Multiple sequence alignment - TraesCS5D01G093400

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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 TraesCS5D01G093400 chr5D 100.000 3563 0 0 1 3563 102279243 102275681 0.000000e+00 6580
1 TraesCS5D01G093400 chr5A 91.501 2459 139 39 694 3096 97565749 97563305 0.000000e+00 3319
2 TraesCS5D01G093400 chr5A 94.419 430 17 4 3115 3538 97563318 97562890 0.000000e+00 654
3 TraesCS5D01G093400 chr5B 91.033 1171 58 23 1922 3058 111682038 111680881 0.000000e+00 1537
4 TraesCS5D01G093400 chr5B 90.488 799 57 12 790 1587 111683471 111682691 0.000000e+00 1037
5 TraesCS5D01G093400 chr5B 85.894 794 92 10 3 786 111699918 111699135 0.000000e+00 828
6 TraesCS5D01G093400 chr5B 92.874 435 14 11 3137 3563 111680857 111680432 1.820000e-172 616
7 TraesCS5D01G093400 chr5B 87.723 448 45 9 1580 2021 111682504 111682061 6.820000e-142 514
8 TraesCS5D01G093400 chr2D 93.703 397 18 4 2404 2793 610857979 610858375 3.960000e-164 588


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 TraesCS5D01G093400 chr5D 102275681 102279243 3562 True 6580.0 6580 100.0000 1 3563 1 chr5D.!!$R1 3562
1 TraesCS5D01G093400 chr5A 97562890 97565749 2859 True 1986.5 3319 92.9600 694 3538 2 chr5A.!!$R1 2844
2 TraesCS5D01G093400 chr5B 111680432 111683471 3039 True 926.0 1537 90.5295 790 3563 4 chr5B.!!$R2 2773
3 TraesCS5D01G093400 chr5B 111699135 111699918 783 True 828.0 828 85.8940 3 786 1 chr5B.!!$R1 783

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
227 228 0.035458 GTCCTGTCCTTGTCACCCTG 59.965 60.000 0.00 0.0 0.0 4.45 F
1223 1237 0.036294 GCCTTAGGTCGGAGCTTGTT 60.036 55.000 15.66 0.0 0.0 2.83 F
1236 1250 1.007387 CTTGTTTCTTGCGCCACCC 60.007 57.895 4.18 0.0 0.0 4.61 F
2376 2746 0.038166 TGATGTGTTCCTGCCCCTTC 59.962 55.000 0.00 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1242 1256 0.108138 AGTGCCGACCTAATCACTGC 60.108 55.000 0.0 0.0 38.25 4.40 R
2068 2410 0.686224 TAAGTGTGGTGGGGGTTACG 59.314 55.000 0.0 0.0 0.00 3.18 R
2498 2870 1.153429 CGCTTAACGGGAGGAAGGG 60.153 63.158 0.0 0.0 38.44 3.95 R
3395 3786 0.322816 TGCTTCAGTTGGGGAGCATC 60.323 55.000 0.0 0.0 0.00 3.91 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
23 24 2.909076 GCAAAATTGACACAGTTGCG 57.091 45.000 0.00 0.00 35.69 4.85
24 25 1.522258 GCAAAATTGACACAGTTGCGG 59.478 47.619 0.00 0.00 35.69 5.69
25 26 1.522258 CAAAATTGACACAGTTGCGGC 59.478 47.619 0.00 0.00 0.00 6.53
66 67 1.009078 CGCGTGTCCAACATCATCAT 58.991 50.000 0.00 0.00 0.00 2.45
114 115 6.069665 TCGTAGTAGCAAAAATTTACGACG 57.930 37.500 13.95 13.95 43.20 5.12
115 116 5.855925 TCGTAGTAGCAAAAATTTACGACGA 59.144 36.000 17.02 17.02 45.89 4.20
122 123 6.318628 AGCAAAAATTTACGACGATTGCATA 58.681 32.000 18.60 0.00 42.95 3.14
123 124 6.804295 AGCAAAAATTTACGACGATTGCATAA 59.196 30.769 18.60 0.00 42.95 1.90
149 150 2.273370 TGTCTCGCGATAGAACCAAC 57.727 50.000 10.36 0.00 39.76 3.77
157 158 1.735700 CGATAGAACCAACGCAGCTCA 60.736 52.381 0.00 0.00 39.76 4.26
161 162 1.153168 AACCAACGCAGCTCACACT 60.153 52.632 0.00 0.00 0.00 3.55
165 166 1.063806 CAACGCAGCTCACACTCTAC 58.936 55.000 0.00 0.00 0.00 2.59
169 170 1.513158 CAGCTCACACTCTACGGGG 59.487 63.158 0.00 0.00 0.00 5.73
172 173 1.533469 GCTCACACTCTACGGGGTGT 61.533 60.000 0.00 0.00 45.96 4.16
182 183 1.802365 CTACGGGGTGTTTGTAGCAAC 59.198 52.381 0.00 0.00 30.29 4.17
184 185 1.161563 CGGGGTGTTTGTAGCAACGT 61.162 55.000 0.00 0.00 0.00 3.99
190 191 2.094575 GTGTTTGTAGCAACGTGTGACA 59.905 45.455 0.00 0.00 0.00 3.58
193 194 0.872451 TGTAGCAACGTGTGACACCG 60.872 55.000 10.52 7.99 0.00 4.94
208 209 3.803082 CCGATTGTGGCAGCACCG 61.803 66.667 0.00 0.00 43.94 4.94
212 213 3.196207 ATTGTGGCAGCACCGTCCT 62.196 57.895 0.00 0.00 43.94 3.85
221 222 1.668151 GCACCGTCCTGTCCTTGTC 60.668 63.158 0.00 0.00 0.00 3.18
227 228 0.035458 GTCCTGTCCTTGTCACCCTG 59.965 60.000 0.00 0.00 0.00 4.45
228 229 1.302832 CCTGTCCTTGTCACCCTGC 60.303 63.158 0.00 0.00 0.00 4.85
229 230 1.302832 CTGTCCTTGTCACCCTGCC 60.303 63.158 0.00 0.00 0.00 4.85
233 234 2.738521 CTTGTCACCCTGCCGTCG 60.739 66.667 0.00 0.00 0.00 5.12
250 251 1.461127 GTCGTCATGCTCACCAGTTTC 59.539 52.381 0.00 0.00 0.00 2.78
255 256 2.082231 CATGCTCACCAGTTTCAGAGG 58.918 52.381 0.00 0.00 0.00 3.69
271 274 2.106511 CAGAGGTAGAGAGAGGAGAGGG 59.893 59.091 0.00 0.00 0.00 4.30
273 276 2.372172 GAGGTAGAGAGAGGAGAGGGAG 59.628 59.091 0.00 0.00 0.00 4.30
302 305 1.568504 TGAGAACGCCCCTTCATAGT 58.431 50.000 0.00 0.00 0.00 2.12
326 329 1.484444 CCTAGGGGTAGCCATGGAGC 61.484 65.000 18.40 4.80 0.00 4.70
340 343 3.257873 CCATGGAGCTGTATCTCTCGATT 59.742 47.826 5.56 0.00 33.70 3.34
347 350 3.319405 GCTGTATCTCTCGATTGGGAAGA 59.681 47.826 0.00 0.00 0.00 2.87
351 354 6.341316 TGTATCTCTCGATTGGGAAGAAAAG 58.659 40.000 0.00 0.00 0.00 2.27
353 356 5.078411 TCTCTCGATTGGGAAGAAAAGAG 57.922 43.478 0.00 0.00 0.00 2.85
367 370 5.832539 AGAAAAGAGGGAAGAATGAGTGA 57.167 39.130 0.00 0.00 0.00 3.41
375 378 3.118445 GGGAAGAATGAGTGAAGGAGAGG 60.118 52.174 0.00 0.00 0.00 3.69
376 379 3.118445 GGAAGAATGAGTGAAGGAGAGGG 60.118 52.174 0.00 0.00 0.00 4.30
380 383 2.103153 TGAGTGAAGGAGAGGGTTGT 57.897 50.000 0.00 0.00 0.00 3.32
390 393 4.753186 AGGAGAGGGTTGTAGAGAAAAGA 58.247 43.478 0.00 0.00 0.00 2.52
393 396 6.960542 AGGAGAGGGTTGTAGAGAAAAGATAA 59.039 38.462 0.00 0.00 0.00 1.75
394 397 7.125053 AGGAGAGGGTTGTAGAGAAAAGATAAG 59.875 40.741 0.00 0.00 0.00 1.73
447 450 4.917415 GGACAACAAAACATATGAGTGTGC 59.083 41.667 10.38 5.53 31.49 4.57
452 455 3.334583 AAACATATGAGTGTGCGGTCT 57.665 42.857 10.38 0.00 31.49 3.85
464 467 1.671379 GCGGTCTCCCTGGTTGTTC 60.671 63.158 0.00 0.00 0.00 3.18
483 486 3.896317 GATCCAGGTAGATCGTGCC 57.104 57.895 0.00 0.00 33.78 5.01
485 488 1.464376 ATCCAGGTAGATCGTGCCGG 61.464 60.000 0.00 0.00 35.65 6.13
531 534 2.889018 GGTCGGCCGGATCGAAAC 60.889 66.667 27.83 14.16 38.42 2.78
586 596 3.944087 ACTGCAAGGACATAAACCTCTC 58.056 45.455 0.00 0.00 39.30 3.20
600 610 1.227205 CTCTCTGGCTCCATCGCAC 60.227 63.158 0.00 0.00 0.00 5.34
602 612 1.521010 CTCTGGCTCCATCGCACTG 60.521 63.158 0.00 0.00 0.00 3.66
604 614 3.963687 CTGGCTCCATCGCACTGCA 62.964 63.158 1.11 0.00 0.00 4.41
605 615 3.200593 GGCTCCATCGCACTGCAG 61.201 66.667 13.48 13.48 0.00 4.41
606 616 3.200593 GCTCCATCGCACTGCAGG 61.201 66.667 19.93 8.27 0.00 4.85
642 652 3.314541 AAACATGAGTACGGAGACACC 57.685 47.619 0.00 0.00 0.00 4.16
664 674 4.973663 CCGACAAAAACGCAAAACTCTTAT 59.026 37.500 0.00 0.00 0.00 1.73
677 687 5.816955 AAACTCTTATATCTGAGGCCCTC 57.183 43.478 2.98 2.98 34.84 4.30
727 737 3.579151 AGAAGGAGAGGGACTGTGTAAAC 59.421 47.826 0.00 0.00 41.55 2.01
728 738 2.258109 AGGAGAGGGACTGTGTAAACC 58.742 52.381 0.00 0.00 41.55 3.27
759 770 1.825474 CGCTCCTCTCTCAAACCCTAA 59.175 52.381 0.00 0.00 0.00 2.69
933 944 3.176411 TGGGCCTGGTATATCTGATCTG 58.824 50.000 4.53 0.00 0.00 2.90
984 995 2.110226 GTTTTAGATCTCGCCGTCTCG 58.890 52.381 0.00 0.00 0.00 4.04
987 998 4.965858 GATCTCGCCGTCTCGCCG 62.966 72.222 0.00 0.00 0.00 6.46
1177 1191 1.524863 AATACGGCCTCTCGATCCCG 61.525 60.000 0.00 10.40 45.80 5.14
1197 1211 2.219458 GGTCTCGTCCGTCATCTGATA 58.781 52.381 0.00 0.00 0.00 2.15
1223 1237 0.036294 GCCTTAGGTCGGAGCTTGTT 60.036 55.000 15.66 0.00 0.00 2.83
1232 1246 1.081175 GGAGCTTGTTTCTTGCGCC 60.081 57.895 4.18 0.00 39.24 6.53
1236 1250 1.007387 CTTGTTTCTTGCGCCACCC 60.007 57.895 4.18 0.00 0.00 4.61
1242 1256 1.791103 TTCTTGCGCCACCCGAAAAG 61.791 55.000 4.18 0.00 40.02 2.27
1258 1272 1.739067 AAAGCAGTGATTAGGTCGGC 58.261 50.000 0.00 0.00 0.00 5.54
1267 1281 2.236146 TGATTAGGTCGGCACTCATGTT 59.764 45.455 0.00 0.00 0.00 2.71
1300 1314 5.105106 TGACTATCTAGGCGTTTTTCATGGA 60.105 40.000 0.00 0.00 32.65 3.41
1301 1315 5.930135 ACTATCTAGGCGTTTTTCATGGAT 58.070 37.500 0.00 0.00 0.00 3.41
1306 1320 1.134946 GGCGTTTTTCATGGATGAGGG 59.865 52.381 0.00 0.00 38.19 4.30
1357 1372 4.154942 ACTTGGGCAGTGATTTCTTTCAT 58.845 39.130 0.00 0.00 32.83 2.57
1384 1399 6.338214 TGATCTCTAGGATATTGAGTGTGC 57.662 41.667 0.00 0.00 34.33 4.57
1423 1438 3.454812 ACGCTTAGTTTCCAGGTATCCAT 59.545 43.478 0.00 0.00 0.00 3.41
1445 1460 6.449698 CATAGGATTTTTGTGAGTTTGCAGT 58.550 36.000 0.00 0.00 0.00 4.40
1500 1515 3.375782 AATTTGAGCTGCCTGTTGTTC 57.624 42.857 0.00 0.00 0.00 3.18
1504 1519 1.860484 GAGCTGCCTGTTGTTCTGCC 61.860 60.000 0.00 0.00 0.00 4.85
1523 1538 5.663106 TCTGCCTAGATAGTTGAAACCTGAT 59.337 40.000 0.00 0.00 0.00 2.90
1542 1557 8.297470 ACCTGATATTAGTTTCAATGCATTGT 57.703 30.769 32.67 19.50 38.84 2.71
1562 1577 7.558991 CATTGTAGTTCGTTATCTGCTATGTG 58.441 38.462 0.00 0.00 30.48 3.21
1563 1578 5.041287 TGTAGTTCGTTATCTGCTATGTGC 58.959 41.667 0.00 0.00 43.25 4.57
1591 1800 2.890945 GGTTTGAGTGGCTATTGTGGTT 59.109 45.455 0.00 0.00 0.00 3.67
1632 1841 4.142227 TGAGTTAGGTTCGTGCCTATTCTC 60.142 45.833 19.63 19.63 40.47 2.87
1646 1855 1.284657 ATTCTCGATGAAGCGTGCAG 58.715 50.000 0.00 0.00 38.18 4.41
1663 1872 3.215975 TGCAGCTTTGCATCATATAGCA 58.784 40.909 0.00 0.00 40.23 3.49
1860 2086 6.784031 AGGTTACTCTCTGAATTGTTCCATT 58.216 36.000 0.00 0.00 0.00 3.16
1899 2125 9.918630 AGTTGATAAAGGATTTTGATTCTGTTG 57.081 29.630 0.00 0.00 40.09 3.33
1929 2155 6.376299 ACGTCTAGGTGATTGTGTCTATGTTA 59.624 38.462 0.00 0.00 0.00 2.41
1973 2199 8.125978 ACATTTGTGGTGAAATAATGATGTCT 57.874 30.769 0.00 0.00 32.15 3.41
1977 2203 7.943079 TGTGGTGAAATAATGATGTCTGATT 57.057 32.000 0.00 0.00 0.00 2.57
1982 2208 9.294030 GGTGAAATAATGATGTCTGATTGTTTC 57.706 33.333 0.00 0.00 38.84 2.78
1983 2209 9.003112 GTGAAATAATGATGTCTGATTGTTTCG 57.997 33.333 0.00 0.00 40.12 3.46
2011 2237 3.595190 ATTGCCCACTAGAATAACCCC 57.405 47.619 0.00 0.00 0.00 4.95
2021 2247 6.329197 CCACTAGAATAACCCCTTCATCCTTA 59.671 42.308 0.00 0.00 0.00 2.69
2038 2380 9.429109 TTCATCCTTACCTTGTGTATATAGTCA 57.571 33.333 0.00 0.00 0.00 3.41
2041 2383 9.656323 ATCCTTACCTTGTGTATATAGTCAGAA 57.344 33.333 0.00 0.00 0.00 3.02
2063 2405 5.698741 AGTGGACAGATTGGTCATTCATA 57.301 39.130 0.00 0.00 39.59 2.15
2067 2409 8.274322 AGTGGACAGATTGGTCATTCATAAATA 58.726 33.333 0.00 0.00 39.59 1.40
2068 2410 8.345565 GTGGACAGATTGGTCATTCATAAATAC 58.654 37.037 0.00 0.00 39.59 1.89
2071 2413 9.256477 GACAGATTGGTCATTCATAAATACGTA 57.744 33.333 0.00 0.00 37.73 3.57
2077 2419 5.471116 GGTCATTCATAAATACGTAACCCCC 59.529 44.000 0.00 0.00 0.00 5.40
2091 2434 4.384427 CGTAACCCCCACCACACTTAATAT 60.384 45.833 0.00 0.00 0.00 1.28
2096 2439 4.461198 CCCCACCACACTTAATATTCCTC 58.539 47.826 0.00 0.00 0.00 3.71
2107 2451 9.829507 ACACTTAATATTCCTCATCTCTTTCAG 57.170 33.333 0.00 0.00 0.00 3.02
2119 2463 7.176340 CCTCATCTCTTTCAGAAATTTCAACCT 59.824 37.037 19.99 0.00 33.62 3.50
2195 2565 1.672030 CAATGCGCTGGTGGAGACA 60.672 57.895 9.73 0.00 38.70 3.41
2376 2746 0.038166 TGATGTGTTCCTGCCCCTTC 59.962 55.000 0.00 0.00 0.00 3.46
2515 2888 1.451567 GCCCTTCCTCCCGTTAAGC 60.452 63.158 0.00 0.00 0.00 3.09
2657 3035 2.935849 TCTGGTATTGCTGTGTAATGCG 59.064 45.455 0.00 0.00 0.00 4.73
2709 3087 1.134128 CCTTTTGCCTTGCCCTTTGTT 60.134 47.619 0.00 0.00 0.00 2.83
2711 3089 0.908198 TTTGCCTTGCCCTTTGTTGT 59.092 45.000 0.00 0.00 0.00 3.32
2728 3106 5.590530 TGTTGTGGCATCTACTTTTGTTT 57.409 34.783 0.00 0.00 0.00 2.83
2733 3111 5.769662 TGTGGCATCTACTTTTGTTTGAGAT 59.230 36.000 0.00 0.00 0.00 2.75
2762 3140 1.921243 TAGGACGATGCACATGAACG 58.079 50.000 0.00 0.05 0.00 3.95
2776 3154 1.018910 TGAACGCATCATGCCATCAG 58.981 50.000 3.38 0.00 41.12 2.90
3038 3416 2.575735 TGAGTTGTTCTATGCATCCCCA 59.424 45.455 0.19 0.00 0.00 4.96
3045 3423 1.980765 TCTATGCATCCCCATGTCCTC 59.019 52.381 0.19 0.00 31.86 3.71
3086 3464 4.025480 GCCTTTTTCTGCACTTGTGAATTG 60.025 41.667 4.79 0.00 0.00 2.32
3087 3465 4.508861 CCTTTTTCTGCACTTGTGAATTGG 59.491 41.667 4.79 0.00 0.00 3.16
3088 3466 4.734398 TTTTCTGCACTTGTGAATTGGT 57.266 36.364 4.79 0.00 0.00 3.67
3089 3467 4.734398 TTTCTGCACTTGTGAATTGGTT 57.266 36.364 4.79 0.00 0.00 3.67
3090 3468 3.988379 TCTGCACTTGTGAATTGGTTC 57.012 42.857 4.79 0.00 34.85 3.62
3091 3469 3.554934 TCTGCACTTGTGAATTGGTTCT 58.445 40.909 4.79 0.00 35.33 3.01
3092 3470 3.953612 TCTGCACTTGTGAATTGGTTCTT 59.046 39.130 4.79 0.00 35.33 2.52
3093 3471 4.044336 TGCACTTGTGAATTGGTTCTTG 57.956 40.909 4.79 0.00 35.33 3.02
3094 3472 2.796593 GCACTTGTGAATTGGTTCTTGC 59.203 45.455 4.79 0.00 35.33 4.01
3095 3473 3.491447 GCACTTGTGAATTGGTTCTTGCT 60.491 43.478 4.79 0.00 35.33 3.91
3096 3474 4.685924 CACTTGTGAATTGGTTCTTGCTT 58.314 39.130 0.00 0.00 35.33 3.91
3097 3475 5.111293 CACTTGTGAATTGGTTCTTGCTTT 58.889 37.500 0.00 0.00 35.33 3.51
3098 3476 5.232838 CACTTGTGAATTGGTTCTTGCTTTC 59.767 40.000 0.00 0.00 35.33 2.62
3099 3477 5.127682 ACTTGTGAATTGGTTCTTGCTTTCT 59.872 36.000 0.00 0.00 35.33 2.52
3100 3478 5.596836 TGTGAATTGGTTCTTGCTTTCTT 57.403 34.783 0.00 0.00 35.33 2.52
3101 3479 5.976458 TGTGAATTGGTTCTTGCTTTCTTT 58.024 33.333 0.00 0.00 35.33 2.52
3102 3480 6.405538 TGTGAATTGGTTCTTGCTTTCTTTT 58.594 32.000 0.00 0.00 35.33 2.27
3103 3481 6.878389 TGTGAATTGGTTCTTGCTTTCTTTTT 59.122 30.769 0.00 0.00 35.33 1.94
3104 3482 7.064490 TGTGAATTGGTTCTTGCTTTCTTTTTC 59.936 33.333 0.00 0.00 35.33 2.29
3105 3483 7.278646 GTGAATTGGTTCTTGCTTTCTTTTTCT 59.721 33.333 0.00 0.00 35.33 2.52
3106 3484 7.823799 TGAATTGGTTCTTGCTTTCTTTTTCTT 59.176 29.630 0.00 0.00 35.33 2.52
3107 3485 8.565896 AATTGGTTCTTGCTTTCTTTTTCTTT 57.434 26.923 0.00 0.00 0.00 2.52
3108 3486 9.665719 AATTGGTTCTTGCTTTCTTTTTCTTTA 57.334 25.926 0.00 0.00 0.00 1.85
3109 3487 8.702163 TTGGTTCTTGCTTTCTTTTTCTTTAG 57.298 30.769 0.00 0.00 0.00 1.85
3110 3488 7.264947 TGGTTCTTGCTTTCTTTTTCTTTAGG 58.735 34.615 0.00 0.00 0.00 2.69
3111 3489 6.701841 GGTTCTTGCTTTCTTTTTCTTTAGGG 59.298 38.462 0.00 0.00 0.00 3.53
3112 3490 6.405278 TCTTGCTTTCTTTTTCTTTAGGGG 57.595 37.500 0.00 0.00 0.00 4.79
3113 3491 6.133356 TCTTGCTTTCTTTTTCTTTAGGGGA 58.867 36.000 0.00 0.00 0.00 4.81
3114 3492 6.609616 TCTTGCTTTCTTTTTCTTTAGGGGAA 59.390 34.615 0.00 0.00 0.00 3.97
3115 3493 6.800072 TGCTTTCTTTTTCTTTAGGGGAAA 57.200 33.333 0.00 0.00 0.00 3.13
3116 3494 7.373617 TGCTTTCTTTTTCTTTAGGGGAAAT 57.626 32.000 0.00 0.00 33.51 2.17
3117 3495 7.801104 TGCTTTCTTTTTCTTTAGGGGAAATT 58.199 30.769 0.00 0.00 33.51 1.82
3120 3498 7.684317 TTCTTTTTCTTTAGGGGAAATTGGT 57.316 32.000 0.00 0.00 33.51 3.67
3135 3513 5.394553 GGAAATTGGTTCTTGCTTATGAGGG 60.395 44.000 0.00 0.00 36.40 4.30
3151 3535 7.510675 TTATGAGGGAGAAAATGGTACTCTT 57.489 36.000 0.00 0.00 0.00 2.85
3193 3577 3.947196 CCAGAGCATTTGTGGCTATTACA 59.053 43.478 0.00 0.00 42.78 2.41
3262 3652 0.548682 ACTGTGGAAGGAGATGGCCT 60.549 55.000 3.32 0.00 40.93 5.19
3375 3766 2.641305 GCAATGATGGAGTTCAGCTCT 58.359 47.619 0.00 0.00 43.62 4.09
3395 3786 3.133542 TCTGCACTTCATCTCAGTATGGG 59.866 47.826 0.00 0.00 38.61 4.00
3477 3868 0.098376 CAGAAAGCAGCTCGGCAATC 59.902 55.000 0.00 0.00 35.83 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.421888 GCAACTGTGTCAATTTTGCTACG 59.578 43.478 2.29 0.00 39.57 3.51
1 2 3.421888 CGCAACTGTGTCAATTTTGCTAC 59.578 43.478 7.07 0.00 40.34 3.58
66 67 7.774134 AGCATCAACATTTGCTACATCATTAA 58.226 30.769 0.00 0.00 46.92 1.40
78 79 4.826500 GCTACTACGAGCATCAACATTTG 58.173 43.478 0.00 0.00 42.36 2.32
92 93 6.069665 TCGTCGTAAATTTTTGCTACTACG 57.930 37.500 0.00 2.55 36.57 3.51
138 139 1.661112 GTGAGCTGCGTTGGTTCTATC 59.339 52.381 0.00 0.00 0.00 2.08
149 150 1.515088 CCGTAGAGTGTGAGCTGCG 60.515 63.158 0.00 0.00 39.44 5.18
157 158 1.125633 ACAAACACCCCGTAGAGTGT 58.874 50.000 0.00 0.00 44.42 3.55
161 162 1.340088 TGCTACAAACACCCCGTAGA 58.660 50.000 0.00 0.00 35.65 2.59
165 166 1.161563 ACGTTGCTACAAACACCCCG 61.162 55.000 0.00 0.00 0.00 5.73
169 170 2.094575 TGTCACACGTTGCTACAAACAC 59.905 45.455 0.00 0.00 0.00 3.32
172 173 1.666700 GGTGTCACACGTTGCTACAAA 59.333 47.619 0.73 0.00 34.83 2.83
182 183 1.859398 CCACAATCGGTGTCACACG 59.141 57.895 0.73 6.42 46.44 4.49
184 185 0.884259 CTGCCACAATCGGTGTCACA 60.884 55.000 5.12 0.00 46.44 3.58
190 191 2.672996 GGTGCTGCCACAATCGGT 60.673 61.111 0.00 0.00 43.88 4.69
193 194 2.690778 GGACGGTGCTGCCACAATC 61.691 63.158 0.00 0.00 43.88 2.67
208 209 0.035458 CAGGGTGACAAGGACAGGAC 59.965 60.000 0.00 0.00 0.00 3.85
212 213 2.836154 GGCAGGGTGACAAGGACA 59.164 61.111 0.00 0.00 0.00 4.02
221 222 2.815211 CATGACGACGGCAGGGTG 60.815 66.667 10.27 0.00 0.00 4.61
227 228 3.188786 GGTGAGCATGACGACGGC 61.189 66.667 0.00 0.00 0.00 5.68
228 229 1.807165 CTGGTGAGCATGACGACGG 60.807 63.158 0.00 0.00 0.00 4.79
229 230 0.667487 AACTGGTGAGCATGACGACG 60.667 55.000 0.00 0.00 0.00 5.12
233 234 2.740981 CTCTGAAACTGGTGAGCATGAC 59.259 50.000 0.00 0.00 0.00 3.06
250 251 2.106511 CCCTCTCCTCTCTCTACCTCTG 59.893 59.091 0.00 0.00 0.00 3.35
255 256 1.423921 CCCTCCCTCTCCTCTCTCTAC 59.576 61.905 0.00 0.00 0.00 2.59
271 274 1.363744 CGTTCTCATGCTTGACCCTC 58.636 55.000 0.00 0.00 0.00 4.30
273 276 1.648467 GGCGTTCTCATGCTTGACCC 61.648 60.000 0.00 0.00 35.00 4.46
340 343 4.353788 TCATTCTTCCCTCTTTTCTTCCCA 59.646 41.667 0.00 0.00 0.00 4.37
347 350 5.073691 TCCTTCACTCATTCTTCCCTCTTTT 59.926 40.000 0.00 0.00 0.00 2.27
351 354 3.772025 TCTCCTTCACTCATTCTTCCCTC 59.228 47.826 0.00 0.00 0.00 4.30
353 356 3.118445 CCTCTCCTTCACTCATTCTTCCC 60.118 52.174 0.00 0.00 0.00 3.97
367 370 5.155905 TCTTTTCTCTACAACCCTCTCCTT 58.844 41.667 0.00 0.00 0.00 3.36
402 405 6.815142 GTCCCATACTATGTACGTCAAGTTTT 59.185 38.462 0.00 0.00 0.00 2.43
403 406 6.071221 TGTCCCATACTATGTACGTCAAGTTT 60.071 38.462 0.00 0.00 0.00 2.66
404 407 5.419788 TGTCCCATACTATGTACGTCAAGTT 59.580 40.000 0.00 0.00 0.00 2.66
405 408 4.951715 TGTCCCATACTATGTACGTCAAGT 59.048 41.667 0.00 0.00 0.00 3.16
406 409 5.509716 TGTCCCATACTATGTACGTCAAG 57.490 43.478 0.00 0.00 0.00 3.02
407 410 5.185442 TGTTGTCCCATACTATGTACGTCAA 59.815 40.000 0.00 0.00 0.00 3.18
408 411 4.705991 TGTTGTCCCATACTATGTACGTCA 59.294 41.667 0.00 0.00 0.00 4.35
409 412 5.252969 TGTTGTCCCATACTATGTACGTC 57.747 43.478 0.00 0.00 0.00 4.34
410 413 5.664294 TTGTTGTCCCATACTATGTACGT 57.336 39.130 0.00 0.00 0.00 3.57
417 420 8.325787 ACTCATATGTTTTGTTGTCCCATACTA 58.674 33.333 1.90 0.00 0.00 1.82
418 421 7.121168 CACTCATATGTTTTGTTGTCCCATACT 59.879 37.037 1.90 0.00 0.00 2.12
421 424 5.774690 ACACTCATATGTTTTGTTGTCCCAT 59.225 36.000 1.90 0.00 0.00 4.00
430 433 3.436704 AGACCGCACACTCATATGTTTTG 59.563 43.478 1.90 1.42 0.00 2.44
435 438 1.539065 GGGAGACCGCACACTCATATG 60.539 57.143 0.00 0.00 43.64 1.78
436 439 0.753262 GGGAGACCGCACACTCATAT 59.247 55.000 0.00 0.00 43.64 1.78
452 455 0.613260 CTGGATCGAACAACCAGGGA 59.387 55.000 17.55 0.00 44.96 4.20
559 562 6.245408 AGGTTTATGTCCTTGCAGTATTCAA 58.755 36.000 0.00 0.00 30.18 2.69
586 596 3.200593 GCAGTGCGATGGAGCCAG 61.201 66.667 0.00 0.00 36.02 4.85
617 627 6.203338 GGTGTCTCCGTACTCATGTTTTTAAA 59.797 38.462 0.00 0.00 0.00 1.52
618 628 5.697633 GGTGTCTCCGTACTCATGTTTTTAA 59.302 40.000 0.00 0.00 0.00 1.52
634 644 0.041576 GCGTTTTTGTCGGTGTCTCC 60.042 55.000 0.00 0.00 0.00 3.71
642 652 7.744715 AGATATAAGAGTTTTGCGTTTTTGTCG 59.255 33.333 0.00 0.00 0.00 4.35
646 656 8.237267 CCTCAGATATAAGAGTTTTGCGTTTTT 58.763 33.333 3.90 0.00 0.00 1.94
783 794 9.141400 GATTTTTAGTCCGGCTATCTTATACTG 57.859 37.037 0.00 0.00 0.00 2.74
984 995 4.816984 TCGGAGAGGGGAGACGGC 62.817 72.222 0.00 0.00 0.00 5.68
1142 1155 2.740580 CGTATTATCAGGGGTGCGTGTT 60.741 50.000 0.00 0.00 0.00 3.32
1177 1191 1.025812 ATCAGATGACGGACGAGACC 58.974 55.000 0.00 0.00 0.00 3.85
1197 1211 2.438411 CTCCGACCTAAGGCTATCGAT 58.562 52.381 2.16 2.16 36.70 3.59
1223 1237 1.791103 CTTTTCGGGTGGCGCAAGAA 61.791 55.000 10.83 3.87 43.02 2.52
1232 1246 2.420022 CCTAATCACTGCTTTTCGGGTG 59.580 50.000 0.00 0.00 0.00 4.61
1236 1250 2.348666 CCGACCTAATCACTGCTTTTCG 59.651 50.000 0.00 0.00 0.00 3.46
1242 1256 0.108138 AGTGCCGACCTAATCACTGC 60.108 55.000 0.00 0.00 38.25 4.40
1258 1272 4.384056 AGTCAGAGGAACAAACATGAGTG 58.616 43.478 0.00 0.00 0.00 3.51
1267 1281 3.632604 CGCCTAGATAGTCAGAGGAACAA 59.367 47.826 0.00 0.00 0.00 2.83
1300 1314 7.126421 ACACATCTTCAGTAACTTATCCCTCAT 59.874 37.037 0.00 0.00 0.00 2.90
1301 1315 6.440647 ACACATCTTCAGTAACTTATCCCTCA 59.559 38.462 0.00 0.00 0.00 3.86
1306 1320 9.469807 CCAGATACACATCTTCAGTAACTTATC 57.530 37.037 0.00 0.00 39.62 1.75
1367 1382 3.312828 GAGCGCACACTCAATATCCTAG 58.687 50.000 11.47 0.00 36.65 3.02
1373 1388 2.616842 TCTATCGAGCGCACACTCAATA 59.383 45.455 11.47 0.00 36.42 1.90
1382 1397 2.220363 CGTACTAGTTCTATCGAGCGCA 59.780 50.000 11.47 0.00 0.00 6.09
1384 1399 2.475864 AGCGTACTAGTTCTATCGAGCG 59.524 50.000 0.00 0.00 0.00 5.03
1401 1416 2.835764 TGGATACCTGGAAACTAAGCGT 59.164 45.455 0.00 0.00 0.00 5.07
1423 1438 5.009610 GGACTGCAAACTCACAAAAATCCTA 59.990 40.000 0.00 0.00 0.00 2.94
1445 1460 3.004315 GCGTGATTTGAAACTTGAAGGGA 59.996 43.478 0.00 0.00 0.00 4.20
1500 1515 5.344743 TCAGGTTTCAACTATCTAGGCAG 57.655 43.478 0.00 0.00 0.00 4.85
1523 1538 8.941977 ACGAACTACAATGCATTGAAACTAATA 58.058 29.630 38.99 20.91 40.14 0.98
1591 1800 4.809193 ACTCAGCTAGGTGAGATAATCCA 58.191 43.478 43.28 14.80 46.02 3.41
1646 1855 5.765176 TCAACATGCTATATGATGCAAAGC 58.235 37.500 0.00 0.00 42.74 3.51
1648 1857 8.298854 GGTAATCAACATGCTATATGATGCAAA 58.701 33.333 0.00 0.00 42.74 3.68
1655 1864 4.094887 GCGGGGTAATCAACATGCTATATG 59.905 45.833 0.00 0.00 0.00 1.78
1657 1866 3.071747 TGCGGGGTAATCAACATGCTATA 59.928 43.478 0.00 0.00 0.00 1.31
1663 1872 1.283613 TCCTTGCGGGGTAATCAACAT 59.716 47.619 0.00 0.00 35.33 2.71
1860 2086 5.652014 CCTTTATCAACTCCAGCATAAACCA 59.348 40.000 0.00 0.00 0.00 3.67
1899 2125 5.056894 ACACAATCACCTAGACGTTCTAC 57.943 43.478 0.00 0.00 0.00 2.59
1929 2155 9.084533 ACAAATGTTAATTATGTTACCTGTGGT 57.915 29.630 0.00 0.00 40.16 4.16
1973 2199 6.375736 TGGGCAATACTATTTCGAAACAATCA 59.624 34.615 13.81 0.00 0.00 2.57
1977 2203 5.250200 AGTGGGCAATACTATTTCGAAACA 58.750 37.500 13.81 0.00 0.00 2.83
1982 2208 8.709646 GTTATTCTAGTGGGCAATACTATTTCG 58.290 37.037 0.00 0.00 30.83 3.46
1983 2209 9.000486 GGTTATTCTAGTGGGCAATACTATTTC 58.000 37.037 0.00 0.00 30.83 2.17
2011 2237 9.915629 GACTATATACACAAGGTAAGGATGAAG 57.084 37.037 0.00 0.00 35.14 3.02
2021 2247 6.895756 TCCACTTCTGACTATATACACAAGGT 59.104 38.462 0.00 0.00 0.00 3.50
2038 2380 4.042062 TGAATGACCAATCTGTCCACTTCT 59.958 41.667 0.00 0.00 34.25 2.85
2041 2383 4.581309 ATGAATGACCAATCTGTCCACT 57.419 40.909 0.00 0.00 34.25 4.00
2063 2405 1.704070 TGTGGTGGGGGTTACGTATTT 59.296 47.619 0.00 0.00 0.00 1.40
2067 2409 1.347243 AAGTGTGGTGGGGGTTACGT 61.347 55.000 0.00 0.00 0.00 3.57
2068 2410 0.686224 TAAGTGTGGTGGGGGTTACG 59.314 55.000 0.00 0.00 0.00 3.18
2071 2413 4.571148 GGAATATTAAGTGTGGTGGGGGTT 60.571 45.833 0.00 0.00 0.00 4.11
2077 2419 7.504403 AGAGATGAGGAATATTAAGTGTGGTG 58.496 38.462 0.00 0.00 0.00 4.17
2135 2480 5.978919 ACAACAAAGCAGATGTTACAATGTG 59.021 36.000 0.00 0.00 38.90 3.21
2195 2565 2.880890 GTCAACACAGTCCTTGAAGCAT 59.119 45.455 0.00 0.00 0.00 3.79
2234 2604 1.620819 GACTCCTCTTGCTTGTCCAGA 59.379 52.381 0.00 0.00 0.00 3.86
2273 2643 2.037772 GGAGTGCTTCAGGAACTTCTCA 59.962 50.000 0.00 0.00 34.60 3.27
2376 2746 4.463891 AGATGGGCAATGTTAGAAACTTGG 59.536 41.667 0.00 0.00 0.00 3.61
2441 2811 2.584835 TAAGCAGCAGTGGGTTCATT 57.415 45.000 0.00 0.00 0.00 2.57
2497 2869 1.451567 GCTTAACGGGAGGAAGGGC 60.452 63.158 0.00 0.00 0.00 5.19
2498 2870 1.153429 CGCTTAACGGGAGGAAGGG 60.153 63.158 0.00 0.00 38.44 3.95
2515 2888 4.808895 TCTATTAAGTAGCACAATGTGGCG 59.191 41.667 15.78 0.00 33.64 5.69
2657 3035 5.587844 ACAGATCTTGCACTATGATGTTTCC 59.412 40.000 0.00 0.00 0.00 3.13
2709 3087 5.129634 TCTCAAACAAAAGTAGATGCCACA 58.870 37.500 0.00 0.00 0.00 4.17
2711 3089 6.003326 TGATCTCAAACAAAAGTAGATGCCA 58.997 36.000 0.00 0.00 0.00 4.92
2728 3106 7.093354 GCATCGTCCTATATTCTTTGATCTCA 58.907 38.462 0.00 0.00 0.00 3.27
2733 3111 5.912892 TGTGCATCGTCCTATATTCTTTGA 58.087 37.500 0.00 0.00 0.00 2.69
2744 3122 1.361668 GCGTTCATGTGCATCGTCCT 61.362 55.000 0.00 0.00 0.00 3.85
3038 3416 2.305343 AGAAGCAAGCTCAAGAGGACAT 59.695 45.455 0.00 0.00 0.00 3.06
3069 3447 3.953612 AGAACCAATTCACAAGTGCAGAA 59.046 39.130 0.00 0.00 37.29 3.02
3086 3464 6.701841 CCCTAAAGAAAAAGAAAGCAAGAACC 59.298 38.462 0.00 0.00 0.00 3.62
3087 3465 6.701841 CCCCTAAAGAAAAAGAAAGCAAGAAC 59.298 38.462 0.00 0.00 0.00 3.01
3088 3466 6.609616 TCCCCTAAAGAAAAAGAAAGCAAGAA 59.390 34.615 0.00 0.00 0.00 2.52
3089 3467 6.133356 TCCCCTAAAGAAAAAGAAAGCAAGA 58.867 36.000 0.00 0.00 0.00 3.02
3090 3468 6.405278 TCCCCTAAAGAAAAAGAAAGCAAG 57.595 37.500 0.00 0.00 0.00 4.01
3091 3469 6.800072 TTCCCCTAAAGAAAAAGAAAGCAA 57.200 33.333 0.00 0.00 0.00 3.91
3092 3470 6.800072 TTTCCCCTAAAGAAAAAGAAAGCA 57.200 33.333 0.00 0.00 30.48 3.91
3093 3471 7.173218 CCAATTTCCCCTAAAGAAAAAGAAAGC 59.827 37.037 0.00 0.00 36.83 3.51
3094 3472 8.210946 ACCAATTTCCCCTAAAGAAAAAGAAAG 58.789 33.333 0.00 0.00 36.83 2.62
3095 3473 8.096621 ACCAATTTCCCCTAAAGAAAAAGAAA 57.903 30.769 0.00 0.00 36.83 2.52
3096 3474 7.684317 ACCAATTTCCCCTAAAGAAAAAGAA 57.316 32.000 0.00 0.00 36.83 2.52
3097 3475 7.567250 AGAACCAATTTCCCCTAAAGAAAAAGA 59.433 33.333 0.00 0.00 36.83 2.52
3098 3476 7.735917 AGAACCAATTTCCCCTAAAGAAAAAG 58.264 34.615 0.00 0.00 36.83 2.27
3099 3477 7.684317 AGAACCAATTTCCCCTAAAGAAAAA 57.316 32.000 0.00 0.00 36.83 1.94
3100 3478 7.505258 CAAGAACCAATTTCCCCTAAAGAAAA 58.495 34.615 0.00 0.00 36.83 2.29
3101 3479 6.463755 GCAAGAACCAATTTCCCCTAAAGAAA 60.464 38.462 0.00 0.00 37.61 2.52
3102 3480 5.011635 GCAAGAACCAATTTCCCCTAAAGAA 59.988 40.000 0.00 0.00 34.32 2.52
3103 3481 4.526650 GCAAGAACCAATTTCCCCTAAAGA 59.473 41.667 0.00 0.00 34.32 2.52
3104 3482 4.528206 AGCAAGAACCAATTTCCCCTAAAG 59.472 41.667 0.00 0.00 34.32 1.85
3105 3483 4.488770 AGCAAGAACCAATTTCCCCTAAA 58.511 39.130 0.00 0.00 34.32 1.85
3106 3484 4.126520 AGCAAGAACCAATTTCCCCTAA 57.873 40.909 0.00 0.00 34.32 2.69
3107 3485 3.825908 AGCAAGAACCAATTTCCCCTA 57.174 42.857 0.00 0.00 34.32 3.53
3108 3486 2.702270 AGCAAGAACCAATTTCCCCT 57.298 45.000 0.00 0.00 34.32 4.79
3109 3487 4.466015 TCATAAGCAAGAACCAATTTCCCC 59.534 41.667 0.00 0.00 34.32 4.81
3110 3488 5.394553 CCTCATAAGCAAGAACCAATTTCCC 60.395 44.000 0.00 0.00 34.32 3.97
3111 3489 5.394553 CCCTCATAAGCAAGAACCAATTTCC 60.395 44.000 0.00 0.00 34.32 3.13
3112 3490 5.418840 TCCCTCATAAGCAAGAACCAATTTC 59.581 40.000 0.00 0.00 33.95 2.17
3113 3491 5.332743 TCCCTCATAAGCAAGAACCAATTT 58.667 37.500 0.00 0.00 0.00 1.82
3114 3492 4.934356 TCCCTCATAAGCAAGAACCAATT 58.066 39.130 0.00 0.00 0.00 2.32
3115 3493 4.228210 TCTCCCTCATAAGCAAGAACCAAT 59.772 41.667 0.00 0.00 0.00 3.16
3116 3494 3.587061 TCTCCCTCATAAGCAAGAACCAA 59.413 43.478 0.00 0.00 0.00 3.67
3117 3495 3.181329 TCTCCCTCATAAGCAAGAACCA 58.819 45.455 0.00 0.00 0.00 3.67
3120 3498 5.653769 CCATTTTCTCCCTCATAAGCAAGAA 59.346 40.000 0.00 0.00 0.00 2.52
3151 3535 7.336931 GCTCTGGAAACATAGGTCTTAATTTGA 59.663 37.037 0.00 0.00 41.51 2.69
3162 3546 4.142315 CCACAAATGCTCTGGAAACATAGG 60.142 45.833 0.00 0.00 41.51 2.57
3193 3577 8.898761 TCTATTTTATTTGTGTGATACCGCAAT 58.101 29.630 0.00 0.00 35.01 3.56
3262 3652 7.123397 GCTATATGATATTCCTCCTCACTGTGA 59.877 40.741 10.50 10.50 0.00 3.58
3375 3766 3.106827 TCCCATACTGAGATGAAGTGCA 58.893 45.455 0.00 0.00 0.00 4.57
3395 3786 0.322816 TGCTTCAGTTGGGGAGCATC 60.323 55.000 0.00 0.00 0.00 3.91
3477 3868 8.231837 CCAAGTTTTTATGCAAATTTGATCAGG 58.768 33.333 22.31 2.26 36.12 3.86
3532 3924 7.360017 CGAGATACATGCTTGAAGTACACAAAA 60.360 37.037 6.60 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.