Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019409.1 Corchorus olitorius cultivar O-4 contig19442, 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: 47080
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:61 original size:39 final size:39
Alignment explanation
Indices: 7--98 Score: 175
Period size: 39 Copynumber: 2.4 Consensus size: 39
1 TGTGAC
7 ATGCTGATGTGGCAAAAATTATTATGTTATTCACTTTTT
1 ATGCTGATGTGGCAAAAATTATTATGTTATTCACTTTTT
*
46 ATGCTGATGTGGCAAAAATTATTATTTTATTCACTTTTT
1 ATGCTGATGTGGCAAAAATTATTATGTTATTCACTTTTT
85 ATGCTGATGTGGCA
1 ATGCTGATGTGGCA
99 TGCCACGTGA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.45
Consensus pattern (39 bp):
ATGCTGATGTGGCAAAAATTATTATGTTATTCACTTTTT
Found at i:2058 original size:33 final size:33
Alignment explanation
Indices: 2016--2099 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 33
2006 CTTTCTCCAA
* * **
2016 GTGGCATTGCCATGTCAGACTAGTCCGACCCAC
1 GTGGCATTGCCACGTCAGACAAAACCGACCCAC
* **
2049 GTGGCATTGCCACGTCGGACAAAACCGTGCCAC
1 GTGGCATTGCCACGTCAGACAAAACCGACCCAC
2082 GTGGCATTGCCACGTCAG
1 GTGGCATTGCCACGTCAG
2100 TGACGATCAG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.21, C:0.32, G:0.27, T:0.19
Consensus pattern (33 bp):
GTGGCATTGCCACGTCAGACAAAACCGACCCAC
Found at i:2239 original size:71 final size:71
Alignment explanation
Indices: 2148--2290 Score: 277
Period size: 71 Copynumber: 2.0 Consensus size: 71
2138 TCTCGCCGTA
*
2148 GCCGGTAGTAGCGTCGGAGGAGAGGAAATTGAAGCAAGTAAAACAAAATAGGAAGAAATTAGGAA
1 GCCGGTAGTAGCGTCGGAGGAGAGGAAATTGAAGCAAGTAAAACAAAATAGGAAGAAACTAGGAA
2213 ATTAAG
66 ATTAAG
2219 GCCGGTAGTAGCGTCGGAGGAGAGGAAATTGAAGCAAGTAAAACAAAATAGGAAGAAACTAGGAA
1 GCCGGTAGTAGCGTCGGAGGAGAGGAAATTGAAGCAAGTAAAACAAAATAGGAAGAAACTAGGAA
2284 ATTAAG
66 ATTAAG
2290 G
1 G
2291 GTGGGCACTT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.45, C:0.09, G:0.31, T:0.15
Consensus pattern (71 bp):
GCCGGTAGTAGCGTCGGAGGAGAGGAAATTGAAGCAAGTAAAACAAAATAGGAAGAAACTAGGAA
ATTAAG
Found at i:18096 original size:21 final size:21
Alignment explanation
Indices: 18067--18111 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
18057 TTGGGTTAAC
*
18067 AGTCTCATCTTTGGGTTTTTT
1 AGTCCCATCTTTGGGTTTTTT
18088 AGTCCCATCTTTGGGTTTTTT
1 AGTCCCATCTTTGGGTTTTTT
18109 AGT
1 AGT
18112 TCGTTGAGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.11, C:0.16, G:0.20, T:0.53
Consensus pattern (21 bp):
AGTCCCATCTTTGGGTTTTTT
Found at i:19066 original size:17 final size:17
Alignment explanation
Indices: 19044--19080 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
19034 CTAACTTCTA
*
19044 CTTCTAAATATCGTTTT
1 CTTCTAAACATCGTTTT
*
19061 CTTCTAAACATGGTTTT
1 CTTCTAAACATCGTTTT
19078 CTT
1 CTT
19081 TAATTGTCCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.19, G:0.08, T:0.51
Consensus pattern (17 bp):
CTTCTAAACATCGTTTT
Found at i:24906 original size:32 final size:32
Alignment explanation
Indices: 24865--24925 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
24855 AAATATGTTT
24865 GAAAAATAAGGATATAAT-GATCGATTCAATTA
1 GAAAAATAAGGATATAATAG-TCGATTCAATTA
*
24897 GAAAAATAAGGGTATAATAGTCGATTCAA
1 GAAAAATAAGGATATAATAGTCGATTCAA
24926 AAGTTTTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
32 26 0.96
33 1 0.04
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (32 bp):
GAAAAATAAGGATATAATAGTCGATTCAATTA
Found at i:46636 original size:319 final size:321
Alignment explanation
Indices: 45810--47080 Score: 1804
Period size: 319 Copynumber: 3.9 Consensus size: 321
45800 TTATTTGGTT
* *
45810 AAAGGTTAAAGGTTTTTTCACGCTTCTAAATATCATTTTTCCAACTTTTTTCCGAATAAATTT-T
1 AAAGATTAAAGGTTTTTTCACGCTTCT-AATATCATTTTTCCAACTTTTTTCCGAATTAATTTCT
* * *
45874 AATTAAATCAAAACAAGATTCAGATACTCGTAGAAACAAATCCTTAAATCCAACGAGGCTGAGAT
65 AATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAACGTGGCTGAGAT
* * *
45939 TTGGTTAGGATAAATATAGATATTTCAAGGAGTCTTTGCGCCCAAAATCATGTAAAACTAACCCG
130 TTGGTT-TGATAAATATAGATATTTCAAGGAGTCTTTGAGCCAAAAATCATGTAAAACTAACCCG
*
46004 GGCTCCGGAACGCGTTTTTAGGCAAAAACCGTGATGGTTTGTACACGATTTCGGCTAAAAACTGA
194 GGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGG--TGTACACGATTTCGGCTAAAAACTGA
* * *
46069 CCCGAAAAGTTTTTTCTCAATTCTCTTGCCACAATACTTATAAAAAATAAATAATTCAACGCCAA
257 CCCGAAAAGTTTTTCCTCAATTTTCTTGCCACAATACTTATAAAAAATATATAATTCAACGCCAA
* *
46134 AAAGATTAAAGGATTTTTCACGCTTCTAATATCA-TTTTCCAACTTTTTTCCGAATTAAATTCTA
1 AAAGATTAAAGGTTTTTTCACGCTTCTAATATCATTTTTCCAACTTTTTTCCGAATTAATTTCTA
* *
46198 ATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAACGTGGCTGTGATT
66 ATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAACGTGGCTGAGATT
* * * *
46263 TGGTTTGATGAATATAGATATTTCAAGGAGTCTTT-ACGCCCAAAATCATGTAAAACTAAGCTGG
131 TGGTTTGATAAATATAGATATTTCAAGGAGTCTTTGA-GCCAAAAATCATGTAAAACTAACCCGG
*
46327 GCTCCGGAACGCGTTTTTAGCCAAAAACCGTGAT-G-GTACACGATTTCGGCTAAAAACTGGCCC
195 GCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTGTACACGATTTCGGCTAAAAACTGACCC
*
46390 GAAAAGTTTTTCCTCAATTTTCTTGCCACAATACTTAAAAAAAATATATAATTCAACGCCAA
260 GAAAAGTTTTTCCTCAATTTTCTTGCCACAATACTTATAAAAAATATATAATTCAACGCCAA
*
46452 AAAGATTAAAGGTTTTTTCACGCTTCTAATATCAGTTTTCCAACTTTTTTCCGAATTAATTTCTA
1 AAAGATTAAAGGTTTTTTCACGCTTCTAATATCATTTTTCCAACTTTTTTCCGAATTAATTTCTA
* * * *
46517 ATTAAATCGAAACAAGATTCGGATACTTGTAAAAACAAATCCTTAAATCTAACGTGCCTGAGATT
66 ATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAACGTGGCTGAGATT
* * * **
46582 TGGTTTGATAAATATAGATATTTCAAGGAGTTTTTGAACCAAAAATCATGTAAAACTGACCAAGG
131 TGGTTTGATAAATATAGATATTTCAAGGAGTCTTTGAGCCAAAAATCATGTAAAACTAACCCGGG
* *
46647 CTCCGGAACGCGTTTTTTTTGCCAAAAAACGGTGATGGTTAGTACACGATTTCGGCTAAAAACTG
196 CTCCGGAACGCG--TTTTTAGCC-AAAAACCGTGATGG-T-GTACACGATTTCGGCTAAAAACTG
* *
46712 ACCCGAAAAGTTTTTCCTCGATTTTCTTGCCACAATACTTATAAAAAATATATAATTCACCGCCA
256 ACCCGAAAAGTTTTTCCTCAATTTTCTTGCCACAATACTTATAAAAAATATATAATTCAACGCCA
46777 A
321 A
*
46778 AAAGATTAAAGGTTTTTTCACGCTTCTAATATAATTTTTCCCAAC-TTTTTCCGAATTAACTTTC
1 AAAGATTAAAGGTTTTTTCACGCTTCTAATATCATTTTT-CCAACTTTTTTCCGAATTAA-TTTC
* * *
46842 TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGAGA
64 TAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAACGTGGCTGAGA
* * * * * * *
46907 TTTGGTTAGATAAATATAGATATTTCAAGGACTCTTTGCACCCAAAAA-CATGCAAAATTGAGCC
129 TTTGGTTTGATAAATATAGATATTTCAAGGAGTCTTTG-AGCCAAAAATCATGTAAAACTAACCC
** * * * * *
46971 GGGCTCTAGAACGCGTTCTTAACCAAAAACCGTGATGATTAGTACATGATTTCGGCTAAAATCT-
193 GGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATG-GT-GTACACGATTTCGGCTAAAAACTG
* * ** *
47035 ATCCCGAAAAGTTTTT-CTAAATTTTTTTGTAACAATACTTAGAAAA
256 A-CCCGAAAAGTTTTTCCTCAATTTTCTTGCCACAATACTTATAAAA
Statistics
Matches: 856, Mismatches: 75, Indels: 33
0.89 0.08 0.03
Matches are distributed among these distances:
318 118 0.14
319 155 0.18
320 1 0.00
321 9 0.01
322 122 0.14
323 100 0.12
324 74 0.09
325 6 0.01
326 137 0.16
327 126 0.15
328 8 0.01
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (321 bp):
AAAGATTAAAGGTTTTTTCACGCTTCTAATATCATTTTTCCAACTTTTTTCCGAATTAATTTCTA
ATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAACGTGGCTGAGATT
TGGTTTGATAAATATAGATATTTCAAGGAGTCTTTGAGCCAAAAATCATGTAAAACTAACCCGGG
CTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTGTACACGATTTCGGCTAAAAACTGACCCG
AAAAGTTTTTCCTCAATTTTCTTGCCACAATACTTATAAAAAATATATAATTCAACGCCAA
Done.