Multiple sequence alignment - TraesCS6D01G342200

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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 TraesCS6D01G342200 chr6D 100.000 5591 0 0 1 5591 441624274 441618684 0.000000e+00 10325
1 TraesCS6D01G342200 chr6D 86.068 323 32 8 1070 1386 460156751 460157066 8.970000e-88 335
2 TraesCS6D01G342200 chr6A 97.220 3705 76 15 1353 5039 590077952 590074257 0.000000e+00 6246
3 TraesCS6D01G342200 chr6A 90.980 1408 64 35 1 1365 590080188 590078801 0.000000e+00 1838
4 TraesCS6D01G342200 chr6A 90.417 480 19 11 5138 5591 590074257 590073779 1.720000e-169 606
5 TraesCS6D01G342200 chr6B 90.578 2664 143 42 54 2639 667075955 667073322 0.000000e+00 3430
6 TraesCS6D01G342200 chr6B 94.484 1396 73 2 3049 4443 667072922 667071530 0.000000e+00 2148
7 TraesCS6D01G342200 chr6B 87.389 563 52 12 4417 4968 667071493 667070939 3.680000e-176 628
8 TraesCS6D01G342200 chr6B 86.737 377 40 6 1160 1533 101435593 101435962 1.450000e-110 411
9 TraesCS6D01G342200 chr6B 86.431 339 38 4 2317 2647 117907752 117907414 1.140000e-96 364
10 TraesCS6D01G342200 chr6B 91.903 247 20 0 1842 2088 117907990 117907744 4.150000e-91 346
11 TraesCS6D01G342200 chr6B 92.199 141 11 0 5447 5587 667070885 667070745 3.420000e-47 200
12 TraesCS6D01G342200 chrUn 100.000 415 0 0 1944 2358 477231703 477231289 0.000000e+00 767
13 TraesCS6D01G342200 chrUn 85.185 243 26 3 1580 1822 8489226 8489458 2.010000e-59 241
14 TraesCS6D01G342200 chr2A 91.552 509 38 4 1578 2085 736738624 736739128 0.000000e+00 697
15 TraesCS6D01G342200 chr2A 87.021 339 36 1 2317 2647 736739123 736739461 5.290000e-100 375
16 TraesCS6D01G342200 chr2A 85.165 364 40 6 1169 1527 578015979 578015625 1.480000e-95 361
17 TraesCS6D01G342200 chr2A 84.802 329 38 7 911 1235 736736646 736736966 2.510000e-83 320
18 TraesCS6D01G342200 chr3D 91.349 393 30 4 1695 2085 156977500 156977890 8.240000e-148 534
19 TraesCS6D01G342200 chr3D 88.889 378 29 6 1160 1533 443672964 443672596 2.370000e-123 453
20 TraesCS6D01G342200 chr3D 85.460 337 34 10 2641 2974 477825804 477826128 2.500000e-88 337
21 TraesCS6D01G342200 chr3D 92.271 207 15 1 2441 2646 477825570 477825776 5.480000e-75 292
22 TraesCS6D01G342200 chr3D 80.967 331 47 9 1614 1940 443672591 443672273 1.200000e-61 248
23 TraesCS6D01G342200 chr3D 83.871 279 23 5 2317 2587 156977885 156978149 4.330000e-61 246
24 TraesCS6D01G342200 chr4B 85.904 376 41 6 1160 1532 580716756 580716390 1.890000e-104 390
25 TraesCS6D01G342200 chr4B 92.623 244 18 0 1842 2085 97058641 97058398 8.910000e-93 351
26 TraesCS6D01G342200 chr4B 84.071 339 40 4 2317 2647 97058403 97058071 1.170000e-81 315
27 TraesCS6D01G342200 chr7A 87.850 321 30 4 2336 2647 59609400 59609080 8.850000e-98 368
28 TraesCS6D01G342200 chr5D 85.714 336 35 8 2641 2974 461620779 461621103 5.360000e-90 342
29 TraesCS6D01G342200 chr5D 92.754 207 12 2 2441 2646 461620547 461620751 4.240000e-76 296
30 TraesCS6D01G342200 chr5A 85.312 320 27 6 2336 2647 544168577 544168884 4.210000e-81 313
31 TraesCS6D01G342200 chr1B 90.870 230 19 2 1578 1806 45380582 45380354 1.960000e-79 307
32 TraesCS6D01G342200 chr1B 85.214 257 28 2 1578 1834 635879227 635878981 7.190000e-64 255
33 TraesCS6D01G342200 chr2B 90.583 223 20 1 1578 1799 764523887 764524109 1.520000e-75 294
34 TraesCS6D01G342200 chr4A 91.960 199 11 3 1338 1533 56472995 56472799 1.980000e-69 274
35 TraesCS6D01G342200 chr5B 84.047 257 31 2 1578 1834 22357054 22356808 7.240000e-59 239
36 TraesCS6D01G342200 chr5B 92.568 148 10 1 2441 2587 441695016 441694869 1.580000e-50 211
37 TraesCS6D01G342200 chr2D 88.710 186 13 2 1350 1532 592104109 592104289 2.620000e-53 220
38 TraesCS6D01G342200 chr4D 92.029 138 11 0 2450 2587 49768239 49768376 1.590000e-45 195
39 TraesCS6D01G342200 chr3A 93.548 124 7 1 1695 1817 157997027 157996904 3.440000e-42 183


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 TraesCS6D01G342200 chr6D 441618684 441624274 5590 True 10325.000000 10325 100.000000 1 5591 1 chr6D.!!$R1 5590
1 TraesCS6D01G342200 chr6A 590073779 590080188 6409 True 2896.666667 6246 92.872333 1 5591 3 chr6A.!!$R1 5590
2 TraesCS6D01G342200 chr6B 667070745 667075955 5210 True 1601.500000 3430 91.162500 54 5587 4 chr6B.!!$R2 5533
3 TraesCS6D01G342200 chr6B 117907414 117907990 576 True 355.000000 364 89.167000 1842 2647 2 chr6B.!!$R1 805
4 TraesCS6D01G342200 chr2A 736736646 736739461 2815 False 464.000000 697 87.791667 911 2647 3 chr2A.!!$F1 1736
5 TraesCS6D01G342200 chr3D 156977500 156978149 649 False 390.000000 534 87.610000 1695 2587 2 chr3D.!!$F1 892
6 TraesCS6D01G342200 chr3D 443672273 443672964 691 True 350.500000 453 84.928000 1160 1940 2 chr3D.!!$R1 780
7 TraesCS6D01G342200 chr3D 477825570 477826128 558 False 314.500000 337 88.865500 2441 2974 2 chr3D.!!$F2 533
8 TraesCS6D01G342200 chr4B 97058071 97058641 570 True 333.000000 351 88.347000 1842 2647 2 chr4B.!!$R2 805
9 TraesCS6D01G342200 chr5D 461620547 461621103 556 False 319.000000 342 89.234000 2441 2974 2 chr5D.!!$F1 533

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
317 323 0.178846 TTCACTTCCCATCCCCCTCA 60.179 55.000 0.00 0.0 0.00 3.86 F
318 324 0.178846 TCACTTCCCATCCCCCTCAA 60.179 55.000 0.00 0.0 0.00 3.02 F
623 654 0.251519 GAAGCCCCATCCATCCATCC 60.252 60.000 0.00 0.0 0.00 3.51 F
665 696 0.692756 CTCCTTTCTCCCCCTCCCTC 60.693 65.000 0.00 0.0 0.00 4.30 F
1273 1338 1.202582 CCTCAGTGTCTAGGACAACGG 59.797 57.143 1.77 0.0 44.49 4.44 F
2965 5453 1.377333 GGGGCACTTGTCTGTAGCC 60.377 63.158 0.00 0.0 44.48 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1432 3764 1.084370 GCCTCGTGCATCTGTACCAC 61.084 60.000 0.00 0.0 40.77 4.16 R
1772 4115 1.506493 GCGGCTGTGAGATGGATAAG 58.494 55.000 0.00 0.0 0.00 1.73 R
1889 4240 9.507329 AAGTACAAATCATAAGATTCACTGTGT 57.493 29.630 7.79 4.3 43.52 3.72 R
2932 5419 2.755103 GTGCCCCTTTTATCCAGTTCTG 59.245 50.000 0.00 0.0 0.00 3.02 R
3524 6012 2.731572 CTGCCCTCATTCATCCACTTT 58.268 47.619 0.00 0.0 0.00 2.66 R
5142 7715 0.035343 GTGGGGAGTAGAACCTTGGC 60.035 60.000 0.00 0.0 0.00 4.52 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
27 28 0.647925 GTTCGCCGAAGAAGATGCTC 59.352 55.000 0.00 0.00 0.00 4.26
34 35 2.935201 CCGAAGAAGATGCTCCAAGAAG 59.065 50.000 0.00 0.00 0.00 2.85
49 50 3.941483 CCAAGAAGCGTTCCACAGATATT 59.059 43.478 0.00 0.00 0.00 1.28
50 51 4.201851 CCAAGAAGCGTTCCACAGATATTG 60.202 45.833 0.00 0.00 0.00 1.90
107 108 6.204359 CAAAGTCTCCTCAAACAAATCACAG 58.796 40.000 0.00 0.00 0.00 3.66
117 118 3.814504 ACAAATCACAGGAATCACCCT 57.185 42.857 0.00 0.00 40.05 4.34
118 119 3.690460 ACAAATCACAGGAATCACCCTC 58.310 45.455 0.00 0.00 40.05 4.30
120 121 3.641434 AATCACAGGAATCACCCTCTG 57.359 47.619 0.00 0.00 40.05 3.35
121 122 2.030027 TCACAGGAATCACCCTCTGT 57.970 50.000 0.00 0.00 40.62 3.41
317 323 0.178846 TTCACTTCCCATCCCCCTCA 60.179 55.000 0.00 0.00 0.00 3.86
318 324 0.178846 TCACTTCCCATCCCCCTCAA 60.179 55.000 0.00 0.00 0.00 3.02
333 354 0.889186 CTCAACCCCAAGAACCACCG 60.889 60.000 0.00 0.00 0.00 4.94
341 362 2.147387 AAGAACCACCGCACCTCCT 61.147 57.895 0.00 0.00 0.00 3.69
343 364 3.607370 GAACCACCGCACCTCCTCC 62.607 68.421 0.00 0.00 0.00 4.30
376 397 2.100983 AACCAAACCCCCATCCCCA 61.101 57.895 0.00 0.00 0.00 4.96
438 463 3.134792 GTGCGAGCCGAGAGAGGA 61.135 66.667 0.00 0.00 0.00 3.71
620 651 1.648302 CCTGAAGCCCCATCCATCCA 61.648 60.000 0.00 0.00 0.00 3.41
621 652 0.481567 CTGAAGCCCCATCCATCCAT 59.518 55.000 0.00 0.00 0.00 3.41
622 653 0.479815 TGAAGCCCCATCCATCCATC 59.520 55.000 0.00 0.00 0.00 3.51
623 654 0.251519 GAAGCCCCATCCATCCATCC 60.252 60.000 0.00 0.00 0.00 3.51
664 695 1.398234 CTCCTTTCTCCCCCTCCCT 59.602 63.158 0.00 0.00 0.00 4.20
665 696 0.692756 CTCCTTTCTCCCCCTCCCTC 60.693 65.000 0.00 0.00 0.00 4.30
666 697 1.694525 CCTTTCTCCCCCTCCCTCC 60.695 68.421 0.00 0.00 0.00 4.30
667 698 1.694525 CTTTCTCCCCCTCCCTCCC 60.695 68.421 0.00 0.00 0.00 4.30
668 699 2.191846 TTTCTCCCCCTCCCTCCCT 61.192 63.158 0.00 0.00 0.00 4.20
669 700 2.196304 TTTCTCCCCCTCCCTCCCTC 62.196 65.000 0.00 0.00 0.00 4.30
670 701 4.179599 CTCCCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
837 869 1.343142 GATTTGGGCGGTTTTCTTGGT 59.657 47.619 0.00 0.00 0.00 3.67
884 916 4.988598 CCACCAACCTGCGCGTCT 62.989 66.667 8.43 0.00 0.00 4.18
906 938 3.001838 TCGTGTGAAATTCGTGTTCTTGG 59.998 43.478 0.00 0.00 0.00 3.61
907 939 3.042887 GTGTGAAATTCGTGTTCTTGGC 58.957 45.455 0.00 0.00 0.00 4.52
908 940 2.948979 TGTGAAATTCGTGTTCTTGGCT 59.051 40.909 0.00 0.00 0.00 4.75
924 980 1.303155 GCTCTGCTTCTGCTGGGTT 60.303 57.895 0.00 0.00 40.24 4.11
1053 1115 4.171186 GGGATGGACCAGTTCCCT 57.829 61.111 21.77 0.00 45.17 4.20
1267 1332 2.808919 CCTGTTCCTCAGTGTCTAGGA 58.191 52.381 0.00 0.00 42.19 2.94
1268 1333 2.494073 CCTGTTCCTCAGTGTCTAGGAC 59.506 54.545 0.00 0.00 41.63 3.85
1269 1334 3.157881 CTGTTCCTCAGTGTCTAGGACA 58.842 50.000 0.00 0.00 41.63 4.02
1270 1335 3.572642 TGTTCCTCAGTGTCTAGGACAA 58.427 45.455 1.77 0.00 44.49 3.18
1271 1336 3.321111 TGTTCCTCAGTGTCTAGGACAAC 59.679 47.826 1.77 0.00 44.49 3.32
1272 1337 2.160205 TCCTCAGTGTCTAGGACAACG 58.840 52.381 1.77 0.00 44.49 4.10
1273 1338 1.202582 CCTCAGTGTCTAGGACAACGG 59.797 57.143 1.77 0.00 44.49 4.44
1287 1354 3.002965 GGACAACGGACAACCACTAAAAG 59.997 47.826 0.00 0.00 35.59 2.27
1291 1358 5.008316 ACAACGGACAACCACTAAAAGATTC 59.992 40.000 0.00 0.00 35.59 2.52
1432 3764 8.313292 TGACCTGAATTTATGATTCCCTTTTTG 58.687 33.333 0.00 0.00 0.00 2.44
1434 3766 8.096414 ACCTGAATTTATGATTCCCTTTTTGTG 58.904 33.333 0.00 0.00 0.00 3.33
1772 4115 5.355350 CCCTGTCATCAGTAAGTTCCAAATC 59.645 44.000 0.00 0.00 39.82 2.17
1824 4167 4.467198 ACTGGTCTTGGTAATAGGAACG 57.533 45.455 0.00 0.00 0.00 3.95
2615 4987 2.555199 ACTTGCCGAGCATTATCTGTC 58.445 47.619 0.00 0.00 38.76 3.51
2932 5419 8.999431 TGAAACAAGTAAATGAGTAATCTGGTC 58.001 33.333 0.00 0.00 0.00 4.02
2965 5453 1.377333 GGGGCACTTGTCTGTAGCC 60.377 63.158 0.00 0.00 44.48 3.93
3023 5511 9.003658 GCATGTAGTATATGCTAAACCAGAAAT 57.996 33.333 20.98 0.00 45.64 2.17
3134 5622 5.897050 TCACAAGTTTAACCGATTGCTTTT 58.103 33.333 0.00 0.00 0.00 2.27
3524 6012 2.829741 GGCAAGCCCAATTACAACAA 57.170 45.000 0.00 0.00 0.00 2.83
3947 6435 0.400594 GTACCAAAGTGGGAGCTGGT 59.599 55.000 0.00 0.00 43.37 4.00
4157 6645 3.316308 GCAGAATGTTTGGACAGACAAGT 59.684 43.478 0.00 0.00 39.58 3.16
4248 6736 0.659957 GAATGCGTCTGAATCAGGCC 59.340 55.000 9.49 0.00 31.65 5.19
4354 6842 6.592607 CGACCTTTTTAACCTCTTGCATACTA 59.407 38.462 0.00 0.00 0.00 1.82
4427 6925 8.982685 AGTACAGCGATACATCATAATCTTTTG 58.017 33.333 0.00 0.00 0.00 2.44
4470 7020 7.329962 CCTAGTAGAGCGATACATATATCCTCG 59.670 44.444 0.00 4.51 38.66 4.63
4592 7146 0.179048 CTCGGGGCTTGCATATGACA 60.179 55.000 6.97 1.06 0.00 3.58
4603 7157 0.179048 CATATGACAAGAGGCCGCCA 60.179 55.000 13.15 0.00 0.00 5.69
4632 7186 0.459237 CCACGTCACTCTGCATCCTC 60.459 60.000 0.00 0.00 0.00 3.71
4706 7261 7.118496 AGCTAGTGTTGCTGATCTTTAGTAT 57.882 36.000 0.00 0.00 39.56 2.12
4859 7424 3.584848 AGGTGAGTAATCTATGATGGGCC 59.415 47.826 0.00 0.00 0.00 5.80
4882 7447 4.250464 TCGACCTGGAATTTGTATGTCAC 58.750 43.478 0.00 0.00 0.00 3.67
4883 7448 4.020573 TCGACCTGGAATTTGTATGTCACT 60.021 41.667 0.00 0.00 0.00 3.41
4884 7449 4.093408 CGACCTGGAATTTGTATGTCACTG 59.907 45.833 0.00 0.00 0.00 3.66
4886 7451 3.129287 CCTGGAATTTGTATGTCACTGCC 59.871 47.826 0.00 0.00 0.00 4.85
4887 7452 3.758023 CTGGAATTTGTATGTCACTGCCA 59.242 43.478 0.00 0.00 0.00 4.92
4888 7453 4.343231 TGGAATTTGTATGTCACTGCCAT 58.657 39.130 0.00 0.00 0.00 4.40
4889 7454 4.398988 TGGAATTTGTATGTCACTGCCATC 59.601 41.667 0.00 0.00 0.00 3.51
4890 7455 4.398988 GGAATTTGTATGTCACTGCCATCA 59.601 41.667 0.00 0.00 0.00 3.07
4898 7463 2.171027 TGTCACTGCCATCATGCATAGA 59.829 45.455 0.00 0.00 41.16 1.98
4901 7470 1.773052 ACTGCCATCATGCATAGACCT 59.227 47.619 0.00 0.00 41.16 3.85
4941 7514 1.075212 TGTGGCTGGTGAAATCCATCA 59.925 47.619 0.00 0.00 36.84 3.07
4952 7525 6.723515 TGGTGAAATCCATCAAAAACCTGATA 59.276 34.615 0.00 0.00 34.20 2.15
4957 7530 7.722949 AATCCATCAAAAACCTGATACATGT 57.277 32.000 2.69 2.69 34.20 3.21
4958 7531 6.513806 TCCATCAAAAACCTGATACATGTG 57.486 37.500 9.11 0.00 34.20 3.21
4980 7553 5.648960 GTGGGCATGAATTTGGATTTGAATT 59.351 36.000 0.00 0.00 0.00 2.17
5024 7597 7.337938 TCCATGAATTAGCTGTCTGTTCATAA 58.662 34.615 0.00 0.00 37.12 1.90
5050 7623 6.908870 AAACTTCAATCAACAAAAGAAGCC 57.091 33.333 0.00 0.00 39.33 4.35
5051 7624 4.610945 ACTTCAATCAACAAAAGAAGCCG 58.389 39.130 0.00 0.00 39.33 5.52
5052 7625 3.011949 TCAATCAACAAAAGAAGCCGC 57.988 42.857 0.00 0.00 0.00 6.53
5053 7626 2.360483 TCAATCAACAAAAGAAGCCGCA 59.640 40.909 0.00 0.00 0.00 5.69
5055 7628 0.383949 TCAACAAAAGAAGCCGCACC 59.616 50.000 0.00 0.00 0.00 5.01
5056 7629 0.597377 CAACAAAAGAAGCCGCACCC 60.597 55.000 0.00 0.00 0.00 4.61
5057 7630 1.744320 AACAAAAGAAGCCGCACCCC 61.744 55.000 0.00 0.00 0.00 4.95
5058 7631 1.903404 CAAAAGAAGCCGCACCCCT 60.903 57.895 0.00 0.00 0.00 4.79
5059 7632 1.603739 AAAAGAAGCCGCACCCCTC 60.604 57.895 0.00 0.00 0.00 4.30
5060 7633 3.569200 AAAGAAGCCGCACCCCTCC 62.569 63.158 0.00 0.00 0.00 4.30
5069 7642 4.452733 CACCCCTCCGCTTCCGAC 62.453 72.222 0.00 0.00 36.29 4.79
5089 7662 4.292178 CATCGCCGCCCTCCTCTC 62.292 72.222 0.00 0.00 0.00 3.20
5093 7666 4.851214 GCCGCCCTCCTCTCCTCT 62.851 72.222 0.00 0.00 0.00 3.69
5094 7667 2.520741 CCGCCCTCCTCTCCTCTC 60.521 72.222 0.00 0.00 0.00 3.20
5095 7668 2.520741 CGCCCTCCTCTCCTCTCC 60.521 72.222 0.00 0.00 0.00 3.71
5096 7669 2.520741 GCCCTCCTCTCCTCTCCG 60.521 72.222 0.00 0.00 0.00 4.63
5097 7670 2.520741 CCCTCCTCTCCTCTCCGC 60.521 72.222 0.00 0.00 0.00 5.54
5098 7671 2.904866 CCTCCTCTCCTCTCCGCG 60.905 72.222 0.00 0.00 0.00 6.46
5099 7672 3.591835 CTCCTCTCCTCTCCGCGC 61.592 72.222 0.00 0.00 0.00 6.86
5102 7675 3.222855 CTCTCCTCTCCGCGCCAT 61.223 66.667 0.00 0.00 0.00 4.40
5103 7676 3.496875 CTCTCCTCTCCGCGCCATG 62.497 68.421 0.00 0.00 0.00 3.66
5104 7677 4.598894 CTCCTCTCCGCGCCATGG 62.599 72.222 7.63 7.63 0.00 3.66
5106 7679 3.933722 CCTCTCCGCGCCATGGAT 61.934 66.667 18.40 0.00 34.32 3.41
5107 7680 2.664185 CTCTCCGCGCCATGGATG 60.664 66.667 18.40 8.13 34.32 3.51
5108 7681 4.916293 TCTCCGCGCCATGGATGC 62.916 66.667 18.40 17.55 34.32 3.91
5132 7705 4.980805 GTTGCCACCGTCTCCGCA 62.981 66.667 0.00 0.00 0.00 5.69
5133 7706 4.680237 TTGCCACCGTCTCCGCAG 62.680 66.667 0.00 0.00 31.86 5.18
5137 7710 4.680237 CACCGTCTCCGCAGCCAA 62.680 66.667 0.00 0.00 0.00 4.52
5138 7711 4.681978 ACCGTCTCCGCAGCCAAC 62.682 66.667 0.00 0.00 0.00 3.77
5156 7729 1.810030 CGCCGCCAAGGTTCTACTC 60.810 63.158 0.00 0.00 43.70 2.59
5166 7739 0.910338 GGTTCTACTCCCCACCCTTC 59.090 60.000 0.00 0.00 0.00 3.46
5179 7752 2.190578 CCTTCGCCATCCAGACCC 59.809 66.667 0.00 0.00 0.00 4.46
5188 7761 3.957435 ATCCAGACCCTCGTCCGCA 62.957 63.158 0.00 0.00 40.12 5.69
5190 7763 2.105128 CAGACCCTCGTCCGCATC 59.895 66.667 0.00 0.00 40.12 3.91
5205 7778 2.110627 ATCGAGCAGCATCAGGGC 59.889 61.111 0.00 0.00 0.00 5.19
5285 7858 1.827315 TTGTTTCCAGCTCGTTCGCG 61.827 55.000 0.00 0.00 42.98 5.87
5422 8018 2.431683 TCAGCAGCCCTGACCAAC 59.568 61.111 0.00 0.00 45.44 3.77
5433 8029 2.102925 CCCTGACCAACACAGCAAAAAT 59.897 45.455 0.00 0.00 34.47 1.82
5436 8032 4.278170 CCTGACCAACACAGCAAAAATCTA 59.722 41.667 0.00 0.00 34.47 1.98
5440 8036 6.488344 TGACCAACACAGCAAAAATCTACATA 59.512 34.615 0.00 0.00 0.00 2.29
5518 8114 2.899303 ACGAACATTCCAAATCCCCT 57.101 45.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.351111 GCTTCTTGGAGCATCTTCTTCG 59.649 50.000 0.00 0.00 42.25 3.79
17 18 1.277557 ACGCTTCTTGGAGCATCTTCT 59.722 47.619 1.57 0.00 42.83 2.85
27 28 1.813513 ATCTGTGGAACGCTTCTTGG 58.186 50.000 0.00 0.00 42.39 3.61
34 35 3.806257 CGCAATATCTGTGGAACGC 57.194 52.632 0.00 0.00 42.39 4.84
71 72 3.071747 AGGAGACTTTGGTCCTTGACTTC 59.928 47.826 0.00 0.00 40.54 3.01
107 108 2.704572 CTCACAACAGAGGGTGATTCC 58.295 52.381 0.00 0.00 42.62 3.01
117 118 1.413118 TCTCTGTGGCTCACAACAGA 58.587 50.000 8.96 3.40 44.08 3.41
118 119 2.245159 TTCTCTGTGGCTCACAACAG 57.755 50.000 8.96 7.99 44.08 3.16
120 121 2.481952 GTGATTCTCTGTGGCTCACAAC 59.518 50.000 8.96 0.58 44.08 3.32
121 122 2.104622 TGTGATTCTCTGTGGCTCACAA 59.895 45.455 8.96 0.00 44.08 3.33
317 323 2.203437 GCGGTGGTTCTTGGGGTT 60.203 61.111 0.00 0.00 0.00 4.11
318 324 3.494254 TGCGGTGGTTCTTGGGGT 61.494 61.111 0.00 0.00 0.00 4.95
346 367 3.204467 TTTGGTTGGAGGGAGCGGG 62.204 63.158 0.00 0.00 0.00 6.13
347 368 1.971695 GTTTGGTTGGAGGGAGCGG 60.972 63.158 0.00 0.00 0.00 5.52
348 369 1.971695 GGTTTGGTTGGAGGGAGCG 60.972 63.158 0.00 0.00 0.00 5.03
376 397 4.824515 CGGGGAGGAGAGAGCGGT 62.825 72.222 0.00 0.00 0.00 5.68
438 463 3.650950 AATCCCGCACTGCACCCT 61.651 61.111 1.11 0.00 0.00 4.34
620 651 1.086565 TGGATTGGGACCTGGGGAT 59.913 57.895 0.00 0.00 0.00 3.85
621 652 1.928567 GTGGATTGGGACCTGGGGA 60.929 63.158 0.00 0.00 0.00 4.81
622 653 2.683475 GTGGATTGGGACCTGGGG 59.317 66.667 0.00 0.00 0.00 4.96
623 654 2.215451 CTGGTGGATTGGGACCTGGG 62.215 65.000 0.00 0.00 32.98 4.45
667 698 4.806339 AAGCGGGGAGGGAGGGAG 62.806 72.222 0.00 0.00 0.00 4.30
668 699 4.798682 GAAGCGGGGAGGGAGGGA 62.799 72.222 0.00 0.00 0.00 4.20
669 700 4.806339 AGAAGCGGGGAGGGAGGG 62.806 72.222 0.00 0.00 0.00 4.30
670 701 3.157949 GAGAAGCGGGGAGGGAGG 61.158 72.222 0.00 0.00 0.00 4.30
671 702 1.268283 AAAGAGAAGCGGGGAGGGAG 61.268 60.000 0.00 0.00 0.00 4.30
791 823 3.870607 TTGCAGAGGGAGGGAGGCA 62.871 63.158 0.00 0.00 0.00 4.75
837 869 2.821437 CCCTAGACTCCAACCAAGAGA 58.179 52.381 0.00 0.00 35.27 3.10
884 916 3.001838 CCAAGAACACGAATTTCACACGA 59.998 43.478 0.00 0.00 0.00 4.35
906 938 1.303155 AACCCAGCAGAAGCAGAGC 60.303 57.895 0.00 0.00 45.49 4.09
907 939 0.035881 TCAACCCAGCAGAAGCAGAG 59.964 55.000 0.00 0.00 45.49 3.35
908 940 0.035881 CTCAACCCAGCAGAAGCAGA 59.964 55.000 0.00 0.00 45.49 4.26
924 980 1.946768 CGGAAGCAAACCAAGAACTCA 59.053 47.619 0.00 0.00 0.00 3.41
1267 1332 3.876341 TCTTTTAGTGGTTGTCCGTTGT 58.124 40.909 0.00 0.00 36.30 3.32
1268 1333 5.432885 AATCTTTTAGTGGTTGTCCGTTG 57.567 39.130 0.00 0.00 36.30 4.10
1269 1334 4.517832 GGAATCTTTTAGTGGTTGTCCGTT 59.482 41.667 0.00 0.00 36.30 4.44
1270 1335 4.070009 GGAATCTTTTAGTGGTTGTCCGT 58.930 43.478 0.00 0.00 36.30 4.69
1271 1336 4.154195 CAGGAATCTTTTAGTGGTTGTCCG 59.846 45.833 0.00 0.00 36.30 4.79
1272 1337 5.070685 ACAGGAATCTTTTAGTGGTTGTCC 58.929 41.667 0.00 0.00 0.00 4.02
1273 1338 6.438763 CAACAGGAATCTTTTAGTGGTTGTC 58.561 40.000 0.00 0.00 0.00 3.18
1287 1354 3.432252 CGTGACAACTACCAACAGGAATC 59.568 47.826 0.00 0.00 0.00 2.52
1291 1358 1.508632 CCGTGACAACTACCAACAGG 58.491 55.000 0.00 0.00 0.00 4.00
1432 3764 1.084370 GCCTCGTGCATCTGTACCAC 61.084 60.000 0.00 0.00 40.77 4.16
1434 3766 4.110493 GCCTCGTGCATCTGTACC 57.890 61.111 0.00 0.00 40.77 3.34
1772 4115 1.506493 GCGGCTGTGAGATGGATAAG 58.494 55.000 0.00 0.00 0.00 1.73
1889 4240 9.507329 AAGTACAAATCATAAGATTCACTGTGT 57.493 29.630 7.79 4.30 43.52 3.72
2932 5419 2.755103 GTGCCCCTTTTATCCAGTTCTG 59.245 50.000 0.00 0.00 0.00 3.02
2965 5453 8.622948 AATCTTGTTAAAAGGTGTAGAGAAGG 57.377 34.615 0.00 0.00 0.00 3.46
3063 5551 7.339212 ACCTATTTGTGCACATCTAGCATTTAA 59.661 33.333 22.39 8.08 44.79 1.52
3134 5622 5.928976 AGCCTATATTTCTGCATGTACACA 58.071 37.500 0.00 0.00 0.00 3.72
3524 6012 2.731572 CTGCCCTCATTCATCCACTTT 58.268 47.619 0.00 0.00 0.00 2.66
3947 6435 1.072489 TGTATCGTGCCACCAAAGGAA 59.928 47.619 0.00 0.00 0.00 3.36
4248 6736 2.396955 CGCTCTGCAGCCTTTGAGG 61.397 63.158 9.47 0.00 43.56 3.86
4483 7034 5.916883 GCAAAACCATCATTAGATCAATCGG 59.083 40.000 0.00 0.00 30.20 4.18
4484 7035 6.732154 AGCAAAACCATCATTAGATCAATCG 58.268 36.000 0.00 0.00 30.20 3.34
4632 7186 1.067974 TCGGGGAACATGCGTATACAG 59.932 52.381 3.32 0.00 0.00 2.74
4859 7424 4.330074 GTGACATACAAATTCCAGGTCGAG 59.670 45.833 0.00 0.00 0.00 4.04
4884 7449 1.202855 ACCAGGTCTATGCATGATGGC 60.203 52.381 10.16 0.63 0.00 4.40
4886 7451 3.812262 TCAACCAGGTCTATGCATGATG 58.188 45.455 10.16 0.00 0.00 3.07
4887 7452 4.508551 TTCAACCAGGTCTATGCATGAT 57.491 40.909 10.16 0.00 0.00 2.45
4888 7453 3.998913 TTCAACCAGGTCTATGCATGA 57.001 42.857 10.16 1.87 0.00 3.07
4889 7454 5.125900 TCAAATTCAACCAGGTCTATGCATG 59.874 40.000 10.16 0.00 0.00 4.06
4890 7455 5.263599 TCAAATTCAACCAGGTCTATGCAT 58.736 37.500 3.79 3.79 0.00 3.96
4898 7463 5.782893 TTTCGATTCAAATTCAACCAGGT 57.217 34.783 0.00 0.00 0.00 4.00
4901 7470 5.925397 CCACATTTCGATTCAAATTCAACCA 59.075 36.000 0.00 0.00 0.00 3.67
4941 7514 3.505386 TGCCCACATGTATCAGGTTTTT 58.495 40.909 0.00 0.00 0.00 1.94
4957 7530 4.904895 TTCAAATCCAAATTCATGCCCA 57.095 36.364 0.00 0.00 0.00 5.36
4958 7531 6.374894 TCAAATTCAAATCCAAATTCATGCCC 59.625 34.615 0.00 0.00 0.00 5.36
4980 7553 4.301505 GCCTGACGAGCCATTCAA 57.698 55.556 0.00 0.00 0.00 2.69
5024 7597 9.045223 GGCTTCTTTTGTTGATTGAAGTTTATT 57.955 29.630 0.00 0.00 37.17 1.40
5039 7612 2.200337 GGGGTGCGGCTTCTTTTGT 61.200 57.895 0.00 0.00 0.00 2.83
5040 7613 1.866853 GAGGGGTGCGGCTTCTTTTG 61.867 60.000 0.00 0.00 0.00 2.44
5041 7614 1.603739 GAGGGGTGCGGCTTCTTTT 60.604 57.895 0.00 0.00 0.00 2.27
5043 7616 4.035102 GGAGGGGTGCGGCTTCTT 62.035 66.667 0.00 0.00 0.00 2.52
5052 7625 4.452733 GTCGGAAGCGGAGGGGTG 62.453 72.222 0.00 0.00 0.00 4.61
5072 7645 4.292178 GAGAGGAGGGCGGCGATG 62.292 72.222 12.98 0.00 0.00 3.84
5076 7649 4.851214 AGAGGAGAGGAGGGCGGC 62.851 72.222 0.00 0.00 0.00 6.53
5077 7650 2.520741 GAGAGGAGAGGAGGGCGG 60.521 72.222 0.00 0.00 0.00 6.13
5078 7651 2.520741 GGAGAGGAGAGGAGGGCG 60.521 72.222 0.00 0.00 0.00 6.13
5079 7652 2.520741 CGGAGAGGAGAGGAGGGC 60.521 72.222 0.00 0.00 0.00 5.19
5080 7653 2.520741 GCGGAGAGGAGAGGAGGG 60.521 72.222 0.00 0.00 0.00 4.30
5081 7654 2.904866 CGCGGAGAGGAGAGGAGG 60.905 72.222 0.00 0.00 0.00 4.30
5082 7655 3.591835 GCGCGGAGAGGAGAGGAG 61.592 72.222 8.83 0.00 0.00 3.69
5085 7658 3.222855 ATGGCGCGGAGAGGAGAG 61.223 66.667 8.83 0.00 0.00 3.20
5086 7659 3.531207 CATGGCGCGGAGAGGAGA 61.531 66.667 8.83 0.00 0.00 3.71
5087 7660 4.598894 CCATGGCGCGGAGAGGAG 62.599 72.222 8.83 0.00 0.00 3.69
5089 7662 3.933722 ATCCATGGCGCGGAGAGG 61.934 66.667 8.83 2.99 35.56 3.69
5090 7663 2.664185 CATCCATGGCGCGGAGAG 60.664 66.667 8.83 0.54 35.56 3.20
5091 7664 4.916293 GCATCCATGGCGCGGAGA 62.916 66.667 8.83 0.00 35.56 3.71
5134 7707 4.038080 GAACCTTGGCGGCGTTGG 62.038 66.667 9.37 8.82 35.61 3.77
5135 7708 1.669760 TAGAACCTTGGCGGCGTTG 60.670 57.895 9.37 0.00 35.61 4.10
5136 7709 1.670083 GTAGAACCTTGGCGGCGTT 60.670 57.895 9.37 1.94 35.61 4.84
5137 7710 2.047560 GTAGAACCTTGGCGGCGT 60.048 61.111 9.37 0.00 35.61 5.68
5138 7711 1.810030 GAGTAGAACCTTGGCGGCG 60.810 63.158 0.51 0.51 35.61 6.46
5139 7712 1.449778 GGAGTAGAACCTTGGCGGC 60.450 63.158 0.00 0.00 35.61 6.53
5140 7713 1.221021 GGGAGTAGAACCTTGGCGG 59.779 63.158 0.00 0.00 39.35 6.13
5141 7714 1.221021 GGGGAGTAGAACCTTGGCG 59.779 63.158 0.00 0.00 0.00 5.69
5142 7715 0.035343 GTGGGGAGTAGAACCTTGGC 60.035 60.000 0.00 0.00 0.00 4.52
5143 7716 0.618981 GGTGGGGAGTAGAACCTTGG 59.381 60.000 0.00 0.00 0.00 3.61
5144 7717 0.618981 GGGTGGGGAGTAGAACCTTG 59.381 60.000 0.00 0.00 33.02 3.61
5145 7718 0.496841 AGGGTGGGGAGTAGAACCTT 59.503 55.000 0.00 0.00 33.02 3.50
5146 7719 0.496841 AAGGGTGGGGAGTAGAACCT 59.503 55.000 0.00 0.00 33.02 3.50
5147 7720 0.910338 GAAGGGTGGGGAGTAGAACC 59.090 60.000 0.00 0.00 0.00 3.62
5148 7721 0.535797 CGAAGGGTGGGGAGTAGAAC 59.464 60.000 0.00 0.00 0.00 3.01
5149 7722 1.262640 GCGAAGGGTGGGGAGTAGAA 61.263 60.000 0.00 0.00 0.00 2.10
5150 7723 1.684734 GCGAAGGGTGGGGAGTAGA 60.685 63.158 0.00 0.00 0.00 2.59
5156 7729 4.506255 GGATGGCGAAGGGTGGGG 62.506 72.222 0.00 0.00 0.00 4.96
5166 7739 3.432051 GACGAGGGTCTGGATGGCG 62.432 68.421 0.00 0.00 40.15 5.69
5188 7761 2.110627 GCCCTGATGCTGCTCGAT 59.889 61.111 0.00 0.00 0.00 3.59
5205 7778 4.760047 CTGGTCGCCGAACCCCAG 62.760 72.222 7.72 7.72 38.65 4.45
5378 7951 3.654143 AGCATGTGGAGCCAGGCA 61.654 61.111 15.80 0.00 44.17 4.75
5385 7981 0.322277 AAGGTGCTCAGCATGTGGAG 60.322 55.000 0.54 10.34 41.91 3.86
5422 8018 9.767684 TTTTACGATATGTAGATTTTTGCTGTG 57.232 29.630 0.00 0.00 33.75 3.66
5440 8036 9.543783 GTCTCCTATTGAGGTTATTTTTACGAT 57.456 33.333 0.00 0.00 44.19 3.73
5469 8065 6.543100 AGATTACCTTTGAAAAACACGTGGTA 59.457 34.615 21.57 5.24 31.58 3.25
5475 8071 8.739461 CGTAACAAGATTACCTTTGAAAAACAC 58.261 33.333 0.00 0.00 31.42 3.32
5518 8114 5.090652 GATGAAATCGCTGCGGTTATTTA 57.909 39.130 21.91 3.70 31.13 1.40


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

AutoCloner maintained by Alex Coulton.