Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019028.1 Corchorus olitorius cultivar O-4 contig19061, 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: 9859
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Found at i:409 original size:9 final size:9
Alignment explanation
Indices: 391--419 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
381 TTAATTCATT
391 TAATTT-CA
1 TAATTTCCA
399 TAATTTCCA
1 TAATTTCCA
408 TAATTTCCA
1 TAATTTCCA
417 TAA
1 TAA
420 GTAATTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (9 bp):
TAATTTCCA
Found at i:651 original size:18 final size:18
Alignment explanation
Indices: 604--651 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
594 TATCTTTCTA
*
604 TAATTAATAAAAAAAGTT
1 TAATTAATAAAAAAAATT
622 TAA-TAACTAAAAAAAATAT
1 TAATTAA-TAAAAAAAAT-T
641 TAATTAA-AAAA
1 TAATTAATAAAA
652 TTATTATACT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 3 0.12
18 16 0.62
19 4 0.15
20 3 0.12
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
TAATTAATAAAAAAAATT
Found at i:908 original size:15 final size:16
Alignment explanation
Indices: 890--927 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
880 ATATCATCAT
890 AATATAT-CTTTAAAA
1 AATATATCCTTTAAAA
*
905 AATAAATCCTTTAAAA
1 AATATATCCTTTAAAA
921 AATATAT
1 AATATAT
928 TCTTAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (16 bp):
AATATATCCTTTAAAA
Found at i:3007 original size:2 final size:2
Alignment explanation
Indices: 2995--3035 Score: 66
Period size: 2 Copynumber: 20.5 Consensus size: 2
2985 TTCGTGATTT
2995 TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA T
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3036 GGGTAATTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 34 0.92
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4325 original size:2 final size:2
Alignment explanation
Indices: 4314--4355 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
4304 AAGGAAATAG
*
4314 TA TA -A TA TA TA TA TA TA TA TA TA AA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4354 TA
1 TA
4356 CCTCTTAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:4799 original size:21 final size:20
Alignment explanation
Indices: 4754--4801 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
4744 ATTCAAAATA
* **
4754 AAATAAAAACTACCTATTTT
1 AAATAAAAACTACCCATTAG
4774 AAATAAAAACTACCCATTAG
1 AAATAAAAACTACCCATTAG
4794 AGAATAAA
1 A-AATAAA
4802 TTTAATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.56, C:0.15, G:0.04, T:0.25
Consensus pattern (20 bp):
AAATAAAAACTACCCATTAG
Found at i:5492 original size:21 final size:20
Alignment explanation
Indices: 5468--5507 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
5458 ACTAACCACA
5468 AATGGCACAAAACCCACATAG
1 AATGG-ACAAAACCCACATAG
*
5489 AATGGATAAAACCCACATA
1 AATGGACAAAACCCACATA
5508 CATTTTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (20 bp):
AATGGACAAAACCCACATAG
Found at i:5742 original size:63 final size:63
Alignment explanation
Indices: 5595--5738 Score: 236
Period size: 62 Copynumber: 2.3 Consensus size: 63
5585 TCTGATCACT
* *
5595 TTAATAATGTTTATGTATTATTGTTATCCTAAAGGAGGAGGGGAAAAATAAAAGTTAATGAATA
1 TTAAT-ATATTTATTTATTATTGTTATCCTAAAGGAGGAGGGGAAAAATAAAAGTTAATGAATA
* *
5659 TTAATATATTTATTTATTATTGTTATCTTAAAGGAGGAGGGG-AAAATAAAAGTTAATGGATA
1 TTAATATATTTATTTATTATTGTTATCCTAAAGGAGGAGGGGAAAAATAAAAGTTAATGAATA
5721 TTAATATATTTATTTATT
1 TTAATATATTTATTTATT
5739 TATTTATGTA
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
62 37 0.49
63 34 0.45
64 5 0.07
ACGTcount: A:0.40, C:0.02, G:0.17, T:0.40
Consensus pattern (63 bp):
TTAATATATTTATTTATTATTGTTATCCTAAAGGAGGAGGGGAAAAATAAAAGTTAATGAATA
Found at i:6338 original size:2 final size:2
Alignment explanation
Indices: 6290--6321 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6280 TCTAGTCTAG
6290 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6322 GGTATGGTTA
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7639 original size:5 final size:5
Alignment explanation
Indices: 7576--7620 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
7566 TTATTGTTCA
* *
7576 AATTC AATTT AA--T AATTT CA-TT AATTT AATTT AATTT AATTT AAT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT AAT
7621 AATTATTGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
3 3 0.09
4 3 0.09
5 28 0.82
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (5 bp):
AATTT
Found at i:9841 original size:1 final size:1
Alignment explanation
Indices: 9835--9859 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
9825 CTGAGGTTTG
9835 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.