Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009333.1 Corchorus capsularis cultivar CVL-1 contig09354, 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: 10952
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:254 original size:14 final size:14
Alignment explanation
Indices: 237--273 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
227 TAGGTTTTAC
*
237 AAATTAGGGACATG
1 AAATTAGGGACAGG
*
251 AAATTAGGAACAGG
1 AAATTAGGGACAGG
265 AAATTAGGG
1 AAATTAGGG
274 TTACACCCAA
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:0.46, C:0.05, G:0.30, T:0.19
Consensus pattern (14 bp):
AAATTAGGGACAGG
Found at i:350 original size:6 final size:6
Alignment explanation
Indices: 332--387 Score: 60
Period size: 6 Copynumber: 9.5 Consensus size: 6
322 GAACTCACGG
* * * * *
332 AAGGAA AAAGAA AAGG-A AACGAA AAGTAA AATGAA AAGTAA AAGGAA
1 AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA
379 AAGGAA AAG
1 AAGGAA AAG
388 AACTTACTGT
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
5 4 0.10
6 35 0.90
ACGTcount: A:0.68, C:0.02, G:0.25, T:0.05
Consensus pattern (6 bp):
AAGGAA
Found at i:468 original size:28 final size:28
Alignment explanation
Indices: 412--486 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
402 TACAAAGTCT
*
412 CGAATCGAAGGAGAGGAGAACGGCTCTG
1 CGAATCGAAGGAGAGGAGAACGGCGCTG
** * *
440 CGAATCGATTGAGAGGGGAACGTCGCTG
1 CGAATCGAAGGAGAGGAGAACGGCGCTG
* *
468 CG-CTCGACGGAGAGGAGAA
1 CGAATCGAAGGAGAGGAGAA
487 GGAAGAAAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
27 13 0.34
28 25 0.66
ACGTcount: A:0.29, C:0.19, G:0.40, T:0.12
Consensus pattern (28 bp):
CGAATCGAAGGAGAGGAGAACGGCGCTG
Found at i:541 original size:17 final size:18
Alignment explanation
Indices: 506--544 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
496 TCGAAAAACA
*
506 CTTAGGAAATTTTTGTGC
1 CTTAGGAAATTTTTATGC
524 CTTAGGAAA-TTTTATGC
1 CTTAGGAAATTTTTATGC
541 CTTA
1 CTTA
545 AATGGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.44
Consensus pattern (18 bp):
CTTAGGAAATTTTTATGC
Found at i:4788 original size:22 final size:22
Alignment explanation
Indices: 4760--4802 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
4750 AATTGAATTC
4760 GAAGAATTCAAATTGAAGCATG
1 GAAGAATTCAAATTGAAGCATG
*
4782 GAAGAATTGAAATTGAAGCAT
1 GAAGAATTCAAATTGAAGCAT
4803 TGACATTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.07, G:0.23, T:0.23
Consensus pattern (22 bp):
GAAGAATTCAAATTGAAGCATG
Found at i:4831 original size:58 final size:58
Alignment explanation
Indices: 4724--4915 Score: 262
Period size: 58 Copynumber: 3.3 Consensus size: 58
4714 GAAGGAGGTT
* ** * * * * *
4724 TTGAATAATTGAAATCAAAACATTGA-AATT-GAATTCGAAGAATTCAAATTGAAGCA
1 TTGAAGAATTGAAATTGAAGCATTGACATTTGGAATTTGAAGAACTGAAATTGAAGCA
* *
4780 TGGAAGAATTGAAATTGAAGCATTGACATTTGGAATTTGAAGAACTGAAATTGAAGCG
1 TTGAAGAATTGAAATTGAAGCATTGACATTTGGAATTTGAAGAACTGAAATTGAAGCA
*
4838 TTGAAGAATTGAAATTGAAGCATTGACATTTGGAATTTGAAGAACTGAAATTTAAGCA
1 TTGAAGAATTGAAATTGAAGCATTGACATTTGGAATTTGAAGAACTGAAATTGAAGCA
4896 TTGAAGAATTGAAAATTGAA
1 TTGAAGAATTG-AAATTGAA
4916 ATTGAAGCGT
Statistics
Matches: 120, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
56 21 0.17
57 3 0.03
58 88 0.73
59 8 0.07
ACGTcount: A:0.44, C:0.07, G:0.20, T:0.29
Consensus pattern (58 bp):
TTGAAGAATTGAAATTGAAGCATTGACATTTGGAATTTGAAGAACTGAAATTGAAGCA
Found at i:4841 original size:22 final size:22
Alignment explanation
Indices: 4816--4863 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
4806 CATTTGGAAT
*
4816 TTGAAGAACTGAAATTGAAGCG
1 TTGAAGAACTGAAATTGAAGCA
*
4838 TTGAAGAATTGAAATTGAAGCA
1 TTGAAGAACTGAAATTGAAGCA
4860 TTGA
1 TTGA
4864 CATTTGGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.27
Consensus pattern (22 bp):
TTGAAGAACTGAAATTGAAGCA
Found at i:4849 original size:8 final size:8
Alignment explanation
Indices: 4770--4994 Score: 65
Period size: 8 Copynumber: 30.2 Consensus size: 8
4760 GAAGAATTCA
4770 AATTGAAG
1 AATTGAAG
* *
4778 CATGGAAG
1 AATTGAAG
4786 AATTG-A-
1 AATTGAAG
4792 AATTGAAG
1 AATTGAAG
* *
4800 CATTG-AC
1 AATTGAAG
*
4807 ATTTG--G
1 AATTGAAG
4813 AATTTGAAG
1 AA-TTGAAG
*
4822 AACTG-A-
1 AATTGAAG
4828 AATTGAAG
1 AATTGAAG
**
4836 CGTTGAAG
1 AATTGAAG
4844 AATTG-A-
1 AATTGAAG
4850 AATTGAAG
1 AATTGAAG
* *
4858 CATTG-AC
1 AATTGAAG
*
4865 ATTTG--G
1 AATTGAAG
4871 AATTTGAAG
1 AA-TTGAAG
*
4880 AACTG-A-
1 AATTGAAG
*
4886 AATTTAAG
1 AATTGAAG
*
4894 CATTGAAG
1 AATTGAAG
4902 AATTGAA-
1 AATTGAAG
4909 AATTG-A-
1 AATTGAAG
4915 AATTGAAG
1 AATTGAAG
** **
4923 CGTCAAAG
1 AATTGAAG
*
4931 ATTTG-A-
1 AATTGAAG
*
4937 AATTGAGG
1 AATTGAAG
* *
4945 CATTGAAT
1 AATTGAAG
*
4953 AATTGAGG
1 AATTGAAG
4961 AATTGAAG
1 AATTGAAG
* *
4969 CATTGAAT
1 AATTGAAG
4977 AATTGAAG
1 AATTGAAG
*
4985 AATTAAAG
1 AATTGAAG
4993 AA
1 AA
4995 AGATCACCCT
Statistics
Matches: 149, Mismatches: 50, Indels: 36
0.63 0.21 0.15
Matches are distributed among these distances:
6 29 0.19
7 29 0.19
8 85 0.57
9 6 0.04
ACGTcount: A:0.43, C:0.06, G:0.23, T:0.28
Consensus pattern (8 bp):
AATTGAAG
Found at i:4856 original size:36 final size:36
Alignment explanation
Indices: 4782--4857 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
4772 TTGAAGCATG
* * *
4782 GAAGAATTGAAATTGAAGCATTGACATTTGGAATTT
1 GAAGAACTGAAATTGAAGCATTGACAATTGGAAATT
* *
4818 GAAGAACTGAAATTGAAGCGTTGAAGAATT-GAAATT
1 GAAGAACTGAAATTGAAGCATTG-ACAATTGGAAATT
4854 GAAG
1 GAAG
4858 CATTGACATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 30 0.88
37 4 0.12
ACGTcount: A:0.42, C:0.05, G:0.25, T:0.28
Consensus pattern (36 bp):
GAAGAACTGAAATTGAAGCATTGACAATTGGAAATT
Found at i:4964 original size:24 final size:24
Alignment explanation
Indices: 4937--4988 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
4927 AAAGATTTGA
* *
4937 AATTGAGGCATTGAATAATTGAGG
1 AATTGAAGCATTGAATAATTGAAG
4961 AATTGAAGCATTGAATAATTGAAG
1 AATTGAAGCATTGAATAATTGAAG
4985 AATT
1 AATT
4989 AAAGAAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.04, G:0.23, T:0.31
Consensus pattern (24 bp):
AATTGAAGCATTGAATAATTGAAG
Found at i:5040 original size:16 final size:18
Alignment explanation
Indices: 5009--5041 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
4999 CACCCTGGAT
5009 CATTGAAGTAAATTGAAG
1 CATTGAAGTAAATTGAAG
5027 CATTGAA-T-AATTGAA
1 CATTGAAGTAAATTGAA
5042 ATTGAAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.30
Consensus pattern (18 bp):
CATTGAAGTAAATTGAAG
Found at i:5273 original size:50 final size:50
Alignment explanation
Indices: 5154--5308 Score: 133
Period size: 50 Copynumber: 3.1 Consensus size: 50
5144 AATTGAAACA
* * *
5154 TTGAAATATTGAA-ATTGAAACATTGAAGAATTGAAACATTGATGGATTGAAA
1 TTGAAA-AATGAACATTGAAACATTG-A-AATTGAAACATTGAAGGATTGAAT
** *
5206 TTG-AATTTGAAGCATTGAGGA-ATTGAAATTGAAACATTGAAGGATTGAAT
1 TTGAAAAATGAA-CATTGA-AACATTGAAATTGAAACATTGAAGGATTGAAT
* * *
5256 TTGAAGAAATGAA-ATTGAAACATTGAAGTTG-GA-ATTGAAGAATTGAAT
1 TTGAA-AAATGAACATTGAAACATTGAAATTGAAACATTGAAGGATTGAAT
5304 TTGAA
1 TTGAA
5309 TTTGAAGAAT
Statistics
Matches: 87, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
48 19 0.22
49 2 0.02
50 44 0.51
51 4 0.05
52 17 0.20
53 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.31
Consensus pattern (50 bp):
TTGAAAAATGAACATTGAAACATTGAAATTGAAACATTGAAGGATTGAAT
Found at i:5329 original size:14 final size:14
Alignment explanation
Indices: 5134--5336 Score: 80
Period size: 14 Copynumber: 14.8 Consensus size: 14
5124 GGAAGAGCTA
5134 GAAGAATTGAAATT
1 GAAGAATTGAAATT
5148 GAA-ACATTGAAATATT
1 GAAGA-ATTG-AA-ATT
5164 G-A-AATTGAAACATT
1 GAAGAATTG-AA-ATT
5178 GAAGAATTGAAACATT
1 GAAGAATTG-AA-ATT
* *
5194 GATGGATTGAAATT
1 GAAGAATTGAAATT
*
5208 G-A-ATTTGAAGCATT
1 GAAGAATTGAA--ATT
*
5222 GAGGAATTGAAATT
1 GAAGAATTGAAATT
5236 GAA-ACATTG-AA--
1 GAAGA-ATTGAAATT
*
5247 G--G-ATTGAATTT
1 GAAGAATTGAAATT
*
5258 GAAGAAATGAAATT
1 GAAGAATTGAAATT
*
5272 GAA-ACATTGAAGTT
1 GAAGA-ATTGAAATT
5286 G--GAATTGAAGAATT
1 GAAGAATTG-A-AATT
* *
5300 G-A-ATTTGAATTT
1 GAAGAATTGAAATT
5312 GAAGAATTGAAATT
1 GAAGAATTGAAATT
*
5326 GAAGCATTGAA
1 GAAGAATTGAA
5337 GAATTTGAAG
Statistics
Matches: 145, Mismatches: 20, Indels: 48
0.68 0.09 0.23
Matches are distributed among these distances:
8 4 0.03
9 1 0.01
11 2 0.01
12 13 0.09
13 10 0.07
14 79 0.54
15 7 0.05
16 29 0.20
ACGTcount: A:0.45, C:0.03, G:0.22, T:0.30
Consensus pattern (14 bp):
GAAGAATTGAAATT
Found at i:5335 original size:22 final size:22
Alignment explanation
Indices: 5065--5341 Score: 157
Period size: 22 Copynumber: 12.5 Consensus size: 22
5055 AGAGTCGAAT
*
5065 TTGAAGAATTGAAACTGAAGCA
1 TTGAAGAATTGAAATTGAAGCA
* * *
5087 ATGAA-ATGTTGAAATTGAAACA
1 TTGAAGA-ATTGAAATTGAAGCA
*
5109 TTGAATG-ATCG-AATTGGAAG-A
1 TTGAA-GAATTGAAATT-GAAGCA
* *
5130 GCTAGAAGAATTGAAATTGAAACA
1 --TTGAAGAATTGAAATTGAAGCA
*
5154 TTGAA-ATATTGAAATTGAAACA
1 TTGAAGA-ATTGAAATTGAAGCA
* *
5176 TTGAAGAATTGAAACATTGATGGA
1 TTGAAGAATTG-AA-ATTGAAGCA
*
5200 TTG-A-AATTGAATTTGAAGCA
1 TTGAAGAATTGAAATTGAAGCA
* *
5220 TTGAGGAATTGAAATTGAAACA
1 TTGAAGAATTGAAATTGAAGCA
* * *
5242 TTGAAGGATTGAATTTGAAGAA
1 TTGAAGAATTGAAATTGAAGCA
*
5264 ATG-A-AATTGAAACATTGAAG--
1 TTGAAGAATTG-AA-ATTGAAGCA
*
5284 TTG--GAATTGAAGAATTGAATTTGAA
1 TTGAAGAATTG-A-AATTGAA---GCA
5309 TTTGAAGAATTGAAATTGAAGCA
1 -TTGAAGAATTGAAATTGAAGCA
5332 TTGAAGAATT
1 TTGAAGAATT
5342 TGAAGAAAGA
Statistics
Matches: 197, Mismatches: 31, Indels: 54
0.70 0.11 0.19
Matches are distributed among these distances:
20 28 0.14
21 13 0.07
22 108 0.55
23 17 0.09
24 14 0.07
26 10 0.05
27 1 0.01
28 6 0.03
ACGTcount: A:0.44, C:0.04, G:0.22, T:0.29
Consensus pattern (22 bp):
TTGAAGAATTGAAATTGAAGCA
Found at i:5335 original size:28 final size:27
Alignment explanation
Indices: 5200--5336 Score: 104
Period size: 28 Copynumber: 5.0 Consensus size: 27
5190 CATTGATGGA
* *
5200 TTGA-AATTGAATTTGAAGCATTGAGGAA
1 TTGAGAATTGAAATTGAAGCATTGA--AT
*
5228 TTGA-AATTGAAACATTGAAGGATTGAAT
1 TTGAGAATTG-AA-ATTGAAGCATTGAAT
* * *
5256 TTGAAGAAATGAAATTGAAACATTGAAG
1 TTG-AGAATTGAAATTGAAGCATTGAAT
*
5284 TTG-GAATTGAAGAATTGAA--TTTGAAT
1 TTGAGAATTG-A-AATTGAAGCATTGAAT
5310 TTGAAGAATTGAAATTGAAGCATTGAA
1 TTG-AGAATTGAAATTGAAGCATTGAA
5337 GAATTTGAAG
Statistics
Matches: 88, Mismatches: 11, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
26 20 0.23
27 2 0.02
28 46 0.52
29 5 0.06
30 15 0.17
ACGTcount: A:0.43, C:0.03, G:0.23, T:0.31
Consensus pattern (27 bp):
TTGAGAATTGAAATTGAAGCATTGAAT
Found at i:5346 original size:9 final size:8
Alignment explanation
Indices: 5134--5348 Score: 69
Period size: 8 Copynumber: 27.8 Consensus size: 8
5124 GGAAGAGCTA
5134 GAAGAATT
1 GAAGAATT
5142 G-A-AATT
1 GAAGAATT
5148 GAA-ACATT
1 GAAGA-ATT
5156 GAA-ATATT
1 GAAGA-ATT
5164 G-A-AATT
1 GAAGAATT
5170 GAA-ACATT
1 GAAGA-ATT
5178 GAAGAATT
1 GAAGAATT
5186 GAA-ACATT
1 GAAGA-ATT
* *
5194 GATGGATT
1 GAAGAATT
5202 GAAATTGAATTT
1 G-AA--GAA-TT
*
5214 GAAGCATT
1 GAAGAATT
*
5222 GAGGAATT
1 GAAGAATT
5230 G-A-AATT
1 GAAGAATT
5236 GAA-ACATT
1 GAAGA-ATT
*
5244 GAAGGATT
1 GAAGAATT
*
5252 G-A-ATTT
1 GAAGAATT
*
5258 GAAGAAAT
1 GAAGAATT
5266 G-A-AATT
1 GAAGAATT
5272 GAA-ACATT
1 GAAGA-ATT
5280 GAAG--TT
1 GAAGAATT
5286 G--GAATT
1 GAAGAATT
5292 GAAGAATT
1 GAAGAATT
5300 GAATTTGAATTT
1 GAA---GAA-TT
5312 GAAGAATT
1 GAAGAATT
5320 G-A-AATT
1 GAAGAATT
*
5326 GAAGCATT
1 GAAGAATT
5334 GAAGAATTT
1 GAAGAA-TT
5343 GAAGAA
1 GAAGAA
5349 AGACCACCTT
Statistics
Matches: 160, Mismatches: 17, Indels: 59
0.68 0.07 0.25
Matches are distributed among these distances:
4 1 0.01
6 32 0.20
7 17 0.11
8 80 0.50
9 15 0.09
11 7 0.04
12 8 0.05
ACGTcount: A:0.45, C:0.03, G:0.22, T:0.30
Consensus pattern (8 bp):
GAAGAATT
Found at i:5414 original size:58 final size:58
Alignment explanation
Indices: 5331--5628 Score: 377
Period size: 58 Copynumber: 5.2 Consensus size: 58
5321 AAATTGAAGC
* * * ** ***
5331 ATTGAAGAATTTGAAGAAAGACCACCTTGGATCATTGAAGTAAATTGAAACATTGAGCG
1 ATTGAAGAA-TTGAAGAAAGATCACCCTGGATCTTTGAAGTAAATTGAAGTATTGAATA
* * * * * *
5390 ATTGAAGAATTGAAGAAAGACCACCCTGGAGCATTGAAGTAAACTGAAGGATTGAATG
1 ATTGAAGAATTGAAGAAAGATCACCCTGGATCTTTGAAGTAAATTGAAGTATTGAATA
* *
5448 ATTGAGGAATCGAAGAAAGATCACCCTGGATCTTTGAAGTAAATTGAAGTATTGAATA
1 ATTGAAGAATTGAAGAAAGATCACCCTGGATCTTTGAAGTAAATTGAAGTATTGAATA
* * *
5506 ATTGAGGAATTGAAGAAAGATCACCCCGGATTTTTGAAGTAAATTGAAGTATTGAATA
1 ATTGAAGAATTGAAGAAAGATCACCCTGGATCTTTGAAGTAAATTGAAGTATTGAATA
*
5564 ATTGAAGAATTGAAGAAAGATCACCCTGGATCTTTGAAGT--ATTGAA-TAATTGAAGA
1 ATTGAAGAATTGAAGAAAGATCACCCTGGATCTTTGAAGTAAATTGAAGT-ATTGAATA
5620 ATTGAAGAA
1 ATTGAAGAA
5629 AGGCCACCCT
Statistics
Matches: 216, Mismatches: 22, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
55 1 0.00
56 22 0.10
58 184 0.85
59 9 0.04
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (58 bp):
ATTGAAGAATTGAAGAAAGATCACCCTGGATCTTTGAAGTAAATTGAAGTATTGAATA
Found at i:5579 original size:8 final size:8
Alignment explanation
Indices: 5547--5580 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
5537 TTTTGAAGTA
5547 AATTGAAG
1 AATTGAAG
* *
5555 TATTGAAT
1 AATTGAAG
5563 AATTGAAG
1 AATTGAAG
5571 AATTGAAG
1 AATTGAAG
5579 AA
1 AA
5581 AGATCACCCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (8 bp):
AATTGAAG
Found at i:6465 original size:6 final size:6
Alignment explanation
Indices: 6454--6506 Score: 74
Period size: 6 Copynumber: 8.8 Consensus size: 6
6444 TTTTCATTCT
6454 TTTTTC TTTTTC TTTTTC TTTTTC -TTTTC TTCTTTC TTTTT- TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT-TTTC TTTTTC TTTTTC
6501 ATTTTT
1 -TTTTT
6507 TCGTGCACTT
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.23
6 22 0.51
7 11 0.26
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:6490 original size:30 final size:30
Alignment explanation
Indices: 6450--6506 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
6440 CTTCTTTTCA
*
6450 TTCTTTTTTCTTTTTCTTTTTC-TTTTTCTT
1 TTCTTCTTTCTTTTT-TTTTTCATTTTTCTT
6480 TTCTTCTTTCTTTTTTTTTTCATTTTT
1 TTCTTCTTTCTTTTTTTTTTCATTTTT
6507 TCGTGCACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (30 bp):
TTCTTCTTTCTTTTTTTTTTCATTTTTCTT
Found at i:7417 original size:13 final size:13
Alignment explanation
Indices: 7384--7418 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
7374 TGCTTTTTCA
*
7384 TTTTTTCCTCCTT
1 TTTTTTCTTCCTT
*
7397 TTTTTTCTTCTTT
1 TTTTTTCTTCCTT
7410 TTTTTTCTT
1 TTTTTTCTT
7419 TTTCATCCGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTCTTCCTT
Found at i:10901 original size:2 final size:2
Alignment explanation
Indices: 10894--10920 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10884 AACCCTAAAT
10894 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 T
10921 GGACTAGGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.