Multiple sequence alignment - TraesCS1A01G320300

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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 TraesCS1A01G320300 chr1A 100.000 4132 0 0 1 4132 511004371 511008502 0.000000e+00 7631
1 TraesCS1A01G320300 chr1D 90.377 3346 186 50 1 3272 414277632 414280915 0.000000e+00 4270
2 TraesCS1A01G320300 chr1D 88.846 780 70 10 3346 4118 414281096 414281865 0.000000e+00 942
3 TraesCS1A01G320300 chr1B 88.705 3267 213 77 1 3165 558996980 559000192 0.000000e+00 3845
4 TraesCS1A01G320300 chr1B 87.237 619 70 7 3162 3777 559000352 559000964 0.000000e+00 697
5 TraesCS1A01G320300 chr1B 87.054 224 23 5 3790 4010 559072794 559073014 8.870000e-62 248


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 TraesCS1A01G320300 chr1A 511004371 511008502 4131 False 7631 7631 100.0000 1 4132 1 chr1A.!!$F1 4131
1 TraesCS1A01G320300 chr1D 414277632 414281865 4233 False 2606 4270 89.6115 1 4118 2 chr1D.!!$F1 4117
2 TraesCS1A01G320300 chr1B 558996980 559000964 3984 False 2271 3845 87.9710 1 3777 2 chr1B.!!$F2 3776

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
849 868 0.583917 GAGCGCATAAACTAGCCAGC 59.416 55.0 11.47 0.00 0.0 4.85 F
1743 1840 0.319900 ATTCGCCATAGCTAGCACCG 60.320 55.0 18.83 11.31 36.6 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2334 2474 0.033090 CCGTATCCGTCTAAAGGGCC 59.967 60.0 0.0 0.0 0.0 5.80 R
3273 3614 0.539986 ACGCCCGATACTGTTTGGAT 59.460 50.0 0.0 0.0 0.0 3.41 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
31 32 5.360714 AGATGTTGTTTTGTTCTGTCCATGT 59.639 36.000 0.00 0.00 0.00 3.21
32 33 5.398603 TGTTGTTTTGTTCTGTCCATGTT 57.601 34.783 0.00 0.00 0.00 2.71
67 68 8.702438 CAAAAATGTTAGATGTGAAATGGTGTC 58.298 33.333 0.00 0.00 0.00 3.67
115 116 2.430921 CGCGTCTTGGCTCGACTT 60.431 61.111 0.00 0.00 0.00 3.01
123 124 3.059800 GTCTTGGCTCGACTTTGTTGTAC 60.060 47.826 0.00 0.00 0.00 2.90
144 145 2.290260 CCACTTCACTCCCACTTATGCA 60.290 50.000 0.00 0.00 0.00 3.96
146 147 4.012374 CACTTCACTCCCACTTATGCAAT 58.988 43.478 0.00 0.00 0.00 3.56
158 159 5.122239 CCACTTATGCAATATCATGTACCCG 59.878 44.000 0.00 0.00 0.00 5.28
283 287 3.025978 CACAATTCATGGTGGGTGCTAT 58.974 45.455 0.00 0.00 0.00 2.97
300 304 5.134661 GTGCTATACCACTAGAGAAGGACT 58.865 45.833 0.00 0.00 33.02 3.85
334 338 1.416401 TGTTCTGGAACACACCTCTCC 59.584 52.381 11.53 0.00 45.42 3.71
348 352 2.106684 ACCTCTCCCCTTCAAGAAACAC 59.893 50.000 0.00 0.00 0.00 3.32
380 384 4.676546 GCACATTTTAGATGGCCTCTTTC 58.323 43.478 3.32 0.00 35.28 2.62
381 385 4.731773 GCACATTTTAGATGGCCTCTTTCG 60.732 45.833 3.32 0.00 35.28 3.46
382 386 4.635765 CACATTTTAGATGGCCTCTTTCGA 59.364 41.667 3.32 0.00 35.28 3.71
386 390 6.834168 TTTTAGATGGCCTCTTTCGAAAAT 57.166 33.333 12.41 0.93 35.28 1.82
393 402 6.436843 TGGCCTCTTTCGAAAATAAGAATC 57.563 37.500 12.41 0.58 30.55 2.52
405 414 9.611284 TCGAAAATAAGAATCTGTTGAACAATG 57.389 29.630 0.00 0.00 0.00 2.82
560 576 1.803334 TCATGGCGTTACACTGGAAC 58.197 50.000 0.00 0.00 0.00 3.62
655 671 2.673368 CGACCAGTTTCAACTCTATGCC 59.327 50.000 0.00 0.00 37.08 4.40
686 702 1.202348 GCAAGGGTCCAAAGATTTCCG 59.798 52.381 0.00 0.00 0.00 4.30
715 731 3.490759 CATGAGGACGTGCGGTGC 61.491 66.667 0.00 0.00 37.22 5.01
772 788 3.438297 ACACATATGCGTACACTCTCC 57.562 47.619 1.58 0.00 0.00 3.71
780 796 1.734748 GTACACTCTCCGCCTAGCC 59.265 63.158 0.00 0.00 0.00 3.93
809 828 7.309621 CCAGCCAAAATATTCTAATCCCATCAG 60.310 40.741 0.00 0.00 0.00 2.90
848 867 0.855349 CGAGCGCATAAACTAGCCAG 59.145 55.000 11.47 0.00 0.00 4.85
849 868 0.583917 GAGCGCATAAACTAGCCAGC 59.416 55.000 11.47 0.00 0.00 4.85
850 869 0.815615 AGCGCATAAACTAGCCAGCC 60.816 55.000 11.47 0.00 0.00 4.85
851 870 1.095228 GCGCATAAACTAGCCAGCCA 61.095 55.000 0.30 0.00 0.00 4.75
852 871 0.940126 CGCATAAACTAGCCAGCCAG 59.060 55.000 0.00 0.00 0.00 4.85
886 905 2.195683 CCCCCATCCATCAACCCG 59.804 66.667 0.00 0.00 0.00 5.28
887 906 2.195683 CCCCATCCATCAACCCGG 59.804 66.667 0.00 0.00 0.00 5.73
903 923 1.510383 CGGAGGTCAGAGCTCACAG 59.490 63.158 27.07 15.66 44.10 3.66
927 947 1.672356 CACAAAGTCAGAGCCCCCG 60.672 63.158 0.00 0.00 0.00 5.73
928 948 2.045926 CAAAGTCAGAGCCCCCGG 60.046 66.667 0.00 0.00 0.00 5.73
957 1013 2.266055 CTCGTGCCCTTCACTCCC 59.734 66.667 0.00 0.00 43.46 4.30
958 1014 3.316573 CTCGTGCCCTTCACTCCCC 62.317 68.421 0.00 0.00 43.46 4.81
959 1015 3.636231 CGTGCCCTTCACTCCCCA 61.636 66.667 0.00 0.00 43.46 4.96
960 1016 2.352805 GTGCCCTTCACTCCCCAG 59.647 66.667 0.00 0.00 42.38 4.45
1007 1066 3.872728 CTCGATCGACGACCCGCA 61.873 66.667 15.15 0.00 46.45 5.69
1149 1217 1.519455 CGTGATCAGCGGGACTTCC 60.519 63.158 0.00 0.00 0.00 3.46
1170 1238 4.115199 ATGAGTTCGGGGCCTGCC 62.115 66.667 7.74 0.00 0.00 4.85
1215 1289 3.718210 ATCGCCGTTCTTCCTCGCC 62.718 63.158 0.00 0.00 0.00 5.54
1253 1327 2.032178 GGACGCAATCCTTCATGTAAGC 59.968 50.000 0.00 0.00 45.22 3.09
1272 1346 8.780846 TGTAAGCAGGAATTAAATCGTTCTTA 57.219 30.769 2.51 2.51 0.00 2.10
1273 1347 8.662141 TGTAAGCAGGAATTAAATCGTTCTTAC 58.338 33.333 19.83 19.83 40.77 2.34
1274 1348 7.923414 AAGCAGGAATTAAATCGTTCTTACT 57.077 32.000 0.00 0.00 0.00 2.24
1275 1349 7.541122 AGCAGGAATTAAATCGTTCTTACTC 57.459 36.000 0.00 0.00 0.00 2.59
1298 1383 7.511028 ACTCTATTAGCTAGGCTACTCCATTTT 59.489 37.037 0.00 0.00 41.12 1.82
1308 1393 4.072131 GCTACTCCATTTTGTTGACTCCA 58.928 43.478 0.00 0.00 0.00 3.86
1339 1425 9.995003 CCTTAATAATACTCTTCTGAGCATCTT 57.005 33.333 0.00 0.00 43.85 2.40
1482 1570 4.162690 ATCCGCCTCCCGTTCTGC 62.163 66.667 0.00 0.00 34.38 4.26
1490 1578 3.793888 CCCGTTCTGCCTACCCCC 61.794 72.222 0.00 0.00 0.00 5.40
1576 1664 1.515736 GTAGCTACGGTGACACGCC 60.516 63.158 8.40 0.00 37.37 5.68
1730 1827 2.678336 CAAACTCCTCAAGGTATTCGCC 59.322 50.000 0.00 0.00 36.34 5.54
1743 1840 0.319900 ATTCGCCATAGCTAGCACCG 60.320 55.000 18.83 11.31 36.60 4.94
1827 1944 2.032681 AGAACTGAACCTGCGGCC 59.967 61.111 0.00 0.00 0.00 6.13
1902 2019 2.509561 GCGAAGAAGCCTCGGACC 60.510 66.667 0.00 0.00 0.00 4.46
1935 2058 0.443869 CGATGCCGACTTTCAAGGTG 59.556 55.000 0.00 0.00 38.22 4.00
2034 2167 9.696572 AAATATATTTATGCTCTCTGCCATCAT 57.303 29.630 8.99 0.00 42.00 2.45
2035 2168 8.905660 ATATATTTATGCTCTCTGCCATCATC 57.094 34.615 0.00 0.00 42.00 2.92
2036 2169 4.426736 TTTATGCTCTCTGCCATCATCA 57.573 40.909 0.00 0.00 42.00 3.07
2039 2172 0.945813 GCTCTCTGCCATCATCAAGC 59.054 55.000 0.00 0.00 35.15 4.01
2058 2193 3.059634 GCGATCGAGCTATAAGCCTAG 57.940 52.381 21.57 0.00 43.77 3.02
2077 2212 8.017418 AGCCTAGAATGCCTACTTGATATATC 57.983 38.462 5.73 5.73 0.00 1.63
2179 2318 2.551504 GGTCTCGCCTTTTGGAAAGGTA 60.552 50.000 17.94 8.30 44.07 3.08
2208 2347 2.907042 CACCCTCCTACTTCCTTTCTGT 59.093 50.000 0.00 0.00 0.00 3.41
2256 2396 6.782298 AGAGTACTTAACTTTCTTTTCGCC 57.218 37.500 0.00 0.00 39.07 5.54
2291 2431 2.101770 GCTCTGCAATTCGCCTGC 59.898 61.111 0.00 0.00 41.33 4.85
2311 2451 3.256383 TGCAAGTTGCTGAGTATTTGCAT 59.744 39.130 27.17 0.00 43.95 3.96
2434 2574 5.123979 GTGAGTACCAAAATTCCCTAAGCAG 59.876 44.000 0.00 0.00 0.00 4.24
2489 2641 3.059597 CGCTTACTTATTGCAGATTCCCG 60.060 47.826 0.00 0.00 0.00 5.14
2501 2656 2.362397 CAGATTCCCGAACAGCTAGCTA 59.638 50.000 18.86 0.00 0.00 3.32
2502 2657 2.362717 AGATTCCCGAACAGCTAGCTAC 59.637 50.000 18.86 10.97 0.00 3.58
2508 2663 1.993370 CGAACAGCTAGCTACCACAAC 59.007 52.381 18.86 4.28 0.00 3.32
2539 2698 0.445829 TGATGCACACGCCATTAACG 59.554 50.000 0.00 0.00 37.32 3.18
2589 2751 2.102252 CTCTCCCTACTTCATCAGGTGC 59.898 54.545 0.00 0.00 0.00 5.01
2629 2791 1.213182 TCCAGCACAAACAGGTACCAA 59.787 47.619 15.94 0.00 0.00 3.67
2701 2863 5.902613 TGCATTTTTCTCATGAACTAGGG 57.097 39.130 0.00 0.00 31.02 3.53
2822 2984 4.410400 CCGGAGTTCTGGCACCCC 62.410 72.222 0.00 0.00 35.28 4.95
2915 3077 1.118838 AACTCAGCTAGCTAGGCAGG 58.881 55.000 18.86 3.79 0.00 4.85
3020 3194 2.163412 ACAGTGTTGAAGCAAAAGCGAA 59.837 40.909 0.00 0.00 0.00 4.70
3145 3322 7.440198 TGAAGAGAATCATATGCACTAGGAAG 58.560 38.462 0.00 0.00 37.82 3.46
3172 3512 6.735130 AGTAAAATGGAACTACTTTGCACAC 58.265 36.000 0.00 0.00 38.54 3.82
3175 3515 3.120321 TGGAACTACTTTGCACACGAT 57.880 42.857 0.00 0.00 29.00 3.73
3183 3523 4.624336 ACTTTGCACACGATGTTTAACA 57.376 36.364 0.00 0.00 0.00 2.41
3190 3530 4.317291 GCACACGATGTTTAACATTTCGAC 59.683 41.667 22.46 6.01 39.27 4.20
3192 3532 4.512198 ACACGATGTTTAACATTTCGACCA 59.488 37.500 22.46 0.00 39.27 4.02
3230 3571 2.337879 AAAGGTCCAGCTCCACGCAA 62.338 55.000 0.00 0.00 42.61 4.85
3250 3591 3.040147 ACGGACATGATGAAAGAACGT 57.960 42.857 0.00 0.00 0.00 3.99
3262 3603 2.519377 AAGAACGTGGTGAATCGTCA 57.481 45.000 0.00 0.00 39.39 4.35
3273 3614 7.279090 ACGTGGTGAATCGTCATATAAAAATCA 59.721 33.333 0.00 0.00 35.80 2.57
3316 3657 4.651994 CAGCATTGCTCTTAGTAAAACGG 58.348 43.478 8.54 0.00 36.40 4.44
3325 3666 8.780846 TGCTCTTAGTAAAACGGATATTTTGA 57.219 30.769 0.00 0.00 33.80 2.69
3329 3671 9.715121 TCTTAGTAAAACGGATATTTTGAGTGT 57.285 29.630 0.00 0.00 33.80 3.55
3338 3680 9.832445 AACGGATATTTTGAGTGTATTACATCT 57.168 29.630 0.00 0.00 0.00 2.90
3365 3813 3.496884 TCCTTAAACTTAAGCAGTGCACG 59.503 43.478 19.20 7.77 38.99 5.34
3368 3816 5.121768 CCTTAAACTTAAGCAGTGCACGTAT 59.878 40.000 19.20 1.89 38.99 3.06
3428 3878 0.176449 CTCTGCATCATCGTGGTCCA 59.824 55.000 0.00 0.00 0.00 4.02
3463 3914 3.335484 AGGGCTATTTTGGTCCCTAAACA 59.665 43.478 0.00 0.00 46.75 2.83
3497 3948 5.238650 ACCTTACTTTGGTCGAAATCACAAG 59.761 40.000 0.00 0.00 31.03 3.16
3500 3951 3.003689 ACTTTGGTCGAAATCACAAGCTG 59.996 43.478 0.00 0.00 0.00 4.24
3589 4041 2.361737 GGAGCAAGTTCCCCAGCC 60.362 66.667 0.00 0.00 0.00 4.85
3614 4066 6.020281 CACGAGACTGTTCAGTAGCATATTTC 60.020 42.308 5.40 0.00 0.00 2.17
3621 4073 6.314018 TGTTCAGTAGCATATTTCTTTTGCG 58.686 36.000 0.00 0.00 41.22 4.85
3665 4117 4.712051 AGCATACTCATTTGCCCTATGA 57.288 40.909 0.00 0.00 39.72 2.15
3672 4124 5.075493 ACTCATTTGCCCTATGATTCCATC 58.925 41.667 0.00 0.00 34.31 3.51
3696 4148 7.922382 TCATGAATTCTAGAGGAAAAGAAGGT 58.078 34.615 7.05 0.00 37.49 3.50
3708 4160 3.864789 AAAGAAGGTGTGAGGTGACAT 57.135 42.857 0.00 0.00 0.00 3.06
3716 4168 3.560025 GGTGTGAGGTGACATTGAGGATT 60.560 47.826 0.00 0.00 0.00 3.01
3742 4194 2.127708 AGGGAGACAGTTTGGTGACTT 58.872 47.619 0.00 0.00 0.00 3.01
3743 4195 2.509964 AGGGAGACAGTTTGGTGACTTT 59.490 45.455 0.00 0.00 0.00 2.66
3750 4202 6.126409 AGACAGTTTGGTGACTTTTATGGAA 58.874 36.000 0.00 0.00 0.00 3.53
3754 4206 5.245977 AGTTTGGTGACTTTTATGGAATGGG 59.754 40.000 0.00 0.00 0.00 4.00
3771 4223 0.251832 GGGGTGTCAGAGAGAGGTGA 60.252 60.000 0.00 0.00 0.00 4.02
3777 4229 3.095332 TGTCAGAGAGAGGTGAGGAATG 58.905 50.000 0.00 0.00 0.00 2.67
3779 4231 1.829849 CAGAGAGAGGTGAGGAATGCA 59.170 52.381 0.00 0.00 0.00 3.96
3784 4236 0.257039 GAGGTGAGGAATGCATGGGT 59.743 55.000 0.00 0.00 0.00 4.51
3788 4240 3.721575 AGGTGAGGAATGCATGGGTATTA 59.278 43.478 0.00 0.00 28.83 0.98
3789 4241 4.167892 AGGTGAGGAATGCATGGGTATTAA 59.832 41.667 0.00 0.00 28.83 1.40
3790 4242 5.079643 GGTGAGGAATGCATGGGTATTAAT 58.920 41.667 0.00 0.00 28.83 1.40
3791 4243 5.183904 GGTGAGGAATGCATGGGTATTAATC 59.816 44.000 0.00 0.00 28.83 1.75
3795 4247 7.510001 TGAGGAATGCATGGGTATTAATCAAAT 59.490 33.333 0.00 0.00 28.83 2.32
3825 4277 9.965824 ATCGGACCTAAATGCAAAATAAAATAG 57.034 29.630 0.00 0.00 0.00 1.73
3848 4300 3.042871 TCAAATGCCCTTGATTTGCAC 57.957 42.857 0.00 0.00 39.60 4.57
3854 4306 3.139850 TGCCCTTGATTTGCACAAAATG 58.860 40.909 0.00 0.00 38.64 2.32
3889 4342 1.475280 CTTCCATGTCCATTGTGCCAG 59.525 52.381 0.00 0.00 0.00 4.85
3904 4357 1.202114 TGCCAGATTTGCCGTGAAATC 59.798 47.619 7.86 7.86 41.02 2.17
3916 4369 6.043327 TGCCGTGAAATCGTGATATTTTAG 57.957 37.500 0.00 0.00 0.00 1.85
3919 4372 6.237996 GCCGTGAAATCGTGATATTTTAGTCA 60.238 38.462 0.00 0.00 0.00 3.41
3920 4373 7.337718 CCGTGAAATCGTGATATTTTAGTCAG 58.662 38.462 0.00 0.00 0.00 3.51
3934 4387 0.972883 AGTCAGACTGGAGCTCCAAC 59.027 55.000 34.30 27.61 46.97 3.77
3939 4392 3.030291 CAGACTGGAGCTCCAACTAGAT 58.970 50.000 34.30 16.39 46.97 1.98
3953 4406 9.561069 GCTCCAACTAGATTAAGGATCAAAATA 57.439 33.333 0.00 0.00 37.22 1.40
3969 4424 7.285401 GGATCAAAATAGCCATTTTAGGAGTCA 59.715 37.037 2.43 0.00 41.41 3.41
3977 4432 7.573968 AGCCATTTTAGGAGTCATGTAATTC 57.426 36.000 0.00 0.00 0.00 2.17
4032 4487 0.486879 AAAATGGCCAGACTTCCCCA 59.513 50.000 13.05 0.00 0.00 4.96
4046 4501 1.378382 CCCCACCATGTTGCGATGA 60.378 57.895 0.00 0.00 0.00 2.92
4049 4504 1.477700 CCCACCATGTTGCGATGAAAT 59.522 47.619 0.00 0.00 0.00 2.17
4069 4524 5.576447 AATAAAAGTATCAAGGGCCAACG 57.424 39.130 6.18 0.00 0.00 4.10
4070 4525 2.871096 AAAGTATCAAGGGCCAACGA 57.129 45.000 6.18 0.00 0.00 3.85
4073 4528 1.837439 AGTATCAAGGGCCAACGATCA 59.163 47.619 6.18 0.00 0.00 2.92
4074 4529 2.439507 AGTATCAAGGGCCAACGATCAT 59.560 45.455 6.18 0.00 0.00 2.45
4094 4549 4.651503 TCATAGGAGAGGTTTTAGCTGAGG 59.348 45.833 0.00 0.00 0.00 3.86
4098 4553 2.941720 GAGAGGTTTTAGCTGAGGCATG 59.058 50.000 0.00 0.00 41.70 4.06
4101 4556 1.753073 GGTTTTAGCTGAGGCATGCAT 59.247 47.619 21.36 13.78 41.70 3.96
4107 4562 3.565764 AGCTGAGGCATGCATAGTTTA 57.434 42.857 21.36 0.00 41.70 2.01
4112 4567 2.880890 GAGGCATGCATAGTTTACCCAG 59.119 50.000 21.36 0.00 0.00 4.45
4118 4573 5.663456 CATGCATAGTTTACCCAGCAAAAT 58.337 37.500 0.00 0.00 35.45 1.82
4119 4574 5.070770 TGCATAGTTTACCCAGCAAAATG 57.929 39.130 0.00 0.00 0.00 2.32
4120 4575 4.526262 TGCATAGTTTACCCAGCAAAATGT 59.474 37.500 0.00 0.00 0.00 2.71
4121 4576 5.011533 TGCATAGTTTACCCAGCAAAATGTT 59.988 36.000 0.00 0.00 0.00 2.71
4122 4577 6.209589 TGCATAGTTTACCCAGCAAAATGTTA 59.790 34.615 0.00 0.00 0.00 2.41
4123 4578 6.751888 GCATAGTTTACCCAGCAAAATGTTAG 59.248 38.462 0.00 0.00 0.00 2.34
4124 4579 5.722021 AGTTTACCCAGCAAAATGTTAGG 57.278 39.130 0.00 0.00 0.00 2.69
4125 4580 4.526650 AGTTTACCCAGCAAAATGTTAGGG 59.473 41.667 0.00 0.00 42.07 3.53
4126 4581 2.990740 ACCCAGCAAAATGTTAGGGA 57.009 45.000 0.00 0.00 39.60 4.20
4127 4582 2.807676 ACCCAGCAAAATGTTAGGGAG 58.192 47.619 0.00 0.00 39.60 4.30
4128 4583 2.102578 CCCAGCAAAATGTTAGGGAGG 58.897 52.381 0.00 0.00 38.60 4.30
4129 4584 2.291540 CCCAGCAAAATGTTAGGGAGGA 60.292 50.000 0.00 0.00 38.60 3.71
4130 4585 3.019564 CCAGCAAAATGTTAGGGAGGAG 58.980 50.000 0.00 0.00 0.00 3.69
4131 4586 3.308402 CCAGCAAAATGTTAGGGAGGAGA 60.308 47.826 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 1.139256 TGGTACAACAAAGTCGAGCCA 59.861 47.619 0.00 0.00 31.92 4.75
110 111 3.869246 AGTGAAGTGGTACAACAAAGTCG 59.131 43.478 2.54 0.00 44.16 4.18
112 113 4.196971 GGAGTGAAGTGGTACAACAAAGT 58.803 43.478 2.54 0.00 44.16 2.66
115 116 2.506231 TGGGAGTGAAGTGGTACAACAA 59.494 45.455 2.54 0.00 44.16 2.83
123 124 2.290260 TGCATAAGTGGGAGTGAAGTGG 60.290 50.000 0.00 0.00 0.00 4.00
144 145 6.479972 TCTCAAACTCGGGTACATGATATT 57.520 37.500 0.00 0.00 0.00 1.28
146 147 7.670140 AGATATCTCAAACTCGGGTACATGATA 59.330 37.037 0.00 0.00 0.00 2.15
158 159 8.654230 TGCATCAAGTTAGATATCTCAAACTC 57.346 34.615 17.39 8.41 31.15 3.01
283 287 8.840200 ATATTTCAAGTCCTTCTCTAGTGGTA 57.160 34.615 0.00 0.00 0.00 3.25
318 322 0.838122 AGGGGAGAGGTGTGTTCCAG 60.838 60.000 0.00 0.00 32.50 3.86
329 333 3.492102 TGTGTTTCTTGAAGGGGAGAG 57.508 47.619 0.00 0.00 0.00 3.20
334 338 3.023832 ACACCTTGTGTTTCTTGAAGGG 58.976 45.455 0.00 0.00 45.08 3.95
348 352 2.031245 TCTAAAATGTGCGCACACCTTG 60.031 45.455 42.74 29.10 46.86 3.61
380 384 9.398170 ACATTGTTCAACAGATTCTTATTTTCG 57.602 29.630 0.00 0.00 0.00 3.46
382 386 8.981647 GCACATTGTTCAACAGATTCTTATTTT 58.018 29.630 0.00 0.00 0.00 1.82
386 390 6.631971 TGCACATTGTTCAACAGATTCTTA 57.368 33.333 0.00 0.00 0.00 2.10
393 402 9.195411 AGTAATAATTTGCACATTGTTCAACAG 57.805 29.630 10.39 0.00 0.00 3.16
442 451 6.556495 TGCTATCACTCTATCTCCCTCAAATT 59.444 38.462 0.00 0.00 0.00 1.82
443 452 6.080682 TGCTATCACTCTATCTCCCTCAAAT 58.919 40.000 0.00 0.00 0.00 2.32
444 453 5.458595 TGCTATCACTCTATCTCCCTCAAA 58.541 41.667 0.00 0.00 0.00 2.69
450 459 7.947282 AGTAGTTTTGCTATCACTCTATCTCC 58.053 38.462 0.00 0.00 31.50 3.71
487 496 8.970020 TCCAACAATATCAATTTGCTATCACTT 58.030 29.630 0.00 0.00 0.00 3.16
488 497 8.408601 GTCCAACAATATCAATTTGCTATCACT 58.591 33.333 0.00 0.00 0.00 3.41
490 499 8.523915 AGTCCAACAATATCAATTTGCTATCA 57.476 30.769 0.00 0.00 0.00 2.15
491 500 8.844244 AGAGTCCAACAATATCAATTTGCTATC 58.156 33.333 0.00 0.00 0.00 2.08
492 501 8.757982 AGAGTCCAACAATATCAATTTGCTAT 57.242 30.769 0.00 0.00 0.00 2.97
493 502 8.461222 CAAGAGTCCAACAATATCAATTTGCTA 58.539 33.333 0.00 0.00 0.00 3.49
509 518 6.073657 CGACCGTTTTTAATACAAGAGTCCAA 60.074 38.462 0.00 0.00 0.00 3.53
560 576 1.298041 GTTTGCGTGTGGTCAACCG 60.298 57.895 0.00 0.00 39.43 4.44
587 603 2.677979 GCGGAGGAGTTTTCGGTGC 61.678 63.158 0.00 0.00 0.00 5.01
655 671 2.435586 CCCTTGCTGACTCGCTGG 60.436 66.667 0.00 0.00 0.00 4.85
686 702 2.176273 CCTCATGCAGTGCCGCTAC 61.176 63.158 13.72 0.00 0.00 3.58
715 731 2.286294 GCTATGTGCGGATCAAGTCAAG 59.714 50.000 0.00 0.00 0.00 3.02
780 796 5.279156 GGGATTAGAATATTTTGGCTGGCTG 60.279 44.000 2.00 0.00 0.00 4.85
809 828 1.135774 GTCCGTTCCTGGATTTTTCGC 60.136 52.381 0.00 0.00 40.91 4.70
886 905 0.902516 ACCTGTGAGCTCTGACCTCC 60.903 60.000 16.19 0.00 0.00 4.30
887 906 0.530288 GACCTGTGAGCTCTGACCTC 59.470 60.000 16.19 0.54 0.00 3.85
903 923 2.079925 GGCTCTGACTTTGTGATGACC 58.920 52.381 0.00 0.00 0.00 4.02
927 947 4.194720 ACGAGCACGATCGAGGCC 62.195 66.667 24.34 15.99 45.56 5.19
928 948 2.951745 CACGAGCACGATCGAGGC 60.952 66.667 24.34 23.26 45.56 4.70
929 949 2.951745 GCACGAGCACGATCGAGG 60.952 66.667 24.34 14.40 45.56 4.63
930 950 2.951745 GGCACGAGCACGATCGAG 60.952 66.667 24.34 16.03 45.56 4.04
957 1013 1.078848 GACAGTACTGGCTGGCTGG 60.079 63.158 26.12 0.00 41.18 4.85
958 1014 1.078848 GGACAGTACTGGCTGGCTG 60.079 63.158 27.55 13.56 43.78 4.85
959 1015 2.294078 GGGACAGTACTGGCTGGCT 61.294 63.158 27.55 4.81 43.78 4.75
960 1016 2.124507 TTGGGACAGTACTGGCTGGC 62.125 60.000 27.55 11.62 43.58 4.85
1000 1059 8.677300 ACAATCAATGATTTATATATGCGGGTC 58.323 33.333 5.63 0.00 28.87 4.46
1001 1060 8.579850 ACAATCAATGATTTATATATGCGGGT 57.420 30.769 5.63 0.00 28.87 5.28
1002 1061 9.859427 AAACAATCAATGATTTATATATGCGGG 57.141 29.630 5.63 0.00 28.87 6.13
1031 1090 2.756207 TCAATCGATCGGTGTAGTGGAA 59.244 45.455 16.41 0.00 0.00 3.53
1131 1199 1.519455 GGAAGTCCCGCTGATCACG 60.519 63.158 9.75 9.75 0.00 4.35
1149 1217 4.547367 GGCCCCGAACTCATCCCG 62.547 72.222 0.00 0.00 0.00 5.14
1194 1268 1.447838 GAGGAAGAACGGCGATGCA 60.448 57.895 16.62 0.00 0.00 3.96
1197 1271 2.202756 GCGAGGAAGAACGGCGAT 60.203 61.111 16.62 0.00 0.00 4.58
1215 1289 0.033920 TCCAATCCATCTGCGGATCG 59.966 55.000 4.63 0.00 45.39 3.69
1272 1346 5.586155 TGGAGTAGCCTAGCTAATAGAGT 57.414 43.478 0.00 0.00 43.07 3.24
1273 1347 7.475137 AAATGGAGTAGCCTAGCTAATAGAG 57.525 40.000 0.00 0.00 43.07 2.43
1274 1348 7.290248 ACAAAATGGAGTAGCCTAGCTAATAGA 59.710 37.037 0.00 0.00 43.07 1.98
1275 1349 7.445945 ACAAAATGGAGTAGCCTAGCTAATAG 58.554 38.462 0.00 0.00 43.07 1.73
1320 1406 5.424895 AGACCAAGATGCTCAGAAGAGTATT 59.575 40.000 0.00 0.00 45.60 1.89
1327 1413 1.895798 ACGAGACCAAGATGCTCAGAA 59.104 47.619 0.00 0.00 0.00 3.02
1334 1420 1.012086 CCATGCACGAGACCAAGATG 58.988 55.000 0.00 0.00 0.00 2.90
1339 1425 1.517361 CTAGCCATGCACGAGACCA 59.483 57.895 0.00 0.00 0.00 4.02
1482 1570 2.123428 CGTCGGTGTAGGGGGTAGG 61.123 68.421 0.00 0.00 0.00 3.18
1601 1689 4.560743 TGGTGGTGCTGCTGCGAA 62.561 61.111 11.21 0.00 43.34 4.70
1664 1761 2.786495 CGGTGACCTCTGGATCGGG 61.786 68.421 0.00 0.00 0.00 5.14
1669 1766 3.695606 GCTGCGGTGACCTCTGGA 61.696 66.667 0.00 0.00 0.00 3.86
1730 1827 3.584406 AGCTATTCGGTGCTAGCTATG 57.416 47.619 17.23 5.31 46.70 2.23
1957 2080 7.216973 AGAACGATCAGTTATACTATGGGAC 57.783 40.000 0.00 0.00 44.35 4.46
1958 2081 7.039923 GGAAGAACGATCAGTTATACTATGGGA 60.040 40.741 0.00 0.00 44.35 4.37
1968 2101 9.078990 AGATATATGTGGAAGAACGATCAGTTA 57.921 33.333 0.00 0.00 44.35 2.24
2020 2153 0.945813 GCTTGATGATGGCAGAGAGC 59.054 55.000 0.00 0.00 44.65 4.09
2034 2167 2.351835 GGCTTATAGCTCGATCGCTTGA 60.352 50.000 11.09 0.00 41.99 3.02
2035 2168 1.989165 GGCTTATAGCTCGATCGCTTG 59.011 52.381 11.09 4.24 41.99 4.01
2036 2169 1.889829 AGGCTTATAGCTCGATCGCTT 59.110 47.619 11.09 0.44 41.99 4.68
2039 2172 4.948608 TTCTAGGCTTATAGCTCGATCG 57.051 45.455 9.36 9.36 41.99 3.69
2058 2193 7.602517 AAAGCGATATATCAAGTAGGCATTC 57.397 36.000 13.11 0.00 0.00 2.67
2077 2212 4.030529 CACGGCAAATTCTATTCAAAAGCG 59.969 41.667 0.00 0.00 0.00 4.68
2179 2318 3.523972 GGAAGTAGGAGGGTGAAAAGGAT 59.476 47.826 0.00 0.00 0.00 3.24
2186 2325 3.173965 CAGAAAGGAAGTAGGAGGGTGA 58.826 50.000 0.00 0.00 0.00 4.02
2208 2347 9.847224 CTACTAAGCTAATAATGGAGGGAAAAA 57.153 33.333 0.00 0.00 0.00 1.94
2256 2396 9.481340 TTGCAGAGCAATATAGTATAAACAGAG 57.519 33.333 0.00 0.00 43.99 3.35
2291 2431 5.306532 AGATGCAAATACTCAGCAACTTG 57.693 39.130 0.00 0.00 38.04 3.16
2311 2451 1.378531 CCGGGCATCGATCAAAAAGA 58.621 50.000 0.00 0.00 42.43 2.52
2334 2474 0.033090 CCGTATCCGTCTAAAGGGCC 59.967 60.000 0.00 0.00 0.00 5.80
2349 2489 1.514087 GTGGAGAACCGATGCCGTA 59.486 57.895 0.00 0.00 39.42 4.02
2434 2574 4.844349 TGGAGCATCTATAATTAGGGGC 57.156 45.455 0.00 0.00 33.73 5.80
2489 2641 3.320673 AGTTGTGGTAGCTAGCTGTTC 57.679 47.619 27.68 16.14 0.00 3.18
2501 2656 6.209192 TGCATCATGAAAAGATTAGTTGTGGT 59.791 34.615 0.00 0.00 0.00 4.16
2502 2657 6.529125 GTGCATCATGAAAAGATTAGTTGTGG 59.471 38.462 0.00 0.00 0.00 4.17
2508 2663 4.731961 GCGTGTGCATCATGAAAAGATTAG 59.268 41.667 0.00 0.00 42.15 1.73
2539 2698 1.952296 CTGCATGCAGAGATAAACCCC 59.048 52.381 38.90 0.00 46.30 4.95
2647 2809 7.516198 AGTGAGATGAAATTAAACAAGCAGT 57.484 32.000 0.00 0.00 0.00 4.40
2664 2826 9.798994 GAGAAAAATGCAATTCATAAGTGAGAT 57.201 29.630 11.38 0.00 33.67 2.75
2701 2863 3.186047 CGGCGTCACCATCCGAAC 61.186 66.667 0.00 0.00 45.53 3.95
2915 3077 7.799914 CACAATCACACACACATATATGCATAC 59.200 37.037 8.99 0.00 0.00 2.39
3024 3198 6.586293 GCACATTGCTGATTGCTTAAAAGCT 61.586 40.000 15.25 0.00 45.55 3.74
3145 3322 8.347035 TGTGCAAAGTAGTTCCATTTTACTAAC 58.653 33.333 0.00 0.00 0.00 2.34
3155 3332 2.605837 TCGTGTGCAAAGTAGTTCCA 57.394 45.000 0.00 0.00 0.00 3.53
3172 3512 5.003402 GCAATGGTCGAAATGTTAAACATCG 59.997 40.000 0.00 0.00 37.97 3.84
3175 3515 4.979197 GTGCAATGGTCGAAATGTTAAACA 59.021 37.500 0.00 0.00 0.00 2.83
3183 3523 2.746904 TCAATCGTGCAATGGTCGAAAT 59.253 40.909 0.22 0.00 37.16 2.17
3190 3530 2.619646 TGGATCATCAATCGTGCAATGG 59.380 45.455 0.00 0.00 34.99 3.16
3192 3532 4.202080 CCTTTGGATCATCAATCGTGCAAT 60.202 41.667 0.00 0.00 34.99 3.56
3230 3571 2.736721 CACGTTCTTTCATCATGTCCGT 59.263 45.455 0.00 0.00 0.00 4.69
3250 3591 8.783093 GGATGATTTTTATATGACGATTCACCA 58.217 33.333 0.00 0.00 33.38 4.17
3273 3614 0.539986 ACGCCCGATACTGTTTGGAT 59.460 50.000 0.00 0.00 0.00 3.41
3324 3665 8.662781 TTAAGGATTGCAGATGTAATACACTC 57.337 34.615 8.34 0.00 33.99 3.51
3325 3666 8.893727 GTTTAAGGATTGCAGATGTAATACACT 58.106 33.333 8.34 0.00 33.99 3.55
3334 3676 6.855836 TGCTTAAGTTTAAGGATTGCAGATG 58.144 36.000 12.23 0.00 40.31 2.90
3338 3680 6.012658 CACTGCTTAAGTTTAAGGATTGCA 57.987 37.500 12.23 5.05 39.76 4.08
3342 3684 4.154195 CGTGCACTGCTTAAGTTTAAGGAT 59.846 41.667 16.19 0.18 39.76 3.24
3387 3837 3.895656 GGCCAGAGGTTTAACTTCCTTTT 59.104 43.478 0.00 0.00 33.83 2.27
3394 3844 1.003696 GCAGAGGCCAGAGGTTTAACT 59.996 52.381 5.01 0.00 0.00 2.24
3403 3853 1.332889 ACGATGATGCAGAGGCCAGA 61.333 55.000 5.01 0.00 40.13 3.86
3428 3878 6.462909 CCAAAATAGCCCTTTTGAGAGTTTGT 60.463 38.462 18.15 0.00 44.97 2.83
3497 3948 1.032014 TTCCAGAGTTGCCAAACAGC 58.968 50.000 0.00 0.00 38.88 4.40
3500 3951 1.268539 CGTGTTCCAGAGTTGCCAAAC 60.269 52.381 0.00 0.00 36.47 2.93
3589 4041 2.706555 TGCTACTGAACAGTCTCGTG 57.293 50.000 10.81 0.49 42.54 4.35
3614 4066 2.153366 ATGAGGGCAAAACGCAAAAG 57.847 45.000 0.00 0.00 45.17 2.27
3621 4073 2.794350 CGTTGAACAATGAGGGCAAAAC 59.206 45.455 0.00 0.00 0.00 2.43
3665 4117 9.352191 CTTTTCCTCTAGAATTCATGATGGAAT 57.648 33.333 8.44 0.00 39.11 3.01
3672 4124 7.609532 ACACCTTCTTTTCCTCTAGAATTCATG 59.390 37.037 8.44 0.00 33.44 3.07
3678 4130 5.012148 CCTCACACCTTCTTTTCCTCTAGAA 59.988 44.000 0.00 0.00 0.00 2.10
3696 4148 3.072915 ACAATCCTCAATGTCACCTCACA 59.927 43.478 0.00 0.00 0.00 3.58
3708 4160 2.233922 GTCTCCCTTCGACAATCCTCAA 59.766 50.000 0.00 0.00 0.00 3.02
3716 4168 1.070134 CCAAACTGTCTCCCTTCGACA 59.930 52.381 0.00 0.00 38.94 4.35
3742 4194 3.849574 TCTCTGACACCCCATTCCATAAA 59.150 43.478 0.00 0.00 0.00 1.40
3743 4195 3.455910 CTCTCTGACACCCCATTCCATAA 59.544 47.826 0.00 0.00 0.00 1.90
3750 4202 0.415429 ACCTCTCTCTGACACCCCAT 59.585 55.000 0.00 0.00 0.00 4.00
3754 4206 1.181786 CCTCACCTCTCTCTGACACC 58.818 60.000 0.00 0.00 0.00 4.16
3771 4223 7.038799 GGATTTGATTAATACCCATGCATTCCT 60.039 37.037 0.00 0.00 0.00 3.36
3777 4229 5.957842 TCGGATTTGATTAATACCCATGC 57.042 39.130 0.00 0.00 0.00 4.06
3779 4231 5.880332 CCGATCGGATTTGATTAATACCCAT 59.120 40.000 30.62 0.00 37.50 4.00
3795 4247 1.116308 TGCATTTAGGTCCGATCGGA 58.884 50.000 32.59 32.59 42.90 4.55
3830 4282 3.488778 TTGTGCAAATCAAGGGCATTT 57.511 38.095 0.00 0.00 40.05 2.32
3831 4283 3.488778 TTTGTGCAAATCAAGGGCATT 57.511 38.095 0.00 0.00 40.05 3.56
3843 4295 2.093288 TCAAGGTTGCCATTTTGTGCAA 60.093 40.909 0.00 0.00 44.64 4.08
3848 4300 4.634199 AGATTGTCAAGGTTGCCATTTTG 58.366 39.130 0.00 0.00 0.00 2.44
3854 4306 2.238521 TGGAAGATTGTCAAGGTTGCC 58.761 47.619 0.00 0.00 0.00 4.52
3889 4342 2.892373 TCACGATTTCACGGCAAATC 57.108 45.000 10.01 10.01 38.79 2.17
3904 4357 5.460419 GCTCCAGTCTGACTAAAATATCACG 59.540 44.000 10.47 0.00 0.00 4.35
3939 4392 9.707957 TCCTAAAATGGCTATTTTGATCCTTAA 57.292 29.630 25.80 6.91 44.12 1.85
3953 4406 6.260936 CGAATTACATGACTCCTAAAATGGCT 59.739 38.462 0.00 0.00 0.00 4.75
3998 4453 6.064060 TGGCCATTTTCTAGTCATATGAAGG 58.936 40.000 7.07 0.94 0.00 3.46
4010 4465 2.025321 GGGGAAGTCTGGCCATTTTCTA 60.025 50.000 5.51 0.00 0.00 2.10
4011 4466 1.272704 GGGGAAGTCTGGCCATTTTCT 60.273 52.381 5.51 0.00 0.00 2.52
4013 4468 0.486879 TGGGGAAGTCTGGCCATTTT 59.513 50.000 5.51 0.10 0.00 1.82
4032 4487 6.024552 ACTTTTATTTCATCGCAACATGGT 57.975 33.333 0.00 0.00 0.00 3.55
4046 4501 5.712917 TCGTTGGCCCTTGATACTTTTATTT 59.287 36.000 0.00 0.00 0.00 1.40
4049 4504 4.289238 TCGTTGGCCCTTGATACTTTTA 57.711 40.909 0.00 0.00 0.00 1.52
4069 4524 6.412362 TCAGCTAAAACCTCTCCTATGATC 57.588 41.667 0.00 0.00 0.00 2.92
4070 4525 5.306678 CCTCAGCTAAAACCTCTCCTATGAT 59.693 44.000 0.00 0.00 0.00 2.45
4073 4528 3.389656 GCCTCAGCTAAAACCTCTCCTAT 59.610 47.826 0.00 0.00 35.50 2.57
4074 4529 2.766828 GCCTCAGCTAAAACCTCTCCTA 59.233 50.000 0.00 0.00 35.50 2.94
4094 4549 2.023673 TGCTGGGTAAACTATGCATGC 58.976 47.619 11.82 11.82 0.00 4.06
4098 4553 5.072040 ACATTTTGCTGGGTAAACTATGC 57.928 39.130 0.00 0.00 0.00 3.14
4101 4556 5.712917 CCCTAACATTTTGCTGGGTAAACTA 59.287 40.000 0.00 0.00 0.00 2.24
4107 4562 2.557452 CCTCCCTAACATTTTGCTGGGT 60.557 50.000 0.00 0.00 36.23 4.51


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

AutoCloner maintained by Alex Coulton.