Multiple sequence alignment - TraesCS7A01G202400

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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 TraesCS7A01G202400 chr7A 100.000 1821 0 0 1 1821 164183122 164181302 0.000000e+00 3363.0
1 TraesCS7A01G202400 chr7A 86.783 1203 89 29 584 1768 164394420 164393270 0.000000e+00 1277.0
2 TraesCS7A01G202400 chr7A 100.000 639 0 0 2126 2764 164180997 164180359 0.000000e+00 1181.0
3 TraesCS7A01G202400 chr7A 77.778 270 50 4 187 450 125929701 125929436 1.020000e-34 158.0
4 TraesCS7A01G202400 chr7A 98.810 84 1 0 14 97 152877873 152877790 1.710000e-32 150.0
5 TraesCS7A01G202400 chr7A 79.399 233 32 11 819 1047 163991289 163991069 1.710000e-32 150.0
6 TraesCS7A01G202400 chr7A 75.649 308 46 19 757 1047 163948768 163948473 2.890000e-25 126.0
7 TraesCS7A01G202400 chr7D 89.260 1257 97 24 582 1821 163216028 163214793 0.000000e+00 1539.0
8 TraesCS7A01G202400 chr7D 87.823 1240 100 19 597 1819 163251654 163250449 0.000000e+00 1406.0
9 TraesCS7A01G202400 chr7D 95.462 639 25 3 2126 2763 163214722 163214087 0.000000e+00 1016.0
10 TraesCS7A01G202400 chr7D 84.841 818 106 11 1001 1809 163199875 163199067 0.000000e+00 808.0
11 TraesCS7A01G202400 chr7D 88.889 90 8 1 14 101 635385890 635385979 2.910000e-20 110.0
12 TraesCS7A01G202400 chr7B 82.521 1785 193 56 93 1819 125364135 125362412 0.000000e+00 1458.0
13 TraesCS7A01G202400 chr7B 92.290 882 57 8 942 1819 125356068 125355194 0.000000e+00 1242.0
14 TraesCS7A01G202400 chr7B 90.000 970 67 16 856 1819 125244379 125243434 0.000000e+00 1227.0
15 TraesCS7A01G202400 chr7B 92.496 653 39 2 1170 1819 125313255 125312610 0.000000e+00 926.0
16 TraesCS7A01G202400 chr7B 92.343 653 40 2 1170 1819 125280443 125279798 0.000000e+00 920.0
17 TraesCS7A01G202400 chr7B 84.790 927 117 17 901 1811 125186655 125185737 0.000000e+00 909.0
18 TraesCS7A01G202400 chr7B 83.299 958 123 21 864 1809 125192025 125191093 0.000000e+00 848.0
19 TraesCS7A01G202400 chr7B 85.885 751 63 28 572 1303 125208208 125207482 0.000000e+00 760.0
20 TraesCS7A01G202400 chr7B 91.667 552 36 2 1271 1819 125221189 125220645 0.000000e+00 756.0
21 TraesCS7A01G202400 chr7B 87.810 484 52 3 2215 2697 125362314 125361837 6.680000e-156 560.0
22 TraesCS7A01G202400 chr7B 85.366 287 28 11 572 848 125244797 125244515 4.510000e-73 285.0
23 TraesCS7A01G202400 chr7B 85.366 287 28 11 572 848 125280852 125280570 4.510000e-73 285.0
24 TraesCS7A01G202400 chr7B 85.366 287 28 11 572 848 125314733 125314451 4.510000e-73 285.0
25 TraesCS7A01G202400 chr7B 82.059 340 30 15 612 923 125230961 125230625 7.590000e-66 261.0
26 TraesCS7A01G202400 chr7B 81.765 340 31 15 612 923 125267137 125266801 3.530000e-64 255.0
27 TraesCS7A01G202400 chr7B 90.265 113 9 2 2586 2696 125203852 125203740 2.220000e-31 147.0
28 TraesCS7A01G202400 chr7B 96.386 83 1 2 17 98 351015453 351015372 4.800000e-28 135.0
29 TraesCS7A01G202400 chr7B 93.151 73 5 0 2126 2198 125204239 125204167 1.050000e-19 108.0
30 TraesCS7A01G202400 chr7B 100.000 49 0 0 14 62 729021051 729021099 1.050000e-14 91.6
31 TraesCS7A01G202400 chrUn 85.366 287 28 11 572 848 332928290 332928008 4.510000e-73 285.0
32 TraesCS7A01G202400 chr2A 79.399 233 44 3 220 450 703565123 703564893 7.920000e-36 161.0
33 TraesCS7A01G202400 chr5A 81.383 188 33 2 264 450 301364337 301364523 4.770000e-33 152.0
34 TraesCS7A01G202400 chr5A 80.000 190 32 6 264 450 641588670 641588856 4.800000e-28 135.0
35 TraesCS7A01G202400 chr5A 78.431 204 42 2 283 484 590673414 590673617 6.210000e-27 132.0
36 TraesCS7A01G202400 chr5A 78.140 215 39 8 240 450 315263430 315263640 2.230000e-26 130.0
37 TraesCS7A01G202400 chr5A 86.316 95 6 7 14 101 10015754 10015848 2.270000e-16 97.1
38 TraesCS7A01G202400 chr3B 97.561 82 0 1 15 96 794566796 794566717 3.710000e-29 139.0
39 TraesCS7A01G202400 chr3B 98.039 51 1 0 16 66 794979306 794979256 3.790000e-14 89.8
40 TraesCS7A01G202400 chr6B 80.105 191 31 6 264 450 581872419 581872232 4.800000e-28 135.0
41 TraesCS7A01G202400 chr1A 77.632 228 46 4 187 411 11666373 11666598 1.730000e-27 134.0
42 TraesCS7A01G202400 chr1A 90.909 88 6 1 17 102 53355478 53355391 1.740000e-22 117.0
43 TraesCS7A01G202400 chr1D 75.451 277 62 5 177 450 416141307 416141580 2.230000e-26 130.0
44 TraesCS7A01G202400 chr3D 98.077 52 1 0 14 65 38220593 38220542 1.050000e-14 91.6


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 TraesCS7A01G202400 chr7A 164180359 164183122 2763 True 2272.000000 3363 100.0000 1 2764 2 chr7A.!!$R6 2763
1 TraesCS7A01G202400 chr7A 164393270 164394420 1150 True 1277.000000 1277 86.7830 584 1768 1 chr7A.!!$R5 1184
2 TraesCS7A01G202400 chr7D 163250449 163251654 1205 True 1406.000000 1406 87.8230 597 1819 1 chr7D.!!$R2 1222
3 TraesCS7A01G202400 chr7D 163214087 163216028 1941 True 1277.500000 1539 92.3610 582 2763 2 chr7D.!!$R3 2181
4 TraesCS7A01G202400 chr7D 163199067 163199875 808 True 808.000000 808 84.8410 1001 1809 1 chr7D.!!$R1 808
5 TraesCS7A01G202400 chr7B 125355194 125356068 874 True 1242.000000 1242 92.2900 942 1819 1 chr7B.!!$R6 877
6 TraesCS7A01G202400 chr7B 125361837 125364135 2298 True 1009.000000 1458 85.1655 93 2697 2 chr7B.!!$R12 2604
7 TraesCS7A01G202400 chr7B 125185737 125186655 918 True 909.000000 909 84.7900 901 1811 1 chr7B.!!$R1 910
8 TraesCS7A01G202400 chr7B 125191093 125192025 932 True 848.000000 848 83.2990 864 1809 1 chr7B.!!$R2 945
9 TraesCS7A01G202400 chr7B 125220645 125221189 544 True 756.000000 756 91.6670 1271 1819 1 chr7B.!!$R3 548
10 TraesCS7A01G202400 chr7B 125243434 125244797 1363 True 756.000000 1227 87.6830 572 1819 2 chr7B.!!$R9 1247
11 TraesCS7A01G202400 chr7B 125312610 125314733 2123 True 605.500000 926 88.9310 572 1819 2 chr7B.!!$R11 1247
12 TraesCS7A01G202400 chr7B 125279798 125280852 1054 True 602.500000 920 88.8545 572 1819 2 chr7B.!!$R10 1247
13 TraesCS7A01G202400 chr7B 125203740 125208208 4468 True 338.333333 760 89.7670 572 2696 3 chr7B.!!$R8 2124

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
577 588 0.179137 TAGCTCATTGCCGTCGTCAG 60.179 55.0 0.0 0.0 44.23 3.51 F
1463 5026 0.180171 CGGGGGTGTCTATCATGCAA 59.820 55.0 0.0 0.0 0.00 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1544 5107 0.034059 CATAGATGGCGTCCTCCACC 59.966 60.0 2.37 0.0 39.25 4.61 R
2492 6121 0.255890 GGAGCCTGAAGGTATGCCAA 59.744 55.0 1.54 0.0 37.57 4.52 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
30 31 5.547181 CGTAAGGGAATTTCTTGGAAGTC 57.453 43.478 0.00 0.00 0.00 3.01
31 32 5.246307 CGTAAGGGAATTTCTTGGAAGTCT 58.754 41.667 0.00 0.00 0.00 3.24
32 33 6.403878 CGTAAGGGAATTTCTTGGAAGTCTA 58.596 40.000 0.00 0.00 0.00 2.59
33 34 6.535508 CGTAAGGGAATTTCTTGGAAGTCTAG 59.464 42.308 0.00 0.00 0.00 2.43
34 35 6.704056 AAGGGAATTTCTTGGAAGTCTAGA 57.296 37.500 0.00 0.00 0.00 2.43
35 36 6.704056 AGGGAATTTCTTGGAAGTCTAGAA 57.296 37.500 0.00 0.00 35.90 2.10
36 37 7.277405 AGGGAATTTCTTGGAAGTCTAGAAT 57.723 36.000 0.00 0.00 37.16 2.40
37 38 7.703755 AGGGAATTTCTTGGAAGTCTAGAATT 58.296 34.615 4.86 4.86 37.16 2.17
38 39 8.836735 AGGGAATTTCTTGGAAGTCTAGAATTA 58.163 33.333 5.23 0.00 37.16 1.40
39 40 9.114952 GGGAATTTCTTGGAAGTCTAGAATTAG 57.885 37.037 5.23 0.15 37.16 1.73
40 41 9.674068 GGAATTTCTTGGAAGTCTAGAATTAGT 57.326 33.333 5.23 0.00 37.16 2.24
139 140 2.362077 GCACCGATAAATTTGCCCTCAT 59.638 45.455 0.00 0.00 0.00 2.90
141 142 3.631686 CACCGATAAATTTGCCCTCATGA 59.368 43.478 0.00 0.00 0.00 3.07
144 145 5.473504 ACCGATAAATTTGCCCTCATGATAC 59.526 40.000 0.00 0.00 0.00 2.24
146 147 6.878923 CCGATAAATTTGCCCTCATGATACTA 59.121 38.462 0.00 0.00 0.00 1.82
148 149 8.950210 CGATAAATTTGCCCTCATGATACTATT 58.050 33.333 0.00 0.00 0.00 1.73
154 155 7.559335 TTGCCCTCATGATACTATTAGATGT 57.441 36.000 0.00 0.00 0.00 3.06
155 156 6.939622 TGCCCTCATGATACTATTAGATGTG 58.060 40.000 0.00 0.00 0.00 3.21
157 158 7.673926 TGCCCTCATGATACTATTAGATGTGTA 59.326 37.037 0.00 0.00 0.00 2.90
158 159 8.700051 GCCCTCATGATACTATTAGATGTGTAT 58.300 37.037 0.00 0.00 0.00 2.29
169 170 9.481340 ACTATTAGATGTGTATGTGTATGCAAG 57.519 33.333 0.00 0.00 30.51 4.01
170 171 9.481340 CTATTAGATGTGTATGTGTATGCAAGT 57.519 33.333 0.00 0.00 30.51 3.16
171 172 7.770801 TTAGATGTGTATGTGTATGCAAGTC 57.229 36.000 0.00 0.00 30.51 3.01
172 173 5.733676 AGATGTGTATGTGTATGCAAGTCA 58.266 37.500 0.00 0.00 30.51 3.41
173 174 5.814188 AGATGTGTATGTGTATGCAAGTCAG 59.186 40.000 0.00 0.00 30.51 3.51
174 175 4.893608 TGTGTATGTGTATGCAAGTCAGT 58.106 39.130 0.00 0.00 30.51 3.41
175 176 5.304778 TGTGTATGTGTATGCAAGTCAGTT 58.695 37.500 0.00 0.00 30.51 3.16
176 177 6.459923 TGTGTATGTGTATGCAAGTCAGTTA 58.540 36.000 0.00 0.00 30.51 2.24
177 178 6.367695 TGTGTATGTGTATGCAAGTCAGTTAC 59.632 38.462 0.00 0.00 30.51 2.50
185 186 6.652900 TGTATGCAAGTCAGTTACAAATAGCA 59.347 34.615 0.00 0.00 0.00 3.49
189 190 5.629435 GCAAGTCAGTTACAAATAGCAAACC 59.371 40.000 0.00 0.00 0.00 3.27
192 193 6.735130 AGTCAGTTACAAATAGCAAACCAAC 58.265 36.000 0.00 0.00 0.00 3.77
195 196 8.293867 GTCAGTTACAAATAGCAAACCAACATA 58.706 33.333 0.00 0.00 0.00 2.29
217 218 2.574369 TGGTTGGACGGTTATGAGGATT 59.426 45.455 0.00 0.00 0.00 3.01
218 219 3.775866 TGGTTGGACGGTTATGAGGATTA 59.224 43.478 0.00 0.00 0.00 1.75
219 220 4.141801 TGGTTGGACGGTTATGAGGATTAG 60.142 45.833 0.00 0.00 0.00 1.73
223 226 6.989155 TGGACGGTTATGAGGATTAGTATT 57.011 37.500 0.00 0.00 0.00 1.89
224 227 6.989659 TGGACGGTTATGAGGATTAGTATTC 58.010 40.000 0.00 0.00 0.00 1.75
226 229 6.210984 GGACGGTTATGAGGATTAGTATTCCT 59.789 42.308 12.47 12.47 46.41 3.36
228 231 8.350852 ACGGTTATGAGGATTAGTATTCCTAG 57.649 38.462 12.58 3.52 43.75 3.02
231 234 7.364851 GGTTATGAGGATTAGTATTCCTAGCCC 60.365 44.444 12.58 6.38 43.75 5.19
233 236 5.665701 TGAGGATTAGTATTCCTAGCCCAT 58.334 41.667 12.58 0.00 43.75 4.00
238 241 7.345914 AGGATTAGTATTCCTAGCCCATCATAC 59.654 40.741 11.19 0.00 41.89 2.39
244 247 5.708736 TTCCTAGCCCATCATACTTCAAA 57.291 39.130 0.00 0.00 0.00 2.69
246 249 5.869579 TCCTAGCCCATCATACTTCAAATC 58.130 41.667 0.00 0.00 0.00 2.17
247 250 5.006386 CCTAGCCCATCATACTTCAAATCC 58.994 45.833 0.00 0.00 0.00 3.01
250 253 6.266131 AGCCCATCATACTTCAAATCCTAA 57.734 37.500 0.00 0.00 0.00 2.69
252 255 6.547510 AGCCCATCATACTTCAAATCCTAAAC 59.452 38.462 0.00 0.00 0.00 2.01
255 258 9.627123 CCCATCATACTTCAAATCCTAAACTTA 57.373 33.333 0.00 0.00 0.00 2.24
259 262 9.457436 TCATACTTCAAATCCTAAACTTAACCC 57.543 33.333 0.00 0.00 0.00 4.11
260 263 8.683615 CATACTTCAAATCCTAAACTTAACCCC 58.316 37.037 0.00 0.00 0.00 4.95
262 265 5.245584 TCAAATCCTAAACTTAACCCCGT 57.754 39.130 0.00 0.00 0.00 5.28
269 272 1.232621 AACTTAACCCCGTTGCTCGC 61.233 55.000 0.00 0.00 38.35 5.03
308 311 3.729526 AAGTTCTTTCGATGATGTGCG 57.270 42.857 0.00 0.00 0.00 5.34
310 313 2.413112 AGTTCTTTCGATGATGTGCGTG 59.587 45.455 0.00 0.00 0.00 5.34
311 314 2.078849 TCTTTCGATGATGTGCGTGT 57.921 45.000 0.00 0.00 0.00 4.49
317 320 1.469079 CGATGATGTGCGTGTAGTGGA 60.469 52.381 0.00 0.00 0.00 4.02
319 322 2.078849 TGATGTGCGTGTAGTGGAAG 57.921 50.000 0.00 0.00 0.00 3.46
320 323 1.337728 TGATGTGCGTGTAGTGGAAGG 60.338 52.381 0.00 0.00 0.00 3.46
325 328 0.601558 GCGTGTAGTGGAAGGAGACA 59.398 55.000 0.00 0.00 0.00 3.41
353 357 5.502153 GTTATCTACGAGGTGTCTGTGAT 57.498 43.478 0.00 0.00 0.00 3.06
361 365 1.964223 AGGTGTCTGTGATGACTTCGT 59.036 47.619 0.00 0.00 37.79 3.85
362 366 2.365617 AGGTGTCTGTGATGACTTCGTT 59.634 45.455 0.00 0.00 37.79 3.85
368 372 7.027760 GTGTCTGTGATGACTTCGTTAATCTA 58.972 38.462 0.00 0.00 37.79 1.98
371 375 8.587950 GTCTGTGATGACTTCGTTAATCTAAAG 58.412 37.037 0.00 0.00 34.39 1.85
373 377 9.140286 CTGTGATGACTTCGTTAATCTAAAGAA 57.860 33.333 0.00 0.00 35.45 2.52
382 386 5.454554 TCGTTAATCTAAAGAAGATGCGTCG 59.545 40.000 0.00 0.00 44.56 5.12
388 392 0.459237 AAGAAGATGCGTCGGCTCAG 60.459 55.000 0.00 0.00 40.82 3.35
395 399 2.401592 CGTCGGCTCAGTCTCTCG 59.598 66.667 0.00 0.00 0.00 4.04
396 400 2.101233 CGTCGGCTCAGTCTCTCGA 61.101 63.158 0.00 0.00 0.00 4.04
409 413 2.034053 GTCTCTCGAAGGTGCTCATAGG 59.966 54.545 0.00 0.00 0.00 2.57
411 415 1.063942 TCTCGAAGGTGCTCATAGGGA 60.064 52.381 0.00 0.00 0.00 4.20
416 420 3.511477 GAAGGTGCTCATAGGGATAGGA 58.489 50.000 0.00 0.00 0.00 2.94
418 422 3.448934 AGGTGCTCATAGGGATAGGATG 58.551 50.000 0.00 0.00 0.00 3.51
421 425 4.160626 GGTGCTCATAGGGATAGGATGTAC 59.839 50.000 0.00 0.00 0.00 2.90
423 427 5.423610 GTGCTCATAGGGATAGGATGTACAT 59.576 44.000 8.43 8.43 0.00 2.29
424 428 5.423290 TGCTCATAGGGATAGGATGTACATG 59.577 44.000 14.43 0.00 0.00 3.21
425 429 5.423610 GCTCATAGGGATAGGATGTACATGT 59.576 44.000 14.43 2.69 0.00 3.21
426 430 6.629068 GCTCATAGGGATAGGATGTACATGTG 60.629 46.154 14.43 0.00 0.00 3.21
427 431 6.322931 TCATAGGGATAGGATGTACATGTGT 58.677 40.000 14.43 0.00 0.00 3.72
428 432 7.475299 TCATAGGGATAGGATGTACATGTGTA 58.525 38.462 14.43 2.04 0.00 2.90
472 483 0.992072 CGTCTGCGTCTGTATTGTGG 59.008 55.000 0.00 0.00 0.00 4.17
475 486 3.581755 GTCTGCGTCTGTATTGTGGTAA 58.418 45.455 0.00 0.00 0.00 2.85
476 487 3.612860 GTCTGCGTCTGTATTGTGGTAAG 59.387 47.826 0.00 0.00 0.00 2.34
539 550 7.935520 TCTAGTATATGCTCACTTGAACAGAG 58.064 38.462 0.00 0.00 0.00 3.35
543 554 6.734104 ATATGCTCACTTGAACAGAGAAAC 57.266 37.500 0.00 0.00 0.00 2.78
551 562 6.376864 TCACTTGAACAGAGAAACAATTTCCA 59.623 34.615 0.00 0.00 40.54 3.53
554 565 8.260114 ACTTGAACAGAGAAACAATTTCCATTT 58.740 29.630 0.00 0.00 40.54 2.32
555 566 9.101655 CTTGAACAGAGAAACAATTTCCATTTT 57.898 29.630 0.00 0.00 40.54 1.82
556 567 9.447157 TTGAACAGAGAAACAATTTCCATTTTT 57.553 25.926 0.00 0.00 40.54 1.94
576 587 0.245266 TTAGCTCATTGCCGTCGTCA 59.755 50.000 0.00 0.00 44.23 4.35
577 588 0.179137 TAGCTCATTGCCGTCGTCAG 60.179 55.000 0.00 0.00 44.23 3.51
590 624 0.963856 TCGTCAGGGTCACGCAGTAT 60.964 55.000 0.00 0.00 41.61 2.12
608 642 5.100259 CAGTATATTTATCACCGCGTAGGG 58.900 45.833 4.92 0.00 46.96 3.53
617 656 2.897207 CGCGTAGGGGGTCAATCA 59.103 61.111 0.00 0.00 36.55 2.57
627 666 2.369394 GGGGTCAATCAATCGCTTTCT 58.631 47.619 0.00 0.00 0.00 2.52
630 669 2.030946 GGTCAATCAATCGCTTTCTCCG 59.969 50.000 0.00 0.00 0.00 4.63
632 671 3.125316 GTCAATCAATCGCTTTCTCCGTT 59.875 43.478 0.00 0.00 0.00 4.44
642 681 3.187637 CGCTTTCTCCGTTTGAATTACCA 59.812 43.478 0.00 0.00 0.00 3.25
698 739 0.250945 TAATTGCCGCCTGTTCACCA 60.251 50.000 0.00 0.00 0.00 4.17
741 784 5.291128 CACCTCGTATGCACTAGTAAAAAGG 59.709 44.000 0.00 0.00 0.00 3.11
744 787 6.761714 CCTCGTATGCACTAGTAAAAAGGAAT 59.238 38.462 0.00 0.00 0.00 3.01
772 816 4.466567 TGCTAATCACGTTGAACAAGTG 57.533 40.909 0.00 0.00 37.24 3.16
788 833 1.945387 AGTGAAGCTGCATGTATCCG 58.055 50.000 0.00 0.00 0.00 4.18
790 835 2.093500 AGTGAAGCTGCATGTATCCGAA 60.093 45.455 0.00 0.00 0.00 4.30
816 862 4.832248 TCCTCTGCGTGTAAAATCAAGAT 58.168 39.130 0.00 0.00 0.00 2.40
817 863 5.972935 TCCTCTGCGTGTAAAATCAAGATA 58.027 37.500 0.00 0.00 0.00 1.98
923 1111 3.136443 TGATTACACCCACCATCTCATCC 59.864 47.826 0.00 0.00 0.00 3.51
924 1112 1.119684 TACACCCACCATCTCATCCG 58.880 55.000 0.00 0.00 0.00 4.18
926 1114 2.111878 CCCACCATCTCATCCGCC 59.888 66.667 0.00 0.00 0.00 6.13
934 1122 0.467384 ATCTCATCCGCCCAAGTCTG 59.533 55.000 0.00 0.00 0.00 3.51
981 1169 6.265196 TCAAATAAAATCAGAAGCCACACACT 59.735 34.615 0.00 0.00 0.00 3.55
989 1178 6.599356 TCAGAAGCCACACACTTAGTATAA 57.401 37.500 0.00 0.00 0.00 0.98
997 1188 9.198475 AGCCACACACTTAGTATAAAGTAGTAT 57.802 33.333 0.00 0.00 37.61 2.12
1034 1227 4.142271 CGCTCTCTCTTGGATTAGTGTCTT 60.142 45.833 0.00 0.00 0.00 3.01
1050 1243 4.813697 AGTGTCTTTCTGCTTGTCTTCTTC 59.186 41.667 0.00 0.00 0.00 2.87
1067 1260 3.853330 CGCGTCTTGGTCATGCGG 61.853 66.667 0.00 0.00 44.00 5.69
1116 1309 2.836360 GCCGACCCGACCTATGGA 60.836 66.667 0.00 0.00 0.00 3.41
1140 1333 3.429141 TCGGTGAGGCTCGACGAC 61.429 66.667 23.51 10.94 0.00 4.34
1200 2125 1.874019 CGCACGCTACAGCTTCGAT 60.874 57.895 0.00 0.00 39.32 3.59
1242 2167 3.764466 CTCGCCTCCGACAAGCCT 61.764 66.667 0.00 0.00 38.82 4.58
1300 2225 5.675538 AGATCAGGATGGCAGTAAGTTAAC 58.324 41.667 0.00 0.00 36.16 2.01
1303 2228 6.222038 TCAGGATGGCAGTAAGTTAACTAG 57.778 41.667 8.92 0.97 36.16 2.57
1304 2229 4.811557 CAGGATGGCAGTAAGTTAACTAGC 59.188 45.833 8.92 10.60 0.00 3.42
1393 4956 0.604578 TTGCAGGGGTACGACTACAC 59.395 55.000 0.00 0.00 0.00 2.90
1403 4966 2.488820 GACTACACCTCCGGCGTC 59.511 66.667 6.01 0.00 0.00 5.19
1418 4981 2.266055 GTCTGGCAGTTCGAGGGG 59.734 66.667 15.27 0.00 0.00 4.79
1442 5005 4.682334 TACGTCCCCTCCGGCACA 62.682 66.667 0.00 0.00 0.00 4.57
1463 5026 0.180171 CGGGGGTGTCTATCATGCAA 59.820 55.000 0.00 0.00 0.00 4.08
1466 5029 2.565841 GGGGTGTCTATCATGCAAGTC 58.434 52.381 0.00 0.00 0.00 3.01
1544 5107 1.226603 GTACTACGACCGGCAGCTG 60.227 63.158 10.11 10.11 0.00 4.24
2260 5888 7.756722 CCATAGTTTCAATGAAAACAAGCTAGG 59.243 37.037 10.27 8.57 40.77 3.02
2361 5990 7.914427 TTATAGACAACCACCTCATGATAGT 57.086 36.000 0.00 0.00 0.00 2.12
2362 5991 9.429109 TTTATAGACAACCACCTCATGATAGTA 57.571 33.333 0.00 0.00 0.00 1.82
2372 6001 6.323996 CCACCTCATGATAGTAGTGGTAAGAA 59.676 42.308 15.50 0.00 39.91 2.52
2454 6083 0.473755 CATATGTGCCTAGGGGTGCA 59.526 55.000 11.72 0.00 34.54 4.57
2492 6121 0.807667 CAGACGCGCTAGCCTGATTT 60.808 55.000 5.73 0.00 41.18 2.17
2493 6122 0.108138 AGACGCGCTAGCCTGATTTT 60.108 50.000 5.73 0.00 41.18 1.82
2586 6215 1.860641 TTACTCGGGAATCCTGCTCA 58.139 50.000 2.50 0.00 0.00 4.26
2638 6267 2.686572 GGCTTTCCCCATACCCCGT 61.687 63.158 0.00 0.00 0.00 5.28
2663 6292 2.047769 TAAAGTAGACCAAGGCCCCA 57.952 50.000 0.00 0.00 0.00 4.96
2711 6340 4.295051 CACAACTTGGACAATTAAACCCG 58.705 43.478 0.00 0.00 0.00 5.28
2731 6360 3.565902 CCGTGACTATCTAGTGCATCTCA 59.434 47.826 0.00 0.00 36.50 3.27
2743 6372 2.164624 GTGCATCTCACCTAGTTCGTCT 59.835 50.000 0.00 0.00 39.79 4.18
2755 6384 5.163405 ACCTAGTTCGTCTACCATAGTCGTA 60.163 44.000 3.18 0.00 38.25 3.43
2763 6392 2.846039 ACCATAGTCGTAGAGTTGCG 57.154 50.000 0.00 0.00 42.19 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.332828 ACTTCCAAGAAATTCCCTTACGG 58.667 43.478 0.00 0.00 0.00 4.02
8 9 5.246307 AGACTTCCAAGAAATTCCCTTACG 58.754 41.667 0.00 0.00 0.00 3.18
9 10 7.621796 TCTAGACTTCCAAGAAATTCCCTTAC 58.378 38.462 0.00 0.00 0.00 2.34
10 11 7.808279 TCTAGACTTCCAAGAAATTCCCTTA 57.192 36.000 0.00 0.00 0.00 2.69
11 12 6.704056 TCTAGACTTCCAAGAAATTCCCTT 57.296 37.500 0.00 0.00 0.00 3.95
12 13 6.704056 TTCTAGACTTCCAAGAAATTCCCT 57.296 37.500 0.00 0.00 0.00 4.20
13 14 7.946381 AATTCTAGACTTCCAAGAAATTCCC 57.054 36.000 0.00 0.00 33.26 3.97
14 15 9.674068 ACTAATTCTAGACTTCCAAGAAATTCC 57.326 33.333 0.00 0.00 33.26 3.01
92 93 9.025041 CCCACACATACACATCTAATCTATCTA 57.975 37.037 0.00 0.00 0.00 1.98
93 94 7.526192 GCCCACACATACACATCTAATCTATCT 60.526 40.741 0.00 0.00 0.00 1.98
94 95 6.591834 GCCCACACATACACATCTAATCTATC 59.408 42.308 0.00 0.00 0.00 2.08
95 96 6.043127 TGCCCACACATACACATCTAATCTAT 59.957 38.462 0.00 0.00 0.00 1.98
96 97 5.365314 TGCCCACACATACACATCTAATCTA 59.635 40.000 0.00 0.00 0.00 1.98
97 98 4.164030 TGCCCACACATACACATCTAATCT 59.836 41.667 0.00 0.00 0.00 2.40
98 99 4.273480 GTGCCCACACATACACATCTAATC 59.727 45.833 0.00 0.00 46.61 1.75
122 123 6.808008 AGTATCATGAGGGCAAATTTATCG 57.192 37.500 0.09 0.00 0.00 2.92
127 128 9.458727 CATCTAATAGTATCATGAGGGCAAATT 57.541 33.333 0.09 0.00 0.00 1.82
144 145 9.481340 ACTTGCATACACATACACATCTAATAG 57.519 33.333 0.00 0.00 0.00 1.73
146 147 7.986889 TGACTTGCATACACATACACATCTAAT 59.013 33.333 0.00 0.00 0.00 1.73
148 149 6.872920 TGACTTGCATACACATACACATCTA 58.127 36.000 0.00 0.00 0.00 1.98
149 150 5.733676 TGACTTGCATACACATACACATCT 58.266 37.500 0.00 0.00 0.00 2.90
150 151 5.582269 ACTGACTTGCATACACATACACATC 59.418 40.000 0.00 0.00 0.00 3.06
151 152 5.491070 ACTGACTTGCATACACATACACAT 58.509 37.500 0.00 0.00 0.00 3.21
152 153 4.893608 ACTGACTTGCATACACATACACA 58.106 39.130 0.00 0.00 0.00 3.72
154 155 6.459923 TGTAACTGACTTGCATACACATACA 58.540 36.000 0.00 0.00 0.00 2.29
155 156 6.961359 TGTAACTGACTTGCATACACATAC 57.039 37.500 0.00 0.00 0.00 2.39
157 158 6.875948 TTTGTAACTGACTTGCATACACAT 57.124 33.333 0.00 0.00 0.00 3.21
158 159 6.875948 ATTTGTAACTGACTTGCATACACA 57.124 33.333 0.00 0.00 0.00 3.72
159 160 6.961554 GCTATTTGTAACTGACTTGCATACAC 59.038 38.462 0.00 0.00 0.00 2.90
160 161 6.652900 TGCTATTTGTAACTGACTTGCATACA 59.347 34.615 0.00 0.00 0.00 2.29
163 164 6.573664 TTGCTATTTGTAACTGACTTGCAT 57.426 33.333 0.00 0.00 0.00 3.96
164 165 6.205784 GTTTGCTATTTGTAACTGACTTGCA 58.794 36.000 0.00 0.00 0.00 4.08
166 167 6.734137 TGGTTTGCTATTTGTAACTGACTTG 58.266 36.000 0.00 0.00 0.00 3.16
167 168 6.952773 TGGTTTGCTATTTGTAACTGACTT 57.047 33.333 0.00 0.00 0.00 3.01
169 170 6.500041 TGTTGGTTTGCTATTTGTAACTGAC 58.500 36.000 0.00 0.00 0.00 3.51
170 171 6.701145 TGTTGGTTTGCTATTTGTAACTGA 57.299 33.333 0.00 0.00 0.00 3.41
171 172 9.075519 CATATGTTGGTTTGCTATTTGTAACTG 57.924 33.333 0.00 0.00 0.00 3.16
172 173 8.250332 CCATATGTTGGTTTGCTATTTGTAACT 58.750 33.333 1.24 0.00 40.99 2.24
173 174 8.406172 CCATATGTTGGTTTGCTATTTGTAAC 57.594 34.615 1.24 0.00 40.99 2.50
192 193 4.065088 CCTCATAACCGTCCAACCATATG 58.935 47.826 0.00 0.00 0.00 1.78
195 196 2.193127 TCCTCATAACCGTCCAACCAT 58.807 47.619 0.00 0.00 0.00 3.55
204 205 7.259161 GCTAGGAATACTAATCCTCATAACCG 58.741 42.308 0.00 0.00 44.01 4.44
210 211 5.087923 TGGGCTAGGAATACTAATCCTCA 57.912 43.478 0.00 0.00 44.01 3.86
217 218 7.246027 TGAAGTATGATGGGCTAGGAATACTA 58.754 38.462 0.00 0.00 32.12 1.82
218 219 6.084738 TGAAGTATGATGGGCTAGGAATACT 58.915 40.000 0.00 0.00 33.41 2.12
219 220 6.360370 TGAAGTATGATGGGCTAGGAATAC 57.640 41.667 0.00 0.00 0.00 1.89
223 226 5.221925 GGATTTGAAGTATGATGGGCTAGGA 60.222 44.000 0.00 0.00 0.00 2.94
224 227 5.006386 GGATTTGAAGTATGATGGGCTAGG 58.994 45.833 0.00 0.00 0.00 3.02
226 229 5.912149 AGGATTTGAAGTATGATGGGCTA 57.088 39.130 0.00 0.00 0.00 3.93
228 231 6.547510 AGTTTAGGATTTGAAGTATGATGGGC 59.452 38.462 0.00 0.00 0.00 5.36
233 236 9.457436 GGGTTAAGTTTAGGATTTGAAGTATGA 57.543 33.333 0.00 0.00 0.00 2.15
238 241 5.708697 ACGGGGTTAAGTTTAGGATTTGAAG 59.291 40.000 0.00 0.00 0.00 3.02
244 247 3.009805 AGCAACGGGGTTAAGTTTAGGAT 59.990 43.478 0.00 0.00 0.00 3.24
246 249 2.745821 GAGCAACGGGGTTAAGTTTAGG 59.254 50.000 0.00 0.00 0.00 2.69
247 250 2.414138 CGAGCAACGGGGTTAAGTTTAG 59.586 50.000 0.00 0.00 38.46 1.85
250 253 1.232621 GCGAGCAACGGGGTTAAGTT 61.233 55.000 5.57 0.00 42.83 2.66
252 255 1.024579 ATGCGAGCAACGGGGTTAAG 61.025 55.000 0.57 0.00 42.83 1.85
255 258 1.460273 AAAATGCGAGCAACGGGGTT 61.460 50.000 0.57 0.00 42.83 4.11
258 261 4.963815 AAAAATGCGAGCAACGGG 57.036 50.000 0.57 0.00 42.83 5.28
296 299 1.469079 CCACTACACGCACATCATCGA 60.469 52.381 0.00 0.00 0.00 3.59
299 302 2.621338 CTTCCACTACACGCACATCAT 58.379 47.619 0.00 0.00 0.00 2.45
300 303 1.337728 CCTTCCACTACACGCACATCA 60.338 52.381 0.00 0.00 0.00 3.07
308 311 4.675671 CGAGAATGTCTCCTTCCACTACAC 60.676 50.000 0.00 0.00 40.34 2.90
310 313 3.444388 ACGAGAATGTCTCCTTCCACTAC 59.556 47.826 0.00 0.00 40.34 2.73
311 314 3.698289 ACGAGAATGTCTCCTTCCACTA 58.302 45.455 0.00 0.00 40.34 2.74
333 336 4.575236 GTCATCACAGACACCTCGTAGATA 59.425 45.833 0.00 0.00 38.40 1.98
335 338 2.747989 GTCATCACAGACACCTCGTAGA 59.252 50.000 0.00 0.00 38.40 2.59
344 348 6.025749 AGATTAACGAAGTCATCACAGACA 57.974 37.500 0.00 0.00 45.00 3.41
353 357 7.009265 CGCATCTTCTTTAGATTAACGAAGTCA 59.991 37.037 12.09 0.00 40.50 3.41
361 365 4.506654 GCCGACGCATCTTCTTTAGATTAA 59.493 41.667 0.00 0.00 41.78 1.40
362 366 4.049186 GCCGACGCATCTTCTTTAGATTA 58.951 43.478 0.00 0.00 41.78 1.75
368 372 0.037326 TGAGCCGACGCATCTTCTTT 60.037 50.000 0.00 0.00 37.52 2.52
371 375 1.142778 GACTGAGCCGACGCATCTTC 61.143 60.000 0.00 0.00 37.52 2.87
373 377 1.999071 GAGACTGAGCCGACGCATCT 61.999 60.000 0.00 0.00 37.52 2.90
378 382 1.636570 TTCGAGAGACTGAGCCGACG 61.637 60.000 0.00 0.00 41.84 5.12
380 384 1.027255 CCTTCGAGAGACTGAGCCGA 61.027 60.000 0.00 0.00 41.84 5.54
382 386 0.172352 CACCTTCGAGAGACTGAGCC 59.828 60.000 0.00 0.00 41.84 4.70
388 392 2.034053 CCTATGAGCACCTTCGAGAGAC 59.966 54.545 0.00 0.00 41.84 3.36
395 399 3.511477 TCCTATCCCTATGAGCACCTTC 58.489 50.000 0.00 0.00 0.00 3.46
396 400 3.637821 TCCTATCCCTATGAGCACCTT 57.362 47.619 0.00 0.00 0.00 3.50
421 425 9.330063 ACACTCATCCTTATTAATGTACACATG 57.670 33.333 0.00 0.00 36.56 3.21
433 437 7.438459 GCAGACGTTTATACACTCATCCTTATT 59.562 37.037 0.00 0.00 0.00 1.40
434 438 6.924060 GCAGACGTTTATACACTCATCCTTAT 59.076 38.462 0.00 0.00 0.00 1.73
435 439 6.270815 GCAGACGTTTATACACTCATCCTTA 58.729 40.000 0.00 0.00 0.00 2.69
436 440 5.109903 GCAGACGTTTATACACTCATCCTT 58.890 41.667 0.00 0.00 0.00 3.36
437 441 4.683832 GCAGACGTTTATACACTCATCCT 58.316 43.478 0.00 0.00 0.00 3.24
456 467 3.845178 TCTTACCACAATACAGACGCAG 58.155 45.455 0.00 0.00 0.00 5.18
457 468 3.945981 TCTTACCACAATACAGACGCA 57.054 42.857 0.00 0.00 0.00 5.24
483 494 9.865321 TTATTCTTAGCACGTATTTCTTACTGT 57.135 29.630 0.00 0.00 0.00 3.55
516 527 7.881775 TCTCTGTTCAAGTGAGCATATACTA 57.118 36.000 0.00 0.00 34.81 1.82
524 535 4.882671 TTGTTTCTCTGTTCAAGTGAGC 57.117 40.909 0.00 0.00 30.37 4.26
527 538 6.563422 TGGAAATTGTTTCTCTGTTCAAGTG 58.437 36.000 2.84 0.00 39.59 3.16
554 565 2.147958 ACGACGGCAATGAGCTAAAAA 58.852 42.857 0.00 0.00 44.79 1.94
555 566 1.730064 GACGACGGCAATGAGCTAAAA 59.270 47.619 0.00 0.00 44.79 1.52
556 567 1.337354 TGACGACGGCAATGAGCTAAA 60.337 47.619 0.00 0.00 44.79 1.85
560 571 2.456119 CCTGACGACGGCAATGAGC 61.456 63.158 4.25 0.00 44.65 4.26
569 580 4.337060 TGCGTGACCCTGACGACG 62.337 66.667 0.00 0.00 39.21 5.12
576 587 5.510861 GGTGATAAATATACTGCGTGACCCT 60.511 44.000 0.00 0.00 0.00 4.34
577 588 4.689345 GGTGATAAATATACTGCGTGACCC 59.311 45.833 0.00 0.00 0.00 4.46
590 624 1.619827 CCCCCTACGCGGTGATAAATA 59.380 52.381 12.47 0.00 0.00 1.40
608 642 2.356069 GGAGAAAGCGATTGATTGACCC 59.644 50.000 0.00 0.00 0.00 4.46
616 655 3.536158 TTCAAACGGAGAAAGCGATTG 57.464 42.857 0.00 0.00 0.00 2.67
617 656 4.766404 AATTCAAACGGAGAAAGCGATT 57.234 36.364 0.00 0.00 0.00 3.34
642 681 5.624292 GCTGTTATTTTCGTGTTACCGATT 58.376 37.500 0.00 0.00 36.62 3.34
698 739 3.134804 GGTGACATTGGCTGACTAGGTAT 59.865 47.826 0.00 0.00 0.00 2.73
751 795 4.123506 TCACTTGTTCAACGTGATTAGCA 58.876 39.130 0.00 0.00 33.15 3.49
752 796 4.725556 TCACTTGTTCAACGTGATTAGC 57.274 40.909 0.00 0.00 33.15 3.09
770 814 1.939974 TCGGATACATGCAGCTTCAC 58.060 50.000 0.00 0.00 0.00 3.18
772 816 2.555199 ACTTCGGATACATGCAGCTTC 58.445 47.619 0.00 0.00 0.00 3.86
850 896 6.170506 GGCGATTTATCACCATATACCTTCA 58.829 40.000 0.00 0.00 0.00 3.02
861 1040 1.202698 AGGCTCTGGCGATTTATCACC 60.203 52.381 0.00 0.00 39.81 4.02
862 1041 2.246719 AGGCTCTGGCGATTTATCAC 57.753 50.000 0.00 0.00 39.81 3.06
926 1114 1.203287 TCTCTCGATGCACAGACTTGG 59.797 52.381 0.00 0.00 0.00 3.61
934 1122 3.127895 AGTTGTACTCTCTCTCGATGCAC 59.872 47.826 0.00 0.00 0.00 4.57
961 1149 6.296026 ACTAAGTGTGTGGCTTCTGATTTTA 58.704 36.000 0.00 0.00 0.00 1.52
989 1178 3.243907 GCGAGGAGCCATTGATACTACTT 60.244 47.826 0.00 0.00 40.81 2.24
997 1188 3.723235 GAGCGCGAGGAGCCATTGA 62.723 63.158 12.10 0.00 44.76 2.57
1034 1227 1.139989 CGCGAAGAAGACAAGCAGAA 58.860 50.000 0.00 0.00 0.00 3.02
1050 1243 3.853330 CCGCATGACCAAGACGCG 61.853 66.667 3.53 3.53 45.25 6.01
1300 2225 7.717568 AGTACAACTAATGATGTGGTAGCTAG 58.282 38.462 0.00 0.00 31.59 3.42
1303 2228 6.019801 CGAAGTACAACTAATGATGTGGTAGC 60.020 42.308 0.00 0.00 31.59 3.58
1304 2229 7.033791 ACGAAGTACAACTAATGATGTGGTAG 58.966 38.462 0.00 0.00 41.94 3.18
1369 4930 1.911269 TCGTACCCCTGCAAGCAGA 60.911 57.895 22.76 0.17 46.30 4.26
1370 4931 1.741770 GTCGTACCCCTGCAAGCAG 60.742 63.158 14.91 14.91 43.26 4.24
1371 4932 0.901114 TAGTCGTACCCCTGCAAGCA 60.901 55.000 0.00 0.00 0.00 3.91
1403 4966 1.218316 GTACCCCTCGAACTGCCAG 59.782 63.158 0.00 0.00 0.00 4.85
1442 5005 0.180406 GCATGATAGACACCCCCGTT 59.820 55.000 0.00 0.00 0.00 4.44
1544 5107 0.034059 CATAGATGGCGTCCTCCACC 59.966 60.000 2.37 0.00 39.25 4.61
1603 5166 0.595567 GTACACGGTGAGCGTTGACA 60.596 55.000 16.29 0.00 0.00 3.58
1668 5231 3.383825 ACACCGAACTTGAAGTAGTGAGT 59.616 43.478 22.06 7.99 31.95 3.41
2260 5888 5.452078 TCATTGAAACAGGTCAATCCAAC 57.548 39.130 0.00 0.00 44.58 3.77
2361 5990 3.508402 TCACGTGATGCTTCTTACCACTA 59.492 43.478 15.76 0.00 0.00 2.74
2362 5991 2.299013 TCACGTGATGCTTCTTACCACT 59.701 45.455 15.76 0.00 0.00 4.00
2372 6001 4.065088 ACTAAACATTGTCACGTGATGCT 58.935 39.130 23.12 4.52 0.00 3.79
2423 6052 7.875041 CCCTAGGCACATATGAATGTATATAGC 59.125 40.741 10.38 0.00 44.70 2.97
2426 6055 6.678411 ACCCCTAGGCACATATGAATGTATAT 59.322 38.462 10.38 0.00 39.88 0.86
2492 6121 0.255890 GGAGCCTGAAGGTATGCCAA 59.744 55.000 1.54 0.00 37.57 4.52
2493 6122 1.635817 GGGAGCCTGAAGGTATGCCA 61.636 60.000 1.54 0.00 35.60 4.92
2586 6215 1.133976 GTAGGACTCAAGGCCATGCAT 60.134 52.381 5.01 0.00 0.00 3.96
2627 6256 4.784177 ACTTTATACAAACGGGGTATGGG 58.216 43.478 6.25 1.04 33.68 4.00
2638 6267 5.503002 GGGCCTTGGTCTACTTTATACAAA 58.497 41.667 0.84 0.00 0.00 2.83
2663 6292 1.306654 TATCAGTTGGCCCTCGGGT 60.307 57.895 0.00 0.00 37.65 5.28
2671 6300 1.672881 GTGGCATGTCTATCAGTTGGC 59.327 52.381 0.00 0.00 0.00 4.52
2703 6332 4.463539 TGCACTAGATAGTCACGGGTTTAA 59.536 41.667 0.00 0.00 33.46 1.52
2711 6340 4.582656 AGGTGAGATGCACTAGATAGTCAC 59.417 45.833 0.00 1.77 46.86 3.67
2731 6360 4.125703 CGACTATGGTAGACGAACTAGGT 58.874 47.826 3.43 0.00 44.50 3.08
2743 6372 3.957671 CGCAACTCTACGACTATGGTA 57.042 47.619 0.00 0.00 0.00 3.25


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

AutoCloner maintained by Alex Coulton.