Multiple sequence alignment - TraesCS4A01G251800

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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 TraesCS4A01G251800 chr4A 100.000 1553 0 0 1 1553 563513448 563511896 0.000000e+00 2868.0
1 TraesCS4A01G251800 chr4A 100.000 1125 0 0 1868 2992 563511581 563510457 0.000000e+00 2078.0
2 TraesCS4A01G251800 chr4A 89.712 1147 71 16 1868 2992 594731088 594732209 0.000000e+00 1421.0
3 TraesCS4A01G251800 chr4A 95.802 786 17 8 775 1547 594730293 594731075 0.000000e+00 1254.0
4 TraesCS4A01G251800 chr4A 89.412 1020 68 15 1868 2861 594738265 594739270 0.000000e+00 1249.0
5 TraesCS4A01G251800 chr4A 89.314 1020 70 14 1868 2861 594710816 594709810 0.000000e+00 1243.0
6 TraesCS4A01G251800 chr4A 98.714 622 5 1 1 622 594729682 594730300 0.000000e+00 1101.0
7 TraesCS4A01G251800 chr4A 87.296 795 63 24 790 1553 594711642 594710855 0.000000e+00 874.0
8 TraesCS4A01G251800 chr4A 86.341 798 68 23 790 1553 594737456 594738246 0.000000e+00 832.0
9 TraesCS4A01G251800 chr4A 82.992 782 64 29 790 1545 563228598 563227860 0.000000e+00 643.0
10 TraesCS4A01G251800 chr4A 94.872 117 6 0 1869 1985 563227844 563227728 1.830000e-42 183.0
11 TraesCS4A01G251800 chr4A 92.366 131 5 2 2863 2992 594709515 594709389 6.590000e-42 182.0
12 TraesCS4A01G251800 chr4A 91.791 134 6 2 2860 2992 594739562 594739691 6.590000e-42 182.0
13 TraesCS4A01G251800 chr4A 87.417 151 15 2 35 185 688603366 688603220 1.430000e-38 171.0
14 TraesCS4A01G251800 chr4D 90.862 1149 72 15 1868 2992 8627179 8626040 0.000000e+00 1509.0
15 TraesCS4A01G251800 chr4D 90.285 772 48 10 775 1545 8598701 8597956 0.000000e+00 985.0
16 TraesCS4A01G251800 chr4D 87.072 789 67 19 790 1553 8627970 8627192 0.000000e+00 859.0
17 TraesCS4A01G251800 chr4D 97.521 363 5 1 1 363 8599284 8598926 4.240000e-173 617.0
18 TraesCS4A01G251800 chr4D 95.565 248 9 1 377 622 8598941 8598694 2.160000e-106 396.0
19 TraesCS4A01G251800 chr4D 94.776 134 4 2 1868 1999 8597945 8597813 3.910000e-49 206.0
20 TraesCS4A01G251800 chr4D 89.474 114 11 1 28 141 509754650 509754762 3.110000e-30 143.0
21 TraesCS4A01G251800 chr4D 82.178 101 2 6 2258 2344 8597645 8597547 4.140000e-09 73.1
22 TraesCS4A01G251800 chr4B 93.438 762 42 5 790 1545 15926659 15925900 0.000000e+00 1123.0
23 TraesCS4A01G251800 chr4B 90.598 234 17 2 2760 2992 15925075 15924846 3.750000e-79 305.0
24 TraesCS4A01G251800 chr4B 86.047 301 20 2 2420 2700 15925380 15925082 1.350000e-78 303.0
25 TraesCS4A01G251800 chr2B 100.000 151 0 0 623 773 792984616 792984766 2.270000e-71 279.0
26 TraesCS4A01G251800 chr1A 100.000 151 0 0 623 773 494797640 494797490 2.270000e-71 279.0
27 TraesCS4A01G251800 chr6D 96.689 151 5 0 623 773 433702082 433702232 4.950000e-63 252.0
28 TraesCS4A01G251800 chr6D 87.200 125 14 2 2129 2251 467149861 467149985 1.120000e-29 141.0
29 TraesCS4A01G251800 chr6D 83.721 86 11 2 2706 2788 10715365 10715450 8.890000e-11 78.7
30 TraesCS4A01G251800 chr5B 86.709 158 20 1 616 773 546918799 546918643 1.100000e-39 174.0
31 TraesCS4A01G251800 chr5B 87.302 126 13 2 2129 2251 659822589 659822714 1.120000e-29 141.0
32 TraesCS4A01G251800 chr5A 86.260 131 16 2 2129 2257 530074820 530074690 1.120000e-29 141.0
33 TraesCS4A01G251800 chr6A 86.154 130 15 3 2126 2252 602619441 602619312 1.450000e-28 137.0
34 TraesCS4A01G251800 chr3D 84.783 138 18 3 2117 2251 597753250 597753387 5.200000e-28 135.0
35 TraesCS4A01G251800 chr1B 84.112 107 17 0 2715 2821 34206924 34206818 1.470000e-18 104.0
36 TraesCS4A01G251800 chr6B 80.672 119 21 2 2671 2788 20087231 20087348 1.140000e-14 91.6
37 TraesCS4A01G251800 chr6B 85.526 76 11 0 2706 2781 20032463 20032538 2.470000e-11 80.5
38 TraesCS4A01G251800 chr2A 78.689 122 25 1 2669 2789 727176186 727176065 2.470000e-11 80.5


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 TraesCS4A01G251800 chr4A 563510457 563513448 2991 True 2473.000000 2868 100.000000 1 2992 2 chr4A.!!$R3 2991
1 TraesCS4A01G251800 chr4A 594729682 594732209 2527 False 1258.666667 1421 94.742667 1 2992 3 chr4A.!!$F1 2991
2 TraesCS4A01G251800 chr4A 594709389 594711642 2253 True 766.333333 1243 89.658667 790 2992 3 chr4A.!!$R4 2202
3 TraesCS4A01G251800 chr4A 594737456 594739691 2235 False 754.333333 1249 89.181333 790 2992 3 chr4A.!!$F2 2202
4 TraesCS4A01G251800 chr4A 563227728 563228598 870 True 413.000000 643 88.932000 790 1985 2 chr4A.!!$R2 1195
5 TraesCS4A01G251800 chr4D 8626040 8627970 1930 True 1184.000000 1509 88.967000 790 2992 2 chr4D.!!$R2 2202
6 TraesCS4A01G251800 chr4D 8597547 8599284 1737 True 455.420000 985 92.065000 1 2344 5 chr4D.!!$R1 2343
7 TraesCS4A01G251800 chr4B 15924846 15926659 1813 True 577.000000 1123 90.027667 790 2992 3 chr4B.!!$R1 2202

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
737 740 0.03779 GGAGGATCTATCGGCTGCAC 60.038 60.0 0.5 0.0 33.73 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2292 2485 1.085893 CATCACATGGCACGCTACAA 58.914 50.0 0.0 0.0 0.0 2.41 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
435 436 9.469807 GTTGATCTAACAGTTGTGATATCCTAG 57.530 37.037 0.00 0.00 39.16 3.02
536 537 6.894654 ACTATGATCTTTGGTTCTCTCTCTCA 59.105 38.462 0.00 0.00 0.00 3.27
537 538 6.617782 ATGATCTTTGGTTCTCTCTCTCAA 57.382 37.500 0.00 0.00 0.00 3.02
538 539 6.425210 TGATCTTTGGTTCTCTCTCTCAAA 57.575 37.500 0.00 0.00 0.00 2.69
539 540 6.830912 TGATCTTTGGTTCTCTCTCTCAAAA 58.169 36.000 0.00 0.00 0.00 2.44
613 616 0.169672 GCACTTCATGAACAGCGCAT 59.830 50.000 11.47 0.00 0.00 4.73
614 617 1.401931 GCACTTCATGAACAGCGCATT 60.402 47.619 11.47 2.63 0.00 3.56
615 618 2.159531 GCACTTCATGAACAGCGCATTA 60.160 45.455 11.47 0.00 0.00 1.90
616 619 3.670359 GCACTTCATGAACAGCGCATTAA 60.670 43.478 11.47 0.00 0.00 1.40
617 620 3.848019 CACTTCATGAACAGCGCATTAAC 59.152 43.478 11.47 0.00 0.00 2.01
618 621 3.501828 ACTTCATGAACAGCGCATTAACA 59.498 39.130 11.47 3.26 0.00 2.41
619 622 3.745332 TCATGAACAGCGCATTAACAG 57.255 42.857 11.47 0.00 0.00 3.16
620 623 2.159531 TCATGAACAGCGCATTAACAGC 60.160 45.455 11.47 0.00 0.00 4.40
653 656 6.874704 GCTATACAGCCGACACTTATTAAAC 58.125 40.000 0.00 0.00 42.37 2.01
654 657 5.961395 ATACAGCCGACACTTATTAAACG 57.039 39.130 0.00 0.00 0.00 3.60
655 658 3.916761 ACAGCCGACACTTATTAAACGA 58.083 40.909 0.00 0.00 0.00 3.85
656 659 3.676646 ACAGCCGACACTTATTAAACGAC 59.323 43.478 0.00 0.00 0.00 4.34
657 660 3.676172 CAGCCGACACTTATTAAACGACA 59.324 43.478 0.00 0.00 0.00 4.35
658 661 3.676646 AGCCGACACTTATTAAACGACAC 59.323 43.478 0.00 0.00 0.00 3.67
659 662 3.480825 GCCGACACTTATTAAACGACACG 60.481 47.826 0.00 0.00 0.00 4.49
660 663 3.480825 CCGACACTTATTAAACGACACGC 60.481 47.826 0.00 0.00 0.00 5.34
662 665 2.159934 ACACTTATTAAACGACACGCGC 60.160 45.455 5.73 0.00 46.04 6.86
663 666 2.060284 ACTTATTAAACGACACGCGCA 58.940 42.857 5.73 0.00 46.04 6.09
664 667 2.159934 ACTTATTAAACGACACGCGCAC 60.160 45.455 5.73 0.00 46.04 5.34
665 668 0.362845 TATTAAACGACACGCGCACG 59.637 50.000 5.73 12.50 46.04 5.34
666 669 1.276820 ATTAAACGACACGCGCACGA 61.277 50.000 22.34 4.88 46.04 4.35
667 670 2.132916 TTAAACGACACGCGCACGAC 62.133 55.000 22.34 5.38 46.04 4.34
671 674 3.979961 GACACGCGCACGACGTTT 61.980 61.111 5.73 4.55 42.96 3.60
672 675 4.273951 ACACGCGCACGACGTTTG 62.274 61.111 5.73 0.00 42.96 2.93
676 679 4.383602 GCGCACGACGTTTGCCAT 62.384 61.111 15.24 0.00 46.11 4.40
677 680 2.202171 CGCACGACGTTTGCCATC 60.202 61.111 15.24 0.00 36.57 3.51
678 681 2.667318 CGCACGACGTTTGCCATCT 61.667 57.895 15.24 0.00 36.57 2.90
679 682 1.348538 CGCACGACGTTTGCCATCTA 61.349 55.000 15.24 0.00 36.57 1.98
680 683 0.370273 GCACGACGTTTGCCATCTAG 59.630 55.000 11.10 0.00 33.58 2.43
681 684 0.370273 CACGACGTTTGCCATCTAGC 59.630 55.000 0.00 0.00 0.00 3.42
682 685 0.739813 ACGACGTTTGCCATCTAGCC 60.740 55.000 0.00 0.00 0.00 3.93
683 686 0.739462 CGACGTTTGCCATCTAGCCA 60.739 55.000 0.00 0.00 0.00 4.75
684 687 1.668419 GACGTTTGCCATCTAGCCAT 58.332 50.000 0.00 0.00 0.00 4.40
685 688 1.599542 GACGTTTGCCATCTAGCCATC 59.400 52.381 0.00 0.00 0.00 3.51
686 689 0.583438 CGTTTGCCATCTAGCCATCG 59.417 55.000 0.00 0.00 0.00 3.84
687 690 0.947244 GTTTGCCATCTAGCCATCGG 59.053 55.000 0.00 0.00 0.00 4.18
698 701 4.160635 CCATCGGCGGCGTTGTTC 62.161 66.667 31.86 0.00 0.00 3.18
699 702 4.160635 CATCGGCGGCGTTGTTCC 62.161 66.667 31.06 0.00 0.00 3.62
700 703 4.388499 ATCGGCGGCGTTGTTCCT 62.388 61.111 31.06 5.57 0.00 3.36
701 704 3.009192 ATCGGCGGCGTTGTTCCTA 62.009 57.895 31.06 9.62 0.00 2.94
702 705 2.901051 ATCGGCGGCGTTGTTCCTAG 62.901 60.000 31.06 0.00 0.00 3.02
703 706 2.263540 GGCGGCGTTGTTCCTAGA 59.736 61.111 9.37 0.00 0.00 2.43
704 707 1.810030 GGCGGCGTTGTTCCTAGAG 60.810 63.158 9.37 0.00 0.00 2.43
705 708 1.080025 GCGGCGTTGTTCCTAGAGT 60.080 57.895 9.37 0.00 0.00 3.24
706 709 0.171903 GCGGCGTTGTTCCTAGAGTA 59.828 55.000 9.37 0.00 0.00 2.59
707 710 1.202382 GCGGCGTTGTTCCTAGAGTAT 60.202 52.381 9.37 0.00 0.00 2.12
708 711 2.728922 CGGCGTTGTTCCTAGAGTATC 58.271 52.381 0.00 0.00 0.00 2.24
709 712 2.543238 CGGCGTTGTTCCTAGAGTATCC 60.543 54.545 0.00 0.00 33.66 2.59
710 713 2.694109 GGCGTTGTTCCTAGAGTATCCT 59.306 50.000 0.00 0.00 33.66 3.24
711 714 3.887716 GGCGTTGTTCCTAGAGTATCCTA 59.112 47.826 0.00 0.00 33.66 2.94
712 715 4.261530 GGCGTTGTTCCTAGAGTATCCTAC 60.262 50.000 0.00 0.00 33.66 3.18
713 716 4.554330 GCGTTGTTCCTAGAGTATCCTACG 60.554 50.000 0.00 0.00 33.66 3.51
714 717 4.024218 CGTTGTTCCTAGAGTATCCTACGG 60.024 50.000 0.00 0.00 33.66 4.02
715 718 4.785346 TGTTCCTAGAGTATCCTACGGT 57.215 45.455 0.00 0.00 33.66 4.83
716 719 4.458397 TGTTCCTAGAGTATCCTACGGTG 58.542 47.826 0.00 0.00 33.66 4.94
717 720 3.784511 TCCTAGAGTATCCTACGGTGG 57.215 52.381 0.00 0.00 33.66 4.61
718 721 2.374504 TCCTAGAGTATCCTACGGTGGG 59.625 54.545 3.80 3.80 33.66 4.61
719 722 2.554785 CCTAGAGTATCCTACGGTGGGG 60.555 59.091 10.89 3.29 33.66 4.96
720 723 1.229131 AGAGTATCCTACGGTGGGGA 58.771 55.000 10.89 8.72 33.66 4.81
721 724 1.145325 AGAGTATCCTACGGTGGGGAG 59.855 57.143 10.89 0.00 34.89 4.30
722 725 0.187851 AGTATCCTACGGTGGGGAGG 59.812 60.000 10.89 0.00 34.89 4.30
723 726 0.186873 GTATCCTACGGTGGGGAGGA 59.813 60.000 10.89 5.26 43.46 3.71
724 727 1.947041 ATCCTACGGTGGGGAGGAT 59.053 57.895 10.89 7.48 43.34 3.24
725 728 0.178929 ATCCTACGGTGGGGAGGATC 60.179 60.000 10.89 0.00 45.17 3.36
726 729 1.233369 CCTACGGTGGGGAGGATCT 59.767 63.158 2.00 0.00 33.73 2.75
727 730 0.481567 CCTACGGTGGGGAGGATCTA 59.518 60.000 2.00 0.00 33.73 1.98
728 731 1.077334 CCTACGGTGGGGAGGATCTAT 59.923 57.143 2.00 0.00 33.73 1.98
729 732 2.448453 CTACGGTGGGGAGGATCTATC 58.552 57.143 0.00 0.00 33.73 2.08
730 733 0.539901 ACGGTGGGGAGGATCTATCG 60.540 60.000 0.00 0.00 33.73 2.92
731 734 1.251527 CGGTGGGGAGGATCTATCGG 61.252 65.000 0.00 0.00 33.73 4.18
732 735 1.545706 GGTGGGGAGGATCTATCGGC 61.546 65.000 0.00 0.00 33.73 5.54
733 736 0.543174 GTGGGGAGGATCTATCGGCT 60.543 60.000 0.00 0.00 33.73 5.52
734 737 0.542938 TGGGGAGGATCTATCGGCTG 60.543 60.000 0.00 0.00 33.73 4.85
735 738 1.594310 GGGAGGATCTATCGGCTGC 59.406 63.158 0.00 0.00 33.73 5.25
736 739 1.188219 GGGAGGATCTATCGGCTGCA 61.188 60.000 0.50 0.00 33.73 4.41
737 740 0.037790 GGAGGATCTATCGGCTGCAC 60.038 60.000 0.50 0.00 33.73 4.57
738 741 0.676184 GAGGATCTATCGGCTGCACA 59.324 55.000 0.50 0.00 0.00 4.57
739 742 1.274728 GAGGATCTATCGGCTGCACAT 59.725 52.381 0.50 0.00 0.00 3.21
740 743 1.274728 AGGATCTATCGGCTGCACATC 59.725 52.381 0.50 0.00 0.00 3.06
741 744 1.344458 GATCTATCGGCTGCACATCG 58.656 55.000 0.50 0.00 0.00 3.84
742 745 0.676184 ATCTATCGGCTGCACATCGT 59.324 50.000 0.50 0.00 0.00 3.73
743 746 0.249031 TCTATCGGCTGCACATCGTG 60.249 55.000 0.50 0.00 36.51 4.35
752 755 3.729804 CACATCGTGCACACACCA 58.270 55.556 18.64 0.00 44.40 4.17
753 756 2.246841 CACATCGTGCACACACCAT 58.753 52.632 18.64 0.00 44.40 3.55
754 757 0.166597 CACATCGTGCACACACCATC 59.833 55.000 18.64 0.00 44.40 3.51
755 758 1.291184 ACATCGTGCACACACCATCG 61.291 55.000 18.64 0.00 44.40 3.84
756 759 1.005037 ATCGTGCACACACCATCGT 60.005 52.632 18.64 0.00 44.40 3.73
757 760 1.291184 ATCGTGCACACACCATCGTG 61.291 55.000 18.64 0.00 44.40 4.35
770 773 5.395325 CACCATCGTGTGTAGATCAATTC 57.605 43.478 0.00 0.00 35.10 2.17
771 774 4.271049 CACCATCGTGTGTAGATCAATTCC 59.729 45.833 0.00 0.00 35.10 3.01
772 775 3.490896 CCATCGTGTGTAGATCAATTCCG 59.509 47.826 0.00 0.00 0.00 4.30
773 776 3.861276 TCGTGTGTAGATCAATTCCGT 57.139 42.857 0.00 0.00 0.00 4.69
822 825 3.893521 TCGATTATTGGACCCTTTTCCC 58.106 45.455 0.00 0.00 34.33 3.97
851 854 1.704641 TGACTGTCCAGCTACTGTGT 58.295 50.000 5.17 0.00 32.42 3.72
1213 1240 2.569059 CCAAGATCATGTCGCATCCTT 58.431 47.619 0.00 0.00 0.00 3.36
1409 1452 1.303317 ACGAGCTCCGGCCAAATTT 60.303 52.632 8.47 0.00 43.93 1.82
1416 1459 0.614294 TCCGGCCAAATTTAGACGGA 59.386 50.000 26.87 26.87 46.85 4.69
1417 1460 1.210967 TCCGGCCAAATTTAGACGGAT 59.789 47.619 26.87 0.00 44.53 4.18
1437 1480 4.473520 CAGGAACAGCCGGCGGAT 62.474 66.667 33.66 24.23 43.43 4.18
1540 1639 2.163826 GCGATATGCTTGTGTGTGTG 57.836 50.000 0.00 0.00 41.73 3.82
1545 1644 1.462616 ATGCTTGTGTGTGTGTGTGT 58.537 45.000 0.00 0.00 0.00 3.72
1546 1645 0.520847 TGCTTGTGTGTGTGTGTGTG 59.479 50.000 0.00 0.00 0.00 3.82
1547 1646 0.798009 GCTTGTGTGTGTGTGTGTGC 60.798 55.000 0.00 0.00 0.00 4.57
1549 1648 1.231296 TTGTGTGTGTGTGTGTGCGT 61.231 50.000 0.00 0.00 0.00 5.24
1551 1650 1.669437 TGTGTGTGTGTGTGCGTGT 60.669 52.632 0.00 0.00 0.00 4.49
1552 1651 1.225991 GTGTGTGTGTGTGCGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
2014 2202 5.769484 TTACACCAAGTTATTTTTGCGGA 57.231 34.783 0.00 0.00 0.00 5.54
2081 2269 0.107165 AGCCTTGCGGGTTTCCTATC 60.107 55.000 0.00 0.00 37.94 2.08
2142 2332 8.433421 TTTTGTATGGGAACTTTCGATCTATC 57.567 34.615 0.00 0.00 0.00 2.08
2233 2426 2.390938 CGACGACTACAAGCACTGAAA 58.609 47.619 0.00 0.00 0.00 2.69
2251 2444 2.664851 CAAGCCGAAGACACGCCA 60.665 61.111 0.00 0.00 0.00 5.69
2253 2446 1.302511 AAGCCGAAGACACGCCATT 60.303 52.632 0.00 0.00 0.00 3.16
2290 2483 9.903682 CATCATCTATGAAAGAAAACAAGTGTT 57.096 29.630 0.00 0.00 40.69 3.32
2301 2504 6.427150 AGAAAACAAGTGTTATTGTAGCGTG 58.573 36.000 0.00 0.00 42.49 5.34
2309 2512 2.675844 GTTATTGTAGCGTGCCATGTGA 59.324 45.455 0.00 0.00 0.00 3.58
2329 2536 5.294799 TGTGATGTTTATAATTCCCGAACCG 59.705 40.000 0.00 0.00 0.00 4.44
2330 2537 5.524646 GTGATGTTTATAATTCCCGAACCGA 59.475 40.000 0.00 0.00 0.00 4.69
2467 2678 3.805207 CCGTGGTTCTCCCCTTATAAAG 58.195 50.000 0.00 0.00 0.00 1.85
2544 2778 0.397535 AGATGCGCATCCCCCAAAAT 60.398 50.000 39.38 20.63 38.58 1.82
2558 2792 6.498538 TCCCCCAAAATATAACAGTGTCATT 58.501 36.000 0.00 0.00 0.00 2.57
2596 2830 3.281727 TGATGAATGTCTTAGGGTGCC 57.718 47.619 0.00 0.00 0.00 5.01
2597 2831 2.846206 TGATGAATGTCTTAGGGTGCCT 59.154 45.455 0.00 0.00 37.71 4.75
2612 2846 2.028876 GTGCCTGGGTAAACAACTTGT 58.971 47.619 0.00 0.00 0.00 3.16
2645 2879 2.747446 ACACTAAACCGGCATTCATGTC 59.253 45.455 0.00 0.00 0.00 3.06
2690 2924 4.956075 GGGATGTAAATTTGTGACCCTCAT 59.044 41.667 0.00 0.00 33.99 2.90
2701 2935 4.050313 CCCTCATGGTTCCCTCGA 57.950 61.111 0.00 0.00 0.00 4.04
2703 2937 0.179000 CCCTCATGGTTCCCTCGAAG 59.821 60.000 0.00 0.00 0.00 3.79
2801 3035 5.459505 ACTAAAGAGGGCTAGAGAATGCTA 58.540 41.667 0.00 0.00 0.00 3.49
2848 3082 1.568606 CCTGATCATCTGCTCACACG 58.431 55.000 0.00 0.00 0.00 4.49
2877 3404 7.042797 ACATGCTAGTTTGAACAACTTCATT 57.957 32.000 0.00 0.00 36.26 2.57
2898 3425 2.125552 TCCGACCGCTGAAGCATG 60.126 61.111 2.79 0.00 42.21 4.06
2899 3426 3.869272 CCGACCGCTGAAGCATGC 61.869 66.667 10.51 10.51 42.21 4.06
2900 3427 3.120385 CGACCGCTGAAGCATGCA 61.120 61.111 21.98 0.00 42.21 3.96
2901 3428 2.466982 CGACCGCTGAAGCATGCAT 61.467 57.895 21.98 8.13 42.21 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
435 436 9.193133 CAATCATTAAATCATCAATTCTGCTCC 57.807 33.333 0.00 0.00 0.00 4.70
613 616 0.606096 TAGCAGTGCTCCGCTGTTAA 59.394 50.000 23.64 0.00 43.09 2.01
614 617 0.824109 ATAGCAGTGCTCCGCTGTTA 59.176 50.000 23.64 0.77 43.09 2.41
615 618 0.824109 TATAGCAGTGCTCCGCTGTT 59.176 50.000 23.64 0.00 43.09 3.16
616 619 0.103208 GTATAGCAGTGCTCCGCTGT 59.897 55.000 23.64 2.78 43.09 4.40
617 620 0.103026 TGTATAGCAGTGCTCCGCTG 59.897 55.000 23.64 1.61 43.89 5.18
618 621 0.387202 CTGTATAGCAGTGCTCCGCT 59.613 55.000 23.64 7.75 40.44 5.52
619 622 2.892305 CTGTATAGCAGTGCTCCGC 58.108 57.895 23.64 12.94 40.44 5.54
630 633 6.914215 TCGTTTAATAAGTGTCGGCTGTATAG 59.086 38.462 0.00 0.00 0.00 1.31
631 634 6.692681 GTCGTTTAATAAGTGTCGGCTGTATA 59.307 38.462 0.00 0.00 0.00 1.47
632 635 5.517770 GTCGTTTAATAAGTGTCGGCTGTAT 59.482 40.000 0.00 0.00 0.00 2.29
633 636 4.858692 GTCGTTTAATAAGTGTCGGCTGTA 59.141 41.667 0.00 0.00 0.00 2.74
634 637 3.676646 GTCGTTTAATAAGTGTCGGCTGT 59.323 43.478 0.00 0.00 0.00 4.40
635 638 3.676172 TGTCGTTTAATAAGTGTCGGCTG 59.324 43.478 0.00 0.00 0.00 4.85
636 639 3.676646 GTGTCGTTTAATAAGTGTCGGCT 59.323 43.478 0.00 0.00 0.00 5.52
637 640 3.480825 CGTGTCGTTTAATAAGTGTCGGC 60.481 47.826 0.00 0.00 0.00 5.54
638 641 3.480825 GCGTGTCGTTTAATAAGTGTCGG 60.481 47.826 0.00 0.00 0.00 4.79
639 642 3.642210 GCGTGTCGTTTAATAAGTGTCG 58.358 45.455 0.00 0.00 0.00 4.35
640 643 3.642210 CGCGTGTCGTTTAATAAGTGTC 58.358 45.455 0.00 0.00 0.00 3.67
641 644 2.159934 GCGCGTGTCGTTTAATAAGTGT 60.160 45.455 8.43 0.00 41.07 3.55
642 645 2.159947 TGCGCGTGTCGTTTAATAAGTG 60.160 45.455 8.43 0.00 41.07 3.16
643 646 2.060284 TGCGCGTGTCGTTTAATAAGT 58.940 42.857 8.43 0.00 41.07 2.24
644 647 2.414985 GTGCGCGTGTCGTTTAATAAG 58.585 47.619 8.43 0.00 41.07 1.73
645 648 1.201683 CGTGCGCGTGTCGTTTAATAA 60.202 47.619 12.43 0.00 41.07 1.40
646 649 0.362845 CGTGCGCGTGTCGTTTAATA 59.637 50.000 12.43 0.00 41.07 0.98
647 650 1.129009 CGTGCGCGTGTCGTTTAAT 59.871 52.632 12.43 0.00 41.07 1.40
648 651 1.943202 TCGTGCGCGTGTCGTTTAA 60.943 52.632 20.50 0.00 41.07 1.52
649 652 2.353261 TCGTGCGCGTGTCGTTTA 60.353 55.556 20.50 0.00 41.07 2.01
650 653 3.979961 GTCGTGCGCGTGTCGTTT 61.980 61.111 20.50 0.00 41.07 3.60
654 657 3.979961 AAACGTCGTGCGCGTGTC 61.980 61.111 20.50 10.41 46.11 3.67
655 658 4.273951 CAAACGTCGTGCGCGTGT 62.274 61.111 20.50 16.27 46.11 4.49
659 662 4.383602 ATGGCAAACGTCGTGCGC 62.384 61.111 15.58 0.00 46.11 6.09
660 663 1.348538 TAGATGGCAAACGTCGTGCG 61.349 55.000 15.58 0.00 43.18 5.34
661 664 0.370273 CTAGATGGCAAACGTCGTGC 59.630 55.000 14.18 14.18 40.15 5.34
662 665 0.370273 GCTAGATGGCAAACGTCGTG 59.630 55.000 0.00 0.00 40.15 4.35
663 666 0.739813 GGCTAGATGGCAAACGTCGT 60.740 55.000 0.00 0.00 40.15 4.34
664 667 2.006772 GGCTAGATGGCAAACGTCG 58.993 57.895 0.00 0.00 40.15 5.12
681 684 4.160635 GAACAACGCCGCCGATGG 62.161 66.667 0.37 0.00 40.97 3.51
682 685 4.160635 GGAACAACGCCGCCGATG 62.161 66.667 0.00 0.00 42.17 3.84
683 686 2.901051 CTAGGAACAACGCCGCCGAT 62.901 60.000 0.00 0.00 38.29 4.18
684 687 3.636313 CTAGGAACAACGCCGCCGA 62.636 63.158 0.00 0.00 38.29 5.54
685 688 3.186047 CTAGGAACAACGCCGCCG 61.186 66.667 0.00 0.00 41.14 6.46
686 689 1.810030 CTCTAGGAACAACGCCGCC 60.810 63.158 0.00 0.00 0.00 6.13
687 690 0.171903 TACTCTAGGAACAACGCCGC 59.828 55.000 0.00 0.00 0.00 6.53
688 691 2.543238 GGATACTCTAGGAACAACGCCG 60.543 54.545 0.00 0.00 0.00 6.46
689 692 3.095102 GGATACTCTAGGAACAACGCC 57.905 52.381 0.00 0.00 0.00 5.68
709 712 2.448453 GATAGATCCTCCCCACCGTAG 58.552 57.143 0.00 0.00 0.00 3.51
710 713 1.271762 CGATAGATCCTCCCCACCGTA 60.272 57.143 0.00 0.00 39.76 4.02
711 714 0.539901 CGATAGATCCTCCCCACCGT 60.540 60.000 0.00 0.00 39.76 4.83
712 715 1.251527 CCGATAGATCCTCCCCACCG 61.252 65.000 0.00 0.00 39.76 4.94
713 716 1.545706 GCCGATAGATCCTCCCCACC 61.546 65.000 0.00 0.00 39.76 4.61
714 717 0.543174 AGCCGATAGATCCTCCCCAC 60.543 60.000 0.00 0.00 39.76 4.61
715 718 0.542938 CAGCCGATAGATCCTCCCCA 60.543 60.000 0.00 0.00 39.76 4.96
716 719 1.893919 GCAGCCGATAGATCCTCCCC 61.894 65.000 0.00 0.00 39.76 4.81
717 720 1.188219 TGCAGCCGATAGATCCTCCC 61.188 60.000 0.00 0.00 39.76 4.30
718 721 0.037790 GTGCAGCCGATAGATCCTCC 60.038 60.000 0.00 0.00 39.76 4.30
719 722 0.676184 TGTGCAGCCGATAGATCCTC 59.324 55.000 0.00 0.00 39.76 3.71
720 723 1.274728 GATGTGCAGCCGATAGATCCT 59.725 52.381 0.00 0.00 39.76 3.24
721 724 1.719600 GATGTGCAGCCGATAGATCC 58.280 55.000 0.00 0.00 39.76 3.36
722 725 1.336332 ACGATGTGCAGCCGATAGATC 60.336 52.381 8.96 0.00 39.76 2.75
723 726 0.676184 ACGATGTGCAGCCGATAGAT 59.324 50.000 8.96 0.00 39.76 1.98
724 727 0.249031 CACGATGTGCAGCCGATAGA 60.249 55.000 8.96 0.00 39.76 1.98
725 728 2.219847 CACGATGTGCAGCCGATAG 58.780 57.895 8.96 0.00 0.00 2.08
726 729 4.418337 CACGATGTGCAGCCGATA 57.582 55.556 8.96 0.00 0.00 2.92
735 738 0.166597 GATGGTGTGTGCACGATGTG 59.833 55.000 13.13 0.00 46.13 3.21
736 739 1.291184 CGATGGTGTGTGCACGATGT 61.291 55.000 13.13 0.00 46.13 3.06
737 740 1.291184 ACGATGGTGTGTGCACGATG 61.291 55.000 13.13 0.00 46.13 3.84
738 741 1.005037 ACGATGGTGTGTGCACGAT 60.005 52.632 13.13 0.00 46.13 3.73
739 742 1.953642 CACGATGGTGTGTGCACGA 60.954 57.895 13.13 0.00 46.13 4.35
740 743 2.550772 CACGATGGTGTGTGCACG 59.449 61.111 13.13 0.00 46.13 5.34
749 752 4.442706 GGAATTGATCTACACACGATGGT 58.557 43.478 0.00 0.00 0.00 3.55
750 753 3.490896 CGGAATTGATCTACACACGATGG 59.509 47.826 0.00 0.00 0.00 3.51
751 754 4.112634 ACGGAATTGATCTACACACGATG 58.887 43.478 0.00 0.00 0.00 3.84
752 755 4.386867 ACGGAATTGATCTACACACGAT 57.613 40.909 0.00 0.00 0.00 3.73
753 756 3.861276 ACGGAATTGATCTACACACGA 57.139 42.857 0.00 0.00 0.00 4.35
754 757 5.346551 TGTTAACGGAATTGATCTACACACG 59.653 40.000 0.26 0.00 0.00 4.49
755 758 6.672357 GCTGTTAACGGAATTGATCTACACAC 60.672 42.308 18.81 0.00 0.00 3.82
756 759 5.350365 GCTGTTAACGGAATTGATCTACACA 59.650 40.000 18.81 0.00 0.00 3.72
757 760 5.500290 CGCTGTTAACGGAATTGATCTACAC 60.500 44.000 18.81 0.00 0.00 2.90
758 761 4.565166 CGCTGTTAACGGAATTGATCTACA 59.435 41.667 18.81 0.00 0.00 2.74
759 762 4.802039 TCGCTGTTAACGGAATTGATCTAC 59.198 41.667 18.81 0.00 0.00 2.59
760 763 4.802039 GTCGCTGTTAACGGAATTGATCTA 59.198 41.667 18.81 0.00 0.00 1.98
761 764 3.617263 GTCGCTGTTAACGGAATTGATCT 59.383 43.478 18.81 0.00 0.00 2.75
762 765 3.617263 AGTCGCTGTTAACGGAATTGATC 59.383 43.478 18.81 0.00 0.00 2.92
763 766 3.596214 AGTCGCTGTTAACGGAATTGAT 58.404 40.909 18.81 0.00 0.00 2.57
764 767 3.034721 AGTCGCTGTTAACGGAATTGA 57.965 42.857 18.81 6.79 0.00 2.57
765 768 6.764877 ATATAGTCGCTGTTAACGGAATTG 57.235 37.500 18.81 4.56 0.00 2.32
766 769 8.086522 ACATATATAGTCGCTGTTAACGGAATT 58.913 33.333 18.81 4.78 0.00 2.17
767 770 7.600065 ACATATATAGTCGCTGTTAACGGAAT 58.400 34.615 18.81 8.68 0.00 3.01
768 771 6.973843 ACATATATAGTCGCTGTTAACGGAA 58.026 36.000 18.81 2.26 0.00 4.30
769 772 6.564709 ACATATATAGTCGCTGTTAACGGA 57.435 37.500 18.81 4.24 0.00 4.69
770 773 6.639686 ACAACATATATAGTCGCTGTTAACGG 59.360 38.462 10.24 10.24 0.00 4.44
771 774 7.149015 GGACAACATATATAGTCGCTGTTAACG 60.149 40.741 0.26 0.00 31.93 3.18
772 775 7.115947 GGGACAACATATATAGTCGCTGTTAAC 59.884 40.741 15.75 0.00 39.81 2.01
773 776 7.149973 GGGACAACATATATAGTCGCTGTTAA 58.850 38.462 15.75 0.00 39.81 2.01
822 825 2.484417 GCTGGACAGTCATATGTGAGGG 60.484 54.545 2.17 0.00 34.36 4.30
851 854 0.759959 TGCAGTTACTGTCCGGGAAA 59.240 50.000 14.23 0.00 33.43 3.13
979 982 2.112297 TTGGTTGTCCGGCTGGTC 59.888 61.111 12.43 6.68 36.30 4.02
1213 1240 1.456196 CCGAGCAGAGCCGGATAGAA 61.456 60.000 5.05 0.00 42.08 2.10
1329 1372 2.091499 TCCGACCTTATTAGGCAGAGGA 60.091 50.000 0.00 0.00 46.22 3.71
1409 1452 0.824109 CTGTTCCTGCCATCCGTCTA 59.176 55.000 0.00 0.00 0.00 2.59
1437 1480 0.539669 TGAACTGGTCGAGCTCTGGA 60.540 55.000 16.64 0.00 0.00 3.86
1466 1510 5.704515 AGCTAGCCTAAACTAATCATGCATG 59.295 40.000 21.07 21.07 0.00 4.06
1467 1511 5.704515 CAGCTAGCCTAAACTAATCATGCAT 59.295 40.000 12.13 0.00 0.00 3.96
1468 1512 5.059161 CAGCTAGCCTAAACTAATCATGCA 58.941 41.667 12.13 0.00 0.00 3.96
1469 1513 4.453819 CCAGCTAGCCTAAACTAATCATGC 59.546 45.833 12.13 0.00 0.00 4.06
2014 2202 4.412528 ACTCCCAAACCTAGAAAGACAAGT 59.587 41.667 0.00 0.00 0.00 3.16
2188 2378 5.121380 AGGTGGTCTATGAATCTGCATTT 57.879 39.130 0.00 0.00 0.00 2.32
2189 2379 4.785346 AGGTGGTCTATGAATCTGCATT 57.215 40.909 0.00 0.00 0.00 3.56
2192 2384 3.658709 GCTAGGTGGTCTATGAATCTGC 58.341 50.000 0.00 0.00 0.00 4.26
2290 2483 2.682155 TCACATGGCACGCTACAATA 57.318 45.000 0.00 0.00 0.00 1.90
2292 2485 1.085893 CATCACATGGCACGCTACAA 58.914 50.000 0.00 0.00 0.00 2.41
2301 2504 5.240623 TCGGGAATTATAAACATCACATGGC 59.759 40.000 0.00 0.00 33.60 4.40
2309 2512 6.531021 AGATCGGTTCGGGAATTATAAACAT 58.469 36.000 0.00 0.00 0.00 2.71
2467 2678 6.756542 GGTTATATCACCTTTGCCATGTTTTC 59.243 38.462 0.00 0.00 33.50 2.29
2544 2778 5.159273 TGCCAGACAATGACACTGTTATA 57.841 39.130 0.00 0.00 0.00 0.98
2579 2813 1.281867 CCAGGCACCCTAAGACATTCA 59.718 52.381 0.00 0.00 29.64 2.57
2593 2827 2.445682 ACAAGTTGTTTACCCAGGCA 57.554 45.000 1.64 0.00 0.00 4.75
2596 2830 2.809696 CGGGTACAAGTTGTTTACCCAG 59.190 50.000 32.35 24.46 45.32 4.45
2597 2831 2.437281 TCGGGTACAAGTTGTTTACCCA 59.563 45.455 32.35 22.07 45.32 4.51
2612 2846 2.431782 GGTTTAGTGTATGGCTCGGGTA 59.568 50.000 0.00 0.00 0.00 3.69
2690 2924 2.011122 AGAAGACTTCGAGGGAACCA 57.989 50.000 9.53 0.00 43.73 3.67
2700 2934 6.205658 ACATTTGGTTGAGCTAAGAAGACTTC 59.794 38.462 7.14 7.14 37.53 3.01
2701 2935 6.064717 ACATTTGGTTGAGCTAAGAAGACTT 58.935 36.000 0.00 0.00 39.81 3.01
2703 2937 5.948992 ACATTTGGTTGAGCTAAGAAGAC 57.051 39.130 0.00 0.00 0.00 3.01
2848 3082 8.307882 GAAGTTGTTCAAACTAGCATGTATGCC 61.308 40.741 12.88 0.00 42.43 4.40
2877 3404 2.048222 CTTCAGCGGTCGGAGCAA 60.048 61.111 8.06 0.00 37.01 3.91
2921 3448 8.574251 TTTGCAGGTTATACACTCATTTACAT 57.426 30.769 0.00 0.00 0.00 2.29
2922 3449 7.120579 CCTTTGCAGGTTATACACTCATTTACA 59.879 37.037 0.00 0.00 35.06 2.41


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

AutoCloner maintained by Alex Coulton.