Multiple sequence alignment - TraesCS5D01G149600

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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 TraesCS5D01G149600 chr5D 100.000 3100 0 0 1 3100 238558791 238555692 0.000000e+00 5725.0
1 TraesCS5D01G149600 chr5D 91.753 97 8 0 1381 1477 342712637 342712541 5.390000e-28 135.0
2 TraesCS5D01G149600 chr5B 95.116 2580 69 17 477 3016 266500886 266503448 0.000000e+00 4013.0
3 TraesCS5D01G149600 chr5B 87.528 449 35 6 5 436 266499818 266500262 1.660000e-137 499.0
4 TraesCS5D01G149600 chr5B 90.722 97 9 0 1381 1477 402751166 402751070 2.510000e-26 130.0
5 TraesCS5D01G149600 chr5B 95.775 71 3 0 3030 3100 69812778 69812708 7.020000e-22 115.0
6 TraesCS5D01G149600 chr5B 97.059 68 2 0 3033 3100 464321828 464321761 7.020000e-22 115.0
7 TraesCS5D01G149600 chr5B 86.747 83 11 0 1378 1460 704916515 704916597 3.290000e-15 93.5
8 TraesCS5D01G149600 chr5A 93.646 2282 64 25 461 2704 316084499 316086737 0.000000e+00 3336.0
9 TraesCS5D01G149600 chr5A 84.337 415 27 10 1 394 316083695 316084092 3.780000e-99 372.0
10 TraesCS5D01G149600 chr5A 91.244 217 19 0 2821 3037 316087069 316087285 2.340000e-76 296.0
11 TraesCS5D01G149600 chr5A 100.000 32 0 0 405 436 316084085 316084116 3.340000e-05 60.2
12 TraesCS5D01G149600 chr4D 85.078 516 55 15 1001 1506 107710734 107710231 9.920000e-140 507.0
13 TraesCS5D01G149600 chr4D 81.522 276 43 6 1001 1270 506607107 506606834 1.450000e-53 220.0
14 TraesCS5D01G149600 chr4B 84.676 509 54 13 1001 1503 168984879 168985369 1.290000e-133 486.0
15 TraesCS5D01G149600 chr4A 83.871 527 61 16 1001 1515 468603250 468603764 6.010000e-132 481.0
16 TraesCS5D01G149600 chr4A 82.418 273 39 7 1001 1267 724782636 724782905 2.400000e-56 230.0
17 TraesCS5D01G149600 chr7A 82.051 273 40 7 1001 1267 12429646 12429377 1.120000e-54 224.0
18 TraesCS5D01G149600 chr7D 81.655 278 39 10 1001 1270 13029511 13029238 1.450000e-53 220.0
19 TraesCS5D01G149600 chr6A 98.507 67 1 0 3034 3100 1090370 1090304 5.430000e-23 119.0
20 TraesCS5D01G149600 chr3D 97.101 69 2 0 3032 3100 336539268 336539200 1.950000e-22 117.0
21 TraesCS5D01G149600 chr3D 96.970 66 2 0 3035 3100 583869074 583869009 9.090000e-21 111.0
22 TraesCS5D01G149600 chr3D 88.764 89 8 2 2843 2930 123305962 123305875 1.180000e-19 108.0
23 TraesCS5D01G149600 chr3D 84.946 93 14 0 2839 2931 541196945 541196853 9.150000e-16 95.3
24 TraesCS5D01G149600 chr3B 95.833 72 3 0 3029 3100 138269310 138269239 1.950000e-22 117.0
25 TraesCS5D01G149600 chr3A 95.833 72 2 1 3029 3100 62573392 62573462 7.020000e-22 115.0
26 TraesCS5D01G149600 chr2A 97.059 68 2 0 3033 3100 569281069 569281136 7.020000e-22 115.0
27 TraesCS5D01G149600 chr2D 92.405 79 5 1 3023 3100 564440795 564440717 9.090000e-21 111.0
28 TraesCS5D01G149600 chr2D 95.652 69 3 0 2839 2907 646251252 646251184 9.090000e-21 111.0
29 TraesCS5D01G149600 chr2D 90.000 80 4 4 1378 1455 108313429 108313506 1.970000e-17 100.0
30 TraesCS5D01G149600 chr2D 86.022 93 12 1 2831 2923 512165833 512165924 7.070000e-17 99.0
31 TraesCS5D01G149600 chr2B 89.655 87 9 0 2837 2923 781580586 781580500 9.090000e-21 111.0
32 TraesCS5D01G149600 chr6D 88.172 93 10 1 2830 2921 305736590 305736682 3.270000e-20 110.0
33 TraesCS5D01G149600 chr1A 87.234 94 10 2 2831 2923 449669417 449669509 4.230000e-19 106.0


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 TraesCS5D01G149600 chr5D 238555692 238558791 3099 True 5725.00 5725 100.00000 1 3100 1 chr5D.!!$R1 3099
1 TraesCS5D01G149600 chr5B 266499818 266503448 3630 False 2256.00 4013 91.32200 5 3016 2 chr5B.!!$F2 3011
2 TraesCS5D01G149600 chr5A 316083695 316087285 3590 False 1016.05 3336 92.30675 1 3037 4 chr5A.!!$F1 3036
3 TraesCS5D01G149600 chr4D 107710231 107710734 503 True 507.00 507 85.07800 1001 1506 1 chr4D.!!$R1 505
4 TraesCS5D01G149600 chr4A 468603250 468603764 514 False 481.00 481 83.87100 1001 1515 1 chr4A.!!$F1 514

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
124 125 0.038166 CTGCCTCAAGCCCTTACCAA 59.962 55.0 0.0 0.0 42.71 3.67 F
972 1769 0.396435 TCGAGCTGCCAAAAGGAGAA 59.604 50.0 0.0 0.0 35.54 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1940 2812 0.676184 TGGCCTCGTCATCATAGCTC 59.324 55.0 3.32 0.0 0.0 4.09 R
2352 3254 0.848735 CATCATCCCATCCCCAGTGT 59.151 55.0 0.00 0.0 0.0 3.55 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
73 74 3.152261 CTAGTGAGGACATCGACAACC 57.848 52.381 0.00 0.00 0.00 3.77
87 88 1.000274 GACAACCATGTTGAACAGCCC 60.000 52.381 13.46 0.00 40.74 5.19
88 89 1.039068 CAACCATGTTGAACAGCCCA 58.961 50.000 3.74 0.00 0.00 5.36
124 125 0.038166 CTGCCTCAAGCCCTTACCAA 59.962 55.000 0.00 0.00 42.71 3.67
148 170 5.618056 ATTGCTCAGTTTGACACATACAG 57.382 39.130 0.00 0.00 0.00 2.74
153 175 5.290493 TCAGTTTGACACATACAGAACCT 57.710 39.130 0.00 0.00 0.00 3.50
155 177 4.452455 CAGTTTGACACATACAGAACCTCC 59.548 45.833 0.00 0.00 0.00 4.30
190 212 3.005791 CCAAACCAAGTCCAACCATCTTC 59.994 47.826 0.00 0.00 0.00 2.87
209 231 8.811017 CCATCTTCTATTGAATCCTCTAAGCTA 58.189 37.037 0.00 0.00 0.00 3.32
282 304 8.718102 TCATAATCAAGTTTAAGCACTACTCC 57.282 34.615 0.00 0.00 0.00 3.85
286 308 7.674471 ATCAAGTTTAAGCACTACTCCTTTC 57.326 36.000 0.00 0.00 0.00 2.62
328 350 7.047891 GGGAGTGAATGACTTCATGTATTGTA 58.952 38.462 0.00 0.00 43.08 2.41
335 357 6.795098 TGACTTCATGTATTGTAACCACAC 57.205 37.500 0.00 0.00 33.30 3.82
336 358 6.530120 TGACTTCATGTATTGTAACCACACT 58.470 36.000 0.00 0.00 33.30 3.55
387 409 6.349300 AGGCATACTGGTTGTTAGATACAAG 58.651 40.000 0.00 0.00 46.95 3.16
388 410 6.070194 AGGCATACTGGTTGTTAGATACAAGT 60.070 38.462 0.00 0.00 46.95 3.16
389 411 6.598064 GGCATACTGGTTGTTAGATACAAGTT 59.402 38.462 0.00 0.00 46.95 2.66
436 458 7.930217 TGGTCAGAACTTCAGTAAAAATCTTG 58.070 34.615 0.00 0.00 0.00 3.02
438 460 8.286097 GGTCAGAACTTCAGTAAAAATCTTGAG 58.714 37.037 0.00 0.00 0.00 3.02
440 462 7.993183 TCAGAACTTCAGTAAAAATCTTGAGGT 59.007 33.333 0.00 0.00 0.00 3.85
441 463 8.072567 CAGAACTTCAGTAAAAATCTTGAGGTG 58.927 37.037 0.00 0.00 0.00 4.00
442 464 6.319141 ACTTCAGTAAAAATCTTGAGGTGC 57.681 37.500 0.00 0.00 0.00 5.01
443 465 5.827797 ACTTCAGTAAAAATCTTGAGGTGCA 59.172 36.000 0.00 0.00 0.00 4.57
444 466 6.491403 ACTTCAGTAAAAATCTTGAGGTGCAT 59.509 34.615 0.00 0.00 0.00 3.96
445 467 6.258230 TCAGTAAAAATCTTGAGGTGCATG 57.742 37.500 0.00 0.00 0.00 4.06
446 468 5.769662 TCAGTAAAAATCTTGAGGTGCATGT 59.230 36.000 0.00 0.00 0.00 3.21
448 470 6.583806 CAGTAAAAATCTTGAGGTGCATGTTC 59.416 38.462 0.00 0.00 0.00 3.18
449 471 4.525912 AAAATCTTGAGGTGCATGTTCC 57.474 40.909 0.00 0.00 0.00 3.62
450 472 2.885135 ATCTTGAGGTGCATGTTCCA 57.115 45.000 10.09 0.00 0.00 3.53
451 473 2.189594 TCTTGAGGTGCATGTTCCAG 57.810 50.000 10.09 0.00 0.00 3.86
453 475 2.637382 TCTTGAGGTGCATGTTCCAGTA 59.363 45.455 10.09 0.00 0.00 2.74
454 476 2.768253 TGAGGTGCATGTTCCAGTAG 57.232 50.000 10.09 0.00 0.00 2.57
455 477 1.977854 TGAGGTGCATGTTCCAGTAGT 59.022 47.619 10.09 0.00 0.00 2.73
457 479 3.003480 GAGGTGCATGTTCCAGTAGTTC 58.997 50.000 10.09 0.00 0.00 3.01
458 480 2.639839 AGGTGCATGTTCCAGTAGTTCT 59.360 45.455 10.09 0.00 0.00 3.01
459 481 3.073062 AGGTGCATGTTCCAGTAGTTCTT 59.927 43.478 10.09 0.00 0.00 2.52
503 1299 4.989044 ACACTTTACCGTTTTGTTTCCTG 58.011 39.130 0.00 0.00 0.00 3.86
519 1315 4.895224 TTCCTGCACATAGTAGAGTACG 57.105 45.455 0.00 0.00 30.56 3.67
520 1316 3.211865 TCCTGCACATAGTAGAGTACGG 58.788 50.000 0.00 0.00 30.56 4.02
587 1383 2.260434 GTGGTGGCTTGCATGCAG 59.740 61.111 21.50 15.64 34.04 4.41
606 1402 2.035632 AGAAGTCTAGCCAAGGATCCG 58.964 52.381 5.98 0.00 0.00 4.18
625 1421 4.658063 TCCGATTTAAATCCCACACAGTT 58.342 39.130 20.01 0.00 31.68 3.16
856 1653 3.307506 CTCACTCCCCTTCATCATCTCT 58.692 50.000 0.00 0.00 0.00 3.10
871 1668 9.785982 TTCATCATCTCTCTCCTATATATACGG 57.214 37.037 0.00 0.00 0.00 4.02
872 1669 9.160412 TCATCATCTCTCTCCTATATATACGGA 57.840 37.037 9.32 9.32 0.00 4.69
873 1670 9.435688 CATCATCTCTCTCCTATATATACGGAG 57.564 40.741 21.03 21.03 44.48 4.63
879 1676 6.750660 TCTCCTATATATACGGAGAGGGAG 57.249 45.833 23.44 18.48 46.17 4.30
941 1738 3.117171 CCAGCTGCAGACACGAGC 61.117 66.667 20.43 0.00 0.00 5.03
969 1766 0.740868 CGATCGAGCTGCCAAAAGGA 60.741 55.000 10.26 0.00 0.00 3.36
970 1767 1.012841 GATCGAGCTGCCAAAAGGAG 58.987 55.000 0.00 0.00 36.90 3.69
971 1768 0.615331 ATCGAGCTGCCAAAAGGAGA 59.385 50.000 0.00 0.00 35.54 3.71
972 1769 0.396435 TCGAGCTGCCAAAAGGAGAA 59.604 50.000 0.00 0.00 35.54 2.87
973 1770 0.801251 CGAGCTGCCAAAAGGAGAAG 59.199 55.000 0.00 0.00 35.54 2.85
974 1771 1.609061 CGAGCTGCCAAAAGGAGAAGA 60.609 52.381 0.00 0.00 35.54 2.87
975 1772 2.083002 GAGCTGCCAAAAGGAGAAGAG 58.917 52.381 0.00 0.00 35.54 2.85
976 1773 1.701847 AGCTGCCAAAAGGAGAAGAGA 59.298 47.619 0.00 0.00 35.54 3.10
977 1774 2.308275 AGCTGCCAAAAGGAGAAGAGAT 59.692 45.455 0.00 0.00 35.54 2.75
978 1775 2.682352 GCTGCCAAAAGGAGAAGAGATC 59.318 50.000 0.00 0.00 35.54 2.75
979 1776 3.871463 GCTGCCAAAAGGAGAAGAGATCA 60.871 47.826 0.00 0.00 35.54 2.92
980 1777 4.330250 CTGCCAAAAGGAGAAGAGATCAA 58.670 43.478 0.00 0.00 35.54 2.57
989 1804 4.224818 AGGAGAAGAGATCAAAGAAGGTGG 59.775 45.833 0.00 0.00 0.00 4.61
1293 2159 2.721859 CCGTCCAGCGATCGATCA 59.278 61.111 24.40 2.12 44.77 2.92
1363 2232 8.328758 ACATGATCTAATTACAACTCTTTGGGA 58.671 33.333 0.00 0.00 37.00 4.37
1859 2731 0.460109 TCATGTCCTTCGACCGCATG 60.460 55.000 10.41 10.41 38.32 4.06
1862 2734 1.215647 GTCCTTCGACCGCATGTCT 59.784 57.895 0.00 0.00 42.13 3.41
1890 2762 1.678970 GCCGGGCTGGTTTTCATCT 60.679 57.895 15.16 0.00 41.21 2.90
1899 2771 2.151202 TGGTTTTCATCTCTGGCGTTC 58.849 47.619 0.00 0.00 0.00 3.95
1900 2772 1.468914 GGTTTTCATCTCTGGCGTTCC 59.531 52.381 0.00 0.00 0.00 3.62
1901 2773 1.128692 GTTTTCATCTCTGGCGTTCCG 59.871 52.381 0.00 0.00 34.14 4.30
1962 2834 0.319040 CTATGATGACGAGGCCACCG 60.319 60.000 5.01 11.15 0.00 4.94
2352 3254 8.418662 AGAGACGTTTACTAATGGTGCATATTA 58.581 33.333 0.00 0.00 0.00 0.98
2353 3255 8.361592 AGACGTTTACTAATGGTGCATATTAC 57.638 34.615 0.00 0.00 0.00 1.89
2354 3256 7.982919 AGACGTTTACTAATGGTGCATATTACA 59.017 33.333 0.00 0.00 0.00 2.41
2355 3257 7.912383 ACGTTTACTAATGGTGCATATTACAC 58.088 34.615 0.00 0.00 37.31 2.90
2356 3258 7.767198 ACGTTTACTAATGGTGCATATTACACT 59.233 33.333 0.00 0.00 38.14 3.55
2357 3259 8.061857 CGTTTACTAATGGTGCATATTACACTG 58.938 37.037 0.00 0.00 38.14 3.66
2473 3377 1.944778 GCATGATGCGACTAAGGGC 59.055 57.895 0.00 0.00 31.71 5.19
2629 3534 4.336713 AGTGAAGCCTTCTGTTTTTGTCTC 59.663 41.667 5.96 0.00 0.00 3.36
2790 3897 4.262121 CCCTGATCACATTCACTGCAAAAA 60.262 41.667 0.00 0.00 0.00 1.94
2902 4034 5.267776 TGTTAGCTTGCAAAAACGTCTTAC 58.732 37.500 0.00 0.00 0.00 2.34
2908 4040 5.116528 GCTTGCAAAAACGTCTTACATTACC 59.883 40.000 0.00 0.00 0.00 2.85
2909 4041 5.110940 TGCAAAAACGTCTTACATTACCC 57.889 39.130 0.00 0.00 0.00 3.69
2916 4048 2.033801 CGTCTTACATTACCCGACGGAT 59.966 50.000 17.49 0.00 42.49 4.18
2987 4119 5.999205 ACCATTTCTCAATGCATGGTTAA 57.001 34.783 0.00 0.00 46.00 2.01
3023 4155 5.650266 TCTGCTTCCAAAGAAAAACTACACA 59.350 36.000 0.00 0.00 0.00 3.72
3025 4157 5.163561 TGCTTCCAAAGAAAAACTACACAGG 60.164 40.000 0.00 0.00 0.00 4.00
3040 4172 8.442632 AACTACACAGGTTTAAAAACTACTCC 57.557 34.615 5.62 0.00 38.89 3.85
3041 4173 6.994496 ACTACACAGGTTTAAAAACTACTCCC 59.006 38.462 5.62 0.00 38.89 4.30
3042 4174 6.009908 ACACAGGTTTAAAAACTACTCCCT 57.990 37.500 5.62 0.00 38.89 4.20
3043 4175 6.060136 ACACAGGTTTAAAAACTACTCCCTC 58.940 40.000 5.62 0.00 38.89 4.30
3044 4176 6.126565 ACACAGGTTTAAAAACTACTCCCTCT 60.127 38.462 5.62 0.00 38.89 3.69
3045 4177 6.204882 CACAGGTTTAAAAACTACTCCCTCTG 59.795 42.308 5.62 4.67 38.89 3.35
3046 4178 6.126565 ACAGGTTTAAAAACTACTCCCTCTGT 60.127 38.462 5.62 5.20 38.89 3.41
3047 4179 6.427242 CAGGTTTAAAAACTACTCCCTCTGTC 59.573 42.308 5.62 0.00 38.89 3.51
3048 4180 5.704515 GGTTTAAAAACTACTCCCTCTGTCC 59.295 44.000 5.62 0.00 38.89 4.02
3049 4181 5.494390 TTAAAAACTACTCCCTCTGTCCC 57.506 43.478 0.00 0.00 0.00 4.46
3050 4182 2.715763 AAACTACTCCCTCTGTCCCA 57.284 50.000 0.00 0.00 0.00 4.37
3051 4183 2.950990 AACTACTCCCTCTGTCCCAT 57.049 50.000 0.00 0.00 0.00 4.00
3052 4184 4.348020 AAACTACTCCCTCTGTCCCATA 57.652 45.455 0.00 0.00 0.00 2.74
3053 4185 4.348020 AACTACTCCCTCTGTCCCATAA 57.652 45.455 0.00 0.00 0.00 1.90
3054 4186 4.561254 ACTACTCCCTCTGTCCCATAAT 57.439 45.455 0.00 0.00 0.00 1.28
3055 4187 5.681494 ACTACTCCCTCTGTCCCATAATA 57.319 43.478 0.00 0.00 0.00 0.98
3056 4188 6.234404 ACTACTCCCTCTGTCCCATAATAT 57.766 41.667 0.00 0.00 0.00 1.28
3057 4189 7.358255 ACTACTCCCTCTGTCCCATAATATA 57.642 40.000 0.00 0.00 0.00 0.86
3058 4190 7.776745 ACTACTCCCTCTGTCCCATAATATAA 58.223 38.462 0.00 0.00 0.00 0.98
3059 4191 7.896496 ACTACTCCCTCTGTCCCATAATATAAG 59.104 40.741 0.00 0.00 0.00 1.73
3060 4192 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
3061 4193 7.313731 ACTCCCTCTGTCCCATAATATAAGAA 58.686 38.462 0.00 0.00 0.00 2.52
3062 4194 7.235812 ACTCCCTCTGTCCCATAATATAAGAAC 59.764 40.741 0.00 0.00 0.00 3.01
3063 4195 6.210784 TCCCTCTGTCCCATAATATAAGAACG 59.789 42.308 0.00 0.00 0.00 3.95
3064 4196 6.014499 CCCTCTGTCCCATAATATAAGAACGT 60.014 42.308 0.00 0.00 0.00 3.99
3065 4197 7.442656 CCTCTGTCCCATAATATAAGAACGTT 58.557 38.462 0.00 0.00 0.00 3.99
3066 4198 7.931948 CCTCTGTCCCATAATATAAGAACGTTT 59.068 37.037 0.46 0.00 0.00 3.60
3067 4199 9.326413 CTCTGTCCCATAATATAAGAACGTTTT 57.674 33.333 0.46 0.00 0.00 2.43
3068 4200 9.675464 TCTGTCCCATAATATAAGAACGTTTTT 57.325 29.630 9.22 9.22 0.00 1.94
3082 4214 8.707938 AAGAACGTTTTTAACACTAGTGTAGT 57.292 30.769 28.13 16.41 44.13 2.73
3083 4215 8.707938 AGAACGTTTTTAACACTAGTGTAGTT 57.292 30.769 28.13 21.46 44.13 2.24
3084 4216 9.154847 AGAACGTTTTTAACACTAGTGTAGTTT 57.845 29.630 28.13 15.32 44.13 2.66
3085 4217 9.413611 GAACGTTTTTAACACTAGTGTAGTTTC 57.586 33.333 28.13 16.53 44.13 2.78
3086 4218 8.477984 ACGTTTTTAACACTAGTGTAGTTTCA 57.522 30.769 28.13 9.00 44.13 2.69
3087 4219 8.934825 ACGTTTTTAACACTAGTGTAGTTTCAA 58.065 29.630 28.13 13.55 44.13 2.69
3088 4220 9.757859 CGTTTTTAACACTAGTGTAGTTTCAAA 57.242 29.630 28.13 16.98 44.13 2.69
3092 4224 9.757859 TTTAACACTAGTGTAGTTTCAAAAACG 57.242 29.630 28.13 0.00 44.13 3.60
3093 4225 6.973229 ACACTAGTGTAGTTTCAAAAACGT 57.027 33.333 26.91 0.00 42.90 3.99
3094 4226 7.368480 ACACTAGTGTAGTTTCAAAAACGTT 57.632 32.000 26.91 0.00 42.90 3.99
3095 4227 7.458677 ACACTAGTGTAGTTTCAAAAACGTTC 58.541 34.615 26.91 0.00 42.90 3.95
3096 4228 7.332678 ACACTAGTGTAGTTTCAAAAACGTTCT 59.667 33.333 26.91 0.00 42.90 3.01
3097 4229 8.173130 CACTAGTGTAGTTTCAAAAACGTTCTT 58.827 33.333 15.06 0.00 36.76 2.52
3098 4230 9.369904 ACTAGTGTAGTTTCAAAAACGTTCTTA 57.630 29.630 0.00 0.00 34.86 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 1.252904 CCCCTGGGCTGTTCAACATG 61.253 60.000 7.39 0.00 0.00 3.21
87 88 2.750657 GGGTGATCCTCTGCCCCTG 61.751 68.421 0.00 0.00 35.18 4.45
88 89 2.367512 GGGTGATCCTCTGCCCCT 60.368 66.667 0.00 0.00 35.18 4.79
124 125 7.105588 TCTGTATGTGTCAAACTGAGCAATAT 58.894 34.615 0.00 0.00 0.00 1.28
167 189 2.176798 AGATGGTTGGACTTGGTTTGGA 59.823 45.455 0.00 0.00 0.00 3.53
209 231 7.320399 AGATTTTTGTTTGAACGAACCTCTTT 58.680 30.769 0.00 0.00 32.22 2.52
218 240 9.672086 TTGATAAGGTAGATTTTTGTTTGAACG 57.328 29.630 0.00 0.00 0.00 3.95
282 304 5.045578 TCCCTGGTTAAATCTGAGGAGAAAG 60.046 44.000 0.00 0.00 0.00 2.62
286 308 3.777522 ACTCCCTGGTTAAATCTGAGGAG 59.222 47.826 0.00 0.00 44.25 3.69
328 350 6.989169 GCAGATATATTCTTGAGAGTGTGGTT 59.011 38.462 0.00 0.00 29.93 3.67
401 423 7.453393 ACTGAAGTTCTGACCAATAGATTCAA 58.547 34.615 15.84 0.00 28.41 2.69
436 458 2.770164 ACTACTGGAACATGCACCTC 57.230 50.000 9.61 0.00 38.20 3.85
438 460 3.059352 AGAACTACTGGAACATGCACC 57.941 47.619 0.00 0.00 38.20 5.01
440 462 4.350368 TCAAGAACTACTGGAACATGCA 57.650 40.909 0.00 0.00 38.20 3.96
441 463 5.525378 CCTATCAAGAACTACTGGAACATGC 59.475 44.000 0.00 0.00 38.20 4.06
442 464 6.644347 ACCTATCAAGAACTACTGGAACATG 58.356 40.000 0.00 0.00 38.20 3.21
443 465 6.875972 ACCTATCAAGAACTACTGGAACAT 57.124 37.500 0.00 0.00 38.20 2.71
444 466 7.576287 CGTTACCTATCAAGAACTACTGGAACA 60.576 40.741 0.00 0.00 31.69 3.18
445 467 6.750963 CGTTACCTATCAAGAACTACTGGAAC 59.249 42.308 0.00 0.00 31.69 3.62
446 468 6.660521 TCGTTACCTATCAAGAACTACTGGAA 59.339 38.462 0.00 0.00 31.69 3.53
448 470 6.446781 TCGTTACCTATCAAGAACTACTGG 57.553 41.667 0.00 0.00 0.00 4.00
449 471 8.928270 ATTTCGTTACCTATCAAGAACTACTG 57.072 34.615 0.00 0.00 0.00 2.74
450 472 9.939802 AAATTTCGTTACCTATCAAGAACTACT 57.060 29.630 0.00 0.00 0.00 2.57
453 475 9.379791 CCTAAATTTCGTTACCTATCAAGAACT 57.620 33.333 0.00 0.00 0.00 3.01
454 476 9.159364 ACCTAAATTTCGTTACCTATCAAGAAC 57.841 33.333 0.00 0.00 0.00 3.01
457 479 9.590451 TGTACCTAAATTTCGTTACCTATCAAG 57.410 33.333 0.00 0.00 0.00 3.02
458 480 9.369904 GTGTACCTAAATTTCGTTACCTATCAA 57.630 33.333 0.00 0.00 0.00 2.57
459 481 8.752187 AGTGTACCTAAATTTCGTTACCTATCA 58.248 33.333 0.00 0.00 0.00 2.15
503 1299 1.334779 CCGCCGTACTCTACTATGTGC 60.335 57.143 0.00 0.00 0.00 4.57
519 1315 0.960364 TCAAGGCATTTCACTCCGCC 60.960 55.000 0.00 0.00 45.23 6.13
520 1316 0.169009 GTCAAGGCATTTCACTCCGC 59.831 55.000 0.00 0.00 0.00 5.54
587 1383 2.032620 TCGGATCCTTGGCTAGACTTC 58.967 52.381 10.75 0.00 0.00 3.01
606 1402 4.165779 CGCAACTGTGTGGGATTTAAATC 58.834 43.478 18.22 18.22 33.45 2.17
625 1421 1.675720 TACTGCTGCATCCTAGCGCA 61.676 55.000 11.47 0.00 44.01 6.09
870 1667 2.370189 CTCTCTCTCTCTCTCCCTCTCC 59.630 59.091 0.00 0.00 0.00 3.71
871 1668 3.041946 ACTCTCTCTCTCTCTCCCTCTC 58.958 54.545 0.00 0.00 0.00 3.20
872 1669 2.774234 CACTCTCTCTCTCTCTCCCTCT 59.226 54.545 0.00 0.00 0.00 3.69
873 1670 2.771943 TCACTCTCTCTCTCTCTCCCTC 59.228 54.545 0.00 0.00 0.00 4.30
874 1671 2.774234 CTCACTCTCTCTCTCTCTCCCT 59.226 54.545 0.00 0.00 0.00 4.20
875 1672 2.771943 TCTCACTCTCTCTCTCTCTCCC 59.228 54.545 0.00 0.00 0.00 4.30
876 1673 3.706594 TCTCTCACTCTCTCTCTCTCTCC 59.293 52.174 0.00 0.00 0.00 3.71
877 1674 5.069648 TGATCTCTCACTCTCTCTCTCTCTC 59.930 48.000 0.00 0.00 0.00 3.20
878 1675 4.964897 TGATCTCTCACTCTCTCTCTCTCT 59.035 45.833 0.00 0.00 0.00 3.10
879 1676 5.282055 TGATCTCTCACTCTCTCTCTCTC 57.718 47.826 0.00 0.00 0.00 3.20
941 1738 1.461778 CAGCTCGATCGTCTTTCTCG 58.538 55.000 15.94 0.00 0.00 4.04
969 1766 4.322349 CGACCACCTTCTTTGATCTCTTCT 60.322 45.833 0.00 0.00 0.00 2.85
970 1767 3.929610 CGACCACCTTCTTTGATCTCTTC 59.070 47.826 0.00 0.00 0.00 2.87
971 1768 3.307059 CCGACCACCTTCTTTGATCTCTT 60.307 47.826 0.00 0.00 0.00 2.85
972 1769 2.234908 CCGACCACCTTCTTTGATCTCT 59.765 50.000 0.00 0.00 0.00 3.10
973 1770 2.028020 ACCGACCACCTTCTTTGATCTC 60.028 50.000 0.00 0.00 0.00 2.75
974 1771 1.978580 ACCGACCACCTTCTTTGATCT 59.021 47.619 0.00 0.00 0.00 2.75
975 1772 2.347731 GACCGACCACCTTCTTTGATC 58.652 52.381 0.00 0.00 0.00 2.92
976 1773 1.337823 CGACCGACCACCTTCTTTGAT 60.338 52.381 0.00 0.00 0.00 2.57
977 1774 0.032952 CGACCGACCACCTTCTTTGA 59.967 55.000 0.00 0.00 0.00 2.69
978 1775 0.032952 TCGACCGACCACCTTCTTTG 59.967 55.000 0.00 0.00 0.00 2.77
979 1776 0.974383 ATCGACCGACCACCTTCTTT 59.026 50.000 0.00 0.00 0.00 2.52
980 1777 0.531200 GATCGACCGACCACCTTCTT 59.469 55.000 0.00 0.00 0.00 2.52
989 1804 1.364171 CTCCCCATGATCGACCGAC 59.636 63.158 0.00 0.00 0.00 4.79
1293 2159 2.124151 GCCATGGCCAACCTCGAT 60.124 61.111 27.24 0.00 36.63 3.59
1876 2748 0.813821 GCCAGAGATGAAAACCAGCC 59.186 55.000 0.00 0.00 0.00 4.85
1940 2812 0.676184 TGGCCTCGTCATCATAGCTC 59.324 55.000 3.32 0.00 0.00 4.09
2104 2979 4.849813 TCCAGCTAGTACCACAGTAGTA 57.150 45.455 0.00 0.00 33.97 1.82
2105 2980 3.733883 TCCAGCTAGTACCACAGTAGT 57.266 47.619 0.00 0.00 36.13 2.73
2106 2981 5.401531 TTTTCCAGCTAGTACCACAGTAG 57.598 43.478 0.00 0.00 33.81 2.57
2257 3137 4.145052 TCATAGCGATCTCCAAGAAGCTA 58.855 43.478 15.16 15.16 43.43 3.32
2352 3254 0.848735 CATCATCCCATCCCCAGTGT 59.151 55.000 0.00 0.00 0.00 3.55
2353 3255 1.073444 CTCATCATCCCATCCCCAGTG 59.927 57.143 0.00 0.00 0.00 3.66
2354 3256 1.061111 TCTCATCATCCCATCCCCAGT 60.061 52.381 0.00 0.00 0.00 4.00
2355 3257 1.738474 TCTCATCATCCCATCCCCAG 58.262 55.000 0.00 0.00 0.00 4.45
2356 3258 2.060275 CTTCTCATCATCCCATCCCCA 58.940 52.381 0.00 0.00 0.00 4.96
2357 3259 2.342659 TCTTCTCATCATCCCATCCCC 58.657 52.381 0.00 0.00 0.00 4.81
2439 3343 3.203716 TCATGCTTGCAGATCAGATCAC 58.796 45.455 13.14 4.97 0.00 3.06
2473 3377 5.936686 ACATTCAAGAACAGACATGACAG 57.063 39.130 0.00 0.00 0.00 3.51
2629 3534 6.594284 TGCAGAATCAATCAACTAGAATCG 57.406 37.500 0.00 0.00 0.00 3.34
2742 3647 4.778143 GCCGTTGCCGACAGGGAT 62.778 66.667 0.00 0.00 37.83 3.85
2902 4034 1.070786 CCCCATCCGTCGGGTAATG 59.929 63.158 12.29 7.93 42.77 1.90
2908 4040 1.042229 TGTATTACCCCATCCGTCGG 58.958 55.000 4.39 4.39 0.00 4.79
2909 4041 3.675228 GCTATGTATTACCCCATCCGTCG 60.675 52.174 0.00 0.00 0.00 5.12
2916 4048 5.690865 CTGAAAAGGCTATGTATTACCCCA 58.309 41.667 0.00 0.00 0.00 4.96
3023 4155 6.465464 GGACAGAGGGAGTAGTTTTTAAACCT 60.465 42.308 1.90 0.00 39.71 3.50
3025 4157 5.704515 GGGACAGAGGGAGTAGTTTTTAAAC 59.295 44.000 0.00 0.00 39.17 2.01
3056 4188 9.801873 ACTACACTAGTGTTAAAAACGTTCTTA 57.198 29.630 32.15 9.27 41.83 2.10
3057 4189 8.707938 ACTACACTAGTGTTAAAAACGTTCTT 57.292 30.769 32.15 5.99 41.83 2.52
3058 4190 8.707938 AACTACACTAGTGTTAAAAACGTTCT 57.292 30.769 32.15 6.43 41.83 3.01
3059 4191 9.413611 GAAACTACACTAGTGTTAAAAACGTTC 57.586 33.333 32.15 18.68 41.83 3.95
3060 4192 8.934825 TGAAACTACACTAGTGTTAAAAACGTT 58.065 29.630 32.15 18.96 41.83 3.99
3061 4193 8.477984 TGAAACTACACTAGTGTTAAAAACGT 57.522 30.769 32.15 14.98 41.83 3.99
3062 4194 9.757859 TTTGAAACTACACTAGTGTTAAAAACG 57.242 29.630 32.15 14.43 41.83 3.60
3066 4198 9.757859 CGTTTTTGAAACTACACTAGTGTTAAA 57.242 29.630 32.15 19.14 41.83 1.52
3067 4199 8.934825 ACGTTTTTGAAACTACACTAGTGTTAA 58.065 29.630 32.15 15.50 41.83 2.01
3068 4200 8.477984 ACGTTTTTGAAACTACACTAGTGTTA 57.522 30.769 32.15 17.04 41.83 2.41
3069 4201 7.368480 ACGTTTTTGAAACTACACTAGTGTT 57.632 32.000 32.15 15.56 41.83 3.32
3070 4202 6.973229 ACGTTTTTGAAACTACACTAGTGT 57.027 33.333 30.13 30.13 46.87 3.55
3071 4203 7.681903 AGAACGTTTTTGAAACTACACTAGTG 58.318 34.615 21.44 21.44 39.39 2.74
3072 4204 7.838771 AGAACGTTTTTGAAACTACACTAGT 57.161 32.000 0.46 0.00 41.73 2.57


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

AutoCloner maintained by Alex Coulton.