Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007886.1 Hibiscus syriacus cultivar Beakdansim tig00110266_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: 1254954
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 7
Found at i:517059 original size:20 final size:20
Alignment explanation
Indices: 517034--517071 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
517024 TCTAATAAAT
517034 TATTTAAAATAAATCAATCG
1 TATTTAAAATAAATCAATCG
517054 TATTTAAAATAAATCAAT
1 TATTTAAAATAAATCAAT
517072 TCATATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.37
Consensus pattern (20 bp):
TATTTAAAATAAATCAATCG
Found at i:517080 original size:20 final size:20
Alignment explanation
Indices: 516917--517078 Score: 83
Period size: 22 Copynumber: 7.2 Consensus size: 20
516907 ATACTAATAT
516917 TATTTAAAATAAATCAATCCA
1 TATTTAAAATAAATCAAT-CA
516938 TATTTTAAAATAAATCAATTCA
1 TA-TTTAAAATAAATCAA-TCA
* *
516960 TACTAATAAATTATTAAATAAATCA
1 TA-T-TTAAA--A-TAAATCAATCA
**
516985 TACAACTACAATATAAATCAATC-
1 T--ATTTA-AA-ATAAATCAATCA
* *
517008 TATTTAAAAAAATTCATCTAATAAA
1 TATTTAAAATAA---ATC-AAT-CA
*
517033 TTATTTAAAATAAATCAATCG
1 -TATTTAAAATAAATCAATCA
517054 TATTTAAAATAAATCAATTCA
1 TATTTAAAATAAATCAA-TCA
517075 TATT
1 TATT
517079 AATAAACTAT
Statistics
Matches: 110, Mismatches: 14, Indels: 34
0.70 0.09 0.22
Matches are distributed among these distances:
19 3 0.03
20 19 0.17
21 11 0.10
22 26 0.24
23 12 0.11
24 9 0.08
25 9 0.08
26 20 0.18
27 1 0.01
ACGTcount: A:0.52, C:0.11, G:0.01, T:0.36
Consensus pattern (20 bp):
TATTTAAAATAAATCAATCA
Found at i:517217 original size:53 final size:54
Alignment explanation
Indices: 517117--517327 Score: 335
Period size: 53 Copynumber: 4.0 Consensus size: 54
517107 ACAACTACAT
*
517117 AATAAATCAATCCATGTTTTAAAAT-AATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* * *
517170 AATAATTCAATCTATATTTTAAAATAAATCAATCGATACTAAT-AATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
517223 AAT-AATCAATCCATATTTTAAAATAAATCAATCC--ACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
517274 AATAAATCAATCCATATTTT-AAATAAATCAATCCATACTAATAAATCATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
517327 A
1 A
517328 TAATTATTTT
Statistics
Matches: 145, Mismatches: 8, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
50 6 0.04
51 27 0.19
52 44 0.30
53 52 0.36
54 16 0.11
ACGTcount: A:0.50, C:0.13, G:0.01, T:0.36
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:517300 original size:26 final size:24
Alignment explanation
Indices: 517220--517367 Score: 81
Period size: 21 Copynumber: 6.3 Consensus size: 24
517210 AATAATTATT
517220 TAAAAT-AATCAATCCATA-TTT-
1 TAAAATAAATCAATCCATATTTTA
*
517241 TAAAATAAATCAATCCACTAATAAATTATT
1 TAAAATAAATCAATCCA-T-AT---TT-TA
517271 TAAAATAAATCAATCCATA-TTT-
1 TAAAATAAATCAATCCATATTTTA
* *
517293 T-AAATAAATCAATCCATA-CTAA
1 TAAAATAAATCAATCCATATTTTA
517315 TAAATCATTTAAAT-AAT---TA-TTT-
1 TAAA--A--TAAATCAATCCATATTTTA
517337 TAAAATAAATCAATCCATATTTT-
1 TAAAATAAATCAATCCATATTTTA
517360 TAAAATAA
1 TAAAATAA
517368 TTATTTTAAA
Statistics
Matches: 103, Mismatches: 4, Indels: 38
0.71 0.03 0.26
Matches are distributed among these distances:
18 5 0.05
19 3 0.03
20 1 0.01
21 24 0.23
22 18 0.17
23 18 0.17
24 3 0.03
25 1 0.01
26 3 0.03
27 5 0.05
28 3 0.03
29 2 0.02
30 17 0.17
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.36
Consensus pattern (24 bp):
TAAAATAAATCAATCCATATTTTA
Found at i:519847 original size:23 final size:23
Alignment explanation
Indices: 519792--519849 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
519782 GGGCGGTTAT
*
519792 ATATATTATATTTAATATTTTGAG
1 ATATATTAT-TTTAATATTTTGAA
* *
519816 ATTTTTTATTTT-ATATTGTTGAA
1 ATATATTATTTTAATATT-TTGAA
519839 ATATATTATTT
1 ATATATTATTT
519850 AATTATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 5 0.18
23 16 0.57
24 7 0.25
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (23 bp):
ATATATTATTTTAATATTTTGAA
Found at i:519925 original size:42 final size:40
Alignment explanation
Indices: 519837--519933 Score: 124
Period size: 42 Copynumber: 2.4 Consensus size: 40
519827 TATATTGTTG
** *
519837 AAATATATTA-TTTAATTATTAAAAATAAAAAATTATTAT
1 AAATATATTATTTTAACAATTAAAAATAAAAAATAATTAT
* *
519876 AAATATATTATTTTAACAACTTGAAATATAATAAATAATTAT
1 AAATATATTATTTTAACAA-TT-AAAAATAAAAAATAATTAT
519918 AAATATATTATTTTAA
1 AAATATATTATTTTAA
519934 TTATTTTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
39 10 0.20
40 6 0.12
41 2 0.04
42 32 0.64
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (40 bp):
AAATATATTATTTTAACAATTAAAAATAAAAAATAATTAT
Found at i:521176 original size:51 final size:51
Alignment explanation
Indices: 521102--521204 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 51
521092 AATGTCATTC
521102 AATAAATTCTATTAACATTATATAAGTTTATACTTAGTATATCAAATATTA
1 AATAAATTCTATTAACATTATATAAGTTTATACTTAGTATATCAAATATTA
* *
521153 AATAAATTCTATTAACATTATATAAGTTTATATTTAGTATATGAAATATTA
1 AATAAATTCTATTAACATTATATAAGTTTATACTTAGTATATCAAATATTA
521204 A
1 A
521205 TTCTTAACGA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.44
Consensus pattern (51 bp):
AATAAATTCTATTAACATTATATAAGTTTATACTTAGTATATCAAATATTA
Found at i:525149 original size:31 final size:31
Alignment explanation
Indices: 525108--525172 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
525098 CTCGAGTTAG
* *
525108 AAAACTGTAAGAGTAAGCTTGATTCGACTCA
1 AAAACGGTAAGAGTAAGCTTGACTCGACTCA
525139 AAAACGGTAAGAGTAAGCTTGACTCGACTCA
1 AAAACGGTAAGAGTAAGCTTGACTCGACTCA
525170 AAA
1 AAA
525173 CTTGCAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.22
Consensus pattern (31 bp):
AAAACGGTAAGAGTAAGCTTGACTCGACTCA
Found at i:526650 original size:14 final size:14
Alignment explanation
Indices: 526633--526686 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
526623 CGGATTTAGG
526633 GTTTAGGGTTTAAT
1 GTTTAGGGTTTAAT
**
526647 GTTTAATGTTT-AT
1 GTTTAGGGTTTAAT
* *
526660 AGTTTAGGATTTAAG
1 -GTTTAGGGTTTAAT
526675 GTTTAGGGTTTA
1 GTTTAGGGTTTA
526687 TACTTTAGGA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
13 2 0.06
14 28 0.90
15 1 0.03
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (14 bp):
GTTTAGGGTTTAAT
Found at i:526651 original size:21 final size:21
Alignment explanation
Indices: 526632--526686 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
526622 TCGGATTTAG
526632 GGTTTAGGGTTTAATG-TTTAA
1 GGTTTAGGGTTTAA-GATTTAA
* ** *
526653 TGTTTATAGTTTAGGATTTAA
1 GGTTTAGGGTTTAAGATTTAA
526674 GGTTTAGGGTTTA
1 GGTTTAGGGTTTA
526687 TACTTTAGGA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (21 bp):
GGTTTAGGGTTTAAGATTTAA
Found at i:526667 original size:28 final size:28
Alignment explanation
Indices: 526633--526726 Score: 95
Period size: 28 Copynumber: 3.4 Consensus size: 28
526623 CGGATTTAGG
*
526633 GTTTAGGGTTTAATGTTTAATGTTTATA
1 GTTTAGGATTTAATGTTTAATGTTTATA
* **
526661 GTTTAGGATTTAAGGTTTAGGGTTTATA
1 GTTTAGGATTTAATGTTTAATGTTTATA
*
526689 CTTTAGGATTT-ATGATTT-ATGTTT-TA
1 GTTTAGGATTTAATG-TTTAATGTTTATA
526715 GGTTTTAGGATT
1 -G-TTTAGGATT
526727 CATTATAAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
26 2 0.04
27 6 0.11
28 46 0.85
ACGTcount: A:0.23, C:0.01, G:0.23, T:0.52
Consensus pattern (28 bp):
GTTTAGGATTTAATGTTTAATGTTTATA
Found at i:526693 original size:14 final size:14
Alignment explanation
Indices: 526655--526701 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
526645 ATGTTTAATG
526655 TTTATAGTTTAGGA
1 TTTATAGTTTAGGA
*
526669 TTTA-AGGTTTAGGG
1 TTTATA-GTTTAGGA
*
526683 TTTATACTTTAGGA
1 TTTATAGTTTAGGA
526697 TTTAT
1 TTTAT
526702 GATTTATGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 1 0.04
14 26 0.93
15 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.21, T:0.51
Consensus pattern (14 bp):
TTTATAGTTTAGGA
Found at i:526700 original size:21 final size:21
Alignment explanation
Indices: 526676--526726 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
526666 GGATTTAAGG
*
526676 TTTAGGGTTTATACTTTAGGA
1 TTTAGGATTTATACTTTAGGA
* ** *
526697 TTTATGATTTATGTTTTAGGT
1 TTTAGGATTTATACTTTAGGA
526718 TTTAGGATT
1 TTTAGGATT
526727 CATTATAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.02, G:0.22, T:0.55
Consensus pattern (21 bp):
TTTAGGATTTATACTTTAGGA
Found at i:526707 original size:14 final size:14
Alignment explanation
Indices: 526662--526726 Score: 51
Period size: 14 Copynumber: 4.6 Consensus size: 14
526652 ATGTTTATAG
* *
526662 TTTAGGATTTAAGG
1 TTTAGGATTTATGA
*
526676 TTTAGGGTTTAT-A
1 TTTAGGATTTATGA
526689 CTTTAGGATTTATGA
1 -TTTAGGATTTATGA
* * * *
526704 TTTATGTTTTAGGT
1 TTTAGGATTTATGA
526718 TTTAGGATT
1 TTTAGGATT
526727 CATTATAAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
14 38 0.97
15 1 0.03
ACGTcount: A:0.23, C:0.02, G:0.23, T:0.52
Consensus pattern (14 bp):
TTTAGGATTTATGA
Found at i:531938 original size:60 final size:60
Alignment explanation
Indices: 531786--532019 Score: 393
Period size: 60 Copynumber: 3.9 Consensus size: 60
531776 CAAATATCAT
*
531786 TGAACTATACTCAATTGATCT-CTTTCATCCTTCAACTTTCAAAAGTTACAATATGG-T-C
1 TGAACTATACTCAATTGAT-TACTTTCATCCTTCAACTTTCAAAAATTACAATATGGTTAC
531844 GTGAACTATACTCAATTGATTACTTTCATCCTTCAACTTTCAAAAATTACAATATGGTTAC
1 -TGAACTATACTCAATTGATTACTTTCATCCTTCAACTTTCAAAAATTACAATATGGTTAC
531905 TGAACTATACTCAATTGATTACTTTCATCCTTCAACTTTCAAAAATTACAATATGGTTAC
1 TGAACTATACTCAATTGATTACTTTCATCCTTCAACTTTCAAAAATTACAATATGGTTAC
* * *
531965 TGAACTATACTCAATTGATCACTTTCATCCTTAAACTTTCAAAAGTTACAATATG
1 TGAACTATACTCAATTGATTACTTTCATCCTTCAACTTTCAAAAATTACAATATG
532020 ATCATTATAA
Statistics
Matches: 168, Mismatches: 4, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
58 1 0.01
59 53 0.32
60 113 0.67
61 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.38
Consensus pattern (60 bp):
TGAACTATACTCAATTGATTACTTTCATCCTTCAACTTTCAAAAATTACAATATGGTTAC
Found at i:532689 original size:2 final size:2
Alignment explanation
Indices: 532684--532728 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
532674 AAAAAAAGAA
532684 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
532726 AT A
1 AT A
532729 ACAATGTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:534371 original size:36 final size:36
Alignment explanation
Indices: 534238--534614 Score: 315
Period size: 36 Copynumber: 10.3 Consensus size: 36
534228 TAATAATATA
* *
534238 AAAAT-ATTTTCAAAAATTATATAATATATATTTTCCC
1 AAAATAATTTTCAAAAACTATATATTATATATTTT--C
** * *
534275 AAAATGTTTTTTAAAAACTATACAATATATATATTTTC
1 AAAATAATTTTCAAAAACTATA-TAT-TATATATTTTC
534313 AAAA-ATATTTT-AAAAACTATATATTATATATTTTC
1 AAAATA-ATTTTCAAAAACTATATATTATATATTTTC
*
534348 AAAATAATTTTAAAAAACTATATA-T-TATATTTTC
1 AAAATAATTTTCAAAAACTATATATTATATATTTTC
*
534382 AAAATAATTTTAAAAAACTATATA-T-TATATTTTC
1 AAAATAATTTTCAAAAACTATATATTATATATTTTC
* * * *
534416 AAAATATTTTTTAAAAGCTATATAATATATATATTT-
1 AAAATAATTTTCAAAAACTATATATTATATAT-TTTC
** *
534452 AAAATGTTTTTCAAAAACTATATAATATATATTTTC
1 AAAATAATTTTCAAAAACTATATATTATATATTTTC
**
534488 AAAATGTTTTTCAAAAACTATATATATTATATATATATTTC
1 AAAATAATTTTCAAAAAC--TATATA-T-TATATAT-TTTC
*
534529 AAAAT-GTTTT-AAAAACTATATATTATATTTAAGTTTTC
1 AAAATAATTTTCAAAAACTATATATTATA--T-A-TTTTC
* ** * *
534567 AAAAAATATTTTTTAAAACCATATATTATATAATTTCC
1 AAAATA-ATTTTCAAAAACTATATATTATAT-ATTTTC
*
534605 AAAATGATTT
1 AAAATAATTT
534615 CAAGCTATAT
Statistics
Matches: 295, Mismatches: 23, Indels: 44
0.81 0.06 0.12
Matches are distributed among these distances:
34 64 0.22
35 29 0.10
36 68 0.23
37 29 0.10
38 45 0.15
39 11 0.04
40 25 0.08
41 24 0.08
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (36 bp):
AAAATAATTTTCAAAAACTATATATTATATATTTTC
Found at i:534557 original size:42 final size:40
Alignment explanation
Indices: 534244--534551 Score: 234
Period size: 34 Copynumber: 8.4 Consensus size: 40
534234 TATAAAAATA
534244 TTTTCAAAAA-T-TATATA--ATATATATTTTCCCAAAATGT
1 TTTTCAAAAACTATATATATTATATATATTTT--CAAAATGT
* * *
534282 TTTTTAAAAACTATACA-A-TATATATATTTTCAAAAAT-A
1 TTTTCAAAAACTATATATATTATATATATTTTC-AAAATGT
**
534320 TTTT-AAAAAC--TATATA-T-TATATATTTTCAAAATAA
1 TTTTCAAAAACTATATATATTATATATATTTTCAAAATGT
* **
534355 TTTT-AAAAA--A-CTATA-TAT-TATATTTTCAAAATAA
1 TTTTCAAAAACTATATATATTATATATATTTTCAAAATGT
* *
534389 TTTT-AAAAA--A-CTATA-TAT-TATATTTTCAAAATAT
1 TTTTCAAAAACTATATATATTATATATATTTTCAAAATGT
* *
534423 TTTTTAAAAGCTATATA-A-TATATATA-TTT-AAAATGT
1 TTTTCAAAAACTATATATATTATATATATTTTCAAAATGT
534459 TTTTCAAAAAC--TATATA--ATATATATTTTCAAAATGT
1 TTTTCAAAAACTATATATATTATATATATTTTCAAAATGT
534495 TTTTCAAAAACTATATATATTATATATATATTTCAAAATG-
1 TTTTCAAAAACTATATATATTATATATAT-TTTCAAAATGT
534535 TTTT-AAAAACTATATAT
1 TTTTCAAAAACTATATAT
534552 TATATTTAAG
Statistics
Matches: 238, Mismatches: 11, Indels: 41
0.82 0.04 0.14
Matches are distributed among these distances:
34 74 0.31
35 33 0.14
36 35 0.15
37 14 0.06
38 26 0.11
39 20 0.08
40 26 0.11
41 10 0.04
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (40 bp):
TTTTCAAAAACTATATATATTATATATATTTTCAAAATGT
Found at i:536442 original size:2 final size:2
Alignment explanation
Indices: 536437--536461 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
536427 ATATGCCTAA
536437 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
536462 TGTGCACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:537700 original size:16 final size:16
Alignment explanation
Indices: 537679--537709 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
537669 AAAAACAATT
*
537679 TAAATATTAAATATTA
1 TAAATAGTAAATATTA
537695 TAAATAGTAAATATT
1 TAAATAGTAAATATT
537710 TAATAAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TAAATAGTAAATATTA
Found at i:546023 original size:20 final size:20
Alignment explanation
Indices: 545998--546051 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
545988 AGTTGCACAC
* *
545998 AAAGTTTTGAAACTACGGGG
1 AAAGTTTCGAAACTACAGGG
546018 AAAGTTTCGAAACTACAGGG
1 AAAGTTTCGAAACTACAGGG
546038 AAAGTTTCGAAACT
1 AAAGTTTCGAAACT
546052 CTTCGGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (20 bp):
AAAGTTTCGAAACTACAGGG
Found at i:546121 original size:20 final size:18
Alignment explanation
Indices: 546098--546164 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 18
546088 CCAAAGTATT
546098 GAAACTTTAATGAAAGTTTC
1 GAAACTTT-A-GAAAGTTTC
*
546118 GAAACTCTTGAGATAGTTTC
1 GAAACT-TT-AGAAAGTTTC
* *
546138 GAAACTATAGGAAAGTATC
1 GAAACTTTA-GAAAGTTTC
546157 GAAACTTT
1 GAAACTTT
546165 TTGGGCTTCT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 1 0.03
19 15 0.38
20 20 0.51
21 3 0.08
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (18 bp):
GAAACTTTAGAAAGTTTC
Found at i:546160 original size:19 final size:19
Alignment explanation
Indices: 546090--546162 Score: 56
Period size: 20 Copynumber: 3.7 Consensus size: 19
546080 CGTTGGACCC
* * *
546090 AAAGTATTGAAACTTTAATG
1 AAAGTATCGAAACTAT-AGG
* * *
546110 AAAGTTTCGAAACTCTTGAG
1 AAAGTATCGAAACTATAG-G
* *
546130 ATAGTTTCGAAACTATAGG
1 AAAGTATCGAAACTATAGG
546149 AAAGTATCGAAACT
1 AAAGTATCGAAACT
546163 TTTTGGGCTT
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
19 13 0.31
20 29 0.69
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (19 bp):
AAAGTATCGAAACTATAGG
Found at i:546335 original size:19 final size:20
Alignment explanation
Indices: 546313--546357 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
546303 TAAAAGACTC
*
546313 ATTTTAAAGATTTGACAA-A
1 ATTTTAAAGATTTGAAAATA
**
546332 ATTTTAGGGATTTGAAAATA
1 ATTTTAAAGATTTGAAAATA
546352 ATTTTA
1 ATTTTA
546358 CGAAAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.42, C:0.02, G:0.13, T:0.42
Consensus pattern (20 bp):
ATTTTAAAGATTTGAAAATA
Found at i:547590 original size:31 final size:31
Alignment explanation
Indices: 547538--547612 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
547528 GTTACGTCGG
* *
547538 GACCATATTGCAAACGGACTAAATGTT-AGGA
1 GACCATATTGCAAACAGACTAAATATTGA-GA
* *
547569 GACCATATTGCAAATATACTAAATATTGAGA
1 GACCATATTGCAAACAGACTAAATATTGAGA
*
547600 GACTATATTGCAA
1 GACCATATTGCAA
547613 GTTTTAAAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
31 37 0.97
32 1 0.03
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (31 bp):
GACCATATTGCAAACAGACTAAATATTGAGA
Found at i:551344 original size:23 final size:23
Alignment explanation
Indices: 551314--551394 Score: 107
Period size: 23 Copynumber: 3.7 Consensus size: 23
551304 GCACTCCTGC
551314 AGTGCATCCATGCACCTGCCACT
1 AGTGCATCCATGCACCTGCCACT
*
551337 AGTGCATCGATGCACCTGCCACT
1 AGTGCATCCATGCACCTGCCACT
*
551360 AGTGCATCGATGCACCATG---C-
1 AGTGCATCCATGCACC-TGCCACT
551380 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
551395 TCAATTTCAA
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
20 14 0.25
21 1 0.02
23 38 0.69
24 2 0.04
ACGTcount: A:0.23, C:0.35, G:0.21, T:0.21
Consensus pattern (23 bp):
AGTGCATCCATGCACCTGCCACT
Found at i:553067 original size:16 final size:16
Alignment explanation
Indices: 553046--553134 Score: 70
Period size: 16 Copynumber: 6.0 Consensus size: 16
553036 TTTTAATAAC
553046 TATATTTATATATTAT
1 TATATTTATATATTAT
553062 TATATTT-TA-ATTAT
1 TATATTTATATATTAT
553076 TA-A--T-TAT-TTAT
1 TATATTTATATATTAT
*
553087 TATATTTA-ATAATTAA
1 TATATTTATAT-ATTAT
*
553103 TAT-TATTAAATATTAT
1 TATAT-TTATATATTAT
*
553119 TATATTTATTTATTAT
1 TATATTTATATATTAT
553135 ATTCATTTAA
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
11 9 0.15
12 1 0.02
13 1 0.02
14 10 0.17
15 3 0.05
16 32 0.54
17 3 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATATTTATATATTAT
Found at i:553131 original size:13 final size:13
Alignment explanation
Indices: 553058--553143 Score: 59
Period size: 13 Copynumber: 6.2 Consensus size: 13
553048 TATTTATATA
*
553058 TTATTATATTTTAA
1 TTATTATA-TTTAT
553072 TTATTA-A-TTAT
1 TTATTATATTTAT
553083 TTATTATATTTAAT
1 TTATTATATTT-AT
* *
553097 AATTAATATTATTAAAT
1 --TTATTA-TATT-TAT
553114 ATTATTATATTTAT
1 -TTATTATATTTAT
*
553128 TTATTATATTCAT
1 TTATTATATTTAT
553141 TTA
1 TTA
553144 ATTTCTACTT
Statistics
Matches: 59, Mismatches: 6, Indels: 15
0.74 0.08 0.19
Matches are distributed among these distances:
11 9 0.15
12 1 0.02
13 18 0.31
14 10 0.17
15 4 0.07
16 11 0.19
17 6 0.10
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATTATATTTAT
Found at i:553606 original size:17 final size:17
Alignment explanation
Indices: 553586--553621 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
553576 CATATAAAAT
553586 ATAAGAAAATATCTAAA
1 ATAAGAAAATATCTAAA
* *
553603 ATAAGAGAATATTTAAA
1 ATAAGAAAATATCTAAA
553620 AT
1 AT
553622 TTTTAGAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (17 bp):
ATAAGAAAATATCTAAA
Found at i:555394 original size:2 final size:2
Alignment explanation
Indices: 555387--555431 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
555377 AGCACATTCT
555387 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
555429 TA T
1 TA T
555432 TCACACAGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:556902 original size:2 final size:2
Alignment explanation
Indices: 556895--556923 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
556885 AGATCTTTTA
556895 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
556924 CCCCTATCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:557110 original size:12 final size:12
Alignment explanation
Indices: 557085--557154 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
557075 ACGGAGATAT
* *
557085 CAGAAATCAAAA
1 CAGAATTCAGAA
557097 CAGAATTCAGAA
1 CAGAATTCAGAA
557109 CA-AATATCAGAA
1 CAGAAT-TCAGAA
* *
557121 CAGAATCCAGAT
1 CAGAATTCAGAA
* *
557133 TAGAAATCAGAA
1 CAGAATTCAGAA
*
557145 CATAATTCAG
1 CAGAATTCAG
557155 GTCATATATC
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
11 3 0.07
12 39 0.87
13 3 0.07
ACGTcount: A:0.53, C:0.17, G:0.13, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:557141 original size:48 final size:48
Alignment explanation
Indices: 557084--557191 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 48
557074 CACGGAGATA
557084 TCAGAAATCAAAACAGAATTCAGAACAAATATCAGAACAGAATCC-AG
1 TCAGAAATCAAAACAGAATTCAGAACAAATATCAGAACAGAATCCAAG
* * * ** * * *
557131 ATTAGAAATCAGAACATAATTCAGGTCATATATCATAACAGAATTCAAG
1 -TCAGAAATCAAAACAGAATTCAGAACAAATATCAGAACAGAATCCAAG
557180 TCAGAAATCAAA
1 TCAGAAATCAAA
557192 TAAAATATTT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
48 47 0.96
49 2 0.04
ACGTcount: A:0.51, C:0.17, G:0.12, T:0.20
Consensus pattern (48 bp):
TCAGAAATCAAAACAGAATTCAGAACAAATATCAGAACAGAATCCAAG
Found at i:557189 original size:24 final size:25
Alignment explanation
Indices: 557083--557189 Score: 89
Period size: 24 Copynumber: 4.4 Consensus size: 25
557073 ACACGGAGAT
*
557083 ATCAGAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* *
557107 AACA-AATATCAGAACAGAA-TCCAG
1 ATCAGAA-ATCAGAACAGAATTCAAG
* *
557131 ATTAGAAATCAGAACATAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * * *
557155 GTCATATATCATAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAAG
557180 -TCAGAAATCA
1 ATCAGAAATCA
557190 AATAAAATAT
Statistics
Matches: 65, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
23 4 0.06
24 55 0.85
25 6 0.09
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:563216 original size:170 final size:170
Alignment explanation
Indices: 562797--563307 Score: 803
Period size: 170 Copynumber: 3.0 Consensus size: 170
562787 CAAAAGTTAA
* * *
562797 CGTTAAGTTTTAAAAAATAGAAAGTTTAGGAACTAAAACAAATCAAAACTGATAGTTTAGGTACT
1 CGTTAAGTTTTAAAAAATAGAAAGTTTAGGTACTAAAACAGATCAAAATTGATAGTTTAGGTACT
*
562862 AAACACGTTAAATTTTTAACGGCAGATACTAAAATAAAACAAAAACTAAATATTAAGTATGATTT
66 AAACACGTTAAGTTTTTAACGGCAGATACTAAAATAAAACAAAAACTAAATATTAAGTATGATTT
* *
562927 AGGGAAAAAAAATAAAAGTTTAAGTACTAAAACGGATCAAAAC
131 --TG-AAAAAAATTAAAGTTTAAGTACTAAAACGGATCAAAAC
* *
562970 CGTTATG-TTTAAAAAATAGAAAGTTTAGGTACTAAAACAGATAAAAATTGATAGTTTAGGTACT
1 CGTTAAGTTTTAAAAAATAGAAAGTTTAGGTACTAAAACAGATCAAAATTGATAGTTTAGGTACT
* *
563034 AAACATGTTAAGTTTTTAACGGCAGATACTAAAATAAAATAAAAACTAAATATTAAGTATGATTT
66 AAACACGTTAAGTTTTTAACGGCAGATACTAAAATAAAACAAAAACTAAATATTAAGTATGATTT
563099 TGAAAAAAATTAAAGTTTAAGTACTAAAACGGATCAAAAC
131 TGAAAAAAATTAAAGTTTAAGTACTAAAACGGATCAAAAC
*
563139 CGTTAAGTTTTAAAAAATAGAAAGTTTAGGTACTAAAACAGATCAAAATTGATAGTTTATGTACT
1 CGTTAAGTTTTAAAAAATAGAAAGTTTAGGTACTAAAACAGATCAAAATTGATAGTTTAGGTACT
* * *
563204 AAACGA-GTTAAGTTTTTAACGGAAAATACTAAAATAAAACAAAAACTAAATATTAAGCATGATT
66 AAAC-ACGTTAAGTTTTTAACGGCAGATACTAAAATAAAACAAAAACTAAATATTAAGTATGATT
* * *
563268 TT-AAAAAAATTAAAAGTTTGAGTACTAAAATGGATTAAAA
130 TTGAAAAAAATT-AAAGTTTAAGTACTAAAACGGATCAAAA
563308 TTAATAGTTT
Statistics
Matches: 315, Mismatches: 20, Indels: 9
0.92 0.06 0.03
Matches are distributed among these distances:
169 52 0.17
170 141 0.45
171 1 0.00
172 115 0.37
173 6 0.02
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29
Consensus pattern (170 bp):
CGTTAAGTTTTAAAAAATAGAAAGTTTAGGTACTAAAACAGATCAAAATTGATAGTTTAGGTACT
AAACACGTTAAGTTTTTAACGGCAGATACTAAAATAAAACAAAAACTAAATATTAAGTATGATTT
TGAAAAAAATTAAAGTTTAAGTACTAAAACGGATCAAAAC
Found at i:565279 original size:21 final size:21
Alignment explanation
Indices: 565253--565322 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 21
565243 ATTTTGGACT
565253 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
565274 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
565295 ATCGCAACGAATTTGG-A-AA
1 ATCGCAACGAATTTGGAATAA
565314 ATCGCAACG
1 ATCGCAACG
565323 CGAACTTCGA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
19 16 0.41
21 14 0.36
23 9 0.23
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:565327 original size:40 final size:42
Alignment explanation
Indices: 565249--565341 Score: 172
Period size: 40 Copynumber: 2.3 Consensus size: 42
565239 TGCGATTTTG
565249 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
565291 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
565331 GACTATCGCAA
1 GACTATCGCAA
565342 TGCGAATATG
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 30 0.59
41 1 0.02
42 20 0.39
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:565338 original size:21 final size:21
Alignment explanation
Indices: 565274--565347 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
565264 TTTGGAATAA
565274 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * **
565295 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
565314 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
565335 ATCGCAATGCGAA
1 ATCGCAACGCGAA
565348 TATGTAAATC
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
19 15 0.36
21 27 0.64
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:566688 original size:14 final size:14
Alignment explanation
Indices: 566669--566696 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
566659 AAGTGAAAGA
566669 ATAGTTATATAATT
1 ATAGTTATATAATT
566683 ATAGTTATATAATT
1 ATAGTTATATAATT
566697 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:569003 original size:21 final size:22
Alignment explanation
Indices: 568971--569012 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
568961 TCTGATCAAT
*
568971 GTTTTCTTTG-TTCTTTTTGGG
1 GTTTTCTTTGTTTCGTTTTGGG
568992 GTTTT-TTATGTTTCGTTTTGG
1 GTTTTCTT-TGTTTCGTTTTGG
569013 AGTGTTGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 2 0.11
21 7 0.39
22 9 0.50
ACGTcount: A:0.02, C:0.07, G:0.24, T:0.67
Consensus pattern (22 bp):
GTTTTCTTTGTTTCGTTTTGGG
Found at i:575061 original size:12 final size:12
Alignment explanation
Indices: 575044--575069 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
575034 TGGAGGTAGA
575044 GGTGATAGAGGT
1 GGTGATAGAGGT
575056 GGTGATAGAGGT
1 GGTGATAGAGGT
575068 GG
1 GG
575070 CTACGGAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.54, T:0.23
Consensus pattern (12 bp):
GGTGATAGAGGT
Found at i:575085 original size:30 final size:30
Alignment explanation
Indices: 575050--575144 Score: 118
Period size: 30 Copynumber: 3.2 Consensus size: 30
575040 TAGAGGTGAT
*
575050 AGAGGTGGTGATAGAGGTGGCTACGGAGGC
1 AGAGGTGGCGATAGAGGTGGCTACGGAGGC
* * *
575080 CGAGGTGGCGATAGAGGTGGCTACAGAGGT
1 AGAGGTGGCGATAGAGGTGGCTACGGAGGC
* * * *
575110 AGAGGTGGCGATAGGGGAGGCTATGGAGGT
1 AGAGGTGGCGATAGAGGTGGCTACGGAGGC
575140 AGAGG
1 AGAGG
575145 ACGTGGAAGG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.24, C:0.09, G:0.51, T:0.16
Consensus pattern (30 bp):
AGAGGTGGCGATAGAGGTGGCTACGGAGGC
Found at i:582484 original size:18 final size:18
Alignment explanation
Indices: 582461--582502 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
582451 AGGGATTATC
582461 AGTGGTCCTACGGGACAT
1 AGTGGTCCTACGGGACAT
*
582479 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTACGGGACAT
582497 AGTGGT
1 AGTGGT
582503 TATTCGGGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTACGGGACAT
Found at i:582508 original size:18 final size:18
Alignment explanation
Indices: 582461--582513 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
582451 AGGGATTATC
* *
582461 AGTGGTCCTACGGGACAT
1 AGTGGTCATTCGGGACAT
*
582479 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGGACAT
*
582497 AGTGGTTATTCGGGACA
1 AGTGGTCATTCGGGACA
582514 AATATTCAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.21, C:0.19, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:590054 original size:47 final size:47
Alignment explanation
Indices: 589985--590078 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
589975 GGTGTTACAG
589985 GTATTGACTAGTGAGGCCAGGTGAGTGCATATTAGTGGGTATATGAT
1 GTATTGACTAGTGAGGCCAGGTGAGTGCATATTAGTGGGTATATGAT
590032 GTATTGACTAGTGAGGCCAGGTGAGTGCATATTAGTGGGTATATGAT
1 GTATTGACTAGTGAGGCCAGGTGAGTGCATATTAGTGGGTATATGAT
590079 ATTGTATATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.26, C:0.09, G:0.34, T:0.32
Consensus pattern (47 bp):
GTATTGACTAGTGAGGCCAGGTGAGTGCATATTAGTGGGTATATGAT
Found at i:592580 original size:21 final size:21
Alignment explanation
Indices: 592554--592594 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
592544 TTGAAATCAC
592554 TGTAGCAGTGCATCGATACAT
1 TGTAGCAGTGCATCGATACAT
592575 TGTAGCAGTGCATCGATACA
1 TGTAGCAGTGCATCGATACA
592595 CATTTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (21 bp):
TGTAGCAGTGCATCGATACAT
Found at i:599754 original size:2 final size:2
Alignment explanation
Indices: 599747--599787 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
599737 TTGAATACAT
599747 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
599788 ACAATGTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:601215 original size:15 final size:14
Alignment explanation
Indices: 601183--601227 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
601173 CTAATGTAAA
601183 AAATACAATATAATT
1 AAATA-AATATAATT
601198 AAATAAATATAATGT
1 AAATAAATATAAT-T
*
601213 AAAT-AATTTAATT
1 AAATAAATATAATT
601226 AA
1 AA
601228 CTATTTTCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 3 0.11
14 15 0.54
15 10 0.36
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (14 bp):
AAATAAATATAATT
Found at i:604875 original size:20 final size:20
Alignment explanation
Indices: 604810--604880 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
604800 ATTGTTCGCT
* * *
604810 AGTATTGATATTGACACTTT
1 AGTATCGATATTGACCCTTA
* *
604830 AGTATTGATATTGGCCCTTCA
1 AGTATCGATATTGACCCTT-A
*
604851 A-TATCGATATTGACCCCTA
1 AGTATCGATATTGACCCTTA
*
604870 AGTATCAATAT
1 AGTATCGATAT
604881 CTAACTATTG
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
19 2 0.05
20 39 0.93
21 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (20 bp):
AGTATCGATATTGACCCTTA
Found at i:610371 original size:21 final size:21
Alignment explanation
Indices: 610345--610391 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
610335 AGTTCCCAAT
* *
610345 AATAACAAAATCGGTAGAAAA
1 AATAACAAAACCGATAGAAAA
*
610366 AATAACAAAACCGATAGAAAT
1 AATAACAAAACCGATAGAAAA
610387 AATAA
1 AATAA
610392 TGTTTCCGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.64, C:0.11, G:0.11, T:0.15
Consensus pattern (21 bp):
AATAACAAAACCGATAGAAAA
Found at i:611053 original size:22 final size:22
Alignment explanation
Indices: 611028--611071 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
611018 TTATAAAATG
611028 ATCATTAAATTTATCAAATCAT
1 ATCATTAAATTTATCAAATCAT
611050 ATCATTAAATTTATCAAATCAT
1 ATCATTAAATTTATCAAATCAT
611072 TACAAAACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (22 bp):
ATCATTAAATTTATCAAATCAT
Found at i:611144 original size:32 final size:31
Alignment explanation
Indices: 611104--611197 Score: 91
Period size: 31 Copynumber: 3.0 Consensus size: 31
611094 TATAATAATC
*
611104 GTAAAATTTTGATAAATTTAATTATCATTTT
1 GTAAAATTTTGATAAATTTAATGATCATTTT
* * * *
611135 GTAACAA-TTTAATAAAATCTAATGATTATTCT
1 GTAA-AATTTTGAT-AAATTTAATGATCATTTT
* * *
611167 GCAATATTTTGATAAATTTAATGACCATTTT
1 GTAAAATTTTGATAAATTTAATGATCATTTT
611198 ACAATCGTTC
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
31 24 0.50
32 24 0.50
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (31 bp):
GTAAAATTTTGATAAATTTAATGATCATTTT
Found at i:615336 original size:61 final size:59
Alignment explanation
Indices: 615251--615400 Score: 194
Period size: 61 Copynumber: 2.5 Consensus size: 59
615241 TATTATTTGA
* * **
615251 ATTATCTTAGAATTCAAATATTAAATGAGTGATTGTGG-TTGAATTGAAATAATTAAAATAT
1 ATTATCTTAAAATTCAAATATTAAATGAGTGATTG-GGATTAAATCAAAATAATT-AAA-AT
* * **
615312 ATTATCTTAAAATTCAATTTTTAAACAAGTGATTGGGATTAAATCAAAATAATTAAAAT
1 ATTATCTTAAAATTCAAATATTAAATGAGTGATTGGGATTAAATCAAAATAATTAAAAT
615371 ATTATCTTAAAATTCAAATATTAAATGAGT
1 ATTATCTTAAAATTCAAATATTAAATGAGT
615401 TATCTTAAAA
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
59 28 0.37
60 5 0.07
61 43 0.57
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (59 bp):
ATTATCTTAAAATTCAAATATTAAATGAGTGATTGGGATTAAATCAAAATAATTAAAAT
Found at i:617581 original size:20 final size:20
Alignment explanation
Indices: 617558--617619 Score: 106
Period size: 20 Copynumber: 3.1 Consensus size: 20
617548 GCAATGTGAA
*
617558 TACGTATTCGCATTGCGATT
1 TACGTATTCGCGTTGCGATT
*
617578 TACGTAATCGCGTTGCGATT
1 TACGTATTCGCGTTGCGATT
617598 TACGTATTCGCGTTGCGATT
1 TACGTATTCGCGTTGCGATT
617618 TA
1 TA
617620 GTAAATCGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (20 bp):
TACGTATTCGCGTTGCGATT
Found at i:617602 original size:40 final size:40
Alignment explanation
Indices: 617504--617623 Score: 120
Period size: 40 Copynumber: 3.0 Consensus size: 40
617494 GATTCTGACT
* * **
617504 ATCGCGTTGCGATTTTCCTAATTCGCAACGCGA-TTACGTAA
1 ATCGCGTTGCGATTTACGT-ATTCGCATTGCGATTTACGT-A
** * *
617545 ATCGCAATGTGA-ATACGTATTCGCATTGCGATTTACGTA
1 ATCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTA
*
617584 ATCGCGTTGCGATTTACGTATTCGCGTTGCGATTTA-GTA
1 ATCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTA
617623 A
1 A
617624 ATCGTAACGA
Statistics
Matches: 64, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
39 25 0.39
40 30 0.47
41 9 0.14
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (40 bp):
ATCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTA
Found at i:617832 original size:22 final size:22
Alignment explanation
Indices: 617807--617862 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
617797 CTCTCTCCGG
617807 CGACATCCGTTCCTATATCCAA
1 CGACATCCGTTCCTATATCCAA
617829 CGACATCCGTTCCTATATCCAA
1 CGACATCCGTTCCTATATCCAA
617851 CGACATCC-TTCC
1 CGACATCCGTTCC
617863 CCATCCGGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 4 0.12
22 30 0.88
ACGTcount: A:0.25, C:0.39, G:0.09, T:0.27
Consensus pattern (22 bp):
CGACATCCGTTCCTATATCCAA
Found at i:621142 original size:33 final size:33
Alignment explanation
Indices: 621105--621284 Score: 243
Period size: 33 Copynumber: 5.3 Consensus size: 33
621095 GGAAATTACT
*
621105 ATCGCAATGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
* *
621138 ATCGCAACGAGATAATCGCAATGTGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
*
621171 ATCGCAACGCGGAAATGACTATCGCAATGCGAAATGAAA
1 ATCGCAA--C-GAGA-GA--ATCGCAATGCGAAATGAAA
*
621210 ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
* *
621243 ATCGCAACGAGGGAATCGCAAAGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
621276 ATCGCAACG
1 ATCGCAACG
621285 CGAATTTAGT
Statistics
Matches: 130, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
33 95 0.73
35 2 0.02
36 6 0.05
37 2 0.02
39 25 0.19
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
Found at i:621208 original size:72 final size:66
Alignment explanation
Indices: 621105--621284 Score: 252
Period size: 72 Copynumber: 2.6 Consensus size: 66
621095 GGAAATTACT
* * * *
621105 ATCGCAATGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGTGAAATGAA
1 ATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAA
621170 A
66 A
*
621171 ATCGCAACGCGGAAATGACTATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGA
1 ATCGCAACGAGG----GA--ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGA
621236 AATGAAA
60 AATGAAA
*
621243 ATCGCAACGAGGGAATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACG
621285 CGAATTTAGT
Statistics
Matches: 101, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
66 36 0.36
68 2 0.02
70 2 0.02
72 61 0.60
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.14
Consensus pattern (66 bp):
ATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAA
A
Found at i:621225 original size:14 final size:14
Alignment explanation
Indices: 621206--621263 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
621196 AATGCGAAAT
621206 GAAAATCGCAACGA
1 GAAAATCGCAACGA
621220 GAAAATCGCAATGCGAAA
1 GAAAATCGCAA--CG--A
621238 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
**
621253 GGGAATCGCAA
1 GAAAATCGCAA
621264 AGCGAAATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 20 0.54
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 11 0.30
ACGTcount: A:0.47, C:0.19, G:0.24, T:0.10
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:621229 original size:105 final size:106
Alignment explanation
Indices: 621078--621286 Score: 312
Period size: 105 Copynumber: 2.0 Consensus size: 106
621068 CAATCATATT
* * ** * *
621078 AATGTCTATCGCAACGCGGAAATTACTATCGCAATGAGAGAATCGCAATGCGAAATGAAAATCGC
1 AATGACTATCGCAACGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGC
* * *
621143 AACGAGATAATCGCAATGTGAAATGAAAATCGCAACGCGGA
66 AACGAGAGAATCGCAAAGCGAAATGAAAATCGCAACGCGGA
*
621184 AATGACTATCGCAATGC-GAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGC
1 AATGACTATCGCAACGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGC
*
621248 AACGAGGGAATCGCAAAGCGAAATGAAAATCGCAACGCG
66 AACGAGAGAATCGCAAAGCGAAATGAAAATCGCAACGCG
621287 AATTTAGTTT
Statistics
Matches: 92, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
105 77 0.84
106 15 0.16
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (106 bp):
AATGACTATCGCAACGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGC
AACGAGAGAATCGCAAAGCGAAATGAAAATCGCAACGCGGA
Found at i:621319 original size:19 final size:19
Alignment explanation
Indices: 621284--621329 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
621274 AAATCGCAAC
*
621284 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
621303 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
621322 TCGATTTT
1 GCGATTTT
621330 GTCATTGCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.15, G:0.24, T:0.48
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:621343 original size:33 final size:33
Alignment explanation
Indices: 621301--621392 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
621291 TAGTTTCGCG
* * *
621301 TTGCGATTTT-AGTTTCGCGTTTCGATTTTGTCA
1 TTGCGATTTTCA-TTTCGCATTGCGATTTTCTCA
*
621334 TTGCGATTTTCATTTCGCATTGCGATTTTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCTCA
*
621367 TTACGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
621393 AGTCATTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
33 52 0.98
34 1 0.02
ACGTcount: A:0.14, C:0.18, G:0.18, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCTCA
Found at i:621356 original size:19 final size:19
Alignment explanation
Indices: 621332--621392 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 19
621322 TCGATTTTGT
621332 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
621351 CATTGCGATTTTC---TCG
1 CATTGCGATTTTCATTTCG
*
621367 --TTACGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
621384 CATTGCGAT
1 CATTGCGAT
621393 AGTCATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 19 0.54
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.46
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:621518 original size:14 final size:14
Alignment explanation
Indices: 621499--621535 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
621489 CATCAATTAA
621499 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
621513 ACAAATCATCTTTT
1 ACAAATCAACTTTT
621527 ACAAATCAA
1 ACAAATCAA
621536 TTAAACAATA
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:622950 original size:21 final size:21
Alignment explanation
Indices: 622884--622950 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
622874 GTGAATCGGG
*
622884 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
622904 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
622926 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
622947 CTCT
1 CTCT
622951 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:623450 original size:94 final size:94
Alignment explanation
Indices: 623288--623485 Score: 335
Period size: 94 Copynumber: 2.1 Consensus size: 94
623278 TAACAAAGAC
* * * *
623288 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCATAGTGTTAAAGAATACA
1 AAATTTACTATCAACCAAAAAACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAA
623353 CAGTTTAGCAGAATTGGCAGCAACCGAAT
66 CAGTTTAGCAGAATTGGCAGCAACCGAAT
623382 AAATTTAC-ATCAACCAAAAAACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAA
1 AAATTTACTATCAACCAAAAAACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATAA
*
623446 ACAGTTTAGCAGTATTGGCAGCAACCGAAT
65 ACAGTTTAGCAGAATTGGCAGCAACCGAAT
623476 AAATTTACTA
1 AAATTTACTA
623486 AGCAATCTAA
Statistics
Matches: 97, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
93 17 0.18
94 79 0.81
95 1 0.01
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (94 bp):
AAATTTACTATCAACCAAAAAACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAA
CAGTTTAGCAGAATTGGCAGCAACCGAAT
Found at i:625211 original size:20 final size:20
Alignment explanation
Indices: 625188--625262 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
625178 TGAAATGAAA
625188 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
*
625208 ATCGCAACGCG-GAAATGACT
1 ATCGCAACGAGAG-AATGACT
* **
625228 ATCGCAACGTGA-AATGAAA
1 ATCGCAACGAGAGAATGACT
*
625247 ATCGTAACGAGAGAAT
1 ATCGCAACGAGAGAAT
625263 TGCAACGCGA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
19 16 0.35
20 30 0.65
ACGTcount: A:0.41, C:0.19, G:0.24, T:0.16
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:625250 original size:19 final size:19
Alignment explanation
Indices: 625179--625310 Score: 103
Period size: 19 Copynumber: 7.1 Consensus size: 19
625169 TCTTTTGGTT
*
625179 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
625198 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
625218 GGAAATGACTATCGCAACGT
1 -GAAATGAAAATCGCAACGC
*
625238 GAAATGAAAATCGTAA--C
1 GAAATGAAAATCGCAACGC
* *
625255 G--A-GAGAATTGCAACGC
1 GAAATGAAAATCGCAACGC
*
625271 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
625290 GAAATGAAAATTGCAATGC
1 GAAATGAAAATCGCAACGC
625309 GA
1 GA
625311 TTTTGGTTTC
Statistics
Matches: 89, Mismatches: 17, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
14 8 0.09
15 1 0.01
16 2 0.02
17 1 0.01
18 1 0.01
19 44 0.49
20 30 0.34
21 2 0.02
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.16
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:625356 original size:21 final size:20
Alignment explanation
Indices: 625337--625408 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
625327 CGATTCTCTC
625337 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
* ** *
625357 CATTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
625378 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
625398 GTTGCGATTTT
1 GTTGCGATTTT
625409 AAGTTTAGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 29 0.67
21 14 0.33
ACGTcount: A:0.14, C:0.17, G:0.18, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:626085 original size:20 final size:20
Alignment explanation
Indices: 625965--626088 Score: 178
Period size: 20 Copynumber: 6.2 Consensus size: 20
625955 GCTTTAAAAA
*
625965 TCGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGTAT
* *
625985 ACGCATTGCGATTTACGTAT
1 TCGCGTTGCGATTTACGTAT
*
626005 TCTCGTTGCGATTTACAG-AT
1 TCGCGTTGCGATTTAC-GTAT
* *
626025 ACGCGTTGCGATTTACGTAA
1 TCGCGTTGCGATTTACGTAT
626045 TCGCGTTGCGATTTACGTAT
1 TCGCGTTGCGATTTACGTAT
626065 TCGCGTTGCGATTTACGTAT
1 TCGCGTTGCGATTTACGTAT
626085 TCGC
1 TCGC
626089 ATTGTAAATT
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
19 1 0.01
20 89 0.98
21 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (20 bp):
TCGCGTTGCGATTTACGTAT
Found at i:626137 original size:21 final size:21
Alignment explanation
Indices: 626085--626137 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
626075 ATTTACGTAT
**
626085 TCGCATTGTAAATTAGGAAAA
1 TCGCATTGCGAATTAGGAAAA
** * *
626106 TCGCAACGCGAATTTGGGAAA
1 TCGCATTGCGAATTAGGAAAA
626127 TCGCATTGCGA
1 TCGCATTGCGA
626138 TAGTCAGAAT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (21 bp):
TCGCATTGCGAATTAGGAAAA
Found at i:628686 original size:20 final size:20
Alignment explanation
Indices: 628658--628713 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 20
628648 GAATTTAACC
*
628658 AAAATTTCAATTTTTTTAAA
1 AAAAATTCAATTTTTTTAAA
628678 AAAAATTCAATTTTTTTTAAA
1 AAAAATTCAA-TTTTTTTAAA
*
628699 AAAAAATCATATTTT
1 AAAAATTCA-ATTTT
628714 ATGATTTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 9 0.28
21 22 0.69
22 1 0.03
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.46
Consensus pattern (20 bp):
AAAAATTCAATTTTTTTAAA
Found at i:629391 original size:15 final size:15
Alignment explanation
Indices: 629373--629444 Score: 92
Period size: 15 Copynumber: 4.9 Consensus size: 15
629363 TTTCGGAAAA
629373 TGAATTACTGGAATT
1 TGAATTACTGGAATT
*
629388 TGAACTACTGGAATT
1 TGAATTACTGGAATT
* * **
629403 TGAACTACTGAAAAA
1 TGAATTACTGGAATT
629418 TGAATTACTGGAATT
1 TGAATTACTGGAATT
629433 TGAATT-CTGGAA
1 TGAATTACTGGAA
629445 AATGAATTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
14 6 0.12
15 43 0.88
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:629748 original size:90 final size:89
Alignment explanation
Indices: 629654--629820 Score: 196
Period size: 90 Copynumber: 1.9 Consensus size: 89
629644 ACTTATTTAT
* * * * *
629654 TATTAAAAATAAT-TTATTTA-TTATTAAA-TAGTATTTTTATAATTTTATTAATAAAAAATATT
1 TATTAAAAATAATATTAATTATTTATTAAAGTAATAGTGTTAT-ATTCTATT--TAAAAAATATT
*
629716 AATTTTGTATATTTTAGTGAAACAAAAA
63 AA-TTAGTATATTTTAGTGAAACAAAAA
* * *
629744 TATTATAAATTATATTAATTATTTATTAAAGTAATAGTGTTATATTCTATTTTAAAAATATTAAT
1 TATTAAAAATAATATTAATTATTTATTAAAGTAATAGTGTTATATTCTATTTAAAAAATATTAAT
629809 TAGTATATTTTA
66 TAGTATATTTTA
629821 AATATCTTTA
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
89 12 0.18
90 23 0.35
91 6 0.09
92 15 0.23
93 9 0.14
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (89 bp):
TATTAAAAATAATATTAATTATTTATTAAAGTAATAGTGTTATATTCTATTTAAAAAATATTAAT
TAGTATATTTTAGTGAAACAAAAA
Found at i:629876 original size:28 final size:27
Alignment explanation
Indices: 629838--629890 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 27
629828 TTATTAAAAT
629838 ATTATTTAAATATATAAATAATATTATTC
1 ATTATTTAAATATATAAA-AAT-TTATTC
629867 ATTA-TTAAATATATAAAAATTTAT
1 ATTATTTAAATATATAAAAATTTAT
629891 ATTATATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 4 0.17
27 3 0.12
28 13 0.54
29 4 0.17
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
ATTATTTAAATATATAAAAATTTATTC
Found at i:629880 original size:19 final size:20
Alignment explanation
Indices: 629828--629880 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
629818 TTAAATATCT
629828 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
629847 ATATATAAATAATATTA-TTCA
1 TTAT-TAAAT-ATATTATTTAA
629868 TTATTAAATATAT
1 TTATTAAATATAT
629881 AAAAATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 6 0.21
22 6 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:629893 original size:28 final size:27
Alignment explanation
Indices: 629837--630002 Score: 81
Period size: 29 Copynumber: 5.8 Consensus size: 27
629827 TTTATTAAAA
629837 TATTATTTAAATATATAAATAATATTAT
1 TATTA-TTAAATATATAAATAATATTAT
*
629865 TCATTATTAAATATATAAAAATTTATATTAT
1 T-ATTATTAAATATAT--AAA-TAATATTAT
*
629896 ATATTATTAAA-ATAAAAATATAATATCT-T
1 -TATTATTAAATAT-ATAA-ATAATAT-TAT
** * *
629925 ATATTATTATAATATAATTGATTATTTTAT
1 -TATTATTA-AATAT-ATAAATAATATTAT
* * *
629955 ATAATATTAAAAATAT-AATATTA-TAT
1 -TATTATTAAATATATAAATAATATTAT
629981 TATTA-TAAATATTAATAAATAA
1 TATTATTAAATA-T-ATAAATAA
630003 ATAAATAATA
Statistics
Matches: 107, Mismatches: 17, Indels: 29
0.70 0.11 0.19
Matches are distributed among these distances:
24 5 0.05
25 5 0.05
26 5 0.05
27 7 0.07
28 13 0.12
29 26 0.24
30 23 0.21
31 22 0.21
32 1 0.01
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (27 bp):
TATTATTAAATATATAAATAATATTAT
Found at i:629909 original size:60 final size:59
Alignment explanation
Indices: 629836--629986 Score: 150
Period size: 59 Copynumber: 2.6 Consensus size: 59
629826 CTTTATTAAA
*
629836 ATATTATTTAAATATATAA-ATAATATTATTCATTATTA-AATATATAAAAATTTATATTAT
1 ATATTATTAAAATATATAATATAATATTATT-ATTATTATAATATA-AAAAA-TTATATTAT
* *** *
629896 ATATTATTAAAATA-AAAATATAATATCT-TATATTATTATAATATAATTGATTATTTTAT
1 ATATTATTAAAATATATAATATAATAT-TAT-TATTATTATAATATAAAAAATTATATTAT
* *
629955 ATAATATTAAAA-ATATAATATTATATTATTAT
1 ATATTATTAAAATATATAATATAATATTATTAT
629987 AAATATTAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
58 5 0.07
59 33 0.43
60 30 0.39
61 8 0.11
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (59 bp):
ATATTATTAAAATATATAATATAATATTATTATTATTATAATATAAAAAATTATATTAT
Found at i:629927 original size:29 final size:28
Alignment explanation
Indices: 629836--629938 Score: 86
Period size: 29 Copynumber: 3.5 Consensus size: 28
629826 CTTTATTAAA
*
629836 ATATTATTTAAATATATAAA-TAATATTAT
1 ATATTA-TTAAA-ATAAAAATTAATATTAT
*
629865 -TCATTATTAAATATATAAAAATTTATATTAT
1 AT-ATTATT-AA-A-ATAAAAATTAATATTAT
629896 ATATTATTAAAATAAAAATATAATATCT-T
1 ATATTATTAAAATAAAAAT-TAATAT-TAT
*
629925 ATATTATTATAATA
1 ATATTATTAAAATA
629939 TAATTGATTA
Statistics
Matches: 63, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
28 11 0.17
29 26 0.41
30 11 0.17
31 14 0.22
32 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
ATATTATTAAAATAAAAATTAATATTAT
Found at i:629979 original size:22 final size:23
Alignment explanation
Indices: 629954--629997 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
629944 GATTATTTTA
629954 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
629976 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
629998 AATAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:630249 original size:42 final size:42
Alignment explanation
Indices: 630190--630305 Score: 187
Period size: 42 Copynumber: 2.8 Consensus size: 42
630180 ATGAATTACG
* * *
630190 TTCCGGAAAACCAATTACGTGAAACAAACACTGGAAAATATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
630232 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
* *
630274 TTTCGGAAAATGAATTACGTGAAACAAACACG
1 TTCCGGAAAACGAATTACGTGAAACAAACACG
630306 AGAATTCGGG
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.20
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:636003 original size:48 final size:47
Alignment explanation
Indices: 635919--636013 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 47
635909 ATTGATAATA
635919 TGCACATACACCCTACAAACACATAGGCTTGAATTTGAATCCTCTAT
1 TGCACATACACCCTACAAACACATAGGCTTGAATTTGAATCCTCTAT
*
635966 TGCACATACACCCTACAACACACATGGGCTTGAATTTGAATCCTCTAT
1 TGCACATACACCCTACAA-ACACATAGGCTTGAATTTGAATCCTCTAT
636014 GGAGAGTAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 18 0.39
48 28 0.61
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (47 bp):
TGCACATACACCCTACAAACACATAGGCTTGAATTTGAATCCTCTAT
Found at i:643506 original size:16 final size:16
Alignment explanation
Indices: 643485--643515 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
643475 ATGTTATATG
643485 AAAGAAAGAAAATGAA
1 AAAGAAAGAAAATGAA
*
643501 AAAGAAAGAGAATGA
1 AAAGAAAGAAAATGA
643516 GTGAAGAGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (16 bp):
AAAGAAAGAAAATGAA
Found at i:643980 original size:2 final size:2
Alignment explanation
Indices: 643973--644004 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
643963 TTTTATGGTA
643973 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
644005 GGTTTGCTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:651024 original size:19 final size:17
Alignment explanation
Indices: 650980--651024 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
650970 ACACAGAGCA
650980 AAAAAAAAGAATAAAAG
1 AAAAAAAAGAATAAAAG
*
650997 AATAAAAAAGAAATTAAAG
1 AA-AAAAAAG-AATAAAAG
651016 AAAAGAAAA
1 AAAA-AAAA
651025 AAAAGAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 2 0.08
18 9 0.38
19 13 0.54
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (17 bp):
AAAAAAAAGAATAAAAG
Found at i:651039 original size:24 final size:23
Alignment explanation
Indices: 650992--651049 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
650982 AAAAAAGAAT
**
650992 AAAAGAATAAAAAAGAAATTAAAG
1 AAAAGAA-AAAAAAGAAAACAAAG
651016 AAAAGAAAAAAAAGAGAAACAAAG
1 AAAAGAAAAAAAAGA-AAACAAAG
*
651040 AGAA-AAAAAA
1 AAAAGAAAAAA
651050 GGGGACGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 14 0.47
24 16 0.53
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (23 bp):
AAAAGAAAAAAAAGAAAACAAAG
Found at i:651041 original size:10 final size:10
Alignment explanation
Indices: 651016--651048 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
651006 GAAATTAAAG
651016 AAAAGA-AAA
1 AAAAGAGAAA
651025 AAAAGAGAAA
1 AAAAGAGAAA
*
651035 CAAAGAGAAA
1 AAAAGAGAAA
651045 AAAA
1 AAAA
651049 AGGGGACGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 6 0.29
10 15 0.71
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAGAGAAA
Found at i:652117 original size:33 final size:32
Alignment explanation
Indices: 652080--652154 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 32
652070 GCATCGTTAA
*
652080 AGATTCAACAACAAATGTTGGGGCAATATTTGG
1 AGATTCAACAACAAATATTGGGG-AATATTTGG
*** *
652113 AGATTCAACATTGAATATTGGGGTATATTTGG
1 AGATTCAACAACAAATATTGGGGAATATTTGG
*
652145 GGATTCAACA
1 AGATTCAACA
652155 TCCTGATGCA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 17 0.47
33 19 0.53
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.31
Consensus pattern (32 bp):
AGATTCAACAACAAATATTGGGGAATATTTGG
Found at i:652522 original size:43 final size:41
Alignment explanation
Indices: 652431--652554 Score: 149
Period size: 43 Copynumber: 2.9 Consensus size: 41
652421 ACGAAGGGGC
*
652431 CATCCACGATTTCAACTCCACGGCGGAGGATATCGTACCAA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAA
* *
652472 CGGATCCATGATTTCAACTCCACGACGGAGGATATCGTGCTCACA
1 C--ATCCACGATTTCAACTCCACGACGGAGGATATCGTAC-CA-A
* * * *
652517 CATCCACGGTTTCAACTTCACGACGAAGGAAATCGTAC
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTAC
652555 ACACAAGCAG
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
41 1 0.01
43 65 0.93
44 2 0.03
45 2 0.03
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (41 bp):
CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAA
Found at i:652987 original size:37 final size:37
Alignment explanation
Indices: 652937--653010 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
652927 GTCCAACGGG
**
652937 CAATCTAAAGCCTTCACTGAAGAGTAGTGAAGCAAAT
1 CAATCTAAAGCCTTCACAAAAGAGTAGTGAAGCAAAT
*
652974 CAATCTTAAGCCTTCACAAAAGAGTAGTGAAGCAAAT
1 CAATCTAAAGCCTTCACAAAAGAGTAGTGAAGCAAAT
653011 TCAGATCTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.22
Consensus pattern (37 bp):
CAATCTAAAGCCTTCACAAAAGAGTAGTGAAGCAAAT
Found at i:653280 original size:110 final size:110
Alignment explanation
Indices: 653012--653310 Score: 456
Period size: 110 Copynumber: 2.7 Consensus size: 110
653002 GAAGCAAATT
653012 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCCCTCTTTTTCAAGATTTGATATTCCCTG
1 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCCCTCTTTTTCAAGATTTGA-ATTCCCTG
* * * *
653077 AGTGACAGCGGAACAAATCTGCTCTGATTCAATGGATTAACTCTCC
65 AGTGACAGCGGAACAAATCTACCCTGATTCAATGAATCAACTCTCC
* * * *
653123 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCTCTCTCTTTCAAGATTTG-ATTCTCTGG
1 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCCCTCTTTTTCAAGATTTGAATTCCCTGA
* *
653187 GTGACAGCGGAACAAAGTCTACCCTGATTCAATGAATCAATTTTCC
66 GTGACAGCGGAACAAA-TCTACCCTGATTCAATGAATCAACTCTCC
* *
653233 CAGATCTGATATTCCCTCAGAGGAAGCGAAACAGATCCCTATTTTTCAAGATTTGATATTCCCTG
1 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCCCTCTTTTTCAAGATTTGA-ATTCCCTG
653298 AGTGACAGCGGAA
65 AGTGACAGCGGAA
653311 TAGATCCCTC
Statistics
Matches: 169, Mismatches: 16, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
109 23 0.14
110 74 0.44
111 53 0.31
112 19 0.11
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (110 bp):
CAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCCCTCTTTTTCAAGATTTGAATTCCCTGA
GTGACAGCGGAACAAATCTACCCTGATTCAATGAATCAACTCTCC
Found at i:653465 original size:3 final size:3
Alignment explanation
Indices: 653453--653482 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
653443 CGTCTTTTAA
653453 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
653483 TAATTATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:655095 original size:2 final size:2
Alignment explanation
Indices: 655088--655133 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
655078 TTTTATGGTA
655088 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
655130 AT AT
1 AT AT
655134 GGTTTGCTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:679011 original size:36 final size:36
Alignment explanation
Indices: 678952--679024 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 36
678942 GTTGAAAAAT
*
678952 ATTTATATATTTTCTTTAAAAAATT-AAATTCATAAA
1 ATTTATAAATTTTCTTTAAAAAATTGAAATT-ATAAA
*
678988 ATTTATACAATTTT-TTTACAAAATTGAAATTATAAA
1 ATTTATA-AATTTTCTTTAAAAAATTGAAATTATAAA
679024 A
1 A
679025 ATGTTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 23 0.70
37 10 0.30
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.45
Consensus pattern (36 bp):
ATTTATAAATTTTCTTTAAAAAATTGAAATTATAAA
Found at i:679365 original size:23 final size:23
Alignment explanation
Indices: 679330--679383 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
679320 CAACCAAACG
* *
679330 GGGAATGTGGATTCCATTCCCAT
1 GGGAATCTAGATTCCATTCCCAT
* *
679353 GGGAATCTAGATTTCATTCTCAT
1 GGGAATCTAGATTCCATTCCCAT
679376 GGGAATCT
1 GGGAATCT
679384 CACATTCCTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (23 bp):
GGGAATCTAGATTCCATTCCCAT
Found at i:686950 original size:17 final size:17
Alignment explanation
Indices: 686925--686961 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
686915 GACAATTAAA
* *
686925 TTTATTTTAATTTATTT
1 TTTAATTTAATATATTT
686942 TTTAATTTAATATATTT
1 TTTAATTTAATATATTT
686959 TTT
1 TTT
686962 CACCAATCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTAATTTAATATATTT
Found at i:691315 original size:32 final size:30
Alignment explanation
Indices: 691253--691315 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 30
691243 TTGATATTTG
*
691253 AATTTTAGATAATATTAATTGAACTTTTAA
1 AATTTTAGATAATATTAATTGAACTCTTAA
691283 AATTTTAGATAAGATATTAATTTG-ACTCTTAA
1 AATTTTAGAT-A-ATATTAA-TTGAACTCTTAA
691315 A
1 A
691316 CTTTAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 10 0.34
31 1 0.03
32 15 0.52
33 3 0.10
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (30 bp):
AATTTTAGATAATATTAATTGAACTCTTAA
Found at i:693891 original size:22 final size:19
Alignment explanation
Indices: 693865--693914 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 19
693855 AATTTGTAAC
693865 AATAATTTAATCAGTAAAATAT
1 AATAATTTAA--A-TAAAATAT
693887 AATAATTTTAAATAAAATAT
1 AATAA-TTTAAATAAAATAT
693907 AACTAATT
1 AA-TAATT
693915 ATTATAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 12 0.46
21 4 0.15
22 5 0.19
23 5 0.19
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (19 bp):
AATAATTTAAATAAAATAT
Found at i:693924 original size:21 final size:22
Alignment explanation
Indices: 693879--693936 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 22
693869 ATTTAATCAG
693879 TAAAATATAA-TAATT-TTAAA
1 TAAAATATAACTAATTATTAAA
*
693899 TAAAATATAACTAATTATTATA
1 TAAAATATAACTAATTATTAAA
*
693921 -AAAATAAAACTAATTA
1 TAAAATATAACTAATTA
693937 AAAGATCATA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 10 0.29
21 20 0.59
22 4 0.12
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (22 bp):
TAAAATATAACTAATTATTAAA
Found at i:710881 original size:32 final size:32
Alignment explanation
Indices: 710845--710908 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
710835 AGGTTGTGTG
710845 GTCAAGTTGTGAACTTGTGCATCTGTTTCGCA
1 GTCAAGTTGTGAACTTGTGCATCTGTTTCGCA
710877 GTCAAGTTGTGAACTTGTGCATCTGTTTCGCA
1 GTCAAGTTGTGAACTTGTGCATCTGTTTCGCA
710909 ATTGAAGAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (32 bp):
GTCAAGTTGTGAACTTGTGCATCTGTTTCGCA
Found at i:718973 original size:9 final size:9
Alignment explanation
Indices: 718959--718992 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
718949 CTAAGTTAAA
718959 TTAATTATT
1 TTAATTATT
718968 TTAATTATT
1 TTAATTATT
718977 TTAATTATTT
1 TTAATTA-TT
718987 TTAATT
1 TTAATT
718993 TTAAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTAATTATT
Found at i:719443 original size:24 final size:25
Alignment explanation
Indices: 719395--719450 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
719385 GTGGCAGAAC
719395 AACAGGGTGAAAAAAGAGAATGAAA
1 AACAGGGTGAAAAAAGAGAATGAAA
**
719420 AACAGGGTGAGCAAA-AGAATGAAA
1 AACAGGGTGAAAAAAGAGAATGAAA
719444 AA-AGGGT
1 AACAGGGT
719451 CAGATGCACA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 11 0.38
25 13 0.45
ACGTcount: A:0.55, C:0.05, G:0.30, T:0.09
Consensus pattern (25 bp):
AACAGGGTGAAAAAAGAGAATGAAA
Found at i:721100 original size:192 final size:192
Alignment explanation
Indices: 720773--721156 Score: 741
Period size: 192 Copynumber: 2.0 Consensus size: 192
720763 GAACAAATGC
*
720773 CTGAATATGATTATTCAATCTCACGTATGATCTACTTTCAACTTGTTCCACCAGTGCATACTTTA
1 CTGAATATGATTATTCAATCTAACGTATGATCTACTTTCAACTTGTTCCACCAGTGCATACTTTA
*
720838 TTTACTCCTTCCACAAGCATATTCTTAAATGGCCAACTTTTAAAAGATAACCAATCTATTATGCT
66 TTTACTCCTTCCACAAGCATATTCTTAAATGGCCAACTTTTAAAAGAGAACCAATCTATTATGCT
720903 ATTATGAAATAGCCAAGAATCTTCTAAGTTCTAAGGATACCTTAATGATATCTAATAAAAAT
131 ATTATGAAATAGCCAAGAATCTTCTAAGTTCTAAGGATACCTTAATGATATCTAATAAAAAT
720965 CTGAATATGATTATTCAATCTAACGTATGATCTACTTTCAACTTGTTCCACCAGTGCATACTTTA
1 CTGAATATGATTATTCAATCTAACGTATGATCTACTTTCAACTTGTTCCACCAGTGCATACTTTA
*
721030 TTTACTCCTTCCACAAGCATATTCTTAAATGGCCAACTTTTAAAAGAGAGCCAATCTATTATGCT
66 TTTACTCCTTCCACAAGCATATTCTTAAATGGCCAACTTTTAAAAGAGAACCAATCTATTATGCT
721095 ATTATGAAATAGCCAAGAATCTTCTAAGTTCTAAGGATACCTTAATGATATCTAATAAAAAT
131 ATTATGAAATAGCCAAGAATCTTCTAAGTTCTAAGGATACCTTAATGATATCTAATAAAAAT
721157 TTCTCACCAA
Statistics
Matches: 189, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
192 189 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (192 bp):
CTGAATATGATTATTCAATCTAACGTATGATCTACTTTCAACTTGTTCCACCAGTGCATACTTTA
TTTACTCCTTCCACAAGCATATTCTTAAATGGCCAACTTTTAAAAGAGAACCAATCTATTATGCT
ATTATGAAATAGCCAAGAATCTTCTAAGTTCTAAGGATACCTTAATGATATCTAATAAAAAT
Found at i:727373 original size:20 final size:20
Alignment explanation
Indices: 727348--727418 Score: 142
Period size: 20 Copynumber: 3.5 Consensus size: 20
727338 ACATGCCAGA
727348 AGTATCGATACTCAAGAAAG
1 AGTATCGATACTCAAGAAAG
727368 AGTATCGATACTCAAGAAAG
1 AGTATCGATACTCAAGAAAG
727388 AGTATCGATACTCAAGAAAG
1 AGTATCGATACTCAAGAAAG
727408 AGTATCGATAC
1 AGTATCGATAC
727419 CAGTCATTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.21
Consensus pattern (20 bp):
AGTATCGATACTCAAGAAAG
Found at i:728752 original size:25 final size:25
Alignment explanation
Indices: 728722--728808 Score: 90
Period size: 25 Copynumber: 3.6 Consensus size: 25
728712 TTTTAAAACT
*
728722 TCAAACATTTTTCTAAATTCTTTCA
1 TCAAACATTTTTCAAAATTCTTTCA
* * *
728747 TCAAACATTATTCAAAATCCTTTCT
1 TCAAACATTTTTCAAAATTCTTTCA
* *
728772 TAAAACA-TTTTCAAAACTT-GTTCA
1 TCAAACATTTTTCAAAA-TTCTTTCA
728796 TCAAAC-TTTTTCA
1 TCAAACATTTTTCA
728809 CCTTTTGAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
24 22 0.44
25 28 0.56
ACGTcount: A:0.36, C:0.21, G:0.01, T:0.43
Consensus pattern (25 bp):
TCAAACATTTTTCAAAATTCTTTCA
Found at i:730451 original size:3 final size:3
Alignment explanation
Indices: 730443--730480 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
730433 CCAACGTTTT
730443 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
730481 TTAATAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:730757 original size:20 final size:20
Alignment explanation
Indices: 730725--730762 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
730715 ATCAACAATG
730725 AAATCAAAACAAATCTAATA
1 AAATCAAAACAAATCTAATA
730745 AAAT-AAAACCAAATCTAA
1 AAATCAAAA-CAAATCTAA
730763 CCCATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.66, C:0.16, G:0.00, T:0.18
Consensus pattern (20 bp):
AAATCAAAACAAATCTAATA
Found at i:731853 original size:33 final size:32
Alignment explanation
Indices: 731794--731868 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 32
731784 TTTATGTGTA
731794 ATGTACATATTTATTATTTATCTATGTATTAT
1 ATGTACATATTTATTATTTATCTATGTATTAT
* *
731826 ATGTACATATTTATTTATTTGTTTATGTATTAT
1 ATGTACATATTTA-TTATTTATCTATGTATTAT
731859 ATGTACATAT
1 ATGTACATAT
731869 ATTCTTTTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 13 0.32
33 27 0.68
ACGTcount: A:0.31, C:0.05, G:0.08, T:0.56
Consensus pattern (32 bp):
ATGTACATATTTATTATTTATCTATGTATTAT
Found at i:732109 original size:14 final size:15
Alignment explanation
Indices: 732090--732120 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
732080 ATGTACATCT
732090 ATTTTATTTT-ATTC
1 ATTTTATTTTAATTC
732104 ATTTTATTTTAATTC
1 ATTTTATTTTAATTC
732119 AT
1 AT
732121 AAAGTATCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTTATTTTAATTC
Found at i:736258 original size:27 final size:27
Alignment explanation
Indices: 736222--736273 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
736212 TTTATGGCGA
736222 CCTACAAGGTCGCCCGGAGTGCATGGC
1 CCTACAAGGTCGCCCGGAGTGCATGGC
736249 CCTACAAGGTCGCCCGGAGTGCATG
1 CCTACAAGGTCGCCCGGAGTGCATG
736274 CACAAGGTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.19, C:0.33, G:0.33, T:0.15
Consensus pattern (27 bp):
CCTACAAGGTCGCCCGGAGTGCATGGC
Found at i:736644 original size:18 final size:18
Alignment explanation
Indices: 736623--736664 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
736613 ATTTACACGA
736623 CTAAGCATACCTACACTG
1 CTAAGCATACCTACACTG
*
736641 CTAAGCTTACCTACACTG
1 CTAAGCATACCTACACTG
736659 CTAAGC
1 CTAAGC
736665 GTAGTTGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.31, C:0.33, G:0.12, T:0.24
Consensus pattern (18 bp):
CTAAGCATACCTACACTG
Found at i:739573 original size:57 final size:57
Alignment explanation
Indices: 739497--739632 Score: 188
Period size: 57 Copynumber: 2.4 Consensus size: 57
739487 AGAAAAACCC
*
739497 AACAATGAAAAAATAACTAAGCTTAAACA-ACTAC-CCCTTCCCTATACACAG-GACACCA
1 AACAATG-AAAAATAACTAAGCTTAAACAGA-AACTCCC-TCCCTATACACAGAG-CACCA
* *
739555 AACAATGAAAAATAACTAAGCTTAAACAGAAACTCCCTCCCTGTACACAGAGTACCA
1 AACAATGAAAAATAACTAAGCTTAAACAGAAACTCCCTCCCTATACACAGAGCACCA
739612 AACAATGAAAAATAACTAAGC
1 AACAATGAAAAATAACTAAGC
739633 AGACCCTATA
Statistics
Matches: 72, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
57 60 0.83
58 12 0.17
ACGTcount: A:0.49, C:0.26, G:0.09, T:0.17
Consensus pattern (57 bp):
AACAATGAAAAATAACTAAGCTTAAACAGAAACTCCCTCCCTATACACAGAGCACCA
Found at i:741581 original size:16 final size:17
Alignment explanation
Indices: 741560--741602 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
741550 AAATTCCTAG
*
741560 TAATCTTATTTTC-TGA
1 TAATCTTATTCTCATGA
741576 TAATCTTTATTCTCATTGA
1 TAATC-TTATTCTCA-TGA
741595 TAATCTTA
1 TAATCTTA
741603 CGTTCCGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 5 0.22
17 7 0.30
18 3 0.13
19 8 0.35
ACGTcount: A:0.28, C:0.14, G:0.05, T:0.53
Consensus pattern (17 bp):
TAATCTTATTCTCATGA
Found at i:742729 original size:20 final size:21
Alignment explanation
Indices: 742704--742755 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
742694 TTTTCCCAAT
*
742704 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
742724 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
742745 TCGCAATGCGA
1 TCGCAATGCGA
742756 TACTTACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:742768 original size:41 final size:41
Alignment explanation
Indices: 742741--742818 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
742731 GCGAATTGGG
* * *
742741 AAAATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTTACTATCGCAACGCGATAATAC
*
742782 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTTACTATCGCAACGCGATA
742819 CTGACTTTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTTACTATCGCAACGCGATAATAC
Found at i:742769 original size:20 final size:20
Alignment explanation
Indices: 742744--742837 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
742734 AATTGGGAAA
*
742744 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
742764 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
742785 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
742805 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
742825 TTCGCAACGCGAT
1 ATCGCAACGCGAT
742838 TTACATAATC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.71
21 12 0.19
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:743053 original size:22 final size:22
Alignment explanation
Indices: 743025--743068 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
743015 CACTCTCTCA
743025 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
743047 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
743069 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:744619 original size:18 final size:18
Alignment explanation
Indices: 744598--744642 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
744588 TCCACTTCGG
* *
744598 GAGCCATCACCTCGCCCA
1 GAGCCATCACCCCACCCA
*
744616 GAGCTATCACCCCACCCA
1 GAGCCATCACCCCACCCA
744634 GAGCCATCA
1 GAGCCATCA
744643 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.47, G:0.16, T:0.11
Consensus pattern (18 bp):
GAGCCATCACCCCACCCA
Found at i:745199 original size:19 final size:19
Alignment explanation
Indices: 745107--745208 Score: 70
Period size: 19 Copynumber: 5.6 Consensus size: 19
745097 TAGTTTACTT
* **
745107 TCGCAACACGAAATGACTA
1 TCGCAACGCGAAATGAAAA
****
745126 TCGCAACGCGGAAATGGCTT
1 TCGCAACGC-GAAATGAAAA
*
745146 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
745165 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
745179 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
745198 TCGCAATGCGA
1 TCGCAACGCGA
745209 TTTGTGTTTC
Statistics
Matches: 66, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
14 10 0.15
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 34 0.52
20 16 0.24
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.15
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:745251 original size:13 final size:14
Alignment explanation
Indices: 745220--745272 Score: 99
Period size: 14 Copynumber: 3.9 Consensus size: 14
745210 TTGTGTTTCG
745220 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
745234 CGTTGCGATTTT-T
1 CGTTGCGATTTTGT
745247 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
745261 CGTTGCGATTTT
1 CGTTGCGATTTT
745273 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.34
14 25 0.66
ACGTcount: A:0.08, C:0.15, G:0.26, T:0.51
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Done.