Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013041.1 Corchorus olitorius cultivar O-4 contig13074, 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: 20386
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:496 original size:79 final size:79
Alignment explanation
Indices: 360--509 Score: 282
Period size: 79 Copynumber: 1.9 Consensus size: 79
350 CAAGTTATCA
360 AAGTTGACTGCACATTGGTCCTCTTTCATCATTAATCAAGAAATTTTCAGTTACAACATCAGACT
1 AAGTTGACTGCACATTGGTCCTCTTTCATCATTAATCAAGAAATTTTCAGTTACAACATCAGACT
425 CAGAGTTATTTTTC
66 CAGAGTTATTTTTC
* *
439 AAGTTGACTGCACATTGGTCCTCTTTCATCATTAATCAAGAAATTTTCAGTTGCAACATCAGATT
1 AAGTTGACTGCACATTGGTCCTCTTTCATCATTAATCAAGAAATTTTCAGTTACAACATCAGACT
504 CAGAGT
66 CAGAGT
510 CATTGTCCAA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 69 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (79 bp):
AAGTTGACTGCACATTGGTCCTCTTTCATCATTAATCAAGAAATTTTCAGTTACAACATCAGACT
CAGAGTTATTTTTC
Found at i:716 original size:50 final size:50
Alignment explanation
Indices: 582--700 Score: 220
Period size: 50 Copynumber: 2.4 Consensus size: 50
572 TCCGAATGCT
582 CAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
1 CAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
632 CAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
1 CAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
**
682 TGGGCTTTTCCACAAGCCA
1 CAGGCTTTTCCACAAGCCA
701 CATCCGGTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 67 1.00
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.26
Consensus pattern (50 bp):
CAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
Found at i:801 original size:50 final size:50
Alignment explanation
Indices: 728--933 Score: 385
Period size: 50 Copynumber: 4.1 Consensus size: 50
718 TGCATTACCT
728 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
778 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
*
828 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATATGCGGGAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
*
878 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
*
928 TCTTAA
1 TTTTAA
934 TATGTTAGAT
Statistics
Matches: 152, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 152 1.00
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.27
Consensus pattern (50 bp):
TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
Found at i:1250 original size:27 final size:27
Alignment explanation
Indices: 1213--1300 Score: 99
Period size: 27 Copynumber: 3.3 Consensus size: 27
1203 GGGATTTTGG
1213 GGTCATTTGCATGTTCAGGGGCATTTT
1 GGTCATTTGCATGTTCAGGGGCATTTT
* * * *
1240 AGTCATTTGCACG-TCTAAGGGCATTTC
1 GGTCATTTGCATGTTC-AGGGGCATTTT
*
1267 GGTCATTTGTATGTTC-GGAGGCATTTT
1 GGTCATTTGCATGTTCAGG-GGCATTTT
1294 GGTCATT
1 GGTCATT
1301 CTAGATTCAC
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
26 3 0.06
27 44 0.90
28 2 0.04
ACGTcount: A:0.17, C:0.16, G:0.27, T:0.40
Consensus pattern (27 bp):
GGTCATTTGCATGTTCAGGGGCATTTT
Found at i:1606 original size:36 final size:36
Alignment explanation
Indices: 1559--1648 Score: 171
Period size: 36 Copynumber: 2.5 Consensus size: 36
1549 TATGCATTTT
1559 TTATTAGTAATTAGGCATCATCATTCACATTAGTAA
1 TTATTAGTAATTAGGCATCATCATTCACATTAGTAA
*
1595 TTATTAGTAATTAGGCATCATCGTTCACATTAGTAA
1 TTATTAGTAATTAGGCATCATCATTCACATTAGTAA
1631 TTATTAGTAATTAGGCAT
1 TTATTAGTAATTAGGCAT
1649 TGCATTCACA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (36 bp):
TTATTAGTAATTAGGCATCATCATTCACATTAGTAA
Found at i:8973 original size:3 final size:3
Alignment explanation
Indices: 8965--8989 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
8955 GTTACTAACC
8965 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
8990 ATATATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:11357 original size:21 final size:21
Alignment explanation
Indices: 11314--11358 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
11304 GTAAGTGATG
*
11314 AAGTAGTGAATTTGATGATTA
1 AAGTAGTGAATTTGATGAATA
11335 AAGTGAGTGAATTTG-TGAATA
1 AAGT-AGTGAATTTGATGAATA
11356 AAG
1 AAG
11359 GTAATAGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.40, C:0.00, G:0.27, T:0.33
Consensus pattern (21 bp):
AAGTAGTGAATTTGATGAATA
Done.