Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005830.1 Corchorus capsularis cultivar CVL-1 contig05848, 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: 8018
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:38 original size:1 final size:1
Alignment explanation
Indices: 28--84 Score: 60
Period size: 1 Copynumber: 57.0 Consensus size: 1
18 ACTTTCCTTC
* * * * **
28 TTTTTGTTTTTGTTTTTTTTTTTTGTTTTTGTTTTTTTTTTTTGATTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
85 GCATTTTCAG
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.02, C:0.00, G:0.09, T:0.89
Consensus pattern (1 bp):
T
Found at i:50 original size:13 final size:13
Alignment explanation
Indices: 28--85 Score: 82
Period size: 13 Copynumber: 4.5 Consensus size: 13
18 ACTTTCCTTC
*
28 TTTTTGTTTTTGT
1 TTTTTGTTTTTTT
*
41 TTTTT-TTTTTTG
1 TTTTTGTTTTTTT
53 TTTTTGTTTTTTT
1 TTTTTGTTTTTTT
66 TTTTTGATTTTTTT
1 TTTTTG-TTTTTTT
80 TTTTTG
1 TTTTTG
86 CATTTTCAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
12 10 0.25
13 17 0.43
14 13 0.32
ACGTcount: A:0.02, C:0.00, G:0.10, T:0.88
Consensus pattern (13 bp):
TTTTTGTTTTTTT
Found at i:52 original size:19 final size:19
Alignment explanation
Indices: 28--84 Score: 98
Period size: 19 Copynumber: 3.0 Consensus size: 19
18 ACTTTCCTTC
28 TTTTTGTTTTTGTTTTTTT
1 TTTTTGTTTTTGTTTTTTT
47 TTTTTGTTTTTGTTTTTTT
1 TTTTTGTTTTTGTTTTTTT
66 TTTTTGATTTTT-TTTTTTT
1 TTTTTG-TTTTTGTTTTTTT
85 GCATTTTCAG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 32 0.86
20 5 0.14
ACGTcount: A:0.02, C:0.00, G:0.09, T:0.89
Consensus pattern (19 bp):
TTTTTGTTTTTGTTTTTTT
Found at i:5161 original size:144 final size:143
Alignment explanation
Indices: 4897--5518 Score: 776
Period size: 144 Copynumber: 4.3 Consensus size: 143
4887 TCTGAAACTT
4897 AAGACGCCGCTAAATAGTGGCGTATGAGGTCCTAAACGCCGCCATCCATCTTTAATTTCTCTGAG
1 AAGACGCCGCTAAATAGTGGCGTATGAGGTCCTAAACGCCG----CCATCTTTAATTTCTCTGAG
* *
4962 GAAGGCAAATTTGGTAAACAAGAAGGCTAAAAGATAGCGGCGTCTGGGTTCAAGACGCCGCTAAA
62 GAAGGCAAATTGGGTAAAAAAGAAGGCTAAAAGATAGCGGCGTCTGGGTTCAAGACGCCGCTAAA
*
5027 TAGTGGTGTCTGTGTCC
127 TAGTGGCGTCTGTGTCC
*
5044 CAGACGCCGCTAAATAGTGGCGTATGAGGTCCTAAACGCCGCCATCTTTAATTTTCTCTGAGGAA
1 AAGACGCCGCTAAATAGTGGCGTATGAGGTCCTAAACGCCGCCATCTTTAA-TTTCTCTGAGGAA
5109 GGCAAATTGGGTAAAAAAGAAGGCTAAAAGATAGCGGCGTCTGGGTTCAAGACGCCGCTAAATAG
65 GGCAAATTGGGTAAAAAAGAAGGCTAAAAGATAGCGGCGTCTGGGTTCAAGACGCCGCTAAATAG
* *
5174 TGGCATATGTGTCC
130 TGGCGTCTGTGTCC
*
5188 AAGACGCCGCTAAATAGTGGCGTATGAGGTCCTAAACGCCGCCATC------TT-TCTGAGGCAG
1 AAGACGCCGCTAAATAGTGGCGTATGAGGTCCTAAACGCCGCCATCTTTAATTTCTCTGAGGAAG
* *
5246 GCGAATTGGGTAAAAAAGAAGGCTAAAAGATAGCGGCGCGGCGTCTGGGTACAAGACGCCGCTAA
66 GCAAATTGGGTAAAAAAGAAGGCTAAAAGATA-----GCGGCGTCTGGGTTCAAGACGCCGCTAA
*
5311 ATAGTGGCGTCTGGGTCC
126 ATAGTGGCGTCTGTGTCC
* * * * *
5329 AATACGCCGCTAAATAGTGGCGTATGAGGTCCTACACGCCGCCATCTTTATTTTTTTATCCGAGG
1 AAGACGCCGCTAAATAGTGGCGTATGAGGTCCTAAACGCCGCCATCTTTA---ATTTCTCTGAGG
* * * * * * *
5394 AAGGCAAATTGGGTAAAAATGAAAGCTAAAAGATAGTGGCGTCTTGAGGTTC-GGACGCCTCCAT
63 AAGGCAAATTGGGTAAAAAAGAAGGCTAAAAGATAGCGGCGTC-TG-GGTTCAAGACGCCGCTAA
* * *
5458 TTAGCGGCGTTCT-TGAACC
126 ATAGTGGCG-TCTGTG-TCC
* * *
5477 TAGACGCCGCTAAATAGTGGCGTCTAAGGTCCTAAACGCCGC
1 AAGACGCCGCTAAATAGTGGCGTATGAGGTCCTAAACGCCGC
5519 TATATATAAT
Statistics
Matches: 420, Mismatches: 35, Indels: 39
0.85 0.07 0.08
Matches are distributed among these distances:
136 40 0.10
137 2 0.00
141 86 0.20
143 10 0.02
144 132 0.31
146 7 0.02
147 58 0.14
148 46 0.11
150 2 0.00
151 37 0.09
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (143 bp):
AAGACGCCGCTAAATAGTGGCGTATGAGGTCCTAAACGCCGCCATCTTTAATTTCTCTGAGGAAG
GCAAATTGGGTAAAAAAGAAGGCTAAAAGATAGCGGCGTCTGGGTTCAAGACGCCGCTAAATAGT
GGCGTCTGTGTCC
Found at i:5323 original size:31 final size:31
Alignment explanation
Indices: 5285--5351 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
5275 ATAGCGGCGC
5285 GGCGTCTGGGTACAAGACGCCGCTAAATAGT
1 GGCGTCTGGGTACAAGACGCCGCTAAATAGT
* *
5316 GGCGTCTGGGTCCAATACGCCGCTAAATAGT
1 GGCGTCTGGGTACAAGACGCCGCTAAATAGT
5347 GGCGT
1 GGCGT
5352 ATGAGGTCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.22, C:0.24, G:0.33, T:0.21
Consensus pattern (31 bp):
GGCGTCTGGGTACAAGACGCCGCTAAATAGT
Found at i:5368 original size:32 final size:31
Alignment explanation
Indices: 5285--5370 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 31
5275 ATAGCGGCGC
* * *
5285 GGCGTCTGGGTACAAGACGCCGCTAAATAGT
1 GGCGTATGGGTCCAACACGCCGCTAAATAGT
* *
5316 GGCGTCTGGGTCCAATACGCCGCTAAATAGT
1 GGCGTATGGGTCCAACACGCCGCTAAATAGT
*
5347 GGCGTATGAGGTCCTACACGCCGC
1 GGCGTATG-GGTCCAACACGCCGC
5371 CATCTTTATT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
31 36 0.73
32 13 0.27
ACGTcount: A:0.22, C:0.27, G:0.31, T:0.20
Consensus pattern (31 bp):
GGCGTATGGGTCCAACACGCCGCTAAATAGT
Found at i:6224 original size:9 final size:9
Alignment explanation
Indices: 6212--6299 Score: 59
Period size: 9 Copynumber: 10.8 Consensus size: 9
6202 CCAACCCGAA
6212 ACCCGAATG
1 ACCCGAATG
6221 ACCCGAA--
1 ACCCGAATG
* **
6228 ATCTAAATG
1 ACCCGAATG
6237 ACCCGAA--
1 ACCCGAATG
*
6244 ACCCGTATG
1 ACCCGAATG
6253 ACCCGAA--
1 ACCCGAATG
*
6260 ACCCGAATA
1 ACCCGAATG
6269 ACCCGAAT-
1 ACCCGAATG
*
6277 -CCAG-ATG
1 ACCCGAATG
6284 ACCCGAATG
1 ACCCGAATG
6293 ACCCGAA
1 ACCCGAA
6300 AAAAGTGCCT
Statistics
Matches: 60, Mismatches: 10, Indels: 18
0.68 0.11 0.20
Matches are distributed among these distances:
6 2 0.03
7 20 0.33
8 3 0.05
9 35 0.58
ACGTcount: A:0.38, C:0.34, G:0.17, T:0.11
Consensus pattern (9 bp):
ACCCGAATG
Found at i:6224 original size:16 final size:16
Alignment explanation
Indices: 6205--6290 Score: 102
Period size: 16 Copynumber: 5.4 Consensus size: 16
6195 AACCCGTCCA
6205 ACCCGAAACCCGAATG
1 ACCCGAAACCCGAATG
* **
6221 ACCCGAAATCTAAATG
1 ACCCGAAACCCGAATG
*
6237 ACCCGAAACCCGTATG
1 ACCCGAAACCCGAATG
*
6253 ACCCGAAACCCGAATA
1 ACCCGAAACCCGAATG
* *
6269 ACCCGAATCCAG-ATG
1 ACCCGAAACCCGAATG
6284 ACCCGAA
1 ACCCGAA
6291 TGACCCGAAA
Statistics
Matches: 58, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
15 9 0.16
16 49 0.84
ACGTcount: A:0.38, C:0.35, G:0.16, T:0.10
Consensus pattern (16 bp):
ACCCGAAACCCGAATG
Found at i:6273 original size:32 final size:31
Alignment explanation
Indices: 6204--6299 Score: 102
Period size: 32 Copynumber: 3.0 Consensus size: 31
6194 GAACCCGTCC
* **
6204 AACCCGAAACCCGAATGACCCGAAATCTAAAT
1 AACCCGAAACCCG-ATGACCCGAAACCCGAAT
*
6236 GACCCGAAACCCGTATGACCCGAAACCCGAAT
1 AACCCGAAACCCG-ATGACCCGAAACCCGAAT
* *
6268 AACCCGAATCCAGATGACCCGAATGACCCGAA
1 AACCCGAAACCCGATGACCCGAA--ACCCGAA
6300 AAAAGTGCCT
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
31 10 0.19
32 37 0.69
33 7 0.13
ACGTcount: A:0.39, C:0.34, G:0.17, T:0.10
Consensus pattern (31 bp):
AACCCGAAACCCGATGACCCGAAACCCGAAT
Found at i:6810 original size:42 final size:42
Alignment explanation
Indices: 6742--6823 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
6732 TGTTGACACA
*
6742 TACCCCACATGATAATTAATTATGTATTTAATATTCAAAACC
1 TACCCCACATGATAATCAATTATGTATTTAATATTCAAAACC
* *
6784 TACCTCACCTGATAATCAATTATGTATTTAATATTCAAAA
1 TACCCCACATGATAATCAATTATGTATTTAATATTCAAAA
6824 TTAATATCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.37
Consensus pattern (42 bp):
TACCCCACATGATAATCAATTATGTATTTAATATTCAAAACC
Found at i:7067 original size:16 final size:16
Alignment explanation
Indices: 7048--7150 Score: 120
Period size: 16 Copynumber: 6.5 Consensus size: 16
7038 AACCCGCCCA
7048 ACCCGAGACCCGAATG
1 ACCCGAGACCCGAATG
*
7064 ACCCGATACCCGAATG
1 ACCCGAGACCCGAATG
*
7080 ACCCG-GAACCCGTATG
1 ACCCGAG-ACCCGAATG
* *
7096 ACCCAAGACCCGAATA
1 ACCCGAGACCCGAATG
* *
7112 ACCCGA-ACTCAAATG
1 ACCCGAGACCCGAATG
*
7127 ACCCGAAACCCGAATG
1 ACCCGAGACCCGAATG
7143 ACCCGAGA
1 ACCCGAGA
7151 AAACTGCCTG
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
15 12 0.17
16 58 0.82
17 1 0.01
ACGTcount: A:0.35, C:0.37, G:0.19, T:0.09
Consensus pattern (16 bp):
ACCCGAGACCCGAATG
Found at i:7084 original size:32 final size:32
Alignment explanation
Indices: 7002--7150 Score: 123
Period size: 32 Copynumber: 4.8 Consensus size: 32
6992 CTGACCCAGT
* *
7002 TGACCCGAAACCCGAGTGACCCGAG-GCC-AA
1 TGACCCGAAACCCGAATGACCCGAGACCCGAA
* ****
7032 -AACCCG-AACCCGCCCAACCCGAGACCCGAA
1 TGACCCGAAACCCGAATGACCCGAGACCCGAA
* *
7062 TGACCCGATACCCGAATGACCCG-GAACCCGTA
1 TGACCCGAAACCCGAATGACCCGAG-ACCCGAA
* * *
7094 TGACCC-AAGACCCGAATAACCCGA-ACTCAAA
1 TGACCCGAA-ACCCGAATGACCCGAGACCCGAA
7125 TGACCCGAAACCCGAATGACCCGAGA
1 TGACCCGAAACCCGAATGACCCGAGA
7151 AAACTGCCTG
Statistics
Matches: 91, Mismatches: 19, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
28 13 0.14
29 7 0.08
30 2 0.02
31 31 0.34
32 38 0.42
ACGTcount: A:0.34, C:0.39, G:0.20, T:0.07
Consensus pattern (32 bp):
TGACCCGAAACCCGAATGACCCGAGACCCGAA
Done.