Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 133 of 230
Found at i:38730973 original size:44 final size:42
Alignment explanation
Indices: 38730925--38731062 Score: 146
Period size: 40 Copynumber: 3.3 Consensus size: 42
38730915 AAGGAGAGGG
38730925 AAGAAAGAAAAAGAAGGAAAGAAAGGGAAAGGAGAAGAGAAAAA
1 AAGAAAGAAAAAGAA-G-AAGAAAGGGAAAGGAGAAGAGAAAAA
*
38730969 AAGAAAG--AAAGAAGAAGAGAA-GGAAAGGAGAAGAAAAAAGA
1 AAGAAAGAAAAAGAAGAAGA-AAGGGAAAGGAGAAGAGAAAA-A
*
38731010 AAGAATGAAAGAAGAAGAAGAAGAGGG-AA-G-GAAG-GAAAAA
1 AAGAAAGAAA-AAGAAGAAGAA-AGGGAAAGGAGAAGAGAAAAA
*
38731050 AAGAAAAAAAAAG
1 AAGAAAGAAAAAG
38731063 GTAATTTTAT
Statistics
Matches: 82, Mismatches: 5, Indels: 19
0.77 0.05 0.18
Matches are distributed among these distances:
39 3 0.04
40 30 0.37
41 14 0.17
42 10 0.12
43 3 0.04
44 20 0.24
45 2 0.02
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (42 bp):
AAGAAAGAAAAAGAAGAAGAAAGGGAAAGGAGAAGAGAAAAA
Found at i:38731011 original size:45 final size:45
Alignment explanation
Indices: 38730925--38731059 Score: 129
Period size: 44 Copynumber: 3.0 Consensus size: 45
38730915 AAGGAGAGGG
* * *
38730925 AAGAAAGAAA-AAGAAG-GAAAGAAAGG-GAAAGGAGAAGAGAAAAA
1 AAGAAAGAAAGAAGAAGAGAAGGAAAGGAG-AA-GAAAAAAGAAAAA
*
38730969 AAGAAAGAAAGAAGAAGAGAAGGAAAGGAGAAGAAAAAAGAAAGA
1 AAGAAAGAAAGAAGAAGAGAAGGAAAGGAGAAGAAAAAAGAAAAA
* * *
38731014 ATGAAAG-AAGAAGAAGA-AGAGGGAAGGA-AGGAAAAAAAGAAAAA
1 AAGAAAGAAAGAAGAAGAGA-AGGAAAGGAGAAG-AAAAAAGAAAAA
38731058 AA
1 AA
38731060 AAGGTAATTT
Statistics
Matches: 77, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
43 3 0.04
44 40 0.52
45 22 0.29
46 11 0.14
47 1 0.01
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (45 bp):
AAGAAAGAAAGAAGAAGAGAAGGAAAGGAGAAGAAAAAAGAAAAA
Found at i:38731020 original size:25 final size:26
Alignment explanation
Indices: 38730895--38731058 Score: 85
Period size: 26 Copynumber: 6.3 Consensus size: 26
38730885 AGGAGAGGGA
* *
38730895 AAGAAAGAAAG-AGAGAAAGAAAGGAG
1 AAGAAA-AAAGAAGAGAAGGAAAGAAG
* * *
38730921 AGGGAAGAAAGAAAAAGAAGGAAAGAA-
1 A-AGAAAAAAG-AAGAGAAGGAAAGAAG
* **
38730948 AGGGAAAGGAGAAGAGAA--AAA-AAG
1 A-AGAAAAAAGAAGAGAAGGAAAGAAG
* *
38730972 AAAGAAAGAAGAAGAGAAGGAAAGGAG
1 -AAGAAAAAAGAAGAGAAGGAAAGAAG
*
38730999 AAGAAAAAAGAA-AGAATGAAAGAAG
1 AAGAAAAAAGAAGAGAAGGAAAGAAG
*
38731024 AAGAAGAAGAGGGAAG-GAAGGAAA-AA-
1 AAGAA-AA-A-AGAAGAGAAGGAAAGAAG
38731050 AAGAAAAAA
1 AAGAAAAAA
38731059 AAAGGTAATT
Statistics
Matches: 108, Mismatches: 18, Indels: 27
0.71 0.12 0.18
Matches are distributed among these distances:
23 2 0.02
24 18 0.17
25 19 0.18
26 32 0.30
27 16 0.15
28 21 0.19
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (26 bp):
AAGAAAAAAGAAGAGAAGGAAAGAAG
Found at i:38731025 original size:41 final size:40
Alignment explanation
Indices: 38730895--38731032 Score: 135
Period size: 40 Copynumber: 3.5 Consensus size: 40
38730885 AGGAGAGGGA
* * *
38730895 AAGAAAGAA-AGAGAGAAAGAAAGGAGAGGGAAGAAAGAAA-
1 AAGAAAGAAGA-AGAGAAGGAAAGGAGA-AGAAAAAAGAAAG
* *
38730935 AAG-AAGGA-AAGA-AAGGGAAAGGAGAAGAGAAAA-AAAG
1 AAGAAAGAAGAAGAGAA-GGAAAGGAGAAGAAAAAAGAAAG
38730972 AAAGAAAGAAGAAGAGAAGGAAAGGAGAAGAAAAAAGAAAG
1 -AAGAAAGAAGAAGAGAAGGAAAGGAGAAGAAAAAAGAAAG
38731013 AATGAAAGAAGAAGAAGAAG
1 AA-GAAAGAAGAAG-AGAAG
38731033 AGGGAAGGAA
Statistics
Matches: 82, Mismatches: 7, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
36 3 0.04
37 7 0.09
38 15 0.18
39 9 0.11
40 26 0.32
41 17 0.21
42 5 0.06
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (40 bp):
AAGAAAGAAGAAGAGAAGGAAAGGAGAAGAAAAAAGAAAG
Found at i:38732291 original size:159 final size:156
Alignment explanation
Indices: 38731857--38732303 Score: 396
Period size: 159 Copynumber: 2.8 Consensus size: 156
38731847 TTCCCCCTTA
* * * *
38731857 ACACTAAATTAATAAATTTCAAACATGATGCACTGAAATAATATAAAATTATAAAAGACTAAGTT
1 ACACTAAA-TAATAAATTTCAAACATAATGCACTGAAATAATATAAAATTATAAAATA-GAA-AT
38731922 TATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAATGGCAGAAGTAAGAGT
63 TATGATATTTTTTAAAGTAATAAAATGC-GAG-AAAAAATACGAACAAATGGCAGAAGTAAGAGT
* * *
38731987 GTATTACTAACTTTTATAAAATTCAGAAATAATT
126 GTATTA-T-A-TTTTACAAAATTAAGAAATAATC
* * * **
38732021 A-A-TACAA-AAT--ATTTCAAAGAAAATGTACTGAAATAATATAAAACAATAAAATACGAGAAT
1 ACACTA-AATAATAAATTTCAAACATAATGCACTGAAATAATATAAAATTATAAAATA-GA-AAT
* * **
38732081 AAT-ATAATTTTATTTAAAGTAATAAAAAT-CGAGAAAATAATACGAGCAAATGGCAGGGGTAAG
63 TATGAT-A-TTT-TTTAAAGTAAT-AAAATGCGAGAAAA-AATACGAACAAATGGCAGAAGTAAG
* *
38732144 GGT-TATT-T-TTTTACACCAAATTAATTTAAATAA-C
123 AGTGTATTATATTTTACA--AAATTAA--GAAATAATC
* *
38732178 ACACTAGAGTAATAAATTTCAAACATTATGCACTGAAATAATGA-AAAATTATAAAATTAGAAAT
1 ACACTA-AATAATAAATTTCAAACATAATGCACTGAAATAAT-ATAAAATTATAAAA-TAGAAAT
* *
38732242 TATGATATTTTTTAAAGTAATAAAATGCGAAGAAAAAATACGAATAAATGGCTGAAGTAAGA
63 TATGATATTTTTTAAAGTAATAAAATGCG-AGAAAAAATACGAACAAATGGCAGAAGTAAGA
38732304 TTTATTTACT
Statistics
Matches: 229, Mismatches: 33, Indels: 47
0.74 0.11 0.15
Matches are distributed among these distances:
154 6 0.03
156 6 0.03
157 2 0.01
158 14 0.06
159 86 0.38
160 43 0.19
161 21 0.09
162 44 0.19
163 6 0.03
164 1 0.00
ACGTcount: A:0.51, C:0.08, G:0.13, T:0.29
Consensus pattern (156 bp):
ACACTAAATAATAAATTTCAAACATAATGCACTGAAATAATATAAAATTATAAAATAGAAATTAT
GATATTTTTTAAAGTAATAAAATGCGAGAAAAAATACGAACAAATGGCAGAAGTAAGAGTGTATT
ATATTTTACAAAATTAAGAAATAATC
Found at i:38737463 original size:15 final size:12
Alignment explanation
Indices: 38737426--38737456 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
38737416 AAAAAAATTT
*
38737426 ATACTCAAAATA
1 ATACACAAAATA
38737438 ATACACAAAATA
1 ATACACAAAATA
38737450 ATACACA
1 ATACACA
38737457 CTAAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.61, C:0.19, G:0.00, T:0.19
Consensus pattern (12 bp):
ATACACAAAATA
Found at i:38737496 original size:26 final size:26
Alignment explanation
Indices: 38737462--38737514 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
38737452 ACACACTAAA
* *
38737462 ATTATTAATTTTATACTCAAATTAAT
1 ATTAATAATTTTATACTCAAAATAAT
38737488 ATTAATAATTTTATACTCAAAATAAT
1 ATTAATAATTTTATACTCAAAATAAT
38737514 A
1 A
38737515 CACACTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (26 bp):
ATTAATAATTTTATACTCAAAATAAT
Found at i:38737712 original size:3 final size:3
Alignment explanation
Indices: 38737704--38737729 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
38737694 TCTTAATACT
38737704 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
38737730 TAATAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:38737820 original size:19 final size:21
Alignment explanation
Indices: 38737796--38737834 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
38737786 ACTAAAACAA
*
38737796 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
38737815 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
38737835 ATCAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:38738004 original size:27 final size:27
Alignment explanation
Indices: 38737966--38738041 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
38737956 ATAATACGAG
38737966 TGGTGCCGCCAATGGCATTGGCACCAT
1 TGGTGCCGCCAATGGCATTGGCACCAT
** *
38737993 TGGTGCCGCCAATGGTTTTGGCACCTT
1 TGGTGCCGCCAATGGCATTGGCACCAT
**
38738020 TGGTGCCGCCAATATCATTGGC
1 TGGTGCCGCCAATGGCATTGGC
38738042 GTGACCAGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.16, C:0.28, G:0.29, T:0.28
Consensus pattern (27 bp):
TGGTGCCGCCAATGGCATTGGCACCAT
Found at i:38738126 original size:27 final size:27
Alignment explanation
Indices: 38738091--38738165 Score: 116
Period size: 27 Copynumber: 2.7 Consensus size: 27
38738081 TTTTTTGTTT
38738091 TTTTGATATATTTTGGTAAATAAAAAAA
1 TTTT-ATATATTTTGGTAAATAAAAAAA
38738119 TTTTATATATTTTGGTAAATAAAAAAA
1 TTTTATATATTTTGGTAAATAAAAAAA
*
38738146 -GTTATAATATTTTGGTAAAT
1 TTTTAT-ATATTTTGGTAAAT
38738166 TTTTATTTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
26 4 0.09
27 37 0.82
28 4 0.09
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.45
Consensus pattern (27 bp):
TTTTATATATTTTGGTAAATAAAAAAA
Found at i:38744387 original size:18 final size:18
Alignment explanation
Indices: 38744364--38744404 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
38744354 GAATTGTGCA
*
38744364 AACCCATATATGAATGTG
1 AACCCATATATGAATGCG
* *
38744382 AACCCATGTATGCATGCG
1 AACCCATATATGAATGCG
38744400 AACCC
1 AACCC
38744405 TATTAAAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (18 bp):
AACCCATATATGAATGCG
Found at i:38746809 original size:6 final size:6
Alignment explanation
Indices: 38746710--38746791 Score: 148
Period size: 6 Copynumber: 13.8 Consensus size: 6
38746700 ACAACCTATT
38746710 AAAAT- AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
*
38746757 AAAATC AAAATC AAAATC AAAATC AAAATT AAAAT
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAAT
38746792 AAGGATGAAA
Statistics
Matches: 75, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
5 5 0.07
6 70 0.93
ACGTcount: A:0.68, C:0.13, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAATC
Found at i:38756764 original size:17 final size:18
Alignment explanation
Indices: 38756731--38756764 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
38756721 TTGATTCTAC
*
38756731 ATTAAAATAAGTTCATAA
1 ATTAAAATAAATTCATAA
38756749 ATTAAAA-AAATTCATA
1 ATTAAAATAAATTCATA
38756765 CTTCAACCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (18 bp):
ATTAAAATAAATTCATAA
Found at i:38757617 original size:11 final size:11
Alignment explanation
Indices: 38757581--38757639 Score: 77
Period size: 11 Copynumber: 5.4 Consensus size: 11
38757571 TAAATCCTTT
*
38757581 CTCTC-AATTT
1 CTCTCAAATTC
38757591 CTCTCCAATATT-
1 CTCT-CAA-ATTC
38757603 CTCTCAAATTC
1 CTCTCAAATTC
38757614 CTCTCAAATTC
1 CTCTCAAATTC
38757625 CTCTCAAATTC
1 CTCTCAAATTC
38757636 CTCT
1 CTCT
38757640 TAAAAAAGCT
Statistics
Matches: 45, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
10 7 0.16
11 30 0.67
12 5 0.11
13 3 0.07
ACGTcount: A:0.24, C:0.36, G:0.00, T:0.41
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:38758118 original size:41 final size:41
Alignment explanation
Indices: 38758052--38758133 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
38758042 GTGGAGACTC
* *
38758052 GAGATGCATACATTCCATCTTCCATGTGGAGAGTGTACTAT
1 GAGACGCACACATTCCATCTTCCATGTGGAGAGTGTACTAT
38758093 GAGACGCACACATTCCATCTTCCATGTGGAGAGTGTACTAT
1 GAGACGCACACATTCCATCTTCCATGTGGAGAGTGTACTAT
38758134 CACTTTGGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (41 bp):
GAGACGCACACATTCCATCTTCCATGTGGAGAGTGTACTAT
Found at i:38760005 original size:35 final size:34
Alignment explanation
Indices: 38759921--38760017 Score: 124
Period size: 34 Copynumber: 2.8 Consensus size: 34
38759911 ATTTTGAATA
*
38759921 TTTTGATATTATTTGATGTAATAAAATAGAAATTC
1 TTTT-ATATTATTTAATGTAATAAAATAGAAATTC
*
38759956 TTATATATTATTTAATGTAATAAAATAGAAAATTAC
1 TTTTATATTATTTAATGTAATAAAATAG-AAATT-C
*
38759992 TTTTATATT-TTTAATATAATAGAAAT
1 TTTTATATTATTTAATGTAATA-AAAT
38760018 TCTTTTAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
34 23 0.42
35 19 0.35
36 13 0.24
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (34 bp):
TTTTATATTATTTAATGTAATAAAATAGAAATTC
Found at i:38763438 original size:103 final size:103
Alignment explanation
Indices: 38763302--38763774 Score: 437
Period size: 95 Copynumber: 4.7 Consensus size: 103
38763292 CACGTGGGAG
* * * * * * * *
38763302 TTTTTTTTAAATTAACAAATAATTTAATTAAGTAACCCTAAACCCCAAACCCTAATTTATTTGAG
1 TTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCCAAACCCTAATTTATTTAAT
*
38763367 TTTTCTTTAAAAA-CGTTAAACACTAAACCCTAATCTAA
66 TTTTCTTTAAAAACCCTT-AACACTAAACCCTAATCTAA
*
38763405 TTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAAACCCTAATTTATTTAAT
1 TTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCCAAACCCTAATTTATTTAAT
*
38763470 TTTTCCTTAAAAACCCTTAACACTAAACCCTAATCTAA
66 TTTTCTTTAAAAACCCTTAACACTAAACCCTAATCTAA
* * *
38763508 TTTTGTT-AAATTTATAATTAAATTACTCAAGTAACCCT-------AAACCCTAATTTATTTGAT
1 TTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCCAAACCCTAATTTATTTAAT
* * * *
38763565 TTTTCCTTAAAAACCCTTAACACTAAACCTTAATTTGA
66 TTTTCTTTAAAAACCCTTAACACTAAACCCTAATCTAA
* * *
38763603 --TTTTTAAAATTTTTTAATTAATTTACTCAAGTAA-GCT------TAAACCCTAATTTAATTTA
1 TTTTTTTAAAA-TTTATAATTAATTTACTCAAGTAACCCTAAACCCCAAACCCTAATTT-ATTTA
* *** * *
38763659 TTTTTTCTTTAAAAATTATAAACACGAAACCCTAATCTAA
64 ATTTTTCTTTAAAAACCCTTAACACTAAACCCTAATCTAA
** * * * * * ** *
38763699 -TTTTAAAAAATTT-TAATTAATTTAATTAAGAAACTCTAAACCCTAATTCCTTATTTATTTAAT
1 TTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCCAAACCCTAATTTATTTAA-
38763762 TTTTTCTTTAAAA
65 TTTTTCTTTAAAA
38763775 CCATAAACCT
Statistics
Matches: 314, Mismatches: 42, Indels: 29
0.82 0.11 0.08
Matches are distributed among these distances:
93 4 0.01
94 5 0.02
95 104 0.33
96 39 0.12
97 7 0.02
101 5 0.02
102 53 0.17
103 94 0.30
104 3 0.01
ACGTcount: A:0.39, C:0.17, G:0.03, T:0.41
Consensus pattern (103 bp):
TTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCCAAACCCTAATTTATTTAAT
TTTTCTTTAAAAACCCTTAACACTAAACCCTAATCTAA
Found at i:38763496 original size:43 final size:43
Alignment explanation
Indices: 38763438--38763605 Score: 138
Period size: 43 Copynumber: 3.7 Consensus size: 43
38763428 TTACTCAAGT
* *
38763438 AACCCTAAACCCTAAACCCTAATTTATTTAATTTTTCCTTAAA
1 AACCCTTAACACTAAACCCTAATTTATTTAATTTTTCCTTAAA
* * **
38763481 AACCCTTAACACTAAACCCTAATCTAATTTTGTTAAATTTATAATTAAA
1 AACCCTTAACACTAAACCCTAA--T--TTAT-TT-AATTTTTCCTTAAA
* ** * *
38763530 TTACTCAAGTAACCCTAAACCCTAATTTATTTGATTTTTCCTTAAA
1 -AAC-C-CTTAACACTAAACCCTAATTTATTTAATTTTTCCTTAAA
*
38763576 AACCCTTAACACTAAACCTTAATTTGATTT
1 AACCCTTAACACTAAACCCTAATTT-ATTT
38763606 TTAAAATTTT
Statistics
Matches: 95, Mismatches: 20, Indels: 19
0.71 0.15 0.14
Matches are distributed among these distances:
43 37 0.39
44 5 0.05
45 3 0.03
46 10 0.11
47 5 0.05
48 5 0.05
49 11 0.12
50 3 0.03
51 1 0.01
52 15 0.16
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (43 bp):
AACCCTTAACACTAAACCCTAATTTATTTAATTTTTCCTTAAA
Found at i:38763583 original size:95 final size:94
Alignment explanation
Indices: 38763342--38763746 Score: 438
Period size: 95 Copynumber: 4.2 Consensus size: 94
38763332 AGTAACCCTA
* * * *
38763342 AACCCCAAACCCTAATTTATTTGAGTTTTCTTTAAAAA-CGTTAAACACTAAACCCTAATCTAAT
1 AACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTT-AACACTAAACCCTAATCTAA-
38763406 TTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCT
64 -TTTTTAAAATTTATAATTAATTTACTCAAG------T
*
38763444 AAACCCTAAACCCTAATTTATTTAATTTTTCCTTAAAAACCCTTAACACTAAACCCTAATCTAAT
1 -AACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTTAACACTAAACCCTAATCTAAT
* *
38763509 TTTGTTAAATTTATAATTAAATTACTCAAGT
65 TTT-TAAAATTTATAATTAATTTACTCAAGT
* * *
38763540 AACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTTAACACTAAACCTTAATTTGATT
1 AACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTTAACACTAAACCCTAATCTAATT
*
38763605 TTTAAAATTTTTTAATTAATTTACTCAAGT
66 TTTAAAA-TTTATAATTAATTTACTCAAGT
* * * *** * *
38763635 AAGCTTAAACCCTAATTTAATTT-ATTTTTTCTTTAAAAATTATAAACACGAAACCCTAATCTAA
1 AACCCTAAACCCTAATTT-ATTTGA-TTTTTCCTTAAAAACCCTTAACACTAAACCCTAATCTAA
* * * *
38763699 TTTTAAAAAATTT-TAATTAATTTAATTAAGA
64 TTTT-TAAAATTTATAATTAATTTACTCAAGT
*
38763730 AACTCTAAACCCTAATT
1 AACCCTAAACCCTAATT
38763747 CCTTATTTAT
Statistics
Matches: 264, Mismatches: 32, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
94 4 0.02
95 129 0.49
96 42 0.16
97 4 0.02
101 4 0.02
102 24 0.09
103 54 0.20
104 3 0.01
ACGTcount: A:0.40, C:0.18, G:0.03, T:0.40
Consensus pattern (94 bp):
AACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTTAACACTAAACCCTAATCTAATT
TTTAAAATTTATAATTAATTTACTCAAGT
Found at i:38768837 original size:29 final size:27
Alignment explanation
Indices: 38768804--38768888 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 27
38768794 GTATAGGGAT
38768804 GCACCGAAGTGCAATAACAGAACAGAGTA
1 GCACC-AAGTGC-ATAACAGAACAGAGTA
** *
38768833 GCACCAGAGTGCCATGTCAGAACAGAATA
1 GCACCA-AGTG-CATAACAGAACAGAGTA
*
38768862 GCACTCAAGTGCTTAATCAGAACAGAG
1 GCAC-CAAGTGCATAA-CAGAACAGAG
38768889 CGACACTGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
28 3 0.07
29 39 0.87
30 3 0.07
ACGTcount: A:0.40, C:0.22, G:0.24, T:0.14
Consensus pattern (27 bp):
GCACCAAGTGCATAACAGAACAGAGTA
Found at i:38771647 original size:2 final size:2
Alignment explanation
Indices: 38771642--38771673 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
38771632 ATATATATAT
*
38771642 AG AG AG AG AG AG AG AG AG AG AG TG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
38771674 TGAGTGAGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (2 bp):
AG
Found at i:38771674 original size:10 final size:10
Alignment explanation
Indices: 38771645--38771677 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
38771635 TATATATAGA
*
38771645 GAGAGAGAGA
1 GAGAGAGAGT
38771655 GAGAGAGAGT
1 GAGAGAGAGT
38771665 GAGAGAGAGT
1 GAGAGAGAGT
38771675 GAG
1 GAG
38771678 TGAGCAGCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.52, T:0.06
Consensus pattern (10 bp):
GAGAGAGAGT
Found at i:38771678 original size:14 final size:14
Alignment explanation
Indices: 38771642--38771681 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
38771632 ATATATATAT
*
38771642 AGAGAGAGAGAGAG
1 AGAGAGAGTGAGAG
38771656 AGAGAGAGTGAGAG
1 AGAGAGAGTGAGAG
*
38771670 AGAGTGAGTGAG
1 AGAGAGAGTGAG
38771682 CAGCTAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.50, T:0.07
Consensus pattern (14 bp):
AGAGAGAGTGAGAG
Found at i:38773332 original size:27 final size:27
Alignment explanation
Indices: 38773285--38773338 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
38773275 CATTCAATTA
*
38773285 TTTATATTTTTCATATTTTTATAGTAT
1 TTTATATTTTTCATATTTTTAAAGTAT
38773312 TTTA-ATTTATTCA-ATATTTTAAAGTAT
1 TTTATATTT-TTCATAT-TTTTAAAGTAT
38773339 AAAATTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (27 bp):
TTTATATTTTTCATATTTTTAAAGTAT
Found at i:38780755 original size:15 final size:13
Alignment explanation
Indices: 38780720--38780745 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38780710 AATATCCTTC
38780720 GTGACTGGAATTT
1 GTGACTGGAATTT
38780733 GTGACTGGAATTT
1 GTGACTGGAATTT
38780746 TTAAGACTGG
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:0.23, C:0.08, G:0.31, T:0.38
Consensus pattern (13 bp):
GTGACTGGAATTT
Found at i:38781267 original size:27 final size:27
Alignment explanation
Indices: 38781230--38781307 Score: 147
Period size: 27 Copynumber: 2.9 Consensus size: 27
38781220 CATAACATAG
*
38781230 ACACATTAAGTTAGTATCAAACTAGAC
1 ACACATCAAGTTAGTATCAAACTAGAC
38781257 ACACATCAAGTTAGTATCAAACTAGAC
1 ACACATCAAGTTAGTATCAAACTAGAC
38781284 ACACATCAAGTTAGTATCAAACTA
1 ACACATCAAGTTAGTATCAAACTA
38781308 CTCTACTTAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.45, C:0.21, G:0.10, T:0.24
Consensus pattern (27 bp):
ACACATCAAGTTAGTATCAAACTAGAC
Found at i:38796396 original size:16 final size:16
Alignment explanation
Indices: 38796375--38796406 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
38796365 ATTTTGTTGC
*
38796375 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
38796391 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
38796407 CTTTCAATCA
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:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:38796692 original size:51 final size:50
Alignment explanation
Indices: 38796630--38796825 Score: 236
Period size: 51 Copynumber: 3.9 Consensus size: 50
38796620 GATACCGATT
* *
38796630 CACATAATAGCCTGCACATAGTACTACACATGTGACCATCACTGTCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACT-TCCGGTA
** *
38796681 CATGTAGTAGCCTGCACATAGTACTACACATGTGATCGA--AGCTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGA-CCATCA-CT-TCCGGTA
* * * *
38796732 CGCATAGTAGCCTGCACATTGTACTACACATGCGACCTATCA-TTCTGGTA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACC-ATCACTTCCGGTA
*
38796782 CACATAGTAGCCTACACATAGTACTACACATGTGACCATCACTT
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTT
38796826 TCAGTTTATC
Statistics
Matches: 122, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
49 4 0.03
50 43 0.35
51 72 0.59
52 2 0.02
53 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.26
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTTCCGGTA
Found at i:38796810 original size:12 final size:13
Alignment explanation
Indices: 38796780--38796812 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
38796770 ATCATTCTGG
38796780 TACACATAGTAGCC
1 TACACATAGTA-CC
38796794 TACACATAGTA-C
1 TACACATAGTACC
38796806 TACACAT
1 TACACAT
38796813 GTGACCATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
14 11 0.58
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.24
Consensus pattern (13 bp):
TACACATAGTACC
Found at i:38796813 original size:101 final size:102
Alignment explanation
Indices: 38796632--38796816 Score: 275
Period size: 101 Copynumber: 1.8 Consensus size: 102
38796622 TACCGATTCA
* ** *
38796632 CATAATAGCCTGCACATAGTACTACACATGTGACCATCACTGTCCGATACATGTAGTAGCCTGCA
1 CATAATAGCCTGCACATAGTACTACACATGCGACCATCACTGTCCGATACACATAGTAGCCTACA
38796697 CATAGTACTACACATGTGATCGAAGCTATCCGGTACG
66 CATAGTACTACACATGTGATCGAAGCTATCCGGTACG
* * * *
38796734 CATAGTAGCCTGCACATTGTACTACACATGCGACCTATCA-T-TCTGGTACACATAGTAGCCTAC
1 CATAATAGCCTGCACATAGTACTACACATGCGACC-ATCACTGTCCGATACACATAGTAGCCTAC
38796797 ACATAGTACTACACATGTGA
65 ACATAGTACTACACATGTGA
38796817 CCATCACTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
101 37 0.50
102 33 0.45
103 4 0.05
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.25
Consensus pattern (102 bp):
CATAATAGCCTGCACATAGTACTACACATGCGACCATCACTGTCCGATACACATAGTAGCCTACA
CATAGTACTACACATGTGATCGAAGCTATCCGGTACG
Found at i:38807760 original size:9 final size:9
Alignment explanation
Indices: 38807748--38807799 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
38807738 TATTAAAAAC
38807748 GAGAGACTT
1 GAGAGACTT
38807757 GAGAGACTT
1 GAGAGACTT
**
38807766 GAGAGGGTTT
1 GAGA-GACTT
38807776 GAGAGAAC-T
1 GAGAG-ACTT
*
38807785 GAGAGAGTT
1 GAGAGACTT
38807794 GAGAGA
1 GAGAGA
38807800 AGGATATGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
8 1 0.03
9 27 0.77
10 7 0.20
ACGTcount: A:0.35, C:0.06, G:0.40, T:0.19
Consensus pattern (9 bp):
GAGAGACTT
Found at i:38807779 original size:19 final size:17
Alignment explanation
Indices: 38807748--38807799 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
38807738 TATTAAAAAC
*
38807748 GAGAGACTTGAGAGACTT
1 GAGAGAGTTGAGAGAC-T
*
38807766 GAGAGGGTTTGAGAGAACT
1 GAGAGAG-TTGAGAG-ACT
38807785 GAGAGAGTTGAGAGA
1 GAGAGAGTTGAGAGA
38807800 AGGATATGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 1 0.03
18 12 0.41
19 14 0.48
20 2 0.07
ACGTcount: A:0.35, C:0.06, G:0.40, T:0.19
Consensus pattern (17 bp):
GAGAGAGTTGAGAGACT
Found at i:38809711 original size:14 final size:14
Alignment explanation
Indices: 38809694--38809720 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38809684 TGAAGAGATG
38809694 TGTGTGAAATGAGT
1 TGTGTGAAATGAGT
38809708 TGTGTGAAATGAG
1 TGTGTGAAATGAG
38809721 GAAGGGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (14 bp):
TGTGTGAAATGAGT
Found at i:38810243 original size:27 final size:28
Alignment explanation
Indices: 38810190--38810243 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
38810180 AAAAATAATT
*
38810190 AAAATTAAATATGTTAATAATTTAAGTG
1 AAAATTAAATATGTTAATAATTAAAGTG
* *
38810218 AAAATTAATTAT-TTTATAATTAAAGT
1 AAAATTAAATATGTTAATAATTAAAGT
38810244 ATGAATTTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (28 bp):
AAAATTAAATATGTTAATAATTAAAGTG
Found at i:38810449 original size:14 final size:15
Alignment explanation
Indices: 38810430--38810458 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
38810420 GCCAAAAGAC
38810430 ATCTTCTAAC-CACA
1 ATCTTCTAACACACA
38810444 ATCTTCTAACACACA
1 ATCTTCTAACACACA
38810459 TACACCCGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.38, C:0.34, G:0.00, T:0.28
Consensus pattern (15 bp):
ATCTTCTAACACACA
Found at i:38812935 original size:21 final size:22
Alignment explanation
Indices: 38812892--38812944 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
38812882 GGGAGAGCAC
*
38812892 TAAATTAATTCTAATTTAAACA-
1 TAAA-TAAATCTAATTTAAACAT
38812914 TAAATAAATCTAA-TTAATACAT
1 TAAATAAATCTAATTTAA-ACAT
*
38812936 TAATTAAAT
1 TAAATAAAT
38812945 TATAGTACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 4 0.15
21 11 0.41
22 12 0.44
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATAAATCTAATTTAAACAT
Found at i:38818611 original size:25 final size:25
Alignment explanation
Indices: 38818574--38818647 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 25
38818564 AGGTCATGAG
** *
38818574 AGCTTACTAATTCTCAGCTCGTATA
1 AGCTTACCGATTCACAGCTCGTATA
* *
38818599 AGCTTACCGATTCACAACTCGTGA-G
1 AGCTTACCGATTCACAGCTCGT-ATA
*
38818624 AGCATACCGATTCACAGCTCGTAT
1 AGCTTACCGATTCACAGCTCGTAT
38818648 GAGCATACAT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
24 1 0.03
25 38 0.95
26 1 0.03
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.28
Consensus pattern (25 bp):
AGCTTACCGATTCACAGCTCGTATA
Found at i:38818651 original size:25 final size:25
Alignment explanation
Indices: 38818583--38818655 Score: 94
Period size: 25 Copynumber: 2.9 Consensus size: 25
38818573 GAGCTTACTA
* * *
38818583 ATTCTCAGCTCGTATAAGCTTACCG
1 ATTCACAGCTCGTATGAGCATACCG
*
38818608 ATTCACAACTCGTGA-GAGCATACCG
1 ATTCACAGCTCGT-ATGAGCATACCG
38818633 ATTCACAGCTCGTATGAGCATAC
1 ATTCACAGCTCGTATGAGCATAC
38818656 ATGTACAAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
24 1 0.02
25 39 0.95
26 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (25 bp):
ATTCACAGCTCGTATGAGCATACCG
Found at i:38822023 original size:115 final size:115
Alignment explanation
Indices: 38821821--38822050 Score: 399
Period size: 115 Copynumber: 2.0 Consensus size: 115
38821811 CAATAGTGGA
*
38821821 ATTCATAGTCCAAGTCATGGGTAAATGATATCCTCTCATTGGTATTACATGGTTGATGAAAAGTA
1 ATTCATAGCCCAAGTCATGGGTAAATGATATCCTCTCATTGGTATTACATGGTTGATGAAAAGTA
*
38821886 AACAGAGGTAAAATTGGGATGAGAAAATTATTTAATATAAACATTGAAGT
66 AACAGAGGTAAAATTGGGATGAGAAAATTATTTAATATAAACATTAAAGT
* *
38821936 ATTCATAGCCCGAGTCATGGGTAAATGATATCCTTTCATTGGTATTACATGGTTGATGAAAAGTA
1 ATTCATAGCCCAAGTCATGGGTAAATGATATCCTCTCATTGGTATTACATGGTTGATGAAAAGTA
*
38822001 AA-TGAAGGTAAAATTGGGATGAGAAAATTATTTAATATAAACATTAAAGT
66 AACAG-AGGTAAAATTGGGATGAGAAAATTATTTAATATAAACATTAAAGT
38822051 TTATTTTGGG
Statistics
Matches: 109, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
114 1 0.01
115 108 0.99
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.32
Consensus pattern (115 bp):
ATTCATAGCCCAAGTCATGGGTAAATGATATCCTCTCATTGGTATTACATGGTTGATGAAAAGTA
AACAGAGGTAAAATTGGGATGAGAAAATTATTTAATATAAACATTAAAGT
Found at i:38826328 original size:15 final size:15
Alignment explanation
Indices: 38826306--38826343 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
38826296 TTATATATAT
*
38826306 ATTGAATTTTGATTCA
1 ATTGAATTTTAATT-A
38826322 A-TGAATTTTAATTA
1 ATTGAATTTTAATTA
38826336 ATTGAATT
1 ATTGAATT
38826344 AATTGTTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 17 0.85
16 1 0.05
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.50
Consensus pattern (15 bp):
ATTGAATTTTAATTA
Found at i:38830263 original size:35 final size:35
Alignment explanation
Indices: 38830222--38830293 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
38830212 TAATTGATTT
* *
38830222 AGCTTTGACAATTGGAGTTCCCGAACAGTCATTGA
1 AGCTTTGACAATTGAAGTTCCCAAACAGTCATTGA
*
38830257 AGCTTTGACAATTGAAGTTCCCAAATAGTCATTGA
1 AGCTTTGACAATTGAAGTTCCCAAACAGTCATTGA
38830292 AG
1 AG
38830294 TGGACTTAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (35 bp):
AGCTTTGACAATTGAAGTTCCCAAACAGTCATTGA
Found at i:38840572 original size:25 final size:25
Alignment explanation
Indices: 38840538--38840610 Score: 119
Period size: 25 Copynumber: 2.9 Consensus size: 25
38840528 AGGGTTATCG
*
38840538 ATTTATAGCTCGAGAGAGCATACTA
1 ATTTATAGCTCGAGAGAGCATACAA
*
38840563 ATTTATAGCTCGAGAAAGCATACAA
1 ATTTATAGCTCGAGAGAGCATACAA
*
38840588 ATTTATAGCTCGTGAGAGCATAC
1 ATTTATAGCTCGAGAGAGCATAC
38840611 GGATCTTCAG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.27
Consensus pattern (25 bp):
ATTTATAGCTCGAGAGAGCATACAA
Found at i:38842067 original size:20 final size:20
Alignment explanation
Indices: 38842030--38842067 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38842020 TGCAGTGTTG
*
38842030 AAAAATTCTACTATTTTTTA
1 AAAAATTCTACTAGTTTTTA
38842050 AAAAATTCT-CTGAGTTTT
1 AAAAATTCTACT-AGTTTT
38842068 CGATATAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (20 bp):
AAAAATTCTACTAGTTTTTA
Found at i:38858036 original size:20 final size:20
Alignment explanation
Indices: 38857988--38858028 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
38857978 AAATATCTTG
38857988 ATTTGATTTGATTTCAATCA
1 ATTTGATTTGATTTCAATCA
*
38858008 ATTTGATTTGATTTTAATCA
1 ATTTGATTTGATTTCAATCA
38858028 A
1 A
38858029 ATTTATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (20 bp):
ATTTGATTTGATTTCAATCA
Found at i:38858818 original size:82 final size:82
Alignment explanation
Indices: 38858732--38858938 Score: 299
Period size: 82 Copynumber: 2.5 Consensus size: 82
38858722 ATTCATTCCA
* * * *
38858732 TTCAACAGATTTTATTCCATTTTGATTTTGTTTCCAAACGAGAATTAATTGTATAATTCTATTTC
1 TTCAACATATTTTATTCCATTTTGATTTTGTTTCCAAACAAGAATTAAATGGATAATTCTATTTC
*
38858797 -GAGATTTATTCTCGCCG
66 AG-GATTTATTCCCGCCG
* * * *
38858814 TTCAACATATTTTATTCTATTTTGATTTTGTTTCTAAACAATAATTAAATGGATAATTCTGTTTC
1 TTCAACATATTTTATTCCATTTTGATTTTGTTTCCAAACAAGAATTAAATGGATAATTCTATTTC
38858879 AGGATTTATTCCCGCCG
66 AGGATTTATTCCCGCCG
* *
38858896 TTTAACATATTTTATTCGATTTTGATTTTGTTTCCAAACAAGA
1 TTCAACATATTTTATTCCATTTTGATTTTGTTTCCAAACAAGA
38858939 CATAATTAAG
Statistics
Matches: 111, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
82 110 0.99
83 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.46
Consensus pattern (82 bp):
TTCAACATATTTTATTCCATTTTGATTTTGTTTCCAAACAAGAATTAAATGGATAATTCTATTTC
AGGATTTATTCCCGCCG
Found at i:38858953 original size:82 final size:81
Alignment explanation
Indices: 38858711--38858966 Score: 284
Period size: 82 Copynumber: 3.1 Consensus size: 81
38858701 ATAAAATCTG
* ** * * *
38858711 TTTCGGGATTTATTCATTCCATTCAACAGATTTTATTCCATTTTGATTTTGTTTCCAAACGAGAA
1 TTTCAGGATTTATTCACGCCGTTCAACATATTTTATTCCATTTTGATTTTGTTTCCAAACAAGAA
38858776 TTAATT-GTATAATTCTA
66 TTAATTAG--TAATTCTA
* * * *
38858793 TTTC-GAGATTTATTCTCGCCGTTCAACATATTTTATTCTATTTTGATTTTGTTTCTAAACAATA
1 TTTCAG-GATTTATTCACGCCGTTCAACATATTTTATTCCATTTTGATTTTGTTTCCAAACAAGA
* * *
38858857 ATTAAATGGATAATTCTG
65 ATTAATTAG-TAATTCTA
* * *
38858875 TTTCAGGATTTATTCCCGCCGTTTAACATATTTTATTCGATTTTGATTTTGTTTCCAAACAAGAC
1 TTTCAGGATTTATTCACGCCGTTCAACATATTTTATTCCATTTTGATTTTGTTTCCAAACAAGA-
*
38858940 A-TAATTAAGTAATTGTA
65 ATTAATT-AGTAATTCTA
38858957 TTTCAGGATT
1 TTTCAGGATT
38858967 CAATCCTGTC
Statistics
Matches: 149, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
81 1 0.01
82 144 0.97
83 4 0.03
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (81 bp):
TTTCAGGATTTATTCACGCCGTTCAACATATTTTATTCCATTTTGATTTTGTTTCCAAACAAGAA
TTAATTAGTAATTCTA
Found at i:38861535 original size:81 final size:82
Alignment explanation
Indices: 38861183--38861554 Score: 374
Period size: 82 Copynumber: 4.5 Consensus size: 82
38861173 AAAAAAATAA
* * **
38861183 AATTGAATAAAATCTATTTCGAGACTTATTCCTTCCGTTCAACAGATTTTATTCCATTTTGATTT
1 AATTGAAT-AATTCTATTTCGAGATTTATTCCCGCCGTTCAACAGATTTTATTCCATTTTGATTT
* * ** * *
38861248 TTTTTCAAAATGATAACT
65 TGTTTCCAAACAAGAATT
* *
38861266 AATTGAATAATTCTATTTCGGGGTTTATTCCCGCCGTTCAACAGATTTTATTCCATTTTGATTTT
1 AATTGAATAATTCTATTTCGAGATTTATTCCCGCCGTTCAACAGATTTTATTCCATTTTGATTTT
*
38861331 GTTTCCAAACTAGAATT
66 GTTTCCAAACAAGAATT
* * * * * * *
38861348 AATTGTATAATTCTACTTCTAGATTTATTCTCGCCGCTCAACATATTTTATTCTATTTTGATTTT
1 AATTGAATAATTCTATTTCGAGATTTATTCCCGCCGTTCAACAGATTTTATTCCATTTTGATTTT
*
38861413 GTTTCCAAACAATAATT
66 GTTTCCAAACAAGAATT
* * * * * * * * *
38861430 AAATGAATAATTTTTTTTAG-GATTTATTCCCGCCATTTAACAAATTTTATTCGATTTTCATTTT
1 AATTGAATAATTCTATTTCGAGATTTATTCCCGCCGTTCAACAGATTTTATTCCATTTTGATTTT
*
38861494 -TTTCCAAACAAGATTT
66 GTTTCCAAACAAGAATT
* * * *
38861510 AATTAAATAATTTTATTTTC-AGATTTGA-TCCTGCCGGTCAACAGA
1 AATTGAATAATTCTA-TTTCGAGATTT-ATTCCCGCCGTTCAACAGA
38861555 ATTGATTCTG
Statistics
Matches: 238, Mismatches: 48, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
80 26 0.11
81 57 0.24
82 147 0.62
83 8 0.03
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.45
Consensus pattern (82 bp):
AATTGAATAATTCTATTTCGAGATTTATTCCCGCCGTTCAACAGATTTTATTCCATTTTGATTTT
GTTTCCAAACAAGAATT
Found at i:38866088 original size:20 final size:20
Alignment explanation
Indices: 38866063--38866111 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
38866053 AAATATCTTG
38866063 ATTTGATTTGATTCTAATCA
1 ATTTGATTTGATTCTAATCA
* *
38866083 ATTTGATTTGATTTTATTCA
1 ATTTGATTTGATTCTAATCA
*
38866103 AATTGATTT
1 ATTTGATTT
38866112 AAAAGCTCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.55
Consensus pattern (20 bp):
ATTTGATTTGATTCTAATCA
Found at i:38869105 original size:27 final size:28
Alignment explanation
Indices: 38869071--38869240 Score: 131
Period size: 27 Copynumber: 6.3 Consensus size: 28
38869061 TACCCCTGAA
38869071 GGTAAAATGACCGAAATACCCTCAGT-G
1 GGTAAAATGACCGAAATACCCTCAGTAG
*
38869098 GGTAAAATGATCGAAATACCCTC-G-ATG
1 GGTAAAATGACCGAAATACCCTCAGTA-G
* * * *
38869125 GGTAATATGATCGTAATACCCT-TGTAG
1 GGTAAAATGACCGAAATACCCTCAGTAG
* * * *
38869152 GGTAAAATGACTGTAATGCCC-CTGTAG
1 GGTAAAATGACCGAAATACCCTCAGTAG
* *
38869179 GGTAAAATGACCGTAATGCCC-CAGTAG
1 GGTAAAATGACCGAAATACCCTCAGTAG
* * *
38869206 GGTAACATAACC-ATAATACCCT-TGTAG
1 GGTAAAATGACCGA-AATACCCTCAGTAG
*
38869233 AGTAAAAT
1 GGTAAAAT
38869241 AATTGTCATG
Statistics
Matches: 120, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
26 1 0.01
27 118 0.98
28 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (28 bp):
GGTAAAATGACCGAAATACCCTCAGTAG
Found at i:38869183 original size:81 final size:81
Alignment explanation
Indices: 38869071--38869240 Score: 184
Period size: 81 Copynumber: 2.1 Consensus size: 81
38869061 TACCCCTGAA
* * *
38869071 GGTAAAATGACCGAAATACCCTCAGTGGGTAAAATGATCGAAATACCCTC-G-ATGGGTAATATG
1 GGTAAAATGACCGAAATACCCTCAGTGGGTAAAATGACCGAAATACCC-CAGTA-GGGTAACATA
* *
38869134 ATCGTAATACCCTTGTAG
64 ACCATAATACCCTTGTAG
* * * * * *
38869152 GGTAAAATGACTGTAATGCCC-CTGTAGGGTAAAATGACCGTAATGCCCCAGTAGGGTAACATAA
1 GGTAAAATGACCGAAATACCCTCAGT-GGGTAAAATGACCGAAATACCCCAGTAGGGTAACATAA
38869216 CCATAATACCCTTGTAG
65 CCATAATACCCTTGTAG
*
38869233 AGTAAAAT
1 GGTAAAAT
38869241 AATTGTCATG
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
80 4 0.05
81 69 0.93
82 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (81 bp):
GGTAAAATGACCGAAATACCCTCAGTGGGTAAAATGACCGAAATACCCCAGTAGGGTAACATAAC
CATAATACCCTTGTAG
Found at i:38869232 original size:54 final size:54
Alignment explanation
Indices: 38869071--38869240 Score: 148
Period size: 54 Copynumber: 3.1 Consensus size: 54
38869061 TACCCCTGAA
* * * *
38869071 GGTAAAATGACCGAAATACCCTCAGT-GGGTAAAATGATCGA-AATACCCTCG-ATG
1 GGTAAAATGACCGTAATACCC-CAGTAGGGTAAAAT-AACCATAATACCCTTGTA-G
* * ** * ** * *
38869125 GGTAATATGATCGTAATACCCTTGTAGGGTAAAATGACTGTAATGCCCCTGTAG
1 GGTAAAATGACCGTAATACCCCAGTAGGGTAAAATAACCATAATACCCTTGTAG
* *
38869179 GGTAAAATGACCGTAATGCCCCAGTAGGGTAACATAACCATAATACCCTTGTAG
1 GGTAAAATGACCGTAATACCCCAGTAGGGTAAAATAACCATAATACCCTTGTAG
*
38869233 AGTAAAAT
1 GGTAAAAT
38869241 AATTGTCATG
Statistics
Matches: 89, Mismatches: 24, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
53 3 0.03
54 85 0.96
55 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (54 bp):
GGTAAAATGACCGTAATACCCCAGTAGGGTAAAATAACCATAATACCCTTGTAG
Found at i:38869325 original size:23 final size:24
Alignment explanation
Indices: 38869289--38869355 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 24
38869279 CCTCGAAGTC
* *
38869289 AAATGATTGTTTTGTCTGTGGTT-
1 AAATGACTGATTTGTCTGTGGTTG
*
38869312 AAATGACTGATTTGTCTGTGTTTG
1 AAATGACTGATTTGTCTGTGGTTG
**
38869336 GTATGACTGATTTGTCTGTG
1 AAATGACTGATTTGTCTGTG
38869356 ATTTGAATGG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.18, C:0.07, G:0.27, T:0.48
Consensus pattern (24 bp):
AAATGACTGATTTGTCTGTGGTTG
Found at i:38869369 original size:24 final size:23
Alignment explanation
Indices: 38869290--38869371 Score: 92
Period size: 24 Copynumber: 3.5 Consensus size: 23
38869280 CTCGAAGTCA
* * * *
38869290 AATGATTGTTTTGTCTGTGGTTA
1 AATGACTGATTTGTCTGTGTTTG
38869313 AATGACTGATTTGTCTGTGTTTGG
1 AATGACTGATTTGTCTGTGTTT-G
*
38869337 TATGACTGATTTGTCTGTGATTTG
1 AATGACTGATTTGTCTGTG-TTTG
*
38869361 AATGGCTGATT
1 AATGACTGATT
38869372 CTGAGCATGG
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
23 19 0.38
24 28 0.56
25 3 0.06
ACGTcount: A:0.18, C:0.07, G:0.27, T:0.48
Consensus pattern (23 bp):
AATGACTGATTTGTCTGTGTTTG
Found at i:38869644 original size:64 final size:64
Alignment explanation
Indices: 38869543--38869689 Score: 240
Period size: 64 Copynumber: 2.3 Consensus size: 64
38869533 TTTACTGCGA
38869543 TGCTACTGATGGCTTTGTGTCGATCATATTACCATTACTAATGGTTGTGTGCCGATCATATCAC
1 TGCTACTGATGGCTTTGTGTCGATCATATTACCATTACTAATGGTTGTGTGCCGATCATATCAC
* * **
38869607 TGCTACTGAAGGCTTTGTGTCGATCATGTTACCATTACTGGTGGTTGTGTGCCGATCATATCAC
1 TGCTACTGATGGCTTTGTGTCGATCATATTACCATTACTAATGGTTGTGTGCCGATCATATCAC
* *
38869671 TACTACTGATGGCTCTGTG
1 TGCTACTGATGGCTTTGTG
38869690 CCAATCACAT
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 76 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (64 bp):
TGCTACTGATGGCTTTGTGTCGATCATATTACCATTACTAATGGTTGTGTGCCGATCATATCAC
Found at i:38869678 original size:32 final size:32
Alignment explanation
Indices: 38869545--38869696 Score: 128
Period size: 32 Copynumber: 4.8 Consensus size: 32
38869535 TACTGCGATG
* * *
38869545 CTACTGATGGCTT-TGTGTCGATCATATTACCA
1 CTACTGATGG-TTGTGTGCCGATCATATCACTA
* * *
38869577 TTACTAATGGTTGTGTGCCGATCATATCACTG
1 CTACTGATGGTTGTGTGCCGATCATATCACTA
* * * * *
38869609 CTACTGAAGGCTT-TGTGTCGATCATGTTACCA
1 CTACTGATGG-TTGTGTGCCGATCATATCACTA
* *
38869641 TTACTGGTGGTTGTGTGCCGATCATATCACTA
1 CTACTGATGGTTGTGTGCCGATCATATCACTA
* * *
38869673 CTACTGATGGCTCTGTGCCAATCA
1 CTACTGATGGTTGTGTGCCGATCA
38869697 CATTACTGTA
Statistics
Matches: 91, Mismatches: 26, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
31 4 0.04
32 85 0.93
33 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.36
Consensus pattern (32 bp):
CTACTGATGGTTGTGTGCCGATCATATCACTA
Found at i:38869733 original size:22 final size:22
Alignment explanation
Indices: 38869708--38869754 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
38869698 ATTACTGTAC
* * * *
38869708 TTATGGCTTGTAGTTATTCTGT
1 TTATAGCTTATAGCTATCCTGT
38869730 TTATAGCTTATAGCTATCCTGT
1 TTATAGCTTATAGCTATCCTGT
38869752 TTA
1 TTA
38869755 CGACTCTTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.13, G:0.17, T:0.51
Consensus pattern (22 bp):
TTATAGCTTATAGCTATCCTGT
Found at i:38869795 original size:26 final size:26
Alignment explanation
Indices: 38869766--38869819 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
38869756 GACTCTTAGC
* *
38869766 CATTCTGACTACTGCCAGCTCTGCTG
1 CATTATGACTACTGCCAGCTATGCTG
* *
38869792 CATTATTACTACTGGCAGCTATGCTG
1 CATTATGACTACTGCCAGCTATGCTG
38869818 CA
1 CA
38869820 ATATTGGTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.20, C:0.30, G:0.19, T:0.31
Consensus pattern (26 bp):
CATTATGACTACTGCCAGCTATGCTG
Found at i:38869824 original size:26 final size:26
Alignment explanation
Indices: 38869773--38869824 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
38869763 AGCCATTCTG
* *
38869773 ACTACTGCCAGCTCTGCTGCATTATT
1 ACTACTGCCAGCTATGCTGCAATATT
*
38869799 ACTACTGGCAGCTATGCTGCAATATT
1 ACTACTGCCAGCTATGCTGCAATATT
38869825 GGTGTGAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (26 bp):
ACTACTGCCAGCTATGCTGCAATATT
Found at i:38870595 original size:20 final size:20
Alignment explanation
Indices: 38870566--38870627 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 20
38870556 GGTGTTACAA
*
38870566 CATTACTGGCAGCTTATCTG
1 CATTATTGGCAGCTTATCTG
* *
38870586 CATTATTGGCAGTTTATTTG
1 CATTATTGGCAGCTTATCTG
* *
38870606 CATTATTGACAGCTTGTCTG
1 CATTATTGGCAGCTTATCTG
38870626 CA
1 CA
38870628 CTGCTGGCAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (20 bp):
CATTATTGGCAGCTTATCTG
Found at i:38870636 original size:40 final size:40
Alignment explanation
Indices: 38870566--38870693 Score: 139
Period size: 40 Copynumber: 3.2 Consensus size: 40
38870556 GGTGTTACAA
* * * * * *
38870566 CATTACTGGCAGCTTATCTGCATTATTGGCAGTTTATTTG
1 CATTACTGACAGCTTGTCTGCACTACTGGCAATTTATCTG
* * *
38870606 CATTATTGACAGCTTGTCTGCACTGCTGGCAATTTATCTA
1 CATTACTGACAGCTTGTCTGCACTACTGGCAATTTATCTG
** *
38870646 CATTACTGGTAGCTTGTCTGTACTACTGGCAATTTATCTG
1 CATTACTGACAGCTTGTCTGCACTACTGGCAATTTATCTG
*
38870686 CATCACTG
1 CATTACTG
38870694 GTGGCTTGTC
Statistics
Matches: 72, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 72 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (40 bp):
CATTACTGACAGCTTGTCTGCACTACTGGCAATTTATCTG
Found at i:38870694 original size:40 final size:40
Alignment explanation
Indices: 38870616--38870703 Score: 131
Period size: 40 Copynumber: 2.2 Consensus size: 40
38870606 CATTATTGAC
* *
38870616 AGCTTGTCTGCACTGCTGGCAATTTATCTACATTACTGGT
1 AGCTTGTCTGCACTACTGGCAATTTATCTACATCACTGGT
* *
38870656 AGCTTGTCTGTACTACTGGCAATTTATCTGCATCACTGGT
1 AGCTTGTCTGCACTACTGGCAATTTATCTACATCACTGGT
*
38870696 GGCTTGTC
1 AGCTTGTC
38870704 CATAAATTGG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.38
Consensus pattern (40 bp):
AGCTTGTCTGCACTACTGGCAATTTATCTACATCACTGGT
Found at i:38875190 original size:41 final size:41
Alignment explanation
Indices: 38875145--38875342 Score: 245
Period size: 41 Copynumber: 4.8 Consensus size: 41
38875135 GCTTATTAAA
* * * * *
38875145 ATACACAGGCATAAAGCCTTCTAGGCACAAAGCCAGATATG
1 ATACACCGGCATGAAGCCTGCTAGGCATAAAGCCTGATATG
*
38875186 ATACACCGGCACGAAGCCTGCTAGGCATAAAGCCTGATATG
1 ATACACCGGCATGAAGCCTGCTAGGCATAAAGCCTGATATG
*
38875227 GTACACCGGCATGAAGCCTGCTAGGCATAAAGCCTGATATG
1 ATACACCGGCATGAAGCCTGCTAGGCATAAAGCCTGATATG
* * *
38875268 GTACACCGGCATGAAGCCTGTTAGGCATAAAGCCTGTTAT-
1 ATACACCGGCATGAAGCCTGCTAGGCATAAAGCCTGATATG
* * * * *
38875308 AGTTCACCGACATAAAGCCTGCTAGGAACAAAGCC
1 A-TACACCGGCATGAAGCCTGCTAGGCATAAAGCC
38875343 CGAGTATCAT
Statistics
Matches: 139, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
41 139 1.00
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (41 bp):
ATACACCGGCATGAAGCCTGCTAGGCATAAAGCCTGATATG
Found at i:38875217 original size:82 final size:81
Alignment explanation
Indices: 38875117--38875342 Score: 256
Period size: 82 Copynumber: 2.8 Consensus size: 81
38875107 CATCGGCATA
* * * * *
38875117 AAGCCTGTGAGGTATAAAGCTTATTAAAATACACAGGCATAAAGCCTTCTAGGCACAAAGCCAGA
1 AAGCCTGT-AGGCATAAAGCTTATTATAGTACACCGGCATAAAGCCTGCTAGGCACAAAGCCAGA
38875182 TATGATACACCGGCACG
65 TATGATACACCGGCACG
* * * * *
38875199 AAGCCTGCTAGGCATAAAGCCTGA-TATGGTACACCGGCATGAAGCCTGCTAGGCATAAAGCCTG
1 AAGCCTG-TAGGCATAAAG-CTTATTATAGTACACCGGCATAAAGCCTGCTAGGCACAAAGCCAG
* *
38875263 ATATGGTACACCGGCATG
64 ATATGATACACCGGCACG
* * * * *
38875281 AAGCCTGTTAGGCATAAAGCCTGTTATAGTTCACCGACATAAAGCCTGCTAGGAACAAAGCC
1 AAGCCTG-TAGGCATAAAGCTTATTATAGTACACCGGCATAAAGCCTGCTAGGCACAAAGCC
38875343 CGAGTATCAT
Statistics
Matches: 119, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
81 1 0.01
82 114 0.96
83 4 0.03
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (81 bp):
AAGCCTGTAGGCATAAAGCTTATTATAGTACACCGGCATAAAGCCTGCTAGGCACAAAGCCAGAT
ATGATACACCGGCACG
Found at i:38875300 original size:16 final size:16
Alignment explanation
Indices: 38875275--38875306 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
38875265 ATGGTACACC
*
38875275 GGCATGAAGCCTGTTA
1 GGCATAAAGCCTGTTA
38875291 GGCATAAAGCCTGTTA
1 GGCATAAAGCCTGTTA
38875307 TAGTTCACCG
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:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (16 bp):
GGCATAAAGCCTGTTA
Found at i:38878615 original size:22 final size:22
Alignment explanation
Indices: 38878575--38878616 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
38878565 AAAGTTAAAT
38878575 ATAAAATAATTTAATATAATGA
1 ATAAAATAATTTAATATAATGA
*
38878597 ATAAATTATATTTAA-ATAAT
1 ATAAAATA-ATTTAATATAAT
38878617 TTAATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
ATAAAATAATTTAATATAATGA
Found at i:38878651 original size:33 final size:32
Alignment explanation
Indices: 38878582--38878670 Score: 126
Period size: 33 Copynumber: 2.8 Consensus size: 32
38878572 AATATAAAAT
* * *
38878582 AATTTAATATAATGAATAAAT-TATATTTAAAT
1 AATTTAATATAATG-ATACATAAATATTTAAAC
38878614 AATTTAATATAATGATACATGAAATATTTAAAC
1 AATTTAATATAATGATACAT-AAATATTTAAAC
38878647 AATTTAATATAATGATACATAAAT
1 AATTTAATATAATGATACATAAAT
38878671 TAGAAACTAA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
31 5 0.10
32 18 0.35
33 29 0.56
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.39
Consensus pattern (32 bp):
AATTTAATATAATGATACATAAATATTTAAAC
Found at i:38879268 original size:19 final size:20
Alignment explanation
Indices: 38879244--38879307 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 20
38879234 TAAATGTTGA
*
38879244 AATTTTTATAAA-TATTTTG
1 AATTTTTAAAAATTATTTTG
38879263 AA-TTTTAAAAATTATTTTG
1 AATTTTTAAAAATTATTTTG
* * *
38879282 AATTTTTGAAATTTAATTT-
1 AATTTTTAAAAATTATTTTG
38879301 AATTTTT
1 AATTTTT
38879308 TTGTAATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
18 8 0.21
19 18 0.46
20 13 0.33
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
AATTTTTAAAAATTATTTTG
Found at i:38884340 original size:12 final size:11
Alignment explanation
Indices: 38884312--38884347 Score: 63
Period size: 11 Copynumber: 3.2 Consensus size: 11
38884302 AGCAACCTCC
38884312 CCCCTATTGTA
1 CCCCTATTGTA
38884323 CCCCTATTGTA
1 CCCCTATTGTA
38884334 CCACCTATTGTA
1 CC-CCTATTGTA
38884346 CC
1 CC
38884348 TCCGGTTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.19, C:0.39, G:0.08, T:0.33
Consensus pattern (11 bp):
CCCCTATTGTA
Found at i:38895205 original size:9 final size:9
Alignment explanation
Indices: 38895184--38895224 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
38895174 ATGTAAGAAT
38895184 TAAAAATTCA
1 TAAAAATT-A
38895194 TAAAAATTA
1 TAAAAATTA
38895203 TAAAAATTA
1 TAAAAATTA
*
38895212 T-AAATTTA
1 TAAAAATTA
38895220 TAAAA
1 TAAAA
38895225 TCCTTTCAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 7 0.24
9 14 0.48
10 8 0.28
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (9 bp):
TAAAAATTA
Found at i:38895220 original size:17 final size:19
Alignment explanation
Indices: 38895184--38895224 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
38895174 ATGTAAGAAT
38895184 TAAAAATTCATAAAAATTA
1 TAAAAATTCATAAAAATTA
*
38895203 TAAAAATT-AT-AAATTTA
1 TAAAAATTCATAAAAATTA
38895220 TAAAA
1 TAAAA
38895225 TCCTTTCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.52
18 2 0.10
19 8 0.38
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
TAAAAATTCATAAAAATTA
Found at i:38897110 original size:19 final size:19
Alignment explanation
Indices: 38897086--38897139 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
38897076 AATCATATAT
38897086 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
38897105 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
*
38897124 TTTAAGATTGCATATC
1 TCTAAGATTGCATATC
38897140 CTTGAAGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:38897137 original size:38 final size:41
Alignment explanation
Indices: 38897063--38897139 Score: 115
Period size: 38 Copynumber: 1.9 Consensus size: 41
38897053 AAATTAAATC
38897063 TCTAAGATTACAAAATCATATATTCTAAGATTGCATATCATA
1 TCTAAGATTACAAAATCA-ATATTCTAAGATTGCATATCATA
*
38897105 TCTAAGATTAC-ATATC-ATATT-TAAGATTGCATATC
1 TCTAAGATTACAAAATCAATATTCTAAGATTGCATATC
38897140 CTTGAAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 14 0.41
39 5 0.15
41 4 0.12
42 11 0.32
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (41 bp):
TCTAAGATTACAAAATCAATATTCTAAGATTGCATATCATA
Found at i:38897910 original size:101 final size:101
Alignment explanation
Indices: 38897739--38898224 Score: 726
Period size: 101 Copynumber: 4.8 Consensus size: 101
38897729 CCATCTTTAG
* * * *
38897739 TCTTTTAAATTGTAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAACCTGTTCCACTACAC
1 TCTTTTTAATTGCAATGTTGGGGAAACGAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACAC
* *
38897804 CGCCAGGGAAGTAAAATTTACCGTTTGCCGCTTTAA
66 CGCCAGGGAAGTAAAATTCACCGTTTGCCGCTTCAA
* *
38897840 TCTTTTTAATTGCAATGTTGGGGAAACGAGATTCGCCGTCGTAGCTTCAATCTATTCCGCTACAC
1 TCTTTTTAATTGCAATGTTGGGGAAACGAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACAC
* *
38897905 TGCCAGGGAAGTAAAATTCACCGTTTGCGGCTTCAA
66 CGCCAGGGAAGTAAAATTCACCGTTTGCCGCTTCAA
* *
38897941 TCTTTTTAATTGCAATGTTGGGGAAACGAGATTCGCTGTCGTAGCTTTAATCTGTTCCACTACAC
1 TCTTTTTAATTGCAATGTTGGGGAAACGAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACAC
* **
38898006 CGCTAGGGAAGTAAAATTTGCCGTTT-CCGGCTTCAA
66 CGCCAGGGAAGTAAAATTCACCGTTTGCC-GCTTCAA
* * *
38898042 TCTTTTTAATTGCAATGCTAGGGAAACGAGATTCGCCGTCATAGCTTCAATCTGTTCCACTACAC
1 TCTTTTTAATTGCAATGTTGGGGAAACGAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACAC
** *
38898107 CGCCAGGGAAGTAAAATTCGTCG-TTGCGGCTTCAA
66 CGCCAGGGAAGTAAAATTCACCGTTTGCCGCTTCAA
*
38898142 TCTTTTTAATTGCAATGTTGGGGAAACTAGATTCGCCGTCG-AGCTTCAATCTGTTCCACTACAC
1 TCTTTTTAATTGCAATGTTGGGGAAACGAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACAC
* *
38898206 CGCCAGGGGAGTAAGATTC
66 CGCCAGGGAAGTAAAATTC
38898225 GTTGTTGCGG
Statistics
Matches: 349, Mismatches: 34, Indels: 6
0.90 0.09 0.02
Matches are distributed among these distances:
99 40 0.11
100 47 0.13
101 262 0.75
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (101 bp):
TCTTTTTAATTGCAATGTTGGGGAAACGAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACAC
CGCCAGGGAAGTAAAATTCACCGTTTGCCGCTTCAA
Found at i:38897965 original size:51 final size:51
Alignment explanation
Indices: 38897809--38897965 Score: 118
Period size: 51 Copynumber: 3.1 Consensus size: 51
38897799 TACACCGCCA
* * *
38897809 GGGAAGTAAAATTTACCGTTTGCCGCTTTAATCTTTTTAATTGCAATGTTG
1 GGGAAGTAAAATTCACCGTTTGCAGCTTCAATCTTTTTAATTGCAATGTTG
*** * * * * * **** * * ***
38897860 GGGAAACGAGATTCGCCG-TCGTAGCTTCAATCTATTCCGCTACACTGCCA
1 GGGAAGTAAAATTCACCGTTTGCAGCTTCAATCTTTTTAATTGCAATGTTG
*
38897910 GGGAAGTAAAATTCACCGTTTGCGGCTTCAATCTTTTTAATTGCAATGTTG
1 GGGAAGTAAAATTCACCGTTTGCAGCTTCAATCTTTTTAATTGCAATGTTG
38897961 GGGAA
1 GGGAA
38897966 ACGAGATTCG
Statistics
Matches: 67, Mismatches: 38, Indels: 2
0.63 0.36 0.02
Matches are distributed among these distances:
50 31 0.46
51 36 0.54
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (51 bp):
GGGAAGTAAAATTCACCGTTTGCAGCTTCAATCTTTTTAATTGCAATGTTG
Found at i:38898080 original size:51 final size:50
Alignment explanation
Indices: 38897824--38898193 Score: 142
Period size: 50 Copynumber: 7.4 Consensus size: 50
38897814 GTAAAATTTA
* * * *
38897824 CCGTTTGCCGCTTTAATCTTTTTAATTGCAATGTTGGGGAAACGAGATTCG
1 CCGTTT-CGGCTTCAATCTTTTTAATTGCAATGCTAGGGAAACGAGATTCG
* **** * * * *** * *
38897875 CCG--TCGTAGCTTCAATCTATTCCGCTACACTGCCAGGGAAGTAAAATTCA
1 CCGTTTCG--GCTTCAATCTTTTTAATTGCAATGCTAGGGAAACGAGATTCG
* *
38897925 CCGTTTGCGGCTTCAATCTTTTTAATTGCAATGTTGGGGAAACGAGATTCG
1 CCGTTT-CGGCTTCAATCTTTTTAATTGCAATGCTAGGGAAACGAGATTCG
* * * ** * * ** *** * *
38897976 -C-TGTCGTAGCTTTAATCTGTTCCACTACACCGCTAGGGAAGTAAAATTTG
1 CCGTTTCG--GCTTCAATCTTTTTAATTGCAATGCTAGGGAAACGAGATTCG
38898026 CCGTTTCCGGCTTCAATCTTTTTAATTGCAATGCTAGGGAAACGAGATTCG
1 CCGTTT-CGGCTTCAATCTTTTTAATTGCAATGCTAGGGAAACGAGATTCG
* * * ** * * ** * *** *
38898077 CCGTCAT-AGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAAATTCG
1 CCGT-TTCGGCTTCAATCTTTTTAATTGCAATGCTAGGGAAACGAGATTCG
* * * * *
38898127 TCGTTGCGGCTTCAATCTTTTTAATTGCAATGTTGGGGAAACTAGATTCG
1 CCGTTTCGGCTTCAATCTTTTTAATTGCAATGCTAGGGAAACGAGATTCG
38898177 CCG--TCGAGCTTCAATCT
1 CCGTTTCG-GCTTCAATCT
38898194 GTTCCACTAC
Statistics
Matches: 210, Mismatches: 96, Indels: 28
0.63 0.29 0.08
Matches are distributed among these distances:
48 5 0.02
49 13 0.06
50 120 0.57
51 64 0.30
52 4 0.02
53 4 0.02
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.32
Consensus pattern (50 bp):
CCGTTTCGGCTTCAATCTTTTTAATTGCAATGCTAGGGAAACGAGATTCG
Found at i:38898223 original size:49 final size:49
Alignment explanation
Indices: 38898070--38898225 Score: 120
Period size: 50 Copynumber: 3.1 Consensus size: 49
38898060 TAGGGAAACG
* *
38898070 AGATTCGCCGTCATAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTA
1 AGATTCGCCGTC-GAGCTTCAATCTGTTCCACTACACCGCCAGGGGAGTA
* * * ** * * ** ** *
38898120 AAATTCGTCGTTGCG-GCTTCAATCTTTTTAATTGCAATG-TTGGGGA-AA
1 AGATTCGCCG-T-CGAGCTTCAATCTGTTCCACTACACCGCCAGGGGAGTA
38898168 CTAGATTCGCCGTCGAGCTTCAATCTGTTCCACTACACCGCCAGGGGAGTA
1 --AGATTCGCCGTCGAGCTTCAATCTGTTCCACTACACCGCCAGGGGAGTA
38898219 AGATTCG
1 AGATTCG
38898226 TTGTTGCGGC
Statistics
Matches: 73, Mismatches: 26, Indels: 15
0.64 0.23 0.13
Matches are distributed among these distances:
48 3 0.04
49 29 0.40
50 38 0.52
51 2 0.03
52 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.28
Consensus pattern (49 bp):
AGATTCGCCGTCGAGCTTCAATCTGTTCCACTACACCGCCAGGGGAGTA
Found at i:38898607 original size:44 final size:44
Alignment explanation
Indices: 38898558--38898767 Score: 244
Period size: 44 Copynumber: 5.0 Consensus size: 44
38898548 GAAGTAAGAT
* *
38898558 TCACAATCTTCAACCTATTCCACTACTAACCAGGGAGATAGGAC
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
38898602 TCACAATCTTCAACCTATTCCACTGCTGACCA-GGAGATAGG--
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
*
38898643 -----A--TTC-ACCTATTCCACTGCTGACCAGGGAGATAGGAT
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
* * * *
38898679 TTACAATTTTCAAACTATTCCACTACTGACCAGGGAGATAGGAC
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
* * * *
38898723 TTACAATTTTCAACCTATTCCATTGCTGACCAGTGAGATAGGAC
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
38898767 T
1 T
38898768 AGGGTCATCG
Statistics
Matches: 146, Mismatches: 9, Indels: 22
0.82 0.05 0.12
Matches are distributed among these distances:
33 20 0.14
34 12 0.08
36 1 0.01
41 1 0.01
43 12 0.08
44 100 0.68
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.27
Consensus pattern (44 bp):
TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
Found at i:38898656 original size:33 final size:34
Alignment explanation
Indices: 38898614--38898679 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 34
38898604 ACAATCTTCA
38898614 ACCTATTCCACTGCTGACCA-GGAGATAGGATTC
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTC
38898647 ACCTATTCCACTGCTGACCAGGGAGATAGGATT
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATT
38898680 TACAATTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 20 0.62
34 12 0.38
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (34 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGATTC
Found at i:38898697 original size:77 final size:78
Alignment explanation
Indices: 38898570--38898721 Score: 234
Period size: 77 Copynumber: 2.0 Consensus size: 78
38898560 ACAATCTTCA
* *
38898570 ACCTATTCCACTACTAACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACCA-
1 ACCTATTCCACTACTAACCAGGGAGATAGGACTCACAATCTTCAAACTATTCCACTACTGACCAG
38898634 GGAGATAGGATTC
66 GGAGATAGGATTC
* * * * *
38898647 ACCTATTCCACTGCTGACCAGGGAGATAGGATTTACAATTTTCAAACTATTCCACTACTGACCAG
1 ACCTATTCCACTACTAACCAGGGAGATAGGACTCACAATCTTCAAACTATTCCACTACTGACCAG
38898712 GGAGATAGGA
66 GGAGATAGGA
38898722 CTTACAATTT
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
77 57 0.85
78 10 0.15
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (78 bp):
ACCTATTCCACTACTAACCAGGGAGATAGGACTCACAATCTTCAAACTATTCCACTACTGACCAG
GGAGATAGGATTC
Found at i:38900162 original size:16 final size:17
Alignment explanation
Indices: 38900122--38900168 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 17
38900112 CCTTGGCCTC
*
38900122 TCTTTTTCCTCTTATTCTT
1 TCTTTTT-CT-TTTTTCTT
38900141 TCTTTTTCTTTTTTCTT
1 TCTTTTTCTTTTTTCTT
38900158 T-TTTTTCTTTT
1 TCTTTTTCTTTT
38900169 CCTTTTTCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 10 0.37
17 8 0.30
18 2 0.07
19 7 0.26
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (17 bp):
TCTTTTTCTTTTTTCTT
Found at i:38905410 original size:19 final size:19
Alignment explanation
Indices: 38905386--38905477 Score: 157
Period size: 19 Copynumber: 4.8 Consensus size: 19
38905376 AATCATATCT
38905386 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
38905405 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
38905424 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
38905443 TCTAATATTACATATCATA
1 TCTAAGATTGCATATCATA
38905462 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
38905478 CTTGAAGATT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 67 1.00
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:38905435 original size:38 final size:38
Alignment explanation
Indices: 38905363--38905477 Score: 176
Period size: 38 Copynumber: 2.9 Consensus size: 38
38905353 AAATTAAATC
*
38905363 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTAC-ATATCATA---TCTAAGATTGCATATCATA
38905405 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
*
38905443 TCTAATATTACATATCATATCTAAGATTGCATATC
1 TCTAAGATTACATATCATATCTAAGATTGCATATC
38905478 CTTGAAGATT
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
38 53 0.75
41 7 0.10
42 11 0.15
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:38905681 original size:16 final size:16
Alignment explanation
Indices: 38905655--38905687 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
38905645 TGTATATTAA
38905655 AGTTTTTTT-AATTTT
1 AGTTTTTTTAAATTTT
38905670 AGTTTTTATTAAATTTT
1 AGTTTTT-TTAAATTTT
38905687 A
1 A
38905688 ATGAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (16 bp):
AGTTTTTTTAAATTTT
Found at i:38911592 original size:16 final size:17
Alignment explanation
Indices: 38911561--38911594 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
38911551 ATTAGAAATG
*
38911561 AATAATTTATATATAAA
1 AATAAATTATATATAAA
38911578 AATAAATTA-ATATAAA
1 AATAAATTATATATAAA
38911594 A
1 A
38911595 TTATGTTCAT
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AATAAATTATATATAAA
Found at i:38913102 original size:15 final size:15
Alignment explanation
Indices: 38913084--38913145 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
38913074 AAGGTTTTTG
* *
38913084 AATTATTATTTAATT
1 AATTATAATTAAATT
38913099 AATTATAATTAAATT
1 AATTATAATTAAATT
38913114 -ATTA-AAGTTAAA--
1 AATTATAA-TTAAATT
* *
38913126 AAATAGAATTAAATT
1 AATTATAATTAAATT
38913141 AATTA
1 AATTA
38913146 GTTATTGTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
13 10 0.26
14 11 0.29
15 17 0.45
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (15 bp):
AATTATAATTAAATT
Found at i:38914288 original size:50 final size:50
Alignment explanation
Indices: 38914207--38914332 Score: 153
Period size: 50 Copynumber: 2.5 Consensus size: 50
38914197 CTCGCCACTT
* *
38914207 AGGCTTTCCAAATTATACACCACATAGGCCTTTCAGAAAACTAGACACAA
1 AGGCTTTCCAAATTATATACCACATAAGCCTTTCAGAAAACTAGACACAA
* * * ** * * *
38914257 AGGTTTTCCAAATAATATACCACATAAGCCTTTTAGGTATCTCGCCACAA
1 AGGCTTTCCAAATTATATACCACATAAGCCTTTCAGAAAACTAGACACAA
*
38914307 AGGCTTTCCAAATTATATGCCACATA
1 AGGCTTTCCAAATTATATACCACATA
38914333 GGCACCACAT
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 63 1.00
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.27
Consensus pattern (50 bp):
AGGCTTTCCAAATTATATACCACATAAGCCTTTCAGAAAACTAGACACAA
Found at i:38915323 original size:25 final size:26
Alignment explanation
Indices: 38915269--38915324 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
38915259 TAGCTTAATG
*
38915269 AAGAAGAATAGAACATTTAGGTTAGA
1 AAGAAGAATAGAACATTGAGGTTAGA
*
38915295 AAGAAGAACTAGAACGTTGA-G-TAGA
1 AAGAAGAA-TAGAACATTGAGGTTAGA
38915320 AAGAA
1 AAGAA
38915325 AAACCATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 9 0.33
26 9 0.33
27 9 0.33
ACGTcount: A:0.52, C:0.05, G:0.25, T:0.18
Consensus pattern (26 bp):
AAGAAGAATAGAACATTGAGGTTAGA
Found at i:38916628 original size:28 final size:28
Alignment explanation
Indices: 38916571--38916628 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
38916561 AGCTACAGAA
* *
38916571 GCTTTCCTTCTAGAGTCTCTCCATAGAG
1 GCTTTCCTTCTAGAGTCTCTCCACAAAG
38916599 GCTTTCCTTCTAGAGTCT-TGCCACAAAG
1 GCTTTCCTTCTAGAGTCTCT-CCACAAAG
38916627 GC
1 GC
38916629 ATCCTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.33
Consensus pattern (28 bp):
GCTTTCCTTCTAGAGTCTCTCCACAAAG
Found at i:38916649 original size:29 final size:29
Alignment explanation
Indices: 38916618--38916801 Score: 170
Period size: 29 Copynumber: 6.3 Consensus size: 29
38916608 CTAGAGTCTT
*
38916618 GCCACAAAGGCATCCTTTTAATAGAGATT
1 GCCACAAAGGCATCCTTTTAATAGAGATA
* *
38916647 GCCACAAAGGCTTCCTTTTAATAAAGATA
1 GCCACAAAGGCATCCTTTTAATAGAGATA
* * * *
38916676 GCCACAAAGACTTCCTTTTAACAAAGATA
1 GCCACAAAGGCATCCTTTTAATAGAGATA
**
38916705 GCCACAAAGGTGTCCTTTTAATAGAGATA
1 GCCACAAAGGCATCCTTTTAATAGAGATA
* ** * *
38916734 GCCACAAATGTGTCCTTTTAATCAGATATT
1 GCCACAAAGGCATCCTTTTAAT-AGAGATA
* * ** *
38916764 GTCATAAAGAAATCTTTTTAATCAGAGATA
1 GCCACAAAGGCATCCTTTTAAT-AGAGATA
*
38916794 CCCACAAA
1 GCCACAAA
38916802 AGCTTTCTTT
Statistics
Matches: 129, Mismatches: 25, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
29 98 0.76
30 31 0.24
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (29 bp):
GCCACAAAGGCATCCTTTTAATAGAGATA
Found at i:38916781 original size:87 final size:89
Alignment explanation
Indices: 38916618--38916801 Score: 207
Period size: 87 Copynumber: 2.1 Consensus size: 89
38916608 CTAGAGTCTT
*
38916618 GCCACAAAGGCATCCTTTTAATAGAGATTGCCACAAAGGCTTCCTTTTAATAAAGATAGCCACAA
1 GCCACAAAGGCATCCTTTTAATAGAGATAGCCACAAAGGCTTCCTTTTAATAAAGATAGCCACAA
**
38916683 AGACTTCC-TTTTAA-CAAAGATA
66 AGAAATCCTTTTTAATCAAAGATA
** * * *
38916705 GCCACAAAGGTGTCCTTTTAATAGAGATAGCCACAAATG-TGTCCTTTTAAT-CAGATATTGTCA
1 GCCACAAAGGCATCCTTTTAATAGAGATAGCCACAAAGGCT-TCCTTTTAATAAAGATA--GCCA
* *
38916768 TAAAGAAAT-CTTTTTAATCAGAGATA
63 CAAAGAAATCCTTTTTAATCAAAGATA
*
38916794 CCCACAAA
1 GCCACAAA
38916802 AGCTTTCTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
86 6 0.07
87 46 0.57
88 15 0.19
89 14 0.17
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (89 bp):
GCCACAAAGGCATCCTTTTAATAGAGATAGCCACAAAGGCTTCCTTTTAATAAAGATAGCCACAA
AGAAATCCTTTTTAATCAAAGATA
Found at i:38926103 original size:15 final size:15
Alignment explanation
Indices: 38926085--38926118 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
38926075 AAAATAATAA
38926085 AAAAGGAAATAAATG
1 AAAAGGAAATAAATG
*
38926100 AAAAGTAAATAAATG
1 AAAAGGAAATAAATG
38926115 AAAA
1 AAAA
38926119 AAACAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (15 bp):
AAAAGGAAATAAATG
Found at i:38931378 original size:17 final size:17
Alignment explanation
Indices: 38931356--38931388 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
38931346 CGATTTGAGA
38931356 TGTGGAATTAAATTAGG
1 TGTGGAATTAAATTAGG
38931373 TGTGGAATTAAATTAG
1 TGTGGAATTAAATTAG
38931389 CTTGATCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.36
Consensus pattern (17 bp):
TGTGGAATTAAATTAGG
Found at i:38939826 original size:29 final size:29
Alignment explanation
Indices: 38939763--38939832 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
38939753 TCATCGACAA
38939763 ATGAAAAGGGATAGCTTCAGCTATCGAGT
1 ATGAAAAGGGATAGCTTCAGCTATCGAGT
*
38939792 ACGAAAAGGGATAGCTTCAGCTATCGA-T
1 ATGAAAAGGGATAGCTTCAGCTATCGAGT
*
38939820 GATGAAAAAGGAT
1 -ATGAAAAGGGAT
38939833 GGTGATAACC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 1 0.03
29 36 0.97
ACGTcount: A:0.39, C:0.13, G:0.27, T:0.21
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCAGCTATCGAGT
Found at i:38939853 original size:29 final size:30
Alignment explanation
Indices: 38939821--38939893 Score: 121
Period size: 29 Copynumber: 2.5 Consensus size: 30
38939811 GCTATCGATG
*
38939821 ATGAAAAAGGATGGTGATAACCATC-AACA
1 ATGAAAAGGGATGGTGATAACCATCGAACA
*
38939850 ATGAAAAGGGATGGTGATGACCATCGAACA
1 ATGAAAAGGGATGGTGATAACCATCGAACA
38939880 ATGAAAAGGGATGG
1 ATGAAAAGGGATGG
38939894 CTTCGACTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 23 0.56
30 18 0.44
ACGTcount: A:0.44, C:0.11, G:0.29, T:0.16
Consensus pattern (30 bp):
ATGAAAAGGGATGGTGATAACCATCGAACA
Found at i:38939906 original size:30 final size:30
Alignment explanation
Indices: 38939763--38940011 Score: 122
Period size: 30 Copynumber: 8.4 Consensus size: 30
38939753 TCATCGACAA
*
38939763 ATGAAAAGGGATAGCTTC-AGCTATCG-AGT
1 ATGAAAAGGGATAGCTTCGA-CTATCGAACT
*
38939792 ACGAAAAGGGATAGCTTC-AGCTATCG-A-T
1 ATGAAAAGGGATAGCTTCGA-CTATCGAACT
* * * * *
38939820 GATGAAAAAGGAT-GGTGAT-AACCATC-AACA
1 -ATGAAAAGGGATAGCT--TCGACTATCGAACT
* * *
38939850 ATGAAAAGGGAT-GGTGAT-GACCATCGAACA
1 ATGAAAAGGGATAGCT--TCGACTATCGAACT
* *
38939880 ATGAAAAGGGATGGCTTCGACTATCGATCT
1 ATGAAAAGGGATAGCTTCGACTATCGAACT
* * * * * * *
38939910 GTGGAAAGAGATAGCTCCGGCTATCAAATT
1 ATGAAAAGGGATAGCTTCGACTATCGAACT
* * *
38939940 ATGAAAAGGGATAGCTTCGGCTGTCGAAGT
1 ATGAAAAGGGATAGCTTCGACTATCGAACT
* * * *
38939970 ATGAAAAGGGATAACTTCGATTATCAAATT
1 ATGAAAAGGGATAGCTTCGACTATCGAACT
*
38940000 ATGAAAAAGGAT
1 ATGAAAAGGGAT
38940012 GTATCAACAT
Statistics
Matches: 176, Mismatches: 35, Indels: 17
0.77 0.15 0.07
Matches are distributed among these distances:
28 3 0.02
29 65 0.37
30 106 0.60
31 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.22
Consensus pattern (30 bp):
ATGAAAAGGGATAGCTTCGACTATCGAACT
Found at i:38940782 original size:43 final size:42
Alignment explanation
Indices: 38940734--38940860 Score: 106
Period size: 43 Copynumber: 3.1 Consensus size: 42
38940724 TGGTATAAAC
38940734 TTGGTTAAGTATGAGTTTAACAATTGACCAATTTGTGTTTATA
1 TTGGTTAAGTAT-AGTTTAACAATTGACCAATTTGTGTTTATA
* * *** * * *
38940777 TTGGTT-GGTA-A----AACAAATGGTAAATATG-GTATAAA
1 TTGGTTAAGTATAGTTTAACAATTGACCAATTTGTGTTTATA
38940812 CTTGGTTAAGTATTAGTTTAACAATTGACCAATTTGTGTTTATA
1 -TTGGTTAAGTA-TAGTTTAACAATTGACCAATTTGTGTTTATA
38940856 TTGGT
1 TTGGT
38940861 ACATGTTTTA
Statistics
Matches: 59, Mismatches: 16, Indels: 18
0.63 0.17 0.19
Matches are distributed among these distances:
35 5 0.08
36 18 0.31
37 3 0.05
39 1 0.02
40 1 0.02
42 3 0.05
43 23 0.39
44 5 0.08
ACGTcount: A:0.32, C:0.06, G:0.20, T:0.42
Consensus pattern (42 bp):
TTGGTTAAGTATAGTTTAACAATTGACCAATTTGTGTTTATA
Found at i:38940830 original size:79 final size:80
Alignment explanation
Indices: 38940697--38940860 Score: 303
Period size: 79 Copynumber: 2.1 Consensus size: 80
38940687 TGGTATGTTT
38940697 TTGGTTAGTAAAACAAATGGTACAATATGGTATAAACTTGGTTAAGTATGAGTTTAACAATTGAC
1 TTGGTTAGTAAAACAAATGGTACAATATGGTATAAACTTGGTTAAGTATGAGTTTAACAATTGAC
38940762 CAATTTGTGTTTATA
66 CAATTTGTGTTTATA
* *
38940777 TTGGTTGGTAAAACAAATGGTA-AATATGGTATAAACTTGGTTAAGTATTAGTTTAACAATTGAC
1 TTGGTTAGTAAAACAAATGGTACAATATGGTATAAACTTGGTTAAGTATGAGTTTAACAATTGAC
38940841 CAATTTGTGTTTATA
66 CAATTTGTGTTTATA
38940856 TTGGT
1 TTGGT
38940861 ACATGTTTTA
Statistics
Matches: 82, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
79 61 0.74
80 21 0.26
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.39
Consensus pattern (80 bp):
TTGGTTAGTAAAACAAATGGTACAATATGGTATAAACTTGGTTAAGTATGAGTTTAACAATTGAC
CAATTTGTGTTTATA
Found at i:38947180 original size:29 final size:29
Alignment explanation
Indices: 38947115--38947184 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
38947105 TCATCGACGA
* *
38947115 ATGAAAAGGGATAGCTTTGGCTATCGAAT
1 ATGAAAAGGGATAACTTCGGCTATCGAAT
* * * *
38947144 ACGGAAAGGGATAACTTCGGCTATTGATT
1 ATGAAAAGGGATAACTTCGGCTATCGAAT
*
38947173 GTGAAAAGGGAT
1 ATGAAAAGGGAT
38947185 GGTGATGACC
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.34, C:0.10, G:0.30, T:0.26
Consensus pattern (29 bp):
ATGAAAAGGGATAACTTCGGCTATCGAAT
Found at i:38947244 original size:30 final size:30
Alignment explanation
Indices: 38947174--38947363 Score: 161
Period size: 30 Copynumber: 6.4 Consensus size: 30
38947164 CTATTGATTG
* *
38947174 TGAAAAGGGATGGTGATGACCATC-AACAA
1 TGAAAAGGGATGGTGACGACCATCGAACTA
* *
38947203 AGAATAGGGATGGTGACGACCATCGAACTA
1 TGAAAAGGGATGGTGACGACCATCGAACTA
** ** *
38947233 TGAAAAGGGATGGCT-TTGAATATCGATCTA
1 TGAAAAGGGATGG-TGACGACCATCGAACTA
* * * * * *
38947263 TGAAAAGGGATAGCT-TCGGCTATCAAATTA
1 TGAAAAGGGAT-GGTGACGACCATCGAACTA
*
38947293 TGAAAAGGGATGGTGACGACCATCGAACAA
1 TGAAAAGGGATGGTGACGACCATCGAACTA
* * * *
38947323 TGAAAAGGGATGGTGACAACCGTCAAATTA
1 TGAAAAGGGATGGTGACGACCATCGAACTA
38947353 TGAAAAGGGAT
1 TGAAAAGGGAT
38947364 AGGTTTGGCT
Statistics
Matches: 127, Mismatches: 30, Indels: 7
0.77 0.18 0.04
Matches are distributed among these distances:
29 23 0.18
30 102 0.80
31 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.28, T:0.21
Consensus pattern (30 bp):
TGAAAAGGGATGGTGACGACCATCGAACTA
Found at i:38947349 original size:60 final size:60
Alignment explanation
Indices: 38947174--38947363 Score: 197
Period size: 60 Copynumber: 3.2 Consensus size: 60
38947164 CTATTGATTG
* * * *
38947174 TGAAAAGGGATGGTGATGACCATC-AACAAAGAATAGGGATGGTGACGACCATCGAACTA
1 TGAAAAGGGATGGTGATGACCATCGAACAATGAAAAGGGATGGTGACGACCATCAAATTA
* ** * * * * * *
38947233 TGAAAAGGGATGGCT-TTGAATATCGATCTATGAAAAGGGATAGCT-TCGGCTATCAAATTA
1 TGAAAAGGGATGG-TGATGACCATCGAACAATGAAAAGGGAT-GGTGACGACCATCAAATTA
* * *
38947293 TGAAAAGGGATGGTGACGACCATCGAACAATGAAAAGGGATGGTGACAACCGTCAAATTA
1 TGAAAAGGGATGGTGATGACCATCGAACAATGAAAAGGGATGGTGACGACCATCAAATTA
38947353 TGAAAAGGGAT
1 TGAAAAGGGAT
38947364 AGGTTTGGCT
Statistics
Matches: 101, Mismatches: 25, Indels: 9
0.75 0.19 0.07
Matches are distributed among these distances:
59 22 0.22
60 77 0.76
61 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.28, T:0.21
Consensus pattern (60 bp):
TGAAAAGGGATGGTGATGACCATCGAACAATGAAAAGGGATGGTGACGACCATCAAATTA
Found at i:38947355 original size:90 final size:90
Alignment explanation
Indices: 38947208--38947393 Score: 232
Period size: 90 Copynumber: 2.1 Consensus size: 90
38947198 AACAAAGAAT
* *** * *
38947208 AGGGATGGTGACGACCATCGAACTATGAAAAGGGATGGCTTTGAATATCGATCTATGAAAAGGGA
1 AGGGATGGTGACGACCATCGAACAATGAAAAGGGATGGCTGACAACATCAATCTATGAAAAGGGA
*
38947273 TAGCTTCGGCTATCAAATTATGAAA
66 TAGCTTCGGCTATCAAACTATGAAA
*
38947298 AGGGATGGTGACGACCATCGAACAATGAAAAGGGATGG-TGACAACCGTCAAAT-TATGAAAAGG
1 AGGGATGGTGACGACCATCGAACAATGAAAAGGGATGGCTGACAA-CATC-AATCTATGAAAAGG
* * * *
38947361 GATAGGTTTGGCTGTCGAACTATGAAA
64 GATAGCTTCGGCTATCAAACTATGAAA
38947388 AGGGAT
1 AGGGAT
38947394 AACTTTGATT
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
89 3 0.04
90 77 0.94
91 2 0.02
ACGTcount: A:0.36, C:0.13, G:0.29, T:0.22
Consensus pattern (90 bp):
AGGGATGGTGACGACCATCGAACAATGAAAAGGGATGGCTGACAACATCAATCTATGAAAAGGGA
TAGCTTCGGCTATCAAACTATGAAA
Found at i:38947394 original size:30 final size:29
Alignment explanation
Indices: 38947174--38947393 Score: 129
Period size: 30 Copynumber: 7.4 Consensus size: 29
38947164 CTATTGATTG
* *
38947174 TGAAAAGGGATGGTGAT-GACCATC-AACAA
1 TGAAAAGGGATGGT--TCGACTATCGAACTA
* * * *
38947203 AGAATAGGGATGGTGACGACCATCGAACTA
1 TGAAAAGGGATGGT-TCGACTATCGAACTA
* * *
38947233 TGAAAAGGGATGGCTTTGAATATCGATCTA
1 TGAAAAGGGATGG-TTCGACTATCGAACTA
* * * *
38947263 TGAAAAGGGATAGCTTCGGCTATCAAATTA
1 TGAAAAGGGAT-GGTTCGACTATCGAACTA
* * *
38947293 TGAAAAGGGATGGTGACGACCATCGAACAA
1 TGAAAAGGGATGGT-TCGACTATCGAACTA
* * ** * *
38947323 TGAAAAGGGATGGTGACAACCGTCAAATTA
1 TGAAAAGGGATGGT-TCGACTATCGAACTA
* * *
38947353 TGAAAAGGGATAGGTTTGGCTGTCGAACTA
1 TGAAAAGGGAT-GGTTCGACTATCGAACTA
38947383 TGAAAAGGGAT
1 TGAAAAGGGAT
38947394 AACTTTGATT
Statistics
Matches: 147, Mismatches: 38, Indels: 11
0.75 0.19 0.06
Matches are distributed among these distances:
29 21 0.14
30 121 0.82
31 5 0.03
ACGTcount: A:0.37, C:0.13, G:0.29, T:0.21
Consensus pattern (29 bp):
TGAAAAGGGATGGTTCGACTATCGAACTA
Found at i:38951991 original size:150 final size:150
Alignment explanation
Indices: 38951720--38952020 Score: 530
Period size: 150 Copynumber: 2.0 Consensus size: 150
38951710 AGAATGTGAT
* *
38951720 TGGTGTACCACCTGGATACAATCAACCAATGCTGCGGCAAAATGTGTAACAAAGCTTGTCATCTT
1 TGGTGTACCACCTGCATACAATCAACCAATGCTGCGGCAAAATGTGCAACAAAGCTTGTCATCTT
** *
38951785 CAACATCATTTATGGAAGCTCTCTTAAAGGAGTATATGGCTAAGAATGATGTAATTATTCAGAGC
66 CAACATCAACTATAGAAGCTCTCTTAAAGGAGTATATGGCTAAGAATGATGTAATTATTCAGAGC
38951850 CAGGTAGCTTTCTTAAGAGC
131 CAGGTAGCTTTCTTAAGAGC
* * *
38951870 TGGTGTACCACTTGCATACAGTCAACCAATGCTGCGGCAAAATGTGCAACAAAGTTTGTCATCTT
1 TGGTGTACCACCTGCATACAATCAACCAATGCTGCGGCAAAATGTGCAACAAAGCTTGTCATCTT
38951935 CAACATCAACTATAGAAGCTCTCTTAAAGGAGTATATGGCTAAGAATGATGTAATTATTCAGAGC
66 CAACATCAACTATAGAAGCTCTCTTAAAGGAGTATATGGCTAAGAATGATGTAATTATTCAGAGC
38952000 CAGGTAGCTTTCTTAAGAGC
131 CAGGTAGCTTTCTTAAGAGC
38952020 T
1 T
38952021 CTAGAGAATC
Statistics
Matches: 143, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
150 143 1.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (150 bp):
TGGTGTACCACCTGCATACAATCAACCAATGCTGCGGCAAAATGTGCAACAAAGCTTGTCATCTT
CAACATCAACTATAGAAGCTCTCTTAAAGGAGTATATGGCTAAGAATGATGTAATTATTCAGAGC
CAGGTAGCTTTCTTAAGAGC
Found at i:38968423 original size:28 final size:28
Alignment explanation
Indices: 38968391--38968635 Score: 375
Period size: 28 Copynumber: 8.8 Consensus size: 28
38968381 AACAGTATTG
*
38968391 TGTGGGCCTTAGCCCAATACAGCAACAA
1 TGTGGGCCTTAGCCCAATACAGTAACAA
* *
38968419 TGTGGGCCCTAGCCTAATACAGTAACAA
1 TGTGGGCCTTAGCCCAATACAGTAACAA
* *
38968447 TATGGGTCTTAGCCCAATACAGTAACAA
1 TGTGGGCCTTAGCCCAATACAGTAACAA
*
38968475 TGTGGGCCTTAGCCCAAAACA-TCAACAA
1 TGTGGGCCTTAGCCCAATACAGT-AACAA
*
38968503 TGTGGGCCTTAGCCCAATACAATAACAA
1 TGTGGGCCTTAGCCCAATACAGTAACAA
*
38968531 TGTGGGCTTTAGCCCAATACAGTAACAA
1 TGTGGGCCTTAGCCCAATACAGTAACAA
**
38968559 TGTGGGCCTTAGCCCAATACAACAACAA
1 TGTGGGCCTTAGCCCAATACAGTAACAA
*
38968587 TGTGGGCCTTAGCCCAAAACAGTAACAA
1 TGTGGGCCTTAGCCCAATACAGTAACAA
38968615 TGTGGGCCTTAGCCCAATACA
1 TGTGGGCCTTAGCCCAATACA
38968636 ATATCGGTAT
Statistics
Matches: 195, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
27 1 0.01
28 193 0.99
29 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (28 bp):
TGTGGGCCTTAGCCCAATACAGTAACAA
Found at i:38968860 original size:27 final size:27
Alignment explanation
Indices: 38968822--38968893 Score: 126
Period size: 27 Copynumber: 2.7 Consensus size: 27
38968812 GGGACCCGTG
38968822 GGGGTAATTCGGTTATTTTATCCTATA
1 GGGGTAATTCGGTTATTTTATCCTATA
*
38968849 GGGGTAATTCGGTTATTTTATCCTGTA
1 GGGGTAATTCGGTTATTTTATCCTATA
*
38968876 GGGGTAATTCGGTCATTT
1 GGGGTAATTCGGTTATTT
38968894 ACTGACCTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.19, C:0.11, G:0.26, T:0.43
Consensus pattern (27 bp):
GGGGTAATTCGGTTATTTTATCCTATA
Found at i:38975900 original size:23 final size:22
Alignment explanation
Indices: 38975848--38975900 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
38975838 TCCACGTCTT
*
38975848 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
38975870 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
38975893 TTTCTTTT
1 TTTCTTTT
38975901 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:38984643 original size:37 final size:35
Alignment explanation
Indices: 38984580--38984648 Score: 86
Period size: 37 Copynumber: 1.9 Consensus size: 35
38984570 ATTCCAACAA
*
38984580 TAATATTATTTTAATAGTTTAATATTAAATTTAATC
1 TAATATTATCTTAATAGTTTAATATT-AATTTAATC
*
38984616 TAATACTTATCTTAATAGTATT-TTATTAATTTA
1 TAATA-TTATCTTAATAGT-TTAATATTAATTTA
38984649 TTATTAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 11 0.38
37 16 0.55
38 2 0.07
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (35 bp):
TAATATTATCTTAATAGTTTAATATTAATTTAATC
Found at i:38984782 original size:59 final size:62
Alignment explanation
Indices: 38984666--38984782 Score: 150
Period size: 62 Copynumber: 1.9 Consensus size: 62
38984656 ATTGATTATC
* * * * *
38984666 TTAAAATTAAATTTCATTTAATGTTTATCTTGTAGATAAACATTCTATTATTTTAATAAGAT
1 TTAAAATTAAATTTAATCTAATATTTATCTTGTAGATAAACATTATATTAATTTAATAAGAT
* *
38984728 TTAATATTAAATTTAATCTAATATTTATC-T-T-GATAAATATTATATTAATTTAATA
1 TTAAAATTAAATTTAATCTAATATTTATCTTGTAGATAAACATTATATTAATTTAATA
38984783 TTAAATTGAT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 21 0.44
60 1 0.02
61 1 0.02
62 25 0.52
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (62 bp):
TTAAAATTAAATTTAATCTAATATTTATCTTGTAGATAAACATTATATTAATTTAATAAGAT
Found at i:38986784 original size:50 final size:50
Alignment explanation
Indices: 38986673--38986920 Score: 207
Period size: 50 Copynumber: 4.9 Consensus size: 50
38986663 ATTTGGGTAA
* *
38986673 AGAGATCCCATGTAAGACCATGTCTGGGACATGGAATTGGCATTATTGAGATTATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGC---ATCGAG---ATG
* **
38986729 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCATCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATG
* ** * * * * *
38986779 AGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCAATATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATG
* * * *
38986829 AGA-ACTCTCATGTAAGACCATATCTGGGATATGGCATTGGTAGTAC-A-A-G
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-T-CGAGATG
* * *
38986878 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
38986921 GTTATTATCA
Statistics
Matches: 159, Mismatches: 29, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
48 1 0.01
49 35 0.22
50 78 0.49
51 1 0.01
52 1 0.01
53 5 0.03
56 38 0.24
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATG
Found at i:38989883 original size:40 final size:38
Alignment explanation
Indices: 38989789--38989887 Score: 110
Period size: 40 Copynumber: 2.5 Consensus size: 38
38989779 GAAATCCTTG
*
38989789 TTATAATTATTGTAATTAT-AATTTAGGATCAAATATTA
1 TTATAATTA-TGTAATTATAAATTTAGGATCAAACATTA
* ** *
38989827 TTATAATTACTATAATTATAAATTTTTTGCTCAAACATTA
1 TTATAATTA-TGTAATTATAAA-TTTAGGATCAAACATTA
38989867 TTATAATTATGGTAATTATAA
1 TTATAATTAT-GTAATTATAA
38989888 CTATTATATT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
38 17 0.33
39 3 0.06
40 31 0.61
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.47
Consensus pattern (38 bp):
TTATAATTATGTAATTATAAATTTAGGATCAAACATTA
Found at i:38992698 original size:31 final size:31
Alignment explanation
Indices: 38992661--38992722 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
38992651 AGATAATTTT
38992661 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
38992692 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
38992723 TAATTTGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:38998887 original size:31 final size:31
Alignment explanation
Indices: 38998850--38998910 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
38998840 AGATAATTTT
38998850 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
38998881 AAAGAGTTTTATTAGGATTCAATTACTCTT
1 AAAGAGTTTTATTAGGATTCAATTACTCTT
38998911 TTAATTTGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.43
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:39000837 original size:11 final size:11
Alignment explanation
Indices: 39000821--39000845 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39000811 TTTTGAGTAA
39000821 TTTGGTTAAGT
1 TTTGGTTAAGT
39000832 TTTGGTTAAGT
1 TTTGGTTAAGT
39000843 TTT
1 TTT
39000846 ATAATGGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.24, T:0.60
Consensus pattern (11 bp):
TTTGGTTAAGT
Found at i:39003961 original size:17 final size:17
Alignment explanation
Indices: 39003939--39003973 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
39003929 TTAGCAGTCA
*
39003939 ATCGTGAGGCTGGAATT
1 ATCGTGAGACTGGAATT
39003956 ATCGTGAGACTGGAATT
1 ATCGTGAGACTGGAATT
39003973 A
1 A
39003974 ACATTCGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.11, G:0.31, T:0.29
Consensus pattern (17 bp):
ATCGTGAGACTGGAATT
Found at i:39015129 original size:25 final size:25
Alignment explanation
Indices: 39015022--39015145 Score: 153
Period size: 25 Copynumber: 5.0 Consensus size: 25
39015012 CGAATACTTC
39015022 ATAGCTCATGAGAGCATA-CTGATTT
1 ATAGCTCATGAGAGCATATC-GATTT
*
39015047 ATAGCTCATGAGAGCATACCGATTT
1 ATAGCTCATGAGAGCATATCGATTT
* *
39015072 ATAGCTCATGAGAGGATATTGATTT
1 ATAGCTCATGAGAGCATATCGATTT
* * *
39015097 ATAGCTCGTGGGAGCATATCGATCT
1 ATAGCTCATGAGAGCATATCGATTT
*
39015122 ATAGCTCGA-GTGAGCATATCGATT
1 ATAGCTC-ATGAGAGCATATCGATT
39015146 CACAGCTCCT
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
25 85 0.99
26 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (25 bp):
ATAGCTCATGAGAGCATATCGATTT
Found at i:39015152 original size:25 final size:25
Alignment explanation
Indices: 39015099--39015153 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
39015089 ATTGATTTAT
* *
39015099 AGCTCGTGGGAGCATATCGATCTAT
1 AGCTCGAGGGAGCATATCGATCTAC
*
39015124 AGCTCGAGTGAGCATATCGAT-TCAC
1 AGCTCGAGGGAGCATATCGATCT-AC
39015149 AGCTC
1 AGCTC
39015154 CTATGAGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 1 0.04
25 25 0.96
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.25
Consensus pattern (25 bp):
AGCTCGAGGGAGCATATCGATCTAC
Found at i:39031341 original size:22 final size:22
Alignment explanation
Indices: 39031293--39031344 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
39031283 TACTTCATGG
* * *
39031293 AGTGTGAACACATTTATGTTTT
1 AGTGTGAACACACTTAAGTGTT
39031315 AGTGTGAACA-ACTTAAGTGTT
1 AGTGTGAACACACTTAAGTGTT
39031336 AGGTGTGAA
1 A-GTGTGAA
39031345 TGTGTTTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.37
Consensus pattern (22 bp):
AGTGTGAACACACTTAAGTGTT
Found at i:39050392 original size:29 final size:29
Alignment explanation
Indices: 39050360--39050419 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
39050350 ATATTAGTTG
39050360 TTATTTAAAAGTATTTTGTTAAGTGATTT
1 TTATTTAAAAGTATTTTGTTAAGTGATTT
39050389 TTATTTAAAAGTATTTTGTTAAGTGATTT
1 TTATTTAAAAGTATTTTGTTAAGTGATTT
39050418 TT
1 TT
39050420 GATAAATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (29 bp):
TTATTTAAAAGTATTTTGTTAAGTGATTT
Found at i:39059573 original size:15 final size:15
Alignment explanation
Indices: 39059550--39059611 Score: 65
Period size: 15 Copynumber: 4.2 Consensus size: 15
39059540 CGAATAAAAT
39059550 TTTAAATTTTTATAA
1 TTTAAATTTTTATAA
*
39059565 TTTATATTTTTATAA
1 TTTAAATTTTTATAA
* *
39059580 TTTTAAAGTATTA-AA
1 -TTTAAATTTTTATAA
*
39059595 -TTAAAATTTTATAA
1 TTTAAATTTTTATAA
39059609 TTT
1 TTT
39059612 TAGAATGAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 9 0.24
14 2 0.05
15 18 0.47
16 9 0.24
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (15 bp):
TTTAAATTTTTATAA
Done.