Multiple sequence alignment - TraesCS2A01G546700

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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 TraesCS2A01G546700 chr2A 100.000 3407 0 0 1 3407 755341916 755338510 0.000000e+00 6292.0
1 TraesCS2A01G546700 chr2A 93.183 1819 79 25 988 2799 755118507 755120287 0.000000e+00 2630.0
2 TraesCS2A01G546700 chr2A 90.782 358 8 6 3075 3407 755174078 755174435 4.010000e-124 455.0
3 TraesCS2A01G546700 chr2A 86.667 180 11 3 2835 3001 755120287 755120466 1.610000e-43 187.0
4 TraesCS2A01G546700 chr2D 93.378 1797 103 12 637 2420 624054540 624052747 0.000000e+00 2645.0
5 TraesCS2A01G546700 chr2D 92.552 1544 105 5 1014 2552 623947750 623949288 0.000000e+00 2206.0
6 TraesCS2A01G546700 chr2D 87.117 326 19 6 2699 3001 623951951 623952276 7.000000e-92 348.0
7 TraesCS2A01G546700 chr2D 84.906 371 18 8 3071 3407 623955149 623955515 1.170000e-89 340.0
8 TraesCS2A01G546700 chr2D 95.062 81 4 0 2998 3078 623955047 623955127 9.920000e-26 128.0
9 TraesCS2A01G546700 chr2D 88.660 97 6 1 2615 2711 623950394 623950485 2.780000e-21 113.0
10 TraesCS2A01G546700 chr2B 93.910 1445 88 0 976 2420 765792960 765791516 0.000000e+00 2182.0
11 TraesCS2A01G546700 chr2B 93.333 1440 87 6 988 2420 765586440 765587877 0.000000e+00 2119.0
12 TraesCS2A01G546700 chr2B 90.823 316 21 7 637 945 765793391 765793077 1.890000e-112 416.0
13 TraesCS2A01G546700 chr2B 79.310 464 77 13 1 447 765794307 765793846 1.190000e-79 307.0
14 TraesCS2A01G546700 chr2B 87.546 273 16 5 2747 3001 765588293 765588565 1.990000e-77 300.0
15 TraesCS2A01G546700 chr2B 83.657 361 15 16 3071 3407 765590635 765590975 1.990000e-77 300.0
16 TraesCS2A01G546700 chr2B 79.310 348 56 12 6 338 765795035 765794689 2.640000e-56 230.0
17 TraesCS2A01G546700 chr2B 100.000 48 0 0 2676 2723 765588252 765588299 4.680000e-14 89.8
18 TraesCS2A01G546700 chr4A 87.602 984 103 10 981 1949 677272514 677273493 0.000000e+00 1123.0
19 TraesCS2A01G546700 chr5D 83.305 1192 163 24 1129 2305 238670466 238669296 0.000000e+00 1066.0
20 TraesCS2A01G546700 chr7A 83.139 1198 163 25 1129 2305 262852442 262853621 0.000000e+00 1057.0
21 TraesCS2A01G546700 chr7B 83.138 1192 162 25 1129 2299 222553191 222554364 0.000000e+00 1051.0
22 TraesCS2A01G546700 chr7D 85.528 691 42 28 2350 3001 534447897 534447226 0.000000e+00 669.0
23 TraesCS2A01G546700 chr7D 83.446 737 99 12 1583 2305 246388398 246389125 0.000000e+00 664.0
24 TraesCS2A01G546700 chr7D 88.950 362 14 11 3071 3407 534444132 534443772 1.130000e-114 424.0


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 TraesCS2A01G546700 chr2A 755338510 755341916 3406 True 6292.00 6292 100.00000 1 3407 1 chr2A.!!$R1 3406
1 TraesCS2A01G546700 chr2A 755118507 755120466 1959 False 1408.50 2630 89.92500 988 3001 2 chr2A.!!$F2 2013
2 TraesCS2A01G546700 chr2D 624052747 624054540 1793 True 2645.00 2645 93.37800 637 2420 1 chr2D.!!$R1 1783
3 TraesCS2A01G546700 chr2D 623947750 623955515 7765 False 627.00 2206 89.65940 1014 3407 5 chr2D.!!$F1 2393
4 TraesCS2A01G546700 chr2B 765791516 765795035 3519 True 783.75 2182 85.83825 1 2420 4 chr2B.!!$R1 2419
5 TraesCS2A01G546700 chr2B 765586440 765590975 4535 False 702.20 2119 91.13400 988 3407 4 chr2B.!!$F1 2419
6 TraesCS2A01G546700 chr4A 677272514 677273493 979 False 1123.00 1123 87.60200 981 1949 1 chr4A.!!$F1 968
7 TraesCS2A01G546700 chr5D 238669296 238670466 1170 True 1066.00 1066 83.30500 1129 2305 1 chr5D.!!$R1 1176
8 TraesCS2A01G546700 chr7A 262852442 262853621 1179 False 1057.00 1057 83.13900 1129 2305 1 chr7A.!!$F1 1176
9 TraesCS2A01G546700 chr7B 222553191 222554364 1173 False 1051.00 1051 83.13800 1129 2299 1 chr7B.!!$F1 1170
10 TraesCS2A01G546700 chr7D 246388398 246389125 727 False 664.00 664 83.44600 1583 2305 1 chr7D.!!$F1 722
11 TraesCS2A01G546700 chr7D 534443772 534447897 4125 True 546.50 669 87.23900 2350 3407 2 chr7D.!!$R1 1057

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
216 231 0.034337 TAGGGGTGTGCGTCAGTTTC 59.966 55.0 0.0 0.0 0.0 2.78 F
958 2040 0.110486 AGCCGACACTCCAAAACCAT 59.890 50.0 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1539 2700 3.692406 ACGAGCTTCCCGGTGACC 61.692 66.667 0.00 0.00 0.00 4.02 R
2945 6903 1.559368 TTAGTTGGCCAGCCGTACTA 58.441 50.000 16.95 12.91 39.42 1.82 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
28 29 9.748708 TGAAGAAGTTCATTAATTGTGGAAAAG 57.251 29.630 5.50 0.00 37.79 2.27
29 30 9.965824 GAAGAAGTTCATTAATTGTGGAAAAGA 57.034 29.630 5.50 0.00 32.36 2.52
32 33 9.912634 GAAGTTCATTAATTGTGGAAAAGATCA 57.087 29.630 0.00 0.00 0.00 2.92
33 34 9.696917 AAGTTCATTAATTGTGGAAAAGATCAC 57.303 29.630 0.00 0.00 34.71 3.06
34 35 8.023128 AGTTCATTAATTGTGGAAAAGATCACG 58.977 33.333 0.00 0.00 36.74 4.35
35 36 7.680442 TCATTAATTGTGGAAAAGATCACGA 57.320 32.000 0.00 0.00 36.74 4.35
36 37 7.751732 TCATTAATTGTGGAAAAGATCACGAG 58.248 34.615 0.00 0.00 36.74 4.18
41 42 6.539649 TTGTGGAAAAGATCACGAGTTTAG 57.460 37.500 0.00 0.00 36.74 1.85
42 43 5.849510 TGTGGAAAAGATCACGAGTTTAGA 58.150 37.500 0.00 0.00 36.74 2.10
46 47 7.746475 GTGGAAAAGATCACGAGTTTAGAAATG 59.254 37.037 0.00 0.00 0.00 2.32
112 127 6.544928 AAAAACCAGTGAAAAAGTCCAGAT 57.455 33.333 0.00 0.00 0.00 2.90
117 132 5.238650 ACCAGTGAAAAAGTCCAGATAAACG 59.761 40.000 0.00 0.00 0.00 3.60
123 138 8.500773 GTGAAAAAGTCCAGATAAACGAATGTA 58.499 33.333 0.00 0.00 0.00 2.29
139 154 7.329588 ACGAATGTAGAAAGGAAAACAAACT 57.670 32.000 0.00 0.00 0.00 2.66
140 155 7.193595 ACGAATGTAGAAAGGAAAACAAACTG 58.806 34.615 0.00 0.00 0.00 3.16
153 168 6.981559 GGAAAACAAACTGGTGTATAAAAGCA 59.018 34.615 0.00 0.00 0.00 3.91
154 169 7.655732 GGAAAACAAACTGGTGTATAAAAGCAT 59.344 33.333 0.00 0.00 0.00 3.79
159 174 3.447229 ACTGGTGTATAAAAGCATTGCCC 59.553 43.478 4.70 0.00 0.00 5.36
164 179 5.507985 GGTGTATAAAAGCATTGCCCTGATC 60.508 44.000 4.70 0.00 0.00 2.92
173 188 2.514824 GCCCTGATCGGCTGAACC 60.515 66.667 0.00 0.00 46.10 3.62
175 190 1.153289 CCCTGATCGGCTGAACCAG 60.153 63.158 16.96 16.96 39.03 4.00
177 192 0.036010 CCTGATCGGCTGAACCAGTT 60.036 55.000 20.27 0.00 39.03 3.16
179 194 2.271800 CTGATCGGCTGAACCAGTTAC 58.728 52.381 16.09 0.00 39.03 2.50
182 197 1.045407 TCGGCTGAACCAGTTACAGT 58.955 50.000 0.00 0.00 39.03 3.55
184 199 2.629137 TCGGCTGAACCAGTTACAGTAA 59.371 45.455 0.00 0.00 39.03 2.24
186 201 3.335579 GGCTGAACCAGTTACAGTAAGG 58.664 50.000 0.00 0.00 38.86 2.69
193 208 6.438108 TGAACCAGTTACAGTAAGGCTATGTA 59.562 38.462 0.00 0.00 0.00 2.29
216 231 0.034337 TAGGGGTGTGCGTCAGTTTC 59.966 55.000 0.00 0.00 0.00 2.78
240 255 2.906047 GCCTATAAGTGGCGCAGAG 58.094 57.895 10.83 0.00 41.03 3.35
253 1000 0.597637 CGCAGAGGACGCCGAATAAT 60.598 55.000 0.00 0.00 0.00 1.28
256 1003 2.731976 GCAGAGGACGCCGAATAATAAG 59.268 50.000 0.00 0.00 0.00 1.73
272 1019 7.483691 CGAATAATAAGTGGGTAAAGTTTGTGC 59.516 37.037 0.00 0.00 0.00 4.57
278 1025 2.432146 TGGGTAAAGTTTGTGCATTGCA 59.568 40.909 7.38 7.38 35.60 4.08
280 1027 4.064388 GGGTAAAGTTTGTGCATTGCATT 58.936 39.130 15.49 6.39 41.91 3.56
320 1067 5.764192 AGATGAGCAAGGATTAATCTTCAGC 59.236 40.000 14.95 14.21 0.00 4.26
321 1068 5.108187 TGAGCAAGGATTAATCTTCAGCT 57.892 39.130 20.29 20.29 32.60 4.24
326 1073 5.586243 GCAAGGATTAATCTTCAGCTGTACA 59.414 40.000 14.67 0.00 0.00 2.90
327 1074 6.094048 GCAAGGATTAATCTTCAGCTGTACAA 59.906 38.462 14.67 0.00 0.00 2.41
338 1085 8.850454 TCTTCAGCTGTACAAAATAAAACAAC 57.150 30.769 14.67 0.00 0.00 3.32
345 1092 7.856894 GCTGTACAAAATAAAACAACCGTAGAA 59.143 33.333 0.00 0.00 0.00 2.10
352 1099 4.563337 AAAACAACCGTAGAAGGCTTTC 57.437 40.909 0.00 0.00 33.69 2.62
356 1103 3.081804 CAACCGTAGAAGGCTTTCCAAT 58.918 45.455 4.73 0.00 33.64 3.16
363 1110 6.403309 CCGTAGAAGGCTTTCCAATAAAAGTC 60.403 42.308 4.73 0.00 40.40 3.01
371 1118 5.163612 GCTTTCCAATAAAAGTCTGGCTAGG 60.164 44.000 0.00 0.00 38.30 3.02
372 1119 5.514500 TTCCAATAAAAGTCTGGCTAGGT 57.486 39.130 0.00 0.00 0.00 3.08
375 1122 5.104900 TCCAATAAAAGTCTGGCTAGGTCTC 60.105 44.000 0.00 0.00 0.00 3.36
379 1126 2.614134 AGTCTGGCTAGGTCTCAGTT 57.386 50.000 0.00 0.00 0.00 3.16
384 1131 4.402793 GTCTGGCTAGGTCTCAGTTGATTA 59.597 45.833 0.00 0.00 0.00 1.75
385 1132 5.023452 TCTGGCTAGGTCTCAGTTGATTAA 58.977 41.667 0.00 0.00 0.00 1.40
468 1218 9.558396 AAAAAGGAAATTTTGCATGAATCTACA 57.442 25.926 0.00 0.00 40.27 2.74
469 1219 9.729281 AAAAGGAAATTTTGCATGAATCTACAT 57.271 25.926 0.00 0.00 39.67 2.29
472 1222 8.970020 AGGAAATTTTGCATGAATCTACATACA 58.030 29.630 0.00 0.00 0.00 2.29
482 1232 7.117523 GCATGAATCTACATACAAGATCTCACC 59.882 40.741 0.00 0.00 32.48 4.02
483 1233 6.739112 TGAATCTACATACAAGATCTCACCG 58.261 40.000 0.00 0.00 32.48 4.94
500 1250 3.110358 CACCGATATTGCGTCGACTTTA 58.890 45.455 14.70 0.00 41.40 1.85
504 1542 4.280461 CGATATTGCGTCGACTTTAGACT 58.720 43.478 14.70 0.00 41.40 3.24
509 1547 4.494350 TGCGTCGACTTTAGACTTAACT 57.506 40.909 14.70 0.00 36.53 2.24
511 1549 6.187125 TGCGTCGACTTTAGACTTAACTAT 57.813 37.500 14.70 0.00 36.53 2.12
529 1567 9.719279 CTTAACTATGTCTTAAGTCTAAGTCGG 57.281 37.037 1.63 0.00 36.63 4.79
530 1568 6.134040 ACTATGTCTTAAGTCTAAGTCGGC 57.866 41.667 1.63 0.00 36.63 5.54
531 1569 5.887035 ACTATGTCTTAAGTCTAAGTCGGCT 59.113 40.000 1.63 0.00 36.63 5.52
532 1570 4.436242 TGTCTTAAGTCTAAGTCGGCTG 57.564 45.455 1.63 0.00 36.63 4.85
533 1571 4.077108 TGTCTTAAGTCTAAGTCGGCTGA 58.923 43.478 1.63 0.00 36.63 4.26
534 1572 4.156190 TGTCTTAAGTCTAAGTCGGCTGAG 59.844 45.833 0.00 0.00 36.63 3.35
535 1573 4.395542 GTCTTAAGTCTAAGTCGGCTGAGA 59.604 45.833 0.00 0.00 36.63 3.27
536 1574 5.066764 GTCTTAAGTCTAAGTCGGCTGAGAT 59.933 44.000 7.52 0.00 34.83 2.75
537 1575 5.297278 TCTTAAGTCTAAGTCGGCTGAGATC 59.703 44.000 7.52 1.72 34.83 2.75
538 1576 3.006112 AGTCTAAGTCGGCTGAGATCA 57.994 47.619 7.52 0.00 34.83 2.92
590 1628 4.597004 TGTAAACCAATTATTACGGGCCA 58.403 39.130 4.39 0.00 35.30 5.36
591 1629 4.398673 TGTAAACCAATTATTACGGGCCAC 59.601 41.667 4.39 0.00 35.30 5.01
592 1630 3.375647 AACCAATTATTACGGGCCACT 57.624 42.857 4.39 0.00 0.00 4.00
593 1631 3.375647 ACCAATTATTACGGGCCACTT 57.624 42.857 4.39 0.00 0.00 3.16
594 1632 3.020984 ACCAATTATTACGGGCCACTTG 58.979 45.455 4.39 0.00 0.00 3.16
595 1633 3.020984 CCAATTATTACGGGCCACTTGT 58.979 45.455 4.39 0.00 0.00 3.16
596 1634 3.445805 CCAATTATTACGGGCCACTTGTT 59.554 43.478 4.39 0.00 0.00 2.83
597 1635 4.420168 CAATTATTACGGGCCACTTGTTG 58.580 43.478 4.39 0.00 0.00 3.33
598 1636 2.863132 TATTACGGGCCACTTGTTGT 57.137 45.000 4.39 0.00 0.00 3.32
599 1637 2.863132 ATTACGGGCCACTTGTTGTA 57.137 45.000 4.39 0.00 0.00 2.41
600 1638 2.634815 TTACGGGCCACTTGTTGTAA 57.365 45.000 4.39 0.00 0.00 2.41
601 1639 2.634815 TACGGGCCACTTGTTGTAAA 57.365 45.000 4.39 0.00 0.00 2.01
647 1702 3.558321 CCCGATTACAGGAACCAAAGACA 60.558 47.826 0.00 0.00 0.00 3.41
665 1720 1.134670 ACATTCTCCGGCTGCTAGTTC 60.135 52.381 0.00 0.00 0.00 3.01
736 1791 2.483188 CGGCATACTAGTTGGGACTTCC 60.483 54.545 0.00 0.00 37.33 3.46
749 1804 3.414700 CTTCCGACCAGTGCACGC 61.415 66.667 12.01 1.57 0.00 5.34
771 1826 1.441729 GGCCGTCCGATCTGAATCA 59.558 57.895 0.00 0.00 31.76 2.57
788 1843 7.097192 TCTGAATCAAAAACAGCTATCGTACT 58.903 34.615 0.00 0.00 0.00 2.73
802 1857 6.092670 AGCTATCGTACTACGTCAAAGTTGTA 59.907 38.462 8.42 0.00 43.14 2.41
804 1859 7.430502 GCTATCGTACTACGTCAAAGTTGTAAT 59.569 37.037 8.42 0.00 43.14 1.89
805 1860 7.731556 ATCGTACTACGTCAAAGTTGTAATC 57.268 36.000 8.42 0.00 43.14 1.75
806 1861 5.790003 TCGTACTACGTCAAAGTTGTAATCG 59.210 40.000 8.42 0.00 43.14 3.34
807 1862 5.002840 CGTACTACGTCAAAGTTGTAATCGG 59.997 44.000 0.00 0.00 36.74 4.18
809 1864 3.116079 ACGTCAAAGTTGTAATCGGGT 57.884 42.857 0.00 0.00 0.00 5.28
810 1865 3.469739 ACGTCAAAGTTGTAATCGGGTT 58.530 40.909 0.00 0.00 0.00 4.11
811 1866 4.630111 ACGTCAAAGTTGTAATCGGGTTA 58.370 39.130 0.00 0.00 0.00 2.85
893 1951 0.858583 CGCACACGTCAATCAGAACA 59.141 50.000 0.00 0.00 33.53 3.18
909 1967 1.199327 GAACACGATCACGACTCCAGA 59.801 52.381 0.00 0.00 42.66 3.86
917 1976 2.037136 ACGACTCCAGACCGTACGG 61.037 63.158 32.22 32.22 42.03 4.02
945 2027 4.021368 ACCAGTATATAATCACCAGCCGAC 60.021 45.833 0.00 0.00 0.00 4.79
958 2040 0.110486 AGCCGACACTCCAAAACCAT 59.890 50.000 0.00 0.00 0.00 3.55
1056 2214 1.847328 TGGTGCTCCTCGTCATCTTA 58.153 50.000 6.34 0.00 34.23 2.10
1482 2643 1.002134 CGTCAAGAACCAGGGCCAT 60.002 57.895 6.18 0.00 0.00 4.40
1539 2700 1.197721 GTGGAAGGCGTCAACAAGATG 59.802 52.381 2.86 0.00 36.29 2.90
1549 2710 0.036164 CAACAAGATGGTCACCGGGA 59.964 55.000 6.32 0.00 0.00 5.14
1551 2712 0.324943 ACAAGATGGTCACCGGGAAG 59.675 55.000 6.32 0.00 0.00 3.46
2246 3432 4.722700 CTGTTGCAGGGACCGGGG 62.723 72.222 6.32 0.00 0.00 5.73
2310 3497 2.203337 ACCTGCGCCAAGAGCAAA 60.203 55.556 4.18 0.00 44.67 3.68
2446 3699 6.975772 AGCTTTTTGTTTTCATAACGTAGCAA 59.024 30.769 0.00 0.00 0.00 3.91
2480 3737 5.962433 TCCGAGAGTCCTTGTAAATACTTG 58.038 41.667 0.00 0.00 0.00 3.16
2481 3738 5.479375 TCCGAGAGTCCTTGTAAATACTTGT 59.521 40.000 0.00 0.00 0.00 3.16
2482 3739 6.660521 TCCGAGAGTCCTTGTAAATACTTGTA 59.339 38.462 0.00 0.00 0.00 2.41
2520 3780 7.124147 GGAGGAATCATTCTTTTTCCAATGGTA 59.876 37.037 0.00 0.00 41.15 3.25
2673 5095 8.333984 TCCTAATATGATCCACGGTAAGAGATA 58.666 37.037 0.00 0.00 0.00 1.98
2674 5096 8.407064 CCTAATATGATCCACGGTAAGAGATAC 58.593 40.741 0.00 0.00 0.00 2.24
2675 5097 7.776618 AATATGATCCACGGTAAGAGATACA 57.223 36.000 0.00 0.00 36.14 2.29
2676 5098 5.713792 ATGATCCACGGTAAGAGATACAG 57.286 43.478 0.00 0.00 36.14 2.74
2677 5099 4.533815 TGATCCACGGTAAGAGATACAGT 58.466 43.478 0.00 0.00 42.63 3.55
2745 6646 2.911143 GCTAGCTAGCTGGGCCAA 59.089 61.111 33.71 4.87 45.62 4.52
2769 6709 0.667487 TGAGCAAAGAGTTCGCCTCG 60.667 55.000 0.00 0.00 45.44 4.63
2771 6711 0.249911 AGCAAAGAGTTCGCCTCGTT 60.250 50.000 0.00 0.00 45.44 3.85
2893 6844 0.247460 CAGGTCCATCGTTCAGAGCA 59.753 55.000 0.00 0.00 0.00 4.26
2917 6871 3.851098 AGCTTCTACTGAAACGACATCC 58.149 45.455 0.00 0.00 0.00 3.51
2940 6898 7.565680 TCCCTGATAATTTGGAGTTTCTAGTC 58.434 38.462 0.00 0.00 0.00 2.59
2945 6903 7.552687 TGATAATTTGGAGTTTCTAGTCGCAAT 59.447 33.333 0.00 0.00 0.00 3.56
2959 6918 1.153249 GCAATAGTACGGCTGGCCA 60.153 57.895 4.71 4.71 35.37 5.36
2973 6932 2.481471 GGCCAACTAATCCGCCAGC 61.481 63.158 0.00 0.00 41.25 4.85
2977 6937 3.400599 AACTAATCCGCCAGCCCCG 62.401 63.158 0.00 0.00 0.00 5.73
3001 6961 1.134946 GCCCGTTGATCCCATCTTTTG 59.865 52.381 0.00 0.00 0.00 2.44
3002 6962 2.446435 CCCGTTGATCCCATCTTTTGT 58.554 47.619 0.00 0.00 0.00 2.83
3003 6963 2.423538 CCCGTTGATCCCATCTTTTGTC 59.576 50.000 0.00 0.00 0.00 3.18
3004 6964 2.423538 CCGTTGATCCCATCTTTTGTCC 59.576 50.000 0.00 0.00 0.00 4.02
3005 6965 3.081061 CGTTGATCCCATCTTTTGTCCA 58.919 45.455 0.00 0.00 0.00 4.02
3051 10857 5.469760 GGTTTGCCAATGATTTTAGTTTGCT 59.530 36.000 0.00 0.00 34.09 3.91
3061 10867 3.488778 TTTAGTTTGCTACCGTGGGAA 57.511 42.857 0.00 0.00 0.00 3.97
3119 11072 9.365311 CAAATAACGAATAATAAAGGTACGCAG 57.635 33.333 0.00 0.00 0.00 5.18
3263 11246 7.803189 TGTGAAATTTTAGAATCTTTGAGCGAC 59.197 33.333 0.00 0.00 0.00 5.19
3357 11343 6.872628 AGGTGCTTAAGGTGTAAAAGTAAC 57.127 37.500 4.29 0.00 0.00 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.748708 CTTTTCCACAATTAATGAACTTCTTCA 57.251 29.630 0.00 0.00 40.77 3.02
3 4 9.965824 TCTTTTCCACAATTAATGAACTTCTTC 57.034 29.630 0.00 0.00 0.00 2.87
7 8 9.696917 GTGATCTTTTCCACAATTAATGAACTT 57.303 29.630 0.00 0.00 33.72 2.66
9 10 8.020819 TCGTGATCTTTTCCACAATTAATGAAC 58.979 33.333 0.00 0.00 33.13 3.18
13 14 7.687941 ACTCGTGATCTTTTCCACAATTAAT 57.312 32.000 0.00 0.00 33.13 1.40
15 16 7.504924 AAACTCGTGATCTTTTCCACAATTA 57.495 32.000 0.00 0.00 33.13 1.40
23 24 9.665264 AAACATTTCTAAACTCGTGATCTTTTC 57.335 29.630 0.00 0.00 0.00 2.29
96 111 7.228706 ACATTCGTTTATCTGGACTTTTTCACT 59.771 33.333 0.00 0.00 0.00 3.41
97 112 7.360361 ACATTCGTTTATCTGGACTTTTTCAC 58.640 34.615 0.00 0.00 0.00 3.18
100 115 8.842358 TCTACATTCGTTTATCTGGACTTTTT 57.158 30.769 0.00 0.00 0.00 1.94
105 120 7.039882 TCCTTTCTACATTCGTTTATCTGGAC 58.960 38.462 0.00 0.00 0.00 4.02
110 125 9.887406 TTGTTTTCCTTTCTACATTCGTTTATC 57.113 29.630 0.00 0.00 0.00 1.75
112 127 9.505995 GTTTGTTTTCCTTTCTACATTCGTTTA 57.494 29.630 0.00 0.00 0.00 2.01
117 132 7.435192 CACCAGTTTGTTTTCCTTTCTACATTC 59.565 37.037 0.00 0.00 0.00 2.67
123 138 8.528044 TTATACACCAGTTTGTTTTCCTTTCT 57.472 30.769 0.00 0.00 0.00 2.52
139 154 3.446873 CAGGGCAATGCTTTTATACACCA 59.553 43.478 4.82 0.00 0.00 4.17
140 155 3.699038 TCAGGGCAATGCTTTTATACACC 59.301 43.478 4.82 0.00 0.00 4.16
159 174 2.271800 GTAACTGGTTCAGCCGATCAG 58.728 52.381 0.00 0.00 41.21 2.90
164 179 2.736144 TACTGTAACTGGTTCAGCCG 57.264 50.000 0.00 0.00 41.21 5.52
168 183 5.247564 ACATAGCCTTACTGTAACTGGTTCA 59.752 40.000 7.44 0.00 0.00 3.18
171 186 6.685620 GCATACATAGCCTTACTGTAACTGGT 60.686 42.308 7.44 5.42 0.00 4.00
173 188 6.516718 AGCATACATAGCCTTACTGTAACTG 58.483 40.000 0.00 0.00 0.00 3.16
175 190 7.091443 CCTAGCATACATAGCCTTACTGTAAC 58.909 42.308 0.00 0.00 0.00 2.50
177 192 5.715279 CCCTAGCATACATAGCCTTACTGTA 59.285 44.000 0.00 0.00 0.00 2.74
179 194 4.081420 CCCCTAGCATACATAGCCTTACTG 60.081 50.000 0.00 0.00 0.00 2.74
182 197 3.838317 CACCCCTAGCATACATAGCCTTA 59.162 47.826 0.00 0.00 0.00 2.69
184 199 2.260822 CACCCCTAGCATACATAGCCT 58.739 52.381 0.00 0.00 0.00 4.58
186 201 2.872038 GCACACCCCTAGCATACATAGC 60.872 54.545 0.00 0.00 0.00 2.97
193 208 2.244117 CTGACGCACACCCCTAGCAT 62.244 60.000 0.00 0.00 0.00 3.79
235 250 2.433868 TATTATTCGGCGTCCTCTGC 57.566 50.000 6.85 0.00 0.00 4.26
238 253 3.057734 CCACTTATTATTCGGCGTCCTC 58.942 50.000 6.85 0.00 0.00 3.71
240 255 2.140717 CCCACTTATTATTCGGCGTCC 58.859 52.381 6.85 0.00 0.00 4.79
253 1000 5.737635 GCAATGCACAAACTTTACCCACTTA 60.738 40.000 0.00 0.00 0.00 2.24
256 1003 2.799978 GCAATGCACAAACTTTACCCAC 59.200 45.455 0.00 0.00 0.00 4.61
272 1019 3.186909 CCAGTTCATGAGCAATGCAATG 58.813 45.455 12.41 11.10 36.11 2.82
278 1025 3.920231 TCTAGCCAGTTCATGAGCAAT 57.080 42.857 12.41 0.00 0.00 3.56
280 1027 2.767960 TCATCTAGCCAGTTCATGAGCA 59.232 45.455 12.41 0.00 0.00 4.26
314 1061 7.096640 CGGTTGTTTTATTTTGTACAGCTGAAG 60.097 37.037 23.35 0.00 32.04 3.02
315 1062 6.693545 CGGTTGTTTTATTTTGTACAGCTGAA 59.306 34.615 23.35 3.60 32.04 3.02
320 1067 9.377383 CTTCTACGGTTGTTTTATTTTGTACAG 57.623 33.333 0.00 0.00 0.00 2.74
321 1068 8.344098 CCTTCTACGGTTGTTTTATTTTGTACA 58.656 33.333 0.00 0.00 0.00 2.90
326 1073 6.644248 AGCCTTCTACGGTTGTTTTATTTT 57.356 33.333 0.00 0.00 0.00 1.82
327 1074 6.644248 AAGCCTTCTACGGTTGTTTTATTT 57.356 33.333 0.00 0.00 0.00 1.40
335 1082 2.178912 TGGAAAGCCTTCTACGGTTG 57.821 50.000 0.00 0.00 34.31 3.77
338 1085 5.414765 ACTTTTATTGGAAAGCCTTCTACGG 59.585 40.000 0.00 0.00 39.65 4.02
345 1092 3.511540 GCCAGACTTTTATTGGAAAGCCT 59.488 43.478 0.00 0.00 39.65 4.58
352 1099 5.104259 AGACCTAGCCAGACTTTTATTGG 57.896 43.478 0.00 0.00 35.06 3.16
356 1103 4.417437 ACTGAGACCTAGCCAGACTTTTA 58.583 43.478 0.00 0.00 0.00 1.52
363 1110 3.902881 AATCAACTGAGACCTAGCCAG 57.097 47.619 0.00 0.00 0.00 4.85
385 1132 9.730705 TCACTTGATTGAGATTTGATTAAGTCT 57.269 29.630 0.00 0.00 35.80 3.24
447 1197 9.585099 TTGTATGTAGATTCATGCAAAATTTCC 57.415 29.630 7.49 0.00 43.42 3.13
452 1202 9.399797 AGATCTTGTATGTAGATTCATGCAAAA 57.600 29.630 10.25 0.00 44.76 2.44
453 1203 8.969260 AGATCTTGTATGTAGATTCATGCAAA 57.031 30.769 10.25 0.00 44.76 3.68
454 1204 8.206189 TGAGATCTTGTATGTAGATTCATGCAA 58.794 33.333 0.00 9.09 43.87 4.08
455 1205 7.654923 GTGAGATCTTGTATGTAGATTCATGCA 59.345 37.037 0.00 0.00 38.30 3.96
456 1206 7.117523 GGTGAGATCTTGTATGTAGATTCATGC 59.882 40.741 0.00 0.00 32.64 4.06
457 1207 7.328005 CGGTGAGATCTTGTATGTAGATTCATG 59.672 40.741 0.00 0.00 32.64 3.07
458 1208 7.231519 TCGGTGAGATCTTGTATGTAGATTCAT 59.768 37.037 0.00 0.00 32.64 2.57
459 1209 6.546034 TCGGTGAGATCTTGTATGTAGATTCA 59.454 38.462 0.00 0.00 32.64 2.57
460 1210 6.971602 TCGGTGAGATCTTGTATGTAGATTC 58.028 40.000 0.00 0.00 32.64 2.52
461 1211 6.961360 TCGGTGAGATCTTGTATGTAGATT 57.039 37.500 0.00 0.00 32.64 2.40
462 1212 8.815565 ATATCGGTGAGATCTTGTATGTAGAT 57.184 34.615 0.00 0.00 40.66 1.98
463 1213 8.515414 CAATATCGGTGAGATCTTGTATGTAGA 58.485 37.037 0.00 0.00 38.13 2.59
464 1214 7.274468 GCAATATCGGTGAGATCTTGTATGTAG 59.726 40.741 0.00 0.00 42.22 2.74
465 1215 7.090808 GCAATATCGGTGAGATCTTGTATGTA 58.909 38.462 0.00 0.00 42.22 2.29
466 1216 5.928839 GCAATATCGGTGAGATCTTGTATGT 59.071 40.000 0.00 0.00 42.22 2.29
467 1217 5.061435 CGCAATATCGGTGAGATCTTGTATG 59.939 44.000 0.00 0.00 42.22 2.39
468 1218 5.164233 CGCAATATCGGTGAGATCTTGTAT 58.836 41.667 0.00 0.00 42.22 2.29
469 1219 4.037565 ACGCAATATCGGTGAGATCTTGTA 59.962 41.667 0.00 0.00 42.22 2.41
472 1222 3.643763 GACGCAATATCGGTGAGATCTT 58.356 45.455 0.00 0.00 40.66 2.40
474 1224 1.979469 CGACGCAATATCGGTGAGATC 59.021 52.381 0.00 0.00 40.66 2.75
482 1232 4.280461 AGTCTAAAGTCGACGCAATATCG 58.720 43.478 10.46 0.00 41.00 2.92
483 1233 7.431668 AGTTAAGTCTAAAGTCGACGCAATATC 59.568 37.037 10.46 0.01 36.53 1.63
504 1542 8.186821 GCCGACTTAGACTTAAGACATAGTTAA 58.813 37.037 10.09 0.00 38.88 2.01
509 1547 5.884232 TCAGCCGACTTAGACTTAAGACATA 59.116 40.000 10.09 0.00 38.88 2.29
511 1549 4.077108 TCAGCCGACTTAGACTTAAGACA 58.923 43.478 10.09 0.00 38.88 3.41
518 1556 2.948979 CTGATCTCAGCCGACTTAGACT 59.051 50.000 0.00 0.00 37.15 3.24
519 1557 3.347958 CTGATCTCAGCCGACTTAGAC 57.652 52.381 0.00 0.00 37.15 2.59
581 1619 2.634815 TTACAACAAGTGGCCCGTAA 57.365 45.000 0.00 0.00 0.00 3.18
582 1620 2.634815 TTTACAACAAGTGGCCCGTA 57.365 45.000 0.00 0.00 0.00 4.02
583 1621 1.765230 TTTTACAACAAGTGGCCCGT 58.235 45.000 0.00 0.00 0.00 5.28
584 1622 2.873133 TTTTTACAACAAGTGGCCCG 57.127 45.000 0.00 0.00 0.00 6.13
604 1642 9.768662 ATCGGGTTACAACGTAAATTTATCTAT 57.231 29.630 0.31 0.00 0.00 1.98
606 1644 8.496707 AATCGGGTTACAACGTAAATTTATCT 57.503 30.769 0.31 0.00 0.00 1.98
607 1645 9.636965 GTAATCGGGTTACAACGTAAATTTATC 57.363 33.333 6.29 0.00 41.87 1.75
635 1679 2.084546 CCGGAGAATGTCTTTGGTTCC 58.915 52.381 0.00 0.00 0.00 3.62
647 1702 0.103208 CGAACTAGCAGCCGGAGAAT 59.897 55.000 5.05 0.00 0.00 2.40
788 1843 4.255833 ACCCGATTACAACTTTGACGTA 57.744 40.909 0.00 0.00 0.00 3.57
809 1864 2.232941 GACCTCAGATCCAACGGTGTAA 59.767 50.000 0.00 0.00 0.00 2.41
810 1865 1.822990 GACCTCAGATCCAACGGTGTA 59.177 52.381 0.00 0.00 0.00 2.90
811 1866 0.608640 GACCTCAGATCCAACGGTGT 59.391 55.000 0.00 0.00 0.00 4.16
871 1929 0.388520 TCTGATTGACGTGTGCGAGG 60.389 55.000 0.00 0.00 42.00 4.63
877 1935 2.502213 TCGTGTTCTGATTGACGTGT 57.498 45.000 0.00 0.00 33.56 4.49
893 1951 1.645704 CGGTCTGGAGTCGTGATCGT 61.646 60.000 8.05 0.00 38.33 3.73
909 1967 2.769652 TACTGGTCTGGCCGTACGGT 62.770 60.000 33.34 14.25 41.21 4.83
917 1976 5.482908 CTGGTGATTATATACTGGTCTGGC 58.517 45.833 0.00 0.00 0.00 4.85
945 2027 4.032900 CGATCGACTTATGGTTTTGGAGTG 59.967 45.833 10.26 0.00 0.00 3.51
1539 2700 3.692406 ACGAGCTTCCCGGTGACC 61.692 66.667 0.00 0.00 0.00 4.02
2409 3642 8.308207 TGAAAACAAAAAGCTGTAACCTAAACT 58.692 29.630 0.00 0.00 0.00 2.66
2616 4944 8.321353 TGACCATGATCATATACCATTCCTTAC 58.679 37.037 8.15 0.00 0.00 2.34
2623 4951 8.489489 GGAACTATGACCATGATCATATACCAT 58.511 37.037 10.32 11.47 40.08 3.55
2673 5095 3.791320 TCACCTCCCTCAATTCTACTGT 58.209 45.455 0.00 0.00 0.00 3.55
2674 5096 4.826274 TTCACCTCCCTCAATTCTACTG 57.174 45.455 0.00 0.00 0.00 2.74
2675 5097 4.846940 AGTTTCACCTCCCTCAATTCTACT 59.153 41.667 0.00 0.00 0.00 2.57
2676 5098 5.167303 AGTTTCACCTCCCTCAATTCTAC 57.833 43.478 0.00 0.00 0.00 2.59
2677 5099 5.783360 TGTAGTTTCACCTCCCTCAATTCTA 59.217 40.000 0.00 0.00 0.00 2.10
2745 6646 2.421424 GGCGAACTCTTTGCTCATGAAT 59.579 45.455 0.00 0.00 40.04 2.57
2769 6709 8.474006 AAGTGGTTTTTGAACATGAGTTTAAC 57.526 30.769 0.00 0.00 38.30 2.01
2771 6711 7.547370 CCAAAGTGGTTTTTGAACATGAGTTTA 59.453 33.333 0.00 0.00 39.79 2.01
2893 6844 6.043411 GGATGTCGTTTCAGTAGAAGCTATT 58.957 40.000 0.00 0.00 34.71 1.73
2917 6871 6.018669 GCGACTAGAAACTCCAAATTATCAGG 60.019 42.308 0.00 0.00 0.00 3.86
2940 6898 2.244651 GGCCAGCCGTACTATTGCG 61.245 63.158 0.00 0.00 0.00 4.85
2945 6903 1.559368 TTAGTTGGCCAGCCGTACTA 58.441 50.000 16.95 12.91 39.42 1.82
2959 6918 2.595655 GGGGCTGGCGGATTAGTT 59.404 61.111 0.00 0.00 0.00 2.24
2984 6944 3.081061 TGGACAAAAGATGGGATCAACG 58.919 45.455 0.00 0.00 0.00 4.10
3051 10857 6.052405 ACACATACTTAAATTCCCACGGTA 57.948 37.500 0.00 0.00 0.00 4.02
3119 11072 9.617523 ATCCAAATATTTCAACATTTCAATCCC 57.382 29.630 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.