Multiple sequence alignment - TraesCS7D01G491600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G491600 chr7D 100.000 6210 0 0 1 6210 600855642 600861851 0.000000e+00 11468.0
1 TraesCS7D01G491600 chr7D 80.130 307 53 5 1 300 179918801 179918496 8.100000e-54 222.0
2 TraesCS7D01G491600 chr7D 79.299 314 42 10 464 764 453167334 453167031 1.370000e-46 198.0
3 TraesCS7D01G491600 chr7D 93.684 95 5 1 355 448 600855940 600856034 2.330000e-29 141.0
4 TraesCS7D01G491600 chr7D 93.684 95 5 1 299 393 600855996 600856089 2.330000e-29 141.0
5 TraesCS7D01G491600 chr7B 95.652 3266 96 17 358 3604 680066037 680069275 0.000000e+00 5203.0
6 TraesCS7D01G491600 chr7B 94.690 2373 74 21 3603 5955 680069534 680071874 0.000000e+00 3637.0
7 TraesCS7D01G491600 chr7B 93.577 1012 50 11 4902 5907 707830915 707831917 0.000000e+00 1495.0
8 TraesCS7D01G491600 chr7B 96.013 903 26 6 3155 4052 707826051 707826948 0.000000e+00 1459.0
9 TraesCS7D01G491600 chr7B 93.955 397 20 1 1 393 680065731 680066127 1.150000e-166 597.0
10 TraesCS7D01G491600 chr7B 96.013 301 11 1 4617 4917 707830595 707830894 7.240000e-134 488.0
11 TraesCS7D01G491600 chr7B 96.708 243 7 1 4203 4444 707827395 707827637 2.700000e-108 403.0
12 TraesCS7D01G491600 chr7B 98.507 134 1 1 4072 4204 707827138 707827271 1.040000e-57 235.0
13 TraesCS7D01G491600 chr7B 89.189 185 3 5 4438 4622 707827974 707828141 1.360000e-51 215.0
14 TraesCS7D01G491600 chr7B 77.895 190 37 4 628 814 689420777 689420590 5.090000e-21 113.0
15 TraesCS7D01G491600 chr7B 85.897 78 7 4 5431 5507 707867693 707867767 5.160000e-11 80.5
16 TraesCS7D01G491600 chr7A 93.696 2919 128 32 3336 6210 692780431 692783337 0.000000e+00 4320.0
17 TraesCS7D01G491600 chr7A 94.516 1641 63 14 632 2266 692777692 692779311 0.000000e+00 2507.0
18 TraesCS7D01G491600 chr7A 96.599 1029 28 6 2321 3344 692779317 692780343 0.000000e+00 1700.0
19 TraesCS7D01G491600 chr7A 77.994 359 69 6 1 352 271867063 271866708 3.770000e-52 217.0
20 TraesCS7D01G491600 chr7A 80.663 181 19 10 461 635 116545630 116545460 6.540000e-25 126.0
21 TraesCS7D01G491600 chr3D 85.252 278 39 2 1020 1296 416200409 416200685 1.020000e-72 285.0
22 TraesCS7D01G491600 chr2A 80.635 315 54 5 1 308 249588140 249587826 2.890000e-58 237.0
23 TraesCS7D01G491600 chr2A 81.944 144 23 2 633 776 158514877 158515017 1.090000e-22 119.0
24 TraesCS7D01G491600 chr1B 83.203 256 32 6 1 249 188531648 188531899 2.250000e-54 224.0
25 TraesCS7D01G491600 chr1B 79.333 300 36 17 474 758 662628286 662627998 2.960000e-43 187.0
26 TraesCS7D01G491600 chr5B 78.729 362 49 13 463 811 423354585 423354931 3.770000e-52 217.0
27 TraesCS7D01G491600 chr5B 79.195 149 29 2 664 811 290132518 290132665 1.100000e-17 102.0
28 TraesCS7D01G491600 chr5B 95.349 43 0 2 192 232 232376623 232376665 4.020000e-07 67.6
29 TraesCS7D01G491600 chr3A 79.365 315 57 5 1 308 185291813 185291500 1.360000e-51 215.0
30 TraesCS7D01G491600 chr3A 80.268 299 48 6 2 291 439076222 439076518 1.360000e-51 215.0
31 TraesCS7D01G491600 chr3A 77.152 302 41 16 5616 5906 574313848 574314132 3.880000e-32 150.0
32 TraesCS7D01G491600 chr6A 83.182 220 31 4 1 215 316550090 316549872 4.910000e-46 196.0
33 TraesCS7D01G491600 chr6A 74.744 293 51 12 5619 5906 616096895 616096621 6.580000e-20 110.0
34 TraesCS7D01G491600 chr6A 77.368 190 36 5 628 814 586860043 586859858 8.510000e-19 106.0
35 TraesCS7D01G491600 chr2D 77.322 366 58 13 461 811 95182299 95182654 6.350000e-45 193.0
36 TraesCS7D01G491600 chr6B 78.431 306 50 11 461 761 566527654 566527360 1.060000e-42 185.0
37 TraesCS7D01G491600 chr6B 92.000 50 4 0 580 629 406445594 406445545 3.110000e-08 71.3
38 TraesCS7D01G491600 chr5D 77.982 327 44 16 478 786 210220438 210220754 4.950000e-41 180.0
39 TraesCS7D01G491600 chr5D 77.211 294 60 4 1 287 413029252 413029545 1.380000e-36 165.0
40 TraesCS7D01G491600 chr5D 84.146 82 10 1 1010 1091 88184944 88184866 6.680000e-10 76.8
41 TraesCS7D01G491600 chr1A 85.294 170 23 2 644 811 416518323 416518492 2.300000e-39 174.0
42 TraesCS7D01G491600 chr1A 76.433 314 48 13 461 759 576567741 576567439 5.020000e-31 147.0
43 TraesCS7D01G491600 chr4B 76.271 295 56 8 461 750 120506547 120506262 1.800000e-30 145.0
44 TraesCS7D01G491600 chr5A 81.152 191 19 11 456 641 7803762 7803584 3.020000e-28 137.0
45 TraesCS7D01G491600 chr2B 80.606 165 31 1 645 808 556223551 556223715 6.540000e-25 126.0
46 TraesCS7D01G491600 chr3B 91.489 47 4 0 583 629 553843592 553843638 1.440000e-06 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G491600 chr7D 600855642 600861851 6209 False 11468.000000 11468 100.000000 1 6210 1 chr7D.!!$F1 6209
1 TraesCS7D01G491600 chr7B 680065731 680071874 6143 False 3145.666667 5203 94.765667 1 5955 3 chr7B.!!$F2 5954
2 TraesCS7D01G491600 chr7B 707826051 707831917 5866 False 715.833333 1495 95.001167 3155 5907 6 chr7B.!!$F3 2752
3 TraesCS7D01G491600 chr7A 692777692 692783337 5645 False 2842.333333 4320 94.937000 632 6210 3 chr7A.!!$F1 5578

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
780 795 0.178068 AGTGCAGTTCAGACGGTTGT 59.822 50.000 0.00 0.00 0.00 3.32 F
786 801 0.391597 GTTCAGACGGTTGTGGGAGA 59.608 55.000 0.00 0.00 0.00 3.71 F
1782 1805 1.388065 CCGACGAGGAGGAGATGCTT 61.388 60.000 0.00 0.00 45.00 3.91 F
2658 2683 0.829333 CATGGACTGCTGCTAGGTCT 59.171 55.000 15.81 1.24 0.00 3.85 F
2986 3014 0.246635 GCTGGCGAGTCAGGAGTTTA 59.753 55.000 6.84 0.00 35.43 2.01 F
3592 3720 1.077265 CATGGTTTCCCAGGCCACT 59.923 57.895 5.01 0.00 46.15 4.00 F
4070 4467 1.632422 CGAATCCTTGTTTGCCATGC 58.368 50.000 0.00 0.00 0.00 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 1805 0.603569 GGCAGTCGAAGAGGTTCTCA 59.396 55.000 0.00 0.0 36.95 3.27 R
1857 1880 4.814147 TGATAATGATCATGAGCTCGACC 58.186 43.478 12.92 0.0 37.15 4.79 R
2986 3014 2.299326 AAGGCCAGCTTGAGACAATT 57.701 45.000 5.01 0.0 0.00 2.32 R
3841 4231 0.618981 GTGGCAGGCTACTAGGGTTT 59.381 55.000 0.09 0.0 0.00 3.27 R
4001 4391 1.267121 GGTCTGAGGAAGTAGGTGCA 58.733 55.000 0.00 0.0 0.00 4.57 R
5003 8528 1.792118 AAGGCAGAAAACCGGCGAAC 61.792 55.000 9.30 0.0 36.81 3.95 R
5998 9537 0.704076 CCTTCATCCCCCACTTCCAA 59.296 55.000 0.00 0.0 0.00 3.53 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 5.379732 TTTGAAAGGAAACTCAACGTTGT 57.620 34.783 26.47 8.55 42.68 3.32
106 107 3.806949 TCCTCATACAAGCTGGGTTTT 57.193 42.857 0.00 0.00 0.00 2.43
149 154 3.118261 AGCATGACTGTCCGGTTATGATT 60.118 43.478 13.45 0.63 35.93 2.57
153 158 2.351726 GACTGTCCGGTTATGATTGTGC 59.648 50.000 0.00 0.00 0.00 4.57
159 164 1.608590 CGGTTATGATTGTGCCATCCC 59.391 52.381 0.00 0.00 0.00 3.85
216 221 9.919348 CTACAAAATTTTCAAACAACAGAATGG 57.081 29.630 0.00 0.00 43.62 3.16
225 230 7.176589 TCAAACAACAGAATGGTTAGGTTTT 57.823 32.000 0.00 0.00 43.62 2.43
226 231 7.262048 TCAAACAACAGAATGGTTAGGTTTTC 58.738 34.615 0.00 0.00 43.62 2.29
290 295 5.014808 AGCATATTTGGGTGAAGAAATGC 57.985 39.130 0.00 0.00 38.95 3.56
292 297 5.045872 GCATATTTGGGTGAAGAAATGCTC 58.954 41.667 0.00 0.00 36.44 4.26
297 302 2.827322 TGGGTGAAGAAATGCTCCATTG 59.173 45.455 0.00 0.00 34.04 2.82
299 304 3.511146 GGGTGAAGAAATGCTCCATTGAA 59.489 43.478 0.00 0.00 34.04 2.69
308 313 7.949434 AGAAATGCTCCATTGAATCTTTATCC 58.051 34.615 0.00 0.00 34.04 2.59
327 332 2.107378 TCCATTGTCACAAGCCTAACCA 59.893 45.455 0.00 0.00 0.00 3.67
328 333 3.091545 CCATTGTCACAAGCCTAACCAT 58.908 45.455 0.00 0.00 0.00 3.55
329 334 3.119388 CCATTGTCACAAGCCTAACCATG 60.119 47.826 0.00 0.00 0.00 3.66
330 335 1.533625 TGTCACAAGCCTAACCATGC 58.466 50.000 0.00 0.00 0.00 4.06
331 336 1.202867 TGTCACAAGCCTAACCATGCA 60.203 47.619 0.00 0.00 0.00 3.96
332 337 1.470098 GTCACAAGCCTAACCATGCAG 59.530 52.381 0.00 0.00 0.00 4.41
333 338 0.813184 CACAAGCCTAACCATGCAGG 59.187 55.000 0.00 0.00 45.67 4.85
334 339 0.698238 ACAAGCCTAACCATGCAGGA 59.302 50.000 0.00 0.00 41.22 3.86
335 340 1.285962 ACAAGCCTAACCATGCAGGAT 59.714 47.619 0.00 1.54 41.22 3.24
336 341 2.509548 ACAAGCCTAACCATGCAGGATA 59.490 45.455 0.00 0.00 41.22 2.59
337 342 3.053693 ACAAGCCTAACCATGCAGGATAA 60.054 43.478 0.00 0.00 41.22 1.75
338 343 3.498774 AGCCTAACCATGCAGGATAAG 57.501 47.619 0.00 0.00 41.22 1.73
339 344 1.882623 GCCTAACCATGCAGGATAAGC 59.117 52.381 0.00 0.00 41.22 3.09
375 380 7.698836 AATAATTTTATCGATTGCCACAAGC 57.301 32.000 1.71 0.00 44.14 4.01
463 468 5.163713 GCAGGATAATCTTTATCGATTGCCC 60.164 44.000 1.71 0.00 35.40 5.36
497 502 1.970917 GCTTCAATGGCGGACGACAG 61.971 60.000 6.37 0.00 36.12 3.51
499 504 3.168271 CAATGGCGGACGACAGTG 58.832 61.111 13.68 13.68 42.86 3.66
539 544 2.753966 CGCCTTCAATGTGGAGCGG 61.754 63.158 0.00 0.00 39.89 5.52
541 546 1.675310 CCTTCAATGTGGAGCGGCA 60.675 57.895 1.45 0.00 0.00 5.69
560 565 0.663688 ACGCTCTACAGGCTACATCG 59.336 55.000 0.00 0.00 0.00 3.84
681 696 1.003718 CCTCCCCCACGTTTGTCTC 60.004 63.158 0.00 0.00 0.00 3.36
689 704 1.011333 CACGTTTGTCTCCGGTTTGT 58.989 50.000 0.00 0.00 0.00 2.83
700 715 1.064611 TCCGGTTTGTGGGAGAAAACA 60.065 47.619 0.00 0.00 37.89 2.83
701 716 1.960689 CCGGTTTGTGGGAGAAAACAT 59.039 47.619 0.00 0.00 37.89 2.71
712 727 2.618045 GGAGAAAACATGTCCGGACCAT 60.618 50.000 31.19 20.64 30.78 3.55
735 750 3.930504 GGACCGATACAGGACCGT 58.069 61.111 0.00 0.00 36.47 4.83
774 789 0.946221 CCGGACAGTGCAGTTCAGAC 60.946 60.000 0.00 0.00 0.00 3.51
780 795 0.178068 AGTGCAGTTCAGACGGTTGT 59.822 50.000 0.00 0.00 0.00 3.32
786 801 0.391597 GTTCAGACGGTTGTGGGAGA 59.608 55.000 0.00 0.00 0.00 3.71
924 941 1.506493 CCACTGTCACTGAAGCACTC 58.494 55.000 0.00 0.00 0.00 3.51
942 959 2.290705 ACTCCCGATTTTTCGAACCCAT 60.291 45.455 0.00 0.00 34.64 4.00
943 960 2.354821 CTCCCGATTTTTCGAACCCATC 59.645 50.000 0.00 0.00 34.64 3.51
944 961 2.026636 TCCCGATTTTTCGAACCCATCT 60.027 45.455 0.00 0.00 34.64 2.90
1314 1337 3.343788 CTCGCTCCTCACCCACGAC 62.344 68.421 0.00 0.00 0.00 4.34
1467 1490 2.361865 AACCTCTCGCGGCTCTCT 60.362 61.111 6.13 0.00 0.00 3.10
1566 1589 4.194720 GCCGACCTCGTCTGCGAT 62.195 66.667 0.00 0.00 46.80 4.58
1782 1805 1.388065 CCGACGAGGAGGAGATGCTT 61.388 60.000 0.00 0.00 45.00 3.91
1857 1880 3.702048 TTCGTCAAGGCCGAGGGG 61.702 66.667 0.00 0.00 35.49 4.79
2051 2074 6.319658 CAGCTGCTCCATTCCTTCTTATTTTA 59.680 38.462 0.00 0.00 0.00 1.52
2172 2196 6.649141 TGCCGCTAGGTTCATATTATAGTTTG 59.351 38.462 0.00 0.00 40.50 2.93
2267 2291 8.495949 ACAAGCTTGTATCATAATTGTATACGC 58.504 33.333 30.25 0.00 40.16 4.42
2269 2293 9.923143 AAGCTTGTATCATAATTGTATACGCTA 57.077 29.630 0.00 0.00 28.86 4.26
2658 2683 0.829333 CATGGACTGCTGCTAGGTCT 59.171 55.000 15.81 1.24 0.00 3.85
2968 2996 5.063944 TCTGAAAATTGACTGATAAGCGAGC 59.936 40.000 0.00 0.00 0.00 5.03
2986 3014 0.246635 GCTGGCGAGTCAGGAGTTTA 59.753 55.000 6.84 0.00 35.43 2.01
3094 3124 7.716799 TGTTAATTGCTTCTGAAATATGGGT 57.283 32.000 0.00 0.00 0.00 4.51
3255 3285 5.931724 TGGATTGTATGTATATGAACCTGCG 59.068 40.000 0.00 0.00 0.00 5.18
3326 3356 6.038997 ACCACCAGTTATCTACAGAGTTTC 57.961 41.667 0.00 0.00 0.00 2.78
3327 3357 5.780793 ACCACCAGTTATCTACAGAGTTTCT 59.219 40.000 0.00 0.00 0.00 2.52
3328 3358 6.071278 ACCACCAGTTATCTACAGAGTTTCTC 60.071 42.308 0.00 0.00 0.00 2.87
3510 3638 3.837213 ATGGTTGCACTTGAAGATTCG 57.163 42.857 0.00 0.00 0.00 3.34
3592 3720 1.077265 CATGGTTTCCCAGGCCACT 59.923 57.895 5.01 0.00 46.15 4.00
3716 4106 1.707427 AGACAGAAAACCAGGCCTCAT 59.293 47.619 0.00 0.00 0.00 2.90
3841 4231 6.405278 TGAAGTATCTGTCAGTTGTTGAGA 57.595 37.500 0.00 0.00 36.21 3.27
3988 4378 4.479619 CTGAATAAACTGGCACTGAAAGC 58.520 43.478 0.00 0.00 37.60 3.51
4001 4391 4.035675 GCACTGAAAGCTACTTGTTTGAGT 59.964 41.667 0.00 0.00 37.60 3.41
4070 4467 1.632422 CGAATCCTTGTTTGCCATGC 58.368 50.000 0.00 0.00 0.00 4.06
4673 8162 3.152341 CTCCACCAAGCTTCTGAAACAT 58.848 45.455 0.00 0.00 0.00 2.71
4734 8223 1.972660 ATCTGGCACTCCGGGTAAGC 61.973 60.000 0.00 0.45 39.31 3.09
4854 8343 6.310941 TCCCTGTCATTAATTTTCAGGAACA 58.689 36.000 21.93 9.94 45.76 3.18
4946 8471 3.350833 ACTTCAGGCATGTCATTCCTTC 58.649 45.455 0.63 0.00 0.00 3.46
5003 8528 1.603172 GGGATCTAGCGTGAATGGTCG 60.603 57.143 0.00 0.00 0.00 4.79
5068 8593 6.089954 GCATTCTTCAAGTAGGCAATGTTTTC 59.910 38.462 0.00 0.00 0.00 2.29
5301 8830 4.261614 GCTTTGTTTGTAAACTAGCCAGCT 60.262 41.667 16.91 0.00 39.30 4.24
5477 9007 6.264832 TGTGATTTTTGTGTCATTGTCACTC 58.735 36.000 13.77 4.95 36.57 3.51
5507 9037 2.192664 TGGCGCTTCCAAGTTTATCA 57.807 45.000 7.64 0.00 43.21 2.15
5508 9038 2.722094 TGGCGCTTCCAAGTTTATCAT 58.278 42.857 7.64 0.00 43.21 2.45
5756 9291 2.638744 AGCTTTGCTTGGCTCACTC 58.361 52.632 0.00 0.00 33.89 3.51
5793 9328 1.120530 ATTATCCTCTTGGCGTCGGT 58.879 50.000 0.00 0.00 0.00 4.69
5825 9360 4.154347 CCACTGCTCGCCCCTCTC 62.154 72.222 0.00 0.00 0.00 3.20
5827 9362 4.390556 ACTGCTCGCCCCTCTCCT 62.391 66.667 0.00 0.00 0.00 3.69
5873 9410 3.716195 CCATCCTGCCCCGTGTCA 61.716 66.667 0.00 0.00 0.00 3.58
5874 9411 2.436646 CATCCTGCCCCGTGTCAC 60.437 66.667 0.00 0.00 0.00 3.67
5914 9452 3.505835 CTCCGTCCTCTTAGGAGCT 57.494 57.895 0.00 0.00 46.90 4.09
5963 9502 2.364579 TGGTGGGGGTAGTAGCCG 60.365 66.667 12.18 0.00 36.39 5.52
5966 9505 1.986210 GTGGGGGTAGTAGCCGTGT 60.986 63.158 12.18 0.00 36.39 4.49
5971 9510 1.039233 GGGTAGTAGCCGTGTGCCTA 61.039 60.000 1.88 0.00 42.71 3.93
5973 9512 0.248377 GTAGTAGCCGTGTGCCTACG 60.248 60.000 3.15 3.15 42.71 3.51
5999 9538 3.788766 GACATGCGCGGCGAGTTT 61.789 61.111 28.54 6.64 0.00 2.66
6000 9539 3.982424 GACATGCGCGGCGAGTTTG 62.982 63.158 28.54 17.94 0.00 2.93
6001 9540 4.817063 CATGCGCGGCGAGTTTGG 62.817 66.667 28.54 4.55 0.00 3.28
6004 9543 4.445545 GCGCGGCGAGTTTGGAAG 62.446 66.667 28.54 0.00 0.00 3.46
6005 9544 3.041940 CGCGGCGAGTTTGGAAGT 61.042 61.111 19.16 0.00 0.00 3.01
6006 9545 2.556287 GCGGCGAGTTTGGAAGTG 59.444 61.111 12.98 0.00 0.00 3.16
6012 9551 0.328258 CGAGTTTGGAAGTGGGGGAT 59.672 55.000 0.00 0.00 0.00 3.85
6023 9562 4.191015 GGGGGATGAAGGGGCGAC 62.191 72.222 0.00 0.00 0.00 5.19
6090 9664 3.681835 GTGGCCTCACGGACGAGT 61.682 66.667 3.32 0.00 43.41 4.18
6095 9669 2.651361 CTCACGGACGAGTTGGCT 59.349 61.111 0.00 0.00 0.00 4.75
6103 9677 1.006102 ACGAGTTGGCTGGTCTTCG 60.006 57.895 0.00 0.00 0.00 3.79
6105 9679 1.301716 GAGTTGGCTGGTCTTCGCA 60.302 57.895 0.00 0.00 0.00 5.10
6106 9680 1.294659 GAGTTGGCTGGTCTTCGCAG 61.295 60.000 0.00 0.00 0.00 5.18
6128 9702 2.985847 GGCCTCTTGCTTTGCGGT 60.986 61.111 0.00 0.00 40.92 5.68
6129 9703 2.256461 GCCTCTTGCTTTGCGGTG 59.744 61.111 0.00 0.00 36.87 4.94
6133 9707 4.705519 CTTGCTTTGCGGTGGCGG 62.706 66.667 0.00 0.00 44.10 6.13
6176 9750 1.308069 TTGATCTTGGCTTCCTGCGC 61.308 55.000 0.00 0.00 44.05 6.09
6180 9754 4.927782 TTGGCTTCCTGCGCGTGT 62.928 61.111 8.43 0.00 44.05 4.49
6204 9778 2.269241 CCCTTCCTCTTGGCCGAC 59.731 66.667 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 0.113190 AACCCAAGCCTTCCTTCCTG 59.887 55.000 0.00 0.00 0.00 3.86
58 59 3.935203 CTCGGGAGTCTAGTACGTTACAA 59.065 47.826 0.00 0.00 0.00 2.41
106 107 1.062880 GGTTCGAGTTGTTTGTCGCAA 59.937 47.619 0.00 0.00 36.11 4.85
153 158 3.689347 TCATCAGAAACAACAGGGATGG 58.311 45.455 0.00 0.00 34.42 3.51
211 216 2.095372 CCGAGCGAAAACCTAACCATTC 59.905 50.000 0.00 0.00 0.00 2.67
215 220 2.368655 TACCGAGCGAAAACCTAACC 57.631 50.000 0.00 0.00 0.00 2.85
216 221 5.050567 CCAATATACCGAGCGAAAACCTAAC 60.051 44.000 0.00 0.00 0.00 2.34
225 230 1.991121 AGTCCCAATATACCGAGCGA 58.009 50.000 0.00 0.00 0.00 4.93
226 231 3.255149 AGTTAGTCCCAATATACCGAGCG 59.745 47.826 0.00 0.00 0.00 5.03
290 295 8.133627 GTGACAATGGATAAAGATTCAATGGAG 58.866 37.037 0.00 0.00 26.82 3.86
292 297 7.774134 TGTGACAATGGATAAAGATTCAATGG 58.226 34.615 0.00 0.00 26.82 3.16
297 302 6.096001 AGGCTTGTGACAATGGATAAAGATTC 59.904 38.462 0.00 0.00 0.00 2.52
299 304 5.513233 AGGCTTGTGACAATGGATAAAGAT 58.487 37.500 0.00 0.00 0.00 2.40
308 313 3.674138 GCATGGTTAGGCTTGTGACAATG 60.674 47.826 0.00 0.00 0.00 2.82
349 354 9.410556 GCTTGTGGCAATCGATAAAATTATTAT 57.589 29.630 0.00 0.00 41.35 1.28
350 355 8.795786 GCTTGTGGCAATCGATAAAATTATTA 57.204 30.769 0.00 0.00 41.35 0.98
351 356 7.698836 GCTTGTGGCAATCGATAAAATTATT 57.301 32.000 0.00 0.00 41.35 1.40
479 484 0.670546 ACTGTCGTCCGCCATTGAAG 60.671 55.000 0.00 0.00 0.00 3.02
493 498 1.154188 GACGCGACCTCTCACTGTC 60.154 63.158 15.93 0.00 0.00 3.51
515 520 1.243342 CCACATTGAAGGCGGCTCAA 61.243 55.000 13.70 17.97 37.22 3.02
539 544 0.103208 ATGTAGCCTGTAGAGCGTGC 59.897 55.000 0.00 0.00 34.64 5.34
541 546 0.663688 CGATGTAGCCTGTAGAGCGT 59.336 55.000 0.00 0.00 34.64 5.07
549 554 1.534163 CATTCATGCCGATGTAGCCTG 59.466 52.381 0.00 0.00 0.00 4.85
613 619 1.774300 CCCTGGCCCACCTAAAACT 59.226 57.895 0.00 0.00 36.63 2.66
640 646 2.420466 GGGAATCCGGACCGCTAC 59.580 66.667 6.12 0.00 0.00 3.58
681 696 1.394618 TGTTTTCTCCCACAAACCGG 58.605 50.000 0.00 0.00 32.76 5.28
689 704 1.060729 TCCGGACATGTTTTCTCCCA 58.939 50.000 0.00 0.00 0.00 4.37
712 727 0.323633 TCCTGTATCGGTCCGTGGAA 60.324 55.000 11.88 0.00 0.00 3.53
774 789 1.365699 CCGTAAATCTCCCACAACCG 58.634 55.000 0.00 0.00 0.00 4.44
780 795 1.518774 GCGACCCGTAAATCTCCCA 59.481 57.895 0.00 0.00 0.00 4.37
786 801 0.107848 CTCCAAGGCGACCCGTAAAT 60.108 55.000 0.00 0.00 35.76 1.40
899 916 1.053835 TTCAGTGACAGTGGGCTGGA 61.054 55.000 10.39 0.79 46.62 3.86
900 917 0.604780 CTTCAGTGACAGTGGGCTGG 60.605 60.000 10.39 0.00 46.62 4.85
924 941 2.365582 AGATGGGTTCGAAAAATCGGG 58.634 47.619 0.00 0.00 0.00 5.14
942 959 0.039764 TGGCTCGAGGAGGAAGAAGA 59.960 55.000 15.58 0.00 0.00 2.87
943 960 0.174617 GTGGCTCGAGGAGGAAGAAG 59.825 60.000 15.58 0.00 0.00 2.85
944 961 1.258445 GGTGGCTCGAGGAGGAAGAA 61.258 60.000 15.58 0.00 0.00 2.52
1347 1370 2.599281 TCGGTGAGGTCGGCAAGA 60.599 61.111 0.00 0.00 0.00 3.02
1350 1373 3.371063 GAGTCGGTGAGGTCGGCA 61.371 66.667 0.00 0.00 34.34 5.69
1782 1805 0.603569 GGCAGTCGAAGAGGTTCTCA 59.396 55.000 0.00 0.00 36.95 3.27
1857 1880 4.814147 TGATAATGATCATGAGCTCGACC 58.186 43.478 12.92 0.00 37.15 4.79
2172 2196 7.649306 CCATTTTCAGCTTTATATTGGCTACAC 59.351 37.037 0.00 0.00 34.71 2.90
2304 2328 5.356470 GCCTTATCAGAAATTGAGCAGAACT 59.644 40.000 0.00 0.00 39.68 3.01
2671 2697 7.887996 TTTTCAGCTTTATTTACATTGGCTG 57.112 32.000 0.00 0.00 44.51 4.85
2968 2996 2.743636 TTAAACTCCTGACTCGCCAG 57.256 50.000 0.00 0.00 0.00 4.85
2986 3014 2.299326 AAGGCCAGCTTGAGACAATT 57.701 45.000 5.01 0.00 0.00 2.32
3094 3124 7.403312 TTTCTTGTTCACAGGAATCTGAAAA 57.597 32.000 5.43 0.00 43.49 2.29
3255 3285 5.140747 AGTATATTTGTCGATCCTCTGCC 57.859 43.478 0.00 0.00 0.00 4.85
3510 3638 4.386652 CAGTAAACAGCATGGCAAAACATC 59.613 41.667 0.00 0.00 43.62 3.06
3716 4106 2.719531 TGCTGTTTCTGGTTGTGGTA 57.280 45.000 0.00 0.00 0.00 3.25
3827 4217 3.644966 AGGGTTTCTCAACAACTGACA 57.355 42.857 0.00 0.00 34.15 3.58
3841 4231 0.618981 GTGGCAGGCTACTAGGGTTT 59.381 55.000 0.09 0.00 0.00 3.27
3988 4378 4.632153 AGTAGGTGCACTCAAACAAGTAG 58.368 43.478 17.98 0.00 0.00 2.57
4001 4391 1.267121 GGTCTGAGGAAGTAGGTGCA 58.733 55.000 0.00 0.00 0.00 4.57
4070 4467 2.035704 TGCAGCACCAACAACCTATTTG 59.964 45.455 0.00 0.00 41.49 2.32
4673 8162 6.734137 CCACTAGCTGAAACATACAAACAAA 58.266 36.000 0.00 0.00 0.00 2.83
4734 8223 5.335504 GGAAGAAAGACTGAATGAAGCCTTG 60.336 44.000 0.00 0.00 0.00 3.61
4854 8343 5.719085 ACTCTATTCTTGTCCTCATCTGTGT 59.281 40.000 0.00 0.00 0.00 3.72
4946 8471 8.830580 ACTCAACAACATATGATTTATTCGAGG 58.169 33.333 10.38 0.00 0.00 4.63
5003 8528 1.792118 AAGGCAGAAAACCGGCGAAC 61.792 55.000 9.30 0.00 36.81 3.95
5068 8593 7.518161 TCAACAAGCTGATTAATAAACTGTCG 58.482 34.615 0.00 0.00 0.00 4.35
5418 8948 7.414436 TGTCAAAACTGATGCAAGTAAGTAAC 58.586 34.615 0.00 0.00 0.00 2.50
5477 9007 2.158957 TGGAAGCGCCACTAAATCTAGG 60.159 50.000 2.29 0.00 43.33 3.02
5541 9071 6.259167 CGAAAAAGAACCGTGAATATATGGGA 59.741 38.462 0.00 0.00 0.00 4.37
5552 9082 6.689669 AGAATTTGTTACGAAAAAGAACCGTG 59.310 34.615 0.00 0.00 37.69 4.94
5590 9120 7.481275 AAAATTGACAGTAACAAGGCAAATG 57.519 32.000 0.00 0.00 0.00 2.32
5716 9251 1.956477 TGCCTTTCTTTCCAAGCTGAC 59.044 47.619 0.00 0.00 0.00 3.51
5756 9291 6.043706 AGGATAATACACCATCCTCTTCTTGG 59.956 42.308 0.00 0.00 46.62 3.61
5870 9407 3.647771 GGTGGTGGAGGGGGTGAC 61.648 72.222 0.00 0.00 0.00 3.67
5871 9408 3.869934 AGGTGGTGGAGGGGGTGA 61.870 66.667 0.00 0.00 0.00 4.02
5914 9452 1.539496 CCCGTTTGTCCAACTCTTCGA 60.539 52.381 0.00 0.00 32.53 3.71
5998 9537 0.704076 CCTTCATCCCCCACTTCCAA 59.296 55.000 0.00 0.00 0.00 3.53
5999 9538 1.214305 CCCTTCATCCCCCACTTCCA 61.214 60.000 0.00 0.00 0.00 3.53
6000 9539 1.615262 CCCTTCATCCCCCACTTCC 59.385 63.158 0.00 0.00 0.00 3.46
6001 9540 1.615262 CCCCTTCATCCCCCACTTC 59.385 63.158 0.00 0.00 0.00 3.01
6002 9541 2.626467 GCCCCTTCATCCCCCACTT 61.626 63.158 0.00 0.00 0.00 3.16
6003 9542 3.023735 GCCCCTTCATCCCCCACT 61.024 66.667 0.00 0.00 0.00 4.00
6004 9543 4.506255 CGCCCCTTCATCCCCCAC 62.506 72.222 0.00 0.00 0.00 4.61
6005 9544 4.750695 TCGCCCCTTCATCCCCCA 62.751 66.667 0.00 0.00 0.00 4.96
6006 9545 4.191015 GTCGCCCCTTCATCCCCC 62.191 72.222 0.00 0.00 0.00 5.40
6058 9632 3.077556 CACGAGGCAGGCCCTACT 61.078 66.667 6.70 0.00 46.60 2.57
6080 9654 2.738521 CCAGCCAACTCGTCCGTG 60.739 66.667 0.00 0.00 0.00 4.94
6081 9655 3.222354 GACCAGCCAACTCGTCCGT 62.222 63.158 0.00 0.00 28.59 4.69
6082 9656 2.432628 GACCAGCCAACTCGTCCG 60.433 66.667 0.00 0.00 28.59 4.79
6085 9659 1.006102 CGAAGACCAGCCAACTCGT 60.006 57.895 0.00 0.00 0.00 4.18
6111 9685 2.985847 ACCGCAAAGCAAGAGGCC 60.986 61.111 0.00 0.00 46.50 5.19
6112 9686 2.256461 CACCGCAAAGCAAGAGGC 59.744 61.111 0.00 0.00 45.30 4.70
6145 9719 3.849953 GATCAACGTCGTGGCCGC 61.850 66.667 6.11 6.11 0.00 6.53
6147 9721 1.635663 CCAAGATCAACGTCGTGGCC 61.636 60.000 0.00 0.00 40.08 5.36
6151 9725 1.429463 GAAGCCAAGATCAACGTCGT 58.571 50.000 0.00 0.00 0.00 4.34
6156 9730 0.449388 CGCAGGAAGCCAAGATCAAC 59.551 55.000 0.00 0.00 41.38 3.18


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.