Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000433.1 Hibiscus syriacus cultivar Beakdansim tig00000795_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: 46893
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:2320 original size:46 final size:47
Alignment explanation
Indices: 2226--2321 Score: 131
Period size: 46 Copynumber: 2.1 Consensus size: 47
2216 CGACTCGGGT
* * * * *
2226 TTTTTTTGTTTTTGATGGATTGTTTAATGATTGGTAATGGCTACTGG
1 TTTTTTTGTTCTTGATGGAGTGTTTAATGATTGGTAATGACCAATGG
*
2273 TTTTTTTGTTCTTGATGGAGTG-TTAATGGTTGGTAATGACCAATGG
1 TTTTTTTGTTCTTGATGGAGTGTTTAATGATTGGTAATGACCAATGG
2319 TTT
1 TTT
2322 CTCCTCTGTC
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
46 23 0.53
47 20 0.47
ACGTcount: A:0.18, C:0.05, G:0.26, T:0.51
Consensus pattern (47 bp):
TTTTTTTGTTCTTGATGGAGTGTTTAATGATTGGTAATGACCAATGG
Found at i:4621 original size:31 final size:31
Alignment explanation
Indices: 4583--4643 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
4573 GAACCAATCT
*
4583 CGTTGGTAAGTGT-TTAATTATTTAAATAACC
1 CGTTGGTAAGT-TATTAATTATATAAATAACC
4614 CGTTGGTAAGTTATTAATTATATAAATAAC
1 CGTTGGTAAGTTATTAATTATATAAATAAC
4644 ATGCATTCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 1 0.04
31 27 0.96
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (31 bp):
CGTTGGTAAGTTATTAATTATATAAATAACC
Found at i:5040 original size:15 final size:15
Alignment explanation
Indices: 5020--5055 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
5010 TTTTGAGTAT
5020 ATTACCGGGAATGTC
1 ATTACCGGGAATGTC
5035 ATTACCGGGAATGTC
1 ATTACCGGGAATGTC
5050 ATTACC
1 ATTACC
5056 TCTTTTTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (15 bp):
ATTACCGGGAATGTC
Found at i:5528 original size:18 final size:16
Alignment explanation
Indices: 5482--5531 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
5472 CAAATACAAC
5482 ATTCCC-AGTAATCTT
1 ATTCCCTAGTAATCTT
*
5497 ATTCCCTGGTAATCTT
1 ATTCCCTAGTAATCTT
5513 ATTCTCACTAGTAATCTT
1 ATTC-C-CTAGTAATCTT
5531 A
1 A
5532 CATTCCGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 6 0.20
16 12 0.40
17 1 0.03
18 11 0.37
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.42
Consensus pattern (16 bp):
ATTCCCTAGTAATCTT
Found at i:10405 original size:22 final size:22
Alignment explanation
Indices: 10380--10443 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
10370 ATATTGTATG
10380 CATGTAGTGCATATGAGGTTAA
1 CATGTAGTGCATATGAGGTTAA
10402 CA--T-GTGCATA--A--TAT-A
1 CATGTAGTGCATATGAGGT-TAA
10417 CATGTAGTGCATATGAGGTTAA
1 CATGTAGTGCATATGAGGTTAA
10439 CATGT
1 CATGT
10444 GCATAGTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 18
0.65 0.00 0.35
Matches are distributed among these distances:
15 4 0.12
16 1 0.03
17 2 0.06
18 7 0.21
19 7 0.21
20 2 0.06
21 1 0.03
22 9 0.27
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (22 bp):
CATGTAGTGCATATGAGGTTAA
Found at i:10410 original size:19 final size:19
Alignment explanation
Indices: 10386--10448 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
10376 TATGCATGTA
10386 GTGCATATGAGGTTAACAT
1 GTGCATATGAGGTTAACAT
10405 GTGCATA--A---TATACATGT
1 GTGCATATGAGGTTA-ACA--T
10422 AGTGCATATGAGGTTAACAT
1 -GTGCATATGAGGTTAACAT
10442 GTGCATA
1 GTGCATA
10449 GTATCCATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 18
0.66 0.00 0.34
Matches are distributed among these distances:
14 2 0.06
15 3 0.09
17 2 0.06
18 7 0.20
19 14 0.40
20 2 0.06
22 3 0.09
23 2 0.06
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (19 bp):
GTGCATATGAGGTTAACAT
Found at i:10430 original size:37 final size:37
Alignment explanation
Indices: 10380--10458 Score: 140
Period size: 37 Copynumber: 2.1 Consensus size: 37
10370 ATATTGTATG
10380 CATGTAGTGCATATGAGGTTAACATGTGCATAATATA
1 CATGTAGTGCATATGAGGTTAACATGTGCATAATATA
* *
10417 CATGTAGTGCATATGAGGTTAACATGTGCATAGTATC
1 CATGTAGTGCATATGAGGTTAACATGTGCATAATATA
10454 CATGT
1 CATGT
10459 GTGGGTGAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.33
Consensus pattern (37 bp):
CATGTAGTGCATATGAGGTTAACATGTGCATAATATA
Found at i:11705 original size:19 final size:20
Alignment explanation
Indices: 11636--11710 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
11626 AATTTTGAGC
* *
11636 ATCAGTACTGTTCATACAGT
1 ATCAGTACTATTCATACAAT
** *
11656 ATTGGTACTATTTATACAAT
1 ATCAGTACTATTCATACAAT
* *
11676 ATTAATACTATTCATACAAT
1 ATCAGTACTATTCATACAAT
11696 A-CAGTACTATTCATA
1 ATCAGTACTATTCATA
11711 AAACCATTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
19 12 0.27
20 33 0.73
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (20 bp):
ATCAGTACTATTCATACAAT
Found at i:14437 original size:23 final size:23
Alignment explanation
Indices: 14377--14442 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 23
14367 AAACCAATCC
*
14377 ATATTTATATAAATTAATTTTATAT
1 ATATTTATATAAA-T-ATTTGATAT
*
14402 ATAGTTTCTATAAATATTTGA-AT
1 ATA-TTTATATAAATATTTGATAT
14425 ATATTTATAATAAA-ATTT
1 ATATTTAT-ATAAATATTT
14443 TATAAAACAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
22 8 0.22
23 10 0.28
24 5 0.14
25 4 0.11
26 9 0.25
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (23 bp):
ATATTTATATAAATATTTGATAT
Found at i:14528 original size:20 final size:21
Alignment explanation
Indices: 14505--14546 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
14495 TTTAAACTAA
14505 TTAA-AAATAATTTTAATATT
1 TTAATAAATAATTTTAATATT
* *
14525 TTAATAAATTATTTTATTATT
1 TTAATAAATAATTTTAATATT
14546 T
1 T
14547 AGTCTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAATAAATAATTTTAATATT
Found at i:15276 original size:25 final size:25
Alignment explanation
Indices: 15240--15288 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
15230 ATCTTCAATC
* *
15240 TCTTACATAACACACTCCTTTCATA
1 TCTTACACAACAAACTCCTTTCATA
*
15265 TCTTACACAACAAACTCTTTTCAT
1 TCTTACACAACAAACTCCTTTCAT
15289 CTAACCAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.31, G:0.00, T:0.37
Consensus pattern (25 bp):
TCTTACACAACAAACTCCTTTCATA
Found at i:19960 original size:46 final size:46
Alignment explanation
Indices: 19880--19972 Score: 134
Period size: 46 Copynumber: 2.0 Consensus size: 46
19870 CGACTTGGGT
* *
19880 TTTTTTTGTTTTTGATGGATTGTTTAATGATTGGTAATGGCTACTGG
1 TTTTTTTGTTCTTGATGGA-TGTTTAATGATTGGTAATGGCCACTGG
*
19927 TTTTTTTGTTCTTGATGGA-GTATTAATGGTTGGTAATGGCCACTGG
1 TTTTTTTGTTCTTGATGGATGT-TTAATGATTGGTAATGGCCACTGG
19973 ATTCTCCTCT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
45 2 0.05
46 22 0.52
47 18 0.43
ACGTcount: A:0.17, C:0.06, G:0.27, T:0.49
Consensus pattern (46 bp):
TTTTTTTGTTCTTGATGGATGTTTAATGATTGGTAATGGCCACTGG
Found at i:20451 original size:55 final size:55
Alignment explanation
Indices: 20382--20708 Score: 398
Period size: 55 Copynumber: 6.0 Consensus size: 55
20372 TTCGAATGAT
* *
20382 GGGTCCGCTTCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAGCAAAC
1 GGGTCCGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAAC
* * * * *
20437 GTGTCTGTTCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCTTCAATAAAC
1 GGGTCCGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAAC
*
20492 GGGTCCGCTCCCTATTCGTTCAGGGAGTAT-AGAACTCGAACAATCTTCATA-AAAC
1 GGGTCCGCTCCCTATTCCTTCAGGGAGTATAAG-ACTCGAACAATCTTCA-ACAAAC
* * * *
20547 GGGTCTGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCAATAAAC
1 GGGTCCGCTCCCTATTCCTTCAGGGAGTATAAG-ACTCGAACAATCTTCAACAAAC
* * * *
20602 GGGTCCGCTCCCTATTCGTTCAGGGAGTATAAAACTCGAGCAATCTTCAACGAAC
1 GGGTCCGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAAC
** * *
20657 TTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACAAAC
1 GGGTCCGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAAC
20708 G
1 G
20709 AGTTTGCTTC
Statistics
Matches: 237, Mismatches: 31, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
51 14 0.06
54 3 0.01
55 218 0.92
56 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (55 bp):
GGGTCCGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAAC
Found at i:20648 original size:165 final size:165
Alignment explanation
Indices: 20393--20693 Score: 442
Period size: 165 Copynumber: 1.8 Consensus size: 165
20383 GGTCCGCTTC
* * * * *
20393 CTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAGCAAACGTGTCTGTTCCCTATTCATTC
1 CTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCCGCTCCCTATTCATTC
* * * *
20458 AGGGAGTATAAGACTCGAACAATCTTCAATAAACGGGTCCGCTCCCTATTCGTTCAGGGAGTATA
66 AGGGAGTATAAAACTCGAACAATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATA
20523 GAACTCGAACAATCTTCATAAAACGGGTCTGCTCT
131 GAACTCGAACAATCTTCATAAAACGGGTCTGCTCT
* *
20558 CTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCAATAAACGGGTCCGCTCCCTATTCGTT
1 CTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAAACGGGTCCGCTCCCTATTCATT
* * **
20622 CAGGGAGTATAAAACTCGAGCAATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTAT
65 CAGGGAGTATAAAACTCGAACAATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTAT
*
20687 AGGACTC
130 AGAACTC
20694 AATCTTCAAC
Statistics
Matches: 119, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
164 2 0.02
165 117 0.98
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (165 bp):
CTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCCGCTCCCTATTCATTC
AGGGAGTATAAAACTCGAACAATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATA
GAACTCGAACAATCTTCATAAAACGGGTCTGCTCT
Found at i:22131 original size:24 final size:24
Alignment explanation
Indices: 22099--22145 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
22089 TTTTCATCAT
22099 TTTTTTCTCTTTTTCCCTTTTTTA
1 TTTTTTCTCTTTTTCCCTTTTTTA
22123 TTTTTTCTCTTTTTCCCTTTTTT
1 TTTTTTCTCTTTTTCCCTTTTTT
22146 TAATTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTTTTCTCTTTTTCCCTTTTTTA
Found at i:22169 original size:12 final size:11
Alignment explanation
Indices: 22153--22191 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
22143 TTTTAATTAT
22153 TTTTTTATTTC
1 TTTTTTATTTC
*
22164 TCTTTTTTTTTC
1 T-TTTTTATTTC
22176 TTTTTTCATTTC
1 TTTTTT-ATTTC
22188 TTTT
1 TTTT
22192 CAGGCGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 6 0.25
12 18 0.75
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTATTTC
Found at i:22179 original size:24 final size:25
Alignment explanation
Indices: 22116--22188 Score: 69
Period size: 26 Copynumber: 2.9 Consensus size: 25
22106 TCTTTTTCCC
* * *
22116 TTTTTTATT-TTTTCTCTTTTTCCCT
1 TTTTTTATTATTTTTTC-ATTTCTCT
*
22141 TTTTTTAATTATTTTTTTATTTCTCT
1 TTTTTT-ATTATTTTTTCATTTCTCT
*
22167 TTTTTT-TTCTTTTTTCATTTCT
1 TTTTTTATTATTTTTTCATTTCT
22189 TTTCAGGCGA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
24 14 0.35
25 6 0.15
26 15 0.38
27 5 0.12
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTTTTATTATTTTTTCATTTCTCT
Found at i:31915 original size:45 final size:47
Alignment explanation
Indices: 31847--31944 Score: 128
Period size: 45 Copynumber: 2.1 Consensus size: 47
31837 CGTTATTCAC
* *
31847 AAAAAGAAATCCTAACCATATGATATCTAATTCGCATGC-TTGTTCG
1 AAAAAGAAATCCTAACCACATGATATCTAATTCGCATGCATTATTCG
* * *
31893 AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCATTTATTCG
1 AAAAAGAAATCCTAACCACATGATATCTAATTCGCATGCA-TTATTCG
31940 AAAAA
1 AAAAA
31945 ACGAAAATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
45 26 0.58
46 8 0.18
47 11 0.24
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (47 bp):
AAAAAGAAATCCTAACCACATGATATCTAATTCGCATGCATTATTCG
Found at i:34773 original size:46 final size:47
Alignment explanation
Indices: 34693--34788 Score: 140
Period size: 46 Copynumber: 2.1 Consensus size: 47
34683 CGACTCGGGT
* * * *
34693 TTTTTTTGTTTTTGATGGATTGTTTAATGATTGGTAATGGCTACTGG
1 TTTTTTTGTTCTTGATGGAGTGTTTAATGATTGGTAATGACCACTGG
*
34740 TTTTTTTGTTCTTGATGGAGTG-TTAATGGTTGGTAATGACCACTGG
1 TTTTTTTGTTCTTGATGGAGTGTTTAATGATTGGTAATGACCACTGG
34786 TTT
1 TTT
34789 CTCCTTTGTC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
46 24 0.55
47 20 0.45
ACGTcount: A:0.17, C:0.06, G:0.26, T:0.51
Consensus pattern (47 bp):
TTTTTTTGTTCTTGATGGAGTGTTTAATGATTGGTAATGACCACTGG
Found at i:37110 original size:31 final size:31
Alignment explanation
Indices: 37072--37132 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
37062 GAACCAATCT
*
37072 CGTTGGTAAGTGT-TTAATTATTTAAATAACC
1 CGTTGGTAAGT-TATTAATTATATAAATAACC
37103 CGTTGGTAAGTTATTAATTATATAAATAAC
1 CGTTGGTAAGTTATTAATTATATAAATAAC
37133 ATGCATTCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 1 0.04
31 27 0.96
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (31 bp):
CGTTGGTAAGTTATTAATTATATAAATAACC
Found at i:37529 original size:15 final size:15
Alignment explanation
Indices: 37509--37544 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
37499 TTTTGAGTAT
37509 ATTACCGGGAATGTC
1 ATTACCGGGAATGTC
37524 ATTACCGGGAATGTC
1 ATTACCGGGAATGTC
37539 ATTACC
1 ATTACC
37545 TCTTTTTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (15 bp):
ATTACCGGGAATGTC
Found at i:38001 original size:16 final size:18
Alignment explanation
Indices: 37979--38022 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 18
37969 ACAACATTCC
37979 AGTAATCTTATTC-C-CT
1 AGTAATCTTATTCTCACT
*
37995 GGTAATCTTATTCTCACT
1 AGTAATCTTATTCTCACT
38013 AGTAATCTTA
1 AGTAATCTTA
38023 CATTCCGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 12 0.50
17 1 0.04
18 11 0.46
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.43
Consensus pattern (18 bp):
AGTAATCTTATTCTCACT
Found at i:40735 original size:16 final size:16
Alignment explanation
Indices: 40714--40745 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40704 TCCGTAGCCG
40714 ATCCGAAAAATCGGAT
1 ATCCGAAAAATCGGAT
*
40730 ATCCGAAAATTCGGAT
1 ATCCGAAAAATCGGAT
40746 CGAATATCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (16 bp):
ATCCGAAAAATCGGAT
Found at i:42920 original size:22 final size:22
Alignment explanation
Indices: 42895--42958 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
42885 ATATTGTATG
42895 CATGTAGTGCATATGAGGTTAA
1 CATGTAGTGCATATGAGGTTAA
42917 CA--T-GTGCATA--A--TAT-A
1 CATGTAGTGCATATGAGGT-TAA
42932 CATGTAGTGCATATGAGGTTAA
1 CATGTAGTGCATATGAGGTTAA
42954 CATGT
1 CATGT
42959 GCATAGTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 18
0.65 0.00 0.35
Matches are distributed among these distances:
15 4 0.12
16 1 0.03
17 2 0.06
18 7 0.21
19 7 0.21
20 2 0.06
21 1 0.03
22 9 0.27
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (22 bp):
CATGTAGTGCATATGAGGTTAA
Found at i:42925 original size:19 final size:19
Alignment explanation
Indices: 42901--42963 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
42891 TATGCATGTA
42901 GTGCATATGAGGTTAACAT
1 GTGCATATGAGGTTAACAT
42920 GTGCATA--A---TATACATGT
1 GTGCATATGAGGTTA-ACA--T
42937 AGTGCATATGAGGTTAACAT
1 -GTGCATATGAGGTTAACAT
42957 GTGCATA
1 GTGCATA
42964 GTATCCATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 18
0.66 0.00 0.34
Matches are distributed among these distances:
14 2 0.06
15 3 0.09
17 2 0.06
18 7 0.20
19 14 0.40
20 2 0.06
22 3 0.09
23 2 0.06
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (19 bp):
GTGCATATGAGGTTAACAT
Found at i:42945 original size:37 final size:37
Alignment explanation
Indices: 42895--42973 Score: 140
Period size: 37 Copynumber: 2.1 Consensus size: 37
42885 ATATTGTATG
42895 CATGTAGTGCATATGAGGTTAACATGTGCATAATATA
1 CATGTAGTGCATATGAGGTTAACATGTGCATAATATA
* *
42932 CATGTAGTGCATATGAGGTTAACATGTGCATAGTATC
1 CATGTAGTGCATATGAGGTTAACATGTGCATAATATA
42969 CATGT
1 CATGT
42974 GTGGGTGAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.33
Consensus pattern (37 bp):
CATGTAGTGCATATGAGGTTAACATGTGCATAATATA
Done.