Multiple sequence alignment - TraesCS4D01G072500

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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 TraesCS4D01G072500 chr4D 100.000 6718 0 0 1 6718 47492921 47499638 0.000000e+00 12406.0
1 TraesCS4D01G072500 chr4D 77.095 179 34 7 6197 6372 211055645 211055819 5.550000e-16 97.1
2 TraesCS4D01G072500 chr4B 95.954 2620 79 21 3256 5860 69317271 69319878 0.000000e+00 4226.0
3 TraesCS4D01G072500 chr4B 93.208 2076 90 20 870 2904 69312550 69314615 0.000000e+00 3005.0
4 TraesCS4D01G072500 chr4B 89.747 673 47 13 1 666 69311379 69312036 0.000000e+00 841.0
5 TraesCS4D01G072500 chr4B 87.832 641 36 19 6049 6683 69319891 69320495 0.000000e+00 713.0
6 TraesCS4D01G072500 chr4B 97.039 304 8 1 2900 3202 69316970 69317273 1.670000e-140 510.0
7 TraesCS4D01G072500 chr4B 77.654 179 33 7 6197 6372 327535920 327536094 1.190000e-17 102.0
8 TraesCS4D01G072500 chr4A 95.692 2066 50 9 4655 6718 550496448 550494420 0.000000e+00 3286.0
9 TraesCS4D01G072500 chr4A 91.326 1637 91 25 1 1611 550501489 550499878 0.000000e+00 2189.0
10 TraesCS4D01G072500 chr4A 91.766 1008 62 11 2856 3857 550499044 550498052 0.000000e+00 1382.0
11 TraesCS4D01G072500 chr4A 96.055 507 19 1 4112 4618 550496952 550496447 0.000000e+00 824.0
12 TraesCS4D01G072500 chr4A 91.000 500 31 9 1661 2159 550499534 550499048 0.000000e+00 662.0
13 TraesCS4D01G072500 chr4A 95.273 275 12 1 3870 4143 550497258 550496984 1.030000e-117 435.0
14 TraesCS4D01G072500 chr4A 90.741 54 3 1 6112 6165 379043571 379043622 3.360000e-08 71.3
15 TraesCS4D01G072500 chr7B 81.595 163 20 9 2294 2451 5497283 5497126 7.070000e-25 126.0
16 TraesCS4D01G072500 chr7D 80.702 171 19 13 2295 2459 7719369 7719207 3.290000e-23 121.0
17 TraesCS4D01G072500 chr6A 80.702 171 17 15 2299 2460 457611075 457611238 1.180000e-22 119.0
18 TraesCS4D01G072500 chr6A 86.111 72 6 4 6102 6171 134174223 134174292 2.600000e-09 75.0
19 TraesCS4D01G072500 chr3D 80.447 179 16 17 2292 2461 324408328 324408160 1.180000e-22 119.0
20 TraesCS4D01G072500 chr5D 81.132 159 18 12 2295 2445 361150378 361150532 4.260000e-22 117.0
21 TraesCS4D01G072500 chr5D 80.000 175 20 14 2294 2461 438945984 438945818 1.530000e-21 115.0
22 TraesCS4D01G072500 chr5D 79.235 183 25 12 2294 2469 467851709 467851885 1.530000e-21 115.0
23 TraesCS4D01G072500 chr5D 83.333 72 10 2 6111 6182 485358335 485358404 1.560000e-06 65.8
24 TraesCS4D01G072500 chr1A 80.925 173 11 19 2296 2459 20253257 20253416 4.260000e-22 117.0
25 TraesCS4D01G072500 chr6B 87.692 65 7 1 6107 6171 198379037 198379100 2.600000e-09 75.0
26 TraesCS4D01G072500 chr6D 89.474 57 3 3 6126 6181 157976961 157976907 1.210000e-07 69.4
27 TraesCS4D01G072500 chr1D 90.566 53 2 3 6110 6162 445041143 445041094 4.350000e-07 67.6
28 TraesCS4D01G072500 chr5B 86.885 61 5 3 6110 6170 660592550 660592607 1.560000e-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 TraesCS4D01G072500 chr4D 47492921 47499638 6717 False 12406 12406 100.000000 1 6718 1 chr4D.!!$F1 6717
1 TraesCS4D01G072500 chr4B 69311379 69320495 9116 False 1859 4226 92.756000 1 6683 5 chr4B.!!$F2 6682
2 TraesCS4D01G072500 chr4A 550494420 550501489 7069 True 1463 3286 93.518667 1 6718 6 chr4A.!!$R1 6717

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
312 317 0.392193 ATCGAGGCAAAGCACAGAGG 60.392 55.000 0.00 0.0 0.00 3.69 F
1254 1589 0.034337 TTCCTCCGTCTTCCCGTTTG 59.966 55.000 0.00 0.0 0.00 2.93 F
1383 1736 0.985549 CACGAAGCTTGCTCTACGAC 59.014 55.000 2.10 0.0 0.00 4.34 F
1637 1993 1.106285 CCATTGGCTCTTGGGTAAGC 58.894 55.000 0.00 0.0 37.80 3.09 F
2474 3128 0.394216 AAAGCATCATACAGCGGCCA 60.394 50.000 2.24 0.0 35.48 5.36 F
3687 6705 0.110486 GGCCTGTTGGTTCCTTCTGA 59.890 55.000 0.00 0.0 35.27 3.27 F
4208 8072 2.833794 AGACGCACAGCAGAACTAAAA 58.166 42.857 0.00 0.0 0.00 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1922 2574 0.251354 TGCCAGATGAGACTCTTGGC 59.749 55.000 26.05 26.05 38.68 4.52 R
2375 3029 0.528901 GCTACCGTGTGTGTGTGTCA 60.529 55.000 0.00 0.00 0.00 3.58 R
2387 3041 0.944311 CTTTGCTCGTGTGCTACCGT 60.944 55.000 0.00 0.00 0.00 4.83 R
2671 3325 2.545742 GGCAGGAAAATGTGTTGGTCAC 60.546 50.000 0.00 0.00 46.31 3.67 R
3944 7745 1.293179 GAGCAATGGGGGTGCAAAC 59.707 57.895 0.00 0.00 44.74 2.93 R
5141 9018 3.242220 GCATCTTAGACGCATCACAACAG 60.242 47.826 0.00 0.00 0.00 3.16 R
6058 9937 0.103390 TTCGTCGTCTCAGTTGGCAA 59.897 50.000 0.00 0.00 0.00 4.52 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
131 133 5.379732 TTTATTACAAGGGGCACGAAAAG 57.620 39.130 0.00 0.00 0.00 2.27
252 254 6.223852 ACATCACAGACTCGTTAAACTTGAT 58.776 36.000 0.00 0.00 0.00 2.57
281 286 1.905354 GGGCCAGGCAGGAATATGC 60.905 63.158 15.19 0.00 45.74 3.14
312 317 0.392193 ATCGAGGCAAAGCACAGAGG 60.392 55.000 0.00 0.00 0.00 3.69
354 359 4.873259 GGACCAGAAAGATAGCTCAAGAAC 59.127 45.833 0.00 0.00 0.00 3.01
396 401 2.092592 GTCAACCGGGGATTACCAAGAT 60.093 50.000 6.32 0.00 42.91 2.40
433 438 1.030457 TAGAAAGATCGCTCGGGGAC 58.970 55.000 0.00 0.00 0.00 4.46
434 439 0.970937 AGAAAGATCGCTCGGGGACA 60.971 55.000 0.00 0.00 0.00 4.02
435 440 0.528684 GAAAGATCGCTCGGGGACAG 60.529 60.000 0.00 0.00 0.00 3.51
436 441 0.970937 AAAGATCGCTCGGGGACAGA 60.971 55.000 0.00 0.00 0.00 3.41
437 442 1.388065 AAGATCGCTCGGGGACAGAG 61.388 60.000 0.00 0.00 38.68 3.35
438 443 2.043852 ATCGCTCGGGGACAGAGT 60.044 61.111 0.00 0.00 37.99 3.24
439 444 2.343163 GATCGCTCGGGGACAGAGTG 62.343 65.000 4.02 4.02 44.91 3.51
440 445 4.135153 CGCTCGGGGACAGAGTGG 62.135 72.222 2.68 0.00 41.19 4.00
441 446 2.680352 GCTCGGGGACAGAGTGGA 60.680 66.667 0.00 0.00 37.99 4.02
443 448 1.592223 CTCGGGGACAGAGTGGAAC 59.408 63.158 0.00 0.00 0.00 3.62
461 470 0.759346 ACTCCAAAGACGCAGAAGGT 59.241 50.000 0.00 0.00 0.00 3.50
501 510 6.923928 TCACAATTTATCAGAATCGCATGA 57.076 33.333 0.00 0.00 0.00 3.07
591 600 2.031683 GGATCGCCGAAAACTATTGGTG 59.968 50.000 0.00 0.00 35.95 4.17
597 606 4.473199 GCCGAAAACTATTGGTGAAGAAC 58.527 43.478 0.00 0.00 0.00 3.01
669 680 3.861797 CGGTCCTGAATCCGGGGG 61.862 72.222 0.00 0.00 42.61 5.40
677 688 4.516326 AATCCGGGGGAGGGAGGG 62.516 72.222 0.00 0.00 36.91 4.30
773 784 2.674462 CGACTGGTACGAGTCTCTCAGA 60.674 54.545 28.38 0.00 40.33 3.27
779 790 4.255301 GGTACGAGTCTCTCAGAAGAAGA 58.745 47.826 0.00 0.00 0.00 2.87
792 803 5.436175 TCAGAAGAAGACAGAGATCGAGAT 58.564 41.667 0.00 0.00 0.00 2.75
857 868 1.516386 CGACGAACCCGATGAGGTG 60.516 63.158 0.00 0.00 40.05 4.00
858 869 1.590147 GACGAACCCGATGAGGTGT 59.410 57.895 0.00 0.00 40.05 4.16
859 870 0.813184 GACGAACCCGATGAGGTGTA 59.187 55.000 0.00 0.00 40.05 2.90
860 871 0.815734 ACGAACCCGATGAGGTGTAG 59.184 55.000 0.00 0.00 40.05 2.74
863 874 1.623542 AACCCGATGAGGTGTAGGGC 61.624 60.000 0.00 0.00 45.75 5.19
864 875 1.762460 CCCGATGAGGTGTAGGGCT 60.762 63.158 0.00 0.00 38.74 5.19
865 876 0.469331 CCCGATGAGGTGTAGGGCTA 60.469 60.000 0.00 0.00 38.74 3.93
975 1310 4.063967 TACGAGCCACACGCCCAG 62.064 66.667 0.00 0.00 38.78 4.45
1250 1585 2.722201 CCCTTCCTCCGTCTTCCCG 61.722 68.421 0.00 0.00 0.00 5.14
1253 1588 0.320697 CTTCCTCCGTCTTCCCGTTT 59.679 55.000 0.00 0.00 0.00 3.60
1254 1589 0.034337 TTCCTCCGTCTTCCCGTTTG 59.966 55.000 0.00 0.00 0.00 2.93
1346 1681 1.873903 GCAGCTTCGTTCAGACCTTCA 60.874 52.381 0.00 0.00 0.00 3.02
1358 1693 6.149474 CGTTCAGACCTTCACTTATCCAAATT 59.851 38.462 0.00 0.00 0.00 1.82
1365 1718 8.472007 ACCTTCACTTATCCAAATTGTAAACA 57.528 30.769 0.00 0.00 0.00 2.83
1379 1732 3.985008 TGTAAACACGAAGCTTGCTCTA 58.015 40.909 2.10 0.00 0.00 2.43
1380 1733 3.739300 TGTAAACACGAAGCTTGCTCTAC 59.261 43.478 2.10 0.00 0.00 2.59
1383 1736 0.985549 CACGAAGCTTGCTCTACGAC 59.014 55.000 2.10 0.00 0.00 4.34
1395 1748 3.181490 TGCTCTACGACAATGCGTAATCT 60.181 43.478 10.11 0.00 44.98 2.40
1409 1762 9.046296 CAATGCGTAATCTAAGAAACCTCTAAT 57.954 33.333 0.00 0.00 0.00 1.73
1424 1779 4.202161 ACCTCTAATTCTGTGTCGCCATAG 60.202 45.833 0.00 0.00 0.00 2.23
1470 1825 7.538575 AGGTGCTTGTACATGAATTGAATAAC 58.461 34.615 12.65 0.00 0.00 1.89
1533 1889 1.129058 ACCTATTTAGTGAGGGGCGG 58.871 55.000 0.00 0.00 37.14 6.13
1561 1917 4.757594 TCATTGCTTTGAACAGCTTTGTT 58.242 34.783 0.00 0.00 40.79 2.83
1597 1953 4.279420 AGCTCTACGAAGATGATGTATGCA 59.721 41.667 0.00 0.00 0.00 3.96
1617 1973 4.901868 GCATTTGCATATTGGATTCCCAT 58.098 39.130 0.00 0.00 40.84 4.00
1637 1993 1.106285 CCATTGGCTCTTGGGTAAGC 58.894 55.000 0.00 0.00 37.80 3.09
1651 2007 3.054361 TGGGTAAGCTGATCCCTTCTTTC 60.054 47.826 17.99 0.00 41.58 2.62
1652 2008 3.054361 GGGTAAGCTGATCCCTTCTTTCA 60.054 47.826 12.22 0.00 38.29 2.69
1703 2353 6.801862 GGAAGTTTTTGACGACCAATATCTTG 59.198 38.462 0.00 0.00 34.23 3.02
1727 2377 5.249393 GGGAGGATTATAGAGCATTTCCAGA 59.751 44.000 0.00 0.00 0.00 3.86
1731 2381 7.173722 AGGATTATAGAGCATTTCCAGATTGG 58.826 38.462 0.00 0.00 39.43 3.16
1742 2392 6.458210 CATTTCCAGATTGGGGTATAAATGC 58.542 40.000 6.38 0.00 38.32 3.56
1845 2496 2.100584 TCGCTCAAAACTGGCAAAATGT 59.899 40.909 0.00 0.00 0.00 2.71
1862 2513 5.783100 AAATGTGTGCAGTTCAACTTTTG 57.217 34.783 0.00 0.00 0.00 2.44
1863 2514 2.605030 TGTGTGCAGTTCAACTTTTGC 58.395 42.857 0.00 0.00 37.09 3.68
1864 2515 2.230992 TGTGTGCAGTTCAACTTTTGCT 59.769 40.909 2.30 0.00 37.45 3.91
1865 2516 3.441922 TGTGTGCAGTTCAACTTTTGCTA 59.558 39.130 2.30 0.00 37.45 3.49
1921 2573 5.393461 GCCATTTCCTTTTGTGGAGTATGAG 60.393 44.000 0.00 0.00 37.43 2.90
1922 2574 5.126061 CCATTTCCTTTTGTGGAGTATGAGG 59.874 44.000 0.00 0.00 37.43 3.86
1923 2575 3.350219 TCCTTTTGTGGAGTATGAGGC 57.650 47.619 0.00 0.00 0.00 4.70
1955 2607 6.017400 TCATCTGGCAATCTTTTCTTGAAC 57.983 37.500 0.00 0.00 0.00 3.18
2009 2661 7.654022 ACCAAAAGTTTGAACTAATGGAGAA 57.346 32.000 23.65 0.00 42.77 2.87
2011 2663 7.147976 CCAAAAGTTTGAACTAATGGAGAAGG 58.852 38.462 16.79 0.00 42.77 3.46
2023 2675 2.348472 TGGAGAAGGTTGGACAATCCT 58.652 47.619 0.00 2.93 37.46 3.24
2030 2682 6.552008 AGAAGGTTGGACAATCCTCATAAAA 58.448 36.000 6.64 0.00 37.46 1.52
2170 2822 2.673258 TCTATCCGGTGGATTGCTACA 58.327 47.619 0.00 0.00 39.79 2.74
2273 2925 7.319646 TGATTCACAGCCGCTTTAATTTATTT 58.680 30.769 0.00 0.00 0.00 1.40
2351 3003 1.876416 GCAAACCACTAGAGCCAACGA 60.876 52.381 0.00 0.00 0.00 3.85
2369 3023 5.449862 CCAACGAGTTCAACAAAGATCCAAA 60.450 40.000 0.00 0.00 0.00 3.28
2375 3029 5.363580 AGTTCAACAAAGATCCAAACCACAT 59.636 36.000 0.00 0.00 0.00 3.21
2387 3041 2.121291 AACCACATGACACACACACA 57.879 45.000 0.00 0.00 0.00 3.72
2388 3042 1.378531 ACCACATGACACACACACAC 58.621 50.000 0.00 0.00 0.00 3.82
2404 3058 1.663388 CACGGTAGCACACGAGCAA 60.663 57.895 0.00 0.00 36.85 3.91
2414 3068 1.457303 CACACGAGCAAAGTACAGAGC 59.543 52.381 0.00 0.00 0.00 4.09
2471 3125 4.882671 AACTAAAAGCATCATACAGCGG 57.117 40.909 0.00 0.00 35.48 5.52
2474 3128 0.394216 AAAGCATCATACAGCGGCCA 60.394 50.000 2.24 0.00 35.48 5.36
2546 3200 4.262635 GGAAATGTGGAGAAGAGTGAGTCA 60.263 45.833 0.00 0.00 0.00 3.41
2671 3325 7.412672 GCCCAAGAAACACTACTAAACGAATAG 60.413 40.741 0.00 0.00 0.00 1.73
2739 3393 5.043732 TGGTTGGGTGGAAGGAACATAATAT 60.044 40.000 0.00 0.00 0.00 1.28
2783 3437 6.783892 TTCATTTGTGCTGGCTTTAAATTC 57.216 33.333 0.00 0.00 0.00 2.17
2824 3478 5.655090 TGTAGCTTACTAGATGCACAGGTTA 59.345 40.000 0.00 0.00 27.07 2.85
2872 3526 8.578448 TGAATCACCATTCATCTTAATTGTCA 57.422 30.769 0.00 0.00 42.99 3.58
3119 6135 1.394917 CTCGATTTGAAGCGGAACCTG 59.605 52.381 1.35 0.00 38.53 4.00
3346 6363 2.090967 CCAAACGAATCAAAATGCTGCG 59.909 45.455 0.00 0.00 0.00 5.18
3367 6384 4.083802 GCGGTATTTATTCCATGAGCTGAC 60.084 45.833 0.00 0.00 0.00 3.51
3399 6416 5.376854 ACTCTTGCATTAGTTTTTCGCAT 57.623 34.783 0.00 0.00 31.67 4.73
3406 6423 7.082700 TGCATTAGTTTTTCGCATATCTCAA 57.917 32.000 0.00 0.00 0.00 3.02
3631 6649 8.442632 TGATGATCAACTGGTAGATTCATTTC 57.557 34.615 0.00 0.00 0.00 2.17
3669 6687 4.181010 CCTCCACATGCCTCCGGG 62.181 72.222 0.00 0.00 0.00 5.73
3687 6705 0.110486 GGCCTGTTGGTTCCTTCTGA 59.890 55.000 0.00 0.00 35.27 3.27
3845 6863 4.635765 TCTTTTGCCCTTGATAATCTGTCG 59.364 41.667 0.00 0.00 0.00 4.35
4208 8072 2.833794 AGACGCACAGCAGAACTAAAA 58.166 42.857 0.00 0.00 0.00 1.52
4424 8288 4.401022 TGAGTGTCTTCAATGCCAGATTT 58.599 39.130 0.00 0.00 0.00 2.17
4428 8292 6.182627 AGTGTCTTCAATGCCAGATTTATGA 58.817 36.000 0.00 0.00 0.00 2.15
4586 8450 8.938801 AATAATCCCTACATTGTATGCATTGA 57.061 30.769 3.54 0.00 32.21 2.57
4627 8491 3.568007 TGCTGGTTCCAACTAAATGTGAC 59.432 43.478 0.00 0.00 0.00 3.67
4628 8492 3.568007 GCTGGTTCCAACTAAATGTGACA 59.432 43.478 0.00 0.00 0.00 3.58
4629 8493 4.320494 GCTGGTTCCAACTAAATGTGACAG 60.320 45.833 0.00 0.00 0.00 3.51
4630 8494 5.042463 TGGTTCCAACTAAATGTGACAGA 57.958 39.130 0.00 0.00 0.00 3.41
4633 8497 6.039270 TGGTTCCAACTAAATGTGACAGAAAG 59.961 38.462 0.00 0.00 0.00 2.62
4676 8550 3.221771 CCATTCAACACTCAAACTGGGA 58.778 45.455 0.00 0.00 0.00 4.37
4731 8605 6.856895 GCTTTTGCATGAGTAGGTTAGAAAT 58.143 36.000 0.00 0.00 46.58 2.17
4780 8654 3.006967 AGCAGTGTTTCGATCTGGTACTT 59.993 43.478 9.25 0.00 37.99 2.24
4782 8656 3.123621 CAGTGTTTCGATCTGGTACTTGC 59.876 47.826 0.00 0.00 0.00 4.01
4783 8657 3.064207 GTGTTTCGATCTGGTACTTGCA 58.936 45.455 0.00 0.00 0.00 4.08
4980 8857 5.539955 ACTCAGTTATCCCTTTTGCACAAAT 59.460 36.000 0.00 0.00 0.00 2.32
5017 8894 4.756084 ATGACTAGTTTTTGCAGTCTGC 57.244 40.909 18.32 18.32 45.29 4.26
5053 8930 7.011828 ACGTGCATCTATACAAAACCAATAC 57.988 36.000 0.00 0.00 0.00 1.89
5141 9018 1.010350 CTCGGCAATTGCGCTGATC 60.010 57.895 23.48 8.10 45.97 2.92
5335 9213 7.720957 TGCATAGGCTCTATTTTGTATGTCATT 59.279 33.333 0.00 0.00 41.91 2.57
5356 9234 8.440833 GTCATTGTTTTCTAGTATTACAGCGTT 58.559 33.333 0.00 0.00 0.00 4.84
5439 9318 7.283127 TGATCCTTATTGTGCTTTCAACTATCC 59.717 37.037 0.00 0.00 0.00 2.59
5491 9370 1.785041 CTGGTGACAAGTTGTGGCCG 61.785 60.000 14.57 7.79 42.06 6.13
5502 9381 0.535335 TTGTGGCCGACAGAGGTATC 59.465 55.000 0.00 0.00 35.44 2.24
5948 9827 1.692395 TCAATCGCATGGAGGGGGA 60.692 57.895 0.00 0.00 0.00 4.81
5997 9876 5.312895 TGCTAGTGTTTGAAAAGATGGCTA 58.687 37.500 0.00 0.00 0.00 3.93
6005 9884 2.500098 TGAAAAGATGGCTACCTACGCT 59.500 45.455 0.00 0.00 0.00 5.07
6009 9888 1.409427 AGATGGCTACCTACGCTGTTC 59.591 52.381 0.00 0.00 0.00 3.18
6047 9926 3.603532 CAGCTCTTATTGCCAACTGAGA 58.396 45.455 7.17 0.00 0.00 3.27
6048 9927 3.373439 CAGCTCTTATTGCCAACTGAGAC 59.627 47.826 7.17 0.97 0.00 3.36
6049 9928 2.680339 GCTCTTATTGCCAACTGAGACC 59.320 50.000 7.17 0.00 0.00 3.85
6050 9929 3.869912 GCTCTTATTGCCAACTGAGACCA 60.870 47.826 7.17 0.00 0.00 4.02
6051 9930 3.937706 CTCTTATTGCCAACTGAGACCAG 59.062 47.826 0.00 0.00 45.76 4.00
6063 9942 3.942829 CTGAGACCAGTTCTTATTGCCA 58.057 45.455 0.00 0.00 33.22 4.92
6064 9943 4.326826 CTGAGACCAGTTCTTATTGCCAA 58.673 43.478 0.00 0.00 33.22 4.52
6065 9944 4.072131 TGAGACCAGTTCTTATTGCCAAC 58.928 43.478 0.00 0.00 33.22 3.77
6066 9945 4.202461 TGAGACCAGTTCTTATTGCCAACT 60.202 41.667 0.00 0.00 33.22 3.16
6067 9946 4.074970 AGACCAGTTCTTATTGCCAACTG 58.925 43.478 4.39 4.39 44.47 3.16
6068 9947 4.072131 GACCAGTTCTTATTGCCAACTGA 58.928 43.478 11.69 0.00 46.74 3.41
6069 9948 4.074970 ACCAGTTCTTATTGCCAACTGAG 58.925 43.478 11.69 5.61 46.74 3.35
6099 9978 2.508663 GTACGGAGCCACCTTCGC 60.509 66.667 0.00 0.00 44.09 4.70
6100 9979 4.124351 TACGGAGCCACCTTCGCG 62.124 66.667 0.00 0.00 44.09 5.87
6358 10239 6.018016 AGCAAATGAAACTAATTTGGTGTTGC 60.018 34.615 11.51 0.00 0.00 4.17
6661 10543 8.987599 AATTTATCGCGTATTAAGAACATGTG 57.012 30.769 5.77 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 133 0.254747 TGGGAACATGATTCGACCCC 59.745 55.000 0.00 0.00 36.82 4.95
252 254 0.896479 GCCTGGCCCCGACTTTTTAA 60.896 55.000 7.66 0.00 0.00 1.52
281 286 3.013276 TGCCTCGATTAGATTACTGCG 57.987 47.619 0.00 0.00 0.00 5.18
312 317 2.092807 TCCGGGTTTAGTTATTGGCTCC 60.093 50.000 0.00 0.00 0.00 4.70
386 391 6.668283 ACCGTCTGCCTATATATCTTGGTAAT 59.332 38.462 0.00 0.00 0.00 1.89
396 401 9.696572 ATCTTTCTAATACCGTCTGCCTATATA 57.303 33.333 0.00 0.00 0.00 0.86
438 443 0.756294 TCTGCGTCTTTGGAGTTCCA 59.244 50.000 0.00 0.00 45.94 3.53
439 444 1.801178 CTTCTGCGTCTTTGGAGTTCC 59.199 52.381 0.00 0.00 0.00 3.62
440 445 1.801178 CCTTCTGCGTCTTTGGAGTTC 59.199 52.381 0.00 0.00 0.00 3.01
441 446 1.141053 ACCTTCTGCGTCTTTGGAGTT 59.859 47.619 0.00 0.00 0.00 3.01
443 448 2.611518 CTACCTTCTGCGTCTTTGGAG 58.388 52.381 0.00 0.00 0.00 3.86
444 449 1.275291 CCTACCTTCTGCGTCTTTGGA 59.725 52.381 0.00 0.00 0.00 3.53
445 450 1.726853 CCTACCTTCTGCGTCTTTGG 58.273 55.000 0.00 0.00 0.00 3.28
446 451 1.079503 GCCTACCTTCTGCGTCTTTG 58.920 55.000 0.00 0.00 0.00 2.77
447 452 0.389948 CGCCTACCTTCTGCGTCTTT 60.390 55.000 0.00 0.00 43.12 2.52
448 453 1.215647 CGCCTACCTTCTGCGTCTT 59.784 57.895 0.00 0.00 43.12 3.01
449 454 2.885861 CGCCTACCTTCTGCGTCT 59.114 61.111 0.00 0.00 43.12 4.18
501 510 1.476074 CGCGAATTTGCAACAACTGT 58.524 45.000 17.78 0.00 34.15 3.55
552 561 0.391263 CCGTTCTTGGTGGTAGAGCC 60.391 60.000 0.00 0.00 37.90 4.70
586 595 1.270305 CCTCGCTGAGTTCTTCACCAA 60.270 52.381 5.15 0.00 0.00 3.67
591 600 0.174617 CTCCCCTCGCTGAGTTCTTC 59.825 60.000 5.15 0.00 0.00 2.87
597 606 3.465403 CCCACTCCCCTCGCTGAG 61.465 72.222 0.00 0.00 34.73 3.35
677 688 3.090532 ACTCGCCCTTCCATCCCC 61.091 66.667 0.00 0.00 0.00 4.81
681 692 3.411517 CCCCACTCGCCCTTCCAT 61.412 66.667 0.00 0.00 0.00 3.41
758 769 4.691685 TGTCTTCTTCTGAGAGACTCGTAC 59.308 45.833 14.64 0.00 34.22 3.67
773 784 4.531854 TCCATCTCGATCTCTGTCTTCTT 58.468 43.478 0.00 0.00 0.00 2.52
779 790 4.501229 GCTTCATTCCATCTCGATCTCTGT 60.501 45.833 0.00 0.00 0.00 3.41
792 803 2.707791 CCTCTCCCATAGCTTCATTCCA 59.292 50.000 0.00 0.00 0.00 3.53
857 868 1.830836 GGCCCAGTTCTAGCCCTAC 59.169 63.158 0.00 0.00 41.00 3.18
858 869 1.760875 CGGCCCAGTTCTAGCCCTA 60.761 63.158 0.00 0.00 44.13 3.53
859 870 3.083997 CGGCCCAGTTCTAGCCCT 61.084 66.667 0.00 0.00 44.13 5.19
860 871 4.176752 CCGGCCCAGTTCTAGCCC 62.177 72.222 0.00 0.00 44.13 5.19
862 873 2.871216 GAACCCGGCCCAGTTCTAGC 62.871 65.000 20.29 0.59 39.42 3.42
863 874 1.221021 GAACCCGGCCCAGTTCTAG 59.779 63.158 20.29 0.00 39.42 2.43
864 875 2.652095 CGAACCCGGCCCAGTTCTA 61.652 63.158 23.22 0.00 40.18 2.10
865 876 4.016706 CGAACCCGGCCCAGTTCT 62.017 66.667 23.22 0.00 40.18 3.01
975 1310 2.046604 GTGGGTAAGGTGGTCGCC 60.047 66.667 0.00 0.00 0.00 5.54
1250 1585 1.145162 CGGCAGCAACCAACACAAAC 61.145 55.000 0.00 0.00 0.00 2.93
1253 1588 3.898509 GCGGCAGCAACCAACACA 61.899 61.111 3.18 0.00 44.35 3.72
1346 1681 7.040686 AGCTTCGTGTTTACAATTTGGATAAGT 60.041 33.333 0.78 0.00 0.00 2.24
1358 1693 2.833794 AGAGCAAGCTTCGTGTTTACA 58.166 42.857 0.00 0.00 0.00 2.41
1365 1718 0.596577 TGTCGTAGAGCAAGCTTCGT 59.403 50.000 0.00 0.00 36.95 3.85
1379 1732 5.063060 GGTTTCTTAGATTACGCATTGTCGT 59.937 40.000 10.17 10.17 45.49 4.34
1380 1733 5.291128 AGGTTTCTTAGATTACGCATTGTCG 59.709 40.000 0.00 0.07 0.00 4.35
1383 1736 6.910536 AGAGGTTTCTTAGATTACGCATTG 57.089 37.500 0.00 0.00 0.00 2.82
1395 1748 5.867716 GCGACACAGAATTAGAGGTTTCTTA 59.132 40.000 0.00 0.00 34.79 2.10
1424 1779 8.538039 GCACCTTAACTACGAATATTTACTGTC 58.462 37.037 0.00 0.00 0.00 3.51
1433 1788 6.923012 TGTACAAGCACCTTAACTACGAATA 58.077 36.000 0.00 0.00 0.00 1.75
1507 1863 5.163131 GCCCCTCACTAAATAGGTAATGGAA 60.163 44.000 0.00 0.00 0.00 3.53
1508 1864 4.349930 GCCCCTCACTAAATAGGTAATGGA 59.650 45.833 0.00 0.00 0.00 3.41
1533 1889 3.883997 TTCAAAGCAATGAACCGGC 57.116 47.368 0.00 0.00 34.50 6.13
1561 1917 4.311606 TCGTAGAGCTGCAAATTACACAA 58.688 39.130 1.02 0.00 0.00 3.33
1597 1953 5.156649 TGGATGGGAATCCAATATGCAAAT 58.843 37.500 4.96 0.00 46.90 2.32
1614 1970 4.251443 CTTACCCAAGAGCCAATGGATGG 61.251 52.174 2.05 5.17 42.38 3.51
1617 1973 1.340991 GCTTACCCAAGAGCCAATGGA 60.341 52.381 2.05 0.00 39.12 3.41
1637 1993 3.659183 ATGGGTGAAAGAAGGGATCAG 57.341 47.619 0.00 0.00 0.00 2.90
1703 2353 5.249393 TCTGGAAATGCTCTATAATCCTCCC 59.751 44.000 0.00 0.00 0.00 4.30
1727 2377 4.532834 ACGACAAGCATTTATACCCCAAT 58.467 39.130 0.00 0.00 0.00 3.16
1731 2381 3.377172 AGCAACGACAAGCATTTATACCC 59.623 43.478 0.00 0.00 0.00 3.69
1742 2392 3.904136 ATTCTTCCAAGCAACGACAAG 57.096 42.857 0.00 0.00 0.00 3.16
1845 2496 4.916983 ATAGCAAAAGTTGAACTGCACA 57.083 36.364 10.09 0.00 37.26 4.57
1862 2513 9.333724 TGCCCAAAAAGTACTAAATACTATAGC 57.666 33.333 0.00 0.00 43.79 2.97
1891 2543 3.831911 CCACAAAAGGAAATGGCCTAAGA 59.168 43.478 3.32 0.00 37.26 2.10
1904 2556 2.290896 TGGCCTCATACTCCACAAAAGG 60.291 50.000 3.32 0.00 0.00 3.11
1905 2557 3.071874 TGGCCTCATACTCCACAAAAG 57.928 47.619 3.32 0.00 0.00 2.27
1921 2573 0.463474 GCCAGATGAGACTCTTGGCC 60.463 60.000 24.05 0.00 35.33 5.36
1922 2574 0.251354 TGCCAGATGAGACTCTTGGC 59.749 55.000 26.05 26.05 38.68 4.52
1923 2575 2.775911 TTGCCAGATGAGACTCTTGG 57.224 50.000 13.59 13.59 0.00 3.61
1955 2607 6.638610 TGGTTGGTGCATAAAATTCAATAGG 58.361 36.000 0.00 0.00 0.00 2.57
2009 2661 6.953520 TGAATTTTATGAGGATTGTCCAACCT 59.046 34.615 0.00 0.00 39.61 3.50
2023 2675 8.559536 GCAGGTCGAATCTATTGAATTTTATGA 58.440 33.333 0.00 0.00 0.00 2.15
2030 2682 5.282055 TCTGCAGGTCGAATCTATTGAAT 57.718 39.130 15.13 0.00 0.00 2.57
2040 2692 0.468226 ACTTGGTTCTGCAGGTCGAA 59.532 50.000 15.13 9.67 0.00 3.71
2249 2901 7.612266 CAAATAAATTAAAGCGGCTGTGAATC 58.388 34.615 1.81 0.00 0.00 2.52
2273 2925 3.627395 ATTAACTGTGAAGATCCGGCA 57.373 42.857 0.00 0.00 0.00 5.69
2351 3003 4.709397 TGTGGTTTGGATCTTTGTTGAACT 59.291 37.500 0.00 0.00 0.00 3.01
2369 3023 1.378531 GTGTGTGTGTGTCATGTGGT 58.621 50.000 0.00 0.00 0.00 4.16
2375 3029 0.528901 GCTACCGTGTGTGTGTGTCA 60.529 55.000 0.00 0.00 0.00 3.58
2387 3041 0.944311 CTTTGCTCGTGTGCTACCGT 60.944 55.000 0.00 0.00 0.00 4.83
2388 3042 0.944311 ACTTTGCTCGTGTGCTACCG 60.944 55.000 0.00 0.00 0.00 4.02
2461 3115 4.830765 GCCGTGGCCGCTGTATGA 62.831 66.667 15.69 0.00 34.56 2.15
2512 3166 8.047310 TCTTCTCCACATTTCCCTCTAATTTAC 58.953 37.037 0.00 0.00 0.00 2.01
2546 3200 8.345724 AGAGACAAATCTAAATGCATTTCACT 57.654 30.769 27.28 11.92 34.34 3.41
2601 3255 8.618677 GCTCCTTTGTTTAGTAAACTAGTGTTT 58.381 33.333 22.87 0.00 46.74 2.83
2602 3256 7.991460 AGCTCCTTTGTTTAGTAAACTAGTGTT 59.009 33.333 22.87 11.78 41.90 3.32
2626 3280 7.981225 TCTTGGGCAAGAAAATATGATAAAAGC 59.019 33.333 0.00 0.00 43.79 3.51
2642 3296 5.560183 CGTTTAGTAGTGTTTCTTGGGCAAG 60.560 44.000 0.00 0.00 39.71 4.01
2658 3312 6.747125 TGTGTTGGTCACTATTCGTTTAGTA 58.253 36.000 0.00 0.00 46.27 1.82
2671 3325 2.545742 GGCAGGAAAATGTGTTGGTCAC 60.546 50.000 0.00 0.00 46.31 3.67
2783 3437 9.013490 GTAAGCTACACATTGCTAATTGAATTG 57.987 33.333 0.00 0.00 38.75 2.32
2824 3478 7.465116 TCAAGAGAGAAAATTCAAGGGAGATT 58.535 34.615 0.00 0.00 0.00 2.40
2904 3561 9.048446 TGAACAAACAAGTATAGGTTAACACTC 57.952 33.333 8.10 0.00 0.00 3.51
2905 3562 8.967664 TGAACAAACAAGTATAGGTTAACACT 57.032 30.769 8.10 4.99 0.00 3.55
3217 6234 3.940209 TGAGCCCACTTAAATGCAAAG 57.060 42.857 0.00 0.00 0.00 2.77
3290 6307 5.852282 AAACCTATTTGGATGTGGCATAC 57.148 39.130 0.00 0.00 39.71 2.39
3346 6363 6.651225 GGTAGTCAGCTCATGGAATAAATACC 59.349 42.308 0.00 0.00 0.00 2.73
3399 6416 9.066892 AGCTTTCATACAACAAACTTTGAGATA 57.933 29.630 8.55 0.00 0.00 1.98
3669 6687 1.815003 CATCAGAAGGAACCAACAGGC 59.185 52.381 0.00 0.00 0.00 4.85
3687 6705 7.120579 TGAGATAGTTTAAAAATGTCACGCCAT 59.879 33.333 7.27 0.00 0.00 4.40
3781 6799 4.667573 TCTACACAGGAGTTGATCAGACT 58.332 43.478 9.42 9.42 0.00 3.24
3845 6863 2.270874 ATCAACCCTCATGGACCGGC 62.271 60.000 0.00 0.00 38.00 6.13
3889 7688 2.715046 TCATTGAGATGCTTTTCGCCT 58.285 42.857 0.00 0.00 38.05 5.52
3944 7745 1.293179 GAGCAATGGGGGTGCAAAC 59.707 57.895 0.00 0.00 44.74 2.93
4208 8072 5.650266 TGGGTTATACACAAGCGATGAAAAT 59.350 36.000 0.00 0.00 0.00 1.82
4424 8288 6.538742 GCACCATTTTAGCTAGTCAACTCATA 59.461 38.462 0.00 0.00 0.00 2.15
4428 8292 4.010349 GGCACCATTTTAGCTAGTCAACT 58.990 43.478 0.00 0.00 0.00 3.16
4586 8450 7.826690 ACCAGCAAATAAATCGACTTTATGTT 58.173 30.769 11.21 7.28 39.46 2.71
4780 8654 3.419943 TGCATATGGAAGAAACTGTGCA 58.580 40.909 4.56 0.00 38.83 4.57
4782 8656 6.194463 CGTTATGCATATGGAAGAAACTGTG 58.806 40.000 7.36 0.00 0.00 3.66
4783 8657 5.220854 GCGTTATGCATATGGAAGAAACTGT 60.221 40.000 7.36 0.00 45.45 3.55
5053 8930 7.024171 TGTTGCGGTAAATAACACATACATTG 58.976 34.615 0.00 0.00 30.06 2.82
5070 8947 6.037172 GTCTAATTGACTAATCATGTTGCGGT 59.963 38.462 0.00 0.00 42.21 5.68
5141 9018 3.242220 GCATCTTAGACGCATCACAACAG 60.242 47.826 0.00 0.00 0.00 3.16
5335 9213 7.327761 GTGAGAACGCTGTAATACTAGAAAACA 59.672 37.037 0.00 0.00 0.00 2.83
5344 9222 4.491676 TGGAAGTGAGAACGCTGTAATAC 58.508 43.478 0.00 0.00 36.93 1.89
5356 9234 5.221601 GCAGAGGAATCATATGGAAGTGAGA 60.222 44.000 2.13 0.00 0.00 3.27
5439 9318 3.417069 TTATGTGGAAGTGGGTCTGTG 57.583 47.619 0.00 0.00 0.00 3.66
5491 9370 4.220821 TGTGGAAGACAAGATACCTCTGTC 59.779 45.833 0.00 0.00 33.43 3.51
5502 9381 9.177608 TGGAAATATAGAAATGTGGAAGACAAG 57.822 33.333 0.00 0.00 38.36 3.16
5535 9414 4.157246 CCCCAACTTAAGGCTAAAGGTTT 58.843 43.478 7.53 0.00 0.00 3.27
5900 9779 5.338463 GGACATAACTCCACCTTCTTTAGCT 60.338 44.000 0.00 0.00 0.00 3.32
5901 9780 4.876679 GGACATAACTCCACCTTCTTTAGC 59.123 45.833 0.00 0.00 0.00 3.09
5902 9781 6.049955 TGGACATAACTCCACCTTCTTTAG 57.950 41.667 0.00 0.00 35.23 1.85
5903 9782 5.546499 ACTGGACATAACTCCACCTTCTTTA 59.454 40.000 0.00 0.00 35.23 1.85
5904 9783 4.351111 ACTGGACATAACTCCACCTTCTTT 59.649 41.667 0.00 0.00 35.23 2.52
5905 9784 3.910627 ACTGGACATAACTCCACCTTCTT 59.089 43.478 0.00 0.00 35.23 2.52
5906 9785 3.261897 CACTGGACATAACTCCACCTTCT 59.738 47.826 0.00 0.00 35.23 2.85
5907 9786 3.600388 CACTGGACATAACTCCACCTTC 58.400 50.000 0.00 0.00 35.23 3.46
5948 9827 4.404073 ACTCACACAAACACTCTCTCTCTT 59.596 41.667 0.00 0.00 0.00 2.85
6005 9884 0.172578 CCATCGAGCACCTACGAACA 59.827 55.000 0.00 0.00 41.65 3.18
6009 9888 2.279517 GGCCATCGAGCACCTACG 60.280 66.667 0.00 0.00 0.00 3.51
6047 9926 4.074970 CTCAGTTGGCAATAAGAACTGGT 58.925 43.478 13.19 0.00 44.43 4.00
6048 9927 4.154918 GTCTCAGTTGGCAATAAGAACTGG 59.845 45.833 13.19 6.09 44.43 4.00
6049 9928 4.143030 CGTCTCAGTTGGCAATAAGAACTG 60.143 45.833 1.92 5.76 45.27 3.16
6050 9929 3.997021 CGTCTCAGTTGGCAATAAGAACT 59.003 43.478 1.92 0.00 0.00 3.01
6051 9930 3.994392 TCGTCTCAGTTGGCAATAAGAAC 59.006 43.478 1.92 0.00 0.00 3.01
6052 9931 3.994392 GTCGTCTCAGTTGGCAATAAGAA 59.006 43.478 1.92 0.00 0.00 2.52
6053 9932 3.585862 GTCGTCTCAGTTGGCAATAAGA 58.414 45.455 1.92 4.15 0.00 2.10
6054 9933 2.345641 CGTCGTCTCAGTTGGCAATAAG 59.654 50.000 1.92 1.60 0.00 1.73
6055 9934 2.029739 TCGTCGTCTCAGTTGGCAATAA 60.030 45.455 1.92 0.00 0.00 1.40
6056 9935 1.542472 TCGTCGTCTCAGTTGGCAATA 59.458 47.619 1.92 0.00 0.00 1.90
6057 9936 0.317160 TCGTCGTCTCAGTTGGCAAT 59.683 50.000 1.92 0.00 0.00 3.56
6058 9937 0.103390 TTCGTCGTCTCAGTTGGCAA 59.897 50.000 0.00 0.00 0.00 4.52
6059 9938 0.596600 GTTCGTCGTCTCAGTTGGCA 60.597 55.000 0.00 0.00 0.00 4.92
6060 9939 0.318784 AGTTCGTCGTCTCAGTTGGC 60.319 55.000 0.00 0.00 0.00 4.52
6061 9940 2.983402 TAGTTCGTCGTCTCAGTTGG 57.017 50.000 0.00 0.00 0.00 3.77
6062 9941 3.822996 ACATAGTTCGTCGTCTCAGTTG 58.177 45.455 0.00 0.00 0.00 3.16
6063 9942 4.435253 CGTACATAGTTCGTCGTCTCAGTT 60.435 45.833 0.00 0.00 0.00 3.16
6064 9943 3.061831 CGTACATAGTTCGTCGTCTCAGT 59.938 47.826 0.00 0.00 0.00 3.41
6065 9944 3.543656 CCGTACATAGTTCGTCGTCTCAG 60.544 52.174 0.00 0.00 0.00 3.35
6066 9945 2.349580 CCGTACATAGTTCGTCGTCTCA 59.650 50.000 0.00 0.00 0.00 3.27
6067 9946 2.604914 TCCGTACATAGTTCGTCGTCTC 59.395 50.000 0.00 0.00 0.00 3.36
6068 9947 2.606725 CTCCGTACATAGTTCGTCGTCT 59.393 50.000 0.00 0.00 0.00 4.18
6069 9948 2.848751 GCTCCGTACATAGTTCGTCGTC 60.849 54.545 0.00 0.00 0.00 4.20
6334 10215 6.135400 GCAACACCAAATTAGTTTCATTTGC 58.865 36.000 0.67 0.00 39.40 3.68
6466 10347 9.090103 CAGTACAGTTATATTCCCTCTATTCCA 57.910 37.037 0.00 0.00 0.00 3.53
6556 10437 8.344098 ACATTACGAAACATAAACGAAAAGGAA 58.656 29.630 0.00 0.00 0.00 3.36
6557 10438 7.863666 ACATTACGAAACATAAACGAAAAGGA 58.136 30.769 0.00 0.00 0.00 3.36
6558 10439 8.496872 AACATTACGAAACATAAACGAAAAGG 57.503 30.769 0.00 0.00 0.00 3.11
6661 10543 9.537848 CGGATATTTTATTAAAATAGACCACGC 57.462 33.333 26.11 13.59 44.09 5.34
6686 10568 6.518395 CCATGAACACTTTTTAATACACGACG 59.482 38.462 0.00 0.00 0.00 5.12


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

AutoCloner maintained by Alex Coulton.