Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019122.1 Corchorus olitorius cultivar O-4 contig19155, 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: 64119
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:723 original size:2 final size:2
Alignment explanation
Indices: 700--740 Score: 50
Period size: 2 Copynumber: 20.5 Consensus size: 2
690 TTTCTTTTCC
700 TA TA TA T- TA CTA GTA TA T- 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 TA TA T
741 TCTTTTCCTC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
1 2 0.06
2 29 0.83
3 4 0.11
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5964 original size:29 final size:30
Alignment explanation
Indices: 5906--5966 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
5896 GTTCTAATTG
* *
5906 ATGTATACATATAAATTATTCAATTTTATT
1 ATGTATAAATATAAATTATTCAATTATATT
*
5936 ATGTATAAATAT-AATTATTTAATTATATT
1 ATGTATAAATATAAATTATTCAATTATATT
5965 AT
1 AT
5967 ATTATTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (30 bp):
ATGTATAAATATAAATTATTCAATTATATT
Found at i:6952 original size:60 final size:60
Alignment explanation
Indices: 6881--7017 Score: 170
Period size: 60 Copynumber: 2.3 Consensus size: 60
6871 AACGTTTGTT
* *
6881 AAAATGTTCAAATAAGGGTCC-GATCTTTTAATTT-AGCCAAATAAGAGCCTGACATTATCG
1 AAAATGCTCAAATAAGGG-CCTGATCTTTTAATTTGA-CCAAATAAGAGCCTAACATTATCG
* * * * * *
6941 AAAATGCTCAAATAAGTGCCTGATTTTTTTATTTGACCAAATAAGGGTCTAACGTTATCG
1 AAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGACCAAATAAGAGCCTAACATTATCG
7001 AAAATGCTCAAATAAGG
1 AAAATGCTCAAATAAGG
7018 ACTTGGCGTC
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
59 2 0.03
60 63 0.95
61 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (60 bp):
AAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGACCAAATAAGAGCCTAACATTATCG
Found at i:7131 original size:60 final size:60
Alignment explanation
Indices: 7058--7223 Score: 217
Period size: 60 Copynumber: 2.8 Consensus size: 60
7048 ATTTTCGATG
* *
7058 CCAGGCCCTTATTTAAGCATTTTGGCAAACATTAGGTCGTTATTTGGCCAAATTAAAAGA
1 CCAGGCCCTTATTTAAGCATTTTGGCAAACGTTAGGTCCTTATTTGGCCAAATTAAAAGA
* * *
7118 CCAGGCCCTTATTTGAGTATTTTGACAAACGTTAGGTCCTTATTTGGCCAAATTAAAAGA
1 CCAGGCCCTTATTTAAGCATTTTGGCAAACGTTAGGTCCTTATTTGGCCAAATTAAAAGA
* * * * **
7178 TCAGACCCCTATTTGAA-CAGTTTGGCAAACGTTAGACCCTTATTTG
1 CCAGGCCCTTATTT-AAGCATTTTGGCAAACGTTAGGTCCTTATTTG
7224 AGCAATTAGC
Statistics
Matches: 91, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
60 90 0.99
61 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (60 bp):
CCAGGCCCTTATTTAAGCATTTTGGCAAACGTTAGGTCCTTATTTGGCCAAATTAAAAGA
Found at i:10945 original size:53 final size:53
Alignment explanation
Indices: 10882--11044 Score: 317
Period size: 53 Copynumber: 3.1 Consensus size: 53
10872 TGTTTATTCA
*
10882 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATACAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
10935 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
10988 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
11041 ATTG
1 ATTG
11045 GATTTAAAGA
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
53 109 1.00
ACGTcount: A:0.51, C:0.18, G:0.07, T:0.23
Consensus pattern (53 bp):
ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
Found at i:18998 original size:52 final size:52
Alignment explanation
Indices: 18920--19022 Score: 170
Period size: 52 Copynumber: 2.0 Consensus size: 52
18910 GTTTGTTTTA
* * *
18920 AAAGGGAGCTAAACCTTGGTCTAAAATCGTGTCTAAATTTGAGGAGTTCATC
1 AAAGGGAGCTAAACCTTGGACTAAAATCGTGCCTAAATTTAAGGAGTTCATC
*
18972 AAAGGGGGCTAAACCTTGGACTAAAATCGTGCCTAAATTTAAGGAGTTCAT
1 AAAGGGAGCTAAACCTTGGACTAAAATCGTGCCTAAATTTAAGGAGTTCAT
19023 TTGACATTGC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (52 bp):
AAAGGGAGCTAAACCTTGGACTAAAATCGTGCCTAAATTTAAGGAGTTCATC
Found at i:37829 original size:3 final size:3
Alignment explanation
Indices: 37823--37860 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
37813 GGGGAAAGAG
37823 AAT AAT AAT AAT AAT AAT AAT AATT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT A
37861 CACCTAAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:45800 original size:26 final size:28
Alignment explanation
Indices: 45756--45814 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 28
45746 CCATTGTTTA
45756 TAAAAAAATATATGTAAAA-TT-TAATT
1 TAAAAAAATATATGTAAAAGTTGTAATT
45782 TAAAAAAATATAT-TGAAAAGGTTGTAATT
1 TAAAAAAATATATGT-AAAA-GTTGTAATT
45811 TAAA
1 TAAA
45815 GTTTATAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
25 1 0.03
26 17 0.59
28 2 0.07
29 9 0.31
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (28 bp):
TAAAAAAATATATGTAAAAGTTGTAATT
Found at i:60308 original size:2 final size:2
Alignment explanation
Indices: 60303--60327 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
60293 TTTTTTATTT
60303 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 T
60328 TAAACATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:62932 original size:22 final size:22
Alignment explanation
Indices: 62904--62983 Score: 110
Period size: 22 Copynumber: 3.7 Consensus size: 22
62894 ATTATGCTAT
62904 TATATATAAAATATATTTATGA
1 TATATATAAAATATATTTATGA
* *
62926 TATATATAGAATATATGTA--A
1 TATATATAAAATATATTTATGA
* *
62946 AATATATAAATTATATTTATGA
1 TATATATAAAATATATTTATGA
62968 TATATATAAAATATAT
1 TATATATAAAATATAT
62984 ATAACAAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 16 0.33
22 32 0.67
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (22 bp):
TATATATAAAATATATTTATGA
Found at i:62961 original size:31 final size:31
Alignment explanation
Indices: 62904--62984 Score: 83
Period size: 33 Copynumber: 2.5 Consensus size: 31
62894 ATTATGCTAT
** *
62904 TATATATAAAATATATTTATGATATATATAGA
1 TATATATAAAATATATAAATTATATATAT-GA
* *
62936 -ATATATGTAAAATATATAAATTATATTTATGA
1 TATATAT-AAAA-TATATAAATTATATATATGA
62968 TATATATAAAATATATA
1 TATATATAAAATATATA
62985 TAACAAATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
31 12 0.30
32 8 0.20
33 20 0.50
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (31 bp):
TATATATAAAATATATAAATTATATATATGA
Found at i:62992 original size:13 final size:11
Alignment explanation
Indices: 62904--62987 Score: 73
Period size: 11 Copynumber: 7.8 Consensus size: 11
62894 ATTATGCTAT
62904 TATATATAAAA
1 TATATATAAAA
* **
62915 TATATTTATGA
1 TATATATAAAA
*
62926 TATATATAGAA
1 TATATATAAAA
*
62937 TATATGT-AAA
1 TATATATAAAA
*
62947 -ATATATAAAT
1 TATATATAAAA
* **
62957 TATATTTATGA
1 TATATATAAAA
62968 TATATATAAAA
1 TATATATAAAA
62979 TATATATAA
1 TATATATAA
62988 CAAATTTTTT
Statistics
Matches: 54, Mismatches: 17, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
9 5 0.09
10 4 0.07
11 45 0.83
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (11 bp):
TATATATAAAA
Done.