Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024343.1 Corchorus olitorius cultivar O-4 contig24376, 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: 3829
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:339 original size:7 final size:7
Alignment explanation
Indices: 327--359 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
317 CTCCATCAAA
327 AATTTTC
1 AATTTTC
334 AATTTTC
1 AATTTTC
*
341 -ACTTTC
1 AATTTTC
347 AATTTTC
1 AATTTTC
354 AATTTT
1 AATTTT
360 TCTTTTGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.27, C:0.15, G:0.00, T:0.58
Consensus pattern (7 bp):
AATTTTC
Found at i:348 original size:13 final size:13
Alignment explanation
Indices: 330--354 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
320 CATCAAAAAT
330 TTTCAATTTTCAC
1 TTTCAATTTTCAC
343 TTTCAATTTTCA
1 TTTCAATTTTCA
355 ATTTTTCTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTCAATTTTCAC
Found at i:373 original size:8 final size:8
Alignment explanation
Indices: 356--416 Score: 79
Period size: 8 Copynumber: 7.6 Consensus size: 8
346 CAATTTTCAA
*
356 TTTTTCTT
1 TTTTTGTT
*
364 TTGTT-TT
1 TTTTTGTT
371 TTTTTGTT
1 TTTTTGTT
379 TTTTTGTT
1 TTTTTGTT
387 TTTTGTGTT
1 TTTT-TGTT
396 TTTTTGTT
1 TTTTTGTT
*
404 TGTTTGTT
1 TTTTTGTT
412 TTTTT
1 TTTTT
417 TTGCATATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
7 6 0.13
8 33 0.70
9 8 0.17
ACGTcount: A:0.00, C:0.02, G:0.13, T:0.85
Consensus pattern (8 bp):
TTTTTGTT
Found at i:383 original size:18 final size:18
Alignment explanation
Indices: 356--419 Score: 78
Period size: 18 Copynumber: 3.6 Consensus size: 18
346 CAATTTTCAA
356 TTTTTCTTTTGTTTTTTT-
1 TTTTT-TTTTGTTTTTTTG
374 TTGTTTTTTTG-TTTTTTG
1 TT-TTTTTTTGTTTTTTTG
* *
392 TGTTTTTTTGTTTGTTTG
1 TTTTTTTTTGTTTTTTTG
410 TTTTTTTTTG
1 TTTTTTTTTG
420 CATATTTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
17 14 0.35
18 23 0.57
19 3 0.08
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (18 bp):
TTTTTTTTTGTTTTTTTG
Found at i:397 original size:25 final size:25
Alignment explanation
Indices: 362--415 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
352 TCAATTTTTC
* *
362 TTTTGTTTTTTTTTGTTTTTTTGTT
1 TTTTGTGTTTTTTTGTTTGTTTGTT
387 TTTTGTGTTTTTTTGTTTGTTTGTT
1 TTTTGTGTTTTTTTGTTTGTTTGTT
412 TTTT
1 TTTT
416 TTTGCATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (25 bp):
TTTTGTGTTTTTTTGTTTGTTTGTT
Found at i:417 original size:17 final size:17
Alignment explanation
Indices: 362--419 Score: 80
Period size: 17 Copynumber: 3.3 Consensus size: 17
352 TCAATTTTTC
*
362 TTTTGTTTTTTTTTGTTT
1 TTTTG-TTTTTTGTGTTT
380 TTTTGTTTTTTGTGTTT
1 TTTTGTTTTTTGTGTTT
*
397 TTTTGTTTGTTTGTTTTT
1 TTTTGTTT-TTTGTGTTT
415 TTTTG
1 TTTTG
420 CATATTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
17 19 0.51
18 18 0.49
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (17 bp):
TTTTGTTTTTTGTGTTT
Found at i:2170 original size:12 final size:13
Alignment explanation
Indices: 2153--2182 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
2143 CTTGATAAAT
2153 CATGAAAATGT-G
1 CATGAAAATGTAG
2165 CATGAAAATGTAG
1 CATGAAAATGTAG
2178 CATGA
1 CATGA
2183 CATGGCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.23
Consensus pattern (13 bp):
CATGAAAATGTAG
Done.