Multiple sequence alignment - TraesCS6B01G308300

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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 TraesCS6B01G308300 chr6B 100.000 3427 0 0 1 3427 552244213 552247639 0.000000e+00 6329.0
1 TraesCS6B01G308300 chr6A 89.256 2783 176 64 418 3113 507093394 507096140 0.000000e+00 3369.0
2 TraesCS6B01G308300 chr6A 85.941 441 43 5 1 427 507092808 507093243 1.450000e-123 453.0
3 TraesCS6B01G308300 chr6A 83.219 292 38 9 3140 3427 507096444 507096728 1.220000e-64 257.0
4 TraesCS6B01G308300 chr6D 89.007 2720 155 69 349 2977 366539274 366541940 0.000000e+00 3234.0
5 TraesCS6B01G308300 chr6D 91.989 362 13 3 1 347 366538821 366539181 8.540000e-136 494.0
6 TraesCS6B01G308300 chr3D 81.971 771 97 24 1338 2097 574998900 574999639 1.750000e-172 616.0
7 TraesCS6B01G308300 chr3D 74.869 191 31 10 2467 2649 575027809 575027990 1.710000e-08 71.3
8 TraesCS6B01G308300 chr7A 95.789 95 2 2 2790 2883 561707750 561707843 5.920000e-33 152.0
9 TraesCS6B01G308300 chr4B 94.845 97 3 1 2789 2883 14344272 14344368 2.130000e-32 150.0
10 TraesCS6B01G308300 chr4B 89.831 59 2 4 3148 3205 637339936 637339991 4.740000e-09 73.1
11 TraesCS6B01G308300 chr7B 95.556 90 2 2 2790 2878 524519515 524519603 3.560000e-30 143.0
12 TraesCS6B01G308300 chr5D 79.048 210 42 2 3163 3371 456750784 456750576 3.560000e-30 143.0
13 TraesCS6B01G308300 chr7D 95.506 89 2 2 2790 2877 496099163 496099250 1.280000e-29 141.0
14 TraesCS6B01G308300 chr7D 95.506 89 2 2 2790 2877 496106737 496106824 1.280000e-29 141.0
15 TraesCS6B01G308300 chr1B 90.566 106 8 2 2788 2892 661576819 661576923 4.610000e-29 139.0
16 TraesCS6B01G308300 chr1D 90.566 106 5 4 2788 2892 475655484 475655585 5.970000e-28 135.0
17 TraesCS6B01G308300 chr2A 83.824 68 10 1 3164 3230 748223093 748223026 2.860000e-06 63.9


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 TraesCS6B01G308300 chr6B 552244213 552247639 3426 False 6329.000000 6329 100.000000 1 3427 1 chr6B.!!$F1 3426
1 TraesCS6B01G308300 chr6A 507092808 507096728 3920 False 1359.666667 3369 86.138667 1 3427 3 chr6A.!!$F1 3426
2 TraesCS6B01G308300 chr6D 366538821 366541940 3119 False 1864.000000 3234 90.498000 1 2977 2 chr6D.!!$F1 2976
3 TraesCS6B01G308300 chr3D 574998900 574999639 739 False 616.000000 616 81.971000 1338 2097 1 chr3D.!!$F1 759

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
968 1255 0.394216 TTTCCGGCAGTCCCATGATG 60.394 55.0 0.00 0.0 0.00 3.07 F
979 1266 1.019673 CCCATGATGGACAAGAAGCG 58.980 55.0 14.26 0.0 40.96 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1911 2256 0.178068 GGGGCTAAGCACGAGATCAA 59.822 55.0 0.0 0.0 29.41 2.57 R
2658 3039 0.394216 TCAATCGACATTGCCCCCTG 60.394 55.0 0.0 0.0 39.56 4.45 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
42 43 4.894784 TGGTACTTCTAAACAGAAGGCAG 58.105 43.478 16.48 0.00 46.93 4.85
77 78 3.077359 ACACATTGAACTTAGCTGGAGC 58.923 45.455 0.00 0.00 42.49 4.70
149 164 1.835483 CGACAGTTGACAGTGCAGGC 61.835 60.000 0.00 0.00 0.00 4.85
152 167 1.301244 AGTTGACAGTGCAGGCGAG 60.301 57.895 0.00 0.00 0.00 5.03
174 189 6.508563 CGAGTAACATATGCTGACATGTGAAC 60.509 42.308 1.15 0.00 45.48 3.18
191 206 5.826586 TGTGAACGTCAAACTGCATATTTT 58.173 33.333 0.00 0.00 0.00 1.82
220 235 7.962441 AGGTACAAAAATGTAGCCTGAAAAAT 58.038 30.769 12.93 0.00 41.98 1.82
332 347 2.400408 CGTGTCAAAAAGGCGAAATTCG 59.600 45.455 11.47 11.47 43.89 3.34
342 357 1.673920 GGCGAAATTCGGGCAAATAGA 59.326 47.619 17.49 0.00 40.84 1.98
347 362 4.970003 CGAAATTCGGGCAAATAGATTGTC 59.030 41.667 7.61 0.00 43.10 3.18
415 521 9.090103 AGTATCCTTAATGATAAGTGATCCGAA 57.910 33.333 2.44 0.00 37.42 4.30
533 813 2.287009 GCACCAAACTCGAACAGGAAAG 60.287 50.000 0.00 0.00 0.00 2.62
534 814 3.202906 CACCAAACTCGAACAGGAAAGA 58.797 45.455 0.00 0.00 0.00 2.52
535 815 3.625764 CACCAAACTCGAACAGGAAAGAA 59.374 43.478 0.00 0.00 0.00 2.52
536 816 3.877508 ACCAAACTCGAACAGGAAAGAAG 59.122 43.478 0.00 0.00 0.00 2.85
539 820 5.277538 CCAAACTCGAACAGGAAAGAAGAAG 60.278 44.000 0.00 0.00 0.00 2.85
615 896 5.765182 ACATCTGTTTGGTGAAGACTTAAGG 59.235 40.000 7.53 0.00 0.00 2.69
666 947 4.980590 TGTAAATAACCAATTCTGCAGCG 58.019 39.130 9.47 0.00 0.00 5.18
790 1076 7.288810 ACCAAAGATTTAAACATGAGCAAGA 57.711 32.000 0.00 0.00 0.00 3.02
791 1077 7.373493 ACCAAAGATTTAAACATGAGCAAGAG 58.627 34.615 0.00 0.00 0.00 2.85
792 1078 6.309737 CCAAAGATTTAAACATGAGCAAGAGC 59.690 38.462 0.00 0.00 42.56 4.09
867 1153 1.770658 CAAGGGCCATATCAGGTGAGA 59.229 52.381 6.18 0.00 0.00 3.27
924 1210 2.727607 GCTAGCTAGCGATCGATCAGTG 60.728 54.545 28.89 10.03 39.82 3.66
925 1211 1.313772 AGCTAGCGATCGATCAGTGT 58.686 50.000 24.40 8.38 0.00 3.55
926 1212 2.495084 AGCTAGCGATCGATCAGTGTA 58.505 47.619 24.40 9.03 0.00 2.90
927 1213 3.078097 AGCTAGCGATCGATCAGTGTAT 58.922 45.455 24.40 3.96 0.00 2.29
967 1254 0.394352 GTTTCCGGCAGTCCCATGAT 60.394 55.000 0.00 0.00 0.00 2.45
968 1255 0.394216 TTTCCGGCAGTCCCATGATG 60.394 55.000 0.00 0.00 0.00 3.07
969 1256 2.203252 CCGGCAGTCCCATGATGG 60.203 66.667 3.98 3.98 37.25 3.51
970 1257 2.745308 CCGGCAGTCCCATGATGGA 61.745 63.158 14.26 0.00 40.96 3.41
978 1265 2.425143 TCCCATGATGGACAAGAAGC 57.575 50.000 14.26 0.00 40.96 3.86
979 1266 1.019673 CCCATGATGGACAAGAAGCG 58.980 55.000 14.26 0.00 40.96 4.68
1017 1304 1.873069 GCCATGGATTCAGAGCTCTCG 60.873 57.143 18.40 9.98 34.09 4.04
1022 1309 2.556189 TGGATTCAGAGCTCTCGATAGC 59.444 50.000 14.96 14.51 43.11 2.97
1069 1356 1.070577 CGTGTTGTTGCTCTTCTTCGG 60.071 52.381 0.00 0.00 0.00 4.30
1071 1358 1.134220 TGTTGTTGCTCTTCTTCGGGT 60.134 47.619 0.00 0.00 0.00 5.28
1136 1429 4.838152 GCTGCCGAGCGGGATTCA 62.838 66.667 11.30 0.00 38.47 2.57
1137 1430 2.109799 CTGCCGAGCGGGATTCAT 59.890 61.111 11.30 0.00 38.47 2.57
1140 1433 1.302033 GCCGAGCGGGATTCATGAT 60.302 57.895 11.30 0.00 38.47 2.45
1466 1774 2.025321 AGAACCAGGGAAAATGCGGTAT 60.025 45.455 0.00 0.00 0.00 2.73
1509 1826 3.133901 ACATTGCATTGCACATCCATGAT 59.866 39.130 21.22 5.12 38.71 2.45
1557 1888 2.613595 TGCGCACCATGTATCTGAAATC 59.386 45.455 5.66 0.00 0.00 2.17
1589 1920 2.604686 TGCTGGGCCTTCTCGACT 60.605 61.111 4.53 0.00 0.00 4.18
1727 2059 1.605710 GACTTCGCCTACGCCTACATA 59.394 52.381 0.00 0.00 39.84 2.29
1756 2094 4.157120 GGGGATCCACACCGACGG 62.157 72.222 15.23 13.61 29.82 4.79
1909 2254 6.703319 TGATGGACATTGATTGCTTTGATTT 58.297 32.000 0.00 0.00 0.00 2.17
1910 2255 6.592220 TGATGGACATTGATTGCTTTGATTTG 59.408 34.615 0.00 0.00 0.00 2.32
1911 2256 5.856156 TGGACATTGATTGCTTTGATTTGT 58.144 33.333 0.00 0.00 0.00 2.83
2073 2431 5.649970 TCCAGTTCTACAAAGGGGTAAAA 57.350 39.130 0.00 0.00 0.00 1.52
2074 2432 5.627135 TCCAGTTCTACAAAGGGGTAAAAG 58.373 41.667 0.00 0.00 0.00 2.27
2088 2446 5.185828 AGGGGTAAAAGAAATGATCAAGTGC 59.814 40.000 0.00 0.00 0.00 4.40
2092 2455 8.470002 GGGTAAAAGAAATGATCAAGTGCTATT 58.530 33.333 0.00 0.00 0.00 1.73
2103 2466 8.607441 TGATCAAGTGCTATTTACCATGATAC 57.393 34.615 0.00 0.00 30.16 2.24
2108 2471 9.764363 CAAGTGCTATTTACCATGATACTAGAA 57.236 33.333 0.00 0.00 0.00 2.10
2111 2474 9.542462 GTGCTATTTACCATGATACTAGAACAA 57.458 33.333 0.00 0.00 0.00 2.83
2162 2525 6.179906 ACCCTGGTAATTATCTCATCTGTG 57.820 41.667 0.00 0.00 0.00 3.66
2163 2526 5.072329 ACCCTGGTAATTATCTCATCTGTGG 59.928 44.000 0.00 0.00 0.00 4.17
2167 2532 5.163205 TGGTAATTATCTCATCTGTGGGTGG 60.163 44.000 0.00 0.00 0.00 4.61
2169 2534 2.568546 TATCTCATCTGTGGGTGGGT 57.431 50.000 0.00 0.00 0.00 4.51
2180 2545 2.194597 GGTGGGTGTGTGGCTTGA 59.805 61.111 0.00 0.00 0.00 3.02
2204 2569 0.179001 AGGGGGTGTTTGAAGGAACG 60.179 55.000 0.00 0.00 32.18 3.95
2318 2683 2.690881 TGGGGCGAGCAAGGGTAT 60.691 61.111 0.00 0.00 0.00 2.73
2319 2684 1.383386 TGGGGCGAGCAAGGGTATA 60.383 57.895 0.00 0.00 0.00 1.47
2339 2704 0.252881 TCAGGATCAAGAGGGGCACT 60.253 55.000 0.00 0.00 0.00 4.40
2371 2736 3.030209 GCGTCTGCGACATCTACAA 57.970 52.632 8.91 0.00 41.33 2.41
2375 2740 3.439293 CGTCTGCGACATCTACAAGATT 58.561 45.455 8.91 0.00 41.33 2.40
2389 2754 6.143915 TCTACAAGATTGCCTCTTACCCTAT 58.856 40.000 0.00 0.00 42.48 2.57
2400 2765 5.570844 GCCTCTTACCCTATCAAGAACAACA 60.571 44.000 0.00 0.00 30.68 3.33
2402 2767 6.070767 CCTCTTACCCTATCAAGAACAACAGA 60.071 42.308 0.00 0.00 30.68 3.41
2408 2773 2.702592 TCAAGAACAACAGAACGGGT 57.297 45.000 0.00 0.00 0.00 5.28
2435 2800 1.001393 GGGGGCCTGATTTTGTCGA 60.001 57.895 0.84 0.00 0.00 4.20
2444 2809 3.126171 CCTGATTTTGTCGACGGCATAAA 59.874 43.478 11.62 10.06 0.00 1.40
2449 2815 2.371910 TGTCGACGGCATAAATGTCA 57.628 45.000 11.62 0.00 32.91 3.58
2462 2828 6.529125 GGCATAAATGTCACTGAAACTCATTG 59.471 38.462 0.00 0.00 31.41 2.82
2463 2829 7.086376 GCATAAATGTCACTGAAACTCATTGT 58.914 34.615 0.00 0.00 30.26 2.71
2465 2831 9.121517 CATAAATGTCACTGAAACTCATTGTTC 57.878 33.333 0.00 0.00 38.03 3.18
2466 2832 4.794248 TGTCACTGAAACTCATTGTTCG 57.206 40.909 0.00 0.00 38.03 3.95
2467 2833 4.188462 TGTCACTGAAACTCATTGTTCGT 58.812 39.130 0.00 0.00 38.03 3.85
2469 2835 5.198274 GTCACTGAAACTCATTGTTCGTTC 58.802 41.667 0.00 0.00 38.03 3.95
2470 2836 4.873259 TCACTGAAACTCATTGTTCGTTCA 59.127 37.500 0.00 0.00 38.03 3.18
2473 2839 6.141211 CACTGAAACTCATTGTTCGTTCATTG 59.859 38.462 0.00 0.00 38.03 2.82
2507 2885 0.810648 TGGATGCAACATCGCCTTTC 59.189 50.000 0.00 0.00 0.00 2.62
2513 2891 3.122297 TGCAACATCGCCTTTCTTTTTG 58.878 40.909 0.00 0.00 0.00 2.44
2560 2940 4.075963 ACAAGTTAGGCGGTCTGTAAAA 57.924 40.909 0.00 0.00 0.00 1.52
2594 2974 3.813166 GGTGAGAAAATCTGGTTGTTCGA 59.187 43.478 0.00 0.00 0.00 3.71
2600 2980 0.250124 ATCTGGTTGTTCGACGGCAA 60.250 50.000 0.00 0.00 0.00 4.52
2638 3018 5.060506 TGTATTTCTCTTCTGTTTTCGGCA 58.939 37.500 0.00 0.00 0.00 5.69
2658 3039 0.759060 AAACACAGTGGGGAAAGGGC 60.759 55.000 5.31 0.00 0.00 5.19
2679 3060 0.394352 GGGGGCAATGTCGATTGAGT 60.394 55.000 2.94 0.00 41.49 3.41
2724 3137 4.742201 CTGACACCGCCGTCCAGG 62.742 72.222 0.63 0.00 44.97 4.45
2733 3146 3.083349 CCGTCCAGGGCATCAGGA 61.083 66.667 0.00 0.00 35.97 3.86
2737 3150 3.414193 CCAGGGCATCAGGAGGCA 61.414 66.667 8.27 0.00 40.32 4.75
2739 3152 1.000521 CAGGGCATCAGGAGGCAAA 60.001 57.895 8.27 0.00 40.32 3.68
2750 3163 1.840635 AGGAGGCAAATAGGACAGGAC 59.159 52.381 0.00 0.00 0.00 3.85
2751 3164 1.473434 GGAGGCAAATAGGACAGGACG 60.473 57.143 0.00 0.00 0.00 4.79
2752 3165 0.541863 AGGCAAATAGGACAGGACGG 59.458 55.000 0.00 0.00 0.00 4.79
2754 3167 1.065709 GGCAAATAGGACAGGACGGAA 60.066 52.381 0.00 0.00 0.00 4.30
2756 3169 2.678336 GCAAATAGGACAGGACGGAAAG 59.322 50.000 0.00 0.00 0.00 2.62
2760 3173 4.903045 ATAGGACAGGACGGAAAGAAAA 57.097 40.909 0.00 0.00 0.00 2.29
2761 3174 3.127425 AGGACAGGACGGAAAGAAAAG 57.873 47.619 0.00 0.00 0.00 2.27
2767 3182 6.374613 GGACAGGACGGAAAGAAAAGATAAAT 59.625 38.462 0.00 0.00 0.00 1.40
2769 3184 8.857694 ACAGGACGGAAAGAAAAGATAAATAA 57.142 30.769 0.00 0.00 0.00 1.40
2869 3284 3.726557 TCAAGTCTCGGTAGGACCTTA 57.273 47.619 0.00 0.00 35.66 2.69
2872 3287 5.759059 TCAAGTCTCGGTAGGACCTTATTA 58.241 41.667 0.00 0.00 35.66 0.98
2931 3353 4.955450 TGCATGGTAATTGCTGAGGTATTT 59.045 37.500 0.00 0.00 40.77 1.40
2955 3377 1.017387 CGAGCAGCCCAAAACCTATC 58.983 55.000 0.00 0.00 0.00 2.08
2956 3378 1.017387 GAGCAGCCCAAAACCTATCG 58.983 55.000 0.00 0.00 0.00 2.92
2957 3379 0.328258 AGCAGCCCAAAACCTATCGT 59.672 50.000 0.00 0.00 0.00 3.73
2958 3380 0.451783 GCAGCCCAAAACCTATCGTG 59.548 55.000 0.00 0.00 0.00 4.35
2962 3384 2.570302 AGCCCAAAACCTATCGTGTACT 59.430 45.455 0.00 0.00 0.00 2.73
2963 3385 3.770933 AGCCCAAAACCTATCGTGTACTA 59.229 43.478 0.00 0.00 0.00 1.82
2964 3386 3.867493 GCCCAAAACCTATCGTGTACTAC 59.133 47.826 0.00 0.00 0.00 2.73
3017 3444 6.092259 AGAGTTACAAAAATACGAGCACATCC 59.908 38.462 0.00 0.00 0.00 3.51
3019 3446 4.419522 ACAAAAATACGAGCACATCCAC 57.580 40.909 0.00 0.00 0.00 4.02
3030 3457 1.097547 CACATCCACCATCTTCGGGC 61.098 60.000 0.00 0.00 0.00 6.13
3049 3481 1.047002 CCATCCTGGAGCCTAGACAG 58.953 60.000 1.52 0.00 40.96 3.51
3057 3489 2.070654 GAGCCTAGACAGAGCTCGCC 62.071 65.000 8.37 1.38 43.18 5.54
3075 3507 2.477375 CGCCTGCTACAACGTTTCTTAA 59.523 45.455 0.00 0.00 0.00 1.85
3076 3508 3.423123 CGCCTGCTACAACGTTTCTTAAG 60.423 47.826 0.00 0.00 0.00 1.85
3077 3509 3.497262 GCCTGCTACAACGTTTCTTAAGT 59.503 43.478 0.00 0.00 0.00 2.24
3078 3510 4.610680 GCCTGCTACAACGTTTCTTAAGTG 60.611 45.833 0.00 0.00 0.00 3.16
3079 3511 4.748102 CCTGCTACAACGTTTCTTAAGTGA 59.252 41.667 0.00 0.00 0.00 3.41
3080 3512 5.408604 CCTGCTACAACGTTTCTTAAGTGAT 59.591 40.000 0.00 0.00 0.00 3.06
3081 3513 6.401153 CCTGCTACAACGTTTCTTAAGTGATC 60.401 42.308 0.00 0.00 0.00 2.92
3082 3514 5.407387 TGCTACAACGTTTCTTAAGTGATCC 59.593 40.000 0.00 0.00 0.00 3.36
3089 3525 5.105752 CGTTTCTTAAGTGATCCAGGAGAG 58.894 45.833 1.63 0.00 0.00 3.20
3100 3536 3.765432 TCCAGGAGAGATGAAAGGAGA 57.235 47.619 0.00 0.00 0.00 3.71
3113 3549 2.738013 AAGGAGAAGCTTGCATTTGC 57.262 45.000 2.10 0.00 42.50 3.68
3135 3646 4.734108 GCACGAGTCTAGTCCTTTATCACC 60.734 50.000 0.00 0.00 0.00 4.02
3141 3652 5.053145 GTCTAGTCCTTTATCACCTGCATG 58.947 45.833 0.00 0.00 0.00 4.06
3145 3656 5.128919 AGTCCTTTATCACCTGCATGATTC 58.871 41.667 8.05 0.00 39.97 2.52
3156 3869 5.993441 CACCTGCATGATTCCTTTTCTTTTT 59.007 36.000 0.00 0.00 0.00 1.94
3175 3888 5.986004 TTTTTCTGAGAGAAACTTCCGAC 57.014 39.130 0.00 0.00 43.25 4.79
3183 3896 5.422331 TGAGAGAAACTTCCGACCTATTCAT 59.578 40.000 0.00 0.00 0.00 2.57
3194 3907 9.875691 CTTCCGACCTATTCATAATCAATCATA 57.124 33.333 0.00 0.00 0.00 2.15
3210 3923 6.908825 TCAATCATAGCAGTACAAAAACACC 58.091 36.000 0.00 0.00 0.00 4.16
3211 3924 5.897377 ATCATAGCAGTACAAAAACACCC 57.103 39.130 0.00 0.00 0.00 4.61
3212 3925 4.076394 TCATAGCAGTACAAAAACACCCC 58.924 43.478 0.00 0.00 0.00 4.95
3248 3961 9.665719 AAATTAAAACAATATCCATTGACCACC 57.334 29.630 4.46 0.00 43.67 4.61
3269 3982 4.058124 CCTAGCAGCGATTACAAGCATTA 58.942 43.478 0.00 0.00 35.48 1.90
3270 3983 4.511454 CCTAGCAGCGATTACAAGCATTAA 59.489 41.667 0.00 0.00 35.48 1.40
3278 3991 3.757745 TTACAAGCATTAAAGCGAGCC 57.242 42.857 0.00 0.00 40.15 4.70
3279 3992 0.447801 ACAAGCATTAAAGCGAGCCG 59.552 50.000 0.00 0.00 40.15 5.52
3283 3996 1.006832 GCATTAAAGCGAGCCGAAGA 58.993 50.000 0.00 0.00 0.00 2.87
3285 3998 1.999735 CATTAAAGCGAGCCGAAGACA 59.000 47.619 0.00 0.00 0.00 3.41
3286 3999 2.380084 TTAAAGCGAGCCGAAGACAT 57.620 45.000 0.00 0.00 0.00 3.06
3288 4001 1.639298 AAAGCGAGCCGAAGACATGC 61.639 55.000 0.00 0.00 0.00 4.06
3289 4002 2.510238 GCGAGCCGAAGACATGCT 60.510 61.111 0.00 0.00 38.24 3.79
3290 4003 2.806856 GCGAGCCGAAGACATGCTG 61.807 63.158 0.00 0.00 34.99 4.41
3293 4006 2.747460 GCCGAAGACATGCTGCCA 60.747 61.111 0.00 0.00 0.00 4.92
3295 4008 2.020131 CCGAAGACATGCTGCCATC 58.980 57.895 0.00 0.00 0.00 3.51
3296 4009 0.463295 CCGAAGACATGCTGCCATCT 60.463 55.000 0.00 0.00 0.00 2.90
3298 4011 1.741706 CGAAGACATGCTGCCATCTTT 59.258 47.619 10.32 0.00 0.00 2.52
3301 4014 0.815734 GACATGCTGCCATCTTTGCT 59.184 50.000 0.00 0.00 0.00 3.91
3305 4018 0.679002 TGCTGCCATCTTTGCTCCTC 60.679 55.000 0.00 0.00 0.00 3.71
3306 4019 1.382692 GCTGCCATCTTTGCTCCTCC 61.383 60.000 0.00 0.00 0.00 4.30
3326 4039 2.579684 CTAACCGGAGCTGGGCAGAC 62.580 65.000 9.46 0.00 0.00 3.51
3351 4064 2.614983 GTTGTTGTAGACAGCCGGAAAA 59.385 45.455 5.05 0.00 39.94 2.29
3354 4067 2.004583 TGTAGACAGCCGGAAAATCG 57.995 50.000 5.05 0.00 0.00 3.34
3357 4070 0.320374 AGACAGCCGGAAAATCGTCA 59.680 50.000 5.05 0.00 0.00 4.35
3364 4077 2.286418 GCCGGAAAATCGTCATGCTAAG 60.286 50.000 5.05 0.00 0.00 2.18
3368 4081 3.312697 GGAAAATCGTCATGCTAAGACCC 59.687 47.826 0.00 0.00 32.41 4.46
3369 4082 2.622064 AATCGTCATGCTAAGACCCC 57.378 50.000 0.00 0.00 32.41 4.95
3373 4086 2.039216 TCGTCATGCTAAGACCCCAAAA 59.961 45.455 0.00 0.00 32.41 2.44
3376 4089 4.273318 GTCATGCTAAGACCCCAAAAGAT 58.727 43.478 0.00 0.00 0.00 2.40
3377 4090 4.096984 GTCATGCTAAGACCCCAAAAGATG 59.903 45.833 0.00 0.00 0.00 2.90
3412 4126 2.283298 CAACCATCACCGATGAAGAGG 58.717 52.381 5.54 0.00 42.09 3.69
3415 4129 1.210478 CCATCACCGATGAAGAGGGTT 59.790 52.381 5.54 0.00 42.09 4.11
3423 4137 4.459685 ACCGATGAAGAGGGTTATAGATCG 59.540 45.833 0.00 0.00 33.06 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 2.550487 TGTGTCCATTACGCAAGCC 58.450 52.632 0.00 0.00 45.44 4.35
52 53 4.012374 CCAGCTAAGTTCAATGTGTCCAT 58.988 43.478 0.00 0.00 0.00 3.41
77 78 3.848019 GCAAGTTAATTGACATCTGTGCG 59.152 43.478 2.93 0.00 41.83 5.34
130 145 1.835483 GCCTGCACTGTCAACTGTCG 61.835 60.000 0.00 0.00 0.00 4.35
149 164 5.043248 TCACATGTCAGCATATGTTACTCG 58.957 41.667 4.29 0.00 35.46 4.18
152 167 5.063438 ACGTTCACATGTCAGCATATGTTAC 59.937 40.000 4.29 1.32 35.46 2.50
174 189 5.920273 ACCTTCAAAAATATGCAGTTTGACG 59.080 36.000 13.91 12.55 40.11 4.35
191 206 6.065374 TCAGGCTACATTTTTGTACCTTCAA 58.935 36.000 0.00 0.00 0.00 2.69
220 235 4.568072 AAGTGTGTATATGCAGACCCAA 57.432 40.909 15.89 0.00 33.71 4.12
312 327 2.724174 CCGAATTTCGCCTTTTTGACAC 59.276 45.455 13.26 0.00 38.82 3.67
332 347 6.759497 AACTTGTAGACAATCTATTTGCCC 57.241 37.500 0.00 0.00 39.03 5.36
415 521 4.192429 GGCACCAGCTTTTCATGTTATT 57.808 40.909 0.00 0.00 41.70 1.40
485 761 1.684983 CCATTGGCTTGCAGAATAGGG 59.315 52.381 0.00 0.00 0.00 3.53
545 826 8.046708 TGTGATGGTATCAAACTACTTGCTATT 58.953 33.333 0.00 0.00 41.69 1.73
636 917 7.491682 CAGAATTGGTTATTTACAAGGATGGG 58.508 38.462 0.00 0.00 0.00 4.00
666 947 1.587613 CGGCTAGACGAAGCAGCTC 60.588 63.158 14.40 0.00 44.64 4.09
867 1153 1.679680 CAAGCAAGCGATTCATCCCAT 59.320 47.619 0.00 0.00 0.00 4.00
967 1254 1.597854 CAGCACCGCTTCTTGTCCA 60.598 57.895 0.00 0.00 36.40 4.02
968 1255 0.674895 ATCAGCACCGCTTCTTGTCC 60.675 55.000 0.00 0.00 36.40 4.02
969 1256 1.160137 AATCAGCACCGCTTCTTGTC 58.840 50.000 0.00 0.00 36.40 3.18
970 1257 2.472695 TAATCAGCACCGCTTCTTGT 57.527 45.000 0.00 0.00 36.40 3.16
971 1258 3.242870 GGATTAATCAGCACCGCTTCTTG 60.243 47.826 17.07 0.00 36.40 3.02
973 1260 2.565841 GGATTAATCAGCACCGCTTCT 58.434 47.619 17.07 0.00 36.40 2.85
974 1261 1.261619 CGGATTAATCAGCACCGCTTC 59.738 52.381 17.07 0.00 36.40 3.86
976 1263 0.178068 ACGGATTAATCAGCACCGCT 59.822 50.000 17.07 0.94 46.18 5.52
977 1264 0.582005 GACGGATTAATCAGCACCGC 59.418 55.000 17.07 4.90 46.18 5.68
979 1266 0.582005 GCGACGGATTAATCAGCACC 59.418 55.000 17.07 5.68 0.00 5.01
1017 1304 7.527084 AACTATCAACAAGAAGAACGCTATC 57.473 36.000 0.00 0.00 0.00 2.08
1022 1309 6.690957 TGCAAAAACTATCAACAAGAAGAACG 59.309 34.615 0.00 0.00 0.00 3.95
1071 1358 1.687840 CGAGGGGTCATGGTGGGTA 60.688 63.158 0.00 0.00 0.00 3.69
1095 1388 1.681327 GTCCTCCTGCGAGTACCCA 60.681 63.158 0.00 0.00 33.93 4.51
1129 1422 4.317488 GAGCTGAAGAGATCATGAATCCC 58.683 47.826 0.00 0.00 37.44 3.85
1134 1427 2.100418 CCACGAGCTGAAGAGATCATGA 59.900 50.000 0.00 0.00 37.44 3.07
1136 1429 2.100584 GACCACGAGCTGAAGAGATCAT 59.899 50.000 0.00 0.00 37.44 2.45
1137 1430 1.474478 GACCACGAGCTGAAGAGATCA 59.526 52.381 0.00 0.00 33.97 2.92
1140 1433 1.587043 CCGACCACGAGCTGAAGAGA 61.587 60.000 0.00 0.00 42.66 3.10
1308 1601 1.810030 GTAGCCGGCCTTGAACTCG 60.810 63.158 26.15 0.00 0.00 4.18
1455 1763 3.016736 CCTTGTCTCCATACCGCATTTT 58.983 45.455 0.00 0.00 0.00 1.82
1466 1774 2.259917 TCAGAGATTGCCTTGTCTCCA 58.740 47.619 0.00 0.00 41.36 3.86
1509 1826 3.070734 GCTAGCTGAAATCCTGAGATGGA 59.929 47.826 7.70 0.00 40.82 3.41
1727 2059 2.535317 ATCCCCTGGTTGCCCACT 60.535 61.111 0.00 0.00 35.17 4.00
1733 2071 1.000896 GGTGTGGATCCCCTGGTTG 60.001 63.158 9.90 0.00 0.00 3.77
1756 2094 0.674534 CATGAGGTAGGGGTAGTCGC 59.325 60.000 0.00 0.00 0.00 5.19
1873 2217 6.053650 TCAATGTCCATCAGATTAGAGCAAG 58.946 40.000 0.00 0.00 0.00 4.01
1876 2220 6.568081 GCAATCAATGTCCATCAGATTAGAGC 60.568 42.308 7.27 5.00 29.87 4.09
1909 2254 1.405526 GGGCTAAGCACGAGATCAACA 60.406 52.381 0.00 0.00 0.00 3.33
1910 2255 1.291132 GGGCTAAGCACGAGATCAAC 58.709 55.000 0.00 0.00 0.00 3.18
1911 2256 0.178068 GGGGCTAAGCACGAGATCAA 59.822 55.000 0.00 0.00 29.41 2.57
2036 2394 0.906756 CTGGAAGTCTCTGCTCCCCA 60.907 60.000 0.00 0.00 0.00 4.96
2073 2431 8.627403 CATGGTAAATAGCACTTGATCATTTCT 58.373 33.333 0.00 0.00 36.42 2.52
2074 2432 8.623903 TCATGGTAAATAGCACTTGATCATTTC 58.376 33.333 0.00 0.00 36.42 2.17
2108 2471 7.725251 ACACTTGACCATTTTGTATCATTTGT 58.275 30.769 0.00 0.00 0.00 2.83
2125 2488 7.933215 ATTACCAGGGTAAATAACACTTGAC 57.067 36.000 14.42 0.00 39.51 3.18
2155 2518 0.890542 CACACACCCACCCACAGATG 60.891 60.000 0.00 0.00 0.00 2.90
2162 2525 2.912025 CAAGCCACACACCCACCC 60.912 66.667 0.00 0.00 0.00 4.61
2163 2526 2.193536 GTCAAGCCACACACCCACC 61.194 63.158 0.00 0.00 0.00 4.61
2167 2532 1.789078 CTGCAGTCAAGCCACACACC 61.789 60.000 5.25 0.00 0.00 4.16
2169 2534 1.526686 CCTGCAGTCAAGCCACACA 60.527 57.895 13.81 0.00 0.00 3.72
2180 2545 0.468029 CTTCAAACACCCCCTGCAGT 60.468 55.000 13.81 0.00 0.00 4.40
2204 2569 1.963338 GTCCAGCTGAGTGCCACAC 60.963 63.158 17.39 0.00 44.23 3.82
2318 2683 2.050144 GTGCCCCTCTTGATCCTGATA 58.950 52.381 0.00 0.00 0.00 2.15
2319 2684 0.842635 GTGCCCCTCTTGATCCTGAT 59.157 55.000 0.00 0.00 0.00 2.90
2371 2736 5.219739 TCTTGATAGGGTAAGAGGCAATCT 58.780 41.667 0.00 0.00 41.27 2.40
2375 2740 4.101114 TGTTCTTGATAGGGTAAGAGGCA 58.899 43.478 0.00 0.00 34.68 4.75
2389 2754 2.680841 CAACCCGTTCTGTTGTTCTTGA 59.319 45.455 0.00 0.00 38.58 3.02
2400 2765 3.576259 CCACCCCCAACCCGTTCT 61.576 66.667 0.00 0.00 0.00 3.01
2435 2800 4.072131 AGTTTCAGTGACATTTATGCCGT 58.928 39.130 0.00 0.00 0.00 5.68
2444 2809 4.816385 ACGAACAATGAGTTTCAGTGACAT 59.184 37.500 12.74 0.00 44.38 3.06
2449 2815 6.201517 CAATGAACGAACAATGAGTTTCAGT 58.798 36.000 0.00 0.00 41.51 3.41
2462 2828 2.405892 AGCACTTGCAATGAACGAAC 57.594 45.000 0.00 0.00 45.16 3.95
2463 2829 2.095768 GCTAGCACTTGCAATGAACGAA 60.096 45.455 10.63 0.00 45.16 3.85
2465 2831 1.197492 TGCTAGCACTTGCAATGAACG 59.803 47.619 14.93 0.00 45.16 3.95
2466 2832 2.589014 GTGCTAGCACTTGCAATGAAC 58.411 47.619 35.25 9.05 42.37 3.18
2467 2833 1.197492 CGTGCTAGCACTTGCAATGAA 59.803 47.619 37.42 2.51 42.37 2.57
2469 2835 0.518636 ACGTGCTAGCACTTGCAATG 59.481 50.000 37.42 25.15 42.37 2.82
2470 2836 0.518636 CACGTGCTAGCACTTGCAAT 59.481 50.000 37.42 17.78 42.37 3.56
2473 2839 1.021390 ATCCACGTGCTAGCACTTGC 61.021 55.000 36.32 18.42 42.48 4.01
2507 2885 4.384247 TGTTGCTTCGTGTTCAACAAAAAG 59.616 37.500 8.26 8.26 44.62 2.27
2513 2891 1.202132 TGCTGTTGCTTCGTGTTCAAC 60.202 47.619 0.00 0.00 40.17 3.18
2560 2940 3.644966 TTTCTCACCGGAGCCAAATAT 57.355 42.857 9.46 0.00 41.13 1.28
2594 2974 2.297701 ACAACTGAACTGAATTGCCGT 58.702 42.857 0.00 0.00 0.00 5.68
2600 2980 8.682936 AGAGAAATACAACAACTGAACTGAAT 57.317 30.769 0.00 0.00 0.00 2.57
2638 3018 1.788229 CCCTTTCCCCACTGTGTTTT 58.212 50.000 7.08 0.00 0.00 2.43
2658 3039 0.394216 TCAATCGACATTGCCCCCTG 60.394 55.000 0.00 0.00 39.56 4.45
2679 3060 1.341976 TGGATGTCTGGATCCGACAGA 60.342 52.381 29.75 17.30 44.52 3.41
2724 3137 1.143684 TCCTATTTGCCTCCTGATGCC 59.856 52.381 0.00 0.00 0.00 4.40
2728 3141 1.839994 CCTGTCCTATTTGCCTCCTGA 59.160 52.381 0.00 0.00 0.00 3.86
2729 3142 1.839994 TCCTGTCCTATTTGCCTCCTG 59.160 52.381 0.00 0.00 0.00 3.86
2733 3146 0.541863 CCGTCCTGTCCTATTTGCCT 59.458 55.000 0.00 0.00 0.00 4.75
2737 3150 4.903045 TTCTTTCCGTCCTGTCCTATTT 57.097 40.909 0.00 0.00 0.00 1.40
2739 3152 4.530946 TCTTTTCTTTCCGTCCTGTCCTAT 59.469 41.667 0.00 0.00 0.00 2.57
2786 3201 3.118112 AGACCATAGGACCTTTGCTGATG 60.118 47.826 0.00 0.00 0.00 3.07
2791 3206 3.432326 CCACTAGACCATAGGACCTTTGC 60.432 52.174 0.00 0.00 0.00 3.68
2884 3300 8.125448 GCAAGAAGTAGTCCTATGCAAAAATAG 58.875 37.037 0.00 0.00 32.80 1.73
2886 3302 6.434028 TGCAAGAAGTAGTCCTATGCAAAAAT 59.566 34.615 0.00 0.00 39.15 1.82
2897 3313 5.449177 GCAATTACCATGCAAGAAGTAGTCC 60.449 44.000 0.00 0.00 43.29 3.85
2931 3353 3.490031 TTTTGGGCTGCTCGGCTCA 62.490 57.895 0.00 0.00 41.36 4.26
2987 3409 7.116519 GTGCTCGTATTTTTGTAACTCTCTTCT 59.883 37.037 0.00 0.00 0.00 2.85
2995 3422 5.793457 GTGGATGTGCTCGTATTTTTGTAAC 59.207 40.000 0.00 0.00 0.00 2.50
3017 3444 1.526917 GGATGGCCCGAAGATGGTG 60.527 63.158 0.00 0.00 0.00 4.17
3019 3446 1.228063 CAGGATGGCCCGAAGATGG 60.228 63.158 0.00 0.00 40.87 3.51
3049 3481 2.161486 CGTTGTAGCAGGCGAGCTC 61.161 63.158 10.69 2.73 45.26 4.09
3057 3489 5.900339 TCACTTAAGAAACGTTGTAGCAG 57.100 39.130 10.09 0.00 0.00 4.24
3075 3507 3.710677 CCTTTCATCTCTCCTGGATCACT 59.289 47.826 0.00 0.00 0.00 3.41
3076 3508 3.708631 TCCTTTCATCTCTCCTGGATCAC 59.291 47.826 0.00 0.00 0.00 3.06
3077 3509 3.966006 CTCCTTTCATCTCTCCTGGATCA 59.034 47.826 0.00 0.00 0.00 2.92
3078 3510 4.222336 TCTCCTTTCATCTCTCCTGGATC 58.778 47.826 0.00 0.00 0.00 3.36
3079 3511 4.277788 TCTCCTTTCATCTCTCCTGGAT 57.722 45.455 0.00 0.00 0.00 3.41
3080 3512 3.765432 TCTCCTTTCATCTCTCCTGGA 57.235 47.619 0.00 0.00 0.00 3.86
3081 3513 3.432046 GCTTCTCCTTTCATCTCTCCTGG 60.432 52.174 0.00 0.00 0.00 4.45
3082 3514 3.451902 AGCTTCTCCTTTCATCTCTCCTG 59.548 47.826 0.00 0.00 0.00 3.86
3089 3525 4.715527 AATGCAAGCTTCTCCTTTCATC 57.284 40.909 0.00 0.00 29.45 2.92
3113 3549 4.641094 AGGTGATAAAGGACTAGACTCGTG 59.359 45.833 0.00 0.00 0.00 4.35
3125 3636 4.467769 AGGAATCATGCAGGTGATAAAGG 58.532 43.478 3.28 0.00 37.85 3.11
3156 3869 3.231818 AGGTCGGAAGTTTCTCTCAGAA 58.768 45.455 0.00 0.00 31.28 3.02
3158 3871 4.993029 ATAGGTCGGAAGTTTCTCTCAG 57.007 45.455 0.00 0.00 0.00 3.35
3168 3881 8.783833 ATGATTGATTATGAATAGGTCGGAAG 57.216 34.615 0.00 0.00 0.00 3.46
3171 3884 7.765819 TGCTATGATTGATTATGAATAGGTCGG 59.234 37.037 0.00 0.00 0.00 4.79
3194 3907 2.445682 TGGGGTGTTTTTGTACTGCT 57.554 45.000 0.00 0.00 0.00 4.24
3230 3943 4.165950 TGCTAGGTGGTCAATGGATATTGT 59.834 41.667 0.00 0.00 43.33 2.71
3233 3946 3.244700 GCTGCTAGGTGGTCAATGGATAT 60.245 47.826 0.00 0.00 0.00 1.63
3234 3947 2.104792 GCTGCTAGGTGGTCAATGGATA 59.895 50.000 0.00 0.00 0.00 2.59
3241 3954 1.136305 GTAATCGCTGCTAGGTGGTCA 59.864 52.381 0.00 0.00 0.00 4.02
3248 3961 5.657470 TTAATGCTTGTAATCGCTGCTAG 57.343 39.130 0.00 0.00 0.00 3.42
3269 3982 1.639298 GCATGTCTTCGGCTCGCTTT 61.639 55.000 0.00 0.00 0.00 3.51
3270 3983 2.103042 GCATGTCTTCGGCTCGCTT 61.103 57.895 0.00 0.00 0.00 4.68
3279 3992 2.734492 GCAAAGATGGCAGCATGTCTTC 60.734 50.000 5.19 0.00 44.57 2.87
3283 3996 0.815734 GAGCAAAGATGGCAGCATGT 59.184 50.000 5.19 0.00 39.31 3.21
3285 3998 0.033405 AGGAGCAAAGATGGCAGCAT 60.033 50.000 5.19 0.00 0.00 3.79
3286 3999 0.679002 GAGGAGCAAAGATGGCAGCA 60.679 55.000 5.19 0.00 0.00 4.41
3288 4001 0.750911 GGGAGGAGCAAAGATGGCAG 60.751 60.000 0.00 0.00 0.00 4.85
3289 4002 1.210204 AGGGAGGAGCAAAGATGGCA 61.210 55.000 0.00 0.00 0.00 4.92
3290 4003 0.839946 TAGGGAGGAGCAAAGATGGC 59.160 55.000 0.00 0.00 0.00 4.40
3293 4006 1.486726 CGGTTAGGGAGGAGCAAAGAT 59.513 52.381 0.00 0.00 0.00 2.40
3295 4008 0.107654 CCGGTTAGGGAGGAGCAAAG 60.108 60.000 0.00 0.00 35.97 2.77
3296 4009 0.545787 TCCGGTTAGGGAGGAGCAAA 60.546 55.000 0.00 0.00 41.52 3.68
3298 4011 2.775030 TCCGGTTAGGGAGGAGCA 59.225 61.111 0.00 0.00 41.52 4.26
3305 4018 4.176752 GCCCAGCTCCGGTTAGGG 62.177 72.222 16.30 16.30 42.55 3.53
3306 4019 3.391665 CTGCCCAGCTCCGGTTAGG 62.392 68.421 0.00 0.00 42.97 2.69
3326 4039 1.531149 CGGCTGTCTACAACAACAAGG 59.469 52.381 0.00 0.00 37.45 3.61
3327 4040 1.531149 CCGGCTGTCTACAACAACAAG 59.469 52.381 0.00 0.00 37.45 3.16
3351 4064 1.496060 TGGGGTCTTAGCATGACGAT 58.504 50.000 0.00 0.00 35.45 3.73
3354 4067 3.686016 TCTTTTGGGGTCTTAGCATGAC 58.314 45.455 0.00 0.00 0.00 3.06
3357 4070 3.635591 CCATCTTTTGGGGTCTTAGCAT 58.364 45.455 0.00 0.00 42.33 3.79
3377 4090 1.298339 GTTGTTGATATGGCGCGCC 60.298 57.895 42.35 42.35 0.00 6.53
3379 4092 0.662619 ATGGTTGTTGATATGGCGCG 59.337 50.000 0.00 0.00 0.00 6.86
3380 4093 1.675483 TGATGGTTGTTGATATGGCGC 59.325 47.619 0.00 0.00 0.00 6.53
3381 4094 2.033299 GGTGATGGTTGTTGATATGGCG 59.967 50.000 0.00 0.00 0.00 5.69
3382 4095 2.033299 CGGTGATGGTTGTTGATATGGC 59.967 50.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.