Multiple sequence alignment - TraesCS1B01G077700

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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 TraesCS1B01G077700 chr1B 100.000 2747 0 0 1 2747 60535415 60532669 0.000000e+00 5073
1 TraesCS1B01G077700 chr1B 90.897 1483 69 28 894 2320 60047786 60049258 0.000000e+00 1930
2 TraesCS1B01G077700 chr1B 90.829 1483 70 28 894 2320 59961350 59962822 0.000000e+00 1925
3 TraesCS1B01G077700 chr1B 86.752 1638 82 58 455 2001 59912326 59913919 0.000000e+00 1698
4 TraesCS1B01G077700 chr1B 86.508 1638 85 55 455 2001 59854858 59856450 0.000000e+00 1676
5 TraesCS1B01G077700 chr1B 85.149 1212 62 40 873 2029 59926923 59928071 0.000000e+00 1133
6 TraesCS1B01G077700 chr1B 92.715 453 23 5 2303 2747 60050616 60051066 0.000000e+00 645
7 TraesCS1B01G077700 chr1B 92.274 453 26 5 2303 2747 59964180 59964631 3.860000e-178 634
8 TraesCS1B01G077700 chr1B 82.385 738 59 33 127 836 59926228 59926922 6.600000e-161 577
9 TraesCS1B01G077700 chr1B 84.565 609 58 24 1184 1772 94300527 94301119 3.070000e-159 571
10 TraesCS1B01G077700 chr1B 90.909 429 17 9 1615 2029 60021222 60021642 8.590000e-155 556
11 TraesCS1B01G077700 chr1B 86.193 507 38 12 2127 2624 59856656 59857139 1.130000e-143 520
12 TraesCS1B01G077700 chr1B 87.557 442 40 7 1 439 59854284 59854713 5.280000e-137 497
13 TraesCS1B01G077700 chr1B 85.078 516 40 16 2127 2628 59914125 59914617 2.460000e-135 492
14 TraesCS1B01G077700 chr1B 82.218 523 63 18 2118 2624 60037954 60038462 9.090000e-115 424
15 TraesCS1B01G077700 chr1B 81.992 522 66 16 2118 2624 59944240 59944748 4.230000e-113 418
16 TraesCS1B01G077700 chr1B 81.818 396 50 14 206 590 59917131 59917515 2.050000e-81 313
17 TraesCS1B01G077700 chr1B 84.581 227 23 7 578 801 59961003 59961220 5.960000e-52 215
18 TraesCS1B01G077700 chr1B 84.581 227 23 7 578 801 60047439 60047656 5.960000e-52 215
19 TraesCS1B01G077700 chr1D 86.671 1718 102 56 450 2118 40488759 40490398 0.000000e+00 1786
20 TraesCS1B01G077700 chr1D 87.229 1613 86 57 454 2001 40228198 40229755 0.000000e+00 1727
21 TraesCS1B01G077700 chr1D 87.483 1470 81 48 454 1872 40432880 40434297 0.000000e+00 1600
22 TraesCS1B01G077700 chr1D 85.714 1624 95 62 551 2118 40325377 40326919 0.000000e+00 1587
23 TraesCS1B01G077700 chr1D 85.345 1624 102 63 551 2118 40244038 40245581 0.000000e+00 1555
24 TraesCS1B01G077700 chr1D 86.917 1414 68 53 641 2001 40201967 40203316 0.000000e+00 1478
25 TraesCS1B01G077700 chr1D 88.754 987 44 29 1151 2118 40380988 40381926 0.000000e+00 1146
26 TraesCS1B01G077700 chr1D 87.955 880 44 34 1150 2001 40315861 40316706 0.000000e+00 981
27 TraesCS1B01G077700 chr1D 87.206 680 56 15 1184 1862 33028074 33028723 0.000000e+00 745
28 TraesCS1B01G077700 chr1D 84.871 661 71 16 2 655 40174785 40175423 8.290000e-180 640
29 TraesCS1B01G077700 chr1D 85.799 507 46 12 2118 2607 40203479 40203976 5.250000e-142 514
30 TraesCS1B01G077700 chr1D 82.979 329 41 10 257 572 40171761 40172087 1.610000e-72 283
31 TraesCS1B01G077700 chr1A 85.543 1501 92 54 1006 2423 39832218 39833676 0.000000e+00 1454
32 TraesCS1B01G077700 chr1A 81.548 1382 146 49 13 1341 39756963 39758288 0.000000e+00 1038
33 TraesCS1B01G077700 chr1A 86.912 680 50 20 1184 1861 31945899 31946541 0.000000e+00 726
34 TraesCS1B01G077700 chrUn 84.266 1411 85 50 681 2029 335951177 335949842 0.000000e+00 1249
35 TraesCS1B01G077700 chrUn 82.218 523 63 18 2118 2624 329120382 329119874 9.090000e-115 424
36 TraesCS1B01G077700 chrUn 82.218 523 63 18 2118 2624 385766628 385766120 9.090000e-115 424
37 TraesCS1B01G077700 chrUn 91.257 183 12 1 2569 2747 474545355 474545173 2.110000e-61 246


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 TraesCS1B01G077700 chr1B 60532669 60535415 2746 True 5073.000000 5073 100.000000 1 2747 1 chr1B.!!$R1 2746
1 TraesCS1B01G077700 chr1B 60047439 60051066 3627 False 930.000000 1930 89.397667 578 2747 3 chr1B.!!$F9 2169
2 TraesCS1B01G077700 chr1B 59961003 59964631 3628 False 924.666667 1925 89.228000 578 2747 3 chr1B.!!$F8 2169
3 TraesCS1B01G077700 chr1B 59854284 59857139 2855 False 897.666667 1676 86.752667 1 2624 3 chr1B.!!$F5 2623
4 TraesCS1B01G077700 chr1B 59926228 59928071 1843 False 855.000000 1133 83.767000 127 2029 2 chr1B.!!$F7 1902
5 TraesCS1B01G077700 chr1B 59912326 59917515 5189 False 834.333333 1698 84.549333 206 2628 3 chr1B.!!$F6 2422
6 TraesCS1B01G077700 chr1B 94300527 94301119 592 False 571.000000 571 84.565000 1184 1772 1 chr1B.!!$F4 588
7 TraesCS1B01G077700 chr1B 60037954 60038462 508 False 424.000000 424 82.218000 2118 2624 1 chr1B.!!$F3 506
8 TraesCS1B01G077700 chr1B 59944240 59944748 508 False 418.000000 418 81.992000 2118 2624 1 chr1B.!!$F1 506
9 TraesCS1B01G077700 chr1D 40488759 40490398 1639 False 1786.000000 1786 86.671000 450 2118 1 chr1D.!!$F8 1668
10 TraesCS1B01G077700 chr1D 40228198 40229755 1557 False 1727.000000 1727 87.229000 454 2001 1 chr1D.!!$F2 1547
11 TraesCS1B01G077700 chr1D 40432880 40434297 1417 False 1600.000000 1600 87.483000 454 1872 1 chr1D.!!$F7 1418
12 TraesCS1B01G077700 chr1D 40325377 40326919 1542 False 1587.000000 1587 85.714000 551 2118 1 chr1D.!!$F5 1567
13 TraesCS1B01G077700 chr1D 40244038 40245581 1543 False 1555.000000 1555 85.345000 551 2118 1 chr1D.!!$F3 1567
14 TraesCS1B01G077700 chr1D 40380988 40381926 938 False 1146.000000 1146 88.754000 1151 2118 1 chr1D.!!$F6 967
15 TraesCS1B01G077700 chr1D 40201967 40203976 2009 False 996.000000 1478 86.358000 641 2607 2 chr1D.!!$F10 1966
16 TraesCS1B01G077700 chr1D 40315861 40316706 845 False 981.000000 981 87.955000 1150 2001 1 chr1D.!!$F4 851
17 TraesCS1B01G077700 chr1D 33028074 33028723 649 False 745.000000 745 87.206000 1184 1862 1 chr1D.!!$F1 678
18 TraesCS1B01G077700 chr1D 40171761 40175423 3662 False 461.500000 640 83.925000 2 655 2 chr1D.!!$F9 653
19 TraesCS1B01G077700 chr1A 39832218 39833676 1458 False 1454.000000 1454 85.543000 1006 2423 1 chr1A.!!$F3 1417
20 TraesCS1B01G077700 chr1A 39756963 39758288 1325 False 1038.000000 1038 81.548000 13 1341 1 chr1A.!!$F2 1328
21 TraesCS1B01G077700 chr1A 31945899 31946541 642 False 726.000000 726 86.912000 1184 1861 1 chr1A.!!$F1 677
22 TraesCS1B01G077700 chrUn 335949842 335951177 1335 True 1249.000000 1249 84.266000 681 2029 1 chrUn.!!$R2 1348
23 TraesCS1B01G077700 chrUn 329119874 329120382 508 True 424.000000 424 82.218000 2118 2624 1 chrUn.!!$R1 506
24 TraesCS1B01G077700 chrUn 385766120 385766628 508 True 424.000000 424 82.218000 2118 2624 1 chrUn.!!$R3 506

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
206 3231 0.109723 TGGCTGCGTCCTTTTAGGTT 59.89 50.0 0.0 0.0 36.53 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2168 5841 0.591741 GGCTTCTCGGTCGTCGTATG 60.592 60.0 0.0 0.0 40.32 2.39 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
71 3095 2.111043 CCACAACACTGGCCGACT 59.889 61.111 0.00 0.00 0.00 4.18
80 3104 3.535629 CTGGCCGACTTGCTCCACA 62.536 63.158 0.00 0.00 0.00 4.17
125 3149 2.662866 TCACGAATCTCGGAAGGGTAT 58.337 47.619 0.67 0.00 45.59 2.73
156 3181 3.706055 TGGAGCTCCAAGACAACAC 57.294 52.632 33.41 2.42 44.35 3.32
168 3193 3.627395 AGACAACACCAGTCAGTCAAA 57.373 42.857 0.00 0.00 38.46 2.69
179 3204 0.389025 TCAGTCAAAGCAGCGTCTGA 59.611 50.000 10.46 0.00 32.44 3.27
180 3205 1.001293 TCAGTCAAAGCAGCGTCTGAT 59.999 47.619 10.46 1.72 32.44 2.90
191 3216 2.673523 GTCTGATGGGCACTGGCT 59.326 61.111 2.14 0.00 40.87 4.75
204 3229 0.321653 ACTGGCTGCGTCCTTTTAGG 60.322 55.000 0.00 0.00 36.46 2.69
205 3230 0.321653 CTGGCTGCGTCCTTTTAGGT 60.322 55.000 0.00 0.00 36.53 3.08
206 3231 0.109723 TGGCTGCGTCCTTTTAGGTT 59.890 50.000 0.00 0.00 36.53 3.50
207 3232 1.244816 GGCTGCGTCCTTTTAGGTTT 58.755 50.000 0.00 0.00 36.53 3.27
208 3233 1.611977 GGCTGCGTCCTTTTAGGTTTT 59.388 47.619 0.00 0.00 36.53 2.43
210 3235 3.119955 GGCTGCGTCCTTTTAGGTTTTAG 60.120 47.826 0.00 0.00 36.53 1.85
211 3236 3.669824 GCTGCGTCCTTTTAGGTTTTAGC 60.670 47.826 0.00 0.00 36.53 3.09
212 3237 2.815503 TGCGTCCTTTTAGGTTTTAGCC 59.184 45.455 0.00 0.00 36.53 3.93
215 3240 3.816523 CGTCCTTTTAGGTTTTAGCCACA 59.183 43.478 0.00 0.00 36.53 4.17
216 3241 4.276431 CGTCCTTTTAGGTTTTAGCCACAA 59.724 41.667 0.00 0.00 36.53 3.33
217 3242 5.526115 GTCCTTTTAGGTTTTAGCCACAAC 58.474 41.667 0.00 0.00 36.53 3.32
218 3243 5.068067 GTCCTTTTAGGTTTTAGCCACAACA 59.932 40.000 0.00 0.00 36.53 3.33
219 3244 5.836358 TCCTTTTAGGTTTTAGCCACAACAT 59.164 36.000 0.00 0.00 36.53 2.71
220 3245 5.925969 CCTTTTAGGTTTTAGCCACAACATG 59.074 40.000 0.00 0.00 0.00 3.21
222 3247 1.618343 AGGTTTTAGCCACAACATGCC 59.382 47.619 0.00 0.00 0.00 4.40
223 3248 1.337728 GGTTTTAGCCACAACATGCCC 60.338 52.381 0.00 0.00 0.00 5.36
224 3249 1.342819 GTTTTAGCCACAACATGCCCA 59.657 47.619 0.00 0.00 0.00 5.36
225 3250 0.965439 TTTAGCCACAACATGCCCAC 59.035 50.000 0.00 0.00 0.00 4.61
227 3252 1.788518 TAGCCACAACATGCCCACCT 61.789 55.000 0.00 0.00 0.00 4.00
228 3253 2.209315 GCCACAACATGCCCACCTT 61.209 57.895 0.00 0.00 0.00 3.50
229 3254 0.897863 GCCACAACATGCCCACCTTA 60.898 55.000 0.00 0.00 0.00 2.69
230 3255 1.176527 CCACAACATGCCCACCTTAG 58.823 55.000 0.00 0.00 0.00 2.18
232 3257 1.072266 ACAACATGCCCACCTTAGGA 58.928 50.000 4.77 0.00 0.00 2.94
236 3261 0.469917 CATGCCCACCTTAGGACGAT 59.530 55.000 4.77 0.00 0.00 3.73
237 3262 0.759346 ATGCCCACCTTAGGACGATC 59.241 55.000 4.77 0.00 0.00 3.69
238 3263 1.067582 GCCCACCTTAGGACGATCG 59.932 63.158 14.88 14.88 0.00 3.69
239 3264 1.389609 GCCCACCTTAGGACGATCGA 61.390 60.000 24.34 0.00 0.00 3.59
240 3265 0.669077 CCCACCTTAGGACGATCGAG 59.331 60.000 24.34 8.02 0.00 4.04
243 3268 1.108132 ACCTTAGGACGATCGAGGGC 61.108 60.000 24.34 7.75 0.00 5.19
244 3269 0.824182 CCTTAGGACGATCGAGGGCT 60.824 60.000 24.34 0.00 0.00 5.19
245 3270 1.033574 CTTAGGACGATCGAGGGCTT 58.966 55.000 24.34 6.98 0.00 4.35
246 3271 0.744874 TTAGGACGATCGAGGGCTTG 59.255 55.000 24.34 0.00 0.00 4.01
247 3272 1.107538 TAGGACGATCGAGGGCTTGG 61.108 60.000 24.34 0.00 0.00 3.61
250 3275 2.892425 CGATCGAGGGCTTGGTGC 60.892 66.667 10.26 0.00 41.94 5.01
251 3276 2.892425 GATCGAGGGCTTGGTGCG 60.892 66.667 0.00 0.00 44.05 5.34
253 3278 3.254024 ATCGAGGGCTTGGTGCGTT 62.254 57.895 0.00 0.00 44.05 4.84
255 3280 3.365265 GAGGGCTTGGTGCGTTGG 61.365 66.667 0.00 0.00 44.05 3.77
260 3285 3.222855 CTTGGTGCGTTGGGCCAA 61.223 61.111 16.66 16.66 42.61 4.52
261 3286 2.759973 TTGGTGCGTTGGGCCAAA 60.760 55.556 22.82 1.98 42.61 3.28
262 3287 2.697992 CTTGGTGCGTTGGGCCAAAG 62.698 60.000 25.30 25.30 41.15 2.77
273 3298 4.362476 GCCAAAGCCCGCACCAAG 62.362 66.667 0.00 0.00 0.00 3.61
291 3316 3.572642 CAAGGGGTTAGTTTGGAAACCT 58.427 45.455 4.40 0.00 43.87 3.50
292 3317 3.964688 CAAGGGGTTAGTTTGGAAACCTT 59.035 43.478 4.40 0.00 43.87 3.50
293 3318 3.840991 AGGGGTTAGTTTGGAAACCTTC 58.159 45.455 4.40 0.00 43.87 3.46
294 3319 3.205733 AGGGGTTAGTTTGGAAACCTTCA 59.794 43.478 4.40 0.00 43.87 3.02
295 3320 4.140782 AGGGGTTAGTTTGGAAACCTTCAT 60.141 41.667 4.40 0.00 43.87 2.57
296 3321 4.219944 GGGGTTAGTTTGGAAACCTTCATC 59.780 45.833 4.40 0.00 43.87 2.92
297 3322 4.830600 GGGTTAGTTTGGAAACCTTCATCA 59.169 41.667 4.40 0.00 43.87 3.07
298 3323 5.303333 GGGTTAGTTTGGAAACCTTCATCAA 59.697 40.000 4.40 0.00 43.87 2.57
299 3324 6.447162 GGTTAGTTTGGAAACCTTCATCAAG 58.553 40.000 0.00 0.00 41.63 3.02
302 3327 4.405358 AGTTTGGAAACCTTCATCAAGCAA 59.595 37.500 0.00 0.00 39.71 3.91
303 3328 5.070847 AGTTTGGAAACCTTCATCAAGCAAT 59.929 36.000 0.00 0.00 39.71 3.56
306 3331 5.540911 TGGAAACCTTCATCAAGCAATTTC 58.459 37.500 0.00 0.00 0.00 2.17
307 3332 5.070180 TGGAAACCTTCATCAAGCAATTTCA 59.930 36.000 0.00 0.00 31.90 2.69
308 3333 5.636543 GGAAACCTTCATCAAGCAATTTCAG 59.363 40.000 0.00 0.00 31.90 3.02
309 3334 6.409524 AAACCTTCATCAAGCAATTTCAGA 57.590 33.333 0.00 0.00 0.00 3.27
311 3336 6.600882 ACCTTCATCAAGCAATTTCAGATT 57.399 33.333 0.00 0.00 0.00 2.40
312 3337 7.001099 ACCTTCATCAAGCAATTTCAGATTT 57.999 32.000 0.00 0.00 0.00 2.17
313 3338 7.447594 ACCTTCATCAAGCAATTTCAGATTTT 58.552 30.769 0.00 0.00 0.00 1.82
314 3339 8.587608 ACCTTCATCAAGCAATTTCAGATTTTA 58.412 29.630 0.00 0.00 0.00 1.52
315 3340 9.595823 CCTTCATCAAGCAATTTCAGATTTTAT 57.404 29.630 0.00 0.00 0.00 1.40
320 3345 8.991243 TCAAGCAATTTCAGATTTTATTGAGG 57.009 30.769 0.00 0.00 31.29 3.86
321 3346 8.805175 TCAAGCAATTTCAGATTTTATTGAGGA 58.195 29.630 0.00 0.00 31.29 3.71
386 3411 9.189156 TCATTTGTAGGGATTGAAATCTTTAGG 57.811 33.333 3.21 0.00 35.73 2.69
387 3412 9.189156 CATTTGTAGGGATTGAAATCTTTAGGA 57.811 33.333 3.21 0.00 35.73 2.94
388 3413 9.768215 ATTTGTAGGGATTGAAATCTTTAGGAA 57.232 29.630 3.21 0.00 35.73 3.36
389 3414 9.594936 TTTGTAGGGATTGAAATCTTTAGGAAA 57.405 29.630 3.21 0.00 35.73 3.13
391 3416 9.768215 TGTAGGGATTGAAATCTTTAGGAAATT 57.232 29.630 3.21 0.00 35.73 1.82
411 3436 2.586258 TTTTTAAGGCTTGCGTTGCA 57.414 40.000 10.69 0.00 36.47 4.08
412 3437 1.846541 TTTTAAGGCTTGCGTTGCAC 58.153 45.000 10.69 0.00 38.71 4.57
414 3439 1.885560 TTAAGGCTTGCGTTGCACTA 58.114 45.000 10.69 0.00 38.71 2.74
415 3440 2.107950 TAAGGCTTGCGTTGCACTAT 57.892 45.000 10.69 0.00 38.71 2.12
417 3442 2.332063 AGGCTTGCGTTGCACTATAT 57.668 45.000 0.00 0.00 38.71 0.86
419 3444 3.016736 AGGCTTGCGTTGCACTATATTT 58.983 40.909 0.00 0.00 38.71 1.40
420 3445 3.443681 AGGCTTGCGTTGCACTATATTTT 59.556 39.130 0.00 0.00 38.71 1.82
424 3449 6.020678 GGCTTGCGTTGCACTATATTTTAAAG 60.021 38.462 0.00 0.00 38.71 1.85
426 3451 7.272515 GCTTGCGTTGCACTATATTTTAAAGAA 59.727 33.333 0.00 0.00 38.71 2.52
427 3452 9.123709 CTTGCGTTGCACTATATTTTAAAGAAA 57.876 29.630 0.00 0.00 38.71 2.52
429 3454 9.464714 TGCGTTGCACTATATTTTAAAGAAAAA 57.535 25.926 0.00 0.00 36.10 1.94
447 3472 3.586100 AAAATTACACCATTGCGACCC 57.414 42.857 0.00 0.00 0.00 4.46
448 3473 2.507407 AATTACACCATTGCGACCCT 57.493 45.000 0.00 0.00 0.00 4.34
449 3474 2.507407 ATTACACCATTGCGACCCTT 57.493 45.000 0.00 0.00 0.00 3.95
450 3475 2.279935 TTACACCATTGCGACCCTTT 57.720 45.000 0.00 0.00 0.00 3.11
451 3476 2.279935 TACACCATTGCGACCCTTTT 57.720 45.000 0.00 0.00 0.00 2.27
452 3477 2.279935 ACACCATTGCGACCCTTTTA 57.720 45.000 0.00 0.00 0.00 1.52
484 3634 0.945813 TTTTTCTAACACCGGCGTGG 59.054 50.000 6.01 0.00 44.86 4.94
498 3655 1.797441 CGTGGGAGAGAGTGAGTCG 59.203 63.158 0.00 0.00 0.00 4.18
553 3748 1.024271 AATGGGCGTATCATGTGTGC 58.976 50.000 0.00 0.00 0.00 4.57
574 3773 4.022475 GCATTCGTTTATTCTTCGAGCAC 58.978 43.478 0.00 0.00 35.13 4.40
575 3774 4.201724 GCATTCGTTTATTCTTCGAGCACT 60.202 41.667 0.00 0.00 35.13 4.40
576 3775 4.903638 TTCGTTTATTCTTCGAGCACTG 57.096 40.909 0.00 0.00 35.13 3.66
667 3874 7.025485 TCAAATATGCATCACTAATCGCAAA 57.975 32.000 0.19 0.00 38.01 3.68
679 3916 5.062934 CACTAATCGCAAACGGATAGAACAA 59.937 40.000 0.00 0.00 40.63 2.83
680 3917 4.336532 AATCGCAAACGGATAGAACAAC 57.663 40.909 0.00 0.00 40.63 3.32
681 3918 2.756829 TCGCAAACGGATAGAACAACA 58.243 42.857 0.00 0.00 40.63 3.33
682 3919 3.132160 TCGCAAACGGATAGAACAACAA 58.868 40.909 0.00 0.00 40.63 2.83
683 3920 3.749088 TCGCAAACGGATAGAACAACAAT 59.251 39.130 0.00 0.00 40.63 2.71
801 4056 0.725118 GAGTCGAGAACGGACACACG 60.725 60.000 0.00 0.00 40.21 4.49
853 4119 0.179009 CCCCGGTATCTCGTGGACTA 60.179 60.000 0.00 0.00 29.10 2.59
855 4121 1.607628 CCCGGTATCTCGTGGACTAAG 59.392 57.143 0.00 0.00 0.00 2.18
891 4238 3.363378 CCATCAAACAAGCTATCGATCGC 60.363 47.826 13.69 13.69 0.00 4.58
906 4257 2.992817 ATCGCCATCTCCCTCTCGCT 62.993 60.000 0.00 0.00 0.00 4.93
909 4264 2.334653 CATCTCCCTCTCGCTCGC 59.665 66.667 0.00 0.00 0.00 5.03
910 4265 3.283684 ATCTCCCTCTCGCTCGCG 61.284 66.667 0.00 0.00 41.35 5.87
1155 4542 2.810852 CAAGAAGTGCAAGAACTCCTCC 59.189 50.000 0.00 0.00 0.00 4.30
1347 4755 0.037590 AATACAAGAAGCCCCGCACA 59.962 50.000 0.00 0.00 0.00 4.57
1597 5056 1.067212 AGCTGCCTCGGACTAATAACG 59.933 52.381 0.00 0.00 0.00 3.18
1599 5058 0.818938 TGCCTCGGACTAATAACGCA 59.181 50.000 0.00 0.00 0.00 5.24
1831 5331 7.454380 TGTGGAATTCAATCCCATAACTTCTTT 59.546 33.333 7.93 0.00 38.82 2.52
1940 5458 6.091305 GGTCATTTTTCTGCAGCTTAATTTCC 59.909 38.462 9.47 8.38 0.00 3.13
1941 5459 5.863397 TCATTTTTCTGCAGCTTAATTTCCG 59.137 36.000 9.47 0.00 0.00 4.30
1981 5513 1.002033 CAACTTGAAGTGCACAGCTCC 60.002 52.381 21.04 3.41 0.00 4.70
2011 5547 3.851458 TGCATGGATAGCAGATGAGTT 57.149 42.857 0.00 0.00 37.02 3.01
2012 5548 4.160642 TGCATGGATAGCAGATGAGTTT 57.839 40.909 0.00 0.00 37.02 2.66
2168 5841 6.095440 ACATGCAGTTACCCATTAATTCAGTC 59.905 38.462 0.00 0.00 0.00 3.51
2187 5860 0.591741 CATACGACGACCGAGAAGCC 60.592 60.000 0.00 0.00 41.76 4.35
2246 5919 5.068591 GGGAAGATATAAACACGCCCATTTT 59.931 40.000 0.00 0.00 34.47 1.82
2265 5938 6.536224 CCATTTTCCCATGATAAAGTTGAAGC 59.464 38.462 0.00 0.00 0.00 3.86
2271 5944 4.639310 CCATGATAAAGTTGAAGCTGAGCT 59.361 41.667 0.00 0.00 42.56 4.09
2331 7383 3.292500 CTGCAGCTGGAGACGAGCA 62.293 63.158 29.60 10.21 37.08 4.26
2423 7488 0.815734 AACGAGACGGACCATAGGTG 59.184 55.000 0.00 0.00 35.25 4.00
2451 7521 2.564947 AGTCACTAGGAAGCACTCAAGG 59.435 50.000 0.00 0.00 0.00 3.61
2505 7577 3.981375 TCCTCTACTCTAGCATCCCACTA 59.019 47.826 0.00 0.00 0.00 2.74
2526 7602 7.547370 CCACTACACTTCAAAATCCAACAAAAA 59.453 33.333 0.00 0.00 0.00 1.94
2543 7619 8.404000 CCAACAAAAATTGAACCAAATGAATGA 58.596 29.630 0.00 0.00 0.00 2.57
2643 7724 1.327690 TATCTGCCCGGTCACTGTCC 61.328 60.000 0.00 0.00 0.00 4.02
2645 7733 3.164977 TGCCCGGTCACTGTCCAA 61.165 61.111 0.00 0.00 0.00 3.53
2652 7740 2.936498 CCGGTCACTGTCCAATCATAAC 59.064 50.000 0.00 0.00 0.00 1.89
2704 7794 1.990160 AACGTCTGGGGCTGTTTGGA 61.990 55.000 0.00 0.00 0.00 3.53
2728 7822 1.402107 CCCAAACCCAGCCCATATGC 61.402 60.000 0.00 0.00 0.00 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 3069 1.299541 CAGTGTTGTGGCGAGACTTT 58.700 50.000 0.00 0.00 0.00 2.66
80 3104 1.947456 GTTCGGGTCTCTTGCTGTTTT 59.053 47.619 0.00 0.00 0.00 2.43
125 3149 2.027192 GGAGCTCCACTGTGTTATGGAA 60.027 50.000 28.43 0.00 44.42 3.53
156 3181 0.882042 ACGCTGCTTTGACTGACTGG 60.882 55.000 0.00 0.00 0.00 4.00
168 3193 3.709633 TGCCCATCAGACGCTGCT 61.710 61.111 0.00 0.00 0.00 4.24
191 3216 2.815503 GGCTAAAACCTAAAAGGACGCA 59.184 45.455 0.00 0.00 37.67 5.24
211 3236 1.176527 CTAAGGTGGGCATGTTGTGG 58.823 55.000 0.00 0.00 0.00 4.17
212 3237 1.176527 CCTAAGGTGGGCATGTTGTG 58.823 55.000 0.00 0.00 0.00 3.33
215 3240 0.035439 CGTCCTAAGGTGGGCATGTT 60.035 55.000 0.00 0.00 0.00 2.71
216 3241 0.907704 TCGTCCTAAGGTGGGCATGT 60.908 55.000 0.00 0.00 0.00 3.21
217 3242 0.469917 ATCGTCCTAAGGTGGGCATG 59.530 55.000 0.00 0.00 0.00 4.06
218 3243 0.759346 GATCGTCCTAAGGTGGGCAT 59.241 55.000 0.00 0.00 0.00 4.40
219 3244 1.672854 CGATCGTCCTAAGGTGGGCA 61.673 60.000 7.03 0.00 0.00 5.36
220 3245 1.067582 CGATCGTCCTAAGGTGGGC 59.932 63.158 7.03 0.00 0.00 5.36
222 3247 0.669077 CCTCGATCGTCCTAAGGTGG 59.331 60.000 15.94 1.50 0.00 4.61
223 3248 0.669077 CCCTCGATCGTCCTAAGGTG 59.331 60.000 15.94 4.71 0.00 4.00
224 3249 1.108132 GCCCTCGATCGTCCTAAGGT 61.108 60.000 15.94 0.00 0.00 3.50
225 3250 0.824182 AGCCCTCGATCGTCCTAAGG 60.824 60.000 15.94 13.57 0.00 2.69
227 3252 0.744874 CAAGCCCTCGATCGTCCTAA 59.255 55.000 15.94 0.00 0.00 2.69
228 3253 1.107538 CCAAGCCCTCGATCGTCCTA 61.108 60.000 15.94 0.00 0.00 2.94
229 3254 2.427245 CCAAGCCCTCGATCGTCCT 61.427 63.158 15.94 4.52 0.00 3.85
230 3255 2.107141 CCAAGCCCTCGATCGTCC 59.893 66.667 15.94 2.19 0.00 4.79
232 3257 2.579201 CACCAAGCCCTCGATCGT 59.421 61.111 15.94 0.00 0.00 3.73
236 3261 3.936203 AACGCACCAAGCCCTCGA 61.936 61.111 0.00 0.00 41.38 4.04
237 3262 3.726517 CAACGCACCAAGCCCTCG 61.727 66.667 0.00 0.00 41.38 4.63
238 3263 3.365265 CCAACGCACCAAGCCCTC 61.365 66.667 0.00 0.00 41.38 4.30
239 3264 4.974721 CCCAACGCACCAAGCCCT 62.975 66.667 0.00 0.00 41.38 5.19
243 3268 2.697992 CTTTGGCCCAACGCACCAAG 62.698 60.000 0.00 0.00 43.93 3.61
244 3269 2.759973 TTTGGCCCAACGCACCAA 60.760 55.556 0.00 0.00 41.61 3.67
245 3270 3.222855 CTTTGGCCCAACGCACCA 61.223 61.111 0.00 0.00 40.31 4.17
246 3271 4.662961 GCTTTGGCCCAACGCACC 62.663 66.667 19.09 0.00 38.28 5.01
259 3284 4.994756 CCCCTTGGTGCGGGCTTT 62.995 66.667 0.00 0.00 40.54 3.51
266 3291 6.534479 GTTTCCAAACTAACCCCTTGGTGC 62.534 50.000 0.35 0.00 39.29 5.01
267 3292 3.069016 GTTTCCAAACTAACCCCTTGGTG 59.931 47.826 0.35 0.00 39.29 4.17
268 3293 3.302161 GTTTCCAAACTAACCCCTTGGT 58.698 45.455 0.35 0.00 40.47 3.67
269 3294 2.631062 GGTTTCCAAACTAACCCCTTGG 59.369 50.000 2.32 0.00 40.88 3.61
270 3295 3.572642 AGGTTTCCAAACTAACCCCTTG 58.427 45.455 0.00 0.00 43.89 3.61
271 3296 3.985553 AGGTTTCCAAACTAACCCCTT 57.014 42.857 0.00 0.00 43.89 3.95
272 3297 3.205733 TGAAGGTTTCCAAACTAACCCCT 59.794 43.478 0.00 0.00 43.89 4.79
273 3298 3.568443 TGAAGGTTTCCAAACTAACCCC 58.432 45.455 0.00 0.00 43.89 4.95
275 3300 6.399639 TTGATGAAGGTTTCCAAACTAACC 57.600 37.500 2.32 0.00 43.31 2.85
276 3301 5.920840 GCTTGATGAAGGTTTCCAAACTAAC 59.079 40.000 2.32 0.00 38.89 2.34
277 3302 5.596361 TGCTTGATGAAGGTTTCCAAACTAA 59.404 36.000 2.32 0.00 38.89 2.24
278 3303 5.136828 TGCTTGATGAAGGTTTCCAAACTA 58.863 37.500 2.32 0.00 38.89 2.24
280 3305 4.320608 TGCTTGATGAAGGTTTCCAAAC 57.679 40.909 0.00 0.00 38.17 2.93
281 3306 5.549742 ATTGCTTGATGAAGGTTTCCAAA 57.450 34.783 0.00 0.00 0.00 3.28
282 3307 5.549742 AATTGCTTGATGAAGGTTTCCAA 57.450 34.783 0.00 0.00 0.00 3.53
283 3308 5.070180 TGAAATTGCTTGATGAAGGTTTCCA 59.930 36.000 0.00 0.00 0.00 3.53
284 3309 5.540911 TGAAATTGCTTGATGAAGGTTTCC 58.459 37.500 0.00 0.00 0.00 3.13
285 3310 6.449698 TCTGAAATTGCTTGATGAAGGTTTC 58.550 36.000 0.00 0.00 0.00 2.78
286 3311 6.409524 TCTGAAATTGCTTGATGAAGGTTT 57.590 33.333 0.00 0.00 0.00 3.27
287 3312 6.600882 ATCTGAAATTGCTTGATGAAGGTT 57.399 33.333 0.00 0.00 0.00 3.50
289 3314 7.900782 AAAATCTGAAATTGCTTGATGAAGG 57.099 32.000 0.00 0.00 0.00 3.46
294 3319 9.595823 CCTCAATAAAATCTGAAATTGCTTGAT 57.404 29.630 0.00 0.00 30.99 2.57
295 3320 8.805175 TCCTCAATAAAATCTGAAATTGCTTGA 58.195 29.630 0.00 0.00 30.99 3.02
296 3321 8.991243 TCCTCAATAAAATCTGAAATTGCTTG 57.009 30.769 0.00 0.00 30.99 4.01
360 3385 9.189156 CCTAAAGATTTCAATCCCTACAAATGA 57.811 33.333 0.00 0.00 36.04 2.57
361 3386 9.189156 TCCTAAAGATTTCAATCCCTACAAATG 57.811 33.333 0.00 0.00 36.04 2.32
363 3388 9.594936 TTTCCTAAAGATTTCAATCCCTACAAA 57.405 29.630 0.00 0.00 36.04 2.83
364 3389 9.768215 ATTTCCTAAAGATTTCAATCCCTACAA 57.232 29.630 0.00 0.00 36.04 2.41
365 3390 9.768215 AATTTCCTAAAGATTTCAATCCCTACA 57.232 29.630 0.00 0.00 36.04 2.74
392 3417 2.159170 AGTGCAACGCAAGCCTTAAAAA 60.159 40.909 0.00 0.00 45.86 1.94
393 3418 1.407258 AGTGCAACGCAAGCCTTAAAA 59.593 42.857 0.00 0.00 45.86 1.52
394 3419 1.028905 AGTGCAACGCAAGCCTTAAA 58.971 45.000 0.00 0.00 45.86 1.52
395 3420 1.885560 TAGTGCAACGCAAGCCTTAA 58.114 45.000 0.00 0.00 45.86 1.85
397 3422 2.107950 TATAGTGCAACGCAAGCCTT 57.892 45.000 0.00 0.00 45.86 4.35
398 3423 2.332063 ATATAGTGCAACGCAAGCCT 57.668 45.000 0.00 0.00 45.86 4.58
399 3424 3.420839 AAATATAGTGCAACGCAAGCC 57.579 42.857 0.00 0.00 45.86 4.35
400 3425 6.745450 TCTTTAAAATATAGTGCAACGCAAGC 59.255 34.615 0.00 0.00 45.86 4.01
401 3426 8.667987 TTCTTTAAAATATAGTGCAACGCAAG 57.332 30.769 0.00 0.00 45.86 4.01
403 3428 9.464714 TTTTTCTTTAAAATATAGTGCAACGCA 57.535 25.926 0.00 0.00 36.77 5.24
426 3451 3.576550 AGGGTCGCAATGGTGTAATTTTT 59.423 39.130 0.00 0.00 0.00 1.94
427 3452 3.161866 AGGGTCGCAATGGTGTAATTTT 58.838 40.909 0.00 0.00 0.00 1.82
429 3454 2.507407 AGGGTCGCAATGGTGTAATT 57.493 45.000 0.00 0.00 0.00 1.40
433 3458 2.279935 TAAAAGGGTCGCAATGGTGT 57.720 45.000 0.00 0.00 0.00 4.16
434 3459 3.651803 TTTAAAAGGGTCGCAATGGTG 57.348 42.857 0.00 0.00 0.00 4.17
435 3460 4.674281 TTTTTAAAAGGGTCGCAATGGT 57.326 36.364 0.14 0.00 0.00 3.55
465 3615 0.945813 CCACGCCGGTGTTAGAAAAA 59.054 50.000 20.30 0.00 42.80 1.94
484 3634 1.135731 CACGCGACTCACTCTCTCC 59.864 63.158 15.93 0.00 0.00 3.71
498 3655 6.315393 TGAAACTATTTATCCTTCCTTCACGC 59.685 38.462 0.00 0.00 0.00 5.34
533 3720 1.405105 GCACACATGATACGCCCATTT 59.595 47.619 0.00 0.00 0.00 2.32
553 3748 5.251081 CAGTGCTCGAAGAATAAACGAATG 58.749 41.667 0.00 0.00 34.09 2.67
574 3773 4.959596 AAATGAATACAGACAGCAGCAG 57.040 40.909 0.00 0.00 0.00 4.24
575 3774 5.241285 TGAAAAATGAATACAGACAGCAGCA 59.759 36.000 0.00 0.00 0.00 4.41
576 3775 5.570589 GTGAAAAATGAATACAGACAGCAGC 59.429 40.000 0.00 0.00 0.00 5.25
690 3928 1.602377 CCAGACCGGAACAAAACTGTC 59.398 52.381 9.46 0.00 36.56 3.51
720 3960 1.189524 AGGGGACACGGAAATGACGA 61.190 55.000 0.00 0.00 34.93 4.20
721 3961 0.533491 TAGGGGACACGGAAATGACG 59.467 55.000 0.00 0.00 37.36 4.35
722 3962 1.553704 AGTAGGGGACACGGAAATGAC 59.446 52.381 0.00 0.00 0.00 3.06
760 4010 3.169733 GGTTCGAGTCTGTAAAGCTACG 58.830 50.000 0.00 0.00 0.00 3.51
761 4011 3.120060 TCGGTTCGAGTCTGTAAAGCTAC 60.120 47.826 0.00 0.00 0.00 3.58
762 4012 3.076621 TCGGTTCGAGTCTGTAAAGCTA 58.923 45.455 0.00 0.00 0.00 3.32
801 4056 3.448686 AGTAGTTGATCGCTATGTGCAC 58.551 45.455 10.75 10.75 43.06 4.57
816 4071 4.501071 CGGGGCGCATATTTATAGTAGTT 58.499 43.478 10.83 0.00 0.00 2.24
853 4119 2.762887 TGATGGAGATGAAGAGTCGCTT 59.237 45.455 0.00 0.00 40.25 4.68
855 4121 2.879002 TGATGGAGATGAAGAGTCGC 57.121 50.000 0.00 0.00 0.00 5.19
891 4238 3.038280 CGAGCGAGAGGGAGATGG 58.962 66.667 0.00 0.00 0.00 3.51
928 4283 3.135167 GCCATTGATTTTGGTGGATGGAT 59.865 43.478 4.47 0.00 36.92 3.41
929 4284 2.500910 GCCATTGATTTTGGTGGATGGA 59.499 45.455 4.47 0.00 36.92 3.41
930 4285 2.236644 TGCCATTGATTTTGGTGGATGG 59.763 45.455 0.00 0.00 36.57 3.51
931 4286 3.527533 CTGCCATTGATTTTGGTGGATG 58.472 45.455 0.00 0.00 36.57 3.51
1347 4755 1.226688 CGACGATGACGACATGGCT 60.227 57.895 4.80 0.00 42.66 4.75
1629 5100 1.699656 CGAACATGGCCTTCTGCGAG 61.700 60.000 3.32 0.00 42.61 5.03
1630 5101 1.741401 CGAACATGGCCTTCTGCGA 60.741 57.895 3.32 0.00 42.61 5.10
1831 5331 8.421249 AGATGAATGAAACAAAAGGGATTACA 57.579 30.769 0.00 0.00 0.00 2.41
1905 5423 4.622220 GCAGAAAAATGACCATGAAGGCAT 60.622 41.667 0.00 0.00 43.14 4.40
1906 5424 3.306225 GCAGAAAAATGACCATGAAGGCA 60.306 43.478 0.00 0.00 43.14 4.75
1907 5425 3.256558 GCAGAAAAATGACCATGAAGGC 58.743 45.455 0.00 0.00 43.14 4.35
1908 5426 4.491676 CTGCAGAAAAATGACCATGAAGG 58.508 43.478 8.42 0.00 45.67 3.46
1909 5427 3.924686 GCTGCAGAAAAATGACCATGAAG 59.075 43.478 20.43 0.00 0.00 3.02
1940 5458 1.393539 AGCGCTACAGCACATTAAACG 59.606 47.619 8.99 0.00 42.21 3.60
1941 5459 2.415168 TGAGCGCTACAGCACATTAAAC 59.585 45.455 11.50 0.00 42.21 2.01
1959 5490 1.945394 AGCTGTGCACTTCAAGTTGAG 59.055 47.619 19.41 4.49 0.00 3.02
1981 5513 3.940852 TGCTATCCATGCAAACTGTAGTG 59.059 43.478 0.00 0.00 37.51 2.74
2137 5810 8.988546 ATTAATGGGTAACTGCATGTGTAATA 57.011 30.769 0.00 0.00 0.00 0.98
2168 5841 0.591741 GGCTTCTCGGTCGTCGTATG 60.592 60.000 0.00 0.00 40.32 2.39
2187 5860 2.159734 GCGAGAACTGTTTCTGCATCTG 60.160 50.000 0.00 0.00 42.53 2.90
2246 5919 5.178096 TCAGCTTCAACTTTATCATGGGA 57.822 39.130 0.00 0.00 0.00 4.37
2265 5938 4.130118 ACTCACCTACAAACAAAGCTCAG 58.870 43.478 0.00 0.00 0.00 3.35
2271 5944 4.024387 GCATTCGACTCACCTACAAACAAA 60.024 41.667 0.00 0.00 0.00 2.83
2451 7521 2.429571 TGGTGTACGCGCGAGAAC 60.430 61.111 39.36 28.53 0.00 3.01
2505 7577 8.558973 TCAATTTTTGTTGGATTTTGAAGTGT 57.441 26.923 0.00 0.00 0.00 3.55
2526 7602 5.757320 TGCGTTTTCATTCATTTGGTTCAAT 59.243 32.000 0.00 0.00 0.00 2.57
2611 7692 2.084546 GGCAGATAGTTTTGAGCGGTT 58.915 47.619 0.00 0.00 0.00 4.44
2643 7724 5.981315 GCCTTGGATGACAATGTTATGATTG 59.019 40.000 0.00 0.00 38.65 2.67
2645 7733 4.586001 GGCCTTGGATGACAATGTTATGAT 59.414 41.667 0.00 0.00 38.65 2.45
2652 7740 1.044790 GGGGGCCTTGGATGACAATG 61.045 60.000 0.84 0.00 38.65 2.82
2704 7794 2.122592 GGCTGGGTTTGGGGGTTT 60.123 61.111 0.00 0.00 0.00 3.27
2728 7822 2.280797 CGCCCCATATCCACACCG 60.281 66.667 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.