Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167849.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_12, 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: 22966848
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 129000 characters in sequence are not A, C, G, or T
File 93 of 129
Found at i:15215315 original size:15 final size:15
Alignment explanation
Indices: 15215289--15215336 Score: 64
Period size: 14 Copynumber: 3.3 Consensus size: 15
15215279 ACATGTTATG
15215289 TATAAT-AAATAAAT
1 TATAATCAAATAAAT
15215303 TATAATCAAATAAAT
1 TATAATCAAATAAAT
*
15215318 T-TAAACAAATAAAT
1 TATAATCAAATAAAT
*
15215332 CATAA
1 TATAA
15215337 ATAATCATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (15 bp):
TATAATCAAATAAAT
Found at i:15215509 original size:13 final size:14
Alignment explanation
Indices: 15215491--15215521 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
15215481 ATTCATATTG
15215491 AATACATCCCA-TT
1 AATACATCCCATTT
15215504 AATACATCCCATTT
1 AATACATCCCATTT
15215518 AATA
1 AATA
15215522 GTAAAATCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.42, C:0.26, G:0.00, T:0.32
Consensus pattern (14 bp):
AATACATCCCATTT
Found at i:15219574 original size:50 final size:49
Alignment explanation
Indices: 15219515--15219630 Score: 128
Period size: 50 Copynumber: 2.3 Consensus size: 49
15219505 CAATACATCT
* *
15219515 AATTATTTCATCATTTAAG-TCAAATTAAAAGTATTCTTTTTT-GAATTTTTA
1 AATT-TTTCACCATTTAAGCT-AAATTAAAA-T-TTCTTTTTTAAAATTTTTA
* * *
15219566 AATTTTTCACCATTTAAGCTTATTTAAAATTTTTTTTTTCAAAATTTTTA
1 AATTTTTCACCATTTAAGCTAAATTAAAATTTCTTTTTT-AAAATTTTTA
15219616 AATTTTTCACCATTT
1 AATTTTTCACCATTT
15219631 GAACCTATTT
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
48 8 0.14
49 1 0.02
50 43 0.75
51 5 0.09
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.53
Consensus pattern (49 bp):
AATTTTTCACCATTTAAGCTAAATTAAAATTTCTTTTTTAAAATTTTTA
Found at i:15219802 original size:24 final size:25
Alignment explanation
Indices: 15219756--15219802 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
15219746 TCACATAAAG
*
15219756 ATTTCTTAAGATTTTACTATTTGAA
1 ATTTCTTAAGATTTTAATATTTGAA
*
15219781 ATTT-TTAAGATTTTAATCTTTG
1 ATTTCTTAAGATTTTAATATTTG
15219803 GATAATTGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (25 bp):
ATTTCTTAAGATTTTAATATTTGAA
Found at i:15220921 original size:8 final size:8
Alignment explanation
Indices: 15220906--15220946 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
15220896 CTCTATCACC
15220906 TATTTTTT
1 TATTTTTT
*
15220914 TGTTTTTT
1 TATTTTTT
15220922 TA-TTTTT
1 TATTTTTT
15220929 TATTTTTT
1 TATTTTTT
15220937 TATTTTTT
1 TATTTTTT
15220945 TA
1 TA
15220947 ATTAATAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 7 0.23
8 23 0.77
ACGTcount: A:0.12, C:0.00, G:0.02, T:0.85
Consensus pattern (8 bp):
TATTTTTT
Found at i:15220946 original size:16 final size:16
Alignment explanation
Indices: 15220906--15220946 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
15220896 CTCTATCACC
*
15220906 TATTTTTTTGTTTTTT
1 TATTTTTTTATTTTTT
15220922 TA-TTTTTTATTTTTT
1 TATTTTTTTATTTTTT
15220937 TATTTTTTTA
1 TATTTTTTTA
15220947 ATTAATAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.12, C:0.00, G:0.02, T:0.85
Consensus pattern (16 bp):
TATTTTTTTATTTTTT
Found at i:15227923 original size:13 final size:14
Alignment explanation
Indices: 15227886--15227923 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
15227876 ATTTGTTAAA
*
15227886 ATTATTTTTTATCT
1 ATTATTTTTAATCT
*
15227900 ATGATTTTTAATC-
1 ATTATTTTTAATCT
15227913 ATTATTTTTAA
1 ATTATTTTTAA
15227924 ATTATTAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (14 bp):
ATTATTTTTAATCT
Found at i:15229911 original size:32 final size:31
Alignment explanation
Indices: 15229856--15229947 Score: 87
Period size: 32 Copynumber: 2.8 Consensus size: 31
15229846 TTTTTATATC
*
15229856 AATATAAATAATTACACGT-AATTTTAATATAA
1 AATATAAATAAATACA--TAAATTTTAATATAA
**
15229888 AATATAACATAAATACATAAATTTTTAATATTT
1 AATATAA-ATAAATACATAAA-TTTTAATATAA
* *
15229921 TATATAAATAAATACCTAAATTATTAA
1 AATATAAATAAATACATAAATT-TTAA
15229948 GTTTACCTAC
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
31 3 0.06
32 25 0.49
33 23 0.45
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.39
Consensus pattern (31 bp):
AATATAAATAAATACATAAATTTTAATATAA
Found at i:15230112 original size:28 final size:28
Alignment explanation
Indices: 15230057--15230113 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
15230047 AAATTAATAT
* * * *
15230057 AAAAATATATTTTTAAAATCATTCAAAA
1 AAAAATACATTGTTAAAATCAATAAAAA
*
15230085 AAAAATACATTGTTAAAATTAATAAAAA
1 AAAAATACATTGTTAAAATCAATAAAAA
15230113 A
1 A
15230114 TCAAAACAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (28 bp):
AAAAATACATTGTTAAAATCAATAAAAA
Found at i:15232467 original size:29 final size:30
Alignment explanation
Indices: 15232396--15232469 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
15232386 AAAATAGTTC
* *
15232396 TTTAAGGATTTAATTAGACAAAAATATTAT
1 TTTAAGAATTTAATTAGACAAAAATAATAT
*
15232426 TTTAA-AAGCTTAATTAGACAAAAA-AATAT
1 TTTAAGAA-TTTAATTAGACAAAAATAATAT
15232455 TTTAAGAATTTAATT
1 TTTAAGAATTTAATT
15232470 TGGTATAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
29 16 0.42
30 22 0.58
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (30 bp):
TTTAAGAATTTAATTAGACAAAAATAATAT
Found at i:15233297 original size:21 final size:18
Alignment explanation
Indices: 15233274--15233311 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
15233264 ATTTAATTCT
*
15233274 ATTATTAAAAAATAATTA
1 ATTATTATAAAATAATTA
15233292 ATTATTATAAAATAATTA
1 ATTATTATAAAATAATTA
15233310 AT
1 AT
15233312 AAATATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTATTATAAAATAATTA
Found at i:15233327 original size:21 final size:18
Alignment explanation
Indices: 15233277--15233318 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
15233267 TAATTCTATT
* *
15233277 ATTAAAAAATAATTAATT
1 ATTATAAAATAATTAATA
15233295 ATTATAAAATAATTAATA
1 ATTATAAAATAATTAATA
*
15233313 AATATA
1 ATTATA
15233319 TTAAAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTATAAAATAATTAATA
Found at i:15235593 original size:20 final size:20
Alignment explanation
Indices: 15235551--15235594 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
15235541 ACTTTATATA
* *
15235551 TATTTAATAAATAAATTTTT
1 TATTAAATAAATAAATTTGT
15235571 TATTAAATAATATAAA-TTGT
1 TATTAAATAA-ATAAATTTGT
15235591 TATT
1 TATT
15235595 TTAGATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TATTAAATAAATAAATTTGT
Found at i:15235775 original size:24 final size:24
Alignment explanation
Indices: 15235748--15235831 Score: 66
Period size: 25 Copynumber: 3.5 Consensus size: 24
15235738 TAAATACCCA
15235748 TAAAAATAAAAATAATAATAAATT
1 TAAAAATAAAAATAATAATAAATT
*** * *
15235772 T-AAAATATCTATTA-AATATAATA
1 TAAAAATAAAAATAATAATA-AATT
*
15235795 CAAAAATAAAAATAAT-ATAAATATT
1 TAAAAATAAAAATAATAAT-AA-ATT
15235820 TAAAAATAAAAA
1 TAAAAATAAAAA
15235832 CAAAAAATAT
Statistics
Matches: 43, Mismatches: 12, Indels: 9
0.67 0.19 0.14
Matches are distributed among these distances:
22 4 0.09
23 12 0.28
24 13 0.30
25 14 0.33
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (24 bp):
TAAAAATAAAAATAATAATAAATT
Found at i:15236107 original size:13 final size:13
Alignment explanation
Indices: 15236089--15236113 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15236079 TTTTATTAAT
15236089 ATTATTATATTTA
1 ATTATTATATTTA
15236102 ATTATTATATTT
1 ATTATTATATTT
15236114 TTTTGTCTTC
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTATTATATTTA
Found at i:15242104 original size:78 final size:78
Alignment explanation
Indices: 15241953--15242104 Score: 218
Period size: 79 Copynumber: 1.9 Consensus size: 78
15241943 TTGCCTAGAA
* *
15241953 CAATCAATGATCTATGGAAGATAAAATCAAATGATACGAGAATTCCATGAAAACTAAAGGTACTC
1 CAATCAATCATCTATAGAAGATAAAATCAAATGATACGAGAATTCCATGAAAACTAAAGGTACTC
15242018 AGAAATGAAGGAG
66 AGAAATGAAGGAG
* * * *
15242031 CAATCAAATCATCTATATAAGATAAAATCAAATGATACGAGGA-TCCATGAAAA-TTAAGAGTAG
1 CAATC-AATCATCTATAGAAGATAAAATCAAATGATACGAGAATTCCATGAAAACTAAAG-GTAC
15242094 TCAGAAATGAA
64 TCAGAAATGAA
15242105 TATCCTGATT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
77 4 0.06
78 29 0.44
79 33 0.50
ACGTcount: A:0.49, C:0.12, G:0.17, T:0.22
Consensus pattern (78 bp):
CAATCAATCATCTATAGAAGATAAAATCAAATGATACGAGAATTCCATGAAAACTAAAGGTACTC
AGAAATGAAGGAG
Found at i:15245088 original size:19 final size:19
Alignment explanation
Indices: 15245066--15245112 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
15245056 TTTTATTAGA
*
15245066 AATTTTTTTATTTA-AGTT
1 AATTTATTTATTTACAGTT
15245084 GAATTTATTTATTTACAGTT
1 -AATTTATTTATTTACAGTT
*
15245104 AATTAATTT
1 AATTTATTT
15245113 TAAATTAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 21 0.84
20 4 0.16
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (19 bp):
AATTTATTTATTTACAGTT
Found at i:15245525 original size:16 final size:17
Alignment explanation
Indices: 15245496--15245529 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
15245486 ACACAGATCC
*
15245496 ATTAAATCACACCAAAT
1 ATTAAATCAAACCAAAT
15245513 ATTAAA-CAAACCAAAT
1 ATTAAATCAAACCAAAT
15245529 A
1 A
15245530 CAAAATACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.59, C:0.21, G:0.00, T:0.21
Consensus pattern (17 bp):
ATTAAATCAAACCAAAT
Found at i:15247075 original size:9 final size:9
Alignment explanation
Indices: 15247063--15247096 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
15247053 TGATTATTCA
15247063 AATTAAATC
1 AATTAAATC
15247072 AATTAAATC
1 AATTAAATC
* *
15247081 AATCAATTC
1 AATTAAATC
15247090 AATTAAA
1 AATTAAA
15247097 ACTAAATTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (9 bp):
AATTAAATC
Found at i:15247349 original size:11 final size:11
Alignment explanation
Indices: 15247333--15247381 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
15247323 TTATGTAAAG
15247333 TATTATATTTA
1 TATTATATTTA
15247344 TATTATATTTA
1 TATTATATTTA
* *
15247355 TATAAAATTATA
1 TATTATATT-TA
*
15247367 TATCATAATTTA
1 TATTAT-ATTTA
15247379 TAT
1 TAT
15247382 CGATATAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
11 18 0.56
12 11 0.34
13 3 0.09
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (11 bp):
TATTATATTTA
Found at i:15255499 original size:15 final size:16
Alignment explanation
Indices: 15255471--15255512 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
15255461 TTTGAAATTT
* *
15255471 TAATCTATACATAATA
1 TAATTTATATATAATA
15255487 -AATTTATATATAATA
1 TAATTTATATATAATA
15255502 TAATTTATATA
1 TAATTTATATA
15255513 ATTTTAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATTTATATATAATA
Found at i:15256752 original size:371 final size:371
Alignment explanation
Indices: 15256069--15256811 Score: 1486
Period size: 371 Copynumber: 2.0 Consensus size: 371
15256059 GCTACAAGTT
15256069 GTAAGACGAGAATTTCAACCATCAACCGACTCGTGTCTTTCCTTCCATATTCTGGTATTAAGAAA
1 GTAAGACGAGAATTTCAACCATCAACCGACTCGTGTCTTTCCTTCCATATTCTGGTATTAAGAAA
15256134 TTCTTTCACTAATGGACTCAATTGCTTCATTTCATATCAATAACAATAGTTGCCAGTTAAACTTA
66 TTCTTTCACTAATGGACTCAATTGCTTCATTTCATATCAATAACAATAGTTGCCAGTTAAACTTA
15256199 TGACAAGATTATCAGAATAAAAAGGTGAGGTTACAGTCAGATCGGTGCTTTCCTTCGTCAGTTTA
131 TGACAAGATTATCAGAATAAAAAGGTGAGGTTACAGTCAGATCGGTGCTTTCCTTCGTCAGTTTA
15256264 ATTAGCAAACTACAAGACTTAAGACAAGATTATCAAACAAACCCAGAATTCATTTCTATATTAAA
196 ATTAGCAAACTACAAGACTTAAGACAAGATTATCAAACAAACCCAGAATTCATTTCTATATTAAA
15256329 TATGGGAAATGAAGACAAATCAGAAACGACATGGCAAGGAGACGAAGGAACATCAGCTTGTTTTG
261 TATGGGAAATGAAGACAAATCAGAAACGACATGGCAAGGAGACGAAGGAACATCAGCTTGTTTTG
15256394 TGGTGCACACGTTCAGTTCAAAGCTATGGCAATGAACACTATCAAG
326 TGGTGCACACGTTCAGTTCAAAGCTATGGCAATGAACACTATCAAG
15256440 GTAAGACGAGAATTTCAACCATCAACCGACTCGTGTCTTTCCTTCCATATTCTGGTATTAAGAAA
1 GTAAGACGAGAATTTCAACCATCAACCGACTCGTGTCTTTCCTTCCATATTCTGGTATTAAGAAA
15256505 TTCTTTCACTAATGGACTCAATTGCTTCATTTCATATCAATAACAATAGTTGCCAGTTAAACTTA
66 TTCTTTCACTAATGGACTCAATTGCTTCATTTCATATCAATAACAATAGTTGCCAGTTAAACTTA
15256570 TGACAAGATTATCAGAATAAAAAGGTGAGGTTACAGTCAGATCGGTGCTTTCCTTCGTCAGTTTA
131 TGACAAGATTATCAGAATAAAAAGGTGAGGTTACAGTCAGATCGGTGCTTTCCTTCGTCAGTTTA
15256635 ATTAGCAAACTACAAGACTTAAGACAAGATTATCAAACAAACCCAGAATTCATTTCTATATTAAA
196 ATTAGCAAACTACAAGACTTAAGACAAGATTATCAAACAAACCCAGAATTCATTTCTATATTAAA
15256700 TATGGGAAATGAAGACAAATCAGAAACGACATGGCAAGGAGACGAAGGAACATCAGCTTGTTTTG
261 TATGGGAAATGAAGACAAATCAGAAACGACATGGCAAGGAGACGAAGGAACATCAGCTTGTTTTG
15256765 TGGTGCACACGTTCAGTTCAAAGCTATGGCAATGAACACTATCAAG
326 TGGTGCACACGTTCAGTTCAAAGCTATGGCAATGAACACTATCAAG
15256811 G
1 G
15256812 GGATAGGATT
Statistics
Matches: 372, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
371 372 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (371 bp):
GTAAGACGAGAATTTCAACCATCAACCGACTCGTGTCTTTCCTTCCATATTCTGGTATTAAGAAA
TTCTTTCACTAATGGACTCAATTGCTTCATTTCATATCAATAACAATAGTTGCCAGTTAAACTTA
TGACAAGATTATCAGAATAAAAAGGTGAGGTTACAGTCAGATCGGTGCTTTCCTTCGTCAGTTTA
ATTAGCAAACTACAAGACTTAAGACAAGATTATCAAACAAACCCAGAATTCATTTCTATATTAAA
TATGGGAAATGAAGACAAATCAGAAACGACATGGCAAGGAGACGAAGGAACATCAGCTTGTTTTG
TGGTGCACACGTTCAGTTCAAAGCTATGGCAATGAACACTATCAAG
Found at i:15258084 original size:26 final size:25
Alignment explanation
Indices: 15258036--15258086 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
15258026 ATGTAAAATA
**
15258036 AAAAAATTCATATTATATTTTATAT
1 AAAAAATTCATATTATAACTTATAT
*
15258061 AAAAAATTACATCTTATAACTTATAT
1 AAAAAATT-CATATTATAACTTATAT
15258087 CAATTCAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (25 bp):
AAAAAATTCATATTATAACTTATAT
Found at i:15262596 original size:20 final size:20
Alignment explanation
Indices: 15262551--15262610 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
15262541 ATATTTAAAT
*
15262551 TATTAAAAATTAAAA-TTTGA
1 TATT-AAAATTAAAATTTTAA
15262571 TCATTAAAATTAAAATTTTAA
1 T-ATTAAAATTAAAATTTTAA
* *
15262592 TATTATATTTATAAATTTT
1 TATTAAAATTA-AAATTTT
15262611 GCAACTGTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 19 0.56
21 15 0.44
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
TATTAAAATTAAAATTTTAA
Found at i:15263208 original size:18 final size:17
Alignment explanation
Indices: 15263185--15263218 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
15263175 AACTTTAAAT
15263185 AATAATATATTATAATAA
1 AATAATATATTA-AATAA
*
15263203 AATAATTTATTAAATA
1 AATAATATATTAAATA
15263219 TTATATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATAATATATTAAATAA
Found at i:15273071 original size:2 final size:2
Alignment explanation
Indices: 15273060--15273089 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
15273050 CTGCATTTTC
15273060 AT AT -T 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 AT A
15273090 CACACACACA
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:15273094 original size:2 final size:2
Alignment explanation
Indices: 15273089--15273119 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
15273079 ATATATATAT
*
15273089 AC AC AC AC AC AC AC AC AC AC AC AC AT AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
15273120 TGCACCATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.45, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:15273242 original size:11 final size:11
Alignment explanation
Indices: 15273226--15273250 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
15273216 TGCATTCATA
15273226 TATATATATAT
1 TATATATATAT
15273237 TATATATATAT
1 TATATATATAT
15273248 TAT
1 TAT
15273251 TTTAAGGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATATATATAT
Found at i:15274432 original size:2 final size:2
Alignment explanation
Indices: 15274427--15274459 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
15274417 AAGTTTATTC
15274427 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15274460 GTCAATTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:15277710 original size:14 final size:14
Alignment explanation
Indices: 15277680--15277728 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
15277670 ATTATATGAT
15277680 ATAAAAATAATATAA
1 ATAAAAAT-ATATAA
*
15277695 ATAAAAATATAAAA
1 ATAAAAATATATAA
15277709 AT-AAAATATTATAA
1 ATAAAAATA-TATAA
15277723 ATAAAA
1 ATAAAA
15277729 TAAAAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 6 0.20
14 13 0.43
15 11 0.37
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
ATAAAAATATATAA
Found at i:15277738 original size:14 final size:14
Alignment explanation
Indices: 15277683--15277738 Score: 60
Period size: 14 Copynumber: 4.0 Consensus size: 14
15277673 ATATGATATA
*
15277683 AAAATAATATAAAT
1 AAAATAATAAAAAT
15277697 AAAA-ATATAAAAAT
1 AAAATA-ATAAAAAT
* *
15277711 AAAATATTATAAAT
1 AAAATAATAAAAAT
*
15277725 AAAATAAAAAAAAT
1 AAAATAATAAAAAT
15277739 TATATATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
13 1 0.03
14 32 0.94
15 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
AAAATAATAAAAAT
Found at i:15277740 original size:21 final size:20
Alignment explanation
Indices: 15277703--15277742 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
15277693 AAATAAAAAT
* *
15277703 ATAAAAATAAAATATTATAA
1 ATAAAAAAAAAAAATTATAA
15277723 ATAAAATAAAAAAAATTATA
1 ATAAAA-AAAAAAAATTATA
15277743 TATTTTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
ATAAAAAAAAAAAATTATAA
Found at i:15277744 original size:23 final size:25
Alignment explanation
Indices: 15277682--15277744 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
15277672 TATATGATAT
*
15277682 AAAAATAATATAAATAAAAATATAAA
1 AAAAATTATATAAAT-AAAATATAAA
*
15277708 AATAAAATATTATAAAT-AAA-ATAAA
1 AA-AAATTA-TATAAATAAAATATAAA
15277733 AAAAATTATATA
1 AAAAATTATATA
15277745 TTTTTATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
23 4 0.12
24 5 0.16
25 7 0.22
26 5 0.16
27 4 0.12
28 7 0.22
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (25 bp):
AAAAATTATATAAATAAAATATAAA
Found at i:15277746 original size:28 final size:28
Alignment explanation
Indices: 15277683--15277736 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
15277673 ATATGATATA
* *
15277683 AAAATAATATAAATAAAAATATAAAAAT
1 AAAATATTATAAATAAAAATAAAAAAAT
15277711 AAAATATTATAAAT-AAAATAAAAAAA
1 AAAATATTATAAATAAAAATAAAAAAA
15277737 ATTATATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (28 bp):
AAAATATTATAAATAAAAATAAAAAAAT
Found at i:15280430 original size:2 final size:2
Alignment explanation
Indices: 15280411--15280444 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
15280401 TCATCCAAAA
* *
15280411 AT AT AT AC AT AT AC 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
15280445 GCATCTCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:15285748 original size:18 final size:17
Alignment explanation
Indices: 15285708--15285760 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 17
15285698 ATCAAATCAC
*
15285708 ATTTAAATCGAATTTTAA
1 ATTTAAATC-AAATTTAA
15285726 A-TTAAACTCAAATTTAA
1 ATTTAAA-TCAAATTTAA
15285743 ATTTAAATTCAAATTTAA
1 ATTTAAA-TCAAATTTAA
15285761 TACTATATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 13 0.42
18 18 0.58
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.42
Consensus pattern (17 bp):
ATTTAAATCAAATTTAA
Found at i:15289030 original size:26 final size:24
Alignment explanation
Indices: 15288981--15289045 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 24
15288971 ATTAAAAAAA
15288981 AAATTCG-A-TTAAA-TTTAAATT
1 AAATTCGAATTTAAATTTTAAATT
15289002 AAATTTCGAATCTTAAATTTTAAATT
1 AAA-TTCGAAT-TTAAATTTTAAATT
*
15289028 AAATTCGAATTCAAATTT
1 AAATTCGAATTTAAATTT
15289046 AATATTTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
21 3 0.08
22 4 0.11
23 1 0.03
24 7 0.18
25 12 0.32
26 11 0.29
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.43
Consensus pattern (24 bp):
AAATTCGAATTTAAATTTTAAATT
Found at i:15289432 original size:20 final size:20
Alignment explanation
Indices: 15289409--15289455 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
15289399 AGTAAACGCA
*
15289409 TGTTTGTCCATGTAAGGATG
1 TGTTTGACCATGTAAGGATG
15289429 TGTTTGACCATGTAAGGATG
1 TGTTTGACCATGTAAGGATG
15289449 TGTTTGA
1 TGTTTGA
15289456 TATTTTACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.21, C:0.09, G:0.30, T:0.40
Consensus pattern (20 bp):
TGTTTGACCATGTAAGGATG
Found at i:15290145 original size:17 final size:17
Alignment explanation
Indices: 15290119--15290153 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
15290109 AACCAAACCA
*
15290119 AAATGGAAATTAGCTAT
1 AAATGAAAATTAGCTAT
*
15290136 AAATGAAAATTAGGTAT
1 AAATGAAAATTAGCTAT
15290153 A
1 A
15290154 TACTACAAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.17, T:0.29
Consensus pattern (17 bp):
AAATGAAAATTAGCTAT
Found at i:15290304 original size:14 final size:14
Alignment explanation
Indices: 15290285--15290332 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
15290275 TTAATTAATT
15290285 TTTATATATATATA
1 TTTATATATATATA
*
15290299 TTTATATAATGATATT
1 TTTATAT-AT-ATATA
* *
15290315 TTTAAATATTTATA
1 TTTATATATATATA
15290329 TTTA
1 TTTA
15290333 AAAAATAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 14 0.50
15 4 0.14
16 10 0.36
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
TTTATATATATATA
Found at i:15290318 original size:30 final size:30
Alignment explanation
Indices: 15290282--15290346 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
15290272 TTTTTAATTA
* * * *
15290282 ATTTTTATATATATATATTTATATAATGAT
1 ATTTTTAAATATATATATTTAAAAAATAAT
*
15290312 ATTTTTAAATATTTATATTTAAAAAATAAT
1 ATTTTTAAATATATATATTTAAAAAATAAT
15290342 ATTTT
1 ATTTT
15290347 ATTAATTTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (30 bp):
ATTTTTAAATATATATATTTAAAAAATAAT
Found at i:15291444 original size:20 final size:19
Alignment explanation
Indices: 15291399--15291445 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
15291389 ACATTATTTA
*
15291399 ATATTCAAATTATTTTTTT
1 ATATTTAAATTATTTTTTT
* *
15291418 A-ACTTAAATTGTATTTTTT
1 ATATTTAAATTAT-TTTTTT
15291437 ATATTTAAA
1 ATATTTAAA
15291446 ATTTTTAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 8 0.36
19 8 0.36
20 6 0.27
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.57
Consensus pattern (19 bp):
ATATTTAAATTATTTTTTT
Found at i:15302037 original size:15 final size:15
Alignment explanation
Indices: 15302013--15302048 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
15302003 CAGAGAAAGT
*
15302013 CTTCTGCATCAAAAA
1 CTTCTACATCAAAAA
*
15302028 CTTCTACATCAAAAT
1 CTTCTACATCAAAAA
15302043 CTTCTA
1 CTTCTA
15302049 GACCTCGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (15 bp):
CTTCTACATCAAAAA
Found at i:15308514 original size:11 final size:11
Alignment explanation
Indices: 15308478--15308516 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
15308468 TTTATAAATT
15308478 ATTTAAATTAA
1 ATTTAAATTAA
* *
15308489 ATTAAAATAAA
1 ATTTAAATTAA
*
15308500 ATTTAAATTTA
1 ATTTAAATTAA
15308511 ATTTAA
1 ATTTAA
15308517 TTATTGTTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATTTAAATTAA
Found at i:15321113 original size:10 final size:10
Alignment explanation
Indices: 15321098--15321155 Score: 71
Period size: 10 Copynumber: 5.8 Consensus size: 10
15321088 ACTTTTATTA
*
15321098 TCTCTCTTTC
1 TCTCTCTCTC
*
15321108 TCTCTCTATC
1 TCTCTCTCTC
15321118 TCTCTCTCTC
1 TCTCTCTCTC
15321128 TCTCTCTCTC
1 TCTCTCTCTC
* *
15321138 TCTCCCTCCC
1 TCTCTCTCTC
*
15321148 TCCCTCTC
1 TCTCTCTC
15321156 GCTCCCCCCT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 42 1.00
ACGTcount: A:0.02, C:0.52, G:0.00, T:0.47
Consensus pattern (10 bp):
TCTCTCTCTC
Found at i:15321123 original size:4 final size:4
Alignment explanation
Indices: 15321098--15321155 Score: 71
Period size: 4 Copynumber: 14.5 Consensus size: 4
15321088 ACTTTTATTA
* * *
15321098 TCTC TCTT TCTC TCTC TATC TCTC TCTC TCTC TCTC TCTC TCTC CCTC
1 TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC
* *
15321146 CCTC CCTC TC
1 TCTC TCTC TC
15321156 GCTCCCCCCT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.02, C:0.52, G:0.00, T:0.47
Consensus pattern (4 bp):
TCTC
Found at i:15321160 original size:10 final size:10
Alignment explanation
Indices: 15321106--15321161 Score: 53
Period size: 10 Copynumber: 5.8 Consensus size: 10
15321096 TATCTCTCTT
* *
15321106 TCTCTCTCTA
1 TCTCTCCCTC
*
15321116 TCTCTCTCTC
1 TCTCTCCCTC
*
15321126 TCTCTCTCTC
1 TCTCTCCCTC
15321136 TCTCTCCCTC
1 TCTCTCCCTC
15321146 -C-CTCCCTC
1 TCTCTCCCTC
*
15321154 TCGCTCCC
1 TCTCTCCC
15321162 CCCTTGTGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.17
9 2 0.05
10 33 0.79
ACGTcount: A:0.02, C:0.55, G:0.02, T:0.41
Consensus pattern (10 bp):
TCTCTCCCTC
Found at i:15322613 original size:2 final size:2
Alignment explanation
Indices: 15322606--15322652 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
15322596 AACCTTCGTT
* *
15322606 TC TC TC TC TC TC TC TC TC TC TC TC TG T- TC TG TC -C TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
15322646 TC TC TC T
1 TC TC TC T
15322653 TTCCTTTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.00, C:0.45, G:0.04, T:0.51
Consensus pattern (2 bp):
TC
Found at i:15324654 original size:32 final size:32
Alignment explanation
Indices: 15324594--15324654 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
15324584 AAATAATATA
* *
15324594 AAAATCAAATTAAATTCAAATATTATAAATCT
1 AAAATCAAATCAAATTCAAATATAATAAATCT
*
15324626 AAAATCAAATCAGATTCGAAATA-AATAAA
1 AAAATCAAATCAAATTC-AAATATAATAAA
15324655 CTTTCAATCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 20 0.80
33 5 0.20
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.28
Consensus pattern (32 bp):
AAAATCAAATCAAATTCAAATATAATAAATCT
Found at i:15325456 original size:13 final size:13
Alignment explanation
Indices: 15325438--15325462 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15325428 CTTTCAAGCC
15325438 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
15325451 AAAAAAGAAAAA
1 AAAAAAGAAAAA
15325463 CCTTAATATT
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAA
Found at i:15326528 original size:17 final size:18
Alignment explanation
Indices: 15326488--15326528 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
15326478 AAATTAAGAT
*
15326488 AATTTATTTATTGGTTAA
1 AATTTATTTATTCGTTAA
*
15326506 AA-TTATTT-TTCTTTAA
1 AATTTATTTATTCGTTAA
15326522 AATTTAT
1 AATTTAT
15326529 ATAATTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 8 0.40
17 10 0.50
18 2 0.10
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (18 bp):
AATTTATTTATTCGTTAA
Found at i:15336338 original size:160 final size:160
Alignment explanation
Indices: 15336074--15336397 Score: 621
Period size: 160 Copynumber: 2.0 Consensus size: 160
15336064 ATTTCTAGTT
15336074 CAAAGAAGTGCCAGATAGTTCGGAAAGACACGTACGAAAAGTAAACTTTAAGCTGCTTGGATGCG
1 CAAAGAAGTGCCAGATAGTTCGGAAAGACACGTACGAAAAGTAAACTTTAAGCTGCTTGGATGCG
* *
15336139 CGGCCAAATGCAAAGACGTAAATGCATAAACTATCTTACAGAAATCAGGACAAAAAATGTTAGGA
66 CAGCCAAATGCAAAGACGTAAATGCATAAACTATCTTACAGAAATCAGGACAAAAAATGGTAGGA
15336204 CCATGAAAATTAACTTCCTAATAATATCTG
131 CCATGAAAATTAACTTCCTAATAATATCTG
15336234 CAAAGAAGTGCCAGATAGTTCGGAAAGACACGTACGAAAAGTAAACTTTAAGCTGCTTGGATGCG
1 CAAAGAAGTGCCAGATAGTTCGGAAAGACACGTACGAAAAGTAAACTTTAAGCTGCTTGGATGCG
15336299 CAGCCAAATGCAAAGACGTAAATGCATAAACTATCTTACAGAAATCAGGACAAAAAATGGTAGGA
66 CAGCCAAATGCAAAGACGTAAATGCATAAACTATCTTACAGAAATCAGGACAAAAAATGGTAGGA
*
15336364 CCATGAAAATTAACTTCTTAATAATATCTG
131 CCATGAAAATTAACTTCCTAATAATATCTG
15336394 CAAA
1 CAAA
15336398 AGCAATGACG
Statistics
Matches: 161, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
160 161 1.00
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.22
Consensus pattern (160 bp):
CAAAGAAGTGCCAGATAGTTCGGAAAGACACGTACGAAAAGTAAACTTTAAGCTGCTTGGATGCG
CAGCCAAATGCAAAGACGTAAATGCATAAACTATCTTACAGAAATCAGGACAAAAAATGGTAGGA
CCATGAAAATTAACTTCCTAATAATATCTG
Found at i:15342410 original size:8 final size:8
Alignment explanation
Indices: 15342397--15342421 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
15342387 GACAGGGAAA
15342397 GGCAAATG
1 GGCAAATG
15342405 GGCAAATG
1 GGCAAATG
15342413 GGCAAATG
1 GGCAAATG
15342421 G
1 G
15342422 CAATACAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.40, T:0.12
Consensus pattern (8 bp):
GGCAAATG
Found at i:15347765 original size:20 final size:20
Alignment explanation
Indices: 15347728--15347766 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
15347718 ATTAATACAA
*
15347728 AATTAATTTTATTCATCAAT
1 AATTAAATTTATTCATCAAT
15347748 AATTAAATTT-TTCTATCAA
1 AATTAAATTTATTC-ATCAA
15347767 ATGTGAGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTAAATTTATTCATCAAT
Found at i:15361199 original size:75 final size:75
Alignment explanation
Indices: 15361052--15361198 Score: 253
Period size: 74 Copynumber: 2.0 Consensus size: 75
15361042 GAAAATTTTA
15361052 TTTCCAGAAAGACCAGAGGGTTTTGCCCTTCCAGGAATGGCTTTGGTAAACGATACCGTAAGTGG
1 TTTCCAGAAAGACCAGAGGGTTTTGCCCTTCCAGGAATGGCTTTGGTAAACGATACCGTAAGTGG
15361117 GATTTTTTGG
66 GATTTTTTGG
* *
15361127 TTTCCAGAAAGACCAGAGGGTTTTG-CCTTCCTGGAATGGCTTTGGTAAA-GTATACTGTAAGTG
1 TTTCCAGAAAGACCAGAGGGTTTTGCCCTTCCAGGAATGGCTTTGGTAAACG-ATACCGTAAGTG
15361190 GGATTTTTT
65 GGATTTTTT
15361199 TTTTTTAATC
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
73 1 0.01
74 43 0.62
75 25 0.36
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (75 bp):
TTTCCAGAAAGACCAGAGGGTTTTGCCCTTCCAGGAATGGCTTTGGTAAACGATACCGTAAGTGG
GATTTTTTGG
Found at i:15365630 original size:147 final size:147
Alignment explanation
Indices: 15365363--15365656 Score: 516
Period size: 147 Copynumber: 2.0 Consensus size: 147
15365353 AACCCAATTG
* *
15365363 AAAGCACTAGACATCCCATTACATAATTCCCATGTGAGAATATCCCCAAATAATAAAAGCCATTA
1 AAAGCACTAGACATCCCAATAAATAATTCCCATGTGAGAATATCCCCAAATAATAAAAGCCATTA
** *
15365428 GGAATGATTCAACACTTTGAAACAAGAAATTCCTTGATGAAATTTCACCTCTTAAGCTTGCCAAG
66 CAAATGATTCAACACTTTGAAACAAGAAATTCATTGATGAAATTTCACCTCTTAAGCTTGCCAAG
15365493 CCCTCTATTTCCTACAA
131 CCCTCTATTTCCTACAA
* *
15365510 AAAGCACTAGACATCCCAATAAATGATTCCCATGTGAGAATATCCCCAAATAATCAAAGCCATTA
1 AAAGCACTAGACATCCCAATAAATAATTCCCATGTGAGAATATCCCCAAATAATAAAAGCCATTA
15365575 CAAATGATTCAACACTTTGAAACAAGAAATTCATTGATGAAATTTCACCTCTTAAGCTTGCCAAG
66 CAAATGATTCAACACTTTGAAACAAGAAATTCATTGATGAAATTTCACCTCTTAAGCTTGCCAAG
*
15365640 CCCTCTGTTTCCTACAA
131 CCCTCTATTTCCTACAA
15365657 TTATGCAGCT
Statistics
Matches: 139, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
147 139 1.00
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.27
Consensus pattern (147 bp):
AAAGCACTAGACATCCCAATAAATAATTCCCATGTGAGAATATCCCCAAATAATAAAAGCCATTA
CAAATGATTCAACACTTTGAAACAAGAAATTCATTGATGAAATTTCACCTCTTAAGCTTGCCAAG
CCCTCTATTTCCTACAA
Found at i:15366257 original size:2 final size:2
Alignment explanation
Indices: 15366250--15366283 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
15366240 TCAGCCTCCA
15366250 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
15366284 ACCGTAGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:15378892 original size:19 final size:20
Alignment explanation
Indices: 15378858--15378897 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
15378848 AAATTGTTTG
15378858 AGAAAATATTTTTTATTTTTT
1 AGAAAATA-TTTTTATTTTTT
15378879 AGAAAATA-TTTTATTTTTT
1 AGAAAATATTTTTATTTTTT
15378898 GTTTTTAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.58
21 8 0.42
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
AGAAAATATTTTTATTTTTT
Found at i:15378902 original size:25 final size:24
Alignment explanation
Indices: 15378867--15378933 Score: 91
Period size: 25 Copynumber: 2.8 Consensus size: 24
15378857 GAGAAAATAT
15378867 TTTTTATTTTTTAGAAAATATTTTA
1 TTTTT-TTTTTTAGAAAATATTTTA
15378892 TTTTTTGTTTTTAGAAAATATTTT-
1 TTTTTT-TTTTTAGAAAATATTTTA
**
15378916 TTACTTTTTTTAGAAAAT
1 TTTTTTTTTTTAGAAAAT
15378934 GTATATGTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.31
24 5 0.13
25 22 0.56
ACGTcount: A:0.30, C:0.01, G:0.06, T:0.63
Consensus pattern (24 bp):
TTTTTTTTTTTAGAAAATATTTTA
Found at i:15381633 original size:26 final size:27
Alignment explanation
Indices: 15381578--15381634 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
15381568 ACTGCAGAAA
* * *
15381578 TTCAAGTAAAACCAGTGATAAATATTT
1 TTCAAGTAAAACCAGTAACAAATATAT
15381605 TTCAAGTAAAACCAG-AACAAATATAT
1 TTCAAGTAAAACCAGTAACAAATATAT
15381631 TTCA
1 TTCA
15381635 TTATTTCTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 12 0.44
27 15 0.56
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.30
Consensus pattern (27 bp):
TTCAAGTAAAACCAGTAACAAATATAT
Found at i:15381938 original size:3 final size:3
Alignment explanation
Indices: 15381930--15381972 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
15381920 TTGTTTTGTA
15381930 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
15381973 GACTTAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:15397028 original size:3 final size:3
Alignment explanation
Indices: 15397020--15397063 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
15397010 AAAGACAAAA
* *
15397020 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG GAG AAG AAG GAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
15397064 ACCTTATATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:15398721 original size:21 final size:23
Alignment explanation
Indices: 15398677--15398727 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 23
15398667 GATTAAAAAA
15398677 AATTATATATTTTTTATTTTTTT
1 AATTATATATTTTTTATTTTTTT
*
15398700 AATTA-ATTTTTTTTA-TTTTTT
1 AATTATATATTTTTTATTTTTTT
15398721 AA-TATAT
1 AATTATAT
15398728 TCTAAGAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 2 0.08
21 10 0.38
22 9 0.35
23 5 0.19
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (23 bp):
AATTATATATTTTTTATTTTTTT
Found at i:15403835 original size:112 final size:112
Alignment explanation
Indices: 15403638--15403862 Score: 414
Period size: 112 Copynumber: 2.0 Consensus size: 112
15403628 TGATTGTTCT
15403638 TACAAGACCATGTAGCTTGTTTAACGCTGACCTCGTCAGAAATGGGGCTTTAGTTCAGGGATTTC
1 TACAAGACCATGTAGCTTGTTTAACGCTGACCTCGTCAGAAATGGGGCTTTAGTTCAGGGATTTC
15403703 TCTTGTTTTTTCATTCTTTGTCTAGTTTTCCTGTACTATATATCAGC
66 TCTTGTTTTTTCATTCTTTGTCTAGTTTTCCTGTACTATATATCAGC
* *
15403750 TACAAGACCATGTAGCTTGTTTAACGCTGACCTCGTCAGAACTGGGGCTTTAGTTCAGGGGTTTC
1 TACAAGACCATGTAGCTTGTTTAACGCTGACCTCGTCAGAAATGGGGCTTTAGTTCAGGGATTTC
* *
15403815 TCTTGTTTTTTCATTTTTTGTCTAGTTTTCCTGTACTATCTATCAGC
66 TCTTGTTTTTTCATTCTTTGTCTAGTTTTCCTGTACTATATATCAGC
15403862 T
1 T
15403863 TGTACTCTTT
Statistics
Matches: 109, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
112 109 1.00
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.42
Consensus pattern (112 bp):
TACAAGACCATGTAGCTTGTTTAACGCTGACCTCGTCAGAAATGGGGCTTTAGTTCAGGGATTTC
TCTTGTTTTTTCATTCTTTGTCTAGTTTTCCTGTACTATATATCAGC
Found at i:15413985 original size:26 final size:25
Alignment explanation
Indices: 15413935--15413985 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
15413925 TGAATAAAAT
*
15413935 TCAAATTTGATTTGATCATTATTGAA
1 TCAAATTTGATTTGA-CATAATTGAA
15413961 TCAAATTTGAGTTTGA-ATAACTTGA
1 TCAAATTTGA-TTTGACATAA-TTGA
15413986 TTTATTGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 3 0.14
26 14 0.64
27 5 0.23
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (25 bp):
TCAAATTTGATTTGACATAATTGAA
Found at i:15414100 original size:23 final size:21
Alignment explanation
Indices: 15414056--15414101 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
15414046 ATCAAGTTTT
* *
15414056 TTATTTTAATAAATATTTTTA
1 TTATTTTAATAAAAATTATTA
15414077 TTATTTTAATTTAAAAATTATTA
1 TTATTTTAA--TAAAAATTATTA
15414100 TT
1 TT
15414102 TTATCTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
23 12 0.57
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTATTTTAATAAAAATTATTA
Found at i:15414110 original size:26 final size:26
Alignment explanation
Indices: 15414054--15414110 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
15414044 TAATCAAGTT
* *
15414054 TTTTATTTTAATAAATATTTTTATTA
1 TTTTAATTTAATAAATATTATTATTA
15414080 TTTTAATTTAA-AAATTATTATT-TTA
1 TTTTAATTTAATAAA-TATTATTATTA
15414105 TCTTTA
1 T-TTTA
15414111 TATATATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 7 0.26
26 20 0.74
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTTAATTTAATAAATATTATTATTA
Found at i:15414281 original size:11 final size:11
Alignment explanation
Indices: 15414239--15414288 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
15414229 TCTTGAATCA
*
15414239 AAATCAAATTT
1 AAATTAAATTT
*
15414250 ATAATTAAAATT
1 A-AATTAAATTT
*
15414262 CAATTAAATTT
1 AAATTAAATTT
15414273 AAATTAAATTTT
1 AAATTAAA-TTT
15414285 AAAT
1 AAAT
15414289 AATAAATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
11 17 0.53
12 15 0.47
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (11 bp):
AAATTAAATTT
Found at i:15422212 original size:2 final size:2
Alignment explanation
Indices: 15422205--15422235 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
15422195 AAATACAGCT
15422205 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
15422236 CAATCACTTT
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:15424059 original size:35 final size:34
Alignment explanation
Indices: 15423999--15424074 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 34
15423989 AAGAACAATA
*
15423999 AAAT-TTTTATTTTTATTTTTAAATTTTTCAAAATT
1 AAATATTTTATTTTTATTTATAAATTTTT-AAAA-T
15424034 AAATATTTTA-TTTTA-TTATATAATTTTTAAAAT
1 AAATATTTTATTTTTATTTATA-AATTTTTAAAAT
15424067 ATAATATT
1 A-AATATT
15424075 ACAATTCTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
33 2 0.05
34 14 0.38
35 16 0.43
36 5 0.14
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (34 bp):
AAATATTTTATTTTTATTTATAAATTTTTAAAAT
Found at i:15426348 original size:2 final size:2
Alignment explanation
Indices: 15426341--15426366 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15426331 TTTAATATGC
15426341 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
15426367 GCATATGCTT
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:15427210 original size:2 final size:2
Alignment explanation
Indices: 15427168--15427193 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15427158 GACAATTATC
15427168 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
15427194 CAGTGACAAA
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:15436510 original size:29 final size:30
Alignment explanation
Indices: 15436477--15436538 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
15436467 ATGAATATAA
*
15436477 TTATA-ATAAAATAAAATTGGAAAATTTAT
1 TTATATATAAAATAAAATTCGAAAATTTAT
* * * *
15436506 TTATATTTTAAATAAAATTCTAAATTTTAT
1 TTATATATAAAATAAAATTCGAAAATTTAT
15436536 TTA
1 TTA
15436539 AGTATTAAGC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 5 0.19
30 22 0.81
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (30 bp):
TTATATATAAAATAAAATTCGAAAATTTAT
Found at i:15438814 original size:2 final size:2
Alignment explanation
Indices: 15438807--15438836 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15438797 GGTGAAAAAC
15438807 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
15438837 ATATTAGCGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:15440596 original size:16 final size:18
Alignment explanation
Indices: 15440577--15440612 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
15440567 AATTTTTTAA
15440577 AAATTAAAAT-T-AAAAT
1 AAATTAAAATATGAAAAT
15440593 AAATTAAAATATGAAAAT
1 AAATTAAAATATGAAAAT
15440611 AA
1 AA
15440613 GAAAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 1 0.06
18 7 0.39
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
AAATTAAAATATGAAAAT
Found at i:15440793 original size:7 final size:7
Alignment explanation
Indices: 15440781--15440809 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
15440771 CCTTTTTTAG
15440781 AAATAAA
1 AAATAAA
15440788 AAAT-AA
1 AAATAAA
15440794 AAATAAA
1 AAATAAA
15440801 AAATAAA
1 AAATAAA
15440808 AA
1 AA
15440810 CAAAAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAATAAA
Found at i:15440799 original size:13 final size:13
Alignment explanation
Indices: 15440781--15440815 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
15440771 CCTTTTTTAG
15440781 AAATAAAAAATAA
1 AAATAAAAAATAA
15440794 AAATAAAAAATAA
1 AAATAAAAAATAA
*
15440807 AAACAAAAA
1 AAATAAAAA
15440816 TATTTTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.86, C:0.03, G:0.00, T:0.11
Consensus pattern (13 bp):
AAATAAAAAATAA
Found at i:15457672 original size:31 final size:30
Alignment explanation
Indices: 15457615--15457672 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 30
15457605 TTTAAAATTT
**
15457615 AATTTAAATTAAATTAAAATTTAATTTTTA
1 AATTTAAATTAAATTAAAATAAAATTTTTA
* *
15457645 AATTTAATATTTACTTAAAATAAAATTT
1 AATTTAA-ATTAAATTAAAATAAAATTT
15457673 AAATTACTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 7 0.30
31 16 0.70
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (30 bp):
AATTTAAATTAAATTAAAATAAAATTTTTA
Found at i:15457674 original size:36 final size:37
Alignment explanation
Indices: 15457593--15457674 Score: 107
Period size: 36 Copynumber: 2.3 Consensus size: 37
15457583 AGGTTCGACT
*
15457593 TAAAATTT-ATTGTTTAAAATTTAATTTAAATTAAAT
1 TAAAATTTAATTGTTTAAAATTTAATTTAAATTAAAA
* *
15457629 TAAAATTTAATT-TTT-AAATTTAATATTTACTTAAAA
1 TAAAATTTAATTGTTTAAAATTTAAT-TTAAATTAAAA
15457665 TAAAATTTAA
1 TAAAATTTAA
15457675 ATTACTTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
35 9 0.22
36 29 0.71
37 3 0.07
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (37 bp):
TAAAATTTAATTGTTTAAAATTTAATTTAAATTAAAA
Found at i:15457881 original size:18 final size:19
Alignment explanation
Indices: 15457857--15457908 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
15457847 ATTTAAATAT
15457857 TTAAATTTAATTTATTCAA
1 TTAAATTTAATTTATTCAA
* * *
15457876 -TAAATTAAATTTTTTGAA
1 TTAAATTTAATTTATTCAA
15457894 TTTAAATTTAATTTA
1 -TTAAATTTAATTTA
15457909 ATAATAATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 15 0.58
20 11 0.42
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (19 bp):
TTAAATTTAATTTATTCAA
Found at i:15464741 original size:10 final size:10
Alignment explanation
Indices: 15464726--15464751 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
15464716 CGATGTTATA
15464726 TATATATATG
1 TATATATATG
15464736 TATATATATG
1 TATATATATG
15464746 TATATA
1 TATATA
15464752 ACATCTTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (10 bp):
TATATATATG
Found at i:15471189 original size:27 final size:27
Alignment explanation
Indices: 15471159--15471215 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
15471149 TTAAAGTTCG
* *
15471159 TTTATATTTGTTTA-TTGTATTTTTATT
1 TTTA-ATTTGTTTAGTTATAATTTTATT
*
15471186 TTTAATTTTTTTAGTTATAATTTTATT
1 TTTAATTTGTTTAGTTATAATTTTATT
15471213 TTT
1 TTT
15471216 TAAAATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (27 bp):
TTTAATTTGTTTAGTTATAATTTTATT
Found at i:15472226 original size:21 final size:22
Alignment explanation
Indices: 15472168--15472228 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 22
15472158 GTTGTTATTA
* *
15472168 TTATTCATTTATGATATTATTACG
1 TTATTCATTTATTAT-TTA-TACT
*
15472192 TTATCTTATGTTATTATTTATA-T
1 TTAT-TCAT-TTATTATTTATACT
15472215 TTATTCATTTATTA
1 TTATTCATTTATTA
15472229 CAAGCCTGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
21 6 0.19
22 3 0.10
23 4 0.13
24 6 0.19
25 6 0.19
26 6 0.19
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.61
Consensus pattern (22 bp):
TTATTCATTTATTATTTATACT
Found at i:15482393 original size:55 final size:55
Alignment explanation
Indices: 15482299--15482405 Score: 169
Period size: 55 Copynumber: 1.9 Consensus size: 55
15482289 TTTCCTTATT
*
15482299 GGATTTTAGATGCACTATCTTGCCTTTCTTAGTGAGTTATTTTAACTTTACATAA
1 GGATTTTAGATGCACTATCTTGCCTTTCATAGTGAGTTATTTTAACTTTACATAA
* * * *
15482354 GGATTTTAGATTCACTCTCTTGCCTTTCATATTGTGTTATTTTAACTTTACA
1 GGATTTTAGATGCACTATCTTGCCTTTCATAGTGAGTTATTTTAACTTTACA
15482406 ATCTTCTCAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 47 1.00
ACGTcount: A:0.23, C:0.16, G:0.13, T:0.48
Consensus pattern (55 bp):
GGATTTTAGATGCACTATCTTGCCTTTCATAGTGAGTTATTTTAACTTTACATAA
Found at i:15483558 original size:3 final size:3
Alignment explanation
Indices: 15483550--15483586 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
15483540 GATTTCAAAG
15483550 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
15483587 GTTCTTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:15485371 original size:3 final size:3
Alignment explanation
Indices: 15485363--15485388 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
15485353 GAGAAATTGC
15485363 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
15485389 CGTGGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:15491290 original size:6 final size:6
Alignment explanation
Indices: 15491279--15491360 Score: 64
Period size: 6 Copynumber: 13.7 Consensus size: 6
15491269 ATATTATTTT
**
15491279 TAAATA TAAATA TATAAT- T-AA-A TAAATA TAAATA TGTATA TAAAATA
1 TAAATA TAAATA TA-AATA TAAATA TAAATA TAAATA TAAATA T-AAATA
* *
15491326 TAAATA TAAA-A TTAAATA AATAATA TATATA TAAA
1 TAAATA TAAATA -TAAATA TA-AATA TAAATA TAAA
15491361 AAAATCAAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
4 3 0.05
5 3 0.05
6 41 0.68
7 13 0.22
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (6 bp):
TAAATA
Found at i:15491312 original size:41 final size:40
Alignment explanation
Indices: 15491258--15491363 Score: 124
Period size: 41 Copynumber: 2.6 Consensus size: 40
15491248 ATTTGATTTG
* * * *
15491258 AAATTAATAAAATAT-TATTTTTAAATATAAATATATAATT
1 AAATAAATAAAATATGTA-TATAAAATATAAATATAAAATT
15491298 AAATAAATATAAATATGTATATAAAATATAAATATAAAATT
1 AAATAAATA-AAATATGTATATAAAATATAAATATAAAATT
* * *
15491339 AAATAAATAATATATATATAAAAAA
1 AAATAAATAAAATATGTATATAAAA
15491364 ATCAAATTGA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
40 21 0.37
41 34 0.60
42 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (40 bp):
AAATAAATAAAATATGTATATAAAATATAAATATAAAATT
Found at i:15491326 original size:13 final size:13
Alignment explanation
Indices: 15491280--15491361 Score: 71
Period size: 13 Copynumber: 6.2 Consensus size: 13
15491270 TATTATTTTT
15491280 AAATATAAATATA
1 AAATATAAATATA
*
15491293 TAAT-TAAATAAATA
1 AAATATAAAT--ATA
**
15491307 TAAATATGTATATA
1 -AAATATAAATATA
15491321 AAATATAAATATA
1 AAATATAAATATA
15491334 AAAT-TAAATA-A
1 AAATATAAATATA
*
15491345 ATAATATATATATA
1 A-AATATAAATATA
15491359 AAA
1 AAA
15491362 AAATCAAATT
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
11 2 0.04
12 14 0.25
13 25 0.45
14 8 0.15
15 3 0.05
16 3 0.05
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (13 bp):
AAATATAAATATA
Found at i:15491365 original size:41 final size:41
Alignment explanation
Indices: 15491280--15491363 Score: 125
Period size: 41 Copynumber: 2.1 Consensus size: 41
15491270 TATTATTTTT
* * *
15491280 AAATATAAATATATAATTAAATAAATATAAATATGTATATA
1 AAATATAAATATAAAATTAAATAAATATAAATATATATAAA
*
15491321 AAATATAAATATAAAATTAAATAAATA-ATATATATATAAA
1 AAATATAAATATAAAATTAAATAAATATAAATATATATAAA
15491361 AAA
1 AAA
15491364 ATCAAATTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 13 0.33
41 26 0.67
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (41 bp):
AAATATAAATATAAAATTAAATAAATATAAATATATATAAA
Found at i:15492927 original size:16 final size:16
Alignment explanation
Indices: 15492908--15492938 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
15492898 AACATCTAAA
*
15492908 ATTTTAATTTTTTTAT
1 ATTTAAATTTTTTTAT
15492924 ATTTAAATTTTTTTA
1 ATTTAAATTTTTTTA
15492939 ACATAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTAAATTTTTTTAT
Found at i:15494457 original size:23 final size:23
Alignment explanation
Indices: 15494430--15494500 Score: 58
Period size: 23 Copynumber: 3.1 Consensus size: 23
15494420 AAAAAAAATT
15494430 AATTTTAATATATTTAATATTAA
1 AATTTTAATATATTTAATATTAA
* *
15494453 AA-TTTAAT-TTTTTAGTAAATTAA
1 AATTTTAATATATTTA--ATATTAA
* *
15494476 AATTTT-ATAAATTTTAATGTTAA
1 AATTTTAATATA-TTTAATATTAA
15494499 AA
1 AA
15494501 ATAAAAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
21 5 0.14
22 6 0.16
23 19 0.51
24 3 0.08
25 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (23 bp):
AATTTTAATATATTTAATATTAA
Found at i:15496520 original size:18 final size:18
Alignment explanation
Indices: 15496493--15496551 Score: 82
Period size: 18 Copynumber: 3.3 Consensus size: 18
15496483 AGAAGAAGAA
*
15496493 GAAGAGGATGACGACGAC
1 GAAGATGATGACGACGAC
* *
15496511 GAAGATGATGATGACGGC
1 GAAGATGATGACGACGAC
*
15496529 GAAGATGATGACGACGAT
1 GAAGATGATGACGACGAC
15496547 GAAGA
1 GAAGA
15496552 CGGAGAAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.39, C:0.12, G:0.37, T:0.12
Consensus pattern (18 bp):
GAAGATGATGACGACGAC
Found at i:15496526 original size:15 final size:15
Alignment explanation
Indices: 15496508--15496548 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
15496498 GGATGACGAC
*
15496508 GACGAAGATGATGAT
1 GACGACGATGATGAT
* *
15496523 GACGGCGAAGATGAT
1 GACGACGATGATGAT
15496538 GACGACGATGA
1 GACGACGATGA
15496549 AGACGGAGAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.37, C:0.12, G:0.37, T:0.15
Consensus pattern (15 bp):
GACGACGATGATGAT
Found at i:15496574 original size:27 final size:27
Alignment explanation
Indices: 15496514--15496575 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
15496504 CGACGACGAA
* * * *
15496514 GATGATGATGACGGCGAAGATGATGAC
1 GATGATGAAGACGGAGAAGAAGAGGAC
* *
15496541 GACGATGAAGACGGAGAAGAAGAGGAT
1 GATGATGAAGACGGAGAAGAAGAGGAC
15496568 GATGATGA
1 GATGATGA
15496576 TGAAGTGCAG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.39, C:0.08, G:0.39, T:0.15
Consensus pattern (27 bp):
GATGATGAAGACGGAGAAGAAGAGGAC
Found at i:15496646 original size:12 final size:12
Alignment explanation
Indices: 15496631--15496679 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
15496621 AGTTGATGAT
*
15496631 GATGAGGATGAC
1 GATGAGGACGAC
*
15496643 GATGAGGACGAA
1 GATGAGGACGAC
* *
15496655 GATGATGAAGAC
1 GATGAGGACGAC
*
15496667 GACGAGGACGAC
1 GATGAGGACGAC
15496679 G
1 G
15496680 GTGAAGGCGG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.37, C:0.12, G:0.41, T:0.10
Consensus pattern (12 bp):
GATGAGGACGAC
Found at i:15508119 original size:52 final size:53
Alignment explanation
Indices: 15507964--15508120 Score: 205
Period size: 52 Copynumber: 3.0 Consensus size: 53
15507954 TATAATCATA
* * * *
15507964 CAAACTTGCCCATTAAGAATCC-CTTTCATCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATCCTCTTTCTTCTTAGAATTCTTCTCTTGCAAGT
15508016 CAAACTTGCCTATTAAGAAT-CTCTTTCCTT-TTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCTCTTT-CTTCTTAGAATTCTTCTCTTGCAAGT
* * * *
15508068 CAAACTTACCTATTAAGAATCCTCTTT-TTCTTGGAATTCTTCTTTTACAAGT
1 CAAACTTGCCTATTAAGAATCCTCTTTCTTCTTAGAATTCTTCTCTTGCAAGT
15508120 C
1 C
15508121 TTTTTGTCCA
Statistics
Matches: 93, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
51 3 0.03
52 82 0.88
53 8 0.09
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (53 bp):
CAAACTTGCCTATTAAGAATCCTCTTTCTTCTTAGAATTCTTCTCTTGCAAGT
Found at i:15508161 original size:11 final size:11
Alignment explanation
Indices: 15508145--15508175 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
15508135 GCAATATCTG
15508145 ACAAATCTCAA
1 ACAAATCTCAA
15508156 ACAAATCTCAA
1 ACAAATCTCAA
15508167 ACAAATCTC
1 ACAAATCTC
15508176 TTATGAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:15509140 original size:52 final size:52
Alignment explanation
Indices: 15508998--15509154 Score: 192
Period size: 52 Copynumber: 3.0 Consensus size: 52
15508988 TATAACCATA
* * * *
15508998 CAAACTTGCCCATTAAGAATCCCTTTCATCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTCTTCTTAGAATTCTTCTCTTGCAAGT
* * *
15509050 TAAACTTGCCTATTAAGAATCTCTTTCCTT-TTAAAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCCTTT-CTTCTTAGAATTCTTCTCTTGCAAGT
* * *
15509102 CAAACTTACCTATTAAGAATCCCCTTT-TTCTTGGAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAAT-CCCTTTCTTCTTAGAATTCTTCTCTTGCAAGT
15509154 C
1 C
15509155 TTCTTGTCCA
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
51 2 0.02
52 80 0.90
53 7 0.08
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCCTTTCTTCTTAGAATTCTTCTCTTGCAAGT
Found at i:15509195 original size:11 final size:11
Alignment explanation
Indices: 15509179--15509209 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
15509169 GCAATATCTG
15509179 ACAAATCTCAA
1 ACAAATCTCAA
15509190 ACAAATCTCAA
1 ACAAATCTCAA
15509201 ACAAATCTC
1 ACAAATCTC
15509210 TTATGGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:15517232 original size:17 final size:15
Alignment explanation
Indices: 15517210--15517250 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
15517200 ATAGAATTTA
15517210 ATGTAAAAATAAATAAT
1 ATGTAAAAATAAAT--T
15517227 ATGTAAAAA-AAATT
1 ATGTAAAAATAAATT
15517241 AT-TAAAAATA
1 ATGTAAAAATA
15517251 TCGTTTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 6 0.26
14 4 0.17
16 4 0.17
17 9 0.39
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
ATGTAAAAATAAATT
Found at i:15532861 original size:23 final size:23
Alignment explanation
Indices: 15532817--15532861 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
15532807 ATTGGTAAAA
*
15532817 AAAGAAAGAAGAAGGGAAAAGAG
1 AAAGAAAGAAGAAAGGAAAAGAG
15532840 AAAGAAAGAA-AAAGGAAGAAGA
1 AAAGAAAGAAGAAAGGAA-AAGA
15532862 AAAAACTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (23 bp):
AAAGAAAGAAGAAAGGAAAAGAG
Found at i:15535315 original size:21 final size:21
Alignment explanation
Indices: 15535272--15535319 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
15535262 AGATAATTTT
* *
15535272 AAATTATAAAAATTAATATTG
1 AAATAATAAAAATTAATAGTG
15535293 AAATAATAAAAATT-ATGAGTG
1 AAATAATAAAAATTAAT-AGTG
15535314 -AATAAT
1 AAATAAT
15535320 TGTCTAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (21 bp):
AAATAATAAAAATTAATAGTG
Found at i:15537321 original size:21 final size:21
Alignment explanation
Indices: 15537295--15537334 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
15537285 ACGTTTTATC
15537295 TTCTTGACCTTGTAAGACCTT
1 TTCTTGACCTTGTAAGACCTT
15537316 TTCTTGACCTTGTAAGACC
1 TTCTTGACCTTGTAAGACC
15537335 CCGTTTAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (21 bp):
TTCTTGACCTTGTAAGACCTT
Found at i:15565832 original size:26 final size:26
Alignment explanation
Indices: 15565776--15565839 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 26
15565766 CATTTAGGCG
*
15565776 AAATTTTAAAAAAAATTTTGCTTAGA
1 AAATTTTAAAAAAAATTTTGATTAGA
* * * * *
15565802 GAATTTTAAAGAAATTTTTTATTTGA
1 AAATTTTAAAAAAAATTTTGATTAGA
*
15565828 AAATTTTTAAAA
1 AAATTTTAAAAA
15565840 TTTCATCTTT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.44
Consensus pattern (26 bp):
AAATTTTAAAAAAAATTTTGATTAGA
Found at i:15566149 original size:9 final size:9
Alignment explanation
Indices: 15566135--15566176 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
15566125 GAGAATACAT
15566135 ATAAAATAA
1 ATAAAATAA
15566144 ATAAAATAA
1 ATAAAATAA
*
15566153 CT-AAATAA
1 ATAAAATAA
15566161 ATAAAATAA
1 ATAAAATAA
15566170 ATAAAAT
1 ATAAAAT
15566177 TAGAAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 7 0.23
9 23 0.77
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (9 bp):
ATAAAATAA
Found at i:15566160 original size:17 final size:17
Alignment explanation
Indices: 15566138--15566174 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
15566128 AATACATATA
*
15566138 AAATAAATAAAATAACT
1 AAATAAATAAAATAAAT
15566155 AAATAAATAAAATAAAT
1 AAATAAATAAAATAAAT
15566172 AAA
1 AAA
15566175 ATTAGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (17 bp):
AAATAAATAAAATAAAT
Found at i:15566190 original size:26 final size:27
Alignment explanation
Indices: 15566133--15566192 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
15566123 AAGAGAATAC
* *
15566133 ATATAAAATAAATAAAATAACTAAATA
1 ATATAAAATAAATAAAATAACGAAAAA
*
15566160 A-ATAAAATAAATAAAATTA-GAAAAA
1 ATATAAAATAAATAAAATAACGAAAAA
15566185 ATATAAAA
1 ATATAAAA
15566193 AATGGCTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 5 0.17
26 23 0.79
27 1 0.03
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (27 bp):
ATATAAAATAAATAAAATAACGAAAAA
Found at i:15566528 original size:20 final size:20
Alignment explanation
Indices: 15566499--15566536 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
15566489 GTCGAATGTT
15566499 TCATCAAAAACTAGAAAAAA
1 TCATCAAAAACTAGAAAAAA
* *
15566519 TCATCGAAAATTAGAAAA
1 TCATCAAAAACTAGAAAA
15566537 TATTGTTGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.08, T:0.18
Consensus pattern (20 bp):
TCATCAAAAACTAGAAAAAA
Found at i:15567053 original size:4 final size:4
Alignment explanation
Indices: 15567044--15567085 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
15567034 ATAAATCTAA
* *
15567044 AAAT AAAT AAAT AAGT AAAT AGAT AAAT -AAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
15567086 ATATAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:15567088 original size:16 final size:15
Alignment explanation
Indices: 15567044--15567085 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
15567034 ATAAATCTAA
15567044 AAATAAATAAATAAGT
1 AAATAAATAAATAA-T
*
15567060 AAATAGATAAATAAT
1 AAATAAATAAATAAT
15567075 AAATAAATAAA
1 AAATAAATAAA
15567086 ATATAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAATAAATAAT
Found at i:15567438 original size:44 final size:43
Alignment explanation
Indices: 15567381--15567749 Score: 220
Period size: 45 Copynumber: 8.3 Consensus size: 43
15567371 GCTCAATGAG
* * *
15567381 TTTGAAAAGATAAATAATGCTTTTCTAAATAAATGTTCAACCACT
1 TTTGAAAA-ATAAATAAAGCTTTTCT-AATAAAGGTTCAACCAAT
* ** * *
15567426 TTTGAAAAATAAAT-AAGGTTTCTCTAA-ACAGAGACTCAACGATT
1 TTTGAAAAATAAATAAAGCTTT-TCTAATA-A-AGGTTCAACCAAT
* *
15567470 TTTGAAAAATAAATAAATAAAGCTTTTCTAATTAAAGGCTCAA-TAAT
1 TTTG---AA-AAATAAATAAAGCTTTTCTAA-TAAAGGTTCAACCAAT
* * *
15567517 TTTGAAAAATAAATAAAG-TTCATCTAATTAGAGGTTCAA-TAAT
1 TTTGAAAAATAAATAAAGCTT-TTCTAA-TAAAGGTTCAACCAAT
15567560 TTTG-AAAA-AAATAAAG-TTTCTCTAAT-AAGAGTTCAA-CAAT
1 TTTGAAAAATAAATAAAGCTTT-TCTAATAAAG-GTTCAACCAAT
* * * * *
15567600 TTTGATAAAATAAATAAAACTCTTCTAATAAGAGGTTCATCGACT
1 TTTGA-AAAATAAATAAAGCTTTTCTAATAA-AGGTTCAACCAAT
* * ** * * *
15567645 TCTGAAAAATAAATAATGCTCCTCTAATCAGAAGGCTCAACGATT
1 TTTGAAAAATAAATAAAGCTTTTCTAAT-A-AAGGTTCAACCAAT
* * *
15567690 TTTAAAAAATAAATTAAA-CTTTTTCTAATCAGAGGTTCAACCACT
1 TTTGAAAAATAAA-TAAAGC-TTTTCTAAT-AAAGGTTCAACCAAT
15567735 TTTGAAAAATAAATA
1 TTTGAAAAATAAATA
15567750 GAACTCCTAT
Statistics
Matches: 261, Mismatches: 39, Indels: 49
0.75 0.11 0.14
Matches are distributed among these distances:
39 2 0.01
40 14 0.05
41 15 0.06
42 11 0.04
43 56 0.21
44 53 0.20
45 61 0.23
46 13 0.05
47 8 0.03
48 20 0.08
49 7 0.03
50 1 0.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (43 bp):
TTTGAAAAATAAATAAAGCTTTTCTAATAAAGGTTCAACCAAT
Found at i:15567543 original size:43 final size:43
Alignment explanation
Indices: 15567381--15567799 Score: 203
Period size: 45 Copynumber: 9.5 Consensus size: 43
15567371 GCTCAATGAG
* * * * * *
15567381 TTTGAAAAGATAAATAATGCTTTTCTAAATAAATGTTCAACCACT
1 TTTGAAAA-ATAAATAAAGCTTCTCTAATTAAAGGTTCAA-TAAT
* * ** * ** * *
15567426 TTTGAAAAATAAATAAGGTTTCTCTAAACAGAGACTCAACGATT
1 TTTGAAAAATAAATAAAGCTTCTCTAATTAAAGGTTCAA-TAAT
* *
15567470 TTTGAAAAATAAATAAATAAAGCTTTTCTAATTAAAGGCTCAATAAT
1 TTTG---AA-AAATAAATAAAGCTTCTCTAATTAAAGGTTCAATAAT
*
15567517 TTTGAAAAATAAATAAAG-TTCATCTAATTAGAGGTTCAATAAT
1 TTTGAAAAATAAATAAAGCTTC-TCTAATTAAAGGTTCAATAAT
* *
15567560 TTTG-AAAA-AAATAAAGTTTCTCTAA-T-AAGAGTTCAACAAT
1 TTTGAAAAATAAATAAAGCTTCTCTAATTAAAG-GTTCAATAAT
* *
15567600 TTTGATAAAATAAATAAAAC-TCTTCTAA-TAAGAGGTTC-ATCGACT
1 TTTGA-AAAATAAATAAAGCTTC-TCTAATTAA-AGGTTCAAT--AAT
* * * * * * *
15567645 TCTGAAAAATAAATAATGCTCCTCTAATCAGAAGGCTCAACGATT
1 TTTGAAAAATAAATAAAGCTTCTCTAATTA-AAGGTTCAA-TAAT
* * * * * *
15567690 TTTAAAAAATAAATTAAA-CTTTTTCTAATCAGAGGTTCAACCACT
1 TTTGAAAAATAAA-TAAAGC-TTCTCTAATTAAAGGTTCAA-TAAT
* * * *
15567735 TTTGAAAAATAAATAGAA-CTCCTATAATCAGAA-GTTCAATAAC
1 TTTGAAAAATAAATA-AAGCTTCTCTAATTA-AAGGTTCAATAAT
15567778 TTTGAAAAAAATAAATAAAGCT
1 TTTG--AAAAATAAATAAAGCT
15567800 CATCGACAAT
Statistics
Matches: 294, Mismatches: 53, Indels: 54
0.73 0.13 0.13
Matches are distributed among these distances:
39 2 0.01
40 14 0.05
41 13 0.04
42 15 0.05
43 54 0.18
44 72 0.24
45 76 0.26
46 14 0.05
47 8 0.03
48 26 0.09
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.32
Consensus pattern (43 bp):
TTTGAAAAATAAATAAAGCTTCTCTAATTAAAGGTTCAATAAT
Found at i:15567584 original size:41 final size:41
Alignment explanation
Indices: 15567484--15567613 Score: 151
Period size: 43 Copynumber: 3.2 Consensus size: 41
15567474 AAAAATAAAT
* *
15567484 AAATAAAGCTTT-TCTAATTAAAGGCTCAATAATTTTGAAAAA
1 AAATAAAG-TTTCTCTAATTAGAGGTTCAATAATTTTG-AAAA
15567526 TAAATAAAG-TTCATCTAATTAGAGGTTCAATAATTTTGAAAA
1 -AAATAAAGTTTC-TCTAATTAGAGGTTCAATAATTTTGAAAA
* * *
15567568 AAATAAAGTTTCTCTAATAAGA-GTTCAACAATTTTG-ATA
1 AAATAAAGTTTCTCTAATTAGAGGTTCAATAATTTTGAAAA
15567607 AAATAAA
1 AAATAAA
15567614 TAAAACTCTT
Statistics
Matches: 79, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
39 9 0.11
40 13 0.16
41 19 0.24
42 7 0.09
43 31 0.39
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.34
Consensus pattern (41 bp):
AAATAAAGTTTCTCTAATTAGAGGTTCAATAATTTTGAAAA
Found at i:15567653 original size:84 final size:84
Alignment explanation
Indices: 15567484--15567743 Score: 231
Period size: 84 Copynumber: 3.0 Consensus size: 84
15567474 AAAAATAAAT
* ** * *
15567484 AAATAAAGCTTT-TCTAATTAA-AGGCTCAATAATTTTGAAAAATAAATAAAGTTCATCTAATTA
1 AAATAAAG-TTTCTCTAA-TAAGAGGCTCAACAATTTTGAAAAATAAATAAAACTCTTCTAATAA
*
15567547 GAGGTTCAAT-AATTTTGAAAA
64 GAGGTTC-ATCACTTTTGAAAA
*
15567568 AAATAAAGTTTCTCTAATAAGA-GTTCAACAATTTTGATAAAATAAATAAAACTCTTCTAATAAG
1 AAATAAAGTTTCTCTAATAAGAGGCTCAACAATTTTGA-AAAATAAATAAAACTCTTCTAATAAG
*
15567632 AGGTTCATCGACTTCTGAAAAA
65 AGGTTCATC-ACTTTTG-AAAA
* * * * * * * *
15567654 TAAATAATGCTCCTCTAATCAGAAGGCTCAACGATTTTTAAAAAATAAATTAAACTTTTTCTAAT
1 -AAATAAAGTTTCTCTAATAAG-AGGCTCAAC-AATTTTGAAAAATAAATAAAAC-TCTTCTAAT
* *
15567719 CAGAGGTTCAACCACTTTTGAAAA
62 AAGAGGTTC-ATCACTTTTGAAAA
15567743 A
1 A
15567744 TAAATAGAAC
Statistics
Matches: 144, Mismatches: 20, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
83 21 0.15
84 42 0.29
85 5 0.03
86 4 0.03
87 17 0.12
88 2 0.01
89 23 0.16
90 28 0.19
91 2 0.01
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (84 bp):
AAATAAAGTTTCTCTAATAAGAGGCTCAACAATTTTGAAAAATAAATAAAACTCTTCTAATAAGA
GGTTCATCACTTTTGAAAA
Found at i:15567744 original size:90 final size:90
Alignment explanation
Indices: 15567480--15567768 Score: 274
Period size: 90 Copynumber: 3.3 Consensus size: 90
15567470 TTTGAAAAAT
** * * * * *
15567480 AAATAAATAAAGCTTTTCTAATTA-AAGGCTCAATAA-TTTTGAAAAATAAA-TAAAGTTCATCT
1 AAATAAATAAAGCTCCTCTAATCAGAAGGCTCAACAATTTTTAAAAAATAAATTAAACTTCTTCT
* * *
15567542 AATTAGAGGTTCAA-TAATTTTG-A
66 AATAAGAGGTTCAACCACTTTTGAA
* * * * * * *
15567565 AAA-AAATAAAGTTTCTCTAATAAG-A-GTTCAACAATTTTGATAAAATAAATAAAAC-TCTTCT
1 AAATAAATAAAGCTCCTCTAATCAGAAGGCTCAACAATTTTTAAAAAATAAATTAAACTTCTTCT
* * *
15567626 AATAAGAGGTTCATCGACTTCTGAA
66 AATAAGAGGTTCAACCACTTTTGAA
* * *
15567651 AAATAAATAATGCTCCTCTAATCAGAAGGCTCAACGATTTTTAAAAAATAAATTAAACTTTTTCT
1 AAATAAATAAAGCTCCTCTAATCAGAAGGCTCAACAATTTTTAAAAAATAAATTAAACTTCTTCT
*
15567716 AATCAGAGGTTCAACCACTTTTGAA
66 AATAAGAGGTTCAACCACTTTTGAA
*
15567741 AAATAAATAGAA-CTCCTATAATCAGAAG
1 AAATAAATA-AAGCTCCTCTAATCAGAAG
15567769 TTCAATAACT
Statistics
Matches: 162, Mismatches: 32, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
83 7 0.04
84 46 0.28
85 11 0.07
86 4 0.02
87 17 0.10
88 1 0.01
89 25 0.15
90 50 0.31
91 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (90 bp):
AAATAAATAAAGCTCCTCTAATCAGAAGGCTCAACAATTTTTAAAAAATAAATTAAACTTCTTCT
AATAAGAGGTTCAACCACTTTTGAA
Found at i:15567787 original size:90 final size:87
Alignment explanation
Indices: 15567589--15567796 Score: 229
Period size: 90 Copynumber: 2.3 Consensus size: 87
15567579 CTCTAATAAG
* * *
15567589 AGTTCAACAATTTTGATAAAATAAATAAAACTCTTCTAATAAGAGGTTCATCGACTTCTGAAAAA
1 AGTTCAACAA-TTTGAAAAAATAAATAAAACTCTTCTAATAAGAGGTTCAACCACTTCTGAAAAA
* *
15567654 TAAATAATGCTCCTCTAATCAGA
65 TAAATAATACTCCTATAATCAGA
* * * * * * *
15567677 AGGCTCAACGATTTTTAAAAAATAAATTAAACTTTTTCTAATCAGAGGTTCAACCACTTTTGAAA
1 A-GTTCAAC-AATTTGAAAAAATAAATAAAAC-TCTTCTAATAAGAGGTTCAACCACTTCTGAAA
15567742 AATAAATAGA-ACTCCTATAATCAGA
63 AATAAATA-ATACTCCTATAATCAGA
*
15567767 AGTTCAATAACTTTGAAAAAAATAAATAAA
1 AGTTCAACAA-TTTG-AAAAAATAAATAAA
15567797 GCTCATCGAC
Statistics
Matches: 97, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
88 2 0.02
89 31 0.32
90 63 0.65
91 1 0.01
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.30
Consensus pattern (87 bp):
AGTTCAACAATTTGAAAAAATAAATAAAACTCTTCTAATAAGAGGTTCAACCACTTCTGAAAAAT
AAATAATACTCCTATAATCAGA
Found at i:15568378 original size:11 final size:11
Alignment explanation
Indices: 15568362--15568394 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
15568352 ATATATTGGA
15568362 TTTTTTCAAAT
1 TTTTTTCAAAT
*
15568373 TTTTTTTAAAT
1 TTTTTTCAAAT
15568384 TTTTTTCAAAT
1 TTTTTTCAAAT
15568395 AAATGATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTTTTCAAAT
Found at i:15576215 original size:10 final size:9
Alignment explanation
Indices: 15576202--15576268 Score: 52
Period size: 8 Copynumber: 7.6 Consensus size: 9
15576192 CTTTTATCTC
*
15576202 TTTTTACAT
1 TTTTTTCAT
*
15576211 TTTTTCTCTTT
1 TTTTT-TC-AT
15576222 TTTTTTCA-
1 TTTTTTCAT
15576230 TTTTTT-AT
1 TTTTTTCAT
*
15576238 TTTTTTTAT
1 TTTTTTCAT
15576247 TTTTTT--T
1 TTTTTTCAT
15576254 TTTTTCTCAT
1 TTTTT-TCAT
15576264 TTTTT
1 TTTTT
15576269 CATCCATTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
7 7 0.15
8 13 0.27
9 13 0.27
10 9 0.19
11 6 0.12
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:15576231 original size:20 final size:19
Alignment explanation
Indices: 15576202--15576268 Score: 63
Period size: 16 Copynumber: 3.7 Consensus size: 19
15576192 CTTTTATCTC
*
15576202 TTTTTACATTTTTTCTCTTT
1 TTTTTACATTTTTTAT-TTT
*
15576222 TTTTTTCATTTTTTA-TTT
1 TTTTTACATTTTTTATTTT
15576240 TTTTT--ATTTTTT-TTTT
1 TTTTTACATTTTTTATTTT
*
15576256 TTTCT-CATTTTTT
1 TTTTTACATTTTTT
15576269 CATCCATTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
16 14 0.33
17 7 0.17
18 8 0.19
20 13 0.31
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTACATTTTTTATTTT
Done.