Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013385.1 Corchorus capsularis cultivar CVL-1 contig13406, 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: 36836
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:391 original size:20 final size:20
Alignment explanation
Indices: 350--391 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
340 TTAGTATGGA
* * *
350 AAAATTTTTGTTTTTTTTAG
1 AAAATTTTTATTTATTTAAG
370 AAAATTTTTATTTATTTAAG
1 AAAATTTTTATTTATTTAAG
390 AA
1 AA
392 CTTATAATGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (20 bp):
AAAATTTTTATTTATTTAAG
Found at i:618 original size:4 final size:4
Alignment explanation
Indices: 611--641 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
601 TAAAAAAAAC
611 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATT
642 GCCAAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:1681 original size:139 final size:140
Alignment explanation
Indices: 1521--1851 Score: 513
Period size: 139 Copynumber: 2.4 Consensus size: 140
1511 AGGTTAGTGA
* * *
1521 TCGTTAGTTAATTTTGCCAATCAAAGTCGTAATTGATTGATAATTATTTAATTTTACCAT-AAAT
1 TCGTTAGTTAATTTTGCCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAAT
* *
1585 CACTACCAAAAAAATTAACATAAAGAAATAAATCAATTAGTAATTATGTT-ACCAAAAAATAAAT
66 CACCACC-AAAAAATTAACATAAAGAAATAAATCAATTAGTAATTATGTTAACAAAAAAATAAAT
1649 TATTCAACATG
130 TATTCAACATG
* *
1660 TCGTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATGATTATATGATTTTACCATAAAAT
1 TCGTTAGTTAATTTTGCCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAAT
* * *
1725 CGCCACCAAAAAATTACCATAAATAAATAAATCAATTAGTAATTATGTTAACAAAAAAATAAATT
66 CACCACCAAAAAATTAACATAAAGAAATAAATCAATTAGTAATTATGTTAACAAAAAAATAAATT
* *
1790 ATTGAATATG
131 ATTCAACATG
* *
1800 TCGTCAGTTAATTTTGCCAATCAAAGTTGTAATTGATTGATGATTATGTAAT
1 TCGTTAGTTAATTTTGCCAATCAAAGTTGTAATTGATTGATGATTATATAAT
1852 CAAAGTTATA
Statistics
Matches: 174, Mismatches: 16, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
139 95 0.55
140 79 0.45
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.36
Consensus pattern (140 bp):
TCGTTAGTTAATTTTGCCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAAT
CACCACCAAAAAATTAACATAAAGAAATAAATCAATTAGTAATTATGTTAACAAAAAAATAAATT
ATTCAACATG
Found at i:10269 original size:27 final size:27
Alignment explanation
Indices: 10231--10291 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
10221 AGTTGACGAA
* *
10231 ACAGCAAGGTTTTGCTTCTACTTTTGG
1 ACAGCAAGGTTTTGATTCTACTCTTGG
10258 ACAGCAAGGTTTTGATTCTACTCTTGG
1 ACAGCAAGGTTTTGATTCTACTCTTGG
*
10285 GCAGCAA
1 ACAGCAA
10292 TCAAGTAGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (27 bp):
ACAGCAAGGTTTTGATTCTACTCTTGG
Found at i:11130 original size:29 final size:29
Alignment explanation
Indices: 11066--11121 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
11056 TGATTTAGGG
* *
11066 CTAAACTTAACTTATAAATTACTCTAAGA
1 CTAAGCTTAACTTACAAATTACTCTAAGA
*
11095 CTAAGCTTAACTTACAAGTTACTCTAA
1 CTAAGCTTAACTTACAAATTACTCTAA
11122 CTACGAGCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (29 bp):
CTAAGCTTAACTTACAAATTACTCTAAGA
Found at i:11975 original size:60 final size:59
Alignment explanation
Indices: 11902--12064 Score: 236
Period size: 60 Copynumber: 2.7 Consensus size: 59
11892 GCTAATTGTT
** * * * *
11902 CAAATAAGAGCCTAACGTTTGATAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGT
1 CAAATAAG-GCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGGC
*
11962 TAAATAAAGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGGC
1 CAAAT-AAGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGGC
12022 CAAATAAGGACCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
1 CAAATAAGG-CCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
12065 TATCTCACAC
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
59 4 0.04
60 86 0.92
61 3 0.03
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (59 bp):
CAAATAAGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGGC
Found at i:12059 original size:31 final size:30
Alignment explanation
Indices: 11963--12066 Score: 90
Period size: 31 Copynumber: 3.4 Consensus size: 30
11953 TAATTTGGTT
11963 AAATAAAGGCCTAACGTTTGCCAAAATGCTC
1 AAAT-AAGGCCTAACGTTTGCCAAAATGCTC
* * **
11994 AAATAAGGGCCCGATC-TTTG--AATTTGGC-C
1 AAATAA-GG-CCTAACGTTTGCCAAAAT-GCTC
12023 AAATAAGGACCTAACGTTTGCCAAAATGCTC
1 AAATAAGG-CCTAACGTTTGCCAAAATGCTC
12054 AAATAAGGGCCTA
1 AAATAA-GGCCTA
12067 TCTCACACGC
Statistics
Matches: 56, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
28 6 0.11
29 14 0.25
30 6 0.11
31 24 0.43
32 6 0.11
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (30 bp):
AAATAAGGCCTAACGTTTGCCAAAATGCTC
Found at i:12134 original size:31 final size:31
Alignment explanation
Indices: 12093--12227 Score: 161
Period size: 31 Copynumber: 4.4 Consensus size: 31
12083 AACTGACACC
12093 AGGCCCTTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTTCGATAACGTT
* *
12124 AGACCCTTATTTGAGCATTTTTGATAACGTT
1 AGGCCCTTATTTGAGCATTTTCGATAACGTT
* * *
12155 AGGCCCTTATTTG-GCCATATT--A-AAAGATC
1 AGGCCCTTATTTGAG-CATTTTCGATAACG-TT
* *
12184 GGGCCCTTATTTGAGCATTTTCAATAACGTT
1 AGGCCCTTATTTGAGCATTTTCGATAACGTT
12215 AGGCCCTTATTTG
1 AGGCCCTTATTTG
12228 GCCAAATTAA
Statistics
Matches: 87, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
28 3 0.03
29 19 0.22
30 2 0.02
31 60 0.69
32 3 0.03
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCATTTTCGATAACGTT
Found at i:12194 original size:29 final size:29
Alignment explanation
Indices: 12156--12256 Score: 116
Period size: 29 Copynumber: 3.4 Consensus size: 29
12146 GATAACGTTA
12156 GGCCCTTATTTGGCCATATTAAAAGATCG
1 GGCCCTTATTTGGCCATATTAAAAGATCG
* **
12185 GGCCCTTATTTGAG-CATTTTCAATAACG-TTA
1 GGCCCTTATTTG-GCCATATT-AA-AA-GATCG
*
12216 GGCCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGGCCATATTAAAAGATCG
12245 GGCCCTTATTTG
1 GGCCCTTATTTG
12257 AGCATTTTGG
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
28 1 0.02
29 32 0.54
30 6 0.10
31 19 0.32
32 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.34
Consensus pattern (29 bp):
GGCCCTTATTTGGCCATATTAAAAGATCG
Found at i:12199 original size:60 final size:60
Alignment explanation
Indices: 12127--12264 Score: 249
Period size: 60 Copynumber: 2.3 Consensus size: 60
12117 TAACGTTAGA
** *
12127 CCCTTATTTGAGCATTTTTGATAACGTTAGGCCCTTATTTGGCCATATTAAAAGATCGGG
1 CCCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGG
12187 CCCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGG
1 CCCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGG
12247 CCCTTATTTGAGCATTTT
1 CCCTTATTTGAGCATTTT
12265 GGCAAACATT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 75 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGG
Found at i:12282 original size:60 final size:60
Alignment explanation
Indices: 12127--12287 Score: 238
Period size: 60 Copynumber: 2.7 Consensus size: 60
12117 TAACGTTAGA
*
12127 CCCTTATTTGAGCATTTTTG-ATAACGTTAGGCCCTTATTTGGCCATATTAAAAGATCGGG
1 CCCTTATTTGAGCA-TTTTGCATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGG
12187 CCCTTATTTGAGCATTTT-CAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGG
1 CCCTTATTTGAGCATTTTGC-ATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGG
* **
12247 CCCTTATTTGAGCATTTTGGCA-AACATTAAACCCTTATTTG
1 CCCTTATTTGAGCATTTT-GCATAACGTTAGGCCCTTATTTG
12288 AGCAATTAGC
Statistics
Matches: 93, Mismatches: 4, Indels: 8
0.89 0.04 0.08
Matches are distributed among these distances:
59 4 0.04
60 87 0.94
61 1 0.01
62 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTGCATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGG
Found at i:28148 original size:12 final size:12
Alignment explanation
Indices: 28131--28155 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28121 CTTTGTAAAA
28131 CGCCGGAGCTCT
1 CGCCGGAGCTCT
28143 CGCCGGAGCTCT
1 CGCCGGAGCTCT
28155 C
1 C
28156 TCATCCTTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.44, G:0.32, T:0.16
Consensus pattern (12 bp):
CGCCGGAGCTCT
Done.