Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013252.1 Corchorus capsularis cultivar CVL-1 contig13273, 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: 24893
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Found at i:585 original size:297 final size:297
Alignment explanation
Indices: 51--632 Score: 1110
Period size: 297 Copynumber: 2.0 Consensus size: 297
41 TCGAAAAATC
*
51 TTTGTTCATGAGTTTTGATGTTGTTTTACTTGAATGATTTTGAATAATTGAGGTTTGAAAGTTTG
1 TTTGTTCATGAGTTTTGATGTTGTTTTACTTGAATGATTTTGAATAATTGAGATTTGAAAGTTTG
116 AAGGTCGAGAGAATTTGAGAGAATTAAAAAATTTGAAATTTGATGGAAAATAAAGCAAATGGTAA
66 AAGGTCGAGAGAATTTGAGAGAATTAAAAAATTTGAAATTTGATGGAAAATAAAGCAAATGGTAA
* *
181 AATAGTCTAAAGGGGGACGGTGGCTAGTAAAAGGGGCGGTATTTAGTAATCCACTTTAAGTTATT
131 AATAGTCTAAAGGGGGACGGTGGCTAGTAAAAAGGGCGGTATTTAGTAATCCACTTTAAATTATT
* *
246 TTTAATGTCGGAAATGATAACGTGTGATGTTTTTAAAATGAAAAAATGAAATAAACAGAGAGTTG
196 TTTAATGTCGGAAATGATAACGTGCGATGTTTTTAAAATGAAAAAATGAAATAAACAAAGAGTTG
311 ATTGGGTGAAACCAAAAAGTAAATCCACTTTAAATTA
261 ATTGGGTGAAACCAAAAAGTAAATCCACTTTAAATTA
348 TTTGTTCATGAGTTTTGATGTTGTTTTACTTGAATGATTTTGAATAATTGAGATTTGAAAGTTTG
1 TTTGTTCATGAGTTTTGATGTTGTTTTACTTGAATGATTTTGAATAATTGAGATTTGAAAGTTTG
413 AAGGTCGAGAGAATTTGAGAGAATTAAAAAATTTGAAATTTGATGGAAAATAAAGCAAATGGTAA
66 AAGGTCGAGAGAATTTGAGAGAATTAAAAAATTTGAAATTTGATGGAAAATAAAGCAAATGGTAA
478 AATAGTCTAAAGGGGGACGGTGGCTAGTAAAAAGGGCGGTATTTAGTAATCCACTTTAAATTATT
131 AATAGTCTAAAGGGGGACGGTGGCTAGTAAAAAGGGCGGTATTTAGTAATCCACTTTAAATTATT
*
543 TTTAATGTCGGAAATGATAACGTGCGCTGTTTTTAAAATGAAAAAATGAAATAAACAAAGAGTTG
196 TTTAATGTCGGAAATGATAACGTGCGATGTTTTTAAAATGAAAAAATGAAATAAACAAAGAGTTG
608 ATTGGGTGAAACCAAAAAGTAAATC
261 ATTGGGTGAAACCAAAAAGTAAATC
633 AAGAGAAAAT
Statistics
Matches: 279, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
297 279 1.00
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.33
Consensus pattern (297 bp):
TTTGTTCATGAGTTTTGATGTTGTTTTACTTGAATGATTTTGAATAATTGAGATTTGAAAGTTTG
AAGGTCGAGAGAATTTGAGAGAATTAAAAAATTTGAAATTTGATGGAAAATAAAGCAAATGGTAA
AATAGTCTAAAGGGGGACGGTGGCTAGTAAAAAGGGCGGTATTTAGTAATCCACTTTAAATTATT
TTTAATGTCGGAAATGATAACGTGCGATGTTTTTAAAATGAAAAAATGAAATAAACAAAGAGTTG
ATTGGGTGAAACCAAAAAGTAAATCCACTTTAAATTA
Found at i:678 original size:9 final size:9
Alignment explanation
Indices: 666--690 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
656 CACACCCAAC
666 AAACCCACT
1 AAACCCACT
675 AAACCCACT
1 AAACCCACT
684 AAACCCA
1 AAACCCA
691 ACCGCCGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.44, G:0.00, T:0.08
Consensus pattern (9 bp):
AAACCCACT
Found at i:6863 original size:15 final size:15
Alignment explanation
Indices: 6835--6870 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
6825 TATGAAATCG
*
6835 AAGAAAAAGCTTTGA
1 AAGAAGAAGCTTTGA
*
6850 AAGAAGAAGTTTTGA
1 AAGAAGAAGCTTTGA
6865 AAGAAG
1 AAGAAG
6871 CTGTAGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.25, T:0.19
Consensus pattern (15 bp):
AAGAAGAAGCTTTGA
Found at i:15432 original size:32 final size:33
Alignment explanation
Indices: 15391--15456 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
15381 TGCCAACTCT
15391 AGAGTCTAGACAT-TACAAAAAATGTAAAACCA
1 AGAGTCTAGACATGTACAAAAAATGTAAAACCA
*
15423 AGAGTCTAGACTTGTACAAAAAATGTAAAACCA
1 AGAGTCTAGACATGTACAAAAAATGTAAAACCA
15456 A
1 A
15457 TTCAAATTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 12 0.38
33 20 0.62
ACGTcount: A:0.52, C:0.15, G:0.14, T:0.20
Consensus pattern (33 bp):
AGAGTCTAGACATGTACAAAAAATGTAAAACCA
Found at i:23236 original size:48 final size:48
Alignment explanation
Indices: 23143--23244 Score: 129
Period size: 48 Copynumber: 2.1 Consensus size: 48
23133 CAATAAACAG
*
23143 CCTCCATCGGCTTGGCTTTTCAATGCAACGTCGTTTGATATTGGCAGCT
1 CCTCCATCCGCTTGGCTTTTCAATGCAACGTCGTTTGA-ATTGGCAGCT
*
23192 CCTCC-TCCGCTTGGCTTTTCAATAATGCAATGTCGTTTG-A-TGGCAGCT
1 CCTCCATCCGCTTGGCTTTTC---AATGCAACGTCGTTTGAATTGGCAGCT
23240 CCTCC
1 CCTCC
23245 GCTACATCGT
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
48 27 0.56
49 6 0.12
51 15 0.31
ACGTcount: A:0.16, C:0.29, G:0.21, T:0.34
Consensus pattern (48 bp):
CCTCCATCCGCTTGGCTTTTCAATGCAACGTCGTTTGAATTGGCAGCT
Done.