Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016678.1 Corchorus olitorius cultivar O-4 contig16711, 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: 9091
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:1841 original size:78 final size:78
Alignment explanation
Indices: 1712--1858 Score: 267
Period size: 78 Copynumber: 1.9 Consensus size: 78
1702 AAAGGAAAAC
* *
1712 AAAGGATATAGGTTTTCTTGTTTGGATTGTTAAAAATTAGCCAGGTAGAGGAAATGAATCACCAT
1 AAAGGATATAGGTTTTCTTGTTTGGATTGTTAAAAATTAGCCAGGGAGAGGAAAAGAATCACCAT
1777 ACCAGTTGTTAAT
66 ACCAGTTGTTAAT
*
1790 AAAGGATATAGGTTTTCTTGTTTGGATTGTTAAAAATTAGTCAGGGAGAGGAAAAGAATCACCAT
1 AAAGGATATAGGTTTTCTTGTTTGGATTGTTAAAAATTAGCCAGGGAGAGGAAAAGAATCACCAT
1855 ACCA
66 ACCA
1859 TACCAGTTGT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 66 1.00
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.31
Consensus pattern (78 bp):
AAAGGATATAGGTTTTCTTGTTTGGATTGTTAAAAATTAGCCAGGGAGAGGAAAAGAATCACCAT
ACCAGTTGTTAAT
Found at i:7748 original size:22 final size:22
Alignment explanation
Indices: 7723--8290 Score: 383
Period size: 22 Copynumber: 26.4 Consensus size: 22
7713 TCAAAGACAA
*
7723 TTTGATAACCACACTGTGAAAT
1 TTTGATAACCACACTATGAAAT
7745 TTTGATAACCACACTAT-ACAAT
1 TTTGATAACCACACTATGA-AAT
*
7767 TTTGATAAACCTTC-CTATGAAAT
1 TTTGAT-AACC-ACACTATGAAAT
* *
7790 TTCGGTAACCACACTATGAAAT
1 TTTGATAACCACACTATGAAAT
*
7812 TTTGATAACCTTC-CTATGAAAT
1 TTTGATAACC-ACACTATGAAAT
* * *
7834 TTCGGTAACCACACTATTAAAT
1 TTTGATAACCACACTATGAAAT
* * *
7856 TTCGATAACCTCCCTATGAAA-
1 TTTGATAACCACACTATGAAAT
* * *
7877 TTTGATAACCTCTCTATAAAAT
1 TTTGATAACCACACTATGAAAT
* * *
7899 TTTAATAACCAAACTATAAAAT
1 TTTGATAACCACACTATGAAAT
7921 TTT-AGT-A--ACA-TATGAAAT
1 TTTGA-TAACCACACTATGAAAT
* *
7939 TTTGTTAA-C-CTCTATGAAAT
1 TTTGATAACCACACTATGAAAT
* * *
7959 TTTGGTAATCACATTATG-AAT
1 TTTGATAACCACACTATGAAAT
*
7980 TTT-AGTAACCTTCA-TATGAAAT
1 TTTGA-TAACC-ACACTATGAAAT
*
8002 TTTGATAACCACACTGTGAAAT
1 TTTGATAACCACACTATGAAAT
* * * *
8024 TTTGATAATCTCTCTATAAAAT
1 TTTGATAACCACACTATGAAAT
* *
8046 CTTGATAACCTTCA-TATGAAAT
1 TTTGATAACC-ACACTATGAAAT
* *
8068 TTTGGTAACCTTC-CTATGAAA-
1 TTTGATAACC-ACACTATGAAAT
*
8089 TTTGATAACCTC-CTTATGAAAT
1 TTTGATAACCACAC-TATGAAAT
**
8111 TCAGATAACCACACTATGAAAT
1 TTTGATAACCACACTATGAAAT
** *
8133 TCGGATAACCTTC-CTATGAAAT
1 TTTGATAACC-ACACTATGAAAT
**
8155 TCGGATAACCACACTATGAAAT
1 TTTGATAACCACACTATGAAAT
* * *
8177 TTTAATAACC-CCCTATGAATT
1 TTTGATAACCACACTATGAAAT
8198 TTTG-TAACCACAC--TGAAAT
1 TTTGATAACCACACTATGAAAT
****
8217 TTTGATAA-CTTTTTAATGAAAT
1 TTTGATAACCACACT-ATGAAAT
* * *
8239 TTTTATAACCATAATATGAAAT
1 TTTGATAACCACACTATGAAAT
* *
8261 TTTGGTAACCACACTATGAAGT
1 TTTGATAACCACACTATGAAAT
*
8283 TGTGATAA
1 TTTGATAA
8291 TTTCCTTATG
Statistics
Matches: 437, Mismatches: 76, Indels: 66
0.75 0.13 0.11
Matches are distributed among these distances:
18 11 0.03
19 14 0.03
20 26 0.06
21 71 0.16
22 289 0.66
23 24 0.05
24 2 0.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (22 bp):
TTTGATAACCACACTATGAAAT
Found at i:8186 original size:109 final size:108
Alignment explanation
Indices: 7726--8195 Score: 380
Period size: 109 Copynumber: 4.4 Consensus size: 108
7716 AAGACAATTT
* *
7726 GATAACCACACTGTGAAATTTTGATAACCACACTAT-ACAATTTTGATAAACCTTCC-TATGAAA
1 GATAACCACACTATGAAATTTTGATAACC-CCCTATGA-AA-TTTGAT-AACC-TCCTTATGAAA
*
7789 TTTC-GGTAACCACACTATGAAATTTTGATAACCTTCCTATGAAATTTCG
61 TTTCAGATAACCACACTATGAAATTTTGATAACC-TCCTATGAAA-TTCG
* * *
7838 G-TAACCACACTATTAAATTTCGATAACCTCCCTATGAAATTTGATAACCT-CTCTATAAAATTT
1 GATAACCACACTATGAAATTTTGATAACC-CCCTATGAAATTTGATAACCTCCT-TATGAAATTT
* * * * **
7901 TA-ATAACCAAACTATAAAATTTT-AGTAA---CATATGAAATTTT
64 CAGATAACCACACTATGAAATTTTGA-TAACCTCCTATGAAATTCG
* * * * ** * * *
7942 GTTAA-C-CTCTATGAAATTTTGGTAATCACATTATG-AATTTTAGTAACCTTCATATGAAATTT
1 GATAACCACACTATGAAATTTTGATAA-CCCCCTATGAAATTTGA-TAACCTCCTTATGAAATTT
* * * * *
8004 -TGATAACCACACTGTGAAATTTTGATAATCTCTCTAT-AAAATCTT
64 CAGATAACCACACTATGAAATTTTGATAACCTC-CTATGAAATTC-G
* * *
8049 GATAACCTTCA-TATGAAATTTTGGTAACCTTCCTATGAAATTTGATAACCTCCTTATGAAA-TT
1 GATAACC-ACACTATGAAATTTTGATAACC-CCCTATGAAATTTGATAACCTCCTTATGAAATTT
**
8112 CAGATAACCACACTATGAAATTCGGATAACCTTCCTATGAAATTCG
64 CAGATAACCACACTATGAAATTTTGATAACC-TCCTATGAAATTCG
*
8158 GATAACCACACTATGAAATTTTAATAACCCCCTATGAA
1 GATAACCACACTATGAAATTTTGATAACCCCCTATGAA
8196 TTTTTGTAAC
Statistics
Matches: 283, Mismatches: 50, Indels: 54
0.73 0.13 0.14
Matches are distributed among these distances:
102 6 0.02
103 56 0.20
104 7 0.02
105 11 0.04
106 5 0.02
107 9 0.03
108 16 0.06
109 120 0.42
110 20 0.07
111 31 0.11
112 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.35
Consensus pattern (108 bp):
GATAACCACACTATGAAATTTTGATAACCCCCTATGAAATTTGATAACCTCCTTATGAAATTTCA
GATAACCACACTATGAAATTTTGATAACCTCCTATGAAATTCG
Done.