Multiple sequence alignment - TraesCS6D01G225900

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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 TraesCS6D01G225900 chr6D 100.000 5119 0 0 1 5119 317484264 317489382 0.000000e+00 9454.0
1 TraesCS6D01G225900 chr6A 94.345 4315 167 43 838 5119 455042788 455047058 0.000000e+00 6545.0
2 TraesCS6D01G225900 chr6A 86.667 510 61 6 308 816 455039603 455040106 4.480000e-155 558.0
3 TraesCS6D01G225900 chr6B 95.050 2505 96 14 1680 4178 506710301 506707819 0.000000e+00 3914.0
4 TraesCS6D01G225900 chr6B 91.252 743 42 11 951 1686 506711149 506710423 0.000000e+00 990.0
5 TraesCS6D01G225900 chr6B 92.432 370 22 5 4176 4540 506707658 506707290 1.630000e-144 523.0
6 TraesCS6D01G225900 chr6B 93.878 343 16 4 4546 4885 506707246 506706906 3.530000e-141 512.0
7 TraesCS6D01G225900 chr6B 91.961 311 12 8 1 300 506717294 506716986 1.700000e-114 424.0
8 TraesCS6D01G225900 chr6B 94.239 243 10 3 4880 5119 506706844 506706603 8.100000e-98 368.0
9 TraesCS6D01G225900 chr6B 93.590 234 15 0 513 746 506715937 506715704 2.930000e-92 350.0
10 TraesCS6D01G225900 chr6B 100.000 28 0 0 917 944 506714559 506714532 9.000000e-03 52.8
11 TraesCS6D01G225900 chrUn 92.920 113 8 0 2897 3009 273323038 273322926 1.140000e-36 165.0
12 TraesCS6D01G225900 chrUn 92.920 113 8 0 2897 3009 366017932 366017820 1.140000e-36 165.0
13 TraesCS6D01G225900 chrUn 92.920 113 8 0 2897 3009 432254609 432254497 1.140000e-36 165.0
14 TraesCS6D01G225900 chr4D 92.920 113 8 0 2897 3009 123380331 123380443 1.140000e-36 165.0
15 TraesCS6D01G225900 chr4D 92.920 113 8 0 2897 3009 123591116 123591228 1.140000e-36 165.0
16 TraesCS6D01G225900 chr3D 92.920 113 8 0 2897 3009 523756379 523756491 1.140000e-36 165.0
17 TraesCS6D01G225900 chr2D 92.920 113 8 0 2897 3009 635049761 635049873 1.140000e-36 165.0


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 TraesCS6D01G225900 chr6D 317484264 317489382 5118 False 9454.000 9454 100.00000 1 5119 1 chr6D.!!$F1 5118
1 TraesCS6D01G225900 chr6A 455039603 455047058 7455 False 3551.500 6545 90.50600 308 5119 2 chr6A.!!$F1 4811
2 TraesCS6D01G225900 chr6B 506706603 506717294 10691 True 891.725 3914 94.05025 1 5119 8 chr6B.!!$R1 5118

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
948 4663 0.110056 TCACGCGAGTTTCTACGGTC 60.110 55.000 15.93 0.0 46.40 4.79 F
1215 8316 0.741221 CTGTAGGGCTCGTTGGCTTC 60.741 60.000 5.03 0.0 41.48 3.86 F
1410 8511 1.270358 GGATTCTCCTATGCCCGTGAC 60.270 57.143 0.00 0.0 32.53 3.67 F
1725 8953 1.402968 AGAAATGTGCATGACATCCGC 59.597 47.619 0.00 0.0 45.12 5.54 F
2993 10228 2.799412 CTCTTTAGATGCCATCACTCGC 59.201 50.000 7.56 0.0 0.00 5.03 F
3891 11128 0.884704 AGCTTGCCACTGGTACAACG 60.885 55.000 0.00 0.0 38.70 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2415 9649 1.873591 CCAACAGGAGAAACTTGGACG 59.126 52.381 0.00 0.0 36.06 4.79 R
2991 10226 3.976339 CAGAGATCTGGGGTAAGCG 57.024 57.895 0.00 0.0 40.20 4.68 R
3435 10670 8.498054 ACTTGAACTGATTATACCAGAACATG 57.502 34.615 7.99 0.0 35.69 3.21 R
3568 10803 7.471721 TGGTCAATAAGATCGCACAAAATTAG 58.528 34.615 0.00 0.0 0.00 1.73 R
4065 11302 1.069204 GACGATGCCTATTCCAGCTCA 59.931 52.381 0.00 0.0 0.00 4.26 R
5077 12596 0.830444 ATAGCGAAGGGGCCGATGTA 60.830 55.000 0.00 0.0 0.00 2.29 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
35 36 6.207417 TCTGAGAGATTTTCCAACACATTTCC 59.793 38.462 0.00 0.00 0.00 3.13
36 37 5.243730 TGAGAGATTTTCCAACACATTTCCC 59.756 40.000 0.00 0.00 0.00 3.97
37 38 5.147032 AGAGATTTTCCAACACATTTCCCA 58.853 37.500 0.00 0.00 0.00 4.37
41 42 5.620738 TTTTCCAACACATTTCCCAATGA 57.379 34.783 1.97 0.00 42.35 2.57
42 43 5.822132 TTTCCAACACATTTCCCAATGAT 57.178 34.783 1.97 0.00 42.35 2.45
47 48 6.709846 TCCAACACATTTCCCAATGATTTTTC 59.290 34.615 1.97 0.00 42.35 2.29
195 207 6.910433 CACCGCAATCAAAACTAATGTATACC 59.090 38.462 0.00 0.00 0.00 2.73
284 296 2.086610 ATGGAAGTGCACCCAAAGTT 57.913 45.000 17.32 2.73 35.85 2.66
289 301 2.022764 AGTGCACCCAAAGTTTTTGC 57.977 45.000 14.63 6.65 0.00 3.68
303 1266 3.742369 AGTTTTTGCCATTCAATGCTTCG 59.258 39.130 0.00 0.00 34.12 3.79
320 1283 7.801547 ATGCTTCGTTGAAATTAAATGAGTG 57.198 32.000 0.00 0.00 0.00 3.51
321 1284 5.629020 TGCTTCGTTGAAATTAAATGAGTGC 59.371 36.000 5.81 5.81 0.00 4.40
372 1335 4.290155 CAAGCACACTGTATTGTGTTTCC 58.710 43.478 2.77 0.00 44.74 3.13
373 1336 3.003275 AAGCACACTGTATTGTGTTTCCG 59.997 43.478 5.23 0.00 44.74 4.30
374 1337 6.556391 AAGCACACTGTATTGTGTTTCCGC 62.556 45.833 5.23 0.00 44.74 5.54
376 1339 3.187478 CACTGTATTGTGTTTCCGCTG 57.813 47.619 0.00 0.00 33.61 5.18
378 1341 0.878416 TGTATTGTGTTTCCGCTGCC 59.122 50.000 0.00 0.00 0.00 4.85
380 1343 1.268352 GTATTGTGTTTCCGCTGCCAA 59.732 47.619 0.00 0.00 0.00 4.52
381 1344 0.968405 ATTGTGTTTCCGCTGCCAAT 59.032 45.000 0.00 0.00 0.00 3.16
382 1345 0.749649 TTGTGTTTCCGCTGCCAATT 59.250 45.000 0.00 0.00 0.00 2.32
383 1346 1.610363 TGTGTTTCCGCTGCCAATTA 58.390 45.000 0.00 0.00 0.00 1.40
384 1347 1.957177 TGTGTTTCCGCTGCCAATTAA 59.043 42.857 0.00 0.00 0.00 1.40
385 1348 2.362397 TGTGTTTCCGCTGCCAATTAAA 59.638 40.909 0.00 0.00 0.00 1.52
386 1349 3.006323 TGTGTTTCCGCTGCCAATTAAAT 59.994 39.130 0.00 0.00 0.00 1.40
387 1350 4.218635 TGTGTTTCCGCTGCCAATTAAATA 59.781 37.500 0.00 0.00 0.00 1.40
388 1351 5.164954 GTGTTTCCGCTGCCAATTAAATAA 58.835 37.500 0.00 0.00 0.00 1.40
389 1352 5.635700 GTGTTTCCGCTGCCAATTAAATAAA 59.364 36.000 0.00 0.00 0.00 1.40
390 1353 6.146347 GTGTTTCCGCTGCCAATTAAATAAAA 59.854 34.615 0.00 0.00 0.00 1.52
391 1354 6.367422 TGTTTCCGCTGCCAATTAAATAAAAG 59.633 34.615 0.00 0.00 0.00 2.27
392 1355 5.906113 TCCGCTGCCAATTAAATAAAAGA 57.094 34.783 0.00 0.00 0.00 2.52
393 1356 5.646606 TCCGCTGCCAATTAAATAAAAGAC 58.353 37.500 0.00 0.00 0.00 3.01
394 1357 5.417580 TCCGCTGCCAATTAAATAAAAGACT 59.582 36.000 0.00 0.00 0.00 3.24
395 1358 5.516339 CCGCTGCCAATTAAATAAAAGACTG 59.484 40.000 0.00 0.00 0.00 3.51
396 1359 5.004726 CGCTGCCAATTAAATAAAAGACTGC 59.995 40.000 0.00 0.00 0.00 4.40
397 1360 5.868801 GCTGCCAATTAAATAAAAGACTGCA 59.131 36.000 0.00 0.00 0.00 4.41
398 1361 6.183360 GCTGCCAATTAAATAAAAGACTGCAC 60.183 38.462 0.00 0.00 0.00 4.57
399 1362 6.162777 TGCCAATTAAATAAAAGACTGCACC 58.837 36.000 0.00 0.00 0.00 5.01
400 1363 5.288472 GCCAATTAAATAAAAGACTGCACCG 59.712 40.000 0.00 0.00 0.00 4.94
401 1364 6.616947 CCAATTAAATAAAAGACTGCACCGA 58.383 36.000 0.00 0.00 0.00 4.69
411 1393 1.303236 CTGCACCGATCCCCAAACA 60.303 57.895 0.00 0.00 0.00 2.83
414 1396 0.894835 GCACCGATCCCCAAACAAAT 59.105 50.000 0.00 0.00 0.00 2.32
418 1400 1.750778 CCGATCCCCAAACAAATCAGG 59.249 52.381 0.00 0.00 0.00 3.86
420 1402 2.684881 CGATCCCCAAACAAATCAGGAG 59.315 50.000 0.00 0.00 0.00 3.69
424 1406 1.273327 CCCAAACAAATCAGGAGTGGC 59.727 52.381 0.00 0.00 0.00 5.01
444 1426 0.322456 TTTGATTCCAGAGGGGTGCG 60.322 55.000 0.00 0.00 38.11 5.34
447 1429 2.595009 GATTCCAGAGGGGTGCGTCC 62.595 65.000 0.00 0.00 38.11 4.79
459 1441 2.285773 TGCGTCCTGATGTGCTCCT 61.286 57.895 0.00 0.00 0.00 3.69
469 1451 3.807538 GTGCTCCTCGTCCGCGTA 61.808 66.667 4.92 0.00 39.49 4.42
470 1452 2.827190 TGCTCCTCGTCCGCGTAT 60.827 61.111 4.92 0.00 39.49 3.06
482 1464 3.419922 CGTCCGCGTATGTATGTTTACTC 59.580 47.826 4.92 0.00 0.00 2.59
491 1473 9.073368 GCGTATGTATGTTTACTCCATATACAG 57.927 37.037 0.00 0.00 37.56 2.74
517 1499 5.762279 AGGAGAAAAACCCTAGTTGTTGAA 58.238 37.500 0.00 0.00 33.36 2.69
562 1544 1.597663 ACAACAGAAAGGCGTCGAAAG 59.402 47.619 0.00 0.00 0.00 2.62
627 1609 7.428020 CAATGAGAAACATGAAACTGAAGGAA 58.572 34.615 0.00 0.00 39.39 3.36
631 1613 4.453480 AACATGAAACTGAAGGAAGGGA 57.547 40.909 0.00 0.00 0.00 4.20
645 1627 2.238521 GAAGGGAAATGTGAGTTGGCA 58.761 47.619 0.00 0.00 0.00 4.92
724 1706 7.255451 GGTCAATACCACAAAGTCATTCAAGAA 60.255 37.037 0.00 0.00 45.98 2.52
742 1724 8.561738 TTCAAGAATGGTACTTTGAAGGATAC 57.438 34.615 0.00 0.00 0.00 2.24
753 1735 4.857871 TTGAAGGATACGCTCAAATTCG 57.142 40.909 0.00 0.00 39.40 3.34
763 1745 1.156736 CTCAAATTCGCACGGGTCTT 58.843 50.000 0.00 0.00 0.00 3.01
764 1746 0.871722 TCAAATTCGCACGGGTCTTG 59.128 50.000 0.00 0.00 0.00 3.02
765 1747 0.729140 CAAATTCGCACGGGTCTTGC 60.729 55.000 0.00 0.00 36.57 4.01
776 1758 2.035442 GGTCTTGCGGCTTGGAGAC 61.035 63.158 0.00 9.26 38.19 3.36
804 1786 4.026062 TCGCGAAATATTTGATCCTTCGTG 60.026 41.667 6.20 7.92 46.13 4.35
847 4555 3.243334 TGCATCAAATTTGTCACAAGCGA 60.243 39.130 17.47 0.00 0.00 4.93
865 4573 5.536554 AGCGATACAGTCTGAATGTTTTG 57.463 39.130 16.37 12.90 32.02 2.44
870 4578 6.803320 CGATACAGTCTGAATGTTTTGCAAAT 59.197 34.615 16.37 1.69 32.02 2.32
871 4579 7.326789 CGATACAGTCTGAATGTTTTGCAAATT 59.673 33.333 16.37 4.29 32.02 1.82
888 4600 9.495754 TTTGCAAATTATTTTGAAACCTTTTCG 57.504 25.926 8.05 0.00 44.11 3.46
889 4601 7.128976 TGCAAATTATTTTGAAACCTTTTCGC 58.871 30.769 13.02 0.00 44.11 4.70
948 4663 0.110056 TCACGCGAGTTTCTACGGTC 60.110 55.000 15.93 0.00 46.40 4.79
1084 8179 8.993404 AAATCAAAATCAATTCCAGGGAAAAA 57.007 26.923 4.63 0.00 37.69 1.94
1085 8180 7.984422 ATCAAAATCAATTCCAGGGAAAAAC 57.016 32.000 4.63 0.00 37.69 2.43
1086 8181 6.893583 TCAAAATCAATTCCAGGGAAAAACA 58.106 32.000 4.63 0.00 37.69 2.83
1087 8182 6.991531 TCAAAATCAATTCCAGGGAAAAACAG 59.008 34.615 4.63 0.00 37.69 3.16
1088 8183 6.745794 AAATCAATTCCAGGGAAAAACAGA 57.254 33.333 4.63 0.17 37.69 3.41
1215 8316 0.741221 CTGTAGGGCTCGTTGGCTTC 60.741 60.000 5.03 0.00 41.48 3.86
1236 8337 3.917760 CGGCGGGAGGAGATGGAC 61.918 72.222 0.00 0.00 0.00 4.02
1239 8340 2.835431 CGGGAGGAGATGGACGCT 60.835 66.667 0.00 0.00 0.00 5.07
1357 8458 2.101917 TCCGGAATCGAAGGTATTGGTC 59.898 50.000 0.00 0.00 39.00 4.02
1359 8460 2.805657 CGGAATCGAAGGTATTGGTCCC 60.806 54.545 0.00 0.00 39.00 4.46
1360 8461 2.438392 GGAATCGAAGGTATTGGTCCCT 59.562 50.000 0.00 0.00 0.00 4.20
1361 8462 3.118000 GGAATCGAAGGTATTGGTCCCTT 60.118 47.826 0.00 0.00 43.72 3.95
1369 8470 2.581246 GGTATTGGTCCCTTCTTTCCCT 59.419 50.000 0.00 0.00 0.00 4.20
1384 8485 5.277250 TCTTTCCCTTTCCCTTTGTTCTTT 58.723 37.500 0.00 0.00 0.00 2.52
1385 8486 5.362717 TCTTTCCCTTTCCCTTTGTTCTTTC 59.637 40.000 0.00 0.00 0.00 2.62
1386 8487 4.258457 TCCCTTTCCCTTTGTTCTTTCA 57.742 40.909 0.00 0.00 0.00 2.69
1387 8488 4.814967 TCCCTTTCCCTTTGTTCTTTCAT 58.185 39.130 0.00 0.00 0.00 2.57
1388 8489 4.588528 TCCCTTTCCCTTTGTTCTTTCATG 59.411 41.667 0.00 0.00 0.00 3.07
1389 8490 4.344968 CCCTTTCCCTTTGTTCTTTCATGT 59.655 41.667 0.00 0.00 0.00 3.21
1397 8498 6.385033 CCTTTGTTCTTTCATGTGGATTCTC 58.615 40.000 0.00 0.00 0.00 2.87
1399 8500 5.246981 TGTTCTTTCATGTGGATTCTCCT 57.753 39.130 0.00 0.00 37.46 3.69
1410 8511 1.270358 GGATTCTCCTATGCCCGTGAC 60.270 57.143 0.00 0.00 32.53 3.67
1422 8523 2.047844 CGTGACTCTGCCCCTGTG 60.048 66.667 0.00 0.00 0.00 3.66
1439 8540 4.060900 CCTGTGAGCATGATTACGCTTAT 58.939 43.478 0.00 0.00 38.99 1.73
1440 8541 5.230182 CCTGTGAGCATGATTACGCTTATA 58.770 41.667 0.00 0.00 38.99 0.98
1478 8579 2.603173 GCGAGCTGTTTCAGTTTTCCTG 60.603 50.000 0.00 0.00 42.97 3.86
1509 8610 4.839668 TGGTTAGGGTGATTTTTGAACG 57.160 40.909 0.00 0.00 0.00 3.95
1517 8618 5.983118 AGGGTGATTTTTGAACGATTTTGTC 59.017 36.000 0.00 0.00 0.00 3.18
1519 8620 6.074356 GGGTGATTTTTGAACGATTTTGTCAG 60.074 38.462 0.00 0.00 0.00 3.51
1522 8623 8.469125 GTGATTTTTGAACGATTTTGTCAGTAC 58.531 33.333 0.00 0.00 0.00 2.73
1545 8646 5.095490 CCGTTGCTGTTTTAGGATCAATTC 58.905 41.667 0.00 0.00 0.00 2.17
1580 8681 4.062991 CTGGTTACCCCAATCGTAATAGC 58.937 47.826 0.00 0.00 44.65 2.97
1645 8746 5.925969 TGATCAATGCGCGAGAAATAATAGA 59.074 36.000 12.10 0.00 0.00 1.98
1649 8750 2.626266 TGCGCGAGAAATAATAGAGGGA 59.374 45.455 12.10 0.00 0.00 4.20
1668 8769 7.126061 AGAGGGAAAAGGGGAAACAAATATAG 58.874 38.462 0.00 0.00 0.00 1.31
1725 8953 1.402968 AGAAATGTGCATGACATCCGC 59.597 47.619 0.00 0.00 45.12 5.54
1820 9049 6.985059 AGAACTGAAACTGACTGTAGGTTTAC 59.015 38.462 9.50 5.97 34.00 2.01
1871 9100 5.685520 TCAGGCTGGTTATGTTATGTGTA 57.314 39.130 15.73 0.00 0.00 2.90
1910 9144 6.595326 TCTCACTTCTGTTTGCTATGGTTATG 59.405 38.462 0.00 0.00 0.00 1.90
1959 9193 8.572185 GTCATACTTAGATGATCTACAGAAGCA 58.428 37.037 0.78 0.00 38.11 3.91
2381 9615 6.294473 TGCATTTTCTCTCTCTCAAAACTCT 58.706 36.000 0.00 0.00 0.00 3.24
2415 9649 4.785511 TGACTGTCTACTACCAGAAAGC 57.214 45.455 9.51 0.00 33.74 3.51
2717 9952 6.255887 CACGGTAGTCAGAATTCTTCATAACC 59.744 42.308 4.86 9.08 0.00 2.85
2893 10128 6.431198 TCATCCTGAATAACGCCTAAAAAC 57.569 37.500 0.00 0.00 0.00 2.43
2931 10166 9.515020 CTTTAAATTATGCAATACGTTCACCAT 57.485 29.630 0.00 0.00 0.00 3.55
2991 10226 3.559242 GCACTCTTTAGATGCCATCACTC 59.441 47.826 7.56 0.00 33.06 3.51
2993 10228 2.799412 CTCTTTAGATGCCATCACTCGC 59.201 50.000 7.56 0.00 0.00 5.03
3435 10670 7.106890 AGAGTTCTTTTACTGGCTAATCTTCC 58.893 38.462 0.00 0.00 0.00 3.46
3599 10834 4.811024 GTGCGATCTTATTGACCATCTTGA 59.189 41.667 0.00 0.00 0.00 3.02
3602 10837 6.203530 TGCGATCTTATTGACCATCTTGATTC 59.796 38.462 0.00 0.00 0.00 2.52
3891 11128 0.884704 AGCTTGCCACTGGTACAACG 60.885 55.000 0.00 0.00 38.70 4.10
4082 11319 6.830873 ATTAAATGAGCTGGAATAGGCATC 57.169 37.500 0.00 0.00 0.00 3.91
4140 11378 4.498009 GCCTGGTAATGAAATTCCATGTCG 60.498 45.833 0.00 0.00 37.87 4.35
4208 11609 3.058293 TGACAATGGTCTGTTCAATTCGC 60.058 43.478 1.02 0.00 44.61 4.70
4239 11640 5.897250 TCAGGTACTAACTAAGATGCATCCA 59.103 40.000 23.06 10.54 36.02 3.41
4426 11833 2.218603 TCGGGAGCTGAGTTTGTTTTC 58.781 47.619 0.00 0.00 0.00 2.29
4435 11842 7.225734 GGAGCTGAGTTTGTTTTCTAGGATATC 59.774 40.741 0.00 0.00 0.00 1.63
4479 11886 6.369615 AGCATTCAAATTACAAACATTCCTGC 59.630 34.615 0.00 0.00 0.00 4.85
4504 11911 6.356556 TGTGATCAGTTCCTTTTCTTCAGAA 58.643 36.000 0.00 0.00 0.00 3.02
4525 11932 9.209175 TCAGAAGATTCTTAAGCTAACAGTTTC 57.791 33.333 0.00 0.00 34.74 2.78
4544 11989 2.733517 TCGAATTTTGTTTTGCCGGTC 58.266 42.857 1.90 0.00 0.00 4.79
4562 12007 5.221048 GCCGGTCTAAATTAGAATGTGCATT 60.221 40.000 4.04 0.00 36.40 3.56
4738 12186 1.874872 TGCGACGTTTCCCCTTAAAAG 59.125 47.619 0.00 0.00 0.00 2.27
4740 12188 2.745821 GCGACGTTTCCCCTTAAAAGAT 59.254 45.455 0.00 0.00 0.00 2.40
4789 12238 4.164843 ACAGTGGTGGACATTTACAAGT 57.835 40.909 0.00 0.00 0.00 3.16
4790 12239 5.298989 ACAGTGGTGGACATTTACAAGTA 57.701 39.130 0.00 0.00 0.00 2.24
4791 12240 5.876357 ACAGTGGTGGACATTTACAAGTAT 58.124 37.500 0.00 0.00 0.00 2.12
4807 12256 9.520204 TTTACAAGTATACAAAGCCGATACTAC 57.480 33.333 5.50 0.00 35.76 2.73
4878 12394 1.518572 CGACATGGCACGACCCTAC 60.519 63.158 0.00 0.00 37.83 3.18
5000 12519 1.385743 CGCAGTTAGCAACTCGTGTAC 59.614 52.381 0.00 0.00 46.13 2.90
5113 12632 2.481952 GCTATGCATGACGGGATCTTTC 59.518 50.000 10.16 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 6.064060 TGTGTTGGAAAATCTCTCAGATTGT 58.936 36.000 0.00 0.00 43.67 2.71
23 24 6.711645 AGAAAAATCATTGGGAAATGTGTTGG 59.288 34.615 0.00 0.00 0.00 3.77
47 48 6.254589 CGCTCTCAGTTTTCCACTTAAGATAG 59.745 42.308 10.09 0.00 30.92 2.08
65 66 8.630037 TCTAGAATTATTACAATGACGCTCTCA 58.370 33.333 0.00 0.00 0.00 3.27
145 146 8.587608 TGATTAATTGCACCTTTCTCAGAATTT 58.412 29.630 0.00 0.00 0.00 1.82
149 150 6.500684 GTGATTAATTGCACCTTTCTCAGA 57.499 37.500 0.00 0.00 0.00 3.27
195 207 7.697710 AGCAATTTCATTTGTGTATATGTGACG 59.302 33.333 0.00 0.00 0.00 4.35
229 241 5.772521 ACCAGAATGAAGCATTGTAAACAC 58.227 37.500 0.00 0.00 39.69 3.32
274 286 3.539604 TGAATGGCAAAAACTTTGGGTG 58.460 40.909 0.00 0.00 0.00 4.61
284 296 3.383620 ACGAAGCATTGAATGGCAAAA 57.616 38.095 7.35 0.00 40.48 2.44
289 301 7.579589 TTAATTTCAACGAAGCATTGAATGG 57.420 32.000 7.35 0.00 43.65 3.16
303 1266 7.589954 AGTTGTACGCACTCATTTAATTTCAAC 59.410 33.333 0.00 0.00 0.00 3.18
320 1283 3.362693 GCTGACAGTAAACAGTTGTACGC 60.363 47.826 3.99 0.00 36.62 4.42
321 1284 3.799963 TGCTGACAGTAAACAGTTGTACG 59.200 43.478 3.99 0.00 36.62 3.67
372 1335 5.004726 GCAGTCTTTTATTTAATTGGCAGCG 59.995 40.000 0.00 0.00 0.00 5.18
373 1336 5.868801 TGCAGTCTTTTATTTAATTGGCAGC 59.131 36.000 0.00 0.00 0.00 5.25
374 1337 6.311200 GGTGCAGTCTTTTATTTAATTGGCAG 59.689 38.462 0.00 0.00 0.00 4.85
375 1338 6.162777 GGTGCAGTCTTTTATTTAATTGGCA 58.837 36.000 0.00 0.00 0.00 4.92
376 1339 5.288472 CGGTGCAGTCTTTTATTTAATTGGC 59.712 40.000 0.00 0.00 0.00 4.52
378 1341 7.432252 GGATCGGTGCAGTCTTTTATTTAATTG 59.568 37.037 0.00 0.00 0.00 2.32
380 1343 6.039382 GGGATCGGTGCAGTCTTTTATTTAAT 59.961 38.462 0.00 0.00 0.00 1.40
381 1344 5.355910 GGGATCGGTGCAGTCTTTTATTTAA 59.644 40.000 0.00 0.00 0.00 1.52
382 1345 4.879545 GGGATCGGTGCAGTCTTTTATTTA 59.120 41.667 0.00 0.00 0.00 1.40
383 1346 3.694566 GGGATCGGTGCAGTCTTTTATTT 59.305 43.478 0.00 0.00 0.00 1.40
384 1347 3.279434 GGGATCGGTGCAGTCTTTTATT 58.721 45.455 0.00 0.00 0.00 1.40
385 1348 2.421529 GGGGATCGGTGCAGTCTTTTAT 60.422 50.000 0.00 0.00 0.00 1.40
386 1349 1.065709 GGGGATCGGTGCAGTCTTTTA 60.066 52.381 0.00 0.00 0.00 1.52
387 1350 0.322546 GGGGATCGGTGCAGTCTTTT 60.323 55.000 0.00 0.00 0.00 2.27
388 1351 1.299976 GGGGATCGGTGCAGTCTTT 59.700 57.895 0.00 0.00 0.00 2.52
389 1352 1.488705 TTGGGGATCGGTGCAGTCTT 61.489 55.000 0.00 0.00 0.00 3.01
390 1353 1.488705 TTTGGGGATCGGTGCAGTCT 61.489 55.000 0.00 0.00 0.00 3.24
391 1354 1.002624 TTTGGGGATCGGTGCAGTC 60.003 57.895 0.00 0.00 0.00 3.51
392 1355 1.303317 GTTTGGGGATCGGTGCAGT 60.303 57.895 0.00 0.00 0.00 4.40
393 1356 0.893270 TTGTTTGGGGATCGGTGCAG 60.893 55.000 0.00 0.00 0.00 4.41
394 1357 0.468214 TTTGTTTGGGGATCGGTGCA 60.468 50.000 0.00 0.00 0.00 4.57
395 1358 0.894835 ATTTGTTTGGGGATCGGTGC 59.105 50.000 0.00 0.00 0.00 5.01
396 1359 2.164219 CTGATTTGTTTGGGGATCGGTG 59.836 50.000 0.00 0.00 0.00 4.94
397 1360 2.446435 CTGATTTGTTTGGGGATCGGT 58.554 47.619 0.00 0.00 0.00 4.69
398 1361 1.750778 CCTGATTTGTTTGGGGATCGG 59.249 52.381 0.00 0.00 0.00 4.18
399 1362 2.684881 CTCCTGATTTGTTTGGGGATCG 59.315 50.000 0.00 0.00 0.00 3.69
400 1363 3.445096 CACTCCTGATTTGTTTGGGGATC 59.555 47.826 0.00 0.00 0.00 3.36
401 1364 3.434309 CACTCCTGATTTGTTTGGGGAT 58.566 45.455 0.00 0.00 0.00 3.85
411 1393 3.766051 GGAATCAAAGCCACTCCTGATTT 59.234 43.478 0.00 0.00 38.35 2.17
414 1396 1.704628 TGGAATCAAAGCCACTCCTGA 59.295 47.619 0.00 0.00 0.00 3.86
418 1400 2.363683 CCTCTGGAATCAAAGCCACTC 58.636 52.381 0.00 0.00 0.00 3.51
420 1402 1.467920 CCCTCTGGAATCAAAGCCAC 58.532 55.000 0.00 0.00 0.00 5.01
424 1406 1.467920 GCACCCCTCTGGAATCAAAG 58.532 55.000 0.00 0.00 38.00 2.77
444 1426 0.179124 GACGAGGAGCACATCAGGAC 60.179 60.000 0.00 0.00 0.00 3.85
447 1429 1.226802 CGGACGAGGAGCACATCAG 60.227 63.158 0.00 0.00 0.00 2.90
459 1441 2.565210 AAACATACATACGCGGACGA 57.435 45.000 12.47 0.00 43.93 4.20
470 1452 8.803235 CCTAGCTGTATATGGAGTAAACATACA 58.197 37.037 0.00 0.00 33.98 2.29
482 1464 5.998363 GGGTTTTTCTCCTAGCTGTATATGG 59.002 44.000 0.00 0.00 0.00 2.74
530 1512 5.412594 GCCTTTCTGTTGTGATCTAATGACA 59.587 40.000 0.00 0.00 0.00 3.58
534 1516 4.579869 ACGCCTTTCTGTTGTGATCTAAT 58.420 39.130 0.00 0.00 0.00 1.73
562 1544 8.024145 TCATCTTTTCCTACTATCTTCTTCCC 57.976 38.462 0.00 0.00 0.00 3.97
589 1571 0.674581 CTCATTGCCGCCTTCAGACA 60.675 55.000 0.00 0.00 0.00 3.41
627 1609 2.158475 TCTTGCCAACTCACATTTCCCT 60.158 45.455 0.00 0.00 0.00 4.20
631 1613 3.565307 TCCTTCTTGCCAACTCACATTT 58.435 40.909 0.00 0.00 0.00 2.32
645 1627 6.485830 TGATAATCCGTTGATCTCCTTCTT 57.514 37.500 0.00 0.00 0.00 2.52
724 1706 4.161565 TGAGCGTATCCTTCAAAGTACCAT 59.838 41.667 0.00 0.00 0.00 3.55
742 1724 2.098298 CCCGTGCGAATTTGAGCG 59.902 61.111 0.00 0.00 35.87 5.03
804 1786 6.451393 TGCACAAAATACCACATAACCTTTC 58.549 36.000 0.00 0.00 0.00 2.62
865 4573 7.128976 TGCGAAAAGGTTTCAAAATAATTTGC 58.871 30.769 0.00 0.00 44.52 3.68
870 4578 9.751542 TTATCTTGCGAAAAGGTTTCAAAATAA 57.248 25.926 1.99 0.00 0.00 1.40
871 4579 9.751542 TTTATCTTGCGAAAAGGTTTCAAAATA 57.248 25.926 1.99 0.00 0.00 1.40
902 4614 8.978539 AGCTCTTTCCGTTTTCAAATTTATTTC 58.021 29.630 0.00 0.00 0.00 2.17
906 4618 7.434013 GTGAAGCTCTTTCCGTTTTCAAATTTA 59.566 33.333 0.00 0.00 34.77 1.40
907 4619 6.255670 GTGAAGCTCTTTCCGTTTTCAAATTT 59.744 34.615 0.00 0.00 34.77 1.82
908 4620 5.748630 GTGAAGCTCTTTCCGTTTTCAAATT 59.251 36.000 0.00 0.00 34.77 1.82
909 4621 5.281727 GTGAAGCTCTTTCCGTTTTCAAAT 58.718 37.500 0.00 0.00 34.77 2.32
948 4663 4.557690 CGACGGTACAGTTCAGTAAATCAG 59.442 45.833 0.00 0.00 0.00 2.90
1160 8255 1.993653 CCATCAACTGGCAGGGAGA 59.006 57.895 20.34 13.38 38.47 3.71
1357 8458 2.899900 CAAAGGGAAAGGGAAAGAAGGG 59.100 50.000 0.00 0.00 0.00 3.95
1359 8460 4.895889 AGAACAAAGGGAAAGGGAAAGAAG 59.104 41.667 0.00 0.00 0.00 2.85
1360 8461 4.878968 AGAACAAAGGGAAAGGGAAAGAA 58.121 39.130 0.00 0.00 0.00 2.52
1361 8462 4.536295 AGAACAAAGGGAAAGGGAAAGA 57.464 40.909 0.00 0.00 0.00 2.52
1363 8464 5.026790 TGAAAGAACAAAGGGAAAGGGAAA 58.973 37.500 0.00 0.00 0.00 3.13
1369 8470 4.959210 TCCACATGAAAGAACAAAGGGAAA 59.041 37.500 0.00 0.00 0.00 3.13
1397 8498 1.227380 GCAGAGTCACGGGCATAGG 60.227 63.158 0.00 0.00 0.00 2.57
1399 8500 2.731571 GGGCAGAGTCACGGGCATA 61.732 63.158 0.00 0.00 40.55 3.14
1410 8511 1.451567 CATGCTCACAGGGGCAGAG 60.452 63.158 0.00 0.00 41.88 3.35
1422 8523 7.545362 AATCCATATAAGCGTAATCATGCTC 57.455 36.000 0.00 0.00 46.58 4.26
1439 8540 4.991056 GCTCGCATCTCAGTTAAATCCATA 59.009 41.667 0.00 0.00 0.00 2.74
1440 8541 3.812053 GCTCGCATCTCAGTTAAATCCAT 59.188 43.478 0.00 0.00 0.00 3.41
1483 8584 7.868415 CGTTCAAAAATCACCCTAACCAAATAA 59.132 33.333 0.00 0.00 0.00 1.40
1484 8585 7.230913 TCGTTCAAAAATCACCCTAACCAAATA 59.769 33.333 0.00 0.00 0.00 1.40
1494 8595 5.751028 TGACAAAATCGTTCAAAAATCACCC 59.249 36.000 0.00 0.00 0.00 4.61
1509 8610 3.250040 ACAGCAACGGTACTGACAAAATC 59.750 43.478 7.93 0.00 37.35 2.17
1517 8618 3.395639 TCCTAAAACAGCAACGGTACTG 58.604 45.455 0.00 0.00 39.86 2.74
1519 8620 3.998341 TGATCCTAAAACAGCAACGGTAC 59.002 43.478 0.00 0.00 0.00 3.34
1522 8623 4.701956 ATTGATCCTAAAACAGCAACGG 57.298 40.909 0.00 0.00 0.00 4.44
1610 8711 3.365264 GCGCATTGATCAGACAAGTCAAA 60.365 43.478 0.30 0.00 35.70 2.69
1616 8717 1.001624 CTCGCGCATTGATCAGACAA 58.998 50.000 8.75 0.00 0.00 3.18
1645 8746 7.051696 TCTATATTTGTTTCCCCTTTTCCCT 57.948 36.000 0.00 0.00 0.00 4.20
1820 9049 7.487509 TCCACAATGCATAAAAATACAATGACG 59.512 33.333 0.00 0.00 0.00 4.35
1871 9100 4.346418 AGAAGTGAGATGTTCCACAGTTCT 59.654 41.667 0.00 0.00 43.56 3.01
1893 9127 5.415701 AGGAACACATAACCATAGCAAACAG 59.584 40.000 0.00 0.00 0.00 3.16
1910 9144 2.622942 TGCACATGGAGAAAAGGAACAC 59.377 45.455 0.00 0.00 0.00 3.32
1991 9225 4.299586 TGCCATGAACTACTCATTTGGA 57.700 40.909 0.00 0.00 42.46 3.53
2415 9649 1.873591 CCAACAGGAGAAACTTGGACG 59.126 52.381 0.00 0.00 36.06 4.79
2468 9702 8.924511 AATGGAAGAAAAGTTCAGAAGATACA 57.075 30.769 0.00 0.00 0.00 2.29
2893 10128 5.691754 GCATAATTTAAAGAAGCCCATTCCG 59.308 40.000 0.00 0.00 38.84 4.30
2931 10166 5.483685 TCCTTTTTCTGAAGATCCGAGAA 57.516 39.130 0.00 0.00 0.00 2.87
2991 10226 3.976339 CAGAGATCTGGGGTAAGCG 57.024 57.895 0.00 0.00 40.20 4.68
3435 10670 8.498054 ACTTGAACTGATTATACCAGAACATG 57.502 34.615 7.99 0.00 35.69 3.21
3472 10707 8.789762 GGTTGTTTACAATGGTAACTTAGATGT 58.210 33.333 0.00 0.00 39.14 3.06
3568 10803 7.471721 TGGTCAATAAGATCGCACAAAATTAG 58.528 34.615 0.00 0.00 0.00 1.73
3891 11128 5.915196 GCCAAAACTCTGTGAAAAGTGATAC 59.085 40.000 0.00 0.00 0.00 2.24
4065 11302 1.069204 GACGATGCCTATTCCAGCTCA 59.931 52.381 0.00 0.00 0.00 4.26
4082 11319 1.135972 CCAAGGCAAACATTCTCGACG 60.136 52.381 0.00 0.00 0.00 5.12
4140 11378 2.488545 ACGACGGGTCTATGATAGCATC 59.511 50.000 0.00 0.00 35.94 3.91
4208 11609 9.130312 GCATCTTAGTTAGTACCTGATTAATCG 57.870 37.037 10.80 5.78 0.00 3.34
4239 11640 2.616510 GCACCAGTTAGCACATTCTCCT 60.617 50.000 0.00 0.00 0.00 3.69
4435 11842 7.329962 TGAATGCTTGCACATTTCATAGAAAAG 59.670 33.333 4.24 0.00 40.31 2.27
4479 11886 7.307870 CTTCTGAAGAAAAGGAACTGATCACAG 60.308 40.741 12.01 0.00 40.86 3.66
4504 11911 8.779354 ATTCGAAACTGTTAGCTTAAGAATCT 57.221 30.769 6.67 0.00 0.00 2.40
4525 11932 2.738135 AGACCGGCAAAACAAAATTCG 58.262 42.857 0.00 0.00 0.00 3.34
4738 12186 2.031044 TTGATACGTTGGCGCGCATC 62.031 55.000 34.42 24.61 42.83 3.91
4740 12188 2.738904 TTGATACGTTGGCGCGCA 60.739 55.556 34.42 16.55 42.83 6.09
4771 12220 7.675962 TTGTATACTTGTAAATGTCCACCAC 57.324 36.000 4.17 0.00 0.00 4.16
4789 12238 4.516321 TGAGCGTAGTATCGGCTTTGTATA 59.484 41.667 0.00 0.00 0.00 1.47
4790 12239 3.317149 TGAGCGTAGTATCGGCTTTGTAT 59.683 43.478 0.00 0.00 0.00 2.29
4791 12240 2.684374 TGAGCGTAGTATCGGCTTTGTA 59.316 45.455 0.00 0.00 0.00 2.41
4807 12256 1.288419 TATGTTGTGCGGTGTGAGCG 61.288 55.000 0.00 0.00 42.73 5.03
5000 12519 5.399301 GGAAACAAAGATTGTGTTGTGATCG 59.601 40.000 0.00 0.00 44.59 3.69
5077 12596 0.830444 ATAGCGAAGGGGCCGATGTA 60.830 55.000 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.