Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021625.1 Corchorus olitorius cultivar O-4 contig21658, 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: 12644
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Found at i:1137 original size:38 final size:38
Alignment explanation
Indices: 1041--1188 Score: 226
Period size: 38 Copynumber: 3.9 Consensus size: 38
1031 GGCTGTGCAT
*
1041 AGTGGACCCGTACCTCAGGGGGTTAAACTGATGGTAAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGT-AAG
* *
1080 AGTGGACCCATACCACAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
*
1118 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
* *
1156 GGTGGACCCGTGCCTCAGGGGGTT-AACTGTTGG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGG
1189 CTAGACTCGA
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
37 9 0.09
38 61 0.60
39 32 0.31
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.22
Consensus pattern (38 bp):
AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
Found at i:1229 original size:6 final size:6
Alignment explanation
Indices: 1218--1249 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1208 CGTTAACGGA
1218 TGATTG TGATTG TGATTG TGATTG TGATTG TG
1 TGATTG TGATTG TGATTG TGATTG TGATTG TG
1250 GTGCAGCCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (6 bp):
TGATTG
Found at i:1493 original size:12 final size:12
Alignment explanation
Indices: 1476--1509 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
1466 TGATGAGTAA
1476 GCATTGGGGATT
1 GCATTGGGGATT
1488 GCATTGGGGATT
1 GCATTGGGGATT
1500 GCATTGGGGA
1 GCATTGGGGA
1510 GAGTGATCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.18, C:0.09, G:0.44, T:0.29
Consensus pattern (12 bp):
GCATTGGGGATT
Found at i:2069 original size:19 final size:18
Alignment explanation
Indices: 2036--2071 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2026 CTGAAATTAT
2036 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
2054 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
2072 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:2185 original size:8 final size:8
Alignment explanation
Indices: 2172--2197 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2162 AAAGTAGTGA
2172 AAATTATC
1 AAATTATC
2180 AAATTATC
1 AAATTATC
2188 AAATTATC
1 AAATTATC
2196 AA
1 AA
2198 TTTCACATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.35
Consensus pattern (8 bp):
AAATTATC
Found at i:2967 original size:18 final size:19
Alignment explanation
Indices: 2930--2967 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
2920 CTCCTCTATC
*
2930 ATGAAAAGCACTTCTTTTT
1 ATGAAAAGCAATTCTTTTT
*
2949 ATGAAAA-CAATTTTTTTT
1 ATGAAAAGCAATTCTTTTT
2967 A
1 A
2968 ATTACCCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.45
Consensus pattern (19 bp):
ATGAAAAGCAATTCTTTTT
Found at i:12214 original size:19 final size:18
Alignment explanation
Indices: 12181--12216 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12171 CTGAAATTAT
12181 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
12199 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
12217 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Done.