Multiple sequence alignment - TraesCS6A01G129500

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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 TraesCS6A01G129500 chr6A 100.000 2731 0 0 1 2731 101536731 101539461 0.000000e+00 5044.0
1 TraesCS6A01G129500 chr6A 93.943 743 41 3 1990 2731 599935018 599934279 0.000000e+00 1120.0
2 TraesCS6A01G129500 chr6A 93.809 743 39 4 1989 2731 51469525 51468790 0.000000e+00 1110.0
3 TraesCS6A01G129500 chr6A 100.000 28 0 0 1565 1592 383479424 383479451 5.000000e-03 52.8
4 TraesCS6A01G129500 chr6D 90.810 1469 86 22 550 1988 84213165 84214614 0.000000e+00 1919.0
5 TraesCS6A01G129500 chr6D 88.650 511 45 7 1 499 84212649 84213158 6.470000e-171 610.0
6 TraesCS6A01G129500 chr7D 94.110 747 41 2 1985 2731 552301567 552302310 0.000000e+00 1133.0
7 TraesCS6A01G129500 chr7D 93.935 742 43 1 1990 2731 13065430 13064691 0.000000e+00 1120.0
8 TraesCS6A01G129500 chr7D 93.289 745 47 2 1987 2731 604060130 604060871 0.000000e+00 1096.0
9 TraesCS6A01G129500 chr5D 93.935 742 43 1 1990 2731 372104928 372104189 0.000000e+00 1120.0
10 TraesCS6A01G129500 chr5D 93.801 742 44 1 1990 2731 480019014 480019753 0.000000e+00 1114.0
11 TraesCS6A01G129500 chr3A 93.566 746 45 2 1987 2731 686571212 686570469 0.000000e+00 1109.0
12 TraesCS6A01G129500 chr3D 93.531 742 46 1 1990 2731 94245173 94244434 0.000000e+00 1103.0
13 TraesCS6A01G129500 chr6B 89.655 116 11 1 1611 1725 160658995 160659110 2.190000e-31 147.0
14 TraesCS6A01G129500 chr2D 100.000 29 0 0 1578 1606 435936065 435936093 1.000000e-03 54.7
15 TraesCS6A01G129500 chr1D 100.000 29 0 0 1578 1606 456977924 456977896 1.000000e-03 54.7


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 TraesCS6A01G129500 chr6A 101536731 101539461 2730 False 5044.0 5044 100.000 1 2731 1 chr6A.!!$F1 2730
1 TraesCS6A01G129500 chr6A 599934279 599935018 739 True 1120.0 1120 93.943 1990 2731 1 chr6A.!!$R2 741
2 TraesCS6A01G129500 chr6A 51468790 51469525 735 True 1110.0 1110 93.809 1989 2731 1 chr6A.!!$R1 742
3 TraesCS6A01G129500 chr6D 84212649 84214614 1965 False 1264.5 1919 89.730 1 1988 2 chr6D.!!$F1 1987
4 TraesCS6A01G129500 chr7D 552301567 552302310 743 False 1133.0 1133 94.110 1985 2731 1 chr7D.!!$F1 746
5 TraesCS6A01G129500 chr7D 13064691 13065430 739 True 1120.0 1120 93.935 1990 2731 1 chr7D.!!$R1 741
6 TraesCS6A01G129500 chr7D 604060130 604060871 741 False 1096.0 1096 93.289 1987 2731 1 chr7D.!!$F2 744
7 TraesCS6A01G129500 chr5D 372104189 372104928 739 True 1120.0 1120 93.935 1990 2731 1 chr5D.!!$R1 741
8 TraesCS6A01G129500 chr5D 480019014 480019753 739 False 1114.0 1114 93.801 1990 2731 1 chr5D.!!$F1 741
9 TraesCS6A01G129500 chr3A 686570469 686571212 743 True 1109.0 1109 93.566 1987 2731 1 chr3A.!!$R1 744
10 TraesCS6A01G129500 chr3D 94244434 94245173 739 True 1103.0 1103 93.531 1990 2731 1 chr3D.!!$R1 741

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
501 514 0.035439 GGTGCAGCTAGCCCACTAAA 60.035 55.0 25.98 1.03 44.83 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1844 1884 0.031043 TCGTACACACAACTCCCGTG 59.969 55.0 0.0 0.0 40.32 4.94 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
124 129 5.904362 AATCTGAAGCCCAACTTACATTC 57.096 39.130 0.00 0.00 39.29 2.67
126 131 2.420022 CTGAAGCCCAACTTACATTCGG 59.580 50.000 0.00 0.00 39.29 4.30
181 186 6.164876 TCCACCACATTTGCTATGAATTTTG 58.835 36.000 6.42 0.00 0.00 2.44
183 188 6.091169 CCACCACATTTGCTATGAATTTTGAC 59.909 38.462 6.42 0.00 0.00 3.18
243 248 4.543689 TGTCCTAATATTCCGTCACCTCT 58.456 43.478 0.00 0.00 0.00 3.69
260 265 4.935808 CACCTCTAAATAAGTCACACCACC 59.064 45.833 0.00 0.00 0.00 4.61
262 267 4.322499 CCTCTAAATAAGTCACACCACCGT 60.322 45.833 0.00 0.00 0.00 4.83
263 268 4.562082 TCTAAATAAGTCACACCACCGTG 58.438 43.478 0.00 0.00 46.11 4.94
292 297 0.690762 GGCTTACCACCACCTCTTCA 59.309 55.000 0.00 0.00 35.26 3.02
350 355 1.718757 GATGGCCGACAACCTCATGC 61.719 60.000 0.00 0.00 0.00 4.06
355 360 2.444624 CGACAACCTCATGCGTCCG 61.445 63.158 0.00 0.00 0.00 4.79
366 371 3.202706 GCGTCCGAGGAAATGGGC 61.203 66.667 0.00 0.00 0.00 5.36
367 372 2.513897 CGTCCGAGGAAATGGGCC 60.514 66.667 0.00 0.00 0.00 5.80
368 373 2.998949 GTCCGAGGAAATGGGCCT 59.001 61.111 4.53 0.00 38.81 5.19
372 377 1.821332 CGAGGAAATGGGCCTGCTC 60.821 63.158 4.53 3.67 35.44 4.26
392 398 1.867233 CAAGAAGGTGACGTGTTGGAG 59.133 52.381 0.00 0.00 38.98 3.86
416 422 0.325296 ATGACAACCGCCTCCTAGGA 60.325 55.000 11.98 11.98 37.67 2.94
418 424 2.299503 GACAACCGCCTCCTAGGAGC 62.300 65.000 30.56 23.61 37.67 4.70
419 425 2.038975 AACCGCCTCCTAGGAGCA 59.961 61.111 30.56 0.32 37.67 4.26
420 426 2.359967 AACCGCCTCCTAGGAGCAC 61.360 63.158 30.56 22.81 37.67 4.40
427 433 2.672098 CCTCCTAGGAGCACTATGTGT 58.328 52.381 30.56 0.00 37.67 3.72
440 453 4.627058 CACTATGTGTGGCGGTATAATGA 58.373 43.478 0.00 0.00 42.68 2.57
456 469 7.042335 GGTATAATGATATTCCGAACTGGGAG 58.958 42.308 0.00 0.00 37.40 4.30
457 470 6.688073 ATAATGATATTCCGAACTGGGAGT 57.312 37.500 0.00 0.00 37.40 3.85
459 472 5.730296 ATGATATTCCGAACTGGGAGTAG 57.270 43.478 0.00 0.00 37.40 2.57
462 475 1.640917 TTCCGAACTGGGAGTAGCTT 58.359 50.000 0.00 0.00 37.40 3.74
463 476 0.895530 TCCGAACTGGGAGTAGCTTG 59.104 55.000 0.00 0.00 38.76 4.01
465 478 0.895530 CGAACTGGGAGTAGCTTGGA 59.104 55.000 0.00 0.00 0.00 3.53
466 479 1.134965 CGAACTGGGAGTAGCTTGGAG 60.135 57.143 0.00 0.00 0.00 3.86
472 485 2.193993 GGGAGTAGCTTGGAGGGTTAA 58.806 52.381 0.00 0.00 0.00 2.01
477 490 4.652822 AGTAGCTTGGAGGGTTAAGTTTG 58.347 43.478 0.00 0.00 0.00 2.93
488 501 3.443976 GGTTAAGTTTGTTGTGGTGCAG 58.556 45.455 0.00 0.00 0.00 4.41
493 506 0.667993 TTTGTTGTGGTGCAGCTAGC 59.332 50.000 18.08 6.62 45.96 3.42
499 512 1.612146 TGGTGCAGCTAGCCCACTA 60.612 57.895 25.98 20.96 44.83 2.74
501 514 0.035439 GGTGCAGCTAGCCCACTAAA 60.035 55.000 25.98 1.03 44.83 1.85
502 515 1.408822 GGTGCAGCTAGCCCACTAAAT 60.409 52.381 25.98 0.14 44.83 1.40
503 516 2.369394 GTGCAGCTAGCCCACTAAATT 58.631 47.619 22.19 0.00 44.83 1.82
505 518 3.016736 TGCAGCTAGCCCACTAAATTTC 58.983 45.455 12.13 0.00 44.83 2.17
506 519 3.016736 GCAGCTAGCCCACTAAATTTCA 58.983 45.455 12.13 0.00 37.23 2.69
507 520 3.443681 GCAGCTAGCCCACTAAATTTCAA 59.556 43.478 12.13 0.00 37.23 2.69
508 521 4.439289 GCAGCTAGCCCACTAAATTTCAAG 60.439 45.833 12.13 0.00 37.23 3.02
509 522 4.096984 CAGCTAGCCCACTAAATTTCAAGG 59.903 45.833 12.13 0.00 0.00 3.61
510 523 4.017126 GCTAGCCCACTAAATTTCAAGGT 58.983 43.478 2.29 0.00 0.00 3.50
511 524 4.096532 GCTAGCCCACTAAATTTCAAGGTC 59.903 45.833 2.29 0.00 0.00 3.85
512 525 4.388577 AGCCCACTAAATTTCAAGGTCT 57.611 40.909 0.00 0.00 0.00 3.85
513 526 5.514500 AGCCCACTAAATTTCAAGGTCTA 57.486 39.130 0.00 0.00 0.00 2.59
514 527 5.501156 AGCCCACTAAATTTCAAGGTCTAG 58.499 41.667 0.00 0.00 0.00 2.43
515 528 5.250774 AGCCCACTAAATTTCAAGGTCTAGA 59.749 40.000 0.00 0.00 0.00 2.43
516 529 5.354513 GCCCACTAAATTTCAAGGTCTAGAC 59.645 44.000 14.87 14.87 0.00 2.59
533 546 7.541122 GTCTAGACCTGTCATGTATTTTTCC 57.459 40.000 12.13 0.00 0.00 3.13
534 547 7.331791 GTCTAGACCTGTCATGTATTTTTCCT 58.668 38.462 12.13 0.00 0.00 3.36
535 548 7.278868 GTCTAGACCTGTCATGTATTTTTCCTG 59.721 40.741 12.13 0.00 0.00 3.86
536 549 5.256474 AGACCTGTCATGTATTTTTCCTGG 58.744 41.667 0.00 0.00 0.00 4.45
537 550 5.014123 AGACCTGTCATGTATTTTTCCTGGA 59.986 40.000 0.00 0.00 0.00 3.86
538 551 5.831103 ACCTGTCATGTATTTTTCCTGGAT 58.169 37.500 0.00 0.00 0.00 3.41
539 552 6.256053 ACCTGTCATGTATTTTTCCTGGATT 58.744 36.000 0.00 0.00 0.00 3.01
540 553 6.378280 ACCTGTCATGTATTTTTCCTGGATTC 59.622 38.462 0.00 0.00 0.00 2.52
541 554 6.377996 CCTGTCATGTATTTTTCCTGGATTCA 59.622 38.462 0.00 0.00 0.00 2.57
542 555 7.069085 CCTGTCATGTATTTTTCCTGGATTCAT 59.931 37.037 0.00 0.00 0.00 2.57
543 556 8.365060 TGTCATGTATTTTTCCTGGATTCATT 57.635 30.769 0.00 0.00 0.00 2.57
544 557 8.814931 TGTCATGTATTTTTCCTGGATTCATTT 58.185 29.630 0.00 0.00 0.00 2.32
545 558 9.305925 GTCATGTATTTTTCCTGGATTCATTTC 57.694 33.333 0.00 0.00 0.00 2.17
546 559 9.033711 TCATGTATTTTTCCTGGATTCATTTCA 57.966 29.630 0.00 0.00 0.00 2.69
547 560 9.656040 CATGTATTTTTCCTGGATTCATTTCAA 57.344 29.630 0.00 0.00 0.00 2.69
548 561 9.880157 ATGTATTTTTCCTGGATTCATTTCAAG 57.120 29.630 0.00 0.00 0.00 3.02
576 589 6.505044 TTTGGTGATGTCATCAATCTTCAG 57.495 37.500 17.11 0.00 45.32 3.02
579 592 5.104235 TGGTGATGTCATCAATCTTCAGGAT 60.104 40.000 17.11 0.00 41.69 3.24
595 608 1.664321 GGATTTGCCTGCTCAGCCTG 61.664 60.000 0.00 0.00 0.00 4.85
597 610 0.329261 ATTTGCCTGCTCAGCCTGTA 59.671 50.000 0.00 0.00 0.00 2.74
620 633 3.595691 GTGCTATGTGCGCCTCTAT 57.404 52.632 4.18 0.00 45.73 1.98
630 643 3.373748 TGTGCGCCTCTATGTTTGTATTG 59.626 43.478 4.18 0.00 0.00 1.90
673 688 7.027778 ACGATATTTGCAAGGAAAGGAATAC 57.972 36.000 0.00 0.00 0.00 1.89
675 690 7.285401 ACGATATTTGCAAGGAAAGGAATACAT 59.715 33.333 0.00 0.00 0.00 2.29
796 811 8.043113 TCTTCAGCATTGCTCTATTTTCTTCTA 58.957 33.333 8.54 0.00 36.40 2.10
839 854 5.840940 ACTTAACTAAGCAATGACGACAC 57.159 39.130 0.00 0.00 36.79 3.67
856 871 4.384846 ACGACACATGAACTAAACTAAGCG 59.615 41.667 0.00 0.00 0.00 4.68
860 875 2.103537 TGAACTAAACTAAGCGGGGC 57.896 50.000 0.00 0.00 0.00 5.80
892 907 3.074412 GCCACGAATATCCCGATCAATT 58.926 45.455 4.73 0.00 0.00 2.32
897 912 3.372206 CGAATATCCCGATCAATTCTGCC 59.628 47.826 0.00 0.00 0.00 4.85
901 916 0.820891 CCCGATCAATTCTGCCCTGG 60.821 60.000 0.00 0.00 0.00 4.45
925 940 4.501915 CCCTGCCAATGTGCAATATAAAGG 60.502 45.833 0.00 0.00 41.51 3.11
926 941 4.341806 CCTGCCAATGTGCAATATAAAGGA 59.658 41.667 0.00 0.00 41.51 3.36
940 955 9.171877 GCAATATAAAGGAGGATAATGAGAAGG 57.828 37.037 0.00 0.00 0.00 3.46
944 959 4.972751 AGGAGGATAATGAGAAGGAAGC 57.027 45.455 0.00 0.00 0.00 3.86
947 962 4.555262 GAGGATAATGAGAAGGAAGCTCG 58.445 47.826 0.00 0.00 35.15 5.03
951 966 6.098409 AGGATAATGAGAAGGAAGCTCGTTAA 59.902 38.462 0.00 0.00 43.30 2.01
955 970 4.174009 TGAGAAGGAAGCTCGTTAATTCG 58.826 43.478 0.00 0.00 35.15 3.34
965 980 0.098728 CGTTAATTCGGCAGGGCAAG 59.901 55.000 0.00 0.00 0.00 4.01
967 982 0.039035 TTAATTCGGCAGGGCAAGGT 59.961 50.000 0.00 0.00 0.00 3.50
968 983 0.393808 TAATTCGGCAGGGCAAGGTC 60.394 55.000 0.00 0.00 0.00 3.85
969 984 2.424842 AATTCGGCAGGGCAAGGTCA 62.425 55.000 0.00 0.00 0.00 4.02
970 985 2.215451 ATTCGGCAGGGCAAGGTCAT 62.215 55.000 0.00 0.00 0.00 3.06
971 986 1.558167 TTCGGCAGGGCAAGGTCATA 61.558 55.000 0.00 0.00 0.00 2.15
972 987 1.819632 CGGCAGGGCAAGGTCATAC 60.820 63.158 0.00 0.00 0.00 2.39
982 997 3.118408 GGCAAGGTCATACTCATACACCA 60.118 47.826 0.00 0.00 0.00 4.17
1041 1056 2.592993 GCAGGTCAGTGCTACCCCA 61.593 63.158 0.00 0.00 40.54 4.96
1176 1191 0.464554 ACGTACCCTACTACCTCGCC 60.465 60.000 0.00 0.00 0.00 5.54
1179 1194 0.255890 TACCCTACTACCTCGCCGTT 59.744 55.000 0.00 0.00 0.00 4.44
1201 1216 1.379044 CCCCAGGGTTAGCTGCTTG 60.379 63.158 7.79 0.00 0.00 4.01
1207 1222 0.036875 GGGTTAGCTGCTTGACCTGT 59.963 55.000 24.73 0.00 32.73 4.00
1237 1252 4.339872 TGCCTTGATCAGCAAAATGTTT 57.660 36.364 7.14 0.00 35.69 2.83
1238 1253 5.465532 TGCCTTGATCAGCAAAATGTTTA 57.534 34.783 7.14 0.00 35.69 2.01
1239 1254 5.851720 TGCCTTGATCAGCAAAATGTTTAA 58.148 33.333 7.14 0.00 35.69 1.52
1243 1258 7.041848 GCCTTGATCAGCAAAATGTTTAACTTT 60.042 33.333 2.23 0.00 35.74 2.66
1259 1277 9.095065 TGTTTAACTTTCCTTTAGATCTATCGC 57.905 33.333 2.58 0.00 0.00 4.58
1263 1281 7.296628 ACTTTCCTTTAGATCTATCGCTGAT 57.703 36.000 2.58 0.00 0.00 2.90
1266 1284 8.410673 TTTCCTTTAGATCTATCGCTGATACT 57.589 34.615 2.58 0.00 0.00 2.12
1275 1293 8.293867 AGATCTATCGCTGATACTAGTGTTTTC 58.706 37.037 5.39 0.00 0.00 2.29
1278 1296 3.512329 TCGCTGATACTAGTGTTTTCCCA 59.488 43.478 5.39 0.00 0.00 4.37
1282 1300 5.396884 GCTGATACTAGTGTTTTCCCATCCT 60.397 44.000 5.39 0.00 0.00 3.24
1288 1306 3.767711 AGTGTTTTCCCATCCTCCTTTC 58.232 45.455 0.00 0.00 0.00 2.62
1291 1309 3.397618 TGTTTTCCCATCCTCCTTTCTGA 59.602 43.478 0.00 0.00 0.00 3.27
1303 1321 5.367937 TCCTCCTTTCTGATTATCTCAAGGG 59.632 44.000 13.69 7.67 32.37 3.95
1318 1336 0.984995 AAGGGAAGGAGAAGAACCCG 59.015 55.000 0.00 0.00 44.57 5.28
1325 1343 2.973945 AGGAGAAGAACCCGAAATTCG 58.026 47.619 8.62 8.62 40.07 3.34
1338 1356 2.603560 CGAAATTCGTGGAGGAAGTAGC 59.396 50.000 7.29 0.00 34.72 3.58
1344 1362 1.984570 TGGAGGAAGTAGCTGCGCT 60.985 57.895 9.73 8.09 43.41 5.92
1360 1378 1.202698 GCGCTCTATGGGAAGGAACAT 60.203 52.381 0.00 0.00 0.00 2.71
1369 1387 2.224769 TGGGAAGGAACATCACTTGGTC 60.225 50.000 0.00 0.00 41.69 4.02
1381 1399 6.177610 ACATCACTTGGTCGTGGTAATTAAT 58.822 36.000 0.00 0.00 35.63 1.40
1392 1412 7.063308 GGTCGTGGTAATTAATAAACTCGTGAA 59.937 37.037 0.00 0.00 0.00 3.18
1411 1431 2.586258 ACGTTTGATCATCTCCCTCG 57.414 50.000 0.00 0.00 0.00 4.63
1413 1433 2.196749 CGTTTGATCATCTCCCTCGTG 58.803 52.381 0.00 0.00 0.00 4.35
1500 1532 0.391661 TGAGATCCAAGCTTGCGACC 60.392 55.000 21.43 10.75 0.00 4.79
1515 1547 1.140375 GACCGCGGACCTCGTAAAT 59.860 57.895 35.90 4.22 41.72 1.40
1551 1583 1.313091 GCCCAACCCGGTCAATTCTC 61.313 60.000 0.00 0.00 0.00 2.87
1570 1602 2.863137 CTCGCTCAATCTAGCTTGAACC 59.137 50.000 10.08 4.13 40.49 3.62
1573 1605 1.936547 CTCAATCTAGCTTGAACCGCC 59.063 52.381 10.08 0.00 34.86 6.13
1634 1674 2.288825 ACTTGTGATCTGGGTGTACGTG 60.289 50.000 0.00 0.00 0.00 4.49
1644 1684 0.461339 GGTGTACGTGCAGGGGTATG 60.461 60.000 6.58 0.00 0.00 2.39
1728 1768 1.228063 CCAGCACCTCAGCAGTTGT 60.228 57.895 0.00 0.00 36.85 3.32
1748 1788 4.136051 TGTGAACTTGACTCATGCATGAA 58.864 39.130 28.39 12.90 36.18 2.57
1749 1789 4.763279 TGTGAACTTGACTCATGCATGAAT 59.237 37.500 28.39 20.87 36.18 2.57
1750 1790 5.093457 GTGAACTTGACTCATGCATGAATG 58.907 41.667 28.39 20.32 36.18 2.67
1772 1812 5.522456 TGCATGATCAAGCGGAATAAATTC 58.478 37.500 17.34 0.00 36.08 2.17
1780 1820 4.877323 AGCGGAATAAATTCGGAACTTC 57.123 40.909 12.80 0.00 38.83 3.01
1844 1884 7.066163 TCACCATGTTCATGATGATGTAAAGAC 59.934 37.037 13.51 0.00 0.00 3.01
1847 1887 6.407475 TGTTCATGATGATGTAAAGACACG 57.593 37.500 0.00 0.00 38.76 4.49
1881 1921 2.239654 ACGAATGGGAATCTGTCACCAT 59.760 45.455 0.00 0.00 45.18 3.55
1887 1927 3.826157 TGGGAATCTGTCACCATTTCAAC 59.174 43.478 0.00 0.00 0.00 3.18
1913 1953 1.710809 GGGGTTGGGGCATATATGTCT 59.289 52.381 16.58 0.00 31.84 3.41
1951 1991 6.638610 TGAGGATGTTTTTCACATTGTGTTT 58.361 32.000 16.06 0.00 46.96 2.83
1979 2019 5.512298 TGATGATTGATTGTTGTCTCCCAT 58.488 37.500 0.00 0.00 0.00 4.00
1981 2021 4.920999 TGATTGATTGTTGTCTCCCATCA 58.079 39.130 0.00 0.00 0.00 3.07
2057 2097 9.464714 GTACACTCATTCGATACAATATTCACT 57.535 33.333 0.00 0.00 0.00 3.41
2079 2119 4.164843 ACATAGGGCGGTACATCATTTT 57.835 40.909 0.00 0.00 0.00 1.82
2092 2132 8.405531 CGGTACATCATTTTCAAGAATACCATT 58.594 33.333 0.00 0.00 32.89 3.16
2203 2243 4.175787 ACTTCGAGATACTCAACGCTTT 57.824 40.909 0.00 0.00 0.00 3.51
2212 2252 6.166279 AGATACTCAACGCTTTCATCTTCAA 58.834 36.000 0.00 0.00 0.00 2.69
2225 2265 3.118992 TCATCTTCAAGTCACGCATAGCT 60.119 43.478 0.00 0.00 0.00 3.32
2230 2270 0.898320 AAGTCACGCATAGCTGACCT 59.102 50.000 0.00 3.73 37.39 3.85
2231 2271 1.763968 AGTCACGCATAGCTGACCTA 58.236 50.000 0.00 0.00 37.39 3.08
2252 2292 0.687354 GTCATAGTCCCCCGATGCAT 59.313 55.000 0.00 0.00 0.00 3.96
2265 2305 1.603931 CGATGCATGAGACGCTACCAT 60.604 52.381 2.46 0.00 0.00 3.55
2275 2315 3.670625 AGACGCTACCATAAAAGTGCAA 58.329 40.909 0.00 0.00 0.00 4.08
2283 2323 6.538742 GCTACCATAAAAGTGCAATCAGTCTA 59.461 38.462 0.00 0.00 0.00 2.59
2422 2462 1.305381 CCCTTCCTCGTCCCTGACT 60.305 63.158 0.00 0.00 0.00 3.41
2470 2510 2.103771 GGACTCCATGAAGCTAGCATCA 59.896 50.000 23.57 23.57 0.00 3.07
2519 2559 4.130255 GGGACCAGCCACTACTCA 57.870 61.111 0.00 0.00 38.95 3.41
2520 2560 2.609046 GGGACCAGCCACTACTCAT 58.391 57.895 0.00 0.00 38.95 2.90
2521 2561 0.179000 GGGACCAGCCACTACTCATG 59.821 60.000 0.00 0.00 38.95 3.07
2560 2600 1.223487 GCTAATCCGGCCCAACAGA 59.777 57.895 0.00 0.00 0.00 3.41
2575 2615 5.479027 GCCCAACAGACCTTTTCCTTTATTA 59.521 40.000 0.00 0.00 0.00 0.98
2591 2631 6.894654 TCCTTTATTATGAAAATCCACTGGCA 59.105 34.615 0.00 0.00 0.00 4.92
2698 2738 9.431887 CCAAAGATCAAATCATTTCTCAAATGT 57.568 29.630 8.46 0.00 46.46 2.71
2708 2748 4.982241 TTTCTCAAATGTCAGGTCCTCT 57.018 40.909 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 6.403049 TGGACTAGAATTTTCTAACATCGCA 58.597 36.000 0.00 0.25 39.15 5.10
78 79 3.384789 GGCTATCACCACTGATACACTCA 59.615 47.826 0.00 0.00 38.21 3.41
79 80 3.384789 TGGCTATCACCACTGATACACTC 59.615 47.826 0.00 0.00 38.21 3.51
89 93 3.065925 GCTTCAGATTTGGCTATCACCAC 59.934 47.826 3.64 0.00 40.19 4.16
141 146 9.479549 AATGTGGTGGATAGAATAGACAAATTT 57.520 29.630 0.00 0.00 0.00 1.82
147 152 6.058183 AGCAAATGTGGTGGATAGAATAGAC 58.942 40.000 0.00 0.00 33.11 2.59
148 153 6.252599 AGCAAATGTGGTGGATAGAATAGA 57.747 37.500 0.00 0.00 33.11 1.98
151 156 6.604171 TCATAGCAAATGTGGTGGATAGAAT 58.396 36.000 0.00 0.00 36.66 2.40
218 223 6.208994 AGAGGTGACGGAATATTAGGACATAC 59.791 42.308 0.00 0.00 0.00 2.39
243 248 3.068560 GCACGGTGGTGTGACTTATTTA 58.931 45.455 10.60 0.00 46.13 1.40
260 265 0.378257 GTAAGCCATGACCATGCACG 59.622 55.000 4.53 0.00 37.49 5.34
262 267 0.330941 TGGTAAGCCATGACCATGCA 59.669 50.000 4.53 0.00 40.87 3.96
263 268 3.189568 TGGTAAGCCATGACCATGC 57.810 52.632 4.53 1.33 40.87 4.06
350 355 2.513897 GGCCCATTTCCTCGGACG 60.514 66.667 0.00 0.00 0.00 4.79
355 360 0.323725 TTGAGCAGGCCCATTTCCTC 60.324 55.000 0.00 0.00 0.00 3.71
358 363 1.475682 CTTCTTGAGCAGGCCCATTTC 59.524 52.381 0.00 0.00 0.00 2.17
366 371 0.034059 ACGTCACCTTCTTGAGCAGG 59.966 55.000 0.00 0.00 34.50 4.85
367 372 1.143305 CACGTCACCTTCTTGAGCAG 58.857 55.000 0.00 0.00 0.00 4.24
368 373 0.464036 ACACGTCACCTTCTTGAGCA 59.536 50.000 0.00 0.00 0.00 4.26
372 377 1.867233 CTCCAACACGTCACCTTCTTG 59.133 52.381 0.00 0.00 0.00 3.02
392 398 1.017387 GGAGGCGGTTGTCATTGATC 58.983 55.000 0.00 0.00 0.00 2.92
419 425 4.948341 TCATTATACCGCCACACATAGT 57.052 40.909 0.00 0.00 0.00 2.12
420 426 7.224753 GGAATATCATTATACCGCCACACATAG 59.775 40.741 0.00 0.00 0.00 2.23
427 433 5.046878 AGTTCGGAATATCATTATACCGCCA 60.047 40.000 0.00 0.00 40.12 5.69
440 453 3.577919 AGCTACTCCCAGTTCGGAATAT 58.422 45.455 0.00 0.00 36.56 1.28
456 469 4.395625 ACAAACTTAACCCTCCAAGCTAC 58.604 43.478 0.00 0.00 0.00 3.58
457 470 4.717279 ACAAACTTAACCCTCCAAGCTA 57.283 40.909 0.00 0.00 0.00 3.32
459 472 3.383505 ACAACAAACTTAACCCTCCAAGC 59.616 43.478 0.00 0.00 0.00 4.01
462 475 3.292460 CCACAACAAACTTAACCCTCCA 58.708 45.455 0.00 0.00 0.00 3.86
463 476 3.067601 CACCACAACAAACTTAACCCTCC 59.932 47.826 0.00 0.00 0.00 4.30
465 478 2.429250 GCACCACAACAAACTTAACCCT 59.571 45.455 0.00 0.00 0.00 4.34
466 479 2.166664 TGCACCACAACAAACTTAACCC 59.833 45.455 0.00 0.00 0.00 4.11
472 485 1.949525 CTAGCTGCACCACAACAAACT 59.050 47.619 1.02 0.00 0.00 2.66
477 490 2.335712 GGGCTAGCTGCACCACAAC 61.336 63.158 15.72 0.00 45.15 3.32
488 501 4.017126 ACCTTGAAATTTAGTGGGCTAGC 58.983 43.478 6.04 6.04 0.00 3.42
493 506 6.986904 GTCTAGACCTTGAAATTTAGTGGG 57.013 41.667 12.13 0.00 0.00 4.61
509 522 7.278868 CAGGAAAAATACATGACAGGTCTAGAC 59.721 40.741 14.87 14.87 0.00 2.59
510 523 7.331026 CAGGAAAAATACATGACAGGTCTAGA 58.669 38.462 0.00 0.00 0.00 2.43
511 524 6.540189 CCAGGAAAAATACATGACAGGTCTAG 59.460 42.308 0.00 0.00 0.00 2.43
512 525 6.214615 TCCAGGAAAAATACATGACAGGTCTA 59.785 38.462 0.00 0.00 0.00 2.59
513 526 5.014123 TCCAGGAAAAATACATGACAGGTCT 59.986 40.000 0.00 0.00 0.00 3.85
514 527 5.253330 TCCAGGAAAAATACATGACAGGTC 58.747 41.667 0.00 0.00 0.00 3.85
515 528 5.255397 TCCAGGAAAAATACATGACAGGT 57.745 39.130 0.00 0.00 0.00 4.00
516 529 6.377996 TGAATCCAGGAAAAATACATGACAGG 59.622 38.462 0.00 0.00 0.00 4.00
517 530 7.395190 TGAATCCAGGAAAAATACATGACAG 57.605 36.000 0.00 0.00 0.00 3.51
518 531 7.959658 ATGAATCCAGGAAAAATACATGACA 57.040 32.000 0.00 0.00 0.00 3.58
519 532 9.305925 GAAATGAATCCAGGAAAAATACATGAC 57.694 33.333 0.00 0.00 0.00 3.06
520 533 9.033711 TGAAATGAATCCAGGAAAAATACATGA 57.966 29.630 0.00 0.00 0.00 3.07
521 534 9.656040 TTGAAATGAATCCAGGAAAAATACATG 57.344 29.630 0.00 0.00 0.00 3.21
522 535 9.880157 CTTGAAATGAATCCAGGAAAAATACAT 57.120 29.630 0.00 0.00 0.00 2.29
523 536 8.869109 ACTTGAAATGAATCCAGGAAAAATACA 58.131 29.630 0.00 0.00 0.00 2.29
524 537 9.710900 AACTTGAAATGAATCCAGGAAAAATAC 57.289 29.630 0.00 0.00 0.00 1.89
526 539 9.631257 AAAACTTGAAATGAATCCAGGAAAAAT 57.369 25.926 0.00 0.00 0.00 1.82
527 540 9.460019 AAAAACTTGAAATGAATCCAGGAAAAA 57.540 25.926 0.00 0.00 0.00 1.94
551 564 7.287512 TGAAGATTGATGACATCACCAAAAA 57.712 32.000 17.77 2.68 39.39 1.94
554 567 4.945543 CCTGAAGATTGATGACATCACCAA 59.054 41.667 17.77 4.19 39.39 3.67
561 574 4.400251 GGCAAATCCTGAAGATTGATGACA 59.600 41.667 0.00 0.00 44.75 3.58
562 575 4.643784 AGGCAAATCCTGAAGATTGATGAC 59.356 41.667 0.00 0.00 44.75 3.06
589 602 1.069823 CATAGCACCCTCTACAGGCTG 59.930 57.143 14.16 14.16 38.72 4.85
592 605 1.202580 GCACATAGCACCCTCTACAGG 60.203 57.143 0.00 0.00 44.79 4.00
595 608 0.876342 GCGCACATAGCACCCTCTAC 60.876 60.000 0.30 0.00 46.13 2.59
597 610 2.187946 GCGCACATAGCACCCTCT 59.812 61.111 0.30 0.00 46.13 3.69
646 661 5.708948 TCCTTTCCTTGCAAATATCGTTTG 58.291 37.500 0.00 0.00 0.00 2.93
650 665 7.026631 TGTATTCCTTTCCTTGCAAATATCG 57.973 36.000 0.00 0.00 0.00 2.92
662 677 9.651913 TTAAGCAATTTTCATGTATTCCTTTCC 57.348 29.630 0.00 0.00 0.00 3.13
707 722 4.196626 CATGTGTTGCAAGGATGGAATT 57.803 40.909 0.00 0.00 39.21 2.17
796 811 1.243902 CCAACGGCCACAAGTGTATT 58.756 50.000 2.24 0.00 0.00 1.89
839 854 2.354821 GCCCCGCTTAGTTTAGTTCATG 59.645 50.000 0.00 0.00 0.00 3.07
872 887 4.389992 CAGAATTGATCGGGATATTCGTGG 59.610 45.833 0.00 0.00 33.38 4.94
901 916 0.754472 ATATTGCACATTGGCAGGGC 59.246 50.000 0.00 0.00 45.88 5.19
914 929 9.171877 CCTTCTCATTATCCTCCTTTATATTGC 57.828 37.037 0.00 0.00 0.00 3.56
925 940 4.038642 ACGAGCTTCCTTCTCATTATCCTC 59.961 45.833 0.00 0.00 0.00 3.71
926 941 3.964031 ACGAGCTTCCTTCTCATTATCCT 59.036 43.478 0.00 0.00 0.00 3.24
940 955 1.327764 CCTGCCGAATTAACGAGCTTC 59.672 52.381 0.00 0.00 35.09 3.86
944 959 0.742990 TGCCCTGCCGAATTAACGAG 60.743 55.000 0.00 0.00 35.09 4.18
947 962 0.455815 CCTTGCCCTGCCGAATTAAC 59.544 55.000 0.00 0.00 0.00 2.01
951 966 2.044946 GACCTTGCCCTGCCGAAT 60.045 61.111 0.00 0.00 0.00 3.34
955 970 0.464554 GAGTATGACCTTGCCCTGCC 60.465 60.000 0.00 0.00 0.00 4.85
965 980 4.021016 GGGAGATGGTGTATGAGTATGACC 60.021 50.000 0.00 0.00 0.00 4.02
967 982 4.814967 TGGGAGATGGTGTATGAGTATGA 58.185 43.478 0.00 0.00 0.00 2.15
968 983 5.551305 TTGGGAGATGGTGTATGAGTATG 57.449 43.478 0.00 0.00 0.00 2.39
969 984 5.846164 TGATTGGGAGATGGTGTATGAGTAT 59.154 40.000 0.00 0.00 0.00 2.12
970 985 5.215845 TGATTGGGAGATGGTGTATGAGTA 58.784 41.667 0.00 0.00 0.00 2.59
971 986 4.040047 TGATTGGGAGATGGTGTATGAGT 58.960 43.478 0.00 0.00 0.00 3.41
972 987 4.694760 TGATTGGGAGATGGTGTATGAG 57.305 45.455 0.00 0.00 0.00 2.90
982 997 3.748083 CCATTGACGATGATTGGGAGAT 58.252 45.455 4.07 0.00 38.03 2.75
1161 1176 0.255890 TAACGGCGAGGTAGTAGGGT 59.744 55.000 16.62 0.00 0.00 4.34
1176 1191 0.177373 GCTAACCCTGGGGAGTAACG 59.823 60.000 18.88 0.00 38.96 3.18
1179 1194 0.981277 GCAGCTAACCCTGGGGAGTA 60.981 60.000 18.88 5.32 38.96 2.59
1201 1216 0.329596 AGGCAAGGGATTGACAGGTC 59.670 55.000 0.00 0.00 30.64 3.85
1207 1222 2.947243 GCTGATCAAGGCAAGGGATTGA 60.947 50.000 0.00 0.00 37.36 2.57
1233 1248 9.095065 GCGATAGATCTAAAGGAAAGTTAAACA 57.905 33.333 6.52 0.00 39.76 2.83
1234 1249 9.315525 AGCGATAGATCTAAAGGAAAGTTAAAC 57.684 33.333 6.52 0.00 39.76 2.01
1237 1252 8.234136 TCAGCGATAGATCTAAAGGAAAGTTA 57.766 34.615 6.52 0.00 39.76 2.24
1238 1253 7.113658 TCAGCGATAGATCTAAAGGAAAGTT 57.886 36.000 6.52 0.00 39.76 2.66
1239 1254 6.716934 TCAGCGATAGATCTAAAGGAAAGT 57.283 37.500 6.52 0.00 39.76 2.66
1243 1258 8.322828 ACTAGTATCAGCGATAGATCTAAAGGA 58.677 37.037 6.52 1.43 39.76 3.36
1253 1271 5.921408 GGGAAAACACTAGTATCAGCGATAG 59.079 44.000 0.00 0.00 0.00 2.08
1259 1277 6.240549 AGGATGGGAAAACACTAGTATCAG 57.759 41.667 0.00 0.00 0.00 2.90
1263 1281 4.695606 AGGAGGATGGGAAAACACTAGTA 58.304 43.478 0.00 0.00 0.00 1.82
1266 1284 4.601857 AGAAAGGAGGATGGGAAAACACTA 59.398 41.667 0.00 0.00 0.00 2.74
1275 1293 5.309020 TGAGATAATCAGAAAGGAGGATGGG 59.691 44.000 0.00 0.00 32.77 4.00
1278 1296 6.044171 CCCTTGAGATAATCAGAAAGGAGGAT 59.956 42.308 0.86 0.00 39.68 3.24
1282 1300 6.126652 CCTTCCCTTGAGATAATCAGAAAGGA 60.127 42.308 0.86 0.00 39.68 3.36
1288 1306 6.326064 TCTTCTCCTTCCCTTGAGATAATCAG 59.674 42.308 0.00 0.00 39.68 2.90
1291 1309 6.126623 GGTTCTTCTCCTTCCCTTGAGATAAT 60.127 42.308 0.00 0.00 37.46 1.28
1303 1321 3.371285 CGAATTTCGGGTTCTTCTCCTTC 59.629 47.826 10.95 0.00 36.00 3.46
1318 1336 3.619038 CAGCTACTTCCTCCACGAATTTC 59.381 47.826 0.00 0.00 0.00 2.17
1325 1343 4.504132 CGCAGCTACTTCCTCCAC 57.496 61.111 0.00 0.00 0.00 4.02
1338 1356 0.465705 TTCCTTCCCATAGAGCGCAG 59.534 55.000 11.47 0.00 0.00 5.18
1344 1362 4.080356 CCAAGTGATGTTCCTTCCCATAGA 60.080 45.833 0.00 0.00 0.00 1.98
1360 1378 7.879160 AGTTTATTAATTACCACGACCAAGTGA 59.121 33.333 0.00 0.00 44.43 3.41
1369 1387 6.890870 CGTTCACGAGTTTATTAATTACCACG 59.109 38.462 0.00 5.04 43.02 4.94
1381 1399 5.924254 AGATGATCAAACGTTCACGAGTTTA 59.076 36.000 6.30 0.00 43.02 2.01
1392 1412 1.825474 ACGAGGGAGATGATCAAACGT 59.175 47.619 0.00 1.76 0.00 3.99
1411 1431 4.158025 ACATCTAGTGTGGCTACTGTACAC 59.842 45.833 0.64 3.89 43.71 2.90
1413 1433 4.985538 ACATCTAGTGTGGCTACTGTAC 57.014 45.455 0.64 0.00 40.28 2.90
1500 1532 2.856346 CGCATTTACGAGGTCCGCG 61.856 63.158 13.96 13.96 43.32 6.46
1515 1547 0.750182 GGCAGGCCTTAATTACCGCA 60.750 55.000 0.00 0.00 0.00 5.69
1570 1602 7.958567 TGAAACTAAATATAAGACGTTTTGGCG 59.041 33.333 0.83 0.00 37.94 5.69
1606 1646 6.814954 ACACCCAGATCACAAGTAAGATAT 57.185 37.500 0.00 0.00 0.00 1.63
1621 1661 2.579657 CCCTGCACGTACACCCAGA 61.580 63.158 0.00 0.00 0.00 3.86
1622 1662 2.047274 CCCTGCACGTACACCCAG 60.047 66.667 0.00 0.00 0.00 4.45
1634 1674 1.883084 CGCGTTCTCATACCCCTGC 60.883 63.158 0.00 0.00 0.00 4.85
1644 1684 2.202676 CAGGCTCCTCGCGTTCTC 60.203 66.667 5.77 0.00 40.44 2.87
1722 1762 3.313249 TGCATGAGTCAAGTTCACAACTG 59.687 43.478 0.00 0.00 41.91 3.16
1728 1768 5.305139 CATTCATGCATGAGTCAAGTTCA 57.695 39.130 27.25 11.53 38.19 3.18
1748 1788 5.717078 ATTTATTCCGCTTGATCATGCAT 57.283 34.783 27.30 17.93 0.00 3.96
1749 1789 5.518848 AATTTATTCCGCTTGATCATGCA 57.481 34.783 27.30 12.95 0.00 3.96
1750 1790 4.614284 CGAATTTATTCCGCTTGATCATGC 59.386 41.667 20.66 20.66 33.28 4.06
1751 1791 5.049474 TCCGAATTTATTCCGCTTGATCATG 60.049 40.000 0.00 0.00 33.28 3.07
1752 1792 5.063204 TCCGAATTTATTCCGCTTGATCAT 58.937 37.500 0.00 0.00 33.28 2.45
1753 1793 4.447290 TCCGAATTTATTCCGCTTGATCA 58.553 39.130 0.00 0.00 33.28 2.92
1754 1794 5.007724 AGTTCCGAATTTATTCCGCTTGATC 59.992 40.000 0.00 0.00 33.28 2.92
1755 1795 4.881850 AGTTCCGAATTTATTCCGCTTGAT 59.118 37.500 0.00 0.00 33.28 2.57
1756 1796 4.258543 AGTTCCGAATTTATTCCGCTTGA 58.741 39.130 0.00 0.00 33.28 3.02
1757 1797 4.616181 AGTTCCGAATTTATTCCGCTTG 57.384 40.909 0.00 0.00 33.28 4.01
1772 1812 2.161609 GGGCACATGTAAAGAAGTTCCG 59.838 50.000 0.00 0.00 0.00 4.30
1780 1820 2.945447 CATGGTGGGCACATGTAAAG 57.055 50.000 0.00 0.00 40.54 1.85
1844 1884 0.031043 TCGTACACACAACTCCCGTG 59.969 55.000 0.00 0.00 40.32 4.94
1847 1887 2.073816 CCATTCGTACACACAACTCCC 58.926 52.381 0.00 0.00 0.00 4.30
1861 1901 2.401583 TGGTGACAGATTCCCATTCG 57.598 50.000 0.00 0.00 35.01 3.34
1881 1921 4.206943 AACCCCGGCCCGTTGAAA 62.207 61.111 0.85 0.00 0.00 2.69
1951 1991 6.095860 GGAGACAACAATCAATCATCAATGGA 59.904 38.462 0.00 0.00 0.00 3.41
2057 2097 4.967084 AAATGATGTACCGCCCTATGTA 57.033 40.909 0.00 0.00 0.00 2.29
2203 2243 3.118992 AGCTATGCGTGACTTGAAGATGA 60.119 43.478 0.00 0.00 0.00 2.92
2212 2252 1.763968 TAGGTCAGCTATGCGTGACT 58.236 50.000 15.75 8.91 42.37 3.41
2230 2270 1.899814 GCATCGGGGGACTATGACATA 59.100 52.381 0.00 0.00 0.00 2.29
2231 2271 0.687354 GCATCGGGGGACTATGACAT 59.313 55.000 0.00 0.00 0.00 3.06
2252 2292 3.259064 GCACTTTTATGGTAGCGTCTCA 58.741 45.455 0.00 0.00 0.00 3.27
2301 2341 7.014422 CCGGTCTCTACATAGGTATTTCTCTTT 59.986 40.741 0.00 0.00 0.00 2.52
2422 2462 3.253838 GCCAGTGTGGGGGTGGTA 61.254 66.667 0.00 0.00 38.19 3.25
2470 2510 5.304101 TGCAGGTTGGTTCAAGATTAATGTT 59.696 36.000 0.00 0.00 0.00 2.71
2500 2540 1.612442 GAGTAGTGGCTGGTCCCCA 60.612 63.158 0.00 0.00 0.00 4.96
2519 2559 4.100189 CGGAGTTCCTAATTCTCTGGACAT 59.900 45.833 0.00 0.00 32.76 3.06
2520 2560 3.447586 CGGAGTTCCTAATTCTCTGGACA 59.552 47.826 0.00 0.00 32.76 4.02
2521 2561 3.738590 GCGGAGTTCCTAATTCTCTGGAC 60.739 52.174 0.00 0.00 35.76 4.02
2552 2592 7.396055 TCATAATAAAGGAAAAGGTCTGTTGGG 59.604 37.037 0.00 0.00 0.00 4.12
2575 2615 2.026641 CCGATGCCAGTGGATTTTCAT 58.973 47.619 15.20 6.10 0.00 2.57
2587 2627 2.038820 TGCATATCATTCTCCGATGCCA 59.961 45.455 2.96 0.00 41.76 4.92
2591 2631 4.356405 TTGGTGCATATCATTCTCCGAT 57.644 40.909 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.