Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167982.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_24, 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: 18142777
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 63000 characters in sequence are not A, C, G, or T
File 50 of 84
Found at i:11485675 original size:74 final size:75
Alignment explanation
Indices: 11485548--11485690 Score: 186
Period size: 74 Copynumber: 1.9 Consensus size: 75
11485538 AGTATCAATT
* * * *
11485548 TTTCTTAAAATTAAAATTTCAAAACAATATATTTTTGAGAAAAAGTTGAAAGTATTAATTTTTCT
1 TTTCTTAAAATTAAAATTTCAAAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAA-TTTCCT
11485613 TAAAAGTAAAA
65 TAAAAGTAAAA
*
11485624 TTTC-TAAAA-TAAAATTTTCAAAAAAAAATA-TTTTGA-AGAAAAGTTGGAAGTATCAATTTCC
1 TTTCTTAAAATTAAAA-TTTCAAAAAAAAATATTTTTGAGA-AAAAGTTGAAAGTATCAATTTCC
11485685 TTAAAA
64 TTAAAA
11485691 AAATAAAAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
73 11 0.18
74 27 0.45
75 18 0.30
76 4 0.07
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.37
Consensus pattern (75 bp):
TTTCTTAAAATTAAAATTTCAAAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTCCTT
AAAAGTAAAA
Found at i:11485712 original size:61 final size:62
Alignment explanation
Indices: 11485629--11485752 Score: 155
Period size: 61 Copynumber: 2.0 Consensus size: 62
11485619 TAAAATTTCT
* * **
11485629 AAAATAAAATTTTCAAAAAAAAATATTTTGAA-GAAAAGTTGGAAGTATCAA-TTTCCTTAAA
1 AAAATAAAATTATCAAAAAAAAACATTTT-AAGGAAAAGTTAAAAGTATCAATTTTCCTTAAA
* *
11485690 AAAATAAAAATTATC-AAGAAAAACATTTTAAGGAAAAGTTAAAAGTATTAATTTTCCTTAAA
1 AAAAT-AAAATTATCAAAAAAAAACATTTTAAGGAAAAGTTAAAAGTATCAATTTTCCTTAAA
11485752 A
1 A
11485753 TAAAAATTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
60 2 0.04
61 33 0.61
62 19 0.35
ACGTcount: A:0.54, C:0.06, G:0.09, T:0.31
Consensus pattern (62 bp):
AAAATAAAATTATCAAAAAAAAACATTTTAAGGAAAAGTTAAAAGTATCAATTTTCCTTAAA
Found at i:11494270 original size:14 final size:15
Alignment explanation
Indices: 11494252--11494290 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
11494242 ATAAAAATAA
11494252 AAAAAATAAAAAATG
1 AAAAAATAAAAAATG
* *
11494267 -AAAAACAAAAATTG
1 AAAAAATAAAAAATG
11494281 AAAAAATAAA
1 AAAAAATAAA
11494291 GACAAAAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAAAATG
Found at i:11495032 original size:16 final size:16
Alignment explanation
Indices: 11495011--11495041 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11495001 TACATAGCAT
11495011 GCATTGAATTTCGCAC
1 GCATTGAATTTCGCAC
*
11495027 GCATTGTATTTCGCA
1 GCATTGAATTTCGCA
11495042 TAGCATATAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (16 bp):
GCATTGAATTTCGCAC
Found at i:11495463 original size:43 final size:43
Alignment explanation
Indices: 11495303--11495603 Score: 273
Period size: 43 Copynumber: 7.0 Consensus size: 43
11495293 GTCAATGAGT
* * *
11495303 AATTTA-TTTTTTCAAAGTTGTTGAGCCTCTGTTTAAAGAAGC
1 AATTTATTTTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGC
* * *
11495345 AATTTA-TTTTTTCAAAGTCGTTGAGCCTCTATTTAAAAGAG-
1 AATTTATTTTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGC
*
11495386 -ATTTATTTATTTCTCCAAAGTCGTT-AACCTCTGTTTAGAGGAGC
1 AATTTATTT-TTT-T-CAAAGTCGTTGAGCCTCTGTTTAGAGGAGC
*
11495430 AATTTATTTTTTTCAAAGTCATTGAGCCTCTGTTTAGAGGAGC
1 AATTTATTTTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGC
* * *
11495473 --TTTATTTATTTCTTCAAAGTCGTTGAGCTTCTATTTAGATGAGC
1 AATTTA-TT-TTT-TTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGC
* *
11495517 TATGTTTATTTTTTT--AAGTCGTTGAGCCTCTGATTAGAGGAG-
1 -A-ATTTATTTTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGC
* * * *
11495559 ATATGTTTATTTTTTT-TAAGTTGTTGAGCCTCTGCTTAGAAGAGC
1 A-A--TTTATTTTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGC
11495604 TTTGTTTATG
Statistics
Matches: 219, Mismatches: 22, Indels: 33
0.80 0.08 0.12
Matches are distributed among these distances:
40 5 0.02
41 8 0.04
42 51 0.23
43 71 0.32
44 65 0.30
45 10 0.05
46 3 0.01
47 2 0.01
48 4 0.02
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.44
Consensus pattern (43 bp):
AATTTATTTTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGC
Found at i:11495510 original size:44 final size:44
Alignment explanation
Indices: 11495304--11495623 Score: 301
Period size: 44 Copynumber: 7.4 Consensus size: 44
11495294 TCAATGAGTA
* * * *
11495304 ATTTATTTTTTCAAAGTTGTTGAGCCTCTGTTTAAAGAAGC--A
1 ATTTATTTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTT
* * * *
11495346 ATTTATTTTTTCAAAGTCGTTGAGCCTCTATTTAAAAGAGATTT
1 ATTTATTTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTT
* * * *
11495390 ATTTATTTCTCCAAAGTCGTT-AACCTCTGTTTAGAGGAGC--A
1 ATTTATTTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTT
*
11495431 ATTTATTTTTTTCAAAGTCATTGAGCCTCTGTTTAGAGGAGCTTT
1 ATTTA-TTTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTT
* * * * *
11495476 ATTTATTTCTTCAAAGTCGTTGAGCTTCTATTTAGATGAGCTAT
1 ATTTATTTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTT
* * * * *
11495520 GTTTATTTTTT-TAAGTCGTTGAGCCTCTGATTAGAGGAGATAT
1 ATTTATTTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTT
* ** * * *
11495563 GTTTATTTTTTTTAAGTTGTTGAGCCTCTGCTTAGAAGAGCTTT
1 ATTTATTTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTT
* *
11495607 GTTTATGTTTCTCAAAG
1 ATTTAT-TTTTTCAAAG
11495624 GCATATGAGC
Statistics
Matches: 229, Mismatches: 41, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
41 5 0.02
42 49 0.21
43 69 0.30
44 94 0.41
45 12 0.05
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.45
Consensus pattern (44 bp):
ATTTATTTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTT
Found at i:11495546 original size:87 final size:85
Alignment explanation
Indices: 11495304--11495603 Score: 325
Period size: 87 Copynumber: 3.5 Consensus size: 85
11495294 TCAATGAGTA
* * *
11495304 ATTTATTTTTTCAAAGTTGTTGAGCCTCTGTTTA-AAGAAGCAATTTATTTTTTCAAAGTCGTTG
1 ATTTATTTCTTCAAAGTCGTTGAGCCTCTGTTTAGAAG-AGCAATTTATTTTTT-TAAGTCGTTG
* * *
11495368 AGCCTCTATTTAAAAGAGATTT
64 AGCCTCTGTTTAGAGGAGATTT
* * * *
11495390 ATTTATTTCTCCAAAGTCGTT-AACCTCTGTTTAGAGGAGCAATTTATTTTTTTCAAAGTCATTG
1 ATTTATTTCTTCAAAGTCGTTGAGCCTCTGTTTAGAAGAGCAATTTATTTTTTT--AAGTCGTTG
*
11495454 AGCCTCTGTTTAGAGGAGCTTT
64 AGCCTCTGTTTAGAGGAGATTT
* * * *
11495476 ATTTATTTCTTCAAAGTCGTTGAGCTTCTATTTAGATGAGCTATGTTTATTTTTTTAAGTCGTTG
1 ATTTATTTCTTCAAAGTCGTTGAGCCTCTGTTTAGAAGAGC-A-ATTTATTTTTTTAAGTCGTTG
* *
11495541 AGCCTCTGATTAGAGGAGATAT
64 AGCCTCTGTTTAGAGGAGATTT
* * ** * *
11495563 GTTTATTTTTTTTAAGTTGTTGAGCCTCTGCTTAGAAGAGC
1 ATTTATTTCTTCAAAGTCGTTGAGCCTCTGTTTAGAAGAGC
11495604 TTTGTTTATG
Statistics
Matches: 178, Mismatches: 30, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
85 26 0.15
86 66 0.37
87 74 0.42
88 1 0.01
89 11 0.06
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.44
Consensus pattern (85 bp):
ATTTATTTCTTCAAAGTCGTTGAGCCTCTGTTTAGAAGAGCAATTTATTTTTTTAAGTCGTTGAG
CCTCTGTTTAGAGGAGATTT
Found at i:11495844 original size:4 final size:4
Alignment explanation
Indices: 11495835--11495943 Score: 86
Period size: 4 Copynumber: 28.5 Consensus size: 4
11495825 CATTTTTATT
* * *
11495835 TTTA TTTA TTTA TTTA -TTA -TTA -TTA -TTA TTTA TCTA TTAA TATA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * * *
11495879 TTTT TTTA TTTA TCTA TTAA TATT- TTTA -TTA TTTA TCTA TTAA TTAA
1 TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA
11495926 TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TT
11495944 ATCTATTAGT
Statistics
Matches: 85, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
3 17 0.20
4 67 0.79
5 1 0.01
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (4 bp):
TTTA
Found at i:11495858 original size:24 final size:24
Alignment explanation
Indices: 11495830--11495950 Score: 119
Period size: 24 Copynumber: 5.2 Consensus size: 24
11495820 ATTTGCATTT
11495830 TTATTTTTATTTATTTATTTATTA
1 TTATTTTTATTTATTTATTTATTA
* * *
11495854 TTATTATTATTTATCTA-TTAATA
1 TTATTTTTATTTATTTATTTATTA
*
11495877 -TA-TTTT-TTTATTTATCTATTA
1 TTATTTTTATTTATTTATTTATTA
* *
11495898 ATATTTTTA-TTATTTATCTATTAA
1 TTATTTTTATTTATTTATTTATT-A
*
11495922 TTA-ATTTATTTATTTATTTATTA
1 TTATTTTTATTTATTTATTTATTA
11495945 TCTATT
1 T-TATT
11495951 AGTATATATA
Statistics
Matches: 78, Mismatches: 11, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
20 7 0.09
21 7 0.09
22 4 0.05
23 28 0.36
24 32 0.41
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (24 bp):
TTATTTTTATTTATTTATTTATTA
Found at i:11495911 original size:47 final size:47
Alignment explanation
Indices: 11495833--11495967 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 47
11495823 TGCATTTTTA
*
11495833 TTTTTATTTATTTATTTATTATTATTATTATTTATCTATTAA-TATATT
1 TTTTTATTTATTTA-TTAATATTATTATTATTTATCTATTAATTA-ATT
* *
11495881 TTTTTATTTATCTATTAATATTTTTATTATTTATCTATTAATTAATT
1 TTTTTATTTATTTATTAATATTATTATTATTTATCTATTAATTAATT
* *
11495928 TATTTATTTATTTATTATCTATTAGTATATATATTTATCT
1 TTTTTATTTATTTATTA-ATATTA-T-TAT-TATTTATCT
11495968 TTTTTTTTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
47 43 0.57
48 19 0.25
49 1 0.01
50 3 0.04
51 9 0.12
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.66
Consensus pattern (47 bp):
TTTTTATTTATTTATTAATATTATTATTATTTATCTATTAATTAATT
Found at i:11497016 original size:59 final size:58
Alignment explanation
Indices: 11496819--11497027 Score: 242
Period size: 59 Copynumber: 3.6 Consensus size: 58
11496809 TTTTTAAATG
*
11496819 ATTTTTCTTAAAAATAAAATTCTAAAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCA
1 ATTTTTCTTAAAAATAAAATTTTAAAAAAAATATTTTT-GGAAAAAGTTGAAAGTATCA
* * * * ** *
11496878 ATTTTCCTT-AAAATTAAATTTAAAAAAAAAGCA-TTTTGGGGAAAGTTGAAAGTATTA
1 ATTTTTCTTAAAAATAAAATTTTAAAAAAAA-TATTTTTGGAAAAAGTTGAAAGTATCA
* *
11496935 ATTTTTCTTAAAATTAAAATTTTACAAAAAAATATTTTTGGAAAAAGTTAAAAGTATCA
1 ATTTTTCTTAAAAATAAAATTTTA-AAAAAAATATTTTTGGAAAAAGTTGAAAGTATCA
* * *
11496994 ATTTTTTTTGAAAGTAAAATTTTTAAAATAAAAT
1 ATTTTTCTTAAAAATAAAA-TTTTAAAA-AAAAT
11497028 TTTCAAAAAA
Statistics
Matches: 124, Mismatches: 20, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
57 25 0.20
58 34 0.27
59 55 0.44
60 10 0.08
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.38
Consensus pattern (58 bp):
ATTTTTCTTAAAAATAAAATTTTAAAAAAAATATTTTTGGAAAAAGTTGAAAGTATCA
Found at i:11497025 original size:14 final size:14
Alignment explanation
Indices: 11496998--11497045 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
11496988 GTATCAATTT
*
11496998 TTTTTGAAAGTAAAA
1 TTTTT-AAAATAAAA
11497013 TTTTTAAAATAAAA
1 TTTTTAAAATAAAA
* *
11497027 TTTTCAAAAAAAACA
1 TTTTTAAAATAAA-A
11497042 TTTT
1 TTTT
11497046 GAAGAAAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 19 0.66
15 10 0.34
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (14 bp):
TTTTTAAAATAAAA
Found at i:11497101 original size:62 final size:62
Alignment explanation
Indices: 11497018--11497142 Score: 164
Period size: 62 Copynumber: 2.0 Consensus size: 62
11497008 TAAAATTTTT
* *
11497018 AAAATAAAATTTTCAAAAAAAACATTTTGAA-GAAAAGTTAGAAT-TACCAATTTTCCTTAAA
1 AAAATAAAATTATCAAAAAAAACATTTTGAAGGAAAAATT-GAATGTACCAATTTTCCTTAAA
* * * *
11497079 AAAATAAAAATTATCAAGAAAAACATTTTTAAGGAAAAATTGAATGTATCAATTTTTCTTAAA
1 AAAAT-AAAATTATCAAAAAAAACATTTTGAAGGAAAAATTGAATGTACCAATTTTCCTTAAA
11497142 A
1 A
11497143 TAAAAATTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
61 5 0.09
62 27 0.49
63 23 0.42
ACGTcount: A:0.53, C:0.08, G:0.07, T:0.32
Consensus pattern (62 bp):
AAAATAAAATTATCAAAAAAAACATTTTGAAGGAAAAATTGAATGTACCAATTTTCCTTAAA
Found at i:11507882 original size:23 final size:25
Alignment explanation
Indices: 11507840--11507885 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
11507830 CGTATTTGAT
*
11507840 TATTGATTGTTATCTATTGCTTCTG
1 TATTGATTGTGATCTATTGCTTCTG
11507865 TATTG-TTGTGAT-TATTGCTTC
1 TATTGATTGTGATCTATTGCTTC
11507886 AGGCGCAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 6 0.30
25 5 0.25
ACGTcount: A:0.15, C:0.11, G:0.17, T:0.57
Consensus pattern (25 bp):
TATTGATTGTGATCTATTGCTTCTG
Found at i:11513360 original size:175 final size:175
Alignment explanation
Indices: 11513069--11513412 Score: 654
Period size: 175 Copynumber: 2.0 Consensus size: 175
11513059 AAACAGGGCC
11513069 CTCATACCAACTCACAAGATGGAAAGAGGGGAAAAGGGTGAGACATCACATGGACCAACAGAAGC
1 CTCATACCAACTCACAAGATGGAAAGAGGGGAAAAGGGTGAGACATCACATGGACCAACAGAAGC
*
11513134 AATATGGAGTCCCACATCATTATTGTCCATGTTTTTTCCTCATTCTTAGTGTCTTTCGGGTGTAA
66 AATATGGAGTCCCACAACATTATTGTCCATGTTTTTTCCTCATTCTTAGTGTCTTTCGGGTGTAA
11513199 TTGAGAAATTAAATACCATAATTATAATGCTTAGGAGACTACCTT
131 TTGAGAAATTAAATACCATAATTATAATGCTTAGGAGACTACCTT
11513244 CTCATACCAACTCACAAGATGGAAAGAGGGGAAAAGGGTGAGACATCACATGGA-CAGACAGAAG
1 CTCATACCAACTCACAAGATGGAAAGAGGGGAAAAGGGTGAGACATCACATGGACCA-ACAGAAG
11513308 CAATATGGAGTCCCACAACATTATTGTCCATGTTTTTTCCTCATTCTTAGTGTCTTTCGGGTGTA
65 CAATATGGAGTCCCACAACATTATTGTCCATGTTTTTTCCTCATTCTTAGTGTCTTTCGGGTGTA
*
11513373 ATTGAGAAATTAACTACCATAATTATAATGCTTAGGAGAC
130 ATTGAGAAATTAAATACCATAATTATAATGCTTAGGAGAC
11513413 AGTATTACCT
Statistics
Matches: 166, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
174 2 0.01
175 164 0.99
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (175 bp):
CTCATACCAACTCACAAGATGGAAAGAGGGGAAAAGGGTGAGACATCACATGGACCAACAGAAGC
AATATGGAGTCCCACAACATTATTGTCCATGTTTTTTCCTCATTCTTAGTGTCTTTCGGGTGTAA
TTGAGAAATTAAATACCATAATTATAATGCTTAGGAGACTACCTT
Found at i:11515322 original size:2 final size:2
Alignment explanation
Indices: 11515315--11515358 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
11515305 AATCCAAAAG
*
11515315 AT AT AT AT AT AT AT AT AT AT AG 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
11515357 AT
1 AT
11515359 TCTTCTCAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11516643 original size:13 final size:13
Alignment explanation
Indices: 11516625--11516671 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
11516615 TTGATATTAT
11516625 TATAATTATAATA
1 TATAATTATAATA
11516638 TATAATTATTAATA
1 TATAATTA-TAATA
11516652 T-TACATT-TAATTA
1 TATA-ATTATAA-TA
11516665 TATAATT
1 TATAATT
11516672 TTATAATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.10
13 16 0.53
14 11 0.37
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (13 bp):
TATAATTATAATA
Found at i:11516692 original size:28 final size:27
Alignment explanation
Indices: 11516632--11516686 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
11516622 TATTATAATT
*
11516632 ATAA-TATATAATTATTAATATTACAT
1 ATAATTATATAATTATTAATATTACAA
* *
11516658 TTAATTATATAATTTTATAATATTACAA
1 ATAATTATATAATTAT-TAATATTACAA
11516686 A
1 A
11516687 ATATTACATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
26 3 0.13
27 10 0.43
28 10 0.43
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (27 bp):
ATAATTATATAATTATTAATATTACAA
Found at i:11523513 original size:2 final size:2
Alignment explanation
Indices: 11523506--11523535 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11523496 TTACTTATCC
11523506 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
11523536 AAGGTTTCAA
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:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:11527378 original size:24 final size:21
Alignment explanation
Indices: 11527351--11527398 Score: 51
Period size: 22 Copynumber: 2.1 Consensus size: 21
11527341 TTTAACTGTA
*
11527351 ATTTCTTGCCTTTTTTTTTTCTTT
1 ATTTCTTG--TTTTTATTTT-TTT
*
11527375 ATTTTTTGTTTTTATTTTTTT
1 ATTTCTTGTTTTTATTTTTTT
11527396 ATT
1 ATT
11527399 GGTGAAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 6 0.27
22 9 0.41
24 7 0.32
ACGTcount: A:0.08, C:0.08, G:0.04, T:0.79
Consensus pattern (21 bp):
ATTTCTTGTTTTTATTTTTTT
Found at i:11527381 original size:14 final size:13
Alignment explanation
Indices: 11527362--11527395 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
11527352 TTTCTTGCCT
11527362 TTTTTTTTTCTTTA
1 TTTTTTTTT-TTTA
*
11527376 TTTTTTGTTTTTA
1 TTTTTTTTTTTTA
11527389 TTTTTTT
1 TTTTTTT
11527396 ATTGGTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.06, C:0.03, G:0.03, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTTTA
Found at i:11530094 original size:3 final size:3
Alignment explanation
Indices: 11530086--11530230 Score: 103
Period size: 3 Copynumber: 48.3 Consensus size: 3
11530076 TAAAACATGG
* * * * * * * *
11530086 ATT ATT ATT ATT ATT ATT ATG ATC ATC ATC ATC ATC ATC ATT ATC A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
11530133 CTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATCC
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
* * * * * * * * *
11530179 ATC ATC ATC ATT ATT ATA ATA ATA ATA ATT ATT ATA ATT GTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
11530227 ATT A
1 ATT A
11530231 GAGGTATTTT
Statistics
Matches: 125, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
3 123 0.98
4 2 0.02
ACGTcount: A:0.36, C:0.09, G:0.01, T:0.54
Consensus pattern (3 bp):
ATT
Found at i:11540195 original size:27 final size:27
Alignment explanation
Indices: 11540165--11540252 Score: 149
Period size: 27 Copynumber: 3.2 Consensus size: 27
11540155 TCATATGCCC
11540165 ACTCTTCTCATCATAACATATATGAAT
1 ACTCTTCTCATCATAACATATATGAAT
* *
11540192 ACTCTTTTTTATCATAACATATATGAAT
1 ACTC-TTCTCATCATAACATATATGAAT
11540220 ACTCTTCTCATCATAACATATATGAAT
1 ACTCTTCTCATCATAACATATATGAAT
11540247 ACTCTT
1 ACTCTT
11540253 TTTTATCATA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
27 31 0.55
28 25 0.45
ACGTcount: A:0.35, C:0.20, G:0.03, T:0.41
Consensus pattern (27 bp):
ACTCTTCTCATCATAACATATATGAAT
Found at i:11540212 original size:28 final size:28
Alignment explanation
Indices: 11540174--11540263 Score: 155
Period size: 28 Copynumber: 3.2 Consensus size: 28
11540164 CACTCTTCTC
11540174 ATCATAACATATATGAATACTCTTTTTT
1 ATCATAACATATATGAATACTCTTTTTT
* *
11540202 ATCATAACATATATGAATACTC-TTCTC
1 ATCATAACATATATGAATACTCTTTTTT
11540229 ATCATAACATATATGAATACTCTTTTTT
1 ATCATAACATATATGAATACTCTTTTTT
11540257 ATCATAA
1 ATCATAA
11540264 ATCAAACTAT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
27 25 0.44
28 32 0.56
ACGTcount: A:0.38, C:0.17, G:0.03, T:0.42
Consensus pattern (28 bp):
ATCATAACATATATGAATACTCTTTTTT
Found at i:11547037 original size:14 final size:13
Alignment explanation
Indices: 11547009--11547051 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
11546999 AATAAATATT
11547009 AAAAGTGAAAAAA
1 AAAAGTGAAAAAA
*
11547022 AAAGGT-AAACAAA
1 AAAAGTGAAA-AAA
11547035 AAAAGTGAAAAAA
1 AAAAGTGAAAAAA
11547048 AAAA
1 AAAA
11547052 ATTAAAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 3 0.12
13 20 0.77
14 3 0.12
ACGTcount: A:0.77, C:0.02, G:0.14, T:0.07
Consensus pattern (13 bp):
AAAAGTGAAAAAA
Found at i:11547058 original size:13 final size:13
Alignment explanation
Indices: 11547016--11547058 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
11547006 ATTAAAAGTG
*
11547016 AAAAAAAAAGGTA
1 AAAAAAAAAGTTA
*
11547029 AACAAAAAAAGTGA
1 AA-AAAAAAAGTTA
*
11547043 AAAAAAAAAATTA
1 AAAAAAAAAGTTA
11547056 AAA
1 AAA
11547059 TGAGTAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.79, C:0.02, G:0.09, T:0.09
Consensus pattern (13 bp):
AAAAAAAAAGTTA
Found at i:11548348 original size:19 final size:17
Alignment explanation
Indices: 11548309--11548351 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
11548299 TTAAAGGAAG
*
11548309 AAAAAAATTAGAAAAAT
1 AAAAAAATTAGAAAAAC
*
11548326 AAAAAAATTACAGAAAAGC
1 AAAAAAATT--AGAAAAAC
11548345 AAAAAAA
1 AAAAAAA
11548352 ACAAGTCAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 9 0.41
19 13 0.59
ACGTcount: A:0.77, C:0.05, G:0.07, T:0.12
Consensus pattern (17 bp):
AAAAAAATTAGAAAAAC
Found at i:11549198 original size:2 final size:2
Alignment explanation
Indices: 11549191--11549221 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11549181 TCAATTCCTC
11549191 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
11549222 AAGCAACACA
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:11551559 original size:16 final size:16
Alignment explanation
Indices: 11551535--11551589 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
11551525 TTGGAGTGAC
11551535 TTTAAGGTTTGGAGAG
1 TTTAAGGTTTGGAGAG
* *
11551551 TTTAGGGTTT-G-G-T
1 TTTAAGGTTTGGAGAG
*
11551564 TTTAAGGCTTGGAGAG
1 TTTAAGGTTTGGAGAG
*
11551580 TTTAGGGTTT
1 TTTAAGGTTT
11551590 TGATTTTAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 6
0.69 0.17 0.14
Matches are distributed among these distances:
13 8 0.28
14 2 0.07
15 2 0.07
16 17 0.59
ACGTcount: A:0.18, C:0.02, G:0.36, T:0.44
Consensus pattern (16 bp):
TTTAAGGTTTGGAGAG
Found at i:11551577 original size:29 final size:29
Alignment explanation
Indices: 11551535--11551647 Score: 122
Period size: 29 Copynumber: 3.9 Consensus size: 29
11551525 TTGGAGTGAC
* *
11551535 TTTAAGGTTTGGAGAGTTTAGGGTTTGGT
1 TTTAAGGCTTGGAGAGTTTAGGGTTTGAT
11551564 TTTAAGGCTTGGAGAGTTTAGGGTTTTGAT
1 TTTAAGGCTTGGAGAGTTTAGGG-TTTGAT
* * *
11551594 TTTAAGGCTT-GAG-CTTTAATGTTTTGAT
1 TTTAAGGCTTGGAGAGTTT-AGGGTTTGAT
* * *
11551622 TTTAGGGTTTGGAAAGTTTAGGGTTT
1 TTTAAGGCTTGGAGAGTTTAGGGTTT
11551648 TAGTGTTTGG
Statistics
Matches: 69, Mismatches: 11, Indels: 8
0.78 0.12 0.09
Matches are distributed among these distances:
28 17 0.25
29 34 0.49
30 18 0.26
ACGTcount: A:0.19, C:0.03, G:0.32, T:0.46
Consensus pattern (29 bp):
TTTAAGGCTTGGAGAGTTTAGGGTTTGAT
Found at i:11551620 original size:28 final size:30
Alignment explanation
Indices: 11551535--11551648 Score: 99
Period size: 30 Copynumber: 3.9 Consensus size: 30
11551525 TTGGAGTGAC
* * * *
11551535 TTTAAGGTTTGGAGAGTTT-AGGGTTTGGT
1 TTTAAGGCTTGGAGACTTTAAGGTTTTGAT
* *
11551564 TTTAAGGCTTGGAGAGTTTAGGGTTTTGAT
1 TTTAAGGCTTGGAGACTTTAAGGTTTTGAT
*
11551594 TTTAAGGCTT-GAG-CTTTAATGTTTTGAT
1 TTTAAGGCTTGGAGACTTTAAGGTTTTGAT
* * * * *
11551622 TTTAGGGTTTGGAAAGTTTAGGGTTTT
1 TTTAAGGCTTGGAGACTTTAAGGTTTT
11551649 AGTGTTTGGG
Statistics
Matches: 69, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
28 20 0.29
29 23 0.33
30 26 0.38
ACGTcount: A:0.19, C:0.03, G:0.32, T:0.46
Consensus pattern (30 bp):
TTTAAGGCTTGGAGACTTTAAGGTTTTGAT
Found at i:11551947 original size:3 final size:3
Alignment explanation
Indices: 11551939--11551992 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
11551929 AAGTATTTTA
11551939 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
11551987 TAT TAT
1 TAT TAT
11551993 GTAAGGGTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:11553825 original size:37 final size:37
Alignment explanation
Indices: 11553749--11553829 Score: 110
Period size: 37 Copynumber: 2.2 Consensus size: 37
11553739 CAAGTTAAGT
*
11553749 AATAAAGAAAACAATTAGGACAACACCATAAGTCCAAAA
1 AATAAAG-AAACAATTAGGACAACACCACAAGTCC-AAA
**
11553788 AATAAAG-AACAATTAGGACAACACCACAAGTTGAAA
1 AATAAAGAAACAATTAGGACAACACCACAAGTCCAAA
11553824 AATAAA
1 AATAAA
11553830 AAAAAATGAC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
36 9 0.23
37 23 0.59
39 7 0.18
ACGTcount: A:0.59, C:0.16, G:0.11, T:0.14
Consensus pattern (37 bp):
AATAAAGAAACAATTAGGACAACACCACAAGTCCAAA
Found at i:11554035 original size:22 final size:22
Alignment explanation
Indices: 11554007--11554049 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
11553997 ACTGCAAGTC
*
11554007 AAAATTATGCCCAAAGATCTTT
1 AAAATTATACCCAAAGATCTTT
*
11554029 AAAATTATACCCGAAGATCTT
1 AAAATTATACCCAAAGATCTT
11554050 AGAGATTGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (22 bp):
AAAATTATACCCAAAGATCTTT
Found at i:11554224 original size:22 final size:22
Alignment explanation
Indices: 11554197--11554287 Score: 76
Period size: 22 Copynumber: 4.1 Consensus size: 22
11554187 ACTGCAAGTT
11554197 AAAATTATGCCCAGAGGTCTTA
1 AAAATTATGCCCAGAGGTCTTA
* *
11554219 AAAATTATGTCCAGAGCTCTTA
1 AAAATTATGCCCAGAGGTCTTA
* * * *
11554241 GAGATTGTGCCC-GAAGGTTTTA
1 AAAATTATGCCCAG-AGGTCTTA
* * *
11554263 GAGAATTATGCCTAGAAGTCTTA
1 -AAAATTATGCCCAGAGGTCTTA
11554286 AA
1 AA
11554288 GAATCGATCA
Statistics
Matches: 50, Mismatches: 16, Indels: 6
0.69 0.22 0.08
Matches are distributed among these distances:
21 1 0.02
22 35 0.70
23 13 0.26
24 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (22 bp):
AAAATTATGCCCAGAGGTCTTA
Found at i:11554242 original size:190 final size:192
Alignment explanation
Indices: 11553997--11554482 Score: 536
Period size: 190 Copynumber: 2.6 Consensus size: 192
11553987 CCAGGACAGT
* * * * * *
11553997 ACTGCAAGTCAAAATTATGCCCAAAGATCTTTAAAATTATACCCGAAGATCTTAGAGATTGTGCT
1 ACTGCAAGTTAAAATTATGCCCAGAGGTCTTAAAAATTATACCAGAAGATCTTAGAGATTGTGCC
* * *
11554062 AAAAGGTTTTAGAGAATTATGTCAAAAAGTCTTAAAGAATCGA-CTGAGATAATACCGCAATTCA
66 AAAAGGTTTTAGAGAATTATGCCAAAAAGTCTTAAAGAATCGATCAG-GACAATACCGCAATTCA
* * * * **
11554126 AAAAATAAGAAAACGA-TGGGATAACACCATAAGTC-AAAAGTAAAGAATCGATCGGGACAAC
130 AAAAATAAAAAAACGACTGAGACAAAACCATAAGTCAAAAAGTAAAGAATCGATCGAAACAAC
* *
11554187 ACTGCAAGTTAAAATTATGCCCAGAGGTCTTAAAAATTATGTCCAG-AGCTCTTAGAGATTGTGC
1 ACTGCAAGTTAAAATTATGCCCAGAGGTCTTAAAAATTAT-ACCAGAAGATCTTAGAGATTGTGC
** * * *
11554251 CCGAAGGTTTTAGAGAATTATGCCTAGAAGTCTTAAAGAATCGATCAGGACAATACCGTAATTCA
65 CAAAAGGTTTTAGAGAATTATGCCAAAAAGTCTTAAAGAATCGATCAGGACAATACCGCAATTCA
* * * * *
11554316 AAAAATAAAAAAATGACTGAGACAAAATCATGAGTCAAAAAGTAAAGAATCGATTGAAACAAT
130 AAAAATAAAAAAACGACTGAGACAAAACCATAAGTCAAAAAGTAAAGAATCGATCGAAACAAC
* * * * * *
11554379 ACCGCAAGTTAAAATTATGCCTAGAGGTCTT--AGATTATGCTC-GAAGGTCTTGGAGATTGTGC
1 ACTGCAAGTTAAAATTATGCCCAGAGGTCTTAAAAATTATAC-CAGAAGATCTTAGAGATTGTGC
* * ** * * *
11554441 CCAGAGGTCATAGAGAATTATGCCCAAAGGTTTTAAAGAATC
65 CAAAAGGTTTTAGAGAATTATGCCAAAAAGTCTTAAAGAATC
11554483 AACCAAGACA
Statistics
Matches: 249, Mismatches: 41, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
189 2 0.01
190 177 0.71
191 19 0.08
192 51 0.20
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (192 bp):
ACTGCAAGTTAAAATTATGCCCAGAGGTCTTAAAAATTATACCAGAAGATCTTAGAGATTGTGCC
AAAAGGTTTTAGAGAATTATGCCAAAAAGTCTTAAAGAATCGATCAGGACAATACCGCAATTCAA
AAAATAAAAAAACGACTGAGACAAAACCATAAGTCAAAAAGTAAAGAATCGATCGAAACAAC
Found at i:11554417 original size:20 final size:20
Alignment explanation
Indices: 11554392--11554454 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
11554382 GCAAGTTAAA
11554392 ATTATGCCTAGAGGTCTTAG
1 ATTATGCCTAGAGGTCTTAG
*
11554412 ATTATG-CTCGAAGGTCTTGGAG
1 ATTATGCCTAG-AGGTCTT--AG
* * *
11554434 ATTGTGCCCAGAGGTCATAG
1 ATTATGCCTAGAGGTCTTAG
11554454 A
1 A
11554455 GAATTATGCC
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
19 3 0.09
20 16 0.47
22 13 0.38
23 2 0.06
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (20 bp):
ATTATGCCTAGAGGTCTTAG
Found at i:11554471 original size:23 final size:22
Alignment explanation
Indices: 11554410--11554471 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
11554400 TAGAGGTCTT
* * * *
11554410 AGATTATGCTCGAAGGTCTTGG
1 AGATTATGCCCAAAGGTCATAG
* *
11554432 AGATTGTGCCCAGAGGTCATAG
1 AGATTATGCCCAAAGGTCATAG
11554454 AGAATTATGCCCAAAGGT
1 AG-ATTATGCCCAAAGGT
11554472 TTTAAAGAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 18 0.58
23 13 0.42
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (22 bp):
AGATTATGCCCAAAGGTCATAG
Found at i:11554891 original size:41 final size:41
Alignment explanation
Indices: 11554832--11554954 Score: 192
Period size: 41 Copynumber: 3.0 Consensus size: 41
11554822 ACTCTAAATG
* * * * *
11554832 TCTTGTTTGAAAAAGGTTCTTCCTAAACAAAGGCTTTGAAA
1 TCTTGATTGAAAATGGTTCCTCTTAAACAAAAGCTTTGAAA
11554873 TCTTGATTGAAAATGGTTCCTCTTAAACAAAAGCTTTGAAA
1 TCTTGATTGAAAATGGTTCCTCTTAAACAAAAGCTTTGAAA
*
11554914 TCTTGATTGAAAATGGTTCCTCTTAAGCAAAAGCTTTGAAA
1 TCTTGATTGAAAATGGTTCCTCTTAAACAAAAGCTTTGAAA
11554955 CTTTAAAAAC
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 76 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (41 bp):
TCTTGATTGAAAATGGTTCCTCTTAAACAAAAGCTTTGAAA
Found at i:11555829 original size:9 final size:8
Alignment explanation
Indices: 11555805--11555842 Score: 60
Period size: 8 Copynumber: 4.8 Consensus size: 8
11555795 AAAGAAATCC
11555805 TTTTA-TT
1 TTTTATTT
11555812 TTTTATTT
1 TTTTATTT
11555820 TTTTATTT
1 TTTTATTT
11555828 TTTTACTTT
1 TTTTA-TTT
11555837 TTTTAT
1 TTTTAT
11555843 GCCCTATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 5 0.17
8 16 0.55
9 8 0.28
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTATTT
Found at i:11555837 original size:17 final size:16
Alignment explanation
Indices: 11555805--11555842 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
11555795 AAAGAAATCC
11555805 TTTTA-TTTTTTATTT
1 TTTTATTTTTTTATTT
11555820 TTTTATTTTTTTACTTT
1 TTTTATTTTTTTA-TTT
11555837 TTTTAT
1 TTTTAT
11555843 GCCCTATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.24
16 7 0.33
17 9 0.43
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTATTTTTTTATTT
Found at i:11560580 original size:17 final size:19
Alignment explanation
Indices: 11560559--11560603 Score: 67
Period size: 17 Copynumber: 2.5 Consensus size: 19
11560549 TTTTTGAAAA
11560559 CTTTTTTTGTTTTTTG-TT
1 CTTTTTTTGTTTTTTGCTT
*
11560577 -TTTTTTTTTTTTTTGCTT
1 CTTTTTTTGTTTTTTGCTT
11560595 CTTTTTTTG
1 CTTTTTTTG
11560604 CTTGTTAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 14 0.61
18 2 0.09
19 7 0.30
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (19 bp):
CTTTTTTTGTTTTTTGCTT
Found at i:11562350 original size:14 final size:14
Alignment explanation
Indices: 11562331--11562443 Score: 61
Period size: 14 Copynumber: 7.8 Consensus size: 14
11562321 GTTTGGAAGG
11562331 TTTAGGGTTTTGAT
1 TTTAGGGTTTTGAT
11562345 TTTAGGGTTTTAAGGA-
1 TTTAGGGTTTT---GAT
*
11562361 TTTAGAGTTTGTG-T
1 TTTAGGGTTT-TGAT
* * *
11562375 TTTAAGGTTTGGAGAG
1 TTTAGGGTTT--TGAT
** *
11562391 TTTAAAGTTTCGAT
1 TTTAGGGTTTTGAT
*
11562405 TTTAGGG-TTTGAGG
1 TTTAGGGTTTTGA-T
11562419 TTTAGGGTTTTGAT
1 TTTAGGGTTTTGAT
*
11562433 TTTAGGATTTT
1 TTTAGGGTTTT
11562444 AAAGGTTTAG
Statistics
Matches: 76, Mismatches: 14, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
13 4 0.05
14 44 0.58
15 7 0.09
16 18 0.24
17 3 0.04
ACGTcount: A:0.19, C:0.01, G:0.29, T:0.50
Consensus pattern (14 bp):
TTTAGGGTTTTGAT
Found at i:11562365 original size:30 final size:29
Alignment explanation
Indices: 11562327--11562459 Score: 135
Period size: 30 Copynumber: 4.5 Consensus size: 29
11562317 TAAGGTTTGG
11562327 AAGGTTTAGGGTTTTGATTTTAGGGTTTT
1 AAGGTTTAGGGTTTTGATTTTAGGGTTTT
* * *
11562356 AAGGATTTAGAGTTTGTG-TTTTAAGGTTTG
1 AAGG-TTTAGGGTTT-TGATTTTAGGGTTTT
* ** *
11562386 GAGAGTTTAAAGTTTCGATTTTAGGG-TTT
1 AAG-GTTTAGGGTTTTGATTTTAGGGTTTT
* *
11562415 GAGGTTTAGGGTTTTGATTTTAGGATTTT
1 AAGGTTTAGGGTTTTGATTTTAGGGTTTT
11562444 AAAGGTTTAGGGTTTT
1 -AAGGTTTAGGGTTTT
11562460 AGTGTTTGTG
Statistics
Matches: 85, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
28 18 0.21
29 13 0.15
30 51 0.60
31 3 0.04
ACGTcount: A:0.21, C:0.01, G:0.30, T:0.48
Consensus pattern (29 bp):
AAGGTTTAGGGTTTTGATTTTAGGGTTTT
Found at i:11570624 original size:19 final size:19
Alignment explanation
Indices: 11570569--11570627 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
11570559 TATTCGATAT
*
11570569 TTAAATTATCAATATATAA
1 TTAAATTATAAATATATAA
* ** *
11570588 TTTTAATT-TACTTTTATAA
1 -TTAAATTATAAATATATAA
11570607 TTAAATTATAAATATATAA
1 TTAAATTATAAATATATAA
11570626 TT
1 TT
11570628 TTATTTTACT
Statistics
Matches: 29, Mismatches: 9, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
18 6 0.21
19 17 0.59
20 6 0.21
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAATTATAAATATATAA
Found at i:11578557 original size:20 final size:20
Alignment explanation
Indices: 11578532--11578569 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11578522 TAATACAGAT
**
11578532 ATATATTTTTAATTTTTTTC
1 ATATATTTGAAATTTTTTTC
11578552 ATATATTTGAAATTTTTT
1 ATATATTTGAAATTTTTT
11578570 AATTTGCATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (20 bp):
ATATATTTGAAATTTTTTTC
Found at i:11579472 original size:27 final size:25
Alignment explanation
Indices: 11579413--11579472 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 25
11579403 ATAATTTATT
**
11579413 ATATTATTTTTTTATTATAATTTTTG
1 ATATT-TTTTTTTATTATAATTTTAC
11579439 ATAATTTTATTTTTATTATAATATTTAC
1 AT-ATTTT-TTTTTATTATAAT-TTTAC
11579467 ATATTT
1 ATATTT
11579473 ATGTTAACGC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 4 0.14
27 20 0.69
28 5 0.17
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (25 bp):
ATATTTTTTTTTATTATAATTTTAC
Found at i:11581087 original size:17 final size:18
Alignment explanation
Indices: 11581055--11581088 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11581045 ATATTTTATT
11581055 AATTAAAATAATAAAAAA
1 AATTAAAATAATAAAAAA
*
11581073 AATTTAAAT-ATAAAAA
1 AATTAAAATAATAAAAA
11581089 TTTGATTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AATTAAAATAATAAAAAA
Found at i:11581340 original size:14 final size:14
Alignment explanation
Indices: 11581321--11581376 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
11581311 GCGTAAGTTT
11581321 TTTTTTTATTTTGA
1 TTTTTTTATTTTGA
**
11581335 TTTTTTGGGTTTT-A
1 TTTTTT-TATTTTGA
*
11581349 TTTTAGATTATTTTGA
1 TTTT--TTTATTTTGA
11581365 TTTTTTTATTTT
1 TTTTTTTATTTT
11581377 TCTATTTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
14 18 0.56
15 8 0.25
16 6 0.19
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.75
Consensus pattern (14 bp):
TTTTTTTATTTTGA
Found at i:11581349 original size:20 final size:22
Alignment explanation
Indices: 11581324--11581363 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
11581314 TAAGTTTTTT
11581324 TTTTATTTT-GATT-TTTTGGG
1 TTTTATTTTAGATTATTTTGGG
11581344 TTTTATTTTAGATTATTTTG
1 TTTTATTTTAGATTATTTTG
11581364 ATTTTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 4 0.22
22 5 0.28
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (22 bp):
TTTTATTTTAGATTATTTTGGG
Found at i:11581368 original size:21 final size:20
Alignment explanation
Indices: 11581324--11581368 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
11581314 TAAGTTTTTT
*
11581324 TTTTATTTTGATTTTTTGGG
1 TTTTATTTTGATTTTTTGGA
11581344 TTTTATTTTAGATTATTTT-GA
1 TTTTATTTT-GATT-TTTTGGA
11581365 TTTT
1 TTTT
11581369 TTTATTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
21 9 0.41
22 4 0.18
ACGTcount: A:0.16, C:0.00, G:0.13, T:0.71
Consensus pattern (20 bp):
TTTTATTTTGATTTTTTGGA
Found at i:11581382 original size:22 final size:21
Alignment explanation
Indices: 11581357--11581397 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
11581347 TATTTTAGAT
*
11581357 TATTTTGATTTTTTTATTTTTC
1 TATTTTGA-TTTATTATTTTTC
*
11581379 TATTTTTATTTATTATTTT
1 TATTTTGATTTATTATTTT
11581398 AATTGAGCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.78
Consensus pattern (21 bp):
TATTTTGATTTATTATTTTTC
Found at i:11581586 original size:34 final size:35
Alignment explanation
Indices: 11581548--11581629 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 35
11581538 TAGTATCTAT
* *
11581548 TTGCATGATAATTTTTATATGATATAAT-ATATTA
1 TTGCATGATAATTTTTACATGACATAATAATATTA
* **
11581582 TTGCATGAT-ATTATTACATGACATTTTAATATTA
1 TTGCATGATAATTTTTACATGACATAATAATATTA
*
11581616 TTGTATGATAATTT
1 TTGCATGATAATTT
11581630 ATATTAATAG
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
33 13 0.33
34 23 0.59
35 3 0.08
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (35 bp):
TTGCATGATAATTTTTACATGACATAATAATATTA
Found at i:11581630 original size:21 final size:21
Alignment explanation
Indices: 11581610--11581656 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
11581600 TGACATTTTA
*
11581610 ATATT-ATTGTATGATAATTT
1 ATATTAATAGTATGATAATTT
*
11581630 ATATTAATAGTATGATTATATT
1 ATATTAATAGTATGATAAT-TT
11581652 ATATT
1 ATATT
11581657 TGCATGATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 11 0.48
22 7 0.30
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (21 bp):
ATATTAATAGTATGATAATTT
Found at i:11589495 original size:174 final size:174
Alignment explanation
Indices: 11589199--11589525 Score: 457
Period size: 174 Copynumber: 1.9 Consensus size: 174
11589189 GCAACCAGGA
* *
11589199 TTCAGATTGCATGGAAGAATTTTGTTTGCAGATCTCTACGCAAACAAACTTATGCTGCAACTAAA
1 TTCAGATTGCATGGAAGAATTTTGTCTGCAGATCTCTACGCAAACAAACTTATGCTGCAACCAAA
11589264 ATTCAGAGCCATTATCGCAGTTGGCAGTTAAGAAGGAGTTTTATGAAACAAAAGCAAGCAATAAC
66 ATTCAGAGCCATTATCGCAGTTGGCAGTTAAGAAGGAGTTTTATGAAACAAAAGCAAGCAATAAC
11589329 AAAAATTCAAAGTAATTTTCGACAACTGAAATGTTGGAGAGCCT
131 AAAAATTCAAAGTAATTTTCGACAACTGAAATGTTGGAGAGCCT
* * *
11589373 TTCAGATTGCTTGGAAGGAA-TTTGTCTGTAGATCTCT-C-CAAAATCAGACATT-TGCTGCAAC
1 TTCAGATTGCATGGAA-GAATTTTGTCTGCAGATCTCTACGC-AAA-CAAAC-TTATGCTGCAAC
* ** * * * *
11589434 CAAAATTCAGAGTCATT-TCCGTTGTTGGCAGTTCAGGAGGAGTTTTATGAAGCAGAAGCAAGCA
62 CAAAATTCAGAGCCATTAT-CGCAGTTGGCAGTTAAGAAGGAGTTTTATGAAACAAAAGCAAGCA
*
11589498 ATAATAAAAATTCAAAGTAATTTTCGAC
126 ATAACAAAAATTCAAAGTAATTTTCGAC
11589526 GGCTAAAATG
Statistics
Matches: 135, Mismatches: 13, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
172 1 0.01
173 5 0.04
174 124 0.92
175 5 0.04
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (174 bp):
TTCAGATTGCATGGAAGAATTTTGTCTGCAGATCTCTACGCAAACAAACTTATGCTGCAACCAAA
ATTCAGAGCCATTATCGCAGTTGGCAGTTAAGAAGGAGTTTTATGAAACAAAAGCAAGCAATAAC
AAAAATTCAAAGTAATTTTCGACAACTGAAATGTTGGAGAGCCT
Found at i:11592308 original size:21 final size:23
Alignment explanation
Indices: 11592242--11592306 Score: 82
Period size: 21 Copynumber: 2.9 Consensus size: 23
11592232 ACTTTCTCAG
11592242 CAGGTTCCTGTAATCCTCTTATA
1 CAGGTTCCTGTAATCCTCTTATA
* *
11592265 CAGAATT--TG-GATCCTCTTATA
1 CAG-GTTCCTGTAATCCTCTTATA
11592286 CAGGTTCCTGTAATCCTCTTA
1 CAGGTTCCTGTAATCCTCTTA
11592307 CATAAACCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 2 0.06
21 14 0.41
22 4 0.12
23 12 0.35
24 2 0.06
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (23 bp):
CAGGTTCCTGTAATCCTCTTATA
Found at i:11593163 original size:14 final size:14
Alignment explanation
Indices: 11593144--11593172 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
11593134 AAATGTAATT
11593144 TAAATTTTAAAAAA
1 TAAATTTTAAAAAA
11593158 TAAATTTTAAAAAA
1 TAAATTTTAAAAAA
11593172 T
1 T
11593173 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAATTTTAAAAAA
Found at i:11608100 original size:20 final size:20
Alignment explanation
Indices: 11608068--11608106 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
11608058 TTTCATCACC
11608068 AAAAAAAAAAAGAA-AAAAG
1 AAAAAAAAAAAGAACAAAAG
*
11608087 AAAATAAAAGAAGAACAAAA
1 AAAA-AAAAAAAGAACAAAA
11608107 TCACGAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 9 0.53
21 4 0.24
ACGTcount: A:0.85, C:0.03, G:0.10, T:0.03
Consensus pattern (20 bp):
AAAAAAAAAAAGAACAAAAG
Found at i:11620863 original size:19 final size:19
Alignment explanation
Indices: 11620839--11620880 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
11620829 CAATGGTCAG
11620839 TATGGCAATTAGTGTCTAC
1 TATGGCAATTAGTGTCTAC
*
11620858 TATGGCAGTTAGTGTCTAC
1 TATGGCAATTAGTGTCTAC
11620877 TATG
1 TATG
11620881 TATATTCACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (19 bp):
TATGGCAATTAGTGTCTAC
Found at i:11624138 original size:30 final size:30
Alignment explanation
Indices: 11624080--11624163 Score: 109
Period size: 30 Copynumber: 2.8 Consensus size: 30
11624070 TCACTTTATT
* *
11624080 TAAATAGGTTTTTATA-TTTTTA-TTACATC
1 TAAATAAGTTTTTA-ACTTTTAATTTACATC
11624109 TAAATAAGTTTTTAACTTTTAATTTACATC
1 TAAATAAGTTTTTAACTTTTAATTTACATC
* *
11624139 TAAATAAATTCTTAACTTTTAATTT
1 TAAATAAGTTTTTAACTTTTAATTT
11624164 GTATTTAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
28 1 0.02
29 18 0.37
30 30 0.61
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.52
Consensus pattern (30 bp):
TAAATAAGTTTTTAACTTTTAATTTACATC
Found at i:11624173 original size:30 final size:30
Alignment explanation
Indices: 11624106--11624207 Score: 118
Period size: 30 Copynumber: 3.4 Consensus size: 30
11624096 TTTTTATTAC
* * **
11624106 ATCTAAATAAGTTTTTAACTTTTAATTTAC
1 ATCTAAATAAATTCTTAACTTTTAATTTGT
11624136 ATCTAAATAAATTCTTAACTTTTAATTTGT
1 ATCTAAATAAATTCTTAACTTTTAATTTGT
*
11624166 ATTTAAATAAA-TCTTAA-TAATTTAATTTGT
1 ATCTAAATAAATTCTTAACT--TTTAATTTGT
*
11624196 ACCTAAATAAAT
1 ATCTAAATAAAT
11624208 CCAAAAATAA
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
28 1 0.02
29 6 0.10
30 55 0.89
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (30 bp):
ATCTAAATAAATTCTTAACTTTTAATTTGT
Found at i:11626776 original size:27 final size:26
Alignment explanation
Indices: 11626737--11626791 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
11626727 TTAGATTAAT
*
11626737 TATAATTAATATAGT-TTTATTAAAAA
1 TATAATTAATATA-TATTTATAAAAAA
11626763 TATATATTAATATATATTTATAAAAAA
1 TATA-ATTAATATATATTTATAAAAAA
11626790 TA
1 TA
11626792 CTTAAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (26 bp):
TATAATTAATATATATTTATAAAAAA
Found at i:11633549 original size:42 final size:44
Alignment explanation
Indices: 11633476--11633584 Score: 116
Period size: 42 Copynumber: 2.4 Consensus size: 44
11633466 AAAAATATTT
* * *
11633476 TTATTATTTATTTAATTTTATATTTATATATTATATTAATAAAA
1 TTATTATTTATATAATTTTATATTTAAATATTAAATTAATAAAA
11633520 TTATTATTTA-AT-ATTTTA-ATTTAAAATATTAAATTAATAAAA
1 TTATTATTTATATAATTTTATATTT-AAATATTAAATTAATAAAA
*
11633562 ATACTATATTTATGATTAATTTT
1 TTA-T-TATTTAT-A-TAATTTT
11633585 CTGATGTTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
41 4 0.07
42 25 0.46
43 2 0.04
44 16 0.30
46 1 0.02
47 1 0.02
48 5 0.09
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (44 bp):
TTATTATTTATATAATTTTATATTTAAATATTAAATTAATAAAA
Found at i:11633806 original size:16 final size:16
Alignment explanation
Indices: 11633785--11633825 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
11633775 TGTCAGCAGT
* *
11633785 TTTTTTTTTTTTTAAG
1 TTTTTTTATTTTTAAC
*
11633801 TTTTTTAATTTTTAAC
1 TTTTTTTATTTTTAAC
11633817 TTTTTTTAT
1 TTTTTTTAT
11633826 GTAAAATGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.78
Consensus pattern (16 bp):
TTTTTTTATTTTTAAC
Found at i:11635750 original size:29 final size:31
Alignment explanation
Indices: 11635718--11635798 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 31
11635708 ATAATTTATT
*
11635718 TTATATTTATATATATTATTTTAAT-AAA-A
1 TTATATTTATATATATTAATTTAATAAAATA
*
11635747 TTATTATTTA-ATATCTTAATTTAATAAAAATA
1 TTA-TATTTATATATATTAATTTAAT-AAAATA
*
11635779 TTATATTTATACATAATTAA
1 TTATATTTATATAT-ATTAA
11635799 AATGTAATCC
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
29 16 0.38
30 6 0.14
31 9 0.21
32 7 0.17
33 4 0.10
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (31 bp):
TTATATTTATATATATTAATTTAATAAAATA
Found at i:11636169 original size:21 final size:21
Alignment explanation
Indices: 11636124--11636164 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
11636114 AATAGCAATC
11636124 AATTTTTTTTTGTTATTTTAA
1 AATTTTTTTTTGTTATTTTAA
11636145 AATTTATTTATTT-TTATTTT
1 AATTT-TTT-TTTGTTATTTT
11636165 TAATTAGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 10 0.56
23 3 0.17
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (21 bp):
AATTTTTTTTTGTTATTTTAA
Found at i:11640060 original size:19 final size:20
Alignment explanation
Indices: 11640036--11640083 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
11640026 TTTTTTATTG
11640036 AAAATTAATATAT-ATCTAT-
1 AAAATTAATAT-TCATCTATA
*
11640055 AAAATTAATATTCATTTATA
1 AAAATTAATATTCATCTATA
11640075 AAAATTAAT
1 AAAATTAAT
11640084 TAAAACAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 1 0.04
19 16 0.62
20 9 0.35
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAATTAATATTCATCTATA
Found at i:11641028 original size:21 final size:21
Alignment explanation
Indices: 11641004--11641062 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
11640994 ATAAATACTA
11641004 ATAATTTAATTTTGATTTGAT
1 ATAATTTAATTTTGATTTGAT
* * ***
11641025 ATAATATAAGTAAAATTTGAT
1 ATAATTTAATTTTGATTTGAT
*
11641046 ATAATTTTGATTTTGAT
1 ATAA-TTTAATTTTGAT
11641063 AATCTTTTAT
Statistics
Matches: 26, Mismatches: 11, Indels: 1
0.68 0.29 0.03
Matches are distributed among these distances:
21 20 0.77
22 6 0.23
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (21 bp):
ATAATTTAATTTTGATTTGAT
Found at i:11641116 original size:21 final size:21
Alignment explanation
Indices: 11641077--11641131 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
11641067 TTTTATATGT
* **
11641077 TTTGATAACCTTTGTTAAAAG
1 TTTGATAACTTTTAATAAAAG
*
11641098 TTTGATAACTTTTAATAAAAT
1 TTTGATAACTTTTAATAAAAG
*
11641119 TTTGGTAACTTTT
1 TTTGATAACTTTT
11641132 GGTACAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.49
Consensus pattern (21 bp):
TTTGATAACTTTTAATAAAAG
Found at i:11641140 original size:21 final size:21
Alignment explanation
Indices: 11641092--11641154 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
11641082 TAACCTTTGT
* *
11641092 TAAAAGTTTGATAACTTTTAA
1 TAAAATTTTGGTAACTTTTAA
**
11641113 TAAAATTTTGGTAACTTTTGG
1 TAAAATTTTGGTAACTTTTAA
*
11641134 TACAATTTTGGTAATCTTTTA
1 TAAAATTTTGGTAA-CTTTTA
11641155 TGTTAGTTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 30 0.86
22 5 0.14
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.48
Consensus pattern (21 bp):
TAAAATTTTGGTAACTTTTAA
Found at i:11641220 original size:21 final size:21
Alignment explanation
Indices: 11641176--11641269 Score: 68
Period size: 21 Copynumber: 4.6 Consensus size: 21
11641166 TAACTAATTA
** *
11641176 TGATATAATTTTTGTAACCAT
1 TGATATAATTTTAATAACCTT
*
11641197 TGATATAATTTTAATAATCTT
1 TGATATAATTTTAATAACCTT
* * * *
11641218 TGATA-AA-ATT-GTAGCTTCT
1 TGATATAATTTTAATAACCT-T
*
11641237 TGATGTAATTTTAATAACCTT
1 TGATATAATTTTAATAACCTT
*
11641258 TCATATAATTTT
1 TGATATAATTTT
11641270 GGTAATTTAT
Statistics
Matches: 53, Mismatches: 16, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
18 3 0.06
19 7 0.13
20 4 0.08
21 35 0.66
22 4 0.08
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.49
Consensus pattern (21 bp):
TGATATAATTTTAATAACCTT
Found at i:11641613 original size:22 final size:22
Alignment explanation
Indices: 11641574--11641700 Score: 98
Period size: 22 Copynumber: 5.8 Consensus size: 22
11641564 GACAATTAAG
* * *
11641574 TTATCATTTATTTTCTACTATA
1 TTATCAATGATTTACTACTATA
*
11641596 TTATCAATGATCTACTACTATGA
1 TTATCAATGATTTACTACTAT-A
* *
11641619 -TATCAATGATTTACT-TTTTAA
1 TTATCAATGATTTACTACTAT-A
*
11641640 TTATCATTGATTTACTACTA-A
1 TTATCAATGATTTACTACTATA
* * *
11641661 TTTATAAATGATTTACCACTAAA
1 -TTATCAATGATTTACTACTATA
**
11641684 TTATTGATGATTTACTA
1 TTATCAATGATTTACTA
11641701 TTAAGTTACT
Statistics
Matches: 83, Mismatches: 17, Indels: 10
0.75 0.15 0.09
Matches are distributed among these distances:
21 4 0.05
22 76 0.92
23 3 0.04
ACGTcount: A:0.34, C:0.13, G:0.06, T:0.48
Consensus pattern (22 bp):
TTATCAATGATTTACTACTATA
Found at i:11641713 original size:22 final size:22
Alignment explanation
Indices: 11641668--11641719 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
11641658 TAATTTATAA
*
11641668 ATGATTTACCACTAAATTATTG
1 ATGATTTACCACTAAATTACTG
* * *
11641690 ATGATTTACTATTAAGTTACTG
1 ATGATTTACCACTAAATTACTG
*
11641712 ATAATTTA
1 ATGATTTA
11641720 TTATAAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.44
Consensus pattern (22 bp):
ATGATTTACCACTAAATTACTG
Found at i:11641768 original size:21 final size:20
Alignment explanation
Indices: 11641710--11641768 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
11641700 ATTAAGTTAC
*
11641710 TGATAATTTATTATAAATTA
1 TGATAATTTATTATAATTTA
* *
11641730 TAATTGATTT-TTATTAATTTA
1 TGA-TAATTTATTA-TAATTTA
11641751 TCGATAATTTATTATAAT
1 T-GATAATTTATTATAAT
11641769 ATAAATAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
20 5 0.17
21 21 0.70
22 4 0.13
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (20 bp):
TGATAATTTATTATAATTTA
Found at i:11642526 original size:14 final size:15
Alignment explanation
Indices: 11642509--11642537 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11642499 TTAGCAAATC
11642509 AATT-AAAACAAAAA
1 AATTAAAAACAAAAA
11642523 AATTAAAAACAAAAA
1 AATTAAAAACAAAAA
11642538 GAGAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (15 bp):
AATTAAAAACAAAAA
Found at i:11643342 original size:13 final size:13
Alignment explanation
Indices: 11643324--11643348 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11643314 AAATATGAGT
11643324 ATTTTAATTTTTA
1 ATTTTAATTTTTA
11643337 ATTTTAATTTTT
1 ATTTTAATTTTT
11643349 TTATGTATGT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTAATTTTTA
Found at i:11643491 original size:28 final size:28
Alignment explanation
Indices: 11643437--11643491 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
11643427 ATGGTTTTAA
* *
11643437 TTTTATAGTATTTGTAATTGTTGAATTC
1 TTTTATAATATTTGTAATTGTTAAATTC
* *
11643465 TTTTATAATTTTTGTAATTTTTAAATT
1 TTTTATAATATTTGTAATTGTTAAATT
11643492 TGGAAGAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.62
Consensus pattern (28 bp):
TTTTATAATATTTGTAATTGTTAAATTC
Found at i:11649067 original size:3 final size:3
Alignment explanation
Indices: 11649061--11649091 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
11649051 GTTGTTGTTG
11649061 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
11649092 CATAATCATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:11650048 original size:19 final size:19
Alignment explanation
Indices: 11650020--11650073 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
11650010 TGTTTGTAAG
*
11650020 TTTTTCTTTTTTTATTTTA
1 TTTTTATTTTTTTATTTTA
*
11650039 TTTTTATTTTTTGATTTTA
1 TTTTTATTTTTTTATTTTA
11650058 --TTTATTTTTGTTATTT
1 TTTTTATTTTT-TTATTT
11650074 GTTTAAGATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 9 0.29
18 5 0.16
19 17 0.55
ACGTcount: A:0.13, C:0.02, G:0.04, T:0.81
Consensus pattern (19 bp):
TTTTTATTTTTTTATTTTA
Found at i:11650074 original size:23 final size:24
Alignment explanation
Indices: 11650029--11650074 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
11650019 GTTTTTCTTT
*
11650029 TTTTATTTTATTTTTATTTTTTGA
1 TTTTATTTTATTTTTATTATTTGA
*
11650053 TTTTA-TTTATTTTTGTTATTTG
1 TTTTATTTTATTTTTATTATTTG
11650075 TTTAAGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (24 bp):
TTTTATTTTATTTTTATTATTTGA
Found at i:11650337 original size:20 final size:22
Alignment explanation
Indices: 11650301--11650346 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
11650291 TTTTACTCAA
11650301 AAATAAAAGTAAAAAAAAAGAT
1 AAATAAAAGTAAAAAAAAAGAT
*
11650323 AAATAAAA-T-AAAAAAATGAT
1 AAATAAAAGTAAAAAAAAAGAT
11650343 AAAT
1 AAAT
11650347 TATTTAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.61
21 1 0.04
22 8 0.35
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (22 bp):
AAATAAAAGTAAAAAAAAAGAT
Found at i:11662634 original size:40 final size:40
Alignment explanation
Indices: 11662585--11662791 Score: 169
Period size: 40 Copynumber: 5.3 Consensus size: 40
11662575 GAATTTAAAG
* * * *
11662585 TAAAGTTTCATTACCTCTGATCATATAAGCCTTTTAAATT
1 TAAAGTTTCATTACCTCTGGTCAGAGAAGCCTTTTGAATT
* * *
11662625 TAAAGTTTCATTATCTTTGGTCAAAGAAGCC------ATT
1 TAAAGTTTCATTACCTCTGGTCAGAGAAGCCTTTTGAATT
* *
11662659 TAAAGTTTTA-TAGCCTCTGGTCAGAGAAACCTTTTTGAATT
1 TAAAGTTTCATTA-CCTCTGGTCAGAGAAGCC-TTTTGAATT
* * * *
11662700 TAAAGTTTCATTGCCTCTAGTTAGAGAAGCTTTTTGAATT
1 TAAAGTTTCATTACCTCTGGTCAGAGAAGCCTTTTGAATT
* * * * *
11662740 TAAAGTTTCATTGCCTCTGGTTAGATG-GGCTTTTTTAATT
1 TAAAGTTTCATTACCTCTGGTCAGA-GAAGCCTTTTGAATT
11662780 TAAAGTTTCATT
1 TAAAGTTTCATT
11662792 GTCTTTAGTC
Statistics
Matches: 138, Mismatches: 19, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
33 2 0.01
34 26 0.19
40 82 0.59
41 27 0.20
42 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.43
Consensus pattern (40 bp):
TAAAGTTTCATTACCTCTGGTCAGAGAAGCCTTTTGAATT
Found at i:11662716 original size:41 final size:40
Alignment explanation
Indices: 11662656--11662792 Score: 186
Period size: 40 Copynumber: 3.4 Consensus size: 40
11662646 CAAAGAAGCC
* * * *
11662656 ATTTAAAGTTTTATAGCCTCTGGTCAGAGAAACCTTTTTGA
1 ATTTAAAGTTTCATTGCCTCTGGTTAGAG-AAGCTTTTTGA
*
11662697 ATTTAAAGTTTCATTGCCTCTAGTTAGAGAAGCTTTTTGA
1 ATTTAAAGTTTCATTGCCTCTGGTTAGAGAAGCTTTTTGA
* *
11662737 ATTTAAAGTTTCATTGCCTCTGGTTAGATG-GGCTTTTTTA
1 ATTTAAAGTTTCATTGCCTCTGGTTAGA-GAAGCTTTTTGA
11662777 ATTTAAAGTTTCATTG
1 ATTTAAAGTTTCATTG
11662793 TCTTTAGTCA
Statistics
Matches: 87, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
40 61 0.70
41 26 0.30
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.44
Consensus pattern (40 bp):
ATTTAAAGTTTCATTGCCTCTGGTTAGAGAAGCTTTTTGA
Found at i:11662820 original size:34 final size:33
Alignment explanation
Indices: 11662777--11662903 Score: 101
Period size: 34 Copynumber: 3.6 Consensus size: 33
11662767 GGCTTTTTTA
*
11662777 ATTTAAAGTTTCATTGTCTTTAGTCAAAAGAGTC
1 ATTTAAAGTTTCATTGCCTTTA-TCAAAAGAGTC
** * *
11662811 ATTTAAAGTTTTGTTGCCTCTTATCAGAGGAGTC
1 ATTTAAAGTTTCATTGCCT-TTATCAAAAGAGTC
**
11662845 TTTTAAATTTAAAGTTTCATTGCCTTTAATCAAAAGAACC
1 ------ATTTAAAGTTTCATTGCCTTT-ATCAAAAGAGTC
*
11662885 ATTTAAAGTTTCATAGCCT
1 ATTTAAAGTTTCATTGCCT
11662904 CTAATCAGAG
Statistics
Matches: 73, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
34 43 0.59
35 3 0.04
39 2 0.03
40 25 0.34
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.41
Consensus pattern (33 bp):
ATTTAAAGTTTCATTGCCTTTATCAAAAGAGTC
Found at i:11662854 original size:74 final size:74
Alignment explanation
Indices: 11662585--11662927 Score: 257
Period size: 74 Copynumber: 4.5 Consensus size: 74
11662575 GAATTTAAAG
* ** ** *
11662585 TAAAGTTTCATTA-CCTCTGATCATATAAGCCTTTTAAATTTAAAGTTTCATTATCTTTGGTC-A
1 TAAAGTTTCA-TAGCCTCTGATCAGAGGAG-CTTTTAAATTTAAAGTTTCATTGCCTTTAGTCAA
*
11662648 AAGAAGCCATT
64 AAGTAGCCATT
* * * * * * *
11662659 TAAAGTTTTATAGCCTCTGGTCAGAGAAACCTTTTTGAATTTAAAGTTTCATTGCCTCTAGTTAG
1 TAAAGTTTCATAGCCTCTGATCAGAG-GAGC-TTTTAAATTTAAAGTTTCATTGCCTTTAGTCA-
* *
11662724 AGAAGCTTTTTG-AATT
63 A-AAG----TAGCCATT
* * * * *
11662740 TAAAGTTTCATTGCCTCTGGTTAGATGG-GCTTTTTTAATTTAAAGTTTCATTGTCTTTAGTCAA
1 TAAAGTTTCATAGCCTCTGATCAGA-GGAGC-TTTTAAATTTAAAGTTTCATTGCCTTTAGTCAA
*
11662804 AAG-AGTCATT
64 AAGTAGCCATT
** * * *
11662814 TAAAGTTTTGTTGCCTCTTATCAGAGGAGTCTTTTAAATTTAAAGTTTCATTGCCTTTAATCAAA
1 TAAAGTTTCATAGCCTCTGATCAGAGGAG-CTTTTAAATTTAAAGTTTCATTGCCTTTAGTCAAA
*
11662879 AG-AACCATT
65 AGTAGCCATT
* *
11662888 TAAAGTTTCATAGCCTCTAATCAGAGGAGCTTTTTAATTT
1 TAAAGTTTCATAGCCTCTGATCAGAGGAGCTTTTAAATTT
11662928 TAAGAACTTC
Statistics
Matches: 215, Mismatches: 40, Indels: 29
0.76 0.14 0.10
Matches are distributed among these distances:
73 15 0.07
74 107 0.50
75 28 0.13
77 1 0.00
78 6 0.03
79 1 0.00
80 30 0.14
81 25 0.12
82 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.41
Consensus pattern (74 bp):
TAAAGTTTCATAGCCTCTGATCAGAGGAGCTTTTAAATTTAAAGTTTCATTGCCTTTAGTCAAAA
GTAGCCATT
Found at i:11662930 original size:40 final size:39
Alignment explanation
Indices: 11662656--11662927 Score: 172
Period size: 40 Copynumber: 7.1 Consensus size: 39
11662646 CAAAGAAGCC
* * * * *
11662656 ATTTAAAGTTTTATAGCCTCTGGTCAGAGAAACCTTTTTGA
1 ATTTAAAGTTTCATTGCCTCTAGTCAGAG-GAGCTTTTT-A
* *
11662697 ATTTAAAGTTTCATTGCCTCTAGTTAGAGAAGCTTTTTGA
1 ATTTAAAGTTTCATTGCCTCTAGTCAGAGGAGCTTTTT-A
* *
11662737 ATTTAAAGTTTCATTGCCTCTGGTTAGATGG-GCTTTTTTA
1 ATTTAAAGTTTCATTGCCTCTAGTCAGA-GGAGC-TTTTTA
* * * * *
11662777 ATTTAAAGTTTCATTGTCTTTAGTCAAAAGAG-----TC
1 ATTTAAAGTTTCATTGCCTCTAGTCAGAGGAGCTTTTTA
** *
11662811 ATTTAAAGTTTTGTTGCCTCTTA-TCAGAGGAGTCTTTTAA
1 ATTTAAAGTTTCATTGCCTC-TAGTCAGAGGAG-CTTTTTA
* * * * * *
11662851 ATTTAAAGTTTCATTGCCTTTAATCAAAAGAAC-----C
1 ATTTAAAGTTTCATTGCCTCTAGTCAGAGGAGCTTTTTA
* *
11662885 ATTTAAAGTTTCATAGCCTCTAATCAGAGGAGCTTTTTA
1 ATTTAAAGTTTCATTGCCTCTAGTCAGAGGAGCTTTTTA
11662924 ATTT
1 ATTT
11662928 TAAGAACTTC
Statistics
Matches: 180, Mismatches: 35, Indels: 34
0.72 0.14 0.14
Matches are distributed among these distances:
34 52 0.29
35 2 0.01
39 8 0.04
40 87 0.48
41 31 0.17
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.42
Consensus pattern (39 bp):
ATTTAAAGTTTCATTGCCTCTAGTCAGAGGAGCTTTTTA
Found at i:11663095 original size:41 final size:39
Alignment explanation
Indices: 11663050--11663336 Score: 188
Period size: 40 Copynumber: 7.5 Consensus size: 39
11663040 TAGAGGATCC
*
11663050 ATTTAAAATTTCATTGCCTCTAGTTAAATGAGCCTTTTTGA
1 ATTTAAAGTTTCATTGCCTCTAGTTAAA-GAGCC-TTTTGA
*
11663091 ATTTAAAGTTTCATTGCCTTTAGTTAAAAGAGCC------
1 ATTTAAAGTTTCATTGCCTCTAGTT-AAAGAGCCTTTTGA
* ** * *
11663125 ATTTAAAATTTTGTTGCTTCTAGTTAAAGAGCCTTTTAA
1 ATTTAAAGTTTCATTGCCTCTAGTTAAAGAGCCTTTTGA
** * * *
11663164 ATTTAAAGTTTTGTTGCCTTTAGTTAGAAGAACTTTTTGA
1 ATTTAAAGTTTCATTGCCTCTAGTTA-AAGAGCCTTTTGA
* * * *
11663204 ATTTAAAGTTTCATTGCATTTGGTT-AAGAG-----T-C
1 ATTTAAAGTTTCATTGCCTCTAGTTAAAGAGCCTTTTGA
** * *
11663236 ATTTAAAGTTTTGTTGCCTCTTA-TTAGAATAACCTTTTGA
1 ATTTAAAGTTTCATTGCCTC-TAGTTA-AAGAGCCTTTTGA
* * * *
11663276 ATTTAAAGTTTCGTTGCCTTTGGTTAGAAGAGCCTTCTGA
1 ATTTAAAGTTTCATTGCCTCTAGTTA-AAGAGCCTTTTGA
*
11663316 ATTTAAAGTTTTATTGCCTCT
1 ATTTAAAGTTTCATTGCCTCT
11663337 GATTAGAGGA
Statistics
Matches: 192, Mismatches: 36, Indels: 37
0.72 0.14 0.14
Matches are distributed among these distances:
32 18 0.09
33 10 0.05
34 23 0.12
38 4 0.02
39 25 0.13
40 81 0.42
41 28 0.15
42 3 0.02
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (39 bp):
ATTTAAAGTTTCATTGCCTCTAGTTAAAGAGCCTTTTGA
Found at i:11663101 original size:75 final size:72
Alignment explanation
Indices: 11663010--11663194 Score: 217
Period size: 75 Copynumber: 2.5 Consensus size: 72
11663000 TTTTCTTAGA
* * *
11663010 TTTTTAATTTAAAGTTTCGTTGCTTCCAGTTAGAGGATCCATTTAAAATTTCATTGCCTCTAGTT
1 TTTTTAATTTAAAGTTTCGTTGCTT-CAGTTAAAAGAGCCATTTAAAATTTCATTGCCTCTAGTT
11663075 AAATGAGCC
65 AAA-GAGCC
* * ** *
11663084 TTTTTGAATTTAAAGTTTCATTGCCTTTAGTTAAAAGAGCCATTTAAAATTTTGTTGCTTCTAGT
1 TTTTT-AATTTAAAGTTTCGTTG-CTTCAGTTAAAAGAGCCATTTAAAATTTCATTGCCTCTAGT
11663149 TAAAGAGCC
64 TAAAGAGCC
* * * *
11663158 TTTTAAATTTAAAGTTTTGTTGCCTTTAGTTAGAAGA
1 TTTTTAATTTAAAGTTTCGTTG-CTTCAGTTAAAAGA
11663195 ACTTTTTGAA
Statistics
Matches: 97, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
73 29 0.30
74 14 0.14
75 51 0.53
76 3 0.03
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (72 bp):
TTTTTAATTTAAAGTTTCGTTGCTTCAGTTAAAAGAGCCATTTAAAATTTCATTGCCTCTAGTTA
AAGAGCC
Found at i:11663247 original size:72 final size:72
Alignment explanation
Indices: 11663164--11663367 Score: 230
Period size: 72 Copynumber: 2.7 Consensus size: 72
11663154 AGCCTTTTAA
*
11663164 ATTTAAAGTTTTGTTGCCT-TTAGTTAGAAGAACTTTTTGAATTTAAAGTTTCATTGCATTTGGT
1 ATTTAAAGTTTTGTTGCCTCTTA-TTAGAAGAACCTTTTGAATTTAAAGTTTCATTGCATTTGGT
11663228 TAAGAGTC
65 TAAGAGTC
* * *
11663236 ATTTAAAGTTTTGTTGCCTCTTATTAGAATAACCTTTTGAATTTAAAGTTTCGTTGCCTTTGGTT
1 ATTTAAAGTTTTGTTGCCTCTTATTAGAAGAACCTTTTGAATTTAAAGTTTCATTGCATTTGGTT
11663301 AGAAGAGCCTTC
66 --AAGAG---TC
* * * * *
11663313 TGAATTTAAAGTTTTATTGCCTCTGATTAGAGGAATCTTTTAATATTTAAAGTTT
1 ---ATTTAAAGTTTTGTTGCCTCTTATTAGAAGAACCTTTTGA-ATTTAAAGTTT
11663368 GTTGCCTCAA
Statistics
Matches: 112, Mismatches: 10, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
72 57 0.51
73 3 0.03
74 5 0.04
77 2 0.02
80 34 0.30
81 11 0.10
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.46
Consensus pattern (72 bp):
ATTTAAAGTTTTGTTGCCTCTTATTAGAAGAACCTTTTGAATTTAAAGTTTCATTGCATTTGGTT
AAGAGTC
Found at i:11663292 original size:40 final size:40
Alignment explanation
Indices: 11663236--11663375 Score: 158
Period size: 40 Copynumber: 3.5 Consensus size: 40
11663226 GTTAAGAGTC
*
11663236 ATTTAAAGTTTTGTTGCCTCTTATTAGAATAACCTTTTGA
1 ATTTAAAGTTTTGTTGCCTCTTATTAGAAGAACCTTTTGA
* * * *
11663276 ATTTAAAGTTTCGTTGCCT-TTGGTTAGAAGAGCCTTCTGA
1 ATTTAAAGTTTTGTTGCCTCTT-ATTAGAAGAACCTTTTGA
* * * * *
11663316 ATTTAAAGTTTTATTGCCTCTGATTAGAGGAATCTTTTAA
1 ATTTAAAGTTTTGTTGCCTCTTATTAGAAGAACCTTTTGA
11663356 TATTTAAAG-TTTGTTGCCTC
1 -ATTTAAAGTTTTGTTGCCTC
11663376 AAGTCAGATG
Statistics
Matches: 82, Mismatches: 15, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
39 2 0.02
40 71 0.87
41 9 0.11
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (40 bp):
ATTTAAAGTTTTGTTGCCTCTTATTAGAAGAACCTTTTGA
Found at i:11663302 original size:112 final size:112
Alignment explanation
Indices: 11663050--11663332 Score: 338
Period size: 112 Copynumber: 2.5 Consensus size: 112
11663040 TAGAGGATCC
* * * * *
11663050 ATTTAAAATTTCATTGCCTCTAGTTA-AATGAGCCTTTTTGAATTTAAAGTTTCATTGCCTTTAG
1 ATTTAAAGTTTCGTTGCCTTTAGTTAGAA-GA-ACTTTTTGAATTTAAAGTTTCATTGCATTTAG
* *
11663114 TTAAAAGAGCCATTTAAAATTTTGTTGCTTCTAGTTAAAGAGCCTTTTAA
64 TT-AAAGAGCCATTTAAAATTTTGTTGCCTCTAGTTAAAGAACCTTTTAA
* *
11663164 ATTTAAAGTTTTGTTGCCTTTAGTTAGAAGAACTTTTTGAATTTAAAGTTTCATTGCATTTGGTT
1 ATTTAAAGTTTCGTTGCCTTTAGTTAGAAGAACTTTTTGAATTTAAAGTTTCATTGCATTTAGTT
* * * *
11663229 -AAGAGTCATTTAAAGTTTTGTTGCCTCTTA-TTAGAATAACCTTTTGA
66 AAAGAGCCATTTAAAATTTTGTTGCCTC-TAGTTA-AAGAACCTTTTAA
* * * * *
11663276 ATTTAAAGTTTCGTTGCCTTTGGTTAGAAGAGCCTTCTGAATTTAAAGTTTTATTGC
1 ATTTAAAGTTTCGTTGCCTTTAGTTAGAAGAACTTTTTGAATTTAAAGTTTCATTGC
11663333 CTCTGATTAG
Statistics
Matches: 147, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
111 27 0.18
112 63 0.43
113 31 0.21
114 24 0.16
115 2 0.01
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.45
Consensus pattern (112 bp):
ATTTAAAGTTTCGTTGCCTTTAGTTAGAAGAACTTTTTGAATTTAAAGTTTCATTGCATTTAGTT
AAAGAGCCATTTAAAATTTTGTTGCCTCTAGTTAAAGAACCTTTTAA
Found at i:11663389 original size:80 final size:80
Alignment explanation
Indices: 11663236--11663391 Score: 197
Period size: 80 Copynumber: 1.9 Consensus size: 80
11663226 GTTAAGAGTC
* * * * *** *
11663236 ATTTAAAGTTTTGTTGCCTCTTATTAGAATAACCTTTTGAATTTAAAGTTTCGTTGCCTTTGGTT
1 ATTTAAAGTTTTATTGCCTCTGATTAGAAGAACCTTTTAAATTTAAAGTTTCGTTGCCTCAAGTC
11663301 AGAAGAGCCTTCTGA
66 AGAAGAGCCTTCTGA
* *
11663316 ATTTAAAGTTTTATTGCCTCTGATTAGAGGAATCTTTTAATATTTAAAGTTT-GTTGCCTCAAGT
1 ATTTAAAGTTTTATTGCCTCTGATTAGAAGAACCTTTTAA-ATTTAAAGTTTCGTTGCCTCAAGT
*
11663380 CAGATGAGCCTT
65 CAGAAGAGCCTT
11663392 TTTAAATTTT
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
80 53 0.83
81 11 0.17
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.43
Consensus pattern (80 bp):
ATTTAAAGTTTTATTGCCTCTGATTAGAAGAACCTTTTAAATTTAAAGTTTCGTTGCCTCAAGTC
AGAAGAGCCTTCTGA
Found at i:11663630 original size:3 final size:3
Alignment explanation
Indices: 11663622--11663651 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
11663612 ATTTTGTTTA
11663622 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
11663652 CAATTAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:11665062 original size:11 final size:11
Alignment explanation
Indices: 11665046--11665088 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 11
11665036 AGATTTATTT
11665046 AAATAATATAA
1 AAATAATATAA
11665057 AAATAATA-AA
1 AAATAATATAA
11665067 AAATAATAATGAA
1 AAATAAT-AT-AA
11665080 ATAATAATA
1 A-AATAATA
11665089 ATAATTGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 9 0.32
11 9 0.32
13 4 0.14
14 6 0.21
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (11 bp):
AAATAATATAA
Found at i:11665070 original size:21 final size:24
Alignment explanation
Indices: 11665046--11665089 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
11665036 AGATTTATTT
11665046 AAATAAT-AT-AAA-AATAATAAA
1 AAATAATAATGAAATAATAATAAA
11665067 AAATAATAATGAAATAATAATAA
1 AAATAATAATGAAATAATAATAA
11665090 TAATTGATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.35
22 2 0.10
23 3 0.15
24 8 0.40
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (24 bp):
AAATAATAATGAAATAATAATAAA
Found at i:11665264 original size:22 final size:23
Alignment explanation
Indices: 11665229--11665292 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
11665219 AAATTTTTTT
* *
11665229 AAAATAATATAATAAAAAAGATA
1 AAAATAATACAATAAAAAAGAAA
* * *
11665252 AAAACAATA-AATAGAAAATAAA
1 AAAATAATACAATAAAAAAGAAA
11665274 AAAATAATTACAATAAAAA
1 AAAATAA-TACAATAAAAA
11665293 TTAATTAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
22 16 0.48
23 10 0.30
24 7 0.21
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (23 bp):
AAAATAATACAATAAAAAAGAAA
Found at i:11669970 original size:3 final size:3
Alignment explanation
Indices: 11669962--11669995 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
11669952 TTATATATTA
11669962 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG T
11669996 AGTAGTAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:11674563 original size:5 final size:6
Alignment explanation
Indices: 11674552--11674580 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
11674542 TTCTTTGTCC
11674552 TTTTTG -TTTTG TTTTTG TTTTTG TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
11674581 GTATTGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (6 bp):
TTTTTG
Found at i:11676149 original size:2 final size:2
Alignment explanation
Indices: 11676142--11676166 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11676132 ACAAAGCCCA
11676142 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 A
11676167 AAGGGGGGGG
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:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11677804 original size:16 final size:16
Alignment explanation
Indices: 11677785--11677819 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
11677775 AAATTAACTG
*
11677785 CAAATAAAAAAACTTA
1 CAAAGAAAAAAACTTA
*
11677801 CAAAGAAAATAACTTA
1 CAAAGAAAAAAACTTA
11677817 CAA
1 CAA
11677820 GGATTTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.66, C:0.14, G:0.03, T:0.17
Consensus pattern (16 bp):
CAAAGAAAAAAACTTA
Found at i:11698215 original size:2 final size:2
Alignment explanation
Indices: 11698208--11698236 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11698198 AGATGTTACA
11698208 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 A
11698237 CCTATTCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11699119 original size:21 final size:22
Alignment explanation
Indices: 11699084--11699126 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
11699074 AGCACCAATC
*
11699084 CAAATATTTGGACA-TTTAAAA
1 CAAATATTTGAACATTTTAAAA
*
11699105 CAAATATTTTAACATTTTAAAA
1 CAAATATTTGAACATTTTAAAA
11699127 GGAGGTTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (22 bp):
CAAATATTTGAACATTTTAAAA
Found at i:11703635 original size:19 final size:20
Alignment explanation
Indices: 11703607--11703645 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
11703597 ATCCGACATT
11703607 ATTAAAAAATTATTT-TTTA
1 ATTAAAAAATTATTTATTTA
*
11703626 ATTAATAAATTATTTATTTA
1 ATTAAAAAATTATTTATTTA
11703646 TATATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTAAAAAATTATTTATTTA
Found at i:11703702 original size:21 final size:21
Alignment explanation
Indices: 11703672--11703722 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
11703662 GATATTTTTA
11703672 AATA-TTTATATTTAAAAAAT
1 AATATTTTATATTTAAAAAAT
*
11703692 AATATTTTATATTTTAAAAAT
1 AATATTTTATATTTAAAAAAT
11703713 AATATTTTAT
1 AATATTTTAT
11703723 TAATTTCGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATTTTATATTTAAAAAAT
Found at i:11704065 original size:19 final size:20
Alignment explanation
Indices: 11704041--11704080 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
11704031 TTTATGTTAT
11704041 AAAAATT-TAAAATATATAA
1 AAAAATTATAAAATATATAA
11704060 AAAAATTAATAAAATATATAA
1 AAAAATT-ATAAAATATATAA
11704081 TTCGATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.37
21 12 0.63
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAAATTATAAAATATATAA
Found at i:11719249 original size:86 final size:86
Alignment explanation
Indices: 11719104--11719276 Score: 319
Period size: 86 Copynumber: 2.0 Consensus size: 86
11719094 TGACCCGAAG
* *
11719104 ATCTTACAATTTTATCCTACAAAAGACGTCTCACAAGTTTGAGAGGCGTTACAATCTCCTCACTT
1 ATCTTACAATTTTATCCTACAAAAGACGCCTCACAAGTTTGAGAGGCGTTACAATCTCCTCACCT
11719169 TTAATACTTGACGTCCTTGTC
66 TTAATACTTGACGTCCTTGTC
*
11719190 ATCTTACAATTTTATCTTACAAAAGACGCCTCACAAGTTTGAGAGGCGTTACAATCTCCTCACCT
1 ATCTTACAATTTTATCCTACAAAAGACGCCTCACAAGTTTGAGAGGCGTTACAATCTCCTCACCT
11719255 TTAATACTTGACGTCCTTGTC
66 TTAATACTTGACGTCCTTGTC
11719276 A
1 A
11719277 AGCCGAGTTC
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
86 84 1.00
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (86 bp):
ATCTTACAATTTTATCCTACAAAAGACGCCTCACAAGTTTGAGAGGCGTTACAATCTCCTCACCT
TTAATACTTGACGTCCTTGTC
Found at i:11719395 original size:25 final size:25
Alignment explanation
Indices: 11719361--11719409 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
11719351 TCGCACTCAA
11719361 CCTGCGAGATATTATCTACTTTGAC
1 CCTGCGAGATATTATCTACTTTGAC
*
11719386 CCTGCGAGATATTATCTGCTTTGA
1 CCTGCGAGATATTATCTACTTTGA
11719410 ATCGAAAGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.37
Consensus pattern (25 bp):
CCTGCGAGATATTATCTACTTTGAC
Found at i:11720751 original size:2 final size:2
Alignment explanation
Indices: 11720744--11720772 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11720734 TTTATATTTG
11720744 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11720773 CGGTGGCCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11740047 original size:6 final size:6
Alignment explanation
Indices: 11740038--11740093 Score: 55
Period size: 6 Copynumber: 9.5 Consensus size: 6
11740028 CCCATTTGCA
* *
11740038 TTTTAT TTTTAT TTTT-T ATTTAT TTATTAAT TTTTA- -TTAAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TT-TT-AT TTTTAT TTTTAT TTTTAT
11740085 TTTTAT TTT
1 TTTTAT TTT
11740094 ATCATTTATC
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
4 3 0.07
5 4 0.10
6 26 0.63
7 4 0.10
8 4 0.10
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:11740075 original size:10 final size:10
Alignment explanation
Indices: 11740060--11740085 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
11740050 TTTTTATTTA
11740060 TTTATTAATT
1 TTTATTAATT
11740070 TTTATTAATT
1 TTTATTAATT
11740080 TTTATT
1 TTTATT
11740086 TTTATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTATTAATT
Found at i:11740644 original size:20 final size:20
Alignment explanation
Indices: 11740621--11740660 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
11740611 GAGAAAAAAA
11740621 AGAGA-AAAGAGGGAAAGGAG
1 AGAGAGAAAGAGGG-AAGGAG
*
11740641 AGAGAGAGAGAGGGAAGGAG
1 AGAGAGAAAGAGGGAAGGAG
11740661 GCAATCTGCG
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:0.50, T:0.00
Consensus pattern (20 bp):
AGAGAGAAAGAGGGAAGGAG
Found at i:11742432 original size:32 final size:31
Alignment explanation
Indices: 11742384--11742447 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 31
11742374 AAATTACAAT
**
11742384 TCTTTTAAAGCATATTTTACACAGTTTCATA
1 TCTTTTAAAGCATATTTTACACAACTTCATA
*
11742415 TCTTTTACAATCATATTTTACACAACTTCATA
1 TCTTTTA-AAGCATATTTTACACAACTTCATA
11742447 T
1 T
11742448 ATTGATCTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 7 0.24
32 22 0.76
ACGTcount: A:0.33, C:0.19, G:0.03, T:0.45
Consensus pattern (31 bp):
TCTTTTAAAGCATATTTTACACAACTTCATA
Found at i:11744408 original size:9 final size:9
Alignment explanation
Indices: 11744394--11744423 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
11744384 GGTAAATTTT
11744394 TAATTAAAA
1 TAATTAAAA
11744403 TAATTAAAA
1 TAATTAAAA
11744412 TATATTAAAA
1 TA-ATTAAAA
11744422 TA
1 TA
11744424 TAAAAGCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAATTAAAA
Found at i:11744420 original size:10 final size:10
Alignment explanation
Indices: 11744396--11744425 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
11744386 TAAATTTTTA
11744396 ATTAAAATA-
1 ATTAAAATAT
11744405 ATTAAAATAT
1 ATTAAAATAT
11744415 ATTAAAATAT
1 ATTAAAATAT
11744425 A
1 A
11744426 AAAGCTCGAT
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:11752867 original size:11 final size:11
Alignment explanation
Indices: 11752851--11752877 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
11752841 ACTCAAGGTC
11752851 AAATTTGATCA
1 AAATTTGATCA
11752862 AAATTTGATCA
1 AAATTTGATCA
11752873 AAATT
1 AAATT
11752878 AATTAAACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (11 bp):
AAATTTGATCA
Found at i:11753954 original size:14 final size:15
Alignment explanation
Indices: 11753892--11753954 Score: 60
Period size: 14 Copynumber: 4.3 Consensus size: 15
11753882 CAAAAAAAAA
11753892 AAAAAAAGAGAAGAAG
1 AAAAAAAGAG-AGAAG
* *
11753908 AAAAAAAGAAATG-TG
1 AAAAAAAGAGA-GAAG
*
11753923 AAAAAAAAAGAGAA-
1 AAAAAAAGAGAGAAG
11753937 AAAAAAAGAGA-AAG
1 AAAAAAAGAGAGAAG
11753951 AAAA
1 AAAA
11753955 GTTAGAAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
13 2 0.05
14 15 0.39
15 11 0.29
16 10 0.26
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (15 bp):
AAAAAAAGAGAGAAG
Found at i:11753955 original size:11 final size:12
Alignment explanation
Indices: 11753883--11753954 Score: 58
Period size: 12 Copynumber: 5.6 Consensus size: 12
11753873 CTGAAAACAC
11753883 AAAAAAAAA-A-
1 AAAAAAAAAGAG
11753893 AAAAAAGAGAAGAAG
1 AAAAAA-A-AAG-AG
*
11753908 AAAAAAAGAAATGTG
1 -AAAAAA-AAA-GAG
11753923 AAAAAAAAAGAG
1 AAAAAAAAAGAG
11753935 AAAAAAAAAGAG
1 AAAAAAAAAGAG
11753947 AAAGAAAA
1 AAA-AAAA
11753955 GTTAGAAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
10 6 0.12
11 1 0.02
12 19 0.37
13 7 0.13
14 7 0.13
15 3 0.06
16 9 0.17
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.03
Consensus pattern (12 bp):
AAAAAAAAAGAG
Found at i:11753964 original size:35 final size:33
Alignment explanation
Indices: 11753890--11753956 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
11753880 CACAAAAAAA
* * *
11753890 AAAAAAAAAGAGAAGAAGAAAAAAAGAAATGTG
1 AAAAAAAAAGAGAAAAAAAAAAAAAGAAAAGTG
11753923 AAAAAAAAAGAGAAAAAAAAAGAGAAAGAAAAGT
1 AAAAAAAAAGAGAAAAAAAAA-A-AAAGAAAAGT
11753957 TAGAAAAAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 19 0.66
34 1 0.03
35 9 0.31
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.04
Consensus pattern (33 bp):
AAAAAAAAAGAGAAAAAAAAAAAAAGAAAAGTG
Found at i:11754243 original size:169 final size:170
Alignment explanation
Indices: 11753964--11754304 Score: 560
Period size: 169 Copynumber: 2.0 Consensus size: 170
11753954 AGTTAGAAAA
* *
11753964 AGCTTAAATAAGGTATAATCTCCATTTTCTTTTCTTGCATTCCATTATACCTTTATCTCATTTTC
1 AGCTTAAAGAAGGTATAATCTCCATTTTCTTTTCTTGCATTCCATTACACCTTTATCTCATTTTC
*
11754029 ATAACATTTTTACATTGGTTCTTCATTCATTTTTCTATTTTTCTTTTGAAAAATTTGTAATTCTT
66 ATAACATTTTTACATTGGTTATTCATTCATTTTTCTATTTTTCTTTTGAAAAATTTGTAATTCTT
11754094 TTTC-TTTTTTTTTTTTTATCA-AAGCTTGAATCAAAATTT
131 TTTCTTTTTTTTTTTTTTATCACAA-CTTGAATCAAAATTT
* * *
11754133 AGCTTAAAGAATGTATAATCTCTATTTTCTTTTCTTGCATTTCATTACACCTTTATCTCATTTTC
1 AGCTTAAAGAAGGTATAATCTCCATTTTCTTTTCTTGCATTCCATTACACCTTTATCTCATTTTC
* * *
11754198 ATAACATTTTTATATTGGTTATTCATTCATTTTTCTATTTTTCTTTTGAGAAATTTGTAGTTCTT
66 ATAACATTTTTACATTGGTTATTCATTCATTTTTCTATTTTTCTTTTGAAAAATTTGTAATTCTT
*
11754263 TTTCTTTTTTTTTTTTTTTATCACAACTTGAATCAAATTTT
131 TTTC-TTTTTTTTTTTTTTATCACAACTTGAATCAAAATTT
11754304 A
1 A
11754305 TCTAACTAGT
Statistics
Matches: 159, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
169 125 0.79
171 32 0.20
172 2 0.01
ACGTcount: A:0.24, C:0.15, G:0.06, T:0.55
Consensus pattern (170 bp):
AGCTTAAAGAAGGTATAATCTCCATTTTCTTTTCTTGCATTCCATTACACCTTTATCTCATTTTC
ATAACATTTTTACATTGGTTATTCATTCATTTTTCTATTTTTCTTTTGAAAAATTTGTAATTCTT
TTTCTTTTTTTTTTTTTTATCACAACTTGAATCAAAATTT
Found at i:11755134 original size:7 final size:7
Alignment explanation
Indices: 11755118--11755258 Score: 85
Period size: 7 Copynumber: 20.3 Consensus size: 7
11755108 TAAAACCCTA
*
11755118 AAACCAT
1 AAACCTT
11755125 AAACCTT
1 AAACCTT
*
11755132 AAACATT
1 AAACCTT
11755139 AAACCTT
1 AAACCTT
*
11755146 AAACCCT
1 AAACCTT
11755153 AAACC-T
1 AAACCTT
*
11755159 AAGCCTT
1 AAACCTT
**
11755166 AAATTTT
1 AAACCTT
*
11755173 AAACCCT
1 AAACCTT
11755180 AAATCC-T
1 AAA-CCTT
*
11755187 AAAACTT
1 AAACCTT
11755194 AAACCTT
1 AAACCTT
11755201 AAA-CTAT
1 AAACCT-T
*
11755208 AGATCC-T
1 A-AACCTT
*
11755215 AAACCCT
1 AAACCTT
*
11755222 AAA-TTCT
1 AAACCT-T
11755229 AAACCTT
1 AAACCTT
*
11755236 GAACCTT
1 AAACCTT
*
11755243 AAATCTT
1 AAACCTT
*
11755250 AAACTTT
1 AAACCTT
11755257 AA
1 AA
11755259 CCTAGACCCT
Statistics
Matches: 102, Mismatches: 23, Indels: 18
0.71 0.16 0.13
Matches are distributed among these distances:
6 11 0.11
7 86 0.84
8 4 0.04
9 1 0.01
ACGTcount: A:0.45, C:0.25, G:0.02, T:0.28
Consensus pattern (7 bp):
AAACCTT
Done.