Multiple sequence alignment - TraesCS6A01G136000

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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 TraesCS6A01G136000 chr6A 100.000 2672 0 0 1 2672 107263534 107266205 0.000000e+00 4935.0
1 TraesCS6A01G136000 chr5D 93.323 1962 84 18 734 2672 289355419 289353482 0.000000e+00 2854.0
2 TraesCS6A01G136000 chr5D 92.730 1912 87 22 796 2672 289421183 289419289 0.000000e+00 2713.0
3 TraesCS6A01G136000 chr5D 88.814 295 24 5 1 287 289356421 289356128 1.180000e-93 353.0
4 TraesCS6A01G136000 chr5D 91.176 238 15 3 1 232 289421757 289421520 4.290000e-83 318.0
5 TraesCS6A01G136000 chr5D 78.039 255 19 12 824 1041 29876506 29876252 2.790000e-25 126.0
6 TraesCS6A01G136000 chr5D 91.667 84 5 2 305 388 289496845 289496764 6.040000e-22 115.0
7 TraesCS6A01G136000 chr5D 90.698 86 8 0 361 446 289727576 289727491 6.040000e-22 115.0
8 TraesCS6A01G136000 chr5D 91.803 61 4 1 361 420 289421517 289421457 1.700000e-12 84.2
9 TraesCS6A01G136000 chr5D 100.000 32 0 0 542 573 289355772 289355741 2.870000e-05 60.2
10 TraesCS6A01G136000 chr1B 91.579 1900 98 29 796 2655 426497058 426495181 0.000000e+00 2566.0
11 TraesCS6A01G136000 chr1B 97.171 919 24 2 1755 2672 133110648 133109731 0.000000e+00 1552.0
12 TraesCS6A01G136000 chr1B 96.844 919 26 3 1755 2672 426481238 426480322 0.000000e+00 1533.0
13 TraesCS6A01G136000 chr1B 96.627 919 24 4 1755 2672 133123277 133122365 0.000000e+00 1519.0
14 TraesCS6A01G136000 chr1B 86.974 1021 64 19 722 1709 133124259 133123275 0.000000e+00 1085.0
15 TraesCS6A01G136000 chr1B 91.200 750 58 4 968 1709 398962051 398962800 0.000000e+00 1013.0
16 TraesCS6A01G136000 chr1B 88.075 805 82 7 969 1767 398840324 398839528 0.000000e+00 942.0
17 TraesCS6A01G136000 chr1B 91.186 295 20 3 1 289 133125257 133124963 1.930000e-106 396.0
18 TraesCS6A01G136000 chr1B 89.416 274 24 3 1 269 133112269 133111996 9.160000e-90 340.0
19 TraesCS6A01G136000 chr1B 88.973 263 24 3 29 286 426482874 426482612 1.190000e-83 320.0
20 TraesCS6A01G136000 chr1B 84.918 305 33 8 1 292 426497875 426497571 2.010000e-76 296.0
21 TraesCS6A01G136000 chr1B 90.511 137 13 0 305 441 426497590 426497454 5.880000e-42 182.0
22 TraesCS6A01G136000 chr1B 89.051 137 15 0 305 441 426482625 426482489 1.270000e-38 171.0
23 TraesCS6A01G136000 chr1B 85.542 83 2 3 796 868 426482150 426482068 7.930000e-11 78.7
24 TraesCS6A01G136000 chr1B 97.727 44 1 0 796 839 133111555 133111512 2.850000e-10 76.8
25 TraesCS6A01G136000 chr1B 100.000 32 0 0 542 573 133124614 133124583 2.870000e-05 60.2
26 TraesCS6A01G136000 chr7A 91.597 1785 93 18 793 2547 628645448 628647205 0.000000e+00 2412.0
27 TraesCS6A01G136000 chr7A 98.268 866 14 1 1808 2672 628384988 628384123 0.000000e+00 1515.0
28 TraesCS6A01G136000 chr7A 87.768 981 76 22 834 1774 626992695 626991719 0.000000e+00 1107.0
29 TraesCS6A01G136000 chr7A 86.142 1068 69 29 736 1759 628386018 628384986 0.000000e+00 1079.0
30 TraesCS6A01G136000 chr7A 90.580 138 13 0 304 441 627120032 627119895 1.630000e-42 183.0
31 TraesCS6A01G136000 chr7A 89.209 139 10 2 1635 1768 627006967 627006829 4.570000e-38 169.0
32 TraesCS6A01G136000 chr7A 97.872 47 1 0 1722 1768 580503759 580503713 6.130000e-12 82.4
33 TraesCS6A01G136000 chr7A 93.617 47 3 0 767 813 627008733 627008687 1.330000e-08 71.3
34 TraesCS6A01G136000 chr7A 95.000 40 2 0 1772 1811 628383879 628383840 2.220000e-06 63.9
35 TraesCS6A01G136000 chr7B 97.152 913 17 2 1761 2672 589736202 589737106 0.000000e+00 1533.0
36 TraesCS6A01G136000 chr7B 86.667 1020 69 17 722 1709 588878366 588877382 0.000000e+00 1068.0
37 TraesCS6A01G136000 chr7B 86.130 1031 66 30 722 1709 589919807 589920803 0.000000e+00 1040.0
38 TraesCS6A01G136000 chr7B 79.860 998 126 31 820 1766 537825707 537824734 0.000000e+00 660.0
39 TraesCS6A01G136000 chr7B 89.527 296 19 6 1 285 588879282 588878988 5.440000e-97 364.0
40 TraesCS6A01G136000 chr7B 90.152 264 19 4 29 286 589734528 589734790 1.190000e-88 337.0
41 TraesCS6A01G136000 chr7B 86.014 143 12 4 304 438 589734776 589734918 2.140000e-31 147.0
42 TraesCS6A01G136000 chr7B 92.157 102 8 0 824 925 498300126 498300025 7.710000e-31 145.0
43 TraesCS6A01G136000 chr7B 95.000 80 4 0 362 441 588823882 588823803 2.790000e-25 126.0
44 TraesCS6A01G136000 chr7B 90.411 73 3 2 722 794 498300171 498300103 2.830000e-15 93.5
45 TraesCS6A01G136000 chr7B 97.727 44 1 0 767 810 589919901 589919944 2.850000e-10 76.8
46 TraesCS6A01G136000 chr7B 100.000 32 0 0 542 573 588878637 588878606 2.870000e-05 60.2
47 TraesCS6A01G136000 chr7D 88.644 907 65 13 797 1671 518768806 518769706 0.000000e+00 1070.0
48 TraesCS6A01G136000 chr7D 87.014 901 72 26 796 1661 545267073 545266183 0.000000e+00 974.0
49 TraesCS6A01G136000 chr7D 77.655 998 130 42 817 1768 509573867 509572917 3.050000e-144 521.0
50 TraesCS6A01G136000 chr7D 78.991 852 110 26 817 1642 509598800 509597992 3.940000e-143 518.0
51 TraesCS6A01G136000 chr2B 88.790 901 62 16 796 1657 182133881 182132981 0.000000e+00 1068.0
52 TraesCS6A01G136000 chr2B 85.011 914 77 20 763 1662 135512529 135513396 0.000000e+00 874.0
53 TraesCS6A01G136000 chr2B 90.638 235 18 2 1 231 127790867 127790633 2.580000e-80 309.0
54 TraesCS6A01G136000 chr2B 82.657 271 15 7 817 1055 127790210 127789940 7.490000e-51 211.0
55 TraesCS6A01G136000 chr2B 88.811 143 16 0 304 446 182134279 182134137 2.730000e-40 176.0
56 TraesCS6A01G136000 chr2B 87.413 143 18 0 304 446 127790614 127790472 5.920000e-37 165.0
57 TraesCS6A01G136000 chrUn 89.744 78 8 0 820 897 65755206 65755283 1.690000e-17 100.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G136000 chr6A 107263534 107266205 2671 False 4935.000000 4935 100.000000 1 2672 1 chr6A.!!$F1 2671
1 TraesCS6A01G136000 chr5D 289353482 289356421 2939 True 1089.066667 2854 94.045667 1 2672 3 chr5D.!!$R4 2671
2 TraesCS6A01G136000 chr5D 289419289 289421757 2468 True 1038.400000 2713 91.903000 1 2672 3 chr5D.!!$R5 2671
3 TraesCS6A01G136000 chr1B 426495181 426497875 2694 True 1014.666667 2566 89.002667 1 2655 3 chr1B.!!$R5 2654
4 TraesCS6A01G136000 chr1B 398962051 398962800 749 False 1013.000000 1013 91.200000 968 1709 1 chr1B.!!$F1 741
5 TraesCS6A01G136000 chr1B 398839528 398840324 796 True 942.000000 942 88.075000 969 1767 1 chr1B.!!$R1 798
6 TraesCS6A01G136000 chr1B 133122365 133125257 2892 True 765.050000 1519 93.696750 1 2672 4 chr1B.!!$R3 2671
7 TraesCS6A01G136000 chr1B 133109731 133112269 2538 True 656.266667 1552 94.771333 1 2672 3 chr1B.!!$R2 2671
8 TraesCS6A01G136000 chr1B 426480322 426482874 2552 True 525.675000 1533 90.102500 29 2672 4 chr1B.!!$R4 2643
9 TraesCS6A01G136000 chr7A 628645448 628647205 1757 False 2412.000000 2412 91.597000 793 2547 1 chr7A.!!$F1 1754
10 TraesCS6A01G136000 chr7A 626991719 626992695 976 True 1107.000000 1107 87.768000 834 1774 1 chr7A.!!$R2 940
11 TraesCS6A01G136000 chr7A 628383840 628386018 2178 True 885.966667 1515 93.136667 736 2672 3 chr7A.!!$R5 1936
12 TraesCS6A01G136000 chr7B 589734528 589737106 2578 False 672.333333 1533 91.106000 29 2672 3 chr7B.!!$F1 2643
13 TraesCS6A01G136000 chr7B 537824734 537825707 973 True 660.000000 660 79.860000 820 1766 1 chr7B.!!$R1 946
14 TraesCS6A01G136000 chr7B 589919807 589920803 996 False 558.400000 1040 91.928500 722 1709 2 chr7B.!!$F2 987
15 TraesCS6A01G136000 chr7B 588877382 588879282 1900 True 497.400000 1068 92.064667 1 1709 3 chr7B.!!$R4 1708
16 TraesCS6A01G136000 chr7D 518768806 518769706 900 False 1070.000000 1070 88.644000 797 1671 1 chr7D.!!$F1 874
17 TraesCS6A01G136000 chr7D 545266183 545267073 890 True 974.000000 974 87.014000 796 1661 1 chr7D.!!$R3 865
18 TraesCS6A01G136000 chr7D 509572917 509573867 950 True 521.000000 521 77.655000 817 1768 1 chr7D.!!$R1 951
19 TraesCS6A01G136000 chr7D 509597992 509598800 808 True 518.000000 518 78.991000 817 1642 1 chr7D.!!$R2 825
20 TraesCS6A01G136000 chr2B 135512529 135513396 867 False 874.000000 874 85.011000 763 1662 1 chr2B.!!$F1 899
21 TraesCS6A01G136000 chr2B 182132981 182134279 1298 True 622.000000 1068 88.800500 304 1657 2 chr2B.!!$R2 1353
22 TraesCS6A01G136000 chr2B 127789940 127790867 927 True 228.333333 309 86.902667 1 1055 3 chr2B.!!$R1 1054

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
615 937 0.034059 AACAGACGCAAGGGTGAGAG 59.966 55.0 0.0 0.0 46.39 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1697 2559 1.063616 CCTGCACTGCTGATGATTTCG 59.936 52.381 9.36 0.0 0.0 3.46 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 44 2.159366 ACGATAACGAGTTCAGCTCCAG 60.159 50.000 0.00 0.00 41.10 3.86
53 54 1.373497 CAGCTCCAGTGTCGACCAC 60.373 63.158 14.12 11.25 44.89 4.16
259 281 6.198650 TGATTTTCCATCAGCTACATTGTG 57.801 37.500 0.00 0.00 0.00 3.33
266 288 5.355071 TCCATCAGCTACATTGTGATTCAAC 59.645 40.000 0.00 0.00 38.97 3.18
267 289 4.926860 TCAGCTACATTGTGATTCAACG 57.073 40.909 0.00 0.00 38.97 4.10
268 290 4.314961 TCAGCTACATTGTGATTCAACGT 58.685 39.130 0.00 0.00 38.97 3.99
269 291 4.152223 TCAGCTACATTGTGATTCAACGTG 59.848 41.667 0.00 0.00 38.97 4.49
270 292 3.120199 AGCTACATTGTGATTCAACGTGC 60.120 43.478 0.00 0.00 38.97 5.34
271 293 2.314561 ACATTGTGATTCAACGTGCG 57.685 45.000 0.00 0.00 38.97 5.34
272 294 1.870402 ACATTGTGATTCAACGTGCGA 59.130 42.857 0.00 0.00 38.97 5.10
273 295 2.483877 ACATTGTGATTCAACGTGCGAT 59.516 40.909 0.00 0.00 38.97 4.58
274 296 2.592796 TTGTGATTCAACGTGCGATG 57.407 45.000 0.00 0.00 0.00 3.84
275 297 1.507562 TGTGATTCAACGTGCGATGT 58.492 45.000 0.00 0.00 0.00 3.06
276 298 1.870402 TGTGATTCAACGTGCGATGTT 59.130 42.857 0.00 0.00 0.00 2.71
277 299 2.289274 TGTGATTCAACGTGCGATGTTT 59.711 40.909 0.00 0.00 0.00 2.83
278 300 2.902484 GTGATTCAACGTGCGATGTTTC 59.098 45.455 0.00 0.19 0.00 2.78
279 301 2.545946 TGATTCAACGTGCGATGTTTCA 59.454 40.909 0.00 2.64 0.00 2.69
280 302 3.188254 TGATTCAACGTGCGATGTTTCAT 59.812 39.130 0.00 0.00 0.00 2.57
281 303 2.592796 TCAACGTGCGATGTTTCATG 57.407 45.000 0.00 0.00 0.00 3.07
282 304 1.870402 TCAACGTGCGATGTTTCATGT 59.130 42.857 0.00 0.00 34.21 3.21
283 305 2.289274 TCAACGTGCGATGTTTCATGTT 59.711 40.909 0.00 0.00 41.53 2.71
284 306 3.042189 CAACGTGCGATGTTTCATGTTT 58.958 40.909 0.00 0.00 39.58 2.83
285 307 3.347958 ACGTGCGATGTTTCATGTTTT 57.652 38.095 0.00 0.00 0.00 2.43
286 308 3.701241 ACGTGCGATGTTTCATGTTTTT 58.299 36.364 0.00 0.00 0.00 1.94
334 356 8.870160 TCATGTTTTGTTGTTCCTATTTTCTG 57.130 30.769 0.00 0.00 0.00 3.02
345 367 2.564771 CTATTTTCTGCGGCATCCAGA 58.435 47.619 1.75 0.00 37.54 3.86
354 376 1.566211 CGGCATCCAGAGATAGGGAT 58.434 55.000 0.00 0.00 44.65 3.85
371 393 2.356069 GGGATCTCGGAATCTTTGCAAC 59.644 50.000 0.00 0.00 0.00 4.17
379 409 3.091545 GGAATCTTTGCAACCTGGATCA 58.908 45.455 0.00 0.00 0.00 2.92
448 594 2.409378 GGCATGTTCAATTTGACAAGCG 59.591 45.455 15.88 7.16 29.56 4.68
471 617 3.368236 GCAATCACAGAACTCCGAGTTAC 59.632 47.826 13.85 7.94 38.80 2.50
474 632 2.225019 TCACAGAACTCCGAGTTACGAC 59.775 50.000 13.85 1.95 45.77 4.34
484 642 0.737715 GAGTTACGACCTGCAGCTGG 60.738 60.000 17.12 16.57 0.00 4.85
491 649 2.111669 CCTGCAGCTGGACACACA 59.888 61.111 17.12 2.34 0.00 3.72
494 652 1.081892 CTGCAGCTGGACACACATAC 58.918 55.000 17.12 0.00 0.00 2.39
499 657 2.877786 CAGCTGGACACACATACAAACA 59.122 45.455 5.57 0.00 0.00 2.83
500 658 2.878406 AGCTGGACACACATACAAACAC 59.122 45.455 0.00 0.00 0.00 3.32
501 659 2.616376 GCTGGACACACATACAAACACA 59.384 45.455 0.00 0.00 0.00 3.72
502 660 3.253188 GCTGGACACACATACAAACACAT 59.747 43.478 0.00 0.00 0.00 3.21
503 661 4.786507 CTGGACACACATACAAACACATG 58.213 43.478 0.00 0.00 0.00 3.21
504 662 3.004210 TGGACACACATACAAACACATGC 59.996 43.478 0.00 0.00 0.00 4.06
505 663 3.253188 GGACACACATACAAACACATGCT 59.747 43.478 0.00 0.00 0.00 3.79
506 664 4.221342 GACACACATACAAACACATGCTG 58.779 43.478 0.00 0.00 0.00 4.41
508 666 3.004629 CACACATACAAACACATGCTGGT 59.995 43.478 0.00 0.00 0.00 4.00
518 685 0.883833 ACATGCTGGTTAAGTGCTGC 59.116 50.000 0.00 0.00 0.00 5.25
573 895 5.181245 TGCTGGTTAAGATGTTTAACTCTGC 59.819 40.000 9.01 12.62 35.73 4.26
575 897 6.621596 GCTGGTTAAGATGTTTAACTCTGCAG 60.622 42.308 7.63 7.63 35.73 4.41
578 900 6.348540 GGTTAAGATGTTTAACTCTGCAGTGG 60.349 42.308 19.27 13.13 35.73 4.00
580 902 4.319177 AGATGTTTAACTCTGCAGTGGAC 58.681 43.478 19.27 12.11 31.06 4.02
581 903 3.552132 TGTTTAACTCTGCAGTGGACA 57.448 42.857 19.27 14.16 31.06 4.02
582 904 3.466836 TGTTTAACTCTGCAGTGGACAG 58.533 45.455 19.27 9.09 36.44 3.51
584 906 0.976641 TAACTCTGCAGTGGACAGGG 59.023 55.000 19.27 0.00 41.64 4.45
585 907 1.460305 ACTCTGCAGTGGACAGGGT 60.460 57.895 19.27 0.00 44.08 4.34
586 908 1.056700 ACTCTGCAGTGGACAGGGTT 61.057 55.000 19.27 0.00 46.78 4.11
587 909 0.109342 CTCTGCAGTGGACAGGGTTT 59.891 55.000 14.67 0.00 35.78 3.27
592 914 1.750682 GCAGTGGACAGGGTTTCAGTT 60.751 52.381 0.00 0.00 0.00 3.16
595 917 3.071023 CAGTGGACAGGGTTTCAGTTAGA 59.929 47.826 0.00 0.00 0.00 2.10
608 930 3.390135 TCAGTTAGAAACAGACGCAAGG 58.610 45.455 0.00 0.00 46.39 3.61
609 931 2.480419 CAGTTAGAAACAGACGCAAGGG 59.520 50.000 0.00 0.00 46.39 3.95
610 932 2.104281 AGTTAGAAACAGACGCAAGGGT 59.896 45.455 0.00 0.00 46.39 4.34
612 934 0.468226 AGAAACAGACGCAAGGGTGA 59.532 50.000 0.00 0.00 46.39 4.02
614 936 0.468226 AAACAGACGCAAGGGTGAGA 59.532 50.000 0.00 0.00 46.39 3.27
615 937 0.034059 AACAGACGCAAGGGTGAGAG 59.966 55.000 0.00 0.00 46.39 3.20
617 939 0.318441 CAGACGCAAGGGTGAGAGAA 59.682 55.000 0.00 0.00 46.39 2.87
618 940 0.605589 AGACGCAAGGGTGAGAGAAG 59.394 55.000 0.00 0.00 46.39 2.85
619 941 0.318762 GACGCAAGGGTGAGAGAAGT 59.681 55.000 0.00 0.00 46.39 3.01
625 947 3.406764 CAAGGGTGAGAGAAGTGGAAAG 58.593 50.000 0.00 0.00 0.00 2.62
626 948 2.695585 AGGGTGAGAGAAGTGGAAAGT 58.304 47.619 0.00 0.00 0.00 2.66
627 949 3.049344 AGGGTGAGAGAAGTGGAAAGTT 58.951 45.455 0.00 0.00 0.00 2.66
628 950 3.071747 AGGGTGAGAGAAGTGGAAAGTTC 59.928 47.826 0.00 0.00 0.00 3.01
645 1073 8.084073 TGGAAAGTTCTGCATTTTAGATTTCTG 58.916 33.333 0.00 0.00 29.97 3.02
647 1075 5.958955 AGTTCTGCATTTTAGATTTCTGGC 58.041 37.500 0.00 0.00 0.00 4.85
650 1078 4.400251 TCTGCATTTTAGATTTCTGGCAGG 59.600 41.667 15.73 0.00 45.49 4.85
652 1080 4.400251 TGCATTTTAGATTTCTGGCAGGAG 59.600 41.667 15.73 0.00 0.00 3.69
653 1081 4.641989 GCATTTTAGATTTCTGGCAGGAGA 59.358 41.667 15.73 1.04 0.00 3.71
654 1082 5.126061 GCATTTTAGATTTCTGGCAGGAGAA 59.874 40.000 15.73 7.92 0.00 2.87
655 1083 6.558909 CATTTTAGATTTCTGGCAGGAGAAC 58.441 40.000 15.73 1.29 31.53 3.01
697 1176 2.447408 TAGTTATGCCTGGACTCGGA 57.553 50.000 0.00 0.00 0.00 4.55
707 1186 2.482664 CCTGGACTCGGATTCAGACATG 60.483 54.545 0.00 0.00 0.00 3.21
709 1188 1.134699 GGACTCGGATTCAGACATGCA 60.135 52.381 0.00 0.00 0.00 3.96
714 1193 1.688772 GGATTCAGACATGCATGCCT 58.311 50.000 26.53 18.73 0.00 4.75
715 1194 1.337071 GGATTCAGACATGCATGCCTG 59.663 52.381 30.67 30.67 39.29 4.85
732 1292 2.741878 GCCTGCGCTAGTTGGAAAGATA 60.742 50.000 9.73 0.00 0.00 1.98
789 1353 2.416107 TAGCTATGCATGCCTGGGCC 62.416 60.000 16.68 0.00 41.09 5.80
790 1354 2.981909 CTATGCATGCCTGGGCCG 60.982 66.667 16.68 1.63 41.09 6.13
791 1355 3.480679 CTATGCATGCCTGGGCCGA 62.481 63.158 16.68 0.00 41.09 5.54
868 1559 1.404583 GGATTCAAATTGCTTGCCGCT 60.405 47.619 0.00 0.00 40.11 5.52
1239 2065 2.035626 CCCGCCAACATCAAGGGT 59.964 61.111 0.00 0.00 37.36 4.34
1278 2116 4.496336 AGCAGCGGCAAGGATCCC 62.496 66.667 12.44 0.00 44.61 3.85
1290 2128 0.688087 AGGATCCCAAGAGTCCGACC 60.688 60.000 8.55 0.00 37.12 4.79
1697 2559 0.107459 GGGTGATGGAAGCAGAGGAC 60.107 60.000 0.00 0.00 24.12 3.85
1830 2708 6.095160 TCGAGTTAAGCTAGTCCTTCCTAAAG 59.905 42.308 0.00 0.00 0.00 1.85
1904 2782 8.561738 TTAATCACCAAGATTTCTAGTGTTCC 57.438 34.615 9.31 0.00 44.48 3.62
1956 2834 2.284754 AGAGTGTCAGCAGAGTCTCA 57.715 50.000 1.94 0.00 31.33 3.27
1997 2875 4.612264 ACCTTGTTAAGATGTGTACGGT 57.388 40.909 0.00 0.00 0.00 4.83
2004 2882 9.362539 CTTGTTAAGATGTGTACGGTATAGTTT 57.637 33.333 0.00 0.00 0.00 2.66
2319 3197 0.739462 CTTAGGCATTGGCGTCGTGA 60.739 55.000 4.38 0.00 42.47 4.35
2583 3462 2.808543 GGAAAAGTGTGTACTGAGGCAG 59.191 50.000 0.00 0.00 37.19 4.85
2626 3505 6.898041 TCTGATTTCACAATACTTCGTTTGG 58.102 36.000 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 0.665369 ATTCGAACCGTGGTCGACAC 60.665 55.000 18.91 12.39 46.78 3.67
53 54 3.381949 GGGTCTAGAATGATTCGAACCG 58.618 50.000 0.00 0.00 33.79 4.44
54 55 3.381949 CGGGTCTAGAATGATTCGAACC 58.618 50.000 0.00 14.33 32.88 3.62
130 140 4.139038 GCCGTAAAAAGCCCATAATCCTA 58.861 43.478 0.00 0.00 0.00 2.94
232 252 4.517285 TGTAGCTGATGGAAAATCAGTCC 58.483 43.478 14.89 5.91 45.38 3.85
259 281 3.181826 TGAAACATCGCACGTTGAATC 57.818 42.857 8.01 6.17 0.00 2.52
293 315 2.366916 ACATGAAACATCCCCGCAAAAA 59.633 40.909 0.00 0.00 0.00 1.94
294 316 1.967066 ACATGAAACATCCCCGCAAAA 59.033 42.857 0.00 0.00 0.00 2.44
295 317 1.626686 ACATGAAACATCCCCGCAAA 58.373 45.000 0.00 0.00 0.00 3.68
296 318 1.626686 AACATGAAACATCCCCGCAA 58.373 45.000 0.00 0.00 0.00 4.85
297 319 1.626686 AAACATGAAACATCCCCGCA 58.373 45.000 0.00 0.00 0.00 5.69
298 320 2.288763 ACAAAACATGAAACATCCCCGC 60.289 45.455 0.00 0.00 0.00 6.13
299 321 3.658757 ACAAAACATGAAACATCCCCG 57.341 42.857 0.00 0.00 0.00 5.73
300 322 4.702831 ACAACAAAACATGAAACATCCCC 58.297 39.130 0.00 0.00 0.00 4.81
301 323 5.236263 GGAACAACAAAACATGAAACATCCC 59.764 40.000 0.00 0.00 0.00 3.85
302 324 6.048509 AGGAACAACAAAACATGAAACATCC 58.951 36.000 0.00 0.00 0.00 3.51
334 356 1.188219 TCCCTATCTCTGGATGCCGC 61.188 60.000 0.00 0.00 33.71 6.53
345 367 4.020662 GCAAAGATTCCGAGATCCCTATCT 60.021 45.833 0.00 0.00 45.46 1.98
354 376 2.426522 CAGGTTGCAAAGATTCCGAGA 58.573 47.619 0.00 0.00 0.00 4.04
357 379 1.533625 TCCAGGTTGCAAAGATTCCG 58.466 50.000 0.00 0.00 0.00 4.30
379 409 6.531923 CCATGTATGATCTCAGAAACCTGAT 58.468 40.000 0.00 0.00 39.70 2.90
448 594 1.338200 ACTCGGAGTTCTGTGATTGCC 60.338 52.381 4.45 0.00 0.00 4.52
471 617 2.740055 GTGTCCAGCTGCAGGTCG 60.740 66.667 17.16 10.29 0.00 4.79
474 632 0.036105 TATGTGTGTCCAGCTGCAGG 60.036 55.000 17.12 4.46 0.00 4.85
484 642 4.221342 CAGCATGTGTTTGTATGTGTGTC 58.779 43.478 0.00 0.00 0.00 3.67
491 649 5.564651 GCACTTAACCAGCATGTGTTTGTAT 60.565 40.000 0.00 0.00 32.92 2.29
494 652 3.052036 GCACTTAACCAGCATGTGTTTG 58.948 45.455 0.00 0.00 32.92 2.93
499 657 0.883833 GCAGCACTTAACCAGCATGT 59.116 50.000 0.00 0.00 0.00 3.21
500 658 1.131883 GAGCAGCACTTAACCAGCATG 59.868 52.381 0.00 0.00 0.00 4.06
501 659 1.004044 AGAGCAGCACTTAACCAGCAT 59.996 47.619 0.00 0.00 0.00 3.79
502 660 0.397941 AGAGCAGCACTTAACCAGCA 59.602 50.000 0.00 0.00 0.00 4.41
503 661 0.801251 CAGAGCAGCACTTAACCAGC 59.199 55.000 0.00 0.00 0.00 4.85
504 662 1.002430 TCCAGAGCAGCACTTAACCAG 59.998 52.381 0.00 0.00 0.00 4.00
505 663 1.055849 TCCAGAGCAGCACTTAACCA 58.944 50.000 0.00 0.00 0.00 3.67
506 664 2.409948 ATCCAGAGCAGCACTTAACC 57.590 50.000 0.00 0.00 0.00 2.85
508 666 3.701205 TCAATCCAGAGCAGCACTTAA 57.299 42.857 0.00 0.00 0.00 1.85
518 685 7.468357 GCATCAAGGTCTTATTTCAATCCAGAG 60.468 40.741 0.00 0.00 0.00 3.35
573 895 2.348411 AACTGAAACCCTGTCCACTG 57.652 50.000 0.00 0.00 0.00 3.66
575 897 3.764237 TCTAACTGAAACCCTGTCCAC 57.236 47.619 0.00 0.00 0.00 4.02
585 907 4.272504 CCTTGCGTCTGTTTCTAACTGAAA 59.727 41.667 0.00 0.00 40.36 2.69
586 908 3.807622 CCTTGCGTCTGTTTCTAACTGAA 59.192 43.478 0.00 0.00 40.36 3.02
587 909 3.390135 CCTTGCGTCTGTTTCTAACTGA 58.610 45.455 0.00 0.00 37.07 3.41
592 914 1.689813 TCACCCTTGCGTCTGTTTCTA 59.310 47.619 0.00 0.00 0.00 2.10
595 917 0.468226 TCTCACCCTTGCGTCTGTTT 59.532 50.000 0.00 0.00 0.00 2.83
599 921 0.605589 CTTCTCTCACCCTTGCGTCT 59.394 55.000 0.00 0.00 0.00 4.18
600 922 0.318762 ACTTCTCTCACCCTTGCGTC 59.681 55.000 0.00 0.00 0.00 5.19
601 923 0.034059 CACTTCTCTCACCCTTGCGT 59.966 55.000 0.00 0.00 0.00 5.24
602 924 0.671781 CCACTTCTCTCACCCTTGCG 60.672 60.000 0.00 0.00 0.00 4.85
603 925 0.687354 TCCACTTCTCTCACCCTTGC 59.313 55.000 0.00 0.00 0.00 4.01
604 926 3.181450 ACTTTCCACTTCTCTCACCCTTG 60.181 47.826 0.00 0.00 0.00 3.61
605 927 3.049344 ACTTTCCACTTCTCTCACCCTT 58.951 45.455 0.00 0.00 0.00 3.95
608 930 4.061596 CAGAACTTTCCACTTCTCTCACC 58.938 47.826 0.00 0.00 0.00 4.02
609 931 3.496507 GCAGAACTTTCCACTTCTCTCAC 59.503 47.826 0.00 0.00 0.00 3.51
610 932 3.134623 TGCAGAACTTTCCACTTCTCTCA 59.865 43.478 0.00 0.00 0.00 3.27
612 934 3.845781 TGCAGAACTTTCCACTTCTCT 57.154 42.857 0.00 0.00 0.00 3.10
614 936 5.859205 AAAATGCAGAACTTTCCACTTCT 57.141 34.783 0.00 0.00 0.00 2.85
615 937 6.970484 TCTAAAATGCAGAACTTTCCACTTC 58.030 36.000 0.00 0.00 0.00 3.01
617 939 7.530426 AATCTAAAATGCAGAACTTTCCACT 57.470 32.000 0.00 0.00 0.00 4.00
618 940 8.084684 AGAAATCTAAAATGCAGAACTTTCCAC 58.915 33.333 0.00 0.00 28.07 4.02
619 941 8.084073 CAGAAATCTAAAATGCAGAACTTTCCA 58.916 33.333 0.00 0.00 28.07 3.53
625 947 5.713025 TGCCAGAAATCTAAAATGCAGAAC 58.287 37.500 0.00 0.00 0.00 3.01
626 948 5.105635 CCTGCCAGAAATCTAAAATGCAGAA 60.106 40.000 9.53 0.00 45.84 3.02
627 949 4.400251 CCTGCCAGAAATCTAAAATGCAGA 59.600 41.667 9.53 0.00 45.84 4.26
628 950 4.400251 TCCTGCCAGAAATCTAAAATGCAG 59.600 41.667 0.00 0.00 43.37 4.41
645 1073 6.601217 AGAAATCTAAAATCAGTTCTCCTGCC 59.399 38.462 0.00 0.00 41.25 4.85
647 1075 8.783833 TCAGAAATCTAAAATCAGTTCTCCTG 57.216 34.615 0.00 0.00 42.97 3.86
650 1078 9.442047 TTCCTCAGAAATCTAAAATCAGTTCTC 57.558 33.333 0.00 0.00 0.00 2.87
662 1137 8.938883 AGGCATAACTAATTCCTCAGAAATCTA 58.061 33.333 0.00 0.00 35.09 1.98
663 1138 7.718753 CAGGCATAACTAATTCCTCAGAAATCT 59.281 37.037 0.00 0.00 35.09 2.40
665 1140 6.774656 CCAGGCATAACTAATTCCTCAGAAAT 59.225 38.462 0.00 0.00 35.09 2.17
709 1188 0.322456 TTTCCAACTAGCGCAGGCAT 60.322 50.000 11.47 0.00 43.41 4.40
714 1193 4.465632 TTCTATCTTTCCAACTAGCGCA 57.534 40.909 11.47 0.00 0.00 6.09
715 1194 4.260415 GCTTTCTATCTTTCCAACTAGCGC 60.260 45.833 0.00 0.00 0.00 5.92
716 1195 4.870426 TGCTTTCTATCTTTCCAACTAGCG 59.130 41.667 0.00 0.00 0.00 4.26
732 1292 5.006386 AGACTCGGATTCAAATTGCTTTCT 58.994 37.500 0.00 0.00 0.00 2.52
789 1353 2.257974 TTGAATCCGAGTCGAAGTCG 57.742 50.000 15.64 10.71 40.53 4.18
790 1354 4.377124 GGTTTTTGAATCCGAGTCGAAGTC 60.377 45.833 15.64 2.31 0.00 3.01
791 1355 3.497262 GGTTTTTGAATCCGAGTCGAAGT 59.503 43.478 15.64 0.00 0.00 3.01
868 1559 0.322277 ACGCGGGAGACAGAGAAGTA 60.322 55.000 12.47 0.00 0.00 2.24
1052 1844 2.597805 AGGAGTGCAGGTCGTCGT 60.598 61.111 0.00 0.00 0.00 4.34
1278 2116 1.216710 GAGGCAGGTCGGACTCTTG 59.783 63.158 8.23 5.89 39.94 3.02
1446 2284 1.721664 CGATCTCCTGCCGACGGTTA 61.722 60.000 16.73 4.23 0.00 2.85
1637 2475 1.446907 CATCGCTTGAGCAAAGTCCT 58.553 50.000 3.65 0.00 42.21 3.85
1697 2559 1.063616 CCTGCACTGCTGATGATTTCG 59.936 52.381 9.36 0.00 0.00 3.46
1830 2708 7.872163 TTAAATGAAACTCATGTGTGAATGC 57.128 32.000 0.31 0.00 37.15 3.56
1904 2782 4.952335 ACTAATGGCTGAAAGGGATTGAAG 59.048 41.667 0.00 0.00 0.00 3.02
2250 3128 1.412361 GGAGGGTCAGCATAGTCTCCT 60.412 57.143 0.00 0.00 38.13 3.69
2319 3197 6.511767 CGTCAGAAACTGCAACTTTAACTCAT 60.512 38.462 0.00 0.00 0.00 2.90
2583 3462 6.111669 TCAGAGATGAATCCATTGGATCTC 57.888 41.667 18.45 19.22 42.27 2.75
2626 3505 1.832883 TGGTTATGTGCATCACCACC 58.167 50.000 12.65 7.91 39.44 4.61


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

AutoCloner maintained by Alex Coulton.