Multiple sequence alignment - TraesCS2D01G486300

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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 TraesCS2D01G486300 chr2D 100.000 5206 0 0 1 5206 586793965 586788760 0.000000e+00 9614
1 TraesCS2D01G486300 chr2D 73.794 1244 262 47 1100 2306 618660264 618659048 2.880000e-117 433
2 TraesCS2D01G486300 chr2D 76.009 446 95 11 1109 1551 586907680 586908116 2.440000e-53 220
3 TraesCS2D01G486300 chr2D 82.008 239 33 6 2970 3203 310087885 310088118 1.480000e-45 195
4 TraesCS2D01G486300 chr2B 93.374 3637 177 22 641 4237 708240519 708236907 0.000000e+00 5323
5 TraesCS2D01G486300 chr2B 92.222 540 20 6 1 523 708241366 708240832 0.000000e+00 745
6 TraesCS2D01G486300 chr2B 86.036 222 15 8 4601 4822 708236522 708236317 1.890000e-54 224
7 TraesCS2D01G486300 chr2B 94.400 125 7 0 518 642 708240802 708240678 5.320000e-45 193
8 TraesCS2D01G486300 chr2A 91.974 1819 122 8 518 2324 721603246 721601440 0.000000e+00 2529
9 TraesCS2D01G486300 chr2A 87.517 2251 163 34 2945 5179 721600927 721598779 0.000000e+00 2492
10 TraesCS2D01G486300 chr2A 90.780 282 16 5 1 274 721603944 721603665 8.240000e-98 368
11 TraesCS2D01G486300 chr2A 86.429 280 12 7 265 523 721603545 721603271 3.070000e-72 283
12 TraesCS2D01G486300 chr2A 77.737 274 54 7 1376 1647 721659943 721660211 1.500000e-35 161
13 TraesCS2D01G486300 chr7A 83.264 239 31 4 2970 3203 575456209 575456443 1.470000e-50 211
14 TraesCS2D01G486300 chr5D 81.590 239 34 6 2970 3203 438366414 438366647 6.880000e-44 189
15 TraesCS2D01G486300 chr4B 79.275 193 35 3 3008 3199 598722139 598722327 4.230000e-26 130
16 TraesCS2D01G486300 chr7D 82.979 141 18 5 5048 5187 496785064 496785199 7.080000e-24 122


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 TraesCS2D01G486300 chr2D 586788760 586793965 5205 True 9614.00 9614 100.000 1 5206 1 chr2D.!!$R1 5205
1 TraesCS2D01G486300 chr2D 618659048 618660264 1216 True 433.00 433 73.794 1100 2306 1 chr2D.!!$R2 1206
2 TraesCS2D01G486300 chr2B 708236317 708241366 5049 True 1621.25 5323 91.508 1 4822 4 chr2B.!!$R1 4821
3 TraesCS2D01G486300 chr2A 721598779 721603944 5165 True 1418.00 2529 89.175 1 5179 4 chr2A.!!$R1 5178

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
317 459 2.230130 TTGCCCATGGGAACTTTAGG 57.770 50.0 36.00 4.56 37.50 2.69 F
1257 1619 0.109342 CCAACTGTGAGCACCCTCTT 59.891 55.0 0.00 0.00 38.93 2.85 F
1746 2120 0.537143 AGGTCACGTACGGGTACACA 60.537 55.0 18.57 0.00 35.87 3.72 F
2853 3240 0.786581 CGCGCGCATCTATTTGATCT 59.213 50.0 32.61 0.00 32.05 2.75 F
4052 4472 0.178767 TCTGCATCCAGGAATCACCG 59.821 55.0 0.00 0.00 44.74 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1821 2195 0.535780 TCTTCCAAGTGCTGGTGCTG 60.536 55.000 0.0 0.0 46.51 4.41 R
2616 3002 0.717784 GGCAAGTACCGTTTAGTCGC 59.282 55.000 0.0 0.0 0.00 5.19 R
3539 3957 0.309302 CGATGGTGAGGCTAGAGTCG 59.691 60.000 0.0 0.0 0.00 4.18 R
4160 4583 0.033503 TAGTGAGATCCGCCTGACCA 60.034 55.000 0.0 0.0 0.00 4.02 R
5015 5528 1.005394 GCGTTGGAAGGAAGGTCGA 60.005 57.895 0.0 0.0 0.00 4.20 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
47 48 4.498520 CCTGCGGCGTCTCGTCAT 62.499 66.667 9.37 0.00 0.00 3.06
51 52 4.175489 CGGCGTCTCGTCATCCGT 62.175 66.667 0.00 0.00 37.94 4.69
164 165 2.399611 CTTCGGTCGCCAAATCGC 59.600 61.111 0.00 0.00 0.00 4.58
317 459 2.230130 TTGCCCATGGGAACTTTAGG 57.770 50.000 36.00 4.56 37.50 2.69
445 604 8.294954 TGGTGACTAAAGGTCTAAATCTCTAG 57.705 38.462 0.00 0.00 44.74 2.43
446 605 7.894364 TGGTGACTAAAGGTCTAAATCTCTAGT 59.106 37.037 0.00 0.00 44.74 2.57
487 646 5.047943 CCATCGTAATACCCAGAGTCTTAGG 60.048 48.000 4.66 4.66 0.00 2.69
533 727 9.097257 TCTTGTTGATGAAAAGTCAAATTTTCC 57.903 29.630 11.73 0.82 44.81 3.13
578 772 5.071788 ACTTTCTCACTGATTGACCTTACCA 59.928 40.000 0.00 0.00 0.00 3.25
729 1086 5.728621 GCTGCATGGACACATATATATTGCG 60.729 44.000 0.00 5.44 34.99 4.85
765 1122 8.201554 CACACTTGCAACTTCTATATATGTGT 57.798 34.615 0.00 0.63 34.67 3.72
766 1123 9.313118 CACACTTGCAACTTCTATATATGTGTA 57.687 33.333 10.96 0.00 33.34 2.90
767 1124 9.884636 ACACTTGCAACTTCTATATATGTGTAA 57.115 29.630 9.96 0.00 32.96 2.41
804 1161 2.320781 CATCTAGTCCGTTCCCTCCAT 58.679 52.381 0.00 0.00 0.00 3.41
873 1232 5.391736 GCTGTTAGTCAGAGTCTTAGCGTTA 60.392 44.000 0.00 0.00 46.27 3.18
1008 1367 1.543429 GGAAGGTCCCTAATGATGGCG 60.543 57.143 0.00 0.00 0.00 5.69
1093 1455 1.337728 CCGGTGCTACTGACACATTCA 60.338 52.381 0.00 0.00 39.87 2.57
1243 1605 2.133641 GTTTGCTGGGTGGCCAACT 61.134 57.895 22.79 0.00 35.73 3.16
1248 1610 1.601759 CTGGGTGGCCAACTGTGAG 60.602 63.158 22.79 7.98 0.00 3.51
1257 1619 0.109342 CCAACTGTGAGCACCCTCTT 59.891 55.000 0.00 0.00 38.93 2.85
1272 1634 1.524863 CTCTTGACGACACCTCCGGT 61.525 60.000 0.00 0.00 35.62 5.28
1303 1665 2.923035 CCAGTGACACGGGGGACT 60.923 66.667 16.26 0.00 29.33 3.85
1316 1678 1.219393 GGGACTTTCTCCTGCTCGG 59.781 63.158 0.00 0.00 39.39 4.63
1317 1679 1.545706 GGGACTTTCTCCTGCTCGGT 61.546 60.000 0.00 0.00 39.39 4.69
1382 1747 1.071987 CAGTGGAGGCACAGCTTCA 59.928 57.895 3.56 0.00 36.34 3.02
1402 1767 2.526873 AGTCCGGCAACCTGGTCT 60.527 61.111 0.00 0.00 0.00 3.85
1429 1794 3.416156 GACCAGAGAAGCAAAACCATCT 58.584 45.455 0.00 0.00 0.00 2.90
1485 1850 2.918248 CCCGGCATGAAGATGGGA 59.082 61.111 0.00 0.00 42.77 4.37
1579 1944 4.735132 GCCGCGTGCTGGAGTACA 62.735 66.667 4.92 0.00 36.87 2.90
1581 1946 2.049526 CGCGTGCTGGAGTACACA 60.050 61.111 0.00 0.00 36.57 3.72
1662 2027 1.322538 GGAATGGGCGCTGGTTCAAT 61.323 55.000 7.64 0.00 0.00 2.57
1689 2054 3.507009 GAGGCCTCGACGTACGCT 61.507 66.667 19.06 1.58 42.26 5.07
1746 2120 0.537143 AGGTCACGTACGGGTACACA 60.537 55.000 18.57 0.00 35.87 3.72
1755 2129 3.330720 GGGTACACAGCCAGGCCT 61.331 66.667 8.22 0.00 42.27 5.19
1833 2207 4.996434 GACGCCAGCACCAGCACT 62.996 66.667 0.00 0.00 45.49 4.40
1869 2249 4.265056 GGGCCAAGGGACGTGTGT 62.265 66.667 4.39 0.00 35.66 3.72
1905 2285 4.309950 GGGGCGTTCGGTCTGTGT 62.310 66.667 0.00 0.00 0.00 3.72
2383 2769 9.809395 AGTATACTGGCTCAATTAGATAGTACA 57.191 33.333 4.10 0.00 31.84 2.90
2610 2996 3.186119 GAGAAGGAAGCACAAGATCTCG 58.814 50.000 0.00 0.00 0.00 4.04
2616 3002 3.247173 GGAAGCACAAGATCTCGCATAAG 59.753 47.826 12.64 0.00 0.00 1.73
2737 3124 4.629200 CCTCAAAGTTCAGCTATGACAGTC 59.371 45.833 0.00 0.00 34.35 3.51
2740 3127 1.478510 AGTTCAGCTATGACAGTCCCG 59.521 52.381 0.00 0.00 34.35 5.14
2853 3240 0.786581 CGCGCGCATCTATTTGATCT 59.213 50.000 32.61 0.00 32.05 2.75
2901 3288 6.174720 TGTTTGATCAACTTCAGGTCTACT 57.825 37.500 7.89 0.00 36.21 2.57
2925 3335 5.760253 TCTGCAGCAGTTTAATTATAGGCTC 59.240 40.000 22.10 0.00 32.61 4.70
3004 3414 2.356135 GATTGCGGTGAAGAGGCTTAA 58.644 47.619 0.00 0.00 0.00 1.85
3022 3432 4.974792 GCAGTCTGCTCTCACGAA 57.025 55.556 17.89 0.00 40.96 3.85
3023 3433 3.201342 GCAGTCTGCTCTCACGAAA 57.799 52.632 17.89 0.00 40.96 3.46
3571 3989 0.319555 ACCATCGTCAACTCACCGTG 60.320 55.000 0.00 0.00 0.00 4.94
3641 4059 2.425312 TCGTTTGCAAATGTTCAGTGGT 59.575 40.909 26.39 0.00 0.00 4.16
3644 4062 3.988379 TTGCAAATGTTCAGTGGTCTC 57.012 42.857 0.00 0.00 0.00 3.36
3645 4063 2.929641 TGCAAATGTTCAGTGGTCTCA 58.070 42.857 0.00 0.00 0.00 3.27
3667 4085 6.061441 TCACAGATGATTTTACTGGTGTGTT 58.939 36.000 0.00 0.00 36.33 3.32
3798 4218 2.033194 GGACAAAGGAACGGCGAGG 61.033 63.158 16.62 0.00 0.00 4.63
3877 4297 4.816385 TCTTGGCCGTATCTCATGAAAATC 59.184 41.667 0.00 0.00 0.00 2.17
3934 4354 1.768684 TTGTGGGAGCAGGACAGGAC 61.769 60.000 0.00 0.00 0.00 3.85
3942 4362 1.310933 GCAGGACAGGACAATGGCTG 61.311 60.000 0.00 0.00 0.00 4.85
3954 4374 2.489329 ACAATGGCTGTTCTTGATTCGG 59.511 45.455 0.00 0.00 32.99 4.30
3977 4397 1.062505 GTGAATCTCCCTCCCCTCTCT 60.063 57.143 0.00 0.00 0.00 3.10
3990 4410 1.745264 CTCTCTCGGCCTGATTCCC 59.255 63.158 0.00 0.00 0.00 3.97
3995 4415 0.533755 CTCGGCCTGATTCCCACATC 60.534 60.000 0.00 0.00 0.00 3.06
4009 4429 0.803768 CACATCGGCTCTGAACTCGG 60.804 60.000 0.00 0.00 0.00 4.63
4052 4472 0.178767 TCTGCATCCAGGAATCACCG 59.821 55.000 0.00 0.00 44.74 4.94
4160 4583 2.413310 ACCGAACAAGGTTTGTGACT 57.587 45.000 0.00 0.00 44.59 3.41
4249 4674 6.149973 TGAAATCAGAGTTTACAAGAGCATGG 59.850 38.462 0.00 0.00 0.00 3.66
4297 4722 4.038080 CTTGTTCCGTTGGCCGCC 62.038 66.667 1.04 1.04 34.38 6.13
4326 4751 6.584184 AGCGTATTCGAAGATGAAGATATGTG 59.416 38.462 15.91 0.00 39.71 3.21
4440 4872 5.277779 GCTGGCATTAAAATGTATACTCGCA 60.278 40.000 4.17 0.00 38.65 5.10
4466 4898 7.715265 TCTCTTCTCACAGTTTGAATTACAC 57.285 36.000 0.00 0.00 32.21 2.90
4478 4910 8.918658 CAGTTTGAATTACACATGAGAATTTGG 58.081 33.333 0.00 0.00 0.00 3.28
4483 4915 1.547372 ACACATGAGAATTTGGGCTGC 59.453 47.619 0.00 0.00 0.00 5.25
4486 4918 3.019564 ACATGAGAATTTGGGCTGCTAC 58.980 45.455 0.00 0.00 0.00 3.58
4488 4920 2.715046 TGAGAATTTGGGCTGCTACTG 58.285 47.619 0.00 0.00 0.00 2.74
4508 4976 1.960763 TGGCACATGCGTGAGTGAC 60.961 57.895 14.17 3.93 46.80 3.67
4509 4977 1.960763 GGCACATGCGTGAGTGACA 60.961 57.895 14.17 0.00 46.80 3.58
4516 4984 1.859383 TGCGTGAGTGACAAATCGAA 58.141 45.000 0.00 0.00 0.00 3.71
4528 4996 5.180492 GTGACAAATCGAAGGGAAACATGTA 59.820 40.000 0.00 0.00 0.00 2.29
4569 5038 4.218852 TGACAGACGGTGTGTGTTCATATA 59.781 41.667 16.23 0.00 40.10 0.86
4570 5039 5.142061 ACAGACGGTGTGTGTTCATATAA 57.858 39.130 10.40 0.00 36.66 0.98
4571 5040 5.730550 ACAGACGGTGTGTGTTCATATAAT 58.269 37.500 10.40 0.00 36.66 1.28
4626 5117 2.903135 GGCTATGGTAAGGCAGATCTCT 59.097 50.000 0.00 0.00 41.51 3.10
4647 5138 2.845586 TGGATCATCAGTTCATCACCCA 59.154 45.455 0.00 0.00 0.00 4.51
4677 5168 3.306088 GCTGCTGGAGTTCTACTGTTGTA 60.306 47.826 0.00 0.00 0.00 2.41
4679 5170 3.639561 TGCTGGAGTTCTACTGTTGTACA 59.360 43.478 0.00 0.00 0.00 2.90
4697 5188 5.001232 TGTACAGTACTGAAAAATGGCTCC 58.999 41.667 29.30 3.54 0.00 4.70
4707 5198 0.332632 AAATGGCTCCCTGCAGCTTA 59.667 50.000 8.66 0.00 45.15 3.09
4756 5250 2.557869 AGGCAGGACCCAATACACTAA 58.442 47.619 0.00 0.00 40.58 2.24
4770 5264 8.612619 CCCAATACACTAACAAAATAGCTACTG 58.387 37.037 0.00 0.00 0.00 2.74
4783 5277 1.699634 AGCTACTGCCTCTGTTCCAAA 59.300 47.619 0.00 0.00 40.80 3.28
4784 5278 2.307098 AGCTACTGCCTCTGTTCCAAAT 59.693 45.455 0.00 0.00 40.80 2.32
4785 5279 3.084786 GCTACTGCCTCTGTTCCAAATT 58.915 45.455 0.00 0.00 0.00 1.82
4786 5280 3.127721 GCTACTGCCTCTGTTCCAAATTC 59.872 47.826 0.00 0.00 0.00 2.17
4789 5283 2.892852 CTGCCTCTGTTCCAAATTCCAA 59.107 45.455 0.00 0.00 0.00 3.53
4791 5285 3.258872 TGCCTCTGTTCCAAATTCCAATG 59.741 43.478 0.00 0.00 0.00 2.82
4792 5286 3.511146 GCCTCTGTTCCAAATTCCAATGA 59.489 43.478 0.00 0.00 0.00 2.57
4793 5287 4.021192 GCCTCTGTTCCAAATTCCAATGAA 60.021 41.667 0.00 0.00 34.33 2.57
4794 5288 5.473039 CCTCTGTTCCAAATTCCAATGAAC 58.527 41.667 0.00 0.00 36.67 3.18
4795 5289 5.244626 CCTCTGTTCCAAATTCCAATGAACT 59.755 40.000 0.00 0.00 36.98 3.01
4796 5290 6.088016 TCTGTTCCAAATTCCAATGAACTG 57.912 37.500 0.00 0.00 36.98 3.16
4797 5291 5.598005 TCTGTTCCAAATTCCAATGAACTGT 59.402 36.000 0.00 0.00 36.98 3.55
4798 5292 6.775142 TCTGTTCCAAATTCCAATGAACTGTA 59.225 34.615 0.00 0.00 36.98 2.74
4842 5336 7.605410 AAACAAAGGGTGTAGATTGTATACG 57.395 36.000 0.00 0.00 40.60 3.06
4881 5376 4.923281 GCAAACTTGACACTGAAAACAACT 59.077 37.500 0.00 0.00 0.00 3.16
4889 5384 6.507900 TGACACTGAAAACAACTGTTCAAAA 58.492 32.000 0.00 0.00 37.25 2.44
4903 5398 9.299963 CAACTGTTCAAAATTTAGTGTGATGAA 57.700 29.630 0.00 0.00 0.00 2.57
4904 5399 9.868277 AACTGTTCAAAATTTAGTGTGATGAAA 57.132 25.926 0.00 0.00 0.00 2.69
4905 5400 9.868277 ACTGTTCAAAATTTAGTGTGATGAAAA 57.132 25.926 0.00 0.00 0.00 2.29
4987 5482 0.320073 TCACATCGTCGGTTCAACCC 60.320 55.000 0.00 0.00 33.75 4.11
4989 5484 0.037605 ACATCGTCGGTTCAACCCTC 60.038 55.000 0.00 0.00 33.75 4.30
4990 5485 0.739813 CATCGTCGGTTCAACCCTCC 60.740 60.000 0.00 0.00 33.75 4.30
4992 5487 1.080025 CGTCGGTTCAACCCTCCTC 60.080 63.158 0.00 0.00 33.75 3.71
5003 5516 2.586792 CCTCCTCTTGCCCCTTCG 59.413 66.667 0.00 0.00 0.00 3.79
5004 5517 2.124942 CTCCTCTTGCCCCTTCGC 60.125 66.667 0.00 0.00 0.00 4.70
5006 5519 2.437359 CCTCTTGCCCCTTCGCAG 60.437 66.667 0.00 0.00 40.53 5.18
5009 5522 2.747855 CTTGCCCCTTCGCAGTCC 60.748 66.667 0.00 0.00 40.53 3.85
5013 5526 4.148825 CCCCTTCGCAGTCCCTCG 62.149 72.222 0.00 0.00 0.00 4.63
5015 5528 3.764466 CCTTCGCAGTCCCTCGCT 61.764 66.667 0.00 0.00 0.00 4.93
5019 5532 4.838486 CGCAGTCCCTCGCTCGAC 62.838 72.222 0.00 0.00 0.00 4.20
5020 5533 4.500116 GCAGTCCCTCGCTCGACC 62.500 72.222 0.00 0.00 0.00 4.79
5021 5534 2.752238 CAGTCCCTCGCTCGACCT 60.752 66.667 0.00 0.00 0.00 3.85
5022 5535 2.035940 AGTCCCTCGCTCGACCTT 59.964 61.111 0.00 0.00 0.00 3.50
5035 5551 2.032071 ACCTTCCTTCCAACGCGG 59.968 61.111 12.47 0.00 0.00 6.46
5036 5552 2.746277 CCTTCCTTCCAACGCGGG 60.746 66.667 12.47 2.26 34.36 6.13
5037 5553 2.746277 CTTCCTTCCAACGCGGGG 60.746 66.667 12.47 12.41 34.36 5.73
5074 5590 2.048503 GTGCCTTAGCGTCACCGT 60.049 61.111 0.00 0.00 44.31 4.83
5075 5591 2.048597 TGCCTTAGCGTCACCGTG 60.049 61.111 0.00 0.00 44.31 4.94
5076 5592 2.260434 GCCTTAGCGTCACCGTGA 59.740 61.111 0.00 0.00 36.15 4.35
5078 5594 1.585006 CCTTAGCGTCACCGTGACT 59.415 57.895 25.37 13.05 44.85 3.41
5082 5598 4.961511 GCGTCACCGTGACTGCCA 62.962 66.667 25.37 0.00 44.85 4.92
5083 5599 2.279851 CGTCACCGTGACTGCCAA 60.280 61.111 25.37 0.00 44.85 4.52
5084 5600 2.594962 CGTCACCGTGACTGCCAAC 61.595 63.158 25.37 2.61 44.85 3.77
5086 5602 4.012895 CACCGTGACTGCCAACGC 62.013 66.667 0.00 0.00 0.00 4.84
5088 5604 4.988598 CCGTGACTGCCAACGCCT 62.989 66.667 0.00 0.00 0.00 5.52
5089 5605 3.414700 CGTGACTGCCAACGCCTC 61.415 66.667 0.00 0.00 0.00 4.70
5090 5606 2.280797 GTGACTGCCAACGCCTCA 60.281 61.111 0.00 0.00 0.00 3.86
5091 5607 2.280797 TGACTGCCAACGCCTCAC 60.281 61.111 0.00 0.00 0.00 3.51
5092 5608 2.031163 GACTGCCAACGCCTCACT 59.969 61.111 0.00 0.00 0.00 3.41
5093 5609 2.281070 ACTGCCAACGCCTCACTG 60.281 61.111 0.00 0.00 0.00 3.66
5094 5610 3.730761 CTGCCAACGCCTCACTGC 61.731 66.667 0.00 0.00 0.00 4.40
5164 5680 2.298661 TTCCCCTTCTTCCTCGCCC 61.299 63.158 0.00 0.00 0.00 6.13
5182 5698 4.489771 CCCGGGACATCCTGCCAC 62.490 72.222 18.48 0.00 41.13 5.01
5183 5699 3.402681 CCGGGACATCCTGCCACT 61.403 66.667 0.69 0.00 41.13 4.00
5184 5700 2.124983 CGGGACATCCTGCCACTG 60.125 66.667 0.00 0.00 35.28 3.66
5185 5701 2.439156 GGGACATCCTGCCACTGC 60.439 66.667 0.00 0.00 35.95 4.40
5186 5702 2.439156 GGACATCCTGCCACTGCC 60.439 66.667 0.00 0.00 36.33 4.85
5187 5703 2.439156 GACATCCTGCCACTGCCC 60.439 66.667 0.00 0.00 36.33 5.36
5188 5704 4.052518 ACATCCTGCCACTGCCCC 62.053 66.667 0.00 0.00 36.33 5.80
5197 5713 3.953775 CACTGCCCCGTCCCAGTT 61.954 66.667 0.00 0.00 40.12 3.16
5198 5714 3.175710 ACTGCCCCGTCCCAGTTT 61.176 61.111 0.00 0.00 39.11 2.66
5199 5715 2.672996 CTGCCCCGTCCCAGTTTG 60.673 66.667 0.00 0.00 0.00 2.93
5200 5716 4.278513 TGCCCCGTCCCAGTTTGG 62.279 66.667 0.00 0.00 37.25 3.28
5203 5719 4.278513 CCCGTCCCAGTTTGGCCA 62.279 66.667 0.00 0.00 35.79 5.36
5204 5720 2.035626 CCGTCCCAGTTTGGCCAT 59.964 61.111 6.09 0.00 35.79 4.40
5205 5721 1.606313 CCGTCCCAGTTTGGCCATT 60.606 57.895 6.09 0.00 35.79 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.690633 GAGATGGAGGAGGTGCCCA 60.691 63.158 0.00 0.00 37.37 5.36
47 48 4.361971 ACGGGAGCTCAGGACGGA 62.362 66.667 17.19 0.00 0.00 4.69
68 69 4.162690 CCTACCGTGCTCCAGCCC 62.163 72.222 0.00 0.00 41.18 5.19
164 165 3.217743 GTCTACCTCCTCGCCGGG 61.218 72.222 2.18 0.00 0.00 5.73
196 205 1.216178 CCTCTTGGGCAATTTGGCG 59.784 57.895 15.79 3.77 44.78 5.69
301 439 1.474330 GTGCCTAAAGTTCCCATGGG 58.526 55.000 26.30 26.30 0.00 4.00
302 440 1.272425 TGGTGCCTAAAGTTCCCATGG 60.272 52.381 4.14 4.14 0.00 3.66
355 497 7.833682 ACATCATTGTGGTAAATATCCAGTCAA 59.166 33.333 0.00 0.00 35.49 3.18
394 536 5.493809 GTCCTTGGTTATTACTACAAGCCA 58.506 41.667 0.00 0.00 39.09 4.75
395 537 4.880120 GGTCCTTGGTTATTACTACAAGCC 59.120 45.833 0.00 0.00 39.09 4.35
477 636 6.271159 ACTGAATGAGGAAAACCTAAGACTCT 59.729 38.462 0.00 0.00 0.00 3.24
478 637 6.468543 ACTGAATGAGGAAAACCTAAGACTC 58.531 40.000 0.00 0.00 0.00 3.36
487 646 7.931275 ACAAGAAACTACTGAATGAGGAAAAC 58.069 34.615 0.00 0.00 0.00 2.43
533 727 5.900425 AGTCAACATGTCAGCTAGATGTAG 58.100 41.667 8.04 0.00 41.02 2.74
729 1086 1.009675 CAAGTGTGCAACTGCGGAC 60.010 57.895 0.00 0.00 45.83 4.79
768 1125 8.943002 CGGACTAGATGTGGTATTTTTAGTTTT 58.057 33.333 0.00 0.00 0.00 2.43
769 1126 8.098912 ACGGACTAGATGTGGTATTTTTAGTTT 58.901 33.333 0.00 0.00 0.00 2.66
770 1127 7.618137 ACGGACTAGATGTGGTATTTTTAGTT 58.382 34.615 0.00 0.00 0.00 2.24
771 1128 7.179076 ACGGACTAGATGTGGTATTTTTAGT 57.821 36.000 0.00 0.00 0.00 2.24
772 1129 7.224167 GGAACGGACTAGATGTGGTATTTTTAG 59.776 40.741 0.00 0.00 0.00 1.85
792 1149 4.835927 CTCGAATGGAGGGAACGG 57.164 61.111 0.00 0.00 39.22 4.44
804 1161 5.800296 TGAATTTGTCCACTTATCCTCGAA 58.200 37.500 0.00 0.00 0.00 3.71
854 1213 8.503458 AACTAATAACGCTAAGACTCTGACTA 57.497 34.615 0.00 0.00 0.00 2.59
887 1246 1.621992 GAGGGGCGATCTGATACAGA 58.378 55.000 3.95 3.95 44.99 3.41
982 1341 4.637288 TCATTAGGGACCTTCCTCCTAA 57.363 45.455 0.00 0.00 44.30 2.69
1008 1367 4.762251 AGGATTTGAAGAGTGCAGTTTACC 59.238 41.667 0.00 0.00 0.00 2.85
1093 1455 0.610232 GTGACATTCTGGCCCTTGCT 60.610 55.000 0.00 0.00 37.74 3.91
1146 1508 5.995446 GGAGAGAAGAATCCCAGTGTAAAT 58.005 41.667 0.00 0.00 0.00 1.40
1243 1605 1.112916 TCGTCAAGAGGGTGCTCACA 61.113 55.000 2.21 0.00 0.00 3.58
1248 1610 1.668151 GGTGTCGTCAAGAGGGTGC 60.668 63.158 0.00 0.00 0.00 5.01
1290 1652 1.477685 GGAGAAAGTCCCCCGTGTCA 61.478 60.000 0.00 0.00 39.88 3.58
1303 1665 2.172483 GAGCCACCGAGCAGGAGAAA 62.172 60.000 5.19 0.00 45.00 2.52
1316 1678 4.394712 CCACCTCACCGGAGCCAC 62.395 72.222 9.46 0.00 39.96 5.01
1374 1739 2.948720 GCCGGACTCCTGAAGCTGT 61.949 63.158 5.05 0.00 0.00 4.40
1382 1747 3.322466 CCAGGTTGCCGGACTCCT 61.322 66.667 5.05 5.68 0.00 3.69
1402 1767 3.462483 TTTGCTTCTCTGGTCGTGTAA 57.538 42.857 0.00 0.00 0.00 2.41
1429 1794 1.593209 GGTCGAACGACTGCCACAA 60.593 57.895 22.98 0.00 44.04 3.33
1599 1964 3.164977 TCCCGTTGCCACAGGACA 61.165 61.111 0.00 0.00 0.00 4.02
1671 2036 3.507009 GCGTACGTCGAGGCCTCT 61.507 66.667 29.73 14.17 42.86 3.69
1689 2054 2.032634 GTGCAGCGGGAAATCGTGA 61.033 57.895 0.00 0.00 0.00 4.35
1722 2096 2.117156 CCCGTACGTGACCTCCGAT 61.117 63.158 15.21 0.00 0.00 4.18
1729 2103 0.730494 GCTGTGTACCCGTACGTGAC 60.730 60.000 15.21 9.29 38.85 3.67
1821 2195 0.535780 TCTTCCAAGTGCTGGTGCTG 60.536 55.000 0.00 0.00 46.51 4.41
1828 2202 3.133141 GAAGAAGGTCTTCCAAGTGCT 57.867 47.619 6.72 0.00 45.34 4.40
1851 2228 3.953775 CACACGTCCCTTGGCCCT 61.954 66.667 0.00 0.00 0.00 5.19
1971 2351 0.981183 TTTCCCTCATGTACCACGCT 59.019 50.000 0.00 0.00 0.00 5.07
2381 2767 9.838339 CAGACCAATCCTAATAAAATCTACTGT 57.162 33.333 0.00 0.00 0.00 3.55
2395 2781 4.365514 TTTTGCAGTCAGACCAATCCTA 57.634 40.909 0.00 0.00 0.00 2.94
2455 2841 3.543680 AAATCATGTCAGGTACGGAGG 57.456 47.619 0.00 0.00 30.07 4.30
2610 2996 3.442100 AGTACCGTTTAGTCGCTTATGC 58.558 45.455 0.00 0.00 0.00 3.14
2616 3002 0.717784 GGCAAGTACCGTTTAGTCGC 59.282 55.000 0.00 0.00 0.00 5.19
2660 3047 4.037089 TCGATTAACATAAGCGCAGTAGGA 59.963 41.667 11.47 0.00 0.00 2.94
2669 3056 5.277058 CCAAGTCAGCTCGATTAACATAAGC 60.277 44.000 0.00 0.00 0.00 3.09
2701 3088 1.471684 CTTTGAGGAATGCAGTCTGCC 59.528 52.381 21.99 6.69 44.23 4.85
2869 3256 5.686841 TGAAGTTGATCAAACAAGCAAATCG 59.313 36.000 10.35 0.00 41.61 3.34
2901 3288 5.684704 AGCCTATAATTAAACTGCTGCAGA 58.315 37.500 34.28 13.82 35.18 4.26
2938 3348 8.927675 ACCCTAGTGATTGTACAATTGTTAAA 57.072 30.769 21.63 11.83 0.00 1.52
2943 3353 7.630242 ATTGACCCTAGTGATTGTACAATTG 57.370 36.000 21.63 3.24 0.00 2.32
3035 3445 4.103153 ACCTCCACTTCTCTTGTGAAATCA 59.897 41.667 0.00 0.00 37.60 2.57
3139 3549 1.098050 GCTCTTGTTGGGCATGTAGG 58.902 55.000 0.00 0.00 0.00 3.18
3539 3957 0.309302 CGATGGTGAGGCTAGAGTCG 59.691 60.000 0.00 0.00 0.00 4.18
3571 3989 3.473625 GGAGAGTAGAGTAGAGTGGCTC 58.526 54.545 0.00 0.00 0.00 4.70
3635 4053 6.091849 CAGTAAAATCATCTGTGAGACCACTG 59.908 42.308 0.00 0.00 43.55 3.66
3636 4054 6.169094 CAGTAAAATCATCTGTGAGACCACT 58.831 40.000 0.00 0.00 43.55 4.00
3641 4059 5.934043 CACACCAGTAAAATCATCTGTGAGA 59.066 40.000 0.00 0.00 37.87 3.27
3644 4062 5.947228 ACACACCAGTAAAATCATCTGTG 57.053 39.130 0.00 0.00 0.00 3.66
3645 4063 7.665559 ACATAACACACCAGTAAAATCATCTGT 59.334 33.333 0.00 0.00 0.00 3.41
3701 4121 2.045926 GCCCGCAATGACTCTGGT 60.046 61.111 0.00 0.00 0.00 4.00
3798 4218 2.046892 TGAAAGGAGCCTCTGCGC 60.047 61.111 0.00 0.00 44.33 6.09
3877 4297 7.617935 GCAAAACAAAAGAGAATCGCTAACATG 60.618 37.037 0.00 0.00 42.67 3.21
3934 4354 2.733227 GCCGAATCAAGAACAGCCATTG 60.733 50.000 0.00 0.00 0.00 2.82
3942 4362 1.153353 TTCACCGCCGAATCAAGAAC 58.847 50.000 0.00 0.00 0.00 3.01
3954 4374 2.506472 GGGAGGGAGATTCACCGC 59.494 66.667 0.00 0.00 0.00 5.68
3977 4397 1.526887 GATGTGGGAATCAGGCCGA 59.473 57.895 0.00 0.00 0.00 5.54
3990 4410 0.803768 CCGAGTTCAGAGCCGATGTG 60.804 60.000 0.00 0.00 0.00 3.21
3995 4415 2.492090 CTCCCGAGTTCAGAGCCG 59.508 66.667 0.00 0.00 0.00 5.52
4009 4429 1.396653 CCCAATCTGAATGCACCTCC 58.603 55.000 0.00 0.00 0.00 4.30
4160 4583 0.033503 TAGTGAGATCCGCCTGACCA 60.034 55.000 0.00 0.00 0.00 4.02
4207 4631 4.952262 TTTCAAATCTTGATCAGAGCCG 57.048 40.909 0.00 0.00 39.84 5.52
4249 4674 1.099879 ATGAGCTCGCTTGGGCATTC 61.100 55.000 9.64 0.00 38.60 2.67
4260 4685 6.307155 ACAAGATAAACGAAAAATGAGCTCG 58.693 36.000 9.64 0.00 38.53 5.03
4297 4722 5.511571 TCTTCATCTTCGAATACGCTACTG 58.488 41.667 0.00 0.00 39.58 2.74
4326 4751 4.895961 AGGAAGTTACACTTTCTGGTAGC 58.104 43.478 0.00 0.00 42.30 3.58
4364 4791 3.765511 CCATGGACAAGGAACACATCAAT 59.234 43.478 5.56 0.00 0.00 2.57
4396 4824 3.119495 AGCATTTCCTTACCATTTGCGAC 60.119 43.478 0.00 0.00 33.99 5.19
4397 4825 3.088532 AGCATTTCCTTACCATTTGCGA 58.911 40.909 0.00 0.00 33.99 5.10
4440 4872 8.778358 GTGTAATTCAAACTGTGAGAAGAGATT 58.222 33.333 2.41 0.00 37.61 2.40
4466 4898 3.066342 CAGTAGCAGCCCAAATTCTCATG 59.934 47.826 0.00 0.00 0.00 3.07
4478 4910 2.747855 GTGCCACCAGTAGCAGCC 60.748 66.667 0.00 0.00 40.28 4.85
4483 4915 1.375908 ACGCATGTGCCACCAGTAG 60.376 57.895 6.08 0.00 37.91 2.57
4486 4918 2.669229 TCACGCATGTGCCACCAG 60.669 61.111 6.08 0.00 46.01 4.00
4488 4920 2.669569 ACTCACGCATGTGCCACC 60.670 61.111 6.08 0.00 46.01 4.61
4508 4976 6.035843 CCAATACATGTTTCCCTTCGATTTG 58.964 40.000 2.30 0.00 0.00 2.32
4509 4977 5.714806 ACCAATACATGTTTCCCTTCGATTT 59.285 36.000 2.30 0.00 0.00 2.17
4516 4984 5.074115 TCGAAAACCAATACATGTTTCCCT 58.926 37.500 2.30 0.00 33.76 4.20
4528 4996 7.010183 CGTCTGTCATTAGTATCGAAAACCAAT 59.990 37.037 0.00 0.00 0.00 3.16
4569 5038 8.552296 AGACAACAATCCTACCTATCAAAGATT 58.448 33.333 0.00 0.00 0.00 2.40
4570 5039 8.095452 AGACAACAATCCTACCTATCAAAGAT 57.905 34.615 0.00 0.00 0.00 2.40
4571 5040 7.364762 GGAGACAACAATCCTACCTATCAAAGA 60.365 40.741 0.00 0.00 32.51 2.52
4626 5117 2.845586 TGGGTGATGAACTGATGATCCA 59.154 45.455 0.00 0.00 0.00 3.41
4671 5162 5.825679 AGCCATTTTTCAGTACTGTACAACA 59.174 36.000 21.99 7.88 0.00 3.33
4677 5168 3.074538 AGGGAGCCATTTTTCAGTACTGT 59.925 43.478 21.99 0.00 0.00 3.55
4679 5170 3.690460 CAGGGAGCCATTTTTCAGTACT 58.310 45.455 0.00 0.00 0.00 2.73
4681 5172 2.224992 TGCAGGGAGCCATTTTTCAGTA 60.225 45.455 0.00 0.00 44.83 2.74
4682 5173 1.260544 GCAGGGAGCCATTTTTCAGT 58.739 50.000 0.00 0.00 37.23 3.41
4683 5174 1.203994 CTGCAGGGAGCCATTTTTCAG 59.796 52.381 5.57 0.00 44.83 3.02
4684 5175 1.259609 CTGCAGGGAGCCATTTTTCA 58.740 50.000 5.57 0.00 44.83 2.69
4685 5176 0.108472 GCTGCAGGGAGCCATTTTTC 60.108 55.000 17.12 0.00 44.83 2.29
4686 5177 0.543646 AGCTGCAGGGAGCCATTTTT 60.544 50.000 17.12 0.00 44.83 1.94
4687 5178 0.543646 AAGCTGCAGGGAGCCATTTT 60.544 50.000 17.12 0.00 44.83 1.82
4697 5188 3.072944 GCTCTGGATTATAAGCTGCAGG 58.927 50.000 17.12 0.00 32.31 4.85
4707 5198 7.577303 TCCAACTCTAATTTGCTCTGGATTAT 58.423 34.615 0.00 0.00 0.00 1.28
4745 5239 8.122952 GCAGTAGCTATTTTGTTAGTGTATTGG 58.877 37.037 0.00 0.00 37.91 3.16
4756 5250 4.559862 ACAGAGGCAGTAGCTATTTTGT 57.440 40.909 0.00 0.00 41.70 2.83
4770 5264 3.511146 TCATTGGAATTTGGAACAGAGGC 59.489 43.478 0.00 0.00 42.39 4.70
4818 5312 7.163441 ACGTATACAATCTACACCCTTTGTTT 58.837 34.615 3.32 0.00 39.91 2.83
4823 5317 5.590259 ACGTACGTATACAATCTACACCCTT 59.410 40.000 21.41 0.00 0.00 3.95
4839 5333 1.962412 CCGCAACTGTTACGTACGTA 58.038 50.000 23.60 23.60 0.00 3.57
4840 5334 1.277495 GCCGCAACTGTTACGTACGT 61.277 55.000 25.98 25.98 0.00 3.57
4841 5335 1.276820 TGCCGCAACTGTTACGTACG 61.277 55.000 15.01 15.01 0.00 3.67
4842 5336 0.860533 TTGCCGCAACTGTTACGTAC 59.139 50.000 11.76 4.79 0.00 3.67
4950 5445 6.970043 CGATGTGAGTTTTGTTAGGTCAAAAA 59.030 34.615 6.24 0.00 44.93 1.94
4967 5462 1.068474 GGTTGAACCGACGATGTGAG 58.932 55.000 0.00 0.00 0.00 3.51
4987 5482 2.124942 GCGAAGGGGCAAGAGGAG 60.125 66.667 0.00 0.00 0.00 3.69
4989 5484 2.437359 CTGCGAAGGGGCAAGAGG 60.437 66.667 0.00 0.00 43.39 3.69
4990 5485 1.743252 GACTGCGAAGGGGCAAGAG 60.743 63.158 0.00 0.00 43.39 2.85
4992 5487 2.747855 GGACTGCGAAGGGGCAAG 60.748 66.667 0.00 0.00 43.39 4.01
5003 5516 4.500116 GGTCGAGCGAGGGACTGC 62.500 72.222 0.00 0.00 41.55 4.40
5004 5517 2.272918 GAAGGTCGAGCGAGGGACTG 62.273 65.000 9.28 0.00 41.55 3.51
5006 5519 2.490685 GAAGGTCGAGCGAGGGAC 59.509 66.667 9.28 0.00 0.00 4.46
5009 5522 1.139947 GAAGGAAGGTCGAGCGAGG 59.860 63.158 9.28 0.00 0.00 4.63
5013 5526 1.014564 CGTTGGAAGGAAGGTCGAGC 61.015 60.000 6.48 6.48 0.00 5.03
5015 5528 1.005394 GCGTTGGAAGGAAGGTCGA 60.005 57.895 0.00 0.00 0.00 4.20
5018 5531 2.032071 CCGCGTTGGAAGGAAGGT 59.968 61.111 4.92 0.00 42.00 3.50
5019 5532 2.746277 CCCGCGTTGGAAGGAAGG 60.746 66.667 4.92 0.00 42.00 3.46
5020 5533 2.746277 CCCCGCGTTGGAAGGAAG 60.746 66.667 4.92 0.00 42.00 3.46
5052 5568 3.488090 GACGCTAAGGCACGGCAC 61.488 66.667 0.00 0.00 37.24 5.01
5074 5590 2.280797 GTGAGGCGTTGGCAGTCA 60.281 61.111 0.00 0.00 42.47 3.41
5075 5591 2.031163 AGTGAGGCGTTGGCAGTC 59.969 61.111 0.00 0.00 42.47 3.51
5076 5592 2.281070 CAGTGAGGCGTTGGCAGT 60.281 61.111 0.00 0.00 42.47 4.40
5180 5696 3.491598 AAACTGGGACGGGGCAGTG 62.492 63.158 0.00 0.00 40.47 3.66
5181 5697 3.175710 AAACTGGGACGGGGCAGT 61.176 61.111 0.00 0.00 40.47 4.40
5182 5698 2.672996 CAAACTGGGACGGGGCAG 60.673 66.667 0.00 0.00 40.47 4.85
5183 5699 4.278513 CCAAACTGGGACGGGGCA 62.279 66.667 0.00 0.00 40.47 5.36
5186 5702 3.583882 ATGGCCAAACTGGGACGGG 62.584 63.158 10.96 0.00 39.59 5.28
5187 5703 1.606313 AATGGCCAAACTGGGACGG 60.606 57.895 10.96 0.00 39.59 4.79
5188 5704 4.095590 AATGGCCAAACTGGGACG 57.904 55.556 10.96 0.00 39.59 4.79


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

AutoCloner maintained by Alex Coulton.