Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004016.1 Corchorus capsularis cultivar CVL-1 contig04024, 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: 13834
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:4769 original size:32 final size:32
Alignment explanation
Indices: 4725--4802 Score: 131
Period size: 32 Copynumber: 2.4 Consensus size: 32
4715 TCTAGCTTCA
*
4725 ATTAATGTTGTTCCCACCAATTT-AAATGCATG
1 ATTAATGGTGTTCCCACC-ATTTGAAATGCATG
4757 ATTAATGGTGTTCCCACCATTTGAAATGCATG
1 ATTAATGGTGTTCCCACCATTTGAAATGCATG
4789 ATTAATGGTGTTCC
1 ATTAATGGTGTTCC
4803 ACCTTTTTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
31 4 0.09
32 40 0.91
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (32 bp):
ATTAATGGTGTTCCCACCATTTGAAATGCATG
Found at i:8498 original size:19 final size:19
Alignment explanation
Indices: 8444--8503 Score: 53
Period size: 19 Copynumber: 3.5 Consensus size: 19
8434 AATTAATTGA
8444 TTAATTCATCATTG-GCCC
1 TTAATTCATCATTGTGCCC
8462 TTAAATT-A-CA--GT--CC
1 TT-AATTCATCATTGTGCCC
8476 TTAATTCATCATTGTGCCC
1 TTAATTCATCATTGTGCCC
*
8495 TTAAATCAT
1 TTAATTCAT
8504 AGTTCATATT
Statistics
Matches: 33, Mismatches: 1, Indels: 15
0.67 0.02 0.31
Matches are distributed among these distances:
13 4 0.12
14 5 0.15
15 3 0.09
17 4 0.12
18 3 0.09
19 14 0.42
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.40
Consensus pattern (19 bp):
TTAATTCATCATTGTGCCC
Found at i:8517 original size:33 final size:32
Alignment explanation
Indices: 8445--8517 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 32
8435 ATTAATTGAT
* *
8445 TAATTCATCATTGGCCCTTAAATTACAGTCCT
1 TAATTCATCATTGGCCCTTAAATCACAGTCCA
* *
8477 TAATTCATCATTGTGCCCTTAAATCATAGTTCA
1 TAATTCATCATTG-GCCCTTAAATCACAGTCCA
*
8510 TATTTCAT
1 TAATTCAT
8518 AAGCCACCCC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
32 13 0.37
33 22 0.63
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (32 bp):
TAATTCATCATTGGCCCTTAAATCACAGTCCA
Found at i:10593 original size:2 final size:2
Alignment explanation
Indices: 10580--10617 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
10570 TTTCACCACC
10580 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10618 TCTAAAGTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11128 original size:18 final size:18
Alignment explanation
Indices: 11107--11144 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
11097 GTGGTTGAAT
**
11107 CGATCAGACCGGTTAAAC
1 CGATCAGACCAATTAAAC
11125 CGATCAGACCAATTAAAC
1 CGATCAGACCAATTAAAC
11143 CG
1 CG
11145 CGAAGTGCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.37, C:0.29, G:0.18, T:0.16
Consensus pattern (18 bp):
CGATCAGACCAATTAAAC
Found at i:11628 original size:150 final size:151
Alignment explanation
Indices: 11467--11754 Score: 488
Period size: 150 Copynumber: 1.9 Consensus size: 151
11457 AATTACTTTA
* * *
11467 TTTTTACCATTTTATTATTTTTCATTAAAAATTTGGATATATTAAAATTTTTTAATATGTAATTT
1 TTTTTACCATTTTACTATTTTTCATTAAAAACTTGGATATATTAAAATTTTTTAATATATAATTT
* * * *
11532 GATTCTACTAAAAACTCTATTTTCATTTAATTAAATTC-ATATTTTTATAATTATTTTATTTTTA
66 GATTATACTAAAAACTCTATTTTAATTTAATTAAATTCAATACTTTTATAATTACTTTATTTTTA
11596 CCATTGTAATTTAAAATATTT
131 CCATTGTAATTTAAAATATTT
*
11617 TTTTTACCATTTTACTATTTTTCATTAAAAACTTGGATATATTAAAATTTTTTAATATATAGTTT
1 TTTTTACCATTTTACTATTTTTCATTAAAAACTTGGATATATTAAAATTTTTTAATATATAATTT
*
11682 GGTTATACTAAAAACTCTATTTTAATTTAATTAAATTCAATACTTTTATAATTACTTTATTTTTA
66 GATTATACTAAAAACTCTATTTTAATTTAATTAAATTCAATACTTTTATAATTACTTTATTTTTA
11747 CCATTGTA
131 CCATTGTA
11755 TTTTTACCAT
Statistics
Matches: 128, Mismatches: 9, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
150 96 0.75
151 32 0.25
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.53
Consensus pattern (151 bp):
TTTTTACCATTTTACTATTTTTCATTAAAAACTTGGATATATTAAAATTTTTTAATATATAATTT
GATTATACTAAAAACTCTATTTTAATTTAATTAAATTCAATACTTTTATAATTACTTTATTTTTA
CCATTGTAATTTAAAATATTT
Found at i:11758 original size:14 final size:14
Alignment explanation
Indices: 11739--11768 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
11729 ATAATTACTT
11739 TATTTTTACCATTG
1 TATTTTTACCATTG
11753 TATTTTTACCATTG
1 TATTTTTACCATTG
11767 TA
1 TA
11769 ATTCAATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.07, T:0.57
Consensus pattern (14 bp):
TATTTTTACCATTG
Done.