Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003805.1 Hibiscus syriacus cultivar Beakdansim tig00008145_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: 2300233
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 11
Found at i:2286872 original size:23 final size:23
Alignment explanation
Indices: 2286846--2286908 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
2286836 ATATAACCAC
2286846 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2286869 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2286892 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2286909 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2287301 original size:23 final size:23
Alignment explanation
Indices: 2287275--2287337 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
2287265 ATATAACCAC
2287275 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2287298 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2287321 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2287338 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2287731 original size:23 final size:23
Alignment explanation
Indices: 2287705--2287767 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
2287695 ATATAACCAC
2287705 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2287728 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2287751 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2287768 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2288162 original size:23 final size:23
Alignment explanation
Indices: 2288136--2288198 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
2288126 ATATAACCAC
2288136 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2288159 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2288182 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2288199 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2288579 original size:21 final size:20
Alignment explanation
Indices: 2288549--2288618 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 20
2288539 GATAGATACT
*
2288549 TTACAATATAACCACTACCTA
1 TTACATTATAA-CACTACCTA
* *
2288570 TTACATTATATAAACGAACCTA
1 TTACATTATA-ACAC-TACCTA
* *
2288592 TTACATTATAAGCGCTATCTA
1 TTACATTATAA-CACTACCTA
2288613 TTACAT
1 TTACAT
2288619 CATATTTTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
21 22 0.56
22 17 0.44
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.34
Consensus pattern (20 bp):
TTACATTATAACACTACCTA
Found at i:2289017 original size:23 final size:23
Alignment explanation
Indices: 2288991--2289053 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
2288981 ATATAACCAC
2288991 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2289014 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2289037 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2289054 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2289443 original size:23 final size:23
Alignment explanation
Indices: 2289417--2289479 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
2289407 ATATAACCAC
2289417 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2289440 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2289463 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2289480 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2289875 original size:23 final size:23
Alignment explanation
Indices: 2289849--2289911 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
2289839 ATATAACCAC
2289849 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2289872 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2289895 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2289912 GTTACCTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2290328 original size:22 final size:23
Alignment explanation
Indices: 2290274--2290335 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
2290264 ATATAACAAC
2290274 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2290297 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2290320 TA-CTATTACATCATAT
1 TACCTATTACATTATAT
2290336 TTTTACTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 13 0.36
23 23 0.64
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2290735 original size:23 final size:23
Alignment explanation
Indices: 2290699--2290760 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
2290689 ATATAACCAC
2290699 TACCTA-TACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2290721 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2290744 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2290761 TTTACCTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 6 0.17
23 30 0.83
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.35
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2290972 original size:12 final size:12
Alignment explanation
Indices: 2290942--2290980 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
2290932 TAAAATTTTA
*
2290942 TTAAATTTT-AT
1 TTAATTTTTAAT
2290953 TT-ATTTTTAAT
1 TTAATTTTTAAT
2290964 TTAATTTTTAAT
1 TTAATTTTTAAT
2290976 TTAAT
1 TTAAT
2290981 AATATATATC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 5 0.20
11 6 0.24
12 14 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTAATTTTTAAT
Found at i:2291165 original size:23 final size:23
Alignment explanation
Indices: 2291139--2291201 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
2291129 ATATAACCAC
2291139 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2291162 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2291185 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2291202 TTTACCTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2291587 original size:23 final size:23
Alignment explanation
Indices: 2291561--2291623 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
2291551 ATATAACCAC
2291561 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2291584 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2291607 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2291624 TTTACCTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2292016 original size:22 final size:23
Alignment explanation
Indices: 2291985--2292046 Score: 90
Period size: 22 Copynumber: 2.7 Consensus size: 23
2291975 ATATAACCAC
2291985 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2292008 TA-CTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2292030 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2292047 GTTTACCTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2292040 original size:23 final size:23
Alignment explanation
Indices: 2291975--2292046 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
2291965 ATACTTTACA
* *
2291975 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
2291998 ATATAAACGATA-CTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
2292020 ATATAAGCGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
2292043 ATAT
1 ATAT
2292047 GTTTACCTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 20 0.48
23 22 0.52
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:2292432 original size:23 final size:23
Alignment explanation
Indices: 2292406--2292468 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
2292396 ATATAACAAC
2292406 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2292429 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2292452 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2292469 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2292860 original size:23 final size:23
Alignment explanation
Indices: 2292834--2292894 Score: 81
Period size: 21 Copynumber: 2.7 Consensus size: 23
2292824 ATATAACCAC
2292834 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2292857 TACCTATTACA-T-TATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2292878 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2292895 TTTTACCTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 18 0.55
22 1 0.03
23 14 0.42
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2292889 original size:21 final size:21
Alignment explanation
Indices: 2292819--2292889 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
2292809 GGATAGATAC
* * *
2292819 TTACAATATAACCACTACCTA
1 TTACATTATAAACGCTACCTA
*
2292840 TTACATTATATAAACGATACCTA
1 TTACA-T-TATAAACGCTACCTA
*
2292863 TTACATTATAAGCGCTACCTA
1 TTACATTATAAACGCTACCTA
2292884 TTACAT
1 TTACAT
2292890 CATATTTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
21 24 0.57
22 1 0.02
23 17 0.40
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.34
Consensus pattern (21 bp):
TTACATTATAAACGCTACCTA
Found at i:2293292 original size:22 final size:23
Alignment explanation
Indices: 2293257--2293318 Score: 90
Period size: 22 Copynumber: 2.7 Consensus size: 23
2293247 ATATAACCAC
2293257 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2293280 TACCTA-TACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2293302 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2293319 TTTACCTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.35
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2293695 original size:20 final size:21
Alignment explanation
Indices: 2293680--2293736 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
2293670 AATATACCAC
2293680 TACCTATTACATTATAAAACGA
1 TACCTATTACATTATAAAAC-A
* *
2293702 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATA-AAAC-A
2293725 TACCTATTACAT
1 TACCTATTACAT
2293737 CATATTTTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 16 0.50
23 16 0.50
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.35
Consensus pattern (21 bp):
TACCTATTACATTATAAAACA
Found at i:2293732 original size:23 final size:23
Alignment explanation
Indices: 2293679--2293741 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
2293669 CAATATACCA
2293679 CTACCTATTACATTATA-AAACG
1 CTACCTATTACATTATATAAACG
* *
2293701 ATACCTATTACATTATATAAGCG
1 CTACCTATTACATTATATAAACG
*
2293724 CTACCTATTACATCATAT
1 CTACCTATTACATTATAT
2293742 TTTACCTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 16 0.44
23 20 0.56
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (23 bp):
CTACCTATTACATTATATAAACG
Found at i:2294150 original size:23 final size:22
Alignment explanation
Indices: 2294093--2294162 Score: 81
Period size: 21 Copynumber: 3.2 Consensus size: 22
2294083 ATACTTTACA
*
2294093 ATATAACCACTACCTATTACATT
1 ATATAA-CGCTACCTATTACATT
*
2294116 ATA-AACGATACCTATTACATT
1 ATATAACGCTACCTATTACATT
*
2294137 ATATAAGCGCTACCTA-TACATC
1 ATATAA-CGCTACCTATTACATT
2294159 ATAT
1 ATAT
2294163 TTTTACCTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
21 17 0.41
22 13 0.32
23 11 0.27
ACGTcount: A:0.40, C:0.23, G:0.04, T:0.33
Consensus pattern (22 bp):
ATATAACGCTACCTATTACATT
Found at i:2294579 original size:23 final size:23
Alignment explanation
Indices: 2294526--2294586 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
2294516 AATATAACCC
2294526 TACCTATTACA-TAT-TAAACGA
1 TACCTATTACATTATATAAACGA
* *
2294547 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
* *
2294570 TATCTATTACATCATAT
1 TACCTATTACATTATAT
2294587 TTTTACCTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.32
22 3 0.09
23 20 0.59
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2294966 original size:21 final size:21
Alignment explanation
Indices: 2294936--2295006 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
2294926 GATAGATACT
*
2294936 TTACAATATAACCACTACCTA
1 TTACATTATAACCACTACCTA
*
2294957 TTACATTATAAACGA-TACCTA
1 TTACATTAT-AACCACTACCTA
* *
2294978 TTACATTATATAAGCGCTACCTA
1 TTACA-T-TATAACCACTACCTA
2295001 TTACAT
1 TTACAT
2295007 CATATGTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
21 19 0.46
22 8 0.20
23 14 0.34
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.34
Consensus pattern (21 bp):
TTACATTATAACCACTACCTA
Found at i:2294998 original size:23 final size:22
Alignment explanation
Indices: 2294941--2295011 Score: 90
Period size: 23 Copynumber: 3.2 Consensus size: 22
2294931 ATACTTTACA
*
2294941 ATATAACCACTACCTATTACATT
1 ATATAA-CGCTACCTATTACATT
*
2294964 ATA-AACGATACCTATTACATT
1 ATATAACGCTACCTATTACATT
*
2294985 ATATAAGCGCTACCTATTACATC
1 ATATAA-CGCTACCTATTACATT
2295008 ATAT
1 ATAT
2295012 GTTTACCTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.40
22 4 0.10
23 21 0.50
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.34
Consensus pattern (22 bp):
ATATAACGCTACCTATTACATT
Found at i:2295408 original size:23 final size:23
Alignment explanation
Indices: 2295372--2295428 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
2295362 ATATAACCAC
2295372 TACCTA-TACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2295394 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
2295417 TACCTATTACAT
1 TACCTATTACAT
2295429 CATGTTTACC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 6 0.19
23 26 0.81
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.35
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2295813 original size:22 final size:23
Alignment explanation
Indices: 2295785--2295855 Score: 92
Period size: 22 Copynumber: 3.2 Consensus size: 23
2295775 ATACTTTACA
2295785 ATATAACCACTACCTA-TACATT
1 ATATAACCACTACCTATTACATT
*
2295807 ATATAACGA-TACCTATTACATT
1 ATATAACCACTACCTATTACATT
* * *
2295829 ATATAAGCGCTACCTATTACATC
1 ATATAACCACTACCTATTACATT
2295852 ATAT
1 ATAT
2295856 GTTTACCTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
21 6 0.14
22 20 0.48
23 16 0.38
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.34
Consensus pattern (23 bp):
ATATAACCACTACCTATTACATT
Found at i:2296226 original size:21 final size:21
Alignment explanation
Indices: 2296201--2296272 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 21
2296191 GATAGATACT
2296201 TTACAATATAACAACTACCTA
1 TTACAATATAACAACTACCTA
*
2296222 TTACATTATATA-AACGATACCTA
1 TTACAATATA-ACAAC--TACCTA
*
2296245 TTACATTATATAAGC-GCTACCTA
1 TTACA--ATATAA-CAACTACCTA
2296268 TTACA
1 TTACA
2296273 TCATATTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
21 12 0.29
22 1 0.02
23 22 0.54
24 1 0.02
25 5 0.12
ACGTcount: A:0.42, C:0.21, G:0.04, T:0.33
Consensus pattern (21 bp):
TTACAATATAACAACTACCTA
Found at i:2296242 original size:23 final size:23
Alignment explanation
Indices: 2296216--2296278 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
2296206 ATATAACAAC
2296216 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2296239 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2296262 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2296279 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2296669 original size:23 final size:23
Alignment explanation
Indices: 2296643--2296704 Score: 90
Period size: 22 Copynumber: 2.7 Consensus size: 23
2296633 ATATAACCAC
2296643 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2296666 TACCTATTACA-TATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2296688 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2296705 TTTTACCTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.35
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2297075 original size:21 final size:21
Alignment explanation
Indices: 2297050--2297119 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 21
2297040 GATAGATACT
2297050 TTACAATATAACCACTACCTA
1 TTACAATATAACCACTACCTA
*
2297071 TTACATTATATAAACGA-TA-CTA
1 TTACA--ATAT-AACCACTACCTA
* * *
2297093 TTACATTAATAAGCGCTACCTA
1 TTACAAT-ATAACCACTACCTA
2297115 TTACA
1 TTACA
2297120 TCATATTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 11
0.70 0.09 0.20
Matches are distributed among these distances:
20 3 0.08
21 9 0.24
22 16 0.42
23 6 0.16
24 4 0.11
ACGTcount: A:0.41, C:0.21, G:0.04, T:0.33
Consensus pattern (21 bp):
TTACAATATAACCACTACCTA
Found at i:2297096 original size:22 final size:23
Alignment explanation
Indices: 2297065--2297125 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
2297055 ATATAACCAC
2297065 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2297088 TA-CTATTACATTA-ATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2297109 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2297126 TTTTACCTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 8 0.24
22 21 0.64
23 4 0.12
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.36
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2297509 original size:23 final size:23
Alignment explanation
Indices: 2297483--2297540 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
2297473 ATATAACCAC
2297483 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2297506 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
2297529 TACCTATTACAT
1 TACCTATTACAT
2297541 CATTTTTTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2297931 original size:22 final size:22
Alignment explanation
Indices: 2297891--2297965 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
2297881 GATAGATACT
*
2297891 TTACA-ATAT-AACCATACCTA
1 TTACATATATAAACGATACCTA
2297911 TTACATATATAAACGATACCTA
1 TTACATATATAAACGATACCTA
* *
2297933 TTACATTATATAAGCGCTACCTA
1 TTACA-TATATAAACGATACCTA
2297956 -TACATCATAT
1 TTACAT-ATAT
2297966 TTTACTATTA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
20 5 0.10
21 5 0.10
22 23 0.48
23 15 0.31
ACGTcount: A:0.41, C:0.21, G:0.04, T:0.33
Consensus pattern (22 bp):
TTACATATATAAACGATACCTA
Found at i:2298349 original size:23 final size:23
Alignment explanation
Indices: 2298323--2298384 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
2298313 ATATAACCAC
2298323 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2298346 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2298369 TATCTATTACA-TATAT
1 TACCTATTACATTATAT
2298385 TTTTACCTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 5 0.14
23 31 0.86
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.39
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2298796 original size:23 final size:23
Alignment explanation
Indices: 2298734--2298805 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
2298724 ATACTTTACA
* *
2298734 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
2298757 ATA-AAACGATACCTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
2298779 ATATAAGCGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
2298802 ATAT
1 ATAT
2298806 GTTTACCTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 19 0.45
23 23 0.55
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.33
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:2299599 original size:23 final size:23
Alignment explanation
Indices: 2299573--2299635 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
2299563 ATATAACCAC
2299573 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
2299596 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
2299619 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2299636 TTTACCTATA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2300034 original size:23 final size:22
Alignment explanation
Indices: 2299987--2300047 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
2299977 ACAATAACCA
2299987 CTACCTA-TACATTATA-AACG
1 CTACCTATTACATTATATAACG
*
2300007 ATACCTATTACATTATATAAGCG
1 CTACCTATTACATTATATAA-CG
*
2300030 CTACCTATTACATCATAT
1 CTACCTATTACATTATAT
2300048 TTTTACCTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 6 0.17
21 9 0.26
22 2 0.06
23 18 0.51
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.34
Consensus pattern (22 bp):
CTACCTATTACATTATATAACG
Found at i:2300099 original size:21 final size:22
Alignment explanation
Indices: 2300065--2300108 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
2300055 TATTATATTG
2300065 AAAGTGTCCATACTT-TTTATAA
1 AAAGTGTCCATACTTCTTT-TAA
*
2300087 AAAG-GTCGATACTTCTTTTAA
1 AAAGTGTCCATACTTCTTTTAA
2300108 A
1 A
2300109 GTTATGTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (22 bp):
AAAGTGTCCATACTTCTTTTAA
Done.