Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011240.1 Corchorus capsularis cultivar CVL-1 contig11261, 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: 38052
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:328 original size:2 final size:2
Alignment explanation
Indices: 321--351 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
311 ATTTAGTATG
321 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 T
352 TTCGTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3846 original size:13 final size:15
Alignment explanation
Indices: 3820--3852 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
3810 TGCGTAAGGT
3820 AAAAAAAAGCAAAA-
1 AAAAAAAAGCAAAAG
3834 AAAAAAAAG-AAAAG
1 AAAAAAAAGCAAAAG
3848 AAAAA
1 AAAAA
3853 GGTTTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGCAAAAG
Found at i:4883 original size:34 final size:35
Alignment explanation
Indices: 4805--4888 Score: 152
Period size: 35 Copynumber: 2.4 Consensus size: 35
4795 AGTTTTTGAA
4805 GATCAGAGTTGATCTCATTCCAAGAAGTTTTCAAC
1 GATCAGAGTTGATCTCATTCCAAGAAGTTTTCAAC
*
4840 GATCAGAGTTGATCTCATTCCAAGAAGTTTT-AAT
1 GATCAGAGTTGATCTCATTCCAAGAAGTTTTCAAC
4874 GATCAGAGTTGATCT
1 GATCAGAGTTGATCT
4889 TAGGATGATC
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
34 17 0.35
35 31 0.65
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (35 bp):
GATCAGAGTTGATCTCATTCCAAGAAGTTTTCAAC
Found at i:5023 original size:89 final size:88
Alignment explanation
Indices: 4819--5032 Score: 263
Period size: 89 Copynumber: 2.4 Consensus size: 88
4809 AGAGTTGATC
* * *
4819 TCATTCCAAGAAGTTTTCA-ACGATCAGAGTTGATCTCATTCCAAGAAGTTTTAATGATCAGAGT
1 TCATTCCAAGAAATTTTCAGA-GGTCAGAGTTGATCTCATTCCAAGAAGTTTCAATGATCAGAGT
* *
4883 TGATCTTAGGATGATCCGATGTGG
65 TGATCTCAGGATAATCCGATGTGG
* * *
4907 TCATTCCAAGAAATTTTCAGCGGTCAGAGTTGATTTCATTTCAAGAAGTTTCCAATGATCAGAGT
1 TCATTCCAAGAAATTTTCAGAGGTCAGAGTTGATCTCATTCCAAGAAGTTT-CAATGATCAGAGT
*
4972 TGATCTCA-GATTAATCCGGTGTGG
65 TGATCTCAGGA-TAATCCGATGTGG
** *
4996 TCATTCCAA-AAAGTTTTTGGAGTTCAGAGTTGATCTC
1 TCATTCCAAGAAA-TTTTCAGAGGTCAGAGTTGATCTC
5033 CAATTGATCC
Statistics
Matches: 108, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
88 50 0.46
89 58 0.54
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (88 bp):
TCATTCCAAGAAATTTTCAGAGGTCAGAGTTGATCTCATTCCAAGAAGTTTCAATGATCAGAGTT
GATCTCAGGATAATCCGATGTGG
Found at i:5077 original size:54 final size:55
Alignment explanation
Indices: 4942--5086 Score: 179
Period size: 54 Copynumber: 2.7 Consensus size: 55
4932 AGAGTTGATT
* *
4942 TCATTTCAAGAAGTTTCC-AATGATCAGAGTTGATCT-CAGATTAATCCGGTGTGG
1 TCATTCCAAGAAGTTTCCGAA-GATCAGAGTTGATCTCCAGATTAATCCGGTGCGG
* ** * * *
4996 TCATTCCAAAAAGTTTTTGGAGTTCAGAGTTGATCTCCA-ATTGATCCGGTGCGG
1 TCATTCCAAGAAGTTTCCGAAGATCAGAGTTGATCTCCAGATTAATCCGGTGCGG
*
5050 TCATTCCAAGAAGTTTCCGAAGATCAGAGTTTATCTC
1 TCATTCCAAGAAGTTTCCGAAGATCAGAGTTGATCTC
5087 ATTCCAAGAA
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 72 0.96
55 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (55 bp):
TCATTCCAAGAAGTTTCCGAAGATCAGAGTTGATCTCCAGATTAATCCGGTGCGG
Found at i:5096 original size:35 final size:34
Alignment explanation
Indices: 5050--5365 Score: 319
Period size: 35 Copynumber: 9.1 Consensus size: 34
5040 TCCGGTGCGG
* *
5050 TCATTCCAAGAAGTTTCCGAAGATCAGAGTTTATC
1 TCATTCCAAGAAGTTTCC-ATGATCAGAGTTGATC
* *
5085 TCATTCCAAGAAGTTTCCAACGATCAGAGTTGATG
1 TCATTCCAAGAAGTTTCC-ATGATCAGAGTTGATC
* ** * *
5120 TCATTCCAAAAAGTGTTTGAAGATCAGATTTGATC
1 TCATTCCAAGAAGT-TTCCATGATCAGAGTTGATC
* * * *
5155 TCATTCCAAGAAATTTTCAGCGATCCGAGTTGATC
1 TCATTCCAAGAAGTTTCCA-TGATCAGAGTTGATC
* *
5190 TTATTCCAAGAAGTTTCCATGGTCAGAGTTGATC
1 TCATTCCAAGAAGTTTCCATGATCAGAGTTGATC
* *
5224 TCATTTCAAGTAGTTTTCCATGATCAGAGTTGATC
1 TCATTCCAAGAAG-TTTCCATGATCAGAGTTGATC
* **
5259 TCATTTCAAGAAGTTTTAGATGATCAGAGTTGATC
1 TCATTCCAAGAAG-TTTCCATGATCAGAGTTGATC
* *
5294 CCATTTCAA-ATAGTTTTCCATGATCAGAGTTGATC
1 TCATTCCAAGA-AG-TTTCCATGATCAGAGTTGATC
* * *
5329 TCATTTCAAGAAGTTTTCGATGGTCAGAGTTGATC
1 TCATTCCAAGAAG-TTTCCATGATCAGAGTTGATC
5364 TC
1 TC
5366 GAGTTGATCC
Statistics
Matches: 241, Mismatches: 35, Indels: 10
0.84 0.12 0.03
Matches are distributed among these distances:
34 27 0.11
35 211 0.88
36 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (34 bp):
TCATTCCAAGAAGTTTCCATGATCAGAGTTGATC
Found at i:6757 original size:17 final size:17
Alignment explanation
Indices: 6737--6776 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
6727 TATTATTTAT
*
6737 TATTATCTATTTAGTAC
1 TATTATCTATTTAATAC
6754 TATTATCTATTTAATAC
1 TATTATCTATTTAATAC
6771 TATTAT
1 TATTAT
6777 TTATCTATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.55
Consensus pattern (17 bp):
TATTATCTATTTAATAC
Found at i:6898 original size:24 final size:22
Alignment explanation
Indices: 6871--6936 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 22
6861 TGTCCATTTG
6871 TTTATATATCTATTTATCTTTTT
1 TTTATATATCTATTTA-CTTTTT
*
6894 ATTTATCTATACT-TTTACTTTTT
1 -TTTATATAT-CTATTTACTTTTT
6917 TTTATAGTTATCTA-TTACTT
1 TTTATA--TATCTATTTACTT
6937 AATTATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
22 5 0.14
23 14 0.39
24 15 0.42
25 2 0.06
ACGTcount: A:0.23, C:0.11, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTATATATCTATTTACTTTTT
Found at i:8460 original size:22 final size:22
Alignment explanation
Indices: 8347--8745 Score: 184
Period size: 22 Copynumber: 18.5 Consensus size: 22
8337 CTCTGCGTCA
***
8347 TTATCAAAATTTCATAGTAAAG
1 TTATCAAAATTTCATAGTGTGG
* *
8369 TTATTAAAAGTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGTGG
* * *
8391 TTATTAAAATTTTATAGTGTTG
1 TTATCAAAATTTCATAGTGTGG
* * ** *
8413 TAATTAAAATTTCATACGAAT-A
1 TTATCAAAATTTCATA-GTGTGG
8435 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGTGG
* *** *
8457 TTATCACAATTTCATAACATAG
1 TTATCAAAATTTCATAGTGTGG
**
8479 TT-TCCAAAATCCCA-A-----G
1 TTAT-CAAAATTTCATAGTGTGG
* *
8495 TTATCAAAATTTCAGAG-GAAT-A
1 TTATCAAAATTTCATAGTG--TGG
* *
8517 TTATCAAAGTTTCATAATGTGG
1 TTATCAAAATTTCATAGTGTGG
* * *
8539 TTATCAAAATTTCAGAGGGAGG
1 TTATCAAAATTTCATAGTGTGG
* *
8561 TTATCAAAATTTAATAGTGTAG
1 TTATCAAAATTTCATAGTGTGG
* * *
8583 TTATCGAAATTTCATAGGGAGG
1 TTATCAAAATTTCATAGTGTGG
** *
8605 -TGCCAAAATTTCAAAGTGTGG
1 TTATCAAAATTTCATAGTGTGG
* *
8626 TTATCGAAATTTCATAG-AT-G
1 TTATCAAAATTTCATAGTGTGG
* *
8646 TTATCAAGATTAT-ATAAG-GAGG
1 TTATCAAAATT-TCAT-AGTGTGG
* ** *
8668 TTATCAAAATGTGGTTGTGTGG
1 TTATCAAAATTTCATAGTGTGG
* *
8690 TTATTAAAATTTCACA-TG-GAG
1 TTATCAAAATTTCATAGTGTG-G
* *
8711 ATTATCAAAATTTCATTGTGTGA
1 -TTATCAAAATTTCATAGTGTGG
8734 TTATCAAAATTT
1 TTATCAAAATTT
8746 GATATGAGTA
Statistics
Matches: 277, Mismatches: 78, Indels: 44
0.69 0.20 0.11
Matches are distributed among these distances:
16 11 0.04
17 2 0.01
20 13 0.05
21 29 0.10
22 216 0.78
23 5 0.02
24 1 0.00
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGG
Found at i:9485 original size:19 final size:19
Alignment explanation
Indices: 9461--9504 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
9451 AGTTTCAACT
*
9461 TTCAACCTTGAATATATTA
1 TTCAACCTTCAATATATTA
* *
9480 TTCAACCTTCAATATGTTC
1 TTCAACCTTCAATATATTA
9499 TTCAAC
1 TTCAAC
9505 TGGACTCTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.41
Consensus pattern (19 bp):
TTCAACCTTCAATATATTA
Found at i:11461 original size:156 final size:156
Alignment explanation
Indices: 11182--11552 Score: 381
Period size: 156 Copynumber: 2.4 Consensus size: 156
11172 CATCTTGGCC
* ** * * * * *** *
11182 AAGTTTCATCTCAAACAGACTTAAGATGAAAAACTTATGCAAGTTTTTCAGTTAAGGTCAGTTTG
1 AAGTTTCAGCTCATTCAGACTTAGGATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACCTA
* * * * **
11247 GGGTGAGAAACCAACTTCACTATGATAGGGAGTTTTGTTTTACTTAAAATTTTTTCCATAGTCTT
66 GGGAGAGAAACCAACTTCACCATCATAGGGAGCTCGGTTTTACTTAAAATTTTTTCCATAGTCTT
* * * * **
11312 ATGGAGATACTCTAAGTCTCGTGGCC
131 ATGGAAAGAATCTAAGTCCCGTGGAA
*
11338 AAGTTTCAGCTTCATT-GGACTTAGGATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACCT
1 AAGTTTCAGC-TCATTCAGACTTAGGATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACCT
* * ** *
11402 AGGGAGAGAAACCTAGTTCACCATCA-AGGGGAGCTCGGTTTTACTTGGATTTTTTTCCATAGTC
65 AGGGAGAGAAACCAACTTCACCATCATA-GGGAGCTCGGTTTTACTTAAAATTTTTTCCATAGTC
* * *
11466 TTGTGGAAAGAATTTAAGTCCCTTGGAA
129 TTATGGAAAGAATCTAAGTCCCGTGGAA
* *
11494 AAGTTTCAGCTCATTCAGACAT-GAAATG-AAAACTTATGCTAGTTTTTCATTTAAGGACA
1 AAGTTTCAGCTCATTCAGACTTAG-GATGAAAAACTTATGCTAGTTTTTCATTTAAGGACA
11553 GTTTGAGGTG
Statistics
Matches: 176, Mismatches: 35, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
155 38 0.22
156 135 0.77
157 3 0.02
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (156 bp):
AAGTTTCAGCTCATTCAGACTTAGGATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACCTA
GGGAGAGAAACCAACTTCACCATCATAGGGAGCTCGGTTTTACTTAAAATTTTTTCCATAGTCTT
ATGGAAAGAATCTAAGTCCCGTGGAA
Found at i:17804 original size:21 final size:21
Alignment explanation
Indices: 17780--17819 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
17770 ATGGATTCTC
* *
17780 AAAATAACTAAATTAAACTTG
1 AAAACAACTAAATAAAACTTG
*
17801 AAAACAATTAAATAAAACT
1 AAAACAACTAAATAAAACT
17820 AAACTAGAGA
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:0.62, C:0.10, G:0.03, T:0.25
Consensus pattern (21 bp):
AAAACAACTAAATAAAACTTG
Found at i:20501 original size:19 final size:18
Alignment explanation
Indices: 20468--20504 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
20458 TTGAAATAAT
20468 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
20486 TCTTCAAATTATCTTCAAG
1 TCTTC-AATGATCTTCAAG
20505 AAGTCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:20818 original size:15 final size:16
Alignment explanation
Indices: 20798--20827 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20788 TGTTAGTTAA
20798 TCAAAA-ATCAATTTT
1 TCAAAAGATCAATTTT
20813 TCAAAAGATCAATTT
1 TCAAAAGATCAATTT
20828 GAATTCACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (16 bp):
TCAAAAGATCAATTTT
Found at i:20959 original size:15 final size:15
Alignment explanation
Indices: 20939--20968 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20929 CATCATTCTT
20939 AAGTAGCTATAATCA
1 AAGTAGCTATAATCA
*
20954 AAGTAGCTCTAATCA
1 AAGTAGCTATAATCA
20969 CTTACCATTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (15 bp):
AAGTAGCTATAATCA
Found at i:26676 original size:21 final size:21
Alignment explanation
Indices: 26650--26691 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
26640 GCACAAGTGA
*
26650 CCGGCCATGCGACTTGGAGAT
1 CCGGCCACGCGACTTGGAGAT
26671 CCGGCCACGCGACTTGGAGAT
1 CCGGCCACGCGACTTGGAGAT
26692 GCCCGACCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.31, G:0.33, T:0.17
Consensus pattern (21 bp):
CCGGCCACGCGACTTGGAGAT
Found at i:26713 original size:33 final size:33
Alignment explanation
Indices: 26671--26777 Score: 162
Period size: 33 Copynumber: 3.2 Consensus size: 33
26661 ACTTGGAGAT
*
26671 CCGGCCACGCGACTTGGAGATGCCCGACCATCA
1 CCGGCCACGCGACTTGGAGATGCCCGGCCATCA
*
26704 CCGGCCACGCGACTCGGAGATGCCCGGCCATCA
1 CCGGCCACGCGACTTGGAGATGCCCGGCCATCA
* *
26737 CCGGCCACGCGACATGGACATGCCCGGCCA-CA
1 CCGGCCACGCGACTTGGAGATGCCCGGCCATCA
26769 CTCGGCCAC
1 C-CGGCCAC
26778 ATGATTCGGC
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
32 3 0.04
33 65 0.96
ACGTcount: A:0.20, C:0.43, G:0.28, T:0.09
Consensus pattern (33 bp):
CCGGCCACGCGACTTGGAGATGCCCGGCCATCA
Found at i:26777 original size:66 final size:66
Alignment explanation
Indices: 26671--26810 Score: 176
Period size: 66 Copynumber: 2.1 Consensus size: 66
26661 ACTTGGAGAT
* * * *
26671 CCGGCCACGCGACTTGGAGATGCCCGACCATCACCGGCCACGCGACTCGGAGATGCCCGGCCATC
1 CCGGCCACGCGACATGGACATGCCCGACCATCACCGGCCACACGACTCGGACATGCCCGGCCA-C
26736 -A
65 AA
* * * *
26737 CCGGCCACGCGACATGGACATGCCCGGCCA-CACTCGGCCACATGATTCGGCCATGCCCGGCCAC
1 CCGGCCACGCGACATGGACATGCCCGACCATCAC-CGGCCACACGACTCGGACATGCCCGGCCAC
26801 AA
65 AA
26803 CCGGCCAC
1 CCGGCCAC
26811 ATGATCCTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
65 4 0.06
66 60 0.94
ACGTcount: A:0.20, C:0.43, G:0.27, T:0.10
Consensus pattern (66 bp):
CCGGCCACGCGACATGGACATGCCCGACCATCACCGGCCACACGACTCGGACATGCCCGGCCACA
A
Found at i:27760 original size:7 final size:8
Alignment explanation
Indices: 27732--27765 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
27722 CACCTTCTTG
27732 AAAAATTC
1 AAAAATTC
*
27740 AAAAATTT
1 AAAAATTC
27748 AGAAAATTC
1 A-AAAATTC
27757 AAAAATTC
1 AAAAATTC
27765 A
1 A
27766 TAACCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.62, C:0.09, G:0.03, T:0.26
Consensus pattern (8 bp):
AAAAATTC
Found at i:27856 original size:5 final size:5
Alignment explanation
Indices: 27839--27877 Score: 69
Period size: 5 Copynumber: 7.6 Consensus size: 5
27829 GTTATATCGA
27839 AAAAT ATAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
27878 TTTCGACCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 28 0.85
6 5 0.15
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:33279 original size:33 final size:33
Alignment explanation
Indices: 33241--33348 Score: 121
Period size: 33 Copynumber: 3.3 Consensus size: 33
33231 AGCACAAGTG
*
33241 ACCGGCCACGCGACTTGGAGATGCCC-GCGCAAC
1 ACCGGCCACGCGACATGGAGATGCCCGGC-CAAC
* *
33274 ACCGGCCATGCGACATGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACATGGAGATGCCCGGCCAAC
* ** *
33307 ACCGGCCACGCGATATGGCCAAGCCCGGCC-AC
1 ACCGGCCACGCGACATGGAGATGCCCGGCCAAC
33339 ACCCGGCCAC
1 A-CCGGCCAC
33349 ATGACTCGGC
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
32 2 0.03
33 60 0.94
34 2 0.03
ACGTcount: A:0.21, C:0.42, G:0.29, T:0.08
Consensus pattern (33 bp):
ACCGGCCACGCGACATGGAGATGCCCGGCCAAC
Found at i:33360 original size:33 final size:33
Alignment explanation
Indices: 33323--33385 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
33313 CACGCGATAT
* *
33323 GGCCAAGCCCGGCCACACCCGGCCACATGACTC
1 GGCCAAGCCCAGCCACAACCGGCCACATGACTC
* *
33356 GGCCATGCCCAGCCACAACCGGCCATATGA
1 GGCCAAGCCCAGCCACAACCGGCCACATGA
33386 TCCTTTAGCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.24, C:0.44, G:0.24, T:0.08
Consensus pattern (33 bp):
GGCCAAGCCCAGCCACAACCGGCCACATGACTC
Found at i:34483 original size:64 final size:64
Alignment explanation
Indices: 34405--34580 Score: 217
Period size: 64 Copynumber: 2.8 Consensus size: 64
34395 GCGACAAAGT
* * * * *
34405 TCCAGCTTTTCCAAAGTTCACGCCGCAGTAGGAGTCCATGCGGCAGCTTGATACCACGCGGCAA
1 TCCAGCTTTCCCAAAGTTCACGCCACAGTAGGAATCCATACGACAGCTTGATACCACGCGGCAA
* ** * * * * *
34469 TCCAGCTTTCCCAAAGTTCACGTCACAACAGGATTCCATACGACAGCTTGTTCCCATGCGGCTA
1 TCCAGCTTTCCCAAAGTTCACGCCACAGTAGGAATCCATACGACAGCTTGATACCACGCGGCAA
* *
34533 TCCAGCTCTCCCAAAGTTCATGCCACAGTAGGAATCCATACGACAGCT
1 TCCAGCTTTCCCAAAGTTCACGCCACAGTAGGAATCCATACGACAGCT
34581 AGAGACGGTG
Statistics
Matches: 94, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
64 94 1.00
ACGTcount: A:0.26, C:0.32, G:0.20, T:0.22
Consensus pattern (64 bp):
TCCAGCTTTCCCAAAGTTCACGCCACAGTAGGAATCCATACGACAGCTTGATACCACGCGGCAA
Done.