Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019856.1 Corchorus olitorius cultivar O-4 contig19889, 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: 19510
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:375 original size:24 final size:25
Alignment explanation
Indices: 346--395 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
336 GGACTCAATA
346 CTGAGCCC-AAAGCAAATGTAACTT
1 CTGAGCCCAAAAGCAAATGTAACTT
370 CTGAGCCCAAAAGCAAATGTAACTT
1 CTGAGCCCAAAAGCAAATGTAACTT
395 C
1 C
396 CAATAATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.20
Consensus pattern (25 bp):
CTGAGCCCAAAAGCAAATGTAACTT
Found at i:1345 original size:30 final size:29
Alignment explanation
Indices: 1302--1358 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 29
1292 TTAGGATTAG
1302 TTATTTATGCTTTAATTTTCAA-TTTCCT
1 TTATTTATGCTTTAATTTTCAAGTTTCCT
1330 TTATCTTATGTCTTTAATTTTCAAGTTTC
1 TTAT-TTATG-CTTTAATTTTCAAGTTTC
1359 ATTAATAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 4 0.15
29 5 0.19
30 13 0.50
31 4 0.15
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (29 bp):
TTATTTATGCTTTAATTTTCAAGTTTCCT
Found at i:2924 original size:18 final size:19
Alignment explanation
Indices: 2890--2925 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2880 TGAAGACTTA
*
2890 TTGAAGACAATTTGAAGAT
1 TTGAACACAATTTGAAGAT
2909 TTGAACACAA-TTGAAGA
1 TTGAACACAATTTGAAGA
2926 ATTATTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.28
Consensus pattern (19 bp):
TTGAACACAATTTGAAGAT
Found at i:4248 original size:22 final size:22
Alignment explanation
Indices: 4206--4248 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
4196 TTTCTAATTA
**
4206 ATTGTTTTCTTTAATTTTCTTG
1 ATTGTTTTCTTTAATACTCTTG
4228 ATTGTTTTC-TTAGATACTCTT
1 ATTGTTTTCTTTA-ATACTCTT
4249 AATTACTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.16, C:0.12, G:0.09, T:0.63
Consensus pattern (22 bp):
ATTGTTTTCTTTAATACTCTTG
Found at i:13350 original size:32 final size:32
Alignment explanation
Indices: 13323--13544 Score: 336
Period size: 32 Copynumber: 6.9 Consensus size: 32
13313 CTTGTTCTGA
*
13323 AGACGCCGCTAAATAAGGGCGTTTTGTTTTGT
1 AGACGCCGCTAAATAAGGGCGTTTTGTTTTTT
*
13355 AGACGCCGCTAATTAAGGGCGTTTTGTTTTTT
1 AGACGCCGCTAAATAAGGGCGTTTTGTTTTTT
*
13387 AGACGCCGCTAATTAAGGGCGTTTTGTTTTTT
1 AGACGCCGCTAAATAAGGGCGTTTTGTTTTTT
* *
13419 AGACGCTGCTAAATAAGGGTGTTTTGTTTTTT
1 AGACGCCGCTAAATAAGGGCGTTTTGTTTTTT
* *
13451 AGACGCCGCTAAATAAAGGCTTTTTGTTTTTT
1 AGACGCCGCTAAATAAGGGCGTTTTGTTTTTT
* * * *
13483 AGACGCAGCTACATAAGGGCGTTTTGTTCTAT
1 AGACGCCGCTAAATAAGGGCGTTTTGTTTTTT
*
13515 AGACGCCGCTAAATAAGGGCGTTTTCTTTT
1 AGACGCCGCTAAATAAGGGCGTTTTGTTTT
13545 CACACATGCT
Statistics
Matches: 171, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 171 1.00
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (32 bp):
AGACGCCGCTAAATAAGGGCGTTTTGTTTTTT
Found at i:13566 original size:64 final size:63
Alignment explanation
Indices: 13308--13566 Score: 211
Period size: 64 Copynumber: 4.0 Consensus size: 63
13298 TATATATAGC
* * * * *
13308 GGCGTCTTGTTCTGA-AGACGCCGCTAAATAAGGGCGTTTTGTTTTGTAGACGC-CGCTAATTAA
1 GGCGTTTTGTTCT-ATAGACGCCGCTAAATAAGGGCGTTTTTTTTTATACACGCTC-C-AAATAA
13371 G
63 G
* * * * *
13372 GGCGTTTTGTTTTTTAGACGCCGCTAATTAAGGGCGTTTTGTTTTT-TAGACGCTGCTAAATAAG
1 GGCGTTTTGTTCTATAGACGCCGCTAAATAAGGGCGTTTT-TTTTTATACACGCT-CCAAATAAG
* * * * * * * * *
13436 GGTGTTTTGTTTTTTAGACGCCGCTAAATAAAGGC-TTTTTGTTTTTTAGACGCAGCTACATAAG
1 GGCGTTTTGTTCTATAGACGCCGCTAAATAAGGGCGTTTTT-TTTTATACACGC-TCCAAATAAG
* * * *
13500 GGCGTTTTGTTCTATAGACGCCGCTAAATAAGGGCGTTTTCTTTTCACACATGCTCCAAATCAG
1 GGCGTTTTGTTCTATAGACGCCGCTAAATAAGGGCGTTTT-TTTTTATACACGCTCCAAATAAG
13564 GGC
1 GGC
13567 TTTCATTTAT
Statistics
Matches: 161, Mismatches: 25, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
62 1 0.01
63 8 0.05
64 135 0.84
65 15 0.09
66 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (63 bp):
GGCGTTTTGTTCTATAGACGCCGCTAAATAAGGGCGTTTTTTTTTATACACGCTCCAAATAAG
Found at i:15949 original size:27 final size:27
Alignment explanation
Indices: 15889--15982 Score: 136
Period size: 27 Copynumber: 3.5 Consensus size: 27
15879 CGACCCGAGG
* *
15889 CGAAATGGGAGGATCCACTGCT-GGGT
1 CGAAGTGGAAGGATCCACTGCTGGGGT
*
15915 CGAAGTGGGAGGATCCACTGCTGGGGT
1 CGAAGTGGAAGGATCCACTGCTGGGGT
*
15942 CGAAGTGGAAGGATCCACTACTGGGGT
1 CGAAGTGGAAGGATCCACTGCTGGGGT
*
15969 CGAAGCGGAAGGAT
1 CGAAGTGGAAGGAT
15983 TTACTGCGGT
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
26 21 0.33
27 42 0.67
ACGTcount: A:0.24, C:0.18, G:0.40, T:0.17
Consensus pattern (27 bp):
CGAAGTGGAAGGATCCACTGCTGGGGT
Done.