Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006907.1 Hibiscus syriacus cultivar Beakdansim tig00017647_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 557747
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 3
Found at i:168105 original size:20 final size:21
Alignment explanation
Indices: 168058--168105 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
168048 GCTCAGGTTT
*
168058 GTTTTATTTAGGTTATATATTA
1 GTTTT-TTTAGGTTATATATAA
*
168080 GGTTTTTTAGGTTA-ATATAA
1 GTTTTTTTAGGTTATATATAA
168100 GTTTTT
1 GTTTTT
168106 AGTCCTCCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 10 0.43
21 9 0.39
22 4 0.17
ACGTcount: A:0.25, C:0.00, G:0.17, T:0.58
Consensus pattern (21 bp):
GTTTTTTTAGGTTATATATAA
Found at i:168299 original size:23 final size:23
Alignment explanation
Indices: 168267--168317 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
168257 TTTGTGTTTG
168267 TTTTTATTTAAGTT-TATGTTTTAA
1 TTTTTATTTAA-TTCTATG-TTTAA
168291 TTTTT-TTTAATTCGTATGTTTAA
1 TTTTTATTTAATTC-TATGTTTAA
168314 TTTT
1 TTTT
168318 ATCTACATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 2 0.08
23 14 0.56
24 9 0.36
ACGTcount: A:0.22, C:0.02, G:0.08, T:0.69
Consensus pattern (23 bp):
TTTTTATTTAATTCTATGTTTAA
Found at i:170088 original size:39 final size:39
Alignment explanation
Indices: 170037--170135 Score: 99
Period size: 45 Copynumber: 2.4 Consensus size: 39
170027 TAAATGCTTG
*
170037 CGAACTATATATCATAGGTTTATTTTTCGAACAAGCATA
1 CGAACTAGATATCATAGGTTTATTTTTCGAACAAGCATA
* * *
170076 CGAACTAGATATCATGCGGTTAGGTTTATTTTTTGAATAAGCATG
1 CGAACTAGATATCA------TAGGTTTATTTTTCGAACAAGCATA
*
170121 CGAATTAGATATCAT
1 CGAACTAGATATCAT
170136 GCGGTTAGGA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
39 14 0.29
45 35 0.71
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36
Consensus pattern (39 bp):
CGAACTAGATATCATAGGTTTATTTTTCGAACAAGCATA
Found at i:170104 original size:45 final size:45
Alignment explanation
Indices: 170051--170154 Score: 154
Period size: 45 Copynumber: 2.3 Consensus size: 45
170041 CTATATATCA
170051 TAGGTTTATTTTTCGAACAAGCATACGAACTAGATATCATGCGGT
1 TAGGTTTATTTTTCGAACAAGCATACGAACTAGATATCATGCGGT
* * * *
170096 TAGGTTTATTTTTTGAATAAGCATGCGAATTAGATATCATGCGGT
1 TAGGTTTATTTTTCGAACAAGCATACGAACTAGATATCATGCGGT
*
170141 TAGGATTTCTTTTT
1 TAGG-TTTATTTTT
170155 GTGAATAACA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 45 0.85
46 8 0.15
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (45 bp):
TAGGTTTATTTTTCGAACAAGCATACGAACTAGATATCATGCGGT
Found at i:176631 original size:7 final size:7
Alignment explanation
Indices: 176600--176761 Score: 82
Period size: 7 Copynumber: 22.4 Consensus size: 7
176590 TTTCGCCTGA
176600 AAAAAAG
1 AAAAAAG
* *
176607 AGAAAAT
1 AAAAAAG
*
176614 AAGAAAG
1 AAAAAAG
176621 -AAAAAG
1 AAAAAAG
176627 AAAAAATG
1 AAAAAA-G
*
176635 AAAAAATC
1 AAAAAA-G
*
176643 AAGAAAAT
1 AA-AAAAG
176651 AAAAAATG
1 AAAAAA-G
*
176659 AAAAATG
1 AAAAAAG
***
176666 GTGAAAG
1 AAAAAAG
176673 AAAAAA-
1 AAAAAAG
176679 ATGAAAAA-
1 A--AAAAAG
*
176687 AAAGAAG
1 AAAAAAG
176694 AAAAAAAG
1 -AAAAAAG
*
176702 AAAAGAG
1 AAAAAAG
*
176709 AAAATA-
1 AAAAAAG
*
176715 AAAAATG
1 AAAAAAG
176722 AAAAAATG
1 AAAAAA-G
176730 -AAAAAG
1 AAAAAAG
176736 AAGAAAAG
1 AA-AAAAG
176744 AGAAAAAG
1 A-AAAAAG
176752 AAAAAAG
1 AAAAAAG
176759 AAA
1 AAA
176762 TAAAAGGAGG
Statistics
Matches: 118, Mismatches: 24, Indels: 26
0.70 0.14 0.15
Matches are distributed among these distances:
6 15 0.13
7 56 0.47
8 42 0.36
9 5 0.04
ACGTcount: A:0.77, C:0.01, G:0.16, T:0.07
Consensus pattern (7 bp):
AAAAAAG
Found at i:176632 original size:8 final size:8
Alignment explanation
Indices: 176598--176767 Score: 66
Period size: 8 Copynumber: 21.1 Consensus size: 8
176588 TATTTCGCCT
176598 GAAAAAAA
1 GAAAAAAA
176606 GAGAAAATAA
1 GA-AAAA-AA
176616 GAAAGAAAAA
1 G-AA-AAAAA
*
176626 GAAAAAAT
1 GAAAAAAA
*
176634 GAAAAAAT
1 GAAAAAAA
* *
176642 CAAGAAAA
1 GAAAAAAA
* *
176650 TAAAAAAT
1 GAAAAAAA
*
176658 G-AAAAAT
1 GAAAAAAA
***
176665 G-GTGAAA
1 GAAAAAAA
176672 GAAAAAAA
1 GAAAAAAA
176680 TGAAAAAAAA
1 -G-AAAAAAA
176690 GAAGAAAAA
1 GAA-AAAAA
*
176699 -AAGAAAA
1 GAAAAAAA
*
176706 G-AGAAAA
1 GAAAAAAA
* *
176713 TAAAAAAT
1 GAAAAAAA
*
176721 GAAAAAAT
1 GAAAAAAA
176729 G--AAAAA
1 GAAAAAAA
*
176735 GAAGAAAA
1 GAAAAAAA
*
176743 GAGAAAAA
1 GAAAAAAA
176751 G-AAAAAA
1 GAAAAAAA
176758 GAAATAAAA
1 GAAA-AAAA
176767 G
1 G
176768 GAGGGTTCAA
Statistics
Matches: 123, Mismatches: 25, Indels: 27
0.70 0.14 0.15
Matches are distributed among these distances:
6 5 0.04
7 26 0.21
8 56 0.46
9 18 0.15
10 14 0.11
11 4 0.03
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.07
Consensus pattern (8 bp):
GAAAAAAA
Found at i:176683 original size:13 final size:12
Alignment explanation
Indices: 176622--176727 Score: 58
Period size: 13 Copynumber: 8.5 Consensus size: 12
176612 ATAAGAAAGA
176622 AAAAGAAAAAATG
1 AAAA-AAAAAATG
**
176635 AAAAAATCAA-G
1 AAAAAAAAAATG
176646 AAAATAAAAAATG
1 AAAA-AAAAAATG
***
176659 --AAAAATGGTG
1 AAAAAAAAAATG
176669 AAAGAAAAAAATG
1 AAA-AAAAAAATG
176682 AAAAAAAAGAA-G
1 AAAAAAAA-AATG
*
176694 AAAAAAAGAAAAGAG
1 -AAAAAA-AAAA-TG
176709 AAAATAAAAAATG
1 AAAA-AAAAAATG
176722 AAAAAA
1 AAAAAA
176728 TGAAAAAGAA
Statistics
Matches: 71, Mismatches: 11, Indels: 23
0.68 0.10 0.22
Matches are distributed among these distances:
10 5 0.07
11 7 0.10
12 17 0.24
13 29 0.41
14 10 0.14
15 3 0.04
ACGTcount: A:0.76, C:0.01, G:0.14, T:0.08
Consensus pattern (12 bp):
AAAAAAAAAATG
Found at i:176736 original size:63 final size:66
Alignment explanation
Indices: 176644--176767 Score: 168
Period size: 63 Copynumber: 1.9 Consensus size: 66
176634 GAAAAAATCA
** *
176644 AGAAAATAAAAAATGAAAAATGGTGAAAGAA-AAAA-ATGAAAAA-AAAGAAGAAA-AAAAGAAA
1 AGAAAATAAAAAATGAAAAATGGAAAAAGAAGAAAAGA-GAAAAAGAAAAAAGAAATAAAAGAAA
176705 AG
65 AG
176707 AGAAAATAAAAAATGAAAAAAT-GAAAAAGAAGAAAAGAGAAAAAGAAAAAAGAAATAAAAG
1 AGAAAATAAAAAATG-AAAAATGGAAAAAGAAGAAAAGAGAAAAAGAAAAAAGAAATAAAAG
176768 GAGGGTTCAA
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
63 22 0.42
64 16 0.30
65 10 0.19
66 5 0.09
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (66 bp):
AGAAAATAAAAAATGAAAAATGGAAAAAGAAGAAAAGAGAAAAAGAAAAAAGAAATAAAAGAAAA
G
Found at i:176756 original size:37 final size:34
Alignment explanation
Indices: 176617--176761 Score: 68
Period size: 36 Copynumber: 4.0 Consensus size: 34
176607 AGAAAATAAG
*
176617 AAAGAAAAAGAAAAAATGAAAAAATCAAGAAAATA-AA
1 AAAGAAAAAGAAAAAA-G-AAAAA--AAGAAAAGAGAA
***
176654 AAATGAAAAATGGTGAAAGAAAAAAATGAAAA-A-AA
1 AAA-GAAAAA-GAAAAAAGAAAAAAA-GAAAAGAGAA
176689 AGAAGAAAAA-AAGAAAAGAGAAAATAA-AAAATGA-AA
1 A-AAGAAAAAGAA-AAAAGA-AAAA-AAGAAAA-GAGAA
* *
176725 AAATGAAAAAGAAGAAAAGAGAAAAAGAAAAAAGAA
1 AAA-GAAAAAGAA-AAAAGAAAAAAAGAAAAGAGAA
176761 A
1 A
176762 TAAAAGGAGG
Statistics
Matches: 87, Mismatches: 8, Indels: 27
0.71 0.07 0.22
Matches are distributed among these distances:
34 9 0.10
35 21 0.24
36 29 0.33
37 17 0.20
38 7 0.08
39 4 0.05
ACGTcount: A:0.77, C:0.01, G:0.16, T:0.07
Consensus pattern (34 bp):
AAAGAAAAAGAAAAAAGAAAAAAAGAAAAGAGAA
Found at i:176823 original size:45 final size:45
Alignment explanation
Indices: 176764--176849 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
176754 AAAAGAAATA
*
176764 AAAGGAGGGTTCAAGATGAAAACCCAAAAAGGGCGTCTTGAAACC
1 AAAGGAGGGTTCAAGATGAAAACCCAAAAAGGGCGACTTGAAACC
* **
176809 AAAGGA-GGTCTCAAGTTGAAAACCCGCAAAGGGCGACTTGA
1 AAAGGAGGGT-TCAAGATGAAAACCCAAAAAGGGCGACTTGA
176850 GTTTTGTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 3 0.08
45 33 0.92
ACGTcount: A:0.40, C:0.19, G:0.28, T:0.14
Consensus pattern (45 bp):
AAAGGAGGGTTCAAGATGAAAACCCAAAAAGGGCGACTTGAAACC
Found at i:178165 original size:55 final size:54
Alignment explanation
Indices: 178102--178460 Score: 350
Period size: 55 Copynumber: 6.5 Consensus size: 54
178092 GATTGAGTCT
178102 TATACTCTCTGGTAGAATAGGGAGCAGACTCGTTTGTTGAAGATTGTTCGAGTTC
1 TATACTCTCT-GTAGAATAGGGAGCAGACTCGTTTGTTGAAGATTGTTCGAGTTC
** * *
178157 TATACTCTCTGGTAGAATAGGGAGTGGGCTCGTTTGTTGAAGATTGTCCGAGTTC
1 TATACTCTCT-GTAGAATAGGGAGCAGACTCGTTTGTTGAAGATTGTTCGAGTTC
* * * *
178212 TATACTCTCTGGTAGAATAAGGAGCGGACTCGTTTGTTGAAGATTGTTTGGGTTC
1 TATACTCTCT-GTAGAATAGGGAGCAGACTCGTTTGTTGAAGATTGTTCGAGTTC
** *
178267 TATACTCTCTAGTAGAATAGAAAG-AGGACCCGTTT-TATGAAGATTGTTCGAGTTC
1 TATACTCTCT-GTAGAATAGGGAGCA-GACTCGTTTGT-TGAAGATTGTTCGAGTTC
* * * * * * *
178322 TATACTCCCTGAACGAATAGGGAGCGGACCCATTTATTGAAGATTGATCGAG-TC
1 TATACTCTCTGTA-GAATAGGGAGCAGACTCGTTTGTTGAAGATTGTTCGAGTTC
* * * *
178376 TTATACTCCCTGAATGAATAGGGAGCAGACAT-GTTTGCTGAAGATTGGTCGAG-TC
1 -TATACTCTCTGTA-GAATAGGGAGCAGAC-TCGTTTGTTGAAGATTGTTCGAGTTC
* * *
178431 TTATACTCCCTGAAGGGATAGGGAGCAGAC
1 -TATACTCTCTGTA-GAATAGGGAGCAGAC
178461 ATGTCATTCG
Statistics
Matches: 263, Mismatches: 34, Indels: 14
0.85 0.11 0.05
Matches are distributed among these distances:
54 5 0.02
55 257 0.98
56 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (54 bp):
TATACTCTCTGTAGAATAGGGAGCAGACTCGTTTGTTGAAGATTGTTCGAGTTC
Found at i:178438 original size:165 final size:165
Alignment explanation
Indices: 178096--178438 Score: 387
Period size: 165 Copynumber: 2.1 Consensus size: 165
178086 TATGAAGATT
* ** *
178096 GAGTCTTATACTCTCTGGTAGAATAGGGAGCAGACTCGTTTGTTGAAGATTGTTCGAGTTCTATA
1 GAGTCTTATACTCTCTAGTAGAATAGAAAGCAGACCCGTTTGTTGAAGATTGTTCGAGTTCTATA
* * * * * * * * *
178161 CTCTCTGGTAGAATAGGGAGTGGGCTCGTTTGTTGAAGATTGTCCGAGTTCTATACTCTCTGGTA
66 CTCCCTGGAAGAATAGGGAGCGGACCCATTTATTGAAGATTGTCCGAGTTCTATACTCCCTGATA
* * * *
178226 GAATAAGGAGCGGACTCGTTTGTTGAAGATTGTTT
131 GAATAAGGAGCAGACTCGTTTGCTGAAGATTGGTC
*
178261 GGGT-TCTATACTCTCTAGTAGAATAGAAAG-AGGACCCGTTT-TATGAAGATTGTTCGAGTTCT
1 GAGTCT-TATACTCTCTAGTAGAATAGAAAGCA-GACCCGTTTGT-TGAAGATTGTTCGAGTTCT
178323 ATACTCCCT-GAACGAATAGGGAGCGGACCCATTTATTGAAGATTGAT-CGAG-TCTTATACTCC
63 ATACTCCCTGGAA-GAATAGGGAGCGGACCCATTTATTGAAGATTG-TCCGAGTTC-TATACTCC
*
178385 CTGA-ATGAATAGGGAGCAGACAT-GTTTGCTGAAGATTGGTC
125 CTGATA-GAATAAGGAGCAGAC-TCGTTTGCTGAAGATTGGTC
178426 GAGTCTTATACTC
1 GAGTCTTATACTC
178439 CCTGAAGGGA
Statistics
Matches: 149, Mismatches: 20, Indels: 18
0.80 0.11 0.10
Matches are distributed among these distances:
164 8 0.05
165 138 0.93
166 3 0.02
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (165 bp):
GAGTCTTATACTCTCTAGTAGAATAGAAAGCAGACCCGTTTGTTGAAGATTGTTCGAGTTCTATA
CTCCCTGGAAGAATAGGGAGCGGACCCATTTATTGAAGATTGTCCGAGTTCTATACTCCCTGATA
GAATAAGGAGCAGACTCGTTTGCTGAAGATTGGTC
Found at i:180191 original size:19 final size:21
Alignment explanation
Indices: 180150--180191 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
180140 GTTTGTTTTA
*
180150 TTTAGGTTATATATTAGGTTT
1 TTTAGGTTATATATTAAGTTT
180171 TTTAGGTTA-ATA-TAAGTTT
1 TTTAGGTTATATATTAAGTTT
180190 TT
1 TT
180192 AGACCTCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 3 0.15
21 9 0.45
ACGTcount: A:0.26, C:0.00, G:0.17, T:0.57
Consensus pattern (21 bp):
TTTAGGTTATATATTAAGTTT
Found at i:180191 original size:20 final size:21
Alignment explanation
Indices: 180144--180191 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
180134 GCTCAGGTTT
*
180144 GTTTTATTTAGGTTATATATTA
1 GTTTT-TTTAGGTTATATATAA
*
180166 GGTTTTTTAGGTTA-ATATAA
1 GTTTTTTTAGGTTATATATAA
180186 GTTTTT
1 GTTTTT
180192 AGACCTCCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 10 0.43
21 9 0.39
22 4 0.17
ACGTcount: A:0.25, C:0.00, G:0.17, T:0.58
Consensus pattern (21 bp):
GTTTTTTTAGGTTATATATAA
Found at i:180384 original size:22 final size:22
Alignment explanation
Indices: 180354--180404 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
180344 TTGTGTTTGT
180354 TTTTATTTAAGTT-TATGTTTTAA
1 TTTTATTTAA-TTCTATG-TTTAA
180377 TTTT-TTTAATTCGTATGTTTAA
1 TTTTATTTAATTC-TATGTTTAA
180399 TTTTAT
1 TTTTAT
180405 CTACATTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 2 0.08
22 14 0.56
23 9 0.36
ACGTcount: A:0.24, C:0.02, G:0.08, T:0.67
Consensus pattern (22 bp):
TTTTATTTAATTCTATGTTTAA
Found at i:182745 original size:492 final size:491
Alignment explanation
Indices: 181822--182804 Score: 1885
Period size: 492 Copynumber: 2.0 Consensus size: 491
181812 AAAGTAAAAA
181822 AAATGTGATTCAAACCAGAGTTTCTCAAAAATTAATTTATATTATGAAATGAATATATTATAATT
1 AAATGTGATTCAAACCAGAGTTTCTCAAAAATTAATTTATATTATGAAATGAATATATTATAATT
181887 AATATCAATGGTTTAATCTTAAAATAATTTATTGATTGTCACCTAACAAATAACAATTTTAAGAG
66 AATATCAATGGTTTAATCTTAAAATAATTTATTGATTGTCACCTAACAAATAACAATTTTAAGAG
*
181952 ATCATAGCATAATACAACTATCAACAATAAGTTGGTTTTGTGGGATGAGACAATATATTTTTAAA
131 ATCATAGCATAATACAACTATCAACAATAAATTGGTTTTGTGGGATGAGACAATATATTTTTAAA
182017 CAATGCCAATAGTTTGAATTCTGGTGTTTATGAATAGAGCAAATTGGGTTGGGAGGGTCACCCTT
196 CAATGCCAATAGTTTGAATTCTGGTGTTTATGAATAGAGCAAATTGGGTTGGGAGGGTCACCCTT
182082 ACCTCTGTAATATCCGATTCATATTAGTCGATTAATAAATCGAAAACCAATAATTATACCAAAAA
261 ACCTCTGTAATATCCGATTCATATTAGTCGATTAATAAATCGAAAACCAATAATTATACCAAAAA
182147 AATAAGATACTATTGTTGGAATTTTAAAAGACAACCAATAACTAATTAGATGTTGACATGTATTA
326 AATAAGATACTATTGTTGGAATTTTAAAAGACAACCAATAACTAATTAGATGTTGACATGTATTA
182212 GAATCTTATTAGAAATACAAAAGTCTATAATAAAAGGAAGCAACCTCGGTGATATAAAGGAGTGT
391 GAATCTTATTAGAAATACAAAAGTCTATAATAAAAGGAAGCAACCTCGGTGATATAAAGGAGTGT
*
182277 TATTCTCTTTCGAGATTTTGTGTTCAAGTAGTTGAG
456 TATTCTCTTTCGAGATTTCGTGTTCAAGTAGTTGAG
*
182313 AAATGTGATTCAAACTAGAGTTTCTCAAAAATTAATTTATATTATGAAATGAATATATTATAATT
1 AAATGTGATTCAAACCAGAGTTTCTCAAAAATTAATTTATATTATGAAATGAATATATTATAATT
*
182378 AATGTCAATGGTTTAATCTTAAAATAATTTATTGATTGTCACCTAACAAATAACAATTTTAAGAG
66 AATATCAATGGTTTAATCTTAAAATAATTTATTGATTGTCACCTAACAAATAACAATTTTAAGAG
*
182443 ATCATAGCATACTACAACTATCAACAATAAATTGGTTTTGTGGGATGAGACAATATATCTTTTAA
131 ATCATAGCATAATACAACTATCAACAATAAATTGGTTTTGTGGGATGAGACAATATAT-TTTTAA
* *
182508 ACAATGTCAATATTTTGAATTCTGGTGTTTATGAATAGAGCAAATTGGGTTGGGAGGGTCACCCT
195 ACAATGCCAATAGTTTGAATTCTGGTGTTTATGAATAGAGCAAATTGGGTTGGGAGGGTCACCCT
182573 TACCTCTGTAATATCCGATTCATATTAGTCGATTAATAAATCGAAAACCAATAATTATACCAAAA
260 TACCTCTGTAATATCCGATTCATATTAGTCGATTAATAAATCGAAAACCAATAATTATACCAAAA
182638 AAATAAGATACTATTGTTGGAATTTTAAAAGACAACCAATAACTAATTAGATGTTGACATGTATT
325 AAATAAGATACTATTGTTGGAATTTTAAAAGACAACCAATAACTAATTAGATGTTGACATGTATT
*
182703 AGAATCTTATTAGAAGTACAAAAGTCTATAATAAAAGGAAGCAACCTCGGTGATATAAAGGAGTG
390 AGAATCTTATTAGAAATACAAAAGTCTATAATAAAAGGAAGCAACCTCGGTGATATAAAGGAGTG
182768 TTATTCTCTTTCGAGATTTCGTGTTCAAGTAGTTGAG
455 TTATTCTCTTTCGAGATTTCGTGTTCAAGTAGTTGAG
182805 TCTGTAGGGT
Statistics
Matches: 483, Mismatches: 8, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
491 184 0.38
492 299 0.62
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (491 bp):
AAATGTGATTCAAACCAGAGTTTCTCAAAAATTAATTTATATTATGAAATGAATATATTATAATT
AATATCAATGGTTTAATCTTAAAATAATTTATTGATTGTCACCTAACAAATAACAATTTTAAGAG
ATCATAGCATAATACAACTATCAACAATAAATTGGTTTTGTGGGATGAGACAATATATTTTTAAA
CAATGCCAATAGTTTGAATTCTGGTGTTTATGAATAGAGCAAATTGGGTTGGGAGGGTCACCCTT
ACCTCTGTAATATCCGATTCATATTAGTCGATTAATAAATCGAAAACCAATAATTATACCAAAAA
AATAAGATACTATTGTTGGAATTTTAAAAGACAACCAATAACTAATTAGATGTTGACATGTATTA
GAATCTTATTAGAAATACAAAAGTCTATAATAAAAGGAAGCAACCTCGGTGATATAAAGGAGTGT
TATTCTCTTTCGAGATTTCGTGTTCAAGTAGTTGAG
Found at i:183866 original size:21 final size:21
Alignment explanation
Indices: 183840--183972 Score: 203
Period size: 21 Copynumber: 6.3 Consensus size: 21
183830 GTTTACCGTG
*
183840 ATTGCGACCATAGCGGGTGCT
1 ATTGCGGCCATAGCGGGTGCT
*
183861 ATTGCGGTCATAGCGGGTGCT
1 ATTGCGGCCATAGCGGGTGCT
*
183882 ATTGCGGCCATAGCAGGTGCT
1 ATTGCGGCCATAGCGGGTGCT
*
183903 ATTGCGGCCATAGCGGGTGTT
1 ATTGCGGCCATAGCGGGTGCT
183924 ATTGCGGCCATAGCGGGTGCT
1 ATTGCGGCCATAGCGGGTGCT
** *
183945 ATTGCGGCCATAGCAAGCGCT
1 ATTGCGGCCATAGCGGGTGCT
183966 ATTGCGG
1 ATTGCGG
183973 GTATAGCAAG
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 102 1.00
ACGTcount: A:0.17, C:0.23, G:0.35, T:0.25
Consensus pattern (21 bp):
ATTGCGGCCATAGCGGGTGCT
Found at i:197793 original size:18 final size:18
Alignment explanation
Indices: 197770--197808 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
197760 CCTGCTGCTC
197770 CAGATTCAGCAGCAGCAA
1 CAGATTCAGCAGCAGCAA
197788 CAGATTCAGCAGCAGCAA
1 CAGATTCAGCAGCAGCAA
197806 CAG
1 CAG
197809 CAGCAAACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.28, G:0.23, T:0.10
Consensus pattern (18 bp):
CAGATTCAGCAGCAGCAA
Found at i:207645 original size:60 final size:60
Alignment explanation
Indices: 207522--207669 Score: 152
Period size: 60 Copynumber: 2.5 Consensus size: 60
207512 TTACATATTT
* * * * * * * * * * *
207522 GGATGAAATTGGAATATTCAAAAGTTTAGGGATTAATTTAGAATGAGAGTTATACTTTGA
1 GGATGAAATTAGAATATTTAAAAATTAAAGGACTAATTTAAAATAAGAGTCAAACTTTAA
*
207582 GGATGAAATTAGAATATTTAAAAATTAAAGGACTAATTTAAAATAAGAGTCAAAGTTTAA
1 GGATGAAATTAGAATATTTAAAAATTAAAGGACTAATTTAAAATAAGAGTCAAACTTTAA
* * * *
207642 GGATAAAATTTGAATGTTTAAAATTTAA
1 GGATGAAATTAGAATATTTAAAAATTAA
207670 GGATGAATTT
Statistics
Matches: 72, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 72 1.00
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.34
Consensus pattern (60 bp):
GGATGAAATTAGAATATTTAAAAATTAAAGGACTAATTTAAAATAAGAGTCAAACTTTAA
Found at i:208573 original size:34 final size:35
Alignment explanation
Indices: 208499--208573 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
208489 AAAACAATCC
* *
208499 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCAAATTTCCAAAATAAT
*
208534 TCAATTTCATTCTAAACCTAAATTT-CAAAATAAT
1 TCAATTTCATTCTAAACCCAAATTTCCAAAATAAT
208568 TCAATT
1 TCAATT
208574 AAATTTAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
34 14 0.38
35 23 0.62
ACGTcount: A:0.40, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCAAATTTCCAAAATAAT
Found at i:209116 original size:130 final size:130
Alignment explanation
Indices: 208970--209217 Score: 433
Period size: 130 Copynumber: 1.9 Consensus size: 130
208960 TATTTATATA
* **
208970 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
*
209035 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
209100 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
209165 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
209218 GAAGAAAATT
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 111 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:209187 original size:23 final size:21
Alignment explanation
Indices: 209144--209190 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
209134 AATTAATCAT
209144 TTAACCAGGATCTGACATGTG
1 TTAACCAGGATCTGACATGTG
* *
209165 TTAACACATGATCATGATATGTG
1 TTAAC-CAGGATC-TGACATGTG
209188 TTA
1 TTA
209191 TTGGTGACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (21 bp):
TTAACCAGGATCTGACATGTG
Found at i:209248 original size:130 final size:129
Alignment explanation
Indices: 208984--209248 Score: 318
Period size: 130 Copynumber: 2.0 Consensus size: 129
208974 ATTTGGTCCT
* ** *
208984 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
*** * * **** *
209049 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
209114 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * *
209179 TGATATGTGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
209243 -A
128 CA
209244 AAATT
1 AAATT
209249 TGGGTCTTGG
Statistics
Matches: 114, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
130 101 0.89
132 8 0.07
133 5 0.04
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:209576 original size:28 final size:27
Alignment explanation
Indices: 209545--209607 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
209535 AGTTGATACA
*
209545 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
209573 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
209601 ATATTTT
1 ATATTTT
209608 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:209708 original size:16 final size:18
Alignment explanation
Indices: 209687--209720 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
209677 ATTTCTTATT
209687 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
209703 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
209721 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:211900 original size:16 final size:17
Alignment explanation
Indices: 211868--211900 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
211858 TTTAATTATG
211868 ATATACTTATGTTTTAA
1 ATATACTTATGTTTTAA
*
211885 ATATATTTAT-TTTTAA
1 ATATACTTATGTTTTAA
211901 CTATTTAGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (17 bp):
ATATACTTATGTTTTAA
Found at i:213101 original size:34 final size:35
Alignment explanation
Indices: 213032--213106 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 35
213022 AAAACAGTCC
* * *
213032 TCAATTTTATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
213067 TCAATTTCATTCTAAA-CCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
213101 TCAATT
1 TCAATT
213107 AAATTCAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 21 0.58
35 15 0.42
ACGTcount: A:0.40, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:213644 original size:130 final size:130
Alignment explanation
Indices: 213503--213750 Score: 487
Period size: 130 Copynumber: 1.9 Consensus size: 130
213493 TATTTATATA
*
213503 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
213568 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
213633 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
213698 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
66 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
213751 GAAGAAAATT
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
130 117 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:213781 original size:130 final size:129
Alignment explanation
Indices: 213517--213781 Score: 372
Period size: 130 Copynumber: 2.0 Consensus size: 129
213507 ATTTGGTCCT
*
213517 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
*** * * **** *
213582 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
213647 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
*
213712 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
213776 -A
128 CA
213777 AAATT
1 AAATT
213782 TGGGTCTTGG
Statistics
Matches: 120, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
130 107 0.89
132 8 0.07
133 5 0.04
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:214108 original size:28 final size:27
Alignment explanation
Indices: 214077--214139 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
214067 AGTTGATACA
*
214077 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
214105 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
214133 ATATTTT
1 ATATTTT
214140 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:214240 original size:16 final size:18
Alignment explanation
Indices: 214219--214252 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
214209 ATTTCTTATT
214219 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
214235 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
214253 TACATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:215000 original size:21 final size:20
Alignment explanation
Indices: 214974--215071 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
214964 ATCAGTTTCC
214974 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* **
214995 AAAATCGCAATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
** *
215014 ACAAATTCGCATTGCGATTTTCA
1 A-AAA-TCGCAACGCGATTTT-G
* *
215037 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
215057 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
215072 ACACATAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 19 0.31
21 38 0.61
22 3 0.05
23 1 0.02
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:215100 original size:20 final size:20
Alignment explanation
Indices: 215038--215231 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
215028 CGATTTTCAA
* ** *
215038 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
215058 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
215078 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
215098 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
215118 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
215138 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
215158 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
215178 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
215198 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
215219 AAATCGCAACGCG
1 AAATCGCAACGCG
215232 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:215122 original size:60 final size:60
Alignment explanation
Indices: 215038--215231 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
215028 CGATTTTCAA
* ** * *
215038 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
215098 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
215158 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
215219 AAATCGCAACGCG
1 AAATCGCAACGCG
215232 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:215649 original size:33 final size:33
Alignment explanation
Indices: 215610--215680 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
215600 TTCACTTAGA
*
215610 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
215643 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
215676 TTTCA
1 TTTCA
215681 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:215804 original size:20 final size:20
Alignment explanation
Indices: 215760--215835 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
215750 TGCAGAAGAG
* *
215760 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGACAA
**
215781 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGACAA
*
215801 TCGCAACGAGAAAATGACAA
1 TCGCAACGAGAGAATGACAA
215821 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
215836 CGCAACGCGA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 36 0.77
21 11 0.23
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAGAATGACAA
Found at i:215824 original size:40 final size:41
Alignment explanation
Indices: 215759--215835 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 41
215749 TTGCAGAAGA
215759 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
*
215800 GTCGCAACGAGA-AAATGACAATCGCAACGAGAGAAT
1 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAAT
215836 CGCAACGCGA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 23 0.66
41 12 0.34
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
Found at i:215857 original size:19 final size:19
Alignment explanation
Indices: 215772--215877 Score: 78
Period size: 19 Copynumber: 5.7 Consensus size: 19
215762 GCAACGAGAT
*
215772 AAATGAAAATCGCAACGAG
1 AAATGAAAATCGCAACGCG
*** *
215791 AGAATGACTGTCGCAACGAG
1 A-AATGAAAATCGCAACGCG
*
215811 AAAATGACAATCGCAA--CG
1 -AAATGAAAATCGCAACGCG
*
215829 --A-GAGAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
215845 AAATGAAAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
**
215864 AAACCAAAATCGCA
1 AAATGAAAATCGCA
215878 TTGCGATTTT
Statistics
Matches: 70, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
18 2 0.03
19 27 0.39
20 27 0.39
21 1 0.01
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.10
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCG
Found at i:215895 original size:19 final size:19
Alignment explanation
Indices: 215873--216000 Score: 78
Period size: 19 Copynumber: 7.1 Consensus size: 19
215863 GAAACCAAAA
*
215873 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
215892 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
215906 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
215925 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
215939 TCTCGTTGCGATTGTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
215959 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
215979 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
215999 TC
1 TC
216001 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.23
16 5 0.06
17 6 0.07
19 22 0.25
20 19 0.22
21 15 0.17
ACGTcount: A:0.11, C:0.25, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:215914 original size:14 final size:14
Alignment explanation
Indices: 215895--215951 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
215885 TTTCATTTCG
215895 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
215909 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
215928 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
215942 CGTTGCGATT
1 CGTTGCGATT
215952 GTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:215920 original size:33 final size:33
Alignment explanation
Indices: 215878--216000 Score: 156
Period size: 33 Copynumber: 3.5 Consensus size: 33
215868 CAAAATCGCA
215878 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
215911 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
215944 TTGCGATTGTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
215985 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
216001 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
33 44 0.56
34 2 0.03
35 6 0.08
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.03
41 20 0.25
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:215962 original size:21 final size:21
Alignment explanation
Indices: 215936--216000 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
215926 CGCGTTGCGA
215936 TTCTCTCGTTGCGATTGTCAT
1 TTCTCTCGTTGCGATTGTCAT
**
215957 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTGTCAT
*
215977 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTGTCAT
215998 TTC
1 TTC
216001 AACCAAAAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
20 17 0.45
21 21 0.55
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTGTCAT
Found at i:215997 original size:20 final size:20
Alignment explanation
Indices: 215935--215998 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
215925 TCGCGTTGCG
215935 ATTCTCTCGTTGCGATTGTC
1 ATTCTCTCGTTGCGATTGTC
**
215955 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTGTC
*
215976 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTGTC
215996 ATT
1 ATT
215999 TCAACCAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
20 20 0.53
21 18 0.47
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.45
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTGTC
Found at i:217853 original size:93 final size:93
Alignment explanation
Indices: 217694--218160 Score: 904
Period size: 93 Copynumber: 5.1 Consensus size: 93
217684 TAGATTGCTT
*
217694 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
217759 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
217787 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
217852 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
217880 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
217945 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
217972 AGTAAATTTGTTCGGTTGC-GCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
218036 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
218064 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
218129 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
218156 AGTAA
1 AGTAA
218161 TGCAATCCAT
Statistics
Matches: 371, Mismatches: 1, Indels: 5
0.98 0.00 0.01
Matches are distributed among these distances:
91 62 0.17
92 64 0.17
93 245 0.66
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:218074 original size:184 final size:186
Alignment explanation
Indices: 217694--218160 Score: 904
Period size: 184 Copynumber: 2.5 Consensus size: 186
217684 TAGATTGCTT
*
217694 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
217759 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
217824 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
217880 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
217945 TTTGTCTTTGTTTTGTC-TTTGGTTGAAAGTAAATTTGTTCGGTTGC-GCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
218008 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
218064 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
218129 TTTGTCTTTGTTTTGTCTTTTGGTTG-AAGTAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAA
218161 TGCAATCCAT
Statistics
Matches: 279, Mismatches: 1, Indels: 4
0.98 0.00 0.01
Matches are distributed among these distances:
184 161 0.58
185 37 0.13
186 81 0.29
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:218248 original size:19 final size:19
Alignment explanation
Indices: 218208--218336 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
218198 TAGTTTACTT
* *
218208 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
218228 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
218247 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
218266 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
218280 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
218299 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
218313 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
218332 TCGCA
1 TCGCA
218337 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:218287 original size:33 final size:32
Alignment explanation
Indices: 218244--218336 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
218234 CGCGAAACCA
**
218244 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
218276 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
218309 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
218337 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:218334 original size:52 final size:52
Alignment explanation
Indices: 218208--218336 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
218198 TAGTTTACTT
**
218208 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
218260 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
218313 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
218337 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:218354 original size:19 final size:19
Alignment explanation
Indices: 218332--218450 Score: 123
Period size: 19 Copynumber: 6.8 Consensus size: 19
218322 GAAACCAAAA
*
218332 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
218351 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
218367 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
218384 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
218400 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
218417 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
218436 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
218451 AAGTTTCTTG
Statistics
Matches: 83, Mismatches: 7, Indels: 20
0.75 0.06 0.18
Matches are distributed among these distances:
14 15 0.18
16 11 0.13
17 11 0.13
19 46 0.55
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:218373 original size:14 final size:14
Alignment explanation
Indices: 218354--218410 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
218344 TTTCATTTCG
218354 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
218368 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
218385 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
218401 CGTTGCGATT
1 CGTTGCGATT
218411 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:218379 original size:33 final size:33
Alignment explanation
Indices: 218337--218429 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
218327 CAAAATCGCA
*
218337 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
218370 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
218403 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
218430 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:218466 original size:20 final size:19
Alignment explanation
Indices: 218401--218457 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
218391 GCGATTCTGT
218401 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTT-AGTTTCG
*
218420 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTAGTTTCG
218439 CGTTGCGATTTTAAGTTTC
1 CGTTGCGATTTT-AGTTTC
218458 TTGTTGCGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 29 0.85
20 5 0.15
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.47
Consensus pattern (19 bp):
CGTTGCGATTTTAGTTTCG
Found at i:220407 original size:14 final size:14
Alignment explanation
Indices: 220388--220423 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
220378 ATTGTTTAAT
220388 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
220402 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
220416 TGATTTGT
1 TGATTTGT
220424 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:220546 original size:19 final size:19
Alignment explanation
Indices: 220530--220645 Score: 144
Period size: 19 Copynumber: 6.6 Consensus size: 19
220520 AAAAATGACT
220530 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
220549 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
220568 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
220582 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
220601 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
220621 ATCGCAA--CGAAA-G--A
1 ATCGCAATGCGAAATGAAA
220635 ATCGCAATGCG
1 ATCGCAATGCG
220646 TTTATAATTT
Statistics
Matches: 87, Mismatches: 2, Indels: 19
0.81 0.02 0.18
Matches are distributed among these distances:
14 18 0.21
15 1 0.01
16 5 0.06
17 6 0.07
18 2 0.02
19 39 0.45
20 16 0.18
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:220659 original size:53 final size:53
Alignment explanation
Indices: 220530--220645 Score: 216
Period size: 53 Copynumber: 2.2 Consensus size: 53
220520 AAAAATGACT
*
220530 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAAAGA
220582 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAAAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAAAGA
220635 ATCGCAATGCG
1 ATCGCAATGCG
220646 TTTATAATTT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAAAGA
Found at i:220689 original size:33 final size:33
Alignment explanation
Indices: 220652--220804 Score: 157
Period size: 33 Copynumber: 4.5 Consensus size: 33
220642 TGCGTTTATA
220652 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
220685 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * *** * *
220725 GTTGCG-ATTTTAATT-TCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
220756 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
220789 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
220805 TTCATTTCGC
Statistics
Matches: 95, Mismatches: 16, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
31 6 0.06
32 7 0.07
33 52 0.55
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.08
39 5 0.05
40 6 0.06
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:220698 original size:19 final size:19
Alignment explanation
Indices: 220674--220889 Score: 231
Period size: 19 Copynumber: 12.4 Consensus size: 19
220664 GATTCTCTCG
220674 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
220693 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
220712 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
220726 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
220745 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
220764 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
220778 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
220797 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
220816 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
220830 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
220850 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
220864 TTGGGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
220882 TTGCGATT
1 TTGCGATT
220890 CTCTCGTTGC
Statistics
Matches: 165, Mismatches: 10, Indels: 44
0.75 0.05 0.20
Matches are distributed among these distances:
13 5 0.03
14 23 0.14
15 1 0.01
16 22 0.13
17 19 0.12
18 8 0.05
19 75 0.45
20 12 0.07
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:220834 original size:33 final size:33
Alignment explanation
Indices: 220693--220903 Score: 216
Period size: 33 Copynumber: 6.2 Consensus size: 33
220683 TCATTTCGCA
220693 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* *
220726 TTGCGATTTTAATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
220762 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
220797 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
220830 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
220864 TTGGGA-TTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
220896 TTGCGATT
1 TTGCGATT
220904 GTAATTTCCG
Statistics
Matches: 145, Mismatches: 18, Indels: 30
0.75 0.09 0.16
Matches are distributed among these distances:
31 10 0.07
32 25 0.17
33 59 0.41
34 20 0.14
35 6 0.04
36 4 0.03
37 2 0.01
38 8 0.06
39 3 0.02
40 8 0.06
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:220834 original size:85 final size:86
Alignment explanation
Indices: 220693--220911 Score: 277
Period size: 85 Copynumber: 2.6 Consensus size: 86
220683 TCATTTCGCA
* **
220693 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTAATTTCGCATTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCGATTGCAATTTCGCATTGCGATTTTCAT
220758 TT-CGCATTGCGATTCTC-TCG
66 TTCCGCATTGCGATTCTCAT-G
* * * *
220778 TTGCGATTTTCATTTCGCATTGCGATT-T-TCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCG-ATTGCAATT-TCGCATTGCGATTTTC
*
220841 ATTTCCGCATTGCGATTTTCATG
64 ATTTCCGCATTGCGATTCTCATG
* * *
220864 TTGGGA-TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATTTC
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCGATTGCAATTTC
220912 CGTGTTGCGA
Statistics
Matches: 115, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
83 6 0.05
84 7 0.06
85 67 0.58
86 28 0.24
87 7 0.06
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (86 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCGATTGCAATTTCGCATTGCGATTTTCAT
TTCCGCATTGCGATTCTCATG
Found at i:220886 original size:104 final size:104
Alignment explanation
Indices: 220652--220889 Score: 372
Period size: 104 Copynumber: 2.3 Consensus size: 104
220642 TGCGTTTATA
* *
220652 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTCTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
220717 ATTCTCTCGTTGCGATTTTAATTTCGCATTGCGATTTTC
66 ATTCTCTCGTTGCGATTTTAATTTCGCATTGCGATTTTC
* *
220756 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTCTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
*
220821 ATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
66 ATTCTCTCGTTGCGATTTTAATTT-CGCATTGCGATTTTC
* * *
220861 ATGTTGGGATTTC-ATT-TCGCATTGCGATT
1 AT-TTCGCATTGCGATTCTCGCATTGCGATT
220890 CTCTCGTTGC
Statistics
Matches: 126, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
104 99 0.79
105 20 0.16
106 7 0.06
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (104 bp):
ATTTCGCATTGCGATTCTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTCTCTCGTTGCGATTTTAATTTCGCATTGCGATTTTC
Found at i:220889 original size:52 final size:52
Alignment explanation
Indices: 220652--220862 Score: 404
Period size: 52 Copynumber: 4.0 Consensus size: 52
220642 TGCGTTTATA
220652 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
220704 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
220756 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
220808 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
220861 AT
1 AT
220863 GTTGGGATTT
Statistics
Matches: 156, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
52 139 0.89
53 17 0.11
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:223180 original size:12 final size:12
Alignment explanation
Indices: 223163--223187 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
223153 TCTTCGGGGA
223163 CTTTTTCTTCTT
1 CTTTTTCTTCTT
223175 CTTTTTCTTCTT
1 CTTTTTCTTCTT
223187 C
1 C
223188 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:223396 original size:24 final size:24
Alignment explanation
Indices: 223362--223408 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
223352 CTGAAACATC
223362 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
223386 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
223409 GACCAATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:224117 original size:20 final size:20
Alignment explanation
Indices: 224089--224298 Score: 228
Period size: 20 Copynumber: 10.5 Consensus size: 20
224079 AAATTTCAGT
* * * *
224089 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
224109 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
224129 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
224149 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
224169 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
224189 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
224209 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
224229 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
224249 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
224269 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
224289 GTTGCGATTT
1 GTTGCGATTT
224299 TGATATTCGC
Statistics
Matches: 165, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.02
20 159 0.96
21 3 0.02
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:224307 original size:20 final size:20
Alignment explanation
Indices: 224270--224361 Score: 80
Period size: 21 Copynumber: 4.5 Consensus size: 20
224260 CGGATACGCG
* *
224270 TTGCGATTTATG-TGTTCGCG
1 TTGCGATTT-TGATATTCGCA
224290 TTGCGATTTTGATATTCGCA
1 TTGCGATTTTGATATTCGCA
* *
224310 TTGCGATTTTTGAAAATCGCA
1 TTGCGA-TTTTGATATTCGCA
* *
224331 ATGCGAATTTG-TACTATCGCA
1 TTGCGATTTTGATA-T-TCGCA
224352 TTGCGATTTT
1 TTGCGATTTT
224362 CAAGAATCGC
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
19 3 0.05
20 25 0.43
21 30 0.52
ACGTcount: A:0.21, C:0.15, G:0.22, T:0.42
Consensus pattern (20 bp):
TTGCGATTTTGATATTCGCA
Found at i:224370 original size:21 final size:20
Alignment explanation
Indices: 224285--224383 Score: 90
Period size: 21 Copynumber: 4.8 Consensus size: 20
224275 ATTTATGTGT
* * *
224285 TCGCGTTGCGATTTTGATAT
1 TCGCATTGCGATTTTGAAAA
224305 TCGCATTGCGATTTTTGAAAA
1 TCGCATTGCGA-TTTTGAAAA
* * **
224326 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTG-AAAA
*
224347 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
224368 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
224384 GGAACTGATT
Statistics
Matches: 62, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
20 15 0.24
21 47 0.76
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:224378 original size:42 final size:41
Alignment explanation
Indices: 224285--224383 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 41
224275 ATTTATGTGT
*
224285 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTTGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTTCAAAA
** *
224326 TCGCAATGCGAATTTG-TACTATCGCATTGCGA-TTTTCAAGAA
1 TCGCGTTGCGATTTTGATA-T-TCGCATTGCGATTTTTCAA-AA
224368 TCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTG
224384 GGAACTGATT
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
40 2 0.04
41 20 0.42
42 26 0.54
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTTCAAAA
Found at i:225658 original size:31 final size:33
Alignment explanation
Indices: 225623--225692 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
225613 TTTAAAACTA
*
225623 ATTTATTATTTAT-ATTTTA-ATAATATTTTAT-
1 ATTTATTATTAATAATTTTAGA-AATATTTTATC
*
225654 ATTTATTATTAATAATTTTAGAATTATTTTATC
1 ATTTATTATTAATAATTTTAGAAATATTTTATC
225687 ATTTAT
1 ATTTAT
225693 ATTCTAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 12 0.35
32 15 0.44
33 7 0.21
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (33 bp):
ATTTATTATTAATAATTTTAGAAATATTTTATC
Found at i:225666 original size:20 final size:19
Alignment explanation
Indices: 225631--225673 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
225621 TAATTTATTA
225631 TTTATATTTTAATAAT-AT
1 TTTATATTTTAATAATAAT
*
225649 TTTATATTTATTATTAATAAT
1 TTTATA-TT-TTAATAATAAT
225670 TTTA
1 TTTA
225674 GAATTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 6 0.29
19 2 0.10
20 7 0.33
21 6 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTATATTTTAATAATAAT
Found at i:225680 original size:21 final size:20
Alignment explanation
Indices: 225643--225681 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
225633 TATATTTTAA
* *
225643 TAATATTTTATATTTATTAT
1 TAATATTTTAGAATTATTAT
225663 TAATAATTTTAGAATTATT
1 TAAT-ATTTTAGAATTATT
225682 TTATCATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TAATATTTTAGAATTATTAT
Found at i:225685 original size:23 final size:21
Alignment explanation
Indices: 225635--225685 Score: 50
Period size: 20 Copynumber: 2.4 Consensus size: 21
225625 TTATTATTTA
* *
225635 TATTTTAATAATATTTTATAT
1 TATTTTATTAATATTTTAAAT
*
225656 T-TATTATTAATAATTTTAGAAT
1 TATTTTATTAAT-ATTTTA-AAT
225678 TATTTTAT
1 TATTTTAT
225686 CATTTATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
20 8 0.35
21 7 0.30
22 3 0.13
23 5 0.22
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TATTTTATTAATATTTTAAAT
Found at i:226215 original size:15 final size:15
Alignment explanation
Indices: 226195--226223 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
226185 TGACAACGCC
226195 TGTACGCGCTGCAGT
1 TGTACGCGCTGCAGT
226210 TGTACGCGCTGCAG
1 TGTACGCGCTGCAG
226224 AGGAATGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.28, G:0.34, T:0.24
Consensus pattern (15 bp):
TGTACGCGCTGCAGT
Found at i:228413 original size:16 final size:16
Alignment explanation
Indices: 228388--228420 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
228378 TAATAAATAA
228388 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
228404 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
228420 A
1 A
228421 AAATTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:228511 original size:16 final size:16
Alignment explanation
Indices: 228490--228559 Score: 122
Period size: 16 Copynumber: 4.4 Consensus size: 16
228480 TAATAAATAA
228490 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
228506 ACGAACATAAACAAAC
1 ACGAACATAAACGAAC
*
228522 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
228538 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
228554 ACGAAC
1 ACGAAC
228560 GTTGGAGACC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.57, C:0.24, G:0.11, T:0.07
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:229315 original size:10 final size:10
Alignment explanation
Indices: 229300--229361 Score: 52
Period size: 10 Copynumber: 5.4 Consensus size: 10
229290 ATAAATGAAT
229300 GAACATAAAC
1 GAACATAAAC
229310 GAACATAATCGAAC
1 GAACAT-A---AAC
229324 GAACATAAAC
1 GAACATAAAC
229334 GAACATAACCAAAC
1 GAACAT----AAAC
229348 GAACATAAAC
1 GAACATAAAC
229358 GAAC
1 GAAC
229362 GTTCACGAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
10 23 0.52
11 1 0.02
13 1 0.02
14 19 0.43
ACGTcount: A:0.56, C:0.23, G:0.11, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:229324 original size:14 final size:13
Alignment explanation
Indices: 229307--229362 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 13
229297 AATGAACATA
229307 AACGAACATAATCG
1 AACGAACATAA-CG
229321 AACGAACAT-A--
1 AACGAACATAACG
*
229331 AACGAACATAACCA
1 AACGAACATAA-CG
229345 AACGAACATAAACG
1 AACGAACAT-AACG
229359 AACG
1 AACG
229363 TTCACGAACG
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
10 9 0.25
11 1 0.03
13 1 0.03
14 23 0.64
15 2 0.06
ACGTcount: A:0.55, C:0.23, G:0.12, T:0.09
Consensus pattern (13 bp):
AACGAACATAACG
Found at i:229327 original size:24 final size:24
Alignment explanation
Indices: 229287--229361 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 24
229277 GATTGGGTTA
*
229287 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
229311 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* *
229335 AACATAACCAAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
229359 AAC
1 AAC
229362 GTTCACGAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 3 0.06
24 44 0.94
ACGTcount: A:0.57, C:0.20, G:0.11, T:0.12
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:230266 original size:37 final size:38
Alignment explanation
Indices: 230193--230276 Score: 127
Period size: 37 Copynumber: 2.2 Consensus size: 38
230183 GTGCAAAATA
230193 TTTTTAGGATGAATATATATATATATTAATAATATAAC
1 TTTTTAGGATGAATATATATATATATTAATAATATAAC
* *
230231 TTTTTTAGGATG-A-ATATGTATGTATTAATAATATAAC
1 -TTTTTAGGATGAATATATATATATATTAATAATATAAC
230268 TTTTTAGGA
1 TTTTTAGGA
230277 CACTATAAGT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
36 9 0.21
37 22 0.51
38 1 0.02
39 11 0.26
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.46
Consensus pattern (38 bp):
TTTTTAGGATGAATATATATATATATTAATAATATAAC
Found at i:236556 original size:2 final size:2
Alignment explanation
Indices: 236549--236610 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
236539 TATTCTCAAG
236549 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
236591 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
236611 CTTAAATGAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:237746 original size:27 final size:23
Alignment explanation
Indices: 237693--237739 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
237683 ATCTAGTTAC
237693 TGTTGGAAAAGTAATTGAATGAA
1 TGTTGGAAAAGTAATTGAATGAA
237716 TGTTGGAAAAGTAATTGAATGAA
1 TGTTGGAAAAGTAATTGAATGAA
237739 T
1 T
237740 TAATGTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.26, T:0.32
Consensus pattern (23 bp):
TGTTGGAAAAGTAATTGAATGAA
Found at i:252176 original size:23 final size:23
Alignment explanation
Indices: 252123--252178 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
252113 CGGTCAACAT
* * *
252123 GACCCGATCCGCCTGTCCGACCT
1 GACCCGACCCGCCTGTCCAACCC
252146 GACCCGACCCGCCTGTCCAACCC
1 GACCCGACCCGCCTGTCCAACCC
*
252169 GACTCGACCC
1 GACCCGACCC
252179 ACTTGTTCCG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.16, C:0.52, G:0.20, T:0.12
Consensus pattern (23 bp):
GACCCGACCCGCCTGTCCAACCC
Found at i:257787 original size:43 final size:43
Alignment explanation
Indices: 257721--257827 Score: 153
Period size: 43 Copynumber: 2.5 Consensus size: 43
257711 CCGGGATCCG
* *
257721 ACCAACTGACCCGACTCGACCTGACCCGGTCCGAACCCACCCT
1 ACCAGCTGACCCGACTAGACCTGACCCGGTCCGAACCCACCCT
* *
257764 ACCAGCTGACCCGACTAGACCTGATCCGGTCCGACCCCACCCT
1 ACCAGCTGACCCGACTAGACCTGACCCGGTCCGAACCCACCCT
*
257807 ACCAGACTG-CCCGACTTGACC
1 ACCAG-CTGACCCGACTAGACC
257828 CGATCTGACC
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
43 55 0.95
44 3 0.05
ACGTcount: A:0.22, C:0.47, G:0.18, T:0.13
Consensus pattern (43 bp):
ACCAGCTGACCCGACTAGACCTGACCCGGTCCGAACCCACCCT
Found at i:259409 original size:24 final size:24
Alignment explanation
Indices: 259367--259434 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
259357 TTTATTTGAT
* * *
259367 TTCTGTTATGATTTTTGATCCAGA
1 TTCTATTATGATATCTGATCCAGA
***
259391 TTCTATTATGATATCTGATATGGA
1 TTCTATTATGATATCTGATCCAGA
259415 TTC-AGTTATGATATCTGATC
1 TTCTA-TTATGATATCTGATC
259435 TGAATTCTGT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
23 1 0.03
24 35 0.97
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.47
Consensus pattern (24 bp):
TTCTATTATGATATCTGATCCAGA
Found at i:259441 original size:24 final size:24
Alignment explanation
Indices: 259396--259441 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
259386 CCAGATTCTA
*
259396 TTATGATATCTGATATGGATTCAG
1 TTATGATATCTGATATGAATTCAG
*
259420 TTATGATATCTGATCTGAATTC
1 TTATGATATCTGATATGAATTC
259442 TGTTCTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.43
Consensus pattern (24 bp):
TTATGATATCTGATATGAATTCAG
Found at i:259581 original size:30 final size:30
Alignment explanation
Indices: 259542--259615 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 30
259532 TAAGGCGACC
*
259542 CTTGGGTAGGCTCTACGGCCTTGAG-ATTTT
1 CTTGGGTAGGCTCT-CGGCCATGAGAATTTT
* *
259572 CTTGTGTAGGCCTCTTGGCCATGAGAATTTT
1 CTTGGGTAGG-CTCTCGGCCATGAGAATTTT
259603 CTTGGGTAGGCTC
1 CTTGGGTAGGCTC
259616 GTAGAGCCCA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 20 0.53
31 18 0.47
ACGTcount: A:0.14, C:0.20, G:0.30, T:0.36
Consensus pattern (30 bp):
CTTGGGTAGGCTCTCGGCCATGAGAATTTT
Found at i:260134 original size:27 final size:26
Alignment explanation
Indices: 260083--260134 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
260073 AGTTGTATTT
*
260083 TGTTTCATATTCGAGTCTGAAAAATC
1 TGTTTCATATTCGAATCTGAAAAATC
*
260109 TGTTTCAT-TTCTGAATACTGATAAAT
1 TGTTTCATATTC-GAAT-CTGAAAAAT
260135 TTTATTTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 3 0.14
26 11 0.50
27 8 0.36
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.42
Consensus pattern (26 bp):
TGTTTCATATTCGAATCTGAAAAATC
Found at i:262351 original size:27 final size:28
Alignment explanation
Indices: 262300--262356 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 28
262290 TACGATAATG
262300 CCCTTAAAGTGTAAAATGACCTAAA-TA
1 CCCTTAAAGTGTAAAATGACCTAAAGTA
* *
262327 CCCTTAAAGTGTAAAATGGCTTAAAGTA
1 CCCTTAAAGTGTAAAATGACCTAAAGTA
262355 CC
1 CC
262357 TCTAAACCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.26
Consensus pattern (28 bp):
CCCTTAAAGTGTAAAATGACCTAAAGTA
Found at i:263219 original size:24 final size:24
Alignment explanation
Indices: 263177--263240 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
263167 TTTATCTGAT
* *
263177 TTCTGTTATGATTTTTGAT-TCAGA
1 TTCTGTTATGATATCTGATAT-AGA
* *
263201 TTCTATTATGATATCTGATATGGA
1 TTCTGTTATGATATCTGATATAGA
263225 TTCTGTTATGATATCT
1 TTCTGTTATGATATCT
263241 CATCTGAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 33 0.97
25 1 0.03
ACGTcount: A:0.23, C:0.09, G:0.16, T:0.52
Consensus pattern (24 bp):
TTCTGTTATGATATCTGATATAGA
Found at i:263251 original size:24 final size:24
Alignment explanation
Indices: 263200--263260 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
263190 TTTGATTCAG
* * *
263200 ATTCTATTATGATATCTGATATGG
1 ATTCTGTTATGATATCTCATATGA
*
263224 ATTCTGTTATGATATCTCATCTGA
1 ATTCTGTTATGATATCTCATATGA
*
263248 ATTCTGTTCTGAT
1 ATTCTGTTATGAT
263261 TTCTAATTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.48
Consensus pattern (24 bp):
ATTCTGTTATGATATCTCATATGA
Found at i:263484 original size:32 final size:31
Alignment explanation
Indices: 263419--263484 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
263409 GGCTCTGCAA
* *
263419 CCCTGAGATTTTCTTGGGTAGGCCTCCGTGG
1 CCCTGAGATTTTCTTAGGTAGGCCTCAGTGG
263450 CCCTGAGAATTTTCTTAGGTAGGCTCTCAG-GG
1 CCCTGAG-ATTTTCTTAGGTAGGC-CTCAGTGG
263482 CCC
1 CCC
263485 AAGGCACTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 7 0.23
32 20 0.65
33 4 0.13
ACGTcount: A:0.14, C:0.27, G:0.29, T:0.30
Consensus pattern (31 bp):
CCCTGAGATTTTCTTAGGTAGGCCTCAGTGG
Found at i:265326 original size:15 final size:15
Alignment explanation
Indices: 265306--265337 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
265296 AGTTTACAAC
265306 TTTGCCATTATAAAG
1 TTTGCCATTATAAAG
*
265321 TTTGCCCTTATAAAG
1 TTTGCCATTATAAAG
265336 TT
1 TT
265338 CAAAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (15 bp):
TTTGCCATTATAAAG
Found at i:268927 original size:18 final size:18
Alignment explanation
Indices: 268903--268956 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
268893 AGGGTGAAAC
268903 TATAAAAGTGTTTATAAAA
1 TATAAAAGTGTTTA-AAAA
* *
268922 -ATAAAATTAACTTTAAAAA
1 TATAAAAGT--GTTTAAAAA
268941 TATAAAAGTGTTTAAA
1 TATAAAAGTGTTTAAA
268957 TTAAAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
18 13 0.46
19 4 0.14
20 11 0.39
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (18 bp):
TATAAAAGTGTTTAAAAA
Found at i:270781 original size:30 final size:30
Alignment explanation
Indices: 270733--270802 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
270723 TAAGAGTTAG
*
270733 ATTAGTATTTTATATAAATTT-TAAGGTCAA
1 ATTAATATTTTATATAAATTTAT-AGGTCAA
* *
270763 ATTAATATTTTGTCTAAATTTATAGGTCAA
1 ATTAATATTTTATATAAATTTATAGGTCAA
*
270793 ATTAAAATTT
1 ATTAATATTT
270803 AACCATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 34 0.97
31 1 0.03
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (30 bp):
ATTAATATTTTATATAAATTTATAGGTCAA
Found at i:273476 original size:76 final size:76
Alignment explanation
Indices: 273350--273501 Score: 295
Period size: 76 Copynumber: 2.0 Consensus size: 76
273340 ATTTCTGAAA
273350 ATTGTTGTCTTTTTTGTGCATATATTTGATAATTCACATGAGCTTCTGTGTGTGCTTATAAAGAG
1 ATTGTTGTCTTTTTTGTGCATATATTTGATAATTCACATGAGCTTCTGTGTGTGCTTATAAAGAG
273415 TTAGCTTGGTT
66 TTAGCTTGGTT
*
273426 ATTGTTGTCTTTTTTGTGCATATATTTGATAATTCACATGAGCTTCTGTGTGTGTTTATAAAGAG
1 ATTGTTGTCTTTTTTGTGCATATATTTGATAATTCACATGAGCTTCTGTGTGTGCTTATAAAGAG
273491 TTAGCTTGGTT
66 TTAGCTTGGTT
273502 TTGCATGTTT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.48
Consensus pattern (76 bp):
ATTGTTGTCTTTTTTGTGCATATATTTGATAATTCACATGAGCTTCTGTGTGTGCTTATAAAGAG
TTAGCTTGGTT
Found at i:276762 original size:35 final size:35
Alignment explanation
Indices: 276716--276827 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
276706 AAAACAGTCC
* * *
276716 TCAATTTCATTCTAAACCCCAATTTTCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
276751 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
** * *
276786 TCAATTAAATTCTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
276821 TCAATTT
1 TCAATTT
276828 AAGGTTTAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 67 1.00
ACGTcount: A:0.41, C:0.22, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:278203 original size:35 final size:35
Alignment explanation
Indices: 278163--278274 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 35
278153 TCTAACCCTT
* * *
278163 AAATTGAAGTATTTTAGAATTTGGGGTTTAGAATT
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
* *
278198 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
* *
278233 AAATTGAATTACTTTGGAAATTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
278268 AAATTGA
1 AAATTGA
278275 GGACTGTTTT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.35, C:0.01, G:0.23, T:0.41
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
Found at i:279496 original size:29 final size:29
Alignment explanation
Indices: 279454--279512 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
279444 ATATTCACCT
279454 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
279483 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
279512 A
1 A
279513 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:285780 original size:14 final size:14
Alignment explanation
Indices: 285761--285787 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
285751 CAATGGATTG
285761 CTTGGTACTATTTT
1 CTTGGTACTATTTT
285775 CTTGGTACTATTT
1 CTTGGTACTATTT
285788 GTCGTCAGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (14 bp):
CTTGGTACTATTTT
Found at i:287153 original size:18 final size:19
Alignment explanation
Indices: 287111--287153 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
287101 AAAATAAAAA
*
287111 GACTGAATTAAATGGAAAG
1 GACTGGATTAAATGGAAAG
*
287130 CA-TGGATTAAAT-GAAAG
1 GACTGGATTAAATGGAAAG
287147 GACTGGA
1 GACTGGA
287154 ATACCCTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
17 6 0.30
18 13 0.65
19 1 0.05
ACGTcount: A:0.44, C:0.07, G:0.28, T:0.21
Consensus pattern (19 bp):
GACTGGATTAAATGGAAAG
Found at i:287177 original size:27 final size:27
Alignment explanation
Indices: 287147--287213 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
287137 TAAATGAAAG
* *
287147 GACTGGAATACCCTTGAAC-TCTAAAAT
1 GACTGAAATACCCTTAAACAT-TAAAAT
*
287174 GACTAAAATACCCTTAAACATTAAAAT
1 GACTGAAATACCCTTAAACATTAAAAT
287201 GACTGAAATACCC
1 GACTGAAATACCC
287214 CGAGCTTCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 34 0.97
28 1 0.03
ACGTcount: A:0.43, C:0.22, G:0.10, T:0.24
Consensus pattern (27 bp):
GACTGAAATACCCTTAAACATTAAAAT
Found at i:288333 original size:39 final size:39
Alignment explanation
Indices: 288246--288323 Score: 115
Period size: 39 Copynumber: 2.0 Consensus size: 39
288236 ACACTAAGAC
*
288246 TAGGGTAAGTCCTTATCTCTAGATCCTTTGCTTTGTGCA
1 TAGGGTAAGTCCTTATCTCTAGATCCTTTGCATTGTGCA
288285 TAGGGTAAGTCCTTA-C-CGTAGACTCCTTTGCATTGTGCA
1 TAGGGTAAGTCCTTATCTC-TAGA-TCCTTTGCATTGTGCA
288324 CTTGGTAAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
37 1 0.03
38 5 0.14
39 30 0.83
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (39 bp):
TAGGGTAAGTCCTTATCTCTAGATCCTTTGCATTGTGCA
Found at i:288606 original size:17 final size:16
Alignment explanation
Indices: 288565--288610 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 16
288555 TAGAGGGTAT
288565 TACTATTG-TTTTAAA
1 TACTATTGTTTTTAAA
*
288580 -AATA-TGTTTTTAAA
1 TACTATTGTTTTTAAA
288594 CTACTATTGTTTTTAAA
1 -TACTATTGTTTTTAAA
288611 AGATTTGTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 2 0.08
14 10 0.40
16 3 0.12
17 10 0.40
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.52
Consensus pattern (16 bp):
TACTATTGTTTTTAAA
Found at i:291705 original size:40 final size:39
Alignment explanation
Indices: 291661--291776 Score: 153
Period size: 39 Copynumber: 2.9 Consensus size: 39
291651 TACACTAAAA
* *
291661 AATAAAAAACTCTCCATCTTCCAAGA-ACTCTTAAATTCAC
1 AATAAAAAACTCT--AACTCCCAAGAGACTCTTAAATTCAC
* * *
291701 AATAAAATACTCTAACTCCCAAGAGAGTCTTAATTTCAC
1 AATAAAAAACTCTAACTCCCAAGAGACTCTTAAATTCAC
*
291740 AATAAAACACTCTAACTCCCAAGAGACTCTTAAATTC
1 AATAAAAAACTCTAACTCCCAAGAGACTCTTAAATTC
291777 CTCCCATTAA
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
38 9 0.13
39 46 0.69
40 12 0.18
ACGTcount: A:0.42, C:0.26, G:0.05, T:0.27
Consensus pattern (39 bp):
AATAAAAAACTCTAACTCCCAAGAGACTCTTAAATTCAC
Found at i:291740 original size:39 final size:39
Alignment explanation
Indices: 291681--291776 Score: 158
Period size: 39 Copynumber: 2.5 Consensus size: 39
291671 TCTCCATCTT
*
291681 CCAAGA-ACTCTTAAATTCACAATAAAATACTCTAACTC
1 CCAAGAGACTCTTAAATTCACAATAAAACACTCTAACTC
* *
291719 CCAAGAGAGTCTTAATTTCACAATAAAACACTCTAACTC
1 CCAAGAGACTCTTAAATTCACAATAAAACACTCTAACTC
291758 CCAAGAGACTCTTAAATTC
1 CCAAGAGACTCTTAAATTC
291777 CTCCCATTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
38 6 0.12
39 46 0.88
ACGTcount: A:0.42, C:0.26, G:0.06, T:0.26
Consensus pattern (39 bp):
CCAAGAGACTCTTAAATTCACAATAAAACACTCTAACTC
Found at i:296791 original size:32 final size:32
Alignment explanation
Indices: 296703--296792 Score: 85
Period size: 32 Copynumber: 2.8 Consensus size: 32
296693 TAAAGTATTT
* *
296703 CCTTGAGTAGGCTCAAAGGCCCCAAGGTATCC
1 CCTTTAGTAGGCTCTAAGGCCCCAAGGTATCC
* **
296735 CCTTTAGTAGGCTCTTAGAACCCAAGGTA--C
1 CCTTTAGTAGGCTCTAAGGCCCCAAGGTATCC
* *
296765 ACTCTTAGGTAGGCTCTCAGGCCCCAAG
1 CCT-TTA-GTAGGCTCTAAGGCCCCAAG
296793 ATAATCCCTT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
30 3 0.06
31 3 0.06
32 41 0.87
ACGTcount: A:0.24, C:0.30, G:0.23, T:0.22
Consensus pattern (32 bp):
CCTTTAGTAGGCTCTAAGGCCCCAAGGTATCC
Found at i:301357 original size:21 final size:20
Alignment explanation
Indices: 301320--301367 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
301310 TATATTTTAA
* *
301320 TAATATTTTATATTTATTAT
1 TAATATTTTAGAATTATTAT
301340 TAATAATTTTAGAATTATT-T
1 TAAT-ATTTTAGAATTATTAT
*
301360 TATTATTT
1 TAATATTT
301368 ATATTCTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 4 0.17
20 8 0.33
21 12 0.50
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TAATATTTTAGAATTATTAT
Found at i:301362 original size:23 final size:21
Alignment explanation
Indices: 301312--301364 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
301302 TTCTTATTTA
* *
301312 TATTTTAATAATATTTTATAT
1 TATTTTATTAATATTTTAAAT
*
301333 T-TATTATTAATAATTTTAGAAT
1 TATTTTATTAAT-ATTTTA-AAT
301355 TATTTTATTA
1 TATTTTATTA
301365 TTTATATTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 8 0.32
21 7 0.28
22 3 0.12
23 7 0.28
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TATTTTATTAATATTTTAAAT
Found at i:305122 original size:15 final size:15
Alignment explanation
Indices: 305102--305131 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
305092 TGTCAAAGTT
305102 AGTAGATCACGTGAA
1 AGTAGATCACGTGAA
*
305117 AGTAGATCATGTGAA
1 AGTAGATCACGTGAA
305132 CATATTGATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.27, T:0.23
Consensus pattern (15 bp):
AGTAGATCACGTGAA
Found at i:309101 original size:2 final size:2
Alignment explanation
Indices: 309089--309120 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
309079 TTAACCGAAA
309089 AT AT A- AT AT AT AT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
309121 TACTTAGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:309107 original size:13 final size:13
Alignment explanation
Indices: 309089--309119 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
309079 TTAACCGAAA
309089 ATATAATATATAT
1 ATATAATATATAT
309102 ATATAATATATAT
1 ATATAATATATAT
309115 ATATA
1 ATATA
309120 TTACTTAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATATAATATATAT
Found at i:310884 original size:3 final size:3
Alignment explanation
Indices: 310872--310912 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
310862 ATTTTGTTAA
310872 TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
310913 TCTTTCTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:312209 original size:45 final size:46
Alignment explanation
Indices: 312121--312211 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 46
312111 TTGAAAAAGC
* *
312121 CTGAGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
312167 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
312212 TTCGATGTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 22 0.51
46 21 0.49
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
Found at i:314997 original size:44 final size:43
Alignment explanation
Indices: 314898--314998 Score: 98
Period size: 44 Copynumber: 2.3 Consensus size: 43
314888 GCATGGTCTT
* * *
314898 GTGCATCGATGCACCTTCAAGGCGTGCATCGGTGCATCTTCAT
1 GTGCATCGATGCACATTCAAGGCGTGCATCGATGCATCTTCAA
* * *
314941 GATGAATTGATGCACATTCAAAGG-GATGCATCGATGCA-CTGTTAA
1 G-TGCATCGATGCACATTC-AAGGCG-TGCATCGATGCATCT-TCAA
314986 GTGCATCGATGCA
1 GTGCATCGATGCA
314999 TGAAGCACAA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
43 1 0.02
44 27 0.59
45 18 0.39
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.27
Consensus pattern (43 bp):
GTGCATCGATGCACATTCAAGGCGTGCATCGATGCATCTTCAA
Found at i:320160 original size:21 final size:22
Alignment explanation
Indices: 320128--320169 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
320118 CGAAGGACCG
320128 CGTAGAAATGCACCGAAGTGCA
1 CGTAGAAATGCACCGAAGTGCA
*
320150 CGTAG-AATGCACCGTAGTGC
1 CGTAGAAATGCACCGAAGTGC
320170 CATATAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.31, C:0.24, G:0.29, T:0.17
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCA
Found at i:323622 original size:65 final size:65
Alignment explanation
Indices: 323500--323625 Score: 155
Period size: 65 Copynumber: 1.9 Consensus size: 65
323490 TGCACTAAGA
** * *
323500 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAGCATAAGTGCATCTATGCATGGTCTT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAAAAGAATAAGTGCATCGATGCATGGTCTT
* * ** *
323565 GTGCATCGATGCATAAAATTCATTCGATG-TTCAAAATAATAATTGGTTCATCGATGCATGG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAA-AAGAATAAGTGCATCGATGCATGG
323626 ATTGGTGCGT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
64 5 0.10
65 46 0.90
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.33
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAAAAGAATAAGTGCATCGATGCATGGTCTT
Found at i:327191 original size:3 final size:3
Alignment explanation
Indices: 327144--327226 Score: 60
Period size: 3 Copynumber: 26.7 Consensus size: 3
327134 GGATAAAAAA
* * * * *
327144 TAT TAT AAT TAT TAA TAT TAA TAT TAA TAT TAA TAT TGA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT
* *
327189 TAT TATT TATT TAT TAT TAA TAT TAAT TAG TAT TAT TA
1 TAT TA-T TA-T TAT TAT TAT TAT T-AT TAT TAT TAT TA
327227 CACTGTTTTG
Statistics
Matches: 62, Mismatches: 14, Indels: 8
0.74 0.17 0.10
Matches are distributed among these distances:
2 1 0.02
3 50 0.81
4 11 0.18
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:327223 original size:6 final size:6
Alignment explanation
Indices: 327153--327215 Score: 72
Period size: 6 Copynumber: 10.2 Consensus size: 6
327143 ATATTATAAT
* * * *
327153 TATTAA TATTAA TATTAA TATTAA TATTGA TATTAT TATTATT TATTTAT
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTA-A TA-TTAA
327203 TATTAA TATTAA T
1 TATTAA TATTAA T
327216 TAGTATTATT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
6 42 0.82
7 6 0.12
8 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (6 bp):
TATTAA
Found at i:330985 original size:13 final size:14
Alignment explanation
Indices: 330958--330990 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
330948 TTTTTTCATC
330958 TTTTAAAATTATAT
1 TTTTAAAATTATAT
330972 TTTTAAAATGTAT-T
1 TTTTAAAAT-TATAT
330986 TTTTA
1 TTTTA
330991 GGTAATCGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 15 0.83
15 3 0.17
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (14 bp):
TTTTAAAATTATAT
Found at i:333652 original size:78 final size:78
Alignment explanation
Indices: 333554--333780 Score: 327
Period size: 78 Copynumber: 2.9 Consensus size: 78
333544 AGATAGTAAG
*
333554 TAAACATTAAAAGAATGTAATTTTGATTATAACTCTTTTAATTGATATCTAATTCGGAATAATTA
1 TAAACATT-AAAGATTGTAATTTTGATTATAACTCTTTTAATTGATATCTAATTCGGAATAATTA
333619 AATAAGATTTTAAA
65 AATAAGATTTTAAA
333633 TAAGA-ATTAAAGATTGTAATTTTGATTATAACTCTTTTAATTGATATCTAATTCGGAATAATTA
1 TAA-ACATTAAAGATTGTAATTTTGATTATAACTCTTTTAATTGATATCTAATTCGGAATAATTA
333697 AATAAGATTTTAAA
65 AATAAGATTTTAAA
** * * * *
333711 TAAACATTAAAGATTGTAATTCAGATTACAATTC-TTTAA-TGTATATTTAATT-TGAATTAATT
1 TAAACATTAAAGATTGTAATTTTGATTATAACTCTTTTAATTG-ATATCTAATTCGGAA-TAATT
333773 AAATAAGA
64 AAATAAGA
333781 AATTTATTAA
Statistics
Matches: 137, Mismatches: 7, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
76 5 0.04
77 28 0.20
78 97 0.71
79 6 0.04
80 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (78 bp):
TAAACATTAAAGATTGTAATTTTGATTATAACTCTTTTAATTGATATCTAATTCGGAATAATTAA
ATAAGATTTTAAA
Found at i:338253 original size:22 final size:22
Alignment explanation
Indices: 338211--338253 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
338201 GAGTAGTTAA
* *
338211 CTTGTTTTATATTCATTAAACT
1 CTTGTTGTATATTCATGAAACT
338233 CTTGTTGTATGATT-ATGAAAC
1 CTTGTTGTAT-ATTCATGAAAC
338254 CTAGAAAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.49
Consensus pattern (22 bp):
CTTGTTGTATATTCATGAAACT
Done.