Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019289.1 Corchorus olitorius cultivar O-4 contig19322, 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: 37720
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:2028 original size:66 final size:66
Alignment explanation
Indices: 1878--2112 Score: 236
Period size: 65 Copynumber: 3.6 Consensus size: 66
1868 CGAAATTCGC
* * * * *
1878 CCTTT-GACCGAAAGGGCATTTTTGGAAA-GTAGA-A-TAAACTGAAATGCAAAAATGA-TGAAA
1 CCTTTCGACCGAAAGGGTATTTTTGGAAATGAAAATACTAAACTTAAATGC-AAAA-GACGGAAA
1938 CTGA
64 -TGA
*
1942 CCCTTTC-ACCGAAAGGGTATTTTTGGAAATGAAAATACTACACTTAAATGCAAAAGACGGAAAT
1 -CCTTTCGACCGAAAGGGTATTTTTGGAAATGAAAATACTAAACTTAAATGCAAAAGACGGAAAT
2006 GA
65 GA
* *
2008 CCTTTCGATCGAAAGGGTA-TTTTGGAAATTTGAAAAT--TAAACTTAAATGGAAAAGACGGAAA
1 CCTTTCGACCGAAAGGGTATTTTTGGAAA--TGAAAATACTAAACTTAAATGCAAAAGACGGAAA
2070 TGA
64 TGA
* * * *
2073 CCCTTCGACCGAAAGGGTGTTTTGGGAATTTGAAAATACT
1 CCTTTCGACCGAAAGGGTATTTTTGGAA-ATGAAAATACT
2113 TACAACCTTT
Statistics
Matches: 144, Mismatches: 14, Indels: 22
0.80 0.08 0.12
Matches are distributed among these distances:
65 90 0.62
66 26 0.18
67 17 0.12
68 11 0.08
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (66 bp):
CCTTTCGACCGAAAGGGTATTTTTGGAAATGAAAATACTAAACTTAAATGCAAAAGACGGAAATG
A
Found at i:6096 original size:2 final size:2
Alignment explanation
Indices: 6089--6114 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6079 CCCAAATTGA
6089 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
6115 TTAACAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7919 original size:38 final size:38
Alignment explanation
Indices: 7822--7967 Score: 197
Period size: 38 Copynumber: 3.8 Consensus size: 38
7812 CTGTGCATAA
* * *
7822 TGGACCCGTACCTCAGGGGGTTAAACTGATGGTAAAGAG
1 TGGACCCATGCCTCAGGGGGTTAAACTGTTGGT-AAGAG
* *
7861 TGGACCCATACCAT-ATGGGGTTAAACTGTTGGTAAGAG
1 TGGACCCATGCC-TCAGGGGGTTAAACTGTTGGTAAGAG
*
7899 TGGATCCATGCCTCAGGGGGTTAAACTGTTGGTAAGAG
1 TGGACCCATGCCTCAGGGGGTTAAACTGTTGGTAAGAG
*
7937 TGGACCCGTGCCTCAGGGGGTT-AACTGTTGG
1 TGGACCCATGCCTCAGGGGGTTAAACTGTTGG
7968 CTAGACTCGA
Statistics
Matches: 97, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
37 10 0.10
38 58 0.60
39 28 0.29
40 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.34, T:0.25
Consensus pattern (38 bp):
TGGACCCATGCCTCAGGGGGTTAAACTGTTGGTAAGAG
Found at i:8008 original size:6 final size:6
Alignment explanation
Indices: 7997--8028 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
7987 CGTTAACAGA
7997 TGATTG TGATTG TGATTG TGATTG TGATTG TG
1 TGATTG TGATTG TGATTG TGATTG TGATTG TG
8029 GTGCAGCCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (6 bp):
TGATTG
Found at i:9764 original size:21 final size:21
Alignment explanation
Indices: 9740--9787 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
9730 ATCGCATGAT
9740 TTTTGATAATGCGTTCATTGC
1 TTTTGATAATGCGTTCATTGC
9761 TTTTGATAATGCGTTCATTGC
1 TTTTGATAATGCGTTCATTGC
9782 TTTTGA
1 TTTTGA
9788 AACGGTGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (21 bp):
TTTTGATAATGCGTTCATTGC
Found at i:17150 original size:13 final size:13
Alignment explanation
Indices: 17132--17174 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
17122 TTATTATAGG
17132 TTCTTTC-TTTCTT
1 TTCTTTCTTTTC-T
17145 TTCTTTCTATTTCT
1 TTCTTTCT-TTTCT
*
17159 TTTTTTCTTTTCT
1 TTCTTTCTTTTCT
17172 TTC
1 TTC
17175 ATTTGAGACC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 14 0.54
14 8 0.31
15 4 0.15
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (13 bp):
TTCTTTCTTTTCT
Found at i:17165 original size:23 final size:22
Alignment explanation
Indices: 17132--17178 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
17122 TTATTATAGG
17132 TTCTTTCTTTCTTTTCTTTCTAT
1 TTCTTTCTTTCTTTTCTTTC-AT
*
17155 TTCTTTTTTTCTTTTCTTTCAT
1 TTCTTTCTTTCTTTTCTTTCAT
17177 TT
1 TT
17179 GAGACCATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (22 bp):
TTCTTTCTTTCTTTTCTTTCAT
Found at i:20900 original size:36 final size:36
Alignment explanation
Indices: 20853--20924 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
20843 CTGTAATTAG
20853 GGGTGAGCATAAAAAACCAAAACCGACAAAAGCGAT
1 GGGTGAGCATAAAAAACCAAAACCGACAAAAGCGAT
*
20889 GGGTGAGCATAAAAAATCAAAACCGACAAAAGCGAT
1 GGGTGAGCATAAAAAACCAAAACCGACAAAAGCGAT
20925 CGACATGACC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.50, C:0.18, G:0.22, T:0.10
Consensus pattern (36 bp):
GGGTGAGCATAAAAAACCAAAACCGACAAAAGCGAT
Found at i:21716 original size:26 final size:26
Alignment explanation
Indices: 21667--21718 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
21657 GTTTTGGCAA
*
21667 CATGTGAAGAAAATTGTTAGCAAAGC
1 CATGTGAAGAAAATTATTAGCAAAGC
21693 CATGTGAAGAAAATTTATTA-CAAAGC
1 CATGTGAAGAAAA-TTATTAGCAAAGC
21719 AAGATGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (26 bp):
CATGTGAAGAAAATTATTAGCAAAGC
Found at i:23089 original size:31 final size:31
Alignment explanation
Indices: 23054--23125 Score: 144
Period size: 31 Copynumber: 2.3 Consensus size: 31
23044 AATCCCACAA
23054 AACAATAGCAAAACAGGAGCTCCAACTCATG
1 AACAATAGCAAAACAGGAGCTCCAACTCATG
23085 AACAATAGCAAAACAGGAGCTCCAACTCATG
1 AACAATAGCAAAACAGGAGCTCCAACTCATG
23116 AACAATAGCA
1 AACAATAGCA
23126 GCAAATTGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.47, C:0.25, G:0.15, T:0.12
Consensus pattern (31 bp):
AACAATAGCAAAACAGGAGCTCCAACTCATG
Found at i:28015 original size:2 final size:2
Alignment explanation
Indices: 28010--28042 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
28000 TGTGTGTGTG
28010 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28043 CCATATTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30922 original size:14 final size:15
Alignment explanation
Indices: 30885--30927 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
30875 GCAATTTTTA
30885 AATGTTAAGTTAATT
1 AATGTTAAGTTAATT
30900 CAATG--AAGTTAATT
1 -AATGTTAAGTTAATT
30914 -ATGTTAAGTTAATT
1 AATGTTAAGTTAATT
30928 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.12
14 18 0.72
16 4 0.16
ACGTcount: A:0.40, C:0.02, G:0.14, T:0.44
Consensus pattern (15 bp):
AATGTTAAGTTAATT
Found at i:32008 original size:13 final size:12
Alignment explanation
Indices: 31990--32034 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 12
31980 ATTTTATTAC
31990 TGTTTTATTAAAT
1 TGTTTTA-TAAAT
32003 TGTTTTATAAAT
1 TGTTTTATAAAT
*
32015 GGTTTTAAATAAAT
1 TGTTTT--ATAAAT
32029 TGTTTT
1 TGTTTT
32035 GGGTGCATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.36
13 7 0.25
14 11 0.39
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (12 bp):
TGTTTTATAAAT
Found at i:32418 original size:21 final size:21
Alignment explanation
Indices: 32392--32435 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
32382 TAGCACCAAG
32392 GAGATGCCAAAGATGCCATTT
1 GAGATGCCAAAGATGCCATTT
32413 GAGATGCCAAAGATGCCATTT
1 GAGATGCCAAAGATGCCATTT
32434 GA
1 GA
32436 TCCATTGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (21 bp):
GAGATGCCAAAGATGCCATTT
Found at i:34380 original size:16 final size:17
Alignment explanation
Indices: 34359--34396 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
34349 GAAAATACAA
34359 AAAAAAATGCAAAT-GC
1 AAAAAAATGCAAATAGC
*
34375 AAAAAAATGGAAATAGC
1 AAAAAAATGCAAATAGC
34392 AAAAA
1 AAAAA
34397 TACAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.68, C:0.08, G:0.13, T:0.11
Consensus pattern (17 bp):
AAAAAAATGCAAATAGC
Done.