Multiple sequence alignment - TraesCS5A01G133300

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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 TraesCS5A01G133300 chr5A 100.000 2626 0 0 1 2626 299774811 299772186 0.000000e+00 4850
1 TraesCS5A01G133300 chr5A 81.752 274 20 14 298 564 208946496 208946746 4.430000e-48 202
2 TraesCS5A01G133300 chr3A 97.974 1876 33 3 754 2626 662139748 662141621 0.000000e+00 3249
3 TraesCS5A01G133300 chr3A 97.203 429 10 1 1 429 662124726 662125152 0.000000e+00 725
4 TraesCS5A01G133300 chr1D 97.818 1879 29 2 754 2626 156777486 156779358 0.000000e+00 3232
5 TraesCS5A01G133300 chr1D 98.582 564 8 0 1 564 156776933 156777496 0.000000e+00 998
6 TraesCS5A01G133300 chr6A 97.141 1889 35 4 754 2626 99978031 99976146 0.000000e+00 3171
7 TraesCS5A01G133300 chr6A 96.491 399 11 2 8 403 100058273 100057875 0.000000e+00 656
8 TraesCS5A01G133300 chr4A 98.778 1227 15 0 754 1980 41896016 41897242 0.000000e+00 2183
9 TraesCS5A01G133300 chr4A 91.300 1069 52 12 1559 2626 725869206 725868178 0.000000e+00 1421
10 TraesCS5A01G133300 chr4A 97.518 564 13 1 1 564 41895464 41896026 0.000000e+00 963
11 TraesCS5A01G133300 chr4A 94.014 568 29 2 1 564 725870434 725869868 0.000000e+00 856
12 TraesCS5A01G133300 chr4A 94.799 423 22 0 754 1176 725869878 725869456 0.000000e+00 660
13 TraesCS5A01G133300 chr4A 95.385 260 12 0 1252 1511 725869454 725869195 5.230000e-112 414
14 TraesCS5A01G133300 chr1A 98.680 1212 15 1 754 1965 452025865 452024655 0.000000e+00 2148
15 TraesCS5A01G133300 chr1A 94.118 1377 57 7 1252 2621 548228465 548227106 0.000000e+00 2073
16 TraesCS5A01G133300 chr1A 97.340 564 14 1 1 564 452026417 452025855 0.000000e+00 957
17 TraesCS5A01G133300 chr1A 95.599 568 20 2 1 564 548229445 548228879 0.000000e+00 905
18 TraesCS5A01G133300 chr1A 95.035 423 21 0 754 1176 548228889 548228467 0.000000e+00 665
19 TraesCS5A01G133300 chr1A 98.974 195 1 1 568 762 105904897 105904704 5.380000e-92 348
20 TraesCS5A01G133300 chr2B 92.520 1377 61 13 1252 2626 493242792 493244128 0.000000e+00 1934
21 TraesCS5A01G133300 chr2B 94.542 568 26 2 1 564 493241812 493242378 0.000000e+00 872
22 TraesCS5A01G133300 chr2B 95.035 423 21 0 754 1176 493242368 493242790 0.000000e+00 665
23 TraesCS5A01G133300 chr2B 99.479 192 1 0 562 753 763841075 763841266 1.500000e-92 350
24 TraesCS5A01G133300 chr2B 100.000 184 0 0 568 751 126951879 126952062 9.000000e-90 340
25 TraesCS5A01G133300 chr4B 91.538 650 40 5 754 1403 570344619 570345253 0.000000e+00 881
26 TraesCS5A01G133300 chr4B 89.796 539 42 6 36 564 570344094 570344629 0.000000e+00 678
27 TraesCS5A01G133300 chr2A 99.482 193 1 0 567 759 775435556 775435364 4.160000e-93 351
28 TraesCS5A01G133300 chr2A 98.974 195 1 1 563 757 377320212 377320019 5.380000e-92 348
29 TraesCS5A01G133300 chr2A 98.000 200 1 3 564 762 218143043 218142846 6.960000e-91 344
30 TraesCS5A01G133300 chr1B 99.482 193 1 0 563 755 520261984 520262176 4.160000e-93 351
31 TraesCS5A01G133300 chr6B 98.477 197 3 0 557 753 28503840 28503644 5.380000e-92 348
32 TraesCS5A01G133300 chr7A 92.208 231 12 5 529 756 493009122 493008895 3.260000e-84 322
33 TraesCS5A01G133300 chr3D 87.273 275 32 2 1429 1702 350130046 350130318 7.060000e-81 311
34 TraesCS5A01G133300 chr5B 85.811 296 33 7 1429 1722 468630265 468629977 3.280000e-79 305
35 TraesCS5A01G133300 chr7D 85.714 280 32 5 1429 1702 606446030 606446307 3.310000e-74 289
36 TraesCS5A01G133300 chr3B 82.222 270 18 11 298 560 462622199 462621953 3.430000e-49 206
37 TraesCS5A01G133300 chrUn 87.963 108 11 2 2334 2441 31522499 31522394 2.740000e-25 126
38 TraesCS5A01G133300 chr5D 88.889 90 8 2 2532 2620 419805005 419804917 2.760000e-20 110
39 TraesCS5A01G133300 chr7B 87.356 87 10 1 2535 2620 521177405 521177319 5.980000e-17 99


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 TraesCS5A01G133300 chr5A 299772186 299774811 2625 True 4850.000000 4850 100.000000 1 2626 1 chr5A.!!$R1 2625
1 TraesCS5A01G133300 chr3A 662139748 662141621 1873 False 3249.000000 3249 97.974000 754 2626 1 chr3A.!!$F2 1872
2 TraesCS5A01G133300 chr1D 156776933 156779358 2425 False 2115.000000 3232 98.200000 1 2626 2 chr1D.!!$F1 2625
3 TraesCS5A01G133300 chr6A 99976146 99978031 1885 True 3171.000000 3171 97.141000 754 2626 1 chr6A.!!$R1 1872
4 TraesCS5A01G133300 chr4A 41895464 41897242 1778 False 1573.000000 2183 98.148000 1 1980 2 chr4A.!!$F1 1979
5 TraesCS5A01G133300 chr4A 725868178 725870434 2256 True 837.750000 1421 93.874500 1 2626 4 chr4A.!!$R1 2625
6 TraesCS5A01G133300 chr1A 452024655 452026417 1762 True 1552.500000 2148 98.010000 1 1965 2 chr1A.!!$R2 1964
7 TraesCS5A01G133300 chr1A 548227106 548229445 2339 True 1214.333333 2073 94.917333 1 2621 3 chr1A.!!$R3 2620
8 TraesCS5A01G133300 chr2B 493241812 493244128 2316 False 1157.000000 1934 94.032333 1 2626 3 chr2B.!!$F3 2625
9 TraesCS5A01G133300 chr4B 570344094 570345253 1159 False 779.500000 881 90.667000 36 1403 2 chr4B.!!$F1 1367

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
604 616 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.0 12.44 8.34 40.8 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2561 2657 0.459585 CCACCAGTACCCGACAATCG 60.46 60.0 0.0 0.0 40.07 3.34 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
553 565 6.897706 TGTTGATGATGATTTGTTTCAGGA 57.102 33.333 0.00 0.00 0.00 3.86
554 566 7.470935 TGTTGATGATGATTTGTTTCAGGAT 57.529 32.000 0.00 0.00 0.00 3.24
555 567 8.578448 TGTTGATGATGATTTGTTTCAGGATA 57.422 30.769 0.00 0.00 0.00 2.59
556 568 9.192642 TGTTGATGATGATTTGTTTCAGGATAT 57.807 29.630 0.00 0.00 0.00 1.63
557 569 9.459640 GTTGATGATGATTTGTTTCAGGATATG 57.540 33.333 0.00 0.00 0.00 1.78
558 570 7.654568 TGATGATGATTTGTTTCAGGATATGC 58.345 34.615 0.00 0.00 0.00 3.14
559 571 6.063640 TGATGATTTGTTTCAGGATATGCG 57.936 37.500 0.00 0.00 0.00 4.73
560 572 4.898829 TGATTTGTTTCAGGATATGCGG 57.101 40.909 0.00 0.00 0.00 5.69
561 573 4.269183 TGATTTGTTTCAGGATATGCGGT 58.731 39.130 0.00 0.00 0.00 5.68
562 574 5.432645 TGATTTGTTTCAGGATATGCGGTA 58.567 37.500 0.00 0.00 0.00 4.02
563 575 5.295787 TGATTTGTTTCAGGATATGCGGTAC 59.704 40.000 0.00 0.00 0.00 3.34
564 576 3.188159 TGTTTCAGGATATGCGGTACC 57.812 47.619 0.16 0.16 0.00 3.34
565 577 2.502130 TGTTTCAGGATATGCGGTACCA 59.498 45.455 13.54 0.00 0.00 3.25
566 578 3.135712 TGTTTCAGGATATGCGGTACCAT 59.864 43.478 13.54 0.87 0.00 3.55
567 579 3.401033 TTCAGGATATGCGGTACCATG 57.599 47.619 13.54 0.00 0.00 3.66
568 580 2.604139 TCAGGATATGCGGTACCATGA 58.396 47.619 13.54 0.00 0.00 3.07
569 581 2.969262 TCAGGATATGCGGTACCATGAA 59.031 45.455 13.54 0.00 0.00 2.57
570 582 3.006859 TCAGGATATGCGGTACCATGAAG 59.993 47.826 13.54 0.00 0.00 3.02
571 583 2.303022 AGGATATGCGGTACCATGAAGG 59.697 50.000 13.54 0.00 45.67 3.46
572 584 2.615493 GGATATGCGGTACCATGAAGGG 60.615 54.545 13.54 0.00 43.89 3.95
573 585 0.762418 TATGCGGTACCATGAAGGGG 59.238 55.000 13.54 0.00 43.89 4.79
574 586 0.986019 ATGCGGTACCATGAAGGGGA 60.986 55.000 13.54 0.00 43.89 4.81
575 587 1.146263 GCGGTACCATGAAGGGGAG 59.854 63.158 13.54 0.00 43.89 4.30
576 588 1.146263 CGGTACCATGAAGGGGAGC 59.854 63.158 13.54 0.00 43.89 4.70
577 589 1.532238 GGTACCATGAAGGGGAGCC 59.468 63.158 7.15 0.00 43.89 4.70
578 590 0.988678 GGTACCATGAAGGGGAGCCT 60.989 60.000 7.15 0.00 43.89 4.58
579 591 0.919710 GTACCATGAAGGGGAGCCTT 59.080 55.000 0.00 0.00 43.89 4.35
580 592 0.918983 TACCATGAAGGGGAGCCTTG 59.081 55.000 0.00 0.00 43.89 3.61
581 593 1.076485 CCATGAAGGGGAGCCTTGG 60.076 63.158 0.00 0.00 0.00 3.61
582 594 1.755783 CATGAAGGGGAGCCTTGGC 60.756 63.158 2.97 2.97 0.00 4.52
583 595 3.350031 ATGAAGGGGAGCCTTGGCG 62.350 63.158 5.95 0.00 0.00 5.69
591 603 3.605749 GAGCCTTGGCGCAGTGGTA 62.606 63.158 10.83 0.00 0.00 3.25
592 604 2.671619 GCCTTGGCGCAGTGGTAA 60.672 61.111 10.83 0.00 0.00 2.85
593 605 2.265182 GCCTTGGCGCAGTGGTAAA 61.265 57.895 10.83 0.00 0.00 2.01
594 606 1.875963 CCTTGGCGCAGTGGTAAAG 59.124 57.895 10.83 0.71 0.00 1.85
595 607 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
596 608 1.228124 TTGGCGCAGTGGTAAAGCT 60.228 52.632 10.83 0.00 0.00 3.74
597 609 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
602 614 1.878775 CAGTGGTAAAGCTGCTGCC 59.121 57.895 12.44 7.07 40.80 4.85
603 615 0.607489 CAGTGGTAAAGCTGCTGCCT 60.607 55.000 12.44 2.45 40.80 4.75
604 616 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35
605 617 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
606 618 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
607 619 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
608 620 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
609 621 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
610 622 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
611 623 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
612 624 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
613 625 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
614 626 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
615 627 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
616 628 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
631 643 2.859165 TGAGGTCATGGGTTCAAGTC 57.141 50.000 0.00 0.00 0.00 3.01
632 644 1.351017 TGAGGTCATGGGTTCAAGTCC 59.649 52.381 0.00 0.00 0.00 3.85
633 645 1.630878 GAGGTCATGGGTTCAAGTCCT 59.369 52.381 0.00 0.00 0.00 3.85
634 646 1.352352 AGGTCATGGGTTCAAGTCCTG 59.648 52.381 0.00 0.00 0.00 3.86
635 647 1.614317 GGTCATGGGTTCAAGTCCTGG 60.614 57.143 0.00 0.00 0.00 4.45
636 648 1.351017 GTCATGGGTTCAAGTCCTGGA 59.649 52.381 0.00 0.00 0.00 3.86
637 649 2.061848 TCATGGGTTCAAGTCCTGGAA 58.938 47.619 0.00 0.00 0.00 3.53
638 650 2.445145 TCATGGGTTCAAGTCCTGGAAA 59.555 45.455 0.00 0.00 0.00 3.13
639 651 2.358322 TGGGTTCAAGTCCTGGAAAC 57.642 50.000 0.00 0.00 0.00 2.78
640 652 1.566703 TGGGTTCAAGTCCTGGAAACA 59.433 47.619 0.00 0.00 32.36 2.83
654 666 4.431416 TGGAAACAGCCTCTTACAGAAA 57.569 40.909 0.00 0.00 35.01 2.52
655 667 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
656 668 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
657 669 4.762251 GGAAACAGCCTCTTACAGAAATGT 59.238 41.667 0.00 0.00 0.00 2.71
658 670 5.938125 GGAAACAGCCTCTTACAGAAATGTA 59.062 40.000 0.00 0.00 0.00 2.29
659 671 6.092807 GGAAACAGCCTCTTACAGAAATGTAG 59.907 42.308 0.00 0.00 0.00 2.74
660 672 5.091261 ACAGCCTCTTACAGAAATGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
661 673 4.080863 ACAGCCTCTTACAGAAATGTAGGG 60.081 45.833 0.00 0.66 0.00 3.53
662 674 4.162320 CAGCCTCTTACAGAAATGTAGGGA 59.838 45.833 0.00 0.00 0.00 4.20
663 675 4.783227 AGCCTCTTACAGAAATGTAGGGAA 59.217 41.667 0.00 0.00 0.00 3.97
664 676 5.250774 AGCCTCTTACAGAAATGTAGGGAAA 59.749 40.000 0.00 0.00 0.00 3.13
665 677 5.586643 GCCTCTTACAGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
666 678 6.116126 CCTCTTACAGAAATGTAGGGAAAGG 58.884 44.000 0.00 0.00 0.00 3.11
667 679 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
668 680 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
669 681 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
670 682 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
671 683 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
672 684 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
673 685 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
674 686 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
675 687 0.535797 GTAGGGAAAGGCTGCGTACT 59.464 55.000 0.00 0.00 34.81 2.73
676 688 1.753073 GTAGGGAAAGGCTGCGTACTA 59.247 52.381 0.00 0.00 34.81 1.82
677 689 1.497161 AGGGAAAGGCTGCGTACTAT 58.503 50.000 0.00 0.00 0.00 2.12
678 690 2.674420 AGGGAAAGGCTGCGTACTATA 58.326 47.619 0.00 0.00 0.00 1.31
679 691 2.628657 AGGGAAAGGCTGCGTACTATAG 59.371 50.000 0.00 0.00 0.00 1.31
680 692 2.626743 GGGAAAGGCTGCGTACTATAGA 59.373 50.000 6.78 0.00 0.00 1.98
681 693 3.552478 GGGAAAGGCTGCGTACTATAGAC 60.552 52.174 6.78 0.00 0.00 2.59
682 694 3.552478 GGAAAGGCTGCGTACTATAGACC 60.552 52.174 6.78 0.00 0.00 3.85
683 695 1.618487 AGGCTGCGTACTATAGACCC 58.382 55.000 6.78 0.00 0.00 4.46
684 696 1.133575 AGGCTGCGTACTATAGACCCA 60.134 52.381 6.78 0.00 0.00 4.51
685 697 1.684983 GGCTGCGTACTATAGACCCAA 59.315 52.381 6.78 0.00 0.00 4.12
686 698 2.101917 GGCTGCGTACTATAGACCCAAA 59.898 50.000 6.78 0.00 0.00 3.28
687 699 3.381949 GCTGCGTACTATAGACCCAAAG 58.618 50.000 6.78 0.00 0.00 2.77
688 700 3.181478 GCTGCGTACTATAGACCCAAAGT 60.181 47.826 6.78 0.00 0.00 2.66
689 701 4.360563 CTGCGTACTATAGACCCAAAGTG 58.639 47.826 6.78 0.00 0.00 3.16
690 702 3.131577 TGCGTACTATAGACCCAAAGTGG 59.868 47.826 6.78 0.00 37.25 4.00
691 703 3.131755 GCGTACTATAGACCCAAAGTGGT 59.868 47.826 6.78 0.00 42.79 4.16
696 708 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
697 709 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
698 710 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
699 711 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
700 712 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
701 713 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
702 714 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
703 715 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
704 716 2.606826 GTGGTCGGACCCTTCCCT 60.607 66.667 23.81 0.00 38.99 4.20
705 717 2.606519 TGGTCGGACCCTTCCCTG 60.607 66.667 23.81 0.00 38.99 4.45
706 718 3.400054 GGTCGGACCCTTCCCTGG 61.400 72.222 16.55 0.00 38.99 4.45
707 719 2.284405 GTCGGACCCTTCCCTGGA 60.284 66.667 0.00 0.00 38.99 3.86
708 720 2.284405 TCGGACCCTTCCCTGGAC 60.284 66.667 0.00 0.00 38.99 4.02
709 721 3.400054 CGGACCCTTCCCTGGACC 61.400 72.222 0.00 0.00 38.99 4.46
710 722 3.015753 GGACCCTTCCCTGGACCC 61.016 72.222 0.00 0.00 35.57 4.46
711 723 2.125225 GACCCTTCCCTGGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
712 724 2.204151 ACCCTTCCCTGGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
713 725 3.732849 CCCTTCCCTGGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
714 726 4.101448 CCTTCCCTGGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
715 727 4.785453 CTTCCCTGGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
740 752 3.558674 GAGCTACATGCACCAGGTT 57.441 52.632 0.00 0.00 45.94 3.50
741 753 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
742 754 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
743 755 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
744 756 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
745 757 1.788518 TACATGCACCAGGTTGCCCT 61.789 55.000 10.46 0.00 42.25 5.19
746 758 1.909781 CATGCACCAGGTTGCCCTT 60.910 57.895 10.46 0.00 42.25 3.95
747 759 1.152269 ATGCACCAGGTTGCCCTTT 60.152 52.632 10.46 0.00 42.25 3.11
748 760 0.763986 ATGCACCAGGTTGCCCTTTT 60.764 50.000 10.46 0.00 42.25 2.27
749 761 0.980231 TGCACCAGGTTGCCCTTTTT 60.980 50.000 10.46 0.00 42.25 1.94
1129 1141 5.552870 TCTAAACATGATCTAGAAGCCCC 57.447 43.478 0.00 0.00 0.00 5.80
1702 1781 9.610104 TTGGATTTAGTATAGCTGGATTACCTA 57.390 33.333 0.00 0.00 37.04 3.08
1709 1788 5.968528 ATAGCTGGATTACCTACTTCTCG 57.031 43.478 0.00 0.00 37.04 4.04
1735 1814 7.707035 GGATGACGAACAGAGACTAACATTATT 59.293 37.037 0.00 0.00 0.00 1.40
1737 1816 8.239681 TGACGAACAGAGACTAACATTATTTG 57.760 34.615 0.00 0.00 0.00 2.32
1971 2055 5.234466 ACTGAGCTCCAACAACTTATCTT 57.766 39.130 12.15 0.00 0.00 2.40
2128 2218 6.038271 ACTTGTTGTGACCTATGACAGAAAAC 59.962 38.462 0.00 0.00 0.00 2.43
2271 2367 4.225942 TGTATGAGGGAAAGTCTGCATTCT 59.774 41.667 0.00 0.00 0.00 2.40
2561 2657 3.118992 GGCCTGATGTTTCCTTTGAATCC 60.119 47.826 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
197 203 1.454847 CTCCAGCCGAGCCTAGACT 60.455 63.158 0.00 0.00 0.00 3.24
402 414 6.206829 GGCTCAATAGTTGGTAAGAAACACTT 59.793 38.462 0.00 0.00 42.04 3.16
553 565 1.351017 CCCCTTCATGGTACCGCATAT 59.649 52.381 7.57 0.00 0.00 1.78
554 566 0.762418 CCCCTTCATGGTACCGCATA 59.238 55.000 7.57 0.00 0.00 3.14
555 567 0.986019 TCCCCTTCATGGTACCGCAT 60.986 55.000 7.57 0.00 0.00 4.73
556 568 1.613928 TCCCCTTCATGGTACCGCA 60.614 57.895 7.57 0.00 0.00 5.69
557 569 1.146263 CTCCCCTTCATGGTACCGC 59.854 63.158 7.57 0.00 0.00 5.68
558 570 1.146263 GCTCCCCTTCATGGTACCG 59.854 63.158 7.57 0.00 0.00 4.02
559 571 0.988678 AGGCTCCCCTTCATGGTACC 60.989 60.000 4.43 4.43 38.74 3.34
560 572 2.621486 AGGCTCCCCTTCATGGTAC 58.379 57.895 0.00 0.00 38.74 3.34
573 585 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
574 586 2.690653 TTTACCACTGCGCCAAGGCT 62.691 55.000 4.18 0.00 39.32 4.58
575 587 2.200170 CTTTACCACTGCGCCAAGGC 62.200 60.000 4.18 0.00 37.85 4.35
576 588 1.875963 CTTTACCACTGCGCCAAGG 59.124 57.895 4.18 6.21 0.00 3.61
577 589 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
578 590 1.228124 AGCTTTACCACTGCGCCAA 60.228 52.632 4.18 0.00 0.00 4.52
579 591 1.965930 CAGCTTTACCACTGCGCCA 60.966 57.895 4.18 0.00 0.00 5.69
580 592 2.870372 CAGCTTTACCACTGCGCC 59.130 61.111 4.18 0.00 0.00 6.53
584 596 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.00 41.70 3.66
585 597 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
586 598 0.242017 CAAGGCAGCAGCTTTACCAC 59.758 55.000 0.00 0.00 38.07 4.16
587 599 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
588 600 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
589 601 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
590 602 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
591 603 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
592 604 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
593 605 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
594 606 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
595 607 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
596 608 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
597 609 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
598 610 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
599 611 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
611 623 2.025887 GGACTTGAACCCATGACCTCAT 60.026 50.000 0.00 0.00 36.96 2.90
612 624 1.351017 GGACTTGAACCCATGACCTCA 59.649 52.381 0.00 0.00 32.45 3.86
613 625 1.630878 AGGACTTGAACCCATGACCTC 59.369 52.381 0.00 0.00 37.82 3.85
614 626 1.352352 CAGGACTTGAACCCATGACCT 59.648 52.381 0.00 0.00 40.96 3.85
615 627 1.614317 CCAGGACTTGAACCCATGACC 60.614 57.143 0.00 0.00 34.29 4.02
616 628 1.351017 TCCAGGACTTGAACCCATGAC 59.649 52.381 0.00 0.00 0.00 3.06
617 629 1.741028 TCCAGGACTTGAACCCATGA 58.259 50.000 0.00 0.00 0.00 3.07
618 630 2.558359 GTTTCCAGGACTTGAACCCATG 59.442 50.000 0.00 0.00 0.00 3.66
619 631 2.176798 TGTTTCCAGGACTTGAACCCAT 59.823 45.455 0.00 0.00 0.00 4.00
620 632 1.566703 TGTTTCCAGGACTTGAACCCA 59.433 47.619 0.00 0.00 0.00 4.51
621 633 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
622 634 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
623 635 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
624 636 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
625 637 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
626 638 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
627 639 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
628 640 1.439543 AAGAGGCTGTTTCCAGGACT 58.560 50.000 0.00 0.00 39.22 3.85
629 641 2.038557 TGTAAGAGGCTGTTTCCAGGAC 59.961 50.000 0.90 0.00 39.22 3.85
630 642 2.303022 CTGTAAGAGGCTGTTTCCAGGA 59.697 50.000 0.90 0.00 35.89 3.86
631 643 2.303022 TCTGTAAGAGGCTGTTTCCAGG 59.697 50.000 17.71 5.83 38.67 4.45
632 644 3.685139 TCTGTAAGAGGCTGTTTCCAG 57.315 47.619 0.90 9.48 38.67 3.86
644 656 5.250774 AGCCTTTCCCTACATTTCTGTAAGA 59.749 40.000 0.00 0.00 44.68 2.10
645 657 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
646 658 5.253330 CAGCCTTTCCCTACATTTCTGTAA 58.747 41.667 0.00 0.00 37.41 2.41
647 659 4.843728 CAGCCTTTCCCTACATTTCTGTA 58.156 43.478 0.00 0.00 36.79 2.74
648 660 3.690460 CAGCCTTTCCCTACATTTCTGT 58.310 45.455 0.00 0.00 39.49 3.41
649 661 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
650 662 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
651 663 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
652 664 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
653 665 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
654 666 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
655 667 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
656 668 0.535797 AGTACGCAGCCTTTCCCTAC 59.464 55.000 0.00 0.00 0.00 3.18
657 669 2.148446 TAGTACGCAGCCTTTCCCTA 57.852 50.000 0.00 0.00 0.00 3.53
658 670 1.497161 ATAGTACGCAGCCTTTCCCT 58.503 50.000 0.00 0.00 0.00 4.20
659 671 2.626743 TCTATAGTACGCAGCCTTTCCC 59.373 50.000 0.00 0.00 0.00 3.97
660 672 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
661 673 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
662 674 2.364647 GGGTCTATAGTACGCAGCCTTT 59.635 50.000 0.00 0.00 0.00 3.11
663 675 1.962100 GGGTCTATAGTACGCAGCCTT 59.038 52.381 0.00 0.00 0.00 4.35
664 676 1.133575 TGGGTCTATAGTACGCAGCCT 60.134 52.381 13.98 0.00 35.18 4.58
665 677 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
666 678 3.181478 ACTTTGGGTCTATAGTACGCAGC 60.181 47.826 16.00 2.07 40.36 5.25
667 679 4.360563 CACTTTGGGTCTATAGTACGCAG 58.639 47.826 16.00 11.29 40.36 5.18
668 680 3.131577 CCACTTTGGGTCTATAGTACGCA 59.868 47.826 13.98 13.98 37.94 5.24
669 681 3.131755 ACCACTTTGGGTCTATAGTACGC 59.868 47.826 0.00 6.13 43.37 4.42
670 682 4.996788 ACCACTTTGGGTCTATAGTACG 57.003 45.455 0.00 0.00 43.37 3.67
680 692 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
681 693 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
682 694 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
683 695 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
684 696 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
685 697 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
686 698 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
687 699 2.606826 AGGGAAGGGTCCGACCAC 60.607 66.667 19.43 8.70 46.04 4.16
688 700 2.606519 CAGGGAAGGGTCCGACCA 60.607 66.667 19.43 0.00 46.04 4.02
689 701 3.400054 CCAGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
690 702 2.284405 TCCAGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
691 703 2.284405 GTCCAGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
692 704 3.400054 GGTCCAGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
693 705 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
694 706 2.125225 AGGGTCCAGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
695 707 2.204151 CAGGGTCCAGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
696 708 3.732849 GCAGGGTCCAGGGAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
697 709 4.101448 CGCAGGGTCCAGGGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
698 710 4.785453 GCGCAGGGTCCAGGGAAG 62.785 72.222 0.30 0.00 0.00 3.46
710 722 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
713 725 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
714 726 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
715 727 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
716 728 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
722 734 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
723 735 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
724 736 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
725 737 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
726 738 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
748 760 6.017770 CGAATCCCTTGTACCGCATATAAAAA 60.018 38.462 0.00 0.00 0.00 1.94
749 761 5.467399 CGAATCCCTTGTACCGCATATAAAA 59.533 40.000 0.00 0.00 0.00 1.52
750 762 4.992319 CGAATCCCTTGTACCGCATATAAA 59.008 41.667 0.00 0.00 0.00 1.40
751 763 4.281435 TCGAATCCCTTGTACCGCATATAA 59.719 41.667 0.00 0.00 0.00 0.98
752 764 3.827876 TCGAATCCCTTGTACCGCATATA 59.172 43.478 0.00 0.00 0.00 0.86
1129 1141 1.089920 CCGAGCTTGATCTGGTTTGG 58.910 55.000 1.22 0.00 0.00 3.28
1709 1788 4.436242 TGTTAGTCTCTGTTCGTCATCC 57.564 45.455 0.00 0.00 0.00 3.51
1735 1814 9.120538 GAGGGTATAAGATGCAAGAATAAACAA 57.879 33.333 0.00 0.00 0.00 2.83
1737 1816 8.677148 TGAGGGTATAAGATGCAAGAATAAAC 57.323 34.615 0.00 0.00 0.00 2.01
1971 2055 9.449719 GGTCTGATGGTTAAGAAAGAAAATAGA 57.550 33.333 0.00 0.00 0.00 1.98
2128 2218 5.335191 GGCAAACAGAAGTTCTACAGATTGG 60.335 44.000 4.74 0.00 36.84 3.16
2271 2367 6.324770 TCCAGCTTGACATCTACATTGATCTA 59.675 38.462 0.00 0.00 0.00 1.98
2423 2519 6.710278 CATGTTTGGTCTTTAAATGGGGAAT 58.290 36.000 0.00 0.00 0.00 3.01
2486 2582 9.368416 AGTAATATAACAGAGGCAACAGAGATA 57.632 33.333 0.00 0.00 41.41 1.98
2561 2657 0.459585 CCACCAGTACCCGACAATCG 60.460 60.000 0.00 0.00 40.07 3.34


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

AutoCloner maintained by Alex Coulton.