Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007957.1 Hibiscus syriacus cultivar Beakdansim tig00110384_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: 8646418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 43 of 43
Found at i:8624004 original size:21 final size:20
Alignment explanation
Indices: 8623974--8624027 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
8623964 GATAGACACT
*
8623974 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
8623995 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
8624018 TTACATTATA
1 TTACATTATA
8624028 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:8624015 original size:23 final size:23
Alignment explanation
Indices: 8623989--8624051 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
8623979 ATATAACCAT
8623989 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
8624012 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
8624035 TACCTATTACATCATAT
1 TACCTATTACATTATAT
8624052 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:8624470 original size:23 final size:22
Alignment explanation
Indices: 8624408--8624479 Score: 90
Period size: 23 Copynumber: 3.2 Consensus size: 22
8624398 ACACTTTACA
*
8624408 ATATAACCATTACCTATTACATT
1 ATATAACGA-TACCTATTACATT
8624431 ATATAACGATACCTATTACATT
1 ATATAACGATACCTATTACATT
* * *
8624453 ATATAAGGGCTACCTATTACATC
1 ATATAA-CGATACCTATTACATT
8624476 ATAT
1 ATAT
8624480 GTTTACCTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 19 0.43
23 25 0.57
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.36
Consensus pattern (22 bp):
ATATAACGATACCTATTACATT
Found at i:8624517 original size:428 final size:429
Alignment explanation
Indices: 8623564--8625006 Score: 2801
Period size: 428 Copynumber: 3.4 Consensus size: 429
8623554 GCGAGATAGA
8623564 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
*
8623629 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
8623694 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTAC-ATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
* *
8623758 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTA
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGATTTTTT
8623823 AATTTAATAATAATATACCGTAACGTAAAAAAT-AATCATTAGACGCCTATAATTACTAAATTAA
261 AATTTAATAATAATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAA
8623887 TATCTTAAAACTCACTC-AAAGATAACCTTAAATTAATGTTTTCCACAGTG-AAAAAGTATGGAC
326 TATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGAC
8623950 ACTTTTATAAAAAGGATAGACACTTTACAATATAACCAT
391 ACTTTTATAAAAAGGATAGACACTTTACAATATAACCAT
8623989 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
8624054 TTACCTATTATATTGAAAGTGTCCATACTTTTTAT-AAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
8624118 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
8624183 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGATTTTTT
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGATTTTTT
8624248 AATTTAATAATATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTA
261 AATTTAATAATA-ATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTA
8624313 ATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGA
325 ATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGA
8624378 CACTTTTATAAAAAGGATAGACACTTTACAATATAACCAT
390 CACTTTTATAAAAAGGATAGACACTTTACAATATAACCAT
8624418 TACCTATTACATTATAT-AACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
8624482 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
8624547 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
8624612 ATTTCATTTGCAC-AAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGATTTTTT
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGATTTTTT
8624676 AATTTAATAATAATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAA
261 AATTTAATAATAATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAA
8624741 TATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGAC
326 TATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGAC
8624806 ACTTTTATAAAAAGGATAGACACTTTACAATATAACCAT
391 ACTTTTATAAAAAGGATAGACACTTTACAATATAACCAT
8624845 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
8624910 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
8624975 TGTAATTTATGTTTCAATTTTTTTAACAGTGT
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGT
8625007 ACTGCGAATT
Statistics
Matches: 1008, Mismatches: 3, Indels: 11
0.99 0.00 0.01
Matches are distributed among these distances:
424 78 0.08
425 189 0.19
426 21 0.02
427 222 0.22
428 322 0.32
429 176 0.17
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (429 bp):
TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGATTTTTT
AATTTAATAATAATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAA
TATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGAC
ACTTTTATAAAAAGGATAGACACTTTACAATATAACCAT
Found at i:8624665 original size:31 final size:29
Alignment explanation
Indices: 8624625--8624691 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 29
8624615 TCATTTGCAC
*
8624625 AAAA-ATTATTT-GATTGTTTTTATATTTTAT
1 AAAATATTATTTAGA-T-TTTTTA-ATTTAAT
8624655 AAAATATTATTTAGATTTTTTAATTTAAT
1 AAAATATTATTTAGATTTTTTAATTTAAT
8624684 AATAATAT
1 AA-AATAT
8624692 ACCGTAACGT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 8 0.24
30 15 0.45
31 8 0.24
32 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (29 bp):
AAAATATTATTTAGATTTTTTAATTTAAT
Found at i:8624860 original size:21 final size:20
Alignment explanation
Indices: 8624830--8624883 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
8624820 GATAGACACT
*
8624830 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
8624851 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
8624874 TTACATTATA
1 TTACATTATA
8624884 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:8624871 original size:23 final size:23
Alignment explanation
Indices: 8624845--8624907 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
8624835 ATATAACCAT
8624845 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
8624868 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
8624891 TACCTATTACATCATAT
1 TACCTATTACATTATAT
8624908 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:8628107 original size:183 final size:184
Alignment explanation
Indices: 8627465--8628124 Score: 1270
Period size: 184 Copynumber: 3.6 Consensus size: 184
8627455 TTTTAAATGG
* *
8627465 TATGGACATAAAGTACCGACACAATATT-ATAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
8627529 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
8627594 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
8627648 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
8627713 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
*
8627778 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
8627832 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
8627897 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
8627962 GATGTGTAAAATGTCGACAC-TTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
8628015 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
8628080 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATT
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATT
8628125 TTATTAATAT
Statistics
Matches: 471, Mismatches: 5, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
183 170 0.36
184 301 0.64
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (184 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
Found at i:8629499 original size:3 final size:3
Alignment explanation
Indices: 8629491--8629577 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
8629481 ACTTGTTTGG
* * * **
8629491 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
8629539 AGC TTC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
8629578 GTCAGCTTCA
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.24, C:0.34, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:8629514 original size:18 final size:18
Alignment explanation
Indices: 8629491--8629592 Score: 87
Period size: 18 Copynumber: 5.7 Consensus size: 18
8629481 ACTTGTTTGG
8629491 ATCATCATCTTCATCATC
1 ATCATCATCTTCATCATC
* *
8629509 ATCATCATCATCGTCATC
1 ATCATCATCTTCATCATC
* ** * *
8629527 ATCTTCATCGCCAGCTTC
1 ATCATCATCTTCATCATC
* *
8629545 ATCGTCATCATCATCATC
1 ATCATCATCTTCATCATC
* *
8629563 ATCGTCATCTTCATCGTC
1 ATCATCATCTTCATCATC
* *
8629581 AGCTTCATCTTC
1 ATCATCATCTTC
8629593 TGCGACCGAT
Statistics
Matches: 67, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 67 1.00
ACGTcount: A:0.23, C:0.34, G:0.07, T:0.36
Consensus pattern (18 bp):
ATCATCATCTTCATCATC
Found at i:8629558 original size:42 final size:42
Alignment explanation
Indices: 8629499--8629589 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
8629489 GGATCATCAT
*
8629499 CTTCATCATCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
* * *
8629541 CTTCATCGTCATCATCATCATCATCGTCATCTTCATCGTCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
8629583 CTTCATC
1 CTTCATC
8629590 TTCTGCGACC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (42 bp):
CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:8631384 original size:195 final size:198
Alignment explanation
Indices: 8631047--8632445 Score: 2442
Period size: 194 Copynumber: 7.1 Consensus size: 198
8631037 TTTAAATTAG
* * *
8631047 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
8631112 ATTGTACCGGTTAGATT-GAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * *
8631176 CGACAC-GTTT-TATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
8631239 AAA
196 AAA
*
8631242 TATCGACACAAACTATA-TAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
8631306 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
8631371 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTT-ATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGG-AA
8631435 AAAA
195 AAAA
*
8631439 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTTATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
8631504 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
8631568 CGACACTTTTTATATATGGATCG--ACTTTATTGATGCACCTTGTTTTTAATTCATTCT-GGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
8631630 AAA
196 AAA
*
8631633 AATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
8631698 ATTGTACCGGTTAGATTAAAAAATTACATATTACA-T-TACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
8631761 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGG-GAA
8631826 AAAA
195 AAAA
8631830 TATCGACACAAACTATATTAGTGTCG--ACATTATTTAGACTTATTCTCTCATAAAACCGGTAT-
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
8631892 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
8631957 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
8632022 AAA
196 AAA
8632025 TATCGACACAAACTATATTA--GTCGACACATTATTTAGACTTATTCTCTCAT-AAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
8632087 ATTGTACCGGTTAGA-TGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
8632151 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
8632216 CAAA
196 -AAA
8632220 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTT-TTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
8632284 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
8632349 CGACACTTTTTATATATGGATCGACAC-TTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGG-GAA
8632413 AAAA
195 AAAA
*
8632417 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
8632446 TGACCCTTAA
Statistics
Matches: 1160, Mismatches: 22, Indels: 42
0.95 0.02 0.03
Matches are distributed among these distances:
192 18 0.02
193 36 0.03
194 322 0.28
195 252 0.22
196 120 0.10
197 233 0.20
198 179 0.15
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (198 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
AAA
Found at i:8632032 original size:392 final size:396
Alignment explanation
Indices: 8631047--8632445 Score: 2458
Period size: 392 Copynumber: 3.6 Consensus size: 396
8631037 TTTAAATTAG
* * *
8631047 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATT
1 TATCGACACAAACTATATTAGTGTCGA-ACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
8631112 ATTGTACCGGTTAGATT-GAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
65 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
8631176 CGACAC-GTTT-TATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
130 CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCTGGGAAA
*
8631239 AAATATCGACACAAACTATA-TAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGT
195 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
8631303 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
260 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
* * *
8631368 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTT-ATTCATTCTGGG
325 GATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGA
8631432 AAAAAAA
390 AAAAAAA
*
8631439 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTTATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGA-ACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
8631504 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
65 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
8631568 CGACACTTTTTATATATGGATCG--ACTTTATTGATGCACCTTGTTTTTAATTCATTCT-GGAAA
130 CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCTGGGAAA
*
8631630 AAAAATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
195 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
*
8631695 ATAATTGTACCGGTTAGATTAAAAAATTACATATTACA-T-TACTTTTGGGTTCGATGATTTTGG
260 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
8631758 GATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGA
325 GATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGA
8631823 AAAAAAA
390 AAAAAAA
8631830 TATCGACACAAACTATATTAGTGTCG-ACATTATTTAGACTTATTCTCTCATAAAACCGGTAT-A
1 TATCGACACAAACTATATTAGTGTCGAACATTATTTAGACTTATTCTCTCATAAAACCGGTATAA
8631893 TTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
66 TTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
*
8631958 GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAAA
131 GACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCTGGGAAAA
8632023 AATATCGACACAAACTATATTA--GTCGACACATTATTTAGACTTATTCTCTCAT-AAACCGGTA
196 AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTA
8632085 TAATTGTACCGGTTAGA-TGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
261 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
8632149 ATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAA
326 ATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAA
*
8632214 AACAAA
391 AAAAAA
8632220 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTT-TTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGA-ACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
8632284 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
65 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
8632349 CGACACTTTTTATATATGGATCGACAC-TTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
130 CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCTGG-GAA
*
8632413 AAAATATCGACACAAACTATATTAGTATCGACA
194 AAAATATCGACACAAACTATATTAGTGTCGACA
8632446 TGACCCTTAA
Statistics
Matches: 966, Mismatches: 24, Indels: 32
0.95 0.02 0.03
Matches are distributed among these distances:
388 74 0.08
389 93 0.10
390 226 0.23
391 152 0.16
392 364 0.38
393 40 0.04
394 17 0.02
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (396 bp):
TATCGACACAAACTATATTAGTGTCGAACATTATTTAGACTTATTCTCTCATAAAACCGGTATAA
TTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
GACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCATTCTGGGAAAA
AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTA
TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
ATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAA
AAAAAA
Found at i:8632570 original size:19 final size:19
Alignment explanation
Indices: 8632528--8632572 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
8632518 TTCACATAAA
*
8632528 AAAAATATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
8632547 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
8632566 AAAATTA
1 AAAATTA
8632573 ACTCGACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:8634401 original size:33 final size:33
Alignment explanation
Indices: 8634364--8634429 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
8634354 CATCTTAATA
*
8634364 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
8634397 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
8634430 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:8636565 original size:24 final size:24
Alignment explanation
Indices: 8636528--8636580 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
8636518 CCGTTCTATC
8636528 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
8636552 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
8636576 TATTT
1 TATTT
8636581 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:8636770 original size:20 final size:19
Alignment explanation
Indices: 8636724--8636770 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
8636714 TCCGGTATCA
*
8636724 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
8636743 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
8636764 TTTTACC
1 TTTTACC
8636771 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:8638011 original size:14 final size:14
Alignment explanation
Indices: 8637989--8638025 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
8637979 CGCATGCATG
8637989 CTCTAGTTCACTTT
1 CTCTAGTTCACTTT
* *
8638003 CTCTGGTTCATTTT
1 CTCTAGTTCACTTT
8638017 CTCTAGTTC
1 CTCTAGTTC
8638026 GAGCTATTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.11, C:0.27, G:0.11, T:0.51
Consensus pattern (14 bp):
CTCTAGTTCACTTT
Found at i:8645110 original size:16 final size:17
Alignment explanation
Indices: 8645081--8645112 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
8645071 CACTTTTTAA
8645081 TTTTAAACTATAATAAC
1 TTTTAAACTATAATAAC
8645098 TTTTAAA-TATAATAA
1 TTTTAAACTATAATAA
8645113 ATAACGTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTTAAACTATAATAAC
Found at i:8645899 original size:29 final size:29
Alignment explanation
Indices: 8645828--8645904 Score: 113
Period size: 29 Copynumber: 2.7 Consensus size: 29
8645818 CAGTTCCGGG
*
8645828 GGTAGGTCGCCATGCACG-CCGGCGACCT
1 GGTAGGTCGCCATGCACGCCCAGCGACCT
*
8645856 -ATAGGTCGCCATGCACGCCCAGCGACCT
1 GGTAGGTCGCCATGCACGCCCAGCGACCT
*
8645884 GGTAGGTCGCCATGCATGCCC
1 GGTAGGTCGCCATGCACGCCC
8645905 TGACCCCTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
27 16 0.37
28 9 0.21
29 18 0.42
ACGTcount: A:0.17, C:0.36, G:0.31, T:0.16
Consensus pattern (29 bp):
GGTAGGTCGCCATGCACGCCCAGCGACCT
Found at i:8645966 original size:10 final size:10
Alignment explanation
Indices: 8645951--8645996 Score: 56
Period size: 10 Copynumber: 4.3 Consensus size: 10
8645941 CCAACGACCT
8645951 CCATGCACGC
1 CCATGCACGC
8645961 CCATGCACGACC
1 CCATGCACG--C
8645973 TCCATGCACGC
1 -CCATGCACGC
*
8645984 CCAGGCACGC
1 CCATGCACGC
8645994 CCA
1 CCA
8645997 ACGACCTCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
10 21 0.66
11 1 0.03
12 1 0.03
13 9 0.28
ACGTcount: A:0.22, C:0.50, G:0.20, T:0.09
Consensus pattern (10 bp):
CCATGCACGC
Found at i:8645971 original size:23 final size:23
Alignment explanation
Indices: 8645944--8645992 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
8645934 CATGAGCCCA
*
8645944 ACGACCTCCATGCACGCCCATGC
1 ACGACCTCCATGCACGCCCAGGC
8645967 ACGACCTCCATGCACGCCCAGGC
1 ACGACCTCCATGCACGCCCAGGC
8645990 ACG
1 ACG
8645993 CCCAACGACC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.22, C:0.47, G:0.20, T:0.10
Consensus pattern (23 bp):
ACGACCTCCATGCACGCCCAGGC
Found at i:8645979 original size:13 final size:13
Alignment explanation
Indices: 8645944--8645982 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
8645934 CATGAGCCCA
8645944 ACGACCTCCATGC
1 ACGACCTCCATGC
8645957 ACG--C-CCATGC
1 ACGACCTCCATGC
8645967 ACGACCTCCATGC
1 ACGACCTCCATGC
8645980 ACG
1 ACG
8645983 CCCAGGCACG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
10 9 0.39
11 1 0.04
12 1 0.04
13 12 0.52
ACGTcount: A:0.23, C:0.46, G:0.18, T:0.13
Consensus pattern (13 bp):
ACGACCTCCATGC
Done.