Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold425
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: 711097
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
File 2 of 5
Found at i:169817 original size:22 final size:23
Alignment explanation
Indices: 169776--169823 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
169766 AAAATATATA
*
169776 AATATTTATATTATTATAAAAAT
1 AATATTTATAATATTATAAAAAT
* *
169799 AATATTTA-AATATTTTAAAAGT
1 AATATTTATAATATTATAAAAAT
169821 AAT
1 AAT
169824 TAATTGATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
AATATTTATAATATTATAAAAAT
Found at i:170955 original size:33 final size:31
Alignment explanation
Indices: 170918--170979 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 31
170908 ATTTTTTAAA
* *
170918 ATTTTATATTTATTTAATTTAACATTATATTTC
1 ATTTTATATTTATATAAATT-ACA-TATATTTC
*
170951 ATTTTTTATTTATATAAATTACATATATT
1 ATTTTATATTTATATAAATTACATATATT
170980 AAATTTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 6 0.23
32 3 0.12
33 17 0.65
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (31 bp):
ATTTTATATTTATATAAATTACATATATTTC
Found at i:175713 original size:21 final size:21
Alignment explanation
Indices: 175687--175738 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
175677 AAATTATTAC
*
175687 TTAAATTAAAATCAAAT-TAAA
1 TTAAATTAAAAT-AAATCAAAA
* *
175708 TTAAATAAAAATAACTCAAAA
1 TTAAATTAAAATAAATCAAAA
175729 TTAAATTAAA
1 TTAAATTAAA
175739 CATTAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (21 bp):
TTAAATTAAAATAAATCAAAA
Found at i:175929 original size:17 final size:18
Alignment explanation
Indices: 175902--175996 Score: 75
Period size: 16 Copynumber: 5.7 Consensus size: 18
175892 TAATTCACAT
175902 ATTTATATTATAATTATA
1 ATTTATATTATAATTATA
175920 ATTT-TATTAT-ATTATA
1 ATTTATATTATAATTATA
175936 ATTT-TATT-TAAATTAT-
1 ATTTATATTAT-AATTATA
*
175952 -TTTATACTTA-AA--AAA
1 ATTTATA-TTATAATTATA
* *
175967 ATTT-TAATATAATAATA
1 ATTTATATTATAATTATA
175984 ATTTATATTATAA
1 ATTTATATTATAA
175997 AATTTTTAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 22
0.70 0.05 0.25
Matches are distributed among these distances:
14 3 0.05
15 8 0.13
16 21 0.34
17 19 0.31
18 11 0.18
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTATATTATAATTATA
Found at i:175950 original size:22 final size:22
Alignment explanation
Indices: 175904--175957 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
175894 ATTCACATAT
*
175904 TTATATTATAATTATAATTTTA
1 TTATATTATAATTATAATTTAA
*
175926 TTATATTATAATT-TTATTTAAA
1 TTATATTATAATTATAATTT-AA
*
175948 TTATTTTATA
1 TTATATTATA
175958 CTTAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 5 0.18
22 23 0.82
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTATATTATAATTATAATTTAA
Found at i:177634 original size:2 final size:2
Alignment explanation
Indices: 177629--177665 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
177619 TTCTTAAAAA
* *
177629 AT AT AT AT AT AT AT AT GT GT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
177666 CACAACCACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:177942 original size:19 final size:20
Alignment explanation
Indices: 177918--177961 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
177908 AAATTACAAG
*
177918 TATTAACATTTAACTTTT-A
1 TATTAACATTTAAATTTTAA
*
177937 TATTAAGATTTAAATTTTAA
1 TATTAACATTTAAATTTTAA
177957 TATTA
1 TATTA
177962 CGTGAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (20 bp):
TATTAACATTTAAATTTTAA
Found at i:184308 original size:2 final size:2
Alignment explanation
Indices: 184303--184328 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
184293 TTACCCTCAC
184303 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
184329 GTTTTCGAAA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:184674 original size:6 final size:6
Alignment explanation
Indices: 184660--184693 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
184650 AATTAGTTTT
*
184660 TTATGA TTATAA TTATAA TTATAA TTATAA TTAT
1 TTATAA TTATAA TTATAA TTATAA TTATAA TTAT
184694 TATATTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
TTATAA
Found at i:187942 original size:42 final size:42
Alignment explanation
Indices: 187883--187966 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
187873 CCACAAAGAA
187883 AACCAAAATCAAAGTGAGGTGAGGAAATTTTATGTAATAGAG
1 AACCAAAATCAAAGTGAGGTGAGGAAATTTTATGTAATAGAG
187925 AACCAAAATCAAAGTGAGGTGAGGAAATTTTATGTAATAGAG
1 AACCAAAATCAAAGTGAGGTGAGGAAATTTTATGTAATAGAG
187967 GATATTAGAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.45, C:0.07, G:0.24, T:0.24
Consensus pattern (42 bp):
AACCAAAATCAAAGTGAGGTGAGGAAATTTTATGTAATAGAG
Found at i:190700 original size:2 final size:2
Alignment explanation
Indices: 190693--190753 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
190683 AAGTAACATC
190693 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
190735 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
190754 AAAGAAGTTA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:192014 original size:61 final size:61
Alignment explanation
Indices: 191913--192033 Score: 172
Period size: 61 Copynumber: 2.0 Consensus size: 61
191903 CAAATTATTA
* * ***
191913 TTATTATAATTAAACTAATCACCTAAATCTGTGGTAATTACTTACCATAATTGACTAATTG
1 TTATTATAATTAAACTAATCACCAAAATCTATAACAATTACTTACCATAATTGACTAATTG
*
191974 TTATTATAATTAAACCT-ATCACCAAAATCTATAACGATTACTTACCATAATTGACTAATT
1 TTATTATAATTAAA-CTAATCACCAAAATCTATAACAATTACTTACCATAATTGACTAATT
192034 ATAAAGGAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
61 51 0.96
62 2 0.04
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.38
Consensus pattern (61 bp):
TTATTATAATTAAACTAATCACCAAAATCTATAACAATTACTTACCATAATTGACTAATTG
Found at i:196775 original size:20 final size:21
Alignment explanation
Indices: 196731--196777 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
196721 TTCGAAAGTA
*
196731 AAATTTATTTAAAGTTTAAAT
1 AAATTAATTTAAAGTTTAAAT
196752 -AATTAATTT-AA-TTTAAATT
1 AAATTAATTTAAAGTTTAAA-T
196771 AAATTAA
1 AAATTAA
196778 AATTAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 6 0.26
19 3 0.13
20 14 0.61
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
AAATTAATTTAAAGTTTAAAT
Found at i:196900 original size:5 final size:5
Alignment explanation
Indices: 196892--196921 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
196882 AATAAATTTA
196892 TAAAT TAAAT TAAAT TAAATT TAAAT TAAA
1 TAAAT TAAAT TAAAT TAAA-T TAAAT TAAA
196922 AAAATTGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAAAT
Found at i:196907 original size:10 final size:11
Alignment explanation
Indices: 196892--196921 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
196882 AATAAATTTA
196892 TAAATTAAA-T
1 TAAATTAAATT
196902 TAAATTAAATT
1 TAAATTAAATT
196913 TAAATTAAA
1 TAAATTAAA
196922 AAAATTGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TAAATTAAATT
Found at i:196910 original size:23 final size:21
Alignment explanation
Indices: 196879--196921 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
196869 ATTTTAATAA
196879 TAAAATAAATTTATAAATTAAAT
1 TAAAATAAA-TT-TAAATTAAAT
*
196902 TAAATTAAATTTAAATTAAA
1 TAAAATAAATTTAAATTAAA
196922 AAAATTGAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 2 0.11
23 8 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAAATAAATTTAAATTAAAT
Found at i:196917 original size:16 final size:15
Alignment explanation
Indices: 196892--196921 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
196882 AATAAATTTA
196892 TAAATTAAATTAAAT
1 TAAATTAAATTAAAT
196907 TAAATTTAAATTAAA
1 TAAA-TTAAATTAAA
196922 AAAATTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAATTAAATTAAAT
Found at i:197158 original size:2 final size:2
Alignment explanation
Indices: 197151--197190 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
197141 ATGTATGGTA
197151 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
197191 TGTCATTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:197823 original size:30 final size:32
Alignment explanation
Indices: 197787--197848 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
197777 AAATTTAATT
*
197787 ATTTTTAAT-TGAATTAAAAT-TAAAATTAAA
1 ATTTTTAATATGAATTAAAATAAAAAATTAAA
*
197817 ATTTTTAATATTAATTAAAATAAAAAATTAAA
1 ATTTTTAATATGAATTAAAATAAAAAATTAAA
197849 TTAAATTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 9 0.32
31 10 0.36
32 9 0.32
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (32 bp):
ATTTTTAATATGAATTAAAATAAAAAATTAAA
Found at i:205709 original size:316 final size:316
Alignment explanation
Indices: 205136--205757 Score: 1190
Period size: 316 Copynumber: 2.0 Consensus size: 316
205126 TGTCATTAAA
** *
205136 TGAAGCAAATATGTGAGCCACCCCAAAAACATGTTCACCCTCTCGAACAGCTGGTCCAAGGTTAG
1 TGAAGCAAATATGTGAAACACCCCAAAAACATGCTCACCCTCTCGAACAGCTGGTCCAAGGTTAG
205201 TATTCTCCTCCTTGGGCTCCCTAACTTTTCTTCTTGACTACAAAATACCCCCAAATCAAAGAATA
66 TATTCTCCTCCTTGGGCTCCCTAACTTTTCTTCTTGACTACAAAATACCCCCAAATCAAAGAATA
205266 CATCAGCTATCTTATTTGCACCTCAATCTATCAATAAATCTGTCCAATACTAATAGAAACCAAAA
131 CATCAGCTATCTTATTTGCACCTCAATCTATCAATAAATCTGTCCAATACTAATAGAAACCAAAA
*
205331 CACTCCACCCCCAAGTAAATTTTTCCAATCTGAACCTTCACATTTCGAGAGCAAGACAAAGCATT
196 CACTCCACCCCCAAGTAAAATTTTCCAATCTGAACCTTCACATTTCGAGAGCAAGACAAAGCATT
205396 CCACATTTCTAGTTTTATTTTGCTTCAATTTTTTCAAGCACAGATAAATGTGTGCT
261 CCACATTTCTAGTTTTATTTTGCTTCAATTTTTTCAAGCACAGATAAATGTGTGCT
*
205452 TGAAGCAAATATGTGAAACACCCCAAAAACATGCTCGCCCTCTCGAACAGCTGGTCCAAGGTTAG
1 TGAAGCAAATATGTGAAACACCCCAAAAACATGCTCACCCTCTCGAACAGCTGGTCCAAGGTTAG
205517 TATTCTCCTCCTTGGGCTCCCTAACTTTTCTTCTTGACTACAAAATACCCCCAAATCAAAGAATA
66 TATTCTCCTCCTTGGGCTCCCTAACTTTTCTTCTTGACTACAAAATACCCCCAAATCAAAGAATA
*
205582 CATCAGCTATCTTATTTTCACCTCAATCTATCAATAAATCTGTCCAATACTAATAGAAACCAAAA
131 CATCAGCTATCTTATTTGCACCTCAATCTATCAATAAATCTGTCCAATACTAATAGAAACCAAAA
205647 CACTCCACCCCCAAGTAAAATTTTCCAATCTGAACCTTCACATTTCGAGAGCAAGACAAAGCATT
196 CACTCCACCCCCAAGTAAAATTTTCCAATCTGAACCTTCACATTTCGAGAGCAAGACAAAGCATT
205712 CCACATTTCTAGTTTTATTTTGCTTCAATTTTTTCAAGCACAGATA
261 CCACATTTCTAGTTTTATTTTGCTTCAATTTTTTCAAGCACAGATA
205758 CAAATTAAAT
Statistics
Matches: 300, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
316 300 1.00
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.29
Consensus pattern (316 bp):
TGAAGCAAATATGTGAAACACCCCAAAAACATGCTCACCCTCTCGAACAGCTGGTCCAAGGTTAG
TATTCTCCTCCTTGGGCTCCCTAACTTTTCTTCTTGACTACAAAATACCCCCAAATCAAAGAATA
CATCAGCTATCTTATTTGCACCTCAATCTATCAATAAATCTGTCCAATACTAATAGAAACCAAAA
CACTCCACCCCCAAGTAAAATTTTCCAATCTGAACCTTCACATTTCGAGAGCAAGACAAAGCATT
CCACATTTCTAGTTTTATTTTGCTTCAATTTTTTCAAGCACAGATAAATGTGTGCT
Found at i:206271 original size:16 final size:16
Alignment explanation
Indices: 206250--206283 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
206240 CAAATACAGA
206250 TTACTCTCATTTCATT
1 TTACTCTCATTTCATT
* *
206266 TTACTCTCGTTTTATT
1 TTACTCTCATTTCATT
206282 TT
1 TT
206284 GAATAATATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.21, G:0.03, T:0.62
Consensus pattern (16 bp):
TTACTCTCATTTCATT
Found at i:208294 original size:60 final size:60
Alignment explanation
Indices: 208221--208422 Score: 404
Period size: 60 Copynumber: 3.4 Consensus size: 60
208211 CTTGTATGCT
208221 GGAGATATTCCTGAAGCTTGGCAGCTAGAAGAACATTTGATCGACATCACTGACGATGAA
1 GGAGATATTCCTGAAGCTTGGCAGCTAGAAGAACATTTGATCGACATCACTGACGATGAA
208281 GGAGATATTCCTGAAGCTTGGCAGCTAGAAGAACATTTGATCGACATCACTGACGATGAA
1 GGAGATATTCCTGAAGCTTGGCAGCTAGAAGAACATTTGATCGACATCACTGACGATGAA
208341 GGAGATATTCCTGAAGCTTGGCAGCTAGAAGAACATTTGATCGACATCACTGACGATGAA
1 GGAGATATTCCTGAAGCTTGGCAGCTAGAAGAACATTTGATCGACATCACTGACGATGAA
208401 GGAGATATTCCTGAAGCTTGGC
1 GGAGATATTCCTGAAGCTTGGC
208423 TGGAAGAGGG
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 142 1.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (60 bp):
GGAGATATTCCTGAAGCTTGGCAGCTAGAAGAACATTTGATCGACATCACTGACGATGAA
Found at i:208456 original size:165 final size:165
Alignment explanation
Indices: 208281--208587 Score: 560
Period size: 165 Copynumber: 1.9 Consensus size: 165
208271 TGACGATGAA
208281 GGAGATATTCCTGAAGCTTGGCAGCTAGAAGAACATTTGATCGACATCACTGACGATGAAGGAGA
1 GGAGATATTCCTGAAGCTTGGCAGCTAGAAGAACATTTGATCGACATCACTGACGATGAAGGAGA
* * *
208346 TATTCCTGAAGCTTGGCAGCTAGAAGAACATTTGATCGACATCACTGACGATGAAGGAGATATTC
66 TATTCCTGAAGCTTGGCAACTAGAAGAACATTTGATCGACATCACTAACGAAGAAGGAGATATTC
208411 CTGAAGCTTGGCTGGAAGAGGGCATCACGTATGCT
131 CTGAAGCTTGGCTGGAAGAGGGCATCACGTATGCT
*
208446 GGAGATATTCCTGAAGCTTGGCAGCTAGAAGTACATTTGATCGACATCACTGACGATGAAGGAGA
1 GGAGATATTCCTGAAGCTTGGCAGCTAGAAGAACATTTGATCGACATCACTGACGATGAAGGAGA
* *
208511 TTTTCCTGAAGCTTGGCAACTAGGAGAACATTTGATCGACATCACTAACGAAGAAGGAGATATTC
66 TATTCCTGAAGCTTGGCAACTAGAAGAACATTTGATCGACATCACTAACGAAGAAGGAGATATTC
208576 CTGAAGCTTGGC
131 CTGAAGCTTGGC
208588 AGATAGAAGA
Statistics
Matches: 136, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
165 136 1.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.24
Consensus pattern (165 bp):
GGAGATATTCCTGAAGCTTGGCAGCTAGAAGAACATTTGATCGACATCACTGACGATGAAGGAGA
TATTCCTGAAGCTTGGCAACTAGAAGAACATTTGATCGACATCACTAACGAAGAAGGAGATATTC
CTGAAGCTTGGCTGGAAGAGGGCATCACGTATGCT
Found at i:208517 original size:60 final size:60
Alignment explanation
Indices: 208446--208597 Score: 241
Period size: 60 Copynumber: 2.5 Consensus size: 60
208436 CACGTATGCT
* * *
208446 GGAGATATTCCTGAAGCTTGGCAGCTAGAAGTACATTTGATCGACATCACTGACGATGAA
1 GGAGATATTCCTGAAGCTTGGCAGCTAGAAGAACATTTGATCGACATCACTAACGAAGAA
* * *
208506 GGAGATTTTCCTGAAGCTTGGCAACTAGGAGAACATTTGATCGACATCACTAACGAAGAA
1 GGAGATATTCCTGAAGCTTGGCAGCTAGAAGAACATTTGATCGACATCACTAACGAAGAA
*
208566 GGAGATATTCCTGAAGCTTGGCAGATAGAAGA
1 GGAGATATTCCTGAAGCTTGGCAGCTAGAAGA
208598 TGATGGGGAA
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 82 1.00
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.24
Consensus pattern (60 bp):
GGAGATATTCCTGAAGCTTGGCAGCTAGAAGAACATTTGATCGACATCACTAACGAAGAA
Found at i:208519 original size:225 final size:225
Alignment explanation
Indices: 208188--208597 Score: 739
Period size: 225 Copynumber: 1.8 Consensus size: 225
208178 ATGTGATGGA
**
208188 GAAGCTTGGCTGGAAGAGGGCATCTTGTATGCTGGAGATATTCCTGAAGCTTGGCAGCTAGAAGA
1 GAAGCTTGGCTGGAAGAGGGCATCACGTATGCTGGAGATATTCCTGAAGCTTGGCAGCTAGAAGA
*
208253 ACATTTGATCGACATCACTGACGATGAAGGAGATATTCCTGAAGCTTGGCAGCTAGAAGAACATT
66 ACATTTGATCGACATCACTGACGATGAAGGAGATATTCCTGAAGCTTGGCAACTAGAAGAACATT
* * *
208318 TGATCGACATCACTGACGATGAAGGAGATATTCCTGAAGCTTGGCAGCTAGAAGAACATTTGATC
131 TGATCGACATCACTAACGAAGAAGGAGATATTCCTGAAGCTTGGCAGATAGAAGAACATTTGATC
208383 GACATCACTGACGATGAAGGAGATATTCCT
196 GACATCACTGACGATGAAGGAGATATTCCT
*
208413 GAAGCTTGGCTGGAAGAGGGCATCACGTATGCTGGAGATATTCCTGAAGCTTGGCAGCTAGAAGT
1 GAAGCTTGGCTGGAAGAGGGCATCACGTATGCTGGAGATATTCCTGAAGCTTGGCAGCTAGAAGA
* *
208478 ACATTTGATCGACATCACTGACGATGAAGGAGATTTTCCTGAAGCTTGGCAACTAGGAGAACATT
66 ACATTTGATCGACATCACTGACGATGAAGGAGATATTCCTGAAGCTTGGCAACTAGAAGAACATT
208543 TGATCGACATCACTAACGAAGAAGGAGATATTCCTGAAGCTTGGCAGATAGAAGA
131 TGATCGACATCACTAACGAAGAAGGAGATATTCCTGAAGCTTGGCAGATAGAAGA
208598 TGATGGGGAA
Statistics
Matches: 176, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
225 176 1.00
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (225 bp):
GAAGCTTGGCTGGAAGAGGGCATCACGTATGCTGGAGATATTCCTGAAGCTTGGCAGCTAGAAGA
ACATTTGATCGACATCACTGACGATGAAGGAGATATTCCTGAAGCTTGGCAACTAGAAGAACATT
TGATCGACATCACTAACGAAGAAGGAGATATTCCTGAAGCTTGGCAGATAGAAGAACATTTGATC
GACATCACTGACGATGAAGGAGATATTCCT
Found at i:214465 original size:16 final size:16
Alignment explanation
Indices: 214444--214478 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
214434 TTCCGGCATG
214444 AAAAGGAAGACAGGTC
1 AAAAGGAAGACAGGTC
214460 AAAAGGAAGACAGGTC
1 AAAAGGAAGACAGGTC
214476 AAA
1 AAA
214479 TGACTAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.54, C:0.11, G:0.29, T:0.06
Consensus pattern (16 bp):
AAAAGGAAGACAGGTC
Found at i:216088 original size:18 final size:18
Alignment explanation
Indices: 216067--216103 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
216057 ATCTAATTTG
216067 TATATA-TA-AAAATAAA
1 TATATATTATAAAATAAA
*
216083 TATATATTATAACATAAA
1 TATATATTATAAAATAAA
216101 TAT
1 TAT
216104 TAAAAATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 2 0.11
18 10 0.56
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
TATATATTATAAAATAAA
Found at i:216343 original size:5 final size:6
Alignment explanation
Indices: 216291--216349 Score: 50
Period size: 6 Copynumber: 9.7 Consensus size: 6
216281 AAAATAAGCA
* * *
216291 TATATA TATATA TATATA TATATTT TATTGATT TATATT TATATT TA-ATT
1 TATATT TATATT TATATT TATA-TT TA-T-ATT TATATT TATATT TATATT
216341 TA-ATT TATA
1 TATATT TATA
216350 GACACTTTTA
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
5 10 0.21
6 28 0.58
7 4 0.08
8 5 0.10
9 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (6 bp):
TATATT
Found at i:216447 original size:18 final size:19
Alignment explanation
Indices: 216417--216453 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
216407 AAATTTAATG
216417 TTTAAAATATTTAA-ATTT
1 TTTAAAATATTTAATATTT
216435 TTTATAAAT-TTTAATATTT
1 TTTA-AAATATTTAATATTT
216454 AAATATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTAAAATATTTAATATTT
Found at i:216467 original size:25 final size:25
Alignment explanation
Indices: 216422--216477 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
216412 TAATGTTTAA
* * **
216422 AATATTTAAATTTTTTATAAATTTT
1 AATATTTAAATTATATATAAATAAT
216447 AATATTTAAA-TATATATTAAATAAT
1 AATATTTAAATTATATA-TAAATAAT
216472 AATATT
1 AATATT
216478 AATATAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 4 0.15
25 22 0.85
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
AATATTTAAATTATATATAAATAAT
Found at i:216487 original size:15 final size:14
Alignment explanation
Indices: 216453--216518 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 14
216443 TTTTAATATT
216453 TAAATATATATTAAA
1 TAAATA-ATATTAAA
216468 T-AATAATATTAATA
1 TAAATAATATTAA-A
216482 TAAAT-A-ATTAAA
1 TAAATAATATTAAA
216494 -AAATTAA-ATTAAA
1 TAAA-TAATATTAAA
216507 TTCAAATAATAT
1 -T-AAATAATAT
216519 AAGCGTCACA
Statistics
Matches: 43, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
11 3 0.07
12 2 0.05
13 19 0.44
14 7 0.16
15 7 0.16
16 5 0.12
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAATAATATTAAA
Found at i:224937 original size:17 final size:18
Alignment explanation
Indices: 224910--224943 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
224900 GAAATAGTGT
224910 TTTTTTCTTTTTTCTTTC
1 TTTTTTCTTTTTTCTTTC
224928 TTTTTT-TTTTTTCTTT
1 TTTTTTCTTTTTTCTTT
224944 TGTCTTGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (18 bp):
TTTTTTCTTTTTTCTTTC
Found at i:227533 original size:23 final size:22
Alignment explanation
Indices: 227507--227549 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
227497 AGATTTTAGA
227507 TGTTAAAAATTAAATTTTAAATT
1 TGTTAAAAATT-AATTTTAAATT
* *
227530 TGTTAAATATTATTTTTAAA
1 TGTTAAAAATTAATTTTAAA
227550 GTTAAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (22 bp):
TGTTAAAAATTAATTTTAAATT
Found at i:230431 original size:19 final size:19
Alignment explanation
Indices: 230409--230449 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
230399 TTATATAAGT
*
230409 AATAAT-ATATAATATTTTA
1 AATAATAATAAAATA-TTTA
230428 AAT-ATAATAAAATATTTA
1 AATAATAATAAAATATTTA
230446 AATA
1 AATA
230450 TGATATAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATAATAATAAAATATTTA
Found at i:230461 original size:19 final size:18
Alignment explanation
Indices: 230415--230472 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
230405 AAGTAATAAT
230415 ATATAATATTTTAAATATA
1 ATATAATA-TTTAAATATA
* *
230434 ATAAAATATTTAAATATG
1 ATATAATATTTAAATATA
*
230452 ATATAGATATATAAATTATA
1 ATATA-ATATTTAAA-TATA
230472 A
1 A
230473 GATTTGTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 13 0.41
19 15 0.47
20 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
ATATAATATTTAAATATA
Found at i:230831 original size:21 final size:21
Alignment explanation
Indices: 230783--230835 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
230773 TTCTCCGATT
**
230783 ATTTTTTTTTAAAATTTTATA
1 ATTTTTTTTTAAAAAATTATA
*
230804 ATATTTTTTTAAAAAATTAT-
1 ATTTTTTTTTAAAAAATTATA
*
230824 TTTTTTTTTTAA
1 ATTTTTTTTTAA
230836 CGTTGTTGGA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
ATTTTTTTTTAAAAAATTATA
Found at i:231907 original size:53 final size:53
Alignment explanation
Indices: 231809--231914 Score: 142
Period size: 53 Copynumber: 2.0 Consensus size: 53
231799 TATTTGACTT
* *** *
231809 TTAATAATATGATTATTAATATAAAATTAAAATTAAAATTTTTAAATATTTAA
1 TTAATAATATAATTATTAATATAAAATTAAAATTAAAAAAATTAAAAATTTAA
*
231862 TTAATTAATATAATTATT-ATATAAAATTAAGATTAAAAAAATTAAAAATTTAA
1 TTAA-TAATATAATTATTAATATAAAATTAAAATTAAAAAAATTAAAAATTTAA
231915 ATCTCATCTT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
53 34 0.74
54 12 0.26
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (53 bp):
TTAATAATATAATTATTAATATAAAATTAAAATTAAAAAAATTAAAAATTTAA
Found at i:237937 original size:2 final size:2
Alignment explanation
Indices: 237925--237975 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
237915 TTAATAATCT
*
237925 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
237967 TA TA TA TA T
1 TA TA TA TA T
237976 TTAACTTGCA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:238768 original size:25 final size:24
Alignment explanation
Indices: 238718--238768 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 24
238708 TATATTTTTA
*
238718 TCATATTATTTATTTAATATTTTAT
1 TCATATTA-TTATTTAATATTATAT
238743 TCATATTA-TATTTATATAATTATAT
1 TCATATTATTATTTA-AT-ATTATAT
238768 T
1 T
238769 TAAAATTATC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 6 0.26
24 2 0.09
25 15 0.65
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (24 bp):
TCATATTATTATTTAATATTATAT
Found at i:241658 original size:11 final size:11
Alignment explanation
Indices: 241642--241698 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
241632 AAATGTAATT
241642 ATATAAATATA
1 ATATAAATATA
*
241653 ATATAAAAATA
1 ATATAAATATA
241664 AT-TAAAATATA
1 ATAT-AAATATA
241675 ATAT-AATAT-
1 ATATAAATATA
*
241684 ACATAAATA-A
1 ATATAAATATA
241694 ATATA
1 ATATA
241699 TAAAAATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
9 3 0.08
10 14 0.37
11 20 0.53
12 1 0.03
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (11 bp):
ATATAAATATA
Found at i:241696 original size:33 final size:32
Alignment explanation
Indices: 241638--241715 Score: 81
Period size: 33 Copynumber: 2.4 Consensus size: 32
241628 TATTAAATGT
*
241638 AATT-ATATAAATATAATATAAAAATA-ATTAA
1 AATTAATAT-AATATAATATAAAAATATATAAA
241669 AATATAATATAATATACATA-AATAAATATATAAA
1 AAT-TAATATAATATA-ATATAA-AAATATATAAA
*
241703 AATTTATATAATA
1 AATTAATATAATA
241716 GTCAACAACC
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
31 3 0.08
32 9 0.22
33 21 0.52
34 7 0.17
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (32 bp):
AATTAATATAATATAATATAAAAATATATAAA
Found at i:241885 original size:21 final size:19
Alignment explanation
Indices: 241854--241897 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
241844 TTTAAAATTT
*
241854 ATATAATTAATAATATAAA
1 ATATAATTAATAAGATAAA
*
241873 ATATAATTATAATACGATAAA
1 ATATAA-T-TAATAAGATAAA
241894 ATAT
1 ATAT
241898 TCAACCAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 1 0.05
21 14 0.67
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (19 bp):
ATATAATTAATAAGATAAA
Found at i:245523 original size:17 final size:17
Alignment explanation
Indices: 245499--245531 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
245489 CATTTTTTCC
245499 TTTATTTTGT-TTTTTT
1 TTTATTTTGTATTTTTT
245515 TTTATTTTTGTATTTTT
1 TTTA-TTTTGTATTTTT
245532 GCTTGTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.09, C:0.00, G:0.06, T:0.85
Consensus pattern (17 bp):
TTTATTTTGTATTTTTT
Found at i:250792 original size:103 final size:103
Alignment explanation
Indices: 250613--250809 Score: 331
Period size: 103 Copynumber: 1.9 Consensus size: 103
250603 ATAGTTACAA
* *
250613 ATATTCAAATTTGTACTATCTATTATCATCTCTAATTAAGATTAAGCTTTTCAAAACATTATATC
1 ATATTCAAATTTATACTATCTATTATCATCTCTAATTAAGATTAAGATTTTCAAAACATTATATC
250678 GAAGTTTCATTTGATTGATATATATATATTTATTTATC
66 GAAGTTTCATTTGATTGATATATATATATTTATTTATC
* * ***
250716 ATATTTAAATTTATACTATCTATTATCATCTCTAGTTAAGATTAAGATTTTCAAGGTATTATATC
1 ATATTCAAATTTATACTATCTATTATCATCTCTAATTAAGATTAAGATTTTCAAAACATTATATC
250781 GAAGTTTCATTTGATTGATATATATATAT
66 GAAGTTTCATTTGATTGATATATATATAT
250810 ATATATATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 87 1.00
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (103 bp):
ATATTCAAATTTATACTATCTATTATCATCTCTAATTAAGATTAAGATTTTCAAAACATTATATC
GAAGTTTCATTTGATTGATATATATATATTTATTTATC
Found at i:250845 original size:2 final size:2
Alignment explanation
Indices: 250798--250827 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
250788 CATTTGATTG
250798 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
250828 AAATAGAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:252407 original size:30 final size:33
Alignment explanation
Indices: 252337--252407 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 33
252327 TTAAAAATAA
*
252337 ATTTA-ATAATGTATATATTAATATATTTTATC
1 ATTTATATAATGTATATATTAAGATATTTTATC
* *
252369 ATCT-TATAAT-TGTAT-TTAAGATATTTTAT-
1 ATTTATATAATGTATATATTAAGATATTTTATC
252398 ATTTATATAA
1 ATTTATATAA
252408 ATTTTAATAC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
29 3 0.09
30 18 0.55
31 4 0.12
32 8 0.24
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (33 bp):
ATTTATATAATGTATATATTAAGATATTTTATC
Found at i:252938 original size:31 final size:29
Alignment explanation
Indices: 252903--252970 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 29
252893 ATTCAATTAG
*
252903 ATTAAATTGAATCACTAAA-AAATTTATCTAA
1 ATTAAATTGAAT-A-TAAATAAATCTATC-AA
*
252934 ATTAAATTTAATATAAATTAAATCTATCAA
1 ATTAAATTGAATATAAA-TAAATCTATCAA
252964 ATTAAAT
1 ATTAAAT
252971 ATATTATCCG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 4 0.12
30 10 0.30
31 19 0.58
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.38
Consensus pattern (29 bp):
ATTAAATTGAATATAAATAAATCTATCAA
Found at i:255593 original size:11 final size:11
Alignment explanation
Indices: 255577--255636 Score: 63
Period size: 11 Copynumber: 5.6 Consensus size: 11
255567 AAATATGATT
255577 ATATAAATATA
1 ATATAAATATA
*
255588 ATATAAAAATA
1 ATATAAATATA
255599 AT-TAAAATATA
1 ATAT-AAATATA
255610 ATAT-AATATA
1 ATATAAATATA
* *
255620 A-ATAAAAATT
1 ATATAAATATA
255630 ATATAAA
1 ATATAAA
255637 AATTTATGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
9 2 0.05
10 13 0.32
11 25 0.61
12 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATATAAATATA
Found at i:255609 original size:22 final size:22
Alignment explanation
Indices: 255581--255639 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 22
255571 ATGATTATAT
*
255581 AAATATAATATAAAAATAATTA
1 AAATATAATATAAAAATAAATA
*
255603 AAATATAATAT-AATATAAATA
1 AAATATAATATAAAAATAAATA
*
255624 AAA-ATTATATAAAAAT
1 AAATATAATATAAAAAT
255640 TTATGTAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 6 0.19
21 15 0.47
22 11 0.34
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
AAATATAATATAAAAATAAATA
Found at i:255643 original size:12 final size:11
Alignment explanation
Indices: 255574--255640 Score: 50
Period size: 11 Copynumber: 6.3 Consensus size: 11
255564 ATTAAATATG
*
255574 ATTATATAAAT
1 ATTATATAAAA
*
255585 ATAATATAAAA
1 ATTATATAAAA
*
255596 ATAAT-TAAAA
1 ATTATATAAAA
* *
255606 TATAATAT-AAT
1 -ATTATATAAAA
*
255617 A-TAAATAAAA
1 ATTATATAAAA
255627 ATTATATAAAA
1 ATTATATAAAA
255638 ATT
1 ATT
255641 TATGTAATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
9 3 0.07
10 9 0.20
11 32 0.71
12 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATTATATAAAA
Found at i:255649 original size:32 final size:32
Alignment explanation
Indices: 255577--255639 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
255567 AAATATGATT
*
255577 ATATAAATATAATATAAAAATAATTAAAATATA
1 ATAT-AATATAATATAAAAATAATAAAAATATA
255610 ATATAATATAA-ATAAAAATTATATAAAAAT
1 ATATAATATAATATAAAAA-TA-ATAAAAAT
255640 TTATGTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 7 0.26
32 9 0.33
33 11 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (32 bp):
ATATAATATAATATAAAAATAATAAAAATATA
Found at i:256050 original size:34 final size:33
Alignment explanation
Indices: 256002--256120 Score: 184
Period size: 34 Copynumber: 3.5 Consensus size: 33
255992 TGGTAAAAAC
** *
256002 CACCATTTAATCAACAATGACAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAAACTACCAAAT
*
256035 CTACCATTTAGTCAACAATGGTAAACTACCAAAT
1 C-ACCATTTAATCAACAATGGTAAACTACCAAAT
256069 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAAACTACCAAAT
256103 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
256121 TCTCCCACTT
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
33 18 0.23
34 61 0.77
ACGTcount: A:0.44, C:0.27, G:0.05, T:0.24
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:256467 original size:20 final size:20
Alignment explanation
Indices: 256439--256513 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
256429 TCATACCCTG
256439 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
256459 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
256479 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
256499 ATGTATCGATACATT
1 ATGTATCGATACATT
256514 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:256506 original size:40 final size:39
Alignment explanation
Indices: 256439--256516 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
256429 TCATACCCTG
* *
256439 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
256479 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
256517 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:270594 original size:11 final size:11
Alignment explanation
Indices: 270525--270576 Score: 86
Period size: 11 Copynumber: 4.6 Consensus size: 11
270515 CTTTACACCC
270525 AAAAAAAAACA
1 AAAAAAAAACA
*
270536 AAAAAAACACA
1 AAAAAAAAACA
270547 AAAAAAAAACA
1 AAAAAAAAACA
270558 AAACAAAAAACA
1 AAA-AAAAAACA
270570 AAAAAAA
1 AAAAAAA
270577 GAAAAAATAG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
11 27 0.71
12 11 0.29
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:270594 original size:22 final size:20
Alignment explanation
Indices: 270525--270595 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 20
270515 CTTTACACCC
270525 AAAAAAAAACAAAAAAAACACA
1 AAAAAAAAAC-AAAAAAACA-A
270547 AAAAAAAAACAAAACAAA-AA
1 AAAAAAAAACAAAA-AAACAA
*
270567 ACAAAAAAAAGAAAAAATAGCAA
1 A-AAAAAAAACAAAAAA-A-CAA
270590 AAAAAA
1 AAAAAA
270596 TAGAAGGGTC
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
20 4 0.09
21 18 0.42
22 18 0.42
23 3 0.07
ACGTcount: A:0.86, C:0.10, G:0.03, T:0.01
Consensus pattern (20 bp):
AAAAAAAAACAAAAAAACAA
Found at i:270595 original size:1 final size:1
Alignment explanation
Indices: 270525--270583 Score: 55
Period size: 1 Copynumber: 59.0 Consensus size: 1
270515 CTTTACACCC
* * * * * * *
270525 AAAAAAAAACAAAAAAAACACAAAAAAAAAACAAAACAAAAAACAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
270584 TAGCAAAAAA
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:270598 original size:12 final size:11
Alignment explanation
Indices: 270524--270595 Score: 64
Period size: 11 Copynumber: 6.8 Consensus size: 11
270514 CCTTTACACC
270524 CAAAAAAAAA-
1 CAAAAAAAAAG
270534 CAAAAAAAACA-
1 CAAAAAAAA-AG
*
270545 CAAAAAAAAAA
1 CAAAAAAAAAG
*
270556 CAAAACAAAAAA
1 CAAAA-AAAAAG
270568 C-AAAAAAAAG
1 CAAAAAAAAAG
*
270578 --AAAAAATAG
1 CAAAAAAAAAG
270587 CAAAAAAAA
1 CAAAAAAAA
270596 TAGAAGGGTC
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
9 8 0.15
10 15 0.28
11 24 0.44
12 7 0.13
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.01
Consensus pattern (11 bp):
CAAAAAAAAAG
Found at i:271952 original size:114 final size:114
Alignment explanation
Indices: 271812--272744 Score: 1008
Period size: 114 Copynumber: 7.8 Consensus size: 114
271802 GAATGTTCAT
271812 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTC
*
271877 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAATGGCA
66 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
271926 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTC
*
271991 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAACTCAGTGGCA
66 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
272040 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTC
*
272104 AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCA
66 AAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
272154 CCCTTTCAAAGCCCACAAGTTAGTGGTACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTC
* * *
272219 AAAGCCCACAAATCAGTGGCGCTCTTTTCAAAGCCCACAAGTCAGTGGCA
66 AAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCA
* * * * * *
272269 CCCTTTCAAAGCCCACAAGTTAGTGGCAC-CCTTTCAGAGCCCACAAGTTAGTGGCATTC-TTTC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTC
* * *
272332 AAAGCCCACACAAGTCGGTGGCAACCATTTTCAAAGCCCACAGAAGTCGGTGGCAA
66 AAAG-CC-CACAAGTCAGTGGC-ACC-CTTTCAAAGCCCAC--AAGTCAGTGGC-A
* * *
272388 CCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAAC
1 CCC-TTTCAAAG-CC-CACAAGTCAGTGGC-ACTCTTTTCAAAGCCCACA-AA-TCAGTGGC-AC
* * * * *
272453 CCATTTCAAAGCCCACACAAGTCGGTGGCAACCATTTTCAAAGCCCACACAAGTCGGTGGCAA
59 TCTTTTCAAAG-CC-CACAAGTCAGTGGC-ACC-CTTTCAAAG-CC-CACAAGTCAGTGGC-A
* * * * * *
272516 CCCTTTTTAAAGCCCACACAAGTCAGTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGAAAC
1 CCC-TTTCAAAG-CC-CACAAGTCAGTGGC-ACTCTTTTCAAAGCCCACA-AA-TCAGTGG-CAC
* * * * *
272581 CCATTTCAAAGCCCACACAAGTCGGTGGCAACCATTTTCAAAGCCCACACAAGTCGGTGGCAA
59 TCTTTTCAAAG-CC-CACAAGTCAGTGGC-ACC-CTTTCAAAG-CC-CACAAGTCAGTGGC-A
* * * * *
272644 CCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACGAGTCAGTGGCAAT
1 CCC-TTTCAAAG-CC-CACAAGTCAGTGGC-ACTCTTTTCAAAGCCCACA--AATCAGTGGC-AC
* *
272709 TCTTTTCAAGGCCCACATAAGTTAGTGGCACCCTTT
59 TCTTTTCAAAGCCCAC--AAGTCAGTGGCACCCTTT
272745 TTTTTTAAAA
Statistics
Matches: 744, Mismatches: 50, Indels: 38
0.89 0.06 0.05
Matches are distributed among these distances:
113 35 0.05
114 278 0.37
115 92 0.12
116 15 0.02
118 10 0.01
119 4 0.01
120 8 0.01
121 2 0.00
122 12 0.02
123 2 0.00
124 14 0.02
125 1 0.00
126 12 0.02
127 7 0.01
128 246 0.33
129 3 0.00
130 3 0.00
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.21
Consensus pattern (114 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTC
AAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:272369 original size:32 final size:30
Alignment explanation
Indices: 271815--272745 Score: 901
Period size: 32 Copynumber: 31.1 Consensus size: 30
271805 TGTTCATCCC
271815 TTTCAAAG-CC-CACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACACAAGTCAGTGGCAC-CT
271844 TTTCAAAGCCCACA-AA-TCAGTGGCACTCT
1 TTTCAAAGCCCACACAAGTCAGTGGCAC-CT
*
271873 TTTCAAAG-CC-CACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACACAAGTCAGTGGCACCT
* *
271901 TTTCAAAG-CC-CACAAGTCAATGGCACCC
1 TTTCAAAGCCCACACAAGTCAGTGGCACCT
271929 TTTCAAAG-CC-CACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACACAAGTCAGTGGCAC-CT
271958 TTTCAAAGCCCACA-AA-TCAGTGGCACTCT
1 TTTCAAAGCCCACACAAGTCAGTGGCAC-CT
*
271987 TTTCAAAG-CC-CACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACACAAGTCAGTGGCACCT
* *
272015 TTTCAAAG-CC-CACAACTCAGTGGCACCC
1 TTTCAAAGCCCACACAAGTCAGTGGCACCT
272043 TTTCAAAG-CC-CACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACACAAGTCAGTGGCAC-CT
*
272072 TTTCAAAG-CC-CACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACACAAGTCAGTGGCACCT
*
272100 TTTCAAAG-CC-CACAAGTCAGTGGCACTCC
1 TTTCAAAGCCCACACAAGTCAGTGGCAC-CT
* *
272129 TTTCAAAG-CC-CACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACACAAGTCAGTGGCACCT
* * *
272157 TTTCAAAG-CC-CACAAGTTAGTGGTACTCC
1 TTTCAAAGCCCACACAAGTCAGTGGCAC-CT
272186 TTTCAAAG-CC-CACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACACAAGTCAGTGGCAC-CT
*
272215 TTTCAAAGCCCACA-AA-TCAGTGGCGCTCT
1 TTTCAAAGCCCACACAAGTCAGTGGCAC-CT
*
272244 TTTCAAAG-CC-CACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACACAAGTCAGTGGCACCT
* *
272272 TTTCAAAG-CC-CACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACACAAGTCAGTGGCACCT
* * *
272300 TTTCAGAG-CC-CACAAGTTAGTGGCA-TT
1 TTTCAAAGCCCACACAAGTCAGTGGCACCT
*
272327 CTTTCAAAGCCCACACAAGTCGGTGGCAACCAT
1 -TTTCAAAGCCCACACAAGTCAGTGGC-ACC-T
* *
272360 TTTCAAAGCCCACAGAAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCAGTGGC-A-CCT
*
272392 TTTCAAAGCCCACACAAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCAGTGGC-A-CCT
* *
272424 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCAGTGGC-A-CCT
*
272456 TTTCAAAGCCCACACAAGTCGGTGGCAACCAT
1 TTTCAAAGCCCACACAAGTCAGTGGC-ACC-T
*
272488 TTTCAAAGCCCACACAAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCAGTGGC-A-CCT
* *
272520 TTTTAAAGCCCACACAAGTCAGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCAGTGGC-A-CCT
* * * *
272552 TTCCAAAGCCCACACAAGTCGGTGGAAACCCA
1 TTTCAAAGCCCACACAAGTCAGTGG-CA-CCT
*
272584 TTTCAAAGCCCACACAAGTCGGTGGCAACCAT
1 TTTCAAAGCCCACACAAGTCAGTGGC-ACC-T
*
272616 TTTCAAAGCCCACACAAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCAGTGGC-A-CCT
* *
272648 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCAGTGGC-A-CCT
* *
272680 TTTCAAAGCCCACACGAGTCAGTGGCAATTCT
1 TTTCAAAGCCCACACAAGTCAGTGGC-A-CCT
* * *
272712 TTTCAAGGCCCACATAAGTTAGTGGCACCCT
1 TTTCAAAGCCCACACAAGTCAGTGGCA-CCT
272743 TTT
1 TTT
272746 TTTTTAAAAA
Statistics
Matches: 822, Mismatches: 51, Indels: 56
0.88 0.05 0.06
Matches are distributed among these distances:
27 6 0.01
28 231 0.28
29 200 0.24
30 24 0.03
31 17 0.02
32 337 0.41
33 7 0.01
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (30 bp):
TTTCAAAGCCCACACAAGTCAGTGGCACCT
Found at i:273334 original size:20 final size:20
Alignment explanation
Indices: 273306--273380 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
273296 TCATACCCTG
273306 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
273326 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
273346 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
273366 ATGTATCGATACATT
1 ATGTATCGATACATT
273381 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:273373 original size:40 final size:39
Alignment explanation
Indices: 273306--273383 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
273296 TCATACCCTG
* *
273306 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
273346 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
273384 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:280967 original size:34 final size:33
Alignment explanation
Indices: 280919--281035 Score: 162
Period size: 34 Copynumber: 3.5 Consensus size: 33
280909 TGGTAAAAAC
** *
280919 CACCATTTAATCAACAATGACAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAAACTACCAAAT
* *
280952 CTACCATTTAGTCAACAATGGTAAACTATCAAAT
1 C-ACCATTTAATCAACAATGGTAAACTACCAAAT
280986 CACTCATTTAATCAACAATGGTAAACTACCAAAT
1 CAC-CATTTAATCAACAATGGTAAACTACCAAAT
*
281020 CATCATTTAATCAACA
1 CACCATTTAATCAACA
281036 CTTTCTTCAT
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
33 16 0.22
34 58 0.78
ACGTcount: A:0.44, C:0.25, G:0.05, T:0.26
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:281129 original size:32 final size:30
Alignment explanation
Indices: 281093--281155 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 30
281083 TATTAACTTA
*
281093 TTTAAATTTATATAACTAATA-ATATAAAATAT
1 TTTAAATATA-ATAA-TAATACA-ATAAAATAT
*
281125 TTTAAATATAATTATAATACAATAAAATAT
1 TTTAAATATAATAATAATACAATAAAATAT
281155 T
1 T
281156 CAAATAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 15 0.54
31 4 0.14
32 9 0.32
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (30 bp):
TTTAAATATAATAATAATACAATAAAATAT
Found at i:281723 original size:13 final size:13
Alignment explanation
Indices: 281693--281753 Score: 50
Period size: 13 Copynumber: 4.6 Consensus size: 13
281683 CTCATAAATT
* *
281693 AAATTCATGACTC
1 AAATTTATGAATC
*
281706 GAATTTATGAATC
1 AAATTTATGAATC
* *
281719 AAATTTATTAATTA
1 AAATTTATGAA-TC
* *
281733 AAATTTGTGAATT
1 AAATTTATGAATC
281746 AAATTTAT
1 AAATTTAT
281754 TAAATAAGAT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
13 27 0.73
14 10 0.27
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.43
Consensus pattern (13 bp):
AAATTTATGAATC
Found at i:281738 original size:14 final size:14
Alignment explanation
Indices: 281719--281766 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
281709 TTTATGAATC
281719 AAATTTATTAATTA
1 AAATTTATTAATTA
* *
281733 AAATTTGTGAATT-
1 AAATTTATTAATTA
*
281746 AAATTTATTAAATA
1 AAATTTATTAATTA
*
281760 AGATTTA
1 AAATTTA
281767 CTGATTGGAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (14 bp):
AAATTTATTAATTA
Found at i:281738 original size:27 final size:27
Alignment explanation
Indices: 281707--281766 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
281697 TCATGACTCG
*
281707 AATTTATGAATCAAATTTATTAATTAA
1 AATTTATGAATCAAATTTATTAAATAA
* *
281734 AATTTGTGAATTAAATTTATTAAATAA
1 AATTTATGAATCAAATTTATTAAATAA
*
281761 GATTTA
1 AATTTA
281767 CTGATTGGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.45
Consensus pattern (27 bp):
AATTTATGAATCAAATTTATTAAATAA
Found at i:282114 original size:23 final size:24
Alignment explanation
Indices: 282088--282133 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
282078 TTAATAATAT
282088 AATTATTAA-AAAAATTAAAATTA
1 AATTATTAATAAAAATTAAAATTA
* *
282111 AATTATTAATTAAGATTAAAATT
1 AATTATTAATAAAAATTAAAATT
282134 TTATAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (24 bp):
AATTATTAATAAAAATTAAAATTA
Found at i:282499 original size:82 final size:82
Alignment explanation
Indices: 282362--282530 Score: 241
Period size: 82 Copynumber: 2.1 Consensus size: 82
282352 TGAAAGTAAT
* *
282362 AAGTATATGTTTAGCAACATAAATAAATACATAAATTTCAATTGATCGATAATTAAAAT-ACGGA
1 AAGTAAATGTTTAGCAACATAAATAAATACATAAACTTCAATTGATCGATAATTAAAATGA-GGA
282426 AAGACATATCATACATAC
65 AAGACATATCATACATAC
* * *
282444 AAGTAAATGTTTAGCGACATAAGTAAATACATAAGCTTCAATTGATCGATAATTAAAATGAGGAA
1 AAGTAAATGTTTAGCAACATAAATAAATACATAAACTTCAATTGATCGATAATTAAAATGAGGAA
* * * *
282509 GGGCATATCATATATGC
66 AGACATATCATACATAC
282526 AAGTA
1 AAGTA
282531 TCCCTGCGTA
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
82 76 0.99
83 1 0.01
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.28
Consensus pattern (82 bp):
AAGTAAATGTTTAGCAACATAAATAAATACATAAACTTCAATTGATCGATAATTAAAATGAGGAA
AGACATATCATACATAC
Found at i:282980 original size:18 final size:19
Alignment explanation
Indices: 282959--282997 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
282949 AAATTCAACC
*
282959 AAAAAGAAAAA-AGAA-AA
1 AAAAAAAAAAAGAGAATAA
282976 AAAAAAAAAAAGAGAATAA
1 AAAAAAAAAAAGAGAATAA
282995 AAA
1 AAA
282998 CATTGGAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 4 0.21
19 5 0.26
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (19 bp):
AAAAAAAAAAAGAGAATAA
Found at i:283027 original size:2 final size:2
Alignment explanation
Indices: 283020--283045 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
283010 AACCTAGGGA
283020 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
283046 CCCCCCCCCC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:286287 original size:32 final size:32
Alignment explanation
Indices: 286262--286327 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
286252 TTTTTTATTT
* *
286262 AAATTATTTTGGATTTGGATCATTTTGAATTC
1 AAATTATTTCGAATTTGGATCATTTTGAATTC
* *
286294 AGATTATTTCGAATTTTGATCATTTT-AGATTC
1 AAATTATTTCGAATTTGGATCATTTTGA-ATTC
286326 AA
1 AA
286328 GTCAATCGGG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
31 1 0.04
32 27 0.96
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.48
Consensus pattern (32 bp):
AAATTATTTCGAATTTGGATCATTTTGAATTC
Found at i:292487 original size:17 final size:16
Alignment explanation
Indices: 292460--292491 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
292450 CTATTCATTA
292460 ATTATATTAAATTTAT
1 ATTATATTAAATTTAT
292476 ATTATAATTAAATTTA
1 ATTAT-ATTAAATTTA
292492 AATACAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTATATTAAATTTAT
Found at i:293927 original size:2 final size:2
Alignment explanation
Indices: 293920--293951 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
293910 AAGGTCACCC
293920 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
293952 CTCACACGCA
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:294844 original size:22 final size:20
Alignment explanation
Indices: 294819--294873 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 20
294809 AGTTATTAAT
294819 TAATTAAAAT-TTATATAAATAA
1 TAATTAAAATATT-T-TAAAT-A
294841 TAATATAAAATATTTTAAATA
1 TAAT-TAAAATATTTTAAATA
*
294862 TAATTATAATAT
1 TAATTAAAATAT
294874 GATAAAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 7 0.23
21 5 0.17
22 9 0.30
23 7 0.23
24 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAATTAAAATATTTTAAATA
Found at i:295200 original size:20 final size:21
Alignment explanation
Indices: 295170--295219 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 21
295160 TTATTCCTTT
*
295170 TTTTTTCTTTCTTTTCTC-TTA
1 TTTTTT-TTTCCTTTCTCATTA
295191 TTTTTTTTTCCTTTCTCGATTA
1 TTTTTTTTTCCTTTCTC-ATTA
295213 TTTTTTT
1 TTTTTTT
295220 AATATTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.38
21 6 0.23
22 10 0.38
ACGTcount: A:0.06, C:0.16, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTTTTTTCCTTTCTCATTA
Found at i:295280 original size:16 final size:16
Alignment explanation
Indices: 295259--295291 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
295249 TTTTAAAAAA
295259 TATTTTTCTT-TTTATT
1 TATTTTT-TTGTTTATT
295275 TATTTTTTTGTTTATT
1 TATTTTTTTGTTTATT
295291 T
1 T
295292 TTTAATGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 14 0.88
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (16 bp):
TATTTTTTTGTTTATT
Found at i:295918 original size:40 final size:35
Alignment explanation
Indices: 295856--295934 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 35
295846 ATGGAATATA
* *
295856 AATTAAATTTATGAATCGAATTTATATATTAAATCTATT
1 AATTAAATTTATAAATC-AAATT-TAT-TT-AATCTATT
*
295895 AATTAAAATTTATAAATTAAATTTATTTAATCTATT
1 AATT-AAATTTATAAATCAAATTTATTTAATCTATT
295931 AATT
1 AATT
295935 GAATCGATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
36 12 0.33
37 2 0.06
38 3 0.08
39 8 0.22
40 11 0.31
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.48
Consensus pattern (35 bp):
AATTAAATTTATAAATCAAATTTATTTAATCTATT
Found at i:297085 original size:2 final size:2
Alignment explanation
Indices: 297078--297113 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
297068 CCTAGGGATT
297078 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
297114 ACACACACAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:297118 original size:2 final size:2
Alignment explanation
Indices: 297113--297140 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
297103 CTCTCTCTCT
297113 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
297141 GGAACAGACA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:300615 original size:26 final size:25
Alignment explanation
Indices: 300560--300615 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
300550 TAATTTTCGA
*
300560 TTTAAAATTTAAATAATATATATTT
1 TTTAAAATTTAAATAATAAATATTT
300585 TTTAAAATTTAATTATAA-AAATATTT
1 TTTAAAATTTAA--ATAATAAATATTT
300611 TTTAA
1 TTTAA
300616 TAAAAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 12 0.43
26 12 0.43
27 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTAAAATTTAAATAATAAATATTT
Found at i:301342 original size:20 final size:21
Alignment explanation
Indices: 301317--301361 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
301307 CATGATACTG
* *
301317 TAAATAAATTAAATA-TTATA
1 TAAATAAATCAAAAATTTATA
*
301337 TAAATATATCAAAAATTTATA
1 TAAATAAATCAAAAATTTATA
301358 TAAA
1 TAAA
301362 ACTAATAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATAAATCAAAAATTTATA
Found at i:304236 original size:17 final size:17
Alignment explanation
Indices: 304185--304243 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
304175 ATATGTTTAT
304185 ATATTTATATTATAT-TC
1 ATATTT-TATTATATATC
* *
304202 GTCTTATTATTA-ATATC
1 ATATT-TTATTATATATC
304219 ATATTTTATTATATATC
1 ATATTTTATTATATATC
304236 ATATTTTA
1 ATATTTTA
304244 ATAATATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 8 0.23
17 26 0.74
18 1 0.03
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.58
Consensus pattern (17 bp):
ATATTTTATTATATATC
Found at i:304249 original size:33 final size:34
Alignment explanation
Indices: 304185--304250 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 34
304175 ATATGTTTAT
* * *
304185 ATATTTATATTATATTCGTCTTATTATTAATATC
1 ATATTTATATTATATTCATATTATTAATAATATC
304219 ATATTT-TATTATATATCATATT-TTAATAATAT
1 ATATTTATATTATAT-TCATATTATTAATAATAT
304251 TTTCGTATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 17 0.61
34 11 0.39
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (34 bp):
ATATTTATATTATATTCATATTATTAATAATATC
Found at i:305565 original size:2 final size:2
Alignment explanation
Indices: 305558--305586 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
305548 AAATAAATAA
305558 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
305587 AAATATAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:306336 original size:21 final size:24
Alignment explanation
Indices: 306312--306361 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 24
306302 GAATTTAAAT
306312 ATAAATTTT-TAG-AATAAAA-AA
1 ATAAATTTTATAGCAATAAAATAA
*
306333 AT-AATTTTATAGCATTAAAATAA
1 ATAAATTTTATAGCAATAAAATAA
306356 ATAAAT
1 ATAAAT
306362 AACTAAACAG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 6 0.25
21 5 0.21
22 6 0.25
23 4 0.17
24 3 0.12
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (24 bp):
ATAAATTTTATAGCAATAAAATAA
Found at i:313012 original size:23 final size:23
Alignment explanation
Indices: 312982--313029 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
312972 TGTGTAGTTT
312982 AAATTATTATTT--ATTTAA-TAA
1 AAATT-TTATTTAAATTTAATTAA
313003 AAATTTTATTTAAATTTAATTAA
1 AAATTTTATTTAAATTTAATTAA
313026 AAAT
1 AAAT
313030 ATATAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.25
21 5 0.21
22 6 0.25
23 7 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AAATTTTATTTAAATTTAATTAA
Found at i:313045 original size:12 final size:11
Alignment explanation
Indices: 312994--313054 Score: 54
Period size: 11 Copynumber: 5.6 Consensus size: 11
312984 ATTATTATTT
*
312994 ATTTAATAAAA
1 ATTTAATATAA
* *
313005 ATTTTATTTAA
1 ATTTAATATAA
313016 ATTTAAT-TAA
1 ATTTAATATAA
**
313026 AAAT-ATATAA
1 ATTTAATATAA
313036 ATATTAATATAA
1 AT-TTAATATAA
313048 ATTTAAT
1 ATTTAAT
313055 TTTTAACAGT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
9 2 0.05
10 9 0.23
11 20 0.51
12 8 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATTTAATATAA
Found at i:314278 original size:6 final size:6
Alignment explanation
Indices: 314267--314298 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
314257 AAGTTATATT
314267 ACTCGG ACTCGG ACTCGG ACTCGG ACTCGG AC
1 ACTCGG ACTCGG ACTCGG ACTCGG ACTCGG AC
314299 GTGAGCGCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.34, G:0.31, T:0.16
Consensus pattern (6 bp):
ACTCGG
Found at i:321326 original size:18 final size:19
Alignment explanation
Indices: 321303--321354 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
321293 ATTAAAAAAA
321303 TAAATAAATAAAATC-TTG
1 TAAATAAATAAAATCATTG
* * *
321321 TAAATATATATAATCATTT
1 TAAATAAATAAAATCATTG
*
321340 TACATAAAATAAAAT
1 TAAAT-AAATAAAAT
321355 TTAATTCGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 13 0.50
19 6 0.23
20 7 0.27
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (19 bp):
TAAATAAATAAAATCATTG
Found at i:321373 original size:25 final size:25
Alignment explanation
Indices: 321345--321397 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
321335 CATTTTACAT
321345 AAAATAA-AATTTA-ATTCGTTATTTA
1 AAAATAATAATTTATATTC-TTA-TTA
*
321370 AAAATAATATTTTATATTCTTATTA
1 AAAATAATAATTTATATTCTTATTA
321395 AAA
1 AAA
321398 GTTTTTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 13 0.52
26 8 0.32
27 4 0.16
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (25 bp):
AAAATAATAATTTATATTCTTATTA
Found at i:321443 original size:14 final size:15
Alignment explanation
Indices: 321426--321462 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
321416 TTTTAATAAT
321426 TTAAATTTAAATT-A
1 TTAAATTTAAATTAA
*
321440 TTAATTTTAAATTAA
1 TTAAATTTAAATTAA
321455 TTAAATTT
1 TTAAATTT
321463 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTAAATTTAAATTAA
Found at i:321473 original size:27 final size:27
Alignment explanation
Indices: 321402--321489 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
321392 TTAAAAGTTT
*
321402 TTTTATATTTGATATTTTAA-TAATTTAAA
1 TTTTATATTT-AT-TTTAAATTAA-TTAAA
* *
321431 TTTAAATTATTAATTTTAAATTAATTAAA
1 TTT-TA-TATTTATTTTAAATTAATTAAA
* * *
321460 TTTTATATTTATTTGAATTTAAATAAA
1 TTTTATATTTATTTTAAATTAATTAAA
321487 TTT
1 TTT
321490 GACTTTGGAT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
27 21 0.44
28 1 0.02
29 16 0.33
30 6 0.12
31 4 0.08
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (27 bp):
TTTTATATTTATTTTAAATTAATTAAA
Found at i:325093 original size:224 final size:227
Alignment explanation
Indices: 324702--325157 Score: 670
Period size: 224 Copynumber: 2.0 Consensus size: 227
324692 GCTTAAAGGC
* *
324702 GGCAGTTTGCATACAATACTTGATTTATGCTTTTGCATTAAAGACCAATATTAAATGAACTGCTC
1 GGCAGTTTGCATACAATACTTGATTTAGGCTTCTGCATTAAAGACCAATATTAAATGAACTGCTC
* *
324767 TAACACTTTGAAACCAGATACGTGGATGACTCTGAAAGAAAAAGCATTGATCTAGTCTTAGTGCT
66 TAACACTTAGAAACCAGATACGTGCATGAC-CTGAAAGAAAAAGCATTGATCTAGTCTTAGTGCT
* *
324832 GGTCATATTAATTAAAGTGCTGTTTGGTTTGTGCTTTTG-CT-TT-TTGTTTTTTGTTCATTTTA
130 AGTCATATTAATTAAAGTGCTGTTTGGTTGGTGCTTTTGTCTCTTGTTGTTTTTTGTTCATTTTA
* *
324894 TTTTTTGCGTTTTTGTTTTAGCATTTATTGCAA
195 TTTTTTGCCTTTTGGTTTTAGCATTTATTGCAA
* * * * *
324927 GGCAGTTTGCATACAATACTTGATTTAGGCTTCTGCATTAATGACCAATTTTGAATTAGCTGCTC
1 GGCAGTTTGCATACAATACTTGATTTAGGCTTCTGCATTAAAGACCAATATTAAATGAACTGCTC
*
324992 TAACACTATAGAAACCAGATACGTGCATGA-CTGAAAGAAAAAGTATTGATCTAGTCTTA-TCGC
66 TAACACT-TAGAAACCAGATACGTGCATGACCTGAAAGAAAAAGCATTGATCTAGTCTTAGT-GC
* *
325055 TAGTCATATTAATTAAGGTTCTGTTTGGTTGGTGCTTTTGCTATCTGCTTGTTGTTTTTTGTTCA
129 TAGTCATATTAATTAAAGTGCTGTTTGGTTGGTGCTTTTG---TCT-CTTGTTGTTTTTTGTTCA
325120 TTTTATTTTTTGCCTTTTGGTTTTAGCATTTATTGCAA
190 TTTTATTTTTTGCCTTTTGGTTTTAGCATTTATTGCAA
325158 AAATAGCTAA
Statistics
Matches: 206, Mismatches: 16, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
223 1 0.00
224 66 0.32
225 65 0.32
226 20 0.10
228 2 0.01
230 2 0.01
231 50 0.24
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (227 bp):
GGCAGTTTGCATACAATACTTGATTTAGGCTTCTGCATTAAAGACCAATATTAAATGAACTGCTC
TAACACTTAGAAACCAGATACGTGCATGACCTGAAAGAAAAAGCATTGATCTAGTCTTAGTGCTA
GTCATATTAATTAAAGTGCTGTTTGGTTGGTGCTTTTGTCTCTTGTTGTTTTTTGTTCATTTTAT
TTTTTGCCTTTTGGTTTTAGCATTTATTGCAA
Found at i:327729 original size:6 final size:6
Alignment explanation
Indices: 327720--327747 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
327710 GATCACCATC
327720 ATCAGG ATCAGG ATCAGG ATCAGG ATCA
1 ATCAGG ATCAGG ATCAGG ATCAGG ATCA
327748 TCTCTCCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.29, T:0.18
Consensus pattern (6 bp):
ATCAGG
Found at i:333264 original size:32 final size:31
Alignment explanation
Indices: 333209--333285 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 31
333199 ATTTAAATAC
* ***
333209 TAATATAAATAAAATATTTTAATATTTTTAAA
1 TAATA-AAATAAAATATTATAATAGACTTAAA
333241 TAATAAAATAAAATTATTATAATAGACTTAAA
1 TAATAAAATAAAA-TATTATAATAGACTTAAA
*
333273 TAAAAAAATAAAA
1 TAATAAAATAAAA
333286 AAAATTCAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 8 0.21
32 31 0.79
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (31 bp):
TAATAAAATAAAATATTATAATAGACTTAAA
Found at i:334441 original size:22 final size:23
Alignment explanation
Indices: 334415--334463 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
334405 AAATATTTTT
334415 ATTTAAAT-TTAATTATAAAAA-A
1 ATTTAAATATTAA-TATAAAAATA
**
334437 ATTTACGTATTAATATAAAAATA
1 ATTTAAATATTAATATAAAAATA
334460 ATTT
1 ATTT
334464 TTTTAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
ATTTAAATATTAATATAAAAATA
Found at i:336121 original size:32 final size:31
Alignment explanation
Indices: 336085--336236 Score: 103
Period size: 31 Copynumber: 4.8 Consensus size: 31
336075 TTTAAATTAG
336085 ATTATTTTATATTTTAATTTTTTTTAATTTGA
1 ATTATTTTA-ATTTTAATTTTTTTTAATTTGA
* * * * *
336117 ATTATTTTAGTTATAAATTATTTTAATTTTA
1 ATTATTTTAATTTTAATTTTTTTTAATTTGA
* *
336148 AGTTATTTTAAGTTTGAATTATTTTTT-ATTTTA
1 A-TTATTTTAA-TTTTAATT-TTTTTTAATTTGA
* * * * * *
336181 GTTA-ATTAAATTTAA-TATCTTAAATTTGA
1 ATTATTTTAATTTTAATTTTTTTTAATTTGA
*
336210 ATTATTTTAAATTTAAATTATTTTTTA
1 ATTATTTT-AATTTTAATT-TTTTTTA
336237 TATAAACTAA
Statistics
Matches: 87, Mismatches: 25, Indels: 15
0.69 0.20 0.12
Matches are distributed among these distances:
28 3 0.03
29 9 0.10
30 6 0.07
31 28 0.32
32 21 0.24
33 15 0.17
34 5 0.06
ACGTcount: A:0.34, C:0.01, G:0.05, T:0.61
Consensus pattern (31 bp):
ATTATTTTAATTTTAATTTTTTTTAATTTGA
Found at i:336221 original size:16 final size:16
Alignment explanation
Indices: 336058--336233 Score: 123
Period size: 16 Copynumber: 11.3 Consensus size: 16
336048 AAGTCGGTTA
*
336058 ATTTTAAATTT-ATTT
1 ATTTTAAATTTGAATT
* *
336073 AATTTAAATTAG-ATT
1 ATTTTAAATTTGAATT
* *
336088 ATTTTATATTTTAATT
1 ATTTTAAATTTGAATT
* *
336104 TTTTTTAATTTGAATT
1 ATTTTAAATTTGAATT
* *
336120 ATTTT-AGTTATAAATT
1 ATTTTAAATT-TGAATT
*
336136 ATTTT-AATTTTAAGTT
1 ATTTTAAATTTGAA-TT
*
336152 ATTTTAAGTTTGAATT
1 ATTTTAAATTTGAATT
** * *
336168 ATTTTTTATTTTAGTT
1 ATTTTAAATTTGAATT
*
336184 A-ATTAAATTT-AA-T
1 ATTTTAAATTTGAATT
*
336197 ATCTTAAATTTGAATT
1 ATTTTAAATTTGAATT
*
336213 ATTTTAAATTTAAATT
1 ATTTTAAATTTGAATT
336229 ATTTT
1 ATTTT
336234 TTATATAAAC
Statistics
Matches: 123, Mismatches: 30, Indels: 15
0.73 0.18 0.09
Matches are distributed among these distances:
13 2 0.02
14 9 0.07
15 33 0.27
16 73 0.59
17 6 0.05
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.60
Consensus pattern (16 bp):
ATTTTAAATTTGAATT
Found at i:336229 original size:61 final size:62
Alignment explanation
Indices: 336141--336258 Score: 166
Period size: 61 Copynumber: 1.9 Consensus size: 62
336131 AAATTATTTT
* * * * * **
336141 AATTTTAAGTTATTTTAAGTTTGAATTATTTTTTATTTTAGTTAATTAAATTTAATATCTTA
1 AATTTGAAGTTATTTTAAATTTAAATTATTTTTTATATAAACTAATTAAATTTAATATCTTA
336203 AATTTGAA-TTATTTTAAATTTAAATTATTTTTTATATAAACTAATTAAATTTAATA
1 AATTTGAAGTTATTTTAAATTTAAATTATTTTTTATATAAACTAATTAAATTTAATA
336259 GTCAAATTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
61 42 0.86
62 7 0.14
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (62 bp):
AATTTGAAGTTATTTTAAATTTAAATTATTTTTTATATAAACTAATTAAATTTAATATCTTA
Found at i:336451 original size:16 final size:17
Alignment explanation
Indices: 336425--336457 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
336415 AAGTTCAAGT
*
336425 CATTCAAATTTTAATCA
1 CATTCAAATTTGAATCA
336442 CATT-AAATTTGAATCA
1 CATTCAAATTTGAATCA
336458 TTTTAATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (17 bp):
CATTCAAATTTGAATCA
Found at i:337349 original size:18 final size:18
Alignment explanation
Indices: 337322--337360 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
337312 TTTCCTTTCA
* *
337322 TTAATTTATTATTATTAT
1 TTAATATATTATTATAAT
*
337340 TTAATATATTTTTATAAT
1 TTAATATATTATTATAAT
337358 TTA
1 TTA
337361 TAAATAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTAATATATTATTATAAT
Found at i:337779 original size:15 final size:17
Alignment explanation
Indices: 337737--337779 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
337727 TGAGAAGTTC
*
337737 AAAAATTATAATTTTTT
1 AAAAAGTATAATTTTTT
*
337754 ATAAAGTATAA-TTTTT
1 AAAAAGTATAATTTTTT
337770 AAAAAG-ATAA
1 AAAAAGTATAA
337780 AAAAATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 4 0.17
16 10 0.43
17 9 0.39
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (17 bp):
AAAAAGTATAATTTTTT
Found at i:341055 original size:2 final size:2
Alignment explanation
Indices: 341048--341073 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
341038 TTATTACATC
341048 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
341074 TGATGAAAAA
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:342020 original size:20 final size:18
Alignment explanation
Indices: 341995--342039 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 18
341985 TTATTTTATT
341995 ATTTTTAAAATATTAAAATA
1 ATTTTT-AAA-ATTAAAATA
*
342015 ATTTTTATAATTAAAATA
1 ATTTTTAAAATTAAAATA
342033 ATATTTT
1 AT-TTTT
342040 TATTATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 11 0.48
19 6 0.26
20 6 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTTTAAAATTAAAATA
Found at i:342029 original size:18 final size:20
Alignment explanation
Indices: 342006--342050 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
341996 TTTTTAAAAT
342006 ATTAAAAT-A-ATTTTTATA
1 ATTAAAATAATATTTTTATA
*
342024 ATTAAAATAATATTTTTATT
1 ATTAAAATAATATTTTTATA
342044 ATTAAAA
1 ATTAAAA
342051 AAAATTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 8 0.33
19 1 0.04
20 15 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTAAAATAATATTTTTATA
Found at i:349878 original size:30 final size:30
Alignment explanation
Indices: 349842--349903 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
349832 GCTAAAAGAA
349842 AACATGGGAAATAGAGAGGACACGAACGGG
1 AACATGGGAAATAGAGAGGACACGAACGGG
349872 AACATGGGAAATAGAGAGGACACGAACGGG
1 AACATGGGAAATAGAGAGGACACGAACGGG
349902 AA
1 AA
349904 GGCCATCCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.45, C:0.13, G:0.35, T:0.06
Consensus pattern (30 bp):
AACATGGGAAATAGAGAGGACACGAACGGG
Found at i:350676 original size:21 final size:21
Alignment explanation
Indices: 350626--350678 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 21
350616 AAATAAGGAA
350626 TTATAAATATTAAAATTTAAAT
1 TTATAAATA-TAAAATTTAAAT
*
350648 TAATTAAATA-AAAATTTAAAAT
1 TTA-TAAATATAAAATTT-AAAT
350670 TTATAAATA
1 TTATAAATA
350679 GTCCTCATGC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 13 0.48
22 8 0.30
23 6 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTATAAATATAAAATTTAAAT
Found at i:351941 original size:2 final size:2
Alignment explanation
Indices: 351934--351964 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
351924 AAAATTATGT
351934 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
351965 CTCAAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:353192 original size:14 final size:14
Alignment explanation
Indices: 353149--353201 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
353139 AATTTTTTTA
*
353149 ATTTTTT-AAATAA
1 ATTTTTTAAAATAT
* *
353162 AATTTTTAAAAAAT
1 ATTTTTTAAAATAT
*
353176 ATTTTTTAAAATGT
1 ATTTTTTAAAATAT
*
353190 ATTTTTTTAAAT
1 ATTTTTTAAAAT
353202 TCATCGAGAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 6 0.19
14 26 0.81
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (14 bp):
ATTTTTTAAAATAT
Found at i:353368 original size:27 final size:30
Alignment explanation
Indices: 353311--353374 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
353301 AAAAAAATTG
* *
353311 ATAAATAATAATATATTAATTATTATTTTTA
1 ATAAAAAATAATATATTAATTA-TATGTTTA
353342 ATAAAAAATAATAT-TTAATTA-A-GTTTA
1 ATAAAAAATAATATATTAATTATATGTTTA
353369 A-AAAAA
1 ATAAAAA
353375 TTATATTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 5 0.16
27 5 0.16
28 1 0.03
30 7 0.23
31 13 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (30 bp):
ATAAAAAATAATATATTAATTATATGTTTA
Found at i:353510 original size:14 final size:15
Alignment explanation
Indices: 353479--353509 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
353469 AATAATATTT
353479 AATTAAGTTTAAAAA
1 AATTAAGTTTAAAAA
353494 AATTAAGTTTAAAAA
1 AATTAAGTTTAAAAA
353509 A
1 A
353510 TAATCAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (15 bp):
AATTAAGTTTAAAAA
Found at i:353984 original size:24 final size:26
Alignment explanation
Indices: 353942--354006 Score: 84
Period size: 24 Copynumber: 2.7 Consensus size: 26
353932 ATTTTAATAA
*
353942 TAATATATTATTTTTTAAAATTT-AT
1 TAATGTATTATTTTTTAAAATTTAAT
353967 TAATGTATT-TTTTTT-AAATTTAAT
1 TAATGTATTATTTTTTAAAATTTAAT
*
353991 T-AGGTATTATTTTTTA
1 TAATGTATTATTTTTTA
354007 TTTTATTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 12 0.34
24 15 0.43
25 8 0.23
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.62
Consensus pattern (26 bp):
TAATGTATTATTTTTTAAAATTTAAT
Found at i:353985 original size:23 final size:24
Alignment explanation
Indices: 353942--354016 Score: 84
Period size: 23 Copynumber: 3.2 Consensus size: 24
353932 ATTTTAATAA
*
353942 TAATATATTATTTTTTAAAATTTAT
1 TAATGTATTATTTTTT-AAATTTAT
353967 TAATGTATT-TTTTTTAAATTTAAT
1 TAATGTATTATTTTTTAAATTT-AT
* *
353991 T-AGGTATTATTTTTT-ATTTTAT
1 TAATGTATTATTTTTTAAATTTAT
354013 TAAT
1 TAAT
354017 AATAATAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
22 3 0.07
23 17 0.40
24 15 0.35
25 8 0.19
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (24 bp):
TAATGTATTATTTTTTAAATTTAT
Found at i:354014 original size:22 final size:23
Alignment explanation
Indices: 353947--354014 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 23
353937 AATAATAATA
* *
353947 TATTATTTTTTAAAATTTATTAATG
1 TATTATTTTTT-AATTTTATT-AGG
*
353972 TATT-TTTTTTAAATTTAATTAGG
1 TATTATTTTTT-AATTTTATTAGG
353995 TATTATTTTTT-ATTTTATTA
1 TATTATTTTTTAATTTTATTA
354015 ATAATAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
22 8 0.21
23 6 0.16
24 20 0.53
25 4 0.11
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (23 bp):
TATTATTTTTTAATTTTATTAGG
Found at i:354136 original size:28 final size:28
Alignment explanation
Indices: 354098--354160 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
354088 TTTTAAAACT
*
354098 TAATTAA-ATATTATTTTTTATTAAAAA
1 TAATTAATATATTATTATTTATTAAAAA
**
354125 TAATTAATATATTATTATTTATTAAATT
1 TAATTAATATATTATTATTTATTAAAAA
354153 TAATTAAT
1 TAATTAAT
354161 TTATAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 7 0.22
28 25 0.78
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TAATTAATATATTATTATTTATTAAAAA
Found at i:354929 original size:2 final size:2
Alignment explanation
Indices: 354922--354959 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
354912 GATCTCATAA
354922 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
354960 GAGTAATTGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:355343 original size:2 final size:2
Alignment explanation
Indices: 355336--355375 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
355326 CATTTGGTTC
355336 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
355376 GCATGGTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:356062 original size:21 final size:21
Alignment explanation
Indices: 356038--356090 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
356028 AGTTGTATTT
*
356038 TTTCATCCAAAAAATACATTC-
1 TTTCATTCAAAAAATACA-TCA
**
356059 TTTCATTCAACCAATACATCA
1 TTTCATTCAAAAAATACATCA
356080 TTTCATTCAAA
1 TTTCATTCAAA
356091 GATACCTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.36
Consensus pattern (21 bp):
TTTCATTCAAAAAATACATCA
Found at i:361167 original size:17 final size:17
Alignment explanation
Indices: 361145--361211 Score: 70
Period size: 17 Copynumber: 4.1 Consensus size: 17
361135 TTGTATTTAA
* *
361145 TTATTTTAAGTTTGAAT
1 TTATTTTAAATTTAAAT
361162 TTATTTTAAATTTAAA-
1 TTATTTTAAATTTAAAT
*
361178 TTATATTAAATTTAAAT
1 TTATTTTAAATTTAAAT
361195 ATT-TTTT--ATTTAAAT
1 -TTATTTTAAATTTAAAT
361210 TT
1 TT
361212 TTGAGATTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
14 2 0.05
15 8 0.18
16 15 0.34
17 17 0.39
18 2 0.05
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
TTATTTTAAATTTAAAT
Done.