Multiple sequence alignment - TraesCS2A01G346200

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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 TraesCS2A01G346200 chr2A 100.000 4239 0 0 1 4239 584524087 584519849 0.000000e+00 7829.0
1 TraesCS2A01G346200 chr2A 85.194 2087 206 49 835 2892 584579325 584577313 0.000000e+00 2047.0
2 TraesCS2A01G346200 chr2A 86.943 314 33 5 2936 3243 584577316 584577005 3.140000e-91 346.0
3 TraesCS2A01G346200 chr2A 80.159 378 53 14 3251 3617 13819090 13818724 3.250000e-66 263.0
4 TraesCS2A01G346200 chr2A 89.005 191 12 3 3627 3817 584577013 584576832 1.190000e-55 228.0
5 TraesCS2A01G346200 chr2D 93.817 2879 112 24 785 3623 440784271 440781419 0.000000e+00 4270.0
6 TraesCS2A01G346200 chr2D 85.388 2101 205 52 835 2892 440969015 440966974 0.000000e+00 2085.0
7 TraesCS2A01G346200 chr2D 93.450 626 24 5 3627 4236 440781369 440780745 0.000000e+00 913.0
8 TraesCS2A01G346200 chr2D 87.608 807 35 15 1 754 440784999 440784205 0.000000e+00 876.0
9 TraesCS2A01G346200 chr2D 86.164 318 32 7 2936 3243 440966978 440966663 2.440000e-87 333.0
10 TraesCS2A01G346200 chr2D 86.275 306 24 8 3627 3915 440966671 440966367 2.460000e-82 316.0
11 TraesCS2A01G346200 chr2D 79.733 375 59 12 3251 3617 27470933 27470568 5.440000e-64 255.0
12 TraesCS2A01G346200 chr2B 93.503 1770 74 12 785 2521 518753933 518752172 0.000000e+00 2593.0
13 TraesCS2A01G346200 chr2B 87.245 1325 103 27 835 2147 518760232 518758962 0.000000e+00 1450.0
14 TraesCS2A01G346200 chr2B 96.239 771 25 2 2514 3281 518752096 518751327 0.000000e+00 1260.0
15 TraesCS2A01G346200 chr2B 86.845 783 51 21 1 754 518754625 518753866 0.000000e+00 828.0
16 TraesCS2A01G346200 chr2B 91.605 405 15 7 3850 4236 518751324 518750921 3.730000e-150 542.0
17 TraesCS2A01G346200 chr2B 89.394 264 21 4 2984 3243 518758072 518757812 4.090000e-85 326.0
18 TraesCS2A01G346200 chr2B 85.560 277 23 8 3655 3915 518757799 518757524 1.500000e-69 274.0
19 TraesCS2A01G346200 chr2B 75.701 321 52 22 233 547 699113289 699113589 2.060000e-28 137.0
20 TraesCS2A01G346200 chr2B 78.475 223 34 9 339 554 699113449 699113664 2.660000e-27 134.0
21 TraesCS2A01G346200 chr7B 82.480 371 48 10 3255 3616 678898026 678897664 4.120000e-80 309.0
22 TraesCS2A01G346200 chr7B 81.579 342 48 10 3250 3582 720969295 720969630 6.990000e-68 268.0
23 TraesCS2A01G346200 chr6B 80.800 375 58 9 3251 3617 34445385 34445753 8.970000e-72 281.0
24 TraesCS2A01G346200 chr5D 80.688 378 52 15 3251 3617 412064424 412064791 1.500000e-69 274.0
25 TraesCS2A01G346200 chr5D 79.825 114 15 6 423 534 400298505 400298398 4.540000e-10 76.8
26 TraesCS2A01G346200 chr3A 80.000 375 62 8 3251 3617 28323444 28323075 9.040000e-67 265.0
27 TraesCS2A01G346200 chr4D 79.947 374 58 10 3252 3617 482521141 482520777 4.200000e-65 259.0
28 TraesCS2A01G346200 chr1D 77.401 177 25 13 378 546 453792832 453792663 1.620000e-14 91.6
29 TraesCS2A01G346200 chr1D 94.444 36 2 0 519 554 408899358 408899393 5.920000e-04 56.5
30 TraesCS2A01G346200 chr3D 85.915 71 9 1 478 547 327612213 327612283 1.630000e-09 75.0
31 TraesCS2A01G346200 chr5B 77.143 140 23 8 402 535 480310200 480310064 5.880000e-09 73.1


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 TraesCS2A01G346200 chr2A 584519849 584524087 4238 True 7829.000000 7829 100.000000 1 4239 1 chr2A.!!$R2 4238
1 TraesCS2A01G346200 chr2A 584576832 584579325 2493 True 873.666667 2047 87.047333 835 3817 3 chr2A.!!$R3 2982
2 TraesCS2A01G346200 chr2D 440780745 440784999 4254 True 2019.666667 4270 91.625000 1 4236 3 chr2D.!!$R2 4235
3 TraesCS2A01G346200 chr2D 440966367 440969015 2648 True 911.333333 2085 85.942333 835 3915 3 chr2D.!!$R3 3080
4 TraesCS2A01G346200 chr2B 518750921 518760232 9311 True 1039.000000 2593 90.055857 1 4236 7 chr2B.!!$R1 4235

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
751 805 0.186386 CGGCCCATATTAAACCCCCA 59.814 55.0 0.00 0.0 0.0 4.96 F
812 866 0.396811 ATATGTTCGTAGGGCCAGCC 59.603 55.0 6.18 0.0 0.0 4.85 F
2089 8552 0.255033 ATAGGTGGCCGAGGGTTTTC 59.745 55.0 0.00 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2075 8538 1.002773 GTCTAAGAAAACCCTCGGCCA 59.997 52.381 2.24 0.0 0.00 5.36 R
2469 8955 1.702401 TGTGTCTAACATTCCCAGCCA 59.298 47.619 0.00 0.0 32.36 4.75 R
3550 10135 1.459209 GCATCGACACAACATCGTTCA 59.541 47.619 0.00 0.0 40.50 3.18 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
78 79 7.559590 AAGTGGCATGCTCTTAGTAATAAAG 57.440 36.000 18.92 0.00 0.00 1.85
82 83 6.183360 TGGCATGCTCTTAGTAATAAAGTTGC 60.183 38.462 18.92 0.00 0.00 4.17
139 163 8.650143 AAAAGAAAATCCTACCATGCTCTTTA 57.350 30.769 0.00 0.00 32.93 1.85
143 167 6.436843 AAATCCTACCATGCTCTTTAAACG 57.563 37.500 0.00 0.00 0.00 3.60
188 212 9.480053 AACATCATGTGATTTTCTAAAACTTGG 57.520 29.630 0.00 0.00 31.21 3.61
211 235 9.979578 TTGGCATGCTATAAAATATGGTAAAAG 57.020 29.630 18.92 0.00 0.00 2.27
312 337 5.634859 GGGCATGTTCTCACTAACAAAATTG 59.365 40.000 0.00 0.00 42.33 2.32
366 411 7.851508 TGTCACGCTCTTTATAATAGAAATGC 58.148 34.615 0.67 0.00 0.00 3.56
370 415 8.935844 CACGCTCTTTATAATAGAAATGCCATA 58.064 33.333 0.67 0.00 0.00 2.74
387 432 8.707938 AATGCCATACTCTTTCAAATAAAAGC 57.292 30.769 0.00 0.00 36.41 3.51
393 438 5.402398 ACTCTTTCAAATAAAAGCGCCATC 58.598 37.500 2.29 0.00 36.41 3.51
394 439 5.183904 ACTCTTTCAAATAAAAGCGCCATCT 59.816 36.000 2.29 0.00 36.41 2.90
395 440 5.640732 TCTTTCAAATAAAAGCGCCATCTC 58.359 37.500 2.29 0.00 36.41 2.75
396 441 5.415701 TCTTTCAAATAAAAGCGCCATCTCT 59.584 36.000 2.29 0.00 36.41 3.10
432 484 8.011106 GTCATGCTTTACAAACAAAATTCCATG 58.989 33.333 0.00 0.00 0.00 3.66
438 490 8.729805 TTTACAAACAAAATTCCATGCTCTTT 57.270 26.923 0.00 0.00 0.00 2.52
450 502 8.652810 ATTCCATGCTCTTTATACAAAAATGC 57.347 30.769 0.00 0.00 0.00 3.56
473 525 7.609960 TGCCATGCTCTTAATAACAAAAATGA 58.390 30.769 0.00 0.00 0.00 2.57
579 631 6.765989 GGAGTAGTACATTGTAAATGCCATGA 59.234 38.462 2.52 0.00 0.00 3.07
583 635 9.450807 GTAGTACATTGTAAATGCCATGATTTC 57.549 33.333 0.00 0.00 0.00 2.17
713 767 4.157246 TCATATATGTTCGTAGGGCCAGT 58.843 43.478 12.42 0.00 0.00 4.00
739 793 0.399454 CAGATCATTCTCCGGCCCAT 59.601 55.000 0.00 0.00 0.00 4.00
740 794 1.625315 CAGATCATTCTCCGGCCCATA 59.375 52.381 0.00 0.00 0.00 2.74
741 795 2.238144 CAGATCATTCTCCGGCCCATAT 59.762 50.000 0.00 0.00 0.00 1.78
742 796 2.915604 AGATCATTCTCCGGCCCATATT 59.084 45.455 0.00 0.00 0.00 1.28
743 797 4.080919 CAGATCATTCTCCGGCCCATATTA 60.081 45.833 0.00 0.00 0.00 0.98
744 798 4.536090 AGATCATTCTCCGGCCCATATTAA 59.464 41.667 0.00 0.00 0.00 1.40
745 799 4.715534 TCATTCTCCGGCCCATATTAAA 57.284 40.909 0.00 0.00 0.00 1.52
746 800 4.394729 TCATTCTCCGGCCCATATTAAAC 58.605 43.478 0.00 0.00 0.00 2.01
747 801 2.943036 TCTCCGGCCCATATTAAACC 57.057 50.000 0.00 0.00 0.00 3.27
748 802 1.422402 TCTCCGGCCCATATTAAACCC 59.578 52.381 0.00 0.00 0.00 4.11
749 803 0.479378 TCCGGCCCATATTAAACCCC 59.521 55.000 0.00 0.00 0.00 4.95
750 804 0.541063 CCGGCCCATATTAAACCCCC 60.541 60.000 0.00 0.00 0.00 5.40
751 805 0.186386 CGGCCCATATTAAACCCCCA 59.814 55.000 0.00 0.00 0.00 4.96
752 806 1.203125 CGGCCCATATTAAACCCCCAT 60.203 52.381 0.00 0.00 0.00 4.00
753 807 2.041891 CGGCCCATATTAAACCCCCATA 59.958 50.000 0.00 0.00 0.00 2.74
754 808 3.309556 CGGCCCATATTAAACCCCCATAT 60.310 47.826 0.00 0.00 0.00 1.78
755 809 4.079672 CGGCCCATATTAAACCCCCATATA 60.080 45.833 0.00 0.00 0.00 0.86
756 810 5.399727 CGGCCCATATTAAACCCCCATATAT 60.400 44.000 0.00 0.00 0.00 0.86
757 811 5.838521 GGCCCATATTAAACCCCCATATATG 59.161 44.000 5.68 5.68 0.00 1.78
758 812 6.440354 GCCCATATTAAACCCCCATATATGT 58.560 40.000 11.73 0.00 30.74 2.29
759 813 6.900743 GCCCATATTAAACCCCCATATATGTT 59.099 38.462 11.73 1.88 30.74 2.71
760 814 7.069455 GCCCATATTAAACCCCCATATATGTTC 59.931 40.741 11.73 0.00 30.74 3.18
761 815 7.563556 CCCATATTAAACCCCCATATATGTTCC 59.436 40.741 11.73 0.00 30.74 3.62
762 816 8.343787 CCATATTAAACCCCCATATATGTTCCT 58.656 37.037 11.73 0.00 30.74 3.36
763 817 9.408648 CATATTAAACCCCCATATATGTTCCTC 57.591 37.037 11.73 0.00 0.00 3.71
764 818 4.741928 AAACCCCCATATATGTTCCTCC 57.258 45.455 11.73 0.00 0.00 4.30
765 819 3.377154 ACCCCCATATATGTTCCTCCA 57.623 47.619 11.73 0.00 0.00 3.86
766 820 2.986728 ACCCCCATATATGTTCCTCCAC 59.013 50.000 11.73 0.00 0.00 4.02
767 821 2.027192 CCCCCATATATGTTCCTCCACG 60.027 54.545 11.73 0.00 0.00 4.94
768 822 2.903784 CCCCATATATGTTCCTCCACGA 59.096 50.000 11.73 0.00 0.00 4.35
769 823 3.326588 CCCCATATATGTTCCTCCACGAA 59.673 47.826 11.73 0.00 0.00 3.85
770 824 4.202419 CCCCATATATGTTCCTCCACGAAA 60.202 45.833 11.73 0.00 0.00 3.46
771 825 5.514834 CCCCATATATGTTCCTCCACGAAAT 60.515 44.000 11.73 0.00 0.00 2.17
772 826 6.296202 CCCCATATATGTTCCTCCACGAAATA 60.296 42.308 11.73 0.00 0.00 1.40
773 827 7.338710 CCCATATATGTTCCTCCACGAAATAT 58.661 38.462 11.73 0.00 0.00 1.28
774 828 7.495934 CCCATATATGTTCCTCCACGAAATATC 59.504 40.741 11.73 0.00 0.00 1.63
775 829 8.260818 CCATATATGTTCCTCCACGAAATATCT 58.739 37.037 11.73 0.00 0.00 1.98
776 830 9.307121 CATATATGTTCCTCCACGAAATATCTC 57.693 37.037 4.43 0.00 0.00 2.75
777 831 4.402056 TGTTCCTCCACGAAATATCTCC 57.598 45.455 0.00 0.00 0.00 3.71
778 832 3.134081 TGTTCCTCCACGAAATATCTCCC 59.866 47.826 0.00 0.00 0.00 4.30
779 833 1.961394 TCCTCCACGAAATATCTCCCG 59.039 52.381 0.00 0.00 0.00 5.14
780 834 1.961394 CCTCCACGAAATATCTCCCGA 59.039 52.381 0.00 0.00 0.00 5.14
781 835 2.029828 CCTCCACGAAATATCTCCCGAG 60.030 54.545 0.00 0.00 0.00 4.63
782 836 2.885266 CTCCACGAAATATCTCCCGAGA 59.115 50.000 0.00 0.00 42.37 4.04
783 837 3.293337 TCCACGAAATATCTCCCGAGAA 58.707 45.455 0.00 0.00 41.36 2.87
784 838 3.702548 TCCACGAAATATCTCCCGAGAAA 59.297 43.478 0.00 0.00 41.36 2.52
785 839 4.344102 TCCACGAAATATCTCCCGAGAAAT 59.656 41.667 0.00 0.00 41.36 2.17
786 840 5.057149 CCACGAAATATCTCCCGAGAAATT 58.943 41.667 0.00 0.00 41.36 1.82
787 841 5.177696 CCACGAAATATCTCCCGAGAAATTC 59.822 44.000 0.00 3.63 41.36 2.17
788 842 5.177696 CACGAAATATCTCCCGAGAAATTCC 59.822 44.000 0.00 0.00 41.36 3.01
789 843 5.070580 ACGAAATATCTCCCGAGAAATTCCT 59.929 40.000 0.00 0.00 41.36 3.36
790 844 5.635700 CGAAATATCTCCCGAGAAATTCCTC 59.364 44.000 0.00 0.00 41.36 3.71
791 845 6.500589 AAATATCTCCCGAGAAATTCCTCA 57.499 37.500 0.00 0.00 41.36 3.86
792 846 6.694445 AATATCTCCCGAGAAATTCCTCAT 57.306 37.500 0.00 0.00 41.36 2.90
793 847 7.798710 AATATCTCCCGAGAAATTCCTCATA 57.201 36.000 0.00 0.00 41.36 2.15
794 848 7.986553 ATATCTCCCGAGAAATTCCTCATAT 57.013 36.000 0.00 0.00 41.36 1.78
795 849 9.494055 AATATCTCCCGAGAAATTCCTCATATA 57.506 33.333 0.00 0.00 41.36 0.86
796 850 7.986553 ATCTCCCGAGAAATTCCTCATATAT 57.013 36.000 0.00 0.00 41.36 0.86
797 851 7.175347 TCTCCCGAGAAATTCCTCATATATG 57.825 40.000 6.36 6.36 33.91 1.78
798 852 6.726299 TCTCCCGAGAAATTCCTCATATATGT 59.274 38.462 12.42 0.00 33.91 2.29
799 853 7.235606 TCTCCCGAGAAATTCCTCATATATGTT 59.764 37.037 12.42 0.00 33.91 2.71
800 854 7.386851 TCCCGAGAAATTCCTCATATATGTTC 58.613 38.462 12.42 7.78 32.86 3.18
801 855 6.311445 CCCGAGAAATTCCTCATATATGTTCG 59.689 42.308 12.42 8.63 32.86 3.95
802 856 6.868864 CCGAGAAATTCCTCATATATGTTCGT 59.131 38.462 12.42 0.00 32.86 3.85
803 857 8.027189 CCGAGAAATTCCTCATATATGTTCGTA 58.973 37.037 12.42 0.00 32.86 3.43
804 858 9.066939 CGAGAAATTCCTCATATATGTTCGTAG 57.933 37.037 12.42 2.40 32.86 3.51
805 859 9.360093 GAGAAATTCCTCATATATGTTCGTAGG 57.640 37.037 12.42 11.06 33.50 3.18
806 860 8.314751 AGAAATTCCTCATATATGTTCGTAGGG 58.685 37.037 12.42 5.42 0.00 3.53
807 861 5.401531 TTCCTCATATATGTTCGTAGGGC 57.598 43.478 12.42 0.00 0.00 5.19
808 862 3.767673 TCCTCATATATGTTCGTAGGGCC 59.232 47.826 12.42 0.00 0.00 5.80
809 863 3.513912 CCTCATATATGTTCGTAGGGCCA 59.486 47.826 12.42 0.00 0.00 5.36
810 864 4.382040 CCTCATATATGTTCGTAGGGCCAG 60.382 50.000 12.42 0.00 0.00 4.85
811 865 3.056107 TCATATATGTTCGTAGGGCCAGC 60.056 47.826 12.42 0.00 0.00 4.85
812 866 0.396811 ATATGTTCGTAGGGCCAGCC 59.603 55.000 6.18 0.00 0.00 4.85
875 933 1.153147 GCTCCGACCCAATCTTCCC 60.153 63.158 0.00 0.00 0.00 3.97
887 945 4.148825 CTTCCCCACTCCTCGCCG 62.149 72.222 0.00 0.00 0.00 6.46
908 966 3.311110 GGTGCCGGTGTCTCCTGA 61.311 66.667 1.90 0.00 0.00 3.86
910 968 1.668151 GTGCCGGTGTCTCCTGAAC 60.668 63.158 1.90 0.00 0.00 3.18
913 971 1.913762 CCGGTGTCTCCTGAACCCT 60.914 63.158 0.00 0.00 0.00 4.34
917 980 1.353091 GTGTCTCCTGAACCCTCCTT 58.647 55.000 0.00 0.00 0.00 3.36
975 1048 0.890683 CTCCAAAGGCAGGCGAAAAT 59.109 50.000 0.00 0.00 0.00 1.82
1178 7621 3.853330 CGTCATCAACCGCGCCAG 61.853 66.667 0.00 0.00 0.00 4.85
1197 7640 1.446272 GAAGGACAAGCCCGACGAG 60.446 63.158 0.00 0.00 37.37 4.18
1261 7712 1.068250 GCTAGGGCGTGGACTGATC 59.932 63.158 0.00 0.00 0.00 2.92
1485 7936 4.116328 TCTTCCAGGTCGCGCTCG 62.116 66.667 5.56 0.00 0.00 5.03
1559 8011 2.858745 ACCAGTGGCTGACGTTTAATT 58.141 42.857 9.78 0.00 32.44 1.40
1562 8014 5.007682 ACCAGTGGCTGACGTTTAATTTAT 58.992 37.500 9.78 0.00 32.44 1.40
1887 8342 5.368145 TGTAGATATTCCAGATGGTTGTGC 58.632 41.667 0.00 0.00 36.34 4.57
1983 8442 3.449737 TGTCCCTCGTACTTAATCCCAAG 59.550 47.826 0.00 0.00 0.00 3.61
2026 8485 6.388689 TCCCATAACCTGGTTTACATAGATGT 59.611 38.462 18.58 0.08 44.30 3.06
2075 8538 3.557898 GCATGCTAGTATGCCACATAGGT 60.558 47.826 29.31 0.00 45.93 3.08
2089 8552 0.255033 ATAGGTGGCCGAGGGTTTTC 59.745 55.000 0.00 0.00 0.00 2.29
2141 8604 8.328758 TCCCCTAATAATGCAATAGTAAGGATG 58.671 37.037 5.63 0.20 0.00 3.51
2196 8669 2.093973 GGTCATATCCCTATGTCCGCTG 60.094 54.545 0.00 0.00 35.03 5.18
2259 8745 5.241403 TGAATATCCTGGTCAGTGTTGTT 57.759 39.130 0.00 0.00 0.00 2.83
2421 8907 5.078411 AGAAACTGATCATGCGTAAGACT 57.922 39.130 0.00 0.00 43.02 3.24
2469 8955 9.631257 TGAAAGTAATATGGTGATGTCATGAAT 57.369 29.630 0.00 0.00 0.00 2.57
2779 9347 4.739195 TCAGTTTTGGTGTACTTGTTTGC 58.261 39.130 0.00 0.00 0.00 3.68
2839 9407 4.081917 GCTCTGAAGTTAGTAGGAAGCTGT 60.082 45.833 0.00 0.00 0.00 4.40
2859 9433 4.489810 TGTGTTGGTTTAAGTGTTGCTTG 58.510 39.130 0.00 0.00 38.05 4.01
2955 9530 3.895041 TCTTTAGAAAAGTTTGGCCCCAG 59.105 43.478 0.00 0.00 0.00 4.45
3199 9784 0.842030 AGATCACCAGGCCCAGTGAA 60.842 55.000 24.72 11.81 45.54 3.18
3305 9890 3.645975 CGGACACCGGTTGCACAC 61.646 66.667 2.97 0.00 44.15 3.82
3315 9900 2.217429 GGTTGCACACCGAAAAATGT 57.783 45.000 0.00 0.00 35.12 2.71
3316 9901 2.545731 GGTTGCACACCGAAAAATGTT 58.454 42.857 0.00 0.00 35.12 2.71
3317 9902 2.933260 GGTTGCACACCGAAAAATGTTT 59.067 40.909 0.00 0.00 35.12 2.83
3318 9903 3.242252 GGTTGCACACCGAAAAATGTTTG 60.242 43.478 0.00 0.00 35.12 2.93
3319 9904 3.510388 TGCACACCGAAAAATGTTTGA 57.490 38.095 0.00 0.00 0.00 2.69
3320 9905 3.849911 TGCACACCGAAAAATGTTTGAA 58.150 36.364 0.00 0.00 0.00 2.69
3321 9906 4.245660 TGCACACCGAAAAATGTTTGAAA 58.754 34.783 0.00 0.00 0.00 2.69
3322 9907 4.690748 TGCACACCGAAAAATGTTTGAAAA 59.309 33.333 0.00 0.00 0.00 2.29
3323 9908 5.179368 TGCACACCGAAAAATGTTTGAAAAA 59.821 32.000 0.00 0.00 0.00 1.94
3324 9909 6.128172 TGCACACCGAAAAATGTTTGAAAAAT 60.128 30.769 0.00 0.00 0.00 1.82
3325 9910 6.744993 GCACACCGAAAAATGTTTGAAAAATT 59.255 30.769 0.00 0.00 0.00 1.82
3326 9911 7.045031 GCACACCGAAAAATGTTTGAAAAATTC 60.045 33.333 0.00 0.00 0.00 2.17
3327 9912 7.427895 CACACCGAAAAATGTTTGAAAAATTCC 59.572 33.333 0.00 0.00 0.00 3.01
3328 9913 7.119846 ACACCGAAAAATGTTTGAAAAATTCCA 59.880 29.630 0.00 0.00 0.00 3.53
3329 9914 7.965107 CACCGAAAAATGTTTGAAAAATTCCAA 59.035 29.630 0.00 0.00 0.00 3.53
3330 9915 8.515414 ACCGAAAAATGTTTGAAAAATTCCAAA 58.485 25.926 0.00 0.00 0.00 3.28
3331 9916 9.346725 CCGAAAAATGTTTGAAAAATTCCAAAA 57.653 25.926 0.00 0.00 34.52 2.44
3405 9990 7.538334 TCAAAATTCGAAACATTGCACTAGATG 59.462 33.333 0.00 0.00 0.00 2.90
3444 10029 3.947196 GACATCAGTGTGATAATTGGCCA 59.053 43.478 0.00 0.00 39.09 5.36
3458 10043 0.612732 TGGCCAAATCTGAAGCCCAG 60.613 55.000 0.61 0.00 45.14 4.45
3566 10158 3.519908 ACATTGAACGATGTTGTGTCG 57.480 42.857 2.22 0.00 44.26 4.35
3575 10167 2.279921 CGATGTTGTGTCGATGCACTAG 59.720 50.000 7.57 0.00 41.40 2.57
3617 10209 4.341806 TCAAACATTTCTGGATGTGCAACT 59.658 37.500 0.00 0.00 40.03 3.16
3619 10211 3.225104 ACATTTCTGGATGTGCAACTGT 58.775 40.909 0.00 0.00 38.75 3.55
3625 10263 1.317613 GGATGTGCAACTGTGGTTCA 58.682 50.000 0.00 0.00 38.04 3.18
3756 10405 2.185004 TTCTGAACTGCCTTAGTGCC 57.815 50.000 0.00 0.00 40.26 5.01
3757 10406 1.352083 TCTGAACTGCCTTAGTGCCT 58.648 50.000 0.00 0.00 40.26 4.75
3842 10491 4.143194 GGTAGTTCCGTTCTTTTTCAGC 57.857 45.455 0.00 0.00 0.00 4.26
3895 10550 2.795470 GTCGGTCTGTTTCAGAGTTCAC 59.205 50.000 0.00 0.00 41.46 3.18
3917 10572 5.294552 CACTTTAGTGCTCCTGTATTTAGCC 59.705 44.000 0.00 0.00 39.39 3.93
4020 10677 0.473755 TCCCGGCATGCATGAAGTAT 59.526 50.000 30.64 0.00 0.00 2.12
4073 10730 4.464947 GAGCTATTTTGCCTTCCCTATGT 58.535 43.478 0.00 0.00 0.00 2.29
4141 10814 0.887836 CGGCTGACCATATGCATGCT 60.888 55.000 20.33 7.07 34.57 3.79
4236 10909 7.604657 TTATATCTGTTTGGTTTGGTTTGGT 57.395 32.000 0.00 0.00 0.00 3.67
4237 10910 4.835284 ATCTGTTTGGTTTGGTTTGGTT 57.165 36.364 0.00 0.00 0.00 3.67
4238 10911 4.625607 TCTGTTTGGTTTGGTTTGGTTT 57.374 36.364 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 7.609918 TGAAGAGCATGGCAACTTTATTACTAA 59.390 33.333 0.00 0.00 30.86 2.24
78 79 3.492011 CACTTTTTGAAGAGCATGGCAAC 59.508 43.478 0.00 0.00 0.00 4.17
82 83 4.572985 TGTCACTTTTTGAAGAGCATGG 57.427 40.909 0.00 0.00 35.39 3.66
139 163 5.777802 TCACATGGCAATTCATAAACGTTT 58.222 33.333 18.90 18.90 0.00 3.60
143 167 6.812656 TGATGTTCACATGGCAATTCATAAAC 59.187 34.615 0.00 0.00 36.57 2.01
241 265 7.201556 GCCTTTTTCTTTTATTAAGAGCATGGC 60.202 37.037 0.00 0.00 0.00 4.40
242 266 7.818930 TGCCTTTTTCTTTTATTAAGAGCATGG 59.181 33.333 0.00 0.00 0.00 3.66
287 312 2.489938 TGTTAGTGAGAACATGCCCC 57.510 50.000 0.00 0.00 34.40 5.80
340 365 8.499162 GCATTTCTATTATAAAGAGCGTGACAT 58.501 33.333 0.00 0.00 0.00 3.06
341 366 7.042051 GGCATTTCTATTATAAAGAGCGTGACA 60.042 37.037 0.00 0.00 0.00 3.58
342 367 7.042051 TGGCATTTCTATTATAAAGAGCGTGAC 60.042 37.037 0.00 0.00 0.00 3.67
343 368 6.989759 TGGCATTTCTATTATAAAGAGCGTGA 59.010 34.615 0.00 0.00 0.00 4.35
344 369 7.189693 TGGCATTTCTATTATAAAGAGCGTG 57.810 36.000 0.00 0.00 0.00 5.34
345 370 7.986085 ATGGCATTTCTATTATAAAGAGCGT 57.014 32.000 0.00 0.00 0.00 5.07
346 371 9.155975 AGTATGGCATTTCTATTATAAAGAGCG 57.844 33.333 4.78 0.00 0.00 5.03
366 411 5.743872 GGCGCTTTTATTTGAAAGAGTATGG 59.256 40.000 7.64 0.00 38.60 2.74
370 415 4.846779 TGGCGCTTTTATTTGAAAGAGT 57.153 36.364 7.64 0.00 38.60 3.24
387 432 6.653183 CATGACACTTTTATAAGAGATGGCG 58.347 40.000 9.85 0.00 35.30 5.69
432 484 6.044682 AGCATGGCATTTTTGTATAAAGAGC 58.955 36.000 0.00 0.00 0.00 4.09
450 502 8.984891 TGTCATTTTTGTTATTAAGAGCATGG 57.015 30.769 0.00 0.00 0.00 3.66
501 553 8.752187 AGAGCATGGCATTTTCTTTATTAAGAA 58.248 29.630 0.00 2.82 46.07 2.52
554 606 6.765989 TCATGGCATTTACAATGTACTACTCC 59.234 38.462 0.00 0.00 0.00 3.85
555 607 7.786178 TCATGGCATTTACAATGTACTACTC 57.214 36.000 0.00 0.00 0.00 2.59
556 608 8.752005 AATCATGGCATTTACAATGTACTACT 57.248 30.769 0.00 0.00 0.00 2.57
557 609 9.450807 GAAATCATGGCATTTACAATGTACTAC 57.549 33.333 0.00 0.00 0.00 2.73
558 610 9.407380 AGAAATCATGGCATTTACAATGTACTA 57.593 29.630 0.00 0.00 0.00 1.82
559 611 8.297470 AGAAATCATGGCATTTACAATGTACT 57.703 30.769 0.00 0.00 0.00 2.73
647 699 3.631250 TGTCATAAATTTCTGGGGAGCC 58.369 45.455 0.00 0.00 0.00 4.70
654 706 5.572896 GGACGCCTTTTGTCATAAATTTCTG 59.427 40.000 0.00 0.00 38.10 3.02
662 714 2.301870 ACAGAGGACGCCTTTTGTCATA 59.698 45.455 0.00 0.00 38.10 2.15
713 767 1.135094 GGAGAATGATCTGGGCTGGA 58.865 55.000 0.00 0.00 35.54 3.86
739 793 7.521468 TGGAGGAACATATATGGGGGTTTAATA 59.479 37.037 16.96 0.00 0.00 0.98
740 794 6.336930 TGGAGGAACATATATGGGGGTTTAAT 59.663 38.462 16.96 0.00 0.00 1.40
741 795 5.677276 TGGAGGAACATATATGGGGGTTTAA 59.323 40.000 16.96 0.00 0.00 1.52
742 796 5.073965 GTGGAGGAACATATATGGGGGTTTA 59.926 44.000 16.96 0.00 0.00 2.01
743 797 4.058731 TGGAGGAACATATATGGGGGTTT 58.941 43.478 16.96 1.65 0.00 3.27
744 798 3.397955 GTGGAGGAACATATATGGGGGTT 59.602 47.826 16.96 2.02 0.00 4.11
745 799 2.986728 GTGGAGGAACATATATGGGGGT 59.013 50.000 16.96 0.00 0.00 4.95
746 800 2.027192 CGTGGAGGAACATATATGGGGG 60.027 54.545 16.96 0.00 0.00 5.40
747 801 2.903784 TCGTGGAGGAACATATATGGGG 59.096 50.000 16.96 0.00 0.00 4.96
748 802 4.617253 TTCGTGGAGGAACATATATGGG 57.383 45.455 16.96 0.00 0.00 4.00
749 803 8.260818 AGATATTTCGTGGAGGAACATATATGG 58.739 37.037 16.96 0.00 0.00 2.74
750 804 9.307121 GAGATATTTCGTGGAGGAACATATATG 57.693 37.037 11.29 11.29 0.00 1.78
751 805 8.478877 GGAGATATTTCGTGGAGGAACATATAT 58.521 37.037 0.00 0.00 0.00 0.86
752 806 7.093465 GGGAGATATTTCGTGGAGGAACATATA 60.093 40.741 0.00 0.00 0.00 0.86
753 807 6.295916 GGGAGATATTTCGTGGAGGAACATAT 60.296 42.308 0.00 0.00 0.00 1.78
754 808 5.011738 GGGAGATATTTCGTGGAGGAACATA 59.988 44.000 0.00 0.00 0.00 2.29
755 809 4.202367 GGGAGATATTTCGTGGAGGAACAT 60.202 45.833 0.00 0.00 0.00 2.71
756 810 3.134081 GGGAGATATTTCGTGGAGGAACA 59.866 47.826 0.00 0.00 0.00 3.18
757 811 3.729966 GGGAGATATTTCGTGGAGGAAC 58.270 50.000 0.00 0.00 0.00 3.62
758 812 2.364324 CGGGAGATATTTCGTGGAGGAA 59.636 50.000 0.00 0.00 0.00 3.36
759 813 1.961394 CGGGAGATATTTCGTGGAGGA 59.039 52.381 0.00 0.00 0.00 3.71
760 814 1.961394 TCGGGAGATATTTCGTGGAGG 59.039 52.381 0.00 0.00 0.00 4.30
761 815 2.885266 TCTCGGGAGATATTTCGTGGAG 59.115 50.000 0.00 2.36 38.80 3.86
762 816 2.940158 TCTCGGGAGATATTTCGTGGA 58.060 47.619 0.00 0.00 38.80 4.02
763 817 3.728076 TTCTCGGGAGATATTTCGTGG 57.272 47.619 0.00 0.00 37.29 4.94
764 818 5.177696 GGAATTTCTCGGGAGATATTTCGTG 59.822 44.000 13.25 0.00 38.57 4.35
765 819 5.070580 AGGAATTTCTCGGGAGATATTTCGT 59.929 40.000 13.25 9.16 38.56 3.85
766 820 5.542779 AGGAATTTCTCGGGAGATATTTCG 58.457 41.667 13.25 0.00 38.56 3.46
767 821 6.525629 TGAGGAATTTCTCGGGAGATATTTC 58.474 40.000 9.25 11.84 38.57 2.17
768 822 6.500589 TGAGGAATTTCTCGGGAGATATTT 57.499 37.500 9.25 2.26 38.57 1.40
769 823 6.694445 ATGAGGAATTTCTCGGGAGATATT 57.306 37.500 9.25 12.27 40.26 1.28
770 824 7.986553 ATATGAGGAATTTCTCGGGAGATAT 57.013 36.000 9.25 3.92 37.29 1.63
771 825 8.918116 CATATATGAGGAATTTCTCGGGAGATA 58.082 37.037 6.92 1.75 37.29 1.98
772 826 7.401493 ACATATATGAGGAATTTCTCGGGAGAT 59.599 37.037 19.63 0.00 37.29 2.75
773 827 6.726299 ACATATATGAGGAATTTCTCGGGAGA 59.274 38.462 19.63 0.00 36.61 3.71
774 828 6.940739 ACATATATGAGGAATTTCTCGGGAG 58.059 40.000 19.63 0.11 36.61 4.30
775 829 6.935240 ACATATATGAGGAATTTCTCGGGA 57.065 37.500 19.63 0.00 36.61 5.14
776 830 6.311445 CGAACATATATGAGGAATTTCTCGGG 59.689 42.308 19.63 0.00 36.61 5.14
777 831 6.868864 ACGAACATATATGAGGAATTTCTCGG 59.131 38.462 19.63 2.54 36.61 4.63
778 832 7.875316 ACGAACATATATGAGGAATTTCTCG 57.125 36.000 19.63 12.91 36.61 4.04
779 833 9.360093 CCTACGAACATATATGAGGAATTTCTC 57.640 37.037 19.63 6.82 0.00 2.87
780 834 8.314751 CCCTACGAACATATATGAGGAATTTCT 58.685 37.037 19.63 0.00 0.00 2.52
781 835 7.064728 GCCCTACGAACATATATGAGGAATTTC 59.935 40.741 19.63 9.96 0.00 2.17
782 836 6.879458 GCCCTACGAACATATATGAGGAATTT 59.121 38.462 19.63 1.78 0.00 1.82
783 837 6.407202 GCCCTACGAACATATATGAGGAATT 58.593 40.000 19.63 2.52 0.00 2.17
784 838 5.104900 GGCCCTACGAACATATATGAGGAAT 60.105 44.000 19.63 3.59 0.00 3.01
785 839 4.222145 GGCCCTACGAACATATATGAGGAA 59.778 45.833 19.63 0.41 0.00 3.36
786 840 3.767673 GGCCCTACGAACATATATGAGGA 59.232 47.826 19.63 6.11 0.00 3.71
787 841 3.513912 TGGCCCTACGAACATATATGAGG 59.486 47.826 19.63 13.85 0.00 3.86
788 842 4.748892 CTGGCCCTACGAACATATATGAG 58.251 47.826 19.63 11.79 0.00 2.90
789 843 3.056107 GCTGGCCCTACGAACATATATGA 60.056 47.826 19.63 0.00 0.00 2.15
790 844 3.262420 GCTGGCCCTACGAACATATATG 58.738 50.000 11.29 11.29 0.00 1.78
791 845 2.236395 GGCTGGCCCTACGAACATATAT 59.764 50.000 0.00 0.00 0.00 0.86
792 846 1.621814 GGCTGGCCCTACGAACATATA 59.378 52.381 0.00 0.00 0.00 0.86
793 847 0.396811 GGCTGGCCCTACGAACATAT 59.603 55.000 0.00 0.00 0.00 1.78
794 848 1.827394 GGCTGGCCCTACGAACATA 59.173 57.895 0.00 0.00 0.00 2.29
795 849 2.590092 GGCTGGCCCTACGAACAT 59.410 61.111 0.00 0.00 0.00 2.71
811 865 1.936767 TTAATCTGGGCTGGGCTGGG 61.937 60.000 0.00 0.00 0.00 4.45
812 866 0.033208 TTTAATCTGGGCTGGGCTGG 60.033 55.000 0.00 0.00 0.00 4.85
813 867 1.106285 GTTTAATCTGGGCTGGGCTG 58.894 55.000 0.00 0.00 0.00 4.85
814 868 0.033109 GGTTTAATCTGGGCTGGGCT 60.033 55.000 0.00 0.00 0.00 5.19
815 869 1.043116 GGGTTTAATCTGGGCTGGGC 61.043 60.000 0.00 0.00 0.00 5.36
816 870 0.397114 GGGGTTTAATCTGGGCTGGG 60.397 60.000 0.00 0.00 0.00 4.45
817 871 0.397114 GGGGGTTTAATCTGGGCTGG 60.397 60.000 0.00 0.00 0.00 4.85
818 872 0.334676 TGGGGGTTTAATCTGGGCTG 59.665 55.000 0.00 0.00 0.00 4.85
819 873 1.318934 ATGGGGGTTTAATCTGGGCT 58.681 50.000 0.00 0.00 0.00 5.19
820 874 2.963101 GTTATGGGGGTTTAATCTGGGC 59.037 50.000 0.00 0.00 0.00 5.36
821 875 4.470602 GAGTTATGGGGGTTTAATCTGGG 58.529 47.826 0.00 0.00 0.00 4.45
822 876 4.134563 CGAGTTATGGGGGTTTAATCTGG 58.865 47.826 0.00 0.00 0.00 3.86
823 877 4.134563 CCGAGTTATGGGGGTTTAATCTG 58.865 47.826 0.00 0.00 0.00 2.90
824 878 3.784202 ACCGAGTTATGGGGGTTTAATCT 59.216 43.478 0.00 0.00 0.00 2.40
825 879 4.132336 GACCGAGTTATGGGGGTTTAATC 58.868 47.826 0.00 0.00 31.66 1.75
868 923 2.066999 GGCGAGGAGTGGGGAAGAT 61.067 63.158 0.00 0.00 0.00 2.40
908 966 1.736491 GGTTTGGGGGAAGGAGGGTT 61.736 60.000 0.00 0.00 0.00 4.11
910 968 2.770827 GGTTTGGGGGAAGGAGGG 59.229 66.667 0.00 0.00 0.00 4.30
913 971 0.847758 GTAGGGGTTTGGGGGAAGGA 60.848 60.000 0.00 0.00 0.00 3.36
917 980 1.230050 GAGGTAGGGGTTTGGGGGA 60.230 63.158 0.00 0.00 0.00 4.81
1178 7621 2.434359 CGTCGGGCTTGTCCTTCC 60.434 66.667 0.00 0.00 34.39 3.46
1261 7712 2.126888 GCATTGCCAACACCGTCG 60.127 61.111 0.00 0.00 0.00 5.12
1485 7936 1.600663 CGAGTACGAGGCATGGATGTC 60.601 57.143 0.00 0.00 42.66 3.06
1559 8011 2.618816 CCTTCCTGCAGGACAGCAATAA 60.619 50.000 35.26 16.79 45.39 1.40
1562 8014 1.073722 CCTTCCTGCAGGACAGCAA 59.926 57.895 35.26 19.10 45.39 3.91
1703 8155 2.664402 ACAGTGAGCAAAGGGTTGAT 57.336 45.000 0.00 0.00 36.83 2.57
1704 8156 3.118038 AGTTACAGTGAGCAAAGGGTTGA 60.118 43.478 0.00 0.00 36.83 3.18
1887 8342 8.252417 TCAAATCAATAATGTGTTTCATCCCAG 58.748 33.333 0.00 0.00 35.48 4.45
2075 8538 1.002773 GTCTAAGAAAACCCTCGGCCA 59.997 52.381 2.24 0.00 0.00 5.36
2089 8552 4.466370 TGATCCTGGTACTTGGTGTCTAAG 59.534 45.833 0.00 0.00 0.00 2.18
2141 8604 9.658799 TCTGCAAGTAGGATTATATAAGATTGC 57.341 33.333 15.14 15.14 39.67 3.56
2249 8735 7.816995 ACTGAAAGCAAATTAAAACAACACTGA 59.183 29.630 0.00 0.00 37.60 3.41
2259 8745 9.462174 CAGTTGTCATACTGAAAGCAAATTAAA 57.538 29.630 8.60 0.00 46.72 1.52
2413 8899 2.732597 GCACCTCAGCTACAGTCTTACG 60.733 54.545 0.00 0.00 0.00 3.18
2469 8955 1.702401 TGTGTCTAACATTCCCAGCCA 59.298 47.619 0.00 0.00 32.36 4.75
2779 9347 2.741122 TAACAAACAACGCACGGAAG 57.259 45.000 0.00 0.00 0.00 3.46
2839 9407 3.516615 GCAAGCAACACTTAAACCAACA 58.483 40.909 0.00 0.00 36.04 3.33
2955 9530 4.759516 TTACGGCAAAAAGGAAGACATC 57.240 40.909 0.00 0.00 0.00 3.06
3199 9784 4.072131 ACGTCACATATTTTCCAGCAGTT 58.928 39.130 0.00 0.00 0.00 3.16
3249 9834 4.169696 CCCCGGCGCACCAGATAA 62.170 66.667 10.83 0.00 34.57 1.75
3297 9882 3.614616 TCAAACATTTTTCGGTGTGCAAC 59.385 39.130 0.00 0.00 37.35 4.17
3305 9890 8.902040 TTTGGAATTTTTCAAACATTTTTCGG 57.098 26.923 0.00 0.00 0.00 4.30
3351 9936 7.961855 TGAAATTTTCTGACAACATTGTTGTG 58.038 30.769 33.51 22.08 42.43 3.33
3414 9999 8.377681 CAATTATCACACTGATGTCAAATTTGC 58.622 33.333 13.54 9.16 37.70 3.68
3458 10043 9.056005 TGACATCAATGTGAACCTAATATAAGC 57.944 33.333 0.00 0.00 41.95 3.09
3487 10072 9.684448 TTGCACGAGATACAAAAATGATAAAAA 57.316 25.926 0.00 0.00 0.00 1.94
3488 10073 9.853555 ATTGCACGAGATACAAAAATGATAAAA 57.146 25.926 0.00 0.00 0.00 1.52
3550 10135 1.459209 GCATCGACACAACATCGTTCA 59.541 47.619 0.00 0.00 40.50 3.18
3582 10174 6.073819 CCAGAAATGTTTGAAAATTTCCGGAC 60.074 38.462 1.83 0.00 40.51 4.79
3586 10178 8.284693 CACATCCAGAAATGTTTGAAAATTTCC 58.715 33.333 13.25 0.00 41.62 3.13
3590 10182 6.289834 TGCACATCCAGAAATGTTTGAAAAT 58.710 32.000 0.00 0.00 37.78 1.82
3595 10187 4.446385 CAGTTGCACATCCAGAAATGTTTG 59.554 41.667 0.00 0.00 37.78 2.93
3596 10188 4.099881 ACAGTTGCACATCCAGAAATGTTT 59.900 37.500 0.00 0.00 37.78 2.83
3617 10209 3.126001 GTGGAACTCAGATGAACCACA 57.874 47.619 19.39 2.42 44.58 4.17
3756 10405 5.929697 TGACAAGCAGATGTAAAGACAAG 57.070 39.130 0.00 0.00 39.59 3.16
3839 10488 4.337763 CAAAGAGTTATTTAGCAGCGCTG 58.662 43.478 32.83 32.83 40.10 5.18
3840 10489 3.181506 GCAAAGAGTTATTTAGCAGCGCT 60.182 43.478 2.64 2.64 43.41 5.92
3841 10490 3.101546 GCAAAGAGTTATTTAGCAGCGC 58.898 45.455 0.00 0.00 0.00 5.92
3842 10491 4.606457 AGCAAAGAGTTATTTAGCAGCG 57.394 40.909 0.00 0.00 0.00 5.18
3895 10550 5.428253 TGGCTAAATACAGGAGCACTAAAG 58.572 41.667 0.00 0.00 37.98 1.85
3952 10609 1.813178 TGCTCGTCAAACAAACAACCA 59.187 42.857 0.00 0.00 0.00 3.67
4020 10677 2.046023 CCGCTGCCATTCTCACCA 60.046 61.111 0.00 0.00 0.00 4.17
4103 10774 2.605338 CCGTGAGCAAATGTGAAACCAG 60.605 50.000 0.00 0.00 34.36 4.00
4169 10842 2.124109 TGAACAACCCTTGCGGCA 60.124 55.556 0.00 0.00 33.26 5.69


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

AutoCloner maintained by Alex Coulton.