Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020645.1 Corchorus olitorius cultivar O-4 contig20678, 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: 4465
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:2305 original size:19 final size:19
Alignment explanation
Indices: 2277--2326 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
2267 CTCCATCAAG
2277 AAATTCGAAAAAAAAAACGA
1 AAATT-GAAAAAAAAAACGA
** **
2297 AAATTGAAAGTAAAAGTGA
1 AAATTGAAAAAAAAAACGA
2316 AAATTGAAAAA
1 AAATTGAAAAA
2327 TAAGATGGAG
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.66, C:0.04, G:0.14, T:0.16
Consensus pattern (19 bp):
AAATTGAAAAAAAAAACGA
Found at i:4043 original size:140 final size:140
Alignment explanation
Indices: 3665--4194 Score: 900
Period size: 140 Copynumber: 3.8 Consensus size: 140
3655 TTCATCATGT
*
3665 TTGCGTTTAAATTTCAATAAACCTTGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCGGGCACC
1 TTGCGTTTAAATTTCAA-AAACCTTGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCGGGCACA
*
3730 ATTTCAGAAGCCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCAT-TTCATTTCATCAAGT
65 ATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATCTT-ATTTCATCAAGT
*
3794 TTCTAATCAAAG
129 TTTTAATCAAAG
* *
3806 TTGTGTTTAAAGTTTAAAAAAACCTTGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCGGGCAC
1 TTGCGTTTAAA-TTT-CAAAAACCTTGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCGGGCAC
*
3871 AATATCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATCTTATTTCATCAAGT
64 AATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATCTTATTTCATCAAGT
3936 TTTTAATCAAAG
129 TTTTAATCAAAG
*
3948 TTGCGTTTAAATTTCAAAAACCTTGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCAGGCACAA
1 TTGCGTTTAAATTTCAAAAACCTTGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCGGGCACAA
*
4013 TTTCAGAAACCTCCGGGTATTAATTTTGATAAATCCTCCGGGTATCATCTTATTTCATCAAGTTT
66 TTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATCTTATTTCATCAAGTTT
4078 TTAATCAAAG
131 TTAATCAAAG
* * *
4088 TTGCGTTTAAATTACAAAAACCTTGCTCAAGGTCGAGTTTACATTTGTAAGACCTCCGGGCACAA
1 TTGCGTTTAAATTTCAAAAACCTTGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCGGGCACAA
* *
4153 TTTTAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGG
66 TTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGG
4195 CATTCCATAT
Statistics
Matches: 368, Mismatches: 18, Indels: 7
0.94 0.05 0.02
Matches are distributed among these distances:
140 222 0.60
141 13 0.04
142 129 0.35
143 4 0.01
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (140 bp):
TTGCGTTTAAATTTCAAAAACCTTGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCGGGCACAA
TTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATCTTATTTCATCAAGTTT
TTAATCAAAG
Found at i:4379 original size:76 final size:76
Alignment explanation
Indices: 4243--4465 Score: 223
Period size: 76 Copynumber: 2.9 Consensus size: 76
4233 TATGTCTTTT
* * *** ** * *
4243 AATCCTGCTCAGGGTCATTTTTTACCAGTCAATTTTAATCCTATTCATGATCATTGCTTTAT-TA
1 AATCCTGCTCAGGATCATTTTTTACCAGTTAATCAAAATCCTGCTCAGGATCATTGCTTTATCAA
* * *
4307 GTCGACTTCAG
66 ATCAACTTCAA
* *
4318 AATCCTGCTCAGGATCATTTCCTTACCAGTTAATCACAATCCTGCTCAGGATCATTGCTTTATCA
1 AATCCTGCTCAGGATCATTT-TTTACCAGTTAATCAAAATCCTGCTCAGGATCATTGCTTTATCA
* *
4383 AATTAATTTCAA
65 AATCAACTTCAA
* * *
4395 AATCCTGCTCAGGATCATCTTTTTATCAAATTAATTTCAAAACCCTGCTCAGGATCATTGCTTTA
1 AATCCTGCTCAGGATCAT-TTTTTA-CCAGTTAA--TCAAAATCCTGCTCAGGATCATTGCTTTA
4460 TCAAAT
62 TCAAAT
Statistics
Matches: 122, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
75 19 0.16
76 34 0.28
77 28 0.23
78 8 0.07
80 33 0.27
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (76 bp):
AATCCTGCTCAGGATCATTTTTTACCAGTTAATCAAAATCCTGCTCAGGATCATTGCTTTATCAA
ATCAACTTCAA
Found at i:4410 original size:40 final size:40
Alignment explanation
Indices: 4313--4465 Score: 197
Period size: 40 Copynumber: 3.9 Consensus size: 40
4303 ATTAGTCGAC
* * * * *
4313 TTCAGAATCCTGCTCAGGATCATTTCCTTA-CCAGTTAA-
1 TTCAAAATCCTGCTCAGGATCATTGCTTTATCAAATTAAT
*
4351 -TCACAATCCTGCTCAGGATCATTGCTTTATCAAATTAAT
1 TTCAAAATCCTGCTCAGGATCATTGCTTTATCAAATTAAT
*
4390 TTCAAAATCCTGCTCAGGATCATCT-TTTTATCAAATTAAT
1 TTCAAAATCCTGCTCAGGATCAT-TGCTTTATCAAATTAAT
*
4430 TTCAAAACCCTGCTCAGGATCATTGCTTTATCAAAT
1 TTCAAAATCCTGCTCAGGATCATTGCTTTATCAAAT
Statistics
Matches: 101, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
37 26 0.26
38 6 0.06
39 1 0.01
40 67 0.66
41 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (40 bp):
TTCAAAATCCTGCTCAGGATCATTGCTTTATCAAATTAAT
Done.