Multiple sequence alignment - TraesCS6A01G060800

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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 TraesCS6A01G060800 chr6A 100.000 5094 0 0 1 5094 32666952 32672045 0.000000e+00 9407.0
1 TraesCS6A01G060800 chr6A 83.229 1437 197 26 1843 3262 32659842 32661251 0.000000e+00 1279.0
2 TraesCS6A01G060800 chr6A 87.446 932 106 6 3268 4188 32661317 32662248 0.000000e+00 1062.0
3 TraesCS6A01G060800 chr6D 93.006 4261 204 35 897 5094 30239842 30235613 0.000000e+00 6131.0
4 TraesCS6A01G060800 chr6D 93.025 3355 165 22 897 4188 30248656 30245308 0.000000e+00 4835.0
5 TraesCS6A01G060800 chr6D 84.719 2369 311 30 1843 4188 30283719 30281379 0.000000e+00 2322.0
6 TraesCS6A01G060800 chr6D 91.196 1204 89 11 2463 3656 30226068 30224872 0.000000e+00 1620.0
7 TraesCS6A01G060800 chr6D 88.847 1318 100 24 1158 2452 30228771 30227478 0.000000e+00 1576.0
8 TraesCS6A01G060800 chr6D 89.744 624 55 4 276 898 30240544 30239929 0.000000e+00 789.0
9 TraesCS6A01G060800 chr6D 86.925 413 42 8 493 898 30249151 30248744 2.160000e-123 453.0
10 TraesCS6A01G060800 chr6D 86.133 375 38 6 84 456 30249503 30249141 4.780000e-105 392.0
11 TraesCS6A01G060800 chr6D 87.059 255 22 5 922 1168 30234379 30234128 1.400000e-70 278.0
12 TraesCS6A01G060800 chr6D 95.312 64 3 0 16 79 30249634 30249571 9.020000e-18 102.0
13 TraesCS6A01G060800 chr6B 93.132 3349 169 17 897 4188 57321820 57325164 0.000000e+00 4854.0
14 TraesCS6A01G060800 chr6B 84.050 1442 191 22 1836 3262 57285340 57286757 0.000000e+00 1352.0
15 TraesCS6A01G060800 chr6B 87.965 914 99 6 3286 4188 57286941 57287854 0.000000e+00 1068.0
16 TraesCS6A01G060800 chr6B 81.680 857 75 30 84 898 57320916 57321732 5.560000e-179 638.0
17 TraesCS6A01G060800 chr6B 82.121 330 45 8 371 687 658804716 658805044 2.340000e-68 270.0
18 TraesCS6A01G060800 chr6B 86.188 181 16 6 4189 4360 63560415 63560595 2.420000e-43 187.0
19 TraesCS6A01G060800 chrUn 87.152 3129 288 65 1106 4164 71717969 71721053 0.000000e+00 3446.0
20 TraesCS6A01G060800 chrUn 86.590 261 24 4 916 1168 71717749 71718006 1.400000e-70 278.0
21 TraesCS6A01G060800 chrUn 84.615 182 19 8 4189 4363 90283812 90283633 6.780000e-39 172.0
22 TraesCS6A01G060800 chr3D 82.242 1329 202 26 1857 3174 604398552 604399857 0.000000e+00 1116.0
23 TraesCS6A01G060800 chr3D 80.440 818 130 24 3296 4103 604399956 604400753 9.440000e-167 597.0
24 TraesCS6A01G060800 chr3D 83.283 329 40 10 372 689 342804322 342803998 6.450000e-74 289.0
25 TraesCS6A01G060800 chr3D 83.784 185 21 9 4192 4372 332489284 332489105 3.150000e-37 167.0
26 TraesCS6A01G060800 chr5D 81.067 1368 222 22 1857 3199 558032788 558034143 0.000000e+00 1057.0
27 TraesCS6A01G060800 chr5D 80.946 719 114 14 3343 4051 558034158 558034863 9.640000e-152 547.0
28 TraesCS6A01G060800 chr5D 85.946 185 10 11 4186 4360 399624601 399624779 3.130000e-42 183.0
29 TraesCS6A01G060800 chr5D 85.405 185 13 10 4189 4360 133248239 133248056 4.050000e-41 180.0
30 TraesCS6A01G060800 chr5D 88.506 87 10 0 1153 1239 557540961 557540875 6.980000e-19 106.0
31 TraesCS6A01G060800 chr5D 82.727 110 15 4 1137 1245 557546910 557546804 1.510000e-15 95.3
32 TraesCS6A01G060800 chr3A 81.125 800 123 19 3296 4086 734130361 734131141 2.610000e-172 616.0
33 TraesCS6A01G060800 chr2D 83.537 328 42 7 371 687 161359804 161359478 3.860000e-76 296.0
34 TraesCS6A01G060800 chr2D 85.635 181 19 6 4189 4364 32016253 32016431 3.130000e-42 183.0
35 TraesCS6A01G060800 chr1D 84.466 309 39 8 387 688 128598497 128598803 3.860000e-76 296.0
36 TraesCS6A01G060800 chr1D 84.466 309 39 8 387 688 128988696 128988390 3.860000e-76 296.0
37 TraesCS6A01G060800 chr1B 82.779 331 43 8 371 688 647924004 647923675 3.000000e-72 283.0
38 TraesCS6A01G060800 chr2A 84.530 181 18 7 4189 4360 709625979 709625800 2.440000e-38 171.0
39 TraesCS6A01G060800 chr7A 84.153 183 20 8 4189 4363 713959517 713959336 8.770000e-38 169.0
40 TraesCS6A01G060800 chr4A 83.077 130 19 2 1135 1261 609819075 609818946 1.160000e-21 115.0
41 TraesCS6A01G060800 chr4A 88.506 87 10 0 1153 1239 609921853 609921767 6.980000e-19 106.0


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 TraesCS6A01G060800 chr6A 32666952 32672045 5093 False 9407.000000 9407 100.000000 1 5094 1 chr6A.!!$F1 5093
1 TraesCS6A01G060800 chr6A 32659842 32662248 2406 False 1170.500000 1279 85.337500 1843 4188 2 chr6A.!!$F2 2345
2 TraesCS6A01G060800 chr6D 30234128 30240544 6416 True 2399.333333 6131 89.936333 276 5094 3 chr6D.!!$R3 4818
3 TraesCS6A01G060800 chr6D 30281379 30283719 2340 True 2322.000000 2322 84.719000 1843 4188 1 chr6D.!!$R1 2345
4 TraesCS6A01G060800 chr6D 30224872 30228771 3899 True 1598.000000 1620 90.021500 1158 3656 2 chr6D.!!$R2 2498
5 TraesCS6A01G060800 chr6D 30245308 30249634 4326 True 1445.500000 4835 90.348750 16 4188 4 chr6D.!!$R4 4172
6 TraesCS6A01G060800 chr6B 57320916 57325164 4248 False 2746.000000 4854 87.406000 84 4188 2 chr6B.!!$F4 4104
7 TraesCS6A01G060800 chr6B 57285340 57287854 2514 False 1210.000000 1352 86.007500 1836 4188 2 chr6B.!!$F3 2352
8 TraesCS6A01G060800 chrUn 71717749 71721053 3304 False 1862.000000 3446 86.871000 916 4164 2 chrUn.!!$F1 3248
9 TraesCS6A01G060800 chr3D 604398552 604400753 2201 False 856.500000 1116 81.341000 1857 4103 2 chr3D.!!$F1 2246
10 TraesCS6A01G060800 chr5D 558032788 558034863 2075 False 802.000000 1057 81.006500 1857 4051 2 chr5D.!!$F2 2194
11 TraesCS6A01G060800 chr3A 734130361 734131141 780 False 616.000000 616 81.125000 3296 4086 1 chr3A.!!$F1 790

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
306 372 0.035915 TTCAAATCGCGGGATCCACA 60.036 50.0 16.02 0.0 30.81 4.17 F
1217 1463 0.253160 TACCACTTCCAGCCTCCCAT 60.253 55.0 0.00 0.0 0.00 4.00 F
2719 4452 0.823356 AACGTGATGCCTTTGTGCCT 60.823 50.0 0.00 0.0 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2298 2611 0.245813 GTACGGGTCAGACAGGTTCC 59.754 60.000 2.17 0.0 0.00 3.62 R
2900 4634 1.892474 TGAAGCACAACCAATTAGGGC 59.108 47.619 0.00 0.0 43.89 5.19 R
4400 6359 0.034960 GAGAAGTGGGGAAGGGAAGC 60.035 60.000 0.00 0.0 0.00 3.86 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
18 19 2.029743 GTTGACGGCTTCCTTTGCA 58.970 52.632 0.00 0.00 0.00 4.08
79 80 0.038310 TCTCGAGGAGAGGAGCAACA 59.962 55.000 13.56 0.00 46.82 3.33
80 81 0.891373 CTCGAGGAGAGGAGCAACAA 59.109 55.000 3.91 0.00 43.20 2.83
82 83 0.318441 CGAGGAGAGGAGCAACAACA 59.682 55.000 0.00 0.00 0.00 3.33
125 189 4.737054 CAAATGCCACTGTTTGATACCTC 58.263 43.478 0.00 0.00 37.48 3.85
128 192 2.037902 TGCCACTGTTTGATACCTCGAA 59.962 45.455 0.00 0.00 0.00 3.71
160 224 5.584551 ATGTTGTTTCCTTCCCTTAGTCT 57.415 39.130 0.00 0.00 0.00 3.24
161 225 5.382664 TGTTGTTTCCTTCCCTTAGTCTT 57.617 39.130 0.00 0.00 0.00 3.01
162 226 5.130350 TGTTGTTTCCTTCCCTTAGTCTTG 58.870 41.667 0.00 0.00 0.00 3.02
163 227 5.131067 GTTGTTTCCTTCCCTTAGTCTTGT 58.869 41.667 0.00 0.00 0.00 3.16
164 228 6.126710 TGTTGTTTCCTTCCCTTAGTCTTGTA 60.127 38.462 0.00 0.00 0.00 2.41
202 266 8.265998 CAGTTTTGTAAATGTTGAAACCGATTC 58.734 33.333 0.00 0.00 38.60 2.52
217 281 8.812329 TGAAACCGATTCAGTAAATTTTGTTTG 58.188 29.630 0.00 0.00 43.08 2.93
218 282 6.763303 ACCGATTCAGTAAATTTTGTTTGC 57.237 33.333 0.00 0.00 0.00 3.68
237 301 7.946207 TGTTTGCATGTAATTTTACAGGAAGA 58.054 30.769 16.73 1.51 45.39 2.87
250 314 9.918630 ATTTTACAGGAAGACAAAATGAAGATG 57.081 29.630 0.00 0.00 31.26 2.90
251 315 8.690203 TTTACAGGAAGACAAAATGAAGATGA 57.310 30.769 0.00 0.00 0.00 2.92
252 316 8.690203 TTACAGGAAGACAAAATGAAGATGAA 57.310 30.769 0.00 0.00 0.00 2.57
306 372 0.035915 TTCAAATCGCGGGATCCACA 60.036 50.000 16.02 0.00 30.81 4.17
365 431 9.144747 CGTTCCACAGATTATATCTATTGAAGG 57.855 37.037 0.00 0.00 37.58 3.46
369 435 9.212641 CCACAGATTATATCTATTGAAGGTGTG 57.787 37.037 0.00 0.00 37.58 3.82
444 510 3.724508 ACTCATGGTAAGCTCAGATCG 57.275 47.619 0.00 0.00 0.00 3.69
477 543 9.874205 CATTTGATTTGGTACCATCTTTTGTAT 57.126 29.630 17.17 0.54 0.00 2.29
480 546 8.821686 TGATTTGGTACCATCTTTTGTATCAT 57.178 30.769 17.17 0.00 28.81 2.45
552 644 4.142403 CCGTCATTGAACAAATACTGCCAT 60.142 41.667 0.00 0.00 0.00 4.40
572 665 8.032045 TGCCATTGAATATTATGTTTGGGATT 57.968 30.769 0.00 0.00 0.00 3.01
588 681 6.865834 TTGGGATTTGGTTAGTTATGCAAT 57.134 33.333 0.00 0.00 0.00 3.56
766 863 0.747255 GCCTCGGTGCTCATTCTCTA 59.253 55.000 0.00 0.00 0.00 2.43
803 902 2.160721 TCTCCTCTCTAAACCGGCAT 57.839 50.000 0.00 0.00 0.00 4.40
820 919 1.888215 CATCGCCTATTCCAGCATGT 58.112 50.000 0.00 0.00 0.00 3.21
824 924 1.221414 GCCTATTCCAGCATGTCGAC 58.779 55.000 9.11 9.11 0.00 4.20
831 931 1.474879 TCCAGCATGTCGACGAATACA 59.525 47.619 11.62 0.00 0.00 2.29
844 944 1.378531 GAATACATTGAGCCCACGCA 58.621 50.000 0.00 0.00 37.52 5.24
847 947 1.836999 TACATTGAGCCCACGCAGGT 61.837 55.000 0.00 0.00 37.52 4.00
893 1008 2.284824 CAGCCTCTTCCTCTGCAGA 58.715 57.895 17.19 17.19 0.00 4.26
913 1118 3.008485 AGAAGCACCTAACTAAGCAGCTT 59.992 43.478 13.46 13.46 42.75 3.74
919 1124 5.064071 GCACCTAACTAAGCAGCTTCTTAAG 59.936 44.000 12.07 5.99 0.00 1.85
967 1172 5.422012 ACACACCCCCATAAATCTTTGATTC 59.578 40.000 0.00 0.00 0.00 2.52
978 1197 9.182214 CATAAATCTTTGATTCCTTCTCCTCAA 57.818 33.333 0.00 0.00 0.00 3.02
995 1214 4.128643 CCTCAATCTCTCATTCCTTCTGC 58.871 47.826 0.00 0.00 0.00 4.26
1110 1329 0.344790 ATGGGAGTGGAGGGAGATGT 59.655 55.000 0.00 0.00 0.00 3.06
1217 1463 0.253160 TACCACTTCCAGCCTCCCAT 60.253 55.000 0.00 0.00 0.00 4.00
1221 1467 1.064166 CACTTCCAGCCTCCCATGAAT 60.064 52.381 0.00 0.00 0.00 2.57
1242 1488 8.993404 TGAATTGGATCAATGGTATGTTCATA 57.007 30.769 0.00 0.00 34.04 2.15
1517 1785 9.113838 AGTTTTGGCAATACTATCATTACAGAG 57.886 33.333 19.68 0.00 0.00 3.35
1523 1791 6.226052 CAATACTATCATTACAGAGCTGCCA 58.774 40.000 0.00 0.00 0.00 4.92
1607 1879 1.390565 ATCTCTTGCTGAATGCTGCC 58.609 50.000 0.00 0.00 43.37 4.85
1631 1903 6.292168 CCGTTAGATTTTGAGTAATACTGCCG 60.292 42.308 0.00 0.00 0.00 5.69
1641 1913 7.050970 TGAGTAATACTGCCGTAAGATGATT 57.949 36.000 0.00 0.00 43.02 2.57
1657 1929 9.474920 GTAAGATGATTATAGCCATAGATGCTC 57.525 37.037 0.00 0.00 40.23 4.26
1730 2004 2.423185 TCGCCAAGATTTATGCCACTTG 59.577 45.455 0.00 0.00 39.24 3.16
1772 2050 3.878699 CCACCGTTAGTGTTACTTTTGGT 59.121 43.478 0.00 0.00 45.74 3.67
1799 2077 6.431234 AGACCAAATTCAGTTAGGCAAAGTAG 59.569 38.462 0.00 0.00 0.00 2.57
1802 2080 6.378280 CCAAATTCAGTTAGGCAAAGTAGGAT 59.622 38.462 0.00 0.00 0.00 3.24
1853 2136 8.957466 CATGGATCATTCTATATCTGTTGCATT 58.043 33.333 0.00 0.00 0.00 3.56
1918 2207 2.085320 CGATCCTCCGGAATCTACGAT 58.915 52.381 5.23 0.00 34.34 3.73
1951 2240 6.871844 AGATCCATGTGGTATGAATATCTCG 58.128 40.000 0.00 0.00 36.34 4.04
1954 2244 3.297830 TGTGGTATGAATATCTCGGCG 57.702 47.619 0.00 0.00 0.00 6.46
1974 2265 5.224135 GGCGCAAACACCTCTAAATAAAAA 58.776 37.500 10.83 0.00 0.00 1.94
1976 2267 5.344933 GCGCAAACACCTCTAAATAAAAAGG 59.655 40.000 0.30 0.00 34.94 3.11
1995 2299 6.374417 AAAGGAGGAGTTGCAGTATTCTAA 57.626 37.500 0.00 0.00 0.00 2.10
1996 2300 5.346181 AGGAGGAGTTGCAGTATTCTAAC 57.654 43.478 0.00 0.00 0.00 2.34
1998 2302 5.248477 AGGAGGAGTTGCAGTATTCTAACAA 59.752 40.000 0.00 0.00 0.00 2.83
2219 2529 0.958822 GACCGGTTCAGCCACAATTT 59.041 50.000 9.42 0.00 36.97 1.82
2298 2611 2.433970 TCCAAAACCTTTTGCTTCCCAG 59.566 45.455 5.16 0.00 44.62 4.45
2591 4321 1.304052 TTTGCGGTATTGCCAGGCT 60.304 52.632 14.15 0.00 36.97 4.58
2719 4452 0.823356 AACGTGATGCCTTTGTGCCT 60.823 50.000 0.00 0.00 0.00 4.75
2900 4634 5.276270 CAGGAATCCATGTAAGCAAATTCG 58.724 41.667 0.61 0.00 0.00 3.34
2911 4645 2.456577 AGCAAATTCGCCCTAATTGGT 58.543 42.857 0.00 0.00 0.00 3.67
3124 4867 3.073650 ACTTGAGCTCAACAAGGGAGATT 59.926 43.478 25.16 0.00 45.92 2.40
3303 5223 9.716556 TTCAGGAGAAGGATAGGTATATATTCC 57.283 37.037 0.14 0.14 0.00 3.01
3338 5259 7.075741 GTGTGTCGTGTATTTTTAAGAGCAAT 58.924 34.615 0.00 0.00 0.00 3.56
3340 5261 8.775527 TGTGTCGTGTATTTTTAAGAGCAATTA 58.224 29.630 0.00 0.00 0.00 1.40
3450 5372 0.178964 CTTCCTGGCTTTTGGACCCA 60.179 55.000 0.00 0.00 31.24 4.51
3525 5447 2.642311 TGGACTTGTTATTCTGGCCTCA 59.358 45.455 3.32 0.00 0.00 3.86
3578 5500 3.838120 TCAGAGTCTACAAATCACAGCG 58.162 45.455 0.00 0.00 0.00 5.18
3619 5541 4.713814 TGTGCTCTGATCTAAGAAGGTCAT 59.286 41.667 0.00 0.00 42.04 3.06
3625 5550 6.344500 TCTGATCTAAGAAGGTCATTGCTTC 58.656 40.000 0.00 0.00 42.04 3.86
3781 5715 4.581309 TGATCTTGCAAAGGAGAGGAAT 57.419 40.909 0.00 0.00 46.24 3.01
3790 5724 7.623999 TGCAAAGGAGAGGAATATATCTCTT 57.376 36.000 5.64 1.68 41.43 2.85
4199 6153 3.861846 AGCCTATCATGGACATGGAGTA 58.138 45.455 11.98 3.50 39.24 2.59
4225 6179 4.363990 CGAGCTCACGTGCACCCT 62.364 66.667 15.40 3.70 34.99 4.34
4248 6202 7.812669 CCCTTTGCTACAGTAAAATCGAAAAAT 59.187 33.333 0.00 0.00 0.00 1.82
4249 6203 9.834628 CCTTTGCTACAGTAAAATCGAAAAATA 57.165 29.630 0.00 0.00 0.00 1.40
4320 6279 2.029200 TCACATGCATGCCAATTTTCGT 60.029 40.909 26.53 0.00 0.00 3.85
4347 6306 6.778821 TGAAATGAGATTTGTGGAGGTCTTA 58.221 36.000 0.00 0.00 31.47 2.10
4348 6307 7.230747 TGAAATGAGATTTGTGGAGGTCTTAA 58.769 34.615 0.00 0.00 31.47 1.85
4349 6308 7.723616 TGAAATGAGATTTGTGGAGGTCTTAAA 59.276 33.333 0.00 0.00 31.47 1.52
4381 6340 3.131046 AGAAAAATCCATGTGGGCGATTC 59.869 43.478 0.00 0.86 36.21 2.52
4388 6347 1.910580 ATGTGGGCGATTCGAGGGTT 61.911 55.000 10.88 0.00 0.00 4.11
4419 6378 0.034960 GCTTCCCTTCCCCACTTCTC 60.035 60.000 0.00 0.00 0.00 2.87
4420 6379 0.621082 CTTCCCTTCCCCACTTCTCC 59.379 60.000 0.00 0.00 0.00 3.71
4421 6380 0.196118 TTCCCTTCCCCACTTCTCCT 59.804 55.000 0.00 0.00 0.00 3.69
4422 6381 0.252742 TCCCTTCCCCACTTCTCCTC 60.253 60.000 0.00 0.00 0.00 3.71
4452 6411 2.894126 CGGAGGCAGACACTAGGATAAT 59.106 50.000 0.00 0.00 0.00 1.28
4476 6435 3.585990 GGCCGCCGATGATGGTTG 61.586 66.667 0.00 0.00 0.00 3.77
4485 6444 1.718757 GATGATGGTTGCGGTGAGGC 61.719 60.000 0.00 0.00 0.00 4.70
4504 6463 4.087892 TCGGCTGCTCCCTTGCTC 62.088 66.667 0.00 0.00 0.00 4.26
4518 6477 0.543410 TTGCTCGGGTGAAGGGACTA 60.543 55.000 0.00 0.00 38.49 2.59
4540 6499 2.215942 GGTACCAAGGCAAGAACCAT 57.784 50.000 7.15 0.00 0.00 3.55
4567 6526 0.390340 GAGGCGACATTGTCTGAGCA 60.390 55.000 14.54 0.00 35.06 4.26
4623 6582 2.972505 CCAGTGCGGTGTGTGGTC 60.973 66.667 0.00 0.00 0.00 4.02
4686 6645 0.038744 CAGTGCCACATCTTCCCCTT 59.961 55.000 0.00 0.00 0.00 3.95
4688 6647 0.890683 GTGCCACATCTTCCCCTTTG 59.109 55.000 0.00 0.00 0.00 2.77
4689 6648 0.251742 TGCCACATCTTCCCCTTTGG 60.252 55.000 0.00 0.00 0.00 3.28
4690 6649 1.607801 GCCACATCTTCCCCTTTGGC 61.608 60.000 0.00 0.00 42.57 4.52
4691 6650 0.040204 CCACATCTTCCCCTTTGGCT 59.960 55.000 0.00 0.00 0.00 4.75
4692 6651 1.467920 CACATCTTCCCCTTTGGCTC 58.532 55.000 0.00 0.00 0.00 4.70
4711 6670 0.460311 CACTTCCCGGCGAATCTAGT 59.540 55.000 9.30 1.12 0.00 2.57
4755 6714 3.428870 GTCACCAGTTGAGTTGTATGACG 59.571 47.826 0.00 0.00 33.71 4.35
4761 6720 3.259876 AGTTGAGTTGTATGACGGGCTAA 59.740 43.478 0.00 0.00 0.00 3.09
4842 6801 1.308998 CAACCCTCACTGGTGTTGTC 58.691 55.000 0.53 0.00 39.73 3.18
4848 6807 1.001406 CTCACTGGTGTTGTCCTCCTC 59.999 57.143 0.53 0.00 0.00 3.71
4849 6808 0.758734 CACTGGTGTTGTCCTCCTCA 59.241 55.000 0.00 0.00 0.00 3.86
4931 6890 3.195698 GGATTGAGCGGTGGCGTC 61.196 66.667 0.00 0.00 46.35 5.19
4954 6913 2.194056 CTCCCTAGGGGCGTCGTA 59.806 66.667 28.19 5.39 43.94 3.43
4964 6923 1.557443 GGGCGTCGTATAGCATGTGC 61.557 60.000 0.00 0.00 42.49 4.57
4993 6952 1.408702 TGCCAACTTTGTTTGAGAGGC 59.591 47.619 0.00 0.00 38.44 4.70
5089 7048 0.963962 GTGGTAGTTCGTCACCCTCA 59.036 55.000 0.00 0.00 33.61 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.040067 CTGCAAAGGAAGCCGTCAAC 60.040 55.000 0.00 0.00 0.00 3.18
1 2 1.795170 GCTGCAAAGGAAGCCGTCAA 61.795 55.000 0.00 0.00 40.09 3.18
2 3 2.260869 GCTGCAAAGGAAGCCGTCA 61.261 57.895 0.00 0.00 40.09 4.35
3 4 2.563427 GCTGCAAAGGAAGCCGTC 59.437 61.111 0.00 0.00 40.09 4.79
7 8 3.752339 CGGGGCTGCAAAGGAAGC 61.752 66.667 0.50 0.00 45.80 3.86
8 9 3.064324 CCGGGGCTGCAAAGGAAG 61.064 66.667 0.50 0.00 0.00 3.46
39 40 2.047179 GGACTGGACGAACAGGGC 60.047 66.667 13.84 6.81 42.75 5.19
79 80 1.745141 GCGGGATTGAGATGAGCTGTT 60.745 52.381 0.00 0.00 0.00 3.16
80 81 0.179062 GCGGGATTGAGATGAGCTGT 60.179 55.000 0.00 0.00 0.00 4.40
82 83 1.617850 CTAGCGGGATTGAGATGAGCT 59.382 52.381 0.00 0.00 37.27 4.09
125 189 7.642071 AGGAAACAACATTGAATTTCATTCG 57.358 32.000 0.00 0.00 42.15 3.34
128 192 6.936335 GGGAAGGAAACAACATTGAATTTCAT 59.064 34.615 0.00 0.00 33.58 2.57
164 228 9.762933 ACATTTACAAAACTGCAGAATTACAAT 57.237 25.926 23.35 7.23 0.00 2.71
208 272 9.553064 TCCTGTAAAATTACATGCAAACAAAAT 57.447 25.926 6.47 0.00 42.26 1.82
217 281 8.810652 TTTTGTCTTCCTGTAAAATTACATGC 57.189 30.769 6.47 0.00 42.26 4.06
249 313 9.288576 ACATCATTGTCTTGTTTCTCTTATTCA 57.711 29.630 0.00 0.00 0.00 2.57
284 350 1.483004 TGGATCCCGCGATTTGAACTA 59.517 47.619 8.23 0.00 0.00 2.24
293 359 2.682136 TTCCTGTGGATCCCGCGA 60.682 61.111 8.23 0.00 36.72 5.87
345 411 8.654997 AGCACACCTTCAATAGATATAATCTGT 58.345 33.333 0.00 0.00 40.51 3.41
347 413 8.874156 TCAGCACACCTTCAATAGATATAATCT 58.126 33.333 0.00 0.00 43.33 2.40
348 414 9.664332 ATCAGCACACCTTCAATAGATATAATC 57.336 33.333 0.00 0.00 0.00 1.75
521 613 6.627395 ATTTGTTCAATGACGGTTCAACTA 57.373 33.333 0.00 0.00 34.61 2.24
531 623 6.389091 TCAATGGCAGTATTTGTTCAATGAC 58.611 36.000 0.00 0.00 0.00 3.06
561 654 6.212388 TGCATAACTAACCAAATCCCAAACAT 59.788 34.615 0.00 0.00 0.00 2.71
572 665 9.104965 GTCACACTATATTGCATAACTAACCAA 57.895 33.333 0.00 0.00 0.00 3.67
588 681 9.727859 TTTAAGGCATACAAAAGTCACACTATA 57.272 29.630 0.00 0.00 0.00 1.31
594 687 6.640907 CCAACTTTAAGGCATACAAAAGTCAC 59.359 38.462 6.81 0.00 40.35 3.67
766 863 1.909302 AGATGGAGGAAATGTCGTGGT 59.091 47.619 0.00 0.00 0.00 4.16
803 902 0.249447 CGACATGCTGGAATAGGCGA 60.249 55.000 0.00 0.00 0.00 5.54
809 908 2.315925 ATTCGTCGACATGCTGGAAT 57.684 45.000 17.16 11.76 0.00 3.01
820 919 1.478916 TGGGCTCAATGTATTCGTCGA 59.521 47.619 0.00 0.00 0.00 4.20
824 924 0.304705 GCGTGGGCTCAATGTATTCG 59.695 55.000 0.00 0.00 35.83 3.34
831 931 2.360350 CACCTGCGTGGGCTCAAT 60.360 61.111 0.00 0.00 41.11 2.57
853 953 3.767044 GAGGAGGAGGAGGAGGGCC 62.767 73.684 0.00 0.00 0.00 5.80
857 957 1.457455 GCAGGAGGAGGAGGAGGAG 60.457 68.421 0.00 0.00 0.00 3.69
858 958 2.235602 CTGCAGGAGGAGGAGGAGGA 62.236 65.000 5.57 0.00 0.00 3.71
893 1008 3.008485 AGAAGCTGCTTAGTTAGGTGCTT 59.992 43.478 15.95 0.00 41.18 3.91
967 1172 4.655186 AGGAATGAGAGATTGAGGAGAAGG 59.345 45.833 0.00 0.00 0.00 3.46
978 1197 1.202627 GCGGCAGAAGGAATGAGAGAT 60.203 52.381 0.00 0.00 0.00 2.75
1110 1329 1.152030 AGACTGTGGGCAGAGGGAA 60.152 57.895 1.30 0.00 45.28 3.97
1119 1338 0.252012 AGACCTCTGGAGACTGTGGG 60.252 60.000 0.00 0.00 44.45 4.61
1217 1463 7.901283 ATGAACATACCATTGATCCAATTCA 57.099 32.000 0.00 0.00 31.05 2.57
1221 1467 9.234827 GATCATATGAACATACCATTGATCCAA 57.765 33.333 9.99 0.00 35.50 3.53
1242 1488 4.581309 ACCAAACCAGAGACATGATCAT 57.419 40.909 1.18 1.18 0.00 2.45
1289 1535 5.563592 TCCAGAAAGCAGAGATGAATGAAA 58.436 37.500 0.00 0.00 0.00 2.69
1492 1760 7.857885 GCTCTGTAATGATAGTATTGCCAAAAC 59.142 37.037 0.00 0.00 0.00 2.43
1501 1769 6.617782 ATGGCAGCTCTGTAATGATAGTAT 57.382 37.500 0.00 0.00 0.00 2.12
1517 1785 4.612932 TTTTTGACACAAAAATGGCAGC 57.387 36.364 15.30 0.00 39.32 5.25
1607 1879 6.255020 ACGGCAGTATTACTCAAAATCTAACG 59.745 38.462 0.00 0.00 0.00 3.18
1631 1903 9.474920 GAGCATCTATGGCTATAATCATCTTAC 57.525 37.037 0.00 0.00 42.78 2.34
1641 1913 2.851805 CGCGAGCATCTATGGCTATA 57.148 50.000 0.00 0.00 42.78 1.31
1657 1929 6.252441 TGAATACTTCCATTTTATTTTGCGCG 59.748 34.615 0.00 0.00 0.00 6.86
1670 1944 7.230108 CACTATTTCTGCCATGAATACTTCCAT 59.770 37.037 0.00 0.00 0.00 3.41
1671 1945 6.543465 CACTATTTCTGCCATGAATACTTCCA 59.457 38.462 0.00 0.00 0.00 3.53
1672 1946 6.767902 TCACTATTTCTGCCATGAATACTTCC 59.232 38.462 0.00 0.00 0.00 3.46
1684 1958 7.445945 AGAAGGTACATATCACTATTTCTGCC 58.554 38.462 0.00 0.00 0.00 4.85
1730 2004 5.464168 GTGGAGCAAATATGGACAATATGC 58.536 41.667 0.00 0.00 31.49 3.14
1772 2050 4.365514 TGCCTAACTGAATTTGGTCTGA 57.634 40.909 0.00 0.00 35.76 3.27
1799 2077 4.098501 CAGTTATGGAAGGGAAAAGCATCC 59.901 45.833 0.00 0.00 38.86 3.51
1906 2195 4.862574 TCTTTTGTGTCATCGTAGATTCCG 59.137 41.667 0.00 0.00 45.12 4.30
1918 2207 3.831323 ACCACATGGATCTTTTGTGTCA 58.169 40.909 4.53 0.00 39.23 3.58
1951 2240 4.428615 TTTATTTAGAGGTGTTTGCGCC 57.571 40.909 4.18 0.00 45.35 6.53
1954 2244 7.039993 TCCTCCTTTTTATTTAGAGGTGTTTGC 60.040 37.037 4.41 0.00 43.80 3.68
1974 2265 4.777896 TGTTAGAATACTGCAACTCCTCCT 59.222 41.667 0.00 0.00 0.00 3.69
1976 2267 7.617041 AATTGTTAGAATACTGCAACTCCTC 57.383 36.000 0.00 0.00 0.00 3.71
2298 2611 0.245813 GTACGGGTCAGACAGGTTCC 59.754 60.000 2.17 0.00 0.00 3.62
2591 4321 5.339008 GACATGTCCAGTCCACTGTTATA 57.661 43.478 15.31 0.00 42.27 0.98
2900 4634 1.892474 TGAAGCACAACCAATTAGGGC 59.108 47.619 0.00 0.00 43.89 5.19
3303 5223 0.042188 CACGACACACCAAAGCTTCG 60.042 55.000 0.00 0.00 0.00 3.79
3338 5259 7.829211 AGAAAACTTGTGCCTGATTAGCTATAA 59.171 33.333 0.00 0.00 0.00 0.98
3340 5261 6.183347 AGAAAACTTGTGCCTGATTAGCTAT 58.817 36.000 0.00 0.00 0.00 2.97
3450 5372 2.555757 GGCTTCACAACAATGCTTCTCT 59.444 45.455 0.00 0.00 0.00 3.10
3525 5447 3.005050 CAGTGTGCTCATCCATGTTGTTT 59.995 43.478 0.00 0.00 0.00 2.83
3685 5617 5.869344 AGACCTGTGCAAAGAAAAGAAAAAC 59.131 36.000 5.12 0.00 0.00 2.43
3790 5724 5.202004 CCTCCTTAGCTTACCAGAGTTCTA 58.798 45.833 0.00 0.00 0.00 2.10
3852 5796 5.302568 GCATCCATCCATCCATTTTCAACTA 59.697 40.000 0.00 0.00 0.00 2.24
4296 6255 4.093703 CGAAAATTGGCATGCATGTGAAAT 59.906 37.500 26.79 19.52 0.00 2.17
4320 6279 5.573219 ACCTCCACAAATCTCATTTCATCA 58.427 37.500 0.00 0.00 0.00 3.07
4349 6308 8.685427 CCCACATGGATTTTTCTTTTTCTTTTT 58.315 29.630 0.00 0.00 37.39 1.94
4352 6311 5.764686 GCCCACATGGATTTTTCTTTTTCTT 59.235 36.000 0.00 0.00 37.39 2.52
4353 6312 5.308014 GCCCACATGGATTTTTCTTTTTCT 58.692 37.500 0.00 0.00 37.39 2.52
4354 6313 4.152223 CGCCCACATGGATTTTTCTTTTTC 59.848 41.667 0.00 0.00 37.39 2.29
4361 6320 2.159254 CGAATCGCCCACATGGATTTTT 60.159 45.455 0.00 0.00 37.39 1.94
4381 6340 1.312815 CGGTACCCTAGTAACCCTCG 58.687 60.000 6.25 0.00 32.01 4.63
4388 6347 3.520623 GGGAAGCGGTACCCTAGTA 57.479 57.895 6.25 0.00 42.56 1.82
4400 6359 0.034960 GAGAAGTGGGGAAGGGAAGC 60.035 60.000 0.00 0.00 0.00 3.86
4402 6361 0.196118 AGGAGAAGTGGGGAAGGGAA 59.804 55.000 0.00 0.00 0.00 3.97
4445 6404 2.031163 GGCCGCGCAGATTATCCT 59.969 61.111 8.75 0.00 0.00 3.24
4465 6424 1.431488 CCTCACCGCAACCATCATCG 61.431 60.000 0.00 0.00 0.00 3.84
4504 6463 0.981277 ACCCATAGTCCCTTCACCCG 60.981 60.000 0.00 0.00 0.00 5.28
4518 6477 1.272480 GGTTCTTGCCTTGGTACCCAT 60.272 52.381 10.07 0.00 31.53 4.00
4540 6499 0.247460 CAATGTCGCCTCTCCACTCA 59.753 55.000 0.00 0.00 0.00 3.41
4554 6513 1.531423 CCTTGCTGCTCAGACAATGT 58.469 50.000 0.00 0.00 0.00 2.71
4567 6526 1.134946 GCATCAATAAACGCCCTTGCT 59.865 47.619 0.00 0.00 34.43 3.91
4578 6537 1.885388 CGCCGGACCGCATCAATAA 60.885 57.895 5.05 0.00 0.00 1.40
4607 6566 2.972505 GGACCACACACCGCACTG 60.973 66.667 0.00 0.00 0.00 3.66
4686 6645 4.697756 CGCCGGGAAGTGAGCCAA 62.698 66.667 2.18 0.00 0.00 4.52
4688 6647 3.682292 ATTCGCCGGGAAGTGAGCC 62.682 63.158 2.18 0.00 38.24 4.70
4689 6648 2.125106 ATTCGCCGGGAAGTGAGC 60.125 61.111 2.18 0.00 38.24 4.26
4690 6649 0.744874 TAGATTCGCCGGGAAGTGAG 59.255 55.000 2.18 0.00 38.24 3.51
4691 6650 0.744874 CTAGATTCGCCGGGAAGTGA 59.255 55.000 2.18 0.00 38.24 3.41
4692 6651 0.460311 ACTAGATTCGCCGGGAAGTG 59.540 55.000 2.18 0.45 38.24 3.16
4704 6663 4.081087 ACCATTAGTGCCAACGACTAGATT 60.081 41.667 0.00 0.00 0.00 2.40
4711 6670 0.319083 ACGACCATTAGTGCCAACGA 59.681 50.000 0.00 0.00 0.00 3.85
4755 6714 3.056749 CGATACTCATACCACCTTAGCCC 60.057 52.174 0.00 0.00 0.00 5.19
4761 6720 3.117625 TGGTCTCGATACTCATACCACCT 60.118 47.826 0.64 0.00 32.24 4.00
4831 6790 1.734655 ATGAGGAGGACAACACCAGT 58.265 50.000 0.00 0.00 0.00 4.00
4916 6875 4.373116 ACGACGCCACCGCTCAAT 62.373 61.111 0.00 0.00 38.22 2.57
4954 6913 2.759191 CACCTATCACGCACATGCTAT 58.241 47.619 1.82 0.00 39.32 2.97
4964 6923 2.151202 ACAAAGTTGGCACCTATCACG 58.849 47.619 0.00 0.00 0.00 4.35
4970 6929 2.689983 CTCTCAAACAAAGTTGGCACCT 59.310 45.455 0.00 0.00 0.00 4.00
4993 6952 2.644992 GGCTCAACACCAAAGCCG 59.355 61.111 0.00 0.00 45.55 5.52


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

AutoCloner maintained by Alex Coulton.