Multiple sequence alignment - TraesCS5D01G355000

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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 TraesCS5D01G355000 chr5D 100.000 4917 0 0 1 4917 436979984 436984900 0.000000e+00 9081.0
1 TraesCS5D01G355000 chr5D 80.640 1250 208 18 1008 2240 445492366 445491134 0.000000e+00 937.0
2 TraesCS5D01G355000 chr5D 84.803 533 81 0 996 1528 445486035 445485503 2.010000e-148 536.0
3 TraesCS5D01G355000 chr5D 83.939 523 84 0 1000 1522 553910501 553911023 7.350000e-138 501.0
4 TraesCS5D01G355000 chr5D 83.918 342 50 3 3290 3627 445490012 445489672 6.140000e-84 322.0
5 TraesCS5D01G355000 chr5D 80.088 457 69 14 3188 3627 553912497 553912948 2.210000e-83 320.0
6 TraesCS5D01G355000 chr5D 85.036 274 34 5 3767 4034 437017716 437017988 6.270000e-69 272.0
7 TraesCS5D01G355000 chr5D 77.500 480 87 10 3220 3687 445403673 445403203 8.110000e-68 268.0
8 TraesCS5D01G355000 chr5D 80.053 376 54 13 3338 3707 437017247 437017607 4.880000e-65 259.0
9 TraesCS5D01G355000 chr5B 95.589 3582 135 13 693 4266 531192088 531195654 0.000000e+00 5718.0
10 TraesCS5D01G355000 chr5B 86.957 552 41 17 150 677 531191493 531192037 4.240000e-165 592.0
11 TraesCS5D01G355000 chr5B 83.333 636 99 4 2358 2987 543298651 543298017 9.170000e-162 580.0
12 TraesCS5D01G355000 chr5B 96.154 312 11 1 2808 3119 531200477 531200787 4.390000e-140 508.0
13 TraesCS5D01G355000 chr5B 83.333 582 59 17 3121 3701 531202249 531202793 2.040000e-138 503.0
14 TraesCS5D01G355000 chr5B 81.343 536 94 4 999 1528 543282510 543281975 9.780000e-117 431.0
15 TraesCS5D01G355000 chr5B 86.598 291 37 2 3338 3627 543297738 543297449 2.210000e-83 320.0
16 TraesCS5D01G355000 chr5B 89.344 244 14 7 4330 4561 531195663 531195906 3.720000e-76 296.0
17 TraesCS5D01G355000 chr5B 76.707 498 93 13 3220 3707 543244265 543243781 6.320000e-64 255.0
18 TraesCS5D01G355000 chr5B 80.702 342 51 7 3765 4101 531207184 531207515 8.170000e-63 252.0
19 TraesCS5D01G355000 chr5B 93.878 147 8 1 24 170 531190649 531190794 2.300000e-53 220.0
20 TraesCS5D01G355000 chr5B 82.063 223 27 10 3808 4026 531202844 531203057 1.410000e-40 178.0
21 TraesCS5D01G355000 chr5B 100.000 28 0 0 1 28 531190608 531190635 9.000000e-03 52.8
22 TraesCS5D01G355000 chr5A 94.200 1862 66 15 485 2319 552266880 552268726 0.000000e+00 2802.0
23 TraesCS5D01G355000 chr5A 94.708 1455 65 1 2310 3764 552268743 552270185 0.000000e+00 2250.0
24 TraesCS5D01G355000 chr5A 84.462 650 99 2 2370 3018 563255050 563254402 1.490000e-179 640.0
25 TraesCS5D01G355000 chr5A 83.398 518 84 2 1001 1517 552298394 552298910 3.440000e-131 479.0
26 TraesCS5D01G355000 chr5A 90.960 354 10 9 4573 4917 552276768 552277108 1.610000e-124 457.0
27 TraesCS5D01G355000 chr5A 87.748 302 34 2 3967 4266 552276165 552276465 2.820000e-92 350.0
28 TraesCS5D01G355000 chr5A 87.797 295 17 10 1 280 552266381 552266671 1.320000e-85 327.0
29 TraesCS5D01G355000 chr5A 82.796 372 47 11 3773 4130 552281694 552282062 2.860000e-82 316.0
30 TraesCS5D01G355000 chr5A 89.571 163 6 4 317 473 552266667 552266824 3.880000e-46 196.0
31 TraesCS5D01G355000 chr4D 80.668 1288 214 23 980 2242 1687297 1688574 0.000000e+00 966.0
32 TraesCS5D01G355000 chr4D 81.435 641 97 8 2358 2994 1688859 1689481 5.680000e-139 505.0
33 TraesCS5D01G355000 chr4D 84.828 290 44 0 3338 3627 2975770 2976059 4.810000e-75 292.0
34 TraesCS5D01G355000 chr1B 83.422 748 106 7 985 1717 553015723 553014979 0.000000e+00 678.0
35 TraesCS5D01G355000 chr1B 83.092 621 105 0 2370 2990 553014248 553013628 2.570000e-157 566.0
36 TraesCS5D01G355000 chr1D 82.588 626 101 4 2369 2987 410458679 410458055 3.350000e-151 545.0
37 TraesCS5D01G355000 chr1A 84.646 508 77 1 2362 2868 506278775 506278268 5.680000e-139 505.0
38 TraesCS5D01G355000 chr2B 87.500 96 11 1 2369 2464 794599566 794599472 5.200000e-20 110.0


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 TraesCS5D01G355000 chr5D 436979984 436984900 4916 False 9081.000000 9081 100.000000 1 4917 1 chr5D.!!$F1 4916
1 TraesCS5D01G355000 chr5D 445485503 445492366 6863 True 598.333333 937 83.120333 996 3627 3 chr5D.!!$R2 2631
2 TraesCS5D01G355000 chr5D 553910501 553912948 2447 False 410.500000 501 82.013500 1000 3627 2 chr5D.!!$F3 2627
3 TraesCS5D01G355000 chr5D 437017247 437017988 741 False 265.500000 272 82.544500 3338 4034 2 chr5D.!!$F2 696
4 TraesCS5D01G355000 chr5B 531190608 531195906 5298 False 1375.760000 5718 93.153600 1 4561 5 chr5B.!!$F2 4560
5 TraesCS5D01G355000 chr5B 543297449 543298651 1202 True 450.000000 580 84.965500 2358 3627 2 chr5B.!!$R3 1269
6 TraesCS5D01G355000 chr5B 543281975 543282510 535 True 431.000000 431 81.343000 999 1528 1 chr5B.!!$R2 529
7 TraesCS5D01G355000 chr5B 531200477 531203057 2580 False 396.333333 508 87.183333 2808 4026 3 chr5B.!!$F3 1218
8 TraesCS5D01G355000 chr5A 552266381 552270185 3804 False 1393.750000 2802 91.569000 1 3764 4 chr5A.!!$F3 3763
9 TraesCS5D01G355000 chr5A 563254402 563255050 648 True 640.000000 640 84.462000 2370 3018 1 chr5A.!!$R1 648
10 TraesCS5D01G355000 chr5A 552298394 552298910 516 False 479.000000 479 83.398000 1001 1517 1 chr5A.!!$F2 516
11 TraesCS5D01G355000 chr5A 552276165 552277108 943 False 403.500000 457 89.354000 3967 4917 2 chr5A.!!$F4 950
12 TraesCS5D01G355000 chr4D 1687297 1689481 2184 False 735.500000 966 81.051500 980 2994 2 chr4D.!!$F2 2014
13 TraesCS5D01G355000 chr1B 553013628 553015723 2095 True 622.000000 678 83.257000 985 2990 2 chr1B.!!$R1 2005
14 TraesCS5D01G355000 chr1D 410458055 410458679 624 True 545.000000 545 82.588000 2369 2987 1 chr1D.!!$R1 618
15 TraesCS5D01G355000 chr1A 506278268 506278775 507 True 505.000000 505 84.646000 2362 2868 1 chr1A.!!$R1 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
978 1857 0.036952 ATGACTGAGTGGAAGCCGTG 60.037 55.000 0.0 0.0 0.00 4.94 F
1406 2285 0.310543 GTGTTCTGCAAATCGTGGCA 59.689 50.000 0.0 0.0 38.52 4.92 F
1929 3024 2.560504 GACCATGCATCACCGTATTCA 58.439 47.619 0.0 0.0 0.00 2.57 F
3282 6126 0.252479 AGCCCACAGAATGCAGAGAG 59.748 55.000 0.0 0.0 42.53 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1913 3008 3.005791 TCGATCTGAATACGGTGATGCAT 59.994 43.478 0.00 0.0 0.00 3.96 R
2329 3694 3.130693 ACCTCATTACTCGGAGCACTTAC 59.869 47.826 4.58 0.0 0.00 2.34 R
3715 6734 0.877071 AGCTTGAAATGCTGACGGTG 59.123 50.000 0.00 0.0 46.52 4.94 R
4281 7420 0.101759 CTGCTGCTGCTGTTGTTGTT 59.898 50.000 17.00 0.0 40.48 2.83 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
102 126 5.926542 TCACTTCATCAACCTCGTCTTAAAG 59.073 40.000 0.00 0.00 0.00 1.85
106 130 5.651530 TCATCAACCTCGTCTTAAAGCTAG 58.348 41.667 0.00 0.00 0.00 3.42
153 177 3.842923 CGAGCGCCAGGATCCAGT 61.843 66.667 15.82 0.00 0.00 4.00
154 178 2.107953 GAGCGCCAGGATCCAGTC 59.892 66.667 15.82 0.00 0.00 3.51
167 913 4.020617 CAGTCCGGCCAGCCTTCA 62.021 66.667 2.24 0.00 0.00 3.02
244 1000 2.553172 CCTGATACGTACCTAGCTGGAC 59.447 54.545 0.00 0.00 39.71 4.02
268 1024 5.176590 CGAATTAGCCAGCTAATGAGAACTC 59.823 44.000 22.16 14.60 45.37 3.01
273 1029 1.123928 AGCTAATGAGAACTCCCGGG 58.876 55.000 16.85 16.85 0.00 5.73
296 1056 4.299978 GTGCTTGACCTCGATTATAGGAC 58.700 47.826 0.00 0.00 37.57 3.85
311 1071 1.568504 AGGACGGGAATTGTAGAGCA 58.431 50.000 0.00 0.00 0.00 4.26
312 1072 2.119495 AGGACGGGAATTGTAGAGCAT 58.881 47.619 0.00 0.00 0.00 3.79
313 1073 3.305720 AGGACGGGAATTGTAGAGCATA 58.694 45.455 0.00 0.00 0.00 3.14
314 1074 3.904339 AGGACGGGAATTGTAGAGCATAT 59.096 43.478 0.00 0.00 0.00 1.78
315 1075 5.084519 AGGACGGGAATTGTAGAGCATATA 58.915 41.667 0.00 0.00 0.00 0.86
377 1137 4.392921 TCGAGATTTGGATTCTCTCACC 57.607 45.455 0.00 0.00 37.96 4.02
395 1159 1.203994 ACCGGTGAGTGCATACTGTAC 59.796 52.381 6.12 0.00 37.25 2.90
414 1178 3.315880 ACTAGGACGGGAAGAGCTAAT 57.684 47.619 0.00 0.00 0.00 1.73
415 1179 3.644335 ACTAGGACGGGAAGAGCTAATT 58.356 45.455 0.00 0.00 0.00 1.40
416 1180 4.031611 ACTAGGACGGGAAGAGCTAATTT 58.968 43.478 0.00 0.00 0.00 1.82
417 1181 5.206587 ACTAGGACGGGAAGAGCTAATTTA 58.793 41.667 0.00 0.00 0.00 1.40
418 1182 5.659971 ACTAGGACGGGAAGAGCTAATTTAA 59.340 40.000 0.00 0.00 0.00 1.52
463 1227 2.287915 GCACTGGGCGTAATTGAGTATG 59.712 50.000 0.00 0.00 0.00 2.39
464 1228 3.531538 CACTGGGCGTAATTGAGTATGT 58.468 45.455 0.00 0.00 0.00 2.29
465 1229 4.689071 CACTGGGCGTAATTGAGTATGTA 58.311 43.478 0.00 0.00 0.00 2.29
466 1230 4.745125 CACTGGGCGTAATTGAGTATGTAG 59.255 45.833 0.00 0.00 0.00 2.74
467 1231 4.202223 ACTGGGCGTAATTGAGTATGTAGG 60.202 45.833 0.00 0.00 0.00 3.18
468 1232 3.962063 TGGGCGTAATTGAGTATGTAGGA 59.038 43.478 0.00 0.00 0.00 2.94
469 1233 4.038763 TGGGCGTAATTGAGTATGTAGGAG 59.961 45.833 0.00 0.00 0.00 3.69
487 1255 7.067421 TGTAGGAGTAGGAGTAGCACATTATT 58.933 38.462 0.00 0.00 0.00 1.40
488 1256 8.222637 TGTAGGAGTAGGAGTAGCACATTATTA 58.777 37.037 0.00 0.00 0.00 0.98
489 1257 7.768807 AGGAGTAGGAGTAGCACATTATTAG 57.231 40.000 0.00 0.00 0.00 1.73
490 1258 6.722129 AGGAGTAGGAGTAGCACATTATTAGG 59.278 42.308 0.00 0.00 0.00 2.69
491 1259 6.720288 GGAGTAGGAGTAGCACATTATTAGGA 59.280 42.308 0.00 0.00 0.00 2.94
492 1260 7.094118 GGAGTAGGAGTAGCACATTATTAGGAG 60.094 44.444 0.00 0.00 0.00 3.69
493 1261 7.299134 AGTAGGAGTAGCACATTATTAGGAGT 58.701 38.462 0.00 0.00 0.00 3.85
494 1262 8.446394 AGTAGGAGTAGCACATTATTAGGAGTA 58.554 37.037 0.00 0.00 0.00 2.59
495 1263 9.245481 GTAGGAGTAGCACATTATTAGGAGTAT 57.755 37.037 0.00 0.00 0.00 2.12
497 1265 8.808092 AGGAGTAGCACATTATTAGGAGTATTC 58.192 37.037 0.00 0.00 0.00 1.75
533 1348 4.540359 TCAGGGATGGCAAAAAGAAATG 57.460 40.909 0.00 0.00 0.00 2.32
547 1362 7.983484 GCAAAAAGAAATGATGGAGTTATGGAT 59.017 33.333 0.00 0.00 0.00 3.41
753 1632 4.330074 CGACTTGAGGTTGCTAAATGGTAG 59.670 45.833 0.00 0.00 0.00 3.18
786 1665 0.527565 CATGAAGGCCCAACGGAAAG 59.472 55.000 0.00 0.00 0.00 2.62
844 1723 2.430465 TCTTCAAGCCATCAAGACTGC 58.570 47.619 0.00 0.00 0.00 4.40
867 1746 4.232221 CCAATTGTCTGTGTGAATTGAGC 58.768 43.478 4.43 0.00 38.72 4.26
909 1788 1.185618 TCCTCACCGGTCTTCACCAG 61.186 60.000 2.59 0.00 44.02 4.00
970 1849 2.029020 TCTTCAACCGATGACTGAGTGG 60.029 50.000 0.00 0.00 37.92 4.00
977 1856 0.247736 GATGACTGAGTGGAAGCCGT 59.752 55.000 0.00 0.00 0.00 5.68
978 1857 0.036952 ATGACTGAGTGGAAGCCGTG 60.037 55.000 0.00 0.00 0.00 4.94
1406 2285 0.310543 GTGTTCTGCAAATCGTGGCA 59.689 50.000 0.00 0.00 38.52 4.92
1913 3008 4.041691 GGCCTATAAGCTATTTCTGGACCA 59.958 45.833 0.00 0.00 0.00 4.02
1929 3024 2.560504 GACCATGCATCACCGTATTCA 58.439 47.619 0.00 0.00 0.00 2.57
1939 3034 4.713824 TCACCGTATTCAGATCGAGTTT 57.286 40.909 0.00 0.00 0.00 2.66
2329 3694 2.551071 GCTGGCCTTATTGGTAGCCTAG 60.551 54.545 3.32 0.00 45.94 3.02
2803 4181 1.202290 GGTGTGCTGTTTGGTGTGAAG 60.202 52.381 0.00 0.00 0.00 3.02
3064 4448 3.140325 TCCTGACGGAAGAAAAGCAAT 57.860 42.857 0.00 0.00 36.03 3.56
3136 5980 2.158959 GGCGTGTCGAAGTGGATCG 61.159 63.158 0.00 0.00 44.04 3.69
3282 6126 0.252479 AGCCCACAGAATGCAGAGAG 59.748 55.000 0.00 0.00 42.53 3.20
3596 6614 5.048713 AGCTTTCAAGTGGAGAAATAAACGG 60.049 40.000 0.00 0.00 34.75 4.44
3627 6645 0.311165 CGTCGACTTCACAGGTCAGT 59.689 55.000 14.70 0.00 33.73 3.41
3647 6666 4.332819 CAGTACTGCCAGTATTAAAGCCAC 59.667 45.833 10.54 0.00 32.65 5.01
3694 6713 6.378280 GGTGATGGAGACCATTTCTATTTTGT 59.622 38.462 4.74 0.00 45.26 2.83
3722 6741 6.507900 TCAATTTTAATTTTCTGCACCGTCA 58.492 32.000 0.00 0.00 0.00 4.35
3960 7061 9.578439 TCTGTATTGATTATGCATCGAGATAAG 57.422 33.333 0.19 0.00 34.08 1.73
3992 7095 2.046314 CCATCTGCCGGTCGGTTT 60.046 61.111 11.25 0.00 37.65 3.27
4037 7140 2.618709 CTGTTCCTTTCTGCGGAGTTTT 59.381 45.455 3.10 0.00 0.00 2.43
4043 7146 5.127491 TCCTTTCTGCGGAGTTTTAAGAAA 58.873 37.500 3.10 0.00 35.96 2.52
4047 7150 5.796350 TCTGCGGAGTTTTAAGAAATAGC 57.204 39.130 3.10 0.00 0.00 2.97
4059 7162 2.711542 AGAAATAGCCCAGTTTGACGG 58.288 47.619 0.00 0.00 0.00 4.79
4063 7166 3.574780 GCCCAGTTTGACGGCTAC 58.425 61.111 0.00 0.00 39.70 3.58
4074 7177 2.172679 TGACGGCTACCACTATGTTCA 58.827 47.619 0.00 0.00 0.00 3.18
4139 7257 7.654923 TGATCATGTCTGTAGTATGCAAGATTC 59.345 37.037 0.00 0.00 0.00 2.52
4160 7278 5.913946 TCCCTCTGATCTCTACAGTGATA 57.086 43.478 0.00 0.00 36.81 2.15
4163 7281 7.990055 TCCCTCTGATCTCTACAGTGATAATA 58.010 38.462 0.00 0.00 36.81 0.98
4168 7286 8.955388 TCTGATCTCTACAGTGATAATATCTGC 58.045 37.037 0.00 0.00 36.81 4.26
4195 7313 3.895656 TGGATTCTAGATTACTCCACGGG 59.104 47.826 8.86 0.00 31.19 5.28
4266 7405 6.130569 ACCTGAACAATTGTTTACCCTGTTA 58.869 36.000 24.02 0.00 38.56 2.41
4267 7406 6.040054 ACCTGAACAATTGTTTACCCTGTTAC 59.960 38.462 24.02 8.54 38.56 2.50
4269 7408 7.266922 TGAACAATTGTTTACCCTGTTACTC 57.733 36.000 24.02 8.02 38.56 2.59
4270 7409 5.934935 ACAATTGTTTACCCTGTTACTCG 57.065 39.130 4.92 0.00 0.00 4.18
4271 7410 4.214758 ACAATTGTTTACCCTGTTACTCGC 59.785 41.667 4.92 0.00 0.00 5.03
4273 7412 3.472283 TGTTTACCCTGTTACTCGCAA 57.528 42.857 0.00 0.00 0.00 4.85
4274 7413 3.132925 TGTTTACCCTGTTACTCGCAAC 58.867 45.455 0.00 0.00 0.00 4.17
4275 7414 3.132925 GTTTACCCTGTTACTCGCAACA 58.867 45.455 0.00 0.00 36.94 3.33
4276 7415 3.472283 TTACCCTGTTACTCGCAACAA 57.528 42.857 0.00 0.00 37.93 2.83
4277 7416 1.589803 ACCCTGTTACTCGCAACAAC 58.410 50.000 0.00 0.00 37.93 3.32
4278 7417 1.134340 ACCCTGTTACTCGCAACAACA 60.134 47.619 0.00 0.00 37.93 3.33
4279 7418 1.944024 CCCTGTTACTCGCAACAACAA 59.056 47.619 0.00 0.00 37.93 2.83
4280 7419 2.286772 CCCTGTTACTCGCAACAACAAC 60.287 50.000 0.00 0.00 37.93 3.32
4281 7420 2.353269 CCTGTTACTCGCAACAACAACA 59.647 45.455 0.00 0.00 37.93 3.33
4282 7421 3.181505 CCTGTTACTCGCAACAACAACAA 60.182 43.478 0.00 0.00 37.93 2.83
4283 7422 3.749404 TGTTACTCGCAACAACAACAAC 58.251 40.909 0.00 0.00 35.53 3.32
4284 7423 3.188667 TGTTACTCGCAACAACAACAACA 59.811 39.130 0.00 0.00 35.53 3.33
4285 7424 2.999507 ACTCGCAACAACAACAACAA 57.000 40.000 0.00 0.00 0.00 2.83
4286 7425 2.591133 ACTCGCAACAACAACAACAAC 58.409 42.857 0.00 0.00 0.00 3.32
4287 7426 2.030717 ACTCGCAACAACAACAACAACA 60.031 40.909 0.00 0.00 0.00 3.33
4288 7427 2.983136 CTCGCAACAACAACAACAACAA 59.017 40.909 0.00 0.00 0.00 2.83
4289 7428 2.726760 TCGCAACAACAACAACAACAAC 59.273 40.909 0.00 0.00 0.00 3.32
4290 7429 2.472861 CGCAACAACAACAACAACAACA 59.527 40.909 0.00 0.00 0.00 3.33
4291 7430 3.421569 CGCAACAACAACAACAACAACAG 60.422 43.478 0.00 0.00 0.00 3.16
4292 7431 3.664014 GCAACAACAACAACAACAACAGC 60.664 43.478 0.00 0.00 0.00 4.40
4293 7432 3.377346 ACAACAACAACAACAACAGCA 57.623 38.095 0.00 0.00 0.00 4.41
4294 7433 3.316283 ACAACAACAACAACAACAGCAG 58.684 40.909 0.00 0.00 0.00 4.24
4295 7434 1.994916 ACAACAACAACAACAGCAGC 58.005 45.000 0.00 0.00 0.00 5.25
4296 7435 1.271934 ACAACAACAACAACAGCAGCA 59.728 42.857 0.00 0.00 0.00 4.41
4297 7436 1.921887 CAACAACAACAACAGCAGCAG 59.078 47.619 0.00 0.00 0.00 4.24
4298 7437 0.179129 ACAACAACAACAGCAGCAGC 60.179 50.000 0.00 0.00 42.56 5.25
4299 7438 0.179132 CAACAACAACAGCAGCAGCA 60.179 50.000 3.17 0.00 45.49 4.41
4300 7439 0.101759 AACAACAACAGCAGCAGCAG 59.898 50.000 3.17 0.00 45.49 4.24
4301 7440 1.660575 CAACAACAGCAGCAGCAGC 60.661 57.895 3.17 0.46 45.49 5.25
4302 7441 2.122797 AACAACAGCAGCAGCAGCA 61.123 52.632 12.92 0.00 45.49 4.41
4303 7442 2.071844 AACAACAGCAGCAGCAGCAG 62.072 55.000 12.92 6.60 45.49 4.24
4314 7453 3.681835 GCAGCAGCAGCAGCCTTT 61.682 61.111 7.26 0.00 46.35 3.11
4315 7454 2.338015 GCAGCAGCAGCAGCCTTTA 61.338 57.895 7.26 0.00 46.35 1.85
4316 7455 1.801332 CAGCAGCAGCAGCCTTTAG 59.199 57.895 6.10 0.00 45.49 1.85
4317 7456 0.959372 CAGCAGCAGCAGCCTTTAGT 60.959 55.000 6.10 0.00 45.49 2.24
4318 7457 0.676151 AGCAGCAGCAGCCTTTAGTC 60.676 55.000 6.10 0.00 45.49 2.59
4319 7458 1.652167 GCAGCAGCAGCCTTTAGTCC 61.652 60.000 0.00 0.00 43.56 3.85
4320 7459 1.028868 CAGCAGCAGCCTTTAGTCCC 61.029 60.000 0.00 0.00 43.56 4.46
4321 7460 1.002134 GCAGCAGCCTTTAGTCCCA 60.002 57.895 0.00 0.00 33.58 4.37
4322 7461 0.609131 GCAGCAGCCTTTAGTCCCAA 60.609 55.000 0.00 0.00 33.58 4.12
4323 7462 1.909700 CAGCAGCCTTTAGTCCCAAA 58.090 50.000 0.00 0.00 0.00 3.28
4324 7463 1.541588 CAGCAGCCTTTAGTCCCAAAC 59.458 52.381 0.00 0.00 0.00 2.93
4325 7464 1.144913 AGCAGCCTTTAGTCCCAAACA 59.855 47.619 0.00 0.00 0.00 2.83
4326 7465 1.960689 GCAGCCTTTAGTCCCAAACAA 59.039 47.619 0.00 0.00 0.00 2.83
4328 7467 3.222603 CAGCCTTTAGTCCCAAACAAGT 58.777 45.455 0.00 0.00 0.00 3.16
4438 7959 0.255033 TGCTGCATCTGCCTCTTGAT 59.745 50.000 0.00 0.00 41.18 2.57
4531 8288 5.817296 TCTGATACCTTCATTTTCATGGTCG 59.183 40.000 0.00 0.00 32.72 4.79
4567 8324 1.271543 TGCAGAGCTTAATGGTGCAGT 60.272 47.619 0.00 0.00 39.17 4.40
4591 8397 0.768622 ACCCAAGTTCCACCGATCAA 59.231 50.000 0.00 0.00 0.00 2.57
4732 9643 1.299620 GCTGTTGTGCTGCTGGTTG 60.300 57.895 0.00 0.00 38.75 3.77
4819 10081 3.363178 GCAGAATACCATTGCTTAACGC 58.637 45.455 0.00 0.00 35.05 4.84
4820 10082 3.065371 GCAGAATACCATTGCTTAACGCT 59.935 43.478 0.00 0.00 40.11 5.07
4823 10085 5.739161 CAGAATACCATTGCTTAACGCTTTC 59.261 40.000 0.00 0.00 40.11 2.62
4824 10086 4.632538 ATACCATTGCTTAACGCTTTCC 57.367 40.909 0.00 0.00 40.11 3.13
4827 10089 4.076394 ACCATTGCTTAACGCTTTCCTTA 58.924 39.130 0.00 0.00 40.11 2.69
4828 10090 4.521256 ACCATTGCTTAACGCTTTCCTTAA 59.479 37.500 0.00 0.00 40.11 1.85
4829 10091 4.857037 CCATTGCTTAACGCTTTCCTTAAC 59.143 41.667 0.00 0.00 40.11 2.01
4830 10092 3.799137 TGCTTAACGCTTTCCTTAACG 57.201 42.857 0.00 0.00 40.11 3.18
4835 10097 3.717350 AACGCTTTCCTTAACGAATCG 57.283 42.857 0.00 0.00 0.00 3.34
4842 10104 6.399039 CGCTTTCCTTAACGAATCGAGATATG 60.399 42.308 10.55 2.30 0.00 1.78
4898 10160 1.080298 GCAAAGCAAGCTCCGCATT 60.080 52.632 10.42 2.16 0.00 3.56
4901 10163 1.470098 CAAAGCAAGCTCCGCATTACT 59.530 47.619 10.42 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 145 3.672295 CTCGTCCCAGCTTCCAGCC 62.672 68.421 0.00 0.00 43.77 4.85
136 160 3.781770 GACTGGATCCTGGCGCTCG 62.782 68.421 21.40 0.00 0.00 5.03
244 1000 5.053145 AGTTCTCATTAGCTGGCTAATTCG 58.947 41.667 20.91 15.54 44.18 3.34
311 1071 7.776969 AGTGTTGGTGATGAAAGAAGCATATAT 59.223 33.333 0.00 0.00 0.00 0.86
312 1072 7.112122 AGTGTTGGTGATGAAAGAAGCATATA 58.888 34.615 0.00 0.00 0.00 0.86
313 1073 5.948162 AGTGTTGGTGATGAAAGAAGCATAT 59.052 36.000 0.00 0.00 0.00 1.78
314 1074 5.316167 AGTGTTGGTGATGAAAGAAGCATA 58.684 37.500 0.00 0.00 0.00 3.14
315 1075 4.147321 AGTGTTGGTGATGAAAGAAGCAT 58.853 39.130 0.00 0.00 0.00 3.79
377 1137 2.941453 AGTACAGTATGCACTCACCG 57.059 50.000 0.00 0.00 38.67 4.94
395 1159 4.674281 AAATTAGCTCTTCCCGTCCTAG 57.326 45.455 0.00 0.00 0.00 3.02
414 1178 7.525360 GCTCATCAATCAAACCTTCCCTTTAAA 60.525 37.037 0.00 0.00 0.00 1.52
415 1179 6.071391 GCTCATCAATCAAACCTTCCCTTTAA 60.071 38.462 0.00 0.00 0.00 1.52
416 1180 5.418840 GCTCATCAATCAAACCTTCCCTTTA 59.581 40.000 0.00 0.00 0.00 1.85
417 1181 4.221482 GCTCATCAATCAAACCTTCCCTTT 59.779 41.667 0.00 0.00 0.00 3.11
418 1182 3.766051 GCTCATCAATCAAACCTTCCCTT 59.234 43.478 0.00 0.00 0.00 3.95
454 1218 6.943718 GCTACTCCTACTCCTACATACTCAAT 59.056 42.308 0.00 0.00 0.00 2.57
463 1227 7.527568 AATAATGTGCTACTCCTACTCCTAC 57.472 40.000 0.00 0.00 0.00 3.18
464 1228 7.889073 CCTAATAATGTGCTACTCCTACTCCTA 59.111 40.741 0.00 0.00 0.00 2.94
465 1229 6.722129 CCTAATAATGTGCTACTCCTACTCCT 59.278 42.308 0.00 0.00 0.00 3.69
466 1230 6.720288 TCCTAATAATGTGCTACTCCTACTCC 59.280 42.308 0.00 0.00 0.00 3.85
467 1231 7.449086 ACTCCTAATAATGTGCTACTCCTACTC 59.551 40.741 0.00 0.00 0.00 2.59
468 1232 7.299134 ACTCCTAATAATGTGCTACTCCTACT 58.701 38.462 0.00 0.00 0.00 2.57
469 1233 7.527568 ACTCCTAATAATGTGCTACTCCTAC 57.472 40.000 0.00 0.00 0.00 3.18
495 1263 8.985922 CCATCCCTGAATCATATACTAGATGAA 58.014 37.037 0.00 0.00 36.90 2.57
497 1265 7.147602 TGCCATCCCTGAATCATATACTAGATG 60.148 40.741 0.00 0.00 0.00 2.90
503 1297 6.899393 TTTTGCCATCCCTGAATCATATAC 57.101 37.500 0.00 0.00 0.00 1.47
547 1362 6.049149 CGGCTCCTCTGAAGTCAATAATAAA 58.951 40.000 0.00 0.00 0.00 1.40
768 1647 1.250840 GCTTTCCGTTGGGCCTTCAT 61.251 55.000 4.53 0.00 0.00 2.57
786 1665 5.615289 TGGATGGATTAGAGAAAGCTAAGC 58.385 41.667 0.00 0.00 36.34 3.09
844 1723 4.801891 CTCAATTCACACAGACAATTGGG 58.198 43.478 10.83 1.44 37.86 4.12
909 1788 7.061688 TCTTATTGGAAGTAGAGGAGAGGTAC 58.938 42.308 0.00 0.00 0.00 3.34
977 1856 3.447040 GCTTTTGCCTGCTGTCCA 58.553 55.556 0.00 0.00 40.15 4.02
1406 2285 3.178540 AACCTCTTGTCGCCGCCTT 62.179 57.895 0.00 0.00 0.00 4.35
1913 3008 3.005791 TCGATCTGAATACGGTGATGCAT 59.994 43.478 0.00 0.00 0.00 3.96
1929 3024 8.024145 AGGATTTTAGGATACAAACTCGATCT 57.976 34.615 0.00 0.00 41.41 2.75
1939 3034 5.631481 GCACCCAGAAGGATTTTAGGATACA 60.631 44.000 0.00 0.00 39.89 2.29
2329 3694 3.130693 ACCTCATTACTCGGAGCACTTAC 59.869 47.826 4.58 0.00 0.00 2.34
2803 4181 3.876320 GCTCTTTTGTGATGAGGAGATCC 59.124 47.826 0.00 0.00 31.83 3.36
3627 6645 4.019681 ACAGTGGCTTTAATACTGGCAGTA 60.020 41.667 28.04 28.04 44.56 2.74
3647 6666 4.862574 CCACAAGCATCATCATTCAAACAG 59.137 41.667 0.00 0.00 0.00 3.16
3694 6713 9.482627 ACGGTGCAGAAAATTAAAATTGAAATA 57.517 25.926 0.00 0.00 0.00 1.40
3707 6726 1.538047 ATGCTGACGGTGCAGAAAAT 58.462 45.000 10.46 0.98 44.04 1.82
3715 6734 0.877071 AGCTTGAAATGCTGACGGTG 59.123 50.000 0.00 0.00 46.52 4.94
3960 7061 3.679389 CAGATGGGTAATAGACATGGGC 58.321 50.000 0.00 0.00 0.00 5.36
3992 7095 4.329392 TGCTGCAGATCAAGAAATGAAGA 58.671 39.130 20.43 0.00 42.54 2.87
4037 7140 4.258543 CCGTCAAACTGGGCTATTTCTTA 58.741 43.478 0.00 0.00 0.00 2.10
4043 7146 4.637771 GCCGTCAAACTGGGCTAT 57.362 55.556 0.00 0.00 43.52 2.97
4047 7150 0.953960 GTGGTAGCCGTCAAACTGGG 60.954 60.000 0.00 0.00 0.00 4.45
4059 7162 3.310774 CAGCACATGAACATAGTGGTAGC 59.689 47.826 0.00 0.00 41.51 3.58
4063 7166 5.178061 TCTAACAGCACATGAACATAGTGG 58.822 41.667 0.00 6.13 33.98 4.00
4074 7177 2.038952 TCTGGCAGTTCTAACAGCACAT 59.961 45.455 15.27 0.00 42.43 3.21
4139 7257 8.821686 ATATTATCACTGTAGAGATCAGAGGG 57.178 38.462 0.00 0.00 36.81 4.30
4168 7286 7.761704 CCGTGGAGTAATCTAGAATCCATAATG 59.238 40.741 17.36 10.65 41.81 1.90
4195 7313 3.077359 ACAGAATTTAGCACTGAGGCAC 58.923 45.455 0.00 0.00 35.85 5.01
4266 7405 2.030717 TGTTGTTGTTGTTGTTGCGAGT 60.031 40.909 0.00 0.00 0.00 4.18
4267 7406 2.590073 TGTTGTTGTTGTTGTTGCGAG 58.410 42.857 0.00 0.00 0.00 5.03
4269 7408 2.472861 TGTTGTTGTTGTTGTTGTTGCG 59.527 40.909 0.00 0.00 0.00 4.85
4270 7409 3.664014 GCTGTTGTTGTTGTTGTTGTTGC 60.664 43.478 0.00 0.00 0.00 4.17
4271 7410 3.492383 TGCTGTTGTTGTTGTTGTTGTTG 59.508 39.130 0.00 0.00 0.00 3.33
4273 7412 3.316283 CTGCTGTTGTTGTTGTTGTTGT 58.684 40.909 0.00 0.00 0.00 3.32
4274 7413 2.092524 GCTGCTGTTGTTGTTGTTGTTG 59.907 45.455 0.00 0.00 0.00 3.33
4275 7414 2.288702 TGCTGCTGTTGTTGTTGTTGTT 60.289 40.909 0.00 0.00 0.00 2.83
4276 7415 1.271934 TGCTGCTGTTGTTGTTGTTGT 59.728 42.857 0.00 0.00 0.00 3.32
4277 7416 1.921887 CTGCTGCTGTTGTTGTTGTTG 59.078 47.619 0.00 0.00 0.00 3.33
4278 7417 1.736696 GCTGCTGCTGTTGTTGTTGTT 60.737 47.619 8.53 0.00 36.03 2.83
4279 7418 0.179129 GCTGCTGCTGTTGTTGTTGT 60.179 50.000 8.53 0.00 36.03 3.32
4280 7419 0.179132 TGCTGCTGCTGTTGTTGTTG 60.179 50.000 17.00 0.00 40.48 3.33
4281 7420 0.101759 CTGCTGCTGCTGTTGTTGTT 59.898 50.000 17.00 0.00 40.48 2.83
4282 7421 1.731700 CTGCTGCTGCTGTTGTTGT 59.268 52.632 17.00 0.00 40.48 3.32
4283 7422 1.660575 GCTGCTGCTGCTGTTGTTG 60.661 57.895 22.10 3.65 39.81 3.33
4284 7423 2.071844 CTGCTGCTGCTGCTGTTGTT 62.072 55.000 27.67 0.00 39.81 2.83
4285 7424 2.517638 TGCTGCTGCTGCTGTTGT 60.518 55.556 27.67 0.00 39.81 3.32
4286 7425 2.255554 CTGCTGCTGCTGCTGTTG 59.744 61.111 27.67 13.98 39.81 3.33
4298 7437 0.959372 ACTAAAGGCTGCTGCTGCTG 60.959 55.000 26.79 16.73 40.48 4.41
4299 7438 0.676151 GACTAAAGGCTGCTGCTGCT 60.676 55.000 26.79 12.99 40.48 4.24
4300 7439 1.652167 GGACTAAAGGCTGCTGCTGC 61.652 60.000 21.42 21.42 39.59 5.25
4301 7440 1.028868 GGGACTAAAGGCTGCTGCTG 61.029 60.000 15.64 0.77 39.59 4.41
4302 7441 1.301293 GGGACTAAAGGCTGCTGCT 59.699 57.895 15.64 0.00 39.59 4.24
4303 7442 0.609131 TTGGGACTAAAGGCTGCTGC 60.609 55.000 7.10 7.10 38.76 5.25
4304 7443 1.541588 GTTTGGGACTAAAGGCTGCTG 59.458 52.381 0.00 0.00 0.00 4.41
4305 7444 1.144913 TGTTTGGGACTAAAGGCTGCT 59.855 47.619 0.00 0.00 0.00 4.24
4306 7445 1.616159 TGTTTGGGACTAAAGGCTGC 58.384 50.000 0.00 0.00 0.00 5.25
4307 7446 3.222603 ACTTGTTTGGGACTAAAGGCTG 58.777 45.455 0.00 0.00 0.00 4.85
4308 7447 3.595190 ACTTGTTTGGGACTAAAGGCT 57.405 42.857 0.00 0.00 0.00 4.58
4309 7448 4.765339 ACATACTTGTTTGGGACTAAAGGC 59.235 41.667 0.00 0.00 29.55 4.35
4310 7449 7.989416 TTACATACTTGTTTGGGACTAAAGG 57.011 36.000 0.00 0.00 37.28 3.11
4311 7450 9.673454 GTTTTACATACTTGTTTGGGACTAAAG 57.327 33.333 0.00 0.00 37.28 1.85
4312 7451 9.411189 AGTTTTACATACTTGTTTGGGACTAAA 57.589 29.630 0.00 0.00 37.28 1.85
4313 7452 8.983702 AGTTTTACATACTTGTTTGGGACTAA 57.016 30.769 0.00 0.00 37.28 2.24
4314 7453 9.492973 GTAGTTTTACATACTTGTTTGGGACTA 57.507 33.333 0.00 0.00 37.28 2.59
4315 7454 7.446319 GGTAGTTTTACATACTTGTTTGGGACT 59.554 37.037 0.00 0.00 37.28 3.85
4316 7455 7.308770 GGGTAGTTTTACATACTTGTTTGGGAC 60.309 40.741 0.00 0.00 37.28 4.46
4317 7456 6.716173 GGGTAGTTTTACATACTTGTTTGGGA 59.284 38.462 0.00 0.00 37.28 4.37
4318 7457 6.490721 TGGGTAGTTTTACATACTTGTTTGGG 59.509 38.462 0.00 0.00 37.28 4.12
4319 7458 7.513371 TGGGTAGTTTTACATACTTGTTTGG 57.487 36.000 0.00 0.00 37.28 3.28
4320 7459 9.458374 CTTTGGGTAGTTTTACATACTTGTTTG 57.542 33.333 0.00 0.00 37.28 2.93
4321 7460 8.635328 CCTTTGGGTAGTTTTACATACTTGTTT 58.365 33.333 0.00 0.00 37.28 2.83
4322 7461 7.255695 GCCTTTGGGTAGTTTTACATACTTGTT 60.256 37.037 0.00 0.00 34.55 2.83
4323 7462 6.208007 GCCTTTGGGTAGTTTTACATACTTGT 59.792 38.462 0.00 0.00 35.97 3.16
4324 7463 6.349860 GGCCTTTGGGTAGTTTTACATACTTG 60.350 42.308 0.00 0.00 34.45 3.16
4325 7464 5.713389 GGCCTTTGGGTAGTTTTACATACTT 59.287 40.000 0.00 0.00 34.45 2.24
4326 7465 5.222171 TGGCCTTTGGGTAGTTTTACATACT 60.222 40.000 3.32 0.00 34.45 2.12
4328 7467 5.014333 TCTGGCCTTTGGGTAGTTTTACATA 59.986 40.000 3.32 0.00 34.45 2.29
4438 7959 2.024176 TCAGCTGGTACTTCTTGGGA 57.976 50.000 15.13 0.00 0.00 4.37
4506 8233 6.484643 CGACCATGAAAATGAAGGTATCAGAT 59.515 38.462 0.00 0.00 42.53 2.90
4567 8324 1.203087 TCGGTGGAACTTGGGTCTCTA 60.203 52.381 0.00 0.00 36.74 2.43
4655 8590 4.137543 TCTTTGCCACTTCCTCTCTTTTC 58.862 43.478 0.00 0.00 0.00 2.29
4819 10081 7.863375 AGACATATCTCGATTCGTTAAGGAAAG 59.137 37.037 14.07 11.28 0.00 2.62
4820 10082 7.713750 AGACATATCTCGATTCGTTAAGGAAA 58.286 34.615 14.07 0.00 0.00 3.13
4828 10090 9.574458 CCAAAATATAGACATATCTCGATTCGT 57.426 33.333 5.89 0.00 36.29 3.85
4829 10091 8.535592 GCCAAAATATAGACATATCTCGATTCG 58.464 37.037 0.00 0.00 36.29 3.34
4830 10092 9.371136 TGCCAAAATATAGACATATCTCGATTC 57.629 33.333 0.00 0.00 36.29 2.52
4835 10097 7.097192 TCCGTGCCAAAATATAGACATATCTC 58.903 38.462 0.00 0.00 36.29 2.75
4842 10104 4.024048 CACCATCCGTGCCAAAATATAGAC 60.024 45.833 0.00 0.00 35.18 2.59


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

AutoCloner maintained by Alex Coulton.