Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013253.1 Corchorus capsularis cultivar CVL-1 contig13274, 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: 43651
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:1789 original size:29 final size:29
Alignment explanation
Indices: 1772--1829 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
1762 TGTTTTGTTC
1772 CCTAAACTTCAATTTTGGACGTTTTATCT
1 CCTAAACTTCAATTTTGGACGTTTTATCT
*
1801 CCTGAACTTCAATTTTGGGACGTTTTATC
1 CCTAAACTTCAATTTT-GGACGTTTTATC
1830 CCCTCATACT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.43
Consensus pattern (29 bp):
CCTAAACTTCAATTTTGGACGTTTTATCT
Found at i:2042 original size:29 final size:29
Alignment explanation
Indices: 1995--2066 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 29
1985 GCAGAGAGGG
*
1995 CAAAATGTCCCAAAATTGAAGTTCAG-GAGA
1 CAAAATGT-CCAAAATTGAAATTCAGTG-GA
*
2025 CAAAATGTCCAAAATTGAAATTTAGTGGA
1 CAAAATGTCCAAAATTGAAATTCAGTGGA
*
2054 CAAAACGTCCAAA
1 CAAAATGTCCAAA
2067 CGCTACAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 29 0.76
30 9 0.24
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.21
Consensus pattern (29 bp):
CAAAATGTCCAAAATTGAAATTCAGTGGA
Found at i:4271 original size:33 final size:33
Alignment explanation
Indices: 4229--4296 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
4219 ATTCACAAGC
**
4229 TGAATATCCTTCATATTTGCACTAACAACCTTG
1 TGAATATCCTTCATATCCGCACTAACAACCTTG
*
4262 TGAATATCCTTCATATCCGCACTAACGACCTTG
1 TGAATATCCTTCATATCCGCACTAACAACCTTG
4295 TG
1 TG
4297 TTCAGCTTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (33 bp):
TGAATATCCTTCATATCCGCACTAACAACCTTG
Found at i:12442 original size:2 final size:2
Alignment explanation
Indices: 12435--12464 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12425 AATATGAAGT
12435 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12465 AAAGAGTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15049 original size:2 final size:2
Alignment explanation
Indices: 15042--15067 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15032 CTAGAAGTTA
15042 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
15068 CTGTTCACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38233 original size:30 final size:31
Alignment explanation
Indices: 38197--38280 Score: 100
Period size: 30 Copynumber: 2.7 Consensus size: 31
38187 CCATGTGTCC
**
38197 TTTTTGTATGCATGGCATGCCACATGATAT-
1 TTTTTGTACACATGGCATGCCACATGATATA
* * *
38227 TTTTTGTACACGTGGCATGCCACGTGGTATA
1 TTTTTGTACACATGGCATGCCACATGATATA
38258 TTTTTGTACA-AGTGGCATGCCAC
1 TTTTTGTACACA-TGGCATGCCAC
38281 GTTGGATGCC
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
30 25 0.54
31 21 0.46
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (31 bp):
TTTTTGTACACATGGCATGCCACATGATATA
Found at i:38265 original size:31 final size:30
Alignment explanation
Indices: 38209--38282 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 30
38199 TTTGTATGCA
* *
38209 TGGCATGCCACATGATATTTTTTGTACACG
1 TGGCATGCCACGTGATATTTTTTGTACAAG
*
38239 TGGCATGCCACGTGGTATATTTTTGTACAAG
1 TGGCATGCCACGTGATAT-TTTTTGTACAAG
38270 TGGCATGCCACGT
1 TGGCATGCCACGT
38283 TGGATGCCCG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 16 0.40
31 24 0.60
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (30 bp):
TGGCATGCCACGTGATATTTTTTGTACAAG
Found at i:38908 original size:21 final size:21
Alignment explanation
Indices: 38865--38908 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
38855 AAAAAAGGGG
* *
38865 TTGCTAAATACCGCCCTAGTT
1 TTGCTAAATACCGCCCCACTT
38886 TTGCTAAATACCGCCCCACTT
1 TTGCTAAATACCGCCCCACTT
38907 TT
1 TT
38909 TACACTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.32, G:0.11, T:0.34
Consensus pattern (21 bp):
TTGCTAAATACCGCCCCACTT
Found at i:38931 original size:14 final size:15
Alignment explanation
Indices: 38907--38950 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
38897 CGCCCCACTT
*
38907 TTTACACTTTTGCCC
1 TTTACACTTTTACCC
38922 TTTA-ACTTTTACCC
1 TTTACACTTTTACCC
38936 TTTTTACACTTTTAC
1 --TTTACACTTTTAC
38951 ACTGAGTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 9 0.36
15 4 0.16
16 4 0.16
17 8 0.32
ACGTcount: A:0.18, C:0.27, G:0.02, T:0.52
Consensus pattern (15 bp):
TTTACACTTTTACCC
Found at i:39030 original size:33 final size:32
Alignment explanation
Indices: 38993--39106 Score: 122
Period size: 33 Copynumber: 3.5 Consensus size: 32
38983 GGCAGAGTCT
* *
38993 CCCCACTGGGGCGGCTTCACCATGGGCAGGCCG
1 CCCCACTGGGGCGGCTTCGCCA-AGGCAGGCCG
* *
39026 CCCCACCGGGGCGGCTTCGCGCAAGGTAGGCCG
1 CCCCACTGGGGCGGCTTCGC-CAAGGCAGGCCG
* *
39059 CCCTCA-TGGGGCGGCTTTGCCACGGCAGGCCG
1 CCC-CACTGGGGCGGCTTCGCCAAGGCAGGCCG
**
39091 CCCCGGTGGGGCGGCT
1 CCCCACTGGGGCGGCT
39107 AGAGCAAACT
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
31 1 0.01
32 23 0.33
33 41 0.59
34 4 0.06
ACGTcount: A:0.10, C:0.39, G:0.39, T:0.12
Consensus pattern (32 bp):
CCCCACTGGGGCGGCTTCGCCAAGGCAGGCCG
Found at i:39247 original size:34 final size:32
Alignment explanation
Indices: 39209--39271 Score: 99
Period size: 34 Copynumber: 1.9 Consensus size: 32
39199 CCGCCCCACC
*
39209 GGGGCGGCCTGCCCAATGGTGAAGCTGCCCTAGT
1 GGGGCGGCCTGCCC-ATGGT-AAGCCGCCCTAGT
39243 GGGGCGGCCTGCCCATGGTAAGCCGCCCT
1 GGGGCGGCCTGCCCATGGTAAGCCGCCCT
39272 CTTGAGGCGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 9 0.32
33 5 0.18
34 14 0.50
ACGTcount: A:0.13, C:0.33, G:0.38, T:0.16
Consensus pattern (32 bp):
GGGGCGGCCTGCCCATGGTAAGCCGCCCTAGT
Found at i:39281 original size:32 final size:34
Alignment explanation
Indices: 39211--39282 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 34
39201 GCCCCACCGG
* *
39211 GGCGGCCTGCCCAATGGTGAAGCTGCCCTAGTGG
1 GGCGGCCTGCCCAATGGTGAAGCCGCCCTAGTGA
**
39245 GGCGGCCTGCCC-ATGGT-AAGCCGCCCTCTTGA
1 GGCGGCCTGCCCAATGGTGAAGCCGCCCTAGTGA
39277 GGCGGC
1 GGCGGC
39283 ACGGGTCATC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 17 0.50
33 5 0.15
34 12 0.35
ACGTcount: A:0.12, C:0.33, G:0.38, T:0.17
Consensus pattern (34 bp):
GGCGGCCTGCCCAATGGTGAAGCCGCCCTAGTGA
Found at i:40138 original size:21 final size:19
Alignment explanation
Indices: 40097--40140 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
40087 ATTCTTTACT
**
40097 AATAAAAATACCACCTTTC
1 AATAAAAATACCACCACTC
40116 AATAAAAATTCACCACCACTC
1 AATAAAAA-T-ACCACCACTC
40137 AATA
1 AATA
40141 TACTAGAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 1 0.05
21 12 0.57
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (19 bp):
AATAAAAATACCACCACTC
Found at i:43363 original size:24 final size:24
Alignment explanation
Indices: 43331--43377 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
43321 TCATTGTACC
43331 TGGTTCTACACATCCAATCAGTTA
1 TGGTTCTACACATCCAATCAGTTA
*
43355 TGGTTCTACATATCCAATCAGTT
1 TGGTTCTACACATCCAATCAGTT
43378 GAGTATTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (24 bp):
TGGTTCTACACATCCAATCAGTTA
Done.