Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168481.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_8, 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: 25818110
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 67000 characters in sequence are not A, C, G, or T
File 106 of 127
Found at i:19562542 original size:25 final size:27
Alignment explanation
Indices: 19562514--19562563 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
19562504 AAATTTAAAA
19562514 AAATATTAAAA-CTTAA-AAAAATCAT
1 AAATATTAAAATCTTAATAAAAATCAT
* *
19562539 AAATCTTAAAATTTTAATAAAAATC
1 AAATATTAAAATCTTAATAAAAATC
19562564 CAAAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.48
26 4 0.19
27 7 0.33
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (27 bp):
AAATATTAAAATCTTAATAAAAATCAT
Found at i:19562546 original size:18 final size:18
Alignment explanation
Indices: 19562504--19562549 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
19562494 TAAATTATAA
19562504 AAAT-TTAAAAAAATATT
1 AAATCTTAAAAAAATATT
*
19562521 AAAACTTAAAAAAATCA-T
1 AAATCTTAAAAAAAT-ATT
19562539 AAATCTTAAAA
1 AAATCTTAAAA
19562550 TTTTAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 3 0.12
18 21 0.84
19 1 0.04
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (18 bp):
AAATCTTAAAAAAATATT
Found at i:19562697 original size:19 final size:20
Alignment explanation
Indices: 19562661--19562698 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19562651 TTGACAATTT
*
19562661 AAAAAAAATTAGTCTTTTTC
1 AAAAAAAATTAGTATTTTTC
*
19562681 AAAAAAATTTAG-ATTTTT
1 AAAAAAAATTAGTATTTTT
19562699 ATTATTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (20 bp):
AAAAAAAATTAGTATTTTTC
Found at i:19562781 original size:34 final size:35
Alignment explanation
Indices: 19562742--19562810 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 35
19562732 TAAGAAAAAA
19562742 ATTTTTATTAAAATTTT-CATGTTTTGAATTTTTT
1 ATTTTTATTAAAATTTTACATGTTTTGAATTTTTT
* *
19562776 ATTTTTATTAAAATTTTGATATTTTTTGAATTTTT
1 ATTTTTATTAAAATTTT-ACATGTTTTGAATTTTT
19562811 ATGTTTTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 17 0.55
36 14 0.45
ACGTcount: A:0.28, C:0.01, G:0.06, T:0.65
Consensus pattern (35 bp):
ATTTTTATTAAAATTTTACATGTTTTGAATTTTTT
Found at i:19562880 original size:18 final size:19
Alignment explanation
Indices: 19562853--19562888 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
19562843 ATTTTAGTTT
19562853 TTTATAATTTTT-AAAATA
1 TTTATAATTTTTGAAAATA
*
19562871 TTTATGATTTTTGAAAAT
1 TTTATAATTTTTGAAAAT
19562889 TAAGAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (19 bp):
TTTATAATTTTTGAAAATA
Found at i:19571469 original size:32 final size:32
Alignment explanation
Indices: 19571414--19571483 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
19571404 ATATCCGAAC
* * * *
19571414 CCGACCCGATCCGATGTTGTATAAAATCAAAT
1 CCGATCCGATCCAATATTATATAAAATCAAAT
19571446 CCGATCCGATCCAATATTATATAAAATCAAAT
1 CCGATCCGATCCAATATTATATAAAATCAAAT
19571478 CCGATC
1 CCGATC
19571484 GGACTTGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26
Consensus pattern (32 bp):
CCGATCCGATCCAATATTATATAAAATCAAAT
Found at i:19571552 original size:11 final size:11
Alignment explanation
Indices: 19571536--19571581 Score: 56
Period size: 11 Copynumber: 3.9 Consensus size: 11
19571526 AATTAAATAT
19571536 ATATATAAAAA
1 ATATATAAAAA
19571547 ATATATAAAATTAA
1 ATATAT-AAA--AA
*
19571561 ATATATATAAA
1 ATATATAAAAA
19571572 ATATATAAAA
1 ATATATAAAA
19571582 TTAAATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
11 17 0.57
12 3 0.10
13 2 0.07
14 8 0.27
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATATATAAAAA
Found at i:19571555 original size:29 final size:29
Alignment explanation
Indices: 19571520--19571603 Score: 115
Period size: 29 Copynumber: 3.0 Consensus size: 29
19571510 TTAAATATAA
19571520 ATATAAAATTAAATATATATATAAAAAAT
1 ATATAAAATTAAATATATATATAAAAAAT
19571549 ATATAAAATT-AA-ATATATAT--AAAAT
1 ATATAAAATTAAATATATATATAAAAAAT
*
19571574 ATATAAAATTAAATATA-AAATTAAAAAAT
1 ATATAAAATTAAATATATATA-TAAAAAAT
19571603 A
1 A
19571604 ATTTTTTTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
25 15 0.31
26 4 0.08
27 12 0.24
28 2 0.04
29 16 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (29 bp):
ATATAAAATTAAATATATATATAAAAAAT
Found at i:19571556 original size:9 final size:9
Alignment explanation
Indices: 19571538--19571582 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
19571528 TTAAATATAT
*
19571538 ATATAAAAA
1 ATATATAAA
19571547 ATATATAAA
1 ATATATAAA
*
19571556 AT-TA-AAT
1 ATATATAAA
19571563 ATATATAAA
1 ATATATAAA
19571572 ATATATAAA
1 ATATATAAA
19571581 AT
1 AT
19571583 TAAATATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
7 4 0.13
8 4 0.13
9 23 0.74
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
ATATATAAA
Found at i:19571604 original size:25 final size:27
Alignment explanation
Indices: 19571520--19571599 Score: 110
Period size: 25 Copynumber: 3.0 Consensus size: 27
19571510 TTAAATATAA
*
19571520 ATATAAAATTAAATATATATATAAAAAAT
1 ATATAAAATTAAATATA-ATAT-TAAAAT
19571549 ATATAAAATTAAATAT-ATA-TAAAAT
1 ATATAAAATTAAATATAATATTAAAAT
*
19571574 ATATAAAATTAAATATAAAATTAAAA
1 ATATAAAATTAAATATAATATTAAAA
19571600 AATAATTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
25 21 0.45
26 2 0.04
27 8 0.17
29 16 0.34
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (27 bp):
ATATAAAATTAAATATAATATTAAAAT
Found at i:19571894 original size:2 final size:2
Alignment explanation
Indices: 19571887--19571920 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
19571877 GATGATGATG
19571887 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19571921 GGTCCATTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19573513 original size:20 final size:20
Alignment explanation
Indices: 19573467--19573506 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
19573457 TAATATTTGA
* *
19573467 AATTGTTAAAATTTAAATTT
1 AATTATTAAAATTAAAATTT
19573487 AATTATTAAAATTAAAATTT
1 AATTATTAAAATTAAAATTT
19573507 TGATATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
AATTATTAAAATTAAAATTT
Found at i:19579195 original size:2 final size:2
Alignment explanation
Indices: 19579190--19579214 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19579180 TGTGTGAGAT
19579190 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
19579215 TATACATTTG
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:19580335 original size:17 final size:17
Alignment explanation
Indices: 19580313--19580345 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
19580303 TACTATCCTG
19580313 GTTATTTATAAATCTAT
1 GTTATTTATAAATCTAT
19580330 GTTATTTATAAATCTA
1 GTTATTTATAAATCTA
19580346 AGTAGTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (17 bp):
GTTATTTATAAATCTAT
Found at i:19583148 original size:166 final size:166
Alignment explanation
Indices: 19582874--19583208 Score: 634
Period size: 166 Copynumber: 2.0 Consensus size: 166
19582864 ATTTAAGTTT
19582874 AGAGAAGAAAATTTAAGAAATATATTACCTAAATTACTGGCTTGACAAATCATGAAAGCAGAAGT
1 AGAGAAGAAAATTTAAGAAATATATTACCTAAATTACTGGCTTGACAAATCATGAAAGCAGAAGT
*
19582939 GATCTATTAGTATTTACGGGTCTCAGCACAGATGCATTTGTTTATGACTTTTGTTAAAAATCACC
66 GATCTATTAGTATTTACGGGTCTCAGCACAGATGCATTTGTTTATGACTTTTGTTAAAAATCAAC
19583004 TGCAGCTGGTGTTATGTGCTGGTTTCACTGGATTTC
131 TGCAGCTGGTGTTATGTGCTGGTTTCACTGGATTTC
*
19583040 AGAGAAGAAAATTTAAGAAATATATTACCTGAATTACTGGCTTGACAAATCATGAAAGCAGAAGT
1 AGAGAAGAAAATTTAAGAAATATATTACCTAAATTACTGGCTTGACAAATCATGAAAGCAGAAGT
* *
19583105 GATCTATTAGTATTTATGGGTCTCAGCACAGGTGCATTTGTTTATGACTTTTGTTAAAAATCAAC
66 GATCTATTAGTATTTACGGGTCTCAGCACAGATGCATTTGTTTATGACTTTTGTTAAAAATCAAC
19583170 TGCAGCTGGTGTTATGTGCTGGTTTCACTGGATTTC
131 TGCAGCTGGTGTTATGTGCTGGTTTCACTGGATTTC
19583206 AGA
1 AGA
19583209 CCTGTTAAAC
Statistics
Matches: 165, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
166 165 1.00
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.34
Consensus pattern (166 bp):
AGAGAAGAAAATTTAAGAAATATATTACCTAAATTACTGGCTTGACAAATCATGAAAGCAGAAGT
GATCTATTAGTATTTACGGGTCTCAGCACAGATGCATTTGTTTATGACTTTTGTTAAAAATCAAC
TGCAGCTGGTGTTATGTGCTGGTTTCACTGGATTTC
Found at i:19587103 original size:3 final size:3
Alignment explanation
Indices: 19587095--19587145 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
19587085 TAAATAAATG
19587095 TAT TAT 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
19587143 TAT
1 TAT
19587146 AAGCTTGTCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:19589580 original size:18 final size:18
Alignment explanation
Indices: 19589557--19589695 Score: 86
Period size: 18 Copynumber: 8.1 Consensus size: 18
19589547 TAATTTACTT
19589557 ATAAATAATATTATATTA
1 ATAAATAATATTATATTA
*
19589575 ATAAATATTATTATA--A
1 ATAAATAATATTATATTA
*
19589591 AT--A-AATA-T-TA-GA
1 ATAAATAATATTATATTA
19589603 AT-AAT-ATATTAATATTA
1 ATAAATAATATT-ATATTA
* *
19589620 ATAAATCATATTATGTTA
1 ATAAATAATATTATATTA
*
19589638 ATAAATCATATATTA-ATAA
1 ATAAAT-A-ATATTATATTA
* *
19589657 ATAATATTATAATATATTA
1 ATAA-ATAATATTATATTA
19589676 ATAAATAATA-TACTATTA
1 ATAAATAATATTA-TATTA
19589694 AT
1 AT
19589696 CTAATATATT
Statistics
Matches: 96, Mismatches: 11, Indels: 28
0.71 0.08 0.21
Matches are distributed among these distances:
11 2 0.02
12 4 0.04
13 7 0.07
14 2 0.02
16 5 0.05
17 5 0.05
18 45 0.47
19 18 0.19
20 8 0.08
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (18 bp):
ATAAATAATATTATATTA
Found at i:19589595 original size:16 final size:16
Alignment explanation
Indices: 19589555--19589600 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
19589545 CATAATTTAC
19589555 TTATAAAT-AATATTA
1 TTATAAATAAATATTA
*
19589570 -TATTAATAAATATTA
1 TTATAAATAAATATTA
19589585 TTATAAATAAATATTA
1 TTATAAATAAATATTA
19589601 GAATAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
16 14 0.52
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTATAAATAAATATTA
Found at i:19589599 original size:13 final size:13
Alignment explanation
Indices: 19589555--19589733 Score: 51
Period size: 13 Copynumber: 12.5 Consensus size: 13
19589545 CATAATTTAC
19589555 TTATAAAT-AATA
1 TTATAAATAAATA
19589567 TTATATTAATAAATATTA
1 TTATA--AAT-AA-A-TA
19589585 TTATAAATAAATA
1 TTATAAATAAATA
19589598 TTAGAATAATATATTAATA
1 TT---ATAA-ATA--AATA
*
19589617 TTAATAAAT-CATA
1 TT-ATAAATAAATA
*
19589630 TTATGTTAATAAATCA
1 TTA--TAAATAAAT-A
*
19589646 TATATTAATAAATA
1 T-TATAAATAAATA
* *
19589660 ATAT-TATAATATA
1 TTATAAATAA-ATA
19589673 TTAATAAATAATATA
1 TT-ATAAATAA-ATA
* * *
19589688 CTATTAATCTAATA
1 TTATAAAT-AAATA
*
19589702 -TATTAATAAATA
1 TTATAAATAAATA
*
19589714 TTATTAATAAATA
1 TTATAAATAAATA
*
19589727 ATATAAA
1 TTATAAA
19589734 GAATAATAAA
Statistics
Matches: 132, Mismatches: 13, Indels: 43
0.70 0.07 0.23
Matches are distributed among these distances:
12 14 0.11
13 40 0.30
14 19 0.14
15 23 0.17
16 12 0.09
17 11 0.08
18 7 0.05
19 6 0.05
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (13 bp):
TTATAAATAAATA
Found at i:19589606 original size:16 final size:15
Alignment explanation
Indices: 19589556--19589727 Score: 80
Period size: 15 Copynumber: 11.6 Consensus size: 15
19589546 ATAATTTACT
19589556 TATAAAT-AATATTA
1 TATAAATAAATATTA
*
19589570 TATTAATAAATATTA
1 TATAAATAAATATTA
19589585 TTATAAATAAATATTA
1 -TATAAATAAATATTA
*
19589601 GAATAATATATTAATATTA
1 -TATAA-ATA--AATATTA
*
19589620 -ATAAAT-CATATTA
1 TATAAATAAATATTA
* *
19589633 TGTTAATAAATCA-TA
1 TATAAATAAAT-ATTA
*
19589648 TATTAATAAATA--A
1 TATAAATAAATATTA
*
19589661 TAT-TATAATATATTA
1 TATAAATAA-ATATTA
*
19589676 -ATAAATAATATACTA
1 TATAAATAA-ATATTA
*
19589691 T-TAATCTAATATATTA
1 TATAA-ATAA-ATATTA
*
19589707 -ATAAAT-ATTATTA
1 TATAAATAAATATTA
19589720 -ATAAATAA
1 TATAAATAA
19589728 TATAAAGAAT
Statistics
Matches: 126, Mismatches: 16, Indels: 32
0.72 0.09 0.18
Matches are distributed among these distances:
12 4 0.03
13 24 0.19
14 15 0.12
15 36 0.29
16 33 0.26
17 7 0.06
19 7 0.06
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (15 bp):
TATAAATAAATATTA
Found at i:19589670 original size:54 final size:55
Alignment explanation
Indices: 19589602--19589719 Score: 129
Period size: 54 Copynumber: 2.2 Consensus size: 55
19589592 TAAATATTAG
* * *
19589602 AATAATA-TATT-A-ATATTAATAAATCATATTA-TGTTAATAAATCATATATTAATA
1 AATAATATTATTAATATATTAATAAATAATA-TACTATTAAT--ATAATATATTAATA
*
19589656 AATAATATTA-TAATATATTAATAAATAATATACTATTAATCTAATATATTAATA
1 AATAATATTATTAATATATTAATAAATAATATACTATTAATATAATATATTAATA
*
19589710 AATATTATTA
1 AATAATATTA
19589720 ATAAATAATA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
54 29 0.53
55 5 0.09
56 21 0.38
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (55 bp):
AATAATATTATTAATATATTAATAAATAATATACTATTAATATAATATATTAATA
Found at i:19589700 original size:23 final size:21
Alignment explanation
Indices: 19589649--19589731 Score: 87
Period size: 23 Copynumber: 3.8 Consensus size: 21
19589639 TAAATCATAT
*
19589649 ATTAATAAATAATATTATAATA
1 ATTAATAAATAATA-TATATTA
19589671 TATTAATAAATAATATACTATTA
1 -ATTAATAAATAATATA-TATTA
* *
19589694 ATCTAATATATTAATAAATATT-
1 AT-TAATA-AATAATATATATTA
19589716 ATTAATAAATAATATA
1 ATTAATAAATAATATA
19589732 AAGAATAATA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
20 7 0.13
21 5 0.10
22 6 0.12
23 27 0.52
24 7 0.13
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTAATAAATAATATATATTA
Found at i:19589796 original size:15 final size:15
Alignment explanation
Indices: 19589776--19589880 Score: 60
Period size: 15 Copynumber: 6.8 Consensus size: 15
19589766 ATATTAACAT
19589776 AATATTTTAATAATA
1 AATATTTTAATAATA
*
19589791 AATATTATTATTAAAATA
1 AATATT-TTA--ATAATA
*
19589809 TAATTATTTTTAAT-ATT
1 -AA-TA-TTTTAATAATA
19589826 AATAATTTTAATAATA
1 AAT-ATTTTAATAATA
*
19589842 AATA-TTT--CAAT-
1 AATATTTTAATAATA
19589853 -ATATTTTAATAATA
1 AATATTTTAATAATA
19589867 AATAATTTTTAATA
1 AAT-A-TTTTAATA
19589881 TTTTAATAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 28
0.67 0.06 0.27
Matches are distributed among these distances:
10 3 0.04
11 3 0.04
12 3 0.04
13 3 0.04
14 3 0.04
15 17 0.25
16 12 0.17
17 10 0.14
18 6 0.09
19 2 0.03
20 5 0.07
21 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.50
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:19589832 original size:19 final size:19
Alignment explanation
Indices: 19589780--19589832 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 19
19589770 TAACATAATA
19589780 TTTTAATAATAA-ATATTAT
1 TTTTAATAATAATA-ATTAT
*
19589799 TATTAA-AAT-ATAATTAT
1 TTTTAATAATAATAATTAT
*
19589816 TTTTAATATTAATAATT
1 TTTTAATAATAATAATT
19589833 TTAATAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 11 0.39
18 6 0.21
19 11 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATAATAATAATTAT
Found at i:19589858 original size:25 final size:26
Alignment explanation
Indices: 19589826--19589890 Score: 91
Period size: 25 Copynumber: 2.6 Consensus size: 26
19589816 TTTTAATATT
19589826 AATA-ATTTTAATAATAAAT-ATTTC
1 AATATATTTTAATAATAAATAATTTC
*
19589850 AATATATTTTAATAATAAATAATTTT
1 AATATATTTTAATAATAAATAATTTC
*
19589876 TA-ATATTTTAATAAT
1 AATATATTTTAATAAT
19589891 TATATTAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
24 4 0.11
25 28 0.76
26 5 0.14
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
AATATATTTTAATAATAAATAATTTC
Found at i:19589908 original size:47 final size:50
Alignment explanation
Indices: 19589824--19589921 Score: 116
Period size: 47 Copynumber: 2.0 Consensus size: 50
19589814 ATTTTTAATA
*
19589824 TTAATAATTTTAATAATAAATATTTCAATATATTTTAATAATAAATAATTT
1 TTAATAATTTTAATAATAAATATTTCAATATATTTTAAAAATAAAT-ATTT
* *
19589875 TTAAT-ATTTTAATAAT-TATA-TT-AATAT-TATTTAAAAATATATATTT
1 TTAATAATTTTAATAATAAATATTTCAATATAT-TTTAAAAATAAATATTT
19589921 T
1 T
19589922 CCAAAAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
46 6 0.14
47 16 0.37
48 2 0.05
49 3 0.07
50 11 0.26
51 5 0.12
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (50 bp):
TTAATAATTTTAATAATAAATATTTCAATATATTTTAAAAATAAATATTT
Found at i:19589917 original size:23 final size:20
Alignment explanation
Indices: 19589875--19589919 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
19589865 TAAATAATTT
*
19589875 TTAATATTTTAATAATTATA
1 TTAATATTTTAAAAATTATA
19589895 TTAATATTATTTAAAAATATATA
1 TTAATA-T-TTTAAAAAT-TATA
19589918 TT
1 TT
19589920 TTCCAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 1 0.05
22 8 0.38
23 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAATATTTTAAAAATTATA
Found at i:19590568 original size:16 final size:17
Alignment explanation
Indices: 19590533--19590572 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
19590523 ACTTTTCCAA
19590533 AAATATTTACAAAAACT
1 AAATATTTACAAAAACT
**
19590550 AAATATTTTGAAAAA-T
1 AAATATTTACAAAAACT
19590566 AAATATT
1 AAATATT
19590573 AGTGCATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (17 bp):
AAATATTTACAAAAACT
Found at i:19590780 original size:17 final size:16
Alignment explanation
Indices: 19590741--19590780 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
19590731 TAAACAAATT
19590741 AAAATACGATTACTTA
1 AAAATACGATTACTTA
*
19590757 AACAATATGATTACTTGA
1 AA-AATACGATTACTT-A
19590775 AAAATA
1 AAAATA
19590781 ATGGATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 16 0.76
18 3 0.14
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (16 bp):
AAAATACGATTACTTA
Found at i:19596565 original size:2 final size:2
Alignment explanation
Indices: 19596558--19596584 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19596548 TGATTGGAAA
19596558 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
19596585 AAAGGCAACA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19598228 original size:18 final size:19
Alignment explanation
Indices: 19598191--19598230 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
19598181 TCTATCAAAA
*
19598191 AAATGTTATACCTCGTAAC
1 AAATGTTATACATCGTAAC
*
19598210 AAATGTTATGCAT-GTAAC
1 AAATGTTATACATCGTAAC
19598228 AAA
1 AAA
19598231 ATAAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (19 bp):
AAATGTTATACATCGTAAC
Found at i:19603020 original size:2 final size:2
Alignment explanation
Indices: 19603013--19603050 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
19603003 TTATGATCTC
*
19603013 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19603051 GCAGGTGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19604976 original size:2 final size:2
Alignment explanation
Indices: 19604969--19604998 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19604959 CACAATGCCC
19604969 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
19604999 ATATGCGTGT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:19611391 original size:6 final size:6
Alignment explanation
Indices: 19611380--19611447 Score: 52
Period size: 6 Copynumber: 11.3 Consensus size: 6
19611370 AATATTATTT
* * *
19611380 TAAATA TAAATA TAAA-A TTAAATA TATATA AAAATA TATAAAA TTAAATA
1 TAAATA TAAATA TAAATA -TAAATA TAAATA TAAATA TA-AATA -TAAATA
*
19611430 T--ATA TATATA TAAATA TA
1 TAAATA TAAATA TAAATA TA
19611448 TAAAATTAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
4 4 0.08
5 1 0.02
6 35 0.71
7 7 0.14
8 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
TAAATA
Found at i:19611404 original size:30 final size:28
Alignment explanation
Indices: 19611380--19611457 Score: 106
Period size: 26 Copynumber: 2.8 Consensus size: 28
19611370 AATATTATTT
19611380 TAAATATAAATATAAAATTAAATATATA
1 TAAATATAAATATAAAATTAAATATATA
*
19611408 TAAA-A-ATATATAAAATTAAATATATA
1 TAAATATAAATATAAAATTAAATATATA
*
19611434 TATATATAAATATATAAAATTAAA
1 TAAATAT-AA-ATATAAAATTAAA
19611458 AAAAAAAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
26 23 0.53
27 2 0.05
28 4 0.09
29 1 0.02
30 13 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
TAAATATAAATATAAAATTAAATATATA
Found at i:19611410 original size:16 final size:16
Alignment explanation
Indices: 19611379--19611457 Score: 59
Period size: 16 Copynumber: 5.3 Consensus size: 16
19611369 AAATATTATT
19611379 TTAAATATAAATATAAAA
1 TTAAATAT--ATATAAAA
19611397 TTAAATATATAT---A
1 TTAAATATATATAAAA
19611410 --AAA-ATATATAAAA
1 TTAAATATATATAAAA
*
19611423 TTAAATATATAT-ATA
1 TTAAATATATATAAAA
19611438 -TATAA-ATATATAAAA
1 TTA-AATATATATAAAA
19611453 TTAAA
1 TTAAA
19611458 AAAAAAAATT
Statistics
Matches: 50, Mismatches: 2, Indels: 21
0.68 0.03 0.29
Matches are distributed among these distances:
10 6 0.12
11 3 0.06
13 2 0.04
14 8 0.16
15 11 0.22
16 12 0.24
18 8 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TTAAATATATATAAAA
Found at i:19611416 original size:10 final size:10
Alignment explanation
Indices: 19611398--19611452 Score: 56
Period size: 10 Copynumber: 5.5 Consensus size: 10
19611388 AATATAAAAT
*
19611398 TAAATATATA
1 TAAAAATATA
19611408 TAAAAATATA
1 TAAAAATATA
* *
19611418 TAAAATTAAA
1 TAAAAATATA
* *
19611428 TATATATATA
1 TAAAAATATA
*
19611438 TATAAATATA
1 TAAAAATATA
19611448 TAAAA
1 TAAAA
19611453 TTAAAAAAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 36 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
TAAAAATATA
Found at i:19611753 original size:2 final size:2
Alignment explanation
Indices: 19611746--19611787 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
19611736 GATGATGATG
19611746 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19611788 GGTCCATTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19620182 original size:17 final size:17
Alignment explanation
Indices: 19620160--19620192 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
19620150 TACTATCCTG
19620160 GTTATTTATAAATCTAT
1 GTTATTTATAAATCTAT
19620177 GTTATTTATAAATCTA
1 GTTATTTATAAATCTA
19620193 AGTAGTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (17 bp):
GTTATTTATAAATCTAT
Found at i:19626798 original size:3 final size:3
Alignment explanation
Indices: 19626790--19626831 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
19626780 TAAATAAATG
19626790 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
19626832 AAGGTTTTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:19629061 original size:13 final size:14
Alignment explanation
Indices: 19629034--19629060 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19629024 TTTGTTTCAA
19629034 AAAAATAATTTTTT
1 AAAAATAATTTTTT
19629048 AAAAATAATTTTT
1 AAAAATAATTTTT
19629061 ATATTTTTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAAAATAATTTTTT
Found at i:19629266 original size:18 final size:18
Alignment explanation
Indices: 19629245--19629415 Score: 113
Period size: 18 Copynumber: 10.1 Consensus size: 18
19629235 AATTTTACTT
19629245 ATAAATAATATTATATTA
1 ATAAATAATATTATATTA
*
19629263 ATAAATATTATTATA--A
1 ATAAATAATATTATATTA
*
19629279 AT--A-AATA-T-TA-GA
1 ATAAATAATATTATATTA
19629291 AT-AAT-ATATTAATATTA
1 ATAAATAATATT-ATATTA
*
19629308 ATAAATAATATTATGTTA
1 ATAAATAATATTATATTA
*
19629326 AT-AAT--CA-TATATTA
1 ATAAATAATATTATATTA
*
19629340 ATAAATAATATTATGTTA
1 ATAAATAATATTATATTA
*
19629358 ATAAATCATATATTA-ATAA
1 ATAAAT-A-ATATTATATTA
* *
19629377 ATAATATTATAATATATTA
1 ATAA-ATAATATTATATTA
19629396 ATAAATAATA-TACTATTA
1 ATAAATAATATTA-TATTA
19629414 AT
1 AT
19629416 CTAATATATT
Statistics
Matches: 121, Mismatches: 14, Indels: 36
0.71 0.08 0.21
Matches are distributed among these distances:
11 2 0.02
12 4 0.03
13 7 0.06
14 10 0.08
15 4 0.03
16 5 0.04
17 9 0.07
18 53 0.44
19 19 0.16
20 8 0.07
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
ATAAATAATATTATATTA
Found at i:19629316 original size:13 final size:13
Alignment explanation
Indices: 19629257--19629450 Score: 93
Period size: 13 Copynumber: 14.3 Consensus size: 13
19629247 AAATAATATT
19629257 ATATTAATAAATA
1 ATATTAATAAATA
*
19629270 TTATT-ATAAATAA
1 ATATTAATAAAT-A
19629283 ATATTAGA-ATAAT-
1 ATATTA-ATA-AATA
*
19629296 ATATTAAT-ATTA
1 ATATTAATAAATA
*
19629308 ATA--AATAATATT
1 ATATTAATAA-ATA
*
19629320 ATGTTAAT-AATCA
1 ATATTAATAAAT-A
19629333 TATATTAATAAATAA
1 -ATATTAATAAAT-A
19629348 TATTATGTTAATAAATCA
1 -A-TA--TTAATAAAT-A
19629366 TATATTAATAAATA
1 -ATATTAATAAATA
19629380 ATATT-AT-AAT-
1 ATATTAATAAATA
19629390 ATATTAATAAATA
1 ATATTAATAAATA
* *
19629403 ATATACTATTAATCTAA
1 ATAT--TAATAA-AT-A
19629420 TATATTAATAAATA
1 -ATATTAATAAATA
*
19629434 TTATTAATAAATA
1 ATATTAATAAATA
19629447 ATAT
1 ATAT
19629451 AAAGAATAAT
Statistics
Matches: 141, Mismatches: 16, Indels: 48
0.69 0.08 0.23
Matches are distributed among these distances:
10 8 0.06
11 8 0.06
12 20 0.14
13 40 0.28
14 13 0.09
15 25 0.18
16 8 0.06
17 3 0.02
18 16 0.11
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (13 bp):
ATATTAATAAATA
Found at i:19629328 original size:14 final size:14
Alignment explanation
Indices: 19629311--19629361 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
19629301 AATATTAATA
19629311 AATAATATTATGTT
1 AATAATATTATGTT
19629325 AATAATCATATAT-TAAT
1 AATAAT-AT-TATGT--T
19629342 AAATAATATTATGTT
1 -AATAATATTATGTT
19629357 AATAA
1 AATAA
19629362 ATCATATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
14 11 0.35
15 4 0.13
16 6 0.19
17 4 0.13
18 6 0.19
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (14 bp):
AATAATATTATGTT
Found at i:19629394 original size:56 final size:54
Alignment explanation
Indices: 19629332--19629439 Score: 146
Period size: 56 Copynumber: 2.0 Consensus size: 54
19629322 GTTAATAATC
* *
19629332 ATATATTAATAAATAATATTA-TGTTAATAAATCATATATTAATAAATAATATTATA
1 ATATATTAATAAATAATA-TACTATTAAT--ATAATATATTAATAAATAATATTATA
* *
19629388 ATATATTAATAAATAATATACTATTAATCTAATATATTAATAAATATTATTA
1 ATATATTAATAAATAATATACTATTAATATAATATATTAATAAATAATATTA
19629440 ATAAATAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
54 21 0.45
55 2 0.04
56 24 0.51
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.44
Consensus pattern (54 bp):
ATATATTAATAAATAATATACTATTAATATAATATATTAATAAATAATATTATA
Found at i:19629420 original size:23 final size:21
Alignment explanation
Indices: 19629369--19629451 Score: 87
Period size: 23 Copynumber: 3.8 Consensus size: 21
19629359 TAAATCATAT
*
19629369 ATTAATAAATAATATTATAATA
1 ATTAATAAATAATA-TATATTA
19629391 TATTAATAAATAATATACTATTA
1 -ATTAATAAATAATATA-TATTA
* *
19629414 ATCTAATATATTAATAAATATT-
1 AT-TAATA-AATAATATATATTA
19629436 ATTAATAAATAATATA
1 ATTAATAAATAATATA
19629452 AAGAATAATA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
20 7 0.13
21 5 0.10
22 6 0.12
23 27 0.52
24 7 0.13
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTAATAAATAATATATATTA
Found at i:19629527 original size:14 final size:14
Alignment explanation
Indices: 19629510--19629536 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19629500 TTTTAATAAT
19629510 AAATATAATTATTA
1 AAATATAATTATTA
19629524 AAATATAATTATT
1 AAATATAATTATT
19629537 TTTTAATATT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATATAATTATTA
Found at i:19629581 original size:25 final size:26
Alignment explanation
Indices: 19629547--19629611 Score: 91
Period size: 25 Copynumber: 2.6 Consensus size: 26
19629537 TTTTAATATT
19629547 AATA-ATTTTAATAATAAAT-ATTTC
1 AATATATTTTAATAATAAATAATTTC
*
19629571 AATATATTTTAATAATAAATAATTTT
1 AATATATTTTAATAATAAATAATTTC
*
19629597 TA-ATATTTTAATAAT
1 AATATATTTTAATAAT
19629612 TATATTAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
24 4 0.11
25 28 0.76
26 5 0.14
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
AATATATTTTAATAATAAATAATTTC
Found at i:19629632 original size:23 final size:21
Alignment explanation
Indices: 19629586--19629642 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 21
19629576 ATTTTAATAA
19629586 TAAATAATT-T-TTAATATTT
1 TAAATAATTATATTAATATTT
19629605 T-AATAATTATATTAATATTATT
1 TAAATAATTATATTAATA-T-TT
19629627 TAAATATATATATATT
1 TAAATA-AT-TATATT
19629643 TTCCAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
18 7 0.23
19 2 0.06
20 6 0.19
21 1 0.03
22 3 0.10
23 4 0.13
24 2 0.06
25 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TAAATAATTATATTAATATTT
Found at i:19629633 original size:58 final size:59
Alignment explanation
Indices: 19629509--19629635 Score: 145
Period size: 59 Copynumber: 2.2 Consensus size: 59
19629499 ATTTTAATAA
* *
19629509 TAAATATAATTATTAAAATATAATTATTTTTTAATATTAATAATTTTAATAATAAATATT
1 TAAATAT-ATTATTAAAATATAATTAATTTTTAATATTAATAATTATAATAATAAATATT
* * *
19629569 TCAATATATT-TTAATAATA-AA-TAATTTTTAATATTTTAATAATTATATTAAT-ATTATT
1 TAAATATATTATTAA-AATATAATTAATTTTTAATA--TTAATAATTATAATAATAAATATT
19629627 TAAATATAT
1 TAAATATAT
19629636 ATATATTTTC
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
57 11 0.19
58 19 0.33
59 22 0.38
60 6 0.10
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (59 bp):
TAAATATATTATTAAAATATAATTAATTTTTAATATTAATAATTATAATAATAAATATT
Found at i:19630290 original size:16 final size:17
Alignment explanation
Indices: 19630255--19630294 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
19630245 ACTTTTCCAA
19630255 AAATATTTACAAAAACT
1 AAATATTTACAAAAACT
**
19630272 AAATATTTTGAAAAA-T
1 AAATATTTACAAAAACT
19630288 AAATATT
1 AAATATT
19630295 AGTGTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (17 bp):
AAATATTTACAAAAACT
Found at i:19630502 original size:17 final size:16
Alignment explanation
Indices: 19630463--19630502 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
19630453 TAAACAAATT
19630463 AAAATACGATTACTTA
1 AAAATACGATTACTTA
*
19630479 AACAATATGATTACTTGA
1 AA-AATACGATTACTT-A
19630497 AAAATA
1 AAAATA
19630503 ATGGATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 16 0.76
18 3 0.14
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (16 bp):
AAAATACGATTACTTA
Found at i:19631695 original size:23 final size:23
Alignment explanation
Indices: 19631665--19631714 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
19631655 GGAAAAAAGA
19631665 AAGAAAAAGTTTGTTGCTTTTTG
1 AAGAAAAAGTTTGTTGCTTTTTG
19631688 AAGAAAAAGTTTGTTGCTTTTTG
1 AAGAAAAAGTTTGTTGCTTTTTG
19631711 AAGA
1 AAGA
19631715 TGCAAAGGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
AAGAAAAAGTTTGTTGCTTTTTG
Found at i:19635335 original size:32 final size:32
Alignment explanation
Indices: 19635294--19635359 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
19635284 AATAACAACC
19635294 AGTTGTTAAGTATGAGATTTTAAATCATATAA
1 AGTTGTTAAGTATGAGATTTTAAATCATATAA
19635326 AGTTGTTAAGTATGAGATTTTAAATCATATAA
1 AGTTGTTAAGTATGAGATTTTAAATCATATAA
19635358 AG
1 AG
19635360 AAAATGACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.41, C:0.03, G:0.17, T:0.39
Consensus pattern (32 bp):
AGTTGTTAAGTATGAGATTTTAAATCATATAA
Found at i:19636365 original size:2 final size:2
Alignment explanation
Indices: 19636358--19636390 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
19636348 TGATTGGAAA
19636358 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
19636391 AAAGGCAACA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19640860 original size:9 final size:9
Alignment explanation
Indices: 19640828--19640853 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
19640818 ATAAGCAAGA
19640828 TTTTTTATG
1 TTTTTTATG
19640837 TTTTTTATG
1 TTTTTTATG
19640846 TTTTTTAT
1 TTTTTTAT
19640854 TTGTTTTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.08, T:0.81
Consensus pattern (9 bp):
TTTTTTATG
Found at i:19642856 original size:2 final size:2
Alignment explanation
Indices: 19642849--19642878 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
19642839 TTATGATCTC
*
19642849 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19642879 GCAGGTGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19644794 original size:2 final size:2
Alignment explanation
Indices: 19644787--19644813 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19644777 CCACAATGCC
19644787 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 T
19644814 ATGCGTGTTT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:19650089 original size:21 final size:20
Alignment explanation
Indices: 19650064--19650112 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
19650054 CATTTTATTA
*
19650064 TTATCAATAACAATTAGATAT
1 TTATCAATAA-AATTAAATAT
*
19650085 TTATCCTAATAAATTTAAATAT
1 TTAT-C-AATAAAATTAAATAT
19650107 TTATCA
1 TTATCA
19650113 TGCATAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
20 1 0.04
21 5 0.21
22 13 0.54
23 5 0.21
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (20 bp):
TTATCAATAAAATTAAATAT
Found at i:19651139 original size:23 final size:23
Alignment explanation
Indices: 19651089--19651146 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
19651079 GGCTGTAGGT
19651089 AGGCTGAACAGGGAGCTAGTCAAA
1 AGGCTG-ACAGGGAGCTAGTCAAA
* * * *
19651113 AGGCTGACAGGGGGCTGGTCGAG
1 AGGCTGACAGGGAGCTAGTCAAA
19651136 AGGCTGACAGG
1 AGGCTGACAGG
19651147 AGTGGCAGCG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 24 0.80
24 6 0.20
ACGTcount: A:0.28, C:0.17, G:0.43, T:0.12
Consensus pattern (23 bp):
AGGCTGACAGGGAGCTAGTCAAA
Found at i:19651234 original size:11 final size:11
Alignment explanation
Indices: 19651208--19651249 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
19651198 TAAAAAAAAA
*
19651208 TTTAATTTAATT
1 TTTAA-TTATTT
19651220 TTTAATTATTT
1 TTTAATTATTT
19651231 TTTAA-T-TTT
1 TTTAATTATTT
19651240 TTTAATTATT
1 TTTAATTATT
19651250 ATATATTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
9 8 0.30
10 2 0.07
11 12 0.44
12 5 0.19
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTAATTATTT
Found at i:19651260 original size:16 final size:16
Alignment explanation
Indices: 19651239--19651287 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
19651229 TTTTTAATTT
19651239 TTTTAATTATTATATA
1 TTTTAATTATTATATA
*
19651255 TTTTAAATATT-TATTA
1 TTTTAATTATTATA-TA
19651271 TTATT-ATTATTA-ATA
1 TT-TTAATTATTATATA
19651286 TT
1 TT
19651288 AATATTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
15 6 0.21
16 20 0.71
17 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTAATTATTATATA
Found at i:19651884 original size:37 final size:37
Alignment explanation
Indices: 19651843--19651958 Score: 112
Period size: 35 Copynumber: 3.1 Consensus size: 37
19651833 CGAGCAAAAT
* *
19651843 ATTAAAGATGACTGGGACTGAACCGTAAGTCGAAAGA
1 ATTAAAGATGACTGGGACTGAATCGCAAGTCGAAAGA
* * * *
19651880 ATTAATGAAATGA-TCGGGATTAAATCGCGAGTC-AAAG-
1 ATTAA--AGATGACT-GGGACTGAATCGCAAGTCGAAAGA
* *
19651917 ATTAAAGATGACTGCGACTGAATCGCAAGTCGACAGA
1 ATTAAAGATGACTGGGACTGAATCGCAAGTCGAAAGA
19651954 ATTAA
1 ATTAA
19651959 TGAAATGATC
Statistics
Matches: 61, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
35 19 0.31
36 4 0.07
37 15 0.25
38 5 0.08
39 18 0.30
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.22
Consensus pattern (37 bp):
ATTAAAGATGACTGGGACTGAATCGCAAGTCGAAAGA
Found at i:19651887 original size:74 final size:74
Alignment explanation
Indices: 19651771--19652758 Score: 1046
Period size: 74 Copynumber: 13.6 Consensus size: 74
19651761 GCGACTTTGA
* * * * *
19651771 ATTAAAGA-GA-TCGGGATTGAACTGCAAGT-TAGAGAATTAATGAAATGACCGAGATTAAACCA
1 ATTAAAGATGACT-GGGACTGAACCGCAAGTCGAGAGAATTAATGAAATGATCGGGATTAAACCA
* *
19651833 CGAGCAAAAT
65 CGAGCCAAAG
* * * *
19651843 ATTAAAGATGACTGGGACTGAACCGTAAGTCGAAAGAATTAATGAAATGATCGGGATTAAATCGC
1 ATTAAAGATGACTGGGACTGAACCGCAAGTCGAGAGAATTAATGAAATGATCGGGATTAAACCAC
*
19651908 GAGTCAAAG
66 GAGCCAAAG
* * *
19651917 ATTAAAGATGACTGCGACTGAATCGCAAGTCGACAGAATTAATGAAATGATCGGGATTAAACCAC
1 ATTAAAGATGACTGGGACTGAACCGCAAGTCGAGAGAATTAATGAAATGATCGGGATTAAACCAC
19651982 GAGCCAAAG
66 GAGCCAAAG
** * * *
19651991 ATTAAAGATGACTAAGACTAAACCGCAAGTCGAGGGAATTAATAAAATGATCGGGATTAAACCAC
1 ATTAAAGATGACTGGGACTGAACCGCAAGTCGAGAGAATTAATGAAATGATCGGGATTAAACCAC
*
19652056 AAGCCAAAG
66 GAGCCAAAG
* * * * **
19652065 ATTAAAGATGACTGGAACTAAACCACAAGTC-AG-GAAATTAATGAAATGACCAAGATTAAACCA
1 ATTAAAGATGACTGGGACTGAACCGCAAGTCGAGAG-AATTAATGAAATGATCGGGATTAAACCA
* *
19652128 CTAGTCAAAG
65 CGAGCCAAAG
* * * *
19652138 ATTAAAGACGATTGGGATTGAACCGCAAGTCG-GACAATTAATGAAATGATC-GGATTAAACCAC
1 ATTAAAGATGACTGGGACTGAACCGCAAGTCGAGAGAATTAATGAAATGATCGGGATTAAACCAC
*
19652201 GAGTCAAAGG
66 GAGCCAAA-G
* *
19652211 A-TAAAAATGACTGGGACTGAACCGCAAGTC-AGAG----AATGAAATGATCGGGATTAAATCAC
1 ATTAAAGATGACTGGGACTGAACCGCAAGTCGAGAGAATTAATGAAATGATCGGGATTAAACCAC
*
19652270 GAGTCAAAG
66 GAGCCAAAG
* * * * * * **
19652279 ATTAAAGACGACTGTGACTGAATCGTAAGTC-AGAGAATTAATAAAATGACCGGGATTAAACTGC
1 ATTAAAGATGACTGGGACTGAACCGCAAGTCGAGAGAATTAATGAAATGATCGGGATTAAACCAC
*
19652343 AAGCCAAAG
66 GAGCCAAAG
** * * *
19652352 ATTAAAGACAATTGGGACTGAACCGTAAGTCGAG-CAATTAATGAAATGATCGGGATTAAACCAC
1 ATTAAAGATGACTGGGACTGAACCGCAAGTCGAGAGAATTAATGAAATGATCGGGATTAAACCAC
19652416 -AGCCAAAGG
66 GAGCCAAA-G
* * * * ** **
19652425 A-TAAAGATGACT-GGATTGAACTGCAAATCGAGAGAATTAATAAAATGATCAAGATTAAACTGC
1 ATTAAAGATGACTGGGACTGAACCGCAAGTCGAGAGAATTAATGAAATGATCGGGATTAAACCAC
*
19652488 GAGTCAAAG
66 GAGCCAAAG
* * * *
19652497 ATTAAAGATGACTGAGACTGAACCGCAAGTCGAGGGAATTAATGAAATGATCGAGATTAAACCAT
1 ATTAAAGATGACTGGGACTGAACCGCAAGTCGAGAGAATTAATGAAATGATCGGGATTAAACCAC
19652562 GAGCCAAAG
66 GAGCCAAAG
* * * * *
19652571 ATTAAAGATGATTGGGACTGAACCGTAAGTC-AGGGAATTAATGAAATGACCCTGGATTAAACCA
1 ATTAAAGATGACTGGGACTGAACCGCAAGTCGAGAGAATTAATGAAATGA-TCGGGATTAAACCA
* *
19652635 TGAGCTAAAAG
65 CGAGC-CAAAG
* * * * * *
19652646 ATTAAAGATGACTGGGACTGAATCGCAAGTC-AAAGAATTAATGAAATGACCGAGATTAAATCAT
1 ATTAAAGATGACTGGGACTGAACCGCAAGTCGAGAGAATTAATGAAATGATCGGGATTAAACCAC
19652710 GAGCCAAAG
66 GAGCCAAAG
* * * *
19652719 GTTAAAAATAACTGGGACTGAATCGCAAGTCGAG-GAATTA
1 ATTAAAGATGACTGGGACTGAACCGCAAGTCGAGAGAATTA
19652759 TATAAGACTG
Statistics
Matches: 774, Mismatches: 119, Indels: 45
0.83 0.13 0.05
Matches are distributed among these distances:
68 14 0.02
69 47 0.06
71 16 0.02
72 95 0.12
73 247 0.32
74 307 0.40
75 48 0.06
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.20
Consensus pattern (74 bp):
ATTAAAGATGACTGGGACTGAACCGCAAGTCGAGAGAATTAATGAAATGATCGGGATTAAACCAC
GAGCCAAAG
Found at i:19652219 original size:34 final size:33
Alignment explanation
Indices: 19652181--19652284 Score: 91
Period size: 34 Copynumber: 3.1 Consensus size: 33
19652171 ACAATTAATG
*
19652181 AAATGATCGGATTAAACCACGAGTCAAAGGATAA
1 AAATGATCGGATTAAACCACGAGTCAAAGAAT-A
* * * * * * *
19652215 AAATGACTGGGACTGAACCGCAAGTCAGAGAATG
1 AAATGA-TCGGATTAAACCACGAGTCAAAGAATA
* *
19652249 AAATGATCGGGATTAAATCACGAGTCAAAGATTA
1 AAATGATC-GGATTAAACCACGAGTCAAAGAATA
19652283 AA
1 AA
19652285 GACGACTGTG
Statistics
Matches: 51, Mismatches: 17, Indels: 4
0.71 0.24 0.06
Matches are distributed among these distances:
33 1 0.02
34 31 0.61
35 19 0.37
ACGTcount: A:0.44, C:0.14, G:0.23, T:0.18
Consensus pattern (33 bp):
AAATGATCGGATTAAACCACGAGTCAAAGAATA
Found at i:19652681 original size:35 final size:35
Alignment explanation
Indices: 19652642--19652749 Score: 90
Period size: 35 Copynumber: 3.0 Consensus size: 35
19652632 CCATGAGCTA
*
19652642 AAAGATTAAAGATGACTGGGACTGAATCGCAAGTC
1 AAAGATTAAAAATGACTGGGACTGAATCGCAAGTC
* * * * *** *
19652677 AAAGAATTAATGAAATGACCGAGATTAAATCATGAGCC
1 AAAG-ATTAA--AAATGACTGGGACTGAATCGCAAGTC
* *
19652715 AAAGGTTAAAAATAACTGGGACTGAATCGCAAGTC
1 AAAGATTAAAAATGACTGGGACTGAATCGCAAGTC
19652750 GAGGAATTAT
Statistics
Matches: 51, Mismatches: 19, Indels: 6
0.67 0.25 0.08
Matches are distributed among these distances:
35 21 0.41
36 5 0.10
37 4 0.08
38 21 0.41
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.20
Consensus pattern (35 bp):
AAAGATTAAAAATGACTGGGACTGAATCGCAAGTC
Found at i:19653835 original size:27 final size:27
Alignment explanation
Indices: 19653804--19653856 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
19653794 TCATTTTTCT
*
19653804 TTTTTTCATC-TTTTCATTTTTTTTTGC
1 TTTTTT-ATCTTTTTCATTTCTTTTTGC
*
19653831 TTTTTTGTCTTTTTCATTTCTTTTTG
1 TTTTTTATCTTTTTCATTTCTTTTTG
19653857 TATATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.06, C:0.13, G:0.06, T:0.75
Consensus pattern (27 bp):
TTTTTTATCTTTTTCATTTCTTTTTGC
Found at i:19653843 original size:19 final size:18
Alignment explanation
Indices: 19653821--19653874 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 18
19653811 ATCTTTTCAT
*
19653821 TTTTTTTTGCTTTTTTGTC
1 TTTTTTTT-CTTTTTTGTA
19653840 TTTTTCATTTC-TTTTTGTA
1 TTTTT--TTTCTTTTTTGTA
19653859 TATTTTTTTCTTTTTT
1 T-TTTTTTTCTTTTTT
19653875 TTAAGCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
18 4 0.13
19 18 0.60
20 5 0.17
21 3 0.10
ACGTcount: A:0.06, C:0.09, G:0.06, T:0.80
Consensus pattern (18 bp):
TTTTTTTTCTTTTTTGTA
Found at i:19665547 original size:24 final size:22
Alignment explanation
Indices: 19665507--19665551 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
19665497 TTTTTAAATA
19665507 TATATTTTTTTAGTTATTATTT
1 TATATTTTTTTAGTTATTATTT
*
19665529 TATATTATTTTTATTTTATTATT
1 TATATT-TTTTTA-GTTATTATT
19665552 ACCAATAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 6 0.30
24 8 0.40
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (22 bp):
TATATTTTTTTAGTTATTATTT
Found at i:19666707 original size:12 final size:12
Alignment explanation
Indices: 19666690--19666719 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
19666680 TTTAAAAAAA
19666690 TTAATTTAATTT
1 TTAATTTAATTT
19666702 TTAA-TTAATTT
1 TTAATTTAATTT
19666713 TTAATTT
1 TTAATTT
19666720 TTTAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTAATTTAATTT
Found at i:19669673 original size:20 final size:21
Alignment explanation
Indices: 19669650--19669691 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
19669640 TTAAAGTATC
19669650 TTTATGAA-AATT-AATAAATA
1 TTTAT-AATAATTAAATAAATA
19669670 TTTATAATAATTAAATAAATA
1 TTTATAATAATTAAATAAATA
19669691 T
1 T
19669692 ATAATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 2 0.10
20 9 0.45
21 9 0.45
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TTTATAATAATTAAATAAATA
Found at i:19677573 original size:23 final size:21
Alignment explanation
Indices: 19677537--19677621 Score: 71
Period size: 22 Copynumber: 3.8 Consensus size: 21
19677527 TTTTCTTTAT
*
19677537 TTATTTTTTTATATTTTAAAA
1 TTATTTTTTAATATTTTAAAA
* **
19677558 TTATGTTTTCTAATATCTTGAACTC
1 TTAT-TTTT-TAATAT-TTTAA-AA
19677583 TTATTTTTTAATAATTTTAAAA
1 TTATTTTTTAAT-ATTTTAAAA
* *
19677605 TTATTATTTATTATTTT
1 TTATTTTTTAATATTTT
19677622 TTTAATTTTC
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
21 9 0.18
22 14 0.28
23 13 0.26
24 10 0.20
25 4 0.08
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (21 bp):
TTATTTTTTAATATTTTAAAA
Found at i:19677898 original size:20 final size:20
Alignment explanation
Indices: 19677859--19677898 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
19677849 TCAAATATCA
*
19677859 AAAATTAAATTTTGATTATT
1 AAAATTAAATTTTGAATATT
19677879 AAAATTAAAATTTT-AATATT
1 AAAATT-AAATTTTGAATATT
19677899 TTATTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
AAAATTAAATTTTGAATATT
Found at i:19683918 original size:2 final size:2
Alignment explanation
Indices: 19683913--19683938 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19683903 CTAAATTTTC
19683913 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
19683939 CCGTTTCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19691039 original size:15 final size:15
Alignment explanation
Indices: 19691019--19691052 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
19691009 AAATATTAAT
*
19691019 AAAGGAAAGGAAAAA
1 AAAGGAAAAGAAAAA
*
19691034 AAAGGAAAAGAAAAG
1 AAAGGAAAAGAAAAA
19691049 AAAG
1 AAAG
19691053 TTTTTTAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (15 bp):
AAAGGAAAAGAAAAA
Found at i:19691127 original size:5 final size:5
Alignment explanation
Indices: 19691110--19691151 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
19691100 TAAAATTAAT
*
19691110 AAAGG AAAAG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AA
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AA
19691152 TTCCAACAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:19702736 original size:2 final size:2
Alignment explanation
Indices: 19702729--19702757 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
19702719 TGGAAAACAA
19702729 AG AG AG AG AG A- AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
19702758 TGGTTTGGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19703244 original size:15 final size:15
Alignment explanation
Indices: 19703204--19703246 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
19703194 AAATATTAAT
*
19703204 AAAGGAAAGGAAAAA
1 AAAGGAAAAGAAAAA
19703219 AAAGGAAAAGAAAAGA
1 AAAGGAAAAGAAAA-A
19703235 AAA-GAAAAGAAA
1 AAAGGAAAAGAAA
19703247 GTTTTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 22 0.85
16 4 0.15
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAAGGAAAAGAAAAA
Found at i:19703267 original size:5 final size:5
Alignment explanation
Indices: 19703208--19703246 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
19703198 ATTAATAAAG
*
19703208 GAAAG GAAAA -AAAA GGAAAA GAAAA GAAAA GAAAA GAAA
1 GAAAA GAAAA GAAAA -GAAAA GAAAA GAAAA GAAAA GAAA
19703247 GTTTTTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
4 4 0.13
5 23 0.74
6 4 0.13
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:19703322 original size:5 final size:5
Alignment explanation
Indices: 19703305--19703341 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
19703295 TAAAATTAAT
*
19703305 AAAGG AAAAG AAAGG AAAGG AAAGG AAAGG AAAGG AA
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AA
19703342 TTCTAACAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:19715033 original size:23 final size:23
Alignment explanation
Indices: 19715007--19715053 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
19714997 ATTCATCTTT
*
19715007 CAGGTATTTATTTATCATAAATG
1 CAGGTATTTATTTATCACAAATG
* *
19715030 CAGGTGTTTATTTATTACAAATG
1 CAGGTATTTATTTATCACAAATG
19715053 C
1 C
19715054 TTTCTATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.43
Consensus pattern (23 bp):
CAGGTATTTATTTATCACAAATG
Found at i:19720510 original size:14 final size:15
Alignment explanation
Indices: 19720488--19720517 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
19720478 AAATTTTAAA
19720488 TTATATTATTTATAT
1 TTATATTATTTATAT
19720503 TTAT-TTATTTATAT
1 TTATATTATTTATAT
19720517 T
1 T
19720518 CTTATCATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTATATTATTTATAT
Found at i:19733907 original size:19 final size:19
Alignment explanation
Indices: 19733883--19733920 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
19733873 TATAAATTAA
*
19733883 TTATGTATTTATTTTATTT
1 TTATGTAATTATTTTATTT
*
19733902 TTATGTAATTCTTTTATTT
1 TTATGTAATTATTTTATTT
19733921 AATAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.71
Consensus pattern (19 bp):
TTATGTAATTATTTTATTT
Found at i:19734864 original size:17 final size:16
Alignment explanation
Indices: 19734838--19734869 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
19734828 AAAATAAATC
19734838 TAATTATTTATATATT
1 TAATTATTTATATATT
19734854 TAATATATTTATATAT
1 TAAT-TATTTATATAT
19734870 AATAAATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTATTTATATATT
Found at i:19735096 original size:12 final size:12
Alignment explanation
Indices: 19735079--19735104 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19735069 GCCTTACTTG
19735079 AAAAATAAAATA
1 AAAAATAAAATA
19735091 AAAAATAAAATA
1 AAAAATAAAATA
19735103 AA
1 AA
19735105 GAATTCTCTT
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAATAAAATA
Found at i:19736483 original size:18 final size:20
Alignment explanation
Indices: 19736460--19736503 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 20
19736450 TTATTTTTTT
19736460 ATATTTTTAT-TTAAAA-TA
1 ATATTTTTATATTAAAATTA
19736478 ATA-TTTTATATTAAAATTA
1 ATATTTTTATATTAAAATTA
19736497 ATATTTT
1 ATATTTT
19736504 ATTAATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.26
18 9 0.39
19 5 0.22
20 3 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATTTTTATATTAAAATTA
Found at i:19736486 original size:17 final size:18
Alignment explanation
Indices: 19736464--19736506 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 18
19736454 TTTTTTATAT
19736464 TTTTATTTAAAA-TAATA
1 TTTTATTTAAAATTAATA
19736481 TTTTATATTAAAATTAATA
1 TTTTAT-TTAAAATTAATA
19736500 TTTTATT
1 TTTTATT
19736507 AATTTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.25
18 7 0.29
19 11 0.46
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTATTTAAAATTAATA
Found at i:19736508 original size:17 final size:17
Alignment explanation
Indices: 19736460--19736508 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
19736450 TTATTTTTTT
19736460 ATATTTTTATTTAAAATA
1 ATATTTTTA-TTAAAATA
19736478 ATATTTTATATTAAAATTA
1 ATATTTT-TATTAAAA-TA
19736497 ATA-TTTTATTAA
1 ATATTTTTATTAA
19736509 TTTTAAATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.21
18 16 0.55
19 7 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATTTTTATTAAAATA
Found at i:19746231 original size:3 final size:3
Alignment explanation
Indices: 19746223--19746254 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
19746213 TCAGTCTTTT
19746223 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
19746255 TTATTATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:19746669 original size:30 final size:28
Alignment explanation
Indices: 19746598--19746669 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 28
19746588 ATTTTTTTGG
*
19746598 ATAAATTCTTATAATTTTATTACATTCAA
1 ATAAATTTTTA-AATTTTATTACATTCAA
* * *
19746627 GTAAATTTTTTAAATTTTAATTTATATTTAA
1 ATAAA-TTTTTAAATTTT-A-TTACATTCAA
19746658 ATAAATTTTTAA
1 ATAAATTTTTAA
19746670 TTTATTTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
29 10 0.29
30 13 0.37
31 12 0.34
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (28 bp):
ATAAATTTTTAAATTTTATTACATTCAA
Found at i:19746671 original size:23 final size:23
Alignment explanation
Indices: 19746637--19746693 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
19746627 GTAAATTTTT
19746637 TAAA-TTTTAATTTATATTTAAA
1 TAAATTTTTAATTTATATTTAAA
*
19746659 TAAATTTTTAATTTATTTTTAAA
1 TAAATTTTTAATTTATATTTAAA
*
19746682 TAAATGTTTAAT
1 TAAATTTTTAAT
19746694 ATAAATTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 4 0.12
23 28 0.88
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TAAATTTTTAATTTATATTTAAA
Found at i:19746712 original size:22 final size:21
Alignment explanation
Indices: 19746685--19746742 Score: 54
Period size: 22 Copynumber: 2.9 Consensus size: 21
19746675 TTTTAAATAA
19746685 ATGTTTAATATAAATTAATATT
1 ATGTTTAATATAAATTAAT-TT
19746707 -TCGTTTGAA-ATAAA--AATTT
1 AT-GTTT-AATATAAATTAATTT
19746726 AT-TTTAATATAAATTAA
1 ATGTTTAATATAAATTAA
19746743 AAAAATTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 14
0.68 0.00 0.32
Matches are distributed among these distances:
17 2 0.07
18 8 0.27
19 2 0.07
20 6 0.20
21 1 0.03
22 9 0.30
23 2 0.07
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (21 bp):
ATGTTTAATATAAATTAATTT
Found at i:19749534 original size:95 final size:92
Alignment explanation
Indices: 19749415--19749693 Score: 264
Period size: 95 Copynumber: 2.9 Consensus size: 92
19749405 TAACAAAAAT
* *
19749415 ATTTTTTTATTTTGTAAACATAATATAAAATTTAAATATATTTACAAATATTATAA-TTCAAATA
1 ATTTTTTTATTTT-TAAATATAATAT-AAATTTAAATATATTTACAAATATTATAATTTAAAATA
* * *
19749479 AATAAGTTTTAAA-TTTTCTATTTTTAAGA
64 AATAAATTTCAAACTTTTCT-TTTTGAAGA
*
19749508 AGTTTTTTTATTTTTCAAAATATAATATATA-TTATAATATTATTATA-AAATATTATAATTTAA
1 A-TTTTTTTATTTTT--AAATATAATATAAATTTA-AATA-TATT-TACAAATATTATAATTTAA
* *
19749571 AATAAACAAATTTCAAACTTTTCTTTTTGAATA
60 AATAAATAAATTTCAAACTTTTCTTTTTGAAGA
* * *
19749604 ATTTTTTCTAATTTTTATATATAATAT-AGTTTAATATATTTTTATCAAA-ATTTATAATTTAAA
1 ATTTTTT-T-ATTTTTAAATATAATATAAATTTAA-ATATATTTA-CAAATA-TTATAATTTAAA
* * *
19749667 ATAAATAAATTCCAAAATTTTATTTTT
61 ATAAATAAATTTCAAACTTTTCTTTTT
19749694 AAATGTAACA
Statistics
Matches: 155, Mismatches: 16, Indels: 28
0.78 0.08 0.14
Matches are distributed among these distances:
93 7 0.05
94 23 0.15
95 85 0.55
96 28 0.18
97 12 0.08
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (92 bp):
ATTTTTTTATTTTTAAATATAATATAAATTTAAATATATTTACAAATATTATAATTTAAAATAAA
TAAATTTCAAACTTTTCTTTTTGAAGA
Found at i:19749561 original size:13 final size:11
Alignment explanation
Indices: 19749528--19749566 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
19749518 TTTTTCAAAA
19749528 TATAATATATAT
1 TATAATAT-TAT
19749540 TATAATATTAT
1 TATAATATTAT
*
19749551 TATAA-AATAT
1 TATAATATTAT
19749561 TATAAT
1 TATAAT
19749567 TTAAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 9 0.36
11 8 0.32
12 8 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
TATAATATTAT
Found at i:19749918 original size:25 final size:24
Alignment explanation
Indices: 19749875--19749922 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
19749865 TTTAAAAAAA
*
19749875 TTTTAAAATTATATATAAAATATAT
1 TTTTAAAATTAAATAT-AAATATAT
19749900 TTTTAAAATTAAACT-TAAATATA
1 TTTTAAAATTAAA-TATAAATATA
19749923 AAAAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 13 0.62
26 1 0.05
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
TTTTAAAATTAAATATAAATATAT
Found at i:19755425 original size:15 final size:15
Alignment explanation
Indices: 19755401--19755437 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
19755391 AATAAAATAA
*
19755401 TTTAATTAATTTAAT
1 TTTAAATAATTTAAT
*
19755416 TTTAAATAATTTGAT
1 TTTAAATAATTTAAT
19755431 TTTAAAT
1 TTTAAAT
19755438 TAATCAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (15 bp):
TTTAAATAATTTAAT
Found at i:19762917 original size:3 final size:3
Alignment explanation
Indices: 19762909--19762934 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
19762899 ATATACTCCT
19762909 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
19762935 TTTTTTTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:19766412 original size:30 final size:30
Alignment explanation
Indices: 19766378--19766455 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 30
19766368 TATTTTGATA
*
19766378 TAAAA-TATAAAATATTTTTTTAAAATTTTG
1 TAAAATTATAAAAT-TTTTATTAAAATTTTG
*
19766408 TAAAATTTATATAATTTTTATTAAAA-TTT-
1 TAAAA-TTATAAAATTTTTATTAAAATTTTG
*
19766437 T-AAATTATAATATTTTTAT
1 TAAAATTATAAAATTTTTAT
19766456 ATTTTTTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
27 13 0.31
28 3 0.07
29 1 0.02
30 8 0.19
31 10 0.24
32 7 0.17
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (30 bp):
TAAAATTATAAAATTTTTATTAAAATTTTG
Found at i:19766469 original size:26 final size:27
Alignment explanation
Indices: 19766434--19766488 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
19766424 TTTATTAAAA
19766434 TTTTAAATTATAATATT-T-TTATATT
1 TTTTAAATTATAATATTATATTATATT
*
19766459 TTTTAATATTATATTATTATATTATATT
1 TTTTAA-ATTATAATATTATATTATATT
19766487 TT
1 TT
19766489 AAATTGTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 6 0.23
26 10 0.38
27 1 0.04
28 9 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTTAAATTATAATATTATATTATATT
Found at i:19768627 original size:66 final size:65
Alignment explanation
Indices: 19768569--19768749 Score: 195
Period size: 67 Copynumber: 2.7 Consensus size: 65
19768559 TTGAACTGTT
*
19768569 GGTCTAAAAAATAAAATGATATGGACCGAGCCAAGATAAAAAATGAATAACTGGGATTGAATCGC
1 GGTCTAAAAAATAAAATGATATGGATCGAGCCAAGATAAAAAATGAATAACTGGGATTGAATCG-
19768634 A
65 A
* * * * * * *
19768635 GGTC-AGAAAAATAAAAATGTTCTAGATCAAGCCGAGATAAAAAAATGAGTAACTGGGGTTGAAT
1 GGTCTA-AAAAAT-AAAATGATATGGATCGAGCCAAGAT-AAAAAATGAATAACTGGGATTGAAT
*
19768699 CGC
63 CGA
**
19768702 GAGT-TAAAAAAGTAAAATGATATGGATCGAGCCAAGATCTAAAATGAA
1 G-GTCTAAAAAA-TAAAATGATATGGATCGAGCCAAGATAAAAAATGAA
19768750 CGATCAAGAT
Statistics
Matches: 92, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
65 1 0.01
66 17 0.18
67 45 0.49
68 29 0.32
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.20
Consensus pattern (65 bp):
GGTCTAAAAAATAAAATGATATGGATCGAGCCAAGATAAAAAATGAATAACTGGGATTGAATCGA
Found at i:19768719 original size:67 final size:64
Alignment explanation
Indices: 19768468--19768720 Score: 165
Period size: 66 Copynumber: 3.8 Consensus size: 64
19768458 GGATTGAGCA
* * * * **
19768468 GAGATAAAAAAACGAGTGACTGGGGTCGAATCATGAG-TAAGAAAAGTAAAATGATTTAGATCGA
1 GAGAT-AAAAAATGAGTAACTGGGATTGAATCGCGAGTTAA-AAAA-TAAAATG-TTTAGATC-A
*
19768532 A-TC
61 AGCC
** * * * * * *
19768535 GAGATAAAAAATGAGCGACTGTGATTGAA-CTGTTG-GTCTAAAAAATAAAATGATATGGACCGA
1 GAGATAAAAAATGAGTAACTGGGATTGAATC-G-CGAGT-TAAAAAATAAAATG-TTTAGATCAA
19768598 GCC
62 GCC
* * *
19768601 AAGATAAAAAATGAATAACTGGGATTGAATCGC-AGGTCAGAAAAATAAAAATGTTCTAGATCAA
1 GAGATAAAAAATGAGTAACTGGGATTGAATCGCGA-GTTA-AAAAAT-AAAATGTT-TAGATCAA
19768665 GCC
62 GCC
*
19768668 GAGATAAAAAAATGAGTAACTGGGGTTGAATCGCGAGTTAAAAAAGTAAAATG
1 GAGAT-AAAAAATGAGTAACTGGGATTGAATCGCGAGTTAAAAAA-TAAAATG
19768721 ATATGGATCG
Statistics
Matches: 146, Mismatches: 26, Indels: 28
0.73 0.13 0.14
Matches are distributed among these distances:
65 3 0.02
66 68 0.47
67 41 0.28
68 33 0.23
69 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.24, T:0.21
Consensus pattern (64 bp):
GAGATAAAAAATGAGTAACTGGGATTGAATCGCGAGTTAAAAAATAAAATGTTTAGATCAAGCC
Found at i:19769054 original size:18 final size:18
Alignment explanation
Indices: 19769001--19769054 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
19768991 AAGATTCACA
19769001 AAGGTTTGCAAGAATTTT
1 AAGGTTTGCAAGAATTTT
19769019 AA-GTTTCGCAA-AAGTTTT
1 AAGGTTT-GCAAGAA-TTTT
*
19769037 AAGGTTTGTAAGAATTTT
1 AAGGTTTGCAAGAATTTT
19769055 CATCATTGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
17 6 0.19
18 19 0.61
19 6 0.19
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (18 bp):
AAGGTTTGCAAGAATTTT
Found at i:19769316 original size:24 final size:24
Alignment explanation
Indices: 19769289--19769373 Score: 79
Period size: 24 Copynumber: 3.6 Consensus size: 24
19769279 CTTTAACATT
* *
19769289 TCATAGCAAAAAATTCAAAGATTC
1 TCATACCAAAAATTTCAAAGATTC
19769313 TCAT-CCGAAAAATTTC-AAGATT-
1 TCATACC-AAAAATTTCAAAGATTC
*
19769335 TCATATCC-AAAATTTCAGAGATTC
1 TCATA-CCAAAAATTTCAAAGATTC
* *
19769359 TCATTCGAAAAATTT
1 TCATACCAAAAATTT
19769374 TGGGATTCAC
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
22 12 0.24
23 13 0.26
24 25 0.50
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (24 bp):
TCATACCAAAAATTTCAAAGATTC
Found at i:19769323 original size:23 final size:23
Alignment explanation
Indices: 19769297--19769372 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
19769287 TTTCATAGCA
19769297 AAAAATTCAAAGATTCTCATCCG
1 AAAAATTCAAAGATTCTCATCCG
19769320 AAAAATTTC-AAGATT-TCATATCC-
1 AAAAA-TTCAAAGATTCTC--ATCCG
* * *
19769343 AAAATTTCAGAGATTCTCATTCG
1 AAAAATTCAAAGATTCTCATCCG
19769366 AAAAATT
1 AAAAATT
19769373 TTGGGATTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
22 8 0.19
23 26 0.60
24 9 0.21
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.32
Consensus pattern (23 bp):
AAAAATTCAAAGATTCTCATCCG
Found at i:19769336 original size:46 final size:46
Alignment explanation
Indices: 19769286--19769373 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 46
19769276 AAACTTTAAC
19769286 ATTTCATAGCAAAAAATTCAAAGATTCTCATCCGAAAAATTTCAAG
1 ATTTCATAGCAAAAAATTCAAAGATTCTCATCCGAAAAATTTCAAG
* * * * *
19769332 ATTTCATATCCAAAATTTCAGAGATTCTCATTCGAAAAATTT
1 ATTTCATAGCAAAAAATTCAAAGATTCTCATCCGAAAAATTT
19769374 TGGGATTCAC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (46 bp):
ATTTCATAGCAAAAAATTCAAAGATTCTCATCCGAAAAATTTCAAG
Found at i:19785393 original size:166 final size:164
Alignment explanation
Indices: 19785119--19785442 Score: 533
Period size: 166 Copynumber: 2.0 Consensus size: 164
19785109 GTTAGTGGGT
* *
19785119 AAAATACTATTTAATAAAAAGTTATTGTATTTAATGCATTAATTTTATTAAATTCCAGAAGAAAC
1 AAAATACTATTTAATAAAAAGTTATTGTATTTAATGCATTAATTTTACTAAATTCCAAAAGAAAC
* *
19785184 TATATATTAATTACATATTTCTTTTTTTAAATATTACCTTAATTATTATATACCGATTAATATTT
66 TATATATTAATTACATATTTCTTTTTTAAAATATTACCTTAATTATTAGATACCGATTAATATTT
19785249 GTT-TATATAAATAAAATCATAACTTAAAAATAAGAG
131 -TTCTATA-AAA-AAAATCATAACTTAAAAATAAGAG
* * *
19785285 AAAATACTATTTAATAAAAAGTTATTGTATTTCATGCATTAATTTTACTAAATTCGAAAAGAAAT
1 AAAATACTATTTAATAAAAAGTTATTGTATTTAATGCATTAATTTTACTAAATTCCAAAAGAAAC
*
19785350 TATATATTAATTACATATTTCTTTTTTAAAATATTACCTTAATTATTAGATACTGATTAATATTT
66 TATATATTAATTACATATTTCTTTTTTAAAATATTACCTTAATTATTAGATACCGATTAATATTT
*
19785415 TTCTATAAAAAAAATCATAATTTAAAAA
131 TTCTATAAAAAAAATCATAACTTAAAAA
19785443 AAAAAAGAGG
Statistics
Matches: 148, Mismatches: 9, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
164 17 0.11
165 5 0.03
166 126 0.85
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.43
Consensus pattern (164 bp):
AAAATACTATTTAATAAAAAGTTATTGTATTTAATGCATTAATTTTACTAAATTCCAAAAGAAAC
TATATATTAATTACATATTTCTTTTTTAAAATATTACCTTAATTATTAGATACCGATTAATATTT
TTCTATAAAAAAAATCATAACTTAAAAATAAGAG
Found at i:19793394 original size:6 final size:6
Alignment explanation
Indices: 19793383--19793416 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
19793373 TGTTGTCATT
* *
19793383 ATTATA ATTATA ATTATA ATTATC ATTATT ATTA
1 ATTATA ATTATA ATTATA ATTATA ATTATA ATTA
19793417 AAAATAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (6 bp):
ATTATA
Found at i:19793680 original size:18 final size:20
Alignment explanation
Indices: 19793659--19793696 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
19793649 AACATAGCTT
19793659 TTTAATAAAA-TT-TTAAAA
1 TTTAATAAAACTTATTAAAA
*
19793677 TTTATTAAAACTTATTAAAA
1 TTTAATAAAACTTATTAAAA
19793697 AGATAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTAATAAAACTTATTAAAA
Found at i:19796667 original size:17 final size:16
Alignment explanation
Indices: 19796647--19796680 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19796637 TGAGTTCTAA
19796647 TCTTCTTCCTTTTCTTT
1 TCTTC-TCCTTTTCTTT
*
19796664 TCTTCTCTTTTTCTTT
1 TCTTCTCCTTTTCTTT
19796680 T
1 T
19796681 TTTAACTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
TCTTCTCCTTTTCTTT
Found at i:19797458 original size:19 final size:20
Alignment explanation
Indices: 19797434--19797474 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
19797424 ATTTTAGGCT
*
19797434 TTAATTCTTGG-GCTTTAAA
1 TTAATTCTTGGACCTTTAAA
*
19797453 TTAATTTTTGGACCTTTAAA
1 TTAATTCTTGGACCTTTAAA
19797473 TT
1 TT
19797475 GAAATAGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.51
Consensus pattern (20 bp):
TTAATTCTTGGACCTTTAAA
Found at i:19809805 original size:62 final size:61
Alignment explanation
Indices: 19809739--19809908 Score: 155
Period size: 62 Copynumber: 2.7 Consensus size: 61
19809729 ATTGAATATA
* *
19809739 TTCAATTTCTAAATGCAAACAATTACATCGTTTCTTTAAACCAAATGCTATAATTAAGTATT
1 TTCAATTTCTAAATGCAAGCAATTACA-CGTTTCTTTAAACCAAACGCTATAATTAAGTATT
* * * *** * * *
19809801 TTCAA-TTCTTAAATCCAAGCAATTACAACATTTCTTTCATTTAAACGCTATAATTGATTTTT
1 TTCAATTTC-TAAATGCAAGCAATTAC-ACGTTTCTTTAAACCAAACGCTATAATTAAGTATT
* * *
19809863 TTAAAATTT-TAAATGCAAGCAATTATGACGTTTCTTTTAACCAAAC
1 TT-CAATTTCTAAATGCAAGCAATTA-CACGTTTCTTTAAACCAAAC
19809909 ACCACAATTG
Statistics
Matches: 84, Mismatches: 19, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
61 3 0.04
62 76 0.90
63 3 0.04
64 2 0.02
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.40
Consensus pattern (61 bp):
TTCAATTTCTAAATGCAAGCAATTACACGTTTCTTTAAACCAAACGCTATAATTAAGTATT
Found at i:19809981 original size:63 final size:62
Alignment explanation
Indices: 19809800--19809982 Score: 197
Period size: 62 Copynumber: 2.9 Consensus size: 62
19809790 AATTAAGTAT
* * * * **
19809800 TTTCAATTCTTAAATCCAAGCAATTACAACATTTCTTTCATTTAAACGCTATAATTGATTTT
1 TTTCAATTCTTAAATCCAAGCAATTACGACATTTCTTTTATTTAAACGCCATAATTGACTAA
* * * * *** * *
19809862 TTTAAAATT-TTAAATGCAAGCAATTATGACGTTTCTTTTAACCAAACACCACAATTGACTAA
1 TTT-CAATTCTTAAATCCAAGCAATTACGACATTTCTTTTATTTAAACGCCATAATTGACTAA
*
19809924 TTTCAATTCTTAAATCCAAGTCAATTACGACATTTTTTTTATTTAAACGCCATAATTGA
1 TTTCAATTCTTAAATCCAAG-CAATTACGACATTTCTTTTATTTAAACGCCATAATTGA
19809983 ATATTTTTAA
Statistics
Matches: 93, Mismatches: 25, Indels: 5
0.76 0.20 0.04
Matches are distributed among these distances:
61 4 0.04
62 55 0.59
63 34 0.37
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.40
Consensus pattern (62 bp):
TTTCAATTCTTAAATCCAAGCAATTACGACATTTCTTTTATTTAAACGCCATAATTGACTAA
Found at i:19810006 original size:125 final size:124
Alignment explanation
Indices: 19809727--19810007 Score: 341
Period size: 124 Copynumber: 2.3 Consensus size: 124
19809717 CTAAATGTCG
* * * * ** * *
19809727 TAATTGAATATATTCAATTTCTAAATGCAAACAATTACATCGTTTCTTTAAACCAAATGCTATAA
1 TAATTGAATATTTTTAATTTTTAAATGCAAGCAATTACATCGTTTCTTTAAACCAAACACCACAA
* * *
19809792 TTAAGTATTTTCAATTCTTAAATCCAAGCAATTACAACATTTCTTTCATTTAAACGCTA
66 TTAACTAATTTCAATTCTTAAATCCAAGCAATTACAACATTTCTTTCATTTAAACGCCA
* * * *
19809851 TAATTG-ATTTTTTTAAAATTTTAAATGCAAGCAATTATGA-CGTTTCTTTTAACCAAACACCAC
1 TAATTGAATATTTTT-AATTTTTAAATGCAAGCAATTA-CATCGTTTCTTTAAACCAAACACCAC
* * * *
19809914 AATTGACTAATTTCAATTCTTAAATCCAAGTCAATTACGACATTTTTTTTATTTAAACGCCA
64 AATTAACTAATTTCAATTCTTAAATCCAAG-CAATTACAACATTTCTTTCATTTAAACGCCA
*
19809976 TAATTGAATATTTTTAATTTTTATATGCAAGC
1 TAATTGAATATTTTTAATTTTTAAATGCAAGC
19810008 CATATTTGTG
Statistics
Matches: 131, Mismatches: 22, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
123 5 0.04
124 70 0.53
125 49 0.37
126 7 0.05
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.41
Consensus pattern (124 bp):
TAATTGAATATTTTTAATTTTTAAATGCAAGCAATTACATCGTTTCTTTAAACCAAACACCACAA
TTAACTAATTTCAATTCTTAAATCCAAGCAATTACAACATTTCTTTCATTTAAACGCCA
Found at i:19819513 original size:31 final size:32
Alignment explanation
Indices: 19819460--19819526 Score: 109
Period size: 31 Copynumber: 2.1 Consensus size: 32
19819450 ATCAAACAAT
*
19819460 TTCTCTTATTCATATATATTATATATTTAAAA
1 TTCTCTTATTCATAAATATTATATATTTAAAA
*
19819492 TTCTCTTATT-TTAAATATTATATATTTAAAA
1 TTCTCTTATTCATAAATATTATATATTTAAAA
19819523 TTCT
1 TTCT
19819527 ATTGATACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
31 23 0.70
32 10 0.30
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (32 bp):
TTCTCTTATTCATAAATATTATATATTTAAAA
Found at i:19819519 original size:15 final size:15
Alignment explanation
Indices: 19819475--19819521 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
19819465 TTATTCATAT
19819475 ATATTATATATTTAA
1 ATATTATATATTTAA
* *
19819490 A-ATTCTCTTATTTTAA
1 ATATTAT-ATA-TTTAA
19819506 ATATTATATATTTAA
1 ATATTATATATTTAA
19819521 A
1 A
19819522 ATTCTATTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
14 4 0.16
15 9 0.36
16 8 0.32
17 4 0.16
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTATATATTTAA
Found at i:19827146 original size:39 final size:39
Alignment explanation
Indices: 19827103--19827181 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
19827093 GAAGTAAAAA
*
19827103 TATGTTATAGAGATTATTGGTGAAATCTTGTGGATGGTT
1 TATGTTATAGAGAATATTGGTGAAATCTTGTGGATGGTT
19827142 TATGTTATAGAGAATATTGGTGAAATCTTGTGGATGGTT
1 TATGTTATAGAGAATATTGGTGAAATCTTGTGGATGGTT
19827181 T
1 T
19827182 TTAACTCGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.27, C:0.03, G:0.28, T:0.43
Consensus pattern (39 bp):
TATGTTATAGAGAATATTGGTGAAATCTTGTGGATGGTT
Found at i:19836423 original size:13 final size:13
Alignment explanation
Indices: 19836391--19836415 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19836381 ATTATTAAGT
19836391 AAAAATTAAAATC
1 AAAAATTAAAATC
19836404 AAAAATTAAAAT
1 AAAAATTAAAAT
19836416 GATAAATTGA
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:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAATTAAAATC
Found at i:19836543 original size:29 final size:29
Alignment explanation
Indices: 19836507--19836597 Score: 69
Period size: 29 Copynumber: 3.1 Consensus size: 29
19836497 ATATTATTTA
19836507 TAAA-AAATTTTGATAAAATTTTTATTAT
1 TAAATAAATTTTGATAAAATTTTTATTAT
* * * **
19836535 TAAATAAATATAGATTAAATTTAAATTAT
1 TAAATAAATTTTGATAAAATTTTTATTAT
* *
19836564 TAACGAT-ATTTTTAATAAAATTTTTTATATAT
1 TAA--ATAAATTTTGATAAAA-TTTTTAT-TAT
19836596 TA
1 TA
19836598 TTTATTTTTA
Statistics
Matches: 46, Mismatches: 12, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
28 4 0.09
29 22 0.48
30 8 0.17
31 7 0.15
32 5 0.11
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.48
Consensus pattern (29 bp):
TAAATAAATTTTGATAAAATTTTTATTAT
Found at i:19836617 original size:17 final size:17
Alignment explanation
Indices: 19836570--19836617 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 17
19836560 TTATTAACGA
*
19836570 TATTTTTA-ATAAAATT
1 TATTTTTATATTAAATT
*
19836586 T-TTTATATATT--ATT
1 TATTTTTATATTAAATT
19836600 TATTTTTATATTAAATT
1 TATTTTTATATTAAATT
19836617 T
1 T
19836618 TATAATTATC
Statistics
Matches: 25, Mismatches: 3, Indels: 7
0.71 0.09 0.20
Matches are distributed among these distances:
14 4 0.16
15 14 0.56
16 3 0.12
17 4 0.16
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTTTTATATTAAATT
Found at i:19838255 original size:11 final size:11
Alignment explanation
Indices: 19838235--19838268 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
19838225 ATTATATAAT
*
19838235 AATATGATATA
1 AATATAATATA
19838246 AATATAATATA
1 AATATAATATA
*
19838257 AAAATAATATA
1 AATATAATATA
19838268 A
1 A
19838269 TTTAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (11 bp):
AATATAATATA
Done.