Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, 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: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 55 of 133
Found at i:11334405 original size:23 final size:22
Alignment explanation
Indices: 11334379--11334496 Score: 76
Period size: 23 Copynumber: 5.2 Consensus size: 22
11334369 CTAAAATCCC
11334379 AAAATCTTAAAACTATAAACCTT
1 AAAATCTTAAAACTA-AAACCTT
* *
11334402 AAAATCATAAACCTTAAAACCTT
1 AAAATCTTAAAAC-TAAAACCTT
* * * *
11334425 GAAACCCTAAAACTCAAAACCCT
1 AAAATCTTAAAACT-AAAACCTT
* *
11334448 -AAATCTTTAAACCCTAAAACCTC
1 AAAATC-TTAAA-ACTAAAACCTT
** * *
11334471 AAAATCCCAAAACCAAAATCTT
1 AAAATCTTAAAACTAAAACCTT
11334493 AAAA
1 AAAA
11334497 CCTCAAACCT
Statistics
Matches: 72, Mismatches: 18, Indels: 11
0.71 0.18 0.11
Matches are distributed among these distances:
22 16 0.22
23 47 0.65
24 9 0.12
ACGTcount: A:0.52, C:0.25, G:0.01, T:0.22
Consensus pattern (22 bp):
AAAATCTTAAAACTAAAACCTT
Found at i:11334421 original size:8 final size:8
Alignment explanation
Indices: 11334395--11334527 Score: 64
Period size: 8 Copynumber: 17.4 Consensus size: 8
11334385 TTAAAACTAT
11334395 AAACCTTA
1 AAACCTTA
* *
11334403 AAATCAT-
1 AAACCTTA
11334410 AAACCTTA
1 AAACCTTA
*
11334418 AAACCTTG
1 AAACCTTA
*
11334426 AAACCCTA
1 AAACCTTA
*
11334434 AAA-CTCA
1 AAACCTTA
*
11334441 AAACCCT-
1 AAACCTTA
* *
11334448 AAATCTTT
1 AAACCTTA
*
11334456 AAACCCTA
1 AAACCTTA
*
11334464 AAACCTCA
1 AAACCTTA
*
11334472 AAATCC-CA
1 AAA-CCTTA
11334480 AAACC--A
1 AAACCTTA
*
11334486 AAATCTTA
1 AAACCTTA
*
11334494 AAACC-TC
1 AAACCTTA
11334501 AAACCTTA
1 AAACCTTA
* *
11334509 AAATCTTG
1 AAACCTTA
*
11334517 AAACCCTA
1 AAACCTTA
11334525 AAA
1 AAA
11334528 TGATATCCTA
Statistics
Matches: 91, Mismatches: 27, Indels: 14
0.69 0.20 0.11
Matches are distributed among these distances:
6 5 0.05
7 23 0.25
8 61 0.67
9 2 0.02
ACGTcount: A:0.50, C:0.28, G:0.02, T:0.21
Consensus pattern (8 bp):
AAACCTTA
Found at i:11334510 original size:15 final size:15
Alignment explanation
Indices: 11334288--11334511 Score: 63
Period size: 15 Copynumber: 14.7 Consensus size: 15
11334278 AAAATTCCAA
11334288 AAACC-TAAAACCTC
1 AAACCTTAAAACCTC
* *
11334302 AAAACCTTAAAA-TTGT
1 -AAACCTTAAAACCT-C
*
11334318 AAATCTTAAAACCTC
1 AAACCTTAAAACCTC
** * *
11334333 GAAACC-CCAAATCTT
1 -AAACCTTAAAACCTC
* *
11334348 AACCCTTAAAACCCC
1 AAACCTTAAAACCTC
11334363 GAAAACC-TAAAATCC-C
1 --AAACCTTAAAA-CCTC
* *
11334379 AAAATCTTAAAA-CTAT
1 -AAACCTTAAAACCT-C
*
11334395 AAACCTTAAAATCAT-
1 AAACCTTAAAA-CCTC
*
11334410 AAACCTTAAAACCTTG
1 AAACCTTAAAACC-TC
*
11334426 AAACCCTAAAA-CTC
1 AAACCTTAAAACCTC
* * * *
11334440 AAAACCCTAAATCTTT
1 -AAACCTTAAAACCTC
*
11334456 AAACCCTAAAACCTC
1 AAACCTTAAAACCTC
* *
11334471 AAAATCC-CAAAACC-A
1 -AAA-CCTTAAAACCTC
*
11334486 AAATCTTAAAACCTC
1 AAACCTTAAAACCTC
11334501 AAACCTTAAAA
1 AAACCTTAAAA
11334512 TCTTGAAACC
Statistics
Matches: 152, Mismatches: 36, Indels: 42
0.66 0.16 0.18
Matches are distributed among these distances:
13 1 0.01
14 16 0.11
15 85 0.56
16 41 0.27
17 9 0.06
ACGTcount: A:0.49, C:0.28, G:0.02, T:0.21
Consensus pattern (15 bp):
AAACCTTAAAACCTC
Found at i:11334521 original size:37 final size:38
Alignment explanation
Indices: 11334439--11334513 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 38
11334429 CCCTAAAACT
* *
11334439 CAAAACCCTAAATCTTTAAACCCTAAAACCTCAAAATCC
1 CAAAA-CCAAAATCTTTAAAACCTAAAACCTCAAAATCC
* *
11334478 CAAAACCAAAATC-TTAAAACCTCAAACCTTAAAATC
1 CAAAACCAAAATCTTTAAAACCTAAAACCTCAAAATC
11334514 TTGAAACCCT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 20 0.62
38 7 0.22
39 5 0.16
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (38 bp):
CAAAACCAAAATCTTTAAAACCTAAAACCTCAAAATCC
Found at i:11337038 original size:21 final size:21
Alignment explanation
Indices: 11336990--11337038 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
11336980 TATCTCCTAC
* *
11336990 ATAATATTTTTAATAATAATG
1 ATAATTTTTTTAAAAATAATG
*
11337011 A-ACATTTTTTTAAAAATAATT
1 ATA-ATTTTTTTAAAAATAATG
11337032 ATAATTT
1 ATAATTT
11337039 AAAAAGTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 1 0.04
21 21 0.91
22 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
ATAATTTTTTTAAAAATAATG
Found at i:11340493 original size:12 final size:12
Alignment explanation
Indices: 11340469--11340541 Score: 67
Period size: 12 Copynumber: 5.8 Consensus size: 12
11340459 TTTATATAAA
11340469 AATTAATTT-TTT
1 AATT-ATTTATTT
11340481 AATTATTTATTT
1 AATTATTTATTT
*
11340493 AATTTTTTTATTT
1 AA-TTATTTATTT
*
11340506 ATATATATTTATAT
1 A-AT-TATTTATTT
*
11340520 AATTATATATTT
1 AATTATTTATTT
*
11340532 AAATATTTAT
1 AATTATTTAT
11340542 ATTTAAAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
11 4 0.08
12 24 0.48
13 13 0.26
14 9 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
AATTATTTATTT
Found at i:11340501 original size:21 final size:22
Alignment explanation
Indices: 11340471--11340516 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
11340461 TATATAAAAA
11340471 TTAATTTTTTAATTAT-T-TAT
1 TTAATTTTTTAATTATATATAT
*
11340491 TTAATTTTTTTATTTATATATAT
1 TTAA-TTTTTTAATTATATATAT
11340514 TTA
1 TTA
11340517 TATAATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 4 0.18
21 11 0.50
22 1 0.05
23 6 0.27
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TTAATTTTTTAATTATATATAT
Found at i:11340518 original size:8 final size:8
Alignment explanation
Indices: 11340507--11340543 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
11340497 TTTTTATTTA
11340507 TATATATT
1 TATATATT
*
11340515 TATATAAT
1 TATATATT
11340523 TATATATT
1 TATATATT
*
11340531 TAAATATT
1 TATATATT
11340539 TATAT
1 TATAT
11340544 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TATATATT
Found at i:11340547 original size:14 final size:16
Alignment explanation
Indices: 11340507--11340561 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
11340497 TTTTTATTTA
*
11340507 TATATATTTATATAAT
1 TATATATTTAAATAAT
11340523 TATATATTTAAAT-AT
1 TATATATTTAAATAAT
*
11340538 T-TATATTTAAAAAAT
1 TATATATTTAAATAAT
*
11340553 AATAT-TTTA
1 TATATATTTA
11340562 TTAATTTCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 10 0.29
15 9 0.26
16 15 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATATTTAAATAAT
Found at i:11340964 original size:11 final size:10
Alignment explanation
Indices: 11340916--11340962 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
11340906 ACGAATTGAA
*
11340916 TTATATATTT
1 TTATAAATTT
*
11340926 TTATTAATTT
1 TTATAAATTT
11340936 TTATATAATTT
1 TTATA-AATTT
11340947 TT-TAAATTT
1 TTATAAATTT
11340956 TTATAAA
1 TTATAAA
11340963 ATAAAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 7 0.22
10 18 0.56
11 7 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTATAAATTT
Found at i:11341036 original size:22 final size:21
Alignment explanation
Indices: 11340979--11341036 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
11340969 ATAATTATTT
*
11340979 TATATAT-AAATTTATTTAAA
1 TATATATAAAATTTATTAAAA
*
11340999 TATATTTAAAATTTTATTAAAA
1 TATATATAAAA-TTTATTAAAA
11341021 TAATATATAAAATTTA
1 T-ATATATAAAATTTA
11341037 AAATTAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 6 0.19
21 3 0.09
22 14 0.44
23 9 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TATATATAAAATTTATTAAAA
Found at i:11347016 original size:13 final size:13
Alignment explanation
Indices: 11346998--11347026 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
11346988 AATAAAATTC
11346998 AAAGCAACTCTGA
1 AAAGCAACTCTGA
11347011 AAAGCAACTCTGA
1 AAAGCAACTCTGA
11347024 AAA
1 AAA
11347027 TGAAAAGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.21, G:0.14, T:0.14
Consensus pattern (13 bp):
AAAGCAACTCTGA
Found at i:11349890 original size:17 final size:16
Alignment explanation
Indices: 11349861--11349894 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
11349851 TAGAGAATTG
11349861 AAAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAAC
*
11349877 AAAAAAGAAGAAAAAAC
1 AAAAAA-AAAAAAAAAC
11349894 A
1 A
11349895 GAGAATGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAAC
Found at i:11351121 original size:20 final size:19
Alignment explanation
Indices: 11351083--11351121 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
11351073 AAAAATAAAT
* *
11351083 ATTTCAAATTTTTTAAAAA
1 ATTTCAAATTATCTAAAAA
11351102 ATTTCAAGATTATCTAAAAA
1 ATTTCAA-ATTATCTAAAAA
11351122 TATTAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (19 bp):
ATTTCAAATTATCTAAAAA
Found at i:11351290 original size:35 final size:35
Alignment explanation
Indices: 11351251--11351320 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
11351241 AATTTTCTAA
11351251 ATGTTTTATA-AAATTTTCTATATTTTTGAATTTTT
1 ATGTTTTATAGAAATTTTCTAT-TTTTTGAATTTTT
* * *
11351286 ATGTTTTCTAGAAATTTTTTATTTTTTTAATTTTT
1 ATGTTTTATAGAAATTTTCTATTTTTTGAATTTTT
11351321 CAAAATCCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 21 0.68
36 10 0.32
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.66
Consensus pattern (35 bp):
ATGTTTTATAGAAATTTTCTATTTTTTGAATTTTT
Found at i:11351303 original size:19 final size:18
Alignment explanation
Indices: 11351251--11351314 Score: 53
Period size: 20 Copynumber: 3.5 Consensus size: 18
11351241 AATTTTCTAA
11351251 ATGTTTTATA-AAATTTTCT
1 ATGTTTT-TAGAAATTTT-T
*
11351270 ATATTTTT-G-AATTTTT
1 ATGTTTTTAGAAATTTTT
11351286 ATGTTTTCTAGAAATTTTTT
1 ATGTTTT-TAGAAA-TTTTT
*
11351306 ATTTTTTTA
1 ATGTTTTTA
11351315 ATTTTTCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
16 7 0.19
17 7 0.19
18 2 0.05
19 10 0.27
20 11 0.30
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (18 bp):
ATGTTTTTAGAAATTTTT
Found at i:11353792 original size:14 final size:14
Alignment explanation
Indices: 11353772--11353805 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
11353762 GCAATCATGC
11353772 AATTATG-CAATAA
1 AATTATGCCAATAA
11353785 ATATTATGCCAATAA
1 A-ATTATGCCAATAA
11353800 AATTAT
1 AATTAT
11353806 CATACGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.05
14 11 0.58
15 7 0.37
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (14 bp):
AATTATGCCAATAA
Found at i:11353855 original size:15 final size:16
Alignment explanation
Indices: 11353817--11353852 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
11353807 ATACGATAAT
*
11353817 ATAAAAT-ATCATGTA
1 ATAAAATCATCATGCA
11353832 ATAAAATCATCATGCA
1 ATAAAATCATCATGCA
11353848 ATAAA
1 ATAAA
11353853 TCACACAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.56, C:0.11, G:0.06, T:0.28
Consensus pattern (16 bp):
ATAAAATCATCATGCA
Found at i:11353936 original size:22 final size:20
Alignment explanation
Indices: 11353878--11353941 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
11353868 TGTAATGATA
* *
11353878 TAATTACTACACAAATATAT
1 TAATTACCATACAAATATAT
*
11353898 TAATTACCATGCAAATATAT
1 TAATTACCATACAAATATAT
11353918 TAATTATCC-TAC-AATAATAT
1 TAATTA-CCATACAAAT-ATAT
11353938 TAAT
1 TAAT
11353942 AATCATGCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 3 0.08
20 33 0.87
21 2 0.05
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.38
Consensus pattern (20 bp):
TAATTACCATACAAATATAT
Found at i:11353937 original size:20 final size:20
Alignment explanation
Indices: 11353914--11353955 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
11353904 CCATGCAAAT
* *
11353914 ATATTAATTATCCTACAATA
1 ATATTAATAATCATACAATA
*
11353934 ATATTAATAATCATGCAATA
1 ATATTAATAATCATACAATA
11353954 AT
1 AT
11353956 TACACAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (20 bp):
ATATTAATAATCATACAATA
Found at i:11354035 original size:28 final size:30
Alignment explanation
Indices: 11353963--11354046 Score: 93
Period size: 30 Copynumber: 2.8 Consensus size: 30
11353953 AATTACACAA
* *
11353963 TAAT-ATCATGTAGTCACACATAAATATAT
1 TAATAATCATGTAATCACAAATAAATATAT
*
11353992 TAATAATCATGCAATCACAAATAAATATA-
1 TAATAATCATGTAATCACAAATAAATATAT
*
11354021 T-ATAATCATATAATCATGCAAATAAA
1 TAATAATCATGTAATCA--CAAATAAA
11354047 AATAAGCATG
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
28 13 0.28
29 5 0.11
30 29 0.62
ACGTcount: A:0.51, C:0.13, G:0.05, T:0.31
Consensus pattern (30 bp):
TAATAATCATGTAATCACAAATAAATATAT
Found at i:11354201 original size:15 final size:15
Alignment explanation
Indices: 11354181--11354209 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11354171 AAAAACATGC
11354181 AATCAAGCAAATAAT
1 AATCAAGCAAATAAT
11354196 AATCAAGCAAATAA
1 AATCAAGCAAATAA
11354210 ATAGGATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.14, G:0.07, T:0.17
Consensus pattern (15 bp):
AATCAAGCAAATAAT
Found at i:11354325 original size:14 final size:14
Alignment explanation
Indices: 11354295--11354338 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
11354285 TTCAATCAAT
*
11354295 AATT-AAAATAAAA
1 AATTCAAAACAAAA
11354308 AATTCAAAA-AAAA
1 AATTCAAAACAAAA
11354321 GAATTCAAAACAAAA
1 -AATTCAAAACAAAA
11354336 AAT
1 AAT
11354339 AAACAAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.29
14 16 0.57
15 4 0.14
ACGTcount: A:0.73, C:0.07, G:0.02, T:0.18
Consensus pattern (14 bp):
AATTCAAAACAAAA
Found at i:11360056 original size:113 final size:113
Alignment explanation
Indices: 11359851--11360062 Score: 248
Period size: 113 Copynumber: 1.9 Consensus size: 113
11359841 AGTTGAGTTA
* ** * * * *
11359851 AAAAAAAAGATATTTTAGATTGAAAACCCAAAAATGGCGGTCTGAACAAAAAAAATGATCATTTA
1 AAAAAAAAGAGATTTTAGATTGAAAACAAAAAAAAGGCAGCCTAAACAAAAAAAATGATCATTTA
* * * *
11359916 AGTTGAAAATCCAAAAGGTTAGTTTAAATAAAAAATTAAAAAAATAAG
66 AGGTGAAAATCCAAAACGATAGCTTAAATAAAAAATTAAAAAAATAAG
* *
11359964 AAAAAAAAGACGA-TTTAGATTGAAAACAAAAAAAAGGCAGCCTAAACTAAAAGAATGATCATTT
1 AAAAAAAAGA-GATTTTAGATTGAAAACAAAAAAAAGGCAGCCTAAACAAAAAAAATGATCATTT
* * *
11360028 AAGGTGAAAA-CCTGAAACGATGGCTTAAATGAAAA
65 AAGGTGAAAATCC-AAAACGATAGCTTAAATAAAAA
11360063 TGGAGCTAAA
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
112 2 0.02
113 78 0.96
114 1 0.01
ACGTcount: A:0.54, C:0.09, G:0.15, T:0.21
Consensus pattern (113 bp):
AAAAAAAAGAGATTTTAGATTGAAAACAAAAAAAAGGCAGCCTAAACAAAAAAAATGATCATTTA
AGGTGAAAATCCAAAACGATAGCTTAAATAAAAAATTAAAAAAATAAG
Found at i:11361109 original size:38 final size:38
Alignment explanation
Indices: 11361014--11361150 Score: 127
Period size: 36 Copynumber: 3.7 Consensus size: 38
11361004 TTATGAAACA
*
11361014 TCATGTTCTTTATTTTTTGACTTGTGGAGTTATCCCGG
1 TCATGTTCTTTATTTTTTGACTTGTGGTGTTATCCCGG
* * ***
11361052 TCA--TTCTTTATTTTATGACTTGTGGTGTTGTTTGGG
1 TCATGTTCTTTATTTTTTGACTTGTGGTGTTATCCCGG
* * ** *
11361088 TTATGTTCATTATTTTTTGACTTGTGGTGTT-TTTCGA
1 TCATGTTCTTTATTTTTTGACTTGTGGTGTTATCCCGG
* * *
11361125 TCATGTTTTTTATTTTCTAACTTGTG
1 TCATGTTCTTTATTTTTTGACTTGTG
11361151 ATGATTGTTT
Statistics
Matches: 81, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
36 29 0.36
37 25 0.31
38 27 0.33
ACGTcount: A:0.13, C:0.11, G:0.20, T:0.56
Consensus pattern (38 bp):
TCATGTTCTTTATTTTTTGACTTGTGGTGTTATCCCGG
Found at i:11361199 original size:35 final size:34
Alignment explanation
Indices: 11361159--11361274 Score: 108
Period size: 35 Copynumber: 3.3 Consensus size: 34
11361149 TGATGATTGT
11361159 TTTTTATTTTATGACTTATGGTGTTGTCCCGATCA
1 TTTTTATTTTAT-ACTTATGGTGTTGTCCCGATCA
* ** *
11361194 TTTTTATTTTTTAACTCGTGGTGTTGTCTCGATCA
1 TTTTTATTTTAT-ACTTATGGTGTTGTCCCGATCA
* * * *
11361229 ATTTTATTTTCA-ACTTATGGTTTTATCCCGAACAAA
1 TTTTTATTTT-ATACTTATGGTGTTGTCCCGATC--A
11361265 TTTTTATTTT
1 TTTTTATTTT
11361275 TCGATTTATG
Statistics
Matches: 64, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
34 15 0.23
35 39 0.61
36 10 0.16
ACGTcount: A:0.20, C:0.14, G:0.13, T:0.53
Consensus pattern (34 bp):
TTTTTATTTTATACTTATGGTGTTGTCCCGATCA
Found at i:11361350 original size:11 final size:11
Alignment explanation
Indices: 11361318--11361352 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
11361308 TGATGTTACC
*
11361318 AAAAAAAAAAC
1 AAAAAAAAAAG
11361329 AAAAAAAAAAG
1 AAAAAAAAAAG
*
11361340 AAAGAAAAAAG
1 AAAAAAAAAAG
11361351 AA
1 AA
11361353 CAAAGTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.89, C:0.03, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:11366725 original size:19 final size:20
Alignment explanation
Indices: 11366691--11366734 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
11366681 TTATGTAAAA
*
11366691 TTGACTTTGTTTGACTAATT
1 TTGACTTTGTTTGACTAAGT
*
11366711 TTGATTTTG-TTGACTAAGT
1 TTGACTTTGTTTGACTAAGT
11366730 TTGAC
1 TTGAC
11366735 CAAATTTAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.52
Consensus pattern (20 bp):
TTGACTTTGTTTGACTAAGT
Found at i:11368519 original size:3 final size:3
Alignment explanation
Indices: 11368502--11368545 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
11368492 CATTTCTTAC
11368502 TAT T-T TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
11368546 ATGAAAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 6 0.16
3 32 0.84
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:11370100 original size:112 final size:110
Alignment explanation
Indices: 11369963--11370179 Score: 355
Period size: 112 Copynumber: 1.9 Consensus size: 110
11369953 AGCAAAAATA
*
11369963 AACAACAACAACAATAAAAATAAT-AACATAAGAGGCTATTTAAACATTTATATGACCTAAGGCT
1 AACAACAACAACAATAAAAATAATAAACATAAGAGGCTATTTAAACATTCATATGACCTAAGGCT
*
11370027 ATTTAAGAAAAAAAAAACCTTTCAATTCTTAATAAACATTTATGCAAC
66 ATTT-A-AAAAAAAAAA-CTTTCAATTATTAATAAACATTTATGCAAC
*
11370075 AACAACAACAACAATAATAATAATAACAACATAAGAGGCTATTTAAACATTCATATGACCTAAGG
1 AACAACAACAACAATAAAAATAAT-A-AACATAAGAGGCTATTTAAACATTCATATGACCTAAGG
11370140 CTATTTAAAAAAAAAAACTTTCAATTATTAATAAACATTT
64 CTATTTAAAAAAAAAAACTTTCAATTATTAATAAACATTT
11370180 TTATTAACTT
Statistics
Matches: 99, Mismatches: 3, Indels: 6
0.92 0.03 0.06
Matches are distributed among these distances:
112 45 0.45
113 10 0.10
114 1 0.01
115 43 0.43
ACGTcount: A:0.52, C:0.15, G:0.06, T:0.27
Consensus pattern (110 bp):
AACAACAACAACAATAAAAATAATAAACATAAGAGGCTATTTAAACATTCATATGACCTAAGGCT
ATTTAAAAAAAAAAACTTTCAATTATTAATAAACATTTATGCAAC
Found at i:11370107 original size:115 final size:112
Alignment explanation
Indices: 11369963--11370179 Score: 362
Period size: 115 Copynumber: 1.9 Consensus size: 112
11369953 AGCAAAAATA
* *
11369963 AACAACAACAACAATAAAAATAATAACATAAGAGGCTATTTAAACATTTATATGACCTAAGGCTA
1 AACAACAACAACAATAAAAATAACAACATAAGAGGCTATTTAAACATTCATATGACCTAAGGCTA
*
11370028 TTTAAGAAAAAAAAAACCTTTCAATTCTTAATAAACATTTATGCAACAAC
66 TTT-A-AAAAAAAAAA-CTTTCAATTATTAATAAACATTTATGCAACAAC
* *
11370078 AACAACAACAATAATAATAATAACAACATAAGAGGCTATTTAAACATTCATATGACCTAAGGCTA
1 AACAACAACAACAATAAAAATAACAACATAAGAGGCTATTTAAACATTCATATGACCTAAGGCTA
11370143 TTTAAAAAAAAAAACTTTCAATTATTAATAAACATTT
66 TTTAAAAAAAAAAACTTTCAATTATTAATAAACATTT
11370180 TTATTAACTT
Statistics
Matches: 97, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
112 22 0.23
113 10 0.10
114 1 0.01
115 64 0.66
ACGTcount: A:0.52, C:0.15, G:0.06, T:0.27
Consensus pattern (112 bp):
AACAACAACAACAATAAAAATAACAACATAAGAGGCTATTTAAACATTCATATGACCTAAGGCTA
TTTAAAAAAAAAAACTTTCAATTATTAATAAACATTTATGCAACAAC
Found at i:11372509 original size:13 final size:12
Alignment explanation
Indices: 11372484--11372524 Score: 57
Period size: 13 Copynumber: 3.3 Consensus size: 12
11372474 GTTTCTGAAA
11372484 GTTT-TTTTTTT
1 GTTTATTTTTTT
11372495 GTTTATTTATTTT
1 GTTTATTT-TTTT
11372508 GTTTATTTTGTTT
1 GTTTATTTT-TTT
11372521 GTTT
1 GTTT
11372525 TTGTTTGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.15
12 4 0.15
13 19 0.70
ACGTcount: A:0.07, C:0.00, G:0.12, T:0.80
Consensus pattern (12 bp):
GTTTATTTTTTT
Found at i:11372552 original size:23 final size:23
Alignment explanation
Indices: 11372491--11372553 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
11372481 AAAGTTTTTT
* *
11372491 TTTTGTTTATTTAT-TTTGTTTA
1 TTTTGTTTGTTTATGTTTGTTGA
* *
11372513 TTTTGTTTGTTTTTGTTTGTTGC
1 TTTTGTTTGTTTATGTTTGTTGA
*
11372536 TTTTGTTTGTTCATGTTT
1 TTTTGTTTGTTTATGTTT
11372554 TCATTATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 12 0.35
23 22 0.65
ACGTcount: A:0.06, C:0.03, G:0.16, T:0.75
Consensus pattern (23 bp):
TTTTGTTTGTTTATGTTTGTTGA
Found at i:11372699 original size:45 final size:46
Alignment explanation
Indices: 11372618--11372894 Score: 167
Period size: 46 Copynumber: 6.0 Consensus size: 46
11372608 GACTTGACCA
* * * *
11372618 TTTGAAAATAAATTTAAAAAACTCATTTTAACAAAGGTTTCA-CACT
1 TTTGAAAATAAATTT-AAAAACTCATTTCAACAAAGGCTTAATAACT
* * ***
11372664 TTTGAAAGTAAATTTAAAAACTTATTTCGGTAAAGGCTTAATAACT
1 TTTGAAAATAAATTTAAAAACTCATTTCAACAAAGGCTTAATAACT
* * * ** *
11372710 TTTGAAAATAAATTTAGAAGCTC-TTAT-AAGTAAAAACTCAATAACT
1 TTTGAAAATAAATTTAAAAACTCATT-TCAA-CAAAGGCTTAATAACT
* * * *
11372756 TTTGAAAATAAATTTAAAAGCTCCTTT-AAGCAAAGGCTCAAGAAC-
1 TTTGAAAATAAATTTAAAAACTCATTTCAA-CAAAGGCTTAATAACT
* * * * * *
11372801 TTTCAAAAAAGGAATTTTAAAACTCACTT-AAGTAAAGGCTTAACAAC-
1 TTTGAAAATA--AATTTAAAAACTCATTTCAA-CAAAGGCTTAATAACT
* * *
11372848 TTTAAAAATAAATTTAAAAACTCCTTT-AAGC-AAGGCTTAACAACT
1 TTTGAAAATAAATTTAAAAACTCATTTCAA-CAAAGGCTTAATAACT
11372893 TT
1 TT
11372895 AAAAATCTCA
Statistics
Matches: 186, Mismatches: 38, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
44 13 0.07
45 48 0.26
46 87 0.47
47 38 0.20
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (46 bp):
TTTGAAAATAAATTTAAAAACTCATTTCAACAAAGGCTTAATAACT
Found at i:11372791 original size:92 final size:93
Alignment explanation
Indices: 11372661--11372894 Score: 228
Period size: 92 Copynumber: 2.5 Consensus size: 93
11372651 AAGGTTTCAC
* ** ** * * * *
11372661 ACTTTTGAAAGTAAATTTAAAAACTTATTTCGGTAAAGGCTTAATAACTTTTGAAAATA-AA-TT
1 ACTTTTGAAAATAAATTTAAAAACTCCTTTAAGCAAAGGCTTAACAACTTTTCAAAAAAGAATTT
* * *
11372724 TAGAAGCTC-TTATAAGTAAAAACTCAATA
66 TA-AAACTCACT-TAAGTAAAAACTCAACA
* * *
11372753 ACTTTTGAAAATAAATTTAAAAGCTCCTTTAAGCAAAGGCTCAAGAAC-TTTCAAAAAAGGAATT
1 ACTTTTGAAAATAAATTTAAAAACTCCTTTAAGCAAAGGCTTAACAACTTTTCAAAAAA-GAATT
** *
11372817 TTAAAACTCACTTAAGTAAAGGCTTAACA
65 TTAAAACTCACTTAAGTAAAAACTCAACA
*
11372846 AC-TTTAAAAATAAATTTAAAAACTCCTTTAAGC-AAGGCTTAACAACTTT
1 ACTTTTGAAAATAAATTTAAAAACTCCTTTAAGCAAAGGCTTAACAACTTT
11372895 AAAAATCTCA
Statistics
Matches: 116, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
91 19 0.16
92 70 0.60
93 22 0.19
94 5 0.04
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (93 bp):
ACTTTTGAAAATAAATTTAAAAACTCCTTTAAGCAAAGGCTTAACAACTTTTCAAAAAAGAATTT
TAAAACTCACTTAAGTAAAAACTCAACA
Found at i:11372883 original size:44 final size:44
Alignment explanation
Indices: 11372760--11372900 Score: 169
Period size: 47 Copynumber: 3.1 Consensus size: 44
11372750 ATAACTTTTG
* * *
11372760 AAAATAAATTTAAAAGCTCCTTTAAGCAAAGGCTCAAGAACTTTCA
1 AAAATAAATTTAAAAACTCCTTTAAGC-AAGGCTTAACAACTTT-A
* *
11372806 AAAA-AGGAATTTTAAAACTCAC-TTAAGTAAAGGCTTAACAACTTTA
1 AAAATA--AATTTAAAAACTC-CTTTAAG-CAAGGCTTAACAACTTTA
11372852 AAAATAAATTTAAAAACTCCTTTAAGCAAGGCTTAACAACTTTA
1 AAAATAAATTTAAAAACTCCTTTAAGCAAGGCTTAACAACTTTA
11372896 AAAAT
1 AAAAT
11372901 CTCATCTTGA
Statistics
Matches: 82, Mismatches: 7, Indels: 14
0.80 0.07 0.14
Matches are distributed among these distances:
44 23 0.28
45 18 0.22
46 9 0.11
47 31 0.38
48 1 0.01
ACGTcount: A:0.48, C:0.15, G:0.09, T:0.28
Consensus pattern (44 bp):
AAAATAAATTTAAAAACTCCTTTAAGCAAGGCTTAACAACTTTA
Found at i:11372944 original size:49 final size:50
Alignment explanation
Indices: 11372889--11373105 Score: 226
Period size: 49 Copynumber: 4.4 Consensus size: 50
11372879 AAGGCTTAAC
11372889 AACTTTAAAAATCTCATC-TTGAAAAGCTCCTCATGAATAAAGGCTTTGA
1 AACTTTAAAAATCTCATCTTTGAAAAGCTCCTCATGAATAAAGGCTTTGA
* * * * ** *
11372938 AACTTT-AAAATCTCGTCTTTGTAAAGATCTTTTTGAATAAAGACTTTGA
1 AACTTTAAAAATCTCATCTTTGAAAAGCTCCTCATGAATAAAGGCTTTGA
* ** * * *
11372987 AACTTT-AAAGTCTCATCTTTGAAAAATTCCTCTTGAACAGAGGCTTT-A
1 AACTTTAAAAATCTCATCTTTGAAAAGCTCCTCATGAATAAAGGCTTTGA
* * * *
11373035 AGACTTTAAAAATCTTTATATTTGAAAAGCTCTTCATGAATAAAGGTTTTGA
1 A-ACTTTAAAAATC-TCATCTTTGAAAAGCTCCTCATGAATAAAGGCTTTGA
11373087 AACTTTAAAAACTCTCATC
1 AACTTTAAAAA-TCTCATC
11373106 CTTAATTGGG
Statistics
Matches: 133, Mismatches: 29, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
48 12 0.09
49 73 0.55
50 5 0.04
51 39 0.29
52 4 0.03
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.36
Consensus pattern (50 bp):
AACTTTAAAAATCTCATCTTTGAAAAGCTCCTCATGAATAAAGGCTTTGA
Found at i:11380916 original size:70 final size:70
Alignment explanation
Indices: 11380824--11381031 Score: 272
Period size: 70 Copynumber: 3.0 Consensus size: 70
11380814 AGAGGTATTT
* * * *
11380824 ACTCCATGACAAATTTTAAACACTAGAAATTTTCATTAATTTCGAACAACTTTTCATTACATGAT
1 ACTCTATGACAAATTTCAAACACTAGAAATTTTCATTAATTTCGAATAACTTTTCATTACATGAA
11380889 GCCAC
66 GCCAC
* * *
11380894 ACTCTATGACAAATTTCCAACACTAGAAATTTTCATTAATTTTGAATAATTTTTCATTACATGAA
1 ACTCTATGACAAATTTCAAACACTAGAAATTTTCATTAATTTCGAATAACTTTTCATTACATGAA
* **
11380959 GTCGT
66 GCCAC
* * * * * *
11380964 ACTCTATAATAAATTTCAAACACTGGAACTTTTCATTGATTGCGAATAACTTTTCATTACATGAA
1 ACTCTATGACAAATTTCAAACACTAGAAATTTTCATTAATTTCGAATAACTTTTCATTACATGAA
11381029 GCC
66 GCC
11381032 CATCATTCTA
Statistics
Matches: 118, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
70 118 1.00
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.37
Consensus pattern (70 bp):
ACTCTATGACAAATTTCAAACACTAGAAATTTTCATTAATTTCGAATAACTTTTCATTACATGAA
GCCAC
Found at i:11387791 original size:20 final size:21
Alignment explanation
Indices: 11387766--11387807 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
11387756 CCCTCATTTT
*
11387766 TTTCCTT-TTTCTTTTTAGGC
1 TTTCCTTATTTCATTTTAGGC
*
11387786 TTTCCTTATTTCATTTTGGGC
1 TTTCCTTATTTCATTTTAGGC
11387807 T
1 T
11387808 AACTTTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.07, C:0.19, G:0.12, T:0.62
Consensus pattern (21 bp):
TTTCCTTATTTCATTTTAGGC
Found at i:11388772 original size:15 final size:16
Alignment explanation
Indices: 11388752--11388781 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11388742 TGAAATAATA
11388752 AAAGAAAA-AAAAAAT
1 AAAGAAAATAAAAAAT
11388767 AAAGAAAATAAAAAA
1 AAAGAAAATAAAAAA
11388782 AAACCTGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.87, C:0.00, G:0.07, T:0.07
Consensus pattern (16 bp):
AAAGAAAATAAAAAAT
Found at i:11392251 original size:21 final size:22
Alignment explanation
Indices: 11392225--11392272 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
11392215 ATTTTCTAAT
11392225 TTTTGAATAT-TCA-TGAGAAAA
1 TTTTGAATATATCAGTG-GAAAA
11392246 TTTTGAATATAGTCAGTGGAAAA
1 TTTTGAATATA-TCAGTGGAAAA
11392269 TTTT
1 TTTT
11392273 TCTTCAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.42
23 12 0.50
24 2 0.08
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.42
Consensus pattern (22 bp):
TTTTGAATATATCAGTGGAAAA
Found at i:11392571 original size:12 final size:12
Alignment explanation
Indices: 11392554--11392589 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
11392544 GATTACTTGT
11392554 AAGCGTGTTTAC
1 AAGCGTGTTTAC
11392566 AAGCGTGTTTAC
1 AAGCGTGTTTAC
*
11392578 AATGCATGTTTA
1 AA-GCGTGTTTA
11392590 AATATACAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 14 0.64
13 8 0.36
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (12 bp):
AAGCGTGTTTAC
Found at i:11392997 original size:2 final size:2
Alignment explanation
Indices: 11392990--11393021 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11392980 TTGTTGTTGA
11392990 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
11393022 TGTAATGACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11394630 original size:18 final size:19
Alignment explanation
Indices: 11394597--11394633 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
11394587 TCACTGTGGA
*
11394597 TTTTAATTTTTATATTATT
1 TTTTAATTTATATATTATT
11394616 TTTTAATTTAT-TATTATT
1 TTTTAATTTATATATTATT
11394634 AAGAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTAATTTATATATTATT
Found at i:11404049 original size:72 final size:72
Alignment explanation
Indices: 11403927--11404072 Score: 186
Period size: 72 Copynumber: 2.0 Consensus size: 72
11403917 AAAATCTAAC
* * ** *
11403927 CTATGACTTTGATGGATTCTTAGGTTAATTTAACCAAAGTAATTACTTAAATCCTCAA-TGTAGT
1 CTATAACTTTGATGGATTCTGAAATTAATTTAACCAAAGTAATTACTTAAATCCTCAACT-CAGT
11403991 TAATCGAG
65 TAATCGAG
*** * *
11403999 CTATAACTTTGATGGATTCTGAAATTAATTTAATTTAAGTGATTACTTAAATCTTCAACTCAGTT
1 CTATAACTTTGATGGATTCTGAAATTAATTTAACCAAAGTAATTACTTAAATCCTCAACTCAGTT
11404064 AATCGAG
66 AATCGAG
11404071 CT
1 CT
11404073 CAAATTTTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
72 62 0.98
73 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (72 bp):
CTATAACTTTGATGGATTCTGAAATTAATTTAACCAAAGTAATTACTTAAATCCTCAACTCAGTT
AATCGAG
Found at i:11410469 original size:63 final size:63
Alignment explanation
Indices: 11410363--11410483 Score: 154
Period size: 63 Copynumber: 1.9 Consensus size: 63
11410353 ATATAAAAAA
* * * *
11410363 ATAAAAAAATTATTTAAGGCATTTCTGTATAGAAAATGCCTTAAATAATCATTTTATATGCAC
1 ATAAAAAAATTATTTAAGGCATTTCTCTATACAAAACGCCTTAAACAATCATTTTATATGCAC
* * * *
11410426 ATAAAAAGATTATTTAAGGCGTTT-TCTATACATAAACGTCTTAAACAATCTTTTTATA
1 ATAAAAAAATTATTTAAGGCATTTCTCTATACA-AAACGCCTTAAACAATCATTTTATA
11410484 AATAAATTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
62 6 0.12
63 43 0.88
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (63 bp):
ATAAAAAAATTATTTAAGGCATTTCTCTATACAAAACGCCTTAAACAATCATTTTATATGCAC
Found at i:11411287 original size:18 final size:18
Alignment explanation
Indices: 11411264--11411298 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11411254 CACCAAACTT
11411264 TTTTTATGTTTTTCTTTC
1 TTTTTATGTTTTTCTTTC
*
11411282 TTTTTATTTTTTTCTTT
1 TTTTTATGTTTTTCTTT
11411299 TTTCAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.09, G:0.03, T:0.83
Consensus pattern (18 bp):
TTTTTATGTTTTTCTTTC
Found at i:11421776 original size:25 final size:25
Alignment explanation
Indices: 11421696--11421776 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
11421686 AAAATTTTCA
* *
11421696 GCCTTCATTGCCG-ACTTCTATTTTAG
1 GCCTTCATTGCCGAAC-CCTA-TTAAG
* *
11421722 GCCTTCATTGCCGAACCCTGTTTAG
1 GCCTTCATTGCCGAACCCTATTAAG
* ** *
11421747 ACCTTCATTGTGGAACCTTATTAAG
1 GCCTTCATTGCCGAACCCTATTAAG
11421772 GCCTT
1 GCCTT
11421777 TATAGCCATT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
25 28 0.62
26 15 0.33
27 2 0.04
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (25 bp):
GCCTTCATTGCCGAACCCTATTAAG
Found at i:11425833 original size:9 final size:9
Alignment explanation
Indices: 11425821--11425854 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
11425811 TTACTTTTTT
11425821 TAAAATATA
1 TAAAATATA
11425830 TAAAATATA
1 TAAAATATA
11425839 TTAATAATATA
1 -TAA-AATATA
11425850 TAAAA
1 TAAAA
11425855 AAGATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 11 0.48
10 6 0.26
11 6 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
TAAAATATA
Found at i:11444345 original size:14 final size:14
Alignment explanation
Indices: 11444326--11444353 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11444316 GTCCAGAAAC
11444326 ATAAAAAAAAAAAA
1 ATAAAAAAAAAAAA
11444340 ATAAAAAAAAAAAA
1 ATAAAAAAAAAAAA
11444354 TCCAAGGATA
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:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (14 bp):
ATAAAAAAAAAAAA
Found at i:11444347 original size:13 final size:13
Alignment explanation
Indices: 11444329--11444354 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11444319 CAGAAACATA
11444329 AAAAAAAAAAAAT
1 AAAAAAAAAAAAT
11444342 AAAAAAAAAAAAT
1 AAAAAAAAAAAAT
11444355 CCAAGGATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAAAAAAAAAAT
Found at i:11446069 original size:15 final size:15
Alignment explanation
Indices: 11446049--11446094 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
11446039 AGAATTTTCA
11446049 TTTTTTCCTTTCTTT
1 TTTTTTCCTTTCTTT
11446064 TTTTTTCCTCTT-TTT
1 TTTTTTCCT-TTCTTT
*
11446079 TATTTCTCCTTTCTTT
1 T-TTTTTCCTTTCTTT
11446095 GTCTATCTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTTCCTTTCTTT
Found at i:11447114 original size:26 final size:27
Alignment explanation
Indices: 11447063--11447117 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 27
11447053 AACTTTGTAA
11447063 TTTTTGTCACATTGGTACCTAAAAATTT
1 TTTTTGTCACATTGGTACCT-AAAATTT
11447091 TTTTTGTCACATTGGTACCT-AAATTT
1 TTTTTGTCACATTGGTACCTAAAATTT
11447117 T
1 T
11447118 CAAATCATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 7 0.26
28 20 0.74
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.49
Consensus pattern (27 bp):
TTTTTGTCACATTGGTACCTAAAATTT
Found at i:11453440 original size:17 final size:17
Alignment explanation
Indices: 11453415--11453450 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
11453405 ATAATGGATG
11453415 AAGTAAAAAAAATGAAA
1 AAGTAAAAAAAATGAAA
*
11453432 AAGTGAAAAAAATGAAA
1 AAGTAAAAAAAATGAAA
11453449 AA
1 AA
11453451 AAAATGAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (17 bp):
AAGTAAAAAAAATGAAA
Found at i:11453442 original size:10 final size:9
Alignment explanation
Indices: 11453420--11453452 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
11453410 GGATGAAGTA
11453420 AAAAAAATG
1 AAAAAAATG
*
11453429 -AAAAAGTG
1 AAAAAAATG
11453437 AAAAAAATG
1 AAAAAAATG
11453446 AAAAAAA
1 AAAAAAA
11453453 AATGAGAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (9 bp):
AAAAAAATG
Found at i:11454644 original size:21 final size:21
Alignment explanation
Indices: 11454619--11454720 Score: 78
Period size: 21 Copynumber: 4.7 Consensus size: 21
11454609 TGTTAAAAAT
11454619 AATGAGAATCTTTGAGTTTTA
1 AATGAGAATCTTTGAGTTTTA
* *
11454640 AATGAGAATCTTTAAAAATTTTTA
1 AATGAGAATCTTT---GAGTTTTA
* * * *
11454664 AATAAGATTATTTTAGTTTTA
1 AATGAGAATCTTTGAGTTTTA
* * * *
11454685 AGTGAGAATTTTTTAATTTTA
1 AATGAGAATCTTTGAGTTTTA
*
11454706 AATGAGAATTTTTGA
1 AATGAGAATCTTTGA
11454721 ATGAGAATCT
Statistics
Matches: 64, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
21 48 0.75
24 16 0.25
ACGTcount: A:0.38, C:0.02, G:0.14, T:0.46
Consensus pattern (21 bp):
AATGAGAATCTTTGAGTTTTA
Found at i:11454723 original size:14 final size:14
Alignment explanation
Indices: 11454701--11454761 Score: 70
Period size: 14 Copynumber: 4.4 Consensus size: 14
11454691 AATTTTTTAA
*
11454701 TTTTAAATGAGAAT
1 TTTTGAATGAGAAT
11454715 TTTTGAATGAGAAT
1 TTTTGAATGAGAAT
* *
11454729 CTTTGAATGAGGAT
1 TTTTGAATGAGAAT
*
11454743 CTTTGAAT-ATGAAT
1 TTTTGAATGA-GAAT
11454757 TTTTG
1 TTTTG
11454762 TCTTTGAGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
13 1 0.02
14 40 0.98
ACGTcount: A:0.33, C:0.03, G:0.20, T:0.44
Consensus pattern (14 bp):
TTTTGAATGAGAAT
Found at i:11455114 original size:21 final size:21
Alignment explanation
Indices: 11455090--11455160 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
11455080 AATTTGGATG
11455090 TGAAATTCTCAAATGCGAAAT
1 TGAAATTCTCAAATGCGAAAT
* *
11455111 TGAAAATCTTGCAAAT-CTGAGATT
1 TGAAATTC-T-CAAATGC-GA-AAT
*
11455135 TGAATTTCTCAAATGC-AAATT
1 TGAAATTCTCAAATGCGAAA-T
11455156 TGAAA
1 TGAAA
11455161 ATCTTACGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
20 1 0.03
21 13 0.34
22 7 0.18
23 9 0.24
24 8 0.21
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (21 bp):
TGAAATTCTCAAATGCGAAAT
Found at i:11455371 original size:18 final size:18
Alignment explanation
Indices: 11455348--11455415 Score: 73
Period size: 18 Copynumber: 3.8 Consensus size: 18
11455338 AATCAATTTC
11455348 TTGCGAATCTGAAAATTA
1 TTGCGAATCTGAAAATTA
* *
11455366 TTGCGAATTTGAAAATTT
1 TTGCGAATCTGAAAATTA
* * *
11455384 TTGCAAATTTGAAAATTC
1 TTGCGAATCTGAAAATTA
* *
11455402 TTGTGAAACTGAAA
1 TTGCGAATCTGAAA
11455416 TCTTTTAACG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (18 bp):
TTGCGAATCTGAAAATTA
Found at i:11455415 original size:36 final size:37
Alignment explanation
Indices: 11455342--11455415 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 37
11455332 CATGAGAATC
* **
11455342 AATTTCTTGCGAATCTGAAAATTATTGCGAATTTGAA
1 AATTTCTTGCAAATCTGAAAATTATTGCGAAACTGAA
* * *
11455379 AATTT-TTGCAAATTTGAAAATTCTTGTGAAACTGAA
1 AATTTCTTGCAAATCTGAAAATTATTGCGAAACTGAA
11455415 A
1 A
11455416 TCTTTTAACG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
36 26 0.84
37 5 0.16
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (37 bp):
AATTTCTTGCAAATCTGAAAATTATTGCGAAACTGAA
Found at i:11455723 original size:9 final size:9
Alignment explanation
Indices: 11455709--11455744 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
11455699 GTTTTATCAT
11455709 TTTATTTTA
1 TTTATTTTA
11455718 TTTA-TTTA
1 TTTATTTTA
11455726 TTTATTTTA
1 TTTATTTTA
*
11455735 TTTGTTTTA
1 TTTATTTTA
11455744 T
1 T
11455745 GGTTAGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (9 bp):
TTTATTTTA
Found at i:11458374 original size:30 final size:29
Alignment explanation
Indices: 11458340--11458425 Score: 95
Period size: 29 Copynumber: 2.9 Consensus size: 29
11458330 AAAATTTGAA
11458340 AAAAATTTCATAGAAAATTCTAAAAAATCT
1 AAAAATTT-ATAGAAAATTCTAAAAAATCT
* * *
11458370 AAAAATTTTTAGGAAATTCTAAAAATTCT
1 AAAAATTTATAGAAAATTCTAAAAAATCT
*
11458399 AAAATATTTA-A-ATAATTCTAACAAAAT
1 AAAA-ATTTATAGAAAATTCTAA-AAAAT
11458426 TATAAATAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
28 8 0.17
29 27 0.57
30 12 0.26
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAAATTTATAGAAAATTCTAAAAAATCT
Found at i:11458397 original size:9 final size:9
Alignment explanation
Indices: 11458353--11458615 Score: 102
Period size: 9 Copynumber: 27.4 Consensus size: 9
11458343 AATTTCATAG
11458353 AAAATTCTA
1 AAAATTCTA
*
11458362 AAAAATCTA
1 AAAATTCTA
*
11458371 AAAATTTTTA
1 AAAA-TTCTA
*
11458381 GGAAATTCTA
1 -AAAATTCTA
11458391 AAAATTCTA
1 AAAATTCTA
11458400 AAATATT-TA
1 AAA-ATTCTA
11458409 AATAATTCTAA
1 AA-AATTCT-A
*
11458420 CAAAATTATA
1 -AAAATTCTA
11458430 AATAATT-TA
1 AA-AATTCTA
*
11458439 AATAATTTTTTA
1 AA-AA--TTCTA
*
11458451 AAAATTCAAA
1 AAAATTC-TA
* *
11458461 AAAAAT-AA
1 AAAATTCTA
* *
11458469 AAAACTCAA
1 AAAATTCTA
*
11458478 AAAATTTTAA
1 AAAATTCT-A
11458488 AAAATTCTA
1 AAAATTCTA
** *
11458497 AACTTTTTGA
1 AAAATTCT-A
** *
11458507 AATTTTTTTA
1 AA-AATTCTA
11458517 AAAATTCTA
1 AAAATTCTA
*
11458526 AAAATTTTA
1 AAAATTCTA
11458535 AAAATTTCTAA
1 AAAA-TTCT-A
11458546 AAAATT-TGA
1 AAAATTCT-A
*
11458555 AAAACTTCAA
1 AAAA-TTCTA
*
11458565 AAAATTTTA
1 AAAATTCTA
* *
11458574 AATACTTGTA
1 AA-AATTCTA
*
11458584 AAAATTCAA
1 AAAATTCTA
11458593 AATAATTCTA
1 AA-AATTCTA
*
11458603 AAAATTATA
1 AAAATTCTA
11458612 AAAA
1 AAAA
11458616 ATAAAAAAGA
Statistics
Matches: 197, Mismatches: 35, Indels: 44
0.71 0.13 0.16
Matches are distributed among these distances:
8 7 0.04
9 97 0.49
10 64 0.32
11 23 0.12
12 6 0.03
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (9 bp):
AAAATTCTA
Found at i:11458489 original size:10 final size:10
Alignment explanation
Indices: 11458328--11458725 Score: 81
Period size: 10 Copynumber: 40.2 Consensus size: 10
11458318 CATATTTAAC
*
11458328 AAAAAATTTGA
1 AAAAAATTT-T
11458339 AAAAAATTTCAT
1 AAAAAATTT--T
* *
11458351 AGAAAATTCT
1 AAAAAATTTT
*
11458361 AAAAAA-TCT
1 AAAAAATTTT
*
11458370 AAAAATTTTT
1 AAAAAATTTT
** *
11458380 AGGAAATTCT
1 AAAAAATTTT
*
11458390 -AAAAATTCT
1 AAAAAATTTT
*
11458399 AAAATA-TTT
1 AAAAAATTTT
* *
11458408 AAATAATTCT
1 AAAAAATTTT
*
11458418 AACAAAATTAT
1 AA-AAAATTTT
*
11458429 AAATAA-TTT
1 AAAAAATTTT
*
11458438 AAATAATTTTT
1 AAA-AAATTTT
* *
11458449 TAAAAA-TTC
1 AAAAAATTTT
**
11458458 AAAAAA-AAT
1 AAAAAATTTT
* *
11458467 AAAAAA-CTC
1 AAAAAATTTT
11458476 AAAAAATTTT
1 AAAAAATTTT
*
11458486 AAAAAATTCT
1 AAAAAATTTT
**
11458496 -AAACTTTTT
1 AAAAAATTTT
* **
11458505 GAAATTTTTT
1 AAAAAATTTT
* *
11458515 TAAAAATTCT
1 AAAAAATTTT
11458525 -AAAAATTTT
1 AAAAAATTTT
11458534 -AAAAATTTCT
1 AAAAAATTT-T
11458544 AAAAAA-TTT
1 AAAAAATTTT
* * *
11458553 GAAAAACTTC
1 AAAAAATTTT
11458563 AAAAAATTTT
1 AAAAAATTTT
* * *
11458573 AAATACTTGT
1 AAAAAATTTT
*
11458583 -AAAAA-TTC
1 AAAAAATTTT
*
11458591 AAAATAATTCT
1 AAAA-AATTTT
*
11458602 -AAAAATTAT
1 AAAAAATTTT
**
11458611 AAAAAA-TAA
1 AAAAAATTTT
11458620 AAAAGAATTTTT
1 AAAA-AA-TTTT
* *
11458632 TAAAATTTTT
1 AAAAAATTTT
** * * * *
11458642 TTATAGTATG
1 AAAAAATTTT
* *
11458652 CAAAATTTTT
1 AAAAAATTTT
*
11458662 TAAAAATTTAT
1 AAAAAATTT-T
*
11458673 CAAAAATTTT
1 AAAAAATTTT
* *
11458683 -GAAAATTCT
1 AAAAAATTTT
*
11458692 AAACAATTTT
1 AAAAAATTTT
11458702 AAAAAATTATT
1 AAAAAATT-TT
11458713 AAAAAAATTTT
1 -AAAAAATTTT
11458724 AA
1 AA
11458726 TGTATAAAAA
Statistics
Matches: 278, Mismatches: 86, Indels: 47
0.68 0.21 0.11
Matches are distributed among these distances:
8 1 0.00
9 97 0.35
10 119 0.43
11 42 0.15
12 19 0.07
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.37
Consensus pattern (10 bp):
AAAAAATTTT
Found at i:11458514 original size:29 final size:29
Alignment explanation
Indices: 11458476--11458589 Score: 95
Period size: 29 Copynumber: 3.9 Consensus size: 29
11458466 TAAAAAACTC
* **
11458476 AAAAAATTTTAAAAAATTCTAAACTTTTT
1 AAAAATTTTTAAAAAATTCTAAAAATTTT
* * *
11458505 GAAATTTTTTTAAAAATTCTAAAAATTTT
1 AAAAATTTTTAAAAAATTCTAAAAATTTT
* * *
11458534 AAAAATTTCTAAAAAATT-TGAAAAACTTC
1 AAAAATTTTTAAAAAATTCT-AAAAATTTT
* * * *
11458563 AAAAAATTTTAAATACTTGTAAAAATT
1 AAAAATTTTTAAAAAATTCTAAAAATT
11458590 CAAAATAATT
Statistics
Matches: 66, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
28 1 0.02
29 64 0.97
30 1 0.02
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (29 bp):
AAAAATTTTTAAAAAATTCTAAAAATTTT
Found at i:11458538 original size:19 final size:19
Alignment explanation
Indices: 11458511--11458617 Score: 99
Period size: 19 Copynumber: 5.6 Consensus size: 19
11458501 TTTTGAAATT
*
11458511 TTTTTAAAAATTCTAAAAA
1 TTTTAAAAAATTCTAAAAA
*
11458530 TTTTAAAAATTTCTAAAAAA
1 TTTTAAAAAATTCT-AAAAA
* * *
11458550 TTTGAAAAACTTCAAAAAA
1 TTTTAAAAAATTCTAAAAA
* * *
11458569 TTTTAAATACTTGTAAAAA
1 TTTTAAAAAATTCTAAAAA
*
11458588 -TTCAAAATAATTCTAAAAA
1 TTTTAAAA-AATTCTAAAAA
*
11458607 TTATAAAAAAT
1 TTTTAAAAAAT
11458618 AAAAAAGAAT
Statistics
Matches: 70, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
18 5 0.07
19 44 0.63
20 21 0.30
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (19 bp):
TTTTAAAAAATTCTAAAAA
Found at i:11458615 original size:29 final size:27
Alignment explanation
Indices: 11458515--11458623 Score: 64
Period size: 29 Copynumber: 3.9 Consensus size: 27
11458505 GAAATTTTTT
* *
11458515 TAAAAATTCTAAAAATTTTAAAAATTTC
1 TAAAAATT-TAAAAATTATAAAAAATTC
* *
11458543 TAAAAAATTTGAAAAACTT-CAAAAAATTT
1 T-AAAAATTT-AAAAA-TTATAAAAAATTC
* *
11458572 TAAATACTTGTAAAAATTCA-AAATAATTC
1 TAAA-AATT-TAAAAATT-ATAAAAAATTC
11458601 TAAAAATTATAAAAA--ATAAAAAA
1 TAAAAATT-TAAAAATTATAAAAAA
11458624 GAATTTTTTA
Statistics
Matches: 64, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
25 1 0.02
26 5 0.08
28 16 0.25
29 39 0.61
30 3 0.05
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (27 bp):
TAAAAATTTAAAAATTATAAAAAATTC
Found at i:11459227 original size:35 final size:35
Alignment explanation
Indices: 11459123--11459277 Score: 108
Period size: 35 Copynumber: 4.6 Consensus size: 35
11459113 GCTAAACTAA
** * *
11459123 GCTTAAATC-TTTCATAATATGTCACA-AAACTGG
1 GCTTAAATCTTTTCATAAGGTGCCAAATAAACTGG
* * * **
11459156 GCTTAAAT-TCTTTCATTAGGTACTAGCTAAACTGG
1 GCTTAAATCT-TTTCATAAGGTGCCAAATAAACTGG
*
11459191 GCTTAAATCTTTTCATAAGGTGCCAAATAAATTGG
1 GCTTAAATCTTTTCATAAGGTGCCAAATAAACTGG
* * * *
11459226 GCTT--A-GTTTTCAT-TGGTGCCAATTAAACTAG
1 GCTTAAATCTTTTCATAAGGTGCCAAATAAACTGG
*
11459257 GCTTAAATTTTTTCATGAAGG
1 GCTTAAATCTTTTCAT-AAGG
11459278 CCAGCTAAAT
Statistics
Matches: 92, Mismatches: 21, Indels: 15
0.72 0.16 0.12
Matches are distributed among these distances:
31 18 0.20
32 7 0.08
33 10 0.11
34 16 0.17
35 38 0.41
36 3 0.03
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (35 bp):
GCTTAAATCTTTTCATAAGGTGCCAAATAAACTGG
Found at i:11459247 original size:31 final size:32
Alignment explanation
Indices: 11459200--11459261 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
11459190 GGCTTAAATC
* *
11459200 TTTTCATAAGGTGCCAAATAAATTGGGCTTAG
1 TTTTCATAAGGTGCCAAATAAACTAGGCTTAG
* *
11459232 TTTTCAT-TGGTGCCAATTAAACTAGGCTTA
1 TTTTCATAAGGTGCCAAATAAACTAGGCTTA
11459262 AATTTTTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 19 0.73
32 7 0.27
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (32 bp):
TTTTCATAAGGTGCCAAATAAACTAGGCTTAG
Found at i:11459559 original size:33 final size:34
Alignment explanation
Indices: 11459108--11459562 Score: 151
Period size: 33 Copynumber: 13.6 Consensus size: 34
11459098 AAAATCTGGC
* * **
11459108 TGCCAGCTAAACTAAGCTTAAATCTTTCATAATA
1 TGCCAGCTAAACTAGGCTTAAATCTTTCATTAGG
* * *
11459142 TGTCA-CAAAACTGGGCTTAAATTCTTTCATTAGG
1 TGCCAGCTAAACTAGGCTTAAA-TCTTTCATTAGG
* * * *
11459176 TACTAGCTAAACTGGGCTTAAATCTTTTCATAAGG
1 TGCCAGCTAAACTAGGCTTAAATC-TTTCATTAGG
** * * *
11459211 TGCCAAATAAATTGGGCTT-AGT-TTTCATT-GG
1 TGCCAGCTAAACTAGGCTTAAATCTTTCATTAGG
** * * *
11459242 TGCCAATTAAACTAGGCTTAAATTTTTTCATGAAG
1 TGCCAGCTAAACTAGGCTTAAA-TCTTTCATTAGG
* * ** *
11459277 -GCCAGCTAAATTGGGCTTATCTCTTTTCATTCATG
1 TGCCAGCTAAACTAGGCTTAAATC-TTTCATT-AGG
* * * * * *
11459312 T-CAATC-AAACT-GGATTTACATCTTTCATGAAG
1 TGCCAGCTAAACTAGG-CTTAAATCTTTCATTAGG
* * * * * *
11459344 T--TAGCCAAACATAGGTTTAATTCATTCATT-GA
1 TGCCAGCTAAAC-TAGGCTTAAATCTTTCATTAGG
* * *
11459376 TGCTAG-TCAAACTGAGTC-TAAAT-TTTTATT-GG
1 TGCCAGCT-AAACT-AGGCTTAAATCTTTCATTAGG
* * * *
11459408 TGCAAGTTAAACTAGGTTTAAATCTTTTCATAAGG
1 TGCCAGCTAAACTAGGCTTAAATC-TTTCATTAGG
* *
11459443 TGCCAGATAAACT-GGACTT-AATTTTTCATT-GG
1 TGCCAGCTAAACTAGG-CTTAAATCTTTCATTAGG
** * **
11459475 TATCAACTAAGTTAGGCTTAAAT-TTTCACTTA-G
1 TGCCAGCTAAACTAGGCTTAAATCTTTCA-TTAGG
* *
11459508 TGCCAGCTAAAATGGGCTTAAATCTTT-ATTAGG
1 TGCCAGCTAAACTAGGCTTAAATCTTTCATTAGG
* *
11459541 TGCCAGTTAAGCTAGGCTTAAA
1 TGCCAGCTAAACTAGGCTTAAA
11459563 ACTTCGTTGG
Statistics
Matches: 308, Mismatches: 83, Indels: 61
0.68 0.18 0.13
Matches are distributed among these distances:
31 22 0.07
32 56 0.18
33 92 0.30
34 79 0.26
35 59 0.19
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (34 bp):
TGCCAGCTAAACTAGGCTTAAATCTTTCATTAGG
Found at i:11459849 original size:66 final size:68
Alignment explanation
Indices: 11459779--11459928 Score: 155
Period size: 65 Copynumber: 2.3 Consensus size: 68
11459769 AGTGCAAACC
* *
11459779 AAACTGGGCTAAAATTTTTC-CTGTTGCTAGCCAAATTAGGCTTAAATCTTTTTATAAG-TACCA
1 AAACTGGGCTAAAATTTTTCACTGATGCCAGCCAAATTAGGCTTAAATCTTTTTATAAGATACCA
11459842 AAT
66 AAT
** * * * * * * **
11459845 AAACTGGG-TTTAA-TTTTCATTGATGCCAGCTAAATTGGGCTTGAATTTTTTTTTAAGATGTCA
1 AAACTGGGCTAAAATTTTTCACTGATGCCAGCCAAATTAGGCTTAAATCTTTTTATAAGATACCA
11459908 AAT
66 AAT
*
11459911 AAATTGGGCTAAAATTTT
1 AAACTGGGCTAAAATTTT
11459929 CAATGGGTGC
Statistics
Matches: 65, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
64 5 0.08
65 33 0.51
66 21 0.32
67 3 0.05
68 3 0.05
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (68 bp):
AAACTGGGCTAAAATTTTTCACTGATGCCAGCCAAATTAGGCTTAAATCTTTTTATAAGATACCA
AAT
Found at i:11460848 original size:20 final size:19
Alignment explanation
Indices: 11460825--11460872 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
11460815 TTTTCCTTTG
*
11460825 TTTTTCTTCATTCTT-TCATT
1 TTTTTCTTC-TT-TTATCACT
11460845 TTTTTCTCTCTTTTATCACT
1 TTTTTCT-TCTTTTATCACT
11460865 TTTTTCTT
1 TTTTTCTT
11460873 TTGCATTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 3 0.12
20 20 0.80
21 2 0.08
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTTCTTCTTTTATCACT
Found at i:11460848 original size:43 final size:44
Alignment explanation
Indices: 11460801--11460899 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 44
11460791 TTCATTTCTT
11460801 TTTTTTTTTTCTCTTTT-TC-CTTTGTTT-TTCTT-CATTCTTTCA
1 TTTTTTTTTTCTCTTTTATCACTTT-TTTCTT-TTGCATTCTTTCA
* *
11460843 -TTTTTTTCTCTCTTTTATCACTTTTTTCTTTTGCATTGTTTCA
1 TTTTTTTTTTCTCTTTTATCACTTTTTTCTTTTGCATTCTTTCA
*
11460886 CTTTTTCTTTTCTC
1 -TTTTTTTTTTCTC
11460900 GGAGTGGATT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
41 15 0.32
42 7 0.15
43 15 0.32
45 10 0.21
ACGTcount: A:0.06, C:0.20, G:0.03, T:0.71
Consensus pattern (44 bp):
TTTTTTTTTTCTCTTTTATCACTTTTTTCTTTTGCATTCTTTCA
Found at i:11464684 original size:15 final size:16
Alignment explanation
Indices: 11464656--11464688 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
11464646 TCATAGACAT
11464656 TTTTTCGTTCTCTATC
1 TTTTTCGTTCTCTATC
*
11464672 TTTTTC-TTTTCTATC
1 TTTTTCGTTCTCTATC
11464687 TT
1 TT
11464689 GAACTTTCGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.06, C:0.21, G:0.03, T:0.70
Consensus pattern (16 bp):
TTTTTCGTTCTCTATC
Found at i:11467923 original size:13 final size:13
Alignment explanation
Indices: 11467905--11467962 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
11467895 ATTTTGCCTT
11467905 GGGTTTCACTTTA
1 GGGTTTCACTTTA
**
11467918 GGGTTT-TGTGTTA
1 GGGTTTCACT-TTA
*
11467931 GAGTTTCACTTTA
1 GGGTTTCACTTTA
*
11467944 GGGTTTCATTTTA
1 GGGTTTCACTTTA
11467957 GGGTTT
1 GGGTTT
11467963 TACTCTAAAG
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
12 1 0.03
13 34 0.94
14 1 0.03
ACGTcount: A:0.14, C:0.09, G:0.28, T:0.50
Consensus pattern (13 bp):
GGGTTTCACTTTA
Found at i:11467924 original size:25 final size:26
Alignment explanation
Indices: 11467896--11467949 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
11467886 GGATTTAGAA
*
11467896 TTTTGCCTT-GGGTTTCACTTTAGGG
1 TTTTGCCTTAGAGTTTCACTTTAGGG
**
11467921 TTTTGTGTTAGAGTTTCACTTTAGGG
1 TTTTGCCTTAGAGTTTCACTTTAGGG
11467947 TTT
1 TTT
11467950 CATTTTAGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.11, C:0.11, G:0.26, T:0.52
Consensus pattern (26 bp):
TTTTGCCTTAGAGTTTCACTTTAGGG
Found at i:11467942 original size:26 final size:26
Alignment explanation
Indices: 11467907--11468001 Score: 102
Period size: 26 Copynumber: 3.7 Consensus size: 26
11467897 TTTGCCTTGG
*
11467907 GTTTCACTTTAGGGTTTTGTGTTAGA
1 GTTTCACTTTAGGGTTTTGTATTAGA
** * *
11467933 GTTTCACTTTAGGGTTTCATTTTAGG
1 GTTTCACTTTAGGGTTTTGTATTAGA
* * **
11467959 GTTTTACTCTAAAGTTTTGTATTAGA
1 GTTTCACTTTAGGGTTTTGTATTAGA
11467985 GTTTCAC-TTAGGGTTTT
1 GTTTCACTTTAGGGTTTT
11468002 AGGATTGACC
Statistics
Matches: 53, Mismatches: 16, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
25 7 0.13
26 46 0.87
ACGTcount: A:0.18, C:0.09, G:0.22, T:0.51
Consensus pattern (26 bp):
GTTTCACTTTAGGGTTTTGTATTAGA
Found at i:11468211 original size:28 final size:27
Alignment explanation
Indices: 11468169--11468222 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
11468159 TCATTAAAAA
*
11468169 TTTTATTATTATTATGATTTATTAATC
1 TTTTATTATTATTATGATTTAATAATC
* *
11468196 TTTTATTATTTTTTATTATTTAATAAT
1 TTTTATTA-TTATTATGATTTAATAAT
11468223 TCCCTAAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (27 bp):
TTTTATTATTATTATGATTTAATAATC
Found at i:11470195 original size:20 final size:20
Alignment explanation
Indices: 11470148--11470214 Score: 68
Period size: 19 Copynumber: 3.3 Consensus size: 20
11470138 AAAATTTTTA
11470148 TTTTATATATTATA-TTATT
1 TTTTATATATTATATTTATT
11470167 ATTCATTATATATTATATTTATT
1 -TT--TTATATATTATATTTATT
*
11470190 TTTTAT-TACTAT-TATTATT
1 TTTTATATATTATAT-TTATT
11470209 TTTTAT
1 TTTTAT
11470215 TTGTTTTTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
18 1 0.02
19 16 0.38
20 6 0.14
22 14 0.33
23 5 0.12
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTATATATTATATTTATT
Found at i:11470202 original size:22 final size:20
Alignment explanation
Indices: 11470148--11470215 Score: 63
Period size: 22 Copynumber: 3.4 Consensus size: 20
11470138 AAAATTTTTA
11470148 TTTTA-TATATTATATTATT
1 TTTTATTATATTATATTATT
11470167 ATTCATTA-TATATTATATTTATT
1 -TT--TTATTATATTATA-TTATT
11470190 TTTTATTACTA-T-TATTATT
1 TTTTATTA-TATTATATTATT
11470209 TTTTATT
1 TTTTATT
11470216 TGTTTTTTCG
Statistics
Matches: 43, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
19 12 0.28
20 7 0.16
21 3 0.07
22 16 0.37
23 5 0.12
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTATTATATTATATTATT
Found at i:11487213 original size:34 final size:34
Alignment explanation
Indices: 11487165--11487229 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
11487155 CATGTTTCTA
*
11487165 TAATTTTTGTTAGGACGTGATGATTGAACCTCAC
1 TAATATTTGTTAGGACGTGATGATTGAACCTCAC
*
11487199 TAATATTTGTTAGGATGTGATGATTGAACCT
1 TAATATTTGTTAGGACGTGATGATTGAACCT
11487230 TACTGCTCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.40
Consensus pattern (34 bp):
TAATATTTGTTAGGACGTGATGATTGAACCTCAC
Found at i:11496046 original size:61 final size:59
Alignment explanation
Indices: 11495789--11496140 Score: 355
Period size: 61 Copynumber: 5.9 Consensus size: 59
11495779 TTATATAAGA
** **
11495789 AAAATTGATACTTTCAACTTTTCCTT-AAA-GCA--TTTT-AAGGTTTTATTTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTTAAAATATATTTTTTGAAAATTTTA-TTTTCAAGG
* *
11495844 AAAATTGATA-TCTTCAACTTTTCCTTAAAAATAATTTTTTTTTGAAAATTTTATTTTTAAGG
1 AAAATTGATACT-TTCAACTTTTCCTT-AAAAT-A-TATTTTTTGAAAATTTTATTTTCAAGG
* * *
11495906 AAAATT-AGTACTTTCAACTTTTTCTCAGAA-ATATTTTTT-AACAATTTTATTTTCAAGG
1 AAAATTGA-TACTTTCAACTTTTCCTTAAAATATATTTTTTGAA-AATTTTATTTTCAAGG
* *
11495964 AAAATTGATACTTTCAACTTTTTCTTAAAATATATTTTTT-AAAATTTTATTTTCAAGAAAA
1 AAAATTGATACTTTCAACTTTTCCTTAAAATATATTTTTTGAAAATTTTATTTTCAAG---G
* * * *
11496025 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTTGAAAATTTTTGTTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCT-TAAAATATATTTTTTGAAAA-TTTTATTTTCAAGG
* * *
11496086 AAAATGGATACTTTCAACTTTTCCTCAAAAATATATTTTTTAAAAATTTTATTTT
1 AAAATTGATACTTTCAACTTTTCCT-TAAAATATATTTTTTGAAAATTTTATTTT
11496141 AGAAAAATCA
Statistics
Matches: 254, Mismatches: 23, Indels: 35
0.81 0.07 0.11
Matches are distributed among these distances:
54 1 0.00
55 24 0.09
57 5 0.02
58 63 0.25
59 13 0.05
60 8 0.03
61 71 0.28
62 45 0.18
63 12 0.05
64 12 0.05
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.48
Consensus pattern (59 bp):
AAAATTGATACTTTCAACTTTTCCTTAAAATATATTTTTTGAAAATTTTATTTTCAAGG
Found at i:11496218 original size:19 final size:21
Alignment explanation
Indices: 11496175--11496226 Score: 72
Period size: 19 Copynumber: 2.5 Consensus size: 21
11496165 AATGCTTACT
*
11496175 TAAATAAATAATTTCAATTTAA
1 TAAATAAATAA-TTCAATATAA
11496197 TAAATAAATAA-T-AATATAA
1 TAAATAAATAATTCAATATAA
11496216 TAAATAAATAA
1 TAAATAAATAA
11496227 ACAATGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 17 0.59
20 1 0.03
22 11 0.38
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAATAAATAATTCAATATAA
Found at i:11496394 original size:31 final size:31
Alignment explanation
Indices: 11496359--11496431 Score: 110
Period size: 31 Copynumber: 2.3 Consensus size: 31
11496349 AGAACGCGGA
* *
11496359 TTGGCTAAAAGTTGGTTGTGCTCGGGTCAGG
1 TTGGCCAAAAGTTGGTTGTGCTCAGGTCAGG
*
11496390 TTGGCCAAAAGTTGGTTGTGCTCAGGTCGGG
1 TTGGCCAAAAGTTGGTTGTGCTCAGGTCAGG
11496421 TTGGACCAAAA
1 TTGG-CCAAAA
11496432 AGAAACGCGT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
31 32 0.84
32 6 0.16
ACGTcount: A:0.21, C:0.15, G:0.36, T:0.29
Consensus pattern (31 bp):
TTGGCCAAAAGTTGGTTGTGCTCAGGTCAGG
Found at i:11496901 original size:22 final size:22
Alignment explanation
Indices: 11496859--11496901 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
11496849 TTAAACACTG
*
11496859 TTTTTATTTCTGTGTCTTGTGA
1 TTTTTATTTCTGTGTCGTGTGA
* *
11496881 TTTTTCTTTCTGTTTCGTGTG
1 TTTTTATTTCTGTGTCGTGTG
11496902 TTCTCGAAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.05, C:0.12, G:0.19, T:0.65
Consensus pattern (22 bp):
TTTTTATTTCTGTGTCGTGTGA
Found at i:11497336 original size:42 final size:41
Alignment explanation
Indices: 11497272--11497733 Score: 245
Period size: 42 Copynumber: 11.1 Consensus size: 41
11497262 TTTAATCAAA
* *
11497272 GCTCCTCTAAGTAGATGCTCAACGACTTTGAGAAACATAAA-T
1 GCTCCTCTAAATAGAGGC-CAACGACTTTGAGAAA-ATAAATT
* *
11497314 GCTCTTCTAAACAGAGGCTCAACGACTTTGAG-AAATAAATT
1 GCTCCTCTAAATAGAGGC-CAACGACTTTGAGAAAATAAATT
** * *
11497355 ATTCCTCTAAATAGAGGCAACACAACTTT-AGAAAAATAAATT
1 GCTCCTCTAAATAGAGGCCA-ACGACTTTGAG-AAAATAAATT
*
11497397 GCTCTTCTAAATAGAGG-CAACGAAACTTTGA-AAAATAAATT
1 GCTCCTCTAAATAGAGGCCAACG--ACTTTGAGAAAATAAATT
* * *
11497438 GTTCCTCTAAATAGAGG-CAACTGAACTTTAAAAAAATAAATT
1 GCTCCTCTAAATAGAGGCCAAC-G-ACTTTGAGAAAATAAATT
* * * * * *
11497480 GTTCTTCTAAATAGA-GACAACAGAATTTTAAAAAAATAAATT
1 GCTCCTCTAAATAGAGGCCAAC-G-ACTTTGAGAAAATAAATT
** * * * * *
11497522 ATTCCTATAAATAAAGG-TAATAGAACTTTGAAAAAAATAAATT
1 GCTCCTCTAAATAGAGGCCAA-CG-ACTTTG-AGAAAATAAATT
* *
11497565 GCTCATCT--ATAGA-GCCAACAAAACTTTGA-AAAATAAATT
1 GCTCCTCTAAATAGAGGCCAAC--GACTTTGAGAAAATAAATT
* * *
11497604 GCTCCTTTAAATAGAGG--AAGTAGAACTTTGAAAAAATAAATT
1 GCTCCTCTAAATAGAGGCCAA--CG-ACTTTGAGAAAATAAATT
* * * *
11497646 GCTTCTTTAAATAGAGG-CAACAAAACTTTGAAAAAATAAATT
1 GCTCCTCTAAATAGAGGCCAAC--GACTTTGAGAAAATAAATT
* * * * * *
11497688 ACTCTTTTAAATAGAGGCAACCACAACTTTGA-AAAATAAAAT
1 GCTCCTCTAAATAGAGGC--CAACGACTTTGAGAAAATAAATT
11497730 GCTC
1 GCTC
11497734 ACTTAATAAA
Statistics
Matches: 341, Mismatches: 50, Indels: 58
0.76 0.11 0.13
Matches are distributed among these distances:
39 16 0.05
40 14 0.04
41 86 0.25
42 194 0.57
43 28 0.08
45 3 0.01
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.28
Consensus pattern (41 bp):
GCTCCTCTAAATAGAGGCCAACGACTTTGAGAAAATAAATT
Found at i:11497413 original size:83 final size:82
Alignment explanation
Indices: 11497296--11497733 Score: 394
Period size: 83 Copynumber: 5.3 Consensus size: 82
11497286 ATGCTCAACG
* * *
11497296 ACTTTGAGAAACATAAA-TGCTCTTCTAAACAGAGGCTCAACGACTTTGAGAAATAAATTATTCC
1 ACTTT-AGAAAAATAAATTGCTCTTCTAAATAGAGGC-CAACGACTTTGAAAAATAAATTATTCC
*
11497360 TCTAAATAGAGGCAACACA
64 TCTAAATAGAGGCAACAGA
*
11497379 ACTTTAGAAAAATAAATTGCTCTTCTAAATAGAGG-CAACGAAACTTTGAAAAATAAATTGTTCC
1 ACTTTAGAAAAATAAATTGCTCTTCTAAATAGAGGCCAACG--ACTTTGAAAAATAAATTATTCC
*
11497443 TCTAAATAGAGGCAACTGA
64 TCTAAATAGAGGCAACAGA
* * * * *
11497462 ACTTTAAAAAAATAAATTGTTCTTCTAAATAGA-GACAACAGAATTTTAAAAAAATAAATTATTC
1 ACTTTAGAAAAATAAATTGCTCTTCTAAATAGAGGCCAAC-G-ACTTT-GAAAAATAAATTATTC
* * * *
11497526 CTATAAATAAAGGTAATAGA
63 CTCTAAATAGAGGCAACAGA
* * * **
11497546 ACTTTGAAAAAAATAAATTGCTCATCT--ATAGA-GCCAACAAAACTTTGAAAAATAAATTGCTC
1 ACTTT-AGAAAAATAAATTGCTCTTCTAAATAGAGGCCAAC--GACTTTGAAAAATAAATTATTC
* *
11497608 CTTTAAATAGAGG-AAGTAGA
63 CTCTAAATAGAGGCAA-CAGA
* *
11497628 ACTTT-GAAAAAATAAATTGCTTCTT-TAAATAGAGG-CAACAAAACTTTGAAAAAATAAATTAC
1 ACTTTAG-AAAAATAAATTGC-TCTTCTAAATAGAGGCCAAC--GACTTTG-AAAAATAAATTAT
* * *
11497690 TCTTTTAAATAGAGGCAACCACA
61 TCCTCTAAATAGAGGCAA-CAGA
*
11497713 ACTTT-GAAAAATAAAATGCTC
1 ACTTTAGAAAAATAAATTGCTC
11497734 ACTTAATAAA
Statistics
Matches: 305, Mismatches: 34, Indels: 32
0.82 0.09 0.09
Matches are distributed among these distances:
81 21 0.07
82 47 0.15
83 133 0.44
84 75 0.25
85 29 0.10
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (82 bp):
ACTTTAGAAAAATAAATTGCTCTTCTAAATAGAGGCCAACGACTTTGAAAAATAAATTATTCCTC
TAAATAGAGGCAACAGA
Found at i:11497591 original size:166 final size:166
Alignment explanation
Indices: 11497346--11497734 Score: 498
Period size: 166 Copynumber: 2.3 Consensus size: 166
11497336 CGACTTTGAG
* * * *
11497346 AAATAAATTATTCCTCTAAATAGAGGCAACACAACTTTAGAAAAATAAATTGCTCTTCTAAATAG
1 AAATAAATTATTCCTATAAATAAAGGCAACACAACTTTAAAAAAATAAATTGCTCATCT-AATAG
* * *
11497411 AGGCAACGAAACTTTGAAAAATAAATTGTTCCTCTAAATAGAGGCAACT-GAACTTTAAAAAAAT
65 AGCCAACAAAACTTTGAAAAATAAATTGCTCCTCTAAATAGAGG-AACTAGAACTTTAAAAAAAT
* *
11497475 AAATTG-TTCTTCTAAATAGAGACAACAGAATTTTAAAA
129 AAATTGCTTCTT-TAAATAGAGACAACAAAACTTTAAAA
* * *
11497513 AAATAAATTATTCCTATAAATAAAGGTAATAGAACTTTGAAAAAAATAAATTGCTCATCT-ATAG
1 AAATAAATTATTCCTATAAATAAAGGCAACACAACTTT-AAAAAAATAAATTGCTCATCTAATAG
* * *
11497577 AGCCAACAAAACTTTGAAAAATAAATTGCTCCTTTAAATAGAGGAAGTAGAACTTTGAAAAAATA
65 AGCCAACAAAACTTTGAAAAATAAATTGCTCCTCTAAATAGAGGAACTAGAACTTTAAAAAAATA
* *
11497642 AATTGCTTCTTTAAATAGAGGCAACAAAACTTTGAAA
130 AATTGCTTCTTTAAATAGAGACAACAAAACTTTAAAA
* * * * * *
11497679 AAATAAATTACTCTTTTAAATAGAGGCAACCACAACTTT-GAAAAATAAAATGCTCA
1 AAATAAATTATTCCTATAAATAAAGGCAA-CACAACTTTAAAAAAATAAATTGCTCA
11497735 CTTAATAAAG
Statistics
Matches: 192, Mismatches: 26, Indels: 10
0.84 0.11 0.04
Matches are distributed among these distances:
165 18 0.09
166 110 0.57
167 45 0.23
168 19 0.10
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (166 bp):
AAATAAATTATTCCTATAAATAAAGGCAACACAACTTTAAAAAAATAAATTGCTCATCTAATAGA
GCCAACAAAACTTTGAAAAATAAATTGCTCCTCTAAATAGAGGAACTAGAACTTTAAAAAAATAA
ATTGCTTCTTTAAATAGAGACAACAAAACTTTAAAA
Found at i:11498775 original size:1 final size:1
Alignment explanation
Indices: 11498769--11498826 Score: 53
Period size: 1 Copynumber: 58.0 Consensus size: 1
11498759 TCCTTAAGTC
** * * * * *
11498769 TTTTTTTTTTCATTTTTTTTTTATTTTTTTATTTTTTTCTCTTTTTTTTTATTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
11498827 CTCAAGCATA
Statistics
Matches: 44, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.07, C:0.05, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:11498786 original size:11 final size:10
Alignment explanation
Indices: 11498770--11498826 Score: 71
Period size: 10 Copynumber: 5.7 Consensus size: 10
11498760 CCTTAAGTCT
11498770 TTTTTTTTTCA
1 TTTTTTTTT-A
11498781 TTTTTTTTT-
1 TTTTTTTTTA
*
11498790 TATTTTTTTA
1 TTTTTTTTTA
* *
11498800 TTTTTTTCTC
1 TTTTTTTTTA
11498810 TTTTTTTTTA
1 TTTTTTTTTA
11498820 TTTTTTT
1 TTTTTTT
11498827 CTCAAGCATA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
9 8 0.21
10 22 0.56
11 9 0.23
ACGTcount: A:0.07, C:0.05, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:11498795 original size:20 final size:20
Alignment explanation
Indices: 11498770--11498829 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
11498760 CCTTAAGTCT
11498770 TTTTTTTTTCATTTTTTT-T-
1 TTTTTTTTT-ATTTTTTTCTC
11498789 TTATTTTTTTATTTTTTTCTC
1 TT-TTTTTTTATTTTTTTCTC
11498810 TTTTTTTTTATTTTTTTCTC
1 TTTTTTTTTATTTTTTTCTC
11498830 AAGCATAGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.26
20 26 0.68
21 2 0.05
ACGTcount: A:0.07, C:0.08, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTTTTTTATTTTTTTCTC
Found at i:11498803 original size:28 final size:28
Alignment explanation
Indices: 11498772--11498826 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
11498762 TTAAGTCTTT
11498772 TTTTTTTCAT-TTTTTTTTTATTTTTTTA
1 TTTTTTTC-TCTTTTTTTTTATTTTTTTA
11498800 TTTTTTTCTCTTTTTTTTTATTTTTTT
1 TTTTTTTCTCTTTTTTTTTATTTTTTT
11498827 CTCAAGCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.07, C:0.05, G:0.00, T:0.87
Consensus pattern (28 bp):
TTTTTTTCTCTTTTTTTTTATTTTTTTA
Found at i:11508364 original size:61 final size:59
Alignment explanation
Indices: 11508182--11508416 Score: 282
Period size: 58 Copynumber: 3.9 Consensus size: 59
11508172 TTTATACAAA
* * *
11508182 GAAAATTGATACTTTCAACTTTTCCTTAAAAATATATATTTTT--AATTTTATTTTTAAG
1 GAAAATTGATACTTTCAACTTTTCCTT-AAAATATTTTTTTTTAAAATTTTATTTTCAAG
* * * *
11508240 GAAAATTGGTACTTCCAACTTTTCTTTAGAAATA---TTTTTTAACAATTTTATTTTCAAA
1 GAAAATTGATACTTTCAACTTTTCCTTA-AAATATTTTTTTTTAA-AATTTTATTTTCAAG
* *
11508298 AAAAATTGATACTTTCAACTTTTCCTTAAAATGTTTTTTTTTGAAAAATTTTATTTTCAAG
1 GAAAATTGATACTTTCAACTTTTCCTTAAAATATTTTTTTTT--AAAATTTTATTTTCAAG
11508359 GAAAATTGATACTTTCAACTTTTCCTTAAAATTATATTTTTTTTGAAAATTTTATTTT
1 GAAAATTGATACTTTCAACTTTTCCTTAAAA-TAT-TTTTTTTT-AAAATTTTATTTT
11508417 AGAAGAATCA
Statistics
Matches: 151, Mismatches: 15, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
55 5 0.03
57 5 0.03
58 66 0.44
60 6 0.04
61 44 0.29
62 17 0.11
63 8 0.05
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.50
Consensus pattern (59 bp):
GAAAATTGATACTTTCAACTTTTCCTTAAAATATTTTTTTTTAAAATTTTATTTTCAAG
Found at i:11508483 original size:4 final size:4
Alignment explanation
Indices: 11508476--11508509 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
11508466 CAATTTAATT
11508476 AATA AAT- AATA ATATA AATA AATA AATA AATA AA
1 AATA AATA AATA A-ATA AATA AATA AATA AATA AA
11508510 CAATGAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.11
4 21 0.75
5 4 0.14
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:11508959 original size:30 final size:30
Alignment explanation
Indices: 11508923--11508981 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
11508913 ATTAGAAACT
* * * *
11508923 TCATCGAAAACTTTGAATTTCGTCGAAAAG
1 TCATCGAAAAATTTAAATCTCGTCCAAAAG
11508953 TCATCGAAAAATTTAAATCTCGTCCAAAA
1 TCATCGAAAAATTTAAATCTCGTCCAAAA
11508982 ATTGCTCGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.29
Consensus pattern (30 bp):
TCATCGAAAAATTTAAATCTCGTCCAAAAG
Found at i:11509134 original size:22 final size:22
Alignment explanation
Indices: 11509109--11509151 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
11509099 ATTGACCTTG
11509109 GCCCAAAGAGGTC-AGATCCCTA
1 GCCCAAAGAGGTCGA-ATCCCTA
*
11509131 GCCCAAATAGGTCGAATCCCT
1 GCCCAAAGAGGTCGAATCCCT
11509152 GGCAATCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.30, C:0.33, G:0.21, T:0.16
Consensus pattern (22 bp):
GCCCAAAGAGGTCGAATCCCTA
Found at i:11511863 original size:17 final size:17
Alignment explanation
Indices: 11511826--11511867 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
11511816 TATTTTGAAT
* * *
11511826 ATTTTAGAAAATTTTAT
1 ATTTTAAAAAATATTAA
11511843 ATTTTAAAAAATATTAA
1 ATTTTAAAAAATATTAA
11511860 A-TTTAAAA
1 ATTTTAAAA
11511868 TATTCAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
ATTTTAAAAAATATTAA
Found at i:11511966 original size:11 final size:11
Alignment explanation
Indices: 11511950--11511983 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
11511940 AAATATTTAA
*
11511950 TTTTAATATTT
1 TTTTAAAATTT
11511961 TTTTAAAATTT
1 TTTTAAAATTT
*
11511972 TTATAAAATTT
1 TTTTAAAATTT
11511983 T
1 T
11511984 CAATATCACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTTAAAATTT
Found at i:11512022 original size:23 final size:21
Alignment explanation
Indices: 11511996--11512051 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 21
11511986 ATATCACTTA
11511996 TTTTTATGTTTCGTTTATAAAT
1 TTTTTATGTTTC-TTTATAAAT
* *
11512018 GTTTTTATATGTTCTTTTTAAAT
1 -TTTTTATGT-TTCTTTATAAAT
*
11512041 TTTTTGTGTTT
1 TTTTTATGTTT
11512052 TTAAAAAGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 2 0.07
22 7 0.25
23 16 0.57
24 3 0.11
ACGTcount: A:0.18, C:0.04, G:0.11, T:0.68
Consensus pattern (21 bp):
TTTTTATGTTTCTTTATAAAT
Found at i:11512321 original size:27 final size:29
Alignment explanation
Indices: 11512260--11512323 Score: 87
Period size: 27 Copynumber: 2.3 Consensus size: 29
11512250 TCATCTAAAT
* * *
11512260 ATTAAAATATATAGAAATTTTCTAAAAAA
1 ATTAAAAAATATAGAAATATTCCAAAAAA
11512289 ATTAAAAAATATA-AAA-ATTCCAAAAAA
1 ATTAAAAAATATAGAAATATTCCAAAAAA
11512316 ATTAAAAA
1 ATTAAAAA
11512324 TAAAATTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 17 0.53
28 3 0.09
29 12 0.38
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.28
Consensus pattern (29 bp):
ATTAAAAAATATAGAAATATTCCAAAAAA
Found at i:11512429 original size:23 final size:24
Alignment explanation
Indices: 11512403--11512447 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
11512393 TTTATTTTAA
11512403 AAAATT-ATA-ATATTTAAAAAAGT
1 AAAATTAATATAT-TTTAAAAAAGT
11512426 AAAATTAATATATTTTAAAAAA
1 AAAATTAATATATTTTAAAAAA
11512448 ATCTAGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 6 0.30
24 12 0.60
25 2 0.10
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
AAAATTAATATATTTTAAAAAAGT
Found at i:11512442 original size:24 final size:23
Alignment explanation
Indices: 11512403--11512447 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
11512393 TTTATTTTAA
11512403 AAAATTATAATATTTAAAAAAGT
1 AAAATTATAATATTTAAAAAAGT
11512426 AAAATTA-ATATATTTTAAAAAA
1 AAAATTATA-ATA-TTTAAAAAA
11512448 ATCTAGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 1 0.05
23 10 0.50
24 9 0.45
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
AAAATTATAATATTTAAAAAAGT
Found at i:11512508 original size:22 final size:22
Alignment explanation
Indices: 11512482--11512532 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
11512472 GCAATATTAA
* *
11512482 ATTTTTTAAAAAATAAAATATG
1 ATTTTTAAAAAAATAAAAAATG
*
11512504 A-TTTTAAAAAAATAAAAAATT
1 ATTTTTAAAAAAATAAAAAATG
11512525 ATTTTTAA
1 ATTTTTAA
11512533 GAATTCCAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
ATTTTTAAAAAAATAAAAAATG
Found at i:11512625 original size:25 final size:25
Alignment explanation
Indices: 11512587--11512642 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
11512577 AAAAAATTAT
* *
11512587 AAAAAATTGAAATAGTGTTAATTTTAA
1 AAAAAATT-AAATA-TCTGAATTTTAA
*
11512614 AAAAAATT-AATATCTGATTTTTAA
1 AAAAAATTAAATATCTGAATTTTAA
11512638 AAAAA
1 AAAAA
11512643 TAAAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 14 0.54
25 4 0.15
27 8 0.31
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (25 bp):
AAAAAATTAAATATCTGAATTTTAA
Found at i:11513748 original size:5 final size:5
Alignment explanation
Indices: 11513738--11513762 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
11513728 AGGGGTCTTT
11513738 TCCTC TCCTC TCCTC TCCTC TCCTC
1 TCCTC TCCTC TCCTC TCCTC TCCTC
11513763 GATGACAACT
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:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (5 bp):
TCCTC
Found at i:11516708 original size:32 final size:32
Alignment explanation
Indices: 11516638--11516701 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
11516628 TTAACATTTT
* *
11516638 TCTTTTTTTTTTTCTTCTTTAATTCTCCTTTC
1 TCTTCTTTTTTCTCTTCTTTAATTCTCCTTTC
*
11516670 TCTTCTTTTTTCTCTT-TTTATTTCTACCTTTC
1 TCTTCTTTTTTCTCTTCTTTAATTCT-CCTTTC
11516702 CATTCTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 8 0.29
32 20 0.71
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.70
Consensus pattern (32 bp):
TCTTCTTTTTTCTCTTCTTTAATTCTCCTTTC
Found at i:11520868 original size:14 final size:15
Alignment explanation
Indices: 11520849--11520877 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11520839 GGTAAATTAG
11520849 AAAG-AAGAAAAAAA
1 AAAGAAAGAAAAAAA
11520863 AAAGAAAGAAAAAAA
1 AAAGAAAGAAAAAAA
11520878 GAAGTAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAAAAAA
Found at i:11522473 original size:2 final size:2
Alignment explanation
Indices: 11522466--11522505 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
11522456 AGATCAAATC
11522466 CT CT CT CT CT CT CT 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 CT CT CT
11522506 AAAGACAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:11523062 original size:24 final size:24
Alignment explanation
Indices: 11523030--11523078 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
11523020 CATAGTATGA
*
11523030 TTTTAAGAAGCGTGACTATGTTAT
1 TTTTAAGAAGCATGACTATGTTAT
* *
11523054 TTTTGAGAAGTATGACTATGTTAT
1 TTTTAAGAAGCATGACTATGTTAT
11523078 T
1 T
11523079 GAGGTTAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.29, C:0.06, G:0.20, T:0.45
Consensus pattern (24 bp):
TTTTAAGAAGCATGACTATGTTAT
Found at i:11531193 original size:30 final size:31
Alignment explanation
Indices: 11531138--11531197 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
11531128 TTAATCTTTT
11531138 ATTTTTTTAATTTTGAAATACTAAATATTTC
1 ATTTTTTTAATTTTGAAATACTAAATATTTC
11531169 ATTTTTATT-ATTATTGAAA-A-TAAATATTT
1 ATTTTT-TTAATT-TTGAAATACTAAATATTT
11531198 TTCATATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 9 0.33
31 10 0.37
32 8 0.30
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.55
Consensus pattern (31 bp):
ATTTTTTTAATTTTGAAATACTAAATATTTC
Found at i:11531201 original size:32 final size:33
Alignment explanation
Indices: 11531134--11531212 Score: 80
Period size: 32 Copynumber: 2.5 Consensus size: 33
11531124 TCTTTTAATC
11531134 TTTT-ATTTTT-TTAATTTTGAAATACTAAATA
1 TTTTCATTTTTATTAATTTTGAAATACTAAATA
11531165 -TTTCATTTTTATT-ATTATTGAAA-A-TAAATA
1 TTTTCATTTTTATTAATT-TTGAAATACTAAATA
* *
11531195 TTTTTCATATTTAATAAT
1 -TTTTCATTTTTATTAAT
11531213 AAATAGTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
30 9 0.22
31 10 0.25
32 19 0.47
33 2 0.05
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.57
Consensus pattern (33 bp):
TTTTCATTTTTATTAATTTTGAAATACTAAATA
Found at i:11531486 original size:22 final size:23
Alignment explanation
Indices: 11531437--11531490 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
11531427 TATAAACAAA
* * *
11531437 TAATATTTTTATCTTTGAATACT
1 TAATATTTTTATCATTAAAAACT
*
11531460 AAATATTTTTAT-ATTAAAAACT
1 TAATATTTTTATCATTAAAAACT
11531482 TAATATTTT
1 TAATATTTT
11531491 AATAGTATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.54
Consensus pattern (23 bp):
TAATATTTTTATCATTAAAAACT
Found at i:11531580 original size:13 final size:14
Alignment explanation
Indices: 11531562--11531591 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
11531552 ATATAATACT
11531562 TTATTATT-AAATA
1 TTATTATTAAAATA
11531575 TTATTATTAAAATA
1 TTATTATTAAAATA
11531589 TTA
1 TTA
11531592 CAATTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTATTATTAAAATA
Found at i:11531683 original size:23 final size:24
Alignment explanation
Indices: 11531632--11531683 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
11531622 AAACCTTGTT
*
11531632 AATATTTTAATGATAAATAATTTTC
1 AATATTTTAATGATAAAT-AGTTTC
*
11531657 AATATTTTAATGATAGAT-GTTTC
1 AATATTTTAATGATAAATAGTTTC
11531680 AATA
1 AATA
11531684 GTTATTACGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 8 0.32
25 17 0.68
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (24 bp):
AATATTTTAATGATAAATAGTTTC
Found at i:11539635 original size:10 final size:11
Alignment explanation
Indices: 11539606--11539635 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
11539596 AAGAAAAACT
11539606 AAGAAAAAAAA
1 AAGAAAAAAAA
11539617 AAGGAAAAAAAA
1 AA-GAAAAAAAA
11539629 AAGAAAA
1 AAGAAAA
11539636 TGGGATGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:11546528 original size:21 final size:21
Alignment explanation
Indices: 11546504--11546565 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
11546494 GGGCCTAAGG
*
11546504 TTAGTTTTAGGGTTTAGGGTT
1 TTAGTTTTAGGGTTTAGAGTT
*
11546525 TTAGTTTTAAGGTTTAGAGTT
1 TTAGTTTTAGGGTTTAGAGTT
*
11546546 TTAG-CTTAGGGTTTAGAGTT
1 TTAGTTTTAGGGTTTAGAGTT
11546566 AGACTCAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 14 0.38
21 23 0.62
ACGTcount: A:0.19, C:0.02, G:0.29, T:0.50
Consensus pattern (21 bp):
TTAGTTTTAGGGTTTAGAGTT
Found at i:11546820 original size:7 final size:7
Alignment explanation
Indices: 11546802--11546875 Score: 61
Period size: 7 Copynumber: 11.3 Consensus size: 7
11546792 GGGCTTAGGG
11546802 TTAAGG-
1 TTAAGGT
11546808 TTAAGGT
1 TTAAGGT
11546815 TTAAGGTT
1 TTAAGG-T
11546823 TTAAGG-
1 TTAAGGT
11546829 TT-A-GT
1 TTAAGGT
* *
11546834 TTTAGGC
1 TTAAGGT
*
11546841 TTAGGGT
1 TTAAGGT
11546848 TTAAGG-
1 TTAAGGT
11546854 TT-AGGT
1 TTAAGGT
*
11546860 TTAGGGT
1 TTAAGGT
11546867 TTAAGGT
1 TTAAGGT
11546874 TT
1 TT
11546876 TGGCTTCAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
4 1 0.02
5 6 0.11
6 13 0.24
7 27 0.50
8 7 0.13
ACGTcount: A:0.23, C:0.01, G:0.31, T:0.45
Consensus pattern (7 bp):
TTAAGGT
Found at i:11546822 original size:19 final size:19
Alignment explanation
Indices: 11546765--11546874 Score: 59
Period size: 19 Copynumber: 5.8 Consensus size: 19
11546755 AAGATTAGGT
*
11546765 TTTAAGGTTTATGTTAAGG
1 TTTAAGGTTTAGGTTAAGG
*
11546784 -TT-AGGTTTGGGCTT-AGG
1 TTTAAGGTTTAGG-TTAAGG
* *
11546801 GTTAAGGTTAAGGTTTAAGG
1 TTTAAGGTTTAGG-TTAAGG
* *
11546821 TTTTAAGG-TTAGTTTTAGG
1 -TTTAAGGTTTAGGTTAAGG
* *
11546840 CTTAGGGTTTAAGGTT-AGG
1 TTTAAGGTTT-AGGTTAAGG
*
11546859 TTTAGGGTTTAAGGTT
1 TTTAAGGTTT-AGGTT
11546875 TTGGCTTCAA
Statistics
Matches: 71, Mismatches: 13, Indels: 14
0.72 0.13 0.14
Matches are distributed among these distances:
17 10 0.14
18 11 0.15
19 34 0.48
20 10 0.14
21 6 0.08
ACGTcount: A:0.22, C:0.02, G:0.33, T:0.44
Consensus pattern (19 bp):
TTTAAGGTTTAGGTTAAGG
Found at i:11546837 original size:12 final size:12
Alignment explanation
Indices: 11546759--11546867 Score: 70
Period size: 12 Copynumber: 9.2 Consensus size: 12
11546749 AGGGTCAAGA
11546759 TTAGGTTTTAAGG
1 TTAGG-TTTAAGG
*
11546772 TTTATG-TTAAGG
1 -TTAGGTTTAAGG
*
11546784 TTAGGTTT-GGG
1 TTAGGTTTAAGG
*
11546795 CTTAGGGTTAAGG
1 -TTAGGTTTAAGG
11546808 TTAAGGTTTAAGG
1 TT-AGGTTTAAGG
11546821 -T---TTTAAGG
1 TTAGGTTTAAGG
*
11546829 TTA-GTTTTAGG
1 TTAGGTTTAAGG
11546840 CTTAGGGTTTAAGG
1 -TTA-GGTTTAAGG
*
11546854 TTAGGTTTAGGG
1 TTAGGTTTAAGG
11546866 TT
1 TT
11546868 TAAGGTTTTG
Statistics
Matches: 76, Mismatches: 9, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
8 7 0.09
9 1 0.01
11 12 0.16
12 31 0.41
13 14 0.18
14 11 0.14
ACGTcount: A:0.21, C:0.02, G:0.33, T:0.44
Consensus pattern (12 bp):
TTAGGTTTAAGG
Found at i:11546842 original size:45 final size:44
Alignment explanation
Indices: 11546778--11546874 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 44
11546768 AAGGTTTATG
* *
11546778 TTAAGGTTAGGTTTGGGCTTAGGG-TTAAGGTTAAGGTTTAAGGTT
1 TTAAGGTTAGGTTTAGGCTTAGGGTTTAAGGTT-AGGTTT-AGGGT
*
11546823 TTAAGGTTAGTTTTAGGCTTAGGGTTTAAGGTTAGGTTTAGGGT
1 TTAAGGTTAGGTTTAGGCTTAGGGTTTAAGGTTAGGTTTAGGGT
11546867 TTAAGGTT
1 TTAAGGTT
11546875 TTGGCTTCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
44 12 0.25
45 28 0.58
46 8 0.17
ACGTcount: A:0.22, C:0.02, G:0.34, T:0.42
Consensus pattern (44 bp):
TTAAGGTTAGGTTTAGGCTTAGGGTTTAAGGTTAGGTTTAGGGT
Done.