Multiple sequence alignment - TraesCS7D01G513400

Loading Multiple Alignment...

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 TraesCS7D01G513400 chr7D 100.000 2797 0 0 1 2797 614534639 614537435 0.000000e+00 5166.0
1 TraesCS7D01G513400 chr7D 84.191 544 79 5 1261 1801 549135038 549135577 3.190000e-144 521.0
2 TraesCS7D01G513400 chr7D 84.007 544 82 3 1260 1801 549274575 549275115 4.130000e-143 518.0
3 TraesCS7D01G513400 chr7D 85.870 184 18 6 951 1129 548916091 548915911 3.680000e-44 189.0
4 TraesCS7D01G513400 chr7D 84.483 174 15 9 956 1124 549134793 549134959 8.020000e-36 161.0
5 TraesCS7D01G513400 chr7D 93.750 48 3 0 2699 2746 540731336 540731289 3.860000e-09 73.1
6 TraesCS7D01G513400 chr7A 92.098 1139 60 7 1246 2380 706900659 706901771 0.000000e+00 1578.0
7 TraesCS7D01G513400 chr7A 88.120 1271 75 20 1 1213 706898923 706900175 0.000000e+00 1441.0
8 TraesCS7D01G513400 chr7A 83.755 554 84 4 1250 1801 634477164 634477713 1.150000e-143 520.0
9 TraesCS7D01G513400 chr7A 83.574 554 85 4 1250 1801 634464234 634464783 5.340000e-142 514.0
10 TraesCS7D01G513400 chr7A 89.441 322 22 8 2476 2797 706901804 706902113 2.020000e-106 396.0
11 TraesCS7D01G513400 chr7A 85.955 178 16 7 956 1129 634605502 634605674 6.150000e-42 182.0
12 TraesCS7D01G513400 chr7A 82.564 195 20 11 956 1143 634464000 634464187 2.880000e-35 159.0
13 TraesCS7D01G513400 chr7A 82.564 195 20 10 956 1143 634476930 634477117 2.880000e-35 159.0
14 TraesCS7D01G513400 chr7A 93.478 46 3 0 2701 2746 622383650 622383605 5.000000e-08 69.4
15 TraesCS7D01G513400 chr7B 90.000 1240 83 26 1 1218 706850106 706851326 0.000000e+00 1565.0
16 TraesCS7D01G513400 chr7B 93.118 712 46 3 1246 1955 706853151 706853861 0.000000e+00 1040.0
17 TraesCS7D01G513400 chr7B 84.317 542 80 3 1262 1801 592718723 592719261 2.470000e-145 525.0
18 TraesCS7D01G513400 chr7B 83.704 540 84 2 1260 1797 592808171 592808708 8.940000e-140 507.0
19 TraesCS7D01G513400 chr7B 83.704 540 84 2 1260 1797 592867962 592868499 8.940000e-140 507.0
20 TraesCS7D01G513400 chr7B 85.380 171 19 4 956 1124 592807932 592808098 3.700000e-39 172.0
21 TraesCS7D01G513400 chr7B 86.250 160 16 4 967 1124 592867734 592867889 4.790000e-38 169.0
22 TraesCS7D01G513400 chr7B 88.321 137 7 2 2129 2256 706854028 706854164 3.730000e-34 156.0
23 TraesCS7D01G513400 chr4B 86.242 298 31 5 1 289 142530126 142529830 5.820000e-82 315.0
24 TraesCS7D01G513400 chr4B 85.235 298 34 5 1 289 95878359 95878063 5.860000e-77 298.0
25 TraesCS7D01G513400 chr6B 84.407 295 36 5 1 286 4264370 4264663 5.900000e-72 281.0
26 TraesCS7D01G513400 chr6B 92.157 51 4 0 2689 2739 607006759 607006809 3.860000e-09 73.1
27 TraesCS7D01G513400 chr2B 87.302 126 16 0 1 126 777527804 777527679 8.070000e-31 145.0
28 TraesCS7D01G513400 chr5A 82.031 128 16 3 2676 2797 578063815 578063941 4.930000e-18 102.0
29 TraesCS7D01G513400 chr4D 90.141 71 6 1 2669 2739 5782351 5782282 1.070000e-14 91.6
30 TraesCS7D01G513400 chr6D 93.750 48 3 0 2692 2739 404601607 404601654 3.860000e-09 73.1
31 TraesCS7D01G513400 chr2A 75.781 128 23 6 2676 2797 411110280 411110405 1.080000e-04 58.4


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 TraesCS7D01G513400 chr7D 614534639 614537435 2796 False 5166.000000 5166 100.000000 1 2797 1 chr7D.!!$F2 2796
1 TraesCS7D01G513400 chr7D 549274575 549275115 540 False 518.000000 518 84.007000 1260 1801 1 chr7D.!!$F1 541
2 TraesCS7D01G513400 chr7D 549134793 549135577 784 False 341.000000 521 84.337000 956 1801 2 chr7D.!!$F3 845
3 TraesCS7D01G513400 chr7A 706898923 706902113 3190 False 1138.333333 1578 89.886333 1 2797 3 chr7A.!!$F4 2796
4 TraesCS7D01G513400 chr7A 634476930 634477713 783 False 339.500000 520 83.159500 956 1801 2 chr7A.!!$F3 845
5 TraesCS7D01G513400 chr7A 634464000 634464783 783 False 336.500000 514 83.069000 956 1801 2 chr7A.!!$F2 845
6 TraesCS7D01G513400 chr7B 706850106 706854164 4058 False 920.333333 1565 90.479667 1 2256 3 chr7B.!!$F4 2255
7 TraesCS7D01G513400 chr7B 592718723 592719261 538 False 525.000000 525 84.317000 1262 1801 1 chr7B.!!$F1 539
8 TraesCS7D01G513400 chr7B 592807932 592808708 776 False 339.500000 507 84.542000 956 1797 2 chr7B.!!$F2 841
9 TraesCS7D01G513400 chr7B 592867734 592868499 765 False 338.000000 507 84.977000 967 1797 2 chr7B.!!$F3 830

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
682 701 0.11131 GCACGCCAAAAATTCGCAAC 60.111 50.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2449 4409 0.249398 GTCCCAGTCAACGCCACTAT 59.751 55.0 0.0 0.0 0.0 2.12 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.342378 TGCTCACATAGGTCATAGAAGTCC 59.658 45.833 0.00 0.00 0.00 3.85
29 30 5.770663 GCTCACATAGGTCATAGAAGTCCTA 59.229 44.000 0.00 0.00 37.04 2.94
62 63 8.882415 ATATGCCAACATTTTCTGATGAAATC 57.118 30.769 0.00 0.00 41.24 2.17
89 90 4.133373 CCCATCAGGCCCAGGTGG 62.133 72.222 16.46 16.46 37.09 4.61
118 119 4.832248 TGTTGGTAGATCCTTGATCACAC 58.168 43.478 0.00 4.19 41.12 3.82
129 130 5.573219 TCCTTGATCACACCATCAATTTCT 58.427 37.500 0.00 0.00 41.06 2.52
160 161 5.324832 AAATGGAACCTCAAGAAAGGAGA 57.675 39.130 0.00 0.00 38.87 3.71
206 216 5.221244 GGTGAGCAGGTATGTCAAAGTTTTT 60.221 40.000 0.00 0.00 0.00 1.94
216 226 5.596836 TGTCAAAGTTTTTCAGATTGGCT 57.403 34.783 0.00 0.00 0.00 4.75
221 231 5.789643 AAGTTTTTCAGATTGGCTAAGCA 57.210 34.783 0.00 0.00 0.00 3.91
270 280 1.341285 TGCTTTCCCATCATGGTCAGG 60.341 52.381 2.07 0.00 35.17 3.86
305 315 5.125417 CCATCTTGGGGTTAACAGTTGTATG 59.875 44.000 8.10 4.42 32.67 2.39
395 405 3.518303 ACCCTCCAATTCACCTACTACAC 59.482 47.826 0.00 0.00 0.00 2.90
403 413 1.074405 TCACCTACTACACTCACCCGT 59.926 52.381 0.00 0.00 0.00 5.28
464 482 7.222611 GCGCAATATGTTAATTCAAACCTTGAT 59.777 33.333 0.30 0.00 39.84 2.57
498 516 1.547372 ACATTTCAACCATGCTGAGGC 59.453 47.619 0.00 0.00 39.26 4.70
586 605 3.283684 CGGCTTGCAACCGTGGAA 61.284 61.111 23.72 0.00 45.70 3.53
587 606 2.625823 CGGCTTGCAACCGTGGAAT 61.626 57.895 23.72 0.00 45.70 3.01
588 607 1.080569 GGCTTGCAACCGTGGAATG 60.081 57.895 0.00 0.00 34.22 2.67
642 661 1.138859 CCACGCTCCTGTATGAATCCA 59.861 52.381 0.00 0.00 0.00 3.41
662 681 6.073447 TCCACTCCTATAAATTCAAGGCAA 57.927 37.500 0.00 0.00 0.00 4.52
682 701 0.111310 GCACGCCAAAAATTCGCAAC 60.111 50.000 0.00 0.00 0.00 4.17
705 724 4.490959 CGAAATGATAGATAATGACGCGCC 60.491 45.833 5.73 0.00 0.00 6.53
733 759 7.461107 CACACACTTCCGAAATATAACGAATT 58.539 34.615 0.00 0.00 0.00 2.17
754 780 7.458198 CGAATTGTTTTTGAAAAACTTGCGTTG 60.458 33.333 27.49 12.67 32.65 4.10
774 800 2.024414 GATTTCCAAATGGAGTCCCCG 58.976 52.381 6.74 0.00 46.36 5.73
818 856 5.435291 AGTTTTCTCCCTGCATGATTAGAG 58.565 41.667 0.00 0.00 0.00 2.43
894 943 1.399215 CGTTTTCACCGGAATTCCACG 60.399 52.381 24.09 18.79 35.14 4.94
895 944 1.605232 GTTTTCACCGGAATTCCACGT 59.395 47.619 24.09 15.79 35.14 4.49
899 948 0.948678 CACCGGAATTCCACGTTGTT 59.051 50.000 24.09 0.00 35.14 2.83
994 1069 3.455327 CACATGTGCTGATCGAGAAGAT 58.545 45.455 13.94 0.00 43.51 2.40
1176 1258 2.431057 TCTGCTCCCTCCGTTCTAATTC 59.569 50.000 0.00 0.00 0.00 2.17
1191 1273 0.465460 AATTCACACGGTGCCACACT 60.465 50.000 8.30 0.00 34.40 3.55
1213 1295 9.268268 ACACTTTTCGATATTCAACTTTGACTA 57.732 29.630 0.00 0.00 36.83 2.59
1220 1302 9.042008 TCGATATTCAACTTTGACTAATAAGCC 57.958 33.333 0.00 0.00 36.83 4.35
1221 1303 9.046296 CGATATTCAACTTTGACTAATAAGCCT 57.954 33.333 0.00 0.00 36.83 4.58
1225 1307 6.407202 TCAACTTTGACTAATAAGCCTCCTC 58.593 40.000 0.00 0.00 31.01 3.71
1237 1510 2.334023 AGCCTCCTCCCAACATCTATC 58.666 52.381 0.00 0.00 0.00 2.08
1334 3237 4.673298 TTCTTCTTCGCCGGCGCA 62.673 61.111 42.78 33.06 39.59 6.09
1520 3423 1.550976 CTGGAAGGCTCCGTCTACTTT 59.449 52.381 2.11 0.00 45.85 2.66
1526 3429 1.271217 GGCTCCGTCTACTTTGGGTTT 60.271 52.381 0.00 0.00 0.00 3.27
1625 3528 4.910195 TCATGCACTTCCTCTACAACAAT 58.090 39.130 0.00 0.00 0.00 2.71
1730 3633 0.179026 CACTCCCGGACGATCTCCTA 60.179 60.000 0.73 0.00 36.80 2.94
1768 3671 1.609580 GGATAAGCACACCGTGGACAA 60.610 52.381 3.03 0.00 33.64 3.18
1840 3744 6.942576 AGTAATTTATCATATTTGCTCGGGCT 59.057 34.615 9.62 0.00 39.59 5.19
1851 3755 1.687123 TGCTCGGGCTTAGTAATCTCC 59.313 52.381 9.62 0.00 39.59 3.71
1852 3756 1.336056 GCTCGGGCTTAGTAATCTCCG 60.336 57.143 0.00 10.57 38.92 4.63
1872 3776 8.330466 TCTCCGTGTGTTTATTTGTGATAAAT 57.670 30.769 0.00 0.00 0.00 1.40
1890 3794 8.702438 GTGATAAATATTTGCAATGGAATTCGG 58.298 33.333 11.05 0.00 31.22 4.30
1891 3795 7.871973 TGATAAATATTTGCAATGGAATTCGGG 59.128 33.333 11.05 0.00 31.22 5.14
1893 3797 3.525268 ATTTGCAATGGAATTCGGGAC 57.475 42.857 0.00 0.00 31.22 4.46
1970 3874 4.262463 GCATCATAACCGGGACTAATGAGA 60.262 45.833 6.32 0.00 30.65 3.27
1977 3881 1.131883 CGGGACTAATGAGACGAACGT 59.868 52.381 0.00 0.00 0.00 3.99
2046 3950 0.893270 TGTGGCGTTGGAATTGAGGG 60.893 55.000 0.00 0.00 0.00 4.30
2249 4207 6.135454 AGATTTGCACACCCATATTTGGATA 58.865 36.000 3.41 0.00 46.92 2.59
2250 4208 6.610830 AGATTTGCACACCCATATTTGGATAA 59.389 34.615 3.41 0.00 46.92 1.75
2251 4209 6.611613 TTTGCACACCCATATTTGGATAAA 57.388 33.333 3.41 0.00 46.92 1.40
2252 4210 6.611613 TTGCACACCCATATTTGGATAAAA 57.388 33.333 3.41 0.00 46.92 1.52
2253 4211 5.971763 TGCACACCCATATTTGGATAAAAC 58.028 37.500 3.41 0.00 46.92 2.43
2254 4212 5.719085 TGCACACCCATATTTGGATAAAACT 59.281 36.000 3.41 0.00 46.92 2.66
2255 4213 6.892456 TGCACACCCATATTTGGATAAAACTA 59.108 34.615 3.41 0.00 46.92 2.24
2256 4214 7.563188 TGCACACCCATATTTGGATAAAACTAT 59.437 33.333 3.41 0.00 46.92 2.12
2257 4215 8.421002 GCACACCCATATTTGGATAAAACTATT 58.579 33.333 3.41 0.00 46.92 1.73
2287 4245 8.496707 TTCGGGTGGATAAAACTAATCTTAAC 57.503 34.615 0.00 0.00 0.00 2.01
2324 4282 6.122277 TCTAAATGAAGCAATACCTCCCAAG 58.878 40.000 0.00 0.00 0.00 3.61
2365 4323 1.153469 GAGGAGGAGCAAGCGAAGG 60.153 63.158 0.00 0.00 0.00 3.46
2366 4324 1.608717 GAGGAGGAGCAAGCGAAGGA 61.609 60.000 0.00 0.00 0.00 3.36
2367 4325 1.153469 GGAGGAGCAAGCGAAGGAG 60.153 63.158 0.00 0.00 0.00 3.69
2368 4326 1.153469 GAGGAGCAAGCGAAGGAGG 60.153 63.158 0.00 0.00 0.00 4.30
2369 4327 1.608717 GAGGAGCAAGCGAAGGAGGA 61.609 60.000 0.00 0.00 0.00 3.71
2370 4328 1.153469 GGAGCAAGCGAAGGAGGAG 60.153 63.158 0.00 0.00 0.00 3.69
2371 4329 1.153469 GAGCAAGCGAAGGAGGAGG 60.153 63.158 0.00 0.00 0.00 4.30
2372 4330 2.821810 GCAAGCGAAGGAGGAGGC 60.822 66.667 0.00 0.00 0.00 4.70
2373 4331 2.985456 CAAGCGAAGGAGGAGGCT 59.015 61.111 0.00 0.00 37.33 4.58
2374 4332 1.298014 CAAGCGAAGGAGGAGGCTT 59.702 57.895 0.00 0.00 45.89 4.35
2375 4333 0.742635 CAAGCGAAGGAGGAGGCTTC 60.743 60.000 0.00 0.00 43.35 3.86
2376 4334 1.904990 AAGCGAAGGAGGAGGCTTCC 61.905 60.000 6.80 6.80 41.57 3.46
2377 4335 2.904131 CGAAGGAGGAGGCTTCCC 59.096 66.667 11.97 2.95 45.24 3.97
2378 4336 1.687493 CGAAGGAGGAGGCTTCCCT 60.687 63.158 11.97 0.00 45.24 4.20
2379 4337 1.911471 GAAGGAGGAGGCTTCCCTG 59.089 63.158 11.97 0.00 45.24 4.45
2380 4338 0.618968 GAAGGAGGAGGCTTCCCTGA 60.619 60.000 11.97 0.00 45.24 3.86
2381 4339 0.045469 AAGGAGGAGGCTTCCCTGAT 59.955 55.000 11.97 0.00 45.24 2.90
2382 4340 0.399806 AGGAGGAGGCTTCCCTGATC 60.400 60.000 11.97 2.05 45.24 2.92
2383 4341 1.745264 GAGGAGGCTTCCCTGATCG 59.255 63.158 11.97 0.00 45.24 3.69
2384 4342 2.110006 GGAGGCTTCCCTGATCGC 59.890 66.667 2.75 0.00 43.12 4.58
2385 4343 2.110006 GAGGCTTCCCTGATCGCC 59.890 66.667 0.00 0.00 43.12 5.54
2386 4344 2.688666 AGGCTTCCCTGATCGCCA 60.689 61.111 9.35 0.00 44.85 5.69
2387 4345 2.257409 GAGGCTTCCCTGATCGCCAA 62.257 60.000 9.35 0.00 43.12 4.52
2388 4346 1.821332 GGCTTCCCTGATCGCCAAG 60.821 63.158 2.54 0.00 42.06 3.61
2420 4380 5.667466 TCCCTGTTATTATGGAGACGTTTC 58.333 41.667 0.00 0.00 0.00 2.78
2423 4383 5.983720 CCTGTTATTATGGAGACGTTTCGAT 59.016 40.000 8.59 8.59 0.00 3.59
2425 4385 6.566141 TGTTATTATGGAGACGTTTCGATCA 58.434 36.000 6.87 0.00 0.00 2.92
2428 4388 2.347697 TGGAGACGTTTCGATCACTG 57.652 50.000 0.00 0.00 0.00 3.66
2433 4393 0.389948 ACGTTTCGATCACTGCCCTC 60.390 55.000 0.00 0.00 0.00 4.30
2434 4394 0.389817 CGTTTCGATCACTGCCCTCA 60.390 55.000 0.00 0.00 0.00 3.86
2435 4395 1.808411 GTTTCGATCACTGCCCTCAA 58.192 50.000 0.00 0.00 0.00 3.02
2436 4396 1.464997 GTTTCGATCACTGCCCTCAAC 59.535 52.381 0.00 0.00 0.00 3.18
2437 4397 0.036388 TTCGATCACTGCCCTCAACC 60.036 55.000 0.00 0.00 0.00 3.77
2438 4398 1.811266 CGATCACTGCCCTCAACCG 60.811 63.158 0.00 0.00 0.00 4.44
2439 4399 1.296715 GATCACTGCCCTCAACCGT 59.703 57.895 0.00 0.00 0.00 4.83
2440 4400 0.741221 GATCACTGCCCTCAACCGTC 60.741 60.000 0.00 0.00 0.00 4.79
2441 4401 1.480212 ATCACTGCCCTCAACCGTCA 61.480 55.000 0.00 0.00 0.00 4.35
2442 4402 1.227823 CACTGCCCTCAACCGTCAA 60.228 57.895 0.00 0.00 0.00 3.18
2443 4403 1.071471 ACTGCCCTCAACCGTCAAG 59.929 57.895 0.00 0.00 0.00 3.02
2444 4404 2.281484 TGCCCTCAACCGTCAAGC 60.281 61.111 0.00 0.00 0.00 4.01
2445 4405 3.056328 GCCCTCAACCGTCAAGCC 61.056 66.667 0.00 0.00 0.00 4.35
2446 4406 2.429930 CCCTCAACCGTCAAGCCA 59.570 61.111 0.00 0.00 0.00 4.75
2447 4407 1.228124 CCCTCAACCGTCAAGCCAA 60.228 57.895 0.00 0.00 0.00 4.52
2448 4408 0.821711 CCCTCAACCGTCAAGCCAAA 60.822 55.000 0.00 0.00 0.00 3.28
2449 4409 1.028905 CCTCAACCGTCAAGCCAAAA 58.971 50.000 0.00 0.00 0.00 2.44
2450 4410 1.613437 CCTCAACCGTCAAGCCAAAAT 59.387 47.619 0.00 0.00 0.00 1.82
2451 4411 2.817258 CCTCAACCGTCAAGCCAAAATA 59.183 45.455 0.00 0.00 0.00 1.40
2452 4412 3.119849 CCTCAACCGTCAAGCCAAAATAG 60.120 47.826 0.00 0.00 0.00 1.73
2453 4413 3.482436 TCAACCGTCAAGCCAAAATAGT 58.518 40.909 0.00 0.00 0.00 2.12
2454 4414 3.252215 TCAACCGTCAAGCCAAAATAGTG 59.748 43.478 0.00 0.00 0.00 2.74
2455 4415 2.159382 ACCGTCAAGCCAAAATAGTGG 58.841 47.619 0.00 0.00 42.05 4.00
2464 4424 3.201726 CCAAAATAGTGGCGTTGACTG 57.798 47.619 0.00 0.00 0.00 3.51
2465 4425 2.095263 CCAAAATAGTGGCGTTGACTGG 60.095 50.000 0.00 0.00 0.00 4.00
2466 4426 1.821216 AAATAGTGGCGTTGACTGGG 58.179 50.000 0.00 0.00 0.00 4.45
2467 4427 0.981183 AATAGTGGCGTTGACTGGGA 59.019 50.000 0.00 0.00 0.00 4.37
2468 4428 0.249398 ATAGTGGCGTTGACTGGGAC 59.751 55.000 0.00 0.00 0.00 4.46
2469 4429 2.149803 TAGTGGCGTTGACTGGGACG 62.150 60.000 0.00 0.00 41.89 4.79
2470 4430 3.542676 TGGCGTTGACTGGGACGT 61.543 61.111 0.00 0.00 41.10 4.34
2471 4431 3.041940 GGCGTTGACTGGGACGTG 61.042 66.667 0.00 0.00 41.10 4.49
2472 4432 3.041940 GCGTTGACTGGGACGTGG 61.042 66.667 0.00 0.00 41.10 4.94
2473 4433 2.357034 CGTTGACTGGGACGTGGG 60.357 66.667 0.00 0.00 34.75 4.61
2474 4434 2.668550 GTTGACTGGGACGTGGGC 60.669 66.667 0.00 0.00 0.00 5.36
2490 4450 1.228657 GGGCGTCTGTTTGGTCACTC 61.229 60.000 0.00 0.00 0.00 3.51
2491 4451 0.249911 GGCGTCTGTTTGGTCACTCT 60.250 55.000 0.00 0.00 0.00 3.24
2492 4452 1.583054 GCGTCTGTTTGGTCACTCTT 58.417 50.000 0.00 0.00 0.00 2.85
2496 4456 4.556233 CGTCTGTTTGGTCACTCTTGATA 58.444 43.478 0.00 0.00 33.11 2.15
2501 4461 8.352942 GTCTGTTTGGTCACTCTTGATATTTTT 58.647 33.333 0.00 0.00 33.11 1.94
2517 4477 2.837291 TTTTTGGCACGCCCAGCT 60.837 55.556 5.42 0.00 46.39 4.24
2518 4478 2.430610 TTTTTGGCACGCCCAGCTT 61.431 52.632 5.42 0.00 46.39 3.74
2519 4479 2.641439 TTTTTGGCACGCCCAGCTTG 62.641 55.000 5.42 0.00 46.39 4.01
2541 4501 3.161450 GCCCGCACTCCCTCCATA 61.161 66.667 0.00 0.00 0.00 2.74
2548 4508 2.037641 CGCACTCCCTCCATATGATTCA 59.962 50.000 3.65 0.00 0.00 2.57
2580 4540 3.854856 GTGAAACCAAGGCAGGCA 58.145 55.556 0.00 0.00 0.00 4.75
2609 4569 1.395826 CCAACTTTTTGGTCGGCCCA 61.396 55.000 2.12 0.00 46.63 5.36
2610 4570 0.678950 CAACTTTTTGGTCGGCCCAT 59.321 50.000 2.12 0.00 44.74 4.00
2617 4577 0.038890 TTGGTCGGCCCATGATTTGA 59.961 50.000 2.12 0.00 44.74 2.69
2619 4579 1.714899 GGTCGGCCCATGATTTGACG 61.715 60.000 0.00 0.00 0.00 4.35
2623 4583 3.525221 CCCATGATTTGACGGGGC 58.475 61.111 0.00 0.00 34.81 5.80
2628 4588 1.366111 ATGATTTGACGGGGCGAACG 61.366 55.000 0.00 0.00 37.36 3.95
2644 4604 2.015227 AACGTGGGCAGCAACCAAAG 62.015 55.000 0.00 0.00 40.24 2.77
2646 4606 1.733402 CGTGGGCAGCAACCAAAGAA 61.733 55.000 0.00 0.00 40.24 2.52
2655 4615 1.204704 GCAACCAAAGAACCCCTATGC 59.795 52.381 0.00 0.00 0.00 3.14
2659 4619 1.006832 CAAAGAACCCCTATGCGTCG 58.993 55.000 0.00 0.00 0.00 5.12
2682 4642 2.586357 GGCGCACGAGGATCCTTC 60.586 66.667 17.42 8.37 0.00 3.46
2696 4656 2.068834 TCCTTCCCCTCGATGAGTAC 57.931 55.000 0.00 0.00 0.00 2.73
2782 4742 1.309499 ACGGAAGAGAGACCTCGCTG 61.309 60.000 4.11 0.00 44.08 5.18
2786 4746 0.968393 AAGAGAGACCTCGCTGACCC 60.968 60.000 4.11 0.00 44.08 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 3.222603 GGGCCTGATGGGTTTAATACTG 58.777 50.000 0.84 0.00 37.43 2.74
89 90 4.518970 TCAAGGATCTACCAACAAACAAGC 59.481 41.667 0.00 0.00 42.04 4.01
118 119 8.313292 TCCATTTACCAAAGAAGAAATTGATGG 58.687 33.333 0.00 0.00 32.56 3.51
129 130 6.369629 TCTTGAGGTTCCATTTACCAAAGAA 58.630 36.000 0.00 0.00 37.53 2.52
160 161 3.127791 ACTTCCCACTCATCAGGATCT 57.872 47.619 0.00 0.00 0.00 2.75
206 216 4.240881 AGGAAATGCTTAGCCAATCTGA 57.759 40.909 0.29 0.00 0.00 3.27
221 231 6.996509 TCTTGCATGAAGCTTTTAAGGAAAT 58.003 32.000 0.00 0.00 45.94 2.17
270 280 2.162681 CCCAAGATGGTGTGGAAGTTC 58.837 52.381 0.00 0.00 37.03 3.01
305 315 5.438761 AAATCATAATTTAGGCCTCGTGC 57.561 39.130 9.68 0.00 33.27 5.34
371 381 3.721087 AGTAGGTGAATTGGAGGGTTG 57.279 47.619 0.00 0.00 0.00 3.77
418 436 5.878116 TGCGCTAATGTAGTAGGTGATTTTT 59.122 36.000 9.73 0.00 0.00 1.94
419 437 5.424757 TGCGCTAATGTAGTAGGTGATTTT 58.575 37.500 9.73 0.00 0.00 1.82
420 438 5.018539 TGCGCTAATGTAGTAGGTGATTT 57.981 39.130 9.73 0.00 0.00 2.17
421 439 4.665833 TGCGCTAATGTAGTAGGTGATT 57.334 40.909 9.73 0.00 0.00 2.57
464 482 2.361438 TGAAATGTGTGCATTGTGAGCA 59.639 40.909 0.00 0.00 43.89 4.26
498 516 1.457346 GTCTCACCAGCTTTGATGGG 58.543 55.000 6.80 0.00 42.48 4.00
585 604 5.951747 TCAAAGCCATTAGTTAGCTTCCATT 59.048 36.000 0.00 0.00 45.77 3.16
586 605 5.509498 TCAAAGCCATTAGTTAGCTTCCAT 58.491 37.500 0.00 0.00 45.77 3.41
587 606 4.917385 TCAAAGCCATTAGTTAGCTTCCA 58.083 39.130 0.00 0.00 45.77 3.53
588 607 6.095440 TGAATCAAAGCCATTAGTTAGCTTCC 59.905 38.462 0.00 0.00 45.77 3.46
589 608 7.088589 TGAATCAAAGCCATTAGTTAGCTTC 57.911 36.000 0.00 0.00 45.77 3.86
607 626 2.237143 AGCGTGGAGAAGGATTGAATCA 59.763 45.455 7.56 0.00 0.00 2.57
642 661 5.358160 GTGCTTGCCTTGAATTTATAGGAGT 59.642 40.000 5.82 0.00 0.00 3.85
662 681 0.249238 TTGCGAATTTTTGGCGTGCT 60.249 45.000 0.00 0.00 37.17 4.40
682 701 4.490959 GGCGCGTCATTATCTATCATTTCG 60.491 45.833 5.47 0.00 0.00 3.46
685 704 3.262420 GGGCGCGTCATTATCTATCATT 58.738 45.455 14.93 0.00 0.00 2.57
705 724 1.434555 TATTTCGGAAGTGTGTGCGG 58.565 50.000 0.00 0.00 32.58 5.69
713 739 9.902196 AAAAACAATTCGTTATATTTCGGAAGT 57.098 25.926 0.00 0.00 36.59 3.01
749 775 3.501950 GACTCCATTTGGAAATCAACGC 58.498 45.455 0.18 0.00 44.91 4.84
754 780 2.024414 CGGGGACTCCATTTGGAAATC 58.976 52.381 0.18 1.88 44.91 2.17
774 800 0.895559 ACCAGCTTTAGGCCTTGTGC 60.896 55.000 12.58 13.18 43.05 4.57
818 856 5.393678 CCTGTAGTCCTGTCTAGAAGCTTTC 60.394 48.000 0.00 0.00 0.00 2.62
894 943 0.027063 CCGTGGTGTGAACGAACAAC 59.973 55.000 0.00 0.00 43.68 3.32
895 944 1.707239 GCCGTGGTGTGAACGAACAA 61.707 55.000 0.00 0.00 43.68 2.83
899 948 2.028484 GAGCCGTGGTGTGAACGA 59.972 61.111 0.00 0.00 43.68 3.85
1176 1258 0.248458 GAAAAGTGTGGCACCGTGTG 60.248 55.000 16.26 0.25 34.49 3.82
1213 1295 3.126453 AGATGTTGGGAGGAGGCTTATT 58.874 45.455 0.00 0.00 0.00 1.40
1218 1300 2.050144 TGATAGATGTTGGGAGGAGGC 58.950 52.381 0.00 0.00 0.00 4.70
1219 1301 3.041211 TGTGATAGATGTTGGGAGGAGG 58.959 50.000 0.00 0.00 0.00 4.30
1220 1302 3.452264 TGTGTGATAGATGTTGGGAGGAG 59.548 47.826 0.00 0.00 0.00 3.69
1221 1303 3.449918 TGTGTGATAGATGTTGGGAGGA 58.550 45.455 0.00 0.00 0.00 3.71
1222 1304 3.912496 TGTGTGATAGATGTTGGGAGG 57.088 47.619 0.00 0.00 0.00 4.30
1225 1307 7.999679 ACATATTTTGTGTGATAGATGTTGGG 58.000 34.615 0.00 0.00 37.11 4.12
1520 3423 1.652947 GGTAGGAGGAGACAAACCCA 58.347 55.000 0.00 0.00 0.00 4.51
1526 3429 3.845559 TCCGGGTAGGAGGAGACA 58.154 61.111 0.00 0.00 45.98 3.41
1601 3504 3.578282 TGTTGTAGAGGAAGTGCATGAGA 59.422 43.478 0.00 0.00 0.00 3.27
1768 3671 1.241315 CCGAAAGTTTGCCCGGATGT 61.241 55.000 0.73 0.00 44.29 3.06
1827 3731 5.510861 GGAGATTACTAAGCCCGAGCAAATA 60.511 44.000 0.00 0.00 43.56 1.40
1832 3736 1.336056 CGGAGATTACTAAGCCCGAGC 60.336 57.143 7.73 0.00 39.31 5.03
1836 3740 2.167900 ACACACGGAGATTACTAAGCCC 59.832 50.000 0.00 0.00 0.00 5.19
1840 3744 8.714179 CACAAATAAACACACGGAGATTACTAA 58.286 33.333 0.00 0.00 0.00 2.24
1872 3776 3.066064 CGTCCCGAATTCCATTGCAAATA 59.934 43.478 1.71 0.00 0.00 1.40
1890 3794 2.602878 TCACTCGCAGTATTTTCGTCC 58.397 47.619 0.00 0.00 0.00 4.79
1891 3795 6.345882 GGAATATCACTCGCAGTATTTTCGTC 60.346 42.308 0.00 0.00 0.00 4.20
1893 3797 5.462068 TGGAATATCACTCGCAGTATTTTCG 59.538 40.000 0.00 0.00 0.00 3.46
1894 3798 6.844696 TGGAATATCACTCGCAGTATTTTC 57.155 37.500 0.00 0.00 0.00 2.29
1970 3874 8.615211 TGATACTGTTATGATACTTACGTTCGT 58.385 33.333 0.00 2.91 0.00 3.85
2259 4217 8.411991 AAGATTAGTTTTATCCACCCGAAAAA 57.588 30.769 0.00 0.00 0.00 1.94
2260 4218 9.517868 TTAAGATTAGTTTTATCCACCCGAAAA 57.482 29.630 0.00 0.00 0.00 2.29
2261 4219 8.949177 GTTAAGATTAGTTTTATCCACCCGAAA 58.051 33.333 0.00 0.00 0.00 3.46
2262 4220 8.102047 TGTTAAGATTAGTTTTATCCACCCGAA 58.898 33.333 0.00 0.00 0.00 4.30
2263 4221 7.622713 TGTTAAGATTAGTTTTATCCACCCGA 58.377 34.615 0.00 0.00 0.00 5.14
2264 4222 7.852971 TGTTAAGATTAGTTTTATCCACCCG 57.147 36.000 0.00 0.00 0.00 5.28
2287 4245 9.897744 TTGCTTCATTTAGAGTCTAAACAAATG 57.102 29.630 24.22 19.42 37.74 2.32
2315 4273 1.412453 TTGTACACCGCTTGGGAGGT 61.412 55.000 0.00 0.00 46.39 3.85
2324 4282 2.613506 GCCCACACTTGTACACCGC 61.614 63.158 0.00 0.00 0.00 5.68
2365 4323 1.745264 CGATCAGGGAAGCCTCCTC 59.255 63.158 0.32 0.00 42.05 3.71
2366 4324 2.439104 GCGATCAGGGAAGCCTCCT 61.439 63.158 0.32 0.00 42.05 3.69
2367 4325 2.110006 GCGATCAGGGAAGCCTCC 59.890 66.667 0.00 0.00 41.59 4.30
2368 4326 2.110006 GGCGATCAGGGAAGCCTC 59.890 66.667 8.29 0.00 45.67 4.70
2371 4329 1.821332 CCTTGGCGATCAGGGAAGC 60.821 63.158 1.96 0.00 44.61 3.86
2372 4330 1.907739 TCCTTGGCGATCAGGGAAG 59.092 57.895 7.41 0.00 46.88 3.46
2373 4331 4.145436 TCCTTGGCGATCAGGGAA 57.855 55.556 7.41 0.00 46.88 3.97
2375 4333 2.037620 CTCCTCCTTGGCGATCAGGG 62.038 65.000 0.00 0.00 43.34 4.45
2376 4334 1.445095 CTCCTCCTTGGCGATCAGG 59.555 63.158 0.00 0.00 35.26 3.86
2377 4335 1.045350 TCCTCCTCCTTGGCGATCAG 61.045 60.000 0.00 0.00 35.26 2.90
2378 4336 0.399091 ATCCTCCTCCTTGGCGATCA 60.399 55.000 0.00 0.00 35.26 2.92
2379 4337 0.320050 GATCCTCCTCCTTGGCGATC 59.680 60.000 0.00 0.00 35.59 3.69
2380 4338 1.124477 GGATCCTCCTCCTTGGCGAT 61.124 60.000 3.84 0.00 32.53 4.58
2381 4339 1.762460 GGATCCTCCTCCTTGGCGA 60.762 63.158 3.84 0.00 32.53 5.54
2382 4340 2.812619 GGGATCCTCCTCCTTGGCG 61.813 68.421 12.58 0.00 36.57 5.69
2383 4341 1.385206 AGGGATCCTCCTCCTTGGC 60.385 63.158 12.58 0.00 36.57 4.52
2384 4342 0.327000 ACAGGGATCCTCCTCCTTGG 60.327 60.000 12.58 0.00 44.48 3.61
2385 4343 1.589414 AACAGGGATCCTCCTCCTTG 58.411 55.000 12.58 1.13 45.40 3.61
2386 4344 3.734344 ATAACAGGGATCCTCCTCCTT 57.266 47.619 12.58 0.00 36.57 3.36
2387 4345 3.734344 AATAACAGGGATCCTCCTCCT 57.266 47.619 12.58 0.00 36.57 3.69
2388 4346 4.226168 CCATAATAACAGGGATCCTCCTCC 59.774 50.000 12.58 0.00 36.57 4.30
2412 4370 0.389948 GGGCAGTGATCGAAACGTCT 60.390 55.000 0.00 0.00 0.00 4.18
2420 4380 1.811266 CGGTTGAGGGCAGTGATCG 60.811 63.158 0.00 0.00 0.00 3.69
2423 4383 1.691195 TTGACGGTTGAGGGCAGTGA 61.691 55.000 0.00 0.00 0.00 3.41
2425 4385 1.071471 CTTGACGGTTGAGGGCAGT 59.929 57.895 0.00 0.00 0.00 4.40
2428 4388 3.056328 GGCTTGACGGTTGAGGGC 61.056 66.667 0.00 0.00 0.00 5.19
2433 4393 3.564511 CACTATTTTGGCTTGACGGTTG 58.435 45.455 0.00 0.00 0.00 3.77
2434 4394 2.556622 CCACTATTTTGGCTTGACGGTT 59.443 45.455 0.00 0.00 0.00 4.44
2435 4395 2.159382 CCACTATTTTGGCTTGACGGT 58.841 47.619 0.00 0.00 0.00 4.83
2436 4396 2.919666 CCACTATTTTGGCTTGACGG 57.080 50.000 0.00 0.00 0.00 4.79
2444 4404 2.095263 CCAGTCAACGCCACTATTTTGG 60.095 50.000 0.00 0.00 39.98 3.28
2445 4405 2.095263 CCCAGTCAACGCCACTATTTTG 60.095 50.000 0.00 0.00 0.00 2.44
2446 4406 2.159382 CCCAGTCAACGCCACTATTTT 58.841 47.619 0.00 0.00 0.00 1.82
2447 4407 1.349688 TCCCAGTCAACGCCACTATTT 59.650 47.619 0.00 0.00 0.00 1.40
2448 4408 0.981183 TCCCAGTCAACGCCACTATT 59.019 50.000 0.00 0.00 0.00 1.73
2449 4409 0.249398 GTCCCAGTCAACGCCACTAT 59.751 55.000 0.00 0.00 0.00 2.12
2450 4410 1.669440 GTCCCAGTCAACGCCACTA 59.331 57.895 0.00 0.00 0.00 2.74
2451 4411 2.426023 GTCCCAGTCAACGCCACT 59.574 61.111 0.00 0.00 0.00 4.00
2452 4412 3.041940 CGTCCCAGTCAACGCCAC 61.042 66.667 0.00 0.00 31.48 5.01
2453 4413 3.542676 ACGTCCCAGTCAACGCCA 61.543 61.111 0.00 0.00 42.47 5.69
2454 4414 3.041940 CACGTCCCAGTCAACGCC 61.042 66.667 0.00 0.00 42.47 5.68
2455 4415 3.041940 CCACGTCCCAGTCAACGC 61.042 66.667 0.00 0.00 42.47 4.84
2456 4416 2.357034 CCCACGTCCCAGTCAACG 60.357 66.667 0.00 0.00 44.22 4.10
2457 4417 2.668550 GCCCACGTCCCAGTCAAC 60.669 66.667 0.00 0.00 0.00 3.18
2458 4418 4.308458 CGCCCACGTCCCAGTCAA 62.308 66.667 0.00 0.00 33.53 3.18
2469 4429 1.525077 TGACCAAACAGACGCCCAC 60.525 57.895 0.00 0.00 0.00 4.61
2470 4430 1.525077 GTGACCAAACAGACGCCCA 60.525 57.895 0.00 0.00 0.00 5.36
2471 4431 1.227853 AGTGACCAAACAGACGCCC 60.228 57.895 0.00 0.00 0.00 6.13
2472 4432 0.249911 AGAGTGACCAAACAGACGCC 60.250 55.000 0.00 0.00 0.00 5.68
2473 4433 1.261619 CAAGAGTGACCAAACAGACGC 59.738 52.381 0.00 0.00 0.00 5.19
2474 4434 2.821546 TCAAGAGTGACCAAACAGACG 58.178 47.619 0.00 0.00 0.00 4.18
2501 4461 2.837291 AAGCTGGGCGTGCCAAAA 60.837 55.556 13.76 0.00 37.98 2.44
2502 4462 3.604667 CAAGCTGGGCGTGCCAAA 61.605 61.111 13.76 0.00 37.98 3.28
2516 4476 3.818787 GAGTGCGGGCATGGCAAG 61.819 66.667 22.06 15.01 42.92 4.01
2520 4480 4.864334 GAGGGAGTGCGGGCATGG 62.864 72.222 0.00 0.00 0.00 3.66
2521 4481 4.864334 GGAGGGAGTGCGGGCATG 62.864 72.222 0.00 0.00 0.00 4.06
2523 4483 3.993865 TATGGAGGGAGTGCGGGCA 62.994 63.158 0.00 0.00 0.00 5.36
2539 4499 5.811613 CCAACAATTTGGCGTTGAATCATAT 59.188 36.000 7.71 0.00 46.09 1.78
2540 4500 5.167121 CCAACAATTTGGCGTTGAATCATA 58.833 37.500 7.71 0.00 46.09 2.15
2541 4501 3.995705 CCAACAATTTGGCGTTGAATCAT 59.004 39.130 7.71 0.00 46.09 2.45
2609 4569 1.366111 CGTTCGCCCCGTCAAATCAT 61.366 55.000 0.00 0.00 0.00 2.45
2610 4570 2.030401 CGTTCGCCCCGTCAAATCA 61.030 57.895 0.00 0.00 0.00 2.57
2623 4583 4.025401 GGTTGCTGCCCACGTTCG 62.025 66.667 0.00 0.00 0.00 3.95
2628 4588 0.249447 GTTCTTTGGTTGCTGCCCAC 60.249 55.000 0.00 0.00 0.00 4.61
2633 4593 2.286365 TAGGGGTTCTTTGGTTGCTG 57.714 50.000 0.00 0.00 0.00 4.41
2644 4604 2.588034 GGCGACGCATAGGGGTTC 60.588 66.667 23.09 0.00 40.72 3.62
2646 4606 3.849951 CTGGCGACGCATAGGGGT 61.850 66.667 23.09 0.00 43.72 4.95
2682 4642 2.201022 CCGGGTACTCATCGAGGGG 61.201 68.421 0.00 0.00 33.35 4.79


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

AutoCloner maintained by Alex Coulton.