Multiple sequence alignment - TraesCS3A01G449700

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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 TraesCS3A01G449700 chr3A 100.000 2582 0 0 1 2582 688916849 688914268 0.000000e+00 4769.0
1 TraesCS3A01G449700 chr3A 91.341 820 41 16 961 1760 688907742 688906933 0.000000e+00 1094.0
2 TraesCS3A01G449700 chr3A 88.263 639 56 10 961 1582 688899033 688898397 0.000000e+00 747.0
3 TraesCS3A01G449700 chr3A 87.583 604 59 8 992 1582 688987045 688986445 0.000000e+00 686.0
4 TraesCS3A01G449700 chr3A 83.543 717 87 16 883 1582 688992937 688993639 2.170000e-180 641.0
5 TraesCS3A01G449700 chr3A 88.115 244 28 1 2102 2344 688906460 688906217 3.250000e-74 289.0
6 TraesCS3A01G449700 chr3A 90.476 126 12 0 1844 1969 688906899 688906774 1.590000e-37 167.0
7 TraesCS3A01G449700 chr3A 100.000 30 0 0 1811 1840 688914996 688914967 3.590000e-04 56.5
8 TraesCS3A01G449700 chr3A 100.000 30 0 0 1854 1883 688915039 688915010 3.590000e-04 56.5
9 TraesCS3A01G449700 chr3D 87.559 1913 135 43 514 2358 552425297 552423420 0.000000e+00 2119.0
10 TraesCS3A01G449700 chr3D 87.966 1529 114 29 961 2457 552416941 552415451 0.000000e+00 1740.0
11 TraesCS3A01G449700 chr3D 94.106 492 17 3 1 492 552434174 552433695 0.000000e+00 737.0
12 TraesCS3A01G449700 chr3D 88.543 611 60 8 976 1582 552289475 552288871 0.000000e+00 732.0
13 TraesCS3A01G449700 chr3D 86.491 607 63 11 992 1582 552609841 552609238 0.000000e+00 649.0
14 TraesCS3A01G449700 chr3D 83.817 241 26 4 2355 2582 552423260 552423020 1.560000e-52 217.0
15 TraesCS3A01G449700 chr3B 87.241 1787 134 38 713 2451 732857677 732855937 0.000000e+00 1951.0
16 TraesCS3A01G449700 chr3B 87.101 690 67 11 957 1633 732845776 732845096 0.000000e+00 761.0
17 TraesCS3A01G449700 chr3B 81.403 898 111 36 717 1582 732841903 732841030 0.000000e+00 682.0
18 TraesCS3A01G449700 chr3B 83.312 791 78 28 1632 2421 732844893 732844156 0.000000e+00 680.0
19 TraesCS3A01G449700 chr3B 89.021 337 11 15 2 327 732859449 732859128 6.700000e-106 394.0
20 TraesCS3A01G449700 chr3B 100.000 35 0 0 2479 2513 732855934 732855900 5.960000e-07 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 TraesCS3A01G449700 chr3A 688914268 688916849 2581 True 1627.333333 4769 100.000000 1 2582 3 chr3A.!!$R4 2581
1 TraesCS3A01G449700 chr3A 688898397 688899033 636 True 747.000000 747 88.263000 961 1582 1 chr3A.!!$R1 621
2 TraesCS3A01G449700 chr3A 688986445 688987045 600 True 686.000000 686 87.583000 992 1582 1 chr3A.!!$R2 590
3 TraesCS3A01G449700 chr3A 688992937 688993639 702 False 641.000000 641 83.543000 883 1582 1 chr3A.!!$F1 699
4 TraesCS3A01G449700 chr3A 688906217 688907742 1525 True 516.666667 1094 89.977333 961 2344 3 chr3A.!!$R3 1383
5 TraesCS3A01G449700 chr3D 552415451 552416941 1490 True 1740.000000 1740 87.966000 961 2457 1 chr3D.!!$R2 1496
6 TraesCS3A01G449700 chr3D 552423020 552425297 2277 True 1168.000000 2119 85.688000 514 2582 2 chr3D.!!$R5 2068
7 TraesCS3A01G449700 chr3D 552288871 552289475 604 True 732.000000 732 88.543000 976 1582 1 chr3D.!!$R1 606
8 TraesCS3A01G449700 chr3D 552609238 552609841 603 True 649.000000 649 86.491000 992 1582 1 chr3D.!!$R4 590
9 TraesCS3A01G449700 chr3B 732855900 732859449 3549 True 803.600000 1951 92.087333 2 2513 3 chr3B.!!$R2 2511
10 TraesCS3A01G449700 chr3B 732841030 732845776 4746 True 707.666667 761 83.938667 717 2421 3 chr3B.!!$R1 1704

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
142 145 0.03601 CGGCAAGTCAAGTCAGGGAT 60.036 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 3495 0.815213 TTCAGTGCGACAGCTGCTTT 60.815 50.0 15.27 0.0 45.42 3.51 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
50 52 7.337942 TGATTTAGCTTTTCCTCTCTTGAATCC 59.662 37.037 0.00 0.00 0.00 3.01
81 83 0.591659 CGAACAGAGTGAGGTGTCGA 59.408 55.000 0.00 0.00 0.00 4.20
82 84 1.663445 CGAACAGAGTGAGGTGTCGAC 60.663 57.143 9.11 9.11 0.00 4.20
83 85 1.609555 GAACAGAGTGAGGTGTCGACT 59.390 52.381 17.92 0.00 0.00 4.18
84 86 0.955178 ACAGAGTGAGGTGTCGACTG 59.045 55.000 17.92 5.62 0.00 3.51
85 87 0.955178 CAGAGTGAGGTGTCGACTGT 59.045 55.000 17.92 0.39 0.00 3.55
86 88 1.068885 CAGAGTGAGGTGTCGACTGTC 60.069 57.143 17.92 10.83 0.00 3.51
87 89 0.110147 GAGTGAGGTGTCGACTGTCG 60.110 60.000 23.33 23.33 42.10 4.35
99 101 1.151668 GACTGTCGAGCATGCAACTT 58.848 50.000 21.98 0.00 0.00 2.66
123 126 4.641954 CTGAACAAGAACATATGACACGC 58.358 43.478 10.38 0.00 0.00 5.34
124 127 3.122780 TGAACAAGAACATATGACACGCG 59.877 43.478 10.38 3.53 0.00 6.01
133 136 0.319986 TATGACACGCGGCAAGTCAA 60.320 50.000 22.66 12.65 44.47 3.18
134 137 1.568612 ATGACACGCGGCAAGTCAAG 61.569 55.000 22.66 0.00 44.47 3.02
135 138 2.203015 ACACGCGGCAAGTCAAGT 60.203 55.556 12.47 0.00 0.00 3.16
136 139 2.159272 GACACGCGGCAAGTCAAGTC 62.159 60.000 12.47 0.31 32.68 3.01
137 140 2.108157 ACGCGGCAAGTCAAGTCA 59.892 55.556 12.47 0.00 0.00 3.41
138 141 1.956170 ACGCGGCAAGTCAAGTCAG 60.956 57.895 12.47 0.00 0.00 3.51
139 142 2.671177 CGCGGCAAGTCAAGTCAGG 61.671 63.158 0.00 0.00 0.00 3.86
140 143 2.328099 GCGGCAAGTCAAGTCAGGG 61.328 63.158 0.00 0.00 0.00 4.45
141 144 1.371183 CGGCAAGTCAAGTCAGGGA 59.629 57.895 0.00 0.00 0.00 4.20
142 145 0.036010 CGGCAAGTCAAGTCAGGGAT 60.036 55.000 0.00 0.00 0.00 3.85
143 146 1.743996 GGCAAGTCAAGTCAGGGATC 58.256 55.000 0.00 0.00 0.00 3.36
144 147 1.003580 GGCAAGTCAAGTCAGGGATCA 59.996 52.381 0.00 0.00 0.00 2.92
186 189 3.904339 ACTTTCCTAGCTTTGAGAGGTCA 59.096 43.478 0.00 0.00 37.30 4.02
206 209 5.268544 GTCACAACTGTAGCGTATCGAATA 58.731 41.667 0.00 0.00 0.00 1.75
215 218 4.098055 AGCGTATCGAATATAGCACTGG 57.902 45.455 0.00 0.00 0.00 4.00
275 281 5.964958 TGCAAAATGAAAGAGAGGTAAGG 57.035 39.130 0.00 0.00 0.00 2.69
309 321 7.706607 GTGTGATATATATGTGCCATCGTGTAT 59.293 37.037 0.00 0.00 0.00 2.29
311 323 9.399403 GTGATATATATGTGCCATCGTGTATAG 57.601 37.037 0.00 0.00 0.00 1.31
318 330 4.036380 TGTGCCATCGTGTATAGAGTGTAG 59.964 45.833 0.00 0.00 0.00 2.74
334 430 7.411486 AGAGTGTAGAATGTACTTGTAGCAT 57.589 36.000 0.00 0.00 0.00 3.79
336 432 6.574350 AGTGTAGAATGTACTTGTAGCATCC 58.426 40.000 0.00 0.00 0.00 3.51
337 433 5.753921 GTGTAGAATGTACTTGTAGCATCCC 59.246 44.000 0.00 0.00 0.00 3.85
364 460 6.095720 ACTTTACAAAAGACAAACGATGGGAA 59.904 34.615 6.41 0.00 0.00 3.97
367 463 1.534729 AAGACAAACGATGGGAAGGC 58.465 50.000 0.00 0.00 0.00 4.35
382 478 2.017559 AAGGCCCGAGATCGTACAGC 62.018 60.000 0.00 0.00 37.74 4.40
396 492 2.324541 GTACAGCATCTGATCCCTCCT 58.675 52.381 0.29 0.00 35.18 3.69
397 493 1.422531 ACAGCATCTGATCCCTCCTC 58.577 55.000 0.29 0.00 35.18 3.71
398 494 0.317799 CAGCATCTGATCCCTCCTCG 59.682 60.000 0.00 0.00 32.44 4.63
399 495 0.105760 AGCATCTGATCCCTCCTCGT 60.106 55.000 0.00 0.00 0.00 4.18
400 496 0.755686 GCATCTGATCCCTCCTCGTT 59.244 55.000 0.00 0.00 0.00 3.85
408 504 0.252103 TCCCTCCTCGTTGGTTAGCT 60.252 55.000 0.00 0.00 37.07 3.32
414 510 4.281182 CCTCCTCGTTGGTTAGCTATGTAT 59.719 45.833 0.00 0.00 37.07 2.29
415 511 5.475909 CCTCCTCGTTGGTTAGCTATGTATA 59.524 44.000 0.00 0.00 37.07 1.47
416 512 6.323203 TCCTCGTTGGTTAGCTATGTATAC 57.677 41.667 0.00 0.00 37.07 1.47
417 513 5.242393 TCCTCGTTGGTTAGCTATGTATACC 59.758 44.000 4.81 4.81 37.07 2.73
433 760 6.961359 TGTATACCAAAGAACTCATCGTTG 57.039 37.500 0.00 0.00 44.22 4.10
434 761 6.693466 TGTATACCAAAGAACTCATCGTTGA 58.307 36.000 0.00 0.00 46.54 3.18
436 763 4.073293 ACCAAAGAACTCATCGTTGACT 57.927 40.909 5.83 0.00 46.54 3.41
441 768 4.527509 AGAACTCATCGTTGACTCACAT 57.472 40.909 0.00 0.00 35.56 3.21
449 776 4.594123 TCGTTGACTCACATCTAAACCA 57.406 40.909 0.00 0.00 0.00 3.67
453 780 8.002984 TCGTTGACTCACATCTAAACCATATA 57.997 34.615 0.00 0.00 0.00 0.86
454 781 8.638873 TCGTTGACTCACATCTAAACCATATAT 58.361 33.333 0.00 0.00 0.00 0.86
455 782 9.908152 CGTTGACTCACATCTAAACCATATATA 57.092 33.333 0.00 0.00 0.00 0.86
470 797 8.962884 AACCATATATATAATCAATGAGCGCA 57.037 30.769 11.47 0.00 0.00 6.09
471 798 9.565090 AACCATATATATAATCAATGAGCGCAT 57.435 29.630 11.47 0.00 35.92 4.73
479 806 9.958234 ATATAATCAATGAGCGCATACTACTAG 57.042 33.333 11.47 0.00 33.44 2.57
480 807 5.713792 ATCAATGAGCGCATACTACTAGT 57.286 39.130 11.47 0.00 33.44 2.57
481 808 6.819397 ATCAATGAGCGCATACTACTAGTA 57.181 37.500 11.47 1.89 34.82 1.82
482 809 6.819397 TCAATGAGCGCATACTACTAGTAT 57.181 37.500 11.47 3.21 41.82 2.12
483 810 7.215719 TCAATGAGCGCATACTACTAGTATT 57.784 36.000 11.47 0.00 39.26 1.89
484 811 8.331730 TCAATGAGCGCATACTACTAGTATTA 57.668 34.615 11.47 2.57 39.26 0.98
485 812 8.451748 TCAATGAGCGCATACTACTAGTATTAG 58.548 37.037 11.47 0.00 39.26 1.73
487 814 5.704053 TGAGCGCATACTACTAGTATTAGCA 59.296 40.000 22.37 10.21 39.26 3.49
488 815 6.374613 TGAGCGCATACTACTAGTATTAGCAT 59.625 38.462 22.37 13.82 39.26 3.79
489 816 6.787225 AGCGCATACTACTAGTATTAGCATC 58.213 40.000 22.37 12.75 39.26 3.91
491 818 6.404403 GCGCATACTACTAGTATTAGCATCCA 60.404 42.308 18.75 0.00 39.26 3.41
493 820 8.837389 CGCATACTACTAGTATTAGCATCCATA 58.163 37.037 2.33 0.00 39.26 2.74
494 821 9.953697 GCATACTACTAGTATTAGCATCCATAC 57.046 37.037 2.33 0.00 39.26 2.39
501 828 9.160496 ACTAGTATTAGCATCCATACTACGTAC 57.840 37.037 0.00 0.00 37.40 3.67
502 829 7.069852 AGTATTAGCATCCATACTACGTACG 57.930 40.000 15.01 15.01 34.95 3.67
503 830 2.701073 AGCATCCATACTACGTACGC 57.299 50.000 16.72 0.00 0.00 4.42
504 831 1.069432 AGCATCCATACTACGTACGCG 60.069 52.381 16.72 3.53 44.93 6.01
505 832 1.959747 CATCCATACTACGTACGCGG 58.040 55.000 16.72 10.82 43.45 6.46
507 834 0.937304 TCCATACTACGTACGCGGAC 59.063 55.000 16.72 12.68 43.45 4.79
532 1035 6.070656 GGATGATTAGAAAATGGGGATGACA 58.929 40.000 0.00 0.00 0.00 3.58
553 1056 5.025453 ACAACTGAAGAATATTGCCCCATT 58.975 37.500 0.00 0.00 0.00 3.16
554 1057 6.194235 ACAACTGAAGAATATTGCCCCATTA 58.806 36.000 0.00 0.00 0.00 1.90
561 1606 4.713321 AGAATATTGCCCCATTATCCATGC 59.287 41.667 0.00 0.00 0.00 4.06
570 1615 3.243501 CCCATTATCCATGCAAAACGAGG 60.244 47.826 0.00 0.00 0.00 4.63
673 1733 9.872757 CACAACAATCTGTAAATAGTACGTTTT 57.127 29.630 0.00 3.62 0.00 2.43
894 2012 6.204108 ACGGGATAACAAACAAAGTAGTTCAG 59.796 38.462 0.00 0.00 0.00 3.02
952 2076 0.374758 CACCGTCCAAATCATCGCAG 59.625 55.000 0.00 0.00 0.00 5.18
964 2088 1.077930 ATCGCAGCATCAACAGCCT 60.078 52.632 0.00 0.00 0.00 4.58
1107 2285 2.839486 TGAAGTCGCTGGTCTTCAAT 57.161 45.000 5.34 0.00 44.29 2.57
1613 2831 4.337145 TCTAGTTCAGGTTCAGGTCTCTC 58.663 47.826 0.00 0.00 0.00 3.20
1617 2835 4.083565 GTTCAGGTTCAGGTCTCTCTAGT 58.916 47.826 0.00 0.00 0.00 2.57
1621 2839 5.014333 TCAGGTTCAGGTCTCTCTAGTTAGT 59.986 44.000 0.00 0.00 0.00 2.24
1623 2841 6.540914 CAGGTTCAGGTCTCTCTAGTTAGTAG 59.459 46.154 0.00 0.00 0.00 2.57
1625 2843 5.695424 TCAGGTCTCTCTAGTTAGTAGCA 57.305 43.478 0.00 0.00 0.00 3.49
1627 2845 5.881443 TCAGGTCTCTCTAGTTAGTAGCAAC 59.119 44.000 0.00 0.00 0.00 4.17
1629 2847 4.635324 GGTCTCTCTAGTTAGTAGCAACGT 59.365 45.833 0.00 0.00 33.50 3.99
1630 2848 5.814705 GGTCTCTCTAGTTAGTAGCAACGTA 59.185 44.000 0.00 0.00 33.50 3.57
1633 2851 6.756074 TCTCTCTAGTTAGTAGCAACGTAGAC 59.244 42.308 0.00 0.00 33.50 2.59
1634 2852 5.814705 TCTCTAGTTAGTAGCAACGTAGACC 59.185 44.000 0.00 0.00 33.50 3.85
1705 3125 1.337167 GGCATGGTGACTCTTTTTGGC 60.337 52.381 0.00 0.00 0.00 4.52
1760 3187 6.533819 TTTCACTACCATAGTTTCAACACG 57.466 37.500 0.00 0.00 36.76 4.49
1803 3230 9.613428 CAGTGATTGTATAAATCTTTGGGAGTA 57.387 33.333 0.30 0.00 0.00 2.59
1804 3231 9.614792 AGTGATTGTATAAATCTTTGGGAGTAC 57.385 33.333 0.30 0.00 0.00 2.73
1805 3232 9.614792 GTGATTGTATAAATCTTTGGGAGTACT 57.385 33.333 0.00 0.00 0.00 2.73
1818 3245 8.488668 TCTTTGGGAGTACTTAGTTTAGTTTGT 58.511 33.333 0.00 0.00 0.00 2.83
1819 3246 8.441312 TTTGGGAGTACTTAGTTTAGTTTGTG 57.559 34.615 0.00 0.00 0.00 3.33
1820 3247 6.527423 TGGGAGTACTTAGTTTAGTTTGTGG 58.473 40.000 0.00 0.00 0.00 4.17
1821 3248 5.936372 GGGAGTACTTAGTTTAGTTTGTGGG 59.064 44.000 0.00 0.00 0.00 4.61
1822 3249 6.239686 GGGAGTACTTAGTTTAGTTTGTGGGA 60.240 42.308 0.00 0.00 0.00 4.37
1823 3250 6.872547 GGAGTACTTAGTTTAGTTTGTGGGAG 59.127 42.308 0.00 0.00 0.00 4.30
1824 3251 7.370905 AGTACTTAGTTTAGTTTGTGGGAGT 57.629 36.000 0.00 0.00 0.00 3.85
1825 3252 8.482852 AGTACTTAGTTTAGTTTGTGGGAGTA 57.517 34.615 0.00 0.00 0.00 2.59
1826 3253 8.363390 AGTACTTAGTTTAGTTTGTGGGAGTAC 58.637 37.037 0.00 0.00 37.22 2.73
1827 3254 7.370905 ACTTAGTTTAGTTTGTGGGAGTACT 57.629 36.000 0.00 0.00 0.00 2.73
1828 3255 7.799081 ACTTAGTTTAGTTTGTGGGAGTACTT 58.201 34.615 0.00 0.00 0.00 2.24
1829 3256 8.927411 ACTTAGTTTAGTTTGTGGGAGTACTTA 58.073 33.333 0.00 0.00 0.00 2.24
1830 3257 9.420551 CTTAGTTTAGTTTGTGGGAGTACTTAG 57.579 37.037 0.00 0.00 0.00 2.18
1831 3258 7.370905 AGTTTAGTTTGTGGGAGTACTTAGT 57.629 36.000 0.00 0.00 0.00 2.24
1832 3259 7.799081 AGTTTAGTTTGTGGGAGTACTTAGTT 58.201 34.615 0.00 0.00 0.00 2.24
1833 3260 8.270030 AGTTTAGTTTGTGGGAGTACTTAGTTT 58.730 33.333 0.00 0.00 0.00 2.66
1834 3261 9.546428 GTTTAGTTTGTGGGAGTACTTAGTTTA 57.454 33.333 0.00 0.00 0.00 2.01
1939 3366 9.703892 CTCCAATATAAGACTTTATGGTCTCAG 57.296 37.037 0.00 0.00 44.67 3.35
2001 3455 1.202580 AGAAGAGGCTGACACACACAC 60.203 52.381 0.00 0.00 0.00 3.82
2020 3474 3.815401 ACACAAACATTAGCCAGTCACTC 59.185 43.478 0.00 0.00 0.00 3.51
2021 3475 3.814842 CACAAACATTAGCCAGTCACTCA 59.185 43.478 0.00 0.00 0.00 3.41
2023 3477 4.067896 CAAACATTAGCCAGTCACTCACT 58.932 43.478 0.00 0.00 34.67 3.41
2034 3488 2.111878 ACTCACTGGCAGTGGCAC 59.888 61.111 38.88 10.29 45.94 5.01
2100 3558 3.456380 AAGTTCAATAGGGCACACCAT 57.544 42.857 0.00 0.00 43.89 3.55
2110 3568 2.158534 AGGGCACACCATAACTTCAACA 60.159 45.455 0.00 0.00 43.89 3.33
2113 3571 3.067461 GGCACACCATAACTTCAACACAA 59.933 43.478 0.00 0.00 35.26 3.33
2114 3572 4.440802 GGCACACCATAACTTCAACACAAA 60.441 41.667 0.00 0.00 35.26 2.83
2115 3573 4.739716 GCACACCATAACTTCAACACAAAG 59.260 41.667 0.00 0.00 0.00 2.77
2191 3809 3.016736 TGCCAGCCTTATTAAACTCAGC 58.983 45.455 0.00 0.00 0.00 4.26
2236 3854 1.855978 CAAAGTGTGTACAACGAGCGA 59.144 47.619 0.00 0.00 0.00 4.93
2239 3857 2.542597 AGTGTGTACAACGAGCGAAAA 58.457 42.857 0.00 0.00 0.00 2.29
2274 3892 1.439228 GGCGACAGAGATAGCTGCA 59.561 57.895 1.02 0.00 39.51 4.41
2275 3893 0.873743 GGCGACAGAGATAGCTGCAC 60.874 60.000 1.02 0.00 39.51 4.57
2309 3928 2.747822 GCGAGCGTCAGACCGTCTA 61.748 63.158 0.00 0.00 0.00 2.59
2322 3941 0.774908 CCGTCTATCTCCCTCCCTCT 59.225 60.000 0.00 0.00 0.00 3.69
2349 3969 2.357952 GGTTGGAATAATTCACCGGCTC 59.642 50.000 0.00 0.00 0.00 4.70
2413 4197 5.024785 AGCCTATAACCGGAGAAAAAGAG 57.975 43.478 9.46 0.00 0.00 2.85
2418 4202 7.094506 GCCTATAACCGGAGAAAAAGAGAAAAA 60.095 37.037 9.46 0.00 0.00 1.94
2427 4211 6.094193 AGAAAAAGAGAAAAATGAGCCCAG 57.906 37.500 0.00 0.00 0.00 4.45
2457 4241 1.227102 GGTGCCTGGCCACATGATA 59.773 57.895 17.53 0.00 37.46 2.15
2477 4261 2.034879 CGCTCACGCCATTTCCACT 61.035 57.895 0.00 0.00 0.00 4.00
2514 5382 0.036952 CTCGTCTGCCAGTTGACCAT 60.037 55.000 0.00 0.00 0.00 3.55
2515 5383 0.037326 TCGTCTGCCAGTTGACCATC 60.037 55.000 0.00 0.00 0.00 3.51
2516 5384 0.036952 CGTCTGCCAGTTGACCATCT 60.037 55.000 0.00 0.00 0.00 2.90
2517 5385 1.731720 GTCTGCCAGTTGACCATCTC 58.268 55.000 0.00 0.00 0.00 2.75
2518 5386 1.002430 GTCTGCCAGTTGACCATCTCA 59.998 52.381 0.00 0.00 0.00 3.27
2520 5388 2.106338 TCTGCCAGTTGACCATCTCAAA 59.894 45.455 0.00 0.00 40.73 2.69
2521 5389 2.227388 CTGCCAGTTGACCATCTCAAAC 59.773 50.000 0.00 0.00 40.73 2.93
2523 5404 2.485814 GCCAGTTGACCATCTCAAACTC 59.514 50.000 0.00 0.00 40.73 3.01
2526 5407 4.503817 CCAGTTGACCATCTCAAACTCTGA 60.504 45.833 0.00 0.00 40.73 3.27
2541 5422 4.278975 ACTCTGACCTTCTCAAACCATC 57.721 45.455 0.00 0.00 0.00 3.51
2542 5423 3.257393 CTCTGACCTTCTCAAACCATCG 58.743 50.000 0.00 0.00 0.00 3.84
2545 5426 4.709886 TCTGACCTTCTCAAACCATCGATA 59.290 41.667 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.152932 ACTTTTCATTTTCACATGTGAGCT 57.847 33.333 26.48 13.62 41.13 4.09
50 52 2.943033 ACTCTGTTCGTTTTCCAACCTG 59.057 45.455 0.00 0.00 0.00 4.00
81 83 0.870393 CAAGTTGCATGCTCGACAGT 59.130 50.000 20.33 4.81 0.00 3.55
82 84 0.453950 GCAAGTTGCATGCTCGACAG 60.454 55.000 22.90 11.95 44.26 3.51
83 85 1.575922 GCAAGTTGCATGCTCGACA 59.424 52.632 22.90 0.00 44.26 4.35
84 86 4.447365 GCAAGTTGCATGCTCGAC 57.553 55.556 22.90 14.41 44.26 4.20
99 101 4.152223 CGTGTCATATGTTCTTGTTCAGCA 59.848 41.667 1.90 0.00 0.00 4.41
119 122 2.162921 CTGACTTGACTTGCCGCGTG 62.163 60.000 4.92 0.00 0.00 5.34
123 126 0.036010 ATCCCTGACTTGACTTGCCG 60.036 55.000 0.00 0.00 0.00 5.69
124 127 1.003580 TGATCCCTGACTTGACTTGCC 59.996 52.381 0.00 0.00 0.00 4.52
133 136 0.832135 ACGGTGTGTGATCCCTGACT 60.832 55.000 0.00 0.00 0.00 3.41
134 137 0.034896 AACGGTGTGTGATCCCTGAC 59.965 55.000 0.00 0.00 0.00 3.51
135 138 0.762418 AAACGGTGTGTGATCCCTGA 59.238 50.000 0.00 0.00 0.00 3.86
136 139 2.465860 TAAACGGTGTGTGATCCCTG 57.534 50.000 0.00 0.00 0.00 4.45
137 140 3.606687 GAATAAACGGTGTGTGATCCCT 58.393 45.455 0.00 0.00 0.00 4.20
138 141 2.350498 CGAATAAACGGTGTGTGATCCC 59.650 50.000 0.00 0.00 0.00 3.85
139 142 3.061697 GTCGAATAAACGGTGTGTGATCC 59.938 47.826 0.00 0.00 0.00 3.36
140 143 3.241552 CGTCGAATAAACGGTGTGTGATC 60.242 47.826 0.00 0.00 36.51 2.92
141 144 2.664568 CGTCGAATAAACGGTGTGTGAT 59.335 45.455 0.00 0.00 36.51 3.06
142 145 2.052891 CGTCGAATAAACGGTGTGTGA 58.947 47.619 0.00 0.00 36.51 3.58
143 146 1.788308 ACGTCGAATAAACGGTGTGTG 59.212 47.619 0.00 0.00 44.21 3.82
144 147 2.138596 ACGTCGAATAAACGGTGTGT 57.861 45.000 0.00 0.00 44.21 3.72
186 189 6.084925 GCTATATTCGATACGCTACAGTTGT 58.915 40.000 0.00 0.00 0.00 3.32
206 209 2.831685 TCAAACGTGACCAGTGCTAT 57.168 45.000 0.00 0.00 0.00 2.97
275 281 6.089016 GGCACATATATATCACACACGTGTAC 59.911 42.308 22.90 0.00 42.83 2.90
309 321 7.933215 TGCTACAAGTACATTCTACACTCTA 57.067 36.000 0.00 0.00 0.00 2.43
311 323 6.697892 GGATGCTACAAGTACATTCTACACTC 59.302 42.308 0.00 0.00 0.00 3.51
318 330 3.877508 GTGGGGATGCTACAAGTACATTC 59.122 47.826 0.00 0.00 0.00 2.67
334 430 4.096682 CGTTTGTCTTTTGTAAAGTGGGGA 59.903 41.667 0.00 0.00 0.00 4.81
336 432 5.238006 TCGTTTGTCTTTTGTAAAGTGGG 57.762 39.130 0.00 0.00 0.00 4.61
337 433 5.685511 CCATCGTTTGTCTTTTGTAAAGTGG 59.314 40.000 0.00 0.00 0.00 4.00
364 460 2.491022 GCTGTACGATCTCGGGCCT 61.491 63.158 0.84 0.00 44.95 5.19
367 463 0.955178 AGATGCTGTACGATCTCGGG 59.045 55.000 4.44 0.00 44.95 5.14
382 478 1.069823 CCAACGAGGAGGGATCAGATG 59.930 57.143 0.00 0.00 41.22 2.90
396 492 6.468333 TTGGTATACATAGCTAACCAACGA 57.532 37.500 18.80 2.52 43.44 3.85
397 493 6.982141 TCTTTGGTATACATAGCTAACCAACG 59.018 38.462 21.33 19.65 46.84 4.10
398 494 8.610035 GTTCTTTGGTATACATAGCTAACCAAC 58.390 37.037 21.33 10.87 46.84 3.77
399 495 8.545472 AGTTCTTTGGTATACATAGCTAACCAA 58.455 33.333 18.80 18.80 45.86 3.67
400 496 8.086143 AGTTCTTTGGTATACATAGCTAACCA 57.914 34.615 9.71 9.71 38.42 3.67
408 504 8.471609 TCAACGATGAGTTCTTTGGTATACATA 58.528 33.333 5.01 0.00 42.02 2.29
414 510 5.209818 AGTCAACGATGAGTTCTTTGGTA 57.790 39.130 0.00 0.00 42.02 3.25
415 511 4.058817 GAGTCAACGATGAGTTCTTTGGT 58.941 43.478 4.36 0.00 42.02 3.67
416 512 4.058124 TGAGTCAACGATGAGTTCTTTGG 58.942 43.478 4.36 0.00 42.02 3.28
417 513 4.507756 TGTGAGTCAACGATGAGTTCTTTG 59.492 41.667 4.36 0.00 42.02 2.77
453 780 9.958234 CTAGTAGTATGCGCTCATTGATTATAT 57.042 33.333 9.73 0.00 34.22 0.86
454 781 8.957466 ACTAGTAGTATGCGCTCATTGATTATA 58.043 33.333 9.73 0.00 34.22 0.98
455 782 7.831753 ACTAGTAGTATGCGCTCATTGATTAT 58.168 34.615 9.73 0.00 34.22 1.28
456 783 7.215719 ACTAGTAGTATGCGCTCATTGATTA 57.784 36.000 9.73 0.00 34.22 1.75
457 784 6.090483 ACTAGTAGTATGCGCTCATTGATT 57.910 37.500 9.73 0.00 34.22 2.57
458 785 5.713792 ACTAGTAGTATGCGCTCATTGAT 57.286 39.130 9.73 0.00 34.22 2.57
459 786 6.819397 ATACTAGTAGTATGCGCTCATTGA 57.181 37.500 19.87 0.00 39.76 2.57
460 787 7.219154 GCTAATACTAGTAGTATGCGCTCATTG 59.781 40.741 20.98 7.89 40.32 2.82
461 788 7.094334 TGCTAATACTAGTAGTATGCGCTCATT 60.094 37.037 27.27 15.48 40.32 2.57
462 789 6.374613 TGCTAATACTAGTAGTATGCGCTCAT 59.625 38.462 27.27 14.81 40.32 2.90
464 791 6.179504 TGCTAATACTAGTAGTATGCGCTC 57.820 41.667 27.27 16.23 40.32 5.03
466 793 5.972382 GGATGCTAATACTAGTAGTATGCGC 59.028 44.000 20.98 22.75 40.32 6.09
468 795 9.953697 GTATGGATGCTAATACTAGTAGTATGC 57.046 37.037 20.98 19.83 40.32 3.14
493 820 1.815421 ATCCGTCCGCGTACGTAGT 60.815 57.895 22.61 5.51 41.27 2.73
494 821 1.368493 CATCCGTCCGCGTACGTAG 60.368 63.158 22.61 8.74 41.27 3.51
496 823 1.996786 AATCATCCGTCCGCGTACGT 61.997 55.000 22.61 2.19 41.27 3.57
497 824 0.041047 TAATCATCCGTCCGCGTACG 60.041 55.000 17.89 17.89 42.49 3.67
500 827 0.742505 TTCTAATCATCCGTCCGCGT 59.257 50.000 4.92 0.00 36.15 6.01
501 828 1.847818 TTTCTAATCATCCGTCCGCG 58.152 50.000 0.00 0.00 37.95 6.46
502 829 3.058914 CCATTTTCTAATCATCCGTCCGC 60.059 47.826 0.00 0.00 0.00 5.54
503 830 3.498397 CCCATTTTCTAATCATCCGTCCG 59.502 47.826 0.00 0.00 0.00 4.79
504 831 3.821033 CCCCATTTTCTAATCATCCGTCC 59.179 47.826 0.00 0.00 0.00 4.79
505 832 4.714632 TCCCCATTTTCTAATCATCCGTC 58.285 43.478 0.00 0.00 0.00 4.79
507 834 5.182001 GTCATCCCCATTTTCTAATCATCCG 59.818 44.000 0.00 0.00 0.00 4.18
508 835 6.070656 TGTCATCCCCATTTTCTAATCATCC 58.929 40.000 0.00 0.00 0.00 3.51
510 837 7.069085 CAGTTGTCATCCCCATTTTCTAATCAT 59.931 37.037 0.00 0.00 0.00 2.45
511 838 6.377996 CAGTTGTCATCCCCATTTTCTAATCA 59.622 38.462 0.00 0.00 0.00 2.57
512 839 6.603201 TCAGTTGTCATCCCCATTTTCTAATC 59.397 38.462 0.00 0.00 0.00 1.75
532 1035 6.494835 GGATAATGGGGCAATATTCTTCAGTT 59.505 38.462 0.00 0.00 0.00 3.16
553 1056 1.562008 TCCCCTCGTTTTGCATGGATA 59.438 47.619 0.00 0.00 0.00 2.59
554 1057 0.331278 TCCCCTCGTTTTGCATGGAT 59.669 50.000 0.00 0.00 0.00 3.41
561 1606 5.240844 AGTCATTTAGTTTCCCCTCGTTTTG 59.759 40.000 0.00 0.00 0.00 2.44
619 1679 0.670162 GCAGAAAGAAAGCAGGCACA 59.330 50.000 0.00 0.00 0.00 4.57
673 1733 6.558771 ATCGCGATTAAAATTGGATGATCA 57.441 33.333 17.62 0.00 0.00 2.92
873 1991 6.966021 TGCCTGAACTACTTTGTTTGTTATC 58.034 36.000 0.00 0.00 0.00 1.75
878 1996 4.321230 GGGATGCCTGAACTACTTTGTTTG 60.321 45.833 0.00 0.00 0.00 2.93
879 1997 3.826729 GGGATGCCTGAACTACTTTGTTT 59.173 43.478 0.00 0.00 0.00 2.83
894 2012 6.374417 TTCACCTATTTATAGAGGGATGCC 57.626 41.667 0.00 0.00 37.06 4.40
952 2076 1.297664 CTCTGCTAGGCTGTTGATGC 58.702 55.000 0.00 0.00 0.00 3.91
964 2088 5.674052 AGAAGAAGAAGATTGCTCTGCTA 57.326 39.130 0.00 0.00 36.25 3.49
1613 2831 5.808042 TGGTCTACGTTGCTACTAACTAG 57.192 43.478 0.00 0.00 0.00 2.57
1678 3098 1.064906 AGAGTCACCATGCCAATCTGG 60.065 52.381 0.00 0.00 41.55 3.86
1679 3099 2.414994 AGAGTCACCATGCCAATCTG 57.585 50.000 0.00 0.00 0.00 2.90
1680 3100 3.446442 AAAGAGTCACCATGCCAATCT 57.554 42.857 0.00 0.00 0.00 2.40
1760 3187 8.730680 ACAATCACTGTATAACCTTGTTTCATC 58.269 33.333 0.00 0.00 36.10 2.92
1800 3227 7.370905 ACTCCCACAAACTAAACTAAGTACT 57.629 36.000 0.00 0.00 0.00 2.73
1803 3230 7.370905 AGTACTCCCACAAACTAAACTAAGT 57.629 36.000 0.00 0.00 0.00 2.24
1804 3231 9.420551 CTAAGTACTCCCACAAACTAAACTAAG 57.579 37.037 0.00 0.00 0.00 2.18
1805 3232 8.927411 ACTAAGTACTCCCACAAACTAAACTAA 58.073 33.333 0.00 0.00 0.00 2.24
1806 3233 8.482852 ACTAAGTACTCCCACAAACTAAACTA 57.517 34.615 0.00 0.00 0.00 2.24
1807 3234 7.370905 ACTAAGTACTCCCACAAACTAAACT 57.629 36.000 0.00 0.00 0.00 2.66
1808 3235 8.442632 AAACTAAGTACTCCCACAAACTAAAC 57.557 34.615 0.00 0.00 0.00 2.01
1809 3236 9.768662 CTAAACTAAGTACTCCCACAAACTAAA 57.231 33.333 0.00 0.00 0.00 1.85
1810 3237 8.927411 ACTAAACTAAGTACTCCCACAAACTAA 58.073 33.333 0.00 0.00 0.00 2.24
1812 3239 7.370905 ACTAAACTAAGTACTCCCACAAACT 57.629 36.000 0.00 0.00 0.00 2.66
1813 3240 7.496920 ACAACTAAACTAAGTACTCCCACAAAC 59.503 37.037 0.00 0.00 0.00 2.93
1814 3241 7.567458 ACAACTAAACTAAGTACTCCCACAAA 58.433 34.615 0.00 0.00 0.00 2.83
1815 3242 7.070322 AGACAACTAAACTAAGTACTCCCACAA 59.930 37.037 0.00 0.00 0.00 3.33
1816 3243 6.552350 AGACAACTAAACTAAGTACTCCCACA 59.448 38.462 0.00 0.00 0.00 4.17
1818 3245 8.746530 CATAGACAACTAAACTAAGTACTCCCA 58.253 37.037 0.00 0.00 32.04 4.37
1819 3246 8.747471 ACATAGACAACTAAACTAAGTACTCCC 58.253 37.037 0.00 0.00 32.04 4.30
1820 3247 9.570488 CACATAGACAACTAAACTAAGTACTCC 57.430 37.037 0.00 0.00 32.04 3.85
1834 3261 9.436957 CAAACTAAGGATAACACATAGACAACT 57.563 33.333 0.00 0.00 0.00 3.16
1854 3281 8.482852 ACTAAACTAAGTACTCCCACAAACTA 57.517 34.615 0.00 0.00 0.00 2.24
1908 3335 9.326413 ACCATAAAGTCTTATATTGGAGTTTCG 57.674 33.333 11.28 6.84 36.73 3.46
1936 3363 5.877012 GTGCCTCTCAATTTATTCTGTCTGA 59.123 40.000 0.00 0.00 0.00 3.27
1939 3366 4.943705 TGGTGCCTCTCAATTTATTCTGTC 59.056 41.667 0.00 0.00 0.00 3.51
2001 3455 4.067896 AGTGAGTGACTGGCTAATGTTTG 58.932 43.478 0.00 0.00 31.75 2.93
2020 3474 3.653009 CGTGTGCCACTGCCAGTG 61.653 66.667 18.02 18.02 45.53 3.66
2025 3479 2.722130 CTTTCTGCGTGTGCCACTGC 62.722 60.000 5.81 5.81 41.78 4.40
2028 3482 2.050985 GCTTTCTGCGTGTGCCAC 60.051 61.111 0.00 0.00 41.78 5.01
2034 3488 1.206072 GACAGCTGCTTTCTGCGTG 59.794 57.895 15.27 0.00 46.63 5.34
2041 3495 0.815213 TTCAGTGCGACAGCTGCTTT 60.815 50.000 15.27 0.00 45.42 3.51
2100 3558 9.840427 CTTTTCTTCTTCTTTGTGTTGAAGTTA 57.160 29.630 0.00 0.00 40.20 2.24
2110 3568 3.627577 TGCGCTCTTTTCTTCTTCTTTGT 59.372 39.130 9.73 0.00 0.00 2.83
2113 3571 3.206150 TGTGCGCTCTTTTCTTCTTCTT 58.794 40.909 9.73 0.00 0.00 2.52
2114 3572 2.838736 TGTGCGCTCTTTTCTTCTTCT 58.161 42.857 9.73 0.00 0.00 2.85
2115 3573 3.187227 TGATGTGCGCTCTTTTCTTCTTC 59.813 43.478 9.73 0.00 0.00 2.87
2191 3809 3.537580 TCCGGTTTCCTCGATAAATTGG 58.462 45.455 0.00 0.00 0.00 3.16
2236 3854 2.132762 CGTCTCTGCGTACTGGTTTTT 58.867 47.619 0.00 0.00 0.00 1.94
2239 3857 1.585006 CCGTCTCTGCGTACTGGTT 59.415 57.895 0.00 0.00 0.00 3.67
2297 3916 2.223745 GAGGGAGATAGACGGTCTGAC 58.776 57.143 20.58 13.34 0.00 3.51
2298 3917 1.143277 GGAGGGAGATAGACGGTCTGA 59.857 57.143 20.58 5.46 0.00 3.27
2309 3928 2.226013 ACCTTTTGAGAGGGAGGGAGAT 60.226 50.000 0.00 0.00 41.31 2.75
2322 3941 5.047660 CCGGTGAATTATTCCAACCTTTTGA 60.048 40.000 11.15 0.00 34.24 2.69
2349 3969 5.062183 CCACTTGTCACGTATTGTACATCTG 59.938 44.000 0.00 0.00 0.00 2.90
2413 4197 1.338105 GGGCAACTGGGCTCATTTTTC 60.338 52.381 0.00 0.00 42.84 2.29
2477 4261 0.534877 AGTGTGCTGTCGCCAATTGA 60.535 50.000 7.12 0.00 34.43 2.57
2514 5382 5.360591 GTTTGAGAAGGTCAGAGTTTGAGA 58.639 41.667 0.00 0.00 36.21 3.27
2515 5383 4.513318 GGTTTGAGAAGGTCAGAGTTTGAG 59.487 45.833 0.00 0.00 36.21 3.02
2516 5384 4.080582 TGGTTTGAGAAGGTCAGAGTTTGA 60.081 41.667 0.00 0.00 36.21 2.69
2517 5385 4.199310 TGGTTTGAGAAGGTCAGAGTTTG 58.801 43.478 0.00 0.00 36.21 2.93
2518 5386 4.503714 TGGTTTGAGAAGGTCAGAGTTT 57.496 40.909 0.00 0.00 36.21 2.66
2520 5388 3.306364 CGATGGTTTGAGAAGGTCAGAGT 60.306 47.826 0.00 0.00 36.21 3.24
2521 5389 3.056536 TCGATGGTTTGAGAAGGTCAGAG 60.057 47.826 0.00 0.00 36.21 3.35
2523 5404 3.319137 TCGATGGTTTGAGAAGGTCAG 57.681 47.619 0.00 0.00 36.21 3.51
2526 5407 3.430374 CCGTATCGATGGTTTGAGAAGGT 60.430 47.826 8.54 0.00 0.00 3.50
2541 5422 1.219522 GAAATGGACGGGCCGTATCG 61.220 60.000 34.29 4.77 41.37 2.92
2542 5423 0.179067 TGAAATGGACGGGCCGTATC 60.179 55.000 34.29 26.16 41.37 2.24
2545 5426 1.451387 GATGAAATGGACGGGCCGT 60.451 57.895 34.81 34.81 45.10 5.68


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

AutoCloner maintained by Alex Coulton.