Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167849.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_12, 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: 22966848
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 129000 characters in sequence are not A, C, G, or T
File 121 of 129
Found at i:20545050 original size:1 final size:1
Alignment explanation
Indices: 20545040--20545069 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
20545030 GGTTGGTATT
*
20545040 GGGGGTGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
20545070 AGGAACAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.97, T:0.03
Consensus pattern (1 bp):
G
Found at i:20547052 original size:28 final size:31
Alignment explanation
Indices: 20547007--20547070 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 31
20546997 ATTTTTTTAT
* *
20547007 AAAATTAAAATTTCATAATTTT-TAATGTAAA
1 AAAATTAAAA-TTCATAATTTTAAAATATAAA
20547038 AAAATTAAAA-T-ATAATTTTAAAATATAAA
1 AAAATTAAAATTCATAATTTTAAAATATAAA
20547067 AAAA
1 AAAA
20547071 GAATTTTAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 8 0.27
29 12 0.40
31 10 0.33
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (31 bp):
AAAATTAAAATTCATAATTTTAAAATATAAA
Found at i:20547060 original size:21 final size:21
Alignment explanation
Indices: 20547036--20547078 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
20547026 TTTTAATGTA
* * *
20547036 AAAAAATTAAAATATAATTTT
1 AAAAAATAAAAAAAGAATTTT
*
20547057 AAAATATAAAAAAAGAATTTT
1 AAAAAATAAAAAAAGAATTTT
20547078 A
1 A
20547079 GATGTTAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAAAATAAAAAAAGAATTTT
Found at i:20550890 original size:13 final size:14
Alignment explanation
Indices: 20550865--20550896 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
20550855 ACAGTTAGTG
20550865 TATAAATTTTATAT
1 TATAAATTTTATAT
20550879 TATAAA-TTTATAT
1 TATAAATTTTATAT
20550892 T-TAAA
1 TATAAA
20550897 ATACGGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.22
13 8 0.44
14 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TATAAATTTTATAT
Found at i:20557332 original size:17 final size:18
Alignment explanation
Indices: 20557310--20557345 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
20557300 ATATCATTGT
*
20557310 ATATGTTAAA-TGATTTA
1 ATATGTCAAATTGATTTA
20557327 ATATGTCAAATTGATTTA
1 ATATGTCAAATTGATTTA
20557345 A
1 A
20557346 AAATAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (18 bp):
ATATGTCAAATTGATTTA
Found at i:20558527 original size:29 final size:26
Alignment explanation
Indices: 20558479--20558531 Score: 70
Period size: 29 Copynumber: 1.9 Consensus size: 26
20558469 CTTCTATTTG
*
20558479 AAAAAAAATGTTTTCAAATACAATAAA
1 AAAAAAAATGTATTCAAATA-AATAAA
20558506 AAAAATAAATCGTATTCAAATAAATA
1 AAAAA-AAAT-GTATTCAAATAAATA
20558532 GATTATTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 5 0.22
28 8 0.35
29 10 0.43
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.26
Consensus pattern (26 bp):
AAAAAAAATGTATTCAAATAAATAAA
Found at i:20559067 original size:41 final size:41
Alignment explanation
Indices: 20558974--20559072 Score: 137
Period size: 43 Copynumber: 2.4 Consensus size: 41
20558964 ATTTAAAATT
*
20558974 ATATAA-TTTATTATAATTTTATATAGATTCTATATTTATAA
1 ATATAATTTTA-TATAATTTTATATAGATTCTATACTTATAA
* *
20559015 ATAATTTATTTTATATAATTTTATATAGATTTTATACTTATAA
1 AT-A-TAATTTTATATAATTTTATATAGATTCTATACTTATAA
20559058 ATATAATTTTATATA
1 ATATAATTTTATATA
20559073 GTATTGTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
41 13 0.25
42 2 0.04
43 32 0.63
44 4 0.08
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (41 bp):
ATATAATTTTATATAATTTTATATAGATTCTATACTTATAA
Found at i:20562573 original size:4 final size:4
Alignment explanation
Indices: 20562564--20562595 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
20562554 AACAAATATA
20562564 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT
20562596 ATGTCTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:20569857 original size:2 final size:2
Alignment explanation
Indices: 20569850--20569892 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
20569840 GCATGAACAA
* *
20569850 AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT GT 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
20569892 A
1 A
20569893 ATTAATTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:20579245 original size:174 final size:175
Alignment explanation
Indices: 20578935--20579271 Score: 577
Period size: 174 Copynumber: 1.9 Consensus size: 175
20578925 CAGATACATC
**
20578935 ATATTTTATGTATATTACAACAAATACATCATATTTTATGTATATTACATCGAGCGAGGTCAACA
1 ATATTTTATGTATACAACAACAAATACATCATATTTTATGTATATTACATCGAGCGAGGTCAACA
* * *
20579000 ATAACCCGACAAATACACCATGTATATATTACAGATAAATTGAAAGTTGGAGTTCAACAAGAATC
66 ATAACCCGACAAATACACCATGTATATATTACAGATAAATTGAAACTAGGAGATCAACAAGAATC
20579065 TGGCTATAGAGTACTGGACAGTGGACACAATAAATATTACAACAA
131 TGGCTATAGAGTACTGGACAGTGGACACAATAAATATTACAACAA
* *
20579110 ATATTTTATGTA-ACAACACCAAATACATCATATTTTATGTATATTACATTGAGCGAGGTCAACA
1 ATATTTTATGTATACAACAACAAATACATCATATTTTATGTATATTACATCGAGCGAGGTCAACA
* *
20579174 ATAACCTGACAAATACACCATGTTTATATTACAGATAAATTGAAACTAGGAGATCAACAAGAATC
66 ATAACCCGACAAATACACCATGTATATATTACAGATAAATTGAAACTAGGAGATCAACAAGAATC
*
20579239 TGGCTATAGAGTACTGGACAGTGGACTCAATAA
131 TGGCTATAGAGTACTGGACAGTGGACACAATAA
20579272 GCAAACAAGT
Statistics
Matches: 152, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
174 140 0.92
175 12 0.08
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (175 bp):
ATATTTTATGTATACAACAACAAATACATCATATTTTATGTATATTACATCGAGCGAGGTCAACA
ATAACCCGACAAATACACCATGTATATATTACAGATAAATTGAAACTAGGAGATCAACAAGAATC
TGGCTATAGAGTACTGGACAGTGGACACAATAAATATTACAACAA
Found at i:20580378 original size:30 final size:30
Alignment explanation
Indices: 20580324--20580390 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
20580314 ATATAGTGTC
*
20580324 AAATATTTTTATTAGAAATATAAAATAATAA
1 AAATA-TTTTATTAAAAATATAAAATAATAA
* *
20580355 CAATATTTT-TTAAAAATTATAAAATATTAA
1 AAATATTTTATTAAAAA-TATAAAATAATAA
20580385 AAATAT
1 AAATAT
20580391 AATTTTTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 6 0.19
30 21 0.68
31 4 0.13
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (30 bp):
AAATATTTTATTAAAAATATAAAATAATAA
Found at i:20585446 original size:27 final size:27
Alignment explanation
Indices: 20585397--20585448 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
20585387 TAAAATTGAA
* *
20585397 TTAATTACATTATTTTTTATATTTTTG
1 TTAATTAAATTAATTTTTATATTTTTG
20585424 TTAATTAAATTGAATTTTT-TATTTT
1 TTAATTAAATT-AATTTTTATATTTT
20585449 AAAAATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (27 bp):
TTAATTAAATTAATTTTTATATTTTTG
Found at i:20585702 original size:17 final size:17
Alignment explanation
Indices: 20585677--20585715 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
20585667 TTTGATTTTT
20585677 AAATT-AAATTAATTAA
1 AAATTAAAATTAATTAA
* *
20585693 AAATTAAAATTATTTTA
1 AAATTAAAATTAATTAA
20585710 AAATTA
1 AAATTA
20585716 TTTTTTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATTAAAATTAATTAA
Found at i:20586629 original size:41 final size:43
Alignment explanation
Indices: 20586572--20586656 Score: 129
Period size: 41 Copynumber: 2.0 Consensus size: 43
20586562 TTAAATTTTT
*
20586572 ATATAATCTATTATAATTTTATATAGA-CTCTACTTATAAATA
1 ATATAATCTATTATAATTTTATATAGATCTATACTTATAAATA
*
20586614 ATATAAT-TTTTATAATTTTATATAGATTCTATACTTATAAATA
1 ATATAATCTATTATAATTTTATATAGA-TCTATACTTATAAATA
20586657 TAAAAACCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
41 18 0.46
42 7 0.18
43 14 0.36
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.48
Consensus pattern (43 bp):
ATATAATCTATTATAATTTTATATAGATCTATACTTATAAATA
Found at i:20586680 original size:20 final size:20
Alignment explanation
Indices: 20586655--20586694 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
20586645 TACTTATAAA
20586655 TATAAAAACCTCTAATTAAT
1 TATAAAAACCTCTAATTAAT
20586675 TATAAAAACCTCTAATTAAT
1 TATAAAAACCTCTAATTAAT
20586695 CGAGAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (20 bp):
TATAAAAACCTCTAATTAAT
Found at i:20586748 original size:22 final size:20
Alignment explanation
Indices: 20586708--20586749 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
20586698 GAATATTTTA
*
20586708 TTTATAGTTTTTATTATAAT
1 TTTATAATTTTTATTATAAT
20586728 TTTATAATTATTTAATTATAAT
1 TTTATAATT-TTT-ATTATAAT
20586750 AAAAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 3 0.16
22 8 0.42
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTATAATTTTTATTATAAT
Found at i:20588639 original size:18 final size:17
Alignment explanation
Indices: 20588611--20588651 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
20588601 TTATTCACCT
*
20588611 TTTTTATTTATTTCTTA
1 TTTTTATTTATTTATTA
*
20588628 TTTTTATATTATTTATTT
1 TTTTTAT-TTATTTATTA
20588646 TTTTTA
1 TTTTTA
20588652 CCAAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTATTTATTTATTA
Found at i:20591438 original size:2 final size:2
Alignment explanation
Indices: 20591431--20591458 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20591421 GATTGATTCT
20591431 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20591459 GATAAACAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20591712 original size:6 final size:6
Alignment explanation
Indices: 20591689--20591735 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
20591679 CACCGAACAA
* * * *
20591689 ATATAT ATATAT ATATAG ATATAG ATACAG ACATAG ATATAG ATATA
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
20591736 ATTAATTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:20594172 original size:17 final size:17
Alignment explanation
Indices: 20594150--20594184 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
20594140 CGCCACCGTT
20594150 CTTGCCGTCC-GTGAAGC
1 CTTGCCG-CCTGTGAAGC
20594167 CTTGCCGCCTGTGAAGC
1 CTTGCCGCCTGTGAAGC
20594184 C
1 C
20594185 GCACTGTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.11, C:0.37, G:0.29, T:0.23
Consensus pattern (17 bp):
CTTGCCGCCTGTGAAGC
Found at i:20594881 original size:98 final size:94
Alignment explanation
Indices: 20594710--20594883 Score: 233
Period size: 94 Copynumber: 1.8 Consensus size: 94
20594700 ATTCACAGAG
* * * * *
20594710 TATTAAATTGTTAGTTTCAGTTCAAATCTTGATAGTTTTTTTTGCCAAAAAATCTGACATGTTCA
1 TATTAAACTATTAGTTTCAGTTCAAATCCTGAAAGTTTTTTTTGCCAAAAAATCTGACAAGTTCA
20594775 ATTACTAAAAATAAGTTTTACCTGAATCA
66 ATTACTAAAAATAAGTTTTACCTGAATCA
**
20594804 TATTAAACTATTAGTTTCAGTTCAAATCCTGACAAGTTTTTTTT-TTATTGAAAAATCCTGACAA
1 TATTAAACTATTAGTTTCAGTTCAAATCCTGA-AAGTTTTTTTTGCCA---AAAAAT-CTGACAA
20594868 GTTCAATTACTAAAAA
61 GTTCAATTACTAAAAA
20594884 AAATAACAAG
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
94 30 0.44
95 10 0.15
97 6 0.09
98 22 0.32
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (94 bp):
TATTAAACTATTAGTTTCAGTTCAAATCCTGAAAGTTTTTTTTGCCAAAAAATCTGACAAGTTCA
ATTACTAAAAATAAGTTTTACCTGAATCA
Found at i:20595812 original size:22 final size:22
Alignment explanation
Indices: 20595758--20595802 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
20595748 ATACATTTTT
*
20595758 TTATTATTTATCTATTCATATA
1 TTATTATTTATCTATTAATATA
20595780 TTATTATTTATCTATTAATATA
1 TTATTATTTATCTATTAATATA
20595802 T
1 T
20595803 ATTTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATTATTTATCTATTAATATA
Found at i:20596643 original size:3 final size:3
Alignment explanation
Indices: 20596631--20596770 Score: 111
Period size: 3 Copynumber: 48.7 Consensus size: 3
20596621 AAATTTTTTT
* *
20596631 TTA TTG TTA TTA TTTA TTA TTA TT- TTA TTA TTA TTA TTA TTA TCA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* ** *
20596676 TTA TTA TTA TTA TTA TTA TTTA TTGA TTA -GA TTA GAA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA -TTA TT-A TTA TTA TTA TTA TTA TTA TTA
*
20596722 TTCC TTA TT- TTA TT- TTA TT- TTA TT- TTA TTA TT- TTA -TA TT-
1 TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20596761 TTA TT- TTA TT
1 TTA TTA TTA TT
20596771 TTTTAAAATG
Statistics
Matches: 109, Mismatches: 14, Indels: 28
0.72 0.09 0.19
Matches are distributed among these distances:
2 19 0.17
3 79 0.72
4 11 0.10
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:20596736 original size:5 final size:5
Alignment explanation
Indices: 20596726--20596772 Score: 69
Period size: 5 Copynumber: 9.4 Consensus size: 5
20596716 TTAATATTCC
*
20596726 TTATT TTATT TTATT TTATT TTATT ATT-TT ATATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT -TTATT TTATT TTATT TTATT TT
20596773 TTAAAATGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
4 1 0.03
5 35 0.92
6 2 0.05
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:20596785 original size:30 final size:30
Alignment explanation
Indices: 20596727--20596785 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
20596717 TAATATTCCT
** *
20596727 TATTTTATTTTATTTTATTTTATTATTTTA
1 TATTTTATTTTATTTTATTAAATGATTTTA
20596757 TATTTTATTTTATTTT-TTAAAATGATTTT
1 TATTTTATTTTATTTTATT-AAATGATTTT
20596786 CTTTAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (30 bp):
TATTTTATTTTATTTTATTAAATGATTTTA
Found at i:20606614 original size:12 final size:12
Alignment explanation
Indices: 20606588--20606617 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
20606578 ACTATGCTTG
20606588 AAAAAAAATGAA
1 AAAAAAAATGAA
20606600 AAAATAAAATGAA
1 AAAA-AAAATGAA
20606613 AAAAA
1 AAAAA
20606618 TGTAAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (12 bp):
AAAAAAAATGAA
Found at i:20606625 original size:31 final size:30
Alignment explanation
Indices: 20606590--20606648 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
20606580 TATGCTTGAA
20606590 AAAAAATGAAAAAAT-AAAATGAAAAAAATGT
1 AAAAAA-GAAAAAATGAAAA-GAAAAAAATGT
*
20606621 AAAAAAGAGAAAATGAAAAGAAAAAAAT
1 AAAAAAGAAAAAATGAAAAGAAAAAAAT
20606649 AAGGAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (30 bp):
AAAAAAGAAAAAATGAAAAGAAAAAAATGT
Found at i:20606657 original size:32 final size:30
Alignment explanation
Indices: 20606590--20606659 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 30
20606580 TATGCTTGAA
*
20606590 AAAAAATGAAAAAATAAAATGAAAAAAATGT
1 AAAAAA-GAAAAAATAAAATGAAAAAAATGG
*
20606621 AAAAAAGAGAAAATGAAAA-GAAAAAAATAAGG
1 AAAAAAGAAAAAAT-AAAATGAAAAAAAT--GG
20606653 AAAAAAG
1 AAAAAAG
20606660 TGAATGAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 16 0.47
31 10 0.29
32 8 0.24
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (30 bp):
AAAAAAGAAAAAATAAAATGAAAAAAATGG
Found at i:20607725 original size:42 final size:41
Alignment explanation
Indices: 20607678--20607887 Score: 199
Period size: 41 Copynumber: 5.0 Consensus size: 41
20607668 CGTCAATGAG
* * *
20607678 CATTTACTTTTTCAAAGTTGTGGTGCTTCTAATTAGAGGAGC
1 CATTTA-TTTTTCAAAGTTGTGGAGCCTCTGATTAGAGGAGC
* * *
20607720 CATTTATTTTTCAAAAGTCGTTGAGCATCTGATTAGAGGAGC
1 CATTTATTTTTC-AAAGTTGTGGAGCCTCTGATTAGAGGAGC
* * * *
20607762 CATTT-TTTTCCAAAGTTATTGAGCCTCTGATTAGAGAAGC
1 CATTTATTTTTCAAAGTTGTGGAGCCTCTGATTAGAGGAGC
*
20607802 CATTTATTTTTCAAAGTTGT-GATGCCTCTGATTAAAGGAGC
1 CATTTATTTTTCAAAGTTGTGGA-GCCTCTGATTAGAGGAGC
** * * *
20607843 TTTGTTTATGTTTCTCAAAGTCGTTGAGCCTCTGCTTAGAGGAGC
1 --CATTTAT-TTT-TCAAAGTTGTGGAGCCTCTGATTAGAGGAGC
20607888 TTTGATCAAA
Statistics
Matches: 141, Mismatches: 19, Indels: 13
0.82 0.11 0.08
Matches are distributed among these distances:
40 32 0.23
41 39 0.28
42 35 0.25
43 5 0.04
44 3 0.02
45 25 0.18
46 2 0.01
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.39
Consensus pattern (41 bp):
CATTTATTTTTCAAAGTTGTGGAGCCTCTGATTAGAGGAGC
Found at i:20607784 original size:40 final size:39
Alignment explanation
Indices: 20607709--20607887 Score: 151
Period size: 40 Copynumber: 4.3 Consensus size: 39
20607699 GGTGCTTCTA
* * *
20607709 ATTAGAGGAGCCATTTATTTTTCAAAAGTCGTTGAGCATCTG
1 ATTAGAGGAGCCA-TT-TTTTTCCAAAGT-TTTGAGCCTCTG
20607751 ATTAGAGGAGCCATTTTTTTCCAAAGTTATTGAGCCTCTG
1 ATTAGAGGAGCCATTTTTTTCCAAAGTT-TTGAGCCTCTG
* * *
20607791 ATTAGAGAAGCCATTTATTTTTCAAAGTTGTGATGCCTCTG
1 ATTAGAGGAGCCATTT-TTTTCCAAAGTTTTGA-GCCTCTG
* ** *
20607832 ATTAAAGGAGCTTTGTTTATGTTTCTCAAAGTCGTTGAGCCTCTG
1 ATTAGAGGAGC--CATTT-T-TTTC-CAAAGT-TTTGAGCCTCTG
*
20607877 CTTAGAGGAGC
1 ATTAGAGGAGC
20607888 TTTGATCAAA
Statistics
Matches: 114, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
40 39 0.34
41 29 0.25
42 13 0.11
43 5 0.04
44 3 0.03
45 22 0.19
46 3 0.03
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.37
Consensus pattern (39 bp):
ATTAGAGGAGCCATTTTTTTCCAAAGTTTTGAGCCTCTG
Found at i:20608089 original size:13 final size:14
Alignment explanation
Indices: 20608066--20608094 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
20608056 AGGTAAGCCC
20608066 ATTTGTTTATTTTT
1 ATTTGTTTATTTTT
20608080 ATTT-TTTATTTTT
1 ATTTGTTTATTTTT
20608093 AT
1 AT
20608095 CTATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.79
Consensus pattern (14 bp):
ATTTGTTTATTTTT
Found at i:20608113 original size:27 final size:27
Alignment explanation
Indices: 20608083--20608235 Score: 95
Period size: 28 Copynumber: 5.7 Consensus size: 27
20608073 TATTTTTATT
20608083 TTTTATTTTTATCTATTTATAAATATA
1 TTTTATTTTTATCTATTTATAAATATA
* *
20608110 TTTT-TTTATTAT-TATTTATCTATTAATA
1 TTTTATTT-TTATCTATTTAT-AAAT-ATA
*
20608138 TTTT-TTATTTATCTA-TTA-ATATATA
1 TTTTATT-TTTATCTATTTATAAATATA
** *
20608163 -TACATTTTTAT-TATTTATTAATATATT
1 TTTTATTTTTATCTATTTA-TAA-ATATA
* ** *
20608190 TTTTATTATTTATCTATTAATGTATATT
1 TTTTATT-TTTATCTATTTATAAATATA
*
20608218 TTTTATATTTATCTATTT
1 TTTTATTTTTATCTATTT
20608236 TATTATTTTT
Statistics
Matches: 97, Mismatches: 16, Indels: 26
0.70 0.12 0.19
Matches are distributed among these distances:
23 2 0.02
24 9 0.09
25 5 0.05
26 12 0.12
27 24 0.25
28 31 0.32
29 9 0.09
30 5 0.05
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (27 bp):
TTTTATTTTTATCTATTTATAAATATA
Found at i:20608121 original size:3 final size:3
Alignment explanation
Indices: 20608115--20608314 Score: 107
Period size: 3 Copynumber: 65.3 Consensus size: 3
20608105 ATATATTTTT
* *
20608115 TTA TTA TTA TTTA TCTA TTA ATA TT- TT- TTA TTTA TCTA TTA ATA TATA
1 TTA TTA TTA -TTA T-TA TTA TTA TTA TTA TTA -TTA T-TA TTA TTA T-TA
* * *
20608163 TACA TTT TTA TTA TTTA TTA ATA -TA TT- TT- TTA TTA TTTA TCTA TTAA
1 T-TA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA -TTA T-TA TT-A
* *
20608210 TGTA -TA TT- TT- TTA -TA TTTA TCTA TT- TTA TTA TTT TTA TTTA TCTT
1 T-TA TTA TTA TTA TTA TTA -TTA T-TA TTA TTA TTA TTA TTA -TTA T-TA
* *
20608255 TTA ATA TTT TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20608302 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
20608315 CATTTTTTGT
Statistics
Matches: 158, Mismatches: 17, Indels: 44
0.72 0.08 0.20
Matches are distributed among these distances:
2 22 0.14
3 95 0.60
4 40 0.25
5 1 0.01
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:20608126 original size:49 final size:49
Alignment explanation
Indices: 20608072--20608303 Score: 138
Period size: 55 Copynumber: 4.6 Consensus size: 49
20608062 GCCCATTTGT
20608072 TTATTTTTATTTTTTATTTTTATCTATTTATAAATATATTTTTTTATTA
1 TTATTTTTATTTTTTATTTTTATCTATTTATAAATATATTTTTTTATTA
* * * **
20608121 TTATTTATCTATTAATATTTTTTATTTATCTATTAATATATATACATTTTTATTA
1 TTATTT-T-TATT--T-TTTATT-TTTATCTATTTATAAATATATTTTTTTATTA
* **
20608176 TTTATTAATATATTTTTTATTATTTATCTA-TTA-ATGTATA-TTTTTTA-TA
1 -TTATT--TTTATTTTTTATT-TTTATCTATTTATAAATATATTTTTTTATTA
* * * *
20608225 TT-TATCTATTTTATTATTTTTATTTATCTT-TTAATAT-TTTTATATTATTA
1 TTATTTTTATTTT-TTATTTTTATCTAT-TTATAAATATATTTT-T-TTATTA
* *
20608275 TTATTATTATTATTATTATTATTAT-TATT
1 TTATTTTTATT-TT-TTATTTTTATCTATT
20608304 ATTATTATTA
Statistics
Matches: 144, Mismatches: 20, Indels: 37
0.72 0.10 0.18
Matches are distributed among these distances:
45 14 0.10
46 5 0.03
47 9 0.06
48 3 0.02
49 11 0.08
50 12 0.08
51 18 0.12
52 14 0.10
53 15 0.10
54 6 0.04
55 27 0.19
56 9 0.06
58 1 0.01
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.67
Consensus pattern (49 bp):
TTATTTTTATTTTTTATTTTTATCTATTTATAAATATATTTTTTTATTA
Found at i:20608207 original size:8 final size:7
Alignment explanation
Indices: 20608071--20608312 Score: 117
Period size: 6 Copynumber: 35.3 Consensus size: 7
20608061 AGCCCATTTG
20608071 TTTATT-
1 TTTATTA
*
20608077 TTTATTT
1 TTTATTA
20608084 TTTATT-
1 TTTATTA
20608090 TTTATCTA
1 TTTAT-TA
*
20608098 TTTATAAA
1 TTTAT-TA
*
20608106 TATATT-
1 TTTATTA
20608112 TTT-TTA
1 TTTATTA
20608118 -TTATTA
1 TTTATTA
20608124 TTTATCTA
1 TTTAT-TA
*
20608132 -TTAATA
1 TTTATTA
*
20608138 TTTTTTA
1 TTTATTA
20608145 TTTATCTA
1 TTTAT-TA
20608153 TTAATATATA
1 TT--TAT-TA
**
20608163 TACATT-
1 TTTATTA
20608169 TTTATTA
1 TTTATTA
20608176 TTTATTAA
1 TTTATT-A
* *
20608184 TATATTT
1 TTTATTA
20608191 TTTATTA
1 TTTATTA
20608198 TTTATCTA
1 TTTAT-TA
*
20608206 TTAATGTA
1 TTTAT-TA
*
20608214 --TATTT
1 TTTATTA
20608219 TTTA-TA
1 TTTATTA
20608225 TTTATCTA
1 TTTAT-TA
20608233 TTTTATTA
1 -TTTATTA
20608241 TTT-TTA
1 TTTATTA
20608247 TTTATCT-
1 TTTAT-TA
*
20608254 TTTAATA
1 TTTATTA
20608261 TTT-TTA
1 TTTATTA
20608267 TATTATTA
1 T-TTATTA
20608275 -TTATTA
1 TTTATTA
20608281 -TTATTA
1 TTTATTA
20608287 -TTATTA
1 TTTATTA
20608293 -TTATTA
1 TTTATTA
20608299 -TTATTA
1 TTTATTA
20608305 -TTATTA
1 TTTATTA
20608311 TT
1 TT
20608313 ATCATTTTTT
Statistics
Matches: 186, Mismatches: 25, Indels: 49
0.72 0.10 0.19
Matches are distributed among these distances:
5 5 0.03
6 75 0.40
7 55 0.30
8 40 0.22
9 5 0.03
10 6 0.03
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.67
Consensus pattern (7 bp):
TTTATTA
Found at i:20608217 original size:78 final size:81
Alignment explanation
Indices: 20608087--20608234 Score: 209
Period size: 78 Copynumber: 1.9 Consensus size: 81
20608077 TTTATTTTTT
*
20608087 ATTTTTATCTATTTATAAATATATTTTTTTATTATTATTTATCTATTAATA-TTTTT-TATTTAT
1 ATTTTTATCTATTTATAAATATATTTTTTTATTATTATCTATCTATTAATATTTTTTATATTTAT
20608150 CTATTAATATATATAC
66 CTATTAATATATATAC
*
20608166 ATTTTTAT-TATTTATTAATATA-TTTTTTATTATTTATCTAT-TAATGT-ATATTTTTTATATT
1 ATTTTTATCTATTTATAAATATATTTTTTTATTA-TTATCTATCT-AT-TAATATTTTTTATATT
20608227 TATCTATT
63 TATCTATT
20608235 TTATTATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
77 11 0.18
78 25 0.40
79 14 0.23
80 12 0.19
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (81 bp):
ATTTTTATCTATTTATAAATATATTTTTTTATTATTATCTATCTATTAATATTTTTTATATTTAT
CTATTAATATATATAC
Found at i:20608251 original size:78 final size:76
Alignment explanation
Indices: 20608076--20608314 Score: 189
Period size: 78 Copynumber: 3.1 Consensus size: 76
20608066 ATTTGTTTAT
* *
20608076 TTTTATTTTTTATTTTTATCTATTTATAAATATATTTTTTTATTATTATTTATCTATTAATATTT
1 TTTTATTATTT-TTTTTATCTATTTATAAATATATTTTTTTATTATTATCTATCTATTAATATTT
20608141 TTTATTTATCTA
65 TTTATTTATCTA
* ** *
20608153 TTAATATATATACATTTTTAT-TATTTATTAATATA-TTTTTTATTATTTATCTAT-TAATGT-A
1 TT-TTAT-TAT-TTTTTTTATCTATTTATAAATATATTTTTTTATTA-TTATCTATCT-AT-TAA
20608214 TATTTTTTATATTTATCTA
60 TA-TTTTT-TATTTATCTA
*
20608233 TTTTATTATTTTTATTTATC--TTT-T-AATAT-TTTTATATTATTATTAT-TAT-TATTATTAT
1 TTTTATTATTTTT-TTTATCTATTTATAAATATATTTT-T-TTATTATTATCTATCTATTAATAT
20608291 TATTATTA-TTAT-TA
63 T-TT-TTATTTATCTA
20608305 TTATTATTAT
1 TT-TTATTAT
20608315 CATTTTTTGT
Statistics
Matches: 135, Mismatches: 10, Indels: 38
0.74 0.05 0.21
Matches are distributed among these distances:
72 4 0.03
73 14 0.10
74 8 0.06
75 13 0.10
76 6 0.04
77 24 0.18
78 36 0.27
79 18 0.13
80 12 0.09
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (76 bp):
TTTTATTATTTTTTTTATCTATTTATAAATATATTTTTTTATTATTATCTATCTATTAATATTTT
TTATTTATCTA
Found at i:20609070 original size:4 final size:4
Alignment explanation
Indices: 20609063--20609107 Score: 53
Period size: 4 Copynumber: 12.2 Consensus size: 4
20609053 GTTTTTTTTC
*
20609063 TTAT TTAT TTAT TTAT TTA- TTA- TTA- TTA- TTAA TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
20609107 T
1 T
20609108 AGATTTGAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
3 12 0.31
4 27 0.69
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:20609246 original size:58 final size:60
Alignment explanation
Indices: 20609176--20609299 Score: 155
Period size: 61 Copynumber: 2.1 Consensus size: 60
20609166 TTTTTAATAA
20609176 TTTTTTTAAAATAAAATTCCAAAAAA-AT-AT-TTTTGAGGAAAAGTTGAAAGTATCAAT
1 TTTTTTTAAAATAAAATTCCAAAAAAGATCATCTTTTGAGGAAAAGTTGAAAGTATCAAT
** * * * * *
20609233 TTTTTTTGAAAATAATTTTCTAAAAAAGGTCTTCTTTTTAGGAAAAGTTGAAAGTATTAAT
1 TTTTTTT-AAAATAAAATTCCAAAAAAGATCATCTTTTGAGGAAAAGTTGAAAGTATCAAT
20609294 TTTTTT
1 TTTTTT
20609300 GTACAAAAGC
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
57 7 0.12
58 16 0.29
59 1 0.02
60 1 0.02
61 31 0.55
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (60 bp):
TTTTTTTAAAATAAAATTCCAAAAAAGATCATCTTTTGAGGAAAAGTTGAAAGTATCAAT
Found at i:20609371 original size:14 final size:14
Alignment explanation
Indices: 20609352--20609395 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
20609342 TAAAGCTGAA
20609352 TCATTTTTTTTCTT
1 TCATTTTTTTTCTT
*
20609366 TCATTTTATTTCTTT
1 TCATTTTTTTTC-TT
*
20609381 TCCTTTTTGTTTCTT
1 TCATTTTT-TTTCTT
20609396 GAATTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 11 0.44
15 10 0.40
16 4 0.16
ACGTcount: A:0.07, C:0.16, G:0.02, T:0.75
Consensus pattern (14 bp):
TCATTTTTTTTCTT
Found at i:20610095 original size:29 final size:29
Alignment explanation
Indices: 20610058--20610117 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
20610048 ATATAATGTC
**
20610058 AAATATTTTTAGTAA-TATAAAATAATAA
1 AAATATTTTTAAAAATTATAAAATAATAA
*
20610086 AAATATTTTTAAAAATTATAAAATATTAA
1 AAATATTTTTAAAAATTATAAAATAATAA
20610115 AAA
1 AAA
20610118 ATATCATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 13 0.46
29 15 0.54
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (29 bp):
AAATATTTTTAAAAATTATAAAATAATAA
Found at i:20614824 original size:28 final size:28
Alignment explanation
Indices: 20614779--20614838 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
20614769 TATCATAATA
* * *
20614779 ATTAATAAATTTATAATTTAAATATTAT
1 ATTAAAAAATTTATAATTCAAATATTAC
*
20614807 ATTAAAAAATTT-TAAATTCAAATTTTAC
1 ATTAAAAAATTTAT-AATTCAAATATTAC
20614835 ATTA
1 ATTA
20614839 TATATTTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (28 bp):
ATTAAAAAATTTATAATTCAAATATTAC
Found at i:20614889 original size:18 final size:18
Alignment explanation
Indices: 20614850--20614891 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
20614840 ATATTTTATT
* *
20614850 ATAATTTAAATACCGTTC
1 ATAATATAAATACCGTTA
20614868 ATAATATAAATACC-TATA
1 ATAATATAAATACCGT-TA
20614886 ATAATA
1 ATAATA
20614892 ATAATTATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.36
Consensus pattern (18 bp):
ATAATATAAATACCGTTA
Found at i:20618464 original size:2 final size:2
Alignment explanation
Indices: 20618457--20618491 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
20618447 CTGCCTTTGA
20618457 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20618492 CAAAAGGGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20620299 original size:2 final size:2
Alignment explanation
Indices: 20620294--20620322 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
20620284 AATGAATGCC
20620294 AT AT AT A- 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
20620323 TACATAATGG
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20622749 original size:27 final size:26
Alignment explanation
Indices: 20622710--20622770 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 26
20622700 AAACAATAAT
* *
20622710 AAAAATTATTATAATTGCAATTAAAA
1 AAAAATTACTATAATTACAATTAAAA
*
20622736 AAAAAGTTACTATAGTTACAATTAAAA
1 AAAAA-TTACTATAATTACAATTAAAA
20622763 AAAAATTA
1 AAAAATTA
20622771 TAAAAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 8 0.26
27 23 0.74
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (26 bp):
AAAAATTACTATAATTACAATTAAAA
Found at i:20624292 original size:2 final size:2
Alignment explanation
Indices: 20624287--20624312 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20624277 AATGAATGCA
20624287 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
20624313 TACATAATGA
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:20626853 original size:39 final size:39
Alignment explanation
Indices: 20626798--20626874 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
20626788 GGACCACATG
*
20626798 GTTATATGTACGAAAAAATTAAAATACCATTAATATTAA
1 GTTATATGTACAAAAAAATTAAAATACCATTAATATTAA
* *
20626837 GTTATATTTACAAAAAACTTAAAATACCATTAATATTA
1 GTTATATGTACAAAAAAATTAAAATACCATTAATATTA
20626875 TTACTTAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (39 bp):
GTTATATGTACAAAAAAATTAAAATACCATTAATATTAA
Found at i:20627822 original size:16 final size:18
Alignment explanation
Indices: 20627791--20627828 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
20627781 CCATATATCA
20627791 ATAAATGTTATATAAAT-
1 ATAAATGTTATATAAATG
*
20627808 ATAAAT-TTTTATAAATG
1 ATAAATGTTATATAAATG
20627825 ATAA
1 ATAA
20627829 TATAATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (18 bp):
ATAAATGTTATATAAATG
Found at i:20628852 original size:14 final size:14
Alignment explanation
Indices: 20628827--20628864 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
20628817 GTAATTAAAG
20628827 AAATAT-AAAATAT
1 AAATATAAAAATAT
20628840 AAATATAAAAATAT
1 AAATATAAAAATAT
*
20628854 AAGTATAAAAA
1 AAATATAAAAA
20628865 AAAAATAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (14 bp):
AAATATAAAAATAT
Found at i:20630060 original size:127 final size:125
Alignment explanation
Indices: 20629733--20630200 Score: 378
Period size: 127 Copynumber: 3.7 Consensus size: 125
20629723 CAATAACTTC
* * * *
20629733 ATTAAAAAAA-TTTTCAAGATTATTGAAA-ATGTTTTT-GTCTAAAAACGCCTTGAGTAATCAAC
1 ATTAAAAAAATTTTTCAGGATTATT-AAAGATATTTTTAGTC-AAAAACACTTTGAGTAATCAA-
* * * **
20629795 TCATAAAAATTTATAAGAAGATTATTAAATACGTTTTTAGCCAAAAATACATTCAATAACCCT
63 TTATAAAAATTTATGAGAGGATTATTAAAGGCGTTTTTAGCCAAAAATACATTCAATAACCCT
*** ** ** * * *
20629858 ATTAAAATTTTTTTTTTGGATTATTAAAGGCATTTTTAGTGAAAAATACTTTGAGTAATCATGTT
1 ATTAAAAAAATTTTTCAGGATTATTAAAGATATTTTTAGTCAAAAACACTTTGAGTAATCA-ATT
***
20629923 ATAAAAATTTATGAGAGGATTATTAAAGGCGTTTTT-GACCAAAAATGTTTTCAATAACCCT
65 ATAAAAATTTATGAGAGGATTATTAAAGGCGTTTTTAG-CCAAAAATACATTCAATAACCCT
* *
20629984 ATTAAAAAAAATTTTTCAGGATTATTTAAGATATTTTTAGTCAAAAACACTTTGAATAATCACAT
1 ATT-AAAAAAATTTTTCAGGATTATTAAAGATATTTTTAGTCAAAAACACTTTGAGTAATCA-AT
* * * * * * * * *
20630049 TTTAAAAATTTATGA-AGGGATTACTAAAGGTGTTTTTAGTCAGAAATGCCTTAAATAACCAT
64 TATAAAAATTTATGAGA-GGATTATTAAAGGCGTTTTTAGCCAAAAATACATTCAATAACCCT
* * * * *
20630111 ATTTTAAAAAAA-ATTTC-GAGCTTATTCAAGGTATTTTTAG-CAAAAA-ATATCTTGAGTAATC
1 A--TTAAAAAAATTTTTCAG-GATTATTAAAGATATTTTTAGTCAAAAACA-CT-TTGAGTAATC
* * *
20630172 ACGTCATAAAAATTTATGAGAAGATTATT
61 A-ATTATAAAAATTTATGAGAGGATTATT
20630201 GAAGATATTT
Statistics
Matches: 274, Mismatches: 55, Indels: 26
0.77 0.15 0.07
Matches are distributed among these distances:
125 12 0.04
126 98 0.36
127 153 0.56
128 9 0.03
129 2 0.01
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (125 bp):
ATTAAAAAAATTTTTCAGGATTATTAAAGATATTTTTAGTCAAAAACACTTTGAGTAATCAATTA
TAAAAATTTATGAGAGGATTATTAAAGGCGTTTTTAGCCAAAAATACATTCAATAACCCT
Found at i:20634453 original size:2 final size:2
Alignment explanation
Indices: 20634446--20634476 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20634436 TTGCCTTTGA
20634446 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20634477 AATAAGAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20638749 original size:22 final size:21
Alignment explanation
Indices: 20638698--20638754 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
20638688 AATTAGGATC
* **
20638698 ATTAAAAATTTATTTGGATAA
1 ATTAAAAATTAATTTAAATAA
*
20638719 ATGATAAAATTAATTTAAATAAA
1 ATTA-AAAATTAATTTAAAT-AA
20638742 ATTAAAAA-TAATT
1 ATTAAAAATTAATT
20638755 ATTATTATCG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
21 8 0.28
22 16 0.55
23 5 0.17
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (21 bp):
ATTAAAAATTAATTTAAATAA
Found at i:20638810 original size:25 final size:25
Alignment explanation
Indices: 20638758--20638807 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
20638748 AATAATTATT
*
20638758 ATTATCGTAATTATGATTAAAATAA
1 ATTATCGTAATTACGATTAAAATAA
*
20638783 ATTATTGTAATTACGATT-AAATAA
1 ATTATCGTAATTACGATTAAAATAA
20638807 A
1 A
20638808 ATTTAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (25 bp):
ATTATCGTAATTACGATTAAAATAA
Found at i:20644377 original size:25 final size:26
Alignment explanation
Indices: 20644319--20644369 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
20644309 TTTTCACGTG
20644319 ATCTATTTTCCTTCTCCACCATTTAT
1 ATCTATTTTCCTTCTCCACCATTTAT
*
20644345 ATCTATTTCTCCTTCTCCACGATTT
1 ATCTATTT-TCCTTCTCCACCATTT
20644370 CTCTATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.18, C:0.31, G:0.02, T:0.49
Consensus pattern (26 bp):
ATCTATTTTCCTTCTCCACCATTTAT
Found at i:20644477 original size:23 final size:23
Alignment explanation
Indices: 20644451--20644495 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
20644441 ATTTTTCATG
20644451 TTTTTT-TTCATTAATTT-CTTTC
1 TTTTTTGTTC-TTAATTTCCTTTC
*
20644473 TTTTTTGTTCTTTATTTCCTTTC
1 TTTTTTGTTCTTAATTTCCTTTC
20644496 CCATTCAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.09, C:0.16, G:0.02, T:0.73
Consensus pattern (23 bp):
TTTTTTGTTCTTAATTTCCTTTC
Found at i:20645882 original size:61 final size:61
Alignment explanation
Indices: 20645817--20646053 Score: 155
Period size: 61 Copynumber: 3.9 Consensus size: 61
20645807 TCTTTTTATT
*
20645817 ATAATTACGAAAATAT-TTCTCTTATCATAA-ATAGCTAAAATTATTAAAATATCCTCCTATC
1 ATAATTACGAAAATATCTT-TCTTATCATAATATAGC-AAAATTATTAAAATATCATCCTATC
** * * * * * * *
20645878 ATAATTATAAAAATATCTTTTTTATTATAATTTATCAAAATTATTATAATATTATCTTATC
1 ATAATTACGAAAATATCTTTCTTATCATAATATAGCAAAATTATTAAAATATCATCCTATC
* * ** * ** * *
20645939 ATAATTACGAAAAGAACTCCCTTATTAT-ATACGGCCAAAATTAATATAATAT-A-CCTTAAATC
1 ATAATTACGAAAATATCTTTCTTATCATAATATAG-CAAAATTATTAAAATATCATCC-T--ATC
* * *
20646001 ATACTTACGAAAATA-CTATTCTTATCATAAT-TGATCAAAATTATTATAATATC
1 ATAATTACGAAAATATCT-TTCTTATCATAATAT-AGCAAAATTATTAAAATATC
20646054 TTTTATATCA
Statistics
Matches: 134, Mismatches: 32, Indels: 18
0.73 0.17 0.10
Matches are distributed among these distances:
59 1 0.01
60 4 0.03
61 83 0.62
62 44 0.33
63 2 0.01
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.40
Consensus pattern (61 bp):
ATAATTACGAAAATATCTTTCTTATCATAATATAGCAAAATTATTAAAATATCATCCTATC
Found at i:20646068 original size:26 final size:25
Alignment explanation
Indices: 20646034--20646085 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
20646024 ATCATAATTG
20646034 ATCAAAATTAT-TATAATATCTTTTAT
1 ATCAAAATTATATA-AATAT-TTTTAT
*
20646060 ATCATAATTATATAAATATTTTTAT
1 ATCAAAATTATATAAATATTTTTAT
20646085 A
1 A
20646086 AATGTTTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 7 0.29
26 15 0.62
27 2 0.08
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (25 bp):
ATCAAAATTATATAAATATTTTTAT
Found at i:20646317 original size:26 final size:26
Alignment explanation
Indices: 20646287--20646352 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 26
20646277 TGAATTAGAT
20646287 AATTATAATTT-TTATTAAAATAAAAA
1 AATTATAATTTATT-TTAAAATAAAAA
20646313 AATTAAATAATTTAATTTTAAAATAAAAA
1 AATT--ATAATTT-ATTTTAAAATAAAAA
*
20646342 TATT-TAATTTA
1 AATTATAATTTA
20646353 CAACCGTGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
25 1 0.03
26 10 0.29
28 7 0.20
29 15 0.43
30 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AATTATAATTTATTTTAAAATAAAAA
Found at i:20648082 original size:22 final size:23
Alignment explanation
Indices: 20648054--20648099 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
20648044 ATCAGAATTG
20648054 TCATATCT-AAGCCTAAAAGTTA
1 TCATATCTCAAGCCTAAAAGTTA
* *
20648076 TCATATCTCAAGCCTTAATGTTA
1 TCATATCTCAAGCCTAAAAGTTA
20648099 T
1 T
20648100 AGGATTTGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.37
Consensus pattern (23 bp):
TCATATCTCAAGCCTAAAAGTTA
Found at i:20655410 original size:21 final size:20
Alignment explanation
Indices: 20655380--20655419 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
20655370 ATGATTGCAT
*
20655380 AATTTAGTTTTCATTCAATTC
1 AATTTAGTTTT-AATCAATTC
*
20655401 AATTTTGTTTTAATCAATT
1 AATTTAGTTTTAATCAATT
20655420 AAAATAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.30, C:0.10, G:0.05, T:0.55
Consensus pattern (20 bp):
AATTTAGTTTTAATCAATTC
Found at i:20660841 original size:20 final size:20
Alignment explanation
Indices: 20660801--20660841 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
20660791 TCCTTTTCCA
**
20660801 TTTTTTTGGGGTTTTTTTTT
1 TTTTTTTGGGGTTTTCGTTT
*
20660821 TTTTTTTGGTGTTTTCGTTT
1 TTTTTTTGGGGTTTTCGTTT
20660841 T
1 T
20660842 CCCTGAAGCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.00, C:0.02, G:0.20, T:0.78
Consensus pattern (20 bp):
TTTTTTTGGGGTTTTCGTTT
Found at i:20662033 original size:18 final size:17
Alignment explanation
Indices: 20662005--20662043 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
20661995 TCATATATTA
20662005 ATAAATTTTATATAAAT-
1 ATAAATTTTATA-AAATG
20662022 ATAAATTTTTATAAAATG
1 ATAAA-TTTTATAAAATG
20662040 ATAA
1 ATAA
20662044 TATAATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
ATAAATTTTATAAAATG
Found at i:20662036 original size:16 final size:17
Alignment explanation
Indices: 20662005--20662036 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20661995 TCATATATTA
20662005 ATAAATTTTATATAAAT
1 ATAAATTTTATATAAAT
20662022 ATAAATTTT-TATAAA
1 ATAAATTTTATATAAA
20662037 ATGATAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAAATTTTATATAAAT
Found at i:20662038 original size:17 final size:18
Alignment explanation
Indices: 20662005--20662043 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
20661995 TCATATATTA
20662005 ATAAATTTTATATAAAT-
1 ATAAATTTTATATAAATG
20662022 ATAAATTTT-TATAAAATG
1 ATAAATTTTATAT-AAATG
20662040 ATAA
1 ATAA
20662044 TATAATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 3 0.15
17 13 0.65
18 4 0.20
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
ATAAATTTTATATAAATG
Found at i:20663914 original size:17 final size:17
Alignment explanation
Indices: 20663892--20663924 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
20663882 AATATTATAT
20663892 ATAATATTTTTGGATTA
1 ATAATATTTTTGGATTA
20663909 ATAATATTTTTGGATT
1 ATAATATTTTTGGATT
20663925 TTTTTTGTTA
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:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (17 bp):
ATAATATTTTTGGATTA
Found at i:20676690 original size:26 final size:26
Alignment explanation
Indices: 20676655--20676712 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
20676645 ATATAAAAAA
* **
20676655 TTATTATTTCAATTTAAAATATTTTT
1 TTATTATTTCAAATTAAAATATAATT
* *
20676681 TTATTTTTTCAAATTAACATATAATT
1 TTATTATTTCAAATTAAAATATAATT
20676707 TTATTA
1 TTATTA
20676713 AAATTTTAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (26 bp):
TTATTATTTCAAATTAAAATATAATT
Found at i:20676819 original size:30 final size:30
Alignment explanation
Indices: 20676757--20676864 Score: 77
Period size: 32 Copynumber: 3.7 Consensus size: 30
20676747 TTCCTCTGTT
* *
20676757 TTATTTTTTTATTTT-TTTGAAATATCTCAAAA
1 TTATTTTTTTATTTTATTT--TATAT-TTAAAA
20676789 TTATTTTTTTATTTTATTTTATATTTAAAA
1 TTATTTTTTTATTTTATTTTATATTTAAAA
* *
20676819 -T-TTTTATT-TTTTA--ATAT-TTTAAAA
1 TTATTTTTTTATTTTATTTTATATTTAAAA
*
20676843 TTATTTTTATTATAATTATTTT
1 TTATTTTT-TTAT-TTTATTTT
20676865 TTAATATTAA
Statistics
Matches: 61, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
24 7 0.11
25 4 0.07
26 4 0.07
27 7 0.11
28 7 0.11
29 4 0.07
30 5 0.08
31 5 0.08
32 15 0.25
33 3 0.05
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.67
Consensus pattern (30 bp):
TTATTTTTTTATTTTATTTTATATTTAAAA
Found at i:20676822 original size:25 final size:24
Alignment explanation
Indices: 20676794--20676844 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
20676784 CAAAATTATT
*
20676794 TTTTTATTTTATT-TTATATTTAAAA
1 TTTTTATTTT-TTAATAT-TTTAAAA
20676819 TTTTTATTTTTTAATATTTTAAAA
1 TTTTTATTTTTTAATATTTTAAAA
20676843 TT
1 TT
20676845 ATTTTTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTTATTTTTTAATATTTTAAAA
Found at i:20676839 original size:24 final size:25
Alignment explanation
Indices: 20676794--20676856 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
20676784 CAAAATTATT
*
20676794 TTTTTATTTTATTTTATATTTAAAA
1 TTTTTATTTTATTATATATTTAAAA
20676819 TTTTTATTTT-TTA-ATATTTTAAAA
1 TTTTTATTTTATTATATA-TTTAAAA
*
20676843 -TTAT-TTTTATTATA
1 TTTTTATTTTATTATA
20676857 ATTATTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 9 0.27
24 10 0.30
25 10 0.30
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (25 bp):
TTTTTATTTTATTATATATTTAAAA
Found at i:20676891 original size:22 final size:20
Alignment explanation
Indices: 20676863--20676919 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 20
20676853 TATAATTATT
20676863 TTTTAATATTAAAAATATAAAA
1 TTTTAATATTAAAAA-AT-AAA
* *
20676885 TTTTAATTTTATGAAAAATTAA
1 TTTTAATATTA--AAAAATAAA
20676907 TTTTAATATTAAA
1 TTTTAATATTAAA
20676920 TACATTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 2 0.07
22 22 0.73
23 2 0.07
24 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
TTTTAATATTAAAAAATAAA
Found at i:20677465 original size:18 final size:18
Alignment explanation
Indices: 20677438--20677473 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20677428 TTGAGATATC
*
20677438 TTTAAAATAATTAATAAA
1 TTTAAAATAATAAATAAA
*
20677456 TTTAATATAATAAATAAA
1 TTTAAAATAATAAATAAA
20677474 AATACATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTTAAAATAATAAATAAA
Found at i:20681913 original size:13 final size:13
Alignment explanation
Indices: 20681895--20681919 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20681885 AAACTTATTT
20681895 TAATATATTAAAA
1 TAATATATTAAAA
20681908 TAATATATTAAA
1 TAATATATTAAA
20681920 TAAAAAATAA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAATATATTAAAA
Found at i:20682074 original size:15 final size:16
Alignment explanation
Indices: 20682054--20682084 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
20682044 TCAAAAAAAT
20682054 TAAATCAAA-CTGAAC
1 TAAATCAAATCTGAAC
20682069 TAAATCAAATCTGAAC
1 TAAATCAAATCTGAAC
20682085 CCTTATCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.52, C:0.19, G:0.06, T:0.23
Consensus pattern (16 bp):
TAAATCAAATCTGAAC
Found at i:20683799 original size:36 final size:36
Alignment explanation
Indices: 20683517--20683798 Score: 325
Period size: 36 Copynumber: 7.8 Consensus size: 36
20683507 AAATACATGG
* * * * **
20683517 TTTGGTCCTTGCCCATAACTCTGTCCACGGCCAGGA
1 TTTGCTCCTTGCCCAGAATTCTGCCCATAGCCAGGA
**
20683553 TTTGCTCCTTGCCCAGAATTCTGAACATAGCCAGGA
1 TTTGCTCCTTGCCCAGAATTCTGCCCATAGCCAGGA
* *
20683589 TTTGCTCCTTGCCCGGAATTCTGCCAATAGCCAGGA
1 TTTGCTCCTTGCCCAGAATTCTGCCCATAGCCAGGA
**
20683625 TTTGCTCCTTGCCCAGAATTCTGAACATAGCCAGGA
1 TTTGCTCCTTGCCCAGAATTCTGCCCATAGCCAGGA
** * *
20683661 TTTGCAGCTTGCCCAGAATTCTGCCAATAGCCAGGG
1 TTTGCTCCTTGCCCAGAATTCTGCCCATAGCCAGGA
*
20683697 TTTGCTCCTTGCCCAGAATTCTGCCCATAACCAGGA
1 TTTGCTCCTTGCCCAGAATTCTGCCCATAGCCAGGA
* ** * *
20683733 TTTAC-CCTTGGACTGAAATTCTGCCCATAGGCAGGA
1 TTTGCTCCTTGCCCAG-AATTCTGCCCATAGCCAGGA
*
20683769 TTTG-TCCCTTGCCCAAAATTCTGCCCATAG
1 TTTGCT-CCTTGCCCAGAATTCTGCCCATAG
20683799 GTGGAACTTG
Statistics
Matches: 206, Mismatches: 37, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
35 7 0.03
36 193 0.94
37 6 0.03
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (36 bp):
TTTGCTCCTTGCCCAGAATTCTGCCCATAGCCAGGA
Found at i:20685974 original size:18 final size:20
Alignment explanation
Indices: 20685951--20685990 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
20685941 ATTAAATAGA
*
20685951 TTCT-AAATT-TGATATTTT
1 TTCTAAAATTGTGAAATTTT
20685969 TTCTAAAATTGTGAAATTTT
1 TTCTAAAATTGTGAAATTTT
20685989 TT
1 TT
20685991 TGTTCAAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 5 0.26
20 10 0.53
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.57
Consensus pattern (20 bp):
TTCTAAAATTGTGAAATTTT
Found at i:20687552 original size:25 final size:25
Alignment explanation
Indices: 20687500--20687546 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
20687490 AAATTTGATG
*
20687500 ATATTTTAAATTTAAATTATTAAAA
1 ATATTTTAAATTTAAATTAATAAAA
*
20687525 ATATTTT-AATTTTAATTAATAA
1 ATATTTTAAATTTAAATTAATAA
20687547 TTAATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
ATATTTTAAATTTAAATTAATAAAA
Found at i:20710860 original size:16 final size:16
Alignment explanation
Indices: 20710836--20710883 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 16
20710826 AAAATGTTTA
*
20710836 TTAAAATATTTAAATT
1 TTAACATATTTAAATT
20710852 TTAACATATTT-AA-T
1 TTAACATATTTAAATT
*
20710866 GTAACA-A-TTAAATT
1 TTAACATATTTAAATT
20710880 TTAA
1 TTAA
20710884 ATTTATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
12 2 0.07
13 3 0.11
14 10 0.37
15 2 0.07
16 10 0.37
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (16 bp):
TTAACATATTTAAATT
Found at i:20711603 original size:22 final size:23
Alignment explanation
Indices: 20711566--20711611 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
20711556 GTTACGTATT
20711566 ATTTTTAATAAAAATATAAATTTA
1 ATTTTTAATAAAAATAT-AATTTA
20711590 ATTTTT-A-AAAAATATAATTTA
1 ATTTTTAATAAAAATATAATTTA
20711611 A
1 A
20711612 AAAATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 8 0.36
23 1 0.05
24 6 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTTTAATAAAAATATAATTTA
Found at i:20711607 original size:16 final size:16
Alignment explanation
Indices: 20711583--20711638 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 16
20711573 ATAAAAATAT
*
20711583 AAATTTAATTTTTAAA
1 AAATATAATTTTTAAA
20711599 AAATATAA--TTTAAA
1 AAATATAATTTTTAAA
*
20711613 AAATAT--TTTTT-GA
1 AAATATAATTTTTAAA
*
20711626 AAATAAAATTTTT
1 AAATATAATTTTT
20711639 TTGTCAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
13 6 0.18
14 15 0.45
15 5 0.15
16 7 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
AAATATAATTTTTAAA
Found at i:20711628 original size:14 final size:14
Alignment explanation
Indices: 20711591--20711639 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
20711581 ATAAATTTAA
20711591 TTTTTAAAAAATAT
1 TTTTTAAAAAATAT
**
20711605 AATTTAAAAAATAT
1 TTTTTAAAAAATAT
*
20711619 TTTTTGAAAATAAAAT
1 TTTTT-AAAA-AATAT
20711635 TTTTT
1 TTTTT
20711640 TGTCAATTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
14 15 0.54
15 4 0.14
16 9 0.32
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (14 bp):
TTTTTAAAAAATAT
Found at i:20712247 original size:18 final size:19
Alignment explanation
Indices: 20712224--20712260 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
20712214 TAAAAAATAA
*
20712224 TTTAATATAATTTA-AAAT
1 TTTAATAAAATTTATAAAT
20712242 TTTAATAAAATTTATAAAT
1 TTTAATAAAATTTATAAAT
20712261 AAATTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTAATAAAATTTATAAAT
Found at i:20712248 original size:39 final size:38
Alignment explanation
Indices: 20712205--20712278 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 38
20712195 TATATAAAAA
20712205 TAATAAAAATAAAAAAT-AATTTAATATAATTTAAAATTT
1 TAATAAAAATAAAAAATAAATTT-A-ATAATTTAAAATTT
* * *
20712244 TAATAAAATTTATAAATAAATTTAATAATTTAAAA
1 TAATAAAAATAAAAAATAAATTTAATAATTTAAAA
20712279 AATGACCTGC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 11 0.35
39 15 0.48
40 5 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (38 bp):
TAATAAAAATAAAAAATAAATTTAATAATTTAAAATTT
Found at i:20719103 original size:22 final size:23
Alignment explanation
Indices: 20719078--20719124 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
20719068 ATGGAATTGC
20719078 TGTTAATTTCTA-TTATTGTTCA
1 TGTTAATTTCTAGTTATTGTTCA
*
20719100 TGTTATTTTCTATGTTATTGTTCA
1 TGTTAATTTCTA-GTTATTGTTCA
20719124 T
1 T
20719125 TCTTCTATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.50
24 11 0.50
ACGTcount: A:0.19, C:0.09, G:0.11, T:0.62
Consensus pattern (23 bp):
TGTTAATTTCTAGTTATTGTTCA
Found at i:20729831 original size:24 final size:24
Alignment explanation
Indices: 20729786--20729834 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
20729776 AATATTAAAC
**
20729786 TTAAGTTCGAATTCGATTTCAAAT
1 TTAAGTTCGAATTCGAGCTCAAAT
20729810 TTAAGGTTCGAATTC-AGCTCAAAT
1 TTAA-GTTCGAATTCGAGCTCAAAT
20729834 T
1 T
20729835 CGATCTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (24 bp):
TTAAGTTCGAATTCGAGCTCAAAT
Found at i:20730017 original size:10 final size:10
Alignment explanation
Indices: 20729993--20730022 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
20729983 TATTTTATCA
20729993 ATTAAAATA-
1 ATTAAAATAT
20730002 ATTAAAATAT
1 ATTAAAATAT
20730012 ATTAAAATAT
1 ATTAAAATAT
20730022 A
1 A
20730023 AAAACTCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:20730435 original size:21 final size:21
Alignment explanation
Indices: 20730405--20730447 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
20730395 AAAGTTTTAA
20730405 AAAATCATAAAAAAATAATTTT
1 AAAATCAT-AAAAAATAATTTT
*
20730427 AAAAT-ATAAAAAATAGTTTT
1 AAAATCATAAAAAATAATTTT
20730447 A
1 A
20730448 GATGCTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 13 0.65
21 2 0.10
22 5 0.25
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAATCATAAAAAATAATTTT
Found at i:20739615 original size:31 final size:31
Alignment explanation
Indices: 20739577--20739638 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
20739567 CTTATAATCT
20739577 CATGATGACCACTATCAGCACTAGGATTAAG
1 CATGATGACCACTATCAGCACTAGGATTAAG
20739608 CATGATGACCACTATCAGCACTAGGATTAAG
1 CATGATGACCACTATCAGCACTAGGATTAAG
20739639 TACACAATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (31 bp):
CATGATGACCACTATCAGCACTAGGATTAAG
Found at i:20743113 original size:22 final size:21
Alignment explanation
Indices: 20742978--20743113 Score: 59
Period size: 21 Copynumber: 6.4 Consensus size: 21
20742968 ATAAAATATA
20742978 AAAATTTTAT-T-TAAATTTTT
1 AAAATTTTATATATAAA-TTTT
* *
20742998 AATAATAATTATATATAAATTTA
1 AA-AAT-TTTATATATAAATTTT
* * * *
20743021 AAAAATTAAAATATATATTTT
1 AAAATTTTATATATAAATTTT
* * *
20743042 -ATATTTTTTATA-AAATATAAT
1 AAAATTTTATATATAAAT-T-TT
*
20743063 ATAAA-TTAATATATAAATTTT
1 A-AAATTTTATATATAAATTTT
*
20743084 AATATTTTATATGATAAA-TTT
1 AAAATTTTATAT-ATAAATTTT
20743105 AAAAGTTTT
1 AAAA-TTTT
20743114 TTTAAAGTTA
Statistics
Matches: 82, Mismatches: 22, Indels: 22
0.65 0.17 0.17
Matches are distributed among these distances:
19 3 0.04
20 12 0.15
21 29 0.35
22 22 0.27
23 12 0.15
24 4 0.05
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (21 bp):
AAAATTTTATATATAAATTTT
Found at i:20743675 original size:2 final size:2
Alignment explanation
Indices: 20743670--20743696 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20743660 GGTTTCAAAG
20743670 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
20743697 ACTTATAGTT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20744558 original size:20 final size:20
Alignment explanation
Indices: 20744529--20744566 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
20744519 TTAAATTATC
20744529 AAATACGATATATCTTATAT
1 AAATACGATATATCTTATAT
*
20744549 AAATATGATATATCTTAT
1 AAATACGATATATCTTAT
20744567 TTTAATCTGA
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:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (20 bp):
AAATACGATATATCTTATAT
Found at i:20744960 original size:31 final size:29
Alignment explanation
Indices: 20744918--20745006 Score: 94
Period size: 31 Copynumber: 3.1 Consensus size: 29
20744908 TTAATTTTTG
*
20744918 TTAAGAGTTTATTTAAATATAAAAATTAAAA
1 TTAAGAATTTATTTAAATAT--AAATTAAAA
**
20744949 TTAAGAATTTATTTAGGTATAAATTAAAA
1 TTAAGAATTTATTTAAATATAAATTAAAA
* *
20744978 TTAA-AATTTATTTGAGTAT-AA-TAAAA
1 TTAAGAATTTATTTAAATATAAATTAAAA
20745004 TTA
1 TTA
20745007 TAAAAAAGTG
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
26 8 0.15
27 2 0.04
28 13 0.25
29 13 0.25
31 17 0.32
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.42
Consensus pattern (29 bp):
TTAAGAATTTATTTAAATATAAATTAAAA
Found at i:20744996 original size:28 final size:29
Alignment explanation
Indices: 20744940--20745006 Score: 97
Period size: 28 Copynumber: 2.4 Consensus size: 29
20744930 TTAAATATAA
20744940 AAATTAAAATTAAGAATTTATTTAGGTAT
1 AAATTAAAATTAAGAATTTATTTAGGTAT
20744969 AAATTAAAATTAA-AATTTATTT-GAGTAT
1 AAATTAAAATTAAGAATTTATTTAG-GTAT
20744997 -AA-TAAAATTA
1 AAATTAAAATTA
20745007 TAAAAAAGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
26 8 0.22
27 3 0.08
28 13 0.35
29 13 0.35
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.40
Consensus pattern (29 bp):
AAATTAAAATTAAGAATTTATTTAGGTAT
Found at i:20745422 original size:11 final size:12
Alignment explanation
Indices: 20745404--20745435 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
20745394 AAATCTCATA
20745404 AGAGATTTGTTT
1 AGAGATTTGTTT
20745416 A-AGATTTG-TT
1 AGAGATTTGTTT
20745426 AGAGATTTGT
1 AGAGATTTGT
20745436 CAGATATTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 3 0.17
11 14 0.78
12 1 0.06
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (12 bp):
AGAGATTTGTTT
Found at i:20745526 original size:52 final size:52
Alignment explanation
Indices: 20745463--20745616 Score: 211
Period size: 52 Copynumber: 3.0 Consensus size: 52
20745453 ACAAGAAGAT
* * *
20745463 TTGCAAAAGAAGAATTCCAAGA-GAAAGATGATTCTTAATAGGTAAGTTTGAC
1 TTGCAAGAGAAGAATTCTAAGAGGAAAGA-GATTCTTAATAGGCAAGTTTGAC
* *
20745515 TTGCAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGCAAGTTTGAC
1 TTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTTGAC
* * * *
20745567 TTACAGGAGAAGAATTCTAAGAGGAGAGAGATTCTTAATGGGCAAGTTTG
1 TTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTTG
20745617 TATGGTTATA
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
52 85 0.94
53 5 0.06
ACGTcount: A:0.40, C:0.09, G:0.25, T:0.26
Consensus pattern (52 bp):
TTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTTGAC
Found at i:20746216 original size:25 final size:24
Alignment explanation
Indices: 20746188--20746243 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
20746178 TGAAGATTCA
20746188 AGATGTGAAAAGAGCCAAAAGTTTG
1 AGATGTG-AAAGAGCCAAAAGTTTG
* **
20746213 AGATATGAAAGAGCTGAAAGTTTG
1 AGATGTGAAAGAGCCAAAAGTTTG
20746237 AGATGTG
1 AGATGTG
20746244 GGAAGAGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 21 0.78
25 6 0.22
ACGTcount: A:0.41, C:0.05, G:0.30, T:0.23
Consensus pattern (24 bp):
AGATGTGAAAGAGCCAAAAGTTTG
Found at i:20746260 original size:25 final size:25
Alignment explanation
Indices: 20746155--20746264 Score: 80
Period size: 25 Copynumber: 4.4 Consensus size: 25
20746145 ATCAAAGCTG
* * *
20746155 AAGGTTTGAAATGTGAGAAGAGTTG
1 AAGGTTTGAGATGTGAAAAGAGTTA
* ** **
20746180 AAGATTCAAGATGTGAAAAGAGCCA
1 AAGGTTTGAGATGTGAAAAGAGTTA
* * *
20746205 AAAGTTTGAGATATG-AAAGAGCTGA
1 AAGGTTTGAGATGTGAAAAGAG-TTA
**
20746230 AA-GTTTGAGATGTGGGAAGAGTTA
1 AAGGTTTGAGATGTGAAAAGAGTTA
20746254 AAGGTTTGAGA
1 AAGGTTTGAGA
20746265 AGTGCATGAT
Statistics
Matches: 64, Mismatches: 18, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
24 21 0.33
25 43 0.67
ACGTcount: A:0.40, C:0.04, G:0.32, T:0.25
Consensus pattern (25 bp):
AAGGTTTGAGATGTGAAAAGAGTTA
Found at i:20746524 original size:11 final size:11
Alignment explanation
Indices: 20746507--20746538 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
20746497 AAATCCCATA
20746507 AGAGATTTGTT
1 AGAGATTTGTT
*
20746518 TGAGATTTGTT
1 AGAGATTTGTT
20746529 AGAGATTTGT
1 AGAGATTTGT
20746539 CAGATATTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (11 bp):
AGAGATTTGTT
Found at i:20746725 original size:11 final size:11
Alignment explanation
Indices: 20746708--20746739 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
20746698 AAATCCCATA
20746708 AGAGATTTGTT
1 AGAGATTTGTT
*
20746719 TGAGATTTGTT
1 AGAGATTTGTT
20746730 AGAGATTTGT
1 AGAGATTTGT
20746740 CAGATATTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (11 bp):
AGAGATTTGTT
Found at i:20746734 original size:201 final size:201
Alignment explanation
Indices: 20746384--20746799 Score: 789
Period size: 201 Copynumber: 2.1 Consensus size: 201
20746374 GACATAAGAG
20746384 AAGAG-AAGATGATTGTGAGACTTCCGTTGTAGGTGGAGCCAAGCATGTCTAGCATGAAGACAGA
1 AAGAGAAAGATGATTGTGAGACTTCCGTTGTAGGTGGAGCCAAGCATGTCTAGCATGAAGACAGA
*
20746448 TGATTGATTGAATTTGAGTCAAGGTGGAGATTGTTGGGAATATTGACTCAAATCCCATAAGAGAT
66 TGATTGATGGAATTTGAGTCAAGGTGGAGATTGTTGGGAATATTGACTCAAATCCCATAAGAGAT
* *
20746513 TTGTTTGAGATTTGTTAGAGATTTGTCAGATATTGCTTGATGGACAAGAAGACTTGCAAAAGAAG
131 TTGTTTGAGATTTGTTAGAGATTTGTCAGATATTGCTTGATGGACAAGAAGACTTGCAAAAAAAA
20746578 AATTCT
196 AATTCT
20746584 AAGAGAAAGATGATTGTGAGACTTCCGTTGTAGGTGGAGCCAAGCATGTCTAGCATGAAGACAGA
1 AAGAGAAAGATGATTGTGAGACTTCCGTTGTAGGTGGAGCCAAGCATGTCTAGCATGAAGACAGA
*
20746649 TGATTGATGGAATTTGAGTCAAGTTGGAGATTGTTGGGAATATTGACTCAAATCCCATAAGAGAT
66 TGATTGATGGAATTTGAGTCAAGGTGGAGATTGTTGGGAATATTGACTCAAATCCCATAAGAGAT
20746714 TTGTTTGAGATTTGTTAGAGATTTGTCAGATATTGCTTGATGGACAAGAAGACTTGCAAAAAAAA
131 TTGTTTGAGATTTGTTAGAGATTTGTCAGATATTGCTTGATGGACAAGAAGACTTGCAAAAAAAA
20746779 AATTCT
196 AATTCT
20746785 AAGAGAAAGATGATT
1 AAGAGAAAGATGATT
20746800 CTTAATAGGT
Statistics
Matches: 211, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
200 5 0.02
201 206 0.98
ACGTcount: A:0.34, C:0.10, G:0.26, T:0.30
Consensus pattern (201 bp):
AAGAGAAAGATGATTGTGAGACTTCCGTTGTAGGTGGAGCCAAGCATGTCTAGCATGAAGACAGA
TGATTGATGGAATTTGAGTCAAGGTGGAGATTGTTGGGAATATTGACTCAAATCCCATAAGAGAT
TTGTTTGAGATTTGTTAGAGATTTGTCAGATATTGCTTGATGGACAAGAAGACTTGCAAAAAAAA
AATTCT
Found at i:20746835 original size:52 final size:52
Alignment explanation
Indices: 20746764--20746920 Score: 208
Period size: 52 Copynumber: 3.0 Consensus size: 52
20746754 TGGACAAGAA
* * * *
20746764 GACTTGCAAAAAAAAAATTCTAAGA-GAAAGATGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGA-GATTCTTAATAGGCAAGTTT
* *
20746816 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTT
* * * *
20746868 GACTTACAGGAGAAGAATTCTAAGAGGAGAGAGATTCTTAATGGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTT
20746920 G
1 G
20746921 TATGGTTATA
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
52 87 0.95
53 5 0.05
ACGTcount: A:0.41, C:0.09, G:0.24, T:0.26
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTT
Found at i:20749062 original size:15 final size:17
Alignment explanation
Indices: 20749025--20749057 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20749015 TGATAAAATA
*
20749025 AAATAAGATGATATTAT
1 AAATAAGATTATATTAT
20749042 AAATAAGATTATATTA
1 AAATAAGATTATATTA
20749058 AATAATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (17 bp):
AAATAAGATTATATTAT
Found at i:20749279 original size:165 final size:164
Alignment explanation
Indices: 20749010--20749317 Score: 431
Period size: 165 Copynumber: 1.9 Consensus size: 164
20749000 TGATATATAA
** * * *
20749010 AATTATGATAAAATAAAATAAGATGATATTATAAATAAGATTATATTAAATAATATTATTTTAGT
1 AATTATGATAAAATAAAATAAGACAATATTATAAATAAAATTAAATTAAATAATATTATTATAGT
* *
20749075 TTATATTTGATACGTGTCAGAATTACGATAGAATAATTTATTTATTAGTTAAAATTAT-TTTTCT
66 TTATATTTGATACGTGTAAAAATTACGATAGAATAATTTATTTATTAGTTAAAATTATATTTTC-
*
20749139 TTAAAAATTATATATATGTCATGTTTTGTGTAAAT
130 TCAAAAATTATATATATGTCATGTTTTGTGTAAAT
** * * *
20749174 AATTATGATATGATAAAATAAGACAATATTATGAATAAAATTAAAATTAAATAATGTTATTATAT
1 AATTATGATAAAATAAAATAAGACAATATTATAAATAAAATT-AAATTAAATAATATTATTATAG
* *
20749239 TTTATATTTGATACGTGTAAAAATTATGAT-GAGATAATTTATTTATTAGTTAAAGTTATATTTT
65 TTTATATTTGATACGTGTAAAAATTACGATAGA-ATAATTTATTTATTAGTTAAAATTATATTTT
*
20749303 CTCAAAATTTATATA
129 CTCAAAAATTATATA
20749318 ATTTAAATTA
Statistics
Matches: 125, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
164 38 0.30
165 82 0.66
166 5 0.04
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (164 bp):
AATTATGATAAAATAAAATAAGACAATATTATAAATAAAATTAAATTAAATAATATTATTATAGT
TTATATTTGATACGTGTAAAAATTACGATAGAATAATTTATTTATTAGTTAAAATTATATTTTCT
CAAAAATTATATATATGTCATGTTTTGTGTAAAT
Found at i:20749357 original size:165 final size:164
Alignment explanation
Indices: 20749010--20749358 Score: 402
Period size: 165 Copynumber: 2.1 Consensus size: 164
20749000 TGATATATAA
* * ** * * *
20749010 AATTATGATAAAATAAAATAAGATGATATTATAAATAAGATTATATTAAATAATATTATTTTAGT
1 AATTAAGATATAATAAAATAAGACAATATTATAAATAAAATTAAATTAAATAATATTATTATAGT
* *
20749075 TTATATTTGATACGTGTCAGAATTACGATAGAATAATTTATTTATTAGTTAAAATTATTTTTCTT
66 TTATATTTGATACGTGTAAAAATTACGATAGAATAATTTATTTATTAGTTAAAATTATTTTTCTT
* * *
20749140 TAAAAATTATATATATGTCATGTTTTGTGTAAAT
131 CAAAAATTATATATATGTAATGTTTTATGTAAAT
* * * * *
20749174 AATTATGATATGATAAAATAAGACAATATTATGAATAAAATTAAAATTAAATAATGTTATTATAT
1 AATTAAGATATAATAAAATAAGACAATATTATAAATAAAATT-AAATTAAATAATATTATTATAG
* *
20749239 TTTATATTTGATACGTGTAAAAATTATGAT-GAGATAATTTATTTATTAGTTAAAGTTATATTTT
65 TTTATATTTGATACGTGTAAAAATTACGATAGA-ATAATTTATTTATTAGTTAAAATTAT-TTTT
* *
20749303 C-TCAAAATTTATATA-ATTTAAAT-TATTTATGT-AAT
128 CTTCAAAAATTATATATATGT-AATGT-TTTATGTAAAT
**
20749338 TTTTAAGAGTATAATAAAATA
1 AATTAAGA-TATAATAAAATA
20749359 TATAAGTTCA
Statistics
Matches: 156, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
164 50 0.32
165 101 0.65
166 5 0.03
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (164 bp):
AATTAAGATATAATAAAATAAGACAATATTATAAATAAAATTAAATTAAATAATATTATTATAGT
TTATATTTGATACGTGTAAAAATTACGATAGAATAATTTATTTATTAGTTAAAATTATTTTTCTT
CAAAAATTATATATATGTAATGTTTTATGTAAAT
Found at i:20749425 original size:21 final size:22
Alignment explanation
Indices: 20749379--20749423 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
20749369 ATTTTATAGA
20749379 TTAAAAATAAAAATTTTCACTT
1 TTAAAAATAAAAATTTTCACTT
20749401 TTAAAAATAAAAATTTTCACTT
1 TTAAAAATAAAAATTTTCACTT
20749423 T
1 T
20749424 AAGATGGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAAAAATAAAAATTTTCACTT
Found at i:20749563 original size:2 final size:2
Alignment explanation
Indices: 20749556--20749594 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
20749546 TATGACAATA
* *
20749556 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20749595 CGTAGGGGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:20755913 original size:22 final size:22
Alignment explanation
Indices: 20755888--20755941 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
20755878 CTCGAAATTA
*
20755888 ATAAAATATTACTTTTTACAAT
1 ATAAAATATTACTTTTTAAAAT
*
20755910 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTACTTTTTAAAAT
20755932 ATAAATATAT
1 ATAAA-ATAT
20755942 AATTATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 25 0.86
23 4 0.14
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (22 bp):
ATAAAATATTACTTTTTAAAAT
Found at i:20755963 original size:18 final size:18
Alignment explanation
Indices: 20755930--20755964 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20755920 ATTTTTTAAA
* *
20755930 ATATAAATATATAATTAT
1 ATATAAATACAAAATTAT
20755948 ATATAAATACAAAATTA
1 ATATAAATACAAAATTA
20755965 AAAAATAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
ATATAAATACAAAATTAT
Found at i:20757318 original size:2 final size:2
Alignment explanation
Indices: 20757307--20757341 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
20757297 GTGATTTAAA
20757307 AT AT -T 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
20757342 TTGGAGGGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:20758779 original size:2 final size:2
Alignment explanation
Indices: 20758772--20758802 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
20758762 GCATGCATGC
*
20758772 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20758803 ATCAAGTGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20767024 original size:89 final size:89
Alignment explanation
Indices: 20766873--20767041 Score: 338
Period size: 89 Copynumber: 1.9 Consensus size: 89
20766863 GAAATATATA
20766873 TTGCATGTTTGCATGTGTGTATATGCATGGTTTTATGTGGGGTGATTATCATTAAATTACTCCTC
1 TTGCATGTTTGCATGTGTGTATATGCATGGTTTTATGTGGGGTGATTATCATTAAATTACTCCTC
20766938 TCAGTTTGTGTAAAAAATTACTTT
66 TCAGTTTGTGTAAAAAATTACTTT
20766962 TTGCATGTTTGCATGTGTGTATATGCATGGTTTTATGTGGGGTGATTATCATTAAATTACTCCTC
1 TTGCATGTTTGCATGTGTGTATATGCATGGTTTTATGTGGGGTGATTATCATTAAATTACTCCTC
20767027 TCAGTTTGTGTAAAA
66 TCAGTTTGTGTAAAA
20767042 TTAAACACAT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 80 1.00
ACGTcount: A:0.23, C:0.11, G:0.21, T:0.44
Consensus pattern (89 bp):
TTGCATGTTTGCATGTGTGTATATGCATGGTTTTATGTGGGGTGATTATCATTAAATTACTCCTC
TCAGTTTGTGTAAAAAATTACTTT
Found at i:20770023 original size:50 final size:50
Alignment explanation
Indices: 20769948--20770042 Score: 145
Period size: 50 Copynumber: 1.9 Consensus size: 50
20769938 AATGGCCACG
* * *
20769948 CATCAGGTTTGAATTGGTTCTGAATGATAACACATTTAGCAAAGACAACA
1 CATCAAGTTTAAATTGGTTCTGAATGAAAACACATTTAGCAAAGACAACA
* *
20769998 CATCAAGTTTAAATTGGTTCTGAATGAAAACACGTTTTGCAAAGA
1 CATCAAGTTTAAATTGGTTCTGAATGAAAACACATTTAGCAAAGA
20770043 AATCTCATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (50 bp):
CATCAAGTTTAAATTGGTTCTGAATGAAAACACATTTAGCAAAGACAACA
Found at i:20792486 original size:28 final size:28
Alignment explanation
Indices: 20792415--20792476 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
20792405 TTTTTATTTT
* *
20792415 TTATAATT-T-ATTATAAAATTTAGTAA
1 TTATAATTATAATAATAAAAATTAGTAA
*
20792441 TTATAATTATAATAATAAAAATTAGTAC
1 TTATAATTATAATAATAAAAATTAGTAA
20792469 TTATAATT
1 TTATAATT
20792477 TTTAAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 8 0.26
27 1 0.03
28 22 0.71
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (28 bp):
TTATAATTATAATAATAAAAATTAGTAA
Found at i:20793423 original size:16 final size:16
Alignment explanation
Indices: 20793389--20793421 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20793379 GTAAAATTAA
20793389 TTATTTATAATTTATT
1 TTATTTATAATTTATT
*
20793405 TTATTTATTA-TTATT
1 TTATTTATAATTTATT
20793420 TT
1 TT
20793422 TAATTTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTATTTATAATTTATT
Found at i:20793570 original size:15 final size:14
Alignment explanation
Indices: 20793540--20793576 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
20793530 TATAATTTTA
*
20793540 TATTTATTTAAATT
1 TATTTAATTAAATT
20793554 TATTTAATTATAATT
1 TATTTAATTA-AATT
20793569 TATTTAAT
1 TATTTAAT
20793577 ATTTTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTTAATTAAATT
Found at i:20793583 original size:24 final size:24
Alignment explanation
Indices: 20793526--20793584 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
20793516 ATATATTATC
* *
20793526 AATTTATAATTTTATATTTATTTA
1 AATTTTTAATTATATATTTATTTA
20793550 AATTTATTTAATTATA-ATTTATTTA
1 AA-TT-TTTAATTATATATTTATTTA
20793575 ATATTTTTAA
1 A-ATTTTTAA
20793585 ATATTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 7 0.23
25 14 0.47
26 9 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
AATTTTTAATTATATATTTATTTA
Found at i:20793623 original size:37 final size:36
Alignment explanation
Indices: 20793534--20793630 Score: 103
Period size: 36 Copynumber: 2.7 Consensus size: 36
20793524 TCAATTTATA
20793534 ATTT-TATATTTATTTAAAT-TTATTT-AATTATAATTT
1 ATTTATATATTTA--TAAATATT-TTTAAATTATAATTT
* *
20793570 ATTTA-ATATTTTTAAATATTTTTAAATTATACTGTT
1 ATTTATATATTTATAAATATTTTTAAATTATAAT-TT
*
20793606 ATTTATATATTTATAAATATGTTTA
1 ATTTATATATTTATAAATATTTTTA
20793631 TTCGTTGAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
34 8 0.15
35 10 0.19
36 17 0.33
37 17 0.33
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (36 bp):
ATTTATATATTTATAAATATTTTTAAATTATAATTT
Found at i:20799170 original size:2 final size:2
Alignment explanation
Indices: 20799163--20799194 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
20799153 AGTAATTGAG
20799163 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
20799195 TGGTTGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20799521 original size:18 final size:19
Alignment explanation
Indices: 20799487--20799533 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
20799477 GATATTTTAT
20799487 TAATTAAAATAATAAAAATA
1 TAATT-AAATAATAAAAATA
* *
20799507 TATTTAAAT-ATAAAAATT
1 TAATTAAATAATAAAAATA
20799525 TAATTAAAT
1 TAATTAAAT
20799534 TCACGAGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 16 0.67
19 4 0.17
20 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAATTAAATAATAAAAATA
Found at i:20801121 original size:12 final size:14
Alignment explanation
Indices: 20801092--20801123 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
20801082 ATTTTCTTAT
20801092 TAAAAATGTGTAAA
1 TAAAAATGTGTAAA
20801106 TAAAAAT-TGT-AA
1 TAAAAATGTGTAAA
20801118 TAAAAA
1 TAAAAA
20801124 ATTTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.44
13 3 0.17
14 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.28
Consensus pattern (14 bp):
TAAAAATGTGTAAA
Done.