Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000300.1 Hibiscus syriacus cultivar Beakdansim tig00000551_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: 67279
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:15331 original size:21 final size:21
Alignment explanation
Indices: 15302--15341 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
15292 CACCTTAGAC
*
15302 TCCACCTGAGTGAGCTTGGTA
1 TCCACCTGAGCGAGCTTGGTA
* *
15323 TCCATCTGAGCGATCTTGG
1 TCCACCTGAGCGAGCTTGG
15342 AGTTAATTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.25, G:0.28, T:0.30
Consensus pattern (21 bp):
TCCACCTGAGCGAGCTTGGTA
Found at i:16646 original size:23 final size:23
Alignment explanation
Indices: 16616--16665 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
16606 AAAACAATTC
16616 GTGCTACTACTGGTTTTCCTTTA
1 GTGCTACTACTGGTTTTCCTTTA
16639 GTGCTACTACTGGTTTTCCTTTA
1 GTGCTACTACTGGTTTTCCTTTA
16662 GTGC
1 GTGC
16666 CATGGTAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (23 bp):
GTGCTACTACTGGTTTTCCTTTA
Found at i:17778 original size:12 final size:12
Alignment explanation
Indices: 17763--17808 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
17753 CGGTTTTTTT
*
17763 ACCGGATAAAAA
1 ACCGGTTAAAAA
17775 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
17790 ACCGGTTAAAAA
1 ACCGGTTAAAAA
17802 ACCGGTT
1 ACCGGTT
17809 TTTATCCGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:17790 original size:15 final size:13
Alignment explanation
Indices: 17769--17809 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
17759 TTTTACCGGA
17769 TAAAAAACCGGTT
1 TAAAAAACCGGTT
17782 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
17796 TAAAAAACCGGTT
1 TAAAAAACCGGTT
17809 T
1 T
17810 TTATCCGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:20120 original size:21 final size:21
Alignment explanation
Indices: 20096--20135 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
20086 TTTATTTTAT
20096 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
20117 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
20136 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:20183 original size:33 final size:33
Alignment explanation
Indices: 20130--20228 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
20120 TTTGTTTCAA
20130 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
20162 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
20195 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
20228 T
1 T
20229 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:20257 original size:13 final size:13
Alignment explanation
Indices: 20214--20268 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
20204 TTGGAAGTAT
20214 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
20227 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
20241 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
20254 TTAAGTATTTGAA
1 TTAAGTATTTCAA
20267 TT
1 TT
20269 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:20708 original size:17 final size:18
Alignment explanation
Indices: 20683--20716 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
20673 GTTTTTTTAT
20683 AACCGGTTTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
20701 AACC-GTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
20717 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:20716 original size:15 final size:16
Alignment explanation
Indices: 20666--20716 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
20656 CTGGAATATT
*
20666 AAAATCGGTTTTTTT-
1 AAAACCGGTTTTTTTA
*
20681 ATAACCGGTTTTTTTAAA
1 AAAACCGGTTTTTTT--A
20699 AAAACC-GTTTTTTTA
1 AAAACCGGTTTTTTTA
20714 AAA
1 AAA
20717 CCGAAACCGG
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 17 0.57
17 8 0.27
18 5 0.17
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (16 bp):
AAAACCGGTTTTTTTA
Found at i:20836 original size:15 final size:17
Alignment explanation
Indices: 20810--20841 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
20800 TTCTATGGGA
20810 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
20826 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
20842 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:42763 original size:15 final size:16
Alignment explanation
Indices: 42745--42775 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42735 TTGAATATAA
42745 TTATAAA-ATAAAAAT
1 TTATAAATATAAAAAT
42760 TTATAAATATAAAAAT
1 TTATAAATATAAAAAT
42776 ATATTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TTATAAATATAAAAAT
Found at i:44052 original size:19 final size:18
Alignment explanation
Indices: 44024--44062 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
44014 AAGATATAAA
44024 TTTTAAAAACTTAAAAAT
1 TTTTAAAAACTTAAAAAT
*
44042 TTTTAAAAAACTTTAAAAT
1 TTTT-AAAAACTTAAAAAT
44061 TT
1 TT
44063 AATAGGTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTTAAAAACTTAAAAAT
Found at i:45339 original size:10 final size:10
Alignment explanation
Indices: 45315--45350 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
45305 ATCAAAAGAA
45315 AAAGAAAAAG
1 AAAGAAAAAG
*
45325 -GAGAAAAAG
1 AAAGAAAAAG
45334 AAAGAAAAAG
1 AAAGAAAAAG
45344 AAAGAAA
1 AAAGAAA
45351 GATAATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:52039 original size:20 final size:20
Alignment explanation
Indices: 52014--52051 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
52004 TTTTGGTGCA
*
52014 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
*
52034 GAGGGAACCGATTCCCCC
1 GAGGGAACCGATACCCCC
52052 TTTGAAGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:56086 original size:16 final size:15
Alignment explanation
Indices: 56060--56089 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
56050 TCGTGTGACC
56060 GGTCATCCCGGGATG
1 GGTCATCCCGGGATG
56075 GGTCAGTCCCGGGAT
1 GGTCA-TCCCGGGAT
56090 ATCGGCCGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.27, G:0.40, T:0.20
Consensus pattern (15 bp):
GGTCATCCCGGGATG
Found at i:56272 original size:18 final size:18
Alignment explanation
Indices: 56249--56289 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
56239 ATCAAAAAAC
*
56249 AATAAAGAAAAATAAGTA
1 AATAAAGAAAAATAAATA
* *
56267 AATAAATAAAATTAAATA
1 AATAAAGAAAAATAAATA
56285 AATAA
1 AATAA
56290 TAATATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (18 bp):
AATAAAGAAAAATAAATA
Found at i:56282 original size:14 final size:14
Alignment explanation
Indices: 56265--56315 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 14
56255 GAAAAATAAG
56265 TAAATAAATAAAAT
1 TAAATAAATAAAAT
56279 TAAATAAATAATAAT
1 TAAATAAATAA-AAT
*
56294 ATAAA-AAATAATAT
1 -TAAATAAATAAAAT
56308 TAATATAA
1 TAA-ATAA
56316 TATATAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
13 3 0.09
14 14 0.44
15 11 0.34
16 4 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAATAAATAAAAT
Found at i:56283 original size:22 final size:22
Alignment explanation
Indices: 56258--56299 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
56248 CAATAAAGAA
*
56258 AAATAAGTAAATAA-ATAAAATT
1 AAATAAAT-AATAATATAAAATT
56280 AAATAAATAATAATATAAAA
1 AAATAAATAATAATATAAAA
56300 AATAATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (22 bp):
AAATAAATAATAATATAAAATT
Found at i:56335 original size:18 final size:18
Alignment explanation
Indices: 56279--56336 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
56269 TAAATAAAAT
56279 TAAATAAATAATAATATAA
1 TAAAT-AATAATAATATAA
* *
56298 AAAATAATATTAATATAA
1 TAAATAATAATAATATAA
* *
56316 TATATAATAATAATACAA
1 TAAATAATAATAATATAA
56334 TAA
1 TAA
56337 TTTTTTTTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 28 0.88
19 4 0.12
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAATAATAATAATATAA
Found at i:56498 original size:36 final size:36
Alignment explanation
Indices: 56408--56728 Score: 187
Period size: 36 Copynumber: 9.2 Consensus size: 36
56398 ATATAATATA
56408 TTTTCAAAATATTTT-AAAACTATATATTATATATTT
1 TTTTCAAAATATTTTAAAAACTATATA-TATATATTT
56444 TTTT-AAAATATTTT-AAAACTATATATATATATTT
1 TTTTCAAAATATTTTAAAAACTATATATATATATTT
* *
56478 TTTTCAAAATGTTTTAAAAACTATAT-TATATATAT
1 TTTTCAAAATATTTTAAAAACTATATATATATATTT
* * * * * * * * *
56513 ATAT--ATATA-TATATATA-TATATAT-TCAAAATG
1 TTTTCAAAATATTTTAAAAACTATATATAT-ATATTT
* * *
56545 TTTT-AAAA-A--CT--ATA-TAT-TATATATATAT
1 TTTTCAAAATATTTTAAAAACTATATATATATATTT
* * * *
56573 -TTTCAAAATGTTTTAAAAACTCTATAT-TGTATATA
1 TTTTCAAAATATTTTAAAAACTATATATATATAT-TT
* * * *
56608 TTTTCATAATTTTTTAAAAACTATATATTATATACATA
1 TTTTCAAAATATTTTAAAAACTATATA-TATATA-TTT
* **
56646 TTTTCAAAATGTTTTAAAAACTATATAT-TATATAAG
1 TTTTCAAAATATTTTAAAAACTATATATATATAT-TT
*
56682 TTTTCAAAAATATTTTAAAAACTATATATTATATATAT
1 TTTTC-AAAATATTTTAAAAACTATATA-TATATATTT
*
56720 ATTTCAAAA
1 TTTTCAAAA
56729 ATCATTTGCA
Statistics
Matches: 221, Mismatches: 41, Indels: 45
0.72 0.13 0.15
Matches are distributed among these distances:
27 3 0.01
28 9 0.04
29 7 0.03
31 8 0.04
32 11 0.05
33 7 0.03
34 19 0.09
35 43 0.19
36 46 0.21
37 27 0.12
38 36 0.16
39 5 0.02
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.48
Consensus pattern (36 bp):
TTTTCAAAATATTTTAAAAACTATATATATATATTT
Found at i:56511 original size:2 final size:2
Alignment explanation
Indices: 56499--56536 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
56489 TTTTAAAAAC
56499 TA TA T- TA TA TA TA 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 TA TA TA TA TA TA TA T
56537 TCAAAATGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:56549 original size:56 final size:53
Alignment explanation
Indices: 56463--56572 Score: 175
Period size: 56 Copynumber: 2.0 Consensus size: 53
56453 ATTTTAAAAC
* *
56463 TATATATATATATTTTTTTCAAAATGTTTTAAAAACTATATTATATATATATATA
1 TATATATATATATTATATTCAAAATGTTTTAAAAACTATA-TAT-TATATATATA
56518 TATATATATATATATATATTCAAAATGTTTTAAAAACTATATATTATATATATA
1 TATATATATATAT-TATATTCAAAATGTTTTAAAAACTATATATTATATATATA
56572 T
1 T
56573 TTTCAAAATG
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
54 11 0.21
55 16 0.31
56 25 0.48
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (53 bp):
TATATATATATATTATATTCAAAATGTTTTAAAAACTATATATTATATATATA
Found at i:56584 original size:94 final size:91
Alignment explanation
Indices: 56428--56608 Score: 256
Period size: 94 Copynumber: 1.9 Consensus size: 91
56418 ATTTTAAAAC
* * * *
56428 TATATATTATATATTTTTTTAAAATATTTTAAAACTATATATATATATTTTTTTCAAAATGTTTT
1 TATATATTATATATATATTCAAAATATTTTAAAACTATATATATATATTATTTTCAAAATGTTTT
56493 AAAAA-CTATATTATATATATATATA
66 AAAAACCTATATTATATATATATATA
*
56518 TATATATATATATATATATTCAAAATGTTTTAAAAACTATATATTATATATATATTTTCAAAATG
1 TATATAT-TATATATATATTCAAAATATTTT-AAAACTATATA-TATATAT-TATTTTCAAAATG
*
56583 TTTTAAAAACTCTATATTGTATATAT
62 TTTTAAAAAC-CTATATTATATATAT
56609 TTTCATAATT
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
90 7 0.09
91 19 0.24
92 11 0.14
93 7 0.09
94 21 0.27
96 14 0.18
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (91 bp):
TATATATTATATATATATTCAAAATATTTTAAAACTATATATATATATTATTTTCAAAATGTTTT
AAAAACCTATATTATATATATATATA
Found at i:56623 original size:74 final size:74
Alignment explanation
Indices: 56518--56728 Score: 318
Period size: 74 Copynumber: 2.8 Consensus size: 74
56508 TATATATATA
* *
56518 TATATATATATATATATATTCAAAATGTTTTAAAAACTATATATTATATATATATTTTCAAAATG
1 TATATAT-TATATATATTTTCAAAATATTTTAAAAACTATATATTATATATATATTTTCAAAATG
56583 TTTTAAAAAC
65 TTTTAAAAAC
* * * * *
56593 TCTATATTGTATATATTTTCATAATTTTTTAAAAACTATATATTATATACATATTTTCAAAATGT
1 TATATATTATATATATTTTCAAAATATTTTAAAAACTATATATTATATATATATTTTCAAAATGT
56658 TTTAAAAAC
66 TTTAAAAAC
56667 TATATATTATATA-AGTTTTCAAAAATATTTTAAAAACTATATATTATATATATA-TTTCAAAA
1 TATATATTATATATA-TTTTC-AAAATATTTTAAAAACTATATATTATATATATATTTTCAAAA
56729 ATCATTTGCA
Statistics
Matches: 123, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
73 1 0.01
74 86 0.70
75 36 0.29
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (74 bp):
TATATATTATATATATTTTCAAAATATTTTAAAAACTATATATTATATATATATTTTCAAAATGT
TTTAAAAAC
Found at i:56649 original size:27 final size:27
Alignment explanation
Indices: 56602--56654 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
56592 CTCTATATTG
* *
56602 TATATATTTTCATAATTTTTTAAAAAC
1 TATATATTATCATAATATTTTAAAAAC
*
56629 TATATATTAT-ATACATATTTTCAAAA
1 TATATATTATCATA-ATATTTTAAAAA
56655 TGTTTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 3 0.14
27 19 0.86
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (27 bp):
TATATATTATCATAATATTTTAAAAAC
Found at i:56747 original size:38 final size:37
Alignment explanation
Indices: 56516--56728 Score: 297
Period size: 38 Copynumber: 5.7 Consensus size: 37
56506 TATATATATA
56516 TATATATATATATATATATATTCAAAATGTTTTAAAAAC
1 TATATAT-TATATATATAT-TTCAAAATGTTTTAAAAAC
56555 TATATATTATATATATATTTTCAAAATGTTTTAAAAAC
1 TATATATTATATATATA-TTTCAAAATGTTTTAAAAAC
* * * *
56593 TCTATATTGTATATAT-TTTCATAATTTTTTAAAAAC
1 TATATATTATATATATATTTCAAAATGTTTTAAAAAC
*
56629 TATATATTATATACATATTTTCAAAATGTTTTAAAAAC
1 TATATATTATATATATA-TTTCAAAATGTTTTAAAAAC
*
56667 TATATATTATATA-AGT-TTTCAAAAATATTTTAAAAAC
1 TATATATTATATATA-TATTTC-AAAATGTTTTAAAAAC
56704 TATATATTATATATATATTTCAAAA
1 TATATATTATATATATATTTCAAAA
56729 ATCATTTGCA
Statistics
Matches: 157, Mismatches: 10, Indels: 16
0.86 0.05 0.09
Matches are distributed among these distances:
36 35 0.22
37 34 0.22
38 80 0.51
39 8 0.05
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (37 bp):
TATATATTATATATATATTTCAAAATGTTTTAAAAAC
Found at i:57584 original size:31 final size:31
Alignment explanation
Indices: 57535--57602 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
57525 AACGTTACAA
* * *
57535 ACAAACGTTACCATTTTAAGTATCTAATGTT
1 ACAAACATTACCATTTTAAATATCTAATATT
* *
57566 ATAAACATTATCATTTTAAATATCTAATATT
1 ACAAACATTACCATTTTAAATATCTAATATT
57597 ACAAAC
1 ACAAAC
57603 GTTGTTTAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.38
Consensus pattern (31 bp):
ACAAACATTACCATTTTAAATATCTAATATT
Found at i:58413 original size:10 final size:10
Alignment explanation
Indices: 58398--58471 Score: 52
Period size: 10 Copynumber: 7.6 Consensus size: 10
58388 ATTTAATAAT
58398 TAAACGAACA
1 TAAACGAACA
58408 TAAACGAAC-
1 TAAACGAACA
58417 ---ACGAACA
1 TAAACGAACA
*
58424 TAAATGAACA
1 TAAACGAACA
*
58434 CAAAC-ATA-A
1 TAAACGA-ACA
58443 TTGAACACGAACA
1 -T-AA-ACGAACA
58456 TAAACGAACA
1 TAAACGAACA
58466 TAAACG
1 TAAACG
58472 TTGGAGATCC
Statistics
Matches: 50, Mismatches: 4, Indels: 20
0.68 0.05 0.27
Matches are distributed among these distances:
6 6 0.12
9 2 0.04
10 32 0.64
11 4 0.08
12 4 0.08
13 2 0.04
ACGTcount: A:0.57, C:0.20, G:0.11, T:0.12
Consensus pattern (10 bp):
TAAACGAACA
Found at i:58422 original size:16 final size:16
Alignment explanation
Indices: 58401--58465 Score: 94
Period size: 16 Copynumber: 4.1 Consensus size: 16
58391 TAATAATTAA
58401 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
58417 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
* **
58433 ACAAACATAATTGAAC
1 ACGAACATAAACGAAC
58449 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
58465 A
1 A
58466 TAAACGTTGG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.57, C:0.22, G:0.11, T:0.11
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:59563 original size:14 final size:14
Alignment explanation
Indices: 59544--59575 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
59534 GATTGGGATA
59544 AACATAAATGAACG
1 AACATAAATGAACG
59558 AACATAAATGAACG
1 AACATAAATGAACG
59572 AACA
1 AACA
59576 AAAACGAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.16, G:0.12, T:0.12
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:59677 original size:40 final size:40
Alignment explanation
Indices: 59627--59728 Score: 195
Period size: 40 Copynumber: 2.5 Consensus size: 40
59617 ATGAGACCTA
*
59627 TGTTCGTGTTCGTTCATTTAATTAAACGAACACAAAATCT
1 TGTTCATGTTCGTTCATTTAATTAAACGAACACAAAATCT
59667 TGTTCATGTTCGTTCATTTAATTAAACGAACACAAAATCT
1 TGTTCATGTTCGTTCATTTAATTAAACGAACACAAAATCT
59707 TGTTCATGTTCGTTCATTTAAT
1 TGTTCATGTTCGTTCATTTAAT
59729 AAATAAACGC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (40 bp):
TGTTCATGTTCGTTCATTTAATTAAACGAACACAAAATCT
Found at i:59943 original size:14 final size:14
Alignment explanation
Indices: 59924--59951 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
59914 AACTATACCC
59924 TTATTCTCAAATAG
1 TTATTCTCAAATAG
59938 TTATTCTCAAATAG
1 TTATTCTCAAATAG
59952 GTGCTTAAAA
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:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
TTATTCTCAAATAG
Found at i:60255 original size:48 final size:48
Alignment explanation
Indices: 60203--60298 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
60193 AATCATACAT
60203 TAAGATATGCAAACGTATACTAAGTATTTAAATTTGAAAATTAAGAGA
1 TAAGATATGCAAACGTATACTAAGTATTTAAATTTGAAAATTAAGAGA
*
60251 TAAGATATGCGAACGTATACTAAGTATTTAAATTTGAAAATTAAGAGA
1 TAAGATATGCAAACGTATACTAAGTATTTAAATTTGAAAATTAAGAGA
60299 GATAAGAGAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (48 bp):
TAAGATATGCAAACGTATACTAAGTATTTAAATTTGAAAATTAAGAGA
Found at i:61934 original size:31 final size:32
Alignment explanation
Indices: 61893--61953 Score: 106
Period size: 31 Copynumber: 1.9 Consensus size: 32
61883 TAGGATAAAC
61893 TACACATTTAATACCTAAACTATCAATTTTAA
1 TACACATTTAATACCTAAACTATCAATTTTAA
*
61925 TACAC-TTTAATACCTAAACTTTCAATTTT
1 TACACATTTAATACCTAAACTATCAATTTT
61954 TTAAAGGCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (32 bp):
TACACATTTAATACCTAAACTATCAATTTTAA
Found at i:65062 original size:16 final size:16
Alignment explanation
Indices: 65041--65074 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
65031 CCATTACACG
* *
65041 TTCAAATTATTTTAAA
1 TTCAAATCAATTTAAA
65057 TTCAAATCAATTTAAA
1 TTCAAATCAATTTAAA
65073 TT
1 TT
65075 GGATTATTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (16 bp):
TTCAAATCAATTTAAA
Done.