Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 63 of 226
Found at i:24542155 original size:16 final size:18
Alignment explanation
Indices: 24542136--24542175 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
24542126 AAATTAATAT
*
24542136 AAAATAA-TCAAATTA-A
1 AAAATAATTCAAAATACA
24542152 AAAA-AATTCAAAATACA
1 AAAATAATTCAAAATACA
24542169 AAAATAA
1 AAAATAA
24542176 ATACATCTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
15 2 0.10
16 11 0.55
17 5 0.25
18 2 0.10
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAATAATTCAAAATACA
Found at i:24542401 original size:21 final size:20
Alignment explanation
Indices: 24542362--24542401 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
24542352 TTTAAAAAAA
*
24542362 TTCAATATTTTAGTTTTTTT
1 TTCAATATTTTAGTCTTTTT
*
24542382 TTCAATTATTTTTGTCTTTT
1 TTCAA-TATTTTAGTCTTTT
24542402 ATATAAACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.70
Consensus pattern (20 bp):
TTCAATATTTTAGTCTTTTT
Found at i:24547885 original size:31 final size:31
Alignment explanation
Indices: 24547843--24547904 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
24547833 AATGACTTAC
* *
24547843 GGGTAAGAGTACATTGTCAACAGAAGCTCAT
1 GGGTAACAGTACATCGTCAACAGAAGCTCAT
24547874 GGGTAACAGTACATCGTCAACAGAAGCTCAT
1 GGGTAACAGTACATCGTCAACAGAAGCTCAT
24547905 AAGAGCTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.21
Consensus pattern (31 bp):
GGGTAACAGTACATCGTCAACAGAAGCTCAT
Found at i:24559219 original size:3 final size:3
Alignment explanation
Indices: 24559211--24559242 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
24559201 ATTAATATGC
24559211 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
24559243 ACTATCTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:24563517 original size:52 final size:53
Alignment explanation
Indices: 24563415--24563523 Score: 166
Period size: 52 Copynumber: 2.1 Consensus size: 53
24563405 AATGATGATG
* * *
24563415 ATAACCTAACATAATATTAACTCCCCCAAACTTATACCTACTCCTATATATATA
1 ATAACCTAACATAATATTAACT-CACCAAACTTATACCTACACATATATATATA
*
24563469 ATAACCTAACATAATATTAACT-ACCAAACTTATGCCTACACATATATATATA
1 ATAACCTAACATAATATTAACTCACCAAACTTATACCTACACATATATATATA
24563521 ATA
1 ATA
24563524 TATTATTATA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
52 29 0.57
54 22 0.43
ACGTcount: A:0.44, C:0.24, G:0.01, T:0.31
Consensus pattern (53 bp):
ATAACCTAACATAATATTAACTCACCAAACTTATACCTACACATATATATATA
Found at i:24563532 original size:3 final size:3
Alignment explanation
Indices: 24563524--24563560 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
24563514 ATATATAATA
24563524 TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
24563561 ACTCTCTCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:24571054 original size:29 final size:31
Alignment explanation
Indices: 24571003--24571064 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 31
24570993 AACCTATATC
*
24571003 TTTATAATTTTTAAAGGATTAAA-TCAAATT
1 TTTATAATTTTTAAAGGAGTAAAGTCAAATT
** *
24571033 TTTAT-ATTTTTAGGGGAGTAAAGTGAAATT
1 TTTATAATTTTTAAAGGAGTAAAGTCAAATT
24571063 TT
1 TT
24571065 ACCTTTACTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.47
Consensus pattern (31 bp):
TTTATAATTTTTAAAGGAGTAAAGTCAAATT
Found at i:24581031 original size:23 final size:24
Alignment explanation
Indices: 24580988--24581033 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
24580978 TATTATTTTA
*
24580988 TGTTAATAATTATTATTTAATTAG
1 TGTTAATAATTATTATATAATTAG
24581012 TGTT-ATAATTA-TATGATAATTA
1 TGTTAATAATTATTAT-ATAATTA
24581034 AAAGTAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 13 0.65
24 4 0.20
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (24 bp):
TGTTAATAATTATTATATAATTAG
Found at i:24582148 original size:14 final size:15
Alignment explanation
Indices: 24582114--24582149 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
24582104 TATAACTAAG
*
24582114 ATTTTTACAACATTC
1 ATTTTTACAACATAC
*
24582129 ATTTTTACAATATAC
1 ATTTTTACAACATAC
24582144 ATTTTT
1 ATTTTT
24582150 CTTTAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTTTACAACATAC
Found at i:24582731 original size:31 final size:34
Alignment explanation
Indices: 24582654--24582736 Score: 82
Period size: 37 Copynumber: 2.4 Consensus size: 34
24582644 GACCTTAAAT
24582654 ATAAATATAAATATAAATTTATATAAAATATATTAAC
1 ATAAATATAAAT-TAAATTTATAT--AATATATTAAC
* *
24582691 AGAACATATAAATTAAATTT-TAT-ATATATTCA-
1 ATAA-ATATAAATTAAATTTATATAATATATTAAC
24582723 ATAAATATAGAATT
1 ATAAATATA-AATT
24582737 TCGATATGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
31 5 0.12
32 7 0.17
33 8 0.20
36 3 0.07
37 10 0.24
38 8 0.20
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (34 bp):
ATAAATATAAATTAAATTTATATAATATATTAAC
Found at i:24584670 original size:43 final size:43
Alignment explanation
Indices: 24584607--24584704 Score: 151
Period size: 43 Copynumber: 2.3 Consensus size: 43
24584597 CAAGTTGCAG
* * *
24584607 GAGACACACGCCTGTGTGGCTAGGCTGTGTGTCTCACACGGTC
1 GAGAGACACACCTGTATGGCTAGGCTGTGTGTCTCACACGGTC
* *
24584650 TAGAGACACACCTGTATGGCTAGGTTGTGTGTCTCACACGGTC
1 GAGAGACACACCTGTATGGCTAGGCTGTGTGTCTCACACGGTC
24584693 GAGAGACACACC
1 GAGAGACACACC
24584705 CGTGTCTCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.21, C:0.27, G:0.30, T:0.22
Consensus pattern (43 bp):
GAGAGACACACCTGTATGGCTAGGCTGTGTGTCTCACACGGTC
Found at i:24586969 original size:21 final size:21
Alignment explanation
Indices: 24586945--24586986 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
24586935 TTTTTTAATT
*
24586945 AATTAACTAACAAAACGTTAA
1 AATTAACTAACAAAACATTAA
**
24586966 AATTTTCTAACAAAACATTAA
1 AATTAACTAACAAAACATTAA
24586987 TACTATCTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.29
Consensus pattern (21 bp):
AATTAACTAACAAAACATTAA
Found at i:24590042 original size:14 final size:14
Alignment explanation
Indices: 24590023--24590053 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
24590013 AATCTTGCAC
24590023 GAGCAGTTGAACAT
1 GAGCAGTTGAACAT
24590037 GAGCAGTTGAACAT
1 GAGCAGTTGAACAT
24590051 GAG
1 GAG
24590054 TCATGAGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.32, T:0.19
Consensus pattern (14 bp):
GAGCAGTTGAACAT
Found at i:24591431 original size:11 final size:11
Alignment explanation
Indices: 24591409--24591441 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
24591399 ATTTAATAAT
24591409 AATTAT-TTTA
1 AATTATATTTA
24591419 AATTATATTTA
1 AATTATATTTA
24591430 AATTATATTTA
1 AATTATATTTA
24591441 A
1 A
24591442 TAATAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.27
11 16 0.73
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
AATTATATTTA
Found at i:24591433 original size:21 final size:19
Alignment explanation
Indices: 24591408--24591468 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 19
24591398 TATTTAATAA
24591408 TAATTATTTTAAATTATATT
1 TAATTATTTTAAATTATA-T
24591428 TAAATTATATTT-AA-TA-A-
1 T-AATTAT-TTTAAATTATAT
24591445 TAATTATTTTAAATTATAT
1 TAATTATTTTAAATTATAT
*
24591464 AAATT
1 TAATT
24591469 CATATAAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 13
0.71 0.02 0.27
Matches are distributed among these distances:
15 3 0.09
16 8 0.24
17 3 0.09
18 1 0.03
19 5 0.15
20 3 0.09
21 8 0.24
22 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TAATTATTTTAAATTATAT
Found at i:24591451 original size:16 final size:15
Alignment explanation
Indices: 24591400--24591456 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 15
24591390 TTGAATGTTA
24591400 TTTAATAATAATTAT
1 TTTAATAATAATTAT
24591415 TTTAAATTATATTTAAATTAT
1 TTT-AA-TA-A--T-AATTAT
24591436 ATTTAATAATAATTAT
1 -TTTAATAATAATTAT
24591452 TTTAA
1 TTTAA
24591457 ATTATATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
15 8 0.23
16 8 0.23
17 3 0.09
18 1 0.03
19 1 0.03
20 3 0.09
21 8 0.23
22 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTAATAATAATTAT
Found at i:24591545 original size:47 final size:46
Alignment explanation
Indices: 24591427--24591562 Score: 108
Period size: 47 Copynumber: 3.0 Consensus size: 46
24591417 TAAATTATAT
24591427 TTAAATTATATTTAATAATAATTA-TTT-TAAATTATATAAATTCA
1 TTAAATTATATTTAATAATAATTATTTTATAAATTATATAAATTCA
* * ** *
24591471 TATAAGA--AAATTT-ATTATCAAGAATTTTATGAAATTATATATCATT-A
1 T-TAA-ATTATATTTAATAAT-AATTATTTTAT-AAATTATATA-AATTCA
* *
24591518 TTAAATTATATTTAATAATAATTA-TTT-TAGATTATACAAATTCA
1 TTAAATTATATTTAATAATAATTATTTTATAAATTATATAAATTCA
24591562 T
1 T
24591563 ATAAGAAAAT
Statistics
Matches: 69, Mismatches: 12, Indels: 22
0.67 0.12 0.21
Matches are distributed among these distances:
43 7 0.10
44 19 0.28
45 8 0.12
46 8 0.12
47 20 0.29
48 7 0.10
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (46 bp):
TTAAATTATATTTAATAATAATTATTTTATAAATTATATAAATTCA
Found at i:24591719 original size:120 final size:120
Alignment explanation
Indices: 24591594--24592011 Score: 703
Period size: 120 Copynumber: 3.5 Consensus size: 120
24591584 AATTATTTTA
* * *
24591594 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATATTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AAATTATATTT
* * * *
24591658 GATAGTATCATATATTATGATTTTAGCAAAGTCATATAAGAATATTGATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
24591714 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
* *
24591779 ATAGTATCATATATTATGATTTGAGTAAATTCATATAATAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
24591834 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATTATTATGTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
*
24591899 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATACTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
24591954 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
24592012 ATGATTAAAT
Statistics
Matches: 280, Mismatches: 16, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
120 272 0.97
121 8 0.03
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:24591749 original size:16 final size:16
Alignment explanation
Indices: 24591728--24591773 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
24591718 TTATTAAATT
24591728 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
24591744 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
24591759 AT-TATGTTAAATTAT
1 ATATAT-TTTAATTAT
24591774 CTTTTATAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 12 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:24591989 original size:16 final size:16
Alignment explanation
Indices: 24591968--24592009 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
24591958 TTATTAAATT
*
24591968 ATATATTTTAATTATA
1 ATATATTTTAATAATA
24591984 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
24591999 AT-TATGTTTAA
1 ATATAT-TTTAA
24592010 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:24591994 original size:15 final size:15
Alignment explanation
Indices: 24591959--24592000 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
24591949 TTAAGAATTT
*
24591959 TATTAAATTAT-ATA
1 TATTTAATTATAATA
24591973 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
24591987 TATTTAATAATAAT
1 TATTTAATTATAAT
24592001 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:24599567 original size:34 final size:32
Alignment explanation
Indices: 24599528--24599601 Score: 85
Period size: 34 Copynumber: 2.2 Consensus size: 32
24599518 AATTAAATTT
* * ** *
24599528 TAATTAAAATCCAATTTTATTTATAATAACACA
1 TAATTAAAATACAAGTTTAAGT-TAATAAAACA
24599561 TAAATTAAAATACAAGTTTAAGTTAATAAAACA
1 T-AATTAAAATACAAGTTTAAGTTAATAAAACA
24599594 TAATTAAA
1 TAATTAAA
24599602 TTTATATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
32 7 0.20
33 11 0.31
34 17 0.49
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.35
Consensus pattern (32 bp):
TAATTAAAATACAAGTTTAAGTTAATAAAACA
Found at i:24604899 original size:3 final size:3
Alignment explanation
Indices: 24604891--24604922 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
24604881 CTAAGCTTAC
24604891 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
24604923 TCTAACTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:24605700 original size:5 final size:5
Alignment explanation
Indices: 24605692--24605746 Score: 53
Period size: 5 Copynumber: 11.2 Consensus size: 5
24605682 TATTTAATTT
* *
24605692 ATATA ATATA ATACA ATATA ATATA TTATATT ATATA ATA-A A-ATA ATAT-
1 ATATA ATATA ATATA ATATA ATATA --ATATA ATATA ATATA ATATA ATATA
24605741 ATATA A
1 ATATA A
24605747 AACATAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
3 1 0.02
4 8 0.20
5 28 0.68
7 4 0.10
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:24605721 original size:27 final size:25
Alignment explanation
Indices: 24605690--24605742 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 25
24605680 TCTATTTAAT
24605690 TTATATAATATAATACAATATAATATA
1 TTATATAATATAATA-AA-ATAATATA
*
24605717 TTATATTATATAATAAAATAATATA
1 TTATATAATATAATAAAATAATATA
24605742 T
1 T
24605743 ATAAAACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 9 0.36
26 2 0.08
27 14 0.56
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
TTATATAATATAATAAAATAATATA
Found at i:24608809 original size:24 final size:25
Alignment explanation
Indices: 24608762--24608812 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
24608752 AATTAAATCT
*
24608762 AACCCAACAGGCCCAAAAATTAAAA
1 AACCCAACAGGCCCAAAAACTAAAA
* *
24608787 AACCTAACA-GCCCACAAACTAAAA
1 AACCCAACAGGCCCAAAAACTAAAA
24608811 AA
1 AA
24608813 GTTTTAGCAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.57, C:0.29, G:0.06, T:0.08
Consensus pattern (25 bp):
AACCCAACAGGCCCAAAAACTAAAA
Found at i:24610400 original size:2 final size:2
Alignment explanation
Indices: 24610393--24610437 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
24610383 TCATTTGTTT
24610393 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
24610435 TA T
1 TA T
24610438 CATCCTTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:24610697 original size:21 final size:20
Alignment explanation
Indices: 24610673--24610719 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
24610663 TTAATTTGTT
*
24610673 TATTCGCTTTCAT-ATCATTGG
1 TATTCGCTTGCATAAT-ATT-G
*
24610694 TATTCACTTGCATAATATTG
1 TATTCGCTTGCATAATATTG
24610714 TATTCG
1 TATTCG
24610720 TGTATTATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.27
21 14 0.64
22 2 0.09
ACGTcount: A:0.23, C:0.17, G:0.13, T:0.47
Consensus pattern (20 bp):
TATTCGCTTGCATAATATTG
Found at i:24612318 original size:30 final size:30
Alignment explanation
Indices: 24612269--24612327 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
24612259 TAAATTAATA
*
24612269 ATAATAAAATTACATTTTAACTCCTTAAAT
1 ATAATAAAATTACAATTTAACTCCTTAAAT
** * *
24612299 ATAATAAAATTTTAATTTAATTCTTTAAA
1 ATAATAAAATTACAATTTAACTCCTTAAA
24612328 AATTGTAAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (30 bp):
ATAATAAAATTACAATTTAACTCCTTAAAT
Found at i:24612650 original size:15 final size:15
Alignment explanation
Indices: 24612630--24612659 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
24612620 ATTTAATTTG
24612630 ATATATTATTTTTTA
1 ATATATTATTTTTTA
24612645 ATATATTATTTTTTA
1 ATATATTATTTTTTA
24612660 CTTTTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATATATTATTTTTTA
Found at i:24613150 original size:135 final size:135
Alignment explanation
Indices: 24612923--24613306 Score: 590
Period size: 135 Copynumber: 2.8 Consensus size: 135
24612913 TCCTTGTTCA
* * * * * * * * *
24612923 TATTTATATTCTGTGAAAATTAACAATTTAATTTATTCATTACTAAGGATATGAAGTACAAGGGT
1 TATTTATATTCTATGAAAACTAAAAATTTAATCTAGTCATTAGTAAGCATATGAATTACAACGGT
* * *
24612988 TGATTTTTATTAATTTATTACATATAAATGGTTAAACGGTTGATTTTTAACTTTGAGGATTTAGT
66 TGATTTTTATTAATTTATTACATATAAATTGTTGAACGGTTGATTTTTAACTTCGAGGATTTAGT
24613053 -TTCCT
131 CTT-CT
24613058 TATTTATATTCTATGAAAACTAAAAATTTAATCTAGTCATTAGTAAGCATATGAATTACAACGGT
1 TATTTATATTCTATGAAAACTAAAAATTTAATCTAGTCATTAGTAAGCATATGAATTACAACGGT
*
24613123 TGATTTTTATTGATTTATTACATATAAATTGTTGAACGGTTGATTTTTAACTTCGAGGATTTAGT
66 TGATTTTTATTAATTTATTACATATAAATTGTTGAACGGTTGATTTTTAACTTCGAGGATTTAGT
24613188 CTTCT
131 CTTCT
* * *
24613193 TATTTATATTCTATGAAAACTAAGAATTTAATCTAGTCATTAGTAAGCATATGAATTATAACCGT
1 TATTTATATTCTATGAAAACTAAAAATTTAATCTAGTCATTAGTAAGCATATGAATTACAACGGT
* *
24613258 TGATTTTTATTAATTTATTACATATAAATTGTTGAACTGTTAATTTTTA
66 TGATTTTTATTAATTTATTACATATAAATTGTTGAACGGTTGATTTTTA
24613307 GATTATTAAT
Statistics
Matches: 229, Mismatches: 19, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
135 227 0.99
136 2 0.01
ACGTcount: A:0.34, C:0.08, G:0.12, T:0.45
Consensus pattern (135 bp):
TATTTATATTCTATGAAAACTAAAAATTTAATCTAGTCATTAGTAAGCATATGAATTACAACGGT
TGATTTTTATTAATTTATTACATATAAATTGTTGAACGGTTGATTTTTAACTTCGAGGATTTAGT
CTTCT
Found at i:24620936 original size:2 final size:2
Alignment explanation
Indices: 24620929--24620971 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
24620919 AACTAACTCA
24620929 AT AT AT AT AT AT 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 AT AT AT
24620971 A
1 A
24620972 AAAGAATGAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24628784 original size:51 final size:50
Alignment explanation
Indices: 24628718--24628817 Score: 128
Period size: 51 Copynumber: 2.0 Consensus size: 50
24628708 AAAAGTATAA
* * * *
24628718 ATATGTATATATATATGGAAATTATAAAGTATATAAAAAATATATATGTAG
1 ATATATATATATATATAGAAATCATAAAATATAT-AAAAATATATATGTAG
* * *
24628769 ATATATATATGTATATATAAATCGTAAAATATATAAAAATATATATGTA
1 ATATATATATATATATAGAAATCATAAAATATATAAAAATATATATGTA
24628818 TATGAATTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
50 15 0.36
51 27 0.64
ACGTcount: A:0.52, C:0.01, G:0.09, T:0.38
Consensus pattern (50 bp):
ATATATATATATATATAGAAATCATAAAATATATAAAAATATATATGTAG
Found at i:24628820 original size:34 final size:33
Alignment explanation
Indices: 24628771--24628849 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 33
24628761 ATATGTAGAT
*
24628771 ATATATATGTATATATAAATCGTAAAATATATAAAA
1 ATATATATG--TATATAAATCATAAAATATA-AAAA
* *
24628807 ATATATATGTATATGAATTATAAAATATAAAAA
1 ATATATATGTATATAAATCATAAAATATAAAAA
24628840 A-ATATATGTA
1 ATATATATGTA
24628850 AAAGGGTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
32 9 0.22
33 5 0.12
34 17 0.43
36 9 0.22
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.37
Consensus pattern (33 bp):
ATATATATGTATATAAATCATAAAATATAAAAA
Found at i:24646580 original size:40 final size:39
Alignment explanation
Indices: 24646532--24646657 Score: 148
Period size: 37 Copynumber: 3.2 Consensus size: 39
24646522 ACCAGTTTGG
*
24646532 CACCCAGTGCCTCATCGGATAATTCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGGATAATTCGAA-TAGTAAATTGA
* * * * *
24646572 CACTCAGTGTCTCATCGGCTAA-ACCAA-AGTAAATTGA
1 CACCCAGTGCCTCATCGGATAATTCGAATAGTAAATTGA
*
24646609 CACCCAGTGCCTCATCGAATTAATTCGAAATAGTAAATTGA
1 CACCCAGTGCCTCATCGGA-TAATTCG-AATAGTAAATTGA
24646650 CACCCAGT
1 CACCCAGT
24646658 ATCTTATCGA
Statistics
Matches: 70, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
37 24 0.34
38 3 0.04
39 4 0.06
40 21 0.30
41 18 0.26
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAATTCGAATAGTAAATTGA
Found at i:24653528 original size:14 final size:15
Alignment explanation
Indices: 24653505--24653538 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
24653495 TAACTTTCTA
24653505 AATA-ACCAAAATT-
1 AATATACCAAAATTC
24653518 AATATACCAAAATTC
1 AATATACCAAAATTC
24653533 AATATA
1 AATATA
24653539 ATATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.21
14 9 0.47
15 6 0.32
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (15 bp):
AATATACCAAAATTC
Found at i:24661598 original size:43 final size:43
Alignment explanation
Indices: 24661490--24661631 Score: 198
Period size: 42 Copynumber: 3.3 Consensus size: 43
24661480 ACGTCGCTAA
* * * *
24661490 CTTTTGCGGCGCTTACA-GAAAAAAACACCGCTAAAGGTCATGTT
1 CTTTAGCGGCGC-T-CAGGAAAAAAACGCCGCTAATGATCATGTT
*
24661534 CTTTAGCGGCGCTTAGG-AAAAAACGCCGCTAATGATCATGTT
1 CTTTAGCGGCGCTCAGGAAAAAAACGCCGCTAATGATCATGTT
*
24661576 CTTTAGCGGCGCTCAGGAAAAAAACGCCACTAATGATCATGTT
1 CTTTAGCGGCGCTCAGGAAAAAAACGCCGCTAATGATCATGTT
24661619 CTTTAGCGGCGCT
1 CTTTAGCGGCGCT
24661632 ATAGCCGCTA
Statistics
Matches: 89, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
42 39 0.44
43 39 0.44
44 11 0.12
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (43 bp):
CTTTAGCGGCGCTCAGGAAAAAAACGCCGCTAATGATCATGTT
Found at i:24662162 original size:12 final size:12
Alignment explanation
Indices: 24662145--24662193 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
24662135 TTTTGAACCT
24662145 CTGCTTCTCTCG
1 CTGCTTCTCTCG
24662157 CTGCTTCTCTCG
1 CTGCTTCTCTCG
* **
24662169 ATGCGGC-CT--
1 CTGCTTCTCTCG
24662178 CTGCTTCTCTCG
1 CTGCTTCTCTCG
24662190 CTGC
1 CTGC
24662194 AGCCTCTGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
9 4 0.14
10 2 0.07
11 2 0.07
12 20 0.71
ACGTcount: A:0.02, C:0.41, G:0.20, T:0.37
Consensus pattern (12 bp):
CTGCTTCTCTCG
Found at i:24662181 original size:21 final size:21
Alignment explanation
Indices: 24662157--24662219 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
24662147 GCTTCTCTCG
* *
24662157 CTGCTTCTCTCGATGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
24662178 CTGCTTCTCTCGCTGCAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
24662199 CTGCTTCCCTCGCTGCTGCCT
1 CTGCTTCTCTCGCTGCAGCCT
24662220 TTGTTTTAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.03, C:0.43, G:0.21, T:0.33
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:24664791 original size:9 final size:9
Alignment explanation
Indices: 24664779--24665064 Score: 187
Period size: 9 Copynumber: 33.4 Consensus size: 9
24664769 ATTATGAAAC
24664779 TTATGTAAG
1 TTATGTAAG
*
24664788 TTATATAAG
1 TTATGTAAG
*
24664797 TTGTGTAAG
1 TTATGTAAG
24664806 TTATGTAAG
1 TTATGTAAG
*
24664815 TTGTGTAAG
1 TTATGTAAG
*
24664824 TTGTGT-A-
1 TTATGTAAG
* *
24664831 TTATGAAAC
1 TTATGTAAG
24664840 TTATGTAAG
1 TTATGTAAG
*
24664849 TTATGT--C
1 TTATGTAAG
24664856 TTATGTAAG
1 TTATGTAAG
*
24664865 TTATGTAAA
1 TTATGTAAG
24664874 TTATGT-A-
1 TTATGTAAG
24664881 TTATGTAAG
1 TTATGTAAG
24664890 TTATGTAAG
1 TTATGTAAG
*
24664899 TTGTGT-A-
1 TTATGTAAG
24664906 TTATGTAAG
1 TTATGTAAG
*
24664915 TTATGTCAG
1 TTATGTAAG
*
24664924 TTGTGT-A-
1 TTATGTAAG
24664931 TTATGTAAG
1 TTATGTAAG
24664940 TTATGTAAG
1 TTATGTAAG
* **
24664949 TTTTTGT-TT
1 -TTATGTAAG
*
24664958 TTGTGT-A-
1 TTATGTAAG
*
24664965 TTATGTAAC
1 TTATGTAAG
* *
24664974 TTATTTAAT
1 TTATGTAAG
*
24664983 TTATGTACG
1 TTATGTAAG
*
24664992 ATATGTATTA-
1 TTATGTA--AG
24665002 TTATGTAAG
1 TTATGTAAG
*
24665011 TTCTGT-A-
1 TTATGTAAG
*
24665018 TTATGTATG
1 TTATGTAAG
24665027 TTATGT-AG
1 TTATGTAAG
24665035 TTATGT-A-
1 TTATGTAAG
24665042 TTATGTAAG
1 TTATGTAAG
* *
24665051 ATATATAAG
1 TTATGTAAG
24665060 CTTAT
1 -TTAT
24665065 ATATAATTAT
Statistics
Matches: 218, Mismatches: 38, Indels: 41
0.73 0.13 0.14
Matches are distributed among these distances:
7 42 0.19
8 25 0.11
9 137 0.63
10 14 0.06
ACGTcount: A:0.29, C:0.02, G:0.19, T:0.49
Consensus pattern (9 bp):
TTATGTAAG
Found at i:24664846 original size:25 final size:25
Alignment explanation
Indices: 24664779--24664950 Score: 245
Period size: 25 Copynumber: 6.8 Consensus size: 25
24664769 ATTATGAAAC
*
24664779 TTATGTAAGTTATATAAGTTGTGTAA
1 TTATGTAAGTTATGTAAGTTGTGT-A
*
24664805 GTTATGTAAGTTGTGTAAGTTGTGTA
1 -TTATGTAAGTTATGTAAGTTGTGTA
* * * *
24664831 TTATGAAACTTATGTAAGTTATGTC
1 TTATGTAAGTTATGTAAGTTGTGTA
* *
24664856 TTATGTAAGTTATGTAAATTATGTA
1 TTATGTAAGTTATGTAAGTTGTGTA
24664881 TTATGTAAGTTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTAAGTTGTGTA
*
24664906 TTATGTAAGTTATGTCAGTTGTGTA
1 TTATGTAAGTTATGTAAGTTGTGTA
24664931 TTATGTAAGTTATGTAAGTT
1 TTATGTAAGTTATGTAAGTT
24664951 TTTGTTTTTG
Statistics
Matches: 130, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
25 107 0.82
26 1 0.01
27 22 0.17
ACGTcount: A:0.30, C:0.02, G:0.22, T:0.47
Consensus pattern (25 bp):
TTATGTAAGTTATGTAAGTTGTGTA
Found at i:24664934 original size:16 final size:16
Alignment explanation
Indices: 24664779--24665041 Score: 113
Period size: 16 Copynumber: 15.4 Consensus size: 16
24664769 ATTATGAAAC
*
24664779 TTATGTAAGTTATATAA
1 TTATGTAAGTTATGT-A
*
24664796 GTTGTGTAAGTTATGTAA
1 -TTATGTAAGTTATGT-A
* *
24664814 GTTGTGTAAGTTGTGTA
1 -TTATGTAAGTTATGTA
* *
24664831 TTATGAAACTTATGTAA
1 TTATGTAAGTTATGT-A
*
24664848 GTTATGT--CTTATGTAA
1 -TTATGTAAGTTATGT-A
*
24664864 GTTATGTAAATTATGTA
1 -TTATGTAAGTTATGTA
24664881 TTATGTAAGTTATGTAA
1 TTATGTAAGTTATGT-A
*
24664898 GTTGTGT-A-TTATGTAA
1 -TTATGTAAGTTATGT-A
* *
24664914 GTTATGTCAGTTGTGTA
1 -TTATGTAAGTTATGTA
24664931 TTATGTAAGTTATGTAA
1 TTATGTAAGTTATGT-A
* ** *
24664948 GTTTTTGT-TTTTGTGTA
1 --TTATGTAAGTTATGTA
* *
24664965 TTATGTAACTTATTTAA
1 TTATGTAAGTTATGT-A
* *
24664982 TTTATGTACGATATGTATTA
1 -TTATGTAAGTTATG---TA
*
24665002 TTATGTAAGTTCTGTA
1 TTATGTAAGTTATGTA
*
24665018 TTATGTATGTTATGTA
1 TTATGTAAGTTATGTA
24665034 GTTATGTA
1 -TTATGTA
24665042 TTATGTAAGA
Statistics
Matches: 194, Mismatches: 33, Indels: 37
0.73 0.12 0.14
Matches are distributed among these distances:
15 5 0.03
16 88 0.45
17 17 0.09
18 66 0.34
19 16 0.08
20 1 0.01
21 1 0.01
ACGTcount: A:0.28, C:0.02, G:0.20, T:0.50
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:24665007 original size:19 final size:19
Alignment explanation
Indices: 24664983--24665054 Score: 58
Period size: 19 Copynumber: 3.7 Consensus size: 19
24664973 CTTATTTAAT
*
24664983 TTATGTACGATATGTATTA
1 TTATGTAAGATATGTATTA
* *
24665002 TTATGTAAGTTCTGTATTA
1 TTATGTAAGATATGTATTA
*
24665021 TGTATGTTATG-TA-GTTATGTA
1 T-TATG-TAAGATATG-TAT-TA
24665042 TTATGTAAGATAT
1 TTATGTAAGATAT
24665055 ATAAGCTTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
19 21 0.51
20 14 0.34
21 6 0.15
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (19 bp):
TTATGTAAGATATGTATTA
Found at i:24665208 original size:21 final size:21
Alignment explanation
Indices: 24665151--24665212 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 21
24665141 AAACTTATAA
*
24665151 ATTTAGAAAACTTATATAGA-T
1 ATTTAGAAAACTTTTATA-ATT
*
24665172 A-TTA-AAACAATATTTATAATT
1 ATTTAGAAA-ACT-TTTATAATT
24665193 ATTTAGAAAACTTTTA-AATT
1 ATTTAGAAAACTTTTATAATT
24665213 TTATAGTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 11
0.70 0.06 0.23
Matches are distributed among these distances:
19 3 0.09
20 10 0.30
21 12 0.36
22 5 0.15
23 3 0.09
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (21 bp):
ATTTAGAAAACTTTTATAATT
Found at i:24666674 original size:15 final size:15
Alignment explanation
Indices: 24666635--24666674 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
24666625 TTAAATCGGG
24666635 GAAATTGGGGGAAAT
1 GAAATTGGGGGAAAT
*
24666650 GGAATTGGGGGAAAT
1 GAAATTGGGGGAAAT
*
24666665 GAAATCGGGG
1 GAAATTGGGG
24666675 AAGTTGGGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.35, C:0.03, G:0.45, T:0.17
Consensus pattern (15 bp):
GAAATTGGGGGAAAT
Found at i:24666683 original size:23 final size:23
Alignment explanation
Indices: 24666652--24666724 Score: 78
Period size: 23 Copynumber: 3.1 Consensus size: 23
24666642 GGGGAAATGG
24666652 AATTGGGGGAAATGAAATCGGGGA
1 AATTGGGGGAAATGAAAT-GGGGA
* *
24666676 AGTTGGGGGAATAGGAAAT-GGGA
1 AATTGGGGGAA-ATGAAATGGGGA
*
24666699 AATT-AGGGAAATGAAATTGGGGA
1 AATTGGGGGAAATGAAA-TGGGGA
24666722 AAT
1 AAT
24666725 CAGAGTGGGG
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
21 5 0.12
22 6 0.15
23 14 0.34
24 10 0.24
25 6 0.15
ACGTcount: A:0.40, C:0.01, G:0.40, T:0.19
Consensus pattern (23 bp):
AATTGGGGGAAATGAAATGGGGA
Found at i:24668479 original size:115 final size:113
Alignment explanation
Indices: 24668246--24669015 Score: 810
Period size: 115 Copynumber: 6.8 Consensus size: 113
24668236 CTATCCAGTT
* *
24668246 GCGGCGTTTTCCTA-TAAGCGCCACTAATTCTAGCATACCTCAAGACC-AAACTCTGCGTTTT-G
1 GCGGCGTTTT-CTAGTAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACTCTGCGTTTTGG
* *
24668308 TTAAGATATGTTGCGGCGCTTTTTGCAAAGCGCCGCTAATACTATGATTTA
65 TTAAGATATTTTGCGGCGC-TTTT-CAAAGCGCCGCTAATACTATGCTTTA
* ** * *
24668359 ACGGCGTTTTCTAGTAAGCGCCACTAATTCTAGTATACATCAAGATTAAAACTATGCGTTTTGTT
1 GCGGCGTTTTCTAGTAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACTCTGCGTTTTGGT
* * *
24668424 TAAGATATTTTGCAGCGCTTTTCAGTAAGCGCCGCTAATACTGTTCTTTA
66 TAAGATATTTTGCGGCGCTTTTCA--AAGCGCCGCTAATACTATGCTTTA
* * ** * * *
24668474 GCGGCGGTTCCCCGTAAGCGCCACTAATTTTAGTATACATCAAGACCAAAACGCTGCGTTTTAGT
1 GCGGCGTTTTCTAGTAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACTCTGCGTTTTGGT
* **
24668539 TAGGATATTTTGCGGCGC-TAGCAAAGAATCGCCGCTAATACTATGCTTTA
66 TAAGATATTTTGCGGCGCTTTTCAAAG---CGCCGCTAATACTATGCTTTA
* * * *
24668589 GCGGCGTTTTAC-CGTAAACGCCACTAATTCTAGTATACATCAATACCAAAA-TGATGCGTTTTG
1 GCGGCGTTTT-CTAGTAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACT-CTGCGTTTTG
* *
24668652 GTTCAA-ATATTTTGCGGCGCTTTTCAAAAGCGCCGCTAATATTAT-CTGTTT
64 GTT-AAGATATTTTGCGGCGCTTTTC-AAAGCGCCGCTAATACTATGCT-TTA
** * *
24668703 GCGGCGTTTTCCTA-TAAGCGCCACTAATTCTAACATACCTCAAGACC-GAACTCTGCGTTTTGG
1 GCGGCGTTTT-CTAGTAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACTCTGCGTTTTGG
* *
24668766 TTAAGATCTTTTGCGGCGCTTTTTGCAAAGCGCCGCTAATACTATGCGTTA
65 TTAAGATATTTTGCGGCGC-TTTT-CAAAGCGCCGCTAATACTATGCTTTA
** * * **
24668817 GCGGCGTTTTCCGGTAAGCGCCACTAATTCTAGGATACATCAACACCAAAAACGATGCGTTTTGG
1 GCGGCGTTTTCTAGTAAGCGCCACTAATTCTAGTATACATCAAGACC-AAAACTCTGCGTTTTGG
* ** * *
24668882 TTAAGATATTTTGCAGCGCATCTCACAAAACGCCGCTAA-A--ACGCTTTA
65 TTAAGATATTTTGCGGCGC-T-TTTCAAAGCGCCGCTAATACTATGCTTTA
** * * * *
24668930 GCGGCGTTTTCTCCTAAACGCCACTAATTCTTGTATACATCAAGACGAAAACGCTGCGTTTTGGT
1 GCGGCGTTTTCTAGTAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACTCTGCGTTTTGGT
*
24668995 TAAGAGATTTTGCGGCGCTTT
66 TAAGATATTTTGCGGCGCTTT
24669016 GTTGTAAACG
Statistics
Matches: 548, Mismatches: 85, Indels: 51
0.80 0.12 0.07
Matches are distributed among these distances:
110 1 0.00
111 1 0.00
112 41 0.07
113 115 0.21
114 139 0.25
115 198 0.36
116 48 0.09
117 5 0.01
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (113 bp):
GCGGCGTTTTCTAGTAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACTCTGCGTTTTGGT
TAAGATATTTTGCGGCGCTTTTCAAAGCGCCGCTAATACTATGCTTTA
Found at i:24668841 original size:228 final size:228
Alignment explanation
Indices: 24668244--24669033 Score: 930
Period size: 228 Copynumber: 3.5 Consensus size: 228
24668234 CACTATCCAG
* *
24668244 TTGCGGCGTTTTCCTATAAGCGCCACTAATTCTAGCATACCTCAAGACCAAACTCTGCGTTTT-G
1 TTGCGGCGTTTTCCTATAAGCGCCACTAATTCTAGCATACATCAAGACCAAACGCTGCGTTTTGG
* * * *
24668308 TTAAGATATGTTGCGGCGCTTTTTGCAAAGCGCCGCTAATACTATGATTTAACGGCGTTTTCTAG
66 TTAAGATATTTTGCGGCGCTTTTTGCAAAGCGCCGCTAATACTATGCTTTAGCGGCGTTTTC-CG
* ** *
24668373 TAAGCGCCACTAATTCTAGTATACATCAAGATTAAAACT-ATGCGTTTTGTTTAAGATATTTTGC
130 TAAGCGCCACTAATTCTAGTATACATCAACACCAAAA-TGATGCGTTTTGGTTAAGATATTTTGC
**
24668437 AGCGCTTTTCAGTAAGCGCCGCTAATACTGT-TCT-T
194 AGCGCTTTTCACAAAGCGCCGCTAATA-T-TATCTGT
* * * ** * * *
24668472 TAGCGGCGGTTCCCCGTAAGCGCCACTAATTTTAGTATACATCAAGACCAAAACGCTGCGTTTTA
1 TTGCGGCGTTTTCCTATAAGCGCCACTAATTCTAGCATACATCAAGACC-AAACGCTGCGTTTTG
* *
24668537 GTTAGGATATTTTGCGGCGC---TAGCAAAGAATCGCCGCTAATACTATGCTTTAGCGGCGTTTT
65 GTTAAGATATTTTGCGGCGCTTTTTGCAAAG---CGCCGCTAATACTATGCTTTAGCGGCGTTTT
* *
24668599 ACCGTAAACGCCACTAATTCTAGTATACATCAATACCAAAATGATGCGTTTTGGTTCAA-ATATT
127 -CCGTAAGCGCCACTAATTCTAGTATACATCAACACCAAAATGATGCGTTTTGGTT-AAGATATT
*
24668663 TTGCGGCGCTTTTCA-AAAGCGCCGCTAATATTATCTGT
190 TTGCAGCGCTTTTCACAAAGCGCCGCTAATATTATCTGT
* * * *
24668701 TTGCGGCGTTTTCCTATAAGCGCCACTAATTCTAACATACCTCAAGACCGAACTCTGCGTTTTGG
1 TTGCGGCGTTTTCCTATAAGCGCCACTAATTCTAGCATACATCAAGACCAAACGCTGCGTTTTGG
* *
24668766 TTAAGATCTTTTGCGGCGCTTTTTGCAAAGCGCCGCTAATACTATGCGTTAGCGGCGTTTTCCGG
66 TTAAGATATTTTGCGGCGCTTTTTGCAAAGCGCCGCTAATACTATGCTTTAGCGGCGTTTTCC-G
* *
24668831 TAAGCGCCACTAATTCTAGGATACATCAACACCAAAAACGATGCGTTTTGGTTAAGATATTTTGC
130 TAAGCGCCACTAATTCTAGTATACATCAACACC-AAAATGATGCGTTTTGGTTAAGATATTTTGC
* * *
24668896 AGCGCATCTCACAAAACGCCGCTAA-A--A-C-GCT
194 AGCGCTTTTCACAAAGCGCCGCTAATATTATCTG-T
* * *
24668927 TTAGCGGCGTTTTCTCCTA-AA-CGCCACTAATTCTTGTATACATCAAGACGAAAACGCTGCGTT
1 TT-GCGGCG-TTT-TCCTATAAGCGCCACTAATTCTAGCATACATCAAGAC-CAAACGCTGCGTT
* *
24668990 TTGGTTAAGAGATTTTGCGGCGCTTTGTTGTAAA-CGCCGCTAAT
62 TTGGTTAAGATATTTTGCGGCGCTTT-TTGCAAAGCGCCGCTAAT
24669034 GATGTTCTTT
Statistics
Matches: 483, Mismatches: 56, Indels: 46
0.83 0.10 0.08
Matches are distributed among these distances:
225 1 0.00
226 4 0.01
227 41 0.08
228 187 0.39
229 116 0.24
230 124 0.26
231 10 0.02
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.32
Consensus pattern (228 bp):
TTGCGGCGTTTTCCTATAAGCGCCACTAATTCTAGCATACATCAAGACCAAACGCTGCGTTTTGG
TTAAGATATTTTGCGGCGCTTTTTGCAAAGCGCCGCTAATACTATGCTTTAGCGGCGTTTTCCGT
AAGCGCCACTAATTCTAGTATACATCAACACCAAAATGATGCGTTTTGGTTAAGATATTTTGCAG
CGCTTTTCACAAAGCGCCGCTAATATTATCTGT
Found at i:24669071 original size:343 final size:341
Alignment explanation
Indices: 24668246--24669053 Score: 926
Period size: 343 Copynumber: 2.4 Consensus size: 341
24668236 CTATCCAGTT
* * * *
24668246 GCGGCG-TTT-TCCTATAAGCGCCACTAATTCTAGCATACCTCAAGACCAAACTCTGCGTTTT-G
1 GCGGCGTTTTCTCCTA-AA-CGCCACTAATTCTAGTATACATCAAGACAAAACGCTGCGTTTTGG
* * ** *
24668308 TTAAGATATGTTGCGGCGCTTTTTGCAAAGCGCCGCTAATACTATGATTTAACGGCG-TTTTCTA
64 TTAAGATATTTTGCGGCGCTTTTTGAAAAGCGCCGCTAATA-T-TTCTTTTACGGCGTTTTTCTA
** * *
24668372 GTAAGCGCCACTAATTCTAGTATACATCAAGATTAAAACTATGCGTTTTGTTTAAGATATTTTGC
127 GTAAGCGCCACTAATTCTAACATACATCAAGATCAAAACTATGCGTTTTGGTTAAGATATTTTGC
* * *
24668437 AGCGCTTTTCAGTAAGCGCCGCTAATACTGTTCTTTAGCGGCGGTTCCCCGTAAGCGCCACTAAT
192 AGCGCTTTTCAG-AAGCGCCGCTAATACTATGCGTTAGCGGCGGTTCCCCGTAAGCGCCACTAAT
* * * * * *
24668502 TTTAGTATACATCAAGACCAAAACGCTGCGTTTTAGTTAGGATATTTTGCGGCGCTAGCAAAGAA
256 TCTAGGATACATCAACACCAAAACGATGCGTTTTAGTTAAGATATTTTGCAGCGCTAGCAAAGAA
*
24668567 TCGCCGCTAATACTATGCTTTA
321 TCGCCGCTAATAC-ACGCTTTA
* * * *
24668589 GCGGCGTTTTAC-CGTAAACGCCACTAATTCTAGTATACATCAATACCAAAATGATGCGTTTTGG
1 GCGGCGTTTT-CTCCTAAACGCCACTAATTCTAGTATACATCAAGA-CAAAACGCTGCGTTTTGG
* * *
24668653 TTCAA-ATATTTTGCGGCGC-TTTTCAAAAGCGCCGCTAATATTATCTGTTTGCGGCGTTTTCCT
64 TT-AAGATATTTTGCGGCGCTTTTTGAAAAGCGCCGCTAATATT-TCT-TTTACGGCGTTTTTCT
* ** * *
24668716 A-TAAGCGCCACTAATTCTAACATACCTCAAGA-CCGAACTCTGCGTTTTGGTTAAGATCTTTTG
126 AGTAAGCGCCACTAATTCTAACATACATCAAGATCAAAACTATGCGTTTTGGTTAAGATATTTTG
* * * *
24668779 CGGCGCTTTTTGCA-AAGCGCCGCTAATACTATGCGTTAGCGGCGTTTTCCGGTAAGCGCCACTA
191 CAGCGC-TTTT-CAGAAGCGCCGCTAATACTATGCGTTAGCGGCGGTTCCCCGTAAGCGCCACTA
* **
24668843 ATTCTAGGATACATCAACACCAAAAACGATGCGTTTTGGTTAAGATATTTTGCAGCGCATCTCAC
254 ATTCTAGGATACATCAACACC-AAAACGATGCGTTTTAGTTAAGATATTTTGCAGCGC-TAGCA-
24668908 AA-AA-CGCCGCTAA-A-ACGCTTTA
316 AAGAATCGCCGCTAATACACGCTTTA
*
24668930 GCGGCGTTTTCTCCTAAACGCCACTAATTCTTGTATACATCAAGACGAAAACGCTGCGTTTTGGT
1 GCGGCGTTTTCTCCTAAACGCCACTAATTCTAGTATACATCAAGAC-AAAACGCTGCGTTTTGGT
* *
24668995 TAAGAGATTTTGCGGCGCTTTGTTGTAAA-CGCCGCTAATGATGTTCTTTTACGGCGTTT
65 TAAGATATTTTGCGGCGCTTT-TTGAAAAGCGCCGCTAAT-AT-TTCTTTTACGGCGTTT
24669054 ATTCAGAAAA
Statistics
Matches: 393, Mismatches: 51, Indels: 43
0.81 0.10 0.09
Matches are distributed among these distances:
340 4 0.01
341 77 0.20
342 24 0.06
343 135 0.34
344 117 0.30
345 32 0.08
346 4 0.01
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.32
Consensus pattern (341 bp):
GCGGCGTTTTCTCCTAAACGCCACTAATTCTAGTATACATCAAGACAAAACGCTGCGTTTTGGTT
AAGATATTTTGCGGCGCTTTTTGAAAAGCGCCGCTAATATTTCTTTTACGGCGTTTTTCTAGTAA
GCGCCACTAATTCTAACATACATCAAGATCAAAACTATGCGTTTTGGTTAAGATATTTTGCAGCG
CTTTTCAGAAGCGCCGCTAATACTATGCGTTAGCGGCGGTTCCCCGTAAGCGCCACTAATTCTAG
GATACATCAACACCAAAACGATGCGTTTTAGTTAAGATATTTTGCAGCGCTAGCAAAGAATCGCC
GCTAATACACGCTTTA
Found at i:24675776 original size:33 final size:33
Alignment explanation
Indices: 24675734--24675799 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
24675724 AGGTATGTTT
24675734 TTTATATCTTACAAAATAGGTAATATTGGCATA
1 TTTATATCTTACAAAATAGGTAATATTGGCATA
24675767 TTTATATCTTACAAAATAGGTAATATTGGCATA
1 TTTATATCTTACAAAATAGGTAATATTGGCATA
24675800 AAGAAAGCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (33 bp):
TTTATATCTTACAAAATAGGTAATATTGGCATA
Found at i:24681470 original size:24 final size:23
Alignment explanation
Indices: 24681442--24681491 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 23
24681432 GCAGCAGGTG
24681442 TCTCTTCCTCT-TTTTCTTCTTTCT
1 TCTCTTCCT-TGTTTTCTTC-TTCT
24681466 TCTCTTCCTTGTTTTCTTCTTCT
1 TCTCTTCCTTGTTTTCTTCTTCT
24681489 TCT
1 TCT
24681492 TTCTTTGGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.66
Consensus pattern (23 bp):
TCTCTTCCTTGTTTTCTTCTTCT
Found at i:24683874 original size:25 final size:25
Alignment explanation
Indices: 24683845--24683892 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
24683835 AAATACAGAC
*
24683845 AACCATAAAATTGTGAACAAAATAT
1 AACCACAAAATTGTGAACAAAATAT
* *
24683870 AACCACGAAATTGTGAATAAAAT
1 AACCACAAAATTGTGAACAAAAT
24683893 TAGGATAACG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.54, C:0.12, G:0.10, T:0.23
Consensus pattern (25 bp):
AACCACAAAATTGTGAACAAAATAT
Found at i:24688230 original size:16 final size:16
Alignment explanation
Indices: 24688195--24688238 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
24688185 TTTTAAATAA
* *
24688195 AAAAACATAGAATTTT
1 AAAAATATAAAATTTT
24688211 AAAAATA-AAAATTTT
1 AAAAATATAAAATTTT
24688226 AAAAAATATAAAA
1 -AAAAATATAAAA
24688239 AATACCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.29
16 13 0.54
17 4 0.17
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (16 bp):
AAAAATATAAAATTTT
Found at i:24692279 original size:20 final size:20
Alignment explanation
Indices: 24692251--24692304 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
24692241 AACACGCAAA
24692251 TTTTGAAACACGAGATTTT-T
1 TTTTGAAACACGA-ATTTTCT
*
24692271 TTTTAAAACACGAATTTTCT
1 TTTTGAAACACGAATTTTCT
24692291 TTTTGAAACACGAA
1 TTTTGAAACACGAA
24692305 AATTTTTAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.16
20 26 0.84
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (20 bp):
TTTTGAAACACGAATTTTCT
Found at i:24692456 original size:36 final size:36
Alignment explanation
Indices: 24692360--24692479 Score: 109
Period size: 36 Copynumber: 3.3 Consensus size: 36
24692350 ATAAAATACG
* * *
24692360 AAACACGAGG-ATTTTTTG-AAACACGAAAATTTATG
1 AAACACG-GGAATTTCTTGAAAACAAGAAAATTTATA
* *
24692395 AAACACGGTCAATTTTCTTGAAAACAAGAAAATTTTTA
1 AAACACGG-GAA-TTTCTTGAAAACAAGAAAATTTATA
* * * * *
24692433 AAAGACGGGAATTTCTTGGAAACACGGAAATTTATG
1 AAACACGGGAATTTCTTGAAAACAAGAAAATTTATA
24692469 AAACACGGGAA
1 AAACACGGGAA
24692480 AAAAATTTTT
Statistics
Matches: 68, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
34 1 0.01
35 7 0.10
36 31 0.46
37 8 0.12
38 21 0.31
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.26
Consensus pattern (36 bp):
AAACACGGGAATTTCTTGAAAACAAGAAAATTTATA
Found at i:24692473 original size:17 final size:17
Alignment explanation
Indices: 24692372--24692476 Score: 75
Period size: 17 Copynumber: 5.8 Consensus size: 17
24692362 ACACGAGGAT
*
24692372 TTTTTGAAACACGAAAA
1 TTTTTGAAACACGGAAA
* *
24692389 TTTATGAAACACGGTCAAT
1 TTTTTGAAACACGG--AAA
* *
24692408 TTTCTTGAAAACAAGAAAA
1 TTT-TTG-AAACACGGAAA
* * *
24692427 TTTTTAAAAGACGGGAA
1 TTTTTGAAACACGGAAA
24692444 TTTCTTGGAAACACGGAAA
1 TTT-TT-GAAACACGGAAA
*
24692463 TTTATGAAACACGG
1 TTTTTGAAACACGG
24692477 GAAAAAAATT
Statistics
Matches: 66, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
17 31 0.47
18 5 0.08
19 22 0.33
20 2 0.03
21 6 0.09
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (17 bp):
TTTTTGAAACACGGAAA
Found at i:24692653 original size:15 final size:16
Alignment explanation
Indices: 24692635--24692667 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
24692625 CGTGACTCTA
*
24692635 TTAAAACACGA-GAAT
1 TTAAAAAACGAGGAAT
24692650 TTAAAAAACGAGGAAT
1 TTAAAAAACGAGGAAT
24692666 TT
1 TT
24692668 TGAATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (16 bp):
TTAAAAAACGAGGAAT
Found at i:24693112 original size:19 final size:19
Alignment explanation
Indices: 24693074--24693119 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
24693064 GCTGCAGTGT
*
24693074 GCTTGCTGGACTGGGTCAG
1 GCTTGCTGGACTGGGACAG
* *
24693093 GCTTGCTGGGCTTGGACAG
1 GCTTGCTGGACTGGGACAG
*
24693112 GCCTGCTG
1 GCTTGCTG
24693120 CCTTTTTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.09, C:0.24, G:0.41, T:0.26
Consensus pattern (19 bp):
GCTTGCTGGACTGGGACAG
Found at i:24693299 original size:3 final size:3
Alignment explanation
Indices: 24693287--24693336 Score: 57
Period size: 3 Copynumber: 16.0 Consensus size: 3
24693277 TCTTTTTTTT
*
24693287 TTC TTCC TTC TTC TTC CTC TT- TTC TTC TTTC TTC TTCC TTC TTC TTC
1 TTC TT-C TTC TTC TTC TTC TTC TTC TTC -TTC TTC TT-C TTC TTC TTC
24693334 TTC
1 TTC
24693337 AAAGTCTAGC
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 2 0.05
3 30 0.73
4 9 0.22
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:24693300 original size:10 final size:10
Alignment explanation
Indices: 24693287--24693333 Score: 67
Period size: 10 Copynumber: 4.6 Consensus size: 10
24693277 TCTTTTTTTT
24693287 TTCTTCCTTC
1 TTCTTCCTTC
*
24693297 TTCTTCCTCTT
1 TTCTTCCT-TC
*
24693308 TTCTTCTTTC
1 TTCTTCCTTC
24693318 TTCTTCCTTC
1 TTCTTCCTTC
24693328 TTCTTC
1 TTCTTC
24693334 TTCAAAGTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 24 0.75
11 8 0.25
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (10 bp):
TTCTTCCTTC
Found at i:24693681 original size:30 final size:30
Alignment explanation
Indices: 24693647--24693726 Score: 117
Period size: 30 Copynumber: 2.7 Consensus size: 30
24693637 GGTTGAAACA
*
24693647 TAATTTTGAGAAAGTTTAGGGGTCAAAATG
1 TAATTTTAAGAAAGTTTAGGGGTCAAAATG
* *
24693677 TAATTTCAAGAAAGTTAAGGGGTCAAAATG
1 TAATTTTAAGAAAGTTTAGGGGTCAAAATG
*
24693707 TAATTTCAA-AAAGTTTAGGG
1 TAATTTTAAGAAAGTTTAGGG
24693727 TTGAAATATA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 10 0.22
30 36 0.78
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.31
Consensus pattern (30 bp):
TAATTTTAAGAAAGTTTAGGGGTCAAAATG
Found at i:24699879 original size:20 final size:20
Alignment explanation
Indices: 24699854--24699891 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
24699844 CAAATGACAA
*
24699854 AAAAATATTAAAATTATTAT
1 AAAAATATAAAAATTATTAT
24699874 AAAAATATAAAAATTATT
1 AAAAATATAAAAATTATT
24699892 GAAATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAATATAAAAATTATTAT
Found at i:24699896 original size:17 final size:18
Alignment explanation
Indices: 24699876--24699910 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
24699866 ATTATTATAA
24699876 AAATATAAA-AATTATTG
1 AAATATAAACAATTATTG
*
24699893 AAATTTAAACAATTATTG
1 AAATATAAACAATTATTG
24699911 GACCGCCGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (18 bp):
AAATATAAACAATTATTG
Found at i:24700491 original size:7 final size:7
Alignment explanation
Indices: 24700479--24700512 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
24700469 ATTTTTTTAA
24700479 AAAAATT
1 AAAAATT
24700486 AAAAATT
1 AAAAATT
24700493 AAAAATT
1 AAAAATT
24700500 AAAAATT
1 AAAAATT
24700507 AAAAAT
1 AAAAAT
24700513 CATTAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAAAATT
Found at i:24708141 original size:17 final size:17
Alignment explanation
Indices: 24708121--24708155 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
24708111 TCCTTTTTCT
24708121 TCTTCTCTTCTCTATTA
1 TCTTCTCTTCTCTATTA
24708138 TCTTCTCTTCTCTATTA
1 TCTTCTCTTCTCTATTA
24708155 T
1 T
24708156 TAAGGGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.29, G:0.00, T:0.60
Consensus pattern (17 bp):
TCTTCTCTTCTCTATTA
Found at i:24720185 original size:54 final size:54
Alignment explanation
Indices: 24720099--24720204 Score: 169
Period size: 54 Copynumber: 2.0 Consensus size: 54
24720089 ATGAAGAGAC
*
24720099 TGGACGTTTCCAAGAATCCCAGTTCAACGAAACTCCGTTTCAGGAGATCAACGG
1 TGGACGTTTCCAAGAATCCCAGTTCAACGAAACTCCATTTCAGGAGATCAACGG
* *
24720153 TGGACGTGTT-CAAGAATCCCAGTTCCAGGAAACTCCATTTCAGGAGATCAAC
1 TGGACGT-TTCCAAGAATCCCAGTTCAACGAAACTCCATTTCAGGAGATCAAC
24720205 AACGTCAACA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
54 46 0.96
55 2 0.04
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (54 bp):
TGGACGTTTCCAAGAATCCCAGTTCAACGAAACTCCATTTCAGGAGATCAACGG
Found at i:24720311 original size:36 final size:36
Alignment explanation
Indices: 24720264--24720337 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
24720254 AGAAGAAGAA
*
24720264 GAAAGAACCAGAAGTGAGGACTTTTCATTCTATAGG
1 GAAAGAACCAGAAGTGAGGACTTTTCACTCTATAGG
*
24720300 GAAAGAACCAGAAGTGAGGACTTTTCACTCTGTAGG
1 GAAAGAACCAGAAGTGAGGACTTTTCACTCTATAGG
24720336 GA
1 GA
24720338 CTGGAACTGG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (36 bp):
GAAAGAACCAGAAGTGAGGACTTTTCACTCTATAGG
Found at i:24728786 original size:4 final size:4
Alignment explanation
Indices: 24728779--24728828 Score: 82
Period size: 4 Copynumber: 12.5 Consensus size: 4
24728769 TGTGTGTGTG
* *
24728779 TGTA TGTA TGCA TGTA TGTA TGTA TGTA TGCA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
24728827 TG
1 TG
24728829 CAACTATTAC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.24, C:0.04, G:0.26, T:0.46
Consensus pattern (4 bp):
TGTA
Found at i:24728804 original size:20 final size:20
Alignment explanation
Indices: 24728779--24728830 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
24728769 TGTGTGTGTG
24728779 TGTATGTATGCATGTATGTA
1 TGTATGTATGCATGTATGTA
24728799 TGTATGTATGCATGTATGTA
1 TGTATGTATGCATGTATGTA
24728819 TGTATGTATGCA
1 TGTATGTATGCA
24728831 ACTATTACTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.44
Consensus pattern (20 bp):
TGTATGTATGCATGTATGTA
Found at i:24735541 original size:24 final size:24
Alignment explanation
Indices: 24735509--24735559 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
24735499 CTAACGTGGC
*
24735509 ATTATAAAAAT-ATAAATATTAAAA
1 ATTAAAAAAATGA-AAATATTAAAA
* *
24735533 ATTAAAAAAGTGAAAATTTTAAAA
1 ATTAAAAAAATGAAAATATTAAAA
24735557 ATT
1 ATT
24735560 TTGATAGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (24 bp):
ATTAAAAAAATGAAAATATTAAAA
Found at i:24736909 original size:21 final size:21
Alignment explanation
Indices: 24736871--24736910 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
24736861 TTTAAAAAAT
**
24736871 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
24736892 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
24736911 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:24736917 original size:22 final size:21
Alignment explanation
Indices: 24736870--24736928 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
24736860 ATTTAAAAAA
* *
24736870 TATTTTTAAAAT-ACTTTTTT
1 TATTTTTAAAATAAATTTTTG
24736890 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAATAAATTTTT-G
24736913 TATTTATTAAAA-AAAT
1 TATTT-TTAAAATAAAT
24736929 AGGCCAGGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 11 0.33
22 14 0.42
23 7 0.21
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTTG
Found at i:24737400 original size:15 final size:15
Alignment explanation
Indices: 24737382--24737431 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
24737372 CGAACCACTG
24737382 CCTCCACCTCCACCT
1 CCTCCACCTCCACCT
*
24737397 CCTCCACTTCCA-CT
1 CCTCCACCTCCACCT
* *
24737411 GCCACCACCTCCGCCT
1 -CCTCCACCTCCACCT
24737427 CCTCC
1 CCTCC
24737432 TTCACCGCTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 2 0.07
15 24 0.86
16 2 0.07
ACGTcount: A:0.12, C:0.64, G:0.04, T:0.20
Consensus pattern (15 bp):
CCTCCACCTCCACCT
Found at i:24737578 original size:132 final size:132
Alignment explanation
Indices: 24737442--24737680 Score: 356
Period size: 132 Copynumber: 1.8 Consensus size: 132
24737432 TTCACCGCTA
* * * *
24737442 CCACTTCCACT-TCCATATCCAGACCCACTTCCGTATCCGGATCCGGACCCATATCCCGACCCTC
1 CCACTTCC-CTATCCAGATCCAGACCCACTTCCGTAACCGGATCCAGACCCATATCCAGACCCTC
24737506 CTCCACTGCCACCACCTCCACCACCGCCA-CTGCCGCCACCACCTCCTCCACCGTTTCCACCACC
65 CTCCACTGCCACCACCTCCACCACCGCCACCT-CCGCCACCACCTCCTCCACCGTTTCCACCACC
24737570 AACG
129 AACG
* * *
24737574 CCACTTCCGTATCCGGATCCAGACCCACTTCCGTAACCGGATCCAGACCCATATCCAGACCCTTC
1 CCACTTCCCTATCCAGATCCAGACCCACTTCCGTAACCGGATCCAGACCCATATCCAGACCCTCC
* * *
24737639 TCCACTGCCACCACCTCCGCCGCCGCCACCTCCGCTACCACC
66 TCCACTGCCACCACCTCCACCACCGCCACCTCCGCCACCACC
24737681 GCCACCTCCT
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
131 1 0.01
132 92 0.97
133 2 0.02
ACGTcount: A:0.20, C:0.52, G:0.11, T:0.17
Consensus pattern (132 bp):
CCACTTCCCTATCCAGATCCAGACCCACTTCCGTAACCGGATCCAGACCCATATCCAGACCCTCC
TCCACTGCCACCACCTCCACCACCGCCACCTCCGCCACCACCTCCTCCACCGTTTCCACCACCAA
CG
Found at i:24737601 original size:24 final size:24
Alignment explanation
Indices: 24737574--24737624 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
24737564 ACCACCAACG
*
24737574 CCACTTCCGTATCCGGATCCAGAC
1 CCACTTCCGTAACCGGATCCAGAC
24737598 CCACTTCCGTAACCGGATCCAGAC
1 CCACTTCCGTAACCGGATCCAGAC
24737622 CCA
1 CCA
24737625 TATCCAGACC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.43, G:0.16, T:0.18
Consensus pattern (24 bp):
CCACTTCCGTAACCGGATCCAGAC
Found at i:24737696 original size:18 final size:18
Alignment explanation
Indices: 24737640--24737697 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
24737630 AGACCCTTCT
* * *
24737640 CCACTGCCACCACCTCCG
1 CCACCGCCACCTCCTCCA
* * *
24737658 CCGCCGCCACCTCCGCTA
1 CCACCGCCACCTCCTCCA
24737676 CCACCGCCACCTCCTCCA
1 CCACCGCCACCTCCTCCA
24737694 CCAC
1 CCAC
24737698 TTCCTATCCC
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.16, C:0.64, G:0.10, T:0.10
Consensus pattern (18 bp):
CCACCGCCACCTCCTCCA
Found at i:24737763 original size:24 final size:24
Alignment explanation
Indices: 24737715--24737764 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
24737705 CCCACCACCA
* * *
24737715 GACCCATACCCCGATCCGGATCCT
1 GACCCATACCCAGACCCGGACCCT
*
24737739 GACCCATACCCAGACCCGTACCCT
1 GACCCATACCCAGACCCGGACCCT
24737763 GA
1 GA
24737765 TCCTTCACCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.24, C:0.46, G:0.16, T:0.14
Consensus pattern (24 bp):
GACCCATACCCAGACCCGGACCCT
Found at i:24741847 original size:25 final size:25
Alignment explanation
Indices: 24741813--24741864 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
24741803 GTGATATCAA
*
24741813 CATAATTTTAATAAAAACCATGTTT
1 CATAAGTTTAATAAAAACCATGTTT
24741838 CATAAGTTTAATAAAAACCATGTTT
1 CATAAGTTTAATAAAAACCATGTTT
24741863 CA
1 CA
24741865 AGAAAAAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (25 bp):
CATAAGTTTAATAAAAACCATGTTT
Found at i:24743502 original size:63 final size:63
Alignment explanation
Indices: 24743395--24743513 Score: 159
Period size: 63 Copynumber: 1.9 Consensus size: 63
24743385 TGCCAGGCCG
** * *
24743395 TGTAACTCACTGTTTGTGAATTAGGGTCATACGGGCCAGGGACACGGGCGTGTGTCTAGGTCA
1 TGTAACTCACTGTTTGTGAATTAAAGTCACACGGGCCAGAGACACGGGCGTGTGTCTAGGTCA
* * *
24743458 TGTAACTCACTGTTT-TGGAATTAAAGTCACACGGGCTAGAGACACTGGTGTGTGTC
1 TGTAACTCACTGTTTGT-GAATTAAAGTCACACGGGCCAGAGACACGGGCGTGTGTC
24743514 CAGGCCGTGT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
62 1 0.02
63 47 0.98
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (63 bp):
TGTAACTCACTGTTTGTGAATTAAAGTCACACGGGCCAGAGACACGGGCGTGTGTCTAGGTCA
Found at i:24744689 original size:16 final size:17
Alignment explanation
Indices: 24744658--24744690 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
24744648 TTAAAGTCAC
24744658 TAAATTAATTTCTTAAT
1 TAAATTAATTTCTTAAT
*
24744675 TAAATT-ATTTTTTAAT
1 TAAATTAATTTCTTAAT
24744691 ACAATTATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TAAATTAATTTCTTAAT
Found at i:24749818 original size:132 final size:132
Alignment explanation
Indices: 24749581--24750411 Score: 1322
Period size: 132 Copynumber: 6.3 Consensus size: 132
24749571 AAACTTGTAG
* * *
24749581 CTTCAACCTTCTCC-ATCGCTACTCAGGGAGACAAGGCTTGGTGGCTTTAATCTGCTTCCCACTA
1 CTTCAACCTTCTCCGCT-GCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA
* ** *
24749645 TCCTGGAAAGATAAGATTTTCCGTCTTCGATCTGCTTCACTACTGCTTAGGGAGATAAGATCTAC
65 TCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTAC
24749710 AAT
130 AAT
*
24749713 CTTCAACCTTCTCCGCTGCTGCTCAAGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
1 CTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
* * *
24749778 CTTGGAAAGATAAGATTCGCCGTCTTCGATCTACTCCACTACTGCTTAGGGAGATGAGATCTATA
66 CTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
24749843 AT
131 AT
* *
24749845 CTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGTTTGGTGGCTTAAATCCGCTTCCCACTAT
1 CTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
* * *
24749910 CTTGGAAAGATAAGATTCGCCGTCTTAGATCTGCTCCACTACTGCTTAGGGAGATGAGATCTATA
66 CTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
24749975 AT
131 AT
*
24749977 CTTCAACCTTCTCCACTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
1 CTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
* *
24750042 CTTGGAAAGATAAGATTCACCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTACA
66 CTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
24750107 AT
131 AT
* *
24750109 CTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGTTTCCCACTAT
1 CTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
* * * *
24750174 CTTGGAAAGATAAGATTTGACGTCTTTGATCTGCTCCACTAGTGCTTAGGGAGATAAGATCTACA
66 CTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
24750239 AT
131 AT
* *
24750241 CTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGTTTCCCACTAT
1 CTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
** * * *
24750306 CTTGGAAAGATAAGATTTACCGTCCTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTACG
66 CTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
24750371 AT
131 AT
* * * *
24750373 CCTCAACCTACTCCGCTGTTGCTCGGGGAGACAAGGCTT
1 CTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTT
24750412 AGTGTTTCAC
Statistics
Matches: 655, Mismatches: 43, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
132 654 1.00
133 1 0.00
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (132 bp):
CTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT
CTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
AT
Found at i:24757211 original size:14 final size:14
Alignment explanation
Indices: 24757192--24757226 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
24757182 CACAACGTGT
24757192 TGAATTCCCAATAA
1 TGAATTCCCAATAA
*
24757206 TGAATTTCCAATAA
1 TGAATTCCCAATAA
24757220 TGAATTC
1 TGAATTC
24757227 TTATTTTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (14 bp):
TGAATTCCCAATAA
Found at i:24767590 original size:2 final size:2
Alignment explanation
Indices: 24767583--24767617 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
24767573 ATGAATGATT
24767583 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
24767618 AAGACTATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:24779234 original size:8 final size:8
Alignment explanation
Indices: 24779221--24779245 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
24779211 TTATCAGCTC
24779221 TTATTATT
1 TTATTATT
24779229 TTATTATT
1 TTATTATT
24779237 TTATTATT
1 TTATTATT
24779245 T
1 T
24779246 CGAATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTATTATT
Found at i:24782622 original size:26 final size:26
Alignment explanation
Indices: 24782593--24782646 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
24782583 ATATAGAATA
24782593 TTGCCTTTATTTTTAAAATTTTATGT
1 TTGCCTTTATTTTTAAAATTTTATGT
24782619 TTGCCTTTATTTTTAAAATTTTATGT
1 TTGCCTTTATTTTTAAAATTTTATGT
24782645 TT
1 TT
24782647 TTGGAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.63
Consensus pattern (26 bp):
TTGCCTTTATTTTTAAAATTTTATGT
Found at i:24783199 original size:25 final size:25
Alignment explanation
Indices: 24783149--24783221 Score: 71
Period size: 26 Copynumber: 3.0 Consensus size: 25
24783139 AGAAAATATG
* **
24783149 AAATAT-A-AAAAAATGTGTATTTA
1 AAATATAATAAAAAATGTATATGAA
24783172 AAATA-AATAAAGAATATGTATATGAA
1 AAATATAATAAA-AA-ATGTATATGAA
*
24783198 AAATATAGTAAAAAATGTATATGA
1 AAATATAATAAAAAATGTATATGA
24783222 GTATATATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
23 6 0.15
24 3 0.07
25 12 0.29
26 15 0.37
27 5 0.12
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (25 bp):
AAATATAATAAAAAATGTATATGAA
Found at i:24783228 original size:2 final size:2
Alignment explanation
Indices: 24783223--24783261 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
24783213 TGTATATGAG
24783223 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24783262 GAAAAATATG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:24799294 original size:2 final size:2
Alignment explanation
Indices: 24799287--24799328 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
24799277 AAGGTTAGAG
24799287 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
24799329 ATAAGAAAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24800345 original size:22 final size:22
Alignment explanation
Indices: 24800320--24800372 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
24800310 CCGACCAAAG
*
24800320 GCTCCGGCGCACCTCCGCCGTA
1 GCTCCGCCGCACCTCCGCCGTA
* *
24800342 GCTCCGCCGTAGCTCCGCCGTA
1 GCTCCGCCGCACCTCCGCCGTA
24800364 GCTCCGCCG
1 GCTCCGCCG
24800373 TAGACGGCAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.08, C:0.49, G:0.28, T:0.15
Consensus pattern (22 bp):
GCTCCGCCGCACCTCCGCCGTA
Found at i:24800346 original size:11 final size:11
Alignment explanation
Indices: 24800332--24800375 Score: 88
Period size: 11 Copynumber: 4.0 Consensus size: 11
24800322 TCCGGCGCAC
24800332 CTCCGCCGTAG
1 CTCCGCCGTAG
24800343 CTCCGCCGTAG
1 CTCCGCCGTAG
24800354 CTCCGCCGTAG
1 CTCCGCCGTAG
24800365 CTCCGCCGTAG
1 CTCCGCCGTAG
24800376 ACGGCAGCCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 33 1.00
ACGTcount: A:0.09, C:0.45, G:0.27, T:0.18
Consensus pattern (11 bp):
CTCCGCCGTAG
Found at i:24801921 original size:16 final size:16
Alignment explanation
Indices: 24801900--24801931 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
24801890 GTAATTATTC
24801900 TTATTATATATGTAAT
1 TTATTATATATGTAAT
24801916 TTATTATATATGTAAT
1 TTATTATATATGTAAT
24801932 GTCCATACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTATTATATATGTAAT
Found at i:24801922 original size:19 final size:20
Alignment explanation
Indices: 24801880--24801926 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
24801870 TGATAGTAAA
*
24801880 TATATAATATGTAATTATTCT
1 TATAT-ATATGTAATTATTAT
24801901 TATTATATATGTAA-T-TTAT
1 TA-TATATATGTAATTATTAT
24801920 TATATAT
1 TATATAT
24801927 GTAATGTCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 5 0.21
19 5 0.21
20 1 0.04
21 10 0.42
22 3 0.12
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (20 bp):
TATATATATGTAATTATTAT
Found at i:24806400 original size:12 final size:12
Alignment explanation
Indices: 24806369--24806403 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
24806359 CCATTTCTTT
*
24806369 TATATATATATA
1 TATATATTTATA
24806381 TATATATTTATA
1 TATATATTTATA
*
24806393 TTTATATTTAT
1 TATATATTTAT
24806404 TTTTTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATATATTTATA
Found at i:24809616 original size:25 final size:25
Alignment explanation
Indices: 24809588--24809636 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
24809578 TGCTCTCTCT
24809588 TGAGCCATATAACAGGAAGCTTATG
1 TGAGCCATATAACAGGAAGCTTATG
* *
24809613 TGAGCCATGTAATAGGAAGCTTAT
1 TGAGCCATATAACAGGAAGCTTAT
24809637 CCAGGCTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (25 bp):
TGAGCCATATAACAGGAAGCTTATG
Found at i:24809682 original size:24 final size:24
Alignment explanation
Indices: 24809653--24809731 Score: 76
Period size: 24 Copynumber: 3.3 Consensus size: 24
24809643 TATATAACGA
24809653 GAAGCTCATAAGAGCCATAATCGG
1 GAAGCTCATAAGAGCCATAATCGG
**
24809677 GAAGCTCATGCGAGCCAATAAT-GG
1 GAAGCTCATAAGAGCC-ATAATCGG
24809701 GTAA-CTC-TGAAGAGCCATTAA-CGG
1 G-AAGCTCAT-AAGAGCCA-TAATCGG
24809725 GAAGCTC
1 GAAGCTC
24809732 CAGATAACCA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
23 4 0.09
24 34 0.76
25 7 0.16
ACGTcount: A:0.34, C:0.22, G:0.27, T:0.18
Consensus pattern (24 bp):
GAAGCTCATAAGAGCCATAATCGG
Found at i:24810614 original size:45 final size:45
Alignment explanation
Indices: 24810548--24810674 Score: 130
Period size: 52 Copynumber: 2.6 Consensus size: 45
24810538 AGCTATCACT
*
24810548 TATCACTTTTCACTTGT-CACTTGATCAGATAAGTGTAGCCGAAGC
1 TATCACTTATCACTT-TCCACTTGATCAGATAAGTGTAGCCGAAGC
*
24810593 TATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGC
1 TATCACTTATCACTTT---C----CACTTGATCAGATAAGTGTAGCCGAAGC
* *
24810645 TATCACTCATCACTTTGTCACTTGATCAGA
1 TATCACTTATCACTTT-CCACTTGATCAGA
24810675 AGTACTCAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 15
0.78 0.06 0.17
Matches are distributed among these distances:
44 1 0.01
45 14 0.20
46 12 0.17
52 42 0.61
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.35
Consensus pattern (45 bp):
TATCACTTATCACTTTCCACTTGATCAGATAAGTGTAGCCGAAGC
Found at i:24810614 original size:52 final size:52
Alignment explanation
Indices: 24810531--24810660 Score: 233
Period size: 52 Copynumber: 2.5 Consensus size: 52
24810521 NNNNNNNNNA
*
24810531 TAGCCGAAGCTATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTG
1 TAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTG
24810583 TAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTG
1 TAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTG
* *
24810635 TAGCTGAAGCTATCACTCATCACTTT
1 TAGCCGAAGCTATCACTTATCACTTT
24810661 GTCACTTGAT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.34
Consensus pattern (52 bp):
TAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTG
Found at i:24812763 original size:25 final size:24
Alignment explanation
Indices: 24812705--24812763 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
24812695 AAGTTCAAGC
* * **
24812705 GAGCCAATATCGGGAAGCTTAGGA
1 GAGCCATTAACGGGAAGCTTAAAA
24812729 GAGCCATTAACGGGAAGCTTACAAA
1 GAGCCATTAACGGGAAGCTTA-AAA
*
24812754 GAGCCTTTAA
1 GAGCCATTAA
24812764 TTAGGAAGCT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 19 0.66
25 10 0.34
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.19
Consensus pattern (24 bp):
GAGCCATTAACGGGAAGCTTAAAA
Found at i:24813471 original size:21 final size:21
Alignment explanation
Indices: 24813431--24813471 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
24813421 GCCCATTTAA
*
24813431 TTCATAAAATTTAGAAATTTT
1 TTCATAAAATTTACAAATTTT
* *
24813452 TTCATAAATTTTACATATTT
1 TTCATAAAATTTACAAATTT
24813472 ACAATGTAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.51
Consensus pattern (21 bp):
TTCATAAAATTTACAAATTTT
Found at i:24822351 original size:17 final size:19
Alignment explanation
Indices: 24822308--24822348 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
24822298 AATAGACATA
24822308 TATTTATTTTTAAAATATT
1 TATTTATTTTTAAAATATT
*
24822327 TATTTATTTTTAATAT-TT
1 TATTTATTTTTAAAATATT
24822345 TATT
1 TATT
24822349 ATTCCCTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTTATTTTTAAAATATT
Found at i:24823438 original size:19 final size:20
Alignment explanation
Indices: 24823397--24823441 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
24823387 TACAAAAAAG
*
24823397 AAAATTCAAAATAATTTTAA
1 AAAATTCAAAATAATTATAA
24823417 AAAATTCAAAAT-ATTCATAA
1 AAAATTCAAAATAATT-ATAA
24823437 AAAAT
1 AAAAT
24823442 CTAAAATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAATTCAAAATAATTATAA
Found at i:24830030 original size:126 final size:126
Alignment explanation
Indices: 24829803--24830054 Score: 477
Period size: 126 Copynumber: 2.0 Consensus size: 126
24829793 GCAGTACATT
*
24829803 TAGCAATTTCAGTTTAATAGTATAATTAAATCCTACCCCACCGCTACACTCCATAGTAAGAATTC
1 TAGCAATTTCAGTTTAACAGTATAATTAAATCCTACCCCACCGCTACACTCCATAGTAAGAATTC
* *
24829868 CCTATAATTCTTATATCCCGAACACTCCAGTTTGTGGATAAACCACCAGCGTTACAAGTTA
66 CCTATAATTCTTATATCCCAAACACTCCAGTCTGTGGATAAACCACCAGCGTTACAAGTTA
24829929 TAGCAATTTCAGTTTAACAGTATAATTAAATCCTACCCCACCGCTACACTCCATAGTAAGAATTC
1 TAGCAATTTCAGTTTAACAGTATAATTAAATCCTACCCCACCGCTACACTCCATAGTAAGAATTC
24829994 CCTATAATTCTTATATCCCAAACACTCCAGTCTGTGGATAAACCACCAGCGTTACAAGTTA
66 CCTATAATTCTTATATCCCAAACACTCCAGTCTGTGGATAAACCACCAGCGTTACAAGTTA
24830055 GTAAGCGTCA
Statistics
Matches: 123, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 123 1.00
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (126 bp):
TAGCAATTTCAGTTTAACAGTATAATTAAATCCTACCCCACCGCTACACTCCATAGTAAGAATTC
CCTATAATTCTTATATCCCAAACACTCCAGTCTGTGGATAAACCACCAGCGTTACAAGTTA
Found at i:24832146 original size:47 final size:48
Alignment explanation
Indices: 24832075--24832173 Score: 119
Period size: 47 Copynumber: 2.1 Consensus size: 48
24832065 CATGGCAATA
*
24832075 TGTGATATGTGGTTTCCATATAAGACCATAGCTGGGCTATGGCATCGG
1 TGTGATATGTGGCTTCCATATAAGACCATAGCTGGGCTATGGCATCGG
* * * * * * *
24832123 TGTGATATGT-GCTTCCGTGTAAGACCATGGTTGGGTTATGGCTTTGG
1 TGTGATATGTGGCTTCCATATAAGACCATAGCTGGGCTATGGCATCGG
24832170 TGTG
1 TGTG
24832174 TGATATGCGA
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
47 33 0.77
48 10 0.23
ACGTcount: A:0.18, C:0.14, G:0.32, T:0.35
Consensus pattern (48 bp):
TGTGATATGTGGCTTCCATATAAGACCATAGCTGGGCTATGGCATCGG
Found at i:24832779 original size:25 final size:25
Alignment explanation
Indices: 24832723--24832804 Score: 89
Period size: 25 Copynumber: 3.4 Consensus size: 25
24832713 GAACCTTAGC
24832723 GTGCTCTCTGATTATTAGCACATCA
1 GTGCTCTCTGATTATTAGCACATCA
* ** *
24832748 GTACTCTCTGATTATTAGCATGTTA
1 GTGCTCTCTGATTATTAGCACATCA
* *
24832773 GTGCTCTCCG---ATTAGCACATCT
1 GTGCTCTCTGATTATTAGCACATCA
24832795 GTGCTCTCTG
1 GTGCTCTCTG
24832805 TATAGCACTT
Statistics
Matches: 46, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
22 17 0.37
25 29 0.63
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (25 bp):
GTGCTCTCTGATTATTAGCACATCA
Found at i:24833764 original size:28 final size:29
Alignment explanation
Indices: 24833713--24833770 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
24833703 TTTTAGTATC
*
24833713 TATTTTTTATAAATTTTTTAA-TTTTAAA
1 TATTTTTTATAAATTTTATAATTTTTAAA
*
24833741 TATTTTTGTAT-AATTTTATGATTTTTAAA
1 TATTTTT-TATAAATTTTATAATTTTTAAA
24833770 T
1 T
24833771 GAAATACCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 15 0.58
29 11 0.42
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (29 bp):
TATTTTTTATAAATTTTATAATTTTTAAA
Found at i:24833865 original size:2 final size:2
Alignment explanation
Indices: 24833860--24833888 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
24833850 TCTTAAAAAA
24833860 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24833889 AATGGAGGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24837356 original size:3 final size:3
Alignment explanation
Indices: 24837350--24837394 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
24837340 ATAATAACGT
24837350 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
24837395 ATGATAATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:24851345 original size:20 final size:22
Alignment explanation
Indices: 24851316--24851360 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
24851306 TTTATTTAAT
*
24851316 TTTTATAAT-AATTATTAATAA
1 TTTTATAATAAATTATTAAAAA
*
24851337 TTTTA-AATAAATTTTTAAAAA
1 TTTTATAATAAATTATTAAAAA
24851358 TTT
1 TTT
24851361 AATTAATTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTATAATAAATTATTAAAAA
Found at i:24851674 original size:21 final size:21
Alignment explanation
Indices: 24851650--24851698 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
24851640 AAGTTATATG
*
24851650 TATTATAGA-TACATGTAAATA
1 TATTATA-ATTACATGTAAAAA
*
24851671 TATTTTAATTACATGTAAAAA
1 TATTATAATTACATGTAAAAA
24851692 TATTATA
1 TATTATA
24851699 TGTGTAGTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (21 bp):
TATTATAATTACATGTAAAAA
Found at i:24851770 original size:20 final size:21
Alignment explanation
Indices: 24851732--24851771 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
24851722 TTAATATCAA
*
24851732 AATTGTGTACCAACTAATATG
1 AATTGTGTACCAACCAATATG
*
24851753 AATTG-GTACCCACCAATAT
1 AATTGTGTACCAACCAATAT
24851772 AAGTCAGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (21 bp):
AATTGTGTACCAACCAATATG
Found at i:24853746 original size:3 final size:3
Alignment explanation
Indices: 24853738--24853806 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
24853728 AAGCCAATGG
24853738 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
24853786 TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
24853807 AGCAGATAAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:24855355 original size:27 final size:27
Alignment explanation
Indices: 24855325--24855379 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
24855315 AAAACAAGCA
24855325 AAAAGAAAAAGAACAAGG-AAAGAAAAG
1 AAAAG-AAAAGAACAAGGAAAAGAAAAG
* *
24855352 AAAAGAAAGGAAGAAGGAAAAGAAAAG
1 AAAAGAAAAGAACAAGGAAAAGAAAAG
24855379 A
1 A
24855380 GGAAGAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 10 0.40
27 15 0.60
ACGTcount: A:0.73, C:0.02, G:0.25, T:0.00
Consensus pattern (27 bp):
AAAAGAAAAGAACAAGGAAAAGAAAAG
Found at i:24855373 original size:17 final size:17
Alignment explanation
Indices: 24855349--24855394 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
24855339 AAGGAAAGAA
24855349 AAGAAAAGAA-AGGAAG
1 AAGAAAAGAAGAGGAAG
24855365 AAGGAAAAGAAAAGAGGAAG
1 AA-GAAAAG--AAGAGGAAG
24855385 AAGAAAAGAA
1 AAGAAAAGAA
24855395 CTAACATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 2 0.08
17 8 0.31
19 8 0.31
20 8 0.31
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (17 bp):
AAGAAAAGAAGAGGAAG
Found at i:24855379 original size:14 final size:15
Alignment explanation
Indices: 24855362--24855394 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
24855352 AAAAGAAAGG
24855362 AAGAAGGAA-AAGAA
1 AAGAAGGAAGAAGAA
24855376 AAG-AGGAAGAAGAA
1 AAGAAGGAAGAAGAA
24855390 AAGAA
1 AAGAA
24855395 CTAACATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 5 0.29
14 11 0.65
15 1 0.06
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (15 bp):
AAGAAGGAAGAAGAA
Found at i:24855394 original size:5 final size:5
Alignment explanation
Indices: 24855325--24855379 Score: 56
Period size: 5 Copynumber: 10.2 Consensus size: 5
24855315 AAAACAAGCA
* *
24855325 AAAAG AAAAAG AACAAG GAAAG AAAAG AAAAG AAAGG AAGAAGG AAAAG
1 AAAAG -AAAAG AA-AAG AAAAG AAAAG AAAAG AAAAG AA-AA-G AAAAG
24855374 AAAAG A
1 AAAAG A
24855380 GGAAGAAGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
5 27 0.64
6 12 0.29
7 3 0.07
ACGTcount: A:0.73, C:0.02, G:0.25, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:24857184 original size:9 final size:9
Alignment explanation
Indices: 24857113--24857294 Score: 61
Period size: 9 Copynumber: 19.4 Consensus size: 9
24857103 TAAAAAAATG
24857113 AAAATTGATA
1 AAAATT-ATA
*
24857123 TAAACTTATA
1 -AAAATTATA
24857133 AAAATTTATA
1 AAAA-TTATA
* *
24857143 AGAATTGTA
1 AAAATTATA
24857152 AAAGA-TATA
1 AAA-ATTATA
* *
24857161 AAAAATCTA
1 AAAATTATA
24857170 ACAAATTATA
1 A-AAATTATA
* *
24857180 AAAATAACCA
1 AAAATTA-TA
24857190 AAATATT-TA
1 AAA-ATTATA
*
24857199 AGATATTATA
1 A-AAATTATA
*
24857209 AAAACATATTA
1 AAAA-TTA-TA
* *
24857220 GAATTCTATA
1 AAAAT-TATA
*
24857230 AAAATCATA
1 AAAATTATA
24857239 AAAA--ATA
1 AAAATTATA
**
24857246 AAAAAAAT-
1 AAAATTATA
24857254 AAAATTGATA
1 AAAATT-ATA
*
24857264 TAAATTAT-
1 AAAATTATA
24857272 AAAATTATAA
1 AAAATTAT-A
*
24857282 AAAATCATA
1 AAAATTATA
24857291 AAAA
1 AAAA
24857295 CTTAAGTTAA
Statistics
Matches: 127, Mismatches: 27, Indels: 36
0.67 0.14 0.19
Matches are distributed among these distances:
7 7 0.06
8 12 0.09
9 49 0.39
10 46 0.36
11 13 0.10
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.29
Consensus pattern (9 bp):
AAAATTATA
Found at i:24860960 original size:16 final size:15
Alignment explanation
Indices: 24860938--24860974 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
24860928 ATATAATATT
*
24860938 TTTTTATATTTATAG
1 TTTTTATATTTAAAG
24860953 TATTTTATATTTAAAG
1 T-TTTTATATTTAAAG
24860969 TTTTTA
1 TTTTTA
24860975 AAAGTTTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (15 bp):
TTTTTATATTTAAAG
Found at i:24861271 original size:5 final size:5
Alignment explanation
Indices: 24861261--24861285 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
24861251 AATAATTCTT
24861261 ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA
24861286 TATTTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:24865372 original size:3 final size:3
Alignment explanation
Indices: 24865364--24865405 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
24865354 AGCCACACAA
24865364 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
24865406 CCATTAAGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:24870125 original size:19 final size:18
Alignment explanation
Indices: 24870103--24870138 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
24870093 ATAATTTTGA
24870103 AAATTCAAAATATTTATAG
1 AAATTC-AAATATTTATAG
*
24870122 AAATTCTAATATTTATA
1 AAATTCAAATATTTATA
24870139 TTTTTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (18 bp):
AAATTCAAATATTTATAG
Done.