Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008105.1 Hibiscus syriacus cultivar Beakdansim tig00110637_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: 5962497
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 29 of 30
Found at i:5667051 original size:120 final size:120
Alignment explanation
Indices: 5666838--5667092 Score: 460
Period size: 120 Copynumber: 2.1 Consensus size: 120
5666828 AAAATTAAAT
*
5666838 AGTAGCTACAAATTAAACAGTTTATTTAAATCTTAAATAAAGGCAGCTAACAACCTTATACAACT
1 AGTAGCTACAAATTAAACAGTTTATTTAAATCCTAAATAAAGGCAGCTAACAACCTTATACAACT
5666903 AATTCGAATGAACAACCAACAACACAAACAAGGACTACAGAGGAAACAAATCAAC
66 AATTCGAATGAACAACCAACAACACAAACAAGGACTACAGAGGAAACAAATCAAC
*
5666958 AGTAGCTACAAATTAAACAGTTTATTTAAATCCTAAATAAAGGCAGCTAATAACCTTATACAAGC
1 AGTAGCTACAAATTAAACAGTTTATTTAAATCCTAAATAAAGGCAGCTAACAACCTTATACAA-C
5667023 -AA-TCTGAATGAACAACCAACAACACAAACAAGGACTACAGAGGAAACAAATCAAC
65 TAATTC-GAATGAACAACCAACAACACAAACAAGGACTACAGAGGAAACAAATCAAC
5667078 AGTAGCTACAAATTA
1 AGTAGCTACAAATTA
5667093 CAGTATATTT
Statistics
Matches: 131, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
119 2 0.02
120 128 0.98
121 1 0.01
ACGTcount: A:0.49, C:0.20, G:0.11, T:0.20
Consensus pattern (120 bp):
AGTAGCTACAAATTAAACAGTTTATTTAAATCCTAAATAAAGGCAGCTAACAACCTTATACAACT
AATTCGAATGAACAACCAACAACACAAACAAGGACTACAGAGGAAACAAATCAAC
Found at i:5667369 original size:19 final size:20
Alignment explanation
Indices: 5667347--5667399 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
5667337 GTTTGAATTC
5667347 GGGTTCGGGTTTTGG-TTTT
1 GGGTTCGGGTTTTGGATTTT
*
5667366 GGGTTCGGG-TTCGGATTTT
1 GGGTTCGGGTTTTGGATTTT
* *
5667385 GGTTTTGGGTTTTGG
1 GGGTTCGGGTTTTGG
5667400 GTTCAGGTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 4 0.14
19 20 0.71
20 4 0.14
ACGTcount: A:0.02, C:0.06, G:0.43, T:0.49
Consensus pattern (20 bp):
GGGTTCGGGTTTTGGATTTT
Found at i:5667372 original size:25 final size:25
Alignment explanation
Indices: 5667344--5667395 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
5667334 CAGGTTTGAA
*
5667344 TTCGGGTTCGGGTTTTGGTTTTGGG
1 TTCGGGTTCGGATTTTGGTTTTGGG
5667369 TTCGGGTTCGGATTTTGGTTTTGGG
1 TTCGGGTTCGGATTTTGGTTTTGGG
5667394 TT
1 TT
5667396 TTGGGTTCAG
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:0.02, C:0.08, G:0.40, T:0.50
Consensus pattern (25 bp):
TTCGGGTTCGGATTTTGGTTTTGGG
Found at i:5667401 original size:32 final size:31
Alignment explanation
Indices: 5667354--5667462 Score: 116
Period size: 32 Copynumber: 3.5 Consensus size: 31
5667344 TTCGGGTTCG
* *
5667354 GGTTTTGGTTTTGGGTTCGGGTTCGGATTTT
1 GGTTTTGGTTTTGGGTTCAGGTTCAGATTTT
5667385 GGTTTTGGGTTTTGGGTTCAGGTTCAGATTTAT
1 GGTTTT-GGTTTTGGGTTCAGGTTCAGATTT-T
** **
5667418 -GTTCAGGTTTTGGGTTCATATTC-GATTTT
1 GGTTTTGGTTTTGGGTTCAGGTTCAGATTTT
*
5667447 GGGTTTGG-TTTGGGTT
1 GGTTTTGGTTTTGGGTT
5667463 TGGGTTTAGG
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
29 9 0.14
30 9 0.14
31 22 0.33
32 25 0.38
33 1 0.02
ACGTcount: A:0.08, C:0.06, G:0.35, T:0.50
Consensus pattern (31 bp):
GGTTTTGGTTTTGGGTTCAGGTTCAGATTTT
Found at i:5667462 original size:6 final size:6
Alignment explanation
Indices: 5667444--5667634 Score: 141
Period size: 6 Copynumber: 31.7 Consensus size: 6
5667434 CATATTCGAT
* ** * *
5667444 TTTGGG TTT-GG TTTGGG TTTGGG TTTAGG TTCAGG TTAGGG TTAGGG
1 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG
* * * *
5667491 TTAGGT TTTGGG TTTGGG TTTGGG TTCGGG TTTGGG TTCGGG TTTGGG
1 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG
* * * * * * *
5667539 TTTTAGG TTTGGG ATTAGG TTAGGG TTTAGG TTAGGG TTTGGG TTCGGG
1 -TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG
* * * ** * **
5667588 TTCGGG TTCGAG TTCAGG TTCGGG TTTGGG TTTTAG TTTAGGG TTTG
1 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTT-GGG TTTG
5667635 AGTTCAAGTT
Statistics
Matches: 149, Mismatches: 33, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
5 5 0.03
6 135 0.91
7 9 0.06
ACGTcount: A:0.08, C:0.04, G:0.43, T:0.45
Consensus pattern (6 bp):
TTTGGG
Found at i:5667648 original size:18 final size:18
Alignment explanation
Indices: 5667569--5667650 Score: 65
Period size: 18 Copynumber: 4.5 Consensus size: 18
5667559 TAGGGTTTAG
* **
5667569 GTTAGGGTTTGGGTTCGG
1 GTTAGGGTTTGAGTTCAA
* * *
5667587 GTTCGGGTTCGAGTTCAG
1 GTTAGGGTTTGAGTTCAA
* * **
5667605 GTTCGGGTTTGGGTTTTA
1 GTTAGGGTTTGAGTTCAA
5667623 GTTTAGGGTTTGAGTTCAA
1 G-TTAGGGTTTGAGTTCAA
5667642 GTTAGGGTT
1 GTTAGGGTT
5667651 AGGTTACAAA
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
18 36 0.72
19 14 0.28
ACGTcount: A:0.11, C:0.07, G:0.40, T:0.41
Consensus pattern (18 bp):
GTTAGGGTTTGAGTTCAA
Found at i:5668443 original size:2 final size:2
Alignment explanation
Indices: 5668436--5668803 Score: 136
Period size: 2 Copynumber: 188.0 Consensus size: 2
5668426 TGTTTATTTA
5668436 AT AT AT AT AT -T 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
* * *
5668477 -T AGT -T AT AT -T AGT -T AT AC AT AC GT AT AT AT ACT AT AT -T
1 AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * *
5668515 A- AT AT AA AT -T AT A- AT AT AT AA ACT AT AT AT -T TT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * * *
5668553 AT TT AT AT AT AT AT AGT TT AT AT AC AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
5668596 ACT AT AT -T A- AT AT AA AT -T AT GT -T TT AT AA ACT AT AT ACT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T
* * * * * * *
5668635 TT TT AT AGT TT AT AC AT AT AT AGT TT AT AT AC AT AGT TT AT AT
1 AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT
* * * * * *
5668678 AT AT AT AGT -T CAC AT AA AC AT A- AT TT AT AT AT AT AG CT -T AT
1 AT AT AT A-T AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
5668719 A- AT A- AT -T AT AT AGT TT AT A- AT AT AA AT AT AGT TT AT AT CT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT
*
5668759 AA ACT -T AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5668800 AT AT
1 AT AT
5668804 TATTTTTTTC
Statistics
Matches: 269, Mismatches: 57, Indels: 80
0.66 0.14 0.20
Matches are distributed among these distances:
1 24 0.09
2 230 0.86
3 15 0.06
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5668609 original size:89 final size:90
Alignment explanation
Indices: 5668500--5668684 Score: 284
Period size: 89 Copynumber: 2.1 Consensus size: 90
5668490 TATACATACG
* *
5668500 TATATATACTATATTAATATAAATTATAATATATAAACTATATA-TTTTATATAATTTATATATA
1 TATATACACTATATTAATATAAATTATAATATATAAACTATATACTTTT-TATAATTTATACATA
5668564 TATAGTTTATATACATA-TATATATA
65 TATAGTTTATATACATAGTATATATA
** * *
5668589 TATATACACTATATTAATATAAATTATGTTTTATAAACTATATACTTTTTATAGTTTATACATAT
1 TATATACACTATATTAATATAAATTATAATATATAAACTATATACTTTTTATAATTTATACATAT
*
5668654 ATAGTTTATATACATAGTTTATATA
66 ATAGTTTATATACATAGTATATATA
5668679 TATATA
1 TATATA
5668685 GTTCACATAA
Statistics
Matches: 87, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
89 70 0.80
90 17 0.20
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.49
Consensus pattern (90 bp):
TATATACACTATATTAATATAAATTATAATATATAAACTATATACTTTTTATAATTTATACATAT
ATAGTTTATATACATAGTATATATA
Found at i:5668670 original size:13 final size:13
Alignment explanation
Indices: 5668639--5668678 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
5668629 TATACTTTTT
*
5668639 ATAGTTTATACATAT
1 ATAGTTTAT--ATAC
5668654 ATAGTTTATATAC
1 ATAGTTTATATAC
5668667 ATAGTTTATATA
1 ATAGTTTATATA
5668679 TATATAGTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 15 0.62
15 9 0.38
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (13 bp):
ATAGTTTATATAC
Found at i:5669920 original size:21 final size:20
Alignment explanation
Indices: 5669894--5670011 Score: 94
Period size: 20 Copynumber: 5.8 Consensus size: 20
5669884 ATCAGTTTCC
5669894 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* **
5669915 AAAATCGCAATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
** *
5669934 ACAAATTCGCATTGCGATTTTCC
1 A-AAA-TCGCAACGCGATTTT-G
* * *
5669957 AGAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
* *
5669977 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
5669997 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
5670012 ACACATAAAT
Statistics
Matches: 80, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
19 1 0.01
20 38 0.47
21 38 0.47
22 2 0.03
23 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:5670040 original size:20 final size:20
Alignment explanation
Indices: 5669959--5670167 Score: 156
Period size: 20 Copynumber: 10.4 Consensus size: 20
5669949 GATTTTCCAG
* ** *
5669959 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* ** *
5669979 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
5669999 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
5670019 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
5670039 AA-CAGCAATACGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
*
5670059 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
5670079 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
5670099 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
5670119 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
5670139 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
5670159 AATCACAAC
1 AATCGCAAC
5670168 ACTGAAATTT
Statistics
Matches: 157, Mismatches: 24, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
19 3 0.02
20 151 0.96
21 3 0.02
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:5670096 original size:40 final size:40
Alignment explanation
Indices: 5670017--5670167 Score: 182
Period size: 40 Copynumber: 3.8 Consensus size: 40
5670007 CGCGAACACA
* *
5670017 TAAATCGCAACGCGTATCCGTAAA-CAGCAATACG-T-ATCCG
1 TAAATCGCAACGAGAATCCGTAAATC-GC-A-ACGATAATCCG
* * *
5670057 TATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCG
*
5670097 TAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCG
* *
5670137 TAAATCGCAACGAGAATCTGTAAATCACAAC
1 TAAATCGCAACGAGAATCCGTAAATCGCAAC
5670168 ACTGAAATTT
Statistics
Matches: 102, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
38 3 0.03
39 2 0.02
40 96 0.94
41 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.21
Consensus pattern (40 bp):
TAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCG
Found at i:5670898 original size:24 final size:24
Alignment explanation
Indices: 5670859--5670905 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5670849 AAATTTGGTC
5670859 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
5670883 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
5670906 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:5671097 original size:12 final size:12
Alignment explanation
Indices: 5671080--5671104 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5671070 ATATAATCCT
5671080 GAAGAAGAAAAA
1 GAAGAAGAAAAA
5671092 GAAGAAGAAAAA
1 GAAGAAGAAAAA
5671104 G
1 G
5671105 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:5673439 original size:33 final size:34
Alignment explanation
Indices: 5673388--5673592 Score: 159
Period size: 34 Copynumber: 5.8 Consensus size: 34
5673378 CGGAAATTAC
* *
5673388 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
*
5673421 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
* * * *
5673455 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCAC
1 AATCGCAA--C--AATGAAAATCGCAATGCGA-AATGAA
*
5673494 AAT-GCGGA-AATGAAAATCGCAATGCGAAATGAA
1 AATCGC-AACAATGAAAATCGCAATGCGAAATGAA
* * *
5673527 AATTGCAACGA-GAGAATCGCAATGCGGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
*
5673561 AATCGCAATGCGAAATGAAAATCGCATTGCGA
1 AATCGCAA--C--AATGAAAATCGCAATGCGA
5673593 TTCTATCGTT
Statistics
Matches: 136, Mismatches: 19, Indels: 29
0.74 0.10 0.16
Matches are distributed among these distances:
32 1 0.01
33 42 0.31
34 50 0.37
36 2 0.01
38 7 0.05
39 34 0.25
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (34 bp):
AATCGCAACAATGAAAATCGCAATGCGAAATGAA
Found at i:5673465 original size:53 final size:53
Alignment explanation
Indices: 5673402--5673586 Score: 318
Period size: 53 Copynumber: 3.5 Consensus size: 53
5673392 GCAACGAGAG
* *
5673402 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGGAAATGAA
*
5673455 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
*
5673508 AATCGCAATGCGAAATGAAAATTGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
5673561 AATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
5673587 TTGCGATTCT
Statistics
Matches: 125, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
53 124 0.99
54 1 0.01
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:5673471 original size:19 final size:19
Alignment explanation
Indices: 5673402--5673592 Score: 196
Period size: 19 Copynumber: 10.7 Consensus size: 19
5673392 GCAACGAGAG
5673402 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5673421 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
5673435 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
5673455 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5673474 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
5673488 AATCACAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
5673508 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
5673527 AATTGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
5673541 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
5673561 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5673580 AATCGCATTGCGA
1 AATCGCAATGCGA
5673593 TTCTATCGTT
Statistics
Matches: 143, Mismatches: 11, Indels: 36
0.75 0.06 0.19
Matches are distributed among these distances:
14 30 0.21
15 2 0.01
16 3 0.02
17 7 0.05
19 60 0.42
20 41 0.29
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:5673626 original size:53 final size:52
Alignment explanation
Indices: 5673563--5673678 Score: 151
Period size: 53 Copynumber: 2.2 Consensus size: 52
5673553 GAAATGAAAA
*
5673563 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTATCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTATCGTTGCGATTTTCATT
** ** ** *
5673615 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTATCGTTGCGATTTTCATT
5673668 TCGCATTGCGA
1 TCGCATTGCGA
5673679 TTTTCATTTC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
52 11 0.20
53 44 0.80
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTATCGTTGCGATTTTCATT
Found at i:5673695 original size:52 final size:53
Alignment explanation
Indices: 5673582--5673698 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
5673572 GAAATGAAAA
5673582 TCGCATTGCGATTCTATCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTATCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
*
5673635 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTATCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
5673687 TCGCATTGCGAT
1 TCGCATTGCGAT
5673699 AGTCATTTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTATCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:5673706 original size:19 final size:19
Alignment explanation
Indices: 5673601--5673698 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
5673591 GATTCTATCG
5673601 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
5673621 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5673640 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
5673654 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5673673 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5673692 TTGCGAT
1 TTGCGAT
5673699 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:5673824 original size:14 final size:14
Alignment explanation
Indices: 5673805--5673841 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
5673795 CATCAATTAC
5673805 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
5673819 ACAAATCATCTTTT
1 ACAAATCAACTTTT
5673833 ACAAATCAA
1 ACAAATCAA
5673842 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:5674759 original size:20 final size:20
Alignment explanation
Indices: 5674728--5674791 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
5674718 TTTTGGTTGA
5674728 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
5674748 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
5674768 AAATGAAAATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
5674789 AAT
1 AAT
5674792 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:5674780 original size:21 final size:21
Alignment explanation
Indices: 5674726--5674790 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
5674716 TCTTTTGGTT
5674726 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
5674747 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
5674767 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
5674788 GAA
1 GAA
5674791 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:5674794 original size:14 final size:14
Alignment explanation
Indices: 5674775--5674830 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 14
5674765 GAGAAATGAA
5674775 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
5674789 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
5674808 AATCGCAACGA-AG
1 AATCGCAACGAGAG
5674821 AATCGCAACG
1 AATCGCAACG
5674831 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
13 11 0.31
14 8 0.23
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:5674813 original size:19 final size:19
Alignment explanation
Indices: 5674726--5674852 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
5674716 TCTTTTGGTT
*
5674726 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*** *
5674745 GAGAATGACTGTCGCAACGAGA
1 GA-AATGAAAATCGCAAC--GC
5674767 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
5674784 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
5674800 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
5674817 G-AA-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
5674832 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
5674851 GA
1 GA
5674853 TTTTGGTTTC
Statistics
Matches: 84, Mismatches: 10, Indels: 28
0.69 0.08 0.23
Matches are distributed among these distances:
13 8 0.10
14 10 0.12
15 4 0.05
16 6 0.07
17 4 0.05
18 1 0.01
19 24 0.29
20 12 0.14
21 11 0.13
22 4 0.05
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:5674828 original size:32 final size:33
Alignment explanation
Indices: 5674726--5674847 Score: 156
Period size: 32 Copynumber: 3.5 Consensus size: 33
5674716 TCTTTTGGTT
*
5674726 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
5674767 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
5674800 GAAATGAAAATCGCAACGA-AGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
5674832 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
5674848 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 1, Indels: 9
0.89 0.01 0.10
Matches are distributed among these distances:
32 29 0.36
33 20 0.25
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.28
ACGTcount: A:0.47, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:5674883 original size:14 final size:14
Alignment explanation
Indices: 5674864--5674920 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5674854 TTTGGTTTCG
5674864 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
5674878 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
5674897 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
5674911 CGTTGCGATT
1 CGTTGCGATT
5674921 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:5674896 original size:33 final size:33
Alignment explanation
Indices: 5674848--5674927 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
5674838 AAAATCGCAA
**
5674848 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
5674881 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
5674914 TGCGATTTTCATTT
1 TGCGATTTTCATTT
5674928 TTCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:5674933 original size:21 final size:21
Alignment explanation
Indices: 5674908--5674981 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
5674898 GTTGCGATTC
5674908 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
5674929 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
5674950 TCACGTTGCGATTTTCATTTC
1 TCTCGTTGCGATTTTCATTTT
5674971 TCTCGTTGCGA
1 TCTCGTTGCGA
5674982 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:5675097 original size:33 final size:33
Alignment explanation
Indices: 5675055--5675125 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
5675045 AATACTAACT
**
5675055 TGAAAATCGCAATTAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
5675088 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
5675121 TGAAA
1 TGAAA
5675126 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.15, G:0.23, T:0.14
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:5675529 original size:20 final size:20
Alignment explanation
Indices: 5675504--5675696 Score: 228
Period size: 20 Copynumber: 9.6 Consensus size: 20
5675494 CTTTAAAAAT
5675504 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
5675524 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
5675544 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
5675565 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
5675585 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
5675605 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
5675625 CACGTTGCGGTTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
5675645 CGCGTTACGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
5675665 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
5675685 CGCGTTGCGATT
1 CGCGTTGCGATT
5675697 CTGGAAAATC
Statistics
Matches: 148, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
20 130 0.88
21 18 0.12
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:5677486 original size:127 final size:127
Alignment explanation
Indices: 5677260--5677508 Score: 417
Period size: 127 Copynumber: 2.0 Consensus size: 127
5677250 TCAAATCATT
* *
5677260 AAGAATAAAATATTAGATGTAGAAGAGTACCTGGATTAATTGATAATTTGCAATCCTTGAATCTT
1 AAGAATAAAATATTAGATGTAGAAGAGTACCTGGATTAATAGATAATTTGCAATCCTTAAATCTT
*
5677325 TCTTCAATTGTGATCTTCCAAGAGGATAGAATTCCCATGAGTACAAACTCTTTGACGGGGAA
66 TCTTCAATTGTGATCTTCCAAGAAGATAGAATTCCCATGAGTACAAACTCTTTGACGGGGAA
* * *
5677387 AAGAATAAAATATTAGATGTGGAAGCGTATCTGGATTAATAGATAATTTGCAATCCTTAAATCTT
1 AAGAATAAAATATTAGATGTAGAAGAGTACCTGGATTAATAGATAATTTGCAATCCTTAAATCTT
* * *
5677452 TCTTCAGTTGTGATCTTCCAAGAAGATAGAATTCCCTTGAGTATAAACTCTTTGACG
66 TCTTCAATTGTGATCTTCCAAGAAGATAGAATTCCCATGAGTACAAACTCTTTGACG
5677509 ATGATTAATT
Statistics
Matches: 113, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
127 113 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (127 bp):
AAGAATAAAATATTAGATGTAGAAGAGTACCTGGATTAATAGATAATTTGCAATCCTTAAATCTT
TCTTCAATTGTGATCTTCCAAGAAGATAGAATTCCCATGAGTACAAACTCTTTGACGGGGAA
Found at i:5677543 original size:91 final size:91
Alignment explanation
Indices: 5677420--5677597 Score: 329
Period size: 91 Copynumber: 2.0 Consensus size: 91
5677410 AGCGTATCTG
5677420 GATTAATAGATAATTTGCAATCCTTAAATCTTTCTTCAGTTGTGATCTTCCAAGAAGATAGAATT
1 GATTAATAGATAATTTGCAATCCTTAAATCTTTCTTCAGTTGTGATCTTCCAAGAAGATAGAATT
5677485 CCCTTGAGTATAAACTCTTTGACGAT
66 CCCTTGAGTATAAACTCTTTGACGAT
* *
5677511 GATTAATTGATAATTTGCAATCCTTGAATCTTTCTTCAGTTGTGATCTTCCAAGAAGATAGAATT
1 GATTAATAGATAATTTGCAATCCTTAAATCTTTCTTCAGTTGTGATCTTCCAAGAAGATAGAATT
*
5677576 CTCTTGAGTATAAACTCTTTGA
66 CCCTTGAGTATAAACTCTTTGA
5677598 TGGGGTTAAG
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (91 bp):
GATTAATAGATAATTTGCAATCCTTAAATCTTTCTTCAGTTGTGATCTTCCAAGAAGATAGAATT
CCCTTGAGTATAAACTCTTTGACGAT
Found at i:5678314 original size:15 final size:15
Alignment explanation
Indices: 5678294--5678323 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5678284 AGTTCTAAAG
5678294 TTTTTTT-TAATTTT
1 TTTTTTTATAATTTT
5678308 TTTTTTTATAATTTT
1 TTTTTTTATAATTTT
5678323 T
1 T
5678324 AGATTAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTTATAATTTT
Found at i:5678579 original size:19 final size:20
Alignment explanation
Indices: 5678555--5678605 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
5678545 CGGCCAAGAG
*
5678555 CATGTATTTTCATT-AAAGT
1 CATGTATTTTCATTAAAAAT
5678574 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATTAAAAAT
5678594 CATGTATTTTCA
1 CATGTATTTTCA
5678606 AAGGGATTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:5680776 original size:31 final size:31
Alignment explanation
Indices: 5680739--5680799 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
5680729 ATAAATGAAG
* *
5680739 AAAATATTAAATTTCATAAAAGA-AAAATAAT
1 AAAATATAAAAATT-ATAAAAGAGAAAATAAT
5680770 AAAATATAAAAATTATAAAAGAGAAAATAA
1 AAAATATAAAAATTATAAAAGAGAAAATAA
5680800 AAATAAAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 8 0.30
31 19 0.70
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.25
Consensus pattern (31 bp):
AAAATATAAAAATTATAAAAGAGAAAATAAT
Found at i:5680932 original size:4 final size:4
Alignment explanation
Indices: 5680925--5680949 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5680915 AAATAAAAGA
5680925 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
5680950 GTCTAAAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:5682407 original size:199 final size:200
Alignment explanation
Indices: 5681819--5683386 Score: 1897
Period size: 200 Copynumber: 7.9 Consensus size: 200
5681809 ATGGCTTCTA
** * * * ** *
5681819 GTTGCTAAATCGTAGTCAACCTTGGTCTTTTTCTCGGTTTAAAGACCTCGGTTTGAAAATTCAAC
1 GTTGCTAAATCACAGCCAACCTAGGTCTTCTTCTCGACTTAAAGACCTCGGTTT-AAACTTCAAC
* * ** * *
5681884 CGGAAAGTAGTTCCTCGATGCTACCATATGGTTGATATGTCC-TCGAGCTAAATGGAATCAAACT
65 CAGAAAGTAGTTCCTCGTTGCTACCATGCGGTTGATATG-CCTTCGAGCTGAATGGAATCGAACT
* * * * *
5681948 CGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGTTGTAAATTCGGTTTGGAGAT
129 CGAAAG-TTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGTTGTAAATTCGGCTGGGAGAT
*
5682013 AGCTCCTT
193 AGTTCCTT
** ** *
5682021 GTTGCTAAATTGCAGCCAACCTAGGTCTTCTTCTCGAGATAAAGACCTCGGTTTAAACTTCAATC
1 GTTGCTAAATCACAGCCAACCTAGGTCTTCTTCTCGACTTAAAGACCTCGGTTTAAACTTCAACC
* * * * *
5682086 GGAAATTAGTTCCTCGTTGCTACCATGCGGTTGATATGCCATT-TAGCTGAATGGAATCAAACTT
66 AGAAAGTAGTTCCTCGTTGCTACCATGCGGTTGATATGCC-TTCGAGCTGAATGGAATCGAACTC
* * * ** * * *
5682150 GAAAGTTTTGCTGACAGATAACCTTTCTTGCCTTAAGCTATGTTGTAAACTCGGTTGGGAGATAG
130 GAAAGTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGTTGTAAATTCGGCTGGGAGATAG
5682215 TTCCTT
195 TTCCTT
* *
5682221 GTTGCTAAATCGCAGCCAACCTAGGTCTTCTTCTCGACTTAAAGACCTCGTTTTAAACTT-AACC
1 GTTGCTAAATCACAGCCAACCTAGGTCTTCTTCTCGACTTAAAGACCTCGGTTTAAACTTCAACC
* * * * *
5682285 ATAAAGTAGTTCCTCGTTGCTACCATGCGGTTGATATGCATTCGAGCCGAATAGAATCGAACTCA
66 AGAAAGTAGTTCCTCGTTGCTACCATGCGGTTGATATGCCTTCGAGCTGAATGGAATCGAACTCG
* * * * *
5682350 AAAGTTTTGTTGACAGATAGCCCTTCTCACATTGAGTTGTGTTGTAAATTCGGTTGGGATATAGT
131 AAAGTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGTTGTAAATTCGGCTGGGAGATAGT
*
5682415 T-TTT
196 TCCTT
** * * *
5682419 GGTTGCTAAATCACAATCAACCTATGTCTTCTTCTCAACTTAAAGACCTTGGTTTAAACTTCAAC
1 -GTTGCTAAATCACAGCCAACCTAGGTCTTCTTCTCGACTTAAAGACCTCGGTTTAAACTTCAAC
* * * * *
5682484 C-GAAAGTAGTTCCTCATTGCTACCATGCGGCTGAGATACCTTTGAGCTGAATGGAATCGAACTC
65 CAGAAAGTAGTTCCTCGTTGCTACCATGCGGTTGATATGCCTTCGAGCTGAATGGAATCGAACTC
* * * * *
5682548 GAAAGTTTTGTTGACAGATAGGCCTTCTCGCCTTAAGCTATGATGTAAACTCGGCTGGGAGATAG
130 GAAAGTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGTTGTAAATTCGGCTGGGAGATAG
5682613 TTCCTT
195 TTCCTT
* * * *
5682619 GTTGATAAATCACCGCCAACCTAAGTCTTCTTCTCGACTTAAAGACCTCGATTTAAACTTCAACC
1 GTTGCTAAATCACAGCCAACCTAGGTCTTCTTCTCGACTTAAAGACCTCGGTTTAAACTTCAACC
* * *
5682684 AGAAAGTAGTTCCTTGTTGCTACCATGTGGTTGATATGCCTTCGAGCTAAATGGAATCGAACTCG
66 AGAAAGTAGTTCCTCGTTGCTACCATGCGGTTGATATGCCTTCGAGCTGAATGGAATCGAACTCG
* * ** *
5682749 AAAGTTTTGTTGACAGATAGTCCTTCTCACCTTGAGCTATGTTGTAAATTCGACCAGGAGATATT
131 AAAGTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGTTGTAAATTCGGCTGGGAGATAGT
*
5682814 TCATT
196 TCCTT
* ** *
5682819 GTTGTTAAATCACAGCCAACCTAGGTCTTCTTCTTAACTTAAAGAACTCGGTTTAAACTTCAACC
1 GTTGCTAAATCACAGCCAACCTAGGTCTTCTTCTCGACTTAAAGACCTCGGTTTAAACTTCAACC
* * * * * * ** *
5682884 GGAAAGTAGTTCCTTGTTGCTACCATACAGTTGAGATACCTTTAAGCTGAATGGAATCAAACTCG
66 AGAAAGTAGTTCCTCGTTGCTACCATGCGGTTGATATGCCTTCGAGCTGAATGGAATCGAACTCG
* * *
5682949 AAAGTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGATGTAAACTCGGCTGGGAGATAGT
131 AAAGTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGTTGTAAATTCGGCTGGGAGATAGT
*
5683014 TCTTT
196 TCCTT
* * * *
5683019 GTTGATAAATCACAACCAACCTAGGTCTTCTTTTCGACTTAAAGACCTCAGTTTAAACTTCAACC
1 GTTGCTAAATCACAGCCAACCTAGGTCTTCTTCTCGACTTAAAGACCTCGGTTTAAACTTCAACC
* * ** *
5683084 AGAAAGTATTTCCTTGTTGCTACCATATGGTTGATATGCCTTCGAGCT--A---AATGGAA-TC-
66 AGAAAGTAGTTCCTCGTTGCTACCATGCGGTTGATATGCCTTCGAGCTGAATGGAATCGAACTCG
* * *
5683142 ---GTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTCAGCTAGGAGATAGT
131 AAAGTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGTTGTAAATTCGGCTGGGAGATAGT
*
5683204 TCATT
196 TCCTT
* * *
5683209 GTTGCTAAATCATAGCCAACCTAGGTCTTCTTCTTGACTTAAAGACCTCGATTTAAACTTCAACC
1 GTTGCTAAATCACAGCCAACCTAGGTCTTCTTCTCGACTTAAAGACCTCGGTTTAAACTTCAACC
* * * * *
5683274 AGAAAATAGTTCCTTGTTGCTACCATGCAGTTGATATGCCTTCTAGCTGAATGGAATCGAACTCA
66 AGAAAGTAGTTCCTCGTTGCTACCATGCGGTTGATATGCCTTCGAGCTGAATGGAATCGAACTCG
* ** *
5683339 AAAGTTTTGTTGATAGATAGCTGTTCTCACCTTGAGCTATGTTTTAAA
131 AAAGTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGTTGTAAA
5683387 CGGTTCCTCA
Statistics
Matches: 1173, Mismatches: 176, Indels: 36
0.85 0.13 0.03
Matches are distributed among these distances:
190 161 0.14
192 1 0.00
194 2 0.00
195 11 0.01
196 2 0.00
198 5 0.00
199 330 0.28
200 549 0.47
201 65 0.06
202 47 0.04
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (200 bp):
GTTGCTAAATCACAGCCAACCTAGGTCTTCTTCTCGACTTAAAGACCTCGGTTTAAACTTCAACC
AGAAAGTAGTTCCTCGTTGCTACCATGCGGTTGATATGCCTTCGAGCTGAATGGAATCGAACTCG
AAAGTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGTTGTAAATTCGGCTGGGAGATAGT
TCCTT
Found at i:5683499 original size:42 final size:42
Alignment explanation
Indices: 5683453--5683759 Score: 127
Period size: 42 Copynumber: 7.2 Consensus size: 42
5683443 TTTAGTTGAC
*
5683453 TCCCCTTCACGGGAAAGCCAAGTGGTATATTCTTCAGGTTGT
1 TCCCCTTCACGGGAAAGCCATGTGGTATATTCTTCAGGTTGT
* * * *
5683495 TCCCCTTGCGA-GTCTG-AA-CCATGTGAG-ATGA-TCTT-TGGATGAC
1 TCCCCTT-C-ACG--GGAAAGCCATGTG-GTAT-ATTCTTCAGGTTG-T
* * *
5683538 TCTCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGT
1 TCCCCTTCACGGGAAAGCCATGTGGTATATTCTTCAGGTTGT
* * * * * *
5683580 TCCCCTTCGCGGGTTTGAA-CCAGGTGAG-ATGA-TCTT-TGGATGAC
1 TCCCCTTCACGGG---AAAGCCATGTG-GTAT-ATTCTTCAGGTTG-T
* * *
5683624 TCCCCTCCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGT
1 TCCCCTTCACGGGAAAGCCATGTGGTATATTCTTCAGGTTGT
* * ** * * *
5683666 TCCCCTTCACGGGTCTGAA-CCAGGTGAAATGA-TCTT-TGGATGAC
1 TCCCCTTCACGGG---AAAGCCATGTGGTAT-ATTCTTCAGGTTG-T
* *
5683710 TCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGT
1 TCCCCTTCACGGGAAAGCCATGTGGTATATTCTTCAGGTTGT
5683752 TCCCCTTC
1 TCCCCTTC
5683760 GCCGGTCTGA
Statistics
Matches: 185, Mismatches: 49, Indels: 62
0.62 0.17 0.21
Matches are distributed among these distances:
40 1 0.01
41 12 0.06
42 78 0.42
43 35 0.19
44 51 0.28
45 8 0.04
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.31
Consensus pattern (42 bp):
TCCCCTTCACGGGAAAGCCATGTGGTATATTCTTCAGGTTGT
Found at i:5683639 original size:86 final size:86
Alignment explanation
Indices: 5683449--5683819 Score: 636
Period size: 86 Copynumber: 4.3 Consensus size: 86
5683439 ATTCTTTAGT
* * * *
5683449 TGACTCCCCTTCACGGGAAAGCCAAGTGGTATATTCTTCAGGTTGTTCCCCTT-GCGAGTCTGAA
1 TGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCGGGTCTGAA
*
5683513 CCATGTGAGATGATCTTTGGA
66 CCAGGTGAGATGATCTTTGGA
* *
5683534 TGACTCTCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCGGGTTTGAA
1 TGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCGGGTCTGAA
5683599 CCAGGTGAGATGATCTTTGGA
66 CCAGGTGAGATGATCTTTGGA
* *
5683620 TGACTCCCCTCCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCACGGGTCTGAA
1 TGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCGGGTCTGAA
*
5683685 CCAGGTGAAATGATCTTTGGA
66 CCAGGTGAGATGATCTTTGGA
*
5683706 TGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCCGGTCTGAA
1 TGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCGGGTCTGAA
5683771 CCAGGTGAGATGATCTTTGGA
66 CCAGGTGAGATGATCTTTGGA
5683792 TGACTCCCCTTCACGGGAAAGTCATGTG
1 TGACTCCCCTTCACGGGAAAGTCATGTG
5683820 AGATGTTCTT
Statistics
Matches: 269, Mismatches: 16, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
85 49 0.18
86 220 0.82
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (86 bp):
TGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCGGGTCTGAA
CCAGGTGAGATGATCTTTGGA
Found at i:5683824 original size:42 final size:42
Alignment explanation
Indices: 5683514--5683829 Score: 163
Period size: 42 Copynumber: 7.4 Consensus size: 42
5683504 GAGTCTGAAC
*
5683514 CATGTGAGATGATCTTTGGATGACTCTCCTTCACGGGAAAGT
1 CATGTGAGATGATCTTTGGATGACTCCCCTTCACGGGAAAGT
* ** * * *
5683556 CATGTG-GTAT-ATTCTTCAGG-TGGTTCCCCTTCGCGGGTTTGAA-C
1 CATGTGAG-ATGA-TCTT-TGGATGACTCCCCTTCACGGG---AAAGT
* *
5683600 CAGGTGAGATGATCTTTGGATGACTCCCCTCCACGGGAAAGT
1 CATGTGAGATGATCTTTGGATGACTCCCCTTCACGGGAAAGT
* ** * *
5683642 CATGTG-GTAT-ATTCTTCAGG-TGGTTCCCCTTCACGGGTCTGAA-C
1 CATGTGAG-ATGA-TCTT-TGGATGACTCCCCTTCACGGG---AAAGT
* *
5683686 CAGGTGAAATGATCTTTGGATGACTCCCCTTCACGGGAAAGT
1 CATGTGAGATGATCTTTGGATGACTCCCCTTCACGGGAAAGT
* ** * *
5683728 CATGTG-GTAT-ATTCTTCAGG-TGGTTCCCCTTCGCCGGTCTG-AA-C
1 CATGTGAG-ATGA-TCTT-TGGATGACTCCCCTTC-ACGG---GAAAGT
*
5683772 CAGGTGAGATGATCTTTGGATGACTCCCCTTCACGGGAAAGT
1 CATGTGAGATGATCTTTGGATGACTCCCCTTCACGGGAAAGT
*
5683814 CATGTGAGATGTTCTT
1 CATGTGAGATGATCTT
5683830 CGAGTGACTC
Statistics
Matches: 198, Mismatches: 44, Indels: 64
0.65 0.14 0.21
Matches are distributed among these distances:
40 1 0.01
41 11 0.06
42 85 0.43
43 18 0.09
44 71 0.36
45 11 0.06
46 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (42 bp):
CATGTGAGATGATCTTTGGATGACTCCCCTTCACGGGAAAGT
Found at i:5688381 original size:31 final size:31
Alignment explanation
Indices: 5688346--5688440 Score: 136
Period size: 31 Copynumber: 3.1 Consensus size: 31
5688336 TATAGCGATA
* *
5688346 TTTTTAAGCGTCGTAAAAAATACATGCGACG
1 TTTTTAAGCGTCGCAAAAAATACATGCGGCG
* *
5688377 TTTTTAAGCATCGCAAAAAATACATACGGCG
1 TTTTTAAGCGTCGCAAAAAATACATGCGGCG
* *
5688408 TTTTTAAGCGCCGCAAAAAACACATGCGGCG
1 TTTTTAAGCGTCGCAAAAAATACATGCGGCG
5688439 TT
1 TT
5688441 ATGAAAAATA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (31 bp):
TTTTTAAGCGTCGCAAAAAATACATGCGGCG
Found at i:5689533 original size:24 final size:24
Alignment explanation
Indices: 5689501--5689546 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
5689491 TCTTCCATAT
5689501 GATGTATAAAACATCTATGTACAC
1 GATGTATAAAACATCTATGTACAC
5689525 GATGTATAAAACATCTATGTAC
1 GATGTATAAAACATCTATGTAC
5689547 CATGTCATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (24 bp):
GATGTATAAAACATCTATGTACAC
Found at i:5698436 original size:43 final size:43
Alignment explanation
Indices: 5698359--5698560 Score: 184
Period size: 43 Copynumber: 4.7 Consensus size: 43
5698349 TGTTAACCAA
* *
5698359 AAACGCCGCAATAGGTAAGATATATAGCGGCGTTTGTTTAT-C
1 AAACGCCGCAATAGGTATGATATTTAGCGGCGTTTGTTTATAC
*
5698401 AAACGCCGTAATAGGTACTGATATTTAGCGGCGTTTGTCTTA-A-
1 AAACGCCGCAATAGGTA-TGATATTTAGCGGCGTTTGT-TTATAC
* *
5698444 AAACGCCGCAATAGGTGTCAATATTTAGCGGCG-TT-TTTATCAC
1 AAACGCCGCAATAGGTAT-GATATTTAGCGGCGTTTGTTTAT-AC
* * * **
5698487 AAACGCCGCAATAAGTGT-TGATATTTTGCGGCATTTTTTTATGG
1 AAACGCCGCAAT-AG-GTATGATATTTAGCGGCGTTTGTTTATAC
* *
5698531 AAACGCCACAATATGTATGGA-ATTTAGCGG
1 AAACGCCGCAATAGGTAT-GATATTTAGCGG
5698561 TATTTTTAGG
Statistics
Matches: 133, Mismatches: 14, Indels: 25
0.77 0.08 0.15
Matches are distributed among these distances:
40 3 0.02
41 1 0.01
42 22 0.17
43 79 0.59
44 21 0.16
45 7 0.05
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (43 bp):
AAACGCCGCAATAGGTATGATATTTAGCGGCGTTTGTTTATAC
Found at i:5698492 original size:86 final size:85
Alignment explanation
Indices: 5698357--5698518 Score: 204
Period size: 86 Copynumber: 1.9 Consensus size: 85
5698347 TTTGTTAACC
* *
5698357 AAAAACGCCGCAATAGGTAAGATATATAGCGGCGTTTGTTTATCAAACGCCGTAATAGGTACTGA
1 AAAAACGCCGCAATAGGTAAGATATATAGCGGCGTTTGTTTATCAAACGCCGCAATAAGTACTGA
5698422 TATTTAGCGGCGTTTGTCTT
66 TATTTAGCGGCGTTTGTCTT
* * *
5698442 AAAAACGCCGCAATAGGTGTCA-ATATTTAGCGGCG-TT-TTTATCACAAACGCCGCAATAAGTG
1 AAAAACGCCGCAATA-G-GTAAGATATATAGCGGCGTTTGTTTAT--CAAACGCCGCAATAAGTA
* *
5698504 TTGATATTTTGCGGC
62 CTGATATTTAGCGGC
5698519 ATTTTTTTAT
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
84 5 0.08
85 17 0.26
86 41 0.62
87 3 0.05
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (85 bp):
AAAAACGCCGCAATAGGTAAGATATATAGCGGCGTTTGTTTATCAAACGCCGCAATAAGTACTGA
TATTTAGCGGCGTTTGTCTT
Found at i:5698697 original size:43 final size:42
Alignment explanation
Indices: 5698636--5698717 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 42
5698626 GATATATTCC
*
5698636 TGGTATATAGCGGCATTTT-TAGTATACAAACGCCGCTAAAAGT
1 TGGTACATAGCGGCATTTTAT-G-ATACAAACGCCGCTAAAAGT
5698679 TGGTACATAGCGGCATTTTATGATACAAACGCCGCTAAA
1 TGGTACATAGCGGCATTTTATGATACAAACGCCGCTAAA
5698718 TAACACAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
42 17 0.46
43 19 0.51
44 1 0.03
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (42 bp):
TGGTACATAGCGGCATTTTATGATACAAACGCCGCTAAAAGT
Found at i:5698711 original size:42 final size:43
Alignment explanation
Indices: 5698636--5698717 Score: 132
Period size: 42 Copynumber: 1.9 Consensus size: 43
5698626 GATATATTCC
*
5698636 TGGTATATAGCGGCATTTTTAGTATACAAACGCCGCTAAAAGT
1 TGGTACATAGCGGCATTTTTAGTATACAAACGCCGCTAAAAGT
5698679 TGGTACATAGCGGCA-TTTTA-TGATACAAACGCCGCTAAA
1 TGGTACATAGCGGCATTTTTAGT-ATACAAACGCCGCTAAA
5698718 TAACACAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
41 1 0.03
42 22 0.59
43 14 0.38
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (43 bp):
TGGTACATAGCGGCATTTTTAGTATACAAACGCCGCTAAAAGT
Found at i:5704488 original size:41 final size:41
Alignment explanation
Indices: 5704431--5704527 Score: 108
Period size: 41 Copynumber: 2.4 Consensus size: 41
5704421 CGGTGTTTTC
* ** * *
5704431 ATAAAAATGCCGCTAAA-ATTCTATTATATTGCGGCGTTTAT
1 ATAAAAATGCCACTAAATATTAAATT-TATTGCCGCGTTTGT
5704472 -TAAAAAATGCCACTAAATATTAAATTTATTGCCGCGTTTGT
1 AT-AAAAATGCCACTAAATATTAAATTTATTGCCGCGTTTGT
*
5704513 ATAAAAACGCCACTA
1 ATAAAAATGCCACTA
5704528 TGGATGAACA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
40 1 0.02
41 39 0.83
42 7 0.15
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.33
Consensus pattern (41 bp):
ATAAAAATGCCACTAAATATTAAATTTATTGCCGCGTTTGT
Found at i:5704596 original size:41 final size:41
Alignment explanation
Indices: 5704541--5704643 Score: 129
Period size: 41 Copynumber: 2.6 Consensus size: 41
5704531 ATGAACATAT
* ***
5704541 TATGGC-G-GTTTTTTATACAAATGCTGTAAAAGTTAGATC
1 TATGGCGGCGTTTTTTATACAAACGCCACAAAAGTTAGATC
*
5704580 TATGGCGGCGTTTTTTATACAAACGCCACAAAAGTTAGGTC
1 TATGGCGGCGTTTTTTATACAAACGCCACAAAAGTTAGATC
* *
5704621 TATAGCGGCGTTTTTGATACAAA
1 TATGGCGGCGTTTTTTATACAAA
5704644 AGCCGCTAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
39 6 0.11
40 1 0.02
41 48 0.87
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (41 bp):
TATGGCGGCGTTTTTTATACAAACGCCACAAAAGTTAGATC
Found at i:5706060 original size:83 final size:82
Alignment explanation
Indices: 5705973--5706173 Score: 219
Period size: 82 Copynumber: 2.4 Consensus size: 82
5705963 CGGTTTTTGC
* * * * **
5705973 ACAAACGCCACTATAAACAATAATATTGCGGCGTTTGTTTGATAAACGCCTCTAAATTACTTCTC
1 ACAAACGCCACTATAAACAATAATATTGCGGCGTTTGTGT-AAAAACACCGCTAAATTACCACTC
5706038 TATAGC-ATCATTTATTGA
65 TATAGCGAT-ATTTATTGA
* * * *
5706056 ACAAACGCCACTATAAACAACACTATCGCGGGGTTTGTGTAAAAACACCGCTAAATTACCACTCT
1 ACAAACGCCACTATAAACAATAATATTGCGGCGTTTGTGTAAAAACACCGCTAAATTACCACTCT
* * *
5706121 ATTGCGGTGTTTATTGA
66 ATAGCGATATTTATTGA
*
5706138 A-ACAACGCCACTATAAAC-ATATATATTACGGCGTTT
1 ACA-AACGCCACTATAAACAATA-ATATTGCGGCGTTT
5706174 TAGCTATAAA
Statistics
Matches: 97, Mismatches: 18, Indels: 7
0.80 0.15 0.06
Matches are distributed among these distances:
81 3 0.03
82 58 0.60
83 36 0.37
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (82 bp):
ACAAACGCCACTATAAACAATAATATTGCGGCGTTTGTGTAAAAACACCGCTAAATTACCACTCT
ATAGCGATATTTATTGA
Found at i:5707698 original size:5 final size:5
Alignment explanation
Indices: 5707652--5707689 Score: 67
Period size: 5 Copynumber: 7.4 Consensus size: 5
5707642 GTCTACAAAA
5707652 ATATT ATATT ATATT ATATT ATATT ATATT ATTATT AT
1 ATATT ATATT ATATT ATATT ATATT ATATT A-TATT AT
5707690 TTTTATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 27 0.84
6 5 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
ATATT
Found at i:5713405 original size:22 final size:22
Alignment explanation
Indices: 5713377--5713423 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
5713367 TGGTGGTTGG
*
5713377 TTTAATGG-ATGTTTAGACTTTA
1 TTTAATGGTATATTTA-ACTTTA
*
5713399 TTTAATGGTATATTTAAGTTTA
1 TTTAATGGTATATTTAACTTTA
5713421 TTT
1 TTT
5713424 TGGTTATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.28, C:0.02, G:0.15, T:0.55
Consensus pattern (22 bp):
TTTAATGGTATATTTAACTTTA
Found at i:5729432 original size:106 final size:106
Alignment explanation
Indices: 5729066--5729955 Score: 1338
Period size: 106 Copynumber: 8.4 Consensus size: 106
5729056 GTCAACAAAT
* * * *
5729066 AATTTCGGAGCCAATTTCAACTTCTCAGTGAAGGATATTGGACTCCAGACAATGCAAGTTCAACT
1 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* *
5729131 TCACGACGAACGGACCGCTGGTTGTCAA-TAACAACTTCCC
66 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
5729171 AATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
1 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* *
5729236 TCACGACGAAGGGACCGCTGGTTGTCAA-TAACAACTTCTC
66 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
5729276 AATTTCAGAGCCAATTTAAACTTCACAGCGAAGGATATTGGACTCTAGACAATGCAAGTTCAACT
1 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* *
5729341 TCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
66 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
5729382 AATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGTCTCCAGACAACGCAAGTTCAACT
1 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* *
5729447 TCACGACGAAGGGACCTCTGGTTGTCAATAAACAACTTCCC
66 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * **
5729488 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACCCCAGATGACGCAAGTTCAACT
1 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* *
5729553 TCACGACGAAGGGACTGCTGGTTGTCAACAAACAACTTCTC
66 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
5729594 AATTTCAGAGCCTATTTCAACTTCACAGTGAAGGATATTGGACTTCAGACGACGCAAGTTCAACT
1 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
*
5729659 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
66 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
5729700 AATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
1 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* *
5729765 TCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
66 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * * *
5729806 AATTACAGAACCAATTTTAACTTCACAGCGAAGGATATTGGACTCCATACAACACAAGTTCAACT
1 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* * *
5729871 TCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTTCC
66 TCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCCC
* * *
5729912 AGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGGACT
1 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACT
5729956 TGGAAGGGGC
Statistics
Matches: 723, Mismatches: 59, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
105 189 0.26
106 534 0.74
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (106 bp):
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
Found at i:5731806 original size:24 final size:24
Alignment explanation
Indices: 5731779--5731829 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
5731769 TATTACTTTC
5731779 TATTAATTTTATTA-TA-TATGTATA
1 TATT-ATTTTATTAGTATTAT-TATA
*
5731803 TATTTTTTTATTAGTATTATTATA
1 TATTATTTTATTAGTATTATTATA
5731827 TAT
1 TAT
5731830 ATATATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 8 0.33
24 13 0.54
25 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (24 bp):
TATTATTTTATTAGTATTATTATA
Found at i:5731815 original size:32 final size:32
Alignment explanation
Indices: 5731779--5731839 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
5731769 TATTACTTTC
* *
5731779 TATTAATTTTATTATATATGTATATATTTTTT
1 TATTAATATTATTATATATATATATATTTTTT
*
5731811 TATTAGTATTATTATATATATATATATTT
1 TATTAATATTATTATATATATATATATTT
5731840 ATATATTTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (32 bp):
TATTAATATTATTATATATATATATATTTTTT
Found at i:5732103 original size:16 final size:15
Alignment explanation
Indices: 5732081--5732116 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
5732071 TATTGTTTTT
5732081 TTTATATTCTATTTA
1 TTTATATTCTATTTA
*
5732096 TATTATATTTTATTTA
1 T-TTATATTCTATTTA
5732112 TTTAT
1 TTTAT
5732117 TTATTAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTATATTCTATTTA
Found at i:5738782 original size:2 final size:2
Alignment explanation
Indices: 5738775--5738802 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5738765 GTTACCCAAT
5738775 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
5738803 CAATAAAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5740265 original size:66 final size:65
Alignment explanation
Indices: 5740183--5740396 Score: 234
Period size: 66 Copynumber: 3.4 Consensus size: 65
5740173 ACAATACTTG
5740183 GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACGACGAATGAGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCAC-ACGAATGAGCCATCCA
5740248 C
65 C
* * * * * **
5740249 GATTTCAACTTCACGACGAAGGATAT-C-GTGC--A-CACAA--GCA-AC-AATGCAACC--CTT
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACACGAATG-AGCCATCCA
*
5740303 G
65 C
* *
5740304 GATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCAC-ACGAATGAGCCATCCA
5740369 C
65 C
5740370 GATTTCAACTTCACGACGAAGGATATC
1 GATTTCAACTTCACGACGAAGGATATC
5740397 GTGCCCACAA
Statistics
Matches: 116, Mismatches: 19, Indels: 26
0.72 0.12 0.16
Matches are distributed among these distances:
55 26 0.22
56 5 0.04
57 7 0.06
59 3 0.03
60 4 0.03
61 4 0.03
62 3 0.03
64 7 0.06
65 4 0.03
66 53 0.46
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.21
Consensus pattern (65 bp):
GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACACGAATGAGCCATCCAC
Found at i:5740522 original size:121 final size:121
Alignment explanation
Indices: 5740179--5740524 Score: 575
Period size: 121 Copynumber: 2.9 Consensus size: 121
5740169 TGAAACAATA
* *
5740179 CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACGACGAATGAGCCA
1 CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCA
*
5740244 TCCACGATTTCAACTTCACGACGAAGGATATCGTGCACACAAGCAACAATGCAACC
66 TCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAACAATGCAACC
*
5740300 CTTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCA
1 CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCA
**
5740365 TCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGTAATGCAACC
66 TCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAACAATGCAACC
* * * *
5740421 CTTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTTACAATGAAGGGGCCA
1 CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCA
* * *
5740486 TCCACTATTTCAAATTTACGACGAAGGATATCGTGCCCA
66 TCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCA
5740525 AGGGATCGAC
Statistics
Matches: 211, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
121 211 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.22
Consensus pattern (121 bp):
CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCA
TCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAACAATGCAACC
Found at i:5740735 original size:85 final size:86
Alignment explanation
Indices: 5740579--5740789 Score: 307
Period size: 85 Copynumber: 2.5 Consensus size: 86
5740569 TAGCCCAGTG
* * * *
5740579 CAGCATAACTCAAGGCGAGAAGGGTTATCTATCATCAAAAGACCTTCGAGTTTGATTACACTCAG
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCCAGTTCGATTACACTCAG
*
5740644 ATCAAAGGCACATCCAATTTA
66 ATCAAAGGCACATCAAATTTA
* * *
5740665 CAGCATAACTCAAGGCGATAAGGGTTATATGTCAAC-CAAGACCTTCCAGTTCGATTACACTCAG
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCCAGTTCGATTACACTCAG
*
5740729 CTCAAAGGCACATCAAATTTA
66 ATCAAAGGCACATCAAATTTA
* * *
5740750 TAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAA
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAA
5740790 ACTAACGAGT
Statistics
Matches: 109, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
85 75 0.69
86 34 0.31
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (86 bp):
CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCCAGTTCGATTACACTCAG
ATCAAAGGCACATCAAATTTA
Found at i:5740801 original size:85 final size:84
Alignment explanation
Indices: 5740579--5740818 Score: 300
Period size: 85 Copynumber: 2.8 Consensus size: 84
5740569 TAGCCCAGTG
* * *
5740579 CAGCATAACTCAAGGCGAGAAGGGTTATCTATCATCAAAAGACCTTCGAGTTTGATTACACTCAG
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAA-A-CTTCGAGTTCGATTACACTCAG
* *
5740644 ATCAAAGGCACATCCAATTTA
64 CTCAAAGGCACATCAAATTTA
* * * * *
5740665 CAGCATAACTCAAGGCGATAAGGGTTATATGTCAACCAAGACCTTCCAGTTCGATTACACTCAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAA-CAAAAACTTCGAGTTCGATTACACTCAGC
5740730 TCAAAGGCACATCAAATTTA
65 TCAAAGGCACATCAAATTTA
* * * * * *
5740750 TAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACTAACGAGTTCGATTTCATTCAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACT-TCGAGTTCGATTACACTCAGC
5740815 TCAA
65 TCAA
5740819 TGACAGCGAG
Statistics
Matches: 131, Mismatches: 21, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
84 6 0.05
85 90 0.69
86 31 0.24
87 4 0.03
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (84 bp):
CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACTTCGAGTTCGATTACACTCAGCT
CAAAGGCACATCAAATTTA
Found at i:5741055 original size:15 final size:16
Alignment explanation
Indices: 5741035--5741087 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 16
5741025 ACAAAAATAT
5741035 TTTATTATA-TTATTA
1 TTTATTATATTTATTA
5741050 TTTATT-TATTTATTA
1 TTTATTATATTTATTA
5741065 -TTATTAATATGTT-TTA
1 TTTATT-ATAT-TTATTA
5741081 TTT-TTAT
1 TTTATTAT
5741088 TTTTTGTAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
14 7 0.21
15 14 0.42
16 8 0.24
17 4 0.12
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (16 bp):
TTTATTATATTTATTA
Found at i:5741059 original size:24 final size:24
Alignment explanation
Indices: 5741032--5741084 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
5741022 TCTACAAAAA
* *
5741032 TATTTTATTA-TATTATTATTTATT
1 TATTTTATTATTATTAATATGT-TT
5741056 TA-TTTATTATTATTAATATGTTT
1 TATTTTATTATTATTAATATGTTT
5741079 TATTTT
1 TATTTT
5741085 TATTTTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (24 bp):
TATTTTATTATTATTAATATGTTT
Found at i:5741065 original size:23 final size:22
Alignment explanation
Indices: 5741035--5741087 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
5741025 ACAAAAATAT
* *
5741035 TTTATTATATTATTATTTATTTA
1 TTTATTATATTAATATGT-TTTA
5741058 TTTATTATTATTAATATGTTTTA
1 TTTATTA-TATTAATATGTTTTA
5741081 TTT-TTAT
1 TTTATTAT
5741088 TTTTTGTAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 1 0.04
22 3 0.11
23 14 0.52
24 9 0.33
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTATTATATTAATATGTTTTA
Found at i:5742480 original size:27 final size:27
Alignment explanation
Indices: 5742446--5742500 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
5742436 TAAACTAAAA
*
5742446 ACTAAATTTTAAATTTTAAAAGATTGG
1 ACTAAATTATAAATTTTAAAAGATTGG
*
5742473 ACTAAATTATAGATTTTAAAAGATTGG
1 ACTAAATTATAAATTTTAAAAGATTGG
5742500 A
1 A
5742501 GGAAGTGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.38
Consensus pattern (27 bp):
ACTAAATTATAAATTTTAAAAGATTGG
Found at i:5746412 original size:18 final size:18
Alignment explanation
Indices: 5746385--5746420 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5746375 CCAGAACCCA
*
5746385 AGGGGTATCGATTCCCCT
1 AGGGGGATCGATTCCCCT
*
5746403 AGGGGGATCGGTTCCCCT
1 AGGGGGATCGATTCCCCT
5746421 TCAAAGGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.28, G:0.33, T:0.25
Consensus pattern (18 bp):
AGGGGGATCGATTCCCCT
Found at i:5752603 original size:12 final size:12
Alignment explanation
Indices: 5752586--5752610 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5752576 TACACCACAT
5752586 GATGGAAAATGG
1 GATGGAAAATGG
5752598 GATGGAAAATGG
1 GATGGAAAATGG
5752610 G
1 G
5752611 TATAATCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.44, T:0.16
Consensus pattern (12 bp):
GATGGAAAATGG
Found at i:5752832 original size:10 final size:10
Alignment explanation
Indices: 5752806--5752877 Score: 56
Period size: 10 Copynumber: 6.6 Consensus size: 10
5752796 TATCACTCCA
5752806 TTTTATTCATAT
1 TTTTATT-AT-T
5752818 TTTTATTATT
1 TTTTATTATT
5752828 TTTTATTATT
1 TTTTATTATT
*
5752838 TTCCCTT-TAATT
1 TT---TTATTATT
*
5752850 TATTTAATATT
1 T-TTTATTATT
5752861 TATTTATTATT
1 T-TTTATTATT
5752872 TTTTAT
1 TTTTAT
5752878 GTAAAATTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
10 20 0.39
11 16 0.31
12 12 0.24
13 3 0.06
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTATTATT
Found at i:5757163 original size:21 final size:20
Alignment explanation
Indices: 5757130--5757175 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
5757120 ATCATTAAAT
5757130 TTATAAAACTTATAAAATTAA
1 TTATAAAACTTATAAAATT-A
* * *
5757151 TTATTAAATTTATGAAATTA
1 TTATAAAACTTATAAAATTA
5757171 TTATA
1 TTATA
5757176 GATAATTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (20 bp):
TTATAAAACTTATAAAATTA
Found at i:5761207 original size:31 final size:30
Alignment explanation
Indices: 5761169--5761247 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 30
5761159 AGTTTCAAAA
* *
5761169 GTAATAAATCGGTCACTAATGATATCGATTT
1 GTAATAAAT-GGTCACTAATGATATCAATCT
* *
5761200 GTAATAAAATGATCACTAATGTTATCAATCT
1 GTAAT-AAATGGTCACTAATGATATCAATCT
*
5761231 GTAACAAAATGGTCACT
1 GTAA-TAAATGGTCACT
5761248 CGACCAACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
31 36 0.90
32 4 0.10
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (30 bp):
GTAATAAATGGTCACTAATGATATCAATCT
Found at i:5762980 original size:33 final size:34
Alignment explanation
Indices: 5762943--5763050 Score: 98
Period size: 33 Copynumber: 3.2 Consensus size: 34
5762933 GGTAAGAAAT
* * *
5762943 TTATTTTTATGTTAGTAT-TTT-TTTAAATAGTTA
1 TTATTTTTATATTAATATATTTATGTAAATA-TTA
5762976 TTATTTTTATATTAATATATTTATGTAAATATTA
1 TTATTTTTATATTAATATATTTATGTAAATATTA
* * *
5763010 TT-TTTTTAT-TAAAATAATATTTATATAATTATTA
1 TTATTTTTATAT-TAAT-ATATTTATGTAAATATTA
5763044 TTTATTT
1 -TTATTT
5763051 AGAATTATTA
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
32 1 0.02
33 26 0.41
34 24 0.38
35 9 0.14
36 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (34 bp):
TTATTTTTATATTAATATATTTATGTAAATATTA
Found at i:5763012 original size:31 final size:33
Alignment explanation
Indices: 5762974--5763046 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 33
5762964 TTTAAATAGT
*
5762974 TATTATTTTTATATT-AAT-ATATTTATGTAAA
1 TATTATTTTTATATTAAATAATATTTATATAAA
* *
5763005 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTATATT-AAATAATATTTATATAAA
5763039 TATTATTT
1 TATTATTT
5763047 ATTTAGAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 14 0.39
33 3 0.08
34 19 0.53
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (33 bp):
TATTATTTTTATATTAAATAATATTTATATAAA
Found at i:5763213 original size:17 final size:17
Alignment explanation
Indices: 5763191--5763244 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
5763181 AATGTTAATA
5763191 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
5763208 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
5763225 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
5763242 TTT
1 TTT
5763245 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:5764802 original size:21 final size:21
Alignment explanation
Indices: 5764772--5764818 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5764762 GCAGGGGTAC
* *
5764772 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
5764793 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
5764814 ATGCC
1 ATGCC
5764819 GTCTCCGCAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.40, G:0.13, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:5764849 original size:21 final size:21
Alignment explanation
Indices: 5764823--5764895 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
5764813 TATGCCGTCT
*
5764823 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
5764844 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
* *
5764865 CCGCCA-AGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
5764886 CCGCAGGGTT
1 CCGCAGGGTT
5764896 TTATACCATA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.04
21 42 0.91
22 2 0.04
ACGTcount: A:0.19, C:0.34, G:0.26, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:5765467 original size:33 final size:33
Alignment explanation
Indices: 5765418--5765513 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 33
5765408 AAATGTTTTT
5765418 AAAATACAAATTATATTATTCAAAATTTAAAATA
1 AAAATACAAATTATATTATTC-AAATTTAAAATA
* * *
5765452 AAAATA-AAATAATATTATTCAAATTTAAATTT
1 AAAATACAAATTATATTATTCAAATTTAAAATA
* *
5765484 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATACAAATTATATTATTC-AAATTTAA
5765514 CATTAAATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
32 16 0.29
33 25 0.45
34 14 0.25
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (33 bp):
AAAATACAAATTATATTATTCAAATTTAAAATA
Found at i:5766142 original size:128 final size:128
Alignment explanation
Indices: 5765914--5766670 Score: 1257
Period size: 128 Copynumber: 5.9 Consensus size: 128
5765904 TTACCTGATT
*
5765914 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * * ** * *
5765979 TGACAAAATAATGGAAGACGCGCCCCCGGGAACGCGTCTTCATGT-CCTCTGAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAAT-AGTGAAATAATAGG
*
5766042 TACTGATATATCTAGTGTCCCTGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
5766107 TGATGAAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
5766170 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
5766235 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
5766298 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *** *
5766363 TGACAAAATAATGGAAGGCGCGCCCCCGAGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
5766426 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
5766491 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
5766554 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* ** * * *
5766619 TGACGAAATAATGGAAGGCGCCCCCCCAAGAACTCACCTTTATGTGAATAGT
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
5766671 ACTCCGATTA
Statistics
Matches: 590, Mismatches: 36, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
127 1 0.00
128 587 0.99
129 2 0.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:5766623 original size:384 final size:384
Alignment explanation
Indices: 5765914--5766670 Score: 1406
Period size: 384 Copynumber: 2.0 Consensus size: 384
5765904 TTACCTGATT
5765914 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
* * *
5765979 TGACAAAATAATGGAAGACGCGCCCCCGGGAACGCGTCTTCATGTCCTCTGAGAAATAATAGGTA
66 TGACAAAATAATGGAAGACGCGCCCCCGAGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGTA
*
5766044 CTGATATATCTAGTGTCCCTGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
131 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
5766109 ATGAAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACT
196 ATGAAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACT
5766174 GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
261 GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
* ** *
5766239 GAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
326 GAAATAATGGAAGGCGCCCCCCCAAGAACGCACCTTCATGTGAATAGTGAAATAATAGG
5766298 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
*
5766363 TGACAAAATAATGGAAGGCGCGCCCCCGAGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGTA
66 TGACAAAATAATGGAAGACGCGCCCCCGAGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGTA
5766428 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
131 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
*
5766493 ATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACT
196 ATGAAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACT
5766558 GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
261 GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
* *
5766623 GAAATAATGGAAGGCGCCCCCCCAAGAACTCACCTTTATGTGAATAGT
326 GAAATAATGGAAGGCGCCCCCCCAAGAACGCACCTTCATGTGAATAGT
5766671 ACTCCGATTA
Statistics
Matches: 361, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
384 361 1.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.23
Consensus pattern (384 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
TGACAAAATAATGGAAGACGCGCCCCCGAGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGTA
CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
ATGAAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACT
GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
GAAATAATGGAAGGCGCCCCCCCAAGAACGCACCTTCATGTGAATAGTGAAATAATAGG
Found at i:5766754 original size:8 final size:8
Alignment explanation
Indices: 5766741--5766781 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
5766731 TCACAATCTT
5766741 TCAAATTC
1 TCAAATTC
5766749 TCAAATTC
1 TCAAATTC
* *
5766757 CCAAACTC
1 TCAAATTC
5766765 T-AAATTC
1 TCAAATTC
5766772 TCAAATTC
1 TCAAATTC
5766780 TC
1 TC
5766782 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:5773234 original size:26 final size:26
Alignment explanation
Indices: 5773204--5773253 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
5773194 TTTAATTAGT
5773204 AATGAACAATAACAGTGAACAGTAAC
1 AATGAACAATAACAGTGAACAGTAAC
* * *
5773230 AATGAACAGTACCCGTGAACAGTA
1 AATGAACAATAACAGTGAACAGTA
5773254 GGGGAATCGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.48, C:0.18, G:0.18, T:0.16
Consensus pattern (26 bp):
AATGAACAATAACAGTGAACAGTAAC
Found at i:5773248 original size:13 final size:13
Alignment explanation
Indices: 5773206--5773253 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
5773196 TAATTAGTAA
*
5773206 TGAACAATAACAG
1 TGAACAGTAACAG
*
5773219 TGAACAGTAACAA
1 TGAACAGTAACAG
* *
5773232 TGAACAGTACCCG
1 TGAACAGTAACAG
5773245 TGAACAGTA
1 TGAACAGTA
5773254 GGGGAATCGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.46, C:0.19, G:0.19, T:0.17
Consensus pattern (13 bp):
TGAACAGTAACAG
Found at i:5773988 original size:40 final size:40
Alignment explanation
Indices: 5773944--5774025 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
5773934 ACCGTAGTGC
* *
5773944 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAACTGTAT
5773984 TACACATAAGGTCGTGCCCACCATATACACCAAACTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAACTGTAT
5774024 TA
1 TA
5774026 TAAACCTACA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.34, C:0.28, G:0.15, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCAAACTGTAT
Found at i:5780624 original size:12 final size:12
Alignment explanation
Indices: 5780607--5780643 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
5780597 TTACTATTCA
*
5780607 TGCTACAATAGC
1 TGCTACAATAAC
*
5780619 TGCTACAGTAAC
1 TGCTACAATAAC
5780631 TGCTACAATAAC
1 TGCTACAATAAC
5780643 T
1 T
5780644 TCCAAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (12 bp):
TGCTACAATAAC
Found at i:5781039 original size:44 final size:44
Alignment explanation
Indices: 5780983--5781114 Score: 142
Period size: 44 Copynumber: 2.9 Consensus size: 44
5780973 AAAATAATAT
*
5780983 AAAATATCTTACCATTTA-TCCTATAAGCTCGTAAGCTTATTTACC
1 AAAATA-CTTACCATTTATTCC-ATAAGCTCATAAGCTTATTTACC
* * *
5781028 AAAATACTTACCATTTAAATTCCATAAACTCATAAGCTTATTTTTCT
1 AAAATACTTACCATTT--ATTCCATAAGCTCATAAGCTTA-TTTACC
* * *
5781075 AATATACTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 AAAATACTTACCATTTATTCCATAAGCTCATAAGCTTATTT
5781115 GCATGGTTAC
Statistics
Matches: 75, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
43 3 0.04
44 30 0.40
45 6 0.08
46 18 0.24
47 18 0.24
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.39
Consensus pattern (44 bp):
AAAATACTTACCATTTATTCCATAAGCTCATAAGCTTATTTACC
Found at i:5797261 original size:13 final size:14
Alignment explanation
Indices: 5797232--5797264 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
5797222 TTATGCACTA
5797232 TTTATTTGTTTTAC
1 TTTATTTGTTTTAC
*
5797246 TTTATTT-TTTTTC
1 TTTATTTGTTTTAC
5797259 TTTATT
1 TTTATT
5797265 GCAGGCATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.12, C:0.06, G:0.03, T:0.79
Consensus pattern (14 bp):
TTTATTTGTTTTAC
Found at i:5814112 original size:18 final size:18
Alignment explanation
Indices: 5814089--5814125 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5814079 GACAAAGGGT
**
5814089 GTGGTGGTTTTGGAGGAG
1 GTGGTGGTGGTGGAGGAG
5814107 GTGGTGGTGGTGGAGGAG
1 GTGGTGGTGGTGGAGGAG
5814125 G
1 G
5814126 GCTTGGAGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.00, G:0.62, T:0.27
Consensus pattern (18 bp):
GTGGTGGTGGTGGAGGAG
Found at i:5814257 original size:75 final size:75
Alignment explanation
Indices: 5814173--5814314 Score: 221
Period size: 75 Copynumber: 1.9 Consensus size: 75
5814163 GGAGGCTTGG
* * **
5814173 TGGTGGCATTGGAAAGGGTGGGGGACTTGGAGGTAGGTTTGGGAAAGGAGGAGACTTTGGTGGTG
1 TGGTGGCATTGGAAAGAGAGGGGGACTTGGAGGTAGGTTTGGGAAAGGAAAAGACTTTGGTGGTG
5814238 GCGGGATTGA
66 GCGGGATTGA
* * *
5814248 TGGTGGCATTGTAAAGAGAGGGGGACTTGGAGGTGGGTTTGGGAAAGGAAAAGGCTTTGGTGGTG
1 TGGTGGCATTGGAAAGAGAGGGGGACTTGGAGGTAGGTTTGGGAAAGGAAAAGACTTTGGTGGTG
5814313 GC
66 GC
5814315 TTTGGAAAGG
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 60 1.00
ACGTcount: A:0.21, C:0.06, G:0.49, T:0.24
Consensus pattern (75 bp):
TGGTGGCATTGGAAAGAGAGGGGGACTTGGAGGTAGGTTTGGGAAAGGAAAAGACTTTGGTGGTG
GCGGGATTGA
Found at i:5814445 original size:30 final size:29
Alignment explanation
Indices: 5814404--5814518 Score: 122
Period size: 30 Copynumber: 3.8 Consensus size: 29
5814394 TTGGTTTTGG
* *
5814404 TGGTGGAATTGGAAAGCGTGGAGGGCTTGA
1 TGGTGGAATTGGAAAG-GAGGAGGCCTTGA
* *
5814434 TGGTGGCATTGGGAAAGGAGGAGGCCTTGG
1 TGGTGGAATT-GGAAAGGAGGAGGCCTTGA
* * *
5814464 TGGTGGAATTGGTAAAGGATGAGGCATCGA
1 TGGTGGAATTGG-AAAGGAGGAGGCCTTGA
*
5814494 TGGTGGTATTGGCAAAGGAGGAGGC
1 TGGTGGAATTGG-AAAGGAGGAGGC
5814519 TTTAGGAAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
29 2 0.03
30 63 0.89
31 6 0.08
ACGTcount: A:0.24, C:0.08, G:0.46, T:0.22
Consensus pattern (29 bp):
TGGTGGAATTGGAAAGGAGGAGGCCTTGA
Found at i:5814465 original size:60 final size:60
Alignment explanation
Indices: 5814400--5814518 Score: 163
Period size: 60 Copynumber: 2.0 Consensus size: 60
5814390 GACATTGGTT
* *
5814400 TTGGTGGTGGAATTGG-AAAGCG-TGGAGGGC-TTGATGGTGGCATTGGGAAAGGAGGAGGCC
1 TTGGTGGTGGAATTGGTAAAG-GAT-GA-GGCATCGATGGTGGCATTGGCAAAGGAGGAGGCC
*
5814460 TTGGTGGTGGAATTGGTAAAGGATGAGGCATCGATGGTGGTATTGGCAAAGGAGGAGGC
1 TTGGTGGTGGAATTGGTAAAGGATGAGGCATCGATGGTGGCATTGGCAAAGGAGGAGGC
5814519 TTTAGGAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
59 3 0.06
60 45 0.85
61 5 0.09
ACGTcount: A:0.24, C:0.08, G:0.46, T:0.23
Consensus pattern (60 bp):
TTGGTGGTGGAATTGGTAAAGGATGAGGCATCGATGGTGGCATTGGCAAAGGAGGAGGCC
Found at i:5814481 original size:96 final size:96
Alignment explanation
Indices: 5814303--5814481 Score: 205
Period size: 96 Copynumber: 1.9 Consensus size: 96
5814293 AGGAAAAGGC
** * * * ** *
5814303 TTTGGTGGTGGCTTTGGAAAGGGTTGAGGACTTGGTGGTCACATTGGAAAAGTCGGATGCCTTGG
1 TTTGGTGGTGGAATTGGAAAGCGTGGAGGACTTGATGGTCACATTGGAAAAGGAGGAGGCCTTGG
*
5814368 AGGAGGTATAGGAAAAGGTGGTGACATTGGT
66 AGGAGGAATAGGAAAAGGTGGTGACATTGGT
* ** *
5814399 TTTGGTGGTGGAATTGGAAAGCGTGGAGGGCTTGATGGTGGCATTGGGAAAGGAGGAGGCCTTGG
1 TTTGGTGGTGGAATTGGAAAGCGTGGAGGACTTGATGGTCACATTGGAAAAGGAGGAGGCCTTGG
* * * *
5814464 TGGTGGAATTGGTAAAGG
66 AGGAGGAATAGGAAAAGG
5814482 ATGAGGCATC
Statistics
Matches: 66, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
96 66 1.00
ACGTcount: A:0.22, C:0.07, G:0.44, T:0.27
Consensus pattern (96 bp):
TTTGGTGGTGGAATTGGAAAGCGTGGAGGACTTGATGGTCACATTGGAAAAGGAGGAGGCCTTGG
AGGAGGAATAGGAAAAGGTGGTGACATTGGT
Found at i:5815770 original size:21 final size:21
Alignment explanation
Indices: 5815746--5815788 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5815736 CCAAATCCAC
5815746 CCTCTTTGGCAAACTCATGCA
1 CCTCTTTGGCAAACTCATGCA
5815767 CCTCTTTGGCAAACTCATGCA
1 CCTCTTTGGCAAACTCATGCA
5815788 C
1 C
5815789 TAATGTCTCA
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:0.23, C:0.35, G:0.14, T:0.28
Consensus pattern (21 bp):
CCTCTTTGGCAAACTCATGCA
Found at i:5824590 original size:161 final size:162
Alignment explanation
Indices: 5824319--5824641 Score: 591
Period size: 161 Copynumber: 2.0 Consensus size: 162
5824309 GAGCAAAAGC
5824319 TACTTTCAGGCTTAACAAATGTATCACTTACTTTGTGTGTGAGCATTGTATAACAAGTAAGCATC
1 TACTTTCAGGCTTAACAAATGTATCACTTACTTTGTGTGTGAGCATTGTATAACAAGTAAGCATC
5824384 ACCGATTAAAATTCAACACGTCAAATTCTAGAGGCAAACGTTCTAGAATTGGTTCATT-TGATAT
66 ACCGATTAAAATTCAACACGTCAAATTCTAGAGGCAAACGTTCTAGAATTGGTTCATTCTG-TAT
5824448 GTCAAGCACCAGTTACAT-CCTAGGCGGAGCAA
130 GTCAAGCACCAGTTACATCCCTAGGCGGAGCAA
5824480 TACTTTCAGGCTTAACAAATGTATCACTTAC-TT-TGTGTGAGCATTGTATAACAAGTAAGCATC
1 TACTTTCAGGCTTAACAAATGTATCACTTACTTTGTGTGTGAGCATTGTATAACAAGTAAGCATC
5824543 ACCGATTAAAATTCAACACGTCAAATTCTAGAGGCAAACGTGTTCTAGAATTGGTTCATTCTGTA
66 ACCGATTAAAATTCAACACGTCAAATTCTAGAGGCAAAC--GTTCTAGAATTGGTTCATTCTGTA
5824608 TGTCAAGCACCAGTTACATCCCTAGGCGGAGCAA
129 TGTCAAGCACCAGTTACATCCCTAGGCGGAGCAA
5824642 AATACTTTTT
Statistics
Matches: 158, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
159 69 0.44
160 2 0.01
161 71 0.45
162 16 0.10
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (162 bp):
TACTTTCAGGCTTAACAAATGTATCACTTACTTTGTGTGTGAGCATTGTATAACAAGTAAGCATC
ACCGATTAAAATTCAACACGTCAAATTCTAGAGGCAAACGTTCTAGAATTGGTTCATTCTGTATG
TCAAGCACCAGTTACATCCCTAGGCGGAGCAA
Found at i:5824785 original size:22 final size:22
Alignment explanation
Indices: 5824754--5824796 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5824744 GGGTGGAACT
*
5824754 TGATTTTAGAAATAAGATCAAA
1 TGATTCTAGAAATAAGATCAAA
5824776 TGATTCTAGAAATAAGATCAA
1 TGATTCTAGAAATAAGATCAA
5824797 GTGTTTCCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.07, G:0.14, T:0.30
Consensus pattern (22 bp):
TGATTCTAGAAATAAGATCAAA
Found at i:5830468 original size:16 final size:16
Alignment explanation
Indices: 5830426--5830473 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
5830416 AAAACATCTA
*
5830426 AAAATAGTAACAACTAG
1 AAAA-AGTAACAGCTAG
*
5830443 AATCAA-TAACAGCTAG
1 AA-AAAGTAACAGCTAG
5830459 AAAAAGTAACAGCTA
1 AAAAAGTAACAGCTA
5830474 TGATGTCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 2 0.08
16 20 0.77
17 3 0.12
18 1 0.04
ACGTcount: A:0.56, C:0.15, G:0.12, T:0.17
Consensus pattern (16 bp):
AAAAAGTAACAGCTAG
Found at i:5837888 original size:50 final size:50
Alignment explanation
Indices: 5837813--5837914 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
5837803 AGAGATAATG
5837813 TCAAATCTGAAGAAACACTTACCTTGCACAGGAGCACCTTGAAGAATTCT
1 TCAAATCTGAAGAAACACTTACCTTGCACAGGAGCACCTTGAAGAATTCT
5837863 TCAAATCTGAAGAAACACTTACCTTGCACAGGAGCACCTTGAAGAATTCT
1 TCAAATCTGAAGAAACACTTACCTTGCACAGGAGCACCTTGAAGAATTCT
5837913 TC
1 TC
5837915 CTAGAAGGTC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25
Consensus pattern (50 bp):
TCAAATCTGAAGAAACACTTACCTTGCACAGGAGCACCTTGAAGAATTCT
Found at i:5839819 original size:2 final size:2
Alignment explanation
Indices: 5839812--5839837 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5839802 ATAAAAACAT
5839812 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
5839838 GAAAGTGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5841007 original size:29 final size:29
Alignment explanation
Indices: 5840965--5841031 Score: 125
Period size: 29 Copynumber: 2.3 Consensus size: 29
5840955 GACCTACGGC
*
5840965 TGCACTCCGGGCGACCTTGTAGGTCGCCA
1 TGCACTCCTGGCGACCTTGTAGGTCGCCA
5840994 TGCACTCCTGGCGACCTTGTAGGTCGCCA
1 TGCACTCCTGGCGACCTTGTAGGTCGCCA
5841023 TGCACTCCT
1 TGCACTCCT
5841032 CCTGCTCCTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.13, C:0.36, G:0.27, T:0.24
Consensus pattern (29 bp):
TGCACTCCTGGCGACCTTGTAGGTCGCCA
Found at i:5845731 original size:14 final size:14
Alignment explanation
Indices: 5845712--5845740 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5845702 AATATGTAGG
5845712 GCTCAAATAGAGCA
1 GCTCAAATAGAGCA
5845726 GCTCAAATAGAGCA
1 GCTCAAATAGAGCA
5845740 G
1 G
5845741 ATGCAAGCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.21, G:0.24, T:0.14
Consensus pattern (14 bp):
GCTCAAATAGAGCA
Found at i:5848384 original size:21 final size:18
Alignment explanation
Indices: 5848339--5848391 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 18
5848329 AAACATTAAT
5848339 TATAAAAGTTAGTATAAA
1 TATAAAAGTTAGTATAAA
* *
5848357 TAAAAAAATTAGTATAAAAAA
1 TATAAAAGTTAGTAT---AAA
5848378 TATAAAAGTTAGTA
1 TATAAAAGTTAGTA
5848392 ATTTACAGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 13 0.46
21 15 0.54
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.30
Consensus pattern (18 bp):
TATAAAAGTTAGTATAAA
Found at i:5848516 original size:11 final size:11
Alignment explanation
Indices: 5848500--5848524 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5848490 ATAATATAAT
5848500 AAATAAATTTA
1 AAATAAATTTA
5848511 AAATAAATTTA
1 AAATAAATTTA
5848522 AAA
1 AAA
5848525 ATTTACTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATAAATTTA
Found at i:5850218 original size:23 final size:21
Alignment explanation
Indices: 5850163--5850220 Score: 55
Period size: 23 Copynumber: 2.7 Consensus size: 21
5850153 CATATCATAT
*
5850163 TGGTATCGATACT-CCTTCTA
1 TGGTATAGATACTCCCTTCTA
* * *
5850183 AGGTATTGGTACTCCCTTTCTA
1 TGGTATAGATACTCCC-TTCTA
5850205 GTGGTATAGATACTCC
1 -TGGTATAGATACTCC
5850221 ATTGGGTATC
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 10 0.34
21 2 0.07
22 5 0.17
23 12 0.41
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.38
Consensus pattern (21 bp):
TGGTATAGATACTCCCTTCTA
Found at i:5857410 original size:20 final size:20
Alignment explanation
Indices: 5857385--5857460 Score: 134
Period size: 20 Copynumber: 3.8 Consensus size: 20
5857375 ATTTAATCTC
5857385 AGTATCGATACTCACCTGAG
1 AGTATCGATACTCACCTGAG
*
5857405 AGTATCGATACTCGCCTGAG
1 AGTATCGATACTCACCTGAG
*
5857425 AGTATCGATACTCGCCTGAG
1 AGTATCGATACTCACCTGAG
5857445 AGTATCGATACTCACC
1 AGTATCGATACTCACC
5857461 CTTCTCAGTA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (20 bp):
AGTATCGATACTCACCTGAG
Found at i:5860774 original size:7 final size:8
Alignment explanation
Indices: 5860756--5860782 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
5860746 CAATTTTACC
5860756 AAAATTGA
1 AAAATTGA
5860764 AAAATTGA
1 AAAATTGA
5860772 AAAATTGA
1 AAAATTGA
5860780 AAA
1 AAA
5860783 GTTAAGGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (8 bp):
AAAATTGA
Found at i:5861941 original size:15 final size:16
Alignment explanation
Indices: 5861921--5861955 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
5861911 GATTTTCAAA
5861921 TCAAAATTTTC-TTTT
1 TCAAAATTTTCATTTT
5861936 TCAAAATTTTCATTTT
1 TCAAAATTTTCATTTT
5861952 TCAA
1 TCAA
5861956 TTTTGAAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.54
Consensus pattern (16 bp):
TCAAAATTTTCATTTT
Found at i:5863355 original size:42 final size:42
Alignment explanation
Indices: 5863309--5863401 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
5863299 TAAGGGAAAT
* * *
5863309 GATCGATCCTTTTCATCGAGGGGTCGATC-CTTTTGTTGAAGG
1 GATCGATCCTTTTCATCGAGGGATCGATCATTTTTG-TAAAGG
* * * *
5863351 GATCGATCTTTTTCCTCTATGGATCGATCATTTTTGTAAAGG
1 GATCGATCCTTTTCATCGAGGGATCGATCATTTTTGTAAAGG
5863393 GATCGATCC
1 GATCGATCC
5863402 CAAAGTTACT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 37 0.88
43 5 0.12
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (42 bp):
GATCGATCCTTTTCATCGAGGGATCGATCATTTTTGTAAAGG
Found at i:5863885 original size:16 final size:15
Alignment explanation
Indices: 5863864--5863902 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
5863854 AGTTTGAATG
5863864 AAAGGAAGAAGACAAA
1 AAAGGAAGAAGA-AAA
*
5863880 AAAGGATGAAGAAAA
1 AAAGGAAGAAGAAAA
*
5863895 AGAGGAAG
1 AAAGGAAG
5863903 CATGACACGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.64, C:0.03, G:0.31, T:0.03
Consensus pattern (15 bp):
AAAGGAAGAAGAAAA
Found at i:5871687 original size:30 final size:29
Alignment explanation
Indices: 5871629--5871960 Score: 287
Period size: 30 Copynumber: 11.1 Consensus size: 29
5871619 TAAAAAGATC
* *
5871629 AAAATAG-AAAAAAAGAAACTTAAGGGACT
1 AAAATAGCAAAAATA-AAATTTAAGGGACT
* * *
5871658 AAAATAGCAAAAATAGGAATTAAAAGGACT
1 AAAATAGCAAAAATA-AAATTTAAGGGACT
* *
5871688 AAAATAGCAAAAATCAAAACTTAAGGGATT
1 AAAATAGCAAAAAT-AAAATTTAAGGGACT
* *
5871718 AAAATAGCAAAAATAAAAATTAAAAGGACT
1 AAAATAGCAAAAAT-AAAATTTAAGGGACT
* * * *
5871748 AAAATAGAAAGAAAAACAAAACTTAAGGGATT
1 AAAATAG---CAAAAATAAAATTTAAGGGACT
*
5871780 AAAATAGCATAAACAT-AAATTTAAAGGACT
1 AAAATAGCA-AAA-ATAAAATTTAAGGGACT
* *
5871810 AAAATAGTAAAAATATACATTTAAGGGACT
1 AAAATAGCAAAAATA-AAATTTAAGGGACT
* *
5871840 AAAATCA-CAAAAACAAAAACTTAAGGGACT
1 AAAAT-AGCAAAAA-TAAAATTTAAGGGACT
* * * *
5871870 AAATTAGTAAAAAT-ACATTTAAAGGACT
1 AAAATAGCAAAAATAAAATTTAAGGGACT
*
5871898 AAAATAGCAAAAACATAAATTTAAGGGACT
1 AAAATAGCAAAAATA-AAATTTAAGGGACT
*
5871928 AAAATAGCAAAACA-AAAACTTAAGGGACT
1 AAAATAGCAAAA-ATAAAATTTAAGGGACT
5871957 AAAA
1 AAAA
5871961 CACAAATAAA
Statistics
Matches: 243, Mismatches: 45, Indels: 30
0.76 0.14 0.09
Matches are distributed among these distances:
28 24 0.10
29 29 0.12
30 162 0.67
31 5 0.02
32 18 0.07
33 5 0.02
ACGTcount: A:0.59, C:0.09, G:0.13, T:0.19
Consensus pattern (29 bp):
AAAATAGCAAAAATAAAATTTAAGGGACT
Found at i:5871783 original size:122 final size:120
Alignment explanation
Indices: 5871634--5871966 Score: 362
Period size: 122 Copynumber: 2.8 Consensus size: 120
5871624 AGATCAAAAT
* *
5871634 AGAAAAAAAGAAACTTAAGGGACTAAAATAGCAAAAATAGGAATTAAAAGGACTAAAATAGCAAA
1 AGAAAAACA-AAACTTAAGGGACTAAAATAGCAAAAATA--AATTTAAAGGACTAAAATAGCAAA
* *
5871699 AATCAAAACTTAAGGGATTAAAAT-AGCAAAAATAAAAA-TTAAAAGGACTAAAATAGAA
63 AATCAAAACTTAAGGGACTAAAATCA-CAAAAACAAAAACTT-AAAGGACTAAAATAGAA
* *
5871757 AGAAAAACAAAACTTAAGGGATTAAAATAGCATAAACATAAATTTAAAGGACTAAAATAGTAAAA
1 AGAAAAACAAAACTTAAGGGACTAAAATAGCA-AAA-ATAAATTTAAAGGACTAAAATAGCAAAA
* * * * *
5871822 AT-ATACATTTAAGGGACTAAAATCACAAAAACAAAAACTTAAGGGACTAAATTAGTA
64 ATCA-AAACTTAAGGGACTAAAATCACAAAAACAAAAACTTAAAGGACTAAAATAGAA
* * * *
5871879 A-AAATAC---ATTTAAAGGACTAAAATAGCAAAAACATAAATTTAAGGGACTAAAATAGC-AAA
1 AGAAAAACAAAACTTAAGGGACTAAAATAGC-AAAA-ATAAATTTAAAGGACTAAAATAGCAAAA
5871939 A-CAAAAACTTAAGGGACTAAAA-CACAAA
64 ATC-AAAACTTAAGGGACTAAAATCACAAA
5871967 TAAAATAAAC
Statistics
Matches: 183, Mismatches: 19, Indels: 23
0.81 0.08 0.10
Matches are distributed among these distances:
116 6 0.03
117 20 0.11
118 44 0.24
119 1 0.01
121 6 0.03
122 89 0.49
123 14 0.08
124 3 0.02
ACGTcount: A:0.59, C:0.10, G:0.13, T:0.18
Consensus pattern (120 bp):
AGAAAAACAAAACTTAAGGGACTAAAATAGCAAAAATAAATTTAAAGGACTAAAATAGCAAAAAT
CAAAACTTAAGGGACTAAAATCACAAAAACAAAAACTTAAAGGACTAAAATAGAA
Found at i:5871910 original size:88 final size:89
Alignment explanation
Indices: 5871629--5871960 Score: 352
Period size: 92 Copynumber: 3.7 Consensus size: 89
5871619 TAAAAAGATC
* * * * ** *
5871629 AAAATAG-AAAAAAAGAAACTTAAGGGACTAAAATAGCAAAAATAGGAA-TTAAAAGGACTAAAA
1 AAAATAGCAAAAATATAAATTTAAGGGACTAAAATAGCAAAAACAAAAACTT-AAGGGACTAAAA
* * * *
5871692 TAG-CAAAAATCAAAACTTAAGGGATT
65 TAGATAAAAAT--AAATTTAAAGGACT
* * * * * *
5871718 AAAATAGCAAAAATAAAAATTAAAAGGACTAAAATAGAAAGAAAAACAAAACTTAAGGGATTAAA
1 AAAATAGCAAAAATATAAATTTAAGGGACTAAAATAGCAA-AAACA-AAAACTTAAGGGACTAAA
*
5871783 ATAGCATAAACATAAATTTAAAGGACT
64 ATAG-ATAAAAATAAATTTAAAGGACT
* * *
5871810 AAAATAGTAAAAATATACATTTAAGGGACTAAAATCA-CAAAAACAAAAACTTAAGGGACTAAAT
1 AAAATAGCAAAAATATAAATTTAAGGGACTAAAAT-AGCAAAAACAAAAACTTAAGGGACTAAAA
*
5871874 TAG-TAAAAATACATTTAAAGGACT
65 TAGATAAAAATAAATTTAAAGGACT
*
5871898 AAAATAGCAAAAACATAAATTTAAGGGACTAAAATAGC-AAAACAAAAACTTAAGGGACTAAAA
1 AAAATAGCAAAAATATAAATTTAAGGGACTAAAATAGCAAAAACAAAAACTTAAGGGACTAAAA
5871961 CACAAATAAA
Statistics
Matches: 204, Mismatches: 31, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
87 25 0.12
88 52 0.25
89 7 0.03
90 46 0.23
91 8 0.04
92 58 0.28
93 3 0.01
94 5 0.02
ACGTcount: A:0.59, C:0.09, G:0.13, T:0.19
Consensus pattern (89 bp):
AAAATAGCAAAAATATAAATTTAAGGGACTAAAATAGCAAAAACAAAAACTTAAGGGACTAAAAT
AGATAAAAATAAATTTAAAGGACT
Found at i:5874128 original size:21 final size:21
Alignment explanation
Indices: 5874098--5874206 Score: 182
Period size: 21 Copynumber: 5.2 Consensus size: 21
5874088 AATATGTAAA
*
5874098 TCGCATTGCGATTTTCCAAAT
1 TCGCGTTGCGATTTTCCAAAT
*
5874119 TCACGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATTTTCCAAAT
*
5874140 TCGCGTTGCGATTTTCTAAAT
1 TCGCGTTGCGATTTTCCAAAT
*
5874161 TCGCGTTGCGATTTTCTAAAT
1 TCGCGTTGCGATTTTCCAAAT
5874182 TCGCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATTTTCCAAAT
5874203 TCGC
1 TCGC
5874207 AACGTGAATC
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 83 1.00
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.39
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCAAAT
Found at i:5874223 original size:42 final size:42
Alignment explanation
Indices: 5874069--5874215 Score: 143
Period size: 42 Copynumber: 3.5 Consensus size: 42
5874059 CGCAACCCAG
* * * *
5874069 TTTCCAATTTCGCAACGCGAATATGTAAA-TCGCATTGCGAT
1 TTTCCAAATTCGCAACGCGAATTTCTAAATTCGCGTTGCGAT
* *** * *
5874110 TTTCCAAATTCACGTTGCGATTTTCCAAATTCGCGTTGCGAT
1 TTTCCAAATTCGCAACGCGAATTTCTAAATTCGCGTTGCGAT
* *** *
5874152 TTTCTAAATTCGCGTTGCGATTTTCTAAATTCGCGTTGCGAT
1 TTTCCAAATTCGCAACGCGAATTTCTAAATTCGCGTTGCGAT
*
5874194 TTTCCAAATTCGCAACGTGAAT
1 TTTCCAAATTCGCAACGCGAAT
5874216 CTGTAAATCG
Statistics
Matches: 86, Mismatches: 19, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
41 20 0.23
42 66 0.77
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (42 bp):
TTTCCAAATTCGCAACGCGAATTTCTAAATTCGCGTTGCGAT
Found at i:5874223 original size:63 final size:63
Alignment explanation
Indices: 5874069--5874227 Score: 196
Period size: 63 Copynumber: 2.6 Consensus size: 63
5874059 CGCAACCCAG
*
5874069 TTTCCAATTTCGCAACGCGAATATGTAAA-TCGCATTGCGATTTTCCAAATTCACGTTGCGAT
1 TTTCCAAATTCGCAACGCGAATATGTAAATTCGCATTGCGATTTTCCAAATTCACGTTGCGAT
*** * * * * * *
5874131 TTTCCAAATTCGCGTTGCGATTTTCTAAATTCGCGTTGCGATTTTCTAAATTCGCGTTGCGAT
1 TTTCCAAATTCGCAACGCGAATATGTAAATTCGCATTGCGATTTTCCAAATTCACGTTGCGAT
* *
5874194 TTTCCAAATTCGCAACGTGAATCTGTAAA-TCGCA
1 TTTCCAAATTCGCAACGCGAATATGTAAATTCGCA
5874228 ACGCGAATTT
Statistics
Matches: 78, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
62 26 0.33
63 52 0.67
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (63 bp):
TTTCCAAATTCGCAACGCGAATATGTAAATTCGCATTGCGATTTTCCAAATTCACGTTGCGAT
Found at i:5874228 original size:20 final size:20
Alignment explanation
Indices: 5874203--5874249 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
5874193 TTTTCCAAAT
*
5874203 TCGCAACGTGAATCTGTAAA
1 TCGCAACGCGAATCTGTAAA
*
5874223 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATCTGTAAA
5874243 TCGCAAC
1 TCGCAAC
5874250 ACAGAAGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGAATCTGTAAA
Found at i:5874266 original size:20 final size:20
Alignment explanation
Indices: 5874243--5874326 Score: 107
Period size: 20 Copynumber: 4.2 Consensus size: 20
5874233 AATTTGTAAA
5874243 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
5874263 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
*
5874283 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* *
5874303 TCGCAACACGGAATTTCAAAT
1 TCGCAACACAGAA-GTCAAAT
5874324 TCG
1 TCG
5874327 TAACTAAATT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
19 2 0.04
20 43 0.78
21 10 0.18
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.19
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:5874267 original size:40 final size:42
Alignment explanation
Indices: 5874223--5874368 Score: 141
Period size: 40 Copynumber: 3.7 Consensus size: 42
5874213 AATCTGTAAA
*
5874223 TCGCAACGCGAATTTGT-AAA-TCGCAACACAGAAGTCAAAT
1 TCGCAACGCGAATTTGTCAAATTCGCAACACAAAAGTCAAAT
*
5874263 TCGCAACGCG-A-TAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACGCGAATTTGTCAAATTCGCAACACAAAAGTCAAAT
* * * **
5874303 TCGCAACACGGAA-TT-TCAAATTCGTAAC-TAAATTTCAAAT
1 TCGCAACGC-GAATTTGTCAAATTCGCAACACAAAAGTCAAAT
*
5874343 TCGCAAC-TGAA-TT-TCAAATTCGCAAC
1 TCGCAACGCGAATTTGTCAAATTCGCAAC
5874369 TAGATTTTCG
Statistics
Matches: 92, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
38 20 0.22
39 4 0.04
40 53 0.58
41 13 0.14
42 2 0.02
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (42 bp):
TCGCAACGCGAATTTGTCAAATTCGCAACACAAAAGTCAAAT
Found at i:5874338 original size:19 final size:19
Alignment explanation
Indices: 5874277--5874388 Score: 109
Period size: 19 Copynumber: 5.7 Consensus size: 19
5874267 AACGCGATAG
* **
5874277 TCAAATTCGCAACACAAAAG
1 TCAAATTCGCAAC-TAAATT
5874297 TCAAATTCGCAAC-ACGGAATT
1 TCAAATTCGCAACTA---AATT
*
5874318 TCAAATTCGTAACTAAATT
1 TCAAATTCGCAACTAAATT
*
5874337 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTAAATT
*
5874356 TCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACTA-AATT
*
5874376 TCGAATTCGCAAC
1 TCAAATTCGCAAC
5874389 ACGAGTTTAA
Statistics
Matches: 79, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
18 1 0.01
19 35 0.44
20 28 0.35
21 14 0.18
22 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (19 bp):
TCAAATTCGCAACTAAATT
Found at i:5874363 original size:38 final size:39
Alignment explanation
Indices: 5874198--5874388 Score: 128
Period size: 40 Copynumber: 4.8 Consensus size: 39
5874188 TGCGATTTTC
5874198 CAAATTCGCAACGT-GAATCTGT-AAA-TCGCAACGCGAATTT
1 CAAATTCGCAAC-TAGAAT-T-TCAAATTCGCAACG-GAATTT
* * * *
5874238 GTAAA-TCGCAACACAGAA-GTCAAATTCGCAACGCG-ATAGT
1 -CAAATTCGCAAC-TAGAATTTCAAATTCGCAACG-GAAT-TT
* **
5874278 CAAATTCGCAAC-ACAAAAGTCAAATTCGCAACACGGAATTT
1 CAAATTCGCAACTA-GAATTTCAAATTCGC-A-ACGGAATTT
* *
5874319 CAAATTCGTAACTA-AATTTCAAATTCGCAACTGAATTT
1 CAAATTCGCAACTAGAATTTCAAATTCGCAACGGAATTT
* *
5874357 CAAATTCGCAACTAGATTTTCGAATTCGCAAC
1 CAAATTCGCAACTAGAATTTCAAATTCGCAAC
5874389 ACGAGTTTAA
Statistics
Matches: 123, Mismatches: 15, Indels: 26
0.75 0.09 0.16
Matches are distributed among these distances:
38 23 0.19
39 26 0.21
40 48 0.39
41 20 0.16
42 6 0.05
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.25
Consensus pattern (39 bp):
CAAATTCGCAACTAGAATTTCAAATTCGCAACGGAATTT
Found at i:5874382 original size:20 final size:20
Alignment explanation
Indices: 5874297--5874388 Score: 118
Period size: 19 Copynumber: 4.7 Consensus size: 20
5874287 AACACAAAAG
5874297 TCAAATTCGCAAC-ACGGAATT
1 TCAAATTCGCAACTA--GAATT
*
5874318 TCAAATTCGTAACTA-AATT
1 TCAAATTCGCAACTAGAATT
5874337 TCAAATTCGCAACT-GAATT
1 TCAAATTCGCAACTAGAATT
*
5874356 TCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACTAGAATT
*
5874376 TCGAATTCGCAAC
1 TCAAATTCGCAAC
5874389 ACGAGTTTAA
Statistics
Matches: 64, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
19 35 0.55
20 16 0.25
21 12 0.19
22 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (20 bp):
TCAAATTCGCAACTAGAATT
Found at i:5874404 original size:39 final size:39
Alignment explanation
Indices: 5874257--5874407 Score: 146
Period size: 40 Copynumber: 3.8 Consensus size: 39
5874247 AACACAGAAG
* * * **
5874257 TCAAATTCGCAACGCG-ATAGTCAAATTCGCAACACAAAAG
1 TCAAATTCGCAACACGAAT-TTCAAATTCGCAAC-TAAATT
*
5874297 TCAAATTCGCAACACGGAATTTCAAATTCGTAACTAAATT
1 TCAAATTCGCAACAC-GAATTTCAAATTCGCAACTAAATT
* *
5874337 TCAAATTCGCAAC-TGAATTTCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACACGAATTTCAAATTCGCAACTA-AATT
* * *
5874376 TCGAATTCGCAACACGAGTTT-AATTTCGCAAC
1 TCAAATTCGCAACACGAATTTCAAATTCGCAAC
5874408 AGGTTTTAGT
Statistics
Matches: 94, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
38 19 0.20
39 25 0.27
40 35 0.37
41 13 0.14
42 2 0.02
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.27
Consensus pattern (39 bp):
TCAAATTCGCAACACGAATTTCAAATTCGCAACTAAATT
Found at i:5874415 original size:18 final size:19
Alignment explanation
Indices: 5874381--5874427 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
5874371 GATTTTCGAA
5874381 TTCGCAACACGAGTTTAAT
1 TTCGCAACACGAGTTTAAT
*
5874400 TTCGCAACA-G-GTTTTAGT
1 TTCGCAACACGAG-TTTAAT
5874418 TTCGCAACAC
1 TTCGCAACAC
5874428 AAATGTTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 1 0.04
18 15 0.60
19 9 0.36
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (19 bp):
TTCGCAACACGAGTTTAAT
Done.