Multiple sequence alignment - TraesCS3D01G288100

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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 TraesCS3D01G288100 chr3D 100.000 3788 0 0 1 3788 397160811 397157024 0.000000e+00 6996.0
1 TraesCS3D01G288100 chr3D 94.311 791 36 6 3004 3788 397149940 397149153 0.000000e+00 1203.0
2 TraesCS3D01G288100 chr3D 90.780 423 35 3 3253 3671 584474692 584475114 2.550000e-156 562.0
3 TraesCS3D01G288100 chr3B 89.007 2065 120 62 21 2053 522779229 522777240 0.000000e+00 2457.0
4 TraesCS3D01G288100 chr3B 90.094 848 53 14 2200 3032 522777102 522776271 0.000000e+00 1072.0
5 TraesCS3D01G288100 chr3B 89.858 424 38 4 3252 3671 10196593 10196171 1.200000e-149 540.0
6 TraesCS3D01G288100 chr3B 88.125 160 14 1 3029 3183 522400166 522400007 6.460000e-43 185.0
7 TraesCS3D01G288100 chr3A 87.005 2224 133 63 21 2168 516635256 516633113 0.000000e+00 2362.0
8 TraesCS3D01G288100 chr3A 90.566 583 35 10 2460 3030 516632538 516631964 0.000000e+00 754.0
9 TraesCS3D01G288100 chr3A 89.362 423 39 5 3254 3671 734516005 734516426 9.320000e-146 527.0
10 TraesCS3D01G288100 chr3A 88.889 243 6 9 2231 2465 516632981 516632752 2.880000e-71 279.0
11 TraesCS3D01G288100 chr3A 100.000 36 0 0 3671 3706 516631090 516631055 2.440000e-07 67.6
12 TraesCS3D01G288100 chr2A 89.527 592 37 11 2629 3207 186284184 186284763 0.000000e+00 726.0
13 TraesCS3D01G288100 chr1D 91.080 426 31 6 3251 3671 403547729 403547306 1.530000e-158 569.0
14 TraesCS3D01G288100 chr7D 90.141 426 36 5 3251 3671 392752895 392753319 1.990000e-152 549.0
15 TraesCS3D01G288100 chr2B 89.810 422 38 4 3254 3671 198012360 198012780 1.550000e-148 536.0
16 TraesCS3D01G288100 chr7B 89.647 425 36 6 3252 3671 538384233 538384654 5.570000e-148 534.0
17 TraesCS3D01G288100 chr7B 89.598 423 39 4 3253 3671 592346598 592347019 2.000000e-147 532.0
18 TraesCS3D01G288100 chr6D 85.329 334 34 7 1231 1552 465420079 465420409 7.840000e-87 331.0
19 TraesCS3D01G288100 chr1B 96.341 82 3 0 1315 1396 600885828 600885747 6.600000e-28 135.0
20 TraesCS3D01G288100 chr1A 95.062 81 4 0 1315 1395 536437783 536437863 1.100000e-25 128.0


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 TraesCS3D01G288100 chr3D 397157024 397160811 3787 True 6996.00 6996 100.0000 1 3788 1 chr3D.!!$R2 3787
1 TraesCS3D01G288100 chr3D 397149153 397149940 787 True 1203.00 1203 94.3110 3004 3788 1 chr3D.!!$R1 784
2 TraesCS3D01G288100 chr3B 522776271 522779229 2958 True 1764.50 2457 89.5505 21 3032 2 chr3B.!!$R3 3011
3 TraesCS3D01G288100 chr3A 516631055 516635256 4201 True 865.65 2362 91.6150 21 3706 4 chr3A.!!$R1 3685
4 TraesCS3D01G288100 chr2A 186284184 186284763 579 False 726.00 726 89.5270 2629 3207 1 chr2A.!!$F1 578

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
436 466 0.445436 CAGCCTCTCATTTGCACGAC 59.555 55.0 0.00 0.0 0.0 4.34 F
2024 2143 0.179040 AGACGCGGGAAGGAAAAACA 60.179 50.0 12.47 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2080 2203 0.104120 GGGGTTTTGCTTCGCTTGTT 59.896 50.0 0.0 0.0 0.0 2.83 R
3240 4353 0.331278 ATTTGCCCCTTCCGACATGA 59.669 50.0 0.0 0.0 0.0 3.07 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
17 18 3.731136 TGCAAAGTCGTGGTCTGC 58.269 55.556 0.00 0.00 0.00 4.26
18 19 1.153269 TGCAAAGTCGTGGTCTGCA 60.153 52.632 0.00 0.00 40.54 4.41
19 20 0.746204 TGCAAAGTCGTGGTCTGCAA 60.746 50.000 0.00 0.00 39.91 4.08
79 80 3.900601 AGGTGACCAGAGCCTATTCTATG 59.099 47.826 3.63 0.00 0.00 2.23
80 81 3.643792 GGTGACCAGAGCCTATTCTATGT 59.356 47.826 0.00 0.00 0.00 2.29
105 110 3.908213 TGAGCGCCCTTGTTTAAAAATC 58.092 40.909 2.29 0.00 0.00 2.17
108 113 3.320826 AGCGCCCTTGTTTAAAAATCTGT 59.679 39.130 2.29 0.00 0.00 3.41
114 119 5.989168 CCCTTGTTTAAAAATCTGTTGTCCC 59.011 40.000 0.00 0.00 0.00 4.46
189 194 2.243957 TCGCCGTCTTGCTTGTGTG 61.244 57.895 0.00 0.00 0.00 3.82
222 231 3.584834 TCACGTTGCAGCGCATATATAT 58.415 40.909 23.44 0.00 38.76 0.86
223 232 4.739195 TCACGTTGCAGCGCATATATATA 58.261 39.130 23.44 0.00 38.76 0.86
252 265 3.537793 CGAAGGGAAAGCTACAAACAC 57.462 47.619 0.00 0.00 0.00 3.32
268 292 6.785488 ACAAACACACACTATACACTGATG 57.215 37.500 0.00 0.00 0.00 3.07
279 303 2.512286 ACTGATGGCCGATGTGCG 60.512 61.111 0.00 0.00 40.47 5.34
362 387 9.841295 TTCCTTGTTTTCAGTTACTTGTATAGT 57.159 29.630 0.00 0.00 41.04 2.12
363 388 9.268268 TCCTTGTTTTCAGTTACTTGTATAGTG 57.732 33.333 0.00 0.00 37.73 2.74
386 411 7.657354 AGTGTTTCTTTTCTTTCAAAAAGCAGT 59.343 29.630 4.61 0.00 43.06 4.40
388 413 7.440856 TGTTTCTTTTCTTTCAAAAAGCAGTGT 59.559 29.630 4.61 0.00 43.06 3.55
393 418 7.721286 TTTCTTTCAAAAAGCAGTGTTTTCA 57.279 28.000 5.36 0.00 0.00 2.69
398 423 8.770438 TTTCAAAAAGCAGTGTTTTCAGTTAT 57.230 26.923 5.36 0.00 0.00 1.89
403 428 9.646427 AAAAAGCAGTGTTTTCAGTTATTTGTA 57.354 25.926 5.36 0.00 0.00 2.41
436 466 0.445436 CAGCCTCTCATTTGCACGAC 59.555 55.000 0.00 0.00 0.00 4.34
495 525 5.801350 TCAGCTCAATTTGTAGTGTATGC 57.199 39.130 0.00 0.00 0.00 3.14
588 622 1.171308 AGCACATTGTCACATGGAGC 58.829 50.000 0.00 0.00 0.00 4.70
694 728 5.943416 TGTATTCAATTTCAACATCGGGAGT 59.057 36.000 0.00 0.00 0.00 3.85
713 747 3.549794 AGTTGCTTCAGACTTTTGAGCT 58.450 40.909 0.00 0.00 0.00 4.09
714 748 4.708177 AGTTGCTTCAGACTTTTGAGCTA 58.292 39.130 0.00 0.00 0.00 3.32
715 749 5.126067 AGTTGCTTCAGACTTTTGAGCTAA 58.874 37.500 0.00 0.00 0.00 3.09
716 750 5.008118 AGTTGCTTCAGACTTTTGAGCTAAC 59.992 40.000 0.00 0.00 0.00 2.34
717 751 4.450976 TGCTTCAGACTTTTGAGCTAACA 58.549 39.130 0.00 0.00 0.00 2.41
899 947 1.599071 CAGTGCGCTTTTCACTTCAGA 59.401 47.619 9.73 0.00 42.38 3.27
900 948 1.599542 AGTGCGCTTTTCACTTCAGAC 59.400 47.619 9.73 0.00 41.61 3.51
901 949 1.599542 GTGCGCTTTTCACTTCAGACT 59.400 47.619 9.73 0.00 0.00 3.24
902 950 1.599071 TGCGCTTTTCACTTCAGACTG 59.401 47.619 9.73 0.00 0.00 3.51
911 959 2.036475 TCACTTCAGACTGAGCTTCACC 59.964 50.000 5.10 0.00 0.00 4.02
932 980 3.924114 TCTCAGAGACTTCGGAGAGAT 57.076 47.619 0.00 0.00 45.66 2.75
938 993 4.991056 CAGAGACTTCGGAGAGATAGAGAG 59.009 50.000 0.00 0.00 38.43 3.20
944 999 5.011125 ACTTCGGAGAGATAGAGAGAGAGAG 59.989 48.000 0.00 0.00 38.43 3.20
950 1005 6.152661 GGAGAGATAGAGAGAGAGAGAGAGAG 59.847 50.000 0.00 0.00 0.00 3.20
969 1024 5.598005 AGAGAGAGAGAGAGAGAGAGAGAAG 59.402 48.000 0.00 0.00 0.00 2.85
1106 1169 1.011333 GAGGACGAGAACGAGGAGAG 58.989 60.000 0.00 0.00 42.66 3.20
1185 1248 1.817209 CGGTGGGGCTAAGACTCTC 59.183 63.158 0.00 0.00 0.00 3.20
1209 1272 0.329261 TCCATCTGGAGCCAAAGGTG 59.671 55.000 0.00 0.00 39.78 4.00
1211 1274 1.681166 CCATCTGGAGCCAAAGGTGAG 60.681 57.143 0.00 0.00 37.39 3.51
1229 1304 3.869832 GTGAGGAATTAACTAACGCCTCC 59.130 47.826 0.00 0.00 37.73 4.30
1232 1307 3.134262 AGGAATTAACTAACGCCTCCCTC 59.866 47.826 0.00 0.00 0.00 4.30
1280 1355 3.056107 TGTGGACACTGCTAGTATTCACC 60.056 47.826 3.91 0.00 0.00 4.02
1281 1356 3.195825 GTGGACACTGCTAGTATTCACCT 59.804 47.826 0.00 0.00 0.00 4.00
1282 1357 3.195610 TGGACACTGCTAGTATTCACCTG 59.804 47.826 0.00 0.00 0.00 4.00
1283 1358 3.190874 GACACTGCTAGTATTCACCTGC 58.809 50.000 0.00 0.00 0.00 4.85
1284 1359 2.567169 ACACTGCTAGTATTCACCTGCA 59.433 45.455 0.00 0.00 33.94 4.41
1285 1360 2.932614 CACTGCTAGTATTCACCTGCAC 59.067 50.000 0.00 0.00 32.37 4.57
1286 1361 2.834549 ACTGCTAGTATTCACCTGCACT 59.165 45.455 0.00 0.00 32.37 4.40
1287 1362 3.193263 CTGCTAGTATTCACCTGCACTG 58.807 50.000 0.00 0.00 32.37 3.66
1288 1363 1.936547 GCTAGTATTCACCTGCACTGC 59.063 52.381 0.00 0.00 0.00 4.40
1289 1364 2.677902 GCTAGTATTCACCTGCACTGCA 60.678 50.000 3.11 3.11 36.92 4.41
1290 1365 2.795231 AGTATTCACCTGCACTGCAT 57.205 45.000 3.64 0.00 38.13 3.96
1291 1366 3.912496 AGTATTCACCTGCACTGCATA 57.088 42.857 3.64 0.00 38.13 3.14
1292 1367 4.220693 AGTATTCACCTGCACTGCATAA 57.779 40.909 3.64 0.00 38.13 1.90
1293 1368 4.785301 AGTATTCACCTGCACTGCATAAT 58.215 39.130 3.64 5.44 38.13 1.28
1294 1369 5.928976 AGTATTCACCTGCACTGCATAATA 58.071 37.500 3.64 4.56 38.13 0.98
1295 1370 6.356556 AGTATTCACCTGCACTGCATAATAA 58.643 36.000 3.64 0.00 38.13 1.40
1296 1371 4.963276 TTCACCTGCACTGCATAATAAC 57.037 40.909 3.64 0.00 38.13 1.89
1297 1372 3.949132 TCACCTGCACTGCATAATAACA 58.051 40.909 3.64 0.00 38.13 2.41
1298 1373 4.525996 TCACCTGCACTGCATAATAACAT 58.474 39.130 3.64 0.00 38.13 2.71
1299 1374 4.336153 TCACCTGCACTGCATAATAACATG 59.664 41.667 3.64 0.00 38.13 3.21
1307 1382 3.565905 GCATAATAACATGCCTCCTGC 57.434 47.619 0.00 0.00 44.55 4.85
1308 1383 3.152341 GCATAATAACATGCCTCCTGCT 58.848 45.455 0.00 0.00 44.55 4.24
1351 1426 1.815421 GTCCATGCACTGCTACGGG 60.815 63.158 1.98 0.00 0.00 5.28
1410 1485 5.365605 TGGAAGGTACCATACGAATGAGAAT 59.634 40.000 15.94 0.00 34.84 2.40
1446 1521 0.741915 TTTTTCGGGGCAGTGTTGAC 59.258 50.000 0.00 0.00 0.00 3.18
1468 1547 5.699143 ACATTCTTTTGATAGGGCATAGCT 58.301 37.500 0.00 0.00 0.00 3.32
1469 1548 6.841601 ACATTCTTTTGATAGGGCATAGCTA 58.158 36.000 0.00 0.00 0.00 3.32
1470 1549 6.939163 ACATTCTTTTGATAGGGCATAGCTAG 59.061 38.462 0.00 0.00 0.00 3.42
1471 1550 6.500589 TTCTTTTGATAGGGCATAGCTAGT 57.499 37.500 0.00 0.00 0.00 2.57
1472 1551 5.858381 TCTTTTGATAGGGCATAGCTAGTG 58.142 41.667 0.00 0.00 0.00 2.74
1473 1552 5.602561 TCTTTTGATAGGGCATAGCTAGTGA 59.397 40.000 0.00 0.00 0.00 3.41
1563 1642 7.538303 AAAAGGAATTGCAAAGTTTGTACAG 57.462 32.000 16.70 0.00 0.00 2.74
1579 1658 3.694364 CAGCTGATCTGGCCGTAAT 57.306 52.632 8.42 0.00 39.15 1.89
1740 1830 1.933853 GCCACCTCGATGTGTTGATAC 59.066 52.381 17.87 0.00 34.35 2.24
1762 1852 0.723414 CAGACATAGCCAAGTGTGCG 59.277 55.000 0.00 0.00 0.00 5.34
1778 1871 3.057019 TGTGCGTTTCTTACTGCTAGTG 58.943 45.455 0.00 0.00 0.00 2.74
1780 1873 3.493503 GTGCGTTTCTTACTGCTAGTGTT 59.506 43.478 0.00 0.00 0.00 3.32
1781 1874 4.025145 GTGCGTTTCTTACTGCTAGTGTTT 60.025 41.667 0.00 0.00 0.00 2.83
1782 1875 5.176223 GTGCGTTTCTTACTGCTAGTGTTTA 59.824 40.000 0.00 0.00 0.00 2.01
1787 1885 8.940924 CGTTTCTTACTGCTAGTGTTTAAAAAC 58.059 33.333 0.00 0.00 39.33 2.43
1998 2112 0.663688 GGAGCAGAGATAAGTCGCGA 59.336 55.000 3.71 3.71 0.00 5.87
1999 2113 1.268352 GGAGCAGAGATAAGTCGCGAT 59.732 52.381 14.06 0.00 0.00 4.58
2023 2142 0.237498 CAGACGCGGGAAGGAAAAAC 59.763 55.000 12.47 0.00 0.00 2.43
2024 2143 0.179040 AGACGCGGGAAGGAAAAACA 60.179 50.000 12.47 0.00 0.00 2.83
2060 2179 3.978723 CTCTGTGCGCCTCCAGTCG 62.979 68.421 4.18 1.26 0.00 4.18
2068 2191 1.156736 CGCCTCCAGTCGTTTCAAAT 58.843 50.000 0.00 0.00 0.00 2.32
2077 2200 8.028938 CCTCCAGTCGTTTCAAATTTTCAATAT 58.971 33.333 0.00 0.00 0.00 1.28
2079 2202 9.834628 TCCAGTCGTTTCAAATTTTCAATATAC 57.165 29.630 0.00 0.00 0.00 1.47
2080 2203 9.619316 CCAGTCGTTTCAAATTTTCAATATACA 57.381 29.630 0.00 0.00 0.00 2.29
2090 2213 9.941991 CAAATTTTCAATATACAACAAGCGAAG 57.058 29.630 0.00 0.00 0.00 3.79
2108 2231 3.494251 CGAAGCAAAACCCCAAATTTCTG 59.506 43.478 0.00 0.00 0.00 3.02
2122 2245 0.036577 TTTCTGCTCTGCTCTGCTCC 60.037 55.000 0.00 0.00 0.00 4.70
2123 2246 1.897225 TTCTGCTCTGCTCTGCTCCC 61.897 60.000 0.00 0.00 0.00 4.30
2128 2256 4.527583 CTGCTCTGCTCCCCTCGC 62.528 72.222 0.00 0.00 0.00 5.03
2156 2284 2.225491 GCTAATGGCGAACAGTGAACAA 59.775 45.455 0.00 0.00 0.00 2.83
2161 2289 0.663153 GCGAACAGTGAACAAAGCCT 59.337 50.000 0.00 0.00 0.00 4.58
2165 2293 0.179045 ACAGTGAACAAAGCCTCGCT 60.179 50.000 0.00 0.00 42.56 4.93
2168 2296 1.525765 TGAACAAAGCCTCGCTGCA 60.526 52.632 0.00 0.00 39.62 4.41
2186 2359 1.202177 GCAGTGGCATGTTACGGAATG 60.202 52.381 0.00 0.00 40.72 2.67
2187 2360 2.083774 CAGTGGCATGTTACGGAATGT 58.916 47.619 0.00 0.00 0.00 2.71
2189 2362 3.309682 CAGTGGCATGTTACGGAATGTAG 59.690 47.826 0.00 0.00 33.75 2.74
2190 2363 3.055385 AGTGGCATGTTACGGAATGTAGT 60.055 43.478 0.00 0.00 33.75 2.73
2191 2364 3.308866 GTGGCATGTTACGGAATGTAGTC 59.691 47.826 0.00 0.00 33.75 2.59
2192 2365 3.055747 TGGCATGTTACGGAATGTAGTCA 60.056 43.478 0.00 0.00 33.75 3.41
2193 2366 4.127171 GGCATGTTACGGAATGTAGTCAT 58.873 43.478 0.00 0.00 33.75 3.06
2194 2367 5.163395 TGGCATGTTACGGAATGTAGTCATA 60.163 40.000 0.00 0.00 33.75 2.15
2195 2368 5.176958 GGCATGTTACGGAATGTAGTCATAC 59.823 44.000 0.00 0.00 33.75 2.39
2196 2369 5.751509 GCATGTTACGGAATGTAGTCATACA 59.248 40.000 0.00 0.00 45.73 2.29
2198 2371 5.334319 TGTTACGGAATGTAGTCATACACG 58.666 41.667 0.00 0.00 44.51 4.49
2205 2383 2.425539 TGTAGTCATACACGTCACCGA 58.574 47.619 0.00 0.00 36.98 4.69
2474 2901 0.389817 TTGGTACTACTGCTGCTGCG 60.390 55.000 11.21 8.29 43.34 5.18
2499 2926 3.889815 CTCATAATTGAGCTCCCACCAA 58.110 45.455 12.15 0.00 42.79 3.67
2510 2937 1.278127 CTCCCACCAACTTCACCGTAT 59.722 52.381 0.00 0.00 0.00 3.06
2516 2943 0.999406 CAACTTCACCGTATGGCTCG 59.001 55.000 0.00 0.00 39.70 5.03
2588 3020 4.337985 TGATTTACGAGTCGAGTGAGTC 57.662 45.455 21.50 9.56 40.54 3.36
2605 3037 0.318275 GTCCTGGACGAGCGATCATC 60.318 60.000 11.71 0.00 0.00 2.92
2618 3050 6.128282 ACGAGCGATCATCTTTAACATTTTGT 60.128 34.615 0.00 0.00 0.00 2.83
2788 3220 0.250814 CCCGGCTCCGAGTAGATAGT 60.251 60.000 10.28 0.00 42.83 2.12
2831 3269 2.290641 GTGGGTGTGACACATTTCACTC 59.709 50.000 18.40 0.00 45.34 3.51
2875 3316 4.600576 TCTCACGCAAGGCACGCA 62.601 61.111 0.00 0.00 46.39 5.24
2916 3357 4.019174 ACCATGGCAAGGAAGAAACTATG 58.981 43.478 16.88 0.00 0.00 2.23
3223 4328 1.595109 CTGTGTGCTGTGCTCGGAA 60.595 57.895 0.00 0.00 0.00 4.30
3245 4358 2.550830 AAGTTGGAGCGAAGTCATGT 57.449 45.000 0.00 0.00 0.00 3.21
3267 4380 1.343142 GGAAGGGGCAAATTTTCGTGT 59.657 47.619 0.00 0.00 0.00 4.49
3307 4420 5.063017 ACCTATTCGAGATCTGACCCTAA 57.937 43.478 0.00 0.00 0.00 2.69
3318 4431 8.462016 CGAGATCTGACCCTAATTTGAATTTTT 58.538 33.333 0.00 0.00 0.00 1.94
3372 4485 1.826720 TCCATGACGGTAGGGTGTAAC 59.173 52.381 0.00 0.00 35.57 2.50
3396 4509 2.741878 TACCGTCAGGGACCTTGGCT 62.742 60.000 6.64 0.00 43.47 4.75
3410 4523 2.025887 CCTTGGCTGTAGGAAACATCCT 60.026 50.000 2.51 2.51 43.56 3.24
3427 4540 1.156736 CCTTACCGCCAAACAGACTG 58.843 55.000 0.00 0.00 0.00 3.51
3474 4587 4.530857 GTGCTCGGCGGTAGGCAT 62.531 66.667 7.21 0.00 46.16 4.40
3606 4720 3.055094 GGTAGCAAAAGGGTCAGATCTCA 60.055 47.826 0.00 0.00 0.00 3.27
3610 4724 4.895297 AGCAAAAGGGTCAGATCTCAAAAA 59.105 37.500 0.00 0.00 0.00 1.94
3644 4759 9.976776 ACTAGGGTCAAATCTCGAATAGATATA 57.023 33.333 0.00 0.00 44.56 0.86
3712 4827 0.890996 CACAAAAAGAGAGGGCCGCT 60.891 55.000 10.44 10.44 0.00 5.52
3713 4828 0.690762 ACAAAAAGAGAGGGCCGCTA 59.309 50.000 10.67 0.00 0.00 4.26
3720 4835 0.822164 GAGAGGGCCGCTACTACAAA 59.178 55.000 10.67 0.00 0.00 2.83
3722 4837 2.626743 GAGAGGGCCGCTACTACAAATA 59.373 50.000 10.67 0.00 0.00 1.40
3723 4838 3.036091 AGAGGGCCGCTACTACAAATAA 58.964 45.455 8.47 0.00 0.00 1.40
3727 4842 1.525619 GCCGCTACTACAAATAAGCCG 59.474 52.381 0.00 0.00 0.00 5.52
3767 4882 2.888447 ATCCGCCTGCCTAGCCATC 61.888 63.158 0.00 0.00 0.00 3.51
3780 4895 4.451241 CCATCCGATCTGGCACTG 57.549 61.111 0.00 0.00 37.80 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.746204 TTGCAGACCACGACTTTGCA 60.746 50.000 0.00 0.00 42.44 4.08
1 2 0.317020 GTTGCAGACCACGACTTTGC 60.317 55.000 0.00 0.00 35.42 3.68
2 3 1.003545 CAGTTGCAGACCACGACTTTG 60.004 52.381 0.00 0.00 0.00 2.77
3 4 1.299541 CAGTTGCAGACCACGACTTT 58.700 50.000 0.00 0.00 0.00 2.66
4 5 1.160329 GCAGTTGCAGACCACGACTT 61.160 55.000 0.00 0.00 41.59 3.01
5 6 1.595382 GCAGTTGCAGACCACGACT 60.595 57.895 0.00 0.00 41.59 4.18
6 7 2.939022 GCAGTTGCAGACCACGAC 59.061 61.111 0.00 0.00 41.59 4.34
16 17 1.135460 GCATCTCTTCCTTGCAGTTGC 60.135 52.381 0.00 0.00 42.50 4.17
17 18 2.095364 GTGCATCTCTTCCTTGCAGTTG 60.095 50.000 0.00 0.00 46.18 3.16
18 19 2.157738 GTGCATCTCTTCCTTGCAGTT 58.842 47.619 0.00 0.00 46.18 3.16
19 20 1.350351 AGTGCATCTCTTCCTTGCAGT 59.650 47.619 0.00 0.00 46.18 4.40
79 80 1.172812 AAACAAGGGCGCTCAAGGAC 61.173 55.000 11.40 0.00 0.00 3.85
80 81 0.398696 TAAACAAGGGCGCTCAAGGA 59.601 50.000 11.40 0.00 0.00 3.36
105 110 0.038159 GAGACACGAGGGGACAACAG 60.038 60.000 0.00 0.00 0.00 3.16
108 113 0.966920 GAAGAGACACGAGGGGACAA 59.033 55.000 0.00 0.00 0.00 3.18
114 119 2.202492 CGCCGAAGAGACACGAGG 60.202 66.667 0.00 0.00 0.00 4.63
252 265 2.100749 TCGGCCATCAGTGTATAGTGTG 59.899 50.000 2.24 0.00 0.00 3.82
268 292 4.465512 CACTTGCGCACATCGGCC 62.466 66.667 11.12 0.00 38.94 6.13
279 303 3.799035 CACATACGTGTCTTTCACTTGC 58.201 45.455 0.00 0.00 44.16 4.01
361 386 7.741652 CACTGCTTTTTGAAAGAAAAGAAACAC 59.258 33.333 12.75 0.00 45.20 3.32
362 387 7.440856 ACACTGCTTTTTGAAAGAAAAGAAACA 59.559 29.630 12.75 2.81 45.20 2.83
363 388 7.796838 ACACTGCTTTTTGAAAGAAAAGAAAC 58.203 30.769 12.75 0.00 45.20 2.78
367 392 8.281893 TGAAAACACTGCTTTTTGAAAGAAAAG 58.718 29.630 4.69 5.89 45.17 2.27
375 400 8.655092 CAAATAACTGAAAACACTGCTTTTTGA 58.345 29.630 0.00 0.00 0.00 2.69
377 402 8.546597 ACAAATAACTGAAAACACTGCTTTTT 57.453 26.923 0.00 0.00 0.00 1.94
386 411 9.685828 GCCTTTACATACAAATAACTGAAAACA 57.314 29.630 0.00 0.00 0.00 2.83
388 413 8.861086 TGGCCTTTACATACAAATAACTGAAAA 58.139 29.630 3.32 0.00 0.00 2.29
393 418 7.122715 TGGATGGCCTTTACATACAAATAACT 58.877 34.615 3.32 0.00 36.28 2.24
398 423 3.699038 GCTGGATGGCCTTTACATACAAA 59.301 43.478 3.32 0.00 38.62 2.83
436 466 0.107017 AGAAGGGACCCAATCATGCG 60.107 55.000 14.60 0.00 0.00 4.73
449 479 7.939039 TGAAAGCATAACCATAGAATAGAAGGG 59.061 37.037 0.00 0.00 0.00 3.95
526 560 3.181507 CGTGGAATCATGCGTTTGAGAAT 60.182 43.478 0.00 0.00 0.00 2.40
530 564 1.731709 CTCGTGGAATCATGCGTTTGA 59.268 47.619 0.00 0.00 0.00 2.69
531 565 1.464608 ACTCGTGGAATCATGCGTTTG 59.535 47.619 0.00 0.00 0.00 2.93
694 728 4.881273 TGTTAGCTCAAAAGTCTGAAGCAA 59.119 37.500 0.00 0.00 0.00 3.91
713 747 7.881232 GGCAGTATAAAAGTGGGCTATATGTTA 59.119 37.037 0.00 0.00 0.00 2.41
714 748 6.715264 GGCAGTATAAAAGTGGGCTATATGTT 59.285 38.462 0.00 0.00 0.00 2.71
715 749 6.238648 GGCAGTATAAAAGTGGGCTATATGT 58.761 40.000 0.00 0.00 0.00 2.29
716 750 5.648092 GGGCAGTATAAAAGTGGGCTATATG 59.352 44.000 0.00 0.00 0.00 1.78
717 751 5.570844 CGGGCAGTATAAAAGTGGGCTATAT 60.571 44.000 0.00 0.00 0.00 0.86
901 949 2.166829 GTCTCTGAGAGGTGAAGCTCA 58.833 52.381 9.97 0.00 38.72 4.26
902 950 2.446435 AGTCTCTGAGAGGTGAAGCTC 58.554 52.381 9.97 1.20 0.00 4.09
932 980 6.101881 TCTCTCTCTCTCTCTCTCTCTCTCTA 59.898 46.154 0.00 0.00 0.00 2.43
933 981 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
938 993 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
944 999 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
950 1005 3.471680 GGCTTCTCTCTCTCTCTCTCTC 58.528 54.545 0.00 0.00 0.00 3.20
969 1024 1.066303 CTCTATCTCACTCACCACGGC 59.934 57.143 0.00 0.00 0.00 5.68
1096 1159 2.756283 CCCCTCGCTCTCCTCGTT 60.756 66.667 0.00 0.00 0.00 3.85
1185 1248 0.677731 TTGGCTCCAGATGGAAAGCG 60.678 55.000 2.65 0.00 44.91 4.68
1209 1272 3.134262 AGGGAGGCGTTAGTTAATTCCTC 59.866 47.826 11.06 11.06 36.59 3.71
1211 1274 3.134262 AGAGGGAGGCGTTAGTTAATTCC 59.866 47.826 0.00 0.00 0.00 3.01
1229 1304 2.818130 GCAGAGGCATCTTAGAGAGG 57.182 55.000 0.00 0.00 40.72 3.69
1272 1347 6.038161 TGTTATTATGCAGTGCAGGTGAATAC 59.962 38.462 24.20 14.49 43.65 1.89
1306 1381 1.812922 CTCCACCGTCTGCATCAGC 60.813 63.158 0.00 0.00 42.57 4.26
1307 1382 1.812922 GCTCCACCGTCTGCATCAG 60.813 63.158 0.00 0.00 0.00 2.90
1308 1383 2.265739 GCTCCACCGTCTGCATCA 59.734 61.111 0.00 0.00 0.00 3.07
1351 1426 0.884704 TCTGAACTTTCCTGGCGCAC 60.885 55.000 10.83 0.00 0.00 5.34
1399 1474 8.244113 GGATTTAAAGGTTCAATTCTCATTCGT 58.756 33.333 0.00 0.00 0.00 3.85
1410 1485 6.517605 CCGAAAAAGGGATTTAAAGGTTCAA 58.482 36.000 0.00 0.00 0.00 2.69
1446 1521 6.939163 ACTAGCTATGCCCTATCAAAAGAATG 59.061 38.462 0.00 0.00 0.00 2.67
1552 1631 3.077359 GCCAGATCAGCTGTACAAACTT 58.923 45.455 14.67 0.00 43.33 2.66
1555 1634 1.675714 CGGCCAGATCAGCTGTACAAA 60.676 52.381 14.67 0.00 43.33 2.83
1558 1637 4.427394 CGGCCAGATCAGCTGTAC 57.573 61.111 14.67 9.09 43.33 2.90
1563 1642 2.246719 AAGATTACGGCCAGATCAGC 57.753 50.000 2.24 0.00 0.00 4.26
1579 1658 4.816385 CCTCTGGCGAATAATTAGCAAAGA 59.184 41.667 0.00 0.00 0.00 2.52
1740 1830 2.417933 GCACACTTGGCTATGTCTGAAG 59.582 50.000 0.00 0.00 0.00 3.02
1762 1852 9.777575 TGTTTTTAAACACTAGCAGTAAGAAAC 57.222 29.630 6.10 1.24 43.45 2.78
1793 1892 5.505780 CCCACCAATAAGAAATGGACACTA 58.494 41.667 0.00 0.00 39.12 2.74
1796 1895 3.707316 CCCCACCAATAAGAAATGGACA 58.293 45.455 0.00 0.00 39.12 4.02
1811 1910 1.692173 TACTAATGCTCCGCCCCACC 61.692 60.000 0.00 0.00 0.00 4.61
1938 2046 2.237751 CGTTGCGCTCCTATTCCCG 61.238 63.158 9.73 0.00 0.00 5.14
1941 2049 1.201343 GAGACGTTGCGCTCCTATTC 58.799 55.000 9.73 0.00 0.00 1.75
1942 2050 0.530744 TGAGACGTTGCGCTCCTATT 59.469 50.000 9.73 0.00 32.33 1.73
1998 2112 1.513158 CTTCCCGCGTCTGACAGAT 59.487 57.895 8.73 0.00 0.00 2.90
1999 2113 2.636412 CCTTCCCGCGTCTGACAGA 61.636 63.158 4.92 0.00 0.00 3.41
2068 2191 6.673106 TGCTTCGCTTGTTGTATATTGAAAA 58.327 32.000 0.00 0.00 0.00 2.29
2077 2200 2.223618 GGGTTTTGCTTCGCTTGTTGTA 60.224 45.455 0.00 0.00 0.00 2.41
2079 2202 1.208259 GGGTTTTGCTTCGCTTGTTG 58.792 50.000 0.00 0.00 0.00 3.33
2080 2203 0.104120 GGGGTTTTGCTTCGCTTGTT 59.896 50.000 0.00 0.00 0.00 2.83
2086 2209 3.494251 CAGAAATTTGGGGTTTTGCTTCG 59.506 43.478 0.00 0.00 0.00 3.79
2090 2213 2.807967 GAGCAGAAATTTGGGGTTTTGC 59.192 45.455 0.00 0.00 0.00 3.68
2091 2214 4.060205 CAGAGCAGAAATTTGGGGTTTTG 58.940 43.478 0.00 0.00 0.00 2.44
2108 2231 3.082701 AGGGGAGCAGAGCAGAGC 61.083 66.667 0.00 0.00 0.00 4.09
2123 2246 1.890979 CATTAGCCCAGCAGCGAGG 60.891 63.158 0.00 0.00 38.01 4.63
2128 2256 1.451927 TTCGCCATTAGCCCAGCAG 60.452 57.895 0.00 0.00 38.78 4.24
2168 2296 2.489938 ACATTCCGTAACATGCCACT 57.510 45.000 0.00 0.00 0.00 4.00
2492 2919 1.448985 CATACGGTGAAGTTGGTGGG 58.551 55.000 0.00 0.00 0.00 4.61
2499 2926 0.606604 AACGAGCCATACGGTGAAGT 59.393 50.000 0.00 0.00 34.93 3.01
2510 2937 2.835701 GATGCTCCGACAACGAGCCA 62.836 60.000 7.31 0.00 42.66 4.75
2516 2943 1.687494 GACGCAGATGCTCCGACAAC 61.687 60.000 2.95 0.00 39.32 3.32
2588 3020 0.387202 AAGATGATCGCTCGTCCAGG 59.613 55.000 4.89 0.00 38.04 4.45
2605 3037 9.956797 CACAAGAACAGAAACAAAATGTTAAAG 57.043 29.630 0.00 0.00 40.14 1.85
2618 3050 3.278574 CCTGGACACACAAGAACAGAAA 58.721 45.455 0.00 0.00 0.00 2.52
2788 3220 6.470278 CACCCTATCAGCTTATCATCATCAA 58.530 40.000 0.00 0.00 0.00 2.57
2875 3316 0.389296 TTGCGTGTGCTGCTACGTAT 60.389 50.000 23.22 0.00 43.34 3.06
2916 3357 4.715297 TGGTCTCCTAGTTACAATCTTCCC 59.285 45.833 0.00 0.00 0.00 3.97
3158 4260 2.311841 ACATTTTCTTTCCCCCGGATCT 59.688 45.455 0.73 0.00 0.00 2.75
3223 4328 3.632145 ACATGACTTCGCTCCAACTTTTT 59.368 39.130 0.00 0.00 0.00 1.94
3240 4353 0.331278 ATTTGCCCCTTCCGACATGA 59.669 50.000 0.00 0.00 0.00 3.07
3245 4358 0.885196 CGAAAATTTGCCCCTTCCGA 59.115 50.000 0.00 0.00 0.00 4.55
3267 4380 7.094549 CGAATAGGTATCACAAAAGGGTCAAAA 60.095 37.037 0.00 0.00 0.00 2.44
3318 4431 3.502211 GCAAAAGGGTCAGATCTCGAAAA 59.498 43.478 0.00 0.00 0.00 2.29
3359 4472 3.236632 GTAGGTTGTTACACCCTACCG 57.763 52.381 23.22 0.00 43.19 4.02
3372 4485 0.903454 AGGTCCCTGACGGTAGGTTG 60.903 60.000 6.49 0.00 36.02 3.77
3382 4495 0.909610 CCTACAGCCAAGGTCCCTGA 60.910 60.000 0.36 0.00 0.00 3.86
3410 4523 3.315765 CCAGTCTGTTTGGCGGTAA 57.684 52.632 0.00 0.00 0.00 2.85
3427 4540 1.093496 GGGTTGTACATGCTACCGCC 61.093 60.000 8.08 0.72 35.58 6.13
3610 4724 6.940298 TCGAGATTTGACCCTAGTTTGATTTT 59.060 34.615 0.00 0.00 0.00 1.82
3613 4727 5.677319 TCGAGATTTGACCCTAGTTTGAT 57.323 39.130 0.00 0.00 0.00 2.57
3644 4759 7.713507 GGCTAAATTTTGTGTTACCCTTTTCTT 59.286 33.333 0.00 0.00 0.00 2.52
3657 4772 8.495148 GTTAAAACATCCTGGCTAAATTTTGTG 58.505 33.333 0.00 0.00 0.00 3.33
3712 4827 8.514330 AAAAATCATCCGGCTTATTTGTAGTA 57.486 30.769 0.00 0.00 0.00 1.82
3713 4828 7.404671 AAAAATCATCCGGCTTATTTGTAGT 57.595 32.000 0.00 0.00 0.00 2.73
3739 4854 2.092429 AGGCAGGCGGATGATTTTTCTA 60.092 45.455 0.00 0.00 0.00 2.10
3740 4855 1.106285 GGCAGGCGGATGATTTTTCT 58.894 50.000 0.00 0.00 0.00 2.52
3767 4882 2.682893 GCTAACAGTGCCAGATCGG 58.317 57.895 0.00 0.00 38.11 4.18


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

AutoCloner maintained by Alex Coulton.