Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010302.1 Corchorus olitorius cultivar O-4 contig10334, 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: 9975
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:94 original size:22 final size:21
Alignment explanation
Indices: 64--233 Score: 101
Period size: 22 Copynumber: 7.8 Consensus size: 21
54 CTTTTCTCCT
*
64 ACTTACTATGAAATTTTGATA
1 ACTTCCTATGAAATTTTGATA
* *
85 ATCTTGCTAT-ATTATTTTGATA
1 A-CTTCCTATGA-AATTTTGATA
* * *
107 ACCTCTCTAAGAAATTATGATA
1 ACTTC-CTATGAAATTTTGATA
* * *
129 ACCTCCCAGTGAAACTTTGATA
1 ACTTCCTA-TGAAATTTTGATA
**
151 ACCACACTATGAAATTTTGAT-
1 ACTTC-CTATGAAATTTTGATA
172 ACTATCCTATGAAATTTTGATA
1 ACT-TCCTATGAAATTTTGATA
** * *
194 ACAACACTATAAAATTGTGATA
1 ACTTC-CTATGAAATTTTGATA
* *
216 ACCTCTATATGAAATTTT
1 ACTTC-CTATGAAATTTT
234 TTTTATGACG
Statistics
Matches: 114, Mismatches: 26, Indels: 17
0.73 0.17 0.11
Matches are distributed among these distances:
21 24 0.21
22 87 0.76
23 3 0.03
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (21 bp):
ACTTCCTATGAAATTTTGATA
Found at i:344 original size:23 final size:23
Alignment explanation
Indices: 301--367 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 23
291 GTACACTATG
* *
301 AAATTTGGATAACCAT-ACTATAA
1 AAATTTTGATAACC-TCCCTATAA
324 AAATTTTGATAACCTCCCTAT-A
1 AAATTTTGATAACCTCCCTATAA
* * *
346 GAATGTTGATAACTTCCCTATA
1 AAATTTTGATAACCTCCCTATA
368 GACTTTCATT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 20 0.54
23 17 0.46
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (23 bp):
AAATTTTGATAACCTCCCTATAA
Found at i:414 original size:22 final size:22
Alignment explanation
Indices: 386--488 Score: 88
Period size: 22 Copynumber: 4.7 Consensus size: 22
376 TTAATCTCAC
*
386 TATGAAATTTTGATAAGCACAA
1 TATGAAATTTTGATAAGCACAT
* *
408 TATGAAATTTTGATTA-C-CTTT
1 TATGAAATTTTGATAAGCAC-AT
*
429 TATGAAATTTTTG-TAATCACAT
1 TATGAAA-TTTTGATAAGCACAT
* *
451 TATGAAAATTTGAT-AGCCACAC
1 TATGAAATTTTGATAAG-CACAT
*
473 TATGAAATTTCGATAA
1 TATGAAATTTTGATAA
489 TCTGCAAAGT
Statistics
Matches: 64, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
20 1 0.02
21 15 0.23
22 46 0.72
23 2 0.03
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAAGCACAT
Found at i:1177 original size:16 final size:16
Alignment explanation
Indices: 1158--1201 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
1148 TCGGGCTGCC
* *
1158 TCGGGTTTGGGTATTT
1 TCGGGTTCGGGTAATT
*
1174 TCGGGCTCGGGTAATT
1 TCGGGTTCGGGTAATT
*
1190 TCAGGTTCGGGT
1 TCGGGTTCGGGT
1202 TCGGGCGGGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.09, C:0.14, G:0.39, T:0.39
Consensus pattern (16 bp):
TCGGGTTCGGGTAATT
Found at i:2601 original size:25 final size:24
Alignment explanation
Indices: 2558--2606 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
2548 GAGTTTCACC
*
2558 ATTTATTTTTTTTACTTTTCTTCT
1 ATTTATTTTTTTTACTTTTATTCT
2582 ATTTATTTATTTTTTA-TTTTATTCT
1 ATTTA-TT-TTTTTTACTTTTATTCT
2607 TCAATGTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 5 0.23
25 10 0.45
26 7 0.32
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (24 bp):
ATTTATTTTTTTTACTTTTATTCT
Found at i:7566 original size:2 final size:2
Alignment explanation
Indices: 7554--7601 Score: 80
Period size: 2 Copynumber: 24.0 Consensus size: 2
7544 CGTGCCATTG
7554 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7595 AT CAT AT
1 AT -AT AT
7602 TAAAAACAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 41 0.93
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.