Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008255.1 Corchorus capsularis cultivar CVL-1 contig08276, 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: 31044
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:273 original size:26 final size:26
Alignment explanation
Indices: 238--303 Score: 105
Period size: 26 Copynumber: 2.5 Consensus size: 26
228 AATTTATTAA
*
238 TAAAATTATTCAGTTTTAACTAAGGT
1 TAAAATTATTCAATTTTAACTAAGGT
*
264 TAAAATTATTTAATTTTAACTAAGGT
1 TAAAATTATTCAATTTTAACTAAGGT
290 TAAAATTATGTCAA
1 TAAAATTAT-TCAA
304 GGTAATTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
26 33 0.92
27 3 0.08
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.42
Consensus pattern (26 bp):
TAAAATTATTCAATTTTAACTAAGGT
Found at i:712 original size:31 final size:31
Alignment explanation
Indices: 659--770 Score: 118
Period size: 31 Copynumber: 3.6 Consensus size: 31
649 CCCTAAACTT
* * **
659 AAAATCAGGACACTTTGTCTCATGAACTTCC
1 AAAATCAAGACATTTTACCTCATGAACTTCC
* *
690 AAAATAAAGACATTTTACCTCATGAACTTTC
1 AAAATCAAGACATTTTACCTCATGAACTTCC
* * * *
721 AAAATCATGACATTTT-CCCCCTGTACTTCCC
1 AAAATCAAGACATTTTACCTCATGAACTT-CC
752 AAAATCAAGACATTTTACC
1 AAAATCAAGACATTTTACC
771 CCCTGATGGA
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
30 9 0.14
31 55 0.83
32 2 0.03
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.30
Consensus pattern (31 bp):
AAAATCAAGACATTTTACCTCATGAACTTCC
Found at i:1957 original size:1 final size:1
Alignment explanation
Indices: 1951--1977 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1941 ATATATATAG
1951 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1978 GAGCGGGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:7117 original size:18 final size:17
Alignment explanation
Indices: 7094--7130 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
7084 ATAACAAACC
7094 ACAATGAGGGAATTAGAA
1 ACAATGAGGGAATTA-AA
7112 ACAATGAGGGAATTAAA
1 ACAATGAGGGAATTAAA
7129 AC
1 AC
7131 TATCCATAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.51, C:0.08, G:0.24, T:0.16
Consensus pattern (17 bp):
ACAATGAGGGAATTAAA
Found at i:9278 original size:319 final size:319
Alignment explanation
Indices: 8699--9322 Score: 1140
Period size: 319 Copynumber: 2.0 Consensus size: 319
8689 CCTCGGCTGG
8699 TTCCCAACTCGCCTCATTTTCGGGTTACCCCTTCCAAAGCACTAAGTATTCCTTCTTTCGTTCAC
1 TTCCCAACTCGCCTCATTTTCGGGTTACCCCTTCCAAAGCACTAAGTATTCCTTCTTTCGTTCAC
*
8764 GTCCCTTCCTTTTACGTCCCACCGCCCGCTCGGCAAGGATGGCTTGCACCTCCTTCTCGAACCTT
66 GTCCCTTCCTCTTACGTCCCACCGCCCGCTCGGCAAGGATGGCTTGCACCTCCTTCTCGAACCTT
*
8829 GTTTTCACGCGGAATAATGCACGTCTTGACTTGCTTCGTTCTGGGTCTTCCTCGTCGGCATGATA
131 GTTTTCACGCGGAATAATGCACGTCTTGACTTGCTTCGTTCTGGGTCTTCCTCGTCAGCATGATA
*
8894 TGGCTTGAGTAAGCTCACGTGGAAGACGGGGCGCATTCGAAACTTATACCCTCGAGGAATATTGA
196 TGGCTTGAGTAAACTCACGTGGAAGACGGGGCGCATTCGAAACTTATACCCTCGAGGAATATTGA
*
8959 GCTTGTAGACTAGCTTGCCTACTCGCCTAAGAACTCGGAAAGGACCCTCATAGACTAGC
261 GCTTGTAGACTAGCTTGCCAACTCGCCTAAGAACTCGGAAAGGACCCTCATAGACTAGC
*
9018 TTCCCAACTCGCCTCATTTTCGGGTTGCCCCTTCCAAAGCACTAAGTATTCCTTCTTTCGTTCAC
1 TTCCCAACTCGCCTCATTTTCGGGTTACCCCTTCCAAAGCACTAAGTATTCCTTCTTTCGTTCAC
*
9083 GTCCCTTCCTCTTACGTCCCACCGTCCGCTCGGCAAGGATGGCTTGCACCTCCTTCTCGAACCTT
66 GTCCCTTCCTCTTACGTCCCACCGCCCGCTCGGCAAGGATGGCTTGCACCTCCTTCTCGAACCTT
* * *
9148 GTTTTCACGCGGAATAGTGCACGTCTTGACTTGCTTCGTTCTGGTTTTTCCTCGTCAGCATGATA
131 GTTTTCACGCGGAATAATGCACGTCTTGACTTGCTTCGTTCTGGGTCTTCCTCGTCAGCATGATA
* *
9213 TGGCTTGAGTAAACTCACGTGGAAGACGGGGTGCATTCGAAACTTATACCCTCGAGGTATATTGA
196 TGGCTTGAGTAAACTCACGTGGAAGACGGGGCGCATTCGAAACTTATACCCTCGAGGAATATTGA
*
9278 GCTTGTAGACTATCTTGCCAACTCGCCTAAGAACTCGGAAAGGAC
261 GCTTGTAGACTAGCTTGCCAACTCGCCTAAGAACTCGGAAAGGAC
9323 TCTTATATTG
Statistics
Matches: 293, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
319 293 1.00
ACGTcount: A:0.20, C:0.30, G:0.21, T:0.30
Consensus pattern (319 bp):
TTCCCAACTCGCCTCATTTTCGGGTTACCCCTTCCAAAGCACTAAGTATTCCTTCTTTCGTTCAC
GTCCCTTCCTCTTACGTCCCACCGCCCGCTCGGCAAGGATGGCTTGCACCTCCTTCTCGAACCTT
GTTTTCACGCGGAATAATGCACGTCTTGACTTGCTTCGTTCTGGGTCTTCCTCGTCAGCATGATA
TGGCTTGAGTAAACTCACGTGGAAGACGGGGCGCATTCGAAACTTATACCCTCGAGGAATATTGA
GCTTGTAGACTAGCTTGCCAACTCGCCTAAGAACTCGGAAAGGACCCTCATAGACTAGC
Found at i:16882 original size:31 final size:31
Alignment explanation
Indices: 16844--17010 Score: 141
Period size: 31 Copynumber: 5.5 Consensus size: 31
16834 TTAGGCTAAT
*
16844 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
* ** **
16875 TGCTCAAATAAGGGCCTGATC-TTT-TTAATT
1 TGCTCAAATAAGGGCCT-AACGTTTGCCAAAA
*
16905 TGGC-CAAATAAGGGCCTAATGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGCCAAAA
* * **
16936 TGCTCAAATAAGGGCCCGATC-TTTG--AATT
1 TGCTCAAATAAGGG-CCTAACGTTTGCCAAAA
*
16965 TGGC-CAAATAAGGGCCTAATGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGCCAAAA
16996 TGCTCAAATAAGGGC
1 TGCTCAAATAAGGGC
17011 TTGTCTCACG
Statistics
Matches: 105, Mismatches: 20, Indels: 22
0.71 0.14 0.15
Matches are distributed among these distances:
28 3 0.03
29 18 0.17
30 26 0.25
31 53 0.50
32 5 0.05
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
Found at i:16915 original size:30 final size:30
Alignment explanation
Indices: 16879--16981 Score: 102
Period size: 30 Copynumber: 3.4 Consensus size: 30
16869 TCAAAATGCT
*
16879 CAAATAAGGGCCTGATCTTTTTAATTTGGC
1 CAAATAAGGGCCTGATCTTTTCAATTTGGC
* * * **
16909 CAAATAAGGGCCTAATGTTTGCCAAAAT-GC
1 CAAATAAGGGCCTGATCTTT-TCAATTTGGC
* *
16939 TCAAATAAGGGCCCGATC-TTTGAATTTGGC
1 -CAAATAAGGGCCTGATCTTTTCAATTTGGC
16969 CAAATAAGGGCCT
1 CAAATAAGGGCCT
16982 AATGTTTGCC
Statistics
Matches: 56, Mismatches: 14, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
29 15 0.27
30 24 0.43
31 17 0.30
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (30 bp):
CAAATAAGGGCCTGATCTTTTCAATTTGGC
Found at i:16990 original size:60 final size:61
Alignment explanation
Indices: 16848--17010 Score: 283
Period size: 60 Copynumber: 2.7 Consensus size: 61
16838 GCTAATTGCT
* * * *
16848 CAAATAAGGGCCTAACGTTTGTCAAAATGCTCAAATAAGGGCCTGATCTTTTTAATTTGGC
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTGAATTTGGC
16909 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCCGATC-TTTGAATTTGGC
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTGAATTTGGC
16969 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGC
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGC
17011 TTGTCTCACG
Statistics
Matches: 98, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
60 53 0.54
61 45 0.46
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (61 bp):
CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTGAATTTGGC
Found at i:17083 original size:31 final size:31
Alignment explanation
Indices: 17040--17178 Score: 117
Period size: 31 Copynumber: 4.5 Consensus size: 31
17030 AATTGACACC
* *
17040 AGGTCCTTATTTGAGCATTTTCGATAACTTT
1 AGGTCCTTATTTGAGCATTTTCAATAACGTT
*
17071 AGGTTCTTATTTGAGCATTTTCAATAACGTT
1 AGGTCCTTATTTGAGCATTTTCAATAACGTT
* ** *
17102 AGGCCCTTATTTG-GCCAAATT-AA-AA-GATC
1 AGGTCCTTATTTGAG-CATTTTCAATAACG-TT
* * *
17131 GGGCCCTTATTTGAGCATTTTGACA-AACGTT
1 AGGTCCTTATTTGAGCATTTTCA-ATAACGTT
*
17162 AGGCCCTTATTTGAGCA
1 AGGTCCTTATTTGAGCA
17179 ATTAGCCAAT
Statistics
Matches: 89, Mismatches: 13, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
28 1 0.01
29 19 0.21
30 5 0.06
31 63 0.71
32 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (31 bp):
AGGTCCTTATTTGAGCATTTTCAATAACGTT
Found at i:24103 original size:22 final size:23
Alignment explanation
Indices: 24078--24120 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
24068 CGTGATGAAC
*
24078 AAGAGAAAA-AGGCACGGAGCCT
1 AAGAGAAAATAAGCACGGAGCCT
24100 AAGAGAAAATAAGCACGGAGC
1 AAGAGAAAATAAGCACGGAGC
24121 TTGGTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.49, C:0.16, G:0.30, T:0.05
Consensus pattern (23 bp):
AAGAGAAAATAAGCACGGAGCCT
Found at i:30060 original size:21 final size:21
Alignment explanation
Indices: 30011--30061 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
30001 TTTTCAGTTA
*
30011 TTTTTCTTTCATGTTTTCACCT
1 TTTTTCTTTCATATTTTCA-CT
*
30033 CTTTTCTTTCA-ATTTTCACT
1 TTTTTCTTTCATATTTTCACT
30053 TTTCTTCTT
1 TTT-TTCTT
30062 ACTCATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 4 0.16
21 11 0.44
22 10 0.40
ACGTcount: A:0.10, C:0.24, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTTTCTTTCATATTTTCACT
Done.