Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397256.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_56.0, 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: 13963513
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 99179 characters in sequence are not A, C, G, or T
File 13 of 29
Found at i:4682522 original size:21 final size:21
Alignment explanation
Indices: 4682460--4682540 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
4682450 TTAGTGATCC
*
4682460 TTGAACTTGTTTGAAT-GATTT
1 TTGAACTTGTTTAAATAG-TTT
*
4682481 TTGAAGTTGTTTAAATAAGTTT
1 TTGAACTTGTTTAAAT-AGTTT
*
4682503 TTGAACTTGTTTGAATAGTTT
1 TTGAACTTGTTTAAATAGTTT
* *
4682524 TTAAACTTTTTTAAATA
1 TTGAACTTGTTTAAATA
4682541 AGCTTTGAAG
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
21 33 0.65
22 17 0.33
23 1 0.02
ACGTcount: A:0.30, C:0.04, G:0.15, T:0.52
Consensus pattern (21 bp):
TTGAACTTGTTTAAATAGTTT
Found at i:4682525 original size:43 final size:43
Alignment explanation
Indices: 4682460--4682542 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
4682450 TTAGTGATCC
* *
4682460 TTGAACTTGTTTGAATGATTTTTGAAGTTGTTTAAATAAGTTT
1 TTGAACTTGTTTGAATGATTTTTAAACTTGTTTAAATAAGTTT
*
4682503 TTGAACTTGTTTGAAT-AGTTTTTAAACTTTTTTAAATAAG
1 TTGAACTTGTTTGAATGA-TTTTTAAACTTGTTTAAATAAG
4682543 CTTTGAAGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 1 0.03
43 35 0.97
ACGTcount: A:0.30, C:0.04, G:0.16, T:0.51
Consensus pattern (43 bp):
TTGAACTTGTTTGAATGATTTTTAAACTTGTTTAAATAAGTTT
Found at i:4682605 original size:21 final size:21
Alignment explanation
Indices: 4682581--4682635 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
4682571 AAAAGTTTCA
4682581 AAATTATTTGAATGAGTTTTG
1 AAATTATTTGAATGAGTTTTG
* *
4682602 AAATTGCTTT-AATGATTTTTG
1 AAATT-ATTTGAATGAGTTTTG
* *
4682623 AACTTGTTTGAAT
1 AAATTATTTGAAT
4682636 AATTTTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 3 0.11
21 22 0.79
22 3 0.11
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (21 bp):
AAATTATTTGAATGAGTTTTG
Found at i:4682640 original size:21 final size:22
Alignment explanation
Indices: 4682587--4682642 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
4682577 TTCAAAATTA
*
4682587 TTTGAATGAGTTTTGAAATTGC
1 TTTGAATGATTTTTGAAATTGC
*
4682609 TTT-AATGATTTTTGAACTTG-
1 TTTGAATGATTTTTGAAATTGC
*
4682629 TTTGAATAATTTTT
1 TTTGAATGATTTTT
4682643 TAAAACTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.10
21 24 0.80
22 3 0.10
ACGTcount: A:0.27, C:0.04, G:0.16, T:0.54
Consensus pattern (22 bp):
TTTGAATGATTTTTGAAATTGC
Found at i:4682833 original size:21 final size:21
Alignment explanation
Indices: 4682808--4682927 Score: 101
Period size: 20 Copynumber: 6.0 Consensus size: 21
4682798 AATGGTTCTG
* * *
4682808 CCCAAAATATATGGATGCATT
1 CCCAAAATGTATCGATACATT
*
4682829 CCC-AAATGTATTGATACATT
1 CCCAAAATGTATCGATACATT
*
4682849 -TCAAAATGTATCGATACATT
1 CCCAAAATGTATCGATACATT
* *
4682869 CCC-AAATGTA-AGATATAGTT
1 CCCAAAATGTATCGATACA-TT
*
4682889 --CAAAATGTATCGATGCATT
1 CCCAAAATGTATCGATACATT
*
4682908 -CCAAAATGTATTGATACATT
1 CCCAAAATGTATCGATACATT
4682928 TGATCCAAAA
Statistics
Matches: 80, Mismatches: 13, Indels: 13
0.75 0.12 0.12
Matches are distributed among these distances:
18 1 0.01
19 15 0.19
20 60 0.75
21 4 0.05
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (21 bp):
CCCAAAATGTATCGATACATT
Found at i:4682835 original size:20 final size:20
Alignment explanation
Indices: 4682825--4682927 Score: 102
Period size: 20 Copynumber: 5.2 Consensus size: 20
4682815 TATATGGATG
*
4682825 CATTCCCAAATGTATTGATA
1 CATTCCCAAATGTATCGATA
* *
4682845 CATTTCAAAATGTATCGATA
1 CATTCCCAAATGTATCGATA
*
4682865 CATTCCCAAATGTA-AGATA
1 CATTCCCAAATGTATCGATA
* * *
4682884 TAGTT-CAAAATGTATCGATG
1 CA-TTCCCAAATGTATCGATA
* *
4682904 CATTCCAAAATGTATTGATA
1 CATTCCCAAATGTATCGATA
4682924 CATT
1 CATT
4682928 TGATCCAAAA
Statistics
Matches: 67, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
19 15 0.22
20 52 0.78
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.34
Consensus pattern (20 bp):
CATTCCCAAATGTATCGATA
Found at i:4682900 original size:39 final size:40
Alignment explanation
Indices: 4682810--4682925 Score: 153
Period size: 39 Copynumber: 2.9 Consensus size: 40
4682800 TGGTTCTGCC
* * * *
4682810 CAAAATATATGGATGCATTCCCAAATGTATTGATACATTT
1 CAAAATGTATCGATGCATTCCCAAATGTATAGATACAGTT
* *
4682850 CAAAATGTATCGATACATTCCCAAATGTA-AGATATAGTT
1 CAAAATGTATCGATGCATTCCCAAATGTATAGATACAGTT
* *
4682889 CAAAATGTATCGATGCATTCCAAAATGTATTGATACA
1 CAAAATGTATCGATGCATTCCCAAATGTATAGATACA
4682926 TTTGATCCAA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
39 34 0.52
40 31 0.48
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.32
Consensus pattern (40 bp):
CAAAATGTATCGATGCATTCCCAAATGTATAGATACAGTT
Found at i:4683008 original size:20 final size:20
Alignment explanation
Indices: 4682983--4683020 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4682973 CTATTTTGTT
*
4682983 CACCAAATCTTCTCTAACAG
1 CACCAAAGCTTCTCTAACAG
4683003 CACCAAAGCTTCTCTAAC
1 CACCAAAGCTTCTCTAAC
4683021 TATAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.37, G:0.05, T:0.24
Consensus pattern (20 bp):
CACCAAAGCTTCTCTAACAG
Found at i:4691869 original size:29 final size:29
Alignment explanation
Indices: 4691833--4691888 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
4691823 GATATTAAAG
*
4691833 ATATCTTGCTTAGCTACTG-TGGATATTGT
1 ATATCTTGCTTAGATAC-GATGGATATTGT
*
4691862 ATATCTTGTTTAGATACGATGGATATT
1 ATATCTTGCTTAGATACGATGGATATT
4691889 ATGAATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.45
Consensus pattern (29 bp):
ATATCTTGCTTAGATACGATGGATATTGT
Found at i:4695992 original size:14 final size:15
Alignment explanation
Indices: 4695966--4695994 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4695956 TAAATTAAAG
4695966 TGAACATGAAATTAA
1 TGAACATGAAATTAA
4695981 TGAACA-GAAATTAA
1 TGAACATGAAATTAA
4695995 AAATTCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.24
Consensus pattern (15 bp):
TGAACATGAAATTAA
Found at i:4697135 original size:19 final size:19
Alignment explanation
Indices: 4697069--4697141 Score: 60
Period size: 19 Copynumber: 3.7 Consensus size: 19
4697059 CTCCTACGAA
*
4697069 AACATAAAAATAAACATAAAT
1 AACAT-AAAATAAACAT-TAT
*
4697090 AACATAAACT-AACATTATT
1 AACATAAAATAAACATTA-T
*
4697109 AACTTAAAATAAACATGTA-
1 AACATAAAATAAACAT-TAT
*
4697128 AACATAAATTAAAC
1 AACATAAAATAAAC
4697142 TAAACTAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
18 1 0.02
19 26 0.60
20 9 0.21
21 7 0.16
ACGTcount: A:0.62, C:0.12, G:0.01, T:0.25
Consensus pattern (19 bp):
AACATAAAATAAACATTAT
Found at i:4706476 original size:15 final size:17
Alignment explanation
Indices: 4706443--4706476 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4706433 CAACTTTATG
4706443 TTGATTTGTTTAGTTAA
1 TTGATTTGTTTAGTTAA
4706460 TTGATTT-TTTA-TTAA
1 TTGATTTGTTTAGTTAA
4706475 TT
1 TT
4706477 TCTTTCATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 4 0.24
17 7 0.41
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.65
Consensus pattern (17 bp):
TTGATTTGTTTAGTTAA
Found at i:4706684 original size:16 final size:17
Alignment explanation
Indices: 4706647--4706687 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
4706637 TGGTATAGTT
4706647 ATGTTGACATGGCACAA
1 ATGTTGACATGGCACAA
4706664 ATGTTGACATGGCAC-A
1 ATGTTGACATGGCACAA
4706680 ATGTTGAC
1 ATGTTGAC
4706688 TTGTCACATG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (17 bp):
ATGTTGACATGGCACAA
Found at i:4707390 original size:47 final size:47
Alignment explanation
Indices: 4707321--4707462 Score: 266
Period size: 47 Copynumber: 3.0 Consensus size: 47
4707311 CTAGAACCAA
4707321 TTGTTTCTCCATATCTTGGTTCTCCTTCTTGGGTTGTTAATTTTCTT
1 TTGTTTCTCCATATCTTGGTTCTCCTTCTTGGGTTGTTAATTTTCTT
4707368 TTGTTTCTCCATATCTTGGTTCTCCTTCTTGGGTTGTTAATTTTCTT
1 TTGTTTCTCCATATCTTGGTTCTCCTTCTTGGGTTGTTAATTTTCTT
* *
4707415 TTGTTTCTCCATATCTTGGTTCTCCTTCTTAGGTTGTTAAGTTTCTT
1 TTGTTTCTCCATATCTTGGTTCTCCTTCTTGGGTTGTTAATTTTCTT
4707462 T
1 T
4707463 CTTTCTTTAT
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 93 1.00
ACGTcount: A:0.09, C:0.19, G:0.15, T:0.57
Consensus pattern (47 bp):
TTGTTTCTCCATATCTTGGTTCTCCTTCTTGGGTTGTTAATTTTCTT
Found at i:4710338 original size:14 final size:14
Alignment explanation
Indices: 4710319--4710347 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4710309 ATATATATAT
4710319 ATACACACACACAC
1 ATACACACACACAC
4710333 ATACACACACACAC
1 ATACACACACACAC
4710347 A
1 A
4710348 CATTTAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.41, G:0.00, T:0.07
Consensus pattern (14 bp):
ATACACACACACAC
Found at i:4728125 original size:31 final size:31
Alignment explanation
Indices: 4728079--4728149 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
4728069 TTGAAGGATT
* * *
4728079 AAATTAAAAATAAGTTAGAGGACCAAATTGA
1 AAATAAAAAAAAAGTTAGAAGACCAAATTGA
*
4728110 AAATAAAAAAAAAGTTAGAAGACCAAATTGT
1 AAATAAAAAAAAAGTTAGAAGACCAAATTGA
4728141 AAATAAAAA
1 AAATAAAAA
4728150 TAAATATTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.62, C:0.06, G:0.13, T:0.20
Consensus pattern (31 bp):
AAATAAAAAAAAAGTTAGAAGACCAAATTGA
Found at i:4729894 original size:32 final size:34
Alignment explanation
Indices: 4729818--4729894 Score: 90
Period size: 32 Copynumber: 2.3 Consensus size: 34
4729808 CTATCGACTT
4729818 AAAAAGTAAAC-TATAAAACAATTAATATCAAAAC
1 AAAAAG-AAACATATAAAACAATTAATATCAAAAC
* *
4729852 AAAAAAAAACATATAAAAC-ATTAA-ATGAAAGA-
1 AAAAAGAAACATATAAAACAATTAATATCAAA-AC
4729884 AAAAAGAAACA
1 AAAAAGAAACA
4729895 AACAAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
32 15 0.39
33 10 0.26
34 13 0.34
ACGTcount: A:0.70, C:0.09, G:0.05, T:0.16
Consensus pattern (34 bp):
AAAAAGAAACATATAAAACAATTAATATCAAAAC
Found at i:4729994 original size:12 final size:11
Alignment explanation
Indices: 4729977--4730027 Score: 54
Period size: 12 Copynumber: 4.7 Consensus size: 11
4729967 AAAGAGTCAC
4729977 ACACAATAAAAA
1 ACACAA-AAAAA
*
4729989 ACACAAACAACA
1 ACACAAA-AAAA
4730001 ACAC-AAAAAA
1 ACACAAAAAAA
4730011 A-A-AAAAAAA
1 ACACAAAAAAA
4730020 ACACAAAA
1 ACACAAAA
4730028 TCAAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
9 8 0.24
10 5 0.15
11 7 0.21
12 13 0.39
ACGTcount: A:0.78, C:0.20, G:0.00, T:0.02
Consensus pattern (11 bp):
ACACAAAAAAA
Found at i:4730008 original size:19 final size:19
Alignment explanation
Indices: 4729977--4730027 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 19
4729967 AAAGAGTCAC
4729977 ACACAATAAAAAACACAAACAACA
1 ACACAA-AAAAAA-A-AAA-AA-A
4730001 ACACAAAAAAAAAAAAAAA
1 ACACAAAAAAAAAAAAAAA
4730020 ACACAAAA
1 ACACAAAA
4730028 TCAAAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 9 0.33
20 2 0.07
21 3 0.11
22 1 0.04
23 6 0.22
24 6 0.22
ACGTcount: A:0.78, C:0.20, G:0.00, T:0.02
Consensus pattern (19 bp):
ACACAAAAAAAAAAAAAAA
Found at i:4730025 original size:24 final size:25
Alignment explanation
Indices: 4729975--4730035 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
4729965 CAAAAGAGTC
* * *
4729975 ACACACAATAAAAAACACAAACAACA
1 ACACA-AAAAAAAAAAAAAAACAACA
4730001 ACACAAAAAAAAAAAAAAAAC-ACA
1 ACACAAAAAAAAAAAAAAAACAACA
*
4730025 AAATCAAAAAA
1 ACA-CAAAAAA
4730036 TAACAAAGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 5 0.17
25 20 0.67
26 5 0.17
ACGTcount: A:0.77, C:0.20, G:0.00, T:0.03
Consensus pattern (25 bp):
ACACAAAAAAAAAAAAAAAACAACA
Found at i:4732011 original size:40 final size:41
Alignment explanation
Indices: 4731951--4732027 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 41
4731941 GATGAAATGA
* * *
4731951 AATGTTTAATGTATGCTATGATGGGTAAGGCCCAATTATTT
1 AATGTTTAATGTAAGCTATGATGAGTAAGACCCAATTATTT
*
4731992 AATGTTT-ATGTAAGTTATGATGAGTAAGACCCAATT
1 AATGTTTAATGTAAGCTATGATGAGTAAGACCCAATT
4732028 GCTCTAAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
40 25 0.78
41 7 0.22
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (41 bp):
AATGTTTAATGTAAGCTATGATGAGTAAGACCCAATTATTT
Found at i:4734308 original size:81 final size:81
Alignment explanation
Indices: 4734179--4734379 Score: 278
Period size: 81 Copynumber: 2.5 Consensus size: 81
4734169 AATATAATTA
* ** * * * ** *
4734179 TTAGAGATAATTTAAATGATCAATAATTAAATTTTGATTGGTCAAAAATATGAAGATTATCTCCA
1 TTAGAGATAAATTGGATGACCAATAACTAATTTTTGATTGGTCAAAAATACAAAGAGTATCTCCA
4734244 AATTATTTTGATTTAT
66 AATTATTTTGATTTAT
*
4734260 TTAGAGATAAATTGGATGACCAATAACTAATTTTTTGATTGGTC-AAAATACAAATAGTATCTCC
1 TTAGAGATAAATTGGATGACCAATAACTAA-TTTTTGATTGGTCAAAAATACAAAGAGTATCTCC
4734324 AAATTATTTTGATTTAT
65 AAATTATTTTGATTTAT
* *
4734341 TTGGAGATAAATTGGATGACCAAGAACTAATTTTTGATT
1 TTAGAGATAAATTGGATGACCAATAACTAATTTTTGATT
4734380 TGTCTAATTT
Statistics
Matches: 107, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
80 9 0.08
81 86 0.80
82 12 0.11
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (81 bp):
TTAGAGATAAATTGGATGACCAATAACTAATTTTTGATTGGTCAAAAATACAAAGAGTATCTCCA
AATTATTTTGATTTAT
Found at i:4744476 original size:18 final size:18
Alignment explanation
Indices: 4744455--4744495 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
4744445 GAACTTAACC
4744455 AATAATTAAAAATTTTAT
1 AATAATTAAAAATTTTAT
* *
4744473 AATAAATAATAATTTTAT
1 AATAATTAAAAATTTTAT
4744491 -ATAAT
1 AATAAT
4744496 ATGTAAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATAATTAAAAATTTTAT
Found at i:4746303 original size:13 final size:13
Alignment explanation
Indices: 4746285--4746309 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4746275 AGAAGCCATT
4746285 AAAAATAAATATA
1 AAAAATAAATATA
4746298 AAAAATAAATAT
1 AAAAATAAATAT
4746310 TTTTAAAAAT
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAATAAATATA
Found at i:4753814 original size:27 final size:28
Alignment explanation
Indices: 4753757--4753817 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
4753747 AAACACCTTA
*
4753757 AACATGGTGTGTAATAACTTTTTATTTC
1 AACATGGCGTGTAATAACTTTTTATTTC
4753785 AACATGGCGTGT-ATCAACTTTTT-TTTC
1 AACATGGCGTGTAAT-AACTTTTTATTTC
4753812 AACATG
1 AACATG
4753818 ACATGTAACT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
27 12 0.39
28 19 0.61
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (28 bp):
AACATGGCGTGTAATAACTTTTTATTTC
Found at i:4753824 original size:27 final size:28
Alignment explanation
Indices: 4753772--4753824 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
4753762 GGTGTGTAAT
* *
4753772 AACTTTTTATTTCAACATGGCGTGTATC
1 AACTTTTTATTTCAACATGACATGTATC
4753800 AACTTTTT-TTTCAACATGACATGTA
1 AACTTTTTATTTCAACATGACATGTA
4753825 ACTTGGTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.43
Consensus pattern (28 bp):
AACTTTTTATTTCAACATGACATGTATC
Found at i:4753911 original size:126 final size:126
Alignment explanation
Indices: 4753686--4753916 Score: 304
Period size: 126 Copynumber: 1.8 Consensus size: 126
4753676 ACATGGTTTA
* * * * *
4753686 AACATGGCATGTAATTTGATCTCTATCTTTGTATTTTACTAAAACATAAACTTTTGGAGTTAAAC
1 AACATGACATGTAACTTGATATCTATCTTTGCATTTCACTAAAACATAAACTTTTGGAGTTAAAC
* *
4753751 ACCTTAAACATGGTGTGTAATAACTTTTTATTTCAACATGGCGTGTATCAACTTTTTTTTC
66 ACCTTAAACATGGCGTGTAACAACTTTTTATTTCAACATGGCGTGTATCAACTTTTTTTTC
* * * * *
4753812 AACATGACATGTAACTTGGTATTTATCTTTGCATTTCATTAATATATAAACTCTTT-GAGTTAAA
1 AACATGACATGTAACTTGATATCTATCTTTGCATTTCACTAAAACATAAACT-TTTGGAGTTAAA
* *
4753876 CACCTTAAATATTGCGTGTAACAACATTTTT-TTTCAACATG
65 CACCTTAAACATGGCGTGTAACAAC-TTTTTATTTCAACATG
4753917 ACGTATAATA
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
126 81 0.91
127 8 0.09
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.42
Consensus pattern (126 bp):
AACATGACATGTAACTTGATATCTATCTTTGCATTTCACTAAAACATAAACTTTTGGAGTTAAAC
ACCTTAAACATGGCGTGTAACAACTTTTTATTTCAACATGGCGTGTATCAACTTTTTTTTC
Found at i:4763183 original size:13 final size:13
Alignment explanation
Indices: 4763165--4763189 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4763155 ATGGCTTCTT
4763165 TGTTGCTTTTTCC
1 TGTTGCTTTTTCC
4763178 TGTTGCTTTTTC
1 TGTTGCTTTTTC
4763190 ACTCATTGAT
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:0.00, C:0.20, G:0.16, T:0.64
Consensus pattern (13 bp):
TGTTGCTTTTTCC
Found at i:4769267 original size:69 final size:70
Alignment explanation
Indices: 4769156--4769298 Score: 191
Period size: 69 Copynumber: 2.0 Consensus size: 70
4769146 AATTCTTAAT
* *
4769156 TATTTCTCCCATTTCCAATCAACTAATAATAATATGTATTT-A-ATCTCCAACAACTATTTTTTT
1 TATTTCTCCCATTTCCAATCAACTAATAATAATATATATTTAAGATCTCCAACAACTATTTTTTC
4769219 CTCATA
66 CT-ATA
* ** * *
4769225 TATTTCTCCTATTTCTGATCAACTAATGATAATATATATTTAATGATCTCCAATAACTATTTTTT
1 TATTTCTCCCATTTCCAATCAACTAATAATAATATATATTTAA-GATCTCCAACAACTATTTTTT
4769290 CCTATA
65 CCTATA
4769296 TAT
1 TAT
4769299 ACAATAAATT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
69 36 0.56
70 1 0.02
71 6 0.09
72 21 0.33
ACGTcount: A:0.33, C:0.19, G:0.03, T:0.45
Consensus pattern (70 bp):
TATTTCTCCCATTTCCAATCAACTAATAATAATATATATTTAAGATCTCCAACAACTATTTTTTC
CTATA
Found at i:4773127 original size:31 final size:33
Alignment explanation
Indices: 4773089--4773174 Score: 99
Period size: 32 Copynumber: 2.7 Consensus size: 33
4773079 CATGTATCCA
4773089 AAACATTTTAGGAAACTTCTAAC-TATTT-CCT
1 AAACATTTTAGGAAACTTCTAACATATTTACCT
* **
4773120 AAACATTTTACGAAA-TT-TTCCATATTTAGCCT
1 AAACATTTTAGGAAACTTCTAACATATTTA-CCT
4773152 AAACATTTTAGGAAACTTTCTAA
1 AAACATTTTAGGAAAC-TTCTAA
4773175 ATCGAGAAGC
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
29 2 0.05
30 7 0.16
31 14 0.33
32 17 0.40
34 2 0.05
35 1 0.02
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.38
Consensus pattern (33 bp):
AAACATTTTAGGAAACTTCTAACATATTTACCT
Found at i:4790483 original size:77 final size:77
Alignment explanation
Indices: 4790398--4790546 Score: 235
Period size: 77 Copynumber: 1.9 Consensus size: 77
4790388 TGAATGAATG
* * *
4790398 TTACTAATAATTATAATAAAAAATATTTTAATGATCATCATTTGATGAATATATATGTATAAGTA
1 TTACTAATAATTATAATAAAAAATATTTTAATGATCACCATTTAATGAATACATATGTATAAGTA
4790463 TAGGTTTAAATC
66 TAGGTTTAAATC
* ** *
4790475 TTACTAATAGTTATAATAAAAAATATTTTAATGATTGCCATTTAATGAATACATATTTATAAGTA
1 TTACTAATAATTATAATAAAAAATATTTTAATGATCACCATTTAATGAATACATATGTATAAGTA
4790540 TAGGTTT
66 TAGGTTT
4790547 TAGATGTTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
77 65 1.00
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.42
Consensus pattern (77 bp):
TTACTAATAATTATAATAAAAAATATTTTAATGATCACCATTTAATGAATACATATGTATAAGTA
TAGGTTTAAATC
Found at i:4793816 original size:13 final size:13
Alignment explanation
Indices: 4793798--4793827 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4793788 AGGCCAAACA
*
4793798 TTATATTTAACCT
1 TTATATCTAACCT
4793811 TTATATCTAACCT
1 TTATATCTAACCT
4793824 TTAT
1 TTAT
4793828 TAGGCCAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (13 bp):
TTATATCTAACCT
Found at i:4794244 original size:50 final size:50
Alignment explanation
Indices: 4794169--4794269 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
4794159 ATTTGGTTGA
4794169 AGCAATTATTAGCAGATTTGGGAGTAACACAAATGTTCCAGCGAAGCTTT
1 AGCAATTATTAGCAGATTTGGGAGTAACACAAATGTTCCAGCGAAGCTTT
4794219 AGCAATTATTAGCAGATTTGGGAGTAACACAAATGTTCCAGCGAAGCTTT
1 AGCAATTATTAGCAGATTTGGGAGTAACACAAATGTTCCAGCGAAGCTTT
4794269 A
1 A
4794270 CTATGATATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.28
Consensus pattern (50 bp):
AGCAATTATTAGCAGATTTGGGAGTAACACAAATGTTCCAGCGAAGCTTT
Found at i:4795644 original size:2 final size:2
Alignment explanation
Indices: 4795633--4795662 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4795623 ATGTTATTAT
4795633 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4795663 TACATGACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4797433 original size:2 final size:2
Alignment explanation
Indices: 4797426--4797455 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4797416 AGTAAATGGA
4797426 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
4797456 TAAATGATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4801440 original size:39 final size:39
Alignment explanation
Indices: 4801396--4801474 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
4801386 TTAAAGTTTT
4801396 CAGCCTTGATTGAATCATACTCAAATTTTACCTAGCTTA
1 CAGCCTTGATTGAATCATACTCAAATTTTACCTAGCTTA
4801435 CAGCCTTGATTGAATCATACTCAAATTTTACCTAGCTTA
1 CAGCCTTGATTGAATCATACTCAAATTTTACCTAGCTTA
4801474 C
1 C
4801475 TTGGTTTAGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.35
Consensus pattern (39 bp):
CAGCCTTGATTGAATCATACTCAAATTTTACCTAGCTTA
Found at i:4803790 original size:21 final size:19
Alignment explanation
Indices: 4803751--4803790 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
4803741 ATATATACCG
*
4803751 ATAAATGATATTTATGAAA
1 ATAAATGATATTCATGAAA
4803770 ATAAATGAATAATTCATGAAA
1 ATAAATG-AT-ATTCATGAAA
4803791 TTACACCTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 2 0.11
21 9 0.50
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (19 bp):
ATAAATGATATTCATGAAA
Found at i:4807044 original size:22 final size:22
Alignment explanation
Indices: 4807019--4807069 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
4807009 AAAGCCTTTC
4807019 ATCTTCTGAGCTTTCTTTGCTT
1 ATCTTCTGAGCTTTCTTTGCTT
*
4807041 ATCTTCTGAGCTTTTTTTGCTT
1 ATCTTCTGAGCTTTCTTTGCTT
4807063 ATCTTCT
1 ATCTTCT
4807070 TCGCCATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.10, C:0.22, G:0.12, T:0.57
Consensus pattern (22 bp):
ATCTTCTGAGCTTTCTTTGCTT
Found at i:4807079 original size:22 final size:22
Alignment explanation
Indices: 4807019--4807080 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
4807009 AAAGCCTTTC
*
4807019 ATCTTCTGAG-CTTTCTTTGCTT
1 ATCTTCTGAGCCATT-TTTGCTT
**
4807041 ATCTTCTGAGCTTTTTTTGCTT
1 ATCTTCTGAGCCATTTTTGCTT
**
4807063 ATCTTCTTCGCCATTTTT
1 ATCTTCTGAGCCATTTTT
4807081 CTTCAATAGC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 31 0.91
23 3 0.09
ACGTcount: A:0.10, C:0.23, G:0.11, T:0.56
Consensus pattern (22 bp):
ATCTTCTGAGCCATTTTTGCTT
Found at i:4808858 original size:32 final size:31
Alignment explanation
Indices: 4808812--4808894 Score: 103
Period size: 32 Copynumber: 2.6 Consensus size: 31
4808802 AGTACTTATG
* **
4808812 AATTTTATTCAATTTAATTTCTATATTTTTTT
1 AATTTTATTCAATTTAATTTCTATA-TCTCAT
* * *
4808844 AATTTTATTTAATTTAATTCCTTTATCTCAT
1 AATTTTATTCAATTTAATTTCTATATCTCAT
4808875 AATTTTATTCAATTTAATTT
1 AATTTTATTCAATTTAATTT
4808895 TTATGACGTG
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 21 0.49
32 22 0.51
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.61
Consensus pattern (31 bp):
AATTTTATTCAATTTAATTTCTATATCTCAT
Found at i:4811133 original size:16 final size:16
Alignment explanation
Indices: 4811104--4811151 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
4811094 AGAGTGAAAA
*
4811104 GAAAAATAGGAAGATG
1 GAAAAATAGAAAGATG
* *
4811120 GAAAAATTGAAAGA-A
1 GAAAAATAGAAAGATG
4811135 GAAAAAGTAGAAAGATG
1 GAAAAA-TAGAAAGATG
4811152 CAAAGAAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 6 0.24
16 19 0.76
ACGTcount: A:0.60, C:0.00, G:0.27, T:0.12
Consensus pattern (16 bp):
GAAAAATAGAAAGATG
Found at i:4813562 original size:34 final size:34
Alignment explanation
Indices: 4813524--4813588 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
4813514 AGAAAAAACT
4813524 TGATAAAGAGAAATATTCTAACTTACTATTTACG
1 TGATAAAGAGAAATATTCTAACTTACTATTTACG
* * * *
4813558 TGATAAAGATAAATATTTTCACTTGCTATTT
1 TGATAAAGAGAAATATTCTAACTTACTATTT
4813589 CTACATGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (34 bp):
TGATAAAGAGAAATATTCTAACTTACTATTTACG
Found at i:4815200 original size:2 final size:2
Alignment explanation
Indices: 4815195--4815227 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4815185 TGTGTGTGTG
4815195 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4815228 TCCATATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4818233 original size:2 final size:2
Alignment explanation
Indices: 4818226--4818250 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4818216 GTGCTAAAAT
4818226 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
4818251 AGGGGAGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4839879 original size:355 final size:353
Alignment explanation
Indices: 4839230--4839934 Score: 966
Period size: 355 Copynumber: 2.0 Consensus size: 353
4839220 GACTTGCTAT
* *
4839230 GACTTATCTTCTTGTGATTCTACTTGTCAAAAAATTTTCTTACTATACGGTAGCCAATGCAAAAT
1 GACTTATCTTCTTGTGATTCTACTTGTCAAAAAATTTTCTCACCATACGGTAGCCAATGCAAAAT
* * * * * * *
4839295 TTCATCACAGGTGTCCAGTTGGGATTAAATGGATAGCCAATTGATGGCCTTCATTGTTTCTTGAT
66 TTAATCACAAGTGTACAGTTAGCATTAAATGGATAGCCAATTGATGGACTTCATTGTTTCTTGAG
* * * *
4839360 AATTGATCTGTTTGTGTAGTTCAGTGGAGAATATGAGTTGAAAAATCCAGGCTAATGGGCCTATG
131 AATTGATCTATTTCTGTAGTTCAGTGGAGAATATGAGTTGAAAAAACCAGACTAATGGGCCTATG
* * * * ** * *
4839425 ATCTTTTTTTCCTTCTTTCATACCTTTACAAATAAAACTTAAAAAATGGGTATACATATTTATTC
196 ATCTTTTTTCCCTTCCTTCATACCTTCACAAATAAAACTTAAAAAACGAATATACATATGTACTC
**
4839490 AACTGTTATGTTACTTTGTTGTCCATTTAAATTTCAAATACAGAAGAGCACTTGACAGTGGCATC
261 AACTGTTATGTTACTTTGTTGTCCATCCAAATTTCAAATACAGAAGAGCACTTGACAGTGGCATC
* *
4839555 CAATGTAGAAGAGCAATGAGTTTGTCAC
326 CAACGTAGAAGAGCAATGAATTTGTCAC
* * * **
4839583 GACTTATCTT-TATGTGATTCTACTT-TCCACAAAATTTTCTCACCATATGGTGGCTGATGCAAA
1 GACTTATCTTCT-TGTGATTCTACTTGT-CAAAAAATTTTCTCACCATACGGTAGCCAATGCAAA
* *
4839646 ATTTAATCACAAAAGTGTATAGTTAGCATTAAATGGATAGCTAATTTG-TGGACTTCATTGTTTC
64 ATTTAATCAC--AAGTGTACAGTTAGCATTAAATGGATAGCCAA-TTGATGGACTTCATTGTTTC
*
4839710 TTGAGAATTGATCTATTTCTGTAGTTCAGTGGAGAATATTAGTTGAAAAAACCAGACTAATGGGC
126 TTGAGAATTGATCTATTTCTGTAGTTCAGTGGAGAATATGAGTTGAAAAAACCAGACTAATGGGC
** * * *
4839775 CTATGATCTTTTTTCCCTTCCTTGGTTCCTTCACAAATAAAACTTAGAGAACGAATATACATATG
191 CTATGATCTTTTTTCCCTTCCTTCATACCTTCACAAATAAAACTTAAAAAACGAATATACATATG
* * *
4839840 TACTGACCTGTTATGTTACTTTGTTGTCCATCCAAATTTCAAATACAGAAGAGCATTTGACAGTG
256 TACTCAACTGTTATGTTACTTTGTTGTCCATCCAAATTTCAAATACAGAAGAGCACTTGACAGTG
*
4839905 GCATCCAACGTAGAAGCGCAATGAATTTGT
321 GCATCCAACGTAGAAGAGCAATGAATTTGT
4839935 TAGTGCTTTT
Statistics
Matches: 305, Mismatches: 42, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
352 2 0.01
353 61 0.20
355 239 0.78
356 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.36
Consensus pattern (353 bp):
GACTTATCTTCTTGTGATTCTACTTGTCAAAAAATTTTCTCACCATACGGTAGCCAATGCAAAAT
TTAATCACAAGTGTACAGTTAGCATTAAATGGATAGCCAATTGATGGACTTCATTGTTTCTTGAG
AATTGATCTATTTCTGTAGTTCAGTGGAGAATATGAGTTGAAAAAACCAGACTAATGGGCCTATG
ATCTTTTTTCCCTTCCTTCATACCTTCACAAATAAAACTTAAAAAACGAATATACATATGTACTC
AACTGTTATGTTACTTTGTTGTCCATCCAAATTTCAAATACAGAAGAGCACTTGACAGTGGCATC
CAACGTAGAAGAGCAATGAATTTGTCAC
Found at i:4851525 original size:4 final size:4
Alignment explanation
Indices: 4851511--4851542 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
4851501 CTAAATTTTC
4851511 AAAT AAAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAA
4851543 AATTAAACCT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:4855417 original size:11 final size:11
Alignment explanation
Indices: 4855401--4855455 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
4855391 GTAGACACTA
4855401 TTTTTATATTT
1 TTTTTATATTT
4855412 TTTTTATTATTT
1 TTTTTA-TATTT
*
4855424 ATTTTAT-TTT
1 TTTTTATATTT
4855434 TATTTT-TATTT
1 T-TTTTATATTT
**
4855445 TGATTATATTT
1 TTTTTATATTT
4855456 GTCTCAATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
10 6 0.17
11 20 0.56
12 10 0.28
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (11 bp):
TTTTTATATTT
Found at i:4855444 original size:12 final size:12
Alignment explanation
Indices: 4855399--4855445 Score: 62
Period size: 12 Copynumber: 4.0 Consensus size: 12
4855389 TTGTAGACAC
*
4855399 TATTTTTATATT
1 TATTTTTATTTT
4855411 T-TTTTTATTATT
1 TATTTTTATT-TT
4855423 TA-TTTTATTTT
1 TATTTTTATTTT
4855434 TATTTTTATTTT
1 TATTTTTATTTT
4855446 GATTATATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
11 11 0.35
12 20 0.65
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (12 bp):
TATTTTTATTTT
Found at i:4858666 original size:31 final size:31
Alignment explanation
Indices: 4858628--4858693 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
4858618 TTAAACAACA
4858628 TAAATTCAATAATTGACTAGTAAGGAATATG
1 TAAATTCAATAATTGACTAGTAAGGAATATG
4858659 TAAATTCAATAATTGACTAGTAAGGAATATG
1 TAAATTCAATAATTGACTAGTAAGGAATATG
4858690 TAAA
1 TAAA
4858694 CATTTAATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.32
Consensus pattern (31 bp):
TAAATTCAATAATTGACTAGTAAGGAATATG
Found at i:4861742 original size:6 final size:6
Alignment explanation
Indices: 4861733--4861785 Score: 79
Period size: 6 Copynumber: 8.8 Consensus size: 6
4861723 CCTCCTTTTC
* * *
4861733 CACCAT CACCTT CACCTT CACCAT CACCAT CACCAT CACCAT CGCCAT
1 CACCAT CACCAT CACCAT CACCAT CACCAT CACCAT CACCAT CACCAT
4861781 CACCA
1 CACCA
4861786 ATCTCTTGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.28, C:0.51, G:0.02, T:0.19
Consensus pattern (6 bp):
CACCAT
Found at i:4880561 original size:2 final size:2
Alignment explanation
Indices: 4880554--4880582 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4880544 TTTCTTTGGT
4880554 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4880583 TAGTTGTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4884302 original size:23 final size:22
Alignment explanation
Indices: 4884257--4884298 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
4884247 GTGTCATTAG
* *
4884257 TTTTTAGGTATTATGAGACTAA
1 TTTTTAAGTATTACGAGACTAA
*
4884279 TTTTTAAGTATTACGTGACT
1 TTTTTAAGTATTACGAGACT
4884299 TAATCATTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.48
Consensus pattern (22 bp):
TTTTTAAGTATTACGAGACTAA
Found at i:4884550 original size:44 final size:44
Alignment explanation
Indices: 4884467--4884572 Score: 113
Period size: 44 Copynumber: 2.4 Consensus size: 44
4884457 TATCAACCAG
* * * * *** *
4884467 TCACACAATACCTAAAAATTAATTATGCAATGTTTAAAAACTAG
1 TCACATAATACTTAAAAACTAATTATACAATGCCCAAAAACTAA
*
4884511 TCATATAATACTTAAAAACTAATTATACAATGCCCAAAAACTAA
1 TCACATAATACTTAAAAACTAATTATACAATGCCCAAAAACTAA
* *
4884555 TTACGTAATACTTAAAAA
1 TCACATAATACTTAAAAA
4884573 TCACCAAAAC
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.50, C:0.16, G:0.05, T:0.29
Consensus pattern (44 bp):
TCACATAATACTTAAAAACTAATTATACAATGCCCAAAAACTAA
Found at i:4884571 original size:22 final size:22
Alignment explanation
Indices: 4884500--4884572 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
4884490 TATGCAATGT
* * *
4884500 TTAAAAACTAGTCATATAATAC
1 TTAAAAACTAATTACATAATAC
* * *
4884522 TTAAAAACTAATTATACAATGC
1 TTAAAAACTAATTACATAATAC
** *
4884544 CCAAAAACTAATTACGTAATAC
1 TTAAAAACTAATTACATAATAC
4884566 TTAAAAA
1 TTAAAAA
4884573 TCACCAAAAC
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.52, C:0.15, G:0.04, T:0.29
Consensus pattern (22 bp):
TTAAAAACTAATTACATAATAC
Found at i:4884743 original size:60 final size:61
Alignment explanation
Indices: 4884675--4884801 Score: 150
Period size: 61 Copynumber: 2.1 Consensus size: 61
4884665 CTTGGCGAAG
* * * *
4884675 AATGCTCAAAATGTTCATAGG-TTTTTCTTT-ATGTATAAAAAATTACTCCAAAATACTTAA
1 AATGCTCAAAACGTTCAAAGGTTTTTTCTTTCATGTATAAAAAACTACT-CAAAATACTCAA
* * * * *
4884735 AATGCTCAAAACGTTTAAAGGTTTTTTTTTTCGTGTATCAAAAACTACTCTAAATACTCAA
1 AATGCTCAAAACGTTCAAAGGTTTTTTCTTTCATGTATAAAAAACTACTCAAAATACTCAA
4884796 AATGCT
1 AATGCT
4884802 TAAAGGTTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
60 18 0.32
61 24 0.43
62 14 0.25
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (61 bp):
AATGCTCAAAACGTTCAAAGGTTTTTTCTTTCATGTATAAAAAACTACTCAAAATACTCAA
Found at i:4889212 original size:30 final size:31
Alignment explanation
Indices: 4889176--4889249 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 31
4889166 ATACAAATAC
*** *
4889176 CTTTTCAAAGTTAAAT-TAGAATTTTTTTTT
1 CTTTTCAAAGTTAAATATAGAATTTCACTAT
* *
4889206 CTTTTCAAGGCT-AATATAGAATTTCACTAT
1 CTTTTCAAAGTTAAATATAGAATTTCACTAT
4889236 CTTTTCAAAGTTAA
1 CTTTTCAAAGTTAA
4889250 GATAGGACGT
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
29 3 0.09
30 30 0.88
31 1 0.03
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.47
Consensus pattern (31 bp):
CTTTTCAAAGTTAAATATAGAATTTCACTAT
Found at i:4889281 original size:30 final size:30
Alignment explanation
Indices: 4889207--4889281 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
4889197 TTTTTTTTTC
* ** *
4889207 TTTTCAAGGCTAATATAGAATTTCACTATC
1 TTTTCAAGGCTAAGATAGAACGTCACTATA
* * * *
4889237 TTTTCAAAGTTAAGATAGGACGTCTCTATA
1 TTTTCAAGGCTAAGATAGAACGTCACTATA
4889267 TTTTCAAGGCTAAGA
1 TTTTCAAGGCTAAGA
4889282 CGAAGGTATG
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (30 bp):
TTTTCAAGGCTAAGATAGAACGTCACTATA
Found at i:4890105 original size:16 final size:17
Alignment explanation
Indices: 4890076--4890110 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
4890066 GATGTGATAA
4890076 TATTTTTCAGATAATTT
1 TATTTTTCAGATAATTT
*
4890093 TATTTTTTA-ATAATTT
1 TATTTTTCAGATAATTT
4890109 TA
1 TA
4890111 AAAAGTACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (17 bp):
TATTTTTCAGATAATTT
Found at i:4893235 original size:18 final size:18
Alignment explanation
Indices: 4893212--4893255 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
4893202 CCAAAGAAAA
4893212 CCAGCAATAAAATAAGGG
1 CCAGCAATAAAATAAGGG
4893230 CCAGCAATAAAATAAGGG
1 CCAGCAATAAAATAAGGG
4893248 CCAGCAAT
1 CCAGCAAT
4893256 CATAAGTCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (18 bp):
CCAGCAATAAAATAAGGG
Found at i:4897054 original size:78 final size:78
Alignment explanation
Indices: 4896924--4897130 Score: 288
Period size: 78 Copynumber: 2.7 Consensus size: 78
4896914 AAGGTATGGG
* * *
4896924 CATGTGGCATTCCTATTATATATTAAGGTATAATGATGTCAATATGTAAATACCATCAAGGTTCA
1 CATGTGGCATTCCTATTATACATTAAGGTATAATGATGACAATATGTAAATACCATCAAGGTCCA
*
4896989 TGTCATAGGTGAA
66 TGTCATAAGTGAA
* *
4897002 CATGTGGCATTCCTATTATACATTAAGGTATAATGATGCCAATATGTCAATACCATCAAGGTCCA
1 CATGTGGCATTCCTATTATACATTAAGGTATAATGATGACAATATGTAAATACCATCAAGGTCCA
* **
4897067 TGTGATAAGTGGG
66 TGTCATAAGTGAA
* * * * *
4897080 TATGTGACATTCCTATTATACATGAAGGTATAATGGTGACAATATATAAAT
1 CATGTGGCATTCCTATTATACATTAAGGTATAATGATGACAATATGTAAAT
4897131 TTAACATCTT
Statistics
Matches: 114, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 114 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (78 bp):
CATGTGGCATTCCTATTATACATTAAGGTATAATGATGACAATATGTAAATACCATCAAGGTCCA
TGTCATAAGTGAA
Found at i:4899806 original size:33 final size:33
Alignment explanation
Indices: 4899764--4899832 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
4899754 ACATCCATTG
4899764 TATACGCCATTCTTGCTGCCAATCCTGCCACTA
1 TATACGCCATTCTTGCTGCCAATCCTGCCACTA
* * *
4899797 TATATGCCATTCTTGCTGCTAATCTTGCCACTA
1 TATACGCCATTCTTGCTGCCAATCCTGCCACTA
4899830 TAT
1 TAT
4899833 TTCTTATGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.22, C:0.30, G:0.12, T:0.36
Consensus pattern (33 bp):
TATACGCCATTCTTGCTGCCAATCCTGCCACTA
Found at i:4910775 original size:49 final size:49
Alignment explanation
Indices: 4910716--4910820 Score: 210
Period size: 49 Copynumber: 2.1 Consensus size: 49
4910706 TTATATGAGG
4910716 CTTGAGTATATTTATACCAAATGTGTTCTATTTCTTCTTGAATTGATTT
1 CTTGAGTATATTTATACCAAATGTGTTCTATTTCTTCTTGAATTGATTT
4910765 CTTGAGTATATTTATACCAAATGTGTTCTATTTCTTCTTGAATTGATTT
1 CTTGAGTATATTTATACCAAATGTGTTCTATTTCTTCTTGAATTGATTT
4910814 CTTGAGT
1 CTTGAGT
4910821 TTTGATGCAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 56 1.00
ACGTcount: A:0.24, C:0.12, G:0.13, T:0.50
Consensus pattern (49 bp):
CTTGAGTATATTTATACCAAATGTGTTCTATTTCTTCTTGAATTGATTT
Found at i:4911202 original size:43 final size:44
Alignment explanation
Indices: 4911155--4911257 Score: 127
Period size: 45 Copynumber: 2.3 Consensus size: 44
4911145 ATTTGGAGCC
* *
4911155 TACGTAACTTTAAAATGATTAAACTCCTT-ATTTGGAATAAGAT
1 TACGTAACTTTAAAAGGAATAAACTCCTTCATTTGGAATAAGAT
** * *
4911198 TACGTAACTTTCAAAAGGAATAAGTTCTTTCATTTGGAATAAGGT
1 TACGTAACTTT-AAAAGGAATAAACTCCTTCATTTGGAATAAGAT
*
4911243 TACATAACTTTAAAA
1 TACGTAACTTTAAAA
4911258 AAAAAAAATT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
43 11 0.22
44 17 0.33
45 23 0.45
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (44 bp):
TACGTAACTTTAAAAGGAATAAACTCCTTCATTTGGAATAAGAT
Found at i:4911377 original size:43 final size:43
Alignment explanation
Indices: 4911275--4911398 Score: 178
Period size: 43 Copynumber: 2.9 Consensus size: 43
4911265 ATTAAATTCA
* * *
4911275 TCATCTGGAATGAGGCTACGTAACTTTGAAA-GGATAAACTCT
1 TCATCTGGAATGAGGCTACATAACTTTGAAATGAATAAACCCT
* *
4911317 TTATCTGGAATGAGGCTACATAACTTTGAAATGAATAACCCCT
1 TCATCTGGAATGAGGCTACATAACTTTGAAATGAATAAACCCT
* *
4911360 TCATCTGGAATGAGGCTACATACCTTTAAAATGAATAAA
1 TCATCTGGAATGAGGCTACATAACTTTGAAATGAATAAA
4911399 GGCTCCTTAT
Statistics
Matches: 72, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 29 0.40
43 43 0.60
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (43 bp):
TCATCTGGAATGAGGCTACATAACTTTGAAATGAATAAACCCT
Found at i:4911566 original size:23 final size:23
Alignment explanation
Indices: 4911526--4911614 Score: 76
Period size: 24 Copynumber: 3.9 Consensus size: 23
4911516 TGAAGACGAT
* *
4911526 TACCTAAA-GATTTCGAAAATGGC
1 TACCCAAAGGATTT-GAAAATAGC
* *
4911549 TACCCAAAGGCTTTGAAAAATAGT
1 TACCCAAAGGATTTG-AAAATAGC
4911573 TACCCAAAGGATTTGAAAGAT-G-
1 TACCCAAAGGATTTGAAA-ATAGC
* *
4911595 TACCTAGAGGATTTGAAAAT
1 TACCCAAAGGATTTGAAAAT
4911615 CATTACTTGG
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
21 2 0.04
22 16 0.29
23 12 0.21
24 26 0.46
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (23 bp):
TACCCAAAGGATTTGAAAATAGC
Found at i:4911605 original size:22 final size:22
Alignment explanation
Indices: 4911580--4911707 Score: 75
Period size: 23 Copynumber: 5.7 Consensus size: 22
4911570 AGTTACCCAA
4911580 AGGATTTGAAAGATGTACCTAG
1 AGGATTTGAAAGATGTACCTAG
* * *
4911602 AGGATTTGAAA-ATCATTACTTGG
1 AGGATTTGAAAGAT--GTACCTAG
* * * *
4911625 AAGTTTTGAAA-ATGGTTACCCAA
1 AGGATTTGAAAGAT-G-TACCTAG
* * *
4911648 AGGTTTTGAAAAATTGTTATCTAG
1 AGGATTTGAAAGA-TG-TACCTAG
4911672 AGGATTTGAAAGATGTACCT-G
1 AGGATTTGAAAGATGTACCTAG
4911693 AAGGATTT-AAAGATG
1 -AGGATTTGAAAGATG
4911708 ATTATCCGGA
Statistics
Matches: 82, Mismatches: 18, Indels: 13
0.73 0.16 0.12
Matches are distributed among these distances:
21 10 0.12
22 22 0.27
23 31 0.38
24 18 0.22
25 1 0.01
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.32
Consensus pattern (22 bp):
AGGATTTGAAAGATGTACCTAG
Found at i:4911653 original size:23 final size:23
Alignment explanation
Indices: 4911525--4911659 Score: 87
Period size: 23 Copynumber: 5.9 Consensus size: 23
4911515 TTGAAGACGA
* * *
4911525 TTACCTAAAGATTTCGAAAATGG
1 TTACCCAAAGGTTTTGAAAATGG
* * *
4911548 CTACCCAAAGGCTTTGAAAAATAG
1 TTACCCAAAGGTTTTG-AAAATGG
*
4911572 TTACCCAAAGGATTTGAAAGAT-G
1 TTACCCAAAGGTTTTGAAA-ATGG
* * * **
4911595 -TACCTAGAGGATTTGAAAATCA
1 TTACCCAAAGGTTTTGAAAATGG
***
4911617 TTACTTGGAA-GTTTTGAAAATGG
1 TTAC-CCAAAGGTTTTGAAAATGG
4911640 TTACCCAAAGGTTTTGAAAA
1 TTACCCAAAGGTTTTGAAAA
4911660 ATTGTTATCT
Statistics
Matches: 85, Mismatches: 21, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
21 2 0.02
22 18 0.21
23 42 0.49
24 23 0.27
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (23 bp):
TTACCCAAAGGTTTTGAAAATGG
Found at i:4911666 original size:24 final size:24
Alignment explanation
Indices: 4911549--4911682 Score: 80
Period size: 24 Copynumber: 5.8 Consensus size: 24
4911539 CGAAAATGGC
* *
4911549 TACCCAAAGGCTTTGAAAAATAGT
1 TACCCAAAGGATTTGAAAAATTGT
*
4911573 TACCCAAAGGATTTGAAAGA-TG-
1 TACCCAAAGGATTTGAAAAATTGT
* * **
4911595 TACCTAGAGGATTTG-AAAATCAT
1 TACCCAAAGGATTTGAAAAATTGT
*** * *
4911618 TACTTGGAA-GTTTTG-AAAATGGT
1 TAC-CCAAAGGATTTGAAAAATTGT
*
4911641 TACCCAAAGGTTTTGAAAAATTGT
1 TACCCAAAGGATTTGAAAAATTGT
* * *
4911665 TATCTAGAGGATTTGAAA
1 TACCCAAAGGATTTGAAA
4911683 GATGTACCTG
Statistics
Matches: 82, Mismatches: 23, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
21 3 0.04
22 15 0.18
23 24 0.29
24 40 0.49
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (24 bp):
TACCCAAAGGATTTGAAAAATTGT
Found at i:4911727 original size:92 final size:92
Alignment explanation
Indices: 4911532--4911700 Score: 241
Period size: 92 Copynumber: 1.8 Consensus size: 92
4911522 CGATTACCTA
4911532 AAGATTTCGAAAATGGCTACCCAAAGGCTTTGAAAAATAGTTACCCAAAGGATTTGAAAGATGTA
1 AAGATTT-GAAAATGGCTACCCAAAGGCTTTGAAAAATAGTTACCCAAAGGATTTGAAAGATGTA
*
4911597 CCTAGAGGATTTGAAAATCATTACTTGG
65 CCTAGAGGATTTGAAAATCATTACTCGG
* * * * * * *
4911625 AAGTTTTGAAAATGGTTACCCAAAGGTTTTGAAAAATTGTTATCTAGAGGATTTGAAAGATGTAC
1 AAGATTTGAAAATGGCTACCCAAAGGCTTTGAAAAATAGTTACCCAAAGGATTTGAAAGATGTAC
4911690 CT-GAAGGATTT
66 CTAG-AGGATTT
4911701 AAAGATGATT
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
91 1 0.01
92 61 0.90
93 6 0.09
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.30
Consensus pattern (92 bp):
AAGATTTGAAAATGGCTACCCAAAGGCTTTGAAAAATAGTTACCCAAAGGATTTGAAAGATGTAC
CTAGAGGATTTGAAAATCATTACTCGG
Found at i:4923422 original size:28 final size:28
Alignment explanation
Indices: 4923390--4923512 Score: 101
Period size: 28 Copynumber: 4.5 Consensus size: 28
4923380 ACTATTGGTT
*
4923390 GTTAAAAGTATTCATCCATTCCTAATAG
1 GTTAAAAGTATTCATCCACTCCTAATAG
**
4923418 GTTAAAAGTATTCATCCACT-CTCGGT-G
1 GTTAAAAGTATTCATCCACTCCT-AATAG
* * * *
4923445 GTTGAAAGTATTTATCCATTCTTAGA-AG
1 GTTAAAAGTATTCATCCACTCCTA-ATAG
* * **
4923473 GTTGAAAGTATTCATCCACCCCTGGTA-
1 GTTAAAAGTATTCATCCACTCCTAATAG
4923500 GTTAAAAGTATTC
1 GTTAAAAGTATTC
4923513 TTATTATTAG
Statistics
Matches: 74, Mismatches: 16, Indels: 11
0.73 0.16 0.11
Matches are distributed among these distances:
27 32 0.43
28 42 0.57
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (28 bp):
GTTAAAAGTATTCATCCACTCCTAATAG
Found at i:4923508 original size:55 final size:54
Alignment explanation
Indices: 4923385--4923512 Score: 159
Period size: 55 Copynumber: 2.3 Consensus size: 54
4923375 TATTCACTAT
* *
4923385 TGGTTGTTAAAAGTATTCATCCATTCCTAATAGGTTAAAAGTATTCATCCACTC
1 TGGTAGTTAAAAGTATTCATCCATTCCTAATAGGTTAAAAGTATTCATCCACCC
* * * * *
4923439 TCGGTGGTTGAAAGTATTTATCCATTCTTAGA-AGGTTGAAAGTATTCATCCACCCC
1 T-GGTAGTTAAAAGTATTCATCCATTCCTA-ATAGGTTAAAAGTATTCATCCA-CCC
4923495 TGGTAGTTAAAAGTATTC
1 TGGTAGTTAAAAGTATTC
4923513 TTATTATTAG
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
54 1 0.02
55 57 0.92
56 4 0.06
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (54 bp):
TGGTAGTTAAAAGTATTCATCCATTCCTAATAGGTTAAAAGTATTCATCCACCC
Found at i:4923979 original size:12 final size:12
Alignment explanation
Indices: 4923962--4924011 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
4923952 ATGATTTGAC
4923962 TATAGTTATATA
1 TATAGTTATATA
4923974 TATAGTTATATA
1 TATAGTTATATA
* * *
4923986 TAAAGATATACA
1 TATAGTTATATA
*
4923998 TAATTGTTATATA
1 T-ATAGTTATATA
4924011 T
1 T
4924012 TTAGCAGTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
12 22 0.73
13 8 0.27
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (12 bp):
TATAGTTATATA
Found at i:4927151 original size:18 final size:18
Alignment explanation
Indices: 4927130--4927170 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 18
4927120 TTATAAAAGA
4927130 AAAAAAAGTCTAGCCAAC
1 AAAAAAAGTCTAGCCAAC
4927148 ---AAAAGTCTAGCCAAC
1 AAAAAAAGTCTAGCCAAC
4927163 AAAAAAAG
1 AAAAAAAG
4927171 GAAGGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
15 15 0.75
18 5 0.25
ACGTcount: A:0.59, C:0.20, G:0.12, T:0.10
Consensus pattern (18 bp):
AAAAAAAGTCTAGCCAAC
Found at i:4927153 original size:15 final size:15
Alignment explanation
Indices: 4927133--4927166 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
4927123 TAAAAGAAAA
4927133 AAAAGTCTAGCCAAC
1 AAAAGTCTAGCCAAC
4927148 AAAAGTCTAGCCAAC
1 AAAAGTCTAGCCAAC
4927163 AAAA
1 AAAA
4927167 AAAGGAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.24, G:0.12, T:0.12
Consensus pattern (15 bp):
AAAAGTCTAGCCAAC
Found at i:4930595 original size:45 final size:45
Alignment explanation
Indices: 4930472--4930612 Score: 178
Period size: 45 Copynumber: 3.2 Consensus size: 45
4930462 CATACCATGA
* * * ** *
4930472 TGTTACACACCATGTACAGAAACATGTTACATATCATGGTTAGAT
1 TGTTACACACCATGTACAAAAATATGTGACACGTCATGATTAGAT
*
4930517 TGTTACACACC--GTATAAAAATATGTGACACGTCATGATTAGAT
1 TGTTACACACCATGTACAAAAATATGTGACACGTCATGATTAGAT
* * *
4930560 TGTTACATACCATGTACAAAAATATGTGATACGTCATGATTAGGT
1 TGTTACACACCATGTACAAAAATATGTGACACGTCATGATTAGAT
4930605 TGTTACAC
1 TGTTACAC
4930613 GTCATGTTAG
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
43 35 0.43
45 47 0.57
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (45 bp):
TGTTACACACCATGTACAAAAATATGTGACACGTCATGATTAGAT
Found at i:4930619 original size:45 final size:46
Alignment explanation
Indices: 4930472--4930629 Score: 164
Period size: 45 Copynumber: 3.5 Consensus size: 46
4930462 CATACCATGA
* * * ** *
4930472 TGTTACACACCATG-TACAGAAACATGTTACATATCATGGTTAGAT
1 TGTTACACACCATGTTACAAAAATATGTGACACGTCATGATTAGAT
*
4930517 TGTTACACACC--G-TATAAAAATATGTGACACGTCATGATTAGAT
1 TGTTACACACCATGTTACAAAAATATGTGACACGTCATGATTAGAT
* * *
4930560 TGTTACATACCATG-TACAAAAATATGTGATACGTCATGATTAGGT
1 TGTTACACACCATGTTACAAAAATATGTGACACGTCATGATTAGAT
** *
4930605 TGTTACACGTCATGTTAGAAAAATA
1 TGTTACACACCATGTTACAAAAATA
4930630 GTATTGTTAC
Statistics
Matches: 95, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
43 35 0.37
45 51 0.54
46 9 0.09
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (46 bp):
TGTTACACACCATGTTACAAAAATATGTGACACGTCATGATTAGAT
Found at i:4930712 original size:25 final size:25
Alignment explanation
Indices: 4930651--4930712 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
4930641 TGTTATGTAC
*
4930651 AAAAACATATTACATGCCATGGTTA
1 AAAAAAATATTACATGCCATGGTTA
** *
4930676 AAAAATGTTATTATATGCCAT-GTTGA
1 AAAAA-AATATTACATGCCATGGTT-A
4930702 AAAAAAATATT
1 AAAAAAATATT
4930713 GTTATTACAC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
25 12 0.40
26 18 0.60
ACGTcount: A:0.47, C:0.10, G:0.11, T:0.32
Consensus pattern (25 bp):
AAAAAAATATTACATGCCATGGTTA
Found at i:4930734 original size:29 final size:31
Alignment explanation
Indices: 4930681--4930775 Score: 124
Period size: 31 Copynumber: 3.1 Consensus size: 31
4930671 GGTTAAAAAA
* *
4930681 TGTTATTATATGCCATGTTGAAAAAAAATAT
1 TGTTATTACACGCCATGTTGAAAAAAAATAT
*
4930712 TGTTATTACACG-CATGTTGAAAAAAAAATAC
1 TGTTATTACACGCCATGTTG-AAAAAAAATAT
*
4930743 TGTTATTACACGCCATATTG--AAAAAATAT
1 TGTTATTACACGCCATGTTGAAAAAAAATAT
4930772 TGTT
1 TGTT
4930776 GTCACATGTC
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
29 12 0.21
30 7 0.12
31 32 0.56
32 6 0.11
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.36
Consensus pattern (31 bp):
TGTTATTACACGCCATGTTGAAAAAAAATAT
Found at i:4936825 original size:29 final size:27
Alignment explanation
Indices: 4936781--4936834 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
4936771 AATAACTTTA
4936781 TAAATTTTATTCAATTTTACTTAAATTCT
1 TAAATTTTATTCAATTTT--TTAAATTCT
* *
4936810 TAAATTTTTTTTAATTTTTTAAATT
1 TAAATTTTATTCAATTTTTTAAATT
4936835 TAACCATCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
29 16 0.70
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (27 bp):
TAAATTTTATTCAATTTTTTAAATTCT
Found at i:4937863 original size:2 final size:2
Alignment explanation
Indices: 4937856--4937896 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
4937846 GAATGCAATT
4937856 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4937897 TTCTTTATAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4939855 original size:51 final size:51
Alignment explanation
Indices: 4939757--4939858 Score: 123
Period size: 51 Copynumber: 2.0 Consensus size: 51
4939747 CGATACTTGG
* * * * * * * *
4939757 ATCAAATGCGATATTTTATACTTATTATTTTTTATTAGTGTCGTGACATAT
1 ATCAAATGCCATACTTTATACATATCATTTTCTACTAGTATCATGACATAT
*
4939808 ATCAAATGCCATACTTTATACATATCGTTTTCTACTAGTATCATGACATAT
1 ATCAAATGCCATACTTTATACATATCATTTTCTACTAGTATCATGACATAT
4939859 CGTGCAATAT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (51 bp):
ATCAAATGCCATACTTTATACATATCATTTTCTACTAGTATCATGACATAT
Found at i:4945609 original size:36 final size:36
Alignment explanation
Indices: 4945530--4945597 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
4945520 TGCTTCCTTC
* *
4945530 GAGCTCCCCTGGTGCTTTCTTGGGGAGTTTGAAATT
1 GAGCTCCCCTGGTGCTTTCTTGGGGAGTCTCAAATT
* *
4945566 GAGCTCCCCTGGTGCTTTTTTTGGGAG-CTCAA
1 GAGCTCCCCTGGTGCTTTCTTGGGGAGTCTCAA
4945598 TTTGGGGCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 3 0.11
36 25 0.89
ACGTcount: A:0.13, C:0.22, G:0.29, T:0.35
Consensus pattern (36 bp):
GAGCTCCCCTGGTGCTTTCTTGGGGAGTCTCAAATT
Found at i:4946411 original size:34 final size:34
Alignment explanation
Indices: 4946366--4946466 Score: 139
Period size: 34 Copynumber: 3.0 Consensus size: 34
4946356 TGTTCTTTAA
* **
4946366 TTTCTGATTTTAACGAATCAAGTAAGTGACTTAT
1 TTTCTAATTTTAAAAAATCAAGTAAGTGACTTAT
*
4946400 TTTCTAGTTTTAAAAAATCAAGTAAGTGACTTAT
1 TTTCTAATTTTAAAAAATCAAGTAAGTGACTTAT
* * *
4946434 TTTCTAATTTTAGAAAATCAGGTAAATGACTTA
1 TTTCTAATTTTAAAAAATCAAGTAAGTGACTTA
4946467 ATATCTCTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 59 1.00
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.41
Consensus pattern (34 bp):
TTTCTAATTTTAAAAAATCAAGTAAGTGACTTAT
Found at i:4947026 original size:27 final size:27
Alignment explanation
Indices: 4946964--4947026 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
4946954 AATTTTAAGA
*
4946964 ATAATTTTACCCACCAGAAGTGAATAG
1 ATAATTTTACCCACCAAAAGTGAATAG
** * *
4946991 ATAGCTTTACCCACCAAAAGTGGATGG
1 ATAATTTTACCCACCAAAAGTGAATAG
4947018 ATAATTTTA
1 ATAATTTTA
4947027 ATTTTACCCA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (27 bp):
ATAATTTTACCCACCAAAAGTGAATAG
Found at i:4947046 original size:33 final size:33
Alignment explanation
Indices: 4946996--4947065 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 33
4946986 AATAGATAGC
4946996 TTTACCCACCAAAAGTGGATGGATAATTTTAA-T
1 TTTACCCACCAAAAGTGGATGGATAA-TTTAAGT
*
4947029 TTTACCCA-CAAAGAGTGGATGTATAATTTAAGT
1 TTTACCCACCAAA-AGTGGATGGATAATTTAAGT
4947062 TTTA
1 TTTA
4947066 TTCACTAGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
32 9 0.26
33 25 0.74
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.36
Consensus pattern (33 bp):
TTTACCCACCAAAAGTGGATGGATAATTTAAGT
Found at i:4947120 original size:28 final size:28
Alignment explanation
Indices: 4947088--4947141 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
4947078 GGATGTATAA
* * *
4947088 TTTAACCCACTAAGAGTAGGTGAATACT
1 TTTAACCCACCAAAAGTAGATGAATACT
*
4947116 TTTAATCCACCAAAAGTAGATGAATA
1 TTTAACCCACCAAAAGTAGATGAATA
4947142 GTAAAAAGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.28
Consensus pattern (28 bp):
TTTAACCCACCAAAAGTAGATGAATACT
Found at i:4947175 original size:21 final size:22
Alignment explanation
Indices: 4947143--4947185 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
4947133 AGATGAATAG
*
4947143 TAAAAAGATATAAGA-AAAAGA
1 TAAAAAGATATAAAATAAAAGA
4947164 TAAAAATG-TATAAAATAAAAGA
1 TAAAAA-GATATAAAATAAAAGA
4947186 AATATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.19
Consensus pattern (22 bp):
TAAAAAGATATAAAATAAAAGA
Found at i:4947321 original size:39 final size:38
Alignment explanation
Indices: 4947261--4947335 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 38
4947251 TGAAATATAT
*
4947261 TGTTGAACTTTATAAGCATCACTGAATGCTAAAAAAAAA
1 TGTTGAACTTTATAA-CATCACTAAATGCTAAAAAAAAA
*
4947300 TGTTGAACTTTATCTAA-ATCACTAAATGCTTAAAAA
1 TGTTGAACTTTA--TAACATCACTAAATGCTAAAAAA
4947336 TATATCAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
39 29 0.91
41 3 0.09
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.32
Consensus pattern (38 bp):
TGTTGAACTTTATAACATCACTAAATGCTAAAAAAAAA
Found at i:4947632 original size:2 final size:2
Alignment explanation
Indices: 4947625--4947653 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4947615 TTTCTTATTT
4947625 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4947654 TAAAAAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4957258 original size:13 final size:13
Alignment explanation
Indices: 4957242--4957277 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
4957232 TTTAGTTTAA
*
4957242 ATTTTGGTTAATT
1 ATTTTAGTTAATT
4957255 ATTTTAGTTAATT
1 ATTTTAGTTAATT
*
4957268 AATTTAGTTA
1 ATTTTAGTTA
4957278 TTTCGTATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (13 bp):
ATTTTAGTTAATT
Found at i:4962468 original size:28 final size:29
Alignment explanation
Indices: 4962409--4962500 Score: 123
Period size: 29 Copynumber: 3.2 Consensus size: 29
4962399 TATTGTATGA
* *
4962409 GTTTGTAGTGATCTTGTTAAAAACCATGG
1 GTTTGTAGTGAACTTGTTAAAAACAATGG
*
4962438 GTTTGTGGTGAACTTGTT-AAAACAATGG
1 GTTTGTAGTGAACTTGTTAAAAACAATGG
* * *
4962466 GTTTATAGTGAGCCTGTTAAAAACAATGG
1 GTTTGTAGTGAACTTGTTAAAAACAATGG
4962495 GTTTGT
1 GTTTGT
4962501 GGTTGAGGCC
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
28 23 0.43
29 31 0.57
ACGTcount: A:0.28, C:0.09, G:0.26, T:0.37
Consensus pattern (29 bp):
GTTTGTAGTGAACTTGTTAAAAACAATGG
Found at i:4964564 original size:17 final size:16
Alignment explanation
Indices: 4964537--4964570 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
4964527 TATTTAGAGA
*
4964537 TAACTTAAGAAGAAGT
1 TAACTTAAGAAAAAGT
4964553 TAACTATAAGAAAAAGT
1 TAACT-TAAGAAAAAGT
4964570 T
1 T
4964571 CTAAGAGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.53, C:0.06, G:0.15, T:0.26
Consensus pattern (16 bp):
TAACTTAAGAAAAAGT
Found at i:4965230 original size:14 final size:15
Alignment explanation
Indices: 4965211--4965261 Score: 61
Period size: 16 Copynumber: 3.5 Consensus size: 15
4965201 TTTGATTTTC
4965211 TTTAGTTTAAATTT-
1 TTTAGTTTAAATTTA
*
4965225 TTTAG-TTAGATTTA
1 TTTAGTTTAAATTTA
*
4965239 GTTAGTTTATAATTTA
1 TTTAGTTTA-AATTTA
4965255 TTTAGTT
1 TTTAGTT
4965262 ACTTGCTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 7 0.23
14 9 0.30
15 3 0.10
16 11 0.37
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (15 bp):
TTTAGTTTAAATTTA
Found at i:4969969 original size:21 final size:21
Alignment explanation
Indices: 4969940--4969980 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4969930 TTAGGGGAGT
* *
4969940 TTTTGTTTTCCTTTCTTTTTA
1 TTTTATTTTCATTTCTTTTTA
*
4969961 TTTTATTTTTATTTCTTTTT
1 TTTTATTTTCATTTCTTTTT
4969981 CTTAAACGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.10, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTATTTTCATTTCTTTTTA
Found at i:4976151 original size:58 final size:58
Alignment explanation
Indices: 4976059--4976234 Score: 218
Period size: 58 Copynumber: 3.1 Consensus size: 58
4976049 AAGGTCTTGT
* * *
4976059 CTTTGCA-TGCATAGCATTTATTAAA--TCATGTAAAATAAATCTATCACATGTATATTA
1 CTTTGCATTGCATAGCATTTATTAAATGTCA--TAAAATAAATCTATCACATGCAAACTA
* *
4976116 CTTTGCATTGCATAGCATTTATTAAATGTCATAAAATAAATCTATCATATCCAAACTA
1 CTTTGCATTGCATAGCATTTATTAAATGTCATAAAATAAATCTATCACATGCAAACTA
* * *
4976174 TTTTGCATTGCATAGCATCTATTAAATTGT-AT-CAATAAATCTATCACATGCAAACTA
1 CTTTGCATTGCATAGCATTTATTAAA-TGTCATAAAATAAATCTATCACATGCAAACTA
4976231 CTTT
1 CTTT
4976235 AGATGATTAT
Statistics
Matches: 104, Mismatches: 11, Indels: 8
0.85 0.09 0.07
Matches are distributed among these distances:
57 32 0.31
58 66 0.63
59 3 0.03
60 3 0.03
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (58 bp):
CTTTGCATTGCATAGCATTTATTAAATGTCATAAAATAAATCTATCACATGCAAACTA
Found at i:4977638 original size:18 final size:18
Alignment explanation
Indices: 4977615--4977652 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
4977605 TTGGGTTTTG
*
4977615 TTTTTCTTTTACAGCTAT
1 TTTTTCTTTTACAGATAT
4977633 TTTTTCTTTTACAGATAT
1 TTTTTCTTTTACAGATAT
4977651 TT
1 TT
4977653 GGTGGCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.13, G:0.05, T:0.63
Consensus pattern (18 bp):
TTTTTCTTTTACAGATAT
Found at i:4980495 original size:16 final size:16
Alignment explanation
Indices: 4980464--4980498 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4980454 CTAAACAATT
**
4980464 AAAATTAAAGCTACTA
1 AAAATTAAAGAAACTA
4980480 AAAATTAAAGAAACTA
1 AAAATTAAAGAAACTA
4980496 AAA
1 AAA
4980499 CTAAAACTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.66, C:0.09, G:0.06, T:0.20
Consensus pattern (16 bp):
AAAATTAAAGAAACTA
Found at i:4980501 original size:6 final size:6
Alignment explanation
Indices: 4980490--4980516 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4980480 AAAATTAAAG
4980490 AAACTA AAACTA AAACTA AAACTA AAA
1 AAACTA AAACTA AAACTA AAACTA AAA
4980517 GAAACAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (6 bp):
AAACTA
Found at i:4988716 original size:19 final size:20
Alignment explanation
Indices: 4988681--4988721 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
4988671 CCTTTTGGAC
4988681 TTTTGGTATTTGCCATCTCT
1 TTTTGGTATTTGCCATCTCT
4988701 TTTTGTGTA-TTG-CATCTCT
1 TTTTG-GTATTTGCCATCTCT
4988720 TT
1 TT
4988722 GGTTATTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.45
20 8 0.40
21 3 0.15
ACGTcount: A:0.10, C:0.17, G:0.15, T:0.59
Consensus pattern (20 bp):
TTTTGGTATTTGCCATCTCT
Found at i:5000611 original size:40 final size:41
Alignment explanation
Indices: 5000567--5000646 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
5000557 ATTTAATTTC
* *
5000567 AAATTTCA-AA-AATTATATTTTTATATAAATCTTTAAAATT
1 AAATTTCATAACAATT-TAATTTTATATAAATCTTAAAAATT
* *
5000607 AAATTTCATAACAATTTAATTTTCTATACATCTTAAAAAT
1 AAATTTCATAACAATTTAATTTTATATAAATCTTAAAAAT
5000647 AATTTACTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 8 0.24
41 22 0.65
42 4 0.12
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.45
Consensus pattern (41 bp):
AAATTTCATAACAATTTAATTTTATATAAATCTTAAAAATT
Found at i:5001055 original size:17 final size:18
Alignment explanation
Indices: 5001013--5001058 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
5001003 AAGGTAAAGT
* *
5001013 TTTTATTTAATTTATTTA
1 TTTTATTTTATTTATTAA
5001031 -TTTA-TTTATTT-TTAA
1 TTTTATTTTATTTATTAA
5001046 TTTTATTTTATTT
1 TTTTATTTTATTT
5001059 GCTCATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 3 0.12
16 10 0.42
17 11 0.46
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTATTTTATTTATTAA
Found at i:5001208 original size:22 final size:21
Alignment explanation
Indices: 5001166--5001213 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
5001156 TATCATGATT
* *
5001166 TTTTATTTTTTATTATGTAAA
1 TTTTATTTTTAATGATGTAAA
*
5001187 TTTTATTTTTAATGATTTTAAA
1 TTTTATTTTTAATGA-TGTAAA
5001209 TTTTA
1 TTTTA
5001214 AAAATTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (21 bp):
TTTTATTTTTAATGATGTAAA
Found at i:5008347 original size:15 final size:15
Alignment explanation
Indices: 5008323--5008357 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5008313 ATTCAACCAA
*
5008323 TATTATAAAATAAAC
1 TATTACAAAATAAAC
*
5008338 TATTACAAAATTAAC
1 TATTACAAAATAAAC
5008353 TATTA
1 TATTA
5008358 AAGGACTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (15 bp):
TATTACAAAATAAAC
Found at i:5008460 original size:14 final size:14
Alignment explanation
Indices: 5008441--5008467 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5008431 CAACATTATA
5008441 AAATAAACTATTAC
1 AAATAAACTATTAC
5008455 AAATAAACTATTA
1 AAATAAACTATTA
5008468 GAGGCTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATAAACTATTAC
Found at i:5011545 original size:24 final size:24
Alignment explanation
Indices: 5011517--5011563 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5011507 ATGCTCCTTG
5011517 TGTAAATC-ATCTCATTGAATACAT
1 TGTAAATCAAT-TCATTGAATACAT
* *
5011541 TGTAATTCAATTCATTTAATACA
1 TGTAAATCAATTCATTGAATACA
5011564 AGCTTAGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.40
Consensus pattern (24 bp):
TGTAAATCAATTCATTGAATACAT
Found at i:5016634 original size:47 final size:46
Alignment explanation
Indices: 5016559--5016648 Score: 171
Period size: 47 Copynumber: 1.9 Consensus size: 46
5016549 CCATTTAAGG
5016559 GGGCTGCTGGAAAATCAAATTTTCCCTCCCAACCGAACTTCTAAAA
1 GGGCTGCTGGAAAATCAAATTTTCCCTCCCAACCGAACTTCTAAAA
5016605 GGGCTGCTGGAAAATTCAAATTTTCCCTCCCAACCGAACTTCTA
1 GGGCTGCTGGAAAA-TCAAATTTTCCCTCCCAACCGAACTTCTA
5016649 GAACCTCCCA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 14 0.33
47 29 0.67
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.26
Consensus pattern (46 bp):
GGGCTGCTGGAAAATCAAATTTTCCCTCCCAACCGAACTTCTAAAA
Found at i:5023510 original size:38 final size:42
Alignment explanation
Indices: 5023468--5023563 Score: 101
Period size: 47 Copynumber: 2.2 Consensus size: 42
5023458 ATGATTTTAT
5023468 TTATTTA-TTA-GATA-AAT-TTTATAAAATGCATGATGTAA
1 TTATTTACTTATGATAGAATATTTATAAAATGCATGATGTAA
*
5023506 TTATTTTACTTACTTGTTAGGTAATATTTATAAAATGCATGATGTAA
1 TTA-TTTACTTA--TGATA-G-AATATTTATAAAATGCATGATGTAA
5023553 TTATTTTACTT
1 TTA-TTTACTT
5023564 TTTTGTTAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 9
0.83 0.02 0.16
Matches are distributed among these distances:
38 3 0.06
39 4 0.08
40 3 0.06
43 3 0.06
46 3 0.06
47 32 0.67
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.49
Consensus pattern (42 bp):
TTATTTACTTATGATAGAATATTTATAAAATGCATGATGTAA
Found at i:5023558 original size:24 final size:24
Alignment explanation
Indices: 5023485--5023558 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
5023475 TTAGATAAAT
5023485 TTTATAAAATGCATGATGTAATTA
1 TTTATAAAATGCATGATGTAATTA
* ** * *
5023509 TTTTACTTACTTG--TTAGGTAA-TA
1 -TTTA-TAAAATGCATGATGTAATTA
5023532 TTTATAAAATGCATGATGTAATTA
1 TTTATAAAATGCATGATGTAATTA
5023556 TTT
1 TTT
5023559 TACTTTTTTG
Statistics
Matches: 35, Mismatches: 10, Indels: 9
0.65 0.19 0.17
Matches are distributed among these distances:
21 4 0.11
22 4 0.11
23 8 0.23
24 11 0.31
25 4 0.11
26 4 0.11
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.47
Consensus pattern (24 bp):
TTTATAAAATGCATGATGTAATTA
Found at i:5023570 original size:47 final size:47
Alignment explanation
Indices: 5023485--5023576 Score: 157
Period size: 47 Copynumber: 2.0 Consensus size: 47
5023475 TTAGATAAAT
*
5023485 TTTATAAAATGCATGATGTAATTATTTTACTTACTTGTTAGGTAATA
1 TTTATAAAATGCATGATGTAATTATTTTACTTACTTGTTAAGTAATA
**
5023532 TTTATAAAATGCATGATGTAATTATTTTACTTTTTTGTTAAGTAA
1 TTTATAAAATGCATGATGTAATTATTTTACTTACTTGTTAAGTAA
5023577 AATTGTATTC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (47 bp):
TTTATAAAATGCATGATGTAATTATTTTACTTACTTGTTAAGTAATA
Found at i:5026923 original size:2 final size:2
Alignment explanation
Indices: 5026918--5026948 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5026908 TATATATATA
5026918 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
5026949 TACTATTGGG
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:5027928 original size:16 final size:16
Alignment explanation
Indices: 5027909--5027944 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5027899 TTTAAATTAT
*
5027909 AAAAACAAGAAAAATG
1 AAAAACAAAAAAAATG
*
5027925 AAAAAGAAAAAAAATG
1 AAAAACAAAAAAAATG
5027941 AAAA
1 AAAA
5027945 GTCATCATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.81, C:0.03, G:0.11, T:0.06
Consensus pattern (16 bp):
AAAAACAAAAAAAATG
Found at i:5030865 original size:14 final size:14
Alignment explanation
Indices: 5030846--5030885 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
5030836 GACAAATGAG
5030846 AAGAAAAAGAGAAA
1 AAGAAAAAGAGAAA
* *
5030860 AAGAAAGAGAGAGA
1 AAGAAAAAGAGAAA
5030874 AAGAAAAAGAGA
1 AAGAAAAAGAGA
5030886 TATGGAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (14 bp):
AAGAAAAAGAGAAA
Found at i:5030874 original size:16 final size:16
Alignment explanation
Indices: 5030846--5030885 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 16
5030836 GACAAATGAG
5030846 AAGAAAAAGAGA-A-A
1 AAGAAAAAGAGAGAGA
5030860 AAG--AAAGAGAGAGA
1 AAGAAAAAGAGAGAGA
5030874 AAGAAAAAGAGA
1 AAGAAAAAGAGA
5030886 TATGGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 7 0.32
13 1 0.05
14 7 0.32
16 7 0.32
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (16 bp):
AAGAAAAAGAGAGAGA
Found at i:5033072 original size:31 final size:31
Alignment explanation
Indices: 5033034--5033372 Score: 219
Period size: 31 Copynumber: 11.0 Consensus size: 31
5033024 ATTTTTAAAG
* *
5033034 TATTGGAATCTCAGTGGAGGAATTCTTAAGA
1 TATTAGAATCTTAGTGGAGGAATTCTTAAGA
* ** * *
5033065 TATTGGAAAATTGGTGGAGGAATTCTTATGA
1 TATTAGAATCTTAGTGGAGGAATTCTTAAGA
* * *
5033096 TATTAG-ATCCTTGGTGGAGAAATTCTTAGGA
1 TATTAGAAT-CTTAGTGGAGGAATTCTTAAGA
* * * *
5033127 TATT-GAAGCCTTAATGGAGGAATTTTTAAGC
1 TATTAGAA-TCTTAGTGGAGGAATTCTTAAGA
* *
5033158 TATTAGAGA-CTTAATGGAGGAATTCTTACGA
1 TATTAGA-ATCTTAGTGGAGGAATTCTTAAGA
* * *
5033189 -AGTTGGAACCTTAGTGGATGAATTCTTAAGA
1 TA-TTAGAATCTTAGTGGAGGAATTCTTAAGA
* *
5033220 TATTAG-ATCCTCAATGGAGGAATTCTTAAGA
1 TATTAGAAT-CTTAGTGGAGGAATTCTTAAGA
* * * *
5033251 AATTGGAATC-TCGATGGAAGAATTCTTAAGA
1 TATTAGAATCTTAG-TGGAGGAATTCTTAAGA
* *
5033282 TATTAG-ATCCTCA-TGGAGGAATTCGTAAGA
1 TATTAGAAT-CTTAGTGGAGGAATTCTTAAGA
* * * *
5033312 TAAT-GAAGCCTTGGTGGAGGAATTCTTAAAA
1 TATTAGAA-TCTTAGTGGAGGAATTCTTAAGA
* ** * *
5033343 TTTTAGAGCCCTGGTGGAGGAATTCTTAAG
1 TATTAGAATCTTAGTGGAGGAATTCTTAAG
5033373 GTGTTGGAAC
Statistics
Matches: 239, Mismatches: 52, Indels: 34
0.74 0.16 0.10
Matches are distributed among these distances:
29 1 0.00
30 28 0.12
31 202 0.85
32 7 0.03
33 1 0.00
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.32
Consensus pattern (31 bp):
TATTAGAATCTTAGTGGAGGAATTCTTAAGA
Found at i:5033122 original size:62 final size:62
Alignment explanation
Indices: 5033048--5033384 Score: 322
Period size: 62 Copynumber: 5.5 Consensus size: 62
5033038 GGAATCTCAG
** * **
5033048 TGGAGGAATTCTTAAGATATTGGAAAATTGGTGGAGGAATTCTTATGATATTAGATCCTTGG
1 TGGAGGAATTCTTAAGATATTGGAACCTTGGTGGAGGAATTCTTAAGATATTAGATCCTTAA
* * ** * * **
5033110 TGGAGAAATTCTTAGGATATT-GAAGCCTTAATGGAGGAATTTTTAAGCTATTAGAGACTTAA
1 TGGAGGAATTCTTAAGATATTGGAA-CCTTGGTGGAGGAATTCTTAAGATATTAGATCCTTAA
* * * *
5033172 TGGAGGAATTCTTACGA-AGTTGGAACCTTAGTGGATGAATTCTTAAGATATTAGATCCTCAA
1 TGGAGGAATTCTTAAGATA-TTGGAACCTTGGTGGAGGAATTCTTAAGATATTAGATCCTTAA
* * * * * *
5033234 TGGAGGAATTCTTAAGAAATTGGAATCTCGATGGAAGAATTCTTAAGATATTAGATCC-TCA
1 TGGAGGAATTCTTAAGATATTGGAACCTTGGTGGAGGAATTCTTAAGATATTAGATCCTTAA
* * * * * * **
5033295 TGGAGGAATTCGTAAGATAAT-GAAGCCTTGGTGGAGGAATTCTTAAAATTTTAGAGCCCTGG
1 TGGAGGAATTCTTAAGATATTGGAA-CCTTGGTGGAGGAATTCTTAAGATATTAGATCCTTAA
* *
5033357 TGGAGGAATTCTTAAGGTGTTGGAACCT
1 TGGAGGAATTCTTAAGATATTGGAACCT
5033385 CGATAGAGGA
Statistics
Matches: 222, Mismatches: 46, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
60 3 0.01
61 49 0.22
62 163 0.73
63 7 0.03
ACGTcount: A:0.32, C:0.10, G:0.25, T:0.32
Consensus pattern (62 bp):
TGGAGGAATTCTTAAGATATTGGAACCTTGGTGGAGGAATTCTTAAGATATTAGATCCTTAA
Found at i:5033814 original size:40 final size:41
Alignment explanation
Indices: 5033756--5033851 Score: 106
Period size: 41 Copynumber: 2.4 Consensus size: 41
5033746 TAAAGCCCCA
* * *
5033756 ATGGAGGAATTCTCATTTC-CTTTCAAAGTT-TTCAGCCTCG
1 ATGGAGGAGTTTTCATTTCACTTTC-AAGTTGTGCAGCCTCG
* * **
5033796 ATGGAGGAGTTTTTATTTCATTTTCAAGTTGTGGTGCCTCG
1 ATGGAGGAGTTTTCATTTCACTTTCAAGTTGTGCAGCCTCG
5033837 ATGGAGGAGTTTTCA
1 ATGGAGGAGTTTTCA
5033852 ATTCTTTTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
40 21 0.46
41 25 0.54
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.40
Consensus pattern (41 bp):
ATGGAGGAGTTTTCATTTCACTTTCAAGTTGTGCAGCCTCG
Found at i:5040632 original size:15 final size:16
Alignment explanation
Indices: 5040612--5040654 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
5040602 ACATAAAATT
*
5040612 AAAATAACTCACT-TA
1 AAAATAACTAACTATA
*
5040627 AAAATAAACTAATTATA
1 AAAAT-AACTAACTATA
5040644 AAAATAACTAA
1 AAAATAACTAA
5040655 AATTAAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 12 0.50
17 7 0.29
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATAACTAACTATA
Found at i:5044890 original size:2 final size:2
Alignment explanation
Indices: 5044885--5044923 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
5044875 TGCTTTTTTG
*
5044885 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5044924 TTGTGAAGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5045075 original size:35 final size:34
Alignment explanation
Indices: 5045018--5045101 Score: 89
Period size: 35 Copynumber: 2.4 Consensus size: 34
5045008 TTGCTCTTGT
5045018 GAAAAAGCTATTGT-AAGCGTTTCACTTAATATTGG
1 GAAAAAGCTATT-TCAAGCGTTTCACTTAATATT-G
* * * *
5045053 GAAAAAGCTATTTCAAGGGTTTCGCTTGATCTTG
1 GAAAAAGCTATTTCAAGCGTTTCACTTAATATTG
*
5045087 TAAAAAGCTCATTTC
1 GAAAAAGCT-ATTTC
5045102 TCTTAGTGGA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
34 10 0.24
35 32 0.76
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (34 bp):
GAAAAAGCTATTTCAAGCGTTTCACTTAATATTG
Found at i:5064878 original size:28 final size:28
Alignment explanation
Indices: 5064820--5064880 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
5064810 TGCCATGCTT
* * *
5064820 AAAAAAATTTTGCTGCACATCATTTTAA
1 AAAAAAATGTTGCTACACATCATGTTAA
* * *
5064848 AAAAAAATGTTGTTACACATTATGTTGA
1 AAAAAAATGTTGCTACACATCATGTTAA
5064876 AAAAA
1 AAAAA
5064881 TGTTATTGTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (28 bp):
AAAAAAATGTTGCTACACATCATGTTAA
Done.