Multiple sequence alignment - TraesCS2D01G524900

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G524900 chr2D 100.000 2132 0 0 1 2132 613321109 613323240 0.000000e+00 3938
1 TraesCS2D01G524900 chr2D 97.087 103 3 0 3 105 19723859 19723961 7.820000e-40 174
2 TraesCS2D01G524900 chr2D 96.117 103 4 0 3 105 19747712 19747814 3.640000e-38 169
3 TraesCS2D01G524900 chr2B 88.145 1299 103 23 3 1286 748699780 748701042 0.000000e+00 1498
4 TraesCS2D01G524900 chr2B 92.967 782 55 0 1351 2132 748701044 748701825 0.000000e+00 1140
5 TraesCS2D01G524900 chr2A 87.904 1298 99 24 5 1286 744978675 744979930 0.000000e+00 1474
6 TraesCS2D01G524900 chr2A 92.967 782 55 0 1351 2132 744979932 744980713 0.000000e+00 1140
7 TraesCS2D01G524900 chr5D 97.170 106 3 0 3 108 473056973 473056868 1.680000e-41 180
8 TraesCS2D01G524900 chr1B 97.170 106 3 0 3 108 34337452 34337557 1.680000e-41 180
9 TraesCS2D01G524900 chr5B 96.226 106 4 0 3 108 617340097 617339992 7.820000e-40 174
10 TraesCS2D01G524900 chr4D 96.226 106 4 0 3 108 446596775 446596670 7.820000e-40 174
11 TraesCS2D01G524900 chr4B 95.283 106 5 0 3 108 381141530 381141425 3.640000e-38 169


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 TraesCS2D01G524900 chr2D 613321109 613323240 2131 False 3938 3938 100.0000 1 2132 1 chr2D.!!$F3 2131
1 TraesCS2D01G524900 chr2B 748699780 748701825 2045 False 1319 1498 90.5560 3 2132 2 chr2B.!!$F1 2129
2 TraesCS2D01G524900 chr2A 744978675 744980713 2038 False 1307 1474 90.4355 5 2132 2 chr2A.!!$F1 2127

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
496 512 1.135915 GCAAACACCATGTGAACACCA 59.864 47.619 0.49 0.0 36.96 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1300 1324 0.252239 TCTAGGGCTTCACTCCTGCA 60.252 55.0 0.0 0.0 34.75 4.41 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
108 110 4.579869 TGTCATTTTTGCCTCTAGAGTCC 58.420 43.478 18.42 9.49 0.00 3.85
109 111 4.041567 TGTCATTTTTGCCTCTAGAGTCCA 59.958 41.667 18.42 11.89 0.00 4.02
140 147 2.380064 TTCCTGTGGCCACTTCATTT 57.620 45.000 34.75 0.00 0.00 2.32
156 163 6.920758 CACTTCATTTGTATTTTTGGGTCGAA 59.079 34.615 0.00 0.00 0.00 3.71
177 184 9.615295 GTCGAATAAATCCTAGTATGAGAAGAC 57.385 37.037 0.00 0.00 0.00 3.01
192 199 2.435805 AGAAGACCGCATGTGGACATAT 59.564 45.455 31.66 13.20 34.26 1.78
242 253 9.661954 TCTATATCCTAGTTTCTCAATTCACCT 57.338 33.333 0.00 0.00 0.00 4.00
252 263 8.709308 AGTTTCTCAATTCACCTATAGCATACT 58.291 33.333 0.00 0.00 0.00 2.12
289 304 5.529800 CCTTTGTTTCCCTAAGAAGTCGAAA 59.470 40.000 0.00 0.00 35.40 3.46
292 307 5.054477 TGTTTCCCTAAGAAGTCGAAACTG 58.946 41.667 11.07 0.00 39.04 3.16
302 317 5.844004 AGAAGTCGAAACTGTAGATGTTGT 58.156 37.500 0.00 0.00 35.36 3.32
303 318 6.281405 AGAAGTCGAAACTGTAGATGTTGTT 58.719 36.000 0.00 0.00 35.36 2.83
308 323 8.885722 AGTCGAAACTGTAGATGTTGTTAAAAA 58.114 29.630 0.00 0.00 33.32 1.94
351 367 3.578978 TCCACTTGTCCCACTAACTGTA 58.421 45.455 0.00 0.00 0.00 2.74
436 452 6.801862 GCTGTATTGGTTTTAAAGTAGCACTG 59.198 38.462 0.00 0.00 0.00 3.66
438 454 8.228035 TGTATTGGTTTTAAAGTAGCACTGTT 57.772 30.769 0.00 0.00 0.00 3.16
439 455 9.339850 TGTATTGGTTTTAAAGTAGCACTGTTA 57.660 29.630 0.00 0.00 0.00 2.41
487 503 2.507484 TCCTCTCAAGCAAACACCATG 58.493 47.619 0.00 0.00 0.00 3.66
488 504 2.158623 TCCTCTCAAGCAAACACCATGT 60.159 45.455 0.00 0.00 0.00 3.21
489 505 2.030540 CCTCTCAAGCAAACACCATGTG 60.031 50.000 0.00 0.00 39.75 3.21
490 506 2.880268 CTCTCAAGCAAACACCATGTGA 59.120 45.455 0.49 0.00 36.96 3.58
491 507 3.286353 TCTCAAGCAAACACCATGTGAA 58.714 40.909 0.49 0.00 36.96 3.18
492 508 3.066621 TCTCAAGCAAACACCATGTGAAC 59.933 43.478 0.49 0.00 36.96 3.18
493 509 2.757314 TCAAGCAAACACCATGTGAACA 59.243 40.909 0.49 0.00 36.96 3.18
494 510 2.859538 CAAGCAAACACCATGTGAACAC 59.140 45.455 0.49 0.00 36.96 3.32
495 511 1.408702 AGCAAACACCATGTGAACACC 59.591 47.619 0.49 0.00 36.96 4.16
496 512 1.135915 GCAAACACCATGTGAACACCA 59.864 47.619 0.49 0.00 36.96 4.17
497 513 2.224018 GCAAACACCATGTGAACACCAT 60.224 45.455 0.49 0.00 36.96 3.55
498 514 3.005261 GCAAACACCATGTGAACACCATA 59.995 43.478 0.49 0.00 36.96 2.74
499 515 4.797471 CAAACACCATGTGAACACCATAG 58.203 43.478 0.49 0.00 36.96 2.23
500 516 3.788227 ACACCATGTGAACACCATAGT 57.212 42.857 0.49 0.00 36.96 2.12
501 517 3.411446 ACACCATGTGAACACCATAGTG 58.589 45.455 0.49 7.46 42.36 2.74
502 518 2.162208 CACCATGTGAACACCATAGTGC 59.838 50.000 2.46 0.00 40.93 4.40
503 519 4.119376 CACCATGTGAACACCATAGTGCT 61.119 47.826 2.46 0.00 40.93 4.40
539 555 5.882000 TGATTCACCATTTCCTCATGTACAG 59.118 40.000 0.33 0.00 0.00 2.74
545 561 6.038603 CACCATTTCCTCATGTACAGTAATGG 59.961 42.308 20.36 20.36 43.89 3.16
608 625 9.844790 TTGATGTATTTCTTTAGCATTTCTGTG 57.155 29.630 0.00 0.00 0.00 3.66
623 640 5.963176 TTTCTGTGCAAGCTCATATGAAA 57.037 34.783 6.90 2.48 0.00 2.69
636 653 9.632638 AAGCTCATATGAAATGGTACTTGTTAT 57.367 29.630 6.90 0.00 0.00 1.89
662 679 7.786030 TCTCATACTTCTGGATTTCCTTACAG 58.214 38.462 0.00 0.00 36.82 2.74
664 681 3.956744 ACTTCTGGATTTCCTTACAGGC 58.043 45.455 0.00 0.00 34.61 4.85
666 683 3.914426 TCTGGATTTCCTTACAGGCTC 57.086 47.619 0.00 0.00 34.61 4.70
682 699 6.506500 ACAGGCTCTTGAATCACTTTATTG 57.493 37.500 0.00 0.00 0.00 1.90
683 700 6.240894 ACAGGCTCTTGAATCACTTTATTGA 58.759 36.000 0.00 0.00 0.00 2.57
689 706 9.630098 GCTCTTGAATCACTTTATTGATTTCAA 57.370 29.630 0.15 0.00 44.59 2.69
706 723 5.560966 TTTCAACTGTGGTTCTTGTTCTC 57.439 39.130 0.00 0.00 32.73 2.87
749 766 5.455326 GGTTGTGGATGAGTAGGCTTGATAT 60.455 44.000 0.00 0.00 0.00 1.63
753 771 7.801104 TGTGGATGAGTAGGCTTGATATTTAA 58.199 34.615 0.00 0.00 0.00 1.52
769 787 9.540538 TTGATATTTAATCTTTTGGGTTCTCCA 57.459 29.630 0.00 0.00 45.43 3.86
781 799 7.896383 TTTGGGTTCTCCATCATATTTAAGG 57.104 36.000 0.00 0.00 46.52 2.69
798 816 6.721571 TTTAAGGAACATTAGCTTCAGTCG 57.278 37.500 0.00 0.00 0.00 4.18
815 833 5.577835 TCAGTCGGTTGTTTTCTTTTGATG 58.422 37.500 0.00 0.00 0.00 3.07
870 888 3.064900 ACCTGACTTTCTTGCAGATCC 57.935 47.619 0.00 0.00 0.00 3.36
908 926 3.125146 TGCGTGATATGAAGTCTGTTTGC 59.875 43.478 0.00 0.00 0.00 3.68
916 934 3.476552 TGAAGTCTGTTTGCGGATTCTT 58.523 40.909 0.00 0.00 31.86 2.52
1086 1104 5.234757 TGACGTGTACTTCCATTTTGTGTAC 59.765 40.000 0.00 0.00 35.43 2.90
1128 1146 4.202080 GGTGAAGTTGTTAAACTGGGGTTC 60.202 45.833 0.00 0.00 46.15 3.62
1135 1153 4.148838 TGTTAAACTGGGGTTCTGATTGG 58.851 43.478 0.00 0.00 34.14 3.16
1138 1156 1.444933 ACTGGGGTTCTGATTGGTCA 58.555 50.000 0.00 0.00 0.00 4.02
1160 1178 1.227674 GAAGCTATCGGCCACTGGG 60.228 63.158 2.24 0.00 43.05 4.45
1174 1192 3.889134 CTGGGCAGCGCTCAAGTCA 62.889 63.158 7.13 0.77 39.14 3.41
1177 1195 1.589716 GGGCAGCGCTCAAGTCATTT 61.590 55.000 7.13 0.00 0.00 2.32
1257 1281 3.390003 TGTTCGTGGGAAGGAACAC 57.610 52.632 9.27 0.00 45.38 3.32
1263 1287 1.066143 CGTGGGAAGGAACACATAGCT 60.066 52.381 0.00 0.00 37.45 3.32
1280 1304 3.699411 AGCTGCTTCATTCTCTCAAGT 57.301 42.857 0.00 0.00 0.00 3.16
1286 1310 4.516698 TGCTTCATTCTCTCAAGTTGAACC 59.483 41.667 7.06 0.00 0.00 3.62
1287 1311 4.083057 GCTTCATTCTCTCAAGTTGAACCC 60.083 45.833 7.06 0.00 0.00 4.11
1288 1312 3.664107 TCATTCTCTCAAGTTGAACCCG 58.336 45.455 7.06 0.00 0.00 5.28
1289 1313 1.878953 TTCTCTCAAGTTGAACCCGC 58.121 50.000 7.06 0.00 0.00 6.13
1290 1314 1.048601 TCTCTCAAGTTGAACCCGCT 58.951 50.000 7.06 0.00 0.00 5.52
1291 1315 1.151668 CTCTCAAGTTGAACCCGCTG 58.848 55.000 7.06 0.00 0.00 5.18
1292 1316 0.884704 TCTCAAGTTGAACCCGCTGC 60.885 55.000 7.06 0.00 0.00 5.25
1293 1317 1.856265 CTCAAGTTGAACCCGCTGCC 61.856 60.000 7.06 0.00 0.00 4.85
1294 1318 2.978010 AAGTTGAACCCGCTGCCG 60.978 61.111 0.00 0.00 0.00 5.69
1299 1323 3.747976 GAACCCGCTGCCGCAAAT 61.748 61.111 0.00 0.00 35.30 2.32
1300 1324 3.281359 GAACCCGCTGCCGCAAATT 62.281 57.895 0.00 0.00 35.30 1.82
1301 1325 3.572196 AACCCGCTGCCGCAAATTG 62.572 57.895 0.00 0.00 35.30 2.32
1303 1327 4.721111 CCGCTGCCGCAAATTGCA 62.721 61.111 18.65 0.00 45.36 4.08
1307 1331 2.964174 TGCCGCAAATTGCAGGAG 59.036 55.556 24.94 10.40 45.36 3.69
1308 1332 1.902918 TGCCGCAAATTGCAGGAGT 60.903 52.632 24.94 0.00 45.36 3.85
1309 1333 1.444895 GCCGCAAATTGCAGGAGTG 60.445 57.895 24.94 7.07 45.36 3.51
1310 1334 1.865788 GCCGCAAATTGCAGGAGTGA 61.866 55.000 24.94 0.00 45.36 3.41
1311 1335 0.597568 CCGCAAATTGCAGGAGTGAA 59.402 50.000 18.65 0.00 45.36 3.18
1312 1336 1.401931 CCGCAAATTGCAGGAGTGAAG 60.402 52.381 18.65 0.00 45.36 3.02
1313 1337 1.706443 GCAAATTGCAGGAGTGAAGC 58.294 50.000 13.73 0.00 44.26 3.86
1314 1338 1.670967 GCAAATTGCAGGAGTGAAGCC 60.671 52.381 13.73 0.00 44.26 4.35
1315 1339 1.067354 CAAATTGCAGGAGTGAAGCCC 60.067 52.381 0.00 0.00 0.00 5.19
1316 1340 0.407139 AATTGCAGGAGTGAAGCCCT 59.593 50.000 0.00 0.00 0.00 5.19
1317 1341 1.289160 ATTGCAGGAGTGAAGCCCTA 58.711 50.000 0.00 0.00 0.00 3.53
1318 1342 0.615331 TTGCAGGAGTGAAGCCCTAG 59.385 55.000 0.00 0.00 0.00 3.02
1319 1343 0.252239 TGCAGGAGTGAAGCCCTAGA 60.252 55.000 0.00 0.00 0.00 2.43
1320 1344 1.127343 GCAGGAGTGAAGCCCTAGAT 58.873 55.000 0.00 0.00 0.00 1.98
1321 1345 1.202627 GCAGGAGTGAAGCCCTAGATG 60.203 57.143 0.00 0.00 0.00 2.90
1322 1346 2.114616 CAGGAGTGAAGCCCTAGATGT 58.885 52.381 0.00 0.00 0.00 3.06
1323 1347 3.300388 CAGGAGTGAAGCCCTAGATGTA 58.700 50.000 0.00 0.00 0.00 2.29
1324 1348 3.320541 CAGGAGTGAAGCCCTAGATGTAG 59.679 52.174 0.00 0.00 0.00 2.74
1325 1349 2.036604 GGAGTGAAGCCCTAGATGTAGC 59.963 54.545 0.00 0.00 0.00 3.58
1326 1350 2.695666 GAGTGAAGCCCTAGATGTAGCA 59.304 50.000 0.00 0.00 0.00 3.49
1327 1351 3.312890 AGTGAAGCCCTAGATGTAGCAT 58.687 45.455 0.00 0.00 0.00 3.79
1328 1352 3.323403 AGTGAAGCCCTAGATGTAGCATC 59.677 47.826 0.00 1.18 0.00 3.91
1329 1353 3.070159 GTGAAGCCCTAGATGTAGCATCA 59.930 47.826 11.12 0.00 0.00 3.07
1330 1354 3.323115 TGAAGCCCTAGATGTAGCATCAG 59.677 47.826 11.12 6.71 0.00 2.90
1331 1355 2.969628 AGCCCTAGATGTAGCATCAGT 58.030 47.619 11.12 0.00 0.00 3.41
1332 1356 3.312890 AGCCCTAGATGTAGCATCAGTT 58.687 45.455 11.12 0.00 0.00 3.16
1333 1357 4.483950 AGCCCTAGATGTAGCATCAGTTA 58.516 43.478 11.12 0.00 0.00 2.24
1334 1358 4.901849 AGCCCTAGATGTAGCATCAGTTAA 59.098 41.667 11.12 0.00 0.00 2.01
1335 1359 5.366768 AGCCCTAGATGTAGCATCAGTTAAA 59.633 40.000 11.12 0.00 0.00 1.52
1336 1360 5.698545 GCCCTAGATGTAGCATCAGTTAAAG 59.301 44.000 11.12 0.48 0.00 1.85
1337 1361 6.686632 GCCCTAGATGTAGCATCAGTTAAAGT 60.687 42.308 11.12 0.00 0.00 2.66
1338 1362 7.275920 CCCTAGATGTAGCATCAGTTAAAGTT 58.724 38.462 11.12 0.00 0.00 2.66
1339 1363 7.225538 CCCTAGATGTAGCATCAGTTAAAGTTG 59.774 40.741 11.12 0.00 0.00 3.16
1340 1364 6.992063 AGATGTAGCATCAGTTAAAGTTGG 57.008 37.500 11.12 0.00 0.00 3.77
1341 1365 6.476378 AGATGTAGCATCAGTTAAAGTTGGT 58.524 36.000 11.12 0.00 0.00 3.67
1342 1366 6.942576 AGATGTAGCATCAGTTAAAGTTGGTT 59.057 34.615 11.12 0.00 0.00 3.67
1343 1367 6.312399 TGTAGCATCAGTTAAAGTTGGTTG 57.688 37.500 0.00 0.00 0.00 3.77
1344 1368 4.243007 AGCATCAGTTAAAGTTGGTTGC 57.757 40.909 0.00 0.00 0.00 4.17
1345 1369 3.005791 AGCATCAGTTAAAGTTGGTTGCC 59.994 43.478 0.00 0.00 0.00 4.52
1346 1370 3.005791 GCATCAGTTAAAGTTGGTTGCCT 59.994 43.478 0.00 0.00 0.00 4.75
1347 1371 4.798574 CATCAGTTAAAGTTGGTTGCCTC 58.201 43.478 0.00 0.00 0.00 4.70
1348 1372 2.875933 TCAGTTAAAGTTGGTTGCCTCG 59.124 45.455 0.00 0.00 0.00 4.63
1349 1373 2.031157 CAGTTAAAGTTGGTTGCCTCGG 60.031 50.000 0.00 0.00 0.00 4.63
1356 1380 4.821589 GGTTGCCTCGGGAGCTCG 62.822 72.222 7.83 0.00 0.00 5.03
1386 1410 7.465781 GCAGCTGAGACTTCTAGAAAATCATTC 60.466 40.741 20.43 8.18 0.00 2.67
1388 1412 6.754209 GCTGAGACTTCTAGAAAATCATTCGA 59.246 38.462 15.42 0.00 0.00 3.71
1395 1419 6.456795 TCTAGAAAATCATTCGAGCAGAGA 57.543 37.500 0.00 0.00 0.00 3.10
1406 1430 2.293677 TCGAGCAGAGAAGTCGAAGTTT 59.706 45.455 0.00 0.00 39.66 2.66
1476 1500 3.691118 TGCCAAATCTGTATTCTGCTGAC 59.309 43.478 0.00 0.00 0.00 3.51
1488 1512 4.548451 TTCTGCTGACAGTCAATCATCT 57.452 40.909 4.41 0.00 44.77 2.90
1499 1523 3.012518 GTCAATCATCTGGTGGGAACAG 58.987 50.000 0.00 0.00 44.46 3.16
1514 1538 7.110155 GGTGGGAACAGAGTTAAATTATCTGA 58.890 38.462 9.78 0.00 44.46 3.27
1517 1541 9.010029 TGGGAACAGAGTTAAATTATCTGAAAC 57.990 33.333 9.78 2.65 42.48 2.78
1539 1563 4.578928 ACTTTGTTCACTCCACATTGTACC 59.421 41.667 0.00 0.00 0.00 3.34
1549 1573 2.487762 CCACATTGTACCGCAAGTGATT 59.512 45.455 0.00 0.00 40.86 2.57
1554 1578 1.621317 TGTACCGCAAGTGATTCTGGA 59.379 47.619 0.00 0.00 0.00 3.86
1558 1582 3.535561 ACCGCAAGTGATTCTGGATTAG 58.464 45.455 0.00 0.00 0.00 1.73
1561 1585 3.935203 CGCAAGTGATTCTGGATTAGTGT 59.065 43.478 0.00 0.00 0.00 3.55
1565 1589 4.265073 AGTGATTCTGGATTAGTGTTGGC 58.735 43.478 0.00 0.00 0.00 4.52
1567 1591 2.107950 TTCTGGATTAGTGTTGGCGG 57.892 50.000 0.00 0.00 0.00 6.13
1602 1626 3.558505 CTCAAGAAATTTGCAGTCCACG 58.441 45.455 0.00 0.00 0.00 4.94
1604 1628 3.820467 TCAAGAAATTTGCAGTCCACGAT 59.180 39.130 0.00 0.00 0.00 3.73
1638 1662 4.427312 GCAAGGAGCATTCACATAAAAGG 58.573 43.478 0.00 0.00 44.79 3.11
1653 1677 9.703892 TCACATAAAAGGAAAAATGGTATTGTG 57.296 29.630 0.00 0.00 0.00 3.33
1661 1685 5.011635 GGAAAAATGGTATTGTGTTCCCACT 59.988 40.000 0.00 0.00 42.34 4.00
1667 1691 5.882040 TGGTATTGTGTTCCCACTTATTGA 58.118 37.500 0.00 0.00 42.34 2.57
1668 1692 6.489603 TGGTATTGTGTTCCCACTTATTGAT 58.510 36.000 0.00 0.00 42.34 2.57
1694 1718 3.192212 GGATCAACTTCAGCCAAAAGGAG 59.808 47.826 0.00 0.00 0.00 3.69
1695 1719 3.576078 TCAACTTCAGCCAAAAGGAGA 57.424 42.857 0.00 0.00 0.00 3.71
1721 1745 4.128925 GTGATTATGAGCTGTCACCTCA 57.871 45.455 0.00 0.30 42.91 3.86
1842 1866 0.460987 CTCTTGATCAGCACGGGGTC 60.461 60.000 0.00 0.00 0.00 4.46
1893 1917 1.587946 GGTTGTTCTTTTGCTGCAACG 59.412 47.619 15.72 9.42 39.95 4.10
1899 1923 1.330521 TCTTTTGCTGCAACGTCAGAC 59.669 47.619 15.72 0.00 36.19 3.51
1903 1927 1.276844 GCTGCAACGTCAGACACAC 59.723 57.895 8.35 0.00 36.19 3.82
1920 1944 6.915300 CAGACACACTAGATAGCACTGATAAC 59.085 42.308 0.00 0.00 0.00 1.89
1934 1958 3.244770 ACTGATAACGGGGAGCAGAAAAA 60.245 43.478 5.85 0.00 0.00 1.94
2052 2076 1.662044 CCAGAAGCCAGGTTGCAAC 59.338 57.895 21.59 21.59 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.196039 TGATCCAAATCCATGCCAAACAG 59.804 43.478 0.00 0.00 0.00 3.16
1 2 3.171528 TGATCCAAATCCATGCCAAACA 58.828 40.909 0.00 0.00 0.00 2.83
126 131 5.179182 CCAAAAATACAAATGAAGTGGCCAC 59.821 40.000 29.22 29.22 0.00 5.01
132 139 6.642707 TCGACCCAAAAATACAAATGAAGT 57.357 33.333 0.00 0.00 0.00 3.01
140 147 7.948034 AGGATTTATTCGACCCAAAAATACA 57.052 32.000 0.00 0.00 0.00 2.29
156 163 6.493802 TGCGGTCTTCTCATACTAGGATTTAT 59.506 38.462 0.00 0.00 0.00 1.40
177 184 2.037121 TGGTAGATATGTCCACATGCGG 59.963 50.000 2.26 0.00 37.15 5.69
192 199 9.601810 AGATACATATGGTGATAAGTTGGTAGA 57.398 33.333 7.80 0.00 0.00 2.59
316 331 8.899306 TGGGACAAGTGGAAGAAGACTTCATAT 61.899 40.741 17.34 3.14 44.77 1.78
317 332 7.657785 TGGGACAAGTGGAAGAAGACTTCATA 61.658 42.308 17.34 0.00 44.77 2.15
318 333 6.930433 TGGGACAAGTGGAAGAAGACTTCAT 61.930 44.000 17.34 5.22 44.77 2.57
319 334 5.671038 TGGGACAAGTGGAAGAAGACTTCA 61.671 45.833 17.34 0.00 44.77 3.02
320 335 3.181454 TGGGACAAGTGGAAGAAGACTTC 60.181 47.826 7.14 7.14 43.34 3.01
321 336 2.777692 TGGGACAAGTGGAAGAAGACTT 59.222 45.455 0.00 0.00 35.13 3.01
322 337 2.104963 GTGGGACAAGTGGAAGAAGACT 59.895 50.000 0.00 0.00 44.16 3.24
323 338 2.104963 AGTGGGACAAGTGGAAGAAGAC 59.895 50.000 0.00 0.00 44.16 3.01
324 339 2.408565 AGTGGGACAAGTGGAAGAAGA 58.591 47.619 0.00 0.00 44.16 2.87
325 340 2.938956 AGTGGGACAAGTGGAAGAAG 57.061 50.000 0.00 0.00 44.16 2.85
351 367 7.174946 CAGTCATACATGTTAAAACTTCCTGGT 59.825 37.037 2.30 0.00 0.00 4.00
455 471 5.809001 TGCTTGAGAGGAACATGAATTAGT 58.191 37.500 0.00 0.00 0.00 2.24
469 485 2.880268 TCACATGGTGTTTGCTTGAGAG 59.120 45.455 0.00 0.00 34.79 3.20
487 503 7.843490 TTAGAATTAGCACTATGGTGTTCAC 57.157 36.000 11.18 0.00 44.65 3.18
488 504 8.264347 TGATTAGAATTAGCACTATGGTGTTCA 58.736 33.333 11.18 0.00 44.65 3.18
489 505 8.662781 TGATTAGAATTAGCACTATGGTGTTC 57.337 34.615 11.18 6.62 44.65 3.18
490 506 9.060347 CATGATTAGAATTAGCACTATGGTGTT 57.940 33.333 11.18 7.46 44.65 3.32
491 507 8.432013 TCATGATTAGAATTAGCACTATGGTGT 58.568 33.333 11.18 0.72 44.65 4.16
492 508 8.837788 TCATGATTAGAATTAGCACTATGGTG 57.162 34.615 4.57 4.57 45.53 4.17
497 513 9.494271 GGTGAATCATGATTAGAATTAGCACTA 57.506 33.333 20.75 0.00 0.00 2.74
498 514 7.994911 TGGTGAATCATGATTAGAATTAGCACT 59.005 33.333 20.75 0.00 0.00 4.40
499 515 8.158169 TGGTGAATCATGATTAGAATTAGCAC 57.842 34.615 20.75 18.92 0.00 4.40
500 516 8.929260 ATGGTGAATCATGATTAGAATTAGCA 57.071 30.769 20.75 16.49 0.00 3.49
554 570 1.065491 TCTGATTAGCCGGTGCATGTT 60.065 47.619 1.90 0.00 41.13 2.71
592 608 3.822735 AGCTTGCACAGAAATGCTAAAGA 59.177 39.130 0.00 0.00 46.28 2.52
604 621 4.097437 ACCATTTCATATGAGCTTGCACAG 59.903 41.667 5.39 0.00 0.00 3.66
608 625 6.183360 ACAAGTACCATTTCATATGAGCTTGC 60.183 38.462 5.39 0.00 34.68 4.01
623 640 9.823647 CAGAAGTATGAGAATAACAAGTACCAT 57.176 33.333 0.00 0.00 0.00 3.55
636 653 8.146053 TGTAAGGAAATCCAGAAGTATGAGAA 57.854 34.615 1.67 0.00 38.89 2.87
662 679 8.246180 TGAAATCAATAAAGTGATTCAAGAGCC 58.754 33.333 6.15 0.00 45.42 4.70
682 699 6.038714 AGAGAACAAGAACCACAGTTGAAATC 59.961 38.462 0.00 0.00 35.94 2.17
683 700 5.888161 AGAGAACAAGAACCACAGTTGAAAT 59.112 36.000 0.00 0.00 35.94 2.17
689 706 4.843728 TGAAAGAGAACAAGAACCACAGT 58.156 39.130 0.00 0.00 0.00 3.55
706 723 7.222611 CCACAACCAACTTAATGTTTCTGAAAG 59.777 37.037 2.48 0.00 36.63 2.62
761 779 8.697507 ATGTTCCTTAAATATGATGGAGAACC 57.302 34.615 0.00 0.00 32.17 3.62
781 799 3.746492 ACAACCGACTGAAGCTAATGTTC 59.254 43.478 0.00 0.00 0.00 3.18
794 812 5.357032 ACTCATCAAAAGAAAACAACCGACT 59.643 36.000 0.00 0.00 0.00 4.18
798 816 9.750125 ATAAGAACTCATCAAAAGAAAACAACC 57.250 29.630 0.00 0.00 0.00 3.77
825 843 4.622740 GCAGGCAAAATTTAGCTACACAAG 59.377 41.667 0.00 0.00 0.00 3.16
870 888 3.689161 TCACGCAATTAAATGTCCTCTGG 59.311 43.478 0.00 0.00 0.00 3.86
930 948 2.156891 GCAAAAATCATGTGCACTGCAG 59.843 45.455 19.41 13.48 40.08 4.41
1086 1104 6.387041 TCACCACCGAGAAAGTATATAGTG 57.613 41.667 0.00 0.00 0.00 2.74
1160 1178 1.198637 AGAAAATGACTTGAGCGCTGC 59.801 47.619 18.48 7.36 0.00 5.25
1169 1187 7.182930 AGGTAGGATTAGGACAGAAAATGACTT 59.817 37.037 0.00 0.00 0.00 3.01
1206 1230 4.841246 GTCATAGTAAGGTCCATCCCAGAT 59.159 45.833 0.00 0.00 36.75 2.90
1207 1231 4.223953 GTCATAGTAAGGTCCATCCCAGA 58.776 47.826 0.00 0.00 36.75 3.86
1239 1263 0.542333 TGTGTTCCTTCCCACGAACA 59.458 50.000 0.00 0.00 44.55 3.18
1240 1264 1.892209 ATGTGTTCCTTCCCACGAAC 58.108 50.000 0.00 0.00 39.07 3.95
1244 1268 2.359900 CAGCTATGTGTTCCTTCCCAC 58.640 52.381 0.00 0.00 0.00 4.61
1257 1281 5.117584 ACTTGAGAGAATGAAGCAGCTATG 58.882 41.667 0.00 0.00 0.00 2.23
1263 1287 4.516698 GGTTCAACTTGAGAGAATGAAGCA 59.483 41.667 10.16 0.00 42.80 3.91
1294 1318 1.670967 GGCTTCACTCCTGCAATTTGC 60.671 52.381 14.49 14.49 45.29 3.68
1295 1319 1.067354 GGGCTTCACTCCTGCAATTTG 60.067 52.381 0.00 0.00 0.00 2.32
1296 1320 1.203100 AGGGCTTCACTCCTGCAATTT 60.203 47.619 0.00 0.00 31.11 1.82
1297 1321 0.407139 AGGGCTTCACTCCTGCAATT 59.593 50.000 0.00 0.00 31.11 2.32
1298 1322 1.211457 CTAGGGCTTCACTCCTGCAAT 59.789 52.381 0.00 0.00 34.75 3.56
1299 1323 0.615331 CTAGGGCTTCACTCCTGCAA 59.385 55.000 0.00 0.00 34.75 4.08
1300 1324 0.252239 TCTAGGGCTTCACTCCTGCA 60.252 55.000 0.00 0.00 34.75 4.41
1301 1325 1.127343 ATCTAGGGCTTCACTCCTGC 58.873 55.000 0.00 0.00 34.75 4.85
1302 1326 2.114616 ACATCTAGGGCTTCACTCCTG 58.885 52.381 0.00 0.00 34.75 3.86
1303 1327 2.559381 ACATCTAGGGCTTCACTCCT 57.441 50.000 0.00 0.00 37.18 3.69
1304 1328 2.036604 GCTACATCTAGGGCTTCACTCC 59.963 54.545 0.00 0.00 0.00 3.85
1305 1329 2.695666 TGCTACATCTAGGGCTTCACTC 59.304 50.000 0.00 0.00 0.00 3.51
1306 1330 2.752030 TGCTACATCTAGGGCTTCACT 58.248 47.619 0.00 0.00 0.00 3.41
1307 1331 3.070159 TGATGCTACATCTAGGGCTTCAC 59.930 47.826 8.87 0.00 35.17 3.18
1308 1332 3.308401 TGATGCTACATCTAGGGCTTCA 58.692 45.455 8.87 0.00 36.82 3.02
1309 1333 3.323403 ACTGATGCTACATCTAGGGCTTC 59.677 47.826 8.87 0.00 0.00 3.86
1310 1334 3.312890 ACTGATGCTACATCTAGGGCTT 58.687 45.455 8.87 0.00 0.00 4.35
1311 1335 2.969628 ACTGATGCTACATCTAGGGCT 58.030 47.619 8.87 0.00 0.00 5.19
1312 1336 3.760580 AACTGATGCTACATCTAGGGC 57.239 47.619 8.87 0.00 0.00 5.19
1313 1337 6.821388 ACTTTAACTGATGCTACATCTAGGG 58.179 40.000 8.87 0.69 0.00 3.53
1314 1338 7.225538 CCAACTTTAACTGATGCTACATCTAGG 59.774 40.741 8.87 2.74 0.00 3.02
1315 1339 7.766278 ACCAACTTTAACTGATGCTACATCTAG 59.234 37.037 8.87 7.14 0.00 2.43
1316 1340 7.620880 ACCAACTTTAACTGATGCTACATCTA 58.379 34.615 8.87 0.00 0.00 1.98
1317 1341 6.476378 ACCAACTTTAACTGATGCTACATCT 58.524 36.000 8.87 0.00 0.00 2.90
1318 1342 6.743575 ACCAACTTTAACTGATGCTACATC 57.256 37.500 0.55 0.55 0.00 3.06
1319 1343 6.570378 GCAACCAACTTTAACTGATGCTACAT 60.570 38.462 0.00 0.00 0.00 2.29
1320 1344 5.278266 GCAACCAACTTTAACTGATGCTACA 60.278 40.000 0.00 0.00 0.00 2.74
1321 1345 5.154222 GCAACCAACTTTAACTGATGCTAC 58.846 41.667 0.00 0.00 0.00 3.58
1322 1346 4.217550 GGCAACCAACTTTAACTGATGCTA 59.782 41.667 0.00 0.00 0.00 3.49
1323 1347 3.005791 GGCAACCAACTTTAACTGATGCT 59.994 43.478 0.00 0.00 0.00 3.79
1324 1348 3.005791 AGGCAACCAACTTTAACTGATGC 59.994 43.478 0.00 0.00 37.17 3.91
1325 1349 4.613622 CGAGGCAACCAACTTTAACTGATG 60.614 45.833 0.00 0.00 37.17 3.07
1326 1350 3.502211 CGAGGCAACCAACTTTAACTGAT 59.498 43.478 0.00 0.00 37.17 2.90
1327 1351 2.875933 CGAGGCAACCAACTTTAACTGA 59.124 45.455 0.00 0.00 37.17 3.41
1328 1352 2.031157 CCGAGGCAACCAACTTTAACTG 60.031 50.000 0.00 0.00 37.17 3.16
1329 1353 2.227194 CCGAGGCAACCAACTTTAACT 58.773 47.619 0.00 0.00 37.17 2.24
1330 1354 1.268625 CCCGAGGCAACCAACTTTAAC 59.731 52.381 0.00 0.00 37.17 2.01
1331 1355 1.143277 TCCCGAGGCAACCAACTTTAA 59.857 47.619 0.00 0.00 37.17 1.52
1332 1356 0.766131 TCCCGAGGCAACCAACTTTA 59.234 50.000 0.00 0.00 37.17 1.85
1333 1357 0.537371 CTCCCGAGGCAACCAACTTT 60.537 55.000 0.00 0.00 37.17 2.66
1334 1358 1.073199 CTCCCGAGGCAACCAACTT 59.927 57.895 0.00 0.00 37.17 2.66
1335 1359 2.750350 CTCCCGAGGCAACCAACT 59.250 61.111 0.00 0.00 37.17 3.16
1336 1360 3.056328 GCTCCCGAGGCAACCAAC 61.056 66.667 0.00 0.00 37.17 3.77
1337 1361 3.249189 AGCTCCCGAGGCAACCAA 61.249 61.111 0.00 0.00 37.17 3.67
1338 1362 3.706373 GAGCTCCCGAGGCAACCA 61.706 66.667 0.87 0.00 37.17 3.67
1339 1363 4.821589 CGAGCTCCCGAGGCAACC 62.822 72.222 8.47 0.00 37.17 3.77
1340 1364 4.821589 CCGAGCTCCCGAGGCAAC 62.822 72.222 8.47 0.00 0.00 4.17
1343 1367 4.214327 CTTCCGAGCTCCCGAGGC 62.214 72.222 8.47 0.00 0.00 4.70
1344 1368 4.214327 GCTTCCGAGCTCCCGAGG 62.214 72.222 8.47 3.34 45.65 4.63
1356 1380 2.757868 TCTAGAAGTCTCAGCTGCTTCC 59.242 50.000 21.77 9.83 39.36 3.46
1364 1388 7.043458 GCTCGAATGATTTTCTAGAAGTCTCAG 60.043 40.741 16.32 6.83 0.00 3.35
1386 1410 2.339728 AACTTCGACTTCTCTGCTCG 57.660 50.000 0.00 0.00 0.00 5.03
1388 1412 2.289133 GGGAAACTTCGACTTCTCTGCT 60.289 50.000 0.00 0.00 0.00 4.24
1395 1419 2.438392 AGGAACAGGGAAACTTCGACTT 59.562 45.455 0.00 0.00 0.00 3.01
1406 1430 2.502947 CAGTCATCATCAGGAACAGGGA 59.497 50.000 0.00 0.00 0.00 4.20
1476 1500 3.012518 GTTCCCACCAGATGATTGACTG 58.987 50.000 0.00 0.00 0.00 3.51
1488 1512 6.884295 CAGATAATTTAACTCTGTTCCCACCA 59.116 38.462 0.00 0.00 33.34 4.17
1514 1538 5.659440 ACAATGTGGAGTGAACAAAGTTT 57.341 34.783 0.00 0.00 0.00 2.66
1517 1541 4.319477 CGGTACAATGTGGAGTGAACAAAG 60.319 45.833 0.00 0.00 0.00 2.77
1527 1551 1.070914 TCACTTGCGGTACAATGTGGA 59.929 47.619 0.00 0.00 37.72 4.02
1529 1553 3.436704 AGAATCACTTGCGGTACAATGTG 59.563 43.478 0.00 0.00 37.72 3.21
1539 1563 3.935203 ACACTAATCCAGAATCACTTGCG 59.065 43.478 0.00 0.00 0.00 4.85
1549 1573 0.392461 GCCGCCAACACTAATCCAGA 60.392 55.000 0.00 0.00 0.00 3.86
1554 1578 1.812571 CTTGAAGCCGCCAACACTAAT 59.187 47.619 0.00 0.00 0.00 1.73
1558 1582 1.576421 CTCTTGAAGCCGCCAACAC 59.424 57.895 0.00 0.00 0.00 3.32
1561 1585 2.672996 GCCTCTTGAAGCCGCCAA 60.673 61.111 0.00 0.00 0.00 4.52
1565 1589 2.046507 AGCTGCCTCTTGAAGCCG 60.047 61.111 0.00 0.00 37.68 5.52
1567 1591 0.803740 CTTGAGCTGCCTCTTGAAGC 59.196 55.000 0.00 0.00 38.93 3.86
1602 1626 2.124736 TTGCGGCCAGGCACTATC 60.125 61.111 15.19 0.00 43.82 2.08
1604 1628 4.408821 CCTTGCGGCCAGGCACTA 62.409 66.667 15.19 0.36 43.82 2.74
1653 1677 4.503714 TCCCTCATCAATAAGTGGGAAC 57.496 45.455 0.00 0.00 40.39 3.62
1667 1691 1.918262 TGGCTGAAGTTGATCCCTCAT 59.082 47.619 0.00 0.00 0.00 2.90
1668 1692 1.361204 TGGCTGAAGTTGATCCCTCA 58.639 50.000 0.00 0.00 0.00 3.86
1694 1718 4.749099 GTGACAGCTCATAATCACCTGATC 59.251 45.833 0.00 0.00 36.31 2.92
1695 1719 4.701765 GTGACAGCTCATAATCACCTGAT 58.298 43.478 0.00 0.00 36.31 2.90
1721 1745 4.298103 ACATCTGATCTTGGAGCAAACT 57.702 40.909 0.00 0.00 0.00 2.66
1814 1838 5.050499 CCGTGCTGATCAAGAGATAAATCAC 60.050 44.000 0.00 0.00 33.72 3.06
1842 1866 4.593864 GGCTCGGGGCTAAGCTCG 62.594 72.222 0.00 0.00 41.46 5.03
1893 1917 4.396478 TCAGTGCTATCTAGTGTGTCTGAC 59.604 45.833 0.00 0.00 0.00 3.51
1899 1923 5.215903 CCGTTATCAGTGCTATCTAGTGTG 58.784 45.833 0.00 0.00 0.00 3.82
1903 1927 4.079970 TCCCCGTTATCAGTGCTATCTAG 58.920 47.826 0.00 0.00 0.00 2.43
1920 1944 2.357009 CTGATGATTTTTCTGCTCCCCG 59.643 50.000 0.00 0.00 0.00 5.73
1934 1958 1.415289 TCTTGAGATGGCGCTGATGAT 59.585 47.619 7.64 0.00 0.00 2.45
2037 2061 1.538849 CCTTTGTTGCAACCTGGCTTC 60.539 52.381 26.14 0.00 34.04 3.86


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

AutoCloner maintained by Alex Coulton.