Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023855.1 Corchorus olitorius cultivar O-4 contig23888, 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: 15237
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5318 original size:22 final size:22
Alignment explanation
Indices: 5290--5334 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
5280 ATCAAGACCA
5290 AGCCAAAGCATACCATCTATTT
1 AGCCAAAGCATACCATCTATTT
5312 AGCCAAAGCATACCATCTATTT
1 AGCCAAAGCATACCATCTATTT
5334 A
1 A
5335 AAAGCATTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.27, G:0.09, T:0.27
Consensus pattern (22 bp):
AGCCAAAGCATACCATCTATTT
Found at i:5340 original size:19 final size:20
Alignment explanation
Indices: 5293--5341 Score: 73
Period size: 22 Copynumber: 2.4 Consensus size: 20
5283 AAGACCAAGC
5293 CAAAGCATACCATCTATTTA
1 CAAAGCATACCATCTATTTA
5313 GCCAAAGCATACCATCTATTTA
1 --CAAAGCATACCATCTATTTA
5335 -AAAGCAT
1 CAAAGCAT
5342 TCCTACCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.26
22 20 0.74
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.27
Consensus pattern (20 bp):
CAAAGCATACCATCTATTTA
Found at i:5822 original size:20 final size:20
Alignment explanation
Indices: 5797--5836 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5787 TGGTGAGAAG
5797 ACTGAATTCTTTAAACCTTC
1 ACTGAATTCTTTAAACCTTC
*
5817 ACTGAATTCTTTAAGCCTTC
1 ACTGAATTCTTTAAACCTTC
5837 CCGGGGACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.25, G:0.07, T:0.40
Consensus pattern (20 bp):
ACTGAATTCTTTAAACCTTC
Found at i:10442 original size:2 final size:2
Alignment explanation
Indices: 10435--10470 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
10425 TTGTTTTATT
10435 TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10471 TCTGACCAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10898 original size:18 final size:18
Alignment explanation
Indices: 10871--10921 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
10861 CCAAGAACCG
*
10871 AAGGTTTGATAGGAGGCA
1 AAGGTATGATAGGAGGCA
10889 AAGGTATGATAGGAGGCA
1 AAGGTATGATAGGAGGCA
10907 AAGGTATGATAGGAG
1 AAGGTATGATAGGAG
10922 TTATAAATTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.37, C:0.04, G:0.39, T:0.20
Consensus pattern (18 bp):
AAGGTATGATAGGAGGCA
Found at i:11664 original size:2 final size:2
Alignment explanation
Indices: 11657--11716 Score: 58
Period size: 2 Copynumber: 32.5 Consensus size: 2
11647 AGTAAATAAG
* *
11657 TA TA TA TA TA -A TA TA TA TC T- TA TA TA TA TA AA T- TA -A T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
11694 TA AA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
11717 TTTGTGTATC
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
1 5 0.10
2 43 0.90
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:12829 original size:22 final size:22
Alignment explanation
Indices: 12757--13070 Score: 114
Period size: 22 Copynumber: 14.4 Consensus size: 22
12747 ATTACTAATT
*
12757 TTTCAT-GGTGAGGTTCTCAAAA
1 TTTCATAGG-GAGGTTATCAAAA
* * * *
12779 TTTCATAGTGTGCTTACCAACAA
1 TTTCATAGGGAGGTTATCAA-AA
12802 -TTCATAGGGAGGTTATCAAAA
1 TTTCATAGGGAGGTTATCAAAA
** ***
12823 TTTCATAACGTTTTTATC-AAA
1 TTTCATAGGGAGGTTATCAAAA
* * **
12844 TTTTATTGGGAGACTATCAAAA
1 TTTCATAGGGAGGTTATCAAAA
* *
12866 TTTCATAGTGAGGTTTTCAAAA
1 TTTCATAGGGAGGTTATCAAAA
* * ** *
12888 TTACATAAGGAAATTAACAAAA
1 TTTCATAGGGAGGTTATCAAAA
* ** * *
12910 ATTCATA-AAAGGTTCTCGAAA
1 TTTCATAGGGAGGTTATCAAAA
* * * * *
12931 TTTCATAAGTAAGTTCTCGAAA
1 TTTCATAGGGAGGTTATCAAAA
* * * *** *
12953 TTCCACAGTGTCATTATCGAAA
1 TTTCATAGGGAGGTTATCAAAA
* *
12975 TTTCATAGGAAGGCTATCAAAA
1 TTTCATAGGGAGGTTATCAAAA
** *
12997 CATCATAGGGAGGTTATGAAAA
1 TTTCATAGGGAGGTTATCAAAA
** * * * *
13019 TTAGATAGTGTGATTATCATAA
1 TTTCATAGGGAGGTTATCAAAA
** *
13041 TTTCATAAAGAGGTTATCACAA
1 TTTCATAGGGAGGTTATCAAAA
13063 TTTCATAG
1 TTTCATAG
13071 TATGGTTATA
Statistics
Matches: 199, Mismatches: 88, Indels: 10
0.67 0.30 0.03
Matches are distributed among these distances:
21 28 0.14
22 168 0.84
23 3 0.02
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (22 bp):
TTTCATAGGGAGGTTATCAAAA
Done.