Multiple sequence alignment - TraesCS4D01G356700

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 TraesCS4D01G356700 chr4D 100.000 5758 0 0 1 5758 505385970 505380213 0.000000e+00 10634.0
1 TraesCS4D01G356700 chr4B 94.760 4981 215 26 809 5758 652236809 652231844 0.000000e+00 7710.0
2 TraesCS4D01G356700 chr4B 95.312 64 3 0 578 641 652248851 652248788 1.020000e-17 102.0
3 TraesCS4D01G356700 chr5A 91.378 2424 149 27 1984 4391 689719271 689716892 0.000000e+00 3264.0
4 TraesCS4D01G356700 chr5A 92.308 1339 74 12 4418 5751 689716914 689715600 0.000000e+00 1875.0
5 TraesCS4D01G356700 chr5A 93.306 971 47 5 863 1815 689720271 689719301 0.000000e+00 1417.0
6 TraesCS4D01G356700 chr5A 85.730 883 72 26 1 862 689724967 689724118 0.000000e+00 883.0
7 TraesCS4D01G356700 chr5A 90.504 516 47 2 1456 1970 689644208 689643694 0.000000e+00 680.0
8 TraesCS4D01G356700 chr5A 85.950 121 15 2 119 238 572159503 572159384 1.680000e-25 128.0
9 TraesCS4D01G356700 chr5A 100.000 31 0 0 2040 2070 689719300 689719270 2.240000e-04 58.4
10 TraesCS4D01G356700 chr6A 78.125 384 64 14 5389 5758 611718012 611717635 5.810000e-55 226.0
11 TraesCS4D01G356700 chr1B 75.309 405 76 16 1009 1398 655067744 655067349 7.670000e-39 172.0
12 TraesCS4D01G356700 chr1B 74.402 418 76 18 1009 1406 654832000 654832406 3.590000e-32 150.0
13 TraesCS4D01G356700 chr2A 89.256 121 11 2 119 238 31880590 31880471 3.590000e-32 150.0
14 TraesCS4D01G356700 chr2A 90.244 41 4 0 1347 1387 197681612 197681572 3.000000e-03 54.7
15 TraesCS4D01G356700 chr4A 89.744 117 11 1 113 228 684280066 684279950 1.290000e-31 148.0
16 TraesCS4D01G356700 chr4A 92.593 81 3 2 6 86 703165631 703165554 4.720000e-21 113.0
17 TraesCS4D01G356700 chr4A 96.970 33 1 0 1032 1064 677675056 677675024 8.060000e-04 56.5
18 TraesCS4D01G356700 chr1A 88.696 115 12 1 113 226 7193310 7193196 7.780000e-29 139.0
19 TraesCS4D01G356700 chr1A 88.034 117 13 1 113 228 31953357 31953241 2.800000e-28 137.0
20 TraesCS4D01G356700 chr7D 87.931 116 13 1 114 228 4906460 4906575 1.010000e-27 135.0
21 TraesCS4D01G356700 chr5D 87.288 118 13 2 119 234 454831896 454831779 3.620000e-27 134.0
22 TraesCS4D01G356700 chr5D 86.777 121 14 2 119 238 455601554 455601435 3.620000e-27 134.0
23 TraesCS4D01G356700 chr5B 85.156 128 16 3 113 238 696730814 696730940 1.680000e-25 128.0
24 TraesCS4D01G356700 chr5B 90.698 86 6 1 1 86 513715845 513715928 4.720000e-21 113.0
25 TraesCS4D01G356700 chr2D 91.860 86 4 2 1 86 484379163 484379081 3.650000e-22 117.0
26 TraesCS4D01G356700 chr3B 91.765 85 3 3 1 85 82825366 82825446 1.310000e-21 115.0
27 TraesCS4D01G356700 chr7A 92.593 81 3 2 6 86 182859367 182859444 4.720000e-21 113.0
28 TraesCS4D01G356700 chr2B 90.805 87 4 3 1 86 473766283 473766200 4.720000e-21 113.0
29 TraesCS4D01G356700 chr6D 90.805 87 3 4 1 86 73502420 73502338 1.700000e-20 111.0
30 TraesCS4D01G356700 chr6D 90.805 87 3 4 1 86 344800313 344800395 1.700000e-20 111.0
31 TraesCS4D01G356700 chr6D 90.805 87 3 4 1 86 344807679 344807761 1.700000e-20 111.0


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 TraesCS4D01G356700 chr4D 505380213 505385970 5757 True 10634.00 10634 100.0000 1 5758 1 chr4D.!!$R1 5757
1 TraesCS4D01G356700 chr4B 652231844 652236809 4965 True 7710.00 7710 94.7600 809 5758 1 chr4B.!!$R1 4949
2 TraesCS4D01G356700 chr5A 689715600 689724967 9367 True 1499.48 3264 92.5444 1 5751 5 chr5A.!!$R3 5750
3 TraesCS4D01G356700 chr5A 689643694 689644208 514 True 680.00 680 90.5040 1456 1970 1 chr5A.!!$R2 514

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
624 657 0.109597 CTCGCACACATCCTTTTGCC 60.110 55.000 0.00 0.0 0.0 4.52 F
837 874 0.110486 AGGTGGACGGCAACAGAAAT 59.890 50.000 0.00 0.0 0.0 2.17 F
2107 6017 0.797579 TAGAGAAACAGGGGGAGGGT 59.202 55.000 0.00 0.0 0.0 4.34 F
2690 6618 0.603569 CACAACTACACTCCGAGCCT 59.396 55.000 0.00 0.0 0.0 4.58 F
3138 7066 0.961019 TTGTGCCCACTGATCTTTGC 59.039 50.000 0.00 0.0 0.0 3.68 F
4159 8094 1.001406 CATCAGATCCCCGGAAGTAGC 59.999 57.143 0.73 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2225 6136 0.521735 GCTTTCCACCTAACGGCTTG 59.478 55.000 0.00 0.0 0.00 4.01 R
2583 6503 3.637432 TCATTTGTGGTCGAATTTGCAC 58.363 40.909 0.00 0.0 0.00 4.57 R
3430 7363 0.322456 TTGGCGAGATGTTCCCAAGG 60.322 55.000 0.00 0.0 33.73 3.61 R
4622 8557 1.263356 AGCGCAACTTAGAGGTACCA 58.737 50.000 15.94 0.0 0.00 3.25 R
4731 8666 1.135286 GCCATTGCAAGTAGGAAGCAC 60.135 52.381 16.86 0.0 38.11 4.40 R
5350 9290 0.614697 GCAGGGGGTTGCCAATACTT 60.615 55.000 0.00 0.0 38.13 2.24 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
19 20 2.992124 TTTGTGACTTGAAGGACCGA 57.008 45.000 0.00 0.00 0.00 4.69
21 22 2.992124 TGTGACTTGAAGGACCGAAA 57.008 45.000 0.00 0.00 0.00 3.46
22 23 3.269538 TGTGACTTGAAGGACCGAAAA 57.730 42.857 0.00 0.00 0.00 2.29
24 25 3.563808 TGTGACTTGAAGGACCGAAAATG 59.436 43.478 0.00 0.00 0.00 2.32
26 27 4.036380 GTGACTTGAAGGACCGAAAATGTT 59.964 41.667 0.00 0.00 0.00 2.71
28 29 5.823570 TGACTTGAAGGACCGAAAATGTTTA 59.176 36.000 0.00 0.00 0.00 2.01
29 30 6.068473 ACTTGAAGGACCGAAAATGTTTAC 57.932 37.500 0.00 0.00 0.00 2.01
30 31 5.009310 ACTTGAAGGACCGAAAATGTTTACC 59.991 40.000 0.00 0.00 0.00 2.85
31 32 3.822167 TGAAGGACCGAAAATGTTTACCC 59.178 43.478 0.00 0.00 0.00 3.69
66 67 5.098663 AGGGACCAAGTCTATACTTTTGGA 58.901 41.667 8.93 0.00 43.60 3.53
71 72 7.317722 ACCAAGTCTATACTTTTGGAGAACT 57.682 36.000 8.93 0.00 43.60 3.01
141 145 7.636326 AGTTTTGGACTAAACGTATCAAGTTG 58.364 34.615 0.00 0.00 41.69 3.16
147 151 6.089150 GGACTAAACGTATCAAGTTGTGAGAC 59.911 42.308 2.11 0.00 43.70 3.36
157 161 3.477210 AGTTGTGAGACTTGAAGGACC 57.523 47.619 0.00 0.00 0.00 4.46
175 179 6.590234 AGGACCAAATGTCTACCAAAAATC 57.410 37.500 0.00 0.00 43.89 2.17
176 180 6.314917 AGGACCAAATGTCTACCAAAAATCT 58.685 36.000 0.00 0.00 43.89 2.40
178 182 7.039714 AGGACCAAATGTCTACCAAAAATCTTC 60.040 37.037 0.00 0.00 43.89 2.87
190 195 6.004574 ACCAAAAATCTTCAGGGACTAAGTC 58.995 40.000 0.00 0.00 36.02 3.01
201 206 7.419711 TCAGGGACTAAGTCTATACTTTTGG 57.580 40.000 0.00 0.00 45.34 3.28
259 283 4.946160 TTGGACCCAACTTATCAGGATT 57.054 40.909 0.00 0.00 0.00 3.01
260 284 4.946160 TGGACCCAACTTATCAGGATTT 57.054 40.909 0.00 0.00 0.00 2.17
261 285 4.599041 TGGACCCAACTTATCAGGATTTG 58.401 43.478 0.00 0.00 0.00 2.32
262 286 4.044065 TGGACCCAACTTATCAGGATTTGT 59.956 41.667 0.00 0.00 0.00 2.83
263 287 4.399303 GGACCCAACTTATCAGGATTTGTG 59.601 45.833 0.00 0.00 0.00 3.33
264 288 4.344104 ACCCAACTTATCAGGATTTGTGG 58.656 43.478 0.00 0.00 0.00 4.17
265 289 3.131046 CCCAACTTATCAGGATTTGTGGC 59.869 47.826 0.00 0.00 0.00 5.01
266 290 3.763360 CCAACTTATCAGGATTTGTGGCA 59.237 43.478 0.00 0.00 0.00 4.92
267 291 4.142315 CCAACTTATCAGGATTTGTGGCAG 60.142 45.833 0.00 0.00 0.00 4.85
268 292 4.307032 ACTTATCAGGATTTGTGGCAGT 57.693 40.909 0.00 0.00 0.00 4.40
269 293 4.012374 ACTTATCAGGATTTGTGGCAGTG 58.988 43.478 0.00 0.00 0.00 3.66
270 294 1.843368 ATCAGGATTTGTGGCAGTGG 58.157 50.000 0.00 0.00 0.00 4.00
271 295 0.251297 TCAGGATTTGTGGCAGTGGG 60.251 55.000 0.00 0.00 0.00 4.61
272 296 1.077265 AGGATTTGTGGCAGTGGGG 59.923 57.895 0.00 0.00 0.00 4.96
273 297 1.076549 GGATTTGTGGCAGTGGGGA 59.923 57.895 0.00 0.00 0.00 4.81
274 298 0.324645 GGATTTGTGGCAGTGGGGAT 60.325 55.000 0.00 0.00 0.00 3.85
275 299 1.106285 GATTTGTGGCAGTGGGGATC 58.894 55.000 0.00 0.00 0.00 3.36
276 300 0.324645 ATTTGTGGCAGTGGGGATCC 60.325 55.000 1.92 1.92 0.00 3.36
277 301 1.434513 TTTGTGGCAGTGGGGATCCT 61.435 55.000 12.58 0.00 0.00 3.24
278 302 0.548926 TTGTGGCAGTGGGGATCCTA 60.549 55.000 12.58 0.00 0.00 2.94
279 303 0.548926 TGTGGCAGTGGGGATCCTAA 60.549 55.000 12.58 0.00 0.00 2.69
280 304 0.623723 GTGGCAGTGGGGATCCTAAA 59.376 55.000 12.58 0.00 0.00 1.85
281 305 1.005450 GTGGCAGTGGGGATCCTAAAA 59.995 52.381 12.58 0.00 0.00 1.52
282 306 1.929494 TGGCAGTGGGGATCCTAAAAT 59.071 47.619 12.58 0.00 0.00 1.82
283 307 3.117663 GTGGCAGTGGGGATCCTAAAATA 60.118 47.826 12.58 0.00 0.00 1.40
284 308 3.529734 TGGCAGTGGGGATCCTAAAATAA 59.470 43.478 12.58 0.00 0.00 1.40
285 309 4.017037 TGGCAGTGGGGATCCTAAAATAAA 60.017 41.667 12.58 0.00 0.00 1.40
286 310 4.959839 GGCAGTGGGGATCCTAAAATAAAA 59.040 41.667 12.58 0.00 0.00 1.52
287 311 5.069119 GGCAGTGGGGATCCTAAAATAAAAG 59.931 44.000 12.58 0.00 0.00 2.27
288 312 5.069119 GCAGTGGGGATCCTAAAATAAAAGG 59.931 44.000 12.58 0.00 0.00 3.11
289 313 6.431722 CAGTGGGGATCCTAAAATAAAAGGA 58.568 40.000 12.58 0.00 45.76 3.36
314 338 3.200605 TGTGGCAGTGGTCTCATCATAAT 59.799 43.478 0.00 0.00 0.00 1.28
318 342 5.072193 TGGCAGTGGTCTCATCATAATGTAT 59.928 40.000 0.00 0.00 34.32 2.29
359 384 4.838904 AAAGGTTGTACTCTATCCACCC 57.161 45.455 0.00 0.00 0.00 4.61
363 388 1.771565 TGTACTCTATCCACCCCACG 58.228 55.000 0.00 0.00 0.00 4.94
374 399 0.802494 CACCCCACGTGTAAATCTGC 59.198 55.000 15.65 0.00 37.73 4.26
380 405 4.201910 CCCCACGTGTAAATCTGCAAATAG 60.202 45.833 15.65 0.00 0.00 1.73
399 424 9.661187 GCAAATAGATGTGATGTATTTTCTCTG 57.339 33.333 0.00 0.00 36.81 3.35
416 448 1.764723 TCTGCTGGCTAGTGCATACAT 59.235 47.619 0.00 0.00 41.91 2.29
484 516 6.691754 AATAATACAACCGCATGACATGAA 57.308 33.333 19.76 0.00 0.00 2.57
487 519 6.691754 AATACAACCGCATGACATGAAATA 57.308 33.333 19.76 2.77 0.00 1.40
545 577 0.458669 CATGCATCCTTGGCCAAGTC 59.541 55.000 37.09 24.57 36.72 3.01
553 585 1.271163 CCTTGGCCAAGTCGGTCTTAA 60.271 52.381 37.09 4.93 41.50 1.85
555 587 2.642154 TGGCCAAGTCGGTCTTAAAA 57.358 45.000 0.61 0.00 41.50 1.52
556 588 3.149005 TGGCCAAGTCGGTCTTAAAAT 57.851 42.857 0.61 0.00 41.50 1.82
557 589 2.817258 TGGCCAAGTCGGTCTTAAAATG 59.183 45.455 0.61 0.00 41.50 2.32
558 590 3.078837 GGCCAAGTCGGTCTTAAAATGA 58.921 45.455 0.00 0.00 35.97 2.57
559 591 3.127030 GGCCAAGTCGGTCTTAAAATGAG 59.873 47.826 0.00 0.00 35.97 2.90
560 592 3.751698 GCCAAGTCGGTCTTAAAATGAGT 59.248 43.478 0.00 0.00 36.97 3.41
561 593 4.933400 GCCAAGTCGGTCTTAAAATGAGTA 59.067 41.667 0.00 0.00 36.97 2.59
562 594 5.063564 GCCAAGTCGGTCTTAAAATGAGTAG 59.936 44.000 0.00 0.00 36.97 2.57
564 596 6.395629 CAAGTCGGTCTTAAAATGAGTAGGA 58.604 40.000 0.00 0.00 34.66 2.94
565 597 6.793505 AGTCGGTCTTAAAATGAGTAGGAT 57.206 37.500 0.00 0.00 0.00 3.24
623 656 0.874390 TCTCGCACACATCCTTTTGC 59.126 50.000 0.00 0.00 0.00 3.68
624 657 0.109597 CTCGCACACATCCTTTTGCC 60.110 55.000 0.00 0.00 0.00 4.52
627 660 1.080569 CACACATCCTTTTGCCGGC 60.081 57.895 22.73 22.73 0.00 6.13
647 680 4.105486 GGCATTATTTTTCCTTGACGAGC 58.895 43.478 0.00 0.00 0.00 5.03
664 697 7.441890 TGACGAGCAACATAAGGAATTTTAA 57.558 32.000 0.00 0.00 0.00 1.52
764 800 7.981102 ATTTTTAGACGAAGCTCCTTTTAGT 57.019 32.000 0.00 0.00 0.00 2.24
791 828 4.385358 AAAATAACCGGGCAAAGCTATG 57.615 40.909 6.32 0.00 0.00 2.23
794 831 0.965363 AACCGGGCAAAGCTATGTGG 60.965 55.000 6.32 0.00 0.00 4.17
837 874 0.110486 AGGTGGACGGCAACAGAAAT 59.890 50.000 0.00 0.00 0.00 2.17
968 4854 4.090588 CGCCGCCCAAACCCTAGA 62.091 66.667 0.00 0.00 0.00 2.43
1408 5294 1.699752 CTTCCCCCTTTGCCCTCAT 59.300 57.895 0.00 0.00 0.00 2.90
1524 5410 3.202706 GAATGGCCGCCGTCTTCC 61.203 66.667 4.10 0.00 0.00 3.46
1644 5530 1.164411 TCAATGAACGAAAGCGCCAT 58.836 45.000 2.29 0.00 42.48 4.40
1749 5645 7.589958 ACAAACCAACCAGTTGATTTATACA 57.410 32.000 12.06 0.00 42.93 2.29
1841 5742 4.019231 GGAGAGAAGGACCTAAACACCATT 60.019 45.833 0.00 0.00 0.00 3.16
1860 5761 6.583912 CCATTAGGTTATAACTCACACACG 57.416 41.667 15.05 0.00 0.00 4.49
1895 5796 3.270027 CGTGTTTGATATTCTCCAGGCA 58.730 45.455 0.00 0.00 0.00 4.75
1913 5814 1.340889 GCACCTGGAAATTTGCAGTCA 59.659 47.619 30.35 3.45 44.06 3.41
1916 5817 2.624838 ACCTGGAAATTTGCAGTCAGTG 59.375 45.455 30.35 20.11 44.06 3.66
2006 5916 1.112113 TGAGCCGAAGATAGGGACAC 58.888 55.000 0.00 0.00 0.00 3.67
2012 5922 1.762957 CGAAGATAGGGACACCATGGT 59.237 52.381 13.00 13.00 40.13 3.55
2024 5934 1.664333 CCATGGTTTGTTGCGGTGC 60.664 57.895 2.57 0.00 0.00 5.01
2107 6017 0.797579 TAGAGAAACAGGGGGAGGGT 59.202 55.000 0.00 0.00 0.00 4.34
2120 6031 2.361070 GGGGAGGGTTTAGAGGGATGTA 60.361 54.545 0.00 0.00 0.00 2.29
2467 6387 6.360370 TCACCTTACTTCAGCAAGAGTAAT 57.640 37.500 6.37 0.00 33.34 1.89
2583 6503 2.480419 AGAACATCTCGCGTTTTCCTTG 59.520 45.455 5.77 0.00 0.00 3.61
2690 6618 0.603569 CACAACTACACTCCGAGCCT 59.396 55.000 0.00 0.00 0.00 4.58
2710 6638 3.535561 CTTAGATGACTTCCGCCACATT 58.464 45.455 0.00 0.00 0.00 2.71
2796 6724 2.837291 GCACACTGCAAACCCCCA 60.837 61.111 0.00 0.00 44.26 4.96
2852 6780 5.295950 AGGTGATCAATTATCTCTTGAGCG 58.704 41.667 0.00 0.00 40.88 5.03
2953 6881 6.030228 GCACTAGCCAACATGAGATTTTAAC 58.970 40.000 0.00 0.00 33.58 2.01
3008 6936 3.388024 TCTTTGGGGACAGAGGAATATCG 59.612 47.826 0.00 0.00 42.60 2.92
3057 6985 7.825331 TTGACAAAGTAAACACCATTGGATA 57.175 32.000 10.37 0.00 0.00 2.59
3083 7011 9.661563 ACACGAATCCAAATAAAGTTGTCTATA 57.338 29.630 0.00 0.00 0.00 1.31
3138 7066 0.961019 TTGTGCCCACTGATCTTTGC 59.039 50.000 0.00 0.00 0.00 3.68
3238 7166 8.078596 GTGAATGAAAGTGATAGTGAAAAGCTT 58.921 33.333 0.00 0.00 0.00 3.74
3332 7262 9.578439 GGAACTATCCATTTCAGAAGAATTTTG 57.422 33.333 0.00 0.00 45.79 2.44
3333 7263 9.578439 GAACTATCCATTTCAGAAGAATTTTGG 57.422 33.333 0.00 0.00 32.89 3.28
3430 7363 8.819643 AGCGTAATATTCTCAAGATAGGTTTC 57.180 34.615 0.00 0.00 0.00 2.78
3435 7368 8.986929 AATATTCTCAAGATAGGTTTCCTTGG 57.013 34.615 0.00 0.00 38.19 3.61
3578 7511 3.776969 AGTCCCTCATTCACTAGATGCAA 59.223 43.478 0.00 0.00 0.00 4.08
3589 7522 8.892723 CATTCACTAGATGCAATTGGTAGTTAA 58.107 33.333 7.72 0.00 0.00 2.01
3698 7631 1.079503 GCTTGCCCTTCTAACACTCG 58.920 55.000 0.00 0.00 0.00 4.18
3720 7653 8.744008 CTCGTCTTAGAGTCAAATTTCTACAA 57.256 34.615 0.00 0.00 33.75 2.41
3743 7676 9.341078 ACAAGTTTCCATGAAGCATTTAAATTT 57.659 25.926 0.00 0.00 0.00 1.82
3829 7762 1.005450 TGCCCAGTAAGAATCCCCAAC 59.995 52.381 0.00 0.00 0.00 3.77
3850 7783 2.598192 CACAAAACACCTCACTTTTGCG 59.402 45.455 3.37 0.00 39.84 4.85
4127 8062 8.704849 TGAATAGGTTTTCATTGGAGAAGAAA 57.295 30.769 0.00 0.00 30.82 2.52
4159 8094 1.001406 CATCAGATCCCCGGAAGTAGC 59.999 57.143 0.73 0.00 0.00 3.58
4325 8260 3.193479 GGGAGCTAAAGTGTCATTTTGGG 59.807 47.826 3.71 0.00 0.00 4.12
4392 8327 1.996191 GTGATGGAGAAGACAACGAGC 59.004 52.381 0.00 0.00 0.00 5.03
4477 8412 4.638865 TGAAAGTCATGCTGATGATTCTGG 59.361 41.667 0.00 0.00 40.78 3.86
4622 8557 6.771267 GCTTATATGGGTTTGCTTACTACCTT 59.229 38.462 0.00 0.00 32.46 3.50
4686 8621 9.736414 CAGATGGATGTTCTAATCCTCAATATT 57.264 33.333 4.93 0.00 45.57 1.28
4731 8666 2.651455 ACACTCCTTGCATGGATGATG 58.349 47.619 20.72 19.44 35.30 3.07
4750 8685 2.161855 TGTGCTTCCTACTTGCAATGG 58.838 47.619 0.00 3.14 38.50 3.16
4793 8728 9.197306 CTCTATCCTCTCTATAGTAGACTGCTA 57.803 40.741 2.52 2.52 0.00 3.49
4830 8765 4.649932 TGTAATCAACACTGCACTCTGCG 61.650 47.826 0.00 0.00 38.75 5.18
4845 8780 3.187700 CTCTGCGGGAATGTACTTGTAC 58.812 50.000 4.14 4.14 0.00 2.90
4879 8814 3.077229 TGAACAAATGCTTTGGTGACG 57.923 42.857 11.59 0.00 41.49 4.35
4884 8819 0.250901 AATGCTTTGGTGACGGAGCT 60.251 50.000 0.00 0.00 40.37 4.09
4893 8828 2.037902 TGGTGACGGAGCTTGACAATTA 59.962 45.455 0.00 0.00 0.00 1.40
4908 8843 8.139350 GCTTGACAATTAATGATCATCCATGAA 58.861 33.333 9.06 0.00 40.69 2.57
5098 9033 4.502087 GCCAAAAATGGAAGCTCTTGTTCT 60.502 41.667 0.00 0.00 0.00 3.01
5171 9108 0.532862 AAGACACTCACGTGCCTTGG 60.533 55.000 11.67 0.79 41.45 3.61
5191 9130 1.208293 GTCCTCACATCCCTTCACCTC 59.792 57.143 0.00 0.00 0.00 3.85
5193 9132 1.577736 CTCACATCCCTTCACCTCCT 58.422 55.000 0.00 0.00 0.00 3.69
5195 9134 1.630369 TCACATCCCTTCACCTCCTTG 59.370 52.381 0.00 0.00 0.00 3.61
5200 9139 1.204113 CCCTTCACCTCCTTGCTCCT 61.204 60.000 0.00 0.00 0.00 3.69
5201 9140 0.251634 CCTTCACCTCCTTGCTCCTC 59.748 60.000 0.00 0.00 0.00 3.71
5202 9141 0.251634 CTTCACCTCCTTGCTCCTCC 59.748 60.000 0.00 0.00 0.00 4.30
5203 9142 1.201429 TTCACCTCCTTGCTCCTCCC 61.201 60.000 0.00 0.00 0.00 4.30
5204 9143 1.614824 CACCTCCTTGCTCCTCCCT 60.615 63.158 0.00 0.00 0.00 4.20
5205 9144 1.162085 ACCTCCTTGCTCCTCCCTT 59.838 57.895 0.00 0.00 0.00 3.95
5265 9204 5.435686 TGAAAGTGCACCTTATGACCTAT 57.564 39.130 14.63 0.00 31.48 2.57
5285 9224 1.859302 TGGGTTGGGGTGATTAATGC 58.141 50.000 0.00 0.00 0.00 3.56
5478 9418 9.886132 GTACTTCTATTAGACAGGGATTCAAAA 57.114 33.333 0.00 0.00 0.00 2.44
5480 9420 9.232473 ACTTCTATTAGACAGGGATTCAAAAAC 57.768 33.333 0.00 0.00 0.00 2.43
5492 9432 5.694458 GGGATTCAAAAACGCTATTGTTGTT 59.306 36.000 1.65 0.00 29.29 2.83
5493 9433 6.346518 GGGATTCAAAAACGCTATTGTTGTTG 60.347 38.462 3.67 3.67 44.74 3.33
5513 9453 5.480772 TGTTGTTAGAAGTTTTTGTTCCCCA 59.519 36.000 0.00 0.00 0.00 4.96
5518 9458 2.838637 AGTTTTTGTTCCCCAGACCA 57.161 45.000 0.00 0.00 0.00 4.02
5635 9576 5.598005 TCTTGTCTTGATTTCCAACATGGTT 59.402 36.000 0.00 0.00 39.03 3.67
5724 9665 4.589908 AGACCAATCAACAACCTACATCC 58.410 43.478 0.00 0.00 0.00 3.51
5735 9676 5.445964 ACAACCTACATCCTGAGTTTGTTT 58.554 37.500 0.00 0.00 0.00 2.83
5755 9696 2.990740 TCCAACCAAGGCCTTTACAT 57.009 45.000 17.61 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 5.189145 TCCAAAAGTATAGACTTGGTCCCTC 59.811 44.000 2.98 0.00 45.50 4.30
48 49 7.878127 TCAAGTTCTCCAAAAGTATAGACTTGG 59.122 37.037 2.98 2.61 45.50 3.61
49 50 8.833231 TCAAGTTCTCCAAAAGTATAGACTTG 57.167 34.615 2.98 0.00 45.50 3.16
51 52 7.310734 CCCTCAAGTTCTCCAAAAGTATAGACT 60.311 40.741 0.00 0.00 37.59 3.24
52 53 6.819146 CCCTCAAGTTCTCCAAAAGTATAGAC 59.181 42.308 0.00 0.00 0.00 2.59
53 54 6.729100 TCCCTCAAGTTCTCCAAAAGTATAGA 59.271 38.462 0.00 0.00 0.00 1.98
137 141 2.771943 TGGTCCTTCAAGTCTCACAACT 59.228 45.455 0.00 0.00 0.00 3.16
141 145 4.137543 ACATTTGGTCCTTCAAGTCTCAC 58.862 43.478 0.00 0.00 0.00 3.51
157 161 7.039784 TCCCTGAAGATTTTTGGTAGACATTTG 60.040 37.037 0.00 0.00 0.00 2.32
175 179 7.982354 CCAAAAGTATAGACTTAGTCCCTGAAG 59.018 40.741 8.96 0.00 45.50 3.02
176 180 7.093024 CCCAAAAGTATAGACTTAGTCCCTGAA 60.093 40.741 8.96 0.00 45.50 3.02
178 182 6.383147 TCCCAAAAGTATAGACTTAGTCCCTG 59.617 42.308 8.96 0.00 45.50 4.45
190 195 6.374613 GTCCCTCAAGTTTCCCAAAAGTATAG 59.625 42.308 0.00 0.00 0.00 1.31
201 206 3.449377 TGTTTTTGGTCCCTCAAGTTTCC 59.551 43.478 0.00 0.00 0.00 3.13
259 283 0.548926 TAGGATCCCCACTGCCACAA 60.549 55.000 8.55 0.00 33.88 3.33
260 284 0.548926 TTAGGATCCCCACTGCCACA 60.549 55.000 8.55 0.00 33.88 4.17
261 285 0.623723 TTTAGGATCCCCACTGCCAC 59.376 55.000 8.55 0.00 33.88 5.01
262 286 1.377690 TTTTAGGATCCCCACTGCCA 58.622 50.000 8.55 0.00 33.88 4.92
263 287 2.755952 ATTTTAGGATCCCCACTGCC 57.244 50.000 8.55 0.00 33.88 4.85
264 288 5.069119 CCTTTTATTTTAGGATCCCCACTGC 59.931 44.000 8.55 0.00 33.13 4.40
265 289 6.431722 TCCTTTTATTTTAGGATCCCCACTG 58.568 40.000 8.55 0.00 35.66 3.66
266 290 6.668133 TCCTTTTATTTTAGGATCCCCACT 57.332 37.500 8.55 0.00 35.66 4.00
274 298 7.234577 ACTGCCACAAATCCTTTTATTTTAGGA 59.765 33.333 0.00 0.00 44.29 2.94
275 299 7.331687 CACTGCCACAAATCCTTTTATTTTAGG 59.668 37.037 0.00 0.00 0.00 2.69
276 300 7.331687 CCACTGCCACAAATCCTTTTATTTTAG 59.668 37.037 0.00 0.00 0.00 1.85
277 301 7.158021 CCACTGCCACAAATCCTTTTATTTTA 58.842 34.615 0.00 0.00 0.00 1.52
278 302 5.997129 CCACTGCCACAAATCCTTTTATTTT 59.003 36.000 0.00 0.00 0.00 1.82
279 303 5.071653 ACCACTGCCACAAATCCTTTTATTT 59.928 36.000 0.00 0.00 0.00 1.40
280 304 4.592778 ACCACTGCCACAAATCCTTTTATT 59.407 37.500 0.00 0.00 0.00 1.40
281 305 4.159557 ACCACTGCCACAAATCCTTTTAT 58.840 39.130 0.00 0.00 0.00 1.40
282 306 3.571590 ACCACTGCCACAAATCCTTTTA 58.428 40.909 0.00 0.00 0.00 1.52
283 307 2.365293 GACCACTGCCACAAATCCTTTT 59.635 45.455 0.00 0.00 0.00 2.27
284 308 1.963515 GACCACTGCCACAAATCCTTT 59.036 47.619 0.00 0.00 0.00 3.11
285 309 1.145738 AGACCACTGCCACAAATCCTT 59.854 47.619 0.00 0.00 0.00 3.36
286 310 0.773644 AGACCACTGCCACAAATCCT 59.226 50.000 0.00 0.00 0.00 3.24
287 311 1.168714 GAGACCACTGCCACAAATCC 58.831 55.000 0.00 0.00 0.00 3.01
288 312 1.896220 TGAGACCACTGCCACAAATC 58.104 50.000 0.00 0.00 0.00 2.17
289 313 2.224843 TGATGAGACCACTGCCACAAAT 60.225 45.455 0.00 0.00 0.00 2.32
290 314 1.142667 TGATGAGACCACTGCCACAAA 59.857 47.619 0.00 0.00 0.00 2.83
295 319 3.813443 ACATTATGATGAGACCACTGCC 58.187 45.455 4.20 0.00 36.73 4.85
333 357 7.120285 GGGTGGATAGAGTACAACCTTTTTAAC 59.880 40.741 0.00 0.00 46.04 2.01
346 371 1.771565 CACGTGGGGTGGATAGAGTA 58.228 55.000 7.95 0.00 43.16 2.59
359 384 5.794687 TCTATTTGCAGATTTACACGTGG 57.205 39.130 21.57 0.44 0.00 4.94
363 388 8.400947 ACATCACATCTATTTGCAGATTTACAC 58.599 33.333 0.00 0.00 32.83 2.90
374 399 9.661187 GCAGAGAAAATACATCACATCTATTTG 57.339 33.333 0.00 0.00 0.00 2.32
380 405 5.505324 GCCAGCAGAGAAAATACATCACATC 60.505 44.000 0.00 0.00 0.00 3.06
399 424 2.540265 AGATGTATGCACTAGCCAGC 57.460 50.000 0.00 0.00 41.13 4.85
463 495 6.691754 ATTTCATGTCATGCGGTTGTATTA 57.308 33.333 8.03 0.00 0.00 0.98
503 535 3.550639 CGTCAGCTTTCATGGCAAAAGAA 60.551 43.478 14.29 6.15 36.09 2.52
504 536 2.030893 CGTCAGCTTTCATGGCAAAAGA 60.031 45.455 14.29 0.12 36.09 2.52
509 541 0.961857 ATGCGTCAGCTTTCATGGCA 60.962 50.000 0.00 0.00 45.42 4.92
545 577 6.636044 GTCGTATCCTACTCATTTTAAGACCG 59.364 42.308 0.00 0.00 0.00 4.79
555 587 9.303116 AGATATTGAAAGTCGTATCCTACTCAT 57.697 33.333 0.00 0.00 0.00 2.90
556 588 8.693120 AGATATTGAAAGTCGTATCCTACTCA 57.307 34.615 0.00 0.00 0.00 3.41
623 656 3.127895 TCGTCAAGGAAAAATAATGCCGG 59.872 43.478 0.00 0.00 0.00 6.13
624 657 4.342772 CTCGTCAAGGAAAAATAATGCCG 58.657 43.478 0.00 0.00 0.00 5.69
627 660 6.148948 TGTTGCTCGTCAAGGAAAAATAATG 58.851 36.000 0.00 0.00 37.04 1.90
741 777 8.362639 TCTACTAAAAGGAGCTTCGTCTAAAAA 58.637 33.333 0.00 0.00 0.00 1.94
747 783 7.417496 TTTTTCTACTAAAAGGAGCTTCGTC 57.583 36.000 0.00 0.00 0.00 4.20
774 810 1.680555 CCACATAGCTTTGCCCGGTTA 60.681 52.381 0.00 0.00 0.00 2.85
775 811 0.965363 CCACATAGCTTTGCCCGGTT 60.965 55.000 0.00 0.00 0.00 4.44
776 812 1.378514 CCACATAGCTTTGCCCGGT 60.379 57.895 0.00 0.00 0.00 5.28
791 828 4.091939 GTAGGCCCGACCCACCAC 62.092 72.222 0.00 0.00 40.58 4.16
794 831 3.782443 CCAGTAGGCCCGACCCAC 61.782 72.222 0.00 0.00 40.58 4.61
837 874 1.159285 CAAAGACGCATCAGGCTTCA 58.841 50.000 0.00 0.00 42.87 3.02
1351 5237 1.888172 CGGGGTTGCACACGTACAA 60.888 57.895 0.00 0.00 0.00 2.41
1524 5410 4.569943 AGCAGTACACTTTCACCATGTAG 58.430 43.478 0.00 0.00 29.67 2.74
1592 5478 2.855514 ATGGCCACCGTTGTTGCAC 61.856 57.895 8.16 0.00 34.91 4.57
1815 5716 2.158066 TGTTTAGGTCCTTCTCTCCCCA 60.158 50.000 0.00 0.00 0.00 4.96
1841 5742 6.432162 ACTCTTCGTGTGTGAGTTATAACCTA 59.568 38.462 12.05 0.00 37.76 3.08
1895 5796 2.624838 CACTGACTGCAAATTTCCAGGT 59.375 45.455 13.60 0.00 33.43 4.00
1913 5814 2.162681 GCCTGCACAAAATCTACCACT 58.837 47.619 0.00 0.00 0.00 4.00
1916 5817 2.636768 GTGCCTGCACAAAATCTACC 57.363 50.000 16.95 0.00 45.53 3.18
1944 5845 2.387476 TAGCCAGGCCATCTGCATCG 62.387 60.000 8.22 0.00 43.89 3.84
2006 5916 1.664333 GCACCGCAACAAACCATGG 60.664 57.895 11.19 11.19 0.00 3.66
2072 5982 0.824109 TCTATCACCAACGCCCTCTG 59.176 55.000 0.00 0.00 0.00 3.35
2081 5991 2.576191 CCCCCTGTTTCTCTATCACCAA 59.424 50.000 0.00 0.00 0.00 3.67
2107 6017 2.632996 CCGCCTCATACATCCCTCTAAA 59.367 50.000 0.00 0.00 0.00 1.85
2120 6031 1.221840 CAAGCTACCACCGCCTCAT 59.778 57.895 0.00 0.00 0.00 2.90
2225 6136 0.521735 GCTTTCCACCTAACGGCTTG 59.478 55.000 0.00 0.00 0.00 4.01
2467 6387 8.699130 TGAAGAATGATCTGATTCAAGCTACTA 58.301 33.333 8.12 0.00 35.59 1.82
2549 6469 3.866651 AGATGTTCTCCCACAAGAATCG 58.133 45.455 0.00 0.00 37.59 3.34
2583 6503 3.637432 TCATTTGTGGTCGAATTTGCAC 58.363 40.909 0.00 0.00 0.00 4.57
2710 6638 3.806949 AGAGTAAAATGTTCCCTGCCA 57.193 42.857 0.00 0.00 0.00 4.92
2796 6724 7.089538 TCATGTTCGATTGCACATTTTGTAAT 58.910 30.769 0.00 0.00 42.69 1.89
2852 6780 8.784043 AGGTAGTAGAAATGATTGTTTTGTGAC 58.216 33.333 0.00 0.00 0.00 3.67
2953 6881 6.795399 TGGAACTAAAGCTTCTGTTCAAAAG 58.205 36.000 29.19 10.44 40.12 2.27
3008 6936 8.950208 AATCCTTCTATTTAGAACTACAGTGC 57.050 34.615 0.00 0.00 37.40 4.40
3057 6985 6.877611 AGACAACTTTATTTGGATTCGTGT 57.122 33.333 0.00 0.00 0.00 4.49
3112 7040 1.619654 TCAGTGGGCACAAATGGAAG 58.380 50.000 0.00 0.00 0.00 3.46
3138 7066 9.820725 TTTCATAAGAAATATTTGGAGGCATTG 57.179 29.630 5.17 0.00 38.76 2.82
3165 7093 9.454859 GATGACTATAGGCTTAAATGGCTTAAT 57.545 33.333 7.23 0.00 42.90 1.40
3430 7363 0.322456 TTGGCGAGATGTTCCCAAGG 60.322 55.000 0.00 0.00 33.73 3.61
3435 7368 0.521735 GGTGTTTGGCGAGATGTTCC 59.478 55.000 0.00 0.00 0.00 3.62
3589 7522 3.037549 TGTTTTGGCAAGAGGATTTGGT 58.962 40.909 0.00 0.00 0.00 3.67
3711 7644 6.899393 TGCTTCATGGAAACTTGTAGAAAT 57.101 33.333 0.00 0.00 35.69 2.17
3720 7653 9.783081 AGAAAATTTAAATGCTTCATGGAAACT 57.217 25.926 18.52 1.48 0.00 2.66
3743 7676 7.733773 TGGGTATCTCTACAGATTCAAAGAA 57.266 36.000 0.00 0.00 40.18 2.52
3751 7684 6.126156 TGACCTACTTGGGTATCTCTACAGAT 60.126 42.308 0.00 0.00 40.55 2.90
3760 7693 3.709653 TGACCATGACCTACTTGGGTATC 59.290 47.826 0.00 0.00 44.81 2.24
3829 7762 2.598192 CGCAAAAGTGAGGTGTTTTGTG 59.402 45.455 8.79 7.74 43.70 3.33
4084 8018 8.806146 ACCTATTCATATGTGTTTTCAAAAGCT 58.194 29.630 1.90 0.00 0.00 3.74
4127 8062 4.407296 GGGGATCTGATGACTACAGAAGTT 59.593 45.833 0.00 0.00 45.44 2.66
4159 8094 6.260050 ACAAACAGTAATATTAGGCATCACCG 59.740 38.462 0.00 0.00 46.52 4.94
4325 8260 5.971792 GCATCGTTTAAAAGAGGGAATAAGC 59.028 40.000 15.69 4.30 0.00 3.09
4392 8327 2.704572 GTTGTCTTCTCCATCACCCAG 58.295 52.381 0.00 0.00 0.00 4.45
4477 8412 2.569404 TCTTCAGCCTCTTCTTCTTCCC 59.431 50.000 0.00 0.00 0.00 3.97
4622 8557 1.263356 AGCGCAACTTAGAGGTACCA 58.737 50.000 15.94 0.00 0.00 3.25
4686 8621 6.721318 AGATGAAAGACTTATGTAAGGCCAA 58.279 36.000 5.01 0.00 42.38 4.52
4731 8666 1.135286 GCCATTGCAAGTAGGAAGCAC 60.135 52.381 16.86 0.00 38.11 4.40
4750 8685 7.852263 AGGATAGAGTACATGTTATTATGGGC 58.148 38.462 2.30 0.00 32.32 5.36
4816 8751 2.116983 ATTCCCGCAGAGTGCAGTGT 62.117 55.000 0.00 0.00 45.36 3.55
4830 8765 3.008704 ACACCTGGTACAAGTACATTCCC 59.991 47.826 12.00 0.00 38.70 3.97
4845 8780 5.277442 GCATTTGTTCAATTTCAACACCTGG 60.277 40.000 0.00 0.00 33.42 4.45
4879 8814 6.263842 TGGATGATCATTAATTGTCAAGCTCC 59.736 38.462 10.14 2.50 0.00 4.70
4908 8843 9.985730 TCAACAATGAGAGCAAATAAGAAAATT 57.014 25.926 0.00 0.00 0.00 1.82
5144 9081 3.802948 ACGTGAGTGTCTTCTCTGTTT 57.197 42.857 0.00 0.00 46.97 2.83
5171 9108 1.208293 GAGGTGAAGGGATGTGAGGAC 59.792 57.143 0.00 0.00 0.00 3.85
5191 9130 1.284313 AGAAGAAGGGAGGAGCAAGG 58.716 55.000 0.00 0.00 0.00 3.61
5193 9132 1.630878 GGAAGAAGAAGGGAGGAGCAA 59.369 52.381 0.00 0.00 0.00 3.91
5195 9134 1.578897 AGGAAGAAGAAGGGAGGAGC 58.421 55.000 0.00 0.00 0.00 4.70
5200 9139 2.890814 ACTCGAAGGAAGAAGAAGGGA 58.109 47.619 0.00 0.00 0.00 4.20
5201 9140 3.686916 AACTCGAAGGAAGAAGAAGGG 57.313 47.619 0.00 0.00 0.00 3.95
5202 9141 3.997681 GGAAACTCGAAGGAAGAAGAAGG 59.002 47.826 0.00 0.00 0.00 3.46
5203 9142 4.888917 AGGAAACTCGAAGGAAGAAGAAG 58.111 43.478 0.00 0.00 32.90 2.85
5204 9143 4.957684 AGGAAACTCGAAGGAAGAAGAA 57.042 40.909 0.00 0.00 32.90 2.52
5205 9144 4.957684 AAGGAAACTCGAAGGAAGAAGA 57.042 40.909 0.00 0.00 42.68 2.87
5265 9204 2.183679 GCATTAATCACCCCAACCCAA 58.816 47.619 0.00 0.00 0.00 4.12
5336 9276 6.446318 TGCCAATACTTTTTGCTTTAGTGAG 58.554 36.000 0.00 0.00 0.00 3.51
5350 9290 0.614697 GCAGGGGGTTGCCAATACTT 60.615 55.000 0.00 0.00 38.13 2.24
5478 9418 6.613755 ACTTCTAACAACAACAATAGCGTT 57.386 33.333 0.00 0.00 0.00 4.84
5480 9420 7.908193 AAAACTTCTAACAACAACAATAGCG 57.092 32.000 0.00 0.00 0.00 4.26
5492 9432 5.358725 GTCTGGGGAACAAAAACTTCTAACA 59.641 40.000 0.00 0.00 0.00 2.41
5493 9433 5.221185 GGTCTGGGGAACAAAAACTTCTAAC 60.221 44.000 0.00 0.00 0.00 2.34
5648 9589 8.653338 ACTACACGTTCATAACACATCATAAAC 58.347 33.333 0.00 0.00 0.00 2.01
5651 9592 7.815549 ACAACTACACGTTCATAACACATCATA 59.184 33.333 0.00 0.00 32.27 2.15
5735 9676 2.757894 TGTAAAGGCCTTGGTTGGAA 57.242 45.000 21.33 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.