Multiple sequence alignment - TraesCS3D01G304800

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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 TraesCS3D01G304800 chr3D 100.000 7540 0 0 1 7540 418775783 418783322 0.000000e+00 13924.0
1 TraesCS3D01G304800 chr3B 89.643 3640 259 61 1 3580 545194679 545198260 0.000000e+00 4525.0
2 TraesCS3D01G304800 chr3B 91.332 1569 81 18 5350 6880 545200370 545201921 0.000000e+00 2093.0
3 TraesCS3D01G304800 chr3B 96.073 662 25 1 6880 7540 545201964 545202625 0.000000e+00 1077.0
4 TraesCS3D01G304800 chr3B 95.882 340 12 1 5018 5355 545198732 545199071 3.980000e-152 549.0
5 TraesCS3D01G304800 chr3B 88.095 420 33 11 3652 4058 545198259 545198674 4.090000e-132 483.0
6 TraesCS3D01G304800 chr3B 93.103 58 4 0 4927 4984 545198673 545198730 1.350000e-12 86.1
7 TraesCS3D01G304800 chr3A 94.844 2851 109 18 772 3608 532325942 532323116 0.000000e+00 4416.0
8 TraesCS3D01G304800 chr3A 96.077 2014 47 14 4888 6880 532322356 532320354 0.000000e+00 3253.0
9 TraesCS3D01G304800 chr3A 94.337 830 30 9 4069 4889 8582037 8582858 0.000000e+00 1256.0
10 TraesCS3D01G304800 chr3A 96.531 663 20 1 6878 7540 532320292 532319633 0.000000e+00 1094.0
11 TraesCS3D01G304800 chr3A 95.540 426 10 5 3655 4071 532322773 532322348 0.000000e+00 673.0
12 TraesCS3D01G304800 chr3A 91.593 452 37 1 1 452 532329250 532328800 2.310000e-174 623.0
13 TraesCS3D01G304800 chr5D 98.301 824 8 3 4072 4889 195557735 195556912 0.000000e+00 1439.0
14 TraesCS3D01G304800 chr5D 98.335 781 8 4 4072 4852 411744361 411743586 0.000000e+00 1365.0
15 TraesCS3D01G304800 chr6D 97.711 830 6 2 4072 4888 451541636 451542465 0.000000e+00 1415.0
16 TraesCS3D01G304800 chr7D 97.800 818 6 2 4072 4888 616902266 616901460 0.000000e+00 1400.0
17 TraesCS3D01G304800 chr7D 96.951 820 12 8 4069 4888 553495395 553496201 0.000000e+00 1363.0
18 TraesCS3D01G304800 chr1D 97.215 826 9 3 4072 4888 201492241 201493061 0.000000e+00 1386.0
19 TraesCS3D01G304800 chr1D 94.903 824 35 3 4072 4888 38599579 38598756 0.000000e+00 1282.0
20 TraesCS3D01G304800 chr4A 94.915 826 27 8 4072 4890 580660516 580659699 0.000000e+00 1279.0
21 TraesCS3D01G304800 chr2A 92.014 864 33 8 4065 4893 582952622 582953484 0.000000e+00 1181.0
22 TraesCS3D01G304800 chr1A 95.040 746 29 5 4151 4889 52540833 52540089 0.000000e+00 1166.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G304800 chr3D 418775783 418783322 7539 False 13924.00 13924 100.000000 1 7540 1 chr3D.!!$F1 7539
1 TraesCS3D01G304800 chr3B 545194679 545202625 7946 False 1468.85 4525 92.354667 1 7540 6 chr3B.!!$F1 7539
2 TraesCS3D01G304800 chr3A 532319633 532329250 9617 True 2011.80 4416 94.917000 1 7540 5 chr3A.!!$R1 7539
3 TraesCS3D01G304800 chr3A 8582037 8582858 821 False 1256.00 1256 94.337000 4069 4889 1 chr3A.!!$F1 820
4 TraesCS3D01G304800 chr5D 195556912 195557735 823 True 1439.00 1439 98.301000 4072 4889 1 chr5D.!!$R1 817
5 TraesCS3D01G304800 chr5D 411743586 411744361 775 True 1365.00 1365 98.335000 4072 4852 1 chr5D.!!$R2 780
6 TraesCS3D01G304800 chr6D 451541636 451542465 829 False 1415.00 1415 97.711000 4072 4888 1 chr6D.!!$F1 816
7 TraesCS3D01G304800 chr7D 616901460 616902266 806 True 1400.00 1400 97.800000 4072 4888 1 chr7D.!!$R1 816
8 TraesCS3D01G304800 chr7D 553495395 553496201 806 False 1363.00 1363 96.951000 4069 4888 1 chr7D.!!$F1 819
9 TraesCS3D01G304800 chr1D 201492241 201493061 820 False 1386.00 1386 97.215000 4072 4888 1 chr1D.!!$F1 816
10 TraesCS3D01G304800 chr1D 38598756 38599579 823 True 1282.00 1282 94.903000 4072 4888 1 chr1D.!!$R1 816
11 TraesCS3D01G304800 chr4A 580659699 580660516 817 True 1279.00 1279 94.915000 4072 4890 1 chr4A.!!$R1 818
12 TraesCS3D01G304800 chr2A 582952622 582953484 862 False 1181.00 1181 92.014000 4065 4893 1 chr2A.!!$F1 828
13 TraesCS3D01G304800 chr1A 52540089 52540833 744 True 1166.00 1166 95.040000 4151 4889 1 chr1A.!!$R1 738

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
502 509 0.036105 TTGCCATCGATGAGTGCAGT 60.036 50.000 26.86 0.00 32.88 4.40 F
1333 4023 0.041576 GTTTGCGTCACCGGAGAAAC 60.042 55.000 9.46 3.09 35.23 2.78 F
2424 5116 2.327568 GTAATGTGCGTGCATTGCTTT 58.672 42.857 10.49 8.33 39.20 3.51 F
3324 6044 0.534412 AGGAGACTGGTGAAGATGCG 59.466 55.000 0.00 0.00 41.13 4.73 F
3643 6366 0.309302 TTGTTCAACAACATCCGCGG 59.691 50.000 22.12 22.12 42.28 6.46 F
4895 7995 1.094073 GGTGCATTCGAGCTCTGCAT 61.094 55.000 26.12 8.30 46.52 3.96 F
5138 8238 2.023404 TCATGAGCCTACCCCTGAAGTA 60.023 50.000 0.00 0.00 0.00 2.24 F
5988 10407 1.811778 ATATGCTTCTGGGGAGCTGA 58.188 50.000 0.00 0.00 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1762 4452 0.179067 CCTTGGGCGCCTCGTAAATA 60.179 55.000 28.56 1.92 0.00 1.40 R
2983 5678 0.036164 TGCCAGTGACGCATAAACCT 59.964 50.000 0.00 0.00 0.00 3.50 R
3633 6356 0.034863 AATACAACCCCGCGGATGTT 60.035 50.000 30.73 25.59 42.18 2.71 R
4556 7636 2.294078 GCAGCTACTCACCCAGGGT 61.294 63.158 4.76 4.76 35.62 4.34 R
5464 9870 3.554752 GGTGCAGTTTAAGGTGTACCGTA 60.555 47.826 9.59 0.00 39.28 4.02 R
5977 10396 1.004044 ACTCAACATTCAGCTCCCCAG 59.996 52.381 0.00 0.00 0.00 4.45 R
6011 10430 1.453197 CCACTTATTCGGTGCCCCC 60.453 63.158 0.00 0.00 33.78 5.40 R
7340 11907 2.063266 CAGTTACAAGCGAGCGGTTAA 58.937 47.619 7.02 0.00 34.20 2.01 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
46 47 7.924412 ACCCAGTTAATATCGTTACATACACAG 59.076 37.037 0.00 0.00 0.00 3.66
188 192 9.978044 AGGACTAGATATTTATTGAAACCGTAC 57.022 33.333 0.00 0.00 0.00 3.67
257 261 0.119155 TGGTCCCTGACTCCTCCAAT 59.881 55.000 0.00 0.00 32.47 3.16
259 263 0.461961 GTCCCTGACTCCTCCAATCG 59.538 60.000 0.00 0.00 0.00 3.34
266 270 3.099905 TGACTCCTCCAATCGAGAATGT 58.900 45.455 0.00 0.00 41.63 2.71
279 283 1.537202 GAGAATGTTCGGCAGCTTTGT 59.463 47.619 0.00 0.00 0.00 2.83
324 329 5.265989 GTTATGTCCCTTGGATTTTGGGTA 58.734 41.667 0.00 0.00 41.58 3.69
340 345 4.516365 TGGGTAGTCGTCTTCTTTTCTC 57.484 45.455 0.00 0.00 0.00 2.87
373 380 0.457443 TGCTTCAGATCATCGTCGCT 59.543 50.000 0.00 0.00 0.00 4.93
374 381 0.851495 GCTTCAGATCATCGTCGCTG 59.149 55.000 0.00 0.00 0.00 5.18
411 418 2.049802 GACGACTTTCGACCGCCA 60.050 61.111 1.94 0.00 43.74 5.69
426 433 1.119635 CGCCACGTCAACAATGTTTG 58.880 50.000 0.00 0.00 0.00 2.93
467 474 1.604693 GGTGGTTCATAGGCGGTATCG 60.605 57.143 0.00 0.00 39.81 2.92
472 479 3.306818 GTTCATAGGCGGTATCGAGTTC 58.693 50.000 0.00 0.00 39.00 3.01
473 480 1.884579 TCATAGGCGGTATCGAGTTCC 59.115 52.381 0.00 0.00 39.00 3.62
478 485 1.725665 CGGTATCGAGTTCCGCTCA 59.274 57.895 11.53 0.00 44.33 4.26
493 500 1.522355 CTCACGGCTTGCCATCGAT 60.522 57.895 12.45 0.00 0.00 3.59
501 508 0.656259 CTTGCCATCGATGAGTGCAG 59.344 55.000 26.86 15.59 32.88 4.41
502 509 0.036105 TTGCCATCGATGAGTGCAGT 60.036 50.000 26.86 0.00 32.88 4.40
517 524 1.972198 CAGTAGGAAGGCGGTGTCA 59.028 57.895 0.00 0.00 0.00 3.58
523 530 2.316108 AGGAAGGCGGTGTCAATTTTT 58.684 42.857 0.00 0.00 0.00 1.94
649 657 1.719709 GACTTAACCGAATGCGCCC 59.280 57.895 4.18 0.00 35.83 6.13
650 658 1.003112 ACTTAACCGAATGCGCCCA 60.003 52.632 4.18 0.00 35.83 5.36
651 659 0.606944 ACTTAACCGAATGCGCCCAA 60.607 50.000 4.18 0.00 35.83 4.12
652 660 0.738389 CTTAACCGAATGCGCCCAAT 59.262 50.000 4.18 0.00 35.83 3.16
655 666 1.247419 AACCGAATGCGCCCAATTGA 61.247 50.000 7.12 0.00 35.83 2.57
671 682 0.756294 TTGACAAAGACAGAGCGGGA 59.244 50.000 0.00 0.00 0.00 5.14
679 690 2.457598 AGACAGAGCGGGACATTTCTA 58.542 47.619 0.00 0.00 0.00 2.10
765 793 3.451402 ACCCCTGGTTTCAAAGATACC 57.549 47.619 0.00 0.44 34.91 2.73
766 794 2.042569 ACCCCTGGTTTCAAAGATACCC 59.957 50.000 4.56 0.00 33.71 3.69
767 795 2.365582 CCCTGGTTTCAAAGATACCCG 58.634 52.381 4.56 0.00 33.71 5.28
768 796 2.365582 CCTGGTTTCAAAGATACCCGG 58.634 52.381 0.00 0.00 33.64 5.73
769 797 2.026636 CCTGGTTTCAAAGATACCCGGA 60.027 50.000 0.73 0.00 39.17 5.14
789 3472 2.294449 AACCCCTTTCTTCTTGCTCC 57.706 50.000 0.00 0.00 0.00 4.70
798 3481 3.802948 TCTTCTTGCTCCGTTATCCTC 57.197 47.619 0.00 0.00 0.00 3.71
869 3553 1.080498 TCTACCCACTCCCAGTTCCAT 59.920 52.381 0.00 0.00 0.00 3.41
870 3554 1.916181 CTACCCACTCCCAGTTCCATT 59.084 52.381 0.00 0.00 0.00 3.16
889 3574 0.254747 TTCCCCAGCACCTAAATCCG 59.745 55.000 0.00 0.00 0.00 4.18
911 3596 3.374984 GGATAACTCTAACCCCCTCTCCA 60.375 52.174 0.00 0.00 0.00 3.86
922 3607 1.981495 CCCCTCTCCACTTCTTGAACT 59.019 52.381 0.00 0.00 0.00 3.01
943 3628 0.251634 CCCTCCTCCAGCTTCTTCAC 59.748 60.000 0.00 0.00 0.00 3.18
1037 3725 0.391263 CCGTGGCTCTTTCCAGGTAC 60.391 60.000 0.00 0.00 39.63 3.34
1078 3766 3.501040 TTCAAACCCCCGTCCTGCC 62.501 63.158 0.00 0.00 0.00 4.85
1115 3803 2.014857 GAATTTGACCTCCCCGCTAAC 58.985 52.381 0.00 0.00 0.00 2.34
1151 3840 1.375140 CACTCTGCAGGCATGTCGT 60.375 57.895 15.13 0.00 0.00 4.34
1152 3841 1.079543 ACTCTGCAGGCATGTCGTC 60.080 57.895 15.13 0.00 0.00 4.20
1153 3842 2.125952 TCTGCAGGCATGTCGTCG 60.126 61.111 15.13 0.00 0.00 5.12
1214 3903 2.972625 TCTGCAAGTCCTCGGTAATTG 58.027 47.619 0.00 0.00 33.76 2.32
1229 3919 1.181098 AATTGCCTGCCTTGACGCTT 61.181 50.000 0.00 0.00 0.00 4.68
1238 3928 2.100584 TGCCTTGACGCTTCAAATTGTT 59.899 40.909 7.10 0.00 41.34 2.83
1256 3946 0.878416 TTGAAAGTAAATGCCGCGCT 59.122 45.000 5.56 0.00 0.00 5.92
1286 3976 4.157840 CGCTGGGCTAAAATTTAGGTTCTT 59.842 41.667 13.89 0.00 0.00 2.52
1287 3977 5.651530 GCTGGGCTAAAATTTAGGTTCTTC 58.348 41.667 13.89 0.00 0.00 2.87
1289 3979 5.562635 TGGGCTAAAATTTAGGTTCTTCGA 58.437 37.500 13.89 0.00 0.00 3.71
1324 4014 2.372350 GTGTTTGCTAGTTTGCGTCAC 58.628 47.619 0.00 0.00 35.36 3.67
1333 4023 0.041576 GTTTGCGTCACCGGAGAAAC 60.042 55.000 9.46 3.09 35.23 2.78
1420 4110 4.513442 TCCATTTTGATCCGTCGAAGATT 58.487 39.130 0.00 0.00 40.67 2.40
1751 4441 3.428045 GGAGGAAACAAATGATTCGCTGG 60.428 47.826 0.00 0.00 0.00 4.85
1762 4452 6.889301 AATGATTCGCTGGATGAATATGTT 57.111 33.333 0.00 0.00 36.24 2.71
2032 4722 4.454504 AGTTTTTATTGTGGCTGTCTACCG 59.545 41.667 0.00 0.00 0.00 4.02
2249 4941 3.756069 CAAGCTAGCTTGTCATGCTTTC 58.244 45.455 38.17 10.18 45.91 2.62
2291 4983 8.087982 AGTGTAATGTAAATGTGAACAGAGTG 57.912 34.615 0.00 0.00 0.00 3.51
2292 4984 7.173218 AGTGTAATGTAAATGTGAACAGAGTGG 59.827 37.037 0.00 0.00 0.00 4.00
2293 4985 6.995686 TGTAATGTAAATGTGAACAGAGTGGT 59.004 34.615 0.00 0.00 0.00 4.16
2294 4986 5.947228 ATGTAAATGTGAACAGAGTGGTG 57.053 39.130 0.00 0.00 0.00 4.17
2295 4987 4.776349 TGTAAATGTGAACAGAGTGGTGT 58.224 39.130 0.00 0.00 0.00 4.16
2296 4988 5.919755 TGTAAATGTGAACAGAGTGGTGTA 58.080 37.500 0.00 0.00 0.00 2.90
2297 4989 5.989168 TGTAAATGTGAACAGAGTGGTGTAG 59.011 40.000 0.00 0.00 0.00 2.74
2298 4990 4.955811 AATGTGAACAGAGTGGTGTAGA 57.044 40.909 0.00 0.00 0.00 2.59
2299 4991 3.728076 TGTGAACAGAGTGGTGTAGAC 57.272 47.619 0.00 0.00 0.00 2.59
2300 4992 2.364324 TGTGAACAGAGTGGTGTAGACC 59.636 50.000 1.06 1.06 43.48 3.85
2301 4993 2.628657 GTGAACAGAGTGGTGTAGACCT 59.371 50.000 10.86 0.00 43.58 3.85
2302 4994 3.069729 GTGAACAGAGTGGTGTAGACCTT 59.930 47.826 10.86 0.00 43.58 3.50
2303 4995 3.709653 TGAACAGAGTGGTGTAGACCTTT 59.290 43.478 10.86 0.00 43.58 3.11
2304 4996 4.897076 TGAACAGAGTGGTGTAGACCTTTA 59.103 41.667 10.86 0.00 43.58 1.85
2337 5029 2.992543 TGACAAAGCCAATATTTTGCGC 59.007 40.909 0.00 0.00 37.71 6.09
2424 5116 2.327568 GTAATGTGCGTGCATTGCTTT 58.672 42.857 10.49 8.33 39.20 3.51
2568 5262 6.584942 CCATGATATGCTTCAATTTTGATCCG 59.415 38.462 0.00 0.00 37.00 4.18
2569 5263 6.698008 TGATATGCTTCAATTTTGATCCGT 57.302 33.333 0.00 0.00 37.00 4.69
2645 5339 6.484364 ACTGGGCAGATTAAAATATTTGGG 57.516 37.500 0.39 0.00 0.00 4.12
2731 5425 9.016438 GGAAAGGTTGACTAAATACCACAATAA 57.984 33.333 0.00 0.00 34.32 1.40
2768 5462 8.577048 AAATATATGCTGCAGCTTTATGAGAT 57.423 30.769 36.61 22.05 42.66 2.75
2854 5548 8.717821 TGTTCTTTCTCAATACTTGAAATACCG 58.282 33.333 0.00 0.00 39.58 4.02
2876 5570 6.136071 CCGTTAGCATTGTATAGCACATTTC 58.864 40.000 0.00 0.00 36.90 2.17
2931 5626 7.149973 CACATCTTCCATTTCAATCTGTTTGT 58.850 34.615 0.00 0.00 36.65 2.83
2978 5673 8.950480 TGGTGGAACATTATATAGGTCCAATAA 58.050 33.333 9.70 0.00 44.52 1.40
2983 5678 9.787435 GAACATTATATAGGTCCAATAACCACA 57.213 33.333 0.00 0.00 42.12 4.17
3012 5707 2.414161 GCGTCACTGGCATAGTTTTTCC 60.414 50.000 0.00 0.00 37.60 3.13
3276 5996 8.947115 GTAGAAGCATATAAACAAAAGGACACT 58.053 33.333 0.00 0.00 0.00 3.55
3324 6044 0.534412 AGGAGACTGGTGAAGATGCG 59.466 55.000 0.00 0.00 41.13 4.73
3579 6302 4.917906 ATCCTGCAAAGTCTAGAGGTTT 57.082 40.909 0.00 0.00 0.00 3.27
3594 6317 1.362355 GTTTGGGGCCAAGTCAACG 59.638 57.895 4.39 0.00 37.24 4.10
3618 6341 2.034104 CCCCCGAGCTTTAAAGTACC 57.966 55.000 16.38 5.53 0.00 3.34
3619 6342 1.407851 CCCCCGAGCTTTAAAGTACCC 60.408 57.143 16.38 0.06 0.00 3.69
3620 6343 1.279846 CCCCGAGCTTTAAAGTACCCA 59.720 52.381 16.38 0.00 0.00 4.51
3621 6344 2.290450 CCCCGAGCTTTAAAGTACCCAA 60.290 50.000 16.38 0.00 0.00 4.12
3622 6345 3.617284 CCCGAGCTTTAAAGTACCCAAT 58.383 45.455 16.38 0.00 0.00 3.16
3623 6346 4.384427 CCCCGAGCTTTAAAGTACCCAATA 60.384 45.833 16.38 0.00 0.00 1.90
3624 6347 5.374071 CCCGAGCTTTAAAGTACCCAATAT 58.626 41.667 16.38 0.00 0.00 1.28
3625 6348 5.826208 CCCGAGCTTTAAAGTACCCAATATT 59.174 40.000 16.38 0.00 0.00 1.28
3626 6349 6.238648 CCCGAGCTTTAAAGTACCCAATATTG 60.239 42.308 16.38 8.58 0.00 1.90
3627 6350 6.317893 CCGAGCTTTAAAGTACCCAATATTGT 59.682 38.462 16.38 0.00 0.00 2.71
3628 6351 7.148137 CCGAGCTTTAAAGTACCCAATATTGTT 60.148 37.037 16.38 3.69 0.00 2.83
3629 6352 7.908601 CGAGCTTTAAAGTACCCAATATTGTTC 59.091 37.037 16.38 2.30 0.00 3.18
3630 6353 8.644374 AGCTTTAAAGTACCCAATATTGTTCA 57.356 30.769 16.38 0.00 0.00 3.18
3631 6354 9.084533 AGCTTTAAAGTACCCAATATTGTTCAA 57.915 29.630 16.38 0.00 0.00 2.69
3632 6355 9.135843 GCTTTAAAGTACCCAATATTGTTCAAC 57.864 33.333 16.38 6.95 0.00 3.18
3635 6358 9.968870 TTAAAGTACCCAATATTGTTCAACAAC 57.031 29.630 4.73 0.00 41.40 3.32
3636 6359 7.589958 AAGTACCCAATATTGTTCAACAACA 57.410 32.000 4.73 0.00 41.40 3.33
3637 6360 7.775053 AGTACCCAATATTGTTCAACAACAT 57.225 32.000 4.73 0.00 41.40 2.71
3638 6361 7.826690 AGTACCCAATATTGTTCAACAACATC 58.173 34.615 4.73 0.00 41.40 3.06
3639 6362 6.036577 ACCCAATATTGTTCAACAACATCC 57.963 37.500 4.73 0.00 41.40 3.51
3640 6363 5.101628 CCCAATATTGTTCAACAACATCCG 58.898 41.667 4.73 0.00 41.40 4.18
3641 6364 4.562394 CCAATATTGTTCAACAACATCCGC 59.438 41.667 4.73 0.00 41.40 5.54
3642 6365 2.330231 ATTGTTCAACAACATCCGCG 57.670 45.000 4.73 0.00 41.40 6.46
3643 6366 0.309302 TTGTTCAACAACATCCGCGG 59.691 50.000 22.12 22.12 42.28 6.46
3644 6367 1.209127 GTTCAACAACATCCGCGGG 59.791 57.895 27.83 13.23 32.14 6.13
3645 6368 1.969064 TTCAACAACATCCGCGGGG 60.969 57.895 27.83 20.49 0.00 5.73
3646 6369 2.671619 CAACAACATCCGCGGGGT 60.672 61.111 27.83 21.21 33.83 4.95
3647 6370 2.114411 AACAACATCCGCGGGGTT 59.886 55.556 27.83 25.67 33.83 4.11
3648 6371 2.265182 AACAACATCCGCGGGGTTG 61.265 57.895 38.42 38.42 45.52 3.77
3649 6372 2.671619 CAACATCCGCGGGGTTGT 60.672 61.111 35.18 28.16 45.94 3.32
3650 6373 1.376166 CAACATCCGCGGGGTTGTA 60.376 57.895 35.18 17.48 43.79 2.41
4007 7041 6.994496 TCTTCAGTTTCATCATTCACTTCTGT 59.006 34.615 0.00 0.00 0.00 3.41
4893 7993 2.806856 CGGTGCATTCGAGCTCTGC 61.807 63.158 17.16 17.16 36.45 4.26
4894 7994 1.742880 GGTGCATTCGAGCTCTGCA 60.743 57.895 21.43 21.43 43.20 4.41
4895 7995 1.094073 GGTGCATTCGAGCTCTGCAT 61.094 55.000 26.12 8.30 46.52 3.96
4908 8008 5.301835 AGCTCTGCATAATGTGTAATCCT 57.698 39.130 0.00 0.00 0.00 3.24
4911 8011 6.877855 AGCTCTGCATAATGTGTAATCCTATG 59.122 38.462 0.00 0.00 0.00 2.23
4924 8024 3.933239 ATCCTATGAGGGAAGCTACCT 57.067 47.619 9.50 9.50 42.18 3.08
5138 8238 2.023404 TCATGAGCCTACCCCTGAAGTA 60.023 50.000 0.00 0.00 0.00 2.24
5198 8300 5.925397 CACATAAAGCATTTTACACTGCCAA 59.075 36.000 0.00 0.00 40.09 4.52
5209 8311 6.870971 TTTACACTGCCAACTAAGGTTTAG 57.129 37.500 0.00 0.00 32.73 1.85
5464 9870 7.173722 AGGAAGAAGACATCAATCAAGACATT 58.826 34.615 0.00 0.00 0.00 2.71
5594 10002 3.588842 TCCTGAAGTCAAAGATCCCATGT 59.411 43.478 0.00 0.00 0.00 3.21
5652 10060 4.142271 TGTCCATTCGAAGTGCTTGTTTTT 60.142 37.500 3.35 0.00 0.00 1.94
5808 10227 9.848710 AAGTTCAATGAAGATAGTGATGATGAT 57.151 29.630 0.00 0.00 0.00 2.45
5901 10320 6.338146 TGGAACATAGATACTGTACAGTTGC 58.662 40.000 32.15 22.95 42.54 4.17
5988 10407 1.811778 ATATGCTTCTGGGGAGCTGA 58.188 50.000 0.00 0.00 0.00 4.26
6284 10727 6.947733 TCTTGTTGGTCATATTGGATGTCTTT 59.052 34.615 0.00 0.00 0.00 2.52
6461 10910 8.683615 TCTTTCCAGGAAAAGTTAAAGAAAGAC 58.316 33.333 15.79 0.00 41.61 3.01
6730 11182 5.631119 AGTTGCTACAAACATACTCCCTTT 58.369 37.500 0.13 0.00 32.21 3.11
6913 11480 0.322008 CAGTTCTGGACCAAGGGAGC 60.322 60.000 0.00 0.00 0.00 4.70
6962 11529 6.368791 GGCACAGTAGCGAAATCATGAATATA 59.631 38.462 0.00 0.00 34.64 0.86
7273 11840 7.041372 GCACACACTTATAAATACCTGGGTATG 60.041 40.741 12.40 2.87 40.73 2.39
7340 11907 4.637091 GTGTAAAACCATTATGTACGGCCT 59.363 41.667 0.00 0.00 0.00 5.19
7415 11982 1.726853 GCTACTTGCCTGTACTGGTG 58.273 55.000 18.89 12.17 35.15 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 7.707464 TGTGTATGTAACGATATTAACTGGGTG 59.293 37.037 0.00 0.00 0.00 4.61
59 60 8.489489 ACTGCCCATCTACAATATTAGATATGG 58.511 37.037 10.16 10.16 36.79 2.74
81 82 5.006153 ACCAACTTTGTAAGGAAAACTGC 57.994 39.130 0.00 0.00 0.00 4.40
188 192 5.163923 GGTCTCGGTAAATAACAAACTTCGG 60.164 44.000 0.00 0.00 0.00 4.30
257 261 0.037326 AAGCTGCCGAACATTCTCGA 60.037 50.000 0.00 0.00 41.44 4.04
259 263 1.537202 ACAAAGCTGCCGAACATTCTC 59.463 47.619 0.00 0.00 0.00 2.87
266 270 3.353836 GGCGACAAAGCTGCCGAA 61.354 61.111 0.00 0.00 39.30 4.30
279 283 0.389817 CAGAAACTCACCGATGGCGA 60.390 55.000 0.00 0.00 40.82 5.54
324 329 3.006003 GTCCCAGAGAAAAGAAGACGACT 59.994 47.826 0.00 0.00 0.00 4.18
340 345 1.078759 GAAGCACATCGTCGTCCCAG 61.079 60.000 0.00 0.00 0.00 4.45
373 380 2.614520 CGATCGAAGCTAGAAGACTCCA 59.385 50.000 10.26 0.00 0.00 3.86
374 381 2.873472 TCGATCGAAGCTAGAAGACTCC 59.127 50.000 16.99 0.00 0.00 3.85
402 409 2.702751 ATTGTTGACGTGGCGGTCGA 62.703 55.000 0.00 0.00 39.83 4.20
411 418 2.020720 TCAGGCAAACATTGTTGACGT 58.979 42.857 2.13 0.00 41.74 4.34
426 433 0.321653 AAACACCATCGGAGTCAGGC 60.322 55.000 0.00 0.00 0.00 4.85
478 485 1.522355 CTCATCGATGGCAAGCCGT 60.522 57.895 24.61 5.30 39.42 5.68
483 490 0.036105 ACTGCACTCATCGATGGCAA 60.036 50.000 24.61 5.34 33.58 4.52
484 491 0.823460 TACTGCACTCATCGATGGCA 59.177 50.000 24.61 22.79 0.00 4.92
488 495 2.363680 CCTTCCTACTGCACTCATCGAT 59.636 50.000 0.00 0.00 0.00 3.59
493 500 1.591703 CGCCTTCCTACTGCACTCA 59.408 57.895 0.00 0.00 0.00 3.41
501 508 2.109425 AATTGACACCGCCTTCCTAC 57.891 50.000 0.00 0.00 0.00 3.18
502 509 2.871096 AAATTGACACCGCCTTCCTA 57.129 45.000 0.00 0.00 0.00 2.94
547 554 8.836413 CCTTACAAAGTCATTCTTGTAGAAACA 58.164 33.333 0.00 0.00 37.82 2.83
628 636 0.024619 GCGCATTCGGTTAAGTCGAC 59.975 55.000 7.70 7.70 36.30 4.20
649 657 2.095567 CCCGCTCTGTCTTTGTCAATTG 60.096 50.000 0.00 0.00 0.00 2.32
650 658 2.154462 CCCGCTCTGTCTTTGTCAATT 58.846 47.619 0.00 0.00 0.00 2.32
651 659 1.347707 TCCCGCTCTGTCTTTGTCAAT 59.652 47.619 0.00 0.00 0.00 2.57
652 660 0.756294 TCCCGCTCTGTCTTTGTCAA 59.244 50.000 0.00 0.00 0.00 3.18
655 666 0.687354 ATGTCCCGCTCTGTCTTTGT 59.313 50.000 0.00 0.00 0.00 2.83
688 699 3.187432 CCGCTCTCTCTTTTGTTTCTTCC 59.813 47.826 0.00 0.00 0.00 3.46
692 703 2.480802 GTCCCGCTCTCTCTTTTGTTTC 59.519 50.000 0.00 0.00 0.00 2.78
696 707 2.393271 ATGTCCCGCTCTCTCTTTTG 57.607 50.000 0.00 0.00 0.00 2.44
746 774 2.735151 GGGTATCTTTGAAACCAGGGG 58.265 52.381 0.00 0.00 34.83 4.79
763 791 0.111832 GAAGAAAGGGGTTTCCGGGT 59.888 55.000 0.00 0.00 41.52 5.28
764 792 0.404426 AGAAGAAAGGGGTTTCCGGG 59.596 55.000 0.00 0.00 41.52 5.73
765 793 1.886542 CAAGAAGAAAGGGGTTTCCGG 59.113 52.381 0.00 0.00 41.52 5.14
766 794 1.269723 GCAAGAAGAAAGGGGTTTCCG 59.730 52.381 0.00 0.00 41.52 4.30
767 795 2.558795 GAGCAAGAAGAAAGGGGTTTCC 59.441 50.000 0.00 0.00 0.00 3.13
768 796 2.558795 GGAGCAAGAAGAAAGGGGTTTC 59.441 50.000 0.00 0.00 0.00 2.78
769 797 2.598565 GGAGCAAGAAGAAAGGGGTTT 58.401 47.619 0.00 0.00 0.00 3.27
798 3481 0.317519 GGCACCGAGGTTTTTCGTTG 60.318 55.000 0.00 0.00 38.88 4.10
869 3553 1.340600 CGGATTTAGGTGCTGGGGAAA 60.341 52.381 0.00 0.00 0.00 3.13
870 3554 0.254747 CGGATTTAGGTGCTGGGGAA 59.745 55.000 0.00 0.00 0.00 3.97
889 3574 3.241156 GGAGAGGGGGTTAGAGTTATCC 58.759 54.545 0.00 0.00 0.00 2.59
911 3596 2.261729 GAGGAGGGGAGTTCAAGAAGT 58.738 52.381 0.00 0.00 0.00 3.01
922 3607 0.618968 GAAGAAGCTGGAGGAGGGGA 60.619 60.000 0.00 0.00 0.00 4.81
982 3670 3.110178 GGTTCTTCGCCCGACGTG 61.110 66.667 0.00 0.00 44.19 4.49
983 3671 2.939261 ATGGTTCTTCGCCCGACGT 61.939 57.895 0.00 0.00 44.19 4.34
1020 3708 0.391263 CGGTACCTGGAAAGAGCCAC 60.391 60.000 10.90 0.00 33.52 5.01
1029 3717 0.899720 GGAACATGACGGTACCTGGA 59.100 55.000 10.90 0.00 0.00 3.86
1037 3725 3.426695 GCTTGAAATGAGGAACATGACGG 60.427 47.826 0.00 0.00 39.39 4.79
1092 3780 1.090052 GCGGGGAGGTCAAATTCTCG 61.090 60.000 0.00 0.00 0.00 4.04
1115 3803 4.814294 CTCGACGGAAAGCGGGGG 62.814 72.222 0.00 0.00 0.00 5.40
1214 3903 1.795170 TTTGAAGCGTCAAGGCAGGC 61.795 55.000 14.67 0.00 44.49 4.85
1229 3919 5.176590 GCGGCATTTACTTTCAACAATTTGA 59.823 36.000 2.79 0.00 40.14 2.69
1238 3928 0.167908 CAGCGCGGCATTTACTTTCA 59.832 50.000 8.83 0.00 0.00 2.69
1243 3933 2.152078 GCAACAGCGCGGCATTTAC 61.152 57.895 8.83 0.00 0.00 2.01
1245 3935 3.615536 GAGCAACAGCGCGGCATTT 62.616 57.895 8.83 0.00 36.85 2.32
1246 3936 4.107051 GAGCAACAGCGCGGCATT 62.107 61.111 8.83 0.00 36.85 3.56
1256 3946 0.536233 TTTTAGCCCAGCGAGCAACA 60.536 50.000 0.00 0.00 0.00 3.33
1264 3954 5.651530 GAAGAACCTAAATTTTAGCCCAGC 58.348 41.667 10.16 0.00 0.00 4.85
1268 3958 5.971792 GCATCGAAGAACCTAAATTTTAGCC 59.028 40.000 10.16 3.03 43.58 3.93
1324 4014 2.434359 GACCCTGCGTTTCTCCGG 60.434 66.667 0.00 0.00 0.00 5.14
1420 4110 4.789075 GAGTACGGCGGCGCTTCA 62.789 66.667 32.57 13.72 0.00 3.02
1669 4359 2.184322 CCGTCATCTCCACCGGTG 59.816 66.667 28.26 28.26 35.78 4.94
1673 4363 2.105128 CTCGCCGTCATCTCCACC 59.895 66.667 0.00 0.00 0.00 4.61
1751 4441 6.241385 GCGCCTCGTAAATAACATATTCATC 58.759 40.000 0.00 0.00 0.00 2.92
1762 4452 0.179067 CCTTGGGCGCCTCGTAAATA 60.179 55.000 28.56 1.92 0.00 1.40
2032 4722 1.039856 AACTGGCCATGTTGACAACC 58.960 50.000 15.59 0.39 0.00 3.77
2072 4763 3.863424 GCGGTAGAAAATGTGAATCTCGA 59.137 43.478 0.00 0.00 0.00 4.04
2073 4764 3.616821 TGCGGTAGAAAATGTGAATCTCG 59.383 43.478 0.00 0.00 0.00 4.04
2249 4941 4.148128 ACACTCTAGAAGATGCATTGGG 57.852 45.455 0.00 0.00 0.00 4.12
2299 4991 6.348540 GCTTTGTCATTGTCTACACCTAAAGG 60.349 42.308 0.00 0.00 42.17 3.11
2300 4992 6.348540 GGCTTTGTCATTGTCTACACCTAAAG 60.349 42.308 0.00 0.00 0.00 1.85
2301 4993 5.472137 GGCTTTGTCATTGTCTACACCTAAA 59.528 40.000 0.00 0.00 0.00 1.85
2302 4994 5.001232 GGCTTTGTCATTGTCTACACCTAA 58.999 41.667 0.00 0.00 0.00 2.69
2303 4995 4.041075 TGGCTTTGTCATTGTCTACACCTA 59.959 41.667 0.00 0.00 0.00 3.08
2304 4996 3.181445 TGGCTTTGTCATTGTCTACACCT 60.181 43.478 0.00 0.00 0.00 4.00
2337 5029 8.746052 TTGATATTTTAACACTCCTACCCATG 57.254 34.615 0.00 0.00 0.00 3.66
2424 5116 0.896479 ATGCTTGCATGCCACAGTGA 60.896 50.000 20.65 1.75 0.00 3.41
2507 5199 7.870445 TGTCATAAAAACTAATTTGAACCAGGC 59.130 33.333 0.00 0.00 0.00 4.85
2618 5312 8.040132 CCAAATATTTTAATCTGCCCAGTTTCA 58.960 33.333 0.00 0.00 0.00 2.69
2645 5339 4.508662 CTTCTGTTCTTGTAGGGTGATCC 58.491 47.826 0.00 0.00 0.00 3.36
2732 5426 9.362539 GCTGCAGCATATATTTATAAGCAAAAT 57.637 29.630 33.36 0.00 41.59 1.82
2745 5439 6.766944 GGATCTCATAAAGCTGCAGCATATAT 59.233 38.462 38.24 27.40 45.16 0.86
2764 5458 4.669318 CACATGTGCAATGAAAGGATCTC 58.331 43.478 13.94 0.00 0.00 2.75
2765 5459 4.713824 CACATGTGCAATGAAAGGATCT 57.286 40.909 13.94 0.00 0.00 2.75
2854 5548 6.438763 GGGAAATGTGCTATACAATGCTAAC 58.561 40.000 0.00 0.00 43.77 2.34
2876 5570 2.051334 TGTTTCAGAATATGGCGGGG 57.949 50.000 0.00 0.00 0.00 5.73
2931 5626 5.182190 ACCACATATTTGTTACGATGCAACA 59.818 36.000 0.00 0.00 32.34 3.33
2978 5673 1.071699 AGTGACGCATAAACCTGTGGT 59.928 47.619 0.00 0.00 37.65 4.16
2983 5678 0.036164 TGCCAGTGACGCATAAACCT 59.964 50.000 0.00 0.00 0.00 3.50
3005 5700 3.517602 AGCTTTGGTCAAACGGAAAAAC 58.482 40.909 0.00 0.00 0.00 2.43
3012 5707 3.064820 ACAGTACAAGCTTTGGTCAAACG 59.935 43.478 0.00 0.00 34.12 3.60
3098 5817 2.794103 AGCATACACTGACAATGCCAA 58.206 42.857 6.27 0.00 45.66 4.52
3469 6192 9.577110 GTCAGCAAGATGAATCAATCAAAATTA 57.423 29.630 0.00 0.00 42.54 1.40
3579 6302 3.723097 TTGCGTTGACTTGGCCCCA 62.723 57.895 0.00 0.00 0.00 4.96
3609 6332 9.968870 GTTGTTGAACAATATTGGGTACTTTAA 57.031 29.630 19.37 4.92 40.59 1.52
3610 6333 9.132923 TGTTGTTGAACAATATTGGGTACTTTA 57.867 29.630 19.37 0.00 40.59 1.85
3611 6334 8.012957 TGTTGTTGAACAATATTGGGTACTTT 57.987 30.769 19.37 3.59 40.59 2.66
3612 6335 7.589958 TGTTGTTGAACAATATTGGGTACTT 57.410 32.000 19.37 4.30 40.59 2.24
3613 6336 7.093945 GGATGTTGTTGAACAATATTGGGTACT 60.094 37.037 18.98 0.00 45.23 2.73
3614 6337 7.033185 GGATGTTGTTGAACAATATTGGGTAC 58.967 38.462 18.98 11.52 45.23 3.34
3615 6338 6.127869 CGGATGTTGTTGAACAATATTGGGTA 60.128 38.462 18.98 2.41 45.23 3.69
3616 6339 5.336372 CGGATGTTGTTGAACAATATTGGGT 60.336 40.000 18.98 6.99 45.23 4.51
3617 6340 5.101628 CGGATGTTGTTGAACAATATTGGG 58.898 41.667 18.98 9.49 45.23 4.12
3618 6341 4.562394 GCGGATGTTGTTGAACAATATTGG 59.438 41.667 18.98 14.86 45.23 3.16
3619 6342 4.262743 CGCGGATGTTGTTGAACAATATTG 59.737 41.667 18.98 14.01 45.23 1.90
3620 6343 4.411327 CGCGGATGTTGTTGAACAATATT 58.589 39.130 18.98 6.01 45.23 1.28
3621 6344 3.181501 CCGCGGATGTTGTTGAACAATAT 60.182 43.478 24.07 18.21 45.23 1.28
3622 6345 2.160615 CCGCGGATGTTGTTGAACAATA 59.839 45.455 24.07 12.05 45.23 1.90
3623 6346 1.068610 CCGCGGATGTTGTTGAACAAT 60.069 47.619 24.07 0.00 45.23 2.71
3624 6347 0.309302 CCGCGGATGTTGTTGAACAA 59.691 50.000 24.07 6.66 45.23 2.83
3625 6348 1.511318 CCCGCGGATGTTGTTGAACA 61.511 55.000 30.73 0.00 46.13 3.18
3626 6349 1.209127 CCCGCGGATGTTGTTGAAC 59.791 57.895 30.73 0.00 0.00 3.18
3627 6350 1.969064 CCCCGCGGATGTTGTTGAA 60.969 57.895 30.73 0.00 0.00 2.69
3628 6351 2.359354 CCCCGCGGATGTTGTTGA 60.359 61.111 30.73 0.00 0.00 3.18
3629 6352 2.265182 AACCCCGCGGATGTTGTTG 61.265 57.895 30.73 6.78 0.00 3.33
3630 6353 2.114411 AACCCCGCGGATGTTGTT 59.886 55.556 30.73 17.80 0.00 2.83
3631 6354 2.671619 CAACCCCGCGGATGTTGT 60.672 61.111 33.87 19.77 35.72 3.32
3632 6355 0.746563 ATACAACCCCGCGGATGTTG 60.747 55.000 37.19 37.19 42.18 3.33
3633 6356 0.034863 AATACAACCCCGCGGATGTT 60.035 50.000 30.73 25.59 42.18 2.71
3634 6357 0.034863 AAATACAACCCCGCGGATGT 60.035 50.000 30.73 27.99 46.23 3.06
3635 6358 1.956297 TAAATACAACCCCGCGGATG 58.044 50.000 30.73 23.86 37.92 3.51
3636 6359 2.684374 GTTTAAATACAACCCCGCGGAT 59.316 45.455 30.73 12.17 0.00 4.18
3637 6360 2.083002 GTTTAAATACAACCCCGCGGA 58.917 47.619 30.73 5.29 0.00 5.54
3638 6361 1.811359 TGTTTAAATACAACCCCGCGG 59.189 47.619 21.04 21.04 0.00 6.46
3639 6362 2.485038 ACTGTTTAAATACAACCCCGCG 59.515 45.455 0.00 0.00 0.00 6.46
3640 6363 5.823209 ATACTGTTTAAATACAACCCCGC 57.177 39.130 0.00 0.00 0.00 6.13
3641 6364 8.949177 AGTAAATACTGTTTAAATACAACCCCG 58.051 33.333 0.00 0.00 34.72 5.73
4556 7636 2.294078 GCAGCTACTCACCCAGGGT 61.294 63.158 4.76 4.76 35.62 4.34
4893 7993 7.335422 GCTTCCCTCATAGGATTACACATTATG 59.665 40.741 0.00 0.00 37.67 1.90
4894 7994 7.238514 AGCTTCCCTCATAGGATTACACATTAT 59.761 37.037 0.00 0.00 37.67 1.28
4895 7995 6.558775 AGCTTCCCTCATAGGATTACACATTA 59.441 38.462 0.00 0.00 37.67 1.90
4908 8008 5.278061 AGTAACAAGGTAGCTTCCCTCATA 58.722 41.667 3.68 0.00 0.00 2.15
4911 8011 3.770388 AGAGTAACAAGGTAGCTTCCCTC 59.230 47.826 3.68 7.57 0.00 4.30
5015 8115 6.157904 CCAAACTGCATATTTGAATGTCACA 58.842 36.000 19.91 0.00 39.01 3.58
5302 8404 6.855914 CACACGATTAACATTTTTAGTGCTGT 59.144 34.615 0.00 0.00 32.22 4.40
5464 9870 3.554752 GGTGCAGTTTAAGGTGTACCGTA 60.555 47.826 9.59 0.00 39.28 4.02
5594 10002 5.452496 GCTCTCCAATATCAACAGCAGTAGA 60.452 44.000 0.00 0.00 0.00 2.59
5652 10060 4.800249 GCACTGAGGCATTTTGATGGAAAA 60.800 41.667 0.00 0.00 37.93 2.29
5671 10079 4.460263 TGTTTTCCTGTAAGACATGCACT 58.540 39.130 0.00 0.00 34.07 4.40
5808 10227 1.490490 ACAGCTTTGTCAACCTCCTCA 59.510 47.619 0.00 0.00 0.00 3.86
5901 10320 4.889409 AGCACCCATCCAATATTACAACTG 59.111 41.667 0.00 0.00 0.00 3.16
5977 10396 1.004044 ACTCAACATTCAGCTCCCCAG 59.996 52.381 0.00 0.00 0.00 4.45
6011 10430 1.453197 CCACTTATTCGGTGCCCCC 60.453 63.158 0.00 0.00 33.78 5.40
6130 10549 2.808543 CTCACTTTCCCTTCAACTTCCG 59.191 50.000 0.00 0.00 0.00 4.30
6461 10910 3.589988 AGCGTCTTTAAGTGACATCTGG 58.410 45.455 10.07 0.00 34.37 3.86
6730 11182 3.635836 TCACATGTCTTGCATTTCCAACA 59.364 39.130 0.00 0.00 35.19 3.33
6913 11480 8.671921 GCCATTCAATATTACTGATGGACTATG 58.328 37.037 16.57 1.62 0.00 2.23
7273 11840 3.522343 ACAACCCTGGGTATAGAACTTCC 59.478 47.826 20.91 0.00 33.12 3.46
7340 11907 2.063266 CAGTTACAAGCGAGCGGTTAA 58.937 47.619 7.02 0.00 34.20 2.01
7415 11982 3.564235 GGGTTTGGTAATCCGTTGAAC 57.436 47.619 0.00 0.00 36.30 3.18
7509 12077 7.667984 AAAACAACGTAAATTTTCTACACGG 57.332 32.000 13.34 1.73 36.95 4.94


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

AutoCloner maintained by Alex Coulton.