Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023042.1 Corchorus olitorius cultivar O-4 contig23075, 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: 12939
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:5821 original size:19 final size:19
Alignment explanation
Indices: 5768--5822 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 19
5758 ATTCTTGACT
5768 TCTTTCTTTTTTTTTTGTG
1 TCTTTCTTTTTTTTTTGTG
5787 T-TATTCTCTTTTTTTTT-TG
1 TCT-TTCT-TTTTTTTTTGTG
5806 CTCTTTCTTTTTTTTTT
1 -TCTTTCTTTTTTTTTT
5823 AACTTTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 1 0.03
19 16 0.50
20 14 0.44
21 1 0.03
ACGTcount: A:0.02, C:0.13, G:0.05, T:0.80
Consensus pattern (19 bp):
TCTTTCTTTTTTTTTTGTG
Found at i:5832 original size:20 final size:20
Alignment explanation
Indices: 5765--5845 Score: 67
Period size: 21 Copynumber: 4.0 Consensus size: 20
5755 CTTATTCTTG
*
5765 ACTTCTTTCTTTTTTTTTTG
1 ACTTCTTTCTTTTTTTTTTA
** *
5785 TGTTATTCTCTTTTTTTTTT-
1 ACTTCTT-TCTTTTTTTTTTA
*
5805 GC-TCTTTCTTTTTTTTTTA
1 ACTTCTTTCTTTTTTTTTTA
*
5824 ACTTTTTTCTATTTTTATTTTA
1 ACTTCTTTCT-TTTTT-TTTTA
5846 TTTTATTTAT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
18 12 0.25
19 4 0.08
20 10 0.21
21 17 0.35
22 5 0.10
ACGTcount: A:0.09, C:0.12, G:0.04, T:0.75
Consensus pattern (20 bp):
ACTTCTTTCTTTTTTTTTTA
Found at i:5839 original size:39 final size:40
Alignment explanation
Indices: 5768--5844 Score: 95
Period size: 39 Copynumber: 1.9 Consensus size: 40
5758 ATTCTTGACT
***
5768 TCTTTCTTTTTTTTTTGTGTTATTCTCTTTTTT-TTTTGC
1 TCTTTCTTTTTTTTTTAACTTATTCTCTTTTTTATTTTGC
*
5807 TCTTTCTTTTTTTTTTAACTT-TTTTCTATTTTTATTTT
1 TCTTTCTTTTTTTTTTAACTTATTCTCT-TTTTTATTTT
5845 ATTTTATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
38 5 0.16
39 23 0.72
40 4 0.12
ACGTcount: A:0.06, C:0.12, G:0.04, T:0.78
Consensus pattern (40 bp):
TCTTTCTTTTTTTTTTAACTTATTCTCTTTTTTATTTTGC
Found at i:7811 original size:107 final size:105
Alignment explanation
Indices: 7640--7844 Score: 347
Period size: 107 Copynumber: 1.9 Consensus size: 105
7630 GTTTAGCCTC
* *
7640 AATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATTA
1 AATTTCACTAAGTTTAGCCCCAAATTAAAATTTCATTTTTATTTTAAGGGTAAATTCCAAAATTA
* *
7705 ATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAACT
66 ATAA--CATTATTATAGGGTTTTAGAAATAAAATACAAAACT
*
7747 AATTTCACTAAGTTTAGCCCCAAATTAAAATTTCATTTTTATTTTAAGGGTAAATTCCATAATTA
1 AATTTCACTAAGTTTAGCCCCAAATTAAAATTTCATTTTTATTTTAAGGGTAAATTCCAAAATTA
7812 ATAACATTATTATAGGGTTTTAGAAATAAAATA
66 ATAACATTATTATAGGGTTTTAGAAATAAAATA
7845 TTTAACTAAT
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
105 27 0.29
107 66 0.71
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.40
Consensus pattern (105 bp):
AATTTCACTAAGTTTAGCCCCAAATTAAAATTTCATTTTTATTTTAAGGGTAAATTCCAAAATTA
ATAACATTATTATAGGGTTTTAGAAATAAAATACAAAACT
Found at i:12532 original size:1 final size:1
Alignment explanation
Indices: 12526--12557 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
12516 AGTCTAATAG
12526 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12558 GCAAGCTGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.