Multiple sequence alignment - TraesCS3B01G084000

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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 TraesCS3B01G084000 chr3B 100.000 3920 0 0 848 4767 52893139 52889220 0.000000e+00 7239.0
1 TraesCS3B01G084000 chr3B 100.000 357 0 0 1 357 52893986 52893630 0.000000e+00 660.0
2 TraesCS3B01G084000 chr3B 90.909 110 2 2 192 297 52893735 52893630 1.790000e-29 141.0
3 TraesCS3B01G084000 chr3B 90.909 110 2 2 252 357 52893795 52893690 1.790000e-29 141.0
4 TraesCS3B01G084000 chr2D 96.682 3014 100 0 848 3861 2341605 2344618 0.000000e+00 5012.0
5 TraesCS3B01G084000 chr2D 81.693 1819 327 6 1466 3281 11425556 11423741 0.000000e+00 1509.0
6 TraesCS3B01G084000 chr2D 94.697 264 12 2 8 271 2340552 2340813 4.440000e-110 409.0
7 TraesCS3B01G084000 chr2D 82.353 357 35 9 3907 4244 2345134 2345481 7.810000e-73 285.0
8 TraesCS3B01G084000 chr2D 82.622 328 21 13 4259 4582 2345528 2345823 1.700000e-64 257.0
9 TraesCS3B01G084000 chr2D 93.567 171 9 2 4598 4767 2345872 2346041 2.200000e-63 254.0
10 TraesCS3B01G084000 chr2D 91.250 80 3 1 252 327 2340734 2340813 6.520000e-19 106.0
11 TraesCS3B01G084000 chr2A 96.547 2809 86 2 1077 3885 2334443 2337240 0.000000e+00 4639.0
12 TraesCS3B01G084000 chr2A 95.436 241 11 0 848 1088 2331370 2331610 7.480000e-103 385.0
13 TraesCS3B01G084000 chr2A 84.058 345 29 11 3907 4233 2338570 2338906 4.630000e-80 309.0
14 TraesCS3B01G084000 chr2A 92.982 57 4 0 4259 4315 2339231 2339287 3.060000e-12 84.2
15 TraesCS3B01G084000 chr4D 85.976 2510 324 22 1368 3863 3714133 3716628 0.000000e+00 2660.0
16 TraesCS3B01G084000 chr4D 86.061 1980 264 8 1379 3350 3420953 3418978 0.000000e+00 2117.0
17 TraesCS3B01G084000 chr4D 79.370 698 120 15 848 1530 3712599 3713287 2.010000e-128 470.0
18 TraesCS3B01G084000 chr4D 83.259 448 64 8 3399 3842 3418961 3418521 7.430000e-108 401.0
19 TraesCS3B01G084000 chr4B 85.218 2503 346 19 1373 3866 4953464 4950977 0.000000e+00 2551.0
20 TraesCS3B01G084000 chr4B 84.331 2489 347 24 1350 3830 6056975 6059428 0.000000e+00 2396.0
21 TraesCS3B01G084000 chr4B 86.864 1964 243 15 1352 3308 6040162 6042117 0.000000e+00 2183.0
22 TraesCS3B01G084000 chr4B 86.605 433 56 2 3382 3813 6042152 6042583 1.200000e-130 477.0
23 TraesCS3B01G084000 chr4B 79.245 689 116 17 848 1530 4954982 4954315 5.620000e-124 455.0
24 TraesCS3B01G084000 chr4B 78.404 727 128 19 848 1567 6055913 6056617 3.380000e-121 446.0
25 TraesCS3B01G084000 chr4A 85.467 2422 323 23 1379 3788 600918291 600915887 0.000000e+00 2495.0
26 TraesCS3B01G084000 chr4A 85.159 2008 289 8 1352 3352 601311418 601313423 0.000000e+00 2049.0
27 TraesCS3B01G084000 chr4A 83.406 687 106 7 848 1530 601309907 601310589 8.710000e-177 630.0
28 TraesCS3B01G084000 chr4A 80.602 665 106 15 848 1508 600919821 600919176 4.290000e-135 492.0
29 TraesCS3B01G084000 chr4A 83.368 487 67 10 3399 3876 601313438 601313919 5.660000e-119 438.0
30 TraesCS3B01G084000 chr2B 90.625 352 19 8 1 348 8710377 8710718 5.620000e-124 455.0
31 TraesCS3B01G084000 chr2B 98.276 58 1 0 848 905 8712224 8712281 8.440000e-18 102.0
32 TraesCS3B01G084000 chr2B 88.525 61 5 2 4364 4424 667794346 667794404 6.620000e-09 73.1


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 TraesCS3B01G084000 chr3B 52889220 52893986 4766 True 2045.250000 7239 95.454500 1 4767 4 chr3B.!!$R1 4766
1 TraesCS3B01G084000 chr2D 11423741 11425556 1815 True 1509.000000 1509 81.693000 1466 3281 1 chr2D.!!$R1 1815
2 TraesCS3B01G084000 chr2D 2340552 2346041 5489 False 1053.833333 5012 90.195167 8 4767 6 chr2D.!!$F1 4759
3 TraesCS3B01G084000 chr2A 2331370 2339287 7917 False 1354.300000 4639 92.255750 848 4315 4 chr2A.!!$F1 3467
4 TraesCS3B01G084000 chr4D 3712599 3716628 4029 False 1565.000000 2660 82.673000 848 3863 2 chr4D.!!$F1 3015
5 TraesCS3B01G084000 chr4D 3418521 3420953 2432 True 1259.000000 2117 84.660000 1379 3842 2 chr4D.!!$R1 2463
6 TraesCS3B01G084000 chr4B 4950977 4954982 4005 True 1503.000000 2551 82.231500 848 3866 2 chr4B.!!$R1 3018
7 TraesCS3B01G084000 chr4B 6055913 6059428 3515 False 1421.000000 2396 81.367500 848 3830 2 chr4B.!!$F2 2982
8 TraesCS3B01G084000 chr4B 6040162 6042583 2421 False 1330.000000 2183 86.734500 1352 3813 2 chr4B.!!$F1 2461
9 TraesCS3B01G084000 chr4A 600915887 600919821 3934 True 1493.500000 2495 83.034500 848 3788 2 chr4A.!!$R1 2940
10 TraesCS3B01G084000 chr4A 601309907 601313919 4012 False 1039.000000 2049 83.977667 848 3876 3 chr4A.!!$F1 3028
11 TraesCS3B01G084000 chr2B 8710377 8712281 1904 False 278.500000 455 94.450500 1 905 2 chr2B.!!$F2 904

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
354 359 0.322546 ATCTGCCCGGGTGACTTTTC 60.323 55.000 24.63 2.41 0.00 2.29 F
1659 6974 0.692476 TGTGTGCTGGAGGTATGCTT 59.308 50.000 0.00 0.00 0.00 3.91 F
1802 7117 2.039418 GGGGGTTTATCCAAATCTGGC 58.961 52.381 0.00 0.00 43.17 4.85 F
2527 7848 3.941483 CCCTTGTAGTAGTGCAAATCAGG 59.059 47.826 2.59 0.49 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2014 7332 0.671781 CCGAGGCTCAGGTTGAACAG 60.672 60.000 15.95 0.0 0.00 3.16 R
2527 7848 0.323816 CCTTTCCTTTCCCCTCTGCC 60.324 60.000 0.00 0.0 0.00 4.85 R
3237 8558 2.024306 GCAAGATAGCCTTTGGTCCCC 61.024 57.143 0.00 0.0 31.42 4.81 R
4390 11684 0.179034 GTGAGCACTCCCATCCCATC 60.179 60.000 0.00 0.0 0.00 3.51 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
71 72 8.830915 TGGGTTATGCTTATCCTAAAATCAAA 57.169 30.769 6.67 0.00 0.00 2.69
144 145 5.185249 AGCGGTTCAGAGTTCAGAGTAATAA 59.815 40.000 0.00 0.00 0.00 1.40
146 147 6.035112 GCGGTTCAGAGTTCAGAGTAATAAAG 59.965 42.308 0.00 0.00 0.00 1.85
148 149 7.062371 CGGTTCAGAGTTCAGAGTAATAAAGTG 59.938 40.741 0.00 0.00 0.00 3.16
160 161 3.829886 AATAAAGTGTCCACGTGCATG 57.170 42.857 10.91 3.82 36.20 4.06
188 189 6.154192 CCATATATCACTCACTAGTCTGGCAT 59.846 42.308 0.00 0.00 31.97 4.40
220 221 1.183549 TCAAACGGAGAGAGGCCTAC 58.816 55.000 4.42 2.65 0.00 3.18
280 281 1.183549 TCAAACGGAGAGAGGCCTAC 58.816 55.000 4.42 2.65 0.00 3.18
293 298 3.652581 GCCTACCTGCCTGACTTTT 57.347 52.632 0.00 0.00 0.00 2.27
322 327 6.021782 CACGACACAACAGTGTAAAATCAAAC 60.022 38.462 0.00 0.00 45.96 2.93
348 353 1.760875 GACCTATCTGCCCGGGTGA 60.761 63.158 24.63 20.87 31.60 4.02
349 354 2.029307 GACCTATCTGCCCGGGTGAC 62.029 65.000 24.63 5.90 31.60 3.67
350 355 1.762460 CCTATCTGCCCGGGTGACT 60.762 63.158 24.63 12.61 0.00 3.41
352 357 0.541863 CTATCTGCCCGGGTGACTTT 59.458 55.000 24.63 8.72 0.00 2.66
353 358 0.988832 TATCTGCCCGGGTGACTTTT 59.011 50.000 24.63 8.37 0.00 2.27
354 359 0.322546 ATCTGCCCGGGTGACTTTTC 60.323 55.000 24.63 2.41 0.00 2.29
355 360 1.228124 CTGCCCGGGTGACTTTTCA 60.228 57.895 24.63 7.74 0.00 2.69
356 361 1.228124 TGCCCGGGTGACTTTTCAG 60.228 57.895 24.63 0.00 30.10 3.02
945 1961 2.476534 GAAGCAACACCACATGGCCG 62.477 60.000 0.00 0.00 39.32 6.13
983 1999 0.751643 AAGTGCGGCAAGAACCAAGT 60.752 50.000 3.23 0.00 0.00 3.16
1066 2088 1.974957 TGGAATCCCTCAACTTCACGA 59.025 47.619 0.00 0.00 0.00 4.35
1171 5037 1.271379 ACCTGCGACACCTAATGCTTT 60.271 47.619 0.00 0.00 0.00 3.51
1575 6887 0.871722 TTCCACGAGAAATTGGCACG 59.128 50.000 0.00 0.00 0.00 5.34
1576 6888 0.953471 TCCACGAGAAATTGGCACGG 60.953 55.000 0.00 0.00 0.00 4.94
1590 6902 1.541233 GGCACGGTAATGGATCTCAGG 60.541 57.143 0.00 0.00 0.00 3.86
1659 6974 0.692476 TGTGTGCTGGAGGTATGCTT 59.308 50.000 0.00 0.00 0.00 3.91
1802 7117 2.039418 GGGGGTTTATCCAAATCTGGC 58.961 52.381 0.00 0.00 43.17 4.85
2185 7503 5.463061 CGCCTTTTGAAGTTGAATCACAATT 59.537 36.000 0.00 0.00 40.76 2.32
2527 7848 3.941483 CCCTTGTAGTAGTGCAAATCAGG 59.059 47.826 2.59 0.49 0.00 3.86
2656 7977 5.971763 AGAAAACCAATGCAACTAACAACA 58.028 33.333 0.00 0.00 0.00 3.33
2894 8215 5.964958 ATGTTCAATCGTGAAATTGAGGT 57.035 34.783 0.24 0.00 45.29 3.85
3180 8501 5.670149 ATGAATTTAGAGCTTGCATCTCG 57.330 39.130 9.86 0.00 35.79 4.04
3237 8558 0.449388 GGAATCTCACAAGGCTTGCG 59.551 55.000 26.45 17.90 0.00 4.85
3706 9042 4.630505 GTCGGTGATGAGCTATCTACGATA 59.369 45.833 16.69 0.00 42.21 2.92
3750 9086 1.391577 TATTTGCACGCTGGCATCAT 58.608 45.000 0.00 0.00 44.48 2.45
3819 9163 5.185056 TCGTATCATGTGGTTTCTTCTCTGA 59.815 40.000 0.00 0.00 0.00 3.27
3831 9179 7.506261 TGGTTTCTTCTCTGATACCTACCTATC 59.494 40.741 0.00 0.00 38.38 2.08
3834 9182 7.395525 TCTTCTCTGATACCTACCTATCTGT 57.604 40.000 0.00 0.00 0.00 3.41
3848 9196 8.718734 CCTACCTATCTGTTTAAAAAGTGTCAC 58.281 37.037 5.29 0.00 0.00 3.67
3850 9198 8.379457 ACCTATCTGTTTAAAAAGTGTCACTC 57.621 34.615 5.82 0.00 0.00 3.51
3892 9240 3.568007 TGGAACATGCAAACCAACTCTAC 59.432 43.478 0.00 0.00 0.00 2.59
3893 9241 3.821033 GGAACATGCAAACCAACTCTACT 59.179 43.478 0.00 0.00 0.00 2.57
3894 9242 4.320494 GGAACATGCAAACCAACTCTACTG 60.320 45.833 0.00 0.00 0.00 2.74
3896 9244 2.340210 TGCAAACCAACTCTACTGCA 57.660 45.000 0.00 0.00 37.46 4.41
3897 9245 2.862541 TGCAAACCAACTCTACTGCAT 58.137 42.857 0.00 0.00 35.02 3.96
3898 9246 2.553602 TGCAAACCAACTCTACTGCATG 59.446 45.455 0.00 0.00 35.02 4.06
3899 9247 2.813754 GCAAACCAACTCTACTGCATGA 59.186 45.455 0.00 0.00 0.00 3.07
3900 9248 3.253188 GCAAACCAACTCTACTGCATGAA 59.747 43.478 0.00 0.00 0.00 2.57
3901 9249 4.787598 CAAACCAACTCTACTGCATGAAC 58.212 43.478 0.00 0.00 0.00 3.18
3902 9250 4.357918 AACCAACTCTACTGCATGAACT 57.642 40.909 0.00 0.00 0.00 3.01
3903 9251 3.668447 ACCAACTCTACTGCATGAACTG 58.332 45.455 0.00 0.00 0.00 3.16
3949 10920 6.292919 GCAGTACGGCTCATTATAGAAAAAGG 60.293 42.308 10.99 0.00 0.00 3.11
3957 10928 7.436376 GGCTCATTATAGAAAAAGGAAACATGC 59.564 37.037 0.00 0.00 0.00 4.06
4037 11008 1.403249 GGTGCTCATTCATGTTGGTGC 60.403 52.381 0.00 2.29 0.00 5.01
4079 11069 3.564133 CCATGTTCTCTTTGATTCCCCCA 60.564 47.826 0.00 0.00 0.00 4.96
4080 11070 3.893753 TGTTCTCTTTGATTCCCCCAA 57.106 42.857 0.00 0.00 0.00 4.12
4101 11091 2.560504 AGTGTTGTTGCTCGATCACAA 58.439 42.857 0.00 0.00 0.00 3.33
4113 11103 4.706527 CTCGATCACAAAAACAGAGCTTC 58.293 43.478 0.00 0.00 0.00 3.86
4122 11112 9.033481 TCACAAAAACAGAGCTTCATTAATTTG 57.967 29.630 0.00 0.00 0.00 2.32
4124 11114 9.598517 ACAAAAACAGAGCTTCATTAATTTGAA 57.401 25.926 12.27 0.00 34.55 2.69
4163 11154 8.306761 TGGCTGGAGATTTATTTTCTTTCTTTC 58.693 33.333 0.00 0.00 0.00 2.62
4164 11155 8.526978 GGCTGGAGATTTATTTTCTTTCTTTCT 58.473 33.333 0.00 0.00 0.00 2.52
4177 11168 6.114187 TCTTTCTTTCTATGCAACCAGAGA 57.886 37.500 0.00 0.00 37.52 3.10
4178 11169 6.533730 TCTTTCTTTCTATGCAACCAGAGAA 58.466 36.000 0.00 0.00 44.91 2.87
4188 11179 4.854399 TGCAACCAGAGAAATTTGTAACG 58.146 39.130 0.00 0.00 0.00 3.18
4191 11182 5.398416 GCAACCAGAGAAATTTGTAACGAAC 59.602 40.000 0.00 0.00 0.00 3.95
4198 11189 9.408069 CAGAGAAATTTGTAACGAACTAGTACT 57.592 33.333 0.00 0.00 0.00 2.73
4254 11508 1.571460 GCGTTTGCTGACTCACTGG 59.429 57.895 0.00 0.00 38.39 4.00
4255 11509 1.845809 GCGTTTGCTGACTCACTGGG 61.846 60.000 0.00 0.00 38.39 4.45
4256 11510 0.532862 CGTTTGCTGACTCACTGGGT 60.533 55.000 0.00 0.00 0.00 4.51
4257 11511 1.680338 GTTTGCTGACTCACTGGGTT 58.320 50.000 0.00 0.00 0.00 4.11
4261 11551 0.250513 GCTGACTCACTGGGTTAGGG 59.749 60.000 3.17 0.00 0.00 3.53
4304 11594 1.153369 CATCCTAGTGTGTGGCGGG 60.153 63.158 0.00 0.00 0.00 6.13
4317 11607 2.590092 GCGGGGTTAGTGGCATCT 59.410 61.111 0.00 0.00 0.00 2.90
4318 11608 1.523938 GCGGGGTTAGTGGCATCTC 60.524 63.158 0.00 0.00 0.00 2.75
4329 11619 6.291377 GTTAGTGGCATCTCAGGAATGATTA 58.709 40.000 0.00 0.00 0.00 1.75
4336 11630 5.007430 GCATCTCAGGAATGATTATATGCCG 59.993 44.000 0.00 0.00 32.95 5.69
4351 11645 1.154469 GCCGCGTCAGTTAACTTGC 60.154 57.895 5.07 9.55 0.00 4.01
4366 11660 1.483827 ACTTGCTGCAGAGCTATGCTA 59.516 47.619 31.40 17.86 46.39 3.49
4376 11670 5.527511 CAGAGCTATGCTATGTACAATGC 57.472 43.478 14.18 14.18 42.12 3.56
4377 11671 4.391216 CAGAGCTATGCTATGTACAATGCC 59.609 45.833 17.11 5.55 42.12 4.40
4378 11672 3.679389 AGCTATGCTATGTACAATGCCC 58.321 45.455 17.11 6.67 36.99 5.36
4379 11673 3.328931 AGCTATGCTATGTACAATGCCCT 59.671 43.478 17.11 9.60 36.99 5.19
4380 11674 3.438087 GCTATGCTATGTACAATGCCCTG 59.562 47.826 17.11 9.95 0.00 4.45
4381 11675 1.679139 TGCTATGTACAATGCCCTGC 58.321 50.000 17.11 7.66 0.00 4.85
4382 11676 1.212688 TGCTATGTACAATGCCCTGCT 59.787 47.619 17.11 0.00 0.00 4.24
4383 11677 1.605710 GCTATGTACAATGCCCTGCTG 59.394 52.381 0.00 0.00 0.00 4.41
4390 11684 0.174845 CAATGCCCTGCTGAACATGG 59.825 55.000 0.00 0.00 37.14 3.66
4393 11687 0.681887 TGCCCTGCTGAACATGGATG 60.682 55.000 0.00 0.00 36.19 3.51
4408 11702 1.348008 GGATGGGATGGGAGTGCTCA 61.348 60.000 1.41 0.00 0.00 4.26
4409 11703 0.179034 GATGGGATGGGAGTGCTCAC 60.179 60.000 1.41 0.00 0.00 3.51
4411 11705 1.997874 GGGATGGGAGTGCTCACCT 60.998 63.158 2.25 0.00 30.24 4.00
4412 11706 1.566298 GGGATGGGAGTGCTCACCTT 61.566 60.000 2.25 0.00 30.24 3.50
4413 11707 0.107459 GGATGGGAGTGCTCACCTTC 60.107 60.000 2.25 6.55 30.24 3.46
4414 11708 0.615331 GATGGGAGTGCTCACCTTCA 59.385 55.000 2.25 0.00 30.24 3.02
4417 11711 1.484444 GGGAGTGCTCACCTTCACCT 61.484 60.000 2.25 0.00 33.90 4.00
4418 11712 0.398318 GGAGTGCTCACCTTCACCTT 59.602 55.000 1.41 0.00 33.90 3.50
4420 11714 1.070758 GAGTGCTCACCTTCACCTTGA 59.929 52.381 0.00 0.00 33.90 3.02
4421 11715 1.701847 AGTGCTCACCTTCACCTTGAT 59.298 47.619 0.00 0.00 33.90 2.57
4422 11716 1.808945 GTGCTCACCTTCACCTTGATG 59.191 52.381 0.00 0.00 0.00 3.07
4423 11717 0.807496 GCTCACCTTCACCTTGATGC 59.193 55.000 0.00 0.00 0.00 3.91
4424 11718 1.081892 CTCACCTTCACCTTGATGCG 58.918 55.000 0.00 0.00 0.00 4.73
4425 11719 0.955428 TCACCTTCACCTTGATGCGC 60.955 55.000 0.00 0.00 0.00 6.09
4429 11723 1.000385 CCTTCACCTTGATGCGCAAAA 60.000 47.619 17.11 11.73 35.74 2.44
4430 11724 2.322161 CTTCACCTTGATGCGCAAAAG 58.678 47.619 17.11 20.80 35.74 2.27
4431 11725 1.603456 TCACCTTGATGCGCAAAAGA 58.397 45.000 28.26 12.88 35.74 2.52
4432 11726 1.952990 TCACCTTGATGCGCAAAAGAA 59.047 42.857 28.26 15.46 35.74 2.52
4433 11727 2.360483 TCACCTTGATGCGCAAAAGAAA 59.640 40.909 28.26 15.20 35.74 2.52
4434 11728 3.122297 CACCTTGATGCGCAAAAGAAAA 58.878 40.909 28.26 11.90 35.74 2.29
4435 11729 3.182972 CACCTTGATGCGCAAAAGAAAAG 59.817 43.478 28.26 18.50 35.74 2.27
4436 11730 3.068024 ACCTTGATGCGCAAAAGAAAAGA 59.932 39.130 28.26 0.00 35.74 2.52
4437 11731 4.050553 CCTTGATGCGCAAAAGAAAAGAA 58.949 39.130 28.26 7.26 35.74 2.52
4438 11732 4.507388 CCTTGATGCGCAAAAGAAAAGAAA 59.493 37.500 28.26 7.32 35.74 2.52
4439 11733 5.388225 TTGATGCGCAAAAGAAAAGAAAC 57.612 34.783 17.11 0.00 32.46 2.78
4440 11734 3.801594 TGATGCGCAAAAGAAAAGAAACC 59.198 39.130 17.11 0.00 0.00 3.27
4441 11735 3.518634 TGCGCAAAAGAAAAGAAACCT 57.481 38.095 8.16 0.00 0.00 3.50
4442 11736 3.186119 TGCGCAAAAGAAAAGAAACCTG 58.814 40.909 8.16 0.00 0.00 4.00
4443 11737 2.033747 GCGCAAAAGAAAAGAAACCTGC 60.034 45.455 0.30 0.00 0.00 4.85
4467 11761 2.256461 CCTTTGCGCCAAGTGAGC 59.744 61.111 18.77 0.00 0.00 4.26
4468 11762 2.256461 CTTTGCGCCAAGTGAGCC 59.744 61.111 12.85 0.00 0.00 4.70
4469 11763 3.273080 CTTTGCGCCAAGTGAGCCC 62.273 63.158 12.85 0.00 0.00 5.19
4494 11788 1.135721 GGTTCAGAAAGGCCATCATGC 59.864 52.381 5.01 0.00 0.00 4.06
4524 11818 2.229543 GTCAAGCTCAATGTTGATGCCA 59.770 45.455 11.11 0.00 36.46 4.92
4582 11876 4.460683 GCGACCACCGTGGCCATA 62.461 66.667 17.99 0.00 42.67 2.74
4583 11877 2.504032 CGACCACCGTGGCCATAT 59.496 61.111 17.99 0.00 42.67 1.78
4584 11878 1.887242 CGACCACCGTGGCCATATG 60.887 63.158 17.99 7.87 42.67 1.78
4585 11879 2.124320 ACCACCGTGGCCATATGC 60.124 61.111 17.99 0.00 42.67 3.14
4594 11888 2.935955 GCCATATGCCGTGTACGC 59.064 61.111 0.00 0.00 38.18 4.42
4595 11889 2.604174 GCCATATGCCGTGTACGCC 61.604 63.158 0.00 0.00 38.18 5.68
4596 11890 1.227409 CCATATGCCGTGTACGCCA 60.227 57.895 0.00 0.00 38.18 5.69
4600 11927 0.741574 TATGCCGTGTACGCCAAAGG 60.742 55.000 0.00 0.00 38.18 3.11
4609 11936 2.004733 GTACGCCAAAGGGACATACAC 58.995 52.381 0.00 0.00 35.59 2.90
4638 11965 2.298610 GCAAGGGGTCTTTAGCATACC 58.701 52.381 0.00 0.00 0.00 2.73
4689 12016 4.130118 CAATAGTATCCCTGAAGGCACAC 58.870 47.826 0.00 0.00 34.51 3.82
4698 12025 1.199327 CTGAAGGCACACATCAAGCTG 59.801 52.381 0.00 0.00 0.00 4.24
4714 12041 2.983229 AGCTGTTGTTGCAGGAGATAG 58.017 47.619 0.00 0.00 37.00 2.08
4757 12085 8.339344 TCAGATCTGCTTCATTTTAATCACAA 57.661 30.769 18.36 0.00 0.00 3.33
4759 12087 7.701078 CAGATCTGCTTCATTTTAATCACAAGG 59.299 37.037 10.38 0.00 0.00 3.61
4761 12089 7.707624 TCTGCTTCATTTTAATCACAAGGAT 57.292 32.000 0.00 0.00 38.05 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 3.587498 AGCATAACCCATACTGCTCCTA 58.413 45.455 0.00 0.00 40.85 2.94
101 102 3.836348 CGCTAATGTACCGAAAACAAACG 59.164 43.478 0.00 0.00 0.00 3.60
144 145 0.944386 GTTCATGCACGTGGACACTT 59.056 50.000 18.88 0.00 0.00 3.16
146 147 1.163420 TGGTTCATGCACGTGGACAC 61.163 55.000 18.88 12.09 28.66 3.67
148 149 1.732941 TATGGTTCATGCACGTGGAC 58.267 50.000 18.88 1.86 0.00 4.02
160 161 7.598278 CCAGACTAGTGAGTGATATATGGTTC 58.402 42.308 0.00 0.00 35.45 3.62
188 189 3.215151 TCCGTTTGATTTTACACTGCCA 58.785 40.909 0.00 0.00 0.00 4.92
220 221 0.322456 TGAAAAGTCATCCGGGCAGG 60.322 55.000 0.00 0.00 42.97 4.85
229 230 2.560504 TGTGTCGTGCTGAAAAGTCAT 58.439 42.857 0.00 0.00 31.85 3.06
293 298 2.676744 CACTGTTGTGTCGTGCTGA 58.323 52.632 0.00 0.00 39.24 4.26
322 327 1.243902 GGCAGATAGGTCTCTCTCCG 58.756 60.000 0.00 0.00 30.42 4.63
945 1961 0.394216 TGATGCCATACCAGGTGCAC 60.394 55.000 8.80 8.80 36.41 4.57
1575 6887 7.540474 TTGTAGATACCTGAGATCCATTACC 57.460 40.000 0.00 0.00 0.00 2.85
1802 7117 9.458727 AATTATTTGAGCTCATATCCATGTAGG 57.541 33.333 21.03 0.00 39.47 3.18
1926 7241 2.546795 CCTTAGTTGAGATAGCTGCCCG 60.547 54.545 0.00 0.00 0.00 6.13
2014 7332 0.671781 CCGAGGCTCAGGTTGAACAG 60.672 60.000 15.95 0.00 0.00 3.16
2185 7503 2.764572 GAGGGATGTTTCCTCCGAAGTA 59.235 50.000 0.00 0.00 43.71 2.24
2527 7848 0.323816 CCTTTCCTTTCCCCTCTGCC 60.324 60.000 0.00 0.00 0.00 4.85
2894 8215 2.545742 CGATGACGGATCTGCACCAATA 60.546 50.000 0.00 0.00 35.72 1.90
3180 8501 3.653539 ATTTTTGCCGTACCAAAGTCC 57.346 42.857 0.00 0.00 36.21 3.85
3237 8558 2.024306 GCAAGATAGCCTTTGGTCCCC 61.024 57.143 0.00 0.00 31.42 4.81
3354 8690 7.768120 TGCAACTAAATGGTTCAAAAGTTCATT 59.232 29.630 0.00 0.00 0.00 2.57
3602 8938 6.261158 GTGAGCATGCGGTATATATCTCTAGA 59.739 42.308 13.01 0.00 0.00 2.43
3706 9042 4.756642 TCGACATGATCTTCACAAGCTTTT 59.243 37.500 0.00 0.00 0.00 2.27
3831 9179 7.278868 ACAGAGAGAGTGACACTTTTTAAACAG 59.721 37.037 10.01 0.00 0.00 3.16
3834 9182 9.095065 GTTACAGAGAGAGTGACACTTTTTAAA 57.905 33.333 10.01 0.00 0.00 1.52
3848 9196 9.521841 TTCCATATATACCAGTTACAGAGAGAG 57.478 37.037 0.00 0.00 0.00 3.20
3850 9198 9.078990 TGTTCCATATATACCAGTTACAGAGAG 57.921 37.037 0.00 0.00 0.00 3.20
3876 9224 2.862541 TGCAGTAGAGTTGGTTTGCAT 58.137 42.857 0.00 0.00 36.71 3.96
3877 9225 2.340210 TGCAGTAGAGTTGGTTTGCA 57.660 45.000 0.00 0.00 39.03 4.08
3896 9244 8.982685 CGTTCAGAAACATATATAGCAGTTCAT 58.017 33.333 0.00 0.00 34.93 2.57
3897 9245 7.979537 ACGTTCAGAAACATATATAGCAGTTCA 59.020 33.333 0.00 0.00 34.93 3.18
3898 9246 8.269424 CACGTTCAGAAACATATATAGCAGTTC 58.731 37.037 0.00 0.00 34.93 3.01
3899 9247 7.254455 GCACGTTCAGAAACATATATAGCAGTT 60.254 37.037 0.00 0.00 34.93 3.16
3900 9248 6.201044 GCACGTTCAGAAACATATATAGCAGT 59.799 38.462 0.00 0.00 34.93 4.40
3901 9249 6.200854 TGCACGTTCAGAAACATATATAGCAG 59.799 38.462 0.00 0.00 34.93 4.24
3902 9250 6.045955 TGCACGTTCAGAAACATATATAGCA 58.954 36.000 0.00 0.00 34.93 3.49
3903 9251 6.201044 ACTGCACGTTCAGAAACATATATAGC 59.799 38.462 22.14 0.00 37.51 2.97
3904 9252 7.700322 ACTGCACGTTCAGAAACATATATAG 57.300 36.000 22.14 0.00 37.51 1.31
3931 10896 7.436376 GCATGTTTCCTTTTTCTATAATGAGCC 59.564 37.037 0.00 0.00 0.00 4.70
3937 10902 6.827586 ACCGCATGTTTCCTTTTTCTATAA 57.172 33.333 0.00 0.00 0.00 0.98
3939 10904 5.944007 ACTACCGCATGTTTCCTTTTTCTAT 59.056 36.000 0.00 0.00 0.00 1.98
3949 10920 2.348666 CAGCACTACTACCGCATGTTTC 59.651 50.000 0.00 0.00 0.00 2.78
3957 10928 5.647589 TGAACTTTATCAGCACTACTACCG 58.352 41.667 0.00 0.00 0.00 4.02
4037 11008 1.225376 TGGCACCGTAGCAAGAAACG 61.225 55.000 0.00 0.00 38.80 3.60
4079 11069 2.942376 TGTGATCGAGCAACAACACTTT 59.058 40.909 4.22 0.00 0.00 2.66
4080 11070 2.560504 TGTGATCGAGCAACAACACTT 58.439 42.857 4.22 0.00 0.00 3.16
4113 11103 7.148373 CCAACCTTTGCATCCTTCAAATTAATG 60.148 37.037 0.00 0.00 33.54 1.90
4122 11112 1.067354 CAGCCAACCTTTGCATCCTTC 60.067 52.381 0.00 0.00 0.00 3.46
4124 11114 0.901580 CCAGCCAACCTTTGCATCCT 60.902 55.000 0.00 0.00 0.00 3.24
4125 11115 0.899717 TCCAGCCAACCTTTGCATCC 60.900 55.000 0.00 0.00 0.00 3.51
4134 11124 5.921962 AGAAAATAAATCTCCAGCCAACC 57.078 39.130 0.00 0.00 0.00 3.77
4163 11154 6.742718 CGTTACAAATTTCTCTGGTTGCATAG 59.257 38.462 0.00 0.00 0.00 2.23
4164 11155 6.428465 TCGTTACAAATTTCTCTGGTTGCATA 59.572 34.615 0.00 0.00 0.00 3.14
4165 11156 5.240623 TCGTTACAAATTTCTCTGGTTGCAT 59.759 36.000 0.00 0.00 0.00 3.96
4166 11157 4.576873 TCGTTACAAATTTCTCTGGTTGCA 59.423 37.500 0.00 0.00 0.00 4.08
4170 11161 7.215085 ACTAGTTCGTTACAAATTTCTCTGGT 58.785 34.615 0.00 0.00 0.00 4.00
4171 11162 7.653767 ACTAGTTCGTTACAAATTTCTCTGG 57.346 36.000 0.00 0.00 0.00 3.86
4211 11202 4.571984 GCGCCTGATGCAACATCATATATA 59.428 41.667 10.48 0.00 41.33 0.86
4212 11203 3.376234 GCGCCTGATGCAACATCATATAT 59.624 43.478 10.48 0.00 41.33 0.86
4221 11212 4.824166 CGCTGCGCCTGATGCAAC 62.824 66.667 9.88 0.00 42.70 4.17
4225 11216 2.202388 CAAACGCTGCGCCTGATG 60.202 61.111 23.51 10.08 0.00 3.07
4237 11491 0.532862 ACCCAGTGAGTCAGCAAACG 60.533 55.000 0.00 0.00 0.00 3.60
4244 11498 1.697432 CAACCCTAACCCAGTGAGTCA 59.303 52.381 0.00 0.00 0.00 3.41
4246 11500 1.815757 ACAACCCTAACCCAGTGAGT 58.184 50.000 0.00 0.00 0.00 3.41
4248 11502 3.798515 AGATACAACCCTAACCCAGTGA 58.201 45.455 0.00 0.00 0.00 3.41
4249 11503 5.888982 ATAGATACAACCCTAACCCAGTG 57.111 43.478 0.00 0.00 0.00 3.66
4250 11504 7.080353 ACATATAGATACAACCCTAACCCAGT 58.920 38.462 0.00 0.00 0.00 4.00
4254 11508 7.387948 CAGCAACATATAGATACAACCCTAACC 59.612 40.741 0.00 0.00 0.00 2.85
4255 11509 8.148351 TCAGCAACATATAGATACAACCCTAAC 58.852 37.037 0.00 0.00 0.00 2.34
4256 11510 8.148351 GTCAGCAACATATAGATACAACCCTAA 58.852 37.037 0.00 0.00 0.00 2.69
4257 11511 7.509318 AGTCAGCAACATATAGATACAACCCTA 59.491 37.037 0.00 0.00 0.00 3.53
4261 11551 8.138074 TGAGAGTCAGCAACATATAGATACAAC 58.862 37.037 0.00 0.00 0.00 3.32
4304 11594 3.118261 TCATTCCTGAGATGCCACTAACC 60.118 47.826 0.00 0.00 0.00 2.85
4317 11607 3.261580 CGCGGCATATAATCATTCCTGA 58.738 45.455 0.00 0.00 35.41 3.86
4318 11608 3.002791 ACGCGGCATATAATCATTCCTG 58.997 45.455 12.47 0.00 0.00 3.86
4329 11619 2.596904 AGTTAACTGACGCGGCATAT 57.403 45.000 18.76 10.49 0.00 1.78
4336 11630 0.586319 TGCAGCAAGTTAACTGACGC 59.414 50.000 9.34 12.30 35.90 5.19
4351 11645 4.248691 TGTACATAGCATAGCTCTGCAG 57.751 45.455 24.15 7.63 44.77 4.41
4366 11660 2.094675 GTTCAGCAGGGCATTGTACAT 58.905 47.619 0.00 0.00 0.00 2.29
4373 11667 4.349682 CCATGTTCAGCAGGGCAT 57.650 55.556 0.00 0.00 42.49 4.40
4377 11671 0.256752 TCCCATCCATGTTCAGCAGG 59.743 55.000 0.00 0.00 0.00 4.85
4378 11672 1.954382 CATCCCATCCATGTTCAGCAG 59.046 52.381 0.00 0.00 0.00 4.24
4379 11673 1.410507 CCATCCCATCCATGTTCAGCA 60.411 52.381 0.00 0.00 0.00 4.41
4380 11674 1.325355 CCATCCCATCCATGTTCAGC 58.675 55.000 0.00 0.00 0.00 4.26
4381 11675 1.496001 TCCCATCCCATCCATGTTCAG 59.504 52.381 0.00 0.00 0.00 3.02
4382 11676 1.496001 CTCCCATCCCATCCATGTTCA 59.504 52.381 0.00 0.00 0.00 3.18
4383 11677 1.496429 ACTCCCATCCCATCCATGTTC 59.504 52.381 0.00 0.00 0.00 3.18
4390 11684 0.179034 GTGAGCACTCCCATCCCATC 60.179 60.000 0.00 0.00 0.00 3.51
4393 11687 1.566298 AAGGTGAGCACTCCCATCCC 61.566 60.000 0.16 0.00 0.00 3.85
4408 11702 0.537143 TTGCGCATCAAGGTGAAGGT 60.537 50.000 12.75 0.00 0.00 3.50
4409 11703 0.597568 TTTGCGCATCAAGGTGAAGG 59.402 50.000 12.75 0.00 35.84 3.46
4411 11705 1.952990 TCTTTTGCGCATCAAGGTGAA 59.047 42.857 22.89 6.42 35.84 3.18
4412 11706 1.603456 TCTTTTGCGCATCAAGGTGA 58.397 45.000 22.89 9.11 35.84 4.02
4413 11707 2.420628 TTCTTTTGCGCATCAAGGTG 57.579 45.000 22.89 7.34 35.84 4.00
4414 11708 3.068024 TCTTTTCTTTTGCGCATCAAGGT 59.932 39.130 22.89 0.00 35.84 3.50
4417 11711 4.269844 GGTTTCTTTTCTTTTGCGCATCAA 59.730 37.500 12.75 6.65 0.00 2.57
4418 11712 3.801594 GGTTTCTTTTCTTTTGCGCATCA 59.198 39.130 12.75 0.00 0.00 3.07
4420 11714 3.803778 CAGGTTTCTTTTCTTTTGCGCAT 59.196 39.130 12.75 0.00 0.00 4.73
4421 11715 3.186119 CAGGTTTCTTTTCTTTTGCGCA 58.814 40.909 5.66 5.66 0.00 6.09
4422 11716 2.033747 GCAGGTTTCTTTTCTTTTGCGC 60.034 45.455 0.00 0.00 0.00 6.09
4423 11717 2.539688 GGCAGGTTTCTTTTCTTTTGCG 59.460 45.455 0.00 0.00 0.00 4.85
4424 11718 2.872245 GGGCAGGTTTCTTTTCTTTTGC 59.128 45.455 0.00 0.00 0.00 3.68
4425 11719 4.122046 CAGGGCAGGTTTCTTTTCTTTTG 58.878 43.478 0.00 0.00 0.00 2.44
4429 11723 1.332195 GCAGGGCAGGTTTCTTTTCT 58.668 50.000 0.00 0.00 0.00 2.52
4430 11724 0.318441 GGCAGGGCAGGTTTCTTTTC 59.682 55.000 0.00 0.00 0.00 2.29
4431 11725 1.121407 GGGCAGGGCAGGTTTCTTTT 61.121 55.000 0.00 0.00 0.00 2.27
4432 11726 1.533994 GGGCAGGGCAGGTTTCTTT 60.534 57.895 0.00 0.00 0.00 2.52
4433 11727 2.118294 GGGCAGGGCAGGTTTCTT 59.882 61.111 0.00 0.00 0.00 2.52
4434 11728 3.984732 GGGGCAGGGCAGGTTTCT 61.985 66.667 0.00 0.00 0.00 2.52
4435 11729 3.529835 AAGGGGCAGGGCAGGTTTC 62.530 63.158 0.00 0.00 0.00 2.78
4436 11730 3.100114 AAAGGGGCAGGGCAGGTTT 62.100 57.895 0.00 0.00 0.00 3.27
4437 11731 3.521452 AAAGGGGCAGGGCAGGTT 61.521 61.111 0.00 0.00 0.00 3.50
4438 11732 4.305956 CAAAGGGGCAGGGCAGGT 62.306 66.667 0.00 0.00 0.00 4.00
4467 11761 2.746277 CTTTCTGAACCGGCCGGG 60.746 66.667 44.99 28.70 43.62 5.73
4468 11762 2.746277 CCTTTCTGAACCGGCCGG 60.746 66.667 42.17 42.17 42.03 6.13
4469 11763 3.431725 GCCTTTCTGAACCGGCCG 61.432 66.667 21.04 21.04 36.56 6.13
4471 11765 1.657751 GATGGCCTTTCTGAACCGGC 61.658 60.000 17.25 17.25 41.75 6.13
4474 11768 1.135721 GCATGATGGCCTTTCTGAACC 59.864 52.381 3.32 0.00 0.00 3.62
4509 11803 1.835121 CGCATGGCATCAACATTGAG 58.165 50.000 0.00 0.00 41.08 3.02
4542 11836 1.146930 CATGGCACCCATACTCGCT 59.853 57.895 0.00 0.00 43.15 4.93
4543 11837 0.250467 ATCATGGCACCCATACTCGC 60.250 55.000 0.00 0.00 43.15 5.03
4549 11843 3.221389 GCGCATCATGGCACCCAT 61.221 61.111 0.30 0.00 46.37 4.00
4585 11879 2.030958 GTCCCTTTGGCGTACACGG 61.031 63.158 3.67 0.00 40.23 4.94
4587 11881 2.004733 GTATGTCCCTTTGGCGTACAC 58.995 52.381 0.00 0.00 33.73 2.90
4588 11882 1.624312 TGTATGTCCCTTTGGCGTACA 59.376 47.619 0.00 0.00 37.59 2.90
4589 11883 2.004733 GTGTATGTCCCTTTGGCGTAC 58.995 52.381 0.00 0.00 33.94 3.67
4592 11886 1.468520 CTTGTGTATGTCCCTTTGGCG 59.531 52.381 0.00 0.00 0.00 5.69
4593 11887 2.790433 TCTTGTGTATGTCCCTTTGGC 58.210 47.619 0.00 0.00 0.00 4.52
4594 11888 4.651778 TCTTCTTGTGTATGTCCCTTTGG 58.348 43.478 0.00 0.00 0.00 3.28
4595 11889 5.392380 GCATCTTCTTGTGTATGTCCCTTTG 60.392 44.000 0.00 0.00 0.00 2.77
4596 11890 4.702131 GCATCTTCTTGTGTATGTCCCTTT 59.298 41.667 0.00 0.00 0.00 3.11
4600 11927 4.095483 CCTTGCATCTTCTTGTGTATGTCC 59.905 45.833 0.00 0.00 0.00 4.02
4609 11936 2.503895 AGACCCCTTGCATCTTCTTG 57.496 50.000 0.00 0.00 0.00 3.02
4638 11965 1.891150 AGCAATTCTTGAGCAACCAGG 59.109 47.619 0.00 0.00 0.00 4.45
4667 11994 4.130118 GTGTGCCTTCAGGGATACTATTG 58.870 47.826 6.96 0.00 42.71 1.90
4689 12016 1.610038 TCCTGCAACAACAGCTTGATG 59.390 47.619 0.00 0.00 36.29 3.07
4698 12025 4.193826 TCAGACTATCTCCTGCAACAAC 57.806 45.455 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.