Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013201.1 Corchorus olitorius cultivar O-4 contig13234, 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: 27393
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:6871 original size:23 final size:23
Alignment explanation
Indices: 6845--6900 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
6835 AGGGCCAAAG
*
6845 TTGTATTCAGGTTAGATACATTA
1 TTGTATCCAGGTTAGATACATTA
6868 TTGTATCCAGGTTAGATACATTA
1 TTGTATCCAGGTTAGATACATTA
* *
6891 TGGCATCCAG
1 TTGTATCCAG
6901 TGATCAGTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.38
Consensus pattern (23 bp):
TTGTATCCAGGTTAGATACATTA
Found at i:22049 original size:148 final size:148
Alignment explanation
Indices: 21781--22080 Score: 600
Period size: 148 Copynumber: 2.0 Consensus size: 148
21771 AAATTAGAAG
21781 CATGATTCAAGCTTAGAAATGCTATCTAGACATCCTTAACTAGTTAAAGCCATGATCCCAAACAC
1 CATGATTCAAGCTTAGAAATGCTATCTAGACATCCTTAACTAGTTAAAGCCATGATCCCAAACAC
21846 ACATATATATGGCATTCAATTTATCTGAATTGCTACTAATGCCTATGTTCTGTAACATTCAGTTT
66 ACATATATATGGCATTCAATTTATCTGAATTGCTACTAATGCCTATGTTCTGTAACATTCAGTTT
21911 GAAAGTTTGGCAGATCAA
131 GAAAGTTTGGCAGATCAA
21929 CATGATTCAAGCTTAGAAATGCTATCTAGACATCCTTAACTAGTTAAAGCCATGATCCCAAACAC
1 CATGATTCAAGCTTAGAAATGCTATCTAGACATCCTTAACTAGTTAAAGCCATGATCCCAAACAC
21994 ACATATATATGGCATTCAATTTATCTGAATTGCTACTAATGCCTATGTTCTGTAACATTCAGTTT
66 ACATATATATGGCATTCAATTTATCTGAATTGCTACTAATGCCTATGTTCTGTAACATTCAGTTT
22059 GAAAGTTTGGCAGATCAA
131 GAAAGTTTGGCAGATCAA
22077 CATG
1 CATG
22081 CAGTTACTGT
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
148 152 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (148 bp):
CATGATTCAAGCTTAGAAATGCTATCTAGACATCCTTAACTAGTTAAAGCCATGATCCCAAACAC
ACATATATATGGCATTCAATTTATCTGAATTGCTACTAATGCCTATGTTCTGTAACATTCAGTTT
GAAAGTTTGGCAGATCAA
Found at i:27155 original size:4 final size:4
Alignment explanation
Indices: 27143--27225 Score: 64
Period size: 4 Copynumber: 20.2 Consensus size: 4
27133 TTGTTTGTTA
* * * *
27143 ATTT GTTT ATTT ATTCAT GTTT ATTAT GTTT A-TT A-TT ATAT ATTT ATTAT
1 ATTT ATTT ATTT ATT--T ATTT ATT-T ATTT ATTT ATTT ATTT ATTT ATT-T
27193 ATTT ATTT ATTT ATTT A-TT ATTCT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATT-T ATTT ATTT A
27226 CTATTTACTA
Statistics
Matches: 64, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
3 9 0.14
4 41 0.64
5 11 0.17
6 3 0.05
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (4 bp):
ATTT
Found at i:27176 original size:23 final size:22
Alignment explanation
Indices: 27146--27232 Score: 81
Period size: 23 Copynumber: 3.9 Consensus size: 22
27136 TTTGTTAATT
*
27146 TGTTTATTTATTCATGTTTATTA
1 TGTTTATTTATT-ATATTTATTA
27169 TGTTTA-TTATTATATATTTATTA
1 TGTTTATTTA-T-TATATTTATTA
*
27192 TATTTATTTATT-TATTTATTA
1 TGTTTATTTATTATATTTATTA
*
27213 T-TCTATTTATTTACTATTTA
1 TGTTTATTTA-TTA-TATTTA
27233 CTATTTAGTC
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
20 7 0.13
21 12 0.22
22 4 0.07
23 28 0.51
24 4 0.07
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.67
Consensus pattern (22 bp):
TGTTTATTTATTATATTTATTA
Found at i:27190 original size:33 final size:33
Alignment explanation
Indices: 27150--27232 Score: 89
Period size: 33 Copynumber: 2.5 Consensus size: 33
27140 TTAATTTGTT
* *
27150 TATTTATTCATGTTTATTATGTTTA-TTATTA-TA
1 TATTTATT-ATATTTATT-TATTTATTTATTATTA
*
27183 TATTTATTATATTTATTTATTTATTTATTATTC
1 TATTTATTATATTTATTTATTTATTTATTATTA
27216 TATTTATTTACTATTTA
1 TATTTA-TTA-TATTTA
27233 CTATTTAGTC
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
31 5 0.12
32 14 0.33
33 15 0.35
34 3 0.07
35 6 0.14
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (33 bp):
TATTTATTATATTTATTTATTTATTTATTATTA
Found at i:27193 original size:9 final size:9
Alignment explanation
Indices: 27150--27223 Score: 63
Period size: 9 Copynumber: 8.9 Consensus size: 9
27140 TTAATTTGTT
27150 TATTTATTCA
1 TATTTATT-A
*
27160 TGTTTATTA
1 TATTTATTA
*
27169 TGTTTA-T-
1 TATTTATTA
27176 TA-TTA-TA
1 TATTTATTA
27183 TATTTATTA
1 TATTTATTA
27192 TATTTATT-
1 TATTTATTA
27200 TATTTATT-
1 TATTTATTA
*
27208 TA-TTATTC
1 TATTTATTA
27216 TATTTATT
1 TATTTATT
27224 TACTATTTAC
Statistics
Matches: 57, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
6 4 0.07
7 8 0.14
8 16 0.28
9 22 0.39
10 7 0.12
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.68
Consensus pattern (9 bp):
TATTTATTA
Found at i:27230 original size:16 final size:15
Alignment explanation
Indices: 27196--27232 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
27186 TTATTATATT
*
27196 TATTTATTTATTTAT
1 TATTTATTTATTTAC
27211 TATTCTATTTATTTAC
1 TATT-TATTTATTTAC
27227 TATTTA
1 TATTTA
27233 CTATTTAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTATTTATTTAC
Found at i:27374 original size:1 final size:1
Alignment explanation
Indices: 27368--27393 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
27358 TTGACTTCTG
27368 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.