Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014320.1 Corchorus capsularis cultivar CVL-1 contig14341, 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: 25763
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1379 original size:18 final size:18
Alignment explanation
Indices: 1353--1388 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1343 GGTAGACATC
*
1353 CATTTTGCAGGGTTATAT
1 CATTGTGCAGGGTTATAT
1371 CATTGTGCAGGGTTATAT
1 CATTGTGCAGGGTTATAT
1389 AGAGTATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.42
Consensus pattern (18 bp):
CATTGTGCAGGGTTATAT
Found at i:1877 original size:2 final size:2
Alignment explanation
Indices: 1865--1906 Score: 66
Period size: 2 Copynumber: 20.0 Consensus size: 2
1855 GTAGATAATC
1865 AT AT CAT AT AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1907 TAAAACTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 34 0.89
3 4 0.11
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3476 original size:26 final size:26
Alignment explanation
Indices: 3426--3479 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
3416 AAACCTGAAA
*
3426 TTTCTAAGAATGTAGTGTTTCTAAAT
1 TTTCTAAGAATGTAGTGTTACTAAAT
*
3452 TTTCTAAGAATGTGAG-GTTAGTAAAT
1 TTTCTAAGAATGT-AGTGTTACTAAAT
3478 TT
1 TT
3480 ATGTAGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (26 bp):
TTTCTAAGAATGTAGTGTTACTAAAT
Found at i:12665 original size:53 final size:52
Alignment explanation
Indices: 12586--12686 Score: 175
Period size: 53 Copynumber: 1.9 Consensus size: 52
12576 TGGGTCTAAA
*
12586 AATGAGATTTCTTAAAAACCCACTTAACATATCAATAATTAAAGGGAATCTT
1 AATGAGATGTCTTAAAAACCCACTTAACATATCAATAATTAAAGGGAATCTT
*
12638 AATGAAGATGTCTTAAAAATCCACTTAACATATCAATAATTAAAGGGAA
1 AATG-AGATGTCTTAAAAACCCACTTAACATATCAATAATTAAAGGGAA
12687 CCTCAAATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 4 0.09
53 42 0.91
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.29
Consensus pattern (52 bp):
AATGAGATGTCTTAAAAACCCACTTAACATATCAATAATTAAAGGGAATCTT
Found at i:19346 original size:11 final size:11
Alignment explanation
Indices: 19330--19361 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
19320 GAAGTTCGTG
19330 TTTGAAGATTA
1 TTTGAAGATTA
*
19341 TTTGAAGATAA
1 TTTGAAGATTA
19352 TTTGAAGATT
1 TTTGAAGATT
19362 TGAAGACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:19358 original size:22 final size:22
Alignment explanation
Indices: 19330--19389 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
19320 GAAGTTCGTG
*
19330 TTTGAAGATTATTTGAAGATAA
1 TTTGAAGATTATTTGAAGACAA
19352 TTTGAAG---ATTTGAAGACAA
1 TTTGAAGATTATTTGAAGACAA
*
19371 -TTGAAGAATTATTTCAAGA
1 TTTGAAG-ATTATTTGAAGA
19390 AGCAAGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 6 0.19
19 11 0.34
22 15 0.47
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37
Consensus pattern (22 bp):
TTTGAAGATTATTTGAAGACAA
Found at i:19364 original size:19 final size:18
Alignment explanation
Indices: 19340--19377 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
19330 TTTGAAGATT
*
19340 ATTTGAAGATAATTTGAAG
1 ATTTGAAGACAA-TTGAAG
19359 ATTTGAAGACAATTGAAG
1 ATTTGAAGACAATTGAAG
19377 A
1 A
19378 ATTATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (18 bp):
ATTTGAAGACAATTGAAG
Found at i:20734 original size:6 final size:6
Alignment explanation
Indices: 20723--20753 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
20713 ATAATTGCTA
20723 TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TA
20754 CTTTGCTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (6 bp):
TAGATT
Done.