Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 71 of 202
Found at i:20987495 original size:12 final size:11
Alignment explanation
Indices: 20987478--20987507 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
20987468 TAAAAAAAAA
20987478 TAAAAAGTATTT
1 TAAAAA-TATTT
20987490 TAAAAATATTT
1 TAAAAATATTT
20987501 TAAAAAT
1 TAAAAAT
20987508 TAAAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (11 bp):
TAAAAATATTT
Found at i:20987523 original size:40 final size:39
Alignment explanation
Indices: 20987431--20987523 Score: 134
Period size: 39 Copynumber: 2.4 Consensus size: 39
20987421 AATTTATTTT
*
20987431 AAAAATTAAAAAAAGTATTTTTAAAATATTTTAAAATTA
1 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTA
*
20987470 AAAAA-AAATAAAAAGTATTTTAAAAATATTTTAAAAATTA
1 AAAAATTAA-AAAAAGTATTTTAAAAATATTTT-AAAATTA
*
20987510 AAAAATTTAAAAAA
1 AAAAATTAAAAAAA
20987524 TAAATATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
38 2 0.04
39 27 0.57
40 17 0.36
41 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (39 bp):
AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTA
Found at i:20987535 original size:17 final size:17
Alignment explanation
Indices: 20987493--20987535 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
20987483 AGTATTTTAA
*
20987493 AAATAT-TTTAAAAATT
1 AAATATATTTAAAAAAT
*
20987509 AAA-AAATTTAAAAAAT
1 AAATATATTTAAAAAAT
20987525 AAATATATTTA
1 AAATATATTTA
20987536 TTATATCGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 1 0.05
16 15 0.68
17 6 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATATATTTAAAAAAT
Found at i:20988937 original size:77 final size:77
Alignment explanation
Indices: 20988810--20988971 Score: 315
Period size: 77 Copynumber: 2.1 Consensus size: 77
20988800 TGAGACAATC
20988810 TTAAAGTGTTATGTCAATAAAATTTTATATATTTCAAGTTCAAAGATTAAAATATATCTAATTGT
1 TTAAAGTGTTATGTCAATAAAATTTTATATATTTCAAGTTCAAAGATTAAAATATATCTAATTGT
*
20988875 CAAGTTCAGTTA
66 CAAGTTCAATTA
20988887 TTAAAGTGTTATGTCAATAAAATTTTATATATTTCAAGTTCAAAGATTAAAATATATCTAATTGT
1 TTAAAGTGTTATGTCAATAAAATTTTATATATTTCAAGTTCAAAGATTAAAATATATCTAATTGT
20988952 CAAGTTCAATTA
66 CAAGTTCAATTA
20988964 TTAAAGTG
1 TTAAAGTG
20988972 GACAAAAAAG
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 84 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (77 bp):
TTAAAGTGTTATGTCAATAAAATTTTATATATTTCAAGTTCAAAGATTAAAATATATCTAATTGT
CAAGTTCAATTA
Found at i:20989340 original size:56 final size:56
Alignment explanation
Indices: 20989274--20989379 Score: 144
Period size: 56 Copynumber: 1.9 Consensus size: 56
20989264 TATATTATGA
20989274 TTTTAGTAAATTA-ATATAAGAATAATTATATTAAGAATT-TTATTAAATTAGATATT
1 TTTTAGTAAATTATATATAAGAATAATTAT-TTAA-AATTATTATTAAATTAGATATT
* * * *
20989330 TTTTATTAAATTATATTTAATAATAATTATTTTAAATTATTATTAAATTA
1 TTTTAGTAAATTATATATAAGAATAATTATTTAAAATTATTATTAAATTA
20989380 TTTATTATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
55 4 0.09
56 26 0.59
57 14 0.32
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (56 bp):
TTTTAGTAAATTATATATAAGAATAATTATTTAAAATTATTATTAAATTAGATATT
Found at i:20989345 original size:17 final size:18
Alignment explanation
Indices: 20989311--20989347 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
20989301 ATATTAAGAA
20989311 TTTTATTAAATTAGATATT
1 TTTTATTAAATTA-ATATT
20989330 TTTTATTAAATT-ATATT
1 TTTTATTAAATTAATATT
20989347 T
1 T
20989348 AATAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTTATTAAATTAATATT
Found at i:20989359 original size:24 final size:24
Alignment explanation
Indices: 20989331--20989409 Score: 69
Period size: 26 Copynumber: 3.4 Consensus size: 24
20989321 TTAGATATTT
20989331 TTTATTAAATTATATTTAATAATAA
1 TTTATTAAATTATATTTAATAAT-A
* *
20989356 TTATTTTAAATTAT-TATTAA-ATTA
1 TT-TATTAAATTATAT-TTAATAATA
*
20989380 TTTATT-ATTTATA-TTAATAAT-
1 TTTATTAAATTATATTTAATAATA
20989401 TTTATTAAA
1 TTTATTAAA
20989410 ATTTAATAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
21 10 0.23
22 8 0.19
23 3 0.07
24 3 0.07
25 5 0.12
26 14 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTATTAAATTATATTTAATAATA
Found at i:20989377 original size:11 final size:11
Alignment explanation
Indices: 20989354--20989386 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
20989344 ATTTAATAAT
20989354 AATTATT-TTA
1 AATTATTATTA
20989364 AATTATTATTA
1 AATTATTATTA
20989375 AATTATTTATTA
1 AATTA-TTATTA
20989387 TTTATATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.33
11 8 0.38
12 6 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
AATTATTATTA
Found at i:20989391 original size:56 final size:56
Alignment explanation
Indices: 20989275--20989391 Score: 139
Period size: 56 Copynumber: 2.1 Consensus size: 56
20989265 ATATTATGAT
* *
20989275 TTTAGTAAATTAATATAAGAATAATTATATTAAGAATTTTATTAAATTAGATATTT
1 TTTATTAAATTAATATAAGAATAATTATATTAAGAATTTTATTAAATTAGATATTA
* * * **
20989331 TTTATTAAATTATATTTAATAATAATTAT-TTTA-AATTATTATTAAATTATTTATTA
1 TTTATTAAATTA-ATATAAGAATAATTATATTAAGAATT-TTATTAAATTAGATATTA
20989387 TTTAT
1 TTTAT
20989392 ATTAATAATT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
55 4 0.08
56 34 0.65
57 14 0.27
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (56 bp):
TTTATTAAATTAATATAAGAATAATTATATTAAGAATTTTATTAAATTAGATATTA
Found at i:20989590 original size:45 final size:44
Alignment explanation
Indices: 20989509--20989598 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
20989499 GCCTCTATTC
20989509 CATTCAACCAAACACAGGAATACTATTACACCTCTATTCCATTA
1 CATTCAACCAAACACAGGAATACTATTACACCTCTATTCCATTA
* * *
20989553 CATTCAACCAAACA-ATTGAATTGCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACA-GGAA-TACTATTACACCTCTATTCCATTA
20989598 C
1 C
20989599 GCCTCTATTC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 17 0.41
45 23 0.56
ACGTcount: A:0.36, C:0.29, G:0.06, T:0.30
Consensus pattern (44 bp):
CATTCAACCAAACACAGGAATACTATTACACCTCTATTCCATTA
Found at i:20989599 original size:16 final size:16
Alignment explanation
Indices: 20989578--20989646 Score: 111
Period size: 16 Copynumber: 4.3 Consensus size: 16
20989568 TTGAATTGCT
20989578 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
20989594 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
**
20989610 ATTACATCTCTATTCC
1 ATTACGCCTCTATTCC
*
20989626 ATTACGCCTCTATTCT
1 ATTACGCCTCTATTCC
20989642 ATTAC
1 ATTAC
20989647 AGCAAACCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.22, C:0.33, G:0.04, T:0.41
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:20993012 original size:16 final size:15
Alignment explanation
Indices: 20992991--20993020 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
20992981 ATATAAATAA
20992991 ATAAATAAATATTTAT
1 ATAAATAAA-ATTTAT
20993007 ATAAATAAAATTTA
1 ATAAATAAAATTTA
20993021 AATGGAACAA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAAATAAAATTTAT
Found at i:20994054 original size:52 final size:52
Alignment explanation
Indices: 20993955--20994068 Score: 129
Period size: 52 Copynumber: 2.2 Consensus size: 52
20993945 GACTCAATGG
** * **
20993955 GGTCAATGTTGCAACAAGCACTTGTTATGGTCATGACACAGACCAACAATAA
1 GGTCAATGTCACAACAAGCACTTATTATGGTCACAACACAGACCAACAATAA
* * * * *
20994007 GGTCAATGTCACAACAAGCACTTATTGTGGTCGCAACACGGATCAACAGTAA
1 GGTCAATGTCACAACAAGCACTTATTATGGTCACAACACAGACCAACAATAA
*
20994059 GGTCAGTGTC
1 GGTCAATGTC
20994069 GTGACATACA
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (52 bp):
GGTCAATGTCACAACAAGCACTTATTATGGTCACAACACAGACCAACAATAA
Found at i:21004302 original size:24 final size:25
Alignment explanation
Indices: 21004267--21004314 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
21004257 TTATGAAATT
21004267 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
21004291 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
21004315 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:21004468 original size:66 final size:63
Alignment explanation
Indices: 21004393--21004603 Score: 192
Period size: 66 Copynumber: 3.4 Consensus size: 63
21004383 AAATATATTT
21004393 AATATTAATTATTTCAAATTTTCATTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTTT-ATTTA-AGTATCATATATTATGATTTGAGTAAATTCATATAA
21004458 G
63 G
* * * * **
21004459 AATATTAATTATTAAGAATTTTA-TTAA--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTTTATTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
*
21004513 AATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATA
1 AATATTAATTAT-TTAAATTT-TA-TTTA-AGTATCATATATTATGATTTGAGTAAATTCATATA
21004577 AG
62 AG
*
21004579 AATATTAATTATTAAGAATTTTATT
1 AATATTAATTATTTA-AATTTTATT
21004604 AAATTATATA
Statistics
Matches: 113, Mismatches: 15, Indels: 35
0.69 0.09 0.21
Matches are distributed among these distances:
53 5 0.04
54 13 0.12
55 5 0.04
56 4 0.04
57 3 0.03
58 1 0.01
59 10 0.09
60 8 0.07
61 10 0.09
62 1 0.01
63 3 0.03
64 4 0.04
65 9 0.08
66 32 0.28
67 5 0.04
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (63 bp):
AATATTAATTATTTAAATTTTATTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:21004493 original size:120 final size:120
Alignment explanation
Indices: 21004355--21004647 Score: 493
Period size: 120 Copynumber: 2.4 Consensus size: 120
21004345 AATTATTTTA
* * *
21004355 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCA-
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTAT-AT
*
21004417 TTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
63 TTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
21004475 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
21004540 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
21004595 AATTTTATTAAATTATATATTTTAATTATAATATATTTAACAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
21004648 TAAATATGAT
Statistics
Matches: 165, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
119 6 0.04
120 157 0.95
121 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:21004515 original size:15 final size:15
Alignment explanation
Indices: 21004480--21004531 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
21004470 TTAAGAATTT
*
21004480 TATTAAATTAT-ATA
1 TATTTAATTATAATA
21004494 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
21004508 TATTTAATAATAAT-
1 TATTTAATTATAATA
21004522 TATGTTAATT
1 TAT-TTAATT
21004532 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:21004797 original size:30 final size:27
Alignment explanation
Indices: 21004746--21004802 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 27
21004736 ATAACAATAC
*
21004746 TTATATATTAATTATTAACAATATTTA
1 TTATATATTAATTAATAACAATATTTA
21004773 TTATATATTAAATAATAATAACAATATTTA
1 TTATATATT-AAT--TAATAACAATATTTA
21004803 ACAATAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 9 0.35
28 3 0.12
30 14 0.54
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (27 bp):
TTATATATTAATTAATAACAATATTTA
Found at i:21004810 original size:16 final size:16
Alignment explanation
Indices: 21004789--21004819 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
21004779 ATTAAATAAT
21004789 AATAACAATATTTAAC
1 AATAACAATATTTAAC
21004805 AATAACAATATTTAA
1 AATAACAATATTTAA
21004820 TAATTTACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (16 bp):
AATAACAATATTTAAC
Found at i:21004884 original size:18 final size:17
Alignment explanation
Indices: 21004856--21004890 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
21004846 ATTATTAAGA
*
21004856 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
21004873 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
21004891 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:21005981 original size:154 final size:154
Alignment explanation
Indices: 21005701--21006010 Score: 550
Period size: 154 Copynumber: 2.0 Consensus size: 154
21005691 CAAACACAAA
* *
21005701 ATGTAAGTGTTACATCTAAAATCTAGGTTAATAGAAATTGAGTTAATGAATTGAGAGTGGTCACG
1 ATGTAAGTGTTACATCTAAAATCTAAGTTAATAAAAATTGAGTTAATGAATTGAGAGTGGTCACG
* *
21005766 CCAAAAAATTTTTATATGATTTTTTACTCATTTTATAATAAATAAGTATCAAGTGTAGTAGTTGA
66 CCAAAAAATTTTTAGATGATTTTTTACTCATTTTATAATAAATAAATATCAAGTGTAGTAGTTGA
21005831 GCAGTAGTGGTGTTGTCATTGATG
131 GCAGTAGTGGTGTTGTCATTGATG
*
21005855 ATGTAAGTGTTACATCTAAAATCTAAGTTAATAAAAATTGGGTTAATGAATTGAGAGTGGTCACG
1 ATGTAAGTGTTACATCTAAAATCTAAGTTAATAAAAATTGAGTTAATGAATTGAGAGTGGTCACG
*
21005920 CTC-AAAATTTTTTAGATGATTTTTTACTCATTTTATAATAAATAAATATCAAGTGTAGTAGTTG
66 C-CAAAAAATTTTTAGATGATTTTTTACTCATTTTATAATAAATAAATATCAAGTGTAGTAGTTG
21005984 AGCAGTAGTGGTGTTGTCATTGATG
130 AGCAGTAGTGGTGTTGTCATTGATG
21006009 AT
1 AT
21006011 CTGTGCTCAA
Statistics
Matches: 149, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
154 148 0.99
155 1 0.01
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.38
Consensus pattern (154 bp):
ATGTAAGTGTTACATCTAAAATCTAAGTTAATAAAAATTGAGTTAATGAATTGAGAGTGGTCACG
CCAAAAAATTTTTAGATGATTTTTTACTCATTTTATAATAAATAAATATCAAGTGTAGTAGTTGA
GCAGTAGTGGTGTTGTCATTGATG
Found at i:21015686 original size:80 final size:80
Alignment explanation
Indices: 21015482--21015845 Score: 376
Period size: 80 Copynumber: 4.6 Consensus size: 80
21015472 CGTTACGCCC
* * * * * * ***
21015482 GATAAGTTCACCGGCACAAAGCGTGCTAGGTAAAAAGCCCTATAA-TCACACTAGCATTTAGCCT
1 GATAAATTCACCGGCACAAAGCCTGCTAGGCACAAAGCCCGATAACT-ACACCAGCACAAAGCCT
* *
21015546 ACTAAGCACTAA--TT
65 GCTAAACACTAAGCTT
* *
21015560 GATAAATTCACCAGCACAAAGCCCTGCTAGGCACAAAGCCCGATAACTACACCGGCACAAAGCCT
1 GATAAATTCACCGGCACAAAG-CCTGCTAGGCACAAAGCCCGATAACTACACCAGCACAAAGCCT
21015625 GCTAAACACTAAGCTT
65 GCTAAACACTAAGCTT
* ** * *
21015641 GATAAATTCATCGGCACAAAGCCTGCTAGGCACAAAGCCTTATAACTACACCATCACAAAGCTTG
1 GATAAATTCACCGGCACAAAGCCTGCTAGGCACAAAGCCCGATAACTACACCAGCACAAAGCCTG
*
21015706 CTAAACATTAAGCTT
66 CTAAACACTAAGCTT
* * * * * * * *
21015721 GATAAATTCACCAGCACGAAGCCTGGTGGGCACAGAGCTCGATAAATACAGC-GACACAAAGCCT
1 GATAAATTCACCGGCACAAAGCCTGCTAGGCACAAAGCCCGATAACTACACCAG-CACAAAGCCT
* *
21015785 GTTAAGCACTAAGCTT
65 GCTAAACACTAAGCTT
* * * *
21015801 GATAAATTCATCGGCACAAAACCTGTTAGGCACAAAGTCCGATAA
1 GATAAATTCACCGGCACAAAGCCTGCTAGGCACAAAGCCCGATAA
21015846 TTTCATAACA
Statistics
Matches: 235, Mismatches: 46, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
78 19 0.08
79 42 0.18
80 153 0.65
81 21 0.09
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (80 bp):
GATAAATTCACCGGCACAAAGCCTGCTAGGCACAAAGCCCGATAACTACACCAGCACAAAGCCTG
CTAAACACTAAGCTT
Found at i:21015828 original size:40 final size:40
Alignment explanation
Indices: 21015541--21015825 Score: 236
Period size: 40 Copynumber: 7.2 Consensus size: 40
21015531 ACTAGCATTT
* *
21015541 AGCCTACTAAGCACTAA--TTGATAAATTCACCAGCACAA
1 AGCCTGCTAAGCACTAAGCTTGATAAATTCACCGGCACAA
* * ** * *
21015579 AGCCCTGCTAGGCACAAAGCCCGATAACTACACCGGCACAA
1 AG-CCTGCTAAGCACTAAGCTTGATAAATTCACCGGCACAA
* *
21015620 AGCCTGCTAAACACTAAGCTTGATAAATTCATCGGCACAA
1 AGCCTGCTAAGCACTAAGCTTGATAAATTCACCGGCACAA
* * * * **
21015660 AGCCTGCTAGGCACAAAGCCTT-ATAACTACACCATCACAA
1 AGCCTGCTAAGCACTAAG-CTTGATAAATTCACCGGCACAA
* * * * *
21015700 AGCTTGCTAAACATTAAGCTTGATAAATTCACCAGCACGA
1 AGCCTGCTAAGCACTAAGCTTGATAAATTCACCGGCACAA
* ** * * * *
21015740 AGCCTGGTGGGCAC-AGAGCTCGATAAATACAGCGACACAA
1 AGCCTGCTAAGCACTA-AGCTTGATAAATTCACCGGCACAA
* *
21015780 AGCCTGTTAAGCACTAAGCTTGATAAATTCATCGGCACAA
1 AGCCTGCTAAGCACTAAGCTTGATAAATTCACCGGCACAA
*
21015820 AACCTG
1 AGCCTG
21015826 TTAGGCACAA
Statistics
Matches: 187, Mismatches: 53, Indels: 12
0.74 0.21 0.05
Matches are distributed among these distances:
38 2 0.01
39 16 0.09
40 147 0.79
41 22 0.12
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.19
Consensus pattern (40 bp):
AGCCTGCTAAGCACTAAGCTTGATAAATTCACCGGCACAA
Found at i:21015845 original size:40 final size:40
Alignment explanation
Indices: 21015750--21015851 Score: 107
Period size: 40 Copynumber: 2.5 Consensus size: 40
21015740 AGCCTGGTGG
* * * *
21015750 GCACAGAGCTCGATAAATACAGCGACACAAAGCCTGTTAA
1 GCACAAAGCTCGATAAATTCATCGACACAAAACCTGTTAA
* * * *
21015790 GCACTAAGCTTGATAAATTCATCGGCACAAAACCTGTTAG
1 GCACAAAGCTCGATAAATTCATCGACACAAAACCTGTTAA
*
21015830 GCACAAAG-TCCGATAATTTCAT
1 GCACAAAGCT-CGATAAATTCAT
21015852 AACATACCAA
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
39 1 0.02
40 49 0.98
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.22
Consensus pattern (40 bp):
GCACAAAGCTCGATAAATTCATCGACACAAAACCTGTTAA
Found at i:21018935 original size:24 final size:24
Alignment explanation
Indices: 21018908--21018954 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
21018898 GAGGAAAAAT
*
21018908 TGGTGGCTTCATCCACGACCTACG
1 TGGTGGCTTCATCCACAACCTACG
*
21018932 TGGTGGCTTCCTCCACAACCTAC
1 TGGTGGCTTCATCCACAACCTAC
21018955 ATGGCAGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.17, C:0.36, G:0.21, T:0.26
Consensus pattern (24 bp):
TGGTGGCTTCATCCACAACCTACG
Found at i:21018964 original size:24 final size:24
Alignment explanation
Indices: 21018913--21018964 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
21018903 AAAATTGGTG
* * **
21018913 GCTTCATCCACGACCTACGTGGTG
1 GCTTCATCCACAACCTACATGGCA
*
21018937 GCTTCCTCCACAACCTACATGGCA
1 GCTTCATCCACAACCTACATGGCA
21018961 GCTT
1 GCTT
21018965 ATCTGTAAAT
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:0.19, C:0.37, G:0.19, T:0.25
Consensus pattern (24 bp):
GCTTCATCCACAACCTACATGGCA
Found at i:21020657 original size:24 final size:24
Alignment explanation
Indices: 21020629--21020703 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
21020619 GAAGAAGAAT
* *
21020629 TGGTGGCTTTGTCCACAACCTACG
1 TGGTGGCTTCGTCCACAACCTACA
* *
21020653 TGGTGGCTTCCTCCACGACCTACA
1 TGGTGGCTTCGTCCACAACCTACA
*
21020677 TGGTGGCTTCGTTCACAACCTACA
1 TGGTGGCTTCGTCCACAACCTACA
21020701 TGG
1 TGG
21020704 CAGCTTATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.17, C:0.31, G:0.24, T:0.28
Consensus pattern (24 bp):
TGGTGGCTTCGTCCACAACCTACA
Found at i:21020923 original size:15 final size:15
Alignment explanation
Indices: 21020900--21020943 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
21020890 ATGTGTTTAC
21020900 TTGTTATTTAACTTA
1 TTGTTATTTAACTTA
*
21020915 TTTTTATTTAACTTA
1 TTGTTATTTAACTTA
21020930 TTGTTATTTAACTT
1 TTGTTATTTAACTT
21020944 GTTATAAGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.64
Consensus pattern (15 bp):
TTGTTATTTAACTTA
Found at i:21026953 original size:37 final size:37
Alignment explanation
Indices: 21026903--21026977 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
21026893 AACAAAATGT
21026903 CTCTTCCAAATTATCATCTCGAGCCATCCTGAACTAG
1 CTCTTCCAAATTATCATCTCGAGCCATCCTGAACTAG
21026940 CTCTTCCAAATTATCATCTCGAGCCATCCTGAACTAG
1 CTCTTCCAAATTATCATCTCGAGCCATCCTGAACTAG
21026977 C
1 C
21026978 CAACTTCCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.27, C:0.33, G:0.11, T:0.29
Consensus pattern (37 bp):
CTCTTCCAAATTATCATCTCGAGCCATCCTGAACTAG
Found at i:21027246 original size:3 final size:3
Alignment explanation
Indices: 21027238--21027291 Score: 92
Period size: 3 Copynumber: 18.0 Consensus size: 3
21027228 AGGCAAGCAA
21027238 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA- GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
21027285 AGAT GAT
1 -GAT GAT
21027292 TTTGGGTAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:21028151 original size:57 final size:56
Alignment explanation
Indices: 21028082--21028193 Score: 206
Period size: 57 Copynumber: 2.0 Consensus size: 56
21028072 AATGTTGTTT
21028082 CTGGTTAAGTGTAATTGACTCCATTTTCTTTCTACCAAAAAAAAAAAAGATTCAAAA
1 CTGGTTAAGTGTAATTGACTCCATTTTCTTTCTACC-AAAAAAAAAAAGATTCAAAA
*
21028139 CTGGTTAAGTGTAATTGACTCCATTTTCTTTCTACCAAAAAGAAAAAGATTCAAA
1 CTGGTTAAGTGTAATTGACTCCATTTTCTTTCTACCAAAAAAAAAAAGATTCAAA
21028194 TCTTGTTATT
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
56 18 0.33
57 36 0.67
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (56 bp):
CTGGTTAAGTGTAATTGACTCCATTTTCTTTCTACCAAAAAAAAAAAGATTCAAAA
Found at i:21035979 original size:18 final size:20
Alignment explanation
Indices: 21035932--21035989 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 20
21035922 TTTTAACTTA
21035932 ATTTAAATT-TAATTAAATT
1 ATTTAAATTATAATTAAATT
21035951 ATTTAAA--ATAATT-AATT
1 ATTTAAATTATAATTAAATT
*
21035968 -TTTAAATTATAAATAAA-T
1 ATTTAAATTATAATTAAATT
21035986 ATTT
1 ATTT
21035990 TTTTCTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
16 6 0.18
17 4 0.12
18 11 0.33
19 12 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTAAATTATAATTAAATT
Found at i:21041209 original size:81 final size:81
Alignment explanation
Indices: 21041074--21041238 Score: 276
Period size: 81 Copynumber: 2.0 Consensus size: 81
21041064 AAATAAGTAA
* * * *
21041074 TTTTAATCAATTAACCACTTTTAGTGTTCAATTTAATCCACATTTCATATTTATGTAAAATTATC
1 TTTTAATCAATTAACCACTTCTAGTATTCAATTTAATCAACATTTCATATTTATGTAAAATTACC
*
21041139 AATTTACCCCTAACAT
66 AATTTACCCCAAACAT
21041155 TTTTAATCAATTAACCACTTCTAGTATTCAATTTAATCAACATTTCATATTTATGTAAAATTACC
1 TTTTAATCAATTAACCACTTCTAGTATTCAATTTAATCAACATTTCATATTTATGTAAAATTACC
*
21041220 AATTTACCCCAAATAT
66 AATTTACCCCAAACAT
21041236 TTT
1 TTT
21041239 AACTTTTTCA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.43
Consensus pattern (81 bp):
TTTTAATCAATTAACCACTTCTAGTATTCAATTTAATCAACATTTCATATTTATGTAAAATTACC
AATTTACCCCAAACAT
Found at i:21043014 original size:37 final size:39
Alignment explanation
Indices: 21042917--21043022 Score: 118
Period size: 37 Copynumber: 2.8 Consensus size: 39
21042907 GTACAAGATA
* *
21042917 AATATTAAATTTAAT-TT-AA-TATTAAGATAATTAGTTT
1 AATATTAAATTTAATATTAAACTATTAAAATAAGTAG-TT
*
21042954 AATATTAAA-TTAATA-AAATACTATTAAAATAAGTA-TT
1 AATATTAAATTTAATATTAA-ACTATTAAAATAAGTAGTT
21042991 AA-ATTAAATTTAATATTAAACTATTAAAATAA
1 AATATTAAATTTAATATTAAACTATTAAAATAA
21043023 TATAATATTA
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
36 11 0.19
37 33 0.56
38 3 0.05
39 12 0.20
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.42
Consensus pattern (39 bp):
AATATTAAATTTAATATTAAACTATTAAAATAAGTAGTT
Found at i:21050492 original size:59 final size:61
Alignment explanation
Indices: 21050419--21050535 Score: 157
Period size: 62 Copynumber: 1.9 Consensus size: 61
21050409 ATCACTTTAG
* * * *
21050419 TATTAAATTAATATAATATTTA-T-CAAGATAAATATTAGATTAAGTTTAATATTAAATCT
1 TATTAAAATAATATAATATTTACTACAAGATAAACATTAAATTAAATTTAATATTAAATCT
* *
21050478 TATTAAAATGATATAATGTTTATCTACAAGATAAACATTAAATTAAATTTAATATTAA
1 TATTAAAATAATATAATATTTA-CTACAAGATAAACATTAAATTAAATTTAATATTAA
21050536 GATAATCAGT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
59 19 0.39
61 1 0.02
62 29 0.59
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (61 bp):
TATTAAAATAATATAATATTTACTACAAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:21053472 original size:11 final size:11
Alignment explanation
Indices: 21053456--21053509 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
21053446 TTTTTTTTAA
21053456 ACCACCACTGG
1 ACCACCACTGG
*
21053467 ACCACCACTGA
1 ACCACCACTGG
** *
21053478 ACCACTGCCGG
1 ACCACCACTGG
*
21053489 ACCACCACCGTG
1 ACCACCACTG-G
21053501 ACCACCACT
1 ACCACCACT
21053510 CTCTTTCTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
11 25 0.74
12 9 0.26
ACGTcount: A:0.28, C:0.48, G:0.15, T:0.09
Consensus pattern (11 bp):
ACCACCACTGG
Found at i:21058149 original size:45 final size:45
Alignment explanation
Indices: 21058085--21058174 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
21058075 AAGACAATTG
*
21058085 GTTAATGCGTCTAACCTTCCTCTATCAAGTGACTAGATTTTTTTA
1 GTTAATGCGTCTAACCTTCCCCTATCAAGTGACTAGATTTTTTTA
* *
21058130 GTTAATGCGTTTAACCTTCCCCTATCAAGTGACTGGATTTTTTTA
1 GTTAATGCGTCTAACCTTCCCCTATCAAGTGACTAGATTTTTTTA
21058175 CACACTAATG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.42
Consensus pattern (45 bp):
GTTAATGCGTCTAACCTTCCCCTATCAAGTGACTAGATTTTTTTA
Found at i:21060392 original size:3 final size:3
Alignment explanation
Indices: 21060384--21060417 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
21060374 ATATGTAGGT
21060384 ATA ATA ATA TATA AT- ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA A
21060418 CAAAATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:21060815 original size:21 final size:21
Alignment explanation
Indices: 21060789--21060866 Score: 138
Period size: 21 Copynumber: 3.7 Consensus size: 21
21060779 AATCATATCT
*
21060789 TCTAAGATTGTATATATCATA
1 TCTAAGATTGCATATATCATA
21060810 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
21060831 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
*
21060852 TCTAAGATTGTATAT
1 TCTAAGATTGCATAT
21060867 CCTCGAAAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:21061634 original size:132 final size:132
Alignment explanation
Indices: 21061397--21062231 Score: 1373
Period size: 132 Copynumber: 6.3 Consensus size: 132
21061387 TCCACTGCAA
* * * *
21061397 CTTCAACCTACTCCGCTGCTGCTCAGTGAGATAAGACTTGGTGGCTTAAATCTGCTTCCCACTAT
1 CTTCAACCTTCTCCGCTGCTGCTCAGAGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
* * *
21061462 CTTGGAAAGATAAGATTTGTCGACTTTGATCTGCTCCACTACTGCTTAGGGAAATAAGATCTACA
66 CTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
21061527 AT
131 AT
* *
21061529 CTTCAACCTTCTCTGCTGCTGCTCAGAGAGACAAGGCTTTGTGGCTTAAATCTGCTTCCCACTAT
1 CTTCAACCTTCTCCGCTGCTGCTCAGAGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
21061594 CTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
66 CTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
21061659 AT
131 AT
* *
21061661 CTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
1 CTTCAACCTTCTCCGCTGCTGCTCAGAGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
* * *
21061726 CTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAAATAAGATCTACA
66 CTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
21061791 AT
131 AT
* *
21061793 ATTCAACCTTCTCCGCTGCTGCTCAGAGAGACAAGGCTTTGTGGCTTAAATCTGCTTCCCACTAT
1 CTTCAACCTTCTCCGCTGCTGCTCAGAGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
* * *
21061858 CTTGGAAAGATAATATTTACCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAAATCTACA
66 CTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
21061923 AT
131 AT
* *
21061925 CTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
1 CTTCAACCTTCTCCGCTGCTGCTCAGAGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
*
21061990 CTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
66 CTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
21062055 AT
131 AT
* * * *
21062057 CTTCAACCTTCTCCGCTGTTGCTCAGAGAGACAAGGATTTGTGGCTCAAATCTGCTTCCCACTAT
1 CTTCAACCTTCTCCGCTGCTGCTCAGAGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
** * * *
21062122 CTTGGAAAGATAAGATTTTTCATCTTTGATCTGCTCTACTACTGCTTAGGGAGATAAGATCTGCA
66 CTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
21062187 AT
131 AT
* *
21062189 CTTCAACGTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTG
1 CTTCAACCTTCTCCGCTGCTGCTCAGAGAGACAAGGCTTGGTG
21062232 TTTCACCGGT
Statistics
Matches: 652, Mismatches: 51, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 652 1.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (132 bp):
CTTCAACCTTCTCCGCTGCTGCTCAGAGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
CTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
AT
Found at i:21061649 original size:44 final size:44
Alignment explanation
Indices: 21061469--21062049 Score: 182
Period size: 44 Copynumber: 13.2 Consensus size: 44
21061459 TATCTTGGAA
* * **
21061469 AGATAAGATTTGTCGACTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * ** * * ** * * *
21061513 AAATAAGATCTACAATCTTCAACCTTCTCTGCTGCTGCTCAGAG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
21061557 AGACAAGGCTTTG-TGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTTGCCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
**
21061601 AGATAAGATTTGCCGTCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * * * *
21061645 AGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** ** * * *
21061689 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* *
21061733 AGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * ** * * * * * * *
21061777 AAATAAGATCTACAATATTCAACCTTCTCCGCTGCTGCTCAGAG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
21061821 AGACAAGGCTTTG-TGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTTGCCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* * **
21061865 AGATAATATTTACCGTCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * ** * * * * *
21061909 AGATAAAATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** ** * * *
21061953 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
*
21061997 AGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
21062041 AGATAAGAT
1 AGATAAGAT
21062050 CTACAATCTT
Statistics
Matches: 356, Mismatches: 153, Indels: 56
0.63 0.27 0.10
Matches are distributed among these distances:
42 24 0.07
43 22 0.06
44 273 0.77
45 22 0.06
46 15 0.04
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (44 bp):
AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:21063471 original size:22 final size:22
Alignment explanation
Indices: 21063445--21063497 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
21063435 TCTCCTTTTG
21063445 TTTTTCTTTTCCTT-TTTCTTT
1 TTTTTCTTTTCCTTCTTTCTTT
*
21063466 CTTTTTCTTTTCTTTCTTTCTTT
1 -TTTTTCTTTTCCTTCTTTCTTT
21063489 TTTTT-TTTT
1 TTTTTCTTTT
21063498 GAAAAATTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 4 0.14
22 18 0.62
23 7 0.24
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (22 bp):
TTTTTCTTTTCCTTCTTTCTTT
Found at i:21063478 original size:15 final size:16
Alignment explanation
Indices: 21063437--21063484 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
21063427 CCTTGGCCTC
*
21063437 TCCTTTTGTTTTTCTTT
1 TCCTTTT-TCTTTCTTT
21063454 TCCTTTTTCTTTCTTT
1 TCCTTTTTCTTTCTTT
*
21063470 TTC-TTTTCTTTCTTT
1 TCCTTTTTCTTTCTTT
21063485 CTTTTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 12 0.41
16 10 0.34
17 7 0.24
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (16 bp):
TCCTTTTTCTTTCTTT
Found at i:21063491 original size:15 final size:15
Alignment explanation
Indices: 21063447--21063491 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
21063437 TCCTTTTGTT
*
21063447 TTTCTTTTCCTTTTTC
1 TTTC-TTTCTTTTTTC
21063463 TTTCTTT-TTCTTTTC
1 TTTCTTTCTT-TTTTC
21063478 TTTCTTTCTTTTTT
1 TTTCTTTCTTTTTT
21063492 TTTTTTGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 1 0.04
15 19 0.73
16 6 0.23
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTCTTTCTTTTTTC
Found at i:21063495 original size:19 final size:19
Alignment explanation
Indices: 21063445--21063494 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 19
21063435 TCTCCTTTTG
21063445 TTTTTCTTTTCCTTTTTCTTTC
1 TTTTTCTTTT-C--TTTCTTTC
21063467 TTTTTCTTTTCTTTCTTTC
1 TTTTTCTTTTCTTTCTTTC
21063486 TTTTT-TTTT
1 TTTTTCTTTT
21063495 TTTGAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.14
19 13 0.46
21 1 0.04
22 10 0.36
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTCTTTTCTTTCTTTC
Found at i:21068279 original size:3 final size:3
Alignment explanation
Indices: 21068271--21068310 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
21068261 ATATGTAGGT
*
21068271 ATA ATA ATA ATA TATA AT- ATA ATA ATA AAA ATA ATA ATA A
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA A
21068311 CAAAATTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:21068294 original size:15 final size:12
Alignment explanation
Indices: 21068273--21068324 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
21068263 ATGTAGGTAT
21068273 AATAATAATATATA
1 AATAATAATA-A-A
21068287 ATATAATAATAAA
1 A-ATAATAATAAA
21068300 AATAATAATAACA
1 AATAATAATAA-A
*
21068313 AA-ATTAATAAA
1 AATAATAATAAA
21068324 A
1 A
21068325 TAGACTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
11 2 0.06
12 17 0.49
13 5 0.14
14 2 0.06
15 9 0.26
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:21068706 original size:21 final size:21
Alignment explanation
Indices: 21068680--21068734 Score: 87
Period size: 19 Copynumber: 2.7 Consensus size: 21
21068670 AATCATATCT
21068680 TCTAAAATTGTATATATCATA
1 TCTAAAATTGTATATATCATA
*
21068701 TCTAAAATTG--CATATCATA
1 TCTAAAATTGTATATATCATA
21068720 TCTAAAATTGTATAT
1 TCTAAAATTGTATAT
21068735 CCTCGAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 18 0.60
21 12 0.40
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (21 bp):
TCTAAAATTGTATATATCATA
Found at i:21068720 original size:24 final size:20
Alignment explanation
Indices: 21068671--21068722 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
21068661 AGATTATAAA
21068671 ATCATATCTTCTAAAATTGT
1 ATCATATCTTCTAAAATTGT
21068691 AT-ATATCATATCTAAAATTGCAT
1 ATCATATC-T-TCTAAAATTG--T
21068714 ATCATATCT
1 ATCATATCT
21068723 AAAATTGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 5 0.19
20 3 0.11
21 10 0.37
23 4 0.15
24 5 0.19
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.42
Consensus pattern (20 bp):
ATCATATCTTCTAAAATTGT
Found at i:21073734 original size:9 final size:9
Alignment explanation
Indices: 21073720--21073750 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
21073710 GGAATTAATT
21073720 TTGAGAGAA
1 TTGAGAGAA
21073729 TTGAGAGAA
1 TTGAGAGAA
*
21073738 TGGAGAGAA
1 TTGAGAGAA
21073747 TTGA
1 TTGA
21073751 ATTTGAGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (9 bp):
TTGAGAGAA
Found at i:21074497 original size:21 final size:21
Alignment explanation
Indices: 21074426--21074499 Score: 105
Period size: 21 Copynumber: 3.6 Consensus size: 21
21074416 AAATTGAAAA
*
21074426 TCAATTTGA-TTTGATTTTAT
1 TCAAATTGATTTTGATTTTAT
* *
21074446 TCAAATTTATTTTTATTTTAT
1 TCAAATTGATTTTGATTTTAT
21074467 TCAAATTGATTTTGATTTTAT
1 TCAAATTGATTTTGATTTTAT
*
21074488 TCAAACTGATTT
1 TCAAATTGATTT
21074500 AAAGGCTCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
20 7 0.15
21 40 0.85
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.58
Consensus pattern (21 bp):
TCAAATTGATTTTGATTTTAT
Found at i:21075038 original size:17 final size:17
Alignment explanation
Indices: 21074997--21075038 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
21074987 AATATGTGTT
*
21074997 TATATTATTTATTTAAA
1 TATATTATTTATATAAA
*
21075014 TATTTTATTTAATATAAA
1 TATATTATTT-ATATAAA
21075032 TA-ATTAT
1 TATATTAT
21075039 AATTATATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATATTATTTATATAAA
Found at i:21076378 original size:7 final size:7
Alignment explanation
Indices: 21076366--21076403 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
21076356 AAGGTAGCAG
21076366 CTCGATC
1 CTCGATC
21076373 CTCGATC
1 CTCGATC
21076380 CTCGATC
1 CTCGATC
21076387 CTCGATC
1 CTCGATC
21076394 CTCGATC
1 CTCGATC
21076401 CTC
1 CTC
21076404 ATGGATCACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.13, C:0.45, G:0.13, T:0.29
Consensus pattern (7 bp):
CTCGATC
Found at i:21076508 original size:15 final size:15
Alignment explanation
Indices: 21076488--21076518 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
21076478 TTAAATGACA
21076488 TGAAAACTATCTTTT
1 TGAAAACTATCTTTT
*
21076503 TGAAAATTATCTTTT
1 TGAAAACTATCTTTT
21076518 T
1 T
21076519 CTATCTGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.52
Consensus pattern (15 bp):
TGAAAACTATCTTTT
Found at i:21076920 original size:17 final size:17
Alignment explanation
Indices: 21076898--21076931 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21076888 CTCCAAAGTC
*
21076898 TCTATTTATAGGTATAA
1 TCTATTTATAGGCATAA
21076915 TCTATTTATAGGCATAA
1 TCTATTTATAGGCATAA
21076932 GAAGTATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (17 bp):
TCTATTTATAGGCATAA
Found at i:21078902 original size:23 final size:23
Alignment explanation
Indices: 21078876--21078919 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
21078866 CCATTACACA
*
21078876 GCTCTTAGTGATCTTCCCGATAG
1 GCTCTTAGTGAGCTTCCCGATAG
*
21078899 GCTCTTTGTGAGCTTCCCGAT
1 GCTCTTAGTGAGCTTCCCGAT
21078920 TAAATGTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.14, C:0.27, G:0.23, T:0.36
Consensus pattern (23 bp):
GCTCTTAGTGAGCTTCCCGATAG
Found at i:21080816 original size:24 final size:23
Alignment explanation
Indices: 21080760--21080853 Score: 77
Period size: 24 Copynumber: 4.1 Consensus size: 23
21080750 AAATGGGCAA
* *
21080760 CATATACATACCAAATTTAACAG
1 CATATATACACCAAATTTAACAG
*
21080783 CACT-TTTACACCAAAATTTAACAG
1 CA-TATATACACC-AAATTTAACAG
* *
21080807 CATATATACAACAAA--TAGGCAG
1 CATATATACACCAAATTTA-ACAG
* *
21080829 CATATACATACCAAATTTAACAG
1 CATATATACACCAAATTTAACAG
21080852 CA
1 CA
21080854 CTTATATATA
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
21 2 0.04
22 15 0.27
23 16 0.29
24 22 0.40
ACGTcount: A:0.47, C:0.22, G:0.06, T:0.24
Consensus pattern (23 bp):
CATATATACACCAAATTTAACAG
Found at i:21081719 original size:42 final size:42
Alignment explanation
Indices: 21081598--21081705 Score: 175
Period size: 41 Copynumber: 2.6 Consensus size: 42
21081588 AGCCCGATAC
21081598 ATTTCACTGGCA-CAAAGCCTGCTAGACATAAAGTCTGAAGTA
1 ATTTCACTGGCATC-AAGCCTGCTAGACATAAAGTCTGAAGTA
*
21081640 A-TTCACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAGTA
1 ATTTCACTGGCATCAAGCCTGCTAGACATAAAGTCTGAAGTA
*
21081681 ATTTCACTGGCATCAACCCTGCTAG
1 ATTTCACTGGCATCAAGCCTGCTAG
21081706 GCATTAAACC
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
41 38 0.62
42 23 0.38
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (42 bp):
ATTTCACTGGCATCAAGCCTGCTAGACATAAAGTCTGAAGTA
Found at i:21081837 original size:2 final size:2
Alignment explanation
Indices: 21081830--21081854 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21081820 GGTCATTATC
21081830 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 T
21081855 CTTATACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21085579 original size:14 final size:15
Alignment explanation
Indices: 21085545--21085589 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
21085535 ATTAGTCTCC
21085545 AATTATAATAAATAT
1 AATTATAATAAATAT
*
21085560 GA-TATAATAAATA-
1 AATTATAATAAATAT
21085573 AATTATAATAAAATAT
1 AATTATAAT-AAATAT
21085589 A
1 A
21085590 CCTGAGATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
13 1 0.04
14 17 0.68
15 6 0.24
16 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (15 bp):
AATTATAATAAATAT
Found at i:21087535 original size:8 final size:8
Alignment explanation
Indices: 21087524--21087568 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
21087514 GCTAAATGTT
21087524 TGTTTATA
1 TGTTTATA
21087532 TGTTTATA
1 TGTTTATA
*
21087540 TATTTATA
1 TGTTTATA
21087548 TG--T-T-
1 TGTTTATA
21087552 TGTTTATA
1 TGTTTATA
21087560 TGTTTATA
1 TGTTTATA
21087568 T
1 T
21087569 CTGGAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
4 2 0.06
5 1 0.03
6 2 0.06
7 1 0.03
8 25 0.81
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.64
Consensus pattern (8 bp):
TGTTTATA
Found at i:21088483 original size:42 final size:42
Alignment explanation
Indices: 21088432--21088551 Score: 197
Period size: 42 Copynumber: 2.9 Consensus size: 42
21088422 CAATTTTTAT
21088432 TATTTATAACAAATTAAAGAGTTATTAATTTAAAATTCTATA
1 TATTTATAACAAATTAAAGAGTTATTAATTTAAAATTCTATA
***
21088474 TATTTATAACAAATTAATA-ACAAATTAATTTAAAATTCTATA
1 TATTTATAACAAATTAA-AGAGTTATTAATTTAAAATTCTATA
21088516 TATTTATAACAAATTAAAGAGTTATTAATTTAAAAT
1 TATTTATAACAAATTAAAGAGTTATTAATTTAAAAT
21088552 ATTTAATAAC
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
41 1 0.01
42 68 0.97
43 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (42 bp):
TATTTATAACAAATTAAAGAGTTATTAATTTAAAATTCTATA
Found at i:21088760 original size:109 final size:106
Alignment explanation
Indices: 21088570--21088782 Score: 270
Period size: 109 Copynumber: 1.9 Consensus size: 106
21088560 ACAAATTATA
21088570 TGGATGAGTAGTGTTTTTTTTGTTAATATAACAACAAGTTAATTAGTATTTAGTAGTTTAAAGAG
1 TGGATGAGTAGTGTTTTTTTTGTTAATATAACAACAAG---ATTAG-ATTTAGTAGTTTAAAGAG
*
21088635 TTACTAAATTAAAATTCTATATATTATAAAAGTATGCATTTAATCTAAG
62 TTACTAAATTAAAATTC----TATTATAAAAGTAAGCATTTAATCTAAG
* *
21088684 TGGATGAGTAGTTTTTTTTTTTAGTTAATATAACAGCAAG-TTA-A-TTAGTAGTTTAAAGAGTT
1 TGGATGAGTAG-TGTTTTTTTT-GTTAATATAACAACAAGATTAGATTTAGTAGTTTAAAGAGTT
* *
21088746 ATTAATTTAAAATTCTATTATAAAAGTAAGCATTTAA
64 ACTAAATTAAAATTCTATTATAAAAGTAAGCATTTAA
21088783 AGAGTTCAAA
Statistics
Matches: 92, Mismatches: 5, Indels: 13
0.84 0.05 0.12
Matches are distributed among these distances:
105 21 0.23
109 31 0.34
110 1 0.01
112 3 0.03
114 11 0.12
115 9 0.10
116 16 0.17
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (106 bp):
TGGATGAGTAGTGTTTTTTTTGTTAATATAACAACAAGATTAGATTTAGTAGTTTAAAGAGTTAC
TAAATTAAAATTCTATTATAAAAGTAAGCATTTAATCTAAG
Found at i:21090993 original size:9 final size:9
Alignment explanation
Indices: 21090979--21091024 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
21090969 GGTTGCAAAA
21090979 AGGACGATG
1 AGGACGATG
21090988 AGGACGATG
1 AGGACGATG
*
21090997 ACGACGATG
1 AGGACGATG
*
21091006 ACGACGATG
1 AGGACGATG
*
21091015 AGGATGATG
1 AGGACGATG
21091024 A
1 A
21091025 TGTTTCTTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.35, C:0.13, G:0.39, T:0.13
Consensus pattern (9 bp):
AGGACGATG
Found at i:21091091 original size:22 final size:22
Alignment explanation
Indices: 21091066--21091130 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 22
21091056 CTTCTAAATA
21091066 TGTTGATGGACAATTTATATTT
1 TGTTGATGGACAATTTATATTT
* *
21091088 TGTT-AT-GA-AA-TTA-AATA
1 TGTTGATGGACAATTTATATTT
21091105 TGTTGATGGACAATTTATATTT
1 TGTTGATGGACAATTTATATTT
21091127 TGTT
1 TGTT
21091131 ATGAAATTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 6 0.18
18 5 0.15
19 4 0.12
20 4 0.12
21 5 0.15
22 10 0.29
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.49
Consensus pattern (22 bp):
TGTTGATGGACAATTTATATTT
Found at i:21091099 original size:19 final size:19
Alignment explanation
Indices: 21091077--21091138 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
21091067 GTTGATGGAC
21091077 AATTTATATTTTGTTATGA
1 AATTTATATTTTGTTATGA
* *
21091096 AA-TTA-AATATGTTGATGGA
1 AATTTATATTTTGTT-AT-GA
21091115 CAATTTATATTTTGTTATGA
1 -AATTTATATTTTGTTATGA
21091135 AATT
1 AATT
21091139 CAATATGTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 6 0.18
18 5 0.15
19 8 0.24
20 4 0.12
21 5 0.15
22 6 0.18
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.50
Consensus pattern (19 bp):
AATTTATATTTTGTTATGA
Found at i:21091103 original size:39 final size:39
Alignment explanation
Indices: 21091060--21091153 Score: 179
Period size: 39 Copynumber: 2.4 Consensus size: 39
21091050 GCTTTCCTTC
21091060 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
1 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
21091099 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
1 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
*
21091138 TCAATATGTTGATGGA
1 TAAATATGTTGATGGA
21091154 TTAATGTATG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.45
Consensus pattern (39 bp):
TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
Found at i:21091172 original size:39 final size:38
Alignment explanation
Indices: 21091060--21091172 Score: 111
Period size: 39 Copynumber: 2.9 Consensus size: 38
21091050 GCTTTCCTTC
* * *
21091060 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
1 TAAATATGTTGATGGACAATGTATA-TATATTATGAAAT
* * *
21091099 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
1 TAAATATGTTGATGGACAATGTATA-TATATTATGAAAT
* *
21091138 TCAATATGTTGATGGATTAATGTATGA-ATATTATG
1 TAAATATGTTGATGGA-CAATGTAT-ATATATTATG
21091173 GTTTGGTGCT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
39 60 0.90
40 6 0.09
41 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.45
Consensus pattern (38 bp):
TAAATATGTTGATGGACAATGTATATATATTATGAAAT
Found at i:21101544 original size:484 final size:484
Alignment explanation
Indices: 21100636--21101596 Score: 1913
Period size: 484 Copynumber: 2.0 Consensus size: 484
21100626 TACGAATTTA
21100636 TTGTCTAGTAAGAGTTTACCTGTCAAGTCCACTGAATTCGTGGTTAAGGTATCGAACCCTTTAGG
1 TTGTCTAGTAAGAGTTTACCTGTCAAGTCCACTGAATTCGTGGTTAAGGTATCGAACCCTTTAGG
21100701 TCAGTATGTCTTAATTAATAAAGTTTGCAAGAATTGTACTTTAATGACTTGGGGTTACAGTTTTT
66 TCAGTATGTCTTAATTAATAAAGTTTGCAAGAATTGTACTTTAATGACTTGGGGTTACAGTTTTT
21100766 TGGCCGATTTGATGCTTTTACCGTTAGATGAATTTGATGTGATTTTGGATATGGGTTGGCTGACT
131 TGGCCGATTTGATGCTTTTACCGTTAGATGAATTTGATGTGATTTTGGATATGGGTTGGCTGACT
21100831 CTGTATGATGCGGTTGTAAACTGCAGACGAAAGCTTATTGTATTGAAATGTCAGAACGGTGAGAC
196 CTGTATGATGCGGTTGTAAACTGCAGACGAAAGCTTATTGTATTGAAATGTCAGAACGGTGAGAC
21100896 TCTTCGTATTGAATCTGATGATTCGAGTGGGTTGCCTATTGTGATATCGGCTACGTTAGCACATA
261 TCTTCGTATTGAATCTGATGATTCGAGTGGGTTGCCTATTGTGATATCGGCTACGTTAGCACATA
21100961 AATATGTGAAGAGGGGTTGTGAGGCTTACCTTGCATATATACTGGATATTAAAGTGTCTGAATTG
326 AATATGTGAAGAGGGGTTGTGAGGCTTACCTTGCATATATACTGGATATTAAAGTGTCTGAATTG
21101026 AAGATTGAATCAGTACCAATGGTTAGTGAATATTTACATGTGTTTCCAAAAGAGTTACCCGGGTT
391 AAGATTGAATCAGTACCAATGGTTAGTGAATATTTACATGTGTTTCCAAAAGAGTTACCCGGGTT
21101091 GCCACCTATTAGAGAGGTTGAGGTTGAGT
456 GCCACCTATTAGAGAGGTTGAGGTTGAGT
21101120 TTGTCTAGTAAGAGTTTACCTGTCAAGTCCACTGAATTCGTGGTTAAGGTATCGAACCCTTTAGG
1 TTGTCTAGTAAGAGTTTACCTGTCAAGTCCACTGAATTCGTGGTTAAGGTATCGAACCCTTTAGG
*
21101185 TCAGTATGTCTTAATTAATAAAGTTTGCAAGAATTGTACTTTAATGACTTGGGGTTACATTTTTT
66 TCAGTATGTCTTAATTAATAAAGTTTGCAAGAATTGTACTTTAATGACTTGGGGTTACAGTTTTT
21101250 TGGCCGATTTGATGCTTTTACCGTTAGATGAATTTGATGTGATTTTGGATATGGGTTGGCTGACT
131 TGGCCGATTTGATGCTTTTACCGTTAGATGAATTTGATGTGATTTTGGATATGGGTTGGCTGACT
21101315 CTGTATGATGCGGTTGTAAACTGCAGACGAAAGCTTATTGTATTGAAATGTCAGAACGGTGAGAC
196 CTGTATGATGCGGTTGTAAACTGCAGACGAAAGCTTATTGTATTGAAATGTCAGAACGGTGAGAC
21101380 TCTTCGTATTGAATCTGATGATTCGAGTGGGTTGCCTATTGTGATATCGGCTACGTTAGCACATA
261 TCTTCGTATTGAATCTGATGATTCGAGTGGGTTGCCTATTGTGATATCGGCTACGTTAGCACATA
21101445 AATATGTGAAGAGGGGTTGTGAGGCTTACCTTGCATATATACTGGATATTAAAGTGTCTGAATTG
326 AATATGTGAAGAGGGGTTGTGAGGCTTACCTTGCATATATACTGGATATTAAAGTGTCTGAATTG
21101510 AAGATTGAATCAGTACCAATGGTTAGTGAATATTTACATGTGTTTCCAAAAGAGTTACCCGGGTT
391 AAGATTGAATCAGTACCAATGGTTAGTGAATATTTACATGTGTTTCCAAAAGAGTTACCCGGGTT
21101575 GCCACCTATTAGAGAGGTTGAG
456 GCCACCTATTAGAGAGGTTGAG
21101597 TTTGCTATTG
Statistics
Matches: 476, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
484 476 1.00
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (484 bp):
TTGTCTAGTAAGAGTTTACCTGTCAAGTCCACTGAATTCGTGGTTAAGGTATCGAACCCTTTAGG
TCAGTATGTCTTAATTAATAAAGTTTGCAAGAATTGTACTTTAATGACTTGGGGTTACAGTTTTT
TGGCCGATTTGATGCTTTTACCGTTAGATGAATTTGATGTGATTTTGGATATGGGTTGGCTGACT
CTGTATGATGCGGTTGTAAACTGCAGACGAAAGCTTATTGTATTGAAATGTCAGAACGGTGAGAC
TCTTCGTATTGAATCTGATGATTCGAGTGGGTTGCCTATTGTGATATCGGCTACGTTAGCACATA
AATATGTGAAGAGGGGTTGTGAGGCTTACCTTGCATATATACTGGATATTAAAGTGTCTGAATTG
AAGATTGAATCAGTACCAATGGTTAGTGAATATTTACATGTGTTTCCAAAAGAGTTACCCGGGTT
GCCACCTATTAGAGAGGTTGAGGTTGAGT
Found at i:21105283 original size:21 final size:22
Alignment explanation
Indices: 21105243--21105284 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
21105233 TAATTTCTCC
* *
21105243 ATAGAATTTTGGATTGAATTGA
1 ATAGAATTATGGATTAAATTGA
21105265 ATAGAATTAT-GATTAAATTG
1 ATAGAATTATGGATTAAATTG
21105285 GTTAAATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.40
Consensus pattern (22 bp):
ATAGAATTATGGATTAAATTGA
Found at i:21106722 original size:31 final size:31
Alignment explanation
Indices: 21106686--21106778 Score: 186
Period size: 31 Copynumber: 3.0 Consensus size: 31
21106676 AGATAATTTT
21106686 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
21106717 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
21106748 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
21106779 TAATTTGTCT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:21107089 original size:3 final size:3
Alignment explanation
Indices: 21107081--21107109 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
21107071 ATCTATCCTT
21107081 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
21107110 TAACTAATTT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:21107336 original size:13 final size:13
Alignment explanation
Indices: 21107320--21107351 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
21107310 AAGAATAAGC
21107320 AAAAAGCGCAAAA
1 AAAAAGCGCAAAA
*
21107333 AAAAACCGCAAAA
1 AAAAAGCGCAAAA
21107346 AAAAAG
1 AAAAAG
21107352 TTGCCTACCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.72, C:0.16, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAGCGCAAAA
Found at i:21112696 original size:3 final size:3
Alignment explanation
Indices: 21112688--21112752 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
21112678 ATCTATCCTT
21112688 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21112736 TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
21112753 TAACTAATTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:21113271 original size:38 final size:36
Alignment explanation
Indices: 21113229--21113318 Score: 121
Period size: 38 Copynumber: 2.5 Consensus size: 36
21113219 TTCTATATGC
* *
21113229 ATATGTGTATAAAAAATAGTTTAATATAAATTGTAT
1 ATATGTGTATAAAAAATAGTTTAATACAAATTATAT
*
21113265 ATATATGTATAATAAAAATAGTTTAATACAAATTATAT
1 ATATGTGTAT-A-AAAAATAGTTTAATACAAATTATAT
21113303 ATA--TGTATAAAAAATA
1 ATATGTGTATAAAAAATA
21113319 TTATGTAAGA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
34 7 0.14
35 1 0.02
36 14 0.29
37 1 0.02
38 26 0.53
ACGTcount: A:0.52, C:0.01, G:0.08, T:0.39
Consensus pattern (36 bp):
ATATGTGTATAAAAAATAGTTTAATACAAATTATAT
Found at i:21113275 original size:36 final size:34
Alignment explanation
Indices: 21113229--21113318 Score: 126
Period size: 36 Copynumber: 2.5 Consensus size: 34
21113219 TTCTATATGC
* *
21113229 ATATGTGTATAAAAAATAGTTTAATATAAATTGTAT
1 ATATATGTATAAAAAATAGTTTAATACAAA-T-TAT
21113265 ATATATGTATAATAAAAATAGTTTAATACAAATTAT
1 ATATATGTAT-A-AAAAATAGTTTAATACAAATTAT
21113301 ATATATGTATAAAAAATA
1 ATATATGTATAAAAAATA
21113319 TTATGTAAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
34 7 0.14
35 1 0.02
36 22 0.44
37 2 0.04
38 18 0.36
ACGTcount: A:0.52, C:0.01, G:0.08, T:0.39
Consensus pattern (34 bp):
ATATATGTATAAAAAATAGTTTAATACAAATTAT
Found at i:21114313 original size:19 final size:18
Alignment explanation
Indices: 21114284--21114320 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
21114274 AAGAAAGAAA
*
21114284 GAAATAAAATAAATAAAT
1 GAAATAAAATAAAAAAAT
21114302 GAAATCAAAATAAAAAAAT
1 GAAAT-AAAATAAAAAAAT
21114321 CGGAGAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (18 bp):
GAAATAAAATAAAAAAAT
Found at i:21117959 original size:7 final size:7
Alignment explanation
Indices: 21117943--21117975 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
21117933 TGGCCTCTCC
21117943 TTTTTC-
1 TTTTTCT
21117949 TTTTTCT
1 TTTTTCT
21117956 TTTTTCT
1 TTTTTCT
21117963 TTTTTCT
1 TTTTTCT
21117970 TTTTTC
1 TTTTTC
21117976 ATCATTTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTCT
Found at i:21118009 original size:17 final size:17
Alignment explanation
Indices: 21117988--21118033 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
21117978 CATTTTCAAT
*
21117988 TTTTTTATTTTCATTTTA
1 TTTTTGATTTT-ATTTTA
*
21118006 TTTTTGATTTTTTTTTA
1 TTTTTGATTTTATTTTA
21118023 TTTTTGATTTT
1 TTTTTGATTTT
21118034 TTTATTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 16 0.62
18 10 0.38
ACGTcount: A:0.13, C:0.02, G:0.04, T:0.80
Consensus pattern (17 bp):
TTTTTGATTTTATTTTA
Found at i:21118034 original size:17 final size:17
Alignment explanation
Indices: 21118001--21118036 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
21117991 TTTATTTTCA
21118001 TTTTATTTTTGATTTTT
1 TTTTATTTTTGATTTTT
21118018 TTTTATTTTTGATTTTT
1 TTTTATTTTTGATTTTT
21118035 TT
1 TT
21118037 ATTAAATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.00, G:0.06, T:0.83
Consensus pattern (17 bp):
TTTTATTTTTGATTTTT
Found at i:21122582 original size:37 final size:35
Alignment explanation
Indices: 21122541--21122630 Score: 128
Period size: 37 Copynumber: 2.5 Consensus size: 35
21122531 TTATATATGC
* * *
21122541 ATATGTGTAT-AAAAAATAGTTTAATATAAATTGT
1 ATATATGTATAAAAAAATAGTTTAATACAAATTAT
21122575 ATTATATGTATAATAAAAATAGTTTAATACAAATTAT
1 A-TATATGTATAA-AAAAATAGTTTAATACAAATTAT
21122612 ATATATGTATAAAAAAATA
1 ATATATGTATAAAAAAATA
21122631 TTATGTAAGA
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
34 1 0.02
35 15 0.30
36 12 0.24
37 22 0.44
ACGTcount: A:0.52, C:0.01, G:0.08, T:0.39
Consensus pattern (35 bp):
ATATATGTATAAAAAAATAGTTTAATACAAATTAT
Found at i:21124362 original size:25 final size:25
Alignment explanation
Indices: 21124306--21124397 Score: 87
Period size: 25 Copynumber: 3.7 Consensus size: 25
21124296 AGGGTTACCG
* * *
21124306 ATTCTAGCTCTTATGAGCTTACAGAT
1 ATTC-AGCTCGTATGAGCTTACCGTT
*
21124332 ACTCAGCTCGTATGAGCTTACCGTT
1 ATTCAGCTCGTATGAGCTTACCGTT
* * *
21124357 GTTCAGCTCGGAAGAGCTTACCGTT
1 ATTCAGCTCGTATGAGCTTACCGTT
* *
21124382 TTTC-TCTCGTATGAGC
1 ATTCAGCTCGTATGAGC
21124398 ATACAGGTAC
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
24 9 0.17
25 42 0.78
26 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.35
Consensus pattern (25 bp):
ATTCAGCTCGTATGAGCTTACCGTT
Found at i:21129628 original size:10 final size:10
Alignment explanation
Indices: 21129613--21129640 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
21129603 TTTCTCAAAA
21129613 AATGGAAATG
1 AATGGAAATG
21129623 AATGGAAATG
1 AATGGAAATG
21129633 AATGGAAA
1 AATGGAAA
21129641 CGTAAGTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.29, T:0.18
Consensus pattern (10 bp):
AATGGAAATG
Found at i:21129675 original size:2 final size:2
Alignment explanation
Indices: 21129668--21129697 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21129658 CTATTTGCAA
21129668 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
21129698 GAATTACTCA
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:21131670 original size:144 final size:142
Alignment explanation
Indices: 21131393--21131683 Score: 431
Period size: 142 Copynumber: 2.0 Consensus size: 142
21131383 CGCGAAAGAG
* * * *
21131393 TTTGTGCCTAGTGCTAGTCGGATAAACCGATGAATGTGTGCTCAGCACTAGTCAGATAAACTGAC
1 TTTGTGCCCAGCGCTAGTCGGATAAACCGAAGAATGTGTGCTCAACACTAGTCAGATAAACTGAC
* * *
21131458 AGAAGTTGCGCCCAGCTAGTTGGATAAACCGACGAAATAAATAGTGAGCCCAGCTCTAGTTGGAT
66 AGAAGTTGCACCCAGCTAGTCGGATAAACCGACGAAATAAATAGTGAGCCCAACTCTAGTTGGAT
21131523 AAACCAACAATA
131 AAACCAACAATA
* * * * *
21131535 TTTGTGCCCAGCGCTAGTTGTATAAACTGAAGAATGTGTGC-CTAACACTAGTTAGATAAATTGA
1 TTTGTGCCCAGCGCTAGTCGGATAAACCGAAGAATGTGTGCTC-AACACTAGTCAGATAAACTGA
21131599 CAGAAGTTGCACCCAGTGCTAGTCGGATAAACCGACGAAATAAATAGTGAGCCCAACTCTAGTTG
65 CAGAAGTTGCACCCA--GCTAGTCGGATAAACCGACGAAATAAATAGTGAGCCCAACTCTAGTTG
*
21131664 GATAAACCAACGATA
128 GATAAACCAACAATA
21131679 TTTGT
1 TTTGT
21131684 AATTATTTAT
Statistics
Matches: 133, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
141 1 0.01
142 67 0.50
144 65 0.49
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (142 bp):
TTTGTGCCCAGCGCTAGTCGGATAAACCGAAGAATGTGTGCTCAACACTAGTCAGATAAACTGAC
AGAAGTTGCACCCAGCTAGTCGGATAAACCGACGAAATAAATAGTGAGCCCAACTCTAGTTGGAT
AAACCAACAATA
Found at i:21137920 original size:3 final size:3
Alignment explanation
Indices: 21137907--21137964 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
21137897 CAATCCAGCT
*
21137907 GAA GGA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
21137955 GAA GAA GAA G
1 GAA GAA GAA G
21137965 GAGGAGGAGG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:21138105 original size:25 final size:25
Alignment explanation
Indices: 21138049--21138109 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
21138039 ATGGATTATC
*
21138049 TTGTTATTATGTTTTTTTTGTATAAT
1 TTGTTATTAT-TTTTTGTTGTATAAT
*
21138075 TT-TTATTATTTTTTGTTGT-TAGT
1 TTGTTATTATTTTTTGTTGTATAAT
21138098 TTAGTTATTATT
1 TT-GTTATTATT
21138110 GTTAGTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 5 0.16
24 9 0.29
25 15 0.48
26 2 0.06
ACGTcount: A:0.18, C:0.00, G:0.11, T:0.70
Consensus pattern (25 bp):
TTGTTATTATTTTTTGTTGTATAAT
Found at i:21138395 original size:76 final size:77
Alignment explanation
Indices: 21138190--21138401 Score: 216
Period size: 76 Copynumber: 2.7 Consensus size: 77
21138180 GTTTAGTTAT
* *
21138190 TAATAATTATTGTTACTTAGTATTATTATTAGTAAAAAACTAATATTATTATTATGGTTAGTTAT
1 TAATTATTATTGTTAGTTAGTATTATTATTAGTAAAAAAC---TATTATTA-T-T-GTTAGTTAT
21138255 TAGGATTAGTAAAAACCC
60 TAGGATTAGTAAAAACCC
* * *** * * ***
21138273 TAATTATTATT-TTAGTTAGTATGATTGTTAGTTTTTACATTA-TATTATTGTTAGTTATTATTT
1 TAATTATTATTGTTAGTTAGTATTATTATTAG-TAAAAAACTATTATTATTGTTAGTTATTAGGA
21138336 TTAGT-AAAACCC
65 TTAGTAAAAACCC
21138348 TAATTATTATTGTTAGTTAGTATTATT-TTGAGTAAAAAACTATTATTATTGTTA
1 TAATTATTATTGTTAGTTAGTATTATTATT-AGTAAAAAACTATTATTATTGTTA
21138402 TTGTGTTAGT
Statistics
Matches: 107, Mismatches: 18, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
75 25 0.23
76 43 0.40
77 1 0.01
78 1 0.01
79 5 0.05
80 2 0.02
82 17 0.16
83 13 0.12
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.50
Consensus pattern (77 bp):
TAATTATTATTGTTAGTTAGTATTATTATTAGTAAAAAACTATTATTATTGTTAGTTATTAGGAT
TAGTAAAAACCC
Found at i:21142580 original size:58 final size:58
Alignment explanation
Indices: 21142489--21142599 Score: 195
Period size: 58 Copynumber: 1.9 Consensus size: 58
21142479 TGATAGCTAC
* *
21142489 ATTGAGTCTAATTAAATCTAGAGTCGAGCTGGATAGGCCCTAAATAGGAGCAAGCCCT
1 ATTGAGTCGAATTAAATCTAGAGTCGAGCTGGATAGGCCCTAAACAGGAGCAAGCCCT
*
21142547 ATTGAGTCGAATTAAATCTAGAGTCGAGTTGGATAGGCCCTAAACAGGAGCAA
1 ATTGAGTCGAATTAAATCTAGAGTCGAGCTGGATAGGCCCTAAACAGGAGCAA
21142600 ACTCTCATAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.23
Consensus pattern (58 bp):
ATTGAGTCGAATTAAATCTAGAGTCGAGCTGGATAGGCCCTAAACAGGAGCAAGCCCT
Found at i:21154637 original size:32 final size:32
Alignment explanation
Indices: 21154586--21154782 Score: 200
Period size: 32 Copynumber: 6.2 Consensus size: 32
21154576 GAATGGCTAC
* * ** *
21154586 AAGCCATAAGT-ACAGTAATATGATTAGCATA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* **
21154617 AAGCCATCAGTAGTAGTAATATGATCAACACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* * *
21154649 CAGCCATCAGTAATAGTAGTATGATCGGTACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* * *
21154681 AAGCCCTCAATAGTAGTAATATGATCGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
*
21154713 CAA-CCATCAGTAATGGTAATATGATCGGCACA
1 -AAGCCATCAGTAATAGTAATATGATCGGCACA
* * * *
21154745 CAGCCATCAGTAATGGTAATATGATTGGTACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
21154777 AAGCCA
1 AAGCCA
21154783 ACAATAGCAT
Statistics
Matches: 137, Mismatches: 26, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
31 11 0.08
32 124 0.91
33 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (32 bp):
AAGCCATCAGTAATAGTAATATGATCGGCACA
Found at i:21154820 original size:26 final size:26
Alignment explanation
Indices: 21154791--21154844 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
21154781 CAACAATAGC
21154791 ATCGCAGCAAAGCTGCCAGCAACAGT
1 ATCGCAGCAAAGCTGCCAGCAACAGT
* *
21154817 ATCGTAGCAAAGCTGCCAGTAACAGT
1 ATCGCAGCAAAGCTGCCAGCAACAGT
21154843 AT
1 AT
21154845 ATGTGGCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (26 bp):
ATCGCAGCAAAGCTGCCAGCAACAGT
Found at i:21154863 original size:27 final size:26
Alignment explanation
Indices: 21154797--21154896 Score: 94
Period size: 27 Copynumber: 3.8 Consensus size: 26
21154787 TAGCATCGCA
** * * *
21154797 GCAAAGCTGCCAGCAACAGTATCGTA
1 GCAAAGCCACCAGTAACAGTATTGTG
**
21154823 GCAAAGCTGCCAGTAACAGTATATGTG
1 GCAAAGCCACCAGTAACAGTAT-TGTG
* *
21154850 GCCAAGCCATCAGTAACAGTGATTGTG
1 GCAAAGCCACCAGTAACAGT-ATTGTG
21154877 GCAAAGCCACCAGT-ACAGTA
1 GCAAAGCCACCAGTAACAGTA
21154897 CTTCCTCCAT
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
25 1 0.02
26 26 0.41
27 34 0.54
28 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (26 bp):
GCAAAGCCACCAGTAACAGTATTGTG
Found at i:21154992 original size:24 final size:24
Alignment explanation
Indices: 21154960--21155093 Score: 151
Period size: 24 Copynumber: 5.6 Consensus size: 24
21154950 CTATGCACGG
**
21154960 AATCAGTCATACAAATCACAGACA
1 AATCAGTCATTTAAATCACAGACA
*
21154984 AATCAGTCATTTAAATCACAGATA
1 AATCAGTCATTTAAATCACAGACA
*
21155008 AATAAGTCATTTAAATCACAGACA
1 AATCAGTCATTTAAATCACAGACA
* * * *
21155032 AATCAGTCATTTACATCTCGGAAA
1 AATCAGTCATTTAAATCACAGACA
* * * *
21155056 AATCATTCATTTACATTACAGGCA
1 AATCAGTCATTTAAATCACAGACA
*
21155080 AATCAATCATTTAA
1 AATCAGTCATTTAA
21155094 CCTCGAGGGG
Statistics
Matches: 92, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 92 1.00
ACGTcount: A:0.45, C:0.19, G:0.08, T:0.28
Consensus pattern (24 bp):
AATCAGTCATTTAAATCACAGACA
Found at i:21155189 original size:26 final size:26
Alignment explanation
Indices: 21155111--21155336 Score: 281
Period size: 27 Copynumber: 8.5 Consensus size: 26
21155101 GGGTAAAATA
*
21155111 GTCATTTTACCCTACAAGGGCATTATG
1 GTCATTTTACCCTAC-AGGGCATTACG
* *
21155138 GTCATTTTACCTTATAGTGGCATTACG
1 GTCATTTTACCCTACAG-GGCATTACG
* *
21155165 ATAATTTTACCCTACAGGGCATTACG
1 GTCATTTTACCCTACAGGGCATTACG
21155191 GTCATTTTACCCTACAGGGCATTACG
1 GTCATTTTACCCTACAGGGCATTACG
*
21155217 GTCATTTTACCCTACAGGGGCGTTACG
1 GTCATTTTACCCTACA-GGGCATTACG
* * **
21155244 GTCATTTTACCCTATAGGGGCGTTATT
1 GTCATTTTACCCTACA-GGGCATTACG
* *
21155271 ATCATTTTACCCTACAGGGGCATTATG
1 GTCATTTTACCCTACA-GGGCATTACG
21155298 GTCATTTTACCCTACAGAGGCATTACG
1 GTCATTTTACCCTACAG-GGCATTACG
*
21155325 ATCATTTTACCC
1 GTCATTTTACCC
21155337 GTCGAAGGTA
Statistics
Matches: 176, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
26 52 0.30
27 124 0.70
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (26 bp):
GTCATTTTACCCTACAGGGCATTACG
Found at i:21155381 original size:26 final size:27
Alignment explanation
Indices: 21155328--21155387 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 27
21155318 CATTACGATC
*
21155328 ATTTTACCCGTCGAAGGTATTTCGGTA
1 ATTTTACCCGTCGAAGGTATTTCAGTA
* *
21155355 ATTTTACCCTTCG-AGGTATTTTAGTA
1 ATTTTACCCGTCGAAGGTATTTCAGTA
21155381 ATTTTAC
1 ATTTTAC
21155388 AACCTTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 18 0.60
27 12 0.40
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (27 bp):
ATTTTACCCGTCGAAGGTATTTCAGTA
Found at i:21155833 original size:53 final size:53
Alignment explanation
Indices: 21155748--21155853 Score: 176
Period size: 53 Copynumber: 2.0 Consensus size: 53
21155738 TGGTCCCAAA
* *
21155748 CGCCATATTTCGGCTTTTACCGTTCTACAGTTACATTGGGGAGTTTACACACC
1 CGCCATATTTCAGCTTTTACCGTTCTACAGTTACAGTGGGGAGTTTACACACC
* *
21155801 CGCCGTATTTCAGCTTTTGCCGTTCTACAGTTACAGTGGGGAGTTTACACACC
1 CGCCATATTTCAGCTTTTACCGTTCTACAGTTACAGTGGGGAGTTTACACACC
21155854 TGATGCAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.33
Consensus pattern (53 bp):
CGCCATATTTCAGCTTTTACCGTTCTACAGTTACAGTGGGGAGTTTACACACC
Found at i:21160616 original size:31 final size:31
Alignment explanation
Indices: 21160556--21160616 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
21160546 CCTGTCATCC
*
21160556 TAGATTTCCCAACAACGATGACCTGCCACCT
1 TAGATTTCCCAACAACGATGACCTACCACCT
* *
21160587 TAGATTTCCCGAA-AATGATGGCCTACCACC
1 TAGATTTCCC-AACAACGATGACCTACCACC
21160617 CCGAGTAGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.30, C:0.33, G:0.15, T:0.23
Consensus pattern (31 bp):
TAGATTTCCCAACAACGATGACCTACCACCT
Found at i:21164187 original size:15 final size:15
Alignment explanation
Indices: 21164167--21164198 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
21164157 CATTTCACTA
*
21164167 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
21164182 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
21164197 TT
1 TT
21164199 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:21173663 original size:19 final size:19
Alignment explanation
Indices: 21173636--21173674 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
21173626 CCCTGTTTTA
21173636 CCCTCTGCCTCTTCTGTTC
1 CCCTCTGCCTCTTCTGTTC
*
21173655 CCCTTTGCCTCTTCTGTTC
1 CCCTCTGCCTCTTCTGTTC
21173674 C
1 C
21173675 TTCCTTCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.00, C:0.46, G:0.10, T:0.44
Consensus pattern (19 bp):
CCCTCTGCCTCTTCTGTTC
Found at i:21176815 original size:16 final size:16
Alignment explanation
Indices: 21176794--21176835 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
21176784 TTATTAAATT
*
21176794 ATATATTTTAATTATA
1 ATATATTTTAATAATA
21176810 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
21176825 AT-TATGTTTAA
1 ATATAT-TTTAA
21176836 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:21176820 original size:15 final size:15
Alignment explanation
Indices: 21176785--21176826 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
21176775 TTAAGAATTT
*
21176785 TATTAAATTAT-ATA
1 TATTTAATTATAATA
21176799 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
21176813 TATTTAATAATAAT
1 TATTTAATTATAAT
21176827 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:21177061 original size:45 final size:44
Alignment explanation
Indices: 21176980--21177070 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
21176970 ATCTCTATTC
*
21176980 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
*** *
21177024 CATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCCATTA
1 CATTCAACCAAACACAAGA-TTACTATTACACCTCTATTCCATTA
21177069 CA
1 CA
21177071 CCTCTAATCC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 16 0.39
45 25 0.61
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
Found at i:21177070 original size:16 final size:16
Alignment explanation
Indices: 21177049--21177081 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
21177039 TTGATTTGCT
*
21177049 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
21177065 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
21177081 A
1 A
21177082 AAACAGCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:21186847 original size:57 final size:55
Alignment explanation
Indices: 21186726--21186854 Score: 134
Period size: 57 Copynumber: 2.3 Consensus size: 55
21186716 TGATTATCTT
* * * * ** *
21186726 AATATTAAATTTAATTTAATGTTTATCTATAAATATTATATTATTTTAATAAGATTT
1 AATATTAAATTTAATCTAATATTTATCAAAAAATATTATATTAAATTAAT-A-ATTA
21186783 AATATTAAATTTAATCTAATATTTATCAACAAAATATTATATTAAATTAAT-ATTA
1 AATATTAAATTTAATCTAATATTTATCAA-AAAATATTATATTAAATTAATAATTA
*
21186838 AAGTAATTAAGTTTAAT
1 AA-T-ATTAAATTTAAT
21186855 TATAGTTGAC
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
55 5 0.08
56 1 0.02
57 37 0.61
58 18 0.30
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (55 bp):
AATATTAAATTTAATCTAATATTTATCAAAAAATATTATATTAAATTAATAATTA
Found at i:21193194 original size:21 final size:21
Alignment explanation
Indices: 21193144--21193196 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
21193134 TTTCTAAAAC
*
21193144 TTTTTATAGTTCTTAATAGTT
1 TTTTTATAATTCTTAATAGTT
** *
21193165 TTTAAATAATTCTTTAT-GTTT
1 TTTTTATAATTCTTAATAG-TT
21193186 TTTTTATAATT
1 TTTTTATAATT
21193197 TTTTGAAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.64
Consensus pattern (21 bp):
TTTTTATAATTCTTAATAGTT
Found at i:21193292 original size:13 final size:13
Alignment explanation
Indices: 21193274--21193298 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21193264 GGTTTTTTTT
21193274 AAAAATATTTATG
1 AAAAATATTTATG
21193287 AAAAATATTTAT
1 AAAAATATTTAT
21193299 TTTTGATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
AAAAATATTTATG
Found at i:21208030 original size:31 final size:28
Alignment explanation
Indices: 21207964--21208030 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 28
21207954 TAAAAATTTG
*
21207964 AAATTTAATTTTTATTTTTTTATTTTTT
1 AAATTTAATTTTTATTTTTTTACTTTTT
**
21207992 ATTTTTAATATTTAATATTTTTTTACTTTTT
1 AAATTTAAT-TTT--TATTTTTTTACTTTTT
21208023 AAATTTAA
1 AAATTTAA
21208031 AAAAATAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 7 0.23
29 3 0.10
31 21 0.68
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (28 bp):
AAATTTAATTTTTATTTTTTTACTTTTT
Found at i:21209662 original size:13 final size:13
Alignment explanation
Indices: 21209621--21209686 Score: 63
Period size: 13 Copynumber: 5.5 Consensus size: 13
21209611 AATTTTGAAT
21209621 TATTTAGTGATAA
1 TATTTAGTGATAA
* *
21209634 TATCTA-T-A-AT
1 TATTTAGTGATAA
21209644 TATTTAGTGATAA
1 TATTTAGTGATAA
21209657 TATTTAG-GAT--
1 TATTTAGTGATAA
*
21209667 TATTTAGTGATAG
1 TATTTAGTGATAA
21209680 TATTTAG
1 TATTTAG
21209687 GAAAAATCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
10 13 0.30
11 5 0.12
12 5 0.12
13 20 0.47
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:21209683 original size:23 final size:23
Alignment explanation
Indices: 21209619--21209688 Score: 104
Period size: 23 Copynumber: 3.0 Consensus size: 23
21209609 TAAATTTTGA
* **
21209619 ATTATTTAGTGATAATATCTATA
1 ATTATTTAGTGATAATATTTAGG
21209642 ATTATTTAGTGATAATATTTAGG
1 ATTATTTAGTGATAATATTTAGG
*
21209665 ATTATTTAGTGATAGTATTTAGG
1 ATTATTTAGTGATAATATTTAGG
21209688 A
1 A
21209689 AAAATCTAGC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.36, C:0.01, G:0.16, T:0.47
Consensus pattern (23 bp):
ATTATTTAGTGATAATATTTAGG
Found at i:21214449 original size:2 final size:2
Alignment explanation
Indices: 21214442--21214495 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
21214432 AAAGAAATAT
* *
21214442 AC AC AC AC AC AA AG AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
21214484 AC AC AC AC AC AC
1 AC AC AC AC AC AC
21214496 GTATGCATCT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.52, C:0.46, G:0.02, T:0.00
Consensus pattern (2 bp):
AC
Found at i:21216106 original size:18 final size:17
Alignment explanation
Indices: 21216077--21216131 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
21216067 TTTTAAAATT
*
21216077 AAAAATATAATTTTTAA
1 AAAAATAAAATTTTTAA
*
21216094 AAAAATTAAAATTATTGAA
1 AAAAA-TAAAATT-TTTAA
* *
21216113 AAACATAAAATTTATAA
1 AAAAATAAAATTTTTAA
21216130 AA
1 AA
21216132 TATATTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
17 10 0.32
18 13 0.42
19 8 0.26
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (17 bp):
AAAAATAAAATTTTTAA
Found at i:21228631 original size:13 final size:13
Alignment explanation
Indices: 21228615--21228641 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
21228605 AAAAAAAAAG
21228615 ATGAAAAATGAAA
1 ATGAAAAATGAAA
21228628 ATGAAAAATGAAA
1 ATGAAAAATGAAA
21228641 A
1 A
21228642 AATGAAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
ATGAAAAATGAAA
Found at i:21228644 original size:8 final size:7
Alignment explanation
Indices: 21228610--21228650 Score: 57
Period size: 7 Copynumber: 5.7 Consensus size: 7
21228600 TTGCAAAAAA
21228610 AAAAGATG
1 AAAA-ATG
21228618 AAAAATG
1 AAAAATG
21228625 -AAAATG
1 AAAAATG
21228631 AAAAATG
1 AAAAATG
21228638 AAAAAATG
1 -AAAAATG
21228646 AAAAA
1 AAAAA
21228651 GTAAAAATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.19
7 14 0.45
8 11 0.35
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:21228657 original size:15 final size:15
Alignment explanation
Indices: 21228609--21228650 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
21228599 ATTGCAAAAA
21228609 AAAAAGATGAAAAATG
1 AAAAA-ATGAAAAATG
21228625 --AAAATGAAAAATG
1 AAAAAATGAAAAATG
21228638 AAAAAATGAAAAA
1 AAAAAATGAAAAA
21228651 GTAAAAATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 10 0.42
14 3 0.12
15 11 0.46
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (15 bp):
AAAAAATGAAAAATG
Found at i:21240857 original size:3 final size:3
Alignment explanation
Indices: 21240849--21240881 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
21240839 TTATAAGTGT
21240849 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
21240882 ATAAACTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:21243180 original size:41 final size:39
Alignment explanation
Indices: 21243116--21243195 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 39
21243106 GTATATGTTG
21243116 ATTGTTGAATTGTCTTAGCATCTTATTACTCGAGTCCAC
1 ATTGTTGAATTGTCTTAGCATCTTATTACTCGAGTCCAC
* *
21243155 ATTGTTGAACTCTGTCTTAGTATCTTATTACTCGGGTCCAC
1 ATTGTTGAA-T-TGTCTTAGCATCTTATTACTCGAGTCCAC
21243196 CAACCGGACC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 9 0.24
40 1 0.03
41 27 0.73
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.41
Consensus pattern (39 bp):
ATTGTTGAATTGTCTTAGCATCTTATTACTCGAGTCCAC
Found at i:21243271 original size:14 final size:13
Alignment explanation
Indices: 21243235--21243280 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
21243225 CATCCAGCCT
21243235 AAAACCAAAAATA
1 AAAACCAAAAATA
*
21243248 AATAAACAAAACATA
1 AA-AACCAAAA-ATA
21243263 AAAACCAAAAAATA
1 AAAACC-AAAAATA
21243277 AAAA
1 AAAA
21243281 ATCCAAGTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 2 0.07
14 17 0.61
15 9 0.32
ACGTcount: A:0.78, C:0.13, G:0.00, T:0.09
Consensus pattern (13 bp):
AAAACCAAAAATA
Found at i:21248474 original size:38 final size:38
Alignment explanation
Indices: 21248423--21248496 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
21248413 TATCGTTGCC
21248423 AAGAAGTGTCATTGTCACCCCAATCATCTAGCTTGTGT
1 AAGAAGTGTCATTGTCACCCCAATCATCTAGCTTGTGT
*
21248461 AAGAAGTGTCATTGTCACCCCTATCATCTAGCTTGT
1 AAGAAGTGTCATTGTCACCCCAATCATCTAGCTTGT
21248497 ATTATTCTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (38 bp):
AAGAAGTGTCATTGTCACCCCAATCATCTAGCTTGTGT
Found at i:21253033 original size:251 final size:251
Alignment explanation
Indices: 21252585--21253067 Score: 727
Period size: 251 Copynumber: 1.9 Consensus size: 251
21252575 ACATTGGTAC
* * *
21252585 GAGGTATGTTGAGGCTCGAAGAATAAAGTTTATTAAAATGAAACAGGGTGATAGTATAGTGGTCG
1 GAGGAATGTTGAGGCTCGAAGAATAAAGTTTATTAAAATGAAACAAGGTGATAGTACAGTGGTCG
* * *
21252650 AGTATAAGGTTGAGTTTCTGAGGTTGAGCTATTATGCTTCGAATATGTTGTCTACTGAGTAGGAT
66 AGTATAAGGTTGAGTTTCTAAGGTTGAGCTATTATGCTTCGAATATGGTGTCTACTGAGCAGGAT
* * * *
21252715 AGGTGTGTACAACTCGAGGATGGGCTAAGGTATGATTTAATGGTTCAGGTTACACCACATTAGGA
131 AAGTGTGTACAACTCAAGGATGAGCTAAGGTATGATTTAAAGGTTCAGGTTACACCACATTAGGA
21252780 GAGGGTGTTTAAGATTCTAGTTGAGAAGGCCAAGATTATAGTTGAGATTCTAGTAT
196 GAGGGTGTTTAAGATTCTAGTTGAGAAGGCCAAGATTATAGTTGAGATTCTAGTAT
* * * **
21252836 GAGGAATGTTGAGGCTCGTAGAATAGAGTTTATTTAGCTGAAACAAGGTGATAAG-ACAGTGGTC
1 GAGGAATGTTGAGGCTCGAAGAATAAAGTTTATTAAAATGAAACAAGGTGAT-AGTACAGTGGTC
*
21252900 GAGTATAAGGTTGAGTTTCTAAGGTTGAG-TCGTTATGCTTCGAATATGGTGTCTACTGAGCAGG
65 GAGTATAAGGTTGAGTTTCTAAGGTTGAGCT-ATTATGCTTCGAATATGGTGTCTACTGAGCAGG
* * * * *
21252964 ATAAGTGTGTATAGCTCAAGGATGAGCTGAGGTATGATTTAAAGGTTCAGGTTGCACCATATTAG
129 ATAAGTGTGTACAACTCAAGGATGAGCTAAGGTATGATTTAAAGGTTCAGGTTACACCACATTAG
* *
21253029 GAGAGGGTGTTTGAGATTCTAGTTGAGAATGCCAAGATT
194 GAGAGGGTGTTTAAGATTCTAGTTGAGAAGGCCAAGATT
21253068 GTAGAGGAGG
Statistics
Matches: 207, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
250 1 0.00
251 204 0.99
252 2 0.01
ACGTcount: A:0.29, C:0.10, G:0.30, T:0.31
Consensus pattern (251 bp):
GAGGAATGTTGAGGCTCGAAGAATAAAGTTTATTAAAATGAAACAAGGTGATAGTACAGTGGTCG
AGTATAAGGTTGAGTTTCTAAGGTTGAGCTATTATGCTTCGAATATGGTGTCTACTGAGCAGGAT
AAGTGTGTACAACTCAAGGATGAGCTAAGGTATGATTTAAAGGTTCAGGTTACACCACATTAGGA
GAGGGTGTTTAAGATTCTAGTTGAGAAGGCCAAGATTATAGTTGAGATTCTAGTAT
Found at i:21255244 original size:13 final size:14
Alignment explanation
Indices: 21255215--21255249 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
21255205 TGGACATATG
*
21255215 GAAATGGATGTTTT
1 GAAATGGATGTTAT
21255229 GAAATGG-TGTTAT
1 GAAATGGATGTTAT
21255242 GAAATGGA
1 GAAATGGA
21255250 CATTGAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (14 bp):
GAAATGGATGTTAT
Done.