Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 55 of 335
Found at i:19420704 original size:18 final size:17
Alignment explanation
Indices: 19420656--19420698 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 17
19420646 TAATTCTAAA
19420656 TATTTCTTAGTTTATTCAT
1 TATTTCTT--TTTATTCAT
19420675 TATTTCCTTTTTATTCATT
1 TATTT-CTTTTTATTCA-T
19420694 TATTT
1 TATTT
19420699 TATTTTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.36
19 11 0.50
20 3 0.14
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTTCTTTTTATTCAT
Found at i:19420704 original size:19 final size:18
Alignment explanation
Indices: 19420666--19420729 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
19420656 TATTTCTTAG
*
19420666 TTTATTCATTATTTCCTT
1 TTTATTCATTATTTCATT
*
19420684 TTTATTCATTTATTTTATT
1 TTTATTCA-TTATTTCATT
* *
19420703 TTTGTTC-TTATCATCATT
1 TTTATTCATTAT-TTCATT
*
19420721 ATTATTCAT
1 TTTATTCAT
19420730 ATTCACCTCT
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
17 4 0.11
18 17 0.47
19 15 0.42
ACGTcount: A:0.20, C:0.12, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTATTCATTATTTCATT
Found at i:19430595 original size:16 final size:16
Alignment explanation
Indices: 19430574--19430606 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
19430564 TTCAAGTCAT
19430574 CGCAACTCTTTTGTCC
1 CGCAACTCTTTTGTCC
19430590 CGCAACTCTTTTGTCC
1 CGCAACTCTTTTGTCC
19430606 C
1 C
19430607 CACTTTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.39, G:0.12, T:0.36
Consensus pattern (16 bp):
CGCAACTCTTTTGTCC
Found at i:19434558 original size:17 final size:16
Alignment explanation
Indices: 19434538--19434592 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
19434528 TAATATTAGT
19434538 ATATAAATAGAAATA-AA
1 ATAT-AATA-AAATAGAA
19434555 ATATAAT-AAATAGAA
1 ATATAATAAAATAGAA
*
19434570 ATATAATAATAGTAGAA
1 ATATAATAA-AATAGAA
19434587 ATATAA
1 ATATAA
19434593 ATAGATAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
14 5 0.15
15 9 0.26
16 4 0.12
17 16 0.47
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.27
Consensus pattern (16 bp):
ATATAATAAAATAGAA
Found at i:19434563 original size:20 final size:20
Alignment explanation
Indices: 19434540--19434577 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
19434530 ATATTAGTAT
19434540 ATAAATAGAAATAAAATATA
1 ATAAATAGAAATAAAATATA
*
19434560 ATAAATAGAAATATAATA
1 ATAAATAGAAATAAAATA
19434578 ATAGTAGAAA
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:0.68, C:0.00, G:0.05, T:0.26
Consensus pattern (20 bp):
ATAAATAGAAATAAAATATA
Found at i:19434573 original size:15 final size:15
Alignment explanation
Indices: 19434548--19434592 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
19434538 ATATAAATAG
19434548 AAATA-AAATATAAT
1 AAATAGAAATATAAT
19434562 AAATAGAAATATAAT
1 AAATAGAAATATAAT
19434577 AATAGTAGAAATATAA
1 AA-A-TAGAAATATAA
19434593 ATAGATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.18
15 11 0.39
16 1 0.04
17 11 0.39
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (15 bp):
AAATAGAAATATAAT
Found at i:19434612 original size:15 final size:14
Alignment explanation
Indices: 19434540--19434655 Score: 62
Period size: 15 Copynumber: 8.1 Consensus size: 14
19434530 ATATTAGTAT
*
19434540 ATAAATAGAAATA-
1 ATAAATAAAAATAG
19434553 A-AATATAATAAATAG
1 ATAA-ATAA-AAATAG
*
19434568 A-AATATAATAATAG
1 ATAA-ATAAAAATAG
* *
19434582 TAGAAATATAAATAG
1 -ATAAATAAAAATAG
19434597 ATAAATAAAAATTAG
1 ATAAATAAAAA-TAG
*
19434612 ATAAATAATAATAG
1 ATAAATAAAAATAG
*
19434626 TATTAGAATAACAA-A-
1 -A-TA-AATAAAAATAG
*
19434641 ATAAATATAAATAG
1 ATAAATAAAAATAG
19434655 A
1 A
19434656 AGCATAAAAA
Statistics
Matches: 82, Mismatches: 10, Indels: 21
0.73 0.09 0.19
Matches are distributed among these distances:
12 8 0.10
13 7 0.09
14 24 0.29
15 31 0.38
16 5 0.06
17 7 0.09
ACGTcount: A:0.65, C:0.01, G:0.08, T:0.27
Consensus pattern (14 bp):
ATAAATAAAAATAG
Found at i:19434617 original size:29 final size:28
Alignment explanation
Indices: 19434560--19434655 Score: 74
Period size: 29 Copynumber: 3.3 Consensus size: 28
19434550 ATAAAATATA
* *
19434560 ATAAATAGA-AATATAATAATAGTAGAAAT
1 ATAAATAGATAA-ATAAAAATAG-ATAAAT
19434589 ATAAATAGATAAATAAAAATTAGATAAAT
1 ATAAATAGATAAATAAAAA-TAGATAAAT
*
19434618 A-ATAATAGTATTAGAATAACAA-A-ATAAAT
1 ATA-AATAG-A-TA-AATAAAAATAGATAAAT
19434647 ATAAATAGA
1 ATAAATAGA
19434656 AGCATAAAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
28 2 0.04
29 38 0.67
30 8 0.14
31 2 0.04
32 7 0.12
ACGTcount: A:0.64, C:0.01, G:0.08, T:0.27
Consensus pattern (28 bp):
ATAAATAGATAAATAAAAATAGATAAAT
Found at i:19439379 original size:47 final size:49
Alignment explanation
Indices: 19439302--19439435 Score: 154
Period size: 46 Copynumber: 2.8 Consensus size: 49
19439292 TGTAACCCGC
*
19439302 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGATGCC-AGTTACAT
* * * * *
19439352 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTC-GA--ACATTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGATGCCAGTTACAT
*
19439395 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGATGCC
19439436 CAAATATTCT
Statistics
Matches: 68, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
43 6 0.09
44 2 0.03
45 2 0.03
46 27 0.40
47 27 0.40
48 2 0.03
49 2 0.03
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (49 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGATGCCAGTTACAT
Found at i:19439450 original size:46 final size:47
Alignment explanation
Indices: 19439305--19439450 Score: 124
Period size: 46 Copynumber: 3.1 Consensus size: 47
19439295 AACCCGCCCA
* * *
19439305 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATC
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCAATTA-TTC
* * * * * *
19439353 TCA-CGAACTCGGACTCAACTCAACGAGTTC-GA---ACATTTGCATCC
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCAATT--ATTC
*
19439397 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCAAATATTC
1 -TAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCAATTATTC
19439445 T-AGTGA
1 TAAGTGA
19439451 CATGTCACTT
Statistics
Matches: 75, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
43 3 0.04
44 1 0.01
45 3 0.04
46 32 0.43
47 28 0.37
48 5 0.07
50 3 0.04
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (47 bp):
TAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCAATTATTC
Found at i:19439704 original size:24 final size:24
Alignment explanation
Indices: 19439673--19439720 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
19439663 TTTAAAATAA
19439673 TAACTATGTTACCAACATTTACAT
1 TAACTATGTTACCAACATTTACAT
19439697 TAACTATGTTACCAACATTTACAT
1 TAACTATGTTACCAACATTTACAT
19439721 ATGAACTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.38
Consensus pattern (24 bp):
TAACTATGTTACCAACATTTACAT
Found at i:19441121 original size:9 final size:9
Alignment explanation
Indices: 19441107--19441165 Score: 91
Period size: 9 Copynumber: 6.6 Consensus size: 9
19441097 TTTATACAAA
19441107 TAATTCGGT
1 TAATTCGGT
19441116 TAATTCGGT
1 TAATTCGGT
19441125 TAATTCGGT
1 TAATTCGGT
* *
19441134 TAATTTGGG
1 TAATTCGGT
*
19441143 TAATTCGGG
1 TAATTCGGT
19441152 TAATTCGGT
1 TAATTCGGT
19441161 TAATT
1 TAATT
19441166 TTATACTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 46 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.44
Consensus pattern (9 bp):
TAATTCGGT
Found at i:19442386 original size:12 final size:11
Alignment explanation
Indices: 19442366--19442394 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
19442356 TCTTTGCACC
19442366 TTCTTTTTTTT
1 TTCTTTTTTTT
19442377 TTCTTTTTTTT
1 TTCTTTTTTTT
19442388 TTCTTTT
1 TTCTTTT
19442395 ATTTCTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:19448884 original size:138 final size:138
Alignment explanation
Indices: 19448715--19448986 Score: 474
Period size: 138 Copynumber: 2.0 Consensus size: 138
19448705 TTTTAAAATT
19448715 TTAAATCAAATAAGTTGCATAATAACATAACAAAGAGAAATGTTAATATAAAACCTAAAAACAAT
1 TTAAATCAAATAAGTTGCATAATAACATAACAAAGAGAAATGTTAATATAAAACCTAAAAACAAT
* * *
19448780 TTAATGCCAATTTTTAAGGAAATTACATATGGTTCTAAAATTCAAAACAAGTACTCCTA-AAAGC
66 TTAATGCCAATTTTTAAAGAAATTACATATGATTCTAAAATTCAAAACAAGGACTCC-ACAAAGC
19448844 ATCCAGACG
130 ATCCAGACG
*
19448853 TTAAATCAAATAAGTTGCATAATAACATAACAAAGAGAAATGTTATTATAAAACCTAAAAACAAT
1 TTAAATCAAATAAGTTGCATAATAACATAACAAAGAGAAATGTTAATATAAAACCTAAAAACAAT
* *
19448918 TTAATGCCAATTTTTAAAGAGATTACATATGATTCTAAAATTCAAAACAGGGACTCCACAAAGCA
66 TTAATGCCAATTTTTAAAGAAATTACATATGATTCTAAAATTCAAAACAAGGACTCCACAAAGCA
19448983 TCCA
131 TCCA
19448987 TACATTATTA
Statistics
Matches: 127, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
137 1 0.01
138 126 0.99
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.27
Consensus pattern (138 bp):
TTAAATCAAATAAGTTGCATAATAACATAACAAAGAGAAATGTTAATATAAAACCTAAAAACAAT
TTAATGCCAATTTTTAAAGAAATTACATATGATTCTAAAATTCAAAACAAGGACTCCACAAAGCA
TCCAGACG
Found at i:19450631 original size:14 final size:13
Alignment explanation
Indices: 19450614--19450675 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 13
19450604 AAATATTAAA
19450614 TTTTTAAGTTTTTT
1 TTTTTAA-TTTTTT
19450628 TTTTT-A-TTTTT
1 TTTTTAATTTTTT
*
19450639 TATTT-ATTTTTAT
1 TTTTTAATTTTT-T
19450652 TTTTT-ATTTTTT
1 TTTTTAATTTTTT
*
19450664 ATTTTTTATTTT
1 -TTTTTAATTTT
19450676 AAAATTTTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
11 10 0.24
12 5 0.12
13 17 0.40
14 10 0.24
ACGTcount: A:0.15, C:0.00, G:0.02, T:0.84
Consensus pattern (13 bp):
TTTTTAATTTTTT
Found at i:19450632 original size:7 final size:7
Alignment explanation
Indices: 19450622--19450675 Score: 74
Period size: 7 Copynumber: 7.4 Consensus size: 7
19450612 AATTTTTAAG
19450622 TTTTT-T
1 TTTTTAT
19450628 TTTTTAT
1 TTTTTAT
19450635 TTTTTATTT
1 TTTTTA--T
19450644 ATTTTTAT
1 -TTTTTAT
19450652 TTTTTAT
1 TTTTTAT
19450659 TTTTTAT
1 TTTTTAT
19450666 TTTTTAT
1 TTTTTAT
19450673 TTT
1 TTT
19450676 AAAATTTTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
6 5 0.11
7 31 0.70
8 1 0.02
9 1 0.02
10 6 0.14
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTAT
Found at i:19450648 original size:31 final size:31
Alignment explanation
Indices: 19450613--19450674 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
19450603 TAAATATTAA
19450613 ATTTTTAAGTTTTT-TTTTTTATTTTTTATTT
1 ATTTTT-AGTTTTTATTTTTTATTTTTTATTT
*
19450644 ATTTTTATTTTTTATTTTTTATTTTTTATTT
1 ATTTTTAGTTTTTATTTTTTATTTTTTATTT
19450675 TAAAATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 6 0.21
31 23 0.79
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (31 bp):
ATTTTTAGTTTTTATTTTTTATTTTTTATTT
Found at i:19450654 original size:24 final size:23
Alignment explanation
Indices: 19450622--19450675 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 23
19450612 AATTTTTAAG
19450622 TTTTTTTTTTTATTTTTTATTTA
1 TTTTTTTTTTTATTTTTTATTTA
19450645 TTTTTATTTTTTATTTTTTATTT-
1 TTTTT-TTTTTTATTTTTTATTTA
*
19450668 TTTATTTT
1 TTTTTTTT
19450676 AAAATTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 3 0.10
23 9 0.31
24 17 0.59
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (23 bp):
TTTTTTTTTTTATTTTTTATTTA
Found at i:19451312 original size:16 final size:15
Alignment explanation
Indices: 19451278--19451321 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
19451268 TTATCTCTTA
*
19451278 CATAA-CCATAAA-T
1 CATAATCCATAAACC
19451291 CATAATCCCATAAACC
1 CATAAT-CCATAAACC
19451307 CATAATCCATAAACC
1 CATAATCCATAAACC
19451322 TTAAAATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 5 0.19
15 16 0.59
16 6 0.22
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (15 bp):
CATAATCCATAAACC
Found at i:19451539 original size:7 final size:7
Alignment explanation
Indices: 19451528--19451571 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
19451518 CTGAACCATG
19451528 AACCCCT
1 AACCCCT
* *
19451535 CACCCTT
1 AACCCCT
19451542 AACCCCT
1 AACCCCT
*
19451549 AACCTCT
1 AACCCCT
19451556 AACCCCT
1 AACCCCT
*
19451563 AACACCT
1 AACCCCT
19451570 AA
1 AA
19451572 ATCTTAAACC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (7 bp):
AACCCCT
Found at i:19451856 original size:41 final size:40
Alignment explanation
Indices: 19451779--19451865 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 40
19451769 TCAAATACAT
19451779 TTAAAACAAATATTAAAACAAGAAACAAATAAAAAATGATA
1 TTAAAACAAATATTAAAACAAGAAACAAATAAAAAAT-ATA
* * * **
19451820 TTAAAACAATTATTAAAACAATAGACAAATTGAAAATATA
1 TTAAAACAAATATTAAAACAAGAAACAAATAAAAAATATA
*
19451860 ATAAAA
1 TTAAAA
19451866 AGTGATTATA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 8 0.20
41 32 0.80
ACGTcount: A:0.66, C:0.07, G:0.05, T:0.23
Consensus pattern (40 bp):
TTAAAACAAATATTAAAACAAGAAACAAATAAAAAATATA
Found at i:19452153 original size:41 final size:41
Alignment explanation
Indices: 19452089--19452257 Score: 232
Period size: 41 Copynumber: 4.1 Consensus size: 41
19452079 ATTATATGAC
* * * *
19452089 TTTTCGCGGCGTTTTATCGAAAGCGCCGCTACTGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
19452130 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
*
19452171 TTTTAACGGCGTTTTACCAAAAGCGCCGCTAATGCTCT-GT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
* * * * *
19452211 TTTTAGCGGCGTTTTAACAAAAAACGCCGCTATTGCTCCGTT
1 TTTTAGCGGCGTTTT-ACCAAAAGCGCCGCTAATGCTCTGGT
19452253 TTTTA
1 TTTTA
19452258 TAATTTTTGT
Statistics
Matches: 115, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
40 16 0.14
41 93 0.81
42 6 0.05
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
Found at i:19453950 original size:26 final size:26
Alignment explanation
Indices: 19453921--19454002 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
19453911 TGATACAAAT
*
19453921 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
19453947 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
19453973 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
19453999 TGAT
1 TGAT
19454003 GGGAATTTCA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:19455515 original size:25 final size:26
Alignment explanation
Indices: 19455487--19455538 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
19455477 TTTACAGTTT
19455487 TACCCCTAGAGATAAATT-ACCGAAA
1 TACCCCTAGAGATAAATTGACCGAAA
* * *
19455512 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGAGATAAATTGACCGAAA
19455538 T
1 T
19455539 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (26 bp):
TACCCCTAGAGATAAATTGACCGAAA
Found at i:19458644 original size:22 final size:20
Alignment explanation
Indices: 19458619--19458660 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
19458609 ATATACACAC
*
19458619 ATAAT-ATATACACGCAATT
1 ATAATAATATACACACAATT
19458638 ATAATAATATACACACAATT
1 ATAATAATATACACACAATT
19458658 ATA
1 ATA
19458661 TTCATGACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.52, C:0.14, G:0.02, T:0.31
Consensus pattern (20 bp):
ATAATAATATACACACAATT
Found at i:19459421 original size:22 final size:22
Alignment explanation
Indices: 19459396--19459437 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
19459386 CATAAAATTA
19459396 AAAAAGAA-AAACGAATCAATCC
1 AAAAAGAATAAA-GAATCAATCC
*
19459418 AAAAATAATAAAGAATCAAT
1 AAAAAGAATAAAGAATCAAT
19459438 TCATTCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.67, C:0.12, G:0.07, T:0.14
Consensus pattern (22 bp):
AAAAAGAATAAAGAATCAATCC
Found at i:19460350 original size:12 final size:11
Alignment explanation
Indices: 19460330--19460360 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
19460320 CAAATGGAAT
19460330 AAAAAAAAAAG
1 AAAAAAAAAAG
19460341 AAAAAGAAAAAG
1 AAAAA-AAAAAG
19460353 AAAAAAAA
1 AAAAAAAA
19460361 GGAAGATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:19460359 original size:22 final size:22
Alignment explanation
Indices: 19460331--19460377 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
19460321 AAATGGAATA
19460331 AAAAAAAAAGAA-AAAGAAAAAG
1 AAAAAAAAAGAAGAAAG-AAAAG
* *
19460353 AAAAAAAAGGAAGATAGAAAAG
1 AAAAAAAAAGAAGAAAGAAAAG
19460375 AAA
1 AAA
19460378 CAGAATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (22 bp):
AAAAAAAAAGAAGAAAGAAAAG
Found at i:19460427 original size:13 final size:13
Alignment explanation
Indices: 19460409--19460434 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19460399 GCAGGGGAGA
19460409 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
19460422 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
19460435 GGGGAAAAGG
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:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AAAAGAAAGAAAG
Found at i:19464042 original size:19 final size:18
Alignment explanation
Indices: 19464003--19464045 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
19463993 CTTTATTATG
19464003 TTTTTGTATTTCAGCATA
1 TTTTTGTATTTCAGCATA
*
19464021 TTTTATGTATTTTAGC-TGA
1 TTTT-TGTATTTCAGCAT-A
19464040 TTTTTG
1 TTTTTG
19464046 AATCATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.19, C:0.07, G:0.14, T:0.60
Consensus pattern (18 bp):
TTTTTGTATTTCAGCATA
Found at i:19464288 original size:64 final size:65
Alignment explanation
Indices: 19464209--19464387 Score: 186
Period size: 67 Copynumber: 2.8 Consensus size: 65
19464199 GACATTATGT
* * *
19464209 TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAAAGCTACGGGATATA-
1 TGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAAAGCTACGAGATAAAC
* * * * * *
19464273 TGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGATA
1 TGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAAAGCTACGAGATA
19464338 AAC
63 AAC
* * *
19464341 TG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGA
1 TGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAG-ACAAGA
19464388 GAGCCAAAAT
Statistics
Matches: 93, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
62 1 0.01
63 15 0.16
64 24 0.26
66 21 0.23
67 30 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (65 bp):
TGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAAAGCTACGAGATAAAC
Found at i:19468105 original size:132 final size:132
Alignment explanation
Indices: 19467859--19468256 Score: 528
Period size: 132 Copynumber: 3.0 Consensus size: 132
19467849 ATCATTCGTT
* * * *
19467859 TAAAAATTCTTTAAAACGAAGGCGATGTTCGATATTTGGCAATTCGCGGAATCGTGCCCTATCGT
1 TAAAAACTCTTTAAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTATCGT
* * * * *
19467924 GCTAGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAATGTCCCATTAGAATTTCACTCATGTTT
66 GCTGGGTTGCAATTTCACGTTTGTTCAAAATAATCGAATATCCCTTTAGAATTTCACTCATGTTT
19467989 TC
131 TC
* ** * *
19467991 TAAAAACTCTTTAAAATGAAGAAAATGTTCGATGTTTGGCAATTTGGGGAGTCGTGCCCTATCGT
1 TAAAAACTCTTTAAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTATCGT
* * *
19468056 GCTGGGTTGCAATTTCCCGTTTGTTCAAAATAATCGAATATCCCTTTAGAATTTCACTCACGTCT
66 GCTGGGTTGCAATTTCACGTTTGTTCAAAATAATCGAATATCCCTTTAGAATTTCACTCATGTTT
19468121 T-
131 TC
* * * * *
19468122 TAAAAACTCTTTAAAGCAAAGGCAATATTCGATGTTTGGAAATTCGGGGAATAGTGCCCTATCGT
1 TAAAAACTCTTTAAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTATCGT
*** * * * *
19468187 GCTGGGTTTTGATTTCACGTTTGTTCAAAATAATCAAATATTCCTTTGGAATTTCACTCGTGTTT
66 GCTGGGTTGCAATTTCACGTTTGTTCAAAATAATCGAATATCCCTTTAGAATTTCACTCATGTTT
19468252 TC
131 TC
19468254 TAA
1 TAA
19468257 GGCGAGGCAA
Statistics
Matches: 229, Mismatches: 36, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
131 111 0.48
132 118 0.52
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (132 bp):
TAAAAACTCTTTAAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTATCGT
GCTGGGTTGCAATTTCACGTTTGTTCAAAATAATCGAATATCCCTTTAGAATTTCACTCATGTTT
TC
Found at i:19469379 original size:20 final size:20
Alignment explanation
Indices: 19469356--19469421 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 20
19469346 TATTATATTA
19469356 ATTATATAAGTTTAATAATT
1 ATTATATAAGTTTAATAATT
**
19469376 ATTATATATA-TTTATATTTTCGTT
1 ATTATATA-AGTTTA-A---TAATT
19469400 ATTATATAAGTTTAATAATT
1 ATTATATAAGTTTAATAATT
19469420 AT
1 AT
19469422 ATTTATAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
20 17 0.47
21 2 0.06
23 2 0.06
24 15 0.42
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (20 bp):
ATTATATAAGTTTAATAATT
Found at i:19470075 original size:18 final size:17
Alignment explanation
Indices: 19470052--19470085 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
19470042 AAGGTTTTAC
19470052 TAATTTAAAATAAAACTG
1 TAATTT-AAATAAAACTG
*
19470070 TAATTTTAATAAAACT
1 TAATTTAAATAAAACT
19470086 TTAAGCGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (17 bp):
TAATTTAAATAAAACTG
Found at i:19472145 original size:17 final size:18
Alignment explanation
Indices: 19472113--19472147 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
19472103 AATTTCATAT
*
19472113 TTAATTTTTAATTAAGTA
1 TTAATTATTAATTAAGTA
19472131 TTAATTATT-ATTAAGTA
1 TTAATTATTAATTAAGTA
19472148 AATATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (18 bp):
TTAATTATTAATTAAGTA
Found at i:19487930 original size:21 final size:18
Alignment explanation
Indices: 19487895--19487933 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 18
19487885 GTTGATATTT
19487895 TTTAAAAAATAAAATATA
1 TTTAAAAAATAAAATATA
19487913 TTTAAAATAATGATAAATATA
1 TTTAAAA-AAT-A-AAATATA
19487934 AAAATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 3 0.17
20 1 0.06
21 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
TTTAAAAAATAAAATATA
Found at i:19488058 original size:19 final size:21
Alignment explanation
Indices: 19488020--19488062 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
19488010 GATAATGATA
*
19488020 TATATAAATTATATATTTTAT
1 TATATAAATTACATATTTTAT
19488041 TATAT-AATTACATA-TTTAT
1 TATATAAATTACATATTTTAT
19488060 TAT
1 TAT
19488063 TTGATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 8 0.38
21 5 0.24
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TATATAAATTACATATTTTAT
Found at i:19492664 original size:2 final size:2
Alignment explanation
Indices: 19492647--19492686 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
19492637 AAATTTTTAT
*
19492647 TA TA GTA TA AA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19492687 ATGGAGAGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 31 0.91
3 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:19499607 original size:43 final size:43
Alignment explanation
Indices: 19499539--19499649 Score: 136
Period size: 43 Copynumber: 2.6 Consensus size: 43
19499529 ATAATCAATG
* *
19499539 AGATCAAGATTACCAGTCCAGGCTAAATCTC-ATCTCCAACATA
1 AGATCAGGATTACCAGTCCAGGCTAAATCCCGAT-TCCAACATA
* *
19499582 TA-ATTAGGATTACCAGTCCAGGCTAAATCCCGATTTCAACATA
1 -AGATCAGGATTACCAGTCCAGGCTAAATCCCGATTCCAACATA
* *
19499625 AGATCAGAATTACCAGTCTAGGCTA
1 AGATCAGGATTACCAGTCCAGGCTA
19499650 GATTCTGTCT
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
42 1 0.02
43 54 0.93
44 3 0.05
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.25
Consensus pattern (43 bp):
AGATCAGGATTACCAGTCCAGGCTAAATCCCGATTCCAACATA
Found at i:19501358 original size:11 final size:11
Alignment explanation
Indices: 19501342--19501372 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
19501332 ATATTACATG
19501342 AAATAATAATA
1 AAATAATAATA
19501353 AAATAATAATA
1 AAATAATAATA
19501364 AAAT-ATAAT
1 AAATAATAAT
19501373 TTAAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.25
11 15 0.75
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AAATAATAATA
Found at i:19506166 original size:21 final size:22
Alignment explanation
Indices: 19506126--19506166 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
19506116 ATGGCATGTC
* *
19506126 ATTAGGGTTATATGCGTGTTTA
1 ATTAGGGATATATGCATGTTTA
19506148 ATTAGGGAT-TATGCATGTT
1 ATTAGGGATATATGCATGTT
19506167 ATTGTGAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.24, C:0.05, G:0.27, T:0.44
Consensus pattern (22 bp):
ATTAGGGATATATGCATGTTTA
Found at i:19515729 original size:21 final size:21
Alignment explanation
Indices: 19515704--19515750 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
19515694 CGTAAAATTT
19515704 TAAATATTTAAAATTTCAAAA
1 TAAATATTTAAAATTTCAAAA
*
19515725 TAAATATTTAAAATTTTAAAA
1 TAAATATTTAAAATTTCAAAA
19515746 -AAATA
1 TAAATA
19515751 AAAAATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATATTTAAAATTTCAAAA
Found at i:19517106 original size:17 final size:18
Alignment explanation
Indices: 19517084--19517124 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
19517074 ATTTTTTTAT
19517084 TTATTTTAATAA-AAGTA
1 TTATTTTAATAAGAAGTA
* *
19517101 TTATTTTTATAAGAATTA
1 TTATTTTAATAAGAAGTA
19517119 TTATTT
1 TTATTT
19517125 ATTTTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TTATTTTAATAAGAAGTA
Found at i:19517914 original size:57 final size:57
Alignment explanation
Indices: 19517826--19517939 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
19517816 TGAGTAGCAT
19517826 TCTCTGGATCGATAAAGCGTACGAAGTCTGGAATGATCTTTGCAAACGTTTTTCTCA
1 TCTCTGGATCGATAAAGCGTACGAAGTCTGGAATGATCTTTGCAAACGTTTTTCTCA
19517883 TCTCTGGATCGATAAAGCGTACGAAGTCTGGAATGATCTTTGCAAACGTTTTTCTCA
1 TCTCTGGATCGATAAAGCGTACGAAGTCTGGAATGATCTTTGCAAACGTTTTTCTCA
19517940 AGGTGGCATC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (57 bp):
TCTCTGGATCGATAAAGCGTACGAAGTCTGGAATGATCTTTGCAAACGTTTTTCTCA
Found at i:19519659 original size:3 final size:3
Alignment explanation
Indices: 19519651--19520046 Score: 257
Period size: 3 Copynumber: 131.0 Consensus size: 3
19519641 ATTTAATATA
* * *
19519651 TAT TAT TAT ATGT TTT TAT TAT T-T TAC TAT TACT TA- TATT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA-T TAT TAT
* *
19519697 CAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* ** *
19519745 TAT TAT TAT TAT TAT CAT TAT TAT TCC TAC TAT TAT TAT TAT T-T GT-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
* * * * * * * *
19519792 TAC TAT TAT TATT TAT TGT CAT TAT CAT TAT TAC GAC TAT CAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* ** * * *
19519838 TAT TAT T-T TATT TAT TAT CAT TAT TAT TCC TAT TTT TGT TAT TTT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * ** * * * * *
19519883 TTT TAC TGC TAA TATT TAT TGT CAT TAT TAT TAC TAT TAT GTTT TAAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT -TAT T-AT
* * *
19519931 TAC TAC TA- CAGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
19519976 TAT TAT TAT TAT TAT TAT TAT TGT TAT CAT TTT TGT AAT TAC TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
19520024 TAT T-G TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
19520047 ATTTTCATCT
Statistics
Matches: 304, Mismatches: 73, Indels: 32
0.74 0.18 0.08
Matches are distributed among these distances:
2 10 0.03
3 274 0.90
4 20 0.07
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:19520116 original size:17 final size:17
Alignment explanation
Indices: 19520084--19520118 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
19520074 ACTTATCTAT
* *
19520084 TTATATTTTCGTTATTA
1 TTATATTTTAGGTATTA
19520101 TTATATTTTAGGTATTA
1 TTATATTTTAGGTATTA
19520118 T
1 T
19520119 ATCCATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.09, T:0.63
Consensus pattern (17 bp):
TTATATTTTAGGTATTA
Found at i:19520153 original size:26 final size:27
Alignment explanation
Indices: 19520097--19520154 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
19520087 TATTTTCGTT
19520097 ATTA-TTATATTTTAGGTATTATATCC
1 ATTATTTATATTTTAGGTATTATATCC
19520123 A-TATTTATA-TTTAGGTATTAATAT-C
1 ATTATTTATATTTTAGGTATT-ATATCC
19520148 ATTATTT
1 ATTATTT
19520155 TACTATTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
25 14 0.48
26 15 0.52
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (27 bp):
ATTATTTATATTTTAGGTATTATATCC
Found at i:19524865 original size:26 final size:26
Alignment explanation
Indices: 19524829--19524938 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
19524819 CATGTAATTC
19524829 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
19524855 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
19524881 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
19524907 TTGTCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
19524933 TTATCA
1 TTATCA
19524939 ATTTGTATCA
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:19531065 original size:75 final size:72
Alignment explanation
Indices: 19530977--19531147 Score: 217
Period size: 75 Copynumber: 2.4 Consensus size: 72
19530967 GGTTTTCCTC
** * *
19530977 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTA-A
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTC--ACA
19531040 CTCAGTATGG
63 CTCAGTATGG
*
19531050 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAC
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAC
19531115 TCAGTATGG
64 TCAGTATGG
19531124 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
19531148 CTTTGCCATG
Statistics
Matches: 89, Mismatches: 5, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
69 21 0.24
72 2 0.02
73 2 0.02
74 19 0.21
75 45 0.51
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (72 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACACTC
AGTATGG
Found at i:19531123 original size:34 final size:35
Alignment explanation
Indices: 19530982--19531149 Score: 193
Period size: 35 Copynumber: 4.7 Consensus size: 35
19530972 TCCTCATTGA
*
19530982 AATACCATACCTACATTTTTCA-ACTCGGTATGGGA-
1 AATACCATACCTACA--TTTCACACTCAGTATGGGAT
*
19531017 AATGCCATACCTACATTTCTTA-ACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTC--ACACTCAGTATGG----GAT
19531057 AATACCATACCTACATTTCACAGCTCAGTAT-GGAT
1 AATACCATACCTACATTTCACA-CTCAGTATGGGAT
19531092 AATACCATACCTACATTTCACACTCAGTAT-GGAT
1 AATACCATACCTACATTTCACACTCAGTATGGGAT
*
19531126 GATACCATACCTACATTTCACACT
1 AATACCATACCTACATTTCACACT
19531150 TTGCCATGGA
Statistics
Matches: 120, Mismatches: 4, Indels: 19
0.84 0.03 0.13
Matches are distributed among these distances:
33 4 0.03
34 35 0.29
35 50 0.42
38 1 0.01
39 4 0.03
40 26 0.22
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.32
Consensus pattern (35 bp):
AATACCATACCTACATTTCACACTCAGTATGGGAT
Found at i:19538515 original size:35 final size:35
Alignment explanation
Indices: 19538471--19538637 Score: 201
Period size: 35 Copynumber: 4.6 Consensus size: 35
19538461 TCCTCATTGA
** *
19538471 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
19538506 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
19538546 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
19538581 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
19538616 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
19538638 CTTTGCCATG
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
35 87 0.74
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:19538554 original size:75 final size:73
Alignment explanation
Indices: 19538466--19538637 Score: 226
Period size: 75 Copynumber: 2.4 Consensus size: 73
19538456 GGTTTTCCTC
** * * **
19538466 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
19538530 TCAGTATGG
65 TCAGTATGG
*
19538539 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
19538604 CTCAGTATGG
64 CTCAGTATGG
19538614 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
19538638 CTTTGCCATG
Statistics
Matches: 89, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 58 0.65
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:19556451 original size:12 final size:12
Alignment explanation
Indices: 19556429--19556458 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
19556419 AAATTATACA
19556429 TTAAT-TTTAAT
1 TTAATATTTAAT
19556440 TTAATATTTAAT
1 TTAATATTTAAT
19556452 TTAATAT
1 TTAATAT
19556459 ATAAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTAATATTTAAT
Found at i:19561669 original size:19 final size:20
Alignment explanation
Indices: 19561637--19561674 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19561627 TATAATTTAA
*
19561637 TTTAAATATATAAACTATAT
1 TTTAAATATATAAAATATAT
19561657 TTTAAATAT-TAAAATATA
1 TTTAAATATATAAAATATA
19561675 ATCATTACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTAAATATATAAAATATAT
Found at i:19561966 original size:20 final size:20
Alignment explanation
Indices: 19561930--19561967 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19561920 TATAAACTCC
*
19561930 ATTAAATTAATTCATTTATT
1 ATTAAATTAATTAATTTATT
19561950 ATTAAA-TATATTAATTTA
1 ATTAAATTA-ATTAATTTA
19561968 ATTTTTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTAAATTAATTAATTTATT
Found at i:19562316 original size:3 final size:3
Alignment explanation
Indices: 19562308--19562350 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
19562298 CTCCTTGTAA
19562308 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
19562351 CCAACCGTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19563611 original size:17 final size:17
Alignment explanation
Indices: 19563586--19563656 Score: 79
Period size: 17 Copynumber: 3.9 Consensus size: 17
19563576 CATAAATATA
19563586 TTATAAAATTATAAAAT
1 TTATAAAATTATAAAAT
* * *
19563603 TTATTAAATAATAAAAA
1 TTATAAAATTATAAAAT
19563620 TTATAAAATTTGATATAAAT
1 TTATAAAA-TT-ATA-AAAT
19563640 TTATTAAAATTATAAAA
1 TTA-TAAAATTATAAAA
19563657 ATGATAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
17 21 0.48
18 4 0.09
19 6 0.14
20 8 0.18
21 5 0.11
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (17 bp):
TTATAAAATTATAAAAT
Found at i:19563663 original size:9 final size:9
Alignment explanation
Indices: 19563585--19563750 Score: 101
Period size: 9 Copynumber: 18.2 Consensus size: 9
19563575 CCATAAATAT
19563585 ATTAT-AAA
1 ATTATAAAA
19563593 ATTATAAAA
1 ATTATAAAA
* *
19563602 TTTAT-TAA
1 ATTATAAAA
*
19563610 ATAATAAAA
1 ATTATAAAA
19563619 ATTATAAAA
1 ATTATAAAA
*
19563628 TTTGATATAAA
1 ATT-ATA-AAA
* *
19563639 TTTATTAAA
1 ATTATAAAA
19563648 ATTATAAAA
1 ATTATAAAA
*
19563657 ATGATAAAA
1 ATTATAAAA
*
19563666 AATATAAAA
1 ATTATAAAA
19563675 A--ATAATAA
1 ATTATAA-AA
* *
19563683 TTTTTAATAA
1 ATTATAA-AA
19563693 ATTATAAAA
1 ATTATAAAA
19563702 ATTATAAAA
1 ATTATAAAA
* *
19563711 GTAATAAATA
1 ATTATAAA-A
19563721 TATT-TAAAA
1 -ATTATAAAA
19563730 TATT-TAAAA
1 -ATTATAAAA
*
19563739 TTTTATAAAA
1 -ATTATAAAA
19563749 AT
1 AT
19563751 CATAGTATAA
Statistics
Matches: 125, Mismatches: 23, Indels: 19
0.75 0.14 0.11
Matches are distributed among these distances:
7 4 0.03
8 12 0.10
9 76 0.61
10 26 0.21
11 7 0.06
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (9 bp):
ATTATAAAA
Found at i:19563747 original size:54 final size:50
Alignment explanation
Indices: 19563585--19563747 Score: 132
Period size: 54 Copynumber: 3.0 Consensus size: 50
19563575 CCATAAATAT
* *
19563585 ATTATAAAATTATAAAATTTATTAAATAA-TAAAAATTATAAAATTTGATATAA
1 ATTATAAAATTATAAAA-ATAATAAATAATTAAAAATT-TAAAATTT--TATAA
* * *
19563638 ATTTATTAAAATTATAAAAATGATAAAAAATATAAAAA-ATAATAATTTTTAATAA
1 A-TTA-TAAAATTATAAAAATAATAAATAAT-TAAAAATTTAA-AA-TTTT-ATAA
*
19563693 ATTATAAAAATTATAAAAGTAATAAATATATTTAAAATATTTAAAATTTTATAA
1 ATTAT-AAAATTATAAAAATAATAAATA-A-TTAAAA-ATTTAAAATTTTATAA
19563747 A
1 A
19563748 AATCATAGTA
Statistics
Matches: 89, Mismatches: 9, Indels: 23
0.74 0.07 0.19
Matches are distributed among these distances:
53 2 0.02
54 41 0.46
55 30 0.34
56 13 0.15
57 3 0.03
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (50 bp):
ATTATAAAATTATAAAAATAATAAATAATTAAAAATTTAAAATTTTATAA
Found at i:19567980 original size:22 final size:22
Alignment explanation
Indices: 19567952--19567994 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
19567942 GCACCCGTTA
19567952 GAAAAATATGCTGGGGAGCTAT
1 GAAAAATATGCTGGGGAGCTAT
19567974 GAAAAATATGCTGGGGAGCTA
1 GAAAAATATGCTGGGGAGCTA
19567995 GTGCCTTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.09, G:0.33, T:0.21
Consensus pattern (22 bp):
GAAAAATATGCTGGGGAGCTAT
Found at i:19573618 original size:2 final size:2
Alignment explanation
Indices: 19573611--19573647 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
19573601 TTCTTTTCCT
19573611 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
19573648 TTTGGGGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:19584134 original size:13 final size:14
Alignment explanation
Indices: 19584118--19584153 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
19584108 CAATCTCATA
19584118 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
19584131 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
19584144 TCTC-ATTTCA
1 TCTCAATTTCA
19584154 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:19584143 original size:18 final size:19
Alignment explanation
Indices: 19584105--19584145 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
19584095 TGGTTCATGT
19584105 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
19584124 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
19584142 TTTC
1 TTTC
19584146 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:19584335 original size:39 final size:38
Alignment explanation
Indices: 19584268--19584402 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
19584258 ACCAATATGG
* * *
19584268 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
19584307 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
19584345 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
19584386 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
19584403 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:19584668 original size:18 final size:19
Alignment explanation
Indices: 19584642--19584680 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
19584632 TTTCAATTCA
19584642 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
19584661 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
19584679 AT
1 AT
19584681 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:19585964 original size:19 final size:19
Alignment explanation
Indices: 19585940--19585986 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
19585930 CTTTCTCCCC
*
19585940 TGTTTCTTTCTGTTT-TTT
1 TGTTTCTTTCTGTTTCTTA
*
19585958 TGCTTTCATTCTGTTTCTTA
1 TG-TTTCTTTCTGTTTCTTA
19585978 TGTTTCTTT
1 TGTTTCTTT
19585987 ACTTATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 2 0.08
19 18 0.75
20 4 0.17
ACGTcount: A:0.04, C:0.15, G:0.11, T:0.70
Consensus pattern (19 bp):
TGTTTCTTTCTGTTTCTTA
Found at i:19586005 original size:5 final size:5
Alignment explanation
Indices: 19585995--19586046 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 5
19585985 TTACTTATTT
* *
19585995 ATATA ATATA ATAT- ATAATTA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATATA ATATA AT-A-TA ATATA ATATA ATATA AT-ATA ATATA
19586042 ATATA
1 ATATA
19586047 TATTTTAACA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 2 0.05
5 28 0.72
6 7 0.18
7 2 0.05
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:19586019 original size:16 final size:17
Alignment explanation
Indices: 19585995--19586048 Score: 56
Period size: 19 Copynumber: 3.0 Consensus size: 17
19585985 TTACTTATTT
19585995 ATATAATATAATATATA
1 ATATAATATAATATATA
19586012 AT-TAATATACTATAATATA
1 ATATAATATA--AT-ATATA
*
19586031 ATAATAATTTAATATATA
1 AT-ATAATATAATATATA
19586049 TTTTAACACA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
16 7 0.23
17 2 0.06
18 7 0.23
19 9 0.29
21 6 0.19
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATAATATAATATATA
Found at i:19586025 original size:21 final size:22
Alignment explanation
Indices: 19585995--19586046 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
19585985 TTACTTATTT
19585995 ATATAATATAATAT-ATAATTA
1 ATATAATATAATATAATAATTA
*
19586016 ATATACTATAATATAATAA-TA
1 ATATAATATAATATAATAATTA
*
19586037 ATTTAATATA
1 ATATAATATA
19586047 TATTTTAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
ATATAATATAATATAATAATTA
Found at i:19586027 original size:26 final size:26
Alignment explanation
Indices: 19585996--19586046 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
19585986 TACTTATTTA
19585996 TATAATATAATATATAA-TTAATATAC
1 TATAATATAATA-ATAATTTAATATAC
19586022 TATAATATAATAATAATTTAATATA
1 TATAATATAATAATAATTTAATATA
19586047 TATTTTAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TATAATATAATAATAATTTAATATAC
Found at i:19590271 original size:17 final size:19
Alignment explanation
Indices: 19590237--19590274 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
19590227 CAAACCTTAA
19590237 TTTTCTCTTTTCTTCTTTC
1 TTTTCTCTTTTCTTCTTTC
19590256 TTTTCTC-TTT-TTCTTTC
1 TTTTCTCTTTTCTTCTTTC
19590273 TT
1 TT
19590275 CCTTCCCCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 3 0.16
19 7 0.37
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTCTCTTTTCTTCTTTC
Found at i:19591074 original size:3 final size:3
Alignment explanation
Indices: 19591066--19591113 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
19591056 AAAATGATCA
19591066 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19591114 GCGCATTTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19591533 original size:22 final size:23
Alignment explanation
Indices: 19591507--19591552 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
19591497 CAACCAAACC
19591507 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
19591529 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
19591552 A
1 A
19591553 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:19591558 original size:23 final size:23
Alignment explanation
Indices: 19591514--19591558 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
19591504 ACCAATTCAA
*
19591514 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
19591537 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
19591559 CACATACCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:19599310 original size:22 final size:23
Alignment explanation
Indices: 19599284--19599329 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
19599274 CAACCAAATC
19599284 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
19599306 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
19599329 A
1 A
19599330 CGTTATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:19606305 original size:8 final size:8
Alignment explanation
Indices: 19606292--19606335 Score: 79
Period size: 8 Copynumber: 5.5 Consensus size: 8
19606282 CTTTTATATT
19606292 TTATTAAA
1 TTATTAAA
19606300 TTATTAAA
1 TTATTAAA
19606308 TTATTAAA
1 TTATTAAA
19606316 TTATTAAA
1 TTATTAAA
*
19606324 TTATTATA
1 TTATTAAA
19606332 TTAT
1 TTAT
19606336 ATACTTAAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (8 bp):
TTATTAAA
Found at i:19606893 original size:8 final size:8
Alignment explanation
Indices: 19606882--19606930 Score: 62
Period size: 8 Copynumber: 5.8 Consensus size: 8
19606872 ATATATTAAT
19606882 TTATATTA
1 TTATATTA
19606890 TTATATTA
1 TTATATTA
19606898 TTATATTA
1 TTATATTA
*
19606906 TTACATTA
1 TTATATTA
19606914 TATATATATA
1 T-TATAT-TA
19606924 TATATAT
1 T-TATAT
19606931 ATATATATGT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
8 24 0.65
9 4 0.11
10 9 0.24
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (8 bp):
TTATATTA
Found at i:19606919 original size:2 final size:2
Alignment explanation
Indices: 19606912--19606938 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19606902 ATTATTACAT
19606912 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 T
19606939 GTAAAACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19607940 original size:12 final size:13
Alignment explanation
Indices: 19607925--19607953 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
19607915 ATGTGAATTG
19607925 ATTT-GTGTGAAA
1 ATTTCGTGTGAAA
19607937 ATTTCGTGTGAAA
1 ATTTCGTGTGAAA
19607950 ATTT
1 ATTT
19607954 TATTGTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.31, C:0.03, G:0.21, T:0.45
Consensus pattern (13 bp):
ATTTCGTGTGAAA
Found at i:19614094 original size:46 final size:45
Alignment explanation
Indices: 19614042--19614245 Score: 188
Period size: 46 Copynumber: 4.5 Consensus size: 45
19614032 GTCGATGCCG
* * *
19614042 TGTCCCAGACAGGTCTTACACTGA-CACATGTAACCGT-GCTGACGCA
1 TGTCCCAGACATGTCTTACACTGAGCACATCT---CGTAGCCGACGCA
*
19614088 TGTCCCATACATGTCTTACACT-AGCACATCTCGTAGCCGACGCA
1 TGTCCCAGACATGTCTTACACTGAGCACATCTCGTAGCCGACGCA
* *
19614132 TGTCCCAGACATGTCTGACACTG-GCTATCATCTCG-AGGCCGATGCA
1 TGTCCCAGACATGTCTTACACTGAGC-A-CATCTCGTA-GCCGACGCA
* * * *
19614178 TGTCCCAGACATGTCTTACACTG-GCTC-TCATACTGTGGCTGATGCA
1 TGTCCCAGACATGTCTTACACTGAGCACATC-T-C-GTAGCCGACGCA
19614224 TGTCCCAGACATGTCTTACACT
1 TGTCCCAGACATGTCTTACACT
19614246 AGCCCTCGTC
Statistics
Matches: 137, Mismatches: 11, Indels: 20
0.82 0.07 0.12
Matches are distributed among these distances:
43 5 0.04
44 32 0.23
45 4 0.03
46 96 0.70
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (45 bp):
TGTCCCAGACATGTCTTACACTGAGCACATCTCGTAGCCGACGCA
Found at i:19614245 original size:92 final size:91
Alignment explanation
Indices: 19614085--19614301 Score: 249
Period size: 92 Copynumber: 2.4 Consensus size: 91
19614075 CCGTGCTGAC
*
19614085 GCATGTCCCATACATGTCTTACACTAG-CACATCTCGTAGCCGACGCATGTCCCAGACATGTCTG
1 GCATGTCCCATACATGTCTTACACTGGCCACATCTCGTAGCCGACGCATGTCCCAGACATGTCTG
* * *
19614149 ACACTGGCTATCATCTCGAGGCCGAT
66 ACACTAGCCATCATCTCAAGGCCGAT
* * * * *
19614175 GCATGTCCCAGACATGTCTTACACTGGCTCTCATACT-GTGGCTGATGCATGTCCCAGACATGTC
1 GCATGTCCCATACATGTCTTACACTGGC-CACAT-CTCGTAGCCGACGCATGTCCCAGACATGTC
* * * *
19614239 TTACACTAGCCCTCGTCTCAATGCCGAT
64 TGACACTAGCCATCATCTCAAGGCCGAT
*
19614267 GCCATGTCTCATACATGGTCTTACACTGGCACACA
1 G-CATGTCCCATACAT-GTCTTACACTGGC-CACA
19614302 AATCTCATGT
Statistics
Matches: 105, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
90 25 0.24
92 50 0.48
93 14 0.13
94 16 0.15
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (91 bp):
GCATGTCCCATACATGTCTTACACTGGCCACATCTCGTAGCCGACGCATGTCCCAGACATGTCTG
ACACTAGCCATCATCTCAAGGCCGAT
Found at i:19614268 original size:46 final size:44
Alignment explanation
Indices: 19614085--19614293 Score: 181
Period size: 46 Copynumber: 4.6 Consensus size: 44
19614075 CCGTGCTGAC
* *
19614085 GCATGTCCCATACATGTCTTACACTAGCACATC-TCGTA-GCCGAC
1 GCATGTCCCAGACATGTCTTACACTAGC-CATCATC-TATGCCGAT
* * * *
19614129 GCATGTCCCAGACATGTCTGACACTGGCTATCATCTCGAGGCCGAT
1 GCATGTCCCAGACATGTCTTACACTAGCCATCATCT--ATGCCGAT
* * *
19614175 GCATGTCCCAGACATGTCTTACACTGGCTC-TCATACTGTGGCTGAT
1 GCATGTCCCAGACATGTCTTACACTAGC-CATCAT-CTAT-GCCGAT
* *
19614221 GCATGTCCCAGACATGTCTTACACTAGCCCTCGTCTCAATGCCGAT
1 GCATGTCCCAGACATGTCTTACACTAGCCATCATCT--ATGCCGAT
* *
19614267 GCCATGTCTCATACATGGTCTTACACT
1 G-CATGTCCCAGACAT-GTCTTACACT
19614294 GGCACACAAA
Statistics
Matches: 137, Mismatches: 16, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
43 4 0.03
44 27 0.20
45 4 0.03
46 77 0.56
47 15 0.11
48 10 0.07
ACGTcount: A:0.22, C:0.32, G:0.19, T:0.27
Consensus pattern (44 bp):
GCATGTCCCAGACATGTCTTACACTAGCCATCATCTATGCCGAT
Found at i:19617970 original size:58 final size:58
Alignment explanation
Indices: 19617880--19617989 Score: 159
Period size: 58 Copynumber: 1.9 Consensus size: 58
19617870 AATATAGTGA
* * *
19617880 TTGGTAGCAATTTCCCATAAGTTGTGGGCTACCGTAGCTCTGTGTGAACATCAATGTG
1 TTGGTAGCAATTTCCCATAAGTCGTGGACTACCGTAGCTCTATGTGAACATCAATGTG
* *
19617938 TTGGTAGTAA-TTCCGCATAAGTCGTGGACTACCGTAGCTCTATGTGAGCATC
1 TTGGTAGCAATTTCC-CATAAGTCGTGGACTACCGTAGCTCTATGTGAACATC
19617990 GAAGTATATG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
57 4 0.09
58 42 0.91
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (58 bp):
TTGGTAGCAATTTCCCATAAGTCGTGGACTACCGTAGCTCTATGTGAACATCAATGTG
Found at i:19624192 original size:6 final size:6
Alignment explanation
Indices: 19624181--19624209 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
19624171 GTTGTTTGTT
19624181 TTCTTG TTCTTG TTCTTG TTCTTG TTCTT
1 TTCTTG TTCTTG TTCTTG TTCTTG TTCTT
19624210 CCCATGGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.17, G:0.14, T:0.69
Consensus pattern (6 bp):
TTCTTG
Found at i:19630034 original size:38 final size:38
Alignment explanation
Indices: 19629973--19630085 Score: 154
Period size: 38 Copynumber: 2.9 Consensus size: 38
19629963 ATTTGATGTG
*
19629973 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTAAAA
1 TATCCGGG-TTAAA-TCCCGCAGGCTTCGTGCTGGTAAAA
**
19630013 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAAA
* * *
19630051 TATCCGGGATAAATCCCGCAGGCCTAGTGCTGGTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTA
19630086 TTATATTCGA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
38 54 0.81
39 5 0.07
40 8 0.12
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.26
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAAA
Found at i:19630086 original size:38 final size:38
Alignment explanation
Indices: 19629989--19630091 Score: 161
Period size: 38 Copynumber: 2.7 Consensus size: 38
19629979 GGCTTAAAGA
** *
19629989 CCCGCAGGCTTCGTGCTGGTAAAATATCCGGGTTAAAT
1 CCCGCAGGCTTCGTGCTGGTATTATATCCGGGATAAAT
19630027 CCCGCAGGCTTCGTGCTGGTATTATATCCGGGATAAAT
1 CCCGCAGGCTTCGTGCTGGTATTATATCCGGGATAAAT
* *
19630065 CCCGCAGGCCTAGTGCTGGTATTATAT
1 CCCGCAGGCTTCGTGCTGGTATTATAT
19630092 TCGAGCCTTC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 60 1.00
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.28
Consensus pattern (38 bp):
CCCGCAGGCTTCGTGCTGGTATTATATCCGGGATAAAT
Found at i:19630146 original size:43 final size:43
Alignment explanation
Indices: 19630068--19630200 Score: 207
Period size: 43 Copynumber: 3.1 Consensus size: 43
19630058 GATAAATCCC
* * * *
19630068 GCAGGCCTAGTGCTGGT-AT-TATATTCGAGCCTTCGTGCCTA
1 GCAGGCTTCGTGCTGGTGATGTGTATTCGGGCCTTCGTGCCTA
19630109 GCAGGCTTCGTGCTGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCTGGTGATGTGTATTCGGGCCTTCGTGCCTA
*
19630152 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCTGGTGATGTGTATTCGGGCCTTCGTGCCTA
19630195 GCAGGC
1 GCAGGC
19630201 GTAATGCCAG
Statistics
Matches: 85, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
41 15 0.18
42 2 0.02
43 68 0.80
ACGTcount: A:0.12, C:0.25, G:0.33, T:0.30
Consensus pattern (43 bp):
GCAGGCTTCGTGCTGGTGATGTGTATTCGGGCCTTCGTGCCTA
Found at i:19636426 original size:2 final size:2
Alignment explanation
Indices: 19636419--19636445 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19636409 AATTTGCTGG
19636419 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 T
19636446 CTTACACTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19638635 original size:13 final size:13
Alignment explanation
Indices: 19638619--19638661 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
19638609 TTTCTTAGTT
19638619 TTTTTTATATTAA
1 TTTTTTATATTAA
*
19638632 TTTTTTGT-TTAA
1 TTTTTTATATTAA
* *
19638644 TTTTTTTTATTTA
1 TTTTTTATATTAA
19638657 TTTTT
1 TTTTT
19638662 ACAAAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (13 bp):
TTTTTTATATTAA
Found at i:19638636 original size:25 final size:25
Alignment explanation
Indices: 19638608--19638661 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 25
19638598 AATTCGATTC
*
19638608 TTTT-CTTAGTTTTTTTTATATTAATT
1 TTTTGCTTAATTTTTTTTAT-TT-ATT
*
19638634 TTTTGTTTAATTTTTTTTATTTATT
1 TTTTGCTTAATTTTTTTTATTTATT
19638659 TTT
1 TTT
19638662 ACAAAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.24
26 6 0.24
27 13 0.52
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.78
Consensus pattern (25 bp):
TTTTGCTTAATTTTTTTTATTTATT
Found at i:19638637 original size:14 final size:13
Alignment explanation
Indices: 19638618--19638661 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
19638608 TTTTCTTAGT
19638618 TTTTTTTATATTAA
1 TTTTTTT-TATTAA
*
19638632 TTTTTTGT-TTAA
1 TTTTTTTTATTAA
*
19638644 TTTTTTTTATTTA
1 TTTTTTTTATTAA
19638657 TTTTT
1 TTTTT
19638662 ACAAAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 11 0.42
13 9 0.35
14 6 0.23
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (13 bp):
TTTTTTTTATTAA
Found at i:19647705 original size:15 final size:15
Alignment explanation
Indices: 19647687--19647717 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
19647677 CTATTGAAGC
*
19647687 AAAAACGATTGCAGG
1 AAAAAAGATTGCAGG
19647702 AAAAAAGATTGCAGG
1 AAAAAAGATTGCAGG
19647717 A
1 A
19647718 CCTTGGTCGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.10, G:0.26, T:0.13
Consensus pattern (15 bp):
AAAAAAGATTGCAGG
Found at i:19652949 original size:10 final size:10
Alignment explanation
Indices: 19652934--19652980 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
19652924 TATGAAATTT
19652934 TAATTTTTTA
1 TAATTTTTTA
19652944 TAA-TTTTTA
1 TAATTTTTTA
* * *
19652953 AAATATTATA
1 TAATTTTTTA
19652963 TTAATTTTTTA
1 -TAATTTTTTA
19652974 TAATTTT
1 TAATTTT
19652981 AAAAAGATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
9 8 0.28
10 14 0.48
11 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:19652967 original size:30 final size:30
Alignment explanation
Indices: 19652933--19652990 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
19652923 ATATGAAATT
* *
19652933 TTAATTTTTTATAATTTTTAAAATATTATA
1 TTAATTTTTTATAATTTTAAAAAGATTATA
19652963 TTAATTTTTTATAATTTTAAAAAGATTA
1 TTAATTTTTTATAATTTTAAAAAGATTA
19652991 AAATATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (30 bp):
TTAATTTTTTATAATTTTAAAAAGATTATA
Found at i:19653003 original size:30 final size:29
Alignment explanation
Indices: 19652933--19653002 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
19652923 ATATGAAATT
* * *
19652933 TTAATTTTTTATAATTTTTAAAATATTATA
1 TTAA-TTTTTATAATTTTAAAAAGATTAAA
19652963 TTAATTTTTTATAATTTTAAAAAGATTAAAA
1 TTAA-TTTTTATAATTTTAAAAAGATT-AAA
19652994 TATAATTTT
1 T-TAATTTT
19653003 ACTTTTACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 25 0.71
31 7 0.20
32 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (29 bp):
TTAATTTTTATAATTTTAAAAAGATTAAA
Found at i:19654325 original size:43 final size:43
Alignment explanation
Indices: 19654277--19654368 Score: 175
Period size: 43 Copynumber: 2.1 Consensus size: 43
19654267 TCAAAACAAC
19654277 ACTTGAATTTTGATCAAAAGTACAATTTAATACATGAATTTTG
1 ACTTGAATTTTGATCAAAAGTACAATTTAATACATGAATTTTG
*
19654320 ACTTGAATTTTGATCAAAAGTACAATTTAATATATGAATTTTG
1 ACTTGAATTTTGATCAAAAGTACAATTTAATACATGAATTTTG
19654363 ACTTGA
1 ACTTGA
19654369 TATAGTTATA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (43 bp):
ACTTGAATTTTGATCAAAAGTACAATTTAATACATGAATTTTG
Found at i:19655508 original size:3 final size:3
Alignment explanation
Indices: 19655500--19655529 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
19655490 TCTCTCCTGC
19655500 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
19655530 CTCAGTTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:19658098 original size:95 final size:95
Alignment explanation
Indices: 19657976--19658170 Score: 390
Period size: 95 Copynumber: 2.1 Consensus size: 95
19657966 AAGTCAAATG
19657976 CAACAAATTTCTTGCATACATGATACATTGATTCAAGGCAAACATTCAAAAAAAATGGTTTTAAT
1 CAACAAATTTCTTGCATACATGATACATTGATTCAAGGCAAACATTCAAAAAAAATGGTTTTAAT
19658041 TTATCTTGAACTTAACGTTAAATTTAACCT
66 TTATCTTGAACTTAACGTTAAATTTAACCT
19658071 CAACAAATTTCTTGCATACATGATACATTGATTCAAGGCAAACATTCAAAAAAAATGGTTTTAAT
1 CAACAAATTTCTTGCATACATGATACATTGATTCAAGGCAAACATTCAAAAAAAATGGTTTTAAT
19658136 TTATCTTGAACTTAACGTTAAATTTAACCT
66 TTATCTTGAACTTAACGTTAAATTTAACCT
19658166 CAACA
1 CAACA
19658171 TTTATTCTCT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 100 1.00
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (95 bp):
CAACAAATTTCTTGCATACATGATACATTGATTCAAGGCAAACATTCAAAAAAAATGGTTTTAAT
TTATCTTGAACTTAACGTTAAATTTAACCT
Found at i:19664658 original size:46 final size:44
Alignment explanation
Indices: 19664554--19664661 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
19664544 TGTCTTTGAC
** * * *
19664554 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
19664598 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
19664644 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
19664662 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:19666347 original size:46 final size:46
Alignment explanation
Indices: 19666297--19666470 Score: 167
Period size: 46 Copynumber: 3.8 Consensus size: 46
19666287 GTTGAGCATC
*
19666297 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTT
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGAT
* * *
19666343 CGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATGT-AACTAGGCAT
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAA-T--G-AT
* ** * **
19666389 CCAAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCC
1 CGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGAT
* *
19666436 CGAGCTCGTTGAGTTGAGTCCGAGTTCTCTTATGG
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
19666471 GCGGGTTACA
Statistics
Matches: 103, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.59
47 25 0.24
48 3 0.03
50 2 0.02
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGAT
Found at i:19666451 original size:93 final size:93
Alignment explanation
Indices: 19666292--19666462 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
19666282 GGATGGTTGA
** * **
19666292 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAGT
19666357 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
19666385 GCATCC-AAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAGCTCGTTGAG
1 GCATCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAG
19666449 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
19666463 TCTTATGGGC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 2 0.03
93 69 0.97
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:19669729 original size:12 final size:12
Alignment explanation
Indices: 19669714--19669739 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19669704 TAAAACTTAG
19669714 TAGGCAATATAA
1 TAGGCAATATAA
19669726 TAGGCAATATAA
1 TAGGCAATATAA
19669738 TA
1 TA
19669740 TGTTTTGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (12 bp):
TAGGCAATATAA
Found at i:19672357 original size:5 final size:5
Alignment explanation
Indices: 19672347--19672428 Score: 164
Period size: 5 Copynumber: 16.4 Consensus size: 5
19672337 ATAAGAATAT
19672347 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
19672397 TATTA TATTA TATTA TATTA TATTA TATTA TA
1 TATTA TATTA TATTA TATTA TATTA TATTA TA
19672429 ACTAAACTAA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 77 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:19676969 original size:43 final size:43
Alignment explanation
Indices: 19676922--19677116 Score: 277
Period size: 43 Copynumber: 4.5 Consensus size: 43
19676912 CATTATAGCA
* *
19676922 TGCTAGGCTCAAAGGCCCGAATACACATCACCGGCATGAAGCC
1 TGCTAGGCTCGAAGGCCCGAATACACATCACCGGCACGAAGCC
*
19676965 TGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCC
1 TGCTAGGCTCGAAGGCCCGAATACACATCACCGGCACGAAGCC
* *
19677008 TGCTAGGCAT-GAAGGCTCGAATACACATCACCAGCACGAAGCC
1 TGCTAGGC-TCGAAGGCCCGAATACACATCACCGGCACGAAGCC
* *
19677051 TGCTAGGCAT-GAAGGCCCGAATACACATCACCGGCACAAAGCA
1 TGCTAGGC-TCGAAGGCCCGAATACACATCACCGGCACGAAGCC
* *
19677094 TGCTAGGCACGAAAGCCCGAATA
1 TGCTAGGCTCGAAGGCCCGAATA
19677117 TAATACCAGC
Statistics
Matches: 138, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
43 138 1.00
ACGTcount: A:0.32, C:0.31, G:0.24, T:0.12
Consensus pattern (43 bp):
TGCTAGGCTCGAAGGCCCGAATACACATCACCGGCACGAAGCC
Found at i:19677067 original size:86 final size:86
Alignment explanation
Indices: 19676918--19677137 Score: 309
Period size: 86 Copynumber: 2.6 Consensus size: 86
19676908 CTGGCATTAT
* * * *
19676918 AGCATGCTAGGCTCAAAGGCCCGAATACACATCACCGGCATGAAGCCTGCTAGGCACGAAGGCCC
1 AGCATGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAAGCCTGCTAGGCACGAAGGCCC
*
19676983 GAATACACATCACCGGCACGA
66 GAATACACATCACCGGCACAA
* * * *
19677004 AGCCTGCTAGGCATGAAGGCTCGAATACACATCACCAGCACGAAGCCTGCTAGGCATGAAGGCCC
1 AGCATGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAAGCCTGCTAGGCACGAAGGCCC
19677069 GAATACACATCACCGGCACAA
66 GAATACACATCACCGGCACAA
* * * *
19677090 AGCATGCTAGGCACGAAAGCCCGAATATA-AT-ACCAGCACTAGGCCTGC
1 AGCATGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAAGCCTGC
19677138 GGGATTTATC
Statistics
Matches: 118, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
84 15 0.13
85 2 0.02
86 101 0.86
ACGTcount: A:0.32, C:0.31, G:0.24, T:0.13
Consensus pattern (86 bp):
AGCATGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAAGCCTGCTAGGCACGAAGGCCC
GAATACACATCACCGGCACAA
Found at i:19682264 original size:22 final size:23
Alignment explanation
Indices: 19682238--19682282 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
19682228 ACCTGATCAG
19682238 AATACGACACAT-AAGTGCCTGA
1 AATACGACACATAAAGTGCCTGA
19682260 AATACGACACATAAAGTGCCTGA
1 AATACGACACATAAAGTGCCTGA
19682283 TCAGTAAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (23 bp):
AATACGACACATAAAGTGCCTGA
Found at i:19682568 original size:27 final size:27
Alignment explanation
Indices: 19682473--19682592 Score: 132
Period size: 23 Copynumber: 4.7 Consensus size: 27
19682463 AAATGTCCAA
19682473 CCAAAACACACCAG----TATAATCCT
1 CCAAAACACACCAGAATATATAATCCT
19682496 CCAAAACACACCAG----TATAATCCT
1 CCAAAACACACCAGAATATATAATCCT
* *
19682519 CCAAAACACACCAGTATCGTATAATCCT
1 CCAAAACACACCAGAAT-ATATAATCCT
19682547 CC-AAACACACCAGAATAATATAATCCAT
1 CCAAAACACACCAGAAT-ATATAATCC-T
19682575 CCAAAACACACCAGAATA
1 CCAAAACACACCAGAATA
19682593 GCACAAAGTG
Statistics
Matches: 87, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
23 37 0.43
27 21 0.24
28 15 0.17
29 14 0.16
ACGTcount: A:0.46, C:0.33, G:0.05, T:0.17
Consensus pattern (27 bp):
CCAAAACACACCAGAATATATAATCCT
Found at i:19687751 original size:11 final size:10
Alignment explanation
Indices: 19687697--19687753 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 10
19687687 TTTCTTCCTG
19687697 TTCTTTCTTT
1 TTCTTTCTTT
*
19687707 TTCTTTCCGTT
1 TTCTTT-CTTT
*
19687718 TTCATTTTTGTCT
1 TTC-TTTCT-T-T
19687731 TTCTTTCTTT
1 TTCTTTCTTT
19687741 TTCTATTCTTT
1 TTCT-TTCTTT
19687752 TT
1 TT
19687754 ATTACTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
10 11 0.29
11 15 0.39
12 8 0.21
13 4 0.11
ACGTcount: A:0.04, C:0.19, G:0.04, T:0.74
Consensus pattern (10 bp):
TTCTTTCTTT
Found at i:19689926 original size:16 final size:17
Alignment explanation
Indices: 19689907--19689944 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
19689897 AATTGAAAAA
19689907 TAAAAAAATT-AAACT-
1 TAAAAAAATTCAAACTC
*
19689922 TTAAAAAATTCAAACTC
1 TAAAAAAATTCAAACTC
19689939 TAAAAA
1 TAAAAA
19689945 GCCTGAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 9 0.47
16 5 0.26
17 5 0.26
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAAAAATTCAAACTC
Found at i:19689929 original size:15 final size:16
Alignment explanation
Indices: 19689909--19689944 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
19689899 TTGAAAAATA
*
19689909 AAAAAATT-AAACTTT
1 AAAAAATTCAAACTCT
19689924 AAAAAATTCAAACTCT
1 AAAAAATTCAAACTCT
19689940 AAAAA
1 AAAAA
19689945 GCCTGAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.64, C:0.11, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAAAATTCAAACTCT
Found at i:19689944 original size:31 final size:30
Alignment explanation
Indices: 19689909--19689978 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
19689899 TTGAAAAATA
* *
19689909 AAAAAATTAAACTTTAAAAAATTCAAACTCT
1 AAAAAATTAAAC-TTAAAAAATTCAAACCCG
** *
19689940 AAAAAGCCTGAACTTAAAAAATTCAAACCCG
1 AAAAA-ATTAAACTTAAAAAATTCAAACCCG
19689971 AAAAAATT
1 AAAAAATT
19689979 GGAGCTTAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
30 1 0.03
31 26 0.84
32 4 0.13
ACGTcount: A:0.57, C:0.16, G:0.04, T:0.23
Consensus pattern (30 bp):
AAAAAATTAAACTTAAAAAATTCAAACCCG
Found at i:19699766 original size:21 final size:21
Alignment explanation
Indices: 19699717--19699775 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
19699707 GTAATAAATC
*
19699717 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
*
19699737 AAACAAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
19699759 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
19699776 TTCTTAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 11 0.34
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:19699852 original size:15 final size:16
Alignment explanation
Indices: 19699822--19699854 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
19699812 AAATAGTTAT
19699822 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
19699839 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
19699854 A
1 A
19699855 AAAATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:19705765 original size:24 final size:24
Alignment explanation
Indices: 19705733--19705804 Score: 90
Period size: 28 Copynumber: 2.8 Consensus size: 24
19705723 TAAGTGATCA
19705733 TTATTTCTCATGTTCTTTTACCTT
1 TTATTTCTCATGTTCTTTTACCTT
* *
19705757 TTATTTCTCATCCTTTGCCCTTTACCTT
1 TTATTTCTCAT--GTT--CTTTTACCTT
19705785 TTATTTCTCATGTTCTTTTA
1 TTATTTCTCATGTTCTTTTA
19705805 GTCTCTTATG
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
24 16 0.40
26 4 0.10
28 20 0.50
ACGTcount: A:0.12, C:0.24, G:0.04, T:0.60
Consensus pattern (24 bp):
TTATTTCTCATGTTCTTTTACCTT
Found at i:19711314 original size:6 final size:6
Alignment explanation
Indices: 19711303--19711351 Score: 71
Period size: 6 Copynumber: 8.2 Consensus size: 6
19711293 AAATAGTTTA
* * *
19711303 CAATTC CAATTC CAATCC CAATCC CAATTC CAATTC CAATTC CCATTC
1 CAATTC CAATTC CAATTC CAATTC CAATTC CAATTC CAATTC CAATTC
19711351 C
1 C
19711352 CCTTCCTCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.31, C:0.41, G:0.00, T:0.29
Consensus pattern (6 bp):
CAATTC
Found at i:19720022 original size:2 final size:2
Alignment explanation
Indices: 19720015--19720048 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
19720005 CAGCACTACT
19720015 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19720049 ATGCATGCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:19721444 original size:10 final size:10
Alignment explanation
Indices: 19721431--19721492 Score: 58
Period size: 10 Copynumber: 6.3 Consensus size: 10
19721421 AATATTAAAA
19721431 AATAATTTTT
1 AATAATTTTT
*
19721441 AAT-ATATTT
1 AATAATTTTT
19721450 AA-ATATTTTT
1 AATA-ATTTTT
19721460 -ATAATTTTT
1 AATAATTTTT
*
19721469 AAAATATTTTT
1 AATA-ATTTTT
*
19721480 AATGATTTTT
1 AATAATTTTT
19721490 AAT
1 AAT
19721493 TTTGAAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
9 14 0.33
10 20 0.48
11 8 0.19
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (10 bp):
AATAATTTTT
Found at i:19721453 original size:20 final size:21
Alignment explanation
Indices: 19721430--19721491 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 21
19721420 AAATATTAAA
19721430 AAATAATTTTTAAT-ATATTT
1 AAATAATTTTTAATAATATTT
*
19721450 AAAT-ATTTTT-ATAATTTTT
1 AAATAATTTTTAATAATATTT
* *
19721469 AAA-ATATTTTTAATGATTTTT
1 AAATA-ATTTTTAATAATATTT
19721490 AA
1 AA
19721492 TTTTGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
18 2 0.06
19 14 0.39
20 10 0.28
21 10 0.28
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
AAATAATTTTTAATAATATTT
Found at i:19721492 original size:28 final size:27
Alignment explanation
Indices: 19721433--19721529 Score: 97
Period size: 28 Copynumber: 3.4 Consensus size: 27
19721423 TATTAAAAAA
* *
19721433 TAATTTTTAATATA-TTTAAATATTTTT
1 TAATTTTTAAAATATTTTTAATA-TTTT
19721460 ATAATTTTTAAAATATTTTTAATGATTTT
1 -TAATTTTTAAAATATTTTTAAT-ATTTT
*
19721489 TAATTTTGAAAAATAATTTTTATATATTTT
1 TAATTTT-TAAAAT-ATTTTTA-ATATTTT
*
19721519 TAAATTTTAAA
1 TAATTTTTAAA
19721530 TTTTAAAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
28 20 0.34
29 18 0.31
30 19 0.32
31 2 0.03
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (27 bp):
TAATTTTTAAAATATTTTTAATATTTT
Found at i:19721532 original size:38 final size:40
Alignment explanation
Indices: 19721460--19721545 Score: 113
Period size: 38 Copynumber: 2.1 Consensus size: 40
19721450 AAATATTTTT
* *
19721460 ATAATTTTTAAAATATTTTTAATGATTTTTAATTTTGAAAA
1 ATAATTTTTAAAATATTTTTAA-GATTTTAAATTTTAAAAA
*
19721501 ATAATTTTT-ATATATTTTTAA-ATTTTAAATTTTAAAAA
1 ATAATTTTTAAAATATTTTTAAGATTTTAAATTTTAAAAA
19721539 ATTAATT
1 A-TAATT
19721546 AAATGTTGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
38 16 0.39
39 5 0.12
40 11 0.27
41 9 0.22
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (40 bp):
ATAATTTTTAAAATATTTTTAAGATTTTAAATTTTAAAAA
Done.