Multiple sequence alignment - TraesCS7A01G280100

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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 TraesCS7A01G280100 chr7A 100.000 3479 0 0 1 3479 299414583 299418061 0.000000e+00 6425.0
1 TraesCS7A01G280100 chr7A 97.534 2757 51 5 724 3479 652482589 652479849 0.000000e+00 4698.0
2 TraesCS7A01G280100 chr6A 97.606 2757 50 4 724 3479 175630097 175632838 0.000000e+00 4711.0
3 TraesCS7A01G280100 chr1A 97.501 2761 54 3 720 3479 582543181 582540435 0.000000e+00 4702.0
4 TraesCS7A01G280100 chr1A 94.964 695 29 6 2 693 558016191 558015500 0.000000e+00 1085.0
5 TraesCS7A01G280100 chr2A 97.500 2760 54 3 721 3479 72953332 72956077 0.000000e+00 4700.0
6 TraesCS7A01G280100 chr2A 93.279 491 31 2 203 693 315764605 315764117 0.000000e+00 723.0
7 TraesCS7A01G280100 chr2A 98.558 208 3 0 2930 3137 507382765 507382558 5.490000e-98 368.0
8 TraesCS7A01G280100 chr2A 93.855 179 8 3 2 179 315764776 315764600 2.060000e-67 267.0
9 TraesCS7A01G280100 chr6B 97.465 2761 54 4 721 3479 707589596 707592342 0.000000e+00 4697.0
10 TraesCS7A01G280100 chr6B 97.279 2756 53 6 724 3479 536839744 536837011 0.000000e+00 4654.0
11 TraesCS7A01G280100 chr6B 98.177 1975 31 1 724 2698 225314119 225316088 0.000000e+00 3443.0
12 TraesCS7A01G280100 chr6B 93.644 881 45 8 724 1597 245661380 245660504 0.000000e+00 1306.0
13 TraesCS7A01G280100 chr6B 93.486 875 40 7 724 1597 646722174 646723032 0.000000e+00 1284.0
14 TraesCS7A01G280100 chr6B 97.735 309 7 0 724 1032 225321894 225321586 1.840000e-147 532.0
15 TraesCS7A01G280100 chr6B 93.226 310 16 2 724 1033 646740641 646740337 5.300000e-123 451.0
16 TraesCS7A01G280100 chr6B 91.693 313 23 3 724 1033 476712964 476712652 6.900000e-117 431.0
17 TraesCS7A01G280100 chr6B 89.841 315 25 5 720 1033 387917477 387917785 7.000000e-107 398.0
18 TraesCS7A01G280100 chr4A 97.425 2757 56 3 724 3479 612039986 612042728 0.000000e+00 4684.0
19 TraesCS7A01G280100 chr4A 95.252 695 28 5 1 693 420017409 420018100 0.000000e+00 1096.0
20 TraesCS7A01G280100 chr3A 97.062 2757 53 5 724 3479 57277795 57275066 0.000000e+00 4617.0
21 TraesCS7A01G280100 chr2B 97.073 2221 37 6 724 2942 183540043 183542237 0.000000e+00 3716.0
22 TraesCS7A01G280100 chr2D 95.058 688 28 5 7 693 52286578 52285896 0.000000e+00 1077.0
23 TraesCS7A01G280100 chr4B 91.035 792 59 8 724 1509 473580525 473579740 0.000000e+00 1059.0
24 TraesCS7A01G280100 chr3D 94.801 654 30 2 1 650 30973503 30972850 0.000000e+00 1016.0
25 TraesCS7A01G280100 chr3D 92.058 554 38 5 1 549 412105346 412104794 0.000000e+00 774.0
26 TraesCS7A01G280100 chr3D 96.503 286 9 1 1 285 477570980 477571265 4.060000e-129 472.0
27 TraesCS7A01G280100 chr3D 93.750 48 1 2 646 693 30972034 30971989 1.730000e-08 71.3
28 TraesCS7A01G280100 chr5B 95.745 611 22 4 1 610 634119303 634119910 0.000000e+00 981.0
29 TraesCS7A01G280100 chr6D 90.927 507 37 6 193 693 169716392 169715889 0.000000e+00 673.0
30 TraesCS7A01G280100 chr3B 88.889 549 46 11 149 693 726178471 726179008 0.000000e+00 662.0
31 TraesCS7A01G280100 chr3B 91.304 138 10 1 1 136 726178264 726178401 1.650000e-43 187.0
32 TraesCS7A01G280100 chr3B 94.595 37 2 0 680 716 608255124 608255160 1.350000e-04 58.4
33 TraesCS7A01G280100 chr4D 89.508 305 28 4 724 1025 374741655 374741958 1.960000e-102 383.0
34 TraesCS7A01G280100 chr4D 85.577 104 11 2 138 241 466837135 466837234 4.750000e-19 106.0
35 TraesCS7A01G280100 chr5A 95.238 42 2 0 680 721 267899003 267898962 2.240000e-07 67.6


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 TraesCS7A01G280100 chr7A 299414583 299418061 3478 False 6425.00 6425 100.0000 1 3479 1 chr7A.!!$F1 3478
1 TraesCS7A01G280100 chr7A 652479849 652482589 2740 True 4698.00 4698 97.5340 724 3479 1 chr7A.!!$R1 2755
2 TraesCS7A01G280100 chr6A 175630097 175632838 2741 False 4711.00 4711 97.6060 724 3479 1 chr6A.!!$F1 2755
3 TraesCS7A01G280100 chr1A 582540435 582543181 2746 True 4702.00 4702 97.5010 720 3479 1 chr1A.!!$R2 2759
4 TraesCS7A01G280100 chr1A 558015500 558016191 691 True 1085.00 1085 94.9640 2 693 1 chr1A.!!$R1 691
5 TraesCS7A01G280100 chr2A 72953332 72956077 2745 False 4700.00 4700 97.5000 721 3479 1 chr2A.!!$F1 2758
6 TraesCS7A01G280100 chr2A 315764117 315764776 659 True 495.00 723 93.5670 2 693 2 chr2A.!!$R2 691
7 TraesCS7A01G280100 chr6B 707589596 707592342 2746 False 4697.00 4697 97.4650 721 3479 1 chr6B.!!$F4 2758
8 TraesCS7A01G280100 chr6B 536837011 536839744 2733 True 4654.00 4654 97.2790 724 3479 1 chr6B.!!$R4 2755
9 TraesCS7A01G280100 chr6B 225314119 225316088 1969 False 3443.00 3443 98.1770 724 2698 1 chr6B.!!$F1 1974
10 TraesCS7A01G280100 chr6B 245660504 245661380 876 True 1306.00 1306 93.6440 724 1597 1 chr6B.!!$R2 873
11 TraesCS7A01G280100 chr6B 646722174 646723032 858 False 1284.00 1284 93.4860 724 1597 1 chr6B.!!$F3 873
12 TraesCS7A01G280100 chr4A 612039986 612042728 2742 False 4684.00 4684 97.4250 724 3479 1 chr4A.!!$F2 2755
13 TraesCS7A01G280100 chr4A 420017409 420018100 691 False 1096.00 1096 95.2520 1 693 1 chr4A.!!$F1 692
14 TraesCS7A01G280100 chr3A 57275066 57277795 2729 True 4617.00 4617 97.0620 724 3479 1 chr3A.!!$R1 2755
15 TraesCS7A01G280100 chr2B 183540043 183542237 2194 False 3716.00 3716 97.0730 724 2942 1 chr2B.!!$F1 2218
16 TraesCS7A01G280100 chr2D 52285896 52286578 682 True 1077.00 1077 95.0580 7 693 1 chr2D.!!$R1 686
17 TraesCS7A01G280100 chr4B 473579740 473580525 785 True 1059.00 1059 91.0350 724 1509 1 chr4B.!!$R1 785
18 TraesCS7A01G280100 chr3D 412104794 412105346 552 True 774.00 774 92.0580 1 549 1 chr3D.!!$R1 548
19 TraesCS7A01G280100 chr3D 30971989 30973503 1514 True 543.65 1016 94.2755 1 693 2 chr3D.!!$R2 692
20 TraesCS7A01G280100 chr5B 634119303 634119910 607 False 981.00 981 95.7450 1 610 1 chr5B.!!$F1 609
21 TraesCS7A01G280100 chr6D 169715889 169716392 503 True 673.00 673 90.9270 193 693 1 chr6D.!!$R1 500
22 TraesCS7A01G280100 chr3B 726178264 726179008 744 False 424.50 662 90.0965 1 693 2 chr3B.!!$F2 692

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
708 719 0.326927 TAAACCTGGCTGTGCTACCC 59.673 55.0 0.00 0.0 0.00 3.69 F
1112 1161 0.039618 ACGCCATGGTTTTGGAGGAT 59.960 50.0 14.67 0.0 40.51 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2375 3394 1.280421 CCCCCTGAACTTCTCCTTCAG 59.720 57.143 1.82 1.82 42.95 3.02 R
3094 4113 0.107703 TCATTGGGGATCTGCGTGAC 60.108 55.000 0.00 0.00 0.00 3.67 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
208 213 9.874215 GTTTTTAAAGTAGTGATCTAAACGCTT 57.126 29.630 0.00 0.00 0.00 4.68
248 253 7.014326 CAGAGGGAGTACTATGCTACATTACAA 59.986 40.741 0.00 0.00 0.00 2.41
258 263 5.685520 TGCTACATTACAAGGTGGTGATA 57.314 39.130 0.00 0.00 0.00 2.15
391 399 4.151883 TCTTTTGATGCTGGCCTTACTTT 58.848 39.130 3.32 0.00 0.00 2.66
396 404 3.947196 TGATGCTGGCCTTACTTTATGTG 59.053 43.478 3.32 0.00 0.00 3.21
453 464 5.186215 TCGTCCATCTTGTGATAAAGGTGTA 59.814 40.000 0.00 0.00 36.69 2.90
457 468 7.552687 GTCCATCTTGTGATAAAGGTGTATTGA 59.447 37.037 0.00 0.00 36.69 2.57
549 560 8.469200 CCATCAAATTATTTTTCAGCTACCTCA 58.531 33.333 0.00 0.00 0.00 3.86
550 561 9.859427 CATCAAATTATTTTTCAGCTACCTCAA 57.141 29.630 0.00 0.00 0.00 3.02
552 563 9.859427 TCAAATTATTTTTCAGCTACCTCAATG 57.141 29.630 0.00 0.00 0.00 2.82
553 564 9.859427 CAAATTATTTTTCAGCTACCTCAATGA 57.141 29.630 0.00 0.00 0.00 2.57
554 565 9.860898 AAATTATTTTTCAGCTACCTCAATGAC 57.139 29.630 0.00 0.00 0.00 3.06
555 566 5.904362 ATTTTTCAGCTACCTCAATGACC 57.096 39.130 0.00 0.00 0.00 4.02
556 567 4.640771 TTTTCAGCTACCTCAATGACCT 57.359 40.909 0.00 0.00 0.00 3.85
557 568 3.616956 TTCAGCTACCTCAATGACCTG 57.383 47.619 0.00 0.00 0.00 4.00
558 569 2.540383 TCAGCTACCTCAATGACCTGT 58.460 47.619 0.00 0.00 0.00 4.00
559 570 3.708451 TCAGCTACCTCAATGACCTGTA 58.292 45.455 0.00 0.00 0.00 2.74
560 571 4.290093 TCAGCTACCTCAATGACCTGTAT 58.710 43.478 0.00 0.00 0.00 2.29
561 572 4.342378 TCAGCTACCTCAATGACCTGTATC 59.658 45.833 0.00 0.00 0.00 2.24
562 573 4.343526 CAGCTACCTCAATGACCTGTATCT 59.656 45.833 0.00 0.00 0.00 1.98
563 574 4.965532 AGCTACCTCAATGACCTGTATCTT 59.034 41.667 0.00 0.00 0.00 2.40
564 575 5.426833 AGCTACCTCAATGACCTGTATCTTT 59.573 40.000 0.00 0.00 0.00 2.52
565 576 5.525378 GCTACCTCAATGACCTGTATCTTTG 59.475 44.000 0.00 0.00 35.89 2.77
566 577 4.848357 ACCTCAATGACCTGTATCTTTGG 58.152 43.478 0.00 0.00 35.49 3.28
567 578 4.536090 ACCTCAATGACCTGTATCTTTGGA 59.464 41.667 0.00 0.00 35.49 3.53
568 579 5.014123 ACCTCAATGACCTGTATCTTTGGAA 59.986 40.000 0.00 0.00 35.49 3.53
569 580 5.945784 CCTCAATGACCTGTATCTTTGGAAA 59.054 40.000 0.00 0.00 35.49 3.13
570 581 6.604795 CCTCAATGACCTGTATCTTTGGAAAT 59.395 38.462 0.00 0.00 35.49 2.17
571 582 7.395190 TCAATGACCTGTATCTTTGGAAATG 57.605 36.000 0.00 0.00 35.49 2.32
572 583 7.174413 TCAATGACCTGTATCTTTGGAAATGA 58.826 34.615 0.00 0.00 35.49 2.57
573 584 7.337689 TCAATGACCTGTATCTTTGGAAATGAG 59.662 37.037 0.00 0.00 35.49 2.90
574 585 5.500234 TGACCTGTATCTTTGGAAATGAGG 58.500 41.667 0.00 0.00 33.23 3.86
575 586 5.014123 TGACCTGTATCTTTGGAAATGAGGT 59.986 40.000 0.00 0.00 33.23 3.85
576 587 5.501156 ACCTGTATCTTTGGAAATGAGGTC 58.499 41.667 0.00 0.00 33.23 3.85
577 588 4.884164 CCTGTATCTTTGGAAATGAGGTCC 59.116 45.833 0.00 0.00 33.23 4.46
578 589 5.500234 CTGTATCTTTGGAAATGAGGTCCA 58.500 41.667 0.00 0.00 43.57 4.02
583 594 2.649531 TGGAAATGAGGTCCAAACGT 57.350 45.000 0.00 0.00 42.29 3.99
584 595 2.938838 TGGAAATGAGGTCCAAACGTT 58.061 42.857 0.00 0.00 42.29 3.99
585 596 3.292460 TGGAAATGAGGTCCAAACGTTT 58.708 40.909 7.96 7.96 42.29 3.60
586 597 3.702045 TGGAAATGAGGTCCAAACGTTTT 59.298 39.130 11.66 0.00 42.29 2.43
587 598 4.202070 TGGAAATGAGGTCCAAACGTTTTC 60.202 41.667 11.66 6.76 42.29 2.29
588 599 4.295870 GAAATGAGGTCCAAACGTTTTCC 58.704 43.478 11.66 13.69 0.00 3.13
589 600 2.421751 TGAGGTCCAAACGTTTTCCA 57.578 45.000 11.66 0.66 0.00 3.53
590 601 2.018515 TGAGGTCCAAACGTTTTCCAC 58.981 47.619 11.66 12.66 0.00 4.02
608 619 2.937591 CACGGTTAGTGTACGACATGT 58.062 47.619 0.00 0.00 45.51 3.21
609 620 3.311106 CACGGTTAGTGTACGACATGTT 58.689 45.455 0.00 0.00 45.51 2.71
610 621 3.362831 CACGGTTAGTGTACGACATGTTC 59.637 47.826 0.00 0.00 45.51 3.18
611 622 3.004629 ACGGTTAGTGTACGACATGTTCA 59.995 43.478 0.00 0.00 0.00 3.18
612 623 4.171005 CGGTTAGTGTACGACATGTTCAT 58.829 43.478 0.00 0.00 30.12 2.57
613 624 5.106197 ACGGTTAGTGTACGACATGTTCATA 60.106 40.000 0.00 0.00 30.12 2.15
614 625 5.228635 CGGTTAGTGTACGACATGTTCATAC 59.771 44.000 0.00 4.08 30.12 2.39
615 626 5.517770 GGTTAGTGTACGACATGTTCATACC 59.482 44.000 0.00 4.30 30.12 2.73
616 627 4.119442 AGTGTACGACATGTTCATACCC 57.881 45.455 0.00 0.00 30.12 3.69
617 628 3.767673 AGTGTACGACATGTTCATACCCT 59.232 43.478 0.00 0.00 30.12 4.34
618 629 4.222145 AGTGTACGACATGTTCATACCCTT 59.778 41.667 0.00 0.00 30.12 3.95
619 630 4.328983 GTGTACGACATGTTCATACCCTTG 59.671 45.833 0.00 0.00 30.12 3.61
620 631 3.695830 ACGACATGTTCATACCCTTGT 57.304 42.857 0.00 0.00 0.00 3.16
621 632 4.811969 ACGACATGTTCATACCCTTGTA 57.188 40.909 0.00 0.00 0.00 2.41
622 633 5.353394 ACGACATGTTCATACCCTTGTAT 57.647 39.130 0.00 0.00 38.21 2.29
623 634 5.357257 ACGACATGTTCATACCCTTGTATC 58.643 41.667 0.00 0.00 35.46 2.24
624 635 5.105106 ACGACATGTTCATACCCTTGTATCA 60.105 40.000 0.00 0.00 35.46 2.15
625 636 5.815222 CGACATGTTCATACCCTTGTATCAA 59.185 40.000 0.00 0.00 35.46 2.57
626 637 6.018751 CGACATGTTCATACCCTTGTATCAAG 60.019 42.308 0.00 2.90 35.46 3.02
627 638 6.721318 ACATGTTCATACCCTTGTATCAAGT 58.279 36.000 0.00 0.00 35.46 3.16
628 639 7.857456 ACATGTTCATACCCTTGTATCAAGTA 58.143 34.615 0.00 0.00 35.46 2.24
629 640 8.325787 ACATGTTCATACCCTTGTATCAAGTAA 58.674 33.333 0.00 0.00 35.46 2.24
630 641 8.830580 CATGTTCATACCCTTGTATCAAGTAAG 58.169 37.037 8.37 0.00 35.46 2.34
631 642 8.141298 TGTTCATACCCTTGTATCAAGTAAGA 57.859 34.615 8.37 0.00 35.46 2.10
632 643 8.258007 TGTTCATACCCTTGTATCAAGTAAGAG 58.742 37.037 8.37 0.00 35.46 2.85
633 644 6.817184 TCATACCCTTGTATCAAGTAAGAGC 58.183 40.000 8.37 0.00 35.46 4.09
634 645 4.124851 ACCCTTGTATCAAGTAAGAGCG 57.875 45.455 8.37 0.00 0.00 5.03
635 646 3.514309 ACCCTTGTATCAAGTAAGAGCGT 59.486 43.478 8.37 0.00 0.00 5.07
636 647 4.113354 CCCTTGTATCAAGTAAGAGCGTC 58.887 47.826 8.37 0.00 0.00 5.19
637 648 4.113354 CCTTGTATCAAGTAAGAGCGTCC 58.887 47.826 8.37 0.00 0.00 4.79
638 649 3.416119 TGTATCAAGTAAGAGCGTCCG 57.584 47.619 0.00 0.00 0.00 4.79
639 650 3.011818 TGTATCAAGTAAGAGCGTCCGA 58.988 45.455 0.00 0.00 0.00 4.55
640 651 2.853731 ATCAAGTAAGAGCGTCCGAG 57.146 50.000 0.00 0.00 0.00 4.63
641 652 1.817357 TCAAGTAAGAGCGTCCGAGA 58.183 50.000 0.00 0.00 0.00 4.04
642 653 1.738350 TCAAGTAAGAGCGTCCGAGAG 59.262 52.381 0.00 0.00 0.00 3.20
659 670 5.814764 CGAGAGGACTAAGTTAGCTACAA 57.185 43.478 9.92 0.00 0.00 2.41
660 671 6.192234 CGAGAGGACTAAGTTAGCTACAAA 57.808 41.667 9.92 0.00 0.00 2.83
661 672 6.028987 CGAGAGGACTAAGTTAGCTACAAAC 58.971 44.000 9.92 0.00 0.00 2.93
662 673 6.349115 CGAGAGGACTAAGTTAGCTACAAACA 60.349 42.308 9.92 0.00 0.00 2.83
663 674 7.299246 AGAGGACTAAGTTAGCTACAAACAA 57.701 36.000 9.92 0.00 0.00 2.83
664 675 7.732996 AGAGGACTAAGTTAGCTACAAACAAA 58.267 34.615 9.92 0.00 0.00 2.83
665 676 7.656542 AGAGGACTAAGTTAGCTACAAACAAAC 59.343 37.037 9.92 0.00 0.00 2.93
666 677 7.506971 AGGACTAAGTTAGCTACAAACAAACT 58.493 34.615 9.92 0.00 31.94 2.66
667 678 7.991460 AGGACTAAGTTAGCTACAAACAAACTT 59.009 33.333 9.92 11.97 41.74 2.66
668 679 8.281194 GGACTAAGTTAGCTACAAACAAACTTC 58.719 37.037 9.92 0.00 40.07 3.01
669 680 8.726870 ACTAAGTTAGCTACAAACAAACTTCA 57.273 30.769 9.92 0.70 40.07 3.02
670 681 9.338622 ACTAAGTTAGCTACAAACAAACTTCAT 57.661 29.630 9.92 0.64 40.07 2.57
672 683 8.856490 AAGTTAGCTACAAACAAACTTCATTG 57.144 30.769 0.00 0.00 35.98 2.82
673 684 7.996385 AGTTAGCTACAAACAAACTTCATTGT 58.004 30.769 0.00 0.00 45.12 2.71
674 685 9.116067 AGTTAGCTACAAACAAACTTCATTGTA 57.884 29.630 0.00 0.00 42.49 2.41
675 686 9.166126 GTTAGCTACAAACAAACTTCATTGTAC 57.834 33.333 0.00 0.00 42.49 2.90
676 687 7.568199 AGCTACAAACAAACTTCATTGTACT 57.432 32.000 0.00 0.00 42.49 2.73
677 688 8.671384 AGCTACAAACAAACTTCATTGTACTA 57.329 30.769 0.00 0.00 42.49 1.82
678 689 8.557029 AGCTACAAACAAACTTCATTGTACTAC 58.443 33.333 0.00 0.00 42.49 2.73
679 690 8.339714 GCTACAAACAAACTTCATTGTACTACA 58.660 33.333 0.00 0.00 42.49 2.74
682 693 9.515020 ACAAACAAACTTCATTGTACTACATTG 57.485 29.630 5.15 5.15 42.49 2.82
683 694 9.729023 CAAACAAACTTCATTGTACTACATTGA 57.271 29.630 8.94 8.94 42.49 2.57
700 711 9.507329 ACTACATTGAATATATAAACCTGGCTG 57.493 33.333 0.00 0.00 0.00 4.85
701 712 9.507329 CTACATTGAATATATAAACCTGGCTGT 57.493 33.333 0.00 0.00 0.00 4.40
702 713 8.169977 ACATTGAATATATAAACCTGGCTGTG 57.830 34.615 0.00 0.00 0.00 3.66
703 714 6.633500 TTGAATATATAAACCTGGCTGTGC 57.367 37.500 0.00 0.00 0.00 4.57
704 715 5.940617 TGAATATATAAACCTGGCTGTGCT 58.059 37.500 0.00 0.00 0.00 4.40
705 716 7.073457 TGAATATATAAACCTGGCTGTGCTA 57.927 36.000 0.00 0.00 0.00 3.49
706 717 6.934645 TGAATATATAAACCTGGCTGTGCTAC 59.065 38.462 0.00 0.00 0.00 3.58
707 718 2.420058 ATAAACCTGGCTGTGCTACC 57.580 50.000 0.00 0.00 0.00 3.18
708 719 0.326927 TAAACCTGGCTGTGCTACCC 59.673 55.000 0.00 0.00 0.00 3.69
709 720 2.748058 AAACCTGGCTGTGCTACCCG 62.748 60.000 0.00 0.00 0.00 5.28
713 724 4.489771 GGCTGTGCTACCCGCCAT 62.490 66.667 0.00 0.00 42.06 4.40
714 725 2.897350 GCTGTGCTACCCGCCATC 60.897 66.667 0.00 0.00 38.05 3.51
715 726 2.203070 CTGTGCTACCCGCCATCC 60.203 66.667 0.00 0.00 38.05 3.51
716 727 3.006133 TGTGCTACCCGCCATCCA 61.006 61.111 0.00 0.00 38.05 3.41
717 728 2.203070 GTGCTACCCGCCATCCAG 60.203 66.667 0.00 0.00 38.05 3.86
718 729 3.479203 TGCTACCCGCCATCCAGG 61.479 66.667 0.00 0.00 38.05 4.45
762 773 2.494471 CCACAATTCAGGCATCACATGT 59.506 45.455 0.00 0.00 0.00 3.21
797 808 4.158384 CGATTGCTAATTTTTGCGTGTCT 58.842 39.130 0.00 0.00 0.00 3.41
1112 1161 0.039618 ACGCCATGGTTTTGGAGGAT 59.960 50.000 14.67 0.00 40.51 3.24
1124 1173 0.107993 TGGAGGATGAAAGCAGCGAG 60.108 55.000 0.00 0.00 0.00 5.03
1710 1802 7.935520 TGCAGTGATTTTGTGTAATTACTTGA 58.064 30.769 16.33 0.00 33.56 3.02
1833 1929 3.514645 CATTGTTGAAGCTATGGGCAAC 58.485 45.455 0.00 0.00 44.79 4.17
2042 2169 6.721318 ACATATCAGCAGGAGGTAAGAAAAA 58.279 36.000 0.00 0.00 0.00 1.94
2492 3511 6.183360 GGTTGTGTAATGACCTAGCATCTAGA 60.183 42.308 0.00 0.00 0.00 2.43
2585 3604 7.950512 TGCTATTCATCCTTTTGTGAGAAAAA 58.049 30.769 0.00 0.00 0.00 1.94
2748 3767 1.202557 ACAATGTTGCAGCAAACCAGG 60.203 47.619 10.11 4.28 0.00 4.45
2849 3868 4.460382 ACTTGATCCATTACAACTTGGCTG 59.540 41.667 0.00 0.00 32.80 4.85
3094 4113 3.871594 CACCTTTAAGCCTCCATACTTCG 59.128 47.826 0.00 0.00 0.00 3.79
3249 4268 6.661377 AGAAGAAAGAGGAAGAAAATTAGGGC 59.339 38.462 0.00 0.00 0.00 5.19
3255 4274 7.559335 AGAGGAAGAAAATTAGGGCAAAAAT 57.441 32.000 0.00 0.00 0.00 1.82
3450 4469 0.037326 TCCTGCAGCTCGACGAAATT 60.037 50.000 8.66 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.678056 TCTGACGTTCTGCAGGTTAAT 57.322 42.857 15.13 0.00 33.05 1.40
181 185 8.219105 AGCGTTTAGATCACTACTTTAAAAACG 58.781 33.333 11.00 11.00 36.66 3.60
248 253 3.780294 TCCTGCTTGTATTATCACCACCT 59.220 43.478 0.00 0.00 0.00 4.00
258 263 8.814038 ATACTCAATTTTCTCCTGCTTGTATT 57.186 30.769 0.00 0.00 0.00 1.89
391 399 8.033178 TCAACAATCTGATATCCCTTCACATA 57.967 34.615 0.00 0.00 0.00 2.29
396 404 8.512956 CATCAATCAACAATCTGATATCCCTTC 58.487 37.037 0.00 0.00 34.90 3.46
549 560 6.604795 CCTCATTTCCAAAGATACAGGTCATT 59.395 38.462 0.00 0.00 0.00 2.57
550 561 6.125029 CCTCATTTCCAAAGATACAGGTCAT 58.875 40.000 0.00 0.00 0.00 3.06
551 562 5.014123 ACCTCATTTCCAAAGATACAGGTCA 59.986 40.000 0.00 0.00 0.00 4.02
552 563 5.501156 ACCTCATTTCCAAAGATACAGGTC 58.499 41.667 0.00 0.00 0.00 3.85
553 564 5.501156 GACCTCATTTCCAAAGATACAGGT 58.499 41.667 0.00 0.00 34.34 4.00
554 565 4.884164 GGACCTCATTTCCAAAGATACAGG 59.116 45.833 0.00 0.00 32.82 4.00
555 566 5.500234 TGGACCTCATTTCCAAAGATACAG 58.500 41.667 0.00 0.00 40.35 2.74
556 567 5.512942 TGGACCTCATTTCCAAAGATACA 57.487 39.130 0.00 0.00 40.35 2.29
564 575 2.649531 ACGTTTGGACCTCATTTCCA 57.350 45.000 0.00 0.00 41.64 3.53
565 576 4.295870 GAAAACGTTTGGACCTCATTTCC 58.704 43.478 15.46 0.00 0.00 3.13
566 577 4.202070 TGGAAAACGTTTGGACCTCATTTC 60.202 41.667 15.46 3.94 0.00 2.17
567 578 3.702045 TGGAAAACGTTTGGACCTCATTT 59.298 39.130 15.46 0.00 0.00 2.32
568 579 3.067601 GTGGAAAACGTTTGGACCTCATT 59.932 43.478 15.46 0.00 0.00 2.57
569 580 2.621526 GTGGAAAACGTTTGGACCTCAT 59.378 45.455 15.46 0.00 0.00 2.90
570 581 2.018515 GTGGAAAACGTTTGGACCTCA 58.981 47.619 15.46 4.47 0.00 3.86
571 582 2.768833 GTGGAAAACGTTTGGACCTC 57.231 50.000 15.46 14.46 0.00 3.85
588 599 9.022536 GTATGAACATGTCGTACACTAACCGTG 62.023 44.444 16.36 0.00 44.91 4.94
589 600 3.004629 TGAACATGTCGTACACTAACCGT 59.995 43.478 0.00 0.00 0.00 4.83
590 601 3.567530 TGAACATGTCGTACACTAACCG 58.432 45.455 0.00 0.00 0.00 4.44
591 602 5.517770 GGTATGAACATGTCGTACACTAACC 59.482 44.000 19.96 13.41 46.63 2.85
592 603 5.517770 GGGTATGAACATGTCGTACACTAAC 59.482 44.000 19.96 10.19 45.35 2.34
593 604 5.653507 GGGTATGAACATGTCGTACACTAA 58.346 41.667 19.96 0.00 45.35 2.24
594 605 5.252969 GGGTATGAACATGTCGTACACTA 57.747 43.478 19.96 5.77 45.35 2.74
595 606 4.119442 GGGTATGAACATGTCGTACACT 57.881 45.455 19.96 0.00 45.35 3.55
597 608 4.020928 ACAAGGGTATGAACATGTCGTACA 60.021 41.667 19.96 11.34 46.63 2.90
598 609 4.501071 ACAAGGGTATGAACATGTCGTAC 58.499 43.478 0.00 8.68 44.85 3.67
599 610 4.811969 ACAAGGGTATGAACATGTCGTA 57.188 40.909 0.00 0.00 0.00 3.43
600 611 3.695830 ACAAGGGTATGAACATGTCGT 57.304 42.857 0.00 0.00 0.00 4.34
601 612 5.356426 TGATACAAGGGTATGAACATGTCG 58.644 41.667 0.00 0.00 40.28 4.35
602 613 6.823689 ACTTGATACAAGGGTATGAACATGTC 59.176 38.462 14.51 0.00 40.28 3.06
603 614 6.721318 ACTTGATACAAGGGTATGAACATGT 58.279 36.000 14.51 0.00 40.28 3.21
604 615 8.731275 TTACTTGATACAAGGGTATGAACATG 57.269 34.615 14.51 0.00 40.28 3.21
605 616 8.768397 TCTTACTTGATACAAGGGTATGAACAT 58.232 33.333 14.51 0.00 40.28 2.71
606 617 8.141298 TCTTACTTGATACAAGGGTATGAACA 57.859 34.615 14.51 0.00 40.28 3.18
607 618 7.224949 GCTCTTACTTGATACAAGGGTATGAAC 59.775 40.741 14.51 2.36 40.28 3.18
608 619 7.272978 GCTCTTACTTGATACAAGGGTATGAA 58.727 38.462 14.51 0.00 40.28 2.57
609 620 6.461092 CGCTCTTACTTGATACAAGGGTATGA 60.461 42.308 14.51 7.47 40.28 2.15
610 621 5.692204 CGCTCTTACTTGATACAAGGGTATG 59.308 44.000 14.51 4.35 40.28 2.39
611 622 5.363005 ACGCTCTTACTTGATACAAGGGTAT 59.637 40.000 14.51 0.00 42.86 2.73
612 623 4.708421 ACGCTCTTACTTGATACAAGGGTA 59.292 41.667 14.51 0.00 0.00 3.69
613 624 3.514309 ACGCTCTTACTTGATACAAGGGT 59.486 43.478 14.51 0.89 0.00 4.34
614 625 4.113354 GACGCTCTTACTTGATACAAGGG 58.887 47.826 14.51 5.98 0.00 3.95
615 626 4.113354 GGACGCTCTTACTTGATACAAGG 58.887 47.826 14.51 0.00 0.00 3.61
616 627 3.791887 CGGACGCTCTTACTTGATACAAG 59.208 47.826 9.51 9.51 0.00 3.16
617 628 3.441222 TCGGACGCTCTTACTTGATACAA 59.559 43.478 0.00 0.00 0.00 2.41
618 629 3.011818 TCGGACGCTCTTACTTGATACA 58.988 45.455 0.00 0.00 0.00 2.29
619 630 3.311871 TCTCGGACGCTCTTACTTGATAC 59.688 47.826 0.00 0.00 0.00 2.24
620 631 3.538591 TCTCGGACGCTCTTACTTGATA 58.461 45.455 0.00 0.00 0.00 2.15
621 632 2.356382 CTCTCGGACGCTCTTACTTGAT 59.644 50.000 0.00 0.00 0.00 2.57
622 633 1.738350 CTCTCGGACGCTCTTACTTGA 59.262 52.381 0.00 0.00 0.00 3.02
623 634 1.202200 CCTCTCGGACGCTCTTACTTG 60.202 57.143 0.00 0.00 0.00 3.16
624 635 1.096416 CCTCTCGGACGCTCTTACTT 58.904 55.000 0.00 0.00 0.00 2.24
625 636 0.252479 TCCTCTCGGACGCTCTTACT 59.748 55.000 0.00 0.00 33.30 2.24
626 637 2.777969 TCCTCTCGGACGCTCTTAC 58.222 57.895 0.00 0.00 33.30 2.34
635 646 3.648507 AGCTAACTTAGTCCTCTCGGA 57.351 47.619 0.00 0.00 36.83 4.55
636 647 4.197750 TGTAGCTAACTTAGTCCTCTCGG 58.802 47.826 0.00 0.00 0.00 4.63
637 648 5.814764 TTGTAGCTAACTTAGTCCTCTCG 57.185 43.478 0.00 0.00 0.00 4.04
638 649 6.921914 TGTTTGTAGCTAACTTAGTCCTCTC 58.078 40.000 0.00 0.00 0.00 3.20
639 650 6.912951 TGTTTGTAGCTAACTTAGTCCTCT 57.087 37.500 0.00 0.00 0.00 3.69
640 651 7.656542 AGTTTGTTTGTAGCTAACTTAGTCCTC 59.343 37.037 0.00 0.00 30.21 3.71
641 652 7.506971 AGTTTGTTTGTAGCTAACTTAGTCCT 58.493 34.615 0.00 0.00 30.21 3.85
642 653 7.725818 AGTTTGTTTGTAGCTAACTTAGTCC 57.274 36.000 0.00 0.00 30.21 3.85
643 654 8.823818 TGAAGTTTGTTTGTAGCTAACTTAGTC 58.176 33.333 8.19 0.00 40.18 2.59
644 655 8.726870 TGAAGTTTGTTTGTAGCTAACTTAGT 57.273 30.769 8.19 0.00 40.18 2.24
646 657 9.944663 CAATGAAGTTTGTTTGTAGCTAACTTA 57.055 29.630 8.19 0.36 40.18 2.24
647 658 8.466798 ACAATGAAGTTTGTTTGTAGCTAACTT 58.533 29.630 7.99 7.99 41.76 2.66
648 659 7.996385 ACAATGAAGTTTGTTTGTAGCTAACT 58.004 30.769 0.00 0.00 36.43 2.24
649 660 9.166126 GTACAATGAAGTTTGTTTGTAGCTAAC 57.834 33.333 0.00 0.00 40.25 2.34
650 661 9.116067 AGTACAATGAAGTTTGTTTGTAGCTAA 57.884 29.630 0.00 0.00 40.25 3.09
651 662 8.671384 AGTACAATGAAGTTTGTTTGTAGCTA 57.329 30.769 0.00 0.00 40.25 3.32
652 663 7.568199 AGTACAATGAAGTTTGTTTGTAGCT 57.432 32.000 0.00 0.00 40.25 3.32
653 664 8.339714 TGTAGTACAATGAAGTTTGTTTGTAGC 58.660 33.333 0.00 0.00 40.25 3.58
656 667 9.515020 CAATGTAGTACAATGAAGTTTGTTTGT 57.485 29.630 12.24 0.00 40.25 2.83
657 668 9.729023 TCAATGTAGTACAATGAAGTTTGTTTG 57.271 29.630 16.93 8.16 35.30 2.93
674 685 9.507329 CAGCCAGGTTTATATATTCAATGTAGT 57.493 33.333 0.00 0.00 0.00 2.73
675 686 9.507329 ACAGCCAGGTTTATATATTCAATGTAG 57.493 33.333 0.00 0.00 0.00 2.74
676 687 9.283768 CACAGCCAGGTTTATATATTCAATGTA 57.716 33.333 0.00 0.00 0.00 2.29
677 688 7.255590 GCACAGCCAGGTTTATATATTCAATGT 60.256 37.037 0.00 0.00 0.00 2.71
678 689 7.040201 AGCACAGCCAGGTTTATATATTCAATG 60.040 37.037 0.00 0.00 0.00 2.82
679 690 7.006509 AGCACAGCCAGGTTTATATATTCAAT 58.993 34.615 0.00 0.00 0.00 2.57
680 691 6.364701 AGCACAGCCAGGTTTATATATTCAA 58.635 36.000 0.00 0.00 0.00 2.69
681 692 5.940617 AGCACAGCCAGGTTTATATATTCA 58.059 37.500 0.00 0.00 0.00 2.57
682 693 6.371825 GGTAGCACAGCCAGGTTTATATATTC 59.628 42.308 0.00 0.00 0.00 1.75
683 694 6.238648 GGTAGCACAGCCAGGTTTATATATT 58.761 40.000 0.00 0.00 0.00 1.28
684 695 5.280521 GGGTAGCACAGCCAGGTTTATATAT 60.281 44.000 1.97 0.00 44.80 0.86
685 696 4.041198 GGGTAGCACAGCCAGGTTTATATA 59.959 45.833 1.97 0.00 44.80 0.86
686 697 3.181443 GGGTAGCACAGCCAGGTTTATAT 60.181 47.826 1.97 0.00 44.80 0.86
687 698 2.171870 GGGTAGCACAGCCAGGTTTATA 59.828 50.000 1.97 0.00 44.80 0.98
688 699 1.064685 GGGTAGCACAGCCAGGTTTAT 60.065 52.381 1.97 0.00 44.80 1.40
689 700 0.326927 GGGTAGCACAGCCAGGTTTA 59.673 55.000 1.97 0.00 44.80 2.01
690 701 1.074951 GGGTAGCACAGCCAGGTTT 59.925 57.895 1.97 0.00 44.80 3.27
691 702 2.757077 GGGTAGCACAGCCAGGTT 59.243 61.111 1.97 0.00 44.80 3.50
692 703 3.706373 CGGGTAGCACAGCCAGGT 61.706 66.667 7.27 0.00 45.82 4.00
703 714 3.560251 CCCCTGGATGGCGGGTAG 61.560 72.222 0.00 0.00 38.88 3.18
719 730 2.525368 ACTTCTGTGCAATTAACCCCC 58.475 47.619 0.00 0.00 0.00 5.40
720 731 3.442625 GGTACTTCTGTGCAATTAACCCC 59.557 47.826 0.00 0.00 0.00 4.95
721 732 4.076394 TGGTACTTCTGTGCAATTAACCC 58.924 43.478 0.00 0.00 0.00 4.11
722 733 4.517453 TGTGGTACTTCTGTGCAATTAACC 59.483 41.667 0.00 0.00 0.00 2.85
762 773 5.601583 TTAGCAATCGTGGTACCAATCTA 57.398 39.130 18.31 8.75 37.45 1.98
1112 1161 0.036732 AATGGTCCTCGCTGCTTTCA 59.963 50.000 0.00 0.00 0.00 2.69
1833 1929 2.664916 CACTTTTGGCATCTTCAACCG 58.335 47.619 0.00 0.00 0.00 4.44
2042 2169 7.649533 TTGCCTTCATATCATCAATCAGTTT 57.350 32.000 0.00 0.00 0.00 2.66
2079 2206 2.756760 TCTGCATCTTTCTTTGCCATCC 59.243 45.455 0.00 0.00 38.08 3.51
2375 3394 1.280421 CCCCCTGAACTTCTCCTTCAG 59.720 57.143 1.82 1.82 42.95 3.02
2503 3522 7.547722 CACCATTAGTACAAGCATACAGTACAA 59.452 37.037 0.00 0.00 40.32 2.41
2585 3604 6.182627 TCCACTTCAAATGCATAGTTCATCT 58.817 36.000 0.00 0.00 0.00 2.90
2748 3767 6.194796 TCCTCTTTTATTGCAATGTACTGC 57.805 37.500 22.27 0.27 42.95 4.40
2815 3834 8.821686 TGTAATGGATCAAGTTGTAATGGATT 57.178 30.769 2.11 0.00 0.00 3.01
2849 3868 5.674933 AGTTAGTTAGTTGCTTCAGTTGC 57.325 39.130 0.00 0.00 0.00 4.17
3066 4085 2.239400 GGAGGCTTAAAGGTGCAACTT 58.761 47.619 12.33 12.33 36.74 2.66
3094 4113 0.107703 TCATTGGGGATCTGCGTGAC 60.108 55.000 0.00 0.00 0.00 3.67
3249 4268 4.082625 TGCTATGGTGAGTGCTGATTTTTG 60.083 41.667 0.00 0.00 0.00 2.44
3255 4274 1.139654 GGATGCTATGGTGAGTGCTGA 59.860 52.381 0.00 0.00 0.00 4.26
3428 4447 1.524008 TTCGTCGAGCTGCAGGAAGA 61.524 55.000 17.12 9.29 0.00 2.87


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

AutoCloner maintained by Alex Coulton.