Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01008960.1 Corchorus olitorius cultivar O-4 contig08987, 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, 731
Length: 1219
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:162 original size:4 final size:4
Alignment explanation
Indices: 153--193 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
143 GGAGTGGCCT
153 TTTA TTTA TTTA TTTA -TTA TTTA --TA TTTA TTTA -TTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
194 ATTTCTCGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
2 2 0.06
3 6 0.18
4 25 0.76
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:181 original size:17 final size:17
Alignment explanation
Indices: 159--197 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
149 GCCTTTTATT
159 TATTTATTTATTATTTA
1 TATTTATTTATTATTTA
176 TATTTATTTATTATTTA
1 TATTTATTTATTATTTA
193 TATTT
1 TATTT
198 CTCGTATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TATTTATTTATTATTTA
Found at i:216 original size:21 final size:21
Alignment explanation
Indices: 190--233 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
180 TATTTATTAT
*
190 TTATATTTCTCGTATATTTAC
1 TTATATTTATCGTATATTTAC
211 TTATATTTATCGTATATTTAC
1 TTATATTTATCGTATATTTAC
232 TT
1 TT
234 TTAAATATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.25, C:0.11, G:0.05, T:0.59
Consensus pattern (21 bp):
TTATATTTATCGTATATTTAC
Found at i:230 original size:11 final size:11
Alignment explanation
Indices: 191--230 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
181 ATTTATTATT
*
191 TATATTTCTCG
1 TATATTTATCG
*
202 TATATTTA-CT
1 TATATTTATCG
212 TATATTTATCG
1 TATATTTATCG
223 TATATTTA
1 TATATTTA
231 CTTTTAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.28, C:0.10, G:0.05, T:0.57
Consensus pattern (11 bp):
TATATTTATCG
Found at i:246 original size:21 final size:21
Alignment explanation
Indices: 201--246 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
191 TATATTTCTC
** *
201 GTATATTTACTTATATTTATC
1 GTATATTTACTTATAAATATA
*
222 GTATATTTACTTTTAAATATA
1 GTATATTTACTTATAAATATA
243 GTAT
1 GTAT
247 TCCCGGCCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.54
Consensus pattern (21 bp):
GTATATTTACTTATAAATATA
Found at i:1069 original size:14 final size:13
Alignment explanation
Indices: 1050--1082 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
1040 GGAAAGTTCA
1050 AAAAATCATCNTTC
1 AAAAATCATC-TTC
1064 AAAAATCATCTTC
1 AAAAATCATCTTC
1077 AAAAAT
1 AAAAAT
1083 TATCATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.52, C:0.18, G:0.00, T:0.27
Consensus pattern (13 bp):
AAAAATCATCTTC
Found at i:1077 original size:13 final size:14
Alignment explanation
Indices: 1050--1088 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
1040 GGAAAGTTCA
*
1050 AAAAATCATCNTTC
1 AAAAATCATCATTC
1064 AAAAATCATC-TTC
1 AAAAATCATCATTC
*
1077 AAAAATTATCAT
1 AAAAATCATCAT
1089 ATATCATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAAATCATCATTC
Found at i:1152 original size:19 final size:19
Alignment explanation
Indices: 1124--1163 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1114 ATAATCCAGA
* *
1124 AATTATAAATTTCTAAAAT
1 AATTAGAAATTTATAAAAT
1143 AATTAGAAATTTATAAAAT
1 AATTAGAAATTTATAAAAT
1162 AA
1 AA
1164 AGTAAAAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
AATTAGAAATTTATAAAAT
Done.