Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013138.1 Corchorus olitorius cultivar O-4 contig13171, 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: 3629
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Found at i:271 original size:13 final size:13
Alignment explanation
Indices: 253--277 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
243 TTTAACCTTA
253 CATGTTCAATTAT
1 CATGTTCAATTAT
266 CATGTTCAATTA
1 CATGTTCAATTA
278 AGCCAAATCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (13 bp):
CATGTTCAATTAT
Found at i:1006 original size:17 final size:18
Alignment explanation
Indices: 984--1027 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
974 TATTTTCCTA
984 TTTCCCTTTCTTCTTTT-
1 TTTCCCTTTCTTCTTTTC
1001 TTTCCCTTT-TTCTTTTC
1 TTTCCCTTTCTTCTTTTC
*
1018 TTTCCTTTTC
1 TTTCCCTTTC
1028 CTTTTCCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 7 0.29
17 17 0.71
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTCCCTTTCTTCTTTTC
Found at i:1015 original size:16 final size:17
Alignment explanation
Indices: 984--1033 Score: 68
Period size: 16 Copynumber: 3.0 Consensus size: 17
974 TATTTTCCTA
984 TTTCCCTTTCTTCTTTT-
1 TTTCCCTTT-TTCTTTTC
1001 TTTCCCTTTTTCTTTTC
1 TTTCCCTTTTTCTTTTC
*
1018 TTT-CCTTTTCCTTTTC
1 TTTCCCTTTTTCTTTTC
1034 CCTTTTTCCT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
16 19 0.61
17 12 0.39
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTCCCTTTTTCTTTTC
Found at i:1055 original size:29 final size:28
Alignment explanation
Indices: 1000--1056 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 28
990 TTTCTTCTTT
*
1000 TTTTCCCTTTTTCTTTTCTTTCCTTTTCC
1 TTTTCCCTTTTTCTTTTCATT-CTTTTCC
*
1029 TTTTCCCTTTTTCCTTTTCCATTTTTTT
1 TTTTCCCTTTTT-CTTTT-CATTCTTTT
1057 TTTTCCTTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 12 0.50
30 9 0.38
31 3 0.12
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (28 bp):
TTTTCCCTTTTTCTTTTCATTCTTTTCC
Found at i:1059 original size:20 final size:20
Alignment explanation
Indices: 976--1064 Score: 76
Period size: 20 Copynumber: 4.4 Consensus size: 20
966 CTTATTATTA
* *
976 TTTTCCTATTTCCCTTTCTTC
1 TTTTCCT-TTTCCTTTTCTTT
*
997 TTTT--TTTCCCTTTTTCTTT
1 TTTTCCTTTTCC-TTTTCTTT
**
1016 TCTTTCCTTTTCCTTTTCCCT
1 T-TTTCCTTTTCCTTTTCTTT
1037 TTTTCCTTTTCCATTTT-TTT
1 TTTTCCTTTTCC-TTTTCTTT
1057 TTTTCCTT
1 TTTTCCTT
1065 CCTTCCTTCC
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
18 4 0.07
19 8 0.15
20 23 0.42
21 15 0.27
22 5 0.09
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTCCTTTTCCTTTTCTTT
Found at i:1062 original size:14 final size:14
Alignment explanation
Indices: 1023--1054 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1013 TTTTCTTTCC
*
1023 TTTTCCTTTTCCCT
1 TTTTCCTTTTCCAT
1037 TTTTCCTTTTCCAT
1 TTTTCCTTTTCCAT
1051 TTTT
1 TTTT
1055 TTTTTTCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTCCTTTTCCAT
Found at i:1149 original size:22 final size:22
Alignment explanation
Indices: 1124--1199 Score: 67
Period size: 22 Copynumber: 3.7 Consensus size: 22
1114 CAGCGGCTTG
*
1124 GGCCGCGCTGGCCAGCTTAGCA
1 GGCCGCGCGGGCCAGCTTAGCA
1146 GGCCGCGCGGGCCAG----GC-
1 GGCCGCGCGGGCCAGCTTAGCA
*
1163 --CCAAGCGCTGGCCAGCTTAGCA
1 GGCC--GCGCGGGCCAGCTTAGCA
1185 GGCCGCGCGGGCCAG
1 GGCCGCGCGGGCCAG
1200 GCCCAAGCGC
Statistics
Matches: 42, Mismatches: 3, Indels: 18
0.67 0.05 0.29
Matches are distributed among these distances:
15 2 0.05
17 10 0.24
18 2 0.05
21 2 0.05
22 24 0.57
24 2 0.05
ACGTcount: A:0.13, C:0.38, G:0.41, T:0.08
Consensus pattern (22 bp):
GGCCGCGCGGGCCAGCTTAGCA
Found at i:1182 original size:39 final size:39
Alignment explanation
Indices: 1128--1214 Score: 174
Period size: 39 Copynumber: 2.2 Consensus size: 39
1118 GGCTTGGGCC
1128 GCGCTGGCCAGCTTAGCAGGCCGCGCGGGCCAGGCCCAA
1 GCGCTGGCCAGCTTAGCAGGCCGCGCGGGCCAGGCCCAA
1167 GCGCTGGCCAGCTTAGCAGGCCGCGCGGGCCAGGCCCAA
1 GCGCTGGCCAGCTTAGCAGGCCGCGCGGGCCAGGCCCAA
1206 GCGCTGGCC
1 GCGCTGGCC
1215 TGCCAGGCTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.14, C:0.39, G:0.39, T:0.08
Consensus pattern (39 bp):
GCGCTGGCCAGCTTAGCAGGCCGCGCGGGCCAGGCCCAA
Done.