Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167826.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_1, 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: 36299135
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Warning! 357000 characters in sequence are not A, C, G, or T
File 12 of 402
Found at i:2546013 original size:113 final size:113
Alignment explanation
Indices: 2545884--2546157 Score: 287
Period size: 112 Copynumber: 2.4 Consensus size: 113
2545874 ACAAAAAACG
* * * * *
2545884 TAATCTTTATTAAAAATAT-AAAAAAATTTATTTTTTTAGAATTTGACAAAGATGGATGTTTTAA
1 TAATATTTATTAAAAATATGAAAAAAA-TTATTTTTTCAAAATTTAACAAAGACGG-TGTTTTAA
*
2545948 GAT-AAAAATGTTGTATTT-ATTAGAAAGATAATATTTCTAAAATAAAAATA
64 GATAAAAAATGTAGTATTTGA-T-GAAAGATAATATTTCTAAAATAAAAATA
* * * * *
2545998 TAATTTTTGTT-AAAATATGAAAAAAA--A-ATTTTCAAAATTTAATAAAGACGGTGTTTTAGGA
1 TAATATTTATTAAAAATATGAAAAAAATTATTTTTTCAAAATTTAACAAAGACGGTGTTTTAAGA
* *
2546059 TAAAAAAAAATGTAGTCTTTGATGAAAGATAATATTTCTAAGATAAAAATA
66 T---AAAAAATGTAGTATTTGATGAAAGATAATATTTCTAAAATAAAAATA
* *
2546110 TAATATTTATTAAAAATATGAAAAAAA-TATATTTT-ACAATTTAACAAA
1 TAATATTTATTAAAAATATGAAAAAAATTATTTTTTCAAAATTTAACAAA
2546158 AATGACGGTT
Statistics
Matches: 135, Mismatches: 16, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
109 10 0.07
110 18 0.13
111 1 0.01
112 36 0.27
113 36 0.27
114 29 0.21
115 5 0.04
ACGTcount: A:0.50, C:0.03, G:0.09, T:0.38
Consensus pattern (113 bp):
TAATATTTATTAAAAATATGAAAAAAATTATTTTTTCAAAATTTAACAAAGACGGTGTTTTAAGA
TAAAAAATGTAGTATTTGATGAAAGATAATATTTCTAAAATAAAAATA
Found at i:2546089 original size:112 final size:111
Alignment explanation
Indices: 2545970--2546237 Score: 305
Period size: 112 Copynumber: 2.4 Consensus size: 111
2545960 GTATTTATTA
*
2545970 GAAAGATAATATTTCTAAAATAAAAATATAATTTTTGTT-AAAATATGAAAAAAA-A-ATTTTCA
1 GAAAGATAATATTTCTAAGATAAAAATATAATTTTTGTTAAAAATATGAAAAAAATATATTTT-A
* *
2546032 AAATTT-A-ATAAA-GACGGTGTTTTAGGATAAAAAAAAATGTAGTCTTTGAT
65 AAATTTAACAAAAATGAC-G-GTTTTAGGAT--AAAAAAA-G-AGTCATTGAT
* * *
2546082 GAAAGATAATATTTCTAAGATAAAAATATAATATTTATTAAAAATATGAAAAAAATATATTTTAC
1 GAAAGATAATATTTCTAAGATAAAAATATAATTTTTGTTAAAAATATGAAAAAAATATATTTTAA
* *
2546147 AATTTAACAAAAATGACGGTTTTATGATAAAAAAAGAGTCATTGTT
66 AATTTAACAAAAATGACGGTTTTAGGATAAAAAAAGAGTCATTGAT
* * * * *
2546193 AAAGAGATGATGTTTTTAAGATAAAAATATAATTTTTGTTGAAAA
1 GAA-AGATAATATTTCTAAGATAAAAATATAATTTTTGTTAAAAA
2546238 GATAATTTTT
Statistics
Matches: 134, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
111 10 0.07
112 72 0.54
113 22 0.16
114 7 0.05
115 15 0.11
116 5 0.04
117 3 0.02
ACGTcount: A:0.50, C:0.03, G:0.12, T:0.35
Consensus pattern (111 bp):
GAAAGATAATATTTCTAAGATAAAAATATAATTTTTGTTAAAAATATGAAAAAAATATATTTTAA
AATTTAACAAAAATGACGGTTTTAGGATAAAAAAAGAGTCATTGAT
Found at i:2546216 original size:40 final size:40
Alignment explanation
Indices: 2546166--2546260 Score: 102
Period size: 40 Copynumber: 2.4 Consensus size: 40
2546156 AAAATGACGG
* * *
2546166 TTTTATGATAAAAAAAGAGTCATTGTT-AAAGAGATGATGT
1 TTTTAAGATAAAAAAAGAATCATTGTTGAAA-AGATAATGT
* * ** *
2546206 TTTTAAGATAAAAATATAATTTTTGTTGAAAAGATAATTT
1 TTTTAAGATAAAAAAAGAATCATTGTTGAAAAGATAATGT
2546246 TTTTAAGATAAAAAA
1 TTTTAAGATAAAAAA
2546261 TATGATTTTT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
40 42 0.93
41 3 0.07
ACGTcount: A:0.46, C:0.01, G:0.14, T:0.39
Consensus pattern (40 bp):
TTTTAAGATAAAAAAAGAATCATTGTTGAAAAGATAATGT
Found at i:2546447 original size:38 final size:37
Alignment explanation
Indices: 2546405--2546485 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 37
2546395 ATATAAAAAA
* * *
2546405 ATAAAACATAAATTATCTTTTACTTAATATTATCATAT
1 ATAAAACATAAAATAT-ATTTACTTAATATTATCATAC
*** *
2546443 ATAAAGTTTAAAATATATTTACTTAATATTATTATAC
1 ATAAAACATAAAATATATTTACTTAATATTATCATAC
2546480 ATAAAA
1 ATAAAA
2546486 TTTATTTATG
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
37 23 0.66
38 12 0.34
ACGTcount: A:0.48, C:0.07, G:0.01, T:0.43
Consensus pattern (37 bp):
ATAAAACATAAAATATATTTACTTAATATTATCATAC
Found at i:2549859 original size:11 final size:11
Alignment explanation
Indices: 2549839--2549878 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
2549829 TTATTTTTTA
*
2549839 TAATAAAATTT
1 TAATATAATTT
2549850 TAATATAATTT
1 TAATATAATTT
2549861 TAATAT-ATTT
1 TAATATAATTT
*
2549871 AAATATAA
1 TAATATAA
2549879 AATAATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TAATATAATTT
Found at i:2551606 original size:21 final size:21
Alignment explanation
Indices: 2551582--2551621 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2551572 TGATTATTTA
* *
2551582 ATTTATTAATTTAAATTTTTT
1 ATTTATTAAATAAAATTTTTT
*
2551603 ATTTTTTAAATAAAATTTT
1 ATTTATTAAATAAAATTTT
2551622 AATAGTAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTATTAAATAAAATTTTTT
Found at i:2561393 original size:3 final size:3
Alignment explanation
Indices: 2561385--2561415 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2561375 ATGATTTATG
2561385 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2561416 TGTTATTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2564862 original size:21 final size:21
Alignment explanation
Indices: 2564838--2564878 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2564828 GGATTCATTA
*
2564838 TACTGTATGAGGGATCACTCG
1 TACTGTAAGAGGGATCACTCG
2564859 TACTGTAAGAGGGATCACTC
1 TACTGTAAGAGGGATCACTC
2564879 TTTCTTTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (21 bp):
TACTGTAAGAGGGATCACTCG
Found at i:2570944 original size:15 final size:15
Alignment explanation
Indices: 2570892--2570952 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 15
2570882 GTAAAATTTA
2570892 TAAAATTT-TT-ATT
1 TAAAATTTATTAATT
* *
2570905 TAAAA-TAATTAAAT
1 TAAAATTTATTAATT
2570919 T-AAA-TTA--AATT
1 TAAAATTTATTAATT
2570930 TAAAATTTATTAATT
1 TAAAATTTATTAATT
2570945 TAAAATTT
1 TAAAATTT
2570953 CGTTACATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
11 4 0.11
12 4 0.11
13 15 0.39
14 3 0.08
15 12 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TAAAATTTATTAATT
Found at i:2571388 original size:2 final size:2
Alignment explanation
Indices: 2571381--2571407 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2571371 GTTGTATACG
2571381 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2571408 GCTATTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2571835 original size:48 final size:48
Alignment explanation
Indices: 2571778--2571877 Score: 139
Period size: 48 Copynumber: 2.1 Consensus size: 48
2571768 GAGGAGGCTC
* * *
2571778 TGGTGGTGGTTTTAGCAG-TGGGGGAGGTGTAGGCAATGGCCGTGGTGG
1 TGGTGGTGGTTATAGCAGCT-GGGGAGGTGTAGGAAATGGCCATGGTGG
* *
2571826 TGGTGGTGGTTATGGCAGCTGGGGAGGTGTGGGAAATGGCCATGGTGG
1 TGGTGGTGGTTATAGCAGCTGGGGAGGTGTAGGAAATGGCCATGGTGG
2571874 TGGT
1 TGGT
2571878 TTTGGCAGTG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 45 0.98
49 1 0.02
ACGTcount: A:0.13, C:0.08, G:0.52, T:0.27
Consensus pattern (48 bp):
TGGTGGTGGTTATAGCAGCTGGGGAGGTGTAGGAAATGGCCATGGTGG
Found at i:2571885 original size:42 final size:43
Alignment explanation
Indices: 2571826--2571924 Score: 118
Period size: 42 Copynumber: 2.3 Consensus size: 43
2571816 GCCGTGGTGG
* *
2571826 TGGTGGTGGTTATGGCAGCTGG-GGAGGTGTGGG-AA-AT-GGCC
1 TGGTGGTGGTTTTGGCAG-TGGTGGAGGCGTGGGCAATATCGG-C
2571867 ATGGTGGTGGTTTTGGCAGTGGTGGAGGCGTGGGCAATATCGGC
1 -TGGTGGTGGTTTTGGCAGTGGTGGAGGCGTGGGCAATATCGGC
2571911 -GGTGGTGGTTTTGG
1 TGGTGGTGGTTTTGG
2571925 ATCCGGCGGT
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
41 3 0.06
42 41 0.80
43 2 0.04
44 3 0.06
45 2 0.04
ACGTcount: A:0.12, C:0.09, G:0.51, T:0.28
Consensus pattern (43 bp):
TGGTGGTGGTTTTGGCAGTGGTGGAGGCGTGGGCAATATCGGC
Found at i:2572066 original size:24 final size:24
Alignment explanation
Indices: 2572015--2572066 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
2572005 GCTACGGTTT
** * *
2572015 TGGCAATGGAGGGGGTGGTGGGGG
1 TGGCAATGGAGGGGGAAGCGGGGA
*
2572039 TGGCAATGGAGGGGGAAGCGGGTA
1 TGGCAATGGAGGGGGAAGCGGGGA
2572063 TGGC
1 TGGC
2572067 GCAGGCTCAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.17, C:0.08, G:0.60, T:0.15
Consensus pattern (24 bp):
TGGCAATGGAGGGGGAAGCGGGGA
Found at i:2576205 original size:3 final size:3
Alignment explanation
Indices: 2576197--2576221 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2576187 TCCCCTCCCA
2576197 ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC A
2576222 CTCTCTAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:2583438 original size:3 final size:3
Alignment explanation
Indices: 2583430--2583458 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2583420 ATATTATCAA
2583430 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2583459 ACAGGATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2598891 original size:15 final size:16
Alignment explanation
Indices: 2598873--2598902 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2598863 TTTGTGTAAG
2598873 TTATT-TTTTAATTGA
1 TTATTGTTTTAATTGA
2598888 TTATTGTTTTAATTG
1 TTATTGTTTTAATTG
2598903 TATTTTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (16 bp):
TTATTGTTTTAATTGA
Found at i:2599095 original size:16 final size:17
Alignment explanation
Indices: 2599074--2599115 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
2599064 ACACTATACA
2599074 TTAAAAATAATAAG-TT
1 TTAAAAATAATAAGATT
2599090 TT-AAAAT-ATAAGATT
1 TTAAAAATAATAAGATT
2599105 TTGAAAAATAA
1 TT-AAAAATAA
2599116 ATTTTTAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 5 0.23
15 9 0.41
16 2 0.09
17 5 0.23
18 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (17 bp):
TTAAAAATAATAAGATT
Found at i:2599189 original size:29 final size:31
Alignment explanation
Indices: 2599146--2599207 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 31
2599136 AATGGTTCTT
2599146 AAATTATAATAAATATTTAATATAGTATTTG
1 AAATTATAATAAATATTTAATATAGTATTTG
*
2599177 AAATT-TAA-AAATATTTAATATGGTATTTG
1 AAATTATAATAAATATTTAATATAGTATTTG
2599206 AA
1 AA
2599208 TGTGATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 22 0.73
30 3 0.10
31 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (31 bp):
AAATTATAATAAATATTTAATATAGTATTTG
Found at i:2602606 original size:231 final size:231
Alignment explanation
Indices: 2602181--2602884 Score: 1108
Period size: 231 Copynumber: 3.0 Consensus size: 231
2602171 GCTTAAAATG
* * * * *
2602181 AGATTGATCATGCTGA--GTAGAGAAGCTGACGTATTGGTA-AAGGGCTGGATGATTACATGTTG
1 AGATTGATCATGTTGAGGGAAGAAAAGCTGACGTATTGG-AGAAGGGCTGGCTGATTATATGTTG
2602243 CAGTTGATCATTTTGAATTCTCTTGTGAACAAGTTTTTATAAACTGCTTTTCCAATAGAGATGCT
65 CAGTTGATCATTTTGAATTCTCTTGTGAACAAGTTTTTATAAACTGCTTTTCCAATAGAGATGCT
2602308 TATTTTGGCTGTTGAAAATGATATCTTAGTACAATCTTTGATAAGTGAAAATGGATGAAGATACT
130 TATTTTGGCTGTTGAAAATGATATCTTAGTACAATCTTTGATAAGTGAAAATGGATGAAGATACT
2602373 AGAATGAAAGATGGAACTTAATGATATAATGGGGTGA
195 AGAATGAAAGATGGAACTTAATGATATAATGGGGTGA
*
2602410 AGATTGATCATGTTGAGGGCAGAAAAGCTGACGTATTGGAGAAGGGCTGGCTGATTATATGTTGC
1 AGATTGATCATGTTGAGGGAAGAAAAGCTGACGTATTGGAGAAGGGCTGGCTGATTATATGTTGC
*
2602475 GGTTGATCATTTTGAATTCTCTTGTGAACAAGTTTTTATAAACTGCTTTTCCAATAGAGATGCTT
66 AGTTGATCATTTTGAATTCTCTTGTGAACAAGTTTTTATAAACTGCTTTTCCAATAGAGATGCTT
2602540 ATTTTGGCTGTTGAAAATGATATCTTAGTACAATCTTTGATAAGTGAAAATGGATGAAGATACTA
131 ATTTTGGCTGTTGAAAATGATATCTTAGTACAATCTTTGATAAGTGAAAATGGATGAAGATACTA
2602605 GAATGAAAGATGGAACTTAATGATATAATGGGGTGA
196 GAATGAAAGATGGAACTTAATGATATAATGGGGTGA
2602641 AGATTGATCATGTTGAGGGAAGAAAAGCTGACGTATTGGAGAAGGGCTGGCTGATTATATGTTGC
1 AGATTGATCATGTTGAGGGAAGAAAAGCTGACGTATTGGAGAAGGGCTGGCTGATTATATGTTGC
* * * *
2602706 AGTTGAGCGTTTTGAATTCTCTTGTGAACAAGTTTTTCTTACCCTTTATAAACAGCTTTTCCATT
66 AGTTGATCATTTTGAATTCTCTTGTGAACAAG------TT----TTTATAAACTGCTTTTCCAAT
* * * **
2602771 AGAGATGCTTATTTCGACTCTTGAAAGGGATATCTTAGTACAATCTTTGATAAGTGAAAATGGAT
121 AGAGATGCTTATTTTGGCTGTTGAAAATGATATCTTAGTACAATCTTTGATAAGTGAAAATGGAT
* * * *
2602836 GAAGCTACTAGAATGAAAGAGGGAACTTAGTGATAGAATGGGGTGA
186 GAAGATACTAGAATGAAAGATGGAACTTAATGATATAATGGGGTGA
2602882 AGA
1 AGA
2602885 CAGACTGCAT
Statistics
Matches: 441, Mismatches: 21, Indels: 14
0.93 0.04 0.03
Matches are distributed among these distances:
229 15 0.03
230 1 0.00
231 299 0.68
237 2 0.00
241 124 0.28
ACGTcount: A:0.32, C:0.10, G:0.25, T:0.33
Consensus pattern (231 bp):
AGATTGATCATGTTGAGGGAAGAAAAGCTGACGTATTGGAGAAGGGCTGGCTGATTATATGTTGC
AGTTGATCATTTTGAATTCTCTTGTGAACAAGTTTTTATAAACTGCTTTTCCAATAGAGATGCTT
ATTTTGGCTGTTGAAAATGATATCTTAGTACAATCTTTGATAAGTGAAAATGGATGAAGATACTA
GAATGAAAGATGGAACTTAATGATATAATGGGGTGA
Found at i:2609559 original size:16 final size:18
Alignment explanation
Indices: 2609540--2609576 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2609530 ATTATCTATT
2609540 TTTAAAGT-TT-ATATAA
1 TTTAAAGTATTAATATAA
*
2609556 TTTAAATTATTAATATAA
1 TTTAAAGTATTAATATAA
2609574 TTT
1 TTT
2609577 TGTAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 9 0.50
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTAAAGTATTAATATAA
Found at i:2610664 original size:32 final size:32
Alignment explanation
Indices: 2610593--2610664 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 32
2610583 AACAAAATAA
* *
2610593 AAAAATTTATATTAACACAACTTATAATATAT
1 AAAATTTTATATAAACACAACTTATAATATAT
*
2610625 -AATTTTTATATAAAACACAA--TATAAATATAT
1 AAAATTTTATAT-AAACACAACTTAT-AATATAT
2610656 AAAATTTTA
1 AAAATTTTA
2610665 ATATTTTACA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
30 3 0.09
31 16 0.48
32 14 0.42
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (32 bp):
AAAATTTTATATAAACACAACTTATAATATAT
Found at i:2611869 original size:24 final size:24
Alignment explanation
Indices: 2611823--2611871 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2611813 TTTTTTAAAT
* *
2611823 ATAAATATTTAAAAATATTATTAA
1 ATAAATATATAAAAATATAATTAA
2611847 ATAAATATATAAATAAT-TAATTAA
1 ATAAATATATAAA-AATATAATTAA
2611871 A
1 A
2611872 AATAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
ATAAATATATAAAAATATAATTAA
Found at i:2622052 original size:2 final size:2
Alignment explanation
Indices: 2622045--2622085 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2622035 TAAATTTATC
2622045 AT AT 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 AT AT A
2622086 AGCGTGGACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2631740 original size:14 final size:14
Alignment explanation
Indices: 2631716--2631770 Score: 76
Period size: 14 Copynumber: 3.9 Consensus size: 14
2631706 TTTTTACATA
2631716 TTAATTAAATTTAAT
1 TTAA-TAAATTTAAT
*
2631731 TTAATAAATTTAAA
1 TTAATAAATTTAAT
*
2631745 TTAATAAA-TAAAT
1 TTAATAAATTTAAT
2631758 TTAATAAATTTAA
1 TTAATAAATTTAA
2631771 ATCAAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
13 11 0.31
14 20 0.57
15 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTAATAAATTTAAT
Found at i:2631742 original size:9 final size:9
Alignment explanation
Indices: 2631728--2631770 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
2631718 AATTAAATTT
2631728 AATTTAATA
1 AATTTAATA
*
2631737 AATTTAAATT
1 AATTT-AATA
*
2631747 AA-TAAATA
1 AATTTAATA
2631755 AATTTAATA
1 AATTTAATA
2631764 AATTTAA
1 AATTTAA
2631771 ATCAAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 5 0.18
9 18 0.64
10 5 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AATTTAATA
Found at i:2631744 original size:6 final size:6
Alignment explanation
Indices: 2631720--2631841 Score: 69
Period size: 6 Copynumber: 19.7 Consensus size: 6
2631710 TACATATTAA
*
2631720 TTAAAT TTAATT TAATAAAT TTAAAT TAATAAA- -TAAAT TT-AA- -TAAAT
1 TTAAAT TTAAAT T--TAAAT TTAAAT T--TAAAT TTAAAT TTAAAT TTAAAT
* *
2631767 TTAAA- TCAAATT TTAAAAC TTAAATT TTAAA- TTAAAT TTAAAT TTAAAT
1 TTAAAT TTAAA-T TT-AAAT TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT
2631816 TTAATAT TATATTAAT TTAAAT TTAA
1 TTAA-AT T-TA--AAT TTAAAT TTAA
2631842 TCAATTATTT
Statistics
Matches: 92, Mismatches: 6, Indels: 36
0.69 0.04 0.27
Matches are distributed among these distances:
3 1 0.01
4 6 0.07
5 11 0.12
6 43 0.47
7 11 0.12
8 16 0.17
9 3 0.03
10 1 0.01
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (6 bp):
TTAAAT
Found at i:2631783 original size:27 final size:26
Alignment explanation
Indices: 2631716--2631813 Score: 71
Period size: 27 Copynumber: 3.8 Consensus size: 26
2631706 TTTTTACATA
*
2631716 TTAATTAAA-TTT-AATTTAATAAAT
1 TTAAATAAATTTTAAATTTAATAAAT
* **
2631740 TTAAATTAATAAATAAATTTAATAAAT
1 TTAAATAAAT-TTTAAATTTAATAAAT
* *
2631767 TTAAATCAAATTTTAAAACTT-A-AATT
1 TTAAAT-AAATTTT-AAATTTAATAAAT
2631793 TTAAATTAAA-TTTAAATTTAA
1 TTAAA-TAAATTTTAAATTTAA
2631814 ATTTAATATT
Statistics
Matches: 57, Mismatches: 10, Indels: 13
0.71 0.12 0.16
Matches are distributed among these distances:
24 12 0.21
25 4 0.07
26 12 0.21
27 21 0.37
28 8 0.14
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
TTAAATAAATTTTAAATTTAATAAAT
Found at i:2631789 original size:19 final size:19
Alignment explanation
Indices: 2631749--2631791 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2631739 TTTAAATTAA
*
2631749 TAAATAAATTTAATAAATT
1 TAAATAAATTTAATAAACT
*
2631768 TAAATCAAATTTTA-AAACT
1 TAAAT-AAATTTAATAAACT
2631787 TAAAT
1 TAAAT
2631792 TTTAAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATAAATTTAATAAACT
Found at i:2631836 original size:46 final size:47
Alignment explanation
Indices: 2631720--2631839 Score: 119
Period size: 46 Copynumber: 2.6 Consensus size: 47
2631710 TACATATTAA
*
2631720 TTAAATTTAAT-TTA-ATAAATTTAAATTAATAAATAAATTTAATAAAT
1 TTAAATTTAATATTATATAAATTTAAATT-TTAAATAAATTT-ATAAAT
* * *
2631767 TTAAA-TCAA-ATTTTA-AAACTTAAATTTTAAATTAAA-TT-TAAAT
1 TTAAATTTAATATTATATAAATTTAAATTTTAAA-TAAATTTATAAAT
*
2631810 TTAAATTTAATATTATATTAATTTAAATTT
1 TTAAATTTAATATTATATAAATTTAAATTT
2631840 AATCAATTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
43 10 0.17
44 3 0.05
45 11 0.19
46 29 0.49
47 6 0.10
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (47 bp):
TTAAATTTAATATTATATAAATTTAAATTTTAAATAAATTTATAAAT
Found at i:2631850 original size:22 final size:22
Alignment explanation
Indices: 2631807--2631850 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2631797 ATTAAATTTA
*
2631807 AATTTAAATTTAATATTATATT
1 AATTTAAATTTAATAATATATT
2631829 AATTTAAATTTAATCAAT-TATT
1 AATTTAAATTTAAT-AATATATT
2631851 TTTTTACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
AATTTAAATTTAATAATATATT
Found at i:2632872 original size:14 final size:13
Alignment explanation
Indices: 2632835--2632868 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
2632825 AATTTTGGAA
2632835 AATTTTAT-TTAT
1 AATTTTATATTAT
*
2632847 AATTTTTTATTAT
1 AATTTTATATTAT
2632860 AATTTTATA
1 AATTTTATA
2632869 ATTAAGCAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
AATTTTATATTAT
Found at i:2648857 original size:21 final size:21
Alignment explanation
Indices: 2648833--2648874 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2648823 ATAGTGAAAA
2648833 TTAAGAATTTAAGA-AAAAATT
1 TTAAGAATTT-AGATAAAAATT
**
2648854 TTAATTATTTAGATAAAAATT
1 TTAAGAATTTAGATAAAAATT
2648875 GAGAGGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.40
Consensus pattern (21 bp):
TTAAGAATTTAGATAAAAATT
Found at i:2653347 original size:2 final size:2
Alignment explanation
Indices: 2653342--2653380 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
2653332 CTCAAAAAAC
* *
2653342 TA TA TA TT TA TA TA TA TT TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2653381 CAATCAAACA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:2653653 original size:32 final size:31
Alignment explanation
Indices: 2653606--2653665 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
2653596 TATATATAAA
* *
2653606 TTTATACATAATAATATTATTAATAATTTAT
1 TTTATAAATAATAATATTATTAAAAATTTAT
*
2653637 TTTATAAATATATAATATTTTTAAAAATT
1 TTTATAAATA-ATAATATTATTAAAAATT
2653666 AAATAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 9 0.36
32 16 0.64
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (31 bp):
TTTATAAATAATAATATTATTAAAAATTTAT
Found at i:2653748 original size:28 final size:28
Alignment explanation
Indices: 2653701--2653761 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
2653691 TAACATCATC
*
2653701 AATTT-ATCATGATATTTTTAAACAATT
1 AATTTAATCATGATATATTTAAACAATT
*
2653728 AATTTAATCAT-ATAATATTTAAATAATT
1 AATTTAATCATGAT-ATATTTAAACAATT
*
2653756 ATTTTA
1 AATTTA
2653762 TTTTTTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 7 0.24
28 22 0.76
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (28 bp):
AATTTAATCATGATATATTTAAACAATT
Found at i:2656942 original size:33 final size:32
Alignment explanation
Indices: 2656896--2657026 Score: 115
Period size: 34 Copynumber: 4.0 Consensus size: 32
2656886 TTTAATTTTT
2656896 TTATAAATTTTT-AAAAATAAACTTTTGAAAAA
1 TTATAAATTTTTAAAAAATAAA-TTTTGAAAAA
*
2656928 TTATAAACTTTTTAAAAAATAAATTTTCAAAAAA
1 TTATAAA-TTTTTAAAAAATAAATTTT-GAAAAA
* * *
2656962 TAATATAATTTTTCAAAAATAAATTCTTG-AAGA
1 TTATA-AATTTTTAAAAAATAAATT-TTGAAAAA
* * *
2656995 TTCTAAATTTATCCAAAAAA-AATTTTTGAAAA
1 TTATAAATTT-T-TAAAAAATAAATTTTGAAAA
2657027 TATTTTTTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 15
0.75 0.10 0.14
Matches are distributed among these distances:
32 15 0.19
33 22 0.28
34 39 0.49
35 4 0.05
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (32 bp):
TTATAAATTTTTAAAAAATAAATTTTGAAAAA
Found at i:2656945 original size:19 final size:18
Alignment explanation
Indices: 2656912--2656981 Score: 56
Period size: 18 Copynumber: 3.9 Consensus size: 18
2656902 ATTTTTAAAA
*
2656912 ATAAACTTTTGAAAAATT
1 ATAAACTTTTAAAAAATT
*
2656930 ATAAACTTTTTAAAAA--
1 ATAAACTTTTAAAAAATT
*
2656946 ATAAA-TTTTCAAAAAATA
1 ATAAACTTTT-AAAAAATT
* *
2656964 ATATAATTTTTCAAAAAT
1 ATA-AACTTTTAAAAAAT
2656982 AAATTCTTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
15 4 0.09
16 10 0.23
18 18 0.41
19 8 0.18
20 4 0.09
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (18 bp):
ATAAACTTTTAAAAAATT
Found at i:2657932 original size:22 final size:22
Alignment explanation
Indices: 2657902--2657946 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2657892 TAATATAATT
*
2657902 TAAAATTAAAAAAAATTATAAA
1 TAAAATTAAAAAAAATTAAAAA
* * *
2657924 TAAATTTAATAAAATTTAAAAA
1 TAAAATTAAAAAAAATTAAAAA
2657946 T
1 T
2657947 TATATTTTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATTAAAAAAAATTAAAAA
Found at i:2657937 original size:21 final size:20
Alignment explanation
Indices: 2657904--2657943 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2657894 ATATAATTTA
2657904 AAATTAAAAAAAATTATAAAT
1 AAATTAAAAAAAATT-TAAAT
* *
2657925 AAATTTAATAAAATTTAAA
1 AAATTAAAAAAAATTTAAA
2657944 AATTATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATTAAAAAAAATTTAAAT
Found at i:2658427 original size:11 final size:11
Alignment explanation
Indices: 2658411--2658435 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2658401 TTTGCATATA
2658411 GTCGTCACACG
1 GTCGTCACACG
2658422 GTCGTCACACG
1 GTCGTCACACG
2658433 GTC
1 GTC
2658436 TAGGTTGGAA
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:0.36, G:0.28, T:0.20
Consensus pattern (11 bp):
GTCGTCACACG
Found at i:2658777 original size:27 final size:27
Alignment explanation
Indices: 2658732--2658791 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
2658722 TTTCAATTTT
*
2658732 TATTA-TAATAAAATAAGATAAAATGA
1 TATTATTAATAAAATAAGATAAAATAA
* * *
2658758 TATTATTAATATAATTAGATTAAATAA
1 TATTATTAATAAAATAAGATAAAATAA
2658785 TATTATT
1 TATTATT
2658792 TTATTTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 5 0.17
27 24 0.83
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (27 bp):
TATTATTAATAAAATAAGATAAAATAA
Found at i:2658892 original size:18 final size:19
Alignment explanation
Indices: 2658869--2658908 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
2658859 TTTAAAATTT
2658869 ATATAATTTAAATTAT-TA
1 ATATAATTTAAATTATATA
*
2658887 ATATAATTTTAATTATATA
1 ATATAATTTAAATTATATA
2658906 ATA
1 ATA
2658909 AAATATGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATAATTTAAATTATATA
Found at i:2659401 original size:23 final size:25
Alignment explanation
Indices: 2659356--2659401 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2659346 ATTTATAAGT
*
2659356 AAAATATATATACATTTACTATTAA
1 AAAATATAAATACATTTACTATTAA
2659381 AAAATATAAATA-ATTTA-TATT
1 AAAATATAAATACATTTACTATT
2659402 TTTAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 5 0.25
25 11 0.55
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (25 bp):
AAAATATAAATACATTTACTATTAA
Found at i:2659408 original size:24 final size:25
Alignment explanation
Indices: 2659355--2659410 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
2659345 AATTTATAAG
*
2659355 TAAAATATATATACATTTACTATTA
1 TAAAATATAAATACATTTACTATTA
* *
2659380 AAAAATATAAATA-ATTTA-TATTTT
1 TAAAATATAAATACATTTACTA-TTA
2659404 TAAAATA
1 TAAAATA
2659411 AAAGAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 2 0.08
24 13 0.50
25 11 0.42
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (25 bp):
TAAAATATAAATACATTTACTATTA
Found at i:2665202 original size:6 final size:6
Alignment explanation
Indices: 2665191--2665224 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
2665181 ATAATCATTA
*
2665191 GTTTGG GTTTGG TTTTGG GTTTGG GTTTGG GTTT
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTT
2665225 TAATCAGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.44, T:0.56
Consensus pattern (6 bp):
GTTTGG
Found at i:2668167 original size:44 final size:43
Alignment explanation
Indices: 2668096--2668182 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 43
2668086 ATTTGGATCT
*
2668096 GATCGTAGCATCATGCGGCATGAATAACATGCTTTTTACCTCA
1 GATCGTAGCATCATCCGGCATGAATAACATGCTTTTTACCTCA
2668139 GATCGTAGCATCAGTCCGGCATGAATAACATGCTTTTTACCTCA
1 GATCGTAGCATCA-TCCGGCATGAATAACATGCTTTTTACCTCA
2668183 TTTCACACTA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
43 13 0.31
44 29 0.69
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (43 bp):
GATCGTAGCATCATCCGGCATGAATAACATGCTTTTTACCTCA
Found at i:2669056 original size:18 final size:18
Alignment explanation
Indices: 2669033--2669085 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
2669023 AACTTTTTTA
2669033 AAAATTTTTATTATATTT
1 AAAATTTTTATTATATTT
*
2669051 AAAA-TTTAATTATA-TT
1 AAAATTTTTATTATATTT
*
2669067 AAAATTTTTTATTACATTT
1 AAAA-TTTTTATTATATTT
2669086 TATTTTATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 6 0.21
17 9 0.31
18 12 0.41
19 2 0.07
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
AAAATTTTTATTATATTT
Found at i:2669068 original size:16 final size:17
Alignment explanation
Indices: 2669042--2669073 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2669032 AAAAATTTTT
2669042 ATTATATTTAAAATTTA
1 ATTATATTTAAAATTTA
2669059 ATTATA-TTAAAATTT
1 ATTATATTTAAAATTT
2669074 TTTATTACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTATATTTAAAATTTA
Found at i:2669694 original size:10 final size:10
Alignment explanation
Indices: 2669679--2669705 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2669669 ATCCACAGGT
2669679 AAAAGAAAGG
1 AAAAGAAAGG
2669689 AAAAGAAAGG
1 AAAAGAAAGG
2669699 AAAAGAA
1 AAAAGAA
2669706 TCGTGTGAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (10 bp):
AAAAGAAAGG
Found at i:2676368 original size:81 final size:82
Alignment explanation
Indices: 2676259--2676420 Score: 245
Period size: 81 Copynumber: 2.0 Consensus size: 82
2676249 CAAAAATAAT
* *
2676259 ATATAGTAATAAATTCATAACAATAAATAATAATCAATAATTCAAAATAT-AAAAAAAATAAAAC
1 ATATAATAATAAATTCATAACAATAAATAACAATCAATAATTCAAAATATAAAAAAAAATAAAAC
* *
2676323 GCATCAAATTTTAATAG
66 ACATCAAAATTTAATAG
* * * *
2676340 ATATAATAATAAATTCATAATAATAAATAACAATTAATAATTTAAGATATAAAAAAAAATAAAAC
1 ATATAATAATAAATTCATAACAATAAATAACAATCAATAATTCAAAATATAAAAAAAAATAAAAC
2676405 ACATCAAAATTTAATA
66 ACATCAAAATTTAATA
2676421 AAAAAATCTT
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
81 44 0.61
82 28 0.39
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.29
Consensus pattern (82 bp):
ATATAATAATAAATTCATAACAATAAATAACAATCAATAATTCAAAATATAAAAAAAAATAAAAC
ACATCAAAATTTAATAG
Found at i:2676574 original size:12 final size:12
Alignment explanation
Indices: 2676524--2676581 Score: 55
Period size: 12 Copynumber: 4.7 Consensus size: 12
2676514 AAAAATAATC
*
2676524 AATAACTAAA-A
1 AATAATTAAATA
2676535 AATAATTAAATA
1 AATAATTAAATA
*
2676547 AATCTCATTAAATA
1 AA--TAATTAAATA
*
2676561 AATAATTCAATA
1 AATAATTAAATA
2676573 AATATATTA
1 AATA-ATTA
2676582 TAAATTTAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
11 9 0.24
12 15 0.39
13 3 0.08
14 11 0.29
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (12 bp):
AATAATTAAATA
Found at i:2677908 original size:27 final size:26
Alignment explanation
Indices: 2677871--2677925 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
2677861 TGCGGTTAGT
* *
2677871 GAAAGCGAGGATGTTG-AGAAGGAGAA
1 GAAAGCGAGGA-ATTGAAGAACGAGAA
2677897 GAAAGGCGAGGAATTGAAGAACGAGAA
1 GAAA-GCGAGGAATTGAAGAACGAGAA
2677924 GA
1 GA
2677926 CGAAGAAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.45, C:0.05, G:0.40, T:0.09
Consensus pattern (26 bp):
GAAAGCGAGGAATTGAAGAACGAGAA
Found at i:2699538 original size:24 final size:24
Alignment explanation
Indices: 2699506--2699554 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2699496 ATTTCTTTCA
*
2699506 TGATACCTGATAACTTTGTTTGTT
1 TGATACCTGATAACTTTATTTGTT
2699530 TGATACCTGATAACTTTATTTGTT
1 TGATACCTGATAACTTTATTTGTT
2699554 T
1 T
2699555 CAGATGAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.12, G:0.14, T:0.51
Consensus pattern (24 bp):
TGATACCTGATAACTTTATTTGTT
Found at i:2713212 original size:32 final size:32
Alignment explanation
Indices: 2713142--2713237 Score: 99
Period size: 31 Copynumber: 3.0 Consensus size: 32
2713132 AAAAATGTTT
* * *
2713142 TTATTT-TAATAAAATAAGGTTCATTTACTTTA
1 TTATTTATAAT-AAATAAAGTTTATTTATTTTA
2713174 TT-TTTATAATAAATAAAGTTTATTTATTTTA
1 TTATTTATAATAAATAAAGTTTATTTATTTTA
* * *
2713205 TTATTTATGATAAGATAAATTTTAATT-TTTTA
1 TTATTTATAATAA-ATAAAGTTTATTTATTTTA
2713237 T
1 T
2713238 ATAAATTATT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
31 23 0.42
32 21 0.38
33 11 0.20
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (32 bp):
TTATTTATAATAAATAAAGTTTATTTATTTTA
Found at i:2715800 original size:33 final size:34
Alignment explanation
Indices: 2715755--2715826 Score: 94
Period size: 33 Copynumber: 2.1 Consensus size: 34
2715745 TTTATATACC
** *
2715755 AAACATGTTTTTTAAATTCA-AAAAATAAAAATTA
1 AAACATGTTTTTTAAA-AAATAAAAATAAAAATGA
2715789 AAACATG-TTTTTAAAAAATAAAAATAAAAATGA
1 AAACATGTTTTTTAAAAAATAAAAATAAAAATGA
2715822 AAACA
1 AAACA
2715827 AAAAATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 1 0.03
33 26 0.76
34 7 0.21
ACGTcount: A:0.61, C:0.06, G:0.04, T:0.29
Consensus pattern (34 bp):
AAACATGTTTTTTAAAAAATAAAAATAAAAATGA
Found at i:2716058 original size:2 final size:2
Alignment explanation
Indices: 2716051--2716080 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2716041 CATACTTTTC
2716051 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2716081 GACAATTAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2717231 original size:20 final size:21
Alignment explanation
Indices: 2717184--2717233 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
2717174 ACAATATTTT
*
2717184 TAATATGATATAATTAAAATTA
1 TAATATTAT-TAATTAAAATTA
* *
2717206 TTATATTATTAATTAAATTTA
1 TAATATTATTAATTAAAATTA
2717227 -AATATTA
1 TAATATTA
2717234 ATTTTAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.25
21 11 0.46
22 7 0.29
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TAATATTATTAATTAAAATTA
Found at i:2717392 original size:20 final size:20
Alignment explanation
Indices: 2717349--2717392 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2717339 CTGATGGAAA
* *
2717349 AAAATGTTATTTGAATTTTG
1 AAAATGTTATTTGAATATTC
2717369 AAAATGTTAATTTG-ATATTC
1 AAAATGTT-ATTTGAATATTC
2717389 AAAA
1 AAAA
2717393 CATTTGGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.43
Consensus pattern (20 bp):
AAAATGTTATTTGAATATTC
Found at i:2718183 original size:3 final size:3
Alignment explanation
Indices: 2718175--2718202 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2718165 AGGGTATCTT
2718175 TAG TAG TAG TAG TAG TAG TAG TAG TAG T
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG T
2718203 CAAGAGCTTT
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:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TAG
Found at i:2722584 original size:156 final size:156
Alignment explanation
Indices: 2722367--2722668 Score: 534
Period size: 156 Copynumber: 1.9 Consensus size: 156
2722357 GATCAAAATG
*
2722367 TTAATTTTGTTTCAATTTCAATTAAACACTGAATTGTTTGAATTCTACACCTCTTTATAAAAATG
1 TTAATTTTGTTTCAATTTCAAATAAACACTGAATTGTTTGAATTCTACACCTCTTTATAAAAATG
*
2722432 CTAAATTTATGCTACCATTATTTTCCTAGGCCATTATGTAAGTCATTGCTTGTGTTGTTGAAAGG
66 CCAAATTTATGCTACCATTATTTTCCTAGGCCATTATGTAAGTCATTGCTTGTGTTGTTGAAAGG
*
2722497 CTTTTAGAATGTTGGACACTGAATTT
131 CTTCTAGAATGTTGGACACTGAATTT
*
2722523 TTAATTTTGTTTCAATTTCAAATAAACACTGAATTGTTTGAATTCTACACCT-TTATGTAAAAAT
1 TTAATTTTGTTTCAATTTCAAATAAACACTGAATTGTTTGAATTCTACACCTCTT-TATAAAAAT
* *
2722587 GCCAAATTTATGCTACCTTTATTTTCCTAGGCCATTATGTAAGTCATTGCTTGTGTTGTTGAAGG
65 GCCAAATTTATGCTACCATTATTTTCCTAGGCCATTATGTAAGTCATTGCTTGTGTTGTTGAAAG
2722652 GCTTCTAGAATGTTGGA
130 GCTTCTAGAATGTTGGA
2722669 TCATTAAATA
Statistics
Matches: 139, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
155 2 0.01
156 137 0.99
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.42
Consensus pattern (156 bp):
TTAATTTTGTTTCAATTTCAAATAAACACTGAATTGTTTGAATTCTACACCTCTTTATAAAAATG
CCAAATTTATGCTACCATTATTTTCCTAGGCCATTATGTAAGTCATTGCTTGTGTTGTTGAAAGG
CTTCTAGAATGTTGGACACTGAATTT
Found at i:2725197 original size:29 final size:29
Alignment explanation
Indices: 2725142--2725198 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
2725132 TAATAAGATG
* *
2725142 AGGTCATGATTCACGAGATTAGGGATTGC
1 AGGTCATGATTCACAAGATTAGAGATTGC
* * *
2725171 AGGTGATGATTCACAATATTTGAGATTG
1 AGGTCATGATTCACAAGATTAGAGATTG
2725199 TAGATGCTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.32
Consensus pattern (29 bp):
AGGTCATGATTCACAAGATTAGAGATTGC
Found at i:2733471 original size:20 final size:20
Alignment explanation
Indices: 2733435--2733473 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2733425 TATTATTTTT
2733435 TAAATATTAAATATTTTAAA
1 TAAATATTAAATATTTTAAA
*
2733455 TAAATTTTACAAT-TTTTAA
1 TAAATATTA-AATATTTTAA
2733474 TACTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAATATTAAATATTTTAAA
Found at i:2751759 original size:22 final size:22
Alignment explanation
Indices: 2751733--2751774 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2751723 TGTATTTATA
*
2751733 TTTGTATCTCTAGAATTAAGTC
1 TTTGTATCCCTAGAATTAAGTC
2751755 TTTGTATCCCTAGAATTAAG
1 TTTGTATCCCTAGAATTAAG
2751775 GACAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (22 bp):
TTTGTATCCCTAGAATTAAGTC
Found at i:2752030 original size:26 final size:25
Alignment explanation
Indices: 2751985--2752043 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
2751975 AAAACTTTCA
*
2751985 GCCTTCATTGCTGACTTCTATTTTAG
1 GCCTTCATTGCTGACTTCTA-TTAAG
2752011 GCCTTCATTG-TCGAAC-TCTATTAAG
1 GCCTTCATTGCT-G-ACTTCTATTAAG
2752036 GCCTTCAT
1 GCCTTCAT
2752044 AGCCATTCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 13 0.43
26 15 0.50
27 2 0.07
ACGTcount: A:0.19, C:0.25, G:0.15, T:0.41
Consensus pattern (25 bp):
GCCTTCATTGCTGACTTCTATTAAG
Found at i:2755772 original size:22 final size:22
Alignment explanation
Indices: 2755747--2755789 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2755737 TATGTATTTA
*
2755747 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
*
2755769 TATTTGTTTCCCTAGAATTAA
1 TATTTGTATCCCTAGAATTAA
2755790 TGACAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.47
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:2758143 original size:10 final size:11
Alignment explanation
Indices: 2758115--2758143 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
2758105 AACAAATATC
2758115 TTATTTTTTAA
1 TTATTTTTTAA
2758126 TTATTTTTTAA
1 TTATTTTTTAA
2758137 TTATTTT
1 TTATTTT
2758144 AATATATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTATTTTTTAA
Found at i:2768424 original size:2 final size:2
Alignment explanation
Indices: 2768417--2768443 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2768407 TGAGTAATCG
2768417 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
2768444 TATGAGAGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2773216 original size:26 final size:26
Alignment explanation
Indices: 2773173--2773229 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
2773163 ATTTTTTGAA
* * *
2773173 TAAAAAAATATATAAAAAATTTATA-T
1 TAAATAAATAAAT-AAAAATTAATATT
*
2773199 TAAATAAATAAATTAAAATTAATATT
1 TAAATAAATAAATAAAAATTAATATT
2773225 TAAAT
1 TAAAT
2773230 TTAATTAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
TAAATAAATAAATAAAAATTAATATT
Found at i:2774839 original size:7 final size:7
Alignment explanation
Indices: 2774827--2774860 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
2774817 CTCTAAATTT
2774827 TAATAAA
1 TAATAAA
2774834 TAATAAA
1 TAATAAA
2774841 TAATAAAA
1 TAAT-AAA
2774849 TAATAAA
1 TAATAAA
2774856 -AATAA
1 TAATAA
2774861 CATATTAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 5 0.19
7 14 0.54
8 7 0.27
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
TAATAAA
Found at i:2774844 original size:14 final size:14
Alignment explanation
Indices: 2774827--2774860 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
2774817 CTCTAAATTT
2774827 TAATAAATAATAAA
1 TAATAAATAATAAA
2774841 TAATAAAATAATAAA
1 TAAT-AAATAATAAA
2774856 -AATAA
1 TAATAA
2774861 CATATTAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 7 0.37
15 10 0.53
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
TAATAAATAATAAA
Found at i:2778098 original size:14 final size:13
Alignment explanation
Indices: 2778042--2778100 Score: 59
Period size: 14 Copynumber: 4.5 Consensus size: 13
2778032 TTAAATAATC
*
2778042 TTAATAAATGATTA
1 TTAATAAAT-TTTA
2778056 TTAATAAATTTTA
1 TTAATAAATTTTA
*
2778069 --AATTAAATTTTT
1 TTAA-TAAATTTTA
2778081 TTAATAAATTTTAA
1 TTAATAAATTTT-A
2778095 TTAATA
1 TTAATA
2778101 GAGTCAATCA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 2 0.05
12 8 0.21
13 11 0.29
14 17 0.45
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (13 bp):
TTAATAAATTTTA
Found at i:2780282 original size:21 final size:21
Alignment explanation
Indices: 2780258--2780309 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
2780248 CCCGAAATTA
2780258 ATAAAATATTTTTTTTTAAAT
1 ATAAAATATTTTTTTTTAAAT
*
2780279 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTTTTTTTTAAAT
2780300 AT-AAATATTT
1 ATAAAATATTT
2780310 AAAAATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 7 0.24
21 22 0.76
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATAAAATATTTTTTTTTAAAT
Found at i:2780317 original size:30 final size:30
Alignment explanation
Indices: 2780281--2780337 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
2780271 TTTTAAATAT
* * *
2780281 AAAATATTATTTTTTAAATATAAATATTTA
1 AAAATATAATTATATAAATATAAATATTTA
*
2780311 AAAATATAATTATATAAATATATATAT
1 AAAATATAATTATATAAATATAAATAT
2780338 AAATAAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
AAAATATAATTATATAAATATAAATATTTA
Found at i:2780325 original size:8 final size:8
Alignment explanation
Indices: 2780298--2780346 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
2780288 TATTTTTTAA
2780298 ATATAAAT
1 ATATAAAT
* *
2780306 ATTTAAAA
1 ATATAAAT
*
2780314 ATATAATT
1 ATATAAAT
2780322 ATATAAAT
1 ATATAAAT
*
2780330 ATATATAT
1 ATATAAAT
*
2780338 AAATAAAT
1 ATATAAAT
2780346 A
1 A
2780347 ATTAATTAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAAAT
Found at i:2781551 original size:21 final size:21
Alignment explanation
Indices: 2781519--2781558 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2781509 TTCATCAATA
*
2781519 TTTTTTTTATT-ATTTTATTG
1 TTTTTTTCATTAATTTTATTG
2781539 TTTTTTTACATTAATTTTAT
1 TTTTTTT-CATTAATTTTAT
2781559 AAACTTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 3 0.18
22 7 0.41
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.75
Consensus pattern (21 bp):
TTTTTTTCATTAATTTTATTG
Found at i:2782158 original size:30 final size:29
Alignment explanation
Indices: 2782122--2782179 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 29
2782112 TTGTTTCATT
*
2782122 AATAAAT-TTATTTTTTATATTAAAAATAAA
1 AATAAATATT-TTTTTT-TAATAAAAATAAA
2782152 AATAAATAATTTTTTTTTAATAAAAATA
1 AATAAAT-ATTTTTTTTTAATAAAAATA
2782180 CTTGAGCGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 17 0.68
31 6 0.24
32 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
AATAAATATTTTTTTTTAATAAAAATAAA
Found at i:2784514 original size:26 final size:26
Alignment explanation
Indices: 2784485--2784537 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
2784475 TTAGATGTAA
*
2784485 TCTGTGTCATAAACATGCTGCATTGC
1 TCTGTGTCATAAACATGCTGCACTGC
* *
2784511 TCTGTGTCGTAAACGTGCTGCACTGC
1 TCTGTGTCATAAACATGCTGCACTGC
2784537 T
1 T
2784538 GTGTCGTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.34
Consensus pattern (26 bp):
TCTGTGTCATAAACATGCTGCACTGC
Found at i:2784544 original size:24 final size:25
Alignment explanation
Indices: 2784486--2784544 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 25
2784476 TAGATGTAAT
* *
2784486 CTGTGTCATAAACATGCTGCATTGC
1 CTGTGTCGTAAACATGCTGCACTGC
*
2784511 TCTGTGTCGTAAACGTGCTGCACTG-
1 -CTGTGTCGTAAACATGCTGCACTGC
2784536 CTGTGTCGT
1 CTGTGTCGT
2784545 CTTTAGTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 9 0.30
26 21 0.70
ACGTcount: A:0.17, C:0.24, G:0.25, T:0.34
Consensus pattern (25 bp):
CTGTGTCGTAAACATGCTGCACTGC
Found at i:2789839 original size:2 final size:2
Alignment explanation
Indices: 2789834--2789877 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
2789824 AAGTATATAC
* *
2789834 GA GA GA GA GA GA GA GA GA GG GA GA GA GA GG GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2789876 GA
1 GA
2789878 AAAGAGCATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2806394 original size:29 final size:31
Alignment explanation
Indices: 2806362--2806429 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
2806352 CATAATTCAA
2806362 ATATCATATTAAAA-ATTT-TTAAAATTTAT
1 ATATCATATTAAAATATTTATTAAAATTTAT
* *
2806391 ATATCAAATTAAAATATTTCATTATAATTTAT
1 ATATCATATTAAAATATTT-ATTAAAATTTAT
*
2806423 AAATCAT
1 ATATCAT
2806430 TCATATTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 13 0.41
30 4 0.12
32 15 0.47
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (31 bp):
ATATCATATTAAAATATTTATTAAAATTTAT
Found at i:2808249 original size:8 final size:8
Alignment explanation
Indices: 2808231--2808264 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
2808221 AAATATAAAA
*
2808231 AATAAAAT
1 AATAAATT
*
2808239 AATTAATT
1 AATAAATT
2808247 AATAAATT
1 AATAAATT
2808255 AATAAATT
1 AATAAATT
2808263 AA
1 AA
2808265 ATTGAACTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AATAAATT
Found at i:2813429 original size:23 final size:24
Alignment explanation
Indices: 2813391--2813439 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
2813381 GATTTTTTTA
2813391 TTAAATAATATAAATT-AT-TATT
1 TTAAATAATATAAATTAATATATT
2813413 TTAAATTAAT-TATAATTAATATATT
1 TTAAA-TAATATA-AATTAATATATT
2813438 TT
1 TT
2813440 TATCGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
22 7 0.30
23 8 0.35
24 2 0.09
25 6 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TTAAATAATATAAATTAATATATT
Found at i:2821652 original size:3 final size:3
Alignment explanation
Indices: 2821646--2821684 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2821636 AATATCATTG
2821646 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2821685 CTAACACCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2821902 original size:21 final size:22
Alignment explanation
Indices: 2821864--2821915 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 22
2821854 TCCGAAATTA
2821864 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
2821886 ATAAAATATTA-TTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
2821907 AT-AAATATT
1 ATAAAATATT
2821916 TAAAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 12 0.40
22 11 0.37
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:2822756 original size:20 final size:21
Alignment explanation
Indices: 2822731--2822769 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2822721 TTCTTCAGTA
2822731 ATTATTATAAA-ATTAATAGC
1 ATTATTATAAAGATTAATAGC
*
2822751 ATTATTCTAAAGATTAATA
1 ATTATTATAAAGATTAATA
2822770 TTTTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (21 bp):
ATTATTATAAAGATTAATAGC
Found at i:2824707 original size:23 final size:24
Alignment explanation
Indices: 2824680--2824730 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
2824670 AATAATAATT
*
2824680 ATTATT-TAA-ATTTTGATTAAAAA
1 ATTATTGTAATATATTGA-TAAAAA
2824703 ATTATTGTAATTATATTGATAAAAA
1 ATTATTGTAA-TATATTGATAAAAA
2824728 ATT
1 ATT
2824731 TAATAACAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 6 0.25
24 3 0.12
25 9 0.38
26 6 0.25
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (24 bp):
ATTATTGTAATATATTGATAAAAA
Found at i:2825849 original size:20 final size:20
Alignment explanation
Indices: 2825812--2825850 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2825802 TATAATTCAC
*
2825812 AAATATATATATAAATAAAA
1 AAATATATATACAAATAAAA
*
2825832 AAATATATATACATATAAA
1 AAATATATATACAAATAAA
2825851 TTTGGGTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATATATATACAAATAAAA
Found at i:2828962 original size:23 final size:23
Alignment explanation
Indices: 2828925--2828977 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
2828915 AAAGATTTAT
* *
2828925 AATAAAAATTTATTTAAATACAA
1 AATAAAAACTCATTTAAATACAA
* * *
2828948 ATTAAAAACTCATTTGAATGCAA
1 AATAAAAACTCATTTAAATACAA
2828971 AATAAAA
1 AATAAAA
2828978 TATAAAATTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.58, C:0.08, G:0.04, T:0.30
Consensus pattern (23 bp):
AATAAAAACTCATTTAAATACAA
Found at i:2834495 original size:25 final size:24
Alignment explanation
Indices: 2834444--2834496 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
2834434 AAATAGTAAT
2834444 AAAAATTACTATAATTATGATTGA
1 AAAAATTACTATAATTATGATTGA
* * *
2834468 AAAAATTATTATTATTGTGATTGA
1 AAAAATTACTATAATTATGATTGA
2834492 AAAAA
1 AAAAA
2834497 ATTAATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (24 bp):
AAAAATTACTATAATTATGATTGA
Found at i:2836833 original size:4 final size:4
Alignment explanation
Indices: 2836824--2836856 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
2836814 CCATAGGCTA
*
2836824 AAAC AAAC AAAC AAAC AAAC AAA- ACAC AAAC AA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AA
2836857 CAATCGAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
3 2 0.08
4 24 0.92
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:2864125 original size:15 final size:16
Alignment explanation
Indices: 2864093--2864341 Score: 98
Period size: 19 Copynumber: 14.4 Consensus size: 16
2864083 TATTTATTAC
*
2864093 TAATAATATAATAATATT
1 TAATAATAT-ATTATA-T
2864111 TAATAATATATTATTTAT
1 TAATAATATATTA--TAT
*
2864129 TAATTAAAATATTAT-T
1 TAA-TAATATATTATAT
2864145 T-ATAA-ATATTATAT
1 TAATAATATATTATAT
*
2864159 TAATAA-ATAATATAT
1 TAATAATATATTATAT
*
2864174 TATATTATATATATTTTAT
1 TA-A-TA-ATATATTATAT
2864193 TAATAATATAATATATATTAT
1 TAAT-A-AT-ATAT-TA-TAT
*
2864214 TAAGTTAATATATTCATAAA
1 TAA--TAATATATT-AT-AT
2864234 TAAT-ATATATTAATAT
1 TAATAATATATT-ATAT
* *
2864250 GATATAA-ATAATATAT
1 TA-ATAATATATTATAT
*
2864266 TAATAGTATTATT-TAT
1 TAATAATA-TATTATAT
* *
2864282 TATTAATATATTATTAA
1 TAATAATATATTA-TAT
* *
2864299 AATATAATATCTTTATAT
1 TA-ATAATAT-ATTATAT
*
2864317 TAACAAAATAATATTATAT
1 T-A-ATAAT-ATATTATAT
2864336 TAATAA
1 TAATAA
2864342 ATAAATAATA
Statistics
Matches: 178, Mismatches: 26, Indels: 55
0.69 0.10 0.21
Matches are distributed among these distances:
13 7 0.04
14 5 0.03
15 22 0.12
16 20 0.11
17 31 0.17
18 30 0.17
19 41 0.23
20 12 0.07
21 8 0.04
22 1 0.01
23 1 0.01
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (16 bp):
TAATAATATATTATAT
Found at i:2864146 original size:34 final size:33
Alignment explanation
Indices: 2864102--2864196 Score: 99
Period size: 33 Copynumber: 2.9 Consensus size: 33
2864092 CTAATAATAT
*
2864102 AATAATATTTAATAATATATTATTTATTAATTAA
1 AATATTATTT-ATAATATATTATTTATTAATTAA
* *
2864136 AATATTATTTATAA-ATATTATATTAATAAATAA
1 AATATTATTTATAATATATTAT-TTATTAATTAA
*
2864169 TATATTATATTAT-ATATA-T-TTTATTAAT
1 AATATTAT-TTATAATATATTATTTATTAAT
2864197 AATATAATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
31 6 0.12
32 8 0.15
33 22 0.42
34 16 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (33 bp):
AATATTATTTATAATATATTATTTATTAATTAA
Found at i:2864196 original size:82 final size:85
Alignment explanation
Indices: 2864110--2864296 Score: 210
Period size: 85 Copynumber: 2.2 Consensus size: 85
2864100 ATAATAATAT
*
2864110 TTAATAATATATTATTTATTAA-TTAAAATATTATTTATAAAT-AT-TATATTAATA-A-ATAAT
1 TTAATAATATATTATTTATTAAGTT--AATA-TATTCATAAATAATATATATTAATAGATATAA-
*
2864170 ATATTATATT-ATA-TA-TATTTTA
62 ATAATATATTAATAGTATTA-TTTA
2864192 TTAATAATATAATATATATTATTAAGTTAATATATTCATAAATAATATATATTAATATGATATAA
1 TTAATAATAT-AT-TAT-TTATTAAGTTAATATATTCATAAATAATATATATTAATA-GATATAA
2864257 ATAATATATTAATAGTATTATTTA
62 ATAATATATTAATAGTATTATTTA
*
2864281 TTATTAATATATTATT
1 TTAATAATATATTATT
2864297 AAAATATAAT
Statistics
Matches: 90, Mismatches: 3, Indels: 20
0.80 0.03 0.18
Matches are distributed among these distances:
82 10 0.11
83 12 0.13
84 9 0.10
85 17 0.19
86 3 0.03
87 13 0.14
88 9 0.10
89 15 0.17
90 2 0.02
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.50
Consensus pattern (85 bp):
TTAATAATATATTATTTATTAAGTTAATATATTCATAAATAATATATATTAATAGATATAAATAA
TATATTAATAGTATTATTTA
Found at i:2864222 original size:23 final size:21
Alignment explanation
Indices: 2864087--2864373 Score: 114
Period size: 21 Copynumber: 14.0 Consensus size: 21
2864077 AGAATCTATT
*
2864087 TATTACTAATAATATAATA-A
1 TATTATTAATAATATAATATA
* *
2864107 TA-T-TTAATAATATATTATT
1 TATTATTAATAATATAATATA
* *
2864126 TATTAATTAA-AATATTATTTA
1 TATT-ATTAATAATATAATATA
*
2864147 TAAATATTATATTAATA-AATA-A
1 T-ATTATTA-A-TAATATAATATA
*
2864169 TA-TATT-ATATTAT-ATATA
1 TATTATTAATAATATAATATA
*
2864187 TTTTATTAATAATATAATATA
1 TATTATTAATAATATAATATA
*
2864208 TATTATT-A-AGT-TAATATA
1 TATTATTAATAATATAATATA
* *
2864226 T-TCATAAATAATAT-ATATTAA
1 TATTATTAATAATATAATA-T-A
* *
2864247 TATGATATAAATAATATATTAATA
1 TAT--TATTAATAATATAAT-ATA
* *
2864271 GTATTATT--TATTATTA-ATA
1 -TATTATTAATAATATAATATA
*
2864290 TATTATTAA-AATATAATATC
1 TATTATTAATAATATAATATA
* * *
2864310 TTTATATTAACAAAATAATAT-
1 TAT-TATTAATAATATAATATA
2864331 TA-TATTAATAA-ATAA-ATAA
1 TATTATTAATAATATAATAT-A
*
2864350 TATTGTATTATTAATATAATATA
1 TA-T-TATTAATAATATAATATA
2864373 T
1 T
2864374 TAGATTACTA
Statistics
Matches: 199, Mismatches: 32, Indels: 69
0.66 0.11 0.23
Matches are distributed among these distances:
17 12 0.06
18 35 0.18
19 32 0.16
20 20 0.10
21 38 0.19
22 27 0.14
23 11 0.06
24 18 0.09
25 5 0.03
26 1 0.01
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (21 bp):
TATTATTAATAATATAATATA
Found at i:2864255 original size:30 final size:29
Alignment explanation
Indices: 2864096--2864255 Score: 88
Period size: 34 Copynumber: 5.0 Consensus size: 29
2864086 TTATTACTAA
* *
2864096 TAATATAATAATATTTAATAATATATTATTTAT
1 TAATA-AATAATATATATTAATATA-TA--TAT
* * *
2864129 TAATTAAAATATTATTTATAAATAT-TATAT
1 TAA-T-AAATAATATATATTAATATATATAT
*
2864159 TAATAAATAATATATTATATTATATATATTTTAT
1 TAATAAAT-A-ATA-TATATTA-ATATA-TATAT
*
2864193 TAATAATATAATATATATTATTAAGTTAATATAT
1 TAATAA-ATAATATATATTAAT-A--T-ATATAT
*
2864227 TCATAAATAATATATATTAATATGATATA
1 TAATAAATAATATATATTAATAT-ATATA
2864256 AATAATATAT
Statistics
Matches: 102, Mismatches: 12, Indels: 29
0.71 0.08 0.20
Matches are distributed among these distances:
28 4 0.04
29 2 0.02
30 14 0.14
31 6 0.06
32 15 0.15
33 20 0.20
34 37 0.36
35 4 0.04
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (29 bp):
TAATAAATAATATATATTAATATATATAT
Found at i:2864347 original size:22 final size:22
Alignment explanation
Indices: 2864322--2864380 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
2864312 TATATTAACA
2864322 AAATAATATTATATTAATAAAT
1 AAATAATATTATATTAATAAAT
* *
2864344 AAATAATATTGTATT-ATTAAT
1 AAATAATATTATATTAATAAAT
*
2864365 ATAAT-ATATTAGATTA
1 A-AATAATATTATATTA
2864381 CTAGTACAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 14 0.45
22 17 0.55
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (22 bp):
AAATAATATTATATTAATAAAT
Found at i:2864430 original size:25 final size:24
Alignment explanation
Indices: 2864401--2864467 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 24
2864391 ATTACTTAGT
2864401 TATATAATGTTATTTATATAATAAA
1 TATATAAT-TTATTTATATAATAAA
2864426 TATATAA--TATTTATATAATAAA
1 TATATAATTTATTTATATAATAAA
* * *
2864448 AATATTATTTTATTAATATA
1 TATA-TAATTTATTTATATA
2864468 TTATTTAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
22 18 0.50
23 2 0.06
25 16 0.44
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (24 bp):
TATATAATTTATTTATATAATAAA
Found at i:2864464 original size:20 final size:22
Alignment explanation
Indices: 2864411--2864465 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
2864401 TATATAATGT
*
2864411 TATTTATATAATAAATATATAA
1 TATTTATATAATAAAAATATAA
*
2864433 TATTTATATAATAAAAATATTA
1 TATTTATATAATAAAAATATAA
2864455 T-TTTAT-TAATA
1 TATTTATATAATA
2864466 TATTATTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 5 0.16
21 5 0.16
22 21 0.68
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TATTTATATAATAAAAATATAA
Found at i:2864699 original size:8 final size:7
Alignment explanation
Indices: 2864688--2864719 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
2864678 AACTGAAAAT
2864688 AAAAAGA
1 AAAAAGA
2864695 AAAAAGA
1 AAAAAGA
2864702 AAAAAGA
1 AAAAAGA
2864709 AAAAACGA
1 AAAAA-GA
2864717 AAA
1 AAA
2864720 CAAAAACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.79
8 5 0.21
ACGTcount: A:0.84, C:0.03, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:2864705 original size:14 final size:15
Alignment explanation
Indices: 2864688--2864733 Score: 60
Period size: 14 Copynumber: 3.1 Consensus size: 15
2864678 AACTGAAAAT
2864688 AAAAAGAAAAAA-GA
1 AAAAAGAAAAAACGA
2864702 AAAAAGAAAAAACGA
1 AAAAAGAAAAAACGA
2864717 AAACAA-AAACAAACGA
1 AAA-AAGAAA-AAACGA
2864733 A
1 A
2864734 CCGCCAAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 12 0.41
15 8 0.28
16 9 0.31
ACGTcount: A:0.80, C:0.09, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAACGA
Found at i:2865367 original size:40 final size:42
Alignment explanation
Indices: 2865314--2865392 Score: 126
Period size: 40 Copynumber: 1.9 Consensus size: 42
2865304 AATAGATAAT
*
2865314 ATTGGTTTAAATTTAATTTAAAA-T-AAAAAAGAAAATTATA
1 ATTGGTGTAAATTTAATTTAAAATTAAAAAAAGAAAATTATA
*
2865354 ATTGGTGTGAATTTAATTTAAAATTAAAAAAAGAAAATT
1 ATTGGTGTAAATTTAATTTAAAATTAAAAAAAGAAAATT
2865393 TTAAATGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 21 0.60
41 1 0.03
42 13 0.37
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (42 bp):
ATTGGTGTAAATTTAATTTAAAATTAAAAAAAGAAAATTATA
Found at i:2874223 original size:2 final size:2
Alignment explanation
Indices: 2874218--2874264 Score: 51
Period size: 2 Copynumber: 23.5 Consensus size: 2
2874208 TGTGTGTGTG
* * *
2874218 TA TA TA TA TA TA TA TA TA TA TA TT TG TA TA TCA TA -A TA GA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
2874260 TA TA T
1 TA TA T
2874265 TATTTTTCTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2878865 original size:28 final size:28
Alignment explanation
Indices: 2878825--2878884 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
2878815 CCTTTACATT
*
2878825 ACATTAACACATTATTATTAATACGCTA
1 ACATTAACACATTATTACTAATACGCTA
* *
2878853 ACATTACCACATTATTACTAATACGCTG
1 ACATTAACACATTATTACTAATACGCTA
2878881 ACAT
1 ACAT
2878885 GGAATTCATC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.22, G:0.05, T:0.33
Consensus pattern (28 bp):
ACATTAACACATTATTACTAATACGCTA
Found at i:2879546 original size:30 final size:31
Alignment explanation
Indices: 2879507--2879581 Score: 73
Period size: 33 Copynumber: 2.4 Consensus size: 31
2879497 ATTATCTTTG
* *
2879507 TATTTTTATTTTAC-TACTAT-TTTATTATTT
1 TATTATTATTTT-CTTACTATATTTATTATCT
* *
2879537 TATTATTATTATCTTACTATGCATTTGTTATCT
1 TATTATTATTTTCTTACTAT--ATTTATTATCT
2879570 TATTATTATTTT
1 TATTATTATTTT
2879582 TTTATTATCT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
29 1 0.03
30 16 0.44
33 19 0.53
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.65
Consensus pattern (31 bp):
TATTATTATTTTCTTACTATATTTATTATCT
Found at i:2880543 original size:11 final size:12
Alignment explanation
Indices: 2880519--2880544 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2880509 TAATTTGGTA
2880519 TTTTGTTTATTT
1 TTTTGTTTATTT
2880531 TTTTGTTTATTT
1 TTTTGTTTATTT
2880543 TT
1 TT
2880545 GTGGTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.85
Consensus pattern (12 bp):
TTTTGTTTATTT
Found at i:2881840 original size:15 final size:15
Alignment explanation
Indices: 2881793--2881843 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
2881783 TATTTTGGTA
*
2881793 TTTTATTTATTTTATT
1 TTTTATTTATTTT-TG
* *
2881809 TTTTATTT-TTATGG
1 TTTTATTTATTTTTG
2881823 TTTTATTTATTTTTG
1 TTTTATTTATTTTTG
2881838 TTTTAT
1 TTTTAT
2881844 GCTATTATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 8 0.28
15 13 0.45
16 8 0.28
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (15 bp):
TTTTATTTATTTTTG
Found at i:2881859 original size:25 final size:26
Alignment explanation
Indices: 2881799--2881862 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 26
2881789 GGTATTTTAT
* * * *
2881799 TTATTTTATTTTTTATTTTTATGGTT
1 TTATTTTAATTTTTAGTTTTATGCTA
2881825 TTA-TTT-ATTTTT-GTTTTATGCTA
1 TTATTTTAATTTTTAGTTTTATGCTA
2881848 TTATTTTAATTTTTA
1 TTATTTTAATTTTTA
2881863 AAAATATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
23 11 0.35
24 8 0.26
25 9 0.29
26 3 0.10
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.73
Consensus pattern (26 bp):
TTATTTTAATTTTTAGTTTTATGCTA
Found at i:2889408 original size:12 final size:12
Alignment explanation
Indices: 2889388--2889418 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2889378 ATCCTGTAGA
*
2889388 ATATGGTAACAG
1 ATATTGTAACAG
2889400 ATATTGTAACAG
1 ATATTGTAACAG
2889412 ATATTGT
1 ATATTGT
2889419 TAGATAATTC
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:0.39, C:0.06, G:0.19, T:0.35
Consensus pattern (12 bp):
ATATTGTAACAG
Found at i:2891062 original size:52 final size:52
Alignment explanation
Indices: 2890980--2891083 Score: 149
Period size: 52 Copynumber: 2.0 Consensus size: 52
2890970 ATAACTATAT
*
2890980 AAACTTGCTTATTAAGAATATATTTCCTCTTAGAATTCTTCTTCTGCAAGTC
1 AAACTTGCCTATTAAGAATATATTTCCTCTTAGAATTCTTCTTCTGCAAGTC
* *
2891032 AAACTTGCCTATTAA-AGATAT-TTTGTCTCTTAGAATTCTTCTTTTGCAAGTC
1 AAACTTGCCTATTAAGA-ATATATTT-CCTCTTAGAATTCTTCTTCTGCAAGTC
2891084 TTTTTATCCA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
51 4 0.09
52 43 0.91
ACGTcount: A:0.28, C:0.18, G:0.11, T:0.43
Consensus pattern (52 bp):
AAACTTGCCTATTAAGAATATATTTCCTCTTAGAATTCTTCTTCTGCAAGTC
Found at i:2891875 original size:92 final size:92
Alignment explanation
Indices: 2891759--2891943 Score: 343
Period size: 92 Copynumber: 2.0 Consensus size: 92
2891749 AACACAACCA
* * *
2891759 AATACATATCCATATACACCCATACATCATACCTATGTGGACCTTCTTAGTCTCCTATAGTCCAC
1 AATACATACCCATATACACCCATACATCATACCTATATGGACCATCTTAGTCTCCTATAGTCCAC
2891824 TCACAAACAAACATACACACCCATAAG
66 TCACAAACAAACATACACACCCATAAG
2891851 AATACATACCCATATACACCCATACATCATACCTATATGGACCATCTTAGTCTCCTATAGTCCAC
1 AATACATACCCATATACACCCATACATCATACCTATATGGACCATCTTAGTCTCCTATAGTCCAC
2891916 TCACAAACAAACATACACACCCATAAG
66 TCACAAACAAACATACACACCCATAAG
2891943 A
1 A
2891944 TGTAAATCTC
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 90 1.00
ACGTcount: A:0.38, C:0.32, G:0.06, T:0.24
Consensus pattern (92 bp):
AATACATACCCATATACACCCATACATCATACCTATATGGACCATCTTAGTCTCCTATAGTCCAC
TCACAAACAAACATACACACCCATAAG
Found at i:2892090 original size:17 final size:17
Alignment explanation
Indices: 2892068--2892107 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
2892058 TTGCCTATTA
*
2892068 AGAATTTCTTTTCTCTT
1 AGAATTTCTTTCCTCTT
2892085 AGAATTTCTTTCCTCTT
1 AGAATTTCTTTCCTCTT
*
2892102 AAAATT
1 AGAATT
2892108 CTTCTTCTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.25, C:0.17, G:0.05, T:0.53
Consensus pattern (17 bp):
AGAATTTCTTTCCTCTT
Found at i:2892215 original size:11 final size:11
Alignment explanation
Indices: 2892199--2892229 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2892189 AACAATATTT
*
2892199 AACAAATCTTA
1 AACAAATCTCA
2892210 AACAAATCTCA
1 AACAAATCTCA
2892221 AACAAATCT
1 AACAAATCT
2892230 GTTATGAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.23
Consensus pattern (11 bp):
AACAAATCTCA
Found at i:2896992 original size:17 final size:18
Alignment explanation
Indices: 2896958--2896995 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
2896948 GTCAAACTTA
2896958 TCTTTTAAGAATTATTTT
1 TCTTTTAAGAATTATTTT
*
2896976 TCTTTTAA-AATTCTTTT
1 TCTTTTAAGAATTATTTT
2896993 TCT
1 TCT
2896996 GTAAGTCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.24, C:0.11, G:0.03, T:0.63
Consensus pattern (18 bp):
TCTTTTAAGAATTATTTT
Found at i:2897797 original size:14 final size:14
Alignment explanation
Indices: 2897778--2897816 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
2897768 AGAATCTCTT
*
2897778 TTCTTTTATAATTC
1 TTCTTTTAGAATTC
2897792 TTCTTTTAGAATTC
1 TTCTTTTAGAATTC
2897806 TTCTTTTAGAA
1 TTCTTTTAGAA
2897817 GTCAAACTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.23, C:0.13, G:0.05, T:0.59
Consensus pattern (14 bp):
TTCTTTTAGAATTC
Found at i:2902060 original size:31 final size:32
Alignment explanation
Indices: 2901987--2902062 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
2901977 TATTAAATAT
* * *
2901987 GATTTCATTTAGTAAAATATTAATGCACGTTT
1 GATTTAATTTAATAAAATATTAATGCACGTTG
*
2902019 GATTTTATTTAATAAAATATTAATGCAC-TTG
1 GATTTAATTTAATAAAATATTAATGCACGTTG
2902050 GATTTAATTTAAT
1 GATTTAATTTAAT
2902063 TTAATTTGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
31 14 0.35
32 26 0.65
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.46
Consensus pattern (32 bp):
GATTTAATTTAATAAAATATTAATGCACGTTG
Found at i:2903618 original size:17 final size:16
Alignment explanation
Indices: 2903596--2903627 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2903586 TGATGATAAT
2903596 TATATAATTAAATTTAA
1 TATATAATT-AATTTAA
2903613 TATATAATTAATTTA
1 TATATAATTAATTTA
2903628 TTTTATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATATAATTAATTTAA
Found at i:2903625 original size:21 final size:21
Alignment explanation
Indices: 2903599--2903668 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
2903589 TGATAATTAT
2903599 ATAATTAAATTTAATATATAA
1 ATAATTAAATTTAATATATAA
* * * *
2903620 TTAATTTATTTTATTATATTAA
1 ATAATTAAATTTAATATA-TAA
*
2903642 AT-ATATAAATTTAA-ATAAAA
1 ATAAT-TAAATTTAATATATAA
2903662 ATAATTA
1 ATAATTA
2903669 TACAAATTAT
Statistics
Matches: 37, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
20 6 0.16
21 21 0.57
22 10 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATAATTAAATTTAATATATAA
Found at i:2905665 original size:21 final size:21
Alignment explanation
Indices: 2905640--2905680 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2905630 GTCCAAGTTT
*
2905640 AATTTTATATGAATTTTATTA
1 AATTTTATATGAAATTTATTA
*
2905661 AATTTTATATTAAATTTATT
1 AATTTTATATGAAATTTATT
2905681 TAGTTATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
AATTTTATATGAAATTTATTA
Found at i:2905666 original size:10 final size:11
Alignment explanation
Indices: 2905640--2905677 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
2905630 GTCCAAGTTT
*
2905640 AATTTTATATG
1 AATTTTATATA
2905651 AATTTTAT-TA
1 AATTTTATATA
2905661 AATTTTATATTA
1 AATTTTATA-TA
2905673 AATTT
1 AATTT
2905678 ATTTAGTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 9 0.38
11 8 0.33
12 7 0.29
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTTATATA
Found at i:2905711 original size:21 final size:20
Alignment explanation
Indices: 2905687--2905728 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
2905677 TATTTAGTTA
2905687 TATTT-TAATTTGTTAATTAAT
1 TATTTATAATTT-TT-ATTAAT
2905708 TATTTAATAATTTTTATTAAT
1 TATTT-ATAATTTTTATTAAT
2905729 ATAATACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 11 0.58
22 2 0.11
23 6 0.32
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TATTTATAATTTTTATTAAT
Done.