Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015091.1 Corchorus olitorius cultivar O-4 contig15124, 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: 45471
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:8287 original size:15 final size:16
Alignment explanation
Indices: 8253--8292 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
8243 CCATTTCGAG
* *
8253 TTCAAGTCATTTTGAA
1 TTCAAGTTATTTTCAA
8269 TTCAAGTTA-TTTCAA
1 TTCAAGTTATTTTCAA
8284 TTCAAGTTA
1 TTCAAGTTA
8293 AGTTTGAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (16 bp):
TTCAAGTTATTTTCAA
Found at i:10215 original size:67 final size:68
Alignment explanation
Indices: 10101--10240 Score: 183
Period size: 67 Copynumber: 2.1 Consensus size: 68
10091 ATGTCTATTA
* * * *
10101 ATTTTATTCTGGCACTTAGACACTAATGATTTCACGAGTTCCTAAACGAGAAATATTAGTGTGAA
1 ATTTTATTCTGGCACTTAGACACTAATGATTTCACCAGATCCCAAACGAGAAATATTAGTCTGAA
10166 T-C
66 TCC
* * * * * *
10168 ATTTTATTCTGGCAGTTAGATATTAATGATTTTACCAGATCCCAAACGAGGAATGTTAGTCTGAA
1 ATTTTATTCTGGCACTTAGACACTAATGATTTCACCAGATCCCAAACGAGAAATATTAGTCTGAA
10233 TCC
66 TCC
10236 ATTTT
1 ATTTT
10241 GTGGCTAAGT
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
67 56 0.90
68 6 0.10
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (68 bp):
ATTTTATTCTGGCACTTAGACACTAATGATTTCACCAGATCCCAAACGAGAAATATTAGTCTGAA
TCC
Found at i:12205 original size:1 final size:1
Alignment explanation
Indices: 12199--12233 Score: 61
Period size: 1 Copynumber: 35.0 Consensus size: 1
12189 TGAAGCAATG
*
12199 TTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12234 AAAAAAATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:16339 original size:13 final size:13
Alignment explanation
Indices: 16321--16346 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16311 CCATAATATG
16321 GAGATAAAAGACT
1 GAGATAAAAGACT
16334 GAGATAAAAGACT
1 GAGATAAAAGACT
16347 TCTTATCTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.23, T:0.15
Consensus pattern (13 bp):
GAGATAAAAGACT
Found at i:17226 original size:16 final size:16
Alignment explanation
Indices: 17202--17257 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
17192 TGTTTATATT
*
17202 TTTAATAATAATTAAA
1 TTTAGTAATAATTAAA
*
17218 TTTAGTAAT--TT-AT
1 TTTAGTAATAATTAAA
*
17231 TTCTAGTACTAATTAAA
1 TT-TAGTAATAATTAAA
17248 TTTAGTAATA
1 TTTAGTAATA
17258 GCATGTATTC
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
13 3 0.10
14 8 0.26
16 17 0.55
17 3 0.10
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (16 bp):
TTTAGTAATAATTAAA
Found at i:17232 original size:30 final size:30
Alignment explanation
Indices: 17198--17256 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
17188 TAAGTGTTTA
*
17198 TATTTTTAATAATAATTAAATTTAGTAATT
1 TATTTCTAATAATAATTAAATTTAGTAATT
* *
17228 TATTTCTAGTACTAATTAAATTTAGTAAT
1 TATTTCTAATAATAATTAAATTTAGTAAT
17257 AGCATGTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (30 bp):
TATTTCTAATAATAATTAAATTTAGTAATT
Found at i:18997 original size:36 final size:36
Alignment explanation
Indices: 18950--19021 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
18940 CTTAACCTCA
*
18950 CTCTGCAGTTACCCTTTTCCCTTAATAGATTAGAAT
1 CTCTGCAGTTACCCTTTCCCCTTAATAGATTAGAAT
**
18986 CTCTGCAGTTACCCTTTCCCCTTGTTAGATTAGAAT
1 CTCTGCAGTTACCCTTTCCCCTTAATAGATTAGAAT
19022 ATGTTGTTGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.22, C:0.26, G:0.12, T:0.39
Consensus pattern (36 bp):
CTCTGCAGTTACCCTTTCCCCTTAATAGATTAGAAT
Found at i:27936 original size:151 final size:153
Alignment explanation
Indices: 27726--28031 Score: 490
Period size: 163 Copynumber: 1.9 Consensus size: 153
27716 GAGAATGTGT
* *
27726 AAATACATTGGCTTCCCTATTTACAAATTGAAGCATGATTATCCAGCTCAATCTTAGTTAGAGAA
1 AAATACATTGACTTCCCTATTTACAAATTGAAGCACGATTATCCAGCTCAATCTTAGTTAGAGAA
27791 TGTG-CA-AATACACACACCACATGATTATCTAGCTCAATTTTAGCTAAAGATTGTGCAAATACA
66 TGTGACACAATACACACACCACATGATTATCTAGCTCAATTTTAGCTAAAGATTGTGCAAATACA
27854 ATGACTTCCCTATTTGAATGTAC
131 ATGACTTCCCTATTTGAATGTAC
27877 AAATACATTGACTTCCCTATTTACAAATTGAAGCACGATTATCCAGCTCAATCTTAGTTAGAGAA
1 AAATACATTGACTTCCCTATTTACAAATTGAAGCACGATTATCCAGCTCAATCTTAGTTAGAGAA
27942 TGTGCAAATACACACACCAATACACACACCACATGATTATCTAGCTCAATTTTAGCTAAAGATTG
66 TGTG---------ACA-CAATACACACACCACATGATTATCTAGCTCAATTTTAGCTAAAGATTG
28007 TGCAAATACAATGACTTCCCTATTT
121 TGCAAATACAATGACTTCCCTATTT
28032 ACAAATTGAA
Statistics
Matches: 141, Mismatches: 2, Indels: 12
0.91 0.01 0.08
Matches are distributed among these distances:
151 67 0.48
161 2 0.01
163 72 0.51
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (153 bp):
AAATACATTGACTTCCCTATTTACAAATTGAAGCACGATTATCCAGCTCAATCTTAGTTAGAGAA
TGTGACACAATACACACACCACATGATTATCTAGCTCAATTTTAGCTAAAGATTGTGCAAATACA
ATGACTTCCCTATTTGAATGTAC
Found at i:27965 original size:12 final size:12
Alignment explanation
Indices: 27948--27972 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27938 AGAATGTGCA
27948 AATACACACACC
1 AATACACACACC
27960 AATACACACACC
1 AATACACACACC
27972 A
1 A
27973 CATGATTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.40, G:0.00, T:0.08
Consensus pattern (12 bp):
AATACACACACC
Found at i:28130 original size:15 final size:17
Alignment explanation
Indices: 28095--28131 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
28085 CTATAACTAC
28095 CAAACATAACAAATATA
1 CAAACATAACAAATATA
*
28112 CAAACA-AATAAAT-TA
1 CAAACATAACAAATATA
28127 CAAAC
1 CAAAC
28132 TAAACTCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 6 0.32
17 6 0.32
ACGTcount: A:0.65, C:0.19, G:0.00, T:0.16
Consensus pattern (17 bp):
CAAACATAACAAATATA
Found at i:35856 original size:50 final size:51
Alignment explanation
Indices: 35793--35890 Score: 180
Period size: 50 Copynumber: 1.9 Consensus size: 51
35783 ATTTGAGAGT
35793 ATTGGGTAAGAGGCCCAAATCTTAT-TCTCATTGGGTAAATTTGTCAGTTA
1 ATTGGGTAAGAGGCCCAAATCTTATATCTCATTGGGTAAATTTGTCAGTTA
*
35843 ATTGGGTTAGAGGCCCAAATCTTATATCTCATTGGGTAAATTTGTCAG
1 ATTGGGTAAGAGGCCCAAATCTTATATCTCATTGGGTAAATTTGTCAG
35891 AAAAAACGAG
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 24 0.52
51 22 0.48
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (51 bp):
ATTGGGTAAGAGGCCCAAATCTTATATCTCATTGGGTAAATTTGTCAGTTA
Done.