Multiple sequence alignment - TraesCS3A01G360500

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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 TraesCS3A01G360500 chr3A 100.000 3233 0 0 1 3233 608342551 608339319 0.000000e+00 5971.0
1 TraesCS3A01G360500 chr3B 89.667 2255 143 42 528 2726 618436392 618434172 0.000000e+00 2791.0
2 TraesCS3A01G360500 chr3B 92.719 467 30 4 2771 3233 618434093 618433627 0.000000e+00 671.0
3 TraesCS3A01G360500 chr3B 81.912 387 39 16 153 531 618439054 618438691 6.780000e-77 298.0
4 TraesCS3A01G360500 chr3D 92.021 965 36 10 770 1704 465023264 465022311 0.000000e+00 1317.0
5 TraesCS3A01G360500 chr3D 96.884 706 20 2 1691 2395 465022294 465021590 0.000000e+00 1181.0
6 TraesCS3A01G360500 chr3D 86.457 731 92 4 3 727 465024212 465023483 0.000000e+00 795.0
7 TraesCS3A01G360500 chr3D 85.714 406 49 8 2835 3233 374029876 374030279 1.390000e-113 420.0
8 TraesCS3A01G360500 chr4B 81.818 781 102 27 2482 3233 660777485 660778254 1.270000e-173 619.0
9 TraesCS3A01G360500 chr4B 81.818 781 102 27 2482 3233 660787328 660788097 1.270000e-173 619.0
10 TraesCS3A01G360500 chr4B 81.690 781 103 27 2482 3233 660772686 660773455 5.930000e-172 614.0
11 TraesCS3A01G360500 chr4A 90.719 334 29 2 1897 2229 629468087 629468419 8.230000e-121 444.0
12 TraesCS3A01G360500 chr5D 89.459 351 31 6 1897 2244 539034441 539034094 3.830000e-119 438.0
13 TraesCS3A01G360500 chr2A 84.165 461 61 10 2782 3233 10347314 10346857 1.380000e-118 436.0
14 TraesCS3A01G360500 chr2A 84.130 460 63 8 2782 3233 10352135 10351678 1.380000e-118 436.0
15 TraesCS3A01G360500 chr2A 84.165 461 61 10 2782 3233 10361780 10361323 1.380000e-118 436.0
16 TraesCS3A01G360500 chr2A 86.070 402 52 4 2835 3233 10356901 10356501 2.300000e-116 429.0
17 TraesCS3A01G360500 chr5B 89.174 351 32 6 1897 2244 680612635 680612288 1.780000e-117 433.0
18 TraesCS3A01G360500 chr4D 100.000 29 0 0 2779 2807 4621839 4621867 2.000000e-03 54.7


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 TraesCS3A01G360500 chr3A 608339319 608342551 3232 True 5971.000000 5971 100.000000 1 3233 1 chr3A.!!$R1 3232
1 TraesCS3A01G360500 chr3B 618433627 618439054 5427 True 1253.333333 2791 88.099333 153 3233 3 chr3B.!!$R1 3080
2 TraesCS3A01G360500 chr3D 465021590 465024212 2622 True 1097.666667 1317 91.787333 3 2395 3 chr3D.!!$R1 2392
3 TraesCS3A01G360500 chr4B 660777485 660778254 769 False 619.000000 619 81.818000 2482 3233 1 chr4B.!!$F2 751
4 TraesCS3A01G360500 chr4B 660787328 660788097 769 False 619.000000 619 81.818000 2482 3233 1 chr4B.!!$F3 751
5 TraesCS3A01G360500 chr4B 660772686 660773455 769 False 614.000000 614 81.690000 2482 3233 1 chr4B.!!$F1 751

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
168 170 0.112995 AAAGCATGGGGTCTGAGCAA 59.887 50.0 9.30 0.0 0.00 3.91 F
506 515 0.323725 CCACCATGGTCCTTTGGGAG 60.324 60.0 16.53 0.0 43.12 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1779 4352 0.694771 ATGAGGAGTGCAGGCTTTGA 59.305 50.000 0.0 0.0 0.00 2.69 R
2445 5019 1.069973 ACATCAACATGCACAACGTCG 60.070 47.619 0.0 0.0 32.57 5.12 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
39 40 4.533815 ACGACATATGTAGAGTCCTCCAA 58.466 43.478 21.06 0.00 0.00 3.53
43 44 6.412362 ACATATGTAGAGTCCTCCAACATC 57.588 41.667 6.56 0.00 37.65 3.06
45 46 2.803956 TGTAGAGTCCTCCAACATCGT 58.196 47.619 0.00 0.00 0.00 3.73
47 48 3.945921 TGTAGAGTCCTCCAACATCGTAG 59.054 47.826 0.00 0.00 0.00 3.51
66 68 2.830370 GGGGCTGCCCTCAATTCG 60.830 66.667 34.99 0.00 44.66 3.34
69 71 2.115291 GGCTGCCCTCAATTCGGTC 61.115 63.158 7.66 0.00 0.00 4.79
76 78 1.614317 CCCTCAATTCGGTCCAAGCTT 60.614 52.381 0.00 0.00 0.00 3.74
82 84 0.611714 TTCGGTCCAAGCTTAGGTCC 59.388 55.000 15.89 15.89 0.00 4.46
90 92 0.417841 AAGCTTAGGTCCCCTCAGGA 59.582 55.000 0.00 0.00 44.91 3.86
100 102 1.428912 TCCCCTCAGGAGCAAATGTTT 59.571 47.619 0.00 0.00 40.93 2.83
103 105 2.629617 CCCTCAGGAGCAAATGTTTGTT 59.370 45.455 0.00 1.15 36.45 2.83
109 111 3.450457 AGGAGCAAATGTTTGTTGGAACA 59.550 39.130 7.26 0.00 43.08 3.18
133 135 3.304911 TGTTTCAGGTCCATTTGTGGA 57.695 42.857 0.00 0.00 35.23 4.02
168 170 0.112995 AAAGCATGGGGTCTGAGCAA 59.887 50.000 9.30 0.00 0.00 3.91
184 186 3.989167 TGAGCAAATTGCAAACATGCTAC 59.011 39.130 26.77 21.31 46.93 3.58
185 187 2.988493 AGCAAATTGCAAACATGCTACG 59.012 40.909 26.02 2.77 45.68 3.51
198 200 1.803334 TGCTACGGAATTTGCGAAGT 58.197 45.000 17.44 0.00 34.49 3.01
204 206 1.243902 GGAATTTGCGAAGTGGGACA 58.756 50.000 0.00 0.00 0.00 4.02
237 239 2.136026 GGGTCCAACCATAAGAGGGAT 58.864 52.381 0.00 0.00 41.02 3.85
249 251 6.161170 ACCATAAGAGGGATCCTTCTTCATTT 59.839 38.462 35.10 18.75 31.76 2.32
261 263 5.053145 CCTTCTTCATTTCCTATGGAGACG 58.947 45.833 0.00 0.00 33.63 4.18
267 269 1.195115 TTCCTATGGAGACGCTGCTT 58.805 50.000 0.00 0.00 31.21 3.91
269 271 0.461548 CCTATGGAGACGCTGCTTCA 59.538 55.000 8.91 0.00 0.00 3.02
288 290 2.743664 TCAAAGACGGATCACATGCTTG 59.256 45.455 0.00 0.00 0.00 4.01
292 294 0.324614 ACGGATCACATGCTTGACCA 59.675 50.000 6.60 0.00 0.00 4.02
297 299 4.202441 GGATCACATGCTTGACCAACTAT 58.798 43.478 6.60 0.00 0.00 2.12
307 309 7.187824 TGCTTGACCAACTATAGAGATTTCT 57.812 36.000 6.78 0.00 37.46 2.52
326 328 6.688073 TTTCTAGAATCAGAAGTGGGAGTT 57.312 37.500 5.89 0.00 35.99 3.01
337 339 2.448453 AGTGGGAGTTCTCCTTACGAG 58.552 52.381 16.95 0.00 40.30 4.18
342 344 2.029290 GGAGTTCTCCTTACGAGCACAA 60.029 50.000 11.20 0.00 37.22 3.33
378 380 6.062095 ACGACCCTGCATATATTTAGCTTTT 58.938 36.000 0.00 0.00 0.00 2.27
379 381 6.546034 ACGACCCTGCATATATTTAGCTTTTT 59.454 34.615 0.00 0.00 0.00 1.94
380 382 7.717875 ACGACCCTGCATATATTTAGCTTTTTA 59.282 33.333 0.00 0.00 0.00 1.52
381 383 8.564574 CGACCCTGCATATATTTAGCTTTTTAA 58.435 33.333 0.00 0.00 0.00 1.52
452 454 1.614317 GCAGGCTCACAACATAAGGGT 60.614 52.381 0.00 0.00 0.00 4.34
463 465 5.649395 CACAACATAAGGGTCAGATTCATGT 59.351 40.000 0.00 0.00 0.00 3.21
469 478 1.207089 GGGTCAGATTCATGTGTCGGA 59.793 52.381 0.00 0.00 0.00 4.55
506 515 0.323725 CCACCATGGTCCTTTGGGAG 60.324 60.000 16.53 0.00 43.12 4.30
533 2844 7.611467 GCAGATATCAACCCATTTCACCATATA 59.389 37.037 5.32 0.00 0.00 0.86
559 2870 1.404391 GGCAGCTTGGATTGATGACTG 59.596 52.381 0.00 0.00 0.00 3.51
564 2875 2.618816 GCTTGGATTGATGACTGGGTCA 60.619 50.000 2.80 2.80 46.90 4.02
579 2890 1.482593 GGGTCATCGAGATTCAGTGGT 59.517 52.381 0.00 0.00 0.00 4.16
583 2894 3.064958 GTCATCGAGATTCAGTGGTCGTA 59.935 47.826 0.00 0.00 34.07 3.43
612 2923 5.588648 CCGACATTCCATATTGTTTAGGTGT 59.411 40.000 0.00 0.00 0.00 4.16
621 2932 6.316390 CCATATTGTTTAGGTGTTGTCCTCTC 59.684 42.308 0.00 0.00 38.86 3.20
631 2942 2.293677 TGTTGTCCTCTCTGAAGACGAC 59.706 50.000 12.34 12.34 42.73 4.34
648 2959 4.159135 AGACGACGATTGTGGGTATTACTT 59.841 41.667 0.00 0.00 0.00 2.24
685 2996 1.264020 CATTTGTGAGGTCGGTGTGTG 59.736 52.381 0.00 0.00 0.00 3.82
687 2998 1.331399 TTGTGAGGTCGGTGTGTGGA 61.331 55.000 0.00 0.00 0.00 4.02
727 3042 3.052036 GTCATGTGTTGTTCAACATGCC 58.948 45.455 18.99 9.05 36.49 4.40
730 3045 0.383949 GTGTTGTTCAACATGCCGGT 59.616 50.000 18.99 0.00 34.86 5.28
735 3050 1.604755 TGTTCAACATGCCGGTTACAC 59.395 47.619 1.90 0.00 0.00 2.90
747 3062 4.002316 GCCGGTTACACTTATTTGTACCA 58.998 43.478 1.90 0.00 31.53 3.25
748 3063 4.093850 GCCGGTTACACTTATTTGTACCAG 59.906 45.833 1.90 0.00 31.53 4.00
750 3065 4.201647 CGGTTACACTTATTTGTACCAGCG 60.202 45.833 0.00 0.00 31.53 5.18
751 3066 4.931002 GGTTACACTTATTTGTACCAGCGA 59.069 41.667 0.00 0.00 31.53 4.93
752 3067 5.063060 GGTTACACTTATTTGTACCAGCGAG 59.937 44.000 0.00 0.00 31.53 5.03
754 3069 4.243270 ACACTTATTTGTACCAGCGAGAC 58.757 43.478 0.00 0.00 0.00 3.36
790 3281 5.439721 TCACCCATTATCACAAATCCAGAG 58.560 41.667 0.00 0.00 0.00 3.35
867 3359 4.978099 ACAAATCTGGTGAGATGTGACTT 58.022 39.130 8.86 0.00 44.21 3.01
868 3360 5.380043 ACAAATCTGGTGAGATGTGACTTT 58.620 37.500 8.86 0.00 44.21 2.66
905 3405 7.666623 ACGGAATTTACACTTGAAATTTCCAT 58.333 30.769 15.48 0.00 36.78 3.41
906 3406 7.812669 ACGGAATTTACACTTGAAATTTCCATC 59.187 33.333 15.48 0.00 36.78 3.51
953 3470 3.631250 TCTCAAACCTAAATGGATGGCC 58.369 45.455 0.00 0.00 39.71 5.36
962 3479 3.303351 AAATGGATGGCCTAGAAGTGG 57.697 47.619 3.32 0.00 34.31 4.00
1056 3573 3.515562 ACACTCCATTCACTCTCTTCCT 58.484 45.455 0.00 0.00 0.00 3.36
1060 3577 2.493675 TCCATTCACTCTCTTCCTCGTG 59.506 50.000 0.00 0.00 0.00 4.35
1098 3615 2.429610 TCACCTCCGCCTGTATTTCTAC 59.570 50.000 0.00 0.00 0.00 2.59
1113 3630 1.001248 CTACTTCCCCGTCCCCTCA 59.999 63.158 0.00 0.00 0.00 3.86
1114 3631 1.305549 TACTTCCCCGTCCCCTCAC 60.306 63.158 0.00 0.00 0.00 3.51
1328 3858 2.322355 AGTGATGTATGAGCACCTGC 57.678 50.000 0.00 0.00 42.32 4.85
1350 3880 5.645067 TGCTCATAAGTTTCTGAATCCAGTG 59.355 40.000 0.00 0.00 41.16 3.66
1351 3881 5.645497 GCTCATAAGTTTCTGAATCCAGTGT 59.355 40.000 0.00 0.00 41.16 3.55
1352 3882 6.402983 GCTCATAAGTTTCTGAATCCAGTGTG 60.403 42.308 0.00 0.00 41.16 3.82
1353 3883 5.412594 TCATAAGTTTCTGAATCCAGTGTGC 59.587 40.000 0.00 0.00 41.16 4.57
1354 3884 2.146342 AGTTTCTGAATCCAGTGTGCG 58.854 47.619 0.00 0.00 41.16 5.34
1355 3885 1.873591 GTTTCTGAATCCAGTGTGCGT 59.126 47.619 0.00 0.00 41.16 5.24
1356 3886 1.511850 TTCTGAATCCAGTGTGCGTG 58.488 50.000 0.00 0.00 41.16 5.34
1357 3887 0.678950 TCTGAATCCAGTGTGCGTGA 59.321 50.000 0.00 0.00 41.16 4.35
1358 3888 0.792640 CTGAATCCAGTGTGCGTGAC 59.207 55.000 0.00 0.00 35.70 3.67
1421 3951 4.277515 TGGGAGAGTTCAGAATTGACTG 57.722 45.455 0.00 0.00 39.02 3.51
1591 4121 4.689612 TCTTCCACATATTCAGGGTAGC 57.310 45.455 0.00 0.00 0.00 3.58
1728 4301 1.667724 GACATGCCATTCTGAACCTCG 59.332 52.381 0.00 0.00 0.00 4.63
2229 4802 1.339151 GGCCTCCAGTTCGTCAAGAAT 60.339 52.381 0.00 0.00 41.49 2.40
2320 4893 5.670792 AACGGAGGTGAATGATTGTACTA 57.329 39.130 0.00 0.00 0.00 1.82
2342 4915 7.099764 ACTAAAGGTGTCATGTGTATCTCTTG 58.900 38.462 0.00 0.00 0.00 3.02
2422 4996 4.499037 AAACCGGTAGAAAACAAGCATC 57.501 40.909 8.00 0.00 0.00 3.91
2423 4997 3.418684 ACCGGTAGAAAACAAGCATCT 57.581 42.857 4.49 0.00 0.00 2.90
2424 4998 3.074412 ACCGGTAGAAAACAAGCATCTG 58.926 45.455 4.49 0.00 0.00 2.90
2425 4999 2.159517 CCGGTAGAAAACAAGCATCTGC 60.160 50.000 0.00 0.00 42.49 4.26
2445 5019 2.262915 CTCAGACGCACCAGTCCC 59.737 66.667 0.00 0.00 41.83 4.46
2462 5036 1.502990 CCCGACGTTGTGCATGTTGA 61.503 55.000 1.30 0.00 0.00 3.18
2463 5037 0.516877 CCGACGTTGTGCATGTTGAT 59.483 50.000 1.30 0.00 0.00 2.57
2464 5038 1.594517 CGACGTTGTGCATGTTGATG 58.405 50.000 0.00 0.00 0.00 3.07
2466 5040 2.601979 CGACGTTGTGCATGTTGATGTT 60.602 45.455 0.00 0.00 31.50 2.71
2467 5041 2.720578 GACGTTGTGCATGTTGATGTTG 59.279 45.455 0.00 0.00 31.50 3.33
2468 5042 2.098934 ACGTTGTGCATGTTGATGTTGT 59.901 40.909 0.00 0.00 31.50 3.32
2469 5043 2.468409 CGTTGTGCATGTTGATGTTGTG 59.532 45.455 0.00 0.00 31.50 3.33
2472 5046 4.907879 TGTGCATGTTGATGTTGTGTTA 57.092 36.364 0.00 0.00 31.50 2.41
2473 5047 5.254339 TGTGCATGTTGATGTTGTGTTAA 57.746 34.783 0.00 0.00 31.50 2.01
2474 5048 5.039984 TGTGCATGTTGATGTTGTGTTAAC 58.960 37.500 0.00 0.00 31.50 2.01
2527 5114 6.954487 TCTGAATAATAGCCAGAAGTACGA 57.046 37.500 0.00 0.00 34.38 3.43
2532 5119 8.803235 TGAATAATAGCCAGAAGTACGATATGT 58.197 33.333 0.00 0.00 0.00 2.29
2533 5120 9.640963 GAATAATAGCCAGAAGTACGATATGTT 57.359 33.333 0.00 0.00 0.00 2.71
2537 5124 5.730550 AGCCAGAAGTACGATATGTTTTCA 58.269 37.500 0.00 0.00 0.00 2.69
2556 5143 1.299648 TGCTGCGGCAGAATAGGTT 59.700 52.632 32.72 0.00 44.28 3.50
2586 5173 7.519328 GCGTTTAATTCTCTGTAAGTTGTTGGA 60.519 37.037 0.00 0.00 33.76 3.53
2596 5183 2.910688 AGTTGTTGGACACGATCAGT 57.089 45.000 0.00 0.00 0.00 3.41
2617 5204 3.164977 TGGGATGGCGCGGGATTA 61.165 61.111 8.83 0.00 0.00 1.75
2628 5215 1.828331 GCGGGATTAACGGATCGTGC 61.828 60.000 0.00 0.00 39.99 5.34
2629 5216 0.528901 CGGGATTAACGGATCGTGCA 60.529 55.000 0.00 0.00 39.99 4.57
2641 5228 0.798776 ATCGTGCACAGCTAGTTTGC 59.201 50.000 18.64 5.65 36.76 3.68
2646 5233 2.744202 GTGCACAGCTAGTTTGCTATGT 59.256 45.455 13.17 0.00 39.44 2.29
2708 5302 2.710698 CGTCGCCAAAACACCGTT 59.289 55.556 0.00 0.00 0.00 4.44
2713 5307 0.317519 CGCCAAAACACCGTTTCCTC 60.318 55.000 0.00 0.00 0.00 3.71
2714 5308 1.029681 GCCAAAACACCGTTTCCTCT 58.970 50.000 0.00 0.00 0.00 3.69
2715 5309 1.407618 GCCAAAACACCGTTTCCTCTT 59.592 47.619 0.00 0.00 0.00 2.85
2716 5310 2.159156 GCCAAAACACCGTTTCCTCTTT 60.159 45.455 0.00 0.00 0.00 2.52
2717 5311 3.443976 CCAAAACACCGTTTCCTCTTTG 58.556 45.455 0.00 0.00 0.00 2.77
2718 5312 3.119280 CCAAAACACCGTTTCCTCTTTGT 60.119 43.478 0.00 0.00 0.00 2.83
2719 5313 3.775661 AAACACCGTTTCCTCTTTGTG 57.224 42.857 0.00 0.00 0.00 3.33
2720 5314 2.413310 ACACCGTTTCCTCTTTGTGT 57.587 45.000 0.00 0.00 32.48 3.72
2721 5315 2.718563 ACACCGTTTCCTCTTTGTGTT 58.281 42.857 0.00 0.00 33.47 3.32
2722 5316 2.681344 ACACCGTTTCCTCTTTGTGTTC 59.319 45.455 0.00 0.00 33.47 3.18
2723 5317 2.943033 CACCGTTTCCTCTTTGTGTTCT 59.057 45.455 0.00 0.00 0.00 3.01
2724 5318 3.377172 CACCGTTTCCTCTTTGTGTTCTT 59.623 43.478 0.00 0.00 0.00 2.52
2725 5319 3.626217 ACCGTTTCCTCTTTGTGTTCTTC 59.374 43.478 0.00 0.00 0.00 2.87
2726 5320 3.877508 CCGTTTCCTCTTTGTGTTCTTCT 59.122 43.478 0.00 0.00 0.00 2.85
2727 5321 4.335594 CCGTTTCCTCTTTGTGTTCTTCTT 59.664 41.667 0.00 0.00 0.00 2.52
2728 5322 5.266242 CGTTTCCTCTTTGTGTTCTTCTTG 58.734 41.667 0.00 0.00 0.00 3.02
2729 5323 5.163754 CGTTTCCTCTTTGTGTTCTTCTTGT 60.164 40.000 0.00 0.00 0.00 3.16
2730 5324 6.621613 GTTTCCTCTTTGTGTTCTTCTTGTT 58.378 36.000 0.00 0.00 0.00 2.83
2731 5325 7.413657 CGTTTCCTCTTTGTGTTCTTCTTGTTA 60.414 37.037 0.00 0.00 0.00 2.41
2732 5326 7.553881 TTCCTCTTTGTGTTCTTCTTGTTAG 57.446 36.000 0.00 0.00 0.00 2.34
2735 5329 7.610305 TCCTCTTTGTGTTCTTCTTGTTAGTTT 59.390 33.333 0.00 0.00 0.00 2.66
2749 5343 8.330466 TCTTGTTAGTTTTGTGTTCTTCAGAA 57.670 30.769 0.00 0.00 0.00 3.02
2813 5471 2.751259 GCATCAGAGCCATGTTTCAGAA 59.249 45.455 0.00 0.00 0.00 3.02
2822 5480 2.270923 CATGTTTCAGAAGCGATCCGA 58.729 47.619 0.00 0.00 0.00 4.55
2845 5504 1.352687 GCTGGAAAAGAGGAGGAGGTT 59.647 52.381 0.00 0.00 0.00 3.50
2868 5527 4.585526 GCGGTGATCGGCGATGGA 62.586 66.667 29.20 10.78 39.69 3.41
2893 5552 0.104855 CATCGCCGAAGAGGGATCAA 59.895 55.000 0.00 0.00 41.48 2.57
2896 5555 1.209504 TCGCCGAAGAGGGATCAAAAT 59.790 47.619 0.00 0.00 41.48 1.82
2899 5558 3.142174 GCCGAAGAGGGATCAAAATAGG 58.858 50.000 0.00 0.00 41.48 2.57
2904 5563 0.178990 AGGGATCAAAATAGGGGCGC 60.179 55.000 0.00 0.00 0.00 6.53
2905 5564 0.467290 GGGATCAAAATAGGGGCGCA 60.467 55.000 10.83 0.00 0.00 6.09
2906 5565 1.620822 GGATCAAAATAGGGGCGCAT 58.379 50.000 10.83 0.00 0.00 4.73
2907 5566 1.541588 GGATCAAAATAGGGGCGCATC 59.458 52.381 10.83 0.00 0.00 3.91
2908 5567 2.229792 GATCAAAATAGGGGCGCATCA 58.770 47.619 10.83 0.00 0.00 3.07
3009 5672 0.878961 GTGGCGTCCCGATCCAATAC 60.879 60.000 0.00 0.00 0.00 1.89
3033 5696 4.155826 CCAATGCTCAACGATTCCAACTAA 59.844 41.667 0.00 0.00 0.00 2.24
3039 5702 5.223449 TCAACGATTCCAACTAAGGTCTT 57.777 39.130 0.00 0.00 0.00 3.01
3115 5778 2.049063 GCACTGCGGAGTTCGACT 60.049 61.111 6.93 0.00 42.43 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.421056 TGGAGGACTCTACATATGTCGTTTT 59.579 40.000 12.68 1.56 0.00 2.43
19 20 5.854010 TGTTGGAGGACTCTACATATGTC 57.146 43.478 12.68 0.00 33.08 3.06
24 25 3.366396 ACGATGTTGGAGGACTCTACAT 58.634 45.455 15.37 15.37 37.45 2.29
25 26 2.803956 ACGATGTTGGAGGACTCTACA 58.196 47.619 9.16 9.16 30.51 2.74
33 34 1.830145 CCCCCTACGATGTTGGAGG 59.170 63.158 0.00 0.00 30.33 4.30
54 56 0.322456 CTTGGACCGAATTGAGGGCA 60.322 55.000 4.92 0.00 38.96 5.36
55 57 1.657751 GCTTGGACCGAATTGAGGGC 61.658 60.000 2.09 0.00 35.57 5.19
82 84 2.242043 ACAAACATTTGCTCCTGAGGG 58.758 47.619 0.00 0.00 41.79 4.30
90 92 3.450457 TCCTGTTCCAACAAACATTTGCT 59.550 39.130 4.25 0.00 41.79 3.91
91 93 3.791245 TCCTGTTCCAACAAACATTTGC 58.209 40.909 4.25 0.00 41.79 3.68
100 102 3.221771 CCTGAAACATCCTGTTCCAACA 58.778 45.455 0.00 0.00 40.14 3.33
103 105 2.224769 GGACCTGAAACATCCTGTTCCA 60.225 50.000 0.00 0.00 40.14 3.53
109 111 3.828451 CACAAATGGACCTGAAACATCCT 59.172 43.478 0.00 0.00 33.34 3.24
125 127 2.046314 CCTCGGCCGTCCACAAAT 60.046 61.111 27.15 0.00 0.00 2.32
133 135 4.572571 TTTGGTTGCCTCGGCCGT 62.573 61.111 27.15 0.00 41.09 5.68
184 186 0.168128 GTCCCACTTCGCAAATTCCG 59.832 55.000 0.00 0.00 0.00 4.30
185 187 1.068541 GTGTCCCACTTCGCAAATTCC 60.069 52.381 0.00 0.00 0.00 3.01
198 200 1.619654 CATGGCTTGAAAGTGTCCCA 58.380 50.000 0.00 0.00 0.00 4.37
204 206 0.482446 TGGACCCATGGCTTGAAAGT 59.518 50.000 6.09 0.00 0.00 2.66
228 230 5.973124 AGGAAATGAAGAAGGATCCCTCTTA 59.027 40.000 22.99 13.10 30.89 2.10
231 233 4.787135 AGGAAATGAAGAAGGATCCCTC 57.213 45.455 8.55 4.91 30.89 4.30
237 239 5.163405 CGTCTCCATAGGAAATGAAGAAGGA 60.163 44.000 0.00 0.00 0.00 3.36
249 251 0.747255 GAAGCAGCGTCTCCATAGGA 59.253 55.000 0.37 0.00 0.00 2.94
261 263 1.129437 GTGATCCGTCTTTGAAGCAGC 59.871 52.381 0.00 0.00 0.00 5.25
267 269 2.743664 CAAGCATGTGATCCGTCTTTGA 59.256 45.455 0.00 0.00 0.00 2.69
269 271 2.744202 GTCAAGCATGTGATCCGTCTTT 59.256 45.455 0.00 0.00 0.00 2.52
297 299 8.061920 TCCCACTTCTGATTCTAGAAATCTCTA 58.938 37.037 9.71 0.00 36.34 2.43
307 309 4.712337 GGAGAACTCCCACTTCTGATTCTA 59.288 45.833 9.50 0.00 43.94 2.10
326 328 3.814577 GCTTGTGCTCGTAAGGAGA 57.185 52.632 0.00 0.00 46.23 3.71
337 339 1.222113 GTCCCCTCCTAGCTTGTGC 59.778 63.158 0.00 0.00 40.05 4.57
342 344 2.279408 GGTCGTCCCCTCCTAGCT 59.721 66.667 0.00 0.00 0.00 3.32
352 354 3.933332 GCTAAATATATGCAGGGTCGTCC 59.067 47.826 0.00 0.00 0.00 4.79
378 380 3.056179 GGGCTTATGGCTGCAACTTTTAA 60.056 43.478 0.50 0.00 41.46 1.52
379 381 2.495669 GGGCTTATGGCTGCAACTTTTA 59.504 45.455 0.50 0.00 41.46 1.52
380 382 1.276138 GGGCTTATGGCTGCAACTTTT 59.724 47.619 0.50 0.00 41.46 2.27
381 383 0.897621 GGGCTTATGGCTGCAACTTT 59.102 50.000 0.50 0.00 41.46 2.66
452 454 3.676291 TGTTCCGACACATGAATCTGA 57.324 42.857 0.00 0.00 0.00 3.27
463 465 6.350445 GGTTTAGGTATTCTAGTGTTCCGACA 60.350 42.308 0.00 0.00 0.00 4.35
469 478 6.691255 TGGTGGTTTAGGTATTCTAGTGTT 57.309 37.500 0.00 0.00 0.00 3.32
506 515 3.319122 GGTGAAATGGGTTGATATCTGCC 59.681 47.826 3.98 5.99 0.00 4.85
533 2844 4.020039 TCATCAATCCAAGCTGCCAAAAAT 60.020 37.500 0.00 0.00 0.00 1.82
559 2870 1.482593 ACCACTGAATCTCGATGACCC 59.517 52.381 0.00 0.00 0.00 4.46
564 2875 3.280295 AGTACGACCACTGAATCTCGAT 58.720 45.455 0.00 0.00 0.00 3.59
579 2890 1.252215 TGGAATGTCGGCCAGTACGA 61.252 55.000 2.24 0.00 38.13 3.43
583 2894 2.092429 ACAATATGGAATGTCGGCCAGT 60.092 45.455 2.24 0.00 37.64 4.00
621 2932 1.336887 ACCCACAATCGTCGTCTTCAG 60.337 52.381 0.00 0.00 0.00 3.02
631 2942 5.646360 ACCAGAAAAGTAATACCCACAATCG 59.354 40.000 0.00 0.00 0.00 3.34
648 2959 4.898861 ACAAATGCTAAAAGGGACCAGAAA 59.101 37.500 0.00 0.00 0.00 2.52
685 2996 6.607689 TGACAAAACATCGAACACATAATCC 58.392 36.000 0.00 0.00 0.00 3.01
687 2998 7.538334 CACATGACAAAACATCGAACACATAAT 59.462 33.333 0.00 0.00 0.00 1.28
727 3042 4.201647 CGCTGGTACAAATAAGTGTAACCG 60.202 45.833 0.00 0.00 40.38 4.44
730 3045 5.865552 GTCTCGCTGGTACAAATAAGTGTAA 59.134 40.000 0.00 0.00 38.70 2.41
750 3065 4.330620 TGGGTGATTTTATTAACGCGTCTC 59.669 41.667 14.44 0.00 0.00 3.36
751 3066 4.255301 TGGGTGATTTTATTAACGCGTCT 58.745 39.130 14.44 5.62 0.00 4.18
752 3067 4.603231 TGGGTGATTTTATTAACGCGTC 57.397 40.909 14.44 0.00 0.00 5.19
754 3069 7.322699 GTGATAATGGGTGATTTTATTAACGCG 59.677 37.037 3.53 3.53 0.00 6.01
834 3325 7.394016 TCTCACCAGATTTGTAGCTGAAATTA 58.606 34.615 0.00 0.00 40.22 1.40
842 3333 4.331168 GTCACATCTCACCAGATTTGTAGC 59.669 45.833 0.00 0.00 37.25 3.58
905 3405 4.346730 TCCATCTTAAAGGACCACGTAGA 58.653 43.478 0.00 0.00 0.00 2.59
906 3406 4.730949 TCCATCTTAAAGGACCACGTAG 57.269 45.455 0.00 0.00 0.00 3.51
953 3470 2.125106 GCCCGTGGCCACTTCTAG 60.125 66.667 32.28 16.85 44.06 2.43
1098 3615 2.284699 AGTGAGGGGACGGGGAAG 60.285 66.667 0.00 0.00 0.00 3.46
1113 3630 4.067944 AGGATTGGTGTCTAGAAGGAGT 57.932 45.455 0.00 0.00 0.00 3.85
1114 3631 4.714308 AGAAGGATTGGTGTCTAGAAGGAG 59.286 45.833 0.00 0.00 0.00 3.69
1328 3858 6.402983 GCACACTGGATTCAGAAACTTATGAG 60.403 42.308 8.39 0.00 43.49 2.90
1350 3880 4.360027 CAGCACGCAGTCACGCAC 62.360 66.667 0.00 0.00 41.61 5.34
1351 3881 2.763627 ATACAGCACGCAGTCACGCA 62.764 55.000 0.00 0.00 41.61 5.24
1352 3882 2.094659 ATACAGCACGCAGTCACGC 61.095 57.895 0.00 0.00 41.61 5.34
1353 3883 1.704010 CATACAGCACGCAGTCACG 59.296 57.895 0.00 0.00 41.61 4.35
1354 3884 1.421485 GCATACAGCACGCAGTCAC 59.579 57.895 0.00 0.00 41.61 3.67
1355 3885 3.874873 GCATACAGCACGCAGTCA 58.125 55.556 0.00 0.00 41.61 3.41
1421 3951 2.097142 CAGCCTTAACAGAGAAGCATGC 59.903 50.000 10.51 10.51 0.00 4.06
1591 4121 8.469309 AAATATAGATTTGGACATCACAAGGG 57.531 34.615 0.00 0.00 33.86 3.95
1779 4352 0.694771 ATGAGGAGTGCAGGCTTTGA 59.305 50.000 0.00 0.00 0.00 2.69
2302 4875 6.879458 ACACCTTTAGTACAATCATTCACCTC 59.121 38.462 0.00 0.00 0.00 3.85
2320 4893 5.702670 CACAAGAGATACACATGACACCTTT 59.297 40.000 0.00 0.00 0.00 3.11
2342 4915 7.985634 ATTTCACACAATGTCAAAGTTACAC 57.014 32.000 0.00 0.00 0.00 2.90
2392 4966 4.426736 TTTCTACCGGTTTTCCTCAGTT 57.573 40.909 15.04 0.00 37.95 3.16
2394 4968 4.131596 TGTTTTCTACCGGTTTTCCTCAG 58.868 43.478 15.04 1.14 37.95 3.35
2425 4999 1.442857 GACTGGTGCGTCTGAGTCG 60.443 63.158 0.00 0.00 0.00 4.18
2426 5000 1.080434 GGACTGGTGCGTCTGAGTC 60.080 63.158 0.00 0.00 35.15 3.36
2427 5001 2.574955 GGGACTGGTGCGTCTGAGT 61.575 63.158 0.00 0.00 34.38 3.41
2428 5002 2.262915 GGGACTGGTGCGTCTGAG 59.737 66.667 0.00 0.00 34.38 3.35
2429 5003 3.680786 CGGGACTGGTGCGTCTGA 61.681 66.667 0.00 0.00 34.38 3.27
2430 5004 3.680786 TCGGGACTGGTGCGTCTG 61.681 66.667 0.00 0.00 34.38 3.51
2431 5005 3.681835 GTCGGGACTGGTGCGTCT 61.682 66.667 0.00 0.00 34.38 4.18
2434 5008 4.657824 AACGTCGGGACTGGTGCG 62.658 66.667 0.00 0.00 0.00 5.34
2435 5009 3.041940 CAACGTCGGGACTGGTGC 61.042 66.667 0.00 0.00 0.00 5.01
2436 5010 1.954146 CACAACGTCGGGACTGGTG 60.954 63.158 0.00 7.00 0.00 4.17
2437 5011 2.420043 CACAACGTCGGGACTGGT 59.580 61.111 0.00 0.00 0.00 4.00
2438 5012 3.041940 GCACAACGTCGGGACTGG 61.042 66.667 0.00 0.00 0.00 4.00
2439 5013 1.667830 ATGCACAACGTCGGGACTG 60.668 57.895 0.00 0.00 0.00 3.51
2440 5014 1.667830 CATGCACAACGTCGGGACT 60.668 57.895 0.00 0.00 0.00 3.85
2445 5019 1.069973 ACATCAACATGCACAACGTCG 60.070 47.619 0.00 0.00 32.57 5.12
2466 5040 7.820386 TGAAGTCTGAAACTAGTTGTTAACACA 59.180 33.333 9.34 7.72 37.17 3.72
2467 5041 8.193250 TGAAGTCTGAAACTAGTTGTTAACAC 57.807 34.615 9.34 4.01 37.17 3.32
2468 5042 8.038944 ACTGAAGTCTGAAACTAGTTGTTAACA 58.961 33.333 9.34 3.59 37.17 2.41
2469 5043 8.421673 ACTGAAGTCTGAAACTAGTTGTTAAC 57.578 34.615 9.34 6.16 37.17 2.01
2472 5046 7.923414 AAACTGAAGTCTGAAACTAGTTGTT 57.077 32.000 9.34 2.02 37.04 2.83
2473 5047 8.258708 ACTAAACTGAAGTCTGAAACTAGTTGT 58.741 33.333 9.34 0.00 37.04 3.32
2474 5048 8.649973 ACTAAACTGAAGTCTGAAACTAGTTG 57.350 34.615 9.34 0.00 37.04 3.16
2527 5114 1.750206 TGCCGCAGCATGAAAACATAT 59.250 42.857 0.00 0.00 46.52 1.78
2556 5143 7.654520 ACAACTTACAGAGAATTAAACGCTACA 59.345 33.333 0.00 0.00 0.00 2.74
2617 5204 0.458543 CTAGCTGTGCACGATCCGTT 60.459 55.000 13.13 0.00 38.32 4.44
2629 5216 2.093973 AGCGACATAGCAAACTAGCTGT 60.094 45.455 0.00 0.00 46.11 4.40
2705 5299 5.163754 ACAAGAAGAACACAAAGAGGAAACG 60.164 40.000 0.00 0.00 0.00 3.60
2708 5302 7.110155 ACTAACAAGAAGAACACAAAGAGGAA 58.890 34.615 0.00 0.00 0.00 3.36
2713 5307 8.638565 CACAAAACTAACAAGAAGAACACAAAG 58.361 33.333 0.00 0.00 0.00 2.77
2714 5308 8.138712 ACACAAAACTAACAAGAAGAACACAAA 58.861 29.630 0.00 0.00 0.00 2.83
2715 5309 7.653647 ACACAAAACTAACAAGAAGAACACAA 58.346 30.769 0.00 0.00 0.00 3.33
2716 5310 7.209471 ACACAAAACTAACAAGAAGAACACA 57.791 32.000 0.00 0.00 0.00 3.72
2717 5311 8.021396 AGAACACAAAACTAACAAGAAGAACAC 58.979 33.333 0.00 0.00 0.00 3.32
2718 5312 8.106247 AGAACACAAAACTAACAAGAAGAACA 57.894 30.769 0.00 0.00 0.00 3.18
2719 5313 8.965986 AAGAACACAAAACTAACAAGAAGAAC 57.034 30.769 0.00 0.00 0.00 3.01
2720 5314 8.788806 TGAAGAACACAAAACTAACAAGAAGAA 58.211 29.630 0.00 0.00 0.00 2.52
2721 5315 8.330466 TGAAGAACACAAAACTAACAAGAAGA 57.670 30.769 0.00 0.00 0.00 2.87
2722 5316 8.450964 TCTGAAGAACACAAAACTAACAAGAAG 58.549 33.333 0.00 0.00 0.00 2.85
2723 5317 8.330466 TCTGAAGAACACAAAACTAACAAGAA 57.670 30.769 0.00 0.00 0.00 2.52
2724 5318 7.915293 TCTGAAGAACACAAAACTAACAAGA 57.085 32.000 0.00 0.00 0.00 3.02
2725 5319 9.573133 AATTCTGAAGAACACAAAACTAACAAG 57.427 29.630 0.00 0.00 36.80 3.16
2726 5320 9.567848 GAATTCTGAAGAACACAAAACTAACAA 57.432 29.630 0.00 0.00 36.80 2.83
2727 5321 8.735315 TGAATTCTGAAGAACACAAAACTAACA 58.265 29.630 7.05 0.00 36.80 2.41
2728 5322 9.226345 CTGAATTCTGAAGAACACAAAACTAAC 57.774 33.333 7.05 0.00 36.80 2.34
2729 5323 9.173021 TCTGAATTCTGAAGAACACAAAACTAA 57.827 29.630 12.17 0.00 36.80 2.24
2730 5324 8.731275 TCTGAATTCTGAAGAACACAAAACTA 57.269 30.769 12.17 0.00 36.80 2.24
2731 5325 7.630242 TCTGAATTCTGAAGAACACAAAACT 57.370 32.000 12.17 0.00 36.80 2.66
2732 5326 6.416161 GCTCTGAATTCTGAAGAACACAAAAC 59.584 38.462 14.97 0.00 36.80 2.43
2735 5329 5.371526 AGCTCTGAATTCTGAAGAACACAA 58.628 37.500 14.97 0.00 36.80 3.33
2749 5343 3.663198 AGAGGGTGGATTAGCTCTGAAT 58.337 45.455 0.00 0.00 0.00 2.57
2803 5461 2.271800 GTCGGATCGCTTCTGAAACAT 58.728 47.619 0.00 0.00 41.45 2.71
2810 5468 1.140589 CAGCTGTCGGATCGCTTCT 59.859 57.895 5.25 0.00 0.00 2.85
2813 5471 1.888436 TTTCCAGCTGTCGGATCGCT 61.888 55.000 13.81 0.00 30.99 4.93
2822 5480 1.627834 CTCCTCCTCTTTTCCAGCTGT 59.372 52.381 13.81 0.00 0.00 4.40
2868 5527 0.108615 CCTCTTCGGCGATGTGTCTT 60.109 55.000 20.25 0.00 0.00 3.01
2893 5552 0.466189 CCACTGATGCGCCCCTATTT 60.466 55.000 4.18 0.00 0.00 1.40
2896 5555 4.175337 GCCACTGATGCGCCCCTA 62.175 66.667 4.18 0.00 0.00 3.53
2904 5563 2.223021 CGTGTAATTTCCGCCACTGATG 60.223 50.000 0.00 0.00 0.00 3.07
2905 5564 2.006888 CGTGTAATTTCCGCCACTGAT 58.993 47.619 0.00 0.00 0.00 2.90
2906 5565 1.434555 CGTGTAATTTCCGCCACTGA 58.565 50.000 0.00 0.00 0.00 3.41
2907 5566 0.179200 GCGTGTAATTTCCGCCACTG 60.179 55.000 6.65 0.00 41.50 3.66
2908 5567 2.168054 GCGTGTAATTTCCGCCACT 58.832 52.632 6.65 0.00 41.50 4.00
2968 5631 3.826754 CCTCAGTGGCGCTCGCTA 61.827 66.667 7.64 5.09 41.60 4.26
3009 5672 1.462616 TGGAATCGTTGAGCATTGGG 58.537 50.000 0.00 0.00 0.00 4.12
3033 5696 1.075601 TCTTCATGGCCCAAAGACCT 58.924 50.000 0.00 0.00 0.00 3.85
3039 5702 1.918262 ACTCTCATCTTCATGGCCCAA 59.082 47.619 0.00 0.00 0.00 4.12
3115 5778 1.686325 GCCTCATCGTCCTTGCCCTA 61.686 60.000 0.00 0.00 0.00 3.53
3164 5827 2.202919 CTGCCATCATCACCGCGA 60.203 61.111 8.23 0.00 0.00 5.87


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

AutoCloner maintained by Alex Coulton.