Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013435.1 Corchorus capsularis cultivar CVL-1 contig13456, 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: 11158
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:453 original size:6 final size:6
Alignment explanation
Indices: 442--467 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
432 AAAGTAAAGC
442 AATCTA AATCTA AATCTA AATCTA AA
1 AATCTA AATCTA AATCTA AATCTA AA
468 GCAGATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (6 bp):
AATCTA
Found at i:4884 original size:15 final size:15
Alignment explanation
Indices: 4864--4968 Score: 72
Period size: 15 Copynumber: 7.0 Consensus size: 15
4854 AAACACTTTT
4864 GGTGCCATCATCTTC
1 GGTGCCATCATCTTC
* *
4879 GGTGCCATCACCTTT
1 GGTGCCATCATCTTC
* *
4894 GGTGCAATTGAT-TTC
1 GGTGCCA-TCATCTTC
* *
4909 GGTGCCACCATCTTT
1 GGTGCCATCATCTTC
*
4924 GGTG-CAGTTGAT-TTC
1 GGTGCCA--TCATCTTC
* * *
4939 GGTGCCACCATTTTG
1 GGTGCCATCATCTTC
4954 GGTGCCATCATCTTC
1 GGTGCCATCATCTTC
4969 CTCCATGGCA
Statistics
Matches: 65, Mismatches: 19, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 6 0.09
15 53 0.82
16 6 0.09
ACGTcount: A:0.14, C:0.27, G:0.24, T:0.35
Consensus pattern (15 bp):
GGTGCCATCATCTTC
Found at i:4897 original size:30 final size:29
Alignment explanation
Indices: 4861--4961 Score: 98
Period size: 30 Copynumber: 3.4 Consensus size: 29
4851 AGTAAACACT
*
4861 TTTGGTGCCA-TCATCTTCGGTGCCATCACC
1 TTTGGTGCCATTCAT-TTCGGTGCCACCA-C
* *
4891 TTTGGTGCAATTGATTTCGGTGCCACCATC
1 TTTGGTGCCATTCATTTCGGTGCCACCA-C
* *
4921 TTTGGTG-CAGTTGATTTCGGTGCCACCAT
1 TTTGGTGCCA-TTCATTTCGGTGCCACCAC
4950 TTTGGGTGCCAT
1 TTT-GGTGCCAT
4962 CATCTTCCTC
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
29 4 0.07
30 52 0.85
31 5 0.08
ACGTcount: A:0.14, C:0.25, G:0.25, T:0.37
Consensus pattern (29 bp):
TTTGGTGCCATTCATTTCGGTGCCACCAC
Found at i:6058 original size:15 final size:15
Alignment explanation
Indices: 6034--6071 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
6024 ATTTGCGTCT
*
6034 TTTC-GCACTAGATG
1 TTTCTGCACTAGATC
6048 TTTCTGCACTAGATC
1 TTTCTGCACTAGATC
*
6063 TCTCTGCAC
1 TTTCTGCAC
6072 CGGCACCACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.18, C:0.29, G:0.16, T:0.37
Consensus pattern (15 bp):
TTTCTGCACTAGATC
Found at i:6228 original size:18 final size:18
Alignment explanation
Indices: 6188--6317 Score: 134
Period size: 18 Copynumber: 7.2 Consensus size: 18
6178 TGTTGAACAA
* *
6188 GTGCGGCCAATTGGTGCG
1 GTGCGGCCACTTGGTGTG
*
6206 ATGCGGCCACTTGGTGTG
1 GTGCGGCCACTTGGTGTG
* * **
6224 GTGCGACCACTTGATAAG
1 GTGCGGCCACTTGGTGTG
* **
6242 GTGCAGCCACTTGGTACG
1 GTGCGGCCACTTGGTGTG
* *
6260 GTGCGGCCATTTGGGGTG
1 GTGCGGCCACTTGGTGTG
*
6278 GTGCGACCACTTGGTGTG
1 GTGCGGCCACTTGGTGTG
*
6296 GTGCGGCCACTGGGTGTG
1 GTGCGGCCACTTGGTGTG
6314 GTGC
1 GTGC
6318 CTGGTGATGC
Statistics
Matches: 90, Mismatches: 22, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 90 1.00
ACGTcount: A:0.12, C:0.22, G:0.41, T:0.25
Consensus pattern (18 bp):
GTGCGGCCACTTGGTGTG
Found at i:6317 original size:54 final size:54
Alignment explanation
Indices: 6188--6317 Score: 161
Period size: 54 Copynumber: 2.4 Consensus size: 54
6178 TGTTGAACAA
* * *
6188 GTGCGGCCAATTGGTGCGATGCGGCCACTTGGTGTGGTGCGACCACTTGATAAG
1 GTGCGGCCACTTGGTGCGGTGCGGCCACTTGGGGTGGTGCGACCACTTGATAAG
* * * * **
6242 GTGCAGCCACTTGGTACGGTGCGGCCATTTGGGGTGGTGCGACCACTTGGTGTG
1 GTGCGGCCACTTGGTGCGGTGCGGCCACTTGGGGTGGTGCGACCACTTGATAAG
* *
6296 GTGCGGCCACTGGGTGTGGTGC
1 GTGCGGCCACTTGGTGCGGTGC
6318 CTGGTGATGC
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 63 1.00
ACGTcount: A:0.12, C:0.22, G:0.41, T:0.25
Consensus pattern (54 bp):
GTGCGGCCACTTGGTGCGGTGCGGCCACTTGGGGTGGTGCGACCACTTGATAAG
Found at i:9263 original size:13 final size:13
Alignment explanation
Indices: 9229--9267 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
9219 TTGGTATTTA
*
9229 TATATATATATAA
1 TATATATATATAT
*
9242 TATAAATATATAT
1 TATATATATATAT
*
9255 TATTTATATATAT
1 TATATATATATAT
9268 AGAAATCTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TATATATATATAT
Found at i:9288 original size:2 final size:2
Alignment explanation
Indices: 9227--9268 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
9217 TTTTGGTATT
* *
9227 TA TA TA TA TA TA TA -A TA TA AA TA TA TA T- TA TT 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
9267 TA
1 TA
9269 GAAATCTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9480 original size:49 final size:49
Alignment explanation
Indices: 9408--9871 Score: 486
Period size: 49 Copynumber: 9.4 Consensus size: 49
9398 CTAACGACTT
*
9408 GGAAATAACAAGTAAAGATGAATGGCTTCCGTCTGGGAAGGGCGCTTTG
1 GGAAATAGCAAGTAAAGATGAATGGCTTCCGTCTGGGAAGGGCGCTTTG
9457 GGAAATAGCAAGTAAAGATGAATGGCTTCCGTCTGGGAAGGGCGCTTTG
1 GGAAATAGCAAGTAAAGATGAATGGCTTCCGTCTGGGAAGGGCGCTTTG
* * *
9506 GGAAATACCAAGTAAAGATGAATGGCTTCCGTCTAGGAAAGGCGCTTTG
1 GGAAATAGCAAGTAAAGATGAATGGCTTCCGTCTGGGAAGGGCGCTTTG
*
9555 GGAAATAGCAAGTAAAGATGAATGGCTTCCGTCTGGGAAGGGCGGTTTG
1 GGAAATAGCAAGTAAAGATGAATGGCTTCCGTCTGGGAAGGGCGCTTTG
* * * * * * *
9604 GGAAATAGCTAGCAAAAATAAATGGCTTCCGTCTAGGAAGGGTGTTTTG
1 GGAAATAGCAAGTAAAGATGAATGGCTTCCGTCTGGGAAGGGCGCTTTG
* * * * *
9653 AGAAATAGCTAGCAAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTG
1 GGAAATAGCAAGTAAAGATGAATGGCTTCCGTCTGGGAAGGGCGCTTTG
* * ** *
9702 GGAAATAGCAAATAAA-A-GAAGTGCCTTCCGTCCAGGAAGGACG-TTTAG
1 GGAAATAGCAAGTAAAGATGAA-TGGCTTCCGTCTGGGAAGGGCGCTTT-G
* * * * * * *
9750 GGAAAAAGCAAATAAAAATTGAGTGCCTTCCGTCCGGGAAGGGCGTTTTG
1 GGAAATAGCAAGTAAAGA-TGAATGGCTTCCGTCTGGGAAGGGCGCTTTG
* * * * * * * * *
9800 GGAAAAAGTTAA-TAAAAATAAACGCCTTCCATCCGGGAAGGGCGTTTTG
1 GGAAATAG-CAAGTAAAGATGAATGGCTTCCGTCTGGGAAGGGCGCTTTG
* * *
9849 GGAAAAAGTAGGTAAAGACTGAA
1 GGAAATAGCAAGTAAAGA-TGAA
9872 AATTAAGAGA
Statistics
Matches: 366, Mismatches: 40, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
47 5 0.01
48 37 0.10
49 279 0.76
50 38 0.10
51 7 0.02
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.22
Consensus pattern (49 bp):
GGAAATAGCAAGTAAAGATGAATGGCTTCCGTCTGGGAAGGGCGCTTTG
Done.