Multiple sequence alignment - TraesCS1D01G067500

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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 TraesCS1D01G067500 chr1D 100.000 5811 0 0 1 5811 49417774 49423584 0.000000e+00 10732.0
1 TraesCS1D01G067500 chr1D 84.843 508 48 12 2199 2696 49419218 49419706 8.750000e-133 484.0
2 TraesCS1D01G067500 chr1D 84.843 508 48 12 1445 1933 49419972 49420469 8.750000e-133 484.0
3 TraesCS1D01G067500 chr1D 81.250 80 14 1 5641 5719 49589671 49589750 4.860000e-06 63.9
4 TraesCS1D01G067500 chr1B 95.538 1860 66 5 3063 4906 69541644 69543502 0.000000e+00 2959.0
5 TraesCS1D01G067500 chr1B 90.390 2258 132 37 1 2201 69539112 69541341 0.000000e+00 2889.0
6 TraesCS1D01G067500 chr1B 97.975 395 6 1 5419 5811 69546569 69546963 0.000000e+00 684.0
7 TraesCS1D01G067500 chr1B 85.827 508 44 13 2203 2696 69540584 69541077 1.120000e-141 514.0
8 TraesCS1D01G067500 chr1B 94.969 159 8 0 2898 3056 69541423 69541581 3.480000e-62 250.0
9 TraesCS1D01G067500 chr1B 92.079 101 7 1 5318 5417 69543990 69544090 2.180000e-29 141.0
10 TraesCS1D01G067500 chr1A 94.976 1851 70 13 3064 4906 48981001 48982836 0.000000e+00 2881.0
11 TraesCS1D01G067500 chr1A 88.828 1468 80 33 1 1446 48978570 48979975 0.000000e+00 1725.0
12 TraesCS1D01G067500 chr1A 86.066 854 53 28 2203 3039 48980011 48980815 0.000000e+00 857.0
13 TraesCS1D01G067500 chr1A 95.674 393 11 2 5419 5811 48992122 48992508 1.370000e-175 627.0
14 TraesCS1D01G067500 chr1A 86.000 500 42 11 1449 1932 48980011 48980498 1.440000e-140 510.0
15 TraesCS1D01G067500 chr1A 95.000 100 5 0 5318 5417 48983268 48983367 2.170000e-34 158.0
16 TraesCS1D01G067500 chr1A 81.250 80 14 1 5641 5719 49100177 49100256 4.860000e-06 63.9
17 TraesCS1D01G067500 chr6D 89.051 274 20 9 1921 2190 411719790 411720057 1.210000e-86 331.0
18 TraesCS1D01G067500 chr6D 80.053 376 46 16 5419 5778 401297015 401296653 9.670000e-63 252.0
19 TraesCS1D01G067500 chr7D 87.970 266 25 6 1930 2193 583059319 583059059 2.030000e-79 307.0
20 TraesCS1D01G067500 chr7D 81.768 181 24 4 5228 5399 285229047 285229227 6.070000e-30 143.0
21 TraesCS1D01G067500 chr6B 87.452 263 24 6 1936 2194 173575568 173575311 1.580000e-75 294.0
22 TraesCS1D01G067500 chr6B 79.644 393 50 17 5419 5794 601869112 601868733 7.470000e-64 255.0
23 TraesCS1D01G067500 chr6A 87.072 263 25 5 1936 2194 109384971 109384714 7.370000e-74 289.0
24 TraesCS1D01G067500 chr5D 85.714 266 25 10 1933 2194 113741613 113741357 9.600000e-68 268.0
25 TraesCS1D01G067500 chr3D 86.992 246 20 11 1930 2172 942562 942326 3.450000e-67 267.0
26 TraesCS1D01G067500 chr3D 84.328 268 37 3 1924 2190 54981542 54981805 2.080000e-64 257.0
27 TraesCS1D01G067500 chr3D 88.485 165 14 3 1929 2092 459073921 459074081 1.650000e-45 195.0
28 TraesCS1D01G067500 chr2D 80.672 238 39 5 5168 5399 203042145 203042381 1.660000e-40 178.0
29 TraesCS1D01G067500 chr2B 80.426 235 41 3 5170 5399 256951777 256952011 2.150000e-39 174.0
30 TraesCS1D01G067500 chr2B 83.117 77 11 2 2110 2184 68202395 68202471 1.040000e-07 69.4
31 TraesCS1D01G067500 chr7B 83.333 180 22 4 5228 5399 275461500 275461321 6.030000e-35 159.0
32 TraesCS1D01G067500 chr7B 83.824 68 5 5 5221 5283 522084376 522084310 6.290000e-05 60.2
33 TraesCS1D01G067500 chr2A 79.487 234 41 5 5168 5399 231349705 231349933 6.030000e-35 159.0
34 TraesCS1D01G067500 chr7A 86.861 137 16 2 5265 5399 323433820 323433956 1.010000e-32 152.0
35 TraesCS1D01G067500 chr5A 81.667 180 28 4 5224 5399 467577830 467578008 1.690000e-30 145.0


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 TraesCS1D01G067500 chr1D 49417774 49423584 5810 False 10732.0 10732 100.000000 1 5811 1 chr1D.!!$F1 5810
1 TraesCS1D01G067500 chr1D 49419218 49420469 1251 False 484.0 484 84.843000 1445 2696 2 chr1D.!!$F3 1251
2 TraesCS1D01G067500 chr1B 69539112 69546963 7851 False 1239.5 2959 92.796333 1 5811 6 chr1B.!!$F1 5810
3 TraesCS1D01G067500 chr1A 48978570 48983367 4797 False 1226.2 2881 90.174000 1 5417 5 chr1A.!!$F3 5416

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
302 307 0.743097 ATTACGTCCTCGCCCACTAC 59.257 55.000 0.0 0.0 41.18 2.73 F
1283 1327 0.532573 GACCACCTGCATCGAGAAGA 59.467 55.000 0.0 0.0 0.00 2.87 F
1318 1362 2.915659 ACCTGCCTCAACGTCGGA 60.916 61.111 0.0 0.0 0.00 4.55 F
2757 2867 3.008485 TGCAGTTTTTCCCCAAACAGTTT 59.992 39.130 0.0 0.0 38.86 2.66 F
3683 3980 2.159382 GTTGATTTGGTCGATGGTGGT 58.841 47.619 0.0 0.0 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1318 1362 0.920763 TCACCTTGGAGGGGATGCAT 60.921 55.000 0.0 0.0 44.45 3.96 R
3058 3283 1.348036 ACTGGACTTGCTGTTCCTACC 59.652 52.381 0.0 0.0 0.00 3.18 R
3061 3286 2.301346 CAAACTGGACTTGCTGTTCCT 58.699 47.619 0.0 0.0 0.00 3.36 R
4268 4565 1.033746 CACATGCCACACCATCCTCC 61.034 60.000 0.0 0.0 0.00 4.30 R
5022 5347 1.028905 TTTGTTCTTTCTGGGCCACG 58.971 50.000 0.0 0.0 0.00 4.94 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
39 40 4.759516 TTCAAGGGACGTTGCTAAATTC 57.240 40.909 0.00 0.00 0.00 2.17
89 90 6.934645 ACACTTCAGGTTCGAAGATAAATCAA 59.065 34.615 0.00 0.00 44.32 2.57
112 113 6.091123 ACTCGCAATACATTCGTAAACTTC 57.909 37.500 0.00 0.00 0.00 3.01
113 114 5.867716 ACTCGCAATACATTCGTAAACTTCT 59.132 36.000 0.00 0.00 0.00 2.85
114 115 6.367969 ACTCGCAATACATTCGTAAACTTCTT 59.632 34.615 0.00 0.00 0.00 2.52
115 116 7.095355 ACTCGCAATACATTCGTAAACTTCTTT 60.095 33.333 0.00 0.00 0.00 2.52
129 134 7.201670 CGTAAACTTCTTTCTTGTGTTTACCCT 60.202 37.037 16.30 0.00 44.48 4.34
227 232 2.095059 CCAGCAATACAAAGACAGTGGC 60.095 50.000 0.00 0.00 0.00 5.01
302 307 0.743097 ATTACGTCCTCGCCCACTAC 59.257 55.000 0.00 0.00 41.18 2.73
359 364 2.355513 GCTCCAGAAGGAATCTCAAGCA 60.356 50.000 0.00 0.00 45.19 3.91
362 367 3.008330 CCAGAAGGAATCTCAAGCAGTG 58.992 50.000 0.00 0.00 35.73 3.66
386 391 5.641209 GTGCTGTGAATAACTCTGAATCAGT 59.359 40.000 10.36 0.00 32.61 3.41
389 394 6.148480 GCTGTGAATAACTCTGAATCAGTGTT 59.852 38.462 26.81 26.81 45.75 3.32
394 399 7.331934 TGAATAACTCTGAATCAGTGTTAGCAC 59.668 37.037 29.39 23.85 46.28 4.40
396 401 6.350194 ATAACTCTGAATCAGTGTTAGCACGA 60.350 38.462 29.39 16.49 46.28 4.35
419 425 1.141019 TGCAAGGACGCGGTAGATC 59.859 57.895 12.47 0.00 33.35 2.75
426 432 1.674962 GGACGCGGTAGATCAGTTAGT 59.325 52.381 12.47 0.00 0.00 2.24
427 433 2.286891 GGACGCGGTAGATCAGTTAGTC 60.287 54.545 12.47 0.00 0.00 2.59
469 491 2.453812 GGTGGTGGTGGTGGTGGTA 61.454 63.158 0.00 0.00 0.00 3.25
473 495 2.038269 GTGGTGGTGGTGGTATGCG 61.038 63.158 0.00 0.00 0.00 4.73
556 578 3.302870 CGTTCTTTTGTTCCGATCAACGT 60.303 43.478 0.00 0.00 40.78 3.99
560 582 5.642686 TCTTTTGTTCCGATCAACGTTTTT 58.357 33.333 0.00 0.00 40.78 1.94
571 593 4.156664 TCAACGTTTTTGTTTCACGGAA 57.843 36.364 0.00 0.00 38.26 4.30
572 594 4.159857 TCAACGTTTTTGTTTCACGGAAG 58.840 39.130 0.00 0.00 38.26 3.46
595 622 7.846101 AGAGAGTGTTGATCCATGTATATGA 57.154 36.000 0.25 0.00 36.36 2.15
644 671 7.661437 TGAGAGAGATTGCTAACTAGAGATCTC 59.339 40.741 15.29 15.29 40.14 2.75
661 688 6.922957 AGAGATCTCGAGCTTTTCATATGTTC 59.077 38.462 16.97 0.00 34.09 3.18
681 708 1.659098 CGTTCCCAGCGATGAAGTTAC 59.341 52.381 0.06 0.00 0.00 2.50
688 716 3.061697 CCAGCGATGAAGTTACGGTAAAC 59.938 47.826 0.06 0.00 36.06 2.01
707 735 6.586082 GGTAAACAAACCATGCATAACTCAAG 59.414 38.462 0.00 0.00 39.50 3.02
710 738 6.403866 ACAAACCATGCATAACTCAAGAAA 57.596 33.333 0.00 0.00 0.00 2.52
713 741 7.933033 ACAAACCATGCATAACTCAAGAAATTT 59.067 29.630 0.00 0.00 0.00 1.82
734 762 8.782533 AATTTAACTTGAACACGACAGATTTC 57.217 30.769 0.00 0.00 0.00 2.17
735 764 7.548196 TTTAACTTGAACACGACAGATTTCT 57.452 32.000 0.00 0.00 0.00 2.52
746 775 3.120199 CGACAGATTTCTGAAAATGCCGT 60.120 43.478 14.29 0.97 46.59 5.68
747 776 4.161333 GACAGATTTCTGAAAATGCCGTG 58.839 43.478 14.29 1.99 46.59 4.94
748 777 3.569701 ACAGATTTCTGAAAATGCCGTGT 59.430 39.130 14.29 2.55 46.59 4.49
781 810 3.628008 TGATTGAATGAGAAGCATGCCT 58.372 40.909 15.66 4.88 37.28 4.75
888 917 3.840666 TCTACAAGGCCATATCCATCCTC 59.159 47.826 5.01 0.00 0.00 3.71
905 934 1.457346 CTCTGCAGGATTGGGTGTTC 58.543 55.000 15.13 0.00 0.00 3.18
1034 1070 2.902343 GCCATAGGCGCTTCCCAC 60.902 66.667 7.64 0.00 39.62 4.61
1283 1327 0.532573 GACCACCTGCATCGAGAAGA 59.467 55.000 0.00 0.00 0.00 2.87
1318 1362 2.915659 ACCTGCCTCAACGTCGGA 60.916 61.111 0.00 0.00 0.00 4.55
1349 1399 4.566278 CCTCCAAGGTGATTGATTGACTGA 60.566 45.833 0.00 0.00 41.83 3.41
1350 1400 4.326826 TCCAAGGTGATTGATTGACTGAC 58.673 43.478 0.00 0.00 41.83 3.51
1391 1441 3.861263 GTCCCGTTCATTCGCGGC 61.861 66.667 6.13 0.00 45.98 6.53
1421 1471 3.774702 GACGCCGCCGAGTGTTTC 61.775 66.667 0.00 0.00 38.29 2.78
2757 2867 3.008485 TGCAGTTTTTCCCCAAACAGTTT 59.992 39.130 0.00 0.00 38.86 2.66
2807 2918 9.950496 AAACAGTATCAAGTCTCATCTTTATGT 57.050 29.630 0.00 0.00 34.50 2.29
2886 2999 8.581253 TGATTTAGGCTATATGATTCTCTCGA 57.419 34.615 2.01 0.00 0.00 4.04
2887 3000 8.681806 TGATTTAGGCTATATGATTCTCTCGAG 58.318 37.037 5.93 5.93 0.00 4.04
2888 3001 8.588290 ATTTAGGCTATATGATTCTCTCGAGT 57.412 34.615 13.13 0.00 0.00 4.18
2889 3002 7.618502 TTAGGCTATATGATTCTCTCGAGTC 57.381 40.000 13.13 2.87 0.00 3.36
2890 3003 5.815581 AGGCTATATGATTCTCTCGAGTCT 58.184 41.667 13.13 0.00 0.00 3.24
2891 3004 6.245408 AGGCTATATGATTCTCTCGAGTCTT 58.755 40.000 13.13 3.54 0.00 3.01
2892 3005 7.398829 AGGCTATATGATTCTCTCGAGTCTTA 58.601 38.462 13.13 5.67 0.00 2.10
2893 3006 8.052748 AGGCTATATGATTCTCTCGAGTCTTAT 58.947 37.037 13.13 12.05 33.65 1.73
2894 3007 9.332502 GGCTATATGATTCTCTCGAGTCTTATA 57.667 37.037 13.13 12.48 32.37 0.98
2925 3038 6.086785 AGCTAAACTTACTCTTGTTCGAGT 57.913 37.500 0.00 0.00 45.62 4.18
2984 3104 4.565817 AGGAAGATTGGCTAGGAAGAGAT 58.434 43.478 0.00 0.00 0.00 2.75
3056 3281 6.576442 GCCAACTAGAAGGGAAAGAGTTCATA 60.576 42.308 0.00 0.00 35.25 2.15
3057 3282 7.394816 CCAACTAGAAGGGAAAGAGTTCATAA 58.605 38.462 0.00 0.00 35.25 1.90
3058 3283 7.550906 CCAACTAGAAGGGAAAGAGTTCATAAG 59.449 40.741 0.00 0.00 35.25 1.73
3059 3284 7.189079 ACTAGAAGGGAAAGAGTTCATAAGG 57.811 40.000 0.00 0.00 35.25 2.69
3061 3286 7.899709 ACTAGAAGGGAAAGAGTTCATAAGGTA 59.100 37.037 0.00 0.00 35.25 3.08
3088 3369 3.627577 CAGCAAGTCCAGTTTGTAACAGT 59.372 43.478 0.00 0.00 0.00 3.55
3094 3375 5.445964 AGTCCAGTTTGTAACAGTTGGAAT 58.554 37.500 0.00 0.00 36.56 3.01
3110 3391 7.872993 ACAGTTGGAATCATATCCTAACATACG 59.127 37.037 0.00 0.00 40.35 3.06
3136 3417 5.390613 GTCAACAACATAATTTGACTCCCG 58.609 41.667 6.47 0.00 43.80 5.14
3140 3421 5.745227 ACAACATAATTTGACTCCCGAGAT 58.255 37.500 0.00 0.00 0.00 2.75
3142 3423 6.986817 ACAACATAATTTGACTCCCGAGATAG 59.013 38.462 0.00 0.00 0.00 2.08
3237 3534 7.155328 ACAACATCTTTCTTATAGGCCTATCG 58.845 38.462 28.75 19.88 0.00 2.92
3239 3536 7.304497 ACATCTTTCTTATAGGCCTATCGTT 57.696 36.000 28.75 8.80 0.00 3.85
3256 3553 7.030165 CCTATCGTTTGTATAGCTCCTACATG 58.970 42.308 9.24 0.00 0.00 3.21
3258 3555 6.459670 TCGTTTGTATAGCTCCTACATGAA 57.540 37.500 0.00 1.27 0.00 2.57
3425 3722 5.996644 TGGAAACACTTCTAACTTCCTTCA 58.003 37.500 0.00 0.00 37.13 3.02
3674 3971 4.274950 TCAGAAGTTTCGGTTGATTTGGTC 59.725 41.667 0.00 0.00 0.00 4.02
3683 3980 2.159382 GTTGATTTGGTCGATGGTGGT 58.841 47.619 0.00 0.00 0.00 4.16
4268 4565 1.288127 GCTTGCCCACAAAGCTGAG 59.712 57.895 1.01 0.00 34.74 3.35
4698 4995 6.240894 TCTAAGGCCATCCACATATGATTTC 58.759 40.000 10.38 0.00 33.74 2.17
4832 5131 1.163420 TAACAGTTGCCAGTGCCACG 61.163 55.000 0.00 0.00 38.14 4.94
4865 5164 8.700722 TGTACATGCCATTGAATTTATGTTTC 57.299 30.769 0.00 0.00 31.84 2.78
4879 5178 6.645884 TTTATGTTTCCTTCTTAGGCCCTA 57.354 37.500 0.00 0.00 41.69 3.53
4886 5185 4.481072 TCCTTCTTAGGCCCTACTACATC 58.519 47.826 0.00 0.00 41.69 3.06
4899 5198 0.249238 CTACATCTGGAGTGAGGCGC 60.249 60.000 0.00 0.00 0.00 6.53
4900 5199 0.684479 TACATCTGGAGTGAGGCGCT 60.684 55.000 7.64 0.00 0.00 5.92
4906 5205 1.078143 GGAGTGAGGCGCTTTGGAT 60.078 57.895 7.64 0.00 0.00 3.41
4908 5207 1.202698 GGAGTGAGGCGCTTTGGATAT 60.203 52.381 7.64 0.00 0.00 1.63
4909 5208 2.565841 GAGTGAGGCGCTTTGGATATT 58.434 47.619 7.64 0.00 0.00 1.28
4910 5209 2.945668 GAGTGAGGCGCTTTGGATATTT 59.054 45.455 7.64 0.00 0.00 1.40
4912 5211 2.682856 GTGAGGCGCTTTGGATATTTGA 59.317 45.455 7.64 0.00 0.00 2.69
4913 5212 3.128589 GTGAGGCGCTTTGGATATTTGAA 59.871 43.478 7.64 0.00 0.00 2.69
4914 5213 3.378112 TGAGGCGCTTTGGATATTTGAAG 59.622 43.478 7.64 0.00 0.00 3.02
4915 5214 3.620488 AGGCGCTTTGGATATTTGAAGA 58.380 40.909 7.64 0.00 0.00 2.87
4916 5215 4.210331 AGGCGCTTTGGATATTTGAAGAT 58.790 39.130 7.64 0.00 0.00 2.40
4917 5216 4.037208 AGGCGCTTTGGATATTTGAAGATG 59.963 41.667 7.64 0.00 0.00 2.90
4918 5217 4.036734 GGCGCTTTGGATATTTGAAGATGA 59.963 41.667 7.64 0.00 0.00 2.92
4919 5218 4.972440 GCGCTTTGGATATTTGAAGATGAC 59.028 41.667 0.00 0.00 0.00 3.06
4920 5219 5.514279 CGCTTTGGATATTTGAAGATGACC 58.486 41.667 0.00 0.00 0.00 4.02
4921 5220 5.297776 CGCTTTGGATATTTGAAGATGACCT 59.702 40.000 0.00 0.00 0.00 3.85
4922 5221 6.183360 CGCTTTGGATATTTGAAGATGACCTT 60.183 38.462 0.00 0.00 37.93 3.50
4923 5222 7.550712 GCTTTGGATATTTGAAGATGACCTTT 58.449 34.615 0.00 0.00 34.68 3.11
4924 5223 8.037166 GCTTTGGATATTTGAAGATGACCTTTT 58.963 33.333 0.00 0.00 34.68 2.27
5046 5373 2.297315 GGCCCAGAAAGAACAAAAGGAG 59.703 50.000 0.00 0.00 0.00 3.69
5048 5375 3.566351 CCCAGAAAGAACAAAAGGAGGT 58.434 45.455 0.00 0.00 0.00 3.85
5112 5439 7.028962 TCACTTATGAAAATGTATGTTGCTGC 58.971 34.615 0.00 0.00 0.00 5.25
5113 5440 6.807720 CACTTATGAAAATGTATGTTGCTGCA 59.192 34.615 0.00 0.00 0.00 4.41
5114 5441 6.808212 ACTTATGAAAATGTATGTTGCTGCAC 59.192 34.615 0.00 0.00 0.00 4.57
5115 5442 3.911868 TGAAAATGTATGTTGCTGCACC 58.088 40.909 0.00 0.00 0.00 5.01
5116 5443 3.253230 GAAAATGTATGTTGCTGCACCC 58.747 45.455 0.00 0.00 0.00 4.61
5117 5444 0.810648 AATGTATGTTGCTGCACCCG 59.189 50.000 0.00 0.00 0.00 5.28
5118 5445 1.656818 ATGTATGTTGCTGCACCCGC 61.657 55.000 0.00 0.00 39.24 6.13
5184 5511 2.988010 TGTACTAGCTCATTGCCTGG 57.012 50.000 0.00 0.00 44.23 4.45
5191 5518 1.503542 CTCATTGCCTGGACGTTGC 59.496 57.895 0.00 0.00 0.00 4.17
5195 5522 0.823356 ATTGCCTGGACGTTGCAACT 60.823 50.000 26.09 13.84 46.60 3.16
5200 5527 0.532862 CTGGACGTTGCAACTGAGGT 60.533 55.000 26.09 16.71 0.00 3.85
5211 5538 6.523201 CGTTGCAACTGAGGTAAACATATTTC 59.477 38.462 26.09 0.00 0.00 2.17
5237 5566 9.229784 CAGTGATTCAATATCAATTACAAGTGC 57.770 33.333 0.00 0.00 0.00 4.40
5250 5579 1.486310 ACAAGTGCCTCAACAGAGACA 59.514 47.619 0.00 0.00 0.00 3.41
5285 5615 1.285280 ATGGTCCTTCCCACATCGAA 58.715 50.000 0.00 0.00 37.31 3.71
5328 5659 8.173775 GTGTTGTAGAATGTGAAGATGATGAAG 58.826 37.037 0.00 0.00 0.00 3.02
5372 5779 8.234525 AGGAGGAGCCCACATAAATAATATTTT 58.765 33.333 3.36 0.00 37.37 1.82
5417 5825 2.203394 AGCGCCTGGGCCATTATG 60.203 61.111 6.72 0.00 37.98 1.90
5435 8320 3.751479 ATGTGCCCAAGGAAGAAAAAC 57.249 42.857 0.00 0.00 0.00 2.43
5453 8338 3.996921 AACTGAGAGTGCTTGGATGAT 57.003 42.857 0.00 0.00 0.00 2.45
5486 8371 7.223777 GCAGAACTTGAGAGTCAACTATTATCC 59.776 40.741 0.00 0.00 34.21 2.59
5606 8491 9.196552 GGAATGAATTGAAGGTTTTTAAGTGAG 57.803 33.333 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 5.616488 TTAGCAACGTCCCTTGAAATTAC 57.384 39.130 0.00 0.00 0.00 1.89
39 40 0.944386 CTTGGTGACCTTGAACCACG 59.056 55.000 2.11 0.00 46.04 4.94
89 90 5.867716 AGAAGTTTACGAATGTATTGCGAGT 59.132 36.000 0.00 0.00 0.00 4.18
112 113 6.202516 TGTCAAAGGGTAAACACAAGAAAG 57.797 37.500 0.00 0.00 0.00 2.62
113 114 6.591750 TTGTCAAAGGGTAAACACAAGAAA 57.408 33.333 0.00 0.00 0.00 2.52
114 115 6.591750 TTTGTCAAAGGGTAAACACAAGAA 57.408 33.333 0.00 0.00 0.00 2.52
115 116 6.605594 AGATTTGTCAAAGGGTAAACACAAGA 59.394 34.615 4.03 0.00 0.00 3.02
129 134 7.388776 ACGAGATCAATCAAGAGATTTGTCAAA 59.611 33.333 0.00 0.00 42.46 2.69
227 232 1.825090 TGGCATAGTTCACTTGCTGG 58.175 50.000 11.42 0.00 36.62 4.85
317 322 3.877559 CTTCTCCCACAAGCACATCATA 58.122 45.455 0.00 0.00 0.00 2.15
359 364 4.607293 TCAGAGTTATTCACAGCACACT 57.393 40.909 0.00 0.00 0.00 3.55
362 367 5.641209 ACTGATTCAGAGTTATTCACAGCAC 59.359 40.000 20.33 0.00 35.18 4.40
368 373 7.331934 GTGCTAACACTGATTCAGAGTTATTCA 59.668 37.037 26.43 23.47 42.89 2.57
411 417 5.710984 ACAACAAGACTAACTGATCTACCG 58.289 41.667 0.00 0.00 0.00 4.02
413 419 7.948278 ACAACAACAAGACTAACTGATCTAC 57.052 36.000 0.00 0.00 0.00 2.59
419 425 6.378582 ACAACAACAACAACAAGACTAACTG 58.621 36.000 0.00 0.00 0.00 3.16
426 432 4.747108 CCAACAACAACAACAACAACAAGA 59.253 37.500 0.00 0.00 0.00 3.02
427 433 4.509600 ACCAACAACAACAACAACAACAAG 59.490 37.500 0.00 0.00 0.00 3.16
473 495 3.368323 CCACCCACATAAAAATGCTGGAC 60.368 47.826 7.91 0.00 0.00 4.02
512 534 1.270412 TGATCGCCGGTTGTTACAACT 60.270 47.619 24.67 6.65 0.00 3.16
556 578 4.698304 ACACTCTCTTCCGTGAAACAAAAA 59.302 37.500 0.00 0.00 35.74 1.94
560 582 3.118920 TCAACACTCTCTTCCGTGAAACA 60.119 43.478 0.00 0.00 35.74 2.83
571 593 7.846101 TCATATACATGGATCAACACTCTCT 57.154 36.000 0.00 0.00 32.61 3.10
572 594 8.933807 CATTCATATACATGGATCAACACTCTC 58.066 37.037 0.00 0.00 26.66 3.20
621 648 6.649141 TCGAGATCTCTAGTTAGCAATCTCTC 59.351 42.308 20.26 0.00 38.07 3.20
625 652 5.181245 AGCTCGAGATCTCTAGTTAGCAATC 59.819 44.000 21.59 6.24 0.00 2.67
644 671 4.494199 GGGAACGAACATATGAAAAGCTCG 60.494 45.833 10.38 9.49 0.00 5.03
661 688 1.659098 GTAACTTCATCGCTGGGAACG 59.341 52.381 0.00 0.00 0.00 3.95
681 708 5.054390 AGTTATGCATGGTTTGTTTACCG 57.946 39.130 10.16 0.00 41.28 4.02
688 716 7.894376 AATTTCTTGAGTTATGCATGGTTTG 57.106 32.000 10.16 0.00 0.00 2.93
707 735 8.782533 AATCTGTCGTGTTCAAGTTAAATTTC 57.217 30.769 0.00 0.00 0.00 2.17
710 738 8.070171 CAGAAATCTGTCGTGTTCAAGTTAAAT 58.930 33.333 2.18 0.00 39.09 1.40
713 741 6.277605 TCAGAAATCTGTCGTGTTCAAGTTA 58.722 36.000 10.06 0.00 44.12 2.24
721 749 4.320494 GGCATTTTCAGAAATCTGTCGTGT 60.320 41.667 10.06 0.00 44.12 4.49
722 750 4.161333 GGCATTTTCAGAAATCTGTCGTG 58.839 43.478 10.06 6.83 44.12 4.35
724 752 3.120199 ACGGCATTTTCAGAAATCTGTCG 60.120 43.478 22.05 22.05 44.12 4.35
727 755 4.164822 ACACGGCATTTTCAGAAATCTG 57.835 40.909 3.99 3.99 45.08 2.90
734 762 3.862267 TGTTTCAAACACGGCATTTTCAG 59.138 39.130 0.00 0.00 36.25 3.02
735 764 3.849911 TGTTTCAAACACGGCATTTTCA 58.150 36.364 0.00 0.00 36.25 2.69
746 775 8.631797 TCTCATTCAATCAATCTGTTTCAAACA 58.368 29.630 2.24 2.24 39.52 2.83
747 776 9.467258 TTCTCATTCAATCAATCTGTTTCAAAC 57.533 29.630 0.00 0.00 0.00 2.93
748 777 9.687210 CTTCTCATTCAATCAATCTGTTTCAAA 57.313 29.630 0.00 0.00 0.00 2.69
781 810 6.601613 TCTCTTTCAGAACCACTAAAAAGCAA 59.398 34.615 0.00 0.00 33.93 3.91
784 813 8.214721 ACTTCTCTTTCAGAACCACTAAAAAG 57.785 34.615 0.00 0.00 36.08 2.27
888 917 1.926511 GCGAACACCCAATCCTGCAG 61.927 60.000 6.78 6.78 0.00 4.41
946 975 4.101790 GTGGCGGGAATGTGTGCG 62.102 66.667 0.00 0.00 0.00 5.34
1034 1070 1.205893 CCTTTCTTCGACAGGAGAGGG 59.794 57.143 9.53 2.79 31.69 4.30
1181 1225 4.539881 GACGTCGCTCTCCTCCGC 62.540 72.222 0.00 0.00 0.00 5.54
1318 1362 0.920763 TCACCTTGGAGGGGATGCAT 60.921 55.000 0.00 0.00 44.45 3.96
1349 1399 3.300765 AAACGGAGAGGGCGTCGT 61.301 61.111 0.96 0.00 37.45 4.34
1350 1400 2.809601 CAAACGGAGAGGGCGTCG 60.810 66.667 0.96 0.00 0.00 5.12
1411 1461 4.703645 TCACAGATCTAGAAACACTCGG 57.296 45.455 0.00 0.00 0.00 4.63
1412 1462 4.502282 GCATCACAGATCTAGAAACACTCG 59.498 45.833 0.00 0.00 0.00 4.18
1413 1463 5.414360 TGCATCACAGATCTAGAAACACTC 58.586 41.667 0.00 0.00 0.00 3.51
1421 1471 3.404224 AGCCATGCATCACAGATCTAG 57.596 47.619 0.00 0.00 0.00 2.43
2696 2806 7.503566 CCCATTTCACCATTTATGACAGATAGT 59.496 37.037 0.00 0.00 0.00 2.12
2697 2807 7.522725 GCCCATTTCACCATTTATGACAGATAG 60.523 40.741 0.00 0.00 0.00 2.08
2698 2808 6.265196 GCCCATTTCACCATTTATGACAGATA 59.735 38.462 0.00 0.00 0.00 1.98
2699 2809 5.069516 GCCCATTTCACCATTTATGACAGAT 59.930 40.000 0.00 0.00 0.00 2.90
2700 2810 4.402155 GCCCATTTCACCATTTATGACAGA 59.598 41.667 0.00 0.00 0.00 3.41
2701 2811 4.160065 TGCCCATTTCACCATTTATGACAG 59.840 41.667 0.00 0.00 0.00 3.51
2702 2812 4.092279 TGCCCATTTCACCATTTATGACA 58.908 39.130 0.00 0.00 0.00 3.58
2757 2867 6.614694 TTTAGCAGGAACAGTATTCTGGTA 57.385 37.500 4.24 0.00 42.23 3.25
2784 2895 8.815189 CACACATAAAGATGAGACTTGATACTG 58.185 37.037 0.00 0.00 36.48 2.74
2805 2916 2.820059 AGATGTTTCGCTCTCACACA 57.180 45.000 0.00 0.00 0.00 3.72
2806 2917 3.743396 AGAAAGATGTTTCGCTCTCACAC 59.257 43.478 9.47 0.00 45.90 3.82
2807 2918 3.995199 AGAAAGATGTTTCGCTCTCACA 58.005 40.909 9.47 0.00 45.90 3.58
2875 2988 8.197439 TGCATTTTATAAGACTCGAGAGAATCA 58.803 33.333 21.68 0.00 39.17 2.57
2876 2989 8.581057 TGCATTTTATAAGACTCGAGAGAATC 57.419 34.615 21.68 6.00 41.32 2.52
2877 2990 8.948631 TTGCATTTTATAAGACTCGAGAGAAT 57.051 30.769 21.68 9.24 41.32 2.40
2878 2991 7.010552 GCTTGCATTTTATAAGACTCGAGAGAA 59.989 37.037 21.68 0.00 41.32 2.87
2879 2992 6.477033 GCTTGCATTTTATAAGACTCGAGAGA 59.523 38.462 21.68 0.83 39.12 3.10
2880 2993 6.478344 AGCTTGCATTTTATAAGACTCGAGAG 59.522 38.462 21.68 0.56 0.00 3.20
2881 2994 6.341316 AGCTTGCATTTTATAAGACTCGAGA 58.659 36.000 21.68 0.00 0.00 4.04
2882 2995 6.595772 AGCTTGCATTTTATAAGACTCGAG 57.404 37.500 11.84 11.84 0.00 4.04
2883 2996 8.388103 GTTTAGCTTGCATTTTATAAGACTCGA 58.612 33.333 0.00 0.00 0.00 4.04
2884 2997 8.391106 AGTTTAGCTTGCATTTTATAAGACTCG 58.609 33.333 0.00 0.00 0.00 4.18
2892 3005 9.846248 CAAGAGTAAGTTTAGCTTGCATTTTAT 57.154 29.630 0.00 0.00 41.43 1.40
2893 3006 8.846211 ACAAGAGTAAGTTTAGCTTGCATTTTA 58.154 29.630 0.00 0.00 41.43 1.52
2894 3007 7.716612 ACAAGAGTAAGTTTAGCTTGCATTTT 58.283 30.769 0.00 0.00 41.43 1.82
2895 3008 7.277174 ACAAGAGTAAGTTTAGCTTGCATTT 57.723 32.000 0.00 0.00 41.43 2.32
2899 3012 5.176958 TCGAACAAGAGTAAGTTTAGCTTGC 59.823 40.000 0.00 0.00 39.51 4.01
2984 3104 6.027025 ACTTCTGTATCTATCCCCACTACA 57.973 41.667 0.00 0.00 0.00 2.74
3056 3281 2.039084 CTGGACTTGCTGTTCCTACCTT 59.961 50.000 0.00 0.00 0.00 3.50
3057 3282 1.625818 CTGGACTTGCTGTTCCTACCT 59.374 52.381 0.00 0.00 0.00 3.08
3058 3283 1.348036 ACTGGACTTGCTGTTCCTACC 59.652 52.381 0.00 0.00 0.00 3.18
3059 3284 2.841442 ACTGGACTTGCTGTTCCTAC 57.159 50.000 0.00 0.00 0.00 3.18
3061 3286 2.301346 CAAACTGGACTTGCTGTTCCT 58.699 47.619 0.00 0.00 0.00 3.36
3088 3369 8.647796 ACTTCGTATGTTAGGATATGATTCCAA 58.352 33.333 0.00 0.00 38.32 3.53
3094 3375 8.002984 TGTTGACTTCGTATGTTAGGATATGA 57.997 34.615 0.00 0.00 0.00 2.15
3136 3417 4.494591 ACCCAATTAGGAGTCCCTATCTC 58.505 47.826 5.25 0.00 44.14 2.75
3140 3421 4.630382 TGTACCCAATTAGGAGTCCCTA 57.370 45.455 5.25 0.00 43.97 3.53
3142 3423 4.263594 TGTTTGTACCCAATTAGGAGTCCC 60.264 45.833 5.25 0.00 41.22 4.46
3227 3524 4.461781 GGAGCTATACAAACGATAGGCCTA 59.538 45.833 16.60 16.60 43.77 3.93
3351 3648 6.606395 ACCAACGTAGATAATTCTCTAGGTGT 59.394 38.462 20.39 14.48 42.80 4.16
3405 3702 6.547510 AGCATTGAAGGAAGTTAGAAGTGTTT 59.452 34.615 0.00 0.00 0.00 2.83
3425 3722 1.684248 GCCTGGTGGATCAGAAGCATT 60.684 52.381 0.00 0.00 36.93 3.56
3674 3971 2.478894 GACAACAGTGTTACCACCATCG 59.521 50.000 8.49 0.00 42.88 3.84
4268 4565 1.033746 CACATGCCACACCATCCTCC 61.034 60.000 0.00 0.00 0.00 4.30
4370 4667 1.677966 CTCCTCCGTCTTCCCGACA 60.678 63.158 0.00 0.00 42.98 4.35
4508 4805 2.618241 GTGCACACCAAGAATCTTGTCA 59.382 45.455 20.18 8.19 0.00 3.58
4698 4995 7.442364 TGAGACAAGTGATAACAGAAAAAGGAG 59.558 37.037 0.00 0.00 0.00 3.69
4774 5071 2.872245 CAGGGCGAAATGACAATCGTAT 59.128 45.455 13.45 0.96 41.01 3.06
4777 5074 1.062587 GACAGGGCGAAATGACAATCG 59.937 52.381 9.05 9.05 41.81 3.34
4832 5131 3.446873 TCAATGGCATGTACAATGAACCC 59.553 43.478 0.00 0.00 0.00 4.11
4865 5164 4.282195 CAGATGTAGTAGGGCCTAAGAAGG 59.718 50.000 16.44 0.00 46.76 3.46
4879 5178 1.107114 CGCCTCACTCCAGATGTAGT 58.893 55.000 0.00 0.00 0.00 2.73
4886 5185 2.037136 CCAAAGCGCCTCACTCCAG 61.037 63.158 2.29 0.00 0.00 3.86
4899 5198 9.933723 AAAAAGGTCATCTTCAAATATCCAAAG 57.066 29.630 0.00 0.00 33.94 2.77
5022 5347 1.028905 TTTGTTCTTTCTGGGCCACG 58.971 50.000 0.00 0.00 0.00 4.94
5023 5348 2.224042 CCTTTTGTTCTTTCTGGGCCAC 60.224 50.000 0.00 0.00 0.00 5.01
5046 5373 9.744468 GACAAATATGTGTATAAAAATGGGACC 57.256 33.333 0.00 0.00 40.74 4.46
5091 5418 6.098679 GGTGCAGCAACATACATTTTCATAA 58.901 36.000 11.86 0.00 0.00 1.90
5122 5449 9.729281 ATGTCTATGAATTTCCAGCAAATTTTT 57.271 25.926 0.00 0.00 43.56 1.94
5127 5454 9.851686 AGTATATGTCTATGAATTTCCAGCAAA 57.148 29.630 0.00 0.00 0.00 3.68
5159 5486 7.180946 TCCAGGCAATGAGCTAGTACATATAAT 59.819 37.037 0.00 0.00 44.79 1.28
5184 5511 2.610374 TGTTTACCTCAGTTGCAACGTC 59.390 45.455 23.21 0.15 0.00 4.34
5191 5518 8.322906 TCACTGAAATATGTTTACCTCAGTTG 57.677 34.615 4.94 2.93 35.35 3.16
5195 5522 9.513906 TTGAATCACTGAAATATGTTTACCTCA 57.486 29.630 0.00 0.00 0.00 3.86
5211 5538 9.229784 GCACTTGTAATTGATATTGAATCACTG 57.770 33.333 0.00 0.00 0.00 3.66
5224 5553 4.713553 TCTGTTGAGGCACTTGTAATTGA 58.286 39.130 0.00 0.00 41.55 2.57
5231 5560 2.245159 TGTCTCTGTTGAGGCACTTG 57.755 50.000 0.00 0.00 46.67 3.16
5237 5566 4.000331 ACTCACAATGTCTCTGTTGAGG 58.000 45.455 0.00 0.00 40.58 3.86
5285 5615 2.025155 ACACGATCTTAGCCGATGACT 58.975 47.619 0.00 0.00 0.00 3.41
5328 5659 5.604650 TCCTCCTAAAATCTCTCATTCCCTC 59.395 44.000 0.00 0.00 0.00 4.30
5385 5793 4.919653 GCTGTCAAGCGAGGATCA 57.080 55.556 0.00 0.00 40.27 2.92
5417 5825 2.693074 TCAGTTTTTCTTCCTTGGGCAC 59.307 45.455 0.00 0.00 0.00 5.01
5435 8320 1.941294 GCATCATCCAAGCACTCTCAG 59.059 52.381 0.00 0.00 0.00 3.35
5453 8338 4.129888 ACTCTCAAGTTCTGCACCTGCA 62.130 50.000 0.00 0.00 40.05 4.41
5486 8371 4.503741 AAATGTCACCCTTCATTTGACG 57.496 40.909 0.00 0.00 42.20 4.35
5628 8513 7.746475 CAGTCAGTGAATTTCGTAATTTCCTTC 59.254 37.037 1.33 0.00 34.16 3.46
5749 8634 1.885887 TCTTGGTGCAGGTGTTTATGC 59.114 47.619 0.00 0.00 42.86 3.14


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

AutoCloner maintained by Alex Coulton.