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 37 of 109
Found at i:5550030 original size:16 final size:16
Alignment explanation
Indices: 5550000--5550029 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5549990 CATTTTATAT
5550000 ATTTTTTAAGTTTTTA
1 ATTTTTTAAGTTTTTA
5550016 ATTTTTTAA-TTTTT
1 ATTTTTTAAGTTTTT
5550030 TTACAAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (16 bp):
ATTTTTTAAGTTTTTA
Found at i:5550345 original size:15 final size:16
Alignment explanation
Indices: 5550325--5550358 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
5550315 TATTTTGTAT
*
5550325 TTATTTTTA-ATTAAA
1 TTATTTTTACAATAAA
5550340 TTATTTTTACAATAAA
1 TTATTTTTACAATAAA
5550356 TTA
1 TTA
5550359 ATATTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATTTTTACAATAAA
Found at i:5550355 original size:16 final size:15
Alignment explanation
Indices: 5550325--5550372 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
5550315 TATTTTGTAT
*
5550325 TTATTTTTAATTAAA
1 TTATTTTTAAATAAA
5550340 TTATTTTTACAATAAA
1 TTATTTTTA-AATAAA
*
5550356 TTAATATTATAAATAAA
1 TT-AT-TTTTAAATAAA
5550373 GATACCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 9 0.32
16 7 0.25
17 8 0.29
18 4 0.14
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATTTTTAAATAAA
Found at i:5550532 original size:2 final size:2
Alignment explanation
Indices: 5550521--5550553 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
5550511 TAAGCTACCC
5550521 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5550554 TTTATTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5558724 original size:17 final size:18
Alignment explanation
Indices: 5558702--5558735 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5558692 AAAAACTTGC
*
5558702 AGAAAAAGAATT-TTAAA
1 AGAAAAAAAATTCTTAAA
5558719 AGAAAAAAAATTCTTAA
1 AGAAAAAAAATTCTTAA
5558736 TGGACAAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.65, C:0.03, G:0.09, T:0.24
Consensus pattern (18 bp):
AGAAAAAAAATTCTTAAA
Found at i:5560812 original size:2 final size:2
Alignment explanation
Indices: 5560805--5560840 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5560795 ATAGAACTCA
5560805 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5560841 TTTAACATGT
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):
AT
Found at i:5561388 original size:29 final size:28
Alignment explanation
Indices: 5561342--5561397 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
5561332 TGAATTATAA
*
5561342 TAAAATATTTAATGTAATACTTAAATTT
1 TAAAATATTTAATATAATACTTAAATTT
* *
5561370 TAAAATTTTATAATATAATATTTAAATT
1 TAAAATATT-TAATATAATACTTAAATT
5561398 ATGAATATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (28 bp):
TAAAATATTTAATATAATACTTAAATTT
Found at i:5563049 original size:29 final size:29
Alignment explanation
Indices: 5563010--5563067 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
5563000 ATAAAAATTA
*
5563010 TAATTTGTATTAAATATTA-ATATATTTTT
1 TAATTTGTATTAAAT-TTATATAAATTTTT
*
5563039 TAATTTTTATTAAATTTATATAAATTTTT
1 TAATTTGTATTAAATTTATATAAATTTTT
5563068 AAAAATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 23 0.88
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (29 bp):
TAATTTGTATTAAATTTATATAAATTTTT
Found at i:5584274 original size:21 final size:22
Alignment explanation
Indices: 5584248--5584290 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5584238 TTTTCTATCC
5584248 TTAATTCCA-AGATACAAATAT
1 TTAATTCCAGAGATACAAATAT
* *
5584269 TTAATTCTAGATATACAAATAT
1 TTAATTCCAGAGATACAAATAT
5584291 ATATACAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.37
Consensus pattern (22 bp):
TTAATTCCAGAGATACAAATAT
Found at i:5593253 original size:17 final size:18
Alignment explanation
Indices: 5593217--5593253 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5593207 ACTTTCAAAA
*
5593217 TTTTCTAAAAATGTTTTT
1 TTTTCTAAAAATGTTATT
5593235 TTTTCTAAAAAT-TTATT
1 TTTTCTAAAAATGTTATT
5593252 TT
1 TT
5593254 CAAGAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTTCTAAAAATGTTATT
Found at i:5593321 original size:58 final size:58
Alignment explanation
Indices: 5593197--5593359 Score: 188
Period size: 58 Copynumber: 2.8 Consensus size: 58
5593187 TTTGTACAAT
* * * *
5593197 AAAAATTGATACTTTCAAAATTTT-CT-AAAAATGTTTTTTTTTCTAAAAATTTATTTTCAAG
1 AAAAATTGATACTTTC-AACTTTTCCTCAAAAA---TATTTTTT-TGAAAACTTATTTTCAAG
* *
5593258 AAAAATTGATATTTTTAACTTTTCCTCAAAAATATTTTTTTGAAAACTTATTTTCAAG
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAACTTATTTTCAAG
* *
5593316 GAAAATTGATACTTTCAACTTTTCTTCAAAAATA-TTTTTTGAAA
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAA
5593360 TTTTATTTAA
Statistics
Matches: 90, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
57 10 0.11
58 46 0.51
59 7 0.08
60 6 0.07
61 16 0.18
62 5 0.06
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.46
Consensus pattern (58 bp):
AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAACTTATTTTCAAG
Found at i:5593434 original size:3 final size:3
Alignment explanation
Indices: 5593421--5593457 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
5593411 AATTTTAATC
5593421 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5593458 AAAATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:5594363 original size:30 final size:30
Alignment explanation
Indices: 5594329--5594479 Score: 125
Period size: 38 Copynumber: 4.9 Consensus size: 30
5594319 AAAAAGATAA
*
5594329 AAAAATATATATATGGATAGATAAATAATT
1 AAAAATATATATATGAATAGATAAATAATT
*
5594359 AAAAATGTATATATTAATATATGGATAGATAAATAATT
1 --AAA---A-ATA-T-ATATATGAATAGATAAATAATT
* *
5594397 AAAAAAATATATATTAATAGATAAATAA-T
1 AAAAATATATATATGAATAGATAAATAATT
*
5594426 AAAAA-ATATATAT---TA-ATAAATAATA
1 AAAAATATATATATGAATAGATAAATAATT
*
5594451 AAAACATATATATATTAATAGATAAATAA
1 AAAA-ATATATATATGAATAGATAAATAA
5594480 GAAAAAGATT
Statistics
Matches: 102, Mismatches: 4, Indels: 27
0.77 0.03 0.20
Matches are distributed among these distances:
24 8 0.08
25 6 0.06
26 1 0.01
27 8 0.08
28 8 0.08
29 6 0.06
30 20 0.20
31 9 0.09
32 5 0.05
33 1 0.01
35 1 0.01
36 6 0.06
37 1 0.01
38 22 0.22
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.33
Consensus pattern (30 bp):
AAAAATATATATATGAATAGATAAATAATT
Found at i:5594386 original size:38 final size:38
Alignment explanation
Indices: 5594337--5594415 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
5594327 AAAAAAATAT
**
5594337 ATATATGGATAGATAAATAATTAAAAATGTATATATTA
1 ATATATGGATAGATAAATAATTAAAAAAATATATATTA
5594375 ATATATGGATAGATAAATAATTAAAAAAATATATATTA
1 ATATATGGATAGATAAATAATTAAAAAAATATATATTA
5594413 ATA
1 ATA
5594416 GATAAATAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (38 bp):
ATATATGGATAGATAAATAATTAAAAAAATATATATTA
Found at i:5594406 original size:28 final size:25
Alignment explanation
Indices: 5594374--5594464 Score: 87
Period size: 30 Copynumber: 3.4 Consensus size: 25
5594364 TGTATATATT
5594374 AATATATGGATAGATAAATAATTAAAAAA
1 AATATAT--ATAGATAAATAA-T-AAAAA
5594403 ATATATATTAATAGATAAATAAT-AAAA
1 A-ATATA-T-ATAGATAAATAATAAAAA
5594430 AATATATATTA-ATAAATAATAAAAA
1 AATATATA-TAGATAAATAATAAAAA
*
5594455 CATATATATA
1 AATATATATA
5594465 TTAATAGATA
Statistics
Matches: 56, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
24 12 0.21
25 14 0.25
26 5 0.09
27 5 0.09
29 2 0.04
30 17 0.30
31 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (25 bp):
AATATATATAGATAAATAATAAAAA
Found at i:5594450 original size:27 final size:27
Alignment explanation
Indices: 5594387--5594485 Score: 121
Period size: 27 Copynumber: 3.7 Consensus size: 27
5594377 ATATGGATAG
*
5594387 ATAAAT-AATTAAAAAAATATATATTA
1 ATAAATAAATAAAAAAAATATATATTA
*
5594413 ATAGATAAATAATAAAAAATATATATTA
1 ATAAATAAATAA-AAAAAATATATATTA
*
5594441 ATAAAT-AATAAAAACATATATATATTA
1 ATAAATAAATAAAAA-AAATATATATTA
* *
5594468 ATAGATAAATAAGAAAAA
1 ATAAATAAATAAAAAAAA
5594486 GATTAATAGA
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
26 8 0.13
27 27 0.44
28 27 0.44
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (27 bp):
ATAAATAAATAAAAAAAATATATATTA
Found at i:5594459 original size:21 final size:23
Alignment explanation
Indices: 5594417--5594527 Score: 61
Period size: 27 Copynumber: 4.7 Consensus size: 23
5594407 ATATTAATAG
*
5594417 ATAAATAATAAAAAATATATATTA
1 ATAAATAAT-AAAAATACATATTA
*
5594441 ATAAATAATAAAAACATATATATATTA
1 ATAAATAAT--AAA-A-ATACATATTA
* *
5594468 ATAGATAAATAAGAAA-A-AGATTA
1 ATAAAT-AATAA-AAATACATATTA
* *
5594491 ATAGATAA-AAAAAT--ATATTT
1 ATAAATAATAAAAATACATATTA
5594511 ATAAATAGATAAAAATA
1 ATAAATA-ATAAAAATA
5594528 AAAATAAACA
Statistics
Matches: 73, Mismatches: 5, Indels: 19
0.75 0.05 0.20
Matches are distributed among these distances:
20 13 0.18
21 3 0.04
22 8 0.11
23 11 0.15
24 10 0.14
25 5 0.07
26 4 0.05
27 16 0.22
28 3 0.04
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.30
Consensus pattern (23 bp):
ATAAATAATAAAAATACATATTA
Found at i:5594470 original size:23 final size:23
Alignment explanation
Indices: 5594417--5594525 Score: 96
Period size: 24 Copynumber: 4.7 Consensus size: 23
5594407 ATATTAATAG
5594417 ATAAATA-ATAAAAAATATATATT
1 ATAAATAGATAAAAAATATATA-T
5594440 AATAAATA-ATAAAAACATATATAT
1 -ATAAATAGATAAAAA-ATATATAT
* * * * * *
5594464 ATTAATAGATAAATAAGAAAAAG
1 ATAAATAGATAAAAAATATATAT
* *
5594487 ATTAATAGATAAAAAAATATATTT
1 ATAAATAGAT-AAAAAATATATAT
5594511 ATAAATAGATAAAAA
1 ATAAATAGATAAAAA
5594526 TAAAAATAAA
Statistics
Matches: 69, Mismatches: 13, Indels: 7
0.78 0.15 0.08
Matches are distributed among these distances:
23 25 0.36
24 37 0.54
25 7 0.10
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (23 bp):
ATAAATAGATAAAAAATATATAT
Found at i:5594507 original size:47 final size:49
Alignment explanation
Indices: 5594387--5594531 Score: 145
Period size: 47 Copynumber: 2.9 Consensus size: 49
5594377 ATATGGATAG
*
5594387 ATAAATAATTAAAAAA-ATATATATTAATAGATAAATAATAAAAAATATATATTA
1 ATAAATAA-TAAAAAATATATATATTAATAGAT--A-AATAAAAAA-A-AGATTA
*
5594441 ATAAATAATAAAAACATATATATATTAATAGATAAATAAGAAAAAGATTA
1 ATAAATAATAAAAA-ATATATATATTAATAGATAAATAAAAAAAAGATTA
* * * *
5594491 ATAGAT-A-AAAAAATATATTTATAAATAGATAAA-AATAAAAA
1 ATAAATAATAAAAAATATATATATTAATAGATAAATAAAAAAAA
5594532 TAAACAAATG
Statistics
Matches: 83, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
46 7 0.08
47 19 0.23
48 5 0.06
49 1 0.01
50 10 0.12
51 1 0.01
52 8 0.10
53 7 0.08
54 9 0.11
55 16 0.19
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.30
Consensus pattern (49 bp):
ATAAATAATAAAAAATATATATATTAATAGATAAATAAAAAAAAGATTA
Found at i:5604273 original size:25 final size:25
Alignment explanation
Indices: 5604239--5604289 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
5604229 TCTCTCTATT
5604239 CTACTTTATATCTAATTGAAGAGAA
1 CTACTTTATATCTAATTGAAGAGAA
5604264 CTACTTTATATCTAATTGAAGAGAA
1 CTACTTTATATCTAATTGAAGAGAA
5604289 C
1 C
5604290 GTTAGGTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (25 bp):
CTACTTTATATCTAATTGAAGAGAA
Found at i:5605334 original size:24 final size:25
Alignment explanation
Indices: 5605307--5605363 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
5605297 TTTATGAATT
* *
5605307 TATTAAATTCGATTTAGAT-AAATC
1 TATTAAATTCAATTTAAATAAAATC
*
5605331 TATTTAAA-TCAATTTAAATAAAATG
1 TA-TTAAATTCAATTTAAATAAAATC
5605356 TATTAAAT
1 TATTAAAT
5605364 GAAAACCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
24 16 0.59
25 11 0.41
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (25 bp):
TATTAAATTCAATTTAAATAAAATC
Found at i:5608768 original size:12 final size:12
Alignment explanation
Indices: 5608702--5608769 Score: 59
Period size: 12 Copynumber: 5.7 Consensus size: 12
5608692 CAAATAAGTT
*
5608702 AATTTTGAATAA
1 AATTTTTAATAA
5608714 AA-TTTTAAT-A
1 AATTTTTAATAA
*
5608724 TATCTTTTAGATAA
1 AAT-TTTTA-ATAA
* *
5608738 TATTTTTATTAA
1 AATTTTTAATAA
*
5608750 AAATTTTAATAA
1 AATTTTTAATAA
5608762 AATTTTTA
1 AATTTTTA
5608770 TCGTTAAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
10 2 0.04
11 6 0.13
12 26 0.58
13 7 0.16
14 4 0.09
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (12 bp):
AATTTTTAATAA
Found at i:5608830 original size:19 final size:19
Alignment explanation
Indices: 5608808--5608844 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5608798 ATTATAAATA
*
5608808 ATATTTTTAATTTTTTTAC
1 ATATTATTAATTTTTTTAC
5608827 ATATTATTAATTTTTTTA
1 ATATTATTAATTTTTTTA
5608845 TTAAACTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (19 bp):
ATATTATTAATTTTTTTAC
Found at i:5609116 original size:5 final size:5
Alignment explanation
Indices: 5609106--5609138 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
5609096 TCTCACTTTA
*
5609106 TTGTT TTGTT TTGTT TTGTT TT-TT TTTTT TTGT
1 TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT TTGT
5609139 AATAACGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (5 bp):
TTGTT
Found at i:5609882 original size:28 final size:27
Alignment explanation
Indices: 5609834--5609887 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
5609824 ATTTGAGACG
*
5609834 TTAAAATTTAAATTTCAATTATTAAAA
1 TTAAAATTTAAATTTCAATTAATAAAA
*
5609861 TTAAAATTTTAATATTT-TATTAATAAA
1 TTAAAA-TTTAA-ATTTCAATTAATAAA
5609888 TTACTTGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 6 0.26
28 13 0.57
29 4 0.17
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (27 bp):
TTAAAATTTAAATTTCAATTAATAAAA
Found at i:5610982 original size:15 final size:15
Alignment explanation
Indices: 5610958--5610987 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5610948 AAAATTACCT
*
5610958 AAATATAAAAATAAA
1 AAATAAAAAAATAAA
5610973 AAATAAAAAAATAAA
1 AAATAAAAAAATAAA
5610988 TCTTTATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAATAAAAAAATAAA
Found at i:5611924 original size:2 final size:2
Alignment explanation
Indices: 5611917--5611949 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5611907 GGTATTTCAA
*
5611917 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5611950 CATAAAGAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5611950 original size:10 final size:10
Alignment explanation
Indices: 5611921--5611953 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
5611911 TTTCAAATAT
*
5611921 ATATATATAT
1 ATATATATAC
5611931 ATATATATAC
1 ATATATATAC
5611941 ATATATATAC
1 ATATATATAC
5611951 ATA
1 ATA
5611954 AAGAGTATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (10 bp):
ATATATATAC
Found at i:5616998 original size:25 final size:24
Alignment explanation
Indices: 5616953--5617002 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
5616943 AGATCTAGAT
*
5616953 AAAATTTTCATTTAGAGATTTCTTA
1 AAAATTTTCATTTAGAAATTT-TTA
5616978 AAAATTTATCATTTA-AAATTTTTA
1 AAAATTT-TCATTTAGAAATTTTTA
5617002 A
1 A
5617003 GAGTCTCATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 4 0.17
25 12 0.52
26 7 0.30
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (24 bp):
AAAATTTTCATTTAGAAATTTTTA
Found at i:5617324 original size:5 final size:4
Alignment explanation
Indices: 5617311--5617351 Score: 64
Period size: 4 Copynumber: 10.0 Consensus size: 4
5617301 AAAAATTATA
*
5617311 AAAT AAAT ATAAT AACT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
5617352 TAAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
4 30 0.88
5 4 0.12
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:5618286 original size:23 final size:23
Alignment explanation
Indices: 5618260--5618312 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
5618250 AAAAAATACT
*
5618260 GATAAATCAAACGTAAAATCAAA
1 GATAAATCAAACGAAAAATCAAA
* * * *
5618283 GATAATTTAAATGAAAAATCATA
1 GATAAATCAAACGAAAAATCAAA
5618306 GATAAAT
1 GATAAAT
5618313 GACTAATCAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.58, C:0.08, G:0.09, T:0.25
Consensus pattern (23 bp):
GATAAATCAAACGAAAAATCAAA
Found at i:5618758 original size:45 final size:45
Alignment explanation
Indices: 5618587--5619066 Score: 376
Period size: 45 Copynumber: 10.8 Consensus size: 45
5618577 CCCGAAGCAG
* * * * *
5618587 AGGCTC-ACAATTTTTAGAAAAACAAATATA-GCTCTTCTAAACAA
1 AGGCTCAACAACTTTGAAAAAAATAAATA-AGGCTCTTCTAATCAA
* ** * * * * * *
5618631 AAGCTCAATGACTTTG-GAAAAGTAAATAA-GCTCCTCCAATTAG
1 AGGCTCAACAACTTTGAAAAAAATAAATAAGGCTCTTCTAATCAA
* * * *
5618674 AGGCAT-AATAACTTTG-AAAAAGTAAATACGGCTCCTCTAAAT-AA
1 AGGC-TCAACAACTTTGAAAAAAATAAATAAGGCTCTTCT-AATCAA
* * *
5618718 AGGCTCAACGACTTTAAAAAAAATAAATAAGGCTCTTCTAAAT-AG
1 AGGCTCAACAACTTTGAAAAAAATAAATAAGGCTCTTCT-AATCAA
* * * * *
5618763 AGACTCAACAATTTTG-AAAGAAT-AACAAGGCTCATT-TAATTAA
1 AGGCTCAACAACTTTGAAAAAAATAAATAAGGCTC-TTCTAATCAA
* * * * * *
5618806 AGGTTCAACAATTTTG-AGAAAATAAATAAGGTTCATCTAATCAG
1 AGGCTCAACAACTTTGAAAAAAATAAATAAGGCTCTTCTAATCAA
* *
5618850 AGGCTCAACAACTTTGAGAAAAGTAAATAAGGCTTCTT-TAATCAA
1 AGGCTCAACAACTTTGAAAAAAATAAATAAGGC-TCTTCTAATCAA
* * * * *
5618895 AGGCTTAACAACTTTGCAAAAAAGTAAATAATGTTCTTCTAATTAGA
1 AGGCTCAACAACTTTG-AAAAAAATAAATAAGGCTCTTCTAATCA-A
5618942 A-GCTCAACAACTTTGAAAAAAAAGTAAATAAGGCTCTTCTAATCAA
1 AGGCTCAACAACTTTG-AAAAAAA-TAAATAAGGCTCTTCTAATCAA
* *
5618988 AGGTTTAACAACTTTGAAAAAAATAAATAAGGCTCTTCTAATCAA
1 AGGCTCAACAACTTTGAAAAAAATAAATAAGGCTCTTCTAATCAA
* * *
5619033 AAGCTCAATAACTTTGAAAAAAGTAAATAAGGCT
1 AGGCTCAACAACTTTGAAAAAAATAAATAAGGCT
5619067 TATCGACAAT
Statistics
Matches: 352, Mismatches: 67, Indels: 33
0.78 0.15 0.07
Matches are distributed among these distances:
42 3 0.01
43 65 0.18
44 70 0.20
45 132 0.38
46 50 0.14
47 32 0.09
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.27
Consensus pattern (45 bp):
AGGCTCAACAACTTTGAAAAAAATAAATAAGGCTCTTCTAATCAA
Found at i:5618845 original size:132 final size:136
Alignment explanation
Indices: 5618648--5619066 Score: 391
Period size: 132 Copynumber: 3.1 Consensus size: 136
5618638 ATGACTTTGG
* * * * * * *
5618648 AAAAGTAAATAA-GCTCCTCCAATTAGAGGCAT-AATAACTTTGAAAAAGTAAATACGGCTCCTC
1 AAAAGTAAACAAGGCTCTTCTAATTAGAAGC-TCAACAACTTTGAAAAAGTAAATAAGGCTCATC
* * *
5618711 TAAAT-AAAGGCTCAACGACTTTAAAAAAAATAAATAAGGCTCTTCTAAAT-AGAGACTCAACAA
65 T-AATCAAAGGCTCAACAACTTTGAAAAAAATAAATAAGGCTCTTCTAAATCAAAGACTCAACAA
*
5618774 TTTTG-AA
129 CTTTGCAA
* * * *
5618781 AGAA-T-AACAAGGCTCATT-TAATTA-AAGGTTCAACAATTTTGAGAAAA-TAAATAAGGTTCA
1 AAAAGTAAACAAGGCTC-TTCTAATTAGAA-GCTCAACAACTTTGA-AAAAGTAAATAAGGCTCA
* * * * *
5618841 TCTAATCAGAGGCTCAACAACTTTGAGAAAAGTAAATAAGGCTTCTT-T-AATCAAAGGCTTAAC
63 TCTAATCAAAGGCTCAACAACTTTGAAAAAAATAAATAAGGC-TCTTCTAAATCAAAGACTCAAC
5618904 AACTTTGCAA
127 AACTTTGCAA
* * * *
5618914 AAAAGTAAATAATGTTCTTCTAATTAGAAGCTCAACAACTTTGAAAAAAAAGTAAATAAGGCTCT
1 AAAAGTAAACAAGGCTCTTCTAATTAGAAGCTCAACAACTTTG---AAAAAGTAAATAAGGCTCA
* * *
5618979 TCTAATCAAAGGTTTAACAACTTTGAAAAAAATAAATAAGGCTCTTCT-AATCAAA-AGCTCAAT
63 TCTAATCAAAGGCTCAACAACTTTGAAAAAAATAAATAAGGCTCTTCTAAATCAAAGA-CTCAAC
5619042 AACTTTG-AA
127 AACTTTGCAA
*
5619051 AAAAGTAAATAAGGCT
1 AAAAGTAAACAAGGCT
5619067 TATCGACAAT
Statistics
Matches: 229, Mismatches: 38, Indels: 34
0.76 0.13 0.11
Matches are distributed among these distances:
131 12 0.05
132 78 0.34
133 17 0.07
134 3 0.01
135 25 0.11
136 2 0.01
137 24 0.10
138 68 0.30
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.27
Consensus pattern (136 bp):
AAAAGTAAACAAGGCTCTTCTAATTAGAAGCTCAACAACTTTGAAAAAGTAAATAAGGCTCATCT
AATCAAAGGCTCAACAACTTTGAAAAAAATAAATAAGGCTCTTCTAAATCAAAGACTCAACAACT
TTGCAA
Found at i:5619415 original size:21 final size:21
Alignment explanation
Indices: 5619386--5619428 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5619376 ACATTTAAAG
*
5619386 ATTCAAATTCTGGAGATTCAC
1 ATTCAAATTCTAGAGATTCAC
* *
5619407 ATTCGAATTCTAGTGATTCAC
1 ATTCAAATTCTAGAGATTCAC
5619428 A
1 A
5619429 CCCAAAAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATTCAAATTCTAGAGATTCAC
Found at i:5619683 original size:49 final size:48
Alignment explanation
Indices: 5619554--5619683 Score: 112
Period size: 49 Copynumber: 2.8 Consensus size: 48
5619544 GTTAAAAAAT
* * **
5619554 TCACATTCAATAAAGCTTAGAGGTTCACATC----TAAGTTTAAAGGT
1 TCACATTCAATAAATCTTAGAGATTCACATCAAGTTAAGTTTAAAGAC
*
5619598 TCTCA-TCGAA-AAAT-TTAGAGATTCACATCCAAAAGTTAAGTTTAAAGAC
1 TCACATTC-AATAAATCTTAGAGATTCACAT-C--AAGTTAAGTTTAAAGAC
*
5619647 TCACATTCAATAAATCTTAGAGTTTCACATCTAAGTT
1 TCACATTCAATAAATCTTAGAGATTCACATC-AAGTT
5619684 TAAAGGTTCT
Statistics
Matches: 67, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
42 13 0.19
43 6 0.09
44 6 0.09
49 22 0.33
50 7 0.10
51 13 0.19
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (48 bp):
TCACATTCAATAAATCTTAGAGATTCACATCAAGTTAAGTTTAAAGAC
Found at i:5619752 original size:21 final size:21
Alignment explanation
Indices: 5619718--5619767 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
5619708 TTAAAAATTT
* *
5619718 TCATTTAAAACTCAAAGATTC
1 TCATTTGAAGCTCAAAGATTC
*
5619739 TTATTTGAAGCTCAAAGATTC
1 TCATTTGAAGCTCAAAGATTC
5619760 TCATTTGA
1 TCATTTGA
5619768 GGATTCATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (21 bp):
TCATTTGAAGCTCAAAGATTC
Found at i:5621262 original size:16 final size:18
Alignment explanation
Indices: 5621231--5621267 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
5621221 TGGCATTCAT
5621231 TTTTTTTCTTTATTTTGC
1 TTTTTTTCTTTATTTTGC
5621249 TTTTTTT-TTT-TTTTGC
1 TTTTTTTCTTTATTTTGC
5621265 TTT
1 TTT
5621268 CTATCTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.47
17 3 0.16
18 7 0.37
ACGTcount: A:0.03, C:0.08, G:0.05, T:0.84
Consensus pattern (18 bp):
TTTTTTTCTTTATTTTGC
Found at i:5623983 original size:23 final size:23
Alignment explanation
Indices: 5623957--5624009 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
5623947 AAAAACTAAT
*
5623957 GATAAATCAAACGTAAAATCAAA
1 GATAAATCAAACGAAAAATCAAA
* * *
5623980 GATAATTTAAACGAAAAATCATA
1 GATAAATCAAACGAAAAATCAAA
5624003 GATAAAT
1 GATAAAT
5624010 GAATAATCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.58, C:0.09, G:0.09, T:0.23
Consensus pattern (23 bp):
GATAAATCAAACGAAAAATCAAA
Found at i:5624727 original size:20 final size:21
Alignment explanation
Indices: 5624704--5624743 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5624694 AAATGAAGGG
5624704 ATGATAAAAG-AGAAAGGAAA
1 ATGATAAAAGAAGAAAGGAAA
**
5624724 ATGATGCAAGAAGAAAGGAA
1 ATGATAAAAGAAGAAAGGAA
5624744 TCACCAGCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.60, C:0.03, G:0.28, T:0.10
Consensus pattern (21 bp):
ATGATAAAAGAAGAAAGGAAA
Found at i:5631432 original size:7 final size:7
Alignment explanation
Indices: 5631420--5631445 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5631410 CAAATAAGCA
5631420 TGTTATC
1 TGTTATC
5631427 TGTTATC
1 TGTTATC
5631434 TGTTATC
1 TGTTATC
5631441 TGTTA
1 TGTTA
5631446 ATCTACATGT
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:0.15, C:0.12, G:0.15, T:0.58
Consensus pattern (7 bp):
TGTTATC
Found at i:5636064 original size:2 final size:2
Alignment explanation
Indices: 5636057--5636082 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5636047 TATTTATTAC
5636057 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
5636083 GATAAATGAT
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:5644240 original size:2 final size:2
Alignment explanation
Indices: 5644233--5644265 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5644223 CCCATTCGAT
5644233 TA 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 TA T
5644266 TTGGAAAGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5646498 original size:16 final size:15
Alignment explanation
Indices: 5646400--5646498 Score: 51
Period size: 16 Copynumber: 6.5 Consensus size: 15
5646390 ATAATTTTAT
*
5646400 AATTTATTAAATATCA
1 AATTTATTAAA-ATTA
* *
5646416 AAATTATTTAAATTA
1 AATTTATTAAAATTA
5646431 TAA-TTA--AAAATTA
1 -AATTTATTAAAATTA
* *
5646444 AATTAATTTAAATATA
1 AATTTATTAAAAT-TA
** *
5646460 TGTTTTTTAAAATTA
1 AATTTATTAAAATTA
**
5646475 AAAATATTAAATATTA
1 AATTTATTAAA-ATTA
5646491 AATTTATT
1 AATTTATT
5646499 TTTTAATAAA
Statistics
Matches: 59, Mismatches: 18, Indels: 12
0.66 0.20 0.13
Matches are distributed among these distances:
12 2 0.03
13 8 0.14
15 18 0.31
16 31 0.53
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (15 bp):
AATTTATTAAAATTA
Found at i:5646656 original size:16 final size:17
Alignment explanation
Indices: 5646624--5646657 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5646614 TAACAATCTT
5646624 TTTTATCTTAATTTAAAA
1 TTTTATCTT-ATTTAAAA
5646642 TTTTATCTT-TTTAAAA
1 TTTTATCTTATTTAAAA
5646658 AAATTTACGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTATCTTATTTAAAA
Found at i:5648007 original size:16 final size:15
Alignment explanation
Indices: 5647986--5648114 Score: 103
Period size: 13 Copynumber: 9.0 Consensus size: 15
5647976 TTAATAAAAT
*
5647986 AATATTTTATTATATA
1 AATATTATATTA-ATA
5648002 AATATTATATTAATA
1 AATATTATATTAATA
5648017 AATA--ATATTAATA
1 AATATTATATTAATA
*
5648030 AATA-T-TGTT-ATA
1 AATATTATATTAATA
**
5648042 TTTATTATATTAAT-
1 AATATTATATTAATA
5648056 AATATTATA-TAAT-
1 AATATTATATTAATA
* * *
5648069 AATATAATATTTATT
1 AATATTATATTAATA
*
5648084 AATAATATATTAATA
1 AATATTATATTAATA
*
5648099 TATTATTATATTAATA
1 -AATATTATATTAATA
5648115 TTAATATTAA
Statistics
Matches: 91, Mismatches: 15, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
12 5 0.05
13 29 0.32
14 13 0.14
15 20 0.22
16 24 0.26
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (15 bp):
AATATTATATTAATA
Found at i:5648041 original size:75 final size:68
Alignment explanation
Indices: 5647961--5648129 Score: 177
Period size: 75 Copynumber: 2.5 Consensus size: 68
5647951 CTACAGTGAC
* * *
5647961 ATTATAATTATTATATTAATAAAATAATATTTTATTATATAAATATTATATTAATAAATAATATT
1 ATTATAATTATTATATTAAT-AAATAATATATAATAATAT-AATATT-TATTAAT-AAT-ATATT
5648026 AATAAATATT
61 AAT--ATATT
* * *
5648036 GTTATATTTATTATATTAAT-AATATTATATAATAATATAATATTTATTAATAATATATTAATAT
1 ATTATAATTATTATATTAATAAATAATATATAATAATATAATATTTATTAATAATATATTAATAT
5648100 ATT
66 ATT
*
5648103 ATTAT-ATTA--ATATTAAT-ATTAATATAT
1 ATTATAATTATTATATTAATAAATAATATAT
5648130 TATTAACAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
64 16 0.19
66 3 0.04
67 9 0.11
69 8 0.10
70 3 0.04
71 7 0.08
72 6 0.07
73 14 0.17
75 18 0.21
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (68 bp):
ATTATAATTATTATATTAATAAATAATATATAATAATATAATATTTATTAATAATATATTAATAT
ATT
Found at i:5648047 original size:4 final size:5
Alignment explanation
Indices: 5648037--5648132 Score: 55
Period size: 5 Copynumber: 19.8 Consensus size: 5
5648027 ATAAATATTG
* * *
5648037 TTATA TT-TA TTATA TTA-A TAATA TTATA -TA-A TAATA TAATA TT-TA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
*
5648082 TTAATA ATATA TTA-A TATATTA TTATA TTAATA TTAATA TTA-A -TATA
1 TT-ATA TTATA TTATA T-TA-TA TTATA TT-ATA TT-ATA TTATA TTATA
5648129 TTAT
1 TTAT
5648133 TAACAAAAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 24
0.71 0.06 0.23
Matches are distributed among these distances:
3 3 0.04
4 18 0.25
5 34 0.47
6 16 0.22
7 2 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (5 bp):
TTATA
Found at i:5648057 original size:36 final size:35
Alignment explanation
Indices: 5648003--5648131 Score: 117
Period size: 36 Copynumber: 3.7 Consensus size: 35
5647993 TATTATATAA
* *
5648003 ATATTATATTAATAAATAATATTAATAAATATTGTT
1 ATATTATATTAATTAAT-ATATTAATAAATATTATT
* *
5648039 ATATT-TATTATATTAATAATATT-ATATAATAATATA
1 ATATTATATTA-ATTAAT-ATATTAATA-AATATTATT
5648075 ATATT-TATTAA-TAATATATTAAT--ATATTATT
1 ATATTATATTAATTAATATATTAATAAATATTATT
5648106 ATATTAATATTAATATTAATATATTA
1 ATATT-ATATT-A-ATTAATATATTA
5648132 TTAACAAAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
31 11 0.14
33 9 0.11
34 7 0.09
35 10 0.13
36 42 0.53
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (35 bp):
ATATTATATTAATTAATATATTAATAAATATTATT
Found at i:5648063 original size:177 final size:175
Alignment explanation
Indices: 5647738--5648088 Score: 437
Period size: 177 Copynumber: 2.0 Consensus size: 175
5647728 CATTGTTACC
* * **
5647738 GCACGGATATTGTTTACAAAAATTATAATTGAACCGCTACACGATGTTATAATTATTATATTAAT
1 GCACGAATATTGTTTACAAAAATTATAATTAAACCGCTACACGACATTATAATTATTATATTAAT
* *
5647803 AAAATAATATTTTTATTATATAAATAATATAAATAAATATTGTTATATTTATTATATTAATAATA
66 AAAATAATATTTTTATTATATAAATAATATAAATAAATAATATTATATTTATTATATT-ATAATA
*
5647868 TTATATAACAATATATTAT-TCATATAATATATTATTTATTAATAAAT
130 TTATATAACAATATATTATAT-A-ATAATATAATATTTATTAATAAAT
* * *
5647915 GCACGAATATTGTTTACAAACATTATAATTAAATCGCTACAGTGACATTATAATTATTATATTAA
1 GCACGAATATTGTTTACAAAAATTATAATTAAACCGCTACA-CGACATTATAATTATTATATTAA
* *
5647980 TAAAATAATA-TTTTATTATATAAATATTATATTAATAAATAATATTAATAAATATTGTTATATT
65 TAAAATAATATTTTTATTATATAAATA--ATATAAATAAATAATATT-AT--AT-TTATTATATT
* *
5648044 -TATTA-TAT-TAA-TA-ATATTATATAATAATATAATATTTATTAATAA
124 ATAATATTATATAACAATATATTATATAATAATATAATATTTATTAATAA
5648089 TATATTAATA
Statistics
Matches: 152, Mismatches: 14, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
176 21 0.14
177 61 0.40
178 32 0.21
179 18 0.12
180 5 0.03
181 4 0.03
182 2 0.01
183 9 0.06
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (175 bp):
GCACGAATATTGTTTACAAAAATTATAATTAAACCGCTACACGACATTATAATTATTATATTAAT
AAAATAATATTTTTATTATATAAATAATATAAATAAATAATATTATATTTATTATATTATAATAT
TATATAACAATATATTATATAATAATATAATATTTATTAATAAAT
Found at i:5648079 original size:67 final size:66
Alignment explanation
Indices: 5647967--5648132 Score: 169
Period size: 67 Copynumber: 2.5 Consensus size: 66
5647957 TGACATTATA
* * * * *
5647967 ATTATTATATTA-ATAAAATAATATTTTATTATATAAATATTATATTAATAAATAATATTAATAA
1 ATTATTATATTATAT-TAATATTAATATATTATATAAATATAATATTAATAAATAATA-TAATAA
5648031 -AT
64 TAT
* * * *
5648033 ATTGTTATATT-TATT-ATATTAATAATATTATATAATAATATAATATTTATTAATAATATATTA
1 ATTATTATATTATATTAATATTAAT-ATATTATAT-A-AATATAATATTAATAAATAATATAATA
5648096 ATAT
63 ATAT
5648100 ATTATTATATTAATATTAATATTAATATATTAT
1 ATTATTATATT-ATATTAATATTAATATATTAT
5648133 TAACAAAAAA
Statistics
Matches: 82, Mismatches: 10, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
64 6 0.07
65 8 0.10
66 18 0.22
67 31 0.38
69 11 0.13
70 8 0.10
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.51
Consensus pattern (66 bp):
ATTATTATATTATATTAATATTAATATATTATATAAATATAATATTAATAAATAATATAATAATA
T
Found at i:5648083 original size:22 final size:23
Alignment explanation
Indices: 5647997--5648122 Score: 95
Period size: 22 Copynumber: 5.5 Consensus size: 23
5647987 ATATTTTATT
*
5647997 ATATAAATATTATATTA-ATAAATA
1 ATATTAATATT-TATTATAT-AATA
* * *
5648021 ATATTAATAAATATTGTTATATTTATT
1 ATATTAAT--AT-TTATTATA-TAATA
*
5648048 ATATTAATA-ATATTATATAATA
1 ATATTAATATTTATTATATAATA
5648070 ATA-TAATATTTATTA-ATAAT-
1 ATATTAATATTTATTATATAATA
5648090 ATATTAATATATTATTATAT--TA
1 ATATTAATAT-TTATTATATAATA
5648112 ATATTAATATT
1 ATATTAATATT
5648123 AATATATTAT
Statistics
Matches: 83, Mismatches: 9, Indels: 23
0.72 0.08 0.20
Matches are distributed among these distances:
20 3 0.04
21 18 0.22
22 27 0.33
23 8 0.10
24 7 0.08
25 1 0.01
26 6 0.07
27 12 0.14
28 1 0.01
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (23 bp):
ATATTAATATTTATTATATAATA
Found at i:5648084 original size:31 final size:27
Alignment explanation
Indices: 5647967--5648134 Score: 154
Period size: 27 Copynumber: 6.3 Consensus size: 27
5647957 TGACATTATA
5647967 ATTATTATATTAATAA-A-A-TAATAT
1 ATTATTATATTAATAATATATTAATAT
* * *
5647991 TTTATTATATAAATATTATATTAATA-
1 ATTATTATATTAATAATATATTAATAT
* **
5648017 A--ATAATATTAATAA-ATATTGTTAT
1 ATTATTATATTAATAATATATTAATAT
5648041 ATTTATTATATTAATAATATTATATAATAAT
1 A-TTATTATATTAATAATA-TAT-TAAT-AT
5648072 ATAATATT-TATTAATAATATATTAATAT
1 AT--TATTATATTAATAATATATTAATAT
*
5648100 ATTATTATATTAATATTAATATTAATAT
1 ATTATTATATTAATAAT-ATATTAATAT
5648128 ATTATTA
1 ATTATTA
5648135 ACAAAAAATG
Statistics
Matches: 116, Mismatches: 13, Indels: 26
0.75 0.08 0.17
Matches are distributed among these distances:
23 7 0.06
24 24 0.21
25 1 0.01
26 5 0.04
27 26 0.22
28 22 0.19
29 7 0.06
30 6 0.05
31 14 0.12
32 4 0.03
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.51
Consensus pattern (27 bp):
ATTATTATATTAATAATATATTAATAT
Found at i:5649420 original size:14 final size:13
Alignment explanation
Indices: 5649379--5649421 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
5649369 CCTTCATTAT
*
5649379 TTCTTCTTCTTTC
1 TTCTTGTTCTTTC
5649392 TTCTTGTTCCTTTC
1 TTCTTGTT-CTTTC
5649406 TTCTTGTTCTGTTC
1 TTCTTGTTCT-TTC
5649420 TT
1 TT
5649422 TTCTTCTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 9 0.33
14 18 0.67
ACGTcount: A:0.00, C:0.26, G:0.07, T:0.67
Consensus pattern (13 bp):
TTCTTGTTCTTTC
Found at i:5649424 original size:19 final size:20
Alignment explanation
Indices: 5649382--5649428 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
5649372 TCATTATTTC
5649382 TTCTTCTTTCTTCTTGTTCCT
1 TTCTTC-TTCTTCTTGTTCCT
* *
5649403 TTCTTCTTGTTC-TGTTCTT
1 TTCTTCTTCTTCTTGTTCCT
5649422 TTCTTCT
1 TTCTTCT
5649429 CATTCCCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 13 0.54
20 5 0.21
21 6 0.25
ACGTcount: A:0.00, C:0.26, G:0.06, T:0.68
Consensus pattern (20 bp):
TTCTTCTTCTTCTTGTTCCT
Found at i:5656927 original size:4 final size:4
Alignment explanation
Indices: 5656918--5656950 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
5656908 AGAAGAGCAT
5656918 TACA TACA TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA T
5656951 TTGCATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:5660685 original size:26 final size:26
Alignment explanation
Indices: 5660655--5660709 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
5660645 AACAAAAGCT
* *
5660655 AATATAA-ATAACAAAAAAATAATAAG
1 AATATAAGATAA-AAAAAAAGAAAAAG
5660681 AATATAATGATAAAAAAAAAGAAAAAG
1 AATATAA-GATAAAAAAAAAGAAAAAG
5660708 AA
1 AA
5660710 ATGGCAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.28
27 14 0.56
28 4 0.16
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.16
Consensus pattern (26 bp):
AATATAAGATAAAAAAAAAGAAAAAG
Found at i:5661763 original size:14 final size:13
Alignment explanation
Indices: 5661731--5661778 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
5661721 TATAACCGTA
5661731 ATTAAAAAATTTT
1 ATTAAAAAATTTT
*
5661744 AATAAAAAATTTAT
1 ATTAAAAAATTT-T
* *
5661758 ATTAAATAAATGTC
1 ATTAAA-AAATTTT
5661772 ATTAAAA
1 ATTAAAA
5661779 TTTATTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 12 0.41
14 12 0.41
15 5 0.17
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (13 bp):
ATTAAAAAATTTT
Found at i:5662883 original size:23 final size:24
Alignment explanation
Indices: 5662838--5662884 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
5662828 TCTAAGGAGA
*
5662838 GTGAGATCAATCTCAATTTTAATT
1 GTGAGATCAATCTAAATTTTAATT
5662862 GTGA-ATCAATC-AAATTTCTAATT
1 GTGAGATCAATCTAAATTT-TAATT
5662885 ATGCAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 12 0.57
24 4 0.19
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (24 bp):
GTGAGATCAATCTAAATTTTAATT
Found at i:5663153 original size:29 final size:29
Alignment explanation
Indices: 5663121--5663242 Score: 97
Period size: 29 Copynumber: 4.2 Consensus size: 29
5663111 TAAATTTTAA
*
5663121 TATTTTATTTAAATAAAATTTTATATTTT
1 TATTTTATTCAAATAAAATTTTATATTTT
* * *
5663150 TATTATATTCAAATAAAATTTT-GATCTT
1 TATTTTATTCAAATAAAATTTTATATTTT
* * * *
5663178 TAATTTACATCTTAAT-AAATTTCTATCTTTT
1 TATTTTA-TTC-AAATAAAATTT-TATATTTT
* * *
5663209 AATTTTATTCAAATAAACTCTTA-ATTTT
1 TATTTTATTCAAATAAAATTTTATATTTT
5663237 TATTTT
1 TATTTT
5663243 TTATATAAAT
Statistics
Matches: 69, Mismatches: 19, Indels: 11
0.70 0.19 0.11
Matches are distributed among these distances:
28 18 0.26
29 33 0.48
30 10 0.14
31 8 0.12
ACGTcount: A:0.36, C:0.07, G:0.01, T:0.56
Consensus pattern (29 bp):
TATTTTATTCAAATAAAATTTTATATTTT
Found at i:5663254 original size:59 final size:58
Alignment explanation
Indices: 5663113--5663256 Score: 135
Period size: 59 Copynumber: 2.4 Consensus size: 58
5663103 AATTTTCCTA
* * * * *
5663113 AATTTTAATATTTTATTTAAATAAAATTTTATATTTTTATTATATTCAAATAAAATTTT
1 AATTTTTATTTTTTATATAAAT-AAATTTTATATTTTAATTATATTCAAATAAAATCTT
* * * ** * * * * *
5663172 GATCTTTAATTTACATCTTAATAAATTTCTATCTTTTAATTTTATTCAAATAAACTCTT
1 AATTTTTATTTTTTATATAAATAAATTT-TATATTTTAATTATATTCAAATAAAATCTT
5663231 AATTTTTATTTTTTATATAAATAAAT
1 AATTTTTATTTTTTATATAAATAAAT
5663257 CCCTAATATA
Statistics
Matches: 63, Mismatches: 21, Indels: 2
0.73 0.24 0.02
Matches are distributed among these distances:
58 6 0.10
59 57 0.90
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (58 bp):
AATTTTTATTTTTTATATAAATAAATTTTATATTTTAATTATATTCAAATAAAATCTT
Found at i:5664962 original size:2 final size:2
Alignment explanation
Indices: 5664925--5664952 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5664915 ATGACCTCTT
5664925 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
5664953 AAGTTATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5666857 original size:22 final size:24
Alignment explanation
Indices: 5666832--5666875 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
5666822 TATATATGAA
5666832 TTTAATAA-AAAAATT-TATATTT
1 TTTAATAATAAAAATTATATATTT
*
5666854 TTTATTAATAAAAATTATATAT
1 TTTAATAATAAAAATTATATAT
5666876 AAAATACAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 7 0.37
24 5 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTAATAATAAAAATTATATATTT
Found at i:5666925 original size:18 final size:18
Alignment explanation
Indices: 5666853--5666929 Score: 61
Period size: 18 Copynumber: 4.2 Consensus size: 18
5666843 AATTTATATT
5666853 TTTTAT-TAATA-AAA-A
1 TTTTATATAATATAAATA
* *
5666868 TTATATATAAAATACAATA
1 TTTTATATAATATA-AATA
* *
5666887 TAATTATATAAATTATTAATA
1 T-TTTATAT-AA-TATAAATA
5666908 TTTTATATAATATAAATA
1 TTTTATATAATATAAATA
5666926 TTTT
1 TTTT
5666930 CAATACTAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
15 5 0.11
16 4 0.09
17 1 0.02
18 13 0.28
19 4 0.09
20 11 0.23
21 7 0.15
22 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTTATATAATATAAATA
Found at i:5667215 original size:13 final size:12
Alignment explanation
Indices: 5667166--5667215 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
5667156 AAAAAATTAT
*
5667166 ATTTATATTATA
1 ATTTATATAATA
* *
5667178 TTTTATATAAAA
1 ATTTATATAATA
5667190 ATTATATATAATA
1 ATT-TATATAATA
5667203 ATTTATATCAATA
1 ATTTATAT-AATA
5667216 TAAAAATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
12 16 0.52
13 15 0.48
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTTATATAATA
Found at i:5667271 original size:24 final size:24
Alignment explanation
Indices: 5667225--5667271 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5667215 ATAAAAATAT
* *
5667225 AAAATATATTTTTTAATTTTTTTA
1 AAAATATATTTTTCAATTATTTTA
5667249 AAAAT-TATTTTTCATATTATTTT
1 AAAATATATTTTTCA-ATTATTTT
5667272 TATATTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
AAAATATATTTTTCAATTATTTTA
Found at i:5671407 original size:29 final size:29
Alignment explanation
Indices: 5671367--5671435 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
5671357 TAAAAATTTA
*
5671367 ATAATTATTTAAGCACATAA-TATTTTATT
1 ATAATTAATTAAG-ACATAATTATTTTATT
**
5671396 ATAATTAATTAAGTTATAATTATTTTATT
1 ATAATTAATTAAGACATAATTATTTTATT
*
5671425 TTGAATTAATT
1 AT-AATTAATT
5671436 GAATCTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.12
29 22 0.65
30 8 0.24
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (29 bp):
ATAATTAATTAAGACATAATTATTTTATT
Found at i:5671455 original size:30 final size:30
Alignment explanation
Indices: 5671421--5671498 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
5671411 ATAATTATTT
* * *
5671421 TATTTTGAATTAATTGAATCT-TTAAGCATA
1 TATTTTTAATTAATTAAAT-TATTAAACATA
*
5671451 TATTTTTATTTAATTAAATTATTAAACATA
1 TATTTTTAATTAATTAAATTATTAAACATA
*
5671481 TATTTTTACTTAATTAAA
1 TATTTTTAATTAATTAAA
5671499 CTTTCGATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 1 0.02
30 41 0.98
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51
Consensus pattern (30 bp):
TATTTTTAATTAATTAAATTATTAAACATA
Found at i:5671751 original size:29 final size:29
Alignment explanation
Indices: 5671687--5671764 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 29
5671677 ATAAATTTTA
* *
5671687 TTATTT-TATTTAAATAATTTTTTATATTT
1 TTATTTATATTTAAATAATATTATA-ATTT
5671716 TTA-TTATATTTAAATAA-ATTATAATTT
1 TTATTTATATTTAAATAATATTATAATTT
*
5671743 TTAATTTATATTCAAAT-ATATT
1 TT-ATTTATATTTAAATAATATT
5671765 GATATTTCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
27 6 0.14
28 8 0.19
29 28 0.67
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (29 bp):
TTATTTATATTTAAATAATATTATAATTT
Found at i:5671771 original size:29 final size:26
Alignment explanation
Indices: 5671708--5671771 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 26
5671698 AAATAATTTT
*
5671708 TTATATTTTTATTATATTTAAATAAA
1 TTATATTTTTATTATATTCAAATAAA
*
5671734 TTATAATTTTTAATTTATATTCAAATATA
1 TTAT-ATTTTT-A-TTATATTCAAATAAA
5671763 TTGATATTT
1 TT-ATATTT
5671772 CAAATAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 4 0.12
27 6 0.19
28 1 0.03
29 19 0.59
30 2 0.06
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (26 bp):
TTATATTTTTATTATATTCAAATAAA
Found at i:5671834 original size:30 final size:29
Alignment explanation
Indices: 5671792--5671894 Score: 98
Period size: 30 Copynumber: 3.5 Consensus size: 29
5671782 ATTAATTAAT
*
5671792 ATTAAAATTTTATTTAAATTCAAATTAAAA
1 ATTAAAAATTTATTTAAATT-AAATTAAAA
* * *
5671822 AATAAAAATTTATTTAGAGTAAATTAAAA
1 ATTAAAAATTTATTTAAATTAAATTAAAA
* * * * *
5671851 TTTAAAGATTCATATAAATGTAAAATAAAA
1 ATTAAAAATTTATTTAAAT-TAAATTAAAA
*
5671881 ATTATAAATTTATT
1 ATTAAAAATTTATT
5671895 GGAATATAAT
Statistics
Matches: 55, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
29 21 0.38
30 34 0.62
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (29 bp):
ATTAAAAATTTATTTAAATTAAATTAAAA
Found at i:5672954 original size:3 final size:3
Alignment explanation
Indices: 5672948--5672976 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5672938 CGATGAGTGC
5672948 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5672977 TGACAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5675281 original size:29 final size:31
Alignment explanation
Indices: 5675230--5675292 Score: 103
Period size: 29 Copynumber: 2.1 Consensus size: 31
5675220 CTTAGACAGA
5675230 AATAACATACACGCTATCTTTTAAAATCAAT
1 AATAACATACACGCTATCTTTTAAAATCAAT
*
5675261 AATAACATAC-C-CTATCTTTTACAATCAAT
1 AATAACATACACGCTATCTTTTAAAATCAAT
5675290 AAT
1 AAT
5675293 TCTTTACCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 20 0.65
30 1 0.03
31 10 0.32
ACGTcount: A:0.44, C:0.21, G:0.02, T:0.33
Consensus pattern (31 bp):
AATAACATACACGCTATCTTTTAAAATCAAT
Found at i:5677357 original size:4 final size:4
Alignment explanation
Indices: 5677348--5677380 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
5677338 ATATATGCAA
5677348 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
5677381 ATGCTCTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:5684937 original size:19 final size:21
Alignment explanation
Indices: 5684913--5684959 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
5684903 TATGGGAATG
*
5684913 AGAAGAAAAGAAC-AGAA-CA
1 AGAAGAAAAGAACAAGAAGAA
*
5684932 AGAAGAAAGGAACAAGAAGAA
1 AGAAGAAAAGAACAAGAAGAA
5684953 AGAAGAA
1 AGAAGAA
5684960 GAAATAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 12 0.50
20 4 0.17
21 8 0.33
ACGTcount: A:0.68, C:0.06, G:0.26, T:0.00
Consensus pattern (21 bp):
AGAAGAAAAGAACAAGAAGAA
Found at i:5684944 original size:14 final size:14
Alignment explanation
Indices: 5684927--5684954 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5684917 GAAAAGAACA
5684927 GAACAAGAAGAAAG
1 GAACAAGAAGAAAG
5684941 GAACAAGAAGAAAG
1 GAACAAGAAGAAAG
5684955 AAGAAGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.29, T:0.00
Consensus pattern (14 bp):
GAACAAGAAGAAAG
Found at i:5686189 original size:8 final size:8
Alignment explanation
Indices: 5686176--5686355 Score: 72
Period size: 8 Copynumber: 22.5 Consensus size: 8
5686166 TTTTTGTTAA
5686176 TAATATAT
1 TAATATAT
5686184 T-A-ATAT
1 TAATATAT
5686190 T-A-ATAT
1 TAATATAT
*
5686196 TAATATAA
1 TAATATAT
5686204 TAATATAT
1 TAATATAT
5686212 TAATATAT
1 TAATATAT
*
5686220 TATTA-AT
1 TAATATAT
*
5686227 AAATATTAT
1 TAATA-TAT
* *
5686236 ATTATATGAA
1 -TAATAT-AT
*
5686246 TATTATAT
1 TAATATAT
*
5686254 TATTATA-
1 TAATATAT
5686261 TAATATAT
1 TAATATAT
5686269 TAATATAAT
1 TAATAT-AT
* *
5686278 AAATATAA
1 TAATATAT
*
5686286 CAATATTTAT
1 TAATA--TAT
5686296 TAATATTAT
1 TAATA-TAT
*
5686305 TTAT-TAAT
1 TAATAT-AT
5686313 ATAATAT-T
1 -TAATATAT
*
5686321 T-ATATAA
1 TAATATAT
*
5686328 TAAAATAT
1 TAATATAT
* *
5686336 TATTTTAT
1 TAATATAT
*
5686344 TAATATAA
1 TAATATAT
5686352 TAAT
1 TAAT
5686356 TATAAAGTCA
Statistics
Matches: 129, Mismatches: 28, Indels: 30
0.69 0.15 0.16
Matches are distributed among these distances:
6 15 0.12
7 16 0.12
8 63 0.49
9 24 0.19
10 11 0.09
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (8 bp):
TAATATAT
Found at i:5686232 original size:31 final size:29
Alignment explanation
Indices: 5686173--5686355 Score: 100
Period size: 28 Copynumber: 6.2 Consensus size: 29
5686163 CATTTTTTGT
*
5686173 TAATAATATATT-A-ATATTAATATTAATA
1 TAATAATATATTAATATATTATTA-TAATA
5686201 TAATAATATATTAATATATTA-T-TAATA
1 TAATAATATATTAATATATTATTATAATA
* * *
5686228 -AATATTATATT-ATATGAATATTATATTA
1 TAATAATATATTAATAT-ATTATTATAATA
5686256 TTATATAATATATTAATATA--A-TA-AATA
1 -TA-ATAATATATTAATATATTATTATAATA
* *
5686283 TAACAATAT-TTATTAATATTATTTATTAATA
1 TAATAATATATTAAT-ATATTA-TTA-TAATA
* *
5686314 TAATATTTATATAATAAAATATTATTTTATTAATA
1 TAATA---ATATATTAATATATTA--TTA-TAATA
5686349 TAATAAT
1 TAATAAT
5686356 TATAAAGTCA
Statistics
Matches: 123, Mismatches: 11, Indels: 38
0.72 0.06 0.22
Matches are distributed among these distances:
24 4 0.03
25 13 0.11
26 15 0.12
27 10 0.08
28 18 0.15
29 5 0.04
30 7 0.06
31 18 0.15
32 6 0.05
34 10 0.08
35 17 0.14
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (29 bp):
TAATAATATATTAATATATTATTATAATA
Found at i:5686258 original size:34 final size:33
Alignment explanation
Indices: 5686175--5686358 Score: 128
Period size: 35 Copynumber: 5.5 Consensus size: 33
5686165 TTTTTTGTTA
* * * *
5686175 ATAATATATTAATATTAATATTAATATAATAATAT
1 ATAATATAATATTATTAATA--AATATTATATTAT
*
5686210 ATTA-AT-ATATTATTAATAAATATTATATTAT
1 ATAATATAATATTATTAATAAATATTATATTAT
* *
5686241 ATGAATATTATATTATTATATAATATATTAATATAAT
1 AT-AATATAATATTATTA-ATAA-ATATT-ATATTAT
* * * *
5686278 A-AATATAACAATATTTATTAATATTAT-TTAT
1 ATAATATAATATTATTAATAAATATTATATTAT
*
5686309 -TAATATAATATTTATATAATAAAATATTATTTTAT
1 ATAATATAATA-TTAT-TAAT-AAATATTATATTAT
5686344 -TAATATAATAATTAT
1 ATAATATAAT-ATTAT
5686359 AAAGTCACTG
Statistics
Matches: 120, Mismatches: 17, Indels: 24
0.75 0.11 0.15
Matches are distributed among these distances:
31 24 0.20
32 6 0.05
33 20 0.17
34 22 0.18
35 35 0.29
36 6 0.05
37 7 0.06
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (33 bp):
ATAATATAATATTATTAATAAATATTATATTAT
Found at i:5686314 original size:82 final size:83
Alignment explanation
Indices: 5686175--5686360 Score: 216
Period size: 82 Copynumber: 2.2 Consensus size: 83
5686165 TTTTTTGTTA
* *
5686175 ATAATATATTAATATTAATATTAATATAATAATATATTAATATATTATTAATAAATATTATA-TT
1 ATAATATATTAATA-TAATA-TAATATAACAATATATTAATATATTATTAATAAATATAATATTT
**
5686239 ATATGAATATTATATTATTAT
64 ATAT-AATAAAATATTATTAT
* * *
5686260 ATAATATATTAATATAATA-AATATAACAATAT-TTATTAATATTATTTATTAATATAATATTTA
1 ATAATATATTAATATAATATAATATAACAATATATTAAT-ATATTATTAATAAATATAATATTTA
*
5686323 TATAATAAAATATTATTTT
65 TATAATAAAATATTATTAT
*
5686342 ATTAATATAATAATTATAA
1 A-TAATATATTAA-TATAA
5686361 AGTCACTGTA
Statistics
Matches: 88, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
81 4 0.05
82 44 0.50
83 16 0.18
84 10 0.11
85 14 0.16
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.48
Consensus pattern (83 bp):
ATAATATATTAATATAATATAATATAACAATATATTAATATATTATTAATAAATATAATATTTAT
ATAATAAAATATTATTAT
Found at i:5686339 original size:19 final size:18
Alignment explanation
Indices: 5686193--5686358 Score: 66
Period size: 19 Copynumber: 9.2 Consensus size: 18
5686183 TTAATATTAA
*
5686193 TATTAATATAATAATATAT
1 TATTTATATAATAA-ATAT
*
5686212 TAATATATTATTAATAAATAT
1 T-ATTTA-TA-TAATAAATAT
*
5686233 TATATTATATGAATATTATAT
1 TAT-TTATAT-AATA-AATAT
5686254 TA-TTATATAAT--ATAT
1 TATTTATATAATAAATAT
5686269 TA---ATATAATAAATA-
1 TATTTATATAATAAATAT
*** * *
5686283 TAACAATATTTATTAATAT
1 TATTTATA-TAATAAATAT
*
5686302 TATTTAT-TAAT--ATAA
1 TATTTATATAATAAATAT
5686317 TATTTATATAATAAAATAT
1 TATTTATATAAT-AAATAT
5686336 TATTT-TATTAATATAATAAT
1 TATTTATA-TAATA-AAT-AT
5686356 TAT
1 TAT
5686359 AAAGTCACTG
Statistics
Matches: 115, Mismatches: 12, Indels: 39
0.69 0.07 0.23
Matches are distributed among these distances:
13 7 0.06
14 2 0.02
15 19 0.17
16 4 0.03
17 6 0.05
18 13 0.11
19 27 0.23
20 16 0.14
21 15 0.13
22 6 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (18 bp):
TATTTATATAATAAATAT
Found at i:5686345 original size:42 final size:41
Alignment explanation
Indices: 5686181--5686345 Score: 163
Period size: 42 Copynumber: 4.0 Consensus size: 41
5686171 GTTAATAATA
*
5686181 TATTAATATTAATATTAATATAATAATATATTAATATATTATT
1 TATTAATA-TAATA-TAATATAATAATATATTATTATATTATT
* * * * * * *
5686224 AATAAATATTATATTATATGAATATTATATTATTATATAATA
1 TATTAATATAATATAATAT-AATAATATATTATTATATTATT
*
5686266 TATTAATATAATA-AATATAACAATAT-TTATTAATATTATT
1 TATTAATATAATATAATATAATAATATATTATT-ATATTATT
* * *
5686306 TATTAATATAATATTTATATAATAAAATATTATTTTATTA
1 TATTAATATAATA-TAATATAATAATATATTATTATATTA
5686346 ATATAATAAT
Statistics
Matches: 97, Mismatches: 20, Indels: 11
0.76 0.16 0.09
Matches are distributed among these distances:
39 5 0.05
40 25 0.26
41 9 0.09
42 47 0.48
43 11 0.11
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (41 bp):
TATTAATATAATATAATATAATAATATATTATTATATTATT
Found at i:5686467 original size:16 final size:15
Alignment explanation
Indices: 5686411--5686467 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
5686401 TTCGTGCATT
*
5686411 TATTAATAAATAATA
1 TATTAATATATAATA
5686426 TATT-ATATGAATAATA
1 TATTAATAT--ATAATA
**
5686442 TATTGTTATATAATA
1 TATTAATATATAATA
5686457 TTATTAATATA
1 -TATTAATATA
5686468 ATAAATATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 18 0.53
17 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (15 bp):
TATTAATATATAATA
Found at i:5687922 original size:27 final size:28
Alignment explanation
Indices: 5687861--5687926 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
5687851 TTTAAAAAAC
*
5687861 ATAT-ATTTAAATTAATTTAATTTTTAA
1 ATATAATTTAAATTAATTTAATATTTAA
* *
5687888 TTATAATTTAAA-TAATTTTGATATTTAA
1 ATATAATTTAAATTAA-TTTAATATTTAA
5687916 ATA-AATTTAAA
1 ATATAATTTAAA
5687927 ATTATCTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 14 0.42
28 19 0.58
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (28 bp):
ATATAATTTAAATTAATTTAATATTTAA
Found at i:5691485 original size:65 final size:65
Alignment explanation
Indices: 5691376--5691505 Score: 242
Period size: 65 Copynumber: 2.0 Consensus size: 65
5691366 TAAAGTCAAC
*
5691376 GGACTATGTAGAGATAAAAGGATAAAATACCTTAACTAAAACCTTGTTTTTACCCATAACTTTCA
1 GGACCATGTAGAGATAAAAGGATAAAATACCTTAACTAAAACCTTGTTTTTACCCATAACTTTCA
*
5691441 GGACCATGTAGGGATAAAAGGATAAAATACCTTAACTAAAACCTTGTTTTTACCCATAACTTTCA
1 GGACCATGTAGAGATAAAAGGATAAAATACCTTAACTAAAACCTTGTTTTTACCCATAACTTTCA
5691506 CAACCTCACC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (65 bp):
GGACCATGTAGAGATAAAAGGATAAAATACCTTAACTAAAACCTTGTTTTTACCCATAACTTTCA
Found at i:5697803 original size:18 final size:18
Alignment explanation
Indices: 5697743--5697804 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 18
5697733 CCATTTTTTA
5697743 AATTAA-AAAAAT-AAAC
1 AATTAATAAAAATAAAAC
*
5697759 -ATTAAT-TAAATGAAATA-
1 AATTAATAAAAAT-AAA-AC
*
5697776 AATCAATAAAAATAAAAC
1 AATTAATAAAAATAAAAC
5697794 AATTAATAAAA
1 AATTAATAAAA
5697805 TAAGATTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
15 9 0.26
17 3 0.09
18 19 0.54
19 4 0.11
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (18 bp):
AATTAATAAAAATAAAAC
Found at i:5704573 original size:19 final size:19
Alignment explanation
Indices: 5704549--5704588 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
5704539 TTTCAGGCAA
5704549 GATTTCAAATAAGAAAAAG
1 GATTTCAAATAAGAAAAAG
5704568 GATTTCAAATAAGAAAAAG
1 GATTTCAAATAAGAAAAAG
5704587 GA
1 GA
5704589 CAACTTAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.57, C:0.05, G:0.17, T:0.20
Consensus pattern (19 bp):
GATTTCAAATAAGAAAAAG
Found at i:5707035 original size:2 final size:2
Alignment explanation
Indices: 5707024--5707054 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5707014 GGCCGCCACT
5707024 TA TA -A 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
5707055 AACTACTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5719099 original size:30 final size:31
Alignment explanation
Indices: 5719065--5719130 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 31
5719055 TGTGAATAAA
* * *
5719065 TAATTTTATTATCTTCATGTTTCTAA-ATTT
1 TAATTATATTATATACATGTTTCTAACATTT
* *
5719095 TAATTATCTTATATACATGTTTTTAACATTT
1 TAATTATATTATATACATGTTTCTAACATTT
5719126 TAATT
1 TAATT
5719131 CACCATTGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 21 0.70
31 9 0.30
ACGTcount: A:0.30, C:0.09, G:0.03, T:0.58
Consensus pattern (31 bp):
TAATTATATTATATACATGTTTCTAACATTT
Found at i:5719874 original size:21 final size:21
Alignment explanation
Indices: 5719850--5719902 Score: 54
Period size: 25 Copynumber: 2.4 Consensus size: 21
5719840 TAATATTTAA
5719850 AATTAAAAA-AAATTAATTATT
1 AATTAAAAATAAATTAATT-TT
*
5719871 AATTTAACAAATTTAATTAATTTT
1 AA-TTAA-AAA-TAAATTAATTTT
5719895 AATTAAAA
1 AATTAAAA
5719903 TTATATGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
21 2 0.07
22 6 0.22
23 7 0.26
24 4 0.15
25 8 0.30
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTAAAAATAAATTAATTTT
Found at i:5720330 original size:36 final size:36
Alignment explanation
Indices: 5720286--5720361 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
5720276 GGTATAGGTG
* *
5720286 AAATGAAATATAATAAGAATAAAAAATAATCATTGA
1 AAATGAAATATAATAAAAATAAAAAATAATCATTAA
* ** *
5720322 AAATGAAATGTTGTAAAAATAAAAAATAATTATTAA
1 AAATGAAATATAATAAAAATAAAAAATAATCATTAA
5720358 AAAT
1 AAAT
5720362 ATTAAATTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.63, C:0.01, G:0.08, T:0.28
Consensus pattern (36 bp):
AAATGAAATATAATAAAAATAAAAAATAATCATTAA
Found at i:5722444 original size:17 final size:16
Alignment explanation
Indices: 5722416--5722463 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
5722406 CCTATTGTAC
5722416 ATTTATA-A-TTTAAT
1 ATTTATATATTTTAAT
5722430 AATTTATATATTTTAAT
1 -ATTTATATATTTTAAT
*
5722447 -TTTATTTATTTT-AT
1 ATTTATATATTTTAAT
5722461 ATT
1 ATT
5722464 AAATATATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
14 2 0.07
15 20 0.69
16 1 0.03
17 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTATATATTTTAAT
Found at i:5727334 original size:5 final size:5
Alignment explanation
Indices: 5727292--5727328 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
5727282 AAAATTTTAA
5727292 ATTAT ATTAT -TT-T A-TAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
5727329 TATATTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 2 0.07
4 4 0.14
5 23 0.79
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
ATTAT
Found at i:5727344 original size:15 final size:16
Alignment explanation
Indices: 5727275--5727345 Score: 67
Period size: 15 Copynumber: 4.5 Consensus size: 16
5727265 TTCATATAAT
**
5727275 AATTATTAAAATTTTA
1 AATTATTATTATTTTA
5727291 AATTA-TATTATTTTA
1 AATTATTATTATTTTA
*
5727306 TATATTA-TATTATATTA
1 -A-ATTATTATTATTTTA
*
5727323 TATTATTA-TATTTTA
1 AATTATTATTATTTTA
5727338 AATTATTA
1 AATTATTA
5727346 AATCTATTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
15 25 0.54
16 8 0.17
17 13 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AATTATTATTATTTTA
Found at i:5728147 original size:32 final size:32
Alignment explanation
Indices: 5728082--5728155 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
5728072 TAGATGTTCG
* *
5728082 ATTTATATATTTATATCATATAAAATATTAAA
1 ATTTATATATTTATATAATATAAAATATAAAA
***
5728114 ATTTATATATTTATATAATATTTTATATAAAA
1 ATTTATATATTTATATAATATAAAATATAAAA
5728146 A-TTATATATT
1 ATTTATATATT
5728156 ATAATTTATA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 9 0.24
32 28 0.76
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (32 bp):
ATTTATATATTTATATAATATAAAATATAAAA
Found at i:5728251 original size:11 final size:11
Alignment explanation
Indices: 5728235--5728278 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
5728225 AAATTTTAAA
*
5728235 TTATATTATTT
1 TTATATTATAT
5728246 TTATATTTTATAT
1 TTATA--TTATAT
5728259 TTATATTATAT
1 TTATATTATAT
5728270 TTATATTAT
1 TTATATTAT
5728279 GTTATCATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 20 0.67
13 10 0.33
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATATTATAT
Found at i:5741710 original size:15 final size:15
Alignment explanation
Indices: 5741690--5741724 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5741680 AAATTTTAAT
*
5741690 ATATTTTTTAGATAA
1 ATATTTTTTAGAAAA
*
5741705 ATATTTTTTATAAAA
1 ATATTTTTTAGAAAA
5741720 ATATT
1 ATATT
5741725 AATAAAGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
ATATTTTTTAGAAAA
Found at i:5741853 original size:12 final size:12
Alignment explanation
Indices: 5741836--5741877 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
5741826 AATTTATATT
5741836 TTTTATTAAATA
1 TTTTATTAAATA
5741848 TTTTATTAAATTA
1 TTTTATTAAA-TA
* *
5741861 TTTT-TAAAAAA
1 TTTTATTAAATA
5741872 TTTTAT
1 TTTTAT
5741878 AGAATTCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 5 0.19
12 15 0.58
13 6 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTTATTAAATA
Found at i:5741883 original size:24 final size:24
Alignment explanation
Indices: 5741847--5741898 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
5741837 TTTATTAAAT
*
5741847 ATTTTATTAAATT-ATTTTTAAAAA
1 ATTTTATTAAATTCA-TTTAAAAAA
5741871 ATTTTA-TAGAATTCATTTAAAAAA
1 ATTTTATTA-AATTCATTTAAAAAA
5741895 ATTT
1 ATTT
5741899 ATGTAAGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 2 0.08
24 22 0.88
25 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
ATTTTATTAAATTCATTTAAAAAA
Found at i:5742599 original size:3 final size:3
Alignment explanation
Indices: 5742591--5742634 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
5742581 AGACTATCTC
5742591 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
5742635 GCAACTGATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5748599 original size:21 final size:20
Alignment explanation
Indices: 5748563--5748602 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
5748553 TGTAAAATAA
5748563 ATAAATATTACTAATATTTT
1 ATAAATATTACTAATATTTT
5748583 ATAAATTATTA-TCAATATTT
1 ATAAA-TATTACT-AATATTT
5748603 AATTATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAAATATTACTAATATTTT
Found at i:5748608 original size:17 final size:16
Alignment explanation
Indices: 5748586--5748617 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
5748576 ATATTTTATA
5748586 AATTATTATCAATATTT
1 AATTATTAT-AATATTT
5748603 AATTATTATAATATT
1 AATTATTATAATATT
5748618 AATGGTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTATTATAATATTT
Found at i:5749576 original size:2 final size:2
Alignment explanation
Indices: 5749569--5749605 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5749559 GAGTTCTATT
5749569 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5749606 ATATATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5749610 original size:2 final size:2
Alignment explanation
Indices: 5749605--5749630 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5749595 TCTCTCTCTC
5749605 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
5749631 GTTTAAAAAA
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):
TA
Found at i:5750842 original size:13 final size:15
Alignment explanation
Indices: 5750818--5750849 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5750808 ATCTCGAGGT
5750818 AAAATAATATA-TAA
1 AAAATAATATATTAA
5750832 AAAATAA-ATATTAA
1 AAAATAATATATTAA
5750846 AAAA
1 AAAA
5750850 AGAAAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 3 0.18
14 14 0.82
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAATAATATATTAA
Found at i:5763972 original size:14 final size:14
Alignment explanation
Indices: 5763953--5763983 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
5763943 TTGGTATGAG
5763953 ATGCATCTCTTATT
1 ATGCATCTCTTATT
5763967 ATGCATCTCTTATT
1 ATGCATCTCTTATT
5763981 ATG
1 ATG
5763984 TATAAGCGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.23, C:0.19, G:0.10, T:0.48
Consensus pattern (14 bp):
ATGCATCTCTTATT
Found at i:5765399 original size:14 final size:14
Alignment explanation
Indices: 5765380--5765425 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
5765370 TTATAATCGA
*
5765380 AAAAAAATTTTAAT
1 AAAAAAATTTTATT
5765394 -AAAAAATTTATATT
1 AAAAAAATTT-TATT
*
5765408 AAATAAATTTTATT
1 AAAAAAATTTTATT
5765422 AAAA
1 AAAA
5765426 TTAATATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 9 0.33
14 10 0.37
15 8 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAAAAAATTTTATT
Found at i:5776405 original size:21 final size:20
Alignment explanation
Indices: 5776364--5776406 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
5776354 AATTTAAAGT
* * *
5776364 AATTTTTTTGATTATTTTAA
1 AATTTTTTTGAATACTCTAA
5776384 AATTTTTTATGAATACTCTAA
1 AATTTTTT-TGAATACTCTAA
5776405 AA
1 AA
5776407 ATAAAAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (20 bp):
AATTTTTTTGAATACTCTAA
Found at i:5782458 original size:17 final size:17
Alignment explanation
Indices: 5782436--5782470 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5782426 ACCTCAAAGA
* *
5782436 TTGAAAAATAAGAAAAT
1 TTGAAAAAAAACAAAAT
5782453 TTGAAAAAAAACAAAAT
1 TTGAAAAAAAACAAAAT
5782470 T
1 T
5782471 CATTGGACAC
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:0.66, C:0.03, G:0.09, T:0.23
Consensus pattern (17 bp):
TTGAAAAAAAACAAAAT
Found at i:5789063 original size:24 final size:24
Alignment explanation
Indices: 5789031--5789087 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
5789021 TATTCCAAAG
5789031 AAGCAAAAGAAGAAAAAGTCTTCC
1 AAGCAAAAGAAGAAAAAGTCTTCC
5789055 AAGCAAAAGAAGAAAAAGTCTTCC
1 AAGCAAAAGAAGAAAAAGTCTTCC
* *
5789079 CAGTAAAAG
1 AAGCAAAAG
5789088 CTCAAAGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.54, C:0.16, G:0.18, T:0.12
Consensus pattern (24 bp):
AAGCAAAAGAAGAAAAAGTCTTCC
Found at i:5803096 original size:24 final size:25
Alignment explanation
Indices: 5803042--5803100 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
5803032 CATTAATAAA
* *
5803042 GTATCATAATTTAATTTATTGATAAT
1 GTATCA-AATTTAATATATTGACAAT
* *
5803068 ATATCAAATTT-ATATGTTGACAAT
1 GTATCAAATTTAATATATTGACAAT
5803092 GTATCAAAT
1 GTATCAAAT
5803101 ATAAACTCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 18 0.64
25 5 0.18
26 5 0.18
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (25 bp):
GTATCAAATTTAATATATTGACAAT
Found at i:5803594 original size:16 final size:16
Alignment explanation
Indices: 5803575--5803606 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5803565 CGAAAATAAT
5803575 ATAAAAAAATTTAAAA
1 ATAAAAAAATTTAAAA
*
5803591 ATAAAACAATTTAAAA
1 ATAAAAAAATTTAAAA
5803607 TTTTAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (16 bp):
ATAAAAAAATTTAAAA
Found at i:5805695 original size:5 final size:5
Alignment explanation
Indices: 5805680--5805711 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
5805670 TATGATGACT
5805680 TAAAA TAAAAA TAAAA TAAAA TAAAA TAAAA T
1 TAAAA T-AAAA TAAAA TAAAA TAAAA TAAAA T
5805712 TACTGATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:5809750 original size:12 final size:11
Alignment explanation
Indices: 5809728--5809789 Score: 56
Period size: 12 Copynumber: 5.5 Consensus size: 11
5809718 TTTTTAATTA
5809728 AAAAATTTAAT
1 AAAAATTTAAT
*
5809739 TAAAATTATAAT
1 AAAAATT-TAAT
5809751 AAAAATTTAAATTT
1 AAAAATTT-AA--T
*
5809765 ATAAATTT-AT
1 AAAAATTTAAT
5809775 -AAAATTTAAT
1 AAAAATTTAAT
5809785 AAAAA
1 AAAAA
5809790 ATTGAATGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
9 6 0.15
10 3 0.07
11 11 0.27
12 13 0.32
14 8 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AAAAATTTAAT
Found at i:5809758 original size:23 final size:21
Alignment explanation
Indices: 5809728--5809789 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 21
5809718 TTTTTAATTA
5809728 AAAAATTTAATTAAAATTATAAT
1 AAAAATTTAATTAAAATT-T-AT
5809751 AAAAATTTAAATTTATAAATTTAT
1 AAAAATTT-AA-TTA-AAATTTAT
*
5809775 -AAAATTTAATAAAAA
1 AAAAATTTAATTAAAA
5809790 ATTGAATGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
20 3 0.09
21 2 0.06
22 2 0.06
23 15 0.43
24 4 0.11
25 4 0.11
26 5 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAAATTTAATTAAAATTTAT
Found at i:5825031 original size:2 final size:2
Alignment explanation
Indices: 5825024--5825051 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5825014 TAAAATGAAC
5825024 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5825052 GGATAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5826668 original size:24 final size:25
Alignment explanation
Indices: 5826614--5826672 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
5826604 CATTAATAAA
* *
5826614 GTATCATAATTTAATTTATTGATAAT
1 GTATCA-AATTTAATATATTGACAAT
* *
5826640 ATATCAAATTT-ATATGTTGACAAT
1 GTATCAAATTTAATATATTGACAAT
5826664 GTATCAAAT
1 GTATCAAAT
5826673 ATAAACTCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 18 0.64
25 5 0.18
26 5 0.18
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (25 bp):
GTATCAAATTTAATATATTGACAAT
Found at i:5829436 original size:5 final size:5
Alignment explanation
Indices: 5829426--5829450 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5829416 TATGATGACT
5829426 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
5829451 ATTACTGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:5835038 original size:2 final size:2
Alignment explanation
Indices: 5835031--5835069 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5835021 TAATTAATGA
5835031 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5835070 CACACATTCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5836918 original size:30 final size:31
Alignment explanation
Indices: 5836882--5836946 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
5836872 ATTTTAATTG
* * *
5836882 TAAATTAATTTAATTTTTAAATCAAAT-TAA
1 TAAATTAATTAAAATTTTAAATAAAATATAA
*
5836912 TAAATTAATTAAAATTTTAATTAAAATATAA
1 TAAATTAATTAAAATTTTAAATAAAATATAA
5836943 TAAA
1 TAAA
5836947 ACCTATATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 23 0.77
31 7 0.23
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (31 bp):
TAAATTAATTAAAATTTTAAATAAAATATAA
Found at i:5837208 original size:14 final size:14
Alignment explanation
Indices: 5837186--5837224 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
5837176 AAAAGATAAA
*
5837186 ATAAATTAATTTTG
1 ATAATTTAATTTTG
5837200 ATAATTTAATTTTG
1 ATAATTTAATTTTG
5837214 ATAATTTAATT
1 ATAATTTAATT
5837225 CAAAATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
ATAATTTAATTTTG
Done.