Multiple sequence alignment - TraesCS3A01G500400

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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 TraesCS3A01G500400 chr3A 100.000 4561 0 0 1 4561 724832020 724827460 0.000000e+00 8423.0
1 TraesCS3A01G500400 chr3A 78.251 869 130 31 3265 4086 724780776 724779920 1.890000e-138 503.0
2 TraesCS3A01G500400 chr3A 78.251 869 130 31 3265 4086 745216440 745217296 1.890000e-138 503.0
3 TraesCS3A01G500400 chr3A 84.536 388 43 6 2836 3217 724746772 724746396 7.210000e-98 368.0
4 TraesCS3A01G500400 chr3A 83.200 250 27 8 3289 3530 724746353 724746111 9.940000e-52 215.0
5 TraesCS3A01G500400 chr3A 85.864 191 14 8 2235 2416 724746963 724746777 1.670000e-44 191.0
6 TraesCS3A01G500400 chr3A 78.646 192 33 7 141 326 57810020 57809831 2.230000e-23 121.0
7 TraesCS3A01G500400 chr3D 91.113 4557 330 39 2 4528 594237764 594242275 0.000000e+00 6102.0
8 TraesCS3A01G500400 chr3D 93.919 3634 187 9 913 4528 594075119 594071502 0.000000e+00 5456.0
9 TraesCS3A01G500400 chr3D 82.042 284 38 11 3925 4205 594201288 594201561 3.550000e-56 230.0
10 TraesCS3A01G500400 chr3D 87.791 172 11 7 2241 2402 593768849 593768678 4.660000e-45 193.0
11 TraesCS3A01G500400 chr3D 91.200 125 10 1 3265 3389 593909064 593908941 7.850000e-38 169.0
12 TraesCS3A01G500400 chr3B 93.182 3359 208 12 913 4255 797460520 797463873 0.000000e+00 4915.0
13 TraesCS3A01G500400 chr3B 87.279 283 32 1 3265 3543 797045654 797045372 2.050000e-83 320.0
14 TraesCS3A01G500400 chr3B 80.634 284 37 14 3925 4205 797456550 797456818 2.150000e-48 204.0
15 TraesCS3A01G500400 chr3B 79.730 296 34 15 4236 4518 797023244 797022962 1.670000e-44 191.0
16 TraesCS3A01G500400 chr3B 79.134 254 49 4 522 774 610551471 610551721 6.070000e-39 172.0
17 TraesCS3A01G500400 chr3B 94.949 99 5 0 4430 4528 797464058 797464156 6.110000e-34 156.0
18 TraesCS3A01G500400 chrUn 86.555 357 40 5 2815 3164 41883065 41883420 1.990000e-103 387.0
19 TraesCS3A01G500400 chrUn 86.723 354 39 5 2818 3164 288264774 288264422 1.990000e-103 387.0
20 TraesCS3A01G500400 chrUn 85.897 312 30 4 3256 3562 41884866 41885168 2.050000e-83 320.0
21 TraesCS3A01G500400 chrUn 93.750 112 7 0 2291 2402 41882956 41883067 7.850000e-38 169.0
22 TraesCS3A01G500400 chrUn 72.759 290 73 5 360 645 12497684 12497397 4.860000e-15 93.5
23 TraesCS3A01G500400 chr6A 79.143 350 68 3 427 774 28668415 28668761 2.120000e-58 237.0
24 TraesCS3A01G500400 chr7D 77.193 399 88 3 378 775 81092194 81092590 3.550000e-56 230.0
25 TraesCS3A01G500400 chr2D 75.626 439 86 17 360 788 72341900 72341473 1.000000e-46 198.0
26 TraesCS3A01G500400 chr2B 76.667 390 69 15 360 742 5817957 5817583 3.600000e-46 196.0
27 TraesCS3A01G500400 chr2B 79.649 285 46 10 493 774 109762978 109762703 1.290000e-45 195.0
28 TraesCS3A01G500400 chr2B 77.483 302 52 13 493 788 109057270 109056979 2.820000e-37 167.0
29 TraesCS3A01G500400 chr2B 72.069 290 75 5 360 645 17208837 17209124 1.050000e-11 82.4
30 TraesCS3A01G500400 chr4D 76.093 343 75 6 427 766 111945890 111946228 6.070000e-39 172.0


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 TraesCS3A01G500400 chr3A 724827460 724832020 4560 True 8423.000000 8423 100.000000 1 4561 1 chr3A.!!$R3 4560
1 TraesCS3A01G500400 chr3A 724779920 724780776 856 True 503.000000 503 78.251000 3265 4086 1 chr3A.!!$R2 821
2 TraesCS3A01G500400 chr3A 745216440 745217296 856 False 503.000000 503 78.251000 3265 4086 1 chr3A.!!$F1 821
3 TraesCS3A01G500400 chr3A 724746111 724746963 852 True 258.000000 368 84.533333 2235 3530 3 chr3A.!!$R4 1295
4 TraesCS3A01G500400 chr3D 594237764 594242275 4511 False 6102.000000 6102 91.113000 2 4528 1 chr3D.!!$F2 4526
5 TraesCS3A01G500400 chr3D 594071502 594075119 3617 True 5456.000000 5456 93.919000 913 4528 1 chr3D.!!$R3 3615
6 TraesCS3A01G500400 chr3B 797456550 797464156 7606 False 1758.333333 4915 89.588333 913 4528 3 chr3B.!!$F2 3615
7 TraesCS3A01G500400 chrUn 41882956 41885168 2212 False 292.000000 387 88.734000 2291 3562 3 chrUn.!!$F1 1271

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
690 695 0.108615 CCGCCTCAAGAAGACGACAT 60.109 55.000 0.00 0.0 0.00 3.06 F
1263 4327 0.178987 ACCTCCTCATCGACGCCTAT 60.179 55.000 0.00 0.0 0.00 2.57 F
1914 4978 1.139058 GCTGTCGGTATGGATGTCCTT 59.861 52.381 0.09 0.0 36.82 3.36 F
3299 7774 0.390866 CGACAGCCACTGATGCTTCT 60.391 55.000 0.78 0.0 36.81 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2160 5224 0.671796 TCCACGTGACGACATCTTGT 59.328 50.000 19.30 0.0 0.00 3.16 R
2250 5314 1.073897 AGGTTTCAGTCCAGCAGCC 59.926 57.895 0.00 0.0 0.00 4.85 R
3426 7913 0.109365 CAGTCACGGCAGACTCTCAG 60.109 60.000 6.62 0.0 45.35 3.35 R
4138 8682 1.679311 CTCCTAGGTGGCAGTTGCA 59.321 57.895 9.08 0.0 44.36 4.08 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
34 35 5.985781 TCATCGAAGTTAAAAAGTCACTGC 58.014 37.500 0.00 0.00 0.00 4.40
38 39 4.554723 CGAAGTTAAAAAGTCACTGCAGGG 60.555 45.833 19.93 15.69 0.00 4.45
39 40 3.222603 AGTTAAAAAGTCACTGCAGGGG 58.777 45.455 17.80 8.84 0.00 4.79
40 41 2.956333 GTTAAAAAGTCACTGCAGGGGT 59.044 45.455 17.80 0.08 0.00 4.95
41 42 1.402787 AAAAAGTCACTGCAGGGGTG 58.597 50.000 17.80 7.23 36.17 4.61
42 43 0.258774 AAAAGTCACTGCAGGGGTGT 59.741 50.000 17.80 0.00 36.25 4.16
43 44 0.179018 AAAGTCACTGCAGGGGTGTC 60.179 55.000 17.80 4.91 36.25 3.67
44 45 1.056700 AAGTCACTGCAGGGGTGTCT 61.057 55.000 17.80 7.31 35.36 3.41
45 46 0.178932 AGTCACTGCAGGGGTGTCTA 60.179 55.000 17.80 0.00 33.02 2.59
46 47 0.905357 GTCACTGCAGGGGTGTCTAT 59.095 55.000 17.80 0.00 36.25 1.98
48 49 2.500098 GTCACTGCAGGGGTGTCTATAA 59.500 50.000 17.80 0.00 36.25 0.98
56 57 5.542635 TGCAGGGGTGTCTATAATACCTAAG 59.457 44.000 0.00 0.00 39.08 2.18
62 63 9.813826 GGGGTGTCTATAATACCTAAGTAGTTA 57.186 37.037 0.00 0.00 39.08 2.24
98 99 6.308766 ACTTTAATTCTTTGAACATGCATCGC 59.691 34.615 0.00 0.00 0.00 4.58
107 108 5.851047 TGAACATGCATCGCTCTATATTG 57.149 39.130 0.00 0.00 0.00 1.90
123 124 7.643569 TCTATATTGTCAAATGTGCCATGTT 57.356 32.000 0.00 0.00 0.00 2.71
131 132 5.456497 GTCAAATGTGCCATGTTATCATTCG 59.544 40.000 0.00 0.00 31.15 3.34
137 138 3.065233 TGCCATGTTATCATTCGCTGAAC 59.935 43.478 0.00 0.00 37.44 3.18
161 162 5.532406 CCTATTTTGTAGCACATGCATACCT 59.468 40.000 6.64 0.00 45.16 3.08
193 194 7.951347 ATTATCCCATCTTGAATAATCCAGC 57.049 36.000 0.00 0.00 0.00 4.85
201 202 5.670485 TCTTGAATAATCCAGCGTACATGT 58.330 37.500 2.69 2.69 0.00 3.21
225 226 9.586435 TGTATACTCTTTATTCACACATGACTG 57.414 33.333 0.00 0.00 33.38 3.51
226 227 9.587772 GTATACTCTTTATTCACACATGACTGT 57.412 33.333 0.00 0.00 33.38 3.55
230 231 8.131100 ACTCTTTATTCACACATGACTGTTTTG 58.869 33.333 0.00 0.00 33.38 2.44
234 235 5.651387 TTCACACATGACTGTTTTGGAAA 57.349 34.783 0.00 0.00 33.38 3.13
239 240 8.420222 TCACACATGACTGTTTTGGAAAATAAT 58.580 29.630 0.00 0.00 31.62 1.28
305 307 7.992180 AATTAATCTTTAAAATCCGCAGCAG 57.008 32.000 0.00 0.00 0.00 4.24
307 309 2.158559 TCTTTAAAATCCGCAGCAGCA 58.841 42.857 0.82 0.00 42.27 4.41
329 333 2.731341 CGCGGAAGTCACCTAGTTACTG 60.731 54.545 0.00 0.00 0.00 2.74
339 343 9.841295 AAGTCACCTAGTTACTGTAAATTTTCA 57.159 29.630 5.79 0.00 0.00 2.69
388 392 9.436957 TTTGCGGAAAGGATTAGATCTATTATC 57.563 33.333 2.58 4.66 0.00 1.75
389 393 8.134202 TGCGGAAAGGATTAGATCTATTATCA 57.866 34.615 13.85 0.00 0.00 2.15
464 469 2.158900 CCCACCACTGGATGATCACTAC 60.159 54.545 0.71 0.00 40.55 2.73
465 470 2.158900 CCACCACTGGATGATCACTACC 60.159 54.545 0.71 2.87 40.55 3.18
470 475 1.676529 CTGGATGATCACTACCGTCGT 59.323 52.381 0.00 0.00 0.00 4.34
472 477 1.333881 GGATGATCACTACCGTCGTCG 60.334 57.143 0.00 0.00 0.00 5.12
516 521 4.936081 CCCGCTCCCCTACCGGAT 62.936 72.222 9.46 0.00 44.55 4.18
518 523 2.203509 CGCTCCCCTACCGGATCT 60.204 66.667 9.46 0.00 0.00 2.75
532 537 2.289694 CCGGATCTGACTTGACCTTGTT 60.290 50.000 2.08 0.00 0.00 2.83
543 548 2.905075 TGACCTTGTTGATGATAGCCG 58.095 47.619 0.00 0.00 0.00 5.52
544 549 2.236146 TGACCTTGTTGATGATAGCCGT 59.764 45.455 0.00 0.00 0.00 5.68
565 570 1.541588 GAAGTCTTGGTGCATGTTCCC 59.458 52.381 0.00 0.00 0.00 3.97
578 583 2.509548 CATGTTCCCCTAAGGACCATCA 59.490 50.000 0.00 0.00 44.07 3.07
599 604 2.320781 CCCTGGATCCTTAGTCATCGT 58.679 52.381 14.23 0.00 0.00 3.73
610 615 0.677288 AGTCATCGTCGTTGAACCCA 59.323 50.000 7.55 0.00 0.00 4.51
625 630 5.314718 TGAACCCATGCATAGATCTGAAT 57.685 39.130 5.18 0.00 0.00 2.57
628 633 5.516059 ACCCATGCATAGATCTGAATCAT 57.484 39.130 5.18 0.88 34.07 2.45
633 638 6.536941 CCATGCATAGATCTGAATCATCTGAG 59.463 42.308 5.18 0.00 37.02 3.35
674 679 1.370051 GAAACGCAAACCTCACCGC 60.370 57.895 0.00 0.00 0.00 5.68
676 681 3.767630 AACGCAAACCTCACCGCCT 62.768 57.895 0.00 0.00 0.00 5.52
690 695 0.108615 CCGCCTCAAGAAGACGACAT 60.109 55.000 0.00 0.00 0.00 3.06
742 747 2.668457 CCAAATGGACGAACTCGAGAAG 59.332 50.000 21.68 11.92 43.39 2.85
747 752 1.743958 GGACGAACTCGAGAAGGATCA 59.256 52.381 21.68 0.00 43.02 2.92
774 779 6.834168 TCCAAAAGACAAACTCAAAGAAGT 57.166 33.333 0.00 0.00 0.00 3.01
776 781 5.289434 CCAAAAGACAAACTCAAAGAAGTGC 59.711 40.000 0.00 0.00 0.00 4.40
797 805 3.779759 CCCTCATCTCACTTTCTTCTCG 58.220 50.000 0.00 0.00 0.00 4.04
805 813 3.728845 TCACTTTCTTCTCGGTTCTTGG 58.271 45.455 0.00 0.00 0.00 3.61
843 854 0.991146 TGGCATTGGCTTCTACTCCA 59.009 50.000 11.84 0.00 40.87 3.86
851 862 2.304761 TGGCTTCTACTCCATCCGTTTT 59.695 45.455 0.00 0.00 0.00 2.43
853 864 4.163458 TGGCTTCTACTCCATCCGTTTTAT 59.837 41.667 0.00 0.00 0.00 1.40
863 874 6.921857 ACTCCATCCGTTTTATAATGTAGACG 59.078 38.462 0.00 0.00 0.00 4.18
919 3978 5.806818 TCGTAGATGGAGGGAGTATTCTAG 58.193 45.833 0.00 0.00 0.00 2.43
1001 4065 1.749638 AGTTCGCCCGAGACGAGAT 60.750 57.895 0.00 0.00 41.18 2.75
1071 4135 1.907255 GCTTACTACCTCCACCACCTT 59.093 52.381 0.00 0.00 0.00 3.50
1242 4306 1.445582 CGCTAACGCCGTCTCCTTT 60.446 57.895 0.00 0.00 0.00 3.11
1263 4327 0.178987 ACCTCCTCATCGACGCCTAT 60.179 55.000 0.00 0.00 0.00 2.57
1279 4343 2.016393 CTATTCCCGCGCTGGACAGA 62.016 60.000 21.11 6.62 42.00 3.41
1284 4348 2.505777 CGCGCTGGACAGACTGAG 60.506 66.667 10.08 0.00 0.00 3.35
1286 4350 2.936912 GCGCTGGACAGACTGAGGT 61.937 63.158 10.08 0.00 0.00 3.85
1569 4633 2.818132 GCGCTGGTCTCTGGCTAT 59.182 61.111 0.00 0.00 0.00 2.97
1575 4639 1.884926 GGTCTCTGGCTATGTGCGC 60.885 63.158 0.00 0.00 44.05 6.09
1576 4640 1.153568 GTCTCTGGCTATGTGCGCA 60.154 57.895 5.66 5.66 44.05 6.09
1597 4661 1.811266 GGTGCGCACGATGAGATGT 60.811 57.895 32.35 0.00 0.00 3.06
1647 4711 3.516700 CTGGGATGGGCTTGAATTCTTTT 59.483 43.478 7.05 0.00 0.00 2.27
1742 4806 2.358737 CGTGGTGAAGGCTGGGTC 60.359 66.667 0.00 0.00 0.00 4.46
1749 4813 1.985116 GAAGGCTGGGTCGGACTCT 60.985 63.158 9.80 0.00 0.00 3.24
1788 4852 1.333169 GCGATGGTTGACATGTATGCG 60.333 52.381 0.00 0.00 40.72 4.73
1797 4861 3.937814 TGACATGTATGCGAAGAAAGGT 58.062 40.909 0.00 0.00 0.00 3.50
1830 4894 1.220529 CTGTTGCGCTCTTCAAGTCA 58.779 50.000 9.73 0.00 0.00 3.41
1914 4978 1.139058 GCTGTCGGTATGGATGTCCTT 59.861 52.381 0.09 0.00 36.82 3.36
1986 5050 1.971357 ACCGAGTTCACATTCTCCAGT 59.029 47.619 0.00 0.00 0.00 4.00
2124 5188 7.493367 ACTTGTACTTCAACTCTGGCTATATC 58.507 38.462 0.00 0.00 32.18 1.63
2160 5224 3.813166 GGTGTTTCAGATCTGTTCCGAAA 59.187 43.478 21.92 11.86 0.00 3.46
2250 5314 7.031372 CACTGACCTTGTTCCATGAATTATTG 58.969 38.462 0.00 0.00 0.00 1.90
2391 5463 1.560505 GGTTCACTGCCATGGGAAAT 58.439 50.000 15.13 0.00 0.00 2.17
2427 5499 3.580022 TGTATGCTAGATCAGGGGATGTG 59.420 47.826 0.00 0.00 32.67 3.21
2535 5607 0.535797 GTGCTAGGGAGGCTTTACGT 59.464 55.000 0.00 0.00 0.00 3.57
2583 5655 2.427095 GGTGGTGCCAAATGAGATTACC 59.573 50.000 0.00 0.00 37.17 2.85
2938 6024 7.721399 TGAGGCTTTTATAAGGGATTCAATCTC 59.279 37.037 0.00 0.00 31.76 2.75
3104 6193 2.420890 GATGCTGGGGAGCTCTCG 59.579 66.667 14.64 0.00 35.49 4.04
3299 7774 0.390866 CGACAGCCACTGATGCTTCT 60.391 55.000 0.78 0.00 36.81 2.85
3426 7913 5.690857 GCACCTATACGAGTAATGAAGAACC 59.309 44.000 0.00 0.00 0.00 3.62
3485 7972 8.430801 AATTGATATCGAAGAGTGAAAAGAGG 57.569 34.615 0.00 0.00 43.63 3.69
3506 7993 6.329723 AGAGGGAAATAATCTTGAGAGATGCT 59.670 38.462 0.00 0.00 41.78 3.79
3512 7999 9.202273 GAAATAATCTTGAGAGATGCTATTCGT 57.798 33.333 0.00 0.00 41.78 3.85
3518 8005 5.282055 TGAGAGATGCTATTCGTTTCCAT 57.718 39.130 0.00 0.00 0.00 3.41
3569 8056 3.383825 CGGATTACTGGTAGTGGCTACTT 59.616 47.826 8.46 0.00 37.16 2.24
3570 8057 4.581824 CGGATTACTGGTAGTGGCTACTTA 59.418 45.833 8.46 0.00 37.16 2.24
3610 8098 9.312904 TCCAAAGTTGAATCCTTGAAGATAAAT 57.687 29.630 0.00 0.00 0.00 1.40
3732 8244 2.685850 AGTTATTCAGGGTGTACGGC 57.314 50.000 0.00 0.00 0.00 5.68
3733 8245 1.903860 AGTTATTCAGGGTGTACGGCA 59.096 47.619 0.00 0.00 0.00 5.69
3800 8313 7.645058 TGCTTTTCTCCCATTTAGGATTAAG 57.355 36.000 0.00 0.00 41.22 1.85
3810 8323 7.237679 TCCCATTTAGGATTAAGATCTGTAGGG 59.762 40.741 0.00 0.00 41.22 3.53
3819 8332 3.710209 AGATCTGTAGGGGCATATTGC 57.290 47.619 0.00 0.00 44.08 3.56
3870 8399 0.251077 CTGCCAGCAGGAAGAAAGGT 60.251 55.000 11.91 0.00 44.27 3.50
3884 8413 5.514310 GGAAGAAAGGTGCCTTAAACTCCTA 60.514 44.000 3.65 0.00 34.84 2.94
3898 8427 1.003233 ACTCCTAAAAAGTGGCCTCCG 59.997 52.381 3.32 0.00 0.00 4.63
3926 8458 5.869579 ACTGAATGGTTGAGTACACTGAAT 58.130 37.500 0.00 0.00 0.00 2.57
3961 8493 1.789464 CGTGCTGATTCTCCTATTCGC 59.211 52.381 0.00 0.00 0.00 4.70
4045 8589 4.653341 AGATATTCTCTCCTTCACCACCTG 59.347 45.833 0.00 0.00 0.00 4.00
4086 8630 2.724174 GCGGTGAGTTTTGGAAATTTCG 59.276 45.455 11.95 0.00 0.00 3.46
4138 8682 5.798132 TGATGAATTGCTGACACTAGTCTT 58.202 37.500 0.00 0.00 45.20 3.01
4193 8737 2.928334 TCACCTCGTAGATACTCACCC 58.072 52.381 0.00 0.00 33.89 4.61
4222 8766 4.120589 CCTAGAAGGCGGTAAGTCAATTC 58.879 47.826 0.00 0.00 0.00 2.17
4289 8957 3.055819 GCAATCTGTCTACCTTGTCCAGA 60.056 47.826 0.00 0.00 36.67 3.86
4350 9024 5.590259 CAGCAGTATAATTTACACTGGCCTT 59.410 40.000 14.86 0.00 40.03 4.35
4364 9038 2.051334 GGCCTTATGTGTGCCATGTA 57.949 50.000 0.00 0.00 44.70 2.29
4388 9062 6.313519 TCAGGAAGCATTACCTTCAGTTAT 57.686 37.500 4.54 0.00 42.31 1.89
4395 9069 5.045578 AGCATTACCTTCAGTTATGGACAGT 60.046 40.000 0.00 0.00 36.27 3.55
4470 9144 9.665719 TGTCATTATTGTGTTAGAGCTTATTGA 57.334 29.630 0.00 0.00 0.00 2.57
4528 9203 4.704540 CCATGTGCCAGTTATCTTGGTTTA 59.295 41.667 0.00 0.00 0.00 2.01
4529 9204 5.360714 CCATGTGCCAGTTATCTTGGTTTAT 59.639 40.000 0.00 0.00 0.00 1.40
4530 9205 6.127366 CCATGTGCCAGTTATCTTGGTTTATT 60.127 38.462 0.00 0.00 0.00 1.40
4531 9206 6.909550 TGTGCCAGTTATCTTGGTTTATTT 57.090 33.333 0.00 0.00 0.00 1.40
4532 9207 8.465999 CATGTGCCAGTTATCTTGGTTTATTTA 58.534 33.333 0.00 0.00 0.00 1.40
4533 9208 8.588290 TGTGCCAGTTATCTTGGTTTATTTAT 57.412 30.769 0.00 0.00 0.00 1.40
4534 9209 8.465999 TGTGCCAGTTATCTTGGTTTATTTATG 58.534 33.333 0.00 0.00 0.00 1.90
4535 9210 8.682710 GTGCCAGTTATCTTGGTTTATTTATGA 58.317 33.333 0.00 0.00 0.00 2.15
4536 9211 8.902806 TGCCAGTTATCTTGGTTTATTTATGAG 58.097 33.333 0.00 0.00 0.00 2.90
4537 9212 9.120538 GCCAGTTATCTTGGTTTATTTATGAGA 57.879 33.333 0.00 0.00 0.00 3.27
4559 9234 9.230122 TGAGATATCTTTGCTAATTGTTTCACA 57.770 29.630 6.70 0.00 0.00 3.58
4560 9235 9.713740 GAGATATCTTTGCTAATTGTTTCACAG 57.286 33.333 6.70 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.272504 CCTGCAGTGACTTTTTAACTTCGA 59.727 41.667 13.81 0.00 0.00 3.71
34 35 7.949006 ACTACTTAGGTATTATAGACACCCCTG 59.051 40.741 0.00 0.00 32.43 4.45
76 77 5.953183 AGCGATGCATGTTCAAAGAATTAA 58.047 33.333 2.46 0.00 0.00 1.40
85 86 5.299949 ACAATATAGAGCGATGCATGTTCA 58.700 37.500 2.46 0.00 0.00 3.18
86 87 5.406477 TGACAATATAGAGCGATGCATGTTC 59.594 40.000 2.46 4.39 0.00 3.18
98 99 7.268199 ACATGGCACATTTGACAATATAGAG 57.732 36.000 0.00 0.00 46.77 2.43
123 124 7.042051 GCTACAAAATAGGTTCAGCGAATGATA 60.042 37.037 0.00 0.00 37.89 2.15
131 132 5.335127 CATGTGCTACAAAATAGGTTCAGC 58.665 41.667 0.00 0.00 0.00 4.26
137 138 5.532406 AGGTATGCATGTGCTACAAAATAGG 59.468 40.000 10.16 0.00 42.66 2.57
172 173 4.202503 ACGCTGGATTATTCAAGATGGGAT 60.203 41.667 0.00 0.00 0.00 3.85
182 183 8.244802 AGAGTATACATGTACGCTGGATTATTC 58.755 37.037 7.96 1.03 34.15 1.75
187 188 6.406692 AAAGAGTATACATGTACGCTGGAT 57.593 37.500 7.96 0.00 35.36 3.41
190 191 8.691727 GTGAATAAAGAGTATACATGTACGCTG 58.308 37.037 7.96 0.00 35.36 5.18
193 194 9.511144 TGTGTGAATAAAGAGTATACATGTACG 57.489 33.333 7.96 0.00 0.00 3.67
278 280 8.655092 TGCTGCGGATTTTAAAGATTAATTTTG 58.345 29.630 0.00 0.00 0.00 2.44
302 304 4.077188 GTGACTTCCGCGTGCTGC 62.077 66.667 4.92 0.00 41.47 5.25
305 307 1.805945 CTAGGTGACTTCCGCGTGC 60.806 63.158 4.92 0.00 43.67 5.34
307 309 1.200948 GTAACTAGGTGACTTCCGCGT 59.799 52.381 4.92 0.00 43.67 6.01
311 313 8.843885 AAATTTACAGTAACTAGGTGACTTCC 57.156 34.615 0.00 0.00 43.67 3.46
360 364 8.519799 AATAGATCTAATCCTTTCCGCAAAAA 57.480 30.769 6.52 0.00 0.00 1.94
392 396 9.621629 TTGAGATATTTTGTACACCCGATAAAT 57.378 29.630 0.00 0.45 0.00 1.40
435 440 3.849574 TCATCCAGTGGTGGGAATCTTTA 59.150 43.478 9.54 0.00 45.11 1.85
437 442 2.278245 TCATCCAGTGGTGGGAATCTT 58.722 47.619 9.54 0.00 45.11 2.40
438 443 1.971149 TCATCCAGTGGTGGGAATCT 58.029 50.000 9.54 0.00 45.11 2.40
448 453 2.541794 CGACGGTAGTGATCATCCAGTG 60.542 54.545 0.00 0.00 0.00 3.66
470 475 3.889044 GTCGATGGCTCGCTCCGA 61.889 66.667 0.00 0.00 44.65 4.55
490 495 4.222847 GGGAGCGGGGACATCGAC 62.223 72.222 0.00 0.00 0.00 4.20
494 499 2.446036 GTAGGGGAGCGGGGACAT 60.446 66.667 0.00 0.00 0.00 3.06
505 510 0.753262 CAAGTCAGATCCGGTAGGGG 59.247 60.000 0.00 0.00 38.33 4.79
516 521 4.687901 TCATCAACAAGGTCAAGTCAGA 57.312 40.909 0.00 0.00 0.00 3.27
518 523 4.937620 GCTATCATCAACAAGGTCAAGTCA 59.062 41.667 0.00 0.00 0.00 3.41
532 537 3.430790 CCAAGACTTCACGGCTATCATCA 60.431 47.826 0.00 0.00 0.00 3.07
543 548 2.030805 GGAACATGCACCAAGACTTCAC 60.031 50.000 0.00 0.00 0.00 3.18
544 549 2.229792 GGAACATGCACCAAGACTTCA 58.770 47.619 0.00 0.00 0.00 3.02
565 570 0.839946 CCAGGGTGATGGTCCTTAGG 59.160 60.000 0.00 0.00 35.47 2.69
578 583 2.320781 CGATGACTAAGGATCCAGGGT 58.679 52.381 15.82 8.85 0.00 4.34
599 604 3.134623 AGATCTATGCATGGGTTCAACGA 59.865 43.478 10.16 0.00 0.00 3.85
610 615 7.324935 GTCTCAGATGATTCAGATCTATGCAT 58.675 38.462 3.79 3.79 33.28 3.96
633 638 4.171005 TCGTTATGTGACGAGATTTGGTC 58.829 43.478 0.00 0.00 46.09 4.02
651 656 1.329599 GTGAGGTTTGCGTTTCTCGTT 59.670 47.619 0.00 0.00 42.13 3.85
674 679 4.753233 AGATTCATGTCGTCTTCTTGAGG 58.247 43.478 0.00 0.00 0.00 3.86
676 681 5.106277 ACGTAGATTCATGTCGTCTTCTTGA 60.106 40.000 0.00 0.00 0.00 3.02
690 695 1.022735 GGAGCTCCGACGTAGATTCA 58.977 55.000 19.06 0.00 0.00 2.57
742 747 7.209475 TGAGTTTGTCTTTTGGATTTTGATCC 58.791 34.615 0.00 0.00 41.10 3.36
747 752 9.154847 CTTCTTTGAGTTTGTCTTTTGGATTTT 57.845 29.630 0.00 0.00 0.00 1.82
754 759 5.410924 GGCACTTCTTTGAGTTTGTCTTTT 58.589 37.500 0.00 0.00 0.00 2.27
774 779 2.909006 AGAAGAAAGTGAGATGAGGGCA 59.091 45.455 0.00 0.00 0.00 5.36
776 781 3.430098 CCGAGAAGAAAGTGAGATGAGGG 60.430 52.174 0.00 0.00 0.00 4.30
797 805 8.910351 ATCTGCTATAAAATAGACCAAGAACC 57.090 34.615 0.00 0.00 0.00 3.62
805 813 8.449397 CAATGCCAGATCTGCTATAAAATAGAC 58.551 37.037 17.76 0.00 0.00 2.59
903 914 3.463704 TCTGCTCTAGAATACTCCCTCCA 59.536 47.826 0.00 0.00 30.84 3.86
919 3978 0.532573 TTCGTGGTCCAGATCTGCTC 59.467 55.000 17.76 11.40 0.00 4.26
984 4046 1.586564 CATCTCGTCTCGGGCGAAC 60.587 63.158 3.56 0.00 37.93 3.95
1053 4117 2.173519 CGAAGGTGGTGGAGGTAGTAA 58.826 52.381 0.00 0.00 0.00 2.24
1134 4198 0.908180 GGAGGAAGAGGGACGGGAAA 60.908 60.000 0.00 0.00 0.00 3.13
1140 4204 1.079057 GTTGCGGAGGAAGAGGGAC 60.079 63.158 0.00 0.00 39.56 4.46
1227 4291 1.895131 AGGTTAAAGGAGACGGCGTTA 59.105 47.619 16.19 0.00 0.00 3.18
1242 4306 0.395311 AGGCGTCGATGAGGAGGTTA 60.395 55.000 9.31 0.00 0.00 2.85
1263 4327 4.373116 GTCTGTCCAGCGCGGGAA 62.373 66.667 31.05 18.87 39.05 3.97
1286 4350 3.068691 CGAAGGTCGCCAGGGAGA 61.069 66.667 0.00 0.00 31.14 3.71
1575 4639 2.733671 CTCATCGTGCGCACCAGTG 61.734 63.158 33.23 26.53 0.00 3.66
1576 4640 2.230994 ATCTCATCGTGCGCACCAGT 62.231 55.000 33.23 17.24 0.00 4.00
1587 4651 2.680312 ACACCCTCAACATCTCATCG 57.320 50.000 0.00 0.00 0.00 3.84
1597 4661 2.507484 CATCAGAGCAAACACCCTCAA 58.493 47.619 0.00 0.00 0.00 3.02
1687 4751 2.158900 CGGCAATATCCCTCACAGAGTT 60.159 50.000 0.00 0.00 0.00 3.01
1742 4806 1.787155 CAAGAAACACGTCAGAGTCCG 59.213 52.381 0.00 0.00 0.00 4.79
1788 4852 4.791974 CTTCACTCAATGCACCTTTCTTC 58.208 43.478 0.00 0.00 0.00 2.87
1797 4861 1.001048 GCAACAGCTTCACTCAATGCA 60.001 47.619 0.00 0.00 31.63 3.96
1830 4894 1.076024 ACCACATTGGGATCAAGCACT 59.924 47.619 0.00 0.00 43.37 4.40
1914 4978 7.336176 TCTGAATACAGACTTAACGCTTCTCTA 59.664 37.037 0.00 0.00 46.55 2.43
1986 5050 4.242475 CCAAGTTACAAGCTCGTATGACA 58.758 43.478 0.00 0.00 0.00 3.58
2124 5188 2.185004 AACACCTGAACCCATCTTCG 57.815 50.000 0.00 0.00 0.00 3.79
2160 5224 0.671796 TCCACGTGACGACATCTTGT 59.328 50.000 19.30 0.00 0.00 3.16
2250 5314 1.073897 AGGTTTCAGTCCAGCAGCC 59.926 57.895 0.00 0.00 0.00 4.85
2427 5499 2.202987 CTCCGGACTGCAGCATCC 60.203 66.667 15.27 13.56 0.00 3.51
2583 5655 2.288825 TGCAGTAAGGACACCGAGAAAG 60.289 50.000 0.00 0.00 0.00 2.62
2833 5917 2.722094 TGGTTGGACTCAATGCATACC 58.278 47.619 0.00 1.30 35.10 2.73
3299 7774 2.636647 TGTCATCTGACTTTGTGCCA 57.363 45.000 11.35 0.00 44.99 4.92
3330 7805 3.071312 TGCCAATTCATCCAACTTTGCTT 59.929 39.130 0.00 0.00 0.00 3.91
3426 7913 0.109365 CAGTCACGGCAGACTCTCAG 60.109 60.000 6.62 0.00 45.35 3.35
3482 7969 6.532826 AGCATCTCTCAAGATTATTTCCCTC 58.467 40.000 0.00 0.00 40.38 4.30
3485 7972 8.655092 CGAATAGCATCTCTCAAGATTATTTCC 58.345 37.037 0.00 0.00 40.38 3.13
3506 7993 6.280855 TCTCTGAAGTGATGGAAACGAATA 57.719 37.500 0.00 0.00 0.00 1.75
3518 8005 2.836372 ACATGAGCCATCTCTGAAGTGA 59.164 45.455 0.00 0.00 40.03 3.41
3569 8056 3.389983 ACTTTGGAACCACTGCACTAGTA 59.610 43.478 0.00 0.00 37.60 1.82
3570 8057 2.172717 ACTTTGGAACCACTGCACTAGT 59.827 45.455 0.00 0.00 41.36 2.57
3610 8098 0.973632 AGGTATGCCAACGTGTCAGA 59.026 50.000 1.54 0.00 37.19 3.27
3709 8221 5.121105 GCCGTACACCCTGAATAACTTATT 58.879 41.667 0.00 0.00 0.00 1.40
3737 8249 7.857885 GTCTTTTAAAGAATCAGAACACCACAG 59.142 37.037 9.14 0.00 39.67 3.66
3782 8295 7.937700 ACAGATCTTAATCCTAAATGGGAGA 57.062 36.000 0.00 0.00 38.92 3.71
3800 8313 3.341823 CTGCAATATGCCCCTACAGATC 58.658 50.000 0.00 0.00 44.23 2.75
3819 8332 3.567164 AGGATTAAATCATCGCAAGGCTG 59.433 43.478 0.00 0.00 38.47 4.85
3870 8399 4.279922 GCCACTTTTTAGGAGTTTAAGGCA 59.720 41.667 0.00 0.00 34.42 4.75
3898 8427 3.568007 TGTACTCAACCATTCAGTTTGGC 59.432 43.478 0.00 0.00 37.81 4.52
3926 8458 1.296392 CACGATGCCTTGGAGGTGA 59.704 57.895 0.00 0.00 37.80 4.02
3961 8493 1.202976 GGGGATGGATCTGGTCAATGG 60.203 57.143 0.00 0.00 0.00 3.16
4118 8662 3.748048 GCAAGACTAGTGTCAGCAATTCA 59.252 43.478 0.00 0.00 45.20 2.57
4138 8682 1.679311 CTCCTAGGTGGCAGTTGCA 59.321 57.895 9.08 0.00 44.36 4.08
4222 8766 8.116136 GGAAACTCAAACAATAAACAAAGCTTG 58.884 33.333 0.00 0.00 0.00 4.01
4326 8998 5.126067 AGGCCAGTGTAAATTATACTGCTG 58.874 41.667 20.07 11.34 43.83 4.41
4328 9000 7.228706 ACATAAGGCCAGTGTAAATTATACTGC 59.771 37.037 20.07 15.75 43.83 4.40
4364 9038 4.851639 ACTGAAGGTAATGCTTCCTGAT 57.148 40.909 0.00 0.00 33.97 2.90
4395 9069 8.556194 GTGAAGTATAAACATGTCAAGACAACA 58.444 33.333 7.02 0.37 45.41 3.33
4470 9144 3.899360 CCATCCAAATGTCCAGGCATTAT 59.101 43.478 8.90 0.00 38.03 1.28


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

AutoCloner maintained by Alex Coulton.