Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007863.1 Corchorus capsularis cultivar CVL-1 contig07884, 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: 15452
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:3547 original size:20 final size:20
Alignment explanation
Indices: 3522--3560 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3512 AATAAGAGCA
3522 CCAATTTGCAAATCAAATGT
1 CCAATTTGCAAATCAAATGT
*
3542 CCAATTTGTAAATCAAATG
1 CCAATTTGCAAATCAAATG
3561 CCTTGCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (20 bp):
CCAATTTGCAAATCAAATGT
Found at i:3910 original size:26 final size:26
Alignment explanation
Indices: 3876--3965 Score: 98
Period size: 26 Copynumber: 3.5 Consensus size: 26
3866 CCACAAAGCT
3876 AAATCACTAAATGAGTGTAACAAACC
1 AAATCACTAAATGAGTGTAACAAACC
* * *
3902 AAATTACTAAATGA---AAACGAAGA-T
1 AAATCACTAAATGAGTGTAAC-AA-ACC
3926 AAATCACTAAATGAGTGTAACAAACC
1 AAATCACTAAATGAGTGTAACAAACC
*
3952 AAATTACTAAATGA
1 AAATCACTAAATGA
3966 AAACGAAGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
23 3 0.06
24 15 0.29
25 2 0.04
26 28 0.55
27 3 0.06
ACGTcount: A:0.53, C:0.14, G:0.11, T:0.21
Consensus pattern (26 bp):
AAATCACTAAATGAGTGTAACAAACC
Found at i:3934 original size:50 final size:50
Alignment explanation
Indices: 3875--3975 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
3865 ACCACAAAGC
3875 TAAATCACTAAATGAGTGTAACAAACCAAATTACTAAATGAAAACGAAGA
1 TAAATCACTAAATGAGTGTAACAAACCAAATTACTAAATGAAAACGAAGA
3925 TAAATCACTAAATGAGTGTAACAAACCAAATTACTAAATGAAAACGAAGA
1 TAAATCACTAAATGAGTGTAACAAACCAAATTACTAAATGAAAACGAAGA
3975 T
1 T
3976 GCAATACCAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.53, C:0.14, G:0.12, T:0.21
Consensus pattern (50 bp):
TAAATCACTAAATGAGTGTAACAAACCAAATTACTAAATGAAAACGAAGA
Found at i:9982 original size:22 final size:22
Alignment explanation
Indices: 9950--10017 Score: 91
Period size: 22 Copynumber: 3.1 Consensus size: 22
9940 CTAAAATTCA
* *
9950 GGACAAGTTCTGCCCATAACTT
1 GGACAACTTCTGCCCAGAACTT
*
9972 GGACAACTTCTGCCAAGAACTT
1 GGACAACTTCTGCCCAGAACTT
* *
9994 GGACAACGTCTGCCCAGGACTT
1 GGACAACTTCTGCCCAGAACTT
10016 GG
1 GG
10018 CCTGTTGAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.22
Consensus pattern (22 bp):
GGACAACTTCTGCCCAGAACTT
Found at i:11663 original size:509 final size:501
Alignment explanation
Indices: 10838--11844 Score: 1457
Period size: 509 Copynumber: 2.0 Consensus size: 501
10828 TGAACCTGGT
* * * * *
10838 TGATAGGAATCTAGTTGTATTAGATTCAAATCTATCCTAGAGACCCGCCAAGAATCTACTTGAAC
1 TGATACGAATCTAGTTGTATTAGATTCAAATCCAACCTAGAGACCCACCAAGAATCGACTTGAAC
* * *
10903 TTCTTCAACTTCTAGAAAGTATGTCGACAACCTTCACAAAGCAAGCTCTCTTCGTTCGTCAGCCC
66 TTCTTCAACTCCTAGAAAGTATGTCGACAACCTTCACAAAGCAAGCCCTCCTCGTTCGTCAGCCC
* * *
10968 TAAGTCTTCAATTAGACCTGCAATTGAACACCTAAGATCATAAGATTCACAAACAATTAAGCAAT
131 TAAGTCCTCAATTAGACCTGCAATTGAACACCTAAGATCACAAGATTCACAAACAACTAAGCAAT
*
11033 CACAACCTAATTGTTTGCTAGGACTCTACAAGATTGAACAACCCTAAGTTTGCTCAAACCAGAAC
196 CACAACCTAATTGCTTGCTAGGACTCTACAAGATTGAACAACCCTAAGTTTGCTCAAACCAGAAC
*
11098 AATGAAGCTAAGATAATCAATTTGGGAAGATGATCCTCAACTTTATTAATCAACTCAACTTATGT
261 AATGAAGCTAAGATAATCAATTTGGGAAGATAATCCTCAACTTTATTAATCAACTCAACTTATGT
* *
11163 TTACAAGAGGGGGATGGTCCCTTTATATAATAGTATGGGACGCATAACCCTTCTCCTAAAGCTAA
326 TTACAAGAGGGGGATGGTCCCTTTATATAATAGTAGGGGACGCATAACCCTTCTCCTAAAACTAA
* *
11228 AAGGAAAACATTACATAAAGGAAGGATCAAGGAAATTGCCTACTCCTTGTCCTACTAGGAAAAGT
391 AAGG--AA-A--ACATAAAGGAAGGAACAAGGAAATAGCCTACTCCTTGTCCTACTAGGAAAAGT
* *
11293 AAATAACATGACTTAATTTAAATAAGGATTGGACTTAGTCAAACAAGGCCTAA
451 AAAT-ACATAACTTAA-TTAAACAAGGATTGGACTTAGTCAAACAAGGCCTAA
* * * *
11346 TGATACGAATCTAGTTGTATTAGATTCAAATCCAACCTTTGAATATCCACCAA-AGTCGACTTGA
1 TGATACGAATCTAGTTGTATTAGATTCAAATCCAACC-TAG-AGACCCACCAAGAATCGACTTGA
** ** * * * * *
11410 ACTTCTTCAACTCCTAGACTTGTATGTCGATGATCTTCACAAAGCTATCCCTCCTCTTTCGTCGG
64 ACTTCTTCAACTCCTAGA-AAGTATGTCGACAACCTTCACAAAGCAAGCCCTCCTCGTTCGTCAG
* **
11475 CCTTAAG-CACTCAATTAGACCTGCAATTGAA-TTCTCAAGATCACAAGATTCACAAACAACTAA
128 CCCTAAGTC-CTCAATTAGACCTGCAATTGAACACCT-AAGATCACAAGATTCACAAACAACTAA
** * * *
11538 GTTATCTCAACCTAATTGCTTGCTAGGACTCTACAAGA-TGAAGAACCCTAAGTTTGCTCAAACT
191 GCAATCACAACCTAATTGCTTGCTAGGACTCTACAAGATTGAACAACCCTAAGTTTGCTCAAACC
11602 AGAACAATGAAGCTAAGATAATCAATTTGGGGAA-ATAATCCTCAACTTTATTAATCAACTCAAC
256 AGAACAATGAAGCTAAGATAATCAATTT-GGGAAGATAATCCTCAACTTTATTAATCAACTCAAC
* *
11666 TTATGTTTACAAGAGGGGGATGGTCCCTTTATATACTAGTAGGGGACGCATTACCCTTCTCCTAA
320 TTATGTTTACAAGAGGGGGATGGTCCCTTTATATAATAGTAGGGGACGCATAACCCTTCTCCTAA
* *
11731 AACTATAAGGAAAACATAAAGGAAGGAACAAGGAAATAGCCTATTCCTTGTCCTACTAGGAAAAG
385 AACTAAAAGGAAAACATAAAGGAAGGAACAAGGAAATAGCCTACTCCTTGTCCTACTAGGAAAAG
*
11796 TAAATACATAACTTAATTAAGCAAGGATTGGACTTAGTCAAACAAGGCC
450 TAAATACATAACTTAATTAAACAAGGATTGGACTTAGTCAAACAAGGCC
11845 CAACCCAATG
Statistics
Matches: 448, Mismatches: 45, Indels: 18
0.88 0.09 0.04
Matches are distributed among these distances:
502 31 0.07
503 10 0.02
504 54 0.12
506 1 0.00
507 2 0.00
508 34 0.08
509 182 0.41
510 134 0.30
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.28
Consensus pattern (501 bp):
TGATACGAATCTAGTTGTATTAGATTCAAATCCAACCTAGAGACCCACCAAGAATCGACTTGAAC
TTCTTCAACTCCTAGAAAGTATGTCGACAACCTTCACAAAGCAAGCCCTCCTCGTTCGTCAGCCC
TAAGTCCTCAATTAGACCTGCAATTGAACACCTAAGATCACAAGATTCACAAACAACTAAGCAAT
CACAACCTAATTGCTTGCTAGGACTCTACAAGATTGAACAACCCTAAGTTTGCTCAAACCAGAAC
AATGAAGCTAAGATAATCAATTTGGGAAGATAATCCTCAACTTTATTAATCAACTCAACTTATGT
TTACAAGAGGGGGATGGTCCCTTTATATAATAGTAGGGGACGCATAACCCTTCTCCTAAAACTAA
AAGGAAAACATAAAGGAAGGAACAAGGAAATAGCCTACTCCTTGTCCTACTAGGAAAAGTAAATA
CATAACTTAATTAAACAAGGATTGGACTTAGTCAAACAAGGCCTAA
Found at i:12233 original size:33 final size:32
Alignment explanation
Indices: 12196--12302 Score: 126
Period size: 33 Copynumber: 3.2 Consensus size: 32
12186 CGCCTAGCGA
*
12196 TGGCCGGT-TGTGGCCGGACATGTCCATGTCGCG
1 TGGCCGGTGT-TGGCCGGACATCTCCA-GTCGCG
* *
12229 TGGCCGGTGTTGGCCGGGCATCTCCGAGTCACG
1 TGGCCGGTGTTGGCCGGACATCTCC-AGTCGCG
* *
12262 TGGCCGGTGTTGGCCGGACTTCTCCAAGTCGCA
1 TGGCCGGTGTTGGCCGGACATCTCC-AGTCGCG
12295 TGGCCGGT
1 TGGCCGGT
12303 CACTAGTGCT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
33 62 0.97
34 2 0.03
ACGTcount: A:0.09, C:0.29, G:0.38, T:0.23
Consensus pattern (32 bp):
TGGCCGGTGTTGGCCGGACATCTCCAGTCGCG
Done.