Multiple sequence alignment - TraesCS5B01G167700

Loading Multiple Alignment...

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 TraesCS5B01G167700 chr5B 100.000 3209 0 0 1 3209 310033899 310037107 0.000000e+00 5927.0
1 TraesCS5B01G167700 chr5B 92.560 2352 87 24 910 3209 312261062 312263377 0.000000e+00 3293.0
2 TraesCS5B01G167700 chr5B 84.861 1222 127 26 1053 2226 309817031 309818242 0.000000e+00 1179.0
3 TraesCS5B01G167700 chr5B 99.520 625 3 0 1 625 310025619 310026243 0.000000e+00 1138.0
4 TraesCS5B01G167700 chr5B 83.647 850 124 12 1347 2186 309665508 309664664 0.000000e+00 785.0
5 TraesCS5B01G167700 chr5B 91.971 137 10 1 626 762 703180425 703180290 1.170000e-44 191.0
6 TraesCS5B01G167700 chr5A 92.610 1475 49 21 910 2326 364198510 364199982 0.000000e+00 2065.0
7 TraesCS5B01G167700 chr5A 81.697 1497 192 48 1053 2487 363919804 363921280 0.000000e+00 1171.0
8 TraesCS5B01G167700 chr5A 80.404 1138 186 30 1079 2186 363598393 363597263 0.000000e+00 832.0
9 TraesCS5B01G167700 chr5A 81.706 1055 118 31 1053 2059 363861970 363862997 0.000000e+00 809.0
10 TraesCS5B01G167700 chr5A 83.029 713 76 18 2356 3036 364200101 364200800 3.540000e-169 604.0
11 TraesCS5B01G167700 chr5A 91.406 128 11 0 2099 2226 363862995 363863122 3.290000e-40 176.0
12 TraesCS5B01G167700 chr5A 96.154 52 2 0 766 817 364198387 364198438 5.700000e-13 86.1
13 TraesCS5B01G167700 chr5D 93.953 1290 44 10 766 2027 275194994 275196277 0.000000e+00 1919.0
14 TraesCS5B01G167700 chr5D 82.231 1497 184 47 1053 2487 275147027 275148503 0.000000e+00 1216.0
15 TraesCS5B01G167700 chr5D 83.628 849 126 11 1347 2186 274572138 274571294 0.000000e+00 785.0
16 TraesCS5B01G167700 chr5D 83.436 652 86 17 1593 2226 274777896 274778543 1.280000e-163 586.0
17 TraesCS5B01G167700 chr5D 86.116 569 44 17 1053 1594 274776068 274776628 5.970000e-162 580.0
18 TraesCS5B01G167700 chr5D 90.746 335 11 5 2012 2326 275196818 275197152 2.290000e-116 429.0
19 TraesCS5B01G167700 chr5D 88.803 259 19 3 2356 2613 275197320 275197569 3.110000e-80 309.0
20 TraesCS5B01G167700 chr5D 85.294 306 29 9 2871 3167 275197725 275198023 5.200000e-78 302.0
21 TraesCS5B01G167700 chr5D 85.915 71 5 2 2614 2679 275197592 275197662 1.600000e-08 71.3
22 TraesCS5B01G167700 chr3A 98.722 626 8 0 1 626 228960489 228959864 0.000000e+00 1112.0
23 TraesCS5B01G167700 chr4A 98.720 625 8 0 1 625 160723937 160723313 0.000000e+00 1110.0
24 TraesCS5B01G167700 chr4A 98.390 621 10 0 5 625 160715076 160714456 0.000000e+00 1092.0
25 TraesCS5B01G167700 chr1B 98.722 626 7 1 1 625 624422470 624421845 0.000000e+00 1110.0
26 TraesCS5B01G167700 chr4B 97.488 637 9 5 1 634 280727966 280728598 0.000000e+00 1081.0
27 TraesCS5B01G167700 chr4B 97.767 627 12 2 1 625 360715843 360715217 0.000000e+00 1079.0
28 TraesCS5B01G167700 chrUn 97.767 627 12 2 1 625 366279793 366279167 0.000000e+00 1079.0
29 TraesCS5B01G167700 chr6A 97.767 627 12 2 1 625 198903716 198903090 0.000000e+00 1079.0
30 TraesCS5B01G167700 chr7B 91.241 137 12 0 626 762 92085159 92085295 1.520000e-43 187.0
31 TraesCS5B01G167700 chr3D 91.667 132 11 0 626 757 70284941 70285072 1.970000e-42 183.0


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 TraesCS5B01G167700 chr5B 310033899 310037107 3208 False 5927.000000 5927 100.000000 1 3209 1 chr5B.!!$F3 3208
1 TraesCS5B01G167700 chr5B 312261062 312263377 2315 False 3293.000000 3293 92.560000 910 3209 1 chr5B.!!$F4 2299
2 TraesCS5B01G167700 chr5B 309817031 309818242 1211 False 1179.000000 1179 84.861000 1053 2226 1 chr5B.!!$F1 1173
3 TraesCS5B01G167700 chr5B 310025619 310026243 624 False 1138.000000 1138 99.520000 1 625 1 chr5B.!!$F2 624
4 TraesCS5B01G167700 chr5B 309664664 309665508 844 True 785.000000 785 83.647000 1347 2186 1 chr5B.!!$R1 839
5 TraesCS5B01G167700 chr5A 363919804 363921280 1476 False 1171.000000 1171 81.697000 1053 2487 1 chr5A.!!$F1 1434
6 TraesCS5B01G167700 chr5A 364198387 364200800 2413 False 918.366667 2065 90.597667 766 3036 3 chr5A.!!$F3 2270
7 TraesCS5B01G167700 chr5A 363597263 363598393 1130 True 832.000000 832 80.404000 1079 2186 1 chr5A.!!$R1 1107
8 TraesCS5B01G167700 chr5A 363861970 363863122 1152 False 492.500000 809 86.556000 1053 2226 2 chr5A.!!$F2 1173
9 TraesCS5B01G167700 chr5D 275147027 275148503 1476 False 1216.000000 1216 82.231000 1053 2487 1 chr5D.!!$F1 1434
10 TraesCS5B01G167700 chr5D 274571294 274572138 844 True 785.000000 785 83.628000 1347 2186 1 chr5D.!!$R1 839
11 TraesCS5B01G167700 chr5D 275194994 275198023 3029 False 606.060000 1919 88.942200 766 3167 5 chr5D.!!$F3 2401
12 TraesCS5B01G167700 chr5D 274776068 274778543 2475 False 583.000000 586 84.776000 1053 2226 2 chr5D.!!$F2 1173
13 TraesCS5B01G167700 chr3A 228959864 228960489 625 True 1112.000000 1112 98.722000 1 626 1 chr3A.!!$R1 625
14 TraesCS5B01G167700 chr4A 160723313 160723937 624 True 1110.000000 1110 98.720000 1 625 1 chr4A.!!$R2 624
15 TraesCS5B01G167700 chr4A 160714456 160715076 620 True 1092.000000 1092 98.390000 5 625 1 chr4A.!!$R1 620
16 TraesCS5B01G167700 chr1B 624421845 624422470 625 True 1110.000000 1110 98.722000 1 625 1 chr1B.!!$R1 624
17 TraesCS5B01G167700 chr4B 280727966 280728598 632 False 1081.000000 1081 97.488000 1 634 1 chr4B.!!$F1 633
18 TraesCS5B01G167700 chr4B 360715217 360715843 626 True 1079.000000 1079 97.767000 1 625 1 chr4B.!!$R1 624
19 TraesCS5B01G167700 chrUn 366279167 366279793 626 True 1079.000000 1079 97.767000 1 625 1 chrUn.!!$R1 624
20 TraesCS5B01G167700 chr6A 198903090 198903716 626 True 1079.000000 1079 97.767000 1 625 1 chr6A.!!$R1 624

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
720 723 0.034089 GAGGTAAGCAGGGTGCCAAT 60.034 55.0 0.0 0.0 46.52 3.16 F
728 731 0.256752 CAGGGTGCCAATCCATGAGA 59.743 55.0 0.0 0.0 38.79 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2108 4036 0.538584 TTGCCATGTTTGGTGTGCAA 59.461 45.000 0.0 0.0 45.57 4.08 R
2228 4159 3.194861 TCCGAGGAATTAAGCAACATCG 58.805 45.455 0.0 0.0 36.56 3.84 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
446 449 4.141937 ACTCAGATATTGTTGCTTCCGCTA 60.142 41.667 0.00 0.00 36.97 4.26
626 629 1.546589 TAAATCGGGGGCGTCACAGT 61.547 55.000 0.00 0.00 0.00 3.55
627 630 2.798148 AAATCGGGGGCGTCACAGTC 62.798 60.000 0.00 0.00 0.00 3.51
628 631 4.988716 TCGGGGGCGTCACAGTCT 62.989 66.667 0.00 0.00 0.00 3.24
629 632 4.436998 CGGGGGCGTCACAGTCTC 62.437 72.222 0.00 0.00 0.00 3.36
630 633 4.083862 GGGGGCGTCACAGTCTCC 62.084 72.222 0.00 0.00 0.00 3.71
631 634 4.083862 GGGGCGTCACAGTCTCCC 62.084 72.222 0.00 0.00 36.25 4.30
632 635 2.997897 GGGCGTCACAGTCTCCCT 60.998 66.667 0.00 0.00 34.19 4.20
634 637 2.433318 GCGTCACAGTCTCCCTGC 60.433 66.667 0.00 0.00 45.68 4.85
635 638 2.262915 CGTCACAGTCTCCCTGCC 59.737 66.667 0.00 0.00 45.68 4.85
636 639 2.262915 GTCACAGTCTCCCTGCCG 59.737 66.667 0.00 0.00 45.68 5.69
637 640 2.117423 TCACAGTCTCCCTGCCGA 59.883 61.111 0.00 0.00 45.68 5.54
638 641 1.533033 TCACAGTCTCCCTGCCGAA 60.533 57.895 0.00 0.00 45.68 4.30
639 642 1.079543 CACAGTCTCCCTGCCGAAG 60.080 63.158 0.00 0.00 45.68 3.79
640 643 1.534235 ACAGTCTCCCTGCCGAAGT 60.534 57.895 0.00 0.00 45.68 3.01
641 644 1.216710 CAGTCTCCCTGCCGAAGTC 59.783 63.158 0.00 0.00 33.59 3.01
642 645 1.985116 AGTCTCCCTGCCGAAGTCC 60.985 63.158 0.00 0.00 0.00 3.85
643 646 2.683933 TCTCCCTGCCGAAGTCCC 60.684 66.667 0.00 0.00 0.00 4.46
644 647 2.685380 CTCCCTGCCGAAGTCCCT 60.685 66.667 0.00 0.00 0.00 4.20
645 648 2.203938 TCCCTGCCGAAGTCCCTT 60.204 61.111 0.00 0.00 0.00 3.95
646 649 2.045926 CCCTGCCGAAGTCCCTTG 60.046 66.667 0.00 0.00 0.00 3.61
647 650 2.045926 CCTGCCGAAGTCCCTTGG 60.046 66.667 0.00 0.00 0.00 3.61
650 653 2.044946 GCCGAAGTCCCTTGGCAT 60.045 61.111 10.53 0.00 46.76 4.40
651 654 2.409870 GCCGAAGTCCCTTGGCATG 61.410 63.158 10.53 0.00 46.76 4.06
652 655 2.409870 CCGAAGTCCCTTGGCATGC 61.410 63.158 9.90 9.90 0.00 4.06
653 656 1.675310 CGAAGTCCCTTGGCATGCA 60.675 57.895 21.36 2.54 0.00 3.96
654 657 1.033746 CGAAGTCCCTTGGCATGCAT 61.034 55.000 21.36 0.00 0.00 3.96
655 658 0.458669 GAAGTCCCTTGGCATGCATG 59.541 55.000 22.70 22.70 0.00 4.06
656 659 0.040058 AAGTCCCTTGGCATGCATGA 59.960 50.000 30.64 7.50 0.00 3.07
657 660 0.040058 AGTCCCTTGGCATGCATGAA 59.960 50.000 30.64 15.16 0.00 2.57
658 661 0.174162 GTCCCTTGGCATGCATGAAC 59.826 55.000 30.64 20.90 0.00 3.18
659 662 0.040058 TCCCTTGGCATGCATGAACT 59.960 50.000 30.64 0.00 0.00 3.01
660 663 0.899720 CCCTTGGCATGCATGAACTT 59.100 50.000 30.64 0.00 0.00 2.66
661 664 1.404986 CCCTTGGCATGCATGAACTTG 60.405 52.381 30.64 13.92 0.00 3.16
662 665 1.404986 CCTTGGCATGCATGAACTTGG 60.405 52.381 30.64 20.17 0.00 3.61
663 666 1.274167 CTTGGCATGCATGAACTTGGT 59.726 47.619 30.64 0.00 0.00 3.67
664 667 2.212812 TGGCATGCATGAACTTGGTA 57.787 45.000 30.64 3.03 0.00 3.25
665 668 1.818060 TGGCATGCATGAACTTGGTAC 59.182 47.619 30.64 8.66 0.00 3.34
666 669 1.818060 GGCATGCATGAACTTGGTACA 59.182 47.619 30.64 0.00 0.00 2.90
667 670 2.159338 GGCATGCATGAACTTGGTACAG 60.159 50.000 30.64 0.00 42.39 2.74
668 671 2.159338 GCATGCATGAACTTGGTACAGG 60.159 50.000 30.64 0.00 42.39 4.00
669 672 1.533625 TGCATGAACTTGGTACAGGC 58.466 50.000 0.00 0.00 39.91 4.85
670 673 0.447801 GCATGAACTTGGTACAGGCG 59.552 55.000 0.00 0.00 39.91 5.52
671 674 0.447801 CATGAACTTGGTACAGGCGC 59.552 55.000 0.00 0.00 39.91 6.53
672 675 0.036164 ATGAACTTGGTACAGGCGCA 59.964 50.000 10.83 0.00 39.91 6.09
673 676 0.882927 TGAACTTGGTACAGGCGCAC 60.883 55.000 10.83 0.00 39.91 5.34
674 677 1.574702 GAACTTGGTACAGGCGCACC 61.575 60.000 10.83 8.98 39.91 5.01
675 678 2.746277 CTTGGTACAGGCGCACCC 60.746 66.667 10.83 0.97 42.39 4.61
676 679 3.545124 CTTGGTACAGGCGCACCCA 62.545 63.158 10.83 4.01 42.39 4.51
677 680 2.819984 CTTGGTACAGGCGCACCCAT 62.820 60.000 10.83 0.00 42.39 4.00
678 681 2.045340 GGTACAGGCGCACCCATT 60.045 61.111 10.83 0.00 36.11 3.16
679 682 2.406616 GGTACAGGCGCACCCATTG 61.407 63.158 10.83 0.00 36.11 2.82
680 683 1.376683 GTACAGGCGCACCCATTGA 60.377 57.895 10.83 0.00 36.11 2.57
681 684 1.376683 TACAGGCGCACCCATTGAC 60.377 57.895 10.83 0.00 36.11 3.18
682 685 2.813226 TACAGGCGCACCCATTGACC 62.813 60.000 10.83 0.00 36.11 4.02
683 686 3.965258 AGGCGCACCCATTGACCA 61.965 61.111 10.83 0.00 36.11 4.02
684 687 2.755469 GGCGCACCCATTGACCAT 60.755 61.111 10.83 0.00 0.00 3.55
685 688 2.491152 GCGCACCCATTGACCATG 59.509 61.111 0.30 0.00 0.00 3.66
686 689 2.045708 GCGCACCCATTGACCATGA 61.046 57.895 0.30 0.00 34.31 3.07
687 690 1.802636 CGCACCCATTGACCATGAC 59.197 57.895 0.00 0.00 34.31 3.06
688 691 0.677731 CGCACCCATTGACCATGACT 60.678 55.000 0.00 0.00 34.31 3.41
689 692 1.098050 GCACCCATTGACCATGACTC 58.902 55.000 0.00 0.00 34.31 3.36
690 693 1.372582 CACCCATTGACCATGACTCG 58.627 55.000 0.00 0.00 34.31 4.18
691 694 0.392998 ACCCATTGACCATGACTCGC 60.393 55.000 0.00 0.00 34.31 5.03
692 695 1.431488 CCCATTGACCATGACTCGCG 61.431 60.000 0.00 0.00 34.31 5.87
693 696 0.460109 CCATTGACCATGACTCGCGA 60.460 55.000 9.26 9.26 34.31 5.87
694 697 0.926155 CATTGACCATGACTCGCGAG 59.074 55.000 33.45 33.45 34.31 5.03
695 698 0.807667 ATTGACCATGACTCGCGAGC 60.808 55.000 34.83 26.13 0.00 5.03
696 699 1.877576 TTGACCATGACTCGCGAGCT 61.878 55.000 34.83 21.95 0.00 4.09
697 700 1.029947 TGACCATGACTCGCGAGCTA 61.030 55.000 34.83 23.97 0.00 3.32
698 701 0.317436 GACCATGACTCGCGAGCTAG 60.317 60.000 34.83 21.28 0.00 3.42
699 702 1.659954 CCATGACTCGCGAGCTAGC 60.660 63.158 34.83 21.39 0.00 3.42
700 703 1.064783 CATGACTCGCGAGCTAGCA 59.935 57.895 34.83 25.83 36.85 3.49
701 704 0.933973 CATGACTCGCGAGCTAGCAG 60.934 60.000 34.83 16.54 36.85 4.24
702 705 1.098129 ATGACTCGCGAGCTAGCAGA 61.098 55.000 34.83 14.73 36.85 4.26
703 706 1.010125 GACTCGCGAGCTAGCAGAG 60.010 63.158 34.83 26.21 40.69 3.35
704 707 2.331098 CTCGCGAGCTAGCAGAGG 59.669 66.667 25.07 8.41 35.63 3.69
705 708 2.438614 TCGCGAGCTAGCAGAGGT 60.439 61.111 18.83 0.00 39.10 3.85
706 709 1.153229 TCGCGAGCTAGCAGAGGTA 60.153 57.895 18.83 0.00 35.50 3.08
707 710 0.746923 TCGCGAGCTAGCAGAGGTAA 60.747 55.000 18.83 0.00 35.50 2.85
708 711 0.317436 CGCGAGCTAGCAGAGGTAAG 60.317 60.000 18.83 0.00 35.50 2.34
709 712 0.596341 GCGAGCTAGCAGAGGTAAGC 60.596 60.000 18.83 6.27 35.50 3.09
710 713 0.741326 CGAGCTAGCAGAGGTAAGCA 59.259 55.000 18.83 0.00 35.50 3.91
711 714 1.268999 CGAGCTAGCAGAGGTAAGCAG 60.269 57.143 18.83 0.00 35.50 4.24
712 715 1.068434 GAGCTAGCAGAGGTAAGCAGG 59.932 57.143 18.83 0.00 35.50 4.85
713 716 0.105778 GCTAGCAGAGGTAAGCAGGG 59.894 60.000 10.63 0.00 0.00 4.45
714 717 1.490574 CTAGCAGAGGTAAGCAGGGT 58.509 55.000 0.00 0.00 0.00 4.34
715 718 1.137872 CTAGCAGAGGTAAGCAGGGTG 59.862 57.143 0.00 0.00 0.00 4.61
716 719 1.746991 GCAGAGGTAAGCAGGGTGC 60.747 63.158 0.00 0.00 45.46 5.01
717 720 1.078143 CAGAGGTAAGCAGGGTGCC 60.078 63.158 0.00 0.00 46.52 5.01
718 721 1.538876 AGAGGTAAGCAGGGTGCCA 60.539 57.895 0.00 0.00 46.52 4.92
719 722 1.133809 AGAGGTAAGCAGGGTGCCAA 61.134 55.000 0.00 0.00 46.52 4.52
720 723 0.034089 GAGGTAAGCAGGGTGCCAAT 60.034 55.000 0.00 0.00 46.52 3.16
721 724 0.034089 AGGTAAGCAGGGTGCCAATC 60.034 55.000 0.00 0.00 46.52 2.67
722 725 1.037579 GGTAAGCAGGGTGCCAATCC 61.038 60.000 0.00 0.00 46.52 3.01
723 726 0.323360 GTAAGCAGGGTGCCAATCCA 60.323 55.000 0.00 0.00 46.52 3.41
724 727 0.630673 TAAGCAGGGTGCCAATCCAT 59.369 50.000 0.00 0.00 46.52 3.41
725 728 0.974010 AAGCAGGGTGCCAATCCATG 60.974 55.000 0.00 0.00 46.52 3.66
726 729 1.380246 GCAGGGTGCCAATCCATGA 60.380 57.895 0.00 0.00 38.79 3.07
727 730 1.389609 GCAGGGTGCCAATCCATGAG 61.390 60.000 0.00 0.00 38.79 2.90
728 731 0.256752 CAGGGTGCCAATCCATGAGA 59.743 55.000 0.00 0.00 38.79 3.27
729 732 1.133575 CAGGGTGCCAATCCATGAGAT 60.134 52.381 0.00 0.00 38.79 2.75
730 733 1.144503 AGGGTGCCAATCCATGAGATC 59.855 52.381 0.00 0.00 32.47 2.75
731 734 1.613836 GGTGCCAATCCATGAGATCC 58.386 55.000 0.00 0.00 32.47 3.36
732 735 1.133699 GGTGCCAATCCATGAGATCCA 60.134 52.381 0.00 0.00 32.47 3.41
733 736 2.490351 GGTGCCAATCCATGAGATCCAT 60.490 50.000 0.00 0.00 32.47 3.41
734 737 3.228453 GTGCCAATCCATGAGATCCATT 58.772 45.455 0.00 0.00 32.47 3.16
735 738 3.640029 GTGCCAATCCATGAGATCCATTT 59.360 43.478 0.00 0.00 32.47 2.32
736 739 3.893200 TGCCAATCCATGAGATCCATTTC 59.107 43.478 0.00 0.00 32.47 2.17
737 740 4.150359 GCCAATCCATGAGATCCATTTCT 58.850 43.478 0.00 0.00 32.47 2.52
738 741 4.217983 GCCAATCCATGAGATCCATTTCTC 59.782 45.833 0.00 0.00 42.10 2.87
739 742 4.765856 CCAATCCATGAGATCCATTTCTCC 59.234 45.833 0.00 0.00 41.24 3.71
740 743 3.758755 TCCATGAGATCCATTTCTCCG 57.241 47.619 0.00 0.00 41.24 4.63
741 744 3.308401 TCCATGAGATCCATTTCTCCGA 58.692 45.455 0.00 0.00 41.24 4.55
742 745 3.323115 TCCATGAGATCCATTTCTCCGAG 59.677 47.826 0.00 0.00 41.24 4.63
743 746 3.323115 CCATGAGATCCATTTCTCCGAGA 59.677 47.826 0.00 0.00 41.24 4.04
744 747 4.202295 CCATGAGATCCATTTCTCCGAGAA 60.202 45.833 6.75 6.75 41.24 2.87
745 748 4.392921 TGAGATCCATTTCTCCGAGAAC 57.607 45.455 10.48 0.00 41.24 3.01
746 749 3.133003 TGAGATCCATTTCTCCGAGAACC 59.867 47.826 10.48 0.00 41.24 3.62
747 750 2.436173 AGATCCATTTCTCCGAGAACCC 59.564 50.000 10.48 0.00 33.26 4.11
748 751 1.651737 TCCATTTCTCCGAGAACCCA 58.348 50.000 10.48 0.00 33.26 4.51
749 752 1.278127 TCCATTTCTCCGAGAACCCAC 59.722 52.381 10.48 0.00 33.26 4.61
750 753 1.359848 CATTTCTCCGAGAACCCACG 58.640 55.000 10.48 0.00 33.26 4.94
751 754 0.391263 ATTTCTCCGAGAACCCACGC 60.391 55.000 10.48 0.00 33.26 5.34
752 755 2.758770 TTTCTCCGAGAACCCACGCG 62.759 60.000 10.48 3.53 33.26 6.01
850 853 7.234661 TGTGGTAAGTTCAAAAAGAAAAGGT 57.765 32.000 0.00 0.00 38.13 3.50
851 854 7.672240 TGTGGTAAGTTCAAAAAGAAAAGGTT 58.328 30.769 0.00 0.00 38.13 3.50
852 855 8.151596 TGTGGTAAGTTCAAAAAGAAAAGGTTT 58.848 29.630 0.00 0.00 38.13 3.27
853 856 8.653338 GTGGTAAGTTCAAAAAGAAAAGGTTTC 58.347 33.333 0.00 0.00 38.13 2.78
888 891 5.876651 AATTCAAAAGGAAAAGGTGAGCT 57.123 34.783 0.00 0.00 39.39 4.09
891 894 4.787551 TCAAAAGGAAAAGGTGAGCTGTA 58.212 39.130 0.00 0.00 0.00 2.74
908 911 2.852413 CTGTATGGTAAACGCGACTCTG 59.148 50.000 15.93 0.00 0.00 3.35
919 938 1.302033 CGACTCTGCAAAGCCTGGT 60.302 57.895 0.00 0.00 0.00 4.00
966 988 3.265737 TCCTTTCACTATAAGCCAAGCCA 59.734 43.478 0.00 0.00 0.00 4.75
967 989 3.378427 CCTTTCACTATAAGCCAAGCCAC 59.622 47.826 0.00 0.00 0.00 5.01
980 1002 2.594592 GCCACAAAGACGCCTGGT 60.595 61.111 0.00 0.00 0.00 4.00
1065 1087 1.218316 GAAGGCGGTCGATGTCCTT 59.782 57.895 12.80 12.80 41.27 3.36
1068 1090 2.577059 GCGGTCGATGTCCTTCCA 59.423 61.111 0.00 0.00 0.00 3.53
1074 1096 1.482593 GTCGATGTCCTTCCAGTGGAT 59.517 52.381 14.00 0.00 35.87 3.41
1327 1359 0.464013 CCTCTCCCTCGACTTCGCTA 60.464 60.000 0.00 0.00 39.60 4.26
2226 4157 4.141135 TGGTGATTGGTAAAACCTCCTTCA 60.141 41.667 0.00 0.00 39.58 3.02
2228 4159 5.125578 GGTGATTGGTAAAACCTCCTTCATC 59.874 44.000 0.00 0.00 39.58 2.92
2229 4160 4.941263 TGATTGGTAAAACCTCCTTCATCG 59.059 41.667 0.00 0.00 39.58 3.84
2230 4161 4.627284 TTGGTAAAACCTCCTTCATCGA 57.373 40.909 0.00 0.00 39.58 3.59
2232 4163 4.513442 TGGTAAAACCTCCTTCATCGATG 58.487 43.478 19.61 19.61 39.58 3.84
2233 4164 4.019681 TGGTAAAACCTCCTTCATCGATGT 60.020 41.667 24.09 4.31 39.58 3.06
2247 4209 4.507756 TCATCGATGTTGCTTAATTCCTCG 59.492 41.667 24.09 0.00 0.00 4.63
2352 4376 2.358957 TGTGGAGCAATCATTCCGAAG 58.641 47.619 0.00 0.00 36.22 3.79
2520 4625 3.864328 TGATTTCATCCCTATCCCGGTA 58.136 45.455 0.00 0.00 0.00 4.02
2529 4634 7.182760 TCATCCCTATCCCGGTATATCATATC 58.817 42.308 0.00 0.00 0.00 1.63
2585 4690 1.683943 ATGGCGATGGAGTTTGATGG 58.316 50.000 0.00 0.00 0.00 3.51
2882 5023 3.877508 GGTGTTATGAGTCTTATGGGTGC 59.122 47.826 0.00 0.00 0.00 5.01
2888 5029 3.441101 TGAGTCTTATGGGTGCTGTACT 58.559 45.455 0.00 0.00 0.00 2.73
2902 5043 6.401796 GGGTGCTGTACTTAGAAACAAATACG 60.402 42.308 0.00 0.00 0.00 3.06
2904 5045 7.329226 GGTGCTGTACTTAGAAACAAATACGTA 59.671 37.037 0.00 0.00 0.00 3.57
3016 5160 5.636903 ACATGATTGTTACCTCTGGCTAT 57.363 39.130 0.00 0.00 29.55 2.97
3169 5319 6.717289 TGGTATGCCTCTTAACAACTACAAT 58.283 36.000 0.16 0.00 35.27 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.341187 ACTACGCTTCTGGTAGCCTCT 60.341 52.381 0.00 0.00 40.78 3.69
626 629 2.683933 GGGACTTCGGCAGGGAGA 60.684 66.667 0.00 0.00 0.00 3.71
627 630 2.685380 AGGGACTTCGGCAGGGAG 60.685 66.667 0.00 0.00 27.25 4.30
639 642 0.174162 GTTCATGCATGCCAAGGGAC 59.826 55.000 22.25 0.00 0.00 4.46
640 643 0.040058 AGTTCATGCATGCCAAGGGA 59.960 50.000 22.25 0.00 0.00 4.20
641 644 0.899720 AAGTTCATGCATGCCAAGGG 59.100 50.000 22.25 0.00 0.00 3.95
642 645 1.404986 CCAAGTTCATGCATGCCAAGG 60.405 52.381 22.25 14.76 0.00 3.61
643 646 1.274167 ACCAAGTTCATGCATGCCAAG 59.726 47.619 22.25 10.23 0.00 3.61
644 647 1.340088 ACCAAGTTCATGCATGCCAA 58.660 45.000 22.25 9.28 0.00 4.52
645 648 1.818060 GTACCAAGTTCATGCATGCCA 59.182 47.619 22.25 8.06 0.00 4.92
646 649 1.818060 TGTACCAAGTTCATGCATGCC 59.182 47.619 22.25 14.20 0.00 4.40
647 650 2.159338 CCTGTACCAAGTTCATGCATGC 60.159 50.000 22.25 11.82 0.00 4.06
648 651 2.159338 GCCTGTACCAAGTTCATGCATG 60.159 50.000 21.07 21.07 28.81 4.06
649 652 2.094675 GCCTGTACCAAGTTCATGCAT 58.905 47.619 0.00 0.00 28.81 3.96
650 653 1.533625 GCCTGTACCAAGTTCATGCA 58.466 50.000 0.00 0.00 28.81 3.96
651 654 0.447801 CGCCTGTACCAAGTTCATGC 59.552 55.000 0.00 0.00 0.00 4.06
652 655 0.447801 GCGCCTGTACCAAGTTCATG 59.552 55.000 0.00 0.00 0.00 3.07
653 656 0.036164 TGCGCCTGTACCAAGTTCAT 59.964 50.000 4.18 0.00 0.00 2.57
654 657 0.882927 GTGCGCCTGTACCAAGTTCA 60.883 55.000 4.18 0.00 0.00 3.18
655 658 1.866925 GTGCGCCTGTACCAAGTTC 59.133 57.895 4.18 0.00 0.00 3.01
656 659 4.058797 GTGCGCCTGTACCAAGTT 57.941 55.556 4.18 0.00 0.00 2.66
662 665 1.376683 TCAATGGGTGCGCCTGTAC 60.377 57.895 17.49 0.00 34.45 2.90
663 666 1.376683 GTCAATGGGTGCGCCTGTA 60.377 57.895 17.49 3.47 34.45 2.74
664 667 2.672996 GTCAATGGGTGCGCCTGT 60.673 61.111 17.49 1.81 34.45 4.00
665 668 3.443045 GGTCAATGGGTGCGCCTG 61.443 66.667 17.49 7.00 34.45 4.85
666 669 3.286694 ATGGTCAATGGGTGCGCCT 62.287 57.895 17.49 0.00 34.45 5.52
667 670 2.755469 ATGGTCAATGGGTGCGCC 60.755 61.111 8.12 8.12 0.00 6.53
668 671 2.045708 TCATGGTCAATGGGTGCGC 61.046 57.895 0.00 0.00 36.86 6.09
669 672 0.677731 AGTCATGGTCAATGGGTGCG 60.678 55.000 0.00 0.00 36.86 5.34
670 673 1.098050 GAGTCATGGTCAATGGGTGC 58.902 55.000 0.00 0.00 36.86 5.01
671 674 1.372582 CGAGTCATGGTCAATGGGTG 58.627 55.000 0.00 0.00 36.86 4.61
672 675 0.392998 GCGAGTCATGGTCAATGGGT 60.393 55.000 0.00 0.00 36.86 4.51
673 676 1.431488 CGCGAGTCATGGTCAATGGG 61.431 60.000 0.00 0.00 36.86 4.00
674 677 0.460109 TCGCGAGTCATGGTCAATGG 60.460 55.000 3.71 0.00 36.86 3.16
675 678 0.926155 CTCGCGAGTCATGGTCAATG 59.074 55.000 27.79 0.00 37.66 2.82
676 679 0.807667 GCTCGCGAGTCATGGTCAAT 60.808 55.000 34.46 0.00 0.00 2.57
677 680 1.446099 GCTCGCGAGTCATGGTCAA 60.446 57.895 34.46 0.00 0.00 3.18
678 681 1.029947 TAGCTCGCGAGTCATGGTCA 61.030 55.000 34.46 10.36 0.00 4.02
679 682 0.317436 CTAGCTCGCGAGTCATGGTC 60.317 60.000 34.46 17.58 0.00 4.02
680 683 1.730487 CTAGCTCGCGAGTCATGGT 59.270 57.895 34.46 18.84 0.00 3.55
681 684 1.659954 GCTAGCTCGCGAGTCATGG 60.660 63.158 34.46 23.12 0.00 3.66
682 685 0.933973 CTGCTAGCTCGCGAGTCATG 60.934 60.000 34.46 22.60 0.00 3.07
683 686 1.098129 TCTGCTAGCTCGCGAGTCAT 61.098 55.000 34.46 23.25 0.00 3.06
684 687 1.710103 CTCTGCTAGCTCGCGAGTCA 61.710 60.000 34.46 24.29 0.00 3.41
685 688 1.010125 CTCTGCTAGCTCGCGAGTC 60.010 63.158 34.46 26.04 0.00 3.36
686 689 2.477176 CCTCTGCTAGCTCGCGAGT 61.477 63.158 34.46 23.50 32.55 4.18
687 690 1.160946 TACCTCTGCTAGCTCGCGAG 61.161 60.000 31.37 31.37 33.48 5.03
688 691 0.746923 TTACCTCTGCTAGCTCGCGA 60.747 55.000 17.23 9.26 0.00 5.87
689 692 0.317436 CTTACCTCTGCTAGCTCGCG 60.317 60.000 17.23 0.00 0.00 5.87
690 693 0.596341 GCTTACCTCTGCTAGCTCGC 60.596 60.000 17.23 2.68 0.00 5.03
691 694 0.741326 TGCTTACCTCTGCTAGCTCG 59.259 55.000 17.23 7.27 34.77 5.03
692 695 1.068434 CCTGCTTACCTCTGCTAGCTC 59.932 57.143 17.23 0.00 34.77 4.09
693 696 1.118838 CCTGCTTACCTCTGCTAGCT 58.881 55.000 17.23 0.00 34.77 3.32
694 697 0.105778 CCCTGCTTACCTCTGCTAGC 59.894 60.000 8.10 8.10 0.00 3.42
695 698 1.137872 CACCCTGCTTACCTCTGCTAG 59.862 57.143 0.00 0.00 0.00 3.42
696 699 1.195115 CACCCTGCTTACCTCTGCTA 58.805 55.000 0.00 0.00 0.00 3.49
697 700 1.986413 CACCCTGCTTACCTCTGCT 59.014 57.895 0.00 0.00 0.00 4.24
698 701 1.746991 GCACCCTGCTTACCTCTGC 60.747 63.158 0.00 0.00 40.96 4.26
699 702 1.078143 GGCACCCTGCTTACCTCTG 60.078 63.158 0.00 0.00 44.28 3.35
700 703 1.133809 TTGGCACCCTGCTTACCTCT 61.134 55.000 0.00 0.00 44.28 3.69
701 704 0.034089 ATTGGCACCCTGCTTACCTC 60.034 55.000 0.00 0.00 44.28 3.85
702 705 0.034089 GATTGGCACCCTGCTTACCT 60.034 55.000 0.00 0.00 44.28 3.08
703 706 1.037579 GGATTGGCACCCTGCTTACC 61.038 60.000 0.00 0.00 44.28 2.85
704 707 0.323360 TGGATTGGCACCCTGCTTAC 60.323 55.000 6.66 0.00 44.28 2.34
705 708 0.630673 ATGGATTGGCACCCTGCTTA 59.369 50.000 6.66 0.00 44.28 3.09
706 709 0.974010 CATGGATTGGCACCCTGCTT 60.974 55.000 6.66 0.00 44.28 3.91
707 710 1.380785 CATGGATTGGCACCCTGCT 60.381 57.895 6.66 0.00 44.28 4.24
708 711 1.380246 TCATGGATTGGCACCCTGC 60.380 57.895 6.66 0.00 44.08 4.85
709 712 0.256752 TCTCATGGATTGGCACCCTG 59.743 55.000 6.66 0.65 0.00 4.45
710 713 1.144503 GATCTCATGGATTGGCACCCT 59.855 52.381 6.66 0.00 34.33 4.34
711 714 1.613836 GATCTCATGGATTGGCACCC 58.386 55.000 0.00 0.00 34.33 4.61
712 715 1.133699 TGGATCTCATGGATTGGCACC 60.134 52.381 0.00 0.00 34.33 5.01
713 716 2.353357 TGGATCTCATGGATTGGCAC 57.647 50.000 0.00 0.00 34.33 5.01
714 717 3.605726 AATGGATCTCATGGATTGGCA 57.394 42.857 0.00 0.00 35.99 4.92
715 718 4.150359 AGAAATGGATCTCATGGATTGGC 58.850 43.478 0.00 0.00 35.99 4.52
716 719 4.765856 GGAGAAATGGATCTCATGGATTGG 59.234 45.833 6.64 0.00 46.24 3.16
717 720 4.454847 CGGAGAAATGGATCTCATGGATTG 59.545 45.833 6.64 0.00 46.24 2.67
718 721 4.349048 TCGGAGAAATGGATCTCATGGATT 59.651 41.667 6.64 0.00 46.24 3.01
719 722 3.906218 TCGGAGAAATGGATCTCATGGAT 59.094 43.478 6.64 0.00 46.24 3.41
720 723 3.308401 TCGGAGAAATGGATCTCATGGA 58.692 45.455 6.64 0.00 46.24 3.41
721 724 3.323115 TCTCGGAGAAATGGATCTCATGG 59.677 47.826 4.96 0.00 46.24 3.66
722 725 4.597404 TCTCGGAGAAATGGATCTCATG 57.403 45.455 4.96 0.00 46.24 3.07
723 726 4.202305 GGTTCTCGGAGAAATGGATCTCAT 60.202 45.833 21.24 0.00 46.24 2.90
724 727 3.133003 GGTTCTCGGAGAAATGGATCTCA 59.867 47.826 21.24 0.00 46.24 3.27
725 728 3.493524 GGGTTCTCGGAGAAATGGATCTC 60.494 52.174 21.24 5.08 44.18 2.75
726 729 2.436173 GGGTTCTCGGAGAAATGGATCT 59.564 50.000 21.24 0.00 35.75 2.75
727 730 2.170607 TGGGTTCTCGGAGAAATGGATC 59.829 50.000 21.24 8.39 35.75 3.36
728 731 2.092914 GTGGGTTCTCGGAGAAATGGAT 60.093 50.000 21.24 0.00 35.75 3.41
729 732 1.278127 GTGGGTTCTCGGAGAAATGGA 59.722 52.381 21.24 4.28 35.75 3.41
730 733 1.739067 GTGGGTTCTCGGAGAAATGG 58.261 55.000 21.24 0.00 35.75 3.16
731 734 1.359848 CGTGGGTTCTCGGAGAAATG 58.640 55.000 21.24 8.60 35.75 2.32
732 735 0.391263 GCGTGGGTTCTCGGAGAAAT 60.391 55.000 21.24 0.00 35.75 2.17
733 736 1.005394 GCGTGGGTTCTCGGAGAAA 60.005 57.895 21.24 4.32 35.75 2.52
734 737 2.654877 GCGTGGGTTCTCGGAGAA 59.345 61.111 16.19 16.19 34.09 2.87
735 738 3.744719 CGCGTGGGTTCTCGGAGA 61.745 66.667 2.97 2.97 0.00 3.71
753 756 4.519437 TCTCCTGGATGCTGCGCG 62.519 66.667 0.00 0.00 0.00 6.86
754 757 2.894387 GTCTCCTGGATGCTGCGC 60.894 66.667 0.00 0.00 0.00 6.09
755 758 2.202987 GGTCTCCTGGATGCTGCG 60.203 66.667 0.00 0.00 0.00 5.18
756 759 0.106819 AATGGTCTCCTGGATGCTGC 60.107 55.000 0.00 0.00 0.00 5.25
757 760 2.295885 GAAATGGTCTCCTGGATGCTG 58.704 52.381 0.00 0.00 0.00 4.41
758 761 1.134280 CGAAATGGTCTCCTGGATGCT 60.134 52.381 0.00 0.00 0.00 3.79
759 762 1.134401 TCGAAATGGTCTCCTGGATGC 60.134 52.381 0.00 0.00 0.00 3.91
760 763 2.988010 TCGAAATGGTCTCCTGGATG 57.012 50.000 0.00 0.00 0.00 3.51
761 764 4.510167 AATTCGAAATGGTCTCCTGGAT 57.490 40.909 0.00 0.00 0.00 3.41
762 765 4.261801 GAAATTCGAAATGGTCTCCTGGA 58.738 43.478 0.00 0.00 0.00 3.86
763 766 4.009675 TGAAATTCGAAATGGTCTCCTGG 58.990 43.478 0.00 0.00 0.00 4.45
764 767 5.124457 ACATGAAATTCGAAATGGTCTCCTG 59.876 40.000 0.00 0.00 0.00 3.86
765 768 5.256474 ACATGAAATTCGAAATGGTCTCCT 58.744 37.500 0.00 0.00 0.00 3.69
766 769 5.567138 ACATGAAATTCGAAATGGTCTCC 57.433 39.130 0.00 0.00 0.00 3.71
767 770 6.528072 GGAAACATGAAATTCGAAATGGTCTC 59.472 38.462 0.00 1.42 0.00 3.36
862 865 6.422100 GCTCACCTTTTCCTTTTGAATTTCTC 59.578 38.462 0.00 0.00 31.67 2.87
875 878 3.073274 ACCATACAGCTCACCTTTTCC 57.927 47.619 0.00 0.00 0.00 3.13
888 891 2.871133 CAGAGTCGCGTTTACCATACA 58.129 47.619 5.77 0.00 0.00 2.29
891 894 0.037697 TGCAGAGTCGCGTTTACCAT 60.038 50.000 5.77 0.00 33.35 3.55
908 911 1.367471 GGTTTGGACCAGGCTTTGC 59.633 57.895 0.00 0.00 45.77 3.68
919 938 1.310904 GCAGGTACGTTTGGTTTGGA 58.689 50.000 0.00 0.00 0.00 3.53
980 1002 2.325484 TGGTTTGTGCCTAGTGAGAGA 58.675 47.619 0.00 0.00 0.00 3.10
1045 1067 1.218316 GGACATCGACCGCCTTCTT 59.782 57.895 0.00 0.00 0.00 2.52
1074 1096 0.178068 GGAGAATGTTGCGGAGGCTA 59.822 55.000 0.00 0.00 40.82 3.93
1840 3196 3.364441 GGTTGCGATGCACAGCCA 61.364 61.111 12.01 0.00 38.71 4.75
1854 3210 2.526873 AGCTGGTCCTCCACGGTT 60.527 61.111 0.00 0.00 39.03 4.44
1905 3267 0.956633 GATACCACCCATCGTCGCTA 59.043 55.000 0.00 0.00 0.00 4.26
2108 4036 0.538584 TTGCCATGTTTGGTGTGCAA 59.461 45.000 0.00 0.00 45.57 4.08
2226 4157 3.809832 CCGAGGAATTAAGCAACATCGAT 59.190 43.478 0.00 0.00 38.49 3.59
2228 4159 3.194861 TCCGAGGAATTAAGCAACATCG 58.805 45.455 0.00 0.00 36.56 3.84
2229 4160 4.816385 TGATCCGAGGAATTAAGCAACATC 59.184 41.667 0.00 0.00 0.00 3.06
2230 4161 4.780815 TGATCCGAGGAATTAAGCAACAT 58.219 39.130 0.00 0.00 0.00 2.71
2232 4163 5.757850 AATGATCCGAGGAATTAAGCAAC 57.242 39.130 0.00 0.00 0.00 4.17
2233 4164 5.299279 GGAAATGATCCGAGGAATTAAGCAA 59.701 40.000 0.00 0.00 38.79 3.91
2352 4376 7.414436 TGTGACTGCAAATTCTAAAACAGTAC 58.586 34.615 0.00 0.00 38.42 2.73
2501 4606 6.209774 TGATATACCGGGATAGGGATGAAAT 58.790 40.000 13.02 0.00 35.15 2.17
2529 4634 7.591006 AATAGTGAATGCTTTGAAATGCAAG 57.409 32.000 7.57 0.00 41.52 4.01
2626 4753 5.820947 GCCTGTAAGCTAATTAAGTGGCTAA 59.179 40.000 14.30 3.08 34.78 3.09
2792 4924 9.859427 TTCCAAACATTAAAAAGAGCATATCAG 57.141 29.630 0.00 0.00 0.00 2.90
2857 4998 4.538490 ACCCATAAGACTCATAACACCCAA 59.462 41.667 0.00 0.00 0.00 4.12
2858 4999 4.080582 CACCCATAAGACTCATAACACCCA 60.081 45.833 0.00 0.00 0.00 4.51
2859 5000 4.451900 CACCCATAAGACTCATAACACCC 58.548 47.826 0.00 0.00 0.00 4.61
2860 5001 3.877508 GCACCCATAAGACTCATAACACC 59.122 47.826 0.00 0.00 0.00 4.16
2861 5002 4.572389 CAGCACCCATAAGACTCATAACAC 59.428 45.833 0.00 0.00 0.00 3.32
2862 5003 4.225042 ACAGCACCCATAAGACTCATAACA 59.775 41.667 0.00 0.00 0.00 2.41
2863 5004 4.770795 ACAGCACCCATAAGACTCATAAC 58.229 43.478 0.00 0.00 0.00 1.89
2864 5005 5.661312 AGTACAGCACCCATAAGACTCATAA 59.339 40.000 0.00 0.00 0.00 1.90
2865 5006 5.208890 AGTACAGCACCCATAAGACTCATA 58.791 41.667 0.00 0.00 0.00 2.15
2869 5010 5.269991 TCTAAGTACAGCACCCATAAGACT 58.730 41.667 0.00 0.00 0.00 3.24
2872 5013 6.170506 TGTTTCTAAGTACAGCACCCATAAG 58.829 40.000 0.00 0.00 0.00 1.73
2888 5029 9.195411 ACGAATGAAGTACGTATTTGTTTCTAA 57.805 29.630 8.17 0.00 38.47 2.10
2902 5043 3.064207 TGCAAGGTCACGAATGAAGTAC 58.936 45.455 0.00 0.00 36.31 2.73
2904 5045 1.873591 GTGCAAGGTCACGAATGAAGT 59.126 47.619 0.00 0.00 36.31 3.01
2912 5053 1.336440 TCCAAAATGTGCAAGGTCACG 59.664 47.619 0.00 0.00 39.73 4.35
3098 5248 2.082140 AATCAGGGTGCATGCATCAT 57.918 45.000 30.97 23.25 0.00 2.45
3179 5330 8.637986 TCACTTGGCAAAATAAGTAGAAATGTT 58.362 29.630 0.00 0.00 35.50 2.71


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

AutoCloner maintained by Alex Coulton.