Multiple sequence alignment - TraesCS2A01G178500

Loading Multiple Alignment...

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 TraesCS2A01G178500 chr2A 100.000 3444 0 0 1 3444 137261710 137258267 0.000000e+00 6360
1 TraesCS2A01G178500 chr2A 98.309 769 11 2 1 768 194173098 194172331 0.000000e+00 1347
2 TraesCS2A01G178500 chr2A 83.701 589 87 8 1597 2180 755060865 755061449 6.500000e-152 547
3 TraesCS2A01G178500 chr2D 89.717 1799 113 27 864 2631 131164432 131162675 0.000000e+00 2231
4 TraesCS2A01G178500 chr2D 85.065 924 93 27 1321 2240 129837262 129838144 0.000000e+00 900
5 TraesCS2A01G178500 chr2D 91.598 607 51 0 1573 2179 129941584 129942190 0.000000e+00 839
6 TraesCS2A01G178500 chr2D 83.447 586 88 8 1600 2180 623791207 623791788 1.410000e-148 536
7 TraesCS2A01G178500 chr2D 79.545 176 24 8 1321 1495 129941394 129941558 7.810000e-22 115
8 TraesCS2A01G178500 chr2B 90.638 1410 89 16 795 2190 184663716 184662336 0.000000e+00 1832
9 TraesCS2A01G178500 chr2B 97.686 778 7 2 1 768 491546885 491546109 0.000000e+00 1327
10 TraesCS2A01G178500 chr2B 83.972 861 96 15 1321 2179 183211537 183212357 0.000000e+00 787
11 TraesCS2A01G178500 chr2B 84.331 568 83 5 1616 2180 751603762 751603198 5.020000e-153 551
12 TraesCS2A01G178500 chr2B 86.325 234 23 4 2404 2631 184662087 184661857 2.650000e-61 246
13 TraesCS2A01G178500 chr2B 83.173 208 14 9 565 768 44114685 44114495 1.640000e-38 171
14 TraesCS2A01G178500 chr4B 97.446 783 10 1 1 773 251999844 251999062 0.000000e+00 1327
15 TraesCS2A01G178500 chr6B 97.561 779 8 1 1 768 717603283 717604061 0.000000e+00 1323
16 TraesCS2A01G178500 chr6B 89.691 97 8 2 672 768 40587064 40587158 4.670000e-24 122
17 TraesCS2A01G178500 chr6A 97.561 779 8 2 1 768 362710541 362711319 0.000000e+00 1323
18 TraesCS2A01G178500 chr6A 97.433 779 9 1 1 768 112107150 112106372 0.000000e+00 1317
19 TraesCS2A01G178500 chr6A 85.024 207 25 6 565 769 14097156 14096954 4.510000e-49 206
20 TraesCS2A01G178500 chr5B 97.561 779 8 4 1 768 52919379 52920157 0.000000e+00 1323
21 TraesCS2A01G178500 chr3B 97.433 779 9 1 1 768 654428486 654427708 0.000000e+00 1317
22 TraesCS2A01G178500 chr3A 97.311 781 10 1 1 770 650005567 650004787 0.000000e+00 1315
23 TraesCS2A01G178500 chr3A 81.805 676 109 8 2758 3422 528524706 528524034 3.880000e-154 555
24 TraesCS2A01G178500 chr3A 77.388 513 92 17 2675 3175 41993951 41993451 2.020000e-72 283
25 TraesCS2A01G178500 chr3D 80.674 771 132 12 2683 3444 488120729 488119967 1.780000e-162 582
26 TraesCS2A01G178500 chr3D 77.500 800 147 25 2631 3417 24218873 24219652 1.890000e-122 449
27 TraesCS2A01G178500 chr7D 85.000 580 75 11 1605 2178 534655136 534654563 2.300000e-161 579
28 TraesCS2A01G178500 chr5D 78.928 802 140 21 2627 3417 451179303 451180086 5.100000e-143 518
29 TraesCS2A01G178500 chr1D 78.634 805 125 31 2636 3412 416092225 416091440 1.110000e-134 490
30 TraesCS2A01G178500 chr1D 77.616 755 149 13 2674 3417 480971623 480970878 1.130000e-119 440
31 TraesCS2A01G178500 chr4D 77.857 700 142 9 2727 3417 3331120 3331815 4.110000e-114 422
32 TraesCS2A01G178500 chr4A 76.645 775 135 26 2630 3391 72971884 72972625 1.500000e-103 387
33 TraesCS2A01G178500 chr1A 76.271 767 157 17 2631 3387 494852438 494853189 5.390000e-103 385
34 TraesCS2A01G178500 chr7A 83.254 209 16 8 565 771 721496196 721496005 1.270000e-39 174
35 TraesCS2A01G178500 chr7B 83.815 173 9 8 599 768 329778736 329778580 2.770000e-31 147
36 TraesCS2A01G178500 chr7B 85.185 135 14 6 637 768 583217014 583217145 2.160000e-27 134
37 TraesCS2A01G178500 chrUn 92.391 92 7 0 676 767 254089717 254089808 7.760000e-27 132
38 TraesCS2A01G178500 chr5A 89.691 97 9 1 672 768 552881003 552881098 4.670000e-24 122


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 TraesCS2A01G178500 chr2A 137258267 137261710 3443 True 6360 6360 100.0000 1 3444 1 chr2A.!!$R1 3443
1 TraesCS2A01G178500 chr2A 194172331 194173098 767 True 1347 1347 98.3090 1 768 1 chr2A.!!$R2 767
2 TraesCS2A01G178500 chr2A 755060865 755061449 584 False 547 547 83.7010 1597 2180 1 chr2A.!!$F1 583
3 TraesCS2A01G178500 chr2D 131162675 131164432 1757 True 2231 2231 89.7170 864 2631 1 chr2D.!!$R1 1767
4 TraesCS2A01G178500 chr2D 129837262 129838144 882 False 900 900 85.0650 1321 2240 1 chr2D.!!$F1 919
5 TraesCS2A01G178500 chr2D 623791207 623791788 581 False 536 536 83.4470 1600 2180 1 chr2D.!!$F2 580
6 TraesCS2A01G178500 chr2D 129941394 129942190 796 False 477 839 85.5715 1321 2179 2 chr2D.!!$F3 858
7 TraesCS2A01G178500 chr2B 491546109 491546885 776 True 1327 1327 97.6860 1 768 1 chr2B.!!$R2 767
8 TraesCS2A01G178500 chr2B 184661857 184663716 1859 True 1039 1832 88.4815 795 2631 2 chr2B.!!$R4 1836
9 TraesCS2A01G178500 chr2B 183211537 183212357 820 False 787 787 83.9720 1321 2179 1 chr2B.!!$F1 858
10 TraesCS2A01G178500 chr2B 751603198 751603762 564 True 551 551 84.3310 1616 2180 1 chr2B.!!$R3 564
11 TraesCS2A01G178500 chr4B 251999062 251999844 782 True 1327 1327 97.4460 1 773 1 chr4B.!!$R1 772
12 TraesCS2A01G178500 chr6B 717603283 717604061 778 False 1323 1323 97.5610 1 768 1 chr6B.!!$F2 767
13 TraesCS2A01G178500 chr6A 362710541 362711319 778 False 1323 1323 97.5610 1 768 1 chr6A.!!$F1 767
14 TraesCS2A01G178500 chr6A 112106372 112107150 778 True 1317 1317 97.4330 1 768 1 chr6A.!!$R2 767
15 TraesCS2A01G178500 chr5B 52919379 52920157 778 False 1323 1323 97.5610 1 768 1 chr5B.!!$F1 767
16 TraesCS2A01G178500 chr3B 654427708 654428486 778 True 1317 1317 97.4330 1 768 1 chr3B.!!$R1 767
17 TraesCS2A01G178500 chr3A 650004787 650005567 780 True 1315 1315 97.3110 1 770 1 chr3A.!!$R3 769
18 TraesCS2A01G178500 chr3A 528524034 528524706 672 True 555 555 81.8050 2758 3422 1 chr3A.!!$R2 664
19 TraesCS2A01G178500 chr3A 41993451 41993951 500 True 283 283 77.3880 2675 3175 1 chr3A.!!$R1 500
20 TraesCS2A01G178500 chr3D 488119967 488120729 762 True 582 582 80.6740 2683 3444 1 chr3D.!!$R1 761
21 TraesCS2A01G178500 chr3D 24218873 24219652 779 False 449 449 77.5000 2631 3417 1 chr3D.!!$F1 786
22 TraesCS2A01G178500 chr7D 534654563 534655136 573 True 579 579 85.0000 1605 2178 1 chr7D.!!$R1 573
23 TraesCS2A01G178500 chr5D 451179303 451180086 783 False 518 518 78.9280 2627 3417 1 chr5D.!!$F1 790
24 TraesCS2A01G178500 chr1D 416091440 416092225 785 True 490 490 78.6340 2636 3412 1 chr1D.!!$R1 776
25 TraesCS2A01G178500 chr1D 480970878 480971623 745 True 440 440 77.6160 2674 3417 1 chr1D.!!$R2 743
26 TraesCS2A01G178500 chr4D 3331120 3331815 695 False 422 422 77.8570 2727 3417 1 chr4D.!!$F1 690
27 TraesCS2A01G178500 chr4A 72971884 72972625 741 False 387 387 76.6450 2630 3391 1 chr4A.!!$F1 761
28 TraesCS2A01G178500 chr1A 494852438 494853189 751 False 385 385 76.2710 2631 3387 1 chr1A.!!$F1 756

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
862 878 0.713883 GCAACGACGACACGATTCAT 59.286 50.0 0.00 0.00 37.03 2.57 F
1446 1486 0.028505 CCCTGCGCTTGATTCATTCG 59.971 55.0 9.73 4.36 0.00 3.34 F
2216 2285 0.108945 TGACAGATCGCTCACTGCTG 60.109 55.0 0.00 0.00 40.11 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2391 2503 0.033601 TTTGTGCCTTGGTGGTGACT 60.034 50.0 0.0 0.0 38.35 3.41 R
2399 2511 0.451783 GCTCGGTATTTGTGCCTTGG 59.548 55.0 0.0 0.0 0.00 3.61 R
3038 3182 0.746063 TGGACACACGTAACGAGGTT 59.254 50.0 0.0 0.0 0.00 3.50 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
20 21 1.003233 GCTGGGAAAGGAAGCGAGT 60.003 57.895 0.00 0.00 0.00 4.18
371 374 8.043710 GGGATGGATCGATTGATTTAGATAGTT 58.956 37.037 0.00 0.00 34.09 2.24
758 774 5.488341 GAGACTACCAACTGCTCCATTAAA 58.512 41.667 0.00 0.00 0.00 1.52
773 789 9.692749 TGCTCCATTAAAAGTAGAGATTATACG 57.307 33.333 0.00 0.00 0.00 3.06
774 790 9.694137 GCTCCATTAAAAGTAGAGATTATACGT 57.306 33.333 0.00 0.00 0.00 3.57
783 799 9.871238 AAAGTAGAGATTATACGTCATTGTTGT 57.129 29.630 0.00 0.00 0.00 3.32
785 801 9.947669 AGTAGAGATTATACGTCATTGTTGTAC 57.052 33.333 0.00 0.00 0.00 2.90
786 802 9.947669 GTAGAGATTATACGTCATTGTTGTACT 57.052 33.333 0.00 0.00 0.00 2.73
807 823 6.707599 ACTTAAGAAAAACTAGTAGCAGCG 57.292 37.500 10.09 0.00 0.00 5.18
826 842 1.392589 GGAACGTGCATGGGATCAAT 58.607 50.000 11.36 0.00 0.00 2.57
827 843 1.750778 GGAACGTGCATGGGATCAATT 59.249 47.619 11.36 0.00 0.00 2.32
828 844 2.948979 GGAACGTGCATGGGATCAATTA 59.051 45.455 11.36 0.00 0.00 1.40
830 846 4.037923 GGAACGTGCATGGGATCAATTAAT 59.962 41.667 11.36 0.00 0.00 1.40
831 847 5.240623 GGAACGTGCATGGGATCAATTAATA 59.759 40.000 11.36 0.00 0.00 0.98
832 848 5.947228 ACGTGCATGGGATCAATTAATAG 57.053 39.130 11.36 0.00 0.00 1.73
833 849 5.376625 ACGTGCATGGGATCAATTAATAGT 58.623 37.500 11.36 0.00 0.00 2.12
853 869 2.743871 GAAAGCCACGCAACGACGAC 62.744 60.000 0.00 0.00 36.70 4.34
854 870 4.578898 AGCCACGCAACGACGACA 62.579 61.111 0.00 0.00 36.70 4.35
855 871 4.349871 GCCACGCAACGACGACAC 62.350 66.667 0.00 0.00 36.70 3.67
856 872 4.042060 CCACGCAACGACGACACG 62.042 66.667 0.00 4.15 36.70 4.49
857 873 3.020105 CACGCAACGACGACACGA 61.020 61.111 0.00 0.00 36.70 4.35
858 874 2.050714 ACGCAACGACGACACGAT 60.051 55.556 0.00 0.00 36.70 3.73
859 875 1.659335 ACGCAACGACGACACGATT 60.659 52.632 0.00 0.00 36.70 3.34
860 876 1.055235 CGCAACGACGACACGATTC 59.945 57.895 0.00 0.00 37.03 2.52
861 877 1.602012 CGCAACGACGACACGATTCA 61.602 55.000 0.00 0.00 37.03 2.57
862 878 0.713883 GCAACGACGACACGATTCAT 59.286 50.000 0.00 0.00 37.03 2.57
878 894 4.142924 CGATTCATCACGTTCATTCCACAA 60.143 41.667 0.00 0.00 0.00 3.33
886 902 2.609491 CGTTCATTCCACAAGGAGACGA 60.609 50.000 0.00 0.00 46.74 4.20
887 903 2.737252 GTTCATTCCACAAGGAGACGAC 59.263 50.000 0.00 0.00 46.74 4.34
889 905 1.001974 CATTCCACAAGGAGACGACCA 59.998 52.381 0.00 0.00 46.74 4.02
1010 1040 1.744374 GCGATACGCGGATATAGCTC 58.256 55.000 12.47 0.00 44.55 4.09
1020 1050 3.654414 CGGATATAGCTCAACCTGAACC 58.346 50.000 0.00 0.00 0.00 3.62
1049 1079 0.319211 CCGAACCAAGCACACGACTA 60.319 55.000 0.00 0.00 0.00 2.59
1059 1089 2.127003 CACGACTAGCACACGCGA 60.127 61.111 15.93 0.00 45.49 5.87
1212 1242 3.276846 GGCAACAACGTCACCGCT 61.277 61.111 0.00 0.00 37.70 5.52
1213 1243 2.052237 GCAACAACGTCACCGCTG 60.052 61.111 0.00 0.00 37.70 5.18
1246 1276 1.819632 GCCATGTGCTACCGAAGGG 60.820 63.158 0.00 0.00 46.49 3.95
1269 1299 3.119096 GCCGACGAAGAGGCCAAC 61.119 66.667 5.01 0.00 45.44 3.77
1294 1324 1.895707 AAGACGGTCCTCGACGTGT 60.896 57.895 4.14 0.00 44.24 4.49
1327 1357 0.747283 GTGCCCTTCTCCTGCAGATG 60.747 60.000 17.39 7.47 35.33 2.90
1444 1484 0.034186 TCCCCTGCGCTTGATTCATT 60.034 50.000 9.73 0.00 0.00 2.57
1445 1485 0.383231 CCCCTGCGCTTGATTCATTC 59.617 55.000 9.73 0.00 0.00 2.67
1446 1486 0.028505 CCCTGCGCTTGATTCATTCG 59.971 55.000 9.73 4.36 0.00 3.34
1447 1487 0.729116 CCTGCGCTTGATTCATTCGT 59.271 50.000 9.73 0.00 0.00 3.85
1448 1488 1.933181 CCTGCGCTTGATTCATTCGTA 59.067 47.619 9.73 4.94 0.00 3.43
1449 1489 2.351418 CCTGCGCTTGATTCATTCGTAA 59.649 45.455 9.73 0.00 0.00 3.18
1486 1528 2.989840 GAGCGGAGATGTATTTGATCGG 59.010 50.000 0.00 0.00 0.00 4.18
1511 1553 5.898606 CGCAACGAACTCAATTCTCAATATC 59.101 40.000 0.00 0.00 34.88 1.63
1512 1554 6.455513 CGCAACGAACTCAATTCTCAATATCA 60.456 38.462 0.00 0.00 34.88 2.15
1566 1612 2.120909 GCCCATCGACCCCATGTTG 61.121 63.158 0.00 0.00 0.00 3.33
1574 1620 2.406002 GACCCCATGTTGACCGGTGT 62.406 60.000 14.63 0.00 0.00 4.16
1674 1720 1.845809 GCACCCTCAAGTTCAGCGTG 61.846 60.000 0.00 0.00 0.00 5.34
1809 1855 2.588314 GAGCCGGAGAGCTGCATG 60.588 66.667 5.05 0.00 45.15 4.06
1863 1909 0.528470 GCTTCCTACTGTGCGAGTCT 59.472 55.000 0.00 0.00 35.96 3.24
1926 1972 4.577246 GCGCCTCTTCTCGCCGAT 62.577 66.667 0.00 0.00 45.01 4.18
1958 2004 3.838271 GGCAGCGATCGTGGAGGA 61.838 66.667 17.81 0.00 0.00 3.71
2190 2236 3.728076 TGCAGGTACGGATCAGATTAC 57.272 47.619 0.00 0.00 0.00 1.89
2211 2280 0.814457 ACTCCTGACAGATCGCTCAC 59.186 55.000 3.32 0.00 0.00 3.51
2216 2285 0.108945 TGACAGATCGCTCACTGCTG 60.109 55.000 0.00 0.00 40.11 4.41
2218 2287 1.133216 GACAGATCGCTCACTGCTGTA 59.867 52.381 0.00 0.00 39.68 2.74
2230 2299 4.450976 TCACTGCTGTACTTGACAAATGT 58.549 39.130 0.00 0.00 37.70 2.71
2231 2300 4.273235 TCACTGCTGTACTTGACAAATGTG 59.727 41.667 0.00 0.00 37.70 3.21
2234 2303 5.356751 ACTGCTGTACTTGACAAATGTGAAA 59.643 36.000 0.00 0.00 37.70 2.69
2236 2305 6.207928 TGCTGTACTTGACAAATGTGAAATG 58.792 36.000 0.00 0.00 37.70 2.32
2237 2306 6.039159 TGCTGTACTTGACAAATGTGAAATGA 59.961 34.615 0.00 0.00 37.70 2.57
2261 2373 1.669795 GCGGCTCCCTTGTTTGATTTG 60.670 52.381 0.00 0.00 0.00 2.32
2276 2388 7.038659 TGTTTGATTTGTTTTAGGTGTGGAAG 58.961 34.615 0.00 0.00 0.00 3.46
2368 2480 2.223340 CGAGTTGCTTGGTTATGCATCC 60.223 50.000 0.19 0.00 36.91 3.51
2369 2481 3.019564 GAGTTGCTTGGTTATGCATCCT 58.980 45.455 0.19 0.00 36.91 3.24
2370 2482 2.756760 AGTTGCTTGGTTATGCATCCTG 59.243 45.455 0.19 0.00 36.91 3.86
2371 2483 1.105457 TGCTTGGTTATGCATCCTGC 58.895 50.000 0.19 8.99 45.29 4.85
2381 2493 1.831286 GCATCCTGCATCCAAGGGG 60.831 63.158 0.00 0.00 44.26 4.79
2382 2494 1.831286 CATCCTGCATCCAAGGGGC 60.831 63.158 0.00 0.00 0.00 5.80
2383 2495 3.078843 ATCCTGCATCCAAGGGGCC 62.079 63.158 0.00 0.00 0.00 5.80
2388 2500 2.060383 GCATCCAAGGGGCCTTTCC 61.060 63.158 0.84 0.00 33.42 3.13
2399 2511 1.603739 GCCTTTCCCCAGTCACCAC 60.604 63.158 0.00 0.00 0.00 4.16
2414 2526 1.272212 CACCACCAAGGCACAAATACC 59.728 52.381 0.00 0.00 43.14 2.73
2423 2535 2.700897 AGGCACAAATACCGAGCTCTAT 59.299 45.455 12.85 0.55 0.00 1.98
2427 2539 5.163652 GGCACAAATACCGAGCTCTATTTTT 60.164 40.000 12.85 6.71 0.00 1.94
2464 2579 8.150945 AGTACAATATATCGCTTCATCTTGGTT 58.849 33.333 0.00 0.00 0.00 3.67
2483 2598 6.358118 TGGTTATGTTTATCTCAATCGCAC 57.642 37.500 0.00 0.00 0.00 5.34
2522 2637 8.903820 GGCATGATAAACTTTACTTAATCAGGT 58.096 33.333 0.00 0.00 0.00 4.00
2532 2647 9.490379 ACTTTACTTAATCAGGTTGTACAGAAG 57.510 33.333 0.00 0.00 0.00 2.85
2571 2691 5.134202 TGACTCGATTCAGCTTTCAGTTA 57.866 39.130 0.65 0.00 0.00 2.24
2586 2706 7.917505 AGCTTTCAGTTATGCTTGTAAATATGC 59.082 33.333 0.00 0.00 30.96 3.14
2601 2722 5.852282 AAATATGCGAGGTTTTTAGGCAT 57.148 34.783 2.23 2.23 45.44 4.40
2628 2749 6.656902 TGCTCAATATCTGATCTTCTGGTTT 58.343 36.000 0.00 0.00 32.14 3.27
2663 2787 2.066999 GGATGACCCTCGGCCTCTT 61.067 63.158 0.00 0.00 0.00 2.85
2664 2788 1.443828 GATGACCCTCGGCCTCTTC 59.556 63.158 0.00 0.00 0.00 2.87
2665 2789 1.002274 ATGACCCTCGGCCTCTTCT 59.998 57.895 0.00 0.00 0.00 2.85
2666 2790 1.333636 ATGACCCTCGGCCTCTTCTG 61.334 60.000 0.00 0.00 0.00 3.02
2667 2791 3.378399 GACCCTCGGCCTCTTCTGC 62.378 68.421 0.00 0.00 0.00 4.26
2668 2792 3.393970 CCCTCGGCCTCTTCTGCA 61.394 66.667 0.00 0.00 0.00 4.41
2669 2793 2.125350 CCTCGGCCTCTTCTGCAC 60.125 66.667 0.00 0.00 0.00 4.57
2748 2879 9.646522 AAATACATCAATAAGTCTAAGCCCATT 57.353 29.630 0.00 0.00 0.00 3.16
2764 2895 3.873952 GCCCATTATCTCGGCAATATCTC 59.126 47.826 0.00 0.00 42.52 2.75
2787 2918 5.239744 TCTCGCTACTCCTATCAACTTGATC 59.760 44.000 7.57 0.00 38.26 2.92
2834 2966 4.759782 CATACCTAGACCTCACACCAAAG 58.240 47.826 0.00 0.00 0.00 2.77
2837 2969 0.690762 TAGACCTCACACCAAAGCCC 59.309 55.000 0.00 0.00 0.00 5.19
2839 2971 0.467290 GACCTCACACCAAAGCCCAA 60.467 55.000 0.00 0.00 0.00 4.12
2840 2972 0.755327 ACCTCACACCAAAGCCCAAC 60.755 55.000 0.00 0.00 0.00 3.77
2841 2973 0.754957 CCTCACACCAAAGCCCAACA 60.755 55.000 0.00 0.00 0.00 3.33
2857 2992 2.524306 CAACATAACTGAAGGCCCCAA 58.476 47.619 0.00 0.00 0.00 4.12
2858 2993 2.215942 ACATAACTGAAGGCCCCAAC 57.784 50.000 0.00 0.00 0.00 3.77
2870 3006 3.977244 CCCAACACCAAGCCGCAC 61.977 66.667 0.00 0.00 0.00 5.34
2872 3008 2.489275 CCAACACCAAGCCGCACTT 61.489 57.895 0.00 0.00 40.05 3.16
2885 3028 1.966451 GCACTTTCGGGTCTGGGTG 60.966 63.158 0.00 0.00 0.00 4.61
2930 3074 1.596752 GGTCACCACATGCACACGA 60.597 57.895 0.00 0.00 0.00 4.35
2959 3103 1.209127 GCCACCGTCGTTTTCCATG 59.791 57.895 0.00 0.00 0.00 3.66
2972 3116 4.398988 CGTTTTCCATGGATCCATCTTCAA 59.601 41.667 24.93 12.29 33.90 2.69
2974 3118 6.572119 CGTTTTCCATGGATCCATCTTCAAAA 60.572 38.462 24.93 20.36 33.90 2.44
2977 3121 8.786710 TTTCCATGGATCCATCTTCAAAATAT 57.213 30.769 24.93 0.00 33.90 1.28
2983 3127 7.815383 TGGATCCATCTTCAAAATATGTACCT 58.185 34.615 11.44 0.00 0.00 3.08
2985 3129 9.793259 GGATCCATCTTCAAAATATGTACCTAA 57.207 33.333 6.95 0.00 0.00 2.69
2996 3140 8.345565 CAAAATATGTACCTAAGCATCAACCTC 58.654 37.037 0.00 0.00 0.00 3.85
2999 3143 0.613260 ACCTAAGCATCAACCTCGCA 59.387 50.000 0.00 0.00 0.00 5.10
3023 3167 2.224066 GCCTATAGTCGATGCCACAACT 60.224 50.000 0.00 0.00 0.00 3.16
3029 3173 4.120331 GATGCCACAACTGCGCCC 62.120 66.667 4.18 0.00 0.00 6.13
3044 3188 3.411351 CCCGACAACGCAACCTCG 61.411 66.667 0.00 0.00 38.29 4.63
3045 3189 2.660552 CCGACAACGCAACCTCGT 60.661 61.111 0.00 0.00 45.58 4.18
3098 3242 2.678934 CCTTGCTGTGCCATGCCT 60.679 61.111 0.00 0.00 0.00 4.75
3134 3278 4.738252 GTCGTAGATGCGTCACATGAAATA 59.262 41.667 8.99 0.00 39.84 1.40
3137 3281 3.872696 AGATGCGTCACATGAAATACCA 58.127 40.909 8.99 0.00 39.84 3.25
3173 3318 2.681778 CCACTGGTCCCTCGAGCT 60.682 66.667 6.99 0.00 37.40 4.09
3176 3321 0.895530 CACTGGTCCCTCGAGCTAAA 59.104 55.000 6.99 0.00 37.40 1.85
3178 3323 1.272536 ACTGGTCCCTCGAGCTAAAGA 60.273 52.381 6.99 0.00 37.40 2.52
3185 3330 2.028020 CCCTCGAGCTAAAGAACACCTT 60.028 50.000 6.99 0.00 36.47 3.50
3200 3345 4.322057 ACACCTTCAAGAATAATGCCCT 57.678 40.909 0.00 0.00 0.00 5.19
3232 3377 0.814010 GACACAAGAGCACCACCGTT 60.814 55.000 0.00 0.00 0.00 4.44
3376 3527 0.250295 CCGAGAGCAGGGTTTTCACA 60.250 55.000 0.00 0.00 0.00 3.58
3426 3577 2.936919 TCTTGTGCACCAGATCACTT 57.063 45.000 16.21 0.00 34.49 3.16
3429 3580 0.109153 TGTGCACCAGATCACTTGCT 59.891 50.000 15.69 0.00 32.85 3.91
3430 3581 1.347378 TGTGCACCAGATCACTTGCTA 59.653 47.619 15.69 0.00 32.85 3.49
3433 3584 2.224499 TGCACCAGATCACTTGCTACAA 60.224 45.455 12.10 0.00 32.85 2.41
3434 3585 2.160417 GCACCAGATCACTTGCTACAAC 59.840 50.000 0.00 0.00 30.08 3.32
3438 3589 2.093310 CAGATCACTTGCTACAACGCTG 59.907 50.000 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.491693 GCCCCTCGATTGATTTTTGTCA 59.508 45.455 0.00 0.00 0.00 3.58
725 740 0.895530 TGGTAGTCTCGCTTTCAGGG 59.104 55.000 0.00 0.00 0.00 4.45
770 786 9.919348 GTTTTTCTTAAGTACAACAATGACGTA 57.081 29.630 1.63 0.00 0.00 3.57
778 794 9.820725 TGCTACTAGTTTTTCTTAAGTACAACA 57.179 29.630 0.00 0.88 0.00 3.33
780 796 8.985805 GCTGCTACTAGTTTTTCTTAAGTACAA 58.014 33.333 0.00 0.00 0.00 2.41
781 797 7.327761 CGCTGCTACTAGTTTTTCTTAAGTACA 59.672 37.037 0.00 0.00 0.00 2.90
782 798 7.201418 CCGCTGCTACTAGTTTTTCTTAAGTAC 60.201 40.741 0.00 0.00 0.00 2.73
783 799 6.810182 CCGCTGCTACTAGTTTTTCTTAAGTA 59.190 38.462 0.00 0.00 0.00 2.24
784 800 5.638234 CCGCTGCTACTAGTTTTTCTTAAGT 59.362 40.000 0.00 0.00 0.00 2.24
785 801 5.867716 TCCGCTGCTACTAGTTTTTCTTAAG 59.132 40.000 0.00 0.00 0.00 1.85
786 802 5.786311 TCCGCTGCTACTAGTTTTTCTTAA 58.214 37.500 0.00 0.00 0.00 1.85
787 803 5.395682 TCCGCTGCTACTAGTTTTTCTTA 57.604 39.130 0.00 0.00 0.00 2.10
788 804 4.267349 TCCGCTGCTACTAGTTTTTCTT 57.733 40.909 0.00 0.00 0.00 2.52
789 805 3.955650 TCCGCTGCTACTAGTTTTTCT 57.044 42.857 0.00 0.00 0.00 2.52
790 806 3.181533 CGTTCCGCTGCTACTAGTTTTTC 60.182 47.826 0.00 0.00 0.00 2.29
791 807 2.735134 CGTTCCGCTGCTACTAGTTTTT 59.265 45.455 0.00 0.00 0.00 1.94
792 808 2.288640 ACGTTCCGCTGCTACTAGTTTT 60.289 45.455 0.00 0.00 0.00 2.43
793 809 1.271656 ACGTTCCGCTGCTACTAGTTT 59.728 47.619 0.00 0.00 0.00 2.66
801 817 3.425713 CATGCACGTTCCGCTGCT 61.426 61.111 0.00 0.00 35.89 4.24
807 823 1.392589 ATTGATCCCATGCACGTTCC 58.607 50.000 0.00 0.00 0.00 3.62
818 834 6.513393 CGTGGCTTTCACTATTAATTGATCCC 60.513 42.308 3.83 0.68 43.94 3.85
826 842 3.120477 CGTTGCGTGGCTTTCACTATTAA 60.120 43.478 0.00 0.00 43.94 1.40
827 843 2.413796 CGTTGCGTGGCTTTCACTATTA 59.586 45.455 0.00 0.00 43.94 0.98
828 844 1.196808 CGTTGCGTGGCTTTCACTATT 59.803 47.619 0.00 0.00 43.94 1.73
830 846 0.249531 TCGTTGCGTGGCTTTCACTA 60.250 50.000 0.00 0.00 43.94 2.74
831 847 1.522806 TCGTTGCGTGGCTTTCACT 60.523 52.632 0.00 0.00 43.94 3.41
832 848 1.368850 GTCGTTGCGTGGCTTTCAC 60.369 57.895 0.00 0.00 42.74 3.18
833 849 2.876879 CGTCGTTGCGTGGCTTTCA 61.877 57.895 0.00 0.00 0.00 2.69
853 869 3.370672 TGGAATGAACGTGATGAATCGTG 59.629 43.478 0.00 0.00 40.19 4.35
854 870 3.370978 GTGGAATGAACGTGATGAATCGT 59.629 43.478 0.00 0.00 42.12 3.73
855 871 3.370672 TGTGGAATGAACGTGATGAATCG 59.629 43.478 0.00 0.00 0.00 3.34
856 872 4.944962 TGTGGAATGAACGTGATGAATC 57.055 40.909 0.00 0.00 0.00 2.52
857 873 4.156556 CCTTGTGGAATGAACGTGATGAAT 59.843 41.667 0.00 0.00 34.57 2.57
858 874 3.501828 CCTTGTGGAATGAACGTGATGAA 59.498 43.478 0.00 0.00 34.57 2.57
859 875 3.073678 CCTTGTGGAATGAACGTGATGA 58.926 45.455 0.00 0.00 34.57 2.92
860 876 3.073678 TCCTTGTGGAATGAACGTGATG 58.926 45.455 0.00 0.00 39.87 3.07
861 877 3.007940 TCTCCTTGTGGAATGAACGTGAT 59.992 43.478 0.00 0.00 42.66 3.06
862 878 2.367241 TCTCCTTGTGGAATGAACGTGA 59.633 45.455 0.00 0.00 42.66 4.35
878 894 2.427506 GCAAAAGATTGGTCGTCTCCT 58.572 47.619 0.00 0.00 37.02 3.69
886 902 2.250924 CCAAGGAGGCAAAAGATTGGT 58.749 47.619 0.00 0.00 37.02 3.67
992 1022 3.099362 GTTGAGCTATATCCGCGTATCG 58.901 50.000 4.92 0.00 38.08 2.92
993 1023 3.128938 AGGTTGAGCTATATCCGCGTATC 59.871 47.826 4.92 0.00 0.00 2.24
1010 1040 2.162681 GTTGGATCTGGGTTCAGGTTG 58.837 52.381 0.00 0.00 41.23 3.77
1020 1050 1.453155 CTTGGTTCGGTTGGATCTGG 58.547 55.000 0.00 0.00 0.00 3.86
1059 1089 2.637383 GCTTCTCCCACTCCGTCGT 61.637 63.158 0.00 0.00 0.00 4.34
1187 1217 4.341502 CGTTGTTGCCGGCCAAGG 62.342 66.667 26.77 22.03 33.21 3.61
1230 1260 1.819632 GCCCCTTCGGTAGCACATG 60.820 63.158 0.00 0.00 0.00 3.21
1253 1283 2.434359 GGTTGGCCTCTTCGTCGG 60.434 66.667 3.32 0.00 0.00 4.79
1327 1357 2.896443 CCCGCTCAGACCCTTCTC 59.104 66.667 0.00 0.00 0.00 2.87
1486 1528 1.194547 TGAGAATTGAGTTCGTTGCGC 59.805 47.619 0.00 0.00 41.84 6.09
1511 1553 2.264794 GCCTGGGTACACGAGGTG 59.735 66.667 13.13 0.00 46.03 4.00
1512 1554 3.001406 GGCCTGGGTACACGAGGT 61.001 66.667 13.13 0.00 46.03 3.85
1566 1612 3.400590 GACGCGTCAACACCGGTC 61.401 66.667 33.09 2.59 0.00 4.79
1574 1620 4.986587 CGACCACCGACGCGTCAA 62.987 66.667 35.71 0.00 41.76 3.18
1807 1853 0.472543 TCCGAGGAGATGATGCCCAT 60.473 55.000 0.00 0.00 38.43 4.00
1809 1855 1.369321 GTCCGAGGAGATGATGCCC 59.631 63.158 0.00 0.00 0.00 5.36
2019 2065 3.192103 AAACTCCCTGCACCCGACC 62.192 63.158 0.00 0.00 0.00 4.79
2190 2236 1.203287 TGAGCGATCTGTCAGGAGTTG 59.797 52.381 0.90 0.00 0.00 3.16
2211 2280 5.422666 TTCACATTTGTCAAGTACAGCAG 57.577 39.130 0.00 0.00 39.87 4.24
2216 2285 8.216453 GCAAATCATTTCACATTTGTCAAGTAC 58.784 33.333 6.32 0.00 40.63 2.73
2218 2287 6.074195 CGCAAATCATTTCACATTTGTCAAGT 60.074 34.615 6.32 0.00 40.63 3.16
2230 2299 0.817013 GGGAGCCGCAAATCATTTCA 59.183 50.000 0.00 0.00 0.00 2.69
2231 2300 1.106285 AGGGAGCCGCAAATCATTTC 58.894 50.000 0.00 0.00 0.00 2.17
2234 2303 0.323725 ACAAGGGAGCCGCAAATCAT 60.324 50.000 0.00 0.00 0.00 2.45
2236 2305 0.603065 AAACAAGGGAGCCGCAAATC 59.397 50.000 0.00 0.00 0.00 2.17
2237 2306 0.318120 CAAACAAGGGAGCCGCAAAT 59.682 50.000 0.00 0.00 0.00 2.32
2261 2373 2.230660 AGCTGCTTCCACACCTAAAAC 58.769 47.619 0.00 0.00 0.00 2.43
2290 2402 1.340405 GGACACCTTGGATGCACATCT 60.340 52.381 10.30 0.00 37.92 2.90
2350 2462 3.155093 CAGGATGCATAACCAAGCAAC 57.845 47.619 0.00 0.00 44.88 4.17
2368 2480 1.305549 AAAGGCCCCTTGGATGCAG 60.306 57.895 0.00 0.00 36.26 4.41
2369 2481 1.305213 GAAAGGCCCCTTGGATGCA 60.305 57.895 0.00 0.00 36.26 3.96
2370 2482 2.060383 GGAAAGGCCCCTTGGATGC 61.060 63.158 0.00 0.00 36.26 3.91
2371 2483 4.362479 GGAAAGGCCCCTTGGATG 57.638 61.111 0.00 0.00 36.26 3.51
2381 2493 1.603739 GTGGTGACTGGGGAAAGGC 60.604 63.158 0.00 0.00 0.00 4.35
2382 2494 1.074951 GGTGGTGACTGGGGAAAGG 59.925 63.158 0.00 0.00 0.00 3.11
2383 2495 0.184933 TTGGTGGTGACTGGGGAAAG 59.815 55.000 0.00 0.00 0.00 2.62
2388 2500 2.282462 GCCTTGGTGGTGACTGGG 60.282 66.667 0.00 0.00 38.35 4.45
2391 2503 0.033601 TTTGTGCCTTGGTGGTGACT 60.034 50.000 0.00 0.00 38.35 3.41
2399 2511 0.451783 GCTCGGTATTTGTGCCTTGG 59.548 55.000 0.00 0.00 0.00 3.61
2427 2539 6.808212 GCGATATATTGTACTAGCGGGTTAAA 59.192 38.462 1.88 0.00 0.00 1.52
2434 2546 7.190191 AGATGAAGCGATATATTGTACTAGCG 58.810 38.462 1.88 0.00 0.00 4.26
2464 2579 5.405269 CCATCGTGCGATTGAGATAAACATA 59.595 40.000 4.17 0.00 31.62 2.29
2483 2598 6.652481 AGTTTATCATGCCTAGATTTCCATCG 59.348 38.462 0.00 0.00 34.17 3.84
2515 2630 5.717078 TCGTACTTCTGTACAACCTGATT 57.283 39.130 0.00 0.00 46.88 2.57
2522 2637 7.972277 GGAGATAATGTTCGTACTTCTGTACAA 59.028 37.037 0.00 0.00 46.88 2.41
2532 2647 5.007430 TCGAGTCAGGAGATAATGTTCGTAC 59.993 44.000 0.00 0.00 0.00 3.67
2571 2691 5.835113 AAACCTCGCATATTTACAAGCAT 57.165 34.783 0.00 0.00 0.00 3.79
2586 2706 2.684881 AGCATGATGCCTAAAAACCTCG 59.315 45.455 14.72 0.00 46.52 4.63
2601 2722 6.042897 ACCAGAAGATCAGATATTGAGCATGA 59.957 38.462 0.00 0.00 44.66 3.07
2628 2749 9.768215 AGGGTCATCCTCTTTTGAAATAAAATA 57.232 29.630 0.00 0.00 44.06 1.40
2654 2778 2.922503 TGGTGCAGAAGAGGCCGA 60.923 61.111 0.00 0.00 0.00 5.54
2743 2874 5.350504 AGAGATATTGCCGAGATAATGGG 57.649 43.478 0.00 0.00 0.00 4.00
2748 2879 3.348119 AGCGAGAGATATTGCCGAGATA 58.652 45.455 0.00 0.00 0.00 1.98
2764 2895 4.902443 TCAAGTTGATAGGAGTAGCGAG 57.098 45.455 0.08 0.00 0.00 5.03
2787 2918 1.962807 TCAAACAATCTGCACCCCTTG 59.037 47.619 0.00 0.00 0.00 3.61
2834 2966 0.817654 GGCCTTCAGTTATGTTGGGC 59.182 55.000 0.00 0.00 37.87 5.36
2837 2969 2.214376 TGGGGCCTTCAGTTATGTTG 57.786 50.000 0.84 0.00 0.00 3.33
2839 2971 1.427368 TGTTGGGGCCTTCAGTTATGT 59.573 47.619 0.84 0.00 0.00 2.29
2840 2972 1.818674 GTGTTGGGGCCTTCAGTTATG 59.181 52.381 0.84 0.00 0.00 1.90
2841 2973 1.272480 GGTGTTGGGGCCTTCAGTTAT 60.272 52.381 0.84 0.00 0.00 1.89
2857 2992 2.542907 CGAAAGTGCGGCTTGGTGT 61.543 57.895 0.00 0.00 37.52 4.16
2858 2993 2.252260 CGAAAGTGCGGCTTGGTG 59.748 61.111 0.00 0.00 37.52 4.17
2870 3006 4.695560 GTCACCCAGACCCGAAAG 57.304 61.111 0.00 0.00 41.56 2.62
2939 3083 0.820074 ATGGAAAACGACGGTGGCAA 60.820 50.000 0.00 0.00 0.00 4.52
2947 3091 3.545703 AGATGGATCCATGGAAAACGAC 58.454 45.455 32.05 13.54 36.70 4.34
2959 3103 9.793259 TTAGGTACATATTTTGAAGATGGATCC 57.207 33.333 4.20 4.20 0.00 3.36
2972 3116 6.706270 CGAGGTTGATGCTTAGGTACATATTT 59.294 38.462 0.00 0.00 0.00 1.40
2974 3118 5.784177 CGAGGTTGATGCTTAGGTACATAT 58.216 41.667 0.00 0.00 0.00 1.78
2977 3121 2.418197 GCGAGGTTGATGCTTAGGTACA 60.418 50.000 0.00 0.00 0.00 2.90
2983 3127 1.737838 CCTTGCGAGGTTGATGCTTA 58.262 50.000 12.40 0.00 38.32 3.09
2985 3129 2.042831 GCCTTGCGAGGTTGATGCT 61.043 57.895 21.55 0.00 45.44 3.79
2996 3140 1.702886 CATCGACTATAGGCCTTGCG 58.297 55.000 12.58 8.36 0.00 4.85
2999 3143 1.344763 GTGGCATCGACTATAGGCCTT 59.655 52.381 12.58 0.81 44.85 4.35
3038 3182 0.746063 TGGACACACGTAACGAGGTT 59.254 50.000 0.00 0.00 0.00 3.50
3044 3188 3.322369 TGTGATGATGGACACACGTAAC 58.678 45.455 0.00 0.00 41.19 2.50
3045 3189 3.669251 TGTGATGATGGACACACGTAA 57.331 42.857 0.00 0.00 41.19 3.18
3069 3213 1.964891 AGCAAGGTCTCGACGACGA 60.965 57.895 9.98 9.98 43.79 4.20
3116 3260 3.623060 GTGGTATTTCATGTGACGCATCT 59.377 43.478 0.00 0.00 35.19 2.90
3134 3278 1.227853 GTTTCAGCGGTGGAGTGGT 60.228 57.895 15.67 0.00 0.00 4.16
3137 3281 2.030562 CGGTTTCAGCGGTGGAGT 59.969 61.111 15.67 0.00 35.16 3.85
3173 3318 7.093945 GGGCATTATTCTTGAAGGTGTTCTTTA 60.094 37.037 0.00 0.00 35.50 1.85
3176 3321 4.706962 GGGCATTATTCTTGAAGGTGTTCT 59.293 41.667 0.00 0.00 33.38 3.01
3178 3323 4.677182 AGGGCATTATTCTTGAAGGTGTT 58.323 39.130 0.00 0.00 0.00 3.32
3200 3345 2.432874 TCTTGTGTCGTTCTTCCCTTGA 59.567 45.455 0.00 0.00 0.00 3.02
3207 3352 1.134521 TGGTGCTCTTGTGTCGTTCTT 60.135 47.619 0.00 0.00 0.00 2.52
3311 3462 1.021390 CGTTCTTCTGCGCCATCCTT 61.021 55.000 4.18 0.00 0.00 3.36
3312 3463 1.448540 CGTTCTTCTGCGCCATCCT 60.449 57.895 4.18 0.00 0.00 3.24
3423 3574 1.227823 TGGCAGCGTTGTAGCAAGT 60.228 52.632 0.00 0.00 40.15 3.16
3426 3577 2.668212 GGTGGCAGCGTTGTAGCA 60.668 61.111 0.00 0.00 40.15 3.49


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

AutoCloner maintained by Alex Coulton.