Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017663.1 Corchorus olitorius cultivar O-4 contig17696, 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: 6864
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:666 original size:199 final size:199
Alignment explanation
Indices: 319--779 Score: 737
Period size: 199 Copynumber: 2.3 Consensus size: 199
309 GGTGATTTAT
* * *
319 TGCACGTGCGGGGTTTAAGGATTGACATGTGTCCCCTTAGGGAAAATGTATTAATATTAAATATT
1 TGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATT
* *
384 TTATTAATTATGAAATGGGATATGTGTCAACTTCTTAACCCGCTTATGAAGTCCAAAATTTACAC
66 TAATTAATTATAAAATGGGATATGTGTCAACTTCTTAACCCGCTTATGAAGTCCAAAATTTACAC
** *
449 TGAAAGTGTATTGTATAATAATCTTATAAGAAAAATTATACTATACACCGTCAGTTG-AGTTTAG
131 TGAAAGTGTACGGTATAATAATCCTATAAGAAAAATTATACTATACACCGTCAG-TGCAGTTTAG
513 CAGAC
195 CAGAC
* * *
518 TGCACGTGCAGGGTTGAAGGGTTGACATGTGTCCCCTTAAGGAATATGTATTGATATTAAATATT
1 TGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATT
* ** *
583 TAATTTATTATAAAATGAGG-TATGTGTCAACTTCTTAATTCGCTTATGGAGTCCAAAATTTACA
66 TAATTAATTATAAAATG-GGATATGTGTCAACTTCTTAACCCGCTTATGAAGTCCAAAATTTACA
*
647 CTGACAGTGTACGGTATAATAATCCTATAAGAAAAATTATACTATACACCGTCAGTGCAGTTTAG
130 CTGAAAGTGTACGGTATAATAATCCTATAAGAAAAATTATACTATACACCGTCAGTGCAGTTTAG
712 CAGAC
195 CAGAC
*
717 TGCACGTGCAGGGTTTAAGGGTTGACATGTGTCTCCTTAGGGAATATGTATTAATATTAAATA
1 TGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATA
780 CACAATTAAT
Statistics
Matches: 240, Mismatches: 20, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
198 2 0.01
199 236 0.98
200 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.34
Consensus pattern (199 bp):
TGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATT
TAATTAATTATAAAATGGGATATGTGTCAACTTCTTAACCCGCTTATGAAGTCCAAAATTTACAC
TGAAAGTGTACGGTATAATAATCCTATAAGAAAAATTATACTATACACCGTCAGTGCAGTTTAGC
AGAC
Found at i:934 original size:24 final size:24
Alignment explanation
Indices: 902--954 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
892 AATTTTGATA
*
902 ATATATACCTTTTTTTGGTATCAT
1 ATATGTACCTTTTTTTGGTATCAT
* *
926 ATATGTACCTTTTTTTGTTATTAT
1 ATATGTACCTTTTTTTGGTATCAT
950 ATATG
1 ATATG
955 GAAAGTTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.57
Consensus pattern (24 bp):
ATATGTACCTTTTTTTGGTATCAT
Found at i:2097 original size:39 final size:38
Alignment explanation
Indices: 2004--2272 Score: 194
Period size: 39 Copynumber: 6.8 Consensus size: 38
1994 AAAATCTTTA
**
2004 ATGGGATCTTTCCCCT-AATTGAAAACTTTGAAAAAGACCAG
1 ATGGGATCTTT-CCCTAAATT-AAAACTTTG-AAAA-ACTTG
*
2045 ATGGGACCTTTCCCTAAATTAAAACTTCTGAAAAACTTG
1 ATGGGATCTTTCCCTAAATTAAAACTT-TGAAAAACTTG
* *
2084 ATGGGATCTTTCCCTAAATTAAAGACTTTAAAAAGAAACTGG
1 ATGGGATCTTTCCCTAAATTAAA-ACTTT--GAA-AAACTTG
* * *
2126 ATGGGATCTTTCTCTAAATCGAAAGAC-TTAAACAAACTTG
1 ATGGGATCTTTCCCTAAAT-TAAA-ACTTTGAA-AAACTTG
* *
2166 ATGGGACCTTTCCC--AATTAGAAA-TCTTG-AAAGCTTG
1 ATGGGATCTTTCCCTAAATTA-AAACT-TTGAAAAACTTG
*
2202 ATGGGACCTTTCCCTAAATTAAAAAC-TTGAGAAATAC-TG
1 ATGGGATCTTTCCCTAAATT-AAAACTTTGA-AAA-ACTTG
* * *
2241 GTGGGATCTTTCCCTAATTTGAAATCTTTGAA
1 ATGGGATCTTTCCCTAAATT-AAAACTTTGAA
2273 TTGAAAACTT
Statistics
Matches: 189, Mismatches: 21, Indels: 38
0.76 0.08 0.15
Matches are distributed among these distances:
36 20 0.11
37 6 0.03
38 14 0.07
39 54 0.29
40 45 0.24
41 18 0.10
42 26 0.14
43 6 0.03
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30
Consensus pattern (38 bp):
ATGGGATCTTTCCCTAAATTAAAACTTTGAAAAACTTG
Found at i:2265 original size:76 final size:78
Alignment explanation
Indices: 2004--2268 Score: 231
Period size: 76 Copynumber: 3.4 Consensus size: 78
1994 AAAATCTTTA
* **
2004 ATGGGATCTTTCCCCTAA-TTGAAAACTTTGAAAAAGACCAGATGGGACCTTTCCCTAAATT-AA
1 ATGGGATCTTT-CCCTAATTTGAAATC-TT-AAAAAGACTGGATGGGACCTTTCCCTAAATTAAA
*
2067 AACTTCTGAAAAACTTG
63 AACTT-AGAAAAACTTG
* * * * *
2084 ATGGGATCTTTCCCTAAATT-AAAGACTTTAAAAAGAAACTGGATGGGATCTTTCTCTAAATCGA
1 ATGGGATCTTTCCCTAATTTGAAA-TC-TTAAAAAG--ACTGGATGGGACCTTTCCCTAAAT-TA
*
2148 AAGACTTA-AACAAACTTG
61 AAAACTTAGAA-AAACTTG
* * * *
2166 ATGGGACCTTTCCC-AATTAGAAATCTT-GAAAG-CTTGATGGGACCTTTCCCTAAATTAAAAAC
1 ATGGGATCTTTCCCTAATTTGAAATCTTAAAAAGACTGGATGGGACCTTTCCCTAAATTAAAAAC
*
2228 TTGAGAAATAC-TG
66 TT-AGAAAAACTTG
*
2241 GTGGGATCTTTCCCTAATTTGAAATCTT
1 ATGGGATCTTTCCCTAATTTGAAATCTT
2269 TGAATTGAAA
Statistics
Matches: 153, Mismatches: 21, Indels: 26
0.76 0.10 0.13
Matches are distributed among these distances:
75 21 0.14
76 36 0.24
77 2 0.01
79 19 0.12
80 20 0.13
81 26 0.17
82 23 0.15
83 6 0.04
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (78 bp):
ATGGGATCTTTCCCTAATTTGAAATCTTAAAAAGACTGGATGGGACCTTTCCCTAAATTAAAAAC
TTAGAAAAACTTG
Found at i:4245 original size:20 final size:20
Alignment explanation
Indices: 4207--4248 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
4197 TTTGTTCCTT
* **
4207 TGGCACCTGAATTCTTGATG
1 TGGCACCTGAACTAGTGATG
4227 TGGCACCTGAACTAGTGATG
1 TGGCACCTGAACTAGTGATG
4247 TG
1 TG
4249 TACTGAGTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (20 bp):
TGGCACCTGAACTAGTGATG
Found at i:5788 original size:58 final size:59
Alignment explanation
Indices: 5566--5878 Score: 402
Period size: 58 Copynumber: 5.3 Consensus size: 59
5556 AAAGTTTTTG
* *
5566 GGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGCCTTAATCTTAAAATTCTTT-TA
1 GGAACTGTCTTCAGATCCATCTATGAGCTGTCTTCAGCCTTAATCTTAAAA-TCTTTCAA
* * * *
5625 GGAATTGTCTTCAGATCTATCTGTGAGCTGTCTTCAGCTTTAATCTTAAAATCTTTCAA
1 GGAACTGTCTTCAGATCCATCTATGAGCTGTCTTCAGCCTTAATCTTAAAATCTTTCAA
** * *
5684 GGAACTGTCTTCAGATCCATCTATGAGCTGTCTTCAATCTCAATCTTAAAATCTTTCGA
1 GGAACTGTCTTCAGATCCATCTATGAGCTGTCTTCAGCCTTAATCTTAAAATCTTTCAA
* * * *
5743 -GAGCTATCTTCAGATCCGTCTATGAGCTGTCTTCAGTCTCT-ATCTTAAAATCTTTC-A
1 GGAACTGTCTTCAGATCCATCTATGAGCTGTCTTCAGCCT-TAATCTTAAAATCTTTCAA
* *
5800 GGAGCTGTCTTCAGATCCATCTATGAGCTGTCTTCAGCCTTAATCTTAAAATTTTTCAA
1 GGAACTGTCTTCAGATCCATCTATGAGCTGTCTTCAGCCTTAATCTTAAAATCTTTCAA
* *
5859 -GAACTATCTTCGGAATCCAT
1 GGAACTGTCTTCAG-ATCCAT
5879 TTCTGATGAA
Statistics
Matches: 224, Mismatches: 24, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
57 2 0.01
58 115 0.51
59 107 0.48
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (59 bp):
GGAACTGTCTTCAGATCCATCTATGAGCTGTCTTCAGCCTTAATCTTAAAATCTTTCAA
Done.