Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008681.1 Hibiscus syriacus cultivar Beakdansim tig00111703_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: 76252
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:10951 original size:23 final size:23
Alignment explanation
Indices: 10924--10969 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
10914 CTAATTTTTA
10924 TTTCATTTTAGTA-CATTTTAGTT
1 TTTCATTTTAGTACCA-TTTAGTT
10947 TTTCATTTTAGTACCATTTAGTT
1 TTTCATTTTAGTACCATTTAGTT
10970 AAAAATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.22, C:0.11, G:0.09, T:0.59
Consensus pattern (23 bp):
TTTCATTTTAGTACCATTTAGTT
Found at i:14144 original size:18 final size:19
Alignment explanation
Indices: 14110--14149 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
14100 TAAATTTAAG
14110 ATAAAATTGATTGAAT-GT
1 ATAAAATTGATTGAATGGT
14128 ATAAATATTGATT-AATGGT
1 ATAAA-ATTGATTGAATGGT
14147 ATA
1 ATA
14150 GTTTATCCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (19 bp):
ATAAAATTGATTGAATGGT
Found at i:20841 original size:15 final size:16
Alignment explanation
Indices: 20809--20841 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
20799 AAAATCTTTC
20809 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
20825 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
20840 TT
1 TT
20842 CTGCCACGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:20864 original size:22 final size:22
Alignment explanation
Indices: 20839--20888 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
20829 CCGTCTGGAT
20839 TTTCTGCCACGATTTGAATATC
1 TTTCTGCCACGATTTGAATATC
20861 TTTCTGCCACGATTTGAATATC
1 TTTCTGCCACGATTTGAATATC
20883 TTTCTG
1 TTTCTG
20889 AAGTTCTTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.44
Consensus pattern (22 bp):
TTTCTGCCACGATTTGAATATC
Found at i:21635 original size:16 final size:16
Alignment explanation
Indices: 21611--21644 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
21601 ATCGCCGACC
*
21611 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
21627 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
21643 CG
1 CG
21645 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:27960 original size:2 final size:2
Alignment explanation
Indices: 27953--27992 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
27943 ATATCTACTC
27953 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
27993 GTGGGTTTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28085 original size:2 final size:2
Alignment explanation
Indices: 28078--28102 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28068 AAAGACTGAG
28078 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 A
28103 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28107 original size:2 final size:2
Alignment explanation
Indices: 28102--28139 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
28092 ATATATATAT
28102 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
28140 GTTAGGATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:33041 original size:2 final size:2
Alignment explanation
Indices: 33034--33073 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
33024 CAGACAAAGA
33034 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
33074 TAAAAAGCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33341 original size:27 final size:26
Alignment explanation
Indices: 33301--33351 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
33291 TTTTTCAATT
* * *
33301 TTTTAATAATAAAAATATTATTTTTAA
1 TTTTAAAAAGAAAAA-ATAATTTTTAA
33328 TTTTAAAAAGAAAAAATAATTTTT
1 TTTTAAAAAGAAAAAATAATTTTT
33352 TAAAAAAACC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 8 0.38
27 13 0.62
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (26 bp):
TTTTAAAAAGAAAAAATAATTTTTAA
Found at i:34307 original size:43 final size:43
Alignment explanation
Indices: 34204--34292 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
34194 TGCGTTCCAA
34204 GAAGAAAAATATATAAAAGATAGAAAATGGATAAAATCAAATG
1 GAAGAAAAATATATAAAAGATAGAAAATGGATAAAATCAAATG
34247 GAAGAAAAATATATAAAAGATAGAAAATGGATAAAATCAAATG
1 GAAGAAAAATATATAAAAGATAGAAAATGGATAAAATCAAATG
34290 GAA
1 GAA
34293 AAGGTTAACT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.63, C:0.02, G:0.17, T:0.18
Consensus pattern (43 bp):
GAAGAAAAATATATAAAAGATAGAAAATGGATAAAATCAAATG
Found at i:39332 original size:2 final size:2
Alignment explanation
Indices: 39327--39351 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39317 TGAACAAATG
39327 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
39352 TTATTATGCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40026 original size:122 final size:120
Alignment explanation
Indices: 39899--40148 Score: 324
Period size: 123 Copynumber: 2.1 Consensus size: 120
39889 TAGGAATATA
* * * * *
39899 TAAAATATATTAAAATAATATGAATAT-ATATATATTTTTTAAAATATATTAACTTAAAAATAAA
1 TAAAATATATTAAAATAATACGAATATAAAAAAAATATTTTAAAATATATTAACTTAAAAATAAA
* *
39963 AATTGTATAAAAAATATATATTTT-TATACGAATTTATATATTTTAAAATATATTAACT
66 AA-T-TATAAAAAATATATATTTTCAATACGAA--TATATATTTTAAAATATATTAACC
* ** * *
40021 TAAAATATTTTATTATTATACGAATATAAAAAAAATATTTTAAAATATATTAACTTAAAAATACA
1 TAAAATATATTAAAATAATACGAATATAAAAAAAATATTTTAAAATATATTAACTTAAAAATAAA
* *
40086 AATTATATAAAATATATATTTTCAATACGAATATATATTTTTAAATATATTAACC
66 AATTATAAAAAATATATATTTTCAATACGAATATATATTTTAAAATATATTAACC
40141 TAAAATAT
1 TAAAATAT
40149 TTTATTATTA
Statistics
Matches: 112, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
120 30 0.27
121 18 0.16
122 30 0.27
123 34 0.30
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (120 bp):
TAAAATATATTAAAATAATACGAATATAAAAAAAATATTTTAAAATATATTAACTTAAAAATAAA
AATTATAAAAAATATATATTTTCAATACGAATATATATTTTAAAATATATTAACC
Found at i:40089 original size:123 final size:120
Alignment explanation
Indices: 39935--40321 Score: 389
Period size: 117 Copynumber: 3.2 Consensus size: 120
39925 TATATATATT
*
39935 TTTTAAAATATATTAACTTAAAAATAAAAATTGTATAAAAAATATATATTTT-TATACGAATTTA
1 TTTTAAAATATATTAACTTAAAAATAAAAA-T-TATAAAAAATATATATTTTCAATACGAA--TA
*
39999 TATATTTTAAAATATATTAACTTAAAATATTTTATTATTATACGAATATAAAAAAAATA
62 TATATTTTAAAATATATTAACCTAAAATATTTTATTATTATACGAATATAAAAAAAATA
* *
40058 TTTTAAAATATATTAACTTAAAAATACAAATTATATAAAATATATATTTTCAATACGAATATATA
1 TTTTAAAATATATTAACTTAAAAATAAAAATTATAAAAAATATATATTTTCAATACGAATATATA
* * * *
40123 TTTTTAAATATATTAACCTAAAATATTTTATTATTATACAAATGTAATACATATATATA
66 TTTTAAAATATATTAACCTAAAATATTTTATTATTATACGAATATAA-A-A-A-AAATA
* *** * * *
40182 TATTT-AAATATATTAAATT-AAAATATTTTATTATTATACA-A-ATA---T-AATACGAATATA
1 T-TTTAAAATATATTAACTTAAAAATA-AAAATTATAAAAAATATATATTTTCAATACGAATATA
* ** * *
40239 T-TTTTAAAATATATTAACTTAAAATATTTTATTATTATAAAAATATAATATTAATATATT
64 TATTTTAAAATATATTAACCTAAAATATTTTATTATTATACGAATATAA-A--AA-AAATA
*
40299 TTTTAAAATATATTAACGTAAAA
1 TTTTAAAATATATTAACTTAAAA
40322 TATTTTATTA
Statistics
Matches: 230, Mismatches: 24, Indels: 25
0.82 0.09 0.09
Matches are distributed among these distances:
116 3 0.01
117 64 0.28
118 17 0.07
119 1 0.00
120 49 0.21
121 19 0.08
122 12 0.05
123 37 0.16
124 25 0.11
125 3 0.01
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (120 bp):
TTTTAAAATATATTAACTTAAAAATAAAAATTATAAAAAATATATATTTTCAATACGAATATATA
TTTTAAAATATATTAACCTAAAATATTTTATTATTATACGAATATAAAAAAAATA
Found at i:40179 original size:59 final size:58
Alignment explanation
Indices: 39997--40382 Score: 422
Period size: 59 Copynumber: 6.5 Consensus size: 58
39987 TATACGAATT
* *
39997 TATATATTTTAAAATATATTAACTTAAAATATTTTATTATTATACGAATATAA-A-AA
1 TATATATTTTTAAATATATTAACTTAAAATATTTTATTATTATACAAATATAATACAA
* * ** ** * * *
40053 -AAATATTTTAAAATATATTAACTTAAAAATACAAATTATATAAAATATATATTTTCAATACGAA
1 TATATATTTTTAAATATATTAACTT-AAAAT--ATTTTAT-TATTATACA-AATAT-AATAC-AA
* *
40117 TATATATTTTTAAATATATTAACCTAAAATATTTTATTATTATACAAATGTAATACATA
1 TATATATTTTTAAATATATTAACTTAAAATATTTTATTATTATACAAATATAATACA-A
* *
40176 TATATATATTTAAATATATTAAATTAAAATATTTTATTATTATACAAATATAATACGAA
1 TATATATTTTTAAATATATTAACTTAAAATATTTTATTATTATACAAATATAATAC-AA
* * *
40235 TATAT-TTTTAAAATATATTAACTTAAAATATTTTATTATTATAAAAATATAATATTAA
1 TATATATTTTTAAATATATTAACTTAAAATATTTTATTATTATACAAATATAATA-CAA
* **
40293 TATAT-TTTTTAAAATATATTAACGTAAAATATTTTATTATTATACAAATATAATATGTA
1 TATATATTTTT-AAATATATTAACTTAAAATATTTTATTATTATACAAATATAATA-CAA
40352 TATATATTTTTTAAAATATATTAACTTAAAA
1 TATATA-TTTTT-AAATATATTAACTTAAAA
40383 ATAAAAATTA
Statistics
Matches: 280, Mismatches: 34, Indels: 27
0.82 0.10 0.08
Matches are distributed among these distances:
55 23 0.08
56 5 0.02
58 62 0.22
59 118 0.42
60 7 0.03
61 31 0.11
62 6 0.02
64 7 0.03
65 21 0.08
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (58 bp):
TATATATTTTTAAATATATTAACTTAAAATATTTTATTATTATACAAATATAATACAA
Found at i:40265 original size:117 final size:116
Alignment explanation
Indices: 39988--40382 Score: 465
Period size: 117 Copynumber: 3.3 Consensus size: 116
39978 ATATATTTTT
*
39988 ATACGAATTTATATATTTTAAAATATATTAACTTAAAATATTTTATTATTATACGAATATAA-AA
1 ATACGAA--TATATATTTTAAAATATATTAACTTAAAATATTTTATTATTATACAAATATAATAA
* ** ** * * *
40052 -AAAATATTTTAAAATATATTAACTTAAAAATACAAATTATATAAAATATATATTTTCA
64 TAATATATTTTAAAATATATTAACTT-AAAAT--ATTTTAT-TATTATACA-AATAT-A
* * *
40110 ATACGAATATATATTTTTAAATATATTAACCTAAAATATTTTATTATTATACAAATGTAATACAT
1 ATACGAATATATATTTTAAAATATATTAACTTAAAATATTTTATTATTATACAAATATAATA-AT
*
40175 ATATATATATTT-AAATATATTAAATTAAAATATTTTATTATTATACAAATATA
65 A-ATATAT-TTTAAAATATATTAACTTAAAATATTTTATTATTATACAAATATA
* *
40228 ATACGAATATAT-TTTTAAAATATATTAACTTAAAATATTTTATTATTATAAAAATATAATATTA
1 ATACGAATATATATTTTAAAATATATTAACTTAAAATATTTTATTATTATACAAATATAATAATA
*
40292 ATATATTTTTTAAAATATATTAACGTAAAATATTTTATTATTATACAAATATA
66 ATATA--TTTTAAAATATATTAACTTAAAATATTTTATTATTATACAAATATA
* *
40345 ATATGTATATATATTTTTTAAAATATATTAACTTAAAA
1 ATACG-A-ATATATATTTTAAAATATATTAACTTAAAA
40383 ATAAAAATTA
Statistics
Matches: 241, Mismatches: 21, Indels: 24
0.84 0.07 0.08
Matches are distributed among these distances:
115 5 0.02
116 5 0.02
117 89 0.37
118 14 0.06
119 9 0.04
120 78 0.32
121 6 0.02
122 8 0.03
123 6 0.02
124 18 0.07
125 3 0.01
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (116 bp):
ATACGAATATATATTTTAAAATATATTAACTTAAAATATTTTATTATTATACAAATATAATAATA
ATATATTTTAAAATATATTAACTTAAAATATTTTATTATTATACAAATATA
Found at i:40393 original size:117 final size:120
Alignment explanation
Indices: 40109--40453 Score: 363
Period size: 117 Copynumber: 2.9 Consensus size: 120
40099 ATATATTTTC
* * * ** * *
40109 AATACGAATATATATTTTTAAATATATTAACCTAAAATATTTTATTATTA-TACAAATGTAATAC
1 AATACGAATATAT-TTTTAAAATATATTAACTTAAAATA-TTAAAAATTAGTA-AAATATTATA-
*
40173 ATAT--ATATATA--TTT-AAATATATTAAATTAAAATATTTTATTATTATACAAATAT
62 ATATGAATATATATTTTTAAAATATATTAACTTAAAATATTTTATTATTATACAAATAT
* **
40227 AATACGAATATATTTTTAAAATATATTAACTTAAAATATTTTATTATTA-TAAAA-A-TATAATA
1 AATACGAATATATTTTTAAAATATATTAACTTAAAATA-TTAAAAATTAGTAAAATATTATAATA
* *
40289 TTAATATAT-TTTTTAAAATATATTAACGTAAAATATTTTATTATTATACAAATAT
65 TGAATATATATTTTTAAAATATATTAACTTAAAATATTTTATTATTATACAAATAT
*
40344 AATATGTATATATATTTTTTAAAATATATTAACTTAAAA-A-TAAAAATTATGTAAAATATTTTT
1 AATACG-A-ATATA-TTTTTAAAATATATTAACTTAAAATATTAAAAATTA-GTAAAATA---TT
*
40407 TTAATATGAATATATATTTTTAAAATATATTAACTTAAAATATTTTA
59 ATAATATGAATATATATTTTTAAAATATATTAACTTAAAATATTTTA
40454 ATATGTTTTA
Statistics
Matches: 198, Mismatches: 13, Indels: 25
0.84 0.06 0.11
Matches are distributed among these distances:
113 4 0.02
114 3 0.02
115 6 0.03
116 6 0.03
117 85 0.43
118 14 0.07
119 11 0.06
120 25 0.13
124 14 0.07
125 30 0.15
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (120 bp):
AATACGAATATATTTTTAAAATATATTAACTTAAAATATTAAAAATTAGTAAAATATTATAATAT
GAATATATATTTTTAAAATATATTAACTTAAAATATTTTATTATTATACAAATAT
Found at i:40401 original size:59 final size:56
Alignment explanation
Indices: 39997--40446 Score: 233
Period size: 59 Copynumber: 7.5 Consensus size: 56
39987 TATACGAATT
* *
39997 TATATATTTTAAAATATATTAACTT-AAAATATTTTATTATTATACGAATATAA-A--AAA
1 TATAT-TTTTAAAATATATTAACTTAAAAATA-ATTATTATTA-A--AATATAATATGTAA
* *
40054 AATA-TTTTAAAATATATTAACTTAAAAATACA-AATTATATAAAATATATATTTTCAATACG-A
1 TATATTTTTAAAATATATTAACTTAAAAATA-ATTATTAT-TAAAATATA-A---T--AT--GTA
40116 A
56 A
* * * * **
40117 TATATATTTTTAAATATATTAACCT-AAAATATTTTATTATTATACAAATGTAATACATATA
1 TATAT-TTTTAAAATATATTAACTTAAAAATA-ATTATTA-T-TA-AAATATAATATGTA-A
* * * *
40178 TATATATTT-AAATATATTAAATT-AAAATATTTTATTATTATACAAATATAATACG-AA
1 TATATTTTTAAAATATATTAACTTAAAAATA-ATTATTA-T-TA-AAATATAATATGTAA
* *
40235 TATATTTTTAAAATATATTAACTTAAAATATTTTATTATTATAAAAATATAATAT-TAA
1 TATATTTTTAAAATATATTAACTTAAAA-A--TAATTATTATTAAAATATAATATGTAA
* *
40293 TATATTTTTTAAAATATATTAACGT-AAAATATTTTATTATTATACAAATATAATATGTATA
1 TATA-TTTTTAAAATATATTAACTTAAAAATA-ATTATTA-T-TA-AAATATAATATGTA-A
** *
40354 TATATTTTTTAAAATATATTAACTTAAAAATAAAAATTATGTAAAATATTTTTTTAATATGAATA
1 TATA-TTTTTAAAATATATTAACTTAAAAATAATTATTAT-TAAAATA------TAATATGTA-A
40419 TATATTTTTAAAATATATTAACTTAAAA
1 TATATTTTTAAAATATATTAACTTAAAA
40447 TATTTTAATA
Statistics
Matches: 319, Mismatches: 34, Indels: 73
0.75 0.08 0.17
Matches are distributed among these distances:
53 6 0.02
54 1 0.00
55 26 0.08
56 14 0.04
57 14 0.04
58 34 0.11
59 81 0.25
60 12 0.04
61 42 0.13
62 7 0.02
63 6 0.02
64 30 0.09
65 35 0.11
66 5 0.02
67 6 0.02
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.45
Consensus pattern (56 bp):
TATATTTTTAAAATATATTAACTTAAAAATAATTATTATTAAAATATAATATGTAA
Found at i:41346 original size:19 final size:20
Alignment explanation
Indices: 41322--41361 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
41312 TGAAAGATTT
*
41322 TAAATTGTTTA-AAATAAAA
1 TAAATTGTTTATAAAGAAAA
*
41341 TAAATTTTTTATAAAGAAAA
1 TAAATTGTTTATAAAGAAAA
41361 T
1 T
41362 TACAAGGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (20 bp):
TAAATTGTTTATAAAGAAAA
Found at i:47678 original size:25 final size:25
Alignment explanation
Indices: 47650--47701 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
47640 AACTGATAGT
*
47650 ACGTTGATAGTTATGATATCCTTAA
1 ACGTTGATAGTTATGATAACCTTAA
47675 ACGTTGATAGTTATGATAACCTTAA
1 ACGTTGATAGTTATGATAACCTTAA
47700 AC
1 AC
47702 TTAGCATCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (25 bp):
ACGTTGATAGTTATGATAACCTTAA
Found at i:49459 original size:14 final size:14
Alignment explanation
Indices: 49440--49523 Score: 53
Period size: 15 Copynumber: 5.7 Consensus size: 14
49430 TAATATGAAT
*
49440 ATATATTTTTTAAA
1 ATATATTATTTAAA
*
49454 ATATATTAACTTAATA
1 ATATATT-ATTTAA-A
* *
49470 ATACAAATTATGTAAA
1 AT--ATATTATTTAAA
*
49486 ATAT-TTTTTTAAA
1 ATATATTATTTAAA
*
49499 ATATATTAACTTAAA
1 ATATATT-ATTTAAA
*
49514 ATATTTTATT
1 ATATATTATT
49524 ATTAATTTAA
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
13 11 0.21
14 12 0.23
15 15 0.29
16 6 0.12
17 4 0.08
18 4 0.08
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (14 bp):
ATATATTATTTAAA
Found at i:49527 original size:21 final size:22
Alignment explanation
Indices: 49499--49548 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
49489 TTTTTTTAAA
49499 ATATATTAACTTAAAATATTTT
1 ATATATTAACTTAAAATATTTT
* * *
49521 AT-TATTAATTTAATATGTTTT
1 ATATATTAACTTAAAATATTTT
49542 ATATATT
1 ATATATT
49549 TATATTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
ATATATTAACTTAAAATATTTT
Found at i:53565 original size:9 final size:9
Alignment explanation
Indices: 53551--53576 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
53541 CTTAAAGTAC
53551 AAAATTTAT
1 AAAATTTAT
53560 AAAATTTAT
1 AAAATTTAT
53569 AAAATTTA
1 AAAATTTA
53577 CGTAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AAAATTTAT
Found at i:63425 original size:197 final size:194
Alignment explanation
Indices: 63059--63453 Score: 627
Period size: 197 Copynumber: 2.0 Consensus size: 194
63049 AAAAAATAAA
*
63059 TAATGTAAATAAATACTTTAATAAAGAAGTAAAAAATAGGGTAAAATACAAAATGTGTACATATA
1 TAATGTAAATAAATACTATAATAAAGAAGTAAAAAATAGGGTAAAATACAAAATGTGTACATATA
*
63124 TATATATATAATATAACATATAAATGAAATAATACTATACTAATAATAAATGTATACGAATGTAT
66 TATATATATAATATAACATATAAATGAAATAATAATATACTAATAATAAA-GTATACGAATGTAT
** *
63189 AAAAAACTAATAATAGTATAAAATATATATAAATATTATAATGTAATATAAAAAGATAATTAAAA
130 AAAAAAAAAATAATAATATAAAATATATATAAATATTATAATGTAATAT-AAAAGATAATTAAAA
63254 C
194 C
63255 TAATGTAAATAAATA-TAATAATAAAGAAGTAAACAAATAGGGTAAAATACAAAATGTGTACATA
1 TAATGTAAATAAATACT-ATAATAAAGAAGTAAA-AAATAGGGTAAAATACAAAATGTGTAC--A
*
63319 TATACATATATATATAATATAACATATAAGTGAAATAATAATATACTAATAATAAA-TATACGAA
62 TAT--ATATATATATAATATAACATATAAATGAAATAATAATATACTAATAATAAAGTATACGAA
*
63383 TGTGTAAAAAAAAAATAATAATAT-AAA-ATATATAAATATTATAATGTAATATAAAAGATAATT
125 TGTATAAAAAAAAAATAATAATATAAAATATATATAAATATTATAATGTAATATAAAAGATAATT
63446 AAAAC
190 AAAAC
63451 TAA
1 TAA
63454 AATCCCGAGA
Statistics
Matches: 186, Mismatches: 7, Indels: 12
0.91 0.03 0.06
Matches are distributed among these distances:
195 1 0.01
196 49 0.26
197 52 0.28
198 3 0.02
199 32 0.17
201 49 0.26
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.30
Consensus pattern (194 bp):
TAATGTAAATAAATACTATAATAAAGAAGTAAAAAATAGGGTAAAATACAAAATGTGTACATATA
TATATATATAATATAACATATAAATGAAATAATAATATACTAATAATAAAGTATACGAATGTATA
AAAAAAAAATAATAATATAAAATATATATAAATATTATAATGTAATATAAAAGATAATTAAAAC
Found at i:64443 original size:3 final size:3
Alignment explanation
Indices: 64431--64467 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
64421 GTAAAGAGAA
64431 AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
64468 CAAATAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:65134 original size:105 final size:105
Alignment explanation
Indices: 64934--65707 Score: 1363
Period size: 105 Copynumber: 7.4 Consensus size: 105
64924 ATATTGTTCC
* ** * *
64934 GAGTCCAATATCCTCCGCCGTGAAGTCGAAATTGGCTCTGAAATTGAG--ATATTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
64997 CAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
65037 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
65102 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
65142 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGAGAAATGTTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
65207 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
65247 GAGTCAAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGGAATTGAGAAATGTTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
65312 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
65352 GAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
65417 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65457 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
65522 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65562 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
65627 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65667 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
65708 GTAAAACATA
Statistics
Matches: 646, Mismatches: 23, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
103 44 0.07
105 602 0.93
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:66443 original size:1 final size:1
Alignment explanation
Indices: 66439--66471 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
66429 TTTTTCTCCC
66439 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
66472 CAACTTAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.