Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019976.1 Corchorus olitorius cultivar O-4 contig20009, 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: 8124
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Found at i:1855 original size:25 final size:24
Alignment explanation
Indices: 1819--1865 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
1809 TCCTTCTATT
1819 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
1842 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
1866 AATTTTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:5537 original size:21 final size:21
Alignment explanation
Indices: 5508--5549 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5498 GCACAAAGAA
*
5508 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCAGAGTTG
*
5529 GTTTTAAGCTCATCAGAGTTG
1 GTTTCAAGCTCATCAGAGTTG
5550 TCTAAGATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (21 bp):
GTTTCAAGCTCATCAGAGTTG
Found at i:6400 original size:41 final size:41
Alignment explanation
Indices: 6340--6464 Score: 141
Period size: 41 Copynumber: 3.1 Consensus size: 41
6330 TTCGTATCAC
* * * *
6340 ATTGGTAAATACT-ATAACACCTTCCGATGAGGAAGGGTAG
1 ATTGGTAAATGCTGACAACACCTTCCGATGAGGAAGGGCAA
*
6380 ATTGG-ACAATGGC-GACAACACC-TCCTGATGAGGGAGGGCAA
1 ATTGGTA-AAT-GCTGACAACACCTTCC-GATGAGGAAGGGCAA
*
6421 ATTGGTAAATGCTGACGACACCTTCCGATGAGGAAGGGCAA
1 ATTGGTAAATGCTGACAACACCTTCCGATGAGGAAGGGCAA
6462 ATT
1 ATT
6465 AGGAATTTAA
Statistics
Matches: 71, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
39 1 0.01
40 13 0.18
41 53 0.75
42 4 0.06
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (41 bp):
ATTGGTAAATGCTGACAACACCTTCCGATGAGGAAGGGCAA
Found at i:6537 original size:46 final size:46
Alignment explanation
Indices: 6481--6943 Score: 510
Period size: 46 Copynumber: 10.0 Consensus size: 46
6471 TTAAACAACT
* * * *
6481 GGGAACTTCCGACCAAGAAGGGGCATTTTTGGGATGAAAGAAAACG
1 GGGACCTTCCGACCAGGAAGGGGCATTTTTGGAATGAAAGAAAACA
** *
6527 GGGACCTTCCGACCAGGAAGTCGCATTTTTGGAATGAAAGAAAACG
1 GGGACCTTCCGACCAGGAAGGGGCATTTTTGGAATGAAAGAAAACA
* * * *
6573 GGGACCTTCCAACCAGGAAGGGGCATTTTTGGAATAAAAAGGAAATA
1 GGGACCTTCCGACCAGGAAGGGGCATTTTTGGAAT-GAAAGAAAACA
* * *
6620 GGGACCTTCCAACCAGGAAGGGACATTTTTGAAAGTG-AAGAAAACTA
1 GGGACCTTCCGACCAGGAAGGGGCATTTTTGGAA-TGAAAGAAAAC-A
6667 -GGACCTTCCGACCAGGAAGGGGCATTTTTGGAATG--AGAAAACA
1 GGGACCTTCCGACCAGGAAGGGGCATTTTTGGAATGAAAGAAAACA
*
6710 GGGACCTT-CGAACCAGGAAGGGGCATTTTTGGACATGATA-AAAACA
1 GGGACCTTCCG-ACCAGGAAGGGGCATTTTTGGA-ATGAAAGAAAACA
* * *
6756 GGAACCTTCCAACCAGGAAGGGGCATTTTTGGAAGTG-AAGAAAACT
1 GGGACCTTCCGACCAGGAAGGGGCATTTTTGGAA-TGAAAGAAAACA
* **
6802 GGGACCTTCCGACCAGGAAGGGGCATTTTTGGAAATGGACATTGAAAAGT
1 GGGACCTTCCGACCAGGAAGGGGCATTTTTGG-AAT-GA-A-AGAAAACA
* * * *
6852 GGGACCTTCCGACCGGGAAGGGGCATTTTTGGTATAAAAGAAAATA
1 GGGACCTTCCGACCAGGAAGGGGCATTTTTGGAATGAAAGAAAACA
* * * *
6898 GGGACCTTCCAATCAAGAAGGGGCATTTTTGGTAA-GAGAGAAAACA
1 GGGACCTTCCGACCAGGAAGGGGCATTTTTGG-AATGAAAGAAAACA
6944 ATTTTTGTTT
Statistics
Matches: 358, Mismatches: 42, Indels: 34
0.82 0.10 0.08
Matches are distributed among these distances:
43 3 0.01
44 36 0.10
45 7 0.02
46 223 0.62
47 47 0.13
48 2 0.01
49 3 0.01
50 37 0.10
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.20
Consensus pattern (46 bp):
GGGACCTTCCGACCAGGAAGGGGCATTTTTGGAATGAAAGAAAACA
Found at i:6807 original size:136 final size:136
Alignment explanation
Indices: 6482--6942 Score: 563
Period size: 136 Copynumber: 3.3 Consensus size: 136
6472 TAAACAACTG
* * *
6482 GGAA-CTTCCGACCAAGAAGGGGCATTTTTGGGA-TGAAAGAAAACGGGGACCTTCCGACCAGGA
1 GGAACCTTCCAACCAAGAAGGGGCATTTTTGGAAGTG-AAGAAAACTGGGACCTTCCGACCAGGA
** * *
6545 AGTCGCATTTTTGGAATGAAAGAAAACGGGGACCTTCCAACCAGGAAGGGGCATTTTTGGAATAA
65 AGGGGCATTTTTGGAATG-AAGAAAACAGGGACCTTCGAACCAGGAAGGGGCATTTTTGGAATAA
6610 AAAGGAAATA
129 AAA--AAATA
* * * * *
6620 GGGACCTTCCAACCAGGAAGGGACATTTTTGAAAGTGAAGAAAACTAGGACCTTCCGACCAGGAA
1 GGAACCTTCCAACCAAGAAGGGGCATTTTTGGAAGTGAAGAAAACTGGGACCTTCCGACCAGGAA
* *
6685 GGGGCATTTTTGGAATG-AGAAAACAGGGACCTTCGAACCAGGAAGGGGCATTTTTGGACATGAT
66 GGGGCATTTTTGGAATGAAGAAAACAGGGACCTTCGAACCAGGAAGGGGCATTTTTGGA-ATAAA
*
6749 AAAAACA
130 AAAAATA
*
6756 GGAACCTTCCAACCAGGAAGGGGCATTTTTGGAAGTGAAGAAAACTGGGACCTTCCGACCAGGAA
1 GGAACCTTCCAACCAAGAAGGGGCATTTTTGGAAGTGAAGAAAACTGGGACCTTCCGACCAGGAA
** * *
6821 GGGGCATTTTTGGAAATGGACATTGAAAAGTGGGACCTTCCG-ACCGGGAAGGGGCATTTTTGGT
66 GGGGCATTTTTGG-AAT-GA-A--GAAAACAGGGACCTT-CGAACCAGGAAGGGGCATTTTTGGA
6885 ATAAAAGAAAATA
125 ATAAAA-AAAATA
* * *
6898 GGGACCTTCCAATCAAGAAGGGGCATTTTTGGTAAGAG-AGAAAAC
1 GGAACCTTCCAACCAAGAAGGGGCATTTTTGG-AAGTGAAGAAAAC
6943 AATTTTTGTT
Statistics
Matches: 281, Mismatches: 30, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
136 78 0.28
137 42 0.15
138 9 0.03
139 65 0.23
140 3 0.01
141 4 0.01
142 74 0.26
143 6 0.02
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.20
Consensus pattern (136 bp):
GGAACCTTCCAACCAAGAAGGGGCATTTTTGGAAGTGAAGAAAACTGGGACCTTCCGACCAGGAA
GGGGCATTTTTGGAATGAAGAAAACAGGGACCTTCGAACCAGGAAGGGGCATTTTTGGAATAAAA
AAAATA
Done.