Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024552.1 Corchorus olitorius cultivar O-4 contig24585, 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: 25057
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:5963 original size:217 final size:217
Alignment explanation
Indices: 5588--6020 Score: 805
Period size: 217 Copynumber: 2.0 Consensus size: 217
5578 CATGTATATA
* * *
5588 TTTTGTCAATAATAATACTCCTTTCATGAAACATGTGAGACAAATATTTATTATTTTGCAGCGTG
1 TTTTGTCAATAATAATACCCCCTTCATGAAACATGTAAGACAAATATTTATTATTTTGCAGCGTG
*
5653 ATCATATATAATTTGTTTGTTTAGTCTTTAGATCATTTTATAAAATAATTTGTTATTCAATTTTA
66 ATCATATAGAATTTGTTTGTTTAGTCTTTAGATCATTTTATAAAATAATTTGTTATTCAATTTTA
5718 AAAATTCAAATTCTTTAATAAAATTATCTTATTCAATAATTTTGTGAAAACTTTGTTTTCCATAT
131 AAAATTCAAATTCTTTAATAAAATTATCTTATTCAATAATTTTGTGAAAACTTTGTTTTCCATAT
*
5783 ATAGATTGCAATGATTGTTATT
196 ATAAATTGCAATGATTGTTATT
5805 TTTTGTCAATAATAATACACCCCTT-ATGAAACATGTAAGACAAATATTTATTATTTTGCAGCGT
1 TTTTGTCAATAATAATAC-CCCCTTCATGAAACATGTAAGACAAATATTTATTATTTTGCAGCGT
5869 GATCATATAGAATTTGTTTGTTTAGTCTTTAGATCATTTTATAAAATAATTTGTTATTCAATTTT
65 GATCATATAGAATTTGTTTGTTTAGTCTTTAGATCATTTTATAAAATAATTTGTTATTCAATTTT
5934 AAAAATTCAAATTCTTTAATAAAATTATCTTATTCAATAATTTTGTGAAAACTTTGTTTTCCATA
130 AAAAATTCAAATTCTTTAATAAAATTATCTTATTCAATAATTTTGTGAAAACTTTGTTTTCCATA
5999 TATAAATTGCAATGATTGTTAT
195 TATAAATTGCAATGATTGTTAT
6021 ATATCCTATT
Statistics
Matches: 210, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
217 206 0.98
218 4 0.02
ACGTcount: A:0.35, C:0.10, G:0.09, T:0.46
Consensus pattern (217 bp):
TTTTGTCAATAATAATACCCCCTTCATGAAACATGTAAGACAAATATTTATTATTTTGCAGCGTG
ATCATATAGAATTTGTTTGTTTAGTCTTTAGATCATTTTATAAAATAATTTGTTATTCAATTTTA
AAAATTCAAATTCTTTAATAAAATTATCTTATTCAATAATTTTGTGAAAACTTTGTTTTCCATAT
ATAAATTGCAATGATTGTTATT
Found at i:6168 original size:108 final size:108
Alignment explanation
Indices: 5948--6165 Score: 402
Period size: 107 Copynumber: 2.0 Consensus size: 108
5938 ATTCAAATTC
5948 TTTAATAAAATTATCTTATTCAATAATTTTGTGAAAACTTTGTTTTCCATATATAAATTGCAATG
1 TTTAATAAAATTATCTTATTCAATAATTTTGTGAAAACTTTGTTTTCCATATATAAATTGCAATG
6013 ATTGTTATATATCCTATTTTGGGAAGAGACGGAAGAATTTTTT
66 ATTGTTATATATCCTATTTTGGGAAGAGACGGAAGAATTTTTT
*
6056 TTTAATAAAATTATCTTATTCAATAATTTTGTGAAAACTTTG-TTTCCATATATAGATTGCAATG
1 TTTAATAAAATTATCTTATTCAATAATTTTGTGAAAACTTTGTTTTCCATATATAAATTGCAATG
**
6120 ATTGTTATATATCCTATTTTGGGAAGAGACGGAAGTTTTTTTT
66 ATTGTTATATATCCTATTTTGGGAAGAGACGGAAGAATTTTTT
6163 TTT
1 TTT
6166 TAAACCACGA
Statistics
Matches: 107, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
107 65 0.61
108 42 0.39
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (108 bp):
TTTAATAAAATTATCTTATTCAATAATTTTGTGAAAACTTTGTTTTCCATATATAAATTGCAATG
ATTGTTATATATCCTATTTTGGGAAGAGACGGAAGAATTTTTT
Found at i:16638 original size:3 final size:3
Alignment explanation
Indices: 16630--16657 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
16620 GCTACCCAAA
16630 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
16658 TAGGCCGTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17136 original size:24 final size:24
Alignment explanation
Indices: 17100--17145 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
17090 AGAAGAGTCA
*
17100 AATACTGAGCATACAACAGTTTGG
1 AATACTGAACATACAACAGTTTGG
*
17124 AATACTGAACATATAACAGTTT
1 AATACTGAACATACAACAGTTT
17146 TGGGATAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (24 bp):
AATACTGAACATACAACAGTTTGG
Found at i:18246 original size:8 final size:8
Alignment explanation
Indices: 18233--18262 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
18223 ACTAAAAATA
18233 ATATATCT
1 ATATATCT
18241 ATATATCT
1 ATATATCT
*
18249 ATATATAT
1 ATATATCT
18257 ATATAT
1 ATATAT
18263 ATGTATTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (8 bp):
ATATATCT
Found at i:20473 original size:17 final size:16
Alignment explanation
Indices: 20421--20469 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
20411 CACCCCCCAT
*
20421 ATCACTAGTGATCTAAG
1 ATCACCAGTGATC-AAG
20438 ATCACCAGTGATGCAAG
1 ATCACCAGTGAT-CAAG
*
20455 ATCACCGGTGATCAA
1 ATCACCAGTGATCAA
20470 AGATTACATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 3 0.10
17 25 0.86
18 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (16 bp):
ATCACCAGTGATCAAG
Found at i:22080 original size:31 final size:31
Alignment explanation
Indices: 22042--22147 Score: 121
Period size: 31 Copynumber: 3.5 Consensus size: 31
22032 AGCCTAATTA
22042 CTCAAATAAGGGCCTAACGTTTGCCAAAATG
1 CTCAAATAAGGGCCTAACGTTTGCCAAAATG
* * **
22073 CTCAAATAAGGGCCTGATC-TTT--TAATTTGG
1 CTCAAATAAGGGCCT-AACGTTTGCCAAAAT-G
*
22103 C-CAAATAAGAGCCTAACGTTTGCCAAAATG
1 CTCAAATAAGGGCCTAACGTTTGCCAAAATG
22133 CTCAAATAAGGGCCT
1 CTCAAATAAGGGCCT
22148 GGCGTCGAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
28 2 0.03
29 18 0.31
30 4 0.07
31 33 0.56
32 2 0.03
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (31 bp):
CTCAAATAAGGGCCTAACGTTTGCCAAAATG
Found at i:22289 original size:60 final size:60
Alignment explanation
Indices: 22187--22347 Score: 252
Period size: 60 Copynumber: 2.7 Consensus size: 60
22177 ACTGACGCCA
**
22187 GACCCTTATTTGAGCATTTTTTTATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
1 GACCCTTATTTGAGCA-TTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
22248 GACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
1 GACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
* * *
22308 GGCCCTTATTTGAGCATTTTGGCA-AACGATAGGCCCTTAT
1 GACCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTAT
22348 CTGAGCAATT
Statistics
Matches: 94, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
60 77 0.82
61 17 0.18
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (60 bp):
GACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
Found at i:22346 original size:31 final size:29
Alignment explanation
Indices: 22189--22354 Score: 97
Period size: 29 Copynumber: 5.5 Consensus size: 29
22179 TGACGCCAGA
* *
22189 CCCTTATTTGAGCATTTTTTTATAACGTTAGG
1 CCCTTATTTGAGCA--TTTTGA-AACGATAGG
** * *
22221 CCCTTATTTG-GCCAAATT-AAAAGATCGG
1 CCCTTATTTGAG-CATTTTGAAACGATAGG
*
22249 ACCCTTATTTGAGCATTTTCGATAACGTTAGG
1 -CCCTTATTTGAGCATTTT-GA-AACGATAGG
** * *
22281 CCCTTATTTG-GCCAAATT-AAAAGATCGGG
1 CCCTTATTTGAG-CATTTTGAAACGAT-AGG
22310 CCCTTATTTGAGCATTTTGGCAAACGATAGG
1 CCCTTATTTGAGCATTTT-G-AAACGATAGG
*
22341 CCCTTATCTGAGCA
1 CCCTTATTTGAGCA
22355 ATTAGCTGTG
Statistics
Matches: 102, Mismatches: 20, Indels: 25
0.69 0.14 0.17
Matches are distributed among these distances:
28 10 0.10
29 32 0.31
30 5 0.05
31 31 0.30
32 24 0.24
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (29 bp):
CCCTTATTTGAGCATTTTGAAACGATAGG
Done.