Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008062.1 Hibiscus syriacus cultivar Beakdansim tig00110557_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: 2089609
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:427211 original size:38 final size:36
Alignment explanation
Indices: 427135--427211 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
427125 GTGCTCACCA
* * *
427135 TTGTCTCTCTTGAGACAGGTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAAGTTCACTTGAAAAAAACT
*
427171 TTGTCTCTCTTGAGACAATTTCACTTGGAAAAAAACCT
1 TTGTCTCTCTTGAGACAAGTTCACTT-GAAAAAAA-CT
427209 TTG
1 TTG
427212 AAATTGTTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 23 0.66
37 7 0.20
38 5 0.14
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAAGTTCACTTGAAAAAAACT
Found at i:427453 original size:37 final size:37
Alignment explanation
Indices: 427383--427454 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
427373 TGGAAGTAAG
* * *
427383 TTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAAAA
* *
427420 TTTTGTCTCCCTTGAGACCGTTTCTCATGAAACAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAA
427455 CAGATATCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (37 bp):
TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAAAA
Found at i:428157 original size:106 final size:106
Alignment explanation
Indices: 428032--428620 Score: 854
Period size: 106 Copynumber: 5.5 Consensus size: 106
428022 GCGCCACCCG
* *
428032 AGACAACACAAGTTTAACTTCACAACGAAGGGACGGATGGTTGTCAACAAACAACTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTT
428097 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
* *** *
428138 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACCACTTTTTAGTTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCA--AT
* * *
428203 CATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACCCG
64 --TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
* * * * * *
428248 GGATAACACAAGTTCAATTTCACAACGAAGGGACGGCTGGTTGTCAATAAATAATTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTT
* * *
428313 TAGAGTCAATTTCAACTTCACAGCGAAGGATTTTGGACTCA
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
* *
428354 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAAACAATTTCCCAGTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AAACAACTTCCCAATT
* *
428419 TCAGAGCCAATTTCAACTTCACAGCGAAGAATATTGAACTCA
65 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
* * * **
428461 AGACAACACAAGTTCAACTTCACAACGAAGGAACGGTTGGTTGTCAACAAACCACTTTTCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
428526 CAAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCA
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
*
428567 AGACAACACAAGTTCAACTTCACAACGAAGAGACGGCTGGTTGTCAACAAACAA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA
428621 TTTTAACTTC
Statistics
Matches: 425, Mismatches: 53, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
106 235 0.55
107 97 0.23
108 2 0.00
110 91 0.21
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (106 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTT
CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
Found at i:428555 original size:213 final size:211
Alignment explanation
Indices: 428032--428857 Score: 971
Period size: 213 Copynumber: 4.0 Consensus size: 211
428022 GCGCCACCCG
* * * *
428032 AGACAACACAAGTTTAACTTCACAACGAAGGGACGGATGGTTGTCAACAAACAACTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTT
*
428097 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACA
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACA
* **
428162 ACGAAGGGACGGCTGGTTGTCAACAAACCACTTTTTAGTTTCATTCAGAGCCAATTTCAACTTCA
131 ACGAAGGGACGGCTGGTTGTCAACAAA-CAATTTCCAG--T--TTCAGAGCCAATTTCAACTTCA
* *
428227 CAGCGAAGGATATT-AGACCCG
191 CAGCGAAGGATATTGA-ACTCA
* * * *
428248 GGATAACACAAGTTCAATTTCACAACGAAGGGACGGCTGGTTGTCAATAAATAATTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTT
* * * *
428313 TAGAGTCAATTTCAACTTCACAGCGAAGGATTTTGGACTCAAGACAACACAAGTTCAACTTCACA
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACA
428378 ACGAAGGGACGGCTGGTTGTCAACAAAACAATTTCCCAGTTTCAGAGCCAATTTCAACTTCACAG
131 ACGAAGGGACGGCTGGTTGTCAAC-AAACAATTT-CCAGTTTCAGAGCCAATTTCAACTTCACAG
*
428443 CGAAGAATATTGAACTCA
194 CGAAGGATATTGAACTCA
* * * * *
428461 AGACAACACAAGTTCAACTTCACAACGAAGGAACGGTTGGTTGTCAACAAACCACTTT-TCAATT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAA-TAATTTCCCAATT
*
428525 TCAAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCAC
65 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCAC
*
428590 AACGAAGAGACGGCTGGTTGTCAACAAAC-A-----A---T---------TTT-AACTTCACAGC
130 AACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCAGTTTCAGAGCCAATTTCAACTTCACAGC
*
428636 GAAGGATATTGGACTCA
195 GAAGGATATTGAACTCA
* * * *
428653 AGACGACACAAGTTCAAATTCACAACGAAGGGACGGCTGGTTGTCAATAAATAATTTCTCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTT
* * * *
428718 CAGAGCCAATTTCAACTTCA-AAGCGAAGGATATTGAACTCGAGATAACACAAGCTCAACTTCAC
66 CAGAGCCAATTTCAACTTCACAA-CGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCAC
* * * * * * * *
428782 -AGGAAAGGGCCGACCGGCTGTCAACAAACAATTTCCCAGTTCCGGAGCCAATTTCAGCTTCAC-
130 AACG-AAGGGACGGCTGGTTGTCAACAAACAATTT-CCAGTTTCAGAGCCAATTTCAACTTCACA
*
428845 GACGGAGGATATT
193 G-CGAAGGATATT
428858 TGACTCGGAA
Statistics
Matches: 527, Mismatches: 55, Indels: 60
0.82 0.09 0.09
Matches are distributed among these distances:
191 8 0.02
192 155 0.29
193 4 0.01
199 1 0.00
202 1 0.00
205 1 0.00
211 5 0.01
212 21 0.04
213 172 0.33
214 5 0.01
215 1 0.00
216 148 0.28
217 5 0.01
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (211 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTT
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACA
ACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCAGTTTCAGAGCCAATTTCAACTTCACAGCG
AAGGATATTGAACTCA
Found at i:428675 original size:43 final size:42
Alignment explanation
Indices: 428536--428683 Score: 147
Period size: 43 Copynumber: 3.5 Consensus size: 42
428526 CAAAGCCAAT
428536 TTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCAAGAC-ACACAAG
*** ** * *
428579 TTCAACTTCACAACGAAGAGACGGCTGGTTGTC-A-ACAAACAAT
1 TTCAACTTCACAACGAAG-GA-TATTGG-ACTCAAGACACACAAG
* *
428622 TTTAACTTCACAGCGAAGGATATTGGACTCAAGACGACACAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCAAGAC-ACACAAG
*
428665 TTCAAATTCACAACGAAGG
1 TTCAACTTCACAACGAAGG
428684 GACGGCTGGT
Statistics
Matches: 80, Mismatches: 19, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
40 2 0.03
41 4 0.05
42 4 0.05
43 60 0.75
44 4 0.05
45 4 0.05
46 2 0.03
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.20
Consensus pattern (42 bp):
TTCAACTTCACAACGAAGGATATTGGACTCAAGACACACAAG
Found at i:428677 original size:86 final size:86
Alignment explanation
Indices: 428532--428710 Score: 295
Period size: 86 Copynumber: 2.1 Consensus size: 86
428522 ATTTCAAAGC
*
428532 CAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAAATTCACAACGAAG
428597 AGACGGCTGGTTGTCAACAAA
66 AGACGGCTGGTTGTCAACAAA
* * *
428618 CAATTTTAACTTCACAGCGAAGGATATTGGACTCAAGACGACACAAGTTCAAATTCACAACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAAATTCACAACGAAG
* *
428683 GGACGGCTGGTTGTCAATAAA
66 AGACGGCTGGTTGTCAACAAA
*
428704 TAATTTC
1 CAATTTC
428711 TCAATTTCAG
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
86 85 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.22
Consensus pattern (86 bp):
CAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAAATTCACAACGAAG
AGACGGCTGGTTGTCAACAAA
Found at i:428769 original size:192 final size:192
Alignment explanation
Indices: 428426--428782 Score: 547
Period size: 192 Copynumber: 1.9 Consensus size: 192
428416 GTTTCAGAGC
*
428426 CAATTTCAACTTCACAGCGAAGAATATTGAACTCAAGACAACACAAGTTCAACTTCACAACGAAG
1 CAATTTCAACTTCACAGCGAAGAATATTGAACTCAAGACAACACAAGTTCAAATTCACAACGAAG
* *
428491 GAACGGTTGGTTGTCAACAAACCACTTTTCAATTTCAAAGCCAATTTCAACTTCACAACGAAGGA
66 GAACGGCTGGTTGTCAACAAACCAATTTTCAATTTCAAAGCCAATTTCAACTTCACAACGAAGGA
* *
428556 TATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGAGACGGCTGGTTGTCAACAAA
131 TATTGAACTCAAGACAACACAAGCTCAACTTCACAACGAAGAGACGGCTGGTTGTCAACAAA
* * * *
428618 CAATTTTAACTTCACAGCGAAGGATATTGGACTCAAGACGACACAAGTTCAAATTCACAACGAAG
1 CAATTTCAACTTCACAGCGAAGAATATTGAACTCAAGACAACACAAGTTCAAATTCACAACGAAG
* * * *
428683 GGACGGCTGGTTGTCAATAAA-TAATTTCTCAATTTCAGAGCCAATTTCAACTTCA-AAGCGAAG
66 GAACGGCTGGTTGTCAACAAACCAATTT-TCAATTTCAAAGCCAATTTCAACTTCACAA-CGAAG
* *
428746 GATATTGAACTCGAGATAACACAAGCTCAACTTCACA
129 GATATTGAACTCAAGACAACACAAGCTCAACTTCACA
428783 GGAAAGGGCC
Statistics
Matches: 148, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
191 6 0.04
192 142 0.96
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.23
Consensus pattern (192 bp):
CAATTTCAACTTCACAGCGAAGAATATTGAACTCAAGACAACACAAGTTCAAATTCACAACGAAG
GAACGGCTGGTTGTCAACAAACCAATTTTCAATTTCAAAGCCAATTTCAACTTCACAACGAAGGA
TATTGAACTCAAGACAACACAAGCTCAACTTCACAACGAAGAGACGGCTGGTTGTCAACAAA
Found at i:428804 original size:106 final size:106
Alignment explanation
Indices: 428618--428843 Score: 256
Period size: 106 Copynumber: 2.1 Consensus size: 106
428608 TGTCAACAAA
* * * * *
428618 CAATTTTAACTTCACAGCGAAGGATATTGGACTCAAGACGACACAAGTTCAAATTCACAACGAAG
1 CAATTTCAACTTCAAAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAAATTCACAACGAAG
* * * * * * *
428683 GGACGGCTGGTTGTCAATAAATAATTTCTCAATTTCAGAGC
66 GGACGACCGGCTGTCAACAAACAATTTCCCAATTCCAGAGC
* * * *
428724 CAATTTCAACTTCAAAGCGAAGGATATTGAACTCGAGATAACACAAGCTCAACTTCAC-AGGAAA
1 CAATTTCAACTTCAAAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAAATTCACAACG-AA
* * *
428788 GGGCCGACCGGCTGTCAACAAACAATTTCCCAGTTCCGGAGC
65 GGGACGACCGGCTGTCAACAAACAATTTCCCAATTCCAGAGC
*
428830 CAATTTCAGCTTCA
1 CAATTTCAACTTCA
428844 CGACGGAGGA
Statistics
Matches: 99, Mismatches: 20, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
105 2 0.02
106 97 0.98
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (106 bp):
CAATTTCAACTTCAAAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAAATTCACAACGAAG
GGACGACCGGCTGTCAACAAACAATTTCCCAATTCCAGAGC
Found at i:430112 original size:17 final size:18
Alignment explanation
Indices: 430086--430125 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
430076 ATTATATGAA
430086 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
430102 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
430120 TATTAT
1 TATTAT
430126 ACGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:438618 original size:2 final size:2
Alignment explanation
Indices: 438611--438637 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
438601 GATGGTCCTT
438611 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
438638 ATTATCTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:444241 original size:26 final size:27
Alignment explanation
Indices: 444192--444243 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
444182 TAAAAGTTAA
*
444192 TATAAATATTTTTAAAAAAATAATTAG
1 TATAAATATATTTAAAAAAATAATTAG
* *
444219 TATAAATA-ATTTAAAATATTAATTA
1 TATAAATATATTTAAAAAAATAATTA
444244 AATTTTAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (27 bp):
TATAAATATATTTAAAAAAATAATTAG
Found at i:448869 original size:20 final size:20
Alignment explanation
Indices: 448846--448888 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
448836 GTCAAATTCA
448846 CAACACGAA-AGTTAAAATCG
1 CAACACGAATAGTT-AAATCG
*
448866 CAACGCGAATAGTTAAATCG
1 CAACACGAATAGTTAAATCG
448886 CAA
1 CAA
448889 TGATAATATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.47, C:0.21, G:0.16, T:0.16
Consensus pattern (20 bp):
CAACACGAATAGTTAAATCG
Found at i:449026 original size:20 final size:20
Alignment explanation
Indices: 448962--449017 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
448952 TGCGAAAATG
448962 AAATTCGCAACGCGAAAGTC
1 AAATTCGCAACGCGAAAGTC
448982 AAATTCGCAACGCGAAAGTC
1 AAATTCGCAACGCGAAAGTC
449002 AAATTCGCAACGCGAA
1 AAATTCGCAACGCGAA
449018 TAGTTAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.41, C:0.25, G:0.20, T:0.14
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAGTC
Found at i:449088 original size:20 final size:20
Alignment explanation
Indices: 449063--449155 Score: 98
Period size: 20 Copynumber: 4.7 Consensus size: 20
449053 TTTTTCAAAT
449063 TCGCAACGCGAATA-GTTAAA
1 TCGCAACGCGAATATG-TAAA
** *
449083 TCGCAACGATAATATGTAAT
1 TCGCAACGCGAATATGTAAA
* * *
449103 TCTCAATGCGAATAGGTAAA
1 TCGCAACGCGAATATGTAAA
**
449123 TCGCAACGATAATATGTAAA
1 TCGCAACGCGAATATGTAAA
449143 TCGCAACGCGAAT
1 TCGCAACGCGAAT
449156 TCTCCAAATT
Statistics
Matches: 56, Mismatches: 16, Indels: 2
0.76 0.22 0.03
Matches are distributed among these distances:
20 55 0.98
21 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:449115 original size:40 final size:40
Alignment explanation
Indices: 449060--449155 Score: 156
Period size: 40 Copynumber: 2.4 Consensus size: 40
449050 CAATTTTTCA
*
449060 AATTCGCAACGCGAATAGTTAAATCGCAACGATAATATGT
1 AATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGT
* *
449100 AATTCTCAATGCGAATAGGTAAATCGCAACGATAATATGT
1 AATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGT
*
449140 AAATCGCAACGCGAAT
1 AATTCGCAACGCGAAT
449156 TCTCCAAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (40 bp):
AATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGT
Found at i:452462 original size:4 final size:4
Alignment explanation
Indices: 452453--452528 Score: 98
Period size: 4 Copynumber: 19.0 Consensus size: 4
452443 TGACAATCGT
* *
452453 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TTTA TTTA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * *
452501 TTTA TTTA TTTA TATA TATA TTTA TATA
1 TATA TATA TATA TATA TATA TATA TATA
452529 ATAAAAAACC
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 68 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (4 bp):
TATA
Found at i:456852 original size:22 final size:22
Alignment explanation
Indices: 456827--456882 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
456817 CTAGCTGGAA
456827 GCATTGCACCTATAGGGTACAT
1 GCATTGCACCTATAGGGTACAT
456849 GCATTGCACCTATAGGGTACAT
1 GCATTGCACCTATAGGGTACAT
456871 GCATTGCACCTA
1 GCATTGCACCTA
456883 AGACAACCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (22 bp):
GCATTGCACCTATAGGGTACAT
Found at i:457909 original size:30 final size:30
Alignment explanation
Indices: 457869--457927 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
457859 TGGTTGATTT
* *
457869 TTATACAAGAATGTTTTCAACCGAAAAATG
1 TTATAAAAGAAGGTTTTCAACCGAAAAATG
*
457899 TTATAAAAGAAGGTTTTCAACTGAAAAAT
1 TTATAAAAGAAGGTTTTCAACCGAAAAAT
457928 ATCAAGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.46, C:0.10, G:0.14, T:0.31
Consensus pattern (30 bp):
TTATAAAAGAAGGTTTTCAACCGAAAAATG
Found at i:458120 original size:59 final size:60
Alignment explanation
Indices: 458048--458169 Score: 201
Period size: 62 Copynumber: 2.0 Consensus size: 60
458038 CAAATTGAGC
* *
458048 ACGATGCTAAGTTACTACCAACTT-AATAAAAAAGAACCCTTTCGATTGCTCGGTTTCAA
1 ACGATGCTAAGTTACTACCAACTTAAATAAAAAAAAACCCTTTCGATTGCTCAGTTTCAA
458107 ACGATGCTAAGTTACTACCAACTTAAAAATAAAAAAAAACCCTTTCGATTGCTCAGTTTCAA
1 ACGATGCTAAGTTACTACCAACTT--AAATAAAAAAAAACCCTTTCGATTGCTCAGTTTCAA
458169 A
1 A
458170 GGGGGGAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
59 24 0.41
62 34 0.59
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.28
Consensus pattern (60 bp):
ACGATGCTAAGTTACTACCAACTTAAATAAAAAAAAACCCTTTCGATTGCTCAGTTTCAA
Found at i:460939 original size:18 final size:18
Alignment explanation
Indices: 460916--460989 Score: 85
Period size: 18 Copynumber: 3.9 Consensus size: 18
460906 CGAGGGTTAC
460916 AGTGGTCCTACGGGACAT
1 AGTGGTCCTACGGGACAT
* *
460934 AGTGGTCATTCGGGACAAT
1 AGTGGTCCTACGGGAC-AT
*
460953 ACAGTGGTCCTACGAGACAT
1 --AGTGGTCCTACGGGACAT
*
460973 AGTGGTCCTTCGGGACA
1 AGTGGTCCTACGGGACA
460990 AATTTCAGTG
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
18 29 0.63
19 2 0.04
20 2 0.04
21 13 0.28
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (18 bp):
AGTGGTCCTACGGGACAT
Found at i:460972 original size:39 final size:39
Alignment explanation
Indices: 460913--460990 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
460903 AGTCGAGGGT
*
460913 TACAGTGGTCCTACGGGACATAGTGGTCATTCGGGACAA
1 TACAGTGGTCCTACGAGACATAGTGGTCATTCGGGACAA
*
460952 TACAGTGGTCCTACGAGACATAGTGGTCCTTCGGGACAA
1 TACAGTGGTCCTACGAGACATAGTGGTCATTCGGGACAA
460991 ATTTCAGTGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (39 bp):
TACAGTGGTCCTACGAGACATAGTGGTCATTCGGGACAA
Found at i:461207 original size:22 final size:23
Alignment explanation
Indices: 461172--461214 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
461162 AAGAATTATA
* *
461172 TGATGTTATGTGTGTT-TATGTG
1 TGATGATATATGTGTTATATGTG
461194 TGATGATATATGTGTTATATG
1 TGATGATATATGTGTTATATG
461215 ATATACAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (23 bp):
TGATGATATATGTGTTATATGTG
Found at i:461257 original size:18 final size:18
Alignment explanation
Indices: 461234--461292 Score: 91
Period size: 18 Copynumber: 3.3 Consensus size: 18
461224 AATGTTAATA
461234 CATGATAGTGATAGAGAT
1 CATGATAGTGATAGAGAT
461252 CATGATAGTGATAGAGAT
1 CATGATAGTGATAGAGAT
** *
461270 GTTGATAATGATAGAGAT
1 CATGATAGTGATAGAGAT
461288 CATGA
1 CATGA
461293 AAAAGATGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.39, C:0.05, G:0.27, T:0.29
Consensus pattern (18 bp):
CATGATAGTGATAGAGAT
Found at i:461327 original size:21 final size:21
Alignment explanation
Indices: 461303--461348 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
461293 AAAAGATGTT
461303 TGTGTTGATAATGAGGGTATA
1 TGTGTTGATAATGAGGGTATA
461324 TGTGTTGATAATGAGGGTATA
1 TGTGTTGATAATGAGGGTATA
461345 TGTG
1 TGTG
461349 CATGTATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.39
Consensus pattern (21 bp):
TGTGTTGATAATGAGGGTATA
Found at i:466441 original size:74 final size:74
Alignment explanation
Indices: 466353--466498 Score: 238
Period size: 74 Copynumber: 2.0 Consensus size: 74
466343 GTGAAACGCA
* * *
466353 AGATATGTTCACATGTTAGGTAGGATGTGAATTAATTCTATGTGCACTTTAAAGATAATTTTTCT
1 AGATATGTTCACATGGTAGGTAAGACGTGAATTAATTCTATGTGCACTTTAAAGATAATTTTTCT
466418 AACATATTG
66 AACATATTG
* *
466427 AGATATGTTCACATGGTAGGTAAGACGTGAATTAGTTCTATGTGCACTTTAAAGATAATTTTTGT
1 AGATATGTTCACATGGTAGGTAAGACGTGAATTAATTCTATGTGCACTTTAAAGATAATTTTTCT
*
466492 AATATAT
66 AACATAT
466499 GTTAAGAGAT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 66 1.00
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (74 bp):
AGATATGTTCACATGGTAGGTAAGACGTGAATTAATTCTATGTGCACTTTAAAGATAATTTTTCT
AACATATTG
Found at i:466552 original size:46 final size:44
Alignment explanation
Indices: 466480--466579 Score: 182
Period size: 46 Copynumber: 2.2 Consensus size: 44
466470 GCACTTTAAA
466480 GATAATTTTTGTAATATATGTTAAGAGATTATTAAAAAAATAAC
1 GATAATTTTTGTAATATATGTTAAGAGATTATTAAAAAAATAAC
466524 GATAATTTTTGTAACATATATGTTAAGAGATTATTAAAAAAATAAC
1 GATAATTTTTGT-A-ATATATGTTAAGAGATTATTAAAAAAATAAC
466570 GATAATTTTT
1 GATAATTTTT
466580 AATATAATAA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
44 12 0.22
45 1 0.02
46 41 0.76
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.40
Consensus pattern (44 bp):
GATAATTTTTGTAATATATGTTAAGAGATTATTAAAAAAATAAC
Found at i:482107 original size:13 final size:13
Alignment explanation
Indices: 482086--482116 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
482076 TACTAGTTTC
*
482086 TGGGGAATAAGAA
1 TGGGAAATAAGAA
482099 TGGGAAATAAGAA
1 TGGGAAATAAGAA
482112 TGGGA
1 TGGGA
482117 TTTAAATGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.39, T:0.16
Consensus pattern (13 bp):
TGGGAAATAAGAA
Found at i:493984 original size:19 final size:20
Alignment explanation
Indices: 493960--494005 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
493950 CGTTGAAGTT
493960 ATATTATATATAA-AGTTTA
1 ATATTATATATAAGAGTTTA
* *
493979 ATATTA-AAATAAGTGTTTA
1 ATATTATATATAAGAGTTTA
493998 A-ATTATAT
1 ATATTATAT
494006 CACATTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.46
Consensus pattern (20 bp):
ATATTATATATAAGAGTTTA
Found at i:503812 original size:24 final size:21
Alignment explanation
Indices: 503794--503899 Score: 80
Period size: 18 Copynumber: 5.0 Consensus size: 21
503784 GCGTAGAATT
503794 TGTCCCGAAGGACCACGTAGA
1 TGTCCCGAAGGACCACGTAGA
* *
503815 TGTCCCGAAGGACCACATATAACACATA
1 TGTCCCGAAGGACCAC--GT-----AGA
503843 TGTCCCGAAGGACCAC-T--A
1 TGTCCCGAAGGACCACGTAGA
503861 TGTCCCGAAGGACCAC-T--A
1 TGTCCCGAAGGACCACGTAGA
*
503879 TGTCCCGAAGGACCGCGTAGA
1 TGTCCCGAAGGACCACGTAGA
503900 CCCTCGACTC
Statistics
Matches: 72, Mismatches: 3, Indels: 20
0.76 0.03 0.21
Matches are distributed among these distances:
18 34 0.47
19 1 0.01
21 17 0.24
23 1 0.01
25 1 0.01
28 18 0.25
ACGTcount: A:0.30, C:0.30, G:0.24, T:0.16
Consensus pattern (21 bp):
TGTCCCGAAGGACCACGTAGA
Found at i:503864 original size:18 final size:18
Alignment explanation
Indices: 503841--503892 Score: 104
Period size: 18 Copynumber: 2.9 Consensus size: 18
503831 ATATAACACA
503841 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
503859 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
503877 TATGTCCCGAAGGACC
1 TATGTCCCGAAGGACC
503893 GCGTAGACCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.27, C:0.33, G:0.23, T:0.17
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:516441 original size:3 final size:3
Alignment explanation
Indices: 516433--516480 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
516423 TCATTTCGTT
*
516433 TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA ATA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
516478 TTA
1 TTA
516481 CAAAATACAT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:516528 original size:13 final size:13
Alignment explanation
Indices: 516510--516546 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
516500 ACGACCCTAA
516510 GCCCATTTACAAG
1 GCCCATTTACAAG
516523 GCCCATTTACAAG
1 GCCCATTTACAAG
*
516536 GCCCGTTTACA
1 GCCCATTTACA
516547 GTTAGCCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.24
Consensus pattern (13 bp):
GCCCATTTACAAG
Found at i:517917 original size:28 final size:27
Alignment explanation
Indices: 517882--517938 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
517872 TTAAAGTGTG
517882 TTTATATTATAATTATAATTTTATTCATTA
1 TTTAT-TTATAA-TATAATTTTATT-ATTA
* *
517912 TTTATTTGTAATATTATTTTATTATTA
1 TTTATTTATAATATAATTTTATTATTA
517939 CTTTTAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.16
28 11 0.44
29 5 0.20
30 5 0.20
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (27 bp):
TTTATTTATAATATAATTTTATTATTA
Found at i:517928 original size:12 final size:11
Alignment explanation
Indices: 517913--517975 Score: 65
Period size: 12 Copynumber: 5.5 Consensus size: 11
517903 TATTCATTAT
517913 TTATTTGTAATA
1 TTATTT-TAATA
*
517925 TTATTTTATTA
1 TTATTTTAATA
517936 TTACTTTTAATA
1 TTA-TTTTAATA
517948 -TATTTTAATTA
1 TTATTTTAA-TA
*
517959 TTACTTTAATTA
1 TTATTTTAA-TA
517971 TTATT
1 TTATT
517976 ATTTTTATCT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
10 6 0.14
11 11 0.25
12 27 0.61
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:517946 original size:23 final size:23
Alignment explanation
Indices: 517920--517975 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 23
517910 TATTTATTTG
517920 TAATATTATTTT-ATTATTACTTT
1 TAATATTATTTTAATTATTAC-TT
517943 TAATA-TATTTTAATTATTACTT
1 TAATATTATTTTAATTATTACTT
517965 TAATTATTATT
1 TAA-TATTATT
517976 ATTTTTATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
22 11 0.37
23 15 0.50
24 4 0.13
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (23 bp):
TAATATTATTTTAATTATTACTT
Found at i:517983 original size:12 final size:12
Alignment explanation
Indices: 517908--517983 Score: 57
Period size: 11 Copynumber: 6.2 Consensus size: 12
517898 AATTTTATTC
*
517908 ATTATTTATTTGT
1 ATTA-TTATTTTT
*
517921 AATATTA-TTTT
1 ATTATTATTTTT
*
517932 ATTATTACTTTT
1 ATTATTATTTTT
* *
517944 AATA-TATTTTA
1 ATTATTATTTTT
517955 ATTATTACTTTAATT
1 ATTATTA-TTT--TT
517970 ATTATTATTTTT
1 ATTATTATTTTT
517982 AT
1 AT
517984 CTTAGTCTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
11 17 0.34
12 16 0.32
13 6 0.12
14 3 0.06
15 8 0.16
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (12 bp):
ATTATTATTTTT
Found at i:520508 original size:12 final size:13
Alignment explanation
Indices: 520491--520519 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
520481 ACATTCACAT
520491 ATTTACA-TTTGC
1 ATTTACATTTTGC
520503 ATTTACATTTTGC
1 ATTTACATTTTGC
520516 ATTT
1 ATTT
520520 TTTTCATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.24, C:0.14, G:0.07, T:0.55
Consensus pattern (13 bp):
ATTTACATTTTGC
Found at i:532634 original size:8 final size:8
Alignment explanation
Indices: 532621--532668 Score: 69
Period size: 8 Copynumber: 5.9 Consensus size: 8
532611 CATATACTCA
532621 AAAAAATG
1 AAAAAATG
532629 AAAAAAATG
1 -AAAAAATG
*
532638 GAAAAATG
1 AAAAAATG
*
532646 GAAAAATG
1 AAAAAATG
532654 AAAAAATG
1 AAAAAATG
532662 AAAAAAT
1 AAAAAAT
532669 TGAATCATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
8 29 0.78
9 8 0.22
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:532650 original size:25 final size:24
Alignment explanation
Indices: 532622--532668 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
532612 ATATACTCAA
*
532622 AAAAATGAAAAAAATGGAAAAATGG
1 AAAAATG-AAAAAATGAAAAAATGG
532647 AAAAATGAAAAAATGAAAAAAT
1 AAAAATGAAAAAATGAAAAAAT
532669 TGAATCATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (24 bp):
AAAAATGAAAAAATGAAAAAATGG
Found at i:535890 original size:75 final size:75
Alignment explanation
Indices: 535766--535905 Score: 208
Period size: 75 Copynumber: 1.9 Consensus size: 75
535756 ATTAACAAGA
* * * *
535766 AGCAAATGCTGGGGCATACTGAAAGCCCCTCTAAATCAGAATCATGAATGTTGATGTATTTTGAA
1 AGCAAATGCTGGGGCATACTAAAAGCCCCTCTAAATCAGAATCAAGAATGTTGACGCATTTTGAA
535831 CATTTATATC
66 CATTTATATC
* * * *
535841 AGCAAATGCTGGGGCATGCTAAAAGCCCCTTTCAATCAGAATGAAGAATGTTGACGCATTTTGAA
1 AGCAAATGCTGGGGCATACTAAAAGCCCCTCTAAATCAGAATCAAGAATGTTGACGCATTTTGAA
535906 TGCTTGTATT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 57 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.28
Consensus pattern (75 bp):
AGCAAATGCTGGGGCATACTAAAAGCCCCTCTAAATCAGAATCAAGAATGTTGACGCATTTTGAA
CATTTATATC
Found at i:535929 original size:75 final size:75
Alignment explanation
Indices: 535766--535933 Score: 201
Period size: 75 Copynumber: 2.2 Consensus size: 75
535756 ATTAACAAGA
* * * * *
535766 AGCAAATGCTGGGGCATACTGAAAGCCCCTCTAAATCAGAATCATGAATGTTGATGTATTTTGAA
1 AGCAAATGCTGGGGCATGCTAAAAGCCCCTCTAAATCAGAATCAAGAATGTTGACGCATTTTGAA
*
535831 CATTTATATC
66 CACTTATATC
* * *
535841 AGCAAATGCTGGGGCATGCTAAAAGCCCCTTTCAATCAGAATGAAGAATGTTGACGCATTTTGAA
1 AGCAAATGCTGGGGCATGCTAAAAGCCCCTCTAAATCAGAATCAAGAATGTTGACGCATTTTGAA
** * *
535906 TGCTTGTATT
66 CACTTATATC
* *
535916 AGCCAATGTTGGGGCATG
1 AGCAAATGCTGGGGCATG
535934 TTGAAGGCCT
Statistics
Matches: 78, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
75 78 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (75 bp):
AGCAAATGCTGGGGCATGCTAAAAGCCCCTCTAAATCAGAATCAAGAATGTTGACGCATTTTGAA
CACTTATATC
Found at i:538031 original size:46 final size:46
Alignment explanation
Indices: 537964--539010 Score: 1837
Period size: 46 Copynumber: 22.8 Consensus size: 46
537954 ACTATTTCCC
537964 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
538010 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
538056 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
*
538102 TTATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
*
538148 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAACCTTCAGG
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAAACCTTCGGG
* * *
538195 TTATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCAGG
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
* *
538241 TCATCTGTAAGTCTTTCAGTGCATGATGTTTTCAAAAACCTTTGGG
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
* *
538287 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCAGG
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
538333 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
*
538379 TCATCTGTAAGTCCTTCAGTGCATGATG-TTTCAAAAACCTTCAGG
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
538424 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
538470 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
538516 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
*
538562 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTTGGG
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
*
538608 TCATCTGTAAGTCCTTCAGTGCATGATATTTTCAAAAACCTTCGGG
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
* * *
538654 TCATCTGTAAGTCTTTTAGTGCATGATGCTTTCAAAAACCTTCGGG
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
*
538700 CCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
538746 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
538792 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
*
538838 TTATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
* * *
538884 TCATCTGTAGGCCCTTCAGTGCATGATGTTTTCAAAAAACCTTCAGG
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAAACCTTCGGG
* * *
538931 TTATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTTGGG
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
* *
538976 TAATCTGTAAGTCCTTCGGTGCATGATGTTTTCAA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAA
539011 CATTTCCATC
Statistics
Matches: 955, Mismatches: 42, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
45 84 0.09
46 785 0.82
47 86 0.09
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.35
Consensus pattern (46 bp):
TCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
Found at i:539144 original size:3 final size:3
Alignment explanation
Indices: 539136--539173 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
539126 TCATTTCGTT
539136 TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
539174 ATATATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:539162 original size:17 final size:17
Alignment explanation
Indices: 539140--539173 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
539130 TTCGTTTTAT
539140 TATTATTATTATTATTA
1 TATTATTATTATTATTA
539157 TATTATTATTATTATTA
1 TATTATTATTATTATTA
539174 ATATATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTATTATTATTATTA
Found at i:539162 original size:20 final size:20
Alignment explanation
Indices: 539137--539179 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
539127 CATTTCGTTT
*
539137 TATTATTATTATTATTATTA
1 TATTATTATTATTATTAATA
539157 TATTATTATTATTATTAATA
1 TATTATTATTATTATTAATA
539177 TAT
1 TAT
539180 ATATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTATTATTATTATTAATA
Found at i:539243 original size:13 final size:13
Alignment explanation
Indices: 539225--539249 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
539215 ACGACCCTAA
539225 GCCCATTTACAAG
1 GCCCATTTACAAG
539238 GCCCATTTACAA
1 GCCCATTTACAA
539250 TTGGCCTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.32, G:0.12, T:0.24
Consensus pattern (13 bp):
GCCCATTTACAAG
Found at i:540833 original size:12 final size:11
Alignment explanation
Indices: 540818--540880 Score: 65
Period size: 12 Copynumber: 5.5 Consensus size: 11
540808 TATTCATTAT
540818 TTATTTGTAATA
1 TTATTT-TAATA
*
540830 TTATTTTATTA
1 TTATTTTAATA
540841 TTACTTTTAATA
1 TTA-TTTTAATA
540853 -TATTTTAATTA
1 TTATTTTAA-TA
*
540864 TTACTTTTATTA
1 TTA-TTTTAATA
540876 TTATT
1 TTATT
540881 ATTTTTATCT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
10 6 0.14
11 13 0.30
12 20 0.45
13 5 0.11
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:540851 original size:23 final size:24
Alignment explanation
Indices: 540825--540880 Score: 89
Period size: 23 Copynumber: 2.4 Consensus size: 24
540815 TATTTATTTG
540825 TAATATTATTTT-ATTATTACTTT
1 TAATATTATTTTAATTATTACTTT
540848 TAATA-TATTTTAATTATTACTTT
1 TAATATTATTTTAATTATTACTTT
*
540871 TATTATTATT
1 TAATATTATT
540881 ATTTTTATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 6 0.20
23 20 0.67
24 4 0.13
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (24 bp):
TAATATTATTTTAATTATTACTTT
Found at i:540881 original size:6 final size:6
Alignment explanation
Indices: 540785--540888 Score: 51
Period size: 6 Copynumber: 17.5 Consensus size: 6
540775 AGTGTGTTTA
* * * *
540785 TATTAT AATTAT AATTAT AATT-T TATTCAT TATTTAT T-TGTAA TATTAT
1 TATTAT TATTAT TATTAT TATTAT TATT-AT TA-TTAT TAT-TAT TATTAT
*
540834 T-TTAT TATTACT T-TTAA TA-TAT T-TTAAT TATTACT T-TTAT TATTAT
1 TATTAT TATTA-T TATTAT TATTAT TATT-AT TATTA-T TATTAT TATTAT
*
540880 TATTTT TAT
1 TATTAT TAT
540889 CTTAGTCTTA
Statistics
Matches: 78, Mismatches: 7, Indels: 26
0.70 0.06 0.23
Matches are distributed among these distances:
5 17 0.22
6 46 0.59
7 13 0.17
8 2 0.03
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (6 bp):
TATTAT
Found at i:540909 original size:2 final size:2
Alignment explanation
Indices: 540897--540959 Score: 99
Period size: 2 Copynumber: 31.5 Consensus size: 2
540887 ATCTTAGTCT
*
540897 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
540939 TA TG TA TG TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
540960 TTGTTTAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:541380 original size:130 final size:129
Alignment explanation
Indices: 541128--541380 Score: 311
Period size: 130 Copynumber: 1.9 Consensus size: 129
541118 ATAATCATAT
* *
541128 TTTAATATTTATATATTTTTTTAATATTAAGAAATTGGTTGTCTTAAAGCACTTAGAAGTATTTT
1 TTTAATATTTATATATTTTTTTAATATTAAGAAATAGGTTGTCTTAAAGCACCTAGAAGTATTTT
* * * *
541193 TCTAATATTCTTAAATAAATAAATATCTTACTTTTATAAATTATATCTATTTTTTAAATAAATGA
66 TATAATATTCTTAAATAAATAAATATCTTAC-TTTATAAATTATAACGATTTGTTAAATAAATGA
*
541258 TTTAATATTTATTTATTTATTTT-ATATTAAGAAA-AGAGTTGTCTTAAAGCACCTAGAAGT-TC
1 TTTAATATTTATATATTT-TTTTAATATTAAGAAATAG-GTTGTCTTAAAGCACCTAGAAGTAT-
* *
541320 TTTTATGATATT-TCTAAATAAATAAATATCTTA-TTTATATA-TATAACAGGATTATGTTAAA
63 TTTTATAATATTCT-TAAATAAATAAATATCTTACTTTATAAATTATAAC--GATT-TGTTAAA
541381 ACACCTAGAT
Statistics
Matches: 107, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
127 5 0.05
128 7 0.07
129 6 0.06
130 85 0.79
131 4 0.04
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (129 bp):
TTTAATATTTATATATTTTTTTAATATTAAGAAATAGGTTGTCTTAAAGCACCTAGAAGTATTTT
TATAATATTCTTAAATAAATAAATATCTTACTTTATAAATTATAACGATTTGTTAAATAAATGA
Found at i:545162 original size:143 final size:142
Alignment explanation
Indices: 544844--545271 Score: 561
Period size: 143 Copynumber: 3.0 Consensus size: 142
544834 ATTGACGATT
* * * * * * *
544844 ATTTAAACTGAACGTTAACTTATTGACTGAGATGTTATAAAATTATATGTTAATGATGCTTATTG
1 ATTTGAACTGGACATTAACTTGTTGACTGAGATGTTATAAAATCATATTTTAATGATGTTTATTG
* * * * *
544909 GCACCATCGTTGCTTTTAAGTACCGACTCGTCTATATAATATTTCAAGCATGAACTCGACATAGA
66 GCACCGTCGTTGC-TTTAAGTACCGACTCGTCGATATAATATTTCAAGCAT-AGCTCGACGTATA
*
544974 ATTTAATGACGACC
129 ATTTAATGATGACC
* *
544988 ATTTGAACTGGACGTTAATTTGTTGACTGAGATGTTATAAAATCATATTTTAATGATGTTTATTG
1 ATTTGAACTGGACATTAACTTGTTGACTGAGATGTTATAAAATCATATTTTAATGATGTTTATTG
* *
545053 GCACCGTCATTGCTATTAAGTACCGAC-AGTCGATATAATATTTCAAGCACTAGCTCGACGTATA
66 GCACCGTCGTTGCT-TTAAGTACCGACTCGTCGATATAATATTTCAAGCA-TAGCTCGACGTATA
545117 ATTTAATGATGACC
129 ATTTAATGATGACC
* *
545131 ATTTGAATTGGACATTAACTTGTTGAGTGAGATGTTATAAAATCATATTTTAATGATGTTTATTG
1 ATTTGAACTGGACATTAACTTGTTGACTGAGATGTTATAAAATCATATTTTAATGATGTTTATTG
* * * * * * *
545196 GTACCGGCGTTGCTTTCAAGTACTGACTCGTCGACAAAATATTTCAAGAAGTAGTTCGACGTATA
66 GCACCGTCGTTGCTTT-AAGTACCGACTCGTCGATATAATATTTCAAGCA-TAGCTCGACGTATA
545261 ATTTAATGATG
129 ATTTAATGATG
545272 TTTATTGTCA
Statistics
Matches: 251, Mismatches: 29, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
142 2 0.01
143 125 0.50
144 124 0.49
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (142 bp):
ATTTGAACTGGACATTAACTTGTTGACTGAGATGTTATAAAATCATATTTTAATGATGTTTATTG
GCACCGTCGTTGCTTTAAGTACCGACTCGTCGATATAATATTTCAAGCATAGCTCGACGTATAAT
TTAATGATGACC
Found at i:545559 original size:24 final size:24
Alignment explanation
Indices: 545532--545578 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
545522 TCTTTATATA
*
545532 TAATAATATTACATATTTAATTAT
1 TAATAATATTACATATTAAATTAT
* *
545556 TAATAATTTTATATATTAAATTA
1 TAATAATATTACATATTAAATTA
545579 AACTAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TAATAATATTACATATTAAATTAT
Found at i:549342 original size:10 final size:10
Alignment explanation
Indices: 549327--549378 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
549317 CGTATGGATG
549327 TAAACGAACA
1 TAAACGAACA
549337 TAAACGAACATAA
1 TAAACGAAC---A
*
549350 TAAACGAACC
1 TAAACGAACA
*
549360 TAAACAAACA
1 TAAACGAACA
*
549370 CAAACGAAC
1 TAAACGAAC
549379 TAACGTAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
10 24 0.71
13 10 0.29
ACGTcount: A:0.60, C:0.23, G:0.08, T:0.10
Consensus pattern (10 bp):
TAAACGAACA
Found at i:549354 original size:23 final size:23
Alignment explanation
Indices: 549327--549409 Score: 87
Period size: 23 Copynumber: 3.6 Consensus size: 23
549317 CGTATGGATG
*
549327 TAAACGAACATAAACGAACATAA
1 TAAACGAACATAAACGAACACAA
* *
549350 TAAACGAACCTAAACAAACACAA
1 TAAACGAACATAAACGAACACAA
* *
549373 -ACGAACTAACGTAAACGAACACAA
1 TA--AACGAACATAAACGAACACAA
*
549397 TAAATGAACATAA
1 TAAACGAACATAA
549410 CTGGAAATAT
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
22 1 0.02
23 28 0.58
24 18 0.38
25 1 0.02
ACGTcount: A:0.59, C:0.20, G:0.08, T:0.12
Consensus pattern (23 bp):
TAAACGAACATAAACGAACACAA
Found at i:549596 original size:14 final size:14
Alignment explanation
Indices: 549579--549614 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
549569 ATTGGGATAA
*
549579 ACATAAATGAACGC
1 ACATAAACGAACGC
*
549593 ACATAAACGAACGG
1 ACATAAACGAACGC
549607 ACATAAAC
1 ACATAAAC
549615 AAACATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.53, C:0.22, G:0.14, T:0.11
Consensus pattern (14 bp):
ACATAAACGAACGC
Found at i:549633 original size:14 final size:14
Alignment explanation
Indices: 549578--549635 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
549568 GATTGGGATA
549578 AACATAAATGAACG
1 AACATAAATGAACG
* *
549592 CACATAAACGAACG
1 AACATAAATGAACG
* *
549606 GACAT--A--AACA
1 AACATAAATGAACG
549616 AACATAAATGAACG
1 AACATAAATGAACG
549630 AACATA
1 AACATA
549636 TTAGTGAACG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
10 7 0.21
12 2 0.06
14 25 0.74
ACGTcount: A:0.57, C:0.19, G:0.12, T:0.12
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:550846 original size:23 final size:20
Alignment explanation
Indices: 550818--550874 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
550808 GCATGGGTAG
550818 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
550842 T-CATCGATTCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
550861 TGCATCGATGCACT
1 TGCATCGATGCACT
550875 TTAAGGGGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 5 0.17
20 11 0.37
21 1 0.03
22 2 0.07
23 10 0.33
24 1 0.03
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:552335 original size:23 final size:23
Alignment explanation
Indices: 552309--552375 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
552299 CATCTATATA
552309 GCACTTCGGTGCATTTCTACGCG
1 GCACTTCGGTGCATTTCTACGCG
* * *
552332 GCACTTAGGTGCAATTCTACGTG
1 GCACTTCGGTGCATTTCTACGCG
* *
552355 GCACTTCGATGCATTTATACG
1 GCACTTCGGTGCATTTCTACG
552376 AGTTGTAGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.31
Consensus pattern (23 bp):
GCACTTCGGTGCATTTCTACGCG
Found at i:564566 original size:27 final size:27
Alignment explanation
Indices: 564535--564589 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
564525 CTTGTACAGC
564535 CCAAAAAAGTGTAATAGTTGCAGCAGA
1 CCAAAAAAGTGTAATAGTTGCAGCAGA
564562 CCAAAAAAGTGTAATAGTTGCAGCAGA
1 CCAAAAAAGTGTAATAGTTGCAGCAGA
564589 C
1 C
564590 TAACATGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.18
Consensus pattern (27 bp):
CCAAAAAAGTGTAATAGTTGCAGCAGA
Found at i:565968 original size:29 final size:29
Alignment explanation
Indices: 565926--566055 Score: 215
Period size: 29 Copynumber: 4.5 Consensus size: 29
565916 ACCCGACCCA
*
565926 GTGACATTTTGGGAATTATTTTGAAAAAT
1 GTGACATTTTGGGAATTATTTTGAAAAAG
* * *
565955 GTGACATTCTGGGAATTATTTTAAAAAAT
1 GTGACATTTTGGGAATTATTTTGAAAAAG
565984 GTGACATTTTGGGAATTATTTTGAAAAAG
1 GTGACATTTTGGGAATTATTTTGAAAAAG
*
566013 GTGACATTCTGGGAATTATTTTGAAAAAG
1 GTGACATTTTGGGAATTATTTTGAAAAAG
566042 GTGACATTTTGGGA
1 GTGACATTTTGGGA
566056 TTTTTGAATG
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 94 1.00
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.38
Consensus pattern (29 bp):
GTGACATTTTGGGAATTATTTTGAAAAAG
Found at i:573650 original size:32 final size:32
Alignment explanation
Indices: 573577--573663 Score: 86
Period size: 32 Copynumber: 2.7 Consensus size: 32
573567 CTAATGTGAC
* *
573577 TCTTAGGTAGGCTCTGCGGCCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGGCCCCTAAGATCAT
** **
573609 TCTCGGGTAGGCCCTGCGG-CCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCCTAAGAT-CAT
**
573641 TCTTAGGTAGGCCCCACGGCCCC
1 TCTTAGGTAGGCCCTGCGGCCCC
573664 GAAATCTATC
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
31 8 0.19
32 32 0.74
33 3 0.07
ACGTcount: A:0.14, C:0.32, G:0.30, T:0.24
Consensus pattern (32 bp):
TCTTAGGTAGGCCCTGCGGCCCCTAAGATCAT
Found at i:573770 original size:25 final size:25
Alignment explanation
Indices: 573718--573770 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
573708 AGGATAACTC
* *
573718 TTTTATGAGATTTATTGCAGTATAA
1 TTTTATGAGATTTACTGCACTATAA
* *
573743 TTTTATGAGATTTACTGGACTATGA
1 TTTTATGAGATTTACTGCACTATAA
573768 TTT
1 TTT
573771 GTTTAGTGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.06, G:0.17, T:0.49
Consensus pattern (25 bp):
TTTTATGAGATTTACTGCACTATAA
Found at i:581330 original size:2 final size:2
Alignment explanation
Indices: 581323--581348 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
581313 ACTTTTGGTC
581323 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
581349 TGGAAGATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:581469 original size:24 final size:23
Alignment explanation
Indices: 581406--581458 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
581396 TCTAAACTAT
581406 TAATTTTAATATGTTTTAGTACC
1 TAATTTTAATATGTTTTAGTACC
581429 TAATTTTAATATGTTTTAGTACC
1 TAATTTTAATATGTTTTAGTACC
*
581452 TTATTTT
1 TAATTTT
581459 TTATTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.57
Consensus pattern (23 bp):
TAATTTTAATATGTTTTAGTACC
Found at i:582222 original size:31 final size:31
Alignment explanation
Indices: 582184--582266 Score: 121
Period size: 31 Copynumber: 2.7 Consensus size: 31
582174 CTTTTAAAAC
**
582184 TTGCAATACAGTCCCCCAACATTTAGTTCAT
1 TTGCAATATGGTCCCCCAACATTTAGTTCAT
* **
582215 TTGCAATATGGTCCCCCAATATTTAGTTTGT
1 TTGCAATATGGTCCCCCAACATTTAGTTCAT
582246 TTGCAATATGGTCCCCCAACA
1 TTGCAATATGGTCCCCCAACA
582267 GTTACGTTGG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.34
Consensus pattern (31 bp):
TTGCAATATGGTCCCCCAACATTTAGTTCAT
Found at i:583302 original size:31 final size:31
Alignment explanation
Indices: 583256--583364 Score: 157
Period size: 31 Copynumber: 3.5 Consensus size: 31
583246 CTTTTAAAAC
* **
583256 TTGCAATAT-AGTCCCCCAACATTTAGTCCAT
1 TTGCAATATGA-TCCCCTAACATTTAGTCTGT
*
583287 TTTCAATATGATCCCCTAACATTTAGTCTGT
1 TTGCAATATGATCCCCTAACATTTAGTCTGT
583318 TTGCAATATGATCCCCTAACATTTAGTCTGT
1 TTGCAATATGATCCCCTAACATTTAGTCTGT
*
583349 TTGCAATATGGTCCCC
1 TTGCAATATGATCCCC
583365 AACGTAACTA
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
31 70 0.99
32 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.37
Consensus pattern (31 bp):
TTGCAATATGATCCCCTAACATTTAGTCTGT
Found at i:587039 original size:2 final size:2
Alignment explanation
Indices: 587032--587059 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
587022 TCAAAGCAAC
587032 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
587060 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:589654 original size:178 final size:180
Alignment explanation
Indices: 589226--589766 Score: 1041
Period size: 178 Copynumber: 3.0 Consensus size: 180
589216 ATTCTTCTTT
589226 AATGAATGAATACAACTCTTCGGTTACTGTATCTATTTCTCTAGGAATTCGCATTTTCAATAACT
1 AATGAATGAATACAACTCTTCGGTTACTGTATCTATTTCTCTAGGAATTCGCATTTTCAATAACT
*
589291 CTTCGGCCCAAATGAATAAACATTCTATTTTCTTATTCATAATTATTTCTCATTCTAAATCGCTA
66 CTTCAGCCCAAATGAATAAACATTCTATTTTCTTATTCATAATTATTTCTCATTCTAAATCGCTA
589356 AACACACACATATATATATATAACGCGGGTTTGACTCCAATTCTATATAG
131 AACACACACATATATATATATAACGCGGGTTTGACTCCAATTCTATATAG
589406 AATGAATGAATACAACTCTTCGGTTACTGTATCTATTTCTCTAGGAATTCGCATTTTCAATAACT
1 AATGAATGAATACAACTCTTCGGTTACTGTATCTATTTCTCTAGGAATTCGCATTTTCAATAACT
589471 CTTCAGCCCAAATGAATAAACATTCTATTTTCTTATTCATAATTATTTCTCATTCTAAATCGCT-
66 CTTCAGCCCAAATGAATAAACATTCTATTTTCTTATTCATAATTATTTCTCATTCTAAATCGCTA
589535 AA-ACACACATATATATATATAACGCGGGTTTGACTCCAATTCTATATAG
131 AACACACACATATATATATATAACGCGGGTTTGACTCCAATTCTATATAG
589584 AATGAATGAATACAACTCTTCGGTTACTGTATCTATTTCTCTAGGAATTCGCATTTTCAATAACT
1 AATGAATGAATACAACTCTTCGGTTACTGTATCTATTTCTCTAGGAATTCGCATTTTCAATAACT
589649 CTTCAGCCCAAATGAATAAACATTCTATTTTCTTATTCATAATTATTTCTCATTCTAAATCGCTA
66 CTTCAGCCCAAATGAATAAACATTCTATTTTCTTATTCATAATTATTTCTCATTCTAAATCGCTA
589714 AACACACACATATATATATATATCACGCGGGTTTGACTCCAATTCTATATAG
131 AACACACACATATATATATATA--ACGCGGGTTTGACTCCAATTCTATATAG
589766 A
1 A
589767 TTATCATGTT
Statistics
Matches: 356, Mismatches: 1, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
178 176 0.49
179 4 0.01
180 147 0.41
182 29 0.08
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (180 bp):
AATGAATGAATACAACTCTTCGGTTACTGTATCTATTTCTCTAGGAATTCGCATTTTCAATAACT
CTTCAGCCCAAATGAATAAACATTCTATTTTCTTATTCATAATTATTTCTCATTCTAAATCGCTA
AACACACACATATATATATATAACGCGGGTTTGACTCCAATTCTATATAG
Found at i:609367 original size:19 final size:19
Alignment explanation
Indices: 609343--609385 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
609333 GATAGAGGCT
*
609343 AGGTTGAGACAGGTTACTA
1 AGGTTGAGACAAGTTACTA
609362 AGGTTGAGACAAGTTACTA
1 AGGTTGAGACAAGTTACTA
*
609381 GGGTT
1 AGGTT
609386 TCGGAAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.30, C:0.09, G:0.33, T:0.28
Consensus pattern (19 bp):
AGGTTGAGACAAGTTACTA
Found at i:614337 original size:57 final size:57
Alignment explanation
Indices: 614274--614386 Score: 226
Period size: 57 Copynumber: 2.0 Consensus size: 57
614264 TTCTTGGGTT
614274 TCAGTAAATGCTTTTCTGTGAAGACTTTGAAAGCTATGGAATAAGCCAGAGTTGAGG
1 TCAGTAAATGCTTTTCTGTGAAGACTTTGAAAGCTATGGAATAAGCCAGAGTTGAGG
614331 TCAGTAAATGCTTTTCTGTGAAGACTTTGAAAGCTATGGAATAAGCCAGAGTTGAG
1 TCAGTAAATGCTTTTCTGTGAAGACTTTGAAAGCTATGGAATAAGCCAGAGTTGAG
614387 ATAGCCTTGC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (57 bp):
TCAGTAAATGCTTTTCTGTGAAGACTTTGAAAGCTATGGAATAAGCCAGAGTTGAGG
Found at i:615265 original size:6 final size:6
Alignment explanation
Indices: 615254--615291 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
615244 TTTGTAGGAT
615254 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AA
615292 TGAAAGTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATTA
Found at i:618180 original size:28 final size:29
Alignment explanation
Indices: 618094--618196 Score: 91
Period size: 31 Copynumber: 3.5 Consensus size: 29
618084 TTTTTATTAG
*
618094 AGTACCTAAAATATTTTTTAGTAAAAATA
1 AGTACCTAAAGTATTTTTTAGTAAAAATA
* * * *
618123 AATACTTAAGGTTATCTTTTTAGTTAAAATA
1 AGTACCTAAAG-TAT-TTTTTAGTAAAAATA
* *
618154 AGTACCTAAAGTATTTTAT-GTCAAAATA
1 AGTACCTAAAGTATTTTTTAGTAAAAATA
* * *
618182 GGTACTTAAATTATT
1 AGTACCTAAAGTATT
618197 CAAATTTTTT
Statistics
Matches: 59, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
28 20 0.34
29 11 0.19
30 6 0.10
31 22 0.37
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.41
Consensus pattern (29 bp):
AGTACCTAAAGTATTTTTTAGTAAAAATA
Found at i:618348 original size:29 final size:30
Alignment explanation
Indices: 618279--618356 Score: 95
Period size: 32 Copynumber: 2.6 Consensus size: 30
618269 AAAAAAATTG
** * *
618279 AATACTTTAGTTACATATTTTGACAAAAAA
1 AATACTTTAAATACTTATATTGACAAAAAA
618309 ATATAACTTTAAATACTTATATTGAC-AAAAA
1 A-AT-ACTTTAAATACTTATATTGACAAAAAA
618340 AATACTTTAAATACTTA
1 AATACTTTAAATACTTA
618357 AATGAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 14 0.33
30 3 0.07
31 8 0.19
32 17 0.40
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.37
Consensus pattern (30 bp):
AATACTTTAAATACTTATATTGACAAAAAA
Found at i:618367 original size:29 final size:30
Alignment explanation
Indices: 618303--618367 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
618293 ATATTTTGAC
* *
618303 AAAAAAATATAACTTTAAATACTTATATTG
1 AAAAAAAAATAACTTTAAATACTTATAATG
*
618333 ACAAAAAAAT-ACTTTAAATACTTA-AATG
1 AAAAAAAAATAACTTTAAATACTTATAATG
618361 AAAAAAA
1 AAAAAAA
618368 TGATATACTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 9 0.29
29 14 0.45
30 8 0.26
ACGTcount: A:0.60, C:0.08, G:0.03, T:0.29
Consensus pattern (30 bp):
AAAAAAAAATAACTTTAAATACTTATAATG
Found at i:626763 original size:111 final size:111
Alignment explanation
Indices: 626624--626845 Score: 392
Period size: 111 Copynumber: 2.0 Consensus size: 111
626614 ATTACAAAAA
*
626624 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACAAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACAAATAATTTAAATTA
*
626689 AATTAAAACATTAAAATGTTACAGTATCA-ACAAAGTGTCGAGATAT
66 AATTAAAACATTAAAATGTTACAGTATCATA-AAAGTGTAGAGATAT
*
626735 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACAAATAATTTAAATTA
*
626800 AATTAAAACATTAAAATGTTACCGTATCATAAAAGTGTAGAGATAT
66 AATTAAAACATTAAAATGTTACAGTATCATAAAAGTGTAGAGATAT
626846 ATGATTTTCA
Statistics
Matches: 106, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
111 105 0.99
112 1 0.01
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACAAATAATTTAAATTA
AATTAAAACATTAAAATGTTACAGTATCATAAAAGTGTAGAGATAT
Found at i:627186 original size:50 final size:50
Alignment explanation
Indices: 627132--627257 Score: 141
Period size: 50 Copynumber: 2.5 Consensus size: 50
627122 AGATACCCAG
* *
627132 GTATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGGCGT-CAGATCACC
1 GTATAGCGCGGATCAGGGGGCGCGCTATACCCACATGGC-TCCAAATCACC
* * * *
627182 GTATATCGCGGGA-CAGGGGACGCTCTATACCCACATGGCTCCAAATCAGC
1 GTATAGCGC-GGATCAGGGGGCGCGCTATACCCACATGGCTCCAAATCACC
*
627232 GTATAGCGC-GATTCAGAGGGCGCGCT
1 GTATAGCGCGGA-TCAGGGGGCGCGCT
627258 TTACTGCTAT
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
48 2 0.03
49 1 0.02
50 56 0.90
51 3 0.05
ACGTcount: A:0.22, C:0.29, G:0.32, T:0.17
Consensus pattern (50 bp):
GTATAGCGCGGATCAGGGGGCGCGCTATACCCACATGGCTCCAAATCACC
Found at i:643195 original size:25 final size:26
Alignment explanation
Indices: 643162--643212 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 26
643152 GAAGGACTCG
643162 TTTTTTATT-TTTAAAATATTTATAT
1 TTTTTTATTATTTAAAATATTTATAT
643187 TTTTTTATTAATTTAAAATATTTATA
1 TTTTTTATT-ATTTAAAATATTTATA
643213 AATTCATAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 9 0.38
27 15 0.62
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTTTTATTATTTAAAATATTTATAT
Found at i:646302 original size:2 final size:2
Alignment explanation
Indices: 646297--646328 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
646287 ACACACACAC
646297 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
646329 TAAACGACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:647388 original size:21 final size:20
Alignment explanation
Indices: 647350--647387 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
647340 GACCGTTTAT
*
647350 AGCCGTTGTGGATGTTTTGG
1 AGCCGTTGGGGATGTTTTGG
647370 AGCCGTTTGGGGAT-TTTT
1 AGCCG-TTGGGGATGTTTT
647388 TTTTTGCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.11, C:0.11, G:0.37, T:0.42
Consensus pattern (20 bp):
AGCCGTTGGGGATGTTTTGG
Found at i:648571 original size:17 final size:18
Alignment explanation
Indices: 648546--648579 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
648536 CAATGTGTAA
*
648546 TCATTCATGT-TAAAAAC
1 TCATGCATGTATAAAAAC
648563 TCATGCATGTATAAAAA
1 TCATGCATGTATAAAAA
648580 TCAATAGGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (18 bp):
TCATGCATGTATAAAAAC
Found at i:650479 original size:20 final size:20
Alignment explanation
Indices: 650454--650505 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
650444 ATCAACTGAT
*
650454 AGTATCAATACTACCTAGAA
1 AGTATCGATACTACCTAGAA
650474 AGTATCGATACTACCTAGAA
1 AGTATCGATACTACCTAGAA
650494 AGTATCGATACT
1 AGTATCGATACT
650506 TCTCTTACCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.27
Consensus pattern (20 bp):
AGTATCGATACTACCTAGAA
Found at i:665681 original size:2 final size:2
Alignment explanation
Indices: 665674--665718 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
665664 AATTTAAAAC
665674 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
665716 AT A
1 AT A
665719 ATGGTGACTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:668927 original size:23 final size:23
Alignment explanation
Indices: 668901--668964 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
668891 CATAACGGCG
* *
668901 GAGCAGTTAGAGTAGAGGCGATA
1 GAGCAGTTGGAGTAGAGGCGACA
*
668924 GAGCAGTTGGAGTAGAGGCGACG
1 GAGCAGTTGGAGTAGAGGCGACA
*
668947 GAGCAGTTGGAATAGAGG
1 GAGCAGTTGGAGTAGAGG
668965 AATGGTTGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.31, C:0.09, G:0.44, T:0.16
Consensus pattern (23 bp):
GAGCAGTTGGAGTAGAGGCGACA
Found at i:669388 original size:45 final size:45
Alignment explanation
Indices: 669268--669843 Score: 875
Period size: 45 Copynumber: 12.8 Consensus size: 45
669258 TAAAATCTCA
* * * ** ** *
669268 TTTGAAAACATCCTGTACTGAAGGTCTTATGGATGACTTGAAGGAC
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-T
* * *
669314 TTT-AAAAGCATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGC
1 TTTGAAAA-CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
669359 TTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* * *
669404 TTTGAAAACATCATGCACTGAAGGTCTTACAGATGGCCCGAAGGA
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
669449 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
669494 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
669539 TTTGAAAACATCATGCACTGAAAGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
669584 TTTGAAAACATCATGCACTGAAGGGCTTACAAATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* * *
669629 TTTGAAAACATCATGCGCTGAAGGGCTTATAGATGACCCGAAGGC
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
669674 TTTGAAAACATCATGCACTGAAAGGCTTACAGATAACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
669719 TTTGAAAATATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* * ** *
669764 TTTGAAAACATCATGCACTGAAGGACTTACAAATGACCAAAAGGC
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
669809 TTTGAAAACATCATGCACTGAAGGGCTTACAGATG
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATG
669844 TGGGAAATAG
Statistics
Matches: 493, Mismatches: 35, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
45 455 0.92
46 38 0.08
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (45 bp):
TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
Found at i:670566 original size:20 final size:21
Alignment explanation
Indices: 670527--670579 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
670517 AATAAAGCTT
670527 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTG-AAAGAGAATCTA
670549 TCATCTTTGAAA-AGAATCTA
1 TCATCTTTGAAAGAGAATCTA
* *
670569 CCATATTTGAA
1 TCATCTTTGAA
670580 GAATGTAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 17 0.59
21 3 0.10
22 9 0.31
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (21 bp):
TCATCTTTGAAAGAGAATCTA
Found at i:672094 original size:75 final size:69
Alignment explanation
Indices: 671926--672097 Score: 218
Period size: 75 Copynumber: 2.4 Consensus size: 69
671916 CATGATGATG
* * * *
671926 TGGGCCTTCAGCATGCCCCAGTATTTGCTGATACAAACGTTCAAAATGTTATTCCAATTTCTGAT
1 TGGGCTTTCAGCATG-CCCAGCATTTGCTAATACAAACGTTCAAAATGATATTCCAATTTCTGAT
671991 TGAAA
65 TGAAA
*
671996 TGGCCTTTCAGCATGCCCTAGCATTTGCTAATACAAACGTTCAAAATGAGCCAATATTCCAATTT
1 TGGGCTTTCAGCATGCCC-AGCATTTGCTAATACAAACGTTCAAAAT--G---ATATTCCAATTT
672061 CTGATTGAAA
60 CTGATTGAAA
*
672071 TGGGCTTTCAGTATGTCCCAGCATTTG
1 TGGGCTTTCAGCATG-CCCAGCATTTG
672098 TTGACGTGAA
Statistics
Matches: 88, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
69 3 0.03
70 39 0.44
72 1 0.01
75 42 0.48
76 3 0.03
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (69 bp):
TGGGCTTTCAGCATGCCCAGCATTTGCTAATACAAACGTTCAAAATGATATTCCAATTTCTGATT
GAAA
Found at i:672114 original size:75 final size:74
Alignment explanation
Indices: 671975--672174 Score: 204
Period size: 75 Copynumber: 2.7 Consensus size: 74
671965 TTCAAAATGT
* * *
671975 TATTCCAATTTCTGATTGAAATGGCCTTTCAGCATGCCCTAGCATTTGCTAATACAAACGTTCAA
1 TATTCCAATTTCTGATTGAAATGGGCTTTCAGCATGCCC-AGCATTTGCTAACACAAACATTCAA
*
672040 AATGAGCCAA
65 AACGAGCCAA
* * * ***
672050 TATTCCAATTTCTGATTGAAATGGGCTTTCAGTATGTCCCAGCATTTGTTGACGTGAACATTCAA
1 TATTCCAATTTCTGATTGAAATGGGCTTTCAGCATG-CCCAGCATTTGCTAACACAAACATTCAA
* * *
672115 AACGCGTCGA
65 AACGAGCCAA
** * *
672125 TATTTCTGA-TTATGATTGAAATGGGCTTTCAGCATACCCCAGCATTTGCT
1 TA-TTCCAATTTCTGATTGAAATGGGCTTTCAGCAT-GCCCAGCATTTGCT
672175 TCTTGTTGAT
Statistics
Matches: 103, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
75 96 0.93
76 7 0.07
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (74 bp):
TATTCCAATTTCTGATTGAAATGGGCTTTCAGCATGCCCAGCATTTGCTAACACAAACATTCAAA
ACGAGCCAA
Found at i:673026 original size:12 final size:12
Alignment explanation
Indices: 673009--673039 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
672999 ATGAGCATAT
673009 GAAGCTTGAAAA
1 GAAGCTTGAAAA
673021 GAAGCTTGAAAA
1 GAAGCTTGAAAA
673033 GAAGCTT
1 GAAGCTT
673040 TTAATGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.10, G:0.26, T:0.19
Consensus pattern (12 bp):
GAAGCTTGAAAA
Found at i:674475 original size:32 final size:32
Alignment explanation
Indices: 674436--674502 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
674426 TGAAGAAATG
* * *
674436 GTTGTTATGTTTATCTGGTAGAGATACTTCTT
1 GTTGTTATGCTCATCTCGTAGAGATACTTCTT
674468 GTTGTTATGCTCATCTCGTAGAGATACTTCTT
1 GTTGTTATGCTCATCTCGTAGAGATACTTCTT
674500 GTT
1 GTT
674503 TATAGACTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.18, C:0.13, G:0.21, T:0.48
Consensus pattern (32 bp):
GTTGTTATGCTCATCTCGTAGAGATACTTCTT
Found at i:674979 original size:9 final size:9
Alignment explanation
Indices: 674938--674980 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
674928 TTTTGATTCA
674938 TTTTTTCC-
1 TTTTTTCCT
*
674946 CTTTTT-CT
1 TTTTTTCCT
*
674954 TTTTTTCTT
1 TTTTTTCCT
674963 TTTTTTCCT
1 TTTTTTCCT
674972 TTTTTTCCT
1 TTTTTTCCT
674981 CTTCAAGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
7 1 0.03
8 10 0.34
9 18 0.62
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTCCT
Found at i:677929 original size:43 final size:44
Alignment explanation
Indices: 677845--677930 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 44
677835 CCGTGCATCA
* * *
677845 AACAAAACTTTTACATGTAGGGGACAGCTTTCAGTCATAACTTT
1 AACAAAACTTTTACATATAGGGGACAACTTTCACTCATAACTTT
* * *
677889 AACAAAAC-TTTACATATAGGGGATAACTTTCCCTCTTAACTT
1 AACAAAACTTTTACATATAGGGGACAACTTTCACTCATAACTT
677931 CTCTAAAACT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 28 0.78
44 8 0.22
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (44 bp):
AACAAAACTTTTACATATAGGGGACAACTTTCACTCATAACTTT
Found at i:678449 original size:36 final size:36
Alignment explanation
Indices: 678389--678457 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
678379 TACCATAAAC
* ** *
678389 TACTTTTGGTATCAATCTGGCAGGATCTTTGTGGAG
1 TACTTTTGGTATCAATATAACAGGATCTATGTGGAG
*
678425 TACTTTTGGTATTAATATAACAGGATCTATGTG
1 TACTTTTGGTATCAATATAACAGGATCTATGTG
678458 TGCATTGCTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.41
Consensus pattern (36 bp):
TACTTTTGGTATCAATATAACAGGATCTATGTGGAG
Found at i:679325 original size:22 final size:22
Alignment explanation
Indices: 679276--679357 Score: 60
Period size: 22 Copynumber: 3.7 Consensus size: 22
679266 TTAATACTTG
679276 AAAATA-AAATAAAATAAAATA
1 AAAATATAAATAAAATAAAATA
*
679297 AAAATATTAATAAAA-AATAATA
1 AAAATATAAATAAAATAA-AATA
* * **
679319 TACATATAAATATTATGAAAATA
1 AAAATATAAATAAAAT-AAAATA
* *
679342 ATAAGTATATATAAAA
1 A-AAATATAAATAAAA
679358 ATTTTGAAAA
Statistics
Matches: 44, Mismatches: 12, Indels: 7
0.70 0.19 0.11
Matches are distributed among these distances:
21 8 0.18
22 21 0.48
23 4 0.09
24 11 0.25
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.28
Consensus pattern (22 bp):
AAAATATAAATAAAATAAAATA
Found at i:679344 original size:29 final size:28
Alignment explanation
Indices: 679281--679367 Score: 83
Period size: 28 Copynumber: 3.1 Consensus size: 28
679271 ACTTGAAAAT
* *
679281 AAAATAA-AATAAAATAAAAATATTAAT-
1 AAAATAATAATATAATATAAATATT-ATG
679308 AAAA-AATAATATACATATAAATATTATG
1 AAAATAATAATATA-ATATAAATATTATG
* *
679336 AAAATAATAAGTAT-ATATAAAAATTTTG
1 AAAATAATAA-TATAATATAAATATTATG
679364 AAAA
1 AAAA
679368 GAAAGAATTA
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
26 2 0.04
27 11 0.22
28 30 0.59
29 5 0.10
30 3 0.06
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (28 bp):
AAAATAATAATATAATATAAATATTATG
Found at i:686949 original size:16 final size:16
Alignment explanation
Indices: 686928--686959 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
686918 TTACAGAAAT
*
686928 TTAAATTAAGATTAAA
1 TTAAATTAAAATTAAA
686944 TTAAATTAAAATTAAA
1 TTAAATTAAAATTAAA
686960 ATTTACATTT
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:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
TTAAATTAAAATTAAA
Found at i:702349 original size:38 final size:37
Alignment explanation
Indices: 702309--702400 Score: 121
Period size: 40 Copynumber: 2.4 Consensus size: 37
702299 AATCATATTT
*
702309 AAAATTTAGTTTTTATTTCATTTTAGTGTCTCACCATTAA
1 AAAATTTAGTTTTTATTTCATTTTAGT-ACTC-CCATT-A
*
702349 AAAATTTAGTTTTTATTTCATTTTAGTACTCCCATTC
1 AAAATTTAGTTTTTATTTCATTTTAGTACTCCCATTA
* *
702386 AAAATTGATTTTTTA
1 AAAATTTAGTTTTTA
702401 AGTTTTGAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
37 13 0.27
38 5 0.10
39 3 0.06
40 27 0.56
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.51
Consensus pattern (37 bp):
AAAATTTAGTTTTTATTTCATTTTAGTACTCCCATTA
Found at i:705045 original size:39 final size:39
Alignment explanation
Indices: 704991--705092 Score: 177
Period size: 39 Copynumber: 2.6 Consensus size: 39
704981 ATAAACAAAA
**
704991 TACTAAAATGAAACAAAAACTAAAGTTTTTAACAGTGGG
1 TACTAAAATGAAACAAAAACTAAAGTTTTTAACAGCAGG
*
705030 TACTAAAATGAAACAAAAACTAAAGTTTTTAACGGCAGG
1 TACTAAAATGAAACAAAAACTAAAGTTTTTAACAGCAGG
705069 TACTAAAATGAAACAAAAACTAAA
1 TACTAAAATGAAACAAAAACTAAA
705093 CTTTAGGTAT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 60 1.00
ACGTcount: A:0.53, C:0.12, G:0.13, T:0.23
Consensus pattern (39 bp):
TACTAAAATGAAACAAAAACTAAAGTTTTTAACAGCAGG
Found at i:707503 original size:17 final size:18
Alignment explanation
Indices: 707470--707508 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
707460 ATATTATGTA
707470 TTTAATTTATTTAAATAT
1 TTTAATTTATTTAAATAT
707488 TTTAATTTATTT-AATAT
1 TTTAATTTATTTAAATAT
707505 TTTA
1 TTTA
707509 CTAATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTAATTTATTTAAATAT
Found at i:708203 original size:21 final size:21
Alignment explanation
Indices: 708177--708355 Score: 240
Period size: 21 Copynumber: 8.6 Consensus size: 21
708167 GTTTCCAGAT
*
708177 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
708198 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
708219 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
*
708239 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTCGACTA
*
708260 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
708281 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
708302 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
* *
708323 TCGCAATGCGAACTTGGATTA
1 TCGCAATGCGAACTTCGACTA
708344 TCGCAATGCGAA
1 TCGCAATGCGAA
708356 TATGTAAATC
Statistics
Matches: 142, Mismatches: 10, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
20 17 0.12
21 125 0.88
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:708396 original size:21 final size:21
Alignment explanation
Indices: 708364--708500 Score: 145
Period size: 21 Copynumber: 6.6 Consensus size: 21
708354 AATATGTAAA
*
708364 TCGCAATGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
708385 TCACATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
* * *
708406 TCGCGTTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* *
708426 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
708447 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
708468 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
*
708489 TCGCGTTGCGAT
1 TCGCATTGCGAT
708501 TTATTCCAAA
Statistics
Matches: 96, Mismatches: 15, Indels: 10
0.79 0.12 0.08
Matches are distributed among these distances:
20 16 0.17
21 79 0.82
22 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:708416 original size:125 final size:125
Alignment explanation
Indices: 708177--708437 Score: 348
Period size: 125 Copynumber: 2.1 Consensus size: 125
708167 GTTTCCAGAT
*
708177 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCG
1 TCGCAATGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCG
* * * * *
708242 CAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGA-ACTTCGACTA
66 CAATGCGATAGTCAACTATCACAATGCGAACTCGAACTATCGCAATGCGATA-GTCGACTA
*
708302 TCGCAATGCGAACTTCGACTATCGCAATGCGAACTTGGATTATCGCAATGCGAATATGTAAATCG
1 TCGCAATGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCG
* * * * **
708367 CAATGCGATAGTCCAAGT-TCACATTGCGATAGTCGAAGT-TCGCGTTGCGATAGTCGACTA
66 CAATGCGATAGT-CAACTATCACAATGCGA-ACTCGAACTATCGCAATGCGATAGTCGACTA
*
708427 TCGCATTGCGA
1 TCGCAATGCGA
708438 TTTACATATT
Statistics
Matches: 119, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
125 110 0.92
126 9 0.08
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (125 bp):
TCGCAATGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCG
CAATGCGATAGTCAACTATCACAATGCGAACTCGAACTATCGCAATGCGATAGTCGACTA
Found at i:709245 original size:21 final size:22
Alignment explanation
Indices: 709220--709301 Score: 100
Period size: 23 Copynumber: 3.8 Consensus size: 22
709210 ATTTTGGACT
709220 ATCGCAA-CGAACTTGGAATAA
1 ATCGCAAGCGAACTTGGAATAA
* *
709241 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA-GCGAACTTGGAATAA
709262 ATCGCAA-CGAACTTGGAATAA
1 ATCGCAAGCGAACTTGGAATAA
709283 ATCGCAAAGCGAACTTGGA
1 ATCGC-AAGCGAACTTGGA
709302 CTATCGCAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
19 10 0.20
21 19 0.37
22 2 0.04
23 20 0.39
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (22 bp):
ATCGCAAGCGAACTTGGAATAA
Found at i:709275 original size:42 final size:42
Alignment explanation
Indices: 709216--709310 Score: 172
Period size: 42 Copynumber: 2.3 Consensus size: 42
709206 TGCAATTTTG
*
709216 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAAAGCGAACTTC
*
709258 GACTATCGCAACGAACTTGGAATAAATCGCAAAGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAAAGCGAACTTC
709300 GACTATCGCAA
1 GACTATCGCAA
709311 TGCGAATATG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAAAGCGAACTTC
Found at i:709307 original size:21 final size:21
Alignment explanation
Indices: 709213--709316 Score: 99
Period size: 21 Copynumber: 5.0 Consensus size: 21
709203 CGTTGCAATT
709213 TTGGACTATCGC-AA-CGAAC
1 TTGGACTATCGCAAAGCGAAC
* *
709232 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAAAGCGAAC
*
709255 TTCGACTATCGC-AA-CGAAC
1 TTGGACTATCGCAAAGCGAAC
*
709274 TTGGAATAAATCGCAAAGCGAAC
1 TTGGACT--ATCGCAAAGCGAAC
*
709297 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAAAGCGAA
709317 TATGTAAATC
Statistics
Matches: 68, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
19 16 0.24
20 1 0.01
21 27 0.40
22 3 0.04
23 21 0.31
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (21 bp):
TTGGACTATCGCAAAGCGAAC
Found at i:710121 original size:41 final size:40
Alignment explanation
Indices: 710063--710144 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 40
710053 TCATACCCAG
* *
710063 GTATAGCGCTGAGCAGGGGTAGCGCTATACCCCTACGTGGC
1 GTATAGCGCGGAGCAGGGGGAGCGCTATACCCC-ACGTGGC
* * *
710104 GTATAGCGCGGATCAGGGGGCGCGCTATATCCCACGTGGC
1 GTATAGCGCGGAGCAGGGGGAGCGCTATACCCCACGTGGC
710144 G
1 G
710145 CCAAATCAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 8 0.22
41 28 0.78
ACGTcount: A:0.18, C:0.27, G:0.37, T:0.18
Consensus pattern (40 bp):
GTATAGCGCGGAGCAGGGGGAGCGCTATACCCCACGTGGC
Found at i:712130 original size:24 final size:24
Alignment explanation
Indices: 712096--712156 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
712086 AAAATTTAGA
*
712096 AGCTCTATTGAAGCCTGAAATTCG
1 AGCTCGATTGAAGCCTGAAATTCG
* *
712120 AGTTTGATTGAAGCCTGAAATTCG
1 AGCTCGATTGAAGCCTGAAATTCG
712144 AGCTCGATTGAAG
1 AGCTCGATTGAAG
712157 TGAAACGATA
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:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (24 bp):
AGCTCGATTGAAGCCTGAAATTCG
Found at i:713767 original size:15 final size:15
Alignment explanation
Indices: 713747--713779 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
713737 TGAAATCCGA
713747 GTACCCGGT-TTTCGG
1 GTACCCGGTCTTT-GG
713762 GTACCCGGTCTTTGG
1 GTACCCGGTCTTTGG
713777 GTA
1 GTA
713780 TTTTCGGCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.09, C:0.24, G:0.33, T:0.33
Consensus pattern (15 bp):
GTACCCGGTCTTTGG
Found at i:713936 original size:22 final size:22
Alignment explanation
Indices: 713908--713953 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
713898 AAATTTTTTT
713908 AAAAATA-AAAATTATATTATTA
1 AAAAATATAAAATTA-ATTATTA
* *
713930 AAAAATATTATATTAATTATTA
1 AAAAATATAAAATTAATTATTA
713952 AA
1 AA
713954 CATATAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAAATATAAAATTAATTATTA
Found at i:714032 original size:24 final size:23
Alignment explanation
Indices: 713999--714047 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
713989 TTTATTAGTT
*
713999 TAATTTAATATATAAAATTATTAA
1 TAATTAAATATATAAAATTA-TAA
* *
714023 TAATTAAATATGTAATATTATAA
1 TAATTAAATATATAAAATTATAA
714046 TA
1 TA
714048 TATAAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TAATTAAATATATAAAATTATAA
Found at i:714364 original size:21 final size:21
Alignment explanation
Indices: 714322--714374 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
714312 ATTCTAACTA
714322 TCGCATTGCGATATCCCAAAT
1 TCGCATTGCGATATCCCAAAT
* * * *
714343 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATATCCCAAAT
*
714364 TCGCAATGCGA
1 TCGCATTGCGA
714375 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGATATCCCAAAT
Found at i:714389 original size:20 final size:20
Alignment explanation
Indices: 714364--714409 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
714354 TTTTCCTAAT
714364 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
714384 TCGCAATGTGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
714404 TCGCAA
1 TCGCAA
714410 CGAGATTCTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:714416 original size:20 final size:20
Alignment explanation
Indices: 714376--714416 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
714366 GCAATGCGAA
* *
714376 TACGTAAATCGCAATGTGAT
1 TACGTAAATCGCAACGAGAT
714396 TACGTAAATCGCAACGAGAT
1 TACGTAAATCGCAACGAGAT
714416 T
1 T
714417 CTGACTACCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (20 bp):
TACGTAAATCGCAACGAGAT
Found at i:714571 original size:20 final size:20
Alignment explanation
Indices: 714546--714759 Score: 243
Period size: 20 Copynumber: 10.6 Consensus size: 20
714536 CTTTAAAAAT
*
714546 CGCGTTGCAATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
714566 CGCGTTGCGATTTTACGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
714588 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
714607 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
714627 CTCGTTACGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
714647 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
714667 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
714687 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
714707 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
714728 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
714749 CTCGTTGCGAT
1 CGCGTTGCGAT
714760 AGTCAGAATC
Statistics
Matches: 161, Mismatches: 26, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.01
20 106 0.66
21 51 0.32
22 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:714781 original size:41 final size:41
Alignment explanation
Indices: 714548--714759 Score: 347
Period size: 41 Copynumber: 5.2 Consensus size: 41
714538 TTAAAAATCG
* *
714548 CGTTGCAATTTACGGATACGCGTTGCGATTTTACGTATTAT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
714589 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
714629 CGTTACGATTTACGGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
714669 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
714710 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
714751 CGTTGCGAT
1 CGTTGCGAT
714760 AGTCAGAATC
Statistics
Matches: 160, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
40 76 0.47
41 84 0.52
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:714791 original size:20 final size:20
Alignment explanation
Indices: 714768--714820 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
714758 ATAGTCAGAA
*
714768 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
714788 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
714808 TCGCGTTGCGATT
1 TCGCGTTGCGATT
714821 ATGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:714793 original size:61 final size:60
Alignment explanation
Indices: 714545--714819 Score: 166
Period size: 61 Copynumber: 4.5 Consensus size: 60
714535 GCTTTAAAAA
* * * * ** **
714545 TCGCGTTGC-AATTTACGGATACGCGTTGCGATTTTACGTATTATCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTTACGGATACGCGTTGCGATGTCACG-AATCGCGTTGCGATTTAATG-T
* * * * * * * * * *
714606 ACGCATTGCGA-TTTACGTATTCTCGTTACGAT-TTACGGATACGCGTTGCGATTTACGTAT
1 TCGCGTTGCGATTTTACGGATACGCGTTGCGATGTCACGAAT-CGCGTTGCGATTTA-ATGT
* * * * * **
714666 TCTCGTTGCGA-TTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTTACGGATACGCGTTGCGATGTCACGAATCG-CGTTGCGATTTAATG-T
* *
714727 ACGCGTTGCGATTTTACGGATACTCGTTGCGATAGTCA-GAATCGCGTTGCGATTTATATGT
1 TCGCGTTGCGATTTTACGGATACGCGTTGCGAT-GTCACGAATCGCGTTGCGATTTA-ATGT
** *
714788 TCGCGTTGCGATTTT-CATATTCGCGTTGCGAT
1 TCGCGTTGCGATTTTACGGATACGCGTTGCGAT
714820 TATGGAAAAT
Statistics
Matches: 166, Mismatches: 39, Indels: 19
0.74 0.17 0.08
Matches are distributed among these distances:
59 1 0.01
60 57 0.34
61 80 0.48
62 26 0.16
63 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (60 bp):
TCGCGTTGCGATTTTACGGATACGCGTTGCGATGTCACGAATCGCGTTGCGATTTAATGT
Found at i:724998 original size:33 final size:32
Alignment explanation
Indices: 724960--725043 Score: 109
Period size: 33 Copynumber: 2.7 Consensus size: 32
724950 ATGGGGGTGA
* *
724960 AGGAGATGGTGGCGGTGGTGACTTGTAATAGT
1 AGGAGATGGTGGCGGTGGTGACTTATAACAGT
*
724992 ACGGAGATGATGGCGGTGGTGACTTATAACAGT
1 A-GGAGATGGTGGCGGTGGTGACTTATAACAGT
*
725025 AAG-GA-GGTGGCGGTGGTGA
1 AGGAGATGGTGGCGGTGGTGA
725044 TGGTAACTTG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
30 13 0.28
31 2 0.04
32 2 0.04
33 29 0.63
ACGTcount: A:0.24, C:0.08, G:0.44, T:0.24
Consensus pattern (32 bp):
AGGAGATGGTGGCGGTGGTGACTTATAACAGT
Found at i:725074 original size:36 final size:36
Alignment explanation
Indices: 725027--725106 Score: 160
Period size: 36 Copynumber: 2.2 Consensus size: 36
725017 ATAACAGTAA
725027 GGAGGTGGCGGTGGTGATGGTAACTTGTAAATGTAG
1 GGAGGTGGCGGTGGTGATGGTAACTTGTAAATGTAG
725063 GGAGGTGGCGGTGGTGATGGTAACTTGTAAATGTAG
1 GGAGGTGGCGGTGGTGATGGTAACTTGTAAATGTAG
725099 GGAGGTGG
1 GGAGGTGG
725107 TGGAGAGGGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.21, C:0.05, G:0.47, T:0.26
Consensus pattern (36 bp):
GGAGGTGGCGGTGGTGATGGTAACTTGTAAATGTAG
Found at i:725202 original size:95 final size:95
Alignment explanation
Indices: 725080--725256 Score: 266
Period size: 95 Copynumber: 1.9 Consensus size: 95
725070 GCGGTGGTGA
* * * *
725080 TGGTAACTTGTAAATGTAGGGAGGTGGTGGAGAGGGAGAT-GAGAGAGGAGGTGATTTATAGTAG
1 TGGTAACTTGTAAACGTAAGGAAGTGGTGGAGAGAGAGATAG-GAGAGGAGGTGATTTATAGTAG
725144 TATGGTGGTGAAGGGCTAGGTGAGAGGGGGG
65 TATGGTGGTGAAGGGCTAGGTGAGAGGGGGG
* * *
725175 TGGTGACTTGTAAACGTAAGGAAGTGGTGGAGAGAGAGATAGGGGAGGAGGTGATTTGTAGTAGT
1 TGGTAACTTGTAAACGTAAGGAAGTGGTGGAGAGAGAGATAGGAGAGGAGGTGATTTATAGTAGT
*
725240 ATGGTGGTGGAGGGCTA
66 ATGGTGGTGAAGGGCTA
725257 AGTGTAACAC
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
95 72 0.99
96 1 0.01
ACGTcount: A:0.27, C:0.03, G:0.47, T:0.24
Consensus pattern (95 bp):
TGGTAACTTGTAAACGTAAGGAAGTGGTGGAGAGAGAGATAGGAGAGGAGGTGATTTATAGTAGT
ATGGTGGTGAAGGGCTAGGTGAGAGGGGGG
Done.