Multiple sequence alignment - TraesCS4B01G041900

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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 TraesCS4B01G041900 chr4B 100.000 3294 0 0 1 3294 28714270 28717563 0.000000e+00 6083
1 TraesCS4B01G041900 chr4A 89.376 1346 91 25 1161 2490 583759012 583757703 0.000000e+00 1646
2 TraesCS4B01G041900 chr4A 86.717 798 47 28 2540 3294 583757525 583756744 0.000000e+00 832
3 TraesCS4B01G041900 chr4A 85.593 354 17 11 822 1158 583759381 583759045 1.130000e-89 340
4 TraesCS4B01G041900 chr4A 92.070 227 12 4 2 227 583760206 583759985 6.860000e-82 315
5 TraesCS4B01G041900 chr4D 88.959 788 47 24 2540 3294 16799102 16799882 0.000000e+00 937
6 TraesCS4B01G041900 chr4D 86.375 778 49 23 417 1152 16796929 16797691 0.000000e+00 797
7 TraesCS4B01G041900 chr4D 88.293 615 37 14 1298 1899 16797835 16798427 0.000000e+00 704
8 TraesCS4B01G041900 chr4D 92.411 448 30 3 2076 2523 16798562 16799005 1.290000e-178 636
9 TraesCS4B01G041900 chr4D 93.963 381 11 8 9 386 16796559 16796930 1.720000e-157 566
10 TraesCS4B01G041900 chr2A 94.194 155 9 0 3089 3243 12281434 12281280 1.530000e-58 237


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 TraesCS4B01G041900 chr4B 28714270 28717563 3293 False 6083.00 6083 100.0000 1 3294 1 chr4B.!!$F1 3293
1 TraesCS4B01G041900 chr4A 583756744 583760206 3462 True 783.25 1646 88.4390 2 3294 4 chr4A.!!$R1 3292
2 TraesCS4B01G041900 chr4D 16796559 16799882 3323 False 728.00 937 90.0002 9 3294 5 chr4D.!!$F1 3285

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
816 916 0.030235 GAAACTCCGCGTGGCTTTTT 59.97 50.0 11.05 9.0 34.14 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2526 2777 0.365523 CAACGGCGAAGATACGTGTG 59.634 55.0 16.62 0.0 41.12 3.82 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
80 81 1.913419 AGAAACGGAATGGCTCCCTTA 59.087 47.619 0.00 0.00 41.87 2.69
120 122 2.352503 AAAAAGGCGCTATTGCTGTG 57.647 45.000 7.64 0.00 36.97 3.66
137 139 1.064758 TGTGTCTGCTTCCCTGTTGTT 60.065 47.619 0.00 0.00 0.00 2.83
138 140 1.604278 GTGTCTGCTTCCCTGTTGTTC 59.396 52.381 0.00 0.00 0.00 3.18
139 141 1.490490 TGTCTGCTTCCCTGTTGTTCT 59.510 47.619 0.00 0.00 0.00 3.01
140 142 1.876156 GTCTGCTTCCCTGTTGTTCTG 59.124 52.381 0.00 0.00 0.00 3.02
141 143 1.768275 TCTGCTTCCCTGTTGTTCTGA 59.232 47.619 0.00 0.00 0.00 3.27
142 144 2.172505 TCTGCTTCCCTGTTGTTCTGAA 59.827 45.455 0.00 0.00 0.00 3.02
143 145 2.551459 CTGCTTCCCTGTTGTTCTGAAG 59.449 50.000 0.00 0.00 36.40 3.02
153 155 5.009010 CCTGTTGTTCTGAAGTTGCAGTTAT 59.991 40.000 0.00 0.00 37.20 1.89
155 157 5.822519 TGTTGTTCTGAAGTTGCAGTTATCT 59.177 36.000 0.00 0.00 37.20 1.98
184 186 2.201732 TGATTTCCAAGCGCGAGTATC 58.798 47.619 12.10 2.61 0.00 2.24
265 288 7.775053 ATTTTGTTTAGATATGTGGTGTGGT 57.225 32.000 0.00 0.00 0.00 4.16
268 291 8.871629 TTTGTTTAGATATGTGGTGTGGTTAT 57.128 30.769 0.00 0.00 0.00 1.89
303 326 8.454106 GTGGAATGTACATGATGGCTATAATTC 58.546 37.037 9.63 0.00 0.00 2.17
307 360 6.711277 TGTACATGATGGCTATAATTCCCTC 58.289 40.000 0.00 0.00 0.00 4.30
308 361 5.184892 ACATGATGGCTATAATTCCCTCC 57.815 43.478 0.00 0.00 0.00 4.30
391 445 6.539173 TCAAATGTACCCTTGTGAACAGTAT 58.461 36.000 0.00 0.00 0.00 2.12
394 448 8.956426 CAAATGTACCCTTGTGAACAGTATAAT 58.044 33.333 0.00 0.00 0.00 1.28
395 449 8.732746 AATGTACCCTTGTGAACAGTATAATC 57.267 34.615 0.00 0.00 0.00 1.75
396 450 7.247456 TGTACCCTTGTGAACAGTATAATCA 57.753 36.000 0.00 0.00 0.00 2.57
397 451 7.101054 TGTACCCTTGTGAACAGTATAATCAC 58.899 38.462 0.00 0.00 42.90 3.06
398 452 5.175859 ACCCTTGTGAACAGTATAATCACG 58.824 41.667 0.00 0.00 44.95 4.35
399 453 5.046878 ACCCTTGTGAACAGTATAATCACGA 60.047 40.000 0.00 0.00 44.95 4.35
400 454 5.872617 CCCTTGTGAACAGTATAATCACGAA 59.127 40.000 0.00 0.00 44.95 3.85
401 455 6.370442 CCCTTGTGAACAGTATAATCACGAAA 59.630 38.462 0.00 0.00 44.95 3.46
402 456 7.094975 CCCTTGTGAACAGTATAATCACGAAAA 60.095 37.037 0.00 0.00 44.95 2.29
403 457 8.286800 CCTTGTGAACAGTATAATCACGAAAAA 58.713 33.333 0.00 0.00 44.95 1.94
469 523 7.853437 TGTTGTTGAATTTTCTACATACGTGTG 59.147 33.333 11.09 11.09 41.25 3.82
486 540 6.626199 ACGTGTGAATTTGTTGAAGAAAAC 57.374 33.333 0.00 0.00 0.00 2.43
487 541 6.386654 ACGTGTGAATTTGTTGAAGAAAACT 58.613 32.000 0.00 0.00 0.00 2.66
488 542 7.531716 ACGTGTGAATTTGTTGAAGAAAACTA 58.468 30.769 0.00 0.00 0.00 2.24
489 543 8.188139 ACGTGTGAATTTGTTGAAGAAAACTAT 58.812 29.630 0.00 0.00 0.00 2.12
494 548 9.232082 TGAATTTGTTGAAGAAAACTATTCACG 57.768 29.630 0.00 0.00 37.15 4.35
530 598 4.093408 CGATGCTCCGAAAAGATTTTCTGA 59.907 41.667 14.31 12.31 43.27 3.27
699 771 6.875948 TTTTAGTGTTCATAGCAGAAGCAA 57.124 33.333 0.00 0.00 45.49 3.91
776 875 8.908786 TTCACAATATATTTTTGGGCAAAACA 57.091 26.923 0.00 0.00 39.70 2.83
804 904 2.509561 GAGCCGAGCCGAAACTCC 60.510 66.667 0.00 0.00 32.79 3.85
816 916 0.030235 GAAACTCCGCGTGGCTTTTT 59.970 50.000 11.05 9.00 34.14 1.94
817 917 1.264826 GAAACTCCGCGTGGCTTTTTA 59.735 47.619 11.05 0.00 34.14 1.52
819 919 0.953960 ACTCCGCGTGGCTTTTTAGG 60.954 55.000 11.05 0.00 34.14 2.69
888 995 2.526375 CCCAAGCCCAAGCCCAAA 60.526 61.111 0.00 0.00 41.25 3.28
889 996 2.586293 CCCAAGCCCAAGCCCAAAG 61.586 63.158 0.00 0.00 41.25 2.77
894 1001 2.526375 CCCAAGCCCAAAGCCCAA 60.526 61.111 0.00 0.00 45.47 4.12
895 1002 1.919816 CCCAAGCCCAAAGCCCAAT 60.920 57.895 0.00 0.00 45.47 3.16
896 1003 0.617249 CCCAAGCCCAAAGCCCAATA 60.617 55.000 0.00 0.00 45.47 1.90
897 1004 0.536724 CCAAGCCCAAAGCCCAATAC 59.463 55.000 0.00 0.00 45.47 1.89
898 1005 0.536724 CAAGCCCAAAGCCCAATACC 59.463 55.000 0.00 0.00 45.47 2.73
899 1006 0.970427 AAGCCCAAAGCCCAATACCG 60.970 55.000 0.00 0.00 45.47 4.02
900 1007 2.423064 GCCCAAAGCCCAATACCGG 61.423 63.158 0.00 0.00 34.35 5.28
901 1008 1.304952 CCCAAAGCCCAATACCGGA 59.695 57.895 9.46 0.00 0.00 5.14
902 1009 0.751643 CCCAAAGCCCAATACCGGAG 60.752 60.000 9.46 0.00 0.00 4.63
903 1010 1.384222 CCAAAGCCCAATACCGGAGC 61.384 60.000 9.46 0.31 0.00 4.70
932 1039 0.249073 CAGCCACCTTATCGTCTCCG 60.249 60.000 0.00 0.00 0.00 4.63
1192 1349 0.726452 GCGTCGTCTGTCTCTGTGTC 60.726 60.000 0.00 0.00 0.00 3.67
1203 1362 3.318275 TGTCTCTGTGTCTGTAGTTCCAC 59.682 47.826 0.00 0.00 0.00 4.02
1223 1383 1.126948 TGATATGCCCGGGATGCTGA 61.127 55.000 29.31 1.94 0.00 4.26
1234 1394 0.749049 GGATGCTGAAAGAATGGGGC 59.251 55.000 0.00 0.00 26.21 5.80
1255 1416 0.180406 AGCTGGTGTCCGTTTCTGTT 59.820 50.000 0.00 0.00 0.00 3.16
1256 1417 1.021968 GCTGGTGTCCGTTTCTGTTT 58.978 50.000 0.00 0.00 0.00 2.83
1257 1418 1.002792 GCTGGTGTCCGTTTCTGTTTC 60.003 52.381 0.00 0.00 0.00 2.78
1259 1420 2.544267 CTGGTGTCCGTTTCTGTTTCTC 59.456 50.000 0.00 0.00 0.00 2.87
1260 1421 2.169769 TGGTGTCCGTTTCTGTTTCTCT 59.830 45.455 0.00 0.00 0.00 3.10
1261 1422 2.544267 GGTGTCCGTTTCTGTTTCTCTG 59.456 50.000 0.00 0.00 0.00 3.35
1265 1426 1.873591 CCGTTTCTGTTTCTCTGTGGG 59.126 52.381 0.00 0.00 0.00 4.61
1266 1427 2.561569 CGTTTCTGTTTCTCTGTGGGT 58.438 47.619 0.00 0.00 0.00 4.51
1267 1428 2.287915 CGTTTCTGTTTCTCTGTGGGTG 59.712 50.000 0.00 0.00 0.00 4.61
1268 1429 3.279434 GTTTCTGTTTCTCTGTGGGTGT 58.721 45.455 0.00 0.00 0.00 4.16
1269 1430 3.644966 TTCTGTTTCTCTGTGGGTGTT 57.355 42.857 0.00 0.00 0.00 3.32
1270 1431 2.917933 TCTGTTTCTCTGTGGGTGTTG 58.082 47.619 0.00 0.00 0.00 3.33
1271 1432 2.503765 TCTGTTTCTCTGTGGGTGTTGA 59.496 45.455 0.00 0.00 0.00 3.18
1272 1433 3.054728 TCTGTTTCTCTGTGGGTGTTGAA 60.055 43.478 0.00 0.00 0.00 2.69
1273 1434 3.013921 TGTTTCTCTGTGGGTGTTGAAC 58.986 45.455 0.00 0.00 0.00 3.18
1274 1435 3.279434 GTTTCTCTGTGGGTGTTGAACT 58.721 45.455 0.00 0.00 0.00 3.01
1275 1436 2.910688 TCTCTGTGGGTGTTGAACTC 57.089 50.000 0.00 0.00 0.00 3.01
1276 1437 1.416401 TCTCTGTGGGTGTTGAACTCC 59.584 52.381 7.86 7.86 0.00 3.85
1277 1438 1.417890 CTCTGTGGGTGTTGAACTCCT 59.582 52.381 15.16 0.00 32.60 3.69
1278 1439 1.843851 TCTGTGGGTGTTGAACTCCTT 59.156 47.619 15.16 0.00 32.60 3.36
1279 1440 1.949525 CTGTGGGTGTTGAACTCCTTG 59.050 52.381 15.16 1.54 32.60 3.61
1280 1441 1.283613 TGTGGGTGTTGAACTCCTTGT 59.716 47.619 15.16 0.00 32.60 3.16
1293 1454 2.821969 ACTCCTTGTGAACCATGAATGC 59.178 45.455 0.00 0.00 0.00 3.56
1322 1483 5.745294 GCACATTTTGCCTGATAATGTAGTG 59.255 40.000 0.00 0.00 46.63 2.74
1338 1500 5.281693 TGTAGTGATTTCTTTGCACATCG 57.718 39.130 0.00 0.00 35.08 3.84
1358 1520 4.441792 TCGATGTGAATGTTACAGGGATG 58.558 43.478 0.00 0.00 0.00 3.51
1363 1525 4.289934 TGTGAATGTTACAGGGATGGGTTA 59.710 41.667 0.00 0.00 0.00 2.85
1382 1544 6.869388 TGGGTTATTTGTTATTTTTCTTCGCC 59.131 34.615 0.00 0.00 0.00 5.54
1396 1558 4.271696 TCTTCGCCATATATGTCCCTTG 57.728 45.455 11.73 0.00 0.00 3.61
1405 1567 6.765036 GCCATATATGTCCCTTGATATGTCTG 59.235 42.308 11.73 0.00 32.62 3.51
1413 1575 4.895889 TCCCTTGATATGTCTGTACAGAGG 59.104 45.833 25.81 18.88 39.49 3.69
1418 1580 6.890979 TGATATGTCTGTACAGAGGAGATG 57.109 41.667 25.81 0.00 39.49 2.90
1424 1586 5.184096 TGTCTGTACAGAGGAGATGTTCTTC 59.816 44.000 25.81 9.72 38.27 2.87
1441 1603 5.817296 TGTTCTTCCATATGTAGATGTGTGC 59.183 40.000 1.24 0.00 0.00 4.57
1443 1605 5.604565 TCTTCCATATGTAGATGTGTGCAG 58.395 41.667 1.24 0.00 0.00 4.41
1449 1611 1.908619 TGTAGATGTGTGCAGGGTGAT 59.091 47.619 0.00 0.00 0.00 3.06
1456 1618 2.159128 TGTGTGCAGGGTGATTGTTTTG 60.159 45.455 0.00 0.00 0.00 2.44
1465 1627 3.625313 GGGTGATTGTTTTGTGGTTTTGG 59.375 43.478 0.00 0.00 0.00 3.28
1477 1643 6.591750 TTGTGGTTTTGGTTCTTCTGTTTA 57.408 33.333 0.00 0.00 0.00 2.01
1483 1649 5.799827 TTTGGTTCTTCTGTTTATTGGGG 57.200 39.130 0.00 0.00 0.00 4.96
1485 1651 5.269554 TGGTTCTTCTGTTTATTGGGGAT 57.730 39.130 0.00 0.00 0.00 3.85
1488 1654 6.556874 TGGTTCTTCTGTTTATTGGGGATTTT 59.443 34.615 0.00 0.00 0.00 1.82
1489 1655 7.730784 TGGTTCTTCTGTTTATTGGGGATTTTA 59.269 33.333 0.00 0.00 0.00 1.52
1490 1656 8.758829 GGTTCTTCTGTTTATTGGGGATTTTAT 58.241 33.333 0.00 0.00 0.00 1.40
1501 1667 6.410222 TTGGGGATTTTATTACAGAAGGGA 57.590 37.500 0.00 0.00 0.00 4.20
1760 1927 1.454201 GCTCTGACCCCTTTGCTAAC 58.546 55.000 0.00 0.00 0.00 2.34
1761 1928 1.271379 GCTCTGACCCCTTTGCTAACA 60.271 52.381 0.00 0.00 0.00 2.41
1762 1929 2.427506 CTCTGACCCCTTTGCTAACAC 58.572 52.381 0.00 0.00 0.00 3.32
1763 1930 2.039084 CTCTGACCCCTTTGCTAACACT 59.961 50.000 0.00 0.00 0.00 3.55
1764 1931 2.038557 TCTGACCCCTTTGCTAACACTC 59.961 50.000 0.00 0.00 0.00 3.51
1765 1932 1.073284 TGACCCCTTTGCTAACACTCC 59.927 52.381 0.00 0.00 0.00 3.85
1766 1933 0.036306 ACCCCTTTGCTAACACTCCG 59.964 55.000 0.00 0.00 0.00 4.63
1767 1934 0.036306 CCCCTTTGCTAACACTCCGT 59.964 55.000 0.00 0.00 0.00 4.69
1768 1935 1.276989 CCCCTTTGCTAACACTCCGTA 59.723 52.381 0.00 0.00 0.00 4.02
1831 1998 6.701841 ACAACACCGTCATGATACATTCTATC 59.298 38.462 0.00 0.00 0.00 2.08
1851 2018 2.784095 TCAGAGGCTTAGCTAGGACCTA 59.216 50.000 15.46 0.13 0.00 3.08
1854 2021 4.219725 CAGAGGCTTAGCTAGGACCTATTC 59.780 50.000 15.46 3.77 0.00 1.75
1858 2033 4.262249 GGCTTAGCTAGGACCTATTCAGTG 60.262 50.000 7.11 0.00 0.00 3.66
1881 2056 6.705825 GTGCTTCCCACATTTCTTTAAAACAT 59.294 34.615 0.00 0.00 44.06 2.71
1934 2110 8.732746 TCCAAAAGGTATAAAAGTAGCATCTC 57.267 34.615 0.00 0.00 0.00 2.75
1962 2138 9.846248 AAAAGATATGAAAATACTGAACAGTGC 57.154 29.630 16.37 3.20 42.52 4.40
1984 2160 8.004215 AGTGCCATGTTTAGAATTTATCCCATA 58.996 33.333 0.00 0.00 0.00 2.74
2029 2205 8.492782 CATCAGGATATTCTATTGGAGGCTTAT 58.507 37.037 0.00 0.00 0.00 1.73
2300 2517 2.163010 TCCTCCGACGAATAAGTGACAC 59.837 50.000 0.00 0.00 0.00 3.67
2335 2552 2.569404 TGCCTCCTGTTTGGTTTTTGTT 59.431 40.909 0.00 0.00 37.07 2.83
2336 2553 3.008485 TGCCTCCTGTTTGGTTTTTGTTT 59.992 39.130 0.00 0.00 37.07 2.83
2386 2603 4.517832 GGTACTCCGTTTCAAGTTTCCATT 59.482 41.667 0.00 0.00 0.00 3.16
2467 2689 9.649167 CATGACATCTCTTCTGTTATATATGCA 57.351 33.333 0.00 0.00 0.00 3.96
2468 2690 9.650539 ATGACATCTCTTCTGTTATATATGCAC 57.349 33.333 0.00 0.00 0.00 4.57
2469 2691 8.864087 TGACATCTCTTCTGTTATATATGCACT 58.136 33.333 0.00 0.00 0.00 4.40
2470 2692 9.138062 GACATCTCTTCTGTTATATATGCACTG 57.862 37.037 0.00 0.00 0.00 3.66
2471 2693 8.864087 ACATCTCTTCTGTTATATATGCACTGA 58.136 33.333 0.00 0.00 0.00 3.41
2472 2694 9.872721 CATCTCTTCTGTTATATATGCACTGAT 57.127 33.333 0.00 0.00 0.00 2.90
2474 2696 9.920133 TCTCTTCTGTTATATATGCACTGATTC 57.080 33.333 0.00 0.00 0.00 2.52
2523 2774 3.118956 TCGTCCCAAGCACAAATGTTTTT 60.119 39.130 0.00 0.00 0.00 1.94
2542 2893 1.348538 TTGCACACGTATCTTCGCCG 61.349 55.000 0.00 0.00 0.00 6.46
2562 2913 2.589407 CGTTGCAAGATTATGTTGTGCG 59.411 45.455 0.00 3.18 38.05 5.34
2602 2953 2.237534 GACAGAGGAGCTCCAGTGGC 62.238 65.000 33.90 27.01 38.89 5.01
2615 2966 1.450312 AGTGGCAGCTCGGTAATGC 60.450 57.895 0.00 0.00 39.25 3.56
2626 2979 1.421410 CGGTAATGCGACTGTCAGGC 61.421 60.000 8.73 0.00 0.00 4.85
2651 3035 2.904697 TGCCACACAAATCATGCAAA 57.095 40.000 0.00 0.00 0.00 3.68
2652 3036 3.189618 TGCCACACAAATCATGCAAAA 57.810 38.095 0.00 0.00 0.00 2.44
2653 3037 3.538591 TGCCACACAAATCATGCAAAAA 58.461 36.364 0.00 0.00 0.00 1.94
2654 3038 4.135306 TGCCACACAAATCATGCAAAAAT 58.865 34.783 0.00 0.00 0.00 1.82
2655 3039 4.579340 TGCCACACAAATCATGCAAAAATT 59.421 33.333 0.00 0.00 0.00 1.82
2689 3073 3.181459 ACCGAAAACCTTTGAATTTGGGG 60.181 43.478 0.00 0.00 36.56 4.96
2712 3096 3.206964 GAATTTGGGGTCTAGCAGTAGC 58.793 50.000 0.00 0.00 42.56 3.58
2713 3097 0.909623 TTTGGGGTCTAGCAGTAGCC 59.090 55.000 0.00 0.00 43.56 3.93
2715 3099 0.252513 TGGGGTCTAGCAGTAGCCAA 60.253 55.000 0.43 0.00 43.56 4.52
2738 3122 4.556942 TTGTGCAAAGTTCAGACATCTG 57.443 40.909 2.24 2.24 45.08 2.90
2757 3144 2.151202 TGCTTCTGAATTTGACCGACC 58.849 47.619 0.00 0.00 0.00 4.79
2767 3154 3.755112 TTTGACCGACCATGTGAGTTA 57.245 42.857 0.00 0.00 0.00 2.24
2768 3155 3.973206 TTGACCGACCATGTGAGTTAT 57.027 42.857 0.00 0.00 0.00 1.89
2769 3156 3.973206 TGACCGACCATGTGAGTTATT 57.027 42.857 0.00 0.00 0.00 1.40
2770 3157 5.408880 TTGACCGACCATGTGAGTTATTA 57.591 39.130 0.00 0.00 0.00 0.98
2782 3169 2.357009 TGAGTTATTAGACGTCCGGCTC 59.643 50.000 13.01 11.66 34.01 4.70
2826 3216 4.032987 CAAAAACCCCGCGACCCG 62.033 66.667 8.23 0.00 0.00 5.28
2871 3273 2.306847 ACGCTCACACAAAAATCCCTT 58.693 42.857 0.00 0.00 0.00 3.95
2874 3276 2.029020 GCTCACACAAAAATCCCTTCCC 60.029 50.000 0.00 0.00 0.00 3.97
2881 3283 0.919710 AAAATCCCTTCCCTCCCTCG 59.080 55.000 0.00 0.00 0.00 4.63
2954 3356 3.839432 CCCGCCTCCTCGTCTTCC 61.839 72.222 0.00 0.00 0.00 3.46
3098 3503 2.178521 CCGGTGTCGTCCTTCTCG 59.821 66.667 0.00 0.00 33.95 4.04
3133 3538 0.321671 TTCTTCACGGGGAGCAAGAG 59.678 55.000 0.00 0.00 0.00 2.85
3271 3677 4.619852 GAGGCGACCTCCTTTTCC 57.380 61.111 13.12 0.00 44.36 3.13
3272 3678 1.984020 GAGGCGACCTCCTTTTCCT 59.016 57.895 13.12 0.00 44.36 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.661536 ATATAGGGAAGGAAAAAGAAAAGGC 57.338 36.000 0.00 0.00 0.00 4.35
120 122 1.876156 CAGAACAACAGGGAAGCAGAC 59.124 52.381 0.00 0.00 0.00 3.51
137 139 5.065914 AGCAAAGATAACTGCAACTTCAGA 58.934 37.500 0.00 0.00 41.17 3.27
138 140 5.368256 AGCAAAGATAACTGCAACTTCAG 57.632 39.130 0.00 0.00 41.17 3.02
139 141 6.881065 AGATAGCAAAGATAACTGCAACTTCA 59.119 34.615 0.00 0.00 41.17 3.02
140 142 7.065085 TCAGATAGCAAAGATAACTGCAACTTC 59.935 37.037 0.00 0.00 41.17 3.01
141 143 6.881065 TCAGATAGCAAAGATAACTGCAACTT 59.119 34.615 0.00 0.00 41.17 2.66
142 144 6.409704 TCAGATAGCAAAGATAACTGCAACT 58.590 36.000 0.00 0.00 41.17 3.16
143 145 6.668541 TCAGATAGCAAAGATAACTGCAAC 57.331 37.500 0.00 0.00 41.17 4.17
153 155 4.333649 CGCTTGGAAATCAGATAGCAAAGA 59.666 41.667 3.55 0.00 29.60 2.52
155 157 3.181497 GCGCTTGGAAATCAGATAGCAAA 60.181 43.478 0.00 0.00 29.60 3.68
184 186 3.879892 GGCTGCTAGTAGAAAATCCTTGG 59.120 47.826 12.54 0.00 0.00 3.61
362 415 2.749621 CACAAGGGTACATTTGAGCTCC 59.250 50.000 12.15 0.00 0.00 4.70
443 497 7.853437 CACACGTATGTAGAAAATTCAACAACA 59.147 33.333 0.00 0.00 36.72 3.33
444 498 8.065407 TCACACGTATGTAGAAAATTCAACAAC 58.935 33.333 0.00 0.00 36.72 3.32
469 523 9.445786 TCGTGAATAGTTTTCTTCAACAAATTC 57.554 29.630 0.00 0.00 34.73 2.17
507 575 5.390885 TTCAGAAAATCTTTTCGGAGCATCG 60.391 40.000 14.73 0.00 46.50 3.84
543 611 5.333721 CCGGGCAAAAATAACAAATCAACAC 60.334 40.000 0.00 0.00 0.00 3.32
674 746 6.845302 TGCTTCTGCTATGAACACTAAAATG 58.155 36.000 0.00 0.00 40.48 2.32
744 843 8.442384 GCCCAAAAATATATTGTGAAAGTGTTG 58.558 33.333 0.00 0.00 0.00 3.33
756 855 8.998377 GTGAAGTGTTTTGCCCAAAAATATATT 58.002 29.630 7.67 0.00 41.37 1.28
761 860 4.583871 TGTGAAGTGTTTTGCCCAAAAAT 58.416 34.783 7.67 0.00 41.37 1.82
766 865 3.196469 TCAATTGTGAAGTGTTTTGCCCA 59.804 39.130 5.13 0.00 0.00 5.36
776 875 1.160137 GCTCGGCTCAATTGTGAAGT 58.840 50.000 11.59 0.00 31.88 3.01
825 932 1.096416 AGTGTCGCTGAGCCTACTAC 58.904 55.000 0.00 0.00 0.00 2.73
827 934 0.528470 GAAGTGTCGCTGAGCCTACT 59.472 55.000 0.00 0.00 0.00 2.57
888 995 2.911143 CTGCTCCGGTATTGGGCT 59.089 61.111 0.00 0.00 0.00 5.19
889 996 2.902343 GCTGCTCCGGTATTGGGC 60.902 66.667 0.00 0.00 0.00 5.36
892 999 2.182842 GGCTGCTGCTCCGGTATTG 61.183 63.158 15.64 0.00 39.59 1.90
893 1000 2.190578 GGCTGCTGCTCCGGTATT 59.809 61.111 15.64 0.00 39.59 1.89
894 1001 2.765807 AGGCTGCTGCTCCGGTAT 60.766 61.111 15.64 0.00 39.59 2.73
895 1002 3.461773 GAGGCTGCTGCTCCGGTA 61.462 66.667 15.64 0.00 39.59 4.02
898 1005 4.834453 CTGGAGGCTGCTGCTCCG 62.834 72.222 15.64 11.62 38.48 4.63
932 1039 1.749033 CAGGATAGAACCCGAGGGC 59.251 63.158 8.33 0.00 39.32 5.19
1044 1159 4.075793 CGGGTGGAGAGGGGGAGA 62.076 72.222 0.00 0.00 0.00 3.71
1125 1240 3.065306 TCGTGCACGAAAGGGGAT 58.935 55.556 37.68 0.00 46.30 3.85
1152 1279 2.811317 CGGCGTGTGCTCCTTCTC 60.811 66.667 0.00 0.00 42.25 2.87
1155 1282 4.626081 AAGCGGCGTGTGCTCCTT 62.626 61.111 9.37 0.00 43.14 3.36
1177 1334 2.809119 ACTACAGACACAGAGACAGACG 59.191 50.000 0.00 0.00 0.00 4.18
1203 1362 0.675837 CAGCATCCCGGGCATATCAG 60.676 60.000 18.49 0.65 0.00 2.90
1223 1383 1.379044 CCAGCTCGCCCCATTCTTT 60.379 57.895 0.00 0.00 0.00 2.52
1234 1394 1.006102 AGAAACGGACACCAGCTCG 60.006 57.895 0.00 0.00 0.00 5.03
1246 1407 2.287915 CACCCACAGAGAAACAGAAACG 59.712 50.000 0.00 0.00 0.00 3.60
1255 1416 2.158813 GGAGTTCAACACCCACAGAGAA 60.159 50.000 0.00 0.00 0.00 2.87
1256 1417 1.416401 GGAGTTCAACACCCACAGAGA 59.584 52.381 0.00 0.00 0.00 3.10
1257 1418 1.417890 AGGAGTTCAACACCCACAGAG 59.582 52.381 0.00 0.00 28.26 3.35
1259 1420 1.949525 CAAGGAGTTCAACACCCACAG 59.050 52.381 0.00 0.00 28.26 3.66
1260 1421 1.283613 ACAAGGAGTTCAACACCCACA 59.716 47.619 0.00 0.00 28.26 4.17
1261 1422 1.676006 CACAAGGAGTTCAACACCCAC 59.324 52.381 0.00 0.00 28.26 4.61
1265 1426 3.013921 TGGTTCACAAGGAGTTCAACAC 58.986 45.455 0.00 0.00 0.00 3.32
1266 1427 3.358111 TGGTTCACAAGGAGTTCAACA 57.642 42.857 0.00 0.00 0.00 3.33
1267 1428 3.882888 TCATGGTTCACAAGGAGTTCAAC 59.117 43.478 0.00 0.00 0.00 3.18
1268 1429 4.163441 TCATGGTTCACAAGGAGTTCAA 57.837 40.909 0.00 0.00 0.00 2.69
1269 1430 3.855255 TCATGGTTCACAAGGAGTTCA 57.145 42.857 0.00 0.00 0.00 3.18
1270 1431 4.616835 GCATTCATGGTTCACAAGGAGTTC 60.617 45.833 0.00 0.00 0.00 3.01
1271 1432 3.256631 GCATTCATGGTTCACAAGGAGTT 59.743 43.478 0.00 0.00 0.00 3.01
1272 1433 2.821969 GCATTCATGGTTCACAAGGAGT 59.178 45.455 0.00 0.00 0.00 3.85
1273 1434 2.165030 GGCATTCATGGTTCACAAGGAG 59.835 50.000 0.00 0.00 0.00 3.69
1274 1435 2.170166 GGCATTCATGGTTCACAAGGA 58.830 47.619 0.00 0.00 0.00 3.36
1275 1436 1.205417 GGGCATTCATGGTTCACAAGG 59.795 52.381 0.00 0.00 0.00 3.61
1276 1437 2.173519 AGGGCATTCATGGTTCACAAG 58.826 47.619 0.00 0.00 0.00 3.16
1277 1438 2.307496 AGGGCATTCATGGTTCACAA 57.693 45.000 0.00 0.00 0.00 3.33
1278 1439 2.945440 GCTAGGGCATTCATGGTTCACA 60.945 50.000 0.00 0.00 38.54 3.58
1279 1440 1.678101 GCTAGGGCATTCATGGTTCAC 59.322 52.381 0.00 0.00 38.54 3.18
1280 1441 1.284491 TGCTAGGGCATTCATGGTTCA 59.716 47.619 0.00 0.00 44.28 3.18
1338 1500 3.885297 CCCATCCCTGTAACATTCACATC 59.115 47.826 0.00 0.00 0.00 3.06
1351 1513 8.539544 AGAAAAATAACAAATAACCCATCCCTG 58.460 33.333 0.00 0.00 0.00 4.45
1358 1520 6.869388 TGGCGAAGAAAAATAACAAATAACCC 59.131 34.615 0.00 0.00 0.00 4.11
1382 1544 9.809096 GTACAGACATATCAAGGGACATATATG 57.191 37.037 11.29 11.29 37.98 1.78
1396 1558 6.892658 ACATCTCCTCTGTACAGACATATC 57.107 41.667 21.74 0.00 34.24 1.63
1405 1567 5.606348 ATGGAAGAACATCTCCTCTGTAC 57.394 43.478 0.00 0.00 0.00 2.90
1413 1575 8.147058 ACACATCTACATATGGAAGAACATCTC 58.853 37.037 7.80 0.00 32.39 2.75
1418 1580 5.817296 TGCACACATCTACATATGGAAGAAC 59.183 40.000 7.80 0.00 0.00 3.01
1424 1586 3.181451 ACCCTGCACACATCTACATATGG 60.181 47.826 7.80 0.00 0.00 2.74
1441 1603 3.817709 AACCACAAAACAATCACCCTG 57.182 42.857 0.00 0.00 0.00 4.45
1443 1605 3.625313 CCAAAACCACAAAACAATCACCC 59.375 43.478 0.00 0.00 0.00 4.61
1449 1611 5.698545 CAGAAGAACCAAAACCACAAAACAA 59.301 36.000 0.00 0.00 0.00 2.83
1456 1618 6.478673 CCAATAAACAGAAGAACCAAAACCAC 59.521 38.462 0.00 0.00 0.00 4.16
1477 1643 6.992235 TCCCTTCTGTAATAAAATCCCCAAT 58.008 36.000 0.00 0.00 0.00 3.16
1483 1649 7.428826 CAATGCCTCCCTTCTGTAATAAAATC 58.571 38.462 0.00 0.00 0.00 2.17
1485 1651 5.656416 CCAATGCCTCCCTTCTGTAATAAAA 59.344 40.000 0.00 0.00 0.00 1.52
1488 1654 3.785887 ACCAATGCCTCCCTTCTGTAATA 59.214 43.478 0.00 0.00 0.00 0.98
1489 1655 2.582636 ACCAATGCCTCCCTTCTGTAAT 59.417 45.455 0.00 0.00 0.00 1.89
1490 1656 1.992557 ACCAATGCCTCCCTTCTGTAA 59.007 47.619 0.00 0.00 0.00 2.41
1491 1657 1.559682 GACCAATGCCTCCCTTCTGTA 59.440 52.381 0.00 0.00 0.00 2.74
1763 1930 7.606135 TGGAATAAATCATACTCCTTACGGA 57.394 36.000 0.00 0.00 37.82 4.69
1764 1931 8.848474 AATGGAATAAATCATACTCCTTACGG 57.152 34.615 0.00 0.00 0.00 4.02
1765 1932 8.936864 GGAATGGAATAAATCATACTCCTTACG 58.063 37.037 0.00 0.00 0.00 3.18
1766 1933 9.793259 TGGAATGGAATAAATCATACTCCTTAC 57.207 33.333 0.00 0.00 0.00 2.34
1768 1935 9.305555 CATGGAATGGAATAAATCATACTCCTT 57.694 33.333 0.00 0.00 41.79 3.36
1811 1978 6.071672 CCTCTGATAGAATGTATCATGACGGT 60.072 42.308 0.00 0.00 33.93 4.83
1831 1998 2.080654 AGGTCCTAGCTAAGCCTCTG 57.919 55.000 0.00 0.00 0.00 3.35
1851 2018 3.771216 AGAAATGTGGGAAGCACTGAAT 58.229 40.909 0.00 0.00 0.00 2.57
1854 2021 5.452078 TTAAAGAAATGTGGGAAGCACTG 57.548 39.130 0.00 0.00 0.00 3.66
1858 2033 6.347644 GCATGTTTTAAAGAAATGTGGGAAGC 60.348 38.462 0.00 0.00 0.00 3.86
1881 2056 8.341892 TGTTACCATTATAACAGTGAAATGCA 57.658 30.769 0.00 0.00 39.56 3.96
1957 2133 6.096705 TGGGATAAATTCTAAACATGGCACTG 59.903 38.462 0.00 0.00 0.00 3.66
1984 2160 7.946219 TCCTGATGGCATAGTTATCATCAAAAT 59.054 33.333 0.00 0.00 43.33 1.82
1987 2163 6.438186 TCCTGATGGCATAGTTATCATCAA 57.562 37.500 0.00 0.00 43.33 2.57
1989 2165 9.270640 GAATATCCTGATGGCATAGTTATCATC 57.729 37.037 0.00 0.00 37.21 2.92
2020 2196 9.899226 CAAGTAGCAAATTAATTATAAGCCTCC 57.101 33.333 0.01 0.00 0.00 4.30
2051 2227 5.738909 ACCATGGAGAGAACTAAACATCTG 58.261 41.667 21.47 0.00 0.00 2.90
2053 2229 6.410540 AGAACCATGGAGAGAACTAAACATC 58.589 40.000 21.47 0.00 0.00 3.06
2300 2517 1.406539 GGAGGCAAATACACATGGCAG 59.593 52.381 0.00 0.00 43.93 4.85
2315 2532 2.979814 ACAAAAACCAAACAGGAGGC 57.020 45.000 0.00 0.00 41.22 4.70
2335 2552 0.804544 GTAGCGCCGTGATGTAGCAA 60.805 55.000 2.29 0.00 0.00 3.91
2336 2553 1.226859 GTAGCGCCGTGATGTAGCA 60.227 57.895 2.29 0.00 0.00 3.49
2386 2603 2.159156 CCCACAATTCATCTACGACGGA 60.159 50.000 0.00 0.00 0.00 4.69
2463 2685 6.776116 ACCATGATGATTTAGAATCAGTGCAT 59.224 34.615 9.01 9.01 36.31 3.96
2464 2686 6.124340 ACCATGATGATTTAGAATCAGTGCA 58.876 36.000 9.01 7.48 36.31 4.57
2465 2687 6.630444 ACCATGATGATTTAGAATCAGTGC 57.370 37.500 9.01 2.98 36.31 4.40
2467 2689 9.857656 ATGTAACCATGATGATTTAGAATCAGT 57.142 29.630 9.01 0.00 36.31 3.41
2485 2736 2.873472 GGACGAAACACACATGTAACCA 59.127 45.455 0.00 0.00 38.45 3.67
2495 2746 0.393132 TGTGCTTGGGACGAAACACA 60.393 50.000 0.00 0.19 35.80 3.72
2497 2748 1.464734 TTTGTGCTTGGGACGAAACA 58.535 45.000 0.00 0.00 0.00 2.83
2523 2774 1.348538 CGGCGAAGATACGTGTGCAA 61.349 55.000 0.00 0.00 35.59 4.08
2526 2777 0.365523 CAACGGCGAAGATACGTGTG 59.634 55.000 16.62 0.00 41.12 3.82
2531 2782 1.355971 TCTTGCAACGGCGAAGATAC 58.644 50.000 16.62 0.00 45.35 2.24
2535 2786 2.095853 ACATAATCTTGCAACGGCGAAG 59.904 45.455 16.62 6.84 45.35 3.79
2538 2789 2.176369 CAACATAATCTTGCAACGGCG 58.824 47.619 4.80 4.80 45.35 6.46
2542 2893 2.916716 CCGCACAACATAATCTTGCAAC 59.083 45.455 0.00 0.00 32.51 4.17
2562 2913 4.681483 GTCTAGCTTGCAAACAAAATGACC 59.319 41.667 0.00 0.00 34.74 4.02
2602 2953 0.458543 ACAGTCGCATTACCGAGCTG 60.459 55.000 0.00 10.35 39.71 4.24
2615 2966 0.445436 GCAATCAAGCCTGACAGTCG 59.555 55.000 0.93 0.00 33.30 4.18
2626 2979 3.369756 GCATGATTTGTGTGGCAATCAAG 59.630 43.478 0.00 0.76 36.89 3.02
2637 3021 9.894783 TTGGATTTAATTTTTGCATGATTTGTG 57.105 25.926 0.00 0.00 0.00 3.33
2651 3035 5.476091 TTTCGGTGCCTTGGATTTAATTT 57.524 34.783 0.00 0.00 0.00 1.82
2652 3036 5.234752 GTTTTCGGTGCCTTGGATTTAATT 58.765 37.500 0.00 0.00 0.00 1.40
2653 3037 4.322424 GGTTTTCGGTGCCTTGGATTTAAT 60.322 41.667 0.00 0.00 0.00 1.40
2654 3038 3.006003 GGTTTTCGGTGCCTTGGATTTAA 59.994 43.478 0.00 0.00 0.00 1.52
2655 3039 2.559231 GGTTTTCGGTGCCTTGGATTTA 59.441 45.455 0.00 0.00 0.00 1.40
2689 3073 3.073274 ACTGCTAGACCCCAAATTCAC 57.927 47.619 0.00 0.00 0.00 3.18
2712 3096 4.431809 TGTCTGAACTTTGCACAAATTGG 58.568 39.130 0.00 0.00 0.00 3.16
2713 3097 5.981315 AGATGTCTGAACTTTGCACAAATTG 59.019 36.000 0.00 0.00 0.00 2.32
2715 3099 5.526115 CAGATGTCTGAACTTTGCACAAAT 58.474 37.500 3.96 0.00 46.59 2.32
2738 3122 2.151202 TGGTCGGTCAAATTCAGAAGC 58.849 47.619 0.00 0.00 0.00 3.86
2757 3144 4.042398 CCGGACGTCTAATAACTCACATG 58.958 47.826 16.46 0.00 0.00 3.21
2767 3154 1.380785 TGGGAGCCGGACGTCTAAT 60.381 57.895 16.46 0.00 0.00 1.73
2768 3155 2.036098 TGGGAGCCGGACGTCTAA 59.964 61.111 16.46 0.00 0.00 2.10
2769 3156 2.753043 GTGGGAGCCGGACGTCTA 60.753 66.667 16.46 0.00 0.00 2.59
2782 3169 3.542676 TATAGCGCGTGGGGTGGG 61.543 66.667 8.43 0.00 0.00 4.61
2826 3216 2.846918 GCAGTCGTGTGCTCGAAC 59.153 61.111 4.75 0.00 41.47 3.95
2943 3345 1.682684 GGCTGGAGGAAGACGAGGA 60.683 63.158 0.00 0.00 0.00 3.71
2948 3350 1.599576 GAGGTGGCTGGAGGAAGAC 59.400 63.158 0.00 0.00 0.00 3.01
2951 3353 1.613630 GAGGAGGTGGCTGGAGGAA 60.614 63.158 0.00 0.00 0.00 3.36
2954 3356 2.985456 GTGAGGAGGTGGCTGGAG 59.015 66.667 0.00 0.00 0.00 3.86
3098 3503 1.079057 GAAGGACGGCAGGAAGGAC 60.079 63.158 0.00 0.00 0.00 3.85
3133 3538 2.428085 GCGTCCTCCTCCTCCTTCC 61.428 68.421 0.00 0.00 0.00 3.46
3227 3632 3.644399 GACGCGGTCCTTGTCCTCC 62.644 68.421 12.47 0.00 0.00 4.30
3258 3663 0.391793 GGAGCAGGAAAAGGAGGTCG 60.392 60.000 0.00 0.00 0.00 4.79
3264 3669 1.539157 GAAGGTGGAGCAGGAAAAGG 58.461 55.000 0.00 0.00 0.00 3.11
3269 3675 2.583441 CGTGGAAGGTGGAGCAGGA 61.583 63.158 0.00 0.00 0.00 3.86
3270 3676 2.046892 CGTGGAAGGTGGAGCAGG 60.047 66.667 0.00 0.00 0.00 4.85
3271 3677 2.743928 GCGTGGAAGGTGGAGCAG 60.744 66.667 0.00 0.00 0.00 4.24
3272 3678 4.329545 GGCGTGGAAGGTGGAGCA 62.330 66.667 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.