Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008826.1 Hibiscus syriacus cultivar Beakdansim tig00112000_pilon, 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: 3884024
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 18
Found at i:2615482 original size:26 final size:28
Alignment explanation
Indices: 2615445--2615520 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 28
2615435 AAGAAGAAAA
2615445 GAAAAT-G-AGAAAAAAGAAAAATGATG
1 GAAAATAGAAGAAAAAAGAAAAATGATG
* *
2615471 GAAAA-A-ACG--AAAAGAAAAA-AATG
1 GAAAATAGAAGAAAAAAGAAAAATGATG
2615494 GAAAATAGAAGAAAAAATGAAAAATGA
1 GAAAATAGAAGAAAAAA-GAAAAATGA
2615521 AAAAAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
23 8 0.21
24 11 0.29
25 2 0.05
26 6 0.16
27 4 0.11
28 6 0.16
29 1 0.03
ACGTcount: A:0.70, C:0.01, G:0.20, T:0.09
Consensus pattern (28 bp):
GAAAATAGAAGAAAAAAGAAAAATGATG
Found at i:2615499 original size:33 final size:32
Alignment explanation
Indices: 2615435--2615531 Score: 92
Period size: 33 Copynumber: 2.9 Consensus size: 32
2615425 GAAGAAGAAA
2615435 AAGAAGAAAAGAAAATGAGAAAAAAGAAAAAT-G
1 AAGAA-AAAAGAAAATGA-AAAAAAGAAAAATAG
* *
2615468 ATGGAAAAAACGAAAA-GAAAAAAATGGAAAATAG
1 A-AGAAAAAA-GAAAATGAAAAAAA-GAAAAATAG
2615502 AAGAAAAAATGAAAAATGAAAAAAA-AAAAA
1 AAGAAAAAA-G-AAAATGAAAAAAAGAAAAA
2615532 GAAAAATGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
32 6 0.11
33 25 0.47
34 14 0.26
35 8 0.15
ACGTcount: A:0.74, C:0.01, G:0.18, T:0.07
Consensus pattern (32 bp):
AAGAAAAAAGAAAATGAAAAAAAGAAAAATAG
Found at i:2615529 original size:20 final size:20
Alignment explanation
Indices: 2615473--2615549 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
2615463 AAATGATGGA
*
2615473 AAAAACGAAAAGAAAAAAATG
1 AAAAATGAAAA-AAAAAAATG
* * *
2615494 GAAAAT-AGAAGAAAAAATG
1 AAAAATGAAAAAAAAAAATG
*
2615513 AAAAATGAAAAAAAAAAAAG
1 AAAAATGAAAAAAAAAAATG
2615533 AAAAATGAAAAAAAAAA
1 AAAAATGAAAAAAAAAA
2615550 GAGAAATAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
19 13 0.28
20 30 0.64
21 4 0.09
ACGTcount: A:0.79, C:0.01, G:0.13, T:0.06
Consensus pattern (20 bp):
AAAAATGAAAAAAAAAAATG
Found at i:2615549 original size:18 final size:18
Alignment explanation
Indices: 2615485--2615560 Score: 73
Period size: 18 Copynumber: 4.1 Consensus size: 18
2615475 AAACGAAAAG
* *
2615485 AAAAAAATGGAAAATAGAA
1 AAAAAAAAGAAAAAT-GAA
* *
2615504 GAAAAAATGAAAAATGAAAA
1 AAAAAAAAGAAAAATG--AA
2615524 AAAAAAAAGAAAAATGAA
1 AAAAAAAAGAAAAATGAA
*
2615542 AAAAAAAAGAGAAAT-AA
1 AAAAAAAAGAAAAATGAA
2615559 AA
1 AA
2615561 GGAGGGTTCA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
17 4 0.08
18 17 0.34
19 13 0.26
20 16 0.32
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (18 bp):
AAAAAAAAGAAAAATGAA
Found at i:2616768 original size:37 final size:37
Alignment explanation
Indices: 2616711--2616793 Score: 132
Period size: 37 Copynumber: 2.2 Consensus size: 37
2616701 GTTGGATCTT
* *
2616711 TGAAACAAATCAATCTTAAGCCTTCACGGAAGAGTAG
1 TGAAGCAAATCAATCTTAAGCCTTCACGGAAGAATAG
2616748 TGAAGCAAATC-ATCTATAAGCCTTCACGGAAGAATAG
1 TGAAGCAAATCAATCT-TAAGCCTTCACGGAAGAATAG
2616785 TGAAGCAAA
1 TGAAGCAAA
2616794 CCCATTTTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
36 4 0.09
37 39 0.91
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.20
Consensus pattern (37 bp):
TGAAGCAAATCAATCTTAAGCCTTCACGGAAGAATAG
Found at i:2617388 original size:55 final size:55
Alignment explanation
Indices: 2616798--2617389 Score: 644
Period size: 55 Copynumber: 10.9 Consensus size: 55
2616788 AGCAAACCCA
* *
2616798 TTTTATGAAGATTGTTCGAGT-TCTATACTCTCTGAAGGAATAGAGAGC-GAACCCG
1 TTTTATGAAGATTGTTCGAGTCT-TATACTCTCTGAAGGAATAGGGAGCAG-ACACG
* * *
2616853 TTTTATGAAGATTGTTCGAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCG
1 TTTTATGAAGATTGTTCGAGTCT-TATACTCTCTGAAGGAATAGGGAGCAGACACG
* *
2616908 TTTTATGAAGATTGTTCGAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGAC-CTG
1 TTTTATGAAGATTGTTCGAGTCT-TATACTCTCTGAAGGAATAGGGAGCAGACAC-G
* * * *
2616963 TTTTTTGAAGATTGTTTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACG
1 TTTTATGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACG
*
2617018 -TTTATTGAAGA----TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACG
1 TTTTA-TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACG
* * *
2617069 -TTTATTGAAGA----TCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGGACCCG
1 TTTTA-TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACG
* * *
2617120 TTTGT-TGAAGATTATTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACG
1 TTT-TATGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACG
* * *
2617175 TTTTATGAAGATTGTTCAAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACG
1 TTTTATGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACG
* * * *
2617230 TTTGT-TGAAGATTGTTTGAGTCTTATACTCCCTGAATGAATAGGGAGCATACACG
1 TTT-TATGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACG
**** * * * * *
2617285 TTTGCCAAAGATTATTTGAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACA
1 TTTTATGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACG
* *
2617340 TTTTATGAAGATTGTTCGAGTCTTATACT-TCCTGAATGAATAAGGAGCAG
1 TTTTATGAAGATTGTTCGAGTCTTATACTCT-CTGAAGGAATAGGGAGCAG
2617390 GCTCGTCATT
Statistics
Matches: 486, Mismatches: 36, Indels: 30
0.88 0.07 0.05
Matches are distributed among these distances:
51 93 0.19
52 2 0.00
53 1 0.00
54 6 0.01
55 381 0.78
56 3 0.01
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (55 bp):
TTTTATGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACG
Found at i:2634907 original size:29 final size:29
Alignment explanation
Indices: 2634865--2634920 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
2634855 TGATTGGTGG
2634865 TAAAATTAAAAAATGATTTATAAAAAAAA
1 TAAAATTAAAAAATGATTTATAAAAAAAA
* *
2634894 TAAAATTATAAAATGATTTCTAAAAAA
1 TAAAATTAAAAAATGATTTATAAAAAA
2634921 TAAAAACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (29 bp):
TAAAATTAAAAAATGATTTATAAAAAAAA
Found at i:2634935 original size:29 final size:29
Alignment explanation
Indices: 2634865--2634938 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
2634855 TGATTGGTGG
*
2634865 TAAAATTAAAAAATGATTTATAAAAAAAA
1 TAAAATAAAAAAATGATTTATAAAAAAAA
* * *
2634894 TAAAATTATAAAATGATTTCTAAAAAATAA
1 TAAAATAAAAAAATGATTTATAAAAAA-AA
2634924 -AAACA-AAAAAAATGA
1 TAAA-ATAAAAAAATGA
2634939 AAACATGAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 36 0.92
30 3 0.08
ACGTcount: A:0.68, C:0.03, G:0.04, T:0.26
Consensus pattern (29 bp):
TAAAATAAAAAAATGATTTATAAAAAAAA
Found at i:2635293 original size:28 final size:27
Alignment explanation
Indices: 2635236--2635316 Score: 72
Period size: 28 Copynumber: 2.9 Consensus size: 27
2635226 TTTAAATTTT
* ** *
2635236 AAATTTAAATAATACCTTAATTTTTTTA
1 AAATTTAAATAAT-CCTCAAACTTTATA
2635264 AAATTTAAATAAGTCCTCAAACTTTATA
1 AAATTTAAATAA-TCCTCAAACTTTATA
* *
2635292 AAATATTAATTAAACCCTCAAACTT
1 AAAT-TTAAAT-AATCCTCAAACTT
2635317 AGTGAAAAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
28 26 0.59
29 16 0.36
30 2 0.05
ACGTcount: A:0.46, C:0.14, G:0.01, T:0.40
Consensus pattern (27 bp):
AAATTTAAATAATCCTCAAACTTTATA
Found at i:2637046 original size:19 final size:19
Alignment explanation
Indices: 2637022--2637058 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2637012 TTCACCGCTG
2637022 GACTCAGAAGGGATCTTCC
1 GACTCAGAAGGGATCTTCC
2637041 GACTCAGAAGGGATCTTC
1 GACTCAGAAGGGATCTTC
2637059 TTAACGTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (19 bp):
GACTCAGAAGGGATCTTCC
Found at i:2641696 original size:55 final size:55
Alignment explanation
Indices: 2641581--2641849 Score: 335
Period size: 55 Copynumber: 4.9 Consensus size: 55
2641571 CTATACGAGA
* ** * * *
2641581 ATTCATCAAC-CTATGATGAATTCTGTGGGT-TGTACACATAGTGCTTGTACGGTG
1 ATTCATCAACTC-ATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTACGGTG
*
2641635 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTACCTGTACGGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTACGGTG
* * *
2641690 ATTCATCAATTTATTATGAATTCCGTGAATATGCACACAAAGTGCCTGTACGGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTACGGTG
* * * * * *
2641745 ACTCGTCAACTCATGATGATTTTCGAGAATATGCACACAAAGTGCATGTACGGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTACGGTG
* * * *
2641800 ACTCATCAACTCATGATAAATTTCGTGAATATGCAAACAAAGTGCCTGTA
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTA
2641850 GTACACATAA
Statistics
Matches: 187, Mismatches: 26, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
54 25 0.13
55 162 0.87
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (55 bp):
ATTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTACGGTG
Found at i:2647879 original size:7 final size:7
Alignment explanation
Indices: 2647856--2647892 Score: 56
Period size: 7 Copynumber: 5.0 Consensus size: 7
2647846 CGTTTGAGAG
2647856 AAGAAGA
1 AAGAAGA
2647863 AGATGAAGA
1 A-A-GAAGA
2647872 AAGAAGA
1 AAGAAGA
2647879 AAGAAGA
1 AAGAAGA
2647886 AAGAAGA
1 AAGAAGA
2647893 GTAATCTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 20 0.71
8 2 0.07
9 6 0.21
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.03
Consensus pattern (7 bp):
AAGAAGA
Found at i:2649350 original size:55 final size:55
Alignment explanation
Indices: 2649275--2649937 Score: 610
Period size: 55 Copynumber: 12.0 Consensus size: 55
2649265 TAAGTGAGAT
* * *
2649275 TTGAAAAATCTTTAGAAAAATGGGTTCGCT-CCTATTCTTTCAGGGAGTATAGGAC
1 TTGAACAATCTTCAG-AAAACGGGTTCGCTCCCTATTCTTTCAGGGAGTATAGGAC
* * * * *
2649330 TTGAAATAATCTTCATAAAATGGGTTCGCTCCCTATTCTTTCAGTGAGTATAAGAC
1 TTG-AACAATCTTCAGAAAACGGGTTCGCTCCCTATTCTTTCAGGGAGTATAGGAC
** * * * * * * *
2649386 TCAAACAATCTTCGGCAAACGGGTCCACTCCCTTTTCTTTCAAGGAGTATATGAC
1 TTGAACAATCTTCAGAAAACGGGTTCGCTCCCTATTCTTTCAGGGAGTATAGGAC
* * * * * *
2649441 TTGAACAATCTTCGGAAAATGTGTAT-GCTCCCTATTTTTTCAGGAAGTATAGGGC
1 TTGAACAATCTTCAGAAAACGGGT-TCGCTCCCTATTCTTTCAGGGAGTATAGGAC
* ** *
2649496 TTGATCAAATCTTTGGAAAAAGGGTTCGCTCCCTATTCTTTCAGGGAGTATAGGAC
1 TTGAAC-AATCTTCAGAAAACGGGTTCGCTCCCTATTCTTTCAGGGAGTATAGGAC
* * * * * *
2649552 TCGAACAATCTT-ATGAAAACGTG-TCTACTCCTTATTCTTTTAGGGAGTATATGAC
1 TTGAACAATCTTCA-GAAAACGGGTTC-GCTCCCTATTCTTTCAGGGAGTATAGGAC
* ** * * *
2649607 TCGAACAATCTTCA-ACAAACGTATCCGATCCCTATTCTTTCAGGGAGTATATGAC
1 TTGAACAATCTTCAGA-AAACGGGTTCGCTCCCTATTCTTTCAGGGAGTATAGGAC
** * * * *
2649662 TCAAACAATCTTCA-ACAAACGTGTCCGTTCCCTATTCTTTCAGGGAGTATATGAC
1 TTGAACAATCTTCAGA-AAACGGGTTCGCTCCCTATTCTTTCAGGGAGTATAGGAC
* * * *
2649717 TTAAACAATCTTCGGAAAACGGG-TCTACTCCCTATTCTTTTAGGGAGTATAGGAC
1 TTGAACAATCTTCAGAAAACGGGTTC-GCTCCCTATTCTTTCAGGGAGTATAGGAC
* * * *
2649772 TTGATCAATCATCAGAAAACGGGTCCGTTCCCTATTCTTTCAGGGAGTATAGGAC
1 TTGAACAATCTTCAGAAAACGGGTTCGCTCCCTATTCTTTCAGGGAGTATAGGAC
* * *
2649827 TAGAACAATCTTCA-ACAAACGTGTAT-GCTCCCTATTCTTTCAGGGAGTATAGTAC
1 TTGAACAATCTTCAGA-AAACGGGT-TCGCTCCCTATTCTTTCAGGGAGTATAGGAC
* *
2649882 TTGAACAATCTTCA-ATAAACGTG-TCTGCTCCCTATTCTTTCAGGGAGTAAAGGAC
1 TTGAACAATCTTCAGA-AAACGGGTTC-GCTCCCTATTCTTTCAGGGAGTATAGGAC
2649937 T
1 T
2649938 CGATCTTGAT
Statistics
Matches: 508, Mismatches: 83, Indels: 34
0.81 0.13 0.05
Matches are distributed among these distances:
53 1 0.00
54 5 0.01
55 420 0.83
56 82 0.16
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (55 bp):
TTGAACAATCTTCAGAAAACGGGTTCGCTCCCTATTCTTTCAGGGAGTATAGGAC
Found at i:2650007 original size:37 final size:36
Alignment explanation
Indices: 2649966--2650168 Score: 165
Period size: 37 Copynumber: 5.4 Consensus size: 36
2649956 CTAATCTTGA
*
2649966 GTGAAGGTTTATAGATGATTCGCTTCACTACTCTTCC
1 GTGAAGGCTTA-AGATGATTCGCTTCACTACTCTTCC
** **** *
2650003 GTGAAGGCTTAAGATGGCTCGGAGGACTTATCATCTTGC
1 GTGAAGGCTTAAGATGATTCGCTTCAC-TA-C-TCTTCC
* * * * *
2650042 TTGGAAGCCTTACTGATGGCTT-GCTTTACTACTCTTCC
1 GT-GAAGGCTTA-AGAT-GATTCGCTTCACTACTCTTCC
* *
2650080 GTGAAGGCTTAAGATTGCTTTGCTTCACTACTCTTCC
1 GTGAAGGCTTAAGA-TGATTCGCTTCACTACTCTTCC
* *
2650117 GTGAAGGCTTAAGATTGATTTGTTTCACTACTCTTCC
1 GTGAAGGCTTAAGA-TGATTCGCTTCACTACTCTTCC
2650154 GTGAAGGCTTAAGAT
1 GTGAAGGCTTAAGAT
2650169 TGACTTTCCC
Statistics
Matches: 134, Mismatches: 24, Indels: 17
0.77 0.14 0.10
Matches are distributed among these distances:
36 17 0.13
37 85 0.63
38 7 0.05
39 7 0.05
40 10 0.07
41 6 0.04
42 2 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (36 bp):
GTGAAGGCTTAAGATGATTCGCTTCACTACTCTTCC
Found at i:2650169 original size:37 final size:37
Alignment explanation
Indices: 2650062--2650171 Score: 193
Period size: 37 Copynumber: 3.0 Consensus size: 37
2650052 TACTGATGGC
* *
2650062 TTGCTTTACTACTCTTCCGTGAAGGCTTAAGATTGCT
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAT
2650099 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAT
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAT
*
2650136 TTGTTTCACTACTCTTCCGTGAAGGCTTAAGATTGA
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGA
2650172 CTTTCCCCAA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (37 bp):
TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAT
Found at i:2652176 original size:11 final size:11
Alignment explanation
Indices: 2652134--2652185 Score: 50
Period size: 11 Copynumber: 4.3 Consensus size: 11
2652124 ATACTCAAAA
2652134 AATATTATTTT
1 AATATTATTTT
*
2652145 ATTTATTTATTATT
1 A-ATA-TTATT-TT
2652159 AATATATTATTTT
1 -A-ATATTATTTT
2652172 AATATTATTTT
1 AATATTATTTT
2652183 AAT
1 AAT
2652186 GAAAATATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
11 14 0.40
12 3 0.09
13 7 0.20
14 7 0.20
15 4 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
AATATTATTTT
Found at i:2652211 original size:28 final size:28
Alignment explanation
Indices: 2652148--2652237 Score: 80
Period size: 28 Copynumber: 3.1 Consensus size: 28
2652138 TTATTTTATT
* *
2652148 TATTTATTAT-TAATATATTATTTTAATAT
1 TATTTAATATATAATATA--ATTTTAATAA
2652177 TATTTTAATGA-A-AATATTAATTATTAA-AA
1 TA-TTTAAT-ATATAATA-TAATT-TTAATAA
2652206 TATTTAATATATAATATAATTTTAATAA
1 TATTTAATATATAATATAATTTTAATAA
2652234 TATT
1 TATT
2652238 ATATTAATAG
Statistics
Matches: 51, Mismatches: 2, Indels: 17
0.73 0.03 0.24
Matches are distributed among these distances:
27 5 0.10
28 18 0.35
29 12 0.24
30 13 0.25
31 3 0.06
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (28 bp):
TATTTAATATATAATATAATTTTAATAA
Found at i:2652365 original size:27 final size:26
Alignment explanation
Indices: 2652292--2652370 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 26
2652282 TAATTTATAA
*
2652292 TAAATTATTAAT-ATAGTTAATATTAT
1 TAAATTATTAATAATA-ATAATATTAT
*
2652318 CTATTAATTTTTAA-AAT-ATAATATTAT
1 -TA--AATTATTAATAATAATAATATTAT
2652345 TAAATTATTAATAATGAATAATATTA
1 TAAATTATTAATAAT-AATAATATTA
2652371 ATTTATACAT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
24 8 0.19
25 3 0.07
26 2 0.05
27 20 0.47
29 10 0.23
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (26 bp):
TAAATTATTAATAATAATAATATTAT
Found at i:2652401 original size:19 final size:19
Alignment explanation
Indices: 2652363--2652408 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2652353 TAATAATGAA
*
2652363 TAATATTAATTTATACATT
1 TAATATTAATTAATACATT
2652382 TAATATTAATATAATA-ATT
1 TAATATTAAT-TAATACATT
*
2652401 TAGTATTA
1 TAATATTA
2652409 TGTTAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
TAATATTAATTAATACATT
Found at i:2652751 original size:30 final size:30
Alignment explanation
Indices: 2652710--2652768 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
2652700 ACAGTTATAG
*
2652710 GTAATTTATTTTACGTAAAATAATTTTCAT
1 GTAATTCATTTTACGTAAAATAATTTTCAT
* * *
2652740 GTAATTCATTTTACTTAAATTATTTTTCA
1 GTAATTCATTTTACGTAAAATAATTTTCA
2652769 GAAAACCAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (30 bp):
GTAATTCATTTTACGTAAAATAATTTTCAT
Found at i:2653316 original size:55 final size:53
Alignment explanation
Indices: 2653235--2653379 Score: 145
Period size: 55 Copynumber: 2.7 Consensus size: 53
2653225 TCAGTTATAT
* *
2653235 TATAATAATA-TATTATATTATATTTTAAATTAATAATGTATAATAAATTATTAA
1 TATAATAATATTA-TATATTATTTTTTAAATTAATAATAT-TAATAAATTATTAA
* *
2653289 TATAATTAATATTATATATTATTTTTTATAAAT-ATAATATTATTAAATTATTAA
1 TATAA-TAATATTATATATTATTTTTTA-AATTAATAATATTAATAAATTATTAA
*
2653343 TAATGAATAATATTA-AT-TTATATATTTAATATTAATA
1 T-AT-AATAATATTATATATTAT-TTTTTAA-ATTAATA
2653380 TAATAATTTA
Statistics
Matches: 77, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
53 5 0.06
54 28 0.36
55 37 0.48
56 7 0.09
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.50
Consensus pattern (53 bp):
TATAATAATATTATATATTATTTTTTAAATTAATAATATTAATAAATTATTAA
Found at i:2653388 original size:19 final size:19
Alignment explanation
Indices: 2653350--2653395 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2653340 TAATAATGAA
*
2653350 TAATATTAATTTATATATT
1 TAATATTAATTAATATATT
2653369 TAATATTAATATAATA-ATT
1 TAATATTAAT-TAATATATT
*
2653388 TAGTATTA
1 TAATATTA
2653396 TGTTAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TAATATTAATTAATATATT
Found at i:2653396 original size:57 final size:54
Alignment explanation
Indices: 2653278--2653386 Score: 130
Period size: 57 Copynumber: 2.0 Consensus size: 54
2653268 TAATGTATAA
** *
2653278 TAAATTATTAATATAATTAATATTATATATTATTTTTTATAAATATAATATTAT
1 TAAATTATTAATATAATTAATATTATATATTATTTAATATAAATATAATAATAT
* *
2653332 TAAATTATTAATAATGAA-TAATATTAATTTATATATTTAATATTAATATAATAAT
1 TAAATTATTAAT-AT-AATTAATATT-ATATAT-TATTTAATATAAATATAATAAT
2653387 TTAGTATTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
54 12 0.26
55 9 0.20
56 7 0.15
57 18 0.39
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (54 bp):
TAAATTATTAATATAATTAATATTATATATTATTTAATATAAATATAATAATAT
Found at i:2653402 original size:30 final size:27
Alignment explanation
Indices: 2653356--2653417 Score: 72
Period size: 30 Copynumber: 2.2 Consensus size: 27
2653346 TGAATAATAT
*
2653356 TAATTTATATATTTAATATTAATA-TAA
1 TAATTTATATATTTAATA-AAATACTAA
2653383 TAATTTAGTATTATGTTAATAAAATACTAA
1 TAATTTA-TA-TAT-TTAATAAAATACTAA
2653413 TAATT
1 TAATT
2653418 AAAATTAGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 7 0.23
28 2 0.07
29 7 0.23
30 14 0.47
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (27 bp):
TAATTTATATATTTAATAAAATACTAA
Found at i:2653719 original size:30 final size:31
Alignment explanation
Indices: 2653684--2653746 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
2653674 AGTTCTAGGT
*
2653684 AATTCATTTTACATAAAATAG-TTTTCATGA
1 AATTCATTTTACATAAAACAGTTTTTCATGA
*
2653714 AATTCATTTTACGTAAAACAGTTTTTCATGA
1 AATTCATTTTACATAAAACAGTTTTTCATGA
2653745 AA
1 AA
2653747 ACTGTTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 19 0.63
31 11 0.37
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.41
Consensus pattern (31 bp):
AATTCATTTTACATAAAACAGTTTTTCATGA
Found at i:2654942 original size:21 final size:21
Alignment explanation
Indices: 2654918--2654960 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2654908 ATTGATGCTT
2654918 AACTCGACTCGTTGCTCGTTA
1 AACTCGACTCGTTGCTCGTTA
2654939 AACTCGACTCGTTGCTCGTTA
1 AACTCGACTCGTTGCTCGTTA
2654960 A
1 A
2654961 GCTCACTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.33
Consensus pattern (21 bp):
AACTCGACTCGTTGCTCGTTA
Found at i:2656046 original size:24 final size:27
Alignment explanation
Indices: 2656013--2656081 Score: 83
Period size: 25 Copynumber: 2.7 Consensus size: 27
2656003 ATTTGATTTT
*
2656013 AATTTTAATATTAATTTTTTAA-A-TA
1 AATTATAATATTAATTTTTTAATATTA
2656038 AATTA-AATATT-ATTTTTTAATATTA
1 AATTATAATATTAATTTTTTAATATTA
*
2656063 TATTATAGATATTAATTTT
1 AATTATA-ATATTAATTTT
2656082 ACTAATTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
23 9 0.24
24 7 0.19
25 10 0.27
26 1 0.03
27 5 0.14
28 5 0.14
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (27 bp):
AATTATAATATTAATTTTTTAATATTA
Found at i:2656059 original size:13 final size:13
Alignment explanation
Indices: 2655977--2656124 Score: 56
Period size: 13 Copynumber: 12.4 Consensus size: 13
2655967 CAAAGAGGTT
2655977 TTATA-TTTAAT-
1 TTATATTTTAATA
*
2655988 TT-TATATT-ATA
1 TTATATTTTAATA
* *
2655999 TTATA-TTTGATT
1 TTATATTTTAATA
2656011 TTA-ATTTTAATA
1 TTATATTTTAATA
*
2656023 TTAATTTTTTAA-A
1 TT-ATATTTTAATA
* *
2656036 -TA-AATTAAATA
1 TTATATTTTAATA
*
2656047 TTATTTTTTAATA
1 TTATATTTTAATA
*
2656060 TTATATTATAGATA
1 TTATATTTTA-ATA
*
2656074 TTA-ATTTTACTA
1 TTATATTTTAATA
*
2656086 --ATTTTTTAA-A
1 TTATATTTTAATA
* *
2656096 -TA-AATTAAATA
1 TTATATTTTAATA
*
2656107 TTATTTTTTAATA
1 TTATATTTTAATA
2656120 TTATA
1 TTATA
2656125 GTATAGATAT
Statistics
Matches: 96, Mismatches: 25, Indels: 30
0.64 0.17 0.20
Matches are distributed among these distances:
10 14 0.15
11 18 0.19
12 21 0.22
13 31 0.32
14 12 0.12
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (13 bp):
TTATATTTTAATA
Found at i:2656074 original size:27 final size:28
Alignment explanation
Indices: 2656020--2656142 Score: 87
Period size: 29 Copynumber: 4.4 Consensus size: 28
2656010 TTTAATTTTA
2656020 ATATTAATTTTTTAA-A-TAAATTA-A-
1 ATATTAATTTTTTAATATTAAATTATAG
*
2656044 ATATT-ATTTTTTAATATTATATTATAG
1 ATATTAATTTTTTAATATTAAATTATAG
* * * *
2656071 ATATTAATTTTACTAATTTTTTAAATAAATTAA
1 ATATTAATTTT-TTAA--TATTAAAT-TA-TAG
* *
2656104 ATATT-ATTTTTTAATATTATAGTATAG
1 ATATTAATTTTTTAATATTAAATTATAG
2656131 ATATTTAATTTT
1 ATA-TTAATTTT
2656143 ATATCAAATA
Statistics
Matches: 75, Mismatches: 12, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
23 9 0.12
24 6 0.08
25 6 0.08
26 1 0.01
27 10 0.13
28 8 0.11
29 13 0.17
31 9 0.12
32 6 0.08
33 7 0.09
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (28 bp):
ATATTAATTTTTTAATATTAAATTATAG
Found at i:2656098 original size:60 final size:61
Alignment explanation
Indices: 2656024--2656143 Score: 224
Period size: 60 Copynumber: 2.0 Consensus size: 61
2656014 ATTTTAATAT
*
2656024 TAATTTTTTAAATAAATTAAATATTATTTTTTAATATTATATTATAGATA-TTAATTTTAC
1 TAATTTTTTAAATAAATTAAATATTATTTTTTAATATTATAGTATAGATATTTAATTTTAC
2656084 TAATTTTTTAAATAAATTAAATATTATTTTTTAATATTATAGTATAGATATTTAATTTTA
1 TAATTTTTTAAATAAATTAAATATTATTTTTTAATATTATAGTATAGATATTTAATTTTA
2656144 TATCAAATAA
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
60 49 0.84
61 9 0.16
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.55
Consensus pattern (61 bp):
TAATTTTTTAAATAAATTAAATATTATTTTTTAATATTATAGTATAGATATTTAATTTTAC
Found at i:2656152 original size:55 final size:57
Alignment explanation
Indices: 2656033--2656157 Score: 175
Period size: 60 Copynumber: 2.2 Consensus size: 57
2656023 TTAATTTTTT
* *
2656033 AAATAAATTAAATATTATTTTTTAATATTATATTATAGATATTAATTTTACTAATTTTTT
1 AAATAAATTAAATATTATTTTTTAATATTATAGTATAGATATTAATTTTACTAA---TTC
2656093 AAATAAATTAAATATTATTTTTTAATATTATAGTATAGATATTTAATTTTA-T-A-TC
1 AAATAAATTAAATATTATTTTTTAATATTATAGTATAGATA-TTAATTTTACTAATTC
2656148 AAATAAATTA
1 AAATAAATTA
2656158 TTTTATATAT
Statistics
Matches: 62, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
55 11 0.18
59 1 0.02
60 41 0.66
61 9 0.15
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (57 bp):
AAATAAATTAAATATTATTTTTTAATATTATAGTATAGATATTAATTTTACTAATTC
Found at i:2656698 original size:31 final size:31
Alignment explanation
Indices: 2656661--2656720 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
2656651 TAGTTGTATG
*
2656661 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATTTCAGTATTGCAAAACTAA
2656692 AATTATTTAAATTTCAGTATTGCAAAACT
1 AATTATTTAAATTTCAGTATTGCAAAACT
2656721 CTTTTAAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
AATTATTTAAATTTCAGTATTGCAAAACTAA
Found at i:2663819 original size:240 final size:244
Alignment explanation
Indices: 2663389--2663834 Score: 720
Period size: 240 Copynumber: 1.8 Consensus size: 244
2663379 CGGTACTGAA
*
2663389 TAGGGTAGGTTATTTCTTGAATGCTTTTGTTTTTGAAGATTGGAGCAGATGGACATCTGTAGCTA
1 TAGGGTAGGTTATTTCTTGAATGCTTTTGTTTTCGAAGATTGGAGCAGATGGACATCTGTAGCTA
2663454 TGTTACTTCTCAATTCTCATTTGTTTTAAAGTACAAGTGTCCAACAAATATCTGAAGGACATGTA
66 TGTTACTTCTCAA-T-T-ATTTGTTTTAAAGTACAAGTGTCCAACAAATATCTGAAGGACATGTA
* * * *
2663519 CGCGTGTCCAAAATATAACCAAAAACTTTGAAACAATTGATGCGCCTTATCTCACACTCCTTGCT
128 CACGTGTCCAAAATATAACCAAAAACTTTGAAACAATCGATGCACCTTATCTCACACTCCTAGCT
2663584 GCATAATTTCTAATTTACTTCATTTTCATGCATTGAATTGTTCACTTTCAAC
193 GCATAATTTCTAATTTACTTCATTTTCATGCATTGAATTGTTCACTTTCAAC
* * *
2663636 TAGGGTAGGTTCTTTCTTGAATTCTTTTGTTTTCGGAGATTGGAGCAGATGGACATCTGTAGCTA
1 TAGGGTAGGTTATTTCTTGAATGCTTTTGTTTTCGAAGATTGGAGCAGATGGACATCTGTAGCTA
* * * *
2663701 TGTTACTTCTCAA-T-TTT-TTTT-AATTACAAGTGTCCAACAAATATTTGAAGGACATGTATAT
66 TGTTACTTCTCAATTATTTGTTTTAAAGTACAAGTGTCCAACAAATATCTGAAGGACATGTACAC
*
2663762 GTGTCCAAAATATAACCAGAAACTTTGAAACAATCGATGCACCTTATCTCACACTCCTAGCTGCA
131 GTGTCCAAAATATAACCAAAAACTTTGAAACAATCGATGCACCTTATCTCACACTCCTAGCTGCA
2663827 TAATTTCT
196 TAATTTCT
2663835 TTTTTTTTTG
Statistics
Matches: 186, Mismatches: 13, Indels: 7
0.90 0.06 0.03
Matches are distributed among these distances:
240 104 0.56
241 4 0.02
242 3 0.02
244 1 0.01
247 74 0.40
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (244 bp):
TAGGGTAGGTTATTTCTTGAATGCTTTTGTTTTCGAAGATTGGAGCAGATGGACATCTGTAGCTA
TGTTACTTCTCAATTATTTGTTTTAAAGTACAAGTGTCCAACAAATATCTGAAGGACATGTACAC
GTGTCCAAAATATAACCAAAAACTTTGAAACAATCGATGCACCTTATCTCACACTCCTAGCTGCA
TAATTTCTAATTTACTTCATTTTCATGCATTGAATTGTTCACTTTCAAC
Found at i:2675867 original size:19 final size:20
Alignment explanation
Indices: 2675831--2675869 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2675821 AAACACTTAA
2675831 AATAATTGAAATAAATAAAT
1 AATAATTGAAATAAATAAAT
2675851 AATAA-TGAAA-AACATAAAT
1 AATAATTGAAATAA-ATAAAT
2675870 CAAATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 11 0.61
20 5 0.28
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.26
Consensus pattern (20 bp):
AATAATTGAAATAAATAAAT
Found at i:2676732 original size:186 final size:188
Alignment explanation
Indices: 2676413--2676805 Score: 645
Period size: 186 Copynumber: 2.1 Consensus size: 188
2676403 AACCGAAATT
* *
2676413 AAATTTTAAATATATTATATATAACATATGGATTCAGCCCAAACCATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGACTCAGCCCAAACCATTTAAAACTCAATTAATAA
*
2676478 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATATATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATACATATAAAATTT
2676543 TTATTTTATAATTATATATCATTTAAATTAATT-GTAAACT-ATTTTTTTGAATT-AAA
131 TTATTTTATAATTATATATCATTTAAATTAATTAG-AAACTGATTTTTTTGAATTAAAA
* *
2676599 AAATATTAAATATATTATATATAACATAT-GAGCTCATCCCAAATCATTTAAAACTCAATTAATA
1 AAATATTAAATATATTATATATAACATATGGA-CTCAGCCCAAACCATTTAAAACTCAATTAATA
*
2676663 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATGCATATAAAATT
65 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATACATATAAAATT
* *
2676728 TTTATTTTATAATTATATATTATTTAAATTAATTAGAAACTGTTTTTTTTGAATTAAAA
130 TTTATTTTATAATTATATATCATTTAAATTAATTAGAAACTGATTTTTTTGAATTAAAA
*
2676787 AAATATTTAAT-TA-TATATA
1 AAATATTAAATATATTATATA
2676806 AATTAAAAAA
Statistics
Matches: 194, Mismatches: 9, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
185 2 0.01
186 164 0.85
187 15 0.08
188 13 0.07
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (188 bp):
AAATATTAAATATATTATATATAACATATGGACTCAGCCCAAACCATTTAAAACTCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATACATATAAAATTT
TTATTTTATAATTATATATCATTTAAATTAATTAGAAACTGATTTTTTTGAATTAAAA
Found at i:2679957 original size:32 final size:32
Alignment explanation
Indices: 2679912--2679979 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
2679902 ATTCTTTTCT
*
2679912 TTCATATACTTGTCATAACTTTCACATTTACA
1 TTCACATACTTGTCATAACTTTCACATTTACA
* *
2679944 TTCACATATTTGTCATAACTTTCACATTTACT
1 TTCACATACTTGTCATAACTTTCACATTTACA
2679976 TTCA
1 TTCA
2679980 TAGCCTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.29, C:0.22, G:0.03, T:0.46
Consensus pattern (32 bp):
TTCACATACTTGTCATAACTTTCACATTTACA
Found at i:2680185 original size:78 final size:78
Alignment explanation
Indices: 2680073--2680253 Score: 240
Period size: 78 Copynumber: 2.3 Consensus size: 78
2680063 CATTTAGTGC
* * * * *
2680073 ATTTTCATCATATGCACCCTATAGTGCTTTATAACCAGTTT-GACACCTTTTAT-CCTTGACACC
1 ATTTTTATCATATGCACCCCATAGTACTTGATAACCAGTTTAG-CACCTTTTATGCCTCGA-ACC
*
2680136 TTTTATGCCTGAATT
64 TTTAATGCCTGAATT
* *
2680151 ATTTTTATTATATGCACCCCATAGTACTTGATAACCAGTTTAGCACCTTTTATGTCTCGAACCTT
1 ATTTTTATCATATGCACCCCATAGTACTTGATAACCAGTTTAGCACCTTTTATGCCTCGAACCTT
*
2680216 TAATGCCTTAATT
66 TAATGCCTGAATT
*
2680229 ATTTTTATCATATTCACCCCATAGT
1 ATTTTTATCATATGCACCCCATAGT
2680254 GCTATTTAAT
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
78 85 0.94
79 5 0.06
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.41
Consensus pattern (78 bp):
ATTTTTATCATATGCACCCCATAGTACTTGATAACCAGTTTAGCACCTTTTATGCCTCGAACCTT
TAATGCCTGAATT
Found at i:2680275 original size:78 final size:77
Alignment explanation
Indices: 2680073--2680276 Score: 239
Period size: 78 Copynumber: 2.6 Consensus size: 77
2680063 CATTTAGTGC
* * * *
2680073 ATTTTCATCATATGCACCCTATAGTGCTTTATAACCAGTTTGACACCTTTTATCCTTGACACCTT
1 ATTTTTATCATATGCACCCCATAGTGCTTT-TAACCAGTTTGGCACCTTTTATCCTCGACACCTT
*
2680138 TTATGCCTGAATT
65 TAATGCCTGAATT
* * * * *
2680151 ATTTTTATTATATGCACCCCATAGTACTTGATAACCAGTTTAGCACCTTTTATGTCTCGA-ACCT
1 ATTTTTATCATATGCACCCCATAGTGCTT-TTAACCAGTTTGGCACCTTTTAT-CCTCGACACCT
*
2680215 TTAATGCCTTAATT
64 TTAATGCCTGAATT
* * *
2680229 ATTTTTATCATATTCACCCCATAGTGCTATTTAATCGGTTTGGCACCT
1 ATTTTTATCATATGCACCCCATAGTGCT-TTTAACCAGTTTGGCACCT
2680277 ATCATGCCTG
Statistics
Matches: 105, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
78 100 0.95
79 5 0.05
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (77 bp):
ATTTTTATCATATGCACCCCATAGTGCTTTTAACCAGTTTGGCACCTTTTATCCTCGACACCTTT
AATGCCTGAATT
Found at i:2683521 original size:17 final size:18
Alignment explanation
Indices: 2683499--2683532 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2683489 TTTTAAAATA
2683499 ATTTTAAGA-AAAAATTT
1 ATTTTAAGACAAAAATTT
2683516 ATTTTAAGACAAAAATT
1 ATTTTAAGACAAAAATT
2683533 GGTCTGTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (18 bp):
ATTTTAAGACAAAAATTT
Found at i:2686824 original size:86 final size:86
Alignment explanation
Indices: 2686679--2686849 Score: 297
Period size: 86 Copynumber: 2.0 Consensus size: 86
2686669 AGCTAACCAT
* * *
2686679 GTCTTAACAGACTGTAAAATAGATATATCATTTCTTATGATGAGTATGTCGTCTACATACAAGAT
1 GTCTTAACAGACTGTAAAATAGATATATCATTTCTTATGATGAGTATGTCATATACATACAAGAC
2686744 TAGGAAAGAAACAATACTCCA
66 TAGGAAAGAAACAATACTCCA
*
2686765 GTCTTAACAGACTGTAAAATAGTTATATCATTTCTTATGATGAGTATGTCATATACATACAAGAC
1 GTCTTAACAGACTGTAAAATAGATATATCATTTCTTATGATGAGTATGTCATATACATACAAGAC
*
2686830 TAGGAAAGAAACAATGCTCC
66 TAGGAAAGAAACAATACTCC
2686850 CATTATATAT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 80 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (86 bp):
GTCTTAACAGACTGTAAAATAGATATATCATTTCTTATGATGAGTATGTCATATACATACAAGAC
TAGGAAAGAAACAATACTCCA
Found at i:2691868 original size:13 final size:13
Alignment explanation
Indices: 2691840--2691873 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
2691830 TTTAATTGTG
2691840 AAAATTGAAAATTT
1 AAAATT-AAAATTT
*
2691854 AAAATTAAGATTT
1 AAAATTAAAATTT
2691867 AAAATTA
1 AAAATTA
2691874 CCCGATTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:2692033 original size:20 final size:20
Alignment explanation
Indices: 2691982--2692033 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 20
2691972 CCAAACAAGA
*
2691982 AAAGGAAAAAAATAATAAATT
1 AAAGG-AAAAAATAATAAATC
2692003 AATA--AATAAAATAATAAATC
1 AA-AGGAA-AAAATAATAAATC
2692023 AAAGGAAAAAA
1 AAAGGAAAAAA
2692034 AGAAAAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 9
0.72 0.03 0.25
Matches are distributed among these distances:
19 3 0.12
20 18 0.69
21 4 0.15
22 1 0.04
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (20 bp):
AAAGGAAAAAATAATAAATC
Found at i:2693450 original size:3 final size:3
Alignment explanation
Indices: 2693437--2693480 Score: 61
Period size: 3 Copynumber: 13.7 Consensus size: 3
2693427 GAAATAAATG
2693437 AAT AAT AAAT AAT AAT AAT AAAT AAT AAT AAAT AAT AAT AAT AA
1 AAT AAT -AAT AAT AAT AAT -AAT AAT AAT -AAT AAT AAT AAT AA
2693481 ATAAATATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 29 0.76
4 9 0.24
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2693484 original size:10 final size:10
Alignment explanation
Indices: 2693437--2693477 Score: 66
Period size: 10 Copynumber: 4.1 Consensus size: 10
2693427 GAAATAAATG
2693437 AATAATAA-A
1 AATAATAATA
2693446 TAATAATAATA
1 -AATAATAATA
2693457 AATAATAATA
1 AATAATAATA
2693467 AATAATAATA
1 AATAATAATA
2693477 A
1 A
2693478 TAAATAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 29 0.97
11 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AATAATAATA
Found at i:2693490 original size:10 final size:11
Alignment explanation
Indices: 2693429--2693491 Score: 67
Period size: 13 Copynumber: 5.5 Consensus size: 11
2693419 ACAAAAAGGA
*
2693429 AATAAATGAAT
1 AATAAATAAAT
2693440 AATAAATAATAAT
1 AATAAAT-A-AAT
2693453 AATAAAT-AAT
1 AATAAATAAAT
2693463 AATAAATAATAAT
1 AATAAAT-A-AAT
2693476 AATAAATAAAT
1 AATAAATAAAT
2693487 -ATAAA
1 AATAAA
2693492 ATTATTTTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
10 15 0.33
11 10 0.22
12 1 0.02
13 20 0.43
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (11 bp):
AATAAATAAAT
Found at i:2693490 original size:13 final size:14
Alignment explanation
Indices: 2693440--2693487 Score: 82
Period size: 13 Copynumber: 3.6 Consensus size: 14
2693430 ATAAATGAAT
2693440 AATAAATAATAAT-
1 AATAAATAATAATA
2693453 AATAAATAATAATA
1 AATAAATAATAATA
2693467 AAT-AATAATAATA
1 AATAAATAATAATA
2693480 AATAAATA
1 AATAAATA
2693488 TAAAATTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
13 26 0.79
14 7 0.21
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AATAAATAATAATA
Found at i:2693491 original size:23 final size:23
Alignment explanation
Indices: 2693429--2693484 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
2693419 ACAAAAAGGA
2693429 AATAAATGAATAATAAATAATAAT
1 AATAAAT-AATAATAAATAATAAT
2693453 AATAAATAATAATAAATAATAAT
1 AATAAATAATAATAAATAATAAT
2693476 AATAAATAA
1 AATAAATAA
2693485 ATATAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 25 0.78
24 7 0.22
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (23 bp):
AATAAATAATAATAAATAATAAT
Found at i:2693580 original size:45 final size:44
Alignment explanation
Indices: 2693508--2693595 Score: 108
Period size: 43 Copynumber: 2.0 Consensus size: 44
2693498 TTTTTAAAAC
* *
2693508 TATATAATATAAATTTTTAGAAATGTTTCTTTTAAAAACTATATAT
1 TATATAATATAAATTTTCAGAAATG-TT-TTTAAAAAACTATATAT
*
2693554 TATAT-ATATAAATTTTCA-AATCTGTTTTTAAAAAACTATATA
1 TATATAATATAAATTTTCAGAA-ATGTTTTTAAAAAACTATATA
2693596 ATTTCCAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
43 15 0.39
44 4 0.11
45 14 0.37
46 5 0.13
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (44 bp):
TATATAATATAAATTTTCAGAAATGTTTTTAAAAAACTATATAT
Found at i:2693756 original size:78 final size:79
Alignment explanation
Indices: 2693602--2693749 Score: 232
Period size: 78 Copynumber: 1.9 Consensus size: 79
2693592 TATAATTTCC
2693602 AAAAAAGTTTTAAAAATTATATATTATATATAAGTTTTCAAAAATGTTTTCAAAAACTATATATT
1 AAAAAAGTTTTAAAAATTATATATTATATATAAGTTTTCAAAAATGTTTTCAAAAACTATATATT
2693667 ATATAAGTTTTCAA
66 ATATAAGTTTTCAA
*
2693681 AAAAAATGTTTTCAAAATCTATATA-T-TATATAAGTTTTC-AAAATGATTTT-AAAAACTATAT
1 AAAAAA-GTTTTAAAAAT-TATATATTATATATAAGTTTTCAAAAATG-TTTTCAAAAACTATAT
2693742 ATTATATA
63 ATTATATA
2693750 TTTTTTCTAA
Statistics
Matches: 65, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
78 25 0.38
79 23 0.35
80 11 0.17
81 6 0.09
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (79 bp):
AAAAAAGTTTTAAAAATTATATATTATATATAAGTTTTCAAAAATGTTTTCAAAAACTATATATT
ATATAAGTTTTCAA
Found at i:2693781 original size:78 final size:79
Alignment explanation
Indices: 2693602--2693804 Score: 227
Period size: 78 Copynumber: 2.6 Consensus size: 79
2693592 TATAATTTCC
*
2693602 AAAAAA-G-TTTTAAAAATTATATATTATATATAAGTTTTCAAAAATGTTTTCAAAAACTATATA
1 AAAAAATGTTTTTAAAAACTATATA-T-TATATAAGTTTTCAAAAATGTTTTCAAAAACTATATA
2693665 TTATATAAGTTTTCAA
64 TTATATAAGTTTTCAA
* *
2693681 AAAAAATGTTTTCAAAATCTATATATTATATAAGTTTTC-AAAATGATTTT-AAAAACTATATAT
1 AAAAAATGTTTTTAAAAACTATATATTATATAAGTTTTCAAAAATG-TTTTCAAAAACTATATAT
** *
2693744 TATATATTTTTTC-T
65 TATATAAGTTTTCAA
** * *
2693758 AAAATGTTTCTTTTAAAAACTATATATTATATACGTATTTTCAAAAA
1 AAAAAATGT-TTTTAAAAACTATATATTATATAAG--TTTTCAAAAA
2693805 CCGTTTGAAA
Statistics
Matches: 105, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
77 6 0.06
78 52 0.50
79 23 0.22
80 7 0.07
81 17 0.16
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (79 bp):
AAAAAATGTTTTTAAAAACTATATATTATATAAGTTTTCAAAAATGTTTTCAAAAACTATATATT
ATATAAGTTTTCAA
Found at i:2693784 original size:41 final size:38
Alignment explanation
Indices: 2693590--2693804 Score: 220
Period size: 41 Copynumber: 5.5 Consensus size: 38
2693580 TTTAAAAAAC
* * *
2693590 TATATAA-TTTCCAAAAAAG-TTTTAAAAATTATATATT
1 TATATAAGTTTTCAAAAATGTTTTTAAAAACTATATA-T
*
2693627 ATATATAAGTTTTCAAAAATGTTTTCAAAAACTATATAT
1 -TATATAAGTTTTCAAAAATGTTTTTAAAAACTATATAT
* *
2693666 TATATAAGTTTTCAAAAAAAATGTTTTCAAAATCTATATAT
1 TATATAAGTTTTC---AAAAATGTTTTTAAAAACTATATAT
*
2693707 TATATAAGTTTTC-AAAATGATTTTAAAAACTATATAT
1 TATATAAGTTTTCAAAAATGTTTTTAAAAACTATATAT
** *
2693744 TATATATTTTTTCTAAAATGTTTCTTTTAAAAACTATATAT
1 TATATAAGTTTTCAAAAATG--T-TTTTAAAAACTATATAT
*
2693785 TATATACGTATTTTCAAAAA
1 TATATAAG--TTTTCAAAAA
2693805 CCGTTTGAAA
Statistics
Matches: 152, Mismatches: 14, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
37 32 0.21
38 26 0.17
39 11 0.07
40 14 0.09
41 60 0.39
43 9 0.06
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (38 bp):
TATATAAGTTTTCAAAAATGTTTTTAAAAACTATATAT
Found at i:2694469 original size:84 final size:84
Alignment explanation
Indices: 2694364--2694636 Score: 289
Period size: 86 Copynumber: 3.2 Consensus size: 84
2694354 TTTTATTGAT
* * * ** *
2694364 AGATAGCCCTTCTTGTCTTGAGCTATATTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
1 AGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
2694429 TCGAAGGTCTTTGGTTGGC
66 TCGAAGGTCTTTGGTTGGC
* * * * * * * * *
2694448 AGATAAACCTTCTAGCCTTGAGTTATGCTACAAATGATATCCCCTCCGAAGCTGAGTGTAATCGA
1 AGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGT-GCCT-TGGAGCTGAGCGTAGTCGA
* *
2694513 ACTTGAAGATCTTTGGTTGGC
64 ACTCGAAGGTCTTTGGTTGGC
* * * *
2694534 AGATAACCCTTATCA-ACTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
1 AGATAACCCTTCT-AGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
*
2694598 CTCGAAGGTCTTT-GTTGCC
65 CTCGAAGGTCTTTGGTTGGC
* *
2694617 AAATAACCCTTCTATCCTTG
1 AGATAACCCTTCTAGCCTTG
2694637 TGTGTTAACT
Statistics
Matches: 148, Mismatches: 37, Indels: 9
0.76 0.19 0.05
Matches are distributed among these distances:
82 1 0.01
83 19 0.13
84 56 0.38
85 6 0.04
86 65 0.44
87 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (84 bp):
AGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
TCGAAGGTCTTTGGTTGGC
Found at i:2705479 original size:18 final size:18
Alignment explanation
Indices: 2705456--2705493 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2705446 CGACCTAGGT
2705456 GCCGATAGGAGCTAGCGA
1 GCCGATAGGAGCTAGCGA
2705474 GCCGATAGGAGCTAGCGA
1 GCCGATAGGAGCTAGCGA
2705492 GC
1 GC
2705494 TAAGGTGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.39, T:0.11
Consensus pattern (18 bp):
GCCGATAGGAGCTAGCGA
Found at i:2706753 original size:18 final size:17
Alignment explanation
Indices: 2706699--2706747 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
2706689 TTGGACTCCT
* *
2706699 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
2706717 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
2706735 AGTGCATTCGATG
1 AGTGCA-TCGATG
2706748 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:2706768 original size:64 final size:61
Alignment explanation
Indices: 2706699--2706878 Score: 177
Period size: 64 Copynumber: 2.8 Consensus size: 61
2706689 TTGGACTCCT
*
2706699 AGTGCATCGGTGCACTAAGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAA-AAAT-AG
1 AGTGCATCGATGCA-TAAGAGTGCATCGATGCATGAA-TGCATTCGATGTTTGAATAAATCAG
* * * *
2706760 CCCGGTGCATCGATGCAT-GGATTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAAT
1 ---AGTGCATCGATGCATAAGA--GTGCATCGATGCAT-GAATGCATTCGATGTTTGAA-TAAAT
2706824 CAG
59 CAG
* *
2706827 AGTGCATCGATGCATAGAGAGTGCATCGGTACATGGAATGCATTCGATGTTT
1 AGTGCATCGATGCATA-AGAGTGCATCGATGCAT-GAATGCATTCGATGTTT
2706879 CAATTTATTC
Statistics
Matches: 97, Mismatches: 11, Indels: 16
0.78 0.09 0.13
Matches are distributed among these distances:
62 2 0.02
63 1 0.01
64 84 0.87
65 2 0.02
66 6 0.06
67 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (61 bp):
AGTGCATCGATGCATAAGAGTGCATCGATGCATGAATGCATTCGATGTTTGAATAAATCAG
Found at i:2706913 original size:21 final size:21
Alignment explanation
Indices: 2706889--2706928 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2706879 CAATTTATTC
2706889 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
2706910 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
2706929 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:2708976 original size:18 final size:17
Alignment explanation
Indices: 2708922--2708970 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
2708912 TTGGACTCCT
* *
2708922 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
2708940 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
2708958 AGTGCATTCGATG
1 AGTGCA-TCGATG
2708971 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:2708991 original size:64 final size:61
Alignment explanation
Indices: 2708922--2709101 Score: 186
Period size: 64 Copynumber: 2.8 Consensus size: 61
2708912 TTGGACTCCT
*
2708922 AGTGCATCGGTGCACTAAGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAA-AAAT-AG
1 AGTGCATCGATGCA-TAAGAGTGCATCGATGCATGAA-TGCATTCGATGTTTGAATAAATCAG
* * * *
2708983 CCTGGTGCATCGATGCAT-GGATTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAAT
1 ---AGTGCATCGATGCATAAGA--GTGCATCGATGCAT-GAATGCATTCGATGTTTGAA-TAAAT
2709047 CAG
59 CAG
*
2709050 AGTGCATCGATGCATAGAGAGTGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGCATCGATGCATA-AGAGTGCATCGATGCAT-GAATGCATTCGATGTTT
2709102 CAATTTATTC
Statistics
Matches: 98, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
62 2 0.02
63 1 0.01
64 85 0.87
65 2 0.02
66 6 0.06
67 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (61 bp):
AGTGCATCGATGCATAAGAGTGCATCGATGCATGAATGCATTCGATGTTTGAATAAATCAG
Found at i:2711190 original size:18 final size:17
Alignment explanation
Indices: 2711136--2711184 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
2711126 TTGGACTCCT
* *
2711136 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
2711154 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
2711172 AGTGCATTCGATG
1 AGTGCA-TCGATG
2711185 TTTGAAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:2711282 original size:19 final size:19
Alignment explanation
Indices: 2711258--2711296 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2711248 TAATTAAATC
2711258 AGAGTGAATCGATGCATGG
1 AGAGTGAATCGATGCATGG
* *
2711277 AGAGTGCATCGGTGCATGG
1 AGAGTGAATCGATGCATGG
2711296 A
1 A
2711297 ATGCATTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.13, G:0.38, T:0.21
Consensus pattern (19 bp):
AGAGTGAATCGATGCATGG
Found at i:2711293 original size:64 final size:64
Alignment explanation
Indices: 2711136--2711341 Score: 217
Period size: 64 Copynumber: 3.3 Consensus size: 64
2711126 TTGGACTCCT
* * * * *
2711136 AGTGCATCGGTGCACT-AAGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAA--AAA-CTG
1 AGTGCATCGATGCA-TGGAGAGTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAG
** * *
2711197 -GTGCATCGATGCATGGATTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCAG
1 AGTGCATCGATGCATGGAGAGTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAG
* * * * *
2711260 AGTGAATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTTTCAATTTATTCATT
1 AGTGCATCGATGCATGGAGAGTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCA--
2711325 G
64 G
2711326 A-TGCATCGATGCATGG
1 AGTGCATCGATGCATGG
2711342 TATTGATGCA
Statistics
Matches: 120, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
59 1 0.01
60 45 0.38
62 3 0.03
63 2 0.02
64 53 0.44
65 14 0.12
66 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.31
Consensus pattern (64 bp):
AGTGCATCGATGCATGGAGAGTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAG
Found at i:2711346 original size:21 final size:21
Alignment explanation
Indices: 2711322--2711361 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2711312 CAATTTATTC
2711322 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
2711343 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
2711362 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:2713983 original size:24 final size:23
Alignment explanation
Indices: 2713912--2713991 Score: 94
Period size: 24 Copynumber: 3.5 Consensus size: 23
2713902 CATGGTCTTG
*
2713912 TGCATCGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGGGA
* *
2713935 TGCATCGGTG--CA-TCATGCGGA
1 TGCATCGATGCACATTCAAG-GGA
2713956 TGCATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
2713980 TGCATCGATGCA
1 TGCATCGATGCA
2713992 TTGTTAAGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
20 4 0.09
21 13 0.28
23 11 0.23
24 17 0.36
25 2 0.04
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.23
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:2714004 original size:44 final size:42
Alignment explanation
Indices: 2713890--2714011 Score: 120
Period size: 44 Copynumber: 2.8 Consensus size: 42
2713880 AAACCCGACA
* *
2713890 GATGCATCGATGCATGGTCTTGTGCATCGATGCACATTCAAGG
1 GATGCATCGATGCATTGT-TAGTGCATCGATGCACATTCAAGG
* * **
2713933 CATGCATCGGTGCATCATG-CGGATGCATCGATGCACATTCAAAGG
1 GATGCATCGATGCAT--TGTTAG-TGCATCGATGCACATTC-AAGG
*
2713978 GATGCATCGATGCATTGTTAAGTGCATCGGTGCA
1 GATGCATCGATGCATTGTT-AGTGCATCGATGCA
2714012 TTAAGCACAA
Statistics
Matches: 63, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
43 16 0.25
44 28 0.44
45 19 0.30
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (42 bp):
GATGCATCGATGCATTGTTAGTGCATCGATGCACATTCAAGG
Found at i:2717582 original size:31 final size:31
Alignment explanation
Indices: 2717459--2717583 Score: 180
Period size: 31 Copynumber: 4.0 Consensus size: 31
2717449 CCCGAAGAAC
* * *
2717459 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
* *
2717490 CAGTTCATATGTCCCGAAGAACATAGGAAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
2717521 TAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2717552 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2717583 C
1 C
2717584 CCTCGACCCT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
31 83 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:2718545 original size:21 final size:21
Alignment explanation
Indices: 2718521--2718564 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2718511 TTTTGTTCGT
* *
2718521 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2718542 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2718563 TT
1 TT
2718565 ACCCAGAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2722261 original size:18 final size:17
Alignment explanation
Indices: 2722207--2722255 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
2722197 TTGGACTCCT
* *
2722207 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
2722225 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
2722243 AGTGCATTCGATG
1 AGTGCA-TCGATG
2722256 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:2722340 original size:64 final size:64
Alignment explanation
Indices: 2722227--2722436 Score: 217
Period size: 64 Copynumber: 3.2 Consensus size: 64
2722217 TGCACTAAGA
* * ** * *
2722227 GTGCATCGATGCATGAAGTGCATTCGATGTTTGAAAAATAACCTG-GTGCATCGATGCATGGATT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTA-AATCAGAGTGCATCGATGCATGGATT
* * **
2722291 GTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCAGAGTGCATCGATGCATGGAGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAGAGTGCATCGATGCATGGATT
* * * * *
2722355 GTGCATTGGTGCATGGAATGCATTCGATGTTTCAATTTATTCATTGA-TGCATCGATGCATGGTA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCA--GAGTGCATCGATGCATGG-A
2722419 TT
63 TT
*
2722421 GATGCATCGGTGCATG
1 G-TGCATCGATGCATG
2722437 CCTTTGAAAA
Statistics
Matches: 122, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
63 4 0.03
64 86 0.70
65 15 0.12
66 4 0.03
67 13 0.11
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAGAGTGCATCGATGCATGGATT
Found at i:2722357 original size:19 final size:19
Alignment explanation
Indices: 2722333--2722383 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
2722323 TAATTAAATC
2722333 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
* *
2722352 AGAGTGCATTGGTGCATGG
1 AGAGTGCATCGATGCATGG
2722371 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
2722384 TTTCAATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 4 0.15
18 5 0.19
19 18 0.67
ACGTcount: A:0.25, C:0.14, G:0.35, T:0.25
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:2722421 original size:21 final size:21
Alignment explanation
Indices: 2722397--2722436 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2722387 CAATTTATTC
2722397 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
2722418 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
2722437 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:2729197 original size:18 final size:17
Alignment explanation
Indices: 2729143--2729191 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
2729133 TTGGACTCCT
* *
2729143 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
2729161 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
2729179 AGTGCATTCGATG
1 AGTGCA-TCGATG
2729192 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:2729274 original size:19 final size:19
Alignment explanation
Indices: 2729250--2729300 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
2729240 TAATTAAATC
2729250 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
2729269 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
2729288 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
2729301 TTTTAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:2729276 original size:64 final size:64
Alignment explanation
Indices: 2729208--2729333 Score: 164
Period size: 64 Copynumber: 2.0 Consensus size: 64
2729198 AAATAGCCTG
*
2729208 GTGCATCGATGCACCAAATGCATTCGATTTTTTAATTAAATCA-GAGTGCATCGATGCATGGAGA
1 GTGCATCGATGCACCAAATGCATTCGATGTTTTAATTAAATCATGA-TGCATCGATGCATGGAGA
* *** * *
2729272 GTGCATCGGTGCATGGAATGCATTCGATGTTTTAATTTATTCATTGATGCATCGATGCATGG
1 GTGCATCGATGCACCAAATGCATTCGATGTTTTAATTAAATCA-TGATGCATCGATGCATGG
2729334 TATTGATGCA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
64 36 0.68
65 15 0.28
66 2 0.04
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCACCAAATGCATTCGATGTTTTAATTAAATCATGATGCATCGATGCATGGAGA
Found at i:2729338 original size:21 final size:21
Alignment explanation
Indices: 2729314--2729353 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2729304 TAATTTATTC
2729314 ATTGATGCATC-GATGCATGGT
1 ATTGATGCATCAG-TGCATGGT
2729335 ATTGATGCATCAGTGCATG
1 ATTGATGCATCAGTGCATG
2729354 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCAGTGCATGGT
Found at i:2730425 original size:168 final size:168
Alignment explanation
Indices: 2730144--2730557 Score: 594
Period size: 168 Copynumber: 2.5 Consensus size: 168
2730134 ACACGCAACA
* * *
2730144 AGTTATGCTGCAAATGATGTGACCTCGAAACTGAGTGTAATCGAACTCGACGGTCTTTGGTTGGC
1 AGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGC
* * * * * *
2730209 AGATAGCCCTTATTGACTTAAGCTATGTTGTAAATAATGTGTCTTTGAGCTGAGCGTAAACGAAC
66 AGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATAATGTGCCTTTGAGCTGAACATAAACGAAC
* * * *
2730274 TCGAAGGTCTTTGTTGGCAGTTAACCCTTCTAGCTTTG
131 TCAAAGGTCTTTATTGGCAGATAACCCTTCTAGCCTTG
* * *
2730312 AGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTTGAAGGTCTTTGGTTGGC
1 AGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGC
* ** *
2730377 AGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAACATAGTCTAAC
66 AGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATAATGTGCCTTTGAGCTGAACATAAACGAAC
2730442 TCAAAGGTCTTTATTGGCAGATAACCCTTCTAGCCTTG
131 TCAAAGGTCTTTATTGGCAGATAACCCTTCTAGCCTTG
* * * * *
2730480 AGTTATGTTGCAAATAATGTGCCATCGAAGCTGAGTGTAATTGAACTCGAAGGTCTTTTGTTGGC
1 AGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGC
*
2730545 AGATAACCCTTCT
66 AGATAGCCCTTCT
2730558 AGCCTTGAGT
Statistics
Matches: 217, Mismatches: 29, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
168 217 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (168 bp):
AGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGC
AGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATAATGTGCCTTTGAGCTGAACATAAACGAAC
TCAAAGGTCTTTATTGGCAGATAACCCTTCTAGCCTTG
Found at i:2730579 original size:85 final size:85
Alignment explanation
Indices: 2730144--2730581 Score: 445
Period size: 85 Copynumber: 5.2 Consensus size: 85
2730134 ACACGCAACA
* * * *
2730144 AGTTATGCTGCAAATGATGTGACC-TCGAAACTGAGTGTAATCGAACTCGACGGTCTTTGGTTGG
1 AGTTATGCTGCAAATAATGTG-CCTTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGG
* * * * *
2730208 CAGATAGCCCTTATTGACTTA
65 CAGATAACCCTTCTAGCCTTG
* * * * * * *
2730229 AGCTATGTTGTAAATAATGTGTCTTTG-AGCTGAGCGTAAACGAACTCGAAGGTC-TTTGTTGGC
1 AGTTATGCTGCAAATAATGTGCCTTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGC
* *
2730292 AGTTAACCCTTCTAGCTTTG
66 AGATAACCCTTCTAGCCTTG
* * * * * *
2730312 AGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTTGAAGGTCTTTGGTTGGC
1 AGTTATGCTGCAAATAATGTGCCTTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGC
* * * *
2730377 AGATAGCCCTTCTCGACTTA
66 AGATAACCCTTCTAGCCTTG
* * * * *** * * * *
2730397 AGCTATGCTGTAAATGATGTGCCTTTG-AGCTGAACATAGTCTAACTCAAAGGTC-TTTATTGGC
1 AGTTATGCTGCAAATAATGTGCCTTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGC
2730460 AGATAACCCTTCTAGCCTTG
66 AGATAACCCTTCTAGCCTTG
* * *
2730480 AGTTATGTTGCAAATAATGTGCCATCGAAGCTGAGTGTAATTGAACTCGAAGGTCTTTTGTTGGC
1 AGTTATGCTGCAAATAATGTGCCTTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGC
2730545 AGATAACCCTTCTAGCCTTG
66 AGATAACCCTTCTAGCCTTG
*
2730565 AGTTATGCTACAAATAA
1 AGTTATGCTGCAAATAA
2730582 ATGAAGAAAT
Statistics
Matches: 280, Mismatches: 68, Indels: 10
0.78 0.19 0.03
Matches are distributed among these distances:
83 85 0.30
84 88 0.31
85 107 0.38
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.32
Consensus pattern (85 bp):
AGTTATGCTGCAAATAATGTGCCTTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGC
AGATAACCCTTCTAGCCTTG
Found at i:2731823 original size:86 final size:88
Alignment explanation
Indices: 2731721--2731898 Score: 261
Period size: 86 Copynumber: 2.0 Consensus size: 88
2731711 ATTATATAAA
*
2731721 TATTATAATAACCTTTATCAGGCTAGCTGAATATTATCCATAAAG-TG-GGCGTTTAACCAATTA
1 TATTATAATAACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCTGAGGCGCTTAACCAATTA
*
2731784 CTCTAGAGGGACAACTCGAGCTT
66 CTCTAGAGGGACAACTCAAGCTT
* * * * *
2731807 TATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCTGAGGTGCTTAACCTATTG
1 TATTATAATAACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCTGAGGCGCTTAACCAATTA
* *
2731872 CTTTAGAGGGACAGCTCAAGCTT
66 CTCTAGAGGGACAACTCAAGCTT
2731895 TATT
1 TATT
2731899 GTATATATAT
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
86 43 0.53
87 2 0.02
88 36 0.44
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (88 bp):
TATTATAATAACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCTGAGGCGCTTAACCAATTA
CTCTAGAGGGACAACTCAAGCTT
Found at i:2731907 original size:2 final size:2
Alignment explanation
Indices: 2731900--2731942 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2731890 AGCTTTATTG
2731900 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2731942 T
1 T
2731943 GTAATTTGGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2735749 original size:20 final size:20
Alignment explanation
Indices: 2735712--2735794 Score: 73
Period size: 20 Copynumber: 4.2 Consensus size: 20
2735702 AGAAAAGGGA
* *
2735712 AAAATAATAAATTGATAAAT
1 AAAATAATAAAATAATAAAT
*
2735732 AAAATACTAAAATAATAAAT
1 AAAATAATAAAATAATAAAT
** *
2735752 CAAAGGAAAAAAATAA-AAAT
1 -AAAATAATAAAATAATAAAT
2735772 -AAA-AATAAAATAGATAAAT
1 AAAATAATAAAATA-ATAAAT
2735791 AAAA
1 AAAA
2735795 AAAGTTAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
17 8 0.16
18 3 0.06
19 4 0.08
20 24 0.48
21 11 0.22
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.20
Consensus pattern (20 bp):
AAAATAATAAAATAATAAAT
Found at i:2737246 original size:41 final size:41
Alignment explanation
Indices: 2737201--2737327 Score: 147
Period size: 42 Copynumber: 3.1 Consensus size: 41
2737191 TGAATAAGAA
* *
2737201 ATAATAATAAATAAATATAAAAAT-TATTTTTTAAAAACTAT
1 ATAATAATAAATAATTTTAAAAATGT-TTTTTTAAAAACTAT
2737242 ATAAT-ATAAAT--TTTTAAAAATGTTTCTTTTAAAAACTAT
1 ATAATAATAAATAATTTTAAAAATGTTT-TTTTAAAAACTAT
* *
2737281 ATATTATATAAA-AATTTTCAAAAATGTTTTTTAAAAAACTAT
1 ATAATA-ATAAATAATTTT-AAAAATGTTTTTTTAAAAACTAT
2737323 ATAAT
1 ATAAT
2737328 TTCCAAAAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
38 10 0.14
39 18 0.24
40 6 0.08
41 10 0.14
42 20 0.27
43 10 0.14
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (41 bp):
ATAATAATAAATAATTTTAAAAATGTTTTTTTAAAAACTAT
Found at i:2737384 original size:29 final size:30
Alignment explanation
Indices: 2737293--2737384 Score: 123
Period size: 30 Copynumber: 3.0 Consensus size: 30
2737283 ATTATATAAA
* *
2737293 AATTTTCAAAAATGTTTTTTAAAAAACTATAT
1 AATTTCCAAAAAAG-TTTTT-AAAAACTATAT
*
2737325 AATTTCCAAAAAAGTTTTTAAAAACTGTAT
1 AATTTCCAAAAAAGTTTTTAAAAACTATAT
*
2737355 AATTTCCAAAAAAG-TTTTAAAAATTATAT
1 AATTTCCAAAAAAGTTTTTAAAAACTATAT
2737384 A
1 A
2737385 TTATATATAA
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
29 14 0.25
30 24 0.44
31 5 0.09
32 12 0.22
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (30 bp):
AATTTCCAAAAAAGTTTTTAAAAACTATAT
Found at i:2737404 original size:39 final size:38
Alignment explanation
Indices: 2737352--2737564 Score: 209
Period size: 41 Copynumber: 5.4 Consensus size: 38
2737342 TTAAAAACTG
* *
2737352 TATAA-TTTCCAAAAAAGTTTT-AAAAATTATATATTATA
1 TATAAGTTTTCAAAAAAGTTTTCAAAAACTATATA-T-TA
*
2737390 TATAAGTTTTCAAAAATGTTTTCAAAAAACTATATATTA
1 TATAAGTTTTCAAAAAAGTTTTC-AAAAACTATATATTA
2737429 TATAAGTTTTCAAAAAAAAGTTTTCAAAAACTATATATTA
1 TATAAGTTTTC--AAAAAAGTTTTCAAAAACTATATATTA
* *
2737469 TATAAGTTTTC-AAAATGATTTT-AAAAACCATATATTA
1 TATAAGTTTTCAAAAAAG-TTTTCAAAAACTATATATTA
* * * *
2737506 TATAATTTTTCTAAAATGTTTATTTTAAAAACTATATATTA
1 TATAAGTTTTCAAAAAAG--T-TTTCAAAAACTATATATTA
*
2737547 TATACGTATTTTCAAAAA
1 TATAAG--TTTTCAAAAA
2737565 CCGTTTGCAA
Statistics
Matches: 151, Mismatches: 12, Indels: 19
0.83 0.07 0.10
Matches are distributed among these distances:
37 29 0.19
38 15 0.10
39 28 0.19
40 30 0.20
41 40 0.26
43 9 0.06
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.42
Consensus pattern (38 bp):
TATAAGTTTTCAAAAAAGTTTTCAAAAACTATATATTA
Found at i:2737430 original size:41 final size:37
Alignment explanation
Indices: 2737229--2737564 Score: 218
Period size: 39 Copynumber: 8.9 Consensus size: 37
2737219 AAAAATTATT
* *
2737229 TTTTAAAAACTATATA--ATATAAATTTTTAAAAATG
1 TTTTAAAAACTATATATTATATAAGTTTTCAAAAATG
*
2737264 TTTCTTTTAAAAACTATATATTATATAAAAATTTTCAAAAATG
1 ----TTTTAAAAACTATATATTATAT--AAGTTTTCAAAAATG
** * * *
2737307 TTTTTTAAA--A-A-ACTATATAA-TTTCCAAAAAAG
1 TTTTAAAAACTATATATTATATAAGTTTTCAAAAATG
* * *
2737339 TTTTTAAAAAC-------TGTATAA-TTTCCAAAAAAG
1 -TTTTAAAAACTATATATTATATAAGTTTTCAAAAATG
*
2737369 TTTTAAAAATTATATATTATATATAAGTTTTCAAAAATG
1 TTTTAAAAACTATATA-T-TATATAAGTTTTCAAAAATG
*
2737408 TTTTCAAAAAACTATATATTATATAAGTTTTCAAAAAAAAG
1 TTTT--AAAAACTATATATTATATAAGTTTTC--AAAAATG
2737449 TTTTCAAAAACTATATATTATATAAGTTTTC-AAAATG
1 TTTT-AAAAACTATATATTATATAAGTTTTCAAAAATG
* * *
2737486 ATTTTAAAAACCATATATTATATAATTTTTCTAAAATG
1 -TTTTAAAAACTATATATTATATAAGTTTTCAAAAATG
*
2737524 TTTATTTTAAAAACTATATATTATATACGTATTTTCAAAAA
1 ----TTTTAAAAACTATATATTATATAAG--TTTTCAAAAA
2737565 CCGTTTGCAA
Statistics
Matches: 247, Mismatches: 23, Indels: 50
0.77 0.07 0.16
Matches are distributed among these distances:
29 9 0.04
30 18 0.07
32 10 0.04
33 9 0.04
35 6 0.02
36 1 0.00
37 30 0.12
38 16 0.06
39 50 0.20
40 27 0.11
41 48 0.19
43 23 0.09
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (37 bp):
TTTTAAAAACTATATATTATATAAGTTTTCAAAAATG
Found at i:2737451 original size:14 final size:14
Alignment explanation
Indices: 2737432--2737458 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2737422 TATATTATAT
2737432 AAGTTTTCAAAAAA
1 AAGTTTTCAAAAAA
2737446 AAGTTTTCAAAAA
1 AAGTTTTCAAAAA
2737459 CTATATATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (14 bp):
AAGTTTTCAAAAAA
Found at i:2737590 original size:2 final size:2
Alignment explanation
Indices: 2737578--2737612 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2737568 TTTGCAAACC
2737578 AT AT A- 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 AT AT AT
2737613 GGACGAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2737705 original size:3 final size:3
Alignment explanation
Indices: 2737699--2737728 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2737689 TATTAAACAT
*
2737699 ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2737729 TCACCTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:2752004 original size:31 final size:28
Alignment explanation
Indices: 2751949--2752050 Score: 105
Period size: 28 Copynumber: 3.5 Consensus size: 28
2751939 TTTCATCTAA
* * *
2751949 GTACCTAAAGTAACTTTTGATCAAAATAA
1 GTACCTAAAGT-ATTTTTGGTCAAAATAG
* *
2751978 GTACTTAAACTTATCTTTTTGGTCAAAATAG
1 GTACCTAAA-GTA--TTTTTGGTCAAAATAG
*
2752009 GCACCTAAAGTATTTTTGGTCAAAATAG
1 GTACCTAAAGTATTTTTGGTCAAAATAG
*
2752037 GTACCCAAAGTATT
1 GTACCTAAAGTATT
2752051 CAATTTTTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
28 28 0.47
29 9 0.15
30 3 0.05
31 20 0.33
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (28 bp):
GTACCTAAAGTATTTTTGGTCAAAATAG
Found at i:2757534 original size:24 final size:24
Alignment explanation
Indices: 2757500--2757584 Score: 143
Period size: 24 Copynumber: 3.5 Consensus size: 24
2757490 CTCTTTGATC
* *
2757500 TCTTGTCTTTACATGTGACTTGAA
1 TCTTGTTTTTATATGTGACTTGAA
*
2757524 TCTTGTTTTTATATGTGTCTTGAA
1 TCTTGTTTTTATATGTGACTTGAA
2757548 TCTTGTTTTTATATGTGACTTGAA
1 TCTTGTTTTTATATGTGACTTGAA
2757572 TCTTGTTTTTATA
1 TCTTGTTTTTATA
2757585 CCCTTCATTC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.19, C:0.11, G:0.15, T:0.55
Consensus pattern (24 bp):
TCTTGTTTTTATATGTGACTTGAA
Found at i:2767005 original size:18 final size:19
Alignment explanation
Indices: 2766977--2767012 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
2766967 AACAACACTT
2766977 TTTTGAATTTTGCTCCACA
1 TTTTGAATTTTGCTCCACA
2766996 TTTT-AATTTTGCTCCAC
1 TTTTGAATTTTGCTCCAC
2767013 CTTACTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.19, C:0.22, G:0.08, T:0.50
Consensus pattern (19 bp):
TTTTGAATTTTGCTCCACA
Found at i:2773253 original size:32 final size:32
Alignment explanation
Indices: 2773217--2773288 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
2773207 TCAATATAAC
*
2773217 ATTTAGATAATGCACAACAGACTTAGTATTGT
1 ATTTAGATAATGCACAACAGACTTAGTATTAT
* * * * *
2773249 ATTTAGATGATGCATAGCAGAGTTAGTGTTAT
1 ATTTAGATAATGCACAACAGACTTAGTATTAT
2773281 ATTTAGAT
1 ATTTAGAT
2773289 CACACACATG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (32 bp):
ATTTAGATAATGCACAACAGACTTAGTATTAT
Found at i:2774799 original size:17 final size:17
Alignment explanation
Indices: 2774777--2774812 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2774767 GAGTATGTTG
2774777 TAAATAGAAAATTATTA
1 TAAATAGAAAATTATTA
*
2774794 TAAATAGAAAATTGTTA
1 TAAATAGAAAATTATTA
2774811 TA
1 TA
2774813 CGCAAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (17 bp):
TAAATAGAAAATTATTA
Found at i:2775932 original size:40 final size:40
Alignment explanation
Indices: 2775877--2776078 Score: 314
Period size: 40 Copynumber: 5.0 Consensus size: 40
2775867 ACCGTAGTAC
*
2775877 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* * * *
2775917 TACACATATGGTCGTGTCCACCATATACAACGAAGTGTAA
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2775957 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* * *
2775997 TACACAAAAGGTCATGCCCACCATATACACTGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
2776037 TACATATAAGGCCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2776077 TA
1 TA
2776079 TAAAGTTGCA
Statistics
Matches: 145, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 145 1.00
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:2776608 original size:45 final size:45
Alignment explanation
Indices: 2776551--2776709 Score: 239
Period size: 45 Copynumber: 3.6 Consensus size: 45
2776541 CATATGTTAG
* * *
2776551 TATGGAA-TAATGGCAAGTGTATTGGTAAAATAAGCTTACGAGCT
1 TATGGAACAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCT
*
2776595 TATGGAACAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCG
1 TATGGAACAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCT
*
2776640 TATGGAACAAATGATAAGTATATTGGTAAAATAAGCTTACGAGCT
1 TATGGAACAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCT
* * *
2776685 TATGGGATAAATGGTAAGTAGATTG
1 TATGGAACAAATGGTAAGTATATTG
2776710 ATAAGAAATG
Statistics
Matches: 104, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
44 7 0.07
45 97 0.93
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.29
Consensus pattern (45 bp):
TATGGAACAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCT
Found at i:2779304 original size:65 final size:63
Alignment explanation
Indices: 2779235--2779395 Score: 164
Period size: 65 Copynumber: 2.5 Consensus size: 63
2779225 GTTTTAATTG
* * * * *
2779235 AACATTGAATAGCTTTTGTGTACCGATACAC-ATACCATGTATCGATGCACTCCATGTATTATTA
1 AACATCGAATA-CTTTTGTGCACCGATACACAAT-CCATGCATCGATGCACCCCATCTATT-TTA
2779299 A
63 A
* * * * *
2779300 AACATCGAATTAATTTTATGCACTGATGCACAATCTATGCATCGATGCACCCCATCTATTTTAA
1 AACATCGAA-TACTTTTGTGCACCGATACACAATCCATGCATCGATGCACCCCATCTATTTTAA
2779364 AACATCGAAT-CATATTTGTGCACCGATACACA
1 AACATCGAATAC-T-TTTGTGCACCGATACACA
2779396 CCCCAGTGCA
Statistics
Matches: 78, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
63 2 0.03
64 28 0.36
65 44 0.56
66 4 0.05
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (63 bp):
AACATCGAATACTTTTGTGCACCGATACACAATCCATGCATCGATGCACCCCATCTATTTTAA
Found at i:2779386 original size:64 final size:65
Alignment explanation
Indices: 2779256--2779395 Score: 169
Period size: 65 Copynumber: 2.2 Consensus size: 65
2779246 GCTTTTGTGT
* * * * *
2779256 ACCGATACAC-ATACCATGTATCGATGCACTCCATGTATTATTAAAACATCGAATTAATTTTATG
1 ACCGATACACAAT-CTATGCATCGATGCACCCCATCTATTATTAAAACATCGAATCAATTTTATG
2779320 C
65 C
* * *
2779321 ACTGATGCACAATCTATGCATCGATGCACCCCATCTATT-TTAAAACATCGAATC-ATATTTGTG
1 ACCGATACACAATCTATGCATCGATGCACCCCATCTATTATTAAAACATCGAATCAAT-TTTATG
2779384 C
65 C
2779385 ACCGATACACA
1 ACCGATACACA
2779396 CCCCAGTGCA
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
63 2 0.03
64 29 0.46
65 30 0.48
66 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.30
Consensus pattern (65 bp):
ACCGATACACAATCTATGCATCGATGCACCCCATCTATTATTAAAACATCGAATCAATTTTATGC
Found at i:2785188 original size:21 final size:21
Alignment explanation
Indices: 2785164--2785220 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 21
2785154 TTTTGCATAA
2785164 TGCATCGATACACTATGAATG
1 TGCATCGATACACTATGAATG
* *
2785185 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGAT--A-CACTATGAATG
*
2785209 TGAATCGATACA
1 TGCATCGATACA
2785221 TCATGAAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
21 10 0.34
22 1 0.03
23 1 0.03
24 17 0.59
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (21 bp):
TGCATCGATACACTATGAATG
Found at i:2785239 original size:45 final size:44
Alignment explanation
Indices: 2785167--2785254 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 44
2785157 TGCATAATGC
*
2785167 ATCGATACACTATGAATGTGCATCGATGCA-TCCCTTTGAATGTGA
1 ATCGATACACTATGAATGTGCACCGATGCACT-CC-TTGAATGTGA
2785212 ATCGATACA-TCATGAA-GATGCACCGATGCACTCCTTGAATGTG
1 ATCGATACACT-ATGAATG-TGCACCGATGCACTCCTTGAATGTG
2785255 CAACGATGCA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
44 11 0.28
45 27 0.69
46 1 0.03
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (44 bp):
ATCGATACACTATGAATGTGCACCGATGCACTCCTTGAATGTGA
Found at i:2787977 original size:65 final size:64
Alignment explanation
Indices: 2787906--2788043 Score: 181
Period size: 65 Copynumber: 2.1 Consensus size: 64
2787896 GTTTTAATTG
* * * * *
2787906 AACATCGAATAGCTTTTGTGTACCGATGCAC-ATACCATGCATCGATGCACTCCATG-TATTATT
1 AACATCGAATAGATTTTATGCACCGATGCACAAT-CCATGCATCGATGCACCCCA-GCTATT-TG
2787969 AA
63 AA
*
2787971 AACATCGAATTGATTTTATGCACCGATGCACAATCCATGCATCGATGCACCCCAGCTATTTGAA
1 AACATCGAATAGATTTTATGCACCGATGCACAATCCATGCATCGATGCACCCCAGCTATTTGAA
2788035 AACATCGAA
1 AACATCGAA
2788044 GAAGATTTGT
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
64 13 0.20
65 50 0.77
66 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.28
Consensus pattern (64 bp):
AACATCGAATAGATTTTATGCACCGATGCACAATCCATGCATCGATGCACCCCAGCTATTTGAA
Found at i:2788077 original size:65 final size:65
Alignment explanation
Indices: 2787940--2788085 Score: 154
Period size: 65 Copynumber: 2.2 Consensus size: 65
2787930 GATGCACATA
* * ** * * *
2787940 CCATGCATCGATGCACTCCATGTATTATTAAAACATCGAATTGATTTTATGCACCGATGCACAAT
1 CCATGCATCGATGCACCCCATGTATTATGAAAACATCGAAAAGATTTTATGCACCAATACACAAC
*
2788005 CCATGCATCGATGCACCCCA-GCTATT-TGAAAACATCGAAGAAGA-TTTGTGCACCAATACACA
1 CCATGCATCGATGCACCCCATG-TATTATGAAAACATCGAA-AAGATTTTATGCACCAATACACA
*
2788067 CC
64 AC
*
2788069 CCAGTGCATTGATGCAC
1 CCA-TGCATCGATGCAC
2788086 TTGGTCAGCC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
64 31 0.46
65 37 0.54
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (65 bp):
CCATGCATCGATGCACCCCATGTATTATGAAAACATCGAAAAGATTTTATGCACCAATACACAAC
Found at i:2799704 original size:31 final size:31
Alignment explanation
Indices: 2799660--2799818 Score: 151
Period size: 31 Copynumber: 5.1 Consensus size: 31
2799650 GAGCATCTTG
*
2799660 GGGCCTAC-GGGCCTACCCAAGAAAGTTCTCA
1 GGGCC-ACGGGGCCTACCCAAGAAAGATCTCA
** * *
2799691 GGGTTACGGGGCCTACCCAAGAAAGATATTA
1 GGGCCACGGGGCCTACCCAAGAAAGATCTCA
* * *
2799722 GGGCCGCAGGGCCTACCCAAGAATGATCTCA
1 GGGCCACGGGGCCTACCCAAGAAAGATCTCA
*
2799753 GGGCCACGGGGCCTACCCAAGTAAA-ATCCCA
1 GGGCCACGGGGCCTACCCAAG-AAAGATCTCA
* ** * * *
2799784 TGGCCACAAGGCCTAACCAAGAATGATCTCG
1 GGGCCACGGGGCCTACCCAAGAAAGATCTCA
2799815 GGGC
1 GGGC
2799819 TGTAGAGCCT
Statistics
Matches: 101, Mismatches: 24, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
30 4 0.04
31 95 0.94
32 2 0.02
ACGTcount: A:0.28, C:0.30, G:0.28, T:0.14
Consensus pattern (31 bp):
GGGCCACGGGGCCTACCCAAGAAAGATCTCA
Found at i:2799762 original size:62 final size:62
Alignment explanation
Indices: 2799660--2799818 Score: 178
Period size: 62 Copynumber: 2.6 Consensus size: 62
2799650 GAGCATCTTG
* * ** **
2799660 GGGCCTAC-GGGCCTACCCAAGAAAGTTCTCAGGGTTACGGGGCCTACCCAAG-AAAGATATTA
1 GGGCC-ACAGGGCCTACCCAAGAATGATCTCAGGGCCACGGGGCCTACCCAAGTAAA-ATACCA
* *
2799722 GGGCCGCAGGGCCTACCCAAGAATGATCTCAGGGCCACGGGGCCTACCCAAGTAAAATCCCA
1 GGGCCACAGGGCCTACCCAAGAATGATCTCAGGGCCACGGGGCCTACCCAAGTAAAATACCA
* * * *
2799784 TGGCCACAAGGCCTAACCAAGAATGATCTCGGGGC
1 GGGCCACAGGGCCTACCCAAGAATGATCTCAGGGC
2799819 TGTAGAGCCT
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
61 1 0.01
62 78 0.95
63 3 0.04
ACGTcount: A:0.28, C:0.30, G:0.28, T:0.14
Consensus pattern (62 bp):
GGGCCACAGGGCCTACCCAAGAATGATCTCAGGGCCACGGGGCCTACCCAAGTAAAATACCA
Found at i:2803997 original size:31 final size:31
Alignment explanation
Indices: 2803959--2804093 Score: 127
Period size: 31 Copynumber: 4.4 Consensus size: 31
2803949 GCCTATAGGA
*
2803959 CTACCCAAGAAAGTTCTCAGGGCCACGAGGC
1 CTACCCAAGAAAGATCTCAGGGCCACGAGGC
* *
2803990 CTTCCCAAGAAAGATC-CTAAGG-C-CGTAGGGC
1 CTACCCAAGAAAGATCTC-AGGGCCACG-A-GGC
*
2804021 CTACCCAAGAATGATCTCAGGGCCAC-AGGTC
1 CTACCCAAGAAAGATCTCAGGGCCACGAGG-C
* * *
2804052 CTACCCAAGAAAAATCCCAGGGCCA-TAGGAC
1 CTACCCAAGAAAGATCTCAGGGCCACGAGG-C
2804083 CTACCCAAGAA
1 CTACCCAAGAA
2804094 TGATATCGGG
Statistics
Matches: 86, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
29 2 0.02
30 5 0.06
31 76 0.88
32 2 0.02
33 1 0.01
ACGTcount: A:0.33, C:0.32, G:0.22, T:0.13
Consensus pattern (31 bp):
CTACCCAAGAAAGATCTCAGGGCCACGAGGC
Found at i:2804059 original size:62 final size:62
Alignment explanation
Indices: 2803948--2804097 Score: 196
Period size: 62 Copynumber: 2.4 Consensus size: 62
2803938 ATCATCTTGG
* * * * *
2803948 GGCCTATAGGA-CTACCCAAGAAAGTTCTCAGGGCCACGAGGCCTTCCCAAGAAAGATCCTAA
1 GGCC-ATAGGACCTACCCAAGAATGATCTCAGGGCCACGAGGCCTACCCAAGAAAAATCCCAA
* * *
2804010 GGCCGTAGGGCCTACCCAAGAATGATCTCAGGGCCAC-AGGTCCTACCCAAGAAAAATCCCAG
1 GGCCATAGGACCTACCCAAGAATGATCTCAGGGCCACGAGG-CCTACCCAAGAAAAATCCCAA
2804072 GGCCATAGGACCTACCCAAGAATGAT
1 GGCCATAGGACCTACCCAAGAATGAT
2804098 ATCGGGGCTG
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
61 7 0.09
62 69 0.91
ACGTcount: A:0.32, C:0.30, G:0.23, T:0.15
Consensus pattern (62 bp):
GGCCATAGGACCTACCCAAGAATGATCTCAGGGCCACGAGGCCTACCCAAGAAAAATCCCAA
Found at i:2804117 original size:62 final size:62
Alignment explanation
Indices: 2803948--2804123 Score: 158
Period size: 62 Copynumber: 2.8 Consensus size: 62
2803938 ATCATCTTGG
* * * * * * *
2803948 GGCCTATAGGA-CTACCCAAGAAAGTTCTCAGGGCCAC-GAGGCCTTCCCAAGAAAGATCCTAA
1 GGCC-ATAGGACCTACCCAAGAATGATATCAGGGCCACAGA-ACCTACCCAAGAAAAATCCCAA
* * * ** *
2804010 GGCCGTAGGGCCTACCCAAGAATGATCTCAGGGCCACAGGTCCTACCCAAGAAAAATCCCAG
1 GGCCATAGGACCTACCCAAGAATGATATCAGGGCCACAGAACCTACCCAAGAAAAATCCCAA
* *** *
2804072 GGCCATAGGACCTACCCAAGAATGATATCGGGGCTGTAGAACCTACCTAAGA
1 GGCCATAGGACCTACCCAAGAATGATATCAGGGCCACAGAACCTACCCAAGA
2804124 GTCACATTAG
Statistics
Matches: 92, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
61 4 0.04
62 87 0.95
63 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.24, T:0.15
Consensus pattern (62 bp):
GGCCATAGGACCTACCCAAGAATGATATCAGGGCCACAGAACCTACCCAAGAAAAATCCCAA
Found at i:2808431 original size:32 final size:31
Alignment explanation
Indices: 2808359--2808431 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
2808349 CCACGTTGCT
* * *
2808359 TATCCAAGAATGATCTTAGGGCCGCAGGGCC
1 TATCCAAGAATGATCTCAGGGACACAGGGCC
*
2808390 TA-CCTAAGAATGATCTCAGGGAACACGGGGCC
1 TATCC-AAGAATGATCTCAGGG-ACACAGGGCC
2808422 TATCCAAGAA
1 TATCCAAGAA
2808432 AAATCCCAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 2 0.06
31 17 0.49
32 14 0.40
33 2 0.06
ACGTcount: A:0.32, C:0.25, G:0.26, T:0.18
Consensus pattern (31 bp):
TATCCAAGAATGATCTCAGGGACACAGGGCC
Found at i:2811864 original size:20 final size:20
Alignment explanation
Indices: 2811835--2811873 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2811825 AGAGCTCATA
*
2811835 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
2811855 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
2811874 GTGGTGAAAA
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:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:2824356 original size:40 final size:40
Alignment explanation
Indices: 2824312--2824418 Score: 178
Period size: 40 Copynumber: 2.7 Consensus size: 40
2824302 AAACTAAGTA
*
2824312 TATATGGTGGGCATGACCTTATGTGTAATACACTTCGGTG
1 TATATGGTGGGCATGACCTTATGTGTAATACACTTCGATG
* *
2824352 TATATGGTGTGCATGACCTTATGTATAATACACTTCGATG
1 TATATGGTGGGCATGACCTTATGTGTAATACACTTCGATG
*
2824392 TATATGGTGGGCACGACCTTATGTGTA
1 TATATGGTGGGCATGACCTTATGTGTA
2824419 GCACTACGGT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (40 bp):
TATATGGTGGGCATGACCTTATGTGTAATACACTTCGATG
Found at i:2826244 original size:17 final size:17
Alignment explanation
Indices: 2826222--2826271 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
2826212 TTAGAAGAGT
*
2826222 GTTTTGGGATATATCGG
1 GTTTTGGGATATATCAG
*
2826239 GTTTTGGTATCTATATCAG
1 GTTTTGGGA--TATATCAG
*
2826258 GTTTTGAGATATAT
1 GTTTTGGGATATAT
2826272 GTGATATCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 13 0.48
19 14 0.52
ACGTcount: A:0.22, C:0.06, G:0.26, T:0.46
Consensus pattern (17 bp):
GTTTTGGGATATATCAG
Found at i:2829857 original size:22 final size:21
Alignment explanation
Indices: 2829831--2829895 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 21
2829821 ACTCGATTGT
2829831 ATATTTACATTTTAATAATTTA
1 ATATTTAC-TTTTAATAATTTA
* *
2829853 ATATTAACTTTCTTAA-AAATT-
1 ATATTTAC-TT-TTAATAATTTA
*
2829874 ATTTATTACTTTTAATAATTTA
1 ATAT-TTACTTTTAATAATTTA
2829896 TTTTATCAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
20 4 0.12
21 9 0.27
22 16 0.48
23 4 0.12
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (21 bp):
ATATTTACTTTTAATAATTTA
Found at i:2831294 original size:16 final size:17
Alignment explanation
Indices: 2831273--2831310 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
2831263 AACGTCTTTT
2831273 AAAAACAATTTTAAGA-
1 AAAAACAATTTTAAGAC
*
2831289 AAAAACATTTTTAAGAC
1 AAAAACAATTTTAAGAC
2831306 AAAAA
1 AAAAA
2831311 AAAGGTCTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.63, C:0.08, G:0.05, T:0.24
Consensus pattern (17 bp):
AAAAACAATTTTAAGAC
Found at i:2833224 original size:83 final size:83
Alignment explanation
Indices: 2832989--2833637 Score: 787
Period size: 83 Copynumber: 7.9 Consensus size: 83
2832979 AACTGAATGA
* ** * * * * *
2832989 AATCGAACTTGAAAATTCTTGTTGACAGATAACCCTTATCGCCTTGAGTTTTACT--ATAATGAT
1 AATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTTGCCTTGAGTTATGCTGCA-AATGAT
2833052 GTGCCTTTGAGCTGAGTGT
65 GTGCCTTTGAGCTGAGTGT
** ** *
2833071 AATCGAACTCGAAGG-CCTTG--GGTAGATAACCCTTCTTGCCTTGAGTTATACTGCAAATGATG
1 AATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATG
2833133 TGCCTTTGAGCTGAGTGT
66 TGCCTTTGAGCTGAGTGT
* * * * *
2833151 AATCGAACTCGAAGGTATTTGTTGACATATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATG
1 AATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATG
2833216 TGCCTTTGAGCTGAGTGT
66 TGCCTTTGAGCTGAGTGT
* *
2833234 AATCGAACTCGAAGGTCTTTG--G-CAGATAACCCTTCTTGCCTTGAGTTTTGCTGCAAAT-ATG
1 AATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATG
* *
2833295 TGCCTTGGAGCTGAGCGT
66 TGCCTTTGAGCTGAGTGT
* * * * * *
2833313 AATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCTCTTTTTGCCTTGAGCTAT-ATAGCAAATGA
1 AATCGAACTCGAAGGT-TTTTGTTGACAGATAACCCTTCTTGCCTTGAGTTATGCT-GCAAATGA
*
2833377 TGTGCCTTTGAGCTGAGTAT
64 TGTGCCTTTGAGCTGAGTGT
** * * *
2833397 AATCGAACTCGAAGGACTTTGTTGATAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
1 AATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATG
*
2833462 TGCCTTTGAACTGAGTGT
66 TGCCTTTGAGCTGAGTGT
* * *
2833480 AATCGAACTCGAAGGTCTTTTGTTGACATATAACCCTTCTTGCCTTGAGTTATGTTGCAAATTAT
1 AATCGAACTCGAAGGT-TTTTGTTGACAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGAT
2833545 GTGCCTTTGAGCTGAGTGT
65 GTGCCTTTGAGCTGAGTGT
* * * *
2833564 AATCGAACTCGAAGGTCTTTTTTTTGGCAGATAACCCTTCTAGCCTTGAAGTTGTGCTGCAAATG
1 AATCGAACTCGAAGG--TTTTTGTTGACAGATAACCCTTCTTGCCTTG-AGTTATGCTGCAAATG
2833629 ATGTGCCTT
63 ATGTGCCTT
2833638 GAACTCGAAG
Statistics
Matches: 486, Mismatches: 65, Indels: 28
0.84 0.11 0.05
Matches are distributed among these distances:
79 62 0.13
80 75 0.15
81 9 0.02
82 14 0.03
83 169 0.35
84 108 0.22
85 26 0.05
86 23 0.05
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (83 bp):
AATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATG
TGCCTTTGAGCTGAGTGT
Found at i:2833263 original size:163 final size:164
Alignment explanation
Indices: 2833007--2833637 Score: 849
Period size: 163 Copynumber: 3.8 Consensus size: 164
2832997 TTGAAAATTC
* *
2833007 TTGTTGACAGATAACCCTTATCGCCTTGAGTT-T-TA-CTATAATGATGTGCCTTTGAGCTGAGT
1 TTGTTGACAGATAACCCTTCTTGCCTTGAGTTATGTAGC-A-AATGATGTGCCTTTGAGCTGAGT
* * * * *
2833069 GTAATCGAACTCGAAGGCCTTGGGTAGATAACCCTTCTTGCCTTGAGTTATACTGCAAATGATGT
64 GTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
*
2833134 GCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT-AT
129 GCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTT
* * * *
2833169 TTGTTGACATATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCTTTGAGCTGAGTGT
1 TTGTTGACAGATAACCCTTCTTGCCTTGAGTTATGTAGCAAATGATGTGCCTTTGAGCTGAGTGT
* *
2833234 AATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGTTTTGCTGCAAAT-ATGTGC
66 AATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
* *
2833298 CTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTT
131 CTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTT
* * * * * * *
2833332 TTGTTGGCAGATAGCTCTTTTTGCCTTGAGCTATATAGCAAATGATGTGCCTTTGAGCTGAGTAT
1 TTGTTGACAGATAACCCTTCTTGCCTTGAGTTATGTAGCAAATGATGTGCCTTTGAGCTGAGTGT
* * *
2833397 AATCGAACTCGAAGGACTTTGTTGATAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
66 AATCGAACTCGAAGGTCTTTG--G-CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATG
*
2833462 TGCCTTTGAACTGAGTGTAATCGAACTCGAAGGTCTT
128 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTT
* * *
2833499 TTGTTGACATATAACCCTTCTTGCCTTGAGTTATGTTGCAAATTATGTGCCTTTGAGCTGAGTGT
1 TTGTTGACAGATAACCCTTCTTGCCTTGAGTTATGTAGCAAATGATGTGCCTTTGAGCTGAGTGT
*
2833564 AATCGAACTCGAAGGTCTTTTTTTTGGCAGATAACCCTTCTAGCCTTGAAGTTGTGCTGCAAATG
66 AATCGAACTCGAAGGTC-----TTTGGCAGATAACCCTTCTAGCCTTG-AGTTATGCTGCAAATG
2833629 ATGTGCCTT
125 ATGTGCCTT
2833638 GAACTCGAAG
Statistics
Matches: 409, Mismatches: 46, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
162 64 0.16
163 154 0.38
164 2 0.00
165 1 0.00
166 32 0.08
167 108 0.26
169 20 0.05
170 24 0.06
172 4 0.01
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (164 bp):
TTGTTGACAGATAACCCTTCTTGCCTTGAGTTATGTAGCAAATGATGTGCCTTTGAGCTGAGTGT
AATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
CTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTT
Found at i:2833444 original size:246 final size:249
Alignment explanation
Indices: 2833011--2833637 Score: 889
Period size: 246 Copynumber: 2.5 Consensus size: 249
2833001 AAATTCTTGT
* * *
2833011 TGACAGATAACCCTTATCGCCTTGAGTTTTACT--ATAATGATGTGCCTTTGAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTTGCCTTGAGTTTTGCTGCA-AAT-ATGTGCCTTTGAGCTGAGTGTAAT
* * *
2833074 CGAACTCGAAGG-C-CTTG--GGTAGATAACCCTTCTTGCCTTGAGTTATACTGCAAATGATGTG
64 CGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATACTGCAAATGATGTG
* *
2833135 CCTTTGAGCTGAGTGTAATCGAACTCGAAGGTATTTGTTGACATATAACCCTTCTAGCCTTGAGT
129 CCTTTGAGCTGAGTATAATCGAACTCGAAGGTATTTGTTGACAGATAACCCTTCTAGCCTTGAGT
* *
2833200 TATGTTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTG
194 TATGCTGTAAATGATGTGCCTTTGAACTGAGTGTAATCGAACTCGAAGGTCTTTTG
* *
2833255 -G-CAGATAACCCTTCTTGCCTTGAGTTTTGCTGCAAATATGTGCCTTGGAGCTGAGCGTAATCG
1 TGACAGATAACCCTTCTTGCCTTGAGTTTTGCTGCAAATATGTGCCTTTGAGCTGAGTGTAATCG
* * *
2833318 AACTCGAAGGTCTTTTGTTGGCAGATAGCTCTTTTTGCCTTGAGCTATA-TAGCAAATGATGTGC
66 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATACT-GCAAATGATGTGC
*
2833382 CTTTGAGCTGAGTATAATCGAACTCGAAGG-ACTTTGTTGATAGATAACCCTTCTAGCCTTGAGT
130 CTTTGAGCTGAGTATAATCGAACTCGAAGGTA-TTTGTTGACAGATAACCCTTCTAGCCTTGAGT
2833446 TATGCTGTAAATGATGTGCCTTTGAACTGAGTGTAATCGAACTCGAAGGTCTTTTG
194 TATGCTGTAAATGATGTGCCTTTGAACTGAGTGTAATCGAACTCGAAGGTCTTTTG
* * *
2833502 TTGACATATAACCCTTCTTGCCTTGAGTTATGTTGCAAATTATGTGCCTTTGAGCTGAGTGTAAT
1 -TGACAGATAACCCTTCTTGCCTTGAGTTTTGCTGCAAA-TATGTGCCTTTGAGCTGAGTGTAAT
* * * * *
2833567 CGAACTCGAAGGTCTTTTTTTTGGCAGATAACCCTTCTAGCCTTGAAGTTGTGCTGCAAATGATG
64 CGAACTCGAAGGTC-TTTTGTTGGCAGATAACCCTTCTTGCCTTG-AGCTATACTGCAAATGATG
2833632 TGCCTT
127 TGCCTT
2833638 GAACTCGAAG
Statistics
Matches: 338, Mismatches: 29, Indels: 23
0.87 0.07 0.06
Matches are distributed among these distances:
242 61 0.18
243 5 0.01
244 4 0.01
245 2 0.01
246 146 0.43
247 4 0.01
249 1 0.00
250 32 0.09
251 37 0.11
252 25 0.07
253 20 0.06
254 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (249 bp):
TGACAGATAACCCTTCTTGCCTTGAGTTTTGCTGCAAATATGTGCCTTTGAGCTGAGTGTAATCG
AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATACTGCAAATGATGTGCC
TTTGAGCTGAGTATAATCGAACTCGAAGGTATTTGTTGACAGATAACCCTTCTAGCCTTGAGTTA
TGCTGTAAATGATGTGCCTTTGAACTGAGTGTAATCGAACTCGAAGGTCTTTTG
Found at i:2833671 original size:69 final size:69
Alignment explanation
Indices: 2833568--2833697 Score: 208
Period size: 69 Copynumber: 1.9 Consensus size: 69
2833558 GAGTGTAATC
** * *
2833568 GAACTCGAAGGTCTTTTTTTTGGCAGATAACCCTTCTAGCCTTGAAGTTGTGCTGCAAATGATGT
1 GAACTCGAAGGTCTTTTGGTTGGCAGATAACCCTTCTAGCCTTG-AGTTATGCTACAAATGATGT
2833633 GCCTT
65 GCCTT
2833638 GAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGA
1 GAACTCGAAGGTCTTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGA
2833698 ACACGATATC
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
68 15 0.27
69 28 0.50
70 13 0.23
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (69 bp):
GAACTCGAAGGTCTTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATGTG
CCTT
Found at i:2838312 original size:20 final size:20
Alignment explanation
Indices: 2838271--2838312 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2838261 CTGAAAAATC
*
2838271 AAATAAAATATTATATGGTA
1 AAATAAAATATTATATGCTA
2838291 AAATAAAATATTGA-ATGCTA
1 AAATAAAATATT-ATATGCTA
2838311 AA
1 AA
2838313 CAAAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.57, C:0.02, G:0.10, T:0.31
Consensus pattern (20 bp):
AAATAAAATATTATATGCTA
Found at i:2838628 original size:22 final size:21
Alignment explanation
Indices: 2838592--2838643 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
2838582 CAAAATGCCA
2838592 AAATTAAAA-TAACAGT-AGCT
1 AAATTAAAATTAACAGTGA-CT
2838612 AAATTAGAAATTAACAGTGACT
1 AAATTA-AAATTAACAGTGACT
2838634 AAATTAAAAT
1 AAATTAAAAT
2838644 AAAATAACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.21
21 7 0.24
22 15 0.52
23 1 0.03
ACGTcount: A:0.56, C:0.08, G:0.10, T:0.27
Consensus pattern (21 bp):
AAATTAAAATTAACAGTGACT
Found at i:2850827 original size:31 final size:30
Alignment explanation
Indices: 2850771--2850839 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 30
2850761 AAAAATTGAC
2850771 TTTATATTCTTTTTGTATTGAATTTTATTCACT
1 TTTA-ATTCTTTTTGTATTGAATTTTA-T-ACT
*
2850804 TTTAATTCTTTTT-TATTGTATTTTATACT
1 TTTAATTCTTTTTGTATTGAATTTTATACT
2850833 TTTAATT
1 TTTAATT
2850840 AAATTGAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
29 10 0.29
30 1 0.03
31 11 0.31
32 9 0.26
33 4 0.11
ACGTcount: A:0.22, C:0.07, G:0.04, T:0.67
Consensus pattern (30 bp):
TTTAATTCTTTTTGTATTGAATTTTATACT
Found at i:2852319 original size:42 final size:42
Alignment explanation
Indices: 2852118--2852637 Score: 404
Period size: 43 Copynumber: 12.0 Consensus size: 42
2852108 TCTTCCTTAG
* * * * * *
2852118 TTTTTGTAATATCATTTTTTACCTTTATATTTGAGGCACTTAA
1 TTTTT-TAATCTCACTTTTTACCTTTATAATTGAAGCCCCTAA
* * *
2852161 CTTTTTTAATCTCACTTTTTACTTTTATAATTGAAGCTCTTAA
1 -TTTTTTAATCTCACTTTTTACCTTTATAATTGAAGCCCCTAA
* * * * **
2852204 TTTTTTTTTCTAGCTCACTTTCTACCTTTATGATTGAAGCCTTTAA
1 ---TTTTTT-AATCTCACTTTTTACCTTTATAATTGAAGCCCCTAA
* * * *
2852250 TTCTTTTAATATCATTTTTTACATTTATAATTGAGGCCCCTAA
1 TT-TTTTAATCTCACTTTTTACCTTTATAATTGAAGCCCCTAA
* * * **** *
2852293 TTTTTTAATCTCACTTTCTACGTTTATAATTAAAGTTTATGA
1 TTTTTTAATCTCACTTTTTACCTTTATAATTGAAGCCCCTAA
* * * **
2852335 TATTTTTAATCTCATTTTTTACCTTCATAATTGATGTTCCTAAA
1 T-TTTTTAATCTCACTTTTTACCTTTATAATTGAAGCCCCT-AA
* * *
2852379 TTTTTCAATCTTACTTTTTACCTTTATAA-TGAAAGCCCATAA
1 TTTTTTAATCTCACTTTTTACCTTTATAATTG-AAGCCCCTAA
* *
2852421 TTTTTTAATCTCACTTTTTACATTTATAATTGAGGCCCCTAA
1 TTTTTTAATCTCACTTTTTACCTTTATAATTGAAGCCCCTAA
*
2852463 TTTATTTTCAATC-CAACTTTTTTACCTTTATAATTG-AGACCCTAA
1 -TT-TTTT-AATCTC-AC-TTTTTACCTTTATAATTGAAGCCCCTAA
* * * * *
2852508 TTTTTTCAATCTCACTTTCTACCTTTATATTTAAAGTCCCAAA
1 TTTTTT-AATCTCACTTTTTACCTTTATAATTGAAGCCCCTAA
* *
2852551 GTTTTTTAATCTTACTTTTTACCTTTATAATTG-AGGCCCTAA
1 -TTTTTTAATCTCACTTTTTACCTTTATAATTGAAGCCCCTAA
*
2852593 TTTTTTTAATC-CAACTTTTTACTTTTATAACTT-AAGCCCCTAA
1 -TTTTTTAATCTC-ACTTTTTACCTTTATAA-TTGAAGCCCCTAA
2852636 TT
1 TT
2852638 GATCATTTTT
Statistics
Matches: 382, Mismatches: 75, Indels: 40
0.77 0.15 0.08
Matches are distributed among these distances:
42 118 0.31
43 174 0.46
44 25 0.07
45 19 0.05
46 46 0.12
ACGTcount: A:0.27, C:0.17, G:0.06, T:0.50
Consensus pattern (42 bp):
TTTTTTAATCTCACTTTTTACCTTTATAATTGAAGCCCCTAA
Found at i:2852350 original size:85 final size:83
Alignment explanation
Indices: 2852162--2852582 Score: 308
Period size: 85 Copynumber: 4.9 Consensus size: 83
2852152 GGCACTTAAC
* * * * * *
2852162 TTTTTTAATCTCACTTTTTACTTTTATAATTGAAGCTCTTAATTTTTTTTTCTAGCTCACTTTCT
1 TTTTTTAATCTCACTTTTTACATTTATAATTGAGGCCCCTAA---TTTTTT-AATCTCACTTTCT
* *
2852227 ACCTTTATGATTGAAGCCTTTA-A
62 ACCTTTATAATTAAAG--TTTATA
* * *
2852250 TTCTTTTAATATCATTTTTTACATTTATAATTGAGGCCCCTAATTTTTTAATCTCACTTTCTACG
1 TT-TTTTAATCTCACTTTTTACATTTATAATTGAGGCCCCTAATTTTTTAATCTCACTTTCTACC
2852315 TTTATAATTAAAGTTTATGA
65 TTTATAATTAAAGTTTAT-A
* * * * ** * * *
2852335 TATTTTTAATCTCATTTTTTACCTTCATAATTGATGTTCCTAAATTTTTCAATCTTACTTTTTAC
1 T-TTTTTAATCTCACTTTTTACATTTATAATTGAGGCCCCT-AATTTTTTAATCTCACTTTCTAC
* ***
2852400 CTTTATAATGAAAGCCCATAA
64 CTTTATAATTAAAGTTTAT-A
*
2852421 TTTTTTAATCTCACTTTTTACATTTATAATTGAGGCCCCTAATTTATTTTCAATC-CAACTTTTT
1 TTTTTTAATCTCACTTTTTACATTTATAATTGAGGCCCCTAA-TT-TTTT-AATCTC-AC-TTTC
* ***
2852485 TACCTTTATAATTGAGACCCTA-A
61 TACCTTTATAATT-AAAGTTTATA
* * * * * * * * *
2852508 TTTTTTCAATCTCACTTTCTACCTTTATATTTAAAGTCCCAAAGTTTTTTAATCTTACTTTTTAC
1 TTTTTT-AATCTCACTTTTTACATTTATAATTGAGGCCCCTAA-TTTTTTAATCTCACTTTCTAC
2852573 CTTTATAATT
64 CTTTATAATT
2852583 GAGGCCCTAA
Statistics
Matches: 273, Mismatches: 47, Indels: 29
0.78 0.13 0.08
Matches are distributed among these distances:
83 4 0.01
84 2 0.01
85 110 0.40
86 52 0.19
87 17 0.06
88 49 0.18
89 39 0.14
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.51
Consensus pattern (83 bp):
TTTTTTAATCTCACTTTTTACATTTATAATTGAGGCCCCTAATTTTTTAATCTCACTTTCTACCT
TTATAATTAAAGTTTATA
Found at i:2854281 original size:85 final size:84
Alignment explanation
Indices: 2854137--2854426 Score: 427
Period size: 77 Copynumber: 3.5 Consensus size: 84
2854127 CTGTCACACT
*
2854137 GTGGCAAACTTAGTTTGATGAAAACAAAACAGTGGCTAAATATTGAGTTTATGCGCTTGTTTGAT
1 GTGGCAAACTTAGTTTGATGAAAA-AAAA-AGTGGCTAAATATTGAGTTTATGGGCTTGTTTGAT
2854202 TGTTTGAATTTTGATTGTGTA
64 TGTTTGAATTTTGATTGTGTA
*
2854223 GTGGCAAACTTAGTTTGATGGAAAAAAAAAGTGGTTAAATATTGAGTTTATGGGC--------TT
1 GTGGCAAACTTAGTTTGAT-GAAAAAAAAAGTGGCTAAATATTGAGTTTATGGGCTTGTTTGATT
2854280 GTTTGAATTTTGATTGTGTA
65 GTTTGAATTTTGATTGTGTA
* *
2854300 GTGGCAAACCTAGTTTGATGGAAAAAACAA-TGGCTAAATATTGAGTTTATGGGCTTGTTTGATT
1 GTGGCAAACTTAGTTTGAT-GAAAAAAAAAGTGGCTAAATATTGAGTTTATGGGCTTGTTTGATT
2854364 GTTTGAATTTTGATTGTGTA
65 GTTTGAATTTTGATTGTGTA
*
2854384 GTGGCAAACTTAGTTTGATGAAAAACAACAGTGGCTAAATATT
1 GTGGCAAACTTAGTTTGATGAAAAA-AAAAGTGGCTAAATATT
2854427 TTTGTTCAAG
Statistics
Matches: 185, Mismatches: 8, Indels: 23
0.86 0.04 0.11
Matches are distributed among these distances:
76 23 0.12
77 50 0.27
83 6 0.03
84 42 0.23
85 36 0.19
86 23 0.12
87 5 0.03
ACGTcount: A:0.31, C:0.07, G:0.24, T:0.38
Consensus pattern (84 bp):
GTGGCAAACTTAGTTTGATGAAAAAAAAAGTGGCTAAATATTGAGTTTATGGGCTTGTTTGATTG
TTTGAATTTTGATTGTGTA
Done.