Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, 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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 182 of 190
Found at i:30903702 original size:2 final size:2
Alignment explanation
Indices: 30903695--30903720 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30903685 ATCCATTTGC
30903695 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
30903721 GTATGGGTAG
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):
TA
Found at i:30905921 original size:30 final size:30
Alignment explanation
Indices: 30905886--30905946 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
30905876 CATTGGAAAT
*
30905886 TCTCAAACAACAGGTGAAACGCATAGGTTA
1 TCTCAAACAACAGGTGAAAAGCATAGGTTA
30905916 TCTCAAACAACAGGTGAAAAGCATAGGTTA
1 TCTCAAACAACAGGTGAAAAGCATAGGTTA
30905946 T
1 T
30905947 TTTAAGTTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21
Consensus pattern (30 bp):
TCTCAAACAACAGGTGAAAAGCATAGGTTA
Found at i:30905978 original size:2 final size:2
Alignment explanation
Indices: 30905964--30906003 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
30905954 TCAAAATCTA
*
30905964 AT AT AT CT A- AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30906004 TACAACATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30906147 original size:26 final size:26
Alignment explanation
Indices: 30906117--30906167 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
30906107 AAACAAAATT
*
30906117 TTTTTAATAAATTATTTAAATTGAATA
1 TTTTGAAT-AATTATTTAAATTGAATA
*
30906144 TTTTGGATAATTATTTAAATTGAA
1 TTTTGAATAATTATTTAAATTGAA
30906168 ATCAATTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (26 bp):
TTTTGAATAATTATTTAAATTGAATA
Found at i:30906804 original size:2 final size:2
Alignment explanation
Indices: 30906797--30906833 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
30906787 GTTCAATCAA
30906797 AT 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 AT A
30906834 CACACACACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30907009 original size:18 final size:19
Alignment explanation
Indices: 30906981--30907016 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
30906971 GCAAAAAAAT
*
30906981 TGAAGAAAATGTTTTTTAA
1 TGAAGAAAATGATTTTTAA
30907000 TGAA-AAAATGATTTTTA
1 TGAAGAAAATGATTTTTA
30907017 TAATTCTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (19 bp):
TGAAGAAAATGATTTTTAA
Found at i:30907014 original size:19 final size:20
Alignment explanation
Indices: 30906981--30907020 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
30906971 GCAAAAAAAT
30906981 TGAAGAAAATGTTTTT-TAA
1 TGAAGAAAATGTTTTTATAA
30907000 TGAA-AAAATGATTTTTATAA
1 TGAAGAAAATG-TTTTTATAA
30907020 T
1 T
30907021 TCTCGAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 9 0.47
20 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (20 bp):
TGAAGAAAATGTTTTTATAA
Found at i:30907919 original size:13 final size:13
Alignment explanation
Indices: 30907901--30907927 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30907891 TGGAGTAAGC
30907901 CGTCAATTTTCTA
1 CGTCAATTTTCTA
30907914 CGTCAATTTTCTA
1 CGTCAATTTTCTA
30907927 C
1 C
30907928 CATTTGTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.07, T:0.44
Consensus pattern (13 bp):
CGTCAATTTTCTA
Found at i:30910894 original size:32 final size:29
Alignment explanation
Indices: 30910837--30910895 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 29
30910827 GAAAATTGAT
30910837 AAAAAAAAAGAAAGTCAAATAATAATTTC
1 AAAAAAAAAGAAAGTCAAATAATAATTTC
*
30910866 AAAAGAAAAGAGAAGATCAAAATAATAATT
1 AAAAAAAAAGA-AAG-TC-AAATAATAATT
30910896 AAGTGAGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 10 0.38
30 3 0.12
31 2 0.08
32 11 0.42
ACGTcount: A:0.66, C:0.05, G:0.10, T:0.19
Consensus pattern (29 bp):
AAAAAAAAAGAAAGTCAAATAATAATTTC
Found at i:30911883 original size:52 final size:52
Alignment explanation
Indices: 30911816--30911961 Score: 186
Period size: 52 Copynumber: 2.8 Consensus size: 52
30911806 AAACTTGTCC
* *
30911816 ATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCTTGTAAGTCAAACTTACCT
1 ATTAAGAATCTCTTTCCTCTTAGAATTCTTCTCTTGCAAGTCAAACTTACCT
* * * * *
30911868 ATTAAGAATCTCTTTCTTTTTAAAATTCTTTTTTTGCAAGTCAAACTTACCT
1 ATTAAGAATCTCTTTCCTCTTAGAATTCTTCTCTTGCAAGTCAAACTTACCT
* * *
30911920 ATTAAGAATCTTCTTT-CTCTTAGAATTATTCTTTTACAAGTC
1 ATTAAGAATC-TCTTTCCTCTTAGAATTCTTCTCTTGCAAGTC
30911962 TTCTTGTCCA
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
52 75 0.94
53 5 0.06
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.45
Consensus pattern (52 bp):
ATTAAGAATCTCTTTCCTCTTAGAATTCTTCTCTTGCAAGTCAAACTTACCT
Found at i:30911998 original size:11 final size:11
Alignment explanation
Indices: 30911982--30912028 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
30911972 TCAAGCAATA
30911982 TCTAACAAATC
1 TCTAACAAATC
30911993 TCTAACAAATC
1 TCTAACAAATC
* *
30912004 CCAAACAAATC
1 TCTAACAAATC
*
30912015 -CAAAACAAATC
1 TC-TAACAAATC
30912026 TCT
1 TCT
30912029 TATGAGATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
10 1 0.03
11 29 0.94
12 1 0.03
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.21
Consensus pattern (11 bp):
TCTAACAAATC
Found at i:30912322 original size:18 final size:19
Alignment explanation
Indices: 30912281--30912325 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
30912271 TTTTATTAGG
30912281 TTAAAAAT-AATTAAATAA
1 TTAAAAATAAATTAAATAA
**
30912299 CAAAAAATAAATTAAA-AA
1 TTAAAAATAAATTAAATAA
30912317 TTAAAAATA
1 TTAAAAATA
30912326 TATATTTCAC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (19 bp):
TTAAAAATAAATTAAATAA
Found at i:30913580 original size:20 final size:21
Alignment explanation
Indices: 30913555--30913608 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
30913545 AATAATTATT
*
30913555 ATATATATAAA-TTTATTTAA
1 ATATATATAAATTTTATTAAA
30913575 ATATAT-TAAAATTTTTATTAAA
1 ATATATAT-AAA-TTTTATTAAA
30913597 ATAATATATAAA
1 AT-ATATATAAA
30913609 AATTTAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 1 0.04
20 9 0.32
22 10 0.36
23 7 0.25
24 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATATATATAAATTTTATTAAA
Found at i:30913591 original size:18 final size:20
Alignment explanation
Indices: 30913555--30913591 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
30913545 AATAATTATT
*
30913555 ATATATATAAATTTATTTAA
1 ATATATATAAAATTATTTAA
30913575 ATATAT-TAAAATT-TTTA
1 ATATATATAAAATTATTTA
30913592 TTAAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 4 0.25
19 6 0.38
20 6 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATATATAAAATTATTTAA
Found at i:30913591 original size:22 final size:24
Alignment explanation
Indices: 30913566--30913609 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
30913556 TATATATAAA
*
30913566 TTTATTTAAAT-ATAT-TAAAATT
1 TTTATTAAAATAATATATAAAATT
30913588 TTTATTAAAATAATATATAAAA
1 TTTATTAAAATAATATATAAAA
30913610 ATTTAAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 4 0.21
24 5 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATTAAAATAATATATAAAATT
Found at i:30916050 original size:29 final size:29
Alignment explanation
Indices: 30916017--30916073 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
30916007 ATGATATAAT
30916017 GATAT-AATATAAATATGATATAAAATTAC
1 GATATGAATAT-AATATGATATAAAATTAC
*
30916046 GATATGAATATAATATGATTTAAAATTA
1 GATATGAATATAATATGATATAAAATTA
30916074 TAGTAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.37
Consensus pattern (29 bp):
GATATGAATATAATATGATATAAAATTAC
Found at i:30923185 original size:2 final size:2
Alignment explanation
Indices: 30923178--30923214 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
30923168 TAACATCACC
30923178 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
30923215 CGTACTCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30924452 original size:1 final size:1
Alignment explanation
Indices: 30924408--30924432 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
30924398 TCTCTTTTGT
30924408 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
30924433 CCGAAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:30926754 original size:21 final size:21
Alignment explanation
Indices: 30926728--30926767 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
30926718 TACCAAAATC
* *
30926728 TATATAAATATATTAAAATAA
1 TATATAAAAAAATTAAAATAA
30926749 TATATAAAAAAATTAAAAT
1 TATATAAAAAAATTAAAAT
30926768 TTAAAAACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TATATAAAAAAATTAAAATAA
Found at i:30928425 original size:29 final size:29
Alignment explanation
Indices: 30928393--30928463 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 29
30928383 TAATCTTGTC
* * * * *
30928393 TATTTGTTTATATACGTATTAGTCATGTT
1 TATTTGTGTACATACATATTAGTAATATT
* *
30928422 TATTCGTGTACATACATATTATTAATATT
1 TATTTGTGTACATACATATTAGTAATATT
30928451 TATTTGTGT-CATA
1 TATTTGTGTACATA
30928464 TTTAAACGAA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
28 4 0.12
29 30 0.88
ACGTcount: A:0.28, C:0.08, G:0.11, T:0.52
Consensus pattern (29 bp):
TATTTGTGTACATACATATTAGTAATATT
Found at i:30929229 original size:35 final size:36
Alignment explanation
Indices: 30929169--30929236 Score: 88
Period size: 35 Copynumber: 1.9 Consensus size: 36
30929159 CCTTTATTTT
*
30929169 ATTTTTTATATTTATTTATGTTT-AAATTCAATATC
1 ATTTTTTATATTTAATTATGTTTAAAATTCAATATC
30929204 ATTTTTTAT-TTTAAATTAT-TATTAAAATTCAAT
1 ATTTTTTATATTT-AATTATGT-TTAAAATTCAAT
30929237 TTCAAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 4 0.14
35 16 0.55
36 9 0.31
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.59
Consensus pattern (36 bp):
ATTTTTTATATTTAATTATGTTTAAAATTCAATATC
Found at i:30929419 original size:23 final size:23
Alignment explanation
Indices: 30929384--30929443 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
30929374 TTTTTATAAT
* *
30929384 ATTATATGATTAATTAATTTAAA
1 ATTAAATGTTTAATTAATTTAAA
* * *
30929407 ATTAGATGTTTAATGATTTTAAA
1 ATTAAATGTTTAATTAATTTAAA
30929430 A-TAAAT-TTTAATTA
1 ATTAAATGTTTAATTA
30929444 TAACTCAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 7 0.23
22 4 0.13
23 20 0.65
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (23 bp):
ATTAAATGTTTAATTAATTTAAA
Found at i:30946821 original size:20 final size:20
Alignment explanation
Indices: 30946793--30946857 Score: 58
Period size: 23 Copynumber: 3.0 Consensus size: 20
30946783 ATTTCATTCG
*
30946793 AAAATAATAAAATATATTTT
1 AAAAAAATAAAATATATTTT
* * *
30946813 AAAAAAATAAATATAAAATTA
1 AAAAAAATAAA-ATATATTTT
30946834 AATAAATAATAAAATAATATTTT
1 AA-AAA-AATAAAAT-ATATTTT
30946857 A
1 A
30946858 TATATATTGG
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
20 10 0.29
21 8 0.24
22 5 0.15
23 11 0.32
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAAAAATAAAATATATTTT
Found at i:30946838 original size:16 final size:17
Alignment explanation
Indices: 30946817--30946848 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
30946807 TATTTTAAAA
30946817 AAATAAAT-ATAAAATT
1 AAATAAATAATAAAATT
30946833 AAATAAATAATAAAAT
1 AAATAAATAATAAAAT
30946849 AATATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AAATAAATAATAAAATT
Found at i:30947673 original size:22 final size:22
Alignment explanation
Indices: 30947645--30947688 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
30947635 AAGAAATGTA
*
30947645 CTAAATTAGATACTTATATATG
1 CTAAATTAAATACTTATATATG
*
30947667 CTAAATTAAATAGTTATATATG
1 CTAAATTAAATACTTATATATG
30947689 AGTGAAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (22 bp):
CTAAATTAAATACTTATATATG
Found at i:30950093 original size:15 final size:15
Alignment explanation
Indices: 30950060--30950092 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
30950050 TTGTCAATGA
30950060 TTTT-TTCAGTACCT
1 TTTTCTTCAGTACCT
30950074 TTTTCTTCAGTAGCCT
1 TTTTCTTCAGTA-CCT
30950090 TTT
1 TTT
30950093 CGTAAAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 7 0.41
16 6 0.35
ACGTcount: A:0.12, C:0.21, G:0.09, T:0.58
Consensus pattern (15 bp):
TTTTCTTCAGTACCT
Found at i:30953036 original size:24 final size:24
Alignment explanation
Indices: 30952980--30953117 Score: 128
Period size: 24 Copynumber: 5.8 Consensus size: 24
30952970 TATTTATTGC
*
30952980 TATTATTA-TTATTTATTAATATA
1 TATTATTATTTATCTATTAATATA
30953003 TA-TATT-TTTATCTATTAATATA
1 TATTATTATTTATCTATTAATATA
* *
30953025 TATTGTTATTTATCTATTAATGTA
1 TATTATTATTTATCTATTAATATA
*
30953049 TATAAATT-TTTAT-TATTAACTAT-
1 TAT-TATTATTTATCTATTAA-TATA
30953072 TATCTATTATTTATCTATTAGTATATA
1 TAT-TATTATTTATCTATTA--ATATA
30953099 TATGTATATATTTAT-TATT
1 TAT-TAT-TATTTATCTATT
30953118 TATCTTTTTT
Statistics
Matches: 95, Mismatches: 9, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
22 20 0.21
23 17 0.18
24 30 0.32
25 7 0.07
26 3 0.03
27 11 0.12
28 7 0.07
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.59
Consensus pattern (24 bp):
TATTATTATTTATCTATTAATATA
Found at i:30953058 original size:48 final size:48
Alignment explanation
Indices: 30952983--30953100 Score: 147
Period size: 48 Copynumber: 2.5 Consensus size: 48
30952973 TTATTGCTAT
*
30952983 TATTA-TTATTTATTAATATATAT--ATTTTTATCTATTAA-TATATAT-
1 TATTATTTATCTATTAATATATATAAATTTTTAT-TATTAACTAT-TATC
* *
30953028 TGTTATTTATCTATTAATGTATATAAATTTTTATTATTAACTATTATC
1 TATTATTTATCTATTAATATATATAAATTTTTATTATTAACTATTATC
*
30953076 TATTATTTATCTATTAGTATATATA
1 TATTATTTATCTATTAATATATATA
30953101 TGTATATATT
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
45 4 0.06
46 16 0.26
47 9 0.15
48 33 0.53
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.58
Consensus pattern (48 bp):
TATTATTTATCTATTAATATATATAAATTTTTATTATTAACTATTATC
Found at i:30953556 original size:17 final size:17
Alignment explanation
Indices: 30953534--30953566 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
30953524 GAAGAAAAAA
30953534 AAGGGAAGAGAGAGAGG
1 AAGGGAAGAGAGAGAGG
30953551 AAGGGAAGAGAGAGAG
1 AAGGGAAGAGAGAGAG
30953567 AAATTAAAAA
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (17 bp):
AAGGGAAGAGAGAGAGG
Found at i:30953920 original size:5 final size:5
Alignment explanation
Indices: 30953897--30953940 Score: 70
Period size: 5 Copynumber: 8.4 Consensus size: 5
30953887 TTTGAATTCC
30953897 TTATT TTATCT TTATTT TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTAT-T TTA-TT TTATT TTATT TTATT TTATT TTATT TT
30953941 TTAATGATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 28 0.76
6 8 0.22
7 1 0.03
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:30954006 original size:18 final size:17
Alignment explanation
Indices: 30953976--30954015 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 17
30953966 CCAAAAACAA
30953976 AAAAAAAATATTTTT-G
1 AAAAAAAATATTTTTGG
30953992 AAAAAAAATGCATTTTTGG
1 AAAAAAAAT--ATTTTTGG
30954011 AAAAA
1 AAAAA
30954016 GTTGAAAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.43
18 6 0.29
19 6 0.29
ACGTcount: A:0.57, C:0.03, G:0.10, T:0.30
Consensus pattern (17 bp):
AAAAAAAATATTTTTGG
Found at i:30954557 original size:16 final size:16
Alignment explanation
Indices: 30954528--30954566 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
30954518 AACTTATTCT
* *
30954528 TTTAGATACTCTTAAG
1 TTTAGGTACCCTTAAG
30954544 TTTAGGTACCCTTAAG
1 TTTAGGTACCCTTAAG
30954560 TTTAGGT
1 TTTAGGT
30954567 GTTCATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.44
Consensus pattern (16 bp):
TTTAGGTACCCTTAAG
Found at i:30955406 original size:3 final size:3
Alignment explanation
Indices: 30955400--30955427 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
30955390 TAAATTTTTC
30955400 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
30955428 GCAGAAGCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:30963108 original size:6 final size:6
Alignment explanation
Indices: 30963099--30963131 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
30963089 GAGAGAGACA
30963099 CCACTT CCACTT CCACTT CCACTT CCACTT CCA
1 CCACTT CCACTT CCACTT CCACTT CCACTT CCA
30963132 AACCTCCCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.52, G:0.00, T:0.30
Consensus pattern (6 bp):
CCACTT
Found at i:30966867 original size:24 final size:24
Alignment explanation
Indices: 30966821--30966867 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
30966811 ATACATTCAG
*
30966821 TTTTATTCTTTGTTTTTCACACAA
1 TTTTATTCTTAGTTTTTCACACAA
30966845 TTTTATTTCTTAGTTTTTC-CACA
1 TTTTA-TTCTTAGTTTTTCACACA
30966868 TGTGGAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.19, C:0.17, G:0.04, T:0.60
Consensus pattern (24 bp):
TTTTATTCTTAGTTTTTCACACAA
Found at i:30972250 original size:17 final size:17
Alignment explanation
Indices: 30972228--30972273 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
30972218 ACAATTAATT
*
30972228 TATAAAATTTTAAAATA
1 TATAAAATTTAAAAATA
*
30972245 TATAAAAATTAAAAATA
1 TATAAAATTTAAAAATA
*
30972262 TATATAATTTAA
1 TATAAAATTTAA
30972274 TTCAATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TATAAAATTTAAAAATA
Found at i:30972377 original size:22 final size:22
Alignment explanation
Indices: 30972349--30972395 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
30972339 ACATCTGAAT
*
30972349 TTAATTTAAATTAAATAAAAAA
1 TTAATTTAAATCAAATAAAAAA
* *
30972371 TTAATTTAAATCAAATCAAACA
1 TTAATTTAAATCAAATAAAAAA
30972393 TTA
1 TTA
30972396 TAATTTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (22 bp):
TTAATTTAAATCAAATAAAAAA
Found at i:30973145 original size:21 final size:20
Alignment explanation
Indices: 30973119--30973182 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
30973109 ATTTTAAATT
30973119 ATTTATAAAAATATATTT-AAA
1 ATTTAT-AAAAT-TATTTAAAA
*
30973140 ATTTATTAAATTATTTAAAA
1 ATTTATAAAATTATTTAAAA
* *
30973160 ATTTA-AAATTTA-ATAAAA
1 ATTTATAAAATTATTTAAAA
30973178 ATTTA
1 ATTTA
30973183 ATTTAAATTC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
18 10 0.26
19 10 0.26
20 12 0.32
21 6 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTATAAAATTATTTAAAA
Found at i:30974429 original size:18 final size:17
Alignment explanation
Indices: 30974408--30974468 Score: 50
Period size: 19 Copynumber: 3.3 Consensus size: 17
30974398 GTTAATTAAA
30974408 ATTTTTATTTTTATTAT
1 ATTTTTATTTTTATTAT
* * *
30974425 GATTTAATATTTTAATGAT
1 -ATTT-TTATTTTTATTAT
30974444 ATTATTTATATTTTATATAT
1 ATT-TTTAT-TTTTAT-TAT
30974464 ATTTT
1 ATTTT
30974469 GAACATGTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
18 10 0.30
19 18 0.55
20 5 0.15
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (17 bp):
ATTTTTATTTTTATTAT
Found at i:30978684 original size:27 final size:29
Alignment explanation
Indices: 30978654--30978709 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
30978644 TAAGTGTAAC
30978654 TTAAAA-AAATAT-AAAATATATTATTTA
1 TTAAAATAAATATAAAAATATATTATTTA
* * *
30978681 TTAAAATCATTATAAAAATATTTTATTTA
1 TTAAAATAAATATAAAAATATATTATTTA
30978710 AAGGATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 6 0.25
28 4 0.17
29 14 0.58
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (29 bp):
TTAAAATAAATATAAAAATATATTATTTA
Found at i:30980098 original size:15 final size:15
Alignment explanation
Indices: 30980078--30980138 Score: 52
Period size: 15 Copynumber: 4.0 Consensus size: 15
30980068 ATAAAATTAT
30980078 TAAAATTTTTTAAAA
1 TAAAATTTTTTAAAA
**
30980093 TAAAATTTTAGAAAA
1 TAAAATTTTTTAAAA
* *
30980108 TTAATAATTATTCAAAA
1 -TAA-AATTTTTTAAAA
*
30980125 -ATAATTTTTTAAAA
1 TAAAATTTTTTAAAA
30980139 ATTATAGATC
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
14 10 0.28
15 14 0.39
16 3 0.08
17 9 0.25
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (15 bp):
TAAAATTTTTTAAAA
Found at i:30980135 original size:33 final size:33
Alignment explanation
Indices: 30980089--30980198 Score: 93
Period size: 32 Copynumber: 3.3 Consensus size: 33
30980079 AAAATTTTTT
**
30980089 AAAATAAAATTTTAGAAAATTAATA-AT-TATTCA
1 AAAATAATTTTTTA-AAAATT-ATAGATCTATTCA
*
30980122 AAAATAATTTTTTAAAAATTATAGATCTCTTCA
1 AAAATAATTTTTTAAAAATTATAGATCTATTCA
** * *
30980155 AAAATTAATTTTCAAAAAATTAT-G-TTTTTTCA
1 AAAA-TAATTTTTTAAAAATTATAGATCTATTCA
30980187 AAAATTAATTTT
1 AAAA-TAATTTT
30980199 CGACAGATGA
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
31 3 0.04
32 26 0.39
33 22 0.33
34 16 0.24
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (33 bp):
AAAATAATTTTTTAAAAATTATAGATCTATTCA
Found at i:30980170 original size:14 final size:14
Alignment explanation
Indices: 30980151--30980199 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 14
30980141 TATAGATCTC
30980151 TTCAAAAATTAATT
1 TTCAAAAATTAATT
*
30980165 TTCAAAAAATTATGTTTT
1 TTC-AAAAATTA---ATT
30980183 TTCAAAAATTAATT
1 TTCAAAAATTAATT
30980197 TTC
1 TTC
30980200 GACAGATGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.28
15 8 0.28
17 8 0.28
18 5 0.17
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (14 bp):
TTCAAAAATTAATT
Found at i:30980192 original size:32 final size:34
Alignment explanation
Indices: 30980118--30980199 Score: 107
Period size: 32 Copynumber: 2.5 Consensus size: 34
30980108 TTAATAATTA
**
30980118 TTCAAAAA-TAATTTTTTAAAAATTATAGATCTC
1 TTCAAAAATTAATTTTCAAAAAATTATAGATCTC
* *
30980151 TTCAAAAATTAATTTTCAAAAAATTAT-G-TTTT
1 TTCAAAAATTAATTTTCAAAAAATTATAGATCTC
30980183 TTCAAAAATTAATTTTC
1 TTCAAAAATTAATTTTC
30980200 GACAGATGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
32 19 0.43
33 9 0.20
34 16 0.36
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (34 bp):
TTCAAAAATTAATTTTCAAAAAATTATAGATCTC
Found at i:30984365 original size:19 final size:20
Alignment explanation
Indices: 30984343--30984385 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
30984333 AAAAATATCT
30984343 ATTTAAT-AAATATATTAAA
1 ATTTAATAAAATATATTAAA
* * *
30984362 ATTTATTAAAATTTTTTAAA
1 ATTTAATAAAATATATTAAA
30984382 ATTT
1 ATTT
30984386 TATACGTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTAATAAAATATATTAAA
Found at i:30984368 original size:10 final size:10
Alignment explanation
Indices: 30984350--30984385 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
30984340 TCTATTTAAT
*
30984350 AAATATATTA
1 AAATTTATTA
30984360 AAATTTATTA
1 AAATTTATTA
*
30984370 AAATTTTTTA
1 AAATTTATTA
30984380 AAATTT
1 AAATTT
30984386 TATACGTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
AAATTTATTA
Found at i:31004506 original size:2 final size:2
Alignment explanation
Indices: 31004499--31004529 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
31004489 GAGAAGACCA
31004499 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
31004530 ATGTAATATA
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:31008544 original size:29 final size:30
Alignment explanation
Indices: 31008484--31008596 Score: 110
Period size: 29 Copynumber: 3.8 Consensus size: 30
31008474 TAATATGATT
*
31008484 TAAAATGAAAAAAT-TATATATAAATTTA-A
1 TAAAAT-AAAAAATATATATATAATTTTATA
*
31008513 TAAAATAAAAAATATAT-TATATTTTTATA
1 TAAAATAAAAAATATATATATAATTTTATA
* **
31008542 TAACATAAATTATA-ATATATAATTTTATA
1 TAAAATAAAAAATATATATATAATTTTATA
*
31008571 TAAAATATAATAAAAATATATA-AATT
1 TAAAATA-AA-AAATATATATATAATT
31008597 ACCAATATTT
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
28 17 0.25
29 38 0.56
30 2 0.03
31 6 0.09
32 5 0.07
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (30 bp):
TAAAATAAAAAATATATATATAATTTTATA
Found at i:31009458 original size:21 final size:21
Alignment explanation
Indices: 31009433--31009479 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
31009423 ACCTATAATC
*
31009433 ATATTCGATTTTACATAAT-AA
1 ATATTCGAATTTA-ATAATAAA
*
31009454 ATATTCGAATTTAATATTAAA
1 ATATTCGAATTTAATAATAAA
31009475 ATATT
1 ATATT
31009480 ATTTTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (21 bp):
ATATTCGAATTTAATAATAAA
Found at i:31009556 original size:18 final size:17
Alignment explanation
Indices: 31009515--31009559 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
31009505 ATTAAAAATT
31009515 AATAAAATAT-TTTTAA
1 AATAAAATATATTTTAA
**
31009531 CTTAAAATATATTTTAA
1 AATAAAATATATTTTAA
31009548 AATATAAATATA
1 AATA-AAATATA
31009560 AAATTAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 8 0.35
17 8 0.35
18 7 0.30
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
AATAAAATATATTTTAA
Found at i:31009702 original size:1 final size:1
Alignment explanation
Indices: 31009696--31009723 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
31009686 CTCAATTTAC
31009696 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
31009724 GACCCTCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:31016098 original size:16 final size:17
Alignment explanation
Indices: 31016079--31016112 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
31016069 GATCGTAAGT
*
31016079 ATTTTTTTG-GTTTGAA
1 ATTTTTTAGTGTTTGAA
31016095 ATTTTTTAGTGTTTGAA
1 ATTTTTTAGTGTTTGAA
31016112 A
1 A
31016113 ATCATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.59
Consensus pattern (17 bp):
ATTTTTTAGTGTTTGAA
Found at i:31016187 original size:16 final size:17
Alignment explanation
Indices: 31016168--31016200 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31016158 TAAAAAAATA
31016168 TTTT-TTTTGAAAATTT
1 TTTTATTTTGAAAATTT
*
31016184 TTTTATTTTTAAAATTT
1 TTTTATTTTGAAAATTT
31016201 AAAATTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTTATTTTGAAAATTT
Found at i:31016781 original size:23 final size:22
Alignment explanation
Indices: 31016728--31016782 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
31016718 ATTAAATCGA
*
31016728 TAAAATTTAATTCGATTAGTAT
1 TAAAATTTAATTCGATTAGAAT
*
31016750 AAAAATTTAATTCGAATTTA-AAT
1 TAAAATTTAATTCG-A-TTAGAAT
31016773 TAAAATTTAA
1 TAAAATTTAA
31016783 ATTTTTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 13 0.46
23 12 0.43
24 3 0.11
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (22 bp):
TAAAATTTAATTCGATTAGAAT
Found at i:31017452 original size:16 final size:16
Alignment explanation
Indices: 31017433--31017475 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
31017423 ATATTTTTTA
*
31017433 ATATAAATATAAAATT
1 ATATAAATATAAAAGT
31017449 ATATATTAATATAAAAGT
1 ATATA--AATATAAAAGT
*
31017467 AAATAAATA
1 ATATAAATA
31017476 ATTAAAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 9 0.39
18 14 0.61
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (16 bp):
ATATAAATATAAAAGT
Found at i:31019271 original size:59 final size:58
Alignment explanation
Indices: 31019133--31019468 Score: 425
Period size: 59 Copynumber: 5.7 Consensus size: 58
31019123 TCTTGTGCAG
**
31019133 AGAAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTGAAAA-TTTATTTTTAA
1 AGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAATTTTATTTTTAA
* * *
31019190 AGAAAATTGATACTTTCAACTTTTTCC-CAAAATTATTTTTTGAAAAATTTAATTTTCAA
1 AGAAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTTG-AAAATTTTATTTTTAA
* *
31019249 AGAAAATTAATACTTTCAACTTTTCCTCAAAAACCCT-TTTTTTG-AAATTTTTTTTTTAA
1 AGAAAATTGATACTTTCAACTTTTCCTCAAAAA---TATTTTTTGAAAATTTTATTTTTAA
31019308 AGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTG-AAATTTTATTTTTAA
1 AGAAAATTGATACTTTCAACTTTTCCTCAAAAATA--TTTTTTGAAAATTTTATTTTTAA
* * *
31019367 GGAAAATTGATACTTTCAACTTTTCCCCAAAAACTTTTTTTTTTTG-AAATTTTATTTTT-A
1 AGAAAATTGATACTTTCAACTTTTCCTCAAAAA----TATTTTTTGAAAATTTTATTTTTAA
31019427 AGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
1 AG-AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
31019469 TGATTTTTAT
Statistics
Matches: 246, Mismatches: 18, Indels: 30
0.84 0.06 0.10
Matches are distributed among these distances:
56 1 0.00
57 41 0.17
58 14 0.06
59 129 0.52
60 2 0.01
61 57 0.23
62 1 0.00
63 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.47
Consensus pattern (58 bp):
AGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAATTTTATTTTTAA
Found at i:31019495 original size:5 final size:5
Alignment explanation
Indices: 31019480--31019571 Score: 54
Period size: 5 Copynumber: 18.8 Consensus size: 5
31019470 GATTTTTATT
* *
31019480 TAAAA -AAAA TAAAA T--AA TAAAA CCAAAA TAAAA GTGAAAA TTAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA -TAAAA TAAAA -T-AAAA TAAAA
* *
31019525 -AAAA TAAAA TAAGAA -AAAG TAAAA CAAAA -ATAAA -AAAA TAAAA TAAA
1 TAAAA TAAAA TAA-AA TAAAA TAAAA TAAAA TA-AAA TAAAA TAAAA TAAA
31019572 GGTAAAAAGA
Statistics
Matches: 69, Mismatches: 7, Indels: 22
0.70 0.07 0.22
Matches are distributed among these distances:
3 3 0.04
4 12 0.17
5 42 0.61
6 8 0.12
7 4 0.06
ACGTcount: A:0.77, C:0.03, G:0.04, T:0.15
Consensus pattern (5 bp):
TAAAA
Found at i:31019577 original size:19 final size:18
Alignment explanation
Indices: 31019482--31019584 Score: 54
Period size: 19 Copynumber: 5.5 Consensus size: 18
31019472 TTTTTATTTA
31019482 AAAAAAATAAAAT-AA-T
1 AAAAAAATAAAATAAAGT
*
31019498 AAAACCAAAATAAAAGTGAAAATT
1 -AAA--AAAATAAAA-T--AAAGT
31019522 AAAAAAATAAAAT-AAG-
1 AAAAAAATAAAATAAAGT
* * *
31019538 -AAAAAGTAAAACAAAAAT
1 AAAAAAATAAAA-TAAAGT
31019556 AAAAAAATAAAATAAAGGT
1 AAAAAAATAAAATAAA-GT
31019575 AAAAAGAATA
1 AAAAA-AATA
31019585 TTAAATAAAC
Statistics
Matches: 66, Mismatches: 7, Indels: 23
0.69 0.07 0.24
Matches are distributed among these distances:
15 10 0.15
17 7 0.11
18 3 0.05
19 25 0.38
20 6 0.09
21 9 0.14
23 5 0.08
24 1 0.02
ACGTcount: A:0.76, C:0.03, G:0.07, T:0.15
Consensus pattern (18 bp):
AAAAAAATAAAATAAAGT
Found at i:31020560 original size:24 final size:21
Alignment explanation
Indices: 31020518--31020615 Score: 99
Period size: 24 Copynumber: 4.3 Consensus size: 21
31020508 AGATAATTAG
31020518 AAAAATAATAATAAGATAAAT
1 AAAAATAATAATAAGATAAAT
31020539 CAAAAATAATATTATAAGATAAAT
1 -AAAAATAATA--ATAAGATAAAT
31020563 AATAATAATAATAATAACAGATAAAT
1 -A-AA-AATAATAAT-A-AGATAAAT
* *
31020589 AAATAT-ATAATTAGATAAAT
1 AAAAATAATAATAAGATAAAT
31020609 AAAAATA
1 AAAAATA
31020616 CATACAAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
20 13 0.20
22 15 0.23
23 2 0.03
24 16 0.25
25 4 0.06
26 15 0.23
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (21 bp):
AAAAATAATAATAAGATAAAT
Found at i:31020592 original size:4 final size:4
Alignment explanation
Indices: 31020583--31020695 Score: 60
Period size: 4 Copynumber: 28.8 Consensus size: 4
31020573 ATAATAACAG
* * * * *
31020583 ATAA ATAA ATAT ATAA TTAG ATAA AT-A A-AA ATAC ATAC A-AA ATAAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT-AA
* * *
31020629 ATGAA AAAA AGAA A-AA ATAAA ATAA ATATA TATTA ATAA AT-A AT-A
1 AT-AA ATAA ATAA ATAA AT-AA ATAA ATA-A -ATAA ATAA ATAA ATAA
31020674 ATAA ATAA ATAA AT-A ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATA
31020696 CATAGGATAT
Statistics
Matches: 86, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
3 18 0.21
4 53 0.62
5 13 0.15
6 2 0.02
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:31020666 original size:14 final size:13
Alignment explanation
Indices: 31020649--31020695 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
31020639 GAAAAAATAA
31020649 AATAAATATATATT
1 AATAAATA-ATATT
*
31020663 AATAAATAATAATA
1 AATAAATAAT-ATT
31020677 AATAAATAA-A-T
1 AATAAATAATATT
31020688 AATAAATA
1 AATAAATA
31020696 CATAGGATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
11 8 0.27
12 1 0.03
13 2 0.07
14 19 0.63
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AATAAATAATATT
Found at i:31020671 original size:18 final size:15
Alignment explanation
Indices: 31020542--31020695 Score: 88
Period size: 16 Copynumber: 10.1 Consensus size: 15
31020532 GATAAATCAA
*
31020542 AAATAATATTATAAGAT
1 AAATAA-ATAATAA-AT
31020559 AAAT-AATAAT-AAT
1 AAATAAATAATAAAT
* *
31020572 -AAT-AATAACAGAT
1 AAATAAATAATAAAT
*
31020585 AAATAAATATATAATT
1 AAATAAATA-ATAAAT
*
31020601 AGATAAATAA-AAAT
1 AAATAAATAATAAAT
*
31020615 ACATACAA-AATAAAAT
1 AAATA-AATAAT-AAAT
* * *
31020631 GAAAAAAAGAAAAAAT
1 -AAATAAATAATAAAT
31020647 AAAATAAATATATATTAAT
1 -AAATAAATA-ATA--AAT
31020666 AAAT-AATAATAAAT
1 AAATAAATAATAAAT
31020680 AAATAAATAATAAAT
1 AAATAAATAATAAAT
31020695 A
1 A
31020696 CATAGGATAT
Statistics
Matches: 108, Mismatches: 16, Indels: 28
0.71 0.11 0.18
Matches are distributed among these distances:
12 8 0.07
13 4 0.04
14 20 0.19
15 22 0.20
16 32 0.30
17 15 0.14
18 4 0.04
19 3 0.03
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (15 bp):
AAATAAATAATAAAT
Found at i:31020716 original size:25 final size:26
Alignment explanation
Indices: 31020662--31020733 Score: 78
Period size: 25 Copynumber: 2.8 Consensus size: 26
31020652 AAATATATAT
*
31020662 TAATAAATA-ATAATAA-ATAAATAAA
1 TAATAAATACATAA-AATATAAAGAAA
**
31020687 TAATAAATACATAGGATATAAAGAAA
1 TAATAAATACATAAAATATAAAGAAA
*
31020713 -AATATATACATAAAATATAAA
1 TAATAAATACATAAAATATAAA
31020734 ATAAGAATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 28 0.72
26 11 0.28
ACGTcount: A:0.67, C:0.03, G:0.04, T:0.26
Consensus pattern (26 bp):
TAATAAATACATAAAATATAAAGAAA
Found at i:31020937 original size:12 final size:12
Alignment explanation
Indices: 31020920--31020965 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
31020910 AACATTTTCA
31020920 TTTTTTGATTTT
1 TTTTTTGATTTT
*
31020932 TTTTTTGTTTTT
1 TTTTTTGATTTT
*
31020944 TTATTTTAATTTT
1 TT-TTTTGATTTT
31020957 TATTTTTGA
1 T-TTTTTGA
31020966 CCAAAGCACC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
12 13 0.46
13 14 0.50
14 1 0.04
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (12 bp):
TTTTTTGATTTT
Found at i:31021061 original size:43 final size:43
Alignment explanation
Indices: 31020976--31021128 Score: 227
Period size: 43 Copynumber: 3.6 Consensus size: 43
31020966 CCAAAGCACC
* * *
31020976 TCTAAACAGAGGCTCAACGACTTT-GAAAAAATAAATAGCTCA
1 TCTAAACAGAGGCACCACGACTTTGGAAAAAATAAATTGCTCA
31021018 TCTAAACAGAGGCACCACGACTTTGGAAAAAATAAATTGCTCA
1 TCTAAACAGAGGCACCACGACTTTGGAAAAAATAAATTGCTCA
* * * *
31021061 TCTAAACAGAGGCACCACGACTTTTGAAAAAGTAAATTACTCC
1 TCTAAACAGAGGCACCACGACTTTGGAAAAAATAAATTGCTCA
*
31021104 TCTAAACAGAGGCACCACAACTTTG
1 TCTAAACAGAGGCACCACGACTTTG
31021129 ACCTCCTTTA
Statistics
Matches: 101, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
42 22 0.22
43 79 0.78
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (43 bp):
TCTAAACAGAGGCACCACGACTTTGGAAAAAATAAATTGCTCA
Found at i:31021141 original size:31 final size:31
Alignment explanation
Indices: 31021100--31021160 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
31021090 AAGTAAATTA
31021100 CTCCTCTAAACAGAGGCACCACAACTTTGAC
1 CTCCTCTAAACAGAGGCACCACAACTTTGAC
* *
31021131 CTCCTTTAAACAGAGGCACCACGACTTTGA
1 CTCCTCTAAACAGAGGCACCACAACTTTGA
31021161 AAAGTAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (31 bp):
CTCCTCTAAACAGAGGCACCACAACTTTGAC
Found at i:31021187 original size:72 final size:74
Alignment explanation
Indices: 31021063--31021199 Score: 233
Period size: 72 Copynumber: 1.9 Consensus size: 74
31021053 ATTGCTCATC
31021063 TAAACAGAGGCACCACGACTTTTGAAAAAGTAAATTACTCCTCTAAACAGAGGCACCACAACTTT
1 TAAACAGAGGCACCACGACTTTTGAAAAAGTAAATTACTCCTCTAAACAGAGGCACCACAACTTT
31021128 GACCTCCTT
66 GACCTCCTT
* * *
31021137 TAAACAGAGGCACCACGAC-TTTG-AAAAGTAAATTGCTCCTCTAAATAGAGGCACCACGACTTT
1 TAAACAGAGGCACCACGACTTTTGAAAAAGTAAATTACTCCTCTAAACAGAGGCACCACAACTTT
31021200 TGAAAGTAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
72 37 0.62
73 4 0.07
74 19 0.32
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (74 bp):
TAAACAGAGGCACCACGACTTTTGAAAAAGTAAATTACTCCTCTAAACAGAGGCACCACAACTTT
GACCTCCTT
Found at i:31021188 original size:41 final size:41
Alignment explanation
Indices: 31021131--31021217 Score: 140
Period size: 41 Copynumber: 2.1 Consensus size: 41
31021121 CAACTTTGAC
*
31021131 CTCCTTTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATTG
1 CTCCTCTAAACAGAGGCACCACGACTTTTG-AAAGTAAATTG
*
31021172 CTCCTCTAAATAGAGGCACCACGACTTTTGAAAGTAAATTG
1 CTCCTCTAAACAGAGGCACCACGACTTTTGAAAGTAAATTG
31021213 CTCCT
1 CTCCT
31021218 TGACAATCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
41 39 0.91
42 4 0.09
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.26
Consensus pattern (41 bp):
CTCCTCTAAACAGAGGCACCACGACTTTTGAAAGTAAATTG
Found at i:31022506 original size:17 final size:17
Alignment explanation
Indices: 31022486--31022519 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31022476 CATTTTCTCA
31022486 TTTTTTCGTTCTTTTTT
1 TTTTTTCGTTCTTTTTT
**
31022503 TTTTTTTTTTCTTTTTT
1 TTTTTTCGTTCTTTTTT
31022520 CTCATTTTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (17 bp):
TTTTTTCGTTCTTTTTT
Found at i:31026620 original size:58 final size:58
Alignment explanation
Indices: 31026433--31026768 Score: 462
Period size: 59 Copynumber: 5.8 Consensus size: 58
31026423 TCTTATGCAG
** *
31026433 GAAAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTAG-AAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTATTTTTAA
* * * * *
31026490 AAAAAATTGATACTTTCAACTTTTTCC-CAAAATTATTTTTTGGAAACTTTGATTTTCAA
1 GAAAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTTTGAAAATTT-ATTTTTAA
**
31026549 GAAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTGAAAATTT-TTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAA-TATTTTTTTGAAAATTTATTTTTAA
* *
31026607 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTTTGAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAA-TATTTTTTTGAAAATTTATTTTTAA
** * *
31026666 GAAAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTTGAAACTTTGATTTTCAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTT-ATTTTTAA
31026725 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGA
31026769 TTTTTATTTA
Statistics
Matches: 247, Mismatches: 25, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
57 33 0.13
58 84 0.34
59 117 0.47
60 13 0.05
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (58 bp):
GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTATTTTTAA
Found at i:31026668 original size:117 final size:117
Alignment explanation
Indices: 31026433--31026768 Score: 475
Period size: 117 Copynumber: 2.9 Consensus size: 117
31026423 TCTTATGCAG
* *
31026433 GAAAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTAG-AAATTTATTTTTAAAAAAAAT
1 GAAAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTTGAAAATTTATTTTTAAGAAAAAT
* *
31026497 TGATACTTTCAACTTTTTCC-C-AAAATTATTTTTTGGAAACTTTGATTTTCAA
66 TGATACTTTCAAC-TTTTCCTCAAAAATT-TTTTTTTGAAAATTTGATTTTCAA
** ** *
31026549 GAAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTGAAAATTT-TTTTTAAGGAAAA
1 GAAAAATTGATACTTTCAACTTTTTTTCAAAAA-TATTTTTTTGAAAATTTATTTTTAAGAAAAA
*
31026613 TTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTTTGAAAATTT-ATTTTTAA
65 TTGATACTTTCAACTTTTCCTCAAAAA-TTTTTTTTTGAAAATTTGATTTTCAA
* *
31026666 GAAAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTTGAAACTTTGATTTTCAAGAAAAA
1 GAAAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTTGAAAATTT-ATTTTTAAGAAAAA
*
31026731 TTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGA
65 TTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTTGA
31026769 TTTTTATTTA
Statistics
Matches: 195, Mismatches: 18, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
116 51 0.26
117 81 0.42
118 61 0.31
119 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (117 bp):
GAAAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTTGAAAATTTATTTTTAAGAAAAAT
TGATACTTTCAACTTTTCCTCAAAAATTTTTTTTTGAAAATTTGATTTTCAA
Found at i:31026673 original size:176 final size:174
Alignment explanation
Indices: 31026435--31026757 Score: 547
Period size: 176 Copynumber: 1.8 Consensus size: 174
31026425 TTATGCAGGA
**
31026435 AAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTAGAAATTTATTTTTAAAAAAAATTGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAATTTATTTTTAAAAAAAATTGA
*
31026500 TACTTTCAACTTTTTCCCAAAATTATTTTTTGGAAACTTTGATTTTCAAGAAAAATTGATACTTT
66 TACTTTCAACTTTTTCCCAAAAATATTTTTTGGAAACTTTGATTTTCAAGAAAAATTGATACTTT
31026565 CAACTTTTCCTCAAAAACCCTTTTTTTGAAAATTTTTTTTAAGG
131 CAACTTTTCCTCAAAAACCCTTTTTTTGAAAATTTTTTTTAAGG
* * *
31026609 AAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTTTGAAAATTTATTTTTAAGAAAAATT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA-TATTTTTTAG-AAATTTATTTTTAAAAAAAATT
** *
31026674 GATACTTTCAACTTTTTTTCAAAAATATTTTTTTGAAACTTTGATTTTCAAGAAAAATTGATACT
64 GATACTTTCAACTTTTTCCCAAAAATATTTTTTGGAAACTTTGATTTTCAAGAAAAATTGATACT
31026739 TTCAACTTTTCCTCAAAAA
129 TTCAACTTTTCCTCAAAAA
31026758 TATTTTTTTG
Statistics
Matches: 138, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
174 29 0.21
175 8 0.06
176 101 0.73
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (174 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAATTTATTTTTAAAAAAAATTGA
TACTTTCAACTTTTTCCCAAAAATATTTTTTGGAAACTTTGATTTTCAAGAAAAATTGATACTTT
CAACTTTTCCTCAAAAACCCTTTTTTTGAAAATTTTTTTTAAGG
Found at i:31026823 original size:14 final size:15
Alignment explanation
Indices: 31026806--31026862 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
31026796 AAACCAAAAC
31026806 AAAAATGAAAATAAA-
1 AAAAAT-AAAATAAAG
31026821 AAAAATAAAAT-AAG
1 AAAAATAAAATAAAG
*
31026835 AAAAAGTAAAACAAA-
1 AAAAA-TAAAATAAAG
*
31026850 AATAA-AAAATAAA
1 AAAAATAAAATAAA
31026863 ATAAAGGTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
13 9 0.25
14 10 0.28
15 15 0.42
16 2 0.06
ACGTcount: A:0.81, C:0.02, G:0.05, T:0.12
Consensus pattern (15 bp):
AAAAATAAAATAAAG
Found at i:31026826 original size:15 final size:15
Alignment explanation
Indices: 31026806--31026845 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
31026796 AAACCAAAAC
31026806 AAAAATGAAAATAA-A
1 AAAAAT-AAAATAAGA
31026821 AAAAATAAAATAAGA
1 AAAAATAAAATAAGA
*
31026836 AAAAGTAAAA
1 AAAAATAAAA
31026846 CAAAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.12
Consensus pattern (15 bp):
AAAAATAAAATAAGA
Found at i:31026830 original size:26 final size:25
Alignment explanation
Indices: 31026782--31026867 Score: 70
Period size: 26 Copynumber: 3.5 Consensus size: 25
31026772 TTATTTAAAG
* *
31026782 AAAATAAAATAATAAAACCAAAACA
1 AAAATAAAATAAAAAAAACAAAACA
* *
31026807 AAAATGAAAATAAAAAAAATAAAATA
1 AAAAT-AAAATAAAAAAAACAAAACA
* * * *
31026833 AGAA-AAAGTAAAACAAA-AATA-A
1 AAAATAAAATAAAAAAAACAAAACA
31026855 AAAATAAAATAAA
1 AAAATAAAATAAA
31026868 GGTAAAAAGA
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
22 4 0.08
23 10 0.20
24 11 0.22
25 5 0.10
26 19 0.39
ACGTcount: A:0.79, C:0.05, G:0.03, T:0.13
Consensus pattern (25 bp):
AAAATAAAATAAAAAAAACAAAACA
Found at i:31026850 original size:29 final size:29
Alignment explanation
Indices: 31026813--31026874 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
31026803 AACAAAAATG
*
31026813 AAAATAAAAAAAATAAAATAAGAA-AAA-GT
1 AAAACAAAAAAAA-AAAATAA-AATAAAGGT
*
31026842 AAAACAAAAATAAAAAATAAAATAAAGGT
1 AAAACAAAAAAAAAAAATAAAATAAAGGT
31026871 AAAA
1 AAAA
31026875 AGAATACTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 2 0.07
28 10 0.34
29 17 0.59
ACGTcount: A:0.79, C:0.02, G:0.06, T:0.13
Consensus pattern (29 bp):
AAAACAAAAAAAAAAAATAAAATAAAGGT
Found at i:31026873 original size:18 final size:17
Alignment explanation
Indices: 31026820--31026875 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 17
31026810 ATGAAAATAA
31026820 AAAAAATAAAAT-AAG-
1 AAAAAATAAAATAAAGT
* * *
31026835 AAAAAGTAAAACAAAAAT
1 AAAAAATAAAA-TAAAGT
31026853 AAAAAATAAAATAAAGGT
1 AAAAAATAAAATAAA-GT
31026871 AAAAA
1 AAAAA
31026876 GAATACTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
15 10 0.32
17 5 0.16
18 16 0.52
ACGTcount: A:0.79, C:0.02, G:0.07, T:0.12
Consensus pattern (17 bp):
AAAAAATAAAATAAAGT
Found at i:31026905 original size:4 final size:4
Alignment explanation
Indices: 31026898--31026924 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
31026888 AACTTAATCT
31026898 AATA AATA AATA AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AAT
31026925 TAAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:31027821 original size:15 final size:15
Alignment explanation
Indices: 31027791--31027833 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
31027781 TAAAAATCAC
31027791 ATAA-AAAAATAGATA
1 ATAAGAAAAATA-ATA
*
31027806 ATTAGAAAAATAATA
1 ATAAGAAAAATAATA
*
31027821 ATAAGATAAATAA
1 ATAAGAAAAATAA
31027834 AAAATAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (15 bp):
ATAAGAAAAATAATA
Found at i:31027839 original size:19 final size:21
Alignment explanation
Indices: 31027811--31027906 Score: 97
Period size: 22 Copynumber: 4.3 Consensus size: 21
31027801 AGATAATTAG
31027811 AAAAATAATAATAAGATAAAT
1 AAAAATAATAATAAGATAAAT
31027832 AAAAAATAATATTATAAGATAAAT
1 -AAAAATAATA--ATAAGATAAAT
*
31027856 AAAAAATAATAATAACAT--AT
1 -AAAAATAATAATAAGATAAAT
*
31027876 AAATAGATATATAATTAGATAAAT
1 AAA-A-ATA-ATAATAAGATAAAT
31027900 AAAAATA
1 AAAAATA
31027907 CATACAAAAT
Statistics
Matches: 64, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
19 3 0.05
20 3 0.05
21 3 0.05
22 27 0.42
23 1 0.02
24 27 0.42
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (21 bp):
AAAAATAATAATAAGATAAAT
Found at i:31027853 original size:24 final size:22
Alignment explanation
Indices: 31027801--31027904 Score: 113
Period size: 24 Copynumber: 4.6 Consensus size: 22
31027791 ATAAAAAAAT
*
31027801 AGATAATTAGAAAAATAATAATA
1 AGATAAATA-AAAAATAATAATA
31027824 AGATAAATAAAAAATAATATTATA
1 AGATAAATAAAAAATAATA--ATA
31027848 AGATAAATAAAAAATAATAATA
1 AGATAAATAAAAAATAATAATA
* * *
31027870 ACAT--ATAAATAGATATATAATT
1 AGATAAATAAA-AAATA-ATAATA
31027892 AGATAAATAAAAA
1 AGATAAATAAAAA
31027905 TACATACAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
20 5 0.07
21 4 0.06
22 24 0.35
23 9 0.13
24 27 0.39
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.27
Consensus pattern (22 bp):
AGATAAATAAAAAATAATAATA
Found at i:31027898 original size:44 final size:45
Alignment explanation
Indices: 31027800--31027904 Score: 124
Period size: 44 Copynumber: 2.3 Consensus size: 45
31027790 CATAAAAAAA
* * *
31027800 TAGATAATTAGAAAAATAATAATAAGATAAATAAAAAATAATATTAT
1 TAGATAAATA-AAAAATAATAATAACAT-AATAAAAAATAATATAAT
* *
31027847 AAGATAAATAAAAAATAATAATAACAT-ATAAATAGAT-ATATAAT
1 TAGATAAATAAAAAATAATAATAACATAATAAA-AAATAATATAAT
31027891 TAGATAAATAAAAA
1 TAGATAAATAAAAA
31027905 TACATACAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
44 24 0.47
45 3 0.06
46 16 0.31
47 8 0.16
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.28
Consensus pattern (45 bp):
TAGATAAATAAAAAATAATAATAACATAATAAAAAATAATATAAT
Found at i:31027960 original size:16 final size:16
Alignment explanation
Indices: 31027935--31027983 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
31027925 AAAGAAAAAA
*
31027935 AATAAAAAAT-ATATAT
1 AATAATAAATAATA-AT
*
31027951 ATTAATAAATAATAAT
1 AATAATAAATAATAAT
31027967 AATAATAAATAATAAT
1 AATAATAAATAATAAT
31027983 A
1 A
31027984 CATAGGATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 26 0.90
17 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAATAAATAATAAT
Found at i:31028031 original size:11 final size:11
Alignment explanation
Indices: 31028010--31028060 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
31028000 AAATATATAC
31028010 ATAAAATATAAA
1 ATAAAA-ATAAA
*
31028022 ATAAGAATAAA
1 ATAAAAATAAA
31028033 ATAAAAATAACA
1 ATAAAAATAA-A
**
31028045 A-AAATGTAAA
1 ATAAAAATAAA
31028055 ATAAAA
1 ATAAAA
31028061 TTAGACTTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
10 2 0.06
11 23 0.72
12 7 0.22
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (11 bp):
ATAAAAATAAA
Found at i:31034422 original size:25 final size:25
Alignment explanation
Indices: 31034352--31034422 Score: 67
Period size: 25 Copynumber: 3.0 Consensus size: 25
31034342 ATAGTGTAAA
*
31034352 ATATTAAAATTTATAT--ATATT-T
1 ATATTATAATTTATATAAATATTAT
* *
31034374 ATATTATATTTTATATAAAAATTAT
1 ATATTATAATTTATATAAATATTAT
* * *
31034399 ATGTTATAATTTATTTTAATATTA
1 ATATTATAATTTATATAAATATTA
31034423 AAATATAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
22 14 0.37
24 4 0.11
25 20 0.53
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (25 bp):
ATATTATAATTTATATAAATATTAT
Found at i:31034426 original size:31 final size:34
Alignment explanation
Indices: 31034351--31034473 Score: 97
Period size: 31 Copynumber: 3.9 Consensus size: 34
31034341 TATAGTGTAA
*
31034351 AATATTAAAATTTATATATATTTATATTATATTTT
1 AATATTAAAA-TTATATATATATATATTATATTTT
* *
31034386 -ATATAAAAATTATATGT-TATA-ATT-TATTTT
1 AATATTAAAATTATATATATATATATTATATTTT
*
31034416 AATATTAAAA-TATA-AAATATATATT-T-TTAATT
1 AATATTAAAATTATATATATATATATTATATT--TT
*
31034448 -ATATTAAAATCATATATA-AT-TATTAT
1 AATATTAAAATTATATATATATATATTAT
31034474 TAAAATTTTA
Statistics
Matches: 72, Mismatches: 8, Indels: 19
0.73 0.08 0.19
Matches are distributed among these distances:
30 16 0.22
31 28 0.39
32 11 0.15
33 9 0.12
34 8 0.11
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (34 bp):
AATATTAAAATTATATATATATATATTATATTTT
Found at i:31034472 original size:24 final size:24
Alignment explanation
Indices: 31034428--31034473 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
31034418 TATTAAAATA
**
31034428 TAAAATATATATTTTTAATTATAT
1 TAAAATATATATAATTAATTATAT
31034452 TAAAATCATATATAATT-ATTAT
1 TAAAAT-ATATATAATTAATTAT
31034474 TAAAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TAAAATATATATAATTAATTATAT
Found at i:31036667 original size:15 final size:15
Alignment explanation
Indices: 31036569--31036657 Score: 76
Period size: 15 Copynumber: 6.0 Consensus size: 15
31036559 TCATTCGAAG
* *
31036569 TTAATAATATTAAAA
1 TTAAAAATATTTAAA
* * *
31036584 ATAAATATTATTTTAA
1 TTAAA-AATATTTAAA
*
31036600 TTAATAAATATAT-AA
1 TTAA-AAATATTTAAA
*
31036615 TT-TAAATA-TTAAA
1 TTAAAAATATTTAAA
31036628 TTAAAAATATTTAAA
1 TTAAAAATATTTAAA
31036643 TTAAAAATATTTAAA
1 TTAAAAATATTTAAA
31036658 ATTTAAATAT
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
12 1 0.02
13 9 0.16
14 5 0.09
15 27 0.47
16 15 0.26
17 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTAAAAATATTTAAA
Found at i:31036667 original size:44 final size:43
Alignment explanation
Indices: 31036574--31036681 Score: 123
Period size: 44 Copynumber: 2.5 Consensus size: 43
31036564 CGAAGTTAAT
* * *
31036574 AATATTAAAAATAAATATTATTTTAATTAATAAATATATAATTTA
1 AATATT-AAAATAAA-AATATTTAAATTAATAAATATAAAATTTA
*
31036619 AATATTAAATTAAAAATATTTAAATTAA-AAATATTTAAAATTTA
1 AATATTAAAATAAAAATATTTAAATTAATAAATA--TAAAATTTA
31036663 AATA-TAAAAT-AAAATATTT
1 AATATTAAAATAAAAATATTT
31036682 TATTATAATT
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
42 14 0.25
43 17 0.30
44 19 0.34
45 6 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (43 bp):
AATATTAAAATAAAAATATTTAAATTAATAAATATAAAATTTA
Found at i:31036672 original size:22 final size:22
Alignment explanation
Indices: 31036613--31036673 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
31036603 ATAAATATAT
*
31036613 AATTTAAATATTAAAT-TAAAA
1 AATTTAAATATAAAATATAAAA
**
31036634 ATATTTAAAT-TAAAAATATTTAA
1 A-ATTTAAATAT-AAAATATAAAA
31036657 AATTTAAATATAAAATA
1 AATTTAAATATAAAATA
31036674 AAATATTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 2 0.06
22 26 0.79
23 5 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTTAAATATAAAATATAAAA
Found at i:31037392 original size:24 final size:24
Alignment explanation
Indices: 31037350--31037412 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
31037340 AATTATATCA
*
31037350 TTTTATTTGATAATAATTTAAAAT
1 TTTTATATGATAATAATTTAAAAT
* * *
31037374 TTTTATATGATAGTGATTTTAAAT
1 TTTTATATGATAATAATTTAAAAT
* *
31037398 TATTA-AAGATAATAA
1 TTTTATATGATAATAA
31037413 AATAATTACC
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
23 7 0.23
24 24 0.77
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (24 bp):
TTTTATATGATAATAATTTAAAAT
Found at i:31037698 original size:8 final size:7
Alignment explanation
Indices: 31037672--31037724 Score: 63
Period size: 7 Copynumber: 7.3 Consensus size: 7
31037662 TCAAAATTGA
31037672 TTTATAT
1 TTTATAT
31037679 TTTATAT
1 TTTATAT
31037686 TTTATAGT
1 TTTATA-T
31037694 TTTAT-T
1 TTTATAT
*
31037700 TTGGATAT
1 TT-TATAT
31037708 TTTATAT
1 TTTATAT
31037715 TTTATGAT
1 TTTAT-AT
31037723 TT
1 TT
31037725 ATTTTTCATA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
6 3 0.08
7 24 0.60
8 13 0.32
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.68
Consensus pattern (7 bp):
TTTATAT
Found at i:31037730 original size:29 final size:29
Alignment explanation
Indices: 31037675--31037729 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
31037665 AAATTGATTT
*
31037675 ATATTTTATATTTTATAGTTTTATTTTGG
1 ATATTTTATATTTTATAGATTTATTTTGG
31037704 ATATTTTATATTTTAT-GATTTATTTT
1 ATATTTTATATTTTATAGATTTATTTT
31037730 TCATATAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.67
Consensus pattern (29 bp):
ATATTTTATATTTTATAGATTTATTTTGG
Found at i:31046393 original size:106 final size:107
Alignment explanation
Indices: 31046195--31046401 Score: 317
Period size: 106 Copynumber: 1.9 Consensus size: 107
31046185 TATTAACCCA
* *
31046195 TAGTATCAAAATGGGTTCTTTACTAGAAAGAATTACTTCAACCAAGAAGGGATCCATAACTTCTA
1 TAGTATCAAAACGGGTTCTTTACAAGAAAGAATTACTTCAACCAAGAAGGGATCCATAACTTCTA
* * *
31046260 TTCTAGTAGTTTATGTACCTACGGATGAT-TTGACCGACCTT
66 TTCTAGCAGTTTATGTACCCACAGATGATATTGACCGACCTT
* * * *
31046301 TAGTATCGAAACGGGTTTTTTACAAGAAAGAATTACTTCTACCAAGGAGGGATCCATAACTTCTA
1 TAGTATCAAAACGGGTTCTTTACAAGAAAGAATTACTTCAACCAAGAAGGGATCCATAACTTCTA
*
31046366 TTCTAGCAGTTTATGTACCCGCAGATGATATTGACC
66 TTCTAGCAGTTTATGTACCCACAGATGATATTGACC
31046402 AACCCTGCCC
Statistics
Matches: 90, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
106 84 0.93
107 6 0.07
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (107 bp):
TAGTATCAAAACGGGTTCTTTACAAGAAAGAATTACTTCAACCAAGAAGGGATCCATAACTTCTA
TTCTAGCAGTTTATGTACCCACAGATGATATTGACCGACCTT
Found at i:31052992 original size:19 final size:18
Alignment explanation
Indices: 31052951--31052996 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
31052941 TGTTTGACAG
31052951 AAAATTGACTAGTCAACA
1 AAAATTGACTAGTCAACA
* *
31052969 AAAATTGGCTGGTCAACA
1 AAAATTGACTAGTCAACA
*
31052987 AAAAATGACT
1 AAAATTGACT
31052997 TGCTGGTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (18 bp):
AAAATTGACTAGTCAACA
Found at i:31053150 original size:18 final size:16
Alignment explanation
Indices: 31053115--31053157 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 16
31053105 GCTTTTGAGC
*
31053115 ATAATTTTACTTATAA
1 ATAATATTACTTATAA
31053131 ATAATATTACATTAATAA
1 ATAATATTAC-TT-ATAA
31053149 ATAATATTA
1 ATAATATTA
31053158 TAATATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 9 0.38
17 2 0.08
18 13 0.54
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATATTACTTATAA
Found at i:31053285 original size:15 final size:15
Alignment explanation
Indices: 31053265--31053305 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
31053255 TATAATTATT
*
31053265 TTTTAATATTAATAA
1 TTTTAATATAAATAA
31053280 TTTTAATAATAAATAA
1 TTTTAAT-ATAAATAA
*
31053296 TTTCAATATA
1 TTTTAATATA
31053306 CTTTAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTTAATATAAATAA
Found at i:31056492 original size:6 final size:6
Alignment explanation
Indices: 31056478--31056555 Score: 61
Period size: 6 Copynumber: 13.3 Consensus size: 6
31056468 AAGATATATG
* * * * * ** *
31056478 TACACA TACATA TACATA TATATA TAGATA TATACA TATGTA TATATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
*
31056526 TAC--A TACATA TACATA TACATA CACATA TA
1 TACATA TACATA TACATA TACATA TACATA TA
31056556 TAAAATGTAT
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
4 4 0.07
6 55 0.93
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.35
Consensus pattern (6 bp):
TACATA
Found at i:31056500 original size:2 final size:2
Alignment explanation
Indices: 31056487--31056587 Score: 60
Period size: 2 Copynumber: 51.0 Consensus size: 2
31056477 GTACACATAC
* * * * *
31056487 AT AT AC AT AT AT AT AT AG AT AT AT AC AT AT GT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * * *
31056529 AT AC AT AT AC AT AT AC AT AC AC AT AT AT A- AA AT GT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
31056570 GT GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
31056588 GGCCATTTGG
Statistics
Matches: 75, Mismatches: 23, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
1 1 0.01
2 74 0.99
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.40
Consensus pattern (2 bp):
AT
Found at i:31056502 original size:12 final size:12
Alignment explanation
Indices: 31056471--31056557 Score: 70
Period size: 12 Copynumber: 7.4 Consensus size: 12
31056461 AAAATTGAAG
* *
31056471 ATATATGTACAC
1 ATATATATACAT
*
31056483 ATACATATACAT
1 ATATATATACAT
*
31056495 ATATATATAGAT
1 ATATATATACAT
* **
31056507 ATATACATATGT
1 ATATATATACAT
31056519 ATATATATAC--
1 ATATATATACAT
*
31056529 ATACATATACAT
1 ATATATATACAT
* *
31056541 ATACATACACAT
1 ATATATATACAT
31056553 ATATA
1 ATATA
31056558 AAATGTATAT
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
10 9 0.15
12 51 0.85
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.36
Consensus pattern (12 bp):
ATATATATACAT
Found at i:31056524 original size:16 final size:16
Alignment explanation
Indices: 31056471--31056557 Score: 79
Period size: 16 Copynumber: 5.6 Consensus size: 16
31056461 AAAATTGAAG
* *
31056471 ATATATGTACACATAC
1 ATATATATATACATAC
* *
31056487 ATATACATAT--ATAT
1 ATATATATATACATAC
* *
31056501 ATAGATATATACATAT
1 ATATATATATACATAC
*
31056517 GTATATATATACATAC
1 ATATATATATACATAC
*
31056533 ATATACATATACATAC
1 ATATATATATACATAC
*
31056549 ACATATATA
1 ATATATATA
31056558 AAATGTATAT
Statistics
Matches: 56, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
14 11 0.20
16 45 0.80
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.36
Consensus pattern (16 bp):
ATATATATATACATAC
Found at i:31056548 original size:20 final size:20
Alignment explanation
Indices: 31056489--31056557 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
31056479 ACACATACAT
* *
31056489 ATACATATATATATAGATAT
1 ATACATATATATATACATAC
* *
31056509 ATACATATGTATATATATAC
1 ATACATATATATATACATAC
*
31056529 ATACATATACATATACATAC
1 ATACATATATATATACATAC
31056549 --ACATATATA
1 ATACATATATA
31056558 AAATGTATAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
18 8 0.19
20 34 0.81
ACGTcount: A:0.49, C:0.12, G:0.03, T:0.36
Consensus pattern (20 bp):
ATACATATATATATACATAC
Found at i:31059690 original size:18 final size:17
Alignment explanation
Indices: 31059669--31059702 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
31059659 CTGCCTTATC
*
31059669 TTTTTCTTATTGTTTTTT
1 TTTTTATTATT-TTTTTT
31059687 TTTTTATTATTTTTTT
1 TTTTTATTATTTTTTT
31059703 ATATTGATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.09, C:0.03, G:0.03, T:0.85
Consensus pattern (17 bp):
TTTTTATTATTTTTTTT
Found at i:31059693 original size:15 final size:15
Alignment explanation
Indices: 31059669--31059702 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
31059659 CTGCCTTATC
*
31059669 TTTTTCTTATTGTTT
1 TTTTTCTTATTATTT
*
31059684 TTTTTTTTATTATTT
1 TTTTTCTTATTATTT
31059699 TTTT
1 TTTT
31059703 ATATTGATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.03, G:0.03, T:0.85
Consensus pattern (15 bp):
TTTTTCTTATTATTT
Found at i:31060681 original size:16 final size:16
Alignment explanation
Indices: 31060660--31060691 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31060650 TACGATGACA
31060660 TTTAAAAAATATTTAT
1 TTTAAAAAATATTTAT
*
31060676 TTTAAAAATTATTTAT
1 TTTAAAAAATATTTAT
31060692 ATATTGTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAAAAAATATTTAT
Found at i:31060682 original size:15 final size:16
Alignment explanation
Indices: 31060659--31060691 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
31060649 GTACGATGAC
31060659 ATTTAAAAAA-TATTT
1 ATTTAAAAAATTATTT
*
31060674 ATTTTAAAAATTATTT
1 ATTTAAAAAATTATTT
31060690 AT
1 AT
31060692 ATATTGTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTAAAAAATTATTT
Found at i:31061437 original size:26 final size:27
Alignment explanation
Indices: 31061380--31061445 Score: 95
Period size: 26 Copynumber: 2.6 Consensus size: 27
31061370 TATTAATATA
*
31061380 ATTATT-AAA-ATATTAAAATATATTT
1 ATTATTAAAATATATTAAAATAGATTT
31061405 ATTATTAAAATATATTAAAAT-GATTT
1 ATTATTAAAATATATTAAAATAGATTT
31061431 ATTATTAAAAT-TATT
1 ATTATTAAAATATATT
31061446 TATATTCAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
25 10 0.26
26 18 0.47
27 10 0.26
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
ATTATTAAAATATATTAAAATAGATTT
Found at i:31061456 original size:16 final size:15
Alignment explanation
Indices: 31061415--31061467 Score: 61
Period size: 16 Copynumber: 3.4 Consensus size: 15
31061405 ATTATTAAAA
*
31061415 TATATTAAAATGATT
1 TATATTAAAATTATT
31061430 TATTATTAAAATTATT
1 TA-TATTAAAATTATT
* *
31061446 TATATTCAAAAATAAT
1 TATATT-AAAATTATT
31061462 TATATT
1 TATATT
31061468 TAATATTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
15 6 0.18
16 27 0.82
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (15 bp):
TATATTAAAATTATT
Found at i:31061577 original size:13 final size:13
Alignment explanation
Indices: 31061559--31061600 Score: 54
Period size: 11 Copynumber: 3.5 Consensus size: 13
31061549 ATAATATAGG
31061559 TTATTACTAATAT
1 TTATTACTAATAT
*
31061572 TTATTAAT-ATA-
1 TTATTACTAATAT
31061583 TTATTAC-AATAT
1 TTATTACTAATAT
31061595 TTATTA
1 TTATTA
31061601 ATTAAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 9 0.36
12 9 0.36
13 7 0.28
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (13 bp):
TTATTACTAATAT
Found at i:31061579 original size:26 final size:24
Alignment explanation
Indices: 31061528--31061631 Score: 99
Period size: 26 Copynumber: 4.3 Consensus size: 24
31061518 TATTATTCTT
*
31061528 TATATTATTTATTAATATATTA-TAA
1 TATATTA-TTACTAATAT-TTATTAA
31061553 TATAGGTTATTACTAATATTTATTAA
1 TATA--TTATTACTAATATTTATTAA
31061579 TATATTATTAC-AATATTTATTAA
1 TATATTATTACTAATATTTATTAA
* ** *
31061602 T-TA-AATTAAAAATATTTATTAT
1 TATATTATTACTAATATTTATTAA
31061624 TATATTAT
1 TATATTAT
31061632 ATTAATAGTA
Statistics
Matches: 68, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
21 4 0.06
22 14 0.21
23 15 0.22
24 9 0.13
25 7 0.10
26 16 0.24
27 3 0.04
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
TATATTATTACTAATATTTATTAA
Found at i:31061654 original size:18 final size:17
Alignment explanation
Indices: 31061614--31061687 Score: 84
Period size: 18 Copynumber: 4.4 Consensus size: 17
31061604 AAATTAAAAA
31061614 TATTTATT-AT-TATAT
1 TATTTATTAATATATAT
*
31061629 TA--TATTAATAGTATAC
1 TATTTATTAATA-TATAT
31061645 TATTTATTAATATATTAT
1 TATTTATTAATATA-TAT
31061663 TATTTATTAATATAATAT
1 TATTTATTAATAT-ATAT
31061681 TATTTAT
1 TATTTAT
31061688 AAGTAAAATT
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
13 4 0.08
14 2 0.04
15 2 0.04
16 6 0.12
17 2 0.04
18 33 0.66
19 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (17 bp):
TATTTATTAATATATAT
Found at i:31075221 original size:15 final size:14
Alignment explanation
Indices: 31075195--31075234 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
31075185 TAAATATTAA
31075195 TTTTAATA-AAATT
1 TTTTAATATAAATT
31075208 TATTTAATATAAATT
1 T-TTTAATATAAATT
31075223 TTTTAATTATAA
1 TTTTAA-TATAA
31075235 TTATTATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.04
14 12 0.50
15 11 0.46
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTTAATATAAATT
Found at i:31076494 original size:42 final size:42
Alignment explanation
Indices: 31076440--31076540 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
31076430 GATAAAATTT
* *
31076440 TAATTTTTATAACTTTTTAATATAATTTGGTAATATTTAATA
1 TAATTTTGATAACTTTTTAATATAATTTGATAATATTTAATA
* * **
31076482 TAATTTTGATAACTTTTTTATATAATTTGATAATTTTTGTTA
1 TAATTTTGATAACTTTTTAATATAATTTGATAATATTTAATA
* *
31076524 CAATTTTGATAAATTTT
1 TAATTTTGATAACTTTT
31076541 GGTAATCTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (42 bp):
TAATTTTGATAACTTTTTAATATAATTTGATAATATTTAATA
Found at i:31076518 original size:20 final size:21
Alignment explanation
Indices: 31076448--31076519 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
31076438 TTTAATTTTT
31076448 ATAACTTTTTAATATAATTTG
1 ATAACTTTTTAATATAATTTG
* *
31076469 GTAA-TATTTAATATAATTTTG
1 ATAACTTTTTAATATAA-TTTG
*
31076490 ATAACTTTTTTATATAATTTG
1 ATAACTTTTTAATATAATTTG
31076511 ATAA-TTTTT
1 ATAACTTTTT
31076520 GTTACAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
20 16 0.36
21 18 0.41
22 10 0.23
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.56
Consensus pattern (21 bp):
ATAACTTTTTAATATAATTTG
Found at i:31076531 original size:21 final size:22
Alignment explanation
Indices: 31076483--31076541 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
31076473 TATTTAATAT
*
31076483 AATTTTGATAACTTTTT-TATAT
1 AATTTTGATAA-TTTTTGTATAC
31076505 AA-TTTGATAATTTTTGT-TAC
1 AATTTTGATAATTTTTGTATAC
*
31076525 AATTTTGATAAATTTTG
1 AATTTTGATAATTTTTG
31076542 GTAATCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
20 9 0.27
21 22 0.67
22 2 0.06
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.56
Consensus pattern (22 bp):
AATTTTGATAATTTTTGTATAC
Found at i:31078041 original size:27 final size:27
Alignment explanation
Indices: 31078018--31078078 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
31078008 ATCAAATCAT
31078018 ATTTAAATATTAAAAAAATAAAATAAA
1 ATTTAAATATTAAAAAAATAAAATAAA
* * *
31078045 ATTTAAATATTATAAATATAAAATTAA
1 ATTTAAATATTAAAAAAATAAAATAAA
31078072 A-TTAAAT
1 ATTTAAAT
31078079 TTGAGACGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
26 6 0.19
27 25 0.81
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
ATTTAAATATTAAAAAAATAAAATAAA
Found at i:31078578 original size:27 final size:27
Alignment explanation
Indices: 31078548--31078612 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
31078538 TAAAATCACG
*
31078548 ATAAAACATAAA-AAAATGATATTATAA
1 ATAAAACA-AAATAAAATAATATTATAA
*
31078575 ATAAAATAAAATAAAATAATATTATAA
1 ATAAAACAAAATAAAATAATATTATAA
31078602 ATGAAAA-AAAA
1 AT-AAAACAAAA
31078613 GGGTTTGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 3 0.09
27 27 0.79
28 4 0.12
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.25
Consensus pattern (27 bp):
ATAAAACAAAATAAAATAATATTATAA
Found at i:31092328 original size:13 final size:13
Alignment explanation
Indices: 31092310--31092335 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31092300 ATGCATATAG
31092310 CAAAAAAAAAAAA
1 CAAAAAAAAAAAA
31092323 CAAAAAAAAAAAA
1 CAAAAAAAAAAAA
31092336 AGATGCACGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
CAAAAAAAAAAAA
Found at i:31105747 original size:34 final size:34
Alignment explanation
Indices: 31105704--31105772 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
31105694 TATCTTAGTA
31105704 TATTGAATCTATCACTTATTAAGATTAAGCAAGC
1 TATTGAATCTATCACTTATTAAGATTAAGCAAGC
31105738 TATTGAATCTATCACTTATTAAGATTAAGCAAGC
1 TATTGAATCTATCACTTATTAAGATTAAGCAAGC
31105772 T
1 T
31105773 TGAAGTCCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (34 bp):
TATTGAATCTATCACTTATTAAGATTAAGCAAGC
Found at i:31114411 original size:18 final size:18
Alignment explanation
Indices: 31114388--31114422 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31114378 CTTTACCAGC
31114388 ATCCTCTCCCTCCTCTGT
1 ATCCTCTCCCTCCTCTGT
**
31114406 ATCCTCTGTCTCCTCTG
1 ATCCTCTCCCTCCTCTG
31114423 CGGCCTCTTT
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:0.06, C:0.46, G:0.09, T:0.40
Consensus pattern (18 bp):
ATCCTCTCCCTCCTCTGT
Done.