Multiple sequence alignment - TraesCS5A01G335900

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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 TraesCS5A01G335900 chr5A 100.000 2954 0 0 1 2954 545049885 545046932 0.000000e+00 5456.0
1 TraesCS5A01G335900 chr5A 80.449 1248 191 29 1025 2254 544728228 544727016 0.000000e+00 904.0
2 TraesCS5A01G335900 chr5A 80.449 1248 191 29 1025 2254 544749819 544748607 0.000000e+00 904.0
3 TraesCS5A01G335900 chr5A 80.449 1248 191 29 1025 2254 544771847 544770635 0.000000e+00 904.0
4 TraesCS5A01G335900 chr5A 80.384 1249 190 31 1025 2254 544794157 544792945 0.000000e+00 898.0
5 TraesCS5A01G335900 chr5A 89.447 199 20 1 446 644 451463574 451463771 1.760000e-62 250.0
6 TraesCS5A01G335900 chr5A 88.500 200 22 1 446 644 659828816 659829015 1.060000e-59 241.0
7 TraesCS5A01G335900 chr5A 81.818 209 26 7 1 208 268578033 268578230 6.550000e-37 165.0
8 TraesCS5A01G335900 chr5D 92.861 1933 73 22 654 2528 429151197 429149272 0.000000e+00 2745.0
9 TraesCS5A01G335900 chr5D 78.864 1268 186 38 1023 2248 439737210 439735983 0.000000e+00 782.0
10 TraesCS5A01G335900 chr5D 78.498 1265 192 38 1023 2248 440064546 440063323 0.000000e+00 756.0
11 TraesCS5A01G335900 chr5D 84.639 638 81 7 1022 1652 429059889 429059262 1.160000e-173 619.0
12 TraesCS5A01G335900 chr5D 86.456 443 48 10 1 438 429151648 429151213 2.660000e-130 475.0
13 TraesCS5A01G335900 chr5D 94.836 213 11 0 2742 2954 429147661 429147449 1.700000e-87 333.0
14 TraesCS5A01G335900 chr5D 81.180 356 62 3 1652 2006 429059218 429058867 6.230000e-72 281.0
15 TraesCS5A01G335900 chr5D 86.124 209 6 4 2555 2741 429149274 429149067 1.390000e-48 204.0
16 TraesCS5A01G335900 chr5B 91.188 2054 109 30 669 2662 518320077 518318036 0.000000e+00 2724.0
17 TraesCS5A01G335900 chr5B 77.355 998 176 35 1023 2009 518490993 518490035 2.000000e-151 545.0
18 TraesCS5A01G335900 chr5B 87.302 441 44 10 1 438 518320539 518320108 7.360000e-136 494.0
19 TraesCS5A01G335900 chr5B 94.737 76 3 1 2667 2741 518317983 518317908 1.860000e-22 117.0
20 TraesCS5A01G335900 chr3D 76.965 738 120 33 1023 1732 129006868 129007583 2.780000e-100 375.0
21 TraesCS5A01G335900 chr2A 89.231 195 21 0 450 644 699240910 699241104 8.180000e-61 244.0
22 TraesCS5A01G335900 chr2A 88.442 199 21 1 446 644 24650804 24651000 3.810000e-59 239.0
23 TraesCS5A01G335900 chr2A 88.442 199 21 1 446 644 24678871 24679067 3.810000e-59 239.0
24 TraesCS5A01G335900 chr2A 88.442 199 21 1 446 644 25658040 25657844 3.810000e-59 239.0
25 TraesCS5A01G335900 chr7A 88.442 199 22 1 450 648 515222514 515222317 3.810000e-59 239.0
26 TraesCS5A01G335900 chr2B 88.500 200 20 2 445 643 536821597 536821400 3.810000e-59 239.0
27 TraesCS5A01G335900 chr2D 87.081 209 25 2 450 656 455942429 455942221 4.920000e-58 235.0
28 TraesCS5A01G335900 chrUn 80.822 146 19 2 2113 2254 447560717 447560577 4.030000e-19 106.0
29 TraesCS5A01G335900 chr4A 75.862 203 32 12 15 214 636968625 636968437 1.460000e-13 87.9


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 TraesCS5A01G335900 chr5A 545046932 545049885 2953 True 5456.000000 5456 100.000000 1 2954 1 chr5A.!!$R5 2953
1 TraesCS5A01G335900 chr5A 544727016 544728228 1212 True 904.000000 904 80.449000 1025 2254 1 chr5A.!!$R1 1229
2 TraesCS5A01G335900 chr5A 544748607 544749819 1212 True 904.000000 904 80.449000 1025 2254 1 chr5A.!!$R2 1229
3 TraesCS5A01G335900 chr5A 544770635 544771847 1212 True 904.000000 904 80.449000 1025 2254 1 chr5A.!!$R3 1229
4 TraesCS5A01G335900 chr5A 544792945 544794157 1212 True 898.000000 898 80.384000 1025 2254 1 chr5A.!!$R4 1229
5 TraesCS5A01G335900 chr5D 429147449 429151648 4199 True 939.250000 2745 90.069250 1 2954 4 chr5D.!!$R4 2953
6 TraesCS5A01G335900 chr5D 439735983 439737210 1227 True 782.000000 782 78.864000 1023 2248 1 chr5D.!!$R1 1225
7 TraesCS5A01G335900 chr5D 440063323 440064546 1223 True 756.000000 756 78.498000 1023 2248 1 chr5D.!!$R2 1225
8 TraesCS5A01G335900 chr5D 429058867 429059889 1022 True 450.000000 619 82.909500 1022 2006 2 chr5D.!!$R3 984
9 TraesCS5A01G335900 chr5B 518317908 518320539 2631 True 1111.666667 2724 91.075667 1 2741 3 chr5B.!!$R2 2740
10 TraesCS5A01G335900 chr5B 518490035 518490993 958 True 545.000000 545 77.355000 1023 2009 1 chr5B.!!$R1 986
11 TraesCS5A01G335900 chr3D 129006868 129007583 715 False 375.000000 375 76.965000 1023 1732 1 chr3D.!!$F1 709

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
381 385 0.391263 GAAACCTACTCCAGCACCCG 60.391 60.0 0.0 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2061 2200 0.106569 TGCCACTTGATGCCTATGGG 60.107 55.0 0.0 0.0 0.0 4.0 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
90 92 5.523916 ACATCAACTGACACTGAACACTAAC 59.476 40.000 0.00 0.00 0.00 2.34
221 225 4.805231 CGTATCACGCACCGGCCA 62.805 66.667 0.00 0.00 33.65 5.36
260 264 2.257371 CCGGTCTTTCGCGTCTGA 59.743 61.111 5.77 0.00 0.00 3.27
266 270 2.029728 GGTCTTTCGCGTCTGATCAATG 59.970 50.000 5.77 0.00 0.00 2.82
273 277 1.469940 GCGTCTGATCAATGTCGGAGT 60.470 52.381 0.00 0.00 34.31 3.85
291 295 1.535444 TGACGTGACTGGATGGGGT 60.535 57.895 0.00 0.00 0.00 4.95
303 307 4.203001 ACTGGATGGGGTGGATATATACCA 60.203 45.833 6.94 3.99 38.74 3.25
350 354 1.349688 TCCTGCCGTCATTAAACAGGT 59.650 47.619 7.19 0.00 46.49 4.00
357 361 3.577667 CGTCATTAAACAGGTACACCGA 58.422 45.455 0.00 0.00 42.08 4.69
365 369 0.599558 CAGGTACACCGACCGAGAAA 59.400 55.000 0.00 0.00 44.88 2.52
368 372 0.600057 GTACACCGACCGAGAAACCT 59.400 55.000 0.00 0.00 0.00 3.50
369 373 1.812571 GTACACCGACCGAGAAACCTA 59.187 52.381 0.00 0.00 0.00 3.08
370 374 0.600057 ACACCGACCGAGAAACCTAC 59.400 55.000 0.00 0.00 0.00 3.18
371 375 0.886563 CACCGACCGAGAAACCTACT 59.113 55.000 0.00 0.00 0.00 2.57
373 377 0.455005 CCGACCGAGAAACCTACTCC 59.545 60.000 0.00 0.00 0.00 3.85
375 379 1.132643 CGACCGAGAAACCTACTCCAG 59.867 57.143 0.00 0.00 0.00 3.86
376 380 0.896226 ACCGAGAAACCTACTCCAGC 59.104 55.000 0.00 0.00 0.00 4.85
377 381 0.895530 CCGAGAAACCTACTCCAGCA 59.104 55.000 0.00 0.00 0.00 4.41
380 384 0.984995 AGAAACCTACTCCAGCACCC 59.015 55.000 0.00 0.00 0.00 4.61
381 385 0.391263 GAAACCTACTCCAGCACCCG 60.391 60.000 0.00 0.00 0.00 5.28
382 386 2.465055 AAACCTACTCCAGCACCCGC 62.465 60.000 0.00 0.00 38.99 6.13
384 388 2.662596 CTACTCCAGCACCCGCAA 59.337 61.111 0.00 0.00 42.27 4.85
385 389 1.741770 CTACTCCAGCACCCGCAAC 60.742 63.158 0.00 0.00 42.27 4.17
392 396 3.353836 GCACCCGCAACGACACAT 61.354 61.111 0.00 0.00 38.36 3.21
395 399 1.959226 ACCCGCAACGACACATCAC 60.959 57.895 0.00 0.00 0.00 3.06
422 426 1.063792 TGGTCTGGCCAACATATGCAT 60.064 47.619 7.01 3.79 45.94 3.96
435 439 2.196742 TATGCATGGAGGAGGAGGTT 57.803 50.000 10.16 0.00 0.00 3.50
438 442 0.620556 GCATGGAGGAGGAGGTTCAA 59.379 55.000 0.00 0.00 0.00 2.69
439 443 1.213926 GCATGGAGGAGGAGGTTCAAT 59.786 52.381 0.00 0.00 0.00 2.57
442 446 4.446889 GCATGGAGGAGGAGGTTCAATAAT 60.447 45.833 0.00 0.00 0.00 1.28
445 449 6.152638 TGGAGGAGGAGGTTCAATAATTTT 57.847 37.500 0.00 0.00 0.00 1.82
446 450 6.561294 TGGAGGAGGAGGTTCAATAATTTTT 58.439 36.000 0.00 0.00 0.00 1.94
515 519 9.862371 AACATAACAAATTTATACGGCATGAAA 57.138 25.926 0.00 0.00 0.00 2.69
516 520 9.515020 ACATAACAAATTTATACGGCATGAAAG 57.485 29.630 0.00 0.00 0.00 2.62
517 521 9.515020 CATAACAAATTTATACGGCATGAAAGT 57.485 29.630 0.00 0.00 0.00 2.66
519 523 8.905103 AACAAATTTATACGGCATGAAAGTAC 57.095 30.769 0.00 0.00 0.00 2.73
520 524 8.046294 ACAAATTTATACGGCATGAAAGTACA 57.954 30.769 0.00 0.00 0.00 2.90
521 525 8.682710 ACAAATTTATACGGCATGAAAGTACAT 58.317 29.630 0.00 0.00 0.00 2.29
522 526 9.515020 CAAATTTATACGGCATGAAAGTACATT 57.485 29.630 0.00 0.00 0.00 2.71
523 527 9.730420 AAATTTATACGGCATGAAAGTACATTC 57.270 29.630 3.88 3.88 0.00 2.67
524 528 7.851387 TTTATACGGCATGAAAGTACATTCA 57.149 32.000 15.26 15.26 43.03 2.57
525 529 7.851387 TTATACGGCATGAAAGTACATTCAA 57.149 32.000 16.68 0.83 42.22 2.69
526 530 6.942532 ATACGGCATGAAAGTACATTCAAT 57.057 33.333 16.68 3.10 42.22 2.57
527 531 9.549078 TTATACGGCATGAAAGTACATTCAATA 57.451 29.630 16.68 7.00 42.22 1.90
528 532 6.751514 ACGGCATGAAAGTACATTCAATAA 57.248 33.333 16.68 0.00 42.22 1.40
529 533 7.333528 ACGGCATGAAAGTACATTCAATAAT 57.666 32.000 16.68 0.00 42.22 1.28
530 534 7.195646 ACGGCATGAAAGTACATTCAATAATG 58.804 34.615 16.68 11.56 46.66 1.90
531 535 7.066887 ACGGCATGAAAGTACATTCAATAATGA 59.933 33.333 16.68 0.00 44.50 2.57
630 634 4.423732 CTTTGATCAAAGTTAATGGGCGG 58.576 43.478 31.54 9.90 42.02 6.13
631 635 3.358111 TGATCAAAGTTAATGGGCGGA 57.642 42.857 0.00 0.00 0.00 5.54
632 636 3.013921 TGATCAAAGTTAATGGGCGGAC 58.986 45.455 0.00 0.00 0.00 4.79
633 637 2.871096 TCAAAGTTAATGGGCGGACT 57.129 45.000 0.00 0.00 0.00 3.85
634 638 3.985019 TCAAAGTTAATGGGCGGACTA 57.015 42.857 0.00 0.00 0.00 2.59
635 639 4.289238 TCAAAGTTAATGGGCGGACTAA 57.711 40.909 0.00 0.00 0.00 2.24
636 640 4.653868 TCAAAGTTAATGGGCGGACTAAA 58.346 39.130 0.00 0.00 0.00 1.85
637 641 5.258051 TCAAAGTTAATGGGCGGACTAAAT 58.742 37.500 0.00 0.00 0.00 1.40
638 642 6.416415 TCAAAGTTAATGGGCGGACTAAATA 58.584 36.000 0.00 0.00 0.00 1.40
639 643 6.885376 TCAAAGTTAATGGGCGGACTAAATAA 59.115 34.615 0.00 0.00 0.00 1.40
640 644 7.393796 TCAAAGTTAATGGGCGGACTAAATAAA 59.606 33.333 0.00 0.00 0.00 1.40
641 645 7.706100 AAGTTAATGGGCGGACTAAATAAAA 57.294 32.000 0.00 0.00 0.00 1.52
642 646 7.706100 AGTTAATGGGCGGACTAAATAAAAA 57.294 32.000 0.00 0.00 0.00 1.94
643 647 7.541162 AGTTAATGGGCGGACTAAATAAAAAC 58.459 34.615 0.00 0.00 0.00 2.43
644 648 5.986501 AATGGGCGGACTAAATAAAAACA 57.013 34.783 0.00 0.00 0.00 2.83
645 649 5.986501 ATGGGCGGACTAAATAAAAACAA 57.013 34.783 0.00 0.00 0.00 2.83
646 650 5.786264 TGGGCGGACTAAATAAAAACAAA 57.214 34.783 0.00 0.00 0.00 2.83
647 651 5.774630 TGGGCGGACTAAATAAAAACAAAG 58.225 37.500 0.00 0.00 0.00 2.77
648 652 5.535406 TGGGCGGACTAAATAAAAACAAAGA 59.465 36.000 0.00 0.00 0.00 2.52
649 653 6.090783 GGGCGGACTAAATAAAAACAAAGAG 58.909 40.000 0.00 0.00 0.00 2.85
650 654 6.090783 GGCGGACTAAATAAAAACAAAGAGG 58.909 40.000 0.00 0.00 0.00 3.69
651 655 6.294342 GGCGGACTAAATAAAAACAAAGAGGT 60.294 38.462 0.00 0.00 0.00 3.85
652 656 7.143340 GCGGACTAAATAAAAACAAAGAGGTT 58.857 34.615 0.00 0.00 0.00 3.50
663 667 6.773976 AAACAAAGAGGTTCATCTTCACAA 57.226 33.333 0.34 0.00 38.59 3.33
666 670 6.122277 ACAAAGAGGTTCATCTTCACAAAGA 58.878 36.000 0.34 0.00 45.36 2.52
712 716 1.503542 GCGGTGGTCAAAGCATCAG 59.496 57.895 0.00 0.00 0.00 2.90
739 743 0.603975 GGTCAACACAGGTCAGAGGC 60.604 60.000 0.00 0.00 0.00 4.70
741 745 1.669115 CAACACAGGTCAGAGGCCG 60.669 63.158 0.00 0.00 0.00 6.13
751 761 0.394192 TCAGAGGCCGATAGCAATGG 59.606 55.000 0.00 0.00 46.50 3.16
756 766 1.166531 GGCCGATAGCAATGGACCAC 61.167 60.000 0.00 0.00 46.50 4.16
776 786 7.203255 ACCACTTACAAAGATTTAAGACTGC 57.797 36.000 0.00 0.00 0.00 4.40
804 815 6.632909 TGCATTTTTCATAGATTTGGGACTG 58.367 36.000 0.00 0.00 0.00 3.51
823 834 6.363473 GGACTGACTTGACATTTTCGTAAAG 58.637 40.000 0.00 0.00 34.02 1.85
831 842 9.821662 ACTTGACATTTTCGTAAAGTAATTAGC 57.178 29.630 0.00 0.00 38.57 3.09
834 845 8.995220 TGACATTTTCGTAAAGTAATTAGCACT 58.005 29.630 0.00 0.00 0.00 4.40
842 853 2.632377 AGTAATTAGCACTGCGCATGT 58.368 42.857 12.24 8.79 46.13 3.21
854 865 4.568359 CACTGCGCATGTATTTTACTCTCT 59.432 41.667 12.24 0.00 0.00 3.10
862 873 8.230486 CGCATGTATTTTACTCTCTTTTGTTCT 58.770 33.333 0.00 0.00 0.00 3.01
882 893 1.272092 TGGGTCCTCTTTGCAAGATGG 60.272 52.381 0.00 3.32 36.82 3.51
995 1010 3.971894 GATCCCACAGATCCGGGT 58.028 61.111 0.00 0.00 45.00 5.28
1740 1857 4.373116 TGCCGCGACAGGGAGTTC 62.373 66.667 8.23 0.00 0.00 3.01
1856 1983 2.047844 CTCTGGTGTCGTGCTGGG 60.048 66.667 0.00 0.00 0.00 4.45
1974 2108 2.639327 GCATTGGTGGGCTGTGGAC 61.639 63.158 0.00 0.00 0.00 4.02
2014 2148 3.009473 TCCCAGGTTCTCAATTCCTCAAG 59.991 47.826 0.00 0.00 0.00 3.02
2036 2170 2.479837 TGCCGTTTATCGTGATGATCC 58.520 47.619 0.00 0.00 38.57 3.36
2037 2171 2.102420 TGCCGTTTATCGTGATGATCCT 59.898 45.455 0.00 0.00 38.57 3.24
2038 2172 3.319689 TGCCGTTTATCGTGATGATCCTA 59.680 43.478 0.00 0.00 38.57 2.94
2039 2173 3.921021 GCCGTTTATCGTGATGATCCTAG 59.079 47.826 0.00 0.00 38.57 3.02
2057 2196 0.539051 AGCTAGAGGACCATGTGTGC 59.461 55.000 0.00 0.00 35.12 4.57
2061 2200 2.034687 AGGACCATGTGTGCCTGC 59.965 61.111 0.00 0.00 35.58 4.85
2194 2360 8.687824 AAACTTGAAACTGTTTGTATCTGTTG 57.312 30.769 11.03 0.00 35.40 3.33
2218 2388 4.838423 TGAACATTAGTCTGGTCTTCAGGA 59.162 41.667 0.00 0.00 43.53 3.86
2300 2470 0.887387 TTGCGCTGAGGTGGGTTTAC 60.887 55.000 9.73 0.00 0.00 2.01
2301 2471 1.003718 GCGCTGAGGTGGGTTTACT 60.004 57.895 0.00 0.00 0.00 2.24
2305 2475 2.167693 CGCTGAGGTGGGTTTACTGATA 59.832 50.000 0.00 0.00 0.00 2.15
2320 2490 8.294577 GGTTTACTGATAAAGTTTTGTGTAGGG 58.705 37.037 0.00 0.00 40.56 3.53
2328 2498 9.457436 GATAAAGTTTTGTGTAGGGGAGAATAA 57.543 33.333 0.00 0.00 0.00 1.40
2353 2523 7.913674 AAAACAACTGTATGATCTTCTCTCC 57.086 36.000 0.00 0.00 0.00 3.71
2354 2524 5.255710 ACAACTGTATGATCTTCTCTCCG 57.744 43.478 0.00 0.00 0.00 4.63
2356 2526 5.186021 ACAACTGTATGATCTTCTCTCCGTT 59.814 40.000 0.00 0.00 0.00 4.44
2357 2527 5.255710 ACTGTATGATCTTCTCTCCGTTG 57.744 43.478 0.00 0.00 0.00 4.10
2429 2621 8.476447 ACCATCTCATAGATATCATGTGCTTAG 58.524 37.037 5.32 1.31 32.12 2.18
2442 2634 0.107831 TGCTTAGTTGGCCGTCTGTT 59.892 50.000 9.36 0.00 0.00 3.16
2443 2635 0.517316 GCTTAGTTGGCCGTCTGTTG 59.483 55.000 9.36 1.98 0.00 3.33
2444 2636 1.876416 GCTTAGTTGGCCGTCTGTTGA 60.876 52.381 9.36 0.00 0.00 3.18
2447 2639 2.112297 TTGGCCGTCTGTTGACCC 59.888 61.111 0.00 0.00 39.94 4.46
2448 2640 2.747443 TTGGCCGTCTGTTGACCCA 61.747 57.895 0.00 0.00 39.94 4.51
2450 2642 3.041940 GCCGTCTGTTGACCCACG 61.042 66.667 0.00 0.00 39.94 4.94
2536 2753 5.888691 TGAAGATGGTTTGCGCTAAATAA 57.111 34.783 9.73 0.00 0.00 1.40
2614 2831 6.156519 CCTGATCCATCACATTTTATGCATG 58.843 40.000 10.16 0.00 32.50 4.06
2700 2968 5.392286 GTTTGTTGGTCGTGTTTGTAGAAA 58.608 37.500 0.00 0.00 0.00 2.52
2738 3007 9.562408 CTTATAATGACCTGACTCTCAGTAGTA 57.438 37.037 0.00 0.00 42.80 1.82
2739 3008 7.811117 ATAATGACCTGACTCTCAGTAGTAC 57.189 40.000 0.00 0.00 42.80 2.73
2740 3009 4.635699 TGACCTGACTCTCAGTAGTACA 57.364 45.455 2.52 0.00 42.80 2.90
2797 4472 1.523758 GTTTGCCGGTGACAGAAGAT 58.476 50.000 1.90 0.00 0.00 2.40
2806 4481 3.506810 GGTGACAGAAGATGAAGACGAG 58.493 50.000 0.00 0.00 0.00 4.18
2814 4489 6.378564 ACAGAAGATGAAGACGAGGAAGATTA 59.621 38.462 0.00 0.00 0.00 1.75
2830 4505 3.454375 AGATTATAAGGCGAACGTGTGG 58.546 45.455 0.00 0.00 0.00 4.17
2848 4523 3.138798 TCCTAGCTCGTGGGCGTC 61.139 66.667 0.00 0.00 39.49 5.19
2868 4543 2.359107 CAGCGAGGAAGCAAGGCA 60.359 61.111 0.00 0.00 40.15 4.75
2870 4545 3.793144 GCGAGGAAGCAAGGCACG 61.793 66.667 0.00 0.00 37.05 5.34
2871 4546 2.048222 CGAGGAAGCAAGGCACGA 60.048 61.111 0.00 0.00 0.00 4.35
2873 4548 1.743252 GAGGAAGCAAGGCACGAGG 60.743 63.158 0.00 0.00 0.00 4.63
2895 4570 0.990374 ATCTCCTGGACAAGCTTGCT 59.010 50.000 26.27 13.39 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 61 4.699735 TCAGTGTCAGTTGATGTTTTGTGT 59.300 37.500 0.00 0.00 0.00 3.72
62 64 5.512788 GTGTTCAGTGTCAGTTGATGTTTTG 59.487 40.000 0.00 0.00 0.00 2.44
196 198 1.536149 GTGCGTGATACGTCTCTGAC 58.464 55.000 0.00 0.00 44.73 3.51
240 244 2.183555 GACGCGAAAGACCGGGAT 59.816 61.111 15.93 0.00 43.85 3.85
251 255 0.525455 CCGACATTGATCAGACGCGA 60.525 55.000 15.93 0.00 0.00 5.87
260 264 1.544246 TCACGTCACTCCGACATTGAT 59.456 47.619 0.00 0.00 45.70 2.57
266 270 1.081376 CCAGTCACGTCACTCCGAC 60.081 63.158 0.00 0.00 41.62 4.79
273 277 1.535444 ACCCCATCCAGTCACGTCA 60.535 57.895 0.00 0.00 0.00 4.35
291 295 7.764617 ACCCATTTGATTGTGGTATATATCCA 58.235 34.615 0.00 0.00 33.55 3.41
350 354 1.812571 GTAGGTTTCTCGGTCGGTGTA 59.187 52.381 0.00 0.00 0.00 2.90
357 361 0.896226 GCTGGAGTAGGTTTCTCGGT 59.104 55.000 0.00 0.00 33.26 4.69
365 369 3.391382 GCGGGTGCTGGAGTAGGT 61.391 66.667 0.00 0.00 38.39 3.08
368 372 2.345991 GTTGCGGGTGCTGGAGTA 59.654 61.111 0.00 0.00 43.34 2.59
369 373 4.988598 CGTTGCGGGTGCTGGAGT 62.989 66.667 0.00 0.00 43.34 3.85
370 374 4.680237 TCGTTGCGGGTGCTGGAG 62.680 66.667 0.00 0.00 43.34 3.86
371 375 4.980805 GTCGTTGCGGGTGCTGGA 62.981 66.667 0.00 0.00 43.34 3.86
373 377 4.012895 GTGTCGTTGCGGGTGCTG 62.013 66.667 0.00 0.00 43.34 4.41
375 379 3.308878 GATGTGTCGTTGCGGGTGC 62.309 63.158 0.00 0.00 43.20 5.01
376 380 1.958715 TGATGTGTCGTTGCGGGTG 60.959 57.895 0.00 0.00 0.00 4.61
377 381 1.959226 GTGATGTGTCGTTGCGGGT 60.959 57.895 0.00 0.00 0.00 5.28
380 384 2.202046 GCGTGATGTGTCGTTGCG 60.202 61.111 0.00 0.00 0.00 4.85
381 385 1.154599 CAGCGTGATGTGTCGTTGC 60.155 57.895 0.00 0.00 32.57 4.17
382 386 1.154599 GCAGCGTGATGTGTCGTTG 60.155 57.895 0.00 0.00 40.21 4.10
384 388 1.300931 AAGCAGCGTGATGTGTCGT 60.301 52.632 0.00 0.00 0.00 4.34
385 389 1.131218 CAAGCAGCGTGATGTGTCG 59.869 57.895 1.43 0.00 0.00 4.35
392 396 2.031012 CCAGACCAAGCAGCGTGA 59.969 61.111 10.26 0.00 0.00 4.35
412 416 2.374504 CCTCCTCCTCCATGCATATGTT 59.625 50.000 0.00 0.00 32.21 2.71
422 426 5.796502 AAATTATTGAACCTCCTCCTCCA 57.203 39.130 0.00 0.00 0.00 3.86
489 493 9.862371 TTTCATGCCGTATAAATTTGTTATGTT 57.138 25.926 0.00 0.00 0.00 2.71
490 494 9.515020 CTTTCATGCCGTATAAATTTGTTATGT 57.485 29.630 0.00 0.00 0.00 2.29
491 495 9.515020 ACTTTCATGCCGTATAAATTTGTTATG 57.485 29.630 0.00 0.00 0.00 1.90
493 497 9.991388 GTACTTTCATGCCGTATAAATTTGTTA 57.009 29.630 0.00 0.00 0.00 2.41
494 498 8.516234 TGTACTTTCATGCCGTATAAATTTGTT 58.484 29.630 0.00 0.00 0.00 2.83
495 499 8.046294 TGTACTTTCATGCCGTATAAATTTGT 57.954 30.769 0.00 0.00 0.00 2.83
496 500 9.515020 AATGTACTTTCATGCCGTATAAATTTG 57.485 29.630 0.00 0.00 0.00 2.32
497 501 9.730420 GAATGTACTTTCATGCCGTATAAATTT 57.270 29.630 14.79 0.00 0.00 1.82
498 502 8.898761 TGAATGTACTTTCATGCCGTATAAATT 58.101 29.630 17.62 0.00 30.82 1.82
499 503 8.445275 TGAATGTACTTTCATGCCGTATAAAT 57.555 30.769 17.62 0.00 30.82 1.40
500 504 7.851387 TGAATGTACTTTCATGCCGTATAAA 57.149 32.000 17.62 0.00 30.82 1.40
501 505 7.851387 TTGAATGTACTTTCATGCCGTATAA 57.149 32.000 21.00 4.38 35.64 0.98
502 506 9.549078 TTATTGAATGTACTTTCATGCCGTATA 57.451 29.630 21.00 13.28 35.64 1.47
503 507 6.942532 ATTGAATGTACTTTCATGCCGTAT 57.057 33.333 21.00 10.39 35.64 3.06
504 508 7.851387 TTATTGAATGTACTTTCATGCCGTA 57.149 32.000 21.00 8.79 35.64 4.02
505 509 6.751514 TTATTGAATGTACTTTCATGCCGT 57.248 33.333 21.00 10.28 35.64 5.68
506 510 7.416817 TCATTATTGAATGTACTTTCATGCCG 58.583 34.615 21.00 11.39 42.71 5.69
609 613 4.082463 GTCCGCCCATTAACTTTGATCAAA 60.082 41.667 19.45 19.45 0.00 2.69
610 614 3.442273 GTCCGCCCATTAACTTTGATCAA 59.558 43.478 3.38 3.38 0.00 2.57
611 615 3.013921 GTCCGCCCATTAACTTTGATCA 58.986 45.455 0.00 0.00 0.00 2.92
612 616 3.279434 AGTCCGCCCATTAACTTTGATC 58.721 45.455 0.00 0.00 0.00 2.92
613 617 3.366052 AGTCCGCCCATTAACTTTGAT 57.634 42.857 0.00 0.00 0.00 2.57
614 618 2.871096 AGTCCGCCCATTAACTTTGA 57.129 45.000 0.00 0.00 0.00 2.69
615 619 5.576447 ATTTAGTCCGCCCATTAACTTTG 57.424 39.130 0.00 0.00 0.00 2.77
616 620 7.706100 TTTATTTAGTCCGCCCATTAACTTT 57.294 32.000 0.00 0.00 0.00 2.66
617 621 7.706100 TTTTATTTAGTCCGCCCATTAACTT 57.294 32.000 0.00 0.00 0.00 2.66
618 622 7.177041 TGTTTTTATTTAGTCCGCCCATTAACT 59.823 33.333 0.00 0.00 0.00 2.24
619 623 7.314393 TGTTTTTATTTAGTCCGCCCATTAAC 58.686 34.615 0.00 0.00 0.00 2.01
620 624 7.463961 TGTTTTTATTTAGTCCGCCCATTAA 57.536 32.000 0.00 0.00 0.00 1.40
621 625 7.463961 TTGTTTTTATTTAGTCCGCCCATTA 57.536 32.000 0.00 0.00 0.00 1.90
622 626 5.986501 TGTTTTTATTTAGTCCGCCCATT 57.013 34.783 0.00 0.00 0.00 3.16
623 627 5.986501 TTGTTTTTATTTAGTCCGCCCAT 57.013 34.783 0.00 0.00 0.00 4.00
624 628 5.535406 TCTTTGTTTTTATTTAGTCCGCCCA 59.465 36.000 0.00 0.00 0.00 5.36
625 629 6.016213 TCTTTGTTTTTATTTAGTCCGCCC 57.984 37.500 0.00 0.00 0.00 6.13
626 630 6.090783 CCTCTTTGTTTTTATTTAGTCCGCC 58.909 40.000 0.00 0.00 0.00 6.13
627 631 6.675026 ACCTCTTTGTTTTTATTTAGTCCGC 58.325 36.000 0.00 0.00 0.00 5.54
628 632 8.347035 TGAACCTCTTTGTTTTTATTTAGTCCG 58.653 33.333 0.00 0.00 0.00 4.79
635 639 9.750125 GTGAAGATGAACCTCTTTGTTTTTATT 57.250 29.630 0.00 0.00 35.63 1.40
636 640 8.912988 TGTGAAGATGAACCTCTTTGTTTTTAT 58.087 29.630 0.00 0.00 35.63 1.40
637 641 8.287439 TGTGAAGATGAACCTCTTTGTTTTTA 57.713 30.769 0.00 0.00 35.63 1.52
638 642 7.169158 TGTGAAGATGAACCTCTTTGTTTTT 57.831 32.000 0.00 0.00 35.63 1.94
639 643 6.773976 TGTGAAGATGAACCTCTTTGTTTT 57.226 33.333 0.00 0.00 35.63 2.43
640 644 6.773976 TTGTGAAGATGAACCTCTTTGTTT 57.226 33.333 0.00 0.00 35.63 2.83
641 645 6.603201 TCTTTGTGAAGATGAACCTCTTTGTT 59.397 34.615 0.00 0.00 36.99 2.83
642 646 6.122277 TCTTTGTGAAGATGAACCTCTTTGT 58.878 36.000 0.00 0.00 36.99 2.83
643 647 6.293845 CCTCTTTGTGAAGATGAACCTCTTTG 60.294 42.308 0.00 0.00 40.93 2.77
644 648 5.767168 CCTCTTTGTGAAGATGAACCTCTTT 59.233 40.000 0.00 0.00 40.93 2.52
645 649 5.072329 TCCTCTTTGTGAAGATGAACCTCTT 59.928 40.000 0.00 0.00 40.93 2.85
646 650 4.594920 TCCTCTTTGTGAAGATGAACCTCT 59.405 41.667 0.00 0.00 40.93 3.69
647 651 4.899502 TCCTCTTTGTGAAGATGAACCTC 58.100 43.478 0.00 0.00 40.93 3.85
648 652 4.982241 TCCTCTTTGTGAAGATGAACCT 57.018 40.909 0.00 0.00 40.93 3.50
649 653 4.637977 GGATCCTCTTTGTGAAGATGAACC 59.362 45.833 3.84 5.48 39.98 3.62
650 654 4.331168 CGGATCCTCTTTGTGAAGATGAAC 59.669 45.833 10.75 0.00 40.93 3.18
651 655 4.020218 ACGGATCCTCTTTGTGAAGATGAA 60.020 41.667 10.75 0.00 40.93 2.57
652 656 3.515502 ACGGATCCTCTTTGTGAAGATGA 59.484 43.478 10.75 0.00 40.93 2.92
663 667 4.202050 GCATTATTTTGCACGGATCCTCTT 60.202 41.667 10.75 0.00 42.31 2.85
666 670 2.362077 GGCATTATTTTGCACGGATCCT 59.638 45.455 10.75 0.00 44.59 3.24
672 676 4.043750 CCATGTAGGCATTATTTTGCACG 58.956 43.478 0.00 0.00 44.59 5.34
712 716 1.741770 CTGTGTTGACCGGCTAGCC 60.742 63.158 24.75 24.75 0.00 3.93
739 743 2.332063 AAGTGGTCCATTGCTATCGG 57.668 50.000 0.00 0.00 0.00 4.18
741 745 5.880332 TCTTTGTAAGTGGTCCATTGCTATC 59.120 40.000 0.00 0.00 0.00 2.08
751 761 7.298854 GCAGTCTTAAATCTTTGTAAGTGGTC 58.701 38.462 0.00 0.00 0.00 4.02
756 766 7.217070 GCAATCGCAGTCTTAAATCTTTGTAAG 59.783 37.037 0.00 0.00 38.36 2.34
776 786 6.979817 TCCCAAATCTATGAAAAATGCAATCG 59.020 34.615 0.00 0.00 0.00 3.34
823 834 4.732285 ATACATGCGCAGTGCTAATTAC 57.268 40.909 18.32 0.00 46.63 1.89
831 842 4.568359 AGAGAGTAAAATACATGCGCAGTG 59.432 41.667 18.32 16.48 0.00 3.66
834 845 6.072728 ACAAAAGAGAGTAAAATACATGCGCA 60.073 34.615 14.96 14.96 0.00 6.09
842 853 7.664318 GGACCCAGAACAAAAGAGAGTAAAATA 59.336 37.037 0.00 0.00 0.00 1.40
854 865 2.693074 GCAAAGAGGACCCAGAACAAAA 59.307 45.455 0.00 0.00 0.00 2.44
882 893 8.360390 AGGAAAGAAATTACAAACCAGTCATTC 58.640 33.333 0.00 0.00 0.00 2.67
1090 1111 0.318762 AGGAACACCAGCTCGAGAAC 59.681 55.000 18.75 0.00 0.00 3.01
1296 1323 4.842292 GGGACGAATACGGGGTTC 57.158 61.111 0.00 0.00 44.46 3.62
1390 1424 2.504681 GCCGCAATCGCCAAACTG 60.505 61.111 0.00 0.00 33.11 3.16
1603 1673 0.307760 CACGTCACCCTGAAGTTTGC 59.692 55.000 0.00 0.00 36.99 3.68
1740 1857 1.227823 TGCGAAATAGATGGGGGCG 60.228 57.895 0.00 0.00 0.00 6.13
1991 2125 2.305927 TGAGGAATTGAGAACCTGGGAC 59.694 50.000 0.00 0.00 33.89 4.46
1992 2126 2.631384 TGAGGAATTGAGAACCTGGGA 58.369 47.619 0.00 0.00 33.89 4.37
1993 2127 3.245052 ACTTGAGGAATTGAGAACCTGGG 60.245 47.826 0.00 0.00 33.89 4.45
2036 2170 2.223923 GCACACATGGTCCTCTAGCTAG 60.224 54.545 15.01 15.01 0.00 3.42
2037 2171 1.757118 GCACACATGGTCCTCTAGCTA 59.243 52.381 0.00 0.00 0.00 3.32
2038 2172 0.539051 GCACACATGGTCCTCTAGCT 59.461 55.000 0.00 0.00 0.00 3.32
2039 2173 0.462759 GGCACACATGGTCCTCTAGC 60.463 60.000 0.00 0.00 0.00 3.42
2061 2200 0.106569 TGCCACTTGATGCCTATGGG 60.107 55.000 0.00 0.00 0.00 4.00
2194 2360 4.932200 CCTGAAGACCAGACTAATGTTCAC 59.068 45.833 0.00 0.00 45.78 3.18
2300 2470 6.472887 TCTCCCCTACACAAAACTTTATCAG 58.527 40.000 0.00 0.00 0.00 2.90
2301 2471 6.442541 TCTCCCCTACACAAAACTTTATCA 57.557 37.500 0.00 0.00 0.00 2.15
2305 2475 8.541899 TTTTATTCTCCCCTACACAAAACTTT 57.458 30.769 0.00 0.00 0.00 2.66
2328 2498 7.118390 CGGAGAGAAGATCATACAGTTGTTTTT 59.882 37.037 0.00 0.00 0.00 1.94
2336 2506 5.506686 TCAACGGAGAGAAGATCATACAG 57.493 43.478 0.00 0.00 0.00 2.74
2347 2517 7.979444 AAAGAAACATATTTCAACGGAGAGA 57.021 32.000 0.00 0.00 45.78 3.10
2348 2518 9.760660 CTAAAAGAAACATATTTCAACGGAGAG 57.239 33.333 0.00 0.00 45.78 3.20
2349 2519 9.496873 TCTAAAAGAAACATATTTCAACGGAGA 57.503 29.630 0.00 0.00 45.78 3.71
2350 2520 9.760660 CTCTAAAAGAAACATATTTCAACGGAG 57.239 33.333 0.00 0.00 45.78 4.63
2351 2521 9.496873 TCTCTAAAAGAAACATATTTCAACGGA 57.503 29.630 0.00 0.00 45.78 4.69
2429 2621 2.258726 GGGTCAACAGACGGCCAAC 61.259 63.158 2.24 0.00 33.01 3.77
2447 2639 1.604693 GCGACCATCTATAACCCCGTG 60.605 57.143 0.00 0.00 0.00 4.94
2448 2640 0.677842 GCGACCATCTATAACCCCGT 59.322 55.000 0.00 0.00 0.00 5.28
2450 2642 1.968493 TCTGCGACCATCTATAACCCC 59.032 52.381 0.00 0.00 0.00 4.95
2648 2867 6.109359 CGAGAATCTGGTCTTTTCCTACAAT 58.891 40.000 0.00 0.00 0.00 2.71
2738 3007 2.277084 GTCGGTCACTGTCAAGTTTGT 58.723 47.619 0.00 0.00 32.98 2.83
2739 3008 1.257936 CGTCGGTCACTGTCAAGTTTG 59.742 52.381 0.00 0.00 32.98 2.93
2740 3009 1.135527 TCGTCGGTCACTGTCAAGTTT 59.864 47.619 0.00 0.00 32.98 2.66
2797 4472 5.507482 CGCCTTATAATCTTCCTCGTCTTCA 60.507 44.000 0.00 0.00 0.00 3.02
2806 4481 4.025979 CACACGTTCGCCTTATAATCTTCC 60.026 45.833 0.00 0.00 0.00 3.46
2814 4489 0.390735 GGACCACACGTTCGCCTTAT 60.391 55.000 0.00 0.00 0.00 1.73
2830 4505 3.412879 GACGCCCACGAGCTAGGAC 62.413 68.421 0.00 0.00 43.93 3.85
2848 4523 2.097038 CCTTGCTTCCTCGCTGTCG 61.097 63.158 0.00 0.00 0.00 4.35
2873 4548 2.163211 GCAAGCTTGTCCAGGAGATTTC 59.837 50.000 26.55 2.37 0.00 2.17
2883 4558 1.294659 CTGTCCGAGCAAGCTTGTCC 61.295 60.000 26.55 17.11 0.00 4.02
2895 4570 2.680352 GCACCCTCCTCTGTCCGA 60.680 66.667 0.00 0.00 0.00 4.55


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

AutoCloner maintained by Alex Coulton.