Multiple sequence alignment - TraesCS4B01G238100

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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 TraesCS4B01G238100 chr4B 100.000 2300 0 0 1 2300 495538238 495540537 0.000000e+00 4248
1 TraesCS4B01G238100 chr1B 96.054 1546 35 15 757 2300 683730388 683731909 0.000000e+00 2494
2 TraesCS4B01G238100 chr7B 95.723 1543 40 15 760 2300 698143912 698142394 0.000000e+00 2460
3 TraesCS4B01G238100 chr6B 95.590 1542 44 17 760 2300 128915867 128914349 0.000000e+00 2449
4 TraesCS4B01G238100 chr3B 95.593 1543 42 15 760 2300 92265607 92264089 0.000000e+00 2449
5 TraesCS4B01G238100 chr3B 95.472 1546 45 14 757 2300 5083386 5084908 0.000000e+00 2444
6 TraesCS4B01G238100 chr3B 93.122 189 12 1 757 945 39820832 39821019 2.250000e-70 276
7 TraesCS4B01G238100 chr5B 95.537 1546 42 16 757 2300 713078466 713079986 0.000000e+00 2447
8 TraesCS4B01G238100 chr2A 95.528 1543 43 15 760 2300 563260392 563258874 0.000000e+00 2444
9 TraesCS4B01G238100 chr2A 95.466 1544 43 16 760 2300 735140543 735139024 0.000000e+00 2438
10 TraesCS4B01G238100 chrUn 95.399 1543 45 17 760 2300 40089612 40088094 0.000000e+00 2433
11 TraesCS4B01G238100 chrUn 95.645 643 26 2 1 641 257943650 257943008 0.000000e+00 1031
12 TraesCS4B01G238100 chrUn 95.334 643 28 2 1 641 233525730 233526372 0.000000e+00 1020
13 TraesCS4B01G238100 chrUn 95.334 643 27 3 1 641 429575731 429575090 0.000000e+00 1018
14 TraesCS4B01G238100 chr2D 95.672 647 25 3 1 645 306152424 306151779 0.000000e+00 1037
15 TraesCS4B01G238100 chr2D 94.868 643 31 2 1 641 637309167 637309809 0.000000e+00 1003
16 TraesCS4B01G238100 chr2D 94.720 644 30 4 1 641 17983910 17983268 0.000000e+00 998
17 TraesCS4B01G238100 chr6A 94.876 644 29 4 1 641 79125773 79126415 0.000000e+00 1003
18 TraesCS4B01G238100 chr6D 94.720 644 30 4 1 641 283186950 283186308 0.000000e+00 998
19 TraesCS4B01G238100 chr4D 94.712 643 31 3 1 641 123688499 123687858 0.000000e+00 996
20 TraesCS4B01G238100 chr7A 93.651 189 12 0 757 945 211228260 211228448 1.350000e-72 283
21 TraesCS4B01G238100 chr3D 93.011 186 11 1 760 945 478073652 478073469 1.050000e-68 270
22 TraesCS4B01G238100 chr5A 86.667 105 14 0 757 861 47443859 47443963 1.440000e-22 117


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 TraesCS4B01G238100 chr4B 495538238 495540537 2299 False 4248 4248 100.000 1 2300 1 chr4B.!!$F1 2299
1 TraesCS4B01G238100 chr1B 683730388 683731909 1521 False 2494 2494 96.054 757 2300 1 chr1B.!!$F1 1543
2 TraesCS4B01G238100 chr7B 698142394 698143912 1518 True 2460 2460 95.723 760 2300 1 chr7B.!!$R1 1540
3 TraesCS4B01G238100 chr6B 128914349 128915867 1518 True 2449 2449 95.590 760 2300 1 chr6B.!!$R1 1540
4 TraesCS4B01G238100 chr3B 92264089 92265607 1518 True 2449 2449 95.593 760 2300 1 chr3B.!!$R1 1540
5 TraesCS4B01G238100 chr3B 5083386 5084908 1522 False 2444 2444 95.472 757 2300 1 chr3B.!!$F1 1543
6 TraesCS4B01G238100 chr5B 713078466 713079986 1520 False 2447 2447 95.537 757 2300 1 chr5B.!!$F1 1543
7 TraesCS4B01G238100 chr2A 563258874 563260392 1518 True 2444 2444 95.528 760 2300 1 chr2A.!!$R1 1540
8 TraesCS4B01G238100 chr2A 735139024 735140543 1519 True 2438 2438 95.466 760 2300 1 chr2A.!!$R2 1540
9 TraesCS4B01G238100 chrUn 40088094 40089612 1518 True 2433 2433 95.399 760 2300 1 chrUn.!!$R1 1540
10 TraesCS4B01G238100 chrUn 257943008 257943650 642 True 1031 1031 95.645 1 641 1 chrUn.!!$R2 640
11 TraesCS4B01G238100 chrUn 233525730 233526372 642 False 1020 1020 95.334 1 641 1 chrUn.!!$F1 640
12 TraesCS4B01G238100 chrUn 429575090 429575731 641 True 1018 1018 95.334 1 641 1 chrUn.!!$R3 640
13 TraesCS4B01G238100 chr2D 306151779 306152424 645 True 1037 1037 95.672 1 645 1 chr2D.!!$R2 644
14 TraesCS4B01G238100 chr2D 637309167 637309809 642 False 1003 1003 94.868 1 641 1 chr2D.!!$F1 640
15 TraesCS4B01G238100 chr2D 17983268 17983910 642 True 998 998 94.720 1 641 1 chr2D.!!$R1 640
16 TraesCS4B01G238100 chr6A 79125773 79126415 642 False 1003 1003 94.876 1 641 1 chr6A.!!$F1 640
17 TraesCS4B01G238100 chr6D 283186308 283186950 642 True 998 998 94.720 1 641 1 chr6D.!!$R1 640
18 TraesCS4B01G238100 chr4D 123687858 123688499 641 True 996 996 94.712 1 641 1 chr4D.!!$R1 640

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
682 685 0.517316 ACTTTCGGTGCGAATTGAGC 59.483 50.0 0.0 0.0 45.28 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2019 2023 0.963856 CAGCAAGCAAGGGATGAGCA 60.964 55.0 0.0 0.0 0.0 4.26 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
46 47 4.777896 TCACTGTGAAGCTAAAGGGTATCT 59.222 41.667 8.27 0.00 0.00 1.98
128 129 8.791327 AACTTTTGTTTCACATTTCCAGAAAT 57.209 26.923 0.00 0.00 40.17 2.17
236 237 3.633065 CCACCTCCCTTTTTCGTAACAAA 59.367 43.478 0.00 0.00 0.00 2.83
263 266 4.422546 AGAAAAACGACCAAAACGACAA 57.577 36.364 0.00 0.00 34.70 3.18
284 287 6.118170 ACAATGAGCAGCATATACAAGACTT 58.882 36.000 0.00 0.00 35.78 3.01
335 338 5.834742 CCCACATGAAGATCAATTATTGGGA 59.165 40.000 12.00 0.00 32.45 4.37
336 339 6.495872 CCCACATGAAGATCAATTATTGGGAT 59.504 38.462 12.00 0.00 32.45 3.85
496 499 4.638421 CGCCCCTTGAAATGTAAATCTACA 59.362 41.667 0.00 0.00 42.22 2.74
516 519 8.522542 TCTACAAAAGTATCCCTTAGACTCTC 57.477 38.462 0.00 0.00 31.48 3.20
645 648 5.528043 TCAAAAAGCAAAGCCTGTTGATA 57.472 34.783 0.00 0.00 0.00 2.15
646 649 5.288804 TCAAAAAGCAAAGCCTGTTGATAC 58.711 37.500 0.00 0.00 0.00 2.24
647 650 5.068987 TCAAAAAGCAAAGCCTGTTGATACT 59.931 36.000 0.00 0.00 0.00 2.12
648 651 5.535753 AAAAGCAAAGCCTGTTGATACTT 57.464 34.783 0.00 0.00 0.00 2.24
649 652 5.535753 AAAGCAAAGCCTGTTGATACTTT 57.464 34.783 0.00 0.00 32.73 2.66
650 653 4.773323 AGCAAAGCCTGTTGATACTTTC 57.227 40.909 0.00 0.00 30.16 2.62
651 654 4.401925 AGCAAAGCCTGTTGATACTTTCT 58.598 39.130 0.00 0.00 30.16 2.52
652 655 4.829492 AGCAAAGCCTGTTGATACTTTCTT 59.171 37.500 0.00 0.00 30.16 2.52
653 656 4.919754 GCAAAGCCTGTTGATACTTTCTTG 59.080 41.667 0.00 0.00 30.16 3.02
654 657 5.507985 GCAAAGCCTGTTGATACTTTCTTGT 60.508 40.000 0.00 0.00 30.16 3.16
655 658 6.507023 CAAAGCCTGTTGATACTTTCTTGTT 58.493 36.000 0.00 0.00 30.16 2.83
656 659 5.695851 AGCCTGTTGATACTTTCTTGTTG 57.304 39.130 0.00 0.00 0.00 3.33
657 660 5.376625 AGCCTGTTGATACTTTCTTGTTGA 58.623 37.500 0.00 0.00 0.00 3.18
658 661 5.239525 AGCCTGTTGATACTTTCTTGTTGAC 59.760 40.000 0.00 0.00 0.00 3.18
659 662 5.562890 GCCTGTTGATACTTTCTTGTTGACC 60.563 44.000 0.00 0.00 0.00 4.02
660 663 5.765182 CCTGTTGATACTTTCTTGTTGACCT 59.235 40.000 0.00 0.00 0.00 3.85
661 664 6.293626 CCTGTTGATACTTTCTTGTTGACCTG 60.294 42.308 0.00 0.00 0.00 4.00
662 665 5.530915 TGTTGATACTTTCTTGTTGACCTGG 59.469 40.000 0.00 0.00 0.00 4.45
663 666 5.560722 TGATACTTTCTTGTTGACCTGGA 57.439 39.130 0.00 0.00 0.00 3.86
664 667 5.305585 TGATACTTTCTTGTTGACCTGGAC 58.694 41.667 0.00 0.00 0.00 4.02
665 668 3.933861 ACTTTCTTGTTGACCTGGACT 57.066 42.857 0.00 0.00 0.00 3.85
666 669 4.236527 ACTTTCTTGTTGACCTGGACTT 57.763 40.909 0.00 0.00 0.00 3.01
667 670 4.600062 ACTTTCTTGTTGACCTGGACTTT 58.400 39.130 0.00 0.00 0.00 2.66
668 671 4.640647 ACTTTCTTGTTGACCTGGACTTTC 59.359 41.667 0.00 0.00 0.00 2.62
669 672 2.833794 TCTTGTTGACCTGGACTTTCG 58.166 47.619 0.00 0.00 0.00 3.46
670 673 1.873591 CTTGTTGACCTGGACTTTCGG 59.126 52.381 0.00 0.00 0.00 4.30
671 674 0.834612 TGTTGACCTGGACTTTCGGT 59.165 50.000 0.00 0.00 0.00 4.69
672 675 1.226746 GTTGACCTGGACTTTCGGTG 58.773 55.000 0.00 0.00 0.00 4.94
673 676 0.534203 TTGACCTGGACTTTCGGTGC 60.534 55.000 0.00 0.00 36.78 5.01
674 677 2.027625 GACCTGGACTTTCGGTGCG 61.028 63.158 0.00 0.00 39.22 5.34
675 678 2.342279 CCTGGACTTTCGGTGCGA 59.658 61.111 0.00 0.00 39.22 5.10
676 679 1.301401 CCTGGACTTTCGGTGCGAA 60.301 57.895 0.00 0.00 44.28 4.70
677 680 0.673644 CCTGGACTTTCGGTGCGAAT 60.674 55.000 0.00 0.00 45.28 3.34
678 681 1.156736 CTGGACTTTCGGTGCGAATT 58.843 50.000 0.00 0.00 45.28 2.17
679 682 0.871722 TGGACTTTCGGTGCGAATTG 59.128 50.000 0.00 0.00 45.28 2.32
680 683 1.153353 GGACTTTCGGTGCGAATTGA 58.847 50.000 0.00 0.00 45.28 2.57
681 684 1.128692 GGACTTTCGGTGCGAATTGAG 59.871 52.381 0.00 0.00 45.28 3.02
682 685 0.517316 ACTTTCGGTGCGAATTGAGC 59.483 50.000 0.00 0.00 45.28 4.26
683 686 0.798776 CTTTCGGTGCGAATTGAGCT 59.201 50.000 0.00 0.00 45.28 4.09
684 687 1.999735 CTTTCGGTGCGAATTGAGCTA 59.000 47.619 0.00 0.00 45.28 3.32
685 688 1.640428 TTCGGTGCGAATTGAGCTAG 58.360 50.000 0.00 0.00 41.05 3.42
686 689 0.815095 TCGGTGCGAATTGAGCTAGA 59.185 50.000 0.00 0.00 31.06 2.43
687 690 1.409064 TCGGTGCGAATTGAGCTAGAT 59.591 47.619 0.00 0.00 31.06 1.98
688 691 2.621526 TCGGTGCGAATTGAGCTAGATA 59.378 45.455 0.00 0.00 31.06 1.98
689 692 2.726760 CGGTGCGAATTGAGCTAGATAC 59.273 50.000 0.00 0.00 35.28 2.24
690 693 2.726760 GGTGCGAATTGAGCTAGATACG 59.273 50.000 0.00 0.00 35.28 3.06
691 694 2.154007 GTGCGAATTGAGCTAGATACGC 59.846 50.000 16.25 16.25 43.98 4.42
692 695 2.394708 GCGAATTGAGCTAGATACGCA 58.605 47.619 17.55 0.00 43.35 5.24
693 696 2.794910 GCGAATTGAGCTAGATACGCAA 59.205 45.455 17.55 3.70 43.35 4.85
694 697 3.245284 GCGAATTGAGCTAGATACGCAAA 59.755 43.478 17.55 0.00 43.35 3.68
695 698 4.260212 GCGAATTGAGCTAGATACGCAAAA 60.260 41.667 17.55 0.00 43.35 2.44
696 699 5.559035 GCGAATTGAGCTAGATACGCAAAAT 60.559 40.000 17.55 0.00 43.35 1.82
697 700 5.842843 CGAATTGAGCTAGATACGCAAAATG 59.157 40.000 0.00 0.00 30.59 2.32
698 701 6.292328 CGAATTGAGCTAGATACGCAAAATGA 60.292 38.462 0.00 0.00 30.59 2.57
699 702 5.718649 TTGAGCTAGATACGCAAAATGAC 57.281 39.130 0.00 0.00 0.00 3.06
700 703 4.119862 TGAGCTAGATACGCAAAATGACC 58.880 43.478 0.00 0.00 0.00 4.02
701 704 3.467803 AGCTAGATACGCAAAATGACCC 58.532 45.455 0.00 0.00 0.00 4.46
702 705 2.221055 GCTAGATACGCAAAATGACCCG 59.779 50.000 0.00 0.00 0.00 5.28
703 706 2.684001 AGATACGCAAAATGACCCGA 57.316 45.000 0.00 0.00 0.00 5.14
704 707 2.980568 AGATACGCAAAATGACCCGAA 58.019 42.857 0.00 0.00 0.00 4.30
705 708 2.936498 AGATACGCAAAATGACCCGAAG 59.064 45.455 0.00 0.00 0.00 3.79
706 709 2.459060 TACGCAAAATGACCCGAAGA 57.541 45.000 0.00 0.00 0.00 2.87
707 710 0.872388 ACGCAAAATGACCCGAAGAC 59.128 50.000 0.00 0.00 0.00 3.01
708 711 1.156736 CGCAAAATGACCCGAAGACT 58.843 50.000 0.00 0.00 0.00 3.24
709 712 1.128692 CGCAAAATGACCCGAAGACTC 59.871 52.381 0.00 0.00 0.00 3.36
710 713 2.427506 GCAAAATGACCCGAAGACTCT 58.572 47.619 0.00 0.00 0.00 3.24
711 714 3.596214 GCAAAATGACCCGAAGACTCTA 58.404 45.455 0.00 0.00 0.00 2.43
712 715 4.192317 GCAAAATGACCCGAAGACTCTAT 58.808 43.478 0.00 0.00 0.00 1.98
713 716 4.636206 GCAAAATGACCCGAAGACTCTATT 59.364 41.667 0.00 0.00 0.00 1.73
714 717 5.815740 GCAAAATGACCCGAAGACTCTATTA 59.184 40.000 0.00 0.00 0.00 0.98
715 718 6.315393 GCAAAATGACCCGAAGACTCTATTAA 59.685 38.462 0.00 0.00 0.00 1.40
716 719 7.676572 GCAAAATGACCCGAAGACTCTATTAAC 60.677 40.741 0.00 0.00 0.00 2.01
717 720 4.627611 TGACCCGAAGACTCTATTAACG 57.372 45.455 0.00 0.00 0.00 3.18
718 721 4.012374 TGACCCGAAGACTCTATTAACGT 58.988 43.478 0.00 0.00 0.00 3.99
719 722 4.142534 TGACCCGAAGACTCTATTAACGTG 60.143 45.833 0.00 0.00 0.00 4.49
720 723 3.760684 ACCCGAAGACTCTATTAACGTGT 59.239 43.478 0.00 0.00 0.00 4.49
721 724 4.103357 CCCGAAGACTCTATTAACGTGTG 58.897 47.826 0.00 0.00 0.00 3.82
722 725 4.103357 CCGAAGACTCTATTAACGTGTGG 58.897 47.826 0.00 0.00 0.00 4.17
723 726 4.142534 CCGAAGACTCTATTAACGTGTGGA 60.143 45.833 0.00 0.00 0.00 4.02
724 727 5.450137 CCGAAGACTCTATTAACGTGTGGAT 60.450 44.000 0.00 0.00 0.00 3.41
725 728 5.681982 CGAAGACTCTATTAACGTGTGGATC 59.318 44.000 0.00 0.00 0.00 3.36
726 729 6.458478 CGAAGACTCTATTAACGTGTGGATCT 60.458 42.308 0.00 0.00 0.00 2.75
727 730 7.254692 CGAAGACTCTATTAACGTGTGGATCTA 60.255 40.741 0.00 0.00 0.00 1.98
728 731 7.499321 AGACTCTATTAACGTGTGGATCTAG 57.501 40.000 0.00 0.00 0.00 2.43
729 732 7.055378 AGACTCTATTAACGTGTGGATCTAGT 58.945 38.462 0.00 0.00 0.00 2.57
730 733 8.209584 AGACTCTATTAACGTGTGGATCTAGTA 58.790 37.037 0.00 0.00 0.00 1.82
731 734 8.380743 ACTCTATTAACGTGTGGATCTAGTAG 57.619 38.462 0.00 0.00 0.00 2.57
732 735 7.992033 ACTCTATTAACGTGTGGATCTAGTAGT 59.008 37.037 0.00 0.00 0.00 2.73
733 736 9.486497 CTCTATTAACGTGTGGATCTAGTAGTA 57.514 37.037 0.00 0.00 0.00 1.82
734 737 9.836864 TCTATTAACGTGTGGATCTAGTAGTAA 57.163 33.333 0.00 0.00 0.00 2.24
735 738 9.875675 CTATTAACGTGTGGATCTAGTAGTAAC 57.124 37.037 0.00 0.00 0.00 2.50
736 739 7.686438 TTAACGTGTGGATCTAGTAGTAACA 57.314 36.000 0.00 0.00 0.00 2.41
737 740 6.579666 AACGTGTGGATCTAGTAGTAACAA 57.420 37.500 0.00 0.00 0.00 2.83
738 741 6.579666 ACGTGTGGATCTAGTAGTAACAAA 57.420 37.500 0.00 0.00 0.00 2.83
739 742 6.385033 ACGTGTGGATCTAGTAGTAACAAAC 58.615 40.000 0.00 0.07 0.00 2.93
740 743 6.208204 ACGTGTGGATCTAGTAGTAACAAACT 59.792 38.462 0.00 0.00 42.62 2.66
741 744 7.088905 CGTGTGGATCTAGTAGTAACAAACTT 58.911 38.462 0.00 0.00 39.80 2.66
742 745 8.239314 CGTGTGGATCTAGTAGTAACAAACTTA 58.761 37.037 0.00 0.00 39.80 2.24
745 748 9.448294 GTGGATCTAGTAGTAACAAACTTATCG 57.552 37.037 0.00 0.00 39.80 2.92
746 749 9.399797 TGGATCTAGTAGTAACAAACTTATCGA 57.600 33.333 0.00 0.00 39.80 3.59
753 756 9.837525 AGTAGTAACAAACTTATCGAACTAGTG 57.162 33.333 0.00 0.00 39.80 2.74
754 757 9.617975 GTAGTAACAAACTTATCGAACTAGTGT 57.382 33.333 0.00 0.00 39.80 3.55
778 781 4.345859 ACTATAGAGTCTCCTGACCTCG 57.654 50.000 6.78 0.00 43.91 4.63
783 786 3.083293 AGAGTCTCCTGACCTCGTTAAC 58.917 50.000 0.00 0.00 43.91 2.01
798 801 5.240844 CCTCGTTAACCAATTGAAGTTTCCT 59.759 40.000 7.12 0.00 0.00 3.36
804 807 9.037737 GTTAACCAATTGAAGTTTCCTAAAACC 57.962 33.333 7.12 0.00 44.87 3.27
808 811 6.407525 CCAATTGAAGTTTCCTAAAACCACCA 60.408 38.462 7.12 0.00 44.87 4.17
809 812 6.994421 ATTGAAGTTTCCTAAAACCACCAT 57.006 33.333 0.00 0.00 44.87 3.55
810 813 6.800072 TTGAAGTTTCCTAAAACCACCATT 57.200 33.333 0.00 0.00 44.87 3.16
823 826 4.771114 ACCACCATTATGAAATCTCCGA 57.229 40.909 0.00 0.00 0.00 4.55
832 835 7.414098 CCATTATGAAATCTCCGACGAAAAGTT 60.414 37.037 0.00 0.00 0.00 2.66
839 842 1.522258 TCCGACGAAAAGTTACGTTGC 59.478 47.619 13.75 0.00 42.74 4.17
847 850 5.629020 ACGAAAAGTTACGTTGCGATTACTA 59.371 36.000 17.49 0.00 39.75 1.82
856 859 4.820716 ACGTTGCGATTACTACTAGATCCT 59.179 41.667 0.00 0.00 0.00 3.24
859 862 7.174599 ACGTTGCGATTACTACTAGATCCTATT 59.825 37.037 0.00 0.00 0.00 1.73
860 863 7.693120 CGTTGCGATTACTACTAGATCCTATTC 59.307 40.741 0.00 0.00 0.00 1.75
861 864 7.304919 TGCGATTACTACTAGATCCTATTCG 57.695 40.000 0.00 0.00 0.00 3.34
863 866 7.278203 TGCGATTACTACTAGATCCTATTCGAG 59.722 40.741 0.00 0.00 0.00 4.04
864 867 7.492020 GCGATTACTACTAGATCCTATTCGAGA 59.508 40.741 0.00 0.00 0.00 4.04
865 868 9.027129 CGATTACTACTAGATCCTATTCGAGAG 57.973 40.741 0.00 0.00 0.00 3.20
868 871 7.786046 ACTACTAGATCCTATTCGAGAGAGA 57.214 40.000 0.00 0.00 43.69 3.10
873 876 6.433847 AGATCCTATTCGAGAGAGAGAGAA 57.566 41.667 0.00 0.00 43.69 2.87
878 881 8.982091 TCCTATTCGAGAGAGAGAGAAAATAA 57.018 34.615 0.00 0.00 43.69 1.40
879 882 9.062524 TCCTATTCGAGAGAGAGAGAAAATAAG 57.937 37.037 0.00 0.00 43.69 1.73
880 883 8.846211 CCTATTCGAGAGAGAGAGAAAATAAGT 58.154 37.037 0.00 0.00 43.69 2.24
881 884 9.878599 CTATTCGAGAGAGAGAGAAAATAAGTC 57.121 37.037 0.00 0.00 43.69 3.01
882 885 6.352682 TCGAGAGAGAGAGAAAATAAGTCG 57.647 41.667 0.00 0.00 34.84 4.18
883 886 5.294799 TCGAGAGAGAGAGAAAATAAGTCGG 59.705 44.000 0.00 0.00 34.84 4.79
884 887 5.065474 CGAGAGAGAGAGAAAATAAGTCGGT 59.935 44.000 0.00 0.00 0.00 4.69
885 888 6.258287 CGAGAGAGAGAGAAAATAAGTCGGTA 59.742 42.308 0.00 0.00 0.00 4.02
886 889 7.201626 CGAGAGAGAGAGAAAATAAGTCGGTAA 60.202 40.741 0.00 0.00 0.00 2.85
887 890 8.528044 AGAGAGAGAGAAAATAAGTCGGTAAT 57.472 34.615 0.00 0.00 0.00 1.89
888 891 9.629878 AGAGAGAGAGAAAATAAGTCGGTAATA 57.370 33.333 0.00 0.00 0.00 0.98
889 892 9.887406 GAGAGAGAGAAAATAAGTCGGTAATAG 57.113 37.037 0.00 0.00 0.00 1.73
890 893 9.411189 AGAGAGAGAAAATAAGTCGGTAATAGT 57.589 33.333 0.00 0.00 0.00 2.12
1068 1071 4.086457 GGTTATGTTTGACAGGGATGGTT 58.914 43.478 0.00 0.00 0.00 3.67
1286 1289 2.098117 CGATGAAGCCAACAGAAATCCC 59.902 50.000 0.00 0.00 0.00 3.85
1471 1474 4.985538 TCTTTCTGGGAACATGCTAAACT 58.014 39.130 0.00 0.00 41.51 2.66
2074 2078 1.679981 TTCCATCCCAGTCCATTCCA 58.320 50.000 0.00 0.00 0.00 3.53
2198 2203 3.767673 TGGAATGGCTCTCTTAGTTACGT 59.232 43.478 0.00 0.00 0.00 3.57
2292 2297 0.846015 CCCCATTCTATGCTGACCCA 59.154 55.000 0.00 0.00 0.00 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.013947 CACAGTGACAAGTCATTTTCTCATTAG 58.986 37.037 6.15 0.00 42.18 1.73
46 47 5.683681 GTTATTTCGTAATCCCCAGGGTAA 58.316 41.667 4.22 0.00 36.47 2.85
128 129 5.862845 TGGTAAACGAACAAATAGGTGGTA 58.137 37.500 0.00 0.00 0.00 3.25
263 266 5.922053 TGAAGTCTTGTATATGCTGCTCAT 58.078 37.500 0.00 0.00 39.17 2.90
297 300 8.133024 TCTTCATGTGGGCAACTTTTATTTAT 57.867 30.769 0.00 0.00 0.00 1.40
298 301 7.531857 TCTTCATGTGGGCAACTTTTATTTA 57.468 32.000 0.00 0.00 0.00 1.40
335 338 5.221966 CCCCATTGGATCAATTTGCCATTAT 60.222 40.000 3.62 0.00 35.39 1.28
336 339 4.102838 CCCCATTGGATCAATTTGCCATTA 59.897 41.667 3.62 0.00 35.39 1.90
414 417 2.943036 TAACGAAATATGGAGGGCCC 57.057 50.000 16.46 16.46 0.00 5.80
496 499 5.721960 TGCTGAGAGTCTAAGGGATACTTTT 59.278 40.000 6.65 0.00 40.64 2.27
516 519 4.100084 TGGGCGTGGATCCTGCTG 62.100 66.667 23.12 8.62 0.00 4.41
556 559 2.016961 GCCACCTGCATACGATGTG 58.983 57.895 0.00 0.00 40.77 3.21
645 648 3.933861 AGTCCAGGTCAACAAGAAAGT 57.066 42.857 0.00 0.00 0.00 2.66
646 649 4.260784 CGAAAGTCCAGGTCAACAAGAAAG 60.261 45.833 0.00 0.00 0.00 2.62
647 650 3.625764 CGAAAGTCCAGGTCAACAAGAAA 59.374 43.478 0.00 0.00 0.00 2.52
648 651 3.202906 CGAAAGTCCAGGTCAACAAGAA 58.797 45.455 0.00 0.00 0.00 2.52
649 652 2.484770 CCGAAAGTCCAGGTCAACAAGA 60.485 50.000 0.00 0.00 0.00 3.02
650 653 1.873591 CCGAAAGTCCAGGTCAACAAG 59.126 52.381 0.00 0.00 0.00 3.16
651 654 1.210967 ACCGAAAGTCCAGGTCAACAA 59.789 47.619 0.00 0.00 31.69 2.83
652 655 0.834612 ACCGAAAGTCCAGGTCAACA 59.165 50.000 0.00 0.00 31.69 3.33
653 656 1.226746 CACCGAAAGTCCAGGTCAAC 58.773 55.000 0.00 0.00 35.85 3.18
654 657 0.534203 GCACCGAAAGTCCAGGTCAA 60.534 55.000 0.00 0.00 35.85 3.18
655 658 1.070786 GCACCGAAAGTCCAGGTCA 59.929 57.895 0.00 0.00 35.85 4.02
656 659 2.027625 CGCACCGAAAGTCCAGGTC 61.028 63.158 0.00 0.00 35.85 3.85
657 660 2.030562 CGCACCGAAAGTCCAGGT 59.969 61.111 0.00 0.00 39.12 4.00
658 661 1.301401 TTCGCACCGAAAGTCCAGG 60.301 57.895 0.00 0.00 43.00 4.45
659 662 4.354155 TTCGCACCGAAAGTCCAG 57.646 55.556 0.00 0.00 43.00 3.86
667 670 0.815095 TCTAGCTCAATTCGCACCGA 59.185 50.000 0.00 0.00 0.00 4.69
668 671 1.858091 ATCTAGCTCAATTCGCACCG 58.142 50.000 0.00 0.00 0.00 4.94
669 672 2.726760 CGTATCTAGCTCAATTCGCACC 59.273 50.000 0.00 0.00 0.00 5.01
670 673 2.154007 GCGTATCTAGCTCAATTCGCAC 59.846 50.000 20.10 0.25 40.16 5.34
671 674 2.223711 TGCGTATCTAGCTCAATTCGCA 60.224 45.455 22.35 22.35 45.27 5.10
672 675 2.394708 TGCGTATCTAGCTCAATTCGC 58.605 47.619 18.93 18.93 40.62 4.70
673 676 5.389642 TTTTGCGTATCTAGCTCAATTCG 57.610 39.130 0.00 0.00 35.28 3.34
674 677 6.848296 GTCATTTTGCGTATCTAGCTCAATTC 59.152 38.462 0.00 0.00 35.28 2.17
675 678 6.238484 GGTCATTTTGCGTATCTAGCTCAATT 60.238 38.462 0.00 0.00 35.28 2.32
676 679 5.237344 GGTCATTTTGCGTATCTAGCTCAAT 59.763 40.000 0.00 0.00 35.28 2.57
677 680 4.570772 GGTCATTTTGCGTATCTAGCTCAA 59.429 41.667 0.00 0.00 35.28 3.02
678 681 4.119862 GGTCATTTTGCGTATCTAGCTCA 58.880 43.478 0.00 0.00 35.28 4.26
679 682 3.495001 GGGTCATTTTGCGTATCTAGCTC 59.505 47.826 0.00 0.00 35.28 4.09
680 683 3.467803 GGGTCATTTTGCGTATCTAGCT 58.532 45.455 0.00 0.00 35.28 3.32
681 684 2.221055 CGGGTCATTTTGCGTATCTAGC 59.779 50.000 0.00 0.00 0.00 3.42
682 685 3.713288 TCGGGTCATTTTGCGTATCTAG 58.287 45.455 0.00 0.00 0.00 2.43
683 686 3.804786 TCGGGTCATTTTGCGTATCTA 57.195 42.857 0.00 0.00 0.00 1.98
684 687 2.684001 TCGGGTCATTTTGCGTATCT 57.316 45.000 0.00 0.00 0.00 1.98
685 688 2.933906 TCTTCGGGTCATTTTGCGTATC 59.066 45.455 0.00 0.00 0.00 2.24
686 689 2.676342 GTCTTCGGGTCATTTTGCGTAT 59.324 45.455 0.00 0.00 0.00 3.06
687 690 2.070783 GTCTTCGGGTCATTTTGCGTA 58.929 47.619 0.00 0.00 0.00 4.42
688 691 0.872388 GTCTTCGGGTCATTTTGCGT 59.128 50.000 0.00 0.00 0.00 5.24
689 692 1.128692 GAGTCTTCGGGTCATTTTGCG 59.871 52.381 0.00 0.00 0.00 4.85
690 693 2.427506 AGAGTCTTCGGGTCATTTTGC 58.572 47.619 0.00 0.00 0.00 3.68
691 694 7.464178 CGTTAATAGAGTCTTCGGGTCATTTTG 60.464 40.741 0.00 0.00 0.00 2.44
692 695 6.534079 CGTTAATAGAGTCTTCGGGTCATTTT 59.466 38.462 0.00 0.00 0.00 1.82
693 696 6.040878 CGTTAATAGAGTCTTCGGGTCATTT 58.959 40.000 0.00 0.00 0.00 2.32
694 697 5.126707 ACGTTAATAGAGTCTTCGGGTCATT 59.873 40.000 0.00 0.00 0.00 2.57
695 698 4.643784 ACGTTAATAGAGTCTTCGGGTCAT 59.356 41.667 0.00 0.00 0.00 3.06
696 699 4.012374 ACGTTAATAGAGTCTTCGGGTCA 58.988 43.478 0.00 0.00 0.00 4.02
697 700 4.142513 ACACGTTAATAGAGTCTTCGGGTC 60.143 45.833 0.00 0.00 0.00 4.46
698 701 3.760684 ACACGTTAATAGAGTCTTCGGGT 59.239 43.478 0.00 0.94 0.00 5.28
699 702 4.103357 CACACGTTAATAGAGTCTTCGGG 58.897 47.826 0.00 0.31 0.00 5.14
700 703 4.103357 CCACACGTTAATAGAGTCTTCGG 58.897 47.826 0.00 0.00 0.00 4.30
701 704 4.978186 TCCACACGTTAATAGAGTCTTCG 58.022 43.478 0.00 0.00 0.00 3.79
702 705 6.797454 AGATCCACACGTTAATAGAGTCTTC 58.203 40.000 0.00 0.00 0.00 2.87
703 706 6.777213 AGATCCACACGTTAATAGAGTCTT 57.223 37.500 0.00 0.00 0.00 3.01
704 707 7.055378 ACTAGATCCACACGTTAATAGAGTCT 58.945 38.462 0.00 0.00 0.00 3.24
705 708 7.261829 ACTAGATCCACACGTTAATAGAGTC 57.738 40.000 0.00 0.00 0.00 3.36
706 709 7.992033 ACTACTAGATCCACACGTTAATAGAGT 59.008 37.037 0.00 0.00 0.00 3.24
707 710 8.380743 ACTACTAGATCCACACGTTAATAGAG 57.619 38.462 0.00 0.00 0.00 2.43
708 711 9.836864 TTACTACTAGATCCACACGTTAATAGA 57.163 33.333 0.00 0.00 0.00 1.98
709 712 9.875675 GTTACTACTAGATCCACACGTTAATAG 57.124 37.037 0.00 0.00 0.00 1.73
710 713 9.394767 TGTTACTACTAGATCCACACGTTAATA 57.605 33.333 0.00 0.00 0.00 0.98
711 714 8.284945 TGTTACTACTAGATCCACACGTTAAT 57.715 34.615 0.00 0.00 0.00 1.40
712 715 7.686438 TGTTACTACTAGATCCACACGTTAA 57.314 36.000 0.00 0.00 0.00 2.01
713 716 7.686438 TTGTTACTACTAGATCCACACGTTA 57.314 36.000 0.00 0.00 0.00 3.18
714 717 6.579666 TTGTTACTACTAGATCCACACGTT 57.420 37.500 0.00 0.00 0.00 3.99
715 718 6.208204 AGTTTGTTACTACTAGATCCACACGT 59.792 38.462 0.00 0.00 34.56 4.49
716 719 6.618811 AGTTTGTTACTACTAGATCCACACG 58.381 40.000 0.00 0.00 34.56 4.49
719 722 9.448294 CGATAAGTTTGTTACTACTAGATCCAC 57.552 37.037 0.00 0.00 35.54 4.02
720 723 9.399797 TCGATAAGTTTGTTACTACTAGATCCA 57.600 33.333 0.00 0.00 35.54 3.41
727 730 9.837525 CACTAGTTCGATAAGTTTGTTACTACT 57.162 33.333 0.00 0.00 35.54 2.57
728 731 9.617975 ACACTAGTTCGATAAGTTTGTTACTAC 57.382 33.333 0.00 0.00 35.54 2.73
733 736 9.538508 AGTTTACACTAGTTCGATAAGTTTGTT 57.461 29.630 0.00 0.00 0.00 2.83
742 745 9.835389 AGACTCTATAGTTTACACTAGTTCGAT 57.165 33.333 0.00 0.00 38.96 3.59
743 746 9.311916 GAGACTCTATAGTTTACACTAGTTCGA 57.688 37.037 0.00 0.00 38.96 3.71
744 747 8.550376 GGAGACTCTATAGTTTACACTAGTTCG 58.450 40.741 1.74 0.00 38.96 3.95
745 748 9.617523 AGGAGACTCTATAGTTTACACTAGTTC 57.382 37.037 1.74 0.00 35.56 3.01
746 749 9.398538 CAGGAGACTCTATAGTTTACACTAGTT 57.601 37.037 1.74 0.00 37.50 2.24
747 750 8.770322 TCAGGAGACTCTATAGTTTACACTAGT 58.230 37.037 1.74 0.00 37.50 2.57
748 751 9.048446 GTCAGGAGACTCTATAGTTTACACTAG 57.952 40.741 1.74 0.00 39.05 2.57
749 752 7.992033 GGTCAGGAGACTCTATAGTTTACACTA 59.008 40.741 1.74 0.00 44.36 2.74
750 753 6.829811 GGTCAGGAGACTCTATAGTTTACACT 59.170 42.308 1.74 0.00 44.36 3.55
751 754 6.829811 AGGTCAGGAGACTCTATAGTTTACAC 59.170 42.308 1.74 0.00 44.36 2.90
752 755 6.971340 AGGTCAGGAGACTCTATAGTTTACA 58.029 40.000 1.74 0.00 44.36 2.41
753 756 6.203338 CGAGGTCAGGAGACTCTATAGTTTAC 59.797 46.154 1.74 0.00 44.36 2.01
754 757 6.126825 ACGAGGTCAGGAGACTCTATAGTTTA 60.127 42.308 1.74 0.00 44.36 2.01
755 758 5.127491 CGAGGTCAGGAGACTCTATAGTTT 58.873 45.833 1.74 0.00 44.36 2.66
756 759 4.164604 ACGAGGTCAGGAGACTCTATAGTT 59.835 45.833 1.74 0.00 44.36 2.24
757 760 3.712733 ACGAGGTCAGGAGACTCTATAGT 59.287 47.826 1.74 0.00 44.36 2.12
758 761 4.345859 ACGAGGTCAGGAGACTCTATAG 57.654 50.000 1.74 0.00 44.36 1.31
778 781 9.037737 GGTTTTAGGAAACTTCAATTGGTTAAC 57.962 33.333 5.42 0.00 43.68 2.01
783 786 5.989168 GGTGGTTTTAGGAAACTTCAATTGG 59.011 40.000 5.42 0.00 43.68 3.16
798 801 7.066525 GTCGGAGATTTCATAATGGTGGTTTTA 59.933 37.037 0.00 0.00 40.67 1.52
804 807 4.368315 TCGTCGGAGATTTCATAATGGTG 58.632 43.478 0.00 0.00 40.67 4.17
808 811 7.611213 AACTTTTCGTCGGAGATTTCATAAT 57.389 32.000 0.00 0.00 40.67 1.28
809 812 7.201376 CGTAACTTTTCGTCGGAGATTTCATAA 60.201 37.037 0.00 0.00 40.67 1.90
810 813 6.252015 CGTAACTTTTCGTCGGAGATTTCATA 59.748 38.462 0.00 0.00 40.67 2.15
823 826 3.865224 AATCGCAACGTAACTTTTCGT 57.135 38.095 0.00 0.00 42.12 3.85
832 835 5.994054 AGGATCTAGTAGTAATCGCAACGTA 59.006 40.000 0.00 0.00 0.00 3.57
839 842 8.929827 TCTCGAATAGGATCTAGTAGTAATCG 57.070 38.462 0.00 0.00 0.00 3.34
847 850 6.724441 TCTCTCTCTCTCGAATAGGATCTAGT 59.276 42.308 0.00 0.00 0.00 2.57
856 859 8.552865 CGACTTATTTTCTCTCTCTCTCGAATA 58.447 37.037 0.00 0.00 0.00 1.75
859 862 5.294799 CCGACTTATTTTCTCTCTCTCTCGA 59.705 44.000 0.00 0.00 0.00 4.04
860 863 5.065474 ACCGACTTATTTTCTCTCTCTCTCG 59.935 44.000 0.00 0.00 0.00 4.04
861 864 6.445357 ACCGACTTATTTTCTCTCTCTCTC 57.555 41.667 0.00 0.00 0.00 3.20
863 866 9.887406 CTATTACCGACTTATTTTCTCTCTCTC 57.113 37.037 0.00 0.00 0.00 3.20
864 867 9.411189 ACTATTACCGACTTATTTTCTCTCTCT 57.589 33.333 0.00 0.00 0.00 3.10
867 870 9.798994 TGAACTATTACCGACTTATTTTCTCTC 57.201 33.333 0.00 0.00 0.00 3.20
901 904 9.570468 ACCAAGAGTAAGTATAGATGAATACGA 57.430 33.333 0.00 0.00 37.41 3.43
919 922 0.036306 CCGGCCAACTTACCAAGAGT 59.964 55.000 2.24 0.00 0.00 3.24
936 939 4.762251 AGAAGAAAGAATGGGAAGAAACCG 59.238 41.667 0.00 0.00 0.00 4.44
1068 1071 8.215050 TCCTTTGAAACCAATAGAAGTTCACTA 58.785 33.333 5.50 0.00 0.00 2.74
1353 1356 4.832823 TCTATATGCTCCGATTGGAACTGA 59.167 41.667 2.51 0.00 45.87 3.41
1440 1443 6.183360 GCATGTTCCCAGAAAGAAGATACTTC 60.183 42.308 0.00 0.00 0.00 3.01
1938 1941 5.506982 GGGCAATAAGCTTGCTTCTTCATAG 60.507 44.000 9.86 0.00 44.36 2.23
1940 1943 3.131755 GGGCAATAAGCTTGCTTCTTCAT 59.868 43.478 9.86 0.00 44.36 2.57
1981 1985 2.623878 TACGTTTTCTTGCTGGGTCA 57.376 45.000 0.00 0.00 0.00 4.02
2019 2023 0.963856 CAGCAAGCAAGGGATGAGCA 60.964 55.000 0.00 0.00 0.00 4.26
2074 2078 4.615513 AGATTCTATTAGCCGCCTATCCT 58.384 43.478 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.