Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015420.1 Corchorus capsularis cultivar CVL-1 contig15441, 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: 62971
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:2423 original size:1 final size:1
Alignment explanation
Indices: 2417--2447 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
2407 TTTTCTTGTC
2417 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2448 GTGATCAGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:4305 original size:6 final size:6
Alignment explanation
Indices: 4296--4344 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
4286 TATCTGGTTG
4296 CCTGAC CCTGAC CCTGAC CCTGAC CCTGAC CCTGAC CCTGAC CCTGAC
1 CCTGAC CCTGAC CCTGAC CCTGAC CCTGAC CCTGAC CCTGAC CCTGAC
4344 C
1 C
4345 GCCTATACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.16, C:0.51, G:0.16, T:0.16
Consensus pattern (6 bp):
CCTGAC
Found at i:5078 original size:14 final size:16
Alignment explanation
Indices: 5048--5091 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
5038 ATAGTTGCAG
*
5048 AGAGAAAGGGAAGAGAA
1 AGAGAAAGAG-AGAGAA
5065 A-A-AAAGAGAGAGAA
1 AGAGAAAGAGAGAGAA
5079 AGAGAAAGAGAGA
1 AGAGAAAGAGAGA
5092 TGGTGGTCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 7 0.29
15 6 0.25
16 10 0.42
17 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (16 bp):
AGAGAAAGAGAGAGAA
Found at i:9036 original size:3 final size:3
Alignment explanation
Indices: 9030--9077 Score: 60
Period size: 3 Copynumber: 14.7 Consensus size: 3
9020 GTCATCATGC
9030 CAT CAT CAT CAT CAT CAT CAT CATT CAT CATT CAT CGAT CATT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CA-T CAT CA-T CAT C-AT CA-T CAT CA
9078 CCCCTCCAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
3 29 0.71
4 12 0.29
ACGTcount: A:0.31, C:0.31, G:0.02, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:15723 original size:27 final size:27
Alignment explanation
Indices: 15635--15727 Score: 84
Period size: 27 Copynumber: 3.5 Consensus size: 27
15625 AAATTACCAG
* * *
15635 GGGCATTTTT-GTTATTTTCGCCTCAA
1 GGGCATTTTTGGTCATTTTCACTTCAA
* * * *
15661 GGGTA-TTCTGGTCATTTTCACTCCTA
1 GGGCATTTTTGGTCATTTTCACTTCAA
*
15687 GGG-GTGTTTTGGTCATTTTCACTTCAA
1 GGGCAT-TTTTGGTCATTTTCACTTCAA
15714 GGGCATTTTTGGTC
1 GGGCATTTTTGGTC
15728 TTTAGGTCCA
Statistics
Matches: 51, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
25 3 0.06
26 18 0.35
27 29 0.57
28 1 0.02
ACGTcount: A:0.14, C:0.18, G:0.24, T:0.44
Consensus pattern (27 bp):
GGGCATTTTTGGTCATTTTCACTTCAA
Found at i:19005 original size:40 final size:40
Alignment explanation
Indices: 18919--19007 Score: 96
Period size: 40 Copynumber: 2.2 Consensus size: 40
18909 CATAGTCAAA
18919 GACTTAATTCATAGAAATTAAGTGGAAGTAATAGTTAAAAT
1 GACTTAATTCATAGAAATTAAGT-GAAGTAATAGTTAAAAT
* *
18960 G-CTTAATTCATGGCAATTAAGT-AAG-AATA-TTAGAAGACT
1 GACTTAATTCATAGAAATTAAGTGAAGTAATAGTTA-AA-A-T
18999 GACTTAATT
1 GACTTAATT
19008 TCAAGGAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
36 3 0.07
37 6 0.14
38 4 0.10
39 2 0.05
40 26 0.62
41 1 0.02
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.33
Consensus pattern (40 bp):
GACTTAATTCATAGAAATTAAGTGAAGTAATAGTTAAAAT
Found at i:19041 original size:36 final size:36
Alignment explanation
Indices: 18993--19129 Score: 172
Period size: 36 Copynumber: 3.8 Consensus size: 36
18983 AGAATATTAG
*
18993 AAGACTGACTTAATTTCAAGGAAATTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
*
19029 AAGACAT-GCTTAATTTCAAGGAAATTAAGT-AA-AA
1 AAGAC-TGGCTTAATTTCAAGGAAATTAGGTAAAGAA
*
19063 AGGACTGGCTTAATTTCAAGAAAGGAAATTAGGTAAAGAA
1 AAGACTGGCTTAATTTC----AAGGAAATTAGGTAAAGAA
*
19103 AAGATTGGCTTAATTTCAAGGAAATTA
1 AAGACTGGCTTAATTTCAAGGAAATTA
19130 AATAAAAAGA
Statistics
Matches: 87, Mismatches: 6, Indels: 16
0.80 0.06 0.15
Matches are distributed among these distances:
33 1 0.01
34 16 0.18
35 2 0.02
36 36 0.41
37 1 0.01
38 12 0.14
39 2 0.02
40 17 0.20
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.26
Consensus pattern (36 bp):
AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
Found at i:19100 original size:74 final size:73
Alignment explanation
Indices: 19010--19200 Score: 249
Period size: 74 Copynumber: 2.6 Consensus size: 73
19000 ACTTAATTTC
* * *
19010 AAGGAAATTAGGTAAAGAAAAGACATGCTTAATTTCAAGGAAATTAAGTAAAAAGGACTGGCTTA
1 AAGGAAATTAGGTAAAGAAAAGACATGCTTAATTTCAAGGAAATTAAATAAAAA-GACCGGCTCA
19075 ATTTCAAGA
65 ATTTCAAGA
*
19084 AAGGAAATTAGGTAAAGAAAAGA-TTGGCTTAATTTCAAGGAAATTAAATAAAAAGACCGGCTCA
1 AAGGAAATTAGGTAAAGAAAAGACAT-GCTTAATTTCAAGGAAATTAAATAAAAAGACCGGCTCA
* * *
19148 GTTTTAGGA
65 ATTTCAAGA
* * * *
19157 AAGGAAATTAGTTAAGGATAAGCACATACTTAATTTCAAGGAAA
1 AAGGAAATTAGGTAAAGAAAAG-ACATGCTTAATTTCAAGGAAA
19201 GAAATTAGGT
Statistics
Matches: 102, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
73 34 0.33
74 67 0.66
75 1 0.01
ACGTcount: A:0.47, C:0.08, G:0.20, T:0.25
Consensus pattern (73 bp):
AAGGAAATTAGGTAAAGAAAAGACATGCTTAATTTCAAGGAAATTAAATAAAAAGACCGGCTCAA
TTTCAAGA
Found at i:19122 original size:40 final size:39
Alignment explanation
Indices: 19010--19122 Score: 130
Period size: 40 Copynumber: 3.0 Consensus size: 39
19000 ACTTAATTTC
19010 AAGGAAATTAGGTAAAGAAAAGACAT-GCTTAATTTC---
1 AAGGAAATTAGGTAAAGAAAAGA-ATGGCTTAATTTCAAG
* * *
19046 AAGGAAATTAAGT-AA-AAAGGACTGGCTTAATTTCAAG
1 AAGGAAATTAGGTAAAGAAAAGAATGGCTTAATTTCAAG
*
19083 AAAGGAAATTAGGTAAAGAAAAGATTGGCTTAATTTCAAG
1 -AAGGAAATTAGGTAAAGAAAAGAATGGCTTAATTTCAAG
19123 GAAATTAAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
33 1 0.02
34 15 0.23
35 2 0.03
36 12 0.19
38 12 0.19
39 2 0.03
40 20 0.31
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.25
Consensus pattern (39 bp):
AAGGAAATTAGGTAAAGAAAAGAATGGCTTAATTTCAAG
Found at i:19222 original size:41 final size:42
Alignment explanation
Indices: 19153--19235 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 42
19143 GCTCAGTTTT
* * *
19153 AGGAAAGGAAATTAGTTAAGGATAAGCACATACTTAATTTCA
1 AGGAAAGGAAATTAGGTAAAGATAAGCACAGACTTAATTTCA
*
19195 AGGAAA-GAAATTAGGTAAAGATCAGCACAGACTTAATTTCA
1 AGGAAAGGAAATTAGGTAAAGATAAGCACAGACTTAATTTCA
19236 CAAGAATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 31 0.84
42 6 0.16
ACGTcount: A:0.46, C:0.11, G:0.19, T:0.24
Consensus pattern (42 bp):
AGGAAAGGAAATTAGGTAAAGATAAGCACAGACTTAATTTCA
Found at i:19268 original size:36 final size:36
Alignment explanation
Indices: 19203--19303 Score: 148
Period size: 36 Copynumber: 2.8 Consensus size: 36
19193 CAAGGAAAGA
* *
19203 AATTAGGTAAAGATCAGCACAGACTTAATTTCACAAG
1 AATTAAGTAAA-ATCAGCAAAGACTTAATTTCACAAG
*
19240 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
1 AATTAAGTAAAATCAGCAAAGACTTAATTTCACAAG
* *
19276 AATTAAGTAAAGTCAGCAAAGATTTAAT
1 AATTAAGTAAAATCAGCAAAGACTTAAT
19304 CCATAGATGA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 48 0.83
37 10 0.17
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.27
Consensus pattern (36 bp):
AATTAAGTAAAATCAGCAAAGACTTAATTTCACAAG
Found at i:19377 original size:11 final size:11
Alignment explanation
Indices: 19362--19437 Score: 111
Period size: 11 Copynumber: 7.1 Consensus size: 11
19352 TTAGGCAAAA
*
19362 GAAAGAAGACA
1 GAAAGAAGACT
19373 GAAAGAAGACT
1 GAAAGAAGACT
*
19384 AAAAGAAGACT
1 GAAAGAAGACT
*
19395 GAAAAAAGACT
1 GAAAGAAGACT
19406 GAAAGAAGACT
1 GAAAGAAGACT
19417 G-AA-AAGACT
1 GAAAGAAGACT
19426 GAAAGAAGACT
1 GAAAGAAGACT
19437 G
1 G
19438 GCTTAATTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
9 7 0.12
10 4 0.07
11 47 0.81
ACGTcount: A:0.58, C:0.09, G:0.25, T:0.08
Consensus pattern (11 bp):
GAAAGAAGACT
Found at i:19472 original size:36 final size:36
Alignment explanation
Indices: 19431--20352 Score: 1260
Period size: 36 Copynumber: 25.7 Consensus size: 36
19421 AGACTGAAAG
19431 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
* *
19467 AAGACTGACTTAGTTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
*
19503 AAGACTGGCTTGATTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
* * *
19539 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
* *
19575 AAGATTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
19611 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
* * * *
19647 AAGTCTAGCTTAGTTTCAGGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
*
19683 AAGACTGGCTTGATTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
** * * *
19719 AAGACTGGCTTAGCTTCAAGGAAACTAGGTAAAGTA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
*
19755 TAGACTGGCTT-ATTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
* * * *
19790 AAGACTGGCTTAGTTTCAAGAAAACTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
*
19826 AAGTCTGGCTTAATTTCAAGGAAATTAAGTAAAG-A
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
* * * * *
19861 AAGAATGCTGGTTTAGTTTCAAGAAAACTAGGTAAAGAA
1 AAG-A--CTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
19900 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
* * *
19936 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
* * *
19972 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
* *
20008 TAGACTGGCTTGATTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
* * *
20044 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
*
20080 AAGACTGGCTTAATTTCAAGAAAATTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
* * *
20116 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
* * * *
20152 AAGACTGGCTTAGTTTCAAGGAAACTAGGAAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
* *
20188 TAGACTGGCTTGATTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
*
20224 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG-A
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
** * *
20259 TGGACTGGCTTAATTTCAAGGAAATTAGGTAAAGGA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
20295 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAA-AA
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
* * *
20330 GACACAGGCTTAATTTC-AGGAAA
1 AAGACTGGCTTAATTTCAAGGAAA
20353 GGAAATTAAG
Statistics
Matches: 784, Mismatches: 96, Indels: 14
0.88 0.11 0.02
Matches are distributed among these distances:
34 6 0.01
35 81 0.10
36 667 0.85
38 26 0.03
39 4 0.01
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.25
Consensus pattern (36 bp):
AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
Found at i:20406 original size:36 final size:32
Alignment explanation
Indices: 20356--20479 Score: 153
Period size: 32 Copynumber: 3.8 Consensus size: 32
20346 CAGGAAAGGA
*
20356 AATTAAGTAAAATAAAGAACTTAATTCAGGGT
1 AATTAAGTAGAATAAAGAACTTAATTCAGGGT
*
20388 AATTAAGTGAAGTCAATAAA-AGGCTTAATTCAGGGT
1 AATTAAGT--AG--AATAAAGA-ACTTAATTCAGGGT
*
20424 AATTAAGTAGAATAAAGAACTTAATTCAAGGT
1 AATTAAGTAGAATAAAGAACTTAATTCAGGGT
*
20456 AATTAAGT-CAATAAAGAACTTAAT
1 AATTAAGTAGAATAAAGAACTTAAT
20480 CTAAAAAGAG
Statistics
Matches: 81, Mismatches: 5, Indels: 13
0.82 0.05 0.13
Matches are distributed among these distances:
31 15 0.19
32 34 0.42
33 1 0.01
34 3 0.04
35 1 0.01
36 27 0.33
ACGTcount: A:0.48, C:0.07, G:0.16, T:0.28
Consensus pattern (32 bp):
AATTAAGTAGAATAAAGAACTTAATTCAGGGT
Found at i:21360 original size:27 final size:27
Alignment explanation
Indices: 21320--21372 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
21310 AGAGATATTC
*
21320 ATGACATAGTGGAGATGCAACAACATT
1 ATGACATAGAGGAGATGCAACAACATT
* * *
21347 ATGATATAGAGGAGTTGCTACAACAT
1 ATGACATAGAGGAGATGCAACAACAT
21373 GCCTTGAAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.25
Consensus pattern (27 bp):
ATGACATAGAGGAGATGCAACAACATT
Found at i:25220 original size:20 final size:21
Alignment explanation
Indices: 25178--25221 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
25168 ATTATTAATC
*
25178 AAAATGAAAGCAATTAAACTT
1 AAAATGAAAGCAAGTAAACTT
25199 AAAAT-AAAGCAAAGTAAA-TT
1 AAAATGAAAGC-AAGTAAACTT
25219 AAA
1 AAA
25222 TCTAAATCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.64, C:0.07, G:0.09, T:0.20
Consensus pattern (21 bp):
AAAATGAAAGCAAGTAAACTT
Found at i:26665 original size:33 final size:33
Alignment explanation
Indices: 26617--26724 Score: 105
Period size: 33 Copynumber: 3.3 Consensus size: 33
26607 AAAGGATCAT
** * *
26617 GTGGCCGGTTGTGGCCGGGCATGGCCATGTCGC
1 GTGGCCGGTCATGGCCGGGCATCGCCAAGTCGC
*
26650 GTGGCCGGTCATGGCCGGGCATCTCCAAGTCGC
1 GTGGCCGGTCATGGCCGGGCATCGCCAAGTCGC
* ** *
26683 ATGGCCGGTGTTGTG-C--GCATCTCCAAGTCGC
1 GTGGCCGGTCATG-GCCGGGCATCGCCAAGTCGC
26714 GTGGCCGGTCA
1 GTGGCCGGTCA
26725 CAAGTGCTTC
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
31 23 0.37
33 39 0.62
34 1 0.02
ACGTcount: A:0.10, C:0.30, G:0.39, T:0.21
Consensus pattern (33 bp):
GTGGCCGGTCATGGCCGGGCATCGCCAAGTCGC
Found at i:27623 original size:30 final size:30
Alignment explanation
Indices: 27589--27648 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
27579 CAATTCTTGC
*
27589 TTCTTGAAATAATTCTTCAAT-AGTCTTCAA
1 TTCTTCAAATAA-TCTTCAATAAGTCTTCAA
*
27619 TTCTTCAAATTATCTTCAATAAGTCTTCAA
1 TTCTTCAAATAATCTTCAATAAGTCTTCAA
27649 ACACGAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.33, C:0.18, G:0.05, T:0.43
Consensus pattern (30 bp):
TTCTTCAAATAATCTTCAATAAGTCTTCAA
Found at i:38271 original size:30 final size:30
Alignment explanation
Indices: 38212--38271 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
38202 AAGTTCGTGT
*
38212 TTGAAGACTTATTGAAGATAATTTGAAGAA
1 TTGAAGACTTATTGAAGATAATTTCAAGAA
*
38242 TTGAAGAC-TATTGAAGAATTATTTCAAGAA
1 TTGAAGACTTATTGAAG-ATAATTTCAAGAA
38272 GCAAGAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.43, C:0.05, G:0.18, T:0.33
Consensus pattern (30 bp):
TTGAAGACTTATTGAAGATAATTTCAAGAA
Found at i:56968 original size:21 final size:21
Alignment explanation
Indices: 56944--56999 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
56934 ATCTTGGAAC
*
56944 CGATTGGAATATTCCTAGAAT
1 CGATTGGAATATTCATAGAAT
* * **
56965 CGATTGTAGTAGACATAGAAT
1 CGATTGGAATATTCATAGAAT
56986 CGATTGGAATATTC
1 CGATTGGAATATTC
57000 TTGCTCCAAA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.32
Consensus pattern (21 bp):
CGATTGGAATATTCATAGAAT
Found at i:57790 original size:33 final size:32
Alignment explanation
Indices: 57753--57857 Score: 111
Period size: 33 Copynumber: 3.2 Consensus size: 32
57743 ATTAGCATCC
* * *
57753 AAAACAGATTTTGTTTCATCACAAACAACACCT
1 AAAACAGATTTAGTATCATCGCAAACAACA-CT
* *
57786 AAAACAGATTTAGTGTCATTGCAAACAACACT
1 AAAACAGATTTAGTATCATCGCAAACAACACT
** *
57818 CAAATTAGGTTTAGTATCATCGCAAACAACATCT
1 -AAAACAGATTTAGTATCATCGCAAACAACA-CT
57852 AAAACA
1 AAAACA
57858 CTCTTTGCAA
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
32 2 0.03
33 55 0.93
34 2 0.03
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.26
Consensus pattern (32 bp):
AAAACAGATTTAGTATCATCGCAAACAACACT
Done.