Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012606.1 Corchorus olitorius cultivar O-4 contig12639, 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: 33867
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Found at i:880 original size:71 final size:71
Alignment explanation
Indices: 764--905 Score: 275
Period size: 71 Copynumber: 2.0 Consensus size: 71
754 TTGCGTTACC
*
764 AATATCTTGTCTTGATTGCATTGTAGTTTGTACTATATTTCAAAGTTGAACCATTGGACACGAGG
1 AATATCTTGTCTTGATTGCATTGTAGTTTGTACTATATTTCAAAGTTGAACCACTGGACACGAGG
829 TTCATT
66 TTCATT
835 AATATCTTGTCTTGATTGCATTGTAGTTTGTACTATATTTCAAAGTTGAACCACTGGACACGAGG
1 AATATCTTGTCTTGATTGCATTGTAGTTTGTACTATATTTCAAAGTTGAACCACTGGACACGAGG
900 TTCATT
66 TTCATT
906 GCGAGACCAA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (71 bp):
AATATCTTGTCTTGATTGCATTGTAGTTTGTACTATATTTCAAAGTTGAACCACTGGACACGAGG
TTCATT
Found at i:6168 original size:20 final size:21
Alignment explanation
Indices: 6131--6173 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
6121 AACCCGTTAA
*
6131 TTAAAGCGTGTCACTCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
*
6152 TTAAA-CGTGTTAATCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
6172 TT
1 TT
6174 GACACGATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (21 bp):
TTAAAGCGTGTCAATCGTGTC
Found at i:6231 original size:42 final size:43
Alignment explanation
Indices: 6161--6243 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 43
6151 CTTAAACGTG
*
6161 TTAATCGTGTCTTGACACGATTAGGACACGAAACACGATAATC
1 TTAATCGTGTCTCGACACGATTAGGACACGAAACACGATAATC
*
6204 TTAATCGTGTC-CGACACGATTCA-GACACGAGACACGATAA
1 TTAATCGTGTCTCGACACGATT-AGGACACGAAACACGATAA
6244 GTCAAACACG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 25 0.68
43 12 0.32
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (43 bp):
TTAATCGTGTCTCGACACGATTAGGACACGAAACACGATAATC
Found at i:17499 original size:13 final size:13
Alignment explanation
Indices: 17481--17517 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
17471 TTAATTATTA
*
17481 GGAGGGTCAAGTT
1 GGAGGGTCAAATT
*
17494 GGAGGGACAAATT
1 GGAGGGTCAAATT
17507 GGAGGGTCAAA
1 GGAGGGTCAAA
17518 AAGAATTATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.32, C:0.08, G:0.43, T:0.16
Consensus pattern (13 bp):
GGAGGGTCAAATT
Found at i:20563 original size:42 final size:42
Alignment explanation
Indices: 20504--20617 Score: 219
Period size: 42 Copynumber: 2.7 Consensus size: 42
20494 TCCTCATGAT
20504 TCACTTGCTGCAGTGGTTCTTCTTTCTCATCTTCAATATTGA
1 TCACTTGCTGCAGTGGTTCTTCTTTCTCATCTTCAATATTGA
20546 TCACTTGCTGCAGTGGTTCTTCTTTCTCATCTTCAATATTGA
1 TCACTTGCTGCAGTGGTTCTTCTTTCTCATCTTCAATATTGA
*
20588 TCACTTGCTGCAGTGGTTCCTCTTTCTCAT
1 TCACTTGCTGCAGTGGTTCTTCTTTCTCAT
20618 TTCCATTCAA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.15, C:0.25, G:0.15, T:0.45
Consensus pattern (42 bp):
TCACTTGCTGCAGTGGTTCTTCTTTCTCATCTTCAATATTGA
Found at i:21355 original size:6 final size:6
Alignment explanation
Indices: 21341--21384 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
21331 TATAGTTTAA
* *
21341 GGGGTT GGGGGT GGGAGT GGGGGT GGGGGT GGGGGT GGGGGT GG
1 GGGGGT GGGGGT GGGGGT GGGGGT GGGGGT GGGGGT GGGGGT GG
21385 ATAAGTTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.02, C:0.00, G:0.80, T:0.18
Consensus pattern (6 bp):
GGGGGT
Found at i:27934 original size:23 final size:23
Alignment explanation
Indices: 27899--27954 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
27889 CCTGAACAAG
* *
27899 TTTCAACATGAAGGACATGAGGA
1 TTTCAAAAAGAAGGACATGAGGA
*
27922 TTTCAAAAAGAAGGACATGTGGA
1 TTTCAAAAAGAAGGACATGAGGA
27945 TTTCAAAAAG
1 TTTCAAAAAG
27955 CTTTTAGTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (23 bp):
TTTCAAAAAGAAGGACATGAGGA
Found at i:33552 original size:28 final size:28
Alignment explanation
Indices: 33520--33578 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
33510 TGTCCAAAGT
33520 TGCTATCATATTAATAACTTGGCCAAAA
1 TGCTATCATATTAATAACTTGGCCAAAA
* * *
33548 TGCTATCATATTAATAAGTTGGGCAAGA
1 TGCTATCATATTAATAACTTGGCCAAAA
33576 TGC
1 TGC
33579 ATTACATTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (28 bp):
TGCTATCATATTAATAACTTGGCCAAAA
Done.