Multiple sequence alignment - TraesCS7D01G322800

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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 TraesCS7D01G322800 chr7D 100.000 4444 0 0 1 4444 412870528 412874971 0.000000e+00 8207.0
1 TraesCS7D01G322800 chr7D 81.537 872 151 9 1 867 219849802 219848936 0.000000e+00 710.0
2 TraesCS7D01G322800 chr7D 94.059 101 5 1 1612 1712 412871992 412872091 7.700000e-33 152.0
3 TraesCS7D01G322800 chr7D 94.059 101 5 1 1465 1564 412872139 412872239 7.700000e-33 152.0
4 TraesCS7D01G322800 chr7D 84.615 130 8 11 2633 2756 412873283 412873160 7.810000e-23 119.0
5 TraesCS7D01G322800 chr7D 100.000 30 0 0 2675 2704 412873174 412873203 6.210000e-04 56.5
6 TraesCS7D01G322800 chr7D 100.000 30 0 0 2647 2676 412873202 412873231 6.210000e-04 56.5
7 TraesCS7D01G322800 chr7A 92.767 2378 118 22 1 2337 474280308 474282672 0.000000e+00 3389.0
8 TraesCS7D01G322800 chr7A 91.950 1118 57 18 2726 3831 474283754 474284850 0.000000e+00 1535.0
9 TraesCS7D01G322800 chr7A 84.943 870 121 8 1 867 219377530 219378392 0.000000e+00 872.0
10 TraesCS7D01G322800 chr7A 96.386 332 11 1 2345 2675 474283423 474283754 3.020000e-151 545.0
11 TraesCS7D01G322800 chr7A 97.000 100 2 1 1467 1565 474281928 474282027 2.750000e-37 167.0
12 TraesCS7D01G322800 chr7A 92.982 114 5 2 4218 4331 474285272 474285382 3.560000e-36 163.0
13 TraesCS7D01G322800 chr7A 85.211 142 8 6 4048 4184 474285068 474285201 2.790000e-27 134.0
14 TraesCS7D01G322800 chr7A 98.246 57 1 0 3853 3909 474284940 474284996 2.830000e-17 100.0
15 TraesCS7D01G322800 chr7A 97.297 37 1 0 3992 4028 716683706 716683742 3.710000e-06 63.9
16 TraesCS7D01G322800 chr7A 100.000 29 0 0 2675 2703 474283726 474283754 2.000000e-03 54.7
17 TraesCS7D01G322800 chr7B 91.367 1251 70 22 2726 3952 427290524 427291760 0.000000e+00 1677.0
18 TraesCS7D01G322800 chr7B 96.012 677 20 5 886 1559 427288724 427289396 0.000000e+00 1094.0
19 TraesCS7D01G322800 chr7B 97.162 458 13 0 1651 2108 427289441 427289898 0.000000e+00 774.0
20 TraesCS7D01G322800 chr7B 95.468 331 12 2 2345 2675 427290197 427290524 3.940000e-145 525.0
21 TraesCS7D01G322800 chr7B 81.674 442 28 20 3962 4376 427291881 427292296 7.170000e-83 318.0
22 TraesCS7D01G322800 chr7B 93.846 65 4 0 4380 4444 427292583 427292647 1.020000e-16 99.0
23 TraesCS7D01G322800 chr7B 93.548 62 4 0 1503 1564 427289441 427289502 4.730000e-15 93.5
24 TraesCS7D01G322800 chr7B 100.000 29 0 0 1701 1729 126740195 126740167 2.000000e-03 54.7
25 TraesCS7D01G322800 chr7B 100.000 29 0 0 2675 2703 427290496 427290524 2.000000e-03 54.7
26 TraesCS7D01G322800 chr2D 88.351 867 97 3 3 867 622369173 622368309 0.000000e+00 1038.0
27 TraesCS7D01G322800 chr1D 83.352 871 137 8 1 867 360146986 360146120 0.000000e+00 798.0
28 TraesCS7D01G322800 chr4B 83.632 837 130 7 1 836 86652660 86651830 0.000000e+00 780.0
29 TraesCS7D01G322800 chr2A 82.549 871 144 8 1 867 262308671 262309537 0.000000e+00 760.0
30 TraesCS7D01G322800 chr1B 82.118 878 140 10 1 867 201759305 201760176 0.000000e+00 736.0
31 TraesCS7D01G322800 chr1B 81.986 866 140 15 8 867 227711485 227710630 0.000000e+00 721.0
32 TraesCS7D01G322800 chr1B 97.778 45 1 0 1566 1610 667043688 667043732 1.330000e-10 78.7
33 TraesCS7D01G322800 chr5A 87.160 405 37 11 1949 2338 463652164 463652568 3.150000e-121 446.0
34 TraesCS7D01G322800 chr5D 94.545 55 1 2 1559 1612 458811306 458811253 2.850000e-12 84.2
35 TraesCS7D01G322800 chr5D 94.872 39 2 0 4008 4046 445400591 445400629 1.330000e-05 62.1
36 TraesCS7D01G322800 chr3B 100.000 45 0 0 1566 1610 99080248 99080292 2.850000e-12 84.2
37 TraesCS7D01G322800 chr3B 95.745 47 2 0 1566 1612 99080264 99080218 4.770000e-10 76.8
38 TraesCS7D01G322800 chr6D 92.982 57 1 3 1566 1620 93644450 93644395 3.680000e-11 80.5
39 TraesCS7D01G322800 chr3D 83.516 91 8 4 3935 4023 373805361 373805276 1.330000e-10 78.7
40 TraesCS7D01G322800 chr4D 97.778 45 0 1 1568 1612 402560158 402560201 4.770000e-10 76.8
41 TraesCS7D01G322800 chr4D 87.500 64 4 3 1549 1612 36591587 36591528 2.220000e-08 71.3
42 TraesCS7D01G322800 chr5B 95.556 45 1 1 1572 1616 617036892 617036849 2.220000e-08 71.3
43 TraesCS7D01G322800 chr5B 85.075 67 7 3 3962 4028 149315665 149315728 1.030000e-06 65.8
44 TraesCS7D01G322800 chr6B 83.333 66 6 5 1700 1761 258467580 258467644 6.210000e-04 56.5


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 TraesCS7D01G322800 chr7D 412870528 412874971 4443 False 1724.8000 8207 97.623600 1 4444 5 chr7D.!!$F1 4443
1 TraesCS7D01G322800 chr7D 219848936 219849802 866 True 710.0000 710 81.537000 1 867 1 chr7D.!!$R1 866
2 TraesCS7D01G322800 chr7A 219377530 219378392 862 False 872.0000 872 84.943000 1 867 1 chr7A.!!$F1 866
3 TraesCS7D01G322800 chr7A 474280308 474285382 5074 False 760.9625 3389 94.317750 1 4331 8 chr7A.!!$F3 4330
4 TraesCS7D01G322800 chr7B 427288724 427292647 3923 False 579.4000 1677 93.634625 886 4444 8 chr7B.!!$F1 3558
5 TraesCS7D01G322800 chr2D 622368309 622369173 864 True 1038.0000 1038 88.351000 3 867 1 chr2D.!!$R1 864
6 TraesCS7D01G322800 chr1D 360146120 360146986 866 True 798.0000 798 83.352000 1 867 1 chr1D.!!$R1 866
7 TraesCS7D01G322800 chr4B 86651830 86652660 830 True 780.0000 780 83.632000 1 836 1 chr4B.!!$R1 835
8 TraesCS7D01G322800 chr2A 262308671 262309537 866 False 760.0000 760 82.549000 1 867 1 chr2A.!!$F1 866
9 TraesCS7D01G322800 chr1B 201759305 201760176 871 False 736.0000 736 82.118000 1 867 1 chr1B.!!$F1 866
10 TraesCS7D01G322800 chr1B 227710630 227711485 855 True 721.0000 721 81.986000 8 867 1 chr1B.!!$R1 859

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
648 670 0.107312 CCATGCAGGAAGGAGGACAG 60.107 60.0 0.00 0.00 41.22 3.51 F
2527 3337 0.110678 TGTCCCATGGGCGTTTTACA 59.889 50.0 27.41 20.45 34.68 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2262 2322 0.253044 TGCACAAGAGGGGTGATAGC 59.747 55.0 0.00 0.0 38.54 2.97 R
4132 5232 0.111061 TTCAGTCTGGCATGGCAAGT 59.889 50.0 23.47 13.5 30.42 3.16 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
32 35 3.369576 CCCTACTTGCTCTCAGGGTTTAC 60.370 52.174 6.02 0.00 42.50 2.01
83 86 4.568956 CAATAAAGCAAAGGAGGTTTGGG 58.431 43.478 0.00 0.00 45.10 4.12
170 175 7.016268 TGGTGTTGGAGTATCTTCTACTTCTTT 59.984 37.037 0.00 0.00 33.73 2.52
217 222 3.428534 GGTTCCAAAATGTGCGTGAAATC 59.571 43.478 0.00 0.00 0.00 2.17
306 311 6.039382 CAGAATGCATCTCAGATTTCAATGGA 59.961 38.462 0.00 0.00 35.73 3.41
307 312 6.605995 AGAATGCATCTCAGATTTCAATGGAA 59.394 34.615 0.00 0.00 30.46 3.53
370 384 0.627986 AGGCTTCCATGAAAGAGGGG 59.372 55.000 0.00 0.00 0.00 4.79
385 399 3.590574 GGGGGTTGGTCTTGCCCT 61.591 66.667 0.00 0.00 42.01 5.19
386 400 2.526110 GGGGTTGGTCTTGCCCTT 59.474 61.111 0.00 0.00 42.01 3.95
387 401 1.606601 GGGGTTGGTCTTGCCCTTC 60.607 63.158 0.00 0.00 42.01 3.46
419 433 8.715191 TTTGTGAAACTTAATGTTGATGCTTT 57.285 26.923 0.00 0.00 39.13 3.51
500 522 5.174037 AGGTTTATCGTTGGAGGAAATGA 57.826 39.130 0.00 0.00 0.00 2.57
508 530 7.938140 ATCGTTGGAGGAAATGAAAAGATTA 57.062 32.000 0.00 0.00 0.00 1.75
526 548 6.363577 AGATTAAGTATTGTGCGGATGTTG 57.636 37.500 0.00 0.00 0.00 3.33
647 669 0.842030 ACCATGCAGGAAGGAGGACA 60.842 55.000 0.00 0.00 41.22 4.02
648 670 0.107312 CCATGCAGGAAGGAGGACAG 60.107 60.000 0.00 0.00 41.22 3.51
690 712 5.562501 GCGGCAATTTTGGATGATTGTTTTT 60.563 36.000 0.00 0.00 36.03 1.94
768 792 2.861462 AGTAGCTCATGAACTCGCTC 57.139 50.000 10.19 3.96 34.14 5.03
791 815 8.736751 CTCGAATAGCTAGATTTTCTTCTACC 57.263 38.462 9.09 0.00 0.00 3.18
820 844 1.740025 GTTCGAGGAGCCTTCAAATGG 59.260 52.381 0.00 0.00 0.00 3.16
922 946 1.229428 TCACTCGAAAGCAAAGCAGG 58.771 50.000 0.00 0.00 0.00 4.85
1143 1167 0.535335 TCGGCATCTGGAACTGGTAC 59.465 55.000 0.00 0.00 0.00 3.34
1167 1194 2.846827 CTCCTTCCTACCACTCCCAAAT 59.153 50.000 0.00 0.00 0.00 2.32
1205 1232 0.254747 TTCCACGCCCCTAAATCCAG 59.745 55.000 0.00 0.00 0.00 3.86
1237 1264 1.418342 ATTCGATCGAAACACGGCGG 61.418 55.000 32.11 2.35 42.82 6.13
1242 1269 0.675522 ATCGAAACACGGCGGGATTT 60.676 50.000 19.75 13.03 42.82 2.17
1265 1293 2.032071 CGTTTTCCCGAGGCTGGT 59.968 61.111 0.00 0.00 0.00 4.00
1291 1319 1.952296 GCTGATGTCATGAATCCCCAC 59.048 52.381 0.00 0.00 0.00 4.61
1342 1370 1.666872 GGTGTACGTGCGCCTCTTT 60.667 57.895 26.49 0.00 36.19 2.52
1559 1587 9.729281 TTTATTTACTACTCCTTTCGTTCCATT 57.271 29.630 0.00 0.00 0.00 3.16
1565 1593 5.080969 ACTCCTTTCGTTCCATTATTCGA 57.919 39.130 0.00 0.00 0.00 3.71
1566 1594 5.109903 ACTCCTTTCGTTCCATTATTCGAG 58.890 41.667 0.00 0.00 33.98 4.04
1568 1596 5.484715 TCCTTTCGTTCCATTATTCGAGTT 58.515 37.500 0.00 0.00 33.98 3.01
1569 1597 5.579511 TCCTTTCGTTCCATTATTCGAGTTC 59.420 40.000 0.00 0.00 33.98 3.01
1570 1598 5.350365 CCTTTCGTTCCATTATTCGAGTTCA 59.650 40.000 0.00 0.00 33.98 3.18
1576 1615 8.293867 TCGTTCCATTATTCGAGTTCAAAATTT 58.706 29.630 0.00 0.00 0.00 1.82
1640 1679 7.442364 ACACATCTCCAATCGGTAAATGATAAG 59.558 37.037 0.00 0.00 0.00 1.73
1681 1720 4.924305 ACATCCATGTGGTTATTGCATC 57.076 40.909 0.00 0.00 40.03 3.91
1850 1895 0.804364 GCTCCAATGTGAACGCATGA 59.196 50.000 0.00 0.00 0.00 3.07
1934 1979 1.247567 ACCATTTGGAGGCAAAGACG 58.752 50.000 3.01 0.00 38.94 4.18
2057 2102 2.141535 TCAAAACCGGCCAAATTTCG 57.858 45.000 0.00 0.00 0.00 3.46
2209 2254 1.447838 CGTGCGCCATGTCTACCTT 60.448 57.895 4.18 0.00 0.00 3.50
2337 2397 1.961277 CCACACACGGCTTCTGACC 60.961 63.158 0.00 0.00 0.00 4.02
2352 3161 6.095580 GGCTTCTGACCGATATGTCTATCATA 59.904 42.308 0.00 0.00 42.30 2.15
2396 3205 5.911752 AGTCATATTGTCTCTGTGATGACC 58.088 41.667 8.73 0.00 42.60 4.02
2527 3337 0.110678 TGTCCCATGGGCGTTTTACA 59.889 50.000 27.41 20.45 34.68 2.41
2590 3400 2.037772 TGCAAGTGTCCTCTCTCCTTTC 59.962 50.000 0.00 0.00 0.00 2.62
2627 3437 6.777580 AGCTTCAAATGGTTCCTTCTTCTTTA 59.222 34.615 0.00 0.00 0.00 1.85
2645 3455 8.053963 TCTTCTTTATAGGATATACTCCCTCCG 58.946 40.741 0.00 0.00 46.27 4.63
2677 3487 8.863872 AATACATGGCATATAAACTTACTCCC 57.136 34.615 0.00 0.00 0.00 4.30
2678 3488 5.631119 ACATGGCATATAAACTTACTCCCC 58.369 41.667 0.00 0.00 0.00 4.81
2679 3489 5.133660 ACATGGCATATAAACTTACTCCCCA 59.866 40.000 0.00 0.00 0.00 4.96
2680 3490 5.718801 TGGCATATAAACTTACTCCCCAA 57.281 39.130 0.00 0.00 0.00 4.12
2681 3491 6.080969 TGGCATATAAACTTACTCCCCAAA 57.919 37.500 0.00 0.00 0.00 3.28
2682 3492 6.678547 TGGCATATAAACTTACTCCCCAAAT 58.321 36.000 0.00 0.00 0.00 2.32
2683 3493 7.817440 TGGCATATAAACTTACTCCCCAAATA 58.183 34.615 0.00 0.00 0.00 1.40
2684 3494 7.722285 TGGCATATAAACTTACTCCCCAAATAC 59.278 37.037 0.00 0.00 0.00 1.89
2685 3495 7.722285 GGCATATAAACTTACTCCCCAAATACA 59.278 37.037 0.00 0.00 0.00 2.29
2686 3496 9.297037 GCATATAAACTTACTCCCCAAATACAT 57.703 33.333 0.00 0.00 0.00 2.29
2688 3498 9.807921 ATATAAACTTACTCCCCAAATACATGG 57.192 33.333 0.00 0.00 40.35 3.66
2689 3499 3.898482 ACTTACTCCCCAAATACATGGC 58.102 45.455 0.00 0.00 39.26 4.40
2690 3500 3.268334 ACTTACTCCCCAAATACATGGCA 59.732 43.478 0.00 0.00 39.26 4.92
2691 3501 4.079212 ACTTACTCCCCAAATACATGGCAT 60.079 41.667 0.00 0.00 39.26 4.40
2692 3502 5.133660 ACTTACTCCCCAAATACATGGCATA 59.866 40.000 0.00 0.00 39.26 3.14
2693 3503 4.747265 ACTCCCCAAATACATGGCATAT 57.253 40.909 0.00 0.00 39.26 1.78
2694 3504 5.858876 ACTCCCCAAATACATGGCATATA 57.141 39.130 0.00 0.00 39.26 0.86
2695 3505 6.212840 ACTCCCCAAATACATGGCATATAA 57.787 37.500 0.00 0.00 39.26 0.98
2696 3506 6.619464 ACTCCCCAAATACATGGCATATAAA 58.381 36.000 0.00 0.00 39.26 1.40
2697 3507 6.493458 ACTCCCCAAATACATGGCATATAAAC 59.507 38.462 0.00 0.00 39.26 2.01
2698 3508 6.619464 TCCCCAAATACATGGCATATAAACT 58.381 36.000 0.00 0.00 39.26 2.66
2699 3509 7.072562 TCCCCAAATACATGGCATATAAACTT 58.927 34.615 0.00 0.00 39.26 2.66
2700 3510 8.228206 TCCCCAAATACATGGCATATAAACTTA 58.772 33.333 0.00 0.00 39.26 2.24
2701 3511 8.303876 CCCCAAATACATGGCATATAAACTTAC 58.696 37.037 0.00 0.00 39.26 2.34
2702 3512 9.077885 CCCAAATACATGGCATATAAACTTACT 57.922 33.333 0.00 0.00 39.26 2.24
2739 3549 6.916360 AGGTTTATATGCCATGTATTTGGG 57.084 37.500 0.00 0.00 37.24 4.12
2837 3647 2.128771 AATTAATGCGCTGACAGGGT 57.871 45.000 19.53 4.12 0.00 4.34
3033 3843 1.418373 CGTGTTCGAGAGCATGTTCA 58.582 50.000 12.41 0.00 39.71 3.18
3054 3864 0.247736 CCACGACCTCAAGGAGAAGG 59.752 60.000 2.30 1.71 38.94 3.46
3055 3865 1.257743 CACGACCTCAAGGAGAAGGA 58.742 55.000 2.30 0.00 38.94 3.36
3059 3869 2.159028 CGACCTCAAGGAGAAGGAATCC 60.159 54.545 2.30 0.00 38.94 3.01
3062 3872 2.437651 CCTCAAGGAGAAGGAATCCTCC 59.562 54.545 0.56 0.00 46.75 4.30
3314 4125 1.075659 GCTCAAGAAGGGGTGCCTT 59.924 57.895 0.00 0.00 0.00 4.35
3326 4137 1.574702 GGTGCCTTGCGTACCTGTTC 61.575 60.000 0.00 0.00 43.57 3.18
3350 4161 1.742761 TCGGGAAGATCTACGACGTT 58.257 50.000 5.50 0.00 0.00 3.99
3377 4188 0.250513 AGATCAGCGGGTTCTTCCAC 59.749 55.000 0.00 0.00 38.11 4.02
3490 4307 3.445450 GGAAAGATCAAAGGGAAGAAGCC 59.555 47.826 0.00 0.00 0.00 4.35
3500 4317 1.539157 GGAAGAAGCCACTGGAAAGG 58.461 55.000 0.00 0.00 0.00 3.11
3529 4346 9.011095 GGAAAGAATAGCCCCAAAAGTATATAC 57.989 37.037 4.60 4.60 0.00 1.47
3530 4347 9.794719 GAAAGAATAGCCCCAAAAGTATATACT 57.205 33.333 9.71 9.71 38.39 2.12
3603 4448 6.314648 TGCATAGTGCTTCTGAGAATTTACAG 59.685 38.462 0.00 6.52 45.31 2.74
3606 4451 4.453819 AGTGCTTCTGAGAATTTACAGCAC 59.546 41.667 21.03 21.03 46.99 4.40
3626 4471 6.807720 CAGCACTGTAATTATGCAAATGTGAA 59.192 34.615 11.15 0.00 41.97 3.18
3627 4472 6.808212 AGCACTGTAATTATGCAAATGTGAAC 59.192 34.615 11.15 0.00 41.97 3.18
3644 4489 3.706373 CCGCTACTGGTGTGGGCT 61.706 66.667 0.00 0.00 0.00 5.19
3672 4528 4.735338 GTGTAAAGAAGTTTGTGAGCAAGC 59.265 41.667 0.00 0.00 35.82 4.01
3679 4535 1.069906 GTTTGTGAGCAAGCGGTGTAG 60.070 52.381 0.00 0.00 35.82 2.74
3681 4537 0.319555 TGTGAGCAAGCGGTGTAGTC 60.320 55.000 0.00 0.00 0.00 2.59
3682 4538 0.038159 GTGAGCAAGCGGTGTAGTCT 60.038 55.000 0.00 0.00 0.00 3.24
3684 4540 1.890489 TGAGCAAGCGGTGTAGTCTAA 59.110 47.619 0.00 0.00 0.00 2.10
3685 4541 2.496070 TGAGCAAGCGGTGTAGTCTAAT 59.504 45.455 0.00 0.00 0.00 1.73
3686 4542 3.056107 TGAGCAAGCGGTGTAGTCTAATT 60.056 43.478 0.00 0.00 0.00 1.40
3687 4543 4.158949 TGAGCAAGCGGTGTAGTCTAATTA 59.841 41.667 0.00 0.00 0.00 1.40
3689 4545 4.868734 AGCAAGCGGTGTAGTCTAATTAAC 59.131 41.667 0.00 0.00 0.00 2.01
3690 4546 4.259690 GCAAGCGGTGTAGTCTAATTAACG 60.260 45.833 0.00 0.00 0.00 3.18
3691 4547 4.037858 AGCGGTGTAGTCTAATTAACGG 57.962 45.455 0.00 0.00 0.00 4.44
3696 4552 5.066505 CGGTGTAGTCTAATTAACGGTACCT 59.933 44.000 10.90 0.00 0.00 3.08
3712 4568 2.736670 ACCTTTTGCTCTGTTGTCCT 57.263 45.000 0.00 0.00 0.00 3.85
3720 4576 1.467734 GCTCTGTTGTCCTGCATGAAG 59.532 52.381 0.00 0.00 0.00 3.02
3735 4591 0.764890 TGAAGTCCTGAACCCTGGTG 59.235 55.000 0.00 0.00 33.58 4.17
3736 4592 0.606673 GAAGTCCTGAACCCTGGTGC 60.607 60.000 0.00 0.00 33.58 5.01
3737 4593 1.352622 AAGTCCTGAACCCTGGTGCA 61.353 55.000 0.00 0.00 33.58 4.57
3792 4649 1.672356 GTTGATCTGGCTGGCGTGT 60.672 57.895 0.00 0.00 0.00 4.49
3793 4650 1.672030 TTGATCTGGCTGGCGTGTG 60.672 57.895 0.00 0.00 0.00 3.82
3824 4681 3.961408 GGTCTGCTCTAGAATTGGTCCTA 59.039 47.826 0.00 0.00 37.12 2.94
3900 4876 6.237901 TGGATTACACAGCTTGACTTTGTAT 58.762 36.000 3.37 0.00 40.38 2.29
3924 4900 7.252965 TCACATTGACAAAATTCGAGTTGTA 57.747 32.000 10.17 0.00 38.07 2.41
3930 4906 5.008217 TGACAAAATTCGAGTTGTACCTTGG 59.992 40.000 10.17 0.00 38.07 3.61
4046 5137 3.323751 TTTGTTTACGGAGGGAGTAGC 57.676 47.619 0.00 0.00 0.00 3.58
4054 5145 1.469423 CGGAGGGAGTAGCGAAGAAAC 60.469 57.143 0.00 0.00 0.00 2.78
4069 5164 1.963515 AGAAACCAAGTTGCCATGTCC 59.036 47.619 0.00 0.00 0.00 4.02
4112 5212 0.674534 AGAAGAGTCGGTCGCTTGTT 59.325 50.000 0.00 0.00 36.38 2.83
4132 5232 3.659092 CGCAGCGAAGGTTGCCAA 61.659 61.111 9.98 0.00 46.38 4.52
4142 5242 1.668793 GGTTGCCAACTTGCCATGC 60.669 57.895 7.62 0.00 0.00 4.06
4186 5301 1.079127 AGATGGAAGGAACGTGCGG 60.079 57.895 0.00 0.00 0.00 5.69
4188 5303 0.672401 GATGGAAGGAACGTGCGGAA 60.672 55.000 0.00 0.00 0.00 4.30
4189 5304 0.035439 ATGGAAGGAACGTGCGGAAT 60.035 50.000 0.00 0.00 0.00 3.01
4191 5306 1.002201 TGGAAGGAACGTGCGGAATAA 59.998 47.619 0.00 0.00 0.00 1.40
4223 5355 2.949644 ACGGTTTCCCTTGAAAACTGAG 59.050 45.455 12.99 2.61 44.43 3.35
4377 5518 5.764131 GTGTTGAACGGTTGATTATTTCCA 58.236 37.500 0.00 0.00 0.00 3.53
4378 5519 5.856455 GTGTTGAACGGTTGATTATTTCCAG 59.144 40.000 0.00 0.00 0.00 3.86
4383 5807 2.936498 CGGTTGATTATTTCCAGACGCT 59.064 45.455 0.00 0.00 0.00 5.07
4420 5844 2.763651 GCTAATCGCCTCCGTTGTT 58.236 52.632 0.00 0.00 35.54 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 35 3.338818 AAGCACGTGTTTCATGTCTTG 57.661 42.857 18.38 0.00 30.47 3.02
83 86 1.691434 CTCATCCAACCCTAGCCTCTC 59.309 57.143 0.00 0.00 0.00 3.20
170 175 6.828273 CCCATAATACACAAATCTTGGTCTGA 59.172 38.462 0.00 0.00 34.12 3.27
235 240 7.451731 TTTCTGTCTTTCCCACCATAGATAT 57.548 36.000 0.00 0.00 0.00 1.63
306 311 6.481434 AGTTAGACGTGAGGGCTATAATTT 57.519 37.500 0.00 0.00 0.00 1.82
307 312 6.481434 AAGTTAGACGTGAGGGCTATAATT 57.519 37.500 0.00 0.00 0.00 1.40
370 384 0.895559 CTGAAGGGCAAGACCAACCC 60.896 60.000 0.00 0.00 44.62 4.11
384 398 4.736126 AAGTTTCACAAAACCCCTGAAG 57.264 40.909 0.00 0.00 44.87 3.02
385 399 6.155393 ACATTAAGTTTCACAAAACCCCTGAA 59.845 34.615 0.00 0.00 44.87 3.02
386 400 5.659079 ACATTAAGTTTCACAAAACCCCTGA 59.341 36.000 0.00 0.00 44.87 3.86
387 401 5.912892 ACATTAAGTTTCACAAAACCCCTG 58.087 37.500 0.00 0.00 44.87 4.45
419 433 6.438108 ACCCTTCATCATGTCATGATCAAAAA 59.562 34.615 22.89 14.24 46.62 1.94
500 522 7.391148 ACATCCGCACAATACTTAATCTTTT 57.609 32.000 0.00 0.00 0.00 2.27
508 530 3.188460 GTCACAACATCCGCACAATACTT 59.812 43.478 0.00 0.00 0.00 2.24
738 762 6.660949 AGTTCATGAGCTACTTTATTTGCCTT 59.339 34.615 10.73 0.00 0.00 4.35
791 815 1.740025 GGCTCCTCGAACCAATTCAAG 59.260 52.381 0.00 0.00 34.14 3.02
922 946 1.257155 GTTTCAGTGTTGACGACCGAC 59.743 52.381 0.00 0.00 31.71 4.79
1104 1128 1.292223 CTTGAAAGGGTCGGAGCGA 59.708 57.895 0.53 0.00 0.00 4.93
1143 1167 1.196012 GGAGTGGTAGGAAGGAGTGG 58.804 60.000 0.00 0.00 0.00 4.00
1167 1194 1.364269 AGATTGGGGAACGGTGGTAA 58.636 50.000 0.00 0.00 0.00 2.85
1205 1232 5.675778 TCGATCGAATTTCACGAGTTTAC 57.324 39.130 16.99 0.00 42.81 2.01
1237 1264 2.745281 TCGGGAAAACGACATCAAATCC 59.255 45.455 0.00 0.00 38.06 3.01
1242 1269 0.672401 GCCTCGGGAAAACGACATCA 60.672 55.000 0.00 0.00 38.06 3.07
1265 1293 2.202919 CATGACATCAGCCGGCGA 60.203 61.111 23.20 21.50 0.00 5.54
1568 1596 7.313646 TGTCGTGGTTTTAGTTCAAATTTTGA 58.686 30.769 7.74 7.74 38.04 2.69
1569 1597 7.513190 TGTCGTGGTTTTAGTTCAAATTTTG 57.487 32.000 2.59 2.59 0.00 2.44
1570 1598 8.030106 TCTTGTCGTGGTTTTAGTTCAAATTTT 58.970 29.630 0.00 0.00 0.00 1.82
1576 1615 6.687081 AATTCTTGTCGTGGTTTTAGTTCA 57.313 33.333 0.00 0.00 0.00 3.18
1640 1679 1.545582 TGCTAGAAATGCACCAAAGCC 59.454 47.619 0.00 0.00 35.31 4.35
1681 1720 5.935789 TGGAACGAAAGGAGTGGTAAATAAG 59.064 40.000 0.00 0.00 0.00 1.73
1850 1895 3.285484 GTTGGCATCAAGATGATCAGGT 58.715 45.455 13.93 0.00 41.20 4.00
1959 2004 3.430929 CGATTAACTGAGGGACCAGAAGG 60.431 52.174 0.00 0.00 37.59 3.46
2057 2102 1.839424 CTTTGATTGGGGACAGGGAC 58.161 55.000 0.00 0.00 44.54 4.46
2206 2251 1.961277 GTCGGTGGCTGTGACAAGG 60.961 63.158 0.00 0.00 32.91 3.61
2209 2254 2.421314 CTGTCGGTGGCTGTGACA 59.579 61.111 6.21 6.21 40.12 3.58
2262 2322 0.253044 TGCACAAGAGGGGTGATAGC 59.747 55.000 0.00 0.00 38.54 2.97
2321 2381 2.029073 CGGTCAGAAGCCGTGTGT 59.971 61.111 0.00 0.00 43.84 3.72
2326 2386 8.282576 ATGATAGACATATCGGTCAGAAGCCG 62.283 46.154 0.00 0.00 42.85 5.52
2352 3161 8.934023 TGACTAGGGAATTAAACAAGAAATGT 57.066 30.769 0.00 0.00 46.82 2.71
2527 3337 3.564225 GGTCCAAGAACTCAACGTCAATT 59.436 43.478 0.00 0.00 0.00 2.32
2590 3400 0.253044 TTGAAGCTGATTCGAGGGGG 59.747 55.000 0.82 0.00 41.14 5.40
2645 3455 6.493458 AGTTTATATGCCATGTATTTGGGGAC 59.507 38.462 0.00 0.00 37.24 4.46
2675 3485 6.916360 AGTTTATATGCCATGTATTTGGGG 57.084 37.500 0.00 0.00 37.24 4.96
2676 3486 9.077885 AGTAAGTTTATATGCCATGTATTTGGG 57.922 33.333 0.00 0.00 37.24 4.12
2686 3496 9.764363 CTCAATACTGAGTAAGTTTATATGCCA 57.236 33.333 0.00 0.00 43.64 4.92
2702 3512 8.585881 GGCATATAAACCTACTCTCAATACTGA 58.414 37.037 0.00 0.00 0.00 3.41
2703 3513 8.367911 TGGCATATAAACCTACTCTCAATACTG 58.632 37.037 0.00 0.00 0.00 2.74
2704 3514 8.492415 TGGCATATAAACCTACTCTCAATACT 57.508 34.615 0.00 0.00 0.00 2.12
2705 3515 9.155975 CATGGCATATAAACCTACTCTCAATAC 57.844 37.037 0.00 0.00 0.00 1.89
2706 3516 8.880244 ACATGGCATATAAACCTACTCTCAATA 58.120 33.333 0.00 0.00 0.00 1.90
2707 3517 7.749666 ACATGGCATATAAACCTACTCTCAAT 58.250 34.615 0.00 0.00 0.00 2.57
2708 3518 7.136822 ACATGGCATATAAACCTACTCTCAA 57.863 36.000 0.00 0.00 0.00 3.02
2709 3519 6.747414 ACATGGCATATAAACCTACTCTCA 57.253 37.500 0.00 0.00 0.00 3.27
2710 3520 9.726438 AAATACATGGCATATAAACCTACTCTC 57.274 33.333 0.00 0.00 0.00 3.20
2711 3521 9.507329 CAAATACATGGCATATAAACCTACTCT 57.493 33.333 0.00 0.00 0.00 3.24
2712 3522 8.730680 CCAAATACATGGCATATAAACCTACTC 58.269 37.037 0.00 0.00 32.78 2.59
2713 3523 7.669722 CCCAAATACATGGCATATAAACCTACT 59.330 37.037 0.00 0.00 39.26 2.57
2714 3524 7.093945 CCCCAAATACATGGCATATAAACCTAC 60.094 40.741 0.00 0.00 39.26 3.18
2715 3525 6.951198 CCCCAAATACATGGCATATAAACCTA 59.049 38.462 0.00 0.00 39.26 3.08
2716 3526 5.779771 CCCCAAATACATGGCATATAAACCT 59.220 40.000 0.00 0.00 39.26 3.50
2717 3527 5.777732 TCCCCAAATACATGGCATATAAACC 59.222 40.000 0.00 0.00 39.26 3.27
2718 3528 6.569610 CGTCCCCAAATACATGGCATATAAAC 60.570 42.308 0.00 0.00 39.26 2.01
2719 3529 5.475220 CGTCCCCAAATACATGGCATATAAA 59.525 40.000 0.00 0.00 39.26 1.40
2720 3530 5.007034 CGTCCCCAAATACATGGCATATAA 58.993 41.667 0.00 0.00 39.26 0.98
2721 3531 4.566697 CCGTCCCCAAATACATGGCATATA 60.567 45.833 0.00 0.00 39.26 0.86
2722 3532 3.420893 CGTCCCCAAATACATGGCATAT 58.579 45.455 0.00 0.00 39.26 1.78
2723 3533 2.488167 CCGTCCCCAAATACATGGCATA 60.488 50.000 0.00 0.00 39.26 3.14
2724 3534 1.691196 CGTCCCCAAATACATGGCAT 58.309 50.000 0.00 0.00 39.26 4.40
2725 3535 0.395036 CCGTCCCCAAATACATGGCA 60.395 55.000 0.00 0.00 39.26 4.92
2739 3549 8.858094 CCTATAAAATATATACTCCCTCCGTCC 58.142 40.741 0.00 0.00 0.00 4.79
2780 3590 8.383175 ACATTTTAGAAAATCCTGACAGAGGTA 58.617 33.333 3.32 0.00 43.37 3.08
2826 3636 1.799181 CGATTCAGTACCCTGTCAGCG 60.799 57.143 0.00 0.00 39.82 5.18
2918 3728 2.181777 GACTCCGTGAGCATGCGA 59.818 61.111 13.01 1.73 32.04 5.10
2948 3758 1.134371 TCCGTTGTGTTGATGGTCACA 60.134 47.619 0.00 0.00 41.81 3.58
3033 3843 1.827969 CTTCTCCTTGAGGTCGTGGAT 59.172 52.381 0.00 0.00 36.34 3.41
3054 3864 2.667137 GATGTCGATCGTGGAGGATTC 58.333 52.381 15.94 0.00 0.00 2.52
3055 3865 1.001268 CGATGTCGATCGTGGAGGATT 60.001 52.381 15.94 0.00 45.43 3.01
3077 3887 2.436539 CGACTCCACGCACATGTCG 61.437 63.158 13.71 13.71 43.03 4.35
3104 3914 2.033194 GTACACGAACCCCAGCAGC 61.033 63.158 0.00 0.00 0.00 5.25
3314 4125 0.935831 CGAACACGAACAGGTACGCA 60.936 55.000 0.00 0.00 0.00 5.24
3326 4137 1.399440 TCGTAGATCTTCCCGAACACG 59.601 52.381 0.00 1.90 0.00 4.49
3350 4161 3.209812 CCGCTGATCTCGTCCCGA 61.210 66.667 0.00 0.00 0.00 5.14
3416 4227 1.301244 CTTCCACACGCTGAGCACT 60.301 57.895 4.88 0.00 0.00 4.40
3490 4307 2.656947 TCTTTCCACCCTTTCCAGTG 57.343 50.000 0.00 0.00 0.00 3.66
3500 4317 2.525105 TTGGGGCTATTCTTTCCACC 57.475 50.000 0.00 0.00 0.00 4.61
3579 4419 6.668541 TGTAAATTCTCAGAAGCACTATGC 57.331 37.500 0.00 0.00 45.46 3.14
3603 4448 6.034898 GGTTCACATTTGCATAATTACAGTGC 59.965 38.462 3.10 3.10 39.26 4.40
3606 4451 5.229887 GCGGTTCACATTTGCATAATTACAG 59.770 40.000 0.00 0.00 0.00 2.74
3626 4471 4.016706 GCCCACACCAGTAGCGGT 62.017 66.667 0.00 0.00 41.07 5.68
3627 4472 3.706373 AGCCCACACCAGTAGCGG 61.706 66.667 0.00 0.00 32.91 5.52
3644 4489 4.590918 TCACAAACTTCTTTACACACCCA 58.409 39.130 0.00 0.00 0.00 4.51
3672 4528 5.066505 AGGTACCGTTAATTAGACTACACCG 59.933 44.000 6.18 0.00 0.00 4.94
3679 4535 6.592994 AGAGCAAAAGGTACCGTTAATTAGAC 59.407 38.462 13.75 2.98 0.00 2.59
3681 4537 6.370718 ACAGAGCAAAAGGTACCGTTAATTAG 59.629 38.462 13.75 5.59 0.00 1.73
3682 4538 6.232692 ACAGAGCAAAAGGTACCGTTAATTA 58.767 36.000 13.75 0.00 0.00 1.40
3684 4540 4.648651 ACAGAGCAAAAGGTACCGTTAAT 58.351 39.130 13.75 2.88 0.00 1.40
3685 4541 4.075963 ACAGAGCAAAAGGTACCGTTAA 57.924 40.909 13.75 0.00 0.00 2.01
3686 4542 3.756933 ACAGAGCAAAAGGTACCGTTA 57.243 42.857 13.75 0.00 0.00 3.18
3687 4543 2.616842 CAACAGAGCAAAAGGTACCGTT 59.383 45.455 7.32 7.32 0.00 4.44
3689 4545 2.218603 ACAACAGAGCAAAAGGTACCG 58.781 47.619 6.18 0.00 0.00 4.02
3690 4546 2.552743 GGACAACAGAGCAAAAGGTACC 59.447 50.000 2.73 2.73 0.00 3.34
3691 4547 3.251004 CAGGACAACAGAGCAAAAGGTAC 59.749 47.826 0.00 0.00 0.00 3.34
3696 4552 1.761449 TGCAGGACAACAGAGCAAAA 58.239 45.000 0.00 0.00 31.42 2.44
3712 4568 1.067295 AGGGTTCAGGACTTCATGCA 58.933 50.000 0.00 0.00 0.00 3.96
3720 4576 1.302832 CTGCACCAGGGTTCAGGAC 60.303 63.158 9.86 0.00 36.11 3.85
3735 4591 6.003234 AGATGAGTCACATATACGTACTGC 57.997 41.667 0.00 0.00 39.56 4.40
3736 4592 8.535690 TCTAGATGAGTCACATATACGTACTG 57.464 38.462 0.00 1.03 39.56 2.74
3737 4593 9.727859 AATCTAGATGAGTCACATATACGTACT 57.272 33.333 5.86 0.00 39.56 2.73
3738 4594 9.762062 CAATCTAGATGAGTCACATATACGTAC 57.238 37.037 5.86 0.00 39.56 3.67
3739 4595 8.947115 CCAATCTAGATGAGTCACATATACGTA 58.053 37.037 5.86 0.00 39.56 3.57
3792 4649 3.541950 GAGCAGACCAGGCACAGCA 62.542 63.158 4.85 0.00 0.00 4.41
3793 4650 1.892819 TAGAGCAGACCAGGCACAGC 61.893 60.000 0.00 0.00 0.00 4.40
3824 4681 1.139095 GCGCGCCTTGTCTACTACT 59.861 57.895 23.24 0.00 0.00 2.57
3900 4876 6.130298 ACAACTCGAATTTTGTCAATGTGA 57.870 33.333 1.80 0.00 29.75 3.58
3930 4906 9.819267 CGGAGGGATTACTATATAATTTCCTTC 57.181 37.037 0.00 0.00 0.00 3.46
3989 5080 9.674824 GAGCGTTTATAGATAACTAAAGTAGCA 57.325 33.333 0.00 0.00 32.04 3.49
3990 5081 9.896263 AGAGCGTTTATAGATAACTAAAGTAGC 57.104 33.333 0.00 0.00 32.04 3.58
4023 5114 3.564053 ACTCCCTCCGTAAACAAAACA 57.436 42.857 0.00 0.00 0.00 2.83
4024 5115 3.434641 GCTACTCCCTCCGTAAACAAAAC 59.565 47.826 0.00 0.00 0.00 2.43
4025 5116 3.667360 GCTACTCCCTCCGTAAACAAAA 58.333 45.455 0.00 0.00 0.00 2.44
4026 5117 2.353011 CGCTACTCCCTCCGTAAACAAA 60.353 50.000 0.00 0.00 0.00 2.83
4027 5118 1.203052 CGCTACTCCCTCCGTAAACAA 59.797 52.381 0.00 0.00 0.00 2.83
4028 5119 0.813184 CGCTACTCCCTCCGTAAACA 59.187 55.000 0.00 0.00 0.00 2.83
4046 5137 2.034558 ACATGGCAACTTGGTTTCTTCG 59.965 45.455 0.00 0.00 45.58 3.79
4054 5145 0.240945 GAACGGACATGGCAACTTGG 59.759 55.000 0.00 0.00 45.58 3.61
4112 5212 3.118454 GCAACCTTCGCTGCGCTA 61.118 61.111 18.65 6.84 0.00 4.26
4132 5232 0.111061 TTCAGTCTGGCATGGCAAGT 59.889 50.000 23.47 13.50 30.42 3.16
4142 5242 3.876274 TCCGAAGAAGATTCAGTCTGG 57.124 47.619 0.00 0.03 37.23 3.86
4186 5301 3.444618 ACCGTTTTCGCTTCGTTATTC 57.555 42.857 0.00 0.00 42.58 1.75
4188 5303 3.364267 GGAAACCGTTTTCGCTTCGTTAT 60.364 43.478 0.00 0.00 41.97 1.89
4189 5304 2.032979 GGAAACCGTTTTCGCTTCGTTA 60.033 45.455 0.00 0.00 41.97 3.18
4191 5306 0.305617 GGAAACCGTTTTCGCTTCGT 59.694 50.000 0.00 0.00 41.97 3.85
4312 5453 2.313172 GCGTCTGTGTGTCTGCCTG 61.313 63.158 0.00 0.00 0.00 4.85
4313 5454 2.029666 GCGTCTGTGTGTCTGCCT 59.970 61.111 0.00 0.00 0.00 4.75
4314 5455 3.406361 CGCGTCTGTGTGTCTGCC 61.406 66.667 0.00 0.00 0.00 4.85
4315 5456 2.742710 TACCGCGTCTGTGTGTCTGC 62.743 60.000 4.92 0.00 0.00 4.26
4336 5477 2.048127 GTCTCCCTGCGTGGTGAC 60.048 66.667 9.80 9.80 40.51 3.67
4344 5485 1.557443 CGTTCAACACGTCTCCCTGC 61.557 60.000 0.00 0.00 44.49 4.85
4345 5486 2.517598 CGTTCAACACGTCTCCCTG 58.482 57.895 0.00 0.00 44.49 4.45
4389 5813 1.269569 CGATTAGCCAGCGTGGTGATA 60.270 52.381 0.00 0.00 40.46 2.15
4418 5842 6.312180 GGCTGAAAGATGGATCAATCAAAAAC 59.688 38.462 12.74 0.47 34.07 2.43
4420 5844 5.969423 GGCTGAAAGATGGATCAATCAAAA 58.031 37.500 12.74 0.00 34.07 2.44


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

AutoCloner maintained by Alex Coulton.