Multiple sequence alignment - TraesCS2D01G258300

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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 TraesCS2D01G258300 chr2D 100.000 3302 0 0 1 3302 314343362 314340061 0.000000e+00 6098.0
1 TraesCS2D01G258300 chr2D 93.157 833 14 6 1 793 206634714 206633885 0.000000e+00 1182.0
2 TraesCS2D01G258300 chr2D 92.206 834 16 8 1 794 528420622 528419798 0.000000e+00 1134.0
3 TraesCS2D01G258300 chr2D 96.648 179 4 2 616 793 206634939 206635116 2.490000e-76 296.0
4 TraesCS2D01G258300 chr2A 92.440 1746 96 17 794 2530 421221133 421222851 0.000000e+00 2460.0
5 TraesCS2D01G258300 chr2A 88.816 456 39 6 2848 3302 421224159 421224603 1.730000e-152 549.0
6 TraesCS2D01G258300 chr2A 92.708 96 7 0 2640 2735 421224009 421224104 4.440000e-29 139.0
7 TraesCS2D01G258300 chr2B 96.925 813 19 2 1427 2239 382582250 382581444 0.000000e+00 1358.0
8 TraesCS2D01G258300 chr2B 89.474 608 41 12 794 1399 382582832 382582246 0.000000e+00 747.0
9 TraesCS2D01G258300 chr2B 94.521 438 17 2 2867 3302 382509345 382508913 0.000000e+00 669.0
10 TraesCS2D01G258300 chr2B 94.292 438 24 1 2445 2881 382562654 382562217 0.000000e+00 669.0
11 TraesCS2D01G258300 chr3D 94.118 833 9 6 1 793 30697086 30696254 0.000000e+00 1230.0
12 TraesCS2D01G258300 chr3D 77.123 424 78 13 1519 1928 383593863 383593445 9.220000e-56 228.0
13 TraesCS2D01G258300 chr3D 88.889 180 10 2 625 794 609964885 609964706 2.580000e-51 213.0
14 TraesCS2D01G258300 chr4D 93.252 815 32 6 1 793 349001635 349002448 0.000000e+00 1179.0
15 TraesCS2D01G258300 chr4D 91.146 192 8 7 616 801 349001409 349001221 5.470000e-63 252.0
16 TraesCS2D01G258300 chr7B 93.284 819 20 7 1 796 58246067 58246873 0.000000e+00 1175.0
17 TraesCS2D01G258300 chr7B 74.696 411 76 17 2878 3261 321109290 321108881 1.230000e-34 158.0
18 TraesCS2D01G258300 chr7B 79.518 166 30 3 3129 3294 706714891 706715052 7.490000e-22 115.0
19 TraesCS2D01G258300 chr7B 84.211 114 18 0 3129 3242 706643872 706643985 9.690000e-21 111.0
20 TraesCS2D01G258300 chr7D 92.883 815 35 6 1 793 436472808 436473621 0.000000e+00 1162.0
21 TraesCS2D01G258300 chr7D 89.385 179 9 2 625 793 94461797 94461975 2.000000e-52 217.0
22 TraesCS2D01G258300 chr7D 89.011 182 10 2 625 796 105674210 105674029 2.000000e-52 217.0
23 TraesCS2D01G258300 chr1D 92.092 822 43 7 1 800 7758574 7759395 0.000000e+00 1138.0
24 TraesCS2D01G258300 chr1D 91.837 833 28 10 1 793 29138035 29137203 0.000000e+00 1125.0
25 TraesCS2D01G258300 chr1D 89.385 179 8 3 625 793 261725292 261725115 7.180000e-52 215.0
26 TraesCS2D01G258300 chr4B 90.681 837 25 13 1 797 483516525 483517348 0.000000e+00 1064.0
27 TraesCS2D01G258300 chr5D 90.675 815 29 13 1 793 414015185 414015974 0.000000e+00 1040.0
28 TraesCS2D01G258300 chr5D 81.759 307 56 0 1519 1825 495779093 495779399 1.180000e-64 257.0
29 TraesCS2D01G258300 chr5D 82.746 284 43 4 2758 3039 352982500 352982779 7.080000e-62 248.0
30 TraesCS2D01G258300 chr5B 96.012 326 12 1 179 504 528512354 528512030 2.260000e-146 529.0
31 TraesCS2D01G258300 chr5B 83.721 129 19 2 3129 3256 526571229 526571102 1.610000e-23 121.0
32 TraesCS2D01G258300 chr5A 81.818 308 54 2 1519 1825 619724757 619725063 1.180000e-64 257.0
33 TraesCS2D01G258300 chr3B 77.594 424 76 14 1519 1928 499190063 499189645 4.260000e-59 239.0
34 TraesCS2D01G258300 chr3B 81.609 174 29 1 3129 3302 727165189 727165019 1.240000e-29 141.0
35 TraesCS2D01G258300 chr3B 83.065 124 12 6 2499 2620 423863640 423863524 1.620000e-18 104.0
36 TraesCS2D01G258300 chr3B 93.182 44 3 0 2539 2582 30006963 30007006 7.650000e-07 65.8
37 TraesCS2D01G258300 chr6D 89.385 179 9 2 625 793 17361281 17361459 2.000000e-52 217.0
38 TraesCS2D01G258300 chr6D 88.889 180 10 2 625 794 17866931 17866752 2.580000e-51 213.0
39 TraesCS2D01G258300 chr6B 75.271 461 82 17 2867 3302 145901477 145901930 1.210000e-44 191.0
40 TraesCS2D01G258300 chr3A 84.746 177 27 0 1546 1722 506467550 506467374 9.420000e-41 178.0
41 TraesCS2D01G258300 chr3A 96.970 33 0 1 2379 2411 157021523 157021492 2.000000e-03 54.7
42 TraesCS2D01G258300 chr7A 73.902 410 80 14 2870 3253 403358589 403358997 4.440000e-29 139.0


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 TraesCS2D01G258300 chr2D 314340061 314343362 3301 True 6098.000000 6098 100.000000 1 3302 1 chr2D.!!$R2 3301
1 TraesCS2D01G258300 chr2D 206633885 206634714 829 True 1182.000000 1182 93.157000 1 793 1 chr2D.!!$R1 792
2 TraesCS2D01G258300 chr2D 528419798 528420622 824 True 1134.000000 1134 92.206000 1 794 1 chr2D.!!$R3 793
3 TraesCS2D01G258300 chr2A 421221133 421224603 3470 False 1049.333333 2460 91.321333 794 3302 3 chr2A.!!$F1 2508
4 TraesCS2D01G258300 chr2B 382581444 382582832 1388 True 1052.500000 1358 93.199500 794 2239 2 chr2B.!!$R3 1445
5 TraesCS2D01G258300 chr3D 30696254 30697086 832 True 1230.000000 1230 94.118000 1 793 1 chr3D.!!$R1 792
6 TraesCS2D01G258300 chr4D 349001635 349002448 813 False 1179.000000 1179 93.252000 1 793 1 chr4D.!!$F1 792
7 TraesCS2D01G258300 chr7B 58246067 58246873 806 False 1175.000000 1175 93.284000 1 796 1 chr7B.!!$F1 795
8 TraesCS2D01G258300 chr7D 436472808 436473621 813 False 1162.000000 1162 92.883000 1 793 1 chr7D.!!$F2 792
9 TraesCS2D01G258300 chr1D 7758574 7759395 821 False 1138.000000 1138 92.092000 1 800 1 chr1D.!!$F1 799
10 TraesCS2D01G258300 chr1D 29137203 29138035 832 True 1125.000000 1125 91.837000 1 793 1 chr1D.!!$R1 792
11 TraesCS2D01G258300 chr4B 483516525 483517348 823 False 1064.000000 1064 90.681000 1 797 1 chr4B.!!$F1 796
12 TraesCS2D01G258300 chr5D 414015185 414015974 789 False 1040.000000 1040 90.675000 1 793 1 chr5D.!!$F2 792

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
721 783 3.753774 CGCAAGACGTGATGCTTTT 57.246 47.368 17.19 0.0 40.39 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2347 2433 0.325296 TGGGGCGAAGTGAGGAGTAT 60.325 55.0 0.0 0.0 0.0 2.12 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
721 783 3.753774 CGCAAGACGTGATGCTTTT 57.246 47.368 17.19 0.00 40.39 2.27
756 818 6.430000 ACTGTATCCTAGTGTTTTTCGCAAAT 59.570 34.615 0.00 0.00 0.00 2.32
923 985 7.301420 AGTCCCGATCCATCATCATATATACT 58.699 38.462 0.00 0.00 0.00 2.12
1196 1258 4.753186 TCTTCTTTCCTAGTCCCACTTCT 58.247 43.478 0.00 0.00 0.00 2.85
1237 1320 2.419198 CCGGGAGCGAGATTCCAG 59.581 66.667 0.00 0.00 36.40 3.86
1250 1333 1.351017 GATTCCAGTTCAGACCCACCA 59.649 52.381 0.00 0.00 0.00 4.17
1252 1335 0.105194 TCCAGTTCAGACCCACCAGA 60.105 55.000 0.00 0.00 0.00 3.86
1260 1343 1.276421 CAGACCCACCAGAACCTACTG 59.724 57.143 0.00 0.00 37.61 2.74
1262 1345 1.002087 GACCCACCAGAACCTACTGTG 59.998 57.143 0.00 0.00 36.30 3.66
1272 1355 0.251474 ACCTACTGTGCCAGACGGTA 60.251 55.000 8.91 2.22 42.84 4.02
1277 1360 0.033504 CTGTGCCAGACGGTAACAGT 59.966 55.000 7.78 0.00 41.02 3.55
1282 1365 2.489329 TGCCAGACGGTAACAGTAGTAC 59.511 50.000 0.00 0.00 33.28 2.73
1287 1370 2.154462 ACGGTAACAGTAGTACGCACT 58.846 47.619 0.00 0.00 38.91 4.40
1290 1373 3.372206 CGGTAACAGTAGTACGCACTAGT 59.628 47.826 0.00 0.00 40.84 2.57
1329 1412 4.988598 ACGCCCCGACAGCACAAG 62.989 66.667 0.00 0.00 0.00 3.16
1422 1505 0.903454 ACGTGGGAACGGAGGAAGAT 60.903 55.000 3.09 0.00 37.45 2.40
1459 1545 5.181056 GCCAAGAAGAAGAAGAAGAAGAAGG 59.819 44.000 0.00 0.00 0.00 3.46
1460 1546 6.529220 CCAAGAAGAAGAAGAAGAAGAAGGA 58.471 40.000 0.00 0.00 0.00 3.36
1462 1548 6.358974 AGAAGAAGAAGAAGAAGAAGGAGG 57.641 41.667 0.00 0.00 0.00 4.30
1464 1550 5.738619 AGAAGAAGAAGAAGAAGGAGGAC 57.261 43.478 0.00 0.00 0.00 3.85
1469 1555 3.440127 AGAAGAAGAAGGAGGACAGGAG 58.560 50.000 0.00 0.00 0.00 3.69
1736 1822 3.019003 ATGAGTGGAAGGACGGCCG 62.019 63.158 26.86 26.86 39.96 6.13
1959 2045 2.785921 CGGAGACTCGACGGACTG 59.214 66.667 0.00 0.00 0.00 3.51
2025 2111 3.716006 CAGCACCACGACGCAAGG 61.716 66.667 0.00 0.00 46.39 3.61
2252 2338 4.564821 CCTCCGTTCCAAAACAGATCCTTA 60.565 45.833 0.00 0.00 34.93 2.69
2280 2366 6.940298 TGTTAGGACAAGATTTTGACCCTAAG 59.060 38.462 22.26 0.00 46.20 2.18
2287 2373 8.392372 ACAAGATTTTGACCCTAAGTTTACTC 57.608 34.615 2.48 0.00 37.73 2.59
2330 2416 5.221263 CCGTACCTTGCTACAGATTATGAGT 60.221 44.000 0.00 0.00 0.00 3.41
2331 2417 6.016527 CCGTACCTTGCTACAGATTATGAGTA 60.017 42.308 0.00 0.00 0.00 2.59
2332 2418 7.078851 CGTACCTTGCTACAGATTATGAGTAG 58.921 42.308 0.00 0.00 38.54 2.57
2333 2419 7.255173 CGTACCTTGCTACAGATTATGAGTAGT 60.255 40.741 0.00 0.00 37.97 2.73
2336 2422 8.978472 ACCTTGCTACAGATTATGAGTAGTAAA 58.022 33.333 0.00 0.00 39.03 2.01
2362 2448 7.427214 AGAAATACTTATACTCCTCACTTCGC 58.573 38.462 0.00 0.00 0.00 4.70
2368 2454 0.325296 ACTCCTCACTTCGCCCCATA 60.325 55.000 0.00 0.00 0.00 2.74
2388 2474 8.076178 CCCCATAATATAAGAGCTTGAAAAACG 58.924 37.037 0.00 0.00 0.00 3.60
2454 2540 6.725101 ATATATGGGGTGGAATGAGTCAAT 57.275 37.500 0.00 0.00 0.00 2.57
2456 2542 3.541242 TGGGGTGGAATGAGTCAATTT 57.459 42.857 0.00 0.00 0.00 1.82
2457 2543 3.430453 TGGGGTGGAATGAGTCAATTTC 58.570 45.455 0.00 0.00 0.00 2.17
2466 2552 9.696917 GTGGAATGAGTCAATTTCTTTTATGTT 57.303 29.630 0.00 0.00 0.00 2.71
2518 2606 9.262358 CTAGTTCTTGGAGGCATACTTTTATAC 57.738 37.037 0.00 0.00 0.00 1.47
2519 2607 7.862675 AGTTCTTGGAGGCATACTTTTATACT 58.137 34.615 0.00 0.00 0.00 2.12
2520 2608 7.988028 AGTTCTTGGAGGCATACTTTTATACTC 59.012 37.037 0.00 0.00 0.00 2.59
2526 3663 9.209048 TGGAGGCATACTTTTATACTCTAGAAA 57.791 33.333 0.00 0.00 0.00 2.52
2550 3687 0.830444 TCTAAGCACCACGGGTCACT 60.830 55.000 0.00 0.00 31.02 3.41
2564 3701 1.954528 TCACTCCGTGACTCGAACC 59.045 57.895 0.00 0.00 37.67 3.62
2565 3702 0.536687 TCACTCCGTGACTCGAACCT 60.537 55.000 0.00 0.00 37.67 3.50
2566 3703 0.387367 CACTCCGTGACTCGAACCTG 60.387 60.000 0.00 0.00 42.86 4.00
2568 3705 0.169230 CTCCGTGACTCGAACCTGAG 59.831 60.000 0.00 0.00 42.86 3.35
2580 3717 4.130857 TCGAACCTGAGTGAGCTAGATAG 58.869 47.826 0.00 0.00 0.00 2.08
2594 3731 5.883503 GCTAGATAGCTACGTGTTATCCT 57.116 43.478 0.00 0.00 45.62 3.24
2597 3734 7.242783 GCTAGATAGCTACGTGTTATCCTAAC 58.757 42.308 0.00 0.00 45.62 2.34
2603 3740 6.746120 AGCTACGTGTTATCCTAACCAATAG 58.254 40.000 0.00 0.00 0.00 1.73
2622 3759 6.183361 CCAATAGGGTGACATCATGTTCTCTA 60.183 42.308 0.00 0.00 0.00 2.43
2624 3761 3.452627 AGGGTGACATCATGTTCTCTACC 59.547 47.826 0.00 0.00 0.00 3.18
2628 3765 3.118629 TGACATCATGTTCTCTACCTGGC 60.119 47.826 0.00 0.00 0.00 4.85
2635 3772 2.950309 TGTTCTCTACCTGGCGATCTAC 59.050 50.000 0.00 0.00 0.00 2.59
2636 3773 2.273538 TCTCTACCTGGCGATCTACC 57.726 55.000 0.00 0.00 0.00 3.18
2641 3789 0.968901 ACCTGGCGATCTACCGTTCA 60.969 55.000 0.00 0.00 0.00 3.18
2647 3795 2.292569 GGCGATCTACCGTTCATCAGTA 59.707 50.000 0.00 0.00 0.00 2.74
2667 3815 1.351017 ACACATTGATCCAACCCTCGT 59.649 47.619 0.00 0.00 0.00 4.18
2696 3844 5.364778 TCATTGTACAAGGCGCTACAATAT 58.635 37.500 24.00 9.11 40.19 1.28
2704 3852 5.466728 ACAAGGCGCTACAATATAATGACTG 59.533 40.000 7.64 0.00 0.00 3.51
2705 3853 3.997021 AGGCGCTACAATATAATGACTGC 59.003 43.478 7.64 0.00 0.00 4.40
2710 3858 3.140325 ACAATATAATGACTGCCCGGG 57.860 47.619 19.09 19.09 0.00 5.73
2739 3887 2.131183 GAGCATCTACAACATCCGAGC 58.869 52.381 0.00 0.00 0.00 5.03
2740 3888 1.759445 AGCATCTACAACATCCGAGCT 59.241 47.619 0.00 0.00 0.00 4.09
2741 3889 2.131183 GCATCTACAACATCCGAGCTC 58.869 52.381 2.73 2.73 0.00 4.09
2742 3890 2.481969 GCATCTACAACATCCGAGCTCA 60.482 50.000 15.40 0.00 0.00 4.26
2743 3891 3.801638 GCATCTACAACATCCGAGCTCAT 60.802 47.826 15.40 0.00 0.00 2.90
2744 3892 4.559502 GCATCTACAACATCCGAGCTCATA 60.560 45.833 15.40 0.29 0.00 2.15
2745 3893 5.718146 CATCTACAACATCCGAGCTCATAT 58.282 41.667 15.40 3.06 0.00 1.78
2746 3894 6.625960 GCATCTACAACATCCGAGCTCATATA 60.626 42.308 15.40 0.00 0.00 0.86
2747 3895 7.487484 CATCTACAACATCCGAGCTCATATAT 58.513 38.462 15.40 0.00 0.00 0.86
2748 3896 6.856895 TCTACAACATCCGAGCTCATATATG 58.143 40.000 15.40 12.77 0.00 1.78
2749 3897 5.474578 ACAACATCCGAGCTCATATATGT 57.525 39.130 15.40 13.38 0.00 2.29
2750 3898 5.473931 ACAACATCCGAGCTCATATATGTC 58.526 41.667 15.40 6.19 0.00 3.06
2751 3899 4.727507 ACATCCGAGCTCATATATGTCC 57.272 45.455 15.40 5.17 0.00 4.02
2752 3900 3.129462 ACATCCGAGCTCATATATGTCCG 59.871 47.826 15.40 10.85 0.00 4.79
2753 3901 2.791655 TCCGAGCTCATATATGTCCGT 58.208 47.619 15.40 0.00 0.00 4.69
2754 3902 2.488153 TCCGAGCTCATATATGTCCGTG 59.512 50.000 15.40 2.14 0.00 4.94
2755 3903 2.416027 CCGAGCTCATATATGTCCGTGG 60.416 54.545 15.40 7.04 0.00 4.94
2756 3904 2.488153 CGAGCTCATATATGTCCGTGGA 59.512 50.000 15.40 0.00 0.00 4.02
2757 3905 3.670895 CGAGCTCATATATGTCCGTGGAC 60.671 52.174 15.40 12.17 44.77 4.02
2766 3914 2.678580 TCCGTGGACAGCGATGGA 60.679 61.111 5.32 0.00 35.80 3.41
2782 3930 3.243877 CGATGGACACGTCATCATTTCTC 59.756 47.826 14.05 0.00 40.58 2.87
2786 3934 3.619038 GGACACGTCATCATTTCTCCTTC 59.381 47.826 0.00 0.00 0.00 3.46
2789 3937 3.868077 CACGTCATCATTTCTCCTTCTCC 59.132 47.826 0.00 0.00 0.00 3.71
2791 3939 3.868077 CGTCATCATTTCTCCTTCTCCAC 59.132 47.826 0.00 0.00 0.00 4.02
2811 3959 2.288666 CAACCACACTCCCCATATTCG 58.711 52.381 0.00 0.00 0.00 3.34
2823 3971 7.875041 CACTCCCCATATTCGAATATCCATATC 59.125 40.741 24.49 0.00 29.35 1.63
2828 3976 8.509690 CCCATATTCGAATATCCATATCAATGC 58.490 37.037 24.49 0.00 29.35 3.56
2835 3983 7.830697 TCGAATATCCATATCAATGCAAATCCT 59.169 33.333 0.00 0.00 0.00 3.24
2836 3984 8.464404 CGAATATCCATATCAATGCAAATCCTT 58.536 33.333 0.00 0.00 0.00 3.36
2837 3985 9.582431 GAATATCCATATCAATGCAAATCCTTG 57.418 33.333 0.00 0.00 35.49 3.61
2846 3994 1.892338 CAAATCCTTGCACGCCCAT 59.108 52.632 0.00 0.00 0.00 4.00
2847 3995 0.179129 CAAATCCTTGCACGCCCATC 60.179 55.000 0.00 0.00 0.00 3.51
2848 3996 0.611618 AAATCCTTGCACGCCCATCA 60.612 50.000 0.00 0.00 0.00 3.07
2849 3997 0.396139 AATCCTTGCACGCCCATCAT 60.396 50.000 0.00 0.00 0.00 2.45
2850 3998 0.473755 ATCCTTGCACGCCCATCATA 59.526 50.000 0.00 0.00 0.00 2.15
2851 3999 0.473755 TCCTTGCACGCCCATCATAT 59.526 50.000 0.00 0.00 0.00 1.78
2852 4000 1.696884 TCCTTGCACGCCCATCATATA 59.303 47.619 0.00 0.00 0.00 0.86
2853 4001 2.079158 CCTTGCACGCCCATCATATAG 58.921 52.381 0.00 0.00 0.00 1.31
2854 4002 2.550855 CCTTGCACGCCCATCATATAGT 60.551 50.000 0.00 0.00 0.00 2.12
2855 4003 2.168326 TGCACGCCCATCATATAGTG 57.832 50.000 0.00 0.00 0.00 2.74
2856 4004 1.416030 TGCACGCCCATCATATAGTGT 59.584 47.619 0.00 0.00 32.74 3.55
2857 4005 2.630580 TGCACGCCCATCATATAGTGTA 59.369 45.455 0.00 0.00 32.74 2.90
2858 4006 3.070302 TGCACGCCCATCATATAGTGTAA 59.930 43.478 0.00 0.00 32.74 2.41
2859 4007 4.062293 GCACGCCCATCATATAGTGTAAA 58.938 43.478 0.00 0.00 32.74 2.01
2860 4008 4.695455 GCACGCCCATCATATAGTGTAAAT 59.305 41.667 0.00 0.00 32.74 1.40
2861 4009 5.390885 GCACGCCCATCATATAGTGTAAATG 60.391 44.000 0.00 0.00 32.74 2.32
2862 4010 4.695455 ACGCCCATCATATAGTGTAAATGC 59.305 41.667 0.00 0.00 0.00 3.56
2863 4011 4.694982 CGCCCATCATATAGTGTAAATGCA 59.305 41.667 0.00 0.00 0.00 3.96
2864 4012 5.390885 CGCCCATCATATAGTGTAAATGCAC 60.391 44.000 0.00 0.00 39.51 4.57
2988 4136 7.482474 TGTCAATTGTTGCGATTATTGATGAT 58.518 30.769 5.13 0.00 38.73 2.45
2989 4137 7.644945 TGTCAATTGTTGCGATTATTGATGATC 59.355 33.333 5.13 0.00 38.73 2.92
2990 4138 7.859377 GTCAATTGTTGCGATTATTGATGATCT 59.141 33.333 5.13 0.00 38.73 2.75
2991 4139 8.407832 TCAATTGTTGCGATTATTGATGATCTT 58.592 29.630 5.13 0.00 33.41 2.40
3025 4173 0.514691 GCCACTTCTTGACTTCAGCG 59.485 55.000 0.00 0.00 0.00 5.18
3026 4174 0.514691 CCACTTCTTGACTTCAGCGC 59.485 55.000 0.00 0.00 0.00 5.92
3052 4200 3.455910 AGAGGTTTATGTCCTGCAGCATA 59.544 43.478 8.66 9.04 35.20 3.14
3066 4214 2.609244 GCAGCATAATCCTCGACTCCTC 60.609 54.545 0.00 0.00 0.00 3.71
3070 4218 1.964552 TAATCCTCGACTCCTCCGTC 58.035 55.000 0.00 0.00 0.00 4.79
3076 4224 0.176219 TCGACTCCTCCGTCTCTCTC 59.824 60.000 0.00 0.00 0.00 3.20
3091 4239 3.057876 TCTCTCTCGCAAGTCTCAACTTC 60.058 47.826 0.00 0.00 43.99 3.01
3125 4273 4.305989 TCAAATTCCTTGCATTATCGCC 57.694 40.909 0.00 0.00 34.76 5.54
3127 4275 1.967319 ATTCCTTGCATTATCGCCGT 58.033 45.000 0.00 0.00 0.00 5.68
3141 4289 1.355066 CGCCGTTTCTCTTGCCTCTC 61.355 60.000 0.00 0.00 0.00 3.20
3179 4327 2.050144 TCTTCAAGTGCAACCTCTCCT 58.950 47.619 0.00 0.00 37.80 3.69
3180 4328 3.239449 TCTTCAAGTGCAACCTCTCCTA 58.761 45.455 0.00 0.00 37.80 2.94
3182 4330 2.609747 TCAAGTGCAACCTCTCCTAGT 58.390 47.619 0.00 0.00 37.80 2.57
3183 4331 2.300152 TCAAGTGCAACCTCTCCTAGTG 59.700 50.000 0.00 0.00 37.80 2.74
3230 4378 7.066284 GCACATCTATGAACATCTTGTACCTTT 59.934 37.037 0.00 0.00 0.00 3.11
3231 4379 8.607459 CACATCTATGAACATCTTGTACCTTTC 58.393 37.037 0.00 0.00 0.00 2.62
3232 4380 7.770897 ACATCTATGAACATCTTGTACCTTTCC 59.229 37.037 0.00 0.00 0.00 3.13
3252 4400 2.421248 CCTCCTCCTTCATCTTCTTGGC 60.421 54.545 0.00 0.00 0.00 4.52
3253 4401 1.561542 TCCTCCTTCATCTTCTTGGCC 59.438 52.381 0.00 0.00 0.00 5.36
3258 4406 4.222336 TCCTTCATCTTCTTGGCCAAAAA 58.778 39.130 20.91 12.43 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1125 1187 2.019156 GCCCTCTTCTTTAGCGGCAAT 61.019 52.381 1.45 0.00 38.32 3.56
1208 1270 2.364579 TCCCGGCATCTACCCGTT 60.365 61.111 0.00 0.00 44.13 4.44
1237 1320 0.765510 AGGTTCTGGTGGGTCTGAAC 59.234 55.000 0.00 0.00 41.65 3.18
1260 1343 1.271656 ACTACTGTTACCGTCTGGCAC 59.728 52.381 0.00 0.00 39.70 5.01
1262 1345 2.476854 CGTACTACTGTTACCGTCTGGC 60.477 54.545 0.00 0.00 39.70 4.85
1287 1370 0.319211 CGTTGGGACTGAACGCACTA 60.319 55.000 0.00 0.00 39.71 2.74
1295 1378 3.228017 TGGTCGCGTTGGGACTGA 61.228 61.111 5.77 0.00 43.54 3.41
1401 1484 0.108945 CTTCCTCCGTTCCCACGTAC 60.109 60.000 0.00 0.00 45.62 3.67
1408 1491 1.202313 CGTCTCATCTTCCTCCGTTCC 60.202 57.143 0.00 0.00 0.00 3.62
1409 1492 1.202313 CCGTCTCATCTTCCTCCGTTC 60.202 57.143 0.00 0.00 0.00 3.95
1410 1493 0.818296 CCGTCTCATCTTCCTCCGTT 59.182 55.000 0.00 0.00 0.00 4.44
1412 1495 1.066587 GCCGTCTCATCTTCCTCCG 59.933 63.158 0.00 0.00 0.00 4.63
1459 1545 1.743321 CGATCCCTGCTCCTGTCCTC 61.743 65.000 0.00 0.00 0.00 3.71
1460 1546 1.760086 CGATCCCTGCTCCTGTCCT 60.760 63.158 0.00 0.00 0.00 3.85
1462 1548 0.537188 TTTCGATCCCTGCTCCTGTC 59.463 55.000 0.00 0.00 0.00 3.51
1464 1550 0.826715 TCTTTCGATCCCTGCTCCTG 59.173 55.000 0.00 0.00 0.00 3.86
1469 1555 3.001736 CGATTTCTTCTTTCGATCCCTGC 59.998 47.826 0.00 0.00 34.92 4.85
2287 2373 7.607223 AGGTACGGTCATTTAGCTAGTAGATAG 59.393 40.741 0.00 0.00 34.31 2.08
2305 2391 4.647853 TCATAATCTGTAGCAAGGTACGGT 59.352 41.667 15.50 3.26 32.01 4.83
2336 2422 7.921745 GCGAAGTGAGGAGTATAAGTATTTCTT 59.078 37.037 0.00 0.00 39.89 2.52
2347 2433 0.325296 TGGGGCGAAGTGAGGAGTAT 60.325 55.000 0.00 0.00 0.00 2.12
2348 2434 0.325296 ATGGGGCGAAGTGAGGAGTA 60.325 55.000 0.00 0.00 0.00 2.59
2349 2435 0.325296 TATGGGGCGAAGTGAGGAGT 60.325 55.000 0.00 0.00 0.00 3.85
2350 2436 0.830648 TTATGGGGCGAAGTGAGGAG 59.169 55.000 0.00 0.00 0.00 3.69
2351 2437 1.507140 ATTATGGGGCGAAGTGAGGA 58.493 50.000 0.00 0.00 0.00 3.71
2353 2439 6.037786 TCTTATATTATGGGGCGAAGTGAG 57.962 41.667 0.00 0.00 0.00 3.51
2354 2440 5.568825 GCTCTTATATTATGGGGCGAAGTGA 60.569 44.000 0.00 0.00 0.00 3.41
2355 2441 4.631813 GCTCTTATATTATGGGGCGAAGTG 59.368 45.833 0.00 0.00 0.00 3.16
2356 2442 4.532521 AGCTCTTATATTATGGGGCGAAGT 59.467 41.667 0.00 0.00 0.00 3.01
2362 2448 8.076178 CGTTTTTCAAGCTCTTATATTATGGGG 58.924 37.037 0.00 0.00 0.00 4.96
2420 2506 6.744822 TCCACCCCATATATACGGTACTTAT 58.255 40.000 3.22 0.00 0.00 1.73
2427 2513 4.469945 ACTCATTCCACCCCATATATACGG 59.530 45.833 0.00 0.00 0.00 4.02
2428 2514 5.186992 TGACTCATTCCACCCCATATATACG 59.813 44.000 0.00 0.00 0.00 3.06
2438 2524 5.728637 AAAGAAATTGACTCATTCCACCC 57.271 39.130 0.00 0.00 0.00 4.61
2440 2526 9.696917 AACATAAAAGAAATTGACTCATTCCAC 57.303 29.630 0.00 0.00 0.00 4.02
2487 2573 1.902508 TGCCTCCAAGAACTAGTCCTG 59.097 52.381 0.00 0.00 0.00 3.86
2489 2575 3.707102 AGTATGCCTCCAAGAACTAGTCC 59.293 47.826 0.00 0.00 0.00 3.85
2526 3663 1.142262 ACCCGTGGTGCTTAGAGTTTT 59.858 47.619 0.00 0.00 32.98 2.43
2550 3687 0.536687 ACTCAGGTTCGAGTCACGGA 60.537 55.000 0.00 0.00 42.70 4.69
2553 3690 1.667467 GCTCACTCAGGTTCGAGTCAC 60.667 57.143 0.00 0.00 44.49 3.67
2573 3710 7.389884 TGGTTAGGATAACACGTAGCTATCTAG 59.610 40.741 0.00 0.00 0.00 2.43
2597 3734 4.785301 AGAACATGATGTCACCCTATTGG 58.215 43.478 0.00 0.00 41.37 3.16
2603 3740 3.452627 AGGTAGAGAACATGATGTCACCC 59.547 47.826 0.00 0.00 0.00 4.61
2611 3748 1.847328 TCGCCAGGTAGAGAACATGA 58.153 50.000 0.00 0.00 42.55 3.07
2613 3750 2.672098 AGATCGCCAGGTAGAGAACAT 58.328 47.619 0.00 0.00 0.00 2.71
2615 3752 2.293955 GGTAGATCGCCAGGTAGAGAAC 59.706 54.545 4.76 0.00 0.00 3.01
2622 3759 0.968901 TGAACGGTAGATCGCCAGGT 60.969 55.000 9.47 2.06 0.00 4.00
2624 3761 1.067060 TGATGAACGGTAGATCGCCAG 59.933 52.381 9.47 5.37 0.00 4.85
2628 3765 4.201881 TGTGTACTGATGAACGGTAGATCG 60.202 45.833 0.00 0.00 40.49 3.69
2635 3772 4.271049 GGATCAATGTGTACTGATGAACGG 59.729 45.833 0.41 0.00 32.40 4.44
2636 3773 4.869861 TGGATCAATGTGTACTGATGAACG 59.130 41.667 0.41 0.00 32.40 3.95
2641 3789 4.228210 AGGGTTGGATCAATGTGTACTGAT 59.772 41.667 0.00 0.00 34.96 2.90
2647 3795 1.351017 ACGAGGGTTGGATCAATGTGT 59.649 47.619 0.00 0.00 0.00 3.72
2667 3815 1.675714 CGCCTTGTACAATGAGCCTCA 60.676 52.381 14.26 0.00 0.00 3.86
2696 3844 2.607568 TTGGCCCGGGCAGTCATTA 61.608 57.895 44.46 18.32 44.11 1.90
2704 3852 2.124695 CTCTAAGTTGGCCCGGGC 60.125 66.667 38.57 38.57 41.06 6.13
2705 3853 2.124695 GCTCTAAGTTGGCCCGGG 60.125 66.667 19.09 19.09 0.00 5.73
2710 3858 4.253685 TGTTGTAGATGCTCTAAGTTGGC 58.746 43.478 0.00 0.00 29.58 4.52
2735 3883 2.488153 TCCACGGACATATATGAGCTCG 59.512 50.000 19.63 16.56 0.00 5.03
2736 3884 3.839293 GTCCACGGACATATATGAGCTC 58.161 50.000 19.63 6.82 44.02 4.09
2737 3885 3.944055 GTCCACGGACATATATGAGCT 57.056 47.619 19.63 0.00 44.02 4.09
2748 3896 2.509336 CCATCGCTGTCCACGGAC 60.509 66.667 9.38 9.38 44.77 4.79
2749 3897 2.678580 TCCATCGCTGTCCACGGA 60.679 61.111 0.00 0.00 0.00 4.69
2750 3898 2.509336 GTCCATCGCTGTCCACGG 60.509 66.667 0.00 0.00 0.00 4.94
2751 3899 2.094659 GTGTCCATCGCTGTCCACG 61.095 63.158 0.00 0.00 0.00 4.94
2752 3900 2.094659 CGTGTCCATCGCTGTCCAC 61.095 63.158 0.00 0.00 0.00 4.02
2753 3901 2.261361 CGTGTCCATCGCTGTCCA 59.739 61.111 0.00 0.00 0.00 4.02
2754 3902 1.805945 GACGTGTCCATCGCTGTCC 60.806 63.158 0.00 0.00 0.00 4.02
2755 3903 0.458543 ATGACGTGTCCATCGCTGTC 60.459 55.000 0.00 0.00 33.90 3.51
2756 3904 0.458543 GATGACGTGTCCATCGCTGT 60.459 55.000 0.00 0.00 32.23 4.40
2757 3905 0.458370 TGATGACGTGTCCATCGCTG 60.458 55.000 10.17 0.00 42.37 5.18
2758 3906 0.461548 ATGATGACGTGTCCATCGCT 59.538 50.000 10.17 0.00 42.37 4.93
2759 3907 1.290203 AATGATGACGTGTCCATCGC 58.710 50.000 10.17 0.00 42.37 4.58
2760 3908 3.190079 AGAAATGATGACGTGTCCATCG 58.810 45.455 10.17 0.00 42.37 3.84
2761 3909 3.557595 GGAGAAATGATGACGTGTCCATC 59.442 47.826 8.40 8.40 40.48 3.51
2762 3910 3.198635 AGGAGAAATGATGACGTGTCCAT 59.801 43.478 0.00 0.00 0.00 3.41
2763 3911 2.567169 AGGAGAAATGATGACGTGTCCA 59.433 45.455 0.00 0.00 0.00 4.02
2766 3914 4.499183 GAGAAGGAGAAATGATGACGTGT 58.501 43.478 0.00 0.00 0.00 4.49
2782 3930 1.543429 GGAGTGTGGTTGTGGAGAAGG 60.543 57.143 0.00 0.00 0.00 3.46
2786 3934 1.073199 GGGGAGTGTGGTTGTGGAG 59.927 63.158 0.00 0.00 0.00 3.86
2789 3937 2.806945 ATATGGGGAGTGTGGTTGTG 57.193 50.000 0.00 0.00 0.00 3.33
2791 3939 2.093181 TCGAATATGGGGAGTGTGGTTG 60.093 50.000 0.00 0.00 0.00 3.77
2811 3959 9.582431 CAAGGATTTGCATTGATATGGATATTC 57.418 33.333 0.00 0.00 40.58 1.75
2828 3976 0.179129 GATGGGCGTGCAAGGATTTG 60.179 55.000 0.79 0.00 37.36 2.32
2831 3979 0.473755 TATGATGGGCGTGCAAGGAT 59.526 50.000 0.79 0.00 0.00 3.24
2833 3981 2.079158 CTATATGATGGGCGTGCAAGG 58.921 52.381 0.79 0.00 0.00 3.61
2835 3983 2.158827 ACACTATATGATGGGCGTGCAA 60.159 45.455 0.00 0.00 0.00 4.08
2836 3984 1.416030 ACACTATATGATGGGCGTGCA 59.584 47.619 0.00 0.00 0.00 4.57
2837 3985 2.169832 ACACTATATGATGGGCGTGC 57.830 50.000 0.00 0.00 0.00 5.34
2838 3986 5.390885 GCATTTACACTATATGATGGGCGTG 60.391 44.000 0.00 0.00 0.00 5.34
2839 3987 4.695455 GCATTTACACTATATGATGGGCGT 59.305 41.667 0.00 0.00 0.00 5.68
2840 3988 4.694982 TGCATTTACACTATATGATGGGCG 59.305 41.667 0.00 0.00 0.00 6.13
2841 3989 5.942872 GTGCATTTACACTATATGATGGGC 58.057 41.667 0.00 0.00 37.58 5.36
2853 4001 7.240674 TCGTTCAATTCATAGTGCATTTACAC 58.759 34.615 0.00 0.00 41.02 2.90
2854 4002 7.371126 TCGTTCAATTCATAGTGCATTTACA 57.629 32.000 0.00 0.00 0.00 2.41
2855 4003 9.370126 GTATCGTTCAATTCATAGTGCATTTAC 57.630 33.333 0.00 0.00 0.00 2.01
2856 4004 9.103861 TGTATCGTTCAATTCATAGTGCATTTA 57.896 29.630 0.00 0.00 0.00 1.40
2857 4005 7.984391 TGTATCGTTCAATTCATAGTGCATTT 58.016 30.769 0.00 0.00 0.00 2.32
2858 4006 7.552458 TGTATCGTTCAATTCATAGTGCATT 57.448 32.000 0.00 0.00 0.00 3.56
2859 4007 7.552458 TTGTATCGTTCAATTCATAGTGCAT 57.448 32.000 0.00 0.00 0.00 3.96
2860 4008 6.976636 TTGTATCGTTCAATTCATAGTGCA 57.023 33.333 0.00 0.00 0.00 4.57
2861 4009 7.464358 ACTTTGTATCGTTCAATTCATAGTGC 58.536 34.615 0.00 0.00 0.00 4.40
2865 4013 9.961266 CGTTTACTTTGTATCGTTCAATTCATA 57.039 29.630 0.00 0.00 0.00 2.15
2866 4014 8.714179 TCGTTTACTTTGTATCGTTCAATTCAT 58.286 29.630 0.00 0.00 0.00 2.57
2867 4015 8.005466 GTCGTTTACTTTGTATCGTTCAATTCA 58.995 33.333 0.00 0.00 0.00 2.57
2868 4016 8.005466 TGTCGTTTACTTTGTATCGTTCAATTC 58.995 33.333 0.00 0.00 0.00 2.17
2869 4017 7.853524 TGTCGTTTACTTTGTATCGTTCAATT 58.146 30.769 0.00 0.00 0.00 2.32
2870 4018 7.410800 TGTCGTTTACTTTGTATCGTTCAAT 57.589 32.000 0.00 0.00 0.00 2.57
2871 4019 6.825284 TGTCGTTTACTTTGTATCGTTCAA 57.175 33.333 0.00 0.00 0.00 2.69
2872 4020 6.825284 TTGTCGTTTACTTTGTATCGTTCA 57.175 33.333 0.00 0.00 0.00 3.18
2873 4021 8.005466 TGAATTGTCGTTTACTTTGTATCGTTC 58.995 33.333 0.00 0.00 0.00 3.95
2874 4022 7.853524 TGAATTGTCGTTTACTTTGTATCGTT 58.146 30.769 0.00 0.00 0.00 3.85
2875 4023 7.410800 TGAATTGTCGTTTACTTTGTATCGT 57.589 32.000 0.00 0.00 0.00 3.73
2950 4098 8.649841 CGCAACAATTGACATCTTTATTCATTT 58.350 29.630 13.59 0.00 0.00 2.32
2957 4105 9.288124 CAATAATCGCAACAATTGACATCTTTA 57.712 29.630 13.59 4.10 32.29 1.85
2963 4111 6.850555 TCATCAATAATCGCAACAATTGACA 58.149 32.000 13.59 0.00 40.18 3.58
2966 4114 8.570096 AAGATCATCAATAATCGCAACAATTG 57.430 30.769 3.24 3.24 0.00 2.32
2981 4129 4.124970 CTCCGCATGAAGAAGATCATCAA 58.875 43.478 0.00 0.00 37.96 2.57
2988 4136 1.406069 GGCTTCTCCGCATGAAGAAGA 60.406 52.381 25.16 9.30 42.37 2.87
2989 4137 1.012841 GGCTTCTCCGCATGAAGAAG 58.987 55.000 20.24 20.24 42.37 2.85
2990 4138 0.324614 TGGCTTCTCCGCATGAAGAA 59.675 50.000 12.59 1.11 42.37 2.52
2991 4139 0.391661 GTGGCTTCTCCGCATGAAGA 60.392 55.000 12.59 0.00 44.77 2.87
3017 4165 0.394565 AACCTCTTGAGCGCTGAAGT 59.605 50.000 31.18 14.49 0.00 3.01
3023 4171 1.666189 GGACATAAACCTCTTGAGCGC 59.334 52.381 0.00 0.00 0.00 5.92
3025 4173 2.680339 GCAGGACATAAACCTCTTGAGC 59.320 50.000 0.00 0.00 35.35 4.26
3026 4174 3.937706 CTGCAGGACATAAACCTCTTGAG 59.062 47.826 5.57 0.00 35.35 3.02
3052 4200 0.256464 AGACGGAGGAGTCGAGGATT 59.744 55.000 0.00 0.00 45.26 3.01
3066 4214 0.098025 GAGACTTGCGAGAGAGACGG 59.902 60.000 8.31 0.00 0.00 4.79
3070 4218 3.057596 AGAAGTTGAGACTTGCGAGAGAG 60.058 47.826 8.31 0.00 45.88 3.20
3076 4224 3.057596 AGAGAGAGAAGTTGAGACTTGCG 60.058 47.826 0.00 0.00 45.88 4.85
3091 4239 6.037391 GCAAGGAATTTGATCTTGAGAGAGAG 59.963 42.308 12.67 0.00 39.97 3.20
3125 4273 2.169832 TTGGAGAGGCAAGAGAAACG 57.830 50.000 0.00 0.00 0.00 3.60
3127 4275 4.647564 AGAATTGGAGAGGCAAGAGAAA 57.352 40.909 0.00 0.00 0.00 2.52
3162 4310 2.300152 CACTAGGAGAGGTTGCACTTGA 59.700 50.000 0.00 0.00 0.00 3.02
3183 4331 4.039124 TGCAAAAGGAGAAAATGGAGTTCC 59.961 41.667 0.00 0.00 0.00 3.62
3189 4337 5.143376 AGATGTGCAAAAGGAGAAAATGG 57.857 39.130 0.00 0.00 0.00 3.16
3193 4341 6.489700 TGTTCATAGATGTGCAAAAGGAGAAA 59.510 34.615 0.00 0.00 0.00 2.52
3199 4347 7.310664 ACAAGATGTTCATAGATGTGCAAAAG 58.689 34.615 0.00 0.00 0.00 2.27
3200 4348 7.218228 ACAAGATGTTCATAGATGTGCAAAA 57.782 32.000 0.00 0.00 0.00 2.44
3230 4378 3.110705 CCAAGAAGATGAAGGAGGAGGA 58.889 50.000 0.00 0.00 0.00 3.71
3231 4379 2.421248 GCCAAGAAGATGAAGGAGGAGG 60.421 54.545 0.00 0.00 0.00 4.30
3232 4380 2.421248 GGCCAAGAAGATGAAGGAGGAG 60.421 54.545 0.00 0.00 0.00 3.69
3260 4408 1.070601 GCCACTTGGACCAGCATTTTT 59.929 47.619 0.00 0.00 37.39 1.94
3261 4409 0.681175 GCCACTTGGACCAGCATTTT 59.319 50.000 0.00 0.00 37.39 1.82


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

AutoCloner maintained by Alex Coulton.