Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014639.1 Corchorus olitorius cultivar O-4 contig14672, 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: 35766
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:4403 original size:2 final size:2
Alignment explanation
Indices: 4398--4429 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4388 GAGAGACTCT
4398 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4430 TAAAATGGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:12543 original size:32 final size:31
Alignment explanation
Indices: 12507--12574 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 31
12497 CGTATTGTTG
12507 ACGTGACATTG-TCACGTCGGAACAAAAATGCC
1 ACGTGACATTGCT-ACGTCGG-ACAAAAATGCC
* * *
12539 ACGTGGCATTGCTACGTTGGACCAAAATGCC
1 ACGTGACATTGCTACGTCGGACAAAAATGCC
12570 ACGTG
1 ACGTG
12575 CTAAGGCCAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 15 0.47
32 16 0.50
33 1 0.03
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.21
Consensus pattern (31 bp):
ACGTGACATTGCTACGTCGGACAAAAATGCC
Found at i:16138 original size:24 final size:26
Alignment explanation
Indices: 16090--16155 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 26
16080 GGGCATGATT
16090 AATTGGTTTTGCTTTTTTTTCTGAGGTA
1 AATTGGTTTTGC--TTTTTTCTGAGGTA
16118 AATTGG-TTTGCTTTTTT-TGAGGTA
1 AATTGGTTTTGCTTTTTTCTGAGGTA
16142 AATTGGTTTTGCTT
1 AATTGGTTTTGCTT
16156 AATTAGATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
24 13 0.35
25 13 0.35
27 5 0.14
28 6 0.16
ACGTcount: A:0.15, C:0.06, G:0.23, T:0.56
Consensus pattern (26 bp):
AATTGGTTTTGCTTTTTTCTGAGGTA
Found at i:20621 original size:94 final size:94
Alignment explanation
Indices: 20460--20646 Score: 365
Period size: 94 Copynumber: 2.0 Consensus size: 94
20450 AAGGGTGATC
*
20460 TGAATTACCACCATAAACCCATGTAATCTTTGATCACCGGTAATCTTGCATATATAAAATCACTA
1 TGAATTACCACCATAAACCCATGTAATCTTTAATCACCGGTAATCTTGCATATATAAAATCACTA
20525 GTGATATGAGGGTAATCCTAACCAGACGT
66 GTGATATGAGGGTAATCCTAACCAGACGT
20554 TGAATTACCACCATAAACCCATGTAATCTTTAATCACCGGTAATCTTGCATATATAAAATCACTA
1 TGAATTACCACCATAAACCCATGTAATCTTTAATCACCGGTAATCTTGCATATATAAAATCACTA
20619 GTGATATGAGGGTAATCCTAACCAGACG
66 GTGATATGAGGGTAATCCTAACCAGACG
20647 CCCCTTAGGA
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 92 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.28
Consensus pattern (94 bp):
TGAATTACCACCATAAACCCATGTAATCTTTAATCACCGGTAATCTTGCATATATAAAATCACTA
GTGATATGAGGGTAATCCTAACCAGACGT
Found at i:23731 original size:19 final size:20
Alignment explanation
Indices: 23707--23751 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
23697 ATCAATTACT
*
23707 TTTTTTACT-TGATTTATTA
1 TTTTTTACTCTAATTTATTA
*
23726 TTTTTT-CTCTAATTTTTTA
1 TTTTTTACTCTAATTTATTA
23745 TTTTTTA
1 TTTTTTA
23752 TTCTTTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 20 0.91
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTTTTACTCTAATTTATTA
Found at i:24349 original size:7 final size:7
Alignment explanation
Indices: 24337--24362 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
24327 TCTAATGCTA
24337 GGAAAAT
1 GGAAAAT
24344 GGAAAAT
1 GGAAAAT
24351 GGAAAAT
1 GGAAAAT
24358 GGAAA
1 GGAAA
24363 GAAAATCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.31, T:0.12
Consensus pattern (7 bp):
GGAAAAT
Found at i:33913 original size:27 final size:27
Alignment explanation
Indices: 33863--33918 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
33853 CTTGGTAAAT
33863 GGTGATGACAAATAAAAAGAAACAGAG
1 GGTGATGACAAATAAAAAGAAACAGAG
* * *
33890 GGTGATGACAAGTAATAAGGAACAGAG
1 GGTGATGACAAATAAAAAGAAACAGAG
33917 GG
1 GG
33919 AGTACTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.48, C:0.07, G:0.32, T:0.12
Consensus pattern (27 bp):
GGTGATGACAAATAAAAAGAAACAGAG
Found at i:34649 original size:19 final size:19
Alignment explanation
Indices: 34620--34668 Score: 89
Period size: 19 Copynumber: 2.5 Consensus size: 19
34610 AGGCAAGCAG
34620 GGAGAGAATGCAGGCCCGAA
1 GGAG-GAATGCAGGCCCGAA
34640 GGAGGAATGCAGGCCCGAA
1 GGAGGAATGCAGGCCCGAA
34659 GGAGGAATGC
1 GGAGGAATGC
34669 CCTGCTCAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 25 0.86
20 4 0.14
ACGTcount: A:0.33, C:0.18, G:0.43, T:0.06
Consensus pattern (19 bp):
GGAGGAATGCAGGCCCGAA
Done.