Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005030.1 Corchorus capsularis cultivar CVL-1 contig05048, 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: 11409
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:897 original size:52 final size:52
Alignment explanation
Indices: 817--951 Score: 202
Period size: 50 Copynumber: 2.6 Consensus size: 52
807 TGTTAATGCA
817 TGTATTTGCTTGATCTTCTCTCTGACTTGAAAATCTAGACTCATCATTTTAC
1 TGTATTTGCTTGATCTTCTCTCTGACTTGAAAATCTAGACTCATCATTTTAC
* * * *
869 TGTATTTGCTTGATCTTCCCTCTAACTTG--AATGTAGGCTCATCATTTTAC
1 TGTATTTGCTTGATCTTCTCTCTGACTTGAAAATCTAGACTCATCATTTTAC
* *
919 TTTGTTTGCTTGATCTTCTCTCTGACTTGAAAA
1 TGTATTTGCTTGATCTTCTCTCTGACTTGAAAA
952 GACTTGAAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
50 44 0.60
52 29 0.40
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (52 bp):
TGTATTTGCTTGATCTTCTCTCTGACTTGAAAATCTAGACTCATCATTTTAC
Found at i:2152 original size:5 final size:5
Alignment explanation
Indices: 2137--2194 Score: 50
Period size: 5 Copynumber: 11.2 Consensus size: 5
2127 CTAAAATAAT
2137 ATATGA ATATA ATATA ATATA ATAT- ATA-A TATATA ATAT- ATAATA
1 ATAT-A ATATA ATATA ATATA ATATA ATATA -ATATA ATATA AT-ATA
2182 TATAATA ATATA A
1 -AT-ATA ATATA A
2195 ATTATATATA
Statistics
Matches: 46, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
4 5 0.11
5 28 0.61
6 7 0.15
7 6 0.13
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:2155 original size:21 final size:20
Alignment explanation
Indices: 2131--2183 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 20
2121 ATAAAACTAA
2131 AATAATATATGAATATAATAT
1 AATAATATAT-AATATAATAT
2152 AAT-ATA-AT-ATATAATAT
1 AATAATATATAATATAATAT
2169 -ATAATATATAATATA
1 AATAATATATAATATA
2184 TAATAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 2 0.07
17 12 0.41
18 2 0.07
19 7 0.24
20 3 0.10
21 3 0.10
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
AATAATATATAATATAATAT
Found at i:2165 original size:7 final size:7
Alignment explanation
Indices: 2132--2194 Score: 83
Period size: 7 Copynumber: 8.6 Consensus size: 7
2122 TAAAACTAAA
2132 ATAATAT
1 ATAATAT
2139 ATGAATAT
1 AT-AATAT
2147 A-ATATAAT
1 ATA-AT-AT
2155 ATAATAT
1 ATAATAT
2162 ATAATAT
1 ATAATAT
2169 ATAATAT
1 ATAATAT
2176 ATAATAT
1 ATAATAT
2183 ATAATAAT
1 ATAAT-AT
2191 ATAA
1 ATAA
2195 ATTATATATA
Statistics
Matches: 51, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
6 1 0.02
7 32 0.63
8 17 0.33
9 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (7 bp):
ATAATAT
Found at i:2203 original size:26 final size:26
Alignment explanation
Indices: 2131--2204 Score: 75
Period size: 26 Copynumber: 2.8 Consensus size: 26
2121 ATAAAACTAA
2131 AATAAT-ATATGAA-TATAATATAATAT
1 AATAATAATAT-AATTAT-ATATAATAT
*
2157 AATATATAATAT-ATAATATATAATAT
1 AATA-ATAATATAATTATATATAATAT
2183 -ATAATAATATAAATTATATATA
1 AATAATAATAT-AATTATATATA
2205 TTTTTTAACA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
24 7 0.17
25 3 0.07
26 23 0.56
27 4 0.10
28 4 0.10
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (26 bp):
AATAATAATATAATTATATATAATAT
Found at i:4303 original size:15 final size:15
Alignment explanation
Indices: 4248--4303 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
4238 ATTCGGATTG
*
4248 AATTTGGGTCAGGTT
1 AATTCGGGTCAGGTT
* *
4263 AATTCGGATTCGGGTT
1 AATTCGG-GTCAGGTT
*
4279 GAATTTGGGTCAGGTT
1 -AATTCGGGTCAGGTT
4295 AATTCGGGT
1 AATTCGGGT
4304 TCGGGTTCAG
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
15 14 0.44
16 12 0.38
17 6 0.19
ACGTcount: A:0.20, C:0.09, G:0.34, T:0.38
Consensus pattern (15 bp):
AATTCGGGTCAGGTT
Found at i:4308 original size:32 final size:32
Alignment explanation
Indices: 4234--4320 Score: 138
Period size: 32 Copynumber: 2.7 Consensus size: 32
4224 CGGGTTTGAA
*
4234 TCGGATTCGGATTGAATTTGGGTCAGGTTAAT
1 TCGGATTCGGGTTGAATTTGGGTCAGGTTAAT
4266 TCGGATTCGGGTTGAATTTGGGTCAGGTTAAT
1 TCGGATTCGGGTTGAATTTGGGTCAGGTTAAT
* * *
4298 TCGGGTTCGGGTTCAGTTTGGGT
1 TCGGATTCGGGTTGAATTTGGGT
4321 TTTGGCCAGA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.16, C:0.10, G:0.36, T:0.38
Consensus pattern (32 bp):
TCGGATTCGGGTTGAATTTGGGTCAGGTTAAT
Found at i:4479 original size:16 final size:16
Alignment explanation
Indices: 4458--4516 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 16
4448 TTTTCATAAA
*
4458 TTTTCGGATTCGGGTT
1 TTTTCGGGTTCGGGTT
* * *
4474 TTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGGGTT
*
4490 TTTTCGGGTTCAGGTT
1 TTTTCGGGTTCGGGTT
4506 TTTTCGGGTTC
1 TTTTCGGGTTC
4517 AAGTTCAGGC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.05, C:0.14, G:0.31, T:0.51
Consensus pattern (16 bp):
TTTTCGGGTTCGGGTT
Found at i:6466 original size:22 final size:22
Alignment explanation
Indices: 6434--6485 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
6424 CGACGTGTTT
*
6434 AATTTTGATAACCTTCCAATGA
1 AATTTTAATAACCTTCCAATGA
6456 AATTTTAATAACCTTCCAATGA
1 AATTTTAATAACCTTCCAATGA
6478 AATTTTAA
1 AATTTTAA
6486 ATTATGATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.38
Consensus pattern (22 bp):
AATTTTAATAACCTTCCAATGA
Found at i:6801 original size:22 final size:22
Alignment explanation
Indices: 6776--7020 Score: 151
Period size: 22 Copynumber: 11.1 Consensus size: 22
6766 GAATTGTTAG
*
6776 TAATCACACTCTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
6798 TAATCATACTATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
* *
6820 TAATCTCGCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
*
6842 TAAATCTTC-CTAT-AAGATTTTGA
1 T-AATC-ACACTATGAA-ATTTTGA
* * * **
6865 TAACCTCCCTATGATTTTTTGA
1 TAATCACACTATGAAATTTTGA
* * *
6887 TAATCTCATTATGAAATTTTGT
1 TAATCACACTATGAAATTTTGA
* * *
6909 TAATCTCCCTATTAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
6931 T-CTACATACTATGAAATTTTGA
1 TAAT-CACACTATGAAATTTTGA
* *
6953 TAA-CCCTCATATGAAATTTTGA
1 TAATCACAC-TATGAAATTTTGA
* * *
6975 -AAACTAAACTATGGAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
* *
6997 TAACCTTCA-TATGAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
7019 TA
1 TA
7021 TCCTCCCAAA
Statistics
Matches: 175, Mismatches: 37, Indels: 22
0.75 0.16 0.09
Matches are distributed among these distances:
21 7 0.04
22 143 0.82
23 23 0.13
24 2 0.01
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:6877 original size:67 final size:66
Alignment explanation
Indices: 6789--6974 Score: 200
Period size: 67 Copynumber: 2.8 Consensus size: 66
6779 TCACACTCTG
* * *
6789 AAATTTTGAT-AATCATACTATGAAATTGTGATAATCTCGCTATGAAATTTTGATAAATCTTCCT
1 AAATTTTGATCAA-CATACTATGAAATTTTGATAATCTC-ATATGAAATTTTGATAAATCTCCCT
6853 A-T
64 ATT
* * ** *
6855 AAGATTTTGAT-AACCTCCCTATGATTTTTTGATAATCTCATTATGAAATTTTG-TTAATCTCCC
1 AA-ATTTTGATCAACAT-ACTATGAAATTTTGATAATCTCA-TATGAAATTTTGATAAATCTCCC
6918 TATT
63 TATT
* *
6922 AAATTTTGATCTACATACTATGAAATTTTGATAACCCTCATATGAAATTTTGA
1 AAATTTTGATCAACATACTATGAAATTTTGATAA-TCTCATATGAAATTTTGA
6975 AAACTAAACT
Statistics
Matches: 99, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
66 49 0.49
67 50 0.51
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (66 bp):
AAATTTTGATCAACATACTATGAAATTTTGATAATCTCATATGAAATTTTGATAAATCTCCCTAT
T
Found at i:6885 original size:45 final size:45
Alignment explanation
Indices: 6787--7020 Score: 187
Period size: 44 Copynumber: 5.3 Consensus size: 45
6777 AATCACACTC
* *
6787 TGAAATTTTGAT-AATCATACTATGAAATTGTGATAATCTCGCTA
1 TGAAATTTTGATAAATCATACTATGAAATTGTGATAACCTCCCTA
* * *
6831 TGAAATTTTGATAAATCTTCCTAT-AAGATTTTGATAACCTCCCTA
1 TGAAATTTTGATAAATCATACTATGAA-ATTGTGATAACCTCCCTA
** * * * *
6876 TGATTTTTTGAT-AATC-TCATTATGAAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAAATCAT-ACTATGAAATTGTGATAACCTCCCTA
* ** * *
6920 TTAAATTTTGATCTA-CATACTATGAAATTTTGATAACC-CTCATA
1 TGAAATTTTGATAAATCATACTATGAAATTGTGATAACCTC-CCTA
* * * * *
6964 TGAAATTTTGA-AAA-CTAAACTATGGAATTTTGATAACCTTCATA
1 TGAAATTTTGATAAATC-ATACTATGAAATTGTGATAACCTCCCTA
7008 TGAAATTTTGATA
1 TGAAATTTTGATA
7021 TCCTCCCAAA
Statistics
Matches: 155, Mismatches: 25, Indels: 19
0.78 0.13 0.10
Matches are distributed among these distances:
43 4 0.03
44 112 0.72
45 39 0.25
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.41
Consensus pattern (45 bp):
TGAAATTTTGATAAATCATACTATGAAATTGTGATAACCTCCCTA
Found at i:7196 original size:22 final size:22
Alignment explanation
Indices: 7147--7250 Score: 93
Period size: 22 Copynumber: 4.8 Consensus size: 22
7137 TCACATTTTG
7147 AAAA-TTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
* * *
7168 GAGATTTTTATAACCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
* * * *
7190 AAAATTTTGTTGACCCCTCTAT
1 AAAATTTTGATAACCTCTTTAT
* * * *
7212 AAAATTCTGATAATCACATTAT
1 AAAATTTTGATAACCTCTTTAT
*
7234 ATAATTTTGATAACCTC
1 AAAATTTTGATAACCTC
7251 GCTTTGAAAT
Statistics
Matches: 61, Mismatches: 21, Indels: 1
0.73 0.25 0.01
Matches are distributed among these distances:
21 2 0.03
22 59 0.97
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (22 bp):
AAAATTTTGATAACCTCTTTAT
Found at i:7261 original size:22 final size:21
Alignment explanation
Indices: 7236--7336 Score: 78
Period size: 22 Copynumber: 4.5 Consensus size: 21
7226 CACATTATAT
* *
7236 AATTTTGATAACCTCGCTTTGA
1 AATTTTGATAACATC-CTATGA
* *
7258 AATTTTGACAACAACACTATGA
1 AATTTTGATAACATC-CTATGA
*
7280 AATTTTGATAATCTTCCTAT-A
1 AATTTTGATAA-CATCCTATGA
7301 AATTTTGATAATCTGATCTCTATGA
1 AATTTTGATAA-C--ATC-CTATGA
*
7326 AATTTCGATAA
1 AATTTTGATAA
7337 TTATTCTATG
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
21 14 0.22
22 31 0.48
23 4 0.06
24 4 0.06
25 11 0.17
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.40
Consensus pattern (21 bp):
AATTTTGATAACATCCTATGA
Found at i:7305 original size:21 final size:24
Alignment explanation
Indices: 7274--7374 Score: 103
Period size: 21 Copynumber: 4.5 Consensus size: 24
7264 GACAACAACA
7274 CTATGAAATTTTGATAATCT-TC-
1 CTATGAAATTTTGATAATCTATCT
7296 CTAT-AAATTTTGATAATCTGATCT
1 CTATGAAATTTTGATAATCT-ATCT
*
7320 CTATGAAATTTCGATAAT-TAT-T
1 CTATGAAATTTTGATAATCTATCT
*
7342 CTATGAGA-TTTGATAAT-T-T-T
1 CTATGAAATTTTGATAATCTATCT
*
7362 CTATCAAATTTTG
1 CTATGAAATTTTG
7375 GTACCCCTTA
Statistics
Matches: 69, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
20 8 0.12
21 28 0.41
22 12 0.17
23 4 0.06
24 5 0.07
25 12 0.17
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.47
Consensus pattern (24 bp):
CTATGAAATTTTGATAATCTATCT
Found at i:7426 original size:22 final size:23
Alignment explanation
Indices: 7397--7451 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
7387 AAATTGAGAC
* *
7397 TTTT-ATAACCTTCA-TATGAAA
1 TTTTGATAACCTACACTATAAAA
7418 TTTTGATAACC-ACACTATAAAA
1 TTTTGATAACCTACACTATAAAA
7440 TTTTGATAACCT
1 TTTTGATAACCT
7452 CCCCATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.40
Consensus pattern (23 bp):
TTTTGATAACCTACACTATAAAA
Found at i:7462 original size:22 final size:22
Alignment explanation
Indices: 7415--7475 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
7405 CCTTCATATG
* * *
7415 AAATTTTGATAACCACACTATA
1 AAATTTTGATAACCTCCCCATA
*
7437 AAATTTTGATAACCTCCCCATT
1 AAATTTTGATAACCTCCCCATA
*
7459 AAATATT-AGTAACCTCC
1 AAATTTTGA-TAACCTCC
7476 TAATGGAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 1 0.03
22 32 0.97
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.33
Consensus pattern (22 bp):
AAATTTTGATAACCTCCCCATA
Found at i:7633 original size:24 final size:22
Alignment explanation
Indices: 7572--7755 Score: 99
Period size: 22 Copynumber: 8.3 Consensus size: 22
7562 TTGTGATAAT
* *
7572 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
*
7594 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
* **
7616 TAACCTGATCCTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTTAA
*
7640 TAACC-ACACTAT-AAAGTTTTCA
1 TAACCAAC-CTATGAAA-TTTTAA
** * **
7662 TAA-CTTCCATATGAAAATTTGG
1 TAACCAACC-TATGAAATTTTAA
* *
7684 TAACC-ACACTGTGAAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
* *
7706 TAACC-TCCTCATGAAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
* * *
7728 TAACCATCTTATGAAATTTTGA
1 TAACCAACCTATGAAATTTTAA
7750 TAACCA
1 TAACCA
7756 CTTAGAGACA
Statistics
Matches: 126, Mismatches: 25, Indels: 22
0.73 0.14 0.13
Matches are distributed among these distances:
21 8 0.06
22 92 0.73
23 8 0.06
24 18 0.14
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.33
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:7644 original size:46 final size:44
Alignment explanation
Indices: 7579--7723 Score: 127
Period size: 44 Copynumber: 3.2 Consensus size: 44
7569 AATTAACCAC
***
7579 CCTATGAAATTTCAATAACCA-ACCTAAGAAATTTTAATAACCTGAT
1 CCTATGAAATTTTGGTAACCACA-CTAAGAAATTTTAATAACCT--T
* *
7625 CCTATGAAATTTTGGTAACCACACTATA-AAGTTTTCATAA-CTT
1 CCTATGAAATTTTGGTAACCACACTA-AGAAATTTTAATAACCTT
* ** *
7668 CCATATGAAAATTTGGTAACCACACTGTGAAATTTTGATAACC-T
1 CC-TATGAAATTTTGGTAACCACACTAAGAAATTTTAATAACCTT
7712 CCTCATGAAATT
1 CCT-ATGAAATT
7724 ATAATAACCA
Statistics
Matches: 82, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
43 4 0.05
44 42 0.51
45 3 0.04
46 31 0.38
47 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (44 bp):
CCTATGAAATTTTGGTAACCACACTAAGAAATTTTAATAACCTT
Found at i:9616 original size:30 final size:31
Alignment explanation
Indices: 9582--9646 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
9572 CGGCAATTTA
* *
9582 GAAATATGTTTTAAAAA-AAATGTATAATTG
1 GAAATATGTTTTAAAAATAAAGGTATAATCG
*
9612 GAAATATGTTTTAAAAATAAGGGTATAATCG
1 GAAATATGTTTTAAAAATAAAGGTATAATCG
9643 GAAA
1 GAAA
9647 ATATAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.49, C:0.02, G:0.17, T:0.32
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAAGGTATAATCG
Found at i:9682 original size:2 final size:2
Alignment explanation
Indices: 9675--9716 Score: 66
Period size: 2 Copynumber: 20.5 Consensus size: 2
9665 TTCGTACTTT
*
9675 TA TA TA TA GTG 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 TA T
9717 GTATTGAAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 36 0.97
3 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9886 original size:23 final size:22
Alignment explanation
Indices: 9859--9902 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
9849 TCTGTCCGAT
9859 TCGA-GACCCGAATGACCCGTAAC
1 TCGAGGACCCG-A-GACCCGTAAC
9882 TCGAGTGACCCGAGACCCGTA
1 TCGAG-GACCCGAGACCCGTA
9903 TGACCCGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 12 0.63
24 1 0.05
25 6 0.32
ACGTcount: A:0.27, C:0.34, G:0.25, T:0.14
Consensus pattern (22 bp):
TCGAGGACCCGAGACCCGTAAC
Found at i:9906 original size:16 final size:15
Alignment explanation
Indices: 9860--9912 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 15
9850 CTGTCCGATT
9860 CGAGACCCGAATGACC
1 CGAGACCCG-ATGACC
*
9876 CGTA-ACTCGAGTGACC
1 CG-AGACCCGA-TGACC
9892 CGAGACCCGTATGACC
1 CGAGACCCG-ATGACC
9908 CGAGA
1 CGAGA
9913 AGTTAACCCG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 2 0.06
16 27 0.87
17 2 0.06
ACGTcount: A:0.28, C:0.34, G:0.26, T:0.11
Consensus pattern (15 bp):
CGAGACCCGATGACC
Found at i:11083 original size:16 final size:16
Alignment explanation
Indices: 11064--11131 Score: 79
Period size: 16 Copynumber: 4.3 Consensus size: 16
11054 AGACTCGGTA
*
11064 GACCCGAGACCCGAAT
1 GACCCGAAACCCGAAT
11080 GACCCGAAACCCGAAT
1 GACCCGAAACCCGAAT
*
11096 AACCCG-AACCC-AGAT
1 GACCCGAAACCCGA-AT
11111 GA-CCGAAAACCCGAAT
1 GACCCG-AAACCCGAAT
11127 GACCC
1 GACCC
11132 AATAAAACTG
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
14 4 0.09
15 8 0.18
16 29 0.66
17 3 0.07
ACGTcount: A:0.37, C:0.38, G:0.19, T:0.06
Consensus pattern (16 bp):
GACCCGAAACCCGAAT
Done.