Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013916.1 Corchorus olitorius cultivar O-4 contig13949, 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: 10258
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:589 original size:36 final size:35
Alignment explanation
Indices: 429--669 Score: 288
Period size: 35 Copynumber: 6.7 Consensus size: 35
419 AAATGCTTTG
* * *
429 GATGGGAACTTTCCCATTTTGAAAACTAAAACTGAAAAT
1 GATGGGAACTTTCCCAATTTGAAAACT-TAA---AAACT
* * * *
468 GACGGGAACTTTCCCTAAATTGAAAA-TGAAAACCT
1 GATGGGAACTTTCCC-AATTTGAAAACTTAAAAACT
*
503 GATGGGAACTTTCCCAATTTGAAAACTTTGAAAACT
1 GATGGGAACTTTCCCAATTTGAAAAC-TTAAAAACT
539 GGATGGGAACTTTCCCAATTTGAAAACTTAAAAAACT
1 -GATGGGAACTTTCCCAATTTGAAAACTT-AAAAACT
* *
576 GGTGGGAACTTTCCCAATTTAAAAACTTAAAAACT
1 GATGGGAACTTTCCCAATTTGAAAACTTAAAAACT
* *
611 GGTGGGAACTTTCCCCATTTGAAAACTT-AAAACT
1 GATGGGAACTTTCCCAATTTGAAAACTTAAAAACT
645 GATGGGAACTTTCCCAATTTGAAAA
1 GATGGGAACTTTCCCAATTTGAAAA
670 AAACTTGAAT
Statistics
Matches: 179, Mismatches: 18, Indels: 15
0.84 0.08 0.07
Matches are distributed among these distances:
34 38 0.21
35 50 0.28
36 34 0.19
37 32 0.18
38 2 0.01
39 15 0.08
40 8 0.04
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (35 bp):
GATGGGAACTTTCCCAATTTGAAAACTTAAAAACT
Found at i:4728 original size:12 final size:12
Alignment explanation
Indices: 4711--4737 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4701 GTCCACGTCT
4711 GTTAGTCACGCC
1 GTTAGTCACGCC
4723 GTTAGTCACGCC
1 GTTAGTCACGCC
4735 GTT
1 GTT
4738 GACGAAGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.30, G:0.26, T:0.30
Consensus pattern (12 bp):
GTTAGTCACGCC
Found at i:7976 original size:24 final size:24
Alignment explanation
Indices: 7944--7995 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
7934 ACTATGAGCA
7944 TTTTTTGTTTTAGAGTACGGGCAT
1 TTTTTTGTTTTAGAGTACGGGCAT
7968 TTTTTTGTTTTAGAGTACGGGCAT
1 TTTTTTGTTTTAGAGTACGGGCAT
7992 TTTT
1 TTTT
7996 AATTGATTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.15, C:0.08, G:0.23, T:0.54
Consensus pattern (24 bp):
TTTTTTGTTTTAGAGTACGGGCAT
Found at i:9899 original size:22 final size:22
Alignment explanation
Indices: 9874--9920 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
9864 TTTTTAGTTG
*
9874 AGTAAAACT-ATAAAAGTAAAAT
1 AGTAAAA-TGATAAAAATAAAAT
*
9896 AGTAAAATGGTAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
9918 AGT
1 AGT
9921 TATAAGGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:9913 original size:93 final size:93
Alignment explanation
Indices: 9813--9981 Score: 320
Period size: 93 Copynumber: 1.8 Consensus size: 93
9803 AATAATATCA
*
9813 TAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTA
1 TAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGACTA
9878 AAACTATAAAAGTAAAATAGTAAAATGG
66 AAACTATAAAAGTAAAATAGTAAAATGG
*
9906 TAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGACTA
1 TAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGACTA
9971 AAACTATAAAA
66 AAACTATAAAA
9982 ATTTAAACAA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.53, C:0.02, G:0.13, T:0.33
Consensus pattern (93 bp):
TAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGACTA
AAACTATAAAAGTAAAATAGTAAAATGG
Found at i:10039 original size:27 final size:28
Alignment explanation
Indices: 10009--10074 Score: 98
Period size: 31 Copynumber: 2.3 Consensus size: 28
9999 TAAGAAATAT
10009 ATTCAAAA-AATAAGGGTATAATAGGCG
1 ATTCAAAATAATAAGGGTATAATAGGCG
10036 ATTCAAAAGATTAATAAGGGTATAATAGGCG
1 ATTC-AAA-A-TAATAAGGGTATAATAGGCG
10067 ATTCAAAA
1 ATTCAAAA
10075 GTTTTACAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
27 4 0.11
28 3 0.09
29 2 0.06
30 3 0.09
31 23 0.66
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (28 bp):
ATTCAAAATAATAAGGGTATAATAGGCG
Found at i:10055 original size:31 final size:31
Alignment explanation
Indices: 10017--10075 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
10007 ATATTCAAAA
10017 AATAAGGGTATAATAGGCGATTCAAAAGATT
1 AATAAGGGTATAATAGGCGATTCAAAAGATT
10048 AATAAGGGTATAATAGGCGATTCAAAAG
1 AATAAGGGTATAATAGGCGATTCAAAAG
10076 TTTTACAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.46, C:0.07, G:0.24, T:0.24
Consensus pattern (31 bp):
AATAAGGGTATAATAGGCGATTCAAAAGATT
Found at i:10218 original size:2 final size:2
Alignment explanation
Indices: 10211--10247 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
10201 TAGTATGATT
10211 TA TA TA TA TA TA 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
10248 TGCATGAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.