Multiple sequence alignment - TraesCS1D01G399500

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 TraesCS1D01G399500 chr1D 100.000 4075 0 0 1382 5456 466102150 466106224 0.000000e+00 7526
1 TraesCS1D01G399500 chr1D 100.000 1078 0 0 1 1078 466100769 466101846 0.000000e+00 1991
2 TraesCS1D01G399500 chr1B 96.502 3230 87 12 1382 4594 643058237 643061457 0.000000e+00 5315
3 TraesCS1D01G399500 chr1B 91.892 814 54 9 4645 5456 643061663 643062466 0.000000e+00 1127
4 TraesCS1D01G399500 chr1B 88.300 641 67 7 4677 5314 599317147 599317782 0.000000e+00 761
5 TraesCS1D01G399500 chr1B 87.768 654 74 5 4674 5325 57805019 57805668 0.000000e+00 760
6 TraesCS1D01G399500 chr1B 95.808 334 5 5 573 898 643057287 643057619 1.040000e-146 531
7 TraesCS1D01G399500 chr1B 92.754 207 7 1 880 1078 643057919 643058125 5.350000e-75 292
8 TraesCS1D01G399500 chr5D 80.853 2298 308 71 2050 4315 1882051 1884248 0.000000e+00 1685
9 TraesCS1D01G399500 chr5D 96.522 575 16 2 1 572 35660862 35660289 0.000000e+00 948
10 TraesCS1D01G399500 chr5D 89.222 167 18 0 1759 1925 412100096 412100262 5.540000e-50 209
11 TraesCS1D01G399500 chr5D 84.177 158 20 4 1392 1549 1881700 1881852 1.220000e-31 148
12 TraesCS1D01G399500 chr2B 83.585 1194 169 14 2012 3187 28149845 28151029 0.000000e+00 1094
13 TraesCS1D01G399500 chr2B 91.581 582 35 7 1 574 659787218 659787793 0.000000e+00 791
14 TraesCS1D01G399500 chr2B 87.768 654 73 6 4676 5325 95792332 95792982 0.000000e+00 758
15 TraesCS1D01G399500 chr2B 80.879 774 123 13 3321 4093 28151148 28151897 2.190000e-163 586
16 TraesCS1D01G399500 chr2B 72.038 633 159 12 3339 3960 8354944 8355569 7.270000e-39 172
17 TraesCS1D01G399500 chr3D 96.187 577 17 3 1 574 143157899 143158473 0.000000e+00 939
18 TraesCS1D01G399500 chr3D 90.123 162 16 0 1760 1921 87926000 87926161 1.540000e-50 211
19 TraesCS1D01G399500 chr3D 89.697 165 15 2 1760 1924 104026066 104025904 5.540000e-50 209
20 TraesCS1D01G399500 chr6A 96.174 575 18 2 1 572 606096594 606096021 0.000000e+00 937
21 TraesCS1D01G399500 chr6A 75.954 262 47 13 3325 3579 69350087 69350339 2.670000e-23 121
22 TraesCS1D01G399500 chr2D 96.181 576 17 3 1 573 575333362 575332789 0.000000e+00 937
23 TraesCS1D01G399500 chr2D 88.244 655 72 4 4676 5329 620552210 620551560 0.000000e+00 778
24 TraesCS1D01G399500 chr2D 88.000 175 19 2 1750 1923 87407354 87407527 7.160000e-49 206
25 TraesCS1D01G399500 chr6D 95.478 575 22 2 1 572 409333354 409333927 0.000000e+00 915
26 TraesCS1D01G399500 chr6D 72.595 343 79 12 2829 3165 29468905 29468572 1.250000e-16 99
27 TraesCS1D01G399500 chr7D 95.304 575 22 3 1 572 579995840 579996412 0.000000e+00 907
28 TraesCS1D01G399500 chr5B 94.692 584 25 4 1 580 325799380 325798799 0.000000e+00 902
29 TraesCS1D01G399500 chr5B 82.406 557 61 20 2332 2863 759920 760464 8.330000e-123 451
30 TraesCS1D01G399500 chr5B 84.400 250 24 2 2948 3182 762486 762735 1.180000e-56 231
31 TraesCS1D01G399500 chr4A 95.848 554 19 2 1 551 675794907 675795459 0.000000e+00 893
32 TraesCS1D01G399500 chr4A 88.073 654 72 5 4674 5325 733340884 733340235 0.000000e+00 771
33 TraesCS1D01G399500 chr4A 91.701 241 14 4 341 577 673051265 673051027 4.070000e-86 329
34 TraesCS1D01G399500 chr4A 89.349 169 18 0 1760 1928 298243723 298243891 4.280000e-51 213
35 TraesCS1D01G399500 chr7B 88.162 642 71 4 4675 5314 538421340 538420702 0.000000e+00 760
36 TraesCS1D01G399500 chr6B 87.846 650 73 5 4678 5325 151215192 151215837 0.000000e+00 758
37 TraesCS1D01G399500 chr6B 76.619 278 44 18 3325 3592 125611625 125611891 3.430000e-27 134
38 TraesCS1D01G399500 chr6B 83.459 133 18 4 3306 3436 703429549 703429419 2.670000e-23 121
39 TraesCS1D01G399500 chr6B 81.818 132 22 2 3306 3436 703502155 703502025 5.780000e-20 110
40 TraesCS1D01G399500 chr4D 87.596 653 77 3 4675 5326 11871521 11872170 0.000000e+00 754
41 TraesCS1D01G399500 chr4D 89.759 166 15 2 1760 1924 36603208 36603044 1.540000e-50 211
42 TraesCS1D01G399500 chr5A 82.268 829 123 18 3286 4093 853530 854355 0.000000e+00 695
43 TraesCS1D01G399500 chr5A 94.045 403 18 4 176 573 287618829 287619230 1.680000e-169 606
44 TraesCS1D01G399500 chr5A 88.760 258 27 2 2939 3195 853162 853418 1.140000e-81 315
45 TraesCS1D01G399500 chr5A 85.283 265 35 4 4092 4355 854321 854582 2.500000e-68 270
46 TraesCS1D01G399500 chr7A 94.839 310 12 3 266 572 109340824 109341132 1.060000e-131 481
47 TraesCS1D01G399500 chr7A 89.571 163 17 0 1760 1922 498937206 498937368 1.990000e-49 207
48 TraesCS1D01G399500 chr3B 89.697 165 17 0 1760 1924 154663205 154663041 1.540000e-50 211


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 TraesCS1D01G399500 chr1D 466100769 466106224 5455 False 4758.500000 7526 100.000 1 5456 2 chr1D.!!$F1 5455
1 TraesCS1D01G399500 chr1B 643057287 643062466 5179 False 1816.250000 5315 94.239 573 5456 4 chr1B.!!$F3 4883
2 TraesCS1D01G399500 chr1B 599317147 599317782 635 False 761.000000 761 88.300 4677 5314 1 chr1B.!!$F2 637
3 TraesCS1D01G399500 chr1B 57805019 57805668 649 False 760.000000 760 87.768 4674 5325 1 chr1B.!!$F1 651
4 TraesCS1D01G399500 chr5D 35660289 35660862 573 True 948.000000 948 96.522 1 572 1 chr5D.!!$R1 571
5 TraesCS1D01G399500 chr5D 1881700 1884248 2548 False 916.500000 1685 82.515 1392 4315 2 chr5D.!!$F2 2923
6 TraesCS1D01G399500 chr2B 28149845 28151897 2052 False 840.000000 1094 82.232 2012 4093 2 chr2B.!!$F4 2081
7 TraesCS1D01G399500 chr2B 659787218 659787793 575 False 791.000000 791 91.581 1 574 1 chr2B.!!$F3 573
8 TraesCS1D01G399500 chr2B 95792332 95792982 650 False 758.000000 758 87.768 4676 5325 1 chr2B.!!$F2 649
9 TraesCS1D01G399500 chr3D 143157899 143158473 574 False 939.000000 939 96.187 1 574 1 chr3D.!!$F2 573
10 TraesCS1D01G399500 chr6A 606096021 606096594 573 True 937.000000 937 96.174 1 572 1 chr6A.!!$R1 571
11 TraesCS1D01G399500 chr2D 575332789 575333362 573 True 937.000000 937 96.181 1 573 1 chr2D.!!$R1 572
12 TraesCS1D01G399500 chr2D 620551560 620552210 650 True 778.000000 778 88.244 4676 5329 1 chr2D.!!$R2 653
13 TraesCS1D01G399500 chr6D 409333354 409333927 573 False 915.000000 915 95.478 1 572 1 chr6D.!!$F1 571
14 TraesCS1D01G399500 chr7D 579995840 579996412 572 False 907.000000 907 95.304 1 572 1 chr7D.!!$F1 571
15 TraesCS1D01G399500 chr5B 325798799 325799380 581 True 902.000000 902 94.692 1 580 1 chr5B.!!$R1 579
16 TraesCS1D01G399500 chr5B 759920 762735 2815 False 341.000000 451 83.403 2332 3182 2 chr5B.!!$F1 850
17 TraesCS1D01G399500 chr4A 675794907 675795459 552 False 893.000000 893 95.848 1 551 1 chr4A.!!$F2 550
18 TraesCS1D01G399500 chr4A 733340235 733340884 649 True 771.000000 771 88.073 4674 5325 1 chr4A.!!$R2 651
19 TraesCS1D01G399500 chr7B 538420702 538421340 638 True 760.000000 760 88.162 4675 5314 1 chr7B.!!$R1 639
20 TraesCS1D01G399500 chr6B 151215192 151215837 645 False 758.000000 758 87.846 4678 5325 1 chr6B.!!$F2 647
21 TraesCS1D01G399500 chr4D 11871521 11872170 649 False 754.000000 754 87.596 4675 5326 1 chr4D.!!$F1 651
22 TraesCS1D01G399500 chr5A 853162 854582 1420 False 426.666667 695 85.437 2939 4355 3 chr5A.!!$F2 1416

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
381 382 0.035534 TTCTTATCCAGCAGCGGCAA 60.036 50.0 12.44 0.0 44.61 4.52 F
932 1285 0.673644 GCTTCAGCCGTTTCCAGCTA 60.674 55.0 0.00 0.0 37.18 3.32 F
975 1328 1.885049 ACAGCCTCTCCACATGGTAT 58.115 50.0 0.00 0.0 36.34 2.73 F
2213 2589 0.523072 CTTCCTTGGTGCCAACATCG 59.477 55.0 0.00 0.0 0.00 3.84 F
3222 5603 0.183492 GTGGGCTATGCTTCATGGGA 59.817 55.0 0.00 0.0 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1538 1902 1.202582 CTGGAGACGTCAATTCGGACT 59.797 52.381 19.50 0.0 35.63 3.85 R
2213 2589 1.904990 GAGAGGAGGGGCAGGAACAC 61.905 65.000 0.00 0.0 0.00 3.32 R
2489 2874 6.441924 TGCATTGAATAATAACCCTTTCCCAA 59.558 34.615 0.00 0.0 0.00 4.12 R
3702 6129 0.396556 TGCCGGCCTGTAGATGTAGA 60.397 55.000 26.77 0.0 0.00 2.59 R
5044 7645 0.759959 TATCGTTGGTGGGTGTGTGT 59.240 50.000 0.00 0.0 0.00 3.72 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
113 114 3.873910 CTTTTGATCGGGACACTGGTAT 58.126 45.455 0.00 0.00 0.00 2.73
230 231 2.706723 AGGCTAGAGGACTACGAGATGA 59.293 50.000 0.00 0.00 0.00 2.92
359 360 4.703575 AGCGGCAATATATGAAGAATGCAT 59.296 37.500 1.45 0.00 38.50 3.96
363 364 7.095523 GCGGCAATATATGAAGAATGCATTTTT 60.096 33.333 14.33 14.45 34.81 1.94
375 376 6.570692 AGAATGCATTTTTCTTATCCAGCAG 58.429 36.000 14.33 0.00 33.94 4.24
377 378 3.111098 GCATTTTTCTTATCCAGCAGCG 58.889 45.455 0.00 0.00 0.00 5.18
378 379 3.699067 CATTTTTCTTATCCAGCAGCGG 58.301 45.455 0.00 0.00 0.00 5.52
379 380 1.094785 TTTTCTTATCCAGCAGCGGC 58.905 50.000 0.00 0.00 41.61 6.53
381 382 0.035534 TTCTTATCCAGCAGCGGCAA 60.036 50.000 12.44 0.00 44.61 4.52
932 1285 0.673644 GCTTCAGCCGTTTCCAGCTA 60.674 55.000 0.00 0.00 37.18 3.32
975 1328 1.885049 ACAGCCTCTCCACATGGTAT 58.115 50.000 0.00 0.00 36.34 2.73
1033 1394 5.812642 GTGATGGTAACCTGAAGTACATGAG 59.187 44.000 0.00 0.00 0.00 2.90
1047 1408 9.354673 TGAAGTACATGAGAGATGTGTATATGA 57.645 33.333 0.00 0.00 33.76 2.15
1752 2116 4.478206 ACTAGTGACTGCAGCATAACAT 57.522 40.909 15.27 0.00 0.00 2.71
1780 2144 3.938289 ACTCTCTCCGTTCCTAAACAC 57.062 47.619 0.00 0.00 34.93 3.32
1817 2181 8.794553 AGAGGTTTCAATATAGACTACATACGG 58.205 37.037 0.00 0.00 0.00 4.02
1953 2318 6.554334 ACTGTACGTATTCTTTTTGCATGT 57.446 33.333 0.00 0.00 0.00 3.21
2000 2373 8.572855 TTGTGTTGATGTTGGAATATGACATA 57.427 30.769 0.00 0.00 34.38 2.29
2008 2381 7.936496 TGTTGGAATATGACATATGTGTGTT 57.064 32.000 14.43 6.33 39.09 3.32
2028 2401 4.157656 TGTTTATGTTAAGCAGACCATGGC 59.842 41.667 13.04 4.70 0.00 4.40
2044 2417 2.126502 GCCACCGGAAATTGCACG 60.127 61.111 9.46 0.00 0.00 5.34
2213 2589 0.523072 CTTCCTTGGTGCCAACATCG 59.477 55.000 0.00 0.00 0.00 3.84
2306 2685 5.244851 TCTGATCTAGACATCATAACAGGGC 59.755 44.000 0.00 0.00 32.21 5.19
2489 2874 5.785940 ACTTCCTACCTTACCATTGACTTCT 59.214 40.000 0.00 0.00 0.00 2.85
2532 2920 6.204495 TCAATGCAAAAATGGTCCTTAAAAGC 59.796 34.615 0.00 0.00 0.00 3.51
2580 2974 2.762745 TCTTCCACCGTTTGCTCTTAC 58.237 47.619 0.00 0.00 0.00 2.34
3222 5603 0.183492 GTGGGCTATGCTTCATGGGA 59.817 55.000 0.00 0.00 0.00 4.37
3693 6120 1.152984 CAATGGCGTGGCATCCCTA 60.153 57.895 9.50 0.00 0.00 3.53
3978 6414 1.981254 CCAAACATGCAATCGTGGTC 58.019 50.000 0.00 0.00 33.54 4.02
4046 6488 3.386237 GAGCGCAGGGTCTGAGGT 61.386 66.667 11.47 3.26 43.82 3.85
4104 6546 1.353694 AGGAAGCTGCTCAAGAATGGT 59.646 47.619 1.00 0.00 0.00 3.55
4236 6678 3.172575 AACGTCGATGCTCACGCG 61.173 61.111 3.53 3.53 39.73 6.01
4355 6797 3.865745 CCTAACGCTCCTAGTGATGTTTG 59.134 47.826 0.00 0.00 0.00 2.93
4362 6804 4.757149 GCTCCTAGTGATGTTTGACTTTGT 59.243 41.667 0.00 0.00 0.00 2.83
4363 6805 5.334414 GCTCCTAGTGATGTTTGACTTTGTG 60.334 44.000 0.00 0.00 0.00 3.33
4366 6808 6.601613 TCCTAGTGATGTTTGACTTTGTGTTT 59.398 34.615 0.00 0.00 0.00 2.83
4367 6809 6.692681 CCTAGTGATGTTTGACTTTGTGTTTG 59.307 38.462 0.00 0.00 0.00 2.93
4369 6811 6.686630 AGTGATGTTTGACTTTGTGTTTGAA 58.313 32.000 0.00 0.00 0.00 2.69
4371 6813 7.818930 AGTGATGTTTGACTTTGTGTTTGAATT 59.181 29.630 0.00 0.00 0.00 2.17
4372 6814 8.110002 GTGATGTTTGACTTTGTGTTTGAATTC 58.890 33.333 0.00 0.00 0.00 2.17
4374 6816 7.344910 TGTTTGACTTTGTGTTTGAATTCAC 57.655 32.000 7.89 0.00 35.43 3.18
4375 6817 7.151308 TGTTTGACTTTGTGTTTGAATTCACT 58.849 30.769 7.89 0.00 35.82 3.41
4446 6888 9.103861 GAGTGCTAGCTATTCTAAGAAACATTT 57.896 33.333 17.23 0.00 0.00 2.32
4547 6990 8.395633 CCTTAGTGTAATATTTCACTTTTCCCG 58.604 37.037 26.45 12.43 43.39 5.14
4558 7001 1.947456 ACTTTTCCCGAGTGCAAGTTC 59.053 47.619 0.00 0.00 0.00 3.01
4605 7048 9.733556 TTACTATTAAATGCTCTGAAAAGGACA 57.266 29.630 0.00 0.00 0.00 4.02
4606 7049 8.045176 ACTATTAAATGCTCTGAAAAGGACAC 57.955 34.615 0.00 0.00 0.00 3.67
4607 7050 6.899393 ATTAAATGCTCTGAAAAGGACACA 57.101 33.333 0.00 0.00 0.00 3.72
4608 7051 6.899393 TTAAATGCTCTGAAAAGGACACAT 57.101 33.333 0.00 0.00 0.00 3.21
4609 7052 7.994425 TTAAATGCTCTGAAAAGGACACATA 57.006 32.000 0.00 0.00 0.00 2.29
4610 7053 6.899393 AAATGCTCTGAAAAGGACACATAA 57.101 33.333 0.00 0.00 0.00 1.90
4611 7054 7.472334 AAATGCTCTGAAAAGGACACATAAT 57.528 32.000 0.00 0.00 0.00 1.28
4612 7055 7.472334 AATGCTCTGAAAAGGACACATAATT 57.528 32.000 0.00 0.00 0.00 1.40
4613 7056 6.899393 TGCTCTGAAAAGGACACATAATTT 57.101 33.333 0.00 0.00 0.00 1.82
4614 7057 6.913170 TGCTCTGAAAAGGACACATAATTTC 58.087 36.000 0.00 0.00 0.00 2.17
4615 7058 6.071952 TGCTCTGAAAAGGACACATAATTTCC 60.072 38.462 0.00 0.00 30.80 3.13
4616 7059 6.151817 GCTCTGAAAAGGACACATAATTTCCT 59.848 38.462 0.00 0.00 41.84 3.36
4617 7060 7.452880 TCTGAAAAGGACACATAATTTCCTG 57.547 36.000 0.00 0.00 39.83 3.86
4618 7061 6.024552 TGAAAAGGACACATAATTTCCTGC 57.975 37.500 0.00 0.00 39.83 4.85
4619 7062 5.774690 TGAAAAGGACACATAATTTCCTGCT 59.225 36.000 0.00 0.00 39.83 4.24
4620 7063 5.904362 AAAGGACACATAATTTCCTGCTC 57.096 39.130 0.00 0.00 39.83 4.26
4621 7064 3.891049 AGGACACATAATTTCCTGCTCC 58.109 45.455 0.00 0.00 38.40 4.70
4622 7065 3.525199 AGGACACATAATTTCCTGCTCCT 59.475 43.478 0.00 0.00 38.40 3.69
4623 7066 3.879892 GGACACATAATTTCCTGCTCCTC 59.120 47.826 0.00 0.00 0.00 3.71
4624 7067 4.517285 GACACATAATTTCCTGCTCCTCA 58.483 43.478 0.00 0.00 0.00 3.86
4625 7068 4.922206 ACACATAATTTCCTGCTCCTCAA 58.078 39.130 0.00 0.00 0.00 3.02
4626 7069 4.702131 ACACATAATTTCCTGCTCCTCAAC 59.298 41.667 0.00 0.00 0.00 3.18
4627 7070 4.701651 CACATAATTTCCTGCTCCTCAACA 59.298 41.667 0.00 0.00 0.00 3.33
4628 7071 5.359009 CACATAATTTCCTGCTCCTCAACAT 59.641 40.000 0.00 0.00 0.00 2.71
4629 7072 5.954150 ACATAATTTCCTGCTCCTCAACATT 59.046 36.000 0.00 0.00 0.00 2.71
4630 7073 6.438425 ACATAATTTCCTGCTCCTCAACATTT 59.562 34.615 0.00 0.00 0.00 2.32
4631 7074 4.796038 ATTTCCTGCTCCTCAACATTTG 57.204 40.909 0.00 0.00 0.00 2.32
4632 7075 2.957402 TCCTGCTCCTCAACATTTGT 57.043 45.000 0.00 0.00 0.00 2.83
4633 7076 3.228188 TCCTGCTCCTCAACATTTGTT 57.772 42.857 0.00 0.00 39.12 2.83
4661 7259 5.170021 GGATTCATGCTTAACATTTGTGCA 58.830 37.500 0.00 0.00 36.64 4.57
4680 7278 6.267817 TGTGCAACTCTTCAATCTCTTTTTG 58.732 36.000 0.00 0.00 38.04 2.44
4724 7322 8.110271 AGATCTATTCATCTTCAATCATGGCAT 58.890 33.333 0.00 0.00 27.71 4.40
4775 7373 7.623999 ATTACATCCAGATTCATAGACCACT 57.376 36.000 0.00 0.00 0.00 4.00
4895 7494 1.003718 GTCGTTGTGCTAAGGCCCT 60.004 57.895 0.00 0.00 37.74 5.19
4930 7529 0.102120 CAAAACAGCAACCGCCTTCA 59.898 50.000 0.00 0.00 39.83 3.02
5011 7610 0.835941 AGCCAGATCCGAGCAAATCT 59.164 50.000 2.49 0.00 32.44 2.40
5014 7613 2.224161 GCCAGATCCGAGCAAATCTACT 60.224 50.000 0.00 0.00 31.10 2.57
5027 7626 7.522889 CGAGCAAATCTACTGAGGATAGATTCA 60.523 40.741 7.52 0.00 44.81 2.57
5033 7634 6.176896 TCTACTGAGGATAGATTCATCGGAG 58.823 44.000 3.37 0.00 42.86 4.63
5039 7640 4.279671 AGGATAGATTCATCGGAGACACAC 59.720 45.833 0.00 0.00 42.51 3.82
5041 7642 2.461695 AGATTCATCGGAGACACACCT 58.538 47.619 0.00 0.00 42.51 4.00
5042 7643 2.428890 AGATTCATCGGAGACACACCTC 59.571 50.000 0.00 0.00 42.51 3.85
5120 7721 5.308825 GAGACCTTTGTTCCATCTTCAGAA 58.691 41.667 0.00 0.00 0.00 3.02
5150 7751 0.601311 GTGTCGCCTTTCTGAGCAGT 60.601 55.000 0.00 0.00 0.00 4.40
5153 7754 0.109272 TCGCCTTTCTGAGCAGTACG 60.109 55.000 0.00 0.00 0.00 3.67
5361 7965 2.679336 GTCTCGAGGGACTACTTCTGAC 59.321 54.545 13.56 0.00 41.55 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 114 2.281091 CTGCTCCCGTACCCCCTA 59.719 66.667 0.00 0.00 0.00 3.53
230 231 3.633418 ACTTCATTCGCTAGTAGGAGGT 58.367 45.455 0.00 0.00 0.00 3.85
359 360 1.472480 GCCGCTGCTGGATAAGAAAAA 59.528 47.619 13.37 0.00 33.53 1.94
363 364 0.181114 ATTGCCGCTGCTGGATAAGA 59.819 50.000 13.37 0.00 38.71 2.10
370 371 3.698029 AAAACTATATTGCCGCTGCTG 57.302 42.857 0.70 0.00 38.71 4.41
375 376 4.561735 TGGCTAAAAACTATATTGCCGC 57.438 40.909 0.00 0.00 41.51 6.53
377 378 6.769608 GCAATGGCTAAAAACTATATTGCC 57.230 37.500 0.00 0.00 41.61 4.52
378 379 5.696270 GGGCAATGGCTAAAAACTATATTGC 59.304 40.000 6.78 0.00 44.76 3.56
379 380 7.054491 AGGGCAATGGCTAAAAACTATATTG 57.946 36.000 6.78 0.00 40.87 1.90
381 382 5.473504 CGAGGGCAATGGCTAAAAACTATAT 59.526 40.000 6.78 0.00 40.87 0.86
738 768 8.019656 TGTCCTAACTCAAACTTCTCTAAAGT 57.980 34.615 0.00 0.00 0.00 2.66
877 912 4.299586 TCAACATGGCTAAGGTGATTGA 57.700 40.909 0.00 0.00 0.00 2.57
950 1303 3.118112 CCATGTGGAGAGGCTGTAAGATT 60.118 47.826 0.00 0.00 37.39 2.40
955 1308 2.543037 TACCATGTGGAGAGGCTGTA 57.457 50.000 5.96 0.00 38.94 2.74
1022 1383 9.838975 CTCATATACACATCTCTCATGTACTTC 57.161 37.037 0.00 0.00 31.88 3.01
1538 1902 1.202582 CTGGAGACGTCAATTCGGACT 59.797 52.381 19.50 0.00 35.63 3.85
1734 2098 3.339253 TGATGTTATGCTGCAGTCACT 57.661 42.857 16.64 6.88 0.00 3.41
1739 2103 4.577693 AGTACCAATGATGTTATGCTGCAG 59.422 41.667 10.11 10.11 0.00 4.41
1752 2116 2.758979 GGAACGGAGAGAGTACCAATGA 59.241 50.000 0.00 0.00 0.00 2.57
1817 2181 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
1953 2318 6.072175 ACAAGTTAAAGTTGCTGAGAAACACA 60.072 34.615 6.03 0.00 31.85 3.72
2000 2373 5.767665 TGGTCTGCTTAACATAAACACACAT 59.232 36.000 0.00 0.00 0.00 3.21
2008 2381 3.287222 GGCCATGGTCTGCTTAACATAA 58.713 45.455 14.67 0.00 0.00 1.90
2028 2401 2.566010 CCGTGCAATTTCCGGTGG 59.434 61.111 0.00 0.00 37.00 4.61
2044 2417 4.135747 AGAGAAGTCATCTGCTTTAGCC 57.864 45.455 0.00 0.00 38.96 3.93
2213 2589 1.904990 GAGAGGAGGGGCAGGAACAC 61.905 65.000 0.00 0.00 0.00 3.32
2489 2874 6.441924 TGCATTGAATAATAACCCTTTCCCAA 59.558 34.615 0.00 0.00 0.00 4.12
3222 5603 4.268828 TGGTCATTCCATTCCCATGAAT 57.731 40.909 0.00 0.00 41.93 2.57
3693 6120 4.681781 GCCTGTAGATGTAGACTTGTGCAT 60.682 45.833 0.00 0.00 0.00 3.96
3702 6129 0.396556 TGCCGGCCTGTAGATGTAGA 60.397 55.000 26.77 0.00 0.00 2.59
4046 6488 1.202794 TCTTGAGCAGGTCATGTTGCA 60.203 47.619 17.31 0.00 42.67 4.08
4104 6546 2.994995 TTCTTCCCGAGCTCCGCA 60.995 61.111 8.47 0.00 36.84 5.69
4383 6825 9.211485 ACCAATCAAGATCAATCACAAAAATTC 57.789 29.630 0.00 0.00 0.00 2.17
4384 6826 8.995220 CACCAATCAAGATCAATCACAAAAATT 58.005 29.630 0.00 0.00 0.00 1.82
4391 6833 4.460382 ACCACACCAATCAAGATCAATCAC 59.540 41.667 0.00 0.00 0.00 3.06
4466 6908 9.982651 TCGGATGAATAACAAAAACCAAAAATA 57.017 25.926 0.00 0.00 0.00 1.40
4467 6909 8.894768 TCGGATGAATAACAAAAACCAAAAAT 57.105 26.923 0.00 0.00 0.00 1.82
4538 6981 1.947456 GAACTTGCACTCGGGAAAAGT 59.053 47.619 0.00 0.00 32.60 2.66
4547 6990 7.810658 TCAAAATATCTTCTGAACTTGCACTC 58.189 34.615 0.00 0.00 0.00 3.51
4594 7037 6.071728 AGCAGGAAATTATGTGTCCTTTTCAG 60.072 38.462 0.00 0.00 39.87 3.02
4595 7038 5.774690 AGCAGGAAATTATGTGTCCTTTTCA 59.225 36.000 0.00 0.00 39.87 2.69
4596 7039 6.272822 AGCAGGAAATTATGTGTCCTTTTC 57.727 37.500 0.00 0.00 39.87 2.29
4597 7040 5.185828 GGAGCAGGAAATTATGTGTCCTTTT 59.814 40.000 0.00 0.00 39.87 2.27
4598 7041 4.706962 GGAGCAGGAAATTATGTGTCCTTT 59.293 41.667 0.00 0.00 39.87 3.11
4599 7042 4.018050 AGGAGCAGGAAATTATGTGTCCTT 60.018 41.667 0.00 0.00 39.87 3.36
4600 7043 3.525199 AGGAGCAGGAAATTATGTGTCCT 59.475 43.478 0.00 0.00 42.72 3.85
4601 7044 3.879892 GAGGAGCAGGAAATTATGTGTCC 59.120 47.826 0.00 0.00 0.00 4.02
4602 7045 4.517285 TGAGGAGCAGGAAATTATGTGTC 58.483 43.478 0.00 0.00 0.00 3.67
4603 7046 4.574674 TGAGGAGCAGGAAATTATGTGT 57.425 40.909 0.00 0.00 0.00 3.72
4604 7047 4.701651 TGTTGAGGAGCAGGAAATTATGTG 59.298 41.667 0.00 0.00 0.00 3.21
4605 7048 4.922206 TGTTGAGGAGCAGGAAATTATGT 58.078 39.130 0.00 0.00 0.00 2.29
4606 7049 6.461110 AATGTTGAGGAGCAGGAAATTATG 57.539 37.500 0.00 0.00 0.00 1.90
4607 7050 6.438425 ACAAATGTTGAGGAGCAGGAAATTAT 59.562 34.615 0.00 0.00 0.00 1.28
4608 7051 5.774690 ACAAATGTTGAGGAGCAGGAAATTA 59.225 36.000 0.00 0.00 0.00 1.40
4609 7052 4.590222 ACAAATGTTGAGGAGCAGGAAATT 59.410 37.500 0.00 0.00 0.00 1.82
4610 7053 4.154942 ACAAATGTTGAGGAGCAGGAAAT 58.845 39.130 0.00 0.00 0.00 2.17
4611 7054 3.565307 ACAAATGTTGAGGAGCAGGAAA 58.435 40.909 0.00 0.00 0.00 3.13
4612 7055 3.228188 ACAAATGTTGAGGAGCAGGAA 57.772 42.857 0.00 0.00 0.00 3.36
4613 7056 2.957402 ACAAATGTTGAGGAGCAGGA 57.043 45.000 0.00 0.00 0.00 3.86
4636 7079 5.813672 GCACAAATGTTAAGCATGAATCCAT 59.186 36.000 0.00 0.00 37.96 3.41
4637 7080 5.170021 GCACAAATGTTAAGCATGAATCCA 58.830 37.500 0.00 0.00 37.96 3.41
4638 7081 5.170021 TGCACAAATGTTAAGCATGAATCC 58.830 37.500 0.00 0.00 37.96 3.01
4639 7082 6.366877 AGTTGCACAAATGTTAAGCATGAATC 59.633 34.615 0.00 0.00 37.96 2.52
4640 7083 6.225318 AGTTGCACAAATGTTAAGCATGAAT 58.775 32.000 0.00 0.00 37.96 2.57
4641 7084 5.599732 AGTTGCACAAATGTTAAGCATGAA 58.400 33.333 0.00 0.00 37.96 2.57
4642 7085 5.009911 AGAGTTGCACAAATGTTAAGCATGA 59.990 36.000 0.00 0.00 37.96 3.07
4643 7086 5.224888 AGAGTTGCACAAATGTTAAGCATG 58.775 37.500 0.00 0.00 37.96 4.06
4698 7296 7.459234 TGCCATGATTGAAGATGAATAGATCT 58.541 34.615 0.00 0.00 33.91 2.75
4724 7322 8.604640 TTTATTATGTCTGGTGTTCGTTGTAA 57.395 30.769 0.00 0.00 0.00 2.41
4775 7373 3.566742 TCAGTGCTTGTAGTCGTCACTAA 59.433 43.478 0.00 0.00 36.84 2.24
4831 7430 3.145551 GCCCTACTTCGGCGAGGA 61.146 66.667 26.26 8.51 36.47 3.71
4895 7494 2.046009 TTTGGTGCGCTGGTCCTACA 62.046 55.000 9.73 0.00 0.00 2.74
5011 7610 5.941058 GTCTCCGATGAATCTATCCTCAGTA 59.059 44.000 0.00 0.00 0.00 2.74
5014 7613 4.520874 GTGTCTCCGATGAATCTATCCTCA 59.479 45.833 0.00 0.00 0.00 3.86
5033 7634 0.814010 GGTGTGTGTGGAGGTGTGTC 60.814 60.000 0.00 0.00 0.00 3.67
5039 7640 2.113139 GGTGGGTGTGTGTGGAGG 59.887 66.667 0.00 0.00 0.00 4.30
5041 7642 1.077357 GTTGGTGGGTGTGTGTGGA 60.077 57.895 0.00 0.00 0.00 4.02
5042 7643 2.477176 CGTTGGTGGGTGTGTGTGG 61.477 63.158 0.00 0.00 0.00 4.17
5043 7644 0.817634 ATCGTTGGTGGGTGTGTGTG 60.818 55.000 0.00 0.00 0.00 3.82
5044 7645 0.759959 TATCGTTGGTGGGTGTGTGT 59.240 50.000 0.00 0.00 0.00 3.72
5133 7734 1.351153 GTACTGCTCAGAAAGGCGAC 58.649 55.000 3.60 0.00 0.00 5.19
5150 7751 4.643463 TGAGATTTGTTAGGGTTTGCGTA 58.357 39.130 0.00 0.00 0.00 4.42
5153 7754 5.010617 TCCTTTGAGATTTGTTAGGGTTTGC 59.989 40.000 0.00 0.00 0.00 3.68
5361 7965 6.019961 GCTTCTATGTTGAGATTGAAGAGTCG 60.020 42.308 13.57 0.00 37.37 4.18


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

AutoCloner maintained by Alex Coulton.