Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012265.1 Corchorus olitorius cultivar O-4 contig12298, 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: 10903
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2888 original size:5 final size:5
Alignment explanation
Indices: 2875--2909 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
2865 TCAAGTAATT
*
2875 AAAGG AAAGA AAAGG AAAGG AAAGG AAAGG AAAGG
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG
2910 GGAGGGAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:3168 original size:20 final size:21
Alignment explanation
Indices: 3135--3181 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
3125 AAAAAAATAG
* *
3135 AAAAAATTAGAAATTTTCAAC
1 AAAAAAATAGAAATCTTCAAC
3156 AAAAAAATA-AAATCTTC-AC
1 AAAAAAATAGAAATCTTCAAC
*
3175 AAGAAAA
1 AAAAAAA
3182 GAGATGAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 8 0.35
20 7 0.30
21 8 0.35
ACGTcount: A:0.64, C:0.11, G:0.04, T:0.21
Consensus pattern (21 bp):
AAAAAAATAGAAATCTTCAAC
Found at i:3453 original size:42 final size:42
Alignment explanation
Indices: 3406--3498 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
3396 CTCGATGAAA
*
3406 TGGATTTGAGAGGAATGGCCAAAGGCTTGTTATTCCTCGTTG
1 TGGATTTGAGAGAAATGGCCAAAGGCTTGTTATTCCTCGTTG
* *
3448 TGGATTTGAGAGAAATGGTCGAAGGCTTGTTATTCCTCGTTG
1 TGGATTTGAGAGAAATGGCCAAAGGCTTGTTATTCCTCGTTG
3490 TCGGATTTG
1 T-GGATTTG
3499 CTAGATTTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
42 40 0.85
43 7 0.15
ACGTcount: A:0.20, C:0.13, G:0.31, T:0.35
Consensus pattern (42 bp):
TGGATTTGAGAGAAATGGCCAAAGGCTTGTTATTCCTCGTTG
Found at i:3704 original size:35 final size:34
Alignment explanation
Indices: 3630--3762 Score: 101
Period size: 35 Copynumber: 3.8 Consensus size: 34
3620 GGATTTGTTG
* *** *
3630 TTGCTTTGTTGATGGAGAACAACTTTGC-TTTGTT
1 TTGCTTTGTTGATGGAGAAGAAC-TTGCAGAAGAT
*
3664 GTTGCTTTGTTGATGGAGAAGAAC-TGGAGAAGAACT
1 -TTGCTTTGTTGATGGAGAAGAACTTGCAGAAG-A-T
* * *
3700 TTGCTTTTTTGATGGAGAA-AACTTTGCTGCAGAT
1 TTGCTTTGTTGATGGAGAAGAAC-TTGCAGAAGAT
3734 TTGCTTTGCTTGATGGAGAAGAACCTTGC
1 TTGCTTTG-TTGATGGAGAAGAA-CTTGC
3763 CTTGCCTTGA
Statistics
Matches: 79, Mismatches: 11, Indels: 15
0.75 0.10 0.14
Matches are distributed among these distances:
33 2 0.03
34 12 0.15
35 52 0.66
36 12 0.15
37 1 0.01
ACGTcount: A:0.23, C:0.12, G:0.27, T:0.38
Consensus pattern (34 bp):
TTGCTTTGTTGATGGAGAAGAACTTGCAGAAGAT
Found at i:7098 original size:21 final size:21
Alignment explanation
Indices: 7074--7139 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
7064 AATTCTCTGT
7074 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* ***
7095 AAATCATAA-AAATTCT-TTGT-
1 AAAT--TAAGAAATACTCAACTC
7115 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
7136 AAAT
1 AAAT
7140 CATAGAAAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 10
0.64 0.16 0.20
Matches are distributed among these distances:
18 3 0.09
19 6 0.19
20 5 0.16
21 9 0.28
22 6 0.19
23 3 0.09
ACGTcount: A:0.52, C:0.15, G:0.05, T:0.29
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:7107 original size:22 final size:22
Alignment explanation
Indices: 7082--7149 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 22
7072 GTAAATTAAG
7082 AAATACTCAACTCAAATCATAA
1 AAATACTCAACTCAAATCATAA
* ***
7104 AAATTCT-TTGT-AAAT--TAA
1 AAATACTCAACTCAAATCATAA
7122 GAAATACTCAACTCAAATCATAGA
1 -AAATACTCAACTCAAATCATA-A
7146 AAAT
1 AAAT
7150 TCTTTGTAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 11
0.63 0.16 0.22
Matches are distributed among these distances:
18 3 0.09
19 6 0.19
20 5 0.16
21 5 0.16
22 6 0.19
23 6 0.19
24 1 0.03
ACGTcount: A:0.51, C:0.16, G:0.04, T:0.28
Consensus pattern (22 bp):
AAATACTCAACTCAAATCATAA
Found at i:7162 original size:42 final size:42
Alignment explanation
Indices: 7061--7181 Score: 219
Period size: 41 Copynumber: 2.9 Consensus size: 42
7051 GCTAAGTCTT
*
7061 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
7103 -AAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
7144 GAAAATTCTTTGTAAATTAAG-AATACTCAACTCAAATC
1 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
7182 CTGATCCTTA
Statistics
Matches: 77, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
41 57 0.74
42 20 0.26
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.31
Consensus pattern (42 bp):
GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:7338 original size:55 final size:57
Alignment explanation
Indices: 7248--7362 Score: 198
Period size: 55 Copynumber: 2.0 Consensus size: 57
7238 TTTATTTTAT
7248 AGAATAATTAAGTAGAGATAAGGGGGGATAAGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAA-GGGGGATAAGATTTATTATAACATTTATTGTGTGAA
*
7306 AGAATAATTAAGTAGAGAT-A-GGGGATATGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAAGGGGGATAAGATTTATTATAACATTTATTGTGTGAA
7361 AG
1 AG
7363 GAAACAAATA
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
55 36 0.64
57 1 0.02
58 19 0.34
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.34
Consensus pattern (57 bp):
AGAATAATTAAGTAGAGATAAGGGGGATAAGATTTATTATAACATTTATTGTGTGAA
Done.