Multiple sequence alignment - TraesCS5A01G428400

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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 TraesCS5A01G428400 chr5A 100.000 2936 0 0 1 2936 613456155 613459090 0.000000e+00 5422.0
1 TraesCS5A01G428400 chr5A 87.965 457 43 6 1318 1772 614367120 614366674 2.000000e-146 529.0
2 TraesCS5A01G428400 chr5A 86.207 377 49 2 1306 1682 614408871 614408498 3.520000e-109 405.0
3 TraesCS5A01G428400 chr5A 91.870 246 20 0 1396 1641 613374354 613374599 7.790000e-91 344.0
4 TraesCS5A01G428400 chr5A 88.961 154 17 0 1122 1275 614367283 614367130 1.070000e-44 191.0
5 TraesCS5A01G428400 chr5A 87.662 154 19 0 1122 1275 614409025 614408872 2.320000e-41 180.0
6 TraesCS5A01G428400 chr5A 92.188 64 4 1 53 115 549939395 549939458 4.030000e-14 89.8
7 TraesCS5A01G428400 chr5A 96.364 55 1 1 965 1019 614409212 614409159 4.030000e-14 89.8
8 TraesCS5A01G428400 chr5D 89.163 2307 158 51 671 2936 490968171 490970426 0.000000e+00 2791.0
9 TraesCS5A01G428400 chr5D 89.563 412 39 3 1306 1716 491846738 491846330 1.210000e-143 520.0
10 TraesCS5A01G428400 chr5D 87.955 440 48 4 3 438 490967449 490967887 5.610000e-142 514.0
11 TraesCS5A01G428400 chr5D 88.835 412 42 3 1306 1716 491796836 491796428 1.210000e-138 503.0
12 TraesCS5A01G428400 chr5D 89.610 154 16 0 1122 1275 492222502 492222349 2.310000e-46 196.0
13 TraesCS5A01G428400 chr5D 89.474 152 13 3 1122 1273 491796987 491796839 3.860000e-44 189.0
14 TraesCS5A01G428400 chr5D 90.845 142 9 3 462 602 490967880 490968018 1.390000e-43 187.0
15 TraesCS5A01G428400 chr5D 88.889 153 15 2 1122 1273 491846892 491846741 1.390000e-43 187.0
16 TraesCS5A01G428400 chr5D 86.585 164 16 3 1092 1255 490954438 490954595 3.010000e-40 176.0
17 TraesCS5A01G428400 chr5D 96.296 54 1 1 966 1019 492222688 492222636 1.450000e-13 87.9
18 TraesCS5A01G428400 chr5D 97.917 48 1 0 972 1019 492068234 492068187 1.880000e-12 84.2
19 TraesCS5A01G428400 chr5D 92.982 57 3 1 621 676 490968060 490968116 6.740000e-12 82.4
20 TraesCS5A01G428400 chr5D 97.436 39 1 0 475 513 4225549 4225511 1.890000e-07 67.6
21 TraesCS5A01G428400 chr5B 88.669 2321 160 44 671 2922 605517942 605520228 0.000000e+00 2734.0
22 TraesCS5A01G428400 chr5B 87.446 462 47 7 1318 1772 606853511 606853054 3.350000e-144 521.0
23 TraesCS5A01G428400 chr5B 88.329 377 41 2 1306 1682 606871001 606870628 1.600000e-122 449.0
24 TraesCS5A01G428400 chr5B 87.190 242 29 1 183 424 4834874 4835113 1.040000e-69 274.0
25 TraesCS5A01G428400 chr5B 87.898 157 19 0 1119 1275 606871158 606871002 5.000000e-43 185.0
26 TraesCS5A01G428400 chr5B 92.857 84 3 2 594 676 605517812 605517893 5.140000e-23 119.0
27 TraesCS5A01G428400 chr5B 93.750 64 3 1 53 115 382215680 382215617 8.660000e-16 95.3
28 TraesCS5A01G428400 chr5B 98.148 54 0 1 966 1019 606871342 606871290 3.120000e-15 93.5
29 TraesCS5A01G428400 chr6D 85.200 250 37 0 184 433 2438025 2437776 1.040000e-64 257.0
30 TraesCS5A01G428400 chr4A 77.917 240 40 11 210 441 678136114 678136348 1.420000e-28 137.0
31 TraesCS5A01G428400 chr4A 92.063 63 4 1 54 115 553487371 553487433 1.450000e-13 87.9
32 TraesCS5A01G428400 chr2B 79.787 188 33 4 258 441 138808192 138808378 6.600000e-27 132.0
33 TraesCS5A01G428400 chr2B 80.833 120 20 3 320 437 24739830 24739712 1.120000e-14 91.6
34 TraesCS5A01G428400 chr2A 84.112 107 17 0 320 426 565374249 565374143 1.440000e-18 104.0
35 TraesCS5A01G428400 chr2A 89.655 58 5 1 462 519 86275581 86275637 4.060000e-09 73.1
36 TraesCS5A01G428400 chr7B 93.651 63 3 1 54 115 567994543 567994605 3.120000e-15 93.5
37 TraesCS5A01G428400 chr7B 81.481 81 8 4 350 424 196656185 196656264 3.160000e-05 60.2
38 TraesCS5A01G428400 chr7D 91.176 68 5 1 53 119 29560340 29560407 1.120000e-14 91.6
39 TraesCS5A01G428400 chr3D 76.879 173 31 9 2045 2215 598112401 598112566 4.030000e-14 89.8
40 TraesCS5A01G428400 chr3B 92.188 64 4 1 56 118 418243070 418243007 4.030000e-14 89.8
41 TraesCS5A01G428400 chr7A 91.935 62 4 1 55 115 66692585 66692646 5.210000e-13 86.1
42 TraesCS5A01G428400 chr4D 89.552 67 6 1 54 119 395711778 395711712 1.880000e-12 84.2


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 TraesCS5A01G428400 chr5A 613456155 613459090 2935 False 5422.000000 5422 100.000000 1 2936 1 chr5A.!!$F3 2935
1 TraesCS5A01G428400 chr5A 614366674 614367283 609 True 360.000000 529 88.463000 1122 1772 2 chr5A.!!$R1 650
2 TraesCS5A01G428400 chr5A 614408498 614409212 714 True 224.933333 405 90.077667 965 1682 3 chr5A.!!$R2 717
3 TraesCS5A01G428400 chr5D 490967449 490970426 2977 False 893.600000 2791 90.236250 3 2936 4 chr5D.!!$F2 2933
4 TraesCS5A01G428400 chr5D 491846330 491846892 562 True 353.500000 520 89.226000 1122 1716 2 chr5D.!!$R4 594
5 TraesCS5A01G428400 chr5D 491796428 491796987 559 True 346.000000 503 89.154500 1122 1716 2 chr5D.!!$R3 594
6 TraesCS5A01G428400 chr5B 605517812 605520228 2416 False 1426.500000 2734 90.763000 594 2922 2 chr5B.!!$F2 2328
7 TraesCS5A01G428400 chr5B 606870628 606871342 714 True 242.500000 449 91.458333 966 1682 3 chr5B.!!$R3 716

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
789 898 0.041488 CTATGCCGACCGACGTAGAC 60.041 60.0 0.0 0.0 40.78 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2497 2715 0.036294 GCAGCCCGTTTTCTAGGAGT 60.036 55.0 0.0 0.0 0.0 3.85 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
43 45 3.056322 TCGGTTCTTGCCTCCTTAGTTAC 60.056 47.826 0.00 0.00 0.00 2.50
51 53 3.130516 TGCCTCCTTAGTTACAGATCACG 59.869 47.826 0.00 0.00 0.00 4.35
67 69 2.734893 ACGCTAGTGAGATAGGGCC 58.265 57.895 10.99 0.00 38.83 5.80
123 125 4.660938 GCCCGCCCTTGTGTCCTT 62.661 66.667 0.00 0.00 0.00 3.36
124 126 2.672996 CCCGCCCTTGTGTCCTTG 60.673 66.667 0.00 0.00 0.00 3.61
125 127 2.672996 CCGCCCTTGTGTCCTTGG 60.673 66.667 0.00 0.00 0.00 3.61
156 158 2.998097 CCAGAGGATGGGCCGAAA 59.002 61.111 0.00 0.00 46.36 3.46
189 191 5.638234 GTCGCACTAGGTAAAACAAGATCTT 59.362 40.000 0.88 0.88 0.00 2.40
191 193 5.637810 CGCACTAGGTAAAACAAGATCTTCA 59.362 40.000 4.57 0.00 0.00 3.02
194 196 6.371825 CACTAGGTAAAACAAGATCTTCACCC 59.628 42.308 4.57 0.40 0.00 4.61
202 204 1.123928 AGATCTTCACCCCCATCGTC 58.876 55.000 0.00 0.00 0.00 4.20
203 205 0.106894 GATCTTCACCCCCATCGTCC 59.893 60.000 0.00 0.00 0.00 4.79
216 218 0.537188 ATCGTCCGGTCATTGCTTCT 59.463 50.000 0.00 0.00 0.00 2.85
224 226 2.346803 GGTCATTGCTTCTGACGCTAA 58.653 47.619 7.67 1.37 43.16 3.09
228 230 3.433274 TCATTGCTTCTGACGCTAAACAG 59.567 43.478 7.67 0.00 35.72 3.16
233 235 3.589988 CTTCTGACGCTAAACAGGTGAT 58.410 45.455 0.00 0.00 35.20 3.06
236 238 1.804151 TGACGCTAAACAGGTGATTGC 59.196 47.619 0.00 0.00 0.00 3.56
243 245 1.909700 AACAGGTGATTGCGGACATT 58.090 45.000 0.00 0.00 0.00 2.71
256 258 1.177401 GGACATTCAGAAAGGTGGGC 58.823 55.000 0.00 0.00 27.58 5.36
266 268 0.112412 AAAGGTGGGCGAGGAAACAT 59.888 50.000 0.00 0.00 0.00 2.71
271 273 0.322456 TGGGCGAGGAAACATTGGAG 60.322 55.000 0.00 0.00 0.00 3.86
287 289 5.822519 ACATTGGAGCAATTATTAGCGAGAA 59.177 36.000 0.00 0.00 31.05 2.87
297 299 7.519008 GCAATTATTAGCGAGAACAAGCTACAT 60.519 37.037 0.00 0.00 44.54 2.29
299 301 2.751166 AGCGAGAACAAGCTACATGT 57.249 45.000 2.69 2.69 42.60 3.21
359 361 6.025896 GTGATGTCAATGTTGAAGCACATAG 58.974 40.000 15.02 0.00 39.21 2.23
366 368 5.567138 ATGTTGAAGCACATAGTTTAGCC 57.433 39.130 0.00 0.00 35.51 3.93
373 375 5.629079 AGCACATAGTTTAGCCAAGTTTC 57.371 39.130 0.00 0.00 0.00 2.78
376 378 5.699839 CACATAGTTTAGCCAAGTTTCCAC 58.300 41.667 0.00 0.00 0.00 4.02
383 385 2.375146 AGCCAAGTTTCCACTTTCGTT 58.625 42.857 0.00 0.00 40.66 3.85
389 391 4.684484 AGTTTCCACTTTCGTTAGGTCT 57.316 40.909 0.00 0.00 0.00 3.85
391 393 3.396260 TTCCACTTTCGTTAGGTCTGG 57.604 47.619 0.00 0.00 0.00 3.86
399 402 0.815734 CGTTAGGTCTGGGACGTCAT 59.184 55.000 18.91 0.00 32.77 3.06
410 413 2.460330 GACGTCATGTCTGGCTTGG 58.540 57.895 11.55 0.00 44.58 3.61
431 434 3.096092 GCCAATCCCATGACCAAAACTA 58.904 45.455 0.00 0.00 0.00 2.24
432 435 3.706086 GCCAATCCCATGACCAAAACTAT 59.294 43.478 0.00 0.00 0.00 2.12
433 436 4.202151 GCCAATCCCATGACCAAAACTATC 60.202 45.833 0.00 0.00 0.00 2.08
434 437 4.342092 CCAATCCCATGACCAAAACTATCC 59.658 45.833 0.00 0.00 0.00 2.59
435 438 3.662759 TCCCATGACCAAAACTATCCC 57.337 47.619 0.00 0.00 0.00 3.85
436 439 2.922955 TCCCATGACCAAAACTATCCCA 59.077 45.455 0.00 0.00 0.00 4.37
437 440 3.335183 TCCCATGACCAAAACTATCCCAA 59.665 43.478 0.00 0.00 0.00 4.12
438 441 4.016666 TCCCATGACCAAAACTATCCCAAT 60.017 41.667 0.00 0.00 0.00 3.16
439 442 4.716287 CCCATGACCAAAACTATCCCAATT 59.284 41.667 0.00 0.00 0.00 2.32
440 443 5.189539 CCCATGACCAAAACTATCCCAATTT 59.810 40.000 0.00 0.00 0.00 1.82
441 444 6.382570 CCCATGACCAAAACTATCCCAATTTA 59.617 38.462 0.00 0.00 0.00 1.40
442 445 7.071071 CCCATGACCAAAACTATCCCAATTTAT 59.929 37.037 0.00 0.00 0.00 1.40
443 446 8.485392 CCATGACCAAAACTATCCCAATTTATT 58.515 33.333 0.00 0.00 0.00 1.40
444 447 9.889128 CATGACCAAAACTATCCCAATTTATTT 57.111 29.630 0.00 0.00 0.00 1.40
446 449 8.536175 TGACCAAAACTATCCCAATTTATTTCC 58.464 33.333 0.00 0.00 0.00 3.13
447 450 8.679344 ACCAAAACTATCCCAATTTATTTCCT 57.321 30.769 0.00 0.00 0.00 3.36
448 451 8.539544 ACCAAAACTATCCCAATTTATTTCCTG 58.460 33.333 0.00 0.00 0.00 3.86
449 452 7.495606 CCAAAACTATCCCAATTTATTTCCTGC 59.504 37.037 0.00 0.00 0.00 4.85
450 453 7.732222 AAACTATCCCAATTTATTTCCTGCA 57.268 32.000 0.00 0.00 0.00 4.41
451 454 7.732222 AACTATCCCAATTTATTTCCTGCAA 57.268 32.000 0.00 0.00 0.00 4.08
452 455 7.732222 ACTATCCCAATTTATTTCCTGCAAA 57.268 32.000 0.00 0.00 0.00 3.68
453 456 8.322905 ACTATCCCAATTTATTTCCTGCAAAT 57.677 30.769 0.00 0.00 38.35 2.32
454 457 9.432982 ACTATCCCAATTTATTTCCTGCAAATA 57.567 29.630 0.00 0.00 36.09 1.40
499 502 7.118496 TGGTGTTTGATGAATAAAACTTGGT 57.882 32.000 5.14 0.00 37.22 3.67
504 507 9.535878 TGTTTGATGAATAAAACTTGGTTTACC 57.464 29.630 5.14 0.00 34.43 2.85
507 510 7.013834 TGATGAATAAAACTTGGTTTACCCCT 58.986 34.615 0.00 0.00 34.43 4.79
546 550 3.720949 TCGTCTTTCTTCTTCCACGAA 57.279 42.857 0.00 0.00 33.58 3.85
548 552 4.049186 TCGTCTTTCTTCTTCCACGAAAG 58.951 43.478 0.00 0.00 42.94 2.62
575 579 1.226746 AACGATAGCCCTAATTGCGC 58.773 50.000 0.00 0.00 42.67 6.09
576 580 0.944311 ACGATAGCCCTAATTGCGCG 60.944 55.000 0.00 0.00 42.67 6.86
577 581 1.497722 GATAGCCCTAATTGCGCGC 59.502 57.895 27.26 27.26 0.00 6.86
578 582 0.951040 GATAGCCCTAATTGCGCGCT 60.951 55.000 33.29 15.25 0.00 5.92
579 583 0.535102 ATAGCCCTAATTGCGCGCTT 60.535 50.000 33.29 21.44 0.00 4.68
595 599 1.372997 CTTGCGTACGTGTCTGCCT 60.373 57.895 17.90 0.00 0.00 4.75
596 600 1.344942 CTTGCGTACGTGTCTGCCTC 61.345 60.000 17.90 0.00 0.00 4.70
597 601 1.802337 TTGCGTACGTGTCTGCCTCT 61.802 55.000 17.90 0.00 0.00 3.69
602 606 3.106672 CGTACGTGTCTGCCTCTAATTC 58.893 50.000 7.22 0.00 0.00 2.17
604 608 2.960819 ACGTGTCTGCCTCTAATTCAC 58.039 47.619 0.00 0.00 0.00 3.18
694 787 8.660373 CAACTGATGAAACTTCCTTGTAGTATC 58.340 37.037 0.00 0.00 0.00 2.24
789 898 0.041488 CTATGCCGACCGACGTAGAC 60.041 60.000 0.00 0.00 40.78 2.59
829 939 1.065600 TCTTGCCTTGTTGCGTTGC 59.934 52.632 0.00 0.00 0.00 4.17
885 995 3.116531 GGGAGCCGTACGTGTTGC 61.117 66.667 15.21 10.30 0.00 4.17
917 1027 2.459442 GCACTGATGCGAGTCCTGC 61.459 63.158 0.00 0.00 43.33 4.85
1305 1466 1.817099 CTTCATCGACCCTGCTGGC 60.817 63.158 3.63 0.00 37.83 4.85
1641 1802 1.407989 GGAAGGATCTGAAGCCCACAG 60.408 57.143 0.00 0.00 36.80 3.66
1659 1820 2.174639 ACAGGAAACCACCAGATCAACA 59.825 45.455 0.00 0.00 0.00 3.33
1660 1821 3.221771 CAGGAAACCACCAGATCAACAA 58.778 45.455 0.00 0.00 0.00 2.83
1661 1822 3.828451 CAGGAAACCACCAGATCAACAAT 59.172 43.478 0.00 0.00 0.00 2.71
1669 1830 3.074412 ACCAGATCAACAATGAACCGAC 58.926 45.455 0.00 0.00 39.49 4.79
1712 1875 6.439599 GTCTTCGAGGATAGAATCGATCAAA 58.560 40.000 0.00 0.00 46.35 2.69
1734 1898 8.458843 TCAAACTTCTTTGTATTTGCTATAGGC 58.541 33.333 1.04 0.00 38.38 3.93
1866 2036 7.646130 TGAAACATTTGTTCACCTCGATTTTAC 59.354 33.333 0.00 0.00 37.25 2.01
1896 2072 3.249917 CAAACCACCACACAACAAGTTC 58.750 45.455 0.00 0.00 0.00 3.01
1900 2076 1.102978 ACCACACAACAAGTTCCAGC 58.897 50.000 0.00 0.00 0.00 4.85
1901 2077 1.102154 CCACACAACAAGTTCCAGCA 58.898 50.000 0.00 0.00 0.00 4.41
1913 2089 9.206870 CAACAAGTTCCAGCATAACATAAAAAT 57.793 29.630 0.00 0.00 0.00 1.82
1989 2179 5.132648 TGGAGGAAGTATCACAAATATGCCT 59.867 40.000 0.00 0.00 0.00 4.75
2006 2197 9.725019 AAATATGCCTAAAAGGAAAAGAAAAGG 57.275 29.630 0.00 0.00 37.67 3.11
2009 2200 7.663043 TGCCTAAAAGGAAAAGAAAAGGTTA 57.337 32.000 0.00 0.00 37.67 2.85
2064 2255 5.414454 CCAGCTAAAGCCTTGTACAATGTAA 59.586 40.000 9.13 0.00 43.38 2.41
2066 2257 7.023575 CAGCTAAAGCCTTGTACAATGTAAAG 58.976 38.462 9.13 4.48 43.38 1.85
2067 2258 6.715264 AGCTAAAGCCTTGTACAATGTAAAGT 59.285 34.615 9.13 0.00 43.38 2.66
2070 2261 6.709018 AAGCCTTGTACAATGTAAAGTGTT 57.291 33.333 9.13 0.00 0.00 3.32
2071 2262 6.709018 AGCCTTGTACAATGTAAAGTGTTT 57.291 33.333 9.13 0.00 0.00 2.83
2072 2263 7.811117 AGCCTTGTACAATGTAAAGTGTTTA 57.189 32.000 9.13 0.00 0.00 2.01
2091 2285 2.808906 AGGGGAGATGCTTGGTAAAC 57.191 50.000 0.00 0.00 0.00 2.01
2100 2294 6.404734 GGAGATGCTTGGTAAACTAAACCATG 60.405 42.308 0.00 0.09 46.16 3.66
2135 2329 8.786898 TCAAATATCCATGCTTATCTTTACAGC 58.213 33.333 0.00 0.00 0.00 4.40
2177 2376 3.056107 TCTGCCGTCTACAAATAAGCACT 60.056 43.478 0.00 0.00 0.00 4.40
2182 2381 3.994392 CGTCTACAAATAAGCACTGGTGT 59.006 43.478 2.64 0.00 0.00 4.16
2253 2459 8.654485 AATGCCTAAAAGATATGCAATATGGA 57.346 30.769 0.00 0.00 40.26 3.41
2254 2460 7.692460 TGCCTAAAAGATATGCAATATGGAG 57.308 36.000 0.00 0.00 40.26 3.86
2255 2461 6.151648 TGCCTAAAAGATATGCAATATGGAGC 59.848 38.462 0.00 0.00 40.26 4.70
2256 2462 6.405176 GCCTAAAAGATATGCAATATGGAGCC 60.405 42.308 0.00 0.00 40.26 4.70
2261 2479 1.174712 ATGCAATATGGAGCCCGCAC 61.175 55.000 0.00 0.00 31.22 5.34
2333 2551 4.987419 GCACGTCGCAAAAAGACA 57.013 50.000 5.30 0.00 41.79 3.41
2335 2553 0.928451 GCACGTCGCAAAAAGACACC 60.928 55.000 5.30 0.00 41.79 4.16
2344 2562 3.057315 CGCAAAAAGACACCCTCAATCAT 60.057 43.478 0.00 0.00 0.00 2.45
2350 2568 6.923199 AAAGACACCCTCAATCATCATTTT 57.077 33.333 0.00 0.00 0.00 1.82
2372 2590 2.282701 TACGCGTTGTTCATAGGGTC 57.717 50.000 20.78 0.00 0.00 4.46
2424 2642 0.107459 ACGTCTCCTCCTACCGGTAC 60.107 60.000 11.16 0.00 0.00 3.34
2437 2655 3.475192 GGTACGGTTGGACTGGGT 58.525 61.111 0.00 0.00 0.00 4.51
2441 2659 2.416747 GTACGGTTGGACTGGGTTTAC 58.583 52.381 0.00 0.00 0.00 2.01
2443 2661 1.202722 ACGGTTGGACTGGGTTTACAG 60.203 52.381 0.00 0.00 44.03 2.74
2449 2667 3.589641 TGGACTGGGTTTACAGGAACTA 58.410 45.455 0.00 0.00 42.75 2.24
2473 2691 1.941377 TGATTTGAGGCCTGCCATTT 58.059 45.000 12.00 0.00 38.92 2.32
2497 2715 3.886123 GCCTAGAGCCTTATGGACAAAA 58.114 45.455 0.00 0.00 34.35 2.44
2502 2720 3.589288 AGAGCCTTATGGACAAAACTCCT 59.411 43.478 0.00 0.00 34.57 3.69
2514 2733 3.146847 CAAAACTCCTAGAAAACGGGCT 58.853 45.455 0.00 0.00 0.00 5.19
2521 2740 2.102109 TAGAAAACGGGCTGCGGACA 62.102 55.000 0.00 0.00 0.00 4.02
2543 2762 2.441375 TGAGAAGACAATGTGGGTCCAA 59.559 45.455 0.00 0.00 35.89 3.53
2544 2763 3.117701 TGAGAAGACAATGTGGGTCCAAA 60.118 43.478 0.00 0.00 35.89 3.28
2562 2781 4.081365 TCCAAAACTCAGACACTACACACA 60.081 41.667 0.00 0.00 0.00 3.72
2564 2783 5.109210 CAAAACTCAGACACTACACACAGA 58.891 41.667 0.00 0.00 0.00 3.41
2568 2787 5.918608 ACTCAGACACTACACACAGAAAAT 58.081 37.500 0.00 0.00 0.00 1.82
2661 2880 7.066284 GCCAAACAAAGATCTTAATCTCTAGCA 59.934 37.037 8.75 0.00 41.54 3.49
2670 2889 2.113860 AATCTCTAGCAAAAGCGGCA 57.886 45.000 1.45 0.00 0.00 5.69
2725 2944 2.173669 CACGACATAGGCCGCCAAG 61.174 63.158 13.15 3.07 0.00 3.61
2726 2945 2.186903 CGACATAGGCCGCCAAGT 59.813 61.111 13.15 6.65 0.00 3.16
2727 2946 1.883084 CGACATAGGCCGCCAAGTC 60.883 63.158 13.15 14.43 0.00 3.01
2739 2958 2.750350 CAAGTCCCCAACGAGGCT 59.250 61.111 0.00 0.00 35.39 4.58
2761 2980 2.368875 AGGTGCCCAAAGATAGTATCCG 59.631 50.000 6.53 0.00 0.00 4.18
2774 2993 5.533154 AGATAGTATCCGGAGAGTTTGTCAG 59.467 44.000 12.49 0.00 0.00 3.51
2815 3034 1.203038 TCAATTCAGCCCAAGCAAGGA 60.203 47.619 0.00 0.00 43.56 3.36
2816 3035 1.203994 CAATTCAGCCCAAGCAAGGAG 59.796 52.381 0.00 0.00 43.56 3.69
2853 3072 6.377327 AATGTTTGTCAGAACGAGATGTTT 57.623 33.333 0.00 0.00 42.09 2.83
2859 3078 6.618287 TGTCAGAACGAGATGTTTCAATTT 57.382 33.333 0.00 0.00 42.09 1.82
2860 3079 7.026631 TGTCAGAACGAGATGTTTCAATTTT 57.973 32.000 0.00 0.00 42.09 1.82
2875 3094 7.172875 TGTTTCAATTTTCATTATGGGCAGTTG 59.827 33.333 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.787725 ACCGATCTTAATGAAGTAACAATCC 57.212 36.000 0.00 0.00 34.03 3.01
7 8 6.315393 GGCAAGAACCGATCTTAATGAAGTAA 59.685 38.462 3.55 0.00 46.80 2.24
21 23 1.640917 ACTAAGGAGGCAAGAACCGA 58.359 50.000 0.00 0.00 33.69 4.69
51 53 2.002505 TGAGGCCCTATCTCACTAGC 57.997 55.000 0.00 0.00 36.46 3.42
84 86 1.250840 GCAAAATCCGAGGCCCTGTT 61.251 55.000 0.00 0.00 0.00 3.16
86 88 2.418083 GGCAAAATCCGAGGCCCTG 61.418 63.158 0.00 0.00 40.55 4.45
111 113 0.250901 CTCCACCAAGGACACAAGGG 60.251 60.000 0.00 0.00 43.07 3.95
114 116 1.715019 CCCCTCCACCAAGGACACAA 61.715 60.000 0.00 0.00 43.07 3.33
156 158 1.038130 CCTAGTGCGACCTACAGCCT 61.038 60.000 0.00 0.00 0.00 4.58
189 191 4.707768 ACCGGACGATGGGGGTGA 62.708 66.667 9.46 0.00 0.00 4.02
191 193 3.995809 ATGACCGGACGATGGGGGT 62.996 63.158 9.46 0.00 34.94 4.95
194 196 2.180204 GCAATGACCGGACGATGGG 61.180 63.158 9.46 0.00 0.00 4.00
202 204 1.970917 GCGTCAGAAGCAATGACCGG 61.971 60.000 0.00 0.00 43.36 5.28
203 205 1.016130 AGCGTCAGAAGCAATGACCG 61.016 55.000 11.18 6.82 43.36 4.79
216 218 1.804151 GCAATCACCTGTTTAGCGTCA 59.196 47.619 0.00 0.00 0.00 4.35
224 226 1.812571 GAATGTCCGCAATCACCTGTT 59.187 47.619 0.00 0.00 0.00 3.16
228 230 1.737838 TCTGAATGTCCGCAATCACC 58.262 50.000 0.00 0.00 31.81 4.02
233 235 1.879380 CACCTTTCTGAATGTCCGCAA 59.121 47.619 0.00 0.00 0.00 4.85
236 238 1.453155 CCCACCTTTCTGAATGTCCG 58.547 55.000 0.00 0.00 0.00 4.79
243 245 1.125093 TTCCTCGCCCACCTTTCTGA 61.125 55.000 0.00 0.00 0.00 3.27
256 258 3.855689 AATTGCTCCAATGTTTCCTCG 57.144 42.857 0.00 0.00 34.04 4.63
266 268 5.182487 TGTTCTCGCTAATAATTGCTCCAA 58.818 37.500 0.00 0.00 0.00 3.53
271 273 5.162000 AGCTTGTTCTCGCTAATAATTGC 57.838 39.130 0.00 0.00 34.11 3.56
287 289 5.356751 TCAAAAGACAACACATGTAGCTTGT 59.643 36.000 13.02 13.02 44.12 3.16
327 329 4.886489 TCAACATTGACATCACAACCTTCA 59.114 37.500 0.00 0.00 32.50 3.02
334 336 3.631227 TGTGCTTCAACATTGACATCACA 59.369 39.130 14.00 14.00 37.96 3.58
338 340 6.579666 AACTATGTGCTTCAACATTGACAT 57.420 33.333 5.91 0.00 41.09 3.06
359 361 4.201980 ACGAAAGTGGAAACTTGGCTAAAC 60.202 41.667 0.00 0.00 46.97 2.01
376 378 1.271656 ACGTCCCAGACCTAACGAAAG 59.728 52.381 0.31 0.00 38.44 2.62
383 385 1.005569 AGACATGACGTCCCAGACCTA 59.994 52.381 14.12 0.00 46.69 3.08
389 391 1.480212 AAGCCAGACATGACGTCCCA 61.480 55.000 14.12 0.00 46.69 4.37
391 393 1.021390 CCAAGCCAGACATGACGTCC 61.021 60.000 14.12 0.00 46.69 4.79
410 413 1.901833 AGTTTTGGTCATGGGATTGGC 59.098 47.619 0.00 0.00 0.00 4.52
418 421 9.889128 AAATAAATTGGGATAGTTTTGGTCATG 57.111 29.630 0.00 0.00 0.00 3.07
457 460 9.889128 CAAACACCATAGAAATTGGGATATTTT 57.111 29.630 0.00 0.00 38.64 1.82
458 461 9.265862 TCAAACACCATAGAAATTGGGATATTT 57.734 29.630 0.00 0.00 38.64 1.40
459 462 8.837099 TCAAACACCATAGAAATTGGGATATT 57.163 30.769 0.00 0.00 38.64 1.28
460 463 8.863086 CATCAAACACCATAGAAATTGGGATAT 58.137 33.333 0.00 0.00 38.64 1.63
474 477 7.734942 ACCAAGTTTTATTCATCAAACACCAT 58.265 30.769 0.00 0.00 35.66 3.55
546 550 4.302559 AGGGCTATCGTTTTCTTTCCTT 57.697 40.909 0.00 0.00 0.00 3.36
548 552 6.495706 CAATTAGGGCTATCGTTTTCTTTCC 58.504 40.000 0.00 0.00 0.00 3.13
575 579 2.763248 CAGACACGTACGCAAGCG 59.237 61.111 16.72 13.50 46.03 4.68
576 580 2.470286 GCAGACACGTACGCAAGC 59.530 61.111 16.72 9.02 45.62 4.01
578 582 1.372499 GAGGCAGACACGTACGCAA 60.372 57.895 16.72 0.00 0.00 4.85
579 583 0.956902 TAGAGGCAGACACGTACGCA 60.957 55.000 16.72 0.00 0.00 5.24
583 587 3.427098 CGTGAATTAGAGGCAGACACGTA 60.427 47.826 0.00 0.00 42.52 3.57
595 599 6.218019 TCGTTTCCTTTCTTCGTGAATTAGA 58.782 36.000 0.00 0.00 34.24 2.10
596 600 6.462073 TCGTTTCCTTTCTTCGTGAATTAG 57.538 37.500 0.00 0.00 34.24 1.73
597 601 7.201496 GCTATCGTTTCCTTTCTTCGTGAATTA 60.201 37.037 0.00 0.00 34.24 1.40
602 606 3.062234 GGCTATCGTTTCCTTTCTTCGTG 59.938 47.826 0.00 0.00 0.00 4.35
604 608 2.608090 GGGCTATCGTTTCCTTTCTTCG 59.392 50.000 0.00 0.00 0.00 3.79
694 787 3.947834 CAGGTGCCCTAAGGATTACAAAG 59.052 47.826 0.00 0.00 33.47 2.77
789 898 1.875364 GTTAGCGGCGGAAGTACGG 60.875 63.158 9.78 0.00 34.93 4.02
795 904 4.440127 GACGGGTTAGCGGCGGAA 62.440 66.667 9.78 0.00 0.00 4.30
829 939 1.007271 ACTGAACCGAGCGTCAGTG 60.007 57.895 13.19 0.00 41.29 3.66
903 1013 2.580815 CTGGCAGGACTCGCATCA 59.419 61.111 6.61 0.00 0.00 3.07
917 1027 1.269988 CGGTGCTGATCATAGTCCTGG 60.270 57.143 0.00 0.00 0.00 4.45
1286 1447 1.599047 CCAGCAGGGTCGATGAAGT 59.401 57.895 0.00 0.00 0.00 3.01
1459 1620 2.677875 CAGCCCCACCTTCTTGCC 60.678 66.667 0.00 0.00 0.00 4.52
1641 1802 3.826157 TCATTGTTGATCTGGTGGTTTCC 59.174 43.478 0.00 0.00 0.00 3.13
1659 1820 1.981256 AACTGCTTGGTCGGTTCATT 58.019 45.000 0.00 0.00 30.15 2.57
1660 1821 2.038557 ACTAACTGCTTGGTCGGTTCAT 59.961 45.455 0.00 0.00 36.91 2.57
1661 1822 1.414919 ACTAACTGCTTGGTCGGTTCA 59.585 47.619 0.00 0.00 36.91 3.18
1669 1830 0.729116 CGCCATGACTAACTGCTTGG 59.271 55.000 0.00 0.00 33.72 3.61
1712 1875 6.663734 AGGCCTATAGCAAATACAAAGAAGT 58.336 36.000 1.29 0.00 46.50 3.01
1866 2036 6.094742 TGTTGTGTGGTGGTTTGCTATATATG 59.905 38.462 0.00 0.00 0.00 1.78
1872 2042 2.130272 TGTTGTGTGGTGGTTTGCTA 57.870 45.000 0.00 0.00 0.00 3.49
1965 2155 5.132648 AGGCATATTTGTGATACTTCCTCCA 59.867 40.000 0.00 0.00 0.00 3.86
2039 2230 3.502123 TTGTACAAGGCTTTAGCTGGT 57.498 42.857 3.59 0.00 41.70 4.00
2042 2233 6.715264 ACTTTACATTGTACAAGGCTTTAGCT 59.285 34.615 19.55 1.62 41.70 3.32
2064 2255 3.562176 CCAAGCATCTCCCCTAAACACTT 60.562 47.826 0.00 0.00 0.00 3.16
2066 2257 2.290960 ACCAAGCATCTCCCCTAAACAC 60.291 50.000 0.00 0.00 0.00 3.32
2067 2258 1.992557 ACCAAGCATCTCCCCTAAACA 59.007 47.619 0.00 0.00 0.00 2.83
2070 2261 3.850173 AGTTTACCAAGCATCTCCCCTAA 59.150 43.478 0.00 0.00 0.00 2.69
2071 2262 3.460825 AGTTTACCAAGCATCTCCCCTA 58.539 45.455 0.00 0.00 0.00 3.53
2072 2263 2.279173 AGTTTACCAAGCATCTCCCCT 58.721 47.619 0.00 0.00 0.00 4.79
2109 2303 8.786898 GCTGTAAAGATAAGCATGGATATTTGA 58.213 33.333 0.00 0.00 36.91 2.69
2110 2304 8.570488 TGCTGTAAAGATAAGCATGGATATTTG 58.430 33.333 0.00 0.00 41.83 2.32
2114 2308 6.233434 CCTGCTGTAAAGATAAGCATGGATA 58.767 40.000 0.00 0.00 45.35 2.59
2118 2312 3.567164 CCCCTGCTGTAAAGATAAGCATG 59.433 47.826 0.00 0.00 45.35 4.06
2156 2355 3.062639 CAGTGCTTATTTGTAGACGGCAG 59.937 47.826 0.00 0.00 0.00 4.85
2159 2358 3.370978 CACCAGTGCTTATTTGTAGACGG 59.629 47.826 0.00 0.00 0.00 4.79
2161 2360 5.941948 AACACCAGTGCTTATTTGTAGAC 57.058 39.130 0.00 0.00 0.00 2.59
2240 2446 1.004628 TGCGGGCTCCATATTGCATAT 59.995 47.619 0.00 0.00 0.00 1.78
2241 2447 0.399833 TGCGGGCTCCATATTGCATA 59.600 50.000 0.00 0.00 0.00 3.14
2242 2448 1.151221 TGCGGGCTCCATATTGCAT 59.849 52.632 0.00 0.00 0.00 3.96
2243 2449 1.823470 GTGCGGGCTCCATATTGCA 60.823 57.895 0.00 0.00 0.00 4.08
2244 2450 1.526917 AGTGCGGGCTCCATATTGC 60.527 57.895 0.00 0.00 0.00 3.56
2245 2451 0.179048 TCAGTGCGGGCTCCATATTG 60.179 55.000 0.00 0.00 0.00 1.90
2246 2452 0.767375 ATCAGTGCGGGCTCCATATT 59.233 50.000 0.00 0.00 0.00 1.28
2247 2453 1.644509 TATCAGTGCGGGCTCCATAT 58.355 50.000 0.00 0.00 0.00 1.78
2248 2454 1.419381 TTATCAGTGCGGGCTCCATA 58.581 50.000 0.00 0.00 0.00 2.74
2249 2455 0.767375 ATTATCAGTGCGGGCTCCAT 59.233 50.000 0.00 0.00 0.00 3.41
2250 2456 0.106708 GATTATCAGTGCGGGCTCCA 59.893 55.000 0.00 0.00 0.00 3.86
2251 2457 0.603975 GGATTATCAGTGCGGGCTCC 60.604 60.000 0.00 0.00 0.00 4.70
2252 2458 0.603975 GGGATTATCAGTGCGGGCTC 60.604 60.000 0.00 0.00 0.00 4.70
2253 2459 1.451936 GGGATTATCAGTGCGGGCT 59.548 57.895 0.00 0.00 0.00 5.19
2254 2460 1.961277 CGGGATTATCAGTGCGGGC 60.961 63.158 0.00 0.00 0.00 6.13
2255 2461 1.961277 GCGGGATTATCAGTGCGGG 60.961 63.158 0.00 0.00 0.00 6.13
2256 2462 1.961277 GGCGGGATTATCAGTGCGG 60.961 63.158 0.00 0.00 0.00 5.69
2261 2479 2.158900 AGTGACTTGGCGGGATTATCAG 60.159 50.000 0.00 0.00 0.00 2.90
2320 2538 1.305201 TGAGGGTGTCTTTTTGCGAC 58.695 50.000 0.00 0.00 0.00 5.19
2333 2551 5.393027 GCGTAACAAAATGATGATTGAGGGT 60.393 40.000 0.00 0.00 0.00 4.34
2335 2553 4.730042 CGCGTAACAAAATGATGATTGAGG 59.270 41.667 0.00 0.00 0.00 3.86
2344 2562 4.274421 TGAACAACGCGTAACAAAATGA 57.726 36.364 14.46 0.00 0.00 2.57
2350 2568 2.288948 ACCCTATGAACAACGCGTAACA 60.289 45.455 14.46 11.08 0.00 2.41
2372 2590 0.179137 TGTTCGCAGCGATGGTCTAG 60.179 55.000 20.32 0.00 35.23 2.43
2395 2613 1.135228 GGAGGAGACGTCTCTTCAAGC 60.135 57.143 40.99 28.02 46.98 4.01
2398 2616 2.355920 GGTAGGAGGAGACGTCTCTTCA 60.356 54.545 40.99 27.87 46.98 3.02
2400 2618 1.407162 CGGTAGGAGGAGACGTCTCTT 60.407 57.143 36.98 32.92 42.48 2.85
2424 2642 1.519408 CTGTAAACCCAGTCCAACCG 58.481 55.000 0.00 0.00 0.00 4.44
2437 2655 7.775093 CCTCAAATCATGGATAGTTCCTGTAAA 59.225 37.037 0.00 0.00 43.07 2.01
2441 2659 4.518211 GCCTCAAATCATGGATAGTTCCTG 59.482 45.833 0.00 0.00 43.07 3.86
2443 2661 3.823304 GGCCTCAAATCATGGATAGTTCC 59.177 47.826 0.00 0.00 42.94 3.62
2449 2667 1.700955 GCAGGCCTCAAATCATGGAT 58.299 50.000 0.00 0.00 0.00 3.41
2454 2672 1.941377 AAATGGCAGGCCTCAAATCA 58.059 45.000 0.00 0.00 36.94 2.57
2479 2697 4.783227 AGGAGTTTTGTCCATAAGGCTCTA 59.217 41.667 0.00 0.00 39.34 2.43
2497 2715 0.036294 GCAGCCCGTTTTCTAGGAGT 60.036 55.000 0.00 0.00 0.00 3.85
2502 2720 1.375013 GTCCGCAGCCCGTTTTCTA 60.375 57.895 0.00 0.00 34.38 2.10
2514 2733 2.289631 ACATTGTCTTCTCATGTCCGCA 60.290 45.455 0.00 0.00 0.00 5.69
2521 2740 2.644299 TGGACCCACATTGTCTTCTCAT 59.356 45.455 0.00 0.00 33.22 2.90
2543 2762 5.339008 TTCTGTGTGTAGTGTCTGAGTTT 57.661 39.130 0.00 0.00 0.00 2.66
2544 2763 5.339008 TTTCTGTGTGTAGTGTCTGAGTT 57.661 39.130 0.00 0.00 0.00 3.01
2562 2781 1.675552 CCGGGCGATGGTAATTTTCT 58.324 50.000 0.00 0.00 0.00 2.52
2564 2783 1.388837 GGCCGGGCGATGGTAATTTT 61.389 55.000 14.21 0.00 0.00 1.82
2596 2815 2.283809 CCTCGGGGATGGAGGTCT 59.716 66.667 0.00 0.00 44.92 3.85
2609 2828 2.202703 CGCCGTAACTTCCCCTCG 60.203 66.667 0.00 0.00 0.00 4.63
2661 2880 0.820871 TTGTGGAAAGTGCCGCTTTT 59.179 45.000 4.51 0.00 46.54 2.27
2706 2925 2.852495 CTTGGCGGCCTATGTCGTGT 62.852 60.000 21.46 0.00 42.91 4.49
2725 2944 1.988406 ACCTAGCCTCGTTGGGGAC 60.988 63.158 0.00 0.00 36.00 4.46
2726 2945 1.987855 CACCTAGCCTCGTTGGGGA 60.988 63.158 0.00 0.00 36.00 4.81
2727 2946 2.584608 CACCTAGCCTCGTTGGGG 59.415 66.667 0.05 0.00 36.00 4.96
2753 2972 4.851843 TCTGACAAACTCTCCGGATACTA 58.148 43.478 3.57 0.00 0.00 1.82
2761 2980 1.343465 TCCGGTTCTGACAAACTCTCC 59.657 52.381 0.00 0.00 0.00 3.71
2815 3034 3.418684 AACATTTGGGTCTAACGAGCT 57.581 42.857 0.00 0.00 37.77 4.09
2816 3035 3.252458 ACAAACATTTGGGTCTAACGAGC 59.748 43.478 9.09 0.00 42.34 5.03
2820 3039 6.206498 GTTCTGACAAACATTTGGGTCTAAC 58.794 40.000 9.09 3.63 42.34 2.34
2853 3072 6.351202 CCTCAACTGCCCATAATGAAAATTGA 60.351 38.462 0.00 0.00 0.00 2.57
2859 3078 2.580322 TCCCTCAACTGCCCATAATGAA 59.420 45.455 0.00 0.00 0.00 2.57
2860 3079 2.204463 TCCCTCAACTGCCCATAATGA 58.796 47.619 0.00 0.00 0.00 2.57
2875 3094 2.893489 ACTCAATGCTTTTGGTTCCCTC 59.107 45.455 1.03 0.00 0.00 4.30
2916 3135 1.369091 CGCACGCTTATTCCCTTGCT 61.369 55.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.