Multiple sequence alignment - TraesCS4A01G459100

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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 TraesCS4A01G459100 chr4A 100.000 3279 0 0 1 3279 724581121 724577843 0.000000e+00 6056.0
1 TraesCS4A01G459100 chr4A 86.221 1183 94 20 998 2134 724782633 724783792 0.000000e+00 1218.0
2 TraesCS4A01G459100 chr4A 93.030 703 44 1 1403 2100 724399909 724399207 0.000000e+00 1022.0
3 TraesCS4A01G459100 chr4A 90.415 626 26 11 751 1342 724400544 724399919 0.000000e+00 793.0
4 TraesCS4A01G459100 chr4A 80.616 552 70 23 2361 2893 724784142 724784675 3.070000e-105 392.0
5 TraesCS4A01G459100 chr4A 89.908 218 18 1 2151 2368 724399099 724398886 8.960000e-71 278.0
6 TraesCS4A01G459100 chr4A 83.794 253 15 18 3045 3277 724784808 724785054 1.980000e-52 217.0
7 TraesCS4A01G459100 chr4A 85.308 211 23 4 2155 2363 724783872 724784076 9.220000e-51 211.0
8 TraesCS4A01G459100 chr4A 88.811 143 10 5 3138 3278 724398387 724398249 1.560000e-38 171.0
9 TraesCS4A01G459100 chr7A 88.894 2170 112 35 1 2099 12653746 12651635 0.000000e+00 2553.0
10 TraesCS4A01G459100 chr7A 88.401 1138 90 16 996 2100 12455348 12454220 0.000000e+00 1332.0
11 TraesCS4A01G459100 chr7A 84.385 1204 110 28 996 2134 12429651 12428461 0.000000e+00 1110.0
12 TraesCS4A01G459100 chr7A 81.242 789 72 42 2523 3279 12650780 12650036 4.750000e-158 568.0
13 TraesCS4A01G459100 chr7A 83.585 597 49 28 2361 2945 12453838 12453279 6.270000e-142 514.0
14 TraesCS4A01G459100 chr7A 87.615 218 21 3 2151 2368 12428391 12428180 7.030000e-62 248.0
15 TraesCS4A01G459100 chr7A 87.685 203 18 3 2151 2353 12651527 12651332 2.540000e-56 230.0
16 TraesCS4A01G459100 chr7A 87.097 155 15 2 2218 2367 12454055 12453901 1.560000e-38 171.0
17 TraesCS4A01G459100 chr7A 92.174 115 4 4 3164 3278 12451471 12451362 1.220000e-34 158.0
18 TraesCS4A01G459100 chr7A 86.667 135 11 4 663 791 12430093 12429960 3.410000e-30 143.0
19 TraesCS4A01G459100 chr7A 80.374 214 15 16 774 965 12455611 12455403 1.590000e-28 137.0
20 TraesCS4A01G459100 chr7A 90.278 72 6 1 663 734 12457518 12457448 3.480000e-15 93.5
21 TraesCS4A01G459100 chr7D 89.876 1699 102 19 466 2100 13098737 13097045 0.000000e+00 2121.0
22 TraesCS4A01G459100 chr7D 84.459 1229 107 29 998 2157 13029514 13028301 0.000000e+00 1134.0
23 TraesCS4A01G459100 chr7D 89.988 809 50 16 1353 2134 13066899 13066095 0.000000e+00 1016.0
24 TraesCS4A01G459100 chr7D 79.171 965 102 60 2361 3278 13027981 13027069 7.890000e-161 577.0
25 TraesCS4A01G459100 chr7D 94.526 274 15 0 998 1271 13067523 13067250 1.090000e-114 424.0
26 TraesCS4A01G459100 chr7D 83.562 219 19 7 2151 2368 13096937 13096735 4.320000e-44 189.0
27 TraesCS4A01G459100 chr7D 95.495 111 3 1 3165 3275 13043738 13043630 3.360000e-40 176.0
28 TraesCS4A01G459100 chr7D 85.616 146 9 7 751 885 13067829 13067685 3.410000e-30 143.0
29 TraesCS4A01G459100 chr7D 81.437 167 21 5 2541 2699 13065594 13065430 9.550000e-26 128.0
30 TraesCS4A01G459100 chr4D 85.602 1146 109 24 997 2099 506607111 506605979 0.000000e+00 1151.0
31 TraesCS4A01G459100 chr4D 82.234 546 67 19 2361 2893 506605595 506605067 8.350000e-121 444.0
32 TraesCS4A01G459100 chr4D 84.836 244 13 17 3053 3278 506604854 506604617 1.180000e-54 224.0
33 TraesCS4A01G459100 chr4D 85.780 218 23 5 2151 2368 506605867 506605658 1.180000e-54 224.0
34 TraesCS4A01G459100 chr4D 85.714 140 8 9 751 885 506607426 506607294 1.590000e-28 137.0
35 TraesCS4A01G459100 chrUn 87.413 143 16 2 253 395 9641115 9640975 2.620000e-36 163.0
36 TraesCS4A01G459100 chr5B 89.655 58 3 3 388 445 321985083 321985029 1.630000e-08 71.3
37 TraesCS4A01G459100 chr5A 89.130 46 5 0 400 445 375871313 375871268 1.270000e-04 58.4
38 TraesCS4A01G459100 chr2A 100.000 28 0 0 419 446 688232449 688232476 6.000000e-03 52.8


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 TraesCS4A01G459100 chr4A 724577843 724581121 3278 True 6056.000000 6056 100.000000 1 3279 1 chr4A.!!$R1 3278
1 TraesCS4A01G459100 chr4A 724398249 724400544 2295 True 566.000000 1022 90.541000 751 3278 4 chr4A.!!$R2 2527
2 TraesCS4A01G459100 chr4A 724782633 724785054 2421 False 509.500000 1218 83.984750 998 3277 4 chr4A.!!$F1 2279
3 TraesCS4A01G459100 chr7A 12650036 12653746 3710 True 1117.000000 2553 85.940333 1 3279 3 chr7A.!!$R3 3278
4 TraesCS4A01G459100 chr7A 12428180 12430093 1913 True 500.333333 1110 86.222333 663 2368 3 chr7A.!!$R1 1705
5 TraesCS4A01G459100 chr7A 12451362 12457518 6156 True 400.916667 1332 86.984833 663 3278 6 chr7A.!!$R2 2615
6 TraesCS4A01G459100 chr7D 13096735 13098737 2002 True 1155.000000 2121 86.719000 466 2368 2 chr7D.!!$R4 1902
7 TraesCS4A01G459100 chr7D 13027069 13029514 2445 True 855.500000 1134 81.815000 998 3278 2 chr7D.!!$R2 2280
8 TraesCS4A01G459100 chr7D 13065430 13067829 2399 True 427.750000 1016 87.891750 751 2699 4 chr7D.!!$R3 1948
9 TraesCS4A01G459100 chr4D 506604617 506607426 2809 True 436.000000 1151 84.833200 751 3278 5 chr4D.!!$R1 2527

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
398 404 0.390603 CGGCCTCCAATCGTTGTACA 60.391 55.0 0.00 0.0 0.00 2.90 F
448 454 0.452184 TTCGAACGTTTTTGCTGGCA 59.548 45.0 0.46 0.0 0.00 4.92 F
1916 4182 0.846015 TTGATCCAATGGAGGCCGAT 59.154 50.0 8.40 0.0 34.05 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1926 4192 1.080569 CGCCGCCATTTTTCTTGCT 60.081 52.632 0.0 0.0 0.00 3.91 R
2016 4282 1.227438 CACCGTCCGTGTTGAGGTT 60.227 57.895 0.0 0.0 37.73 3.50 R
3079 7541 1.420430 ACCTCGTTCCCACTGAGAAA 58.580 50.000 0.0 0.0 31.31 2.52 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
38 39 3.319755 CACTATTGGCCTTGTGCAAAAG 58.680 45.455 9.89 9.89 43.89 2.27
41 42 3.557228 ATTGGCCTTGTGCAAAAGAAA 57.443 38.095 18.67 9.61 43.89 2.52
42 43 3.340814 TTGGCCTTGTGCAAAAGAAAA 57.659 38.095 18.67 6.38 43.89 2.29
43 44 3.340814 TGGCCTTGTGCAAAAGAAAAA 57.659 38.095 18.67 0.00 43.89 1.94
44 45 3.269178 TGGCCTTGTGCAAAAGAAAAAG 58.731 40.909 18.67 1.82 43.89 2.27
45 46 2.613595 GGCCTTGTGCAAAAGAAAAAGG 59.386 45.455 18.67 1.60 43.89 3.11
46 47 3.270027 GCCTTGTGCAAAAGAAAAAGGT 58.730 40.909 18.67 0.00 40.77 3.50
47 48 4.438148 GCCTTGTGCAAAAGAAAAAGGTA 58.562 39.130 18.67 0.00 40.77 3.08
48 49 4.873259 GCCTTGTGCAAAAGAAAAAGGTAA 59.127 37.500 18.67 0.00 40.77 2.85
49 50 5.527214 GCCTTGTGCAAAAGAAAAAGGTAAT 59.473 36.000 18.67 0.00 40.77 1.89
50 51 6.511605 GCCTTGTGCAAAAGAAAAAGGTAATG 60.512 38.462 18.67 0.00 40.77 1.90
51 52 6.538381 CCTTGTGCAAAAGAAAAAGGTAATGT 59.462 34.615 18.67 0.00 0.00 2.71
54 55 6.876257 TGTGCAAAAGAAAAAGGTAATGTTGT 59.124 30.769 0.00 0.00 0.00 3.32
68 69 8.336801 AGGTAATGTTGTGATTCTTTCTAACC 57.663 34.615 0.00 0.00 0.00 2.85
158 160 9.965824 GAGGATTCTTTCTACACATTTCAAAAA 57.034 29.630 0.00 0.00 0.00 1.94
213 218 3.492656 GCATATCGTGAGGCTCCAAGTTA 60.493 47.826 12.86 3.51 0.00 2.24
223 228 2.236395 GGCTCCAAGTTACCTAAGAGCA 59.764 50.000 11.48 0.00 43.09 4.26
278 283 5.204833 TGAAATTCAAAACTTCTTCGCGAG 58.795 37.500 9.59 3.89 0.00 5.03
335 340 2.603560 GAGAATTTCCGACAAGGCTACG 59.396 50.000 0.00 0.00 40.77 3.51
391 397 1.745115 TTTGAGCGGCCTCCAATCG 60.745 57.895 0.00 0.00 37.29 3.34
398 404 0.390603 CGGCCTCCAATCGTTGTACA 60.391 55.000 0.00 0.00 0.00 2.90
402 408 1.670811 CCTCCAATCGTTGTACATGGC 59.329 52.381 7.46 0.00 0.00 4.40
405 411 2.027653 TCCAATCGTTGTACATGGCTGA 60.028 45.455 7.46 0.00 0.00 4.26
407 413 1.640428 ATCGTTGTACATGGCTGACG 58.360 50.000 8.80 8.80 0.00 4.35
416 422 3.300934 ATGGCTGACGCTCGCTGAA 62.301 57.895 0.00 0.00 36.09 3.02
435 441 1.534729 AAGAGGGTGGCATTTCGAAC 58.465 50.000 0.00 0.00 0.00 3.95
442 448 2.217620 GGTGGCATTTCGAACGTTTTTG 59.782 45.455 0.46 0.00 0.00 2.44
443 449 1.855360 TGGCATTTCGAACGTTTTTGC 59.145 42.857 0.46 7.68 0.00 3.68
444 450 2.124122 GGCATTTCGAACGTTTTTGCT 58.876 42.857 0.46 0.00 0.00 3.91
445 451 2.097444 GGCATTTCGAACGTTTTTGCTG 60.097 45.455 0.46 0.00 0.00 4.41
446 452 2.097444 GCATTTCGAACGTTTTTGCTGG 60.097 45.455 0.46 0.00 0.00 4.85
447 453 1.551145 TTTCGAACGTTTTTGCTGGC 58.449 45.000 0.46 0.00 0.00 4.85
448 454 0.452184 TTCGAACGTTTTTGCTGGCA 59.548 45.000 0.46 0.00 0.00 4.92
449 455 0.452184 TCGAACGTTTTTGCTGGCAA 59.548 45.000 0.46 3.72 0.00 4.52
450 456 1.135373 TCGAACGTTTTTGCTGGCAAA 60.135 42.857 15.51 15.51 43.23 3.68
451 457 1.857837 CGAACGTTTTTGCTGGCAAAT 59.142 42.857 19.27 6.24 44.14 2.32
452 458 2.283884 CGAACGTTTTTGCTGGCAAATT 59.716 40.909 19.27 11.70 44.14 1.82
453 459 3.242252 CGAACGTTTTTGCTGGCAAATTT 60.242 39.130 19.27 11.30 44.14 1.82
454 460 4.657055 GAACGTTTTTGCTGGCAAATTTT 58.343 34.783 19.27 11.01 44.14 1.82
455 461 4.693538 ACGTTTTTGCTGGCAAATTTTT 57.306 31.818 19.27 4.73 44.14 1.94
489 495 5.625197 GCTGGCAATTTTAGTTGTGATGGAT 60.625 40.000 0.00 0.00 0.00 3.41
523 529 4.815040 TCAAAAACAGCATGCCATTTTG 57.185 36.364 29.10 29.10 43.12 2.44
579 585 5.991606 AGAAAATGTCACGATGTTCTGAAGA 59.008 36.000 0.00 0.00 0.00 2.87
620 626 2.691984 AAACGTTCGCAAATACCACC 57.308 45.000 0.00 0.00 0.00 4.61
661 667 7.267128 TCGCGAGATAAGAGGGTTTATAAAAA 58.733 34.615 3.71 0.00 33.31 1.94
714 720 2.487934 CTGATTCGGTCCATAGCCAAG 58.512 52.381 0.00 0.00 0.00 3.61
761 2556 5.347364 GGTGAGAGATTTTGAGAGAGAAACG 59.653 44.000 0.00 0.00 0.00 3.60
806 2627 2.769663 AGAGAGGTCGCTAGAGAGAGAA 59.230 50.000 0.00 0.00 32.85 2.87
807 2628 3.199071 AGAGAGGTCGCTAGAGAGAGAAA 59.801 47.826 0.00 0.00 32.85 2.52
808 2629 3.275999 AGAGGTCGCTAGAGAGAGAAAC 58.724 50.000 0.00 0.00 32.85 2.78
809 2630 3.011119 GAGGTCGCTAGAGAGAGAAACA 58.989 50.000 0.00 0.00 32.85 2.83
810 2631 3.013921 AGGTCGCTAGAGAGAGAAACAG 58.986 50.000 0.00 0.00 32.85 3.16
811 2632 3.011119 GGTCGCTAGAGAGAGAAACAGA 58.989 50.000 0.00 0.00 32.85 3.41
918 2781 0.986550 AAACCCCTCCTATCCACCCG 60.987 60.000 0.00 0.00 0.00 5.28
938 2801 3.359654 CGAACGAAACCTGAAAAACCTG 58.640 45.455 0.00 0.00 0.00 4.00
990 2858 1.480137 TCTCTCCAGCAAGCTAAGCTC 59.520 52.381 10.39 0.00 41.14 4.09
1305 3226 2.187958 TGCTTCCTGGCTACACTACAT 58.812 47.619 0.00 0.00 0.00 2.29
1343 3546 2.027625 CCGGTGGCTGACGAGTTTC 61.028 63.158 0.00 0.00 0.00 2.78
1344 3547 1.300620 CGGTGGCTGACGAGTTTCA 60.301 57.895 0.00 0.00 0.00 2.69
1348 3551 1.527311 GTGGCTGACGAGTTTCAGTTC 59.473 52.381 3.10 0.00 44.34 3.01
1370 3573 3.823330 AGGTGGTCGTCGATCGCC 61.823 66.667 27.17 27.17 43.08 5.54
1443 3646 2.031616 TGCGCAAGAAGCTGCTCT 59.968 55.556 8.16 0.00 42.61 4.09
1916 4182 0.846015 TTGATCCAATGGAGGCCGAT 59.154 50.000 8.40 0.00 34.05 4.18
1926 4192 1.758514 GAGGCCGATGACCAGGAGA 60.759 63.158 0.00 0.00 0.00 3.71
1934 4200 2.354103 CGATGACCAGGAGAGCAAGAAA 60.354 50.000 0.00 0.00 0.00 2.52
2016 4282 0.615331 GAGCCTGAACCTGATGGACA 59.385 55.000 0.00 0.00 37.04 4.02
2085 4356 2.428530 GCTCCCATTCCATCAACTTTCC 59.571 50.000 0.00 0.00 0.00 3.13
2100 4374 7.538303 TCAACTTTCCATCAAAAAGAAAAGC 57.462 32.000 2.84 0.00 37.22 3.51
2107 4381 5.050227 TCCATCAAAAAGAAAAGCGCAAATG 60.050 36.000 11.47 0.00 0.00 2.32
2108 4382 4.194381 TCAAAAAGAAAAGCGCAAATGC 57.806 36.364 11.47 0.00 37.78 3.56
2114 4400 1.589779 GAAAAGCGCAAATGCTATGCC 59.410 47.619 11.47 0.00 46.60 4.40
2134 4429 2.827322 CCTGCATGTCTTTTCCATCCAA 59.173 45.455 0.00 0.00 0.00 3.53
2135 4430 3.258872 CCTGCATGTCTTTTCCATCCAAA 59.741 43.478 0.00 0.00 0.00 3.28
2148 4498 6.834168 TTCCATCCAAACTTAATTCTGACC 57.166 37.500 0.00 0.00 0.00 4.02
2149 4506 5.886609 TCCATCCAAACTTAATTCTGACCA 58.113 37.500 0.00 0.00 0.00 4.02
2169 4532 6.719370 TGACCAATATTTCAACTAGCTTGGTT 59.281 34.615 5.61 0.00 43.53 3.67
2249 4614 9.252962 CCTCTTATTTATTTTTATGCAGGCAAG 57.747 33.333 0.00 0.00 0.00 4.01
2292 4657 2.171448 AGCTGTGATGGGTGGATAGAAC 59.829 50.000 0.00 0.00 0.00 3.01
2294 4659 3.434167 GCTGTGATGGGTGGATAGAACAT 60.434 47.826 0.00 0.00 0.00 2.71
2315 4680 9.403110 GAACATATATGATCAAGAATGCCAAAC 57.597 33.333 19.63 0.00 30.86 2.93
2324 4689 4.832266 TCAAGAATGCCAAACATAACCAGT 59.168 37.500 0.00 0.00 38.34 4.00
2338 4708 9.739276 AAACATAACCAGTAATGAGATTGAGAA 57.261 29.630 0.00 0.00 0.00 2.87
2368 4738 8.618702 AATTGTTTGATTGGATGCACATTTTA 57.381 26.923 0.00 0.00 0.00 1.52
2370 4740 5.638657 TGTTTGATTGGATGCACATTTTAGC 59.361 36.000 0.00 0.00 0.00 3.09
2371 4741 4.389890 TGATTGGATGCACATTTTAGCC 57.610 40.909 0.00 0.00 0.00 3.93
2372 4742 3.768215 TGATTGGATGCACATTTTAGCCA 59.232 39.130 0.00 0.00 0.00 4.75
2374 4744 3.804786 TGGATGCACATTTTAGCCATG 57.195 42.857 0.00 0.00 0.00 3.66
2375 4745 3.098377 TGGATGCACATTTTAGCCATGT 58.902 40.909 0.00 0.00 35.10 3.21
2377 4747 4.097741 TGGATGCACATTTTAGCCATGTAC 59.902 41.667 0.00 0.00 32.88 2.90
2433 5216 5.532406 ACACACTCACTGCAATTAATGTTCT 59.468 36.000 0.00 0.00 0.00 3.01
2437 5220 8.629158 ACACTCACTGCAATTAATGTTCTTTTA 58.371 29.630 0.00 0.00 0.00 1.52
2516 5305 6.259550 AGCTTGTGACATAAAATCACTTCC 57.740 37.500 6.68 0.00 45.58 3.46
2517 5306 6.006449 AGCTTGTGACATAAAATCACTTCCT 58.994 36.000 6.68 0.00 45.58 3.36
2568 5361 6.030849 GTGACAGTGTGAGTGTGACTATATC 58.969 44.000 0.00 0.00 33.69 1.63
2571 5364 5.946377 ACAGTGTGAGTGTGACTATATCTCA 59.054 40.000 0.00 0.00 29.04 3.27
2572 5365 6.605194 ACAGTGTGAGTGTGACTATATCTCAT 59.395 38.462 0.00 0.00 37.46 2.90
2589 5390 5.348418 TCTCATTTTTCTTGACTCTTGCG 57.652 39.130 0.00 0.00 0.00 4.85
2646 5448 3.318017 TCTCTTGCGTGAAGAAGCTAAC 58.682 45.455 0.00 0.00 40.33 2.34
2650 5452 1.618837 TGCGTGAAGAAGCTAACCTCT 59.381 47.619 0.00 0.00 0.00 3.69
2662 5464 2.930682 GCTAACCTCTGGTCGTCATTTC 59.069 50.000 0.00 0.00 33.12 2.17
2674 5476 4.414852 GTCGTCATTTCATTGGATTGTGG 58.585 43.478 0.00 0.00 0.00 4.17
2679 5481 6.473131 CGTCATTTCATTGGATTGTGGTTATG 59.527 38.462 0.00 0.00 0.00 1.90
2714 5517 1.116308 TGTTGGTCTTGTGAGTCCGA 58.884 50.000 0.00 0.00 34.28 4.55
2788 5591 5.898174 TGGTATGGCTACGTACATATATGC 58.102 41.667 12.79 1.48 40.19 3.14
2789 5592 5.419471 TGGTATGGCTACGTACATATATGCA 59.581 40.000 12.79 0.00 40.19 3.96
2790 5593 6.097696 TGGTATGGCTACGTACATATATGCAT 59.902 38.462 12.79 3.79 40.19 3.96
2791 5594 6.420903 GGTATGGCTACGTACATATATGCATG 59.579 42.308 10.16 8.05 40.19 4.06
2792 5595 4.754322 TGGCTACGTACATATATGCATGG 58.246 43.478 10.16 2.81 0.00 3.66
2793 5596 4.221924 TGGCTACGTACATATATGCATGGT 59.778 41.667 10.16 8.26 0.00 3.55
2794 5597 5.175859 GGCTACGTACATATATGCATGGTT 58.824 41.667 10.16 0.00 0.00 3.67
2820 5629 7.600375 TGCTAGCTAGTTCTAATTGCATCATAC 59.400 37.037 21.62 0.00 0.00 2.39
2824 5633 7.871973 AGCTAGTTCTAATTGCATCATACAGAG 59.128 37.037 0.00 0.00 0.00 3.35
2826 5635 7.783090 AGTTCTAATTGCATCATACAGAGTG 57.217 36.000 0.00 0.00 0.00 3.51
2828 5640 5.059161 TCTAATTGCATCATACAGAGTGCC 58.941 41.667 0.00 0.00 36.79 5.01
2829 5641 2.785540 TTGCATCATACAGAGTGCCA 57.214 45.000 0.00 0.00 36.79 4.92
2879 5691 2.958818 AGTCTACACTGTGGGTCTTCA 58.041 47.619 13.09 0.00 0.00 3.02
2893 5705 3.694566 GGGTCTTCAATTTCGCATTAGGT 59.305 43.478 0.00 0.00 0.00 3.08
2894 5706 4.438744 GGGTCTTCAATTTCGCATTAGGTG 60.439 45.833 0.00 0.00 0.00 4.00
2895 5707 4.156008 GGTCTTCAATTTCGCATTAGGTGT 59.844 41.667 0.00 0.00 0.00 4.16
2896 5708 5.088739 GTCTTCAATTTCGCATTAGGTGTG 58.911 41.667 0.00 0.00 39.73 3.82
2898 5710 5.935206 TCTTCAATTTCGCATTAGGTGTGTA 59.065 36.000 0.00 0.00 39.38 2.90
2901 5713 7.477144 TCAATTTCGCATTAGGTGTGTATAG 57.523 36.000 0.00 0.00 39.38 1.31
2903 5715 7.766738 TCAATTTCGCATTAGGTGTGTATAGAA 59.233 33.333 0.00 0.00 39.38 2.10
2904 5716 8.559536 CAATTTCGCATTAGGTGTGTATAGAAT 58.440 33.333 0.00 0.00 39.38 2.40
2950 5801 5.745653 ATTTAAGAAAATGTTTCGCGCAG 57.254 34.783 8.75 0.00 33.97 5.18
3078 7540 2.647299 TCATAATTCCTGTGTGTGGGGT 59.353 45.455 0.00 0.00 0.00 4.95
3079 7541 3.075283 TCATAATTCCTGTGTGTGGGGTT 59.925 43.478 0.00 0.00 0.00 4.11
3088 7552 1.676006 GTGTGTGGGGTTTTCTCAGTG 59.324 52.381 0.00 0.00 0.00 3.66
3089 7553 1.318576 GTGTGGGGTTTTCTCAGTGG 58.681 55.000 0.00 0.00 0.00 4.00
3122 7586 4.392940 ACTTGTTGGAGGAGAATTGACTG 58.607 43.478 0.00 0.00 0.00 3.51
3126 7590 1.704628 TGGAGGAGAATTGACTGGCAA 59.295 47.619 0.00 0.00 41.53 4.52
3150 7629 4.935808 ACACAGTACTAATTAACCAGCAGC 59.064 41.667 0.00 0.00 0.00 5.25
3152 7631 4.181578 CAGTACTAATTAACCAGCAGCGT 58.818 43.478 0.00 0.00 0.00 5.07
3153 7632 4.267928 CAGTACTAATTAACCAGCAGCGTC 59.732 45.833 0.00 0.00 0.00 5.19
3154 7633 3.328382 ACTAATTAACCAGCAGCGTCA 57.672 42.857 0.00 0.00 0.00 4.35
3155 7634 3.873910 ACTAATTAACCAGCAGCGTCAT 58.126 40.909 0.00 0.00 0.00 3.06
3156 7635 3.623060 ACTAATTAACCAGCAGCGTCATG 59.377 43.478 0.00 0.00 0.00 3.07
3160 7639 1.372582 AACCAGCAGCGTCATGTATG 58.627 50.000 0.00 0.00 0.00 2.39
3161 7640 1.091771 ACCAGCAGCGTCATGTATGC 61.092 55.000 0.00 0.00 40.71 3.14
3169 7701 5.064325 AGCAGCGTCATGTATGCAATATATG 59.936 40.000 13.65 0.00 46.16 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 9.750125 AGAAAGAATCACAACATTACCTTTTTC 57.250 29.630 0.00 0.00 0.00 2.29
42 43 8.793592 GGTTAGAAAGAATCACAACATTACCTT 58.206 33.333 0.00 0.00 30.73 3.50
43 44 7.942341 TGGTTAGAAAGAATCACAACATTACCT 59.058 33.333 0.00 0.00 30.73 3.08
44 45 8.106247 TGGTTAGAAAGAATCACAACATTACC 57.894 34.615 0.00 0.00 30.73 2.85
45 46 9.959749 TTTGGTTAGAAAGAATCACAACATTAC 57.040 29.630 0.00 0.00 30.73 1.89
46 47 9.959749 GTTTGGTTAGAAAGAATCACAACATTA 57.040 29.630 0.00 0.00 30.73 1.90
47 48 7.647715 CGTTTGGTTAGAAAGAATCACAACATT 59.352 33.333 0.00 0.00 30.73 2.71
48 49 7.012894 TCGTTTGGTTAGAAAGAATCACAACAT 59.987 33.333 0.00 0.00 30.73 2.71
49 50 6.316640 TCGTTTGGTTAGAAAGAATCACAACA 59.683 34.615 0.00 0.00 30.73 3.33
50 51 6.631636 GTCGTTTGGTTAGAAAGAATCACAAC 59.368 38.462 0.00 0.00 0.00 3.32
51 52 6.510478 CGTCGTTTGGTTAGAAAGAATCACAA 60.510 38.462 0.00 0.00 0.00 3.33
54 55 5.051816 ACGTCGTTTGGTTAGAAAGAATCA 58.948 37.500 0.00 0.00 0.00 2.57
67 68 1.225908 GCCGCAATACGTCGTTTGG 60.226 57.895 1.78 0.00 41.42 3.28
68 69 0.110599 TTGCCGCAATACGTCGTTTG 60.111 50.000 1.78 9.29 41.42 2.93
158 160 7.884354 TCAAAATAAGGTATGACTAAACCCGTT 59.116 33.333 0.00 0.00 36.34 4.44
159 161 7.396418 TCAAAATAAGGTATGACTAAACCCGT 58.604 34.615 0.00 0.00 36.34 5.28
223 228 9.851686 TTATGGAAATGAATAGTTGCATAGAGT 57.148 29.630 0.00 0.00 42.94 3.24
278 283 2.107141 CGAGGATGACGGGAAGGC 59.893 66.667 0.00 0.00 0.00 4.35
335 340 5.276207 GCAAAAAGAACTAACGGTCAAAAGC 60.276 40.000 0.00 0.00 0.00 3.51
391 397 0.721718 GAGCGTCAGCCATGTACAAC 59.278 55.000 0.00 0.00 46.67 3.32
398 404 2.786539 TTTCAGCGAGCGTCAGCCAT 62.787 55.000 0.00 0.00 46.67 4.40
402 408 1.075425 CCTCTTTCAGCGAGCGTCAG 61.075 60.000 0.00 0.00 0.00 3.51
405 411 2.262915 CCCTCTTTCAGCGAGCGT 59.737 61.111 0.00 0.00 0.00 5.07
407 413 1.743252 CCACCCTCTTTCAGCGAGC 60.743 63.158 0.00 0.00 0.00 5.03
416 422 1.534729 GTTCGAAATGCCACCCTCTT 58.465 50.000 0.00 0.00 0.00 2.85
454 460 2.621556 ATTGCCAGCTCCCCTAAAAA 57.378 45.000 0.00 0.00 0.00 1.94
455 461 2.621556 AATTGCCAGCTCCCCTAAAA 57.378 45.000 0.00 0.00 0.00 1.52
456 462 2.621556 AAATTGCCAGCTCCCCTAAA 57.378 45.000 0.00 0.00 0.00 1.85
457 463 2.621556 AAAATTGCCAGCTCCCCTAA 57.378 45.000 0.00 0.00 0.00 2.69
458 464 2.580783 ACTAAAATTGCCAGCTCCCCTA 59.419 45.455 0.00 0.00 0.00 3.53
459 465 1.359130 ACTAAAATTGCCAGCTCCCCT 59.641 47.619 0.00 0.00 0.00 4.79
460 466 1.852633 ACTAAAATTGCCAGCTCCCC 58.147 50.000 0.00 0.00 0.00 4.81
461 467 2.562738 ACAACTAAAATTGCCAGCTCCC 59.437 45.455 0.00 0.00 32.47 4.30
462 468 3.255642 TCACAACTAAAATTGCCAGCTCC 59.744 43.478 0.00 0.00 32.47 4.70
463 469 4.503741 TCACAACTAAAATTGCCAGCTC 57.496 40.909 0.00 0.00 32.47 4.09
464 470 4.322198 CCATCACAACTAAAATTGCCAGCT 60.322 41.667 0.00 0.00 32.47 4.24
523 529 3.067320 GCTGAAAATTGCCATCCTCCTAC 59.933 47.826 0.00 0.00 0.00 3.18
579 585 4.888326 TGATGGCAATTTTAGGCAGTTT 57.112 36.364 0.00 0.00 45.09 2.66
620 626 1.857364 CGAACGTTCGTTGGAAGGG 59.143 57.895 35.92 10.64 45.09 3.95
661 667 7.377662 GCTTAAGCACGTAATGTTGTTTAGTTT 59.622 33.333 22.59 0.00 41.59 2.66
714 720 2.894126 TGTCTGTCCCTCTCTGACTTTC 59.106 50.000 0.00 0.00 35.70 2.62
761 2556 1.414919 TCTCTCTCTAGCGACCTCTCC 59.585 57.143 0.00 0.00 0.00 3.71
806 2627 1.589113 GAGACGCAGCCTCTCTGTT 59.411 57.895 12.75 0.00 44.66 3.16
807 2628 2.347322 GGAGACGCAGCCTCTCTGT 61.347 63.158 17.77 0.00 44.66 3.41
808 2629 2.493973 GGAGACGCAGCCTCTCTG 59.506 66.667 17.77 0.00 45.62 3.35
809 2630 2.757917 GGGAGACGCAGCCTCTCT 60.758 66.667 17.77 2.06 35.43 3.10
810 2631 4.200283 CGGGAGACGCAGCCTCTC 62.200 72.222 11.84 11.84 34.47 3.20
918 2781 4.095932 AGTCAGGTTTTTCAGGTTTCGTTC 59.904 41.667 0.00 0.00 0.00 3.95
964 2827 0.673022 GCTTGCTGGAGAGAGGTGTG 60.673 60.000 0.00 0.00 0.00 3.82
990 2858 4.647615 CGCCCCATCGCTCTACGG 62.648 72.222 0.00 0.00 43.89 4.02
1374 3577 4.452733 CGTCCTCCCCGGCAACTC 62.453 72.222 0.00 0.00 0.00 3.01
1557 3760 1.671054 CGTTCATGTTCCAGGCGGT 60.671 57.895 0.00 0.00 0.00 5.68
1810 4040 1.291877 GCTGAAGCCGTCGAACATGT 61.292 55.000 0.00 0.00 34.31 3.21
1909 4175 1.760086 CTCTCCTGGTCATCGGCCT 60.760 63.158 0.00 0.00 0.00 5.19
1916 4182 3.576078 TTTTTCTTGCTCTCCTGGTCA 57.424 42.857 0.00 0.00 0.00 4.02
1926 4192 1.080569 CGCCGCCATTTTTCTTGCT 60.081 52.632 0.00 0.00 0.00 3.91
2016 4282 1.227438 CACCGTCCGTGTTGAGGTT 60.227 57.895 0.00 0.00 37.73 3.50
2085 4356 4.609708 GCATTTGCGCTTTTCTTTTTGATG 59.390 37.500 9.73 0.00 0.00 3.07
2107 4381 2.223665 GGAAAAGACATGCAGGCATAGC 60.224 50.000 6.42 2.20 34.91 2.97
2108 4382 3.018856 TGGAAAAGACATGCAGGCATAG 58.981 45.455 6.42 4.55 34.91 2.23
2109 4383 3.084536 TGGAAAAGACATGCAGGCATA 57.915 42.857 6.42 0.00 34.91 3.14
2114 4400 4.021719 AGTTTGGATGGAAAAGACATGCAG 60.022 41.667 0.00 0.00 45.28 4.41
2220 4585 9.987272 GCCTGCATAAAAATAAATAAGAGGATT 57.013 29.630 0.00 0.00 0.00 3.01
2221 4586 9.146586 TGCCTGCATAAAAATAAATAAGAGGAT 57.853 29.630 0.00 0.00 0.00 3.24
2249 4614 2.225019 CACTTGAGTTCAGCCATGACAC 59.775 50.000 0.00 0.00 34.35 3.67
2338 4708 8.065473 TGTGCATCCAATCAAACAATTAGTAT 57.935 30.769 0.00 0.00 0.00 2.12
2350 4720 3.768215 TGGCTAAAATGTGCATCCAATCA 59.232 39.130 0.00 0.00 0.00 2.57
2389 5167 7.764443 AGTGTGTACATGTGTATATGTTCTTCC 59.236 37.037 9.11 0.00 41.31 3.46
2536 5329 2.764010 ACTCACACTGTCACACACCTAA 59.236 45.455 0.00 0.00 0.00 2.69
2568 5361 5.100751 ACGCAAGAGTCAAGAAAAATGAG 57.899 39.130 0.00 0.00 43.62 2.90
2571 5364 7.078228 GTCATAACGCAAGAGTCAAGAAAAAT 58.922 34.615 0.00 0.00 43.62 1.82
2572 5365 6.037720 TGTCATAACGCAAGAGTCAAGAAAAA 59.962 34.615 0.00 0.00 43.62 1.94
2646 5448 2.679837 CCAATGAAATGACGACCAGAGG 59.320 50.000 0.00 0.00 0.00 3.69
2650 5452 4.078537 ACAATCCAATGAAATGACGACCA 58.921 39.130 0.00 0.00 0.00 4.02
2690 5492 4.385825 GGACTCACAAGACCAACATTGTA 58.614 43.478 0.00 0.00 37.54 2.41
2714 5517 9.593134 GAGATTGATTACAGTGAAGACTAATGT 57.407 33.333 0.00 0.00 0.00 2.71
2788 5591 6.512415 GCAATTAGAACTAGCTAGCAACCATG 60.512 42.308 20.91 12.39 0.00 3.66
2789 5592 5.529060 GCAATTAGAACTAGCTAGCAACCAT 59.471 40.000 20.91 5.19 0.00 3.55
2790 5593 4.876107 GCAATTAGAACTAGCTAGCAACCA 59.124 41.667 20.91 2.90 0.00 3.67
2791 5594 4.876107 TGCAATTAGAACTAGCTAGCAACC 59.124 41.667 20.91 7.34 0.00 3.77
2792 5595 6.258727 TGATGCAATTAGAACTAGCTAGCAAC 59.741 38.462 20.91 11.77 32.83 4.17
2793 5596 6.348498 TGATGCAATTAGAACTAGCTAGCAA 58.652 36.000 20.91 9.96 32.83 3.91
2794 5597 5.917462 TGATGCAATTAGAACTAGCTAGCA 58.083 37.500 20.91 10.60 0.00 3.49
2798 5601 7.730084 TCTGTATGATGCAATTAGAACTAGCT 58.270 34.615 0.00 0.00 0.00 3.32
2800 5603 8.976471 CACTCTGTATGATGCAATTAGAACTAG 58.024 37.037 0.00 0.00 0.00 2.57
2820 5629 9.722056 GTTAGATAATTAAAACATGGCACTCTG 57.278 33.333 0.00 0.00 0.00 3.35
2879 5691 8.677148 ATTCTATACACACCTAATGCGAAATT 57.323 30.769 0.00 0.00 0.00 1.82
3058 7519 3.085952 ACCCCACACACAGGAATTATG 57.914 47.619 0.00 0.00 0.00 1.90
3078 7540 1.766496 ACCTCGTTCCCACTGAGAAAA 59.234 47.619 0.00 0.00 31.31 2.29
3079 7541 1.420430 ACCTCGTTCCCACTGAGAAA 58.580 50.000 0.00 0.00 31.31 2.52
3088 7552 2.148768 CCAACAAGTAACCTCGTTCCC 58.851 52.381 0.00 0.00 0.00 3.97
3089 7553 3.064931 CTCCAACAAGTAACCTCGTTCC 58.935 50.000 0.00 0.00 0.00 3.62
3122 7586 6.563222 TGGTTAATTAGTACTGTGTTTGCC 57.437 37.500 5.39 0.74 0.00 4.52
3126 7590 5.411669 GCTGCTGGTTAATTAGTACTGTGTT 59.588 40.000 5.39 0.17 0.00 3.32
3150 7629 8.767085 TGCATATCATATATTGCATACATGACG 58.233 33.333 0.00 0.00 39.98 4.35
3152 7631 8.780249 GCTGCATATCATATATTGCATACATGA 58.220 33.333 9.63 0.00 43.51 3.07
3153 7632 8.564574 TGCTGCATATCATATATTGCATACATG 58.435 33.333 9.63 0.00 43.51 3.21
3154 7633 8.685838 TGCTGCATATCATATATTGCATACAT 57.314 30.769 9.63 0.00 43.51 2.29
3155 7634 8.564574 CATGCTGCATATCATATATTGCATACA 58.435 33.333 15.78 10.99 43.51 2.29
3156 7635 7.537649 GCATGCTGCATATCATATATTGCATAC 59.462 37.037 15.78 6.75 43.51 2.39
3174 7706 4.481930 TTATATACCGTTTGCATGCTGC 57.518 40.909 20.33 7.88 45.29 5.25


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

AutoCloner maintained by Alex Coulton.