Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, 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: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 39 of 109
Found at i:6043067 original size:19 final size:21
Alignment explanation
Indices: 6043008--6043069 Score: 76
Period size: 23 Copynumber: 3.0 Consensus size: 21
6042998 TATTAATTCA
6043008 ATAAAAATAATATATTTATAT
1 ATAAAAATAATATATTTATAT
6043029 ATAATTAAA-AATATAATTTATAT
1 ATAA--AAATAATAT-ATTTATAT
6043052 -TAAAAATAATAT-TTTATA
1 ATAAAAATAATATATTTATA
6043070 AATACTACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
19 6 0.16
20 3 0.08
21 9 0.24
22 8 0.22
23 11 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAAAAATAATATATTTATAT
Found at i:6043326 original size:27 final size:28
Alignment explanation
Indices: 6043276--6043342 Score: 109
Period size: 27 Copynumber: 2.4 Consensus size: 28
6043266 CTTGGTTGGC
**
6043276 GTTGGCAAAAAAAACGCTGCAGCTGTTA
1 GTTGGCAAAGGAAACGCTGCAGCTGTTA
6043304 GTTGGCAAAGGAAA-GCTGCAGCTGTTA
1 GTTGGCAAAGGAAACGCTGCAGCTGTTA
6043331 GTTGGCAAAGGA
1 GTTGGCAAAGGA
6043343 CTGGACCTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
27 25 0.68
28 12 0.32
ACGTcount: A:0.33, C:0.15, G:0.31, T:0.21
Consensus pattern (28 bp):
GTTGGCAAAGGAAACGCTGCAGCTGTTA
Found at i:6048373 original size:2 final size:2
Alignment explanation
Indices: 6048366--6048396 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
6048356 GACACATACC
*
6048366 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6048397 CTCTTAATTA
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:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6049478 original size:2 final size:2
Alignment explanation
Indices: 6049471--6049514 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
6049461 AGTGCAGTTT
* ** *
6049471 TA TA TA TA AA TA TA TA TA TA TA TA TA CG TA TA TA TG 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
6049513 TA
1 TA
6049515 AATAATTTGG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:6053273 original size:3 final size:3
Alignment explanation
Indices: 6053265--6053302 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
6053255 TTATATACAA
6053265 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6053303 ATAACCTCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6058138 original size:57 final size:57
Alignment explanation
Indices: 6058050--6058166 Score: 234
Period size: 57 Copynumber: 2.1 Consensus size: 57
6058040 CTATAACACA
6058050 TTAAAACCCTTAGGCAGGTTAACTTTAGTCCAAGAAAACTATGACATCTAATTTTAC
1 TTAAAACCCTTAGGCAGGTTAACTTTAGTCCAAGAAAACTATGACATCTAATTTTAC
6058107 TTAAAACCCTTAGGCAGGTTAACTTTAGTCCAAGAAAACTATGACATCTAATTTTAC
1 TTAAAACCCTTAGGCAGGTTAACTTTAGTCCAAGAAAACTATGACATCTAATTTTAC
6058164 TTA
1 TTA
6058167 TACCTATAAC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (57 bp):
TTAAAACCCTTAGGCAGGTTAACTTTAGTCCAAGAAAACTATGACATCTAATTTTAC
Found at i:6064495 original size:13 final size:13
Alignment explanation
Indices: 6064459--6064510 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
6064449 TTATATATAT
**
6064459 TATATTAATACAA
1 TATATTAATTTAA
6064472 T-TATT-ATTTAA
1 TATATTAATTTAA
*
6064483 TATTTTAATTTAA
1 TATATTAATTTAA
6064496 TATATTAATTTAA
1 TATATTAATTTAA
6064509 TA
1 TA
6064511 AATATATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 5 0.15
12 7 0.21
13 21 0.64
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATTAATTTAA
Found at i:6064499 original size:42 final size:45
Alignment explanation
Indices: 6064426--6064529 Score: 119
Period size: 42 Copynumber: 2.3 Consensus size: 45
6064416 AAATAAATTT
*
6064426 TTATTATTTATTTAGTTTTATATTTATATATATT-ATATTAATACAA
1 TTATTATTTATATAGTTTTATATTTATATATATTAAT-TTAATA-AA
6064472 TTATTATTTA-ATA-TTTTA-ATTTA-ATATATTAATTTAATAAA
1 TTATTATTTATATAGTTTTATATTTATATATATTAATTTAATAAA
6064513 TATATTATATTTATATA
1 T-TA-T-TATTTATATA
6064530 TAATTGAGAT
Statistics
Matches: 52, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
41 3 0.06
42 15 0.29
43 8 0.15
44 11 0.21
45 5 0.10
46 10 0.19
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (45 bp):
TTATTATTTATATAGTTTTATATTTATATATATTAATTTAATAAA
Found at i:6064534 original size:42 final size:43
Alignment explanation
Indices: 6064428--6064553 Score: 109
Period size: 42 Copynumber: 2.9 Consensus size: 43
6064418 ATAAATTTTT
* *
6064428 ATTATTTATTTAGTTTTAT-ATTTATATATATTATATTAATACA
1 ATTA-TTATTTAATATTATAATTTATATATATTATATTAATACA
*
6064471 ATTATTATTTAATATTTTAATTTA-ATATATTA-ATTTAATA-A
1 ATTATTATTTAATATTATAATTTATATATATTATA-TTAATACA
* * *
6064512 ATATATTATATTTATA-TATAATTGAGATATAATTTATATTAA
1 AT-TATTAT-TTAATATTATAATTTATATAT-A-TTATATTAA
6064554 AAATAATATT
Statistics
Matches: 69, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
41 4 0.06
42 38 0.55
43 18 0.26
44 1 0.01
45 7 0.10
46 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (43 bp):
ATTATTATTTAATATTATAATTTATATATATTATATTAATACA
Found at i:6066187 original size:21 final size:22
Alignment explanation
Indices: 6066148--6066193 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
6066138 AACTTAAAAT
* *
6066148 TTTAATAAAAATTATAAATAAA
1 TTTAATAAAAATAAAAAATAAA
*
6066170 TTTAAT-AAAATAAAAAATATA
1 TTTAATAAAAATAAAAAATAAA
6066191 TTT
1 TTT
6066194 TATATTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTAATAAAAATAAAAAATAAA
Found at i:6066195 original size:22 final size:22
Alignment explanation
Indices: 6066145--6066195 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
6066135 TATAACTTAA
* *
6066145 AATTTTAATAAAAATTATAAAT
1 AATTTTAATAAAAATAAAAAAT
*
6066167 AAATTTAAT-AAAATAAAAAAT
1 AATTTTAATAAAAATAAAAAAT
6066188 ATATTTTA
1 A-ATTTTA
6066196 TATTTTTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTTTAATAAAAATAAAAAAT
Found at i:6067778 original size:16 final size:17
Alignment explanation
Indices: 6067747--6067781 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6067737 TTTGGTATGA
*
6067747 TTTTCTTTTTTATTGTT
1 TTTTCTTGTTTATTGTT
6067764 TTTTCTTGTTT-TTGTT
1 TTTTCTTGTTTATTGTT
6067780 TT
1 TT
6067782 GATCCCATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.03, C:0.06, G:0.09, T:0.83
Consensus pattern (17 bp):
TTTTCTTGTTTATTGTT
Found at i:6080229 original size:37 final size:39
Alignment explanation
Indices: 6080155--6080232 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
6080145 AAAAATCCCA
* * *
6080155 TGTCATTGTTTGGTTAGATAGAGAAGAAAAGGAAAAAAC
1 TGTCATCGTTTGGTTAGAGAGAAAAGAAAAGGAAAAAAC
* *
6080194 TGTCATCGTTTGGTTATAGAGAAAAGAAAAGAAAAAAAC
1 TGTCATCGTTTGGTTAGAGAGAAAAGAAAAGGAAAAAAC
6080233 ATTGTGGGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.46, C:0.06, G:0.23, T:0.24
Consensus pattern (39 bp):
TGTCATCGTTTGGTTAGAGAGAAAAGAAAAGGAAAAAAC
Found at i:6080934 original size:22 final size:23
Alignment explanation
Indices: 6080906--6080960 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
6080896 ATATTTATTT
*
6080906 TAATAAATTAATTAAATTTTT-A
1 TAATAAATTAAATAAATTTTTAA
*
6080928 TAATAAA-TAAATAATTTTTTAA
1 TAATAAATTAAATAAATTTTTAA
6080950 TAATATAATTA
1 TAATA-AATTA
6080961 TGTGAGATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 11 0.39
22 13 0.46
23 2 0.07
24 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TAATAAATTAAATAAATTTTTAA
Found at i:6081082 original size:16 final size:15
Alignment explanation
Indices: 6081046--6081088 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
6081036 TTTATTAATA
*
6081046 TAAAATTTTAAAATT
1 TAAAATTTTAAAAAT
6081061 TAAAATTTATAAAAAT
1 TAAAATTT-TAAAAAT
* *
6081077 TCAAATTCTAAA
1 TAAAATTTTAAA
6081089 TCGATCCATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAAATTTTAAAAAT
Found at i:6082402 original size:18 final size:20
Alignment explanation
Indices: 6082381--6082424 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
6082371 GATGGGGTCA
*
6082381 TTTTATTAATG-AA-TAAAT
1 TTTTATTAAAGAAATTAAAT
*
6082399 TTTTTTTAAAGAAATTAAAT
1 TTTTATTAAAGAAATTAAAT
6082419 TTTTAT
1 TTTTAT
6082425 ATATTTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 9 0.43
19 2 0.10
20 10 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
TTTTATTAAAGAAATTAAAT
Found at i:6082464 original size:23 final size:23
Alignment explanation
Indices: 6082411--6082470 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
6082401 TTTTTAAAGA
** *
6082411 AATTAAATTTTTATATATTTATT
1 AATTAAATTAATATTTATTTATT
*
6082434 -TTTAAAATTAATATTTATTTATT
1 AATT-AAATTAATATTTATTTATT
6082457 AATTAAA-TAATATT
1 AATTAAATTAATATT
6082471 ATCTGATTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
22 9 0.30
23 19 0.63
24 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
AATTAAATTAATATTTATTTATT
Found at i:6082465 original size:19 final size:18
Alignment explanation
Indices: 6082425--6082462 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
6082415 AAATTTTTAT
6082425 ATATTTATTTTTAAAATTA
1 ATATTTATTTTT-AAATTA
6082444 ATATTTATTTATT-AATTA
1 ATATTTATTT-TTAAATTA
6082462 A
1 A
6082463 ATAATATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 10 0.56
20 2 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATATTTATTTTTAAATTA
Found at i:6084289 original size:14 final size:12
Alignment explanation
Indices: 6084255--6084293 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
6084245 AAAAAAATTT
*
6084255 AATAAATTTTTA
1 AATATATTTTTA
6084267 AATATATTTTTA
1 AATATATTTTTA
6084279 AATAGATATTTTTA
1 AAT--ATATTTTTA
6084293 A
1 A
6084294 TAAAATATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 14 0.58
14 10 0.42
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (12 bp):
AATATATTTTTA
Found at i:6085736 original size:18 final size:18
Alignment explanation
Indices: 6085710--6085744 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6085700 CTAAATTTTT
* *
6085710 TATTTTTATTTTTTTTAC
1 TATTCTTATTATTTTTAC
6085728 TATTCTTATTATTTTTA
1 TATTCTTATTATTTTTA
6085745 TGGTCATCTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (18 bp):
TATTCTTATTATTTTTAC
Found at i:6088838 original size:18 final size:18
Alignment explanation
Indices: 6088804--6088851 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
6088794 ATGGATAAAT
* * *
6088804 TGGTGGTGGAGGTGAATG
1 TGGTGGTGGTGGAGAATA
6088822 TGGTGGTGGTGGAGAATA
1 TGGTGGTGGTGGAGAATA
*
6088840 TGGAGGTGGTGG
1 TGGTGGTGGTGG
6088852 GTAACTGTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.17, C:0.00, G:0.56, T:0.27
Consensus pattern (18 bp):
TGGTGGTGGTGGAGAATA
Found at i:6089143 original size:27 final size:27
Alignment explanation
Indices: 6089113--6089183 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
6089103 GTGGTGGTGA
* *
6089113 TGGTGGAGGAGGTGGAGAGTAAACAGG
1 TGGTGGAGGAGGAGGAGAATAAACAGG
* * * *
6089140 TGGTGGGGGCGGAGGTGAATAAACTGG
1 TGGTGGAGGAGGAGGAGAATAAACAGG
*
6089167 TGGTGGAGGTGGAGGAG
1 TGGTGGAGGAGGAGGAG
6089184 GTGGAGAGTA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.24, C:0.04, G:0.55, T:0.17
Consensus pattern (27 bp):
TGGTGGAGGAGGAGGAGAATAAACAGG
Found at i:6089169 original size:60 final size:60
Alignment explanation
Indices: 6089104--6089217 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
6089094 GGGAGGGCGG
* * *
6089104 TGGTGGT-GATGGTGGAGGAGGTGGAGAGTAAACAGGTGGTGGGGGCGGAGGTGAATAAAC
1 TGGTGGTGGA-GGTGGAGGAGGTGGAGAGTAAACAGGCGGCGGCGGCGGAGGTGAATAAAC
* *
6089164 TGGTGGTGGAGGTGGAGGAGGTGGAGAGTATACAGGCGGCGGCGGCGGTGGTGA
1 TGGTGGTGGAGGTGGAGGAGGTGGAGAGTAAACAGGCGGCGGCGGCGGAGGTGA
6089218 TTGTGGAGTA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
60 46 0.96
61 2 0.04
ACGTcount: A:0.21, C:0.07, G:0.54, T:0.18
Consensus pattern (60 bp):
TGGTGGTGGAGGTGGAGGAGGTGGAGAGTAAACAGGCGGCGGCGGCGGAGGTGAATAAAC
Found at i:6095194 original size:13 final size:14
Alignment explanation
Indices: 6095176--6095204 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6095166 TCTTATCAAA
6095176 TAAAATA-TATAAT
1 TAAAATATTATAAT
6095189 TAAAATATTATAAT
1 TAAAATATTATAAT
6095203 TA
1 TA
6095205 TATAAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAAATATTATAAT
Found at i:6098952 original size:23 final size:24
Alignment explanation
Indices: 6098922--6098972 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
6098912 TAATGTGTTT
*
6098922 ATTTTTTTGTTGAAAATTT-GTAA
1 ATTTTTTTGTTCAAAATTTAGTAA
* *
6098945 ATTTTTTTTTTCAAAATTTATTAA
1 ATTTTTTTGTTCAAAATTTAGTAA
6098969 ATTT
1 ATTT
6098973 AACATAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (24 bp):
ATTTTTTTGTTCAAAATTTAGTAA
Found at i:6106953 original size:2 final size:2
Alignment explanation
Indices: 6106946--6106971 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6106936 AGGCACATAC
6106946 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
6106972 GCATATAGCC
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:6111213 original size:19 final size:19
Alignment explanation
Indices: 6111189--6111227 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
6111179 TCCTATAACT
6111189 TTCAAAATAGTAGTTGCCA
1 TTCAAAATAGTAGTTGCCA
6111208 TTCAAAATAGTAGTTGCCA
1 TTCAAAATAGTAGTTGCCA
6111227 T
1 T
6111228 GCATCCAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (19 bp):
TTCAAAATAGTAGTTGCCA
Found at i:6117393 original size:21 final size:21
Alignment explanation
Indices: 6117353--6117393 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6117343 TCATTGAATC
*
6117353 AAATAATATTATTTTATTAAT
1 AAATAATATTAATTTATTAAT
6117374 AAATAATTATTAATTT-TTAA
1 AAATAA-TATTAATTTATTAA
6117394 AATAAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATAATATTAATTTATTAAT
Found at i:6117417 original size:29 final size:31
Alignment explanation
Indices: 6117372--6117429 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
6117362 TATTTTATTA
6117372 ATAAATAATTATTAA-TTTTTAAAATAAATAT
1 ATAAATAATTATTAATTTTTTAAAA-AAATAT
6117403 ATAAA-AA-TATTAATTTTTTAAAAAAAT
1 ATAAATAATTATTAATTTTTTAAAAAAAT
6117430 TTACTCATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 10 0.38
30 11 0.42
31 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (31 bp):
ATAAATAATTATTAATTTTTTAAAAAAATAT
Found at i:6121917 original size:23 final size:23
Alignment explanation
Indices: 6121890--6121937 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
6121880 TTGGGGAGAT
6121890 AGTTTTTGCAATTGGGAAGAAGG
1 AGTTTTTGCAATTGGGAAGAAGG
6121913 AGTTTTTGCAATTGGGAAGAAGG
1 AGTTTTTGCAATTGGGAAGAAGG
6121936 AG
1 AG
6121938 CTTGAGGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.04, G:0.35, T:0.29
Consensus pattern (23 bp):
AGTTTTTGCAATTGGGAAGAAGG
Found at i:6129822 original size:100 final size:100
Alignment explanation
Indices: 6129649--6129855 Score: 378
Period size: 100 Copynumber: 2.1 Consensus size: 100
6129639 TACCATGAAA
*
6129649 ACATACATCAAGTATATTTTTGTAATAGGAAAACTTCATAGCATTTCTCCTTGAAGCAAGACTCT
1 ACATAAATCAAGTATATTTTTGTAATAGGAAAACTTCATAGCATTTCTCCTTGAAGCAAGACTCT
*
6129714 TGCTTGTGAGTGCTAATCGCATGCATAATCATGGC
66 TGCCTGTGAGTGCTAATCGCATGCATAATCATGGC
*
6129749 ACATAAATCAAGTATGTTTTTGTAATAGGAAAACTTCATAGCATTTCTCCTTGAAGCAAGACTCT
1 ACATAAATCAAGTATATTTTTGTAATAGGAAAACTTCATAGCATTTCTCCTTGAAGCAAGACTCT
*
6129814 TGCCTGTGAGTGTTAATCGCATGCATAATCATGGC
66 TGCCTGTGAGTGCTAATCGCATGCATAATCATGGC
6129849 ACATAAA
1 ACATAAA
6129856 GCGTGATATA
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 103 1.00
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Consensus pattern (100 bp):
ACATAAATCAAGTATATTTTTGTAATAGGAAAACTTCATAGCATTTCTCCTTGAAGCAAGACTCT
TGCCTGTGAGTGCTAATCGCATGCATAATCATGGC
Found at i:6143773 original size:16 final size:15
Alignment explanation
Indices: 6143749--6143843 Score: 73
Period size: 16 Copynumber: 5.9 Consensus size: 15
6143739 ATTTTTTTTT
*
6143749 AGGACTTTGGATTTCA
1 AGGATTTTGGATTT-A
6143765 AGGATTTTGGATTTCA
1 AGGATTTTGGATTT-A
* *
6143781 GGGGGTTTTGGATTTA
1 -AGGATTTTGGATTTA
*
6143797 ATGGATTTTGAATTTTA
1 A-GGATTTTGGA-TTTA
* **
6143814 TGGGGTTTGGATTTA
1 AGGATTTTGGATTTA
6143829 AGGGATTTTGGATTT
1 A-GGATTTTGGATTT
6143844 TTAGAAACCT
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
15 4 0.06
16 42 0.68
17 16 0.26
ACGTcount: A:0.21, C:0.03, G:0.31, T:0.45
Consensus pattern (15 bp):
AGGATTTTGGATTTA
Found at i:6143794 original size:33 final size:32
Alignment explanation
Indices: 6143754--6143843 Score: 119
Period size: 33 Copynumber: 2.8 Consensus size: 32
6143744 TTTTTAGGAC
6143754 TTTGGATTTCAA-GGATTTTGGATTTCAGGGGG
1 TTTGGATTT-AAGGGATTTTGGATTTCAGGGGG
* * * *
6143786 TTTTGGATTTAATGGATTTTGAATTTTATGGGG
1 -TTTGGATTTAAGGGATTTTGGATTTCAGGGGG
6143819 TTTGGATTTAAGGGATTTTGGATTT
1 TTTGGATTTAAGGGATTTTGGATTT
6143844 TTAGAAACCT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
32 25 0.49
33 26 0.51
ACGTcount: A:0.20, C:0.02, G:0.30, T:0.48
Consensus pattern (32 bp):
TTTGGATTTAAGGGATTTTGGATTTCAGGGGG
Found at i:6143846 original size:33 final size:32
Alignment explanation
Indices: 6143754--6143844 Score: 121
Period size: 32 Copynumber: 2.8 Consensus size: 32
6143744 TTTTTAGGAC
*
6143754 TTTGGATTTCAAGGATTTTGGATTTCAGGGGGT
1 TTTGGATTT-AAGGATTTTGGATTTTAGGGGGT
* *
6143787 TTTGGATTTAATGGATTTTGAATTTTATGGGG-
1 TTTGGATTTAA-GGATTTTGGATTTTAGGGGGT
6143819 TTTGGATTTAAGGGATTTTGGATTTT
1 TTTGGATTTAA-GGATTTTGGATTTT
6143845 TAGAAACCTA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
32 26 0.50
33 26 0.50
ACGTcount: A:0.20, C:0.02, G:0.30, T:0.48
Consensus pattern (32 bp):
TTTGGATTTAAGGATTTTGGATTTTAGGGGGT
Found at i:6144368 original size:38 final size:38
Alignment explanation
Indices: 6144323--6144419 Score: 140
Period size: 38 Copynumber: 2.6 Consensus size: 38
6144313 TCAACGCTGA
* * * *
6144323 TCCGGGCGGTCTGATCGGTTCGACGGTTGGATCGACAG
1 TCCGGGCGATCTGACCGGTTCGACGGTCGGATCAACAG
* *
6144361 TTCGGGCGATCTGACCGGTTCGACGGTCGGATCAACGG
1 TCCGGGCGATCTGACCGGTTCGACGGTCGGATCAACAG
6144399 TCCGGGCGATCTGACCGGTTC
1 TCCGGGCGATCTGACCGGTTC
6144420 AGTCCGGTCC
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.13, C:0.27, G:0.37, T:0.23
Consensus pattern (38 bp):
TCCGGGCGATCTGACCGGTTCGACGGTCGGATCAACAG
Found at i:6145506 original size:21 final size:21
Alignment explanation
Indices: 6145482--6145526 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
6145472 ATATTTTAAG
6145482 TTTTAT-TGT-ACATATAATAAA
1 TTTTATATGTAACA-ATAA-AAA
6145503 TTTTATATGTAACAATAAAAA
1 TTTTATATGTAACAATAAAAA
6145524 TTT
1 TTT
6145527 ATCATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 12 0.55
22 7 0.32
23 3 0.14
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (21 bp):
TTTTATATGTAACAATAAAAA
Found at i:6148409 original size:118 final size:118
Alignment explanation
Indices: 6148201--6148430 Score: 406
Period size: 118 Copynumber: 1.9 Consensus size: 118
6148191 CAACTGCATT
* * * *
6148201 CTCTGCTACCTTGTAATGCAGGTGGAATGTGATGAAGCACAACTTCTGGCACTCTTGAGATACAT
1 CTCTGCTACCTTGTAATGCAAGTGGAATGTGATAAAGAACAACTTCTGGCACTCTTCAGATACAT
6148266 ACAACTATCATCTAAAAGAGTAGAACATGGAGAAGAGGTGATTTGTATGTCTA
66 ACAACTATCATCTAAAAGAGTAGAACATGGAGAAGAGGTGATTTGTATGTCTA
*
6148319 CTCTGCTACCTTGTAATGCAAGTGGAATGTGATAAAGAACAACTTCTGGCACTCTTCTGATACAT
1 CTCTGCTACCTTGTAATGCAAGTGGAATGTGATAAAGAACAACTTCTGGCACTCTTCAGATACAT
*
6148384 ACAACTATCATCTAAAAGAGTAGAACATGGATAAGAGGTGATTTGTA
66 ACAACTATCATCTAAAAGAGTAGAACATGGAGAAGAGGTGATTTGTA
6148431 AACCAGCTGC
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
118 106 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (118 bp):
CTCTGCTACCTTGTAATGCAAGTGGAATGTGATAAAGAACAACTTCTGGCACTCTTCAGATACAT
ACAACTATCATCTAAAAGAGTAGAACATGGAGAAGAGGTGATTTGTATGTCTA
Found at i:6153302 original size:15 final size:16
Alignment explanation
Indices: 6153273--6153313 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
6153263 CTTTTCATTT
* *
6153273 TCTTTTTCTTCTTT-A
1 TCTTTTTTTTTTTTAA
6153288 TCTTTTTTTTTTTTAA
1 TCTTTTTTTTTTTTAA
6153304 T-TTTTTTTTT
1 TCTTTTTTTTT
6153314 AGGAGGGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 21 0.91
16 2 0.09
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (16 bp):
TCTTTTTTTTTTTTAA
Found at i:6158800 original size:17 final size:17
Alignment explanation
Indices: 6158780--6158812 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6158770 AGGAGATGAG
6158780 AATTTTTTATTCTTTCT
1 AATTTTTTATTCTTTCT
*
6158797 AATTTTTTATTTTTTC
1 AATTTTTTATTCTTTC
6158813 ACATTATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (17 bp):
AATTTTTTATTCTTTCT
Found at i:6165624 original size:31 final size:31
Alignment explanation
Indices: 6165589--6165652 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
6165579 TTTGGTGTAC
*
6165589 CAGATTGTCGTTTTATATTTGTTAAGGGTTA
1 CAGATTGTCGTTTTATATTTATTAAGGGTTA
*
6165620 CAGATTGTCGTTTTATATTTATTGAGGGTTA
1 CAGATTGTCGTTTTATATTTATTAAGGGTTA
6165651 CA
1 CA
6165653 CGCCAGATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.08, G:0.22, T:0.47
Consensus pattern (31 bp):
CAGATTGTCGTTTTATATTTATTAAGGGTTA
Found at i:6166588 original size:104 final size:104
Alignment explanation
Indices: 6166402--6166601 Score: 310
Period size: 104 Copynumber: 1.9 Consensus size: 104
6166392 CATGTACTTT
* * *
6166402 ATCAAATGTAAAATTAATCATTTTATTTTAATGTATTCAATTAGATCTTTATATATTAATTAATT
1 ATCAAATGTAAAATTAATCATTCTACTTTAATATATTCAATTAGATCTTTATATATTAATTAATT
6166467 ATCGAATTTAAAATTTGATCTAAAATAATTATAAAAAAA
66 ATCGAATTTAAAATTTGATCTAAAATAATTATAAAAAAA
* * *
6166506 ATCAAATGTAAAATTAATCATTCTACTTTAATATGTTCAATTTGATCTTTATATATTGATTAATT
1 ATCAAATGTAAAATTAATCATTCTACTTTAATATATTCAATTAGATCTTTATATATTAATTAATT
* * **
6166571 GTTGAATTTAATGTTTGATCTAAAATAATTA
66 ATCGAATTTAAAATTTGATCTAAAATAATTA
6166602 CGAGAAAATC
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
104 86 1.00
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.45
Consensus pattern (104 bp):
ATCAAATGTAAAATTAATCATTCTACTTTAATATATTCAATTAGATCTTTATATATTAATTAATT
ATCGAATTTAAAATTTGATCTAAAATAATTATAAAAAAA
Found at i:6167214 original size:20 final size:19
Alignment explanation
Indices: 6167164--6167214 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 19
6167154 TATGTTGGAT
6167164 TTAAAATCCAA-TTTGAAA
1 TTAAAATCCAATTTTGAAA
* ** *
6167182 CTAAAATGTAATTTATTAAA
1 TTAAAATCCAATTT-TGAAA
6167202 TTAAAATCCAATT
1 TTAAAATCCAATT
6167215 AATAATTCAA
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
18 8 0.33
19 2 0.08
20 14 0.58
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.37
Consensus pattern (19 bp):
TTAAAATCCAATTTTGAAA
Found at i:6170143 original size:26 final size:24
Alignment explanation
Indices: 6170092--6170176 Score: 66
Period size: 26 Copynumber: 3.3 Consensus size: 24
6170082 TTATAAATAT
6170092 ATATATTAATATATATTTTCAA-TAAAA
1 ATATATT-ATAT-TA-TTT-AATTAAAA
*
6170119 ATATATTAATTTTATTTAATCT-AAA
1 ATATATT-ATATTATTTAAT-TAAAA
*
6170144 ATAATAATTATATTATTTAATAAAAA
1 AT-AT-ATTATATTATTTAATTAAAA
6170170 ATATATT
1 ATATATT
6170177 TACTAAATAT
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
24 5 0.10
25 10 0.20
26 21 0.42
27 14 0.28
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
ATATATTATATTATTTAATTAAAA
Found at i:6170190 original size:17 final size:17
Alignment explanation
Indices: 6170145--6170191 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
6170135 TAATCTAAAA
*
6170145 TAATAATTATAT-TATT
1 TAATAAATATATATATT
*
6170161 TAATAAA-AAATATATT
1 TAATAAATATATATATT
*
6170177 TACTAAATATATATA
1 TAATAAATATATATA
6170192 AATATATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
15 3 0.12
16 16 0.64
17 6 0.24
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATAAATATATATATT
Found at i:6172106 original size:23 final size:23
Alignment explanation
Indices: 6172080--6172125 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
6172070 TAATAAAAGT
6172080 TATTATAATTATAATTAAAAAAA
1 TATTATAATTATAATTAAAAAAA
*
6172103 TATTATAATTATTATTAAAAAAA
1 TATTATAATTATAATTAAAAAAA
6172126 AATTTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TATTATAATTATAATTAAAAAAA
Found at i:6185262 original size:18 final size:17
Alignment explanation
Indices: 6185223--6185281 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 17
6185213 TTTTGATGAG
6185223 ATAA-AAAATAATTATA
1 ATAATAAAATAATTATA
* *
6185239 AAAATAAAATTAATTATT
1 ATAATAAAA-TAATTATA
*
6185257 ATAATAATGA-AATTATAA
1 ATAATAA-AATAATTAT-A
6185275 ATAATAA
1 ATAATAA
6185282 TAAGATATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
16 3 0.09
17 10 0.29
18 20 0.59
19 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
ATAATAAAATAATTATA
Found at i:6185790 original size:5 final size:5
Alignment explanation
Indices: 6185765--6185812 Score: 60
Period size: 5 Copynumber: 9.2 Consensus size: 5
6185755 TTAAAATGTC
* *
6185765 TTATA TTTATA TTATTT TTATA TTATA TTATA TTATG TTATA TTATA T
1 TTATA -TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA TTATA T
6185813 ATGTAGTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
5 28 0.76
6 9 0.24
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (5 bp):
TTATA
Found at i:6188929 original size:6 final size:7
Alignment explanation
Indices: 6188907--6188932 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
6188897 ACTTTTAGGA
6188907 TTTAATT
1 TTTAATT
6188914 TTTAATT
1 TTTAATT
6188921 TTTAATT
1 TTTAATT
6188928 TTTAA
1 TTTAA
6188933 AACTTGTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTAATT
Found at i:6189148 original size:7 final size:7
Alignment explanation
Indices: 6189136--6189160 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6189126 AAAATTTTAA
6189136 AAAATAT
1 AAAATAT
6189143 AAAATAT
1 AAAATAT
6189150 AAAATAT
1 AAAATAT
6189157 AAAA
1 AAAA
6189161 ATCAAAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATAT
Found at i:6191922 original size:22 final size:22
Alignment explanation
Indices: 6191897--6191943 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
6191887 GTTAAGTCTC
6191897 ATGCTTATTCTTAGTTATTATA
1 ATGCTTATTCTTAGTTATTATA
6191919 ATGCTTATTCTTAGTTATTATA
1 ATGCTTATTCTTAGTTATTATA
6191941 ATG
1 ATG
6191944 AAGAAATTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.28, C:0.09, G:0.11, T:0.53
Consensus pattern (22 bp):
ATGCTTATTCTTAGTTATTATA
Found at i:6192034 original size:44 final size:44
Alignment explanation
Indices: 6191983--6192073 Score: 166
Period size: 44 Copynumber: 2.1 Consensus size: 44
6191973 CAACTGTCAC
6191983 GGACCTAAG-AAGAAATCATGAATCATACATTGAATATAATAAGA
1 GGACCTAAGAAAG-AATCATGAATCATACATTGAATATAATAAGA
6192027 GGACCTAAGAAAGAATCATGAATCATACATTGAATATAATAAGA
1 GGACCTAAGAAAGAATCATGAATCATACATTGAATATAATAAGA
6192071 GGA
1 GGA
6192074 TCACTGAAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
44 43 0.93
45 3 0.07
ACGTcount: A:0.49, C:0.11, G:0.18, T:0.22
Consensus pattern (44 bp):
GGACCTAAGAAAGAATCATGAATCATACATTGAATATAATAAGA
Found at i:6193514 original size:6 final size:6
Alignment explanation
Indices: 6193497--6193534 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
6193487 AGTATCTTCC
* *
6193497 TCCTTT TCCTCT TTCTCT TCCTCT TCCTCT TCCTCT TC
1 TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TC
6193535 TTCATCTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (6 bp):
TCCTCT
Found at i:6194754 original size:13 final size:13
Alignment explanation
Indices: 6194738--6194773 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
6194728 AATATGATAT
6194738 AAATATAATATAA
1 AAATATAATATAA
*
6194751 AAATAAAATATAA
1 AAATATAATATAA
6194764 AAA-ATAATAT
1 AAATATAATAT
6194774 GATTTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATATAATATAA
Found at i:6195612 original size:16 final size:18
Alignment explanation
Indices: 6195578--6195614 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
6195568 ATATTTTAAA
6195578 AAATTATATCAATAATTT
1 AAATTATATCAATAATTT
6195596 AAATTATAT-AA-AATTT
1 AAATTATATCAATAATTT
6195612 AAA
1 AAA
6195615 AAAATATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
17 2 0.11
18 9 0.47
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATTATATCAATAATTT
Found at i:6207479 original size:24 final size:24
Alignment explanation
Indices: 6207452--6207502 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
6207442 TTTTATTAAA
*
6207452 AATTTTTTTAATCGTAATTACAAT
1 AATTTTTTTAATCATAATTACAAT
*
6207476 AATTTTTTTAATCATAATTATAAT
1 AATTTTTTTAATCATAATTACAAT
6207500 AAT
1 AAT
6207503 AATAATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (24 bp):
AATTTTTTTAATCATAATTACAAT
Found at i:6207498 original size:21 final size:22
Alignment explanation
Indices: 6207446--6207499 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 22
6207436 TAAATTTTTT
* *
6207446 ATTAAAAATTTTTTTAATCGTA
1 ATTAATAATTTTTTTAATCATA
6207468 ATTACAATAATTTTTTTAATCATA
1 ATT--AATAATTTTTTTAATCATA
6207492 ATT-ATAAT
1 ATTAATAAT
6207500 AATAATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 5 0.18
22 3 0.11
24 20 0.71
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTAATAATTTTTTTAATCATA
Found at i:6218382 original size:10 final size:10
Alignment explanation
Indices: 6218367--6218411 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
6218357 CTGAATCAAA
6218367 TTATATATTT
1 TTATATATTT
6218377 TTATATATTT
1 TTATATATTT
6218387 TTATTATATATT
1 TTA-TATAT-TT
6218399 TTA-A-ATTT
1 TTATATATTT
6218407 TTATA
1 TTATA
6218412 AAATAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 5 0.16
9 3 0.09
10 14 0.44
11 5 0.16
12 5 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTATATATTT
Found at i:6218452 original size:22 final size:21
Alignment explanation
Indices: 6218427--6218480 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 21
6218417 AAAATAATTA
6218427 ATATATATAAAT-TTATTTAA-
1 ATATATATAAATCTTA-TTAAT
*
6218447 ATATATTAAAAATCTTATTAAT
1 ATATA-TATAAATCTTATTAAT
6218469 ATAATATATAAA
1 AT-ATATATAAA
6218481 AAAATTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 5 0.18
21 10 0.36
22 10 0.36
23 3 0.11
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATATATAAATCTTATTAAT
Found at i:6223282 original size:4 final size:4
Alignment explanation
Indices: 6223273--6223307 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
6223263 ATACACAAAG
6223273 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
6223308 ATACCAAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:6223592 original size:20 final size:20
Alignment explanation
Indices: 6223553--6223592 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
6223543 TTCCTTTAGA
* * *
6223553 TTTCTCTTTTTTTTCTCTCT
1 TTTCTCTTTTCTCTCCCTCT
6223573 TTTCTCTTTTCTCTCCCTCT
1 TTTCTCTTTTCTCTCCCTCT
6223593 CTCTTTAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTCTCTTTTCTCTCCCTCT
Found at i:6224078 original size:7 final size:7
Alignment explanation
Indices: 6224068--6224098 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
6224058 TTTTTCCTTT
6224068 TTTTTTG
1 TTTTTTG
6224075 TTTTTTG
1 TTTTTTG
*
6224082 TTTTTTA
1 TTTTTTG
6224089 TTTTTTG
1 TTTTTTG
6224096 TTT
1 TTT
6224099 ATTTTTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.87
Consensus pattern (7 bp):
TTTTTTG
Found at i:6224329 original size:43 final size:43
Alignment explanation
Indices: 6224282--6224419 Score: 159
Period size: 43 Copynumber: 3.2 Consensus size: 43
6224272 TAACATAAAA
* *
6224282 CTCCTCTAAACAGAGGCACAATGACTTTCAAAAATAAATAAGG
1 CTCCTCTAAACAGAAGCACAATGACTTTAAAAAATAAATAAGG
**
6224325 CTCCTCTAAACAGAAGCTTAATGACTTTAAAAAATAAATAAGG
1 CTCCTCTAAACAGAAGCACAATGACTTTAAAAAATAAATAAGG
* ** * * * * *
6224368 CTCTTCTAAGTAAAAGCTCTATAACTCTAAAAAATAAATAAGG
1 CTCCTCTAAACAGAAGCACAATGACTTTAAAAAATAAATAAGG
*
6224411 CTCATCTAA
1 CTCCTCTAA
6224420 GCAAATGTTA
Statistics
Matches: 82, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 82 1.00
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.25
Consensus pattern (43 bp):
CTCCTCTAAACAGAAGCACAATGACTTTAAAAAATAAATAAGG
Found at i:6224420 original size:43 final size:43
Alignment explanation
Indices: 6224300--6224494 Score: 212
Period size: 43 Copynumber: 4.5 Consensus size: 43
6224290 AACAGAGGCA
* * * * *
6224300 CAATGACTTTCAAAAATAAATAAGGCTCCTCTAAACAGAAGCT
1 CAATAACTTTAAAAAATAAATAAGGCTCTTCTAAGCAAAAGCT
* * *
6224343 TAATGACTTTAAAAAATAAATAAGGCTCTTCTAAGTAAAAGCT
1 CAATAACTTTAAAAAATAAATAAGGCTCTTCTAAGCAAAAGCT
* * * * *
6224386 CTATAACTCTAAAAAATAAATAAGGCTCATCTAAGCAAATGTT
1 CAATAACTTTAAAAAATAAATAAGGCTCTTCTAAGCAAAAGCT
* * *
6224429 AAATAACTTTTGAAAAATAAATAAGGCT-TTCTAAGCAAAGGCT
1 CAATAAC-TTTAAAAAATAAATAAGGCTCTTCTAAGCAAAAGCT
* *
6224472 CAATAACTTTGAGAAATAAATAA
1 CAATAACTTTAAAAAATAAATAA
6224495 AGCTTATTGC
Statistics
Matches: 128, Mismatches: 23, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
42 15 0.12
43 95 0.74
44 18 0.14
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.27
Consensus pattern (43 bp):
CAATAACTTTAAAAAATAAATAAGGCTCTTCTAAGCAAAAGCT
Found at i:6225532 original size:10 final size:9
Alignment explanation
Indices: 6225513--6225541 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
6225503 GAATTGAGTC
6225513 TTTC-TTTT
1 TTTCATTTT
6225521 TTTCATTTT
1 TTTCATTTT
6225530 TTTCATTTT
1 TTTCATTTT
6225539 TTT
1 TTT
6225542 AAGCATAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.20
9 16 0.80
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTCATTTT
Found at i:6234657 original size:26 final size:26
Alignment explanation
Indices: 6234603--6234657 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 26
6234593 TCACCTAGAG
*
6234603 ATTTCTTAAGAAATTTATCATTTGAA
1 ATTTCTTAAGAAATTTATCATTGGAA
6234629 ATTT-TTAAG-AATCTTATCATTGGATA
1 ATTTCTTAAGAAAT-TTATCATTGGA-A
6234655 ATT
1 ATT
6234658 GTCAAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 3 0.12
25 15 0.58
26 8 0.31
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.47
Consensus pattern (26 bp):
ATTTCTTAAGAAATTTATCATTGGAA
Found at i:6235909 original size:19 final size:19
Alignment explanation
Indices: 6235858--6235917 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
6235848 CTTTAAATTT
* *
6235858 CAACTCCAAATT-TTAAGTT
1 CAACT-CAAATTCTTCAGTC
* *
6235877 CAATTCAAACTCTTCAGTC
1 CAACTCAAATTCTTCAGTC
*
6235896 CAACTCAAATTCTTCAATC
1 CAACTCAAATTCTTCAGTC
6235915 CAA
1 CAA
6235918 ACAAACAGAT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
18 5 0.15
19 28 0.85
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.32
Consensus pattern (19 bp):
CAACTCAAATTCTTCAGTC
Found at i:6241424 original size:28 final size:26
Alignment explanation
Indices: 6241392--6241459 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 26
6241382 TTGTATTTTG
*
6241392 ATTTAATTTTATATATTAAATATTTAAA
1 ATTTAATTTTATATATT-AAT-TTAAAA
6241420 ATTTAA-TTTA-AT-TTAATTTAAAA
1 ATTTAATTTTATATATTAATTTAAAA
* *
6241443 ATATAATTTTTTATATT
1 ATTTAATTTTATATATT
6241460 TGATTCGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
23 10 0.29
24 6 0.18
25 4 0.12
26 4 0.12
27 4 0.12
28 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
ATTTAATTTTATATATTAATTTAAAA
Found at i:6242165 original size:3 final size:3
Alignment explanation
Indices: 6242157--6242235 Score: 158
Period size: 3 Copynumber: 26.3 Consensus size: 3
6242147 GTGCTTTTGC
6242157 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
6242205 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
6242236 TCGTGGTTAT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:6247761 original size:27 final size:26
Alignment explanation
Indices: 6247693--6247788 Score: 78
Period size: 27 Copynumber: 3.8 Consensus size: 26
6247683 TTTCATAATA
*
6247693 ATTTAAAA-TATAATATAATAATATG
1 ATTTAAAATTATAATAAAATAATATG
** * *
6247718 ATACGAATATAAT-ATAAAAATAATATG
1 AT-TTAAAATTATAAT-AAAATAATATG
*
6247745 ATTTAAAATTATAATAATA-AATAT-
1 ATTTAAAATTATAATAAAATAATATG
6247769 ATTT-AAATT-TAATAAAATAA
1 ATTTAAAATTATAATAAAATAA
6247789 ATTTTTTTAT
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
22 7 0.13
23 7 0.13
24 4 0.07
25 7 0.13
26 14 0.25
27 16 0.29
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (26 bp):
ATTTAAAATTATAATAAAATAATATG
Found at i:6247797 original size:24 final size:24
Alignment explanation
Indices: 6247730--6247815 Score: 72
Period size: 24 Copynumber: 3.7 Consensus size: 24
6247720 ACGAATATAA
* *
6247730 TATAAAAAT-AATATGATTTAAAAT
1 TATAATAATAAATAT-ATTTAAATT
6247754 TATAATAATAAATATATTTAAATT
1 TATAATAATAAATATATTTAAATT
* * *
6247778 TAATAA-AATAAATTTTTTTATATT
1 T-ATAATAATAAATATATTTAAATT
*
6247802 T-TTAT-ATAAATATA
1 TATAATAATAAATATA
6247816 AATTATAATA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
22 9 0.18
24 33 0.65
25 9 0.18
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (24 bp):
TATAATAATAAATATATTTAAATT
Found at i:6247837 original size:31 final size:31
Alignment explanation
Indices: 6247776--6247867 Score: 97
Period size: 31 Copynumber: 3.1 Consensus size: 31
6247766 TATATTTAAA
*
6247776 TTTA-ATAAAATAAATT-TT--TTTAT-ATT
1 TTTATATAAAATAAATTATTAATATATAATT
6247802 TTTATATAAATATAAATTA-TAATATATAATT
1 TTTATATAAA-ATAAATTATTAATATATAATT
* * *
6247833 TTTATGTAAAATATATTATTAATATATAAAT
1 TTTATATAAAATAAATTATTAATATATAATT
6247864 TTTA
1 TTTA
6247868 ATATTATATA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
26 4 0.07
27 5 0.09
28 8 0.15
30 11 0.20
31 27 0.49
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (31 bp):
TTTATATAAAATAAATTATTAATATATAATT
Found at i:6248244 original size:36 final size:37
Alignment explanation
Indices: 6248159--6248244 Score: 131
Period size: 36 Copynumber: 2.4 Consensus size: 37
6248149 GCTGCCCCAG
*
6248159 CACCAACGTCACCACCACCATCGACTAATACTACCTT
1 CACCAACGTCACCACCACCATCGACTAATACTACCGT
6248196 C-CCAACGTCACCACCACCATCGACTAATACTA-CGT
1 CACCAACGTCACCACCACCATCGACTAATACTACCGT
* *
6248231 CACCACCGCCACCA
1 CACCAACGTCACCA
6248245 ACCGCTTCAA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
35 3 0.07
36 41 0.91
37 1 0.02
ACGTcount: A:0.31, C:0.47, G:0.07, T:0.15
Consensus pattern (37 bp):
CACCAACGTCACCACCACCATCGACTAATACTACCGT
Found at i:6248327 original size:21 final size:21
Alignment explanation
Indices: 6248281--6248327 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
6248271 TACTCCCTCC
* *
6248281 CCACCACCTGCCACCCCATCT
1 CCACCACCCGCCACCCCATCA
*
6248302 CCACCACCCGCCACCCCTTCA
1 CCACCACCCGCCACCCCATCA
*
6248323 GCACC
1 CCACC
6248328 TCCGCCTTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.64, G:0.06, T:0.11
Consensus pattern (21 bp):
CCACCACCCGCCACCCCATCA
Found at i:6248555 original size:39 final size:39
Alignment explanation
Indices: 6248494--6248594 Score: 136
Period size: 39 Copynumber: 2.7 Consensus size: 39
6248484 ATCCCCGACA
6248494 AGTTCGGGGACTCCA--T-CACCGCCACCACCTCCAAGG
1 AGTTCGGGGACTCCATCTCCACCGCCACCACCTCCAAGG
* * **
6248530 AGTTCGGGGACTCCATCTCCCCCGCCGCCGTCTCCAAGG
1 AGTTCGGGGACTCCATCTCCACCGCCACCACCTCCAAGG
*
6248569 AGTTCGGGGACTCCATCTCCTCCGCC
1 AGTTCGGGGACTCCATCTCCACCGCC
6248595 GCTGTCGTCT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
36 15 0.26
38 1 0.02
39 41 0.72
ACGTcount: A:0.16, C:0.43, G:0.24, T:0.18
Consensus pattern (39 bp):
AGTTCGGGGACTCCATCTCCACCGCCACCACCTCCAAGG
Found at i:6248595 original size:39 final size:39
Alignment explanation
Indices: 6248522--6248596 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
6248512 CCGCCACCAC
6248522 CTCCAAGGAGTTCGGGGACTCCATCTCCCCCGCCGCCGT
1 CTCCAAGGAGTTCGGGGACTCCATCTCCCCCGCCGCCGT
*
6248561 CTCCAAGGAGTTCGGGGACTCCATCTCCTCCGCCGC
1 CTCCAAGGAGTTCGGGGACTCCATCTCCCCCGCCGC
6248597 TGTCGTCTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.13, C:0.43, G:0.25, T:0.19
Consensus pattern (39 bp):
CTCCAAGGAGTTCGGGGACTCCATCTCCCCCGCCGCCGT
Found at i:6276430 original size:2 final size:2
Alignment explanation
Indices: 6276423--6276458 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6276413 TGTTTATGTT
6276423 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
6276459 AAATAGGCAC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6277606 original size:15 final size:17
Alignment explanation
Indices: 6277586--6277622 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
6277576 ATTTGGCTGC
6277586 CTTTTG-TT-TTTTGTT
1 CTTTTGTTTGTTTTGTT
6277601 CTTTTGTTTGTTTTGTT
1 CTTTTGTTTGTTTTGTT
6277618 -TTTTG
1 CTTTTG
6277623 AATTATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 7 0.35
17 7 0.35
ACGTcount: A:0.00, C:0.05, G:0.16, T:0.78
Consensus pattern (17 bp):
CTTTTGTTTGTTTTGTT
Found at i:6277936 original size:23 final size:23
Alignment explanation
Indices: 6277901--6277944 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
6277891 TTTAATTTGA
*
6277901 TTTAAAATTAATA-AAATATTATT
1 TTTAAAATAAATATAAA-ATTATT
*
6277924 TTTAATATAAATATAAAATTA
1 TTTAAAATAAATATAAAATTA
6277945 AATTAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTAAAATAAATATAAAATTATT
Found at i:6277938 original size:6 final size:6
Alignment explanation
Indices: 6277927--6277974 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
6277917 TATTATTTTT
6277927 AATATA AATATA AA-ATTA AAT-TA ATATATA AATAT- -ATATA AATATA
1 AATATA AATATA AATA-TA AATATA A-ATATA AATATA AATATA AATATA
6277973 AA
1 AA
6277975 ATTAAATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
4 4 0.11
5 4 0.11
6 25 0.69
7 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
AATATA
Found at i:6277946 original size:12 final size:12
Alignment explanation
Indices: 6277931--6277982 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
6277921 ATTTTTAATA
6277931 TAAATATAAAAT
1 TAAATATAAAAT
*
6277943 TAAAT-TAATAT
1 TAAATATAAAAT
*
6277954 ATAAATAT-ATA-
1 -TAAATATAAAAT
6277965 TAAATATAAAAT
1 TAAATATAAAAT
6277977 TAAATA
1 TAAATA
6277983 ATTAATTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
10 7 0.21
11 7 0.21
12 19 0.56
13 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TAAATATAAAAT
Found at i:6277955 original size:18 final size:18
Alignment explanation
Indices: 6277927--6277982 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
6277917 TATTATTTTT
6277927 AATATAAATATAAAATTA
1 AATATAAATATAAAATTA
6277945 AAT-T-AATATATAAA-TA
1 AATATAAATATA-AAATTA
*
6277961 TATATAAATATAAAATTA
1 AATATAAATATAAAATTA
6277979 AATA
1 AATA
6277983 ATTAATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
16 10 0.31
17 8 0.25
18 14 0.44
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AATATAAATATAAAATTA
Found at i:6280744 original size:20 final size:21
Alignment explanation
Indices: 6280719--6280768 Score: 86
Period size: 20 Copynumber: 2.5 Consensus size: 21
6280709 TTCAAAATTA
6280719 ATAAAATATTA-TTTTTAAAT
1 ATAAAATATTATTTTTTAAAT
6280739 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTTAAAT
6280760 AT-AAATATT
1 ATAAAATATT
6280769 TAAATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTTAAAT
Found at i:6281056 original size:2 final size:2
Alignment explanation
Indices: 6281049--6281091 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
6281039 AATCCCTGGT
6281049 GA GA GA GA GA GA 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 GA GA GA GA GA GA
6281091 G
1 G
6281092 GACTAAGGAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6282313 original size:20 final size:20
Alignment explanation
Indices: 6282290--6282386 Score: 95
Period size: 21 Copynumber: 4.8 Consensus size: 20
6282280 TAAAATTTTT
*
6282290 TCAAAAATTACCAAATTGTA
1 TCAAAAATTACCAAATTATA
* *
6282310 TCAATAGTTACCAAATTATA
1 TCAAAAATTACCAAATTATA
* *
6282330 TTATAAATTACCAAAATTATA
1 TCAAAAATTACC-AAATTATA
* *
6282351 TCAAAAGTTACCAAAATTTTA
1 TCAAAAATTACC-AAATTATA
* *
6282372 TAAAAAATTATCAAA
1 TCAAAAATTACCAAA
6282387 ATCAAAATTA
Statistics
Matches: 62, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 28 0.45
21 34 0.55
ACGTcount: A:0.52, C:0.12, G:0.03, T:0.33
Consensus pattern (20 bp):
TCAAAAATTACCAAATTATA
Found at i:6282360 original size:41 final size:42
Alignment explanation
Indices: 6282292--6282388 Score: 126
Period size: 42 Copynumber: 2.4 Consensus size: 42
6282282 AAATTTTTTC
* * *
6282292 AAAAATTACC-AAATTGTATCAATAGTTACC-AAATTATATT
1 AAAAATTACCAAAATTATATCAAAAGTTACCAAAATTATATA
* *
6282332 ATAAATTACCAAAATTATATCAAAAGTTACCAAAATTTTATA
1 AAAAATTACCAAAATTATATCAAAAGTTACCAAAATTATATA
*
6282374 AAAAATTATCAAAAT
1 AAAAATTACCAAAAT
6282389 CAAAATTAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 9 0.19
41 18 0.38
42 21 0.44
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.33
Consensus pattern (42 bp):
AAAAATTACCAAAATTATATCAAAAGTTACCAAAATTATATA
Found at i:6282597 original size:28 final size:27
Alignment explanation
Indices: 6282565--6282628 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
6282555 TTTGATTTCA
6282565 ATATAATATTAAATTTTGATAATTTTTT
1 ATATAAT-TTAAATTTTGATAATTTTTT
**
6282593 ATATAATTTTGATTTTGATAATTTTTT
1 ATATAATTTAAATTTTGATAATTTTTT
* *
6282620 GTAAAATTT
1 ATATAATTT
6282629 TAGTACCCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 25 0.78
28 7 0.22
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (27 bp):
ATATAATTTAAATTTTGATAATTTTTT
Found at i:6282607 original size:27 final size:27
Alignment explanation
Indices: 6282577--6282629 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
6282567 ATAATATTAA
*
6282577 ATTTTGATAATTTTTTATATAATTTTG
1 ATTTTGATAATTTTTTATAAAATTTTG
*
6282604 ATTTTGATAATTTTTTGTAAAATTTT
1 ATTTTGATAATTTTTTATAAAATTTT
6282630 AGTACCCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (27 bp):
ATTTTGATAATTTTTTATAAAATTTTG
Found at i:6282615 original size:15 final size:14
Alignment explanation
Indices: 6282577--6282617 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 14
6282567 ATAATATTAA
6282577 ATTTTGATAATTTT
1 ATTTTGATAATTTT
*
6282591 -TTAT-ATAATTTT
1 ATTTTGATAATTTT
6282603 GATTTTGATAATTTT
1 -ATTTTGATAATTTT
6282618 TTGTAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
12 8 0.36
13 3 0.14
14 3 0.14
15 8 0.36
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.63
Consensus pattern (14 bp):
ATTTTGATAATTTT
Found at i:6282712 original size:42 final size:41
Alignment explanation
Indices: 6282604--6282720 Score: 110
Period size: 42 Copynumber: 2.8 Consensus size: 41
6282594 TATAATTTTG
* * * *
6282604 ATTTTGATAATTTTTTGTAAAATTTTAGTACCCTTTAACATA
1 ATTTTGATAA-TTTTTATAAAATTTTAGTAACCATTAACAAA
* * * * *
6282646 ATTTT-AGTAACTTTTGATATAATTTTGGTAATCATTAATAAA
1 ATTTTGA-TAA-TTTTTATAAAATTTTAGTAACCATTAACAAA
6282688 ATTTTGATAATTTCTTATAAAATTTTAGTAACC
1 ATTTTGATAATTT-TTATAAAATTTTAGTAACC
6282721 TCTTCATGTA
Statistics
Matches: 58, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
41 4 0.07
42 53 0.91
43 1 0.02
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.49
Consensus pattern (41 bp):
ATTTTGATAATTTTTATAAAATTTTAGTAACCATTAACAAA
Found at i:6282724 original size:21 final size:21
Alignment explanation
Indices: 6282621--6282724 Score: 63
Period size: 21 Copynumber: 4.9 Consensus size: 21
6282611 TAATTTTTTG
*
6282621 TAAAATTTTAGT-ACCCTTTAA
1 TAAAATTTTAGTAACTC-TTAA
* * * *
6282642 CATAATTTTAGTAACTTTTGA
1 TAAAATTTTAGTAACTCTTAA
* *
6282663 TATAATTTTGGTAA-TCATTAA
1 TAAAATTTTAGTAACTC-TTAA
*
6282684 TAAAATTTT-GATAATTTCTT-A
1 TAAAATTTTAG-TAA-CTCTTAA
6282705 TAAAATTTTAGTAACCTCTT
1 TAAAATTTTAGTAA-CTCTT
6282725 CATGTAATTT
Statistics
Matches: 65, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
20 2 0.03
21 56 0.86
22 5 0.08
23 2 0.03
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.47
Consensus pattern (21 bp):
TAAAATTTTAGTAACTCTTAA
Found at i:6283159 original size:22 final size:22
Alignment explanation
Indices: 6283143--6283190 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
6283133 CAAATCAATG
*
6283143 ATAATATAATAGTAAATATATA
1 ATAACATAATAGTAAATATATA
6283165 ATAACATAATAGTAAAT-TATTA
1 ATAACATAATAGTAAATATA-TA
6283187 ATAA
1 ATAA
6283191 TTTAGATGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.35
Consensus pattern (22 bp):
ATAACATAATAGTAAATATATA
Found at i:6283191 original size:44 final size:44
Alignment explanation
Indices: 6283143--6283235 Score: 100
Period size: 44 Copynumber: 2.1 Consensus size: 44
6283133 CAAATCAATG
* *
6283143 ATAATATA-ATAGTAAA-TATATAATAACATAATAGTAAATTATTA
1 ATAATATAGAT-GTAAATTATA-AATAACATAATAGTAAATCATAA
* ** *
6283187 ATAATTTAGATGTAAATTATAAATAATTTAGTAGTAAATCATAA
1 ATAATATAGATGTAAATTATAAATAACATAATAGTAAATCATAA
6283231 ATAAT
1 ATAAT
6283236 TATGTTGTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
44 35 0.85
45 6 0.15
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (44 bp):
ATAATATAGATGTAAATTATAAATAACATAATAGTAAATCATAA
Found at i:6283201 original size:22 final size:23
Alignment explanation
Indices: 6283176--6283277 Score: 95
Period size: 22 Copynumber: 4.6 Consensus size: 23
6283166 TAACATAATA
6283176 GTAAATTATTAATAATTTA-GAT
1 GTAAATTATTAATAATTTAGGAT
* *
6283198 GTAAATTATAAATAATTTAGTA-
1 GTAAATTATTAATAATTTAGGAT
* * * *
6283220 GTAAATCATAAATAA-TTATGTT
1 GTAAATTATTAATAATTTAGGAT
* *
6283242 GTAAATCAGTAATAATTTAGGA-
1 GTAAATTATTAATAATTTAGGAT
6283264 GTAAATTAGTTAAT
1 GTAAATTA-TTAAT
6283278 TATTGATAAT
Statistics
Matches: 64, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
21 3 0.05
22 52 0.81
23 9 0.14
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.40
Consensus pattern (23 bp):
GTAAATTATTAATAATTTAGGAT
Found at i:6283236 original size:44 final size:44
Alignment explanation
Indices: 6283174--6283269 Score: 115
Period size: 44 Copynumber: 2.2 Consensus size: 44
6283164 AATAACATAA
* * *
6283174 TAGTAAATTATTAATAATT-TAGATGTAAATTA-TAAATAATTTAG
1 TAGTAAATCATAAATAATTAT-GATGTAAATCAGT-AATAATTTAG
*
6283218 TAGTAAATCATAAATAATTATGTTGTAAATCAGTAATAATTTAG
1 TAGTAAATCATAAATAATTATGATGTAAATCAGTAATAATTTAG
*
6283262 GAGTAAAT
1 TAGTAAAT
6283270 TAGTTAATTA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
44 43 0.96
45 2 0.04
ACGTcount: A:0.47, C:0.02, G:0.11, T:0.40
Consensus pattern (44 bp):
TAGTAAATCATAAATAATTATGATGTAAATCAGTAATAATTTAG
Found at i:6283394 original size:21 final size:22
Alignment explanation
Indices: 6283370--6283420 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
6283360 AGTAAATGAA
6283370 ACTAATTTATCATTAAATT-TC
1 ACTAATTTATCATTAAATTATC
* *
6283391 ACTAATTTATTATTAATTTATC
1 ACTAATTTATCATTAAATTATC
*
6283413 ATTAATTT
1 ACTAATTT
6283421 TTTACTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (22 bp):
ACTAATTTATCATTAAATTATC
Found at i:6283409 original size:11 final size:11
Alignment explanation
Indices: 6283372--6283420 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
6283362 TAAATGAAAC
6283372 TAATTTATCAT
1 TAATTTATCAT
* *
6283383 TAAATT-TCAC
1 TAATTTATCAT
*
6283393 TAATTTATTAT
1 TAATTTATCAT
6283404 TAATTTATCAT
1 TAATTTATCAT
6283415 TAATTT
1 TAATTT
6283421 TTTACTAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
10 8 0.26
11 23 0.74
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (11 bp):
TAATTTATCAT
Found at i:6283486 original size:22 final size:22
Alignment explanation
Indices: 6283372--6283486 Score: 78
Period size: 22 Copynumber: 5.3 Consensus size: 22
6283362 TAAATGAAAC
* * *
6283372 TAATTTATCATTAAATT-TCAC
1 TAATTTTTTATTAAATTATCAT
* *
6283393 TAATTTATTATTAATTTATCAT
1 TAATTTTTTATTAAATTATCAT
*
6283415 TAATTTTTTACTAAA-TA--AT
1 TAATTTTTTATTAAATTATCAT
* *
6283434 TAATTATTAACTATTAAATTACCACT
1 TAATT-TT--TTATTAAATTATCA-T
*
6283460 T-ATTTTTTAATAAATTATCAT
1 TAATTTTTTATTAAATTATCAT
6283481 TAATTT
1 TAATTT
6283487 ACTACTATAT
Statistics
Matches: 74, Mismatches: 11, Indels: 17
0.73 0.11 0.17
Matches are distributed among these distances:
19 7 0.09
20 2 0.03
21 19 0.26
22 36 0.49
23 2 0.03
24 2 0.03
25 4 0.05
26 2 0.03
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (22 bp):
TAATTTTTTATTAAATTATCAT
Found at i:6285013 original size:45 final size:45
Alignment explanation
Indices: 6284952--6285119 Score: 228
Period size: 45 Copynumber: 3.7 Consensus size: 45
6284942 TTTCCAAAAA
* * *
6284952 GTATCATTCTCTGATGCAAGATCAATTCTCTTTCCAGCCAAAACT
1 GTATCATTTTCAGATGCAAGATCAATCCTCTTTCCAGCCAAAACT
* *
6284997 GTATCATTTTCAGATGCAAGTTCAATTCTCTTTCCAGCCAAAACT
1 GTATCATTTTCAGATGCAAGATCAATCCTCTTTCCAGCCAAAACT
* ** *
6285042 GTATCATTTTCAGATGCAAGATCAATCCTCTTTTCTTCCAAAACA
1 GTATCATTTTCAGATGCAAGATCAATCCTCTTTCCAGCCAAAACT
* * *
6285087 ATATCAGTTTCAGATGTAAGATCAATCCTCTTT
1 GTATCATTTTCAGATGCAAGATCAATCCTCTTT
6285120 TCTTCGAAAA
Statistics
Matches: 111, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 111 1.00
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.36
Consensus pattern (45 bp):
GTATCATTTTCAGATGCAAGATCAATCCTCTTTCCAGCCAAAACT
Found at i:6285120 original size:45 final size:45
Alignment explanation
Indices: 6284943--6285136 Score: 219
Period size: 45 Copynumber: 4.3 Consensus size: 45
6284933 GCTATATCCT
* * *
6284943 TTCCAAAA-AGTATCATTCTCTGATGCAAGATCAATTCTCTTTCC
1 TTCCAAAACAGTATCATTTTCAGATGCAAGATCAATCCTCTTTCC
** * * *
6284987 AGCCAAAACTGTATCATTTTCAGATGCAAGTTCAATTCTCTTTCC
1 TTCCAAAACAGTATCATTTTCAGATGCAAGATCAATCCTCTTTCC
** * *
6285032 AGCCAAAACTGTATCATTTTCAGATGCAAGATCAATCCTCTTTTC
1 TTCCAAAACAGTATCATTTTCAGATGCAAGATCAATCCTCTTTCC
* * * *
6285077 TTCCAAAACAATATCAGTTTCAGATGTAAGATCAATCCTCTTTTC
1 TTCCAAAACAGTATCATTTTCAGATGCAAGATCAATCCTCTTTCC
* *
6285122 TTCGAAAACAATATC
1 TTCCAAAACAGTATC
6285137 TCCTTTGCAT
Statistics
Matches: 133, Mismatches: 16, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
44 6 0.05
45 127 0.95
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.35
Consensus pattern (45 bp):
TTCCAAAACAGTATCATTTTCAGATGCAAGATCAATCCTCTTTCC
Found at i:6288366 original size:30 final size:30
Alignment explanation
Indices: 6288332--6288392 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
6288322 GGTTCAGATT
6288332 TCAGACAATGCAGGCTTTAAATTTTATTTA
1 TCAGACAATGCAGGCTTTAAATTTTATTTA
6288362 TCAGACAATGCAGGCTTTAAATTTTATTTA
1 TCAGACAATGCAGGCTTTAAATTTTATTTA
6288392 T
1 T
6288393 AACAGTTACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (30 bp):
TCAGACAATGCAGGCTTTAAATTTTATTTA
Found at i:6289242 original size:10 final size:10
Alignment explanation
Indices: 6289227--6289261 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
6289217 CAAACCTTAA
6289227 AAAAAAAAAC
1 AAAAAAAAAC
*
6289237 AAAAAAAACC
1 AAAAAAAAAC
6289247 AAAAAAAAA-
1 AAAAAAAAAC
6289256 AAAAAA
1 AAAAAA
6289262 TGGAAAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 6 0.26
10 17 0.74
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:6290590 original size:4 final size:4
Alignment explanation
Indices: 6290581--6290608 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
6290571 AAATTTGTAG
6290581 TAAT TAAT TAAT TAAT TAAT TAAT TAAT
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT
6290609 ATCCACAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:6304248 original size:16 final size:16
Alignment explanation
Indices: 6304229--6304259 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6304219 GGCTTGAGCC
6304229 GAAAAAAAAAAAGAAG
1 GAAAAAAAAAAAGAAG
*
6304245 GAAAAAGAAAAAGAA
1 GAAAAAAAAAAAGAA
6304260 AGTCATGGGT
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:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
GAAAAAAAAAAAGAAG
Found at i:6308114 original size:6 final size:6
Alignment explanation
Indices: 6308068--6308130 Score: 51
Period size: 6 Copynumber: 10.7 Consensus size: 6
6308058 TAATATAATA
* * * *
6308068 TTAAAT TTATAT TT-GAT TTAAAAT TTAATAT TTAAAA TTAAGT TTAAAT
1 TTAAAT TTAAAT TTAAAT TT-AAAT TTAA-AT TTAAAT TTAAAT TTAAAT
6308117 TT-AA- TTAAAT TTAA
1 TTAAAT TTAAAT TTAA
6308131 TTATTTTAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
4 2 0.04
5 8 0.18
6 25 0.56
7 10 0.22
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (6 bp):
TTAAAT
Found at i:6308227 original size:25 final size:24
Alignment explanation
Indices: 6308185--6308257 Score: 83
Period size: 25 Copynumber: 2.9 Consensus size: 24
6308175 GAATTAATTT
*
6308185 AATTAAATTTATTAATATTTAAAAATA
1 AATTTAATTT-TT-ATATTTAAAAA-A
*
6308212 AATTTAATTTTTATATTTAATAAA
1 AATTTAATTTTTATATTTAAAAAA
*
6308236 AATTTAATTATTTGTATTTAAA
1 AATTTAATT-TTTATATTTAAA
6308258 TTTAAGTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.24
25 20 0.49
26 2 0.05
27 9 0.22
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (24 bp):
AATTTAATTTTTATATTTAAAAAA
Found at i:6326216 original size:26 final size:27
Alignment explanation
Indices: 6326169--6326228 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 27
6326159 TAATTGATTT
6326169 TTTTAAATAAAAAAATTATTA-TTAAA
1 TTTTAAATAAAAAAATTATTATTTAAA
** *
6326195 TTTTAAATAAAAATTTTTTTATTTAAA
1 TTTTAAATAAAAAAATTATTATTTAAA
*
6326222 ATTTAAA
1 TTTTAAA
6326229 ATAATATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 18 0.62
27 11 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
TTTTAAATAAAAAAATTATTATTTAAA
Found at i:6332609 original size:2 final size:2
Alignment explanation
Indices: 6332602--6332637 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6332592 TTCAATTCTA
6332602 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
6332638 TTTTTTTTTC
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:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:6336425 original size:15 final size:15
Alignment explanation
Indices: 6336405--6336435 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
6336395 AAAATGGTGG
6336405 CAAAATAGAGAAAAA
1 CAAAATAGAGAAAAA
6336420 CAAAATAGAGAAAAA
1 CAAAATAGAGAAAAA
6336435 C
1 C
6336436 TAACTTAATG
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:0.71, C:0.10, G:0.13, T:0.06
Consensus pattern (15 bp):
CAAAATAGAGAAAAA
Found at i:6337923 original size:63 final size:62
Alignment explanation
Indices: 6337856--6337992 Score: 177
Period size: 62 Copynumber: 2.2 Consensus size: 62
6337846 TGTAAAAAAA
* *
6337856 ATTATTGAAGGCATTTCAAGTAAAAATACGCCTTTAATAATCCTATTAAATTTT-TTAGAGGAG
1 ATTATTGAAGGCATTTCAAGT-AAAACACGCCTTTAATAATCCTATTAAATTTTGAT-GAGGAG
* *** * *
6337919 ATTATTGAAGGTATTTTTTGTAAAACACGTCTTTAATAATCCTCTTAAATTTTGATGAGGAG
1 ATTATTGAAGGCATTTCAAGTAAAACACGCCTTTAATAATCCTATTAAATTTTGATGAGGAG
6337981 ATTATTGAAGGC
1 ATTATTGAAGGC
6337993 GTTTTTGACT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
62 46 0.72
63 18 0.28
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (62 bp):
ATTATTGAAGGCATTTCAAGTAAAACACGCCTTTAATAATCCTATTAAATTTTGATGAGGAG
Found at i:6337967 original size:62 final size:60
Alignment explanation
Indices: 6337878--6338180 Score: 213
Period size: 62 Copynumber: 4.8 Consensus size: 60
6337868 ATTTCAAGTA
* *
6337878 AAAATACGCCTTTAATAATCCTATTAAATTTTTTAGAGGAGATTATTGAAGGTATTTTTTGT
1 AAAA-ACGTCTTTAATAATCCTCTTAAA-TTTTTAGAGGAGATTATTGAAGGTATTTTTTGT
* **
6337940 AAAACACGTCTTTAATAATCCTCTTAAATTTTGATGAGGAGATTATTGAAGG-CGTTTTTGACT
1 AAAA-ACGTCTTTAATAATCCTCTTAAATTTTTA-GAGGAGATTATTGAAGGTATTTTTTG--T
* * * * * *
6338003 AAAAATG-CTTTTAATAAT-CTCCTCTAATTTTTTAGAAGAAATTATTGAAGGTATTTTATGC
1 AAAAACGTC-TTTAATAATCCT-CT-TAAATTTTTAGAGGAGATTATTGAAGGTATTTTTTGT
* * * * *
6338064 AAAAA-ATACATTCAATAAT-CTCTTTAAATTTTGATGAGGAGATTATTGAAAGTATTTTTTTAT
1 AAAAACGT-C-TTTAATAATCCTC-TTAAATTTTTA-GAGGAGATTATTGAAGGTA-TTTTTTGT
* * * **
6338127 AAAAAAAC-ACTTTCAATAATCCCCTTCAACTTTTTAGAAAAGATTATTGAAGGT
1 --AAAAACGTCTTT-AATAATCCTCTT-AAATTTTTAGAGGAGATTATTGAAGGT
6338181 GTCCCATCCA
Statistics
Matches: 189, Mismatches: 34, Indels: 34
0.74 0.13 0.13
Matches are distributed among these distances:
61 28 0.15
62 98 0.52
63 25 0.13
64 24 0.13
65 14 0.07
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.40
Consensus pattern (60 bp):
AAAAACGTCTTTAATAATCCTCTTAAATTTTTAGAGGAGATTATTGAAGGTATTTTTTGT
Found at i:6338130 original size:124 final size:125
Alignment explanation
Indices: 6337887--6338180 Score: 307
Period size: 124 Copynumber: 2.4 Consensus size: 125
6337877 AAAAATACGC
** * * * * * *
6337887 CTTT-AATAATCCTATTAAATTTTTTAGAGGAGATTATTGAAGGTATTTTTTGTAAAACACGTCT
1 CTTTCAATAATCCCCTTCAATTTTTTAGAAGAAATTATTGAAGGTATTTTATGCAAAACACATCT
* * **
6337951 TTAATAATCCTCTTAAATTTTGATGAGGAGATTATTGAAGGCGTTTTTGACT-AAAAATG
66 TCAATAATCCTCTTAAATTTTGATGAGGAGATTATTGAAGGAGTTTTTGACTAAAAAACA
* *
6338010 CTTTTAATAATCTCC-TCTAATTTTTTAGAAGAAATTATTGAAGGTATTTTATGCAAAA-A-ATA
1 CTTTCAATAATCCCCTTC-AATTTTTTAGAAGAAATTATTGAAGGTATTTTATGCAAAACACAT-
* * *
6338072 CATTCAATAAT-CTCTTTAAATTTTGATGAGGAGATTATTGAAAGTATTTTTTTA-TAAAAAAAC
64 C-TTCAATAATCCTC-TTAAATTTTGATGAGGAGATTATTG-AAGGAGTTTTTGACT-AAAAAAC
6338135 A
125 A
*
6338136 CTTTCAATAATCCCCTTCAACTTTTTAGAA-AAGATTATTGAAGGT
1 CTTTCAATAATCCCCTTCAATTTTTTAGAAGAA-ATTATTGAAGGT
6338181 GTCCCATCCA
Statistics
Matches: 142, Mismatches: 19, Indels: 17
0.80 0.11 0.10
Matches are distributed among these distances:
122 1 0.01
123 10 0.07
124 77 0.54
125 11 0.08
126 41 0.29
127 2 0.01
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (125 bp):
CTTTCAATAATCCCCTTCAATTTTTTAGAAGAAATTATTGAAGGTATTTTATGCAAAACACATCT
TCAATAATCCTCTTAAATTTTGATGAGGAGATTATTGAAGGAGTTTTTGACTAAAAAACA
Found at i:6343561 original size:3 final size:3
Alignment explanation
Indices: 6343553--6343583 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
6343543 TCATGCCAAC
*
6343553 AAG AAG AAG AAG AAG AAG AAG TAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
6343584 GGTGGGTGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:6349719 original size:17 final size:18
Alignment explanation
Indices: 6349697--6349734 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
6349687 AAATTATTTT
*
6349697 TTTAAA-AATTTATATAA
1 TTTAAATAATTGATATAA
*
6349714 TTTAAATTATTGATATAA
1 TTTAAATAATTGATATAA
6349732 TTT
1 TTT
6349735 TTAAAGCTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTAAATAATTGATATAA
Found at i:6351352 original size:83 final size:83
Alignment explanation
Indices: 6351172--6351339 Score: 291
Period size: 83 Copynumber: 2.0 Consensus size: 83
6351162 TTATTCATAA
*
6351172 TAAAAATAAATTTTAGTAATATTCTAAAATAAAAAATAAAAGATTTAAAAATTAAATTTATTTAC
1 TAAATATAAATTTTAGTAATATTCTAAAATAAAAAATAAAAGATTTAAAAATTAAATTTATTTAC
* *
6351237 TAAATAAGTCTAAGTGCC
66 TAAATAAATCAAAGTGCC
* *
6351255 TAAATATAAATTTTAGTAATATTCTGAAATAAAAAATAAAAGATTTAAAAATTAAATTTATTTAT
1 TAAATATAAATTTTAGTAATATTCTAAAATAAAAAATAAAAGATTTAAAAATTAAATTTATTTAC
6351320 TAAATAAATCAAAGTGCC
66 TAAATAAATCAAAGTGCC
6351338 TA
1 TA
6351340 TCTTTAGCTT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 80 1.00
ACGTcount: A:0.53, C:0.05, G:0.06, T:0.36
Consensus pattern (83 bp):
TAAATATAAATTTTAGTAATATTCTAAAATAAAAAATAAAAGATTTAAAAATTAAATTTATTTAC
TAAATAAATCAAAGTGCC
Found at i:6355260 original size:21 final size:21
Alignment explanation
Indices: 6355234--6355297 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
6355224 ATTATTATTT
6355234 AATTTTTTTCTTTTCTTTTTC
1 AATTTTTTTCTTTTCTTTTTC
6355255 AATTTTTTAT-TTTTCAATTTTTC
1 AATTTTTT-TCTTTTC--TTTTTC
**
6355278 TTTTATTTTTC-TTTCTTTTT
1 AATT-TTTTTCTTTTCTTTTT
6355298 TCTTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
21 18 0.50
22 1 0.03
23 13 0.36
24 4 0.11
ACGTcount: A:0.12, C:0.11, G:0.00, T:0.77
Consensus pattern (21 bp):
AATTTTTTTCTTTTCTTTTTC
Found at i:6355261 original size:14 final size:15
Alignment explanation
Indices: 6355244--6355281 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
6355234 AATTTTTTTC
6355244 TTTTCTTTTTCAATT
1 TTTTCTTTTTCAATT
*
6355259 TTTTATTTTTCAA-T
1 TTTTCTTTTTCAATT
6355273 TTTTCTTTT
1 TTTTCTTTT
6355282 ATTTTTCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTCTTTTTCAATT
Found at i:6356790 original size:10 final size:11
Alignment explanation
Indices: 6356758--6356895 Score: 80
Period size: 11 Copynumber: 12.9 Consensus size: 11
6356748 GCCCACTTCG
*
6356758 TTTTGTATTTTA
1 TTTT-TATTATA
6356770 TTTTTATTATA
1 TTTTTATTATA
6356781 TTTTTA-TATA
1 TTTTTATTATA
*
6356791 -TTTTATTTTA
1 TTTTTATTATA
6356801 -TTTTACTT-TA
1 TTTTTA-TTATA
*
6356811 TTTTGTATTTTA
1 TTTT-TATTATA
6356823 TGTATTTATTAT-
1 T-T-TTTATTATA
6356835 TTATTTATT-TA
1 TT-TTTATTATA
*
6356846 TTATTATTAT-
1 TTTTTATTATA
* *
6356856 TTATTAATATA
1 TTTTTATTATA
* *
6356867 TATTTATTTTA
1 TTTTTATTATA
6356878 -TTTTA-T-TA
1 TTTTTATTATA
6356886 TTTTTATTAT
1 TTTTTATTAT
6356896 TTATCTGTTG
Statistics
Matches: 103, Mismatches: 10, Indels: 27
0.74 0.07 0.19
Matches are distributed among these distances:
8 2 0.02
9 11 0.11
10 34 0.33
11 38 0.37
12 10 0.10
13 6 0.06
14 2 0.02
ACGTcount: A:0.25, C:0.01, G:0.02, T:0.72
Consensus pattern (11 bp):
TTTTTATTATA
Found at i:6356838 original size:4 final size:4
Alignment explanation
Indices: 6356792--6356899 Score: 57
Period size: 4 Copynumber: 26.2 Consensus size: 4
6356782 TTTTATATAT
* *
6356792 TTTA TTTTA TTTTA CTTTA TTT- TGTA TTTTA TGTA TTTA -TTA TTTA
1 TTTA -TTTA -TTTA -TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA
*
6356838 TTTA TTTA -TTA -TTA -TTA TTTA TTAATA TATA TTTA TTTTA TTT- TATTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TT--TA TTTA TTTA -TTTA TTTA T-TTA
*
6356886 TTTT TATTA TTTA T
1 TTTA T-TTA TTTA T
6356900 CTGTTGATAT
Statistics
Matches: 84, Mismatches: 9, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
3 15 0.18
4 42 0.50
5 24 0.29
6 3 0.04
ACGTcount: A:0.26, C:0.01, G:0.02, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:6356842 original size:31 final size:28
Alignment explanation
Indices: 6356763--6357083 Score: 146
Period size: 31 Copynumber: 11.0 Consensus size: 28
6356753 CTTCGTTTTG
6356763 TATT-TTATT-TTTATTATATTTTTATATAT
1 TATTATTATTATTTATT-TATTTTTAT-T-T
6356792 T-TTATT-TTATTTTACTTTATTTTGTATTT
1 TATTATTATTA-TTTA-TTTATTTT-TATTT
6356821 TATGTATTTATTATTTATTTATTTATTATTAT
1 TAT-TA-TTATTATTTATTTATTT-TTATT-T
* *
6356853 TATTTATTAATATATATTTA-TTTTATTT
1 TA-TTATTATTATTTATTTATTTTTATTT
* * *
6356881 TATTATTTTTA-TTATTTATCTGTTGATATA
1 TATTATTATTATTTATTTAT-T-TTTAT-TT
* * * *
6356911 TATGTATTATTATTTATCTATTTATCTAT
1 TAT-TATTATTATTTATTTATTTTTATTT
* **
6356940 TATTATTATTA-TTACTTATCTCTTTA-AA
1 TATTATTATTATTTATTTAT-T-TTTATTT
* *
6356968 TA-TATTATTATTTATCTATTATTATTAT
1 TATTATTATTATTTATTTATTTTTATT-T
* * * *
6356996 TATTATTTATCTATTAATTAATATATTATCCT
1 TATTA-TTAT-TATTTATTTAT-TTTTAT-TT
*
6357028 TATTATTA-TCTTT-TTTA-TTTTATTAT
1 TATTATTATTATTTATTTATTTTTATT-T
*
6357054 T-TTATTATTTACTTTATTTATTTTTTTTT
1 TATTATTA-TTA-TTTATTTATTTTTATTT
6357083 T
1 T
6357084 TCTTTCTTTT
Statistics
Matches: 223, Mismatches: 35, Indels: 68
0.68 0.11 0.21
Matches are distributed among these distances:
25 6 0.03
26 16 0.07
27 23 0.10
28 34 0.15
29 30 0.13
30 30 0.13
31 49 0.22
32 31 0.14
33 4 0.02
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (28 bp):
TATTATTATTATTTATTTATTTTTATTT
Found at i:6356849 original size:3 final size:3
Alignment explanation
Indices: 6356763--6357062 Score: 119
Period size: 3 Copynumber: 96.3 Consensus size: 3
6356753 CTTCGTTTTG
* *
6356763 TAT T-T TAT TTT TAT TA- TAT TTT TAT ATAT T-T TAT T-T TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
* *
6356804 TAC T-T TAT TTT GTAT T-T TAT GTATT TAT TATT TATT TATT TAT TAT
1 TAT TAT TAT TAT -TAT TAT TAT -TA-T TAT TA-T TA-T TA-T TAT TAT
* *
6356850 TAT TATT TAT TAA TAT ATATT TAT T-T TAT T-T TAT TAT TTT TAT TATT
1 TAT TA-T TAT TAT TAT -TA-T TAT TAT TAT TAT TAT TAT TAT TAT TA-T
*
6356897 TAT CTGT TGA- TAT ATAT GTAT TAT TATT TAT CTATT TAT CTAT TAT TAT
1 TAT -TAT T-AT TAT -TAT -TAT TAT TA-T TAT -TA-T TAT -TAT TAT TAT
* * *
6356946 TAT TAT TACT TAT CTCT T-T AAA TA- TAT TAT TATT TAT CTAT TAT TAT
1 TAT TAT TA-T TAT -TAT TAT TAT TAT TAT TAT TA-T TAT -TAT TAT TAT
* **
6356993 TAT TAT TATT TAT CTAT TAAT TAA TA- TAT TAT CCT TAT TAT TAT CT-T
1 TAT TAT TA-T TAT -TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
*
6357040 TTT TAT T-T TAT TAT T-T TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
6357063 TACTTTATTT
Statistics
Matches: 232, Mismatches: 25, Indels: 80
0.69 0.07 0.24
Matches are distributed among these distances:
2 28 0.12
3 132 0.57
4 69 0.30
5 3 0.01
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Done.