Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007295.1 Corchorus capsularis cultivar CVL-1 contig07316, 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: 26873
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:2163 original size:43 final size:43
Alignment explanation
Indices: 2039--2175 Score: 173
Period size: 43 Copynumber: 3.3 Consensus size: 43
2029 AGAAAAGGAA
*
2039 AATTGG-ATTTATTATTCAACAACAATGAATTCGTTTTGGTTTC
1 AATTGGTATTTATTATTCAACAAC-ATGAATTGGTTTTGGTTTC
**
2082 AATTGGTATTTA-TA--C-A-AA-GGGAATTGGTTTTGGTTTC
1 AATTGGTATTTATTATTCAACAACATGAATTGGTTTTGGTTTC
2119 AATTGG-ATTTATTATTCAACAACCATGAATTGGTTTTGGTTTC
1 AATTGGTATTTATTATTCAACAA-CATGAATTGGTTTTGGTTTC
2162 AATTGGTATTTATT
1 AATTGGTATTTATT
2176 GGTATTTATT
Statistics
Matches: 80, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
36 5 0.06
37 24 0.30
39 3 0.04
40 2 0.03
41 3 0.04
43 31 0.39
44 12 0.15
ACGTcount: A:0.28, C:0.09, G:0.18, T:0.45
Consensus pattern (43 bp):
AATTGGTATTTATTATTCAACAACATGAATTGGTTTTGGTTTC
Found at i:2224 original size:15 final size:15
Alignment explanation
Indices: 2204--2235 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2194 GAAAGACACG
2204 TGCTCAATGGTCAAT
1 TGCTCAATGGTCAAT
*
2219 TGCTCAATTGTCAAT
1 TGCTCAATGGTCAAT
2234 TG
1 TG
2236 TGAAGACACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (15 bp):
TGCTCAATGGTCAAT
Found at i:4406 original size:19 final size:19
Alignment explanation
Indices: 4382--4418 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
4372 AATTCAAGAG
4382 TCTTAAAAGGGCAGTGAAC
1 TCTTAAAAGGGCAGTGAAC
4401 TCTTAAAAGGGCAGTGAA
1 TCTTAAAAGGGCAGTGAA
4419 TTGTGATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.14, G:0.27, T:0.22
Consensus pattern (19 bp):
TCTTAAAAGGGCAGTGAAC
Found at i:13628 original size:19 final size:19
Alignment explanation
Indices: 13582--13628 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
13572 CTCAGAACAG
* *
13582 CATAATAGTTTTCAATATA
1 CATAATAATTTACAATATA
*
13601 CATATTAATTTACAATAATA
1 CATAATAATTTACAAT-ATA
13621 -ATAATAAT
1 CATAATAAT
13629 ATTAATTGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (19 bp):
CATAATAATTTACAATATA
Found at i:14304 original size:9 final size:9
Alignment explanation
Indices: 14290--14330 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
14280 CATCGGTGAT
14290 GACGGCGTC
1 GACGGCGTC
14299 GACGGCGTC
1 GACGGCGTC
14308 GACGGCGTC
1 GACGGCGTC
** *
14317 TCCGGCCTC
1 GACGGCGTC
14326 GACGG
1 GACGG
14331 GCTCCGTTGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.10, C:0.37, G:0.41, T:0.12
Consensus pattern (9 bp):
GACGGCGTC
Found at i:15183 original size:17 final size:17
Alignment explanation
Indices: 15163--15216 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
15153 AGGCTCCGCC
15163 GTGGTTGAGCCTCCCTA
1 GTGGTTGAGCCTCCCTA
* * *
15180 GTGG-GGAGGCTCCGC-C
1 GTGGTTGAGCCTCC-CTA
15196 GTGGTTGAGCCTCCCTA
1 GTGGTTGAGCCTCCCTA
15213 GTGG
1 GTGG
15217 GGAGGCTCCG
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
16 12 0.43
17 16 0.57
ACGTcount: A:0.09, C:0.28, G:0.39, T:0.24
Consensus pattern (17 bp):
GTGGTTGAGCCTCCCTA
Found at i:15188 original size:33 final size:33
Alignment explanation
Indices: 15137--15253 Score: 182
Period size: 33 Copynumber: 3.5 Consensus size: 33
15127 CCCATGGTGA
* *
15137 AGCCGCCCCAGTGGGGAGGCTCCGCCGTGGTTG
1 AGCCTCCCTAGTGGGGAGGCTCCGCCGTGGTTG
15170 AGCCTCCCTAGTGGGGAGGCTCCGCCGTGGTTG
1 AGCCTCCCTAGTGGGGAGGCTCCGCCGTGGTTG
*
15203 AGCCTCCCTAGTGGGGAGGCTCCGCCGTGGCTG
1 AGCCTCCCTAGTGGGGAGGCTCCGCCGTGGTTG
*
15236 AG-CTGTCCTAGTGGGGAG
1 AGCCT-CCCTAGTGGGGAG
15254 ACTCAGTGTA
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
32 2 0.03
33 77 0.97
ACGTcount: A:0.10, C:0.30, G:0.41, T:0.19
Consensus pattern (33 bp):
AGCCTCCCTAGTGGGGAGGCTCCGCCGTGGTTG
Found at i:15199 original size:16 final size:16
Alignment explanation
Indices: 15147--15232 Score: 68
Period size: 16 Copynumber: 5.2 Consensus size: 16
15137 AGCCGCCCCA
15147 GTGGGGAGGCTCCGCC
1 GTGGGGAGGCTCCGCC
* * *
15163 GTGGTTGAGCCTCC-CTA
1 GTGG-GGAGGCTCCGC-C
15180 GTGGGGAGGCTCCGCC
1 GTGGGGAGGCTCCGCC
* * *
15196 GTGGTTGAGCCTCC-CTA
1 GTGG-GGAGGCTCCGC-C
15213 GTGGGGAGGCTCCGCC
1 GTGGGGAGGCTCCGCC
15229 GTGG
1 GTGG
15233 CTGAGCTGTC
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
16 28 0.54
17 24 0.46
ACGTcount: A:0.08, C:0.29, G:0.43, T:0.20
Consensus pattern (16 bp):
GTGGGGAGGCTCCGCC
Found at i:21156 original size:2 final size:2
Alignment explanation
Indices: 21149--21187 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
21139 TTAACTAAAT
21149 TA TA TA TA TA -A T- TA TA TA TA TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21188 ATTAAAGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 31 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21429 original size:42 final size:43
Alignment explanation
Indices: 21359--21441 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 43
21349 TTTAAACGTG
*
21359 TTAATCGTGTCTTGACACGATTACGACACGAAACACGATAATC
1 TTAATCGTGTCTCGACACGATTACGACACGAAACACGATAATC
*
21402 TTAATCGTGTC-CGACACGATT-CAGACACGAGACACGATAA
1 TTAATCGTGTCTCGACACGATTAC-GACACGAAACACGATAA
21442 GCCAAACACG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 1 0.03
42 25 0.68
43 11 0.30
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (43 bp):
TTAATCGTGTCTCGACACGATTACGACACGAAACACGATAATC
Done.