Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012334.1 Corchorus capsularis cultivar CVL-1 contig12355, 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: 11387
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Found at i:1342 original size:35 final size:35
Alignment explanation
Indices: 1296--1717 Score: 440
Period size: 35 Copynumber: 12.1 Consensus size: 35
1286 GGATCAACTC
* *
1296 GAGATCAACTCTGACCATCGAAAACTTCTTGAAAT
1 GAGATCAACTCTGATCATCGAAAACTTCTTGGAAT
* * *
1331 GAGATCAACTCTGATCATGGAAAACTACTTGAAAT
1 GAGATCAACTCTGATCATCGAAAACTTCTTGGAAT
* * * * **
1366 GGGATCTACTCTGATAATCTAAAACTTCTTAAAAT
1 GAGATCAACTCTGATCATCGAAAACTTCTTGGAAT
* * *
1401 GAGATCAACTCTGATCATGGATAATTTCTTGGAAT
1 GAGATCAACTCTGATCATCGAAAACTTCTTGGAAT
* *
1436 GAGATCAACTCTGATC-T-TAAAACAATTTTTGGAAT
1 GAGATCAACTCTGATCATCGAAAAC--TTCTTGGAAT
* * *
1471 GAGATCAACTCTGATCGTTGGAAACTTCTTGGAAT
1 GAGATCAACTCTGATCATCGAAAACTTCTTGGAAT
* * *
1506 GAGATCAACTCTGATCATGGAACACTAT-TTGAAAT
1 GAGATCAACTCTGATCATCGAAAACT-TCTTGGAAT
* *
1541 GAGATCAACTCTGACCAT-GGAAACTTCTTGGAAT
1 GAGATCAACTCTGATCATCGAAAACTTCTTGGAAT
* * * *
1575 AAGATCAACTCTGATCGTTGAAAATTTCTTGGAAT
1 GAGATCAACTCTGATCATCGAAAACTTCTTGGAAT
* *
1610 GAGATCAACTCTGATCTTC-AAACACTTTTTTGGAAT
1 GAGATCAACTCTGATCATCGAAA-AC-TTCTTGGAAT
* * * *
1646 GAGATCAACTCTGATCGTTGGAAACTTCTCGGAAT
1 GAGATCAACTCTGATCATCGAAAACTTCTTGGAAT
* *
1681 GAGATCAACTCTGATCTTCGGAAACTTCTTGGAAT
1 GAGATCAACTCTGATCATCGAAAACTTCTTGGAAT
1716 GA
1 GA
1718 CCGCACCGGA
Statistics
Matches: 324, Mismatches: 53, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
33 4 0.01
34 30 0.09
35 254 0.78
36 30 0.09
37 6 0.02
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (35 bp):
GAGATCAACTCTGATCATCGAAAACTTCTTGGAAT
Found at i:1642 original size:175 final size:175
Alignment explanation
Indices: 1296--1696 Score: 588
Period size: 175 Copynumber: 2.3 Consensus size: 175
1286 GGATCAACTC
* * * * *
1296 GAGATCAACTCTGACCATCGAAAACTTCTTGAAATGAGATCAACTCTGATCATGGAAAACTACTT
1 GAGATCAACTCTGATCGTTGGAAACTTCTTGGAATGAGATCAACTCTGATCATGGAAAACTACTT
* * * * * *
1361 GAAATGGGATCTACTCTGATAATCTAAAACTTCTTAAAATGAGATCAACTCTGATCATGGATAAT
66 GAAATGAGATCAACTCTGACAATCGAAAACTTCTTAAAATAAGATCAACTCTGATCATGGAAAAT
1426 TTCTTGGAATGAGATCAACTCTGATCTTAAAACAATTTTTGGAAT
131 TTCTTGGAATGAGATCAACTCTGATCTTAAAACAATTTTTGGAAT
* *
1471 GAGATCAACTCTGATCGTTGGAAACTTCTTGGAATGAGATCAACTCTGATCATGGAACACTATTT
1 GAGATCAACTCTGATCGTTGGAAACTTCTTGGAATGAGATCAACTCTGATCATGGAAAACTACTT
* * ** * *
1536 GAAATGAGATCAACTCTGACCAT-GGAAACTTCTTGGAATAAGATCAACTCTGATCGTTGAAAAT
66 GAAATGAGATCAACTCTGACAATCGAAAACTTCTTAAAATAAGATCAACTCTGATCATGGAAAAT
* *
1600 TTCTTGGAATGAGATCAACTCTGATCTTCAAACACTTTTTTGGAAT
131 TTCTTGGAATGAGATCAACTCTGATCTTAAAACA-ATTTTTGGAAT
*
1646 GAGATCAACTCTGATCGTTGGAAACTTCTCGGAATGAGATCAACTCTGATC
1 GAGATCAACTCTGATCGTTGGAAACTTCTTGGAATGAGATCAACTCTGATC
1697 TTCGGAAACT
Statistics
Matches: 203, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
174 66 0.33
175 137 0.67
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (175 bp):
GAGATCAACTCTGATCGTTGGAAACTTCTTGGAATGAGATCAACTCTGATCATGGAAAACTACTT
GAAATGAGATCAACTCTGACAATCGAAAACTTCTTAAAATAAGATCAACTCTGATCATGGAAAAT
TTCTTGGAATGAGATCAACTCTGATCTTAAAACAATTTTTGGAAT
Found at i:1813 original size:54 final size:52
Alignment explanation
Indices: 1680--1825 Score: 175
Period size: 54 Copynumber: 2.7 Consensus size: 52
1670 CTTCTCGGAA
* *
1680 TGAGATCAACTCTGATCTTCGGAAACTTCTTGGAATGACCGCACCGGATCAAT
1 TGAGATCAACTCTGATCTT-GAAAACTTCTTGGAATGACCACACCGGATCAAT
* * ** *
1733 TGGGGATCAACTCTGAACTCCAAAAACTTCTTGGAATGACCACACCGGATTAAT
1 T-GAGATCAACTCTGATCT-TGAAAACTTCTTGGAATGACCACACCGGATCAAT
*
1787 CTGAGATCAACTCTGATCATTGAAAACTTCTTGAAATGA
1 -TGAGATCAACTCTGATC-TTGAAAACTTCTTGGAATGA
1826 GATCAACTCT
Statistics
Matches: 77, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
53 1 0.01
54 74 0.96
55 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (52 bp):
TGAGATCAACTCTGATCTTGAAAACTTCTTGGAATGACCACACCGGATCAAT
Found at i:1834 original size:35 final size:35
Alignment explanation
Indices: 1788--1860 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
1778 CGGATTAATC
* *
1788 TGAGATCAACTCTGATCATTGAAAACTTCTTGAAA
1 TGAGATCAACTCTGACCACTGAAAACTTCTTGAAA
* * *
1823 TGAGATCAACTCTGACCGCTGAAAATTTCTTGGAA
1 TGAGATCAACTCTGACCACTGAAAACTTCTTGAAA
1858 TGA
1 TGA
1861 CCACACCGGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (35 bp):
TGAGATCAACTCTGACCACTGAAAACTTCTTGAAA
Found at i:1944 original size:88 final size:89
Alignment explanation
Indices: 1737--1948 Score: 320
Period size: 89 Copynumber: 2.4 Consensus size: 89
1727 ATCAATTGGG
* * **
1737 GATCAACTCTGAACTCCAAAAACTTCTTGGAATGACCACACCGGATTAATCTGAGATCAACTCTG
1 GATCAACTCTGACCGCTGAAAACTTCTTGGAATGACCACACCGGATTAATCTGAGATCAACTCTG
1802 ATCATTGAAAACTTCTTGAAATGA
66 ATCATTGAAAACTTCTTGAAATGA
* * *
1826 GATCAACTCTGACCGCTGAAAATTTCTTGGAATGACCACACCGGA-TCATCCTGAGATCAACTTT
1 GATCAACTCTGACCGCTGAAAACTTCTTGGAATGACCACACCGGATTAAT-CTGAGATCAACTCT
1890 GATCATT-AAAACTTCTTGAAATGA
65 GATCATTGAAAACTTCTTGAAATGA
* *
1914 GATCAACTCTGATCGTTGAAAACTTCTTGGAATGA
1 GATCAACTCTGACCGCTGAAAACTTCTTGGAATGA
1949 GATCAACTCT
Statistics
Matches: 112, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
88 52 0.46
89 60 0.54
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (89 bp):
GATCAACTCTGACCGCTGAAAACTTCTTGGAATGACCACACCGGATTAATCTGAGATCAACTCTG
ATCATTGAAAACTTCTTGAAATGA
Found at i:1948 original size:35 final size:34
Alignment explanation
Indices: 1877--1983 Score: 144
Period size: 35 Copynumber: 3.1 Consensus size: 34
1867 CGGATCATCC
* *
1877 TGAGATCAACTTTGATCATT-AAAACTTCTTGAAA
1 TGAGATCAACTCTGATC-TTGAAAACTTCTTGGAA
1911 TGAGATCAACTCTGATCGTTGAAAACTTCTTGGAA
1 TGAGATCAACTCTGATC-TTGAAAACTTCTTGGAA
* *
1946 TGAGATCAACTCTGATCTTCGAAAACTTTTTTGAA
1 TGAGATCAACTCTGATCTT-GAAAACTTCTTGGAA
1981 TGA
1 TGA
1984 TCGCACTGGA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
34 20 0.30
35 46 0.70
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Consensus pattern (34 bp):
TGAGATCAACTCTGATCTTGAAAACTTCTTGGAA
Found at i:2949 original size:11 final size:11
Alignment explanation
Indices: 2918--2955 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
2908 TTTGGAAACC
2918 TTTT-CTTTTT
1 TTTTGCTTTTT
2928 TTTTCGCCTTTTT
1 TTTT-G-CTTTTT
2941 TTTTGCTTTTT
1 TTTTGCTTTTT
2952 TTTT
1 TTTT
2956 TGGACCTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 4 0.16
11 10 0.40
12 1 0.04
13 10 0.40
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (11 bp):
TTTTGCTTTTT
Found at i:2955 original size:12 final size:12
Alignment explanation
Indices: 2918--2957 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
2908 TTTGGAAACC
2918 TTTT-CTTTTTT
1 TTTTGCTTTTTT
* *
2929 TTTCGCCTTTTT
1 TTTTGCTTTTTT
2941 TTTTGCTTTTTT
1 TTTTGCTTTTTT
2953 TTTTG
1 TTTTG
2958 GACCTTACGC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 3 0.12
12 21 0.88
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.80
Consensus pattern (12 bp):
TTTTGCTTTTTT
Found at i:2956 original size:13 final size:12
Alignment explanation
Indices: 2922--2955 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
2912 GAAACCTTTT
2922 CTTTTTTTTTCG
1 CTTTTTTTTTCG
2934 CCTTTTTTTTT-G
1 -CTTTTTTTTTCG
2946 CTTTTTTTTT
1 CTTTTTTTTT
2956 TGGACCTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 1 0.05
13 10 0.48
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (12 bp):
CTTTTTTTTTCG
Found at i:10194 original size:21 final size:21
Alignment explanation
Indices: 10170--10217 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
10160 GGCCTTGTTC
* *
10170 CTGCCTCATTTCTTCTTGCGA
1 CTGCCTCATTTCTCCCTGCGA
*
10191 CTGCCTCATTTCTCCCTGTGA
1 CTGCCTCATTTCTCCCTGCGA
10212 CTGCCT
1 CTGCCT
10218 TAACTGTTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.08, C:0.38, G:0.15, T:0.40
Consensus pattern (21 bp):
CTGCCTCATTTCTCCCTGCGA
Done.