTTAAC-T--
1 TATGAAATTTTGATAATCTCCCTATGAAA-TTTTGATAACATAC
* * * * * *
23737 TATGAAATTTTG-TTATCCTCACTAAGGAATTTTGAAAACCTCAC
1 TATGAAATTTTGATAAT-CTCCCTATGAAATTTTGATAACAT-AC
* * * *
23781 TATGAAATTTTGACAA-CTTCCCAACGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAATC-TCCCTATGAAATTTTGATAA-C-ATAC
** * * * * * *
23826 TATGGGATGTTGATAACCTCCATATGATATATTGATAACCATAT
1 TATGAAATTTTGATAATCTCCCTATGAAATTTTGATAA-CATAC
* * * * * * *
23870 TATGAAAATTTAAAAACCTTCATATG-AATTGTT-AGTAATCACAC
1 TATGAAATTTTGATAATCTCCCTATGAAATT-TTGA-TAA-CATAC
* * * * *
23914 TCTGAAATTTTGATAATCACACTATGAAATTGTGATAACCTCAC
1 TATGAAATTTTGATAATCTCCCTATGAAATTTTGATAACAT-AC
* * * * *
23958 TATGAAATTTTGATAAACATTCCTATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGATAATC-TCCCTATGAAATTTTGAT-AACAT-AC
* * *
24004 TATAAAATTTTGATAATCTCCTTATGAAATCTTGATAAC-TAC
1 TATGAAATTTTGATAATCTCCCTATGAAATTTTGATAACATAC
* ** * *
24046 ----AAATTTTGATAACCTCCCTATGATTTTTTGATAACCTTAT
1 TATGAAATTTTGATAATCTCCCTATGAAATTTTGATAA-CATAC
* * *
24086 TATCAAATTTTGTTAATCTCCCTATGAAATTTTGATCTACATAC
1 TATGAAATTTTGATAATCTCCCTATGAAATTTTGAT-AACATAC
* ** * *
24130 TATGAAATTTTGA-AAACTAAACTATAAAATTTTGATAAGC-TTC
1 TATGAAATTTTGATAATCT-CCCTATGAAATTTTGATAA-CATAC
* *
24173 ATATGAAATTTTGATTATCCTGCC--TGAAATTTTGAT
1 -TATGAAATTTTGATAAT-CTCCCTATGAAATTTTGAT
24209 TACTCCATAA
Statistics
Matches: 374, Mismatches: 107, Indels: 63
0.69 0.20 0.12
Matches are distributed among these distances:
38 29 0.08
39 2 0.01
40 24 0.06
41 3 0.01
42 2 0.01
43 27 0.07
44 193 0.52
45 68 0.18
46 26 0.07
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (43 bp):
TATGAAATTTTGATAATCTCCCTATGAAATTTTGATAACATAC
Found at i:24435 original size:88 final size:88
Alignment explanation
Indices: 24286--24455 Score: 216
Period size: 88 Copynumber: 1.9 Consensus size: 88
24276 CCCAGAAATA
* * **
24286 CCTCTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTTTTTATGAAATTTTGATAAC
1 CCTCTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTGCTTATGAAATTTTGATAAC
** *
24351 CTCTCTATAAAATTTTGTTGACC
66 AACACTATAAAATTTTGTTGACC
* * * *
24374 CCTCTGTGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGGAATTTTGATAA
1 CCTCTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCT-GCTTATGAAATTTTGATAA
*
24438 TAACACTATAAAATTTTG
65 CAACACTATAAAATTTTG
24456 ATAATATTCT
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
88 67 0.97
89 2 0.03
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.42
Consensus pattern (88 bp):
CCTCTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTGCTTATGAAATTTTGATAAC
AACACTATAAAATTTTGTTGACC
Found at i:24515 original size:22 final size:22
Alignment explanation
Indices: 24287--24526 Score: 148
Period size: 22 Copynumber: 10.9 Consensus size: 22
24277 CCAGAAATAC
*
24287 CTCTATGAAATTTTGGTAATCA
1 CTCTATGAAATTTTGATAATCA
* * * *
24309 CAT-TTTGAAAATTTGATAACCT
1 C-TCTATGAAATTTTGATAATCA
* * * *
24331 TTTTATGAAATTTTGATAACCT
1 CTCTATGAAATTTTGATAATCA
* * * * *
24353 CTCTATAAAATTTTGTTGACCC
1 CTCTATGAAATTTTGATAATCA
*
24375 CTCTGTGAAATTTTGATAATCA
1 CTCTATGAAATTTTGATAATCA
* * *
24397 CAT-TATGTAATTTTGATAACCT
1 C-TCTATGAAATTTTGATAATCA
* * * *
24419 CGCTTTGGAATTTTGATAATAA
1 CTCTATGAAATTTTGATAATCA
* *
24441 CACTATAAAATTTTGATAAT-A
1 CTCTATGAAATTTTGATAATCA
*
24462 TTCTTAT-AAATTTTGATAATCTGA
1 CTC-TATGAAATTTTGATAATC--A
*
24486 TCTCTATGAAATTTCGATAATCA
1 -CTCTATGAAATTTTGATAATCA
*
24509 CTCTATGAGA-TTTGATAA
1 CTCTATGAAATTTTGATAA
24527 CCTTATATCA
Statistics
Matches: 168, Mismatches: 40, Indels: 21
0.73 0.17 0.09
Matches are distributed among these distances:
21 23 0.14
22 123 0.73
23 3 0.02
24 4 0.02
25 15 0.09
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (22 bp):
CTCTATGAAATTTTGATAATCA
Found at i:25691 original size:536 final size:540
Alignment explanation
Indices: 24891--25962 Score: 1620
Period size: 537 Copynumber: 2.0 Consensus size: 540
24881 AGGCTCGTTT
* *
24891 GAGTCCATGAAGTCCAAATTGTCAAGTCAGATATTTTGAAATCTAAATCTGATACTCTTAGACCA
1 GAGTCCATGAAGTCCAAACTGTCAAGTCAAATATTTTGAAATCTAAATCTGATACTCTTAGACCA
* * *
24956 ATTTGTTAATATGGAAGCCCAAAGAATAAATCCAAGTCCAATCAGTAATTATGATTCAGTAATGA
66 ATTCGTTAATATGGAAGCCCAAAGAAGAAATCCAAGTCCAATCAGTAATTATGATGCAGTAATGA
* * * * *
25021 TTCAGGCCCGATGCAGCATTGTTAAATCTTATTTAAAGGAGGACTTCACAAGAGTAGTTTTGGAA
131 TTCAGGCCCGATGCAACATTATTAAATCCTATTTAAAGGAGAACTTCACAAGAGCAGTTTTGGAA
* * * ** * * *
25086 GACATTTCATAACTTTTGATTCAGAGTTCTGAAAAATGCAAATGAGGTATCGTTGGAAAGAGGAT
196 GAAAATTCATAACTTTTGATCCAGAACTCAGAAAAATGCAAATGAGGTATCGTTAGAAAGAGAAT
* * *
25151 TCCGAGGTCTACAACTTTTATG-TTATCTTGAAACCTAATTCTGTCGTTTCGGTGGATGATTTTA
261 TCCGAGATCTACAACTTTTATGTTTATCTCGAAACCTAATTCTGCCGTTTCGGTGGATGATTTTA
* * *
25215 CCCTTGAAATTTCTGGTCAGAATTGATCTTCTCCTAAACCGACTTTGAGAATGTTTTAGACGAAA
326 CCCTTAAAATTTCTGGACAGAATTGATCTTCTCCTAAACCGACTTGGAGAATGTTTTAGACGAAA
25280 ATTCAGATGCTAAAAATGATGTGGGGCATCCCTATTGGCCACGTTGGATTCTAATTAATGAGGAT
391 ATTCAGATGCTAAAAATGATGTGGGGCATCCCTATTGGCCACGTTGGATTCTAATTAATGAGGAT
* *
25345 AATCTAAATTGCCATTCTTTTAATAGTGGAATAATT-AAA-A-TA-TTAATAATGGCAATTTAGG
456 AATCTAAATTGCCATTATTTTAATAGTGGAATAATTAAAATATTATTTAATAATGGCAATTTAGA
25406 AATATATTTGAAAAAAAAAA
521 AATATATTTGAAAAAAAAAA
* * *
25426 GAGTCCATGAAGTTCAAACTGTCAAGTCAAAT-TTATTGAAGTCTAAATCTGATATTCTTAGACC
1 GAGTCCATGAAGTCCAAACTGTCAAGTCAAATATT-TTGAAATCTAAATCTGATACTCTTAGA-C
* * *
25490 CAATTCGTTAATATGGAAGCCCAAAGAAGGAGTCCAAGTTCAATCAGTAATTATGATGC-GATAA
64 CAATTCGTTAATATGGAAGCCCAAAGAAGAAATCCAAGTCCAATCAGTAATTATGATGCAG-TAA
* *
25554 TGATTCA-GCCCTGATGTAACATTATTAAATCCTATTTAAAGGAGAACTTCACAATAGCAGTTTT
128 TGATTCAGGCCC-GATGCAACATTATTAAATCCTATTTAAAGGAGAACTTCACAAGAGCAGTTTT
* * *
25618 TGAAGAAAATTCATAACTTTTGATCCAGAACTCAGAAAAATTCAAATGCGGTATCGTTAGAAAGA
192 GGAAGAAAATTCATAACTTTTGATCCAGAACTCAGAAAAATGCAAATGAGGTATCGTTAGAAAGA
* *
25683 GAATTCCGATATCTACAACTTTTATGTTTATCTCGAGACCTAATTCTGCCGTTTCGGTGGATGAT
257 GAATTCCGAGATCTACAACTTTTATGTTTATCTCGAAACCTAATTCTGCCGTTTCGGTGGATGAT
* * *
25748 TTTTCCCTTAAAATTTCTGGACAGAATTGATCTTCTCCTAAACCGACTTGGAGAATGTTTTGGAT
322 TTTACCCTTAAAATTTCTGGACAGAATTGATCTTCTCCTAAACCGACTTGGAGAATGTTTTAGAC
* * * *
25813 GAAAATTCAGATGTTAAAGATGATGTGGGGCATCTCTATTGGCCATGTTGGATTCTAATTAATGA
387 GAAAATTCAGATGCTAAAAATGATGTGGGGCATCCCTATTGGCCACGTTGGATTCTAATTAATGA
* *
25878 GGATAATCTAAATTTCCATTATTTTAATATTGGAATAATTAAAATATTATTTAATAATGGCAATT
452 GGATAATCTAAATTGCCATTATTTTAATAGTGGAATAATTAAAATATTATTTAATAATGGCAATT
25943 TAGAAATATATTTGAAAAAA
517 TAGAAATATATTTGAAAAAA
25963 GGGTACAATT
Statistics
Matches: 480, Mismatches: 48, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
534 2 0.00
535 59 0.12
536 187 0.39
537 192 0.40
538 3 0.01
539 1 0.00
540 2 0.00
541 34 0.07
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (540 bp):
GAGTCCATGAAGTCCAAACTGTCAAGTCAAATATTTTGAAATCTAAATCTGATACTCTTAGACCA
ATTCGTTAATATGGAAGCCCAAAGAAGAAATCCAAGTCCAATCAGTAATTATGATGCAGTAATGA
TTCAGGCCCGATGCAACATTATTAAATCCTATTTAAAGGAGAACTTCACAAGAGCAGTTTTGGAA
GAAAATTCATAACTTTTGATCCAGAACTCAGAAAAATGCAAATGAGGTATCGTTAGAAAGAGAAT
TCCGAGATCTACAACTTTTATGTTTATCTCGAAACCTAATTCTGCCGTTTCGGTGGATGATTTTA
CCCTTAAAATTTCTGGACAGAATTGATCTTCTCCTAAACCGACTTGGAGAATGTTTTAGACGAAA
ATTCAGATGCTAAAAATGATGTGGGGCATCCCTATTGGCCACGTTGGATTCTAATTAATGAGGAT
AATCTAAATTGCCATTATTTTAATAGTGGAATAATTAAAATATTATTTAATAATGGCAATTTAGA
AATATATTTGAAAAAAAAAA
Found at i:30156 original size:2 final size:2
Alignment explanation
Indices: 30149--30173 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30139 TCATTACTAG
30149 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
30174 TCTGATATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30818 original size:22 final size:21
Alignment explanation
Indices: 30784--30826 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
30774 TGTGTGTGTG
* *
30784 TGTGATTGTTTGGTTTCGTAGA
1 TGTGATAGATTGGTTT-GTAGA
30806 TGTGATAGATTGGTTTGTAGA
1 TGTGATAGATTGGTTTGTAGA
30827 GACCGAGCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.19, C:0.02, G:0.33, T:0.47
Consensus pattern (21 bp):
TGTGATAGATTGGTTTGTAGA
Found at i:31367 original size:7 final size:7
Alignment explanation
Indices: 31355--31391 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
31345 GAACAAGTCC
31355 TTGAAGA
1 TTGAAGA
31362 TTGAAGA
1 TTGAAGA
31369 TTGAAGA
1 TTGAAGA
31376 TTGAAGA
1 TTGAAGA
31383 TTGAAGA
1 TTGAAGA
31390 TT
1 TT
31392 TGGTGGAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.27, T:0.32
Consensus pattern (7 bp):
TTGAAGA
Found at i:32055 original size:2 final size:2
Alignment explanation
Indices: 32050--32086 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
32040 GTTGCGTGTG
32050 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
32087 TTATGGACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35431 original size:36 final size:36
Alignment explanation
Indices: 35390--35463 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
35380 TATAAATACC
*
35390 CACCTTATTTTGGCCCTAAACATAACAATCAATTCA
1 CACCTTATGTTGGCCCTAAACATAACAATCAATTCA
35426 CACCTTATGTTGGCCCTAAACATAACAATCAATTCA
1 CACCTTATGTTGGCCCTAAACATAACAATCAATTCA
35462 CA
1 CA
35464 ATTTTATTCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.36, C:0.28, G:0.07, T:0.28
Consensus pattern (36 bp):
CACCTTATGTTGGCCCTAAACATAACAATCAATTCA
Found at i:36309 original size:16 final size:16
Alignment explanation
Indices: 36288--36320 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
36278 TATTTTAGTT
36288 TAATTGCT-TTTATTAA
1 TAATTGCTATTT-TTAA
36304 TAATTGCTATTTTTAA
1 TAATTGCTATTTTTAA
36320 T
1 T
36321 CCCCTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (16 bp):
TAATTGCTATTTTTAA
Found at i:40606 original size:4 final size:4
Alignment explanation
Indices: 40597--40622 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
40587 GGGCATTTTA
40597 TTCT TTCT TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TT
40623 AGTTGGTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:42677 original size:17 final size:18
Alignment explanation
Indices: 42655--42689 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
42645 TGAGGGGGAG
42655 GTTTTTGGAAAA-AAAAA
1 GTTTTTGGAAAACAAAAA
*
42672 GTTTTTTGAAAACAAAAA
1 GTTTTTGGAAAACAAAAA
42690 AATCAACAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.51, C:0.03, G:0.14, T:0.31
Consensus pattern (18 bp):
GTTTTTGGAAAACAAAAA
Found at i:43870 original size:51 final size:50
Alignment explanation
Indices: 43743--43931 Score: 184
Period size: 50 Copynumber: 3.7 Consensus size: 50
43733 ATTTTTGATC
* * * * *
43743 AAAAGATGAAACTTTTAAGTAATTTATGAGTAAAGATTGAATTTTTAGTT
1 AAAAGATGAAACTTTTAAGTAATTTGTGAATAAAGATTGAATCTTTAATG
*
43793 AAAAGATGAAACTTTTAAGTAATTTGTGAATAAAGATTGGATCTTTAATG
1 AAAAGATGAAACTTTTAAGTAATTTGTGAATAAAGATTGAATCTTTAATG
* * * * * *
43843 AGAAGTTGAAACCTTTTAAGCAATTTGTAAATAAA-AATGAAATCTTTAAGTT
1 AAAAGATGAAA-CTTTTAAGTAATTTGTGAATAAAGATTG-AATCTTTAA-TG
* * * *
43895 AAAATATTG-AACTTTTAATTCATTTGTAAATAAAGAT
1 AAAAGA-TGAAACTTTTAAGTAATTTGTGAATAAAGAT
43932 GAAATTTTTG
Statistics
Matches: 114, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
50 56 0.49
51 49 0.43
52 7 0.06
53 2 0.02
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (50 bp):
AAAAGATGAAACTTTTAAGTAATTTGTGAATAAAGATTGAATCTTTAATG
Found at i:44570 original size:41 final size:42
Alignment explanation
Indices: 44534--45008 Score: 370
Period size: 41 Copynumber: 10.9 Consensus size: 42
44524 CTTTTATACA
*
44534 AAAAATGCCCCTTCCTGGTTGGAAGGTCTCTATTTT-ATTCC
1 AAAAATGCCCCTTCCTGGTTGGAAGGTCTCTGTTTTCATTCC
* *
44575 AAAAATGCCCCTTCTTGGTTGGAAGGTCCCTGTTTTCTTTCATTTCC
1 AAAAATGCCCCTTCCTGGTTGGAAGGTCTCTG---T-TTTCA-TTCC
* * * * * *
44622 TAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTTTTCTTTCTTTCC
1 AAAAATGCCCCTTCCTGGTTGGAAGGTCTC---TGT-TTTCATTCC
*
44668 AAAAACGCCCCTTCCTGGTTGGAAGGTC-CTTGTTTTCATTTCC
1 AAAAATGCCCCTTCCTGGTTGGAAGGTCTC-TGTTTTCA-TTCC
* ** *
44711 AAAAATACCCCTTCCAAGTTGGAAGGTCTCTGTTAT-ATTCC
1 AAAAATGCCCCTTCCTGGTTGGAAGGTCTCTGTTTTCATTCC
* * * * **
44752 AAAAATGCCCCTTCCCGGTCGGAAGGTCACAATTTTCTTTTTTCC
1 AAAAATGCCCCTTCCTGGTTGGAAGGTCTC--TGTT-TTCATTCC
* * * * *
44797 AAAAATGCCCCTTCCTGGTCGGAAGGTCACAATTTTCTTTCTTTGC
1 AAAAATGCCCCTTCCTGGTTGGAAGGTCTC---TGT-TTTCATTCC
*
44843 AAAAACGCCCCTTCCTGGTTGGAAGGTC-CTTGTTTTCATTTCC
1 AAAAATGCCCCTTCCTGGTTGGAAGGTCTC-TGTTTTCA-TTCC
*
44886 AAAAATGCCACTTCCTGGTTGGAAGGTCTCTGTTTT-ATTCC
1 AAAAATGCCCCTTCCTGGTTGGAAGGTCTCTGTTTTCATTCC
* * * * *
44927 AAAAATGCCCCTTCCCGGTCGGAAGTTCACAGTTTTCTTTCATTCC
1 AAAAATGCCCCTTCCTGGTTGGAAGGTCTC---TGT-TTTCATTCC
* * *
44973 AAAAATG-CCCTTCCCGGTCGGAAGGTGT-TGTTTTCA
1 AAAAATGCCCCTTCCTGGTTGGAAGGTCTCTGTTTTCA
45009 ATGTTTTATT
Statistics
Matches: 360, Mismatches: 50, Indels: 49
0.78 0.11 0.11
Matches are distributed among these distances:
40 5 0.01
41 89 0.25
42 10 0.03
43 77 0.21
44 6 0.02
45 59 0.16
46 77 0.21
47 36 0.10
50 1 0.00
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.35
Consensus pattern (42 bp):
AAAAATGCCCCTTCCTGGTTGGAAGGTCTCTGTTTTCATTCC
Found at i:44858 original size:175 final size:176
Alignment explanation
Indices: 44534--44998 Score: 745
Period size: 175 Copynumber: 2.6 Consensus size: 176
44524 CTTTTATACA
* ** *
44534 AAAAATGCCCCTTCCTGGTTGGAAGGTCTCTATTTTATTCCAAAAATGCCCCTTCTTGGTTGGAA
1 AAAAATGCCCCTTCCTGGTTGGAAGGTCTCTGTTTTATTCCAAAAATGCCCCTTCCCGGTCGGAA
* * * *
44599 GGTCCCTGTTTTCTTTCATTTCCTAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTTTTCTTTCT
66 GGTCACAGTTTTCTTTC-TTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAATTTTCTTTCT
44664 TTCCAAAAACGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTCC
130 TTCCAAAAACGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTCC
* ** *
44711 AAAAATACCCCTTCCAAGTTGGAAGGTCTCTGTTATATTCCAAAAATGCCCCTTCCCGGTCGGAA
1 AAAAATGCCCCTTCCTGGTTGGAAGGTCTCTGTTTTATTCCAAAAATGCCCCTTCCCGGTCGGAA
* *
44776 GGTCACAATTTTCTTT-TTTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCACAATTTTCTTTCTT
66 GGTCACAGTTTTCTTTCTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAATTTTCTTTCTT
*
44840 TGCAAAAACGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTCC
131 TCCAAAAACGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTCC
*
44886 AAAAATGCCACTTCCTGGTTGGAAGGTCTCTGTTTTATTCCAAAAATGCCCCTTCCCGGTCGGAA
1 AAAAATGCCCCTTCCTGGTTGGAAGGTCTCTGTTTTATTCCAAAAATGCCCCTTCCCGGTCGGAA
* *
44951 GTTCACAGTTTTCTTTCATTCCAAAAATG-CCCTTCCCGGTCGGAAGGT
66 GGTCACAGTTTTCTTTCTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGT
44999 GTTGTTTTCA
Statistics
Matches: 263, Mismatches: 24, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
175 182 0.69
176 11 0.04
177 70 0.27
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (176 bp):
AAAAATGCCCCTTCCTGGTTGGAAGGTCTCTGTTTTATTCCAAAAATGCCCCTTCCCGGTCGGAA
GGTCACAGTTTTCTTTCTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAATTTTCTTTCTT
TCCAAAAACGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTCC
Found at i:44910 original size:89 final size:86
Alignment explanation
Indices: 44534--44998 Score: 392
Period size: 89 Copynumber: 5.3 Consensus size: 86
44524 CTTTTATACA
* * * * *
44534 AAAAATGCCCCTTCCTGGTTGGAAGGTCTCTATTTT-ATTCCAAAAATGCCCCTTCTTGGTTGGA
1 AAAAATGCCCCTTCCTGGTTGGAAGGTCACAATTTTCTTTCCAAAAACGCCCCTTCCTGGTTGGA
* *
44598 AGGTCCCTGTTTTCTTTCATTTCC
66 AGGT-CC-ATTGT-TTTCATTTCC
* * * *
44622 TAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTTTTCTTTCTTTCCAAAAACGCCCCTTCCTGGT
1 AAAAATGCCCCTTCCTGGTTGGAAGGTCACA---AT-TTTCTTTCCAAAAACGCCCCTTCCTGGT
44687 TGGAAGGTCC-TTGTTTTCATTTCC
62 TGGAAGGTCCATTGTTTTCATTTCC
* ** * * * * * *
44711 AAAAATACCCCTTCCAAGTTGGAAGGTCTC--TGTTATATTCCAAAAATGCCCCTTCCCGGTCGG
1 AAAAATGCCCCTTCCTGGTTGGAAGGTCACAATTTTCT-TTCCAAAAACGCCCCTTCCTGGTTGG
*
44774 AAGGTCACAATT-TTCTT-TTTTCC
65 AAGGTC-C-ATTGTT-TTCATTTCC
*
44797 AAAAATGCCCCTTCCTGGTCGGAAGGTCACAATTTTCTTTCTTTGCAAAAACGCCCCTTCCTGGT
1 AAAAATGCCCCTTCCTGGTTGGAAGGTCACAATTTTCTTTC----CAAAAACGCCCCTTCCTGGT
44862 TGGAAGGTCC-TTGTTTTCATTTCC
62 TGGAAGGTCCATTGTTTTCATTTCC
* * ** * * * *
44886 AAAAATGCCACTTCCTGGTTGGAAGGTCTCTGTTTT-ATTCCAAAAATGCCCCTTCCCGGTCGGA
1 AAAAATGCCCCTTCCTGGTTGGAAGGTCACAATTTTCTTTCCAAAAACGCCCCTTCCTGGTTGGA
* *
44950 AGTTCACAGTTTTCTTTCA-TTCC
66 AGGTC-CA-TTGT-TTTCATTTCC
* *
44973 AAAAATG-CCCTTCCCGGTCGGAAGGT
1 AAAAATGCCCCTTCCTGGTTGGAAGGT
44999 GTTGTTTTCA
Statistics
Matches: 308, Mismatches: 47, Indels: 46
0.77 0.12 0.11
Matches are distributed among these distances:
83 3 0.01
84 55 0.18
85 2 0.01
86 48 0.16
87 21 0.07
88 42 0.14
89 72 0.23
90 4 0.01
91 27 0.09
92 5 0.02
93 29 0.09
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (86 bp):
AAAAATGCCCCTTCCTGGTTGGAAGGTCACAATTTTCTTTCCAAAAACGCCCCTTCCTGGTTGGA
AGGTCCATTGTTTTCATTTCC
Found at i:44949 original size:130 final size:130
Alignment explanation
Indices: 44534--45008 Score: 461
Period size: 130 Copynumber: 3.6 Consensus size: 130
44524 CTTTTATACA
* * * * *
44534 AAAAATGCCCCTTCCTGGTTGGAAGGTCTC---TATTTT-ATTCCAAAAATGCCCCTTCTTGGTT
1 AAAAATGCCCCTTCCTGGTCGGAAGGTCACAATTTTTTTCTTTCCAAAAATGCCCCTTCCTGGTT
* *
44595 GGAAGGTCCCTGTTTTCTTTCATTTCCTAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTTTTCT
66 GGAAGGT--C--TTGT-TTTCATTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACA--TTTCT
*
44660 TTCTTTCC
124 TT-ATTCC
* * * * **
44668 AAAAACGCCCCTTCCTGGTTGGAAGGTC-C--TTGTTTTCATTTCCAAAAATACCCCTTCCAAGT
1 AAAAATGCCCCTTCCTGGTCGGAAGGTCACAATTTTTTTC-TTTCCAAAAATGCCCCTTCCTGGT
* *
44730 TGGAAGGTCTCTGTTAT-A-TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAATTTTCTTTT
65 TGGAAGGTCT-TGTTTTCATTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCAC-A-TTTCTTTA
44793 TTCC
127 TTCC
* *
44797 AAAAATGCCCCTTCCTGGTCGGAAGGTCACAATTTTCTTTCTTTGCAAAAACGCCCCTTCCTGGT
1 AAAAATGCCCCTTCCTGGTCGGAAGGTCACAATTTT-TTTCTTTCCAAAAATGCCCCTTCCTGGT
* * * * *
44862 TGGAAGGTCCTTGTTTTCATTTCCAAAAATGCCACTTCCTGGTTGGAAGGTCTC-TGT-TTTATT
65 TGGAAGGT-CTTGTTTTCATTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACATTTCTTTATT
44925 CC
129 CC
* * * * *
44927 AAAAATGCCCCTTCCCGGTCGGAAGTTCACAGTTTTCTTTCATTCCAAAAATG-CCCTTCCCGGT
1 AAAAATGCCCCTTCCTGGTCGGAAGGTCACAATTTT-TTTCTTTCCAAAAATGCCCCTTCCTGGT
* *
44991 CGGAAGGTGTTGTTTTCA
65 TGGAAGGTCTTGTTTTCA
45009 ATGTTTTATT
Statistics
Matches: 295, Mismatches: 34, Indels: 30
0.82 0.09 0.08
Matches are distributed among these distances:
128 9 0.03
129 48 0.16
130 96 0.33
131 4 0.01
132 38 0.13
133 10 0.03
134 63 0.21
136 27 0.09
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.35
Consensus pattern (130 bp):
AAAAATGCCCCTTCCTGGTCGGAAGGTCACAATTTTTTTCTTTCCAAAAATGCCCCTTCCTGGTT
GGAAGGTCTTGTTTTCATTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACATTTCTTTATTCC
Found at i:45041 original size:48 final size:47
Alignment explanation
Indices: 44978--45212 Score: 335
Period size: 48 Copynumber: 4.9 Consensus size: 47
44968 ATTCCAAAAA
* * *
44978 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTACTGTTT
1 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCATT-CCGTTT
**
45026 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTTTATATTTCATTCCCGTTT
1 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCATT-CCGTTT
45074 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCATTCTCGTTT
1 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCATTC-CGTTT
* * *
45122 TGCCCTTCTCGGTCGGAAGGTATTGTCTTCAATATTTCATTTCCGTTT
1 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCA-TTCCGTTT
* * *
45170 CGCCCTTCCCGGTCAGAAGGTGTTGTCTTCAATATTTCATTCC
1 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCATTCC
45213 TGTCTTCAAT
Statistics
Matches: 170, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
47 5 0.03
48 162 0.95
49 3 0.02
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.43
Consensus pattern (47 bp):
TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCATTCCGTTT
Found at i:45218 original size:20 final size:20
Alignment explanation
Indices: 45193--45232 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
45183 CAGAAGGTGT
45193 TGTCTTCAATATTTCATTCC
1 TGTCTTCAATATTTCATTCC
* *
45213 TGTCTTCAATGTTTTATTCC
1 TGTCTTCAATATTTCATTCC
45233 CGTTTTGCCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.23, G:0.07, T:0.53
Consensus pattern (20 bp):
TGTCTTCAATATTTCATTCC
Found at i:64272 original size:31 final size:31
Alignment explanation
Indices: 64237--64303 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
64227 TTGACTTTAT
64237 GGACTGATTTGAACCAATTATGCAACGTTAA
1 GGACTGATTTGAACCAATTATGCAACGTTAA
* ** * * *
64268 GGACTTATTTGAGTCGATTTTGCAACGTTAG
1 GGACTGATTTGAACCAATTATGCAACGTTAA
64299 GGACT
1 GGACT
64304 TAATTAACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (31 bp):
GGACTGATTTGAACCAATTATGCAACGTTAA
Found at i:67941 original size:29 final size:29
Alignment explanation
Indices: 67899--67959 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
67889 ACCTTTCTTT
67899 TTGTATTTGTTCAAGTGCGGGTTGTGCAC
1 TTGTATTTGTTCAAGTGCGGGTTGTGCAC
* *
67928 TTGTGTTTGTTCAAGTGTGGGTTGTGCAC
1 TTGTATTTGTTCAAGTGCGGGTTGTGCAC
67957 TTG
1 TTG
67960 GGATTGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.11, C:0.11, G:0.33, T:0.44
Consensus pattern (29 bp):
TTGTATTTGTTCAAGTGCGGGTTGTGCAC
Found at i:67977 original size:30 final size:29
Alignment explanation
Indices: 67905--67986 Score: 103
Period size: 29 Copynumber: 2.8 Consensus size: 29
67895 CTTTTTGTAT
* * *
67905 TTGTTCAAGTGCGGGTTGTGCACTTGTGT
1 TTGTTCAAGTGTGGGTTGTGCACTTGGGA
67934 TTGTTCAAGTGTGGGTTGTGCACTTGGGA
1 TTGTTCAAGTGTGGGTTGTGCACTTGGGA
**
67963 TTGTTTTGAGTGTGGGTT-TGCACT
1 TTG-TTCAAGTGTGGGTTGTGCACT
67987 CGTGTCAAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 35 0.74
30 12 0.26
ACGTcount: A:0.11, C:0.11, G:0.35, T:0.43
Consensus pattern (29 bp):
TTGTTCAAGTGTGGGTTGTGCACTTGGGA
Found at i:70733 original size:2 final size:2
Alignment explanation
Indices: 70726--70757 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
70716 TAAATCACTC
*
70726 GT GT GT GT GT GT GT GT GT AT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
70758 ATATATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
GT
Found at i:70810 original size:14 final size:15
Alignment explanation
Indices: 70793--70821 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
70783 TACTACAGTT
70793 TACAA-AGTACAAAA
1 TACAATAGTACAAAA
70807 TACAATAGTACAAAA
1 TACAATAGTACAAAA
70822 CGTGTCTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.62, C:0.14, G:0.07, T:0.17
Consensus pattern (15 bp):
TACAATAGTACAAAA
Found at i:74904 original size:15 final size:17
Alignment explanation
Indices: 74870--74906 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
74860 ACCGAAAACA
74870 ACCC-AACCCAGAATTG
1 ACCCGAACCCAGAATTG
74886 ACCCGAACCCA-AA-TG
1 ACCCGAACCCAGAATTG
74901 ACCCGA
1 ACCCGA
74907 CATTTGAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.40
16 6 0.30
17 6 0.30
ACGTcount: A:0.38, C:0.41, G:0.14, T:0.08
Consensus pattern (17 bp):
ACCCGAACCCAGAATTG
Found at i:75454 original size:42 final size:42
Alignment explanation
Indices: 75405--75485 Score: 162
Period size: 42 Copynumber: 1.9 Consensus size: 42
75395 GTATGGTGAC
75405 GGTGCGATTGACATTGTTTAGTAACTGTATAGATGAGATGAT
1 GGTGCGATTGACATTGTTTAGTAACTGTATAGATGAGATGAT
75447 GGTGCGATTGACATTGTTTAGTAACTGTATAGATGAGAT
1 GGTGCGATTGACATTGTTTAGTAACTGTATAGATGAGAT
75486 TACACTATAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.28, C:0.07, G:0.28, T:0.36
Consensus pattern (42 bp):
GGTGCGATTGACATTGTTTAGTAACTGTATAGATGAGATGAT
Found at i:81986 original size:26 final size:26
Alignment explanation
Indices: 81930--81986 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
81920 TCAAAGCTCC
* * *
81930 TTGAACTCGATCTAAACCATAATTAC
1 TTGAACTCAATCTAAACCATAAATAA
*
81956 TTGAACTCAATCTACACCA-AAATAA
1 TTGAACTCAATCTAAACCATAAATAA
81981 TATGAA
1 T-TGAA
81987 TAATTATTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.28
Consensus pattern (26 bp):
TTGAACTCAATCTAAACCATAAATAA
Found at i:87896 original size:18 final size:19
Alignment explanation
Indices: 87851--87896 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
87841 TGTAAATTGA
87851 TTTTCAAATAGTACCAAAT
1 TTTTCAAATAGTACCAAAT
* * *
87870 CTATC-AATAGTACC-ATT
1 TTTTCAAATAGTACCAAAT
87887 TTTTCAAATA
1 TTTTCAAATA
87897 TATTTCTAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 3
0.72 0.17 0.10
Matches are distributed among these distances:
17 5 0.24
18 13 0.62
19 3 0.14
ACGTcount: A:0.39, C:0.17, G:0.04, T:0.39
Consensus pattern (19 bp):
TTTTCAAATAGTACCAAAT
Found at i:88083 original size:165 final size:166
Alignment explanation
Indices: 87874--88346 Score: 611
Period size: 165 Copynumber: 2.8 Consensus size: 166
87864 CCAAATCTAT
* *
87874 CAATAGTACCATTTTTTCAAATATATTTCTAAATTGACATTATTAAAATTTAT-T-ATTTAAAAA
1 CAATTGTACCATTTTTTCAAATATATTTCTAAATTGCCATTATTAAAATTTATATAATTT--AAA
87937 TTAATTATAAAATTTCAATTTAGATCGAATTATAAGTTTGTAAAATTGATTTTCATTGATGAACA
64 TTAATTATAAAATTTCAATTTAGATCGAATTATAAGTTTGTAAAATTGATTTTCATTGATGAACA
**
88002 TGCAAATTTCTACAAATAAT-GGAAACTTTATGTTTTC
129 TGCAAATTTCTACAAATAATAAAAAACTTTATGTTTTC
* * *
88039 CGATTGTACCTTTTTTTCAAATATATTTCTAAATTGCCATTATTAAAATTTAATATAATTT-TAT
1 CAATTGTACCATTTTTTCAAATATATTTCTAAATTGCCATTATTAAAATTT-ATATAATTTAAAT
* * * *
88103 TATTTA-AAAATTTGAATTTAGATCGAATTATAATTTTGTAAATTTGATTTTCATTGATGAACAT
65 TAATTATAAAATTTCAATTTAGATCGAATTATAAGTTTGTAAAATTGATTTTCATTGATGAACAT
*
88167 GCAAATTTCTACGAATAATAAAAAACTTTATGTTTTC
130 GCAAATTTCTACAAATAATAAAAAACTTTATGTTTTC
*
88204 CAATTGTACCCTTTTTTCAAATATATTTCTAAATTGCCATTATTAAAATTTAGTATAATTTTATT
1 CAATTGTACCATTTTTTCAAATATATTTCTAAATTGCCATTATTAAAATTTA-TATAA-TTTA--
* * * * * *
88269 ATTTAAAAATTATAAAATTTTCAATTTAGACCAAATTATAAGTTTGTCAAA-TCATTTT--TTTA
62 AATT---AATTATAAAA-TTTCAATTTAGATCGAATTATAAGTTTGTAAAATTGATTTTCATTGA
*
88331 TGAACATGAAAATTTC
123 TGAACATGCAAATTTC
88347 CTTTACTACT
Statistics
Matches: 268, Mismatches: 26, Indels: 22
0.85 0.08 0.07
Matches are distributed among these distances:
164 74 0.28
165 123 0.46
166 5 0.02
167 1 0.00
168 4 0.01
169 2 0.01
171 18 0.07
172 4 0.01
173 10 0.04
174 27 0.10
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (166 bp):
CAATTGTACCATTTTTTCAAATATATTTCTAAATTGCCATTATTAAAATTTATATAATTTAAATT
AATTATAAAATTTCAATTTAGATCGAATTATAAGTTTGTAAAATTGATTTTCATTGATGAACATG
CAAATTTCTACAAATAATAAAAAACTTTATGTTTTC
Found at i:88157 original size:164 final size:165
Alignment explanation
Indices: 87874--88279 Score: 622
Period size: 165 Copynumber: 2.5 Consensus size: 165
87864 CCAAATCTAT
* * *
87874 CAATAGTACCATTTTTTCAAATATATTTCTAAATTGACATTATTAAAATTT-AT-T-ATTTAAAA
1 CAATTGTACCATTTTTTCAAATATATTTCTAAATTGCCATTATTAAAATTTAATATAATTT---T
*
87936 ATTAATTATAAAATTTCAATTTAGATCGAATTATAAGTTTGTAAAATTGATTTTCATTGATGAAC
63 ATTATTTA-AAAATTTCAATTTAGATCGAATTATAAGTTTGTAAAATTGATTTTCATTGATGAAC
**
88001 ATGCAAATTTCTACAAATAAT-GGAAACTTTATGTTTTC
127 ATGCAAATTTCTACAAATAATAAAAAACTTTATGTTTTC
* *
88039 CGATTGTACCTTTTTTTCAAATATATTTCTAAATTGCCATTATTAAAATTTAATATAATTTTATT
1 CAATTGTACCATTTTTTCAAATATATTTCTAAATTGCCATTATTAAAATTTAATATAATTTTATT
* * *
88104 ATTTAAAAATTTGAATTTAGATCGAATTATAATTTTGTAAATTTGATTTTCATTGATGAACATGC
66 ATTTAAAAATTTCAATTTAGATCGAATTATAAGTTTGTAAAATTGATTTTCATTGATGAACATGC
*
88169 AAATTTCTACGAATAATAAAAAACTTTATGTTTTC
131 AAATTTCTACAAATAATAAAAAACTTTATGTTTTC
* *
88204 CAATTGTACCCTTTTTTCAAATATATTTCTAAATTGCCATTATTAAAATTTAGTATAATTTTATT
1 CAATTGTACCATTTTTTCAAATATATTTCTAAATTGCCATTATTAAAATTTAATATAATTTTATT
88269 ATTTAAAAATT
66 ATTTAAAAATT
88280 ATAAAATTTT
Statistics
Matches: 222, Mismatches: 15, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
164 73 0.33
165 142 0.64
166 2 0.01
167 1 0.00
168 4 0.02
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.45
Consensus pattern (165 bp):
CAATTGTACCATTTTTTCAAATATATTTCTAAATTGCCATTATTAAAATTTAATATAATTTTATT
ATTTAAAAATTTCAATTTAGATCGAATTATAAGTTTGTAAAATTGATTTTCATTGATGAACATGC
AAATTTCTACAAATAATAAAAAACTTTATGTTTTC
Found at i:88271 original size:24 final size:24
Alignment explanation
Indices: 88242--88289 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
88232 CTAAATTGCC
* *
88242 ATTA-TTAAAATTTAGTATAATTTT
1 ATTATTTAAAAATTA-TAAAATTTT
88266 ATTATTTAAAAATTATAAAATTTT
1 ATTATTTAAAAATTATAAAATTTT
88290 CAATTTAGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
ATTATTTAAAAATTATAAAATTTT
Found at i:88397 original size:20 final size:20
Alignment explanation
Indices: 88360--88398 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
88350 TACTACTATT
88360 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
88380 TTTT-AATTTCAATCTTTTA
1 TTTTGAATTT-AATATTTTA
88399 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:88624 original size:22 final size:21
Alignment explanation
Indices: 88575--88799 Score: 135
Period size: 22 Copynumber: 10.1 Consensus size: 21
88565 TGTGGTTAGT
* * *
88575 AAAATTTAATAAGATGGTTATT
1 AAAATTTCATAGGA-GGTTATC
*
88597 ATAATTTCATGAGGAGGTTATC
1 AAAATTTCAT-AGGAGGTTATC
* * ** *
88619 AAAATTCCATAGTGTGAATACC
1 AAAATTTCATAG-GAGGTTATC
*
88641 AAAATTTCATATGGAAGTTATC
1 AAAATTTCATA-GGAGGTTATC
* *
88663 AAAATTTCATGGGAAGGTCATC
1 AAAATTTCATAGG-AGGTTATC
* *
88685 AAAATTTCATAGTGTGGTTACC
1 AAAATTTCATAG-GAGGTTATC
*
88707 AAAATTTCATAGGATCAGGTTATT
1 AAAATTTCATAGG---AGGTTATC
* *
88731 AAAATTTCTTAGGAAGGTTATT
1 AAAATTTCATAGG-AGGTTATC
* * *
88753 GAAATTTCATATTGTGGTTATC
1 AAAATTTCATA-GGAGGTTATC
* * *
88775 ACAATTTTATAGAAAGGTTATC
1 AAAATTTCATAG-GAGGTTATC
88797 AAA
1 AAA
88800 GAGATTATCA
Statistics
Matches: 153, Mismatches: 40, Indels: 20
0.72 0.19 0.09
Matches are distributed among these distances:
21 5 0.03
22 125 0.82
23 6 0.04
24 17 0.11
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (21 bp):
AAAATTTCATAGGAGGTTATC
Found at i:88670 original size:66 final size:68
Alignment explanation
Indices: 88590--88751 Score: 199
Period size: 66 Copynumber: 2.4 Consensus size: 68
88580 TTAATAAGAT
* *
88590 GGTTATTATAATTTCATGAGG-AGGTTATCAAAATTCCATAGTGTGAATACCAAAATTTCATATG
1 GGTTATCAAAATTTCATGAGGAAGGTTATCAAAATTCCATAGTGTGAATACCAAAATTTCATA-G
88654 GA-A
65 GACA
* * **
88657 -GTTATCAAAATTTCATG-GGAAGGTCATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGG
1 GGTTATCAAAATTTCATGAGGAAGGTTATCAAAATTCCATAGTGTGAATACCAAAATTTCATAGG
88720 ATCA
66 A-CA
* *
88724 GGTTATTAAAATTTC-TTAGGAAGGTTAT
1 GGTTATCAAAATTTCATGAGGAAGGTTAT
88752 TGAAATTTCA
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
65 5 0.06
66 52 0.64
67 2 0.02
68 22 0.27
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (68 bp):
GGTTATCAAAATTTCATGAGGAAGGTTATCAAAATTCCATAGTGTGAATACCAAAATTTCATAGG
ACA
Found at i:88858 original size:22 final size:22
Alignment explanation
Indices: 88804--88950 Score: 124
Period size: 22 Copynumber: 6.7 Consensus size: 22
88794 ATCAAAGAGA
* * * *
88804 TTATCAAAATGTCATAGCGAGA
1 TTATCAAAATTTCATAGTGTGG
88826 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGTGG
* *
88848 TTAACAAAATTTCATAAG-GAGG
1 TTATCAAAATTTCAT-AGTGTGG
* * *
88870 TTA-CTAATATTTCAT-GGGAGG
1 TTATC-AAAATTTCATAGTGTGG
88891 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGTGG
* *
88913 TTATCAAAAGTTT-TTAGTATGG
1 TTATCAAAA-TTTCATAGTGTGG
88935 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
88951 TGAAGGTTAT
Statistics
Matches: 103, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
20 1 0.01
21 22 0.21
22 73 0.71
23 7 0.07
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGG
Found at i:88863 original size:44 final size:42
Alignment explanation
Indices: 88804--88964 Score: 146
Period size: 44 Copynumber: 3.7 Consensus size: 42
88794 ATCAAAGAGA
* *
88804 TTATCAAAATGTCATAGCGAGATTATAAGAATTTCATAGTGTGG
1 TTATCAAAATTTCATAG-GAGGTTATAA-AATTTCATAGTGTGG
* * * *
88848 TTAACAAAATTTCATAAGGAGGTTACTAATATTTCAT-GGGAGG
1 TTATCAAAATTTCAT-AGGAGGTTA-TAAAATTTCATAGTGTGG
* * *
88891 TTATCAAAATTTCATAGTGTGGTTATCAAAAGTTT-TTAGTATGG
1 TTATCAAAATTTCATAG-GAGGTTAT-AAAA-TTTCATAGTGTGG
*
88935 TTATCAAAATTTCATATGAAGGTTATAAAA
1 TTATCAAAATTTCATA-GGAGGTTATAAAA
88965 GTCTCATTTT
Statistics
Matches: 95, Mismatches: 15, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
42 3 0.03
43 32 0.34
44 54 0.57
45 6 0.06
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (42 bp):
TTATCAAAATTTCATAGGAGGTTATAAAATTTCATAGTGTGG
Found at i:88947 original size:65 final size:65
Alignment explanation
Indices: 88804--88950 Score: 158
Period size: 65 Copynumber: 2.2 Consensus size: 65
88794 ATCAAAGAGA
*
88804 TTATCAAAATGTCATAGCGAGATTATAAGAATTTCATAGTGTGGTTAACAAAATTTCATAAGGAG
1 TTATCAAAATTTCATAGCGAGATTATAAGAATTTCATAGTGTGGTTAACAAAATTT-ATAAGGAG
88869 G
65 G
* * * * * *
88870 TTA-CTAATATTTCAT-GGGAGGTTATCAA-AATTTCATAGTGTGGTTATCAAAAGTTT-TTAGT
1 TTATC-AAAATTTCATAGCGAGATTAT-AAGAATTTCATAGTGTGGTTAACAAAA-TTTATAAGG
88931 ATGG
63 A-GG
88935 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
88951 TGAAGGTTAT
Statistics
Matches: 67, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
64 4 0.06
65 46 0.69
66 17 0.25
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (65 bp):
TTATCAAAATTTCATAGCGAGATTATAAGAATTTCATAGTGTGGTTAACAAAATTTATAAGGAGG
Found at i:89060 original size:25 final size:21
Alignment explanation
Indices: 89004--89057 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
88994 TAATAGAAAG
*
89004 TTATCAAATCTCATAGAGTGA
1 TTATCAAATTTCATAGAGTGA
89025 TTATCGAAATTTCATAGAGATCGGA
1 TTATC-AAATTTCATAGAG-T--GA
89050 TTATCAAA
1 TTATCAAA
89058 ATTAGGGATG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 5 0.18
22 12 0.43
23 1 0.04
24 3 0.11
25 7 0.25
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (21 bp):
TTATCAAATTTCATAGAGTGA
Found at i:89417 original size:18 final size:18
Alignment explanation
Indices: 89373--89411 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
89363 TTTTTAAGTA
*
89373 AAAATATAATATATAAAT
1 AAAATATTATATATAAAT
*
89391 AAAATATTATATTTAAAT
1 AAAATATTATATATAAAT
89409 AAA
1 AAA
89412 TAATTAGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATATTATATATAAAT
Found at i:89616 original size:22 final size:21
Alignment explanation
Indices: 89588--89667 Score: 79
Period size: 22 Copynumber: 3.7 Consensus size: 21
89578 TGCATCCCTA
*
89588 ATCAAAATTTCATAGTGTTGTT
1 ATCAAAATTTCATAATG-TGTT
* *
89610 ATCAAAATTTCATAAAGAGGTT
1 ATCAAAATTTCATAATG-TGTT
* *
89632 ATCAAATTTTCAAAATGTGATT
1 ATCAAAATTTCATAATGTG-TT
*
89654 ACCAAAATTTCATA
1 ATCAAAATTTCATA
89668 GTGGTATTTC
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
21 1 0.02
22 45 0.98
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.38
Consensus pattern (21 bp):
ATCAAAATTTCATAATGTGTT
Found at i:89842 original size:22 final size:21
Alignment explanation
Indices: 89817--90068 Score: 106
Period size: 22 Copynumber: 11.5 Consensus size: 21
89807 AGTTTACTTT
89817 TCAAAATTTCATAAGAGGGTTA
1 TCAAAATTTCAT-AGAGGGTTA
***
89839 TCAAAATTTCATAGTATATATATAGA
1 TCAAAATTTCATAG-A-GGGT-T--A
89865 TCAAAATTTCATAG-GGAGATTA
1 TCAAAATTTCATAGAGG-G-TTA
*
89887 ACAAAATTTCATA-ATGAGGTTA
1 TCAAAATTTCATAGA-G-GGTTA
** *
89909 TCAAAAAATCATAGGGAGGTTA
1 TCAAAATTTCATAGAG-GGTTA
*
89931 TCAAAATTT-GT--A--GTTA
1 TCAAAATTTCATAGAGGGTTA
*
89947 TCAAGATTTCATA-AGGTCGTTA
1 TCAAAATTTCATAGAGG--GTTA
* *
89969 TCAAAATTTTATAGGGAGGTTTA
1 TCAAAATTTCATA--GAGGGTTA
* * *
89992 TCAAAATTTTATGGGAAGGTTTA
1 TCAAAATTTCAT-AG-AGGGTTA
*
90015 TCAAAATTTCATAGCGAGGTTA
1 TCAAAATTTCATAGAG-GGTTA
* * * *
90037 TCACAATTTTATAGTGTGATTA
1 TCAAAATTTCATAGAG-GGTTA
90059 TCAAAATTTC
1 TCAAAATTTC
90069 TGAGTGTAAT
Statistics
Matches: 175, Mismatches: 32, Indels: 46
0.69 0.13 0.18
Matches are distributed among these distances:
16 12 0.07
17 1 0.01
18 1 0.01
21 4 0.02
22 99 0.57
23 36 0.21
24 3 0.02
25 4 0.02
26 15 0.09
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (21 bp):
TCAAAATTTCATAGAGGGTTA
Found at i:89994 original size:23 final size:23
Alignment explanation
Indices: 89966--90067 Score: 120
Period size: 23 Copynumber: 4.5 Consensus size: 23
89956 CATAAGGTCG
89966 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
89989 TTATCAAAATTTTAT-GGGAAGGT
1 TTATCAAAATTTTATAGGG-AGGT
* *
90012 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAGGGAGGT
* * * *
90034 TTATCACAATTTTATAGTG-TGA
1 TTATCAAAATTTTATAGGGAGGT
90056 TTATCAAAATTT
1 TTATCAAAATTT
90068 CTGAGTGTAA
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.01
22 30 0.43
23 36 0.52
24 2 0.03
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:90145 original size:22 final size:22
Alignment explanation
Indices: 90089--90147 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
90079 TACTAACAAT
* *
90089 TCATATGGAGGTTTTTAAATTT
1 TCATATGGAGGTTATTAAATTA
** *
90111 TCATAACGTGGTTATT-AATATA
1 TCATATGGAGGTTATTAAAT-TA
90133 TCATATGGAGGTTAT
1 TCATATGGAGGTTAT
90148 CAACATCTCA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 3 0.11
22 25 0.89
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.44
Consensus pattern (22 bp):
TCATATGGAGGTTATTAAATTA
Found at i:94275 original size:19 final size:19
Alignment explanation
Indices: 94251--94287 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
94241 CTATTTAGCA
94251 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
*
94270 ACTGTACAGATTAGATTA
1 ACTGTACAGATGAGATTA
94288 GGTACTATAC
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:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:94763 original size:19 final size:20
Alignment explanation
Indices: 94733--94796 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
94723 TTGACACTGT
94733 TTAGCAACTGTACAGATGAGA
1 TTAGC-ACTGTACAGATGAGA
*
94754 TTA-CACTGTACAGATTAGA
1 TTAGCACTGTACAGATGAGA
* *
94773 TTAGGTACTGTACATATGAGA
1 TTA-GCACTGTACAGATGAGA
94794 TTA
1 TTA
94797 TTAGAGCAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 17 0.46
20 1 0.03
21 19 0.51
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31
Consensus pattern (20 bp):
TTAGCACTGTACAGATGAGA
Found at i:94784 original size:21 final size:19
Alignment explanation
Indices: 94739--94796 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
94729 CTGTTTAGCA
94739 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
94758 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--C
*
94779 ACTGTACATATGAGATTA
1 ACTGTACAGATGAGATTA
94797 TTAGAGCAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:94810 original size:488 final size:488
Alignment explanation
Indices: 93894--94849 Score: 1840
Period size: 488 Copynumber: 2.0 Consensus size: 488
93884 CTCCATCCAG
*
93894 AATTGTATGAATTTGAGTATGGTTCAAGCTTCCTTTAAAACACTCCTTGCATTCCCACAACATTG
1 AATTGTAGGAATTTGAGTATGGTTCAAGCTTCCTTTAAAACACTCCTTGCATTCCCACAACATTG
93959 ACTCCTTGCGTGTTGTCTTCCAAAGTAGGGCACTTATCAGTGTAGTTTCCTTGTGAACAAATACC
66 ACTCCTTGCGTGTTGTCTTCCAAAGTAGGGCACTTATCAGTGTAGTTTCCTTGTGAACAAATACC
94024 ACAAACCTTAGGCACACTAGAAAAATTCGAATTGAACAAATCAGTGAGCATAGCGATTTGCTGAT
131 ACAAACCTTAGGCACACTAGAAAAATTCGAATTGAACAAATCAGTGAGCATAGCGATTTGCTGAT
94089 TCGTTTCTTGAAGTTGTTGCTCCAATGAGGTGGAATGTTTAGAGACTTCATTAATTCTTCTTGTA
196 TCGTTTCTTGAAGTTGTTGCTCCAATGAGGTGGAATGTTTAGAGACTTCATTAATTCTTCTTGTA
*
94154 TTGCCTTCTCTTGGTGCATAGTCTTCTCGAGATCCAAACTGTTGATGTTGCGTTTAGTAGAGCGG
261 TTGCCTTCTCTTGGTGCATAGTCTTCTCGAGATCCAAACTGTTGATGCTGCGTTTAGTAGAGCGG
94219 TGCGATAACGGTGCGATTGACACTATTTAGCAACTGTACAGATGAGATTACACTGTACAGATTAG
326 TGCGATAACGGTGCGATTGACACTATTTAGCAACTGTACAGATGAGATTACACTGTACAGATTAG
*
94284 ATTAGGTACTATACATATGAGATTATTAGAGCAGCGATTGAAACGAAGTTTACACTTAAGTTTCG
391 ATTAGGTACTATACATATGAGATTATTAGAGCAGCGATTGAAACGAAGTTTACACTTAAGCTTCG
*
94349 TTTGGGCCCAAAATGAATTTGAGTTTACACTCA
456 ATTGGGCCCAAAATGAATTTGAGTTTACACTCA
*
94382 AATTGTAGGAATTTGAGTATGGTTCAAGCTTCCTTTAAAATACTCCTTGCATTCCCACAACATTG
1 AATTGTAGGAATTTGAGTATGGTTCAAGCTTCCTTTAAAACACTCCTTGCATTCCCACAACATTG
94447 ACTCCTTGCGTGTTGTCTTCCAAAGTAGGGCACTTATCAGTGTAGTTTCCTTGTGAACAAATACC
66 ACTCCTTGCGTGTTGTCTTCCAAAGTAGGGCACTTATCAGTGTAGTTTCCTTGTGAACAAATACC
94512 ACAAACCTTAGGCACACTAGAAAAATTCGAATTGAACAAATCAGTGAGCATAGCGATTTGCTGAT
131 ACAAACCTTAGGCACACTAGAAAAATTCGAATTGAACAAATCAGTGAGCATAGCGATTTGCTGAT
94577 TCGTTTCTTGAAGTTGTTGCTCCAATGAGGTGGAATGTTTAGAGACTTCATTAATTCTTCTTGTA
196 TCGTTTCTTGAAGTTGTTGCTCCAATGAGGTGGAATGTTTAGAGACTTCATTAATTCTTCTTGTA
94642 TTGCCTTCTCTTGGTGCATAGTCTTCTCGAGATCCAAACTGTTGATGCTGCGTTTAGTAGAGCGG
261 TTGCCTTCTCTTGGTGCATAGTCTTCTCGAGATCCAAACTGTTGATGCTGCGTTTAGTAGAGCGG
*
94707 TGCGATAACGGTGCGATTGACACTGTTTAGCAACTGTACAGATGAGATTACACTGTACAGATTAG
326 TGCGATAACGGTGCGATTGACACTATTTAGCAACTGTACAGATGAGATTACACTGTACAGATTAG
* *
94772 ATTAGGTACTGTACATATGAGATTATTAGAGCAGCGATTGAAACGGAGTTTACACTTAAGCTTCG
391 ATTAGGTACTATACATATGAGATTATTAGAGCAGCGATTGAAACGAAGTTTACACTTAAGCTTCG
94837 ATTGGGCCCAAAA
456 ATTGGGCCCAAAA
94850 CGGTGGTGAA
Statistics
Matches: 460, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
488 460 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (488 bp):
AATTGTAGGAATTTGAGTATGGTTCAAGCTTCCTTTAAAACACTCCTTGCATTCCCACAACATTG
ACTCCTTGCGTGTTGTCTTCCAAAGTAGGGCACTTATCAGTGTAGTTTCCTTGTGAACAAATACC
ACAAACCTTAGGCACACTAGAAAAATTCGAATTGAACAAATCAGTGAGCATAGCGATTTGCTGAT
TCGTTTCTTGAAGTTGTTGCTCCAATGAGGTGGAATGTTTAGAGACTTCATTAATTCTTCTTGTA
TTGCCTTCTCTTGGTGCATAGTCTTCTCGAGATCCAAACTGTTGATGCTGCGTTTAGTAGAGCGG
TGCGATAACGGTGCGATTGACACTATTTAGCAACTGTACAGATGAGATTACACTGTACAGATTAG
ATTAGGTACTATACATATGAGATTATTAGAGCAGCGATTGAAACGAAGTTTACACTTAAGCTTCG
ATTGGGCCCAAAATGAATTTGAGTTTACACTCA
Found at i:95783 original size:7 final size:7
Alignment explanation
Indices: 95773--95798 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
95763 GAAAAACTAA
95773 AAAAAAT
1 AAAAAAT
95780 AAAAAAT
1 AAAAAAT
95787 AAAAAAT
1 AAAAAAT
95794 AAAAA
1 AAAAA
95799 GTAGAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:95783 original size:16 final size:16
Alignment explanation
Indices: 95759--95792 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
95749 GCTCTTAATG
*
95759 AAAAGAAAAACTAAAA
1 AAAAGAAAAAATAAAA
*
95775 AAAATAAAAAATAAAA
1 AAAAGAAAAAATAAAA
95791 AA
1 AA
95793 TAAAAAGTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.85, C:0.03, G:0.03, T:0.09
Consensus pattern (16 bp):
AAAAGAAAAAATAAAA
Found at i:96067 original size:26 final size:28
Alignment explanation
Indices: 96037--96088 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
96027 AACACCAATT
*
96037 ATAAAGAAAAGC-AATT-AATCTAAAAA
1 ATAAAGAAAACCAAATTAAATCTAAAAA
*
96063 ATAAAGCAAACCAAATTAAATCTAAA
1 ATAAAGAAAACCAAATTAAATCTAAA
96089 GCTATGACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 10 0.45
27 4 0.18
28 8 0.36
ACGTcount: A:0.63, C:0.12, G:0.06, T:0.19
Consensus pattern (28 bp):
ATAAAGAAAACCAAATTAAATCTAAAAA
Found at i:103526 original size:22 final size:21
Alignment explanation
Indices: 103494--103618 Score: 108
Period size: 22 Copynumber: 5.8 Consensus size: 21
103484 TTGAATTTTT
*
103494 TATGAAATTTTGTTAACTATCC
1 TATGAAATTTTGATAACTA-CC
* *
103516 TATTAAATTTTGATAACCACCC
1 TATGAAATTTTGATAACTA-CC
*
103538 TATGAAATTTTGATAATTACC
1 TATGAAATTTTGATAACTACC
* *
103559 TATGAAATTGTGATAAACAACAC
1 TATGAAATTTTGAT-AACTAC-C
* *
103582 -ATGAAACTTTGATAACCTAAC
1 TATGAAATTTTGATAA-CTACC
* *
103603 TACGAAATTTTAATAA
1 TATGAAATTTTGATAA
103619 ACCTTCATAT
Statistics
Matches: 82, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
21 18 0.22
22 63 0.77
23 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (21 bp):
TATGAAATTTTGATAACTACC
Found at i:103573 original size:43 final size:45
Alignment explanation
Indices: 103494--103597 Score: 124
Period size: 43 Copynumber: 2.4 Consensus size: 45
103484 TTGAATTTTT
* * * * *
103494 TATGAAATTTTGTTAACTATCCTATTAAATTTTGAT-AACCACCC
1 TATGAAATTTTGATAACTATCCTATGAAATTGTGATAAACAACAC
*
103538 TATGAAATTTTGATAATTA-CCTATGAAATTGTGATAAACAACAC
1 TATGAAATTTTGATAACTATCCTATGAAATTGTGATAAACAACAC
*
103582 -ATGAAACTTTGATAAC
1 TATGAAATTTTGATAAC
103598 CTAACTACGA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
43 28 0.55
44 23 0.45
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (45 bp):
TATGAAATTTTGATAACTATCCTATGAAATTGTGATAAACAACAC
Found at i:106293 original size:22 final size:22
Alignment explanation
Indices: 106254--106316 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 22
106244 ATAACAATAC
* ** *
106254 TATGGAATTTTGAGAACCTTTT
1 TATGAAATTTTGTTAACCTTCT
* * *
106276 TATTAATTTTTTTTAACCTTCT
1 TATGAAATTTTGTTAACCTTCT
106298 TATGAAATTTTGTTAACCT
1 TATGAAATTTTGTTAACCT
106317 CCCTAAGGAA
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.27, C:0.11, G:0.10, T:0.52
Consensus pattern (22 bp):
TATGAAATTTTGTTAACCTTCT
Found at i:106350 original size:22 final size:21
Alignment explanation
Indices: 106298--106370 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 21
106288 TTAACCTTCT
* *
106298 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAA-CTCAC
* *
106320 TAAGGAATTTTGA-AGATCTCAC
1 TATGAAATTTTGATA-A-CTCAC
*
106342 TATGAAATTTTGATAACTTAC
1 TATGAAATTTTGATAACTCAC
106363 TATGAAAT
1 TATGAAAT
106371 AACCTCCATA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
21 13 0.32
22 27 0.66
23 1 0.02
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (21 bp):
TATGAAATTTTGATAACTCAC
Found at i:106483 original size:22 final size:22
Alignment explanation
Indices: 106424--106483 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
106414 AAAACCTCCA
*
106424 TATG-AATTGTTAGTAATCACAC
1 TATGAAATTG-TAATAATCACAC
* * *
106446 TCTGAAATTTTGATAATCACAC
1 TATGAAATTGTAATAATCACAC
106468 TATGAAATTGTAATAA
1 TATGAAATTGTAATAA
106484 CCTCGTTATG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
22 26 0.87
23 4 0.13
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (22 bp):
TATGAAATTGTAATAATCACAC
Found at i:106493 original size:22 final size:22
Alignment explanation
Indices: 106468--106573 Score: 108
Period size: 23 Copynumber: 4.7 Consensus size: 22
106458 ATAATCACAC
* *
106468 TATGAAATTGTAAT-AACCTCGT
1 TATGAAATTTTGATAAACCTC-T
*
106490 TATGAAATTTTGATAAACCATCC
1 TATGAAATTTTGATAAACC-TCT
*
106513 TATAAAATTTTGATAAACCTCCT
1 TATGAAATTTTGATAAACCT-CT
*
106536 TATAAAATTTTGAT-AACCTCAT
1 TATGAAATTTTGATAAACCTC-T
*
106558 TATGAAATCTTGATAA
1 TATGAAATTTTGATAA
106574 CTAAATTTTG
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
21 1 0.01
22 31 0.43
23 38 0.53
24 2 0.03
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAAACCTCT
Found at i:106520 original size:23 final size:23
Alignment explanation
Indices: 106482--106573 Score: 116
Period size: 23 Copynumber: 4.0 Consensus size: 23
106472 AAATTGTAAT
* *
106482 AACCTCGTTATGAAATTTTGATA
1 AACCTCCTTATAAAATTTTGATA
106505 AACCATCC-TATAAAATTTTGATA
1 AACC-TCCTTATAAAATTTTGATA
106528 AACCTCCTTATAAAATTTTGAT-
1 AACCTCCTTATAAAATTTTGATA
* * *
106550 AACCTCATTATGAAATCTTGATA
1 AACCTCCTTATAAAATTTTGATA
106573 A
1 A
106574 CTAAATTTTG
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
22 22 0.36
23 37 0.61
24 2 0.03
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (23 bp):
AACCTCCTTATAAAATTTTGATA
Found at i:106574 original size:22 final size:22
Alignment explanation
Indices: 106448--106574 Score: 121
Period size: 22 Copynumber: 5.7 Consensus size: 22
106438 AATCACACTC
* * *
106448 TGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAACCTCATTA
* * *
106470 TGAAATTGTAATAACCTCGTTA
1 TGAAATTTTGATAACCTCATTA
*
106492 TGAAATTTTGATAAACCATC-CTA
1 TGAAATTTTGAT-AACC-TCATTA
* *
106515 TAAAATTTTGATAAACCTCCTTA
1 TGAAATTTTGAT-AACCTCATTA
*
106538 TAAAATTTTGATAACCTCATTA
1 TGAAATTTTGATAACCTCATTA
*
106560 TGAAATCTTGATAAC
1 TGAAATTTTGATAAC
106575 TAAATTTTGA
Statistics
Matches: 88, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
22 50 0.57
23 36 0.41
24 2 0.02
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCATTA
Found at i:106605 original size:22 final size:21
Alignment explanation
Indices: 106577--106651 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 21
106567 TTGATAACTA
106577 AATTTTGATAATCTCCCTATG
1 AATTTTGATAATCTCCCTATG
* * **
106598 ATTTTTTGATAACCTCATTATGG
1 A-ATTTTGATAATCTCCCTAT-G
*
106621 AATTTTGTTAATCTCCCTATG
1 AATTTTGATAATCTCCCTATG
106642 AAATTTTGAT
1 -AATTTTGAT
106652 CTACATACTA
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
21 2 0.05
22 37 0.90
23 2 0.05
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.47
Consensus pattern (21 bp):
AATTTTGATAATCTCCCTATG
Found at i:106669 original size:44 final size:44
Alignment explanation
Indices: 106576--106693 Score: 127
Period size: 44 Copynumber: 2.7 Consensus size: 44
106566 CTTGATAACT
** * *
106576 AAATTTTGATAATCTCCCTATGATTTTTTGATAACCTCATTATG
1 AAATTTTGATAATCTCCCTATGAAATTTTGATAACATCACTATG
* * *
106620 GAATTTTGTTAATCTCCCTATGAAATTTTGATCTACAT-ACTATG
1 AAATTTTGATAATCTCCCTATGAAATTTTGAT-AACATCACTATG
106664 AAATTTTGAT-ATCCTCCC--TGAAATTTTGAT
1 AAATTTTGATAAT-CTCCCTATGAAATTTTGAT
106694 TACTCCATGA
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
42 12 0.19
43 2 0.03
44 46 0.73
45 3 0.05
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (44 bp):
AAATTTTGATAATCTCCCTATGAAATTTTGATAACATCACTATG
Found at i:106825 original size:22 final size:22
Alignment explanation
Indices: 106776--106964 Score: 113
Period size: 22 Copynumber: 8.7 Consensus size: 22
106766 GAAATACCAC
* * *
106776 TATGAAATTTTGGTAATCACGTT
1 TATGAAATTTTGATAACCTC-TT
*
106799 T-TGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAACCTCTT
*
106820 TATGAAACTTTGATAACCTC--
1 TATGAAATTTTGATAACCTCTT
* * * * *
106840 TATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAACCTCTT
*** *
106862 TATGAAATTTTGATAATAACAT
1 TATGAAATTTTGATAACCTCTT
* *
106884 TATGTAATTTTGATAACCTCGCT
1 TATGAAATTTTGATAACCTC-TT
** **
106907 T-TGAAATTTTGATAACAACAC
1 TATGAAATTTTGATAACCTCTT
106928 TATGAAATTTTGATAA--TCTT
1 TATGAAATTTTGATAACCTCTT
106948 CCTAT-AAATTTTGATAA
1 --TATGAAATTTTGATAA
106965 TTCCATCTCT
Statistics
Matches: 128, Mismatches: 31, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
20 16 0.12
21 16 0.12
22 93 0.73
23 3 0.02
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCTT
Found at i:106895 original size:44 final size:44
Alignment explanation
Indices: 106800--106964 Score: 140
Period size: 44 Copynumber: 3.8 Consensus size: 44
106790 AATCACGTTT
* * ** * *
106800 TGAAAATTTGATAACCTCTTTATGAAACTTTGATAAC--CTCTA
1 TGAAATTTTGATAACCCCGCTATGAAATTTTGATAACAACACTA
* * * * * *
106842 TAAAATTTTGTTGACCCCTCTATGAAATTTTGATAATAACATTA
1 TGAAATTTTGATAACCCCGCTATGAAATTTTGATAACAACACTA
* * *
106886 TGTAATTTTGATAACCTCGCTTTGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCCCGCTATGAAATTTTGATAACAACACTA
**
106930 TGAAATTTTGATAATCTTC-CTAT-AAATTTTGATAA
1 TGAAATTTTGATAA-CCCCGCTATGAAATTTTGATAA
106965 TTCCATCTCT
Statistics
Matches: 98, Mismatches: 22, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
42 29 0.30
43 12 0.12
44 54 0.55
45 3 0.03
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.41
Consensus pattern (44 bp):
TGAAATTTTGATAACCCCGCTATGAAATTTTGATAACAACACTA
Found at i:106958 original size:21 final size:23
Alignment explanation
Indices: 106861--107010 Score: 107
Period size: 22 Copynumber: 6.7 Consensus size: 23
106851 GTTGACCCCT
106861 CTATGAAATTTTGATAAT-AACA
1 CTATGAAATTTTGATAATCAACA
* * ** *
106883 TTATGTAATTTTGATAA-CCTCG
1 CTATGAAATTTTGATAATCAACA
*
106905 CTTTGAAATTTTGATAA-CAACA
1 CTATGAAATTTTGATAATCAACA
**
106927 CTATGAAATTTTGATAATCTTC-
1 CTATGAAATTTTGATAATCAACA
* *
106949 CTAT-AAATTTTGATAATTCCATCT
1 CTATGAAATTTTGATAA-T-CAACA
* * *
106973 CTATGAAATATCGATAATC-ACT
1 CTATGAAATTTTGATAATCAACA
*
106995 CTATGAGA-TTTGATAA
1 CTATGAAATTTTGATAA
107011 CTTTCTATCA
Statistics
Matches: 101, Mismatches: 21, Indels: 13
0.75 0.16 0.10
Matches are distributed among these distances:
21 18 0.18
22 62 0.61
23 6 0.06
24 5 0.05
25 10 0.10
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (23 bp):
CTATGAAATTTTGATAATCAACA
Found at i:107079 original size:22 final size:21
Alignment explanation
Indices: 107050--107211 Score: 82
Period size: 22 Copynumber: 7.4 Consensus size: 21
107040 AAATTGAGAC
107050 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCATATGAAA
* **
107071 TTTTGATAACC-AAGCTAAAAAA
1 TTTTGATAACCTCA--TATGAAA
*
107093 TTTTGATAACCACAATATGAAA
1 TTTTGATAACCTC-ATATGAAA
** *
107115 TTTTGATAACCTCCCCATGATA
1 TTTTGATAACCT-CATATGAAA
* *
107137 TATT-AGTAACCTCCTTATGAAA
1 TTTTGA-TAACCT-CATATGAAA
*
107159 TTTTG-TCAACCACACTATGAAA
1 TTTTGAT-AACCTCA-TATGAAA
**
107181 TTCTT-ATAACCTCACTATGCCA
1 TT-TTGATAACCTCA-TATGAAA
107203 TTTTGATAA
1 TTTTGATAA
107212 TCTCTTTGAT
Statistics
Matches: 108, Mismatches: 20, Indels: 25
0.71 0.13 0.16
Matches are distributed among these distances:
20 1 0.01
21 9 0.08
22 93 0.86
23 4 0.04
24 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.36
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:107314 original size:46 final size:43
Alignment explanation
Indices: 107251--107359 Score: 128
Period size: 46 Copynumber: 2.4 Consensus size: 43
107241 GATAACCACA
** *
107251 CTATGAAATTTCAATAACCTTCCTAAGAAATTTTAATAACCTGATC
1 CTATGAAATTTTGATAACCTTCCCAAGAAATTTTAATAA-CT--TC
* *
107297 CTATGAAATTTTGATAACCTTCCCATGAAATTTTGATAACTTC
1 CTATGAAATTTTGATAACCTTCCCAAGAAATTTTAATAACTTC
*
107340 CATATGAAATTTTGGTAACC
1 C-TATGAAATTTTGATAACC
107360 ACACTATGGA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
43 3 0.05
44 17 0.30
45 2 0.04
46 34 0.61
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (43 bp):
CTATGAAATTTTGATAACCTTCCCAAGAAATTTTAATAACTTC
Found at i:107426 original size:22 final size:22
Alignment explanation
Indices: 107216--107426 Score: 180
Period size: 22 Copynumber: 9.5 Consensus size: 22
107206 TGATAATCTC
*
107216 TTTGATAACCTAT-CTATAAAAT
1 TTTGATAACC-ATCCTATGAAAT
*
107238 TATGATAACCA-CACTATGAAAT
1 TTTGATAACCATC-CTATGAAAT
** * *
107260 TTCAATAACCTTCCTAAGAAAT
1 TTTGATAACCATCCTATGAAAT
*
107282 TTTAATAACCTGATCCTATGAAAT
1 TTTGATAACC--ATCCTATGAAAT
* *
107306 TTTGATAACCTTCCCATGAAAT
1 TTTGATAACCATCCTATGAAAT
*
107328 TTTGATAA-CTTCCATATGAAAT
1 TTTGATAACCATCC-TATGAAAT
* *
107350 TTTGGTAACCA-CACTATGGAAT
1 TTTGATAACCATC-CTATGAAAT
107372 TTTGATAACC-TCCTCATGAAAT
1 TTTGATAACCATCCT-ATGAAAT
* * *
107394 TATAATAACCATCTTATGAAAT
1 TTTGATAACCATCCTATGAAAT
*
107416 CTTGATAACCA
1 TTTGATAACCA
107427 CACTAAGACA
Statistics
Matches: 153, Mismatches: 25, Indels: 22
0.76 0.12 0.11
Matches are distributed among these distances:
21 8 0.05
22 120 0.78
23 6 0.04
24 19 0.12
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (22 bp):
TTTGATAACCATCCTATGAAAT
Found at i:108828 original size:21 final size:22
Alignment explanation
Indices: 108768--108848 Score: 103
Period size: 22 Copynumber: 3.8 Consensus size: 22
108758 TGAATATTTT
*
108768 TATGAAATTTTGATAACTATCC
1 TATGAAATTTTGATAATTATCC
* *
108790 TATTAAATTTTGATAATTATGC
1 TATGAAATTTTGATAATTATCC
108812 TATGAAATTTT-ATAATTA-CC
1 TATGAAATTTTGATAATTATCC
* *
108832 TATGAGATTTTGTTAAT
1 TATGAAATTTTGATAAT
108849 CTCCCTATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.22
21 11 0.22
22 29 0.57
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.47
Consensus pattern (22 bp):
TATGAAATTTTGATAATTATCC
Found at i:108856 original size:22 final size:22
Alignment explanation
Indices: 108830--108878 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
108820 TTTATAATTA
108830 CCTATGAGATTTTGTTAATCTC
1 CCTATGAGATTTTGTTAATCTC
*
108852 CCTATTAGATTTTGTTAATCTC
1 CCTATGAGATTTTGTTAATCTC
108874 CCTAT
1 CCTAT
108879 AATTTTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.47
Consensus pattern (22 bp):
CCTATGAGATTTTGTTAATCTC
Found at i:109295 original size:2 final size:2
Alignment explanation
Indices: 109290--109330 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
109280 TAAGGTATAT
* *
109290 AG AG AG AG AG AG AG AG AG AG AG AG TG AG AG AG CG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
109331 ACTACTCCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.02, G:0.49, T:0.02
Consensus pattern (2 bp):
AG
Found at i:110086 original size:45 final size:45
Alignment explanation
Indices: 110016--110106 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
110006 GGAAATCTAA
* *
110016 TCCGGTTTAGCTCTTATAGTGTGATTATACGTTTAAAAATTCAAC
1 TCCGCTTTAGCTCTTATAGTATGATTATACGTTTAAAAATTCAAC
*
110061 TCCGCTTTAGTTCTTATAGTATGATTATACGTTTAAAAATTCAAC
1 TCCGCTTTAGCTCTTATAGTATGATTATACGTTTAAAAATTCAAC
110106 T
1 T
110107 TCTTTGAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (45 bp):
TCCGCTTTAGCTCTTATAGTATGATTATACGTTTAAAAATTCAAC
Found at i:118103 original size:60 final size:60
Alignment explanation
Indices: 118011--118128 Score: 184
Period size: 60 Copynumber: 2.0 Consensus size: 60
118001 AGGGACCCAT
* * *
118011 ATATGACCCAAAATTTTGTATAGGGACTTGTTTGCACAATGCCTT-ATAGTACAGGGACTC
1 ATATCACCCAAAATTTTGTATAGAGACTTGTTTGCACAATG-CTTAACAGTACAGGGACTC
*
118071 ATATCACCCAAAATTTTGTATAGAGATTTGTTTGCACAATGCTTAACAGTACAGGGAC
1 ATATCACCCAAAATTTTGTATAGAGACTTGTTTGCACAATGCTTAACAGTACAGGGAC
118129 CTATGGAGCA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
59 3 0.06
60 50 0.94
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (60 bp):
ATATCACCCAAAATTTTGTATAGAGACTTGTTTGCACAATGCTTAACAGTACAGGGACTC
Found at i:118990 original size:31 final size:31
Alignment explanation
Indices: 118920--119039 Score: 132
Period size: 31 Copynumber: 3.9 Consensus size: 31
118910 CGTGGCATAC
** * *
118920 CACATGTCACTTTTTGAAACACATGGCATGC
1 CACATGTCACTTTTTGGTACACATGGCGTGA
** *
118951 CATGTGTCACTTTTTGGCACACATGGCGTGA
1 CACATGTCACTTTTTGGTACACATGGCGTGA
* * *
118982 TACATGTCACTTTTTGGTACACGTGGCGTGG
1 CACATGTCACTTTTTGGTACACATGGCGTGA
* *
119013 CACATGTCGCTTTTTGGTACACGTGGC
1 CACATGTCACTTTTTGGTACACATGGC
119040 ATGCCATGTC
Statistics
Matches: 75, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.33
Consensus pattern (31 bp):
CACATGTCACTTTTTGGTACACATGGCGTGA
Found at i:119026 original size:62 final size:62
Alignment explanation
Indices: 118921--119039 Score: 148
Period size: 62 Copynumber: 1.9 Consensus size: 62
118911 GTGGCATACC
**
118921 ACATGTCACTTTTTGAAACACATGGCATGCCATGTGTCACTTTTTGGCACACATGGCGTGAT
1 ACATGTCACTTTTTGAAACACATGGCATGCCACATGTCACTTTTTGGCACACATGGCGTGAT
** * * * * * *
118983 ACATGTCACTTTTTGGTACACGTGGCGTGGCACATGTCGCTTTTTGGTACACGTGGC
1 ACATGTCACTTTTTGAAACACATGGCATGCCACATGTCACTTTTTGGCACACATGGC
119040 ATGCCATGTC
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
62 47 1.00
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.33
Consensus pattern (62 bp):
ACATGTCACTTTTTGAAACACATGGCATGCCACATGTCACTTTTTGGCACACATGGCGTGAT
Found at i:120209 original size:28 final size:28
Alignment explanation
Indices: 120156--120209 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
120146 TAAATCTTAC
* **
120156 AAATGTAAATGTAATTTTTTTTTTAGGA
1 AAATGTAAATGTAAATTTTTAGTTAGGA
120184 AAATGTAAATGTAAATTTTTAGTTAG
1 AAATGTAAATGTAAATTTTTAGTTAG
120210 TTTATTTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (28 bp):
AAATGTAAATGTAAATTTTTAGTTAGGA
Found at i:127306 original size:2 final size:2
Alignment explanation
Indices: 127299--127327 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
127289 TACATACATC
127299 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
127328 TTCTTGGCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:127449 original size:18 final size:18
Alignment explanation
Indices: 127421--127462 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
127411 AATATGATGA
127421 TATATTTAATTATTAACGT
1 TATA-TTAATTATTAACGT
127440 TATATTAATTATTAACGT
1 TATATTAATTATTAACGT
127458 TATAT
1 TATAT
127463 ATTTTCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (18 bp):
TATATTAATTATTAACGT
Found at i:127502 original size:25 final size:23
Alignment explanation
Indices: 127446--127494 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
127436 ACGTTATATT
* *
127446 AATTATTAACGTTATATATTTTC
1 AATTGTTAACGTTATATATTTAC
127469 AATTGTTAACGTTACATATATTTAC
1 AATTGTTAACGTT--ATATATTTAC
127494 A
1 A
127495 TTTTTTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 12 0.55
25 10 0.45
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (23 bp):
AATTGTTAACGTTATATATTTAC
Found at i:127797 original size:55 final size:55
Alignment explanation
Indices: 127733--127842 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
127723 CCCCATTCAC
127733 CTATTATCCTATTCGAAATTATACTACTTGCTCTCAATCTTCCCACTTCTCAACA
1 CTATTATCCTATTCGAAATTATACTACTTGCTCTCAATCTTCCCACTTCTCAACA
*
127788 CTATTATCCTATTCGAAATTATACTATTTGCTCTCAATCTTCCCACTTCTCAACA
1 CTATTATCCTATTCGAAATTATACTACTTGCTCTCAATCTTCCCACTTCTCAACA
127843 TGAGATAATT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.27, C:0.30, G:0.04, T:0.39
Consensus pattern (55 bp):
CTATTATCCTATTCGAAATTATACTACTTGCTCTCAATCTTCCCACTTCTCAACA
Found at i:129373 original size:19 final size:19
Alignment explanation
Indices: 129351--129402 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
129341 GGGCTGAAAT
129351 TAATTAATTATTAAATAAA
1 TAATTAATTATTAAATAAA
* * *
129370 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAAATAAA
129389 TAATT-ATTATTAAA
1 TAATTAATTATTAAA
129403 AATCCTACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
18 9 0.35
19 16 0.62
20 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TAATTAATTATTAAATAAA
Done.