Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007395.1 Corchorus capsularis cultivar CVL-1 contig07416, 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: 8278
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:785 original size:19 final size:18
Alignment explanation
Indices: 761--796 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
751 TGAAGATTTC
761 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
780 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
797 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:4303 original size:21 final size:22
Alignment explanation
Indices: 4277--4328 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
4267 GTACAAGTGA
4277 CCGGCCATGCGACTTGGAGAT-
1 CCGGCCATGCGACTTGGAGATG
*
4298 CCGGCCACGCGACTTGGAGATG
1 CCGGCCATGCGACTTGGAGATG
4320 CCTGGCCAT
1 CC-GGCCAT
4329 TACCGGCCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 20 0.74
22 2 0.07
23 5 0.19
ACGTcount: A:0.17, C:0.33, G:0.33, T:0.17
Consensus pattern (22 bp):
CCGGCCATGCGACTTGGAGATG
Found at i:6801 original size:60 final size:60
Alignment explanation
Indices: 6733--6955 Score: 324
Period size: 60 Copynumber: 3.7 Consensus size: 60
6723 GCTAATTGAT
* *
6733 CAAATAAGGACCTAACGTT-TGCCAAAATGTTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGACCTAACGTTAT-CGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
*
6793 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGACCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
* * * * *
6853 CAAATAA-GAGTCTAACCTTATTGAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGA-CCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
* *
6913 CAAATAAGGGCCTAACGTTATCGAAAATGCACAAATAAGGGCC
1 CAAATAAGGACCTAACGTTATCGAAAATGCTCAAATAAGGGCC
6956 TAACGTTATC
Statistics
Matches: 145, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
59 1 0.01
60 142 0.98
61 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (60 bp):
CAAATAAGGACCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:6802 original size:29 final size:29
Alignment explanation
Indices: 6764--6924 Score: 112
Period size: 29 Copynumber: 5.4 Consensus size: 29
6754 CCAAAATGTT
6764 CAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCCGATCTTTTAATTTGGC
* * * **
6793 CAAATAAGGG-CCTAACGTTATCGAAAAT-GC
1 CAAATAAGGGCCCGATC-TT-T-TAATTTGGC
6823 TCAAATAAGGGCCCGATCTTTTAATTTGGC
1 -CAAATAAGGGCCCGATCTTTTAATTTGGC
* * ** * **
6853 CAAATAAGAGTCTAACCTTATTGAAAAT-GC
1 CAAATAAGGGCCCGATCTT-TT-AATTTGGC
* *
6883 TCAAATAAGGGTCTGATCTTTTAATTTGGC
1 -CAAATAAGGGCCCGATCTTTTAATTTGGC
6913 CAAATAAGGGCC
1 CAAATAAGGGCC
6925 TAACGTTATC
Statistics
Matches: 99, Mismatches: 23, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
28 4 0.04
29 43 0.43
30 14 0.14
31 34 0.34
32 4 0.04
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (29 bp):
CAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:6831 original size:31 final size:31
Alignment explanation
Indices: 6793--6984 Score: 157
Period size: 31 Copynumber: 6.3 Consensus size: 31
6783 TTAATTTGGC
6793 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
* * * **
6824 CAAATAAGGGCCCGATC-TT-T-TAATTTGGC-
1 CAAATAAGGG-CCTAACGTTATCGAAAAT-GCT
* * * *
6853 CAAATAAGAGTCTAACCTTATTGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
* * * **
6884 CAAATAAGGGTCTGATC-TT-T-TAATTTGGC-
1 CAAATAAGGGCCT-AACGTTATCGAAAAT-GCT
*
6913 CAAATAAGGGCCTAACGTTATCGAAAATGCA
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
6944 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
6975 CAAATAAGGG
1 CAAATAAGGG
6985 TCTGGTGTCA
Statistics
Matches: 126, Mismatches: 23, Indels: 24
0.73 0.13 0.14
Matches are distributed among these distances:
28 5 0.04
29 31 0.25
30 12 0.10
31 72 0.57
32 6 0.05
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCT
Found at i:7053 original size:31 final size:30
Alignment explanation
Indices: 7018--7122 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 30
7008 ATGAGACAGA
*
7018 CCCTTATTTGAGCATTTTGGCAAACGTTAAG
1 CCCTTATTTGAGCATTTT-GCAAACGTTAGG
** * *
7049 CCCTTATTTG-GCCAAATT--AAAAGATCAGG
1 CCCTTATTTGAG-CATTTTGCAAACG-TTAGG
* *
7078 CCCTTATTTGAGTATTTTGCCAAACATTAGG
1 CCCTTATTTGAGCATTTTG-CAAACGTTAGG
7109 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
7123 ATTAGCCATA
Statistics
Matches: 56, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
28 4 0.07
29 16 0.29
30 2 0.04
31 31 0.55
32 3 0.05
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (30 bp):
CCCTTATTTGAGCATTTTGCAAACGTTAGG
Found at i:7299 original size:34 final size:35
Alignment explanation
Indices: 7259--7325 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
7249 TATTTTGGTG
*
7259 GATGATGAACAAATGAGACA-CAAAAAATGGGGTA
1 GATGATGAACAAATGAGACATAAAAAAATGGGGTA
*
7293 GATGATGCACAAATGAGACATAAAAAAATGGGG
1 GATGATGAACAAATGAGACATAAAAAAATGGGG
7326 AAGAAGATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 19 0.63
35 11 0.37
ACGTcount: A:0.49, C:0.09, G:0.27, T:0.15
Consensus pattern (35 bp):
GATGATGAACAAATGAGACATAAAAAAATGGGGTA
Done.