Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold54
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: 3629595
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8670 characters in sequence are not A, C, G, or T
File 13 of 20
Found at i:2122419 original size:2 final size:2
Alignment explanation
Indices: 2122412--2122456 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
2122402 TTAGGCCTCC
*
2122412 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2122453 AT AT
1 AT AT
2122457 TGAGTAACAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2124997 original size:19 final size:19
Alignment explanation
Indices: 2124960--2125003 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2124950 AATAAATTTA
* **
2124960 AAAAATTTATTATGCTATT
1 AAAAATGTATTATAATATT
*
2124979 TAAAATGTATTATAATATT
1 AAAAATGTATTATAATATT
2124998 AAAAAT
1 AAAAAT
2125004 ATTAATATTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (19 bp):
AAAAATGTATTATAATATT
Found at i:2126816 original size:25 final size:24
Alignment explanation
Indices: 2126784--2126855 Score: 74
Period size: 24 Copynumber: 2.9 Consensus size: 24
2126774 AATATTATTT
2126784 TAAATATTATATATTTTATATAAA
1 TAAATATTATATATTTTATATAAA
* *
2126808 TAATATATTA-ATAATTTATATTATA
1 TAA-ATATTATATATTTTATA-TAAA
*
2126833 TAAATTTTAATATATTTATATAT
1 TAAATATT-ATATATTT-TATAT
2126856 TTATTTTATA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
24 16 0.41
25 13 0.33
26 6 0.15
27 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TAAATATTATATATTTTATATAAA
Found at i:2126833 original size:29 final size:31
Alignment explanation
Indices: 2126799--2126903 Score: 99
Period size: 30 Copynumber: 3.4 Consensus size: 31
2126789 ATTATATATT
2126799 TTATATAAA-TAATATATTAATA-ATTTATA
1 TTATATAAATTAATATATTAATATATTTATA
* *
2126828 TTATATAAATTTTAATATATTTATATATTTATT
1 TTATATAAA--TTAATATATTAATATATTTATA
* * * * *
2126861 TTATATATATT-ATATTTTATTTTATTTTTA
1 TTATATAAATTAATATATTAATATATTTATA
2126891 TTATATATAATTA
1 TTATATA-AATTA
2126904 TATTATATCT
Statistics
Matches: 60, Mismatches: 10, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
29 9 0.15
30 20 0.33
31 5 0.08
32 12 0.20
33 14 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (31 bp):
TTATATAAATTAATATATTAATATATTTATA
Found at i:2126853 original size:38 final size:38
Alignment explanation
Indices: 2126811--2126911 Score: 89
Period size: 38 Copynumber: 2.6 Consensus size: 38
2126801 ATATAAATAA
2126811 TATATTAATAATTTATATTATATAAATTTTAATATATT
1 TATATTAATAATTTATATTATATAAATTTTAATATATT
* * * * *
2126849 TATA-TATTTATTT-TATATATATTATATTTTATTTTATT
1 TATATTAATAATTTATAT-TATA-TAAATTTTAATATATT
* *
2126887 TTTATTATATATAATTATATTATAT
1 TATATTA-ATA-ATTTATATTATAT
2126912 CTAAAAGTTA
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
36 3 0.06
37 11 0.23
38 20 0.42
39 2 0.04
40 2 0.04
41 7 0.15
42 3 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (38 bp):
TATATTAATAATTTATATTATATAAATTTTAATATATT
Found at i:2126861 original size:22 final size:22
Alignment explanation
Indices: 2126819--2126884 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 22
2126809 AATATATTAA
* **
2126819 TAATTTATATTATA-TAAATTT
1 TAATATATATTATATTTTATTT
2126840 TAATATAT-TTATATATTTATTT
1 TAATATATATTATAT-TTTATTT
2126862 T-ATATATATTATATTTTATTT
1 TAATATATATTATATTTTATTT
2126883 TA
1 TA
2126885 TTTTTATTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 5 0.13
21 21 0.55
22 12 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TAATATATATTATATTTTATTT
Found at i:2126868 original size:21 final size:21
Alignment explanation
Indices: 2126836--2126896 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
2126826 TATTATATAA
2126836 ATTTTA-ATATATTTATATATTT
1 ATTTTATATATA-TTATAT-TTT
2126858 ATTTTATATATATTATATTTT
1 ATTTTATATATATTATATTTT
* *
2126879 ATTTTATTTTTATTATAT
1 ATTTTATATATATTATAT
2126897 ATAATTATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 19 0.53
22 12 0.33
23 5 0.14
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTTTATATATATTATATTTT
Found at i:2126907 original size:21 final size:21
Alignment explanation
Indices: 2126868--2126907 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2126858 ATTTTATATA
* * *
2126868 TATTATATTTTATTTTATTTT
1 TATTATATATAATTATATTTT
2126889 TATTATATATAATTATATT
1 TATTATATATAATTATATT
2126908 ATATCTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTATATATAATTATATTTT
Found at i:2127375 original size:20 final size:19
Alignment explanation
Indices: 2127328--2127377 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
2127318 TAATTAATAA
* *
2127328 ATTATTAAAATATATATTT
1 ATTATAAAAATAAATATTT
* *
2127347 ATAAAAAAAATCAAATATTT
1 ATTATAAAAAT-AAATATTT
2127367 ATTATAAAAAT
1 ATTATAAAAAT
2127378 TATTAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTATAAAAATAAATATTT
Found at i:2127386 original size:24 final size:25
Alignment explanation
Indices: 2127326--2127396 Score: 83
Period size: 24 Copynumber: 2.9 Consensus size: 25
2127316 AATAATTAAT
2127326 AAATTATTAAAATATATATTTATAA
1 AAATTATTAAAATATATATTTATAA
* * * *
2127351 AAA-AAATCAAATATTTA-TTATAA
1 AAATTATTAAAATATATATTTATAA
*
2127374 AAATTATTAAAATAAATATTTAT
1 AAATTATTAAAATATATATTTAT
2127397 CATTTAATTA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
23 9 0.26
24 19 0.54
25 7 0.20
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (25 bp):
AAATTATTAAAATATATATTTATAA
Found at i:2127458 original size:17 final size:16
Alignment explanation
Indices: 2127415--2127458 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
2127405 TAGTAGTGAA
*
2127415 ATAAATAATTAATTTT
1 ATAAATAATTAATTAT
*
2127431 TTAAATAAATTAATTAT
1 ATAAAT-AATTAATTAT
2127448 ATAATATAATT
1 ATAA-ATAATT
2127459 TAAATAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 5 0.22
17 16 0.70
18 2 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAAATAATTAATTAT
Found at i:2127647 original size:18 final size:18
Alignment explanation
Indices: 2127601--2127662 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 18
2127591 TGTAATAATT
2127601 TATTTATAATATATTATTAT-
1 TATTTATAA-AT-TT-TTATA
2127621 TATTATATAAATTTTTATA
1 TATT-TATAAATTTTTATA
*
2127640 TATTTATAATTTTTTATTA
1 TATTTATAAATTTTTA-TA
2127659 TATT
1 TATT
2127663 ATATTTTAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
18 15 0.39
19 12 0.32
20 6 0.16
21 5 0.13
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTTATAAATTTTTATA
Found at i:2127657 original size:33 final size:33
Alignment explanation
Indices: 2127600--2127691 Score: 87
Period size: 33 Copynumber: 2.6 Consensus size: 33
2127590 ATGTAATAAT
*
2127600 TTATTTATAATATATTATTATTATTATATAAATTTTTA
1 TTATTT-TAATAT-TT-TTATTA-TAT-TAAATTTTAA
*
2127638 TATATTTATAAT-TTTTTATTATATTATATTTTAA
1 T-TATTT-TAATATTTTTATTATATTAAATTTTAA
*
2127672 TTATTTTATTATTTTTATTA
1 TTATTTTAATATTTTTATTA
2127692 CATATATCTA
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
32 3 0.06
33 14 0.29
34 9 0.18
35 3 0.06
36 6 0.12
37 2 0.04
38 2 0.04
39 10 0.20
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (33 bp):
TTATTTTAATATTTTTATTATATTAAATTTTAA
Found at i:2127664 original size:18 final size:17
Alignment explanation
Indices: 2127620--2127691 Score: 71
Period size: 16 Copynumber: 4.4 Consensus size: 17
2127610 TATATTATTA
2127620 TTATTATA-TA-AATTT
1 TTATTATATTATAATTT
2127635 TTA-TATATTTATAATTTT
1 TTATTATA-TTATAA-TTT
2127653 TTATTATATTAT-ATTT
1 TTATTATATTATAATTT
* * *
2127669 TAATTATTTTATTATTT
1 TTATTATATTATAATTT
2127686 TTATTA
1 TTATTA
2127692 CATATATCTA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
14 4 0.08
15 3 0.06
16 15 0.31
17 12 0.25
18 10 0.21
19 4 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTATATTATAATTT
Found at i:2127678 original size:24 final size:24
Alignment explanation
Indices: 2127638--2127683 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
2127628 TAAATTTTTA
2127638 TATATTTATAATTTTTTATTATAT
1 TATATTTATAATTTTTTATTATAT
2127662 TATATTT-TAATTATTTTATTAT
1 TATATTTATAATT-TTTTATTAT
2127684 TTTTATTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
TATATTTATAATTTTTTATTATAT
Found at i:2127684 original size:8 final size:8
Alignment explanation
Indices: 2127633--2127691 Score: 50
Period size: 9 Copynumber: 7.0 Consensus size: 8
2127623 TTATATAAAT
2127633 TTTTATATA
1 TTTTAT-TA
2127642 TTTATAATT-
1 TTT-T-ATTA
2127651 TTTTATTA
1 TTTTATTA
*
2127659 TATTA-TA
1 TTTTATTA
2127666 TTTTAATTA
1 TTTT-ATTA
2127675 TTTTATTA
1 TTTTATTA
2127683 TTTTTATTA
1 -TTTTATTA
2127692 CATATATCTA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
7 8 0.19
8 10 0.24
9 20 0.48
10 2 0.05
11 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (8 bp):
TTTTATTA
Found at i:2127705 original size:14 final size:14
Alignment explanation
Indices: 2127694--2127723 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2127684 TTTTATTACA
*
2127694 TATATCTAATTAAT
1 TATAACTAATTAAT
2127708 TATAACTAATTAAT
1 TATAACTAATTAAT
2127722 TA
1 TA
2127724 CAACAACTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (14 bp):
TATAACTAATTAAT
Found at i:2132536 original size:2 final size:2
Alignment explanation
Indices: 2132529--2132563 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2132519 AAAATAGCCA
2132529 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 A
2132564 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2132568 original size:2 final size:2
Alignment explanation
Indices: 2132563--2132596 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2132553 ATATATATAT
2132563 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2132597 GTTTCTGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2133107 original size:38 final size:38
Alignment explanation
Indices: 2133056--2133132 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
2133046 GAGACTCTTA
2133056 TTAGCTGTCAAAAATGTCTTCTATTGCCCTAACTTTAC
1 TTAGCTGTCAAAAATGTCTTCTATTGCCCTAACTTTAC
2133094 TTAGCTGTCAAAAATGTCTTCTATTGCCCTAACTTTAC
1 TTAGCTGTCAAAAATGTCTTCTATTGCCCTAACTTTAC
2133132 T
1 T
2133133 CCCTTCTAGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.40
Consensus pattern (38 bp):
TTAGCTGTCAAAAATGTCTTCTATTGCCCTAACTTTAC
Found at i:2136364 original size:16 final size:17
Alignment explanation
Indices: 2136345--2136377 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2136335 ATAATTAATG
2136345 ATATTTTTAATT-TTTT
1 ATATTTTTAATTATTTT
2136361 ATATTTTTAATTATTTT
1 ATATTTTTAATTATTTT
2136378 TAATAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
ATATTTTTAATTATTTT
Found at i:2136375 original size:10 final size:9
Alignment explanation
Indices: 2136345--2136382 Score: 53
Period size: 8 Copynumber: 4.3 Consensus size: 9
2136335 ATAATTAATG
2136345 ATATTTTTA
1 ATATTTTTA
2136354 AT-TTTTT-
1 ATATTTTTA
2136361 ATATTTTTA
1 ATATTTTTA
2136370 ATTATTTTTA
1 A-TATTTTTA
2136380 ATA
1 ATA
2136383 AAAATTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
7 2 0.08
8 10 0.38
9 5 0.19
10 9 0.35
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
ATATTTTTA
Found at i:2136911 original size:18 final size:20
Alignment explanation
Indices: 2136868--2136912 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 20
2136858 TTATGTAGTT
2136868 AATTTTATATTATTAATAAA
1 AATTTTATATTATTAATAAA
2136888 AA-TTTA-ATTA-TAA-AATA
1 AATTTTATATTATTAATAA-A
2136905 AATTTTAT
1 AATTTTAT
2136913 TAAATAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.09
17 6 0.27
18 8 0.36
19 4 0.18
20 2 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTTTATATTATTAATAAA
Found at i:2136921 original size:17 final size:17
Alignment explanation
Indices: 2136877--2136922 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
2136867 TAATTTTATA
2136877 TTATT-AATAA-AAATT
1 TTATTAAATAATAAATT
*
2136892 TAATTATAA-AATAAATT
1 TTATTA-AATAATAAATT
2136909 TTATTAAATAATAA
1 TTATTAAATAATAA
2136923 TTATGTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 4 0.16
16 4 0.16
17 17 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTATTAAATAATAAATT
Found at i:2137323 original size:17 final size:17
Alignment explanation
Indices: 2137303--2137344 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
2137293 ATATAATATG
2137303 AATATAAAAACATATAA
1 AATATAAAAACATATAA
* * *
2137320 AATATATATATATATAA
1 AATATAAAAACATATAA
2137337 AATATAAA
1 AATATAAA
2137345 TAAATTTATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
AATATAAAAACATATAA
Found at i:2137330 original size:23 final size:22
Alignment explanation
Indices: 2137239--2137344 Score: 60
Period size: 23 Copynumber: 4.7 Consensus size: 22
2137229 TATTATTTAA
*
2137239 ATATACAAAAATA-AAAATAT-G
1 ATATA-AAAAATATAAAATATAT
* * *
2137260 ACATAAAAATTA-AAAACCATAT
1 ATATAAAAAATATAAAA-TATAT
* *
2137282 -TATAAAAATAAATATAATATGA-
1 ATATAAAAA-ATATAAAATAT-AT
2137304 ATATAAAAACATATAAAATATAT
1 ATATAAAAA-ATATAAAATATAT
2137327 ATATATATAAAATATAAA
1 ATATA-A-AAAATATAAA
2137345 TAAATTTATA
Statistics
Matches: 64, Mismatches: 12, Indels: 15
0.70 0.13 0.16
Matches are distributed among these distances:
20 10 0.16
21 13 0.20
22 4 0.06
23 26 0.41
24 8 0.12
25 3 0.05
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (22 bp):
ATATAAAAAATATAAAATATAT
Found at i:2137345 original size:23 final size:24
Alignment explanation
Indices: 2137278--2137354 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 24
2137268 ATTAAAAACC
2137278 ATAT-TATAAAA-ATAAATATAAT
1 ATATATATAAAATATAAATATAAT
*
2137300 ATGAATATAAAAACATATAAA-ATATAT
1 AT--ATATATAAA-ATATAAATATA-AT
2137327 ATATATATAAAATATAAATA-AAT
1 ATATATATAAAATATAAATATAAT
*
2137350 TTATA
1 ATATA
2137355 ATACTTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
22 2 0.04
23 6 0.13
24 10 0.22
25 14 0.31
26 4 0.09
27 9 0.20
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (24 bp):
ATATATATAAAATATAAATATAAT
Found at i:2137349 original size:27 final size:27
Alignment explanation
Indices: 2137287--2137354 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
2137277 CATATTATAA
2137287 AAATAAATATA-ATATGAATATAAAAAC
1 AAATAAATATATATAT-AATATAAAAAC
* *
2137314 ATATAAA-ATATATATATATATAAAATAT
1 AAATAAATATATATATA-ATATAAAA-AC
*
2137342 AAATAAATTTATA
1 AAATAAATATATA
2137355 ATACTTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
26 4 0.12
27 18 0.55
28 7 0.21
29 4 0.12
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (27 bp):
AAATAAATATATATATAATATAAAAAC
Found at i:2138278 original size:2 final size:2
Alignment explanation
Indices: 2138271--2138296 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2138261 TTCAGAAAGA
2138271 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
2138297 GCTCATACTG
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:2138623 original size:29 final size:28
Alignment explanation
Indices: 2138558--2138623 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
2138548 AATTATTAAA
* *
2138558 AATTTATATATTTTTTATAATTAAATTT
1 AATTTAAATATTTTTTATAATTAAATAT
* * *
2138586 AAATAAAATATTTTTTATTATTAAATAAT
1 AATTTAAATATTTTTTATAATTAAAT-AT
2138615 AATTTAAAT
1 AATTTAAAT
2138624 CAAATTAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
28 22 0.73
29 8 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
AATTTAAATATTTTTTATAATTAAATAT
Found at i:2139789 original size:11 final size:12
Alignment explanation
Indices: 2139751--2139797 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
2139741 TGATAATTTT
2139751 AAATATAATAAA
1 AAATATAATAAA
2139763 AAATA-AATAATTA
1 AAATATAATAA--A
2139776 AAATATAA-AAA
1 AAATATAATAAA
2139787 AAATTATAATA
1 AAA-TATAATA
2139798 TATAAAAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
11 9 0.30
12 10 0.33
13 9 0.30
14 2 0.07
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
AAATATAATAAA
Found at i:2139797 original size:17 final size:18
Alignment explanation
Indices: 2139771--2139805 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2139761 AAAAATAAAT
2139771 AATTAAAATATA-AAAAA
1 AATTAAAATATATAAAAA
*
2139788 AATTATAATATATAAAAA
1 AATTAAAATATATAAAAA
2139806 GTAACATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AATTAAAATATATAAAAA
Found at i:2145126 original size:25 final size:25
Alignment explanation
Indices: 2145076--2145126 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
2145066 TGTAATATTT
*
2145076 ATTAAAATAATTTAATTAAATAAAA
1 ATTAAAATAATTTAAATAAATAAAA
2145101 ATTAAAA-AATTTATGAATAAATAAAA
1 ATTAAAATAATTTA--AATAAATAAAA
2145127 CATATATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 6 0.26
25 7 0.30
26 10 0.43
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (25 bp):
ATTAAAATAATTTAAATAAATAAAA
Found at i:2148716 original size:3 final size:3
Alignment explanation
Indices: 2148708--2148736 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2148698 ATTTTATCCA
2148708 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2148737 AACAAATTAC
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2149027 original size:24 final size:24
Alignment explanation
Indices: 2148995--2149040 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
2148985 ATTATTTTTA
2148995 ATAAATTT-AATTTAATTAAAAAT
1 ATAAATTTAAATTTAATTAAAAAT
*
2149018 ATAAATTTTAAATTTTATTAAAA
1 ATAAA-TTTAAATTTAATTAAAA
2149041 TTTATTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 3 0.15
25 12 0.60
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAAATTTAAATTTAATTAAAAAT
Found at i:2149246 original size:22 final size:25
Alignment explanation
Indices: 2149203--2149256 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 25
2149193 TTTATATTTT
**
2149203 TTATA-AAAAACATAATTTATA-TA
1 TTATATAAAAACATAATAAATATTA
2149226 -TATATAAAAAC-TAATAAATATTA
1 TTATATAAAAACATAATAAATATTA
2149249 TTATATAA
1 TTATATAA
2149257 TTAAAAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 11 0.42
23 8 0.31
24 7 0.27
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (25 bp):
TTATATAAAAACATAATAAATATTA
Found at i:2149541 original size:25 final size:27
Alignment explanation
Indices: 2149491--2149545 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 27
2149481 AAAATTGATA
2149491 TTAAAAATAATAATTAACATAATATTTTT
1 TTAAAAATAATAATT-A-ATAATATTTTT
2149520 TTAAAAATAATAATT-A-AATATTTTT
1 TTAAAAATAATAATTAATAATATTTTT
2149545 T
1 T
2149546 AATTGAGAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 10 0.38
26 1 0.04
29 15 0.58
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
TTAAAAATAATAATTAATAATATTTTT
Found at i:2149772 original size:12 final size:12
Alignment explanation
Indices: 2149757--2149801 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
2149747 TGAATAAAAT
*
2149757 TATTGAATATTA
1 TATTAAATATTA
*
2149769 TATTAAATATAA
1 TATTAAATATTA
2149781 TA-TAATATATTA
1 TATTAA-ATATTA
2149793 TATTAAATA
1 TATTAAATA
2149802 ATTTTAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 3 0.11
12 22 0.79
13 3 0.11
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (12 bp):
TATTAAATATTA
Found at i:2158606 original size:2 final size:2
Alignment explanation
Indices: 2158599--2158629 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2158589 TGAAAAGGAA
2158599 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 A
2158630 AAATAAGTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2159980 original size:43 final size:43
Alignment explanation
Indices: 2159919--2160005 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
2159909 GTCTTTTAAG
2159919 ACCATGACATGCAGCTTACTGCTGGTAGTCACCAATGGTCCGC
1 ACCATGACATGCAGCTTACTGCTGGTAGTCACCAATGGTCCGC
*
2159962 ACCATGACATGTAGCTTACTGCTGGTAGTCACCAATGGTCCGC
1 ACCATGACATGCAGCTTACTGCTGGTAGTCACCAATGGTCCGC
2160005 A
1 A
2160006 AACTGCTGTC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (43 bp):
ACCATGACATGCAGCTTACTGCTGGTAGTCACCAATGGTCCGC
Found at i:2160038 original size:104 final size:104
Alignment explanation
Indices: 2159858--2160066 Score: 409
Period size: 104 Copynumber: 2.0 Consensus size: 104
2159848 CTCTTTTAAG
2159858 ACCATGACATGTAGCTTACTGCTGGTAGTCACCAATGGTCCGCAAACTGCTGTCTTTTAAGACCA
1 ACCATGACATGTAGCTTACTGCTGGTAGTCACCAATGGTCCGCAAACTGCTGTCTTTTAAGACCA
*
2159923 TGACATGCAGCTTACTGCTGGTAGTCACCAATGGTCCGC
66 TGACATGCAGCTTACTACTGGTAGTCACCAATGGTCCGC
2159962 ACCATGACATGTAGCTTACTGCTGGTAGTCACCAATGGTCCGCAAACTGCTGTCTTTTAAGACCA
1 ACCATGACATGTAGCTTACTGCTGGTAGTCACCAATGGTCCGCAAACTGCTGTCTTTTAAGACCA
2160027 TGACATGCAGCTTACTACTGGTAGTCACCAATGGTCCGC
66 TGACATGCAGCTTACTACTGGTAGTCACCAATGGTCCGC
2160066 A
1 A
2160067 AACTGCTGCA
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 104 1.00
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.27
Consensus pattern (104 bp):
ACCATGACATGTAGCTTACTGCTGGTAGTCACCAATGGTCCGCAAACTGCTGTCTTTTAAGACCA
TGACATGCAGCTTACTACTGGTAGTCACCAATGGTCCGC
Found at i:2162139 original size:27 final size:26
Alignment explanation
Indices: 2162100--2162237 Score: 86
Period size: 27 Copynumber: 5.0 Consensus size: 26
2162090 TTAAAATTTT
*
2162100 TATATAATA--TAAAAATAATATTAA
1 TATATAATATTTAAAAATAATATAAA
2162124 TATATGAATATTTAAATTTTATATAATATAAA
1 TATAT-AATATTTAAA----A-ATAATATAAA
* *
2162156 T-TATTAATATATTAAAATTTATATAAA
1 TATA-TAATAT-TTAAAAATAATATAAA
*
2162183 TATATAATTATTTAAATATAAT-TATAA
1 TATATAA-TATTTAAAAATAATATA-AA
* * *
2162210 TATATAAAAATATAAATATAATATAAA
1 TATAT-AATATTTAAAAATAATATAAA
2162237 T
1 T
2162238 GCATAATTTT
Statistics
Matches: 91, Mismatches: 8, Indels: 27
0.72 0.06 0.21
Matches are distributed among these distances:
24 5 0.05
25 4 0.04
26 2 0.02
27 46 0.51
28 10 0.11
31 8 0.09
32 16 0.18
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (26 bp):
TATATAATATTTAAAAATAATATAAA
Found at i:2162150 original size:32 final size:32
Alignment explanation
Indices: 2162114--2162193 Score: 99
Period size: 32 Copynumber: 2.4 Consensus size: 32
2162104 TAATATAAAA
*
2162114 ATAATATTAATATATGAATAT-TTAAATTTTAT
1 ATAATATTAAT-TATGAATATATTAAAATTTAT
* *
2162146 ATAATATAAATTATTAATATATTAAAATTTAT
1 ATAATATTAATTATGAATATATTAAAATTTAT
2162178 ATAAATATATAATTAT
1 AT-AATAT-TAATTAT
2162194 TTAAATATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 8 0.20
32 22 0.54
33 5 0.12
34 6 0.15
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (32 bp):
ATAATATTAATTATGAATATATTAAAATTTAT
Found at i:2162157 original size:16 final size:17
Alignment explanation
Indices: 2162136--2162237 Score: 69
Period size: 16 Copynumber: 6.3 Consensus size: 17
2162126 TATGAATATT
2162136 TAAATT-TTATATAATA
1 TAAATTATTATATAATA
2162152 TAAATTATTA-AT-ATA
1 TAAATTATTATATAATA
*
2162167 TTAAAAT-TTATATAAATA
1 -TAAATTATTATAT-AATA
2162185 TATAATTATT-TA-AATA
1 TA-AATTATTATATAATA
*
2162201 T-AATTATAATAT-ATA
1 TAAATTATTATATAATA
* *
2162216 -AAAATATAAATATAATA
1 TAAATTAT-TATATAATA
2162233 TAAAT
1 TAAAT
2162238 GCATAATTTT
Statistics
Matches: 68, Mismatches: 5, Indels: 24
0.70 0.05 0.25
Matches are distributed among these distances:
14 6 0.09
15 16 0.24
16 25 0.37
17 8 0.12
18 11 0.16
19 2 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTATTATATAATA
Found at i:2162195 original size:20 final size:20
Alignment explanation
Indices: 2162172--2162231 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
2162162 ATATATTAAA
*
2162172 ATTTATATA-AATATATAATT
1 ATTTAAATATAAT-TATAATT
2162192 ATTTAAATATAATTATAATAT
1 ATTTAAATATAATTATAAT-T
** *
2162213 ATAAAAATATAAATATAAT
1 ATTTAAATATAATTATAAT
2162232 ATAAATGCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 14 0.41
21 20 0.59
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATTTAAATATAATTATAATT
Found at i:2162518 original size:12 final size:12
Alignment explanation
Indices: 2162482--2162534 Score: 56
Period size: 13 Copynumber: 4.3 Consensus size: 12
2162472 ATTTATTTAT
2162482 TAATTATAAAAA
1 TAATTATAAAAA
*
2162494 TTATATATAAAAA
1 TAAT-TATAAAAA
2162507 TAATTATTAAAAA
1 TAATTA-TAAAAA
2162520 T-A-TATAAAAAA
1 TAATTAT-AAAAA
2162531 TAAT
1 TAAT
2162535 AAAGAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
10 1 0.03
11 8 0.24
12 7 0.21
13 18 0.53
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TAATTATAAAAA
Found at i:2162518 original size:25 final size:24
Alignment explanation
Indices: 2162482--2162534 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
2162472 ATTTATTTAT
*
2162482 TAATTATAAAAATTATATATAAAAA
1 TAATTATAAAAAATATATA-AAAAA
*
2162507 TAATTATTAAAAATATATAAAAAA
1 TAATTATAAAAAATATATAAAAAA
2162531 TAAT
1 TAAT
2162535 AAAGAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 9 0.35
25 17 0.65
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
TAATTATAAAAAATATATAAAAAA
Found at i:2162531 original size:11 final size:11
Alignment explanation
Indices: 2162486--2162537 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
2162476 ATTTATTAAT
*
2162486 TATAAAAATTA
1 TATAAAAAATA
2162497 TATATAAAAATAA
1 TATA-AAAAAT-A
*
2162510 TTATTAAAAATA
1 -TATAAAAAATA
2162522 TATAAAAAATA
1 TATAAAAAATA
2162533 -ATAAA
1 TATAAA
2162538 GAAAAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
10 5 0.14
11 14 0.40
12 6 0.17
13 7 0.20
14 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TATAAAAAATA
Found at i:2162543 original size:25 final size:25
Alignment explanation
Indices: 2162489--2162544 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
2162479 TATTAATTAT
* * *
2162489 AAAAATTATATATAAAAATAATTAT
1 AAAAAATATATATAAAAATAATAAG
*
2162514 TAAAAATATATA-AAAAATAATAAAG
1 AAAAAATATATATAAAAATAAT-AAG
2162539 AAAAAA
1 AAAAAA
2162545 AAAAGGTCAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (25 bp):
AAAAAATATATATAAAAATAATAAG
Found at i:2162905 original size:15 final size:15
Alignment explanation
Indices: 2162871--2162913 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2162861 TTTAAATATT
2162871 AAATAAATATTAATA
1 AAATAAATATTAATA
*
2162886 TAATAAATATT-ATAA
1 AAATAAATATTAAT-A
*
2162901 AAATATATATTAA
1 AAATAAATATTAA
2162914 CTTAAATTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 2 0.09
15 20 0.87
16 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATAAATATTAATA
Found at i:2165056 original size:19 final size:17
Alignment explanation
Indices: 2165015--2165057 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
2165005 TAAATTGATT
*
2165015 TTTTAATAAAAATATTA
1 TTTTAATAAAAATATAA
2165032 TATTTAATTAAATAATATAA
1 T-TTTAA-TAAA-AATATAA
2165052 TTTTAA
1 TTTTAA
2165058 ATATAAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 5 0.23
19 9 0.41
20 7 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTAATAAAAATATAA
Found at i:2168702 original size:17 final size:18
Alignment explanation
Indices: 2168667--2168713 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
2168657 AAGATATTAT
* *
2168667 ATTC-AAATTAAATTTAA
1 ATTCAAAATAAAATTAAA
*
2168684 ATT-AAACTAAAATTAAA
1 ATTCAAAATAAAATTAAA
2168701 ATTCAAAATAAAA
1 ATTCAAAATAAAA
2168714 AAAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (18 bp):
ATTCAAAATAAAATTAAA
Found at i:2172156 original size:13 final size:13
Alignment explanation
Indices: 2172138--2172162 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2172128 AAAAGCTTGA
2172138 GTTTAAAAAGTGT
1 GTTTAAAAAGTGT
2172151 GTTTAAAAAGTG
1 GTTTAAAAAGTG
2172163 ATGAAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (13 bp):
GTTTAAAAAGTGT
Found at i:2172268 original size:24 final size:25
Alignment explanation
Indices: 2172241--2172287 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
2172231 GAAATGTAAA
* *
2172241 AAAAATTTAAA-ATAATGAAATTCT
1 AAAAATGTAAAGATAATAAAATTCT
2172265 AAAAATGTAAAGATAATAAAATT
1 AAAAATGTAAAGATAATAAAATT
2172288 ATTTTATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (25 bp):
AAAAATGTAAAGATAATAAAATTCT
Found at i:2177035 original size:15 final size:16
Alignment explanation
Indices: 2177003--2177044 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
2176993 TTTTTAATTT
*
2177003 AAATTAAT-TTTATCA
1 AAATTAATATTTATAA
2177018 AAATTAATATTTA-AA
1 AAATTAATATTTATAA
*
2177033 AAAATAATATTT
1 AAATTAATATTT
2177045 TTATTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTAATATTTATAA
Found at i:2178938 original size:2 final size:2
Alignment explanation
Indices: 2178931--2178958 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2178921 CATCTTTTAT
2178931 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
2178959 GCTGTTGAGT
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:2179800 original size:18 final size:17
Alignment explanation
Indices: 2179776--2179824 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
2179766 ATAAAACTTG
2179776 ATTTATTTTTTAAATAA
1 ATTTATTTTTTAAATAA
* **
2179793 ATTTTATTTTATATTTAA
1 A-TTTATTTTTTAAATAA
2179811 ATTTATTTTTTAAA
1 ATTTATTTTTTAAA
2179825 CTTAATTTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTTATTTTTTAAATAA
Found at i:2179831 original size:18 final size:18
Alignment explanation
Indices: 2179769--2179832 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
2179759 TTTTAATATA
*
2179769 AAACTTGATTTATTTTTT
1 AAACTTAATTTATTTTTT
* *
2179787 AAA-TAAATTT-TATTTT
1 AAACTTAATTTATTTTTT
* *
2179803 ATATTTAAATTTATTTTTT
1 AAACTT-AATTTATTTTTT
2179822 AAACTTAATTT
1 AAACTTAATTT
2179833 TTTATTCAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
16 7 0.20
17 6 0.17
18 13 0.37
19 9 0.26
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (18 bp):
AAACTTAATTTATTTTTT
Found at i:2179893 original size:33 final size:33
Alignment explanation
Indices: 2179828--2179895 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 33
2179818 TTTTAAACTT
* * *
2179828 AATTTTTTATTCAAATGTTTCAAATATTAAATA
1 AATTTTTAATTCAAATCTTTCAAATATAAAATA
* * *
2179861 AATTTTTAATTCAAATCTTTTAACTCTAAAATA
1 AATTTTTAATTCAAATCTTTCAAATATAAAATA
2179894 AA
1 AA
2179896 ACTAATTATC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.44, C:0.09, G:0.01, T:0.46
Consensus pattern (33 bp):
AATTTTTAATTCAAATCTTTCAAATATAAAATA
Found at i:2186847 original size:16 final size:16
Alignment explanation
Indices: 2186826--2186860 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2186816 TACAAATTTT
2186826 TATGTGTGTATATGTA
1 TATGTGTGTATATGTA
2186842 TATGTGTGTATATGTA
1 TATGTGTGTATATGTA
2186858 TAT
1 TAT
2186861 ATATATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (16 bp):
TATGTGTGTATATGTA
Found at i:2189602 original size:23 final size:25
Alignment explanation
Indices: 2189562--2189612 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
2189552 AAATATAAAA
2189562 TTAAAAAAAAAAATTTATA-ATTTT
1 TTAAAAAAAAAAATTTATACATTTT
* * *
2189586 TTAAAAATAATAA-TTATACCTTTT
1 TTAAAAAAAAAAATTTATACATTTT
2189610 TTA
1 TTA
2189613 CTTCAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (25 bp):
TTAAAAAAAAAAATTTATACATTTT
Found at i:2190838 original size:16 final size:16
Alignment explanation
Indices: 2190804--2190836 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2190794 AGCAAGCTTG
2190804 TTTCTTTTTCTTTTCT
1 TTTCTTTTTCTTTTCT
2190820 TTTCTTTTT-TTTT-T
1 TTTCTTTTTCTTTTCT
2190834 TTT
1 TTT
2190837 TTAATTAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 4 0.24
16 9 0.53
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTCTTTTTCTTTTCT
Found at i:2191942 original size:2 final size:2
Alignment explanation
Indices: 2191931--2191963 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2191921 TGAATGTGAC
2191931 CT CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2191964 ACACAAACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:2191973 original size:6 final size:6
Alignment explanation
Indices: 2191964--2192004 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
2191954 CTCTCTCTCT
* *
2191964 ACACAA ACACAA ACACAA ACACAC ACACAC ACACAA ACACA
1 ACACAA ACACAA ACACAA ACACAA ACACAA ACACAA ACACA
2192005 TATACGTCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.61, C:0.39, G:0.00, T:0.00
Consensus pattern (6 bp):
ACACAA
Found at i:2200111 original size:24 final size:24
Alignment explanation
Indices: 2200070--2200132 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
2200060 CATATTTAGA
* * * *
2200070 TAATTTTATATCTATTTACACATT
1 TAATTTTATATTTATTTAAAAAAT
*
2200094 TAATTTTATATTTTTTTAAAAAAT
1 TAATTTTATATTTATTTAAAAAAT
2200118 TAATTTTGATATTTA
1 TAATTTT-ATATTTA
2200133 ATATTTTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 26 0.81
25 6 0.19
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.57
Consensus pattern (24 bp):
TAATTTTATATTTATTTAAAAAAT
Found at i:2200551 original size:30 final size:30
Alignment explanation
Indices: 2200515--2200586 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 30
2200505 TTATTATATT
*
2200515 TTTATATTTAAATAAAATTTTAATATTTAA
1 TTTATATATAAATAAAATTTTAATATTTAA
* * *
2200545 TTTATATATAAATAAGATTTTATTTTTTAA
1 TTTATATATAAATAAAATTTTAATATTTAA
2200575 TTTA-ATA-AAATA
1 TTTATATATAAATA
2200587 TTTAAAAAGC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 5 0.13
29 3 0.08
30 30 0.79
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (30 bp):
TTTATATATAAATAAAATTTTAATATTTAA
Found at i:2200649 original size:29 final size:29
Alignment explanation
Indices: 2200606--2200694 Score: 103
Period size: 29 Copynumber: 3.1 Consensus size: 29
2200596 CTATAAAAGT
* *
2200606 ATTTATTTTTTAATAAGTTTTTATATTTTT-
1 ATTTATATTTAAATAA-TTTTT-TATTTTTA
2200636 A-TTATATTTAAATAATTTTTTATTTTTA
1 ATTTATATTTAAATAATTTTTTATTTTTA
* *
2200664 ATTTATATTTAAATAA-ATTTTATTTTAA
1 ATTTATATTTAAATAATTTTTTATTTTTA
2200692 ATT
1 ATT
2200695 AAAAATTAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
27 7 0.13
28 19 0.36
29 26 0.49
30 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (29 bp):
ATTTATATTTAAATAATTTTTTATTTTTA
Found at i:2200697 original size:17 final size:17
Alignment explanation
Indices: 2200637--2200693 Score: 54
Period size: 16 Copynumber: 3.7 Consensus size: 17
2200627 TATATTTTTA
2200637 TTATATTTAAAT-AATT
1 TTATATTTAAATAAATT
* *
2200653 TTTTATTT---TTAA-T
1 TTATATTTAAATAAATT
2200666 TTATATTTAAATAAATT
1 TTATATTTAAATAAATT
2200683 TTAT-TTTAAAT
1 TTATATTTAAAT
2200694 TAAAAATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
13 9 0.27
14 2 0.06
16 17 0.52
17 5 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATATTTAAATAAATT
Found at i:2200703 original size:28 final size:29
Alignment explanation
Indices: 2200643--2200705 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
2200633 TTTATTATAT
* * * * *
2200643 TTAAATAATTTTTTATTTTTAATTTATAT
1 TTAAATAATATTTTATTTTAAATTAAAAA
2200672 TTAAATAA-ATTTTATTTTAAATTAAAAA
1 TTAAATAATATTTTATTTTAAATTAAAAA
2200700 TTAAAT
1 TTAAAT
2200706 TTATGTTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 21 0.72
29 8 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
TTAAATAATATTTTATTTTAAATTAAAAA
Found at i:2200723 original size:23 final size:24
Alignment explanation
Indices: 2200668--2200724 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
2200658 TTTTTAATTT
*
2200668 ATATTTAAA-TAAATTTTATTTTA
1 ATATTTAAATTAAATTTTATGTTA
*
2200691 A-ATTAAAAATTAAA-TTTATGTTA
1 ATATT-TAAATTAAATTTTATGTTA
2200714 ATATTTAAATT
1 ATATTTAAATT
2200725 TTATTTGGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 3 0.11
23 18 0.64
24 7 0.25
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
ATATTTAAATTAAATTTTATGTTA
Found at i:2200894 original size:12 final size:12
Alignment explanation
Indices: 2200877--2200921 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
2200867 ATACATGTGA
*
2200877 AAATAAATTAAT
1 AAATAAAATAAT
2200889 AAATAAAAT-AT
1 AAATAAAATAAT
*
2200900 -AA-AAAATATT
1 AAATAAAATAAT
2200910 AAATAAAATAAT
1 AAATAAAATAAT
2200922 TCATAATTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
9 5 0.19
10 3 0.11
11 4 0.15
12 15 0.56
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAATAAAATAAT
Found at i:2203137 original size:6 final size:7
Alignment explanation
Indices: 2203128--2203153 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2203118 ATGTTTTTTG
2203128 TTTTTAT
1 TTTTTAT
2203135 TTTTTAT
1 TTTTTAT
2203142 TTTTTAT
1 TTTTTAT
2203149 TTTTT
1 TTTTT
2203154 TGTTGTATAA
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:2206288 original size:2 final size:2
Alignment explanation
Indices: 2206281--2206308 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2206271 ATTCGTAAAA
2206281 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
2206309 TTCTCCACTA
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:2206339 original size:36 final size:36
Alignment explanation
Indices: 2206292--2206364 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
2206282 TATATATATA
2206292 TATATATATATATATATTTCTCCACTACAACATTGT
1 TATATATATATATATATTTCTCCACTACAACATTGT
2206328 TATATATATATATATATTTCTCCACTACAACATTGT
1 TATATATATATATATATTTCTCCACTACAACATTGT
2206364 T
1 T
2206365 GACATTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.36, C:0.16, G:0.03, T:0.45
Consensus pattern (36 bp):
TATATATATATATATATTTCTCCACTACAACATTGT
Found at i:2207928 original size:42 final size:43
Alignment explanation
Indices: 2207882--2207986 Score: 117
Period size: 45 Copynumber: 2.4 Consensus size: 43
2207872 TTTATATAAT
*
2207882 TATAAAATAATTAATTAAATAATTT-AA-ATT-TTTAAATAAATA
1 TATAAAATAATTTATTAAA-AATTTAAATATTATTTAAA-AAATA
* *
2207924 TATAAAATAATATCTATTAAAATTTTAAATATTATTTAAAATATA
1 TATAAAATAAT-T-TATTAAAAATTTAAATATTATTTAAAAAATA
*
2207969 TAAAAAATAATTTATTAA
1 TATAAAATAATTTATTAA
2207987 TACACTTTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
42 11 0.20
43 11 0.20
44 9 0.17
45 17 0.31
46 6 0.11
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (43 bp):
TATAAAATAATTTATTAAAAATTTAAATATTATTTAAAAAATA
Found at i:2209115 original size:19 final size:19
Alignment explanation
Indices: 2209088--2209183 Score: 59
Period size: 19 Copynumber: 4.8 Consensus size: 19
2209078 CTTTCGAGGG
*
2209088 ATTTCTTTTTTCTTTTTCT
1 ATTTTTTTTTTCTTTTTCT
**
2209107 ATTTTTTTTTAATTTTTCT
1 ATTTTTTTTTTCTTTTTCT
* * *
2209126 TTTTTTTAATTATTATTTTT-A
1 ATTTTTT--TT-TTCTTTTTCT
**
2209147 ATTTCTTTCCTTCTTTTTCTT
1 ATTT-TTTTTTTCTTTTTC-T
*
2209168 CTTTTTTTTTTCTTTT
1 ATTTTTTTTTTCTTTT
2209184 AATTTTGTTA
Statistics
Matches: 57, Mismatches: 14, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
19 29 0.51
20 10 0.18
21 8 0.14
22 10 0.18
ACGTcount: A:0.10, C:0.11, G:0.00, T:0.78
Consensus pattern (19 bp):
ATTTTTTTTTTCTTTTTCT
Found at i:2209144 original size:16 final size:16
Alignment explanation
Indices: 2209109--2209145 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2209099 CTTTTTCTAT
* *
2209109 TTTTTTTTAATTTTTC
1 TTTTTTTTAATTATTA
2209125 TTTTTTTTAATTATTA
1 TTTTTTTTAATTATTA
2209141 TTTTT
1 TTTTT
2209146 AATTTCTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTTTTAATTATTA
Found at i:2211237 original size:2 final size:2
Alignment explanation
Indices: 2211230--2211268 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2211220 TTTCTGTTTC
2211230 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2211269 CGTATATGTT
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:2212268 original size:7 final size:7
Alignment explanation
Indices: 2212244--2212285 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
2212234 GGTGGTTCTC
2212244 AAAAAA-
1 AAAAAAT
*
2212250 AAAAAACC
1 AAAAAA-T
2212258 AAAAAAT
1 AAAAAAT
2212265 AAAAAAT
1 AAAAAAT
2212272 AAAAAAT
1 AAAAAAT
2212279 AAAAAAT
1 AAAAAAT
2212286 TTGCAGGTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
6 6 0.18
7 21 0.64
8 6 0.18
ACGTcount: A:0.86, C:0.05, G:0.00, T:0.10
Consensus pattern (7 bp):
AAAAAAT
Found at i:2213995 original size:21 final size:22
Alignment explanation
Indices: 2213958--2214007 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
2213948 TTTTAAAAAA
* *
2213958 TAAT-ATTTTTATTTATTTT-T
1 TAATAATTTGTATATATTTTAT
2213978 TAATAATTTGTATATATTTTAT
1 TAATAATTTGTATATATTTTAT
2214000 TAA-AATTT
1 TAATAATTT
2214008 TAAATATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 4 0.15
21 18 0.69
22 4 0.15
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TAATAATTTGTATATATTTTAT
Found at i:2215384 original size:39 final size:39
Alignment explanation
Indices: 2215341--2215419 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
2215331 AGGATAATTT
*
2215341 TAATAATATTAATTTATAAATTATTAATGATCAATTTAA
1 TAATAATATTAATTTATAAAGTATTAATGATCAATTTAA
* *
2215380 TAATAATATTAATTTATAAAGTATTAATTATCCATTTAA
1 TAATAATATTAATTTATAAAGTATTAATGATCAATTTAA
2215419 T
1 T
2215420 CGAATCTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (39 bp):
TAATAATATTAATTTATAAAGTATTAATGATCAATTTAA
Found at i:2216694 original size:2 final size:2
Alignment explanation
Indices: 2216687--2216720 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2216677 ACGCTGATTT
2216687 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
2216721 GTAGCGAGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2217041 original size:18 final size:19
Alignment explanation
Indices: 2217017--2217078 Score: 65
Period size: 21 Copynumber: 3.2 Consensus size: 19
2217007 TAACAATTAT
*
2217017 TTTAAAAAATATTTTTTTA
1 TTTAAAAAATATTTTTTAA
*
2217036 -TTAAAAATATATTATTTAAA
1 TTTAAAAA-ATATT-TTTTAA
2217056 TTTAAAAAATTATTTTTT-A
1 TTTAAAAAA-TATTTTTTAA
2217075 TTTA
1 TTTA
2217079 TTATCTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 7 0.19
19 10 0.28
20 8 0.22
21 11 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTAAAAAATATTTTTTAA
Found at i:2227101 original size:22 final size:24
Alignment explanation
Indices: 2227057--2227121 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
2227047 ATATTTGTGA
*
2227057 ATATATAA-TTTTTTATATTTTATT
1 ATAT-TAATTTTTTTATATTATATT
*
2227081 TTATTAATTTTTTTATATTATATT
1 ATATTAATTTTTTTATATTATATT
* *
2227105 ATATTTATTTTTATATA
1 ATATTAATTTTTTTATA
2227122 ATACTCATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 3 0.09
24 32 0.91
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
ATATTAATTTTTTTATATTATATT
Found at i:2227134 original size:22 final size:22
Alignment explanation
Indices: 2227090--2227132 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2227080 TTTATTAATT
* *
2227090 TTTTTATATTATATTATATTTA
1 TTTTTATATAATATCATATTTA
2227112 TTTTTATATAATACTCATATT
1 TTTTTATATAATA-TCATATT
2227133 ATATAATTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTTTATATAATATCATATTTA
Found at i:2227806 original size:19 final size:19
Alignment explanation
Indices: 2227784--2227850 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 19
2227774 ATAATGGTAG
2227784 ATATATGATATAAAATATA
1 ATATATGATATAAAATATA
*
2227803 ATATTATG-TTTAAAA-ATA
1 ATA-TATGATATAAAATATA
* ** *
2227821 ATATATTATATTTAATAAA
1 ATATATGATATAAAATATA
*
2227840 ATATATTATAT
1 ATATATGATAT
2227851 GATATGATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 3 0.08
18 10 0.26
19 22 0.56
20 4 0.10
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
ATATATGATATAAAATATA
Found at i:2227818 original size:20 final size:20
Alignment explanation
Indices: 2227795--2227850 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
2227785 TATATGATAT
*
2227795 AAAATATAATATTATGTTTA
1 AAAATATAATATTATATTTA
2227815 AAAATA-ATATATTATATTTA
1 AAAATATA-ATATTATATTTA
2227835 ATAAA-AT-ATATTATAT
1 A-AAATATAATATTATAT
2227851 GATATGATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
19 10 0.31
20 19 0.59
21 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
AAAATATAATATTATATTTA
Found at i:2227949 original size:19 final size:20
Alignment explanation
Indices: 2227889--2227951 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 20
2227879 TATTTAAAAA
2227889 TATATTTATGTTTAA-AA-TTT
1 TATATTTA--TTTAATAATTTT
2227909 TATATTTATTTAATAATTTT
1 TATATTTATTTAATAATTTT
2227929 TAT-TTTA-TTAATAATTATT
1 TATATTTATTTAATAATT-TT
2227948 TATA
1 TATA
2227952 AAGTTTATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
18 14 0.36
19 11 0.28
20 14 0.36
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TATATTTATTTAATAATTTT
Found at i:2228095 original size:23 final size:22
Alignment explanation
Indices: 2228043--2228095 Score: 52
Period size: 23 Copynumber: 2.4 Consensus size: 22
2228033 TATAAATATT
* *
2228043 AAAATTTTTAATTAATTAAATA
1 AAAATTTTTAAATAATTAAACA
* * *
2228065 ATATTTTTTAAAATAATTATACA
1 AAAATTTTT-AAATAATTAAACA
2228088 AAAATTTT
1 AAAATTTT
2228096 GATACTATTC
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
AAAATTTTTAAATAATTAAACA
Found at i:2228198 original size:3 final size:3
Alignment explanation
Indices: 2228190--2228233 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2228180 TGTAGCCGAG
2228190 AAT AAT 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 AAT AAT AA
2228234 AATGGATGAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2228363 original size:2 final size:2
Alignment explanation
Indices: 2228356--2228397 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2228346 CCCATCTGTA
2228356 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2228398 TATTTCTTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2229866 original size:19 final size:18
Alignment explanation
Indices: 2229834--2229870 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
2229824 CTTTGAAACG
*
2229834 TACAATATATATATATAT
1 TACAATATAGATATATAT
2229852 TACATATATAGATATATAT
1 TACA-ATATAGATATATAT
2229871 GCAATTATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (18 bp):
TACAATATAGATATATAT
Found at i:2230964 original size:29 final size:29
Alignment explanation
Indices: 2230915--2230979 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
2230905 GAAAGTAATC
*
2230915 AATTATATATAGGTAACGAGATCAAAGGT
1 AATTATATATAAGTAACGAGATCAAAGGT
** *
2230944 AATTATATATAAGTATGGAGATTAAAGGT
1 AATTATATATAAGTAACGAGATCAAAGGT
*
2230973 ATTTATA
1 AATTATA
2230980 ATTTAAATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.34
Consensus pattern (29 bp):
AATTATATATAAGTAACGAGATCAAAGGT
Found at i:2231433 original size:17 final size:17
Alignment explanation
Indices: 2231400--2231433 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2231390 TGTCAGTGTC
*
2231400 TTAAAAAAAGTTCAAAA
1 TTAAAAAAAGTTAAAAA
*
2231417 TTAAAAAAATTTAAAAA
1 TTAAAAAAAGTTAAAAA
2231434 AAGAATGAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (17 bp):
TTAAAAAAAGTTAAAAA
Found at i:2231734 original size:12 final size:13
Alignment explanation
Indices: 2231711--2231744 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2231701 ATACTTTCAC
2231711 TAAAAAATTAAAA
1 TAAAAAATTAAAA
*
2231724 TAAAAAATAAAAA
1 TAAAAAATTAAAA
*
2231737 CAAAAAAT
1 TAAAAAAT
2231745 GATTATATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (13 bp):
TAAAAAATTAAAA
Found at i:2232134 original size:26 final size:25
Alignment explanation
Indices: 2232078--2232135 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 25
2232068 AAGGTGATTC
*
2232078 AATAAAATCAAAAGTAATTATATAA
1 AATAAAATCAAAAATAATTATATAA
*
2232103 ATATAACAT-AAAAATAATTATAATATA
1 A-ATAAAATCAAAAATAATTAT-ATA-A
2232130 AATAAA
1 AATAAA
2232136 TTATTAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
25 12 0.44
26 13 0.48
27 2 0.07
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (25 bp):
AATAAAATCAAAAATAATTATATAA
Found at i:2232151 original size:16 final size:16
Alignment explanation
Indices: 2232099--2232146 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
2232089 AAGTAATTAT
*
2232099 ATAAA-TATAACATAA
1 ATAAATTATAATATAA
*
2232114 AAATAATTATAATATAA
1 ATA-AATTATAATATAA
2232131 ATAAATTATTAATATA
1 ATAAATTA-TAATATA
2232147 TTAAAATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 2 0.07
16 7 0.26
17 18 0.67
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAAATTATAATATAA
Found at i:2232153 original size:21 final size:18
Alignment explanation
Indices: 2232099--2232174 Score: 54
Period size: 15 Copynumber: 4.3 Consensus size: 18
2232089 AAGTAATTAT
2232099 ATAAATA-TAACATA-AAA
1 ATAAATATTAA-ATATAAA
*
2232116 ATAATTA-T-AATAT-AA
1 ATAAATATTAAATATAAA
2232131 ATAAATTATTAATATATTAAA
1 ATAAA-TATTAA-ATA-TAAA
* *
2232152 ATATATATTAAATATAAT
1 ATAAATATTAAATATAAA
2232170 ATAAA
1 ATAAA
2232175 CATATAAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
15 9 0.19
16 3 0.06
17 8 0.17
18 8 0.17
19 6 0.13
20 7 0.15
21 6 0.13
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAAATATTAAATATAAA
Found at i:2232174 original size:11 final size:11
Alignment explanation
Indices: 2232097--2232174 Score: 56
Period size: 11 Copynumber: 7.1 Consensus size: 11
2232087 AAAAGTAATT
2232097 ATATAAATATAA
1 ATAT-AATATAA
*
2232109 CATA-AAAATAA
1 -ATATAATATAA
*
2232120 TTATAATATAA
1 ATATAATATAA
*
2232131 ATA-AATTATTA
1 ATATAA-TATAA
*
2232142 ATATATTA-AA
1 ATATAATATAA
2232152 ATAT-ATATTAA
1 ATATAATA-TAA
2232163 ATATAATATAA
1 ATATAATATAA
2232174 A
1 A
2232175 CATATAAATT
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
9 2 0.04
10 9 0.18
11 33 0.65
12 4 0.08
13 3 0.06
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (11 bp):
ATATAATATAA
Found at i:2232193 original size:32 final size:31
Alignment explanation
Indices: 2232094--2232193 Score: 84
Period size: 32 Copynumber: 3.2 Consensus size: 31
2232084 ATCAAAAGTA
*
2232094 ATTATATAAATATAACATAAAA-AT-AATTAT
1 ATTAT-TAAATATAATATAAAATATAAATTAT
* * *
2232124 AATA-TAAATA-AATTATTAATATATTAAAATAT
1 ATTATTAAATATAA-TA-TAAAATA-TAAATTAT
2232156 A-TATTAAATATAATATAAACATATAAATTAT
1 ATTATTAAATATAATATAAA-ATATAAATTAT
2232187 ATTATTA
1 ATTATTA
2232194 TAAGATTGGT
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
27 2 0.04
28 7 0.13
29 4 0.07
30 4 0.07
31 14 0.25
32 22 0.40
33 2 0.04
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (31 bp):
ATTATTAAATATAATATAAAATATAAATTAT
Found at i:2232516 original size:19 final size:18
Alignment explanation
Indices: 2232466--2232517 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
2232456 TTTAATAATT
* *
2232466 TAAATAAAATATAATTAA
1 TAAATATAATATAATTTA
2232484 TAAATATAA-A-AATTTA
1 TAAATATAATATAATTTA
*
2232500 TAATATTTAATATAATTT
1 TAA-ATATAATATAATTT
2232518 TTATTATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 8 0.29
17 6 0.21
18 9 0.32
19 5 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAATATAATATAATTTA
Found at i:2235823 original size:14 final size:15
Alignment explanation
Indices: 2235800--2235834 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
2235790 TTAAATACAA
*
2235800 ATTTAGATAATA-AT
1 ATTTAAATAATAGAT
2235814 ATTTAAATAATAGAT
1 ATTTAAATAATAGAT
2235829 ATTTAA
1 ATTTAA
2235835 TGAATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (15 bp):
ATTTAAATAATAGAT
Found at i:2247170 original size:2 final size:2
Alignment explanation
Indices: 2247163--2247196 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2247153 CTGACAAAGA
2247163 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
2247197 TAACCAGCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2247547 original size:3 final size:3
Alignment explanation
Indices: 2247539--2247578 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2247529 GTTTGTCTTT
2247539 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2247579 GTTAATATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2248833 original size:2 final size:2
Alignment explanation
Indices: 2248826--2248875 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2248816 TCAAATCTTG
2248826 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2248868 AT AT AT AT
1 AT AT AT AT
2248876 GACTTGGTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2249058 original size:2 final size:2
Alignment explanation
Indices: 2249051--2249088 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2249041 CCTCCTCAAT
2249051 TA TA TA TA TA 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 TA TA T
2249089 CATGTTGTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2254039 original size:26 final size:27
Alignment explanation
Indices: 2254009--2254063 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
2253999 TTAACTTAAA
2254009 TTACTATTTA-AAA-AATATTTAAA-AAT
1 TTACT-TTTATAAATAA-ATTTAAATAAT
2254035 TTACTTTTATAAATAAATTTAAATAAT
1 TTACTTTTATAAATAAATTTAAATAAT
2254062 TT
1 TT
2254064 TTTTAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 4 0.15
26 15 0.58
27 7 0.27
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (27 bp):
TTACTTTTATAAATAAATTTAAATAAT
Found at i:2254072 original size:26 final size:25
Alignment explanation
Indices: 2254025--2254077 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 25
2254015 TTTAAAAAAT
2254025 ATTTAAAAATTTACTTTTATAAATAA
1 ATTTAAAAATTTA-TTTTATAAATAA
*
2254051 ATTTAAATAATTT-TTTTAATAATTAA
1 ATTTAAA-AATTTATTTT-ATAAATAA
2254077 A
1 A
2254078 AAGTAATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 4 0.17
26 15 0.62
27 5 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
ATTTAAAAATTTATTTTATAAATAA
Found at i:2256820 original size:24 final size:24
Alignment explanation
Indices: 2256788--2256836 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2256778 GTACAGGGAG
2256788 AAATTTCAAAAATGAAGTCAATTA
1 AAATTTCAAAAATGAAGTCAATTA
2256812 AAATTTCAAAAATGAAGTCAATTA
1 AAATTTCAAAAATGAAGTCAATTA
2256836 A
1 A
2256837 TCTTCTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (24 bp):
AAATTTCAAAAATGAAGTCAATTA
Found at i:2258556 original size:18 final size:17
Alignment explanation
Indices: 2258542--2258593 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 17
2258532 TTTTTTTTTG
2258542 TTTTTAGAATTTTTTTAA
1 TTTTTA-AATTTTTTTAA
2258560 TTTTTAAATTTTTATATATA
1 TTTTTAAATTTTT-T-TA-A
2258580 TTTTT--ATTTTTTTA
1 TTTTTAAATTTTTTTA
2258594 TAATTAAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
16 2 0.06
17 8 0.26
18 13 0.42
19 2 0.06
20 6 0.19
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (17 bp):
TTTTTAAATTTTTTTAA
Found at i:2263617 original size:17 final size:17
Alignment explanation
Indices: 2263595--2263651 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
2263585 GTGTAATAAT
2263595 TATATTTAAAATTTTAA
1 TATATTTAAAATTTTAA
2263612 TATA-TTAATAA--TTAA
1 TATATTTAA-AATTTTAA
2263627 T-T-TTATATAAATTTTAA
1 TATATT-TA-AAATTTTAA
2263644 TATATTTA
1 TATATTTA
2263652 TATATTTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 15
0.68 0.00 0.32
Matches are distributed among these distances:
14 2 0.06
15 9 0.28
16 5 0.16
17 11 0.34
18 3 0.09
19 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATATTTAAAATTTTAA
Found at i:2263644 original size:32 final size:29
Alignment explanation
Indices: 2263588--2263663 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 29
2263578 ATTTTATGTG
2263588 TAATAATTATATTTAAAATTTTAATATAT
1 TAATAATTATATTTAAAATTTTAATATAT
*
2263617 TAATAATTAATTTTATATAAATTTTAATATATT
1 TAATAATT-ATATT-TA-AAATTTTAATATA-T
*
2263650 TATATATTTATATT
1 TA-ATAATTATATT
2263664 ATTTTTTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
29 8 0.21
30 4 0.10
31 2 0.05
32 13 0.33
33 7 0.18
34 5 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
TAATAATTATATTTAAAATTTTAATATAT
Found at i:2263656 original size:10 final size:9
Alignment explanation
Indices: 2263626--2263688 Score: 53
Period size: 10 Copynumber: 6.9 Consensus size: 9
2263616 TTAATAATTA
2263626 ATTTTATAT
1 ATTTTATAT
2263635 AAATTTTA-AT
1 --ATTTTATAT
2263645 ATATTTATAT
1 AT-TTTATAT
2263655 A-TTTATATT
1 ATTTTATA-T
2263664 ATTTT-T-T
1 ATTTTATAT
2263671 ATTTTATTAT
1 ATTTTA-TAT
2263681 ATTTTATA
1 ATTTTATA
2263689 ATTACATTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
7 6 0.13
8 8 0.18
9 10 0.22
10 15 0.33
11 6 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
ATTTTATAT
Found at i:2263659 original size:17 final size:17
Alignment explanation
Indices: 2263637--2263688 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
2263627 TTTTATATAA
2263637 ATTTTAATATA-TTTAT
1 ATTTTAATATATTTTAT
*
2263653 ATATTT-ATATTATTTTTT
1 AT-TTTAATA-TATTTTAT
*
2263671 ATTTTATTATATTTTAT
1 ATTTTAATATATTTTAT
2263688 A
1 A
2263689 ATTACATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
16 5 0.17
17 16 0.55
18 8 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTTAATATATTTTAT
Found at i:2263669 original size:28 final size:26
Alignment explanation
Indices: 2263628--2263689 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 26
2263618 AATAATTAAT
2263628 TTTATATAAATTTTAATATATTTA-TATA
1 TTTATATAAATTTT--TAT-TTTATTATA
* *
2263656 TTTATATTATTTTTTATTTTATTATA
1 TTTATATAAATTTTTATTTTATTATA
2263682 TTT-TATAA
1 TTTATATAA
2263690 TTACATTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 8 0.27
26 10 0.33
28 12 0.40
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTATATAAATTTTTATTTTATTATA
Found at i:2263680 original size:15 final size:16
Alignment explanation
Indices: 2263654--2263687 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2263644 TATATTTATA
*
2263654 TATTTATATTATTTTT
1 TATTTATATTATATTT
2263670 TATTT-TATTATATTT
1 TATTTATATTATATTT
2263685 TAT
1 TAT
2263688 AATTACATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTTATATTATATTT
Found at i:2263802 original size:2 final size:2
Alignment explanation
Indices: 2263795--2263831 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2263785 TTTCCTTTCA
2263795 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
2263832 TTCCACCACT
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:2266978 original size:14 final size:16
Alignment explanation
Indices: 2266963--2266995 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2266953 AATTTTAAAA
2266963 TTAA-ATTTTTATAAT
1 TTAACATTTTTATAAT
2266978 TTAACATTTTTAT-AT
1 TTAACATTTTTATAAT
2266993 TTA
1 TTA
2266996 CATATTAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAACATTTTTATAAT
Found at i:2266988 original size:16 final size:14
Alignment explanation
Indices: 2266912--2266995 Score: 50
Period size: 15 Copynumber: 5.9 Consensus size: 14
2266902 TTTAATATTT
2266912 TTTTTATATTTTATAA
1 TTTTTATA-TTTA-AA
*
2266928 TTATTATATTT--A
1 TTTTTATATTTAAA
2266940 TTTGTT-T-TTTAAAA
1 TTT-TTATATTT-AAA
* * *
2266954 ATTTTAAAATTAAA
1 TTTTTATATTTAAA
2266968 TTTTTATAATTTAACA
1 TTTTTAT-ATTTAA-A
2266984 TTTTTATATTTA
1 TTTTTATATTTA
2266996 CATATTAACA
Statistics
Matches: 52, Mismatches: 8, Indels: 17
0.68 0.10 0.22
Matches are distributed among these distances:
11 3 0.06
12 4 0.08
13 4 0.08
14 11 0.21
15 15 0.29
16 15 0.29
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (14 bp):
TTTTTATATTTAAA
Found at i:2267022 original size:22 final size:22
Alignment explanation
Indices: 2266978--2267022 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2266968 TTTTTATAAT
* * *
2266978 TTAACATTTTTATATTTACATA
1 TTAACATATATATATATACATA
*
2267000 TTAACATATATATATATATATA
1 TTAACATATATATATATACATA
2267022 T
1 T
2267023 ATATATATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (22 bp):
TTAACATATATATATATACATA
Done.