Multiple sequence alignment - TraesCS6D01G212300

Loading Multiple Alignment...

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 TraesCS6D01G212300 chr6D 100.000 4162 0 0 1 4162 300327000 300331161 0.000000e+00 7686
1 TraesCS6D01G212300 chr6D 79.105 1699 339 13 297 1987 300889109 300890799 0.000000e+00 1157
2 TraesCS6D01G212300 chr6B 93.590 3042 88 37 1 2946 465148135 465151165 0.000000e+00 4438
3 TraesCS6D01G212300 chr6B 95.530 783 19 8 2966 3734 465151152 465151932 0.000000e+00 1238
4 TraesCS6D01G212300 chr6A 92.235 3052 102 57 1 2950 417446207 417443189 0.000000e+00 4198
5 TraesCS6D01G212300 chr6A 97.032 775 15 3 2966 3733 417443205 417442432 0.000000e+00 1297
6 TraesCS6D01G212300 chr6A 79.258 1697 340 9 297 1987 416658613 416656923 0.000000e+00 1173
7 TraesCS6D01G212300 chr6A 86.111 252 23 11 3917 4162 417442326 417442081 1.150000e-65 261
8 TraesCS6D01G212300 chr2A 77.580 1744 369 21 297 2029 624460535 624458803 0.000000e+00 1035
9 TraesCS6D01G212300 chr2A 76.454 1754 371 34 297 2029 624396586 624394854 0.000000e+00 913
10 TraesCS6D01G212300 chr2A 76.645 1687 366 26 297 1969 166630212 166628540 0.000000e+00 907
11 TraesCS6D01G212300 chr2D 77.104 1747 380 20 293 2029 481963740 481962004 0.000000e+00 992
12 TraesCS6D01G212300 chr2D 76.989 1747 382 19 293 2029 481990649 481988913 0.000000e+00 981
13 TraesCS6D01G212300 chr2D 76.609 1740 373 32 293 2015 481658344 481656622 0.000000e+00 928
14 TraesCS6D01G212300 chr2D 76.491 1727 384 21 300 2015 481690892 481689177 0.000000e+00 920
15 TraesCS6D01G212300 chr2D 76.501 1732 379 26 297 2014 156709584 156707867 0.000000e+00 918
16 TraesCS6D01G212300 chr2D 76.509 1690 371 25 293 1969 156594577 156592901 0.000000e+00 898
17 TraesCS6D01G212300 chr2D 77.762 1403 296 14 635 2029 481601515 481600121 0.000000e+00 848
18 TraesCS6D01G212300 chr1D 77.381 1680 368 12 293 1966 19024740 19023067 0.000000e+00 987
19 TraesCS6D01G212300 chr3D 80.547 1244 231 10 797 2036 5793896 5792660 0.000000e+00 946
20 TraesCS6D01G212300 chr3D 85.366 369 52 2 3088 3455 5790985 5790618 8.440000e-102 381
21 TraesCS6D01G212300 chr3D 86.080 352 47 2 3087 3437 5736828 5737178 1.090000e-100 377
22 TraesCS6D01G212300 chr1B 76.887 1683 371 15 293 1966 28373549 28375222 0.000000e+00 937
23 TraesCS6D01G212300 chrUn 80.567 1199 226 5 840 2036 28820273 28821466 0.000000e+00 917
24 TraesCS6D01G212300 chrUn 81.646 316 58 0 3088 3403 28814339 28814024 3.190000e-66 263
25 TraesCS6D01G212300 chr2B 77.746 1402 298 13 635 2029 564922721 564921327 0.000000e+00 848
26 TraesCS6D01G212300 chr1A 75.860 1686 383 24 293 1966 20925117 20926790 0.000000e+00 837
27 TraesCS6D01G212300 chr3B 86.216 370 49 2 3087 3455 27826702 27826334 2.330000e-107 399
28 TraesCS6D01G212300 chr3B 85.908 369 52 0 3087 3455 12090313 12090681 1.080000e-105 394
29 TraesCS6D01G212300 chr3A 84.824 369 54 2 3088 3455 12161208 12160841 1.830000e-98 370
30 TraesCS6D01G212300 chr3A 84.553 369 57 0 3087 3455 15462757 15462389 2.360000e-97 366


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 TraesCS6D01G212300 chr6D 300327000 300331161 4161 False 7686.000000 7686 100.000000 1 4162 1 chr6D.!!$F1 4161
1 TraesCS6D01G212300 chr6D 300889109 300890799 1690 False 1157.000000 1157 79.105000 297 1987 1 chr6D.!!$F2 1690
2 TraesCS6D01G212300 chr6B 465148135 465151932 3797 False 2838.000000 4438 94.560000 1 3734 2 chr6B.!!$F1 3733
3 TraesCS6D01G212300 chr6A 417442081 417446207 4126 True 1918.666667 4198 91.792667 1 4162 3 chr6A.!!$R2 4161
4 TraesCS6D01G212300 chr6A 416656923 416658613 1690 True 1173.000000 1173 79.258000 297 1987 1 chr6A.!!$R1 1690
5 TraesCS6D01G212300 chr2A 624458803 624460535 1732 True 1035.000000 1035 77.580000 297 2029 1 chr2A.!!$R3 1732
6 TraesCS6D01G212300 chr2A 624394854 624396586 1732 True 913.000000 913 76.454000 297 2029 1 chr2A.!!$R2 1732
7 TraesCS6D01G212300 chr2A 166628540 166630212 1672 True 907.000000 907 76.645000 297 1969 1 chr2A.!!$R1 1672
8 TraesCS6D01G212300 chr2D 481962004 481963740 1736 True 992.000000 992 77.104000 293 2029 1 chr2D.!!$R6 1736
9 TraesCS6D01G212300 chr2D 481988913 481990649 1736 True 981.000000 981 76.989000 293 2029 1 chr2D.!!$R7 1736
10 TraesCS6D01G212300 chr2D 481656622 481658344 1722 True 928.000000 928 76.609000 293 2015 1 chr2D.!!$R4 1722
11 TraesCS6D01G212300 chr2D 481689177 481690892 1715 True 920.000000 920 76.491000 300 2015 1 chr2D.!!$R5 1715
12 TraesCS6D01G212300 chr2D 156707867 156709584 1717 True 918.000000 918 76.501000 297 2014 1 chr2D.!!$R2 1717
13 TraesCS6D01G212300 chr2D 156592901 156594577 1676 True 898.000000 898 76.509000 293 1969 1 chr2D.!!$R1 1676
14 TraesCS6D01G212300 chr2D 481600121 481601515 1394 True 848.000000 848 77.762000 635 2029 1 chr2D.!!$R3 1394
15 TraesCS6D01G212300 chr1D 19023067 19024740 1673 True 987.000000 987 77.381000 293 1966 1 chr1D.!!$R1 1673
16 TraesCS6D01G212300 chr3D 5790618 5793896 3278 True 663.500000 946 82.956500 797 3455 2 chr3D.!!$R1 2658
17 TraesCS6D01G212300 chr1B 28373549 28375222 1673 False 937.000000 937 76.887000 293 1966 1 chr1B.!!$F1 1673
18 TraesCS6D01G212300 chrUn 28820273 28821466 1193 False 917.000000 917 80.567000 840 2036 1 chrUn.!!$F1 1196
19 TraesCS6D01G212300 chr2B 564921327 564922721 1394 True 848.000000 848 77.746000 635 2029 1 chr2B.!!$R1 1394
20 TraesCS6D01G212300 chr1A 20925117 20926790 1673 False 837.000000 837 75.860000 293 1966 1 chr1A.!!$F1 1673

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
988 1015 1.227943 GTCCTGGTTGTGCTGCTCA 60.228 57.895 0.0 0.0 0.00 4.26 F
2222 2462 0.035725 TGATGACTTGGCTCCTGCTG 60.036 55.000 0.0 0.0 39.59 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2371 3199 0.041684 AGGAAAAGGCCCCCAGAATG 59.958 55.0 0.00 0.0 0.0 2.67 R
3892 5201 0.037512 TCTCTTCTCGTCGACCTCGT 60.038 55.0 10.58 0.0 40.8 4.18 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
77 81 3.210232 TCACCCCAAAATACAACGACA 57.790 42.857 0.00 0.00 0.00 4.35
78 82 3.552875 TCACCCCAAAATACAACGACAA 58.447 40.909 0.00 0.00 0.00 3.18
79 83 4.145807 TCACCCCAAAATACAACGACAAT 58.854 39.130 0.00 0.00 0.00 2.71
120 135 1.457346 GGCAGAGCAGCTACACAATT 58.543 50.000 0.00 0.00 34.17 2.32
129 144 5.762045 AGCAGCTACACAATTAACAACAAG 58.238 37.500 0.00 0.00 0.00 3.16
197 215 4.116238 GGCGATAGGAACTGAAGAAGAAG 58.884 47.826 0.00 0.00 41.52 2.85
198 216 4.142138 GGCGATAGGAACTGAAGAAGAAGA 60.142 45.833 0.00 0.00 41.52 2.87
199 217 5.411781 GCGATAGGAACTGAAGAAGAAGAA 58.588 41.667 0.00 0.00 41.52 2.52
268 295 1.755008 CCTCCTCTCCTCCACGGTC 60.755 68.421 0.00 0.00 0.00 4.79
271 298 3.062466 CTCTCCTCCACGGTCGCA 61.062 66.667 0.00 0.00 0.00 5.10
460 487 2.202570 CGGACGAAGCGGTACAGG 60.203 66.667 0.00 0.00 0.00 4.00
988 1015 1.227943 GTCCTGGTTGTGCTGCTCA 60.228 57.895 0.00 0.00 0.00 4.26
1522 1549 0.819259 GGTGGTGCTTGAGCTTGTGA 60.819 55.000 4.44 0.00 42.66 3.58
1750 1777 2.668550 GCGGCGTCCACCTTCTTT 60.669 61.111 9.37 0.00 0.00 2.52
2055 2082 0.599558 TACGGAAGACAAGGACGTGG 59.400 55.000 0.00 0.00 38.34 4.94
2118 2343 4.508662 AGTACGTAGCGGTAGAGTTAGTT 58.491 43.478 0.00 0.00 0.00 2.24
2127 2352 3.707793 GGTAGAGTTAGTTGCTGGATCG 58.292 50.000 0.00 0.00 0.00 3.69
2131 2356 1.276421 AGTTAGTTGCTGGATCGTGCT 59.724 47.619 9.43 0.00 0.00 4.40
2132 2357 2.496070 AGTTAGTTGCTGGATCGTGCTA 59.504 45.455 9.43 0.41 0.00 3.49
2133 2358 3.056107 AGTTAGTTGCTGGATCGTGCTAA 60.056 43.478 9.43 0.00 0.00 3.09
2134 2359 2.472695 AGTTGCTGGATCGTGCTAAA 57.527 45.000 9.43 0.00 0.00 1.85
2152 2384 7.561454 GTGCTAAAGCTGAAAGTCAGAGCATA 61.561 42.308 17.28 0.08 45.75 3.14
2212 2447 8.815141 TTTTTGTGTTTGGATATGATGACTTG 57.185 30.769 0.00 0.00 0.00 3.16
2213 2448 6.513806 TTGTGTTTGGATATGATGACTTGG 57.486 37.500 0.00 0.00 0.00 3.61
2214 2449 4.398988 TGTGTTTGGATATGATGACTTGGC 59.601 41.667 0.00 0.00 0.00 4.52
2222 2462 0.035725 TGATGACTTGGCTCCTGCTG 60.036 55.000 0.00 0.00 39.59 4.41
2256 2496 5.089970 ACTAGATCTGCACTGCATACAAA 57.910 39.130 5.18 0.00 38.13 2.83
2323 3151 9.750125 ATTTCCTTTACAGAAAACTTCAATGTC 57.250 29.630 0.00 0.00 36.83 3.06
2329 3157 6.136541 ACAGAAAACTTCAATGTCCAGAAC 57.863 37.500 0.00 0.00 0.00 3.01
2331 3159 6.152661 ACAGAAAACTTCAATGTCCAGAACAA 59.847 34.615 0.00 0.00 42.37 2.83
2332 3160 7.035004 CAGAAAACTTCAATGTCCAGAACAAA 58.965 34.615 0.00 0.00 42.37 2.83
2341 3169 6.491062 TCAATGTCCAGAACAAATCTTGATGT 59.509 34.615 0.00 0.00 42.37 3.06
2342 3170 7.665145 TCAATGTCCAGAACAAATCTTGATGTA 59.335 33.333 0.00 0.00 42.37 2.29
2348 3176 8.946085 TCCAGAACAAATCTTGATGTATTACAC 58.054 33.333 0.00 0.00 35.73 2.90
2371 3199 4.694509 CCAGCCTATAAGCATGTTCATCTC 59.305 45.833 0.00 0.00 34.23 2.75
2373 3201 5.938710 CAGCCTATAAGCATGTTCATCTCAT 59.061 40.000 0.00 0.00 34.23 2.90
2375 3203 6.654161 AGCCTATAAGCATGTTCATCTCATTC 59.346 38.462 0.00 0.00 34.23 2.67
2376 3204 6.654161 GCCTATAAGCATGTTCATCTCATTCT 59.346 38.462 0.00 0.00 0.00 2.40
2377 3205 7.361031 GCCTATAAGCATGTTCATCTCATTCTG 60.361 40.741 0.00 0.00 0.00 3.02
2378 3206 6.879276 ATAAGCATGTTCATCTCATTCTGG 57.121 37.500 0.00 0.00 0.00 3.86
2379 3207 3.552875 AGCATGTTCATCTCATTCTGGG 58.447 45.455 0.00 0.00 0.00 4.45
2380 3208 2.621998 GCATGTTCATCTCATTCTGGGG 59.378 50.000 0.00 0.00 0.00 4.96
2381 3209 3.220110 CATGTTCATCTCATTCTGGGGG 58.780 50.000 0.00 0.00 0.00 5.40
2471 3412 1.066605 CGTGACTCGTTTATCGGGGAT 59.933 52.381 0.00 0.00 45.43 3.85
2584 3532 4.692625 CCACATCCGCTTAATTAGATCTGG 59.307 45.833 5.18 0.00 0.00 3.86
2627 3583 8.561738 TCTTTCTTTCTTTTTCACTACTGTGT 57.438 30.769 0.00 0.00 44.14 3.72
2628 3584 9.661563 TCTTTCTTTCTTTTTCACTACTGTGTA 57.338 29.630 0.00 0.00 44.14 2.90
2629 3585 9.704098 CTTTCTTTCTTTTTCACTACTGTGTAC 57.296 33.333 0.00 0.00 44.14 2.90
2630 3586 7.459394 TCTTTCTTTTTCACTACTGTGTACG 57.541 36.000 0.00 0.00 44.14 3.67
2641 3602 2.201436 CTGTGTACGGCTCTGCGTCT 62.201 60.000 0.00 0.00 0.00 4.18
2819 3824 4.804139 ACTACGTGAGCATGTATTTACTGC 59.196 41.667 0.00 0.00 32.87 4.40
2845 3850 6.262049 GGTATTTTGTTTCCATTTTTGCCAGT 59.738 34.615 0.00 0.00 0.00 4.00
2905 3910 1.045911 AGGAGGCTACAGCTAGGCAC 61.046 60.000 12.18 5.96 46.03 5.01
2953 3958 5.580661 TGCTTAAAACACGAAAAGTTACCC 58.419 37.500 0.00 0.00 0.00 3.69
2954 3959 4.977963 GCTTAAAACACGAAAAGTTACCCC 59.022 41.667 0.00 0.00 0.00 4.95
2955 3960 3.696281 AAAACACGAAAAGTTACCCCG 57.304 42.857 0.00 0.00 0.00 5.73
3078 4223 5.076873 CAGAAAACAAGAGAATTGGGGGTA 58.923 41.667 0.00 0.00 0.00 3.69
3455 4758 2.639327 GCTCCGTTGCCTGCCATTT 61.639 57.895 0.00 0.00 0.00 2.32
3511 4820 2.441901 AGGAGGAGCAGGAGAGCG 60.442 66.667 0.00 0.00 40.15 5.03
3660 4969 2.433994 GCCTCCTCCTCTCTGCAGG 61.434 68.421 15.13 4.77 34.40 4.85
3790 5099 4.454728 TTGCAGGGTCTCATTTTAATGC 57.545 40.909 0.00 0.00 36.36 3.56
3791 5100 3.700538 TGCAGGGTCTCATTTTAATGCT 58.299 40.909 0.00 0.00 36.36 3.79
3792 5101 4.088634 TGCAGGGTCTCATTTTAATGCTT 58.911 39.130 0.00 0.00 36.36 3.91
3793 5102 5.260424 TGCAGGGTCTCATTTTAATGCTTA 58.740 37.500 0.00 0.00 36.36 3.09
3794 5103 5.714333 TGCAGGGTCTCATTTTAATGCTTAA 59.286 36.000 0.00 0.00 36.36 1.85
3795 5104 6.380846 TGCAGGGTCTCATTTTAATGCTTAAT 59.619 34.615 0.00 0.00 36.36 1.40
3796 5105 6.920210 GCAGGGTCTCATTTTAATGCTTAATC 59.080 38.462 0.00 0.00 36.36 1.75
3797 5106 7.416664 GCAGGGTCTCATTTTAATGCTTAATCA 60.417 37.037 0.00 0.00 36.36 2.57
3798 5107 7.917505 CAGGGTCTCATTTTAATGCTTAATCAC 59.082 37.037 0.00 0.00 36.36 3.06
3799 5108 7.068716 AGGGTCTCATTTTAATGCTTAATCACC 59.931 37.037 0.00 0.00 36.36 4.02
3800 5109 7.203218 GGTCTCATTTTAATGCTTAATCACCC 58.797 38.462 0.00 0.00 36.36 4.61
3801 5110 7.203218 GTCTCATTTTAATGCTTAATCACCCC 58.797 38.462 0.00 0.00 36.36 4.95
3806 5115 7.875327 TTTTAATGCTTAATCACCCCTAGTC 57.125 36.000 0.00 0.00 0.00 2.59
3808 5117 2.124411 TGCTTAATCACCCCTAGTCCC 58.876 52.381 0.00 0.00 0.00 4.46
3826 5135 8.678199 CCTAGTCCCAATTTCTCATAAAAGTTC 58.322 37.037 0.00 0.00 0.00 3.01
3849 5158 8.879759 GTTCTTTCATTTACCTCGATGTAATGA 58.120 33.333 13.10 14.28 31.19 2.57
3859 5168 6.406370 ACCTCGATGTAATGACTGAAAATCA 58.594 36.000 0.00 0.00 0.00 2.57
3883 5192 4.685924 CCACTTATGGCAGCTAAAAATGG 58.314 43.478 0.00 0.00 39.82 3.16
3884 5193 4.160252 CCACTTATGGCAGCTAAAAATGGT 59.840 41.667 0.00 0.00 39.82 3.55
3885 5194 5.359576 CCACTTATGGCAGCTAAAAATGGTA 59.640 40.000 0.00 0.00 39.82 3.25
3886 5195 6.460123 CCACTTATGGCAGCTAAAAATGGTAG 60.460 42.308 0.00 0.00 39.82 3.18
3887 5196 6.318648 CACTTATGGCAGCTAAAAATGGTAGA 59.681 38.462 0.00 0.00 0.00 2.59
3888 5197 6.889722 ACTTATGGCAGCTAAAAATGGTAGAA 59.110 34.615 0.00 0.00 0.00 2.10
3889 5198 7.396055 ACTTATGGCAGCTAAAAATGGTAGAAA 59.604 33.333 0.00 0.00 0.00 2.52
3892 5201 6.242396 TGGCAGCTAAAAATGGTAGAAACTA 58.758 36.000 0.00 0.00 0.00 2.24
3893 5202 6.150474 TGGCAGCTAAAAATGGTAGAAACTAC 59.850 38.462 0.00 0.00 0.00 2.73
3894 5203 6.248631 GCAGCTAAAAATGGTAGAAACTACG 58.751 40.000 0.00 0.00 0.00 3.51
3895 5204 6.091713 GCAGCTAAAAATGGTAGAAACTACGA 59.908 38.462 0.00 0.00 0.00 3.43
3896 5205 7.674240 GCAGCTAAAAATGGTAGAAACTACGAG 60.674 40.741 0.00 0.00 0.00 4.18
3897 5206 6.817140 AGCTAAAAATGGTAGAAACTACGAGG 59.183 38.462 0.00 0.00 0.00 4.63
3898 5207 6.592994 GCTAAAAATGGTAGAAACTACGAGGT 59.407 38.462 0.00 0.00 0.00 3.85
3899 5208 7.201504 GCTAAAAATGGTAGAAACTACGAGGTC 60.202 40.741 0.00 0.00 0.00 3.85
3900 5209 4.367386 AATGGTAGAAACTACGAGGTCG 57.633 45.455 0.00 0.00 46.33 4.79
3901 5210 3.057969 TGGTAGAAACTACGAGGTCGA 57.942 47.619 6.35 0.00 43.02 4.20
3902 5211 2.744202 TGGTAGAAACTACGAGGTCGAC 59.256 50.000 7.13 7.13 43.02 4.20
3903 5212 2.222908 GGTAGAAACTACGAGGTCGACG 60.223 54.545 9.92 0.17 43.02 5.12
3904 5213 1.800805 AGAAACTACGAGGTCGACGA 58.199 50.000 9.92 0.00 43.02 4.20
3905 5214 1.731160 AGAAACTACGAGGTCGACGAG 59.269 52.381 9.92 5.75 43.02 4.18
3906 5215 1.728971 GAAACTACGAGGTCGACGAGA 59.271 52.381 9.92 0.00 43.02 4.04
3907 5216 1.800805 AACTACGAGGTCGACGAGAA 58.199 50.000 9.92 0.00 43.02 2.87
3908 5217 1.357907 ACTACGAGGTCGACGAGAAG 58.642 55.000 9.92 5.81 43.02 2.85
3909 5218 1.067283 ACTACGAGGTCGACGAGAAGA 60.067 52.381 9.92 0.00 43.02 2.87
3910 5219 1.589320 CTACGAGGTCGACGAGAAGAG 59.411 57.143 9.92 0.00 43.02 2.85
3911 5220 0.037512 ACGAGGTCGACGAGAAGAGA 60.038 55.000 9.92 0.00 43.02 3.10
3912 5221 1.077123 CGAGGTCGACGAGAAGAGAA 58.923 55.000 9.92 0.00 43.02 2.87
3913 5222 1.201943 CGAGGTCGACGAGAAGAGAAC 60.202 57.143 9.92 0.00 43.02 3.01
3914 5223 0.797542 AGGTCGACGAGAAGAGAACG 59.202 55.000 9.92 0.00 0.00 3.95
3915 5224 0.179194 GGTCGACGAGAAGAGAACGG 60.179 60.000 9.92 0.00 0.00 4.44
3919 5228 1.725292 CGACGAGAAGAGAACGGACAC 60.725 57.143 0.00 0.00 0.00 3.67
3923 5232 1.340248 GAGAAGAGAACGGACACCACA 59.660 52.381 0.00 0.00 0.00 4.17
3927 5236 1.068741 AGAGAACGGACACCACAGTTC 59.931 52.381 0.00 0.00 42.22 3.01
3938 5247 4.906618 ACACCACAGTTCCTAAATACAGG 58.093 43.478 0.00 0.00 37.00 4.00
3950 5259 9.901172 GTTCCTAAATACAGGGAAGATTAAGAA 57.099 33.333 0.00 0.00 39.43 2.52
3983 5292 3.181458 GGATCGGGGAACAGCTACAAATA 60.181 47.826 0.00 0.00 0.00 1.40
3984 5293 3.255969 TCGGGGAACAGCTACAAATAC 57.744 47.619 0.00 0.00 0.00 1.89
3986 5295 3.199071 TCGGGGAACAGCTACAAATACAT 59.801 43.478 0.00 0.00 0.00 2.29
3989 5298 5.408604 CGGGGAACAGCTACAAATACATATC 59.591 44.000 0.00 0.00 0.00 1.63
3990 5299 5.705905 GGGGAACAGCTACAAATACATATCC 59.294 44.000 0.00 0.00 0.00 2.59
3991 5300 5.705905 GGGAACAGCTACAAATACATATCCC 59.294 44.000 0.00 0.00 35.29 3.85
3992 5301 6.465894 GGGAACAGCTACAAATACATATCCCT 60.466 42.308 0.00 0.00 38.82 4.20
3995 5304 6.900194 ACAGCTACAAATACATATCCCTGTT 58.100 36.000 0.00 0.00 0.00 3.16
3996 5305 6.992715 ACAGCTACAAATACATATCCCTGTTC 59.007 38.462 0.00 0.00 0.00 3.18
4071 5384 4.610605 TCCATACACTCGTCCTGAAAAA 57.389 40.909 0.00 0.00 0.00 1.94
4116 5429 8.204836 TGTTTCTACTGAAGAGAAAGCTAAAGT 58.795 33.333 0.00 0.00 42.17 2.66
4124 5437 3.131400 AGAGAAAGCTAAAGTAGGGAGCG 59.869 47.826 0.00 0.00 41.23 5.03
4125 5438 3.097614 AGAAAGCTAAAGTAGGGAGCGA 58.902 45.455 0.00 0.00 41.23 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 37 8.432013 TGAATCATGCTAATACTATGTGGTTCT 58.568 33.333 0.00 0.00 0.00 3.01
34 38 8.499162 GTGAATCATGCTAATACTATGTGGTTC 58.501 37.037 0.00 0.00 0.00 3.62
36 40 6.936900 GGTGAATCATGCTAATACTATGTGGT 59.063 38.462 0.00 0.00 0.00 4.16
77 81 7.094762 GCCGCAGCTTTACCTAAAGATATTATT 60.095 37.037 8.69 0.00 44.07 1.40
78 82 6.371825 GCCGCAGCTTTACCTAAAGATATTAT 59.628 38.462 8.69 0.00 44.07 1.28
79 83 5.699458 GCCGCAGCTTTACCTAAAGATATTA 59.301 40.000 8.69 0.00 44.07 0.98
120 135 1.301423 GACGTGTGGCCTTGTTGTTA 58.699 50.000 3.32 0.00 0.00 2.41
129 144 1.666553 TGTTGATCGACGTGTGGCC 60.667 57.895 8.59 0.00 0.00 5.36
197 215 3.538392 GCTTAATTCGTTCGTGCATGTTC 59.462 43.478 5.68 0.00 0.00 3.18
198 216 3.488489 GCTTAATTCGTTCGTGCATGTT 58.512 40.909 5.68 0.00 0.00 2.71
199 217 2.473868 CGCTTAATTCGTTCGTGCATGT 60.474 45.455 5.68 0.00 0.00 3.21
268 295 2.792290 CTGAAGCATCGTCCGTGCG 61.792 63.158 8.02 0.00 46.86 5.34
271 298 1.154016 CGTCTGAAGCATCGTCCGT 60.154 57.895 0.00 0.00 0.00 4.69
460 487 2.579738 GAGAGCAGGTCGTTCCCC 59.420 66.667 0.00 0.00 36.75 4.81
988 1015 0.037303 CCAACCATGTCCAGAGTGCT 59.963 55.000 0.00 0.00 0.00 4.40
1063 1090 2.047655 TACGGCTTCAAGGGCACG 60.048 61.111 0.00 0.00 0.00 5.34
1522 1549 0.759436 AGTTCACCGACCACCTCACT 60.759 55.000 0.00 0.00 0.00 3.41
1750 1777 1.074775 GGCCACCACTGTTGATGGA 59.925 57.895 0.00 0.00 39.87 3.41
1795 1822 2.417516 CTGTCCTACATCGCCGGG 59.582 66.667 2.18 0.00 0.00 5.73
2055 2082 2.159627 CCTGCAACTAACGAACCATGTC 59.840 50.000 0.00 0.00 0.00 3.06
2118 2343 0.250234 AGCTTTAGCACGATCCAGCA 59.750 50.000 4.33 0.00 45.16 4.41
2127 2352 3.120373 GCTCTGACTTTCAGCTTTAGCAC 60.120 47.826 4.33 0.00 43.95 4.40
2131 2356 6.183360 GCATTATGCTCTGACTTTCAGCTTTA 60.183 38.462 10.27 0.00 40.96 1.85
2132 2357 5.392811 GCATTATGCTCTGACTTTCAGCTTT 60.393 40.000 10.27 0.00 40.96 3.51
2133 2358 4.096081 GCATTATGCTCTGACTTTCAGCTT 59.904 41.667 10.27 0.00 40.96 3.74
2134 2359 3.626670 GCATTATGCTCTGACTTTCAGCT 59.373 43.478 10.27 0.00 40.96 4.24
2152 2384 5.989777 ACTACTTCTACGTTGTTTGAGCATT 59.010 36.000 0.00 0.00 0.00 3.56
2208 2443 1.374190 CAGTCAGCAGGAGCCAAGT 59.626 57.895 0.00 0.00 43.56 3.16
2211 2446 4.025858 GCCAGTCAGCAGGAGCCA 62.026 66.667 0.00 0.00 43.56 4.75
2212 2447 4.025858 TGCCAGTCAGCAGGAGCC 62.026 66.667 0.00 0.00 43.56 4.70
2222 2462 2.622942 CAGATCTAGTCCTCTGCCAGTC 59.377 54.545 0.00 0.00 33.12 3.51
2304 3112 7.338196 TGTTCTGGACATTGAAGTTTTCTGTAA 59.662 33.333 0.00 0.00 32.00 2.41
2317 3141 6.684686 ACATCAAGATTTGTTCTGGACATTG 58.315 36.000 0.00 0.00 37.23 2.82
2318 3142 6.906157 ACATCAAGATTTGTTCTGGACATT 57.094 33.333 0.00 0.00 37.23 2.71
2323 3151 8.184192 GGTGTAATACATCAAGATTTGTTCTGG 58.816 37.037 0.00 0.00 33.93 3.86
2329 3157 6.319658 AGGCTGGTGTAATACATCAAGATTTG 59.680 38.462 7.83 0.00 38.98 2.32
2331 3159 6.006275 AGGCTGGTGTAATACATCAAGATT 57.994 37.500 7.83 0.00 38.98 2.40
2332 3160 5.636903 AGGCTGGTGTAATACATCAAGAT 57.363 39.130 7.83 0.00 38.98 2.40
2341 3169 6.433847 ACATGCTTATAGGCTGGTGTAATA 57.566 37.500 8.44 0.00 0.00 0.98
2342 3170 5.310409 ACATGCTTATAGGCTGGTGTAAT 57.690 39.130 8.44 0.00 0.00 1.89
2348 3176 4.649692 AGATGAACATGCTTATAGGCTGG 58.350 43.478 8.44 2.91 0.00 4.85
2371 3199 0.041684 AGGAAAAGGCCCCCAGAATG 59.958 55.000 0.00 0.00 0.00 2.67
2373 3201 0.178935 CAAGGAAAAGGCCCCCAGAA 60.179 55.000 0.00 0.00 0.00 3.02
2375 3203 1.610379 CCAAGGAAAAGGCCCCCAG 60.610 63.158 0.00 0.00 0.00 4.45
2376 3204 2.530801 CCAAGGAAAAGGCCCCCA 59.469 61.111 0.00 0.00 0.00 4.96
2377 3205 3.003173 GCCAAGGAAAAGGCCCCC 61.003 66.667 0.00 0.00 45.18 5.40
2627 3583 2.126071 GCAAGACGCAGAGCCGTA 60.126 61.111 0.00 0.00 42.24 4.02
2628 3584 3.521529 AAGCAAGACGCAGAGCCGT 62.522 57.895 0.00 0.00 46.13 5.68
2629 3585 2.740055 AAGCAAGACGCAGAGCCG 60.740 61.111 0.00 0.00 46.13 5.52
2630 3586 2.866028 CAAGCAAGACGCAGAGCC 59.134 61.111 0.00 0.00 46.13 4.70
2641 3602 1.536766 CAAGTCGATGGAAGCAAGCAA 59.463 47.619 0.00 0.00 0.00 3.91
2806 3811 8.682128 AAACAAAATACCGCAGTAAATACATG 57.318 30.769 0.00 0.00 30.59 3.21
2845 3850 0.322816 GCACAGCCATGGAAAGGAGA 60.323 55.000 18.40 0.00 0.00 3.71
2962 3967 7.815549 ACCAGTGAACTTTTCGTGTTTTAATTT 59.184 29.630 0.00 0.00 0.00 1.82
2965 3970 6.256912 ACCAGTGAACTTTTCGTGTTTTAA 57.743 33.333 0.00 0.00 0.00 1.52
2969 3974 6.445357 AATAACCAGTGAACTTTTCGTGTT 57.555 33.333 0.00 0.00 0.00 3.32
2974 3979 7.644157 GTCAGTCAAATAACCAGTGAACTTTTC 59.356 37.037 0.00 0.00 0.00 2.29
2977 3982 5.236478 CGTCAGTCAAATAACCAGTGAACTT 59.764 40.000 0.00 0.00 0.00 2.66
2978 3983 4.750098 CGTCAGTCAAATAACCAGTGAACT 59.250 41.667 0.00 0.00 0.00 3.01
2979 3984 4.084013 CCGTCAGTCAAATAACCAGTGAAC 60.084 45.833 0.00 0.00 0.00 3.18
2981 3986 3.322541 TCCGTCAGTCAAATAACCAGTGA 59.677 43.478 0.00 0.00 0.00 3.41
2982 3987 3.659786 TCCGTCAGTCAAATAACCAGTG 58.340 45.455 0.00 0.00 0.00 3.66
2983 3988 4.253685 CATCCGTCAGTCAAATAACCAGT 58.746 43.478 0.00 0.00 0.00 4.00
2984 3989 3.623060 CCATCCGTCAGTCAAATAACCAG 59.377 47.826 0.00 0.00 0.00 4.00
2986 3991 2.943033 CCCATCCGTCAGTCAAATAACC 59.057 50.000 0.00 0.00 0.00 2.85
3078 4223 3.308473 GGAGCTCCTCAGGTAACCAATTT 60.308 47.826 26.25 0.00 31.08 1.82
3455 4758 2.446994 ACCACCACCCACCGAGAA 60.447 61.111 0.00 0.00 0.00 2.87
3484 4787 4.504916 CTCCTCCTCCGCGCAGTG 62.505 72.222 8.75 0.00 38.04 3.66
3511 4820 0.684805 TCTCCTCCGGCTCTTCTTCC 60.685 60.000 0.00 0.00 0.00 3.46
3660 4969 0.461961 CCCACTAGGCAGTAGCACTC 59.538 60.000 0.00 0.00 44.61 3.51
3766 5075 5.700373 GCATTAAAATGAGACCCTGCAAAAA 59.300 36.000 6.87 0.00 38.70 1.94
3767 5076 5.011943 AGCATTAAAATGAGACCCTGCAAAA 59.988 36.000 6.87 0.00 38.70 2.44
3768 5077 4.527816 AGCATTAAAATGAGACCCTGCAAA 59.472 37.500 6.87 0.00 38.70 3.68
3769 5078 4.088634 AGCATTAAAATGAGACCCTGCAA 58.911 39.130 6.87 0.00 38.70 4.08
3770 5079 3.700538 AGCATTAAAATGAGACCCTGCA 58.299 40.909 6.87 0.00 38.70 4.41
3771 5080 4.725790 AAGCATTAAAATGAGACCCTGC 57.274 40.909 6.87 0.00 38.70 4.85
3772 5081 7.917505 GTGATTAAGCATTAAAATGAGACCCTG 59.082 37.037 6.87 0.00 44.76 4.45
3773 5082 7.068716 GGTGATTAAGCATTAAAATGAGACCCT 59.931 37.037 6.87 0.00 44.76 4.34
3774 5083 7.203218 GGTGATTAAGCATTAAAATGAGACCC 58.797 38.462 6.87 0.00 44.76 4.46
3775 5084 7.203218 GGGTGATTAAGCATTAAAATGAGACC 58.797 38.462 6.87 0.00 44.76 3.85
3776 5085 7.068716 AGGGGTGATTAAGCATTAAAATGAGAC 59.931 37.037 6.87 0.00 44.76 3.36
3777 5086 7.125391 AGGGGTGATTAAGCATTAAAATGAGA 58.875 34.615 6.87 0.00 44.76 3.27
3778 5087 7.352079 AGGGGTGATTAAGCATTAAAATGAG 57.648 36.000 6.87 0.00 44.76 2.90
3779 5088 8.058847 ACTAGGGGTGATTAAGCATTAAAATGA 58.941 33.333 6.87 0.00 44.76 2.57
3780 5089 8.237811 ACTAGGGGTGATTAAGCATTAAAATG 57.762 34.615 0.00 0.00 44.76 2.32
3781 5090 7.505923 GGACTAGGGGTGATTAAGCATTAAAAT 59.494 37.037 0.00 0.00 44.76 1.82
3782 5091 6.831868 GGACTAGGGGTGATTAAGCATTAAAA 59.168 38.462 0.00 0.00 44.76 1.52
3783 5092 6.362248 GGACTAGGGGTGATTAAGCATTAAA 58.638 40.000 0.00 0.00 44.76 1.52
3784 5093 5.163131 GGGACTAGGGGTGATTAAGCATTAA 60.163 44.000 0.00 0.00 45.80 1.40
3785 5094 4.349930 GGGACTAGGGGTGATTAAGCATTA 59.650 45.833 0.00 0.00 0.00 1.90
3786 5095 3.138468 GGGACTAGGGGTGATTAAGCATT 59.862 47.826 0.00 0.00 0.00 3.56
3787 5096 2.711547 GGGACTAGGGGTGATTAAGCAT 59.288 50.000 0.00 0.00 0.00 3.79
3788 5097 2.124411 GGGACTAGGGGTGATTAAGCA 58.876 52.381 0.00 0.00 0.00 3.91
3789 5098 2.124411 TGGGACTAGGGGTGATTAAGC 58.876 52.381 0.00 0.00 0.00 3.09
3790 5099 5.388599 AATTGGGACTAGGGGTGATTAAG 57.611 43.478 0.00 0.00 0.00 1.85
3791 5100 5.494706 AGAAATTGGGACTAGGGGTGATTAA 59.505 40.000 0.00 0.00 0.00 1.40
3792 5101 5.043762 AGAAATTGGGACTAGGGGTGATTA 58.956 41.667 0.00 0.00 0.00 1.75
3793 5102 3.858638 AGAAATTGGGACTAGGGGTGATT 59.141 43.478 0.00 0.00 0.00 2.57
3794 5103 3.459969 GAGAAATTGGGACTAGGGGTGAT 59.540 47.826 0.00 0.00 0.00 3.06
3795 5104 2.844348 GAGAAATTGGGACTAGGGGTGA 59.156 50.000 0.00 0.00 0.00 4.02
3796 5105 2.576191 TGAGAAATTGGGACTAGGGGTG 59.424 50.000 0.00 0.00 0.00 4.61
3797 5106 2.929301 TGAGAAATTGGGACTAGGGGT 58.071 47.619 0.00 0.00 0.00 4.95
3798 5107 5.646692 TTATGAGAAATTGGGACTAGGGG 57.353 43.478 0.00 0.00 0.00 4.79
3799 5108 7.119387 ACTTTTATGAGAAATTGGGACTAGGG 58.881 38.462 0.00 0.00 0.00 3.53
3800 5109 8.581253 AACTTTTATGAGAAATTGGGACTAGG 57.419 34.615 0.00 0.00 0.00 3.02
3801 5110 9.454859 AGAACTTTTATGAGAAATTGGGACTAG 57.545 33.333 0.00 0.00 0.00 2.57
3806 5115 9.933723 ATGAAAGAACTTTTATGAGAAATTGGG 57.066 29.630 4.25 0.00 32.11 4.12
3826 5135 8.331022 CAGTCATTACATCGAGGTAAATGAAAG 58.669 37.037 24.53 17.58 36.86 2.62
3864 5173 6.942532 TCTACCATTTTTAGCTGCCATAAG 57.057 37.500 0.00 0.00 0.00 1.73
3869 5178 5.644977 AGTTTCTACCATTTTTAGCTGCC 57.355 39.130 0.00 0.00 0.00 4.85
3872 5181 6.817140 CCTCGTAGTTTCTACCATTTTTAGCT 59.183 38.462 0.00 0.00 0.00 3.32
3873 5182 6.592994 ACCTCGTAGTTTCTACCATTTTTAGC 59.407 38.462 2.02 0.00 0.00 3.09
3874 5183 7.008992 CGACCTCGTAGTTTCTACCATTTTTAG 59.991 40.741 2.02 0.00 34.11 1.85
3875 5184 6.808212 CGACCTCGTAGTTTCTACCATTTTTA 59.192 38.462 2.02 0.00 34.11 1.52
3876 5185 5.636543 CGACCTCGTAGTTTCTACCATTTTT 59.363 40.000 2.02 0.00 34.11 1.94
3880 5189 3.376546 GTCGACCTCGTAGTTTCTACCAT 59.623 47.826 3.51 0.00 40.80 3.55
3881 5190 2.744202 GTCGACCTCGTAGTTTCTACCA 59.256 50.000 3.51 0.00 40.80 3.25
3882 5191 2.222908 CGTCGACCTCGTAGTTTCTACC 60.223 54.545 10.58 0.00 40.80 3.18
3883 5192 2.668457 TCGTCGACCTCGTAGTTTCTAC 59.332 50.000 10.58 0.00 40.80 2.59
3884 5193 2.926200 CTCGTCGACCTCGTAGTTTCTA 59.074 50.000 10.58 0.00 40.80 2.10
3885 5194 1.731160 CTCGTCGACCTCGTAGTTTCT 59.269 52.381 10.58 0.00 40.80 2.52
3886 5195 1.728971 TCTCGTCGACCTCGTAGTTTC 59.271 52.381 10.58 0.00 40.80 2.78
3887 5196 1.800805 TCTCGTCGACCTCGTAGTTT 58.199 50.000 10.58 0.00 40.80 2.66
3888 5197 1.731160 CTTCTCGTCGACCTCGTAGTT 59.269 52.381 10.58 0.00 40.80 2.24
3889 5198 1.067283 TCTTCTCGTCGACCTCGTAGT 60.067 52.381 10.58 0.00 40.80 2.73
3892 5201 0.037512 TCTCTTCTCGTCGACCTCGT 60.038 55.000 10.58 0.00 40.80 4.18
3893 5202 1.077123 TTCTCTTCTCGTCGACCTCG 58.923 55.000 10.58 0.00 41.45 4.63
3894 5203 1.201943 CGTTCTCTTCTCGTCGACCTC 60.202 57.143 10.58 0.00 0.00 3.85
3895 5204 0.797542 CGTTCTCTTCTCGTCGACCT 59.202 55.000 10.58 0.00 0.00 3.85
3896 5205 0.179194 CCGTTCTCTTCTCGTCGACC 60.179 60.000 10.58 0.00 0.00 4.79
3897 5206 0.795085 TCCGTTCTCTTCTCGTCGAC 59.205 55.000 5.18 5.18 0.00 4.20
3898 5207 0.795085 GTCCGTTCTCTTCTCGTCGA 59.205 55.000 0.00 0.00 0.00 4.20
3899 5208 0.516001 TGTCCGTTCTCTTCTCGTCG 59.484 55.000 0.00 0.00 0.00 5.12
3900 5209 1.401278 GGTGTCCGTTCTCTTCTCGTC 60.401 57.143 0.00 0.00 0.00 4.20
3901 5210 0.597072 GGTGTCCGTTCTCTTCTCGT 59.403 55.000 0.00 0.00 0.00 4.18
3902 5211 0.596577 TGGTGTCCGTTCTCTTCTCG 59.403 55.000 0.00 0.00 0.00 4.04
3903 5212 1.340248 TGTGGTGTCCGTTCTCTTCTC 59.660 52.381 0.00 0.00 0.00 2.87
3904 5213 1.341531 CTGTGGTGTCCGTTCTCTTCT 59.658 52.381 0.00 0.00 0.00 2.85
3905 5214 1.068741 ACTGTGGTGTCCGTTCTCTTC 59.931 52.381 0.00 0.00 0.00 2.87
3906 5215 1.120530 ACTGTGGTGTCCGTTCTCTT 58.879 50.000 0.00 0.00 0.00 2.85
3907 5216 1.068741 GAACTGTGGTGTCCGTTCTCT 59.931 52.381 0.00 0.00 34.47 3.10
3908 5217 1.499049 GAACTGTGGTGTCCGTTCTC 58.501 55.000 0.00 0.00 34.47 2.87
3909 5218 0.106149 GGAACTGTGGTGTCCGTTCT 59.894 55.000 0.00 0.00 36.78 3.01
3910 5219 0.106149 AGGAACTGTGGTGTCCGTTC 59.894 55.000 0.00 0.00 37.18 3.95
3911 5220 1.416243 TAGGAACTGTGGTGTCCGTT 58.584 50.000 0.00 0.00 41.52 4.44
3912 5221 1.416243 TTAGGAACTGTGGTGTCCGT 58.584 50.000 0.00 0.00 41.52 4.69
3913 5222 2.536761 TTTAGGAACTGTGGTGTCCG 57.463 50.000 0.00 0.00 41.52 4.79
3914 5223 4.901868 TGTATTTAGGAACTGTGGTGTCC 58.098 43.478 0.00 0.00 41.52 4.02
3915 5224 4.935808 CCTGTATTTAGGAACTGTGGTGTC 59.064 45.833 0.00 0.00 41.52 3.67
3919 5228 4.837093 TCCCTGTATTTAGGAACTGTGG 57.163 45.455 0.00 0.00 41.52 4.17
3923 5232 9.280456 TCTTAATCTTCCCTGTATTTAGGAACT 57.720 33.333 0.00 0.00 40.42 3.01
3950 5259 3.346146 TCCCCGATCCTAGGATTTCTT 57.654 47.619 25.25 3.26 34.60 2.52
3954 5263 2.330216 CTGTTCCCCGATCCTAGGATT 58.670 52.381 25.25 9.44 34.60 3.01
3956 5265 0.759436 GCTGTTCCCCGATCCTAGGA 60.759 60.000 15.46 15.46 0.00 2.94
4035 5348 9.319143 CGAGTGTATGGAAGAAGAAAGATAAAT 57.681 33.333 0.00 0.00 0.00 1.40
4036 5349 8.311836 ACGAGTGTATGGAAGAAGAAAGATAAA 58.688 33.333 0.00 0.00 0.00 1.40
4039 5352 6.287589 ACGAGTGTATGGAAGAAGAAAGAT 57.712 37.500 0.00 0.00 0.00 2.40
4041 5354 4.865365 GGACGAGTGTATGGAAGAAGAAAG 59.135 45.833 0.00 0.00 0.00 2.62
4043 5356 4.082190 CAGGACGAGTGTATGGAAGAAGAA 60.082 45.833 0.00 0.00 0.00 2.52
4085 5398 9.561069 AGCTTTCTCTTCAGTAGAAACAAATTA 57.439 29.630 0.00 0.00 37.89 1.40
4099 5412 5.337652 GCTCCCTACTTTAGCTTTCTCTTCA 60.338 44.000 0.00 0.00 33.40 3.02
4116 5429 0.753479 CTCTGCTCCTTCGCTCCCTA 60.753 60.000 0.00 0.00 0.00 3.53
4124 5437 3.755905 CCCTTCTTTTTCTCTGCTCCTTC 59.244 47.826 0.00 0.00 0.00 3.46
4125 5438 3.395941 TCCCTTCTTTTTCTCTGCTCCTT 59.604 43.478 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.