Multiple sequence alignment - TraesCS4D01G354300

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 TraesCS4D01G354300 chr4D 100.000 5267 0 0 1 5267 504201945 504196679 0.000000e+00 9727.0
1 TraesCS4D01G354300 chr4D 82.563 476 59 17 2 454 504183030 504182556 1.060000e-106 398.0
2 TraesCS4D01G354300 chr4D 86.486 333 28 9 3959 4283 504187755 504187432 3.020000e-92 350.0
3 TraesCS4D01G354300 chr4D 82.410 307 15 15 4981 5267 504187299 504187012 1.140000e-56 231.0
4 TraesCS4D01G354300 chr4D 82.090 201 16 8 4274 4454 504187507 504187307 2.540000e-33 154.0
5 TraesCS4D01G354300 chr4D 92.647 68 2 1 4219 4283 504197669 504197602 1.560000e-15 95.3
6 TraesCS4D01G354300 chr4D 92.647 68 2 1 4277 4344 504197727 504197663 1.560000e-15 95.3
7 TraesCS4D01G354300 chr5A 88.943 2279 144 48 94 2289 688864016 688861763 0.000000e+00 2713.0
8 TraesCS4D01G354300 chr5A 88.527 1595 90 36 2300 3848 688861639 688860092 0.000000e+00 1845.0
9 TraesCS4D01G354300 chr5A 87.811 1165 67 44 3164 4279 688860764 688859626 0.000000e+00 1295.0
10 TraesCS4D01G354300 chr5A 81.381 478 61 17 2 454 688853970 688853496 1.080000e-96 364.0
11 TraesCS4D01G354300 chr5A 85.455 330 39 7 147 468 688864526 688864198 8.450000e-88 335.0
12 TraesCS4D01G354300 chr5A 84.281 299 25 11 4981 5257 688859157 688858859 6.720000e-69 272.0
13 TraesCS4D01G354300 chr5A 91.509 106 9 0 1 106 688865026 688864921 4.250000e-31 147.0
14 TraesCS4D01G354300 chr4B 89.652 2039 119 32 2300 4298 650743286 650741300 0.000000e+00 2512.0
15 TraesCS4D01G354300 chr4B 92.133 572 21 9 1079 1647 650744790 650744240 0.000000e+00 785.0
16 TraesCS4D01G354300 chr4B 94.856 486 20 4 1 482 650745878 650745394 0.000000e+00 754.0
17 TraesCS4D01G354300 chr4B 88.042 577 38 19 549 1102 650745390 650744822 0.000000e+00 654.0
18 TraesCS4D01G354300 chr4B 88.298 470 32 8 4803 5267 650741297 650740846 4.640000e-150 542.0
19 TraesCS4D01G354300 chr4B 84.259 432 36 16 3856 4287 650731031 650730632 4.940000e-105 392.0
20 TraesCS4D01G354300 chr4B 81.414 495 64 19 2 471 650711191 650710700 3.850000e-101 379.0
21 TraesCS4D01G354300 chr4B 88.737 293 17 10 2012 2291 650743669 650743380 1.400000e-90 344.0
22 TraesCS4D01G354300 chr4B 92.181 243 17 1 1764 2004 650744028 650743786 5.050000e-90 342.0
23 TraesCS4D01G354300 chr4B 80.252 476 75 11 3 465 650746264 650745795 1.820000e-89 340.0
24 TraesCS4D01G354300 chr4B 80.635 315 14 17 4981 5267 650730489 650730194 3.220000e-47 200.0
25 TraesCS4D01G354300 chr4B 90.278 72 3 2 4277 4347 650741378 650741310 2.020000e-14 91.6
26 TraesCS4D01G354300 chr3D 90.541 518 47 2 4465 4980 24569194 24569711 0.000000e+00 684.0
27 TraesCS4D01G354300 chr2A 89.981 519 50 2 4465 4981 537233577 537234095 0.000000e+00 669.0
28 TraesCS4D01G354300 chr2A 89.768 518 49 4 4465 4979 669747264 669746748 0.000000e+00 660.0
29 TraesCS4D01G354300 chr7B 89.695 524 51 3 4465 4985 380072798 380073321 0.000000e+00 665.0
30 TraesCS4D01G354300 chr7B 89.749 517 51 2 4465 4979 648274022 648273506 0.000000e+00 660.0
31 TraesCS4D01G354300 chr4A 89.903 515 51 1 4465 4978 575005575 575005061 0.000000e+00 662.0
32 TraesCS4D01G354300 chrUn 89.749 517 51 2 4465 4979 136394824 136395340 0.000000e+00 660.0
33 TraesCS4D01G354300 chr6A 89.749 517 51 2 4465 4979 591940820 591940304 0.000000e+00 660.0
34 TraesCS4D01G354300 chr3B 88.993 536 55 4 4465 4999 707027375 707026843 0.000000e+00 660.0


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 TraesCS4D01G354300 chr4D 504196679 504201945 5266 True 9727.000000 9727 100.000000 1 5267 1 chr4D.!!$R1 5266
1 TraesCS4D01G354300 chr4D 504182556 504187755 5199 True 283.250000 398 83.387250 2 5267 4 chr4D.!!$R2 5265
2 TraesCS4D01G354300 chr5A 688858859 688865026 6167 True 1101.166667 2713 87.754333 1 5257 6 chr5A.!!$R2 5256
3 TraesCS4D01G354300 chr4B 650740846 650746264 5418 True 707.177778 2512 89.381000 1 5267 9 chr4B.!!$R3 5266
4 TraesCS4D01G354300 chr4B 650730194 650731031 837 True 296.000000 392 82.447000 3856 5267 2 chr4B.!!$R2 1411
5 TraesCS4D01G354300 chr3D 24569194 24569711 517 False 684.000000 684 90.541000 4465 4980 1 chr3D.!!$F1 515
6 TraesCS4D01G354300 chr2A 537233577 537234095 518 False 669.000000 669 89.981000 4465 4981 1 chr2A.!!$F1 516
7 TraesCS4D01G354300 chr2A 669746748 669747264 516 True 660.000000 660 89.768000 4465 4979 1 chr2A.!!$R1 514
8 TraesCS4D01G354300 chr7B 380072798 380073321 523 False 665.000000 665 89.695000 4465 4985 1 chr7B.!!$F1 520
9 TraesCS4D01G354300 chr7B 648273506 648274022 516 True 660.000000 660 89.749000 4465 4979 1 chr7B.!!$R1 514
10 TraesCS4D01G354300 chr4A 575005061 575005575 514 True 662.000000 662 89.903000 4465 4978 1 chr4A.!!$R1 513
11 TraesCS4D01G354300 chrUn 136394824 136395340 516 False 660.000000 660 89.749000 4465 4979 1 chrUn.!!$F1 514
12 TraesCS4D01G354300 chr6A 591940304 591940820 516 True 660.000000 660 89.749000 4465 4979 1 chr6A.!!$R1 514
13 TraesCS4D01G354300 chr3B 707026843 707027375 532 True 660.000000 660 88.993000 4465 4999 1 chr3B.!!$R1 534

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
106 136 1.069568 TGCACAACGCCTTTCATAACG 60.070 47.619 0.00 0.00 41.33 3.18 F
523 1483 1.125021 CTCACTTAGCACGCTCAAACG 59.875 52.381 0.00 0.00 39.50 3.60 F
2232 3528 0.108898 CTGCACTTCTCACTCCGGAG 60.109 60.000 30.11 30.11 36.21 4.63 F
2291 3594 0.240678 TTGTGTTGGATCATGTGCGC 59.759 50.000 0.00 0.00 0.00 6.09 F
3547 5020 0.117140 TCTGTCCCTCCATGGTCTGT 59.883 55.000 12.58 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 3097 1.750778 GACAGAGAGAAGAGGAGCAGG 59.249 57.143 0.00 0.00 0.0 4.85 R
2366 3784 0.109412 AGAAATCGTCACGTCGTCCC 60.109 55.000 0.00 0.00 0.0 4.46 R
3137 4606 0.238289 CGCTGGTGTTGAACATGGTC 59.762 55.000 2.98 2.98 0.0 4.02 R
4115 5658 0.249911 CCCCTAGCGAGCACATAACC 60.250 60.000 0.00 0.00 0.0 2.85 R
4587 6507 0.249911 GAGACAAACCTCCACACGCT 60.250 55.000 0.00 0.00 0.0 5.07 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
37 38 8.214364 TCCCACACATATATTGTATTAACTGCA 58.786 33.333 0.00 0.00 36.57 4.41
78 79 9.220767 GTGAGACTTGAAACATTTATTAGAGGT 57.779 33.333 0.00 0.00 0.00 3.85
91 92 7.936496 TTTATTAGAGGTGATGATTTGCACA 57.064 32.000 0.00 0.00 36.76 4.57
106 136 1.069568 TGCACAACGCCTTTCATAACG 60.070 47.619 0.00 0.00 41.33 3.18
109 290 2.224549 CACAACGCCTTTCATAACGGAA 59.775 45.455 0.00 0.00 0.00 4.30
114 295 2.794631 CGCCTTTCATAACGGAAATGCC 60.795 50.000 9.29 0.00 42.04 4.40
134 315 1.134371 CGGAAGGAGGGAGTGATTTCC 60.134 57.143 0.00 0.00 36.46 3.13
157 541 7.704271 TCCACGTGTACAAATTTAAATCAACA 58.296 30.769 15.65 1.62 0.00 3.33
328 1286 5.297776 CCAAGCTCATTAATCACCAACTAGG 59.702 44.000 0.00 0.00 45.67 3.02
351 1309 4.250464 GACAATCACGATGTCCCTTAACA 58.750 43.478 0.00 0.00 41.02 2.41
385 1343 5.220662 CCACTCGTATGTTTCTTAATGCAGG 60.221 44.000 0.00 0.00 0.00 4.85
409 1367 6.584471 AAATAGGTTCCCACACATATACCA 57.416 37.500 0.00 0.00 0.00 3.25
478 1438 5.157940 AGGCGATGAGATACATAATGCTT 57.842 39.130 0.00 0.00 39.56 3.91
499 1459 1.269166 CGTGGAGTAGCGACAATCAC 58.731 55.000 0.00 3.85 0.00 3.06
523 1483 1.125021 CTCACTTAGCACGCTCAAACG 59.875 52.381 0.00 0.00 39.50 3.60
565 1525 4.311606 ACACGCATATAGTTTCACACACA 58.688 39.130 0.00 0.00 0.00 3.72
593 1553 3.122948 CGTATTAACTGCGCTTGTGAACT 59.877 43.478 9.73 1.18 0.00 3.01
605 1565 4.436852 CGCTTGTGAACTGTGTGTAAAACT 60.437 41.667 0.00 0.00 0.00 2.66
645 1605 2.908015 GGGATGCACTCCGCCTTA 59.092 61.111 0.00 0.00 46.01 2.69
751 1727 8.839343 TCATGCAAGGTGAGTAAATAATATGTG 58.161 33.333 0.00 0.00 0.00 3.21
846 1830 7.916914 ATGCGGGTTACAATATTTATCTACC 57.083 36.000 0.00 0.00 0.00 3.18
909 1894 8.142994 TCATAAAATCCGACTAAAGATTCTGC 57.857 34.615 0.00 0.00 31.54 4.26
1027 2022 9.349713 ACACAACAAATCCAGAGAAGTAAATAA 57.650 29.630 0.00 0.00 0.00 1.40
1028 2023 9.612620 CACAACAAATCCAGAGAAGTAAATAAC 57.387 33.333 0.00 0.00 0.00 1.89
1029 2024 9.574516 ACAACAAATCCAGAGAAGTAAATAACT 57.425 29.630 0.00 0.00 41.49 2.24
1239 2291 2.630580 GCCTGCTGCTCTACTTATACCT 59.369 50.000 0.00 0.00 36.87 3.08
1277 2329 1.452953 TAGCTAGGACCATGTCGGCG 61.453 60.000 0.00 0.00 39.03 6.46
1926 3079 2.052690 ATCCAGGTCCGTCCGTCAG 61.053 63.158 0.00 0.00 41.99 3.51
1930 3083 4.477975 GGTCCGTCCGTCAGCTCG 62.478 72.222 0.00 0.00 0.00 5.03
1944 3097 2.203126 CTCGAAGCCCAGCATCCC 60.203 66.667 0.00 0.00 0.00 3.85
1963 3116 1.619432 CCCTGCTCCTCTTCTCTCTGT 60.619 57.143 0.00 0.00 0.00 3.41
1971 3124 2.027653 CCTCTTCTCTCTGTCCCCAAAC 60.028 54.545 0.00 0.00 0.00 2.93
1981 3134 4.394729 TCTGTCCCCAAACAGTACAAATC 58.605 43.478 0.00 0.00 45.57 2.17
2047 3317 2.887152 GTCAGAAACAGGAGTGGCATTT 59.113 45.455 0.00 0.00 0.00 2.32
2063 3333 5.803967 GTGGCATTTTTCTAATCTTGCTGAG 59.196 40.000 0.00 0.00 0.00 3.35
2064 3334 5.711506 TGGCATTTTTCTAATCTTGCTGAGA 59.288 36.000 0.00 0.00 39.13 3.27
2142 3424 1.505353 GTCCTCTGCACATTGCTGC 59.495 57.895 0.00 0.00 45.31 5.25
2174 3469 4.446719 GCTGAAAAGTTTGCATCTTTCTGG 59.553 41.667 14.71 10.07 34.59 3.86
2201 3497 2.039879 ACCCCACCTGTACTTGATTCAC 59.960 50.000 0.00 0.00 0.00 3.18
2228 3524 0.952984 GTGCCTGCACTTCTCACTCC 60.953 60.000 14.77 0.00 43.12 3.85
2232 3528 0.108898 CTGCACTTCTCACTCCGGAG 60.109 60.000 30.11 30.11 36.21 4.63
2257 3559 4.715896 CATGAGTGGAAGTTGAACATTCG 58.284 43.478 0.00 0.00 0.00 3.34
2260 3562 2.290641 AGTGGAAGTTGAACATTCGCAC 59.709 45.455 0.00 8.76 31.93 5.34
2262 3564 2.548057 TGGAAGTTGAACATTCGCACTC 59.452 45.455 0.00 0.00 0.00 3.51
2266 3568 0.874390 TTGAACATTCGCACTCTGCC 59.126 50.000 0.00 0.00 41.12 4.85
2291 3594 0.240678 TTGTGTTGGATCATGTGCGC 59.759 50.000 0.00 0.00 0.00 6.09
2292 3595 0.606130 TGTGTTGGATCATGTGCGCT 60.606 50.000 9.73 0.00 0.00 5.92
2293 3596 1.338579 TGTGTTGGATCATGTGCGCTA 60.339 47.619 9.73 0.00 0.00 4.26
2295 3598 2.161410 GTGTTGGATCATGTGCGCTAAA 59.839 45.455 9.73 0.00 0.00 1.85
2296 3599 2.816672 TGTTGGATCATGTGCGCTAAAA 59.183 40.909 9.73 0.00 0.00 1.52
2297 3600 3.119884 TGTTGGATCATGTGCGCTAAAAG 60.120 43.478 9.73 0.00 0.00 2.27
2298 3601 2.984562 TGGATCATGTGCGCTAAAAGA 58.015 42.857 9.73 0.27 0.00 2.52
2352 3770 1.679944 CGAGGCAGAATCATTGGTGGT 60.680 52.381 0.00 0.00 0.00 4.16
2366 3784 4.077184 TGGTGGAAGGCCTACGCG 62.077 66.667 5.16 3.53 35.02 6.01
2391 3809 0.241749 ACGTGACGATTTCTACGGCA 59.758 50.000 13.70 0.00 46.66 5.69
2423 3844 2.478031 CGGGACAGATTACACAGAGTCG 60.478 54.545 0.00 0.00 0.00 4.18
2429 3850 2.755655 AGATTACACAGAGTCGTCCTGG 59.244 50.000 0.00 0.00 36.03 4.45
2430 3851 2.281539 TTACACAGAGTCGTCCTGGA 57.718 50.000 0.00 0.00 36.03 3.86
2489 3925 1.615116 CCTGGAGAATGCTTCTGCCAA 60.615 52.381 12.43 0.00 46.27 4.52
2534 3973 1.078918 CAGCACAAGATCAGCCCGA 60.079 57.895 0.00 0.00 0.00 5.14
2550 3989 0.582960 CCGACAACGTACCAAACACC 59.417 55.000 0.00 0.00 37.88 4.16
2563 4002 1.068748 CAAACACCAGTGATGCTCTGC 60.069 52.381 4.48 0.00 0.00 4.26
2566 4005 1.025113 CACCAGTGATGCTCTGCAGG 61.025 60.000 15.13 5.82 43.65 4.85
2585 4024 1.453762 GATGGCCAGCTTGATCAGGC 61.454 60.000 21.39 21.39 46.28 4.85
2760 4202 2.764128 ACATCGGGATCGGGTGCT 60.764 61.111 0.00 0.00 36.95 4.40
2811 4268 5.057843 AGGAGTGGCATGTCATTGATAAT 57.942 39.130 1.89 0.00 0.00 1.28
3006 4472 6.591261 CATCATCGTGCTTGATAAAGATCAG 58.409 40.000 0.00 0.00 43.03 2.90
3007 4473 5.052481 TCATCGTGCTTGATAAAGATCAGG 58.948 41.667 0.00 0.00 43.03 3.86
3025 4494 5.125100 TCAGGTGATCATCTTTGTTTTGC 57.875 39.130 5.51 0.00 0.00 3.68
3085 4554 3.363844 GAGCCTGGACCAGCTCGTC 62.364 68.421 22.14 2.41 30.17 4.20
3094 4563 0.680280 ACCAGCTCGTCCACTCGTAT 60.680 55.000 0.00 0.00 0.00 3.06
3137 4606 0.397941 TCCAGCTCCACTCAACCAAG 59.602 55.000 0.00 0.00 0.00 3.61
3145 4614 2.174639 TCCACTCAACCAAGACCATGTT 59.825 45.455 0.00 0.00 0.00 2.71
3148 4617 3.631686 CACTCAACCAAGACCATGTTCAA 59.368 43.478 0.00 0.00 0.00 2.69
3154 4623 2.294233 CCAAGACCATGTTCAACACCAG 59.706 50.000 0.00 0.00 0.00 4.00
3162 4631 1.375396 TTCAACACCAGCGGATCGG 60.375 57.895 1.50 0.00 0.00 4.18
3264 4733 2.649034 GCCTCGTCGTGACTGGAA 59.351 61.111 11.40 0.00 0.00 3.53
3274 4743 2.430367 GACTGGAACCGGCAACCT 59.570 61.111 0.00 0.00 0.00 3.50
3306 4775 3.249091 CAGATGAACTTGTGAGTCTCCG 58.751 50.000 0.00 0.00 34.21 4.63
3311 4780 0.827925 ACTTGTGAGTCTCCGCTCCA 60.828 55.000 0.00 0.00 34.74 3.86
3547 5020 0.117140 TCTGTCCCTCCATGGTCTGT 59.883 55.000 12.58 0.00 0.00 3.41
3548 5021 0.539051 CTGTCCCTCCATGGTCTGTC 59.461 60.000 12.58 2.06 0.00 3.51
3549 5022 0.178906 TGTCCCTCCATGGTCTGTCA 60.179 55.000 12.58 4.73 0.00 3.58
3550 5023 0.539051 GTCCCTCCATGGTCTGTCAG 59.461 60.000 12.58 0.00 0.00 3.51
3551 5024 0.413434 TCCCTCCATGGTCTGTCAGA 59.587 55.000 12.58 0.00 0.00 3.27
3594 5072 4.655186 CCTCTTCTTCTTCCTCATCCATCT 59.345 45.833 0.00 0.00 0.00 2.90
3595 5073 5.221501 CCTCTTCTTCTTCCTCATCCATCTC 60.222 48.000 0.00 0.00 0.00 2.75
3596 5074 4.653341 TCTTCTTCTTCCTCATCCATCTCC 59.347 45.833 0.00 0.00 0.00 3.71
3597 5075 4.277788 TCTTCTTCCTCATCCATCTCCT 57.722 45.455 0.00 0.00 0.00 3.69
3598 5076 5.409590 TCTTCTTCCTCATCCATCTCCTA 57.590 43.478 0.00 0.00 0.00 2.94
3803 5288 2.488545 TCGCTTCTCTACAGGTCTGTTC 59.511 50.000 9.02 0.00 41.83 3.18
3814 5299 1.001406 AGGTCTGTTCTTCTGCTTCCG 59.999 52.381 0.00 0.00 0.00 4.30
3829 5314 2.426522 CTTCCGTTTGCCATCTCTCAA 58.573 47.619 0.00 0.00 0.00 3.02
4051 5566 7.751768 ATAGAACAGAAGGAAAACAAGGAAG 57.248 36.000 0.00 0.00 0.00 3.46
4104 5629 5.360591 AGTGTTTTAGTCTGACTGGAACTG 58.639 41.667 25.02 0.00 30.64 3.16
4113 5656 2.104792 CTGACTGGAACTGGAAGGACAA 59.895 50.000 0.00 0.00 39.30 3.18
4115 5658 1.421646 ACTGGAACTGGAAGGACAAGG 59.578 52.381 0.00 0.00 39.30 3.61
4119 5662 2.374170 GGAACTGGAAGGACAAGGGTTA 59.626 50.000 0.00 0.00 39.30 2.85
4357 5923 7.224297 TCTAGAAACTTTAGTTCTGCCATGTT 58.776 34.615 0.00 0.00 37.25 2.71
4358 5924 6.319141 AGAAACTTTAGTTCTGCCATGTTC 57.681 37.500 0.00 0.00 37.25 3.18
4386 5954 7.453393 TGTCTCTTGGAATGTTAATTCAGTCT 58.547 34.615 1.28 0.00 43.51 3.24
4388 5956 7.604164 GTCTCTTGGAATGTTAATTCAGTCTCA 59.396 37.037 1.28 0.00 43.51 3.27
4415 6022 0.109532 TGAACGATGGGGTTGAAGCA 59.890 50.000 0.00 0.00 0.00 3.91
4424 6031 1.410083 GGGGTTGAAGCATATGCCTCA 60.410 52.381 22.32 22.32 43.38 3.86
4438 6357 1.227380 CCTCATAGCAGGGACGTGC 60.227 63.158 8.80 8.80 44.35 5.34
4462 6381 6.399669 GCGTGTGCGTTATATATAAGAACCAG 60.400 42.308 5.39 4.04 40.81 4.00
4463 6382 6.859508 CGTGTGCGTTATATATAAGAACCAGA 59.140 38.462 5.39 0.00 0.00 3.86
4531 6450 0.740868 CGGCGGCTTCTTGAAGATGA 60.741 55.000 13.87 0.00 0.00 2.92
4546 6465 5.994250 TGAAGATGAAATAAGGTCCTCCTG 58.006 41.667 0.00 0.00 44.35 3.86
4558 6478 2.494530 CCTCCTGTCTAGCTCCCGC 61.495 68.421 0.00 0.00 0.00 6.13
4584 6504 1.128507 TGATGTTTCAAGCATCGTCGC 59.871 47.619 9.43 0.00 44.02 5.19
4587 6507 1.332065 TGTTTCAAGCATCGTCGCAAA 59.668 42.857 1.90 0.00 0.00 3.68
4645 6565 1.662446 GGTCGGCGTTTGTCTTCGA 60.662 57.895 6.85 0.00 0.00 3.71
4670 6590 0.036765 CCGACTGGATCCGGTTTTCA 60.037 55.000 27.11 0.00 40.78 2.69
4684 6604 4.406069 CGGTTTTCATTCGTCTACGTCTA 58.594 43.478 0.00 0.00 40.80 2.59
4710 6630 0.690192 TGCAGGTTGGATCCTTTCGA 59.310 50.000 14.23 0.00 35.37 3.71
4715 6635 4.372656 CAGGTTGGATCCTTTCGATCTAC 58.627 47.826 14.23 0.00 45.90 2.59
4732 6652 0.815095 TACGCTTCTCTTCATCGGCA 59.185 50.000 0.00 0.00 0.00 5.69
4784 6704 0.669625 GGCCTTAGCACGACGACTTT 60.670 55.000 0.00 0.00 42.56 2.66
4789 6709 0.806868 TAGCACGACGACTTTCCGAT 59.193 50.000 0.00 0.00 0.00 4.18
4820 6740 0.893727 ACAATGTTTGCCCGACTCCC 60.894 55.000 0.00 0.00 0.00 4.30
4821 6741 1.304134 AATGTTTGCCCGACTCCCC 60.304 57.895 0.00 0.00 0.00 4.81
4840 6760 2.764128 GAGGGAGGGGCGATGACA 60.764 66.667 0.00 0.00 0.00 3.58
4848 6768 2.183300 GGCGATGACAGTGGCGTA 59.817 61.111 0.00 0.00 0.00 4.42
4865 6785 1.980232 TACCTTCGGCTCGCTCCAA 60.980 57.895 0.00 0.00 0.00 3.53
4871 6791 2.817423 CGGCTCGCTCCAATGCTTC 61.817 63.158 0.00 0.00 0.00 3.86
4873 6793 1.028868 GGCTCGCTCCAATGCTTCTT 61.029 55.000 0.00 0.00 0.00 2.52
4912 6832 7.541122 GTCTACAGACCTGGATGTAAATTTC 57.459 40.000 0.00 0.00 39.07 2.17
4919 6839 6.656693 AGACCTGGATGTAAATTTCACTTCTG 59.343 38.462 0.00 0.00 0.00 3.02
4955 6875 2.029649 ACCTTGACAATTGATGCACAGC 60.030 45.455 13.59 0.00 0.00 4.40
5074 7018 9.609346 GTATGGGTTGAGTTACATTATAACACT 57.391 33.333 0.00 0.00 0.00 3.55
5144 7091 1.686052 TCCAAGCAATTGGTGGACAAC 59.314 47.619 13.73 0.00 42.94 3.32
5186 7161 5.370679 AGCTCATTCCAAAGCAAAACAATT 58.629 33.333 0.00 0.00 41.06 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 1.069432 TCACTAACAGTCGACGAGTGC 60.069 52.381 28.20 4.23 37.91 4.40
37 38 2.479656 GTCTCACTAACAGTCGACGAGT 59.520 50.000 10.46 10.39 0.00 4.18
91 92 4.091453 CATTTCCGTTATGAAAGGCGTT 57.909 40.909 0.00 0.00 37.63 4.84
106 136 1.453928 CCCTCCTTCCGGCATTTCC 60.454 63.158 0.00 0.00 0.00 3.13
109 290 1.616628 ACTCCCTCCTTCCGGCATT 60.617 57.895 0.00 0.00 0.00 3.56
114 295 1.134371 GGAAATCACTCCCTCCTTCCG 60.134 57.143 0.00 0.00 0.00 4.30
115 296 1.916181 TGGAAATCACTCCCTCCTTCC 59.084 52.381 0.00 0.00 34.22 3.46
119 300 0.613777 ACGTGGAAATCACTCCCTCC 59.386 55.000 0.00 0.00 43.94 4.30
120 301 1.002087 ACACGTGGAAATCACTCCCTC 59.998 52.381 21.57 0.00 43.94 4.30
122 303 2.289195 TGTACACGTGGAAATCACTCCC 60.289 50.000 21.57 0.00 43.94 4.30
123 304 3.034721 TGTACACGTGGAAATCACTCC 57.965 47.619 21.57 0.00 43.94 3.85
126 307 8.563289 TTTAAATTTGTACACGTGGAAATCAC 57.437 30.769 21.57 7.95 42.74 3.06
128 309 9.400638 TGATTTAAATTTGTACACGTGGAAATC 57.599 29.630 21.57 14.50 32.69 2.17
131 312 8.188799 TGTTGATTTAAATTTGTACACGTGGAA 58.811 29.630 21.57 9.26 0.00 3.53
134 315 7.995998 GCTTGTTGATTTAAATTTGTACACGTG 59.004 33.333 15.48 15.48 0.00 4.49
351 1309 2.838202 ACATACGAGTGGGTTTGAGGAT 59.162 45.455 0.00 0.00 0.00 3.24
409 1367 8.988934 CACTAACGGTTCACAGCATATTAATAT 58.011 33.333 1.91 1.91 0.00 1.28
473 1433 1.811266 CGCTACTCCACGCAAGCAT 60.811 57.895 0.00 0.00 45.62 3.79
478 1438 0.457853 GATTGTCGCTACTCCACGCA 60.458 55.000 0.00 0.00 0.00 5.24
499 1459 1.202188 TGAGCGTGCTAAGTGAGATCG 60.202 52.381 0.00 0.00 0.00 3.69
523 1483 1.043673 AGGGAGATACACACGAGGGC 61.044 60.000 0.00 0.00 0.00 5.19
547 1507 9.140286 ACGATATATGTGTGTGAAACTATATGC 57.860 33.333 0.00 0.00 38.04 3.14
565 1525 7.088272 TCACAAGCGCAGTTAATACGATATAT 58.912 34.615 11.47 0.00 0.00 0.86
605 1565 7.070696 TCCCGTCTCCTCTGATAAATATTTTCA 59.929 37.037 5.91 8.94 0.00 2.69
627 1587 3.088941 TAAGGCGGAGTGCATCCCG 62.089 63.158 20.92 20.92 46.50 5.14
645 1605 2.753452 CCTACCGGTATCATCGCTATGT 59.247 50.000 16.25 0.00 34.50 2.29
654 1627 3.657398 TGTTCTCTCCTACCGGTATCA 57.343 47.619 16.25 3.49 0.00 2.15
846 1830 5.676744 CGTTTTTATGACCGTGCATCTAATG 59.323 40.000 0.00 0.00 0.00 1.90
906 1890 9.035607 GGGTAATTATAATATGAGTCATCGCAG 57.964 37.037 9.42 0.00 0.00 5.18
1027 2022 7.546667 CCATTGTTTTGCTGCTGATATTTTAGT 59.453 33.333 0.00 0.00 0.00 2.24
1028 2023 7.546667 ACCATTGTTTTGCTGCTGATATTTTAG 59.453 33.333 0.00 0.00 0.00 1.85
1029 2024 7.331440 CACCATTGTTTTGCTGCTGATATTTTA 59.669 33.333 0.00 0.00 0.00 1.52
1030 2025 6.148150 CACCATTGTTTTGCTGCTGATATTTT 59.852 34.615 0.00 0.00 0.00 1.82
1031 2026 5.640357 CACCATTGTTTTGCTGCTGATATTT 59.360 36.000 0.00 0.00 0.00 1.40
1032 2027 5.047164 TCACCATTGTTTTGCTGCTGATATT 60.047 36.000 0.00 0.00 0.00 1.28
1033 2028 4.463539 TCACCATTGTTTTGCTGCTGATAT 59.536 37.500 0.00 0.00 0.00 1.63
1034 2029 3.825585 TCACCATTGTTTTGCTGCTGATA 59.174 39.130 0.00 0.00 0.00 2.15
1035 2030 2.629137 TCACCATTGTTTTGCTGCTGAT 59.371 40.909 0.00 0.00 0.00 2.90
1059 2054 3.702048 GTGGTGTGGCCCTAGCGA 61.702 66.667 0.00 0.00 41.24 4.93
1277 2329 3.453070 GAGGTCCTCCATGGCGCTC 62.453 68.421 6.96 0.00 35.89 5.03
1367 2422 3.032609 GCGATGATCCTGGACGCG 61.033 66.667 12.66 3.53 39.90 6.01
1543 2598 4.400776 CGTCGTCGTCGTCGTCGT 62.401 66.667 18.87 0.00 45.27 4.34
1544 2599 4.108437 TCGTCGTCGTCGTCGTCG 62.108 66.667 20.39 20.39 45.27 5.12
1545 2600 2.566765 GTCGTCGTCGTCGTCGTC 60.567 66.667 18.44 11.28 45.27 4.20
1546 2601 4.400776 CGTCGTCGTCGTCGTCGT 62.401 66.667 18.87 0.00 45.27 4.34
1880 3033 2.525629 TGGGCGAAGGAGGACACA 60.526 61.111 0.00 0.00 0.00 3.72
1926 3079 2.899339 GGATGCTGGGCTTCGAGC 60.899 66.667 0.00 0.00 41.46 5.03
1930 3083 2.123982 CAGGGGATGCTGGGCTTC 60.124 66.667 0.00 0.00 32.92 3.86
1944 3097 1.750778 GACAGAGAGAAGAGGAGCAGG 59.249 57.143 0.00 0.00 0.00 4.85
1963 3116 4.830600 GGAAAGATTTGTACTGTTTGGGGA 59.169 41.667 0.00 0.00 0.00 4.81
1999 3152 2.320805 TCGTCGACCAAACGAAGTAG 57.679 50.000 10.58 0.00 45.00 2.57
2047 3317 9.388506 CCTAGAAATTCTCAGCAAGATTAGAAA 57.611 33.333 0.00 0.00 32.82 2.52
2142 3424 3.732721 GCAAACTTTTCAGCTGCTACAAG 59.267 43.478 9.47 10.23 31.94 3.16
2174 3469 0.178973 AGTACAGGTGGGGTTTTGGC 60.179 55.000 0.00 0.00 0.00 4.52
2201 3497 2.793946 GTGCAGGCACAATAGGCG 59.206 61.111 18.84 0.00 45.53 5.52
2257 3559 2.256461 CAAAAGGCGGCAGAGTGC 59.744 61.111 13.08 0.00 44.08 4.40
2260 3562 0.318107 CAACACAAAAGGCGGCAGAG 60.318 55.000 13.08 0.00 0.00 3.35
2262 3564 1.300080 CCAACACAAAAGGCGGCAG 60.300 57.895 13.08 0.00 0.00 4.85
2266 3568 2.030007 ACATGATCCAACACAAAAGGCG 60.030 45.455 0.00 0.00 0.00 5.52
2296 3599 9.865321 CTGGAAACAATAACAATCAATCATTCT 57.135 29.630 0.00 0.00 42.06 2.40
2297 3600 9.643693 ACTGGAAACAATAACAATCAATCATTC 57.356 29.630 0.00 0.00 42.06 2.67
2298 3601 9.643693 GACTGGAAACAATAACAATCAATCATT 57.356 29.630 0.00 0.00 42.06 2.57
2366 3784 0.109412 AGAAATCGTCACGTCGTCCC 60.109 55.000 0.00 0.00 0.00 4.46
2377 3795 1.518572 CGGCTGCCGTAGAAATCGT 60.519 57.895 31.72 0.00 42.73 3.73
2403 3824 2.492484 ACGACTCTGTGTAATCTGTCCC 59.508 50.000 0.00 0.00 0.00 4.46
2423 3844 1.198713 TTCTGCTCCAGATCCAGGAC 58.801 55.000 0.00 0.47 40.39 3.85
2429 3850 3.376546 GGTGATGTTTTCTGCTCCAGATC 59.623 47.826 0.00 0.00 40.39 2.75
2430 3851 3.245016 TGGTGATGTTTTCTGCTCCAGAT 60.245 43.478 0.00 0.00 40.39 2.90
2489 3925 1.069823 GCGTCTGGATGATCTCATGGT 59.930 52.381 0.00 0.00 36.57 3.55
2534 3973 2.011222 CACTGGTGTTTGGTACGTTGT 58.989 47.619 0.00 0.00 0.00 3.32
2550 3989 1.300481 CATCCTGCAGAGCATCACTG 58.700 55.000 17.39 0.00 38.13 3.66
2563 4002 0.106868 TGATCAAGCTGGCCATCCTG 60.107 55.000 5.51 1.25 0.00 3.86
2566 4005 1.453762 GCCTGATCAAGCTGGCCATC 61.454 60.000 5.51 0.31 44.36 3.51
2585 4024 0.796312 GTACCCGTGCATGTCTTGTG 59.204 55.000 4.96 0.00 0.00 3.33
2760 4202 1.267574 CCTCTGCTTCCTGGCCACTA 61.268 60.000 0.00 0.00 0.00 2.74
2811 4268 3.620061 CTGTGCTTCAGCTTCTGGA 57.380 52.632 0.00 0.00 42.66 3.86
2966 4432 9.986833 GCACGATGATGCAACAATTTATATATA 57.013 29.630 0.00 0.00 45.39 0.86
2967 4433 8.900511 GCACGATGATGCAACAATTTATATAT 57.099 30.769 0.00 0.00 45.39 0.86
3006 4472 4.240096 CCTGCAAAACAAAGATGATCACC 58.760 43.478 0.00 0.00 0.00 4.02
3007 4473 3.676646 GCCTGCAAAACAAAGATGATCAC 59.323 43.478 0.00 0.00 0.00 3.06
3085 4554 0.249238 GCCTCTGAGCATACGAGTGG 60.249 60.000 0.00 0.00 0.00 4.00
3121 4590 0.398318 GGTCTTGGTTGAGTGGAGCT 59.602 55.000 0.00 0.00 0.00 4.09
3137 4606 0.238289 CGCTGGTGTTGAACATGGTC 59.762 55.000 2.98 2.98 0.00 4.02
3145 4614 2.264480 CCGATCCGCTGGTGTTGA 59.736 61.111 0.00 0.00 0.00 3.18
3154 4623 1.300233 GTCTGATCCACCGATCCGC 60.300 63.158 0.00 0.00 43.82 5.54
3162 4631 4.530857 CGGCCCGGTCTGATCCAC 62.531 72.222 0.00 0.00 0.00 4.02
3274 4743 3.189376 TTCATCTGGGCGGTGCACA 62.189 57.895 20.43 0.00 40.85 4.57
3306 4775 1.625818 TCCTGAAGAAAGAGGTGGAGC 59.374 52.381 0.00 0.00 0.00 4.70
3311 4780 5.284582 AGATGGTATCCTGAAGAAAGAGGT 58.715 41.667 0.00 0.00 0.00 3.85
3547 5020 6.838090 GGGGAGAGTGATATGATATGATCTGA 59.162 42.308 0.00 0.00 0.00 3.27
3548 5021 6.840181 AGGGGAGAGTGATATGATATGATCTG 59.160 42.308 0.00 0.00 0.00 2.90
3549 5022 6.995757 AGGGGAGAGTGATATGATATGATCT 58.004 40.000 0.00 0.00 0.00 2.75
3550 5023 7.068702 AGAGGGGAGAGTGATATGATATGATC 58.931 42.308 0.00 0.00 0.00 2.92
3551 5024 6.995757 AGAGGGGAGAGTGATATGATATGAT 58.004 40.000 0.00 0.00 0.00 2.45
3803 5288 0.883833 ATGGCAAACGGAAGCAGAAG 59.116 50.000 0.00 0.00 0.00 2.85
3814 5299 8.897752 AGATAATTAAGTTGAGAGATGGCAAAC 58.102 33.333 0.00 0.00 0.00 2.93
3829 5314 7.606073 TGTGTATGTGTGTGCAGATAATTAAGT 59.394 33.333 0.00 0.00 33.46 2.24
3888 5403 0.962356 GTGCCCACACCTGAGAATGG 60.962 60.000 0.00 0.00 41.21 3.16
4045 5560 2.620585 GACAGCTTCTGTTTGCTTCCTT 59.379 45.455 0.66 0.00 45.44 3.36
4046 5561 2.158696 AGACAGCTTCTGTTTGCTTCCT 60.159 45.455 0.66 0.00 45.44 3.36
4047 5562 2.225467 AGACAGCTTCTGTTTGCTTCC 58.775 47.619 0.66 0.00 45.44 3.46
4048 5563 4.061596 AGTAGACAGCTTCTGTTTGCTTC 58.938 43.478 0.66 0.00 45.44 3.86
4051 5566 4.810790 TCTAGTAGACAGCTTCTGTTTGC 58.189 43.478 0.00 0.00 45.44 3.68
4104 5629 2.092323 GCACATAACCCTTGTCCTTCC 58.908 52.381 0.00 0.00 0.00 3.46
4113 5656 0.753262 CCTAGCGAGCACATAACCCT 59.247 55.000 0.00 0.00 0.00 4.34
4115 5658 0.249911 CCCCTAGCGAGCACATAACC 60.250 60.000 0.00 0.00 0.00 2.85
4119 5662 0.328258 AAAACCCCTAGCGAGCACAT 59.672 50.000 0.00 0.00 0.00 3.21
4326 5892 9.654663 GGCAGAACTAAAGTTTCTAGAGAATAA 57.345 33.333 0.00 0.00 38.56 1.40
4327 5893 8.812972 TGGCAGAACTAAAGTTTCTAGAGAATA 58.187 33.333 0.00 0.00 38.56 1.75
4328 5894 7.680730 TGGCAGAACTAAAGTTTCTAGAGAAT 58.319 34.615 0.00 0.00 38.56 2.40
4329 5895 7.062749 TGGCAGAACTAAAGTTTCTAGAGAA 57.937 36.000 0.00 0.00 38.56 2.87
4330 5896 6.665992 TGGCAGAACTAAAGTTTCTAGAGA 57.334 37.500 0.00 0.00 38.56 3.10
4331 5897 6.876257 ACATGGCAGAACTAAAGTTTCTAGAG 59.124 38.462 0.00 0.00 38.56 2.43
4332 5898 6.769512 ACATGGCAGAACTAAAGTTTCTAGA 58.230 36.000 0.00 0.00 38.56 2.43
4333 5899 7.389053 AGAACATGGCAGAACTAAAGTTTCTAG 59.611 37.037 0.00 0.00 38.56 2.43
4334 5900 7.224297 AGAACATGGCAGAACTAAAGTTTCTA 58.776 34.615 0.00 0.00 38.56 2.10
4335 5901 6.064717 AGAACATGGCAGAACTAAAGTTTCT 58.935 36.000 0.00 0.00 38.56 2.52
4336 5902 6.319141 AGAACATGGCAGAACTAAAGTTTC 57.681 37.500 0.00 0.00 38.56 2.78
4337 5903 6.715347 AAGAACATGGCAGAACTAAAGTTT 57.285 33.333 0.00 0.00 38.56 2.66
4338 5904 6.096846 ACAAAGAACATGGCAGAACTAAAGTT 59.903 34.615 0.00 0.00 41.64 2.66
4339 5905 5.594317 ACAAAGAACATGGCAGAACTAAAGT 59.406 36.000 0.00 0.00 0.00 2.66
4340 5906 6.016777 AGACAAAGAACATGGCAGAACTAAAG 60.017 38.462 0.00 0.00 0.00 1.85
4341 5907 5.827797 AGACAAAGAACATGGCAGAACTAAA 59.172 36.000 0.00 0.00 0.00 1.85
4342 5908 5.376625 AGACAAAGAACATGGCAGAACTAA 58.623 37.500 0.00 0.00 0.00 2.24
4343 5909 4.973168 AGACAAAGAACATGGCAGAACTA 58.027 39.130 0.00 0.00 0.00 2.24
4357 5923 8.690203 TGAATTAACATTCCAAGAGACAAAGA 57.310 30.769 0.00 0.00 38.50 2.52
4358 5924 8.571336 ACTGAATTAACATTCCAAGAGACAAAG 58.429 33.333 0.00 0.00 38.50 2.77
4386 5954 2.080693 CCCATCGTTCAACCGAAATGA 58.919 47.619 0.00 0.00 40.73 2.57
4388 5956 1.271707 ACCCCATCGTTCAACCGAAAT 60.272 47.619 0.00 0.00 40.73 2.17
4415 6022 1.552337 CGTCCCTGCTATGAGGCATAT 59.448 52.381 0.00 0.00 41.63 1.78
4424 6031 2.184322 CACGCACGTCCCTGCTAT 59.816 61.111 0.00 0.00 34.77 2.97
4455 6374 9.067986 CCTAACAAAACTTAGAAATCTGGTTCT 57.932 33.333 0.00 0.00 40.89 3.01
4457 6376 7.783119 ACCCTAACAAAACTTAGAAATCTGGTT 59.217 33.333 0.00 0.00 0.00 3.67
4459 6378 7.761038 ACCCTAACAAAACTTAGAAATCTGG 57.239 36.000 0.00 0.00 0.00 3.86
4462 6381 9.244799 CACAAACCCTAACAAAACTTAGAAATC 57.755 33.333 0.00 0.00 0.00 2.17
4463 6382 7.709182 GCACAAACCCTAACAAAACTTAGAAAT 59.291 33.333 0.00 0.00 0.00 2.17
4469 6388 3.515901 TGGCACAAACCCTAACAAAACTT 59.484 39.130 0.00 0.00 31.92 2.66
4531 6450 4.625963 AGCTAGACAGGAGGACCTTATTT 58.374 43.478 0.00 0.00 45.36 1.40
4558 6478 0.893270 TGCTTGAAACATCACCGGGG 60.893 55.000 6.32 0.00 0.00 5.73
4584 6504 0.738389 ACAAACCTCCACACGCTTTG 59.262 50.000 0.00 0.00 0.00 2.77
4587 6507 0.249911 GAGACAAACCTCCACACGCT 60.250 55.000 0.00 0.00 0.00 5.07
4670 6590 4.496010 GCAGACACATAGACGTAGACGAAT 60.496 45.833 9.41 0.00 43.02 3.34
4684 6604 1.340405 GGATCCAACCTGCAGACACAT 60.340 52.381 17.39 0.00 0.00 3.21
4710 6630 2.287909 GCCGATGAAGAGAAGCGTAGAT 60.288 50.000 0.00 0.00 0.00 1.98
4715 6635 1.760268 GCTGCCGATGAAGAGAAGCG 61.760 60.000 0.00 0.00 0.00 4.68
4789 6709 5.009210 GGGCAAACATTGTTGTAGTAGACAA 59.991 40.000 2.13 2.49 46.03 3.18
4865 6785 2.029290 ACCTAACGACGACAAGAAGCAT 60.029 45.455 0.00 0.00 0.00 3.79
4871 6791 1.268899 AGACCACCTAACGACGACAAG 59.731 52.381 0.00 0.00 0.00 3.16
4873 6793 1.806542 GTAGACCACCTAACGACGACA 59.193 52.381 0.00 0.00 0.00 4.35
4919 6839 5.362263 TGTCAAGGTAGTACAAAGAACACC 58.638 41.667 2.06 0.00 0.00 4.16
5144 7091 6.276091 TGAGCTTGCTTAGACATAGTACATG 58.724 40.000 0.00 0.00 0.00 3.21
5197 7172 3.759086 TGTGACAGTTTGCCAGTAACAAA 59.241 39.130 0.00 0.00 34.74 2.83


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

AutoCloner maintained by Alex Coulton.